##maf version=1 scoring=autoMZ.v1 a score=19459.000000 s hg19.chr17_gl000204_random 0 82 + 81310 GATCAGGAAGAGTCCTGGGGGGCGGGGGGCGAGCACAGGCAGTGGAAGGGAAGCAAAGCTGCCCCAGATAGGTGGGTGACCC s rheMac2.chr16 74726444 81 + 78773432 GATCGGGGAGAGTCCTGGGGG-CAGGGGGCGAGCACAGGCAGTGGAAAGGAAGCAAGGCTGCCCCAGACAGGTGGGTGACCC i rheMac2.chr16 N 0 C 0 s ponAbe2.chr17 69557946 78 + 73212453 ----AGGAAGAGTCCTGGGGGACAGGGGGCAAGCACAGGCAGTGGAAAGGAAGCAAGGCTGCCCCAGACAGGTGGGTGACAC i ponAbe2.chr17 N 0 C 0 a score=11803.000000 s hg19.chr17_gl000204_random 82 36 + 81310 AGGATGGAGAAGGGCAGCACCTGCGAGTGTTTGCCC s ponAbe2.chr17 69558024 36 + 73212453 AGGAGGGAGAAGGGCAGCACCTGCGAGTGTTTGCCC i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74726525 36 + 78773432 AGGAGGGAGAAGGGCAGCACTTGCAAGTGTCTGCCC i rheMac2.chr16 C 0 C 0 s loxAfr3.scaffold_49 14273547 23 - 17734757 AGGAGAGAGAAGGGA-------------GTTTGTCC i loxAfr3.scaffold_49 N 0 C 0 a score=14075.000000 s hg19.chr17_gl000204_random 118 41 + 81310 CTTGGGGAGTCGAGGGCAGAACCTCCCTCCTTCCTTGCCTG s mm9.chr11 118655889 39 + 121843856 CCTGGGGAGAGGAGAGCAGAGC--CCCTCCCTCCACTCTCA i mm9.chr11 N 0 C 0 s cavPor3.scaffold_76 4287066 26 + 7991924 ------------AGGGCAGAG---CCCTCCTTCCACTCTCG i cavPor3.scaffold_76 N 0 C 0 s ponAbe2.chr17 69558060 41 + 73212453 CTTGGGGAGCCGAGGGCAGAACCTCCCTCCTTCCTTGCCTG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74726561 40 + 78773432 CTTGGGGAGCCGA-GGCAGAACCTCCCTCCTTCCTCGCCTG i rheMac2.chr16 C 0 C 0 s loxAfr3.scaffold_49 14273570 39 - 17734757 TCAGCAGGGTGAGGCACAGAGCA-GCCGCTTTCCCCACAG- i loxAfr3.scaffold_49 C 0 C 0 a score=39519.000000 s hg19.chr17_gl000204_random 159 54 + 81310 GCTTT----CTGCAGAGCCCCTGCCCTCCC--CAAGGAGCACAGACCCAGGCTACTCCCT- s rheMac2.chr16 74726601 54 + 78773432 GCTTT----CTGCAGAACCCCTGCCCTCCC--CAAGGAGCACAGGCCCAGGCTACTCCCT- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69558101 54 + 73212453 GCTTT----CTGCAGAGCCCCTGTCCTCTC--CAAGGAGCACAGACCCAAGCTACTCCCT- i ponAbe2.chr17 C 0 C 0 s cavPor3.scaffold_76 4287092 57 + 7991924 GCTGCCTGACTATGTGGTCCCATCCCTCCC--CAAGAAGCACAGACCC-GGCTACTCCAT- i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118655928 54 + 121843856 GCTCC----CCACAGGGCCTGGTGCCTCCCAACAACACATGCAGA-CC-AGCTGTTCCGC- i mm9.chr11 C 0 C 0 s equCab2.chr11 57930880 53 - 61308211 GCTTT----CTGAGAAGC-TTCACCCTCCC--AAAGGAGCAGAGACCCAGGCTGCTCCCC- i equCab2.chr11 N 0 I 2 s bosTau4.chr19 10742412 40 - 65312493 ------------------CCTTGTCCTCCC--AAAGGAGCACAGACCCAGGCTGCTCCCC- i bosTau4.chr19 N 0 C 0 s loxAfr3.scaffold_49 14273609 52 - 17734757 GCTCT----CTGGGGAGC-CTCATCTGCCA--CAAGGCG-ACAGCCCCAGG-TGCTCCACT i loxAfr3.scaffold_49 C 0 C 0 a score=-31884.000000 s hg19.chr17_gl000204_random 213 85 + 81310 GGGACCTT------------------------------------------GGGA--GGGTCACCTGCAGCCCTTCTGGAGACCACAGGGACCAATAA--CATGCCAC-AGTGACCTCA-GGCCA-TGCA-TGCCC s loxAfr3.scaffold_49 14273661 113 - 17734757 --------GGTGAGTGGAGGCGGCGTCCCTGGGACAGACAGACAGGGTGAGGGAATGGGTAATCAGGTGCCCTT---------CAAAAGGTTGACT---CATGCCCCAGGCAACCTTCAGGCCAACCTG-TGCC- i loxAfr3.scaffold_49 C 0 C 0 s equCab2.chr11 57930935 95 - 61308211 GGGGCAGGA---------GGCGCTGCCCCCAGGGC------------TGTGGGA--GGGCAGTCTGCAGTAATC---------CGAGAGACCAACAA--CACACA---GGGTACCCTC-GGCCCACGTG-TGCC- i equCab2.chr11 I 2 C 0 s canFam2.chr9 59347860 70 - 64418924 GGGACATG------------------------------------------GAGA--GGGTGGTCTGCAGCAATT---------CAAGGCACTGACAACGCACACA---GGTGACCCTC-CGCCA-------GCA- i canFam2.chr9 N 0 C 0 s bosTau4.chr19 10742452 65 - 65312493 -----AAG-----------------------------------------TGGGA--GGGCAGGCCACAGTGATC---------CAAGACCCTGTCAA--CA--------GCAACTCTC-AGCCAAAGTG-TGAA- i bosTau4.chr19 C 0 C 0 s mm9.chr11 118655982 52 + 121843856 GGCACCT--------------------------------------------GGA--GGGTCACCTCAGCTCCCA----------------------------------ATCAACCCTC-GGCCT-GAGGATGTG- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4287149 51 + 7991924 CAGACCA--------------------------------------------GAA--GAGTCATCTGCATCCCTT----------------------------------GGTGACCCTC-AGCCC-CATG-TGCA- i cavPor3.scaffold_76 C 0 C 0 s ponAbe2.chr17 69558155 84 + 73212453 GGGACCTT------------------------------------------GGGA--GGGTCACCTGCAGCCCTTCTGGAGACAACAGGGACCAATAA--CGCGCCAC-AGTGACCTCA-GGCCA-TGCG-TGCC- i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74726655 84 + 78773432 GGGATCTT------------------------------------------GGGA--GGGTCACCTGCAGCCCTTCTGGAGACCACAGGGACCAATAA--TGTGCCAC-AGTGACCTCA-GGCCA-TGTG-TGCC- i rheMac2.chr16 C 0 C 0 a score=220071.000000 s hg19.chr17_gl000204_random 298 183 + 81310 ATTGGAGGACCCTCTGCATTTTTAGAAAGTGAGCTGGAAACATTGGCCTATTATATAATGAAA--------------------GTCCCACA------CACACACACCCTCCCCAA-----------------GAGAAAGC----GATTTTGCTAATTTTTCTCCCGGGCGGCAGGCGCCGTTGCCAGCCTTGGTTGCTAT--GGGGCCCAGTGACTGGTTTGAGTGGTAAAC s rheMac2.chr16 74726739 183 + 78773432 ATTGGAGGACCCTCTGCGTTTCCAGAAAGTGAGCTGGAAACATTGGCCTATTATATAATGAAA--------------------GTCCCCCC------CACACACACCCTCCCCAA-----------------GAGAAAGC----GATTTTGCTAATTTTTCTCCCGGGCGGCAGGCGCCGTTGCCAGCCTTGGTTGCTAT--GGGGCCCAGTGACTGGTTTGAGTGGTAAAC i rheMac2.chr16 C 0 M 422 s ponAbe2.chr17 69558239 181 + 73212453 ATCGGAGGACCCTCTGTGTTTCCAGAAAGTGAGCTGGAAACGTTGGCCTATTATATAATGAAA--------------------GTCCCACA------CACACAC--CCTCCCCAA-----------------GAGAAAGC----GATTTTGCTAATTTTTCTCCCGGGCGGCAGGCACCGTTGCCAGCCTTGGTTGCTAT--GGGGCCCAGTGACTGGTTTGAGTGGTAAAC i ponAbe2.chr17 C 0 C 0 s cavPor3.scaffold_76 4287200 201 + 7991924 ATCC-AAGAGCCTCTGTGTTTCCAGAAAG-GAGCATGAAAAACCAGCCTATTGTATAATGAAAAGCAATGATTTTTCTGAGTACCTCCCCC------TACACACACCCTCCCCCA-----------------AAGAAAGC----GATTTTGCTAATTTTTCTCCTGGGTGCCAGGCGCCGTTGCCAGCCTCAGTTGCTAT--GAGGCCCAGTGACTGGTTTGAGCTGTAAAT i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118656034 161 + 121843856 ATCT---GAACCTC-----------------------AGAGATTGTTCTATTATGTAACGAGAAGCCACGAGCCT--------CCTCACCC------CA-------TCTCTCCAA-----------------AGGAAAGT----GATTTTGATAATTTTTCTCGAAGGTGCCAGGCGCTGTTGCCAGCCTTGGTTGCTAT--GGGGCCTGGTGACTGGCTGCAG-GGTAAAC i mm9.chr11 C 0 C 0 s bosTau4.chr19 10742517 206 - 65312493 ATCCGAGGGCCC-CAGTGCTTCCAGAAGCTG-GCTTGGAGTATCAGTCTGTTATGTAAGGGGAAATGTGTATTTTCCTGAGA-CTCCTCCCC-----TCTCCACACACACCCCCACCTCTATACACATCCTGAAGAGAGCAAGCAAATTCGGTTTTTCTCCTCCCGAGTAGCAGG----------------TGTTGCTGG--GGGATACAGGGACTTGTTTGAGTGGTCAGT i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59347930 212 - 64418924 ATCTGAGGGCCTTCGGTG-TTCCAGAAGGTGAGCTTGAAATATCAGCCTATATTATAATGACAAACAAGGATTTTCCTGAAA-GTCCTTCCCACATGCCCCCACAAACACCCCAA-----------------AGAAAAGCTTGTGAATTTGCTCATTTTCCTTCTG-GGGGCAGGTGCCGTTGCCAGCCATTGCCGCTATGGGGGGCCCAGGGACTGGCTTGAGGGGTCAGC i canFam2.chr9 C 0 C 0 s equCab2.chr11 57931030 203 - 61308211 ATCTGAAGGCCCTGGGCGCTTCCAGAAGGTGGGCTTGAGAGATGAGTCTATTGTATAATGAGAAACGAGGACTTTCCTGCGA-ATCCTTCC------CCACCCCAACATCCCCCA-----------------AAGAAAGCAGGTGATGTGGCTCGTTTTCCTCCTG-GCAGCAGGCGCCGTGGCCAGCTGCTGTTGCTAT--GGGCCCCACGGA--GGTTCGAGTGGTCAGC i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14273774 188 - 17734757 ATCC-GGAGCCCTCAGTTTTTCCCGAAAGTGGGTCTGAAATATCAGCCTATTACGTAATGAAAAACAATGATCCTC-------CCCCCACC------CCAACACGCACCCCC--------------------AAGAAAGC----AACGTTGCTAATTTTTCTCCGA-GCGGCAGACGTGTTAG--AGCCTCTGTTGCTAT--GGGGCACGGTGACTGGTGCT-GCAGCATGC i loxAfr3.scaffold_49 C 0 C 0 s monDom5.chr2 304250753 170 - 541556283 ATTTGAAGATTTCTGGCATTTTGGGAAAACATATACTAAATATTG-------AAATAATGAAAAACATGTTTTTTT-------TTTTTATC----------------------AA-----------------AAGAA-------TACCTTGTTAATTTTTCTCTTGTGTAGCAATTGCTGTTGCCAGGCTTTGTTGCTAA--GGGATAATGCAATTGGTTTGTGCAATACAC i monDom5.chr2 N 0 C 0 a score=12636.000000 s hg19.chr17_gl000204_random 481 150 + 81310 TCAGGGGATTGGAGGAGAGGTTTCCATGGGG--------------AGCCACAGAGTGCAGCTGATGAGAGGCCAC---AGGTCTCCCCACCTAGGGCAGCCCACACGACCAGG---TGTGAAGAGGGCCTCCTG---------GACCCAGAC-----------------CTGGCAGGTGACCCCATAACAGGCATG s ponAbe2.chr17 69558420 150 + 73212453 TCAGGGGATTGGAGGAGAGGTTTCCATGGGG--------------AGCCACACAGTGCAGCAGATGAGAGGCCAC---GGGTCCCCCCACCTGGGGCAGCCCACACGACCAGG---TGTGAAGAGGGCCTCTTG---------GACCCAGAC-----------------CTGGCAGGTGACCCCATAACAGGCATG i ponAbe2.chr17 C 0 C 0 s cavPor3.scaffold_76 4287401 123 + 7991924 GAAGGGGATTGGAGAAGAGGTTTCCATGGGG--------------AGCCACTG-----------------------------CTCCTCACCTG----TGTGCTGGGGACCAGGGGCTGGCAGGAGGGCCTCCAG---------GACTCAGGC-----------------CTGCCAGGTGACATCTCCACAGGTGTG i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118656195 110 + 121843856 TATTGGGATTGGAAAAAAGGTTTCGATGGGG--------------AAGCACAGAGC-------------------------TCCCCTCACC------TGACATGAGGGCCACAGCCGGTGGGAAGGACCTCCTA---------GGATCAGAC-----------------CT---------------TGTAGGTGGG i mm9.chr11 C 0 C 0 s bosTau4.chr19 10742723 99 - 65312493 TCAGATGACTGAAGGAGGGGTGTGTGTGT------------------CCGATGAGC-----------AGGGCTCA---GGCTCCTCTCATCTGGG--GAT---------CAGG---TGGGAAGAAGGACT---------------------------------------CTGCC---------CACCGCTGGC--- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59348142 103 - 64418924 TTGTCAAATTCACAG--------------------------------CCAATGAGT-----------AAGGCCCA---GGCTCCCTTCACCTGGG--GATCGCTGCCACCAGG---TGG---GAAGGGCT---------------------------------------CTGGCAGGTGGCATCACAACCTGCGCG i canFam2.chr9 C 0 C 0 s equCab2.chr11 57931233 129 - 61308211 TCAGAGGATTGAAGGAGAGGTGTCCGTGCG----------------CCCAGTGAGC-----------GAGGCCCA---GGCCCCCTTCACCTGGG--GATCAAGGCCACCAGG---GGGCAAGAAGGGCCTC---------------CAGAG-----------------CTGGCAGGCGACACCACAGCATGCATG i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14273962 144 - 17734757 TCAGAGGACTGGAAGAGAGGTTTCCATGGGA-GCCACACCTTCCTGGCTGAGGAGC-----------CAGGCCCC---AGGTCCCCTCACCTGGGC-CATCAGTGCCCTCAGG---TGGGAAGAAGG----------------GACTCACAG-----------------AAGGCAGGTGATGTTGCAGCACTCACT i loxAfr3.scaffold_49 C 0 C 0 s monDom5.chr2 304250923 182 - 541556283 TCAAGCTATTGGTAGAGAGGTTTCTATAGGGAGTTACATAATTATGGTTGATTAGT-----------GAGGCCTACAGGTTTCAACTCACCTGGTATAATTAACAGCACCAGG---TGGGATAAAAGGCTTAAGGGAAAAAATGATTCAAAGACTATATGGGGCATAATGTGGCAAGTGATGTCACAGCACTCATG i monDom5.chr2 C 0 I 3824 e rheMac2.chr16 74726922 422 + 78773432 M a score=-16498.000000 s hg19.chr17_gl000204_random 631 106 + 81310 AGCCATCTCC--ATGACATCATAACAGGGTCTCTTAATGGGGACATCCCTGTCTGTG-AACCAGGTACAGGCTTCCT---CT-GTGCACATGCATGACACATGCCATATGCAT s ponAbe2.chr17 69558570 105 + 73212453 AGCCATCTCC--ATGACATCATAACAGGGTCTCTTAATGGGGACATCCCTGTCTGTG-AACCAGGTAGAGGCTTCCT---AT-GTGCACATGCATGACACATGCCATATGCA- i ponAbe2.chr17 C 0 I 2597 s cavPor3.scaffold_76 4287524 106 + 7991924 AGTCATCCTG--GCTGTGTGAGAAGAGGGCACTTTAATGGCAGCTTCACTGTCTGTG-GGCACAGTACAGGGCTGCC---GC-ACACACATGGATGGCACGGGTCACACATAG i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118656305 87 + 121843856 AGCCAGCC---------------GCAGGGTGTTTCTGTGCTGGCCTCA----CTGTG-AACACAGTACACTGCTGTCCTTGT-GCACACCTGGGTCACATGGTGCAT-----G i mm9.chr11 C 0 C 0 s bosTau4.chr19 10742822 58 - 65312493 GGTGACCTCC-ATCAGTGTAGCATCACC-------------------TCTGCCTCTG-ACCCTGGCCTGGGGCTGCC---CT------------------------------- i bosTau4.chr19 C 0 I 86 s canFam2.chr9 59348245 80 - 64418924 GGCCACGTCCTGATGGTGTAGAAACAGG----------------------GTCTGTGGACCCTAGCCCAAGGCTGCC---TTCGCT-CCACGTGAGAC-----ATGTATAT-- i canFam2.chr9 C 0 C 0 s equCab2.chr11 57931362 108 - 61308211 AGCAACCTCCTGGAGGTGGAGTAACAGGGAATTTTAACAACGACATAGCTGTCCATGCACCCGGGCACCAGGCTACC---CTTGCTCCCATGTGTGATGGGGGAAGCACAG-- i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14274106 95 - 17734757 AGTGACCTTCTGATGATGTAAGAAGAGATATTTTCAGTGGTGACGGTACTGTGCATGAACCCTGAGATGGGGATACC---TGTGCTCACAGGTGTGAC--------------- i loxAfr3.scaffold_49 C 0 I 89 e monDom5.chr2 304251105 3824 - 541556283 I e rheMac2.chr16 74726922 422 + 78773432 M a score=-14313.000000 s hg19.chr17_gl000204_random 737 47 + 81310 GCACTGCACACGTCTAGATAAGGTGCAGAGCTGGCACTGCCACGGGC s ponAbe2.chr17 69561272 46 + 73212453 GCACCGCTCACATGTAGATA-TGTGCAGAGTTGGCTGTGCCACGGAC i ponAbe2.chr17 I 2597 C 0 s cavPor3.scaffold_76 4287630 36 + 7991924 AAAGGGCGCACATCTGAGGAAGAGGCAGAGCCAGCA----------- i cavPor3.scaffold_76 C 0 I 53 s mm9.chr11 118656392 36 + 121843856 GGATGGCGAGTATCTGTGTAAGTGGGA---------CTG--ATGGGC i mm9.chr11 C 0 I 136 s equCab2.chr11 57931470 14 - 61308211 -GACTCCA-----------GAGACAC--------------------- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59348325 7 - 64418924 -------------------AAGATGC--------------------- i canFam2.chr9 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e bosTau4.chr19 10742880 86 - 65312493 I e loxAfr3.scaffold_49 14274201 89 - 17734757 I e rheMac2.chr16 74726922 422 + 78773432 M a score=-369.000000 s hg19.chr17_gl000204_random 784 193 + 81310 ATGTGTTATGGCCTCATCGAGATGGCTCAGGACTGCGGTGGCATCACCTGCCAGGTCTGGGTCCGGGAGGCCCTCC-TCACACCTGGTGGCACGGGCTGCTGCAGACGGGGGGTCCTAGGGTCTCTCACCAGCCACACCGTGCTGCTTCCCATGGAAACCTCTCCTCTGATGCTTGAGAGAGGCTGATGTGTGG s canFam2.chr9 59348332 64 - 64418924 ---------------------ACGGGG--GGTCTGCTGCAG------------GATGTGGTTAAGAGAGGCCGCGGGTCACTTCTG---------------------------------------TCTCCATCTACTC-------------------------------------------------------- i canFam2.chr9 C 0 C 0 s equCab2.chr11 57931484 63 - 61308211 ---------------------ATGGCT--AGCCCGTCATGG------------GATGTGGGGAAGAGAGGCCAGCAGTCATATAT----------------------------------------TCCCCGACTACTA-------------------------------------------------------- i equCab2.chr11 C 0 C 0 s ponAbe2.chr17 69561318 190 + 73212453 ACATGT-ATGGCGTCATTGAGATGGGTCAGGACTGCGGTGGCATCACCTGCCAGGTCTGGGTCCGGGAGGCCCTCC-TCACACCTGGTGGCGCGGGCTGCTGCAGACGGGG--TCCTAGGACCTCTCACCAGCCACACTGTGCTGCTTCCCATGGAAACCTCTCCTCTGATTCTTGAGAGAGGCTGGTGTGTGG i ponAbe2.chr17 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e bosTau4.chr19 10742880 86 - 65312493 I e cavPor3.scaffold_76 4287666 53 + 7991924 I e mm9.chr11 118656428 136 + 121843856 I e loxAfr3.scaffold_49 14274201 89 - 17734757 I e rheMac2.chr16 74726922 422 + 78773432 M a score=53910.000000 s hg19.chr17_gl000204_random 977 118 + 81310 CTTAGGTCCCCAGAGTAGCGTGCCTTCCTCAGAGATTTCAGGGGATGAGTGATAAATAAAGAAGTGGGTGGAGATGAGGGCAGA--------GCGG-GGAGGA----GGGAGAGAAGGTGGAAAAACTCAA s ponAbe2.chr17 69561508 118 + 73212453 CTTAGGTCCCCAGAGTAGCGTGCCTTCCTCAGAGATTTCAGGGGATGAGTGGTAAATAAAGAAGTGGGTGGAGATGGGGGCAGA--------GTGG-GGAGGA----GGGAGAGAGGGTGGAAAAACCCAA i ponAbe2.chr17 C 0 C 0 s loxAfr3.scaffold_49 14274290 76 - 17734757 TTTAATTTCCCGAAGGAGGGGGCCCTACTCAGAGATTTCAGGTGATAAGCAGAAAATA-------AGGTGGGGGAGGGGGTGG------------------------------------------------ i loxAfr3.scaffold_49 I 89 C 0 s rheMac2.chr16 74727345 123 + 78773432 ---AGGTCCCCAGAGTAGGGTGTCTTTCTCAGAGATTTGAGGGGATGAGTGGTAAATAAAGAAGTGAGTGgggatgggggcagagaggggaggagg-ggagga----gggagacagggtggaaAAACTCAA i rheMac2.chr16 M 422 C 0 s equCab2.chr11 57931547 102 - 61308211 --GAGCTCCCCAAAGCAGAGCGTCTTTTTCGGAGATTTCAGGTGATAAACAGAAAATA-----------AGGAGCTGG----GG--------GGAG-GGAGGA---GGAGACAGAGGGTAGAAAAACTCAC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59348396 103 - 64418924 --TAGTTCCCCAAAGCAAGGTGTCTT----GG-----TCAGGTGATGAGCAGCAGACA--------GCTAGGAGCAGGGCACGG--------GAAG-GGAGGACAGGGAGGGGAAGAATGGAAATACTCAC i canFam2.chr9 C 0 C 0 s bosTau4.chr19 10742966 101 - 65312493 --TAGTTCCCCAAAGTA-------------GGAAATTTCTGGTGA-GGGCAGAAAATAAAA----GAATGGGGGCGGGGGTGGG--------GCAGAGGAGGA--AGGAGGGAAAGGGCAGAAAACCTTAC i bosTau4.chr19 I 86 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e cavPor3.scaffold_76 4287666 53 + 7991924 I e mm9.chr11 118656428 136 + 121843856 I a score=15296.000000 s hg19.chr17_gl000204_random 1095 45 + 81310 AGAACCTTGCTTCCAAATTTCTTTTACATTTTGCCTTCTTTTAAG s equCab2.chr11 57931649 44 - 61308211 ACAGCCTGGCC-CCAGACTCCTTTCCAATGTATTCTTCCTTTAGG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59348499 45 - 64418924 ACGGTCTCGCCTCCAAACTTTGGTCCAATTTATTCTTTTTCTAAG i canFam2.chr9 C 0 C 0 s bosTau4.chr19 10743067 39 - 65312493 AGAGGCT-----CCAAACACCTTTTCAAC-TGTTCTTCCTTTAGG i bosTau4.chr19 C 0 C 0 s cavPor3.scaffold_76 4287719 33 + 7991924 AGAGCTTCTCTTTCGAGTGTTTCTTCCTTTACG------------ i cavPor3.scaffold_76 I 53 C 0 s ponAbe2.chr17 69561626 40 + 73212453 AGAATCTTGCTTCCAAATTTCTTTTAAATTTTGCCTT-----AAG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74727468 45 + 78773432 AGAACCTTGCTTCCAAATTTCCTTTAAATTTGGACTTCTTTTAAG i rheMac2.chr16 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e mm9.chr11 118656428 136 + 121843856 I e loxAfr3.scaffold_49 14274366 0 - 17734757 C a score=51740.000000 s hg19.chr17_gl000204_random 1140 195 + 81310 ATGATC-CCTCTCTTGGTACCAGGTAAA--CTCATGTG-GATGTTGAGGACATGA-------GGCCA--CCTGATGT-CC-CGGGGGCATG--TCCCA-GCTGTG---CACCTGTGGCCAGCACTCCTGGGCC----ACC-----CCCTGCTCTGCCTGCCTGACA--GAGAGGCTT---ACCGCCACC-AGCAGCTCT-GCTCCTG--AGC---TGCCTAACTGCAGATGGTGGGG s rheMac2.chr16 74727513 193 + 78773432 ATGATC-CCC--CTTGGTGCCAGGTAAA--CTCATGTG-TACGTTGAGGACACGA-------GGCCA--CCTGATGT-CC-CGGGGGCATG--TCCCA-GCTGTG---CACCTGTGGCCAGAACTCCTGGGCG----CCC-----CCCTGCTCTGCCTGCCTGACA--GAGAGGCTT---ATCCCCACC-AGCAGCTCC-GCTCCTG--AGC---TTCCTAACTGCAAAGGGTGGGG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69561666 195 + 73212453 ATGATC-CCCCTCTTGGTCCCAGGTAAA--CTCACGTG-GATGTTGAACACATGA-------GGCCA--CCTGATGT-CC-CAGGGGCATG--TCCCA-GCTGTG---TACCTGTGGCCAGCACTCCTGGGCC----ACC-----CCTTGCTCTGCCTGCCTGACA--GAGAGGCTT---ACCCCCACT-GGCAGCTCT-GCTCCTG--AGC---TTCCTAACTGCAGAGGGTGTGG i ponAbe2.chr17 C 0 C 0 s mm9.chr11 118656564 149 + 121843856 --------------------------AT--TATCCCTC-TCTCTC-----CACCATCTTCCCAGCCATCTATCACTTACC-AGGGACTGTGCATCCCA-GCTGTGTGCTGTCTGTGGTCACCAAGCCTGTCCC---ATCT-----TCCCCCT----------------------CCTCCCCCCCCTCCC-CACAGCCTC-------A--GGC---CTTGTCCCAGCAG--------- i mm9.chr11 I 136 C 0 s cavPor3.scaffold_76 4287752 194 + 7991924 AAGAG-------CTTGGTGCAAGGGAAA--TATACATG-GGTGTTGGGGACACAA-------GGCCA--CATTACAT-CC-GTGGACCATG--TCCCA-GCTGTG---TTTTTGTGGTCAGCACACCAGTCCCTATGCCT-----TACTTGTGTACCTGAC--ACA--GAGAGGCCTCAAACCCCACCA-GAGTGGCTC-CTTCAGG--GGC---CCCCTACCTGCAGGTCAGGGGG i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10743106 185 - 65312493 AAGGGC-CTGTG----------AACACA--CACAGGTG--GCTTT---GCCAC---------GGCCA--CGTGATGT-CC-GTGGAGCATG--TTCC--TTTGGA---CACTGGTGCCCAGGACTCTTGTCCT---CACT-----TCCTGCCCTGCCTGCCCAAAATAGCAAGGTTTTAAAAAAATCC--ATGAACTTCTACCCTTGACAGC---TCCTCATCTGCCAAGGTGGGC- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59348544 207 - 64418924 AAGCTCACTGTGCTTGGTGCCTGGTAAAGGCAGGTGTG--ATGCTGGGGACAT---------GGCCA---ATGACGC-CC-ATGAAGCGTG--TTCCA-GCTGGA---TA-CTGTGGCCAGCACTACCATCCC---TGCTCCCTGCCCTGCCCTGCCTGCCCAGGAATGAAAGGCTTCGAAACCCCGCCAAGCAGCTTCTGCTTCTGACAGC---TCCCCAAATGCGAGGGCGGGC- i canFam2.chr9 C 0 C 0 s equCab2.chr11 57931693 199 - 61308211 AAGATC-CTCCGCTCTGCGCCTGGTAAA--CACGTGGG--ACCCTGGAGACAC---------CGTCA--CATCATGT-CC-ATGAAGCGTG--TCCCA-CCTGGA---TGCCTGTGGCCAGCACTTCTGTCCC---CACT-----CCCTGCCCCACCTGCCCAAAAA-GAAAGGCTTCAAAACCCCTCC-AGCAGCTTCCGCTCCTGCCAGT---GCCCCAGCCGGGAAGGTGCGC- i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14274366 183 - 17734757 ------------------------TAAA--TGCATGTAGGACATTGGGGACAC-A-------GGAAA--CATTGCAC-CCTGTGGTGTGTG--TCCCAGGCTGTA-GACACCTGTGGCCGGCACT--TGTCTC---CACC-----CCCTGCTCCATCCCCCAAAAAA-GAAAGGCTTAAGACCTCACCC-AGCAGCTTTGGTTCCTG--ATTCTGCTCTTACCTGCTGTAGGTGGGG i loxAfr3.scaffold_49 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I a score=148214.000000 s hg19.chr17_gl000204_random 1335 360 + 81310 GGCAGCACCTG------------TTCCGTGGGGCTTAGGGCCTCC---GGCTTCC--ATCCATGAGTGCCAGCGTCCC-TGGAACGTGTGCCCCA-CCT-GCCTCCTGCCAGGATCCAGGAGTGG-GCACCTCTC----------------CTCCCTGGGATCACTATGGTCTTTGTTCAGAA-TCACAGTGTTTCTCTCTGCTATGGGCC-TTTGAGTCCT------CCCAGGAAGGGACCTTGAGCAAGGCCTCCGGGAAGTTGGCCTCCTCCTC-TGCTTG-CCCCCTCC--CACCACGCCCTCTGACCCT---------------------------------------------CTGATTTCTCTG---TGGCTCC--TGAGCATGGCCTGTCTCCCTGCA-AGGTGCCACAGGTATGAGAACCCAGGAGACGGTTCTTCTCCAA-CACCCGAGGC s rheMac2.chr16 74727706 371 + 78773432 GGCAGCACCTG------------TTCCGTGGGGCTCAGGCCCTCA---GGC-------TCCATGAGTGCCAGGGTCCC-TGGAATGTGTGCCCCA-CCT-GCCTCCTGCCAGGATCCAGGAGTGG-GAACCTCTCCTCCCGGAGCTGCACTTTCCCTGGGCTCACTATGGTCTTTGTTTGGAA-TCACAGTGTTTCTCTCTGCTATGGGCC-TTTGAGTCCT------CCCAAGAAGGTACCTTGAGCAAGCTCTCTGGGAAGTTGGCCTCCTCCTC-GGCTTG-CCCCCTCC--CACCACGCCCTCTGACCTT---------------------------------------------CTGATTTCTCTG---CAGCTCC--TGAGCATGGCCTGTCTCCCTGCA-AGGTGCCATGGATATGAGGACCCAGGAGACAGTTCTTCTCCAA-CAGCTGAGTC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69561861 375 + 73212453 GGCAGCACCTG------------TTCCGTGGGGCTGAGGCCCTCC---CGCTCCC--ATCCATGAGTGCCAGGGTCCC-TGGAACATGTGTCCCA-CCT-GCCTTCCGCCAGGATCCAGGAGTGG-GCACCTCTCCCCGCCGAGCTGCACTCTCCCTGGGCTCACTATGATCTTTGTTCGGAA-TCACAGTGTTTCTCTCTGCTATGGGCC-TTTGAGTCCT------CCCAGGAAGGGACCTTGAGCAAGGTCTCCAGGAAGTTGGCCTCCTCCTC-TGCTCGCCCCCCTCC--CACCATGCCCTCTGACCCT---------------------------------------------GTGATTCCTGTG---TGGCTCC--TGAGCATGGCCTTTCTCCCCGCA-AGGTGCCACAGGTATGAGAACCCAGGAGATGGTTCTTCTCCAA-CA--TGAGGC i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79177125 359 + 83384210 GGCAGCACCTG------------TTCCGTGGGGATTAGGGCCTCG---GGCTCCC--ATCCATGAGTGCCAGCGTCCA-TGGAACGTGTGCCCCA-CCT-GCCTCCCGGTAGGATCCAGGAGTGG-GCACCTCTC----------------CTCCCTGGGATCACTATGGTCTTTGTTCAGAA-TCACAGAGTTTCTCTGTGCTATGGGCC-TTTGAGTCCT------CCCAGGAAGGGACCTTGAGCAAGGTCTCCGGGAAGTTGGC-TCCTCCTC-TGCTTG-CCCCCTCC--CATCACGCCCTCTGACCCT---------------------------------------------CTGATTTCTCTG---TGGCTCC--TGAGCATGGCCTGTCTCCGTACA-AGATGCCACAGGTATGAGAACCCAGGAGACGGTTCTTCTCCAA-CACCCGAGGC i panTro2.chr17 N 0 C 0 s mm9.chr11 118656713 321 + 121843856 ------------------------------TCGTCCACACTCAAT---GGTATG---------------------------AGA----TCCCCTG-GCT-TCTT---GCCAGACTCTGGCAGCTA-GGGCCTGC--TTCCCATGATC-CATTTAACAACGCTCCTTGTGACTGTAGTTCAGAAGGC--AGGGCTTCTCTCTAACAAG-------------------------GGTGGAGACTTTGAGCAGGGTCTCTGGGATGCTGTCTTCCTcctc-ccctcc-cctcccct--cccctcccctcccctcccctcccctccccacctcttccttcTTTCCCTTCCACCTCTTCCTCTTCTACTCCTGTCT---CAGCCTC--AGTTCCTTGCCTG--TCCCGCCC-AGGTTCC--TGATGTGAGGACCTGGAGG-------------------------- i mm9.chr11 C 0 I 26 s cavPor3.scaffold_76 4287946 308 + 7991924 ---ACAACCAC------------CACCACTTTGTCT-CACCCACC---AGCCTGT---TCCGGAGGCGTCAGTGCCTA-GCAGAAACCTTCCCCGCACT-GCTCCTTGCCAGGTCTCAGAAGCCA-GTGCCTTCATTTCTGATGCTCTCCTTCACCTGGGATCATTCCTGTCTTTGTTCAGAATTCAAAGTGTTTCTCTCTGTGAAGAGCT-TTTCAGTCCT------TTCAGGTGGGGACCTTGAGCAAGGT----------CTGTTTTCATCAAC-TCTctc-ctcctcct--cctcttctttttcctcctc---------------------------------------------ctgctcctgctc---ctgctcc--tgctcct----------cctcc----------------------------------tcctcctcc------------- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10743291 376 - 65312493 AGTGAGACCTGTGTGCACCAATCCACTGAGCTACACT---CCACT---GGCCCTGTGGCCCGAGATCATCAGCATCAAGGGGAATGTTACCCCTG-ACCTGTTTCATGCCA-GTTCCGGGAGCTGTATGCA---GTGTTTCAGGCTCCACTTTCACTGGGCTCGTCCTTGTCTCTGTTCAGAA-TT-CCGTGTTTCTCTCCACTGAGCACTCTGTGAGTGCCCAAGGTCCC---CAGGGTCCCCAGGAAGTGTCT--------------TCCTTTTCATACTGG-GCCCCTCC--CTTCATGCTTCCCCAGCCT---------------------------------------------CTGATTTCTCCT---CAGCTCCTGAGAGCATGGCCTGTCTCCCCTCTTGGGATCC-CGGACTTGGG-CCCTGGA-GGGGGTCATTTTTCAAGCACCAGGGA- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59348751 335 - 64418924 AGCCATCCCTG----------CACCCTGAATCACTCTCCCCCCCGCCAGGCTCCGTGGTTGGCGATCATCAGGGTCCAGTGGGACTTCATGTGGA-CCA-GTTCCATGCCAGGCTCTGGAAGCCG-GTACATCTGTACACCGTGTTCTACTTTAACGGGGCTCATTATTGTCTTTGCTCAGAG-TT-CACTGTTGCTCTCCACTAAGGTCT-TGTGGATGCT------------------CCTTGAACAAGGTCT-----------------------CGCCTG-GCTCTTCC--CACGGAGTTCTCTGAGCTT---------------------------------------------CTGATTTCTGCTG--CAGCCC----------------TCTCCCCTCAGAGGAGCCATGGGCTCGGGAACCAAGA--AAGATTCTTCTCCAA-CACAAGGGAC i canFam2.chr9 C 0 I 1 s equCab2.chr11 57931892 375 - 61308211 GGCGACACCTG----------TCCACCGCATGGCCCTGGCCCTCT---GGCTCTGTGGCCGACAATCATCAGAATCAAGTGGAGCATTATCTGGG-CCCTGTTCCATGCCAGGTTCCAGGAGCTG-GCACACTGGTTTCCCAGGTTCCACTTTAGC-TGGCTCATTATTGTCTTTGTTCAGAA-TG-CAGTGTTTCTCTCCACGAAGCTCT-TGTGAGCTCCTGGGTGC--------AGACCTTGAGCAACATCTGGGGGAAGCTGAGCTTCTTCTC-CACTCG-GCCCTCCCATCTCG-----CTCTGAGCCT---------------------------------------------CTGATTTCTCCTG--CAGCTCC--AGAGCGTGGCCTGTCTCCCCACCGAAGAGCCATGGGCACGGGGACCTGGA-GGAGGTCCTTCTCTAA-GACCAGGGA- i equCab2.chr11 C 0 I 1 s loxAfr3.scaffold_49 14274549 346 - 17734757 AGAGACACCTG------------TGCACTGTGCGTCTCCCCCTCC---AGCTCTGT-CCTCTTGGTCGTCGGGACTGAGAGGAACATTGTCCC---CTC-GGTCCTTG-CAGGGTCTGGGAGCTG-AAACATCTG--TCCCCTCACCAACTCTGCTTGGGCTCATTGTTGTCTTCACTCAGAT-GCAGAGGGTT-CCCTGCACAGTGGTGT-CAGGGGTTCT------CCTGGGTGGGGACCTGGAACAAGGTCTCAGGAAGGCTGCCTCCCTCCTC--ATTCG-CCCCCTCC--CAC-ACACTCTCTGAGCCC---------------------------------------------CCAGTTTCTCCTGCAGTGTTCA--GGAGCAA---CTATCTCCCCACC-------------------------CAAGGTGACCCCTTCCCAG-CACCAGGGAC i loxAfr3.scaffold_49 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I a score=9724.000000 s hg19.chr17_gl000204_random 1695 23 + 81310 AGACGTCAT---GCCTCCTCCCTGCC------- s rheMac2.chr16 74728077 23 + 78773432 AGATATCAT---GCCTCCTCCCTGCC------- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69562236 23 + 73212453 AGACGTCGT---GCCTCCTCCCTGCA------- i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79177484 23 + 83384210 AGACGTCAT---GCCTCCTCCCTGCC------- i panTro2.chr17 C 0 C 0 s mm9.chr11 118657060 23 + 121843856 GGATGACAG---ACCTGTTCCCTGGC------- i mm9.chr11 I 26 C 0 s cavPor3.scaffold_76 4288254 14 + 7991924 ------------tcctcctcctcctc------- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10743667 18 - 65312493 TTGTGCCGC--------CTCCCTGCC------- i bosTau4.chr19 C 0 I 7 s canFam2.chr9 59349087 17 - 64418924 AGGCATCGTGTGGCCTC---------------- i canFam2.chr9 I 1 I 691 s equCab2.chr11 57932268 18 - 61308211 AGGTGCCAC--------CTCCCTGCC------- i equCab2.chr11 I 1 I 729 s loxAfr3.scaffold_49 14274895 30 - 17734757 GGGGCTCCT---GCCTCCTCCTAGGCAAGAGCC i loxAfr3.scaffold_49 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I a score=13066.000000 s hg19.chr17_gl000204_random 1718 39 + 81310 TCTCACTTCCCACTTTGCAGCTTTACTGTCCGCATTGTT s rheMac2.chr16 74728100 39 + 78773432 TCTCACTTCCCACTTTGCAGACTTACTGCCTGCATTGTT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69562259 39 + 73212453 TCTCACTTCCCACTTTGCAGCTTTACTGCCCGCATTGTT i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79177507 39 + 83384210 TCTCACTTCCCACTTTTCAGCTTTACTGCCCGCATTGTT i panTro2.chr17 C 0 C 0 s mm9.chr11 118657083 36 + 121843856 TTTCAGTTCCC---GTGCCGCCATCCCACCTTCGCTGTC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4288268 36 + 7991924 TGTCCCTTACT---CTCTCAGCTTCTGGTCTCCCTAAAG i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10743692 24 - 65312493 TGCAGCTTCCCCCATGGCACCTCT--------------- i bosTau4.chr19 I 7 I 661 s equCab2.chr11 57933015 34 - 61308211 TCTCATTTCCCACTTCGTAGCTTTCCTGCCCTCA----- i equCab2.chr11 I 729 C 0 s canFam2.chr9 59349795 34 - 64418924 TTCCTCTTCTCCTTACGGAGCTTTCCTGCCTCAT----- i canFam2.chr9 I 691 C 0 s loxAfr3.scaffold_49 14274925 19 - 17734757 TACAGCTTCCC----TGCAGCCT---------------- i loxAfr3.scaffold_49 C 0 I 449 e monDom5.chr2 304251105 3824 - 541556283 I a score=148491.000000 s hg19.chr17_gl000204_random 1757 174 + 81310 TGGTTCGCTGAGCCCTAGGAGCTGAGAGA----CTGGTTAACCATGAGGGACTGTGGAGCCAGGAAACATGACTTTGACCATTTGCCCTTCCCACCCTGAA--CCCCACAC-GCTAAGACCAAAGGAGGATGAAGTTTCCAAAATCAACTTCACAATAATGATAGAAAT-------------TAATGAGTTCCA s rheMac2.chr16 74728139 178 + 78773432 TTGTTCCCTGAGCCCTAGGAGCTGAGAGAGGCTCTGGTTAACCAAGAAGGACTGTGGAGCCAGGAAACCCAATCTTGACCATTTGCCCTTCCGACCCTGAA--CCCCACAT-GCTAAGACCAAAGGAGGATGAAGTTTCCAAAATCAACTTCACAATAATGATAGAAAT-------------TAATGAGTTCCA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69562298 178 + 73212453 TTGTTCCCTGAGCCCTAGGAGCTGAGAGAGGCTCTGGTTAACCATGAAGGACTGTGGAGCCAGGAAACATGGCTTTGACCATTTGCCCTTCCCACCCTGAA--CCCCACAC-GCTAGGACCAAAGGAGGATGAAGTTTCCAAAATCAACTTCACAATAATGATAGAAAT-------------TAATGAGTTCCA i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79177546 178 + 83384210 TTGTTCGCTGAGCCCTAGGAGCTGAGAGAGGCTCTGGTTAACCATGAAGGACTGTGGAGCCAGGAAACATGACTTTGACCATTTGCCCTTCCTACCCTGAA--CCCCACAC-GCTAAGACCAAAGGAGGATGAAGTTTCCAAAATCAACTTCACAATAATGATAGAAAT-------------TAATGAGTTCCA i panTro2.chr17 C 0 C 0 s mm9.chr11 118657119 180 + 121843856 TGTTTGGCTGAGTCTGGAGAGCTGAAGGAGGCCCCAGTGAAGCATGAGAGACTCCAGCACAAGGAAGCATGACCCAGATC-CTTGGCCTCCCCAGCCTGAGCCCCCATAATAGCTAAGACGAAGAGGGGGTAACATTTTAAATATAAGCTCTACAATTATGATACAAAT-------------CAATGGCTTCCA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4288304 115 + 7991924 TTCCCCACTGGGCCTCTGTACCACCAAGATGCCT-------GGATATGGGGACCTAGCACCAGGGCGGGTGACA----------AGCCTCCT--GCTTG----CCTCTCATATCC---------------------------------CTCTCC---------ACAAAT-------------TGACAGC-CCTG i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10744377 147 - 65312493 TAGTTGGCTGAGGCCTGAGAGGTGATAGAGGCCCCACTTAAGCATGAAAGGCAGCAGGGCAAGGAAACA-------------------CTCCCACTCTTAT--------------AAGATCAAAAGAAGACAAA-CCTTAAAAATAAACTTTGCAATAATAATAATAAG-------------CAATGATTTCCA i bosTau4.chr19 I 661 I 3 s equCab2.chr11 57933049 153 - 61308211 CGGTTTGCTGAGGCCTGAGAGCTG--AAAGGGCA----------GGAAAGGCCACAGGGCAGGGAAACATGGCT--GCTCATTCGCCCTTCCCACCCCAAG--------------GAGATCAAAAGAGGATGAAGTTTTAAAGATAAGCCTTGCAGGAAAAATAATAAG-------------CAATGATTTCCA i equCab2.chr11 C 0 I 2 s canFam2.chr9 59349829 161 - 64418924 AGGTTTGCTGAGTCCTAGGAGCTGCCATAGGCCC-----------------CCACTAAGCCAGGAAACAACCAT--GATAATTTGTCCTTACCACCCCAAT--------------AAGATCAAAAGAGGATAAAGTTTTCAAAATAAACTTTGCAATAATAATAACAAGCAATGAAAATAAACAATGACTTCAG i canFam2.chr9 C 0 I 7 e monDom5.chr2 304251105 3824 - 541556283 I e loxAfr3.scaffold_49 14274944 449 - 17734757 I a score=75167.000000 s hg19.chr17_gl000204_random 1931 107 + 81310 CACAGATAGGCAGATAGACAGGGGATGACGCATGAATA---------AATGGATACCTGCatagatggataatagatagatgagtagatggat---aggca------------gatggatatagagacata s rheMac2.chr16 74728317 107 + 78773432 CATAGATAGGCAGATAGACAGGGGATGACGCATGAATA---------AATGGATACCTGCatagatggataatagacagatgagtggatggat---aggca------------gatggatatagagacata i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69562476 99 + 73212453 CGTAGATAGGCAGAT----AGGGGATGACGCATGAATA---------AATGGATACCTGCatagatggataatagatagatgag----tggat---aggca------------gatggatatagagacata i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79177724 107 + 83384210 CATAGATAGGCAGATAGACAGGGGATGACGCATGAATA---------AATGGATACCTGCatagatggataatagatagatgagtagatggat---aggca------------gatggatatagagacata i panTro2.chr17 C 0 C 0 s mm9.chr11 118657299 98 + 121843856 GGCAGACAGATAGAAGGATAGATG-----------ACA---------GATGCATGTCTGCATTCACGGGTAAATGCCGGATGGATGAGAAGATGGCAGGGA------------GACAGAGA-ATAGGTATG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4288419 97 + 7991924 GGTGGA---atagatggatagaga------tacacatg---------gatagacagatgcatagataggtaagaggtacatggatagacacat---aggca------------aatggata-CTGGATGTC i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10744527 115 - 65312493 AGGaggtaggtgggaagatacggg--------tggacagtaataggtaatggatatacacatagttggacaatagatacacggatggatggat---aaatacatacat-----gattgataactagatata i bosTau4.chr19 I 3 I 335 s canFam2.chr9 59349997 106 - 64418924 GAGAGGTAGGtggatggat--ggg--------tgggtag--------ggtggatggatgcatgggtg---aatggatgtatcgatagatgagt---gggga-atgggtggggggatggttggatgggtgtg i canFam2.chr9 I 7 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e equCab2.chr11 57933202 2 - 61308211 I e loxAfr3.scaffold_49 14274944 449 - 17734757 I a score=33693.000000 s hg19.chr17_gl000204_random 2038 63 + 81310 cagatagacaggcaggtagacag-----gt-gacagat-gatggatggatgcatagacagatgatggatg s rheMac2.chr16 74728424 63 + 78773432 cagatagacaggcaggtagacag-----gt-gatagat-gatggacagatgcatagacagatgatggatg i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69562575 63 + 73212453 cagatagacaggcaggtagacag-----gt-gatagat-gatggatggatgcatagacagatgatggatg i ponAbe2.chr17 C 0 T 2440 s panTro2.chr17 79177831 63 + 83384210 cagacagacaggcaggtagtcag-----gt-gatagat-gatggatggatgcatagacagatgatggatg i panTro2.chr17 C 0 C 0 s mm9.chr11 118657397 59 + 121843856 TGGTTAGATGCAGGGGTAAGCAAAGGGGAT-GATGGATAAATAAATAGATGCACC-----ATCAT----- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4288516 50 + 7991924 TGTAGACATGCACATATAA---------CT-gataaat-aacagatacatgcata----gatcat----- i cavPor3.scaffold_76 C 0 C 0 s canFam2.chr9 59350103 56 - 64418924 tgggtggatgggtgggtggatgg-----atcgatagat-gagtgggggatg--------ggtgggggatg i canFam2.chr9 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e bosTau4.chr19 10744642 335 - 65312493 I e equCab2.chr11 57933202 2 - 61308211 I e loxAfr3.scaffold_49 14274944 449 - 17734757 I a score=27291.000000 s hg19.chr17_gl000204_random 2101 36 + 81310 gatggacaggtaggtagacagatacatagatggatg s panTro2.chr17 79177894 36 + 83384210 gatggacaggtaggtagacagatacatagatggatG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69560198 36 + 73212453 gatggacaggtaggtagacagatacacagatggatg i ponAbe2.chr17 T 2440 I 2404 s rheMac2.chr16 74728487 36 + 78773432 gatggacaggtaggtaaacagatacatagatggatg i rheMac2.chr16 C 0 C 0 s mm9.chr11 118657456 24 + 121843856 ------------GGAAAACagacacatagctaaatg i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4288566 23 + 7991924 ------------gatgcatgtgtacatgggtggat- i cavPor3.scaffold_76 C 0 C 0 s canFam2.chr9 59350159 34 - 64418924 gatggatgggtgtgtgggtggatAGGTAGGTGGA-- i canFam2.chr9 C 0 M 925 e monDom5.chr2 304251105 3824 - 541556283 I e bosTau4.chr19 10744642 335 - 65312493 I e equCab2.chr11 57933202 2 - 61308211 I e loxAfr3.scaffold_49 14274944 449 - 17734757 I a score=91330.000000 s hg19.chr17_gl000204_random 2137 180 + 81310 attgaacagacagacaatagatcaacaaatgaatggatagacg-------ggtacacacatggatgatagatagatgcatacacagacataggtagatagatcggtagcagataggcaggcaggcaggcagacagacaggAggatggatgaatgaatgaatggatg-------gatggatggatagatagatAG s rheMac2.chr16 74728523 168 + 78773432 attgaacagacagataatagatcaacaaatggatggacagatg-------gatacacacatggatgatagata----catacacagaca----tagatagatcgatagaagat----gggcaggcaggcagatagacagGAGGATGGATGAATGAATACatggatg-------gatagatagatagatagatag i rheMac2.chr16 C 0 I 47 s ponAbe2.chr17 69562638 180 + 73212453 actgaacagacagataatagatcaacaaatggatggataaatg-------gataCACACATGGATgatagatagatacatacagaaacataggtagatagatcgattgcagataggcaggcaggcaggcagatagaccggaggatggatgaacgaatggatggata-------gatggatagatagacagatag i ponAbe2.chr17 I 2404 C 0 s panTro2.chr17 79177930 172 + 83384210 ATTGAACAGACAGACAatagatcaacaaatgaatggatagaca-------ggtacacacatggatgatagatagatacatacacagacataggtagatagatcgatagcagat----aggcaggcaggcagacagacagGAggatgg----atgaatgaatggatg-------gatggatggatagatagatAG i panTro2.chr17 C 0 C 0 s mm9.chr11 118657480 173 + 121843856 gacagacagaaatataatagat--ac--atggatggatcagtaatatctatatacaaatatagatggatgctagacatatatgtgcacatgtaaagat-----aat---aaat----gtacaagtggatggatatacagtcagacagtcagata-atgcataaatgcatatataATTgatgggtaggt----ag i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4288589 160 + 7991924 ----gacagatacaacatagatgaac--atggatggatagatgataaatagatggatagacagacaacagttacatggatggatggaccaatagaGAT-----GATGACAAAT----G-----ACGGAGGAATTgatggagagatatatggatg-atggatggata-------gatggatggatggat------ i cavPor3.scaffold_76 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e bosTau4.chr19 10744642 335 - 65312493 I e equCab2.chr11 57933202 2 - 61308211 I e loxAfr3.scaffold_49 14274944 449 - 17734757 I a score=20316.000000 s hg19.chr17_gl000204_random 2317 73 + 81310 Cagataggcaggcagatagacagaaggatggatggatga----atggatggatggatagatagataggagacaggca s panTro2.chr17 79178102 77 + 83384210 Cagataggcaggcagatagacagaaggatggatggatgaatggatggatggatggatagatagataggagacaagca i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69562818 65 + 73212453 cagataggcaggcagatagacaggaggatgg------------atggatggatggatggatagatagCAGATAGGCA i ponAbe2.chr17 C 0 C 0 s mm9.chr11 118657653 59 + 121843856 ---ttgggtggatggatgggtggagagatgggtgagagg----gtggatggatggatggatgggta----------- i mm9.chr11 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e bosTau4.chr19 10744642 335 - 65312493 I e equCab2.chr11 57933202 2 - 61308211 I e cavPor3.scaffold_76 4288749 0 + 7991924 C e loxAfr3.scaffold_49 14274944 449 - 17734757 I e rheMac2.chr16 74728691 47 + 78773432 I a score=103287.000000 s hg19.chr17_gl000204_random 2390 232 + 81310 gacagataggaggatagacgaatggatgcatagat----agatagcagataggcaggcagatagacaggaggatggatggatggatagatagat-----------------------agataggaagatagatg------------------------gcagatagacaggaagaCAGGCAGGAggat--------ggatggatggatggatggatagataga----cagcagataggcaggcagatagacagga--------ggatggatagatagataggaagatagatggcagataggca s mm9.chr11 118657712 189 + 121843856 gatagataggtggatggatg-atgggtggatggtt---------------------------ggataggtggatgggtgaatg----gatggat-----------------------ggatggatggatggatg-----------------------------------ggtggatgggtaagaggat--------ggatgggtagatggatggat-gatggg----tgatggatggttggataggtggatgggt--------ggataggtagatggatggatggatggat---gaatggatg i mm9.chr11 C 0 C 0 s panTro2.chr17 79178179 236 + 83384210 gacagataggaggatagatgaatggatggatggat----agatagcagataggcaggcagatagacaggaggatggatggatg----gatagat-----------------------agataggaagatagaTG------------------------GCAGATAGGCAGGAAGACAGGCAGGAggatggatggagggatggatggatggatggatagataga----tagcagataggcaggcagatagacagga--------ggatggatagatagataggaagatagatggcagataggca i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69562883 295 + 73212453 GGCAGATAGGAGGATGAATGAATGGATGgatggatggacagatagcagataggcaggcagatagacaggaggatggatggatggatggatggatggatagatagcagataggcaggcagataggaggatggatgaatggatggatggatggacagatagcagataggcaggcagatagacaggaggat--------agatagatagatagGAAGATAGATGGCAGTTAGGCAGGCAGGCAGGCagatagacaggaggatggatggatggatagatagataggaagatagatggcagataggca i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74728738 214 + 78773432 gatggatggatgaatggatggatgggtgggtagat----agatagcagataggcaggcagatagatagacaggaagatg--------gatagat-----------------------agataggaagatagatg------------------------gcagataggcaggcagataggcaagaggat--------ggatggataggtaggtaggtaggtagg-----------taggtaggtagatagatagat--------agatagatagatagatagatagatagat---agatagaca i rheMac2.chr16 I 47 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e bosTau4.chr19 10744642 335 - 65312493 I e equCab2.chr11 57933202 2 - 61308211 I e cavPor3.scaffold_76 4288749 0 + 7991924 C e loxAfr3.scaffold_49 14274944 449 - 17734757 I a score=41497.000000 s hg19.chr17_gl000204_random 2622 61 + 81310 ggcagatag--agacgggaggatggatggatggatg--gatggatg------gatggatggatggatggat s rheMac2.chr16 74728952 63 + 78773432 gacagacagacagacagacagacagacagacagata--gatagata------gatagatagatagatagaa i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69563178 61 + 73212453 ggcagatag--aGACAGGAggatggatggatggatg--gatggatg------gatggatggatgaatagat i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79178415 61 + 83384210 ggcagatag--aGACAGGAGGAAGGAAGGAAggatg--gatggatg------gatggatggatggatggat i panTro2.chr17 C 0 I 160 s mm9.chr11 118657901 59 + 121843856 ggcagat----gggtggaagggtaaatggatagatt--gatgggtg------gatgaatgggtgggtggat i mm9.chr11 C 0 C 0 s equCab2.chr11 57933204 68 - 61308211 GGGAGAGAG--AGA-GAGAGAatggatagatggatgatgatagatgatgaataatggaaggatgggtggtt i equCab2.chr11 I 2 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e bosTau4.chr19 10744642 335 - 65312493 I e cavPor3.scaffold_76 4288749 0 + 7991924 C e loxAfr3.scaffold_49 14274944 449 - 17734757 I a score=49432.000000 s hg19.chr17_gl000204_random 2683 133 + 81310 AGCAGATAGGCAGGCAGGCAGACAGGA--------Ggatggatggatggatagatagatagactgattgat------------------------------------tgactgatcgactgacagactgacagatagatagatagatggatacagatagataTGGATATAGCTCCTC s rheMac2.chr16 74729015 105 + 78773432 agaagataggcaggcagacagacagac--------aggaggatggatggatagattggttgattgatagag----------------------------------------------------------------agagagagagatagatacagatagataTGGATATAGCTCCTC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69563239 177 + 73212453 agcagataggcaggcaggcaggcaggcaggagggtggatggatggatggatagatagatagatagatagatagatagatagatagatagatagatagatagacagacagactgattgattgactgactgactgacagatagatagatgaatacagatagataTGGATATAGCTTCTC i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79178636 133 + 83384210 AGCagataggcaggcaggcagacagga--------ggatggatggatggatagatagatagactgattgat------------------------------------tgactgattgactgacagactgacagatagatagatagatggatacagatagataTGGATATAGCTCCTC i panTro2.chr17 I 160 C 0 s mm9.chr11 118657960 104 + 121843856 ---gggtAGGAAAGTGAGTAGATGTGT--------AGATGTATGGAT-GATAGCTTAATGAACAGATGAGT-----------------------------------------GATTG------------------GAAGAAGCAGAGGCAAAAAGATAGAGATGGA-GTAGGTCCC- i mm9.chr11 C 0 C 0 s equCab2.chr11 57933272 76 - 61308211 -----------------------------------ggctggatggatagatagatacatagatacatagat------------------------------------------------------------acatagatagata-atgcagatagatggataTAGACATACC----- i equCab2.chr11 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e bosTau4.chr19 10744642 335 - 65312493 I e cavPor3.scaffold_76 4288749 0 + 7991924 C e loxAfr3.scaffold_49 14274944 449 - 17734757 I a score=163259.000000 s hg19.chr17_gl000204_random 2816 305 + 81310 TATAGAGGAGAAAATGTAGGGAAAAAAA-CCCCTATATTTTCCCCT-ACACCTTCTCCTTTATGGGTCA-TTCAGAAAGGTCGGTCCAGGTCT-TGACATCGAGTTGGCAGCAGAGGAG----------CCAAGGACTCAAGCC-AGATGAATTCTCACTGGTCACGAG----GTGTCTGACATGTATGCTGGGCGGGCTCAAGTCCAGGTCTGTGCCCATCTCCCTGCAGCAGCACTGGGGCCCCTTGGCCGCCCATGCAGTCCTGGGAA--------TCCAGGCACCAGGGACCAGACCTGACCTGAAACAGGGA--TGTGTGTGG--AGAGGA s equCab2.chr11 57933348 286 - 61308211 ----------------------AAAAAA--TCCTATATTTTTCCTTTGTACCTTCTCCTCCACAGTTCATTTCAGAGAGGTCAGTCCAGGGCTCCGACACCGCGT-GGTGACTGAGCAG----------CCAAGGGTCCAAGCT-CAGACAATTCCCACTGGGCAGGAGTGACGTGGTCTGAACCTGCGTAGGGCCGGCCGCAGTGCAGGTCTCTGTTCATCTCCTGTCAGCAGCACCAGCGCCCCATGACCTCCCCTGGTCTCCCGCATAGCCC---CTCCAGAC-CCTGGGGCTATCCCTGACCTGACACAGCCT--------TGG--AGAGGA i equCab2.chr11 C 0 C 0 s cavPor3.scaffold_76 4288749 237 + 7991924 CATAGATGAAGAAA------GAAAAAAG--CGCCCTATTTCCCCCT---------TCCTTTATGGTTCATTTCAGAAAAGTCGGTCTG----------------TTGGTGGCAGATACT----------CCAAGAATGAAAGCT-----------GCACTGGGCATGAA----GTGGCCTACAT---TGTTGGGCAGGCCCAAGTCCAGGTCTGTAACCATCT-------------------CCTCTTGGCAGTCACCATCGTCTTGGAAATCCC---CTTGAGGTG-CAGGTAGGACCCCT-----------GGGA--TGTGTTTGG--AGGTGA i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118658064 236 + 121843856 ----------------------ACAAAA--CACTCCTTTTCCTCAT-GT-----CTACTTTATAGCTCACTTCAGAAGAAGTGGTCTG-------------GAATCTAGGGTAGAGATGGATAGGTGGACCAAAGGTTCAAGCTCAGATTAA-CCTTCATGGGCACAAG----GCACCTGACACTTGTACTAGGTTGGCCCTAGTCCAGGATGGTGCCCCTCC-------------------TTTTTGTGCAGCC-CCAGGGAC-----AATCTCTAACCTGAGG-----GCTGATGTACCT-----------GGGAATAGTGTT----------- i mm9.chr11 C 0 C 0 s panTro2.chr17 79178769 306 + 83384210 TATAGAGGAGAAAGTGTAGGGAAAAAAAACCCCTATATTTTCCCCT-ACACCTTCTCCTTTATGGGTCA-TTCAGAAAGGTCGGTCCAGGTCT-TGACATCGAGTTGGCAGCAGAGGAG----------CCAAGGACTCAAGCC-AGATGAATTCTCACTGGTCATGAG----GTGTCTGACATGTATGCTGGGCGGGCTCAAGTCCAGGTCTGTGCCCATCTCCCTGCAGCAGCACTGGGGCCCCTTGGCCGCCCATGCAGTCCTGAGAA--------TCCAGGCACCAGGGACCAGACCTGACCTGAAACAGGGA--TGTGTGTGG--AGAGGA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69563416 311 + 73212453 TATAGAGTAGAAAATGTAGAAACAAAAA--CCCTATATTTTCCCCT-ACACCTTCTCCTCTTTGGGTCA-TTCAGAAAGGTCGGTCCAGGTCT-TGACATCGAGTTGGCAGCAGAGGAG----------CCAAGGACACAAGCC-AGATGAATTCCCACTGGTCACGAG----GTGTCTGACATGTATGCTGGGGGGGCTCAAGTCCAGGTCTGTGCCCATCTCCTTGCAGCAGCACTGGGGCCCCTTGGCCGCCCATGTGGTCCTGGGAATCCC---CTCCAGGCACCAGGGTCCAGACCTGACCTGAAACAGGGA--TGTGTGTGTGCAGAGGA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74729120 281 + 78773432 TATAAAGGAGAAAATGTACAAAAAAAAG---CCTATATTTTCCCCT-ATAC---CTCCTTTATGGGTCA-TTCAGAAAGGTTGGTCTGGGTCC-TGACATCGAGTTGGCAGCAGAGGAG----------CCAAGGACTCAAGCC-AGTTGAATTCTCACTGGTCACGAG----CTGTCTGACATGTATGCTGCATGGGCTCAAGTCCAGGTCT------------------------TGGGGCCCCTTGGCCACCTATGTGGTCCTGGGAATCCC---CTCCAGGCACCAGGGACCAGACCTGACCTGAAACAGGGA--TGTGTGTAG--AGAGGA i rheMac2.chr16 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e bosTau4.chr19 10744642 335 - 65312493 I e loxAfr3.scaffold_49 14274944 449 - 17734757 I a score=55617.000000 s hg19.chr17_gl000204_random 3121 62 + 81310 C-----CCCACTCCACGTCAGGGCGCCTGGTCCTGCCTAACGCTCCAGCCTGGACAACTGC---CCTGTG------- s rheMac2.chr16 74729401 62 + 78773432 C-----CCCACTCCACATCAGGGCGCCTGGTCCTGCCTAATGCTCCAGCCTGGACAACTGC---CATGTG------- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69563727 62 + 73212453 C-----CCCACTCCACATCAGGGCGCCTGGTCCTGCCTAATGCTCCAGCCTAGACAACTGT---CCTGTG------- i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79179075 62 + 83384210 C-----CCCACTCCACGTCAGGGCGCCTGGTCCTGCCTAACGCTCCAGCCTGGACAACTGC---CCTGTG------- i panTro2.chr17 C 0 C 0 s mm9.chr11 118658300 60 + 121843856 ------CCCTCACCATGT-AAGTCACCTCGACCTGCCTAGTGATCTGACCAGGACTGCTGC---ACCCTG------- i mm9.chr11 C 0 I 1612 s cavPor3.scaffold_76 4288986 66 + 7991924 GTCACCTCCTCAGCATGT-AAAGCTGCTGGTCCTGCTCCCCGGCCCTCCCTGCATCACTGT---GTTCTT------- i cavPor3.scaffold_76 C 0 I 21 s equCab2.chr11 57933634 65 - 61308211 GTG---TCCACTCCATGTGAAGTCCCCTGGTCCTGCCTCATGCCCCAGCCTGGACGAGGGTG--CCCGTG------- i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14275393 64 - 17734757 -----CCATACTCGGCATCACGTCACCTGGTCCTGC--------CCAGCCTGGATAACTGTGTCCCTGTGTCCCATG i loxAfr3.scaffold_49 I 449 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e bosTau4.chr19 10744642 335 - 65312493 I a score=27341.000000 s hg19.chr17_gl000204_random 3183 89 + 81310 CCTACATTC---------------------------------CCTGTGCCGTCCCTGTCCCC-TGTCCT----------------GCAGGTAAGCAGCT---GACCA---CCTGCTCGCA------------------------------------CCTCACATCT------CCCTATGGCACATGC s rheMac2.chr16 74729463 85 + 78773432 CCTACATTC-------------------------------------TGCTGTCCCTGTCCCC-TATCCT----------------GCAGGTAAGCAGCT---GACCA---CCTGCTCGCA------------------------------------CCTCCCATCT------CCCTATGGCACATGC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69563789 83 + 73212453 CCTACATTC-------------------------------------TGCCGTCCCTGTCCC---ATCCT----------------GCAGGTAAGCAGCT---GACCA---CCTGCTTGCA------------------------------------CCTCCCATCT------CCCTATAGCACATGC i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79179137 89 + 83384210 CCTACATTC---------------------------------CCTGTGCCGTCCCTGTCCCC-TGTCCT----------------GCAGGTAAGCAGCT---GACCA---CCTGCCCGCA------------------------------------CCTCACATCT------CCCTATGGCACATGC i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4289073 107 + 7991924 CCTGTGTTT-------------------------------------GGCCA--CTTGTACTC-AGACCTCTCTGATGGTGGACAGGCAGGGCAGCTGCTTAGGTCCAGGTCCTG-TTGCA------------------------------------CACCCAGCCTCATTGGCCTTCTGCCA---GC i cavPor3.scaffold_76 I 21 C 0 s equCab2.chr11 57933699 106 - 61308211 ---------------------------------------------------TCCCTGTATCAGTGACCC----------------ACCGATAAGGACAT---GGCCA---CCTGCTCTCAGACCTCCTG--GGGGGAGGGGCAGGCTGCTGCTTGGACTCTCAGAT------CTCTGCTGCACATGC i equCab2.chr11 C 0 I 20 s loxAfr3.scaffold_49 14275457 156 - 17734757 CCCACGTCCCTGTCTCAATACCCTCTGTCCCCATGGCTGTGTCCTGCCCTGCTCCTGCCCCT-CCCCCT----------------CCTAATAAGATCCT---GGCCA---CTTGCTGTCAGACCTCCGGCTGGGGCTGGGGCTGCTGCCTGGAC--CCTCACATCT------CCCTATTGCCTGTGC i loxAfr3.scaffold_49 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e bosTau4.chr19 10744642 335 - 65312493 I e mm9.chr11 118658360 1612 + 121843856 I a score=73597.000000 s hg19.chr17_gl000204_random 3272 131 + 81310 --------CCCAC--------CCCACCACCCTTTAGGTGCCACAATGAGCCTGCCAGACCAGACTCCCTCCCTCCACCCACAGCTGCACACAACTGGATGTGGGACCCCAAAAAACA--------GGTTT--------GGCCTCCCTCATT-----------------CCACCAG-GATGG s loxAfr3.scaffold_49 14275613 127 - 17734757 CCAGTCTTCCAGT--------CTCATGGCCCTCAAAGGCAGCCAACCACCCTGCAGGACTGGATTTCCTCCCCATGGCCCCATCCTTGCCCTGA------------CGCAGGAAATG--------GTGCA--------TTTCCAGGTCCCA-----------------GCCCCAA-GGTGG i loxAfr3.scaffold_49 C 0 C 0 s equCab2.chr11 57933825 164 - 61308211 --------TCCACGGGGAATGCTGACCACCCTTCAGGGGTTGCATGGAACCTGCCAGACTGGACTTCCTCCCTCTGCCGAGGGCCAGACACAGCTAGATCTGTGACCCTAGAAAGCA--------GATTCGTTTCCA-GGTCCAGCCCCTCCTGGTGGGCTTCCCCTCGTCCCAGTGGTGG i equCab2.chr11 I 20 C 0 s bosTau4.chr19 10744977 146 - 65312493 --------TCTCCCAAGCACACT-----------AGGGGCTGCATGGAACCTGCCACATTGGACATCCCCTCAC-ACCCACAGCTGAACAGAGCTGGATCTGCGACCCCAGGAAGCA--------GATTCCTTTCCAGGGCCCAGACCATCACGGTGGGACT------GCAGCAG-GGAGA i bosTau4.chr19 I 335 C 0 s cavPor3.scaffold_76 4289180 114 + 7991924 --------CTGGT--------CTGATCACAC-TTAGGTGCTGCGCTGAG---------------------CCACAGCGCACAACAGGACACAGC---ATGTTCATTTCCAAGTCTCAACCCCTGCAGGTG--------GGTCCCCCTCATC-----------------CCACCAG-GATGG i cavPor3.scaffold_76 C 0 C 0 s panTro2.chr17 79179226 131 + 83384210 --------CCCGC--------CCCACCACCCTTTAGGTGCCACAATGAGCCTGCCAGACCAGACTCCCTCCCTCCACCCACAGCTGCACACAACTGGATGTGGGACCCCAAAAAACA--------GGTTT--------GGCCTCCCTCATT-----------------CTACCAG-GATGG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69563872 131 + 73212453 --------CCCGC--------CCCACCACCCTTTAGGTGCCACGATGAGCCTGCCAGACCAGACTCCCTCCCTCCACCCACAGCTGCACACAACTGGATGTGGGACCCCCAAAAACA--------GGTTT--------GGCCTCCCTCATT-----------------CCACCAG-GATGG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74729548 130 + 78773432 --------CCCAC--------CCCACCACCCTTTAGGTGCCACGTTGAGCCTGTGGGACTAGACTCACTCCCTCCGCCCACAACTGCACACAACTGGATATGTTG-TGCAAAAAACA--------GTTTC--------GGCCTCCCTCATT-----------------CCACCAG-GATGG i rheMac2.chr16 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e mm9.chr11 118658360 1612 + 121843856 I a score=25560.000000 s hg19.chr17_gl000204_random 3403 39 + 81310 GGTGATCTGAGCTAAGAGAGGG-AAGGACCTCTAGTTAAA s rheMac2.chr16 74729678 39 + 78773432 GGTGATCTGAGCCAAAAGAGGG-AAGGACCTCCAGTTAAA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69564003 39 + 73212453 GGTGATCTGAGCCAAGAGAGGG-AAGGACCTCTAGTTAAA i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79179357 39 + 83384210 GGTGATCTGAGCTAAGAGAGGG-AAGGACCTCTAGTTAAA i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4289294 39 + 7991924 GATGATCTGGCCCAAGAAATGACAGGGACCTGGGATCAG- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10745123 26 - 65312493 CATAATGTAAAGCAAGGAA-------------GGGTGCA- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57933989 38 - 61308211 GCTGATGTGGGCCAAGGAATGA-CAGGACCCTAGTTCCA- i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14275740 39 - 17734757 GATGATCTGAGCCGAGAAAGGA-CAGGACTCCCCGTTAGT i loxAfr3.scaffold_49 C 0 C 0 s oryLat2.chr15 992599 36 - 30000224 GGAAACCTGCTCTAAGGAG----AACGTTCTCTAAGGAGA i oryLat2.chr15 N 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e mm9.chr11 118658360 1612 + 121843856 I a score=-1676.000000 s hg19.chr17_gl000204_random 3442 59 + 81310 ---TGTAATGGGGAGGGCAGCTT-----GCTCACGTGCAGTCAGAAGAACACGC----ATGAAGGAGAGCG s equCab2.chr11 57934027 59 - 61308211 ---TGTCCGGGGGAGGCCGGTTT-----GCGGGGCTGGAGTCAGGAGAGCATGTGTGAAGGCAGGAA---- i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10745149 56 - 65312493 ---TGTCAGGGGAAGGGCAGTTT-----GCTGAGCCAGAGTCAGGAGAAGATGTG---AAGCAGGGA---- i bosTau4.chr19 C 0 I 36 s dipOrd1.scaffold_46013 7280 53 + 10667 ---TGGAGTGCGCAGGGCGGAGT-----GC------GCAGGACGGGGAGCACGC----AGGATGGAGAGCA i dipOrd1.scaffold_46013 N 0 C 0 s panTro2.chr17 79179396 59 + 83384210 ---TGTAATGGGGAGGGCAGCTT-----GCTCACGTGCAGTCAGAAGAACACGC----ATGAAGGAGACCG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69564042 59 + 73212453 ---TGTAATGTGGAGGGCAGCTT-----GCTCACATTGAGTCAGGAGAACACGC----ATGAAGGAGAGCA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74729717 59 + 78773432 ---TGTAATGGGGAGGGCAGCTT-----GTTCACGTGGAGTCAGGAGAACACGC----ATGAAGGAGAGCG i rheMac2.chr16 C 0 C 0 s ornAna1.Contig15807 5581 41 + 13614 ------agtggggagagcaactg-----aaggggagagagcatgaagggcag------------------- i ornAna1.Contig15807 N 0 I 20 s loxAfr3.scaffold_49 14275779 39 - 17734757 ------CATAAAGGGAACAGCTT-----GCTGGC-TGGGGTCCGAGGAGCA-------------------- i loxAfr3.scaffold_49 C 0 C 0 s cavPor3.scaffold_76 4289333 23 + 7991924 ----------GGTAAAGGGAAGT------------------------------C----AGAGTGGAG---- i cavPor3.scaffold_76 C 0 C 0 s oryLat2.chr15 992635 67 - 30000224 ACCTGTTCTAAGGAGAACGTGCTCTAAGGAGAACCTGCTCCAAGGAGAACCGGC----TCCAAGGAGAACG i oryLat2.chr15 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e mm9.chr11 118658360 1612 + 121843856 I a score=-32244.000000 s hg19.chr17_gl000204_random 3501 136 + 81310 CTCATGAGGGAGAGCTCGCATGGGGGAGCACGTGCACGGAGGAGAGGGTGCACAGGGGAGAACGTGCACAAGGGAGAACGTGCATGATGGAGAACGTG--------------------------------CATGAGAG-AGAGCACGCATGGAGATGGAAGACCATCTC s panTro2.chr17 79179455 136 + 83384210 CCCATGAGGGAGAGCTCGCATGGGGGAGCATGTGCATGGAGGAGAGTGTGCACAGGGGAGAACGTGCACAAGGGAGAACGTGCATGAGGGAGAACGTG--------------------------------CATGAGAG-AGAGCACGCATGGAGATGGAAGACCATCTC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69564101 152 + 73212453 CTCATGAGGGAGGGCGCACATGGGGGAAAGCGTGCATGGAGGAGAGTGTGCACAGGGGAGAACATGCACAAGGGAGAACGTGCATGAGGGAGAATGTG----------------CCTGAGGGAGAACGCACATGAGGG-AGAGCACGCATGGAGACGGAAGACCATCTC i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74729776 168 + 78773432 CTCATGAgggagagcacgcatgggggagagcatgcacaggggagagcacgcacaggggagagcgcgcacaggggagaACGCGCACGAGGGAGAACATGCACGAGGAAGAACATGCACGAGGGAGAACACGCACAAGAG-AGAGCGTGCATGGAGATGGAAGACCATCTC i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_114997.1-227327 157982 148 + 227327 GTCACAGGGGAGAACGGCCAGAGAAGAGAATGACCACAGAAGAGAGTGGCCACAGGGGAAAGCAGCCACAGGGGAGAGCAGGCACAGGGGAGAACAGC----------------CAGAGAAGAGAGTGGCCACAAGGG-AGAGCAGGCACAGAGGAGAGAGGCCA---- i otoGar1.scaffold_114997.1-227327 N 0 N 0 s dipOrd1.scaffold_46013 7333 114 + 10667 CGCAGGACGGGGAGCACGCGGGACGGGGAGCACGCAGGACGGGGAGCACGCAGGACGGGGAGCACGCAGGACGGAGAGCACGCAGGACGGGGAGCACG----------------------------------CAGGAT-GGAGCACGCA-------------------- i dipOrd1.scaffold_46013 C 0 N 0 s cavPor3.scaffold_76 4289356 47 + 7991924 -----------------------------------------------------------------TCA----GGAGAACCGGCAGG-----------------------------------------------AAGAT-TGTGCCCCC-TGCAGCTTGCAGTGCA---- i cavPor3.scaffold_76 C 0 C 0 s equCab2.chr11 57934086 29 - 61308211 GCCAGATTCCAGGTCTC---------------------------------------------CGCTCACTGGGG----------------------------------------------------------------------------------------------- i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14275818 9 - 17734757 ----------------------------------------------------------------------------------------GAGGCG-----------------------------------------AGG------------------------------- i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_301801 6112 115 + 11722 TGCTTAAGGGAGCGTGTGCTTAAGGGAGCGTGTGCTTAAGGGAGCGTGTGCTTAAGGGAGCGTGTGCTTAAGGGAGCGTGTGCTTAAGGGAGCGTGTA---------------------------------ATTAAGGGAGCGTGTGC--------------------- i echTel1.scaffold_301801 N 0 N 0 s ornAna1.Contig15807 5642 101 + 13614 tgcaaaagggagaGCTCGTGAAGGAGAGAGCGCACGAAGGAGAGAGCGCATAAAGGGGAGACTGCGTCAAAGGGAGA--GTGCGTGAAGGGGAAAGGG--------------------------------CATGA---------------------------------- i ornAna1.Contig15807 I 20 N 0 s oryLat2.chr15 992702 133 - 30000224 TTCTCTAAGGAGAACCTGTTCTAAGGAGAACCTGCTCTAAGGAGAACGTGCTCTAAGGAGAACGTGCTCTAAGGAGAACGTGCTCTAAGGAGAACGTG--------------------------------CTCTAAGG-AGAACCTGCTCCAAGGAGAACCG---GCTC i oryLat2.chr15 C 0 N 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e bosTau4.chr19 10745205 36 - 65312493 I e mm9.chr11 118658360 1612 + 121843856 I a score=191697.000000 s hg19.chr17_gl000204_random 3637 318 + 81310 ATCATCTCCAGCCCATAGCTCCTCACCCTAAAACACATCCCTGG----------------------------------------------------------------------------------CAGTGTGCTCCAAGGAGTGACCAAGAGCCAGG-----GTGAGGGTCGTAGGCACGTGTGGGGCCTCCTGCAGACCACAGGTGCCTTGGAGGAGAGGCTGTCATGGGT-CATCTTTGTGTCATCCTTACGTTCAGCTCCACACACACAGCCCCTGGCCCCGATCCAGACCCAAAA-GGG--CCCTGCGAATGTTGGAGAATGAATAGTTGTGTGCTTCAATATCACCTGAACTCAGGAGATCAC------TACTGGAGACACCACCGCAGCCCCAGTGGCCCAC-------------------------------------------GTGTGT s panTro2.chr17 79179591 320 + 83384210 ATCATGTCCAGCCCATAGCTCCTCACCCTAAAACACATCCCTGG----------------------------------------------------------------------------------CAGTGTGCTCCAAGGAGTGACCAAGAGCCAGG-----GTGAGGGTCGTAGGCACGTGTGGGGCCTCCTGCAGACCACAGGCGCCTTGGAGGAGAGGCTGTCATGGGT-CATCTTTGTGTCATCCTTACGTTCAGCTCCACACACACAGCCCCTGGCCCCGATCCAGACCCAAAA-GGG--CCCTGCGAATGTTGGATAATGAACAGTTGTGTGCTTCAATATCACCTGAACTCAGGAGATCAC------TACTGGAGACACCACCGCAGCCCCAGTGGCCCACA-----------------------------------------TGTGTGT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69564253 402 + 73212453 ATCATCTCTAGCCCATGGCTCCTCACCCTAAAACACATCCCCGGCAGTGTGCTCCATGGCTCCTCACCCTAAAACACATCCCCAGCAGTGTGCTCCATGGCTCCTCACCCTAAAACACATCCCCGACAGTGTGCTCCAAGGAGTGACCAAGAGCCAGG-----GTGAGGGTTGTAGGCACATGCAGGGCCTCCTGCAGACCACAGGTGCCTCGGAGGAGAGGCTGTCATGGGT-CATCTTTATGTCATCCTTACGTTCAGCTCCACACACACAGCCCCTGGCCCTGATCCAGACCCAAAA-GGG--CCCTGTGAATGTTGGAGAATGAACAGTTGTGTGCTTCAATATCACCTGAACTCAGGAGATCAC------TACTGGAGACACCACTGCAGCCCCAGTGCCCCACA-----------------------------------------TGTGTGT i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74729944 361 + 78773432 ATCATCTCCAGCCGGTGGCTCCTCACCCTAAAACACATCCCTGG----------------------------------------------------------------------------------CAGGGTGCTCCAAGGAGTGACTAAGAGCCAGG-----GTGAGGTTCGTAAGCACGTGCAGGGCCTCCTGCAGACCACGGGCGCCTCAGAGGAGAGGCTGTCATGGGT-CATCTTTATGTCATCCTTACATTTAGCTCCACACACACAGCCCCTGGTCCCGATACAGACCCAAAA-GGG--CCCTGCGAATGTTGGAGAAAGAACAGTTGTGTGCTTTAATTTCACCTGAACTCAGGAGATCAC------TACTTGAGACACCACCGCAgccccagtggcccacatgtgtgtacctgggacgtcctcctggccccagtggcccacgtgtatgt i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4289403 264 + 7991924 ----CCTGGCGGCCTCAGCTCTTCACCCGGAAACACCTGCTGGG----------------------------------------------------------------------------------GGGTGTG------GGAG---CCCGGAGCCCGGAGTGTGGGAGAGTTGTACACATAT-----GCCTCCTTCAGAAC-TGGGCTCCTCAGACCAGGGCCCATAGTGGGTCCATCTTTG---CATCATTGTGTTTAATCCCAGGCCCCCAACACCACACCCAGTCTTTGCTCCTCAA--GG--CTCTGTAGATGCTAAAGAGGGAAGAGATGTGAACTGTGAGTTCACCCTGATTCAGGAGAT-----------------------------TCCCAG--------------------------------------------------------- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10745241 277 - 65312493 -----TTCCAGAGCTGGGCTCCTCCCACAGAAAGACACACCTCA----------------------------------------------------------------------------------CAGAGTGCTCTGAGGATTAAATAAGAGCCCAG--GGTGAGACTTTCACACACGTATGGAGGTTCTCCTGCTGACCACAGGTT--------------CTCTCTTTTGTCACTCCTTGTACCATCC-TGTGCTTAGCTTGGCACCCACAGCACCAGGTCC--TTTTCTGCCCTTAATGTG--CTCCAAAAATGTTGGAGAATGAATACGTACACATTTGGATTTCATCCTAACTATGGATGTcacctgcaatgcaggagac------------------------------------------------------------------------- i bosTau4.chr19 I 36 I 170 s equCab2.chr11 57934115 300 - 61308211 ------TCCAGACCACGGCTCCTCCCACAGAAACACACATCTCG----------------------------------------------------------------------------------CGGGGTGCTCCACAGAGTGAAGAAGAGCCCGG--CACGAGAGCATAGCATGCACA-GTGGGTTCTCCTGTGGACCACAGG----------------CTGAATTTCATCTATCTTTGCCCCATCC-TATACTTAGCTCAGGACCCACGGCACCGGGCCCAGTTTCAGGCCCCTAAAAGG--CTCCATAAATGTTGGAGAGTGAATAGAAACCCGCTTGGATTTCATCCTCAATCAGGATGTCACC-----AGCCTGAGGCATCTCTCCATCCCTAATGGACAACATGCAC------------------------------------------- i equCab2.chr11 C 0 I 2 s loxAfr3.scaffold_49 14275827 211 - 17734757 ------CCCAGCTC--AGCCCTCCACTCCCCAGCACATCACCTG----------------------------------------------------------------------------------CAGAATG---------------------------------------------------------------------CAGGATTCTCAGAGGAGAGATGGCATTTCCTCCATCTCTGCACCATCTGAGCACTCAGCCCAGTCCCCACAGCCCCTGGCCAGGTCCCCGCCCTTAAA-GGGGCCTCCATACATGCTGGAGAAGGAATAGACAAGTGTTTTCAC-TCATCCTGACTCAGGGTATCAC------CTC-------------------------------------------------------------------------------- i loxAfr3.scaffold_49 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e mm9.chr11 118658360 1612 + 121843856 I a score=40274.000000 s hg19.chr17_gl000204_random 3955 33 + 81310 ACCTGGGACATCATCCT---------GGCCCCGGTGGCCAAA s panTro2.chr17 79179911 33 + 83384210 ACCTGGGACATCATCCT---------GGCCCCAGTGCCCAAA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69564655 33 + 73212453 ACCTGGGACATCATCCT---------GGCCCCAGTGGCCAAA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74730305 33 + 78773432 acctgggacgtcctcct---------ggccccagtggccAAA i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4289667 32 + 7991924 -CCTAAGATATTACCCT---------GCCCACAATGGCCAAC i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10745688 33 - 65312493 GCTTGAGACATCACTCC---------ACCTCCAATGGCCAAC i bosTau4.chr19 I 170 C 0 s equCab2.chr11 57934417 32 - 61308211 ACCTGAGCCATCTC-CC---------GGCCCCAGCGGTCAGA i equCab2.chr11 I 2 C 0 s loxAfr3.scaffold_49 14276038 41 - 17734757 -CCTGAGACCTCTGCCTCCTGCCTTCCACCCCAACAGCCAGC i loxAfr3.scaffold_49 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e mm9.chr11 118658360 1612 + 121843856 I a score=125564.000000 s hg19.chr17_gl000204_random 3988 147 + 81310 ATGCCGTGTGT----CCACTCTGCTGG----------ACAGAGGG-GAAAGAGTAAAGACTGTCAACAGCAAATAAGACAGGCTGGC--GGGTGGGCTAGGGCTGGACGGAGGGCTGTCTTCACTCAACAGCT----CCCCCCGAGGCTACT-GGCTCCCCATGTGAAA s panTro2.chr17 79179944 148 + 83384210 ATGCCATGTGT----CCACTCTGCTGG----------ACAGAGGG-GAAAGAGTAAAGACTGTCAACAGCAAATAAGACAGGCTGGT--GGGTGGGCTAGGGCTGGAGGGAGGGCTGTCTTCACTCAACAGCT---CCCCCCCGAGGCTACT-GGCTCCCCGTGTGAAA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69564688 149 + 73212453 ATGCCGTGTGT----CCACTCTGCTGG----------ACAGAGGG-GAAAGAGTAAAGACTGTCGACAGCAAATCAGACAGGCTGGT--GGGTGGGGTAGGGCTGGAGGGAGGGCTGTCTTCACTCAACAGCT--CCCCTCCTGAGGCTACC-GGCTCCCCGTGTGAAA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74730338 151 + 78773432 ATACCATGTGT----CCACCCTGCCAG----------ACAGAGGG-GAAAGAGTAAAGACTGTCAACAGCAAATCAGACAGGCTGGT--GGGTGAGCTAGGGCTGGAGGGAGGGCTGTCTTCATTCAACAGCTCCCCCCGCCCGAGGCTACT-GGCTCCCCGTGTGAAA i rheMac2.chr16 C 0 C 0 s mm9.chr11 118659972 134 + 121843856 ATGCTGTAGCC----TTGCCCTACTCG----------GTACAGGGTGA---AGATGAGAATCTTACCAGTAGATACCACAG-CTGGT--AGGTGAGGTAGGCTTGGAGTGC---CTGTGTTCACATGACTGCT---ATTCTCTATGGG---------ACTTCTTTAAAA i mm9.chr11 I 1612 C 0 s cavPor3.scaffold_76 4289699 143 + 7991924 AAGCAGGGGCCAACATGTCCCCACTGG----------ACAGATGG-GA---AGTAGGGACTGTTACCGGCAATTGAGATGG---AGC--GGGGAGGGAACATTCGGGGTGT-GACTGTCTTTACTCAGCAGCT---CATCTCTGATGA--CC-AATTCCCTTTGTGAAA i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10745721 133 - 65312493 -------AGGC----GTATCTCTGAGACCCCACCCACACAGAGAA-GAAAGAGTGGAGATTATTACCAG--AAATTGGCAGGCTGGTGGGGGTGG------------------AGTATCTTCACTCAACAGCT---CATTTCT-AGGCCACTAGGCCGCCTATATGAAA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57934449 140 - 61308211 -------GCAC----CCATCTTAGTGG----------ACAGAGAG-GAAAGAACAGAGATTAACAGCA---AGTTGGGCATGCTGGTGGGGGTGGGGCGGCAACTGAGGGTGAGGTACCTTCACTCAACAGCT---CACCTCC-AGGCTACCGGGCCCCCTGTGTGAAA i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14276079 139 - 17734757 ATGCAG-GCAC----CCACCCTACTGG----------ACGGAGGT-GGAAGTGTAGAGACTGTTACCAGCAAACCAGATGGGCT-----GGGGAGGTCGGGGTC--ACAGAGGAGCATCTTCACTCAATGGCT---GGTCTCT-GGGCTA---GGTTCCCTATGTGAAA i loxAfr3.scaffold_49 C 0 I 201 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M a score=165470.000000 s hg19.chr17_gl000204_random 4135 155 + 81310 TGT--------------CGCCACATT-----------------------------------------ATAAGCAGAGTCTCATAAAATT---TCACAGGAAGGTGGCATTAAAATTCTTCTACTCCAAACCACC----CCTCAGCACACACATGCAT-------CTAAGGTTAGAATCCC---------TTCCCCAACAT-CCTACCACgtgcttctcaagctagggaac-------------cccc s panTro2.chr17 79180092 155 + 83384210 TGT--------------CGCCACATT-----------------------------------------ATAAGCAGAGTCTCATAAAATT---TCACAGGAAGGTGGCATTAAAATTCTTCTACTCCAAACCACC----CCTCAGCACACACATGCAT-------CTAAGGTTAGAATCCC---------TTCCCCAACAT-CCTACCACATGCTTCTCAAGCTAGGGAAA-------------CCCC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69564837 155 + 73212453 TGT--------------CGCCACATT-----------------------------------------ATAAGCAGAGTCTCATAAAATT---TCACAGGAAGGTGGCATTAAAATTCTTCTACTCCAAACCACC----TCTCAGCACACACACGCAT-------CTAAGGTTAGAATCCC---------TTCCCCAACAT-CCTACCACGTGCTTCTCAAGCTTGGAAAC-------------CCCC i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74730489 155 + 78773432 TGT--------------TGCCACATT-----------------------------------------ATAAGCAGAGTCTCGTAAAATT---TCAAAGGAAGGTGGCATTAAAATTCTCCTACTCCAAACCACC----CCTCAGCACACACATGCAT-------CTAAGGTTAGAATCCC---------TTCCCCAACAT-CCTACCACATGCTTCTCAAACTAGGGAAC-------------CCCC i rheMac2.chr16 C 0 M 1045 s mm9.chr11 118660106 148 + 121843856 TGT--------------CACAGTATC-----------------------------------------GTATATAGCCT--GGTAAAATG---TCATGTGGAGATATTATTTACATTCTTCTAGTCTAGGCCACC----CTTCAACACACA------------------------ACTCCCATAGCAACTCTCCCATGCATCCCTA-CGaggggttctcaaactggggtcc----------catcccc i mm9.chr11 C 0 I 8 s cavPor3.scaffold_76 4289842 153 + 7991924 TGT--------------CACAGCAAC-----------------------------------------CTAACCAGTGT---CTACAACGGCTTCCCAGGGAGATAACA-TTAAATTCATCTAGCGTAAAGTGCC----CGTTAGCACACA------T-------CTGATGCTAGACTCCC---------CTCCCCTACAGCCCTACCTagtgcttctcaaactgaggaacg---------catgccc i cavPor3.scaffold_76 C 0 I 8 s bosTau4.chr19 10745854 225 - 65312493 tgtcgtctatggggtcgcacagagtcggacatgactgaagcgacttagcagcagcagcAGCAGCATCGTATGAAGAGTCTCATCCAATT---TCACA-GATGACAGCGTTAAAATACATCTAATCCAATCCACCCCCTCCCCAGTACACATGTGCAT-------CTCATGTTAGAAACCC---------TCCCCCGACATCCTCACCAA--GCTTCTCAAACCAGAGACCCACCCCTAACCACCCCC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57934589 153 - 61308211 TGT--------------CACAGCGTT------------------------------------------TACACAGAGTCTCATCGGATC---CCACC-GGAAATCACATTAGAATTCATCCAGTGCAATGCAC-----CCCCAGCACACA--TGCAT-------CTCACGTTAGCATCCC---------TTCCCCCAAGC-----------GCTTCTCAAACCAGGGAACACACCCCACCCGCCCCC i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14276419 160 - 17734757 TGT--------------CTCAGCACT-----------------------------------------GTAAGCAG--TCTCATAGAATT---TCACAGGGAAGT-GTGTTGACGTTCATCCAATCCACACTGCT----CCCCAACACACACGTGCATCCTGCCCCTAACGTAGGAATCTC---------TTCCCCAACATCCCTACCGagtgctccgcaaaatggggagc-------------ccct i loxAfr3.scaffold_49 I 201 I 1 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M a score=557456.000000 s hg19.chr17_gl000204_random 4290 470 + 81310 ctcagcc-cccaagggtgtgcagaggtgagatgagggtggctggccacacagcccacgcatgtgcctcctctcaa-agtatccg----ttctagccaaa-gtgtctgggggaactattactgtcaggttatagccagcacaagcatattgtggattcaatgtaagatgtgcttgaagttttaagagaacaaataagacttcaaagaaatgtcatcctttctctggaccccttctggcaacacacgtccagtccctcaggggtacaggtttaatatt-tcctctcttctggagtcttccggggaaaa-tgtATACCTCCAGGGAAATGCTGTGTGCCTCTCTGTCATCCAAGACAGGCCACTTAATCTCCCTTTGCCTGAGCACAGCCCACTGCACGCA------TGTTCTAGCTCTGTGATGCACCACCAC-----GAAAAAA-ATAACAG--CAGAACCAGCCCTTCCTTTCTATTCACTGAAGGAGAAAA----A s ponAbe2.chr17 69564992 477 + 73212453 CTCAGCC-CGCTAGGGTGTGCAGAGGTGAGATGAGGGTGGCTGGCCACACAGCCCACGCATgtgcctcctctcac-agtatctg----ttctagccaaa-gtgtctgggggaagtattactgtcaggttacagccagcacaagcatattgtggattcaatgtaagatgtgcttgaagttttaagagaacaaataagacttcaaagaaatgtcatcctttctctggaccccttctggcaacacacacccagtccctcaggggtacaggtttaatatt-tcctctcttctgGAGTCTTCCAGGGAAAA-TGTATACCTCCAGGGAAATGCTGTGTGCCTCTCTGTCATCTAAGACAAGCCACTTAATCTCCCTTTGCCTGAGCACAGCCCACTGCACGCA------TGTTCTAGCTCTGTGATGCACCACCAC----AAAAAAAA-ATAACAGAACAGAACCAGCCCTTCCTTTCTATTCAGCGAAGGAGAAAAACTCA i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79180247 474 + 83384210 CTCAGCC-CCCAAGGGTGTGCAGAGGTGAGATGAGGGTGGCTGGCCACACAGCCCACGCATGTGCCTCCTCTCAC-AGTATCCG----TTCTAGCCAAA-GTGTCTGGGGGAACTATTACTGTCAGGTTACAGCCAGCACAAGCATATTGTGGATTCAATGTAAGATGTGCTTGAAGTTTTAAGAGAACAAATAAGACTTCAAAGAAATGTCATCCTTTCTCTGGACCCCTTCTGGCAACACACGCCCAGTCCCTCAGGGGTACAGGTTTAATATT-TCCTCTCTTCTGGAGTCTTCCGGGGAAAA-TGTATACCTCCAGGGAAATGCTGTGTGCCTCTCTGTCATCCAAGACAGGCCACTTAATCTCCCTCTGCCTGAGCACAGCCCACTGCACGCA------TGTTCTAGCTCTGTGATGCACCACCAC-----GAAAAAA-ATAACAG--CAGAACCAGCCCTTCCTTTCTATTCACTGAAGGAGAAAAACTCA i panTro2.chr17 C 0 C 0 s mm9.chr11 118660262 468 + 121843856 cttgtcc-ctcgaggacat-----ag-gatgaggaggcagatcactc-ataggttaacaattgcatctgtct-aa-agcattgc----ctttagttgaacgtgttgtgagaggatgt---tgtaacattacagccagcaaaggtacacagtgggttccatgtaagatgtgcatgtgtttttaagataacaaatacgatttcagggaaatgccatacttcctttgacttgcttctggaagcagatgcccggttccccgggggtagggttttaatattcccccctctttgggagccctcagagggaaaaTGCACACCTCCAGCATGGTGCCACATGCCTCTCCATCATCCACGACAAGCCATTTAATCTCCTCTCCCCTGTGCACAGCCCATCACGTGCA-GCGTGTGTTCCAGCTCTGAGAGACACCTATGTGTTCACCACAAA-ATAACAT-------CATCCTCTTCCGTTATACACCATAAAGGGGGGAAAC--- i mm9.chr11 I 8 C 0 s cavPor3.scaffold_76 4290003 474 + 7991924 ttggtcc-cccaaggatgtacagcag-gaagcaaagccagctgaccctgcgggctgagtatgtcatctgtct--a-agcatctg----ttttagtctaa-gtaccgggagaaaatattactgttatgtcacagtcagcaaaagcatattgtggatttgatgtaagatgtgtgtg-aattttaaaataacaaataagacttcaaagaaatgtcatgctttctctggcccccttctagcaataggcaccgggctccccaggggtacaagtttaatatt-ccttctctctgggagcctttgaggaaaaaCTGCATACCTCCAGTGCAATGCTGCATGCCTCTCTGTCATCCAAGACAAGCCACTGAA-CCCCCATGGCCTGTGTGCAGCCTGCTGCATGCA---GTGTGTCCCAGCTCCACCATGCACCATCATGGTCAAATGAAATACAACGG-------CCAGTCCTCACCTTCTGCTCAGTGAGGGAGGAAAGTGCC i cavPor3.scaffold_76 I 8 C 0 s bosTau4.chr19 10746079 460 - 65312493 TTAAGCCACTCAAGGAATCACGGTGATGAGAT-GGGGTAGCTGA---------ATAAGTATGCACAGCGTTTCACAAGCGT--------TTCAGCCAAA-GTAGTTTggagaaatggtactgttacgttacaagcagcaagagcatactgtggatgagatggaagatctgcatgaatttttaagataacaaataagacatcaaagagatgtca-ggtttccttggacctcttgtggcaacagacatccagtctttcaggggtgcaggtttaatatt-cctggccttttggagtcttcagaggaaaaattCATACCTCCAGTGAAATGCTGTGTGCC-CTCTATCATCCAAGACACACCATTTAATCTCCCTTTTCCAGAGCACAGCTTACTGCATGCAGGTGCATGCTCTACCTCTGGGATGTCCTCTCATGTT---AAAGAA-ATTATAA-------CCAGGCTTTCCTTTAGACTCAGAAAAGGAGAAAAA---- i bosTau4.chr19 C 0 I 4 s equCab2.chr11 57934742 463 - 61308211 TTCAGCCCCTCGAGGCTGTACAGGGGTGACATGGGGGTAGCTGA---------Gtaagcatgtgtatctttctac-agcat--------ttcagccaaa-gcattttggggagacagcactgttttattataaccagcacgagcatattgtggatgagatagaagatttgcataaatttttaagataacaaataagacttcaaagaaatgtcacgcttTCTCTAGACCCCTTCTGGCAACAGACGCCCAGTCTTTTAGGGGAGCAGGTTTAATATG-CCTGCTCTTCTGGAGTCTTCAGAGGAAAAATTCATACCTCCAGTGCAATGCTGTGTGCCTCTCTGTCATCCAAGACAAGCCATTTAATCTCTCTTTGCCTGAGCACAGCCTACTGCGTGCAGGCGCGTGTTCTAGCTCTGGGATGCACCATCGCGTT-AAAAAAAA-ATTATAA-------CCAGTCCTTCCTTTATACTCAG-AAAGGAGAAAAA---- i equCab2.chr11 C 0 I 4 s loxAfr3.scaffold_49 14276580 465 - 17734757 ccccatc-cccaaggacgtacagggatgagg--ggggtggctggagctacagggtgagcacgcgcctctttctac-agcgtccaacttgtttcgtcaaa-ggatttgggggcgatattactgttatgtcacaacgaggactagtacactgtgggttacacgtaagatctgtgtgaatgttaaagatcacaaatacgacttcaaagaaatgccatgcttTCTCTGGACCACTTCTGCCAACAGATG-CCAGTGCCCCGGGAGCACAGGTTTAAGATT-CCTTCCCTCTCGGAATCTTTGGAGGAAAAGTTCCTACCTCCAGTGAAATGCTGTGTGCCTCTCTGTCAGCCAAGACAAGCCAATGAACCCCCCTTTGCCTG-GCACAGCCGACTGCGTACAAGCGA-CATGCTAGCTCTGCCATGCTCCAGCAC----ACTAAAAA-AAAAAAA-----------TCTTTCCTTTATACTTGGAAAGGAATGA------- i loxAfr3.scaffold_49 I 1 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e rheMac2.chr16 74730644 1045 + 78773432 M a score=73959.000000 s hg19.chr17_gl000204_random 4760 158 + 81310 -----ACAGAATTAACTGCTTCATAGACAGTCAAAATAAGCTTTCTGCTGGCCTCAGTGAC-AATGCTTGACATCCATA-ATGCAGAATGGAGGTGAGTCCTGGGTCCCCAGCACCCCTCCTGCTGGAAGAGGC-CAGGACACACGAAG----------------GGTCTCTCATGGGAAGC s ponAbe2.chr17 69565469 158 + 73212453 -----ACAGAATTAACTGCTTCGTAGACAGTCAAAATAAGCTTTCTGCTGGCCTCAGGGAC-AATGCTTGACATCCATA-CTGCAAAACGGAGGTGAGTCCTGGGTCCCCGGCACCCCTCCTGCTGGAATAGGC-CAGGACACATGAAG----------------GGTCTCTCATGGGAACC i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79180721 158 + 83384210 -----ACAGAATTAACTGCTTCATAGACAGTCAAAATAAGCTTTCTGCTGGCCTCAGTGAC-AATGCTTGACATCCATA-ATGCAGAATGGAGGTGAGTCCTGGGTCCCCAGCACCCCTCCTGCTGGAAGAGGC-CAGGACACACGAAG----------------GGTCTCTCATGGGAACC i panTro2.chr17 C 0 C 0 s mm9.chr11 118660730 146 + 121843856 -----------------------CAGGCAG---AACTGAGATCTCAGCCTGTGCCAGCAAA-AGTCCTAGGCATCGATGCAAACAAAGTGGAGA-GAGCCTCGAG-TCCTAGGATTCCCC---CATGATACATACCAG----GAAGAAGTGCCTCCTGGGAACAGGGTCTCCCCGGGGAAGC i mm9.chr11 C 0 I 3590 s cavPor3.scaffold_76 4290477 149 + 7991924 -----ACAGAATCGACTTCTTCATAGACAG---ATATGAGGGTTCTGCCCACCTCAGGAAA-AATACTCAGCATCCCTATCTGCAGAGTGAAGGCAAATCGCAGG-CCACAGCATCCTCTGTGCCGGAGGCAGA-CAG----CAGGGAGCGTCT-----------GGT-------GGGACGC i cavPor3.scaffold_76 C 0 I 13 s bosTau4.chr19 10746543 152 - 65312493 -----CTCAAATTAATTTCTCCATAGA-AGATAAAATAAGGCTTGTACCTGCCTCAGCAAAAATGCCTCAGCCTTCCCAGCTGCCA-ATGGAGGTGGGTGTTGGGCCCAC-GCATGCCTTGTTCTGGAGGCCGG-TAC-----AGTAAG--T-------------AGTCTCCCATTGGAGT- i bosTau4.chr19 I 4 C 0 s equCab2.chr11 57935209 151 - 61308211 -----AAAGAATTCATTTCTTCGTGGACGGACAAAACAAGCCTTTTGTCTGCCTCAGCAAA-ATGCCTCAGCATTCCCATCCCCCAGACGGACGAGGGTCCCAGGTCCAC--CACCCCGTGCGCTGGAGGCTGG-GAA-----GGAGGA----------------AGTCTCCCGTGGGGGG- i equCab2.chr11 I 4 C 0 s pteVam1.scaffold_30799 3643 138 - 4837 -----CCAGAATGGA---CTTCATAGACAGACAAAAGCAGCCTTTTGCCTGTCCCAGCAAA-----------AACGCCATCTGCAAAAAGGA----GGCTTTGGGTCCCC-GCGCCCCTCGTCCTGGAAGCAGG-GGG-----AGCAGGCGC-------------AGCCTCTGGGCGGGGG- i pteVam1.scaffold_30799 N 0 C 0 s loxAfr3.scaffold_49 14277045 163 - 17734757 ACTCAATGGAATTAATTTCTTCATAGAAA----AAATAAGCTTTCTGCTCACCTTAGCAAGGACACCTCAGCACCCCTCTCTGAAAAAGGGAGGTGGATCTTGGGCCCATGGCATTCCTTGCACAAGGCTGTGA-AGG-----ATGAAG-GCCAGTG--------AGCTTCTCCTGGGCATG i loxAfr3.scaffold_49 C 0 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e rheMac2.chr16 74730644 1045 + 78773432 M a score=116217.000000 s hg19.chr17_gl000204_random 4918 124 + 81310 AGCC--ATCGTGGCTCTCAGCTCATGGAAAGCGGGGTACGTGACCAGCACTGGCCAGGGTGCGACGCTTGGGGTATTCGCAGGGAAATGAGGGCAAAGCATTT-TGCAAAGAGCGTGCAGGGCTGGG s ponAbe2.chr17 69565627 124 + 73212453 AGCC--ATCGTGGCTCTCAGCTCATGGAAAGCGGGGTACGTGACCAGCACTGGTCAGGGTGCGACGCTTGGGGTATTCACCGGGAAATGAGGGCAAAGCATTT-TGCAAAGAGCGTGCAGGGCCTGG i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79180879 124 + 83384210 AGCC--ATCGTGGCTCTCAGCTCATGGAAAGCGGGGTACGTGACCAGCACTTGTCAGGGTGCGACACTTGGGGTATTCGCCGGGAAATGAGGGCAAAGCATTT-TGCAAAGAGCGTGCAGGGCTGGG i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4290639 122 + 7991924 AGCC--TCCATGTCTCTGGGCTCAAGGGAGGTGGAGACCATCAGGAATGCTGGTCAGAGGGCCATGCTTGAGGTCTTTCCCACAAAATGAGAACAACATATTT-TGC--AGAGTGTTCTAGATTGGC i cavPor3.scaffold_76 I 13 C 0 s bosTau4.chr19 10746695 109 - 65312493 -GGCCTGCCAGGTATCTGAGCTCCTGGAAAGTGG-----------------GGTCAGAGTGAAATGCTCCATGTATGCCCTGGGGACCGAGAGCAAAGCATTTTTGCAAAGAATGTATGGGGCTATG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57935360 108 - 61308211 -GCC--AGCCTGTACCTGTGCTCCCGGAAAGTGGGGCAC-ACGTGAGAGCTGGGCAGAGTACAATACTCAGCTTACTAACCAGGAAAGGAGAGCAAAGCGTTT---------------GGGGCTGGG i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_30799 3781 122 - 4837 -GGC--ACCGCGTATCTGAGCTACTGGAAAGTGGGGAGCAACGGAAGTGCTGGTCAGAGGGCACAGCTCGGCGCCAGTGCCGGGAAGAGA-ATTAAAGCGTTT-TGCCACAAGTGTACGGGGCTCGG i pteVam1.scaffold_30799 C 0 C 0 s loxAfr3.scaffold_49 14277208 124 - 17734757 GTCC--ACCATGCATTTCAGCTCGTGGAGACTGGGGGACGTGATGGGCACTGGTTGGAGTGTGATGCTCTGAGTATTCACCAGAAAAAGGGGGCAAAGCATTT-TGCAAAGAGTGTACCGGGCTGAG i loxAfr3.scaffold_49 C 0 I 526 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e mm9.chr11 118660876 3590 + 121843856 I e rheMac2.chr16 74730644 1045 + 78773432 M a score=101183.000000 s hg19.chr17_gl000204_random 5042 66 + 81310 CAAAATACTAAATAATTCAAAAATCATGATGACCTTGCCTTGGGAACTTTTGGAGCAACAGAATGG s ponAbe2.chr17 69565751 66 + 73212453 CAAAATACTAAATAATTCAAAAATCATGATGACCTTGCCTTGGGAACTTTTGGAGCAACAGAATGG i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79181003 66 + 83384210 CAAAATACTAAATAATTCAAAAATCATGATGACCTTGCCTTGGGAACTTTTGGAGCAACAGAATGG i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4290761 66 + 7991924 AAAAACTCTTAGAAACTCAAAAATCACAAAGACCTGGCATTGGAAACTTTTTCAGCAACAGAATGA i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10746804 66 - 65312493 TGAAGTACTAAATAACTAAAAAATCATTATGCTCTTGCCTTGGGAACTTTTCGAGCAGCAGAATGG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57935468 65 - 61308211 TGGAACACCAGATAATTCACAAATCATTGTGTCCTTGCCTTGGAAA-TTTTTGAGCAGCAGAACGG i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_30799 3903 65 - 4837 -GAAACGCCAAATTACTGAAGAATCGTCACGTCCTCGCCACGGGGACTTTTTGAGCAACAGAGTGG i pteVam1.scaffold_30799 C 0 C 0 s loxAfr3.scaffold_49 14277858 66 - 17734757 TAAAATACTAAGTAAAACAAAAATCGCTGTAACCTTGCCTGGGAAACTTTTTGACCAAAAGAACAG i loxAfr3.scaffold_49 I 526 C 0 e monDom5.chr2 304251105 3824 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e mm9.chr11 118660876 3590 + 121843856 I e rheMac2.chr16 74730644 1045 + 78773432 M a score=230887.000000 s hg19.chr17_gl000204_random 5108 183 + 81310 TTTAGAATAATGACCCATCCAATGACATTCTGGCTCACAGACAAGAGACAATATTCA-----------AACGCCACCTCTGGTCACCCCTGGCCTGAGGGACATTTGTTTTGGTGGCTGAGGCAGCCGCCAGTTACCCAGT-AC-TGTGGGT-ACAGGCA------TGAGCTTTCTCAGCTACAAAGAGCACGACATAAACAA s loxAfr3.scaffold_49 14277924 201 - 17734757 TCTAGAGTAGTGACCAATCCTATGGCATTCTGGTTCACGAACAAAAGAAAACATCCATGCCATAGCCCAGTGCCACCTCTGGTCACGCCTGCCATGGGTGACAATTGCTTTGGTTGCTGAGTGGGGAGCCGGTTACTCAGC-ACTTGAGTGT-ACAGGCATCTTACTCTTACTCCTTAGCTATGGCTGGTACAGGAGAAACAA i loxAfr3.scaffold_49 C 0 C 0 s pteVam1.scaffold_30799 3968 169 - 4837 TCCAGAGTCGTGACTGCCCCAACGACATGCT-GCCCTCAAACGGGAGGCGGCCCTC------------GACACCACTTCTGGGCAGGTTGGCCACAGGCCGCCTGAGTCCTGTATGCCCAGG-------AGG-CGCCTGGC-AC-TGGGCTA-GCAGGTG------TCCCCTGCCTCAGCCCCAGAGGGGACGTGGAA----A i pteVam1.scaffold_30799 C 0 C 0 s equCab2.chr11 57935533 172 - 61308211 TCTAGAATAGTGACCAATCCAATGACATTCTGGCTCACAAACAAGAGACAAGTTTCA-----------AATGCCACCTCTGGTCACGCCTGGCGTGGGCAACCTTTTTTCCGGTTGTTGAAG-------AGGTTACTTGGC-AC-TTGGGCG-TGTGGCG------TCCACTTCCTCTGCTGCAAACAGCACAAGAGA----A i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10746870 174 - 65312493 TCTAGAACAGTGACCAATCCAATGACATTCTGGCTCACAAACGAGAGAAAACATTCA-----------CAGGCCACCTCTGGTCATGTCAGGCACAGGCGACATTTGTCCTGGTTGTCC----------AGGTTACCTAGC-AC-TCGGGTGTGCAGGCA------TCTGTTTCCTTAGCTGCAAACAGCACAACAGATATTA i bosTau4.chr19 C 0 C 0 s cavPor3.scaffold_76 4290827 163 + 7991924 TTAACCATGATGATC---GCCATGATGGTCTGGCTCATGTGCAAGAGACAACATTCA-----------AATGCCACCTCTGGCCTCGCC----------------TGCTCCAGT-GCTGAAGACATAGCTGGTTGCCTAGC-AC-TGGCCAT-GCAGGTA------TCTGTAACCTTAGCTGCAAATGGCACGGGAGAAATGG i cavPor3.scaffold_76 C 0 C 0 s rheMac2.chr16 74731689 182 + 78773432 TTTAGAATAATGACCCATCCAATGACATTCTGGCTCACAGACAAGAAACAATATTCA-----------AACGTCACCTCTGGTCACCCC-GGCCTGAGGGACATTTGTTTTGGTGGCTGAGGCAGCCGCCGGTTACCCAGC-AC-TGCGGGC-ACAGGCA------TGGGCTTTCTCAGCTACAAATGGCATGACATAAACAA i rheMac2.chr16 M 1045 C 0 s ponAbe2.chr17 69565817 183 + 73212453 TTTAGAATAATGACCCATCCAATGACATTCTGGCTCACAGACAAGAGACAATATTCA-----------AACGCCACCTCTGGTCACCCCTGGCCTGAGGGACATTTGTTTTGGTGGCTGAGGCAGCCGCCAGTTACCCAGC-AC-TGTGGGT-GCAGGCG------TGAGCTTTCTCAGCTACAAAGAGCATGACATAAACAA i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79181069 183 + 83384210 TTTAGAATAATGATCCATCCAATGACATTCTGGCTCACAGACAAGAGACAATATTCA-----------AACGCCACCTCTGGTCACCCCTGGCCTGAGGGACATTTGTTTTGGTGGCTGAGGCAGCCGCCAGTTACCCAGT-AC-TGTGGGT-ACAGGCG------TGAGCTTTCTCAGCTACAAAGAGCACGACATAAACAA i panTro2.chr17 C 0 C 0 s monDom5.chr2 304254929 159 - 541556283 ---AAAAGAATGAGTGATCCAATAACTTACTGACATACAAATTAGAGAAGTTATTTAT----------CACAATACATTTA--------------AAAGAGCATCCA--------ACCATGGCAGCTGGCATTTTTCTAGCTAC-TAAAGGT-AAGGGAA------TTACTGACTTCACCCTGAAAGAGTTTG-CTCAAACAA i monDom5.chr2 I 3824 I 6506 e canFam2.chr9 59350193 925 - 64418924 M e mm9.chr11 118660876 3590 + 121843856 I a score=62236.000000 s hg19.chr17_gl000204_random 5291 93 + 81310 GGAAGGCGCA-----CACACACCTGTCACCTCTCCGGGGACTGCAGTGTTTAAAAGACAGTCATCACCC-AAAGTGCTTTTTAT-AAC----------------AAGAAAGGACTC s panTro2.chr17 79181252 93 + 83384210 GGAAGGCGCA-----CACACACCTGTCACCTCTCCGTGGACTGCAGTGTTTAAAAGACAGTCATCACCC-AAAGTGCTTTTTAT-AAC----------------AAGAAAGGACTC i panTro2.chr17 C 0 M 235 s ponAbe2.chr17 69566000 93 + 73212453 GGAAGGTGCA-----CACACACCTGTCACCTCTCCGTGGACTGCAGTGTTTAAAGGACAGTCATCACCC-AAAGTGCTTTTTAT-AAC----------------AAGAAAGGACTC i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74731871 93 + 78773432 GGAAGGCGCA-----CACACACCTGTCACCTCTCCGTGGACTTCAGTGTTTAAAGGACAATCATCACCC-AAAGTGCTTTTTAT-AAC----------------AAGAAAGGACTC i rheMac2.chr16 C 0 I 2 s cavPor3.scaffold_76 4290990 103 + 7991924 GGA-----CA-----CACAAGCCTACAGTCTCACAGCATATCCTGCTATCTACAGGATCATCATCACCTGAAAATTCTTTGTAC-AACGACATGTTTT--TGAGAAGAAATGTGTT i cavPor3.scaffold_76 C 0 I 3 s bosTau4.chr19 10747044 92 - 65312493 AGA-----TA-----CACAAACCTGCAGCTTCTCAACCAAATACACTGCAGAGCGGATAATCGTGATCTGAAAATTCTTCCTAGTGACAACACGCCTT--------------ACTC i bosTau4.chr19 C 0 I 2 s equCab2.chr11 57935705 110 - 61308211 AGG-----AATCGGGCACACACCTGTAACCTCTCAACCCACCTCGGTGTTTAAAGGATAATCAGCGCCTAATAGTTCTTTGTAC-AGCAATGTGTTCTCTTGAGAGGAGAGGACTC i equCab2.chr11 C 0 I 2 s pteVam1.scaffold_30799 4137 71 - 4837 CAA-----CA-----CACAAGCCTGCGGCT--------------------------GTCATCTGCAC------GGGCTCTGCGG-GGCA--GCGCTTTCTCGAAGGGCATGCACCC i pteVam1.scaffold_30799 C 0 I 2 s loxAfr3.scaffold_49 14278125 91 - 17734757 AGACGG--CA-----C-CAAACCTACAACCTCTCAGCAGATTATAGTGTTTAGAGGAGAATCATCGTTTGAAGGTTCTTTGTAG-AAC----------------AACAAAGTGTTC i loxAfr3.scaffold_49 C 0 I 17 e monDom5.chr2 304255088 6506 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e mm9.chr11 118660876 3590 + 121843856 I a score=-1732.000000 s hg19.chr17_gl000204_random 5384 73 + 81310 TGAACGTTGTCAGGTGAGTAGCACTGCCTGTGTCCCCATGGCCAGGGCATG-TGCAGAG-----CCTGGGTGGACGCAG s ponAbe2.chr17 69566093 73 + 73212453 TGAACGTTGTCAGGTGAGTAGCACTGCCTGCGTCCCCATGGCCAGGGTGTG-TGCAGAG-----CCTGGGTGGACGCAG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74731966 73 + 78773432 TGAACGTTGCCAAGTGAGTAGCACTGCCTGCATGCCCGTGGCCAGGGTGTG-TGCAGAG-----CCTGCGTGGATGCAG i rheMac2.chr16 I 2 C 0 s cavPor3.scaffold_76 4291096 49 + 7991924 CAAATGCTGTTGGATGGG-------ACCTGGCCCCCTA--------GCATG-GGCAAAG----AACTGA---------- i cavPor3.scaffold_76 I 3 C 0 s bosTau4.chr19 10747138 56 - 65312493 TAAATGCTGTTGAGTGAGTAATG-TGCTCCCATCCCCTT-GACAGGGTCTACGATGGA--------------------- i bosTau4.chr19 I 2 C 0 s equCab2.chr11 57935817 57 - 61308211 TAAATG-TGTCCAGTGAGTAAGGCTGCCCCCAGCCTCTTGGACAGGGTCTGCCACAGA--------------------- i equCab2.chr11 I 2 C 0 s pteVam1.scaffold_30799 4210 52 - 4837 AAAACG-TGGCCGAC-AGCAGTGCCACACCC--CCTCTGGGATGGGG--CAGCACAGG--------------------- i pteVam1.scaffold_30799 I 2 C 0 s loxAfr3.scaffold_49 14278233 74 - 17734757 TAAATGGCATGAAACGAGTAACGTCACATCTGTCCGCTCGGGTGGGGTCTGCCACAGAGTGAGGGCTAGGCAAT----- i loxAfr3.scaffold_49 I 17 C 0 e panTro2.chr17 79181345 235 + 83384210 M e monDom5.chr2 304255088 6506 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e mm9.chr11 118660876 3590 + 121843856 I a score=50310.000000 s hg19.chr17_gl000204_random 5457 174 + 81310 GCAGGTTAGCTATCCCAGCCCTA-TGCATCACTCCTGCATCACACCTAGCG-CCCCGTGTG-TGACCCGGGATCCCACCGTTCTCCAGGGTCGAGGGAGAACACTTCAAGAGAGGCGACTAAATCTCCACCAAGCACATTATATCAAATA-CGCt--tcaggaaaaccctttatg------gaaac s panTro2.chr17 79181580 174 + 83384210 GCAGGTTAGCTATCCCAGCCCTA-TGCATGACTCCTGCATCACTCTTAGCG-CCCCGTGTG-TGACCTGGGATCCCACCGTTCTCCAGGGTCAAGGAAGAACACTTCAAGAGAGAAGACTGAATCTCCACCAAGCACATTATATCAAATA-CGCC--TCAGGAAAACCCGTTATG------GAAAC i panTro2.chr17 M 235 C 0 s ponAbe2.chr17 69566166 173 + 73212453 GCAGGTTAGCTATCCCAGCCCTA-TGCATCACTTCTGCATCACACCTAGCG--CCCATATG-TGACCTGGGATCCCACTGTTCTCCAGGGTCGAGGGAGAACACTTCAAGAGAGGCGACTAAATCTCCACCAAGCACATTGTATCAAATA-TGCC--TCAGGAAaaccctttatg------gaaac i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74732039 163 + 78773432 GCAGATTGGCTGGCCCAGCCCCA-TGCATCACTCCTGCATCACACCTCACA--CCTA-----------GGGATCCCACCGTTCTCCAGGGTCAAGGGAGAACACTTCAAGAGAGGCGACTAAATCTCCACCAAGCACAGTATATCAAGGA-CGTC--TCAGGacaaccctttatg------gaaac i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4291145 145 + 7991924 --AGGTTTGTTGCTAAAGCCTTT-GGAGAGATTTCTG-------CCATGTG--TGCATGCG-TGACCCATGA-CCAGCTGCTCCTCAGGGTCAAGAGAG---ACTTCAGGAAGGTACA------------AAAGCA----GTGTCAAGGA-CACCTATCCAGATGATGC-TTATG------GAAAC i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10747194 119 - 65312493 GCAG-----------------------ATTACTCCTACATTACACCTGGGGTGACC-----------AGTGAGTCAACGCTTCCCAGGGGG-AAGGGAGAGTGTTTCA---AGGGCATTTA------TATCAAG-ACATTCTGTGGGA---AGTC--TT-----------TTATG------GAAAC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57935874 160 - 61308211 ACAGGTTTGCCATCACAGCCCCGTTTCGTTATTCCTGCATCGCACCTAGGG-GACCATATG-CGACTCGTGATTCAACTGTTCCCGGGGGGTAAAGGAGAGCATTTCG--AGAGGAAGCTAAAGCAGCATCTAGAACATTGTATCAAAGACAGCC----------------TACG------GAAAG i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_30799 4262 105 - 4837 CGAGGCCTGCTCTCGCGGCCGCACTGGACTGTCCCCACGTCACGCCTCGAG-GACT-------------------------------------------------------GAGGGAGCCC------CATCGAGAACATCGCATCCAA---AGTG----------------TCCGTTCTGTGAAAC i pteVam1.scaffold_30799 C 0 C 0 s loxAfr3.scaffold_49 14278307 163 - 17734757 GCAGGTTTCTGATCAAGCCCATG-TG-ACTGACCCCACTGTGCACTGAGTG-AGCCACGTGCTGACCCACGATTCAAGTCTTCACCCGGGGGAAGGAAGAAGATTCCA-GAGAGACAACGGAGGCGCCATCT-GAATATTACGTCAAAGA-TGCC--CATAGGAAGCTTTT--------------- i loxAfr3.scaffold_49 C 0 I 1277 e monDom5.chr2 304255088 6506 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e mm9.chr11 118660876 3590 + 121843856 I a score=78689.000000 s hg19.chr17_gl000204_random 5631 64 + 81310 ctactatgtgcagcactgtgggagaaac-------aagttgcagcctgtgcccttaaggaactccagaaag s panTro2.chr17 79181754 64 + 83384210 CTACTATGTGCAGCACTGTGGGAGAAAC-------AAGTTGCAGCCTGTGCCCTTAAGGAACTCCAGAAAG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69566339 69 + 73212453 ctactatgtgcagcactgtgggagaaacagag--gaagttgcagcctatgcccttaaggaactccagaaag i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74732202 69 + 78773432 ctactatgtgcagcactgtggtagaaacagag--gaagctgcagCCTGCGCCCTTCAGGAACCCCAGAGAG i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4291290 59 + 7991924 TGGCTGTGCACAAAAGT---GGAGAAAT---------GTAGAGCTCTGGGTCCCTAACATACCCCTCAGAG i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10747313 71 - 65312493 CTACTAGGTGCGAGGCTGTGGGAAGAACACAGAAGCAGCAGAAGCCTGTGCCCTTAAGAAACCCAAGAGag i bosTau4.chr19 C 0 I 419 s equCab2.chr11 57936034 70 - 61308211 CTACTATGTGCAGAGCTGTGGGAGGAACACAGGTGAAGCAGAAG-CCGTGCTCTTGAGAAACCCAAGAGAA i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_30799 4367 41 - 4837 CTGCCATGTACAACCC-----------------------------CCGGGC-CTTGGGAAGCCCAAGAGCG i pteVam1.scaffold_30799 C 0 C 0 s loxAfr3.scaffold_49 14279747 71 - 17734757 CCACCATGCACACAGCTGTGGGAGAAACATAGAAGCAACAGAAGCCTGGGCCCTTAAGGGACCCAAGAGCG i loxAfr3.scaffold_49 I 1277 C 0 e monDom5.chr2 304255088 6506 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e mm9.chr11 118660876 3590 + 121843856 I a score=73442.000000 s hg19.chr17_gl000204_random 5695 152 + 81310 aaaaggggacagG--TGACAAGAG---------ACAT-GACCA-------AAGAG---------GCAGCTCCA----TGCA--CAGATGACGACGACCGCCC--------------------AGCTGCCCTCTG-CAGGTGTGCAG-GAC------CAGAGGGCAGGAAGGTGGGGTGG-GGGTGGGCTCTGGGTCATGCCCACTTGGCCTCCAT s panTro2.chr17 79181818 152 + 83384210 AAAAGGGGACAGG--TGACAAGAG---------ACAT-GACCA-------AAGAG---------GCAGCTCCA----TGCA--CAGATGATGACGACCGCCC--------------------AGCTGCCCTCTG-CAGATGTGCAG-GAC------CAGAGGGCAGGAAGGTGGGGTGG-GGGTGGGCTCTGGGTCATGCCCACTTGGCCTCCAT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69566408 152 + 73212453 aaaaggggacagG--TGACAAGAG---------ACAT-GACCA-------AAGAG---------GCAGCTCCA----TGCA--CAGATGACAACGACCGCCC--------------------AGCTGCCCTCTG-CAGATATGCAG-GAC------CAGAGGGCAGGAAGGTGGGGTGG-GGGTGGGCTCTGGGTCATGCCCACTTGGCCTCCAT i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74732271 153 + 78773432 CAAAGGGGACAGG--CGACGAGAG---------ACAG-GACCA-------AAGAG---------GCAGCTCCA----TGCA--CAGACGACGACGGCCGCCC--------------------AGCTGCCCTCTG-CAGATGTGCAG-GAC------CAGAGGGCAGGAAGCTGGGGTGGAGGGTGGGCTCTGGGTCATGCCCACTTGGCCTCCAT i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4291349 109 + 7991924 ---------------------GAG---------CCCT-G--CA-------GAGGA---------ACAGCCC--------------------AGGGACACCCC--------------------ACCTTCCCTCTACCACAGGCACAGTGCT------CAGAAGTCAGGA----------G-GGACAGGTTCCAGGCCACACCCATTTGACCTCCAA i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10747803 171 - 65312493 CAAAAGAGGGAGGGACCCAAGAGG----AACTTCCAT-GGATA-------GAGAATGTAGAAAGGCAGCCGCA----GTGT--CTGTTTCAT-GTACCTTCC--------------------ATCTGCCCTCTG-TGGACCTGGAG-GGATGGAACCAGAGAGCAGACAGCAGAGA--G-GGGCAGAGCCTGGGTCATACCAACTTGGCATCCAT i bosTau4.chr19 I 419 C 0 s equCab2.chr11 57936104 171 - 61308211 CAAAGGAGACAGGGACCCCGGGAG----GGTTCCCGT-GGGCA-------GAGAGTGAGGAAGAGCAGCCCCA----GGGC--CCGCCCCAT-GCCCCTCGC--------------------AGCTGCCCTCTG-CAGACCCGGAG-GGCAGGCCTCAGAGGACAGGAAACAGAGA--G-GGGCGGGGCCAGAGCTATGCCAACACAGCGGCTGT i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_30799 4408 168 - 4837 CAAAGCAGGCCGG-----CGGGGGATCAGGGACCCGG-GAGCAAGCGGTGGACAGCACAGACCAGCAGAGCCA----GGCCAGCCGCCAAATAGCTTCTCGC--------------------AG----CCCCCG-CAGGCTGGAGG-GACAGGC--CAGCAGACAGAGGGC-GTGG--G-GGGCGGGGCCTGGGCCACGAGGGCAC--CCAC--- i pteVam1.scaffold_30799 C 0 C 0 s loxAfr3.scaffold_49 14279818 170 - 17734757 GAAAGCAAACGGG--GGAGAGGAG---------ACAGAGACCA-------ATGAG---------GAAATTCCAACGGCACA--CAATGGAGAAGAGCCATCCTGCTGCCGGCCTCACTCTGGAGCTGCCCTCTG-CACATGTTGAG-GAT------TGCAGGAGAGAAAGC-------A-GGCAGGGGACTGAGCCGTGCCAACTGGGCATCCCT i loxAfr3.scaffold_49 C 0 C 0 e monDom5.chr2 304255088 6506 - 541556283 I e canFam2.chr9 59350193 925 - 64418924 M e mm9.chr11 118660876 3590 + 121843856 I a score=154837.000000 s hg19.chr17_gl000204_random 5847 187 + 81310 -CCC-----AGAGAGCAGCTCCCCCAAACCTGGAATGATGAGTGTGCCTGACGGGGCCCATCTGAGATAGACCACAGTGGTCA-----------------------------------------------------TACTAGCTGGTGGCAGAGG--------------------------------------------GTTG----------------------------------------------GGAGTGGTAG----------------------------------------------------TCCTTAAA----------------------------ttattttgaaataatttaagaatcacaggaagttgcaaaaatagtacagaaaattcccgtgcacccttc s panTro2.chr17 79181970 187 + 83384210 -CCC-----AGAGAGCAGCTCCCCCAAACCTGGAATGATGAGTGTGCCTGACGGGACCCATCTGAGATAAACCGCAGTGGTCG-----------------------------------------------------TACTAGCTGGTGGCAGAGG--------------------------------------------GTTG----------------------------------------------GGAGTGGTAG----------------------------------------------------TCCTTAAA----------------------------ttattttgaaataatttaagaatcacaagaagttgcaaaaatagtacagaaaattcccgtgcacccttc i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69566560 187 + 73212453 -CCC-----AGAGAACAGCTCCCCCAAACCTGGAATGATGAGTGTGCCTGATGGGACCCATCTGAGACAAACCACAGCGGTCG-----------------------------------------------------CACTAGCTGGTGGCAGAGG--------------------------------------------GTTG----------------------------------------------GGAGTGGTAG----------------------------------------------------TCCTTAAA----------------------------ttattttaaaataatttaagaatcacaagaagttgcaaaaatagtacagaaaattcccgtgcacccttc i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74732424 187 + 78773432 -CCC-----AGAGAGCAGCTCCCCCAAACCTGGAATGATGAGTGTGCCTGACAGGACCCATCTGAGATAAACCACAGTGGCCA-----------------------------------------------------TGTTAGCTGGTGGCAGAGG--------------------------------------------GTTG----------------------------------------------GGAGTGGTAG----------------------------------------------------TCCTTAAA----------------------------ttattttgaaataatttaagaatcacaagaagttgcaaaaatagtacagaaaattcccgtgcacccttc i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4291458 154 + 7991924 -CCC-----AGGAAATAGAACTAATAAACC---------------------CAGGACCCATCACAGAGAAACCACCATGGCCA-----------------------------------------------------TACT-----------GAAG-----------------------------------------------G----------------------------------------------GAAGACACTT----------------------------------------------------tctttaaaaa----------------aaat----tcttattttgaaataatttaagtctcacaagaagctgcaaaaatag------agatctctttgtgcccttc i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10747974 184 - 65312493 --CC-----TGGCATTGTCC-CCAAAAACCTAGAATGATGGATG--CCTGCTGGGATCTTGCCAAGC-AAACCACAGTGGCCA-----------------------------------------------------TGCTGTTT--TGGGGGAGG----------------------------------------------------------------------------------------------TGAGTGTCAT----------------------------------------------------CCttgaaaaa----------------aa---acttgttattttgaaataatttaagacttg-aagaaactgcaaaaatagtgcagagaattctcacatccccttc i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57936275 395 - 61308211 -CCT-----GGAGAGTCGTT-CCCCAAACCCAGGATGCTGGGTGTGCCCGCTGGGACCCCTCCGCAA-AAACCACAGTGGCCATGATGTTTTCGGGGAGGGGGTGCTATCCTTTAAAAAATCTTTTATTTTGGgggggccagcc--cggcggtggcacagtggttatgtggtgtgttccgcttcggtggcccagggttcgagggtttgtatcccagatgccgacctaccaccgctcatcaagccacgctgtggtggcatcccacataaaatagaggaggagggcatggatgttagctcagtgacaatcatcctctcaaaaa----aaAACCCA----AAGT-accttttattttgaaataatttaagactca-aagaaattgcaaaggcagtacagagcattcccatgta-ccttc i equCab2.chr11 C 0 C 0 s canFam2.chr9 59351118 241 - 64418924 -CCC-----AGAGAGTCGCTGCCCCAAACCTGGGAC-CCGTGCAGCTCTGCAGGGACCCGGCAGAGA-AAAC-------------------------------------------GAGGACCTTTT------TAGGGGCCATGC--TGGGGGGGG--------------------------------------------GAGG----------------------------------------------GGAGTGTCATCCTTaaaaaaaaaaaaaaaaa------------------aaaaaTTATTTTACTTTTAAATAATTTAAGACTCACAAGAAGTGGTAttttatttttaaataatttaagactcacaagaagtggtgaaagcagtacagaaaattc--------ccTTC i canFam2.chr9 M 925 C 0 s pteVam1.scaffold_30799 4576 195 - 4837 -CCCTGATGGGAGGGAGGGT-CTGCAAACCCAGGAT-GCGGGCGGGCCC-CCGGGACCCCTCTGACA-ATCC-ACAGTGGCCA----------------------------------------------------GTGCTGTTC--TGGGGCAGG--------------------------------------------GAGC----------------------------------------------GGGCTGT-------------------------------------------------------CCTTTAAAAA----------------AAACAACttttccttttgaaaccatttaagactcacaagaaattacaaaactaccacagagaattcctatgtacccttc i pteVam1.scaffold_30799 C 0 C 0 s loxAfr3.scaffold_49 14279988 193 - 17734757 CCCT-----GGGGAGCCATT--CCCTGACCCAGAACAATGGGCATGCCTGCTGGGGCCCATCCAAGTTTAACCACAATGGCCA---------------------------------------------------AGATCTGACC--TTATTTGGG--------------------------------------------GTGG----------------------------------------------AGGACGAC------------------------------------------------------GCTTTAAA-------------------ACCACctttttgtttttaaataatttaagactcaaaagaagatgcaaaaatagtacagagaattcccacaggcccttc i loxAfr3.scaffold_49 C 0 I 2580 e monDom5.chr2 304255088 6506 - 541556283 I e mm9.chr11 118660876 3590 + 121843856 I a score=107873.000000 s hg19.chr17_gl000204_random 6034 54 + 81310 tattatggactgaatcatgccctctcaaaattca-tacattgaagtcctaacccc s panTro2.chr17 79182157 54 + 83384210 tattatggactgaattgtgccctctcaaaattca-tacattgaagtcctaacccc i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69566747 54 + 73212453 tattatggactgaatcgtgccttctcaaaattca-tacattgaagtcctaacccc i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74732611 54 + 78773432 tattacagactgaatcgtgccctctcaaaattcg-tacgttgaagtgctaacccc i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4291612 53 + 7991924 tgttatgaactgaattatg-tttttaaaaactca-tacattgaagtcctaactct i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10748158 55 - 65312493 tgttacgggctgacttgtgtcccctccaaattcattaagttgaagccctaacccc i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57936670 54 - 61308211 tggtaggggctgatttgtgtctcctgaaaattcc-tacattggagccctgagccc i equCab2.chr11 C 0 C 0 s canFam2.chr9 59351359 54 - 64418924 tgttatgggccgaattgtgtgtcctcaaaatttg-tatgttaaagttcttaaccc i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_30799 4771 53 - 4837 tgttatgggctgaattgtgtccccttgaaattca-catgttgaag-cctaagccc i pteVam1.scaffold_30799 C 0 N 0 e monDom5.chr2 304255088 6506 - 541556283 I e mm9.chr11 118660876 3590 + 121843856 I e loxAfr3.scaffold_49 14280181 2580 - 17734757 I a score=30544.000000 s hg19.chr17_gl000204_random 6088 47 + 81310 t----agtacgttag-a-tgtgaccgcatttggagat-------aggaccctt--------------------accaggc s panTro2.chr17 79182211 47 + 83384210 t----agtacgttag-a-tgtgaccgcatttggagat-------aggaccctt--------------------accaggc i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69566801 47 + 73212453 c----agtacgttag-a-tgtgaccgcatttggagat-------aggaccctt--------------------gccaggc i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74732665 47 + 78773432 c----agtatgttag-a-tatgacctcatttggagat-------aggaccctt--------------------cccaggc i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4291665 46 + 7991924 c----aataaaccagaa-tgtcgctgtctccagagac-------agggtctt----------------------ccaaga i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10748213 72 - 65312493 c----agtacctctg-agtatgactgtatttagagagagtttaaagggtcctt---gactccatgcatgctcagtcatgt i bosTau4.chr19 C 0 I 210 s equCab2.chr11 57936724 66 - 61308211 c----agtacctcag-a--gtgagcgcatctggagag-------agggtctttcaagaggtgatggaggttaaatgaggt i equCab2.chr11 C 0 C 0 s canFam2.chr9 59351413 72 - 64418924 ctagtagttcctcag-aatgtgactatatccggagac-------ggggtctttaaagaagtcattacattaaaatgaggt i canFam2.chr9 C 0 C 0 e monDom5.chr2 304255088 6506 - 541556283 I e mm9.chr11 118660876 3590 + 121843856 I e loxAfr3.scaffold_49 14280181 2580 - 17734757 I a score=114820.000000 s hg19.chr17_gl000204_random 6135 117 + 81310 catatgggtggg-----------------cctcatccac-tctgac-cagtgtccttctaagagaaga--agattaggacacagacat----gcacagatcaaggggcggccatgtgaggacataagg-----------agaagatgaccatc s panTro2.chr17 79182258 117 + 83384210 catacgggtggg-----------------cctcatccac-tctgac-cagtgtccttctaagaggaga--agattaggacacagacat----gcacagatcaaggggcggccatgtgaggacataagg-----------agaagacgaccatc i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69566848 115 + 73212453 catatgggtggt-----------------cctcatccac-tctgacgcagtgtc---ctaagaggaga--agattaggacacagacat----gcacaggtcaaggggtggccatgtgaggacataagg-----------agaagacgaccatc i ponAbe2.chr17 C 0 I 437 s rheMac2.chr16 74732712 109 + 78773432 catatgggtggg-----------------cctcgtccac-tctgac-cagcgtccttctaagaagaga--agattaggacacagacat----gcacagatcaaggggc--------aaagacacaggg-----------agaagacaaccatc i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4291711 129 + 7991924 agttagcaaggggaagtgaggtcaggattcctaatctag-caggag-taggatc---ctgagagaagaggagagcgggacatagacat----gcacagg----gggaagaacatgtaaagatacaagg-----------agaagacaaccgtc i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10748495 110 - 65312493 catatgagtggg----------------ccttaatccaa-tctgac-t-gtgtctttgcaagaagagg--aggttaggacccggacac------acaaa----gggacgaccatgtgaggatgcaga------------aaaagatggccatc i bosTau4.chr19 I 210 C 0 s equCab2.chr11 57936790 117 - 61308211 tata-gggtggg----------------ccctgatccag-taggac-tggtgtccttataagaagaga--ggattaggacacagtcacgtttgcccaga----cggaaggccacgtgaggacacaggg-----------agaagacggccacc i equCab2.chr11 C 0 C 0 s canFam2.chr9 59351485 124 - 64418924 cacg-ggctggt----------------ccctaatccatccatggc-tggtgttcttgt-ggaagagg--gggtgaggacacgcacac----gcccaga----ggggtgaccctgtgagtacacgggggggcggggggcagaaggtggccgac i canFam2.chr9 C 0 C 0 e monDom5.chr2 304255088 6506 - 541556283 I e mm9.chr11 118660876 3590 + 121843856 I e loxAfr3.scaffold_49 14280181 2580 - 17734757 I a score=137578.000000 s hg19.chr17_gl000204_random 6252 155 + 81310 tacaagccaa-agaga--agccttcaaggaaaccaatgctgcc----aacagcttgatct----tagacttctggcctcttgaattttgagaaaattaacctctgttgtgtgag----------cccccaggctgaggggcttcaccatggcagcccaagccgac-caCACACC-TCC s canFam2.chr9 59351609 154 - 64418924 ggcaagcctg-ggaca-gggcctcggaagggaccacccccactgtgggccaccttgatct----gggccacctagcctgcagaactttgagacggt--acacctgt----tcac----------cagcccgtctgtggt-cccagtcacggcagtctgagcaCAGGAGTGCCCC-TCG i canFam2.chr9 C 0 C 0 s equCab2.chr11 57936907 152 - 61308211 tacgagccaa-gaagacaggcttcaggaggaaccagccctgcc----gacacgttgacct----gggactcccagcttccaggactgggagaaaatcaatttccgt----ttac----------cagccagtctgcggcacttagttaggacagcccga-caaactggtgcacc--ca i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10748605 156 - 65312493 tacaacccaa-ggaaagaggcctcagaagaaaccaaccctgtt----cacaccttgacagtagatggacttccagcctccagaactgtgagaaagaaaatttctgt----tcac----------catccagtctg-ggcgctctgtcatggcagcccaagtaaacgaaCGTACC--TT i bosTau4.chr19 C 0 C 0 s cavPor3.scaffold_76 4291840 168 + 7991924 tacaaatgaacagaga--agccttaaaagaaaccagccctgaa----gatgccttcattt----tggacttctggcctccagaattgcaagaaaattactttctgttgcttaagtccccccccccccccaagtctctgatccttcctatggcagtgatagcagactcaggcaCCTTCC i cavPor3.scaffold_76 C 0 C 0 s rheMac2.chr16 74732821 155 + 78773432 tgcaagccaa-agaga--ggtcttcaaagaaaccaatgctgcc----aatagcttgacct----tagacttctggcctcctgaattttgagaaaattaacctctgttgtgtgag----------tccccgggctgaggggcttcgtcatggcagcccaagccgac-caCACACC-TCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69567400 153 + 73212453 tacaagcc-a-agaga--agcctttaaggaaaccaatgctgcc----aacagtttgatct----tagacttctggcctcctgaattttgagaaaattaacctctg-tgtgtgag----------cccccaggctgaggggctttgtcatggcagcccaagccaac-caCACACC-TCC i ponAbe2.chr17 I 437 C 0 s panTro2.chr17 79182375 152 + 83384210 tacaagccaa-agaga--agccttcaaggaaaccaatgctgcc----aacagcttgatct----tagacttctggcct---gaattttgagaaaattaacctctgttgtgtgag----------cccccaggctgaggggcttcaccatggcagcccaagctgac-caCACACC-TCC i panTro2.chr17 C 0 C 0 e monDom5.chr2 304255088 6506 - 541556283 I e mm9.chr11 118660876 3590 + 121843856 I e loxAfr3.scaffold_49 14280181 2580 - 17734757 I a score=32778.000000 s hg19.chr17_gl000204_random 6407 51 + 81310 CACATCT---CATGACCACC---CTCCATTCTCAAGCGAGGACACTGCCCTGGGTCT s panTro2.chr17 79182527 51 + 83384210 CACATCT---CATGACCACC---CTCCATTCTCAAGCGAGGACACTGCCCTGGGTCT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69567553 51 + 73212453 CACATCT---CATGATCACC---CTCCATTCTCAAACGAGGACACTGCCTTGGGTCT i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74732976 51 + 78773432 CACATCT---CATGACCACC---CTCCATTCCCAAGCGAGGACACTGCCCTGGGTCC i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4292008 55 + 7991924 CACCCCTGAGCGAGGCCACCAGTCTATACTGTCAAC--GGGATGCTGTGCTGGACAC i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10748761 25 - 65312493 CACA------------CGTG---ACACATTCCCAAACCAG----------------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57937059 53 - 61308211 cacgtcctg-cgtcaccgtg---gctcatcctcaaaccaggaccctgctctgggtgc i equCab2.chr11 C 0 C 0 s canFam2.chr9 59351763 53 - 64418924 CACAGCCGA-CGTCGCCACG---GCACCTCCTCAAAGCAGCAGCCCACTCTGGGCGT i canFam2.chr9 C 0 C 0 s dasNov2.scaffold_104361 130 51 + 5925 cacatctta-cataaccaca---gtcatttcccaagccaag-caatGTCCTGGGCG- i dasNov2.scaffold_104361 N 0 C 0 e monDom5.chr2 304255088 6506 - 541556283 I e mm9.chr11 118660876 3590 + 121843856 I e loxAfr3.scaffold_49 14280181 2580 - 17734757 I a score=185067.000000 s hg19.chr17_gl000204_random 6458 148 + 81310 GTTGGTCAGTGGCAGAGCTTATTCAAACGTGACAAGTTCTGTGATCTGACCTGTGTGGCCTCTATACcggcacttctcaaaccatctgtggtgaa-ggattcattggtttatttccaattcattctggaccTACAtttttgttt-ctttg s panTro2.chr17 79182578 148 + 83384210 GTTGGTCAGTGGCAGAGCTTATTCAAACGTGACAAGTTCTGTGATCTGACCTGTGTGGCCTCTATACcggcacttctcaaaccatctgtggtgaa-ggactcattgttttatttccaattcattctggacCTACAtttttgttt-ctttg i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69567604 148 + 73212453 GTTGGTCAGTGGCAGAGCTTATTCAAACGTAACAAGTTCCGTGATCTGACCTGTGCAGCCTCTATACTGGCActtctcaaaccatctatggtgaa-ggactcattggtttatttccaattcattctggaccTACAtttttgttt-ctttg i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74733027 148 + 78773432 ACTGGTCAGTGGCAGAGCTTATTCAAACACGACAAGTTCTGTGATCTGACCTGTGTGGCCTCTATACcggcgcttctcaaactatctgcggtgaa-ggactcattggtttatttccaattcattctggacCTACAtttttgttt-ctttg i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4292063 143 + 7991924 ATGCGCCAGCGACACAGCCGATGCCGGGGTTGCCAGCTTTGTGATCTGA-CTGTGCACTCCATGTACGagtgtttctcaaactagctgtggtaga-agaggcattgttttatttctaacttgttagggacctacatttttgctt-a---- i cavPor3.scaffold_76 C 0 I 469 s bosTau4.chr19 10748786 129 - 65312493 ----GTCAACCACAGAGCTTATTCAAACTTCACCAGTTTTGTGATCTGACTC-TGTATCCTCTGCATCTGGgcttctcaaactatgtgtggcaaa-ggcctcac---tct---------tctttgcagatctacatttatt--t-atttg i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57937112 140 - 61308211 acccatcaaccacacggcttatttgaattccaccagttttGCGATCTGACTTGCGCGTCCTCCTTATGCgtgcttctcaaactatctgtgctgaaggactttgc---tttatctccaattcactgcagacctatatttttgct------- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59351816 111 - 64418924 GCCAGCCCACCACACAGCTTATTCGAGCTTCCCTGGTTTTGAGATGGGACCTGTGTGCACTCTCTCT-----CTTGTCAGC---------------GGGCTCAT---TTCATTCCCAAATCACTGGAAATACAT---------------- i canFam2.chr9 C 0 I 23 s loxAfr3.scaffold_49 14282761 143 - 17734757 GTTGGGCAACTCAAGAGCTTATTTAAATGTCACCAGCTTCGTGCTATGACTTGGACATCCTCTATACCAGCCCTTGTCAAATTATCTGGGGTGAA-TGTCAGAGTCCTTCGTTTCCAACGCACAACATGCCTATGCCTTTGTTT------ i loxAfr3.scaffold_49 I 2580 I 381 s dasNov2.scaffold_104361 181 138 + 5925 GCTAATCCGCTGCAGAGCCCATCAGGATTTCGGATG------GATCTGACCTGGTCCAGCCCTATCTGGgcgcttctcagactcgccgtggtgaa-ggacaaattgcttgatttcccattcactgtggacctatagttttgttct----- i dasNov2.scaffold_104361 C 0 C 0 e monDom5.chr2 304255088 6506 - 541556283 I e mm9.chr11 118660876 3590 + 121843856 I a score=52020.000000 s hg19.chr17_gl000204_random 6606 95 + 81310 ttttg-ttttttgagacagggtctcactatgctgcccagctgatctcaaacaccagggctcaaccaatcctcccacctcagcctcctgagtagttg s panTro2.chr17 79182726 95 + 83384210 ttttg-ttttttgagacagggtctcactatgctgcccagctgatctcaaacaccagggctcaaccaatcctcccacctcagcctcctgagtagttg i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69567752 95 + 73212453 ttttg-ttttttgagacagggtctcactatgttgcccagctgatctcaaacaccagggctcaaccaatcctcccacctcagcttcctgagtagttg i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74733175 96 + 78773432 ttttgtttttttgagacagggtctcactatgctgcccagctgatctcaaacaccagggctcaaccaatcctcccacctcagcctcctgagtagctg i rheMac2.chr16 C 0 C 0 e dasNov2.scaffold_104361 319 0 + 5925 C e monDom5.chr2 304255088 6506 - 541556283 I e canFam2.chr9 59351927 23 - 64418924 I e bosTau4.chr19 10748915 0 - 65312493 C e equCab2.chr11 57937252 0 - 61308211 C e cavPor3.scaffold_76 4292206 469 + 7991924 I e mm9.chr11 118660876 3590 + 121843856 I e loxAfr3.scaffold_49 14282904 381 - 17734757 I a score=140345.000000 s hg19.chr17_gl000204_random 6701 159 + 81310 aagtgacaagcCCT-TACTTTTGGTttttagaaaacctataaaaatagaatcactagaaa---aatggaataaa-gaaggcataca-aaaca-----caaagcccaggttcttaacgattagactcatcagacct------------aaaacgactccttca-aatgac--taaaagattctaaa s bosTau4.chr19 10748915 159 - 65312493 ------cagatcta-ta-------tttctttttaagctacaagcatgggattattggaaa---agtggaataaa-aagatt-taca-aaata-----caaagcctgatttctt-attattagattcagtagacacaacagtagacagaaaattgccctttcactctgactgtgaacggttctaaa i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59351950 135 - 64418924 ----------TATA-TA-------------TATTCTCTACAAAAAAGGGATTACTGGAAA---AATGGAATAAA-AAA-------G-AGACAACTTTCTTATTCCAACTGCTC-ATTAGTAGATCCATGAGATAT------------GAAGTTACCCTTACA-GATGACTCTCCCCGCTTACCAC i canFam2.chr9 I 23 C 0 s equCab2.chr11 57937252 133 - 61308211 aaaagaaaaa---------------------aaaagctataaaaaaggaattactggaaa---aatggaataaa-aaa-------g-gaata-----caaagcccaatttcct-gtgattagattcaacagacat------------aaaattactttttca-aattgctgtaaaagattctaaa i equCab2.chr11 C 0 C 0 s panTro2.chr17 79182821 159 + 83384210 aagtgacaagcCCT-TACTTTTGGTttttagaaaacctataaaaatagaatcactagaaa---aatggaataaa-gaaggcataca-aaaca-----caaagcccaggttcttaacgattagactcatcagacct------------aaaatgactccttca-aatgac--taaaagattctaaa i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69567847 159 + 73212453 AAGTGAAAAACCCT-tacttttggtttttagaaaccctataaaaatagaatcactagaaa---aatgggataaa-gaaggcacaca-aaaca-----caaagcccaggttcttaacgattagactcgtcagacct------------aaaatgactccttca-aatgac--taaaagattctaaa i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74733271 159 + 78773432 agatgacaagcCCTATACTTTCGGTTTCCTGAAAACCTATAaaaaaggaatcactagaaa---catggaataaa-gaaggcataca-aagta-----caaagcccaggttttt-atgattagactcatcagacct------------gaaatgactccttca-aatgac--tgtcaaagtctaaa i rheMac2.chr16 C 0 C 0 s dasNov2.scaffold_104361 319 134 + 5925 ------------------------------aaaaaactagaagagt-ggattactagaaataaactggaataaaccaagacatacataaaca-----caaagtccagtttgtt-gttattagattcagtggacgt------------aaaattactctttc--aattgcagcgaaagattctcag i dasNov2.scaffold_104361 C 0 C 0 s loxAfr3.scaffold_49 14283285 132 - 17734757 -----------------------------aaaagagctataaaggc-gaattactagaaa-acagaataaaaaacaaagactta---aaact-----caaagcccaattcctt-cctattagattcaacagacat------------aaaattactcttttg-aatcgctaccaagggctccaaa i loxAfr3.scaffold_49 I 381 C 0 e monDom5.chr2 304255088 6506 - 541556283 I e cavPor3.scaffold_76 4292206 469 + 7991924 I e mm9.chr11 118660876 3590 + 121843856 I a score=38385.000000 s hg19.chr17_gl000204_random 6860 64 + 81310 tgcttaatttca---------------gcttctgtact--ca-gttgc---------------------agggatcag---aagcagcacctcacgggctggcacc s panTro2.chr17 79182980 63 + 83384210 tgcttaatttca---------------gcttctgtact--ca-gtggc---------------------agggatcag---a-gcagcacctcatgggctggcacc i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69568006 64 + 73212453 tgcttaatttca---------------gcttctgtact--ca-gttgc---------------------agggatcag---gagcagcagctcacgggctggcacc i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74733430 62 + 78773432 tgctgactttca---------------gcttccgtact-----gttgc---------------------agggatcag---cagcggcagctcaccggctggcacc i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4292675 102 + 7991924 tacctagtctcaggcaatttgtagaacagcggaacactgact-aacacaGTTAGTTGCTCTTCTCTTGGAGGAGCCAG---CAACAACTGCTCACAGGGAGGCCCT i cavPor3.scaffold_76 I 469 C 0 s mm9.chr11 118664466 55 + 121843856 ---TTGTTCTCA---------------AGTGCAGTATT--CA-AGCCC----------------------GGGGCCAG---TAGCCATGGCTCCCGGGG-----CC i mm9.chr11 I 3590 C 0 s equCab2.chr11 57937385 65 - 61308211 tgtgaactcttg---------------gcttccagact--catctcgc---------------------agggaccag---cggcagcagctcacgggcaggcgct i equCab2.chr11 C 0 C 0 s canFam2.chr9 59352085 63 - 64418924 TCCCCAC-CGCC---------------GTGTCCACACT--CATCTTCT---------------------GGGGACCAG---TGGGCCCAGCTCAGGGGTGGGCTC- i canFam2.chr9 C 0 C 0 s bosTau4.chr19 10749074 64 - 65312493 tgaacactctcg---------------acttctgtccc--catcttgc---------------------tggaatcag----agcagcagctcacaggtgggcact i bosTau4.chr19 C 0 I 283 s loxAfr3.scaffold_49 14283417 65 - 17734757 tgcttcctctca---------------gcttctctgac--cc--tcgg---------------------ggggaccagcagcagcagtagttcacaga-aggcacg i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_104361 453 62 + 5925 tgccgactctca---------------gccttggtgcc--cccatcgt---------------------ggggac------cagtgggggtccccgggcaggcact i dasNov2.scaffold_104361 C 0 C 0 e monDom5.chr2 304255088 6506 - 541556283 I a score=116918.000000 s hg19.chr17_gl000204_random 6924 96 + 81310 catccacagacctcactttgagtagcTGAGATATGGGT--CATGTGAGACGTGT--CCT--CAGCC-----TGT---TGCT-AGGGAGCTGCTGTGGG----TTTGAATTCTGTA s panTro2.chr17 79183043 96 + 83384210 catccacagacctcactttgtgtagcTGAGATATGGGT--CATGTGAGACGTGT--CCT--CAGCC-----TGT---TGCT-AGGGAGCTGCTGTGGG----TTTGAATTctgta i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69568070 96 + 73212453 catccacagacctcactttgagtagcTGGGATATGGGT--CATGTGAGATGTGT--CCT--GAGCC-----TGT---TGCT-AGGGAGCTGCTGTGGG----TTCGAATTctgta i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74733492 96 + 78773432 catccacagacctcactctgagtagcTGGGATATGGGT--CATGTGAGGTGTGT--CCC--GAGCC-----TAT---TGCT-AGGGAGATGCTGTGGG----TTCAAATTCTGTG i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4292777 101 + 7991924 GATCTGTGGTCCTCACTTTGCATAGCTTTGACTTGGGC--CATCTGAGACACAT--CCTGAACAGG-----TGTCATGGCT-GGAGAGTCATTATGGG----CTCCAATTCTGCG i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118664521 99 + 121843856 TATGTGCAGACCTCACTTTGAGTGGTGTTGACCTGAGC--CATCCAGCACGCAC--GCT--CTGAG-----TGTCAGTGTT-GGAGGACTAGGGTGGG----GCTTGATTCTGAC i mm9.chr11 C 0 C 0 s canFam2.chr9 59352148 106 - 64418924 -GTCCACACGCGTCACTTTGAGTAGCTCCACAGTGGAT--CGTTGGAGCTGCATGAGCC--GAGCCAGTGCCGT---CCCC-AGAGAGCCACTGCGGGACGATTCCAACTCTCGA i canFam2.chr9 C 0 C 0 s equCab2.chr11 57937450 103 - 61308211 ggtccttggacctcactttgagtagctctgATTTGGAT--CATACTAGACGTATGTCCT--CAGCCAGGGTTGT---CGCC-AGAGAGCCGCTGTGGG----TTCAAATTCTGGA i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14283482 101 - 17734757 ggcccacggaccacactttgagtagctctgATCTGAATTTCACGTGAcacgtat--tct--gagcc-----tgggttccta-agacagcaaccatgag----tctgaattctgga i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_104361 515 98 + 5925 ggtctgc-gcccacactttgaggggctctgACTTG-ATTACACAACGCACGACC--TCT--GAGTC-----AGCGATCGTGTTGAGAGCTGCTGTGGG----TTGGAACTCTG-- i dasNov2.scaffold_104361 C 0 C 0 e monDom5.chr2 304255088 6506 - 541556283 I e bosTau4.chr19 10749138 283 - 65312493 I a score=11985.000000 s hg19.chr17_gl000204_random 7020 15 + 81310 TGGCCCTG---------GGTTGGT s panTro2.chr17 79183139 15 + 83384210 tggccctg---------ggttggt i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69568166 15 + 73212453 tggccctg---------ggctggt i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74733588 15 + 78773432 TGGCCCTG---------GTCTGGT i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4292878 15 + 7991924 TAGTCTCA---------TGCTGAC i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118664620 10 + 121843856 TGTTCCAG---------Gg----- i mm9.chr11 C 0 I 428 s bosTau4.chr19 10749421 24 - 65312493 tggtaccaggcagcagctgtgaac i bosTau4.chr19 I 283 C 0 s equCab2.chr11 57937553 15 - 61308211 TGGCCCCA---------TGCTAAT i equCab2.chr11 C 0 C 0 s canFam2.chr9 59352254 15 - 64418924 TGGCCCCA---------TGCTAAT i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14283583 15 - 17734757 cagccctg---------ggctagt i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_104361 613 10 + 5925 -----CTG---------CCCCAGT i dasNov2.scaffold_104361 C 0 C 0 e monDom5.chr2 304255088 6506 - 541556283 I a score=138316.000000 s hg19.chr17_gl000204_random 7035 144 + 81310 CATTTATCTGCAGCTCAGCTTCCTCACAGAGCCCGAGTT--GGAACTGTTGTGAGGATTCACG-----ATGATTCATATA-TATTTTGGG---ACGAGAACCTCGGGTAAGATAACCTGCTCA-CATGTGTCATTCAGGGACGTCAGCCTGATGGA s panTro2.chr17 79183154 144 + 83384210 catttatctgcagctcagcttcctcaCAGAGCCCGAGTT--GGAACTGTTGTGAGGATTCACA-----ATGATTCATATA-TATTTTGGG---ACGAGGACCTCGGGTAAGATAACCTGCTCA-CACGTGTCATTCAGGGACGTCAGCCTGATGGA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69568181 144 + 73212453 catttatctgcagctcagcttcctcaCAGAGCCCGAGTT--GGAACTGTTGCGAGGATTCACG-----ATGATTCATATA-AATTTTGGG---ACGAGAACCTCGGGTAAGATAACCTGCTCA-CACGTGTCATTCAGGGACGTCAGCCTGATGGA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74733603 144 + 78773432 CATTTATCTGCAGCTCAGCTTCCTCACAGAGCCTGAGGT--GGAATTGTCATGAGGATTCACG-----ATGATTCATATA-AATTTTGGG---ACGAGAACCTCGGGTAAGATAACCTGCTCA-CACGTGTCATTCGGGGACGTCAGCCTGATGGA i rheMac2.chr16 C 0 C 0 s mm9.chr11 118665058 127 + 121843856 CATTGTCCCGTGGTTCTGTTTT--------------CTC--AGA---GTCGCGATGTCTGACAAGGCAATGTCACCCACA-ACCCTTGGAATGATGAAAATTCCAGACAAGATGGGCTGTACCTCAC--------CA-GCAGGTCACCTTGAGGTA i mm9.chr11 I 428 C 0 s cavPor3.scaffold_76 4292893 150 + 7991924 CATGTAACAGTGGCTCAGTTTTCTCACTGAATTCAGCTC--AGAGTTGTTGTGAAGATTAATGGGG--ATGGTGGGCACATAACCTTGAGATCACAACTATCTCAGATAAGATGCCCTGTGCC-CACGTGTCTTTCA-GGAGGTCAGCTGGACAGA i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10749445 148 - 65312493 cattcctgtatggctcagtttcctcaggagacctagcttagagggttattgtgaggagtaacagag--atgacgcatgtc-aaTCTACAG---ATGAGAACCTTGGAT-AAGATACCCACAAA-CACGTGTCACCCCAGCTTGTCAGCTGGACCAG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57937568 146 - 61308211 CACTCCTCGGAGGCTCAGGGTCCTCatggaacccagctcacagagttgctgtggggatg-acaggg--agggtacatgtc-aaccctgag---aCGA-GAACTGGATC-AGGTAATCTGCACA-TACGTGTCATTCCGGGACATCAGCGTGACCAG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59352269 148 - 64418924 CCTTCATCTGCGGCTCTGTTTCCTCGTGGGacccagcgcacagggttgtcgtgaggattcccaggg--atgacacatgtc-aaCCTGACA---ACGGCGACCTCAGAG-AGACAGCCTGAGTG-TACGTGTCGCTGCAGGACGTCCACCTGACCTG i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14283598 146 - 17734757 aatttaactggggctcagtgttctcatggaccccagctcaccaagctgttgtgaggactaatgggg--atgggacaggta-ag--tagag---aataggaccCCTGTA-AGGTAACCGGCACA-GGTAAGTCACCCCAGGGTGTCAGCGTGAGGGA i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_104361 623 120 + 5925 -GCCTCTCTCTGGCTCAGTTTCGTCTTGGAGCCCAGCTCACA-----------------GATGTGG--GTCGGTGTCGCA-A----AGAG---AACCTCATTCGTACC-ATATAGCCTGGAT-------GTCATCCCAGGACGTTGGTGCAACTTA i dasNov2.scaffold_104361 C 0 C 0 e monDom5.chr2 304255088 6506 - 541556283 I a score=92908.000000 s hg19.chr17_gl000204_random 7179 74 + 81310 TTTCCAGGCCTTGCATACTGTTC-----TGGAC-ACTCCAGGCACACAGATGCCTCCCAC---AAGAAGTTGTGTTACGAGTG s dasNov2.scaffold_104361 743 73 + 5925 TTTCCAAGTCTTCCAAGAGGTT------TAGAG-GCTCCGGACATGCAGAGGTCAACCAC---GGGGGGCAGCTTCTCGTGCG i dasNov2.scaffold_104361 C 0 C 0 s loxAfr3.scaffold_49 14283744 73 - 17734757 TTTCCACGCCATCGCTGCTGTG------TTGGG-GCTGCAGGCATGCAGATGCCTGCCAC---ATGGAGTTGCTTTCCTCGTG i loxAfr3.scaffold_49 C 0 C 0 s canFam2.chr9 59352417 72 - 64418924 TCTCCATGCCTTCCAGACCACAA-----TAGGGAACCCCAGGCCCATGGGTGCCCCCCGCCATGTGAAACGGGTT------TC i canFam2.chr9 C 0 C 0 s equCab2.chr11 57937714 74 - 61308211 CCTCCAAGCCATCAACACTGCTT-----TAGAG-ACGGCAGGCACCCGGATGTCTCCCCC---GTGAGGTTGTTTCATGAGTG i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10749593 74 - 65312493 TCTCCAAGCTCTAAGCCCTGCTG-----TAGAG-ACTCCAGGCCCACGGATGTCTCCCAC---AAGAGGTTGTGTTGTGCGTG i bosTau4.chr19 C 0 C 0 s cavPor3.scaffold_76 4293043 65 + 7991924 TTTCCAGGCCTTCAGCAGCATTT-----GAGAG-ACTCCGGGCACACAGGTGTCTAGCAC---AGAA-----TGCTA----CA i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118665185 74 + 121843856 CCCCCAAGTCTTCTGCACTGTTCGGGGGGGGGG-GCTCTGGGCCCAGGAGCTCCCCTCGT---GGCA-----TGTCAGGAGCA i mm9.chr11 C 0 C 0 s rheMac2.chr16 74733747 74 + 78773432 TTTCCAGGCCTTGCACACTGTTC-----CGGAC-ACTCCAGGCCCACAGATGCCTCCCAC---ATGGAGTTGTGTTACGAGTG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69568325 74 + 73212453 TTTCCAGGCCTTGCACACTGTTC-----TGGAC-ACTCCAGGCACACAGATGCCTCCCAC---ATGAAGTTGTGTTACGAGTG i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79183298 74 + 83384210 TTTCCAGGCCTTGCACACTGTTC-----TGGAC-ACTCCAGGCACACAGATGCCTCCCAC---ATGAAGTTGTGTTAAGAGTG i panTro2.chr17 C 0 C 0 s monDom5.chr2 304261594 61 - 541556283 TTTTCTAGCCTGTCATCATGCTT-----CAGAT------AGGCATATCTGTTTCTCTATT---TTTAAGCAACAA-------- i monDom5.chr2 I 6506 C 0 a score=680305.000000 s hg19.chr17_gl000204_random 7253 210 + 81310 TATTATTTGATCTTTGTT-------GAACTTGGGTTTATC-TTTGCTTGCTTTCAGGCCCTCCCATAATGTTGACATCCTGATGAACCCCCGCTGGTGACGGCAGGTGGCCACACC-CTGCAAGCTCCCTGTAATTCCAGCCATTACTCAGCAA----------TGCTCAGCAATGCAAGGTCACTCAGAAACACCATCTGTCCAAG---------------CTCCATCT---CCC-----CTCCCACCCCA s panTro2.chr17 79183372 210 + 83384210 TATTATTTGATCTTTGTT-------GAACTTGGGTTTATC-TTTGCTTGCTTTCAGACCCTCCCATAATGTTGACATCCTGATGAACCCCCGCTGGTGACGGCAGGTGGCCACACC-CTGCCAGCTCCCTGTAATTCCAGCCATTACTCAGCAA----------CGCTCAGCAATGCAAGGTCACTCAGAAACACCATCTGTCCAAG---------------CTCCGTCT---CCC-----CTCCCACCCCA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69568399 210 + 73212453 TATTATTTGATCTTTGTT-------GAACTTGGGTTTATC-TTTGCTTGCTTTCAGGCCCTCCCATAATGTTGACATCCTGATGAACCCCCGCTGGTGACGGCAGGTGGCCACACC-CTGCAAGCTCCCTGTAATTCCAGCCATTACTCAGCAA----------CGCTCAGCAATGCAAGGTCACTCAGAAACACCATCTGTCCAAG---------------CTCTGTCT---CCC-----CTCCCACCCCA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74733821 209 + 78773432 TGTTATTTGATCTTTGTT-------GAACTTGGGCTTATC-TTTGCTTGCTCTCAGGCCCTCCCATAATGTTGACATCCTGAT-AACTCCCACTGGTGACTGCAGGTGGCCACACC-CTGCAAGCTCCCTGCAATTCCAGCCATTACTCAGCAA----------CGCTCAGCAATGCAAGGTCACTCAGAAACACCATCTGTCCAAG---------------CTCCGTCT---CCC-----CTCCCACCCCA i rheMac2.chr16 C 0 C 0 s mm9.chr11 118665259 220 + 121843856 TCCTATTTGATCTTTGTT-------GAACTTGAGTTCAGC-TTTGATTGCTCTCCCACCCTGCCAGGGTGCTTACATCATAATTGGTGCCCAGTGGTAACTGCAGGAGTCCACATC-CTGCAAGCTTCCT---------GCCAAAGCTCAGCAG----------CAGCCAGTGGTGTAAGGTCAAG-GATGGAGCTGTCTGTCCCAGCAGAGGACAGGGTGACTGTCCCT---CTTTTTTGTTTCCTCTTCT i mm9.chr11 C 0 I 137 s cavPor3.scaffold_76 4293108 198 + 7991924 T--TATTTGATCTTTATT-------GGAC-------------CTGATTGCTTCCAGGCCCTTCCATAATGTTGACATCCTGATTCACCCCCGCTGGTAGCTGCAGGTGGCCACACC-CTGTGAGCTTCCTGAAATTCCAGCCATTACTCAGCAA----------T-GCTTATGACACAAGGTCAC--CATTGCACCATCTGTCTAAG---------------CTCCTTCC---CATTCCTGCTCCCTCCCTG i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10749667 210 - 65312493 TGTTGTTTGATCTTCATT-------GAACTTGGGTTTGTCATCTGGTTGCTTCCAGGTCCTTCCGGAATGCTGGCATCCTGG-TGACCCCCACTGGTAGCTGCGGGTGGCCACACC-CTGCGAGCTTCCTACAGTTCCAGCCACTACTCAGCCA----------CACTCAGCAACACAAGGTCACTCAAAAACACCATCTGTGCATG---------------TGCTACCT---CCT-----CTCCCACCTCA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57937788 212 - 61308211 TGTTATTTGATCTTTGCT------GGAACTCGCGTTTGTCTTCTGATTGCTGCCAGGTCCTGCCTCAGTGTTGACATCCTGATTAACCCCCACTGGGAGCTGCAGGTGGCCACACC-CTGCGAGCTTCCTGCAGCTTCTGCTGCCACTCGGCAG----------CTCTCAGCGACACAAGGTCACTCAGAAACACCATCTGTCCTAG---------------CTCCGCCT---CCT-----CTCCCACCCTA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59352489 218 - 64418924 TGTGAGCTGATCATTGTTGATTTGGGTGCTTGGATTTATCTCCTGATGCCTTCTAGGCCCTTCCATAATGCTGACATCCTAACTAACCCTCACTGGTCGTGGCGGGCAGCCACACC-CCACGAGCCTCCTGTCACTCCAGTCGTTACTCAGCAAC-----ACTCCACTCAGTGACACAAGGTCACTCA-AAACACCA----CCCAAG---------------CTCCACCT---TCT-----CTCCCACCCCA i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14283817 210 - 17734757 TTTTTTTTGATCTTTGTT-------GAGCTTGGGGTTTTCTTTAGATTGCTGCCAGCTCCTTCCAGAATGTGGACATCCTGATTCCCACCCAC-AGTGGCTGCAGGTGGCCACGCC-CTGGGAGCTTCTTGCAGCTCCAGCCATTGCTCAGTGT----------CCCTCAGCAATGCAAGGTCACTCGGAAACACCATCTGTTCACC---------------CACCATCT---CCC-----CTGCCACCCTG i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_104361 816 203 + 5925 TGCTATTCGAGCTTTGTT-------GAACTGGGGTTTATCCTGTGCCTGCTTCTAGATCCTTCTGTGATGCTGACATCCTGATCTGCCCCCACGGGTGACGCCGAGTGACCACCCC-CTGCAAGCCTCCTGCTGC-----CCACAGCTCAGCCC----------CACTCAGGGACGCAAGTTCACTCGAAAACACCATCTGTCCATG---------------C-CCGTCG---CCT-----C--CCACCTGG i dasNov2.scaffold_104361 C 0 C 0 s macEug1.Scaffold58194 6288 223 - 16617 TGTTTCCTGATCTTTGTT-------CATCCCGGGCTTATA--TTGATTCCTTCTAGGTTTCACATTCATGATGGCATCCTGATTAACTCCCACGAGCAACAGCAGGTTGCAACACCACTTCAAGCTTCCTGCAATTCCAACCATTACTCAGCAATGGAAGGAATCACCCAGGGATACAAGGTCATTCAAAAACACCATCTGTCCAAG---------------CACTATCCATATAT-----CCCTATCCCCA i macEug1.Scaffold58194 N 0 I 3 s monDom5.chr2 304261655 219 - 541556283 TATTTCTTGATCTTTGTT-------TGTATTAGACTTCTG--TTGATTCCTTCTAGGTTTCTCATTCATGTT---ATCCTGATTAACTCCTACTAGCAACAGCAGGTTGCAACACTACTTCAAGCTTCCTACAACTCCAACCATTACTCAGCAATGGAGGAAATCACCCAGTGATATAAGGTCATTCAAAACCACCATCTGTCCAAG---------------CACTATCC---ATG---TATCCCTATCTTG i monDom5.chr2 C 0 C 0 a score=25734.000000 s hg19.chr17_gl000204_random 7463 44 + 81310 AAG-GAAAAAA------GAAAAATTAT-TCTGTTCCGCCTCCATTTTT---CTCC s panTro2.chr17 79183582 44 + 83384210 AAG-GAAAAAA------GAAAAATTAT-TCTGTTCCGCCTCCATTTTT---CTCC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69568609 47 + 73212453 AAG-GAAAAAA------GAAAAATTAT-TCTGTTCCGCCTCCATTTTTCTCCTCC i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74734030 47 + 78773432 AAG-GAAAAAA------GAAAAATTAT-TCTGTTCCGCCTCCATTTTTCTCCTCC i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4293306 24 + 7991924 -AG-Gacacac------acacacatatgtgtg----------------------- i cavPor3.scaffold_76 C 0 I 8 s bosTau4.chr19 10749877 45 - 65312493 AAGAAAAAAGA------GAAAAATGAT-TCTATTCTGCCTCCATGTTTTCTC--- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57938000 44 - 61308211 GAG-AAAGAGC------GAAGACTCAT-TCTGTTCCGCCTCCGTGTTTTCTC--- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59352707 36 - 64418924 AAT-AAGCAGA------GAAAAATGAC-CCTGGCC--------TGTTTTCAC--- i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14284027 42 - 17734757 GCG-TAAAGGA------GGACGACGAT-TCCGTCCCACCCCTGTGTGTTC----- i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_104361 1019 42 + 5925 AAG-AACAGGA------GGAAAGTTAT-TCTGTCCCCTCTCCGTGCTTTC----- i dasNov2.scaffold_104361 C 0 C 0 s macEug1.Scaffold58194 6514 41 - 16617 AGG-GAGAAAATCACTCAAAAAACTAT-TC---CCCACTCCTACCC--------- i macEug1.Scaffold58194 I 3 C 0 s monDom5.chr2 304261874 47 - 541556283 AAA-GAGAAAATCACTCAAAAAGCTAT-TC---TCCACTCCCATTCTACTCA--- i monDom5.chr2 C 0 C 0 e mm9.chr11 118665479 137 + 121843856 I a score=-603.000000 s hg19.chr17_gl000204_random 7507 30 + 81310 TCCTCCTAAAAGcacacacacacactcaca s panTro2.chr17 79183626 30 + 83384210 TCCTCCTAAAAGcacacacacacactcaca i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69568656 30 + 73212453 TCCTCCTAAAAGcacacacacacactcaca i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74734077 30 + 78773432 TCCTCCTAAAAGcacacacacactcacaca i rheMac2.chr16 C 0 C 0 s mm9.chr11 118665616 30 + 121843856 cacacacacacacacacacacacacacaca i mm9.chr11 I 137 I 18 s cavPor3.scaffold_76 4293338 30 + 7991924 cacacacacacacacacacacacacacaca i cavPor3.scaffold_76 I 8 C 0 s bosTau4.chr19 10749922 9 - 65312493 ---------------------CCCTACACA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57938044 9 - 61308211 ---------------------TGTCACACA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59352743 9 - 64418924 ---------------------TCTCACACA i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14284069 24 - 17734757 TCATCTTacacacacatacacaca------ i loxAfr3.scaffold_49 C 0 I 361 s dasNov2.scaffold_104361 1061 13 + 5925 ---TGCTACACACACA-------------- i dasNov2.scaffold_104361 C 0 C 0 s macEug1.Scaffold58194 6555 20 - 16617 ------TACTTACACACAAA----Ctaata i macEug1.Scaffold58194 C 0 N 0 s monDom5.chr2 304261921 23 - 541556283 -------AAAACTAAtctctctctctctcc i monDom5.chr2 C 0 C 0 a score=362407.000000 s hg19.chr17_gl000204_random 7537 139 + 81310 cacacacacacgcaGA----ACTAAAGTTAGGCTTGCCTTGACCTCTACTTCTAAATTAATTTTCCTTCCTCAGGCATTTGCTGA--CGCTCCTTTTCTGT--------TCTTTCCCCCACAGAACACAGATGTCTTTGAAAGCACCAATCCT s panTro2.chr17 79183656 137 + 83384210 cacacacac--gcaGA----ACTAAAGTTAGGCTTGCCTTGACCTCTACTTCTAAATTAATTTTCCTTCCTCAGGCATTTGCTGA--CGCTCCTTTTCTGT--------TCTTTCCCCCACAGAACACAGATGTCTTTGAAAGCACCAATCCT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69568686 137 + 73212453 cacacacac--gcaGA----ACTAAAGTTAGGCTTGCCTTGACCTCTACTTCTAAATTAATTTTCCTTCCTCAGGCATTTGCTGA--CGCTCCTTTTCTGT--------TCTTTCCCCCAAAGAACACAGATGTCTTTGAAAGCACCAAGCCT i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74734107 137 + 78773432 cacacacac--gcaGA----ACTAAAGTTAGGCTTGCCTTGACCTCTACTTCTAAATTAATTTTCCTTCCTCAGGCATTTGCTGA--CGCTCCTTTTCTGT--------TCTTTCCCCAACAGAACACAGATGTCTTTGAAAGCACCAAGCCT i rheMac2.chr16 C 0 C 0 s mm9.chr11 118665664 117 + 121843856 cacacacac--acaaacacaGCTCAAGCCCAGCTTGCGCTGTCCCCT-CTTCTGTGT---TCTCCCTTCCTTGGGCCTCTGCCAG------------------------TCCCTCCTCTTCTGAACACAGGTGCCTTTGGAAGCTCC------ i mm9.chr11 I 18 C 0 s cavPor3.scaffold_76 4293368 123 + 7991924 cacacacac--acaGA--------------GGCTTGTCTTGACCCCTACTTCTAGATTAATTTCTCTTCCACGGGTGTTTGTCAACACGC-CTTTTTCTGT--------TCTTTCCTCTGATAAACACAAATGTCTTGGAATGCATCA----- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10749931 139 - 65312493 CAGAGACAC--ACGCA--CCACTGAAGTTAAGCTTGTCTCAACCTCTACTTCTAAATTAATTTTTCTTCCTGAGGCATTTGCTGA--CACTCCCTTTCTGT--------TCTTTGCCCTTCAGAACACAGATGTCTTTGAAAGCACCAGGCCT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57938053 134 - 61308211 CACACACAC--CC-------CCTAAAGTTAAGCTCGTCTCGACCTCTACTTCTAAATTAATTTTCCTTCCGGAAGCATCTGCCGA--CACTCCTTTTCTGC--------TCTTTGCCCCACAGAGCACAGACGTCTTTGAAAGCACCAGGCCT i equCab2.chr11 C 0 C 0 s canFam2.chr9 59352752 137 - 64418924 CGCGTGTAC--GCAGA----ACTAAAGCCAGGCTCGTCCTGACCTCTCCTCCTAAATTAATTTTTCTTCCTCAGACATTTGCTGA--CACTCCTTTTCTGT--------TCTTTGCCGCACAAAACACAAAAGTCTTTGAAAGCACCAGGCCT i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14284454 137 - 17734757 CACACACCG--GCAAC----ACTAAAGCTAGGCTTGTCAAGACTTCAACTTCTAAGTTAATTTTTATTCCTCAGGCATTTATTGA--CACTCCTTTTCTGG--------CCTTGCCCCCACGGATCATAGATGTCTTTGAAAGCACCAGGCCT i loxAfr3.scaffold_49 I 361 C 0 s dasNov2.scaffold_104361 1074 133 + 5925 TTCACCGTG--GCGAA----ACCGAAGCTGGACCTGCCCTGACCTCCACTGCTAAATTAATTTCTCTTCCCCAGCCGTTTGCT------CTCCTTTTCTAT--------TCTTTCTCCCATAGAATACAGATGTCTTTGAAAGCATCAGGCCT i dasNov2.scaffold_104361 C 0 C 0 s monDom5.chr2 304261944 116 - 541556283 ----------------------------------ctctctccctccctcctccactttcctctctccttctcttgccttccctcc--cccttcctttcctttcaatctctctctctcctccctcACCCTAAT-TCTTGCCAATCACCATTTCT i monDom5.chr2 C 0 I 4285 a score=200498.000000 s hg19.chr17_gl000204_random 7676 177 + 81310 GCAAACACTTTGTATATCCTTGCAAATCGGGT----AAAA--------GAATAATTTTCTCCAAATCTATACAAATCCTCACTC-GTCCATTCACCTTTGCCATGGA-ATTCACCGGCAA-CCCCCTCTGAGGAATGCA---CGTGTCA--ATGCAG-AAAAAAAAAAAAAATGAAGAAATTCCGGAATCACATCGAG s panTro2.chr17 79183793 178 + 83384210 GCAAACACTTTGTATATCCTTGCGAATCGGGT----AAAA--------GAATAATTTTCTCCCAATCCATACAAATCCTCACTC-GTCCATTCACCTTTGCCGTGGA-ATTCACCGGCAA-CCCCCTCTGAGGAATGCA---CGTGTCA--ACGCAGGAAAAAAAAAAAAAATGAAGAAATTCTGGAATCACATCGAG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69568823 173 + 73212453 GCAAACACTTTGTGTATCCTTGAAAATCAGGG----AAAA--------GAATAATTTTCTCCCAATCCATACAAATCCTCACTC-ATCCATTCACCTTTGCTGTGGA-ATTCACCAGCAA-CCCCCTCTGAGGAATGTA---CGTGTCA--ATGCAG-----AAGAAAAAAATGAAGAAATTCCGGAATCACATCAAG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74734244 173 + 78773432 GCAAACACTTTGTGTATCCTTGCAAATCGGGT----AAAA--------GAATATTTTTCTCCCAATCCATACAAATCCTCACGC-GTCCATTCACCTTTGCTGTGGA-ATTCACTGACAA-CCCCCTCTGAGGAATGTA---TGTGTCA--ACGCAG-----AAAAAAAAAATGAAGAAATTCCGGAATCACACCAAG i rheMac2.chr16 C 0 C 0 s mm9.chr11 118665781 157 + 121843856 ---------------AGCCCTGAAAA--ACTT----GCAAACCATAACAAACGACTTTCTCCCAATTGGTACACGCCC--GCTG-A--CGCTCACTCTCCGAGTGGA-A--TCACAGCTG-TCCCTCTAACGGTGTGC----TGTGTCT--GTACAA-----AGAGACAGGATGGAGATTCTACGCAGCCAGACCCAG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4293491 171 + 7991924 -CAGATAC----TGTACCCTTGCAAATGAGAT----TAAAACAAAATGAAACAATTTTCTTCCCATTGGTAGAAATCCTGGCTG-GT-CTATGACCCTTCAAGCGGG-A--CGTGTGGTG-GCCCCATGGAAGAGTGAACAGAGTGCCA--GCAC--------GTGACAGAATGAAGAGTCT--GGAGCCAAATCAGG i cavPor3.scaffold_76 C 0 I 23 s bosTau4.chr19 10750070 160 - 65312493 GGGAATACTTAATGTATCCTTGCAAATCGGATTAAAAAAA--------AAATAATTTTCTCCCAATCCATAAAAATCCCTGCTC-GTCTGTTTGCCCTTTGAGTGGA-GTTCACCATCAG-CCCA-----------------CGTGTCG--ACACAG-----AACA---AAGTGAGGGGTCTATGGGATCCGATCCAA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57938187 157 - 61308211 GGGAACACTTAATGTACCCTTGCAAATCG-------AACA--------AAATAATTCTCTCCCAATCCACAGAAATCCTTGCTT-GTCCGTTCGCCCTTTAAGTGGA-GTTCACCGCCAACCCCG-----------------CGTGTCA--ATGTAG-----AAGAAGAAAACGAGGCTTCCGTGGCCTCCGCTCAAG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59352889 145 - 64418924 GGGAATACCTAATGTGTCCTTGTAAATTGG-----AAAAA--------AAAGAATTTTCTCCCAATCCATAAAAATCCTTGCTTCGCCTGTTTGCCCTTTAAGTGAA-GCTCACTGCCAG-CCCG-----------------CGTATTA--ATGCAG-----AAGAAGGAAGTGAGGAT-----------CACCC--- i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14284591 170 - 17734757 AGGAATATTTAA-TTATCCTTGCAAATCAGAT----AAAA--------AAA-AATTTTCTCCTGATCCATAACAATCCTTGCTG-GCCCCTTCACCCTTTAAGCGGG-GCTCTCTGGCAGGCACCATCTGATGAAGGCG---TGCGTCA--GGGTAG-----AAGAACAAGGCCA--GGTCTGCTGAATCAGACCCAG i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_104361 1207 170 + 5925 GGGGACACTTCATTTATCCTTGCAAATCAGAT----GAAA--------AAATAGCTTTCTCCCAATCCATAGCAATCC-TGCAG-GTCCACTCACCCTGTACGTGGGTTCACCCTGGCAGGTCCCACCTGAGGCGCGGT---CGAGTCGATGTGTAA-----GAGGAAAAGG-----ATTCTGACGCATC-GACCAAG i dasNov2.scaffold_104361 C 0 C 0 e monDom5.chr2 304262060 4285 - 541556283 I a score=53639.000000 s hg19.chr17_gl000204_random 7853 53 + 81310 GGGCCT-CAGCCCCAGGTCCCATCTAAGAATGAGGCCAGCAAGAACCACTTAGG s panTro2.chr17 79183971 53 + 83384210 GGGCCT-CAGCCCCAGGTCCCATCTAAGAATGAGGCCAGCAAGAACCACTTAGG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69568996 53 + 73212453 GGGCCT-CAGCCCCACGTCCCATCTAAGAATGAGGCCAGCAAGAACCACTTAGG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74734417 53 + 78773432 GGGCCT-CAGCCCCAGGTCCCATCTAAGAATGAGACCAGCAAGAACCACTTAGG i rheMac2.chr16 C 0 C 0 s mm9.chr11 118665938 51 + 121843856 -GGACT-TTACCTTGGCTCCTGTCTGAGAGTCAT-TCAGCGAGCCCCATATCTG i mm9.chr11 C 0 I 1 s bosTau4.chr19 10750230 51 - 65312493 -GGGCC-TAACCTGGGCACCTGCCTGGCAGTGGAACCAGGAAGCACA-CGTCAA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57938344 52 - 61308211 -GGGCC-TGGGCCGGGTGCCCGTCTGGGAGTGAGACCAGCAACACCAGTGTCGG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59353034 51 - 64418924 -GGAAC-TGGG-TGGGTGCCCGTGGGGCAGTGGGGTCAGCAGGAGAAGTGTCAC i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14284761 45 - 17734757 GGGCTC-AGGGCCCGGGGCCCCTCTGAGAGTGAGACCAGCAAAGAC-------- i loxAfr3.scaffold_49 C 0 I 44 s dasNov2.scaffold_104361 1377 51 + 5925 GGGCCCTCGTCCCCTGTGCCCCTCTGAGAGTGAGGCCAGCCAGAGC--CGTGG- i dasNov2.scaffold_104361 C 0 C 0 e monDom5.chr2 304262060 4285 - 541556283 I e cavPor3.scaffold_76 4293662 23 + 7991924 I a score=37042.000000 s hg19.chr17_gl000204_random 7906 38 + 81310 --CTCTT-GGATGCCGTTGACTCACG--TCcctggtggc---cctt s panTro2.chr17 79184024 38 + 83384210 --CTCTT-GGATGCCGTTGACTCACG--TCCCTGGTGGC---CCTT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69569049 38 + 73212453 --CTCTT-GGAGGCCGTTGACTCAGG--TCCCTGGTGGC---CCTT i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74734470 37 + 78773432 --CTC-T-GGATGCCGTTAACTCAGG--TCCCTGGTGGC---CCTT i rheMac2.chr16 C 0 C 0 s mm9.chr11 118665990 41 + 121843856 --CTCTC-AGATGACACGGA--TAAGAGAGCCTCGTGGCTTTCCGT i mm9.chr11 I 1 C 0 s cavPor3.scaffold_76 4293685 38 + 7991924 --CTCTC-AGATGATGCTGACTCAAGATTGCCACAAG-----CCTT i cavPor3.scaffold_76 I 23 C 0 s bosTau4.chr19 10750281 39 - 65312493 --CTTCT-GGGTGAGGCTGGCTCACAA-ACTCTCATGGC---CCCC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57938396 39 - 61308211 --CCTGC-GGGCGAGGTTGACTCATAA-ACCCTCAGGGC---CCCT i equCab2.chr11 C 0 C 0 s canFam2.chr9 59353085 40 - 64418924 --CCTCTGGGGTGAGGCTGACCCACAA-ACCCTCAGGGC---CCCT i canFam2.chr9 C 0 C 0 s dasNov2.scaffold_104361 1428 42 + 5925 CCCCGTC-CAGTGAGGGTGACTCAAGGGACACTGATGGC---CCCT i dasNov2.scaffold_104361 C 0 I 1769 e monDom5.chr2 304262060 4285 - 541556283 I e loxAfr3.scaffold_49 14284806 44 - 17734757 I a score=74130.000000 s hg19.chr17_gl000204_random 7944 493 + 81310 ga----tc-------attttgaatctaaaacatatggatttatacagattcatgtggaaccttctcatgtttctccatccagaatatctctgtgacgatgcagtcacaagttctg--cagttactt-ctgtgtga-CA---GGG----TCTGTTTGGAT--CAT-GCTTGCACAGGTGTCGATATACCATCCTGGAACA-------CGAGGACTAACCCTCCTTTCCCT------------------CAACGGATGGTGACAATC----ATTTATTGGCTCTCACTGAAGACACAGCCCTTATCGCTGGGGGACTCAGCA-----TCTCAGAGGAGGATGGGCTGTGCATGCAGAGGGAACACA-GGGAGCAAAGTCTGTGCAGAAGGTCACCTCACTCACATTTGACTTTTGTATCCGTGAACTTCAGTGC--------------AGCGTG--TACCCAGGATCTATTTTC---TGCTTCCATTCCCCCTCATTCCCTGGTGCCATTAGTTCCTTTT------------CCTAAAGTCCTCATG---------------------------------------------------GGTCTCCCCCAGC------------------CCTGGACTCTTAC----CTCCAC-----CATCACC s panTro2.chr17 79184062 493 + 83384210 GA----TC-------ATTTTGAATCTAAAACATATGGATTTATACAGATTCATGTGGAACCTTCTCATGTTTCTCCATCCAGAATATCTCTGTGACGATGCAGTCACAAGTTCTG--CAGTTACTT-CTGTGTGA-CA---GGG----TCTGTTTGGAT--CAT-GCTTGCACAGGTGTCGATATACCATCCTGGAACA-------CGAGGACTAACCCTCCTTCCCCT------------------CAACGGATGGTGACAATC----ATTTATTGGCTCTCACTGAAGACACAGCCCTTATCGCTGGGGGACTCAGCA-----TCTCAGAGGAGGATGGGCTGTGCATGCAGAGGGAAGACA-GGGAGCAAAGTCTGTGCAGAAGGTCACCTCACTCACATTTGACTTTTGTATCCGTGAACTTCAGTGC--------------AGCGTG--TACCCAGGATCTATTTTC---TGCCTCCATTCCCCCTCATTCCCTGGTGCCATTAGTTCCTTTT------------CCTAAAGTCCTCATG---------------------------------------------------GGTCTCCCCCAGC------------------CCTGGACTCTTAC----CTCCAC-----CATCACC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69569087 493 + 73212453 GA----TC-------ATTTTGAATCTAAAATGAATGGATTTGTACAGATCCATGTGGAACCTTCTCATGTTTCTCCATCCAGAATATCTCTGTGATGATGCAGTCACAAGTTCTG--CAGTTACTT-CTGTGTGA-CG---GGG----TCTGTTTGGAT--CAT-GCTTGCACAGGTGTTGATATACCATCCCAGAACA-------CGAGGACTAACCCTCCTTCCCCT------------------CAATGGATGGCAACAATC----ATTTATTGGCTCTCACTGAAGACACAGCCCTTATCGCTGGGGGACTCAGCA-----TCTCAGAGGAGGGTGGGCTGTGCATGCAGAGGGAAGACA-GAGAGCAAAGTCTGTACAGAAGGTCACCTCACTCACATTTGACTTTTGTACCCGTGAACTTCAGTGC--------------AGCGTG--TACCCAGGATCTATTTTC---TGCCTCCATTTCCCCTCATTCACTGGTGCCATTAGTTCCTTTT------------CCTAAAGTCCTCATG---------------------------------------------------GGTCTCCCCCAGC------------------CCTGGACTCTTAC----CTCCAC-----CATCACC i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74734507 499 + 78773432 GA----TA-------ATTTTGTATCTAAAACGAATGGATTTCTACAGATCCGTGTGGAACCTTCTCATGTTTCTCCATCCAGAACATCTCTGTGATGGTGCAGTCACAAATTCTG--CAGTTACTT-CTGTGTGA--G---GGG----TCTGTTTGGAT--CGT-GTTTGCACACGTGTCaacataccat-ctggaacataccatcctggaacaCGCCCTCCTTCCCCT------------------CGACGGAGGGCGACAATC----ATTTATTGACTCTCACTGAAGACATGGCCCTGATCGCTGGGGGACTCAGCA-----TCTCAGAGGAGGGTGGGCTGTGCATGCAGAGGGAAAATAGGGGAGCAAAATCTGTGCAGAAGGTCACCTCACTCACATTTGACTTTTGTACCCGTGAACTTCAGTGC--------------AGCGTA--TACCTAGAATCTGTTTCC---TGCCTCAATTTCCCCTCATTCCTTGGTGCCATTAGTTCCTTTT------------CCAAAAGTCCTCATG---------------------------------------------------GGTCTCCTCCAGC------------------CCTGGACTCTTAC----CTTCAC-----CATCACC i rheMac2.chr16 C 0 C 0 s mm9.chr11 118666031 447 + 121843856 GA----TA---GGACCCTGCAATCTCAGGAT-------GCAG-ACAGACCCACCAAGAACCA-CTCCTGTCTCTCTGTCCAGGGTATGCCTTTTAG------GTCACAACTTCTG--CCCATAATTGTTGTGGGT-CA---GGG-----CTATCCATAC--CCCAGAATGCTGTTCTGTGTTGACTCTATCCTGATGGA-------CCAAGATAGTTGCTCCCTGCCTT------------------CTGTAAGCAG------------------TGGCTCTCCCTGA--AGATAGCCCT-GTCCACAGATAGTTCATCA-----TCTCGATAGAAAGTGGGACACCTAGGCACAGAGAGGACT-GAGACCA---------------GTCTCCCTGTGGACGCTTGACTCT--AACAGGTAAACCTGGATGC--------------GGCTCGGAGCTCC----TACTCCTCCGATCGCCTCTGTCCCCTCTC--TCAGTGACATTTATTCTGTCT---------------CCTGGAGCCCTCATG---------------------------------------------------GGCCTTC-------------------------CATGGGTTCCTCTGCTCTCTACCTCTTAGTCCCA i mm9.chr11 C 0 I 8 s cavPor3.scaffold_76 4293723 461 + 7991924 GA----CAA-CAAACCATCTGAACCCAGAGTCAATGG-GCTGTACAAACCCACTTAGAGCCAGCTCCTGCTTCTCTGTCCAGG---CGTCTCTTAT------GTCACGAGCTCTG--CCCAGGAAC----TGGGG-CA---TGAGGCACCTGTTCAGAT--CGC--GATGCCCATGTACACCAGCAC-AGCCTGATGCA-------ACAAGATTGTCCCTCCCTCTCCA------------------CTGCAGACGGTGACAGTC----ACTT-CTGGCTCTCCCAGAAGAGATAGCCGT-ATCGTC-------TTGTCA-----TCC--AAAGACAGGGGGTCCTATAGACACAGAGAAGACA-G-GAACA---------------GTCTCCCAGT-GCCACCTGGCC------CACGTGAGCGTGGGTCCGTGTGTTTCTGGATGGCTTG--ACCCC----TCCTGCTTC---TGCCTTAATGCCCTCTC--TCTCCCACCACCACTGTAGCTTTG------------CCTGGAGTCCTCGAG---------------------------------------------------GGCCTCCCCCA-T------------------TCAAGAGTCTCAC----CTCTAC-----AGCCCCC i cavPor3.scaffold_76 C 0 I 455 s bosTau4.chr19 10750320 441 - 65312493 GG----TA---GCCTGTTTTGAATCTAGAATCAGCGGGTTTGTATAAATCCACGTAGAACT------TCTCTCTCTGCCCAGGACTTCTCCTTTAA------GTCCCAAATTCTCTACTGGGACTG--AATGTGA--------------------------CAA-GTGCACACGTGTGTCAGCATAGCACACTG-AGTG-------TGACACTCGTCCCTGTCTCCCCTGCATGTACCTGCCTGCTGCTGTCAATGGTGATAGTC----ATTTACAGCCCTGTTACGGA--------------------------CGGCCCATAATCTCGCAGGAAGATGGACCATGTGCACACGAGGAGGACT-GGGAATC--------CCAGGAGGCCGCCTCAGCCACCCTGGACTTTCGTATCCGCAGACTTCAATGC--------------AGCGGG--TACCAGG---CTATTTTC---AGCCTCAACTCCTCCTTGTCCCCTGGT-----ATGTTCGTTCC------------TCTCTCTACC--------------------------------------------------------AACCTCCCCCAGT------------------TCTGGATTCTCAC----TCCCAC-----ATT---- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57938435 271 - 61308211 TGATAACA---ACCCATTTTGAGTCTAGAGTCAATGGATTTGCACAAATCCTTGTAGGACCTGCTTGTGTCTCTCTGCCTGGGACGTCTCCTTTAA------GTCA-----------CAGGGACTG--CGTGTGACTG---GGG----CCTGTTCAGATCACGT-GTGCTCACGTGTGTCAACACAGCATGCTGAAGCA-------TGA----------------------------------------------------------------------------------------------------------AGGCC-----TC---------------------------------------------------------AGTGCCTCTTTGCCCTGGCA----------------------------------------------------------------------------------CCGCTTGTCTCT---------TCTTCCGGCTT------------CCTCAGTTCC--------------------------------------------------------AGGTTCTCCCCGT------------------CCCAGATTCTCAC----CCCCAC-----AATCGTG i equCab2.chr11 C 0 I 1 s canFam2.chr9 59353125 392 - 64418924 GGACAATG---ACCCCGTTTGAAGCTAGAATC--------------CACCCATGTGGAGCCCTAGGGTGCCTCC---CCAGGGACAT---CTTGAA------GCCACACATTCCACGCAGCGACTC--TGTGTGA-TG---GGG----ACCCTTCAGGTTCCAT-GGGCACTTGTGTGTCAAC-TAGCGTCCTGAAGCA-------CGACGATTGTCCGTCCCCCCCATGCAC--------------CTGTTCATGGTGACAACC----AATTTCCAGCTCATCCCGAGGACATGGTCCT--TCCCCTGATG-CTCGGCT-----TCCCACAGGGAG-----------GCAGATGGGGA-ACCA-AGTTTTC--------CCAGAAGGCCACCTCGCCCCCACATGACTTCCACATC------------------------------------------------------------------ATCCAGCTTGTCCCTGGGC-----TCTGTTTCCTG------------CCTGTGTCC--------------------------------------------------------------TTCCTTGT-----------------CCCCAGGGCCGTTC----CCCAAC-----TGC---- i canFam2.chr9 C 0 I 1 s loxAfr3.scaffold_49 14284850 559 - 17734757 GA----TAACCACCCATGTTGAACCAAGAATGAatgggtttgtccaaacccgt-tagaactggctcgtgtttctctgcccgctgcat--cctttaa------ggaaaaagctcca--CGCGTAACAGCTAAGTGA-CGGCCGGA----CCACTTTGGAT--CAC-ACGTGCACATACGT---------ATCC----ACG-------TGATG-----CTCTCCTTTCCTC-CACAGACGGACGTTCTACTCTTGATGGTGACAATCCTTTATTTACCTGCTCACCCTGAAGACGTGGCCCCGACCATCAAATGGCTCACAG-----TCTCACAGGGCAG--------GTACACATTAAGAAGCGT-GAGAACCAAGTTTCCCCAG---GCCATGTTACCCACATCTCACTTT-GTATCACTCAACGTCAGGGC--------------TGTTTG--TGCCAGG--CCCTGTTCC---TGCCTTAA-TCCTCCTTGTCTCCTGGTGCCCTTTGTTCCTTTGTGATACAAAGCATCGGGAGTCTCCGGGTGGTGCACACAACAGTTTGCACTCAGCtgctgacctaaaggttagcagttcaaacccatccagcagtgctgcagaagaaagacctggcaatctgc----ctccat-----aa----- i loxAfr3.scaffold_49 I 44 I 127 e dasNov2.scaffold_104361 1470 1769 + 5925 I e monDom5.chr2 304262060 4285 - 541556283 I a score=6595.000000 s hg19.chr17_gl000204_random 8437 74 + 81310 A-----------------CCTGACTCAGTCCCTGCTGCCCGCCCACTGGCCTGCCTCACCACCAGAG----CCCCACGCATCACTAACT-T-CAGCA----- s panTro2.chr17 79184555 74 + 83384210 A-----------------CCTGACTCAGTCCCTGCTGCCCGCCCACTGGCCTGCCTCACCACCAGAG----CCCCACGCATCACTAACT-T-CAGCA----- i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69569580 77 + 73212453 ACC--------------TCCTGACTCAGTCCCTGCTGCACGCCCACTGGCCTGCCTCACCGCCAGAG----CCCCACGCATCACTAACT-T-CAGCA----- i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74735006 74 + 78773432 A-----------------CCTGACTTAGTCCCTGCTGCACGCCCACTGGCCTGCCTCACCGCCAGAG----CCTCACGCATCACTAACT-T-CAGCA----- i rheMac2.chr16 C 0 C 0 s mm9.chr11 118666486 72 + 121843856 A-----------------CTGGGCCTTTTCCCAGC--CCCCACCTCTGGCCT-CTGTATCTGCTGGG----CCTGCTGCAGTCCTAACTCC-CAACA----- i mm9.chr11 I 8 I 2 s bosTau4.chr19 10750761 53 - 65312493 --------------------TCATCCTGTG------------------GGCTCTCCAGCCTTCAGAG----CCTC-CACATTTCTAACC-CGCAGAG----- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57938707 72 - 61308211 -----------------GCCTGACTCTGTTCCCCTCGTA-GGCTGTGGGCCTCCCTTGCCCTCAGGG----CCAC-GGCATTTCTAACT-C-CAGGG----- i equCab2.chr11 I 1 C 0 s canFam2.chr9 59353518 37 - 64418924 -----------------GCCCAACCTCACACCT---------------GGCGCCCCTGCCTCCCGGG----CC----------------------------- i canFam2.chr9 I 1 C 0 s loxAfr3.scaffold_49 14285536 98 - 17734757 -TCCTGAATCGTGCATGGCCTGGGCTTCCTTCCTCCTCAACACCGACGGCCTCTTTCACCTGCAGAGAACTCCTC-CACCTTTCTGCCT-T-CCACCTCTCA i loxAfr3.scaffold_49 I 127 C 0 e dasNov2.scaffold_104361 1470 1769 + 5925 I e monDom5.chr2 304262060 4285 - 541556283 I e cavPor3.scaffold_76 4294184 455 + 7991924 I a score=40963.000000 s hg19.chr17_gl000204_random 8511 171 + 81310 CCCGTGCCCACCCAA-AAA--TGTGTCCACATCCCTCTCTCCCC-AGAGG-------TCTCTTTTTCCCTCTGTTTCTTGGGCCTGACTCCTACCTTTCCTTCCAATTCATTCCTTCCACACC----TCAAGAGC-CCCCTGGAGAGACCTCACAGGCTCCCCTCTCCT--GGCTCAGC-TCTACAACGC s loxAfr3.scaffold_49 14285634 174 - 17734757 CGTTTGCCCAACCAC-AAACCTAAATCTTACTTCCTTTC-CCCC-AAAGG-------TCTCCTTCTCCCTTGCCCTCTGGGGCCTGGCTCCCACTT-TTTTTCTAATCCATCTCACCTGGCCC----CTACAGCC-CTCCAGAGAGACCCTGGCTGGTCCACCCTCCCTCCAGCCTGGCACCTTCAACCC i loxAfr3.scaffold_49 C 0 C 0 s canFam2.chr9 59353555 57 - 64418924 -----------------------------------TCCTCCCTC-----G-------CCTCCTCCACCTT---------------GGCTCTGACCTCTCCTC----------------------------------CTCCAGGGAGACCCTCA------------------------------------- i canFam2.chr9 C 0 C 0 s equCab2.chr11 57938779 149 - 61308211 --------CTCCTAC-------AGCCGATCCTGCTTCCTGCCCCAGGAGG-------CCTCTTCCTCCTTCCCATTCTCAGGCCCGGCTCCGACTTTTCCTTCCAATCCGTTCCTTCCGGGCCTCTTTCTCGAGCGCTCCAGAGAGACCCTCACTGGC----------------CAGGC-TCGGAAAC-- i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10750814 139 - 65312493 --------CTCCTAA-------GTGCCTGACTGCCTCCTTTCCC-CGAGA-------CCTCT--CTCCCTCATCTTGCCAAGCCCGGCTCCAACTTCCTCTTGCAATCTCTTCCTTCAAGCC-----TCCGGAGC-CTCTAGGAAGACCCTCACTGGC----------------CAGGC-TCTGAAA--- i bosTau4.chr19 C 0 C 0 s cavPor3.scaffold_76 4294639 127 + 7991924 CATCCACACACCCAA--------------ATTTACCCCCACCCC-AGG---------TCTCTTCCTGCCTCTGAATCCCAGCCCTGAC---------TCCCTCCAGCCCGTTCCTTCCAAGCT----TCAGAAGC-TCCT-------GCACCACTGGC-----------------CAGC-TCTAAAACCT i cavPor3.scaffold_76 I 455 C 0 s mm9.chr11 118666560 122 + 121843856 TATCTGTCCATTCAGAGAC--TGAGGTTCACTTCCTCCCGCGCC-AGGGACCCTCCCTCCCTCCCTTGCTCAGCACCCCC-CCCCAAC---------TTCCTCCAGGATGCTCTCTTCAGTCC----T--------------------------------------------------T-TATGAGGCCT i mm9.chr11 I 2 C 0 s rheMac2.chr16 74735080 155 + 78773432 CCCGTGCCCACCCAA-AAA--TGTGT----------------CC-AGAGG-------TCTCTTTTTCCCTCTGCTTCTCAGGCCTGGCTCCGACCTTTCCTTCCGATCCATTCCTTCCGCATC----TCAGGAGC-CCCCTGGAGAGACCTCACGGGCTGCCCTCTCCT--GGCCCAGC-TCTACAACGC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69569657 171 + 73212453 CCCGTGCCCACCCAA-AAA--TGTGTCCACATCCCTCTCTCCCC-AGAGG-------TCTCTTTTTCCCTCTGCTTCTTGGGCCTGCCTTCAACCTTTCCTTCCAATCCATTCCTTCCACACC----TCAAGAGC-CCCCTGGAAAGACCTCACAGGCTCCGCTCTCCT--GGCCCAGC-TCTACAACGC i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79184629 171 + 83384210 CCCGTGCCCACCCAA-AAA--TGTGTCCACATCCCTCTCTCCCC-AGAGG-------TCTCTTTTTCCCTCTGTTTCTTGGGCCTGACTCCGACCTTTCCTTCCAATTCATTCCTTCCACACC----TCAAGAGC-CCCCTGGAGAGACCTCACAGGCTCCCCTCTCCT--GGCCCAGC-TCTACAACGC i panTro2.chr17 C 0 C 0 e dasNov2.scaffold_104361 1470 1769 + 5925 I e monDom5.chr2 304262060 4285 - 541556283 I a score=145383.000000 s hg19.chr17_gl000204_random 8682 150 + 81310 CTCCCTCTCCCAC---AGGCAGAGCA-AGACTCCAGTTTCTCTCTCCT------GTGACAAAAGTGTGCGCCCAAAACT-TGCAGCACGAACTGTTTATTTTTAGGTTTAGA-TTTGGGGTCTGGC---------------------TTTTAATTCTTAGTTTGTTCTCAAGTCCGATCTCAG s panTro2.chr17 79184800 150 + 83384210 CTCCCTCTCCCAC---AGGCAGAGCA-AGACTCCAGTTTCTCTCTCCT------GTGACAAAAGTGTGCGCCCAAAACT-TGCAGCACGAACTGTTTATTTTTAGGTTTAGA-TTTGGGGTCTGGC---------------------TTTTAATTCTTAGTTTGTTCTCAAGTCCGATCTCAG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69569828 151 + 73212453 CTCCCTCTCCCAC---AGGCAGAGCA-AGACTCCAGTTTCTCTCTCCT------GTGACAAAAGTGTGCACCCAAAACT-TGCAGCACGAACTGTTTATTTTTAGGTTTAGA-TTTGGGGTCTGGC--------------------TTTTTAATTCTTAGTTTGTTCTCAAGTCCAATCTCAG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74735235 149 + 78773432 CTCCCTCTCCCAC---AGGCAGAGCA-AGACTCCGGTTTCTCTCTCCT------GTGAC--AAGTGTGCGCCCAAAACT-TGCAGCACGAACTGTTTATTTTTAGGTTTAGA-TTTGGGGTCTGGC--------------------TTTTTAATTCTTAGTTTGTTCTCAAGTCCGATCGCAG i rheMac2.chr16 C 0 C 0 s mm9.chr11 118666682 133 + 121843856 TGC-----------------ATGACA-GGGCCCCAGTTTCTCTCTCCT------GTATGAGA-GGATGTGCTCGGAATCACGTGACGCACAGGA--TATTGTTAGGGTGAGA-TGAAGGTGCAGCC---------------------ACTTCGCTCTTAACTGGCTCTCAAGACGGTTTCAG- i mm9.chr11 C 0 I 820 s cavPor3.scaffold_76 4294766 134 + 7991924 CTCTGTCTCC---------GCCAATT-GGAGCAAAACTGTTTTTTCCC------TCTTGATACAGGTATATTTGGAACC-TGCAGCACACACTG--TTATTTTAGGGTTGGG-TTCAGGC----------------------------TTTAATTCCTCATTTGTTCTCAAGAGCATTTTTA- i cavPor3.scaffold_76 C 0 I 1 s bosTau4.chr19 10750953 96 - 65312493 -----TAGCTCCC------------------------------------------------------------AAGACA-TGTGGCAAGGACTGCTTACTTTTAGGTTTAGA-TTTGGGGTCTGTC--------------------TTTTTCATGCTTGGTTTGTTCTTAAGACCAGTCTTAA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57938928 101 - 61308211 CTCCCTCCCCCAC------------------------------------------------------------AAGACT-TGCAGCATGAACCGTTTATTTTTAGGTCTAGA-TTTGGGGTCTGGC--------------------TTTTAAATTTTTTGTTTGCTCTCAAGACTGATCTCAA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59353612 93 - 64418924 -----TGCCCCAC---------------------------------------------------------------ACG-TGCACCACCAACTGTTCGTTTTCAGGCCTGCA-TGTGGGGCCTGGA--------------------TTTTTCATCCCCAGTGTGCTCTCAAGACCCATCTCAG i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14285808 156 - 17734757 CTACCTCACCCGCCACAGGAAGAACAGAGACTTGGGCTTCTCCCTCCCG-----GTGACACAAGTGTGTGCTGGGGACA-TACTGCGCGAATTGTCTATTTTTAGGTGCAGA-TTTCGGGTCTAGC--------------------TTTTTCATTCTTAGCTTGCTCCTGAGACTGAGCCCCA i loxAfr3.scaffold_49 C 0 C 0 s monDom5.chr2 304266345 177 - 541556283 --CTCCTTCTCAG---AGAAGGATTGTAAATTTCTGTTTCTTCCTTCCATAGACAAAAAAAAAGTCTATGCTTAGTACT-TGTAGCACGAACTGTTTATTTTTAGATTTAGATTTTTGGGtcttttcttttttcttttctttttttttttGAAATCTTAGCTTGCTCTCAAGACCGTTCTCAA i monDom5.chr2 I 4285 C 0 e dasNov2.scaffold_104361 1470 1769 + 5925 I a score=39220.000000 s hg19.chr17_gl000204_random 8832 49 + 81310 CAGTGGGA--GGTGGGAAGTGGGTGG---------------GGGACAGA--GAATG-ATCTCAGCTCA-T s panTro2.chr17 79184950 49 + 83384210 CAGTGGGA--GGTGGGAAGTGGGTGG---------------GGGACAGA--GAATG-ATCTCAGCCCA-T i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69569979 49 + 73212453 CAGTGGGA--GGTGGGAAGTGTGTGG---------------GGGACAGA--GAAGG-ATCTCAGCCCA-T i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74735384 49 + 78773432 CAGTGGGA--GGTGGGAAGTGGGCGG---------------GGGACAGA--GAAGG-ATCTCAGCCCA-T i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4294901 48 + 7991924 CTTGGGGT--GGTACGAAGTAG--GG---------------GAGACCCC--GGATGCACCTCAGCCCA-T i cavPor3.scaffold_76 I 1 C 0 s bosTau4.chr19 10751049 48 - 65312493 CAGTAGGATTGGTGGCAAGTGAGTGA-------------------CATG-GAAAGG-ATCTCAGGCAA-A i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57939029 64 - 61308211 CAGCGGGA-TGGTGGGAAGTGGGTGG---AGAACAAATTT-GGGACACAAGAAAGG-AGCTGAGCCAGTC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59353705 68 - 64418924 CCTTGGGA-TGGTGGGAAGTGGGTGGAGCAGAGCAAACTCGGGGACACGAGAAAGA-ATCTCAGCCGACG i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14285964 34 - 17734757 CCGTGGGA-TGGTGGGAGGTGGGTGG---------------GGAGAAGA--G------------------ i loxAfr3.scaffold_49 C 0 I 21 s monDom5.chr2 304266522 39 - 541556283 CTGTGGGA-TGGTGAGATGTGGGTGG---------------GGGAGACA--AAGTG-A------------ i monDom5.chr2 C 0 I 3478 e dasNov2.scaffold_104361 1470 1769 + 5925 I e mm9.chr11 118666815 820 + 121843856 I a score=58912.000000 s hg19.chr17_gl000204_random 8881 77 + 81310 CGTTCCAGGT-GCCTCCCTCTCCACTAGGTCTGTGGACGG----CCTTCTGACCTGGGGTCCTGGGGTTCTTCCAATGTCCA s panTro2.chr17 79184999 77 + 83384210 CGTTCCAGGT-GCCTCCCTCTCCACTAGGTCTGTGGACGG----CCTTCTGACCTGGGGTCCTGGGGTTCTTCCAATGTCCA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69570028 77 + 73212453 CGCACCAGGT-GCCTCCCTCTCCACTAGGTCTGTGGACGG----CCTTCTGACCTGGGGTCCTGGGGTTCTTCCAGTGTCCA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74735433 77 + 78773432 CGCACCAGGC-ACCTCCCTCTCCTCTAGGTCTGTGGACGG----CCTTCTGACCTGGGGTCCTGGGGTTCTTCCGATGTCTA i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4294949 70 + 7991924 TAATACCAGA-AACATTCTTGCCTCTTGGTCTGTGGAGGGGGGACGCTCTGACCTCAAGTTTTGGGGCTCT----------- i cavPor3.scaffold_76 C 0 I 389 s bosTau4.chr19 10751097 73 - 65312493 AGCTCCTGGC-GCTGCAGCTGCCTCTTGAATGACAGACAA----CC-TATGACCTTGGGC-TGGGGTTT-TCAAGAAGT-CG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57939093 76 - 61308211 AACACCAGGC-AGCGCGTCTTCTCCTCGGTTTATGGAGGA----CC-TGTGACCTTGGGTCAGGGGTATCTCAGGAAGTCTA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59353773 75 - 64418924 ACCGGGTGCC-ACCACCTTCTGCTCTGGGTTCCTGCAGGA----CC-TGTGACCTCAGGG-ACGGTTTTATCAAGAAGTGCA i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14286019 78 - 17734757 CGTCTCAGGCAGCCAACACCTCCTCTCGGTTTATGGAGGC----CTTTATAACCTTGGGTCTTGGGTTTTGCAGGAAGTCTA i loxAfr3.scaffold_49 I 21 C 0 e dasNov2.scaffold_104361 1470 1769 + 5925 I e monDom5.chr2 304266561 3478 - 541556283 I e mm9.chr11 118666815 820 + 121843856 I a score=44170.000000 s hg19.chr17_gl000204_random 8958 43 + 81310 CTCTTACAGCTCCCG-TCATTCTGGCCTTGGTTTTACCGCTCAG s panTro2.chr17 79185076 43 + 83384210 CTCTTACAGCTCCAG-TCATTCTGGCCTTGGTTTTACTGCTGAG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69570105 43 + 73212453 CTCTTACAGCTCCAG-TCATTCTGGCCTTGGTTTTACTGCTCAG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74735510 43 + 78773432 CTCTTACAGCTCCAG-TCATTCTGGCCTTGGTTTTACGGCTCGG i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4295408 43 + 7991924 CTCTTACTGCTCACT-TCATCCTGTCCTTTACTGTGCTGAGTGG i cavPor3.scaffold_76 I 389 C 0 s bosTau4.chr19 10751170 41 - 65312493 CTCTTACAGCTTGAG--CGTTCTGGCCTTCAGTTC-TTAATTGG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57939169 43 - 61308211 CTCTTACAGCTCAGAGTCACTCTAGCCTTCACTTC-CTGATCGG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59353848 43 - 64418924 GTCTTCTGGTTCACGGTCATTCTGGCCTTCGCTGC-CCGACGGG i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14286097 33 - 17734757 CTTCCCCAACATGCAGTCATTTCAGCCTTCGTT----------- i loxAfr3.scaffold_49 C 0 I 363 e dasNov2.scaffold_104361 1470 1769 + 5925 I e monDom5.chr2 304266561 3478 - 541556283 I e mm9.chr11 118666815 820 + 121843856 I a score=42004.000000 s hg19.chr17_gl000204_random 9001 55 + 81310 C---------CTGCA--TACCTTC---TTATCATTGTCTTAAAATCAGCCAAGGGATGGTTCTTTTCCA s panTro2.chr17 79185119 55 + 83384210 C---------CTACA--TACCTTC---TTATCATCGTCTTAAAATCAGCCAAGGGATGGTTCTTTTCCA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69570148 55 + 73212453 C---------CTGTA--CACCTTC---TTATCATTGTCTTAAAATCAGCCAAGGGATGGTTCTTTTCCA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74735553 55 + 78773432 G---------CTGTA--CACCTTC---TTATCATTGTCTTAAAATCGGCCAAGGGATGGTTCTTTTTCA i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4295451 64 + 7991924 CAAATGGCATCTCCA--TATCTTC---TGATTGTCATCTTAAAATCACCCAAGCAGCCAGCCTTCCCCG i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10751211 46 - 65312493 C---------TCTTGGGTACATTC---TTATCATTGTTTTTAAAATGAACCAATGACA----------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57939212 53 - 61308211 C---------CTATGAGTACATTA---TTATCATCGTGTCAAAAATG-ACCACCGACAGTTCCTCT--- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59353891 32 - 64418924 C---------CTACAGGCACGTTC---TCGTCGTTGTCTTAAAA------------------------- i canFam2.chr9 C 0 I 210 s loxAfr3.scaffold_49 14286493 58 - 17734757 C---------CTAGG--TACTTTCCTATTATCATTGTCTTCCAAGTGGCCGAGCAATGGTTCTTCTCTT i loxAfr3.scaffold_49 I 363 C 0 e dasNov2.scaffold_104361 1470 1769 + 5925 I e monDom5.chr2 304266561 3478 - 541556283 I e mm9.chr11 118666815 820 + 121843856 I a score=58304.000000 s hg19.chr17_gl000204_random 9056 116 + 81310 GAGCATCTCAGTGTCTGGGTGAGATCAG-GGCC--GAGGGTCAG----GGGACACCTCAGGATGAG-------TCGTG--GGCTGT---AGAGTCATAGTGCCTGGGTTCATCTTCCTCCCTGGCAGCCTTGGAG s panTro2.chr17 79185174 118 + 83384210 GAGCATCTCAGTGTCTGGGTGAGATCAG-GGCCGTGAGGGTCAG----GGGACACCTTGGGATGAG-------TCATG--GGCTGT---AGAGTCATAGTGCCTGGGTTCATCTTCCTCCCTGGCAGCCTTGGAG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69570203 118 + 73212453 GAGCATCTCAGTGTCTGGGTGAGATCAA-GGCCGTGAGGGTCAG----GGCATGCCTCGGGATGTG-------TCGTG--GGCTAT---AGAGTCATAGTGCCCGGGTTCATCTTCCTCCCTGGCAGCCTTGGAG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74735608 118 + 78773432 GAGCTTCTCAGTGTCTGGGTGAGATCAG-GGCTGTGAGGGCCAG----GGGACACCTCAGGATGAG-------TCGTG--GGCTAT---AGAGTCATAGTGCCTGAGCTCATCTTCCTCCTTGGCAGCCTGGGAG i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4295515 120 + 7991924 GAGTGTCCCAATGTCAGAAGAAGATCAG-AGCTATGGCCCTGGA----ACAACACCTTGAGGTGAG-------CCGTGGAGGCCATATCAAAATCACAGCACTGGGGCTTACCTCCTG---TGAAGAGCAGTGGA i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10751257 68 - 65312493 --GTACT------TCTGGGGG------------GTAGGAACAAG---------------------------------------TAT---AAAGG-----TGTCTAGGCTCACCTTCCTCCCCAGTAGTCTTAGAG i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59354133 92 - 64418924 GAGCATC------CTTGTGAAA--------TCTGTGGGGGCAGG---------------GGCAGCG-------GGGGG--ACTCGT---AGAGGT-CAGTGCCTGGGCTCACCTTCCTCCCC-GCAGTCGTGGAA i canFam2.chr9 I 210 C 0 s equCab2.chr11 57939265 95 - 61308211 GAGCATCCCAGGGCTTGGGTGA--------CACTTTGGGACGAGCAATGGGGC------GGCGGAG-------GGGGG--ACATGT---AGAGG--------------TCACCTTCCTCCCCAGTAGTCTTGGAG i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14286551 123 - 17734757 GAGCACCTCAGTGTCTGGGGGAAGTCAATGGCCGGGAGGGGGGT----GTAACTCAATGAGATGAGAATAGTTGGGGG--GCGTGA---GAGATCACAGTGCCTGGG---ATCCCTCCTCCCAGTAGCCTTGGGG i loxAfr3.scaffold_49 C 0 C 0 e dasNov2.scaffold_104361 1470 1769 + 5925 I e monDom5.chr2 304266561 3478 - 541556283 I e mm9.chr11 118666815 820 + 121843856 I a score=289838.000000 s hg19.chr17_gl000204_random 9172 526 + 81310 GATACAGtgggtggaatcatgtccccc-caaaacatgttcc--agccctaacccccaggacctgggaatgtggccttagttggaaataaggtctttgcagatgtgat--gaaggtaa---gaggt---------------gggccccgatccaatgactggtgt------ccttagaagagg--------------aggggaatgagaacacacaggtgcacacacatgcatgc------gtgcacacatgt----------acacacaca------aatg--cacacacacacaGGAAGGTCGTGCGC----GACAGGATACACAGGCATGGGGGTGGGGTTgcctcatgatgatggaggcagagactggact-gacggtgcatctataagccaaggcccacagaggatggccagtggcccccagagccag-gagaaaggcctccgtgtg-tgggacagtttctccctgagaagcaaccccgctgccctcctgattttggat-cctggcctccaggaattggtgagaacgaagagctatc-gtgagaagccacccagtccgtggcattctgtgatggcagtcACGGGACACCGACCCAGAT s panTro2.chr17 79185292 534 + 83384210 GATACAGtgggtggaatcatgtccccc-caaaacatgttcc--agccctaacccccaggacctggaaatgtggccttagttggaaataaggtctttgcagatgtgat--gaaggtaa---gaggt---------------gggccccgatccaatgactggtgt------ccttagaagacg--------------aggggaatgagaacacacaggtgcacacacacacatgc------gtgcacacatgt--------acacacacaca------aatgcacacacacacacaGGAAGGTCGTGCGCGACAGACAGGATACACAGGCATGGGGGTGGGGTTgcctcatgatgatggaggcagagactggact-gacggtgcatctataagccaagacctacagaggatggccagtggcccccagagccag-gagaaaggcctccgtgtg-cgggacagtttctccctgagaagcaaccccgctgccctcctgattttggat-cctggcctccaggaattggcgagaacgaagagctatc-gtgagaagccacccagtccgtggcattctgtgatgacagtcACGGGACACCGACCCAGAT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69570321 516 + 73212453 GATACAGtgggtggaatcatgttcccc-caaaacatgttcc--agccctaacccccaggacctgggaatgtggccttagttggaaataaggtctttgcagatgtgat--caagttaa---gaggt---------------gggccccaatccaatgactggtgt------ccttagaagacg--------------agggaaatgagaacacacaggtgcacacaCACGCATGC------GTGcacacacgc----------acacacaca------aatg--cacacacacacGACA---------------GACAGGATACACAGGCATGGGGGTGGGGTTgcctcgtgatgatggaggcagagactggact-gacggtgcgtctataagccaaggcccacagaggatggccagtggcccccagagccag-gagaaaggcctccgtgtgccgggacagtttctccctgagaagcaaccccactgccaccctgattttggat-cctggcctccaggacttggcgagaacgaagagctatc-gtaagaagccacccagtacatggcgttctgtgatggcagtcacaggacacCGACTCAGAT i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74735726 546 + 78773432 GATACAGtgggtggaatcacatcccct-caaaacatgttcc--atccctaagccccaggacctgggactgtggccttagttggaaataaggtctttgcacatgtgat--caagttaa---gaggt---------------aggccctcatctaatgattggtat------ccttagaagatg--------------atggaaatgagaacacacacatgcacacacatgcatgcatacatgtacacacacacaaatgcacacacacacaca------aatg--cacacacacacaGGAATGTCACGCGCAGCAGACAGG-cagacaggcatgggggtggggttgcctcatgatgatggaggcagagactggact-gacggtgcgtctataagccaaggcccacagaggatggccagtggcccctagagccgg-gagaaaggcctccgtatgctgggaaagctcctccctgagaagcaaccccactgccaccctgattttggat-cccagcctccaggacttggcgaaaacaaagagctatt-gtgtgaagccacccagtctgtggcgttctgtgatggcagtcacaggaCATCGACCCAGAT i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4295635 441 + 7991924 GACATGGtaggtagaat-atgt-cccc-caaaagaagtat----gtcttaacccccaga----------gtgaatttattgagaaataaa-----ttaagatgagat--cacactggactggggt---------------tggccctgacgtagtgactgacgt------ctctgtaaagtg--------------aaggaaatcgggatcc------gctcacacacacatgc--------acacacatgc--------------acaga------aacg---------tcacgtgaag-------------aatgagatacacagacacacggg-gagactgtcacatgatggcagagacagacactgacat-gtcga---------aagtcaaagagcaccaaggaatgtcacagccaccaggagccag-cagggagca----------tgggatggtttccccct-------------actgaccttggggttggggatatctggtgtccaggatcttgcgagaacaaacagttatt-ttcttaagccg---agcctctgcccc------acagcagccgcaggacacaaagacaGA- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10751325 490 - 65312493 GATACAGtaggtagaatggtgtcccccaaaaaggatatcttgaaatcctatcctcaagtatctgtgacaatgaccttatttggacttagggtc--tgcgaatgttgat-caagtaaaaatgaagtcctcctggagtgcgggggtgggggggcggggtgaggggtgctaacccttagccggtgccttcaaaaagcgagggaaaatatggg------------cacacacatacac------acacagaggggc----------gcactgtat------caag---------agacagg----------------gacag-----acagacaccgaggggag-aagccatgcagc----gaggcagagactagaacaaacgt---gtctgccagccaagcaaca-ctgggacaggcagtgaaca-cagaatctg-gagagagaa----------cggg----------------------ccctgctggcaccttgattgcagacctccagccccagggtgt--gagagaataaatctctgttagtcttaaggccgctggcttgtggtcctttgttgcgacggccccaggaCCCTCCCACCAAG i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59354225 429 - 64418924 GATACAGtgggtagaagtacatcccct-gaaggcagctgctggagacctgacccccagaccctgtgactgtgatattatttggactcggggtctttgcaggtatcatcaaggattaagaggagatcctcctggaatgcggtggccctaatgcaatggccggcat------ccttcgaggatg--------------agggaaatgtgga---------------------acac------atgcagaggaca----------tcacctagt------gaag---------gcacagg----------------gacag-----aCAGACACAGAACAGAG-AGGCCATGTGATGACAGAGCAGGGGAATGCCCC-GACGG---GCTTA---------------CAAGGATGGCTGGCAGCCAGCGGGATCCGGGAGGGTGGG----------CGCG----------------------GCCCGGGGACACCTTG-TTCCCAGCATCCAGGCCCCGGGACT--GAG-GGATTGGCTTCTG------CCAA-GCTCCTGGG-TGGGGTG-------------GCCCCAGGGCACGCGT--GGGG i canFam2.chr9 C 0 C 0 s equCab2.chr11 57939360 452 - 61308211 GATATAGtaggtagacttgtatccccc-aaaaggatatattgaagtcctaacgcccagtatctgtgaatgggaccttttttggacttaagatctttgcagatcttaagaccagttaagatgaggtcctactggagtaggacagccctaagccaaaggctggcgt------ccttacgaggtg--------------agggaaatttagacac----atacacatacacacacac------acgcaggggaga----------------aggccgtgaaaag---------acacagg----------------aacag-------agacacagaggggagaaggctgtgtgaagacagaggtagagactggaat-gatgt---gtctacaagccaaggaacaccaaggattgcc-acgaccaccagaatctgagagg-------------------------------------------------------------cagacttctggcctccagaacc--gagagaataaacttctgtt-gtcctaa-tcccccggc-tgtggtgctttgttgcaggagccccagggcgctcatccaGAG i equCab2.chr11 C 0 C 0 e dasNov2.scaffold_104361 1470 1769 + 5925 I e monDom5.chr2 304266561 3478 - 541556283 I e mm9.chr11 118666815 820 + 121843856 I e loxAfr3.scaffold_49 14286674 0 - 17734757 C a score=37699.000000 s hg19.chr17_gl000204_random 9698 107 + 81310 GATCTGAATTTCCAGCCCCACTGGCCAGGCTGACTGTCCTGGGGGCTGCACCTGACACC----CTGTGCTCTGGGGGCCA--------CTGACACCCTGAGGACCAGGCCCTGCT-GGCT------- s panTro2.chr17 79185826 107 + 83384210 GATCTGAATTTCCAGCCCCACTGGCCAGGCTGACTGTCCTGGGGGCTGCACCTGACACC----CTGTGCTCTGGGGGCCA--------CCAACACCCTGCGGACCAGGCCCTGCT-GGCT------- i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69570837 107 + 73212453 GATCTGTACTTCCAGCCCCACTGGCCAGGCTGACTGTCCTGGGGGCTGCACCTAACACC----CTGTGCTCTGGGGGCCA--------CCGGCACCCTGGGGACCAGGCCCTGCT-GGCT------- i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74736272 107 + 78773432 GATCTGAATTTCCAGCCCCACTGGCCAGGTCGACTGTCCTGGGGGCTGCACCTGACACC----CTGGGCTGTGGGGGCCA--------ACGACACTCTAGGGGCCAAGCCCTGCT-GGCT------- i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4296076 108 + 7991924 GGTCTGAATTATGAGACCCATCTACCGGGATCATCAGCCT-GGTGCCACGCCCCACGTC----CTGGGCCCTGGAGACCAGGTTCCACCCTAGAGGCTGGTGGCCACGTCCAG-------------- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10751815 76 - 65312493 CGTCTGAA-TCAGGAGCCCCCCTGT---------------GGGTTCCCCACCCTAAAGCC---CCGGGCTCTAGGA------------------------GCCACTGCTGATGCC-TGCC------- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59354654 96 - 64418924 CATCTGAA-TCAGAACACCACCTCC---------------AGCCACTGAGGCCCAGGACCAGACTGGGGACAGGGACCAG--------GCCGGCTCCCGCGAGATGGCTGTTGCCGCCAC------- i canFam2.chr9 C 0 C 0 s equCab2.chr11 57939812 92 - 61308211 CATCTGAATTTGGAGCCTCACCTAC---------------GGGTTCACCATCTCAAGGC----CTGGGCCCCGGACATGG--------CCCTGCTCCAATGACACGGCTGCTGGC-TCAC------- i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14286674 112 - 17734757 GATCTGAACTGTGAGCCCCCCTTACCAGGCTCACCACCCCGGGCGCAGCACCCAATGC-----CTGGGCCCTGGAGGCTG---------TGATGCCCTGGGGACGTGGCCCCACC-AGACGCTGATC i loxAfr3.scaffold_49 C 0 I 7 e dasNov2.scaffold_104361 1470 1769 + 5925 I e monDom5.chr2 304266561 3478 - 541556283 I e mm9.chr11 118666815 820 + 121843856 I a score=31721.000000 s hg19.chr17_gl000204_random 9805 46 + 81310 CCTCTCCTTGGAT--TATTTCCATCTGGGGAGCAGC-GGCAGGGCC-CTC s dasNov2.scaffold_104361 3239 45 + 5925 CCTCCCCTTCGAC--CCTTGCCCTCCGGG--GCGGCCAGCAGGGCC-ACC i dasNov2.scaffold_104361 I 1769 C 0 s loxAfr3.scaffold_49 14286793 47 - 17734757 ACTCCTCTCAGAC--GTTT-CCATCTGGGGAGCAGCCAGCAGAGCCTCCC i loxAfr3.scaffold_49 I 7 C 0 s equCab2.chr11 57939904 36 - 61308211 ACCGCTGTCTTCTCAGACTGCTCCCTCTGGAGCAGC-------------- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59354750 46 - 64418924 ACTCAGGTCTCAT--GATTCCCATCTGGGGAGCAGCCAGCAGAGCC-TG- i canFam2.chr9 C 0 C 0 s bosTau4.chr19 10751891 46 - 65312493 ACTCCTCTCAGAC--TATTTCCATCTGGGGAGTGGCCAGCAGTGTT-TC- i bosTau4.chr19 C 0 C 0 s cavPor3.scaffold_76 4296184 21 + 7991924 CCTCTTCTCAGAT----------------------------GGCCA-CTC i cavPor3.scaffold_76 C 0 C 0 s rheMac2.chr16 74736379 45 + 78773432 CCTCTCCTTAGAT--TATTTCCATCTGGGGAGCAGC-GGCAGGG-C-CTC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69570944 46 + 73212453 CCTCTCCTTGTAT--AATTTCCATCTGGGGAGCAGC-GGCAGGGCC-CTC i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79185933 46 + 83384210 CCTCTCCTTGGAT--TATTTCCATCTGGGGAGCAGC-GGCAGGGCC-CTC i panTro2.chr17 C 0 C 0 s monDom5.chr2 304270039 46 - 541556283 -ctcctTTCAGAC--ATTTTACATATGGGAAACAGCCAAAAAAACC-ATA i monDom5.chr2 I 3478 C 0 e mm9.chr11 118666815 820 + 121843856 I a score=647648.000000 s hg19.chr17_gl000204_random 9851 325 + 81310 -CCTTCCCGC-TCCAGCGC-TGG----AAC--TACATCTGGAAGCTCTTCTCACCCTTAATTGTTCTTAATGCTTTAACACACGGAGTGACTAATGGGCTCTAATTGG--------------GAGC---GGTGTCCTGGGGAACTC-GCCCACAGCGC-CCTCTGCGACCCGCCCAGTCTCCTCCGCTGCTCACTCA-CAG-----A-GCTCTAAAGTC------A--------CCAAGGAAAA---ATATTGGCCCGTTT-TTCTATTTTTT----------TAAAAAATGTCA-CACCAGTGCCAAAAAGCAGTTTTATCCTTCAGCCAAC-AAGTATAGGGCAAAGAAAAGGATAGAGGCAA------AGCCA--AAAGCAGATGGGACAAAATA s panTro2.chr17 79185979 325 + 83384210 -CCTTCCCGC-TCCAGCGC-TGG----AGC--TACATCTGGAAGCTCTTCTCACCCTTAATTGTTCCTAATGCTTTAACACACGGAGTGACTAATGGGCTCTAATTGG--------------GAGC---GGTGTCCTGGGGAACTC-GCCCACAGCGC-CCTCTGCGACCCGCCCAGTCTCCTCCGCTGCTCACTCA-CAG-----A-GCTCTAAAGTC------A--------CCAAGGAAAA---ATATTGGCCCGTTT-TTCTATTTTTT----------TAAAATATGTCA-CACCAGTGCCAAAACGCAGTTTTATCCTTCAGCCAAC-AAGTATAGGGCAAAGAAAAGGATAGAGGCAA------AGCCA--AAAGCAGATGGGACAAAATA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69570990 324 + 73212453 -CCTTCCCGC-TGCAGCGC-TGG----AAC--TACATCTGGAAGCTCTTCTCACCCTTAATTGTTCTTAATGCTTTAACACACGGAGTGACTAATGGGCTCTAATTGG--------------GAGC---GGTGTCCTGGGGAACTT-GCCCACAGCGC-CCTCTGCGACCCGCCCAGCCTCCTCCGCTGCTCACTCA-CAG-----A-GCTCTAAAGTC------A--------CCAAGGAAAA---ATATTGGCCCATTT-TTCTA-TTTTT----------TAAAAAATGTCA-CACCAATGCCAAAAATCAGTTTTATTCTTCAGCCAAC-AAGTATAGGGCAAAGAAAAGGATAGAGGCGA------AGCCA--AAAGCAGATGGGACAAAATA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74736424 325 + 78773432 -CCTTCCCAC-TCCAGCAC-TGG----AAC--TACATCTGGAAGCTCTTCTCACCCTTAATTGTTCTTAATGCTTTAACACTCGGAGTGACTAATGGGCTGTAATTGG--------------GAGC---GGTGTCCTGGGGAACGC-GCCGACAGCGC-CCTCTGCAACCCGCCCAACCTCCTCCGCCGCTCACTCA-CAG-----A-GCTCAAAAGTC------A--------CCAAGGAAAA---ATATTGGCCCGTTT-TTCTATTTTTT----------AAAAAAATGTCA-CACCAGTGCCAACAAGCAGTTTTATCCTTCAGCCAAC-AAGTATAGGGCGAAGAAAAGGAGGGAGGCGA------AGCCA--GAAGCAGATGGGACAAAATA i rheMac2.chr16 C 0 C 0 s mm9.chr11 118667635 330 + 121843856 -CCTTCCTCG-TCCAG-----GGTGGGAGC--CACACGTGGAA--------CAGCCA-AATAGTTACTAATGTTTTAACACCC-TAGCAACTAATGCATTCTAATTGGGCAACTTAACCCCAGAGT---CAAGACCTGGGGAACTC------CGGGAT-CCTCTGTGACCCTTCCAGCCCCTT-CCTAGCTCCACCA-CAG-----A-GCTCCAAGCCA------C--------CAAGGAAAAA---GTAAGGACCTGGTT-TTCTACTCTTT----------AGGAAAG-GTCG-CAGCAACTCCAACAAGCGGTTTTATCCTTCAACCAAC-AAATGCAAGGCCAGGAAGAGGACAAAGGAGATGGTGCAGCCACCAAGGCCTGTGGGAGACAATA i mm9.chr11 I 820 C 0 s cavPor3.scaffold_76 4296205 337 + 7991924 -CCTTCCAGGCTCCAGCGA-TGGAGCTAGC--TACGTCTGGAGGC-CCTCTCACCCATAATTGTTCTTAATGCTGTAACACAC--GGTGACTAATGGACCCTAATTGGACAGCTTCAGCACCGAGG----GTGGCCTGGGAAACTC-TCTGACAGCAT-CCTCTGTGACCCATGGGGCCTCCT--GGGGCTCACACA-CAG-----A-GTACAAAGGTC------C--------CCAGGATAAC---ATATTGGCTCCTTT-TTCTATTTTTT----------AAAAAAATATCA-CA-CAGCGCTGATAAGCAGTTTTATCCTTCACCTGAC-AAATACAGGACAAAGAAAAGGAGAGAGGAGA------AACCG--AAAGCAGATGGGAGAAAGCA i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10751937 301 - 65312493 -CCTTCCAGC-CCCTGAGC-TGA----AGC--TACATCTGGAAACTCTTCTCACCCTTAATTGTTCTTAATGCTTTAACACACTGAGTGACTAATGGGCTCTAATTGGA-------------CAGCTCCGGCGCGAAGGGGGTGCT--CTGACAGCGC-CCTCTGCCACACGCCCAGCCTCCTGGGCTGCTCACTCC-CAG-----A-GTTCAGAGGTC------A--------CCAACCAAAA---ATATCGG---------------------------------------CC-CACCCCTGCCAACAAGCAGTTTCATCCTTCAACCAGCAAAACACAAGGCACAGAAAAGGATATCGGAAA------AGTCC--AAAGCAGATGGGACAAAATA i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59354796 326 - 64418924 -CCTTCCAGC-ACC--AGCACGA----GGC--TGCATCTGGAAA--CTTCTCACCTTTAATTGTTCTAAATGCTTCAACACCTTGAGTGACTAATGGGCTGTAATTGGA-------------CAGC-----TCTGCGGAGGGGGCT-GCGCCCACCACTCCTCCCCAACCCGCCAG--CCCCAGGGCTGCCCATTCC-CCTCCTCCA-GTTCAAAAGTCAGGAAAA--------AAAAAAAAAA---AAAACAGCAGCCTG-TTCTATTTTT------------TACAAATGCCT-CACTGGTG-CGAC-AGCAGTTTCATCCTTCTACCAAC-AAACACGGGGCAAAGAAAAGGATAGCAGGGA------AGCCA--GA-GCAGACGGAATCAAACA i canFam2.chr9 C 0 C 0 s equCab2.chr11 57939940 309 - 61308211 -----------------GC-TGA----AGC--CACATCTGGAAACTCTTCTCACCCTTAATCGTTCTGAATGCTCTAGCA-CGGGAGTGACTAAC-GGCTCTAATCAGA-------------CAGTG--AGCGTGCAGGGGCAGGT-GCTGACAGTGC-CCTCTGCAACCGGCCGAGCCTCCTGGGCTGCTCGCTCA-CAG-----A-GCTCAAAAGTC------A--------CCCAGAAAAA---ATACTGGTCCTTCC-TCCTATTTTT-----------AAAAAAATGTCA-CACCAGTGCCGACGAGCAGTTTTATCCTTCAGCCAAC-AAATGTGGGGCAAAGAAGAGGACAGAGGAGA------AACCA--AAGGCAGGTGGGACAAAATA i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14286840 322 - 17734757 -CCTCCCAGC-TCCAGTGC---C----AGC--TACATCTGGAAACTCTTCTC-TCCCTAATTGTCCCTAATACTTTAGCACACTGAGTGACTAAGGGGCTCTAATGGGACTGCTCGGGGTG-AAGC---CGCAGCCTGGGGGACAC-GCTCACAGAGC-C--TTGTGACCTCTC---CCTGCT-----GCTCACTCT-CAG-----ACACACAGAAGTC------A--------CCAAGAAAAA---ATACCGGCCCGTTG-TCCGATTCTT------------TAGAAACGTTC-AACCTCTGCCAACAAGCACTTCCATCCTTCAACCAAG-AAATATGGGCCAAGGAAACAGA--AAGGAAA------AGCCA--AAAGCAGGTGGGACAAAATG i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_104361 3284 328 + 5925 -TTTCCCAGC-TCCTGGCT---G----AGCAGAACACCTGGACACTCACCTG-CCCGTGACTGTCTC-AAGGCCCGCACGCTCTGAGGGACTAACGGGCTCTCACTGGACAGCGCCGGCAC-GAGC---GGGGGCT--GGGGACAC-GTGGACAGCAC-CCACTGTGACCTGCC-GGCCTCCT---CAGCTCACGCTCCAG-----ACACGCAAAATTC------A--------CCGAGAAAAA---ACATTGGCCTGTGT-CCCTGATTTT------------TGAAAATTTCA-CACCAGTACCATCGAGCAATTGTCTCCTTCAACCAAC-AAAGAAGGGGAAAGGAAAAGGGT-GGGGGAA------AGCCA--AAGGCAGAC-AGACGAGCCA i dasNov2.scaffold_104361 C 0 C 0 s monDom5.chr2 304270085 360 - 541556283 AGTTCCCAGC-TCCAGTGCATAG----CAC--TACATCTGGAAACTCTTCTCACTCTTAATTGTCCTAAATGCTTTAACACACTGAGTGACTAATAGACACTAATTGGATGACTTTAGCATGGAGC---ATTTACTTGGGGAATGTGGCAGACATTGC-CCTCTAAGACTGCCTGGGACTCAT-----GTTCAGAGG-TAG-----CTGCTGAACAGTT------AACTATTAGCCAAAAAAAGCATATAAAAGCTCTTCCACTGTATTCTTTATTAAAAAAAAAAAAGATGTGAGCATCATGGCCAAAGTATAATTTCATGCCTAAGCCAGC-AAGAATGGGTCAAGGGAATA-ATAAAGGTCA------AAATA--AAAGCAAATTGGATGGAAGA i monDom5.chr2 C 0 I 2718 a score=111756.000000 s hg19.chr17_gl000204_random 10176 59 + 81310 TCACAAATGCCACTGAGGTCTGTGACATCTGTCTAG---AGA-----CAAA-G-----AGTTCTTGGAGGCAA s panTro2.chr17 79186304 59 + 83384210 TCACAAATGCCACTGAGGTCTGTGACATCTGTCTAG---AGA-----CAAA-G-----AGTTCTTGGAGGCAA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69571314 59 + 73212453 TCACAAATGCCACAGAGGTCTGTGACATCTGTCTAG---AGA-----CAAA-A-----AGTTCTTGGAGGCAA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74736749 59 + 78773432 GCACAACTGCCACTGAGGTCTGTGACATCTGTCTGG---AGA-----CAAA-G-----AGTTCTTGGAGGCAA i rheMac2.chr16 C 0 C 0 s mm9.chr11 118667965 44 + 121843856 TCACAAATGCCACCATGCCCTGTAACATCTGTCTAG---AAG---------------------CTGGC----- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4296542 63 + 7991924 TCACGGATGCCACGAAGGTCTGTGGCATCTGTCTAG---AGACAACCCAGG-G-----AGCGCCTGGC-ACAA i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10752238 61 - 65312493 TCACTGGTGCCACCGAGGTTTGTGACATCTGCCCGGGACAGA-----CAGA-------GGTTCTTGGAGGCAA i bosTau4.chr19 C 0 I 306 s canFam2.chr9 59355122 63 - 64418924 TCCCCACCGCCTCCCGGGCTGGTGACAGCTGCCCGGGACACA-----CAGGAG-----GGCCCCCGGGAGCAA i canFam2.chr9 C 0 C 0 s equCab2.chr11 57940249 62 - 61308211 TCGGCAATGCCACCAAGGCTGGCGACATCTGTCTGGGA-AGA-----CAGAAG-----GATTCTTGGAGGCAA i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14287162 64 - 17734757 TCATAAAAGCCACGGGGGCTTGCAACATCTGTCTGC---AGA-----CAGA-CAGAGGAGTTCTTGGAGGCAA i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_104361 3612 57 + 5925 TC--AGAGGCCACTGAGGCTCGGAACGTCCGCCTGG---AGA-----CAGA-T-----GGTTCTTGGGAGTGA i dasNov2.scaffold_104361 C 0 C 0 e monDom5.chr2 304270445 2718 - 541556283 I a score=-23899.000000 s hg19.chr17_gl000204_random 10235 56 + 81310 ACCCCA-CGCCAGTCA------------GTTC-------------AGGGCGTG-TGAAGGATTCCAGCCACACGTTTCCCCTT---------------------- s panTro2.chr17 79186363 56 + 83384210 ACCCCA-CGCCAGTCA------------GTTC-------------AGGGCGTG-TGAAGGATTCTAGCCACACGTTTCCCCTT---------------------- i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69571373 56 + 73212453 ACCCCA-CGCCAGTCA------------GTTC-------------AGGGGGTA-TGAAGGATTCCAGCCACACATTTCCCCTT---------------------- i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74736808 56 + 78773432 ACCCCA-CGCCAGTCA------------GTTC-------------AGGGGGTG-TGAAGGATTCCAGCCACACATTTCCCCTT---------------------- i rheMac2.chr16 C 0 C 0 s mm9.chr11 118668009 61 + 121843856 --CCGG-TATCAGTTGCTTAGG-AATCATCCC---------------AAAGCC-TGGAAGGTTTCAGACGAGAGTTCTCAT------------------------ i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4296605 64 + 7991924 AGCCAG-CACCAATTA---GGG-GAGGGCTCC-------------AGAGAGCC-GGGAAGATTCCAGCCCCGAATCCCCTTCC---------------------- i cavPor3.scaffold_76 C 0 C 0 s canFam2.chr9 59355185 36 - 64418924 -CGCCA-CACTGGTCA------------ATTC-------------ACTGGATGCTAAAGGATT------------------------------------------ i canFam2.chr9 C 0 I 50 s equCab2.chr11 57940311 60 - 61308211 -ACCCAGCACTAGTCA------------ATTCCAGCCACAGCGAAACTGGGTC----------CTGGCCTGCCTTGCATTCTT---------------------- i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14287226 90 - 17734757 ACCCAG-CGCAAGTCAATTAGGTCAATGTTAC-------------AGTGAGCC-TGGAAGATCCCAGCCATAGCGAGTCTGAGTCCAGGCCTTCCTGGCACTCTT i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_104361 3669 80 + 5925 ACCACG-TGCTGGGCAGTGGGG-----GGTGC-------------AG-GAGCC-TGGGGGCTGCC-GCCGCGGCGGGTCCTGG-CCAGGC--TCCTCGCACCCTC i dasNov2.scaffold_104361 C 0 C 0 e monDom5.chr2 304270445 2718 - 541556283 I e bosTau4.chr19 10752299 306 - 65312493 I a score=102390.000000 s hg19.chr17_gl000204_random 10291 188 + 81310 -----------------GAAGGGGAAAGGAAAGAGGGGATAAGGCATCTCTGATGTCTTCTCATCTCCTCTCCGACCCCTGTGAGGGGTA-----AGTGGTGACTGCCAAGTCACCAGAACTGCAGAGAAGGAACCAGATGATAGAGAGGATAGGC--AGAGGCAGGGTGGCAGAATTAGG-GGGTCTGGAAAAGAAAGTGCAGAAAAGCCTG s dasNov2.scaffold_104361 3749 155 + 5925 GGGT------GTGCTTTGCCGGGGCGG-------GGGGAGAAGGCACTGCCGCTCTCGTCTCCTCCCCTCCCAGAGCCCTGC-GGCGGCT-----TGTGGAGACC-CCCACTCACCGGAGCTGC--AGAAGGGACCGAAAGACGTGGAGGCCATGCAAAGAG--------------------AGAGTGGAAAGCTGA---------------- i dasNov2.scaffold_104361 C 0 C 0 s loxAfr3.scaffold_49 14287316 202 - 17734757 GGACTTCTTGGCATCTGGAAGGGGAAGG---ATAGGGGAGAAGGTATCACTGAT---ATCTCGCCCTCCACCCAAGCCCTGCAGGTGGCA-----CAGGGTGATCGCCAACATACCAGAGCCGCAGAGAAAGGACCAAGAGAAGTAGAGGCCAGGCACAGAGGCAGGCTATCAGAGATGGGCACAGTTGGAAGAAAAAGCAAGGAAGGGCTTG i loxAfr3.scaffold_49 C 0 I 1507 s cavPor3.scaffold_76 4296669 165 + 7991924 --------------------CGGGAAAGGAAGGAAGAGAGAGCAACTCCAGGGTGCCTCCTTGTCTCCTGCCTG--CCCCATGGGCCCTG-----CGTG-TGGCTGCACACAGCCCAGAACCACAGGGCATGAG--AG----------GGCTGGGT----GGGCAGGTGGGCCGAG--GGA-GGGTCTTGAA-AAAGAAAGTGTGAAAAGCTG i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118668070 158 + 121843856 ----------------------GGAGAAGACGGAA-----------TCTCAGGAGCCTTCTTACCTCC--------CCTGATGAGTCTTGGATGTCATG-TGACTGTGAACCGTCCCGGACTACAGGGAAAGGA--AGAGGACAATGAGACCGAGC----ATGGAGCTGGGCC-----AGC-AGGTCTGGGA-AGGAGGCATAGAGAAACCTA i mm9.chr11 C 0 C 0 s rheMac2.chr16 74736864 186 + 78773432 -----------------GAAGAGGAAAGG--AGAAGGGATAAGGCATCTCTGATGTCTTCTCATCTCCTCCCCGACCCCTGTGAGGGGTA-----AGTGCTGACTGCCAAGTCACCAGAACTGCAGAGAAGGAACCAGATGATAGAAAGGATAGAC--AGAGGCAGAGTGGCAGAATTAGG-GGCCCTGGAAGAGAACGTACAGAAAAACCTG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69571429 188 + 73212453 -----------------GAAGGGGAAAGGAGAGAGGGGATAAGACATATCTGATGTCTTCTCATCTCCTCTCCAACCCCTGTGAGGGGTA-----AGTGGTGACTGCCAAGTCACCAGAACTGCAGAGAAGGAACCAGATGATAGAGAGGATAGGC--AGAGGCAGGGCGGCAGAATTAGG-GGCTCTGGAAGAGAAAGTGCAGAAAAACCTG i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79186419 188 + 83384210 -----------------GAAGGGGAAAGGAGAGAGGGGATAAGGCATCTCTGATGTCTTCTCATCTCCTCTCCGACCACTGTGAGGGGTG-----AGTGGTGACTGCCAAGTCACCAGAACTGCAGAGAAGGAACCAGATGATAGAGAGGATAGGC--AGAGGCAGGGTGGCAGAATTAGG-GGCTCTGGAAAAGAAAGTGCAGAAAAGCCTG i panTro2.chr17 C 0 C 0 e monDom5.chr2 304270445 2718 - 541556283 I e canFam2.chr9 59355221 50 - 64418924 I e bosTau4.chr19 10752299 306 - 65312493 I e equCab2.chr11 57940371 0 - 61308211 C a score=31881.000000 s hg19.chr17_gl000204_random 10479 51 + 81310 AAGTG-CACACAATTCCTCAGTGGGGTGGCGGGGACAGAGAGAGACAGACAG s panTro2.chr17 79186607 51 + 83384210 AAGTG-CACATAATTCCTCAATGGGGTGGGGGGGACAGAGAGAGACAGACGG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69571617 51 + 73212453 AAGTG-CACACAATTCCTTAATGGGGTGGGGGGGACAGAGAGAGACAGACAG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74737050 48 + 78773432 AAGTG-CACACAATTCCTCAATGGGGTGG-ACGGACAGAGAGAGACAGAC-- i rheMac2.chr16 C 0 C 0 s mm9.chr11 118668228 49 + 121843856 AGGTGAAAGGAAGTCTTGCAATGGGAgggaagag---gggagaggggaggag i mm9.chr11 C 0 I 3 s cavPor3.scaffold_76 4296834 52 + 7991924 AAGGAATATATAATTCCTCAAGGGAAGAGAGGAGACAGAGACAGGGAAGCAG i cavPor3.scaffold_76 C 0 I 248 s dasNov2.scaffold_104361 3904 46 + 5925 AGGTA-GGCGAAACTCCTCGATGGGAACG-Ggagagagaaagagaagg---- i dasNov2.scaffold_104361 C 0 C 0 e monDom5.chr2 304270445 2718 - 541556283 I e canFam2.chr9 59355221 50 - 64418924 I e bosTau4.chr19 10752299 306 - 65312493 I e equCab2.chr11 57940371 0 - 61308211 C e loxAfr3.scaffold_49 14287518 1507 - 17734757 I a score=26173.000000 s hg19.chr17_gl000204_random 10530 32 + 81310 AGACAgaga---aggaggaagaggagggggaatga s panTro2.chr17 79186658 32 + 83384210 AGACAgaga---agtaggaagaggagggggaatga i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69571668 32 + 73212453 AGACagagg---aggaggaagaggaggaggaatga i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74737098 32 + 78773432 AGACAGAGA---AGGAGGAAGAGGAGGAGGCATGA i rheMac2.chr16 C 0 C 0 s mm9.chr11 118668280 32 + 121843856 gaggaggga---aagagagagaggaggggaggagg i mm9.chr11 I 3 C 0 s dasNov2.scaffold_104361 3950 35 + 5925 aaaaagagaaacagagggaagaggagagagagaga i dasNov2.scaffold_104361 C 0 I 27 e monDom5.chr2 304270445 2718 - 541556283 I e canFam2.chr9 59355221 50 - 64418924 I e bosTau4.chr19 10752299 306 - 65312493 I e equCab2.chr11 57940371 0 - 61308211 C e cavPor3.scaffold_76 4296886 248 + 7991924 I e loxAfr3.scaffold_49 14287518 1507 - 17734757 I a score=63154.000000 s hg19.chr17_gl000204_random 10562 94 + 81310 gaaaggaaagaagtagggggagagaaaaaagaa-gaaagaggagaaagaggaaaag-gagacggaagaggaagaagaagaaaaggaggaggaggaA s panTro2.chr17 79186690 94 + 83384210 gaaaggaaagaagtagggggagagaaaaaagaa-gaaagaggagaaagaggaaaag-gagacggaagaggaagaagaagaaaaggaggaggaggaa i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69571700 94 + 73212453 gaaaggaaagaaatagggggagagaaaaaagaa-gcaagaggagaaagaggaaaag-gagacagaagaggaagaagaagaaaaggaagaggaggaa i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74737130 94 + 78773432 GAAAGGAAAGAAGTAGGCAGagagaaaaaagaa-ggaagaggagaaagagaaaaag-gagacagaagaggaagaagaagaaaaggaagaggaggaa i rheMac2.chr16 C 0 C 0 s mm9.chr11 118668312 95 + 121843856 gagagaagaggaggagggaaagagggggaggagtgaaagagggggaggaggggaggagggggaggaggggaggagggagagga-gaggaggaggga i mm9.chr11 C 0 I 22 e dasNov2.scaffold_104361 3985 27 + 5925 I e monDom5.chr2 304270445 2718 - 541556283 I e canFam2.chr9 59355221 50 - 64418924 I e bosTau4.chr19 10752299 306 - 65312493 I e equCab2.chr11 57940371 0 - 61308211 C e cavPor3.scaffold_76 4296886 248 + 7991924 I e loxAfr3.scaffold_49 14287518 1507 - 17734757 I a score=286083.000000 s hg19.chr17_gl000204_random 10656 597 + 81310 GGT-----------gctcaccctgtaaccccagcactttgggaggcctaggtgggtggatcacttgaggtcaggagttcgagaccagcctggccaacagggtgaaaccccgtctctactaaaaatacaaaaattagccaggcgtggtggtgggcgcctgtaatcccagttactcgggaagctgaggcaggagaatctcttaaacccaggaggtagaggttgcagtgagctgagatcgcgccactgcactccagcctgggtgaaagagcaaggctccgtttcaa----aaaaaaataaataaagataaattaaaaaaaaaaaaaAAAAAGAgggcgcggtggctcacacctgtaatcccagcactttgggaggccaaggcaggtggatcacgaggtcaggagatcgagatcatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaacattagccagacgtggtggcgggcgcctgtagtcccagctacttgggaggctgaggcaggagaatggcgtgaacccgggaggcggagtttgcagtgagctgagatcgccccatcgcactccagcctgggcgacagagcgagactccgtcaccgg-aa s panTro2.chr17 79186784 592 + 83384210 ggt-----------gctcaccctgtaaccccagcactttgggaggcctaggtgggtggatcacttgaggtcaggagttcgagaccagcctggccaacagggtgaaaccccgtctctactaaaaatacaaaaattagccaggcgtggtggtgggcgcctgtaatcccagttactcgggaagctgaggcaggagaatctcttaaacccaggaggtagaggttgcagtgagctgagatcgcgccactgcactccagcctgggtgaaagagcaagtctccgtctcaa----aaaaatataaataaagataaatt------aaaaaaaaaaAAGAgggcgcggtggctcatacctgtaatcccagcactttgggaggccaaggcaggcgaatcacgaggtcaggagatcgagatcatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaacattagccagacatggtggcgggtgcctgtagtcccaggtacttgggaggctgaggcaggagaatggtgtgaacccgggaggcggagcttgcagtgagctgagatcgccccatcgcactccagcctgggcaacagagcgaaactccgtcgccgataa i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69571794 597 + 73212453 gGT-----------gctcactctgtaaccccagcactttgggaggccaaggcaggtggatcacttgaggtcaggagtttgagaccagcctggccaacagggtgaaaccccgtctctactaaaaatacaaaaattagccaggcgtggtggtgggcgcctgtaatcccagttacttgggaggctgaggcaggagaatctcttgaacctaggaggtagaggttgcagtgagctgagattgcaccactgtactccagcctgggtgacagagcaaggctccatctcaaaaataaataaataaataaagataaaCT-TTAAAAAAAAAAAAAAAGAgggtgcggttgcttacgcctgtaatcccagcactttgggaggccaaggcaggcggatcacgaggtcaggagatcgagaccatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaacattagccagacgtggtggcgggtgtctgtagtcccagctacttgagaggctgaggcaggagaatggtgtgaacccgggaggcggagcttgcagtgagccgagatcgccccatcgcactccagcctgggcaacagagtgaaactccctcat----aa i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74737224 596 + 78773432 ggccgggcacagtggctcactctgtaaccccagcactttgggaggccgaggtgggtggatcacttgagctcaggagtttgagaccagaatggccaacagggtgaaaccccgtctctactaaaaatacaaaaattagccaggcatgatggcgtgtatctgtaatcccagttactcaggaggctgaggcaggagaatttcttgaacccgggaggtagaggttgcagtgagctgagactgcgccactgcaccccagcctgggtgatagagcaaggctccatctc------aaaaaaataaataaagaTCAATT----------TAAAAACAGAgggtgcagtggctcacacctgtaatcccagcactttgagaggctgagtcaggcagatcatgaggtcaggagattgagaccatcctggctaacacagtgaaacaccgtctctactaaaaatacaaaacattagccggacacggtggtaggcgcctgtagtcccagctacttgggaggctgaggcaggagaatggcgtgaacccgggagatggagttggcagtgagtggagatcgcaccattgcactccagcctgggcaacagagagagactccgtttcaaa-aa i rheMac2.chr16 C 0 C 0 e dasNov2.scaffold_104361 3985 27 + 5925 I e monDom5.chr2 304270445 2718 - 541556283 I e canFam2.chr9 59355221 50 - 64418924 I e bosTau4.chr19 10752299 306 - 65312493 I e equCab2.chr11 57940371 0 - 61308211 C e cavPor3.scaffold_76 4296886 248 + 7991924 I e mm9.chr11 118668407 22 + 121843856 I e loxAfr3.scaffold_49 14287518 1507 - 17734757 I a score=33329.000000 s hg19.chr17_gl000204_random 11253 54 + 81310 aaaaa------------aaaagaGGAGGAGGAGTAGGAAAAAAGGGTGAAACAGAAGCAATGGAGT s rheMac2.chr16 74737820 66 + 78773432 aaaaaaaaaaaaagaggaaaagaGGAGGAGGAGGAGGAAGAAAGGGAGAAACAGAAGCAATGGAGT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69572391 54 + 73212453 aaaaa------------taaagaGGAGGAGGAGGAGGAAGAAAGGGTGAAATAGAAGCAATGGAGT i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79187376 54 + 83384210 aaaaa------------aaaagaggaggaggagtaggaagaAAGGGTGAAACAGAAGCAATGGAGT i panTro2.chr17 C 0 C 0 s equCab2.chr11 57940371 52 - 61308211 AGAGG------------AAAggagagggagagagagagagaaagggagaa--ggaAGCCATAACAA i equCab2.chr11 C 0 I 1 s bosTau4.chr19 10752605 43 - 65312493 -----------------AGAGGAAAGGAAAGGGGACAGAGAAA--GAGAA--TGAA--TATAAGGA i bosTau4.chr19 I 306 I 2 s mm9.chr11 118668429 41 + 121843856 -----------------------ggaggag--gCAGAAAGAAAGGGAGGAATAGAGAGGACGGAGA i mm9.chr11 I 22 C 0 e dasNov2.scaffold_104361 3985 27 + 5925 I e monDom5.chr2 304270445 2718 - 541556283 I e canFam2.chr9 59355221 50 - 64418924 I e cavPor3.scaffold_76 4296886 248 + 7991924 I e loxAfr3.scaffold_49 14287518 1507 - 17734757 I a score=9494.000000 s hg19.chr17_gl000204_random 11307 37 + 81310 GGGGCCCCAGGTCCTTGTCTCATGTCCTCTTTCTCAC s bosTau4.chr19 10752650 28 - 65312493 -GGGTTC--------CAGACTCCTCCCCCTCCCGCAT i bosTau4.chr19 I 2 C 0 s equCab2.chr11 57940424 37 - 61308211 AGTGTCCTACGTCCTCCTCCTCCTCTCCCGGCCTCAC i equCab2.chr11 I 1 C 0 s canFam2.chr9 59355271 33 - 64418924 GGAGCTC----CCGTCCTCCTCCCCTCCCCTCCTCAA i canFam2.chr9 I 50 C 0 s mm9.chr11 118668470 2 + 121843856 GG----------------------------------- i mm9.chr11 C 0 C 0 s rheMac2.chr16 74737886 37 + 78773432 GGGGCCCCAGGTCCTTGTCTTGCATCCTCTTTCTCAC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69572445 35 + 73212453 GGGGCCCCAGGTCCTTGTCTCATGTC--CTTTCTCAC i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79187430 37 + 83384210 GGGGCCCCAGGTCCTTGTCTCGTGTCCTCTTTCTCAC i panTro2.chr17 C 0 C 0 e dasNov2.scaffold_104361 3985 27 + 5925 I e monDom5.chr2 304270445 2718 - 541556283 I e cavPor3.scaffold_76 4296886 248 + 7991924 I e loxAfr3.scaffold_49 14287518 1507 - 17734757 I a score=416393.000000 s hg19.chr17_gl000204_random 11344 439 + 81310 AGGGACATC---CTCAGAGCTTGCTCTGGTGGTGAACAAGCAAAGGGGCAGGGTGGCAGAATTAGGCAGGATCAGAATGAGGGA-CTGAAGTGGCTGAGCCTGGCATCCTTCCTAAA---TATTTTCC---------AAATACATTTCTTAATAGAAAAGGAATCACAGAAGTTTTTAG---GACCCAAGTCTCC--AAAGACTGGCTCAAACTAAAGTCTTCTCATTAAAATATTGGATCCAAGAAGGAAATAAGATG---CCC-CTGTAGGAA--------GGAGAGACCCCAGCAACGTCCTTCAGCTGGGCACCGCCTGTTCCACCCAGGAGCACCTAGGACGAGCTCCTGCA--AAAGGAATGCATTCACTGCAAGCCTGGGA---------GCAACGTCCCATCC-------GCTTCTGGTATAACTAAATGAAGCCATGATCCCCCTCTCCC-----CGCTGCCAAGCA-ACGCTCA----T----GTGCTCCAGGA s panTro2.chr17 79187467 439 + 83384210 AGGGACATC---CTCAGAGCTTGCTCTGGTGGTGAACAAGCAAAGGGGCAGGGTGGCAGAATTCGGCAGGATCAGAATGAGGGA-CTGAAGTGGCTGAGCTTGGCATCCTTCCTAAA---TATTTTCC---------AAATACATTTGTCAATAGAAAAGGACTCACAGAAGTTTTTAG---GACCCACGTCTCC--AAAGACTGGCTCAAACTAAAGTCTTCTCATTAAAATATTGGATCCAAGAAGGAAATAAGATG---CCC-CTGTAGGAA--------GGAGAGACCCCAGCAATGTCCTTCAGCTGGGCACCGCCTGTTCCACCCAGGAGCACCTAGGACGAGCGCCTGCA--AAAGGAATGCATTCACTGCAAGCCTGGGA---------GCAACGTCCCATCC-------GCTTCTGGTATAACTAGATGAAGCCATGATCTTCCTCTCCC-----CGCCGCCAAGCA-ACGCTCA----T----GTGCTCCAGGA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69572480 436 + 73212453 AGGGACATC---CTCAGAGCTTGCTCTGGTGGTGAACAAGCAAAGGGGCAGGGTGGCAGAATTAGGCAGGATCAGAATGAGGGA-CT---ATGGCTGAGCTTGGCACCCTTCCTAAA---TATTTTCC---------AAACACATTTATCAATAGAAAAGGAATCATGGAAGTTTTTAG---GACCCATGTCTCC--AAAGACTGGCTCAAACTAAAGTCTTCTCATTAAAATATTGGATCCAAGAAGGAAATAAGATG---CCC-CTGCAGGAA--------GGAGAGACCCCAGCAACGTCCTTCAGCTGGGCACCGCCTGTTCCACCCAGGAGCACCTAGGACGAGCTCCTGCA--GCAGGAATGCATTCACTGCAAGCCTGGGA---------GCAACGTCCCATCT-------GCTTCTGGTGTAACTAGGTGAAGCCATGATCTCCCTCTCCC-----TGCCACCAAGCA-ACGCTCA----T----GTGCTCCAGGA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74737923 443 + 78773432 AGGGACATC---CTCAGAGCTTGTTCCGAGAACAAGCAAGCAAAGGGGCAAGGTGGCAGAATTAGGCAGGATTAGAATGAGGGA-CTGAAGTGGCTGAGCTTGGCACCCCTCCTAAA---TATTTTCC---------AAATACATTTATCAATAGAAAAGGAATCATGGAAGATTTTAG---GACCCATGTCTCC--AAAGACCGGCTCAAACTAAAGTCTTCTCATTAAAATATTGGATCCAAGAAGGAAATAAGATG---CCC-CCGCAGGAA--------GGAGAGACCCCAGCAACGTCCTTCGGCTGGGCATCGCCTGTTCCACCCAGGAGCACGTAGGACAAGCTCCTGTG--GCAGGAATGCATTCGCTGCAAGCCTGGGA---------GCAACGTCCCATCC-------ACTTCTGGTGTAACTAGATGAAGCCATGATCTCCCTCTTCC-----TGCCGCCAGGCA-ACGCTCAGGCTT----GTGCTCCAGAA i rheMac2.chr16 C 0 C 0 s mm9.chr11 118668472 361 + 121843856 AGGGAAACT---C------------------GGGAGAAGGCA-----GCAGGTAGAGGAAAGTGGGTAGAAAAACCATGGG---------------------------TTTCCCCAG---GGTGAGCC---------CAGTGCA-------------------TCCTGGGAGCTCAT---------------TCC--AA--------------TGAAGTTCCCTAATTAAACCATCAGGTTCTCGAGAGAGCCCAGATG-----A-CTGCAGGAGTCCTGCCCAGGAAGCCCTGTGTGGGGCC-----AATGGGCCCCAACCCTTCTATCCAGCAGCAACTCAGCACAG----TGGG--ACAGCAGCACA-GCAGGGCAGGCTCTGGACAGACAGATGGGAAGGTCTATCTCTAAGTGGCTTCCCATGTGGCTGGGTAAAGCCATGATcacactcctccccacactcctccctaca-ctcctcc----t-----cacacCAGGA i mm9.chr11 C 0 C 0 s canFam2.chr9 59355304 417 - 64418924 GGGCACATC---CCCAGAACGAGCTCCAGCAGCAA--------------------------------GAGCTCAGAAGCAAGGA----TGAAAGCTGATCTCAACGCCCTTCCTGAATCCTCCTTTCC---------AAAACCATTTAGCAATACAAGAGGGACCACAGCTGTTCCCAGAAGGAGCCATGTTTCCCAGAAGACTGGCTCAAGCTAAAGTCTTCCAACGAAACTACCAGGTTC-AGGGG-AAGTGAGATG---CCCGCATGAGAAG--------GCAGAGGCCCCAGCAGCATCCTGAAGGTGGTCCTTCCCTGCCTCAC-CGGCAGCAACCAGGACTTCCTCATGCGTGGCAGGGATGTATTAACTGCAAGTGTCAGA---------AAAACATCCCATTA-------GCTTCTGGTGTAACTAGATAAAGCCGTGCTCTCCCTCTCCC-----CACCACGGGGGAGACGTTTA----CCTCGATGCTCTAGAA i canFam2.chr9 C 0 C 0 s equCab2.chr11 57940461 415 - 61308211 GGGCACATC---CGCAGAATTTGTTCCAGCCAAAA--------------------------------ATGCTCAAAAGGAAGGA-CTGCAGAGGTTGACCTCAGCACCC-TCCAGAATCTTATTTTCC---------AAATACATTTAGTGATAGAACAGGAAGCACAGGTGTTTCTAGAAGGACCCACGTTTCC--AAAGCCCGGCTCAAGCTAAAGTCTTCAAATGAAAGCATCAGGTACAAGAAG-AAATAAGATG---CCC-CCCGAGAAG--------GAGGGAGCACAAGCAGCATCCTTCAGGTGGT-GTTACCTGTTCCGCACGGCAGCAGCCAGGAC-TCCTCGTGCGTGGCAGGAATGCATTAACCGTGAGTGTCAGA---------GAAACATCCCATTA-------GCTCCTGGTGTAACCAGATAAAGCCGCGAGCTGCCTCTCCC-----CACCACCGGGGAGACA-TTA----CCTTGACGCTCTAGAA i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10752678 420 - 65312493 GGGCATATC---CCCAGAACTTGTTCTAGCCGTGA--------------------------------AGGTTCAGAAGCAAGGA----TTAAAGCTGATCTCAGTACCC-TTCCAAATCTTCTTTTCC--------AAAATACATTTAGCAATAGAAGAGCAACCACCAGTGTTTCTAGAAAGATTTGTCTTTCC--AAAGGCTGGCTTCAGCTAAAGTCTTCGAATTAAAATATCAGGCATGAGAAGCAAATAAAAGGTGATTC-TGCAAGAAG--------GGAAAAATACCAGCCTCATCATTCAGGTGGGTATTACCTGTTCCACCCAGCAGCCACCGGGACTTCCTCATGCATGGCAGGAATGTATTAACTGCAAGTGTCAGA---------GAAACATCCCATTA-------GCTTCTGGTGTAACTAGATAAAGTCACGCTCTCCGTCTCCC-----CACCACTGGGGAGACATTTA----CCTCGATGCTCCAGAA i bosTau4.chr19 C 0 C 0 s dasNov2.scaffold_104361 4012 398 + 5925 GGGCACATCATGCCCAGTGCCTGCCCTTGTCATCA--------------------------------CCGTCCAGAGGGGGACAACAGCAGGGGCTGAGCTCAGCCTCCCTCCCGCAGCTGCTTTTCCTGTGGACACTGGGACACTGGGGAGTAGAAG-GGAACCACAGGTGCTTCGGGA--GGCCCATGTTTCC--TAAGGCAGGCCCTCGCTAAGGTCCTCCAGCTAAACCATCAGCGACGAGACGGCGCCCAG--G---CAC-CCGAAGGAA--------GGA-AGAGGCCAGAGGCGTTCCCCG--CGGGAATCGCCTGCTCCACCCCGTAGCAATCGGGCCTTCCTGGTGCGTGACGGGAGCGGATTACCTGGGAGCGTCAGA---------GGAGCATCTCGCTA-------GCTTCTGGCCAAACTAGATAAAGCCGCCACCT-CCTCTCCC-----AGCTCCAGAA------------------------------ i dasNov2.scaffold_104361 I 27 C 0 e monDom5.chr2 304270445 2718 - 541556283 I e cavPor3.scaffold_76 4296886 248 + 7991924 I e loxAfr3.scaffold_49 14287518 1507 - 17734757 I a score=33636.000000 s hg19.chr17_gl000204_random 11783 52 + 81310 AGCCCCACG---------------CACGTTC------CCACGGCTC-----ATGCGGGCAGCCTGTGTCTCGGCTCAG- s dasNov2.scaffold_104361 4410 38 + 5925 CGCTCTGCG---------------CGCACCT------GTA-AGGTG-----ATGCTG-------------CGGCCGTG- i dasNov2.scaffold_104361 C 0 C 0 s bosTau4.chr19 10753098 53 - 65312493 AGCTCCGTG---------------TGCATTA------ATATTGCTG-----ATGCGGGCAGCCTTTGCTGCAGCTTGGC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57940876 56 - 61308211 AGCTCTG-G---------------TGCATTA------ATATTGCTGACGCCATGCCGGCAGCCTTTGCTTCGGCTGGG- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59355721 53 - 64418924 AGCTCTGTG---------------TGCATTA------ATATTGCTG-----ATGCGGGCAGCCTTTGCTTCGCCGGGGC i canFam2.chr9 C 0 C 0 s cavPor3.scaffold_76 4297134 66 + 7991924 AGCCCCACGGAAGACCCCATGCGCAATGTCTGCGTAAGCATCAGAG-----AAATCAGCACCT-------CAGTTCGG- i cavPor3.scaffold_76 I 248 C 0 s mm9.chr11 118668833 69 + 121843856 GGCCTCAGTAAGCGGGGCTGGGGGGATATTC---TAACCACCACAG-----ACTCAGGCAGCCTGTGTA-CAGCTCAG- i mm9.chr11 C 0 C 0 s rheMac2.chr16 74738366 52 + 78773432 AGCCCCACG---------------CACATTC------CCACAGCTG-----ATGCGGGCAGCCTGTGTCTCGGCTTGG- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69572916 52 + 73212453 AGCCCCGCG---------------CACGTTC------CCACAGCTG-----ATGCGGGCAGCCTGTGTCTCGGCTCGG- i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79187906 52 + 83384210 AGCCCCACG---------------CACATTC------CCACGGCTC-----ATGCGGGCAGCCTGTGTCTCGGCTCAG- i panTro2.chr17 C 0 C 0 e monDom5.chr2 304270445 2718 - 541556283 I e loxAfr3.scaffold_49 14287518 1507 - 17734757 I a score=433743.000000 s hg19.chr17_gl000204_random 11835 181 + 81310 CCCTCAAGGGTGC---CATGCTCCCCGTGTGATGGATTCCAGTTTAACAGCTTTTAAAAACAAGCAGACAAGAGACGG-GC-GTGATGGATGAGTGCAGGAAGCACGCTCATTTGGAGATGATTTATGGGAAGT-CATGTGTTGCCGCTCA-TGGG-TG-----TGTCCCTGAGGGTGGGGGCCGG-----GG----------------TGGATG s panTro2.chr17 79187958 181 + 83384210 CCCTCAAGGGTGC---CATGCTCCCCCTGTGATGGATTCCAGTTTAACAGCTTTTAAAAACAAGCAGACAAGAGACGG-GC-ATGATGGATGAGTGCAGGAAGCACGCTCATTTGGAGATGATTTATGGGAAGT-CATGTGTTGCCGCTCA-TGGG-TG-----CGTCCCTGAGGGTGGGGGCCGG-----GG----------------TGGATG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69572968 180 + 73212453 CCCTCAAGGGTGC---CATGCTCCCCCTGTGA-GGATTCCAGTTTAACAGCTTTTAAAAACAAGCAGACAAGAGACAG-GC-GTGATGGATGAGCGCAAGAAGCACGCTTATTCGGAGATGATTTATGGGAAGT-CATGTGTTGCCGCTCA-TGGG-TG-----CGTCCCGGAGGGTGGGGGCCGG-----GG----------------TGGATG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74738418 180 + 78773432 CCCTCGAGGGTGC---CATGCTCCCC-TGTGATGGATTCCAGTTTAACAGCTTTTAAAAACAAGCAGACAAGAGACGG-GC-GTGATGGATGAGTGCAGGAAGCACGCTCATTCGGAGATGATTTATGGGAAGT-CACGTGTTGCCACTCA-TGGG-TG-----CGTCCCCGAGGGTGGGGTCCGG-----GG----------------TGGATG i rheMac2.chr16 C 0 C 0 s mm9.chr11 118668902 177 + 121843856 CCC---AAGGTGTCGGCA-GCATCCC-CGTGATGGATTCTGGTTTAACAGCTTTTAAAAACAAGCAGAGGAGAGCCGG-GC-ATGATGGATGAGTGCAGGAAACACGCTCATTCGGAGATGATTTATGGGATGT-TGCCCGTCG-TGCTCA-TGGGACG-----CAGCTCGAGGG-TGGGGGCCTT-----GG-----------------AGATG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4297200 152 + 7991924 TCC---AAGGTGC---CA-GCACCCC-TGTGATGGATTCTGGTTTAACAGCTTTTAAAAACAAGCGGATG-GAGACAG-GC-CTGATGGATGAGTGCAGG---TGTGCTCA-CCAGAGATGATTTATGGAAAGG-TGCGCGCCA-TGCTCA-CGGG-TG-----CACCTCCGCGAG--------------------------------------- i cavPor3.scaffold_76 C 0 I 27 s canFam2.chr9 59355774 172 - 64418924 CCCCCGAGGATGC---CC---------TGTGATGGATTCCAGTTTAACAGCTTTTAAAAACAAGCAGACAAGAGACGG-GGCGTGATGGATG-GCGTGGGAAGCGCGCTCATTCGGGGATGATTTATGGGAAGT-TGCATGTGGCAGCTCA-GGGG-TC-----CGTCCCCGGGTGGGGGGAGGGG-----TG----------------TAGATG i canFam2.chr9 C 0 C 0 s equCab2.chr11 57940932 159 - 61308211 CCCCCGAGGGTGC---CA---------TGTGATGGATTCCAGTTTAACAGCTTTTAAAAACAAGCAGACAAGAGACAG-GG-GTGATGGATG-ATGTAGGAAGCATGCTTTTTCGGGGATGATTTATGGGGAGT-CGCACGTTGCTGTTCACAGGG-TC-----CATC-----GTGGAGGGTGGGG----------------------------- i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10753151 171 - 65312493 CCCCCGAGGGTGC---CA---------TGTGATGGATTCCAGTTTAACAGCTTTTAAAAACAAGCAGACAAGAGATGA-GC-GTGATGGATG-ATGCAGGAAGCACGCTCATTCGGGAATGATTTATGGGAAGT-CGCATGTTGCCCCTCA-GGGG-TC-----CATCCCCTAGGGTGGGGCCGGG-----GG----------------TAGACA i bosTau4.chr19 C 0 C 0 s dasNov2.scaffold_104361 4448 175 + 5925 GCCCCGGGGGCAT---CATGCTCCCC-TGCGCTGGATCCCAGTTTAACAGCTTTTAAAAATGAACAGAAGAGGGAT-G-GC-ATGACGGATGAGTGGGGAAAGGGTGCTTGTTCCGGGATGATTTATGGGA-GT-CCTGAGTTGTCGCTC--CGGA-TA-----TGACACCGAGCGGGGGGGCGGG-----------------------TGGGTG i dasNov2.scaffold_104361 C 0 I 8 s monDom5.chr2 304273163 199 - 541556283 CCCTTGAGGATCC---CATGTCTCCACAATGATGGATTCTGATTTAATAGCTTCTAAAAACAAGTAGAGGAGAGAAAATGA-GTGATGAATATGTCGAGGAAACAGACTCTTTCTTAGATGATTTATGGGGAATGAGTGAAATGTTGCTCA-CTAA-TA-----CATCCCAGGGTAAGGGGGTCAG-----GGTTTTCCTTTAAGAAATTGGAAG i monDom5.chr2 I 2718 C 0 s eriEur1.scaffold_215579 4033 164 - 5644 ------------------------CCTCATGATGGATTCCAGCTCAGCAGCTTTTACAAACAAGCAGACAAGGCCTAG-GGCCTGATGGATG-GTGCTGGCAG--TGCCTGTGTGGGCATAATTGATGGGAAGT-CATAGGT-----CCCATGGGG-GTGGGagcatccctgtaggtgggagtaaGTAAATGG----------------TGGATG i eriEur1.scaffold_215579 N 0 N 0 e loxAfr3.scaffold_49 14287518 1507 - 17734757 I a score=-67059.000000 s hg19.chr17_gl000204_random 12016 96 + 81310 ------GAT---GAGTTTGGATAGTGTAAG-----------------------------C-TGCACTACCACGGCAG--------GCTCACACT-CAGCCCCATGG---CGTGTGCGGCAGCTCCCGCTCCCATCTCATCACGGCAG s panTro2.chr17 79188139 60 + 83384210 ------GAT---GAGTTTGGATAGCGTAAG-----------------------------C-TGCACTACCACGGCAG--------GCTCACACT-CAGCCCCATGG---CG------------------------------------ i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69573148 60 + 73212453 ------GAT---GAGTTTGGATAGTGTAAG-----------------------------C-TGCACTACCATGGCAG--------GCTCACACT-CAGCCCCACGG---CG------------------------------------ i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74738598 96 + 78773432 ------GAT---GAGTTTGGATAGTGTAAG-----------------------------C-TGCACTACCACGGCAG--------GCTCACTCT-CAACCCCACGG---CGTGCGCGGCAGCCCCAGCTCCCATCTGACCACGGCAG i rheMac2.chr16 C 0 C 0 s mm9.chr11 118669079 58 + 121843856 ------GAT---GTCTTCCAACGCTGAGCA-----------------------------CTTGTAGGGTGTCGGCAG---------------CT-CAACCACA-AA---CATGTAT------------------------------- i mm9.chr11 C 0 C 0 s bosTau4.chr19 10753322 108 - 65312493 ------GAT---GAGTTCTAATGTTGTGGGGTGGGGAACAACAGCCCAAAC--TGCCAGC-TTCACAGCCACAACAC--------ACCCACACC-TGACCCAA-GA---TGAGTGTGGCAGCCCCTGC-TTCGG------------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57941091 43 - 61308211 ------------------CCCTGGCCCAGC--------------CCAGAGCCGCGCTTCT-TGGGCAA----GA-----------------------------------AGAGTG-------------------------------- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59355946 110 - 64418924 ------GAT---GGGTTCCCGTGTTGAAGC---GGGGACAAC-GCCCGACATGTGCCGGC-TGCGCAGTTACGACGC--------TCTCACTGT-CTGCCCCA-ATGCCAGAGTGTGGCAGCCCCTGCTTTCGG------------- i canFam2.chr9 C 0 C 0 s dasNov2.scaffold_104361 4631 103 + 5925 ------GACACAGGGGCTGTCCAGACCAAA-----------------------------G-TCCACGCCTACGGCAGTACCCCACGCTCACACC-TAGCCCCAACA---CAGGCGCGGGGGGCCTGGCTCCAGCCACACACTG---- i dasNov2.scaffold_104361 I 8 C 0 s monDom5.chr2 304273362 102 - 541556283 GTAAATAAC---TAGATTGAAGAGTGTAAG--------------CACTAAC--------C-TACACAACTAGAACAA--------ACTTACATGACAAGCTTA------TGTGAAAGCCTCCCCCAGTTCCTATCACATGAC----- i monDom5.chr2 C 0 I 736 e cavPor3.scaffold_76 4297352 27 + 7991924 I e loxAfr3.scaffold_49 14287518 1507 - 17734757 I a score=-101045.000000 s hg19.chr17_gl000204_random 12112 60 + 81310 GCTCACACTCAGCCCCA-----------TGG------------------------------------------------------------------------------------CATGCGCGGCAGC-ACCCGC---TCCCATCTCATGCTGT----------------------------------CTGCA s panTro2.chr17 79188199 38 + 83384210 ---------------------------------------------------------------------------------------------------------------------TGCGCGGCAGC-ACCCGC---TCCCATCTCATGCTGT----------------------------------CTGTA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69573208 38 + 73212453 ---------------------------------------------------------------------------------------------------------------------TGCGCGGCAGC-CCCCGC---TCCTATCTCATGCTGT----------------------------------CTGCA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74738694 60 + 78773432 GCTCACTCTCAACCCCA-----------CGG------------------------------------------------------------------------------------GGTGCGCTGCAGC-CTCCCC---TCCTGTCTCAGGCTGT----------------------------------CTGCA i rheMac2.chr16 C 0 C 0 s mm9.chr11 118669137 34 + 121843856 GCTC-------------------------------------------------------------------------------------------------------------------CAC-------CCCAGC---CCCAGTCGCCTACAAG----------------------------------AGGCA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4297379 54 + 7991924 GCTCACACAGAGCCCC-------------GG------------------------------------------------------------------------------------CATGCACTA-----CCCTGC---TCCAGTCCCTGCTGTG----------------------------------CTGCG i cavPor3.scaffold_76 I 27 C 0 s bosTau4.chr19 10753430 109 - 65312493 TCACACACTGTCCCCTG-----------TGC------------------------------------------------------TGGAAAAGGTGCCACTGGCCCAACCCAAAGCCACTCTTTCTTG-GATGAGAAAAGTAAACCCTGGTGTG-----------------GACTCTTCCCTGCG-CCCTGCA i bosTau4.chr19 C 0 I 2 s equCab2.chr11 57941134 51 - 61308211 ------AAACTTCCCCT-----------GAC---------------------------------------------------------------------------------------CCCCTGCAGG-TGTGGG---AGCAGCCTCTGAGGGG----------------------------------CCAGA i equCab2.chr11 C 0 I 2 s canFam2.chr9 59356056 140 - 64418924 GTGCACACATGTCCCCG-----------GACGTGGTCATTTTTAAGACGAGCTTGTGGCCCAGCCCAAAGCCAGTCTTGAGCAGAAGGCTGAACTCCGGCTGCACTTCCT-----CCTCCCCTGCAGGCTTCAGG---AGCACCCTCTGAGGTG----------------------------------CAGGA i canFam2.chr9 C 0 I 2 s dasNov2.scaffold_104361 4734 105 + 5925 TCCCATAAGTGGCCACATCCAAAGCAGCTGG------------------------------------------------------------------------------------CAAGTGCCTCTGG-CCCAGT---CCAAAGCTCTTCCTCTTGGGTCTCTCCAGAGGAGACATTCTCCTTCGCCCCTGCA i dasNov2.scaffold_104361 C 0 I 31 e monDom5.chr2 304273464 736 - 541556283 I e loxAfr3.scaffold_49 14287518 1507 - 17734757 I a score=161438.000000 s hg19.chr17_gl000204_random 12172 133 + 81310 T-CAGGGC-A----GAAGACTTTGTTTATCT-------------CTCAGCTCCAGAACAAAGA--TGCTCCCCCAT---CCCCAAAAACATCTAGAGAAGAGACAACCGG-CCACATTCCTTGGCTCCTCTGTGTGACCCCAACAACGAACAGCAATG--------- s dasNov2.scaffold_104361 4870 133 + 5925 T-CAGGGCCA----GAAGGCTTTGCTGACCT-------------GTCAGCTCCAGAATGAGTG--TGCTTCCACCACCCACCAAAACACG-CGGGAGAAGCGACAACCGG-AGGCCGCGTCCGCCTCACCCGAGTGACCCAGACG---CACAGCTCTG--------- i dasNov2.scaffold_104361 I 31 C 0 s loxAfr3.scaffold_49 14289025 116 - 17734757 T-CAGGAC------AGAGGCTTTGT--------------------TCACTCCTTGAACAAAGG--TGCTCTCTAGA---ACCTGGACATATCTGGAGGAGGGACAGCCAGCAGGTC----CTGTCTCATCTGAGCGACCT-GATG---CTCAGCAC----------- i loxAfr3.scaffold_49 I 1507 C 0 s canFam2.chr9 59356198 137 - 64418924 T-CAGAGC-A----GAAGACCTTGTGTGTCT-------------CTCAGCTCCAGGACAAAGG--TGGCCCCCCCG---CCCCAGAAACACCTAGAGAAGGAACACCCGG-CGGTACCCTCTGCTTCATC-TAGTGACCCTGACA---CACAGC-TCAGTGGTTTGG i canFam2.chr9 I 2 C 0 s equCab2.chr11 57941187 125 - 61308211 T-CAGAGC-A----GAAGACCT----CCTCT-------------CTCTGCTCCAGAACAAAGG--CGCTCCCCGGC---CCTCAAAAACATCTGGAGAAGGAACAGCCAG-CTGTGCCCTCTGCTTCATCAGAGTGACCCTGACG---CACAGC-CCA--------- i equCab2.chr11 I 2 C 0 s bosTau4.chr19 10753541 142 - 65312493 T-TTTAGG-A----GCACCTCTCAAGAGGCTAGAGGTCAGACTGTTCATCTCCAGAACAAAGA--TGTTCCCCCAC---CCCAGAAAACATTTGGAGAAGAAACAGCCTG-CTGTGCCCTCTG-TTCGTATGAGCAACCGTAACA---CACAGCACCA--------- i bosTau4.chr19 I 2 C 0 s cavPor3.scaffold_76 4297433 135 + 7991924 CACACGGC-C-----AAAACTTGGTTCACCT-------------CTGGGCTCCAGGACAGTGTGCTTCTGCCACTC---ACGCAAACACATTTGGGGAAGGGACATCCAG-CTGTGCCTGCTGGCTCTGCTAAGTGACCCCAACAGTGCAGAGAGACG--------- i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118669171 138 + 121843856 CAGAAGGC-AGGTGGAAGACTTGACTTTCCC-------------TTCGGCTCCTAAAC-GTGAGCAGCT-CTCCCC---TCTCAGAAACATCTGGAGAAGGAACAGCTGG-TCACAGCCTCTGGTTCCTCTGAGTGACACCCGCAATGGATACAAATA--------- i mm9.chr11 C 0 C 0 s rheMac2.chr16 74738754 131 + 78773432 T-CAGGGC-A----GAAGACTTTGTTTATCT-------------CTCAGCTCCAGAACAAAG----GCGCACCCGT---CCCCAAAAACATCTGGAGAAGAGACAACTGA-CCACACTCCTTGGCTCCTCTGAGTGACCCCAACAATGGACAGCAACG--------- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69573246 129 + 73212453 T-CAGGGC-A----GAAGAC----TTTCTCT-------------CTCAGCTCCAGAACAAAGA--TGCTCCCCCAT---CCCCAAAAACATCTAGAGAAGAGACAAAGGG-CCACATTCCTTGGCTCCACTGAGTGACCCCAACAACGAACAGCAATG--------- i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79188237 133 + 83384210 T-CAGGGC-A----GAAGACTTTGTTTATCT-------------CTCAGCTCCAGAACAAAGA--TGCTCCCCCAT---CCCCAAAAACATCTAGAGAAGAGACAACCGG-CCACATTCCTTGGCTCCTCTGAGTGACCCCAACAACGAACAGCAATG--------- i panTro2.chr17 C 0 C 0 e monDom5.chr2 304273464 736 - 541556283 I a score=500205.000000 s hg19.chr17_gl000204_random 12305 309 + 81310 TGGTTTAGGAAAATTCAGGTTATCCCAT------------GAGAGTGGTGA-----------AGGGGAGGGGAAAGGAAGGGAAGGGTCAGGGTTGGAGGAGCAGATGA-----------CCCTCC-------------TCTGGAG-TTTTTGCTCAGGC-----------CCA-----------TCTCTTCCCTGTG----GACCTGAAAGACCCATCTGCTCCAGGCCTCAGCCACTGCATGTAACAGACAAATCTCGTTTTGCAG------------CATCCATG------TTTTTAATAAGGACTTAGAATTTACTATACAGTAAAACCCAAATTGAATCCATAGTTAAAGGGATGAGCTTTAAAACGGGATCTAATTGACAGGACCCTTTCCGAGG s panTro2.chr17 79188370 321 + 83384210 TGATTTAGGAAAATTCAGGTTATCCCAT------------GAGAGTGGCGA-----------AGGGGAGGGGAAAGGAAGGGAAGGGTTAGGGTTGGAGGAGCAGATGA-----------CCCTCC-------------TCTGGAG-TTTTTGCTCAGGC-----------CCG-----------TCTCTTCCCTGTG----GACCTGAAAGACCCATCTGCTCCAGGCCTCAGCCACTGCGTTTAACAGACAAATCTCGTTTTGCAGCAGATTAATTTCCATCCATG------TTTTTAATAAGGACTTAGAATTTACTATACAGTAAAACCCAAATTGAATCCATATTTAAAGGGATGAGCTTTAAAACGGGATCTAATTGACAGGACCCTTTCCAAGG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69573375 293 + 73212453 TGGTTTAGGAAAATTCAGGTTATCCCAT------------GAGAGTGGCGA-----------AGGGGAGGGGAAAGGAAGGGAAGAGTCAGGGTTGGAGGAGCAGATGA-----------CCCTCC-------------TCTGGAG-TTTTTGCTC------------------------------------------------------AGACCCATCTGCCCCAGGCCTCAGCCTCTGCATGTAACAGACAAATCTTGTTTTGCAGCAGATTAATTTCCATCCATG------TTTTTAATAAGGACTTAGAATTTACTGTACAGTAAAACCCAAATTGAATCCATATTTAAAGGGATGAGCTTTAAAATGGGATCTAATTGACGGGACCCTTTCCAAGG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74738885 321 + 78773432 TGGTTTAGGAAAATTCCTATTACCCCAT------------GAGAATGGCGA-----------AGGCGGGGGGGAAGGAAGGGAAGGGTCAGGGTTGGAGGAGCAGATGA-----------CCCTCC-------------TCTGGAG-CTTTTGCTCAGGT-----------CCA-----------TCTCTTCCCTGTG----GACCTGAAAGACCCATCTGCCCCAGGCCTCAGCCACTGCATGTAACAGACAAATCTCGTTTTGCAGCAGATTAATTTCCATCCATG------TTTTTAATAAGGACTTAGAATTTACTATACGGTAAAACCCAAACTGAATCCATATTTAAAGGGATGAGCTTTAAAATGGGATCTAATTGACGGGATCCTTTCCAAGG i rheMac2.chr16 C 0 C 0 s mm9.chr11 118669309 255 + 121843856 TGGCT---------------------------------------------------------------GAACAGCAGAAGGGACCGGGCAAGCTGGTA-----------------------TGTCC-------------CCTGTAC-CAGTGGGTGACAG-----------ACG-----------TCTCCTTCCAGCA----TGTCTGATGG--ACTGCTGCCCGCAGACT-GGCCACTACA----------ACACCTCATTTTGCAGCAGATTAATGTCCACCCATG------TTTTTAATGAAGTCTTGGAATTGGCTGCACTGTTAGATCTAAATTGACTCCATATTGAAAGAGGTGAGCTTTTAAGTAAGACCTAA-GGACAAGGTCCTGCCTAAAG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4297568 274 + 7991924 TAGTTTGGGAGATT-----CTGTCTCA-------------GAGAGTGACAG-----------GGGCAAGTGAAGAGGAAGGGAGGGGACAACACGCGA-----------------------CCTCCCTGTGGCTTTGGTCCTGGATACTGCGGGTGGAGG-----------GCA-----------TCTCTTCCTGGAA----AGCTACAGAG--CCATCTGCCCGGGGAC----------------------AAATCTCATTCTGTAGCAGACTAATTTCCACCCGTG------TTTTTAATAAGGACTTGGAATTTACTATA---------------TGAGCGCATATGTGAAGGGATGAGCTTTAAAACGGGACCAAACGGATGGGGCCCTTTCT---- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10753683 330 - 65312493 GGCTTTGGAAAGAGTCAGACTGTCCAAT------------GAGAGTGAAGACA---------GGGAAGGGAGAGAGAAAGGGGAGGTTCACGGACAGAAGAGCAGGTGA-----------CGCCCA-------------GCGAGTG-TCTC--TTCCTGATGCTGACAGGTGGG-----------TTCCCTCCCCGTT----GATCTGGAGGACCCATCTGCCCCA-GCCTGTGCCCCTGCATGTAAGAGACAAATCTCACTTTGCGGCAGATTAATATCCACCCATG------TTTTTAATAAGGACTCAGAATTTACTATACAGTAAAACCCAAATCAAATCCTTATTTAAAA-GATGAGCCTCTGGGTGGGTTATAATTTATGGGACACTTTCCAAGG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57941312 331 - 61308211 TGGCATGGGCGGATTCTGACTGTTCAGT------------GAGAGTGGTGACC---------GGGAGGGGAGAGAGGAAAGGGAGGGTCGGGGACAGAAGAGCAGGTTG-----------CGCCCG-------------CCGTGAT-CTTTTGTCCCGCGAGCTGGCAGG-CGG-----------CCCCTTCCCCGTG----GATCTGAAGCACCGATCTGCCCCAGGCCTCCGCCACCACATGTGAGAGACAAATCTCG-TTTGCAACAGATTAATTTCCACCCACG------TTTTTAATAAGGACTCAGAATTTACTATACGGTAAAATGCAAATCGAACCCGTATTTAAGG-GATGAGCTTTAAAACGGGATCTAATTCATGGCACCCTTTCCAAGG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59356335 329 - 64418924 TGGCTTGGGAGGACTCAGGCAGTCAGGT------------GAGAATGGCAA------------GGGGGAGGGAGGGGACGGGGAGGGGCCGGGGCCGAAGAGCCAA-GA-----------CGCCCA-------------CCATGAG-TTTT--TCCAGGGAACCAAGCGA-GTG-----------TCCCTCCCCGGCGACCCGCACCGCAGCACTGATCCATCCCAGGTCTCCATCACCACAC-CAAGAGACAAATCTCATTTTGTAGCAGATTAATTTCCGTCCATG------TTTTTATTAGGGACTCAGAGTTTACTATACAGTAAAATCCAAATTGAATCCATATTTAAAG-GATAAGCCTTAAAATGGGATGTGATTTATGGGACTCTTTCCAAGG i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14289141 302 - 17734757 ---CCTGGGAGAATCCCAGCCATCCCAGT---CTGGT---GAGAGTGGAGT-----------GGAGGCGAGGAGGGGGCGG-------TCGGGTTGGAAGAGCAGGTGA-----------CGCCCA---------------TGACA-CGGCTGTGTG--------------CCATTCACAGTCCCCCCCTGCCCACAG----ACCCGAAAGGACCCATCCACCCC---------------------------AGGATCAACCACACAACAGACCAGCCTCGTTCTGCAGCAGTGCTGTTAATAAGCACACAGAATTCACTGTACGGTAAAATCTCAGCCGAACCCGCGTTTGAAGGGATGAGCTTTAATGTGGGAGCTAATTTATGGCCCCCTCTGAAAGG i loxAfr3.scaffold_49 C 0 I 28 s dasNov2.scaffold_104361 5003 264 + 5925 AGGTCTGGGAGAATTCCGGCTGCGCTGG------------GAGGCTGGTGA-----------GGGGGCAGGGAGA-------------------TGGAAGAGTGGGGGA-----------CGCCCG-----------AGGCTGGCG-TGGCTCTTCC--------------CCA-----------CCCCTGACCTCAG----CCTCTGCAGA----------TAC---------------------------AAATCCCACCTTGCAGCAGGTTCATCTCCATCCACA------TTTCTAAAAAGTGTGCAAAATTGACTCTACAGTAAAATCTACACCGAATCCGTATTGAAAAGGCTGCGCTTTGGAACAGGATCTGATTTATGGGAGCCTTTCCAAGG i dasNov2.scaffold_104361 C 0 C 0 s monDom5.chr2 304274200 358 - 541556283 TGTTTTAGGAACATCTGACTCCCCCTATTGAATTAGTTAAGAAAATGAAATCAGAGGTAGAGGTGGGATAAGAGAAAAGGGGAAAGATCAGAGCTCCAAAAATGAATGGGGAACACTATTTTTTTG-------------GTCAGAG-TTCTTGATGAGAATGC--------CTA-----------GCTCTTCCCTGTC----TAAATGATTGATGAATCTAGCCTAGGCTTCAGCTACTGGAAGTAAGAGACAAATCTTGTTTTACAGCAGATTAATCTCTATTCATG------TTTTTAATAAGCACTCGGAATTTACTATACAGTAAAATTTAAATTGAATCCATATTTAAAAGGACGGGCCTTAAAATGGGGCCTAATTTATGGGGCTTTTTCTGAGG i monDom5.chr2 I 736 C 0 a score=-17348.000000 s hg19.chr17_gl000204_random 12614 59 + 81310 CAGAGGCAATGA------------------ACCAGGGCTGAG---------GCAATGTCCTAGGAGGA-------------------AACTGCTTCCTCC------------------------------CCACA s panTro2.chr17 79188691 59 + 83384210 CAGAGGCAATGA------------------ACCAGGGCTGAG---------GCAATGTCCTAGGAGGA-------------------AACTGCTTCCTCC------------------------------CCACA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69573668 59 + 73212453 CAGAGGCAATGA------------------ACCAGGGCTGAG---------GCAATGTCCTAGAAGGA-------------------AACTGCTTCCTCC------------------------------ACACA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74739206 59 + 78773432 CAGAGGAAATGA------------------ACCGGGGCTGAG---------GCAATGTCCTAGGCGGA-------------------AACGGCTTCCTCC------------------------------CCACT i rheMac2.chr16 C 0 C 0 s mm9.chr11 118669564 55 + 121843856 -GCAAGAAATGC------------------A-GAGGGCAGGG---------TCAAAGGCAG--GAGGA-------------------AATCATTTCTTCT------------------------------CTCAT i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4297842 43 + 7991924 ----------------------------------GGTCCAGG---------TGGGTGATTGCCCAGGA-------------------ATCCGCTGCCTCC------------------------------CTGCA i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10754013 75 - 65312493 CAGAAGAAGGGA------------------GCCAGGGATGGA---------ACGATGGCTAGGAAGGA-------------------AACAGCTTTCCCTCCGTGC--------------CCTGGGCTGACCCTT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57941643 58 - 61308211 CACAGGAAGTCA------------------ACTGGCAGTGGG---------GCAACAGCTGAGGAGGA-------------------AACAGCGTCCTC-------------------------------CCCTC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59356664 118 - 64418924 CCGAGGAGGGGAGTGCCCCCAGGCCCCCAGGCCCCCAGTGAGGACGATTCCGCAGCGACTGGACTGGACCGGGAGTTAGGCTGAATGGTCTGCATGCCCAAGGGG-----------------TGGGACAGCCCCG i canFam2.chr9 C 0 C 0 s dasNov2.scaffold_104361 5267 85 + 5925 CAGGGGAAGGAA----------------------AGGTGAGA---------AGGATCGCCTGGCTGGA-------------------AACAGCTTCCTGGACGCCCTCCCTGGACCCTTTCCTGTCCCACCTGAC i dasNov2.scaffold_104361 C 0 C 0 s monDom5.chr2 304274558 56 - 541556283 -AGGAGAAAGAT------------------ATGAAAAGGGGA---------GGGACAGATGGG--GGA-------------------AAATGCTCTTTCT------------------------------CAGCA i monDom5.chr2 C 0 I 10220 e loxAfr3.scaffold_49 14289443 28 - 17734757 I a score=-1038.000000 s hg19.chr17_gl000204_random 12673 188 + 81310 CTC-------------TCCTTTG------------AAGCAAGGACTCGCCTGCAGTGATGGGGAGTCTCGGTCGAAGGGCT-CCTTGCCAAGGCCATTCCTGAATCA-----------GAAAG---GCCAGCCCGCCTCACTGGG-----GCAAAAGCTCC-TGCAGGCT---TTTCCCTGCCCGGGTTTC-TCCATCACTGTTCTCCAAGTCCCTCTTAGGA---AGCCCCTTCC-----------TCTAG s panTro2.chr17 79188750 188 + 83384210 CTC-------------TCCTTTG------------AAGCAAGGACTCGCCTGCAGTGATGGGGAGTCTCAGTCGAAGGCCT-CCTTGCCAAGGCCATTCCTGAATCA-----------GAAAG---GCCAGCCCACCTCACTGGG-----GCAAAAGCTCC-TGCAGGCT---TTTCCCTGCCCGGGTTTC-TCCATCACTGTTCTCCAAGTCCCTCTTAGGA---AGCCCCTTCC-----------TCTAG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69573727 189 + 73212453 CTG-------------TCCTATG------------AAGCAAGGACTCGCCTGCAGCGATGGGGAGTCTCGCTGGAAGGCCTCCCTTGCCAAGGCCATTCCTGAATCA-----------GAAAG---GCCAGCCCGCCTCACTGGG-----GCAAAAGCTCC-TGCAGGCT---TTTCCCTGCCCGGGTTTC-TCCATTGCTGATCTCCAAGTCCATCTTAGGA---AGCCCCTTCC-----------TCTAG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74739265 188 + 78773432 CTC-------------TCCTTTG------------AAGCAAGGATTCGCCTGCAGTGATGGGGAGTCCCGCTCAAAGGCCT-CCTTGCCAAGGCCATTCCTGAATCA-----------GAAAG---GCCAGCCCGCCTCACTGGG-----GCAAAAGCTCT-TGCAGGCT---TTTCCCTCCCCGGGTTTC-TCCATCACTAATTTCCAAGTCCCTCTTAGGA---AGCCCCTTCC-----------TCTAG i rheMac2.chr16 C 0 C 0 s mm9.chr11 118669619 160 + 121843856 CAT-------------CCCTTG--------------AGCAAGGACACATTGACATTAGTAGAGA-TCACACTAAGTGAGCTACAATGTCAAAGCCATTCCGGGAACT-----------GTGA----CCCAGCTCTGTCCA---GG-----CTGTAGGCTAC-AGCAGGCT---CTTC-----------TGA-CC-----------TCAAAACCACTCTTAGGAGAAGTT--CTTCT-----------CCAA- i mm9.chr11 C 0 I 269 s cavPor3.scaffold_76 4297885 174 + 7991924 AAT-------------CCCTTGG------------AACCCAAGATGCTTCTGCA-GGGCTGGCA-CCACACTACATGGCCTTCAAAGT-GAGGACATTCCTGAACCA-----------GCGC----CCCAGCCCCACCCA---GG--TTCCCATGGGCTTC--TCAGGCT---CTGC-----------TTG-TCCACCGGAG-TGTGGAAGCCACTGGCAGGAGTGGGCCACTGCC-----------CCTG- i cavPor3.scaffold_76 C 0 I 1 s bosTau4.chr19 10754088 180 - 65312493 TTTTGCCCCTACTTGACCCTGAG--------GATCCATCAAGGACACATCTGCAGTGACCAGGAGATACGCTCAACAGTCC------CACACGCCACC---GGGAAT-----------GAAA------CAGC-CTGCTCACCCGA-----GCAGA----------AGGCT---CTTCCTTGT---AATCTC-TCCATCACTGATCCCGGAGCACCACT-GGGG---AGCACTTTCT-----------CCAGG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57941701 159 - 61308211 CTC-------------CTCTGAGCCCTCT--GCCCCAGCAAGGACACCTCTGCAGTGAC--------------------------------AGGGAGCTAAGGGAAC-----------GGAA------CAGCCCCACTCACCGGA-----GCAGAAGCTCC-TGCAGGCT---TCCCCCTGC---AGCTTC-TCCCTCACTGGTCCCCAAGCTCTCCT--GGA---AGCACTTCCT-----------CCCAG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59356782 207 - 64418924 CTC-------------ACCCGAGAA------GCTCCAGCAGATGCTCGCCTACTCTGACC-----TTGCCCGTGACTGACC------CTGAAGCGCTCTGAGGAGGCACCTGCCCGTTGACA------CGCCACCAC-CACAGAAGGTGTGCAGGAGCACCTTACAGCCTGGCTCTCTCCCC---GGCTTCACCCCCCTCCCGACCCCCATCCCTGGC--TGG---CTCTCCTCCTGCCAGCAGAGGCCCAG i canFam2.chr9 C 0 C 0 s dasNov2.scaffold_104361 5352 162 + 5925 CTC-------------CCCCGCCGCGCCCAGGGCTCCGCGATGACAATCCTGCAGCGACGGGG--CAGCATTGATTGACCCTCTGTGCCTGCG--------GGAGTC-----------GAACGCCCCCCCTCACCCCCCACTGGG-----ACAAAGGTGCC-TGCAGCCT---GGTCCCTGCCCAGGTTTC-TCCGTTGCTGGCCT---------------------------------------------- i dasNov2.scaffold_104361 C 0 C 0 e monDom5.chr2 304274614 10220 - 541556283 I e loxAfr3.scaffold_49 14289443 28 - 17734757 I a score=3006.000000 s hg19.chr17_gl000204_random 12861 32 + 81310 TCACATTCCT--------------------TTGG-------------------------GCCATGGA----------------CGGCATCCAC s panTro2.chr17 79188938 32 + 83384210 TCACATTCCT--------------------TTGG-------------------------GCCATGGA----------------CGGCATCCAC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69573916 32 + 73212453 TCACATTCCT--------------------TTGG-------------------------GCCATGGA----------------CGGCATCCAC i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74739453 32 + 78773432 TCACATTCCT--------------------TTGG-------------------------GCCATCGA----------------TGGCATCCAC i rheMac2.chr16 C 0 C 0 s bosTau4.chr19 10754268 73 - 65312493 AGACCTTCCA--------------------CTGTGAAAGGGCATGGAAGATGTATATTTGCAGGGGCTCCATAGGCCCTATGTTGGCATCTGC i bosTau4.chr19 C 0 I 167 s equCab2.chr11 57941860 38 - 61308211 GGACGTTCCA--------------------CTGCGAGTGG-------------------GCAGCGGA----------------AGGCATACAC i equCab2.chr11 C 0 I 232 s canFam2.chr9 59356989 65 - 64418924 GTGCGCTTCACCCGGGAAGATGATGAAATCCCGGGGGAGGGC------------CCTCCGCAGGGGA----------------AGGGACTGGC i canFam2.chr9 C 0 I 51 s dasNov2.scaffold_104361 5514 23 + 5925 ------------------------------TTGGG------------------------ACAATGGA----------------TGGCATCCCC i dasNov2.scaffold_104361 C 0 C 0 e monDom5.chr2 304274614 10220 - 541556283 I e cavPor3.scaffold_76 4298059 1 + 7991924 I e mm9.chr11 118669779 269 + 121843856 I e loxAfr3.scaffold_49 14289443 28 - 17734757 I a score=-11340.000000 s hg19.chr17_gl000204_random 12893 20 + 81310 ATGCCAGA-GCTCTGGTAGCC- s panTro2.chr17 79188970 20 + 83384210 ATGCCAGA-GCTCTGGTAGCC- i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69573948 20 + 73212453 ATGCCAGA-GCTCTGGTAGCC- i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74739485 20 + 78773432 ATGCCAGA-GCTCTGGTAGCC- i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4298060 15 + 7991924 --GCTAG----TTGGGTATCT- i cavPor3.scaffold_76 I 1 C 0 s dasNov2.scaffold_104361 5537 20 + 5925 -CGGCAGCAGTTCTGG-AACCC i dasNov2.scaffold_104361 C 0 N 0 s canFam2.chr9 59357105 5 - 64418924 ----------------GTGCC- i canFam2.chr9 I 51 C 0 s equCab2.chr11 57942130 5 - 61308211 ----------------GCACC- i equCab2.chr11 I 232 C 0 s bosTau4.chr19 10754508 5 - 65312493 ----------------ACACC- i bosTau4.chr19 I 167 C 0 e monDom5.chr2 304274614 10220 - 541556283 I e mm9.chr11 118669779 269 + 121843856 I e loxAfr3.scaffold_49 14289443 28 - 17734757 I a score=73261.000000 s hg19.chr17_gl000204_random 12913 96 + 81310 CAAG--GGGTGGTTTTGGCGGCCCCTTCTCTGAAGCCCATGTCCAGGCTGCAGGGAGAACC-CAGGA---------GC-----TCGCGGGGCAGGAGGGTGTCTA----CA--------------GGCACA s panTro2.chr17 79188990 96 + 83384210 CAAG--GGGTGGTTTTGGCGGCCCCTTCTCTGAAGCCCATGTCCAGGCTGCAGGGAGAACC-CAGGA---------GC-----TCACGGGGCAGGAGGGTGTCTG----CA--------------GGCACA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69573968 96 + 73212453 CAAG--GAGTGGTTTTGGCGGCCCCTTCTCCGAAGCCCATGTCCAGGCCGCAGGGAGAACC-CAGGA---------GC-----TGGCAGGGAAGGAAGATGTCTG----CA--------------GGCACA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74739505 95 + 78773432 CAAA--GGG-GGTTTTGGCAGCCCCTTCTCTGAAGCCCATGTCCAGGCCGCAGGGATAACC-CAGGA---------GC-----ATGCGGAGCAGGAGGGTGTCTG----CA--------------GGCACA i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4298075 98 + 7991924 GCAGCAGGGTGGGTTGGGCAGCAC--TCTCTGGAGCCCATGTTGAGTTCACAAGAAGAGCT---GGG---------GC-----ACAGAGTGTGTGCAGAGGTCAGGAGCCT--------------GGCACA i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10754513 113 - 65312493 CGGA--TAGCAGCTTTGGCAGCCC--CCTCTGAAGCCTGCATCTGGATCCCATTGAGAAAAGCAGGG---------GGCGCCACCATTGGGTGGCCGGGTGTCTG----CAGGGGGTCAGCAGCCAGCAC- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57942135 113 - 61308211 CAGA--GGGGGGGGTTGGCAGCCC--CCTCTGAAGCCTGCATCTGAGTCCCATCAAGAAGAGCAGG----------GTCACCACCGCTGGGTGGGAGGGCATCTG----CAGGGAGTCAGGAGCTGGCACA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59357110 118 - 64418924 CAGG--GGTGGGTCT----GGCTC--CCTCTGGAGCTCCTGTCTGGGTCCCCTGGAGAAGAGTGGGGGGCACCACCGCCGCCGCCACCGGGTGGGAGGGTGTCTG----CA-GGCCCCAGGAGCTGGCACG i canFam2.chr9 C 0 C 0 e monDom5.chr2 304274614 10220 - 541556283 I e mm9.chr11 118669779 269 + 121843856 I e loxAfr3.scaffold_49 14289443 28 - 17734757 I a score=72253.000000 s hg19.chr17_gl000204_random 13009 78 + 81310 CCTGACCTCAGATGTGTGTACATGGCCCTCTTCCTTC-AGACACCCGCCATCCACCATCCTGAAGGTGAATAAAAGACA- s panTro2.chr17 79189086 74 + 83384210 CCTGACCTCAGATGTCTGTACCTGGCCCTCTTCCTTC-AGACACCCACCACCCACCATCCTGAAGGTGAATAAA----A- i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69574064 78 + 73212453 CCTGACCTCAGATGCGCGTACCTGGCCCTTTTCCTTC-AGACACCCGCCACCCACCATCCTGAAGGTGAATAAAAGACA- i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74739600 78 + 78773432 CCTGACCTCAGATACGTGTCCCTGGCCCTCTTCCTTC-AGACACCCACCACCCACCCTCCTGAAGGTGAAAAAAAGACA- i rheMac2.chr16 C 0 C 0 s mm9.chr11 118670048 68 + 121843856 CCTGGATGCTCATCCATGTGCCTGAC-CTCATCCTTC-AGA-------GATCTACCATCCTAGAGCTA--CAAAAGACA- i mm9.chr11 I 269 C 0 s cavPor3.scaffold_76 4298173 71 + 7991924 CCGGCCCACTGAGCCACATGCCTGTC---TGTACTTC-TGA----CTGCATCTGCCCTCCCCAGGCAGATTAAGAGACA- i cavPor3.scaffold_76 C 0 I 531 s bosTau4.chr19 10754626 75 - 65312493 CCTGATCACTGATGGATGTGCTTGGCTCTCTCCCGTCAAGAGGCCCACC-CCCA----CCTGGAGGTGATCAGAAGGTGA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57942248 75 - 61308211 CGGGACCGCCGATCAATATGCCCGGCCCTCTCCCTTC-AGAGACCCGCCACCCG----CCTGAAGTTGATTAAAAGGCGA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59357228 74 - 64418924 CCCGACCACCGCTCAGGGTGCCTGG-CCTCCCTCTTC-TCAGACCCACCACCTG----CCCGAAGTGGATTGAAAGGCAA i canFam2.chr9 C 0 C 0 e monDom5.chr2 304274614 10220 - 541556283 I e loxAfr3.scaffold_49 14289443 28 - 17734757 I a score=286990.000000 s hg19.chr17_gl000204_random 13087 395 + 81310 GGCAGAGATTCAAAGCCACACGCAGG--CCTCAGACTG--CATTGCTCCTTGCTCTGAGGGGCTTCCT-----CTCAGAGGGGCTTCCTTCTCTCC--CCTTGACCTCACCCTTTTA---------------------GAAAAGGAAGA-CTCTGAAAGGCAGATTCC-TCACTTCACAAT--TCAGAGCACACCTTTGGA--ATCAACAAGGGGCTGGACAGTGAACACACCGAG---GGAAGCAGCT-CAGGTCC-AAAAGAGCTTGTGGGGTGACCCCACCAA-CCCTGGACTTCCCAGACGCTCCCTCGG-GGGTGGGCTGGTC-TTGTACTTTCACTGTTGATGACCCCGAGGATTTACCTATTTG-GGGGACACAGGTTCTCAGACCCACAGAAAGGTGAG---GCTGGGCCCCGCAACCTCCTTCTTGGAGGCAGCAG s panTro2.chr17 79189160 395 + 83384210 GGCAGAGATTCAAAGCCACATGCAGG--CCTCAGACCG--CATTGCTCCTTGCTCAGAGGGGCTTCCT-----CTCAGAGGGGCTTCCTTCTCTCC--CCTTGACCTCACCCTTTTA---------------------GAAAAGGAAGA-CTCTGAAAGGCAGATTCC-TCACTTCACAAT--TCAGAGTACACCTTTGGA--ATCAACAAGGGGCTGGACAGTGAACACACCGAG---GGAAGCAGCT-CAGGTCC-AAAAGAGCTTGTGGGGTGACCCCACCAA-CCCTGGACTTCCCAGACCCTCCCTCGG-GGGTGGGCTGGTC-TTGCACTTTCACTGTTGATGACCCCGAGGATTTACCTATTTG-GGGGACACAGGTTCTCAGACCCACAGAAAGGTGAG---GCTGGGCCTCGCAACCTCCTTCTTGGAGGCAGCAG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69574142 396 + 73212453 GGCAGAGATTCAAAGCCACACGCAGG--CCTCAGACCG--CATTGCTCCTTGCTCAGAGGGGCTTCCT-----CTCAGAGGGGCTTCCTTCTCTCC--CCTTGACCTCATCCTTTTA---------------------GCAAAGGAAGA-GTCCGAAATGCAGATTCC-TCACTTCACAAT--TCAGAGCACACCTTTGGA--ATCAACAAGGGGCTGGACAGTGAATACACCGAG---GGAAGCAGCT-CAGGTCC-AAAAGAGCTTGTGGGGTGACCCCACCAACCCCTGGACTTCCCAGACCCTCCCTCAG-GGGTGGGCTTGTC-TTGCGCTTTCATTGTTGATGACCCCGAGGATTTATCTATTTG-GGGGACACAGGTTCTCAGACCCACAGAAAGGTGAG---GCTGGGCCCTGCAACCTCCTTCTTGGAAGCAGCAG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74739678 380 + 78773432 GGCAGAGAGTCAAAGCCACACACAGG--CCTCAGACCT--CATTGCTTCTTG---------------------CTCAGAGGGGCTTCCTTCTCTCC--CCTTGACCTCACCCTTCTA---------------------GAAAAGGAAGA-CTCTGAAATGCAGATTCC-TCACTTCACAAT--TCAGAGCACACCTTTGGA--ATCAACAAGGGGCTGGACAGTGAACACACCGAG---GGAAGCAGCT-CAGGTCC-AAAAGAGCTTGTGGGGTGACCCCACCAGCCCCTGGACTTCCCAGACCCTCCCTCGG-GGGTGGGCTGGTC-TTGTGCTTTCACTGTTGATGACCCTAAGAATTTACCTATTTG-GGGGACATAGGTTCTCAGACCCACAGAAAGGTGAG---GCTGGGCCCTGCAACCTCCTTCTTGGAGGCAGCAG i rheMac2.chr16 C 0 C 0 s mm9.chr11 118670116 314 + 121843856 TGCAGA---------TCACACACAGGTACCTGGGA-----CATACCTCCCTTAGAAGATGGGCTCCCTGTGAGTCCAGA-------------CTCC--CCTTGCCTTCACCCCATGG---------------------GAAGGACAAGA-CTTAGA-----------------TACACAACTGTCAGAAC-TACTTTCTAA--ATGCAC-AGAGGTCAGAATGAGTGTGTGCTAGG---CAAAGACGCT--ACATGT-AAAGTCACTTGGG----------------CTCTGGACTTCCCAGG----TCCATGG-GGACCTGCTGGGCTTTGTGCTTTCAGTTTTAATGACCCCAAAGAGCTCCCT-TTCT-GGGGACACTGGCTCTCTGAAGCCCAGGAAGGTGAA---TGTGGGCC--------------------------- i mm9.chr11 C 0 I 1453 s bosTau4.chr19 10754701 395 - 65312493 CACAGAGCCCAGT-TCCCTCTGCAGG--CTTCAAGCTACTCAGGGCAAACAGGACGCCAGGGTCTTCC-----CTTTGA------TGCCTCTCTCC--CCTGGACTTCACCCCACTGG--------------------AAGGGAGAAGAGCCTTGATGCGC--ATTTC-CTGTTTCACAACT-GCA-AGCACACCTTCAGA--AGCCACGAAGGGGCAGAAAGGGCATGTGCGCCC---AGAAACAGCTCCAGGTGGAAAAGGAGCTTGCGTAGCCAGCCCGCCCAGCCCCAGACGGCTGGAC--CAGCCACCG-GGATCGGCCAGTC-TGGTGCTTTCAAGTTCCACAACACCAAACACTTACTGTTTCAGGAGAATACTGGTTCTCAAACCCACAGAAAGGCGAGGCAGCTGGGCCCTGCAACCTCCTTCACGGAGGCAGCAA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57942323 395 - 61308211 AACACAGAGCCGGCTTCCTCTGCAGG--CCTCAACCTGCTCAGGGCACCTGGGATGCCAGGGTCTTCC-----CTTGGA------TGCTTCTCTCC--CCCTGACTTCGCCCCGCTGC--------------------GAGGAAGAAGA-CTCTCAGATGC--GCATCGCTGCTGCACAATT-TCAGAGCGCGCCTTCGGC--ACGGGCAAGGGGCCGGGCGGTGAGAGAGAGCCTGACAGAAGCAGCTCCAGATTG-AAAGGTGTTTGCACAGCCA-CCCGCCAAGCCCCGAATTTCCCAGA--CCGCCATCA-GGACTGGCCAGTC-AGGTGCTTTGCGCTTTGACGATCTCGAGAATTTCTGTTTTTAGGAAGATGCTGGGTCTCAGACCCACAGAAAAGCGAG---GCTGGGCCCTGCCACCTCCTGCAAGGAGGTACCAA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59357302 358 - 64418924 AGTACAGCCCCGA-GTCCTCTGCAGC--CTTCAAACTGCTCGGCACAACTGGGACACCGGAGTCTTCC-----CCTGGT------GCCTTCTCTCCCGCCCTGACTTCCCCCTGTTGCCCCCCCCCCCCCGCCCCAGGGAGGAAGGAAA-CACGAACACCC--TCTGC-CCACTGCACAATT-TCGGAGGGAGACTTTGTTCAACCAACAAGGGGCTGGAAGGAG--------------AGAAGCAGCTGCAGGTGG-AAAGCAACTTGCACAGGC--CCCACTGAGCGCCGAATTCCCAGGA--CTGCCATCACCCACCAGCCAGTC-TGGTGCTTCTGGCTCCAACAACCCCCAAAACTGACCTTTTCA---------------CCTGA-----------------------GGCCCTGCAACCTCCTTCA----------GA i canFam2.chr9 C 0 C 0 e monDom5.chr2 304274614 10220 - 541556283 I e cavPor3.scaffold_76 4298244 531 + 7991924 I e loxAfr3.scaffold_49 14289443 28 - 17734757 I a score=12697.000000 s hg19.chr17_gl000204_random 13482 28 + 81310 GAAGTGGCATTTTC-AGAGGAGCATGGGA s rheMac2.chr16 74740058 28 + 78773432 GAAGTAGCATTTTC-AGAGGAGCACGGGA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69574538 28 + 73212453 GAAGTGGCATTTTC-AGAGGAGCATAGGA i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79189555 28 + 83384210 GAAGTGGCATTTTC-AGAGGAGCATGGGA i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 39296 28 + 85690 GAAGAAGCCTTTTCTAGAAGAAGA-GGGA i otoGar1.scaffold_94361.1-85690 N 0 C 0 s bosTau4.chr19 10755096 25 - 65312493 G---AATTATCTTC-CCAAGATTCATGGA i bosTau4.chr19 C 0 I 32 s equCab2.chr11 57942718 26 - 61308211 GGAAAAGCATCTTC-TGAGGGGTCACA-- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59357660 19 - 64418924 GGAAAAGCCTCTTC-CAAGA--------- i canFam2.chr9 C 0 C 0 e monDom5.chr2 304274614 10220 - 541556283 I e cavPor3.scaffold_76 4298244 531 + 7991924 I e mm9.chr11 118670430 1453 + 121843856 I e loxAfr3.scaffold_49 14289443 28 - 17734757 I a score=163084.000000 s hg19.chr17_gl000204_random 13510 168 + 81310 GATGGTGCTACCGTCACG-GCCTGCAGGATGTCTGTACGTCAGGGCCCT-CCCCTAGGGACAGAGCTGCACGCATCTT-CTTGGAACTAGGCGTCTGAGGTTCCAGAGACAGAGCATGATCTC--AGGGGGTCTCTCGTCCTGCACTGAGGCCAGCCCCAAACCTCGTGCCCT s rheMac2.chr16 74740086 168 + 78773432 GATGGTGCTACTGTCATG-GCCTGCAGGATGTCTGTACATCGGGGCTCT-CCCCTAGGGACAGAGCTGCAAGCATCTT-CTTGGAACTAGGCCTCTGAGGTTCCAGAGACAGAGCATGATGTC--AGGGGGTCGCTCGTCCTGCGCTGAGGCCAGCCCCAAACCTCGTGTCCA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69574566 168 + 73212453 GATGGTGCTACTGTCACA-GCCTGCAGGATGTCTGTACGTCAGGGCCCT-CCCCTAGGGACAGAGCTGCATGCATCTT-CTTGGAACTAGGCGTCTGAGGTTCCAGAGACAGAGCATGATCTC--AGGGGATCTCTCGTCCTGCACTAAGGCCAGCCCCAAACCTCGTGTCCA i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79189583 168 + 83384210 GACGGTGCTACCGTCACG-GCCTGCAGGATGTCTGTACGTCAGGGCCCT-CCCCTAGGGACAGAGCTGCACGCATCTT-CTTGGAACTAGGCGTCTGAGGTTCCAGAGACAGAGCATGATCTC--AGGGGGTCTCTCGTCCTGCACTGAGGCCAGCCCCAAACCTCGTGTCTT i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 39324 168 + 85690 GATGATGCCACTGTCACC-TGCGGCGGGATGTCTGCATTCCACCATTCT-CCCC--GCGACAGAGCTGTGTGCACCAG-CTTGGAACCAGGAGCCTCAGGCTCCAGGGATGGTGTAAGGCCCCTGCGAGGGCCACTTGTCCCACACTGAGGCCAGCTCCAAACTGTGTGTCCA i otoGar1.scaffold_94361.1-85690 C 0 C 0 s equCab2.chr11 57942744 166 - 61308211 GACGAT-CTTCTGTCACCTGCCTGCAGGACGTCAGCGCTCTGCTGCCCTTCCCCCGGGAGCAGAGCCACCTGCACGTG-TTTGGAAGCAGGAGCCTGAGATGTAGGGGATGGTGCCTGGCC-C----CGGGTCACTTGGCCTGCACCGAGGTCAGCCCCAAACCATGCATCCA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59357679 152 - 64418924 ------------GTCACCTGCCCGCAGGATGTCGGCGCTCTGCTG-----CCTCCAGGGACAGCACCACATATGCTTGCTTTAGAACCAGGGTCCTGAGATTTTGGGGACAGGGAATGACCGC----AGGGTGGCCTGGCCCACACGGAGGTCAGTCACAAGCCATACGTGCC i canFam2.chr9 C 0 I 2 e monDom5.chr2 304274614 10220 - 541556283 I e bosTau4.chr19 10755121 32 - 65312493 I e cavPor3.scaffold_76 4298244 531 + 7991924 I e mm9.chr11 118670430 1453 + 121843856 I e loxAfr3.scaffold_49 14289443 28 - 17734757 I a score=47026.000000 s hg19.chr17_gl000204_random 13678 104 + 81310 ATACTCA------TTTTCTCAGA--CAGCCTGCAAGCACAGTGATCTTGGCACAGAGCGACCTGACCAGGAGCCGTAGTGGATGGCACACCAGTGCTGCCTTCACAGCGACA s rheMac2.chr16 74740254 104 + 78773432 ATATACA------TTTTCTCAGA--CAGCCTGCAAGCACAGTGATCTTGGCACAGAGTGACCTGACCAAGAGCCGTGGCTGATGGCACAGCAGCGCTGCCTTCACCACGACA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69574734 104 + 73212453 ATACACA------TTTTCTCAGA--CAGCCCGCAAGCGCAGTGATCTTGGCACAGAGCGACCTGACCAGGAGCCATAGCGGATGGCACACCAGCGCTGCCTTCACAGCGACA i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79189751 104 + 83384210 CTACTCA------TTTTCTCAGA--CAGCCTGCAAGCACGGTGATCTTGGCACAGAGTGACCTGACCAGGAGCCGTAGTGGATGGCACACCAGTGCTGCCTTCACAGCGACA i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 39492 78 + 85690 ACATAAAC-----CTCTCACAGAGCTAGGTTGCAAGGCCACCGG-CTCAGCACAGAGCAA----------------------------AGAAATGCCGGCTTTACCACAACA i otoGar1.scaffold_94361.1-85690 C 0 C 0 s equCab2.chr11 57942910 96 - 61308211 -------GCAAGGGTGCTTCCGA--CAGCCAACAAAGCTGGCCACCTGTGCACAT-GCAA--TAATAGGGGGCCAAGGGGGACCACACA-TGGCACCAGCTTTATGACA--- i equCab2.chr11 C 0 I 3 e monDom5.chr2 304274614 10220 - 541556283 I e canFam2.chr9 59357831 2 - 64418924 I e bosTau4.chr19 10755121 32 - 65312493 I e cavPor3.scaffold_76 4298244 531 + 7991924 I e mm9.chr11 118670430 1453 + 121843856 I e loxAfr3.scaffold_49 14289443 28 - 17734757 I a score=352640.000000 s hg19.chr17_gl000204_random 13782 438 + 81310 CTGCA-GGGAGCCCCAGGACAGAAAGAGCCAGAAAGAGCAGTGGGATTCCTGCCCTCTAAACAGTCACATTGCT--GC------TTCTCTGTCCC-ATACAGGCTGGGGTGTGTGGCCTTCCTATCTGGGCTCCCCGAGGGGGCCCCTGATGGTTTACGGAATGGGGTGAC--AGCCGTTTCAGCAGAGGAGGGGAGTTGTTTAAGG-GTTTATCTC-AGACATGGGC----CCAGATccaccactcctctcctcccgggtccatggcagagccagtgctccc--------------agggatagagtgcgacagtgggctcgctcgtcagctgt-cccttgct------------------tccactctgtccccctcacagaaggcagagacacctttgtatgtc-----tcaggccattcaatccctcactcagagccctgcagtggctcccaccacccttaagac-aaaatccaaagtcctcagtcccaac s canFam2.chr9 59357833 425 - 64418924 CTAAG-GGGACCCGCAGCACTGAAGGATTTAGAAGGTCCCGAGGGATGGAGACCTTCTGAGCCATCACAGGGCCTGGC------TCCCCTGTCCCTGT------CCCGGTGTCTGACCTTCCTCTGCAGGCTCTCTAA-GGGAACCCCAA-GGTTCA-GCAGAGGAATAGC--AGTCATTTCAGCATAGCAGGGCAGTTGTTTGAAATTCTCACCTC-AAACATGTCC----ACAGACC---CACGTTTCTCATTCTGGGGCCGTGGCACACCCACCACTCCC--------------GGGGA----------CAGCCC----Cagctccctgagtaaccctgct--agctctgacttccct-ccccatctattccccacacagaaggcaacgtcatccacatctaactcaaatctggtgatccaat-------------cccttctgtagctcctaccatctttaagacaaaaaccccaaatccttattcttggc i canFam2.chr9 I 2 C 0 s equCab2.chr11 57943009 466 - 61308211 CTGTG-GGTCCCTGGAGAG--GAAGAATTCAGAAGGTCCTATGGGATCGAGACCTTCTGAATGGTCACTTGGCTTTTC------CCTGCAGGCCCAGTGCAGTCTCGGGTGTATGGTCTTCCTTTCCAGGCTCCCTGA-CAGGTCCCCGATGGCTTA-GGGAATGGGTGAC--CGTCATTTCAGTGTAGCAGGGAAGCTGTTTAAAACgctcatctc-aaacatgtccccagacagacccaacacttttctcatccccggtccacggcgcagtcacccccccctcccccccgccaggaggag----------cagccg----cctcctcacctgtccccctgcttctgccccgacctccttcccccctccattccccacccagaagacaacattctcttcctatcactcgaatcaggccattcagtctctcacccggagcccttcagtggctcccaccatctttaagac-aaaatccaaaatccttacccctggc i equCab2.chr11 I 3 C 0 s otoGar1.scaffold_94361.1-85690 39570 371 + 85690 TGGCACGAGAG----GGAGAGGGAGGACCCAGAGCA------GGGACCACAACCTTCCAGCTGGTCACGCTGCT--GCCACTGGCTCTCTGTCCC--CATCAGTCTGGATGTGCGGCCATCTT-TCTGGGCTCCCTAT-AGGGTCCCTAGTGGTTTCAGCAAGTGGGTATCAGAGCCATTTCAGTACAGAAGGAAACTTGTTTACAG-TCTCATCTCAAGACATAGCT----CTGGAGCTGCCACGTGTCTCGTCCCAGGTCCATGG-ACAGTCAGCCCCTCC--------------CACGACAGAG-----CAGTGA-------------------------C------------------TCCAC----TGCCTCCCACAGAAGGCA-----------------C-----CCCGActctt----------ctcagagcccttcagcggcccctaccacccttaaaac-aaaatctgaactcctc---cccagg i otoGar1.scaffold_94361.1-85690 C 0 C 0 s panTro2.chr17 79189855 434 + 83384210 CTGCA-GGGAGCCCCAGGGCAGAAAGAGCCAGAAAGAGCAGTGGGATTCCTGCCCTCTAAACAGTCACGTTGCT--GC------TTCTCTGTCCC-ATACAGGAAGGGGTGTGTGGCCTTCCTATCTGGGCTCCCCGAGGGGGCCCCTGATGGTTTACGGAATGGGGTGAC--AGCCGTTTCAGCAGAGGAGGGGAGTTGTTTAAGG-GTTTATCTC-AGACACGAGC----CCAGATccaccactcctctcctcccgggtccatggcagagccagtgctccc--------------agggatagagtgcgacagtgg----gctcgtcagctgt-cccttgct------------------tccactctgtccccctcacagaaggcagagacacctttgtatgtc-----tcaggccattcaatccctcactcagagccctgcagtggctcccaccacctttaagac-aaaatccaaagtcctcagtcccaac i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69574838 434 + 73212453 CTGCA-GGGAGCCCCAGGGCAGAAAGAGCCAGAAAGAGCAGTGGGATTCCTGCCCTCTAAACAGTCACATTGCT--GC------TTCTCTGTCCC-ATACAGGCTGGGGTGTGTGGCCTTCCTATCTGCGCTCCCTGAGGGGGTCCCTGATGGTTTACGGAATGGGGTGAC--AGCCATTTCAGCAGAGGAGGGGAGTTGTTTAAGG-GCTTATCTC-AGACATGGGC----CCAGATCTACCACTCCTCTCCTCCTGGGTCCATGGCAGAGCCAGTGCTCCC--------------AGGGATAGAAAGGGACAGTGG----GCTCATCGGCTGT-tccttgct------------------tccactctgtccccctcacagaaggcagcggcatctttgtatgtc-----tcaggccattcaattcctcactcagagccctgcagtggctcccaccacccttaagac-aaaatccaaaatcctcagtcccaac i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74740358 439 + 78773432 CTGCG-GCGAGCCCCAGGGCAGAAGGAGCCAGAACGAGGAGTGGGATTCCTGCCCTCTAAACAGTCACATTGCT--GC------TTCTCTGTCCTGGTACCGGCTGGGGTGTGTGGCCTTCCCATCTGGGCTCCCCGA-GGGGTCCCTGATGGTTTACGGAATGGAGTGAC--AGCTGTTTCAGCAGAGGAGGGGAATTGTTTAAGG-GCTTATCTC-AGACATGGGC----CCAGATCCACCACTCTTCTCCTCCTGGGTCCATGGCAGAGCTAGTGCTCCC--------------GGGGATAGAGTGGGAcagtgg----gctcctcggctgt-cccctgct------------------tccactctgtccccctcacagaaggtggtggcatcttcatacatcccaaatcaggccatttaatccctcactcagaaccctgcagtggctcccaccacccttaagac-aacatccaaaatcctcagccccaac i rheMac2.chr16 C 0 C 0 e monDom5.chr2 304274614 10220 - 541556283 I e bosTau4.chr19 10755121 32 - 65312493 I e cavPor3.scaffold_76 4298244 531 + 7991924 I e mm9.chr11 118670430 1453 + 121843856 I e loxAfr3.scaffold_49 14289443 28 - 17734757 I a score=158830.000000 s hg19.chr17_gl000204_random 14220 197 + 81310 ctaaaggcctctgcatccag-ccctggaccctcttcgtcatctccttcctccacctgcacagcccccggaccccgtgatgccagcccct--------cctgctacttctccagcatgcccacacgttgctgcctcggcgccttggcactggccattccctctgtctggaacactctcccctcagacatcctgggg--tcctccctccc s rheMac2.chr16 74740797 196 + 78773432 ctaaaggccactgcatccag-tcctggaccctcttcgtcatctccttcctctacctgcacagtccccagaccccgggacgccagcccct--------cctgctacttctccagcatgcccgcatgtcgctgcctcagcgccttgg-actggccattccctctgtctggaacgctctcccctcagacatcctgggg--tcctccctccc i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69575272 197 + 73212453 ctaaaggcctctgcatccag-ccctggaccctcttcgtcatctccttcctccatctgcacagcccccggaccctaggacgccaacccct--------cctgctacttctccagcatgcccacacattgctgcctcagcgccttggcactggccattccctctgtctggaacactctcccctcagacatcctgggg--tcctccctccc i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79190289 197 + 83384210 ctaaaggcctctgcatccag-ccctggaccctcttcgtcatctccttcctccacctgcacagcccctggactccgtgacgccagcccct--------cctgctacttctccagcatgcccacacgttgctgcctcggcgccttggcactggccattccctctgtctggaacactctcccctcagacatcctgggg--tcctccctccc i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 39941 180 + 85690 ctgtaggcctctg-acccag--cctggaca--ctgccttgtcccccgcctcagcccacttggccact--------------cagccactcggttgaacctggcagccctgtcgctcacccataca-cgctgccctggggcctttgcacc-tctgttctctctgccagatgc-----tcccccAGACCTGTCAGGG--ACCCACTCCCC i otoGar1.scaffold_94361.1-85690 C 0 I 1633 s equCab2.chr11 57943475 188 - 61308211 ccgaaggcttccgaattgagccccaaccctctctgcctcatctccttccactccctgctcacccactcgtcccc-gcagaccag----------------gcttctcctccagcaggcctgagcatcactgcctcggggcctgtgcact-gctcctgcctcggcctggaccgctcctccctcagacctctgccgg--gtcgccctggc i equCab2.chr11 C 0 C 0 s canFam2.chr9 59358258 167 - 64418924 ctaaaaacttctgaatttaggtgctacactttcta-----------------ccctgctccccaacttggccctggcaggccagtcttc--------tttgctacttctccagca--------------tgcctcagggcctttgcactagccagaccctctgcctgaaccactc--tccacagggctcagctggttgccacccttgc i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14289471 171 - 17734757 CCAAAGGCCTGTGAATCTGTTCCCTGGACAcctt---------ccgcctacccccagcttagccact---cacctgcataccagcctt---------ctggccacttccccctcacgtccgcac--tcctgccatagggcctttgcacaggccgttccctctgcccagaaggctgtcccctcagactcccttgc-------------- i loxAfr3.scaffold_49 I 28 C 0 e monDom5.chr2 304274614 10220 - 541556283 I e bosTau4.chr19 10755121 32 - 65312493 I e cavPor3.scaffold_76 4298244 531 + 7991924 I e mm9.chr11 118670430 1453 + 121843856 I a score=224837.000000 s hg19.chr17_gl000204_random 14417 337 + 81310 ttccttctgtcttggctcacaacatcagca-ccggggcctgccc--ttctgtcctgggcaact-gcagcccccaccattccccgtggtcttaatgcactgcatttatcttcacagcgttat-ggcgcctgaca------ta----------catttattcg--------ccatgtccctgctaaaatataaacaccatgagggccagaacttgaccttgtctccactgcgtctccagcaccccaaacagggctcagcacatcggggg--ctcaaggtt-gtggaatgaac-----aaTGTAGGGCAGTCTGGA--TGGATGAG-CTACGGCAAGAAGA---CCCCAAGGAGCCCTGGAGCAGAGAAGAGC------------------ACCCATGGCC s panTro2.chr17 79190486 337 + 83384210 ttccttctgtcttggctcacaacatcagca-ccggggcctgccc--ctctgtcctgggcaact-gcagcccccaccattccccgtggtcttaatgcactgcatttatcttcacagcgttat-ggttcctgaca------ta----------catttattct--------ccatgtccctgctaaattataaacaccatgagggccagaacttgaccttgtctccactgcgtctccagcaccccaaacagggcttagcacatcggggg--ctcaaggtt-gtggaatgaac-----aaTGTAGGGCAGTCTGGA--TGGATGAG-CTACGGCAAGAAGA---CCCCAAGGAGCCCTGGAGCAGAGAAGAGC------------------ACCCATGGCC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69575469 338 + 73212453 ttcgttctgtctcggctcacaacatcagca-ccagggcctgccc--ttctgtcctgggcaagtcgcagctccaactgttccccatggtcttagcgcactgcatttatcttcactgcattatgggcgcctgaca------ta----------catttattct--------ccatgtccctgctaaa-tataaacaccatgaaggccagaacttgaccttgtctccattgtgtctccagcaccccaaacagggctcagcacattggggg--ctcaaggct-gtggaatgaat-----aaTGCAGGAGAGTCTGGA--TCAATGAG-CTATAGCAAGAAGA---CCCCAGGGAGCCCTGGAGCAGAGAAGAGC------------------ACCCATGGCC i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74740993 339 + 78773432 ttccttctgtctcagctcacaatatcagcacccggggcctgccc--ttctgtcctgtgcaagccacagcccccaacgttcgccttggtcttagcatgctgcgtttatcctcacagcattatgtgcgcctaaca------ta----------catttattct--------ccatgtccctgctaaa-tataaacaccatgagggccagaacttgaccttgtctccactgcgtctccagcaccccaaacagggctcagcacatcggggg--ctcgaggct-gtggaatgaat-----aaTGCAGGACAGTCTGGA--TCGATGAG-CTACGGCAAGAAGA---CCCCAGGGAGCCCTGGAGCAGAGAAAGGC------------------ACCCATGGCC i rheMac2.chr16 C 0 C 0 s equCab2.chr11 57943663 340 - 61308211 tcccctcagcctctgctcacgacgtctgcatccaggccctgccc-tgaccgccctgtgtgaacagcagccgcca-cactcttgatcacctctgcccgcttcctttttcttcatagccccgtcaatccctgacgttatccta----------aatgtgttctttcactctccacgtctccactggaatagaaacacaacgaggacaaggacttgg-tttgtctccatggcatctc-------------------cagcacatgggaggtgctcaagtat----gaatgaat----gaatGCAGACCAGTCAGGGGCCCGATCAGCCCACTGCAGGAAGAGAAGGCTCACATGCCCCGGGGCCGAGACGAGA------------------ACCCACATCC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59358425 331 - 64418924 tcccctcagcctgtgccccgagcagtagcctccaggtcctgcccaggactgtcccaggggaacagcagcctccgccaccctctattgcccttgaccac-----ctttccacagagcctcagcactacccgacactactcta----------caggtgcgtt-----------cgtc-ccactagcacgtgaac--------ggcaagggcttgg-cttgtgtccgctgggtctcccgcctgcaccaca-ggctcagtgcattgggggccctcgaGGAC----GGCTGAATGCCAGCATGCGGCTCAGTCAGTG--CACATCTACCCACCACAAGAAGC-AGGCCCCAAACACCCCGAGGC-----AGGGA------------------GCCCACTTCC i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14289642 373 - 17734757 -ttcttct-tctctgttcacggcgtcagca-ccctggcctgccc--aggacgcctgcataaagagcagcc-ccaccattctctgttgtctgagcctgcgtcattattcttcatctctgtatcactcctgggcattgctttaaatgtgcacccgtttattct--------ccgtgcc-ctactacaagaccaacatcacaatggccgggacttggcttggcctcaactctttgtccagcac-ccaaccagggctcagcccctcagaggccctcaaacatggctgaatgaac----acatGTGGGTCCGTCAG----CAGATGAGCTCACCGCAGGGAGCGAGCCCCACAGCGCCCCGAAGCAGGAGAAAGCATCATTGCAAGCAGTGAGACCCACAGC- i loxAfr3.scaffold_49 C 0 I 70 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e monDom5.chr2 304274614 10220 - 541556283 I e bosTau4.chr19 10755121 32 - 65312493 I e cavPor3.scaffold_76 4298244 531 + 7991924 I e mm9.chr11 118670430 1453 + 121843856 I a score=195080.000000 s hg19.chr17_gl000204_random 14754 279 + 81310 TTCACCAGAGAGAAGCAAGCAGTGCACGCCTGGAGAAGCACCCAGACTGTGCATAGAGACTTCCAATTC--------------TGCAAACTCTGGAA---------AGAGCATCTTTTGATGGGTATTGGAGAGACCAGCCTGTGTCCGGGCCTCTGGTCTC-TTTGTCCAGGGTTCTCGTCGGCATCATCTGCTCAGCCTACAGT-GGGTCATCATGCAAAGCCTGCCTG--CAGGCTTCAGGGCTCCAGTCCTCCCTGCC--------TGGGGG-TCGCTGACCCAC---------------AGCTTTGCATTGTCTATCAGCAGGGA s panTro2.chr17 79190823 271 + 83384210 TTCACCAGAGAGAAGCAAGCAGTGCACGCCTGGAGATGCACCCAGACTGTGCATAGAGACTTCCAATTC--------------TGCAAACTCTGGAA---------AGAGCATCTTTTGATGGGTATTGGAGAGACCAGCCTGTGTCCGGGCCTCTGGTCTC-TTTGTCCAGGGTTCTTGTCGGCATCGTCTGCTCAGCCTA---------CATCATGCAAAGCCTGCCTG--CAGGCTTCAGGGCTCCAGTCCTCCCTGCC--------TGGGGG-TCGCTGACCCAC---------------AGCTTTGCATTGTCTATCAGCAGGGA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69575807 280 + 73212453 TTCACCAGAGAGAAGCAAGCAGTGCACACCTGGAGATGCACCCAGACTATGCGTAGAGATTTCCAATTC--------------TGCGGGCTCTGGAA---------AGGGCATCTTTTGATGGGTACTGGAGAGACCAGCCTGTGTCCGGGCCTCTGGTCTC-TTTGTCCAGGGTTCTTGTTGGTATCCTCTG-TCAGCCCAGAGT-GGGTCATCATGCAAAGCCTGCCTG--CAGGCTTCAGGGCTCCAGTCCTCCCTGAC--------TGGGGGATCGCTGACCCACA-------------GAGCTTTGCGTTGTTTATCAGCAGGG- i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74741332 275 + 78773432 TTCACCAGAGAGAAGCAAGCAGCACATGCCTGGACATGCACCCAGATTGTGCGTGGAGATTTCCGATTC--------------TGCGGGCTCTGGAA---------AGGGCATCTTTTGATGGGTATTGGAGAGACCAGCCTGTGTCTGGGCCTCTGATCTC-TTTGCCTAGGGTTCTT---GGTATCATCTGCTCAGCCCAGAAA-GGGTCGTCATGC-AAGCCTGCCTG--CAGGCTTCAGGGCTCCAGTCCTCCCTGCA--------TGGGGG-TCAATGACCCAC---------------AGCTTTGCCCTGTCTATCATCAGGGA i rheMac2.chr16 C 0 C 0 s equCab2.chr11 57944003 270 - 61308211 GTCATCAAAAGAAAATTATCAGGGCGTACCTGGACCTGCACCAAGGTCATGTGTCAAA---TCTGATTCCTCAGATTCTACAATGGGCCTCTTAAAGAAGATAAGATGGGCTTCTTTTAAGGGACATTGAAGGGACCA---------------CTTGGTCTC---TGCTCAGGATTCTTGTTGGCATCGTCCACTTGGCCCGGACAGGGGCCAGCACAC----------------------AAGGCTCGGGTCTTCCCTGCCCTGCCT--TGGACG-ACAGGGACCCATC--------------AGCTTTGTGCTGCTTCTCAGCAGGGA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59358756 273 - 64418924 GTCAGGAAAAGGAAGTAAGCAGTGCATCCCCGGAGATGC-CCCAGGCCTGGCAGAGAA---CCTCACTC--------------TGTGCACATGAAAG---------CGGGCACCTTTTGAGGGATACTGGAGGGACCGGCCTGTGT-------CCTTGTCTC-CTTGCCCAGAACTCTTATTGGCATCATTTGCTCCGCCCAGGGCAGGATGAGCACAT---GGTGGACTG--CGGTGCGAGGGGTTCAAGTCCTTCTTGCCCCGCCT--CGGGTG-AGCCCGACCCTCC--------------GGTTTTGTGCAGCTTCTCTGCAGGGA i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14290085 265 - 17734757 TCCACCATA-AGAAGTCAGCGGAGCAGCCATGGAGAAGCACC----------------------AACCC--------------TG-------TGCAG---------AGAGTCTCTTT---AGGGTATCAGAGAGGCCAACCTGTAT-------CCTGGCCTCTTTTACCCAGAATTCTCCTTGGCGCCATATCTGCAGCCTAGAACAGGGCTATCAAAC-AAGCATGGCTGCCCCATGTCCAAGGTCTGAGTCTTTtgtaccttgtctcagagatg-acactgacccaccccccctaagacaccagctttgtgttgtttatcagcaggga i loxAfr3.scaffold_49 I 70 I 4 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e monDom5.chr2 304274614 10220 - 541556283 I e bosTau4.chr19 10755121 32 - 65312493 I e cavPor3.scaffold_76 4298244 531 + 7991924 I e mm9.chr11 118670430 1453 + 121843856 I a score=42822.000000 s hg19.chr17_gl000204_random 15033 54 + 81310 ATGGGGCTG-------CACTGAACCTCATGGGGGTTTAAGAAAGAATTCACCtggtgtctg s panTro2.chr17 79191094 54 + 83384210 ATGGGGCTG-------CACTGAACCTCATGGAGGTTtaagaaagaattcacctggtgtctg i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69576087 54 + 73212453 ATGGGGCTG-------CACTGAATCTTACGGGGGTTtaagaaagaattcacctggtgtctg i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74741607 54 + 78773432 ATGGGGCTG-------CACTGAACCTCACGGGGGCTtaagaaagaattcacctggtgtctg i rheMac2.chr16 C 0 C 0 s equCab2.chr11 57944273 61 - 61308211 GCAGGGCTGCATGGAACATGGAGCTCCATGGGGGTGCAAcaaagaattggtctggcttttg i equCab2.chr11 C 0 C 0 s canFam2.chr9 59359029 54 - 64418924 GCGGGGCTG-------CACCGAGCTTCCTGGTGATGGGGTCCAGAACGTGTCTGGGTTTTG i canFam2.chr9 C 0 C 0 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e monDom5.chr2 304274614 10220 - 541556283 I e bosTau4.chr19 10755121 32 - 65312493 I e cavPor3.scaffold_76 4298244 531 + 7991924 I e mm9.chr11 118670430 1453 + 121843856 I e loxAfr3.scaffold_49 14290350 4 - 17734757 I a score=222346.000000 s hg19.chr17_gl000204_random 15087 254 + 81310 tccctggttcctgggaggtgatctctaaaactgctggggtttccaagggataggagtgtcttctgttattcataaaaagccactcctgaccacacctgaccgtgtgctgacctggcaactc---acagggacccgtaggaagcttcaagtgtgaggctggccgtgcacgtgattagagggttggaaatttcactccccacctcaggggagcagagag-ggCTAGAGAC--AGCTCAGTCACGTG--------------------------------------------GCTCGGGGAGCTTGCG- s panTro2.chr17 79191148 254 + 83384210 tccctggttcctgggaggtgatctctaaaactgctggagtttccaagggataggagtgTCTTCTGTTATTCATAAAAAGCCACTCCTGACCACACCTGACCGTGTGCTGACCTGGCAACTC---ACAGGGACCTGTAGGAAGCTTCAAGTGTGAGGCTGGCCGTGCACGTGATTAGAGGGTTGGAAATTTCACTCCCCACCTCAGGGGAGCAGAGAG-GGCTAGAGAC--AGCTCAGTCACGTG--------------------------------------------GTTCAGGGAGCTTTCG- i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69576141 254 + 73212453 tccctagttcctgggaggtgatctctaaaactgctggagtttccaagggataggagtgtcttctgttattcataacaagtcactcctgaccacacctgaccgtgtgctgacctgacaactc---acagggacccgtaggaagcttcaagcgtgaggctggccgtgcacgtgattagagggttggaaacttcactccccacctcaggggagcagagag-ggCTAGAGAC--AGCTCAGTCACGTG--------------------------------------------GCTCGGGGAGCTTTCG- i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74741661 253 + 78773432 tccctcgttcctgggaggtgatctctaaaacctctggagtttccaagggataggagtgtcttctgttAGTCATAACAAGCCACTCCTGCCCATACCTGACCATGTGCTGACCTG-CAACTC---ATAAGGACCCTTAGGAGGCTTCCATCGTGAGGCTGGCCGTGCACGTGATGAGAGGCTTGGAAATTTCACTCCCCACCTCAGGGGAGCAGAGAG-GGCTGGAGAC--AGCTCAGCCACGTG--------------------------------------------ACTCGGGGAGCTTTCG- i rheMac2.chr16 C 0 C 0 s canFam2.chr9 59359083 262 - 64418924 TCCCTGGTTCCAGGGAGGTAACCTCTAACACCTCTGGAATTCCTGAGGGATGGGAGTGTGGTCTGTTATTC------------------CCAGGTCTGGCTTCCTGCTGACTGGGTGGCTCAGGGCGGG--TCCGTAGACA-------------GGC----------ACCTATGGGAGAACTGGTGCTTTGCCTTCCCGGGCAGTGGGAGGAGAGCGGGGCAGGAGCCACGGTCCAGCCTTGTGGCTGATGACATAACAGGACTCCAGTAAAACTCCGGACGTCCGAAGCTCAGGGAGCTTTGTG i canFam2.chr9 C 0 C 0 s felCat3.scaffold_217507 57872 260 + 139435 TccctggttcctgggaggtaacctctaaaacctttggaactcccgagggatgggaatgtcctCTGTTATGC------------------CCACACCCGACTTCACGCTGACTGGGTGACTC---TTGAG--TCCTTAGGCA---------GAGGGAC----------CCTGATTGGAGAGCTGGAGCTTTCACTTCCC---CACTCAGGGGAGAGAGGGACAGGGGACAGAGTCCAGTCTTGGGGCCAATGACATAATAGGACTCCGGTAAAACTCTGGACACTCCCAGCTCAGGCAGCTTTGTG i felCat3.scaffold_217507 N 0 C 0 s equCab2.chr11 57944334 287 - 61308211 tccctggttcccgggaggtcacctctaaaa-tgctggaattcccgagggacaggagtgtctttcattattcacaacaagtcccttttgaccacacctgaccttatcctaaccagggggcta---gcggggacacataggtggttccaaaggaggggc----------actgatgagagggttggaacttccccccacc---tcaggggaggggagagaggctgcagactgagttcagtcacgtggccaatgatgtcataagaccccagtagcactctggacacccaaagctctggg-gctttgtg i equCab2.chr11 C 0 C 0 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e monDom5.chr2 304274614 10220 - 541556283 I e bosTau4.chr19 10755121 32 - 65312493 I e cavPor3.scaffold_76 4298244 531 + 7991924 I e mm9.chr11 118670430 1453 + 121843856 I e loxAfr3.scaffold_49 14290350 4 - 17734757 I a score=101932.000000 s hg19.chr17_gl000204_random 15341 157 + 81310 GTTGGTGAACTTGTGGGTGAACCAGCAGGGTGGTGCATCCTAACACCATGGGGAATGGGTGTGGATGCT------------------CCGAACTCAACCTG-----------TGTGTATCATACGACTGTCATACAACTGTCATTTTTAGTGTAGTGCTTTTTTGTTGCTGTCgttctgtgaactg s rheMac2.chr16 74741914 172 + 78773432 GGTGGTGAACTTGTGGGTGAACCAGCAGGGTGGTGCATCCTAGCTCCATGGCGAGTGGGTGTGGATGTTCCGTATCCAGGACACTGCCCGACCTCAACCTA-----------TGTGTGTCACACGACTGTCATACACCTGTCATTTTTAGTGTAGTGCCTTTTTGT---TGTTgttctgtgaattg i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69576395 157 + 73212453 GTTGGTGAACTTGTGGGTGAACCAGCAGGGTGGTGCATCCTAACTCCACAGGGAATGGGTGTGGATGCT------------------CTGACCTCAACCGG-----------TGTGTATCATATGACTGTCATACAACTGTCATTTTTAGTGTAGTGCTTTTTTGTTGTTGTTgttctgtgaattg i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79191402 157 + 83384210 GTTGGTGAACTTGTGGGTGACCCAGCAGGGTGGTGCATCCTAATTCCATGGGGAATGGGTGTGGATGCT------------------CCGACCTCAACCTG-----------TGTGTATCATACGACTGTCATACAACTGTCATTTTTAGTGTAGTGCTTTTTTGTTGCTGTTgttctgtgaattg i panTro2.chr17 C 0 C 0 s mm9.chr11 118671883 160 + 121843856 GCTGATGAGTATGCAGATGAGCCAGGAGGA-GGGGCTCCCTAACTTCCCAGGAAGGAAGCATGGAAACACAGTTCCCAGGGTTCTC-ACAACCTTCTCCCG-----------AGCG--TCATA----TATCATACAACTGAAATCACACATGTAGCATTTTCTTGG-------GGTCTACAAACAG i mm9.chr11 I 1453 I 3 s canFam2.chr9 59359345 131 - 64418924 ACGGGTGAACGCGTGGATGTGCTGGGAGAGTGACCTGTCCTATCCCTACAGGGTGAGGG----------------------------CAGACCTTGTCCC------------CGTGtgtcctg----catcataaaaatgtagccgtcgatatgg----ctcttaa-------attcagagagtca i canFam2.chr9 C 0 I 3 s felCat3.scaffold_217507 58132 136 + 139435 AGGGGAGAGCACGTGGATGTGCCGGGAGGGTGAGCTGTCCTGACCCTGCAGGGTGAGGG----------------------------CAGACTTCGTCCCA-------TCTACGGGTGTCCCT----TATTACGGAAACGCAACCGTGAGTGTGG----CTCTTAA-------GTTCTGAGAGTca i felCat3.scaffold_217507 C 0 N 0 s equCab2.chr11 57944621 162 - 61308211 gctggtgaccacgtggacgtgctgggagggggacctgtcccaactctccagggagagggtgtggaggctcagcat------------ctggcaccctcccaacctcaccctgcgtgcatcctt----tataac-gaaacctaaccgtcaggagagtgctttctcaa-------gttctgcaagtcg i equCab2.chr11 C 0 I 3 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e monDom5.chr2 304274614 10220 - 541556283 I e bosTau4.chr19 10755121 32 - 65312493 I e cavPor3.scaffold_76 4298244 531 + 7991924 I e loxAfr3.scaffold_49 14290350 4 - 17734757 I a score=120738.000000 s hg19.chr17_gl000204_random 15498 187 + 81310 tagcaaattatcaaaactga-ggggtcctgggaacctctgaatttgccact----ggtcacaagtgcaggtgaccctggcagcttgcattc-------gaagtgagagccatcttacagagcgcttggcccaaaccctgt-ggagtctgacgctgactc-cggcggttagtgtcagagctgaaCGGCAGTCACCCTCTCG-G s canFam2.chr9 59359479 173 - 64418924 tagcaaattatcaaaactga--aggtcatgg--------ggatttgtagctggtaggtcagaagtgcaagtggctcccaaggcttgtggctggcgtctgaagtgggg-cggccctaagggcaaag-ggccccgagcctataggggtctgctgctaACCC------GCTGACCCCGG-----------GGGCTTCCTGCCACA i canFam2.chr9 I 3 C 0 s equCab2.chr11 57944786 200 - 61308211 tagcaaatcattgcaactgagggggttacgggagcccctgaatttatcgccggtcggtcagaggtgcaggtggtccctgagacttgcacctggagtcggaagtggggtcagtgtcgtgggggacg-ggtcctaagcctgt-ggggtctgccactaactccaggtggctcatgccagacttgaagtgCAGTCCTCTTGCTCCA i equCab2.chr11 I 3 C 0 s bosTau4.chr19 10755153 192 - 65312493 tagcaaattatcaaaactgaggcagttgtgggaacctgtgaatttgcaaccacttggtcaggagtgcaaac-gtccttgagatctgcagcta------aaagtgggg-cagtcttgcaggggaca-ggctctaagcctgt-gaggcctgccaataactctaggcggcgagtgccagggttgaaGTACAGTCCAGCCACTGGG i bosTau4.chr19 I 32 C 0 s mm9.chr11 118672046 138 + 121843856 TAGGCAATTATCAAAATCAA-GAGTCCCCAAG---CCCTGTAGGTAGCACG----GAAAATGAATTAAGTC------------------------------GTGTGGGCTGTATTTGAAACCTCT-----------------AAGTGTGACACTGGCCC-TGGTGGCTCCTGTCAGAACC---TGCTGCTCAGCCTG----- i mm9.chr11 I 3 C 0 s panTro2.chr17 79191559 187 + 83384210 tagcaaattatcaaaactga-ggggtcctgggaacctctgaatttgccatt----ggtcacaagtgcaggtgaccctggcagcctgcattc-------aaagtgagagccatcttacagagcgcttggcccaaaccctgt-gtagtctgacgctaactc-tggcggtcagtgtcagagctgaaCGGCAGTCACCCTCTCG-G i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69576552 187 + 73212453 tagcaaattatcaaaactga-ggggtcctgggagcctctgaatttgccatt----ggtcacaagtgcaggtggccctggcagcttccattc-------ggagtgagagccgtcttacagatcgcttggcccaaaccctgt-ggagtctgacgctgactc-tggcggttggtgtcagagctgaacggcagtcaccctgtcg-g i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74742086 173 + 78773432 tagcaaattatcaaaactga-ggggtcctgggaacctctgaatttgccact----ggtcacaagtgcaggtggccttggcaggttgcattc-------gaagtgagagccgtcttacaaagcgctttgcccgaaccctgt-ggagtcggacgctgactc-tggc----agtgtcagagctgaaCGGGGGGC----------- i rheMac2.chr16 C 0 C 0 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e monDom5.chr2 304274614 10220 - 541556283 I e cavPor3.scaffold_76 4298244 531 + 7991924 I e loxAfr3.scaffold_49 14290350 4 - 17734757 I a score=131304.000000 s hg19.chr17_gl000204_random 15685 153 + 81310 GGT----GGGAACAGAGGCATCATGCCGTCCCCTCTAGAGCCACAGGAAGGCTTCAG-GGCC-CTCCCTGAGCCGCGGAGCAATCTGGGCAGCAGAACAC-GAACCGTGCAGGGGAGGGTCAGGCCCTGACTTTGGACTCT--ATGGCATCTT--TGTTGAC-A-----C s loxAfr3.scaffold_49 14290354 137 - 17734757 ggt----gggactgaa--cttcattcggtcccctctctagccaaatgaagacatttgcaggc-atggctggGCCGCTGGGCCTTCTGTGCG----------------------GGGAGGTCAGACCCCACCCTCAGCCTCC--A-GACATCCCCATGCTCAC-AGCGGCC i loxAfr3.scaffold_49 I 4 C 0 s canFam2.chr9 59359652 125 - 64418924 GGTGAAGTGGAATGGAGCAAGCACG--------CACACGGCCTGCTGGAGGCATTAG-ACCCGCTTGCTGGGCTGCAGGGAGATCTGGGCA--------------------GGGGAAGGTCAGACC-------TGGCCTCT--GCAGCATTCT-GTGCTGAC-A-----C i canFam2.chr9 C 0 C 0 s equCab2.chr11 57944986 153 - 61308211 GGC----TGGAATGGGGCCGTCACTTGGT--CCCCTAGGGTCAGATGAAGGCGTTAG-AGCCGCT--CTGGGCTGCAGGGACATCTGGGCAGCAGGACACAGAACCGTCCCGAGCAGGGTCCGACC-CGACCATGGCCTCTAGGCATCATTTC-GTACTGAC-A-----G i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10755345 145 - 65312493 GGA----GGGAGTGCGGCAATCATGAGTTC-CCTCTAGAGCCAGATGAAGGCATCAG-ATCCCATCCCTGGGCCACAGGGGAAAGTGCACG----------GAGCCATGCAAGGGAGGGTCAGACCCCCACCTTGGCCACC--GTGGCATTTC-GTGCTGAC-A-----C i bosTau4.chr19 C 0 C 0 s mm9.chr11 118672184 136 + 121843856 -------AGGGACAGGGA-ATCACTCTATCACCTTAGCAGCAAGATGGAGGCTCACT-GCTG-CTCACTG-GCTTGAGGGCAACCTGGACATTATGTT---------------GGAGGATCAAATCCCAGCCTTGGCCACT--TATACATCTC-ATACTGACAA-----C i mm9.chr11 C 0 C 0 s panTro2.chr17 79191746 153 + 83384210 GGT----GGGAACAGAGCCATCATGCCGTCCCGTCTAGAGCCACAGGAAGGCTTCAG-GGCC-CTCCCTGAGCCGTGGAGCAATCTGGGCAGCAGAACAC-GAACCGTGCAGGGGAGGGGCAGGCCCTGACCTTGGACTCT--ATGGCATCTT--TGTTGAC-A-----C i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69576739 153 + 73212453 ggt----GGGAACGGAGCCATCATGCCATCCCCTCTAGAGCCACACAAAGGCTTCAG-GGCC-CTCTCTGAGCTGCGGAGCAATCTGGGCAGCAGAATAC-GAACCGTGCAGGGGAGGGTCAGGCCCTGACCCTGGACTCT--ATGGCATCTT--TGTTGAC-A-----C i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74742259 153 + 78773432 GGT----GGGAACAGAGGCATTGGGCCGTCCCCTCTAGAGCCGCACGAAGGCTTCAG-GGCC-CTCCCTGAGCTGCGGGGCAATCTGGGCAGCAGAACAT-GAACCGTGCAGGGGAAGGTCAGGCCCTGACCTTGGATTCT--ATGGCATCTC--TGCTGAC-A-----C i rheMac2.chr16 C 0 C 0 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e monDom5.chr2 304274614 10220 - 541556283 I e cavPor3.scaffold_76 4298244 531 + 7991924 I a score=168065.000000 s hg19.chr17_gl000204_random 15838 165 + 81310 CAGACAGTGGACCCCACACCCCGCCCACCCT--CCTTCC--AGGACTAACTGCCCCGCAGCCAGGCTGATGGGCTTCGAGGTA-CAAAGAGCGGTCACTCCTTAAAA-ATTCTAC-CCCATACCTTC----TTGGGCGTCCGTCGATGTTC-----CCCCTCCTACT--------CCACAAAGACACCA s rheMac2.chr16 74742412 164 + 78773432 CAGACAGTGGACCCCACACCCCGCCCACCCT--CCTTCC--AGGACTAACTGCCCCGAAGCCAGGCTGATGGGCTTCAGGGTA-CGAAAAGCGGTCACTCCTTAAAA-ATTCTAC-CCCATACCTTC----CTGGGCATCCGTCGACG-CC-----CCCCTCCTACT--------CCACAAAGACACCA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69576892 161 + 73212453 ----CAGTGGACCCCACACTCCGCCCACCCT--CCTTCC--AGGACTAACTGCCCCGCAGCCAGGCTGATGGACTTCAGGGTA-CGAAGAGCGGTCACTCCTTAAAA-ATTCTAC-CCCATACCTTC----CTGGGCATCCGTCGACGTTC-----CCCCTCCTACT--------CCACAAAGACACCA i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79191899 165 + 83384210 CAGACAGTGGACCCCACACCCCGCCAACCCT--CCTTCC--AGGACTAACTGCCCTGCAGCCAGGCTGATGGGCTTCGAGGTA-CAAAGAGCGGTCACTCCTTACAA-ATTCTAA-CCCATACCTTC----TTGGGCATCCGTCGATGTTC-----CCCCTCCTACT--------CCACAAAGACACCA i panTro2.chr17 C 0 C 0 s mm9.chr11 118672320 151 + 121843856 CTGGCAGGAG--------------CTATTCT--ACTTCC--CAGATTAAGTTCCCCA-AACTGTGCTGATGAGTGTCAGGACA-CAGAGAAC-------------AA-AGTCAATGGCCGTGATTTC----CTGGGGACCTGGGGACTCTCTGTGACTTGACCAACTTGTAGAAGCCACGAAGACGCAA i mm9.chr11 C 0 C 0 s bosTau4.chr19 10755490 153 - 65312493 TAGACAGTGAACTGAGTGCCCTGTCCACCCT--CCTTCC--TGGAATAACCACTCCCCA-CCAGGCTGACAGATTT-----C-------AGTAGCCACTTCTTACAAAATCCCAC-CCAAGGCATTC----CTGCGGTTCTGCGATTC-TC-----CCTGTCCTTCT--------CCCTGAAGACACAG i bosTau4.chr19 C 0 I 9 s equCab2.chr11 57945139 164 - 61308211 CAGACAGTGGATGCTACACCCTGTCC-CACT--CCTTCC--GGGGGTAGCTCCTCCACAGCCAGGCTGATGGATTTCAGGACA-CAGAGAGCAGCCGCTCAGCACAGAATTGCAC-CCAGCACGTTC----CTGGGGATCTGCTGACT-TT-----CCCGTCCCACT--------CCCTGAAGCCACCA i equCab2.chr11 C 0 I 9 s canFam2.chr9 59359777 162 - 64418924 CACACAGCAGACGTGACACCCTGTCC-CCCTGCCTTCCC--AGGGGAAA--ACTCTGCAGCCAGGCTGAGGGATTT-----CA-CGGAGAGCAGGCCCTCCTTACAG-ATTCAGG-CCAGCATCCCCCCCACCGGGGGCCTGCCGACG-CT-----CCCCATCCTGC--------CCCTGAGCCCACAA i canFam2.chr9 C 0 I 13 s loxAfr3.scaffold_49 14290491 166 - 17734757 TGGATAGCGTGCCCCACACTCAGTGTACCCT--CCTTCCCTGGGGCCAATGCCCCTGCAGCCAGCCTGATGG-CTTAAGGGCC-CAGAAAGCAGCTGCCCCTTGGAAAGCTCCAC-ATGCCGCACCC----TTGGGGACTCACCAATC-CC-----CGCCTCCTACT--------CCCTGGAGCCAAAA i loxAfr3.scaffold_49 C 0 I 10 s monDom5.chr2 304284834 166 - 541556283 CAGACAATGTACCCCACAACACTTTCTTCTT--TATCTA--AGGCCTAATTCCTCTGCAGCATATTTGATGAATTTCAATGCATTAGACAGCAGCTGTTTCTTGTAGGGCCTCAG-ATGACTGATTG----CTAGAAATCTGTTGATG-TC-----ATTCTTGCTAC--------AACCAAAGACATTC i monDom5.chr2 I 10220 C 0 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e cavPor3.scaffold_76 4298244 531 + 7991924 I a score=302938.000000 s hg19.chr17_gl000204_random 16003 303 + 81310 TGACTTGAAAGCTATAGAGAGCAGCACAGAA---CGCCCCTACC----CCACAACCCTTGCTGGAAAATCAAATCACCGCATTAAAACGTATTTCCTCCACAAATGCAAACTCTGGGGAT---GG----GCATGGCGGACAGGTGGGGCCGC-CTTACCTGGTAGTGGGAGGTGAGGTCTGCTTTGCTGA-GCGG-GGAGGCCCCAGT-GGGGCT--CCTTCTGGACCGTCC--TTGGCA-AGGAG---GGGGCTGCTGGGGAGGAGT-GGCGACCACAGGAAGA-CTGTTAGCTTCTCAGAGGC---AGAATTTCAACCT-----GCAGGGGGAAAAA s rheMac2.chr16 74742576 301 + 78773432 TGACCTGAAAAC--TAGAGACCGGCAGAGAA---CGTCCCTACC----CCGCAACCCTTTCTGTAAAATAAAATCGCCGCATTAAAATGGATTTTCTCCACAAATGCAAACTCTGGGGAT---GG----GCGTGGTGGACAGGTGGGACCGC-CTTACCTGGTAGTGGGAGGTGAGGTCTGCTTTGCTGT-GCGG-GGAGGCCCCAGT-GGGGCT--CCTTCTGGACCGTCC--TTGGCA-AGGAG---GGGGCTGCTGGGGAGGAGC-AGCGACTGCAGGAAGA-TTGTTAGCGTCTCAGAGAC---AGAATTTCAACCT-----GCAGGGGGAAAAA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69577053 303 + 73212453 TGACCTGAAAGCTATAGACAGCAGCACAGAA---CGCCCCTACC----CCACAACCCTTACTGGAAAATCAAATCGCCGCATTAAAACGTATTTCCTCCACAAATGCAAACTCTGGGGAT---GG----GCATGGTGGACAGGTGGGGCCGC-CTTACCTGGTAGTGGGAGGTGAGGTCTGCTTTGCTGT-GCGG-GGAGGCCCCAGT-GGGGCT--CCTTCTGGACCGTCC--TTGGCA-AGGAG---GGGGCTGCTGGGGAGGAGC-AGCGACCACAGGAAGA-TTGTTAGCTTCTCAGAGAC---AGAATTTCAACCT-----GCAGGGGGAAAAA i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79192064 303 + 83384210 TGACTTGAAAGCTATAGAGAGCAGCACGGAA---CGCCCCTACC----CCACAACCCTTGCTGGAAAATCAAATCGCTGCATTAAAACGTATTTCCTCCACAAATGCAAACTCTGGGGAT---GG----GCGTGGTGGACAGGTGGGGCCGC-CTTACCTGGTAGTGGGAGGTGAGGTCTGCTTTGCTGT-GCGG-GGAGGCCCCAGT-GGGGCT--CCTTCTGGACCGTCC--TTGGCA-AGGAG---GGGGCTGCTGGGGAGGAGT-GGCGACCACAGGAAGA-CTGTTAGCTTCTCAGAGGC---AGAATTTCAACCT-----GCAGGGGAAAAAA i panTro2.chr17 C 0 I 28 s mm9.chr11 118672471 279 + 121843856 -------TGAACTGCAAACACAGGCATAGGA---CACCCTG-------CTACTGCCCCA-CT----ACTGAAGTGGCCTTATT--------AGTGATTCTCGA-CGCAAACTCTGA---T---GCCAAGGCAGAGCAGGGTAGCCTTGTGGC-CTTACCTGTTG-----GGGTGTCGTCTACTTTCCTGTAGCCA-GGGG---CCCGT-GGAAGA--ACTGATGAAGCTTCC--TCAGTA-TGGAGTGTGTGTGTGCCCACGCAGAGT-GGG-ATCGCAAAAAAG-CA-CTAGGTTCTCACAGGC---AGCTTTTCAACCTGAAGAGAAGGaaaacaaa i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4298775 280 + 7991924 TGATGTGTGAGCTGGAGACCCA--CACAGTG---CACCCCG-CC----CCACGACTCCT-CTGTGAAGTGAAATCACCTCAAT--------TCCCACTCTCAAGCGCAAGCTCGGAG--T---GT----GCATGACA-GGTCGTTGGGGAAC-CTTACCTGGTGCC---AGGGGGCGGAGAGAGTGGTGTCGCTG-GGCA---------GAGAGA--CCCGAGGGAGGTTCT--GGGGTA-CGATGTCACTGATATCACTAGAAGAGC-AGGTACCAGGAGAAGG-AC-TTAAATTCTCAGGGAC---AGGTTTTCAATCT-----GAAGGAAAAGAGA i cavPor3.scaffold_76 I 531 C 0 s bosTau4.chr19 10755652 296 - 65312493 CAATCTGCAAACTAGAGCCAGCA--AAAGAA---GGTCCC--------TGTCGTTCCCTCATGTAAAATAAAATCTCCTCATTAAGATGTTTTTCCATCACAAATGCAAACTCTGAGGACAGGTG----TGGTGGCGGGCAGGC---GCGGC-CTTACCTGG-AGTGGCGGGTGAGGT-GGTTCTGTGGCAGCAG-GGAGGCCCCCCT-GGTGTT--CTTTCTGGGGCTCCCCTTGGG----ATGG---AGGGTTACTGGGAAGGAGCGAGTATCAGCAGGAAAA-CCTTCAGAGTCTCAGAGGC---AGCTTTCCAATCT-----GAAGGAAAAGAAA i bosTau4.chr19 I 9 C 0 s equCab2.chr11 57945312 296 - 61308211 CGATCCGCCAGCTGGAGCCATC-----ACAG---CGTCCCCGCCTGCAGTCCATTCCCTTGTGTAAAATCAAGTCGCCTCGTTAAAACGCTTTTCCACCACACACGCAAACCCTGAGGCC---CG----T-GTGGCGGGCGGGC---GCGGC-CTTACCTGGTAGTGGCAGGTGAGGTCTGTTTCGCTGTAGCAC-GGAGGCCCCTCA-GGGGTC--CTTCCTGGAACTTCT--TGGG----GTGG---AGGGCTGCTGGAGAAGAGC-AGGGTCAGCAGAAACA-GCTTCAGGCTCTCAGAAAT---GGGTTTTCAACCT-----GAAGAAAAAGAAA i equCab2.chr11 I 9 C 0 s canFam2.chr9 59359952 281 - 64418924 CGGTCCTCACACCACAGCAAGC-----AGGA---CATCCCCACCC---TGCCATTCTCTCGTGGCAA---------------TAAAACATTTTTCCGTTGCAAATGCAGATGCTAAGGAC---TG----TCCTGGCCGGCG------GCGAC-CTCACCTGGTAGTGGTGGGTGAGGCCTGCTTCACTGCAGCAG-GGAGGCCTCCCACGGGGTT--CTTTCTGGAACTTTC--TCGG----GTAG---AAATTTGCTGAGAAATAGTGAGAATCAGCAGGAAAA-GCTTCAGGTTCTCAGGGACCTGAGATTCTCAACCT-----GAGGgaaaagaaa i canFam2.chr9 I 13 C 0 s loxAfr3.scaffold_49 14290667 283 - 17734757 CAATCTGCAAACCAAGGCAAGG-----AAGA---CACCCTT-------------------CTGCAAAATTAAACCTCCACACCAACATGGTTTCCCATCACAAATGC-TGCCCTCAGGAC---AG----GCTTGGTG-GCCGGCGAGGCAGC-CT-ACCTGGTAGTGGTGGGCGAGGTCCGCTCTGCCACAGCTG-GGGGCCCCCACT-GGGGTT--CTTTCTGGAACTTCC--GTGGGGTAGCGG---AGGGCTGCTGGGGGAGAGCAAGTACCAGCAGAGAAT-CTATCAGGTTCTCAGAAAC---CGATTTTCAACCT-----GAAGAAAAAGAGA i loxAfr3.scaffold_49 I 10 C 0 s monDom5.chr2 304285000 298 - 541556283 ----AGGTCAGGTCTATATAGCAGAAAAGAAGTGCATCTATATC----TGTTTTCATGATCTATAGAATAAAGTCACCACACTAAGGTTTTTATCCCCCA----TCCTATTTGAGAGGAC---AA-------TGTTCAAGGGGCCAAGAGACTCTTACCTGGTAGCACAGGATAACCTCTGTTTTGCTGAACCGATGGTGGCCCTACC-GTGATTACTTTTCTGGAGCTTCA--CTGGTG--CTGG---GAGTGTGGGGGAAGGGAAA-AGTATCAACAGGAAAAGCTGTCAGGTTCTCATAGAC---AGATTTTCAACCT-----GAAAGTAAAGA-- i monDom5.chr2 C 0 C 0 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I a score=71497.000000 s hg19.chr17_gl000204_random 16306 111 + 81310 AGCAAG---TAAAA------AAAT------------TGCCTTTGAAGAAAACATCTTCCTTTT---GATCTAAAACAAACATTTG----GTATTAATAAACCA------GGGAGG--GGGCAGCTTCAAAGCCAACTGTTTGCCACC s rheMac2.chr16 74742877 109 + 78773432 AGCAAG---TAAAA------AAAA------------TGCCTTTGAAGGAAACATCTTCCTTTT---GATCTAAAACAAACATTTG----GTACTAATAAACAA------GG--GG--GGGCAGCTTCAAAGCCAACCATTTGCCACC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69577356 111 + 73212453 AGCACG---TAAAA------AAAT------------GGCCTTTGAAGAAAACATCTTCCTTCT---GATATAAAGCAAACATTTG----GTGTTAATAAACAA------GGGAGG--GGGCAGCTTCAAGGCCAACTGTTTGCCACC i ponAbe2.chr17 C 0 C 0 s mm9.chr11 118672750 96 + 121843856 aacaaaaacaaaaa------acaaaaataaaTGCCCTGCCTTGGAAATAGTC-CCTTCCCTTT---AATAT--AACAAATGCTGGCACACAGTCA---------------------------------------AGAGCCTGCCACC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4299055 104 + 7991924 AACAAAGTTTCTGA------GCAA------------TGCCTTTGAACTGGTTGTCTTCATTTT---TATCT-GAACAAGCTCTAGTGCATTATTAATAAATga------gagggg--agagagagagagagaga------------- i cavPor3.scaffold_76 C 0 I 17 s bosTau4.chr19 10755948 115 - 65312493 AGGAAA----AATG------TAAA------------TGCCTTTGAAGCCAACATGCCTTTTTTTAATATATAAAACAAACACTGG-----TGTTAATAAACAA---GAGAAGAGA--GAGCAGCTTCGAAGCCAATTTGTTGCCATC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57945608 106 - 61308211 AGAAAA----ATCA------TAAA------------TGCTTTTGAAGTAAACATCCATTGTCT---GACATAAAACAAGCATCGG-----TGTTAATAAACAA--------AAGA--GGTCAGCTGTGAAGCCAA-TTGTCGCCACC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59360233 98 - 64418924 agaaaa----gaaaaAGATGTAAA------------CGCCTTTGAAGCAAGCAACCTCTTTTT---GATATAAAACAAACATGGG-----TGTGAGTAACCTA------------------------GAGGTCAC-TGGTGGCCACC i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14290950 110 - 17734757 AGGAAG-----AAA------AAAA------------TGCCTTTGAAGCAAAAATTCTCCTTTT---GATATAAAACAAACATAGG-----TATTAATAAAAAA------GAGAAGACGGGAAGTTTCAAAGCCACCTGGCTGCCATC i loxAfr3.scaffold_49 C 0 C 0 s monDom5.chr2 304285298 114 - 541556283 AGGAAA---AGAAA------AAAA------------TGCCTTTGAAGCAAAGATCCTTCTTTG---GATGTAAAGCAAACAATAG-----TATTAATAATAAACCAAAGAAGAAA--GTGACATTTCAAAGCAAATTGGTTACCA-- i monDom5.chr2 C 0 C 0 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e panTro2.chr17 79192367 28 + 83384210 I a score=-43986.000000 s hg19.chr17_gl000204_random 16417 75 + 81310 AGGGATCGAGGGATTGAGGGATCAGCACC-CT---------------------------CCAAAGGGCACTTT-GCTTTTTATGCCCCAGGGGAGTAAAAGGAA s rheMac2.chr16 74742986 59 + 78773432 --------AGGGATTG--------GCACC-CT---------------------------CCAAAGGGCACTTC-GCTTTTTATGCCCCAGGGGAGTAAAAGGAA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69577467 67 + 73212453 --------AGGGATTGAAGGATCGGCACC-CT---------------------------CCAAAGGGCACTTT-GCTTTTTATGCCCCAGGGGAGTAAAAGGAA i ponAbe2.chr17 C 0 C 0 s mm9.chr11 118672846 55 + 121843856 ----------------AGGAATCAGTCAT-GT---------------GGTACCCGCCCATCCATGGGCACCTAGGCTCTGCCTGGCA----------------- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4299176 102 + 7991924 agagagagagagagagagagagCAGCACT-GTTCAGGTTTGCCCCCAGGGACCAGCGTCCCAGAGAGTACTCTGGGTTTTCATGCCA-AGGGAAGTGAAGGGAA i cavPor3.scaffold_76 I 17 C 0 s bosTau4.chr19 10756063 30 - 65312493 --------------------------------------------------------------AGGGA------------TCACACCCCCAGGGAATCAGGGGAA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57945714 30 - 61308211 --------------------------------------------------------------AGGAA------------TCCCGTCCCAGGGGAAGAAGAGGAA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59360331 30 - 64418924 --------------------------------------------------------------AAGGG------------TCACACCCCAGGGGAAGGAGCAGAG i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14291060 59 - 17734757 ----------------AGGGACCAGCAATGCT---------------------------CTAAAGAGGACTCT--TTTTTAATGCTAAAGGGGAATAAAAGGaa i loxAfr3.scaffold_49 C 0 I 1463 s monDom5.chr2 304285412 53 - 541556283 ---------------------------------------------------TAATCCTATATAATGGCTTTTTTTTTTTGCCCACCTTGGAAGTGTGGTACGGC i monDom5.chr2 C 0 C 0 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e panTro2.chr17 79192367 28 + 83384210 I a score=4535.000000 s hg19.chr17_gl000204_random 16492 42 + 81310 ACTTGCAGAAAACACATCATTAGGACC---CT--ATTGCCAAACAG-C s rheMac2.chr16 74743045 42 + 78773432 ACTTGCAGAAAACACATCATTAGGACC---CT--ATTGCCGAACAA-C i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69577534 42 + 73212453 ACTTGCAGAAAACACATCATTAGGACC---CT--ATTGCCAAATAG-C i ponAbe2.chr17 C 0 C 0 s mm9.chr11 118672901 1 + 121843856 -----------------------------------------------C i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4299278 42 + 7991924 TCTGGAGGAAAACGAAGCA-TGGATCT---CT--GTTGCCAAAACGTC i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10756093 43 - 65312493 CCTTGTGAAAAACAAATCATTAGAGCCGGACT--GCTGCCCAGGG--- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57945744 40 - 61308211 CCGGT--GGAGAAAAATCATTAGGACC---CT--TGTGCCCAACGG-C i equCab2.chr11 C 0 C 0 s canFam2.chr9 59360361 44 - 64418924 CCTGCTGGGAAACAGAGCATTAGGATC---CCGACGTGCCAAGGGG-C i canFam2.chr9 C 0 C 0 s monDom5.chr2 304285465 42 - 541556283 CTTTGAGGCAGTTGAATCATTATGACT---TA--ATTGACAACAAG-C i monDom5.chr2 C 0 I 3704 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e panTro2.chr17 79192367 28 + 83384210 I e loxAfr3.scaffold_49 14291119 1463 - 17734757 I a score=50721.000000 s hg19.chr17_gl000204_random 16534 188 + 81310 CACC-GTG----CAGTCCATCCCAGGGTC---CGCC-------------CCTCtcccagcccgcttgca-------atggtcccccaatcccagg-------gactcttccaccccacc-----acgctggcccctccccatcgcctttcccactaccgcccgctcttgcttcctcccccacccagcctagattccaggacccaccactgtccgcactctcccagcta s rheMac2.chr16 74743087 189 + 78773432 CAACGGTg----cagtccatccccgggtc---cgcc-------------cctctcccagcccacttgcg-------atggtcctccacccccagc-------aactcttccaccccacc-----acgctggctcctccccatcgcctctcccaccgccgcctgctctcgcttcctcccccatccagcctagattccaggacccaccactgtctgcactcccccagcta i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69577576 188 + 73212453 CACC-GTG----CAGTCCATCCCAGGGTC---CGCC-------------CCTCtcccagcccacttgca-------atggtcccccaatcccagc-------gactcttccaccccacc-----acgctggcccctccccatcgcctttcccacctctgcctgctcttgcttcctcccccatccagcctagattccaggacccaccactgtttgcactcccccagcta i ponAbe2.chr17 C 0 C 0 s mm9.chr11 118672902 192 + 121843856 CCAC--TC----TCGGCCATTCGGCCACC---TGCCAGAGCCATTGCCCTCTCAGGCAGCCCATGTCCT-------CTGACTCCCCAATCCCATG-------GACGCTTGTCCCTCCCC-----AAGATGTC----CCCCACCTTCTCCGATGGCTCCTTCTAGCCTCAGTCCCTGTCTCCTCCATCTTAGACTCTA--ACCCGACACATAC-ACACTC-CACAGATA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4299320 160 + 7991924 CCAC---A----TGGGTCATTCTG----C---TGCTGTGATCAT-----GCTCTGGCTTCCCGCTTCCT-------CCGGCCCCC--AGCCCA-G-------GATGCTTGGATGCCACT-----AAGTTG------CTCTGTCTTCTCTCAGGCCCTGTCCTGCTCGCACTTCTGGAAGCCTCCACTGTCAGCCCT-----CCGGCAGCCAC---------------- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10756136 183 - 65312493 ------------TGGG-----ACGTCCTC---TGCA-------------GCTCGCCCAGCTCTCTTGCT-------GTGGAGCCCTGCCCCCAACCCCCTGTGATTCTCTGACTCCGAT-----GTGCCTGTCTCACCCCTCTTTGTCTCCCATCCCCCTCTGCTCTCGCTCCCCGCCTCACCCAGTTCAGATTCCAGGACCCATGGCCACACCACCTCTGACAACTG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57945784 194 - 61308211 GATT-GTGCGCCTGGGCTGCGCCGCCCTCTGGTGCC-------------CTCCCGccagccctcttgac-------gcggtgccccaaccccaac-------aattctctgaccccacg-----gtgctgggcccacatat-cttgtctgatgtcccctcctgctctcacgtgccgcctcacccagtttagattctgggacccactgctgccatcactcctgcaaccc i equCab2.chr11 C 0 C 0 s canFam2.chr9 59360405 186 - 64418924 AGG---------TGGGCTCCCCCAACCCC---TGCC-------------ACGCAGTCAGCCCTCCCACCTCCCACTGTGGTGCCCC--CACCAGC-------TGTCCTTGGACTCCCCTCTCCCATGCTGGCCACAC-----CCAGTCTGGT---CACGCCCCCGCTCACTTCCTGCCTCACCCAGGACAGGGTCCAGGACTCCCCACAGCCACCATTCCCAAAACTC i canFam2.chr9 C 0 I 196 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e loxAfr3.scaffold_49 14291119 1463 - 17734757 I a score=56237.000000 s hg19.chr17_gl000204_random 16722 327 + 81310 ctttgtccctctcttttaaaaatattcatcagatgatgtcactgtcctgatCTGGTGAcacagccttccactggtgtcctgtgtcatttggaagaaacacttaaagttgcttcagtggcc-tgc------aagcca-------gg--tgaatctg-----------------gcttctgtgatt-t--GGGGACTT------------CCTAAGAAAATAA-------------------------CATACGAGGTCTCACATGGGGGCCGT-----------GCGCTCATAGACAGCT---TCACGGTCAACCCC-------C-TTT----------GCCTTTGGGGCTC--------------------TCGGCAGtctggctccctctcctagtatactccctctctcccctgcagccccactggcttcctg--------------gccatccc------------------------------------------tcc------acacag s rheMac2.chr16 74743276 328 + 78773432 ctttgtccctctcttttaaaaatattcatccgatgatgtcactgtcctgatCTGGTGAcacagccttccactggtgtcctgtatcatttggaagaaacacttaaagttgtttcagcggcc-tgc------aagCCA-------GG--TGAGTCGG-----------------GCTTCTATGATT-T--GGGGACTT------------CCTAAGAAGATCA-------------------------GATGCAAGGTCTCACAAGGCGGCTGT-----------GCGCTCGTAGACGGCT---TCATGGCCAACTCT-------CCTTG----------GCCTCTGGGGCTC--------------------TCGGCAGtctggccccctctcctagcacactccctctctcccctgcagccccattggcttcctg--------------gctgtccc------------------------------------------tcc------acgcag i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69577764 327 + 73212453 ctttgtccctctcttttaaaaatattcatcagatgatgtcactgtcctgatCTGGTGAcacagccttccactggtgtcctgtgtcatttggaagaaacacttaaagttgcttcagtggcc-tgc------aagcca-------gg--tgaatctg-----------------gCTTCTATGATG-T--GGGGACTT------------CCTAAGAAAATAA-------------------------CATGCAAGGTCTCACATTGGGGCCGT-----------GCGCTCATAGACAGC----TCATGGTCAACCCC-------CTTTT----------GCCTTTGGGGCTC--------------------TTGGCAGtctggccccctctcctagtacactccctctctcccctgcagccccactggcttcctg--------------gccatccc------------------------------------------tcc------acacag i ponAbe2.chr17 C 0 C 0 s mm9.chr11 118673094 318 + 121843856 CTTCGTCCCTCTCTTTTAGTAGGAATGGTCAGATCAT-GTCCCGTTCTAAC-------CACAACCCTCCCAGGGC------AGTCAATCGGAAGAAACACCCAACATTGCTTTGATGACCATGGTGAACTAACTCAGCCTTTGGG--AGCTCCCA-----------------GTTCACAGGATT-T--GAGG----------------TCTAGGAAAGTAA-------------------------GACCAGATGACAGACCCCG-AGCTAA-----------GCTATCACAGGTGGTC---TCGTGGTAAACCTC-------TCGCT----------GCCGATAGGACTC--------------------GTG--AGCTCTGGAACCTCTCCTATTGCACTCC--CTCATCCCTGTA--CCCA-GGGACTCCAG--------------AATATCAC------------------------------------------TGTAT----ACGCAG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4299480 228 + 7991924 --CTGTCCGGCTCTTTGCAGGAGATTCGCCAGCTGACAGTATTGCCCTGAC-------TACAACCCTCCCACGGT--CCCACTTCATTCAGAGAAAACATGCACAGTTG------------Tggta----aagccagcatttggg--agcctgag-----------------gtctacaggattct--gaggactc---gcg-----ctctaagaaaataa-------------------------gacaagatgacggatgtaa-agctga-----------gAT---GCAG--GGGC---CTGAGGCAGGTCTA--------------------------------------------------------------------------------TGCATTC---------------------------------------------------------------------------------------------------------ACACAG i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10756319 468 - 65312493 CCTTGTCCTTCTCATTCTAACAGATCCCCTTGGTGACTTCACTCTCCTGAT--------GCGTCCCCCCAACGGTGTCCTATTTCATGGGGAAGCAACACCCAGATTTGCTACA-----------------AACCA-------GG--TCAGtccaggtctggggactatgaggcttacatggtt-t--agggggtgagtgtgtccttttctaagaaaataagacaaggtggtggatgcaaaagtaaggtgcagggtcttacccgg-ggctcCATAGGTGCATAGGGCAagttg----ctcagtcgtgtccaactctttgggaccccatggactatacagtccatggaattctccaggccagaatactggagtgggtagtctttcccttctccagggaatcttcccaatccagggattgaaccca--ggtctcctacattgtcggcagattctttaccagctgagccacaagagaagcccaagaatattggaatgggtagcctatcccttctc-- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59360787 308 - 64418924 cCTGGTCCCTCtctttttaagagattctctgggtgaagtcactctcctaac--------atctccctccagcggcgtcctatgtccccgggagaaaacacccagggttgcaacactggcc-tgc------gagCCA-------AG--TGAAACCAGGTTTGGTGACCTCGACGCTTACATGATT-TGCGGGGGGGG-----------GCCTAAGATTACAA-------------AGGCAAAAATCAGCTGCAGGGTCTTGC-TTC-AGCTGT-----------GGGCTCAGTG----CT---tcctggtcaatcct-------cctct----------gcccacgggaccc--------------------tgagcagccc----------------------------------------ccg--ggcctccag--------------gccgtccc------------------------------------------tccgtcccaacgc-- i canFam2.chr9 I 196 C 0 s equCab2.chr11 57945978 322 - 61308211 ccttgtccctctctttttaaaagattcgccaggtgatgtcactctgctgat--------gcatccctccaacggcatcctatttcacc-ggaggaaacatccagactcgctacaatggcc-tac------gag----------agcttgaacccaggtttggggactctgaagcttacatggtt-t--ggggggct-----------ctctaagaaaataagacaagacgatggatgcaacaataagatgcatgctcttgtacgg-ggcTGT-----------GGGTTCGCAG----CT---TCAAGGTCAATCCT-------CCTGT----------GCCCATGGGCCCC--------------------TAGGCAGCCC---------------------------------------------GGGCTCCTGCTGTgcc-------actttccc------------------------------------------ctcctcctaccat-- i equCab2.chr11 C 0 C 0 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e loxAfr3.scaffold_49 14291119 1463 - 17734757 I a score=-13356.000000 s hg19.chr17_gl000204_random 17049 155 + 81310 gcgcatgcctccccgaccc------cacccctgcaccacacctttgcaggt----ctactg---ca--tggaatgctcttccctgcacaattgcaggcctccctccctccctccctccctgcctgcctccctccctccctccttgcctgcctccctccctccctgcctgc s rheMac2.chr16 74743604 101 + 78773432 gcgcatgcctcccggaccc------cacccc-gcaccacgcctttgcacgt----ctactg---ca--tggaatgcttttccctgcacatttgcagggctccttccctccctccctc----------------------------------------------------- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69578091 105 + 73212453 gcgcatgcctccccgaccc------cacccctgcaccacgcctttgcacgt----ctactg---ca--tggaatactgttccctgcACAATTGCAGGGctcgctccctccctccctccct-------------------------------------------------- i ponAbe2.chr17 C 0 I 664 s mm9.chr11 118673412 97 + 121843856 GGTAACTCTTCCTGGTGCC------C------ATAGCACACCT---CGTGT----CCACTGTCACA--TAGGGTGCTC-GCCCTCTATAATTGCATAGCTCTCTCCCTGCTCCAACCCC--------------------------------------------------- i mm9.chr11 C 0 I 91 s bosTau4.chr19 10756787 69 - 65312493 cagtggatcttcccgacccaggaatc------gaaccagggtctcctgcat--------tg---caggcag-attctttacc------aattg----------------------------------------------------------------------------- i bosTau4.chr19 C 0 I 83 s canFam2.chr9 59361095 69 - 64418924 acgcgggcctcc----ccc------t------gcaccacacctttgtgcct---------------------------------------ctg--ttgctcgggaccctcctccct----gcacaa----------------------------------------ctgc i canFam2.chr9 C 0 C 0 s equCab2.chr11 57946300 96 - 61308211 gcctccacccccctg-ccc------c------gccccaggcctttacacccgctgcttctg---ca--cag-atgctcttccctacgtaactg--gtggtctgcccctccctccct----g------------------------------------------------- i equCab2.chr11 C 0 C 0 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e cavPor3.scaffold_76 4299708 0 + 7991924 C e loxAfr3.scaffold_49 14291119 1463 - 17734757 I a score=1182.000000 s hg19.chr17_gl000204_random 17204 51 + 81310 ctgcatccctccctccttccctccttccttgcctccctccctccctccctg s cavPor3.scaffold_76 4299708 44 + 7991924 CTGGGTCCCTCCCACCTCCCCTA-------GCCTCCCAGCTCCCCTCCAGG i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10756939 48 - 65312493 ctgtaccactggcccctccccct--accatgcc-cactccctgcctccccg i bosTau4.chr19 I 83 I 3 s canFam2.chr9 59361164 22 - 64418924 --------ctggattctccctc---------------------cctccctg i canFam2.chr9 C 0 C 0 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e equCab2.chr11 57946396 0 - 61308211 C e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14291119 1463 - 17734757 I e ponAbe2.chr17 69578196 664 + 73212453 I e rheMac2.chr16 74743705 0 + 78773432 C a score=-3883.000000 s hg19.chr17_gl000204_random 17255 36 + 81310 c---ctgcctcccttcctccctccctccctgcct----gcctc s bosTau4.chr19 10756990 40 - 65312493 ---cctgcagtccccaggcctcccagctgtgcctccagaccta i bosTau4.chr19 I 3 I 6 s cavPor3.scaffold_76 4299752 33 + 7991924 CAAGCTGCCTCCCCATCAGTCCCCTGGAATGCC---------- i cavPor3.scaffold_76 C 0 C 0 s ornAna1.Contig103265 3 34 - 1411 ctcctcttctccctctattccctctaccaccccc--------- i ornAna1.Contig103265 N 0 C 0 e otoGar1.scaffold_94361.1-85690 40121 1633 + 85690 I e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e canFam2.chr9 59361186 0 - 64418924 C e equCab2.chr11 57946396 0 - 61308211 C e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14291119 1463 - 17734757 I e ponAbe2.chr17 69578196 664 + 73212453 I e rheMac2.chr16 74743705 0 + 78773432 C a score=-3396.000000 s hg19.chr17_gl000204_random 17291 48 + 81310 cctccctccctgcctgcctccctccctccctccctccctgcctgcctg s otoGar1.scaffold_94361.1-85690 41754 46 + 85690 Ccctcctccccgtgagcatgccgcccgccacccccacc--ccgcgcag i otoGar1.scaffold_94361.1-85690 I 1633 I 3 s ponAbe2.chr17 69578860 47 + 73212453 -ctccctccctccctccctccctccctgcctgcctacctgcctccctc i ponAbe2.chr17 I 664 C 0 s cavPor3.scaffold_76 4299785 18 + 7991924 -CTCCCTACCTATTGTGAG----------------------------- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10757036 48 - 65312493 cctcctcccccgcccccacccccaccccacatcacacctttctaccag i bosTau4.chr19 I 6 C 0 s ornAna1.Contig103265 37 45 - 1411 --ccttcacctctccgcagctaaaccctctttccccctttccctctg- i ornAna1.Contig103265 C 0 C 0 e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e canFam2.chr9 59361186 0 - 64418924 C e equCab2.chr11 57946396 0 - 61308211 C e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14291119 1463 - 17734757 I e rheMac2.chr16 74743705 0 + 78773432 C a score=-715.000000 s hg19.chr17_gl000204_random 17339 48 + 81310 cctgcctgc--ctccctc---cctccctccctgcctgcctg-------cctacctgcctc- s rheMac2.chr16 74743705 48 + 78773432 cctgtctgc--ctccctc---cgttcctccctgcctccctg-------catacctgcctc- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69578907 48 + 73212453 cctccctgt--ctgcctc---cctccctccctgcctgcctg-------cctacctgcctc- i ponAbe2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 41803 60 + 85690 cttgcctgctgctacatcaaatgctcttccctgaatagctgcggggcccctctcctccca- i otoGar1.scaffold_94361.1-85690 I 3 C 0 s cavPor3.scaffold_76 4299803 30 + 7991924 GCTGGTTGC--CCTGGTC---TCCTCTCCCCAG------TG-------------------- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10757084 45 - 65312493 -----ctgtaacatgggc---tgcactcccctacctaagtt-------ggggtttgcccc- i bosTau4.chr19 C 0 I 5 s ornAna1.Contig103265 82 47 - 1411 ctcctccac--ctctccc---ttcccctccccacagcactg---------tactcgtccgc i ornAna1.Contig103265 C 0 C 0 e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e canFam2.chr9 59361186 0 - 64418924 C e equCab2.chr11 57946396 0 - 61308211 C e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14291119 1463 - 17734757 I a score=-3802.000000 s hg19.chr17_gl000204_random 17387 71 + 81310 ggag--ctgtgcaca---tatggcacctttcca------aggccatccaggagcagaacaccccatcaa--------aataacca---gcatc s equCab2.chr11 57946396 71 - 61308211 ggga--ctgt---cc---tatggcacccttccagga---aggccgtcctggccaagaacacc---ccat-------tcaaaaggaacccca-t i equCab2.chr11 C 0 C 0 s canFam2.chr9 59361186 71 - 64418924 gggactctgt---ta---cacagcacccttccagt-----ggccaacctggagccgaacacccttccaa-------tcacagcgg---ctg-c i canFam2.chr9 C 0 C 0 s bosTau4.chr19 10757134 74 - 65312493 gggattccat---ta---catgacacttttccagag---aggtcatctgaaaaccaaacaccttatcag-------aaataacca---ccatc i bosTau4.chr19 I 5 C 0 s cavPor3.scaffold_76 4299833 41 + 7991924 ---A--CTCTGAACATAGTATGTCCCATTT---------AAGCCATCC-------------------------------CAGCCA---G---- i cavPor3.scaffold_76 C 0 C 0 s otoGar1.scaffold_94361.1-85690 41863 66 + 85690 ggga--ctct----------tggtccctttccaatg---aggccatccagaaacagatca-cctataaa--------aataacca---ccacc i otoGar1.scaffold_94361.1-85690 C 0 C 0 s ponAbe2.chr17 69578955 71 + 73212453 ggag--ctgtgcaca---tatggcacctttcca------aggccacccaggagcagaacaccccatcaa--------aacaatca---gcatc i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74743753 71 + 78773432 agaa--ctgtgcaca---tatggcacctttccg------aggccatccaggaacagaacaccccatcaa--------aataacca---gcatt i rheMac2.chr16 C 0 C 0 s ornAna1.Contig103265 129 81 - 1411 tcaa--ctgt----a---tatatttccattaccctatttattttgttaatgaattgtacatcgccttgattctatttagttgcca---ttgtt i ornAna1.Contig103265 C 0 C 0 e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14291119 1463 - 17734757 I a score=42327.000000 s hg19.chr17_gl000204_random 17458 341 + 81310 cctatggcatttccttctccttt-tccccacgaatt----tccccccagggacttagcacatctg-gcttcatgcggatgtgctgg-atcccgccatcccactttgcctccactg-------gaatgcaggc----tccctgag---ggcaggc--atccacaacgg---ctggatttagtgctg-------aatcccca--gtgcccaggat-gtgcctggcacatagctggggctcactccgtattcttctgagtggataagtAAATGAATGAATGA--------ATGAACCCACAAAAG--TTACTCCCCCATTAATACTTCTGGGTTTATTTAGAATCATATCCCACGATC---------ACACCGGAGAGCAGGAATTC-----CCGGG-A--TATGGA----- s rheMac2.chr16 74743824 348 + 78773432 cctctggcatttccttctcctttccccccatgaattccccccccccccgggacttagcacatctg-gcttcacgtggatgtgctgggatcccaccatcctgccttgcctccgctg-------gaatgcaggc----ttcctgag---ggcaggcatattcacatctg---ctggatttagtgctg-------aatcccca--atgcccaggat-gtgcctggcacacagctggggctcgctccatatttttctgagtgaataagtAAATGAATGAA-GA--------ATGAACCCACAAAAG--TTACTCCCCCATTAATACTTCTGGGTTTATTTAGAATCATATCCCACTATC---------ACACCAGAGAGCAGGAATTC-----CCGGG-A--AACGGA----- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69579026 342 + 73212453 cctatggcatttccttctccttt-tcctcatgaata----tccccccagggacttagcacatctg-gcttcatgtggatgtgctgggatcccgccatcccactttgcctccactg-------gaacgcaggc----tccctgag---ggcaggc--atccacatctg---ctggatttagtgctg-------aatcccca--gtgcccaggat-gtgcctggcacatagctggggctcgctccatatttttctgagtggataagtAAATGAATGAATGA--------CTGAACCCACAAAAG--TTACTCCCCCATTAATACTTCTGGGTTTATTTAGAATCATATCCCACTATC---------ACACCAGAGAGCAGGAATTC-----CCGGG-A--TATGGA----- i ponAbe2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 41929 282 + 85690 ccca-ggcattccctgcccccct--ttccATAAACT----GCCCCC--AGGACGGGTCATACGTGTGCCTCCTGC---TGCCTTGG-----------------TTGCCTTGG--G-------GAAAGCAAGCTCTGTCCGTGGG---GACAGAC-----------------TGGgttcagtacta-------tgt-cccg--gtgcctagaac-atgcacag--------tggggctcactccatattttt---------taaGtgaatgaatgaatga--------atgaaCCCACAGGTT--TCTCTTCCCCATCAGTACTTCTGGGTTTATCTAGAACAGTCTCTCATTATC---------ACTCTCTAGACAGGGAAT-----------------GAGAA----- i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4299874 275 + 7991924 --------ACGCCCTGCTCCCTT---CCTATGGACG--CCCCCCCCCCACTACT-----CATCTG-ATGTCAC-TGTAAGCTTTTG------------------CACCCCTGCTG-------GGATGCGTG-----TGCCTGAGGAAGGCAGAC--CTCCGCAGCCAGCCGTGGGACTCACACTG-------AATCCCT----------------------------------GGCTAGTTC--------------AGGTTAAGCAA--GAAGGAAAGA--------ATGCTCCTCTCA------CTCTTTCCCACTGATGCTCCTGGTTGTATTTAGAGCCGTGTCTCATCTTCTGGAGTTAGGCTCCAGGAAGTGGTGAGTC-----CTGTG-GCCCCCAAA----- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10757208 327 - 65312493 cccttggtactccttccttcttt-tccccatgaatt----ttccc---agaaattattgaatctg-ctgtcacatagatgcatttgctgcctgtggtctttctttccccctccctcaacccagaatgccaac----ttcctgcg---ggcagac---acttgatctg---ttttattcatta----------tatctcca--gtgcttggaac-acacctagaacatagctggagctcactcagtattcat---------caagcgaatcaatAAACAA-------------CCCCCAACT---TTTATTCTCATTTTGCACTCTTAGATTTACTTAGAACAGTGTCTCA-TATT---------AGTCTTTAGAGCAGAAATTC-----CCAGGAA--AACAGA----- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59361257 260 - 64418924 cctttggcatcccctcctcctct-gccccatgaatt----tcccc---ggggctgatcacatctg-ctaccacacagatg---------cctgagg---------------------------------------------gca---gataca------tgggtctg---tcttaat----acc--------cgtccccagcgtgcctagacg-gtgcctggcacacagctggcactccctcggtgtttgt---------ccagtgaaggaatGAAGGA-------------------------ACTGTCCCCTATGCACAC-ATCAGGCTTCCGTAGGACACTATCCTA----C---------AGTCCCTGGAGTCAGGATTC-----CCAGG-G--AACACA----- i canFam2.chr9 C 0 C 0 s equCab2.chr11 57946467 326 - 61308211 cccacggcgctccctcctccttt--ccccatgaacc----tcccc---cagga----ctcgtccg-ctagcacacagatgcacttatttcctggggccttccttcgccccacccc---------atgcaagc----accctgag---gatgcac----ttggacctg---ttttactcagcact--------ccacccca--gtgcctgga---acacccggcacatagttggagctcccttagcatttgt---------cgatcgaatgaaCAAATGAAAGAATGGCCGAACCCCCACTTTC-ATTGCCCCGCCTTCACACTTTTGGGTCTATTTAGACCAGTGTCCCATTACC---------ATTCTCCAGAG-CGGGATTC-----CCAGG-A--AACAGA----- i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14292582 314 - 17734757 CTTATGGCATCTGGTACCCTATC-TATTCACTTGTT----TCCTT----------ACTGcatctg-gaatcctatgtatttactcatttcctgttgccttgacttgtccccactg--------aacaaaagc----tccaggaa---ggcaggc--gcttggag--g---ttttattcaatgctc-------tctgccca--gtgcc--agac-atgcctggtacctagttgacgctcactcagtatttgt---------tgagtgaatgaatGAAGGA--------ATGAGCCTTCACTTCTACTGGCCACCGGTTACTACTTCTGGATTGGCTTGGAATATCATTCCACTGTC---------ACTCCCTGGAG------TCT-----CTGGG-T--GGTGGA----- i loxAfr3.scaffold_49 I 1463 I 743 s ornAna1.Contig103265 210 283 - 1411 tttacgagatgttcttcccctcg-actctatttatt----gccat--------tgttcttgtctg---------------------------------tccatctcccccgatta-------gactgtaagc----cc---------gtcaaac--ggcagggactg--tctctatctgttgccgacctgttcatcccaa--gcgcttagtacagtgctctgcacatagtaagcgctcaataaatactatt--------------gaatgaatgaaaga--------tcagagagctgaggggtagaatccccaaat----------------ctgagggcagaggcCCA----A---------GGTCTTAAGGGAAAAGGTCCGAGAACTGAG-G--AGCAGAGGCCA i ornAna1.Contig103265 C 0 C 0 e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e mm9.chr11 118673509 91 + 121843856 I a score=-25905.000000 s hg19.chr17_gl000204_random 17799 51 + 81310 GGGGACT-GAAGGATTCTGTTT----GTTTAGTTGGTGAGGGCTGGCAGGG---------------GGTAG s equCab2.chr11 57946793 63 - 61308211 AGGGGCC--GTGGTTTCTGGGT----GCCTTG-TGGCAGCGGCTGGTTGGGTTCTGT-GGGGGTAAGAAGC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59361517 42 - 64418924 A--GGCC--ACAGGTTGCTGCT----GTTTGG-AGTCAG-----GGTTGGG---------------GGGGC i canFam2.chr9 C 0 C 0 s bosTau4.chr19 10757535 67 - 65312493 AGTGATCTGGTTGTTTGTGTTT----ATTTTGTTGGTGATGGCTGGTTAGGTTTTGTAGAGGGTAGGAGGC i bosTau4.chr19 C 0 C 0 s cavPor3.scaffold_76 4300149 29 + 7991924 AGGGGCT-GGGGG---------------------TGGGAGCGCCGGT--------------------GCAC i cavPor3.scaffold_76 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42211 21 + 85690 GGGGGCT-GGCGG-------------------------------GGCAGTG---------------G---C i otoGar1.scaffold_94361.1-85690 C 0 C 0 s ponAbe2.chr17 69579368 51 + 73212453 GGGGACT-GGAGGATTTTGTTT----GTTTAGTTGGTGAGGGCTGGCAGTG---------------GGTAG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74744172 51 + 78773432 GGGGGCC-GGAGGATTCTGTTT----GTTTGGTTGGTAGGGGCTGGCAGGG---------------GGTAG i rheMac2.chr16 C 0 C 0 s ornAna1.Contig103265 493 55 - 1411 GAGGGCT-GAGGGGTAGTGTCCAGAGGGCTGAGGGGCAAAGGCCAGAAGGC---------------TGAAG i ornAna1.Contig103265 C 0 C 0 e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14292896 743 - 17734757 I a score=114086.000000 s hg19.chr17_gl000204_random 17850 186 + 81310 -----------------------------ACCCAAGCCTGGGAAGTCT--TGTTTGCTTAATTTACTCCAACCCAAACAGTGTATGTGT-GCCATCAGCCAGACAGGACACAAAAACGGTTTAGGAGATCCACTCTGATTAGCCT-GAGAGACTGTCTCTGGGACAGAGTCA--TGAGATCAGGGT----GG-----CCAGGGAGTGGCTGAGCTGTGT---CTCCCTGAATC s rheMac2.chr16 74744223 188 + 78773432 -----------------------------ACCTGAACCTGGAAATTCT--TGTTTGCTTAATTTACTCCAACCCAAACAGTGTATGTGT-GCCGTCAGCCAGACAGGACACAAAAACGATCTAGGAGATCCACTCTGACCAACCC-GAGAGACTGTCTTTGGGATAGAGTCA--TGAGATCGGGGT----GG-----CCAGGGAGTGGCTGAGCTGTGT-GATTCCCTGAATC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69579419 185 + 73212453 -----------------------------ACCCGAGCCCGGGAAGTCT--TGTTTGCTTAATTTACTCCAACCCAAACAGTGTATGTGT-GCCATCAGCCAGACGGGACACAAAAACGGTTTAGGAGATCCACTCTGATTAGCCC-GAGAGACCGTCT-TGGGATAGAGTCA--TGAGATCAGGGT----GG-----CCAGGGAGTGGCTGAGCTGTGT---CTCCCTGAATC i ponAbe2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42232 137 + 85690 -----------------------------ACCCAAGCCTCAGAAGTCTCCTGTCCACTTGGTTTACTCCAACCCAGGCAGCACA--------CAGCAGGCAGGC------------------AGGAGACCCGCTCTGACCCACTC-----------------------------CGAGATGGGGTT----GG-----CCGGGGAGTGGCTGAGCCATGT---CTGCTCACGTC i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4300178 176 + 7991924 -----------------------------ACCTTGGCCCTGGAAGACTTCTGTGTGCTC-ATCTATCCCACTCTGAATAGCGTG--CCT-GCTGCCAGGCTGGTAGAAGGC--ACACAGCTTGGGAGAGCAGCTCC-ATCAGCCT-GC-AGCCTGGCTCTGGGGCCGA------TGCGATCAGGCT----GGGAGTCCCAGGGAGGAGTGGAG---------CTCCTCACCTT i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10757602 182 - 65312493 -----------------------------ACCTGGGCCTTGGAAGTCTTTTCTTTGCTTAATTTATCTCAACCCA------GTGAGTGT-GCCATTAGGCAGACAGGACACATAAACCATTTAGGGGATCCATCCTGATCAGTCCAGAAGGACTGGCTTTGGGGAGGGCTTG--TGAGGTCTTGTT----GG-----CCAGAGGATGGTTCAGCTCTGCCCACCCC----CCC i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59361559 170 - 64418924 -----------------------------ACCTGGGCCTTGTCAGGCCTTTCTTTGCTTAATTCACACCAACCT-------GCATGCAT-GCCAACAGGCAGGTAGGACCCCAAGACCATTCAGGGCATCCTCTCTGGCCAGTCCCCCAAGACCGGCTCCAGGGCAGGGTCC----AAGGCGGGTT----GG-----CTGGGGAGTG--------GTCC---CCCC--AGCCC i canFam2.chr9 C 0 C 0 s equCab2.chr11 57946856 177 - 61308211 -----------------------------ACCCAGGCCTTGG-AAGTCTTTCCCTTCTTGAGTTACTCCAACCTA------GTATGTGT-GCCATCAGGCAGACGGGGCACAAAG-CCCTCGAGGAGAGCCATGCTGAGCAGCCTGGAGACACTGGCTTTGGGGCAGAGTCC--TGAGATCAGGTG----GG-----CCTGGGAGTGGGTGAGCTGTGC---CCCC----CTC i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14293639 162 - 17734757 -----------------------------ACCTGGGTTTTGGAAGTTTT-TCTTTACTTAATTTATTCCAACCCAAATA--GAATGTGT-GCTATCAGGCAGATAGGATACAAAGCTTGTTTAGAGG--------TGGTT------GGAAGACT---TTTGGGTTAGAGTTG--TAAGATCGGGTT----GT-----CGAGGGAGTGGCTGGGCTGTGT---CCAC------- i loxAfr3.scaffold_49 I 743 C 0 s ornAna1.Contig103265 548 201 - 1411 GGCAGAGGTCAGAAGGCTGAAGGGCAGAGATCAGAGAGCTGAGAG-----AGAGAATCCAATGTGCCTCAGCCAGAGGG--GTAGGGGCAGAGACCAGAGATCTGAGGTGCAGAGACCAGAGAGGTGAGGGGCAGTGGCCA-----GAGAG-----CTGCAGGGCAGAGGCCAGAGAGATGAGGGGCAGAGG-----CCAGAGAGGGGCAGAGATCTGA---AGCC------- i ornAna1.Contig103265 C 0 I 29 e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e mm9.chr11 118673509 91 + 121843856 I a score=-5803.000000 s hg19.chr17_gl000204_random 18036 21 + 81310 CCCCCCA------------CCAC--TGGCAC-CACC--- s loxAfr3.scaffold_49 14293801 22 - 17734757 --CCTCA------------GCAGAACGGCTCATCCC--- i loxAfr3.scaffold_49 C 0 C 0 s equCab2.chr11 57947033 34 - 61308211 ACCCCCAGTGGAAAGTCTCCCAG--TGGCGTGTCCC--- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59361729 33 - 64418924 GCCTCCA-TGGAAAGGCTCCCAC--TGGCACATCCC--- i canFam2.chr9 C 0 C 0 s bosTau4.chr19 10757784 34 - 65312493 TACCCCAGTGGAAAGACTCCCAT--TGGCATGTCCC--- i bosTau4.chr19 C 0 C 0 s cavPor3.scaffold_76 4300354 14 + 7991924 CCGCCCA------------CC-------CAT-CA----- i cavPor3.scaffold_76 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42369 22 + 85690 ATCCCTA------------CCAT--TGGCAGATCCC--- i otoGar1.scaffold_94361.1-85690 C 0 C 0 s ponAbe2.chr17 69579604 21 + 73212453 GCCCCCA------------CCAC--TGGCAC-CACC--- i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74744411 21 + 78773432 GCCCCCA------------CCAC--TGGCAG-CACC--- i rheMac2.chr16 C 0 C 0 s fr2.chrUn 234146070 21 + 400509343 CCCCCGA------------CCAC--CAG----CCCCAAA i fr2.chrUn N 0 I 12 e ornAna1.Contig103265 749 29 - 1411 I e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e mm9.chr11 118673509 91 + 121843856 I a score=-26889.000000 s hg19.chr17_gl000204_random 18057 174 + 81310 CAGAAATTTCACAACGGAGTTTTAAACAGC-----AACA--CACAACAATAA---TAAATCTACCAGT----------------TTG----TTTCTTTTCCTAAAATC----CAGTCACTG---------------GACAGAGT---------ACCACCCCCATA--------CCGAA-------GAACCGAAGAGCAGAACC---------AGCATCACAGAGAGCCCAGCAACCCCGGAGCAATGCCTGGGGAA s rheMac2.chr16 74744432 168 + 78773432 CAGAAATTTCACAACGGGGTTTTAAACAAC-----GACGACAACAACAATAA---TACATTAACCAAT----------------TTG----TTTCTTTTCCTAAAATC----CAGTCACTG---------------AATGGAGT---------ACAACCCCCAC-----------------------ACTGAAGAGCAGAACC---------AGCATCCCAGAGAGCTCAGCAGCCCTGGAGCAATGCCTGGGGAA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69579625 174 + 73212453 CAGAAATTTCACAATGGGGTTTTAAACAGC-----AACA--CACAACAATAA---TAAATCTACCAGT----------------TTG----TTTCTTTTCCTAAAATC----CAGTCACTG---------------AACAGAGT---------ACCACCCCCATA--------CTGAA-------GAACTGAAGAGCAGAACC---------AGCATCACAGAGAGCCCAGCAACCCCTGAGCAATGCCTCGGGAA i ponAbe2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42391 149 + 85690 CAGAAATATCACCACAGGGCTCTAAACAAC-----AACA------AAAATAA---TAAAACTACTAGT----------------TTG----CTTCTTTTTCTAAAATG----CAGCTATGG---------------AAGGGAAC---------ACCAGCCCATT------------------------CCAAAAAGCAGGACT---------GGC-CCCTGGAGAGCCTCGT----------CCATCCCT-GGGAA i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4300368 145 + 7991924 CAGAGATCTCACGACAGGGCCTTAGAGGAA-----AAAC--ACTGCTACTGT---TAAAATTCCC--------------------TG----CTTCTTTTCCTACAATG----CAGTTACTT---------------AAGGGAGC---------CCAGCCCCCAG------------------------CCTAATGGCAGGAGC---------AACTTCACAGAGAGTGCTGC----------CAGCCCCT------ i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10757818 159 - 65312493 CAAAAATCTCACAACACAGCTTTGAAACAT-----AATA--------AAGA----AAAAATTGTCAGT----------------TTT----TTCCTTTTCTTAAAATC----CAGTTACTG---------------AACACAGAG--------ATGGCCCCCAT-----------------------CCCAAATGGCAGGGCC---------AACCTCACAGAGTGC-TGCCAACTGCAGAGAAATGCGTGGGCAC i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59361762 161 - 64418924 CAGAAATCCCACAATGGAGCTTTAAAAAAG---GAAAAA--------AAGAA---AAAGACTACCAGT----------------TTG----TTTCTTTTCCTAAAATC----CAGTTACTT---------------AAAGGAGA---------ACCACCCACAT-----------------------CCCAAATGGCAGGGCC---------AACCTCACAGGGCAC-TGCCACCCGCACAGAAATGCCCGGGCAC i canFam2.chr9 C 0 C 0 s equCab2.chr11 57947067 167 - 61308211 CAGAAATCTCACACTGGAGGTTaaaaaaagagagaaaga--------aagaaaggaaaaaCTACCAGT----------------TTG----TTTCTTTCCCTAAAATC----CAGTTTCTT---------------AAGGGAGC---------ACCACTCACAT-----------------------TATAAACGGCAGGGCC---------AACCTCACAGAGCGC-CACCAACCGCAGAGAAATGCCCCAACAC i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14293823 100 - 17734757 CAAAAATCCAACAAGAAGGCTTTAAAAAAA-----AAAA--------ACAAA----------ACCAG----------------------------TTTTCCCAAAGTC----CAACTACTT---------------AAGAAAGC----------CCACCCACAC-----------------------CCTAAACAGCAGGACC----------------------------------------------------- i loxAfr3.scaffold_49 C 0 I 1791 s ornAna1.Contig103265 778 149 - 1411 CAGAAATCT------GAGGCCTGAGGGGAA-----GAGG---CCAGTGAGAA---GAGGGTCATAAGC----------------CTG----AGAG-----CTGAGGGG----CAGAGAGCT---------------GAGAGAGAGAGAGGCCAATGGGCCCCTCAG-------CCAGA-------GGGCTGAAGGGTAGAGGC---TAGACAAGTGAGGGATAGAGG----------------------------- i ornAna1.Contig103265 I 29 N 0 s fr2.chrUn 234146103 192 + 400509343 CAGGAA-----AAATGATGTTGCAGTAAAT-----GATA----------CAG---TAAACCAGCCTGT----------------TTGGGCCTGTCTGGTTCTCTAATC----TGGTCTCTTTCCTCTGTGTATCTAAAGGAGGA---------GGGAACCATaggggaggggcccagagtggaggggcccagagtggaggggcccatagtggaggggcccggag---tggaggggCCCAGAGTGGAG--------- i fr2.chrUn I 12 C 0 s petMar1.Contig17954 12646 148 + 13192 CAAAAATAACCTGAATTAGCTTGAGGGGGA-----AGCA-------CGAAAT---TGTGTTGAATGGTACCTGGGTTCCTTTTAATG----TCTATTTTTTGAGAATCAACACGAGCCCAG---------------TACAAAGC---------ACCAATCACAG-------------------------TACAAGGAGGGCCC---------AGAGACCTGGCGA------------------------------- i petMar1.Contig17954 N 0 C 0 e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e mm9.chr11 118673509 91 + 121843856 I a score=-29520.000000 s hg19.chr17_gl000204_random 18231 48 + 81310 CATCTGCCCTTTCAGGGACCATTGG---TACAG-AGCCCAGTGCCCACTGCT s rheMac2.chr16 74744600 48 + 78773432 CATCTGGCCTTTCAGGGACCATCGG---TGCCG-AGCCCAGTGCCCAGTGCT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69579799 48 + 73212453 CATCTGCCCTTTCAGGGACCACCGG---TGCAG-AGCCCAGTGCCCACTGCT i ponAbe2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42540 42 + 85690 CATGAGCCCCAGCAGGGACCACC---------C-CGCACAGTGCCAGCTGCT i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4300513 29 + 7991924 ------GCCTTAC-----CCACCAG---TACCA-CACTCAGCGC-------- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10757977 47 - 65312493 AACCC-CCTTTTCAGTGGCCATCCG---TGCCA-GGCACAGAGCTAGGACCT i bosTau4.chr19 C 0 I 10 s canFam2.chr9 59361923 48 - 64418924 CACAGGCCTTTTCAGTGACCATCCG---TGCCA-TGCACAGCACCAGGAGCT i canFam2.chr9 C 0 I 9 s equCab2.chr11 57947234 48 - 61308211 CATCTGCCTTTTCAGGGACCATCAG---TGCCA-CACGCAGAGCCAGGAGCT i equCab2.chr11 C 0 I 10 s gasAcu1.chrI 27962925 45 + 28185914 CAGCAGGTCTGTCT-GCAGCCGTCTGTCTGCAGCCGTCTGTCTGCA------ i gasAcu1.chrI N 0 I 2 s danRer6.chr8 22861323 28 + 55568185 --------------GGGTGCACTGG---TAAAG-GGCGTGGATGCT------ i danRer6.chr8 N 0 I 2 s fr2.chrUn 234146295 22 + 400509343 ---------------GGAACCATAG---TGGAGGGGCC------CA------ i fr2.chrUn C 0 I 4 s petMar1.Contig17954 12794 44 + 13192 CAGGTACC----CAGGGACCAGGGA---CCTGG-CGACAGGTACCCAGGGAT i petMar1.Contig17954 C 0 C 0 e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=-20192.000000 s hg19.chr17_gl000204_random 18279 19 + 81310 ---------GGGTGTGGGAGCCACT---CTT s rheMac2.chr16 74744648 19 + 78773432 ---------GGGCGTGGGAGCCACT---TTT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69579847 19 + 73212453 ---------GGGCATGGGAGCCACT---TTT i ponAbe2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42582 19 + 85690 ---------GAGCACAGGAGCTTCT---TTT i otoGar1.scaffold_94361.1-85690 C 0 C 0 s fr2.chrUn 234146321 16 + 400509343 ---------GGAGGGAACCATAGTG------ i fr2.chrUn I 4 I 23 s gasAcu1.chrI 27962972 16 + 28185914 ---------GGGTCTGTCTGCAGCC------ i gasAcu1.chrI I 2 N 0 s oryLat2.scaffold5002 3495 15 + 4714 ---------ggggaggggggcagc------- i oryLat2.scaffold5002 N 0 I 17 s danRer6.chr8 22861353 19 + 55568185 ---------GGGTGTGGGTGCACTGCCA--- i danRer6.chr8 I 2 I 31 s turTru1.scaffold_106006 24168 9 + 145505 -------------------GCCACT---TTT i turTru1.scaffold_106006 N 0 C 0 s petMar1.Contig17954 12838 22 + 13192 AAGAGACCTGGTGACAGGTACC--------- i petMar1.Contig17954 C 0 C 0 e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e canFam2.chr9 59361971 9 - 64418924 I e bosTau4.chr19 10758024 10 - 65312493 I e equCab2.chr11 57947282 10 - 61308211 I e cavPor3.scaffold_76 4300542 0 + 7991924 C e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=-108104.000000 s hg19.chr17_gl000204_random 18298 35 + 81310 CA----ATGGCAAAA--GTGTAAGTAATAGGAAC-------AGTTCCA s rheMac2.chr16 74744667 35 + 78773432 CA----ATGGCAAAA--GTATAAGTAATATGAAC-------AGTTCCA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69579866 35 + 73212453 CA----ATGGCAAAA--GTGTAAGTAATAGGAAC-------AGTTCCA i ponAbe2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42601 42 + 85690 TA----ATGGGAAGT--GTGTGTGACATAGTGTCCCATCCTAACTCCA i otoGar1.scaffold_94361.1-85690 C 0 C 0 s turTru1.scaffold_106006 24177 28 + 145505 CA----AGGGGAGAAACAAGTGTGTGATCTGA---------------- i turTru1.scaffold_106006 C 0 I 8850 s bosTau4.chr19 10758034 8 - 65312493 ------------------------------GA-----GGCCAG----- i bosTau4.chr19 I 10 I 10 s canFam2.chr9 59361980 16 - 64418924 -------GAGGATGG---------------GA---------AGCCGC- i canFam2.chr9 I 9 I 61 s equCab2.chr11 57947292 17 - 61308211 -------GGGGACAG---------------GA---------AGAGCCC i equCab2.chr11 I 10 C 0 s fr2.chrUn 234146360 22 + 400509343 CATAGTGGAGGGGCC--CAGAGTG------------------------ i fr2.chrUn I 23 C 0 s gasAcu1.chrXIII 4066918 17 - 20083130 TA----GGAGCAGGG--CTGGCC------------------------- i gasAcu1.chrXIII N 0 C 0 s oryLat2.scaffold5002 3527 18 + 4714 TG----AAAACAGTT--CTGACTG------------------------ i oryLat2.scaffold5002 I 17 C 0 s danRer6.chr8 22861403 18 + 55568185 TG----GCACAGGAC--GTGGGTG------------------------ i danRer6.chr8 I 31 C 0 s petMar1.Contig17954 12860 31 + 13192 CA----GGGATAAGA--GACCTGGCGACAGGTACCCA----------- i petMar1.Contig17954 C 0 N 0 e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e cavPor3.scaffold_76 4300542 0 + 7991924 C e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=-65085.000000 s hg19.chr17_gl000204_random 18333 40 + 81310 TGGATGAAAT------GCAGCCAGGGAGGTGGCTG-------------GGAGAGGGCCT s rheMac2.chr16 74744702 34 + 78773432 TGGATGAAAT------GCAGCCAAGGAGGTGGCTG-------------GGAGA------ i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69579901 34 + 73212453 TGGATGAAAT------GCAGCCAGGGAGGTGGCTG-------------GGAGA------ i ponAbe2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42643 40 + 85690 TGGTCAAAAG------GCAGAGAGGGAGATGGCTG-------------GGGAGGGCCCT i otoGar1.scaffold_94361.1-85690 C 0 I 10 s equCab2.chr11 57947309 21 - 61308211 TGAGC---------------TCCAAGAGGCCGCTG-------------G---------- i equCab2.chr11 C 0 I 48 s petMar1.Contig42085 12075 46 - 12361 tgggtgtagggtgtctgggtgtagggtgtctgggt-------------gtagagtgtct i petMar1.Contig42085 N 0 C 0 s danRer6.chr8 22861421 25 + 55568185 ---------------------CTGAGGGTGTGGAT-------------GCACTAGCACA i danRer6.chr8 C 0 C 0 s oryLat2.scaffold5002 3545 25 + 4714 ---------------------CAGAGGTTCTGACT-------------GCAAAGGTTCT i oryLat2.scaffold5002 C 0 C 0 s gasAcu1.chrXIII 4066935 25 - 20083130 ---------------------CAGTGCCTGGGGGT-------------GCCTGGGCCCG i gasAcu1.chrXIII C 0 C 0 s fr2.chrUn 234146382 25 + 400509343 ---------------------GAGGGGCCTGGAGT-------------GGAGGGGCCCG i fr2.chrUn C 0 C 0 s cavPor3.scaffold_76 4300542 11 + 7991924 ----------------------AGGTAGGTGGC-------------------------- i cavPor3.scaffold_76 C 0 I 3 s xenTro2.scaffold_1193 113211 27 + 135655 -------------------GTCTGGGTACTGGGGT-------------GTTGGGGGTCT i xenTro2.scaffold_1193 N 0 C 0 s micMur1.scaffold_27997 193 43 + 9776 ----------------GCTGTCAGAGGCCTGGCTGCCGTGGCCTGGCTGCCAGAGGCCT i micMur1.scaffold_27997 N 0 I 29 e turTru1.scaffold_106006 24205 8850 + 145505 I e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e canFam2.chr9 59361996 61 - 64418924 I e bosTau4.chr19 10758042 10 - 65312493 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=2404.000000 s hg19.chr17_gl000204_random 18373 27 + 81310 GGGTGCAGGGGGCCTGGGTG-CAGGGGC- s bosTau4.chr19 10758052 27 - 65312493 GAGCTCCACAGGCCACTTTT-CACGGGG- i bosTau4.chr19 I 10 C 0 s myoLuc1.scaffold_141316 43029 27 + 75010 GGGTGCAGGGGGCCCGGGTG-CAGGGTA- i myoLuc1.scaffold_141316 N 0 C 0 s cavPor3.scaffold_76 4300556 17 + 7991924 GGTTGTCGGACACAGGA------------ i cavPor3.scaffold_76 I 3 C 0 s tupBel1.scaffold_81392.1-4505 1167 27 + 4505 GCGTGCAAGGGCCCTGCGTG-CAGGGCT- i tupBel1.scaffold_81392.1-4505 N 0 C 0 s otoGar1.scaffold_96368.1-179817 149890 27 + 179817 GGTTGAGAGGGACTAGGCTG-TAGAGGG- i otoGar1.scaffold_96368.1-179817 n 10 C 0 s micMur1.scaffold_27997 265 27 + 9776 GGCTGCCGGAGGCCTGGCTG-CTGTGGC- i micMur1.scaffold_27997 I 29 C 0 s dasNov2.scaffold_186432 513 6 + 4438 ----------------------GGGGGC- i dasNov2.scaffold_186432 N 0 C 0 s xenTro2.scaffold_1193 113238 28 + 135655 GGGTACTGGGGGTCTGGGTGTTGGGGGT- i xenTro2.scaffold_1193 C 0 C 0 s fr2.chrUn 234146407 27 + 400509343 GAGTGGAGGGAACCATAGTG-GAGGGGC- i fr2.chrUn C 0 I 1 s gasAcu1.chrXIII 4066960 27 - 20083130 GGGTGCCTGGGCCCGGAGTG-CCTGGGC- i gasAcu1.chrXIII C 0 I 1 s oryLat2.scaffold5002 3570 27 + 4714 GACTGCAAAGGTTCTGAGTG-CAGAGGT- i oryLat2.scaffold5002 C 0 I 196 s danRer6.chr8 22861446 27 + 55568185 GGACGTAGGTGCTGAGGGTC-TGTTGGC- i danRer6.chr8 C 0 I 7 s petMar1.Contig42085 12121 28 - 12361 gggtgCAGGGCGTCTGGGTG-CAGGGCGT i petMar1.Contig42085 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e canFam2.chr9 59361996 61 - 64418924 I e equCab2.chr11 57947330 48 - 61308211 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e ponAbe2.chr17 69579935 0 + 73212453 C e rheMac2.chr16 74744736 0 + 78773432 C a score=26996.000000 s hg19.chr17_gl000204_random 18400 32 + 81310 CT--GGGTGCAGGGGGCCTGGGTGCAG-GGGGCCT s bosTau4.chr19 10758079 9 - 65312493 AG--AGATACA------------------------ i bosTau4.chr19 C 0 I 16 s myoLuc1.scaffold_141316 43056 32 + 75010 CC--GGGTGCAGGGGGCCCGCGTGCAG-GGGGCCC i myoLuc1.scaffold_141316 C 0 C 0 s cavPor3.scaffold_76 4300573 30 + 7991924 ----AGGGGCAGTAACCCTGGCTCTGG-GGTTACT i cavPor3.scaffold_76 C 0 C 0 s tupBel1.scaffold_81392.1-4505 1194 32 + 4505 TC--GTGTGCCCGGACTCTGCATTCAG-GGGCTCA i tupBel1.scaffold_81392.1-4505 C 0 C 0 s otoGar1.scaffold_96368.1-179817 149917 33 + 179817 CTTGGGGTGGAGGGGACCTGG--GTTGAGGGGTCT i otoGar1.scaffold_96368.1-179817 C 0 n 0 s micMur1.scaffold_27997 292 32 + 9776 CT--GGCTGTTGGAGGCCTGGCTGTTG-GAGGCCT i micMur1.scaffold_27997 C 0 C 0 s dasNov2.scaffold_186432 519 32 + 4438 CT--CGGTGGAGGGGCCTTTGGTGGAG-GGGGCCT i dasNov2.scaffold_186432 C 0 C 0 s xenTro2.scaffold_1193 113266 32 + 135655 CT--GGGTACTGGGGGTCTGGGTGTTG-GGGGTCT i xenTro2.scaffold_1193 C 0 C 0 s fr2.chrUn 234146435 32 + 400509343 CG--GAGTGGAGGGGCCCAGAGTGGAG-GGAACCA i fr2.chrUn I 1 C 0 s gasAcu1.chrXIII 4066988 32 - 20083130 CG--GAGTGCCTGGGCCCGGGGTGCCT-GGGCCCG i gasAcu1.chrXIII I 1 C 0 s oryLat2.scaffold5002 3793 32 + 4714 CT--GAGTGCAGAGGTTCTGAGTGCAG-AGGTTCT i oryLat2.scaffold5002 I 196 C 0 s danRer6.chr8 22861480 32 + 55568185 GT--GGGTGCAGATGTTCTGCTGGCAC-AGGGCGT i danRer6.chr8 I 7 C 0 s petMar1.Contig42085 12149 32 - 12361 CT--GGGTGTAGGGTGTCTGGGTGTAG-AGTGTCT i petMar1.Contig42085 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e canFam2.chr9 59361996 61 - 64418924 I e equCab2.chr11 57947330 48 - 61308211 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e ponAbe2.chr17 69579935 0 + 73212453 C e rheMac2.chr16 74744736 0 + 78773432 C a score=-60304.000000 s hg19.chr17_gl000204_random 18432 43 + 81310 GGGTGCAG----------------------GGGGCCTGGGTG-CAGGG-GCCTG---------GGTGCAGGGGGCC s micMur1.scaffold_27997 324 65 + 9776 GGCTGTCGGAGGTTGGAGGCCTGGCTGTCGGAGGCCTGGCTG-CCGTG-GCCTG---------GCTGTTGGAGGCC i micMur1.scaffold_27997 C 0 C 0 s tupBel1.scaffold_81392.1-4505 1226 52 + 4505 ATGTTCAG----------------------GGGCCCCATGTG-CAGGG-CTCTGTGTGCTTGATGTGCAGGGGCCC i tupBel1.scaffold_81392.1-4505 C 0 C 0 s cavPor3.scaffold_76 4300603 37 + 7991924 ---------------GCATTCCTCCTCCACAGAAGTGGAGTG-CCGTG-TCCTT---------------------- i cavPor3.scaffold_76 C 0 C 0 s myoLuc1.scaffold_141316 43088 43 + 75010 GGGTGCAG----------------------GGTACCGGGTGC-AGGGG-GACTG---------GGTGCAGGGGTAC i myoLuc1.scaffold_141316 C 0 C 0 s equCab2.chr11 57947378 31 - 61308211 AGATGCAG----------------------TG-----------AGAGG-GAC-----------GGCCAAGGGAGAC i equCab2.chr11 I 48 C 0 s bosTau4.chr19 10758104 28 - 65312493 ---------------------------------CCCAGGT---CAGTG-GGCTC---------CATGCAAGGAG-- i bosTau4.chr19 I 16 I 1 s dasNov2.scaffold_186432 551 40 + 4438 CGGTGGAG----------------------GGGGCCTCGGTG-GAGGG-GCCTTT--------GGTGGAGGG---- i dasNov2.scaffold_186432 C 0 I 67 s xenTro2.scaffold_1193 113298 44 + 135655 GGGTACCG----------------------GGGGTCTGGGTGTTGGgg-gtctg---------ggtactgggggtc i xenTro2.scaffold_1193 C 0 C 0 s fr2.chrUn 234146467 43 + 400509343 TAGTGGAG----------------------GGGCCTAGAGTG-GAGGG-GCCTG---------GAATGGAggggcc i fr2.chrUn C 0 I 1 s gasAcu1.chrXIII 4067020 38 - 20083130 GGGTGCCT----------------------GGGCCCGGAGTG-CCTGG-GCCCG---------G-----GTGCGTT i gasAcu1.chrXIII C 0 I 1 s oryLat2.scaffold5002 3825 43 + 4714 GACTGCAG----------------------AGGTTCTGACTA-CAGAG-GTTCT---------GACTGCATAGGTT i oryLat2.scaffold5002 C 0 I 1 s danRer6.chr8 22861512 34 + 55568185 GGATGCTG----------------------AGGGTGTGGGTG-CACTG-CC------------------ACAGTAC i danRer6.chr8 C 0 I 1 s petMar1.Contig42085 12181 44 - 12361 GGGTGCAG----------------------GGCgtctgggtg-cagggcgtctg---------ggtgtagggtgtc i petMar1.Contig42085 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_96368.1-179817 149950 0 + 179817 I e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e canFam2.chr9 59361996 61 - 64418924 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e ponAbe2.chr17 69579935 0 + 73212453 C e rheMac2.chr16 74744736 0 + 78773432 C a score=-6515.000000 s hg19.chr17_gl000204_random 18475 24 + 81310 TGGGTG---CAGGGGGCCTGGGTGCAG s myoLuc1.scaffold_141316 43131 24 + 75010 CGGGTG---CAGGGGGACTGGGTGCAA i myoLuc1.scaffold_141316 C 0 I 1 s canFam2.chr9 59362057 24 - 64418924 TCGGTG---CTAACGGCCGTGGGAGAA i canFam2.chr9 I 61 C 0 s equCab2.chr11 57947409 11 - 61308211 ---------------GCCAGGGTAGA- i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10758133 17 - 65312493 TGGATG---------GCTAGGGGAGA- i bosTau4.chr19 I 1 C 0 s cavPor3.scaffold_76 4300640 18 + 7991924 ---------TCCGAAGTCTAAAGGCAG i cavPor3.scaffold_76 C 0 I 11 s tupBel1.scaffold_81392.1-4505 1278 24 + 4505 CGCGTC---CAGGGGCTCCACATTCAG i tupBel1.scaffold_81392.1-4505 C 0 C 0 s micMur1.scaffold_27997 389 24 + 9776 TGGCTG---TCAGAGGCCTGGCTGCCG i micMur1.scaffold_27997 C 0 C 0 s xenTro2.scaffold_1193 113342 24 + 135655 tgggta---ctgggagtctgggtgttg i xenTro2.scaffold_1193 C 0 I 1 s fr2.chrUn 234146511 24 + 400509343 atagtg---gaggggcccagagtggag i fr2.chrUn I 1 I 7 s gasAcu1.chrXIII 4067059 23 - 20083130 TGACTGAGCCTGAG----TGAGCGCTG i gasAcu1.chrXIII I 1 I 3 s oryLat2.scaffold5002 3869 24 + 4714 TGACTG---CAGAGGTTCTGAGTGCAG i oryLat2.scaffold5002 I 1 I 1 s danRer6.chr8 22861547 24 + 55568185 TGGGTG---CTGAGGGTGTGGGTGCAC i danRer6.chr8 I 1 I 7 s petMar1.Contig42085 12225 24 - 12361 tgggtg---tagggtgtctgggtgtag i petMar1.Contig42085 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e dasNov2.scaffold_186432 591 67 + 4438 I e otoGar1.scaffold_96368.1-179817 149950 0 + 179817 I e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e ponAbe2.chr17 69579935 0 + 73212453 C e rheMac2.chr16 74744736 0 + 78773432 C a score=-61139.000000 s hg19.chr17_gl000204_random 18499 31 + 81310 -GGGC---------CTG-GGTGCAGGGGGC-----CTGTGCAGAGGT-- s equCab2.chr11 57947420 12 - 61308211 ------------------GGAGAAGGGGCT------------------- i equCab2.chr11 C 0 C 0 s ponAbe2.chr17 69579935 31 + 73212453 -GGGC---------CTG-GGTGCAGGGGAC-----CTGAGCAGAGGT-- i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74744736 31 + 78773432 -GGGC---------CTG-GGGGCAGGGGAC-----CTGAGCAGAAGT-- i rheMac2.chr16 C 0 C 0 s micMur1.scaffold_27997 413 22 + 9776 -TGGC---------CTG-GCTGTCGGAGGC-----CTG----------- i micMur1.scaffold_27997 C 0 N 0 s tupBel1.scaffold_81392.1-4505 1302 25 + 4505 -GGGC---------TTGAAGTGCAGGGTCC-----CTGCG--------- i tupBel1.scaffold_81392.1-4505 C 0 N 0 s cavPor3.scaffold_76 4300669 25 + 7991924 -TGGC---------GAT-GGGGGAGAAGAC-----------GGAGGT-- i cavPor3.scaffold_76 I 11 C 0 s bosTau4.chr19 10758150 19 - 65312493 -GGGG---------CTG-GGGGAGAAAAGA------------------- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59362081 19 - 64418924 -ATGG---------CTG-GGGGAGGCAGGC------------------- i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_141316 43156 28 + 75010 -AGGG---------CTG-GGTGCAGGGGGCCCGCG--------TGCA-- i myoLuc1.scaffold_141316 I 1 C 0 s xenTro2.scaffold_1193 113367 27 + 135655 -gggt---------ctg-ggtgttgggggt-----ctgggtgt------ i xenTro2.scaffold_1193 I 1 I 13 s fr2.chrUn 234146542 39 + 400509343 -gagtggaggggcccgg-agtggaggggcc-----cagagtgg-agg-- i fr2.chrUn I 7 C 0 s gasAcu1.chrXIII 4067085 39 - 20083130 -GGCTGCGGTGTACCTG-TCTGAGGGGTGT-----TTGAGCGC-GGG-- i gasAcu1.chrXIII I 3 I 12 s oryLat2.scaffold5002 3894 30 + 4714 -GGTT---------CTG-AGTGCAGAGGTT-----CTGACTGC-AGA-- i oryLat2.scaffold5002 I 1 N 0 s danRer6.chr8 22861578 30 + 55568185 -GGAC---------GTG-GGTGCTGAGGGT-----GTGGATGC-ACT-- i danRer6.chr8 I 7 I 3 s petMar1.Contig42085 12249 34 - 12361 ggtgt---------ctg-ggcgcagggtgt-----ctgggtgcagggtg i petMar1.Contig42085 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e dasNov2.scaffold_186432 591 67 + 4438 I e otoGar1.scaffold_96368.1-179817 149950 0 + 179817 I e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=-136675.000000 s hg19.chr17_gl000204_random 18530 28 + 81310 A----------GAGGACTCAGGTGGA-------GGTG-----------------G----------AAGGCAG s myoLuc1.scaffold_141316 43184 37 + 75010 G----------GGGGGCCCGGGTGCA-------GGGG-----------------GACTGGGGTGCAGGG-GG i myoLuc1.scaffold_141316 C 0 C 0 s canFam2.chr9 59362100 22 - 64418924 ---------------GCCCAGGTGGA-------GGAA-----------------A----------GAGG-AG i canFam2.chr9 C 0 C 0 s equCab2.chr11 57947432 16 - 61308211 ---------------CCCCAGGGGGA-------G---------------------------------GG-GA i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10758169 23 - 65312493 --------------GGCTCAACTGGG-------AGTG-----------------G----------AGGG-AG i bosTau4.chr19 C 0 C 0 s cavPor3.scaffold_76 4300694 24 + 7991924 G----------GGACCCTCAGGTGGG-------GGGT-----------------G----------AAG---- i cavPor3.scaffold_76 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42693 17 + 85690 ------------------CAGGTGGA-------GGTA-----------------G----------AAGG--- i otoGar1.scaffold_94361.1-85690 I 10 C 0 s rheMac2.chr16 74744767 28 + 78773432 A----------GAGGACTCAGGTGGA-------GGTG-----------------G----------AAGGCAG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69579966 28 + 73212453 A----------GACGACTCAGGTGGA-------GGTG-----------------G----------AAGGCAG i ponAbe2.chr17 C 0 C 0 s dasNov2.scaffold_186432 658 25 + 4438 ---------------------GTGGA-------GGGG-----------------G-CCTCGGTGGAGGG-AG i dasNov2.scaffold_186432 I 67 C 0 s ornAna1.Ultra272 658328 28 + 11296442 C----------AGGGCCTGAGGTCTA-------GGGG--------TCCT-----G----------AAT---- i ornAna1.Ultra272 N 0 I 7963 s xenTro2.scaffold_1193 113407 23 + 135655 ac--------tgggggtctgggtgtt-------ggga-----------------g----------------- i xenTro2.scaffold_1193 I 13 C 0 s fr2.chrUn 234146581 26 + 400509343 -------------gaACCATAGTGGA-------GGGG---------CCTAGAGTG----------------- i fr2.chrUn C 0 I 7 s gasAcu1.chrXIII 4067136 43 - 20083130 ----------GTGGACCCTTGGTGCATGTTACCGGGGAACGCTGTCCCTAGG--T----------------- i gasAcu1.chrXIII I 12 I 7 s danRer6.chr8 22861611 29 + 55568185 ----------ACAGGACGTAGGTGCT-------GAGG------GTCTGTTGG-------------------- i danRer6.chr8 I 3 I 7 s petMar1.Contig42085 12283 29 - 12361 -tctgggcgcagggtgtctgggtgta-------gggt----------------------------------- i petMar1.Contig42085 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=-98352.000000 s hg19.chr17_gl000204_random 18558 34 + 81310 ----------------CCCAGGTTGGGTAGGAA--------GGGGCT------------CCAGGAAGGGG s myoLuc1.scaffold_141316 43221 40 + 75010 ----------------CCCGGGTGCAGGA--------------GGGCTGGGTGCAGGGGCCCCGGGGTGC i myoLuc1.scaffold_141316 C 0 C 0 s canFam2.chr9 59362122 28 - 64418924 ----------------CCCCCATAGAGGC--------------GGTT------------CCAGGTGGTGA i canFam2.chr9 C 0 C 0 s equCab2.chr11 57947448 28 - 61308211 ----------------CCCAGGTGGAGGA--------------GGGT------------CCAGGTGGTGA i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10758192 28 - 65312493 ----------------CCCACGTGGAGGC--------------AGCT------------CCAGGTAGTGA i bosTau4.chr19 C 0 C 0 s cavPor3.scaffold_76 4300718 12 + 7991924 ---------------------------CAGGGA--------GG-----------------------GGAG i cavPor3.scaffold_76 C 0 C 0 s rheMac2.chr16 74744795 34 + 78773432 ----------------CCCAGGTTGGGcaggaa--------ggggcc------------ccaggaagggg i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69579994 34 + 73212453 ----------------CCCAGGCTGGGTGGGAA--------GGGGCT------------CCACAGAGGGG i ponAbe2.chr17 C 0 C 0 s dasNov2.scaffold_186432 683 19 + 4438 ----------------CCTCAGTGGAGGG--------------GGCC------------CC--------- i dasNov2.scaffold_186432 C 0 N 0 s xenTro2.scaffold_1193 113430 33 + 135655 ----------------tctgggtactgggggtctgggtactgggggt------------ct--------- i xenTro2.scaffold_1193 C 0 N 0 s fr2.chrUn 234146614 26 + 400509343 ----------------CTGGAATGGAGGGGCCC----------------------------ATAGTGGAG i fr2.chrUn I 7 I 1 s gasAcu1.chrXIII 4067186 17 - 20083130 ----------------TGGGGATGAAGAG-------------------------------------GGAG i gasAcu1.chrXIII I 7 I 4 s danRer6.chr8 22861647 17 + 55568185 ----------------CGTGGGTGCAGATGTTC------------------------------------- i danRer6.chr8 I 7 I 178 s petMar1.Contig42085 12312 28 - 12361 gtctgggtgtagggtgtctgggcgcagg------------------------------------------ i petMar1.Contig42085 C 0 N 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 42710 0 + 85690 C e ornAna1.Ultra272 658356 7963 + 11296442 I e panTro2.chr17 79192367 28 + 83384210 I e monDom5.chr2 304285507 3704 - 541556283 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=-27703.000000 s hg19.chr17_gl000204_random 18592 36 + 81310 C-TGGCCTGGTGGGGAGAGAAAGC----AGGC-GGCAGGCTT- s panTro2.chr17 79192395 37 + 83384210 CCTGGCCTGATGGGGAAAGAATGC----AGGC-GGCAGGCAT- i panTro2.chr17 I 28 C 0 s ponAbe2.chr17 69580028 37 + 73212453 CCTGGCCTAGTGGGGAGAGAAAGC----AGGC-GGCAGGCTT- i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74744829 37 + 78773432 ccTGGCCTGGTGGGGAGAGAAAGC----AGGC-AGCAGGCTT- i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42710 22 + 85690 ---GGCCTGGAGGGCAGA-----------------CTGGCCT- i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4300730 27 + 7991924 CCGAGTT-----------GACTGC----AGGTGGGCAGTGCA- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10758220 37 - 65312493 CCCCAGCTGTTGGGGCAAGAAGGC----AGGTAGGCTGGCT-- i bosTau4.chr19 C 0 I 1 s equCab2.chr11 57947476 37 - 61308211 CCCCAGCTCTGGGGCAGAGAAGGC----AGGTAGGCGGTAT-- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59362150 34 - 64418924 -CCGAGCTGATGGGCAGAG--GGC----AAGTAGGTGGGCA-- i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_141316 43261 39 + 75010 AAGGGGCCCGGGTGTAGGG--GGCCTGGGTGCAGGAGGCCT-- i myoLuc1.scaffold_141316 C 0 N 0 s gasAcu1.chrXIII 4067207 34 - 20083130 -CTGGAGTGATGCCG--AAGGAGC----AGG--GGAAGGATTT i gasAcu1.chrXIII I 4 I 995 s danRer6.chr8 22861842 24 + 55568185 -TCAGCCGGATGTGGGTAAGAAGC----A-------------- i danRer6.chr8 I 178 N 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e fr2.chrUn 234146640 1 + 400509343 I e ornAna1.Ultra272 658356 7963 + 11296442 I e monDom5.chr2 304285507 3704 - 541556283 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=66959.000000 s hg19.chr17_gl000204_random 18628 69 + 81310 CTCTGCGACCTAAGTGCTTGATTCTCAGCAGG-AGCACAAAAGGCAAGGGCTAGAACTCACACTGCACCA s panTro2.chr17 79192432 70 + 83384210 ATATGAGAAGCAAGTGCTTGATTCTCAGCAGGGAGCACAAAAGGCAAGGGCTAGAACTCACACTGCACCA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69580065 69 + 73212453 CTCTGCCACCTAAGTGCTTGATTCTCAGCAGG-AGCACAAAAGGCAAGGGCTAGAACTCACACTGCACCA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74744866 69 + 78773432 CTCTGCAACCTGAGTGCTTGATTCTCAGCAGG-AGCAGAAAAGGCAAGAGCTAGAACTCACACTGCACCA i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42732 43 + 85690 C---------------------TCTCAGCC---AGCAGGAGAGGCAC-AGCTGGGG-TCATGTGGC-CTA i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4300757 69 + 7991924 CCCTGGGGCCTCAGGGCTGGGTTCTCAGCAGCTGGCACAAAAGGCAAGGGGC-GCATTCACTCTGCAACA i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10758258 69 - 65312493 CTTGTATAA-TAAACGCTTGATTATCAGCAGCCAGTACAAAAGGCAAGGACCGGCGTTCCTTTTCCACCA i bosTau4.chr19 I 1 C 0 s equCab2.chr11 57947513 68 - 61308211 CTCTTAGAA-TAAGTG-CTGATTCTCAGCAGGCAGCTCAAAAGGCCAGGGCTGGAATTCCCTTTGCACCA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59362184 70 - 64418924 CTCGCAGAGCCAAATGCCTGCTCCTCGGCAGCCAGCACAAGAGGCAGGGGCTGGAACTCATTCTGCACCA i canFam2.chr9 C 0 C 0 s petMar1.Contig31812 3526 43 + 22211 -------TGCAGAGTGCTGGGTGCTGGGTA--------------------CTGGTATCCTGGGTGCAGAG i petMar1.Contig31812 N 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e fr2.chrUn 234146640 1 + 400509343 I e ornAna1.Ultra272 658356 7963 + 11296442 I e monDom5.chr2 304285507 3704 - 541556283 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=-15911.000000 s hg19.chr17_gl000204_random 18697 32 + 81310 GGCCCT---GGGCAGGG---AAGTCCATGGGG-AACTGA s panTro2.chr17 79192502 33 + 83384210 GGCCCT---GGGCAGGG---AAGTCCATGGGGGAACTGA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69580134 32 + 73212453 GGCCCC---GGGCAGGG---AAGTCCGTGGGG-AACTGA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74744935 32 + 78773432 GGCCCT---GGGCAAGG---AGGTCTGTGGAG-GACTGA i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42775 23 + 85690 GGTCCTCTGGAGCAGGG----------------GCCTGC i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4300826 30 + 7991924 GACCCTTCGGGGCGGGG---GGTTCCA------AGCAGG i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10758327 32 - 65312493 GACCTGCTGGATCGGGA---G---CAAGACGG-GGCTGT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57947581 32 - 61308211 GACCCACTGGAACAGGA---G---CAACGTGG-AGATGT i equCab2.chr11 C 0 I 2 s canFam2.chr9 59362254 5 - 64418924 GACCC---------------------------------- i canFam2.chr9 C 0 I 42 s fr2.chrUn 234146641 28 + 400509343 GGCCCA---GAGTGGAG---GGGCCCAGAGTG-GA---- i fr2.chrUn I 1 C 0 s petMar1.Contig31812 3569 34 + 22211 TGCCTA---GTGCAGGGTGCAGGTTGCTGGGG-GTCTG- i petMar1.Contig31812 C 0 N 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e ornAna1.Ultra272 658356 7963 + 11296442 I e monDom5.chr2 304285507 3704 - 541556283 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=24016.000000 s hg19.chr17_gl000204_random 18729 42 + 81310 AGATCTGCACCTAGCCTCCTCTGAGCCTGCTGTCCAC-ACCCC s panTro2.chr17 79192535 42 + 83384210 AGATCTGCGCCTAGCCTCCTCTGAGCCTGCTGTCCAC-ACCCC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69580166 42 + 73212453 AGATCTGCGCCTAGCCTACTCTGAGCCTGCTGTCTAC-ACCCC i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74744967 42 + 78773432 AGATCTGTGCCAAGCCTCCTCTGAGCCTGGTGTCCAC-ACCCC i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42798 33 + 85690 AGTCCTGTCCC---CCTGCCCTG-------TGTCCACAACCCC i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4300856 37 + 7991924 AGTTCCG-----AGCCTCCCCTGGACCTGAGGTCTGC-ACCTC i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10758359 35 - 65312493 GGATGCG-GCCCGGCC------AGGCCCACGCCCCAC-GCCCC i bosTau4.chr19 C 0 I 240 s fr2.chrUn 234146669 27 + 400509343 ------------GGGTCCCGGAgtgcc---tgtcctc-ccccc i fr2.chrUn C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e ornAna1.Ultra272 658356 7963 + 11296442 I e monDom5.chr2 304285507 3704 - 541556283 I e canFam2.chr9 59362259 42 - 64418924 I e equCab2.chr11 57947613 2 - 61308211 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=17240.000000 s hg19.chr17_gl000204_random 18771 37 + 81310 CACAGCCCCAGCTTCCAGCTGTTCCAATGACCGGAGA s panTro2.chr17 79192577 37 + 83384210 CACAGCCCCAGCTTCCAGCTGTTCCAATGACCGGAGG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69580208 37 + 73212453 CATAGCCCCAGCTTCCAGCTGTTTCAATGACCGGAGG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74745009 37 + 78773432 CACAGCCCCAGCTTCCAGCTGCCCCAGTGACCAGAGA i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42831 23 + 85690 TGTGGCCCCAGGCCCCAGCTGCT-------------- i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4300893 26 + 7991924 AGGCTCCCCTGGTTCCAGCTGCGCT-----------G i cavPor3.scaffold_76 C 0 C 0 s fr2.chrUn 234146696 37 + 400509343 agCAGGGCTGGCGCCCCCTTGTGCCGAGGGTAGAATA i fr2.chrUn C 0 N 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e ornAna1.Ultra272 658356 7963 + 11296442 I e monDom5.chr2 304285507 3704 - 541556283 I e canFam2.chr9 59362259 42 - 64418924 I e bosTau4.chr19 10758394 240 - 65312493 I e equCab2.chr11 57947613 2 - 61308211 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=301637.000000 s hg19.chr17_gl000204_random 18808 434 + 81310 AGCAGAAGTTTCTGTAAGCCCTCAAGTCTCCCCTGGTCCCCTTGGGGCTTTCAGGGAGAT--AATAGGATACACTTC-------TGGTCCTGGAGGCGATTCCCAAGCATTTGCTTTAACTC-TCAATATCACCTCCTCCCCAGACAGGGCTCCCAGAGCCAGGATGGAGGCAGGTGGTCCAGGGAGAC--TCCTGCCCCGCTGC-------TCTCTCCCACCAGCCCCAAAGCAGAGGCTGCCCAGGGCCTGGGCGAGAGGAGAGCCTGGGGAGAGGCGGGCTGTCTGCCGGGGCTCTCACCCTTCC--T------GACTTGTCAGTTCTCTTGCCTTTGAGGCGGATGGAGCCCTCCTTCCCAGAGCAGTCCTGGCA----GGGGAGGCG-----------------CCCACAGGAAGG-------------------------------AATGGAAACAGAGTCCATCCCTGGGGATCCCAAGTCATCCCCT-----------GGGG-CCACATGGACA--CCC s panTro2.chr17 79192614 434 + 83384210 AGCAGAAGCTTCTGTAAGCCCTCAAGTCTCCCCTGGTCCCCTTGGGGCTTTCAGGGAGAT--AATAGGATACCCTTC-------TGGTGCTGGAGGCGATTCCCAAGCATTTGCTTTAACTC-TCAATGTCACCTCCTCCCCAGACAGGGCTCCCAGAGCCAGGATGGAGGCAGGTGGTCCAGGGAGAC--TCCTGTCCCGCTGC-------TCTCTCCCACCAGCCCCAAAGCAGAGGCCGCCCAGGGCCTGGGCGAGAGGAGAGCCTGGGGAGAGGCGGGCTGTCTGCCGGGGCTGTCACCCTTCC--T------GACTTGTCAGTTCTCTTGCCTTTGAGGCGGATGGAGCCGTCCTTCCCAGAGCAGTCCTGGCA----GGGGAGGTG-----------------CCCACAGGAAGG-------------------------------AATGGAAACAGAGTCCATCCCTGGGGATCCCAAGTCATCCCCT-----------GGGG-CCACATGGACA--CCG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69580245 434 + 73212453 AGCAGAAGCTTCTGTAAGCCCTCAAGTCTCCCCTGGTCCCATTGGGGCTTTCAGGGAGAT--AATAGGATACCCTTC-------TGGTCCTGGGGGCGATTCCCAAGCATTTGCCTTAACTC-TCAATTTCACCTCCTTCCCAGACAGGGCTCCCAGAGCCAAGATGGAGGCAGGTGGTCCAGGGAGAC--TCCTGCTTGGCTGC-------TCTCTCCCACCAGCCCCAAAGCAGAGGTGGCCCAGGGCCTGGGCGAGAGGAGAGCCTGGGGAGAGGCGGGCTGTCTGCCGGGGCTGTCACCCTTCC--T------GACTTGTCAGTTCTCTTGCCTTTGAGGCGGATGGAGCTGTCCTTCCCAGAGCAGTCCTGGCA----GGGGAGGCG-----------------CCTACAGGAAGG-------------------------------AATGGAAACAGAGTCCGTCCCTGGGGATCCCGAGTCATCCCCC-----------GGGG-CCACATGGACA--CCG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74745046 434 + 78773432 AGCAGAAGCATCTGAAAGCCCTCAAGTCTCCCCTGGTCCTGTCGGGGCTTTCAGGGAGAC--CACAGGATACCCTTC-------TGGTCCTGGAGGCGATTCCCAAGCATTTGCTTCAACTC-TCAACGTCACCTCCTCCCCAGACAGGGTTCCCAGAGCCAGGATGGAGGCAGGTGGTCCAGGGAGAC--TCCTGCCCTGCTGC-------TCTCTCCCACCACCCCCAAAGCAGAAGCAGCCCAGGGCCTGGGTGGGAGGAGAGCCTGGGGAGAGGCGGGCTGTCTGCCGGGGCTGCCACCCTTCC--T------GACTCATCAGTTCTCTTGCCTTTGAGGCGGATGGAGCTGCCCTCCCCAGAGCAGCCCTGGCA----GGGCAGGCG-----------------CCCACAGGAAGG-------------------------------AATGGAAACAGAGTCCATCCCTGGGGATCCCCAGTCATCCCCC-----------GAGG-CCACATGGACA--CTG i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 42854 455 + 85690 -------GCATCTG-AACTCCTTCAGTCCCTCCGGGTACCCTTGGGGTCTTCAGGGAGAT--AATAGGATGCCCTTT-------CTGTCCTGGAAGTGATGCCCAGGTG------------A-TCACTGTCACCTCCT---CAGACAAGTCTCCCAGTGCCTAGATG--AGCAGGTGGTCCTTGACATCAGCCCTGCCCTCCTGCAGTGGGGTCTCTCCCACCACCCCTGAAGCAGAGA-GGCCCAGGATCTGAGTGGGTGGTAAGTCCCAGGAGTGGTCAGCTAGGCAGTGGGGCCATCAGCCACCC--TGGGGGGGGGGGGTCAGTTCTCCCGCCTTCGAGGCTGACAGAGCTGCCCTCCCTAGAACAGCCCAGAC-----GGGGAGGCT-----------------CCCACCAGAAGGCAACAGGGGAAGTCAGGCTCGTCCATGATGAGATAGAAACAGAATCAGTCCCT-GGGACCCTGAATTGCCTCTG-----------GGGGTCCCCATGGACATCTCA i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4300919 442 + 7991924 AGAAGGAGCGGTTG----CCATCCAGAGCTCCTCGTGCCTCCCAGAGGTTTCAGGGAGGTCCCCTGGGATGCCCTTTGGTCCCAGGACCCTGGGTATGACTCCCAAGAGCCTGCTTTGGTTCTTTCAGGTCGCATCTA---CACACACATTTCCCCTAGGCTGGATGGTCGCTGGCAG-------------CTCGGCTCTGCTCT-------TCCCTCTCACCACCTCCAGTACCGAG-------AGGGCCTGGGCTG--GGCTGGCC-------AGGCACACTGCCTGGCAAGGCCACCCTTCTGCCCTT------GTTTATTCTGCTCTCTGGCCTTTGAGGCAGACAGAGCCACC--TCCCAGTGCAGTAGGAGCAGCATGGGAAGGCACCAGGGGTGATGGGCATCCCACAAGGATG---------------------------------TGGGTACAGAAGCCCTTCCTGGGGACACCAGGCTGCTTTGTGGAATGGGTGGGGAG-CCAGATGACCATATGA i cavPor3.scaffold_76 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e ornAna1.Ultra272 658356 7963 + 11296442 I e monDom5.chr2 304285507 3704 - 541556283 I e canFam2.chr9 59362259 42 - 64418924 I e bosTau4.chr19 10758394 240 - 65312493 I e equCab2.chr11 57947613 2 - 61308211 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=29397.000000 s hg19.chr17_gl000204_random 19242 37 + 81310 ATGCTGCCCAGCCTGGCAGCCAGTCCAGGGCCAGGGA s panTro2.chr17 79193048 37 + 83384210 ATGCTGCCCAGCCTGGCAGCCAGTCCAGGGCCAGGGA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69580679 36 + 73212453 ATGCTG-CCAGCCTGGCAGCCAGTCCAGGGCCAGGGA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74745480 37 + 78773432 ATGCTGCCCAGCCTGGCAGCCAGTCCAGGGCCAGGGA i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 43309 24 + 85690 ATGCTGTCCA-------------TCCAGGCCCCTGGG i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4301361 37 + 7991924 AAGCTGCTCGGCCAAGATGCCCACCCAGCATCCAGTA i cavPor3.scaffold_76 C 0 C 0 s equCab2.chr11 57947615 37 - 61308211 ATGCTGCCCAGCCAGCCACGCAGTCAGCGCCCCTGCG i equCab2.chr11 I 2 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e ornAna1.Ultra272 658356 7963 + 11296442 I e monDom5.chr2 304285507 3704 - 541556283 I e canFam2.chr9 59362259 42 - 64418924 I e bosTau4.chr19 10758394 240 - 65312493 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=29900.000000 s hg19.chr17_gl000204_random 19279 173 + 81310 ACATAAACCCTTGAAGGAGAGGGGGAGGAATTAGAGGGAGCAAAGACAGGGTCGGGAGATGTGATGAAAGAACCCAAGA-GAAGCTCCA-ACCCCACTGCTCCCCTCCCCAGCACAGAAATCTTTAAGTGTCATGCCTGAAACCCAGGCCGCCTTCTCTA--GG---TGCTGCTCTTGC-T s panTro2.chr17 79193085 174 + 83384210 ACATAAACCCTCGAAGGAGATGGGGAGGAATTAGAGGGAGCAAAGACAGGGTTGGGAGATGTGATGAAACAACCCAAGA-GAAGCTCCA-ACCCCACTGCTCCCCTCCCCAGCACAGAGATCTTTAAGTGTCATGCCTGAAACCCAGGCCGCCTTCTCTA--GG---TGCTGCTCTTGCTT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69580715 163 + 73212453 ACCTAAACCCTTGAA-GAAATGGGGAGG-ATTAGAGGGAGCAAAGACAGCGTC-CGAGATGTGA-GGAAGGACCCAAGA-GAAGCTCCA-A-CCCACTGCTCCC--TCCCAGCACACAGATCTTT-AGTGTCATGCCTGAAACCCAGG-CACCTTCTCTA---G---TGCTGCTCTTGC-T i ponAbe2.chr17 C 0 M 852 s rheMac2.chr16 74745517 169 + 78773432 ACCTAACCCCTTGAAGGAGATGGGGAGGAATTAGAGGGAGCAAAGACAGGGTGGGGAGATGTGATGAAGGAACCCAACA-GAAGCTCCA-ACCCCACTGCTCCCCTCCCCAGCACAGAGATCTTTACATCTTATGCCTGAAACTCAGGCCACCTTCTCTG--GG---TGCAAATGT----- i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 43333 142 + 85690 A-------CCTGGAGTGTGAGGGAGAAG-------GGACACTAGGACAGCAGG-GGCAAGGCGATAAAGCCCTCCAAG-------CCTG-ACCCTGCTG------------GCAGAGTGACGTTCATCTACCATACCCGGAACCCAGGCCACCTTCTCCA--GG-ACAAATGCCCTCACA- i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4301398 145 + 7991924 CCTAAGTCCTATGAGGGCAGAAAAGAGG-GCTGAAGACAGGAAGGGCAGG----GGAGACA-GATAAAGGCA--------------------CTTGCTG------TGTCCACGACCTTGGTCTT-AATTGTAACTCCTGAACTCCATGCCCCTGATCCCA--GAGACAACTTCCTTTGCA- i cavPor3.scaffold_76 C 0 C 0 s equCab2.chr11 57947652 167 - 61308211 ACCTAAACCCCAGGAGGA--AAGTGACACAGGAAAGGGCGC--AGACAGGGAGGGAGAGGGCAGGACGGGAAATTGAGAGGAGGCCCCACACTCCTGCG------TCCCCAGCACACTGATCTTTATTTACGATTCCTGAAATCCAGGCCACCTTCTGCAGGGG---CGAATGCCTTGCA- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59362301 143 - 64418924 ACCCAAACCCAAGGAGGAG-AGGTGACCAGGGACAGGGAGTAAAGACAGGGCGGG---GAGAAGGGCCAGGAACCCAGA-GAGCCCCCAGATCCTTCAG------GGCCAGGAACCCAGA-----------GAGCCCCCAGATC-----------CTGCA-GGG---TGACGCCGTCACA- i canFam2.chr9 I 42 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e ornAna1.Ultra272 658356 7963 + 11296442 I e monDom5.chr2 304285507 3704 - 541556283 I e bosTau4.chr19 10758394 240 - 65312493 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=32428.000000 s hg19.chr17_gl000204_random 19452 254 + 81310 CCTCCCCCATCC---AGCCTAGATTCCACAT-CCCCCCAGAGGCTGAGCTGAAGGCGGTGCCCCCAGCAGCCCCACACTTCTC-------CACCACA-CCTTGCAA---------GCCAAGCTCACAGGAG--ATTATTTCATTTTCATTTTAACTGGTCCTACCCAGCCCTGTCTGC----AGCCGCCGGCTTAGAAGATGGAGACACGAGCGATCCACAGGCCGCCGAGTCCGG---AGGGCAGGGATCAGCCTCAGGGCAGCCACC-------CCTGCC---TGCGCTCGA s panTro2.chr17 79193259 254 + 83384210 CCTCCCCCATCC---AGCCTAGATTCCACAT-CCCCCCAGAGGCCGAGCTGAAGGCGGTGCCCCCGGCAGCCCCACACCTCTC-------CACCGCA-CCTTGCAA---------GCCAAGCTCACAGGAG--GTTATTTCATTTTCATTTTAACTGGTCCTACCCAGCCCTGTCTGC----AGCCGCCGGCTTAGAGGATGGAGACACGAGCGATCCACAGGCCGCCGAGTCCGG---AGGGCAGGGACCAGCCTCAGCGCAGCCACC-------CCTGCC---TGGGCTCGA i panTro2.chr17 C 0 C 0 s rheMac2.chr16 74745686 228 + 78773432 -----------------------CTTCACAT-CCCCCCAGAGGCCGAGCTGAAGGCGATGCTCCCGGCGCCCCCACACCTCTC-------CTCCGCA-CCTTGCAA---------GCCAAGCTGACAGGAG--GTTA------TTTCATTTTAACGGGTTGTGCCCAGCCCCGCCTGC----AGCCGCCAGCTTAGAGGATGGAGACATGAGCGATCCACAGGCTGCCGAGTCCAG---AGCGCGGGGACCCACCCCAGCGCAGCCACC-------CCTGCC---TGGGCCCGA i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 43475 198 + 85690 ------------------------TCCCC---CCACCCACAGGCTGAGCTG-------TGCCCTGG-------CACCTCTCCA-------CACAGCC-CTTTGCGA---------GCCAAGCTCACCTGAA--ATG-------TTTTATGTCACCGGGTCGTGTACCCCCTGACCTGT----AGCCACTCACTCAGAAAATGGA---------GCTCTTTAGGCCACTGAG-CCTG---AGGGTGGGGACTGTCTCCAATGCAACAA---------CGGACC---TGGACCCAG i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4301543 235 + 7991924 TCTCCCCCACCCCAGAGCCAAGCCCACACACGAACCCCAGA----------AAGGAAGCACCCCTAGCATCC-CACATCTCTCCACTCTGCACCGCC-CCCC-CAA---------GCC-AGCTCCCCCGAGACATTA------TTTCACCTCAACACATCCTGCACAGCCC-ATCTGC----A-CCCCTGGCTTAGAGGATGAAGACAGCGGCAGTT------------------G---GGGGTGGGGACCCATCATGGCACTGTCACCTGCCAGGCCAGCC---TCCACCCGA i cavPor3.scaffold_76 C 0 C 0 s equCab2.chr11 57947819 199 - 61308211 -----------------------TTCC-C---CCACCCACAGGACCAGACGAG-----TGCACCTGG------GCTGACTCTG-------CA-GGCCGCATCGGGA---------GCC-GCCCCCGTGGAG--GGTCT-----TTCCATTTG--TGGGTCCTGCACAGCCG-GCCTGTCCCACGGCACCCACTTAGAGGTGGGA-ATGCA------------------GAGACCGGGACAGGGTAGGGGTTGCTAGCCCTGTGTGCCCC-------CTCGCC---CCCCAGCGA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59362444 222 - 64418924 -----------------------CCCCAC---CCCCCCACACTCCCATGCTGG------GCACCCGGCGC---CCCAGCTCTG-------CACAGCCTCCCCAGGAGTGGCGCAGGCC-CCCACAAGAGAG--GTTAT-----TTTCACTTTGCTGCGCGGTGCACAGCTG-----------CGGCGCTCACTTCGATGGGGGA-GCGTAGGCCATG---GGGTCCCTGGGAGCAGATCGAGGCAGGGATGAGCAGCCCTGTGCTCCCC-------CCCCCCAATCCCAGGCGA i canFam2.chr9 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e ornAna1.Ultra272 658356 7963 + 11296442 I e monDom5.chr2 304285507 3704 - 541556283 I e bosTau4.chr19 10758394 240 - 65312493 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e ponAbe2.chr17 69580878 852 + 73212453 M a score=-28949.000000 s hg19.chr17_gl000204_random 19706 42 + 81310 GCCTCCTTG---------------------GCGCCCCGCACCCCTCCTCTGCCG------------CC-----GGCTAGG s canFam2.chr9 59362666 39 - 64418924 GCTGCCCTG------------------------------C--ACTGCCAGGCCTTGGGGC----ACCC-----GGGCGAG i canFam2.chr9 C 0 C 0 s equCab2.chr11 57948018 45 - 61308211 GCAGCCCCA------------------------------ACGCCTCCCAGGGCGGAGAGCTGGGGTCT-----GGGTGGG i equCab2.chr11 C 0 C 0 s cavPor3.scaffold_76 4301778 44 + 7991924 GGGTCCAGG----CCTGAGCAGCAGCCTGTGTCCTCTAAGCCCCTCCC-------------------------------- i cavPor3.scaffold_76 C 0 C 0 s otoGar1.scaffold_94361.1-85690 43673 18 + 85690 AGAGCCTGG------------------------------AATGCTCCT-------------------------------- i otoGar1.scaffold_94361.1-85690 C 0 C 0 s rheMac2.chr16 74745914 63 + 78773432 GCCTCCTTGGCGTTGGTAGGCGAGTCCTGTGCGTCCTGCATCCCTCCCCTGCCG------------CC-----AGCTGGG i rheMac2.chr16 C 0 C 0 s panTro2.chr17 79193513 42 + 83384210 GCCTCCTTG---------------------GCGCCCCGCACCCCTCCTCTGCCG------------CC-----GGCTAGG i panTro2.chr17 C 0 C 0 s ornAna1.Ultra272 666319 42 + 11296442 GCCTCCCCT---------------------GTGTCCCTCACCCCTTCCCTGGCA------------CCCTTCAGG----- i ornAna1.Ultra272 I 7963 N 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e monDom5.chr2 304285507 3704 - 541556283 I e bosTau4.chr19 10758394 240 - 65312493 I e mm9.chr11 118673509 91 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e ponAbe2.chr17 69580878 852 + 73212453 M a score=133990.000000 s hg19.chr17_gl000204_random 19748 179 + 81310 CGA--AG-------GCGCTGCAT--CCTAGCCCCAC----C------GATAGG-----------------C--CCAGCCTGGTTTTGTTTT----GACCCGAGCTGAGTGGGAGATAACTT---AACAGCTTGTCCCCGATT-------GTAATGGCATGTTTTTCCCCACTCCGCAGTGGGAAACA----CCATCCATCATCCATAGCGCAGAA-CA-----------------CG-G----GCCTATGGCCCCCTCCG s panTro2.chr17 79193555 183 + 83384210 CGA--AG-------GCACTGCGT--CCCAGCCCCAC----C------AATAGG-----------------C--CCAGCCTGGTTTTATTTTCCTCGACCCGAGCTGAGTGGGAGATAACTT---AACAGCTTGTCCCCGATT-------GTAATGGCATGTTTTTCCCCACTCCACAGTGGGAAACA----CCATCCATCACCCATAGCGCAGAA-CA-----------------CG-G----GCCTGTGGCCCCCTCCG i panTro2.chr17 C 0 C 0 s rheMac2.chr16 74745977 178 + 78773432 CGA--AG-------GTGCTGCGT--CCTAGCCCCAC----C------GATAGG-----------------C--CCAGCCTGGTTTTGTTTTCCTCAGCCTGAGCTGAGTGGGAGA-----T---AACAGCTTGTCCCTGATT-------GTAATGGCATGTTTTTCCCCACTGCGCAGTGGGAGACA----CCAACCATCACCCATAGCACAGAC-CA-----------------CA-G----GCCTATGGCCCCCTCCA i rheMac2.chr16 C 0 C 0 s equCab2.chr11 57948063 197 - 61308211 AGAGGAG-------GCCCCGCG-------GCCCCTC----CTGGGCTGCTGGCTCGGGCCCATCGATCGGC--CCAGCTTCATTTTGTTTTCCTCGACCAGAGCTGAACGGGAGATCATTT---AACAGTTTGCCCCTGATT-------ACAACGGCCCATTTTTCCTTCCTCCGCAGTAGGAAACA----CCATTCATCACCCATAGCACAGAC-CA-----------------CG-G----CCCCGTGGCCC------ i equCab2.chr11 C 0 C 0 s canFam2.chr9 59362705 151 - 64418924 AGC-----------------CA-------GCCTCAC----C------ACTGG---------------------CCGGCTGCCCTTTATCGCC-----------TTAAATGAGAGGTCATGT---CCCAGCTTGGCCGGGATT-------GCAAGCACATGTTTGCTCCTACTCTGCAGGAGGAAACA----CCAGCCACCACCCACAGGACAGAA-CC-----------------GG-G----GCCCCTGCCCA------ i canFam2.chr9 C 0 C 0 s monDom5.chr2 304289211 194 - 541556283 G--GAAGAGGTTTAGTCTTGCATTCCCTAGCCCGAT----A------GATTGA-----------------T--GCAGTTTGT-TTTGCTTTCCACCACCAGAGCTGAATGGGAGATAATTT---AACGGCATGTCCCTGACT-------GTAATGGAAC-TTTTCCCTTACTCCACAGTAGGAAACG----CTATCCATCACCAGCTGAACAACA-CA-----------------CA-GCCACCCCCCTGACCTCTGCTG i monDom5.chr2 I 3704 C 0 s choHof1.scaffold_213748 2496 151 + 4094 --------------------CAT--CCCCGCCCCGG----------------------------------C--CCCGATCGG-----------TCAACCTGAGGTGAATGGGAGGCTATTC---CCCGGCGAGTGC-GGGCT-------GCAAGGACCCTCATTTCCTCACTCCGCGGCAGGAGACG----CCGGCCGTCCCTCACGGCGCTCAG-CA-----------------CAcg----gcccgtggcccccg--- i choHof1.scaffold_213748 N 0 C 0 s mm9.chr11 118673600 187 + 121843856 -----------------------------GTCCCAC----C------AAAAGC-----------------C--TCAGGCCGG-TTTGTTTGCTTTGACCCAGGTTGGGTGGGAGAAAACTGAGCGGCAGCCGATCCTCCACC-------ACGGGGGCTCAT-TTCCTTCGCTCTGCAGTGCGAAGTGCCATCCATCCATCATCCACTGCACAGAA-TATCCCAGAACACAGGCTGGA-G----GCCTAAGGCCCCAGCCA i mm9.chr11 I 91 I 101 s otoGar1.scaffold_94361.1-85690 43691 165 + 85690 -----------------------------GCCCCAC----C------AATGCA-----------------C--CCAACCCAGGTTGGTTTTCCTGGCCCCCAGCTGAGTGGGAGCTGATTT---AACAGCTTGTCCCAAGTA-------GTTAATTCACGTTTGCCCTCACTCAGCAGCAGGAGATG----CCACCTGTCACCCACAGTTCAAAA-CA-----------------TG-G----GCCCCTCAGCCCTGCTG i otoGar1.scaffold_94361.1-85690 C 0 C 0 s bosTau4.chr19 10758634 144 - 65312493 ----------------------------------------------------------------------C--CCAGCTCCA-TGTGTTTTCCTCCACCCAAGC-GGATGGGAGATTATCT---AACAGCTTGTCCCTGATT-------GCAGCGGCACATTTTCCCTCCCTCCTCAGCAGGAAACA----CCATCCATCACCCACGGCACAGAAGCC-----------------AG-G----CCCTCAGTTTT------ i bosTau4.chr19 I 240 C 0 s macEug1.Scaffold77160 8014 178 + 8786 ---GGAG-------GTGCTGCATTCCCCGGCCCAATAGATC------AATTGA-----------------C--gcagtttgt-tttgctttctacCACCCGAGCTGAATGGGTGATAATTT---AACCGCATGTCCATGACT-------GTAATGGAAC-TTTTCTCTTACTCCACAGTAGGAAACG----CCATCCATCACCAGCTGAACAACA-CA-----------------CA-G----CCACCCCCC-------- i macEug1.Scaffold77160 N 0 I 13 s cavPor3.scaffold_76 4301822 181 + 7991924 -----AG-------CTGCCTCAC--CTG-GCCCCAC----C------AAAGCC-----------------CAGTCAGCCTGGTTTTGTTTTCCTAGACCAGATCCTTATGGGAGGTAATGG---GACAGCCTGTCCTCTGTCTTTGCTTGTAAAGGCATATCTTTCCTGGCTTTGCA----GAAGCACCTGCCACCCATTA-CCATGGCACAGAA-CA----------------------------TAGGACCACAGCCC i cavPor3.scaffold_76 C 0 I 3 e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e ponAbe2.chr17 69580878 852 + 73212453 M a score=-68039.000000 s hg19.chr17_gl000204_random 19927 67 + 81310 -CGTGCGCTCCTGTACCCC---ACGCCCC--ACCCC--------------------TTGGT-------GCTGCGGGGTTT---------------AGGG-----G-------ACCTCAGGGCTC-----GCC------------ s panTro2.chr17 79193738 67 + 83384210 -CGTGCGCTCCTGCACCCC---ACGCCCC--ACCCC--------------------TTGGT-------GCCGCGGGATTT---------------AGGG-----G-------ACCTCAGGGCTC-----TCC------------ i panTro2.chr17 C 0 C 0 s rheMac2.chr16 74746155 67 + 78773432 -CGTGCACCCCTATGCCCC---ACACCCG--ACCCC--------------------TTGGT-------GCTGCGGGGTTT---------------AGGG-----G-------ACCTCAGGGCTC-----ACT------------ i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 43856 57 + 85690 -TCAGTGTCCTTGCACT--------------GTGCC--------------------CAGGT-------GCCGCGGGGTTT----------------TGG-----A-------ATCATAGGCTTC-----GCC------------ i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4302006 81 + 7991924 -CATGCCCCTCATGGCCCCA-GAAGCCCC--AGCCA--------------------TCAAA-------GTTTTGGGGTGC---------------TGGG-----ATGTCCTTGCCCCTAGCCTCCATGGTGC------------ i cavPor3.scaffold_76 I 3 C 0 s bosTau4.chr19 10758778 65 - 65312493 ---GGGGCCC-------AC---AGGGCCC--ACCCA--------------------GGTGG-----AGTGCCCTGGGTCC---------------CGGGCTGCAG-------AGGAAGGAATTG-----GTC------------ i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59362856 72 - 64418924 ---GGGGTTTTCAACAAAC---AGGACTC--ACCCC--------------------CGGGCAAGTTGGCCCCCCATTCCC---------------CCGG-----G-------GGGGGGTGGTTC-----CCC------------ i canFam2.chr9 C 0 C 0 s equCab2.chr11 57948260 61 - 61308211 ---GGCGCC--------GC---GTGCCCT--GCACC--------------------CCTGC---CCGGCCCCCCAGGTTT---------------CTGG-----G-------ACCACAGGGTTC-----ATC------------ i equCab2.chr11 C 0 C 0 s choHof1.scaffold_213748 2647 84 + 4094 -cgcccgccccctctccgc---gcgccccgTGCCCC--------------------CAGAC-------GCCGCGAGGCCCGGATCCGCGGCCAAGGGGG-----A-------GAGGCTGGCTCC-----GCC------------ i choHof1.scaffold_213748 C 0 C 0 s macEug1.Scaffold77160 8205 90 + 8786 -GCAGTGTCCCCAGATCGCCTTGCTCCTT--ACTCCTACTCCTTTCCCGGATGCAGCAGGA-------GCTGCTGAGTTA---------------TGGA-----G-------ACTGCAGGGTGA-----GCC------------ i macEug1.Scaffold77160 I 13 N 0 s monDom5.chr2 304289405 103 - 541556283 CATGGCATCCCCGGATCACCTTGCTCCTC--ACTCCTACTCTTTTCCCTGCTGCAGCAGCA-------GCTGCTGAGTTA---------------TGGA-----G-------ACTGCAGGGTAA-----GACATGCTCAATACC i monDom5.chr2 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e mm9.chr11 118673787 101 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e ponAbe2.chr17 69580878 852 + 73212453 M a score=-27449.000000 s hg19.chr17_gl000204_random 19994 18 + 81310 CCAG----------------------------------GCTTGT-------GGCTGGCA s panTro2.chr17 79193805 18 + 83384210 CCAG----------------------------------GCTCGT-------GGCTGGCA i panTro2.chr17 C 0 I 10 s rheMac2.chr16 74746222 18 + 78773432 CCAG----------------------------------GCTTGT-------GGCTGGCA i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 43913 18 + 85690 CAGG----------------------------------GCTCAC-------AGCTGCCC i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4302087 18 + 7991924 CCCT----------------------------------GCTCCA-------GGATGCCA i cavPor3.scaffold_76 C 0 I 10 s bosTau4.chr19 10758843 21 - 65312493 CCTTCCT-------------------------------GCCCAT-------GGAGCCCA i bosTau4.chr19 C 0 I 13 s canFam2.chr9 59362928 59 - 64418924 CTTTTTTTTTCCCGGATTGTTAAGGTTAGGGGGAAAAGGCCCAACCAATTAGGTGTTTT i canFam2.chr9 C 0 I 29 s equCab2.chr11 57948321 13 - 61308211 CT------------------------------------GCC----------GGTGACCC i equCab2.chr11 C 0 I 18 s choHof1.scaffold_213748 2731 9 + 4094 CG------------------------------------GTCCGC-------G------- i choHof1.scaffold_213748 C 0 C 0 s monDom5.chr2 304289508 18 - 541556283 CCAG----------------------------------CCTGAG-------AGCTGGGG i monDom5.chr2 C 0 I 8530 e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e mm9.chr11 118673787 101 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e ponAbe2.chr17 69580878 852 + 73212453 M a score=-10312.000000 s hg19.chr17_gl000204_random 20012 72 + 81310 GAAGGAGTGGAACCACGGTGGGAGGCA--AAAGGCCCAGTGA------CCAAGTACCCTTGACG--GCTCTCTAGG---------CCCCGC s rheMac2.chr16 74746240 72 + 78773432 GAAGGAGTGGAACCACAGTGGGAGGCA--AAAGGCCCAGTGA------CCAAGTCCCCTCGAAG--GCTCTCGAGG---------CCCCGC i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 43931 64 + 85690 AAGGGGGCAG---------GAGAGGCA--GGAGG--CAGTGGGGGCCTCCAAG-CTGCACAGGG--GCTCTCCAG-----------CCCTC i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4302115 71 + 7991924 AATGGGGCAG---GGTAATGGGAGGCATGGCAGG--TGACAA------TAAAGTGGCCACAAAGCTGGTCTCGAGG---------TTCTGA i cavPor3.scaffold_76 I 10 I 9 s bosTau4.chr19 10758877 58 - 65312493 GGGGAGGAGG----------------T--AAAGGCCGAGCAG------TGAAGTCACTAGGATACCTCTCTCAAGG---------CCCACA i bosTau4.chr19 I 13 I 5 s canFam2.chr9 59363016 69 - 64418924 CGGAAAAAGGGGGGAAAAAAAGGGGCC--AAAAACC--------------------CCTTGGGCCCCGGACCAAGGGTTTCGGCCTTCCCA i canFam2.chr9 I 29 I 5 s equCab2.chr11 57948352 74 - 61308211 GGGGAGGAGGGACTGAGGTGGGAGGCT--AAAGGCCAAGCAG------TGACGTCGCCAGGAAGCCCCTCTCAAGG---------CCCCCA i equCab2.chr11 I 18 I 5 s choHof1.scaffold_213748 2740 68 + 4094 ----GAACGGGGTGGGGGCGGGGGGCC--AAGGGCCGAGCCA------GGCGGTCTCCAGGGAGCCTCTCTGGGGG---------CCCC-- i choHof1.scaffold_213748 C 0 I 152 e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e panTro2.chr17 79193823 10 + 83384210 I e monDom5.chr2 304289526 8530 - 541556283 I e mm9.chr11 118673787 101 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e ponAbe2.chr17 69580878 852 + 73212453 M a score=-81325.000000 s hg19.chr17_gl000204_random 20084 82 + 81310 AGCCC-GGC-----------AGGGTTGGGAGCGTAGTTGG----GGGCTGGG---------------------CTGGGCTGCAGGTGGCTTC-------------------------TCAGGG--------CGCAGTGGCAGGGACC-AGGGT s rheMac2.chr16 74746312 90 + 78773432 AGCCC-AGC-----------AGGGGTGGGAGCAGAGTGGG----GGCCTGGG---------------------CTGGGCTGCAGGTGGCTTC-------------------------TCAGGGCGAGCCCACGCAGTGGCAGGGACC-ACGGT i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 43995 30 + 85690 AGGCG-AGG-----------TGGGTGAGGAG----------------------------------------------------------------------------------------------------------GGCAGG-----AGGAG i otoGar1.scaffold_94361.1-85690 C 0 C 0 s mm9.chr11 118673888 79 + 121843856 AGCGT-GGC-----------AG-GGTGGAGGAGGAGAGGAGCCAGGCCAGGG---------------------CTGGCTGAAAGATGGGAAA-------------------------GAGG---------------AGATAGATACCTACCCT i mm9.chr11 I 101 C 0 s bosTau4.chr19 10758940 39 - 65312493 AGCTC-AGT-----------TGATAAGGCAAAAAAGCAGAGA--GGCCAAG----------------------CT------------------------------------------------------------------------------ i bosTau4.chr19 I 5 I 5 s canFam2.chr9 59363090 32 - 64418924 GGCCC-CGG------------------------------------GTTAAGG---------------------CCAT--TGCCTGTTTTTCC------------------------------------------------------------- i canFam2.chr9 I 5 I 12 s equCab2.chr11 57948431 114 - 61308211 AGCTC-CGGATAAAGCGAAGAGAAAAGGGAGAACAGAAGAAG--AGCTGAGGGGCGCACTGCACCAGGTGCCCCCATCCCGCCAGCATCCCTCGGGCCCCAGGGACAGGGCCAGAGA------------------------------------ i equCab2.chr11 I 5 I 60 s cavPor3.scaffold_76 4302195 86 + 7991924 -GCTTAGGC-----------AGAGGTGGGGGAGTGGTAGGGCC-TGCAAGGG---------------------TTGGGTGTCTGACTGGAAT-------------------------GGTGGA--------GTCAAAGGGAGTTCCCTAAATT i cavPor3.scaffold_76 I 9 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e panTro2.chr17 79193823 10 + 83384210 I e monDom5.chr2 304289526 8530 - 541556283 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e ponAbe2.chr17 69580878 852 + 73212453 M a score=17400.000000 s hg19.chr17_gl000204_random 20166 27 + 81310 G-GG---CGGGGCCT---GGTCGAGGCCACAGCC s rheMac2.chr16 74746402 27 + 78773432 G-GG---CGGGGCCT---GGTCGAGGCCACAGCC i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 44025 27 + 85690 G-GG---CAAGGGCC---ATCCCAGGCCAGGGCC i otoGar1.scaffold_94361.1-85690 C 0 C 0 s mm9.chr11 118673967 30 + 121843856 T-TG---CAGGGCCCCAGGGTCAAGATCACAGTC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4302281 31 + 7991924 TGCC---CAGAGCCCCAGTGTCAAGAGCACAGTC i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_227219 54 29 + 1029 -GGG---CCGGGCCC-AGGGTGGAGGCCACAGCC i vicPac1.scaffold_227219 N 0 C 0 s bosTau4.chr19 10758984 29 - 65312493 -GGG---CGGGGCCC-AGGGTTAAGGCCACAGCC i bosTau4.chr19 I 5 I 886 s canFam2.chr9 59363134 29 - 64418924 -GGG---AGGGGTTT-GGTTCCTTTCCCACACCC i canFam2.chr9 I 12 C 0 s equCab2.chr11 57948605 32 - 61308211 -GGGCCAGGAGGCCC-AGGGTCAAGGCCACAGCC i equCab2.chr11 I 60 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e panTro2.chr17 79193823 10 + 83384210 I e monDom5.chr2 304289526 8530 - 541556283 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e ponAbe2.chr17 69580878 852 + 73212453 M a score=-32049.000000 s hg19.chr17_gl000204_random 20193 38 + 81310 TACC----------ATTCCCCCAC------------TTCC------TGGGGACAAAAGGGTCCAG----T s rheMac2.chr16 74746429 38 + 78773432 TGCC----------ATTCCCCCAC------------TTGT------TGGGGACAAAAGCGTCCAG----T i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 44052 17 + 85690 TGCT----------A--CCTCGAC-------------------------------------CCCA----T i otoGar1.scaffold_94361.1-85690 C 0 C 0 s mm9.chr11 118673997 27 + 121843856 TGCT----------A--CTCCTG-------------TTGT------CAGCAACAGGC------------T i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4302312 60 + 7991924 TGCTCTCTCCCCCAA--CCCCCGCCCCAACTTGCCATTAT------CAGGGACAAGAGT--CCAGTGTGT i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_227219 83 40 + 1029 TGCC-------------TCCCGGA------------CTCTGGACTGTGGG-ACAAAAGGGCAAGA----T i vicPac1.scaffold_227219 C 0 C 0 s canFam2.chr9 59363163 18 - 64418924 TTCC-------------CCCTTG-----------------------TGGG------------GAT----T i canFam2.chr9 C 0 C 0 s equCab2.chr11 57948637 32 - 61308211 TCCT-------------CTCCAGA------------TTCC------TGGG---CAAAGGGGTGGA----T i equCab2.chr11 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e gasAcu1.chrXIII 4067241 995 - 20083130 I e panTro2.chr17 79193823 10 + 83384210 I e monDom5.chr2 304289526 8530 - 541556283 I e bosTau4.chr19 10759013 886 - 65312493 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e ponAbe2.chr17 69580878 852 + 73212453 M a score=-12211.000000 s hg19.chr17_gl000204_random 20231 107 + 81310 ----CTGTCTCGGGAG---TGAGCTGTGTCCTCCTCATTCTCCGACCTGTATTTATTGCCCCTCACC-----------ATGCGCTGAGTGCAGTGCTCAGAGCACA--------------GCA--------------------GAGCACACAGGGACAC s equCab2.chr11 57948669 141 - 61308211 ----CTGTCCGGGAAG---GGAACTGTGTCTTCCtcattcccggaaccacatttattgcaccccact-----------gtgtgccaagcgcggtgccaggcacctgcagttccagccttggcaggtgcacagcccagcacaggaggcaggcaggGAGCC i equCab2.chr11 C 0 I 1 s canFam2.chr9 59363181 119 - 64418924 ----CAATTTGGGGGG---GTTTCTTTccccccccccccccc----cccc--------ccccccccc-----------ccGCACCAAGCACAGTG--------CTGCGGTCCCAGACT--GTCAGTGCCCAGCCCAGGGCCAGAGGCAGGCAGGGAGCC i canFam2.chr9 C 0 I 1 s vicPac1.scaffold_227219 123 138 + 1029 ----AGGTCGCAGGAG---CGAGCTGCATCTTCCTCCTTCTCGGAATCACCTTTCTTGCTCCCCACC-----------GTGTGCTAAGCTCAGTGCCAGGAACCCGTGGT-CCAGCCTCTGCCAGAGCATGGGGT-GCACAGGAGGCAGGCA-GGAGCC i vicPac1.scaffold_227219 C 0 I 1 s cavPor3.scaffold_76 4302372 138 + 7991924 ----CTCTTTCGGGAGCA-GGAGCTGCATCTTCCTTTCTCT--GAAGCATGTTCATGGCAACCCACA-----------GAGAGCAGAGTACAGTGCCAGGCCCCTACCAT-CCAGCCTTGGCAAGCACACTGCCC-AATTCAGGAACACACGGGG-CGC i cavPor3.scaffold_76 C 0 I 2 s mm9.chr11 118674024 150 + 121843856 ----CTCATTTGTGAGGGTGGGACTGAGTTTTCCTCGCTCTCAGAAGCATAGTTACTGT-GCCCCCATTGTGTACTGTGTGTGCAGAGTGTAGTACCATGTCCCCA-AAT-TTGAGCTGGGCAAGCTTATGTTCC-GGCTGAGGAATACACATGG-CAT i mm9.chr11 C 0 I 2 s otoGar1.scaffold_94361.1-85690 44069 102 + 85690 ----CTGT--TGGGAG---GGGTCTGAGGTTTCCTCACTTTCTGAGCTGTATTGATTGTGCCCCATC-----------CT--GCCAAGTGTGATGCCAGGCCCAGT--------------GCA--------------------GGAGCCACAGAGAGG- i otoGar1.scaffold_94361.1-85690 C 0 C 0 s rheMac2.chr16 74746467 107 + 78773432 ----CTGTCGCAGGAG---CGAGCTGTGTCCTCCTCATTCTCTGAGCCGTATTTATGGCCCCTCACC-----------ATGTGCTGAGTGCAGTGCTCAGAGCACA--------------GCA--------------------GAGCACGCAGGGACAC i rheMac2.chr16 C 0 M 810 s gasAcu1.chrXIII 4068236 90 - 20083130 CTGCCTGCTGCATGAG--------TTTATTTTTCTTCTTCTCCGAATTGGCCTTCTTGGCCTCCAGT-----------CTGCGCTGTCGGCAGGACTTGGCAGGTTCGG-------------------------------------------------- i gasAcu1.chrXIII I 995 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e panTro2.chr17 79193823 10 + 83384210 I e monDom5.chr2 304289526 8530 - 541556283 I e bosTau4.chr19 10759013 886 - 65312493 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e ponAbe2.chr17 69580878 852 + 73212453 M a score=-26675.000000 s hg19.chr17_gl000204_random 20338 29 + 81310 CCC--ACTGTTG-----ACCTTCAAGGGGAAAAG-CC s ponAbe2.chr17 69581731 26 + 73212453 CCC--ACTGTTG-----ACCTTCAAGGGAAA----CC i ponAbe2.chr17 M 852 C 0 s otoGar1.scaffold_94361.1-85690 44171 20 + 85690 -----------G-----TACTGCATGGACAGAGG-AC i otoGar1.scaffold_94361.1-85690 C 0 C 0 s mm9.chr11 118674176 24 + 121843856 CTA--A-----------ACCTGCCCCCCAAAATGGTC i mm9.chr11 I 2 C 0 s cavPor3.scaffold_76 4302512 30 + 7991924 CCA--ACTGTTG-----ACCTTCGTGCAGGAAGGTTG i cavPor3.scaffold_76 I 2 C 0 s vicPac1.scaffold_227219 262 22 + 1029 CCA--ACTGCTGCTGGAATCCAGA------------- i vicPac1.scaffold_227219 I 1 C 0 s canFam2.chr9 59363301 18 - 64418924 CCACGACTGGC------ATCTACG------------- i canFam2.chr9 I 1 C 0 s equCab2.chr11 57948811 18 - 61308211 CCA--ACTGTCG-----ACCTTCGA------------ i equCab2.chr11 I 1 C 0 s gasAcu1.chrXIII 4068326 29 - 20083130 GCA--ACTTGCG-----CACCTCACGGCGAAAAGCC- i gasAcu1.chrXIII C 0 N 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e panTro2.chr17 79193823 10 + 83384210 I e monDom5.chr2 304289526 8530 - 541556283 I e bosTau4.chr19 10759013 886 - 65312493 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e rheMac2.chr16 74746574 810 + 78773432 M a score=5554.000000 s hg19.chr17_gl000204_random 20367 50 + 81310 C--------CTGCAGCCTCCTC--AACTCCCCTTCTTCTGGGAGGTCAGTTGGGGAATTC s ponAbe2.chr17 69581757 48 + 73212453 T--------CTGCGGCCTCCTC--A-CTCCCCTT-TTCTGGGAGGTCAGGTGGGGAATTC i ponAbe2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 44191 49 + 85690 C--------CTGAGGCTGCCTT--ACCCCTCCTGCTACAGGGAGGT-GGGGGAAGAATTC i otoGar1.scaffold_94361.1-85690 C 0 C 0 s mm9.chr11 118674200 58 + 121843856 TGCTAGCAACCTCAGCCTCCTC--CTCTCTGCAGCTGCAGGGAGGACAAGTGGGAAATTC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4302542 52 + 7991924 T--------CCCCAAGCTCCTCAGTTTTTCCCCACTATGGGGAAGTCGAATGAGGAACTC i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_227219 284 41 + 1029 -------------GGTCTCCTG--GCTCTGCCCACTGCAGGGAGGG-GGC---AGGACGC i vicPac1.scaffold_227219 C 0 C 0 s canFam2.chr9 59363319 30 - 64418924 T--------CCACGTCCTTCTT--G---------CTGCAGGCGGTG-GGG---------- i canFam2.chr9 C 0 C 0 s equCab2.chr11 57948829 47 - 61308211 T--------CTCCAGCCTCCTT--GCCCCACC--CTGCAGGGAGGG-GGGTGGGGAACTC i equCab2.chr11 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e panTro2.chr17 79193823 10 + 83384210 I e monDom5.chr2 304289526 8530 - 541556283 I e bosTau4.chr19 10759013 886 - 65312493 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e rheMac2.chr16 74746574 810 + 78773432 M a score=23483.000000 s hg19.chr17_gl000204_random 20417 25 + 81310 TGAGATCCCATCCTGTCCCCTACAC s ponAbe2.chr17 69581805 25 + 73212453 TGAGATCCCATCCTGTCCCCTGCAC i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79193833 25 + 83384210 TGAGATCCCATCCTGTCCCCTACAC i panTro2.chr17 I 10 C 0 s otoGar1.scaffold_94361.1-85690 44240 25 + 85690 CCAGTCCCCATCCTGTCCCCTGCAT i otoGar1.scaffold_94361.1-85690 C 0 I 12 s mm9.chr11 118674258 25 + 121843856 TGAGTTCCCACGATGTCCCCTATAC i mm9.chr11 C 0 I 14 s cavPor3.scaffold_76 4302594 25 + 7991924 TGATCCCTCATCCCATCCTCTGCAC i cavPor3.scaffold_76 C 0 I 6 s vicPac1.scaffold_227219 325 18 + 1029 AGAGGCCC-------CATCCCACAC i vicPac1.scaffold_227219 C 0 C 0 s canFam2.chr9 59363349 10 - 64418924 ---------------ACCCCCACAC i canFam2.chr9 C 0 I 22 s equCab2.chr11 57948876 25 - 61308211 TGAGCCCCATCCCGCATCCCCACCC i equCab2.chr11 C 0 I 1 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e monDom5.chr2 304289526 8530 - 541556283 I e bosTau4.chr19 10759013 886 - 65312493 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e rheMac2.chr16 74746574 810 + 78773432 M a score=-2722.000000 s hg19.chr17_gl000204_random 20442 22 + 81310 ACACATATGCG---T-GCAC-------------------------ATATGC---- s pteVam1.scaffold_60858 575 22 - 1392 ATACATGTGCG---T-GCAC-------------------------ACGTGT---- i pteVam1.scaffold_60858 N 0 C 0 s equCab2.chr11 57948902 16 - 61308211 ACTCACACTCC---A-GAAC----------------------------------- i equCab2.chr11 I 1 C 0 s vicPac1.scaffold_227219 343 19 + 1029 --CCAC-TGCG---A-ACCC-------------------------AAGGGT---- i vicPac1.scaffold_227219 C 0 C 0 s cavPor3.scaffold_76 4302625 49 + 7991924 ACACACACACAGGTT-GCACCTCTGGCTCCAGGACCCCAGGGATGGTACA----- i cavPor3.scaffold_76 I 6 C 0 s mm9.chr11 118674297 22 + 121843856 acacacataca---t-acac-------------------------acacac---- i mm9.chr11 I 14 C 0 s otoGar1.scaffold_94361.1-85690 44277 27 + 85690 ACACACATGTG---TGGCAT-------------------------ACCTGCAGGG i otoGar1.scaffold_94361.1-85690 I 12 C 0 s panTro2.chr17 79193858 22 + 83384210 ACACATATGTG---T-GCAC-------------------------ATATGC---- i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69581830 22 + 73212453 ATACACATGTG---T-GCAC-------------------------ACATGC---- i ponAbe2.chr17 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59363359 22 - 64418924 I e bosTau4.chr19 10759013 886 - 65312493 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e rheMac2.chr16 74746574 810 + 78773432 M a score=-7009.000000 s hg19.chr17_gl000204_random 20464 24 + 81310 TCACA-----T----------ATGCACACGAGCACAGAC s canFam2.chr9 59363381 18 - 64418924 ---------------------ACACAAGGGTTGGCTGGC i canFam2.chr9 I 22 C 0 s pteVam1.scaffold_60858 597 16 - 1392 TCACA-----C----------ATGCACACGT-------- i pteVam1.scaffold_60858 C 0 C 0 s equCab2.chr11 57948918 33 - 61308211 -CACA-----GGGTGGAGGGGATGCAGAGGTTTGCTGTC i equCab2.chr11 C 0 C 0 s vicPac1.scaffold_227219 362 25 + 1029 CC--------------CTGGGGCACAAGGGCTAACTGCC i vicPac1.scaffold_227219 C 0 C 0 s cavPor3.scaffold_76 4302674 29 + 7991924 GCACAGGGAGC----------ACAAAGGTCACTAGTGAC i cavPor3.scaffold_76 C 0 I 10 s mm9.chr11 118674319 24 + 121843856 acaca-----c----------acacacacgaacacaGAC i mm9.chr11 C 0 I 122 s otoGar1.scaffold_94361.1-85690 44304 24 + 85690 acaca-----t----------acacacatgtacacatac i otoGar1.scaffold_94361.1-85690 C 0 C 0 s panTro2.chr17 79193880 24 + 83384210 TCACA-----T----------ATGCACATGAGCACAGAC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69581852 24 + 73212453 TCACA-----T----------ATGCACATGAGCACAGAT i ponAbe2.chr17 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e monDom5.chr2 304289526 8530 - 541556283 I e bosTau4.chr19 10759013 886 - 65312493 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e rheMac2.chr16 74746574 810 + 78773432 M a score=-36896.000000 s hg19.chr17_gl000204_random 20488 19 + 81310 -----GGGC-CAT-CCTGGAC----------CCTA--C s canFam2.chr9 59363399 14 - 64418924 AGCCAGGACCC-T-CC---------------------- i canFam2.chr9 C 0 I 5 s pteVam1.scaffold_60858 613 10 - 1392 -----ACACACAT-TC---------------------- i pteVam1.scaffold_60858 C 0 N 0 s equCab2.chr11 57948951 15 - 61308211 GGCCAGGACTCAT-CC---------------------- i equCab2.chr11 C 0 I 5 s vicPac1.scaffold_227219 387 1 + 1029 ---------------C---------------------- i vicPac1.scaffold_227219 C 0 C 0 s cavPor3.scaffold_76 4302713 15 + 7991924 -----GAGT-CCT-TCTTGAT----------------C i cavPor3.scaffold_76 I 10 C 0 s otoGar1.scaffold_94361.1-85690 44328 33 + 85690 -----agacacacacttagacacacaTTGTTCCTAACC i otoGar1.scaffold_94361.1-85690 C 0 C 0 s panTro2.chr17 79193904 19 + 83384210 -----GGGC-CAT-CCTGGAC----------CCTA--C i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69581876 19 + 73212453 -----GGGC-CAT-CCTGGAC----------CCTA--C i ponAbe2.chr17 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e monDom5.chr2 304289526 8530 - 541556283 I e bosTau4.chr19 10759013 886 - 65312493 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e rheMac2.chr16 74746574 810 + 78773432 M a score=132038.000000 s hg19.chr17_gl000204_random 20507 135 + 81310 CCTCCACCTGCTTCCTCAGGATCTAATCCTCTTGCTTTAATGACAGGG----CCCCCAAATAATAAAGGAGTCCAGGGAGAGGCTTAAGCATCCCCAGAAGGCTGGCTATGGGTGGCAGGGCCCCCAGA---------------AGAG---------CTGGGA s canFam2.chr9 59363418 138 - 64418924 CCTCAACCTGCTTCTTCAGGATCCAACCCCCTGGCTTTAGTAGGGGGA--GCCCTCAAAATAATCTGCAGGTGGGCAGA--GGCTTCAGTTTCCCAGGAAGGCTGGACATAGGTGGTGGGGGTCCCAGGAGGAT----------GAAGGAC-----------A i canFam2.chr9 I 5 C 0 s equCab2.chr11 57948971 155 - 61308211 CCT---CCTGCACCTTCAGGATCCAACCCCCTTGCCTTAAT-GCTGGG--GCCGTCACAATAATTTTGGGGTCCATGGA--GGCTTAAGTTTCCCAAGAAAGCTGGACCTGGGTGGTGGGGGCCCCAGAAGGACGTGATACTAAGGGGGACCTGGAGCTGGAA i equCab2.chr11 I 5 C 0 s bosTau4.chr19 10759899 130 - 65312493 CCTCTATCTG---CTTTGGGATCCACTCTCCTGGCATTAGTGGTGGGG--GCTTTCAAAATAATTTGGGGATCGACAGA--GGCCT--GTTTCCTGGGAAGGCTGGAGAT--ATGATA-------TAGA---------------AAAGGCCTTGGATCTGGAA i bosTau4.chr19 I 886 C 0 s vicPac1.scaffold_227219 388 135 + 1029 CCTCTATTTGCTTCTTCAGGATCCACCCCACTGGCATTAGTGGTGGGG--GCCCTCAAAATAATTTGGGGGTTGA-GGA--GGCTTAAGTTTCCCAGGAAGGCTGTACAC--GTGATA------CCGGA---------------GGAGGCCCTGGATCTGGGA i vicPac1.scaffold_227219 C 0 C 0 s cavPor3.scaffold_76 4302728 130 + 7991924 CTTCTACCTGCTTCTTCAAAATCCAGA-----TTCTTTAATGATTAGGATCCCCCTTCAATAATGTGGGGCCCTAGGGA--TGCTCACATTTCTCAGAAAGACTGGACGTGGGCAGCGGGGAC-ACAGA---------------A-AG---------CTGGAA i cavPor3.scaffold_76 C 0 C 0 s otoGar1.scaffold_94361.1-85690 44361 119 + 85690 CCTCTACCTGCTTCC------TCCAAACCTCTTGCTTTAATCATGGGA-TTCCTCCCAAATAATCTGGGAGTCTGGGGC----CTTCAATTTCTCAGGAAGGCTAGACGTTGGGG---------TCAGA---------------AGGG---------CTGGAC i otoGar1.scaffold_94361.1-85690 C 0 C 0 s panTro2.chr17 79193923 135 + 83384210 CCTCCACCTGCTTCCTCAGGATCTAATCCTCTTGCTTTAATGACAGGG----CCCCCAAATAATAAAGGAGTCCAGGGAGAGGCTTAAGCATCCCCAGAAGGCTGGCTATGGGTGGCAGGGCCCCCAGA---------------AGAG---------CTGGGA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69581895 135 + 73212453 CCTCCACCTGCTTCCTCAGGATCTAATCCTCTTGCTTTAATGACAGGG----CCCCCAAATAATAAAGGAGTCCAGGGAGAGGCTTAAGCATCCCCAGAACGCTGGCTATGGGTGGCAAGGCCACCAGA---------------AGAG---------CTGGGA i ponAbe2.chr17 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e monDom5.chr2 304289526 8530 - 541556283 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I e rheMac2.chr16 74746574 810 + 78773432 M a score=313052.000000 s hg19.chr17_gl000204_random 20642 328 + 81310 AGCATGAG--GAGTG--T---CCTACAAAGGGTG-AGGGCTGTGCC-CTGGGGCTTGGAGGGGGGCCTCAGTCTCAGAG---AAGGATTTTA-AAGACTCCTGTGCCCGCATCTGCAGCTGGCC--------------------------------AGT---TTCCTCTTCGCAGCTCTCAG-----CCTGGCTGCTTCAACCT------GCTGCA--GAACCAG--------CCAGCACTGCTCCCGAGGCAGCACGAGACTGG-GGCAGCCCCTGGTGCTCTGGCCC-CAAAAG-----------------------GTCTCCTCTC-AGATTCTTGTCATTGGAAA---GAGAAGAT-AGAAAAACAAACATCTGG-ACTGCTATAAAGTGTC-CTCTATCAAAA-------------A-ATAAGCAGATACACaaaggg s panTro2.chr17 79194058 328 + 83384210 AGCATGAG--GAGTG--T---CCTACAAAGGGTG-AGGGCTGTGCC-CTGGGGCTTGGAGGGGGGCCTCAGTCTCAGAG---AAGGATTTTA-AAGACTCCTGTGCCCGCATCTGCAGCTGGCC--------------------------------AGT---TTCCTCTTCGCAGCTCTCAG-----CCTGGCTGCTTCGGCCT------GCTGCA--GAACCAG--------CCAGCACTGCTCCCAAGGCAGCACAAGACTGG-GGCAGCCCCTGGTGCTCTGGCCC-CAAAAG-----------------------GCCTCCTCTC-AGATTCTTGTCATTGGAAA---GAGAAGAT-AGAAAAACAAACATTTGG-ACTGCTATAAAGTGTC-TTCTACCAAAA-------------A-ATAAGCAGATACACAAAGGG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69582030 328 + 73212453 AGCGTGAG--GAGCG--T---CCTACAAAGGGTG-AGGGCTGTGCC-CTGGGGTTTGGAGGGGGGCCTCAGTCTCAGAG---AAGGATTTTA-AAGACTCCTGCGCCCCCATCTGCAGCTGGCC--------------------------------AGT---TTCCTCTTCCCAGCTCTCAG-----CCTGGCCGCTTCAGCCT------GCTGCA--GAAACAG--------CCAGCACTGCTCCCAAGGCAGCACAAGACTGG-GGCAGCCCCTGGTGCTCTGGCCC-CAAAAG-----------------------GCCTCCTCTC-AGATTCTTGTTATTGGAAA---GAGAAGAT-AGAAAAACAAACATTTGG-ACTGCTATAAAGTATC-TTCTACCAAAA-------------A-ATAAGCAGATACACAAAGGG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74747385 317 + 78773432 AGCGTGAG--GAGTG--T---CCTACAAAGGGTG-AGGGCTGTGCC-CTGGGGCTTGGA-GGGGGCCTCAGTCTCAGAG---AAGGATTTTA-AAGACCCCTGCGCCCCCATCTGCAGCTGGCC--------------------------------AGT---TTCCTCTTCCCAGCTCTCAG-----CCTAGCCGCTTCAGCCT------GCTGCA--GAACCAG--------CCAGCACTGCTCCCGAGGCAGCACGAAGCTGG-GGCAGCCCCTGGTGCTCTGGCCC-CAAAAG-----------------------ACCTCCTCTC-AGATTCTTGTCA-------------AAGAT-GGAAAAATAAACATTCGG-ACTGCTATAAAGTGTC-TTCTACCAAAA-------------A-ATAAGCAGACACACAAACGA i rheMac2.chr16 M 810 C 0 s otoGar1.scaffold_94361.1-85690 44480 283 + 85690 AGTGTGAG--GCCTGGTT---CTGACACAGGCTG--GGGCTGTGCC-C-GGGCCTGGGTGGGAGGGCTCCATCTCAGAG---CAT--------------------------TTTGCATCCCATC--------------------------------AGT---TTGAGTGTCCTGGCCCACGGAGAGCTCTGGCCACTCCAGCCCGTGGCAGCTGCT--GAGCCAG--------CCA-----GCTCCCAGGGCAGCAAGAGGCTGGAGGCTGCCTTTGGTGCACTGGCCCACAAAAG-----------------------ACC----CTC-AGATTCTGGTCAATGGGGA---GAGAATAT-GGAAAACCAGACACCTGG-ACT-----------TC-TCCTACAAAAA-------------A-ATAAGCA------------- i otoGar1.scaffold_94361.1-85690 C 0 I 632 s cavPor3.scaffold_76 4302858 333 + 7991924 AGTGTCAATTAAGTG--TGAACCTGTCCAGGGAT-AGGGTTATGCC-CTAGTGCTGGGC-GGAAGGCTCAATGTCAGAG---AAGAACTGTA-GTGAC-----CACCACCAGCAGCAGCTTCTC--------------------------------AGTGAGTCCCCATGCCCACTGTGTGT-----GTTGGCCACCCCTACTCCTG---GCTGTT--GAGTCAGGAGGG-TCCTCGCTTTG-TCCCAAGGTGGCAGGAGGCCTG-GGGTGACCCTTGTGCTCCGACTG-CAAAAG-----------------------A-ATCTCCTG-AGATTCTTGTTACTTGTTACTTGATAAAATGGGGAAAAGGAGCATCTTG-ACTTCTAAAAAGAATC-TAT----GAAA-------------A-ATAAGC-----CACACATGA i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_227219 523 347 + 1029 AGTGCCAG--GTGTGG-T---CCTGCCAAAGGCG-AGGGCAGGGAGCCTGGG--CAGGAGGGCGGGCTCCGTCTCAGAG---AAGGACG----TGTGCGTTCGCACTGCCTGCTCCCCCACATC--------------------------------GGC---CTCCCAGGCCCAAGGCCCG------TCTGACCACT------CACGGAGGCTGCT--GGGCCAGCCCAG--TCCAGCTCTGCTCCCCACGGGGTAAGA-------GGCTGCCTTTGAAGCTCCAGCCC-CAAAAGGCTGTTAGACCACTCAGGAGGCTGCCTCCTGTT-AGATTCTTGCCACTGGGGA---G--AAGAT-GGAAAAATAAACACTTTGCATTTCTAGAAAGTGTCTTTCTGC-AAAA-------------ATATAAGCCAACACGGAAAAGG i vicPac1.scaffold_227219 C 0 N 0 s bosTau4.chr19 10760029 375 - 65312493 AGCACCAG--GCATGG-T---CCTGCCAAGGGCGTGGGGCAGGCAGCCTGGG--CAGGAGGGAGGGCTGAGTCTCAGAGGACAGTAAAG----AGCCCATTCCCACTGCCAACCACCCCCCACCCTGACCACCACCACATCTCAGCTGTGGACTGAAGT---CTCCCAGGCCTGTGCCCCAT-----TCTGACCACTCCAGCCCACGGTGGCTGCT--GAGCCAGCCGGGCCTCCAGCTCTGCTCCCAAGGTGGCCAGAGGCTGGGGGCTGCCTTTGGCGCTCCGGCCC-CAAAAG-----------------------GCCTCCTGTT-GGATTCTTGCCACTGGGGA---GAAAAGAT-GGAAAGATAAACACCTGG-ACTTCTAGAAAGTGTC-TTCTGC-AAAA-------------A-ATAAGCCAACACAGAAAGGG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57949126 321 - 61308211 TATGCAAG--GGGTGG-T---CCCGCCAGGGGTG-GGTGCAGGTGG-CTGGG--CAGGAGTG------CTGCCTCCAGG---AAGGACT----ATAACACTCCCACC-CCAACCCCCTCCAATA---------------------------AATAAAGT---GTCCCTGGCTGGGGGCCCAG-----CGCAGCCACTCCAGCCCACGGCAGCTGCT--GAACCAACGCAGCTCCCGGCTCTGCTCCCACAGG--------------GGCTGCCTTTGGGG-TCCAGCCC-CAAAAA-----------------------GCCTCCTGTC-AGACTCTTGCCACTGGGGA---GTGAAGAT-AGAAAAATAAACACCTAG-ACTTCTAGAAAGTGTT-TTCTGC-AAAA-------------A-ATAAGCCAACACACAAATGG i equCab2.chr11 C 0 I 196 s canFam2.chr9 59363556 298 - 64418924 TGCTCCCA--GGGAAG-G---CCTACCACGGGCA-AGGGCAGGGAG-CGGGC--TGGGAGAGG----CCAGTCTCAGGG---CAGGTCTCTCCAGCCCATTCTCACC-----CCTCCTCCCAT------------------------------------------CCCAGCTGCCAGTTCA---------AGTCTCCAAGGCCCATGGCAGC--CACGGAGCCGGCCCAGCTCCCTGTTTTGTTCCCAAGGG--------------GG----------------------CAGAAG-----------------------GCCTCCTGTTGGGATTCCTGCCATTAGGGA---GAGAAGAT-AGAAACATAAACACTGGG-ACTTCTAGAAAGTGTC-TTCAGC-AAAAAAGTCATAATAATA-ATAAGCCAACACACAAA--- i canFam2.chr9 C 0 I 344 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e monDom5.chr2 304289526 8530 - 541556283 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=34304.000000 s hg19.chr17_gl000204_random 20970 65 + 81310 agagggaggtagcagaaggag-------tgagagag--accgagggagggaagaggagggaagga-----AGCCTCTGG s panTro2.chr17 79194386 65 + 83384210 AGAGGGAGGTAGCAAAAGGAG-------TGAGAGTG--ACCGAGGGAGGGAAGAGGAGGGAAGGG-----AGCCTCTGG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69582358 65 + 73212453 AGAGGGAGGTAGCAGAAGGAG-------TGAGAGAG--ACCGAAGGAGGGAAGAGGAGGGAAGGA-----AGCCTCTGG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74747702 65 + 78773432 Agagggaggtaggggaaggag-------tgagagag--acggagggagggaagaagagggaagga-----agCCTCTGG i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4303191 72 + 7991924 AGGAGGAGGGAGGAGAAGGAA-------GGAAAAAGGAACAGATAGACAGAGAATGAAGGCGGGATGAGGAACCGCAGG i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10760404 60 - 65312493 --GCCCAGGCCTCACTGGAGGCTCTTTCTAGAAGAG--ACTGTGTGGATGACAAG---------------GTCCTCTGG i bosTau4.chr19 C 0 I 93 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 44763 632 + 85690 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59363854 344 - 64418924 I e equCab2.chr11 57949447 196 - 61308211 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=73013.000000 s hg19.chr17_gl000204_random 21035 107 + 81310 GGATGAGGCATGTTCACCCAGCCTGGACAGGGGAAGATTGAGGAGGGCCATGGCAGAGGTGTGGGTGAGGCACACAAGGTAGCTGGAGCAGAAGCCACAGGCAGATA s panTro2.chr17 79194451 107 + 83384210 GGATGAGGTGTGTTCACCCAGCCTGGACAGGGGAAGATTGAGGAGGGCCATGGCAGAGGTGTGGGTGAGGCACACAAGGTAGCTGGAGCAGAAGCCACAGGCAGATA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69582423 107 + 73212453 GGATGAGGCATGTTCACCCAGCCTGGACAGGGGAAGATTGAGGAGGGCCATGGCAGAGGTGTGGGTGAGGCACAGAAGGTAGCTGGAGCAGAAGCCACAGGCAGATA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74747767 107 + 78773432 GGACGAGGCACGTTCACCCAGCCTGGACAGGGGAAGGTTGAGGAGGGCCGTGGCAGAGGTGTGGGTGAGGCACACAAGGTAGCTGGAACAGAATCCACAGGCAGATA i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4303263 104 + 7991924 AGACAAGACACATTCGTCCAGCCTGGACACAG--AGCCCCAGGGGGGACAGGGCAGAGA-GGGGTTGAAGTTATCACCGCCGTTGGAGCAGAAGCCACAGGCAGACG i cavPor3.scaffold_76 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 44763 632 + 85690 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59363854 344 - 64418924 I e bosTau4.chr19 10760464 93 - 65312493 I e equCab2.chr11 57949447 196 - 61308211 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=36608.000000 s hg19.chr17_gl000204_random 21142 84 + 81310 GCCCAGGTGAGATGCACTGGCCAGGCAGAGA---GGAGGCTAGGATGGCAGGCCCTGGGCAAGGGCAGA-GAAGGCAGAAGTCAGAT--G s cavPor3.scaffold_76 4303367 72 + 7991924 GGC-----------CCCTGGGCAAGAAGAGA---GAGGGACCAAA----GGGCCCTGGGCCAGGACAGGCAAACGCGAAAATGGGACTGG i cavPor3.scaffold_76 C 0 C 0 s rheMac2.chr16 74747874 84 + 78773432 GTCCAGGTGCGACGCACTGGCCAGGCAGAGA---GTAGGCCAGGACAGCAGGTCCCAGGGAAGGGCAGA-GAAGGCAGAAGTCAGAT--G i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69582530 84 + 73212453 GCCCAGGTGAGGTGCACTGGCCAGGCAGAGA---GGAGGCTAGGACGGCAGTCCCCAGGGAAGGGCAGA-GAAGGCAGAAGTCAGAT--G i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79194558 84 + 83384210 GCCCAGGTGAGATGCACTGGCCAGGCAGAGA---GGAGGCTAGGATGGCAGGCCCTGGGGAAGGGCAGA-GAAGGCAGAAGTCAGAT--G i panTro2.chr17 C 0 C 0 s ornAna1.chr2 50656390 75 - 54797317 GCCCCTGGGTGGTCCATGGACCCTGCGGTCAGCTGGAGGCCCG------GGCCACCAAGAAGGGCCAGA-GGGTCCCCGGGA-------- i ornAna1.chr2 N 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 44763 632 + 85690 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59363854 344 - 64418924 I e bosTau4.chr19 10760464 93 - 65312493 I e equCab2.chr11 57949447 196 - 61308211 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=16522.000000 s hg19.chr17_gl000204_random 21226 38 + 81310 ACCTGCCCT----------GGCTGGCCCCGACGACCTTG--GAC----TCACGA s panTro2.chr17 79194642 38 + 83384210 ACCTGCCCT----------GGCTGGCCCTGACGACCTTG--GAC----TCACGA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69582614 38 + 73212453 ACCTGTCCT----------GGTTGGCCCCAATGACCTTG--GAC----TCACGA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74747958 48 + 78773432 ACCTGCCCTggcgggccccggcgggccccgACGACCTTG--GAC----TCACGA i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4303439 38 + 7991924 GTCAGACTG----------CGCTGACCCAGACGGTCTTA--GAC----GGATAC i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10760557 40 - 65312493 TCCTGTCCT------------CTGCCCCCTGTGGGGCTG--GACACTGTCCTGA i bosTau4.chr19 I 93 C 0 s ornAna1.chr2 50656465 37 - 54797317 GCCTGT-------------GGGTGGGTCGGCCGGCGTCAGCGGC----TCCCGT i ornAna1.chr2 C 0 I 5865 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 44763 632 + 85690 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59363854 344 - 64418924 I e equCab2.chr11 57949447 196 - 61308211 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=25059.000000 s hg19.chr17_gl000204_random 21264 76 + 81310 GTTGCCTTTGGTCAGAAGCGTGGACTTGTGTTGACAAAGATGCTGCAGAGGCCGGGTGGCGGGGAGGCCAGAAGCA---- s bosTau4.chr19 10760597 68 - 65312493 GGGGC---TGAGCAGGGTTGTTGGTCTggg--agagagggggctgaagggggtgag-------gaggtggggagagatga i bosTau4.chr19 C 0 C 0 s cavPor3.scaffold_76 4303477 61 + 7991924 ACCGCC-CTGGTCGGAAGCCCAGGTGTTTGCCCACAGAG----TGAAGAGT---GG-------TGAGTTAGCATTT---- i cavPor3.scaffold_76 C 0 C 0 s rheMac2.chr16 74748006 70 + 78773432 GTTGCCTTTGGTCAGAAGTGTGGACTTGTGTTGACCAAGATGCTGCAGAGGCCAGG------GGGAGCCAGAAGCA---- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69582652 69 + 73212453 GTTGCCTTTGGTCAGAAGCGTGGACTTGTGTTGACCAAGATGCTGCAGAGGCCAGG-------GGTGCCAGAAGCA---- i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79194680 75 + 83384210 GTTGCCTTTGGTCAGAAGCGTGGACTTGTGTTGACAAAGATGCTGCAGAGGCCAGG-GCGGGGGCAGCCAGAAGCA---- i panTro2.chr17 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 44763 632 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59363854 344 - 64418924 I e equCab2.chr11 57949447 196 - 61308211 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=30743.000000 s hg19.chr17_gl000204_random 21340 58 + 81310 AGGGACACGC-ACAGCTAGGAAAGAATGTGCTGAGATGGGGGAGAGGAGAGCCTGGCCG s panTro2.chr17 79194755 58 + 83384210 AGGGACAAGC-ACAGCTAGGAAAGAATGTGCTGAGATGGGGGAGAGGAGAGCCTGGCCG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69582721 58 + 73212453 AGGGACAAGC-ACAGCTAGGAAAGAATGTGCTGAGATGGGGGAGAGGAGAGCCTGGCTG i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74748076 58 + 78773432 AGGGGCAAGC-ACAGCTAGGAAAGAATGTGTTGAGACGGGGGAGGGGAGGGCCTGGCCG i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4303538 45 + 7991924 A--------------CTAGAAAAAGAGGGGGCCAAGAGGAGGCCTGGAGAATGCACCCG i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10760665 52 - 65312493 aagaactggaggaa-----ggaggaagggagagggaacggagagggaagaa--gggTTG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57949643 53 - 61308211 AGGGGCTGGC-ACA-----GGAGGCAGGGAGTGAGTTGGGAGGGGTGAGGACTTGGTCG i equCab2.chr11 I 196 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 44763 632 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59363854 344 - 64418924 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=71278.000000 s hg19.chr17_gl000204_random 21398 135 + 81310 AATCACCATCATCATC---------------CTCGTCCT-------CAGCTCCCCgtcagtgtttgctcactatcgt-gc-cccagcgcctggccaatgctggcacacagtaggcgctcag-cagttttggtgaaatgaacgCTGCAAAGAAGGA------AGTCA s panTro2.chr17 79194813 135 + 83384210 AATCACCATCCTCATC---------------CTCGTCCT-------CAGCCCCCCgtcagtgtttgctcactatcgt-gc-cccagcgcctggccaatgctggcacacagtaggcgctcag-cagttttggtgaaatgaatgGTGCAAAGAAGGA------AGTCA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69582779 135 + 73212453 AATCACCATCCTCATC---------------CTCGTCCT-------CAGTCCCCCgtcagtgtttgctcaccatcgt-gc-cccagcgcctggccaatgctggcacacagtaggcgctcag-cagttttggtgaaatgaatgCTGCAAAGAAGGA------AGTCA i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74748134 135 + 78773432 AACCACCATCCTCATC---------------CTTGTCCT-------TAGCCCCCCgtcagtgttggctcaccactgt-gc-cccagtgcctggccagtgccggcacacagtaggcgctcag-cagtttcggtgaaatgaatgCTGCAAAGAAGGT------GGCCA i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4303583 68 + 7991924 AGCCATCAGCAGCATC---------------TTCACCCA-------CACATCCCCCCAAAAG---------------------------------------GGCAAACCTTAAGGGC-------------------------------AGCAGGA------AGGCA i cavPor3.scaffold_76 C 0 I 61 s bosTau4.chr19 10760717 160 - 65312493 ---AACCATCGTCGTTGAAGTAggactgaatcgagtcccgcaagggcaga---cgggtgttgacctttgctcaccgtggctcctggcacctggcccagggctgcacacagtaggcactcagccgatatttgttaagtgaacaaTGAAAAGAAGGAGAAGGGAGGCG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57949696 145 - 61308211 AATGATTCTCATCATTGAAGCAGAACTGAACCTGGTCCCCTGAAGTCAAA-CCTGGTTGGT--------------------CTCTGCTCCCAGCTCAGTGTGGTACCCAGTGGATGCTTAGCCAATATCTCTTAAATGAACAAGGAAAAGAGGAAGAAGGAAGCCA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59364198 158 - 64418924 catcatcaccatcatcaAAACAGGAC-AAAGCTTATCccgtgagggcagatccaggctggt-ccctctcagcaccgt-gccccctgcccctggccagggctggcacacagcaggtgctcag-cagcacctgctcaacgaacaaGGGAAGGAAGGA----CAAGCCA i canFam2.chr9 I 344 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 44763 632 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=39420.000000 s hg19.chr17_gl000204_random 21533 47 + 81310 -ATCTGGGTGAGTGGCATGGAGCTGGGTAACGTTTCTGATGAAaattc s rheMac2.chr16 74748269 47 + 78773432 -ATCTGGGTGAGTGGTGTGGAGCTGGGTAACGTTTCTGTTGAAAATTC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69582914 47 + 73212453 -ATCTGGGTGAGTGGCGTGGAGCTGGGTAATGTTTCTGATGAAAATTC i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79194948 47 + 83384210 -ATCTGGGTGAGTGGCATGGAGCTGGGTAACGTTTTTGATGAAAATTC i panTro2.chr17 C 0 C 0 s bosTau4.chr19 10760877 48 - 65312493 CGTCGGGGTGGGCAGTGTGCATGGGAGTAATGTTTCTCATTAAAATTC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57949841 40 - 61308211 AGTCTGGGTGAGCAGTATGCAGTTGAGTAATGCTTGTGAT-------- i equCab2.chr11 C 0 I 2 s canFam2.chr9 59364356 33 - 64418924 AGTGTAGGTGAGCCCTGCACAGGTGAGGAACAT--------------- i canFam2.chr9 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 44763 632 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e cavPor3.scaffold_76 4303651 61 + 7991924 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=73220.000000 s hg19.chr17_gl000204_random 21580 153 + 81310 -------------cagcactttgggacgctgaggtgggtggatcacgaggtcaggagtttgagaccatcctggctagcactgtgaaaccctgtctttactaaaaatacaaaaaattagccaggtgtggtggcaggcgcctgtagtcccagctgcttggagaggctg s rheMac2.chr16 74748316 163 + 78773432 CCAGctgtaatcctagcactttgggaggctgaggtgggcggatcacaaggtcaggagatcgagaccatcctggttaacatggtgaaaccctgcctctactaaaaatacaaaaaattagccgggcgtggtggtgg--gcctgtagtcccagttgctcca-gaggctg i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17 69582961 165 + 73212453 TTGGctgtaattccagcactttgggaggctgaggcgggtggatcacgaggtcaggagtttgagaccatcctggctagcactgtgaaaccctgtctctactaaaaatacaaaaaattagccaggcgtggtggcgggcgcctgtagtcccagctgctcag-gaggctg i ponAbe2.chr17 C 0 C 0 s panTro2.chr17 79194995 166 + 83384210 TTGGctgtaattccagcactttgggacgctgaggtgggtcgatcacgaggtcaggagttcgagaccatcctggctagcactgtgaaaccctgtctctattaaaaatacaaaacattagccaggtgtggtggcaggagcctgtagtcccagctgcttggagaggctg i panTro2.chr17 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 44763 632 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59364389 0 - 64418924 C e bosTau4.chr19 10760925 0 - 65312493 C e equCab2.chr11 57949881 2 - 61308211 I e cavPor3.scaffold_76 4303651 61 + 7991924 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=19248.000000 s hg19.chr17_gl000204_random 21733 32 + 81310 aggcaggagaatggtgtgaacccaggaggcgg s panTro2.chr17 79195161 32 + 83384210 aggcaggagaatggtgtgaacccaggaggcgg i panTro2.chr17 C 0 C 0 s ponAbe2.chr17 69583126 32 + 73212453 aggcaggagaatggtgtgaacccaggaggtgg i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74748479 32 + 78773432 aggcaggagaatggcatgagccggggaggcag i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4303712 28 + 7991924 AGGCAGGGGGAGCGTGTG----CGGGAAGCAA i cavPor3.scaffold_76 I 61 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 44763 632 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59364389 0 - 64418924 C e bosTau4.chr19 10760925 0 - 65312493 C e equCab2.chr11 57949881 2 - 61308211 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=21436.000000 s hg19.chr17_gl000204_random 21765 34 + 81310 agcttgcagtgagccgagatcgctccactgcact s cavPor3.scaffold_76 4303740 4 + 7991924 ------------------------------CGCT i cavPor3.scaffold_76 C 0 C 0 s panTro2.chr17 79195193 34 + 83384210 agcttgcggtgagccgagatcgctccactgcact i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0080755 242 34 - 4970 angctgtggtgagccatgattgcaccactgcact i gorGor1.Supercontig_0080755 N 0 C 0 s ponAbe2.chr17 69583158 34 + 73212453 agcttgcagtgagccgagatcgcgccactacact i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74748511 34 + 78773432 agcttgcagtgagccgagatggcgccactgcact i rheMac2.chr16 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 44763 632 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59364389 0 - 64418924 C e bosTau4.chr19 10760925 0 - 65312493 C e equCab2.chr11 57949881 2 - 61308211 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=27513.000000 s hg19.chr17_gl000204_random 21799 49 + 81310 ccagcctgg-gtgacagagcaagaccccatctcagaaaaaaaaaaaaaaa s bosTau4.chr19 10760925 6 - 65312493 CCAGCC-------------------------------------------- i bosTau4.chr19 C 0 C 0 s cavPor3.scaffold_76 4303744 9 + 7991924 CCTGGCTGC----------------------------------------- i cavPor3.scaffold_76 C 0 C 0 s panTro2.chr17 79195227 49 + 83384210 ccagcctgg-gtgacagagcaagaccccatctcagaaaaaaaaaaaaaaa i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0080755 276 50 - 4970 ccagcctggagtgacagagcaagaccccatctcagaaaaaaaaaaaaaaa i gorGor1.Supercontig_0080755 C 0 I 1 s ponAbe2.chr17 69583192 49 + 73212453 ccagcctgg-gtgacagagcaagaccccatctcagaaaaaaaaaaaaaaa i ponAbe2.chr17 C 0 C 0 s rheMac2.chr16 74748545 49 + 78773432 ccagcctgg-gggacagagtgagactccgtctcagaaaaaaaaaaaaaaa i rheMac2.chr16 C 0 I 11 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 44763 632 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59364389 0 - 64418924 C e equCab2.chr11 57949881 2 - 61308211 I e mm9.chr11 118674343 122 + 121843856 I e loxAfr3.scaffold_49 14293923 1791 - 17734757 I a score=43320.000000 s hg19.chr17_gl000204_random 21848 25 + 81310 aaaTTCCTGGGTGACCTGAACACCA s rheMac2.chr16 74748605 25 + 78773432 aaATTCCTGGGTGACCTGAACACGG i rheMac2.chr16 I 11 C 0 s ponAbe2.chr17 69583241 21 + 73212453 ----TCCTGGGTGACCTGAACACCA i ponAbe2.chr17 C 0 N 0 s gorGor1.Supercontig_0080755 327 25 - 4970 aaaTTCCTGGGTGACCTGAACACCA i gorGor1.Supercontig_0080755 I 1 C 0 s panTro2.chr17 79195276 22 + 83384210 ---TTCCTGGGTGACCTGAACACCA i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4303753 19 + 7991924 ----TTCTAGGTGACCAGAAAAC-- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10760931 13 - 65312493 ------------AACCTGAAAACCG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57949883 25 - 61308211 AAATTCCTAGCCGACCTGACAACCA i equCab2.chr11 I 2 C 0 s canFam2.chr9 59364389 22 - 64418924 ---TTCCTAGGTGACCTGACAGGTA i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14295714 25 - 17734757 AAATTCCTCACTGACCTGAAATCCA i loxAfr3.scaffold_49 I 1791 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 44763 632 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e mm9.chr11 118674343 122 + 121843856 I a score=142582.000000 s hg19.chr17_gl000204_random 21873 141 + 81310 ACAAATGGGATAAAGAAG---TTGTC--ACTGATTTGCATCTGACGACGGGATGGTCTT---C-AGGCTCC----------------------TAGAGGTGGGGGTGAGGTGGAATGAACTTCCCATTCTACATGGCAAAGCAAATGAACTCAGCCCACCTAAAACACAGGC- s rheMac2.chr16 74748630 129 + 78773432 ACAAGTGGGATCAAGAAG---TTGTC--ACTGATTTGCATCTGACCACAGGATGGTC-T---C-AGGCTCC----------------------TAGAGGTGGGGGTGAGGTGGAATGACCTTCCCATTCTACATGGCAAAGCAAACGAACTGAGCCCACCT------------ i rheMac2.chr16 C 0 I 273 s ponAbe2.chr17_random 9217182 141 + 17838096 ACAAGTGGGATCAAGAAG---TTGTC--ATTGATTTGCATCTGACAACGGGATGGTCTT---C-AGGCTCC----------------------TAGAGGTGGGGGTGAGGTGGAAAGACCTTCCCATTCTACATGGCAAAGCAAATTAACTGAGCCCACCTAAAACCCAGGC- i ponAbe2.chr17_random N 0 C 0 s gorGor1.Supercontig_0080755 352 141 - 4970 ACAAATGGGATCAAGAAG---TTGTC--ACTGATTTGCATCTGACGACGGGATGGTCTT---C-AGGCTCC----------------------TAGAGGTGGGGGTGAGGTGGAATGAACTTCCCATTCTACATGGCAAAGCAAATGAACTGAGCCCACCTAAAACCCAGGC- i gorGor1.Supercontig_0080755 C 0 C 0 s panTro2.chr17 79195298 141 + 83384210 ACAAATGGGATCAAGAAG---TTGTC--ACTGATTTGCATCTGACGACGGGATGGTCTT---C-AGGCTCC----------------------TAGAGGTGGGGGTGAGGTGGAATGAACTTCCCATTCTACATGGCAAAGCAAATGAACTGAGCCCACCTAAAACCCAGGC- i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 45395 130 + 85690 ---AGTGGAATTGAGAGGAA-TTGTC--GCTCATCTGCACCT-ATCCTGGGGGAGTCTCAGAC-AGACTC-----------------------------TGGAGGTGTGGTG--AGGCCCGTCCCATTCTGTGTGTCAAGGCAAACTAACTAAGCCCACCAAAGACCCC---- i otoGar1.scaffold_94361.1-85690 I 632 C 0 s cavPor3.scaffold_76 4303772 123 + 7991924 AGGCAGGGATTAGACAAG---GCCGCCGGCCACTTTG---TTCACTCCAGGACG--------C-CGACTCC----------------------CAGAAGTGG-GGTGCAGCAGAATGACCTCCACGTTCTACATAGTAAAGCAATCTAA----GCCCACCAGAGC-------- i cavPor3.scaffold_76 C 0 I 7 s speTri1.scaffold_52949 74 125 - 1075 ACACAGGGAGGAGAGGAG---TTGTCATGCCACAGTG-------CCCCGGGACG--------CTCTACGTC----------------------CTG-GGTGG-GGGACACAGAGAGCACCCCTACTTTGTGCACCGCGAAGTGAACTAA-----CACCTCAGAGAACCCTGG- i speTri1.scaffold_52949 N 0 I 1 s bosTau4.chr19 10760944 119 - 65312493 ACACGTGGAATTAA-------CTGTT--CTTAATTATTGCCTGTCAGCGGGATGGTCT----C-CGACTCC----------------------CAGAGGTAG-----------AATGACCTTCACGTTCTACACAGCAAAGCCGACAATCCAGGCCCACCAAAGAC------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57949908 123 - 61308211 ACAAGTGGAATTAA-------TT-GT--CATGACTTGGGTCCATCAGCAGGATGGTCT----C-TGATACC----------------------CAGAGGTGGGGGTGAGGGAGAATGACCTTCACGTTCTAC------AGGCGAACTAACTGAGCCCCCCAGAGAC------- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59364411 106 - 64418924 CTGAGTG-----------------AC--CATAACCCCCGCTCAT------GTGGGTCTG---C-TGATGCC----------------------CAGAGGTGGGGGGAAGGCCAAAT-ACTGTCGCGTCCCCC------AGGTGAAC-ACCTGAGCCCGCCAGACA-------- i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14295739 165 - 17734757 -AGAGTTGAATTAACAGGCATTTGCC--ATTAATTTGTGTCTATCAACTGGGTGGCCT----C-TGATTCCCCAAGATCACCTGGCGAAGGGTCAGAGGTGGAGGTGAGAAAGAATGGCATTCACATTCTGCACGGAGAAGCAAACCACGTAGGTCTGCCGGAGAACCCAGGC i loxAfr3.scaffold_49 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e mm9.chr11 118674343 122 + 121843856 I a score=449895.000000 s hg19.chr17_gl000204_random 22014 203 + 81310 ACCCCAAGACCC--TCACACTCACAGCCTCCTGTGCAGAGAGAGG-ACAAACAGCCAAGCATAC----ATCCTGGATTT--TTTTC---------CGC--AGATCTCCAAATAGA------------------AGGCCACACTTGGACTTCAGCATGCAAGGACAGGCTGGGGACATCACCAGTCCCTTATAAATTAAGGCTC--ATCTGAG---GACATGGCTTCATTTATAGGATTTAAGATGA s ponAbe2.chr17_random 9217323 205 + 17838096 GTCCTGAGACCC--TCACACTCACAGCCTCCTGTGCAGAGAGAGG-ACCAACAGCCAAGCATAC----ATCCTGGATTTTTTTTTC---------CTC--AGATCTCCAAATAGA------------------AGGCCACACTTGGACTTCAGCATGCAAGGACAGGCTGGGGACATTACTAGTCCTTTATAAATTAAGGCTC--ATCTGAG---AACGTGGCTTCATTTATAGGATTTAAGATGA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0080755 493 203 - 4970 ATCCCAAGACCC--TCACACTCACAGCCTCCTGTGCAGAGAGAGG-ACAAACAGCCAAGCAAAC----ATCCTGGATTT--TTTTC---------TGC--AGATCTCCAAATAGA------------------AGGCCACACTTGGACTTCAGCATGCAAGGACAGGCTGAGGACATCACTAGTCCTTTATAAATTAAGGCTC--ATCTGAG---GACATGGCTTCATTTATAGGATTTAAGATGA i gorGor1.Supercontig_0080755 C 0 C 0 s panTro2.chr17 79195439 205 + 83384210 ACCCCAAGACCC--TCACACTCACAGCCTCCTGTGCAGAGAGAGG-ACCAACAGCCAAGCATAC----ATCCTGGATTTCTTTTTT---------CCC--AGATCTCCAAATAGA------------------AGGCCACACTTGGACTTCAGCATGCAAGGACAGGCTGGAGACATCACTAGTCCTTTATAAATTAAGGCTC--ATCTGAG---GACATGGCTTCATTTATAGGATTTAAGATGA i panTro2.chr17 C 0 C 0 s mm9.chr11 118674465 189 + 121843856 ATCCCAAGACTTTGTAACACTCTCAGCAACTCCTGTGGAGA-AAG-CCCTGCAGCAAAGACTAT----GG-CAGACTTT----CCCCAAAGTCGTCCC------CCCC------A------------------AAACTACACATGGC------------TGGGTGGTCTGGGGACACCACTAACTCTTTATAA-ATAATTATCTAACCTGAG---AAAATGGCTTTATTTATAGGATTCCAAATGA i mm9.chr11 I 122 I 565 s cavPor3.scaffold_76 4303902 196 + 7991924 GTTTCAAGACCCC-TCGCATCCTCTGCTGCTCATGCAAACAGGGG-CCCAACAACAAAACTTAA----GT-CAGGCTTC----TCC---------CCA------TCCCAGAGAGA------------------AAGGTACACTTGGACTCCAGGATCTGTGGGCAGGTTGGGGACATCACTGGTCCTTATGAA-CTAAGGATC--ACCTGGG---GAAGTGGCTTTATTTATGAGATTCAAGATGA i cavPor3.scaffold_76 I 7 C 0 s speTri1.scaffold_52949 200 191 - 1075 GTCCCGAGACC---TAGTGCCCTCAGCTGTCCCTGCAGAGA-GAG-C----CAACAAATCC-------AT-CTGGATTT----TCC---------CCA--AAATCCCCAAAGGGG------------------AAGACACACGTGGACTTGAGGACCCAAGGACAGGCTGGGGATGTCAATGGTCCTGTATAATTTAGGGGTC--ATCTGAG---GAAGTGGCTTTATTTATAGGATTCAAGATGT i speTri1.scaffold_52949 I 1 C 0 s otoGar1.scaffold_94361.1-85690 45525 188 + 85690 ------AGACGT-------CCCACAGCCCCTCATGTAGGGAAAGG-CCCAAGAACAGAGATTAC----TTTCTGGAGTT----CTC---------CCC--AGATCTCCAAAGAGA------------------AAGGCACACTGGCACCTCAG-GCCCCAGGACAGGCTGGGGGTG-CACTGCTACTTTATAAATTAAGGACC--ATCTGCA---GGTGTGGAGGCATTTAAAGGACTCAGGATAA i otoGar1.scaffold_94361.1-85690 C 0 C 0 s rheMac2.chr16 74749032 193 + 78773432 ------agaccc--tcacactcacagcctcctgtgcAGAGAGAGG-ACCAACAGCCAAGCATACAGATATCCTGGATTT-TTTTCC---------CCC--AGATCTCCAAATAGA------------------AGACCACACTTGGACTTCAGCATGCAAGG---------GGACATCACTAGTGTTTTATAAATTAAGGCTC--ATCTGAG---GATGTGGCTTCATTTACAGGATTTAAGATGA i rheMac2.chr16 I 273 C 0 s bosTau4.chr19 10761063 174 - 65312493 ---------CCC--TCAGGCTCACAGCTTC-C-TGCAGAGAAAGG-TCCAACAGCCAAGCAGAT----ACTCTGGATTT----GCT---------TCC--AAATCTCCAAG---------------------------------AGACTTCAGGGCCCAAGGACAGGTTGGCGA-GAGAATAGTCCTTTGTAATGTACAAGTT--ACCTGAG---GAAGAGGCTTCATTCACGGGACTCAGGTGGA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57950031 186 - 61308211 ---------TCC--TCACACTCACAGCTTCTCATGCAGAGAGAGG-CCGAACAGCAAAACCTAC----ATTCTGGATTT----TCC---------CCCCAAAATCTCCAAAGAGA------------------ACGGCGCCCTTGGATCTCAGGACCCAAGGACAGGATGAGGGTGACAGCAGTCCTTTATACATGAAGGGCC--ATCTGAG---GCAGTGGCTTACTG-ATGGGATGC------- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59364517 188 - 64418924 -----------C--CCACATGCACGGCTTC-CGGGTGGAGAGGGGTCCCGGCCACAAAGCGTCC----ACTCTGGCTTG----TTT---------TCC--ACATCTCTGAAGAGA------------------AAGGCACACCTGGACCTGAGGACACCTGGGCAGGCCAGGGATGGCAATCGTCCCT--TCCAAGCAGGGTC--ATCTGAG---GAAGTGGCTTCATGTACAGGATGCAAGACAT i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14295904 199 - 17734757 -GTCCTGACCCC--TGACACTCACAGATTCTCGTGCACAGAGAGG-CCCTGCAGCAAAGCCTAT----ATTCTGGATTT-----TT---------CCC--AAATCTCCAAAGAGAACATTTGGGGAAAAGTGTAAAGAAAACTTGGACTTCAGGACCCAAGGACAGACTGGGGACATCAATACTCCTTTATGAGTTAAG--TT--ACCTGAGCAAGATGGGGCTACA------------------- i loxAfr3.scaffold_49 C 0 I 212 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I a score=59919.000000 s hg19.chr17_gl000204_random 22217 48 + 81310 GGCATCACAGAGAGGCAGAAGTGGCCGGTGAGTTGAG--GCGGAGCCCCC s canFam2.chr9 59364705 39 - 64418924 GGTAACACAGAAAAGCAGAGACAACCCGC-----------CAGCACCCCT i canFam2.chr9 C 0 C 0 s equCab2.chr11 57950217 46 - 61308211 GGCAACAGAGAGAAGCAGAGACGTGGCGA--GCTGAC--GCGGAGCCCCT i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10761237 50 - 65312493 GGCAACCCAGAGAAGCAGAGACAGCGGGTGAGCTAACAGGCTGGAGCCCT i bosTau4.chr19 C 0 C 0 s speTri1.scaffold_52949 391 44 - 1075 GGTGCTGCAGAGGAGCAGAAAGGGCCTGGGAGT---G--GAGGAGAAGC- i speTri1.scaffold_52949 C 0 C 0 s cavPor3.scaffold_76 4304098 40 + 7991924 ----AAACAAAGG-GCCCAAAGGGCCTGTGAAC---G--CAGGAGCCCCT i cavPor3.scaffold_76 C 0 C 0 s otoGar1.scaffold_94361.1-85690 45713 34 + 85690 GGAACTGCAGAAGAACA------------GAGTTAAG--AAGGG--CCCT i otoGar1.scaffold_94361.1-85690 C 0 C 0 s panTro2.chr17 79195644 48 + 83384210 GGCATCACAGAGAGGCAGAAGTGGCCGGTGAGTTGAG--GCGGAGCCCCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0080755 696 48 - 4970 GGCATCACAGAGAGGCAGAAGTGGCCGGTGAGTTGAG--GCGGAGCCCCC i gorGor1.Supercontig_0080755 C 0 C 0 s ponAbe2.chr17_random 9217528 48 + 17838096 GGCATCACAGAGAGGCAGAAGTGGCCGGTGAGTTGAG--GCAGAGCCCCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74749225 48 + 78773432 GGCATCACAGAGAGGTAGAAGTAGCTGGTGAGTTGAG--GAGGAGCCCCC i rheMac2.chr16 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e mm9.chr11 118674654 565 + 121843856 I e loxAfr3.scaffold_49 14296103 212 - 17734757 I a score=37370.000000 s hg19.chr17_gl000204_random 22265 45 + 81310 CATTTCACTACCCCCTCCCCGGGCCTACTGACAG-----CA----GCA---CATGG------G----------- s rheMac2.chr16 74749273 45 + 78773432 CATTTTACTACCCCCTCCCCAGGCCTACTGACAG-----CA----GCA---CATGG------G----------- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9217576 45 + 17838096 CATTTCACTACCCCCTCCCTGGGCCTACTGACAG-----CA----GCA---CATGG------G----------- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0080755 744 45 - 4970 CATTTCACTACCACCTCTCCGGGCCTACTGACAG-----CA----GCA---CATGG------G----------- i gorGor1.Supercontig_0080755 C 0 C 0 s panTro2.chr17 79195692 45 + 83384210 CATTTCACCACCCCCTCCCCGGGCCTACTGACAG-----CA----GCA---CATGG------G----------- i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 45747 50 + 85690 CATCTCAGGACCCCCTCCCCA--CTTGCCGCCGG-----CACGGGGCAGGTTTTGA------G----------- i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4304138 49 + 7991924 CATTTTACTG-CCCAACCCCTGGTTT-CCACCAGTTCGGCA----GGG---GGTGGG-----G----------- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_52949 435 31 - 1075 -----------CCCAGCCCCAAGCC--------------CA----GGA---GGCTGGTATCTG----------- i speTri1.scaffold_52949 C 0 C 0 s bosTau4.chr19 10761287 40 - 65312493 CGCTGGA--GCGCCCTCACTGGGCCGCCTGCCAG-----CA----------CACAG------C----------- i bosTau4.chr19 C 0 I 15 s equCab2.chr11 57950263 41 - 61308211 CGTTTTAC-TGCCCCTCCCTGGGCCCGCGGCGGG-----CA----------CACCA------G----------- i equCab2.chr11 C 0 I 9 s canFam2.chr9 59364744 41 - 64418924 CATTTTAC-GCCCCCTCCCTGGGCCTGTGGCTGG-----CA----------CACGG------G----------- i canFam2.chr9 C 0 I 48 s loxAfr3.scaffold_49 14296315 53 - 17734757 CATCTTACTTCCACCCACCTGgggctgctgccag-----ca----------cagga------ggcacctttgtg i loxAfr3.scaffold_49 I 212 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e mm9.chr11 118674654 565 + 121843856 I a score=240855.000000 s hg19.chr17_gl000204_random 22310 203 + 81310 GGAATG---------AGACAATGG-TC-CCCCTCTGGGCAGATGCAGCCTTGCCAGTGCAGGACTTG------------A-ATTCTGAGGCTGTT-------CGTC------------------TTCT-------------CAGAGCATGCTACACTCCATTCTCTGCAACAGCCTGATTGGCATGCCTTGGAACATTCCAGgccatggcaag-----ggaaaagcttggagcaggacccgcaggcctgggttc----tcctcc----cagcccatca s rheMac2.chr16 74749318 203 + 78773432 GGAATG---------AGACGGTGG-TC-CCCCTCTGGGCAGATGCAGCCCTGCCAGTGCAGAACTTG------------A-ATTCTGAGGCTGTT-------CATC------------------TTCT-------------CAGGGCATGCTACACTCCATTCTCTGCAACAGCCTGGTTGGTGTGCCTTGGAACATTTCAGgcaatagcaag-----ggaaaagcttggagcaggacccacaggcctgggttc----tcctcc----caacctatca i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9217621 203 + 17838096 GGAATG---------AGACAATGG-TC-CCCCTCTGGGCAGACGCAGCCCTGCCAGTGCAGGACTTG------------A-ATTCTGAGGCAGTT-------CATC------------------TTCT-------------CAGGGCATGCTACACTCCATTCTCTGCAGCAGCCTGATTGGCGTGCCTTGGAACATTTCAGgcaatggcaag-----ggaaaagcttggagcaggacccgcaggcctgggttc----tcctcc----cagcccatca i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0080755 789 203 - 4970 GGAATG---------AGACAATGG-TC-CCCCTCTGGGCAGATGCAGCCCTGCCAGTGCAGGACTTG------------A-ATTCTGAGGCTGTT-------TGTC------------------TTCT-------------CAGAGCATGCTACACTCCATTCTCTGCAACAGCCTGATTGGCATGCCTTGGAACATTCCAGGCaatggcaag-----gaaaaagcttggagcaggacccgcaggcctgggttc----tcctcc----cagcccatca i gorGor1.Supercontig_0080755 C 0 C 0 s panTro2.chr17 79195737 203 + 83384210 GGAATG---------AGACAGTGG-TC-CCCCTCTGGGCAGATGCAGCCCTGCCAGTGCAGGACTTG------------A-ATTCTGAGGCTGTT-------CGTC------------------TTCT-------------CAGAGCATGCTACACTCCATTCTCTGCAACAGCCTGATTGGCATGCCTTGGAACATTCCAGGCCATGGCAAG-----GGAAAAGCTTGAAGCAGGACCCGCAGGCCTGGGTTC----TCCTCC----CAGCCCATCA i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 45797 208 + 85690 ATCACT---------AGATAATGG--C-ACCCCCTGGGCAGGTGCAGCTCTGGAAGTGCTGGACTTGAATTTAGACTTAA-ATTCCGAGGCCAT---------GCC------------------TGCT-------------CAGGACCCACTGCACACCACTCTCTGTGACAGCCTGAGTGAGACTCCCTGGAGAGTTTCGGGCAAGTTGCTG-----GAAAGAGCCTGAAGCCCGACCCCCAGGCCAGG--------TTCTCC----CAGGCCATTA i otoGar1.scaffold_94361.1-85690 C 0 I 1 s cavPor3.scaffold_76 4304187 222 + 7991924 GGCACACAGAGTACTGGACAAGGGTGG-CCCCTGAAGGCAGATGCA--------AGTGCAGGACTTGAGTTTA------AGGTTCACAAACAAT----------CC------TTTGGTTCAA-GTTCC--------TTGAACGGACCACTCTCTGTCCCATTATCTTTGAAAGCTTGGGTGACATTTTGGGGAGTTT--GGGGCAGTGAGGTG-----GGAAGAACTTGGAACAGGGCTTGTA-----GGGCTCAGCATCCTCC----TAGCCCACCC i cavPor3.scaffold_76 C 0 I 8 s speTri1.scaffold_52949 466 169 - 1075 GGGA-----------GGACAAGGG-GC-CCCCTCTGGGAAAACAC---------------GGTCCTGCGGGTA------A-ATTCAGGGGCTATT-------TATC------TGGAGGCCAA-GTGCCG-------GGGAACAGGCCCCTGTCCAGCTCA------------------GTGACATTCCCAGGAGTTTGGGGGGTGATGGGGTG-----GGAGGA--------------------------GTCCACCAGCTTCC----CAGCCTATCT i speTri1.scaffold_52949 C 0 I 8 s bosTau4.chr19 10761342 178 - 65312493 GGTGT----------GGACAACGG-CGCCCCCTCTGGGCAGATGTGGCCCTGCAAGTGCAGCCCTTG------------A-TCT------------------GCTC---------GGAACAA--GGCA-------------CAGGACAC---CTGCCC------CCATGACAGACTGGGTGAC-TTTTCTGGAGCCTCTGGGGCATCGGGGCA-----GGAAGAACTTGGAGCAT---------------GTTC----CCCTCCAGCTAGCCCCATCT i bosTau4.chr19 I 15 I 8 s equCab2.chr11 57950313 204 - 61308211 GGTGtc---------agacaacag-tg-cccctctgggcagacgtggccccgcaagtgcacgacttg------------A-ACTCCAGAGCCATTGTCACTGGCTCAGGCGTCTGGGAACAAGGGGAA-------------CAGGGCACATACTACCCCGCTATCTGTGACAGCCTGGGCCAC-TTCCCTGGA--------GACCTCGGGGTG-----TGAAGAACTGTCAGCAG---------------ATTC----TCCTCC----AGCCCCATCG i equCab2.chr11 I 9 I 8 s loxAfr3.scaffold_49 14296368 212 - 17734757 gggact---------ggaaaagtg-tc-cttctctgggcagatgaagccctgcaACTGCAG-ACTTG------------A-ATTCC-AGGCTACT-------GATC------------------AGCCGGGAACATGGGAACAGGGCACACCCTACTCAAGTCTCTGTGACAAGCTGGCTGCCATTCCTTGGAGACTCTGGGGCAATGCAGTGTGGGAGGAAGAGCCTGGAGCTGGACTCACA-GCCTGGGTTC----CACTTA----CAGG------ i loxAfr3.scaffold_49 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59364785 48 - 64418924 I e mm9.chr11 118674654 565 + 121843856 I a score=474209.000000 s hg19.chr17_gl000204_random 22513 349 + 81310 ctgtgtgacctggg-ac-atct----gaac-----atccctgatccttt-ccg--catcAACTCACAGGAAGTGTCTACTATGTGGCAGATGCAGACCCAGGTTCCGGA-----CATTCAACAAGGTACACTAGCAACCCCATCCCTGCCCAAAGTGTCTTGGATGTCACCTTCCCTGCC-CCCTGTATGAGGCACACAGAAAGAAGACA-GAAAG-GGCTTTGCACTAAATCACAGCTGCGCTTTCTCCTAATACTCCGAGGAGTCAAATGACCTCTGAAGGCCACCAGAGCCACA-GGCCTC----TTTGTGATG-GTCACACATGGGCTTGTGAAAGAGCCATTTAGG-----------G---------ACATAGCATA-GG------------GGACTCTGA-GACC s panTro2.chr17 79195940 349 + 83384210 CTGTGTGAGCTGGG-AT-ATCT----GAAC-----ATCCCTGATCCTCT-CCC--CGTCAACTCACAGGAAGTGTCTACTACGTGGCAGATGCAGACCCAGGTTCCGGG-----CATTCAACAAGGTACACTAGCAACCCCATCCCTGCCCAAAGTGTCTTGGATGTCACCTTCCCTGCC-CCCTGTATGAGGCACACAGAAAGAAGACA-GAAAG-GGCTTTGCACTAAATCACAGCTGCGCTTTCTCCTAATACTCCAAGGAGTCAAATGACCTCTGAAGGTCACCAGAGCCACA-GGCCTC----TTTGTGATG-GTCACACATGGGCTTGTGAAAGAGCCATTTAGG-----------G---------ACATAGCATA-GG------------GGACTCTGA-GACC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0080755 992 349 - 4970 ctgngtgacctggg-ac-atct----gaac-----atccctgacccttt-ccc--catcAACTCACAGGAAGTGTCTACTATGTGGCAGATGCAGACCCAGGTTCCAGG-----CATTCAACAAGGTACAATAGCAACCCCATCCCTGCCCAAAGTGTCTTGGATGTCACCTtccctgcc-ccctgtatgaggcacacagaaagaagaca-gaaag-ggctttgcactaaatcacagctgcgctTTCTCCTAATACTCCAAGGAGTCAAATGACCTCTGAAGGCCACCAGAGCCACA-GGCCTC----TTTGTGATG-GTCACACATGGGCTTGTGAAAGAGCCATTTAGG-----------G---------ACATAGCATA-GG------------GGACTCTGG-GACC i gorGor1.Supercontig_0080755 C 0 C 0 s ponAbe2.chr17_random 9217824 349 + 17838096 ctgtgtgacctggg-ac-atct----gaac-----atccctgatccttt-ccc--catcAACTCACAGGAAGTGCCTACTATGTGACAGATGCAGACCCAGGTTCCGGA-----CATTCAACAAGATGCAATAGCAACCCCATCCCTGCCCAAAGTGTCTTGGATGTCACCTTCCCTGCC-CCCTGTATGAGGCACACAGAAAGAAGACA-GAAAG-TGCTTTGCACTAAATCACAGCTGCGCTTTCTCCTAATACTCCAAGGAGTCAAATGACCTCTGAAGGCCACCAGAGCCACA-GGCCTC----TTTGTGATG-GTCACACATGGGCTTGTGAAGGAGCCATTTCAG-----------G---------ACATAGCATA-GG------------GGACTCCAA-GACC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74749521 350 + 78773432 ctgtgtgacctggg-ac-atct----gaac-----atccctgatcctttcccc--caGCAACTCACAGGAagtgcctactatgtggcagatgcagacccaggtaccagg-----cattcagcaaggtgcaatagcaaccccatccccgcccAAAGTGTCTTGGATGTCACCTTCCCTGCC-CCCTGCGCAAGGCACACAGAAAGAAGACG-GAAAG-GGCTTTGCACTAAATCACAACTGCACTTTCTCCTAATACTCCAAGGAGTCAAATGACCTCTGAAGGCCACCAGAGCCACA-GGCCTC----TTTGTGATG-GTCAGACATGGGCTTGTGAAAGAGCCATTTAGG-----------G---------ACATAGCATA-GG------------GGACTCCAA-GACC i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_190290 9 350 + 4572 CTGTGTGACCTGGGAAT-CACT----GAAC-----GTTGCTAGTCCTTT-TAC--CACGAACTCCCACGAAGTTCCTACTATGTGCCAGATGAAGACCCAGGCATCCAG-----CATTTGA-AAGGTGCAACAGGGACCCCATCCCTACCTGCAGTGTCTGGAATATCACCTTCCCTGCC-CCCTGCAAAAGGGACAGAGACAGTGTAT--GAAAG-GGCTCTGCAATAAATCAGAGCTGCATTTTCTCCTAATACTCTAGG--------CGACCTCTGAGGACTGCTAGAGCTCAA-AGCCTC------AATGAAG-TTTAGATACCACTTTGTGGAGAAATCACTTGGGGTGGGCTGGGCG---------GGGTAGCACATGG------------GAACTCAGA-GACC i tarSyr1.scaffold_190290 N 0 C 0 s otoGar1.scaffold_94361.1-85690 46006 300 + 85690 CTGTGGACCGTGGG-AC-CTTG----GAAATGCTGGTCCCTGTTCCTGT-CCC--CATCTGCTCCTATGAAGCACCTAGTGTGTGCTAGATGGAGACCCAGGCCCCCGT-----GAGCAGGCAGAGTGAACAGTGACCCCCGTCTGTACCCACAGCGTCTGGAACAG-ACCTTCCC-------------GAGAGACGC---------ACA-GAAGG-GGCCAGGCCCTGAATCAGAGATGTGTTTTATCCT-ATGCCCCAAG----------------GAGGGCTGCT-GAGCGTAA-GGCCTC------TGTGA-G-GTCAGACACAGGCCCATGGTGGAGACGCTTTGC------------------------------A-GC------------GGACGC-GA-GGCC i otoGar1.scaffold_94361.1-85690 I 1 C 0 s cavPor3.scaffold_76 4304417 355 + 7991924 GCCTGTGACCTGG--AC-AGCCTGAACAGG-----GGTTCAGGCCCCT--CCC--CACCAACTCATATGAGGCTCCTGCTCTGTACCAGATGCATCCCCAGCAGCCTGG-----TGTTCGACA-AGCACAACGGCGACTTGGCTCCCATCTACCAGGCCT-GCATGTCATTGCACTGGCCTCCCTGAGAGAGCCACAGAGAAAATAAACG-GAGAG-AGCTTTGCACTAAATCAAAGCAGCATTCTCTCCTAACACCCCAGCAGGCCA---TGCCTTTGCAGGACTGCTGACTCACGGGGCCTCTCTCTCTGTGAAG-GTCAGAAATGCCCCAGGT-AGGGGTGCTGGGGG--------GCAG---------GTGGGGCACA-GG------------GGAGTCCAGAGAAC i cavPor3.scaffold_76 I 8 C 0 s speTri1.scaffold_52949 643 303 - 1075 CCCCGTGACCTGG--AC-AAGC----CAAA-----GGTCCTGATGCTTC-CCC--CATCGACTTGCGGGAGGCG--TACTGTGTGCGA-ATGCAGACGCAG--GCCTGGGCACCTGCTC-----AGTGCAACAGCTCCCCAGTCCCCATC--ATGTGTCT-GGCTCTCGCGGCTCCTGACTCCCTGCAGGAGGCCCAGGGAGGAT-ACCT-GGGAG-AG-TGGGCCCTGAG---------------CTCCTG--ACCGCGAGGACCCA---GATTCCTGTGGGCCACCAGA-------GGCCTGCGGCTCT-----G-GTCAGCTGTGCACTCGTTGAGAGACACCGCAGG-----------G---------GT-GGGCGCA-AG------------G---------GCAC i speTri1.scaffold_52949 I 8 C 0 s bosTau4.chr19 10761528 335 - 65312493 CTGTGTGACCCGGG-ACAAGCA----GAACTAAT-GGCCCTGACCCTTTGCCC--CCTCGACTCGTCTGAAGAGCCTCCTGTGTG-CAGAGGCACGCCAGGGATCGGGA-----TGCTCCATGAG------------------------GCGTGGTGTCTGGAACGTCACCTGATCGG-T-TCCTCCCAGAAGCACAGGGGTAATACATT-CAGAA-GGCTTTGCACTAAATCAGAGGCATTTTCT--CCTAATGCTTCAAGGAGCCAAATGAGCTCTCAGGGCCCCCAGAGCCACA-GGCCTC----TTCATAAAG-GTCAGCCATGAATGCC---AGGAGCCACCTAAG-----------GCAGTGGGGAGGGGCGGGCA-GGAT----------GGAGTAGAG-GGGA i bosTau4.chr19 I 8 C 0 s equCab2.chr11 57950525 351 - 61308211 CTGTGTGACCTGGG-ACCAGCT----GAAC-----ATCCCGGATCCTTCCCCCCACATCCGCTCATACGAAGAGCCGATGACATG-CCGATGCAGACCCAGCAGCCCGG-----CATTCCATGAGCTGCAACAGTGACA--------GTCCATAGTCTCTGGAATGTCACCTGGCCTGCT-CCCTGCCGGCGGCACAGGGAAGGTACGTG-CTGAAGGGCATTGCACTAACTCAGAGCTATGTTCCCACCTGATGCCTC-AGGAGCCAAAT--CCTCTCAGG--CCCCAGAGCTGCA-GGCCTC----GTCGTAAAG-GTCAGATCTGGGCCCCCA-AGGAGCCGCTAAAG-----------G---------GGGCCGGACG-GAATCCAGTGTCTCGGACTCTGG-GGAA i equCab2.chr11 I 8 C 0 s loxAfr3.scaffold_49 14296580 282 - 17734757 CTGTACAGCCTGGG-AC-AG------GAAG---------CTGATGTC---CCT--CGTCTGCTCACGTGAAGCA-CTGCTATGTGCTGAATGCA-------------AG-----T-------AGAGGGCAATAGCAGCCCAGTCCCTGCCTGGA---CCTGGAACATCGCCTGGCCTGCC-GCCCGTCGGAAGCACAGAGGTAACGTATGTGAAGG-GGCTTTGCACTGAATCAGTGCTGGAGTCTCCCTCAGTGCT----------------------------GCTAGCGTTAAA-GGCCAC----TTTGTGAAATGTCAGATGTG-CCACGCTGAGGAGCC---TAAG-----------G---------AGACAGGGCA-GGAT----------GGAGCA-------- i loxAfr3.scaffold_49 C 0 C 0 e choHof1.scaffold_213748 2808 152 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59364785 48 - 64418924 I e mm9.chr11 118674654 565 + 121843856 I a score=147124.000000 s hg19.chr17_gl000204_random 22862 126 + 81310 AGGGG---CTCCAA--------------------------------AG--------GAAGGACCCTAAAATCACCAGAAATCAAGTTTGG---GT-TTTTATAGCATTTTGCTTATCtttt-----------------gttttgttttgt-tttgttttTTAACAAAGATAGCAATATCACCAGAAATATG s panTro2.chr17 79196289 143 + 83384210 AGGGG---CTCCAA--------------------------------AG--------GAAGGACCCTAAAATCACCAGAAATCAAGTTTGG---GT-TTTTATAGCATTTTGCTTATCttttcttttgttttttgttttgttttgttttgt-tttgttttTTAACAAAGATAGCAATATCACCAGAAATATG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0080755 1341 142 - 4970 AGGGG---CTCCAA--------------------------------AG--------GAAGGACCCTAAAATCACCAGAAATCAAGTTTAG---GT-TTTTATAGCATTTTGCTTATCTTCT-ttttgttttgttttttgttttgttttgt-tttgttttTTAACAAAGATAGCAATATCACCAGAAATATG i gorGor1.Supercontig_0080755 C 0 C 0 s ponAbe2.chr17_random 9218173 120 + 17838096 AGGGG---CCCCAA--------------------------------AG--------GAAGGACCCTAAAATCATCAGAAATCAAGTTTGG---GT-TTTTACAGCATTTTGCTTATCTGTT-----------------------TTTTGT-TTTTGTTTTTAACAAAGATAGCAATATCGCCAGAAATATG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74749871 113 + 78773432 AGGG-------------------------------------------------------GGACCCTAAAATCATCAGAAATCAAGTTTGG---GT-TTTTATGTCATTTTGCTCATCTGTT-------------------TTTGTTTTTTGTTTGTTTTTTAACAAAGATAGTGATATCACCAGAAATATG i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_190290 359 99 + 4572 AGGCT---CTCCAA--------------------------------AG--------GAAGG--------ATCATCAGAAATTAAATGTGG---GT-TTTTACTGTATT------------------------------------TTTCCT-TTTTTTTTTAAAGGAAGACACTGGTATAACCAGAAATGTC i tarSyr1.scaffold_190290 C 0 C 0 s otoGar1.scaffold_94361.1-85690 46306 137 + 85690 AAGGT---CTTCAACCTCACCCACTGGAAGGTCTCTCC--------AA--------AGAGGACCCTGAAGTCTTTGGAAATCACGTTTGG---GT-TTTTATTGTACTTTGCTCA------------------------------TTTGT-TTGTTTTTTTAATGAGGACACTAATACCATGGGGACCGTG i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4304772 134 + 7991924 AGGGC---TCTCTGTGCCCATTATAGT-------------------GG-TATCTCTGAGGAACCCTGAAATCTTCAGAAATCAAGTTTTA--TGT-TTTCAGGGTATTTTGCAC------------------------------ATTTGT-TTGTTTTCAAAATGAAGATACAAATATCACCAGGAACACG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_52949 946 120 - 1075 CGGGC---TCTCGGTGCTTATTGTGG--------------------AG-CGTCTGTCAAGGACCCTGGGATCTCCAGAGATCAAGTTCCGGCTGC-TCCC---TCATCTTGTTT------------------------------TCATGT-TTTTT-----AATGGAGACATGAACATCGCCAG------- i speTri1.scaffold_52949 C 0 N 0 s bosTau4.chr19 10761863 123 - 65312493 --------CTCCATTGGTAATAGCAA--------------------AGATTTTCCCAAAGGACTCTGAAATCTTCAGAAATCAAGTTTTG--GGGATTTTGTTGTACCTTGTTT------------------------------GGTTGT-TTT-------AATGAGGATACTAATACTGCCAGAGATGTA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57950876 130 - 61308211 GGTGTGCTCCCCACTTCTTACCACGA--------------------AGATACTTCCAAAGGAGCCTGAGACCTTCAGAAATCAAGTTTTG--GGT-TTTTGTTGTATTTTATTT------------------------------GTTTGC-TTT-------AACGAAGATATTAACATCACCAGAGATGTG i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14296862 140 - 17734757 GGGGG---CTCCAGAGGACAGGGCTCTCCCCGTTGTTACACTGGGAAGGTCTTTCCAAAGGA-CTTGAAATCTTCAAAAATCTAGTTTCT--GGG-TTCTG-------------------------------------------TTGTGT-TTTGTTTTTAAATGGAGAAGCTACTGTCTGCAGGGAAGTG i loxAfr3.scaffold_49 C 0 C 0 s choHof1.scaffold_213748 2960 103 + 4094 ----------------------------------------------AGGTGTTTCCAAA-GA-CCTGAAATCGTCAGAAATCAAGTTTGT--GGT-TTTTGTTGTATT------------------------------------TTGTGT-tttgttttttaatgaaaatggtgactcaaaaagaaacagg i choHof1.scaffold_213748 I 152 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59364785 48 - 64418924 I e mm9.chr11 118674654 565 + 121843856 I a score=429211.000000 s hg19.chr17_gl000204_random 22988 190 + 81310 CTTGCATTCTT-ATTTGGCTTCCTGGAGGGACTCAGAAAATGGCATTTGCAAAATCTCAGAGGACTCCACTCGCACATTTTAG-ATTTTACTTTTCTCCCCAAACTACGCCTTTGCTGGTTCATTTTATTG--CAGAGAGCGGA-AC-TTTTTAGCCTTCTAGTCCT----GCC----AGAAAGttaaaaaaaaaaaaaaaaaa s panTro2.chr17 79196432 190 + 83384210 CCTGCATTCTT-ATTTGGCTTCCTGGAGGGACTCAGAAAATGGCATTTGCAAAATCTCAGAGGACTCCACTCACACATTTTAG-ATTTTACTTTTCTCCCCAAACTACACCTTTGCTGGTTCATTTTATTG--TAGAGAGTGGA-AC-TTTTTAGCCTTCTAGTCCT----TCC----AGAAAGTTaaaaaaaaaaaaaaaaaa i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0080755 1483 160 - 4970 CTTGCATTCTT-ATTTGGCTTCCTGGAGGGACTCAGAAAATGGCATTTGCAAAATCTCAGAGGACTCGACTCGCACATTTTAG-ATTTTACTTTTCTCCCC-AACTACACCTTTGCTGGTTCATTTTATTG--CAGAGAGTGAA-AC-TTTTTAGCCTTCTAGTCCT------------------------------------- i gorGor1.Supercontig_0080755 C 0 M 2340 s ponAbe2.chr17_random 9218293 190 + 17838096 CCTGCATTCTT-ATTTGGCTTCCTGGAAGGACTCAGAAAATGGCATTTGCAAAATCTCAGAGGACTCCACTAGCACATTTTAG-ATTTTACTTTTCTCCCCAAACTACACCTTTGCTGGTTCATTTTATTG--CAGAGAGCAGA-AC-TTTTTAGCCTTCTAGTCCT----GCC----AGAAAGTTAAAAAAAAAAAAAAAAAA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74749984 188 + 78773432 CCCGCATTCTT-ATTTGGCTTCCTGGAGGGACTCAGAAAATGGCACTTGCAAAATCTCAGAGGATTCCACTCGCACATTTTAG-ATTGTGCTTTTCTTCCCAAACTGCACCTTTGCTGGTACATTTTATTG--CAGAGAGCGGA-AC-TTTTTAGCCTTCTAGTCCT----GCC----AGAAAGTTAAAAAAAAAAAAAAAA-- i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_190290 458 186 + 4572 CCCAAATTCTT-GTGTGGCTTCCTGGAAGGTCTCAGGAAATGGTATCTGTAAAATTTCAGGGGACACAACTTGGACATTTTGGAATTGGGCCTTTCTCCTCAAA-----CCTTTGCTGGTTCATTTCATTG--CAGAGAG--AA-AA-TTTCTAGCCTTCCATTTATGCCTGGC----AGAAG--TAAAAAAAAAAAAAAAAGG i tarSyr1.scaffold_190290 C 0 C 0 s otoGar1.scaffold_94361.1-85690 46443 190 + 85690 TCCCCTTTCCT-GCCTGGCTTCCTGGAGGGATGCAGGAAATGGCACCTGCAAAACTCCAGGGG-CTCAGCCTACACATTTCAG-AATTAGGCCTTCTCCTCAAACCACGCCTTTGTTAGCTCCTGTCGTTG--CAGACAG-AAA-AA-ATTTTAGCCCACCAATTCTACCTGGC----AGAAAGTTAAAAAAACAAAATGAA-- i otoGar1.scaffold_94361.1-85690 C 0 I 65 s cavPor3.scaffold_76 4304906 183 + 7991924 CCTGAATTCCC-GTCTGGCCTCCCAGTGGGATCAGAGACCTGGTGGC--CAGAATCCCAGGGGAC-CAACTC-TGTGTCTGAG-AGGGCCCTTCTCCACCC---CCACAACTCTGCCTGTTCATTTCATCC--CAGGGGGGGAA-A---TTTTAGCCTTCCATTTCTGTCTAGC----AGAAAGGTAAAAGAAAAAAAAAAA-- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10761986 180 - 65312493 CCAGCCTCCTT-GTGCGGCTTCCCACAGGGACTCCAGAAATGGAAGCTGAAAAATCCCAAAGGACTCAACATACACATCTTATAAATGGGCCTTTCTCCCCAAACCACACATTCG-TGCTGCATCTCACTG--CAGAGGAGGGAGGC-TTTTAGTTCTCCCGTTTGG-TCTGGT----AG--------------ACAGTAAAAG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57951006 180 - 61308211 CCTGCATTCGG-GTTTGGCTTCCCCGAGGGACACAGGAAATGGCATCTG-CAAATCCCCAGGGACTCAACTTGCCCATCTTAGAATTGGGCCTTTTTCCCCAAACCACAGCTTTGCTGGTTTGTGTCACTG--CAGAGGGAGGA-CC-TTTTTTTCCTTCCGGTTCTGCCTGGC----AG--------------AAAGTAGAAG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59364833 178 - 64418924 CTAACATTCTG-GTTCAAA-TCCCAGAGGGACTCAGGAAATGGCATCAG-CAAATCCCAGGGGACTCAACCCGCCCATC-TAGGATGGGGCCTTTCTCCCCAAACCACACCTTTGCTGGTTCATTTCACTTCCCAGAGGAAG------TTTTTCTGCGACTGGCTCT-CCTGGC----AGGAGCTAAAGGAAA----------- i canFam2.chr9 I 48 I 336 s loxAfr3.scaffold_49 14297002 161 - 17734757 CCTGCGCTC---TTATGGCTTCCCGGACAGACTCAGGAGAA-GCAGCTCCAAAGTGTCAGGGGACTCAACTTGCATGTCTTAGAATTGGGTCTTTCTCCCCAAGCCGCA-CCTGGCTGGCTCATTTCTTGG--CAGAGAGAGAA-AC-TTTCCAGCCTTCCCATTAT----GCC------------------------------ i loxAfr3.scaffold_49 C 0 I 503 s choHof1.scaffold_213748 3063 189 + 4094 cctgtgctcctgttttgccttGTGTAAGGGACTGAGGGAGC-ACATCTCAAAAATCCCGGGACAT---GCTTGCTCCTTTTAGAATTGGGCCTTTCTTCCCAACCCAAATCTTTGCTGGCTCATTTCAAAG--CAGAGACAGAA-ACTTTTCTAGCCTTCCATTTCT----GCCTAATAGAAAGTATTGGGAAAAAAAAA---- i choHof1.scaffold_213748 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e mm9.chr11 118674654 565 + 121843856 I a score=34705.000000 s hg19.chr17_gl000204_random 23178 56 + 81310 a----GAATCAGAGTAATGGCAAGGATTTAACAt-tcttcatttattttattttttgagac s panTro2.chr17 79196622 60 + 83384210 aaaaagaaTCAGAGTAATGGCAAGGATTTAACAt-tctttatttattttattttttgagac i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9218483 50 + 17838096 -----GAATCAGAGTAATGGCAAGGACTTAACAt-tcttt-----ctttattttttgagac i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74750172 50 + 78773432 -----GAATGAGAGTAATGGCAAGGATTTAACAt-tcttt-----ctttattttttgagac i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_190290 644 43 + 4572 -----AAATCAGAGTAGTGGTAAGGATTTAATAT-TC------------ATTTTTTAAAAA i tarSyr1.scaffold_190290 C 0 I 130 s cavPor3.scaffold_76 4305089 40 + 7991924 --------TCAGAGCCACGGCAAAGATTTAGAAT-TC------------ATTTTTTAAAAC i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10762166 30 - 65312493 ----AAGTTCAGAGTAATGGCATAGATTTGCcat--------------------------- i bosTau4.chr19 C 0 I 1029 s equCab2.chr11 57951186 31 - 61308211 ----AAATTCAGAGTAACGGCAAGGATCTGCcata-------------------------- i equCab2.chr11 C 0 I 361 s canFam2.chr9 59365347 24 - 64418924 ----AAATTCAAAGTAAAGGCAAGGATT--------------------------------- i canFam2.chr9 I 336 I 186 s choHof1.scaffold_213748 3252 31 + 4094 ----AAATTCAGATTGATGGCAAGAATTTAGTAT-T------------------------- i choHof1.scaffold_213748 C 0 I 2 e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 46633 65 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e mm9.chr11 118674654 565 + 121843856 I e loxAfr3.scaffold_49 14297163 503 - 17734757 I a score=63352.000000 s hg19.chr17_gl000204_random 23234 148 + 81310 agggtctcactctgtcacccaggctggagtgcagtgacttgaacacagctcactgcagcctccaccgcccaggctcaaacaatcctcctgcctcagtcccccaagtagctgggactacaggtgtgcgccaccatgcctggctaatttt s rheMac2.chr16 74750222 148 + 78773432 agggtctcactctgtcacccaggctggagttcagtgacttgaacacggctcactgcagcctccaccgcccaggttcaagcaatcctcccgcctcagtcccccaagtagcttgaactacaagtgtgcgtcaccatgcctggctaatttt i rheMac2.chr16 C 0 I 29 s ponAbe2.chr17_random 9218533 148 + 17838096 agggtctcactctgtcacccaggctggagtgcaatgacttgaacacggctcactgcagcctccaccgcccaggctcaagcaatcctcccgcctcagtcccctgagtagctgggactacaggtgtgcgccaccatgcctggctaatttt i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79196682 148 + 83384210 agggtctcactctgtcacccaggctggagtgcagtgacttgaacatggctcactgcagcctccaccacccaggctcaagcaatcctcctgcctcagtcccccgagtagctgggactacaggtgtgcgccaccatgcctggctaatttt i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4305129 16 + 7991924 --------------------------------------------------CATT------------------------ACAATATTCCAG---------------------------------------------------------- i cavPor3.scaffold_76 C 0 C 0 e tarSyr1.scaffold_190290 687 130 + 4572 I e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e choHof1.scaffold_213748 3283 2 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 46633 65 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59365371 186 - 64418924 I e bosTau4.chr19 10762196 1029 - 65312493 I e equCab2.chr11 57951217 361 - 61308211 I e mm9.chr11 118674654 565 + 121843856 I e loxAfr3.scaffold_49 14297163 503 - 17734757 I a score=73985.000000 s hg19.chr17_gl000204_random 23382 108 + 81310 tgcattttttgtagagatgggctttcaccatggtgcccaacctggtctcggactcctgagctcaagcgatccacccaccttggcctcccagagtgctgggattacagg s cavPor3.scaffold_76 4305145 49 + 7991924 -------------GAAAGGAGCTGT--TCATGGTACCCATGGTGGT---------------------GGT------------GTCTCCAAAGGACCC----------- i cavPor3.scaffold_76 C 0 C 0 s tarSyr1.scaffold_190290 817 107 + 4572 ttttttttttgtagagacaaggtctcactatgttgcctaggctggtctcgaactcctgggctcaagcaatccttcca-cttggcctcccaaagtgctgggattatagg i tarSyr1.scaffold_190290 I 130 C 0 s rheMac2.chr16 74750399 108 + 78773432 tgtattttttgtagagatgggctttcaccatggtgcccaagctggtctctgactcctgagctcaagcgatccacccaccttggcctcccagagtgctgggattacagg i rheMac2.chr16 I 29 C 0 s ponAbe2.chr17_random 9218681 104 + 17838096 tgcattttttgtagagatgggctttcaccatggtgcccaacctggtctcggactcttgagctcaagcgat----ccaccttggcctcccagagttctgggattccagg i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79196830 108 + 83384210 tgcattttttgtagagatgggctttcaccatggtgcccaacctggtctcggactcctgagctcaagcgatccacccaccttggcctcccagagtgctgggattacagg i panTro2.chr17 C 0 C 0 e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e choHof1.scaffold_213748 3283 2 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 46633 65 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e canFam2.chr9 59365371 186 - 64418924 I e bosTau4.chr19 10762196 1029 - 65312493 I e equCab2.chr11 57951217 361 - 61308211 I e mm9.chr11 118674654 565 + 121843856 I e loxAfr3.scaffold_49 14297163 503 - 17734757 I a score=11743.000000 s hg19.chr17_gl000204_random 23490 22 + 81310 tgtgaggcactgcacctggtcC s panTro2.chr17 79196938 22 + 83384210 tgtgaggcactgcacctggtcC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9218785 22 + 17838096 tgtgaggcactgcacctggtcC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74750507 22 + 78773432 tgtgaggcactgcgcctggtcC i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_190290 924 22 + 4572 catgaaccactgtgcttgactC i tarSyr1.scaffold_190290 C 0 C 0 s canFam2.chr9 59365557 1 - 64418924 ---------------------c i canFam2.chr9 I 186 C 0 s equCab2.chr11 57951578 15 - 61308211 TGGCAGGCATTGCAT------- i equCab2.chr11 I 361 C 0 e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e choHof1.scaffold_213748 3283 2 + 4094 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 46633 65 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e bosTau4.chr19 10762196 1029 - 65312493 I e cavPor3.scaffold_76 4305194 0 + 7991924 C e mm9.chr11 118674654 565 + 121843856 I e loxAfr3.scaffold_49 14297163 503 - 17734757 I a score=24625.000000 s hg19.chr17_gl000204_random 23512 53 + 81310 AACATTCATTTTTTTAAAACCATGGAATTCTCCAAAGGTACTAGAGCTGTGCA s equCab2.chr11 57951593 41 - 61308211 --------TTTTTTTAAAACCATCAAAACATCCAAACCAAAC----CAGCTCA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59365558 53 - 64418924 AGGATTTGTTTTTTAAAAACTACCAACACATCCAAACCAAGCGGAGCCACTTG i canFam2.chr9 C 0 C 0 s cavPor3.scaffold_76 4305194 32 + 7991924 TGAAGTCA-------GAAACCA---AGTTCTT--AGGGTGCCAG--------- i cavPor3.scaffold_76 C 0 C 0 s rheMac2.chr16 74750529 51 + 78773432 AACATTCA--TTTTTAAAACCATGGAATTCTCCAAAGGCACTAGAGCTGCGCA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9218807 53 + 17838096 AACAATCATTTTTTTTGAACCATGGAATTCTCCAAAGGTACTAGAGTCGTGCA i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79196960 53 + 83384210 AACATTCATTTTTTTAAAACCATGGAATTCTCCAAAGGTACTAGAGCTGTGCA i panTro2.chr17 C 0 C 0 s choHof1.scaffold_213748 3285 44 + 4094 ---------TTTTTAAAAGGCATCAAAATATCCAAATGAAAGGAGGCTGCTTA i choHof1.scaffold_213748 I 2 C 0 e tarSyr1.scaffold_190290 946 0 + 4572 C e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 46633 65 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e bosTau4.chr19 10762196 1029 - 65312493 I e mm9.chr11 118674654 565 + 121843856 I e loxAfr3.scaffold_49 14297163 503 - 17734757 I a score=19744.000000 s hg19.chr17_gl000204_random 23565 45 + 81310 CCCTCCCAACTGCAGCATTTCCTCAGGGTATGCAGCCCTCTGGAG s panTro2.chr17 79197013 45 + 83384210 CCCTCCCAACTGCAGCATTTCCTCAGGGTATGCAGCCCTCTGGAG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9218860 45 + 17838096 CCCTCCCAACTGCAGCATTGCCTCAGGGTATGCAGCCCTCTGGAG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74750580 45 + 78773432 CCCTCCGAACTGCAGCACTTCCTCAGGGTATGCAGCCTCCTGGAG i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4305226 26 + 7991924 ------------------TTCCTTAGGGTGCAGAACCCT-TGTAG i cavPor3.scaffold_76 C 0 I 6 s canFam2.chr9 59365611 33 - 64418924 TCCTACCCACTACACTGCCACCATGAACTCAGG------------ i canFam2.chr9 C 0 C 0 s equCab2.chr11 57951634 45 - 61308211 TCCTACAAACTGCACCAGCTCCTCAGGACCTGGAGCCCTCGGCAA i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10763225 41 - 65312493 CCCTGCTAACCATACCCATTTGTTACACTGCGGAGTCCTCA---- i bosTau4.chr19 I 1029 C 0 s choHof1.scaffold_213748 3329 37 + 4094 TCCTACTAGCAGCACTGATTCATCAGGGTATGTGAAC-------- i choHof1.scaffold_213748 C 0 C 0 s loxAfr3.scaffold_49 14297666 18 - 17734757 ---------------------------GTCTGTGACCCTTGTTAA i loxAfr3.scaffold_49 I 503 C 0 e tarSyr1.scaffold_190290 946 0 + 4572 C e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 46633 65 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e mm9.chr11 118674654 565 + 121843856 I a score=27047.000000 s hg19.chr17_gl000204_random 23610 32 + 81310 CTTGCCCGGGGTGCAGTTCCTCAAGGCACTGT s rheMac2.chr16 74750625 32 + 78773432 CTTGCCCGGGGTGCAGTTCCACAAGGCACTGT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9218905 32 + 17838096 CTTGCCCGGGGTGCAGTTCCACAAGGCACTGT i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79197058 32 + 83384210 CTTGCCCGGGGTGCAGTTCCTCAAGGCACTGT i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94361.1-85690 46698 32 + 85690 CTTGCCCACTCCGCAGCTCAGCAAGCCTCTCT i otoGar1.scaffold_94361.1-85690 I 65 C 0 s cavPor3.scaffold_76 4305258 22 + 7991924 CCAACCCACGGTGTGACCCTGC---------- i cavPor3.scaffold_76 I 6 C 0 s canFam2.chr9 59365644 24 - 64418924 -------ACTCTGCAGGTGGGC-AGGCTCCAC i canFam2.chr9 C 0 C 0 s equCab2.chr11 57951679 32 - 61308211 CGTGCCCACTTCGCGGTCCAGCAAGGTGCTGT i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10763266 23 - 65312493 ---------TTCACTTGCCTGCAAGGCACTGT i bosTau4.chr19 C 0 C 0 s loxAfr3.scaffold_49 14297684 30 - 17734757 CTTGCCCA-CTCACAGTTCAGTAAGGCCTTG- i loxAfr3.scaffold_49 C 0 C 0 s choHof1.scaffold_213748 3366 30 + 4094 --TGCCCAGCTCGTGGTTTGGCAAGCCATCGC i choHof1.scaffold_213748 C 0 C 0 e tarSyr1.scaffold_190290 946 0 + 4572 C e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e mm9.chr11 118674654 565 + 121843856 I a score=100126.000000 s hg19.chr17_gl000204_random 23642 114 + 81310 TCTCTTTCCTTCTGTTTTT-----CTTACACTAGCTTCTCCCTGGGTGCCAGTGGTTCTACTTCTGCCATCTTTTCTGGTTAATCCCTCTC---ATACCTTTCAGGGCTGCTGGCTTTGCTC s panTro2.chr17 79197090 114 + 83384210 TCTCTTTCCTTCTGTTTTT-----CTTACACTAGCTTCTCCCTGGGTGCCAGTAGTTCTACTTCTGCCATCTTTTCTGGTTAATCCCTCTC---ATACCTTTCAGGGCTGCTGGCTTTGCTC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9218937 117 + 17838096 TCTCTTTCCTTCTGTTTTT-----CTTACACTAGCTTCTCCCTGGGTGCCAGTGGTTCTACTTCTGCCATCTTTTCGGGTTAATCCCTCTCATGATACCTTTCAGGGCTGCTGGCTTTGCTC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74750657 117 + 78773432 TCTCTTTCCTTCTGTTTTT-----CTTACACTAGCTTCTCCCTGGGTGCCAGTGGCTCTACGTCTGCCGTCTTTTCTGGCTAATCCCTCTCATGATACCTTTCAGGGCTGCTGGCTTTGCTC i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_190290 946 88 + 4572 TTTCCTTCCTTTTGTTTTTTTTCCCTTAAACTAGCTCTTCCCTGTGTGCCCACGGCCTT---TCTGCCATCTTCTCTTGTCAGTTCCTCTC------------------------------- i tarSyr1.scaffold_190290 C 0 C 0 s otoGar1.scaffold_94361.1-85690 46730 108 + 85690 TCTCTCT-------TTTTC-----CTTAAACCATCTG-TCCCTGTGCGCCAAGCTCCCTTCTTCCCCCATCTTCTCTTGTCAGGGCCTCTCATGACGCCTTTCCAGGATGGGGGCTTTGTG- i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4305280 109 + 7991924 ----TCTGCGTCACCTCCC-----CTCCCGCTAGCTGCCCCCTCCCCAACCCTGCCCCCTCGT-GGCCATCTTCCCTCATCCAT-CCTCTG-TGGCAGCCTTCAGGGCTGCTGGCCTCCCT- i cavPor3.scaffold_76 C 0 C 0 s canFam2.chr9 59365668 77 - 64418924 CTCCTGTCCTCATCTCCCT-----CTGAAGCCACCCCGCCT-------CCCCCATCCTCC--------------------------------AGGCACCGTTCCAGG-TGCTGGCGTGCACC i canFam2.chr9 C 0 C 0 s equCab2.chr11 57951711 112 - 61308211 TTTCTTTCCTTATTCTTCT-----CTGAAGCCAGCTCCTCCCTGTGTGCCGCCATCCTTC----TCCTACCTT-TCTCTTCGGTCCCTCTCGGGGCACCTCTCAGGGATGATGGCTTTGTTC i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10763289 114 - 65312493 TTTTCTTCCTTATTTTTCT-----CTGAAACCTGCTTCTCCCTGTGAGCCACGGTCCTTTC---TCCCATCTTCTCTCTTCAGCCTCTCTCAAGGCATCTCTCAGGGATGCCAACGGCATTC i bosTau4.chr19 C 0 C 0 s loxAfr3.scaffold_49 14297714 95 - 17734757 ---GTACCTTCATTTTTTC-----CT-----------------ATGTCCCAACGTCCCTTCT--GCCATTTTCCTCTCGTCAGTCCCTACGGTGTCACCTTCTAGAAGCACGTGCTTCATTC i loxAfr3.scaffold_49 C 0 C 0 s choHof1.scaffold_213748 3396 107 + 4094 ---TTATTTTCCTTTTTCC-----CTTAAACCATCTCCCCAGCACGTTCCCACATCCCTTCT------CTCTCCTTCCAGCA-TCTCTACCCTGCCACCTTCCAGCCATGTGAGCTTTGTTT i choHof1.scaffold_213748 C 0 C 0 e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e mm9.chr11 118674654 565 + 121843856 I a score=95172.000000 s hg19.chr17_gl000204_random 23756 51 + 81310 TCTTCCATTTTCCATCACCCCAATTCCTCCTC----AGCCTCTGTACCCC-CCAAA- s macEug1.Scaffold60637 3664 54 + 15229 TCTACC--TTCTCTTCTTCCACATTTCCTTTCTGATATCTTCCACTCCCC-TCAGAA i macEug1.Scaffold60637 N 0 C 0 s panTro2.chr17 79197204 51 + 83384210 TCTCCCATTTTCCATCACCCCAATTCCTCCTC----AGCCTCTGCACCCC-ACAAA- i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9219054 51 + 17838096 TCTTCCATTTTCCACCACCCCAATGCCTCCTC----AGCCTCTGCACCCC-GCAAA- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74750774 51 + 78773432 TGTTCTGTTTTCCGTCACCCCAGTTCCTCCTC----AGCCTCTGCACCCC-GCAAA- i rheMac2.chr16 C 0 C 0 s bosTau4.chr19 10763403 49 - 65312493 CCCTCAATTTCTCATCACACCTATTCCTCCTC----ATTCTT--CTTCCC-CCAAA- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57951823 51 - 61308211 TCTCCAGTTTCTCATCACCCCGATTCCTCCTC----GTTCTCTGCTTCCC-CCAAA- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59365745 49 - 64418924 TGTCCCATTTCTCCCTTCCCCGATTCCT-CTT----GGTCTTTGC-TCCC-CCACA- i canFam2.chr9 C 0 C 0 s eriEur1.scaffold_354393 86553 45 - 127679 TTCTCTGatactccctcccac----cct--cc----agtCTCTGCTTTCC-TCAAA- i eriEur1.scaffold_354393 N 0 C 0 s loxAfr3.scaffold_49 14297809 52 - 17734757 TCTCCAATTTCCCTTCACCCAGATTTCTCGGC----CATCCCTGCTCCCCACCAAA- i loxAfr3.scaffold_49 C 0 C 0 s choHof1.scaffold_213748 3503 49 + 4094 TCTTCAGTTGCCCTTCA-CCAGGCTCCTCCCC----AGTCTCAGCTCCC--CCAGA- i choHof1.scaffold_213748 C 0 C 0 s tarSyr1.scaffold_190290 1034 40 + 4572 -----------CCATCACCCCAATTTCTTCCC----TGTCTCTGCTTCCC-CCAAA- i tarSyr1.scaffold_190290 C 0 C 0 s otoGar1.scaffold_94361.1-85690 46838 33 + 85690 ------------------TCCAATTCCTCCTT----ACTCTCTGCTTACC-CCGAA- i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4305389 38 + 7991924 -------------GTCATCCTGATTATTCCAT----GGTACATACTTCCC-CCAAA- i cavPor3.scaffold_76 C 0 C 0 e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e mm9.chr11 118674654 565 + 121843856 I a score=107600.000000 s hg19.chr17_gl000204_random 23807 33 + 81310 ---ACATAAGCTCCTA---A-CCAAAATCAGAGTTTAAAA s panTro2.chr17 79197255 33 + 83384210 ---ACATAAGCTCCTA---C-TCAAAATCAGAGTTTAAAA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9219105 33 + 17838096 ---ACATAAGCTCCTG---A-CCAAAATCAGAGTTTAAAA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74750825 33 + 78773432 ---ACATAAGCTCCTA---A-CCAAAAGCAGAGTTTGAAA i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_190290 1074 33 + 4572 ---ACATAAGCTAATA---A-CTGAAATCAGAGTTTTAAA i tarSyr1.scaffold_190290 C 0 C 0 s otoGar1.scaffold_94361.1-85690 46871 36 + 85690 ---ACACAAGCTAATAATGA-CCAAAATCAGAGTTTAAAA i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4305427 33 + 7991924 ---ACATAAGCTCAGC---A-GCAACAACAGGGTTTAAAT i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118675219 33 + 121843856 ---ACACAGACTAAGG---A-CCAACAGGAGCATTTAAGA i mm9.chr11 I 565 C 0 s bosTau4.chr19 10763452 33 - 65312493 ---ACACGAGCTAATA---A-CCAAAACCAGCGCTTGAAA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57951874 33 - 61308211 ---ATATAAGCTAACA---A-CCAAACTCGGAGCTTAAAA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59365794 33 - 64418924 ---ACCCAAGCCAATA---A-CCAGACCCAGAGCTTGACA i canFam2.chr9 C 0 C 0 s eriEur1.scaffold_354393 86598 23 - 127679 ---ACAT--------------CCACTGGCAGAGAGTGAAA i eriEur1.scaffold_354393 C 0 C 0 s loxAfr3.scaffold_49 14297861 33 - 17734757 ---ACATAAGCTTATA---A-CCAAAGTCAGAGTTCAAAA i loxAfr3.scaffold_49 C 0 I 412 s choHof1.scaffold_213748 3552 32 + 4094 ---ACAT-AGCTAATA---A-CCAAGCTCAGAGTCTAAAA i choHof1.scaffold_213748 C 0 C 0 s macEug1.Scaffold60637 3718 29 + 15229 ACCAAAGAAACTAGAA---ATCCAATATGAGG-------- i macEug1.Scaffold60637 C 0 C 0 e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I a score=226125.000000 s hg19.chr17_gl000204_random 23840 76 + 81310 TAGGA------CTCAAACTAAGAAAGCAAAATTTGCTCTTTCTTTAACCAAGAGAA-AAACAACACAGAGCACCTCATTTTA--G s macEug1.Scaffold60637 3747 77 + 15229 TGAGAGGTCTTTTCTGCCTACAAAAGCTAAACATTTTTCCTCTCAGAGTAATAGAATAAACT------AGCTGTTTtgttta--a i macEug1.Scaffold60637 C 0 C 0 s choHof1.scaffold_213748 3584 74 + 4094 TGGGA------CTCA-GCTAAGAGAGCAAACCTCCCCATCCCTTTAAG-ACGGGAA-AAACAACACATGCCACTTCATTTTG--G i choHof1.scaffold_213748 C 0 C 0 s eriEur1.scaffold_354393 86621 68 - 127679 TGGGA------CTCAAACTGAGA--GCAAAACTTGAAATTCCTTGAGTCAGTAGAA-GTAGA------AGCATCTTCTCCCA--G i eriEur1.scaffold_354393 C 0 C 0 s canFam2.chr9 59365827 75 - 64418924 TAAGG------CTCATGCTAAGAAAGCAAAACTTGCCACCTCTTTAGCCAGGAGAA-GGATAATATG-GGCGCTTCACTGCA--A i canFam2.chr9 C 0 C 0 s equCab2.chr11 57951907 74 - 61308211 TGGAA------CCCAAGCTAAGAAGGCAAAACGTGCTATTTCTTCCACCAAGAGCA---ACAACACGCAGCACTTCGTTTCA--G i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10763485 73 - 65312493 TGAGG------CTCAAGCTAAGAAAGCCAAACCTGCTATTTCTTTAACCAGGAGA----AGAACATGAAGCATCACATTTCA--G i bosTau4.chr19 C 0 C 0 s mm9.chr11 118675252 78 + 121843856 TGAGG------CCTGAACCCAGAAAGCACAACTCACTGTGCCTCTAACCCAGAGGG-AAGCACGGCACAGCATGCCATATTTCAG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4305460 76 + 7991924 TGAGC------CTCAAACCTAGGAAGCAAAGCTTGCCACGCTCTTAACCAAGAGAA-AAATAATGTGTGGCAGTGCATCTTC--A i cavPor3.scaffold_76 C 0 C 0 s otoGar1.scaffold_94361.1-85690 46907 76 + 85690 TGGGA------CTCAAACCAAGAAAGCAAAACTTGCTGTTTCTTTAACCAAAAGAA-ACACAGCACGTGGCGGCTCGTGTCG--G i otoGar1.scaffold_94361.1-85690 C 0 C 0 s tarSyr1.scaffold_190290 1107 76 + 4572 TGGGA------CTCAGACTAAGAAAACAAAACTTGTTATTTCTTTATCCGAGAAAG-AACCAACACGGAGCACCTCATTTTA--G i tarSyr1.scaffold_190290 C 0 C 0 s rheMac2.chr16 74750858 76 + 78773432 TGGGA------CTCAAACTAAGAAAGCAAAACTTGCTCTTTCTTTAACCAAGAGAA-AAACAACACAGAGCACCTCATTTTA--G i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9219138 76 + 17838096 TGGGA------CTTAAACTAAGAAAGCAAAATTTGCTCTTTCTTTAACCAAGAGAA-AAACAACATGGAGCACCTCATTTTA--G i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79197288 76 + 83384210 TGGGA------CTCAAACTAAGAACGCAAAATTTACTCTTTCTTTAACCAAGAGAA-AAACAACACAGAGCACCTCATTTTA--G i panTro2.chr17 C 0 C 0 e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304289526 8530 - 541556283 I e loxAfr3.scaffold_49 14297894 412 - 17734757 I a score=173868.000000 s hg19.chr17_gl000204_random 23916 46 + 81310 TAGTAAAGATTATAGGGAATATACAATATTCAGAATAA-ATGAACCT s panTro2.chr17 79197364 46 + 83384210 TAATAAAGATTATAGGGAATATACAATATTCAGAATAA-ATGAACCT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9219214 46 + 17838096 TAGTAAAGATTATAGGGAATATACAATATTCAGAATAA-ATGAAACT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74750934 46 + 78773432 TGGTAAAGATTATAGGGAATATACAATATTCGGAATAA-ATGAGCCT i rheMac2.chr16 C 0 I 349 s tarSyr1.scaffold_190290 1183 46 + 4572 TAGCAAAGATTATAGGGAATGTACAATATTCTGAATAA-ATGAAACT i tarSyr1.scaffold_190290 C 0 C 0 s otoGar1.scaffold_94361.1-85690 46983 46 + 85690 TAGTAAAGATTGGGAGGAATATTCCATATTCTGAGTAA-ATGAACCT i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4305536 46 + 7991924 TAGTAAAGATGATGAGGAACCCACAATATTCCCAGTAA-ATGAACCT i cavPor3.scaffold_76 C 0 I 12 s mm9.chr11 118675330 42 + 121843856 TAGTAAAGATACAGGGAAA--TGCAATATTCCAAGAAA-ATGAGC-- i mm9.chr11 C 0 I 11 s bosTau4.chr19 10763558 46 - 65312493 TTGTAAAGATTACAGAGGATATGTAATATTCTGAATAA-ATGAATCT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57951981 45 - 61308211 TGGTAAAGATTATAGGGAATATTTAATATTCTGAATAA-ACGA-TCT i equCab2.chr11 C 0 C 0 s canFam2.chr9 59365902 46 - 64418924 CAGTAAAGGTTATAGGAAATACATAATATTCAGAATAA-ATGAGTCT i canFam2.chr9 C 0 C 0 s eriEur1.scaffold_354393 86689 45 - 127679 CAGCAAGGGGTCCAGAGAATCTCTGAGATTATGCATAG-CTGG-ACA i eriEur1.scaffold_354393 C 0 C 0 s choHof1.scaffold_213748 3658 45 + 4094 TGGTACAGGTGATAGGGAATATATAATATTCCGAATAA-GTGAGCC- i choHof1.scaffold_213748 C 0 C 0 s macEug1.Scaffold60637 3824 38 + 15229 taattaaaa----aaagaa-----aatattctgaatAATGCAAAcct i macEug1.Scaffold60637 C 0 C 0 s monDom5.chr2 304298056 47 - 541556283 tatttaataatctttaaaaaagaaaatattCTGAATAATACAAATCT i monDom5.chr2 I 8530 C 0 e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e loxAfr3.scaffold_49 14297894 412 - 17734757 I a score=1437006.000000 s hg19.chr17_gl000204_random 23962 238 + 81310 CCTCCCCCTGTTTTTAAACCACT-----CTTGTGAAACCAGCTTAATTCCTGG--CTCCCCTCATGCCTTCTGAATCCTGTCTCTGG----------------------------------------------------CAAA----------AATAATTTGGGTTTTATTCTTCTGGCATCTGGT----GGGAGTCGGTGACAATTTTACTGTAGCTATA------CTTCTT------------CTTTTTTAATACCAGTGTGTTTTAATAATACAGTGTACCTTTTGGTATTGTTGAAATGTTACATTATTCAACGTATCCAACGGG s panTro2.chr17 79197410 238 + 83384210 CCTCCCCCTGTTTTTAAACCAGT-----CTTGTGAAACCATCTTAATTCCTGG--CTCCCCTCATGCCTTCTGAATCCTGTCTCCAG----------------------------------------------------CAAA----------AATAATTTGGGTTTTATTCTTCTGGCATCTGGT----GGGAGTCGGTGACAATTTTACTGTAGCTATA------CTTCTT------------CTTTTTTAATACCAGTGTGTTTTAATAATACAGTGTACCTTTTGGTATTGTTGAAATGTTACATTATTCAATGTATCCAATGGG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9219260 238 + 17838096 CCTCCCCCCATTTTTAAACCACT-----CTTGTGAAACCAGCTTAATTCCTGG--CTCCCCTCATGCCTTCTAAATCCTGTCTCCAG----------------------------------------------------CAAA----------AATAATTTGGGTTTTATTCTTCTGGCATCTGGT----GGGAGTCGGTGACAATTTTACTGTAGCTATA------CTTCTT------------CTTTTTTAATACCAGTGTGTTTTAATAATACAGTGTACCTTTTGGTATTGTTGAAATGTTACATTATTCAACGTATCCAACGGG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74751329 237 + 78773432 cCTCCCCCCGTTTTTAAACCACT-----CTTGTGAAGCCAGCTGAGTTCCTGG--CTCCCCTTGTGCCTTCGGAATCCTGTCTCTGG----------------------------------------------------C-AA----------AATAATTTGGGTTTTATTCTTCTGGCATCTGGT----GGGAGTCGGTGACAATTTTACTGTAGCTACA------CTTCTT------------CTTTTTTAATACCAGTGTGTTTTAATAATACAGTGTACCTTTTGGTATTGTTGAAATGTTACATTATTCAACGTATCCAACAGG i rheMac2.chr16 I 349 C 0 s tarSyr1.scaffold_190290 1229 238 + 4572 CTACCTCCCATTTTGAAACCACT-----CTTGTGAAACCAGCCTCACTCCTGA--CTCCCCTCATGCCTTATGAATCCTGTCTCTGG----------------------------------------------------CAAA----------AATAATTTGGGTTTTATTATTCTGGCATCTGGT----GGGAGTCTGTGACAATTTTACTGTAGCTGCA------CTTCTT------------CTTTTTTAATACCAGTGTGTTTTAATAATACAGTGTACCTTTTGGTATTGTTGAAATGTTACATTATTCAACGTATCCAACGAG i tarSyr1.scaffold_190290 C 0 C 0 s otoGar1.scaffold_94361.1-85690 47029 237 + 85690 CCGCCTCCCATGCTCAAACCACT-----CTTGTGAGACCAGCTTCATCCCTGA--CTCCCCACATGCCTTATGAATCCTGTCTCCGG----------------------------------------------------CAAA----------AATAATTTGGGCTTTATTATTCTGGCATCTGGT----GGGAGTGCGTGACAGTTTTCCTGT-GCCGTG------CGGCTT------------CTTTCTGAGTACGAGTGTGTTTTAATAATACACTGTACCTTTTGGTATTGTTGAAACATTACATTACTCAACGTATCCAACGGG i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4305594 250 + 7991924 CCTCCTCCTGTTTTTAAGCCACG-----CTTGCAAAACCAGCCTCACTCTCTCGTCTCCCCTGATGCCTTATGAATCCTGTCTCCGG----------------------------------------------------CaaaaaaaaataataataatttGGGTTTTATTATTCTGGCATCTGGT----GGGAGTCTGTGACAGTGTTACTGTAGCTACT------CTTCTT------------CCGTTTTAATGCCAGCCTATTTTAATAATACAGTGTACCTTTTGGTATTGTTGAAATGTTACATTATTCAACACATCCAGTAGG i cavPor3.scaffold_76 I 12 C 0 s mm9.chr11 118675383 218 + 121843856 CCTCCTCCCGTTTTTAAATGGCT-----CTTGCGGAGCTGCCTTCACCCTTCA--CTCCCCTCGTGCCTTATGGATCCTGTCCCC-----------------------------------------------------------------------------GGGTTCATTATTCTGACGTGTGGT----GGGAGTC--TGACAGTGTTACTGCGGCTCCA------CTTCTT------------CC--TTTAATGCCAGCCTGTTTTAATAATACAGTGTACCTTTTGGT-TTGGTGAAATGTGACATTATTCCAGGCACCCAGCGGC i mm9.chr11 I 11 C 0 s bosTau4.chr19 10763604 247 - 65312493 CCTCCTCCCATTTTTAAACCACT-----TGTGTGAAACCAGCTCCATTCCTAA--CTCCCCTCATGCCTTATGAATCCTTTCTCTGG----------------------------------------------------CAAA----------AATAATTTGGGTTTTATGATTCTGGCATCTAGT----GGGAGTCTGTGACAATTTTAATGTAGCTCCG------CTGCTGTTGCTTCTTC-TTTTTTTTAATACCAGTGTGTTTTAATAAT--AGTGTACCTTTAGGTATTGTTGAAATGCTACATTATTCAATGTAGCCGACGGG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57952026 258 - 61308211 CCTCCTCCCATTTTTAAACTGCT-----CTCGTGAAACCAGCTTTGTTCCCGA--CTCTCCTCATGCCTTATGAATCCTCTCTCCGG----------------------------------------------------TAAA----------AATAATTTGAGTTTTATTATTCTGGCATCTAGTGCTAGGGAGCCTGTGACAATTTTATCGTAGCTCTGCTTTCTCTTCTTTTCCTTCTTT--TTTTTTAACTACCAATGTCTTTTAATAATACAGGGTACCTTGAGGTATTGTTGAAATGTTACATTATTCAACGCATCCAAGAGG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59365948 293 - 64418924 CCTCCTTCCGTTTTTAAACCA------------GAAACCAGCTTCATTCCTGA--CTCCCCTCATGCCTTGTGAATCCTGTCTCTGGCaaataaataaataaataaataaataaataaataaataaataaataaataaataaa----------taTAATTTGGGTTTTATTATTCTGGCATCTAGT----GGGAGTCTGTGACAATGTTACTGTAGCCAAG------CTGCTCCTGCTTCTTC--CTTTTTTAACACCAGTGAGTTTTAATAATACAGTGTACCTTTAGGTATTGTTGGAATGTTACATTATTCATTGCATCCAACGGG i canFam2.chr9 C 0 C 0 s eriEur1.scaffold_354393 86734 235 - 127679 CCCTCCCCCATTCTCGAACCACT-----C--------------CCACTCCTCA--CTCCCCTCACACCTTATGAATCCTGTCTCcggcaaaggggaa------------------------------------------aaat----------aataatctggGCTTTATTATTCTGGCATCT-GT----GGGAGTTGGTGACAATTTCActgtggct--g------ctgctgctgc--------tttttttaATACCAGTGTGTTTTAATAATACAGTGTACCTTTTGGTATTGTAGAGATGTTACATTATTCAGCATATCCTACGGG i eriEur1.scaffold_354393 C 0 N 0 s choHof1.scaffold_213748 3703 250 + 4094 CCTCCGCCTGGTTTTAAACTGCT-----CTTGGGAAACCAGCTTCATCTCTGA--CTCCCCTCATGCCTTATGAATCCTGTCTCCGG----------------------------------------------------CAAA----------AATAATTTGGGTTTTATTATTCTGGCATCTAGT----GGGAGTCGGTGACAATTTTACTGTAGCTGGG------CTGCTCCCTCTTCTCCTTCTTTTTTAATACCAGTGTGTTTTAATAATACAGTGTACCTTTTGGTATTGTTGAAATGTTACATTATTCAATGTATCCAACAGG i choHof1.scaffold_213748 C 0 C 0 s macEug1.Scaffold60637 3862 246 + 15229 -----acctctttaaaaaaaaatacctacttGGATAACCTCTTCCATTTCTGA--CTTCTTCCTGCCCTTGTGAATCCTGTCTCAGG----------------------------------------------------CGAA----------AATAATTCAGGCTTTATTATTCTGGCATCTAGT----GGGAGTCTGTGACAATTTTACTATAGCTGag------cttccctttctctc----cctttttaatACCAGTGTGTTTTAATAATACAGTGTACCTTTCGGTATTGTTGAAATGTTACATTATTCAATGCATCCAACAGG i macEug1.Scaffold60637 C 0 C 0 s monDom5.chr2 304298103 244 - 541556283 -------ACCTCTTTAAAAAAATACCTACTTGGATAACCTCTTCCATTTCTGA--CTTCTTACAGCCGCTGTGAATCCTGTCTCAGG----------------------------------------------------CGAA----------AATAATTCAGGCTTTATTATTCTGGCATCTAGT----GGGAGTCTGTGACAATTTTACTATAGCTGAG------CTTCCCTTCCTCTC----CCTTTTTAATACCAGTGTGTTTTAATAATACAGTGTACCTTTCTGTATTGTTGAAATGTTACATTATTCAATGCATCCAACAGA i monDom5.chr2 C 0 C 0 e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e loxAfr3.scaffold_49 14297894 412 - 17734757 I a score=750296.000000 s hg19.chr17_gl000204_random 24200 146 + 81310 AAAGGGAAAGGCCTTCTGTAATTTATGTGTCCTCGGT-GCTGTGTTTAAAGCTTGCAAAG-TGGAGGGCTGTAATTTGGGAAGCAATTTTCCCCAAGGTC--G-GGAGAATGGTTTCTGGAGGAGAGGCT-GGAGACTGCCTGAC-----------CCGGGTT s panTro2.chr17 79197648 146 + 83384210 AAAGGGAAGGGCCTTCTGTAATTTATGTGTCCTCGGT-GCTGTGTTTAAAGCTTGCAAAG-TGGAGGGCTGTAATTTGGGAAGCAATTTTCCCCAAGGTC--A-GGAGAATGGTTTCTGGAGGAGAGGCT-GGAGACTGCCTGAC-----------CCAGGTT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9219498 146 + 17838096 AAAGGGAAGGGCCTTCTGTAATTTATGTGTCCTCGGT-GCTGTGTTTAAAGCTTGCAAAG-TGGAGGGCTGTAATTTGGGAAGCAATTTTCCCCAAGGTC--A-GGAGAACGGTTTCTGGAGGAGAGGCT-GGAGACTGCCTGAC-----------CCAGGTT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74751566 146 + 78773432 AAAGGGAAGGGCCTTCTGTAATTTATGTGTCCTCGGC-GCTGTGTTTAAAGCTTGTAACG-TGGAGGGCTGTAATTTGGGAAGCAATTTTCCCCAAGGTC--A-GGAGAACAGTTTCTGGAGGAGAGGCT-GGAGACTGCCTGAC-----------CCGGGCT i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_190290 1467 146 + 4572 AAAGGGATGGGCCTTATGTAATTTATGTGTCCTCCGC-GCTGTGTTTGAAGCTTGCAAAC-TGGAGGGCTGTAATTTGGGAAGCAATTTTCCCCAAGGTC--G-GGGGAACAGTTTCTGGAGAAGAGGAT-GGAGGTTGGCTGAC-----------CCTGGCT i tarSyr1.scaffold_190290 C 0 C 0 s otoGar1.scaffold_94361.1-85690 47266 134 + 85690 AAAGGGAAGGCCCTTATGTAATTTATGTGTCCTCGGC-GATGTGTTTAAAGTCGGCAAAG-TGGAGGGCTGTAATTTGGGAAGCAATTTTCCCCAAGGTC--G-GGGAAACAGTTTCTGGAGG-------------CTTTGTGAC-----------CCGGGCA i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4305844 144 + 7991924 ACTGGGAAGGGCCTCGTGTAATTTATGTGTCCTCTGC-ACTGTGTTTGAAGCTCCCAAAG-TGGAAGG-TGTAATTTGAGAAGTGATTTTTCCCAAGGTC--A-CAGAGACAGTCTCCGGAGAGAAAGCT--GGTGTCATCTGCC-----------CCAAGCT i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118675601 147 + 121843856 AATGAGAAGGGCCTTATGTAATTTATGTGTTCTCCGC-GCTGTGTTTAACACTCCCAAAG-CGGAGGGCTGTAATTTGGGAAGCGATTCTCCCCAAGGTC--A-GGGGAACAGTTTGTAGAGGGAAGGCTGGGGGGCTGTCTGAC-----------CTGAGCT i mm9.chr11 C 0 C 0 s bosTau4.chr19 10763851 158 - 65312493 AATGGGAAGGGCCTCATGTAATTTACGTGTCCCCGGT-GCTGTGTTTAAGGCTTGTGAAA-TGGAGGGGTGTCATTTGGGAAGCAATTTTCCCCAAGGTC--GAGGAAAGCAATTTCTGGAGGAGCGGCT-GGAAACTGTGTGACCCGACTGACAGCCAGGCT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57952284 157 - 61308211 AACGGGAAGGGCCTTATGCAATTTCTGCGTCCCCCGC-GCTGTGTTTAAAGCTTGCGAAA-TGGAGGGGTGTAATTTGGGAAGCAGTTTTCCCCAAGGTC--G-GGGAAGGAATTTCTGGAGGAGCAGCT-GGAGGCTGTGCGACCCTAGTAATAACCAGGCT i equCab2.chr11 C 0 C 0 s canFam2.chr9 59366241 157 - 64418924 AATGAGAAGGCCCTTATGCAATTTATGTGTCCTCCGC-GCTGTGTTTAAAGCTCGGGAAA-TGGAGGGGTGTAATTTGGGAAGCAATTTTCCCCAGGATG--G-GGAAAGCAGTTTCTGGAGGAAAGGCT-GGGGGCTGTGTGACCCTCGTGACAGCCAGGCT i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14298306 133 - 17734757 AATGGGAAGGGCT--GTGCAA-TTATGTGT---------------------CTCGCGCTG-TGGA-GGGTGTAATTTGGGAAGCAATTTTCCCCAAGGTT-GG-GGAAAGCAGTTTCTCAAGAAAAAGCT-GGAGGCTGTCTGACCCTAGTGACA-GCAGGCT i loxAfr3.scaffold_49 I 412 C 0 s choHof1.scaffold_213748 3953 137 + 4094 AATGGGAAGGGCCTGATGTAATTTATGTGTGCTTGGCGGCTGTGTTTAAAGCTTGTGCAG-TGGAGGGGTGTAATTTGGAAAGCAATCTTCCCCAAGATCGGG-GGAAAGCAGTTTCTGGAAGGAAGGCT-GGCGGCTGC----------------------- i choHof1.scaffold_213748 C 0 N 0 s macEug1.Scaffold60637 4108 149 + 15229 AGAGGGATGGTGCTTATGTAATTCATGTGTCCTCCACGGGTGTGTTTAAAATGTGTGTGGTTGGAGGGGTATAATTTGAGAAGCGATTTTCCATAAGGTT-AA-GGAAAGTGGCACCTTTATGAAGGGTC-GGAGATAACCTGGC-----------CCAAGTT i macEug1.Scaffold60637 C 0 N 0 s monDom5.chr2 304298347 149 - 541556283 AGAGGGATGGTGCTTATGTAATTCATGTGTCCTCCATGGGCATGTTTAAAATGTGTGTGGTTGGAGGGGTATAATTTGAGAAGCAATTTTCCATAAGGTT-AA-GGAAAGTGGCACCTTTATGGAAGGTC-GAAGATAACCTGGC-----------TCAAGTT i monDom5.chr2 C 0 I 1812 e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I a score=122504.000000 s hg19.chr17_gl000204_random 24346 143 + 81310 CAGTGGGGCTGGGGGCCC----------------------------AGAA-CCC-TGGCC---ATGAGGCT--GATCC-----TAGTGGTA-----GGGAGTACC---GTGGGCTCAAAAT-CAGAAA---TGTTCCCCAAAATACAGCAACAACAACAAATCCTC---------AGCCTG---GCTATGGCTGG---------------------CT-----TGCTG----------GGCCA s panTro2.chr17 79197794 142 + 83384210 CAGT-GGGCTGGGGGCCC----------------------------AGAA-CCC-TGGCC---ATGAGGCT--GATCC-----TAGTGGTA-----GGGAGTACC---GTGGGCTCAAAAT-CAGAAA---TGTTCCCCAAAATACAGCAGCAACAACAAATCCTC---------AGCCTG---GCTATAGCTGG---------------------CT-----TGCTG----------GGCCA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9219644 142 + 17838096 CATT-GGGCTGGGGGCCC----------------------------AGAA-CCC-CGGCC---ATGAGGCT--GAGCC-----TGGTGGTA-----GGGAGTGCT---GTGGGCTCAAAAT-CAGAAA---TGTTCCCCAAAATACAGCAACAACAACAAATCCTC---------AGCCTG---GCTATGGCTGG---------------------CT-----TGCTG----------GGCCA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74751712 142 + 78773432 CACT-GGGTTGGGGGCCC----------------------------AGAA-CCC-TGGCC---ATGAGGCT--AACCC-----TAGTGGTA-----GGGAGTACT---GTGGGCCCCAAAC-CAGAAA---TGTTCCCCAAAATGCAGCAACAACAACAAATCTTC---------AGCCCG---GCTATGGCTGG---------------------CT-----CGGTA----------GGCCA i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_190290 1613 138 + 4572 C----CGGCTGAAAGCCC----------------------------AGAA-CCCATGGCC---ATGAGGCT--GGGCC-----CTGTGAT------GGGGGAACT---CCGGGTTCCAAAC-CAGAAA---TGTTCCCCTCAATACATTAACAACAAAAAAAC-TC---------AGCCTG---GCTATGGTTGA---------------------CT-----TACTA----------CGTAG i tarSyr1.scaffold_190290 C 0 C 0 s otoGar1.scaffold_94361.1-85690 47400 127 + 85690 G----GGGCTGGGGACCC----------------------------AGAAGCCC-TGCCT---GTGATGCT--GGAAT-----CAG-GCTG-----GAGGGTCTC---CT--GCTCCAAAC-CAGGCA---TGTCCCCCAAA----------TATGACATAACCTC---------AGCCCA---GCTGTGGCTGG---------------------CA-----TGTTA----------GGCTG i otoGar1.scaffold_94361.1-85690 C 0 C 0 s cavPor3.scaffold_76 4305988 170 + 7991924 C----AGGCT-GGGGCCT----------------------------GAAACTCC-CAGCC---ACGAGGCTGGGGAGG-----CAGCTGGG-----GAGAGAGAC---ATGTCCTCCAAATACAAGAACGCTGGTCCAG--------CCGTGGCCCAACAGGCCCCTAGGTGTCAAG--CA---GCTCTTGCTGACATGGGGCTGTCCACTAACCTGTCCCCGCACTA----------GGCCT i cavPor3.scaffold_76 C 0 I 17 s mm9.chr11 118675748 142 + 121843856 C----AGCCCAGGAGCCC----------------------------AGGAGCTC-CAGCT---ATGAGGCT--GGACC-----CAGCAGCA-----G-GAGAACT---CTGCACCTTAAAT-CATAAA---TGGCCCAGATA--AAAACAAAAACAAAAACGCCCC----AGCCCAGCCCA---GCTACGGCCGA---------------------GT-----CACCA----------GGCTT i mm9.chr11 C 0 I 472 s bosTau4.chr19 10764009 138 - 65312493 C----AAGCTGGGGGCTC----------------------------AGAA-CCG-CTGAC---GTGAGGCT--GGGAC-----CAGTGGCC------AAGGGACT---CCATGCCCTGACC-CTGAAA---TGTTCCCAAAA----------CACAGGAGAACTCC---------AGTCTA---GCTACTGCTGG---------------------CT-----CCCTGGGAGCCTTGAAGGCG i bosTau4.chr19 C 0 I 115 s equCab2.chr11 57952441 129 - 61308211 C----GACCTAGGGGCCC----------------------------AGAA-CCC-CTGCCC--CTGAGGCT--GGGAC-----CAGTGGCC------GAAGGACT---CCAGGCCCCAAAC-CAGTAA---TGTTCCCCAAA----------CCCAAGAGAAGGGC---------AGCCCA---GCTATGGCTGG---------------------GT-----GGCTT----------AGGCT i equCab2.chr11 C 0 I 1 s canFam2.chr9 59366398 166 - 64418924 T----ACAGGGGGAGCCCCAGGCCAGAAGTGTCCCCCAAATGCGGGAGAA-CTC-CAGCCCAGCTGTGGCT--GGGGTGCACACAACCGCCTGGTGAGGAGGAGTCACCCAGGGCACGATC-CA--AA---GCTTCCCCAGG----------CTCTC--------C---------AGCGCATTTTCCATGCTTCC---------------------CT-----CACCG----------AATCA i canFam2.chr9 C 0 I 1 s loxAfr3.scaffold_49 14298439 131 - 17734757 T----GGGCAGGGGACCC----------------------------AGAACCCC-TGGCC---ACGAGGCT--GGGAC-----CAGTGGC------GGAGGAACT---CCAGGCCCCAAAC-CATAAA---CGTTCCCAAAAATACA--------AGAAAAATTCC---------AGCCCA---GCTATGGTTGA---------------------CT-----TGCTA----------GGCTA i loxAfr3.scaffold_49 C 0 C 0 e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I a score=549.000000 s hg19.chr17_gl000204_random 24489 19 + 81310 CTTGGG---------------------------------TTT----------CAAGCA--------ACTC--------------- s panTro2.chr17 79197936 19 + 83384210 CTTGGG---------------------------------TTT----------CAAGCA--------ACTC--------------- i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9219786 19 + 17838096 CTTGGG---------------------------------TTT----------CAAGCA--------ATTC--------------- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74751854 19 + 78773432 CTTGGG---------------------------------TTT----------CAAGCA--------ACTC--------------- i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_190290 1751 19 + 4572 TTTGGG---------------------------------TTT----------CGAGCA--------ACTC--------------- i tarSyr1.scaffold_190290 C 0 M 1625 s otoGar1.scaffold_94361.1-85690 47527 19 + 85690 CTTGAG---------------------------------TTT----------CCAGCA--------CCCT--------------- i otoGar1.scaffold_94361.1-85690 C 0 I 29 s bosTau4.chr19 10764262 51 - 65312493 C-TTGGGCAGTGGTGGAGACACCAGGGAGTCACGTGCAAGCC----------CAAGCA--------ACTC--------------- i bosTau4.chr19 I 115 I 28 s equCab2.chr11 57952571 18 - 61308211 C-TTGG---------------------------------GTT----------CCAGCA--------GCTC--------------- i equCab2.chr11 I 1 I 190 s canFam2.chr9 59366565 18 - 64418924 C-CTGG---------------------------------GTC----------CCTGAG--------TCTA--------------- i canFam2.chr9 I 1 I 16 s cavPor3.scaffold_76 4306175 36 + 7991924 -TCAAG---------------------------------GACGGAGACGAGGCAAGCAGATGGGACACTC--------------- i cavPor3.scaffold_76 I 17 I 5 s loxAfr3.scaffold_49 14298570 34 - 17734757 CTTGGG---------------------------------TTT----------CTAGCA--------TTTCCAGACTTTCCTGCCC i loxAfr3.scaffold_49 C 0 C 0 e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e mm9.chr11 118675890 472 + 121843856 I a score=-38230.000000 s hg19.chr17_gl000204_random 24508 18 + 81310 ---------------------------ATTT---AGTTT-------------------------------------------------------------------------------CCA----GTTTCT s panTro2.chr17 79197955 18 + 83384210 ---------------------------ATTT---AGTTT-------------------------------------------------------------------------------CCA----GTTTCT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9219805 18 + 17838096 ---------------------------ATCT---AGTTT-------------------------------------------------------------------------------CCA----GGTTCT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74751873 18 + 78773432 ---------------------------ATCT---AGTTT-------------------------------------------------------------------------------CCA----GGTTCT i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 47575 61 + 85690 ---------------------------ATTTCCGGGCTTT-----CCTGGCAATTC---TCCCTGCACC-------------------ACCCCCCAC------------CAAGGCAGCCCA----GGTTCC i otoGar1.scaffold_94361.1-85690 I 29 C 0 s cavPor3.scaffold_76 4306216 16 + 7991924 ---------------------------ATCT---AGCT--------------------------------------------------------------------------------CTA----TT-TCT i cavPor3.scaffold_76 I 5 C 0 s bosTau4.chr19 10764341 22 - 65312493 ---------------------------ATCC---AAAGC-------------------------------------------------------------------------------CTTCTCAGTCTCT i bosTau4.chr19 I 28 I 132 s canFam2.chr9 59366599 18 - 64418924 ---------------------------ACCG---AGAGC-------------------------------------------------------------------------------CCT----GCTTCG i canFam2.chr9 I 16 C 0 s loxAfr3.scaffold_49 14298604 124 - 17734757 ATTTTTCCTCCCTCCTCTCACCAAGTCAGCC---AGTTTCTTACACCTGGGAGTCAAGGACCCGAGACCCTGGAATGGTAGACTAGGTACTTTAGACAGTTGGGGAACACCAGGTCACCTA----GTTTCT i loxAfr3.scaffold_49 C 0 C 0 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57952589 190 - 61308211 I e mm9.chr11 118675890 472 + 121843856 I a score=2402.000000 s hg19.chr17_gl000204_random 24526 23 + 81310 GG-----------------------------------------------------CCCTT-------------CCAGAGAGCATCA--------------CTG s panTro2.chr17 79197973 23 + 83384210 GG-----------------------------------------------------CCCTT-------------CCAGAGAGCATCA--------------CTG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9219823 23 + 17838096 GG-----------------------------------------------------TCCTT-------------CCAGAGAGCATCA--------------CTG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74751891 21 + 78773432 GG-----------------------------------------------------CCCTT-------------CCAGAGAG--TCA--------------TTG i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 47636 48 + 85690 TG-----------------------------------------------------CACTT--GGAATCTGTGACCCGAGACCTCCAGACGGTGAATTAAGCTG i otoGar1.scaffold_94361.1-85690 C 0 C 0 s mm9.chr11 118676362 76 + 121843856 GGGTCTGCCCTAGCACACCAAGGGAGTGCTGATCACCTAGCATTCCACATGCTGACCCTT-------------AAAGAAAGCACCA--------------CTG i mm9.chr11 I 472 I 10 s cavPor3.scaffold_76 4306232 23 + 7991924 GG-----------------------------------------------------CCCTT-------------CCAGAAAGCAACA--------------TTG i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10764495 23 - 65312493 GG-----------------------------------------------------CCCTT-------------CCAGAAAGCACCA--------------TTC i bosTau4.chr19 I 132 C 0 s canFam2.chr9 59366617 36 - 64418924 GG-----------------------------------------------------CACTCAGGGAACTTGAGGCCAGCAGGCCCTT--------------TCC i canFam2.chr9 C 0 I 2 s loxAfr3.scaffold_49 14298728 29 - 17734757 ---------------------------------------GTACTCTA--------CCATT-------------GCAGAAGGTGCca--------------ttc i loxAfr3.scaffold_49 C 0 C 0 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57952589 190 - 61308211 I a score=14755.000000 s hg19.chr17_gl000204_random 24549 103 + 81310 CTGTGC------TAAACAT-------CCAT-G------------AGTCCCTCCTG-------------C-ATG---GATACTGGGG-CACAGCTGGGA-ACACCACAGGCACCTG---TTGAGGGGCCTGCAGTGTagagagagagagaga s panTro2.chr17 79197996 81 + 83384210 CTGTGC------TAAACAT-------CCAT-G------------AATCCCTCCTG-------------C-ATG---GATACTGGGG-CACAGCTGGGA-ACACCACAGGCACCTG---TTGAGGGGCCT---------------------- i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9219846 101 + 17838096 CTGTGC------TAAACAT-------CCAT-G------------AGTCCCTCCTG-------------C-ATG---GATACTGGGG-CACAGCTAGGA-ACACCACAGGCACCTG---TTGAGGGGCCTGCAGTGT--agagagagagaga i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74751912 93 + 78773432 CTGTGC------TAAACAT-------TCAT-G------------AGTCCCTCCCG-------------C-ATG---GATACTGGGG-CACAGCTGGAA-ACAGCACAGGCACCTG---TTGTGGGACCTGCAGTGT----------AGAGA i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 47684 136 + 85690 CTGCACACTTAGTGAACATCAGGTTACCCT-GCTCCGATATTCTGGTCCTTCCAGAAagcaccattgcc-atgtcagacactggggacacagagaaga-atgccacctggacctt-ccctgtggggcttgcagtgc----------agag- i otoGar1.scaffold_94361.1-85690 C 0 C 0 s mm9.chr11 118676448 56 + 121843856 CTATGC------TGGGGAC-------AAA-------------------------G-----------------G---AACACCATGG--------GGAC-ATGTTGCTAAGAA-------------GCTTACAGTAG--------------- i mm9.chr11 I 10 C 0 s cavPor3.scaffold_76 4306255 69 + 7991924 CTGTGC------TGAGAAT-------AGAT-G-------------------CGGG-----------------G---GACAC----A--------GACA-ATGCTGCAGAAAACTG-TCCCCACAGACTTGCTATGG--------------- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10764518 88 - 65312493 CTGCGA------TGCATGT-------CCATCA------------AGTCCCTT------------------CTA---GATGCTAGGGACACAGGTCGGAGACACCACCCTGATCTGCCCCCAAGAAACTTGC-----------------AGA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57952779 97 - 61308211 CTGTGC------TCaacat-------ccatcg------------agtccctccta-------------tgcta---gatgctggggatacagatgaga-atgccacatggacctgtccccaagcagcctgcagtat------------aga i equCab2.chr11 I 190 C 0 s canFam2.chr9 59366655 97 - 64418924 AAGCAC------TGAACAT-------TCATCA------------AGACCCTCCCA-------------CACTA---GATGCCGGGGACACAGATGAGA-ACACCACGCGGGCCTGTCCTCCAGCGGGCCGCTGTGC------------AGA i canFam2.chr9 I 2 C 0 s loxAfr3.scaffold_49 14298757 109 - 17734757 ctgcgg------tgaacac-------ccactg------------agcccctccag-------------tgttg---gatgctagggatgcaggagtga-acacgacatggacttgtccccagggagcttgcagtttagagggagagatgga i loxAfr3.scaffold_49 C 0 I 2295 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I a score=-11358.000000 s hg19.chr17_gl000204_random 24652 74 + 81310 gagagagagaACAGGT-AAACCACAACCCC---A-GAGGCAGGGTATGGG------ctcctacaagatggcaagctctagaaggt s panTro2.chr17 79198077 12 + 83384210 -------------------------------------------------------------------------gctctagaaggt i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9219947 74 + 17838096 gagagagagaACAGGT-AAACCACAACCCC---A-GAGGCAGGGTATGGG------ctcctacaagatggcaagctctagaaggt i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74752005 77 + 78773432 GAGAGAGAGAACAGGT-AAACCACAACCCCAGGA-GAGGCGgtgtatggg------ctcctacaagatggcaagctccagaatgt i rheMac2.chr16 C 0 I 333 s otoGar1.scaffold_94361.1-85690 47820 44 + 85690 ---------------------------------a-gaggTGGGGTACAGG------CTCACAC-AGCCGGCAGGCACCACAGGCC i otoGar1.scaffold_94361.1-85690 C 0 C 0 s mm9.chr11 118676504 53 + 121843856 ---AGACACAACAGCC-AGCCGACTACCAC---A-GTGGAGGTGGACAAG---------CCTT-GAA-------------AAGG- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4306324 75 + 7991924 ---AGCAATGGCAGGC-AACCAACCATCCC---ACACAGCGGGGGACAAGGGAAGGCTCCTGC-ggatggca-gctcctcaagg- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10764606 75 - 65312493 GGGAGAGATGACGATA-AACCAAAAATCTGGGCT-GAAGTGGGCTAAGGG------TTCACACG-GATGgcaagctccagagag- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57952876 73 - 61308211 gggagagatgaca----aaccaaatatcccagca-gaggtgggataaggg------ctcacatgagatggcaagtgccacagga- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59366752 77 - 64418924 GGGACAGATGACGAAGCAACCAGAGGTCCCATGA-GACATGGGAGAAGGG------CCTGCATGAGACGTAGAGGGCCACGGGG- i canFam2.chr9 C 0 C 0 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=130391.000000 s hg19.chr17_gl000204_random 24726 151 + 81310 tggggccttatttttctcagcaccacagctaagccatcgagaatggtgcctggcacaccccaggtgctaagcaaacatgcttgagtg-agtgcatGAAAGAGTGAAGAGCCAAT-AGAGAGACATGGGTGACGGGTGTCTAGGAACCTAAGCA s panTro2.chr17 79198089 151 + 83384210 tggggccttatttttctcagcaccacagctaagccatcgagaatggtgcctggcacaccccaggtgctaagcaaacatgcttgagtg-agtgcatgaaAGAGTGAAGAGCCAAT-AGAGAGACATGGGTGATGGGTGTCTAGGAACCTAAGCA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9220021 151 + 17838096 tggggccttatttttctcggcaccacagctaagccatcgagaatggtgcctggcacaccccaggtgctaagcaaacatgcttgagtg-agtgcatgaaAGAGTGAAGAGCCAAT-AGACAGACATGGGTGATGGGTGTCTGGGAACCTAAGCA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74752415 150 + 78773432 tggggccttatttttctgagcgccacagctaagccattgagaatggtgcctggcacacccca-gtgctaagcaaacatgcttgagtg-agtgcatGAAAGAGTGAAAAGCCAAT-AGAGAGACATGGGTGATGGGCGTCTGGGAACCTAAGCA i rheMac2.chr16 I 333 C 0 s otoGar1.scaffold_94361.1-85690 47864 135 + 85690 TAGGgcc-tgtcttgctcaatgccacagcta--------agaacggtgactggcacacaacagatgctaagtcaatatgtgtgagtg-TGTACGCCGAGGAG----GTGCTAAC-AGAGAGA---GGGTGACAGGTGCTCGGAAACCTAACCA i otoGar1.scaffold_94361.1-85690 C 0 I 572 s mm9.chr11 118676557 108 + 121843856 AGGGATCTT-CCTTGTACCATGTCACACCTAGG--------------GCCTGGCATAAGGCAAGTGCTATATCGAGACATTTGAGCA-ACTG----ACAGAATAAAATGTCAATGAGAGAGACGGAGA------------------------- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4306399 114 + 7991924 gggaaccttgttttgctccatgccatgcccaaggtgctgggcaccctgcccagtatatagcaggtgtggaaacaatgtgtctgagtg-aat-------------aaatGACTTTCTGATGGGCAGGGA------------------------- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10764681 150 - 65312493 cagaccttcgttttgctcggtgccacattcctggcacctagaacagtgcctgacacgtggcaggtgttaaatgagtgcgttcgagtg-atggaatGAAGGAGTGAAGTGCCACTGAGAGGGATGGGCA--GAGGATGTGTGGAACCCAGGGCA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57952949 148 - 61308211 cagactttaggtctgctcggtggcgtgctcttggcacccagaacagtgcctggcacacagcaggcgctaactgagcatctgggtgagcgatgaacgaatGGACGGAG-TGCAGTGAGAGAGACGGTGA---AGGAGGGGTGGAAACC-CAGCA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59366829 136 - 64418924 CAGATCTGAgttgtgcccggtgg------------gtctagaacggtgcctggcacacaacaggtgctcgggaaacacgtgtgaggg-gctgaatGCACAGACGAGC-GCCACCAATGGAGACGGGTA---AGGGTGTTTGGGATCCTCAGCA i canFam2.chr9 C 0 C 0 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=35995.000000 s hg19.chr17_gl000204_random 24877 113 + 81310 GAG----GTACTGCATTCAT----GGGAG---GTGTTCTGGCTTCCTA----GGGCAGGTGACCAACCCTGGAGTGAATCggagagga-gag---gggaggggaggaaaggagaggggaggggaggggaggg s panTro2.chr17 79198240 112 + 83384210 GAG----GTACTGCATTCAT----GGGAG---GTGTTCTGGCTTCCTA----GGGCAGGTGACCGACCCTGGAGTGAATCggagagaa-ga----gggaggggaggagaggggaggggaggagagaggaggg i panTro2.chr17 C 0 I 333 s ponAbe2.chr17_random 9220172 73 + 17838096 GAG----GTACTGCATTCAT----GGGAG---GTGTTCTGGCTTCCTA----GGGCAGGTGACCGACCCTGGAGTGAATCggagagga-------------------------------------------- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74752565 76 + 78773432 GGG----GTACTGCATTCGT----GGGAG---GTGTTCTAGCTTCCTA----GGGCAGGTGACCGACTCTGGAGTGAATCAGAGAGGGGCA----------------------------------------- i rheMac2.chr16 C 0 C 0 s mm9.chr11 118676665 99 + 121843856 -AA----GCACCACATGCGT----GGGGGAGGGTGTTCTGGCTTCCCAGATGGAGCTGGTGACAGACCCCAGAGAG-------------------GGATggggaagaaagaggaggagaggaggggg----- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4306513 80 + 7991924 --------CACCACACTCGT----GGAGG-GAGTGTTATGGCTCCTGA----------GTAATGGACCCT-----G-------------------GAATGAGTCAAACAGAGGAGGGGGAGTGGGAG----- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10764831 88 - 65312493 GAG----GCTCCTCCCTCATCCTGAGAGG---GTGTTCTTGC-TCCCA----GAGGAGGTG-CCAACCTTGGAGTGAG--CGAGAGAC----TCAAGGAGAGGAGag------------------------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57953097 85 - 61308211 GAG----GCGCCTCACTCATCTCGACGGG---G-GTTCTAGCTTCCCG----GGTGAGGTGACCCACCCTGGAGGGAGTCTTAAAGGT----CCAAGGAGG------------------------------- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59366965 82 - 64418924 GAGGGCAGCACCTCGCTCAGCCCGAGAGG---ATGCTCTTGCTTCCCA----GAGGAGGTGACCCACCCTGGAGGGAGTCCTAAAGGC----T--------------------------------------- i canFam2.chr9 C 0 C 0 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=-3431.000000 s hg19.chr17_gl000204_random 24990 88 + 81310 gaggcgaggggaggggaggggaggggaggggaggggaggggaggggaagggaggggaggggaggggaagggaggggaggggaggggag s cavPor3.scaffold_76 4306593 5 + 7991924 -----------------------------------------------------------------------------------GAGAG i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118676764 43 + 121843856 ----------------------aggaagaagaagagagaggagacggaggaagaagagg-----------------------agaaag i mm9.chr11 C 0 C 0 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e panTro2.chr17 79198352 333 + 83384210 I e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59367047 0 - 64418924 C e bosTau4.chr19 10764919 0 - 65312493 C e equCab2.chr11 57953182 0 - 61308211 C e loxAfr3.scaffold_49 14298866 2295 - 17734757 I e ponAbe2.chr17_random 9220245 0 + 17838096 C e rheMac2.chr16 74752641 0 + 78773432 C a score=271813.000000 s hg19.chr17_gl000204_random 25078 242 + 81310 gggaggagaggggaggggaggagagaggagggcaggTGCAGAGCCTTGGACAGAAGGGGTAGAGGAAATGT---CATCTAGGGAATGCAAATAATAG---AGGAAGTTTAGGACTAGGTg-tagcaggagatgagaccagac-atataagttagaaaccagatcaggaagtaccttgaacaccatgccaaggactttaaaaagccatttgaggaa-ttttaagtaggacatgatgaagatttgggtattcg s cavPor3.scaffold_76 4306598 223 + 7991924 GCCAGGAGAG---------GAAGAAGAGGCAGCAGATCCTG-----------GAGGAGGCCAGGGGGACGT---CTTCTAGGGAACGTAAATAATGGAGCAGGTGGTTTGGGACTGGGTG-TACC-GAAGATGTGACTGGCCAATGTAAGTCAGGAGCCAGATCAAGAAGCACCTTGCATACCAT-CCGAGGAC-TTAAAAAGCCATTTGAAGAA-TTTTAAGCAGGAGACAATGCAGATTTGTGTTTTAG i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118676807 216 + 121843856 agaaggagAG-GCAGGGCAGAGGAAGAGACAGCAGGTGTCAAAT--------GAGAAAGCCACAGGAAAGTGACTTTCTGGG---TGTAGA------------------GAGATGGGACA-AAGC-AGAGACAGGGCTGTCCTGTG-AAGTCAGGAGTCAGATCA--CAGCGCCTTGAAAGCCACACCAAGGACTTTATGAAGTCACTTGGTGAATTTTTAAACGGGAAGCTATGCAGATTCATGTCTTAG i mm9.chr11 C 0 C 0 s panTro2.chr17 79198685 242 + 83384210 gggaggagagaggatgggaggagagaggagggcaggTGCAGAGCCTTGGACAGAAGGGGTAGGGGAAATGT---CATCTAGGGAATGCAAATAATAG---AGGAAGTTTAGGACTAGTGg-tagcaggagatgagaccagac-atataagttagaaaccagatcaggaagtaccttgaacaccatgccaaggattttaaaaagccatttgaggaa-ttttaagtaggacatgatgaagatttgggtattcg i panTro2.chr17 I 333 C 0 s ponAbe2.chr17_random 9220245 238 + 17838096 --gaggagaggggaggggaggacagaggaggGCAGGTGCAGAGCCTTGGACAGAAGGGGCAGGGGAAATAT---CATCTAGGGAATGCAAATAATAG---AGGAAGTTTAGGACTAGggg-tagcaggagatgagaccagac-atat--gtcagaaaccagatcaggaagtaccttgaacaccatgccaaggacttgaaaaagccatttgaggaa-ttttaagcaggacatgatgaagatttgggtattcg i ponAbe2.chr17_random C 0 C 0 s bosTau4.chr19 10764919 219 - 65312493 ----------------------gcggagacagcaggtgcagagccaagcaa-ggaggagcaggtgagatgt---cttcca-gggatgcagataatggggcaggaggtgtgggattggaag-tactgag-gacgacactggcc-a-gcaagtcaagaatcagatcatgaagcaccttgaacgtcacaccaaggactttaaaagctctcttgaagaa-tttcaagcaggaaacgaggcagatgtgtgccttac i bosTau4.chr19 C 0 I 1 s equCab2.chr11 57953182 234 - 61308211 ---------TGGGGGGGGATGGGAGGGGACAGCATATATGGAGCCACGCCA-CGAGGAACAGGTGCCATGT---CTTCCAGGGGGTGCAAATAACGGAGCAGGAGGTTTGCGA-TGCATA-TGCTGGGAGACGAGACTGGCC-ACACAGGTCTGGAACGAGCTCGTGACACACCTTGAACACCAGTCCAAGGACTTTAAAGGGCCACTTGAAGAA-TTTTAAGTGGGAAACTATGCATATTTGTGTCTTGG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59367047 205 - 64418924 ---------TGGGAGCGGAGCAGGTGATCCAGCAGGTATGGAACCACACGG-GAGGGGCTGGAAG--GTGT---CTTCCA-----------------AGCCTGGGACTAG-------ACA-tgctggaagatgaggct-gcc-gtgtaagtcgggaaccagatcatgcggcacctggaacaccacgccaaggacccgcaatggccacttgaagaa-ttttaagcaggaaactatgcagacttgtgtct--- i canFam2.chr9 C 0 I 211 s rheMac2.chr16 74752641 233 + 78773432 ----------GGGAGGGGAGGagagaggagggcaggtgcagagccttggacagaaggggcaggggaaacgt---catctagggaatgcaaataatag---aagaagtttgggactgggggatagcaggagatgagaccagac-atataagtcaggaaccagatcaggaagtaccttgaacaccgtacaaaggactttaaaaagccgtttgaggaa-ttttaagcaggacatgatgcagatttgggtattcg i rheMac2.chr16 C 0 C 0 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=105437.000000 s hg19.chr17_gl000204_random 25320 146 + 81310 gaagcacgctctggtgccgatgtgggctgggtagaggg----gaaaaac--caaggcaggaatctcagta-gggaggtggcccaggtgatccaAT----------GGCCTACGGAAGGGC-GGATGGAG-TTA-GTGACTGTGAACACCAGGACTCGGTGACCAGT s ponAbe2.chr17_random 9220483 147 + 17838096 gaagcacactctggtgccaatgtgggctgggtagaggg----gaaaaac--caaggcaggaatctcagtg-gggaggTGGCCCAGGTGATCCAAT----------GGCTTATGGAAGGGC-GGATGGAGATTA-GTGACTGCGAACACCAGGACTCGGTGACCAGT i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79198927 146 + 83384210 gaagcatgctctggtgccgatgtgggctgggtagatgg----gaaaaac--caaggcaggaatctcagta-gggaggcggcccaggtgatccaAT----------GGCTTACGGAAAGGC-GGATGGAG-TTA-GTGACTGTGAACACCAGGACTCGGTGACCAGT i panTro2.chr17 C 0 C 0 s rheMac2.chr16 74752874 147 + 78773432 gaagcatgctctggtgctgatgtgggcctggtagaggg----gaaaaac--caaggcaggaatctcagcg-gggaggcggcccaggtgatccaAT----------GGCTTACGGAAAGGC-GGATGGAGATTA-GTGACTGCGAACACCAGGATTTGGTGACCAGT i rheMac2.chr16 C 0 C 0 s mm9.chr11 118677023 154 + 121843856 GAGT-GCATCCTGGTGTCTGGGAGGACCCCGCGGACAT----GTGAAAA--CAAGCCAGGAATCTCAATC----AGCCTCTCCAGGCGATCAGATGAGACGTGCAGGCTTTCGGAGGGGCAAGGTGGAAACCA-GATGATGTGGTCAGCAGTGTACAGAAACCAGT i mm9.chr11 C 0 I 698 s cavPor3.scaffold_76 4306821 158 + 7991924 GAATCATGCTTTGGTGCCAGTGCAGACCTGGTGGACAGCGGAGTACAAA--CAAGGCAGGCATCTCAATC----AGCAGCCACAGGTGAGTGGATGAGCACTGCAGACCTTCAGAAGGGC-GGGAGGGGACCA-ATGAACGTTGTCACCAGGACTTGGTGATCGGT i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10765139 151 - 65312493 gatgcttgctctcgtgccaatgtggacaggatggaggg---agtaaaaa-ccaaggcaggaatctcaatcaggaggctgtcaccaggaatcaagtgagaaaCTAAGATTTGGGAAAGGGC-AGAAGGAGGTTG-----GTATGATAGACAGGACTTAGGGA----- i bosTau4.chr19 I 1 I 72 s equCab2.chr11 57953416 137 - 61308211 GAA----------GTGCCACTGTGGATGGG--TGGAGG---TGTGAAAA--CCAAGCAGGAAT---CACCTGGGAGGGAGCTGCCGGGATCACAGGAGAAATGAAGACTCGGGAAGGGGC-GGGCGGAGACGGCTTGAGTGCGATGGACAGGACTCAG-------- i equCab2.chr11 C 0 I 930 s canFam2.chr9 59367463 103 - 64418924 GAAGCTCAATCTGGCACCAGTGAGGATGGGGTGGAAGG---AGTTAAAAATCAAAGCAGGAATCTCCACCTGGAGGCAACCCCTGGCGATCATACAAGAAACTGAG------------------------------------------------------------ i canFam2.chr9 I 211 C 0 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=108304.000000 s hg19.chr17_gl000204_random 25466 208 + 81310 CCCACCCACATGGGAGATGA-GGAAGACGCAAGCCACCTCCCGGGTTTCGGGTTTGTCCAACTACATAAATAGGGGGCCAGTTTGTGATAAGGTGAGGAGGAAGAAGTTGGGCTTGGGAGACCAGGACATCAGGAAATTGCAGTGCAGGGGCCTTCAGCTTGG-TGATGGTGTCATTTATCGCATTATTACCCACAGTCTACTCTGCTAT s ponAbe2.chr17_random 9220630 207 + 17838096 CCCACCCACATGGGAGATGA-GGAAGACACAAGCCACCTGCCGGGTTTCGGGTTTGTCCAACTACATAAATAGGGGGCCAGTTTGTGATAAGGTAAGGAGGAAGAAGGTGGGCTTGGGAGACCATGACATCAGGAAGTTACAGTGCAGGGGCCTTCAGCTTAG-TGATGGTGTCATTTATCGCATTATTACCCACAGTCCACTCTGCTA- i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79199073 208 + 83384210 CCCACCCACATGGGAGATGA-GGAAGACGCAAGCCACCTCCCAGGTTTCGGGTTTGTCAAACTACATAAATAGGGGGCCAGTTTGTGATAAGGTGAGGAGGAGGAAGTTGGGCTTGGGAGACCATGACATCAGGAAGTTGCAGTGCAGGGGCCTTCCGCTTGG-TGATGGTGTCATTTATCGCATTATTACCCATGGTCCACTCTGCTAT i panTro2.chr17 C 0 C 0 s rheMac2.chr16 74753021 207 + 78773432 CCCACCCACATGGGAGATGA-GGAAGACACAAGCCACCTCCCA-GTTTCGGGTTTGTCCAGCTATAAAAATAGGGAGCCAGTTTGTGATAAGGTGAGGAGGAAGAAGGTGGGCTTGGGAGACCAAGACATCAGGAAGTTACAGTGCAGGGGCCTTCAGCTCGG-TGAAGGTGTCATTTATCACATTATCACCTGCAGTCCACTCTGCTAT i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4306979 192 + 7991924 CCCACAGGCAGGGGAGAGGGCGGAGAATGGAAGCCACTGCTGAAGCTTCTGGTTTGCCCAGCTAC-TAGGTAGGGTGCTGGCTTGTAATAAGGTT--------GGAGCGGTGCTGGGAGGCTCATGCTGTTAGGAAAGTTTATAGCAGA---CTTCAGCAGGGCTGACAAGGTGGTTG-----ATTATTACACACAG-CTATGGTGCTAT i cavPor3.scaffold_76 C 0 C 0 s canFam2.chr9 59367566 126 - 64418924 ---ACACACAAGGTGGATAG-AGA------------------------CTGGTCAG------------GATGGTGGGCAGGAccggggcgggggggggggggggA-------------------------------------------GGGTTCCCAGCTGGGTTGATGATGCAGGTTGTTATAGGGTTACGTGTGCTCC-CTACAGTAT i canFam2.chr9 C 0 C 0 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e bosTau4.chr19 10765290 72 - 65312493 I e equCab2.chr11 57953553 930 - 61308211 I e mm9.chr11 118677177 698 + 121843856 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=26911.000000 s hg19.chr17_gl000204_random 25674 35 + 81310 TCCTTACACCTTTTCCTATGTTAAAAATGGCACAA s ponAbe2.chr17_random 9220837 23 + 17838096 ------------TTCCTATGTTAAACATGGCACAA i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79199281 35 + 83384210 TCCTTACACCTTTTCCTATGTTAAAAATGGCACAA i panTro2.chr17 C 0 C 0 s rheMac2.chr16 74753228 35 + 78773432 TCCTTACACCTTTTCCTATGTTAAAAATGGCACGA i rheMac2.chr16 C 0 C 0 s mm9.chr11 118677875 34 + 121843856 TCGTTATCCCCTTTCCTATGTTAAAAATAGCACG- i mm9.chr11 I 698 I 84 s cavPor3.scaffold_76 4307171 34 + 7991924 -CCTGGACGCCTTTCTGGTGTTAAAAATGGCATAA i cavPor3.scaffold_76 C 0 C 0 s canFam2.chr9 59367692 34 - 64418924 TCCTGACACCTCAATATATGTTAACAGCTACCTA- i canFam2.chr9 C 0 C 0 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e bosTau4.chr19 10765290 72 - 65312493 I e equCab2.chr11 57953553 930 - 61308211 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=129378.000000 s hg19.chr17_gl000204_random 25709 255 + 81310 ggccgggcatggtggttcatacctgtaatcccagcactttgggaggccaaggtgggcagatcacttgaggtcaggagttcaagaccagcctggccaacatggtgaaaccctgtctctactaaaaaactacaaaaattagtcaagtatggtggtgcatacctgaaatcccagctactcgagaggcaggagaattgcatgaacctgggaggtggaaattgcggtgagccaagatcatgccattgcactccagcctgg s ponAbe2.chr17_random 9220860 253 + 17838096 ggccgggcatggtggctcatacctgtaatcacagcactttgggaggccaaggtgggcagatcacttgaggtcaggagtttgagaccagcctggccaacatggtgaaaccctgtctt--ctaaaaaactacaaaaattagtcaagtgtggtggcacatacctgaaatcccagctactcgggaggcaggagaattgcacgaacctgggaggtggaaattgcggtgagccaagatcacgccactgcactccagcctgg i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79199316 255 + 83384210 ggccgggcatggtggttcatacctgtaatcccagcactttgggaggccaaggtgggcagatcacttgaggtcaggagttcgagaccagcctggccaacatggtgaaaccctgtctctactaaaaaactacaaaaattagtcaagtatggtggtgcatacctgaaatcccagctactcgagaggcaggagaattgcatgaacctgggaggtggaaattgcggtgagccaagatcatgccactgcactccagcctgg i panTro2.chr17 C 0 C 0 s rheMac2.chr16 74753263 255 + 78773432 ggctgggcacagtggctcatacctgtaatcccagcactttgggaagccaaggtgggcggatcgcttgaggtccggagtttgagaccagcctggccaacgtggtgaaaccctgtctctacttaaaaactacaaaaattagtcaagcgtggcagcacacacctaaaatcccagctattctggaggcaggagaattgcatgaacccgggaggcagaggttgcagtgagccaagatcaggccactgcactccagcctgg i rheMac2.chr16 C 0 C 0 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e gorGor1.Supercontig_0080755 1643 2340 - 4970 M e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59367726 0 - 64418924 C e bosTau4.chr19 10765290 72 - 65312493 I e equCab2.chr11 57953553 930 - 61308211 I e cavPor3.scaffold_76 4307205 0 + 7991924 C e mm9.chr11 118677909 84 + 121843856 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=35900.000000 s hg19.chr17_gl000204_random 25964 42 + 81310 atgacagagcaagactctgtctcaaaaacaaaacaaaaaaga s rheMac2.chr16 74753518 40 + 78773432 atgacagagcaaga--ctgtctcaagaacaaaacaaagaaga i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9221113 42 + 17838096 atgacagagcaagactctgtctcaaaaacaaaacaaaaaaga i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0080755 3983 42 - 4970 ATGACAGAGCAAGACTCTGTCTCAAAAACAAAACAAAAAAGA i gorGor1.Supercontig_0080755 M 2340 C 0 s panTro2.chr17 79199571 42 + 83384210 atgacagagcaagactctgtctcaaaaacaaaacaaaaaaga i panTro2.chr17 C 0 C 0 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59367726 0 - 64418924 C e bosTau4.chr19 10765290 72 - 65312493 I e equCab2.chr11 57953553 930 - 61308211 I e cavPor3.scaffold_76 4307205 0 + 7991924 C e mm9.chr11 118677909 84 + 121843856 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=102226.000000 s hg19.chr17_gl000204_random 26006 106 + 81310 aaTGGCACAGTATGATGTTTCA------AGGCCGATGGGGCTGAGCTCACA-CTGGACATGCTGAGTTTGAAGAGCCCCTGGAATGTCGGGGA--GGAGGGTTGGTCAGT-GGTGG----- s panTro2.chr17 79199613 106 + 83384210 aaTGGCACAATATGATGTTTCA------AGGCCGATGGGGCTGAGCTCACG-TTGGACATGCTGAGTTTGAAGAGCCCCTGGAATGTCGGGGA--GGAGGGTTGGTCAGT-GGTGG----- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0080755 4025 106 - 4970 AATGGCACAATATGATGTTTCA------AGGCCGATGGGGCTGAGCTCACA-TTGGACATGCTGAGTTTGAAGAGCCCCTGGAATGTCGGGGA--GGAGGGTTGGTCAGT-GGTGG----- i gorGor1.Supercontig_0080755 C 0 C 0 s ponAbe2.chr17_random 9221155 106 + 17838096 aaTGGCACAATATGATGTTTCA------AGGCCGATGGGGCTGAGCTCACA-TTGGACACGCTGAGTTTGAAGAGCCCCTGGAATGTCGGGGA--GG-GGGCTGGTCAGTGGGTGG----- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74753558 107 + 78773432 aaTGGCACCATATGATGTTTCA------AGGCCGATGGGGCTGAGCTCACA-TTGGACGTGCTAAGTTTGAAGAGCCCCTGGAATGTCCAGGA--AGGTGGTTGGTCAGTGGGTGG----- i rheMac2.chr16 C 0 C 0 s bosTau4.chr19 10765362 99 - 65312493 AATTGCATAATACAATTTTTCC------AGGTTTGTGGAGTTGGAC---------------ATGTGTTCAAAGCGCCCCTGGTATGTCGGGGG-TGGGGTGATATTTGGTAGATGGTTGGG i bosTau4.chr19 I 72 C 0 s canFam2.chr9 59367726 110 - 64418924 -----------ATAAGGTTTCCCAACCAAGGCTTGTGAGGTTGGCTTCAGACTTGGGCCTGTTGTGCTTGAAGAGCCCCTGGCACATCAGGGGCTGGGGGGATATGTAGCAGGTGGCTGAG i canFam2.chr9 C 0 C 0 s cavPor3.scaffold_76 4307205 92 + 7991924 ----------TACAATGTTTCA------CGGCTGCAGGTG--GAGTTCAGA-CTGGACAGGTTGAACCGGAAGGG--CCTGTGGTGGAGGGAC--AGAGAGATGCTTGGT-AGGGG----- i cavPor3.scaffold_76 C 0 I 99 s mm9.chr11 118677993 73 + 121843856 ----------TAATATATTTCA------AGGCTTGTGGGG--CTGTTAAGA-CTGAACA--------------GA--CCTGAGGT-----GAC--ACAGGAGTAGCTGGG-AGTAG----- i mm9.chr11 I 84 I 5 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57953553 930 - 61308211 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=242942.000000 s hg19.chr17_gl000204_random 26112 217 + 81310 TGCTAGCATCCAAGCT---GGAGAGAATCCTGCCTGCACTGGGGACtgtggcagtccaggctctaagacagc-------ccctgt-gtcttca-cctcctggtgcccagacaccccctggtgtcacctcccctgtcataccagcactggtctgtgtgaccaatagaattcagcagaagtgaaggttcatcaattctaagattaggtcttaaaagagctccatctttctc s rheMac2.chr16 74753665 208 + 78773432 TGCTAGCATCTAAACT---GGAGAGAATCCTGTCTGCACTGGGGACtgtggcag-ccaggttccaagacagc-------ccctgt-gtcttca-cctcctggtgcccaga--------gttgtcccctcgcctgtcataccagcattggtctgtgtgaccaatagaattcagcagaagtgaaggttcatcaattctaagattaggtcttaaaagacctccatctttctc i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9221261 208 + 17838096 TGCTAGCATCTAAGCT---GGAGAGAATCCTGTCTGCATTGGGGACCgtggcag-ccaggctctaagacagc-------ccctgt-gtcttca-cctcctggtgcccaga--------attgtcacctcccctgtcataccagcattggtctgtgtgaccaatagaattcagcagaagtgaagattcatcaattctaagattaggtcttaaaagacctccatctttctc i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0080755 4131 217 - 4970 CGCTAGCATCTAAGCT---GGAGAGAATCCTGCCTGCACTGGGGACtgtggcagtccaggctctaagacagc-------ccctgt-gtcttca-cctcctggtgcccagacaccccctggtgtcacctcccctgtcataccagcattggtctgtgtgaccaatagaattcagcagaagtgaaggttcatcaattctaagattaggtctgaaaagacctccatctttctc i gorGor1.Supercontig_0080755 C 0 C 0 s panTro2.chr17 79199719 217 + 83384210 TGCTAGCATCTAAGCT---GGAGAGAATCCTGCCTGCACTGGGGCCtgtggcagtccaggctctaagacagc-------ccctgt-gtcttca-cctcctggtgcccagacaccccctggtgtcacctcccctgtcataccagcattggtctgtgtgaccaatagaattcagcagaagtaaaagttcatcaattctaagattagatcttaaaagacctccatctttctc i panTro2.chr17 C 0 C 0 s mm9.chr11 118678071 184 + 121843856 TGCTTAGACCTAAGGTTTAAGGAAGAGGCCTCCCTGCTTTGGGGGCCATGGTAA-CCAGCCTCCAGAGTGACTATGTGATCCTAA-CTCTCTACCCTCTTTGTTCC----------------TCACCTCC-------TAGCTGGGTC-ATCTGTGTGAACAAGAGATACAACCAGTAAGGCAGG-----CATATGCAAACTCAGGTCACCGAAGA-------------- i mm9.chr11 I 5 C 0 s bosTau4.chr19 10765461 194 - 65312493 TGCTGGGATCTAAGACTTAGGAAACAGTCTTGTCTGCTTTAGAGATtgtggcag-cccacctccaaggtggc-------ccctataattctca-cctccaatcctcttat--------gtagcccctgctcacatcagaccagggctggtctgtgtaaccacgagaacatggctgaagtgattgtggatcgattctgaggtcaggtcat------------------ac i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59367836 202 - 64418924 TGCCAGGACCTAGGGTTTGGGAGACAATCTTGTCTGCTTTGGGGGCtgtggca--ccagcctccaggacagc-------gctgacagtcctca-cttcctgtcccctggc--------gcagtcccctcccacctcacgccagggctgggctctgcaaccactggaatgcag-tgaagtgatggcgtctcagttctcagatcaggtcatgaatga--------TGTCAC i canFam2.chr9 C 0 C 0 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57953553 930 - 61308211 I e cavPor3.scaffold_76 4307297 99 + 7991924 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=60043.000000 s hg19.chr17_gl000204_random 26329 35 + 81310 tcactctggaggaagtcagccgccctgtcatgagg s rheMac2.chr16 74753873 35 + 78773432 tcactctggaggaagtcagccgccctgtcatgaga i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9221469 35 + 17838096 tcactctggaggaagtcagccgccctgtcatgagg i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0080755 4348 35 - 4970 tcactctggaggaagtcagccgccctgtcatgagg i gorGor1.Supercontig_0080755 C 0 C 0 s panTro2.chr17 79199936 35 + 83384210 tcactctggaggaagtcagccgccctgtcatgagg i panTro2.chr17 C 0 C 0 s mm9.chr11 118678255 15 + 121843856 --------------------CAGCATGGCACCTGG i mm9.chr11 C 0 I 15 s cavPor3.scaffold_76 4307396 35 + 7991924 tcactctggaggaagccagccaccacgccacgagg i cavPor3.scaffold_76 I 99 I 12 s bosTau4.chr19 10765655 35 - 65312493 tcactctgggggaagctggccgccatggcatgagg i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59368038 24 - 64418924 CCGCTCTCA-----------CGCCACATCATGGGG i canFam2.chr9 C 0 C 0 e tarSyr1.scaffold_190290 1770 1625 + 4572 M e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57953553 930 - 61308211 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=454294.000000 s hg19.chr17_gl000204_random 26364 381 + 81310 acactcaggcagccctacagagaggccacctggagaggaactggggcc-ac--agccagcagccac---------------------------------gagagagaccagcttacaagcagatcctccagccccagttgagccttcccatgcctgcggccccggccaacatatcaac--gcaacctcg-aagggacgctgagcc-----------------------------------------------aggcactcagctgagcccctcccagattcctgaacctcagaaaccatgagctaataaatgattgttgtctaaagccattaaatttggggataatctattacacagcaatagata----acAT---AGGGAT----------TAC-AAAAAAATATGAATGGTGG--CTGGAGCCACAGGCATGGAGAAGAACGCGAAGTGAGAAGAC-AGGATGAGAGCAGATTACAGAGGTGAGG s canFam2.chr9 59368062 261 - 64418924 ACACCCATGGG------------------------AGGAACTGGGGCC-CC-------------------------------------------------------------------------TCTTCGAc-------------------------------agccggcatgctgact-acaaccctgtgaaagcctctgagct--------------------------------------------------------gctcag--actctccgactcctgaacccctgaaaccgcaggctaagaaatgatcattgtttaaagctgctaaggtttggggtaaccagt---ggatcaacacatacctgatac---aGGGATTAGACAAGGATCC-------ATGTAAAGGGTGG--CTTTAG--------------------GCCA-GTGAGAAGAT-GGGGTGGG--TGGGAGGTACAGGTGGTG i canFam2.chr9 C 0 C 0 s bosTau4.chr19 10765690 289 - 65312493 acactcaaacggcc-------------------atagtgagtgaggct-tc-------------------------------------------------------------------------ctgccagc-------------------------------agccaacatggtgact-gcaacctctcgaaaga--ctgagct---------------------------------------------acaagcactcagctcagccacccccagattcctgaatcccagaaactgtgagctaataagtgattgttgttgggagtcactacattttagtgtaatccattacagagcaataggtaaATGACCC---GGGAATT---------TCC----AAAATACAAATGGTGG--CTGAAGACATGGGCGTGGATAAGAACACCA-GTGAGAAGAT-GGGA-------GTACAGAACGGGTGATG i bosTau4.chr19 C 0 C 0 s cavPor3.scaffold_76 4307443 305 + 7991924 ccagtggaaaagct-------gagagcac------------tggaagc-tagcggcccacaggtgtaga---------------------------------------------------------cccatccccagct-cgactccacacgcctgcagccctggttgac-t--------gatccctga-cagagacctt-------------------------------------------------------------gctaagctgctcccaggttcctgagtcccagagactaacagctaataactgatggttgtttgtgacc-ctaagttttggagtaacctctcccacagccatagata----actaaCCAGAGAT----------CAT--TGCACACA-----GTCGGAACTGCAGCTGCGTGCGTGGACAAGAAGCCCAAG-GAGAAGAT-GAGATCAG---AGTCATCAGC------- i cavPor3.scaffold_76 I 12 C 0 s mm9.chr11 118678285 393 + 121843856 TCATGGGACCAGCTCTACCGAGAGATCACATGGGCAGGAGGAGGAGGC-TG--AGTCCACTGCCTT--------------------------------------------------------------CATCACAAGCT--GGcttcagatgcctccagcccagacacac-tgtcagtgagaaaccttt-gagataccttgagctttttcttttcttttcctttcttttcctttcttttcttttcttttcttaagca-taagctaagctgtttgccggttctggaaccccagaaaccgagagccaataaacgactgttgttttaagctgctgtgtttgcagataacccatttccaggtgatagtta----acta---aGGGTT----------TAT--AGAAAGCATGAATGTTGT--CTGAAGCTGCAGATGTGCACAGAGCAGCCAGC-AAGAAGGCAGGGAGTAG---AGATGGCAGAGATGATA i mm9.chr11 I 15 C 0 s tarSyr1.scaffold_190290 3459 361 + 4572 acactcaaacagtcctatggagaggtcac----------actgaggcctcc--caccaacaatcatgag---------------------------aatgag-----ccagctttgaagtagactctccggctccagtcaagccttcagatcacagcagaccaaggcgacatactgaca-gcaaccttgtaagggactctgagcc---------------------------------------------aaaaacatccagctaagcatctcccaggttcctgaaccccagaaactatgagataataagtaattgatgtttgacaccattacgttttggggtaacctgttacaca----------------------ggaat----------TAC--AAAAAATATAAATGGTGG--GTGAAACCACAGGCATGGATAAGAACACCAAGTGAGAAGCC-AGGATGAGCACAGATTACGGAGATGATG i tarSyr1.scaffold_190290 M 1625 C 0 s rheMac2.chr16 74753908 413 + 78773432 acactcaggcagccctacagagaggccacttggagaggaactggggcc-ac--agccagcagccatgagagagaccagcttggaagcagatcctccaacaagaggcaccagcttagaagcagatcctccagccccatttgggccttcccatgcctgcagcccgggccaacata--aact-gcaaccttg-aagggatgctgagcc-----------------------------------------------aggcacccagctgagcccctcccagattcgtgaacctcagaaactatgagctaataaatgattgttgtctaaagccattaaatttggggataatctattacacagcaatagata----acAC---AGGGAT----------TACAAAAAAAATATGAATGG-GG--CTGTAGCCACAGTCATGGAGAAGAACACAAAGTGAGAAGAC-GAGATGAGAGCAGATTACAGAGGCGAGG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9221504 415 + 17838096 acactcaggcagccctacagagaggccacctggagaggaactggggcc-ac--agccagcagccacaagacagacgagcttggaagcagatcctccaatgagagagaccagcttacaagcagatcctccagccccatttgagccttcccatgcctgcagccccggccaacatatcaact-gcaacctcg-aagggacgctgagcc-----------------------------------------------aggcacccagctgaacccctcccagattcctgaacctcagaaactatgagctaataaatgattgttgtctgaagccattaaatttggggataatctattacacagcaatagata----acGT---GGGGAT----------TAC-AAAAAAATATGAACGGTGG--CTGGAGCCACAGGCATGCAGAAGAACATGAAGTGAGAAGAT-GGGATGAGAGCAGATTACAGAGGTGAGG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0080755 4383 414 - 4970 acactcaggcagccctacagagaggccacctggagaggaactggggcc-ac--agccagcagccacgagagagacaagcttggaagcagatcctccaatgagagagaccagcttacaagcagatcctccagccccagttgagccttcccatgcctgcagccccagccaacatatcaac--gcaacctcg-aagggacgctgagcc-----------------------------------------------aggcactcagctgagcccctcccagattcctgaacctcagaaaccatgagctaataaatgattgttgtctaaagccattaaatttggggataatctattacacagcaatagata----acAT---GGGGAT----------TAC-AAAAAAATATGAATGGTGG--GTGGAGCCACAGGCATGGAGAAGAACACGAAGTGAGAAGAC-GGGATGAGAGCAGATTACAGAGGTGAGG i gorGor1.Supercontig_0080755 C 0 C 0 s panTro2.chr17 79199971 414 + 83384210 acactcaggcagccctacagagaggccacctggagaggaactggggcc-ac--agccagcagccacgagagagacaagcttggaagcagatcctccaatgagagagaccagcttacaagcagatcctccagccccagttgagccttcccatgcctgcggccccggccaacatatcaac--gcaacctcg-aagggacgctgagcc-----------------------------------------------aggcactcagctgagcccctcccagattcctgaacctcagaaaccatgagcaaataaatgattgttgtctaaagccattaaatttggggataatctattacacagcaatagata----acAT---GGGGAT----------TAC-AAAAAAATATGAATGGTGG--CTGGAGCCACAGGCATGGAGAAGAACACGAAGTGAGAAGAC-GGGATGAGAGCAGATTACAGAGGTGAGG i panTro2.chr17 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57953553 930 - 61308211 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=127816.000000 s hg19.chr17_gl000204_random 26745 85 + 81310 AA-G-G-TCACAC-TGG-GACACGCCAGGAGGCAGT-GGTGGGAGAGAAAGGCCCGTGAGGAGGGAGGAGGAAGAGCCCTCA-AAAGGAGGA s panTro2.chr17 79200385 85 + 83384210 AA-G-G-TCACAC-TGG-GACACGCCAGGAGGCAGT-GGTGGGAGAGAAAGGTCTGTGAGGAGGGAGGAGGAAGAGCCCTCA-AAAGGAGGA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0080755 4797 85 - 4970 AA-G-G-TCACAC-TGG-GACATGCCAGGAGGCAGT-GGTGGGAGAGAAAGGCCCGTGAGGAGGGAGGAGGAAGAGCCCTCA-AAAGGAGGA i gorGor1.Supercontig_0080755 C 0 C 0 s ponAbe2.chr17_random 9221919 85 + 17838096 AA-G-G-TCACAC-TGG-GACACACCAGGAGGCAGT-GGTGGGAGAGAAAGGCCCGTGAGGAGGGAGGAGGAAGAGCCCTCA-AAAGGAGGA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74754321 85 + 78773432 AG-G-G-TCACAC-TGG-GGCACACCAGGAGGCAGT-GGTGGGAGAGAAAGGCTGGTGAGGAGGGATAAGGAAGAGCCCTCA-AAAGGAGGA i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_190290 3820 88 + 4572 AG-G-GATTACACTTGG-GACACACCAGGAGACAGTGGGTAGGAAGGAAAGGCCTGTGAGGAGCAATAAGGAGGAGCCCCCA-AAAGAAGAA i tarSyr1.scaffold_190290 C 0 C 0 s mm9.chr11 118678678 80 + 121843856 TA-CGG-TCACAGCTGA-GACTCTCCAGGAGC---T-GGTGGGTAAGGAAGACTTGCACAGAGGAGCAAGGT----GCCTCA-AAGGGAGAA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4307748 77 + 7991924 -----A-TCAGGGGTGATGACACTACATGG-------GGTGCATAAGAAAGGTTGTCTGAGAGGAACAAGAT-GAGGCCTCA-AAGGGAGGA i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10765979 75 - 65312493 AGAA-G-GAATACCTGA-GACACCCCAGAAGTTGGTGGGAGAGAAAG-------------GAGGAACAAGGACAGGCCCCCA-AGAGAAGGA i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59368323 85 - 64418924 AG-G-G-GCACACCCAG-GTCACCCTGGGAGGCAGCGGGGGTGCAAGAGAAGCTTGTGCAGAGGAACAGGG---GGCCCCTGCAGAGAAGGG i canFam2.chr9 C 0 C 0 s xenTro2.scaffold_787 180921 85 - 417512 AA-G-G-ACACAG-CGG-GGAGCTGGAGGAAGCAGT-GGGGAGCAGGAGGAAGTATGGGGGAGCCAGAGGACACAGCGAGGA-GCGGGAGGA i xenTro2.scaffold_787 N 0 I 60 e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57953553 930 - 61308211 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=37840.000000 s hg19.chr17_gl000204_random 26830 45 + 81310 AGACAAGGCTGAGAAACACAACAAAATCCCAAGGATGAGAG-GTCt s panTro2.chr17 79200470 45 + 83384210 AGACAAGGCTGAGAAACACAACAAAATCCCAAGGATGAGAG-CCCt i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0080755 4882 45 - 4970 AGACAAGGCTGAGAAACACAACAAAATCCCAAGGATGAGAG-CTCt i gorGor1.Supercontig_0080755 C 0 C 0 s ponAbe2.chr17_random 9222004 45 + 17838096 AGACAAGGCTGAGAAACACAACAAAATCCCAAGGATGAGAG-CTCt i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74754406 44 + 78773432 AGACAAGGCTGAG-AACACTACAAAATCCCAAGGATGAGAG-CTCt i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_190290 3908 35 + 4572 CTGTAAGACTGAGAAACACCACAA------AAGTATGAGAG----- i tarSyr1.scaffold_190290 C 0 C 0 s mm9.chr11 118678758 30 + 121843856 G---AAGACAGGGAAACCC-AGAATCCT-----------AGGACC- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4307825 38 + 7991924 AGGCAAGGCTAAGAAACTC-ACAAAACCCAAAGAAAGAG------- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10766054 35 - 65312493 AGATGAGACTGCAAAATACCACAAAAGCCCAAGGA----------- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59368408 31 - 64418924 GGCTAAGGCTGCAAGATGCTACAAATTCCCA--------------- i canFam2.chr9 C 0 I 17 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57953553 930 - 61308211 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=34100.000000 s hg19.chr17_gl000204_random 26875 40 + 81310 attaggctgttcttgcattgctatacagagatgcctgagg s panTro2.chr17 79200515 40 + 83384210 attaggctgttcttgcattgctatacggaaatgcctgagg i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0080755 4927 40 - 4970 attaggctgttcttgcattgctatacagaaatatctgagG i gorGor1.Supercontig_0080755 C 0 N 0 s ponAbe2.chr17_random 9222049 40 + 17838096 attaggctattcttccattgctatacagaaatgcctgagg i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74754450 40 + 78773432 attaggctgttcttacattgctatacagaaatgcctgagg i rheMac2.chr16 C 0 C 0 e tarSyr1.scaffold_190290 3943 0 + 4572 C e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59368439 17 - 64418924 I e bosTau4.chr19 10766089 0 - 65312493 C e equCab2.chr11 57953553 930 - 61308211 I e cavPor3.scaffold_76 4307863 0 + 7991924 C e mm9.chr11 118678788 0 + 121843856 C e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=177849.000000 s hg19.chr17_gl000204_random 26915 339 + 81310 ctgggtcatttatcaagagaagaggtttaattggctcctggttctgcaggctgtacaggaagcaccgtgttggcatctgctcctggtgaggtctcaggaagcttccactcatggtggaagctgaagagggaggaggcgtatcacacggcaagaggggagatgagggaggcaccacactcttttaaacaaccagatctcacatgaactaattgagggacaactcactcatcaccaagggggtggtactaagccatccatgagggatccgcccccatgatccaatcacctcccaccaggccccacctctaacactggcaaatgatttcaacacgagagttg s rheMac2.chr16 74754490 339 + 78773432 ccgggtcatttacaaagaaaagaggtttaattggctcctggttctgcaggctgtataggaagcacagcgtgggcatctgctcctggtgaggtctcaggaagcttccactcatggtggaaggtgaagagggagtaggcgcattacacagcaagaggggagatgagggaggtaccacgctctttcaaacaaccagatctcacatgagctaattgagagacaactcactcatcaccaaggggctggtgctaagccatccatgtgggattcgcccccatgatccaatcacctcccaccaggccccacctctaacactggcaaacgatttcaacatgagagctg i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9222089 339 + 17838096 ctgggtcatttatcaagagaagaggtttaattggctcctggttctgcaggctgtacaggaagcacagtgttggcatctgctcctggtgaggtctcaggaagcttccactcatggtggaaggtaaagagggagtaggtgtattacatggcaagaggggagaagagggaggcaccacactcttttaaacaaccagatctcacacaaactaattgagggacaactcactcatcaccaagggggtggtgctaagccatccatgagggatccgtctccatgatccaatcacctcccaccaggcgccacctctaacactggcaaacgatttcaacatgagagttg i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79200555 339 + 83384210 ctgggtcatttatcaagagaagaggtttaattggctcctggttctgcaggctgtacaggaagcaccatgttggcatctgctcctggtgaggtctcaggaagcttccactcatggtggaaggtgaagagggagtaggcgtattacatggcaagaggggagatgagggaggcaccacactcttttaaacaaccagatctcacatgaactaattgagggacaactcactcatcaccaagggggtggtgctaagccatccatgagggatcctcccccatgatccaatcacctcccaccaggccccacctctaacactggcaaacgatttcaacatgagagttg i panTro2.chr17 C 0 C 0 e tarSyr1.scaffold_190290 3943 0 + 4572 C e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59368439 17 - 64418924 I e bosTau4.chr19 10766089 0 - 65312493 C e equCab2.chr11 57953553 930 - 61308211 I e cavPor3.scaffold_76 4307863 0 + 7991924 C e mm9.chr11 118678788 0 + 121843856 C e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=7721.000000 s hg19.chr17_gl000204_random 27254 42 + 81310 gagggggacacacatccaaaccgtatcaAGAGCATTTCCAGA s panTro2.chr17 79200894 42 + 83384210 gagggggacacgcatccaaaccgtatcaAGAGCATTTCCAGA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9222428 42 + 17838096 gagggggacacacatccaaaccgtaccaAGAGCATTTCCAGA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74754829 41 + 78773432 g-gggagacacatatccgaactgtatcaGGAGCATTTCCAGA i rheMac2.chr16 C 0 C 0 s equCab2.chr11 57954483 36 - 61308211 gaagagcacagaagtccaa---gga---ggagcgtttccaga i equCab2.chr11 I 930 C 0 s bosTau4.chr19 10766089 15 - 65312493 ------------------------A---GGGGCGTTCTCAGA i bosTau4.chr19 C 0 C 0 s tarSyr1.scaffold_190290 3943 8 + 4572 ----------------------------------TTTCCAGG i tarSyr1.scaffold_190290 C 0 C 0 s cavPor3.scaffold_76 4307863 7 + 7991924 ----------------------------------TCTCCAG- i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118678788 13 + 121843856 ----------------------------AGGGTGTTTCCAG- i mm9.chr11 C 0 C 0 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59368439 17 - 64418924 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=357449.000000 s hg19.chr17_gl000204_random 27296 342 + 81310 AGGAGAGCGTCAGATGCTACAA------A--GGCACAGC--AGGACCCCGGCTTCCCAGGGACCAAGTTCTCCCCCTACCCTGTctcagtccagaccttcttacctgccacctccctgcctgg-------ctgctggccccatcacatctctcagatcccactcccagggtcttcggtcttcaatgagaggccttccctgaccacccatgctaaagga-----gtccccaaccccagtttccc------------------ggtcac--tctgtcatagctgcctggcatttgttgcaagttgtaattatattttcatttgtttc-tgtctcagccatgacctatgaaggctg-ggaaatatctgtttcattcactaccataaacc s rheMac2.chr16 74754870 345 + 78773432 AGGAGAGCGTCAGATGCTACAA------A--GGTCCAGC--AGGACCCCGGCTTCCCAGGGACCAAGTTCTCCCCCTACCTTGTCTCAGTCCAGTCCTTCTTACCTGCCACCTCCCTGCCTGG-------CTgctggccccatcgcatccctcagatcccacttccagggtcttcagtcttcaatgagaggccttccctgaccacccaagctaaagga-----gtccccaaccccagtttccc------------------ggtcactttctgtcatagctgcctggcatttgttgcaagttgtaattatattttcatttgtttctttactcagccatgacctatgaaggctg-ggaggtatctgtttccttcactaccataaacc i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9222470 343 + 17838096 AGGAGCGTGTCAGATGCTACAA------A--GGCCCATC--AGGACCCCGGCTTCCCAGGGACCAAGTTCTCCCCCTACCCTGTCTCAGTCCAGACCTTCTTACCTGCCACCTCCCTGCCTGG-------CTGCTGGCCCCATCACATCTCTCAGATCCCACTCCCAGGGTCTTCCGTCTTCAATGAGAGGCCTTCCCAGACCACCCATGCTAAAGGA-----GTCCCAAACCCCAGTTTCCC------------------GGTCAC--TCTGTCATAGCTGCCTGGCATTTGTTGCAAGTTGTAATTATATTTTCATTTGTTTCTTTTCTCAACCATGACCTATGAAGGCTG-GGAAATATCTGTTTCATTCACTACCGTAAACC i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79200936 342 + 83384210 AGGAGAGCATCAGGTGCTACAA------A--GGCCCAGC--AGGACCCCGGCTTCCCAGGGACCAAGTTCTCCCCCTACCCTGTCTCAGTCCAGACCTTCTTACCTGCCACCTCCCTGCCTGG-------CTgctggccccatcacatctctcagatcccactcccagggtcttcggtcttcaatgagaggccttccctgaccacccatgctaaagga-----gtccccaaccccagtttcca------------------ggtcac--tctgtcatagctacctggcatttgttgcaagttgtaattatattttcatttgtttc-tgtctcagccatgacctatgaaggctg-ggaaatatctgtttcattcactaccataaacc i panTro2.chr17 C 0 C 0 s mm9.chr11 118678801 253 + 121843856 AGGAGGGCACCAGCTGTTGCGC---------AGCTTAGA--GCAA------CATCC-AGGCACTC---TCTCGCCCAACAGCGACCTTG-------------------TGCCTCTGCAATGGGTTAGAAGCTGCCAGCCCCATCTCCTCGCTCAG-------------------ACATTTTTAT--AGAGCTCTCCTCTGACAACTAAGGCAAAG--------CTACTGCCCCCAAGTTCCTT------------------GCTCACT-------------------------------GCT---ATTGTATTTCGATGTTCTGCATCACTCCACTCAGGTCCTCGAAGGCTG-GGGAATTTGG-----------CACTACAAACA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4307870 325 + 7991924 AGGAAGGT-TTGGATGCTGCAA------G--GGCTCAAT--GGGATCTGGGCTTCT-AGGAGCCA---GGTCCTCCAACTGCATCCTAGAAGAAAATTTCTCATGTGCTAcctct---------------ttatctggctcctctcatctctcagagctcaagt---ggaaatcacaccttaaa--ggcagactcccctgactatccatgctaaggccacccccccccgcaccccagctccct------------------ggtcaccctctgtcatagcttcctggaacttgttgcaaatt---attatatttc---attatgctctgttctgccatgatctgagaaggctg-gggaatctatgtttcattcaccACCATAAAC- i cavPor3.scaffold_76 C 0 C 0 s tarSyr1.scaffold_190290 3951 331 + 4572 AGG---GCATCAGATACTGCAA------AGCGGTTCAGC--AGGACCCTGACTTCCAAGGGACTAGGTTCTCCTTC-ACTTAAGCCCAGTCCAGACCTATTTTCTTGccacctccttgctttg-------ttgttggctccacta-atctctcagactcca----ggggaaaacacacctttggtgagaggccttccctgatcactcaagctaacaga-----g-----accctcagt---ca------------------agtcattctctgtcatggcttcctggtgcttcttgcaaattataattatattttactttgttcctttattcaaccatagtctgtaaaatctatggaaatatcggtcttgttcaccactgtaaacc i tarSyr1.scaffold_190290 C 0 C 0 s bosTau4.chr19 10766104 319 - 65312493 AGGAAGGCAACAGATTCTTCAA------AGAGGTACGGC--AAGATTG-GAATTCTAAGGGACCCAGCTGTCTCCCA--CCGACCCCAGGTGAGATCTTCTCATTCACTGCTTCCTTGTGAGA-------CTGCTGCCTCCATCCCATCTCTC-GTCctcaagt---ggaaatcacatctct---gggaggctttccccgacaactcaagctagcat------------------agtcccca------------------gttctg---tggtcactctctcttggcacttgttacaaacta--attatattttgatttatctctttacttaatcatagtctgcgagagctg-ggaaatatctgttttgttcaccactgtaaacc i bosTau4.chr19 C 0 I 277 s canFam2.chr9 59368456 258 - 64418924 AGGAGGGCTTCAGATGCTTCAGATTTCTAAGGGACCAGGTTAGAAACC---------AGGGACCCAGTGATCCCCTGACCCCACCCCAAGGGAGATCTTCTCGCTTGCTGCTTCCTTGTGAGA-------C--CCCGAcccatctcatctc---------------------------------------------------------------------------------tcaagtcctc-------------------attctt---------ccccttggtggcacttgtcacaaattgtcattacatttttacttgtttttttactcacccatggcctttgagggctg-gggagcatcagttttgttcaccactgtaaacc i canFam2.chr9 I 17 C 0 s equCab2.chr11 57954519 342 - 61308211 aggagagcatcagatgcttcaa------agaggtccagg--aggagca-gactTCTGAGGGACCAA---ATTCCCCCtccccctcccgtgagag---ctctcgcttgccgcttccttgggaga-------ctgctagctccctcgcatctc---ggcctcacct---ggaaatcatgtctctgacgagaggccttccctgagctcctgagctaccatg-----ggacccatgccaggtccccgtcactcttgtagctgcctgttctt---------ctccttcgtggtacttcttgccaattataattacgtttttgtttgtttctgtactcaactgtggtctatgggggttg-ggaaatacctgctttgttcactactgt-agcc i equCab2.chr11 C 0 C 0 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=69020.000000 s hg19.chr17_gl000204_random 27638 71 + 81310 aagtgcat--------gatatatcctagtttctct-atatt---tgttggat------------aaatggatGGAAA--------GAAAGAAAGATAAAAACC s rheMac2.chr16 74755215 71 + 78773432 aagtgcat--------gaggtatcctaggttctca-atatt---tgttggat------------aaatggatGGAAA--------GAAAGAAAGATAAAAACC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9222813 71 + 17838096 AAGTGCAT--------GATGTATCCTAGTTTCTCT-ATATT---TGTTGGAT------------AAATGGATGGAAA--------GAAAGAAAGACAAAAACC i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79201278 70 + 83384210 aagtgcat--------gatgtatcttagttttttt-atatt---tgttggat------------aaatgga-GGAAA--------GAAAGAAAGATAAAACCC i panTro2.chr17 C 0 C 0 s mm9.chr11 118679054 72 + 121843856 CAGTGCTT--------GATACAGTCTAGGTTCTCA-GTGGTACAGGGTGGAG------------AGATGGGTCAATG--------GATTGATGGGTCAAAA-- i mm9.chr11 C 0 I 277 s cavPor3.scaffold_76 4308195 69 + 7991924 -----CTT--------GATGTTCCCAGTATTTGCT-ggagggagggaaggag------------aaaaagggaaaga--------ggaagggaggaaagaaca i cavPor3.scaffold_76 C 0 I 5 s tarSyr1.scaffold_190290 4282 67 + 4572 ccacacct--------gacacatcctaggttctca-gtatt---tgttggat------------aaatgaatG------------AATGGAAAGACAAAAATC i tarSyr1.scaffold_190290 C 0 C 0 s bosTau4.chr19 10766700 91 - 65312493 ccatttccttctccatgacatatactaggttcttg-atatt---tgttggatgCAAAATCACACGAATGAACAAGTG--------AATGGAAAGATCAAAACT i bosTau4.chr19 I 277 C 0 s canFam2.chr9 59368714 72 - 64418924 cagggccc--------gacatatacgaggttctcaaacatt---tgctggat------------ggatgaatAAGTG--------AATGGAAAAAGCAAAACC i canFam2.chr9 C 0 C 0 s equCab2.chr11 57954861 80 - 61308211 ccgtgccc--------aacacatactgggttcttgaatatc---tgctggct------------gaatgaatgaTTGAGAGAATAAATAGAAAGACCCAAATC i equCab2.chr11 C 0 C 0 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=89677.000000 s hg19.chr17_gl000204_random 27709 58 + 81310 CTGAGTTTCACCTGGAGGCCCAGTTCAACTGGTGGAAAAACCACTTCCCTCCCCAA--GT------------- s panTro2.chr17 79201348 58 + 83384210 CTGAGTTTCACCTGGAGGCCCAGTTCAACTGGTGGAAAAACCATTTCCCTCCCCAA--GT------------- i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9222884 58 + 17838096 CTGAGTTTCACCTGAAGGCCCAGTTCAACTGGTGGAAAAACCATTTCCCTCCCCAA--GT------------- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74755286 57 + 78773432 CTGAGTTTCACCTGGAGGCCCAGTTCAACTGGTGGAAAAACCG-TTCCCTCCCCAA--GT------------- i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_190290 4349 58 + 4572 CTGACTTTCACTTGGTGGCCCAGGTTAACAGGTGAGCAAACCATTTCCCTCTACCC--TT------------- i tarSyr1.scaffold_190290 C 0 C 0 s mm9.chr11 118679403 56 + 121843856 CTTAACTTTACCTAGTAGCCCAGGTCAACTGGTAGACAAGCCATTTCCTTCCTGAA----------------- i mm9.chr11 I 277 I 476 s cavPor3.scaffold_76 4308269 57 + 7991924 CTGAGTTTCACTCAGT-GTCCAGGCCAACAGGTGGACAAACCATTTCCCTGCCACCCC--------------- i cavPor3.scaffold_76 I 5 I 3 s bosTau4.chr19 10766791 69 - 65312493 CTGATTCTCACCTAGTGGCCCCAAATAACTGGTAGACAAACCA--TCCCTTCCCCC--TTCTCCTCTCCACTT i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59368786 68 - 64418924 CTGAGCCTCAGCTGGAGGCCCAGGTTACCTGGTGGACAAACTG--TCTCCTCCCAC--ATC-CCCCTCCACGT i canFam2.chr9 C 0 C 0 s equCab2.chr11 57954941 64 - 61308211 CTGATTCTCACCTAG-TGCCCAGGTTAACTGATGGACAACCCA--CCCCCACCCAC--CTC-CACCCACA--- i equCab2.chr11 C 0 C 0 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=184647.000000 s hg19.chr17_gl000204_random 27767 140 + 81310 CACACACTCG---CCGCGGC----AGTAGGGCTCCTTGGCTCTGGAGGAAAACATAGCTGGGCTGGGGGAGGAGGTGGAGAAGGACAGGAGACTCTGAAGTTGACCCAGACCAGCTCT-TCCATCATTCTAAAAG----TGGGGAAg-------ctgga s panTro2.chr17 79201406 140 + 83384210 CACACACTCG---CCGCGGC----AGTAGGGCTCCTTGGCTCTGGAGGAAAACATAGCTGGGCTGGGGGAGGAGGTGGAGAAGGACAGGAGACTCTGAAGTTGACCCAGACCAGCTCT-TCCATCATTCTGAAAG----TGGGGAAg-------ctgga i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 9222942 140 + 17838096 CACACACTCG---TTGCAGC----AGTAGGGCTCCTTGGCTCTGGAGAAAAACATAGCTGGGCTGGGGGAGGAGGTGGAGAAGGACAGGAGACTCTGAAGTTGACCCAGACCAGCTCT-TCCATCATTCTAAAAG----TGGGGAAg-------ctgga i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74755343 140 + 78773432 CACACACCTG---CCACAGC----AGTAGGGCTCCTTGGCTCTGGAAGAAAACATAGCCAGGCTGGGGGAGGACGTGGAGAAGAACAGGAGACTCTGAAGGTGACCCAGACCAGCTCT-TCCATCATTCCAAAAG----TGGGGAAg-------ctgga i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_190290 4407 138 + 4572 CTCTCTCCCGAACCCTGAGC----AGTAGGGTTCCTTGGTTGCAGAAGAAAACACAGCTGGGCTAGGAGAAGA--TGGGGAAGAAGAGGAGACTCTGAAAGTGACCCAGACAGGCTCT-TCTGTCATTCTAAAA------AGGGAAG-------CTGG- i tarSyr1.scaffold_190290 C 0 N 0 s mm9.chr11 118679935 132 + 121843856 cacacacTCG---CGCGTGC----GCGCGTGCTCTCTTGCTGTAAAGAGAAACTCAGCTGCAATAGCAGAGGATGTGGGGAGGGG-AGAAAACCATGAAGTTGATCCTGACAGGTTC---TCGCTGTGCTAAAAA----CAGGCAAG------------ i mm9.chr11 I 476 I 2 s cavPor3.scaffold_76 4308329 124 + 7991924 CACACTCATA---TCCCTGG----AGGTG-GCTCCTTGGCTGTGGAGGGAAACATATCTGGGATGGCACAGAATGTGGAGCAGAG----AAACCCTGGAGGTGGGCCCAACAAGCTC---CCCTCACATGAAAAG----CAGG---------------- i cavPor3.scaffold_76 I 3 C 0 s bosTau4.chr19 10766860 128 - 65312493 CAC-CACACA---CCGTTATAGG-GGTTGGGCCCCTTGGCTGTGAAGAAAAACACAGTTGGATTGGGAG-GGAGGTGAGGAAAGAGAGAAGACTCTGAAAGCAAGCTCGATGAGCTCT---------------------TGGGGAAGAAGCTGG----A i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59368854 138 - 64418924 ----CCCACA---CCTCTGTAGTGGGCAAGGCCCCGCGGCTGTGAAGGAAAGCACAGACGGGATAGGGA--GAGGTGAGGAAAGAGAGAAGACCCTGAGGGTGACCCAGACAGGCTCTTCCCACCCTTCTCAACACCCCTGGGGAAG------------ i canFam2.chr9 C 0 I 19 s equCab2.chr11 57955005 128 - 61308211 ------CACG---CCTGGGT----GGCAGGGCCCCTC-GCTGTGAAGGAAAACACAGCCCGGATGGGGA-GGAGGTGAGGAAAAAGATAAGACTCTCAAGGGGACCCAGGGGGGCTCTTCTCACGCTTCTAAACA----TGGGGAAG------------ i equCab2.chr11 C 0 I 146 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=53631.000000 s hg19.chr17_gl000204_random 27907 109 + 81310 tacggtggtgcatgcctgtaatcccagctacttaggaggctgaggcaggaggatcacttgagctgaggagtttgaggctagcctgggcaacatagcaagaccccatctc s panTro2.chr17 79201546 109 + 83384210 cacagtggtgcatgcctgtaatcccagctacttaggaggctgaggcaggaggatcacttgagctgaggagtttgaggctagcctgggcaacatagcaagaccccatctc i panTro2.chr17 C 0 M 1752 s ponAbe2.chr17_random 9223082 109 + 17838096 tacagtggtgcatgcctgtaatcccagctacttaggaggctgaggcaggaggatcacttgagctgaggagtttgaggctagcctgggcaacatagcaagaccccatctc i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74755483 109 + 78773432 cacggtggtgcatgcctgtaatcccagttatttaggaggctgaggcaggaggatcacttgagctgaagagtttgaggctagcctgggcaacatagcaagaccccatctc i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4308453 40 + 7991924 ----------------------CCAAGGTCCACAGGA---------------------------------------------CAGGACACCCCACCAATGCCTCACC-- i cavPor3.scaffold_76 C 0 C 0 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59368992 19 - 64418924 I e bosTau4.chr19 10766988 0 - 65312493 C e equCab2.chr11 57955133 146 - 61308211 I e mm9.chr11 118680067 2 + 121843856 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=3341.000000 s hg19.chr17_gl000204_random 28016 40 + 81310 atatctcataaataaataaaTAGTAATTAAAATGAGG----------------------------------------------------------------------------------GCT s ponAbe2.chr17_random 9223191 39 + 17838096 ATATCTCataaataaataaatattaattaaaatGATG-----------------------------------------------------------------------------------CT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74755592 122 + 78773432 atatctcataaataaataaatattaattaaaatgaaggcatctgtaggaagtccaagtggccaccgtattagcaagaccccatctcatatctcataaataaatattaattaaaatgaaggcg i rheMac2.chr16 C 0 C 0 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59368992 19 - 64418924 I e bosTau4.chr19 10766988 0 - 65312493 C e equCab2.chr11 57955133 146 - 61308211 I e cavPor3.scaffold_76 4308493 0 + 7991924 C e mm9.chr11 118680067 2 + 121843856 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=26245.000000 s hg19.chr17_gl000204_random 28056 57 + 81310 TCTTTAGGAATTCCAAGTGGCCACCGTATTTCCTTCAAGCATTCAACAAACATCAAC s mm9.chr11 118680069 56 + 121843856 TCTGTGGGAAACCCAGGCAACCCCC-TACTTCCTTCAGGAATTCAAAAAAGACAGAC i mm9.chr11 I 2 C 0 s ponAbe2.chr17_random 9223230 57 + 17838096 TCTTTAGGAAGTCCAAGTGGCCACCGTATTTCCTTCAAGCATTCAACAAACATCAAC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74755714 57 + 78773432 tctgtaggaagtccaagtggccaccgtattTCCTTCAAGCATTCAACAAACATCAAC i rheMac2.chr16 C 0 C 0 s bosTau4.chr19 10766988 50 - 65312493 ------GGAAGTCCAAGTGACCACTATACTTCCTCCAGGTattcaataaacctgga- i bosTau4.chr19 C 0 I 1 s cavPor3.scaffold_76 4308493 27 + 7991924 -------------------ACCTCC-T----------GGTATCCAGCACATGTGGCC i cavPor3.scaffold_76 C 0 C 0 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59368992 19 - 64418924 I e equCab2.chr11 57955133 146 - 61308211 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=157396.000000 s hg19.chr17_gl000204_random 28113 367 + 81310 AGGCTGAGGCTGTAC--AACTGGGCTAGGTGGTGGGAACC----------------TGTCCCCTCAGCAGTTCAGAGTCTTGGTGGGGAAGCTGGCAGCCAGACAGGG-CAGGAG--AAGATGCAGTGTAAGGGGTGAGGCCTGAAGGCTGACTGTCCCCCTCCACCCTTCCTCCCCGA------GCTGTGAGGCCCTGGGCAAGTAGCATAACGTCT-TAAACTTCCACAGCTTGCCTGTAAGCAGGACTGCTCCCACCGCACAGGC-----TGGCACCAC-CTCTTGTTCCTCACCAACAAAGCACTTGGGCCTGGGCCAGAGCATAGGTCCACATT----GCCATGATTTCaactggtaattacaata------------cactgcagagaagacacacagagcactgtggaca s canFam2.chr9 59369011 325 - 64418924 AGGCTG------------------------GGGGGCAACCGAGGGTGCATCCCACGTGGCCCTCAAGCAGGTCAGAGTC-CAATGGGGATGGAGGCGGCCAGATGGGG-------------------CTAAGGGGTGAGGCCTGGAGGCTGACTGT---CCCCCCACCTG-TGCCCCTG------CCTGAGAGACCTTGC-------------------------------ACTCACCCATGAGGAAGACCACTCCCACCACACAGGTGGTGACAG-GCCCC-TTTGTGCTCCTCACCTGCCAAGTACTCAGGCTTGGGCAGGAGCACGGGTGTGCATT----GCCATGATTTAAACAGATAATTACAATACATTCTGTTGTCTGCAGCAG-AGGGCTGCACACAGCCCTGTGGACA i canFam2.chr9 I 19 C 0 s bosTau4.chr19 10767039 373 - 65312493 agcctg------tgccacatcaaactaggcggtgggaagcaagggtacatcctgcatggcccctcagcagttcacagtc-tagtggggaagtgggcagacaggGGCGT-------------------CTAAGGGGTGAGGCTGGGACGGTG--TGT---CCCCCACCTTGCCACCTCCA------CCTGGGGGATCCTATGCAAGTTGCGTAATCTCTCCTTCCTTCACCGGCTCACCCATGAGG--GGCCACTCCCTCCATACAGGTGGTGATAACACCAC-CTTTTGCCCTCCACCTGCAAAACACTGAAGCCTGGGTGAGAGCATGGGTGTGCACT----GCCATGATTTAAACAGGAAATTGCCATACACTCTGATGGATGCTACAGAAGGGATGCACAGAGCACTGTGGACG i bosTau4.chr19 I 1 C 0 s mm9.chr11 118680125 307 + 121843856 AGCCTG------TGCCCAACTGAACCAGGCAGCAGGAACTAAGAGTGTATCCTGTGTGGCCCTTCAGCAGTGCAGGGTC-AGGTGGGGATATGGACAGCCA---ATGGACATGATAGAACATACAGTGGACAGAGTAAGGCCGGGAGGCCAGCTAG-GCTCTC-------CCTGTCCTT------GCCTCAAGGCCCCAGGCA----------------CAA--------TGCATACCAAAGAGCAAGG-CCTTTCTGCCACACAACTG----TGGAGCATCACCCTTTGCTGTCA-CTGCAGAGCACTTGG-------------------------------GCCA-------GGCTGGCGATTGCAGCT-----------------CAGAGCACGAGCACACCTTTG-GTGGACA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4308520 361 + 7991924 CACGCA------TGCTGTGCCATGTTAGATAGTGGAAACC-AGGGAACATCAAATGCAGATCATCAG-AGTCCAGAGTC-TGGTGGAGCCGTGGGCAGCCAGACAAGGGCAGCAT--GACATCCAGTCTAAGAGAGGAGACCCAAAGCCCAGTGAT-GCCCTCCACCCCACCTCCCCTTCTGTGAGCCT-----CTCCAAGCA----------------CAG-------CTGCTTACCTGCAAGCAGGGCCCTTCCTACCACACAGGTG----TGACAGCCCACCTTTGTTCCTCACCTGAAAGGCACCTGG--CTGGGCT-GAGGATGGGTCCATGTCCCATGACA-------AACAGGAGATTACAGTGCTCCAAGGTGCCAGCTACAGAGCAGGA-CACAGGGTGC-GGGGATG i cavPor3.scaffold_76 C 0 C 0 s ponAbe2.chr17_random 9223287 361 + 17838096 AGGCTG------TGC--AACCGAGCTAGGTGGTGGGAACC----------------CGTCCCTTCAGCAGTTCAGAGTCTTGGTGGGGAAGCTGGCAGCCAGACAGGG-CAGGAG--AAGATGCAGTGTAAGGGGTGAGGCCTGAAGGCTGACTGTCCCCCTCCACCCTTCCTCCCCGa------gctgtgaggccctgggcaagtagcataacctctctaaacatcTGCAGCTTGCCTGTAAGCAGGACTGCTCCCACCGCACAGGC-----TGGCACCAC-CTTTTGTTCCTCACCAGCAAAGCACTTGGGCCTGGGCCAGAGCATAGGTCCACATT----GCCATGATTTCAACCGCTAATTACAATA------------CACTGCAGAGAAGACAC-CAAAGCACTGTGGACA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74755771 361 + 78773432 AGCCTG------TGC--AACTGGGCTAGGTGGTGGGAACC----------------TGTCCCCTCAGCAGTTCAGAGTCTTGGTGGGGAAGCTGGCAGCCAGACAGGG--AGGAG--AAgatgcagtgtaaggggtgaggcctgaaggctgactgtccccctccaccctgcctcccgga------gctatgaagccctgggcaagttgcatagcctctctaaacttccgcagctcgcctgtaaGCAGGACTGCTCCCACCGCACAGGC-----TGGCACCAG-CTTTTGTTCCTCACCAGCAAAGCACTTCAGCCTGGGCCAGAGCACAGGTCCACATT----GCCGTGATTTCAACCAGTAAGTACAATA------------CACTGCAGAGAAGACATACAGAGCACTGTGGACA i rheMac2.chr16 C 0 C 0 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50656502 5865 - 54797317 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57955133 146 - 61308211 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=3167.000000 s hg19.chr17_gl000204_random 28480 177 + 81310 cagggagggtt-ggagtgggctggggaatgagcagctttctgaaggaggtaa-----------cagtggaggct-----------tgaaggagcgggaggcgtggagcagagaagcagctcagagacataaaccctcccatgccc-------------------aggcaaggaggccagaGGG-----CCTGAACAGCTG-AGGGCTTCAGC------AGCAGGACCCAGG s rheMac2.chr16 74756132 177 + 78773432 CAGGGAGGGTT-GGAGTGGGCTGGGGAATGAGCAGCTTTCTGAAGGAGGTAA-----------CAGTGGAGGCT-----------TGAAGGAGTGGGAGGCATGGAGCAGAGAAGCAGCTCGGAGACATAAACCCTCCCATGCCC-------------------AGGCAAGGAGACTGGAGGG-----CCTGCCCAGCTG-AGGGCTTCAGT------GGCAGGACCCAGG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9223648 176 + 17838096 CAGGAAGGGTT-GGAGTGGGCTGGGGAGTGAGCAGCTTTCTGAAGGAGGTAA-----------CAGTAGAGGCT-----------TGAAGGAGCAGGATGCATGGAGCAGAGAAGCAGCTCAGAGACATAAACCCTCCCATGCCC-------------------AGGCAAGGAGGCCAGAGGG-----CCTGACCAGCTG-AGGGCTTCAGC------AGCAGGACC-AGG i ponAbe2.chr17_random C 0 C 0 s cavPor3.scaffold_76 4308881 145 + 7991924 GATGCAGAAGG-GGAAAGAGCTGGGA-----------TGTAGGAGCAGGGAT-----------CAGCAAAGCTG-----------C--------------------------CACAAGCTGGGGTGAGTGAGCCGCCCTGTGCCA-------------------TGACAAGCAGGCCTGA-GC-----CCCGGCCAGCTG-AGCAAATTGGTGGCAGAGGCAAGACCTAAG i cavPor3.scaffold_76 C 0 I 272 s mm9.chr11 118680432 139 + 121843856 CATGAGGAAGG-GCTGGGTGCCGTGAA-----CAGCTTTCTGAATGAAGGAG-----------CATCAGAGCTG-----------T-------------------------GAACCTACTCATGCAGGTG-GCCTGCCTGAGCTA-------------------T-----GCAGATGTCA-GG-----TCCACACAGCTG-ACCACCTCACT-------ACAGAGCTCCAG i mm9.chr11 C 0 C 0 s bosTau4.chr19 10767412 189 - 65312493 CAGGAAGGGTGAGGTACTTTCTGAAGTGTGACCGACTTTCTGAAGGAAGTAA-----------TAGCAGAGCCAAGCACAAAGAGTGGAGCAGAAA--TGCAG--------GAAGGAGGTCAGGTAGGGGAGCCTCACCA-GCCAACTGAGGAGGTCTGAACACAGGGCAGGTGGCAGGAGAG-----ACAGGACAGCTG-GGGGT------------TGAAGGCCCCA-- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59369336 132 - 64418924 TAGGAGGAGTG-GGAGTGGGCTGGGGTGTGACCAGCTTTCAGAAGGGAGTAA-------------------CCA-----------TGGAGCAGCAGGTTGCAG--------GAGGGGGCTCAGCTG--------------------------------------AGGGCAGGTAGCAGGAGAG-------AAGGTGGCCC-AGGCC------------TGAAGGCACCC-- i canFam2.chr9 C 0 C 0 s ornAna1.chr2 50662367 172 - 54797317 CAGGAATCAGG-GAATCAGTTTTGGAACCTAGAAGTGTCCTTGAGGTGGTGGGGAGGGAGACCCAGAAATGTCC-----------TGAGGCAGAGGTGAG-----------GGGGAACCCCA-------AAATGCCCCTGAGATG-------------------GGGGAAAGGGGACCCAGAGATGTCCCTAAGATGCTGTAGGGC----GG------AGGGGGACCCAGG i ornAna1.chr2 I 5865 C 0 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57955133 146 - 61308211 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=13003.000000 s hg19.chr17_gl000204_random 28657 171 + 81310 CTGGAAGT----GAGGCCCGTCAAGGACTGAACCCAACCCTGCCTACAGAGGAGTATCTGTGGCCAGCGGCA-CAGTCACCAACACCAGC-ATCCGGT---CCAGGG---CCACAGCCTGAGATAGCCACACCCAACAGAGGCACAAGAGGACCCACGCAGGAGCCATGCAGAGCTGGAGGTC s rheMac2.chr16 74756309 170 + 78773432 CCAGAAGT----GAGGCCCGCCAAGGACTGAACCCAACCCTGCCTACAGAGCAGTATCTGTGGCCAGCGGCA-CCGTCACCAACACCAGC-ATCTGGG---CCAGGG---CCACAGCCTGAAACAGCCACACCCGGCAGAGGCACAAGAGGA-CCATGCAGGGGCCGTGCAGAGCTGGAGGTC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9223824 171 + 17838096 CCAGAAGT----GAGGCCCACCAAGGACTGAACCCAACCATGCCTACAGAGGAGTATCTGTGGCCAGCGGCA-CGGTCACCAACACCAGC-ATCTGGT---CCAGGG---CCACAGCCTGAGACAGCCACACCCAACAGAGGCACAAGAGGACCCACGCAGGAGCCATACAGAGCTGGAGGTC i ponAbe2.chr17_random C 0 C 0 s mm9.chr11 118680571 169 + 121843856 CCAGAAGGCCCAATAGGCCAGAAGGAAGCAAACCCTACCCTGCCTGGGGGAAGCCATCT-TAGCCAGAAGCC-AGACCA--AAAACTAGC--TCTGAGCACCTAGAG---AACTAGC-----ACGGACAGACCAGGTAGAAATAGACAGGGGCACATTCAGGTGCCCAGCTGAGCAGGAAGTA i mm9.chr11 C 0 C 0 s bosTau4.chr19 10767601 133 - 65312493 -----------AAAGGCCCACTGAAGAATTAGCTCAAATCTGCCTGCAGGGGAGTCCCT-TGGCCAGTGGCATATATCAGAAAGTCAATC--CCTCTG------------------------ACAAACATACTT----------GGAGAGAACCCACCTTGGTATCA--CAGAGCTGGAGGTC i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59369468 122 - 64418924 -----------CCAGGCCAGCTGAAGAGTCAGCCCCAACCTGCCTGCAGGGGGCACAGG-GGGCCCGTGG---ATGCTCACAAACGCAGC--CCTAGG------------------------GCAGG-----------------GTATGGAATCCGGCAGGGGATCA--CAGAGCCGG-GGTC i canFam2.chr9 C 0 C 0 s ornAna1.chr2 50662539 155 - 54797317 ------------ATGTCCCGGAGAGGG--GAGGTGAAGCGTATC--CAGAAATGTCCCT-GAGAGGGGAGGG-AAGATGCTGAGATGAGAGGCCTGGG---TCAAAGGGTACCTTGCC----GTGGGAAGGACCCATGGTTGCAGGAGGGG---TAAACAGAGGCCCTTGCCAGCTGCTCCCC i ornAna1.chr2 C 0 I 79 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57955133 146 - 61308211 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=9321.000000 s hg19.chr17_gl000204_random 28828 73 + 81310 GATGATTTTCATCTG-AACAGGGAGCTGGGC-----CCCGAGGAGGACTTGGAACCACCCAAGTCTGCCCCATCTTTGG s canFam2.chr9 59369590 73 - 64418924 AGTGATCCTC------ACTAGGCTGACAGGAGTGCGCAGGATGGGAGCCTGGAGCTGGCTCTGTGAGCCCATCTCTCAG i canFam2.chr9 C 0 C 0 s bosTau4.chr19 10767734 79 - 65312493 GGTGATTTTCACCAGAACTAGGAAGATGGGCAGGCGTAGGCGGGGATTATGGAGCAGACCAAGTAAGCCCCATCTTCAG i bosTau4.chr19 C 0 C 0 s mm9.chr11 118680740 58 + 121843856 AATGACTT----------AGGTGGGGTGGG-----------GGAGAAGTTGGAAATGGGGAGGCCCACCCTATTTCTGT i mm9.chr11 C 0 C 0 s ponAbe2.chr17_random 9223995 72 + 17838096 AATGATTT-CATCTG-AGCAGGGAGCTGGGC-----CCCGAGGAGGACTTGGAACTGCCCAAGTCTGCCCCATCTTTGG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74756479 46 + 78773432 AATGATTTTCATCTG-AACAGGGAGCTGGGC-----CCCAAGGAGGACTTGG--------------------------- i rheMac2.chr16 C 0 I 17 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50662694 79 - 54797317 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57955133 146 - 61308211 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=-10484.000000 s hg19.chr17_gl000204_random 28901 24 + 81310 G-GGTGGCTGTCTGTCCACGCAGTG s ponAbe2.chr17_random 9224067 24 + 17838096 G-GGCAGCTGTCTGTCCACACAGTG i ponAbe2.chr17_random C 0 C 0 s mm9.chr11 118680798 23 + 121843856 GCAGTAGCTGCCTGT--GAGCATTT i mm9.chr11 C 0 C 0 s bosTau4.chr19 10767813 21 - 65312493 G-CC---ATGTCTGTTCACAAAGCA i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59369663 23 - 64418924 C-CCTGGCTGTCTGTCCAGAGAGC- i canFam2.chr9 C 0 C 0 s ornAna1.chr2 50662773 13 - 54797317 -----AGGTGCCC-----CAAGG-- i ornAna1.chr2 I 79 I 264 s rheMac2.chr16 74756542 9 + 78773432 ----------------CACACAGTG i rheMac2.chr16 I 17 C 0 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57955133 146 - 61308211 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=1143.000000 s hg19.chr17_gl000204_random 28925 20 + 81310 GCCATCTGGGATATGG------------AGGG s canFam2.chr9 59369686 7 - 64418924 ------------TTGG------------GGG- i canFam2.chr9 C 0 C 0 s bosTau4.chr19 10767834 30 - 65312493 GAC-TCTGCGATTTGGGCCCGGGGTGAAGGG- i bosTau4.chr19 C 0 C 0 s mm9.chr11 118680821 20 + 121843856 TTATTCTGAAATTTGA------------AGGT i mm9.chr11 C 0 C 0 s rheMac2.chr16 74756551 20 + 78773432 GCCATCTGGGATATGG------------AGGG i rheMac2.chr16 C 0 M 809 s ponAbe2.chr17_random 9224091 20 + 17838096 GCCATCTGGGATATGG------------AGGG i ponAbe2.chr17_random C 0 C 0 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50662786 264 - 54797317 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57955133 146 - 61308211 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I a score=362.000000 s hg19.chr17_gl000204_random 28945 129 + 81310 TGGCACGTTTGCCACAGTTCAGGT-TCATCCCCATGCGTGCTTCCCCAGGTGTTGTGC-----------CCCGTTAAGGGTCGAAGCCCCC---TCCTCACAGCCCATCCTGTTTC-CCGGTCCCCTCG-------AGGATCTCCACAGGCG s ponAbe2.chr17_random 9224111 129 + 17838096 TGGCATGTTTGCCACAGTTCAGGT-TCATCCCCATGCTTGCTTCCGCAGGTGGTGTGC-----------CCAGTTAAGGGTCGAAGCCCCC---TCCTCACAGCCCGTCCTGTTTC-CTGGTCCCCTCG-------AGGATCTCCACAGGTG i ponAbe2.chr17_random C 0 C 0 s mm9.chr11 118680841 80 + 121843856 ---------TACCGTGTTCCTAATGTTAACCCCATGCTTGGTTCC------------------------------------CAGAACCACCGTGTTCTCTGCACCAATCCTG-------GGGCTGCC------------ATCTC-------- i mm9.chr11 C 0 C 0 s bosTau4.chr19 10767864 131 - 65312493 CAGCCCACTCCCCACAGT-------TAAGCCTCACTC-TGCTT-CCTGGGCATTATCCAAAGCCCACCTCCAGGAAAAGATCAAAGCCACC---TCTTCAC-ACCTGTCCCCTTTCTTCTGCCCTCCTGCAGGCCAGGGACACC-------- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59369693 131 - 64418924 CAGCATGTTCCCCAACCT-------TAATCCCCACACTTGCTTCCCTGGGCCTCAG-CACAGCCCCCCGCCAGGATACTCTGAGCCCCTCC---TCCCCACGGCCCATCACCTTTCTTCTGTGGGGTCGCAGAC--AGGATCCC-------- i canFam2.chr9 C 0 C 0 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50662786 264 - 54797317 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57955133 146 - 61308211 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e loxAfr3.scaffold_49 14298866 2295 - 17734757 I e rheMac2.chr16 74756571 809 + 78773432 M a score=-4924.000000 s hg19.chr17_gl000204_random 29074 66 + 81310 AGTTACC--TGG-CTTAGGTCGGGT-------------GGGAGGTGAAGA-GA-GGAACTTTCTAGTTGCTTTTCTCCAG--CTTG s ponAbe2.chr17_random 9224240 66 + 17838096 AGTTACC--TGG-CTTAGGTTGGGT-------------GGGAGGTGAAGA-GA-GGAACTTTCTAGTTGCTTTTCTCCAG--CTTG i ponAbe2.chr17_random C 0 C 0 s mm9.chr11 118680921 72 + 121843856 ---TACC--TGGCCTTCTGTCAAGTTCTGTATCTACCCAGGGACTGAAGATGA-GGGACT---TAGTTGGTCTTATT-----CTTG i mm9.chr11 C 0 C 0 s bosTau4.chr19 10767995 57 - 65312493 AGCTCAG--GGATGCTCTACTGGGC-------------AGGGACTG-GGA-CAGGGGAGT------------TACCCCAGCACTGG i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59369824 56 - 64418924 AGCTCCC--AGACACCCTCCTGGGC-------------AGGGCCAG-GGA-GA-GGAAGT------------CATCCCAGGGTCGA i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14301161 67 - 17734757 AGTTACCCTGGAGCTGGGATGGGGT-------------GAGAGGTGAGGG-GT-GGGAATTTCCAGTTGG--TTCTCCAGAGCT-- i loxAfr3.scaffold_49 I 2295 C 0 e xenTro2.scaffold_787 181006 60 - 417512 I e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50662786 264 - 54797317 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57955133 146 - 61308211 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e rheMac2.chr16 74756571 809 + 78773432 M a score=-20846.000000 s hg19.chr17_gl000204_random 29140 59 + 81310 GAAGT-GAGG-----------------------CCTTGGAGAAGCCTC--CTGAAGGGGAGAAGGGAGGGAC--------GGCTGGCAGG------GGT- s loxAfr3.scaffold_49 14301228 61 - 17734757 ---GT-GAGT-----------------------CTGTGGAGAAGCCTCAGTGCAGGGGCAGGATGGGAG-----------GGATGTTGGGGTGCCTGGC- i loxAfr3.scaffold_49 C 0 C 0 s canFam2.chr9 59369880 78 - 64418924 GGGTC-GACAGGGACTTTCTAGTTGGCTTTCTCCGCTGGCA---------CTAGGAGGCCTTGTGAGGCTACCCAGCCCTGG-----AGG------GGG- i canFam2.chr9 C 0 C 0 s bosTau4.chr19 10768052 47 - 65312493 GTAGC-GAGA-----------------------CCCTGGCCAAGCTAT--CTAGAGGGCCTGATG---------------GG-----AGG------GGC- i bosTau4.chr19 C 0 C 0 s mm9.chr11 118680993 51 + 121843856 GGGGCAGAAG-----------------------TGGTATATGAGTCCC------AGGCCAGGAGAGAGGCAC--------AG-----AAA------ATC- i mm9.chr11 C 0 C 0 s ponAbe2.chr17_random 9224306 59 + 17838096 GAAGT-AAGG-----------------------CCTTGGAGAAGCCTC--CTGAAGGGGAGAAGGGAGGGAC--------AGCTGGCAGG------GGT- i ponAbe2.chr17_random C 0 C 0 s xenTro2.scaffold_787 181066 52 - 417512 GCAGG-GGGA-----------------------GCTGGAGGAAGCAGC-----AAGGAGTGGAAGGACGCCT--------GG-----GGG------AGCT i xenTro2.scaffold_787 I 60 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50662786 264 - 54797317 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57955133 146 - 61308211 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e rheMac2.chr16 74756571 809 + 78773432 M a score=-44388.000000 s hg19.chr17_gl000204_random 29199 103 + 81310 CGGGAACACCAG------GGGGGAAGCAGAGAAGGGCGG-GGAGTTGGGGGGTGCAGGGGGC-TTCCGGGGGACA--AGGGAGGGGCACTA-GTGTAGAAGCCA--CGATGGGGTG s ponAbe2.chr17_random 9224365 102 + 17838096 CAGGAACACCA-------GGAGGAAGCAGAGAAGTGCAG-GGAGTTGAGGGGTGCAGGGGGC-TTCAGGGAGACA--AGGGAGGGGTACCA-GTGTAGAAGCCA--GGATGGGGTG i ponAbe2.chr17_random C 0 C 0 s mm9.chr11 118681044 75 + 121843856 TGAGTACAGCA-------ACAGGAGAGAGAGAAAGATA---------------GCAGGGGAC--TCTGGGGTAAT--AGGGAGGGGCACCT-GGTTATTGGC-------------- i mm9.chr11 C 0 C 0 s bosTau4.chr19 10768099 58 - 65312493 CGGAAACACCC---------------TCCAGGAAGGAA---------------TCCCTGGGC-TTCAGGAGTGAA--GGAACTGGG------GAACA------------------- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59369958 77 - 64418924 CGGGGGAGGCA---------------CAGAGAAGGGGG---------------GCGCGGGCT-CCCCGCAGTGGGCCTGGGCTGGGCAGATAGCGCAGAAGCCG--CAAT------ i canFam2.chr9 C 0 I 49 s loxAfr3.scaffold_49 14301289 72 - 17734757 CGTGCACTCCAGTGgggagggaggagcagagaagggag--------------------ggac--acaaggaggga--gggaggAGTCGCTG-GGAGA------------------- i loxAfr3.scaffold_49 C 0 C 0 s ornAna1.chr2 50663050 90 - 54797317 GGGTTGCTCTG-------GTGGGAGGCTGGGAAGAGCC---------------TTGGGGGGC-TGGGGAGAGGGA--GAGTCCAGGGGACA-GCGTGGGGTTGGTTTGATGGGAGG i ornAna1.chr2 I 264 I 21 s xenTro2.scaffold_787 181118 92 - 417512 AGAGGACACAG-------CGGGGAGTGGGAGGATGCATGAGGAGTCGGTGGATGCAGGGGGGAGCCAGAGGAAGC--AGTGAGGAGCAGGA-GGATGCATGG-------------- i xenTro2.scaffold_787 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e equCab2.chr11 57955133 146 - 61308211 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e rheMac2.chr16 74756571 809 + 78773432 M a score=-50523.000000 s hg19.chr17_gl000204_random 29302 131 + 81310 --GGGTACA-AGGGCACAA-------------GGAGGTA----------GGA--------agggggaacagggggtggaggtgt----ggggagag---ggagaggggactgggacaggg-------gtgcaaaaa------ggcgggaaggtgggggaggggt-gcagagggtggggaggtg-ggg s ponAbe2.chr17_random 9224467 131 + 17838096 --GGGTACA-AGGGCACaa-------------ggaggtg----------gaa--------agagggaacaaggggtggagatgt----ggggtgag---ggagaggggactgggacaggg-------gtgcaaaaa------ggcaggaaggtgggggaggggt-gcagaaggtggggaggtg-ggg i ponAbe2.chr17_random C 0 I 531 s mm9.chr11 118681119 50 + 121843856 --AGGCTTG-AGGGCA----------------------------------------------GGGGGATAAGAGG-------------------------------------------------------------------GACAAGAAGATGGGGGGGG----GCAGA----------------- i mm9.chr11 C 0 C 0 s bosTau4.chr19 10768157 122 - 65312493 -------CA-GGGGCAAAG-------------GGAGGTG----------TGG--------AGGCAGCACAGGGAGTGGAGATGTGGGAGGGTACAG---TGTGGGGCGATGAGCGCAGGG----------------------CGCAGGGAGGTGTGGGAGGGAC-ACGGGGGGCTGAGATACCTGGA i bosTau4.chr19 C 0 I 1 s equCab2.chr11 57955279 124 - 61308211 --GGGGACACGCGGTACAG-------------GGAGGTGAGCGCAGGGCTGG--------AAACAAGGCAgggagcggggagggaacaggggacag---gaagg------------aggg----------------------tgcaggaagggagaggagaggc--cagagggcaaggaggca-gga i equCab2.chr11 I 146 I 1 s loxAfr3.scaffold_49 14301361 105 - 17734757 ------AGG-TGGGCATCA-------------GAGGGCA-----------------------GGGGTGCAGGAAGTGGGGATGA----AGAGGATG---GGAGAGGCCCAGGGGACAGGGCTG--GGGTGCAAGAATTGGGGTGCAGGAAGGTGGGG------------------------------ i loxAfr3.scaffold_49 C 0 C 0 s ornAna1.chr2 50663161 160 - 54797317 --AGGCATC-AGTGCACGGCTTGGGTCTTGATCAAGGTG----------TGAAATTTAGTAGAGTAGCCAGGGGGTAGACAGTC----GAACTTTGACCAGAGCTGACAGTTGAGTGGAGCTAATGTGTTCAGAGATA----TGTGAGACGATTGGGGAAG------AGAAGATGGAGGCAAGTGGA i ornAna1.chr2 I 21 I 9 s xenTro2.scaffold_787 181210 109 - 417512 GGGAGCCAG-AGGACACAG-------------CGAGGAG----------CAG---------GAGGATGCATGGGGGAGCCAGA-----GGACACAGCAAGGAGCGGGAGGATGCATGGGG----------------------AGTTGGTGGATGCAGGGGGAACTGGAG------------------ i xenTro2.scaffold_787 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59370035 49 - 64418924 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e rheMac2.chr16 74756571 809 + 78773432 M a score=-38457.000000 s hg19.chr17_gl000204_random 29433 68 + 81310 gaggggtgcagagggtggggaggtggggcaggggtactgggg--------cagggatgg--gggtgc-----------------------gggaa------------ggtggg s mm9.chr11 118681169 44 + 121843856 ------TGCAAGAGG-------GCATAGCGGGAGT-----------------GGAATTG--GGGTGC-----------------------AGAAA------------GGTG-- i mm9.chr11 C 0 C 0 s bosTau4.chr19 10768280 68 - 65312493 ATGGGGTGCACTGGG-------AAGGGATGGGG-TGCAGGCA--------CATGGGTAG--AGTCGC-----------------------AGAGGGTATAGACCTgagg---- i bosTau4.chr19 I 1 C 0 s equCab2.chr11 57955404 44 - 61308211 aagga-------gga-------gggaggtgggg------------------atgggtgg--gggcac-----------------------agaggaggt--------gg---- i equCab2.chr11 I 1 C 0 s loxAfr3.scaffold_49 14301466 70 - 17734757 AAGGGGCATAGGCGGTTGAAA-GGGGTACAGGAATGCCTGGAGGC-----GGGGGACTG--GGGCGC-----------------------TGGAG------------GGTGAG i loxAfr3.scaffold_49 C 0 C 0 s ornAna1.chr2 50663330 83 - 54797317 GAGAGGGAAAGGGAG-------GAGAGACAAGATGGTCGAGATCCA-ACAGAGCAGTTT--TGGTGCTTTTGAATTTGCTGCAAAGCAGTAGA-------------------- i ornAna1.chr2 I 9 C 0 s xenTro2.scaffold_787 181319 65 - 417512 --AAGCCGCGAGGAGTGGACA-GATGCATGGGGGAGCCAGAGGACACAGCGTGGAGTGGGAGGATGC-----------------------A---------------------- i xenTro2.scaffold_787 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59370035 49 - 64418924 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e ponAbe2.chr17_random 9224598 531 + 17838096 I e rheMac2.chr16 74756571 809 + 78773432 M a score=705.000000 s hg19.chr17_gl000204_random 29501 36 + 81310 -ggaggggtgcagagggtggg--gaggtgggggaa--aggg s papHam1.Contig660872 0 36 + 1349 -GGAGGGATGCAGAGGGTGGA--GAGGTGAGGGAA--GAGG i papHam1.Contig660872 N 0 C 0 s mm9.chr11 118681213 22 + 121843856 -----------AGAGGGGAGG--AAGGAGTGGGA------G i mm9.chr11 C 0 C 0 s bosTau4.chr19 10768348 39 - 65312493 -gaggggatggaggaggtgggatggagcgaagggac-tgag i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57955448 37 - 61308211 -ggggggacgcagggggcggg--gacacctggagac-tagg i equCab2.chr11 C 0 I 2 s loxAfr3.scaffold_49 14301536 38 - 17734757 -GGAAGGGCTCAAGGTGTGGG--GATGTCTGGAGGCATGGA i loxAfr3.scaffold_49 C 0 C 0 s ornAna1.chr2 50663413 36 - 54797317 -GGAGGCGAGTAGGAAAGAGG--AGAGAGAGGGAA--AGGG i ornAna1.chr2 C 0 I 68 s xenTro2.scaffold_787 181384 35 - 417512 TGGGGAGTCGGTGGATGCAGGGGGGAGCCAGAGGA------ i xenTro2.scaffold_787 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59370035 49 - 64418924 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e ponAbe2.chr17_random 9224598 531 + 17838096 I e rheMac2.chr16 74756571 809 + 78773432 M a score=-1585.000000 s hg19.chr17_gl000204_random 29537 52 + 81310 -----tactggggcagg----ga------tgggggtgcaggaaggtgggaatggAATGCATGGGACA s loxAfr3.scaffold_49 14301574 54 - 17734757 -----CAG-GGTGCAGACTGTGG------GGAAGGGGCAGGAGGCAAGAGACGGAG-GCCTGGGAGG i loxAfr3.scaffold_49 C 0 C 0 s equCab2.chr11 57955487 30 - 61308211 -----cag-ggggcagg----ga------tggggacgcaggaaggt--------------------- i equCab2.chr11 I 2 C 0 s bosTau4.chr19 10768387 40 - 65312493 -----gga-ggggcagg----ag------gaggggagctggcaggtcagtggggaa----------- i bosTau4.chr19 C 0 C 0 s mm9.chr11 118681235 38 + 121843856 -----TAC----CCAAG----GAG-----TGAAGACACAAGAAGTGGGGAGTGGAG----------- i mm9.chr11 C 0 C 0 s papHam1.Contig660872 36 51 + 1349 -----TAC-GGGGCAGG----GA------TGAGGGGGCAGGAAGGTGGGAATGGAGTCCATGGGACA i papHam1.Contig660872 C 0 C 0 s xenTro2.scaffold_787 181419 51 - 417512 ACCAGCGA-AGAGCAGG----AGGACGCATGGGGGAGCCAGAGGACACAGTGGGGA----------- i xenTro2.scaffold_787 C 0 C 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e ornAna1.chr2 50663449 68 - 54797317 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59370035 49 - 64418924 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e ponAbe2.chr17_random 9224598 531 + 17838096 I e rheMac2.chr16 74756571 809 + 78773432 M a score=-49830.000000 s hg19.chr17_gl000204_random 29589 120 + 81310 GGCACAGGTACATAAAGGTGGTTG-GGGGCACA------GGGGTGCAGATGGAG------GGAGGTGGG-----------GGAGAGG-GTATGACAGGGTAGGGCAC--------------GGGGCAGGG-------------GAGGGGTGCAGACATCCACAGTCTGGGTG-- s papHam1.Contig660872 87 122 + 1349 GTGACAGGTACAGAAAGGTGGTTGAGGGGCACA------GGGGTGCAGATGGAG------GGAGGTGGG-----------GGAGAGG-GTATGACAGGGTGGGGCAC-------------AGGGGCAGGG-------------GAGGGATGCAGACACCCACAGTCTGGGTG-- i papHam1.Contig660872 C 0 C 0 s mm9.chr11 118681273 50 + 121843856 -------------------------GAGGTA-----------------------------------GGG-----------AGAGGAG-ACATGGCATG-----------------------AGGGTGAGA-------------GAAGGGTGCG------------CTGAG---- i mm9.chr11 C 0 C 0 s bosTau4.chr19 10768427 99 - 65312493 ---------------------gtgtggggga--------ggggcgcagaaggtg------ggaactaggtggagggaggtggggagg-gCTCAG---------------------------CAGGTAGGGTCGAAGGAGCTGTCTGGAGTCGGGGGG--------CCGGG---- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57955517 70 - 61308211 --------------------------gggta--------ggggtgcagagggtg------ctgacgcgg-----------ggagggg-gcacag---------------------------ggagtggga-------------atggggtgcgggca--------gcggg---- i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14301628 110 - 17734757 GGTGCAGG--------GATGCCTG-GAGGCA--------TGGACTGGGGTGCAG------GGAGGTGGA-----------GGAGGGGTACAGGATAGGGGGATGCCT-------------GGAGGTGGGG-------------ACAGGGTGCAGGCTGTCAGGGAGGGGC---- i loxAfr3.scaffold_49 C 0 C 0 s ornAna1.chr2 50663517 129 - 54797317 --------ACCACCACTCCAAGCATGGGGCA--------GGGGAAATGGAGAAGACCCCTGGGGCTGGGTGGAG------GGGGGGG-CCAGGGTGGGGTTGGGTTGC-TATGGTG----GGAGGCTGGG-------------AAGAGCCTTGGGGGGCTGGGGAGAGGG---- i ornAna1.chr2 I 68 C 0 s xenTro2.scaffold_787 181470 120 - 417512 -------------------------GGGGGAGGACGAATGGGGAGTCGGTGGAC------GCAGCGGCG-AGTG------GGAGGAA-GCAGTGGGGAGTGGGCCATAGTATGAGGACACGGGGGGAGGA-------------CTTTAGTCCAGCCCCCAACAGTCTGAG--GG i xenTro2.scaffold_787 C 0 N 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59370035 49 - 64418924 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e ponAbe2.chr17_random 9224598 531 + 17838096 I e rheMac2.chr16 74756571 809 + 78773432 M a score=-25991.000000 s hg19.chr17_gl000204_random 29709 82 + 81310 CAGGTGTAGGGTGGCAGAAGGTGGT--------TGGGGGTGTAGGCGGTGGACGGGGTGGAGGTTAA---GGCAGAGGCCCCTGTGGGCAG-------GG s papHam1.Contig660872 209 82 + 1349 CAGGGGTGGGGTAGCAGAAGGTAGT--------TGTGGTTGTAGGGGGTGGATGGGGTGGAGGTTAA---GGCAGAGGCTCCTGTGGGCTG-------GG i papHam1.Contig660872 C 0 C 0 s mm9.chr11 118681323 79 + 121843856 -GGGTGTGGAGTGCTGGCCTTGGAC--------TCAGGGAGCAGGGGGTGCCCAAGCTACAGAGTAA------------CCCCAGAGGCAGATTGAGTGG i mm9.chr11 C 0 C 0 s bosTau4.chr19 10768526 57 - 65312493 -GGTTGAGGAGTGAG-------GAT--------GAGACTTGTCTGCAGTTGCTCCAGCC--------------------CCTCCTAGGTGG-------GC i bosTau4.chr19 C 0 I 73 s equCab2.chr11 57955587 53 - 61308211 -ag----ggggtggc-------ggc--------tgggCCCCCGCGCTGTGCTCCGGGCG--------------------CCGCCTGGACCG-------GG i equCab2.chr11 C 0 I 8 s loxAfr3.scaffold_49 14301738 68 - 17734757 -AGGAGGTGGGCACCAGTGCGGGGC--------AGGGTGCTGGAGGGCCCCCCCCAGCCTGGG----------------GCCTGTGGACAG-------CG i loxAfr3.scaffold_49 C 0 I 5 s ornAna1.chr2 50663646 78 - 54797317 -AGAGTCCAGGGGACAGCGTGGGGTTGGTTTGATGGGAGGGTGGGGAGAACCTTGGGTGGGGGCTGGGTGGGCAGATGC--------------------- i ornAna1.chr2 C 0 N 0 e turTru1.scaffold_106006 24205 8850 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59370035 49 - 64418924 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e ponAbe2.chr17_random 9224598 531 + 17838096 I e rheMac2.chr16 74756571 809 + 78773432 M a score=-12005.000000 s hg19.chr17_gl000204_random 29791 33 + 81310 ACCCTGCAGGC----CGGGACCCTGCAGGCCTCCAGC---------- s papHam1.Contig660872 291 18 + 1349 ACCCTGCA--------------CT-----CCCCCAGC---------- i papHam1.Contig660872 C 0 C 0 s mm9.chr11 118681402 31 + 121843856 ACCCCACAGGCAAAGCAGAATTTT----GTTTCCA------------ i mm9.chr11 C 0 C 0 s turTru1.scaffold_106006 33055 28 + 145505 GCCCGGCAGATAGCGCA-----AT----GCCAGCAGC---------- i turTru1.scaffold_106006 I 8850 I 83717 s equCab2.chr11 57955648 28 - 61308211 GCGCGGTCGCGACGGCG-----CT----GCTTCCCGC---------- i equCab2.chr11 I 8 I 4 s loxAfr3.scaffold_49 14301811 43 - 17734757 ACCCTGCCCTTGCTCAGAAGCTCT----TTTCTCACTTATCTCCCCG i loxAfr3.scaffold_49 I 5 C 0 e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59370035 49 - 64418924 I e bosTau4.chr19 10768583 73 - 65312493 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e ponAbe2.chr17_random 9224598 531 + 17838096 I e rheMac2.chr16 74756571 809 + 78773432 M a score=-3249.000000 s hg19.chr17_gl000204_random 29824 53 + 81310 CTCGGCACAGCCTGAGCAGTGGCAGCGTGGCAGATGGGAACGTGCAGAAACAT s papHam1.Contig660872 309 43 + 1349 ATCGGCGCAGCCTGAGCTGTGACAGCGTGGCAGATGGGTAT----------AT i papHam1.Contig660872 C 0 C 0 s mm9.chr11 118681433 20 + 121843856 -----------CTG---------AGTGTAGAAGATAGT-------------GT i mm9.chr11 C 0 C 0 s equCab2.chr11 57955680 23 - 61308211 CTCGGCGCCGCCTGAGC------TGCGCG------------------------ i equCab2.chr11 I 4 C 0 s loxAfr3.scaffold_49 14301854 37 - 17734757 CCTGCCTGTGTCTTCGCCGTGGAAGCATGGCAGTTGG---------------- i loxAfr3.scaffold_49 C 0 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304298496 1812 - 541556283 I e canFam2.chr9 59370035 49 - 64418924 I e bosTau4.chr19 10768583 73 - 65312493 I e cavPor3.scaffold_76 4309026 272 + 7991924 I e ponAbe2.chr17_random 9224598 531 + 17838096 I e rheMac2.chr16 74756571 809 + 78773432 M a score=14116.000000 s hg19.chr17_gl000204_random 29877 33 + 81310 GCAGAAGCATGGCCCCTGGTTAATAAGATTAGG s equCab2.chr11 57955703 32 - 61308211 GCGGAAACCTGGCGCTCGGT-AATAGGATTTTG i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10768656 32 - 65312493 GTGGAAGCACAGCATTTGGT-AATAGGATTTCG i bosTau4.chr19 I 73 C 0 s mm9.chr11 118681453 28 + 121843856 GC-----CAGGATACTAGGTAACCTCGTTTGAG i mm9.chr11 C 0 I 16 s papHam1.Contig660872 352 33 + 1349 GCAGAAGCATGGCCCCTGGTAAATAGGATTGGG i papHam1.Contig660872 C 0 C 0 s monDom5.chr2 304300308 29 - 541556283 ---GAAACGTGGCATTAAAT-AATGAGATTTGG i monDom5.chr2 I 1812 C 0 s loxAfr3.scaffold_49 14301891 13 - 17734757 --------------------TAACAGGATTTTG i loxAfr3.scaffold_49 C 0 C 0 s canFam2.chr9 59370084 29 - 64418924 ---GAAACACGGCGTTTGGT-AATAGGATTTTG i canFam2.chr9 I 49 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e otoGar1.scaffold_94361.1-85690 47999 572 + 85690 I e panTro2.chr17 79201655 1752 + 83384210 M e cavPor3.scaffold_76 4309026 272 + 7991924 I e ponAbe2.chr17_random 9224598 531 + 17838096 I e rheMac2.chr16 74756571 809 + 78773432 M a score=91085.000000 s hg19.chr17_gl000204_random 29910 141 + 81310 ATGTTGAACGGCCGACATGTTCTCCGAGACTGGCTGTATGCCACAAATGGAGGGGACTGCGACCTTAATAGAA-------------------TGCTGAACTTTTGGAAAGTGGAGCAAAATGGAGAGAG------------TCAGAGTT--------------------------------------GGGGACTGAGAGTCCCCCTCTCG- s papHam1.Contig660872 385 141 + 1349 ATGTTGAACAGCCGACATGTTCTCCGAAACTGGCTCTATGCCACAAATGGAGAGAACTGTGACCTTAATAGGA-------------------TGGTAAACTTTTGGAAAGTGGAGAGAAATGAAGAGAG------------CCAGAGTC--------------------------------------GAGGACTGAGGGTCCCCCTCTCT- i papHam1.Contig660872 C 0 C 0 s otoGar1.scaffold_94361.1-85690 48571 189 + 85690 ATGTTG-ACAGTCCACGTTTTCTTCTGAACTGCCTTTATATCACAAATAGCCAGACCTATGACCTT-ATAAAT-------------------TCCAGACCTTTTGGAAAGTGGACATATATGGAGGGGGGACATAGAAAGCCTAGAGTCCTCTCCCCCCAGGCCACACATATAGCCTGCCCTAGGTGGGGGGCATAGGGTGACCTTTCCC- i otoGar1.scaffold_94361.1-85690 I 572 I 2 s mm9.chr11 118681497 95 + 121843856 ATACTAGGTAGCC------TCCTTCGAGAC---------ACTGTAACTAGAAGAGATTGCCACCTTAACAGAT-------------------T-CTGAACTTTTGAAAAACCAAGCCGAAATGAAAGTG------------T--------------------------------------------------------------------- i mm9.chr11 I 16 C 0 s bosTau4.chr19 10768688 138 - 65312493 ATGTTGAACAGCTGACATTTTCTCC-AGACTGGCTTTACATCACCAATGGAGGGGACCAAGGCCTTAACAGGA-------------------TTCT-AAATCTTGCAAAGTGGAGAGAAATGGAGGGGG------------CGGA-ATG--------------------------------------GGGACTCCCAGGGCTCCCTCCCG- i bosTau4.chr19 C 0 I 22 s equCab2.chr11 57955735 139 - 61308211 ATGTTGAACAGCAGACGTTTTCTCCGAGACTGGCTTTAGGTCACAAATGGAGGGGACCGCCACCTTAATAGG--------------------TTCT-AACTTTCGTAAGGTGGAGAGAAACCGAGAGGG------------TGGGAATG--------------------------------------GAGACTCCTGGAGCTCCCTCCCC- i equCab2.chr11 C 0 I 51 s canFam2.chr9 59370113 138 - 64418924 ATGCTGAACAGCCCAACTTTTCTCCGAGACTGGCTTTACGTCACAAATGTAGGGAACTGCGACCTTAATAGGA-------------------TTCT-AACTTTTGGGCCATGGACAGAAATGGGGAGGG------------CGGG-ATA--------------------------------------GAGACTCCTGGA-TGCCCTCCCG- i canFam2.chr9 C 0 I 40 s loxAfr3.scaffold_49 14301904 140 - 17734757 ATGTTGAATAGCCGGCGTTTGCT--GAGACTGGCTTTATGTCACAAATGGAGGGGCCCCCGCCCTTCATAGGA-------------------TTCTGAACTTTGGGGATGTGGAGAGGAATGGGACAAA------------CAAGCAGA--------------------------------------AAGGCTCCTGGGGTCCCTCCCCAG i loxAfr3.scaffold_49 C 0 C 0 s monDom5.chr2 304300337 152 - 541556283 ATGTTGAACAGCAGACTTCCTTCTTGAGACTGACTTAACTTCACAAATGTAGGGAACTATAGGCTTAATGGGAGGTAACCCCAGGCAAAAGGTTCTGAACTTGCAGAAAACAGGAGAAAA----GAAAA------------TGTAAATA--------------------------------------ATTCCTAGAGAGTCTTTCT----- i monDom5.chr2 C 0 I 404 e turTru1.scaffold_106006 33083 83717 + 145505 I e panTro2.chr17 79201655 1752 + 83384210 M e cavPor3.scaffold_76 4309026 272 + 7991924 I e ponAbe2.chr17_random 9224598 531 + 17838096 I e rheMac2.chr16 74756571 809 + 78773432 M a score=45056.000000 s hg19.chr17_gl000204_random 30051 137 + 81310 GGCTGGAGGCCAGGGCT-----ACT---------GGTGACCTG--AGGGCTT--CC----------------------GGGAGTTCAGAGTGGGG-CA-TTTTCAC---TT-CTGGATCCTAAAAGCCGGTGGGCCTGGATG-GGACTCATTCC------TTGGCGTCCTGTTACAGCAA------------CAGGAATGAC s rheMac2.chr16 74757396 138 + 78773432 GGCTGGAGGCCAGGGCT-----ACT---------GGTGACCTG--TGGGGTT--CT----------------------GGGAGTTCAGAGTGGGGACA-TTTTCGC---TT-CTGGGTCCTAAAAGCCAGTGGGTCTGGATG-GGACGCATTCC------TTGGCGTCCTGTTACAGCAA------------CAGGAAAGAC i rheMac2.chr16 M 809 C 0 s papHam1.Contig660872 526 137 + 1349 GGCTGGAGGCCAGGGCC-----ACT---------GGTGACCTG--TGGGGTT--CT----------------------GGGAGTTCAGAGTGGGG-CG-TTTTCAC---TT-CTGGGTCCTAAAAGCCAGTGGGTCTGGATG-GGACGCATTCC------TTGGCGTCCTGTTACAGCAA------------CAGGAAAGAC i papHam1.Contig660872 C 0 C 0 s otoGar1.scaffold_94361.1-85690 48762 141 + 85690 GGCAGGAGCCTGGAG-------ACA---------GGTGACAAG--AGTGGTG--TG----------------------GGGAGTTCCAAGTGGGG-CATTTTTTGC---AT-CTGGA-AATAACAGACAG-GGGCTGGGTAA-AGATTCATTCT------TTGGTTTCCTGTTACAGCAATGATGCCCCT--CAGGC---CC i otoGar1.scaffold_94361.1-85690 I 2 C 0 s mm9.chr11 118681592 109 + 121843856 -------GTTCAAGG--------------------------------GAGGC--CC--------------------CAGGGAGCTCAAAGGTGGA-CT-T---------------------GAAAGCCAGCAAACTTAGCCACAAACTTTCCCAGACAGATAGG------CATGAAACTT---TTCCCTTGCCCGGAGTTCT i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4309298 126 + 7991924 ------------------------T---------GGTGGCACA--AAGGGTT--CC--------------------TGGGGAGTTCAGAGTGGGG-CC-TTTTGGC---TT-GGGGGTCACAAAAGTCAATGGGTCTTGGTGGAGACTCATTCATTC---TTGGCTTCCACTTGCAGGAC---TCCTCTTGCCTG------- i cavPor3.scaffold_76 I 272 C 0 s ponAbe2.chr17_random 9225129 115 + 17838096 -------------------------------------GACCTG--AGGGCTT--CC----------------------AGGAGTTCAGAGTGGGG-CG-TTTTTGC---TTTCTGGGTCCTAAAAGCCAGTGGGCCTGGATG-GGACTCATTCC------TTGGCGTCCTGTTACAGCAA------------CAGGAATGAT i ponAbe2.chr17_random I 531 C 0 s bosTau4.chr19 10768848 134 - 65312493 GACCAGCATTTTGAGGT-----------------GCTGATGGG--AGGGGTG--CT-----------------------AAGGACTTTAGGGGTG-TA-GTGTGGC---CT-TTGGGTCATAAAAGCCAGTGGGCCTGAGTGAAGACTCATTCT------TTGCTCTTGCAATGCAGGAA------------CTGAAATGAC i bosTau4.chr19 I 22 C 0 s equCab2.chr11 57955925 150 - 61308211 GACTGGCGTTTCGGGGC-----ACCGGTCCCTCAGGTGGTGTGACAGGAGCGCCCT-----------------------GGAGTTCAGAGTGGGG-CG-TTGTTGC---TT-CTGGGTCACAAAAGGGGCTGGGCCTGGGTGGAGATTCATTCC------TTGGCTTCCCGGTACAGGAA------------CAGGAACGAC i equCab2.chr11 I 51 C 0 s canFam2.chr9 59370291 124 - 64418924 GGCGGGGGCT------------------------GGTGGTGGG--AGGGGCG--CT-----------------------GGGGCTTTGGAGTGGG-CC-TTGTCCCCTGCT-CCGGGTCCTGACAGCCAGGAGGCCTGCATGGAGACTCCTTCC------TGAGCTCTGTGTTGTAGGAA------------CAGA------ i canFam2.chr9 I 40 C 0 s loxAfr3.scaffold_49 14302044 159 - 17734757 ----AATGCCTGAGGGCCTGCTGCC---------GGAGGCCCG--GTGGGTC--CTGGGACCCAGCCCTGAGGACGCAGGGAGGGCAGACTAGGG-CG-GGTGCGC---TT-CAGGGTCATAGAGGCTGGTGAACCGGGGCAGAGGTTCCTTC-------TTGGTTTCGGTTTCCAGAAG-------------AGGTGTGAC i loxAfr3.scaffold_49 C 0 I 59 e turTru1.scaffold_106006 33083 83717 + 145505 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304300489 404 - 541556283 I a score=19494.000000 s hg19.chr17_gl000204_random 30188 46 + 81310 CAGCGCTC--------------------CTA--------------AAGGCCCCCCACCTGGCCCTGAGAC-------------------CTCCA-TCTCT s rheMac2.chr16 74757534 46 + 78773432 CAGCGCCC--------------------CTA--------------AAGGCCTCCCACCTGGCCCTGAGAC-------------------CTCCA-TCTCT i rheMac2.chr16 C 0 C 0 s papHam1.Contig660872 663 46 + 1349 CAGCGCCC--------------------CTA--------------AAGGCCTCCCACCTGGCCCTGAGAC-------------------CTCCA-TCTCT i papHam1.Contig660872 C 0 C 0 s otoGar1.scaffold_94361.1-85690 48903 59 + 85690 CAGCCCCC--------------------CTCCCCGCTGTGGGCCTGGGGTCCCCCA-CTGGCCCTGAGAT-------------------CTCTA-TCTCT i otoGar1.scaffold_94361.1-85690 C 0 I 276 s mm9.chr11 118681701 30 + 121843856 GATCTGCC--------------------CTG--------------GATCCCTCC-----------------------------------CCCAA-CTTCT i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4309424 61 + 7991924 ---CTCCC--------------------CTA--------------GATCCCCTCTT-TTGGGCCTGAGGTCACCTAGCTTGTCCTGAAACCCCA-TCTGT i cavPor3.scaffold_76 C 0 C 0 s ponAbe2.chr17_random 9225244 46 + 17838096 GAGTGCCC--------------------CTA--------------AAGGCCCCCCACCTGGCCCTGAGAC-------------------CTCCA-TCTCT i ponAbe2.chr17_random C 0 C 0 s bosTau4.chr19 10768982 56 - 65312493 TGTTTCCC---------CTCCCTGGAGTCCA--------------AGTGCCC--GACCTGGCCCTGAGTC-------------------CTCCGTTCTGT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57956075 66 - 61308211 AGCCTCCCCCCGAAGGCCTCTTTCAGACCTA--------------GGGTCTTGGGAAGACGCCCTGAGAC-------------------CTCCA-TCTCT i equCab2.chr11 C 0 C 0 s canFam2.chr9 59370415 48 - 64418924 -----------------CCCCTTCAGAACCT--------------GGGGTTTCAGAACTGGCCCCAAGAC-------------------CTCCA-CCT-G i canFam2.chr9 C 0 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304300489 404 - 541556283 I e loxAfr3.scaffold_49 14302203 59 - 17734757 I a score=20125.000000 s hg19.chr17_gl000204_random 30234 37 + 81310 ---------------------------GCCCACGGTCTGGCTGCATCT---------CCTGGAAGGTTTTGTT s canFam2.chr9 59370463 66 - 64418924 GCTGCACACTCA--GGTCCAAGGGGTTGCCTACAGCCTG--TGTTTCCGGGCAGGTATCT---TGGTTTATTT i canFam2.chr9 C 0 I 247 s equCab2.chr11 57956141 60 - 61308211 GCTGCACACTCACCAGTCTAGGGGTTTG-CTGCAGCCTGGCTGCATCT---------CCT---AGGTGTGTTA i equCab2.chr11 C 0 I 1 s bosTau4.chr19 10769038 60 - 65312493 GGTGCACTCCCA--GGTCTGGGGGTTT--CTGGAGCCTGACTGTGTCT---------CCTGGAAGGTTTTTTA i bosTau4.chr19 C 0 I 1 s cavPor3.scaffold_76 4309485 32 + 7991924 ---------------------------GCCTGCGGCCTTGC-----CC---------ACAGCAGCATTCTCTC i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118681731 37 + 121843856 ---------------------------GCCTACAGCCTGACTGCATTC---------CCTGCAGGAATTTCTC i mm9.chr11 C 0 C 0 s rheMac2.chr16 74757580 37 + 78773432 ---------------------------GCCCACGGTCTGGCTGTATCT---------CCTGGAAGATTTTTTT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9225290 37 + 17838096 ---------------------------GCCCACAGTCTGGCTGTGTCT---------CCTGGAAGATTTTTTT i ponAbe2.chr17_random C 0 C 0 s papHam1.Contig660872 709 37 + 1349 ---------------------------GCCCACGGTCTGGCTGTATCT---------CCTGGAAGATTTTTAT i papHam1.Contig660872 C 0 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e otoGar1.scaffold_94361.1-85690 48962 276 + 85690 I e panTro2.chr17 79201655 1752 + 83384210 M e monDom5.chr2 304300489 404 - 541556283 I e loxAfr3.scaffold_49 14302203 59 - 17734757 I a score=164766.000000 s hg19.chr17_gl000204_random 30271 198 + 81310 TTTT-AATGCTCCTGTCCTGGGGCTC------------------------------TT--CCT-----------CTCTCTAGGCCTAGC----ACACAC--TTCCAGCCTGGGCATCAGGGAAAT--AACTCAAAACCATAACA-CGCTTT----------AAA-----------------AAATACACTAGC-CAGCAACTGCAACAAC---ATTTGCTTTGCACAAACATTTCAAGAGAATTCCCCA------------------------------------------------------------------------------------GATAGTCTTGCT----------GTGGGGGAATTCTAGCCACCA s papHam1.Contig660872 746 196 + 1349 TTT--AATGCTCCCATCCCGGGGCTGC----------------------------ACC--CCT-----------CTCTCTGGGCCCAGC----ACATAC--TTCCAGCCTGGGCATCAGGGAAAT--AACTCAAAACCATAACA-CACTTT----------TAA-----------------AAATACACTTGC-CAGCAACTG---CAAC---ATTTGCTTTGCACAAACATTTCAAGAGAATTCCCCA------------------------------------------------------------------------------------GATAACCCTGCT----------GCGGGAGAATTCTAGCCACTG i papHam1.Contig660872 C 0 C 0 s ponAbe2.chr17_random 9225327 199 + 17838096 TTTTTAATGCTCCTGTCCTGGGGCTG------------------------------TT--CCT-----------CTCTCTAGGCCTAGC----ACACAC--TTCCAGCCTGGGCATCAGGCAAAT--AACTCAAAACCATAACA-CGCTTT----------AAA-----------------AAATACACTTGC-CAGCAACTGCAACAAC---ATTTGCTTTGCACAAACATTTCAAGAGAATTCCCCA------------------------------------------------------------------------------------GATAGTCTTGCT----------GTGGGAGAATTCTAGCCACCA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74757617 196 + 78773432 TTT--AATGCTCCCATTCCGGGGCTGC----------------------------ACC--CCT-----------CTCTCTGGGCCCAGC----ACATAC--TTCCAGCCTGGGCATCAGGGAAAT--AACTCAAAACCGTAACA-CACTTT----------AAA-----------------AAATACACTTGC-CAGCAACTG---CAAC---ATTTGCTTTGCACAAACATTTCAAGAGAATTCCCCA------------------------------------------------------------------------------------GATAACCCTGCT----------GCGGGAGAATTCTAGCCACCG i rheMac2.chr16 C 0 C 0 s mm9.chr11 118681768 199 + 121843856 A----ACTGCTCCCAA-----------------------------------------C--CTAGAGCCTATTGCTTCTCTGCACACAGC----CCACTC--TTCCAGCACGCACATTAGGGAAAT--GGCTTAAGACAGCAGTG-TGTTTT----------AAG-----------------AATCA---TTGC-AAGAGACGC-AGTGAC---ATTTGTAGTGCACAAGTGTTC--GGAAGAATTCCCA------------------------------------------------------------------------------------GGCAAGCCTGCTCTGTTCTGCCCTGGAAGAATTCTAGCCACCA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4309517 179 + 7991924 C----TAGGTTGTCAC-----------------------------------------C--ACA-----------CTCTCTGGA-ACA------CCCCTC--ATCCAGCCTGGGCATTGGGGAAAT--GACTCAAGACAGTCACA-TGCTTTT--------ATAA-----------------AATTA---TCAC-CAGCAACAG-TGAAAC---ACTTGCTTTATCCATGCATTCCAAGAGAACTCCCCA------------------------------------------------------------------------------------GACAGCCCTGCT----------CTGGGAGAACTCCAGCCACGG i cavPor3.scaffold_76 C 0 C 0 s monDom5.chr2 304300893 198 - 541556283 -TTTTA--------------AGGCTGC----------------------------TTCAGTCA-----------ATTCCTGAGCCCAGTCATGGAATTA--TCCCAAAGTTGGCATTAGAGATAT-------AAAATAGTAACAGTGCTTTTTTAAAAAGGCAA-----------------AACAATTATTTC-CAGTGACTATAATAAC---ATTTGCTTTCCACAAACATTCTGAAAGAATTCCTAG------------------------------------------------------------------------------------GACAATACTGCT----------CTGGAAGAATTCTAGCAACCA i monDom5.chr2 I 404 C 0 s otoGar1.scaffold_94361.1-85690 49238 212 + 85690 ----------------cttgaggctccgtctcaaaaaaaaaaaaaaaaaaaaaaaGCC--CCT-----------GTCCTAGGGTTCAA-----GGACAC--GTCCAGCCTGGGCATTGAGGAAAT--AACTCAAAACAGTAACT-GACTTT----------TTA-----------------AAAAATCCTTGCTTAGGGATTGTAACAAT---ATTTGCTTTGCACAGACATTTTGAGAGAATTCCCCA------------------------------------------------------------------------------------CAGGACCCTGCT----------CCTGGAGAATTCTGGCCCCA- i otoGar1.scaffold_94361.1-85690 I 276 C 0 s equCab2.chr11 57956202 173 - 61308211 -------------------------AT----------------------------GCC--CCC-----------CTCCCTGGGCAGGAC----GCACACAGTTCCAGCCTGAGTGTTGGGGAGAT--AACTCACAATGGTAACA-TGCTTT----------AAAG----------------AAATACACTGTT--AGCTACTG---TAAC---ATTCACTTTGCACAAACATTCGTAGAGAATTCCCGG------------------------------------------------------------------------------------GAGGGCCCTGCT----------CTGGGAG-ATTCTAGCCACC- i equCab2.chr11 I 1 C 0 s canFam2.chr9 59370776 259 - 64418924 ------GCGTTCCCTCCCAAGGGCCGC----------------------------ACC--TCC-----------CTCCCTGGGCACAGC----GCACACAGCTCCAGTCCAAG-GATGAGAAAAT--AACTTGCATCAGTAACA-TGCTTT----------AAAA----------------ATACATTTCGCC-AAGCTGCTA---TAAC-----------------AACATTTGC-----ATGCACAGTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGGGCCCTGCT----------CCGAGAGAATGCTAGCCACCA i canFam2.chr9 I 247 C 0 s bosTau4.chr19 10769099 202 - 65312493 ------ATGTTCCCACTGTTGGGTCAC----------------------------ACC--TCT-----------CTCCCTGGGCACAGG----GAATGCAGTTCAAGCCTGAG-TATCAGGAAATAAAACTTAAAATGATAATG-TGCTTA----------AAAAAAAAatatatatatatatatatatCACC-TAGCTACTG---TAACCACATGTCCTTTGCACAAACATTCCA--AGAATTCCC--------------------------------------------------------------------------------------AAGGGCCCTGCT----------GTGGGATAATTC--------- i bosTau4.chr19 I 1 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e panTro2.chr17 79201655 1752 + 83384210 M e loxAfr3.scaffold_49 14302203 59 - 17734757 I a score=143191.000000 s hg19.chr17_gl000204_random 30469 113 + 81310 GGAGAAAGCTGCCC-------AGGCCCTGGCG-GGG-CTTGGC---TTCccagcggtc-cctggccacc-ttgaggacaggaggcaaacagggacagacag--cagc-agaggggtttgaggccacaaca s panTro2.chr17 79203407 110 + 83384210 GGAGAAAGCTGCCC-------AGGCCC-GGCG-GGG-CTTGGC---TTCCCAGCGGTC-CCTGGCCACC-T-GAGGACAGGAGGCAA-CAGGGACAGACAG--CAGC-AGAGGGGTTGAGGGCCACACNA i panTro2.chr17 M 1752 C 0 s ponAbe2.chr17_random 9225526 113 + 17838096 GGAGAAAGCTGCCC-------AGGCCCTGGCG-GGA-CATGGC---TTCTCAGCGGTC-CCTGGCCACC-TTGAGGACAGGAAGCAAACAGGGATAGACAG--CAGC-AGAGGGATTTGAGGCCACAACA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74757813 113 + 78773432 GGAGAAAGCTGCCC-------AGGCCCCAGCG-GGG-Catggt---ttctcagcggtc-cccagccacc-ttgaggacaggaggcaaacagggacagacag--cagc-agagggattcgaggccacaaca i rheMac2.chr16 C 0 C 0 s papHam1.Contig660872 942 114 + 1349 GGAGAAAGCTGCCC-------AGGCCCCAGCG-GGGACATGGC---TTCTCAGCGGTC-CCCAGCCACC-TTGAGGACAGGAGGCAAACAGGGACAGACAG--CAGC-AGAGGGATTCGAGGCCACAACA i papHam1.Contig660872 C 0 C 0 s otoGar1.scaffold_94361.1-85690 49450 106 + 85690 GGAGAAAG--------------GGGCCTGCTGCGGG-TGGGGC---TTCTCAACTATG-TCCCACCATC-CTGAGGACAGGAGGCAAAT-GGGGCAGACTA--CAGG-GAGAGGGTGTGAATCCAAATCA i otoGar1.scaffold_94361.1-85690 C 0 C 0 s mm9.chr11 118681967 89 + 121843856 GAAGGAAGCTATCC-------AGGTCCCTATG-TAG--ACACC---TCACAGACCTTC-------------------TGGGAGGGGA-AGGGAATAGAACGTCTGTCAACAAGGAGATGATG-------- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4309696 114 + 7991924 GGAGAAAGCTGCCC-------AGGTCCCTGTG-TGA--ATGCCAGGTCCTTGAccgtcctccatctccc-ccaagaacaggaggcaa-tggggacagactg--tagccagagggagctgaggcagaca-- i cavPor3.scaffold_76 C 0 C 0 s canFam2.chr9 59371035 115 - 64418924 GGAGAAACCTGCCC-------TGGCCCTGGTGTGGG-CACCAG---TCCTCGGGTGCC-CCCACCTGCC-CTGAGCACAGGAGGCAAACAAGAACAGAGTG--CAACCAGCGGCATCGGAGGTAGAAACA i canFam2.chr9 C 0 C 0 s equCab2.chr11 57956375 114 - 61308211 GGAGAAAGCTG-CC-------TGGTCCTGGTGTGGG-CGCCgg---tcctcggctgtc-cccagctgcc-ctgagcccaggaggaaagcaggggcagaccg--cagcaagaaggatttaaggcaggaaca i equCab2.chr11 C 0 C 0 s monDom5.chr2 304301091 122 - 541556283 GGAGAAAGTAGTTCTTTCTGGATAttctgtaa-aga-ggacag---taaccagctgtt-ctcagtctttgctaaagatagagagtaaacaagaataaactg--tagcctgagggatttcagtatgaaggg i monDom5.chr2 C 0 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e bosTau4.chr19 10769301 0 - 65312493 C e loxAfr3.scaffold_49 14302203 59 - 17734757 I a score=60874.000000 s hg19.chr17_gl000204_random 30582 36 + 81310 gca---taca---gaatttcctggcaggatgtgtc-att-agaG s panTro2.chr17 79203517 36 + 83384210 GCA---TACA---GAATTTCCTGGCAGGATGTGTC-ATT-AGAG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0033591 2 36 + 1388 GCA---TACA---GAATTTCCTGGCAGGATGTGTC-ATT-AGAG i gorGor1.Supercontig_0033591 N 0 C 0 s ponAbe2.chr17_random 9225639 36 + 17838096 GCA---CACA---GTATTTCCTGGCAGGACGTGTC-ATT-AGAG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74757926 36 + 78773432 gca---tgca---gaatttcctggcgggacatgtc-att-agat i rheMac2.chr16 C 0 C 0 s papHam1.Contig660872 1056 36 + 1349 GCA---TGCA---GAATTTCCTGGCGGGACATGTC-ATT-AGAT i papHam1.Contig660872 C 0 C 0 s otoGar1.scaffold_94361.1-85690 49556 40 + 85690 GTG---TGCAAAGGGATTTCTTGGCAAGACGTGTC-ATTCAACG i otoGar1.scaffold_94361.1-85690 C 0 C 0 s mm9.chr11 118682056 34 + 121843856 --------CCGAAGCAACATGGGGTAACATTTGTC-ATT-CAAC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4309810 39 + 7991924 gtg---cacagaaggatttctgggcagcccacgta-att-aaac i cavPor3.scaffold_76 C 0 C 0 s canFam2.chr9 59371150 40 - 64418924 GTC---CACAGAAGAACTTCTTGGCAGGACATGGCGTTT-AAAC i canFam2.chr9 C 0 C 0 s equCab2.chr11 57956489 42 - 61308211 gcatagcacagaaggattttttggcagGACACGGC-TTT-GAAC i equCab2.chr11 C 0 C 0 s monDom5.chr2 304301213 31 - 541556283 -----------gaaattttcctgataaaaaatgtt-agt-gaag i monDom5.chr2 C 0 N 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e bosTau4.chr19 10769301 0 - 65312493 C e loxAfr3.scaffold_49 14302203 59 - 17734757 I a score=73629.000000 s hg19.chr17_gl000204_random 30618 47 + 81310 -CTCT-CCTAGAGACGGCCCTTACCCCACCctttccttgacagcctagg s panTro2.chr17 79203553 47 + 83384210 -CTCT-CCTAGAGAGGGCCCTTACCCCACCctttccttgacagcctggg i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0033591 38 47 + 1388 -CTCT-CCTAGAGAGGGCCCTTACCCCACCCTTTCCTTGACAGCCTGGG i gorGor1.Supercontig_0033591 C 0 C 0 s ponAbe2.chr17_random 9225675 47 + 17838096 -CCCT-CCTAGAGAGGGGCCTTACCCCACCCTTTCCTTGACAGCCTGGG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74757962 47 + 78773432 -CTCT-CCTAGAGAGGGGCCTTACCCCACTCTTCGCTTGACAGCCTGGG i rheMac2.chr16 C 0 C 0 s papHam1.Contig660872 1092 47 + 1349 -CTCT-CCTAGAGAGGGGCCTTACCCCACTCTTCGCTTGACAGCCTGGG i papHam1.Contig660872 C 0 C 0 s otoGar1.scaffold_94361.1-85690 49596 47 + 85690 -CTCT-CCCGGGAAAGGGCCTTCTGCCATCCTTTTCTCGGCAGCTAGGG i otoGar1.scaffold_94361.1-85690 C 0 C 0 s mm9.chr11 118682090 34 + 121843856 --TCT-CCCA---------GCTA-ATGACCCTTTTCTTGACACCT--GG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4309849 46 + 7991924 atgct-cctgggagagagtgtTATATAACCCTGGTGTTTACACCT--GG i cavPor3.scaffold_76 C 0 C 0 s canFam2.chr9 59371190 33 - 64418924 -CCCTGCCTGGGACAAGGTGTCACATGTCCCTTT--------------- i canFam2.chr9 C 0 C 0 s equCab2.chr11 57956531 47 - 61308211 -CCCTGCCCAGGGCAAGGTGTCCCATGGCCCTTT-CTTGACAACCTGGG i equCab2.chr11 C 0 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e bosTau4.chr19 10769301 0 - 65312493 C e loxAfr3.scaffold_49 14302203 59 - 17734757 I a score=196351.000000 s hg19.chr17_gl000204_random 30665 107 + 81310 acacagtgatgcccacctctgagcctcccatgcgt-------------tatcttaggtgttcacgagattgtca----cgtgaa-tgccgaaagcctgcctgcct-cccacggagctgggagctct s canFam2.chr9 59371223 12 - 64418924 -----------------TCT----------TGGA--------------GACCT------------------------------------------------------------------------- i canFam2.chr9 C 0 C 0 s equCab2.chr11 57956578 101 - 61308211 TCACAGTGATGCCCACCTCTGAG-----CATGGA--------------GGTCTCTGATGTTCACAAGATTGTTG----CATGAA-TGCCAAATGCCCACCTGCCC-CCCAGGGGTCTGGAAGCTCT i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10769301 95 - 65312493 GCATAGCGATGCCCACCTCTGAGCCTCCCATATAT-------------GGTCTCAGGTATTTACAAGAGCATCA----CTTGAA-TGCCAAATGCCTGTCTGCCC-CTCACAGG------------ i bosTau4.chr19 C 0 C 0 s cavPor3.scaffold_76 4309895 107 + 7991924 CCACAGCGACGCTCACCTCT-AGCCATCCATGCAT-------------CAGCTCAGGTGTTCACATGACCTGCAGGTGCATGCTGGGCCA----CCTGACTGTCT-TCTTTGGGTCTGGGAACACC i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118682124 96 + 121843856 GCACAGTGGTGC-CACAGCTGAGCAACATAAGCAT-------------CCTCTTGGGTG---GCATGAGATTGA----CAAAAAGTGTCAAAAGCTTGCCTGTCT-CCCATGGGAC--------CT i mm9.chr11 C 0 C 0 s otoGar1.scaffold_94361.1-85690 49643 102 + 85690 GCACGGTGATGCCCACCCT--GCCCTCCCATGCAT-------------TGTCTCA-GTGCTCAC-AGCTTGTCA----CGTTGA-CACCGCATACCCACCGGCCT-CCCA-GGATCTGGGAGCTCT i otoGar1.scaffold_94361.1-85690 C 0 C 0 s papHam1.Contig660872 1139 107 + 1349 GCAAAGCGATGCCCACTTCTGAGCCTCCCATGCAT-------------CATCTCAGGTGTTCACGGGATTGTCA----CGTGCA-TGTGGAAAGCCTGCCTGCCT-CCCACAGAGCTGGGAGCTCT i papHam1.Contig660872 C 0 N 0 s rheMac2.chr16 74758009 107 + 78773432 GCACAGCGATGCCCACTTCTGAGCCTCCCATGCGT-------------CATCTCAGGTGTTCACGGGATTGCCA----CGTGCA-TGTGGAAAGCCTGCCTGCCT-CCCACAGAGCTGGGAGCTCT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 9225722 107 + 17838096 ACACAGTGATGCCCACCTCTGAGCCTCCCATGCAT-------------TATCTTAGGTGTTCACGAGATTGTCA----CGTGAA-TGCCAAAAGCCTGCCTGCCT-CCCACGGAGCTGGGAGCTCT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0033591 85 107 + 1388 ACACAGTGATGCCCACCTCTGAGCCTCCCATGCGT-------------TATCTTAGGTGTTCACGAGATTGTCA----TGTGAA-TGCCGAAAGCCTGCCTGCCT-CCCACGGAGCTGGGAGCTCC i gorGor1.Supercontig_0033591 C 0 C 0 s panTro2.chr17 79203600 107 + 83384210 acacagtgatgcccacctctgagcctcccatgcgt-------------tatcttaggtgttcacgagattgtca----cgtgaa-tgccgaaagcctgcctgcct-cccacggtgctgggagctct i panTro2.chr17 C 0 C 0 s choHof1.scaffold_356533 0 103 + 1257 ------------------CTGAAGCTCCAATGTGGTGGAATTCCACTAGGTCTCACCCACTTACAACACCGCCA----TGTGAA-GGCTGAAGGCCTGTGGACTTCCCCGTGGGTCAGCAACCTCC i choHof1.scaffold_356533 N 0 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e loxAfr3.scaffold_49 14302203 59 - 17734757 I a score=100147.000000 s hg19.chr17_gl000204_random 30772 81 + 81310 tgaggacaATGTCTGCCACGTAGCAGGGCATGGAAATCTTCCT-GAGTGATTTGGGTGTTACCTGTGTGG-------------AGCCG-ATGACCT s panTro2.chr17 79203707 81 + 83384210 tgaggacaatgtctgCCACGTAGCAGGGCATGGAAATCTTCCT-GAGTGATTTGGGTGTTACCTGTGTGG-------------AGCCG-ATGACCT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0033591 192 81 + 1388 TGAGGACAATGTCTGCCACGTAGCAGGGCGTGGAAATCTTCCT-GAGTGATTTGGGTGTTACCTGTGTGG-------------AGCCG-ATGACCT i gorGor1.Supercontig_0033591 C 0 C 0 s ponAbe2.chr17_random 9225829 81 + 17838096 TGAGGACAGTGTCTGCCACGTAGCAGGGAGTGGAAATCTTCCT-GAGTGATTTGGATGTTACCTGTGTGG-------------AGCCG-ATGACCT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74758116 72 + 78773432 TGAGGACAGTGTCTGCCATGTAGAAGGGTGTGGAAATCTTCCT-GAGTGATTTGGGTGTTACCTGTG-----------------------TAACCT i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94361.1-85690 49745 69 + 85690 TGAGGACCATGCCCACCAGGTGGAAGGGCATGGAAATGTTCCC-AAGGGAATTGGGTGTTACCTGCATGG-------------------------- i otoGar1.scaffold_94361.1-85690 C 0 N 0 s mm9.chr11 118682220 77 + 121843856 TTAAGATGGTGTTCCCCACATGGACAGACAAGGACA-TCTTCC-AGGTGACTTGGTTA-CACCTATACAAGGG----------------ATGACCT i mm9.chr11 C 0 I 122 s cavPor3.scaffold_76 4310002 81 + 7991924 TGGGGACGTTGTCTGCTGCATGGAAAT----------CTTTCT-AGGTGACTTGAGTA-CACAGGTTTGGGGG--AGGCAGAAAGCCC-AGGAGCT i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10769396 79 - 65312493 -------AGCGCCTGCCACAC---AGGACTCGGACGTCTTCTT-GGATGAT--GAGTGAGA-CTGTATGGAGG--GGACAACGAGCCG-ATGACCT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 57956679 92 - 61308211 TGAGGACAGCACCTGCCATGCTGAGGGACATGGA--TCTTCCT-GGGTGGCCTGAGTGTGACCTGCAAGGAGGCAGGGCGATGAGCCG-ATGACCT i equCab2.chr11 C 0 C 0 s canFam2.chr9 59371235 42 - 64418924 -----------------------------------------------------GAGTGTGCCCTGCGTGGAGGCAGGACGGTGAGCCG-GGAACCT i canFam2.chr9 C 0 C 0 s choHof1.scaffold_356533 103 95 + 1257 TGAGGATAGCACCTACC-CGGAGAAAGGCACTGGAATCTTCCCAGGGTGACTTGCGTGTAGTctgcgtggaggcagagggatggaccgaatgacct i choHof1.scaffold_356533 C 0 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e loxAfr3.scaffold_49 14302203 59 - 17734757 I a score=519353.000000 s hg19.chr17_gl000204_random 30853 358 + 81310 TT-CACGGTCCTTGCCTGCCTCGGGACCCCTGTTCTGTCAGGC-TGTCCCCA-TGCTA-TCCCTCCCAGCCAGCC-CATCACCTCAAAGAAGCGGGGCTGTCATGAGCCTGCACTGG-CTGAGGCCATCA---TGAGAGCCCTCCTAAGGTGGAAGCGGAAGTCCTGGGT--CCACCCCCTGCATGGCAGCCC-----CC-ACCCAGGTGCACTGCCA-CTCCTCCCCCTGGCCCCATGACTCaaggaactttcctgggagct-gggaaagctgggaaa-tatc-tcaatttaggtcatggctataatggtacagatatttgtcaaaac--tcactggaccata---ctaagacctacgcatttcatagtatgtaaattacc-ct- s panTro2.chr17 79203788 358 + 83384210 TT-CACGGTCCTTGCCTGCCTCGGGACCCCTGTTCGGTCAGGC-TGTCCCCA-CGCTA-TCCCTCCCAGCCAGCC-CATCACCTCAAAGAAGCAGGGCTGTCATGAGCCTGCACTGG-CTGAGGCCATCA---TGAGAGCCCTCCTAAGGTGGAAGCGGAAGTCCTGGGT--CCACCCCCTGCATGGCAGCCC-----CC-ACCCAGGTGCACTGCCA-CTCCTCCCCCTGGCCCCATGACTCaaggaactttcctgggagct-gggaaagctgggaaa-tatc-tcaatttaggtcatggctataatggtacagatatttatcaaaac--tcactggaccata---ctaagacctacgcatttcatagtatgtaaattacc-ct- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0033591 273 358 + 1388 TT-CACGGTCCTTGCCTGCCTCGGGACCCCTGTTCTGTCAGGC-TGTCCCCA-CGCTA-TCCCTCCCAGCCAGCC-CATCAGCTCAAAGAAGTGGGGCTGTCATGAGCCTGCACTGG-CTGAGGCCATCA---TNAGAGCCCTCCTAAGGTGGAAGCGGAAGTCCTGGGT--CCACCCCCTGCATGGCAGCCC-----CC-ACCCAGGTGCACTGCCA-CTCCTCCCCCTGGCCCCATGACTCaaggaactttcctgggagct-gggaaagctgggaaa-tatc-tcagtttaggtcatggctataatggtgcagatatttgtcaaaac--tcattggaccata---ctaagacctatgcatttcatagtatgtaaattacc-ct- i gorGor1.Supercontig_0033591 C 0 C 0 s ponAbe2.chr17_random 9225910 364 + 17838096 TT-CACGGTCCTTGCCTGCCTTGGGACCCCTGTTCTGGCAGGCTTGTCCCCA-CGCTA-TCCCTCCCAGCCAGCC-CATCAGCTCAAAGAAGCGGGGCTGTCATGAGCCTGCATTGG-CTGAGGCCATCA---TGAGAGCCCTCCTAAGATGGAAGCGGAAGTCCTGGGT--CCACCCCCTGCATGGCAGCCC-----CC-ACCCAGATGCACTGCCA-CTCCTCCCCCTGGCCATGTGACTCaaggaactttcctgggagct-gggaaagatggaaaagtatcatcaatttaggtgatggctataatggtgcagatatttgtcttaatcgtcattggaccata---ctaagacctatgcatttcatagtgtgtaaactaCCNNN- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74758188 356 + 78773432 TT-CACGGTCCTTGCCTGCCTCGGGA-CCCTGTTCTGGCAGGC-TGTCCCCA-TGCTG-TCCCTCCCAGCCAGTC-CATCAGCTCAAAGAAGCGGGGCTGTGATGAGCGTGCACTGG-CTGAGGCCATCA---TGAGACCCCCCCTAAGCTGGAAGCAGAAGTCCTGGGT--CCA-CCCCTGCATGGCAGCCC-----CC-ACCCAGGTGCACCACCA-CAATTCCTCCTGGCCCCGTGACTCaaggaactttcttgggagct-gggaaagctgggaaa-gatc-tcaatttagacaatggctataatggcgcagacatctgtcaaaac--tcattggaccata---ctaagacctatgcattccatagtatgtaaattacc-ct- i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4310083 292 + 7991924 TT-CACAGCTCTTTCCTAGCTCGGGACTGGGCTCCAGGAAGGC-TGCCCCCCTTGCTC-CCTCTCCCAGGAAGCC-TTTCAGCCTGCACA--------------------GCACCAG-CT-AACCCATTG---TGAGAG----------------------GTCCTGAGCCACCAGCCCCTGC--TGCTTCCCTTAGTCC-TCCCCAGCCCACCAACT-CCACTCC------------AACACAg-----------aggagat-gggaaggttctaaaa----c-tcaatttaggtgatggctagagagttgtgtacatttgtcagaac--tcttcagatta------taagccctgtgcatttcatagtgtgtaaattaCT-CT- i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10769475 330 - 65312493 TG-CCTGGTTCCTTCCGACCGA-GGCCCCTTCTCCTGTCTGTC-TGTTCCTT-TGCTGCCCACTTTCGGCCAGTCACATTAGCCCAAAGGAGCTGGGGTCTCACAGGCCTGCATTGG-TTGAGGCCATCATCCTGACAGTCCAGCTAAGGCAGGAACTAAGTCCCAGGTT--CACCTGCCTGCATCCTATCAC-----CCCACGAAGGCACTGTAGTGCCTCGTGCC-----------GAATCaaggaactttctcgagagat-ggggaagttct---a-tatc-tcaaattaggtaatagttacacagatgcatacatttgtcaaaac--tgcttggtctata---ttaagacctatacattt---------------------- i bosTau4.chr19 C 0 I 323 s equCab2.chr11 57956771 344 - 61308211 TGCCCAGCCCTTTTCCTG-GGT-GGACTCCTCTCCTGGCTGCC-TGCCCCTT-TGCTG-CCCCTCAGAGCTGGGC-CGTTGGCTCAAAGGAGCTGGGCTGTCACGGGCCTGCTCTGC-TTGAGGCCGTCG---TGAGAATCCTGCTGAGGCTGGAGCTTCAGTCCTGGGC--TCTCCAGCTGCATCGTGTCAC-----CC-ACCCGGCTGCTTCAGCAGCCCCTGCC-----------AGATCaaggagctttctggagagat-gggaaagctcc---a-tatc-tcaattcaggtggtggttagacacgtgtacacattgctcaaaac--tccttagactgta---ctaagatatatacacttcataacatgtaaattact-ct- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59371277 346 - 64418924 TG-CTAGCCCTCTTTTTGCCTT-GGAGCCCTCTACTGGCTAGC-TGTCCCTT-TGCTGCCCCCTCCCCACCTGTC-TGTTAGCTCAAAGGTGCTGGGTTCTCATGGGCCTGCACTGG-TGGAGGCCACCA---CGAGAGTCCTGGTGAGGCTGGAGCTTCAGCCTCTGTC--CACCTCGCTGCATCACATCCT-----CCGGCTCAGGGACTTCAGCA-CCCCTGCC-----------AGatggaggaaccttctggagatgtagggactgttcc---a-tgtc-tcaatgtaggagatggttattcaggtgtatacagttgtcaaaac--tcctttgactgta---ctaagacctgtacatttcacaatatgtaaattact-cc- i canFam2.chr9 C 0 C 0 s choHof1.scaffold_356533 198 276 + 1257 tc-caaggccctttcctgcctg-ggactcctcgCCTTGGAAGC-TGTCTCTT-CACCC-ACTGCTCCAGCCAGCC-CATCGGCTCAAAGGAGCC-GGCCGTCATGGGCCGGCTTTGATCTGAGGCCAAGG---TGAGAATGCAGCTAAGATCAAAGCTTAAGTCCTGGGT--TCA---------------CCT-----CC----------------CA--------------------GACTCAAGAAACttt-----------ggg----------------c------------gagggttatgtgggtgtgttcatgtagcaaaac--tcacggcaccttacacctaagacctgtgcacttcctagtatataaattaaa-cct i choHof1.scaffold_356533 C 0 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e mm9.chr11 118682297 122 + 121843856 I e loxAfr3.scaffold_49 14302203 59 - 17734757 I a score=291835.000000 s hg19.chr17_gl000204_random 31211 199 + 81310 -cagttttttaatt-ta--aaaa------aGTTAACTCCTGGACCGAAAACAGATTT-GAGCAAAAGCCACTGCCTCAGACCCCTAAGGCTTCCAATGGACCGCAGAGTCTTTTATTCAGCCAAAGTC--AGCCAATGGAGCCCA-AGCAATACGTTTGGGAAAAAAAGCAATCATCAATGTAATGATAAGGAAAGTGTCTCATACGTAGTAC s panTro2.chr17 79204146 197 + 83384210 -cagttttTTAATT-TA--AAAA------AGTTACCTCCTGGACCGAAAACAGATT--GAGCAAAAGCCACTGCCTCAGACCCCTAAGGCTTC-AATGGACTGCAGAGTCTTTTATTCAGCCAAAGTC--AGCCAATGGAGCCCA-AGCAATACGTTTGGGAAAAAAAGCAATCATCAATGTAATGATAAGGAAAGTGTCCCATACGTAGTAC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0033591 631 199 + 1388 -caGTTTTTTAATT-TA--AAAN------AGTTACCTCCTAGACTGAAAACAGATTT-GAGCGAAAGCCACTGCCTCAGACCCCTAGGGCTTCCAATGGACTGCAGAATCTTTTATTCAGCCAAAGTC--AGCCAATGGAGCCCA-AGCAATACGTTAGGGAAAAAAAGCAATCATCAATGTAATGATAAGGAAAGTGTCCCATACGTAGTAC i gorGor1.Supercontig_0033591 C 0 C 0 s ponAbe2.chr17_random 9226274 192 + 17838096 -NNNNNNNTTAAAT-TA--AAAA------AGTT-CCTCCTGGA-TGAAAACAGATTT-GAGTGAAAG-CACTGCCTCAGACTCCTAAGGCTTC-GATGGAATGCAGAGTCTTTTA-TCAGCCAAAGTC--AGCCAATGGAGCCC--AGCAATAGGTTTGGGGAAAAAAGC-ATCATCAATGTAATGATAAGGAAAGTGTCCCATATGTAGTAC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74758544 192 + 78773432 -cagttttTTAATT-TA--AAAA------GGTTACCTCCTGGACTGAAAACAGATTT-GAGTGAAAGCCACTGCCTCAGACCC---AGGCGTCCGATGGACTGCAG--TCTTTCATTCAGCCAAAGTC--AGCCAACAGAGCCCA-GTCTATATGTTTGG--AAAAAAACAATCATCAATATAATGATAAGGAAAATGTCCCATACGTAGCAC i rheMac2.chr16 C 0 C 0 s cavPor3.scaffold_76 4310375 196 + 7991924 -CTGTTTTCTAATT-AAAGAAAA------ACTCGCCTCCTGGGCTGGAAACAGAGCTGGAGTCAAAGCGTGTCTTTCAGGCCCCTGAGGCACT-GAAGGGCTGCGGAATCTTTCA-GCGGGCAAAGGCAAAGCCA---GAGCCTATATCAGTATATCCAGGAAAAGAG---AGAATCAGTGTAATGATGCTG-CAGTAGCCCACACTTGGGGC i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10770128 189 - 65312493 -CAGTTTTTAAATT-AA--AAAATT----TGTCAGCTCCTGGACTGACAATAGACCCTGAGTCACAGCCGCTCTCTCAGGTCCCTGAGGCTT-----------CAGAGACTTTCGACTTGCCAGAGTC--AGCGACAGGAGTCAG-ATCAATATGTCTGG--GAAGAAGCAATGATCAGTGTAATGATACTGCGGGTGTCCCATGTTTGGGGC i bosTau4.chr19 I 323 C 0 s equCab2.chr11 57957115 197 - 61308211 -ccatttttaaatt-aa--aaaaTA----AATCACCTCCCGGACTGACAATAGATCTTGAGTCAGAGCCACTCTTTCAAGTCCCTAAGGCTAC-ATGGGGCTGCACAGCATTTCGACTGGCCAGAGTC--AGCGACAGGAGCCAG-ATCAATACGTCTGG--GAAGAAGCA--AATCAGTACAATGATACTGCAGGTGTCCCACATTCGGGGC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59371623 198 - 64418924 -caattttTCAATTAAA--AAAAAA----AATCACCTCCTAGACTGACAATACATCTTGAGTCAGAGCCACTCTCTC-AGTCCCTAAGGCTCT-GACGGGTTGCAGAGCTTTTCAGTTGGCCAGAGTC--AGCGACAGAAGCCCG-ATCAATACGTCTGG--GAAGAAGCAATAATCAGTGTAATGATACTGTATGTGTCCCACGCTC-AGGC i canFam2.chr9 C 0 C 0 s choHof1.scaffold_356533 474 159 + 1257 ccattttttgaatt-aa--aaaaaaAAATAATCCTTCTCTGGACTTAAAATAGATCTTGGGTGAAAGCCACTGTCTCAGTCCTCCAATGTCACCGACCCGCTGCAGAGCCTTCAGCTTGGCCAGAGAA--AACATGCAGGGTCTG-AGAAAGAATCCTGA--------------------------------------CCCCA---------- i choHof1.scaffold_356533 C 0 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e mm9.chr11 118682297 122 + 121843856 I e loxAfr3.scaffold_49 14302203 59 - 17734757 I a score=136237.000000 s hg19.chr17_gl000204_random 31410 181 + 81310 TAGGAGACCTGCCTCGGTGAG-TTTCT--ACCAGCAGTGGCAGGAAGGCCAGAAGCCACCGGTGTC---CA----CACAAAGCCTGG------CTCTTTCCTCATCAGTTCTCTGGCAGTGAGGAGAGGGCA-GGAGTAAA--CACGAAGCTCTAGAACAATGTCCTCTTCCCAGCCCCCCA----------GCTGGCTGCCT-------------GG--------GTAAG s panTro2.chr17 79204343 181 + 83384210 CGGGAGACCTGCCTCGGTGAG-TTTCT--ACCAGCAGTGGCAGGAAGGCCAGAAGCCACCGGTGTC---CA----CCCAAAGCCTGG------CTCTTTCCTCATCAGTTCTCTGGTAGTGAGGAGAGGGCA-GGAGTAAA--CACGAAGCTCTAGAACAATGTCCTCTTCCCAGCCCCCCA----------GCTGGCTGCCT-------------GG--------GTAAG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0033591 830 181 + 1388 CGGGAGACCTGCCTCGGTGAG-TTTCT--ACCAGCAGTNGCAGGAAGGCCAGAAGCCATCGGTGTC---CA----CCCAAAGCCTGG------CTCTTTCCTCATCAGTTCTCTGGTAGTGAGGAGAGGGCA-GGAGTAAA--CACGAAGCTCTAGAACAATGTCCTCTTCCCAGCCCCCCC----------GCTGGCTGCCT-------------GG--------GTAAG i gorGor1.Supercontig_0033591 C 0 C 0 s ponAbe2.chr17_random 9226466 181 + 17838096 CAGGAGACCTGCCTCGGTGAG-TTTCT--ACCAGCAGTGGCAGGAAGGCCAGAAGCCATCGGTGTC---CA----CCCAAAGCCTGG------CTCTTTCCTCATCAGTTCTCTTGTAGTGAGGAGAGGGCA-GGAGTAAA--CAGGAAGCCCTAGAACAATGTCCTCTTCCCAGCCCCCCA----------GCTGGCTGCCT-------------GG--------GTAAG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74758736 176 + 78773432 CGGGAGACCTGCCTCAGTGAG-TTTCT--ACCAGCAGTGGCAAGAGGACCAGAAGCCATCAGTGTC---CA----CCCAAAGCCTGG------CTCTTCCCTCATCAGTTCTCTTGTAGTGAGGAAAGGGCA-GGA-TAAA--CAGGAAGCTCTAGAACAATATCCTCTTCCCAGCCCCTCA----------GATGG----CT-------------GG--------GTAAA i rheMac2.chr16 C 0 C 0 s mm9.chr11 118682419 179 + 121843856 TGAGAGGCATGCCCCAGTGGG-TTTTCAAACTGGCTCTAGTGGGAAGGCC-----CCACCAGGCTA----------CCAAGGCCTGT------ATCATTGCTCATGA----------ATTGAGGAGACAG---GGAAGCAG--CATGGATATCTAGGAT-------TCATCCCAGTCCACCTTGTCTGTGAGTCTAACCCTGGCCTCTCCCTAGTTAG--------CACCA i mm9.chr11 I 122 C 0 s cavPor3.scaffold_76 4310571 169 + 7991924 --TGAGCTGTGCCTCTACTGC-TTCC---ACCAGCAGTGGGAGGAGACCC-----ACACCATGGTACACCA----CCCAGAGCCCAG------AGCTTTGCTCACAAGCTCCTT--TAGTGAGAGGAGAG---GGAAGAAG--TGCGGGG---CAGGATGACACCCTCATGGTAGGCCCCCT----------GCTGACAACGG-------------AG--------CACAT i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10770317 167 - 65312493 AAAGAGACTTGCCCCTGGGGG-CTTCC--AGCAGCAGCAGCAGGAGGGCC-ACAGCCATCAGCATG---CTGTCTCCCAAA------------GCCTCAG--TGTCAGCTCCCTAACAGTAAGAAGAAA----GGAGAGAA--CATGACAACATAGG-AAGTGTCCTCACCCAGACCCC-------------ACC--CTGGCC-------------TG--------GAGAA i bosTau4.chr19 C 0 I 78278 s equCab2.chr11 57957312 169 - 61308211 TGGGAGACTTGCCCCCAGGGG----CC--TCCAGCAGTGGCAGGAAGGCC-ACAGCCATCAGCGTT---CC----------------------ACCTTTG-TCATCGGCTCTCTTGCAGTGGGAAGAGAAAG-GGAGGGCG--CATGATGACACAGGAAAGTGTCCTCACCCCAGACCC-------------ACTGGCTGCCT-------------TGCACGCATGGAGCA i equCab2.chr11 C 0 I 34 s canFam2.chr9 59371821 196 - 64418924 TGAGACACCTGCCCCAGGGGGACTTCC--GCCAGCAGCGGCAGGAAGGCA-ACAGCCACCAGTGTG---CCA---CCCAAACCCTCAGTCCGGACCTTTGCTTGTCAGCTCTCTTGCAAAAAGAAGAGAAAGAAGAGAAAA--CATGACGATACAGGGAAGTGTCCTCCTCCAGGACCCCTGT---------GCTGGCTGCCT-------------TGCACACA--GAGCA i canFam2.chr9 C 0 I 24 s choHof1.scaffold_356533 633 73 + 1257 -----------------------------------------------------------------------GACCCCTGCAGCTGGC------CCCTATGCACAC----------------------------AGAGCAAGGCCCAGAATCCCAAGG--------TTATTCCTGGCACCGCA----------CTTG----------------------------------- i choHof1.scaffold_356533 C 0 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e loxAfr3.scaffold_49 14302203 59 - 17734757 I a score=106013.000000 s hg19.chr17_gl000204_random 31591 126 + 81310 GTGCCAGGTA--GGGATGG------ACATTACATACACA-AGGCTG-----------GTGGTACTGAGGGGCCATCTCTGAAGGTGTGCACCTTACAGCAACACAGAT---GGGCACGGCCAAAGCTGCTCCCC-TC-------CCCTCTGGAGC-CA s panTro2.chr17 79204524 126 + 83384210 GTGCCAGGTA--GGGATGG------ACATTACATACACA-AGGCTG-----------GTGGTACTGAGGGGCCATCTCTGAAGGTGTGCACCTTACAGCAACACAGAT---GGGCACGGCCAAAGCTGCTCCCC-TC-------CCCTCTGGAGC-CA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0033591 1011 126 + 1388 GTGCCAGGTA--GGGATGG------ACATTACATACACA-AGGCTG-----------GTGGTACTGAGGGGCCATCTCTGAAGGTGTGCACCTTACAGCAACACAGAT---GGGCACGGCCACAGCTGCTCCCC-TC-------CCCTCTGGAGC-CA i gorGor1.Supercontig_0033591 C 0 C 0 s ponAbe2.chr17_random 9226647 126 + 17838096 GTGCCAGGTA--GGGATGG------ACATTCCATACACA-AGGCTG-----------GTGATACTGAGGGGCCATCTCTGAAGGTGTGCACCTTAGAGCAACACAGAT---GGGCATGGCCACAGCTGCTCCCC-TC-------CCCTCTGGAGC-CA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74758912 126 + 78773432 GTGCCAGGTA--GAGATGG------ACATTCCATACACA-AGGCTG-----------GTGGTACGGAGGGGATATCTCTGAAGGTGTGCACCTTAGAGCAACACAGAG---GAGCATGGCCACAGCTGCTCCCC-TC-------CCCTGTGGAGC-CA i rheMac2.chr16 C 0 C 0 s mm9.chr11 118682598 113 + 121843856 GCAATAGGCAAAGGGCTAA------AGGCAAAGCACACATAGGATG-----------GGGGTGTTGATGGGCTCTCTCTGATGT----------------GCTCA-CA---AGGCAC------AGCTGTCCCTC-TTATGCTCATCTCTTATGCT-CA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4310740 123 + 7991924 GGAACAAGGATTGGG---------------AAACACTCGTGGGAAGCACTTGGGTGAGGGATATTGATAGGGTCTCTCTGATGCACAGT-CTTTGCAGCAGCCCAGTG---GGGTAT------AGCAGCTCCCC-TT-------TCCTTCGGGAG-C- i cavPor3.scaffold_76 C 0 C 0 s equCab2.chr11 57957515 113 - 61308211 GCACCAGGTA--GGGATGG------ACATGGTGCAC--G-GGGTTG-----------GTGGTATTGAGAGGTGC---------GTATGC-----AGAGCAGTCCAGGT--GGGGCACACCTGCAGCCTCTCCCCTTC-------CCCTCTGGAGCACA i equCab2.chr11 I 34 C 0 s canFam2.chr9 59372041 105 - 64418924 CCTCTGGTTA--GGATCAGGAAGGGACAGGCTGCACATG-GGGTCA-----------GCAGCTCTGAATAGTG------------------------------CAGGT--AGGGCAGGCCCATAGCTGTTCCCCATC-------CCCTCTGGGGCACT i canFam2.chr9 I 24 C 0 s choHof1.scaffold_356533 706 121 + 1257 ---CCAGGTG--GGGATGG-------CACATCACGCTCC-GAGCTG-----------GTGGCATTGAGAGGGGC-CTCCAAAGGTGTGG----TATAG-AGCCTAAATATGGGGAGCAGCTGCCACGGCTCCCTTCC-------CCCTCTGGAGCACA i choHof1.scaffold_356533 C 0 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e bosTau4.chr19 10770484 78278 - 65312493 I e loxAfr3.scaffold_49 14302203 59 - 17734757 I a score=468309.000000 s hg19.chr17_gl000204_random 31717 251 + 81310 ATGGCCACCCCAGCAGGGACTAAGCCAAAGCTTAGAGTCTGCCCAAGACCTCCCCAGGTTAAGAGAGGCTACTGCAGGACTCCAGGAGCTTCCCCACTCCC--TCTGACAGCAACAAGGCCCTGG-CCTTG---GACCAGAC-CCCTAGAAG-AGCAGAT-GTTAGGCAGATGTGCAGGAGGCTCCAGAAGGTT-ATGGTGGGAACAGCTGTGGGTGCTGAG-GAGCAGACAAAAGCAGACAGGAGAGGAGCAGAATGGAGA------------- s panTro2.chr17 79204650 251 + 83384210 ATGGCCACCCCAGCAGGGACTAAGCCAAAGCTTAGAGTCTGCCCAAGACCTCCCCAGGTTAAGAGAGACTACTGCAGGACTCCAGGAGCTTCCCCACTCCC--TCTGACAGCAACAAGGCCCTGG-CCTTG---GACCAGCC-CCCTAGAAG-AGCAGAT-GTTAGGCAGATGTGCAGGAGGCTCCAGAAGGTT-ATGGTGGGAACAGCTGTGGGTGCTGAG-GAGCAGACAAAAGCAGACAGGAGAGGAGCAGAATGGAGA------------- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0033591 1137 250 + 1388 ATGGCCACCCCAGCAGGCACTAAGCCAAAGCTTAGAGTCTGCCCAAGACCTCCCCAGGTTAAGAGAGGCTACTGCAGGACTCCAGGAGCTTCCCCACTCCC--TCTGACAGCAACAAGGCCCTGG-CCTTG---GACCAGCC-CCCTAGAAG-AGCAGAT-GTTAGGCAGATGTGCAGGAGGCTCCAGAA-GTT-ATGGTGGGAACAGCTGTGGGTGCTGAG-GAGCAGACAAAAGCAGACAGGAGAGGAGTAGAATGGAGA------------- i gorGor1.Supercontig_0033591 C 0 N 0 s ponAbe2.chr17_random 9226773 251 + 17838096 ATGGCCACCCCAGCAGGCACTAAGCCAAAGCTTAGAGTCTGCCCAAGACCTCCCCAGGTTAAGAGAGGCTACTGCAGGACTCCAGGAGCTTCCCCACTCCC--TCTGACAGCAACAAGGCCCTGG-CCTTG---GACCAGCC-CCCTAGAAG-AACAGAT-GTTAGGCGGATGTGCAGGAGGCTCCAGAAGGTT-ATGGTGGGAACAGCTGTGGGTGCTGAG-GAGCAGACAAAAGCAGACAGGAGAGGAGCAGAATGGAAA------------- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74759038 251 + 78773432 GTGGTCACCCCAGCAGGCACTGAGCCAATGCTTGGAGTCTGCCCAAGACCTCCCCAGGTTAAGAGAGGCTACTGCAGAACTCCAGGAGCTTCCCCGCTCCC--TCTGGCAGCAACAAGGCACTGG-TCTTG---GACCAGCC-TCCTAGAAC-AGCAGAT-GTTAGGCAGATGTGCAGGAGGCTCCAGAAGGTT-ATGGTGGGAACAGCTGTGGATGCTGAG-GAGCAGACAAAAGCAGACAGGAGAGGAGCAGAATGGAGA------------- i rheMac2.chr16 C 0 C 0 s mm9.chr11 118682711 193 + 121843856 ---GTCTCACCAGCAGCTACCAAG-AAACACCTGGAATCTGCCCAAGACCTCCCTATGTCTGGGGAGATGAACACA-GACCTCCAGAG------AACTTTC--TCTGGCACTGATGAGGCCCTGT-TCTTA---GCTTGGCTTTCATGGGACCAACAGAT-GTTTGG------------------CAGGAGGAT-------GGAACAGC---------TGGG-TTACAGA-----GCAGGCAG-GGTGGTGC----------------------- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4310863 207 + 7991924 ---------CCAGTAGCTACCAAG-AGATGCACACAGTGTGCCCAAGACCTCCC-AGGTCAACAGAGGTGAAT----GACTGCAGGAG-TCTGAAACCTCCCATCTGGCAGTAATAGGAACCTGA-ATTGA---AC-TGGCTGCTCTGGAAGCAACAGAT-GTTTAGCAGATGTGCA--------CAGGATAAC-------AGAACAGCTGTGGATGATGAG-GAACAGA-------AGGTAGAGGAGAGGC----------------------- i cavPor3.scaffold_76 C 0 C 0 s equCab2.chr11 57957628 249 - 61308211 GTGGCCACCCCATCAGCCACCAAGCAAACA-CCAGAGTCTGCCCAAGACCTCCCCAGGTCAAAAGAGGTGGCTGCAGGACTACAGAGGCGTCCCCTCTCTG--TCTGGCAGTGACAAGGCCCTGG-TCTCG---GACAGGCCCCCCTGGAAGCAGCAGATGGTGAGGCCAATGTGCAGGAAGGCTCGGGAAGGTCATGGT-----CAGCTGTTGATGCTGAG-GAGCAGATGAGGGCGGACGGGGGAGAAGCGGGATGGGGA------------- i equCab2.chr11 C 0 I 34 s canFam2.chr9 59372146 253 - 64418924 ATGGCTACCACATTGGCCACGGAGCAAACACCCGGAGTCTGCCCAAGACCACGCCAGGTCAAGACAGGCTGCTCCAGAACTGCAGAGGCCTGCCCTCCCCC--TCCAACAGCGACCAAGCCCTGG-TCTTG---GACAGGCCTCCCTGGAAGCAGCAGATGGTGAAGCCAATGTGCAGGAGGGCTCAGAAGGCCCACGGTGGGAACAGCTGTT-ATGCTGAG-GAACAGCCGAGAACAGA-GGGAGAGAAGCAGGATGGGGA------------- i canFam2.chr9 C 0 I 35 s loxAfr3.scaffold_49 14302262 250 - 17734757 ACAGCCACCACCACAGCTACCAAGCAAACACCTGGAGTCTGCCCCAGACCTCCCCAGGTTGAGACGGGTGGCTGCAGGACTCGGAGGC-----CCTCTCTT--TC--------------CCCTGGTCCTCAGTGGGCGGGCCTCTGTGGAGACGGCAGAT-GTGAAGCAGACGCTCTGGAGAGTCCAGGGGGTC-AGGGC-GAAACAGCTGCAGATGCTGAGAGAGCGGAAAGGGGGAGA-CGGAGGGGCAGAGGGGGAGGTGAGTGCTGCCCAA i loxAfr3.scaffold_49 I 59 C 0 s choHof1.scaffold_356533 827 225 + 1257 CTGGCCACCCCAACAGCCA-CAAGCAAACATCTAGACTCTGCCCAAGATCTCTCCGGGTCAAGAGAAGCAGCTGCAGGACCCGAGTCC----TCCTCTCCT--TCTGGCGGAGACAA-GCCCTGG-CCTCA---GACTGGCCTCCTTGGGGGCAGCAGAT-CCTAAGCAGGTG-TGTGGAGGGTCCAG-------------------------GATGCCGAGGGAGCGGACGAGAGCAGC-AGGAGATGAACGGAATGA----------GCCACA i choHof1.scaffold_356533 C 0 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e bosTau4.chr19 10770484 78278 - 65312493 I a score=42973.000000 s hg19.chr17_gl000204_random 31968 52 + 81310 ----------------TTTACC---TCTTTGGCAAGAGGCTCTTCTGACCACCGCTTGCCCTGCCTTTT-----GG s panTro2.chr17 79204901 52 + 83384210 ----------------TTTACC---TCTTTGGCAAGAGGCTCTTCTGACCACCGCTTGCCCTGCCTTCT-----GG i panTro2.chr17 C 0 N 0 s ponAbe2.chr17_random 9227024 52 + 17838096 ----------------TTTACC---TCTTTGGCAAGAGGCTCTTCTGACCACCCCTTGCCCTGCCTTCT-----GG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 74759289 52 + 78773432 ----------------TTTACC---TCCTTGGCAAGAGGCTCTTCTGACCACCCCTTGCCCTGCCTTCT-----GG i rheMac2.chr16 C 0 C 0 s mm9.chr11 118682904 27 + 121843856 -------------------------------------------TCTGTCGACTGCAT-TCCTATCCATT-----GG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4311070 30 + 7991924 -------------------------------------------TC--TCCACTCCCC-TCCTACCTCTTCTCTGGA i cavPor3.scaffold_76 C 0 C 0 s equCab2.chr11 57957911 50 - 61308211 ----------------TCTGCT---TTCCTGGCAAGAGGCTCCTC--CCCACCTCCTGCTCTGTCTTCT-----GG i equCab2.chr11 I 34 C 0 s canFam2.chr9 59372434 52 - 64418924 ----------------TTCGCT---TCCTCGGCACGAGGATCTTCTGCCCACCTCCTGCCCTGTCTTCT-----AG i canFam2.chr9 I 35 C 0 s loxAfr3.scaffold_49 14302512 68 - 17734757 GCCACCCCCCTCCTGCTTGGCT---GCCTTGACGAGGGGCTCTTCTCTGCCGCTCCAGCCCTGGATCTT-----GA i loxAfr3.scaffold_49 C 0 C 0 s choHof1.scaffold_356533 1052 71 + 1257 ACCCCCTTATCTTTCCCTGGTTTGGGCCCTGGACAAAGGTTCTTCTGTCCACCCCTTGCCCTAGTTTCT-----GA i choHof1.scaffold_356533 C 0 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e bosTau4.chr19 10770484 78278 - 65312493 I a score=82341.000000 s hg19.chr17_gl000204_random 32020 121 + 81310 CTGAG-AACACAGA-CTGAGGCCTGGCAGAGAGAAGGCCTTGCTATGTAAGCCCAGGTTGACTCAGGGCCAGTTTTGGCCTTCAGTATGCTCTCCCTCAGGGATCCCG------CCATGACATCTGCCT s ponAbe2.chr17_random 9227076 122 + 17838096 CTGAGAAACACAGA-CTGAGGCCTGGCAGAGAGATGGCCTTGCTATGTGAGCCCAGGTTGACTCAGGGCCAGTTTTGGCCTTCAATATGCTCTCCCTCAGGGATCCTG------CCATGACATCTGCCT i ponAbe2.chr17_random C 0 N 0 s rheMac2.chr16 74759341 122 + 78773432 CTGAGAAACACAGA-CTGAGGTCTGGCAGAGAGAAAGCCTTGCTGTGTGAGCCCAGGTTGACTCAGGGCCCATTTTGACCTTCAATGTGCTCTCCCTCAGGGATCCCA------CCATGACATTTGCCT i rheMac2.chr16 C 0 C 0 s mm9.chr11 118682931 112 + 121843856 GTGTGAAGCATGGG-TCACAGCCCAGCAGAGAG--------GCTGTCTGAGTCCAGATCGAGTCTGAGCCTGTAGAGTCCTCCACTCTG--CCACCTGGAAGGTCCTG------TCTTGCTCTATGTCA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4311100 126 + 7991924 GTGTGGAGCCCAGA-CCAAGGTCCAGCAGGAAGGAAGCCTAGCTATTCAAACCCCCATCAACTCAGCGCCCACCTTGTCCTCCAGGATG--CCTTCCCGAGGGATCTGGGCTCACCTTGGCATCTGCCT i cavPor3.scaffold_76 C 0 C 0 s equCab2.chr11 57957961 120 - 61308211 GTGTGAA--ACAGG-CCGAGGTCTGGCATAGAGGAGGCCTCCCAACA-AAGCCCAGGCTGACTCGGAGCCCACTGTGGCCCTCAGTCTGCTTTCCCCGAGCGACCCTGG-----CCGTTACACCTGCCT i equCab2.chr11 C 0 C 0 s canFam2.chr9 59372486 104 - 64418924 GAGTGAAACACaga-ccaagggctggcagagaggaggccttt-------------------cttgtactctgctgtggcctccagtctgccctccctgagtgaccctgg-----ccatgaaatctgcct i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14302580 113 - 17734757 GTGTGAAACACAGATACAGACCCACCAGTGAGGGGGGCCTTTCTGCAGGAGCCCAGGGTGACTCGGAGACC-CTAAGGCCTTCCTCATG--CTTGCCAAAGGGATCCCT-----GCATGAC-------- i loxAfr3.scaffold_49 C 0 I 941 s choHof1.scaffold_356533 1123 111 + 1257 GTGTGAAACTGA---CCACGGCCAGGCGTACAGGGGGCCTCTCCACCGCGGCC--GGTCAGCCC----ACC-CTCATGCCTTCAGTCTG--CTCACCCAAGGGTGCTGG-----CCATGA-ATCTGTCT i choHof1.scaffold_356533 C 0 C 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e bosTau4.chr19 10770484 78278 - 65312493 I a score=28124.000000 s hg19.chr17_gl000204_random 32141 22 + 81310 TCATAGGAACTCGTTTTCCTTT s rheMac2.chr16 74759463 22 + 78773432 TCATAGGAACTCATTTTCCTTT i rheMac2.chr16 C 0 C 0 s mm9.chr11 118683043 22 + 121843856 TCTCAGGAATTTGTTTTCTTTC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4311226 21 + 7991924 TCCTAGGAATTC-TTTTCCTTC i cavPor3.scaffold_76 C 0 C 0 s equCab2.chr11 57958081 22 - 61308211 TCTTGGGACCTCATTTGCCTTC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59372590 22 - 64418924 tcttgggacctgattttccttc i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14303634 22 - 17734757 CCCTAGAGCCCCATTTTCCTTC i loxAfr3.scaffold_49 I 941 C 0 s choHof1.scaffold_356533 1234 21 + 1257 -CCTAGGATGTCATTTTTCTCT i choHof1.scaffold_356533 C 0 N 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e bosTau4.chr19 10770484 78278 - 65312493 I a score=61175.000000 s hg19.chr17_gl000204_random 32163 99 + 81310 TGCGCTCCTTTGGGCAGCATTCTTACAATCCAACAGAA-GAATTCTGGCTCTTGTGGAGCTTCATGAAG-GGGGAAGACCTCCC-AAAACCAGTATGGCTCA s rheMac2.chr16 74759485 99 + 78773432 TGCGCTCCTTTGGGCAGCATTCTTACAATCCAACAGAT-GAATTCTGGCTCTTGTGGAGTTCCATCAGG-AGGGAAGACCTCCC-AAAACCAGTATGGCTCA i rheMac2.chr16 C 0 N 0 s mm9.chr11 118683065 100 + 121843856 TAAGATCTTTCTGAT-GTCTTTTTAGAACCCAGCATATGAATTTGGGGCTCATGGAATTTTCCATGGCATAAGGAAGACCTCTG-AGGGTCAGCACAGCTCA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4311247 83 + 7991924 TGAGTTCCTTTGGGCAGTATTTTTACAACCCAGCGGAT-AACTCTTGGCTTGTGGAAAAGTACATGAGGAAAGGAAGACCTCTC------------------ i cavPor3.scaffold_76 C 0 I 68024 s equCab2.chr11 57958103 101 - 61308211 TAAGCTCCTTTGGGCAGCATTCTTACTACCCAGCAGGT-GAGCTTCAGCTCATGCGGAGCTCCATGAGGAAAGGAAGACCTTCCCAAGAGCAGCATGGCTTG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59372612 101 - 64418924 tgAGGTCCTTTGGGTGATGCTCTTACTACCAAGAAGAT-GAGTTTCAGCTCATGCGGAGCTCTATGGCAAACAGAAGACCTCCCCAGGGAAAGCATGGTTTG i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14303656 83 - 17734757 TGAGCCCCTTGGGGCAGCATTCCTCCAACCCAGCAGGT-GAGGTTTGGCTCGGGTTCCAGAACAGGAGGCAAGGACGACCTCTC------------------ i loxAfr3.scaffold_49 C 0 N 0 e turTru1.scaffold_106006 33083 83717 + 145505 I e bosTau4.chr19 10770484 78278 - 65312493 I a score=2516.000000 s hg19.chr17_gl000204_random 32262 12 + 81310 ACAAAGC---------------------------------Gccac s mm9.chr11 118683165 45 + 121843856 GTGAGGCTGCGAGCACACATCAAGATGAAGCAGGGGCAAGGCCTC i mm9.chr11 C 0 I 581 s equCab2.chr11 57958204 40 - 61308211 GCGAAACTAGCAGTACCCATCAGAAAGAGGCTGAG-----GCCAC i equCab2.chr11 C 0 I 8 s canFam2.chr9 59372713 40 - 64418924 GTGAAACTAGGAGTACACATCGGAAAGAAGCCAAG-----GTCAC i canFam2.chr9 C 0 I 8 e turTru1.scaffold_106006 33083 83717 + 145505 I e bosTau4.chr19 10770484 78278 - 65312493 I e cavPor3.scaffold_76 4311330 68024 + 7991924 I a score=16727.000000 s hg19.chr17_gl000204_random 32274 124 + 81310 ctg--cccactcatccatccacccatctacata-----------------------cctacccaaccactcacccatccatctact---cacacagccatccttcca-------cccacccatcc---atctacccattcactcatccatccatccaTAAG-C s mm9.chr11 118683791 130 + 121843856 CTA--CCTATCCATAGAATcatctatccatgtg-----------------------cccaatcatttactcacctgttcatatactaactacatagctgcccattca-------tccgttcaactacaatctatgtatccattcatccgttcatctcttta-a i mm9.chr11 I 581 I 62316 s equCab2.chr11 57958252 126 - 61308211 CTGACtccattcatctacccatccatctatctg-----------------------tgtgtccatccacctatccatccattcacc---catccactcatccgtcaa-------cccatccatcc---atccctccatccctccatccatccatccatccat- i equCab2.chr11 I 8 I 72591 s canFam2.chr9 59372761 155 - 64418924 CTGACTTTattcattcagccatctgtccatctgccatccaaccatttgttccttcatctgtccattgatctatccatccatccact---catccatccatccacccacctgccccccatccaccc---acctgcccatccacccatttacctaccaatcca-- i canFam2.chr9 I 8 I 52888 e turTru1.scaffold_106006 33083 83717 + 145505 I e bosTau4.chr19 10770484 78278 - 65312493 I e cavPor3.scaffold_76 4311330 68024 + 7991924 I a score=1371782.000000 s hg19.chr17_gl000204_random 32398 154 + 81310 CTACCTACAGCGTTTTGGGG--CGTGTTTGTGATGCGGCAGTCGCTGACTGGTACCCCCT-------T--C----CCC-CA--GGCATGAG---GACGTTCCTCAACTTCATCC----CGCTTCCCAGGATTAGCTAGAAACCAAC-AGAGCCATGTGGCTAAATCCATTCTGGTAGGGC s mm9.chr11 118746237 147 + 121843856 ----ctacagtggtttggga--cttgcttgttatacagcggtagctaactgatacaCCCT-------C--T----CCT-ACAACGCATGGA------GACATGAAACTTCATCC----TGCTCATGGTCTTAG--CAAAATCCCATGGGGGATGTGTGGCGGACTTCATCCT-CTAGGGC i mm9.chr11 I 62316 C 0 s dipOrd1.scaffold_53224 610 149 + 10229 ----ctactgagtttgagga--cttgtttgttacacagcggtagttaactgatacaTACT-------C--T-TCCCCC-TCAAGCCATATG------AATCCCAGACTTTAACC----TGCTCCTCACATTCA--GAGAATCCCAC-AGAGACGTGTGGCTGACTTCGCTCT-GTAGGGC i dipOrd1.scaffold_53224 N 0 C 0 s cavPor3.scaffold_76 4379354 133 + 7991924 ----ctatggagttgttggg--ctagtttgttacacagtagtggctaacagatgtaTACT-------C--CATGCTCT-GCA-----------------------ACTTCAGCC----TGCTCCTTGTAGTAG--CAGAACCCCAT-AGAGGCTTGCAGTTAGCTTCACCGT-GTAGGGC i cavPor3.scaffold_76 I 68024 C 0 s speTri1.scaffold_128900 43804 153 + 44573 ----ctaccgagtttta-ga--cctgcttgttatgcaggagtagctaactgatgcaCCCT-------G--C----CCC-CAGAGGCATGAG---GCTGCCCTGCAACCTCATCCTGTGTGCTCCTCAGTCTTA--CGGAGCCCCGT-GGACACACGCGGCTCACGTCTCTCTGGTAGGGC i speTri1.scaffold_128900 N 0 C 0 s papHam1.scaffold8336 30763 149 - 95547 ----ctacagcattttgggg--cgtgtttgtgatgcagcagtcactgactggtaca---T-------T--C----CCC-CAGGGGCATGAG---GATGCTCCTCAACTTCATCC----TGCTTCCCAGGATTAGCTAGAACCCAAC-AGAGCCATGTGGCTAAATCCATACTGGTAGGGC i papHam1.scaffold8336 N 0 C 0 s rheMac2.chr16 75023511 152 + 78773432 ----ctacagcattttgggg--cgtgtttgtgatgcagcagtcgctgactggtacaCCCT-------T--C----CCC-CAGGGGCATGAG---GACGTTCCTCAACTTCATCC----TGCTTCCCAGGATTAGCTAGAACCCAAC-AGAGCCATGTGGCTAAATCCATTCTGGTAGGGC i rheMac2.chr16 N 0 C 0 s ponAbe2.chr17_random 16048952 152 + 17838096 ----ctacagagttttgggg--tgtgtttgtgatgcggcagtcgctgtccggtacGCCCT-------T--C----CCC-CAGGGGCATGAG---GACGCTCCTCAACTTCATTC----TGCTTCCCAGGATTACCTAGAACCCAAC-AGAGCCATGTGGCTACATTCATTCTGGTAGGGC i ponAbe2.chr17_random N 0 C 0 s gorGor1.Supercontig_0007361 2253 152 - 64270 ----CTACAGCGTTTTGGGG--CGTGTTTGTGATGCAGCAGTCACTGACTGGTACACCCT-------T--C----CCC-CAGGGGCATGAA---GACGTTCCTCAACTTCATCC----CGCTTCCCAGGATTAGCTAGAACCCAAC-AGAGCCATGTGGCTAAATCCATTCTGGTAGGGC i gorGor1.Supercontig_0007361 N 0 C 0 s panTro2.chr17 79462041 150 + 83384210 ----ctacagcgttttgggg--cgtgtttgtgatgcggcagtcgctgactggtacaCCCT-------T--C----CCC-CA--GGCATGAG---GACGTTCCTCAACTTCATCC----CGCTTCCCAGGATTAGCTAGAACCCAAC-AGAGCCATGTGGCTAAATCCATTCTGGTAGGGC i panTro2.chr17 N 0 C 0 s tarSyr1.scaffold_131410 3807 139 + 8975 ----ctatagagtttggggg--cttgtttgtgatgaggcattagctgactggttca-CCT-------T--C----CCC-CA-------AAG---GACGCTCTACAATTTCATCC----TACTTCCCAGTAT----TAGAACCCAAT-GGAGGCA-GCATCTAGATTCATTCTGGAAGGGT i tarSyr1.scaffold_131410 N 0 C 0 s bosTau4.chr19 10848762 143 - 65312493 -----------gttaggggg--ctcatttgttacacagctgaagctaactgatac--TCT-------T--C----CCC-TAAAGGAAGGAA---GATGCTCCACAATTTCATTC----TGCTTTTCAGTATTAGATAGAATCCAAC-AGAGACACACAGCTAAATTCAGTCTAGCAGGGT i bosTau4.chr19 I 78278 C 0 s turTru1.scaffold_106006 116800 147 + 145505 ----cttctgagttaggggg--cttgtttgttatacagcag----tacctgacAC--TCT-------T-CC----CCC-TAAAGGCAGGAA---GATGCTCCACAACTTCATCC----TGCTTCTCAGTATTAGACAGAAGCCAAC-AGAGACACACAGCTAAATTCAGTCTGGTAGGGT i turTru1.scaffold_106006 I 83717 C 0 s equCab2.chr11 58030969 151 - 61308211 ----ctaccgagtttggggg--cttatttgttatgcagcagtagctaactgatacaCTCT-------T-CC----TCC-TGAAGGCGTGAA---GACACTCCACAACCTCCTCC----TGCCTCTCAGAGGTAGACAGAACCCAAA-GGAGA--TGCAGCTGGATCCAGTCTGGTACAGT i equCab2.chr11 I 72591 C 0 s canFam2.chr9 59425804 157 - 64418924 ----ctgctgagtttgggga--cttgtttgttatgcaacagtagctaactgatacaCACT-------TCCC----CCC-TAACAGCGTGGGAGAGATGCCCCACAACGTCATCC----CGCTTCTCCGCACTGGATAAAACCCAAT-GGAGACCTGCAGCTAAATCCACTCTGGCAGAGT i canFam2.chr9 I 52888 C 0 s felCat3.scaffold_206428 3264 148 + 132007 ---------gcgtttgggga--cttgtttgttatgtaacactagctaactaatacaTGCT-------T-CC----CCC-TAAGGGCACGAG---GACGCTCTACAACCTCATCC----TGCTTCTCAGTACTGGATAAAACCCGAT-GCAGACCTGCAGCTAAATTCATTCTGGTAGGGC i felCat3.scaffold_206428 N 0 C 0 s myoLuc1.scaffold_4816 4163 154 + 14340 ----ctactgtgcttggggggacttgcttgttatgcagcagtagctaactgatacaCTCT-------T--C----CCC-TGGAGGCATGAA---GATGCTCCACAGTTTCACCC----TGCTTTTCGGCATCAGATAGAACCCAGC-GGAGACAGGCAGCTAAAGCCATTCTGCTAGAGT i myoLuc1.scaffold_4816 N 0 C 0 s pteVam1.scaffold_11245 4468 146 + 48268 ----ctaccgagtttggggg--cttgcttgctgcgcagcaggagctaactgatacGCTCT-------T--C----CCC-TAAAGGCACGAA---GATGCTCCACGCCTTCGACC----TGCCTCTCGGTGT----TAGAACCCGGT-G--GACACGCAGCTCAAGCCGTTCTGGTGGAGT i pteVam1.scaffold_11245 N 0 C 0 s micMur1.scaffold_89264 713 156 + 5251 ctagctacggagtccggggg--cttatttgtgacgcagcagtcgctaactgatacaCCCT-------C--C----CCCGCAAAGGCACGAG---GACGCTCCGCAACTCCCCCC----TGCTTCTCACGACTGCACGGAACCCAAC--GAGACACGCCGCTAAATTCATTCCGGGCGGGT i micMur1.scaffold_89264 N 0 C 0 s otoGar1.scaffold_94362.1-287808 15388 147 + 287808 ccagctac--agtctgggga--cttgtttgtgatgcagcagcagctgactgataca--------------C----CCCACAAAGGAGGGAG---GCTGCTCTGCACCTTCATCC-----ACTTTTCTGTACCAGACAGAAACCAAT--GAGACACACGGCTGCAGTTGCTCT-GGCAGGT i otoGar1.scaffold_94362.1-287808 N 0 C 0 s dasNov2.scaffold_28617 1136 145 + 20752 -------------TTCTAGG--CCTTTTTGTTACGCAGCACTAACTAACTAATACACCCTTTCCCACT-CC----CCC-TAAAGGCATAAG---GTTGTTCTGCAACTTCATCC----CACTTCCC------AGATAGAACCCAAA-AGAAGCATGCTGCTAAATTCATTCTGGTGGGGT i dasNov2.scaffold_28617 N 0 C 0 s proCap1.scaffold_29042 3911 141 + 24616 -------------TTCTGGG--CCTGTTTGTTACACAGCGGTAGCTAGCTGATACACCCT----------T----CCC-CAAAGGCATGAA---GGTGGTTTGCAACCTCACCT----TCCTTCTCACTGTTAGACAGAAGGCAGT-GGAGACAGGCAGC-GGATATGTTCTGGTAGGAT i proCap1.scaffold_29042 N 0 C 0 s loxAfr3.scaffold_49 14419276 144 - 17734757 -------------ttctggg--tgtgtttgtcatacagcagcagctaaatgatacaTCCT-------T-CT----CCC-TAAAGGCATGAG---GATGCTTTGCAACATCACCT----TGCTTCTCAGTGTTAGACAGAACCCAAC-AGAGACAGGCAGCTAGATACATTCCAGTAAGGT i loxAfr3.scaffold_49 N 0 C 0 s calJac1.Contig5139 32488 122 + 225949 ------------------------------------ggcagtcactaactggtacaGCCT-------T--C----CCC-CAGGGGCATGAG---GACGCTCCTCAGCTTCATCC----TGCTTCCCAGGATTAGCTAGAACCCAAC-AGAGCCGTGAGGCTAAACCCATTCTGGTCGGGC i calJac1.Contig5139 N 0 C 0 a score=4029950.000000 s hg19.chr17_gl000204_random 32552 304 + 81310 TTGTAATTGAGCTACTTGGTGAGATCTTCCGTTTGA---T----------------------TTT----CTCTTTTCATATG-TTTT----CAATCAGAAATATCAGAAGCTGCTTTGA---ATGTCCCTGCAGAGTTCT--CAGAAGCATCC-TCTCCCGGGT--------------------TTCTCTGGAGAG------C-CCACCT----------------TGTTTGTT---GGAGAGT-GTATTCTCCTGCAGCTTTTC----------AAAT-GCTACATTTTCCTCTGATGGCAGC-CAGGGC----ATTTGATTGCATGAGA-------GATGGTGA--TGTGGTTGCAA-CTGCTGTCGATATTCC--TTTATGACTCTGAAT------TTGCATCTGT-GCAAGTCTGGTAATAC---- s calJac1.Contig5139 32610 304 + 225949 TTGTAATTGAGTTACTGGATGAGATCTTCGGTTTTA---T----------------------TTT----CTCTTTTCATACG-TTTT----CAATCAGAAATATCAGAAGCTGTTTTGA---AGGTCCCTGCAGAGTTCC--CAGAAGCATCC-TCTCCCAGGT--------------------TTCTCTGGAGAG------C-CTGTCT----------------TATTTGTT---GGAGAGT-GTGTTCTCCTGCAGCTTTTC----------AAAT-GCTCCATTCTCCTCTGACGGCTGC-CGGGGC----TTTCAATTGCCTAAGA-------GATGATGA--CGTGACTGCAA-TGGCCGTCGATACTCC--TTTATGACTCTGAAT------TTGCATCTGT-GCGAGGCTGGTAATAC---- i calJac1.Contig5139 C 0 I 4 s loxAfr3.scaffold_49 14419420 301 - 17734757 TCACCACTAAGCTACCTGATGAGATCTTTAGTTTGA---A----------------------TTT----TCATTTTAATATA-TTTT----CAGTCCGGAATTGAAGATGCCCTTTGGA---ACATCCCTGCAGAGTTCT--AAGAAGCATCC-TTTCCTGGGC--------------------CTCTCCAGAGAGG-----T-GG-CTG----------------TATTTGCT---GGTGAGT-GTGTGCACTCACAGCTTTTC----------AGAC-CCCACACTTCTCT--AATGGCAGC-TGGGGC----ATTTGACTGTGC--GA-------GAGGGTGA--TGTGCCTGTAA-CTGCTGTCAATACTCC-TTTTACGGCTCTGAAT------TTGCATCTCT-GCAAGGCTGGTAATTC---- i loxAfr3.scaffold_49 C 0 I 4 s proCap1.scaffold_29042 4052 304 + 24616 TCACCACTGGGTTACCAGGTGAGACCTTCGTTTTAC---A----------------------TTT----TCATTTTAACACG-TTTT-----AATCCAGAATCAAAGGTGCCACTCGGA---AGATCCCTGCAGAGTGCT--AAGAAACATCC-CTGGCTGGGC--------------------CTCTCCAGAGAGG-----C-GGACTG----------------TGTTTGCT---GGAGAGG-ACAGGCAGCCGCAGCCCTTC----------AAAC-CCTGTCCTTCCCTCAGACGGCAGC-TGGGGC----ATCTGGCTGTGC-AGA-------GAGGGTGA--GGTGCCTGTCA-CCGCTGTCAATATTCC-CTTTACAATGCCGCAT------TTGCATCTGT-GCAAGGCTGGTAATTC---- i proCap1.scaffold_29042 C 0 I 4 s dasNov2.scaffold_28617 1281 308 + 20752 TCATAATTGAGTTACACAGTGAGATCTTTGGTTTAA---A----------------------TGT----TTATTTTAACTTT-TTTTTTTCCCATCAGAAATGTAAGAAGCCATTTAGA---GCCTCTCTCCAGAGTTCT--CAG-AGCATCC-TTTCCCAGGC--------------------TTCTCCAGCGAGG-----C-TCGCTT----------------TGTTTGTT---GGATAAT-GTGTTCTCTCGCAGCTTTTC----------AAA--CCTACATTTTCTTCGGATGGCAGC-TGGGGC----ATTTGATTGTATGAGG-------GATGGCGA--TGTGGTTGTAA-TTGCTGTCGATATTCC-GTTTATGACTCTGAAT------TTGCATCTGT-GCAAGGCTGGTTGTTC---- i dasNov2.scaffold_28617 C 0 I 4 s otoGar1.scaffold_94362.1-287808 15535 304 + 287808 TTATAATTGAGTTACTGGGTGAGAGCTTCAGCTTCATTTT----------------------TTT----TTTTTTTACTATA-TTTT----CAATCAGAGACATCAGAAGCTGTGCCGA---GCCTCCCTGCAGGGTTCT--CAGGAGCATCC-TTTCCAGGGC--------------------TGCTCTGGAGGG------GCCTGTCT----------------TGCTTGCT---GGAAG---CCGCTCT---GCAGCTCTTT----------AGAT-GCCACGTCTCCCTCTGACAGCAGC-CGGGGC----ACCTGATCGTGAGAGA-------GGCGGTGA--TGTGGCTGCCA-TTGCTGTCCATATTCC-TTTTACCACTCTGAAT------TTGCATCTGT-GCAAGGCTGGTAATTC---- i otoGar1.scaffold_94362.1-287808 C 0 I 4 s micMur1.scaffold_89264 869 297 + 5251 TCATAATTGAGCTACTTGGTCAGATCTTCAGTTTGATTTT----------------------TTT----TTCTTTTAATATC-TTTT----CAATCAGAGATATGAGAAGCTGTTCACA---GCGTCCCTGCAGAGCTCT--CAGAAGTGTCC-CTTGCGGGGC--------------------TGCGC-GGAGAG------G-CTGTCT----------------TGTTTGCC---GGGGG-C-CCGCTCTCTCGCCGCTGTTC----------AAGC-GCCACATTTCCCTCGGACGGTGGC-C-AGGC----ATTTGACAGCGCGAGA-------GGCGGTGA--CGGGGTTGCAG-CTGCTGCCGGCGTTCC-TCTTACCACTCTGGAT------CTGCAACTGT-GCAAGGCT------------ i micMur1.scaffold_89264 C 0 M 3270 s pteVam1.scaffold_11245 4614 307 + 48268 TTATAATTGTTTTACTTGCTGAGATCTTTGGCTTAA---A-------------------T-TTTT----TTCTTTCAATATATTTTT----CAATTAAAAATGAAAAGAGCTGTTTGGA---ACATCCCTGCAG--TTTT--CAGAATCACCC-TTTCCTGGGT--------------------TTCTCCAGAGAGG-----T-TTGTTT----------------GGTTTGTT---GGAGAGC-GTGTTCTCTTGCAGCTTTTC----------AAAC-GCTACATTTTCCTCTGGCGGCATC-CAGGGC----ATCTGATCGCATGAGA-------CATGGTGA--CGTGGTTGCAA-TCGCTGTCAACGTTCC-TCTTACGACTCCGAAT------TTGCATCTGT-GCAAGGCTGGTAATTC---- i pteVam1.scaffold_11245 C 0 I 4 s myoLuc1.scaffold_4816 4317 321 + 14340 TGATCACTGATTTCCTTGATGAGATTTCTGTTTTGA---A-------------------TGTTTT----TTCTTCTGATACA-TTTT----CAATCAGAAACGAAAAGAGCCA-TTGGG---ACGTCCCTGCAGA-GTTC--CCGGAGCATCC-TTCC----GG--------------------CTCCCCCGGGCGG-----T-GTGTGTGTGGCGGTGGGAGGGGGGGTTGTTCGCGGGGAGC-GTGTTCTCATG-AGCTTGTC----------AGAC-ACTGCG-TTTCCTCCAGCGGCATC-CGGGGC----CTCTGATCCTGGGAGG-------GGAGGTGA--TGTGGCTGCGATTTGCTGTCAATATTCC-TTCTGCGGCTCCGAAT------TGGCATCTGT-GCGAGGCCGGTAATTC---- i myoLuc1.scaffold_4816 C 0 I 4 s felCat3.scaffold_206428 3412 323 + 132007 TTAGAACTGATTTACTTGGTGAGGTCttttacttta---acttattttttttttttttat-tttt----atttttTACTATA-TTTG----CAATCAGAAATGTAATG------TTGGA---CGGCCCCTGCAAAGTTCT--CAGAAGCATCT-TGTCCTGGGT--------------------TTCTCCAGAGAGG-----C-GTGTTT----------------TGTTTGCG---GGAGAGC-GTGTTCTCTTGCGGCTTTTC----------AAAT-GCTCCATTTTGCTCTGACGGCAGC-CAGGGC----ATTTGATCGCATGAGA-------GATGGTGATGTGTGGTTGCAA-TTGGTGTCAATATTCC-TTTTATGACTCTGAAT------TTGCATCTGT-GCGAGGCTGGTAATTC---- i felCat3.scaffold_206428 C 0 I 4 s canFam2.chr9 59425961 306 - 64418924 TTAGAATTGATCTACTTGGTGAGATCTTTGCCTTAA---A----------------------TTT----TTCTTTTAACACA-TTTT----CCATCAGAAACGTAAGGAGCCACTTGGA---TGGCCCCTGCAGAGTTCT--CAGAAGCATCT-TGTCCCGGGT--------------------TTCTCCAGAGAGG-----C-TTGTTT----------------TGTTTGTT---GGAGAGT-GTGTTCTCTTGCCGCTTTTC----------AAAT-GCTCCATTTTGCTCTGACGGCAGC-CAGGGC----ATTTGATCGCATGAGA-------GATGGTGA--TGTGGTTGCAA-TTGCTGTCAATATTCC-TTTTATGACTCTGAAT------TTGCATCTGT-GCGAGGCTGGTAATTC---- i canFam2.chr9 C 0 I 4 s equCab2.chr11 58031120 297 - 61308211 TTTTAATTGACTTGCTTGGTACGATCTTTGATTTAA---A----------------------TTT----TTCTTTCAATATA-TTTT----CAATCCAAAATGTAAAGAGCTT-TTGGA---ATGTCCCAGCAGAGTTCT--CAGAAGCATCC-TCTCCC-GGC--------------------TTCTCCAGCGAGG-----C-TGGTTT----------------TGTTTGTC---A-------GTGTTC-CCTGCAGCTTTTC----------AAAT-GCCGCCTTTCCCTCCGATGGCAGC-GAGGGC----CTTTGATCGCCCAAGC-------GATGACGA--TGTGGTTGCAC-GTGCCGTCAATATTCC-TTTTAGGATTCTGAAT------TTGCATCCGT-GCGAGGCTGGCAATTC---- i equCab2.chr11 C 0 I 4 s turTru1.scaffold_106006 116947 305 + 145505 TTATAATTGATTCACTTGGTGAGATCTTTGGTTTAA---A----------------------TTT----TTCTTTTAATATA-TTTT----CAATCAGAAACGTAAGGAGCTGTTTGGA---ACGTCCCAGCAGAGTTCT--CAGAAGCATCC-TTTCCTGCGT--------------------TTCTCCAGAGAGG-----C-TTGTTT----------------TGTTTGTT---GGAGAGT-GTGTTCTCTTACAGCTTTTC----------AAAT-GCTACATTTTCCTCTGACGGCAGC-CAGGGC----ATCTGATCGCAAGAAA-------GATGGTGA--TGTGGTTGCAA-TTGCTGTCAATATTCC-TTTTATGACTCTGAAT------TTGCATCTGT-GCAAGGCT-GTAATTC---- i turTru1.scaffold_106006 C 0 I 4 s bosTau4.chr19 10848905 309 - 65312493 TTATAATTGATTTACTTGGTGAG-TCTTTGGTTTAA---A----------------------TTT----TTCTTTTAATATA-TTTT----CAATCAGAAGTGTAAGGAGCTGTTTGGA---ATGTCCCTGCAGAGTTCT--CAGAAGCATCC-TTTCCTGCGT--------------------TTCTCCAGAGAGA-----C-TTGTTT----------------TGTTTGTT---GGAGAGT-GTGTTCTCTTGCAGCTTTTC----------AAAT-GCTACATTTTCCTCTGACGGCAGC-CAGGGCATTTATTTGATCGCAAGAGA-------GATGGTGA--CGTGGTTGCAA-TTGCTGTCAATATTCC-TTTTATGACTCTGAAT------TTGCATCTGT-GCGAGGCTGGTAATTC---- i bosTau4.chr19 C 0 I 4 s tarSyr1.scaffold_131410 3946 301 + 8975 TTAATTATAAGTCACCTGGTGAGATCTTCGGTAAGA---C----------------------TTT----TTCTTTTACTATA-TTTT----CTATCAGAAATATC---AGCTGTCCGCA---ATGACCCTGCAGAGTTCT--CTGAAGCATCC-TTCCCCAGGT--------------------TTCTCTGGAGAGA-----C-CCGTCT----------------TGTTTGTT---AGAGAGT-G-ACTCTCTTGCAGTGTTTC----------AAAT-GCTACATTTTCCTCTGACAGCAGC-CGCGAC----ATTTGATTGTACGAAA-------GATGG-GA--CGTGGCTGCAA-TTGCTGTCGATATTCC-TTTTACGACTCTGAAT------TTGCATCTGT-GCAAGGCTGGTAATTC---- i tarSyr1.scaffold_131410 C 0 I 4 s panTro2.chr17 79462191 304 + 83384210 TTGTAATTGAGCTACTTGGTGAGATCTTCCGTTTGA---T----------------------TTT----CTCTTTTCATATG-TTTT----CAATCAGAAATATCAGAAGCTGCTTCGA---ATGTCCCTGCAGAGTTCT--CAGAAGCATCC-TCTCCTGGGT--------------------TTCTCTGGAGAG------C-CCATCT----------------TGTTTGTT---GGAGAGT-GTATTCTCCTGCAGCTTTTC----------AAAT-GCTACATTTTCCTCTGATGGCAGC-CAGGAC----ATTTGATTGCATGAGA-------GATGGTGA--TGTGGTTGCAA-CTGCTGTCGATATTCC--TTTATGACTCTGAAT------TTGCATCTGT-GCAAGTCTGGTAATAC---- i panTro2.chr17 C 0 I 4 s gorGor1.Supercontig_0007361 2405 304 - 64270 TTGTAATTGAGCTACTTGGTGAGATCTTTGGTTTGG---T----------------------TTT----CTCTTTTCATATG-TTTT----CAATCAGAAATATCAGAAGCTGCTTCGA---ATGTCCCTGCAGAGTTCT--CAGAAGCATCC-TCTCCCGGGT--------------------TTCTCTGGAGAG------C-CCATCT----------------TGTTTGTT---GGAGAGT-GTATTCTCCTGCAGCTTTTC----------AAAT-GCTACATTTTCCTCTGACGGCAGC-CAGGGC----ATTTGATTGCATGAGA-------GATGGTGA--TGTGGTTGCAA-CTGCTGTCGATATTCC--TTTATGACTCTGAAT------TTGCATCTGT-GCAAGTCTGGTAATAC---- i gorGor1.Supercontig_0007361 C 0 I 4 s ponAbe2.chr17_random 16049104 304 + 17838096 TTGTAATTGAGCTACTTGGTGAGACCTTCGGTTTGA---T----------------------TTT----CTCTTTTCATATG-TTTT----CAATCAGAAATATCAGAAGCTGCTTCGA---ATGTCCCTGCAGAGTTCT--CAGAAGCATCC-TCTCCCGGGT--------------------TTCTCTGGAGAA------C-CCATCT----------------TGTTTGTT---GGAGAGT-GCATTCTCCCGCAGCTTTTC----------AAAT-GCTACGTTTTCCTCTGACGGCAGC-CAGGGC----ACTTGATTACATGAGA-------GATGGTGA--TGTGGTTGCAA-CTGCTGTCAATATTCC--TTTATGACTCTGAAT------TTGCATCTGT-GCAAGTCTGGTAATAC---- i ponAbe2.chr17_random C 0 I 4 s rheMac2.chr16 75023663 304 + 78773432 TTGTAATTGAGTCACTTGGTGAGATCTTCAGTTTGA---T----------------------TTT----CTCTTTTCATATG-TTTT----CAATCAGAAATATCAGAAGCTGCTTTGA---ATGTCCCTGCAGAGTTCT--CAGAAGCATCC-TCTCCCGGGT--------------------TTCTCTGGAGAG------C-CCATCT----------------TATTTGTT---GGAGAGT-GTATTCTCCTGCAGCTTTTC----------AAAT-GCTACATTTTCCTCTGACGGCAGC-CAGGGC----ATTTGATTGCATGAGA-------GATGGTGA--TGTGGTTGCAA-CGGCTGTCGATATTCC--TTTATGACTCTGAAT------TTGCATCTGT-GCAAGGCTGGTAATAC---- i rheMac2.chr16 C 0 I 4 s papHam1.scaffold8336 30912 304 - 95547 TTGTAATTGAGTCACTTGGTGAGATCTTCAGTTTGA---T----------------------TTT----CTCTTTTCATATG-TTTT----CAATCAGAAATATCAGAAGCTGCTTTGA---ATGTCCCTGCAGAGTTCT--CAGAAGCATCC-TCTCCCGGGT--------------------TTCTCTGGAGAG------C-CCATCT----------------TATTTGTT---GGAGAGT-GTATTCTCCTGCAGCTTTTC----------AAAT-GCTACATTTTCCTCTGACGGCAGC-CAGGGC----ATTTGATTGCATGAGA-------GATGGTGA--TGTGGTTGCAA-CGGCTGTCGATATTCC--TTTATGACTCTGAAT------TTGCATCTGT-GCAAGGCTGGTAATAC---- i papHam1.scaffold8336 C 0 I 4 s speTri1.scaffold_128900 43957 276 + 44573 TCATAATTGAATTACTTGGTGAGATCTTTGGTTTAA---T----------------------TTTT---TTCTTTTAACACA-TTTT----CCATCAGAAAGAGCAGCAGCTGTTCAGA---GCACTCCTGCAGA-GCCT--CAGAAGCATCC-TTCCCGGGGT--------------------CCCTCCAGAGAGG-----C-TGGTCT----------------TGTCTGCT---GGAGAAC-AGGTCCTCTGGAGGCTTTGT----------GAGT-GCTCCATTTTCCTTC--CAGTGGCGCGGG----------------------------------TGA--CGTGGTAGCCA-TCACTGTGG-----CT--CTTG-GAGTCAGAGT------CTGCACCTGTGGTAAGGCTGGTCATTC---- i speTri1.scaffold_128900 C 0 I 4 s cavPor3.scaffold_76 4379487 294 + 7991924 TTATAATTGAGTTGCTTGGTGAGATTGTTGGTCTAA---T----------------------TTTTTT-TCCTTTTAATACA-TTTT----CAACCAGAAAGAGCAGAAGTTGTTCAAA---TTGCTCCTGTTGAGTTCT--CAGAAGC-GTC-TTCCCTGGGC--------------------CTCTCCGGAGAGG-----C-TCGTGT----------------TGTCTGTT---GAAGAC--ATATCCTCACGAAGCTTTTC---------AGAA--GCCGCATTCTTCTGTGAC-GCAGC-CAGGAC----ACTTAATTGTGTGAGA-------GATGGTGA--TGTGGT-------ATCAGTTG-----CC--TTTATGCCTCCGAAT------CTGCATCTGC-ATGAGGCCGGCAACTC---- i cavPor3.scaffold_76 C 0 I 4 s dipOrd1.scaffold_53224 759 300 + 10229 TCATAATTGAGTTGCTCGGTGAGATCTTTGGTTTAA---T----------------------AT-----TTCTTTTAACATA-TTTT----CAATCAGAAAGAGCAGAAGCGGTTCAGA---GCACCCCTGCAGA-TTCT--CAGGAGCAGCC-TCCCCTGGCT--------------------TTCTCTAGGGAGG-----C-TCATCT----------------TGTCTGCC---GGAGAAT-GTGTCCTCATACAGCTTTTCCAG-TGTGAAAAAT-GTACCATTTGCCTCCAACGGCAGC-CGGG------TGCTGGTTGTCGGGGC------------TGG--TGAGGC-------GGCTGTGC-----CT--TTTATGACTGTGAATTTGCAATCACATCCGT-GCGCAGCTGGTAATTC---- i dipOrd1.scaffold_53224 C 0 I 4 s mm9.chr11 118746384 323 + 121843856 TTATAATTGAGTCACTCGGTGAGGTCTTTGGTTTAA---T----------------------TTTTTTCTTCTTTTAACATA-TTTT----CAATTCGAATGAGCAGATGCAGTTCAGA---GCACTCCTGCTGAGCTCT--CAGAAGCATCC-ATCCCTGGCT--------------------TTCTCCAGAGAGC-----C-TCATCT----------------TGTCTGTC---GGAGACCGGTGTCCTCATGTAGCTTTTTCAGATGTGAAAAACGGGGACGTTTTCCTGCACCAGCAGC-CGGGGC----GCCTGAGTGTGGGAGAGACACGACGTGGCGG--TGTGGCTGCCG-TGGCTGTGC-----CT--TTCACGGCTTGGGCT------TCGCATCTGT-GCGAGGCTGGTGGTTC---- i mm9.chr11 C 0 I 4 s monDom5.chr2 304513039 339 - 541556283 tCACATTTGAGACACTTATAGAGTTCTTTGGtttaa---a---------------------attt----attttttaatat--tttt----CAGTCAAAAATTTAAGAAGTTGTCTAGAGTAATACACTTGAAAAATCCTG-CAACAAAGTTT-TTTTGCAGGTTTTTTTTTTGGGGGGGGGGGTTCTCCACAGGAGATTGTT-TGGTTT----------------TATGTGTA---GCCAAGT-TTAGTCTTCC-CACCTTTCT----------AAGT-CTTACATTTTCCTCCAGAGGCAGC-TGGGGC----ATTTGGTTTTATGAAA-------GATGGTGA--CATAGTTGTAA-TTGCTATCAATATTCCTTTTTGTGTCTCTAATT------TCATATCTGT-GAAGGTCTCACAGCTCATAT i monDom5.chr2 N 0 C 0 s macEug1.Scaffold81348 5176 291 - 9603 --------------------GAGTTCTTTAGTTTAA---A----------------------AAT----TCTCATTAAAAT--TTTT----CAGTcagaaatttatgaaaatatttagatTGGTATCCTTGGAAAGTCTTGCTAGCAGAGTTTATTTTTTAGGT--------------------TTCTCTAcaggaa-----a-ttattt----------------tgtttgta---gCTGAGT-TTAGTCTTCC-CAACTTTCT----------GAGT-CCTACATTTTCCTCCAGAGGCAGC-TGGGAC----ATTGGGTTTTGTTAAA-------GATGGCAA--TGTGGTTGTAA-TTGCTATCAATATTCCTTTTTATGCCTCTAATT------TTGCATCTGT-GAAGTCCTCACAGCTC---- i macEug1.Scaffold81348 N 0 I 4 a score=912800.000000 s hg19.chr17_gl000204_random 32856 44 + 81310 CTGAATTCCAGGCACAAATAAATGAAACTTATTT-AAAATAACTG s otoGar1.scaffold_94362.1-287808 15843 44 + 287808 CTGAATTGCAAGCGCAAATAAATGAAACTTATTT-AAAATAACTG i otoGar1.scaffold_94362.1-287808 I 4 C 0 s tarSyr1.scaffold_131410 4251 44 + 8975 CTGAATTCCAAGCACAAATAAATGAAACTTATTT-AAAATAACTG i tarSyr1.scaffold_131410 I 4 C 0 s calJac1.Contig5139 32918 44 + 225949 CTGAATTCCAAGCACAAACAAATGAAACTTATTT-ACAATAACTG i calJac1.Contig5139 I 4 C 0 s panTro2.chr17 79462499 44 + 83384210 CTGAATTCCAGGCACAAATAAATGAAACTTATTT-AAAATAACTG i panTro2.chr17 I 4 C 0 s gorGor1.Supercontig_0007361 2713 44 - 64270 CTGAATTCCAGGCACAAATAAATGAAACTTATTT-AAAATAACTG i gorGor1.Supercontig_0007361 I 4 C 0 s ponAbe2.chr17_random 16049412 44 + 17838096 CTGAATTCCAGGCACAAATAAATGAAACTTATTT-AAAATAACTA i ponAbe2.chr17_random I 4 C 0 s rheMac2.chr16 75023971 44 + 78773432 CTGAATTCCAGGCACAAACAAATGAAACTTATTT-AAAATAACTG i rheMac2.chr16 I 4 C 0 s papHam1.scaffold8336 31220 44 - 95547 CTGAATTCCAGGCACAAACAAATGAAACTTATTT-AAAATAACTG i papHam1.scaffold8336 I 4 C 0 s mm9.chr11 118746711 45 + 121843856 CTGAATTCTAAGCACAAATAAACGGGACTTATTTAAAAATAACTG i mm9.chr11 I 4 C 0 s dipOrd1.scaffold_53224 1063 43 + 10229 CCGGATCCCAAGCACAAATAGATGAGATTTCCTT--AAACAACTG i dipOrd1.scaffold_53224 I 4 C 0 s cavPor3.scaffold_76 4379785 44 + 7991924 CTGAATTCCATGCACAGATAAAAGAAGCTTATTT-AAAATAACTG i cavPor3.scaffold_76 I 4 C 0 s speTri1.scaffold_128900 44237 43 + 44573 CTGAATTCCAAGTACAGATAAATAAACTTCATTA--AAACCACAG i speTri1.scaffold_128900 I 4 C 0 s ochPri2.scaffold_6980 56372 44 + 61692 CTCAATGCCAAGCACAGAGACATGAAATGCACCT-AAAATAACTG i ochPri2.scaffold_6980 N 0 C 0 s bosTau4.chr19 10849218 44 - 65312493 CTGAATGCCAAGCACAAATAAATGAAACTTATTT-AAAATAACTG i bosTau4.chr19 I 4 C 0 s turTru1.scaffold_106006 117256 44 + 145505 CTGAATGCCAAGCACAAATAACTGAAACTTATTT-AAAATAACTG i turTru1.scaffold_106006 I 4 C 0 s equCab2.chr11 58031421 44 - 61308211 CTGAATGCCAAGCACAAATGAATGAAACTTATTT-AAAACAACTG i equCab2.chr11 I 4 C 0 s canFam2.chr9 59426271 44 - 64418924 CTGAATGCCAAGCACAAATAAATGAAACTTATTT-AAAATAACTG i canFam2.chr9 I 4 C 0 s felCat3.scaffold_206428 3739 44 + 132007 CTGAATGCCAGGCACAAATAAATGAAACTTATTT-AAAATAACTG i felCat3.scaffold_206428 I 4 C 0 s myoLuc1.scaffold_4816 4642 42 + 14340 CTCAGTGCCGAGCGCAAACCAGTGAAACCCATTT-AAAGTAAC-- i myoLuc1.scaffold_4816 I 4 C 0 s pteVam1.scaffold_11245 4925 44 + 48268 GTCCATGCCAAGCACAAAGAAATGAAACTTATTT-AAAATAACTG i pteVam1.scaffold_11245 I 4 C 0 s loxAfr3.scaffold_49 14419725 43 - 17734757 CTGAATGCCAACCACAAAGAAATGAAACTTATTT-AAAATAACT- i loxAfr3.scaffold_49 I 4 I 1 s proCap1.scaffold_29042 4360 43 + 24616 CTGAATGCCAAGCACAAAGAAACGAAACTTATTT-AAAATAACT- i proCap1.scaffold_29042 I 4 I 1 s dasNov2.scaffold_28617 1593 42 + 20752 CTGAATGCCAAGCACAAATAAATGAAACTTATTT-AAAATAAC-- i dasNov2.scaffold_28617 I 4 C 0 s macEug1.Scaffold81348 5471 44 - 9603 CTGAATGCCAAGCACAAATACACTAAACTTACTT-AAAATAACTA i macEug1.Scaffold81348 I 4 C 0 s monDom5.chr2 304513378 43 - 541556283 CCGAATGCCAAGCACAAATACACTAAACTTACTT-AAAATAACA- i monDom5.chr2 C 0 C 0 e micMur1.scaffold_89264 1166 3270 + 5251 M a score=335591.000000 s hg19.chr17_gl000204_random 32900 25 + 81310 -GGAAAAATTCCACACTGGAGGTAA-----------------------------A s otoGar1.scaffold_94362.1-287808 15887 24 + 287808 -GG-AAAATTCTATGCTGGAGGTAA-----------------------------A i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tarSyr1.scaffold_131410 4295 24 + 8975 -GG-AAAATTCCACACTGGAGGCGA-----------------------------A i tarSyr1.scaffold_131410 C 0 C 0 s calJac1.Contig5139 32962 24 + 225949 -GG-AAAATTCCACACTGGAGGTAA-----------------------------A i calJac1.Contig5139 C 0 C 0 s panTro2.chr17 79462543 25 + 83384210 -GGAAAAATTCCACACTGGAGGTAA-----------------------------A i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 2757 25 - 64270 -GGAAAAATTCCACACTGGAGGTAA-----------------------------A i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16049456 25 + 17838096 -GGAAAAATTCCACACTGGAGGTAA-----------------------------A i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75024015 24 + 78773432 -GG-AAAATTCCACACTGGAGGTAA-----------------------------A i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 31264 24 - 95547 -GG-AAAATTCCACACTGGAGGTAA-----------------------------A i papHam1.scaffold8336 C 0 C 0 s mm9.chr11 118746756 24 + 121843856 -GG-AAAATTCCATGCTGGAGTGGG-----------------------------G i mm9.chr11 C 0 I 1 s dipOrd1.scaffold_53224 1106 24 + 10229 -GG-AAAATTCCATGCTAGGGGGAA-----------------------------A i dipOrd1.scaffold_53224 C 0 I 2495 s cavPor3.scaffold_76 4379829 24 + 7991924 -GG-AAAATTCCACGCTGGAGGCAG-----------------------------A i cavPor3.scaffold_76 C 0 I 2 s speTri1.scaffold_128900 44280 24 + 44573 -GG-AAAATTCCACGCTGGAGATAA-----------------------------A i speTri1.scaffold_128900 C 0 I 1 s ochPri2.scaffold_6980 56416 24 + 61692 -GA-AGAATTCCACACTAATGATAC-----------------------------G i ochPri2.scaffold_6980 C 0 I 7 s vicPac1.scaffold_234559 2 24 + 1001 -GG-AAAATTCCATGCTGGAGGTTTG----------------------------- i vicPac1.scaffold_234559 N 0 C 0 s turTru1.scaffold_106006 117300 23 + 145505 -GG-AAAATTCCATGCTGGAGGTTT------------------------------ i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10849262 23 - 65312493 -GG-AAAATTCCATGCTGGAGGTTT------------------------------ i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58031465 21 - 61308211 -GG-AAAATTCCATGCTAGAGGT-------------------------------- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59426315 23 - 64418924 -GG-AAAATTCCATGCTGGAGGTTA------------------------------ i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 3783 23 + 132007 -GG-AAAATTCCATGCTGGAGGtta------------------------------ i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_4816 4684 20 + 14340 -AG-AAAAGTCCACGCTGGAGG--------------------------------- i myoLuc1.scaffold_4816 C 0 I 14 s pteVam1.scaffold_11245 4969 22 + 48268 -GG-AAAATTCCACGCTGGAAGTT------------------------------- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14419769 24 - 17734757 -GG-AAAATTCCATGCTGGAGGCAA-----------------------------A i loxAfr3.scaffold_49 I 1 I 2 s proCap1.scaffold_29042 4404 20 + 24616 -GG-AAAATTCCACACTGGAG---------------------------------A i proCap1.scaffold_29042 I 1 I 2 s dasNov2.scaffold_28617 1635 53 + 20752 -AG-AAAATTCTATACTAGAAGAGAAAggaaggaggaaaggagggagggatggga i dasNov2.scaffold_28617 C 0 I 2 s macEug1.Scaffold81348 5515 24 - 9603 -GG-AAAATTCCACACTAGTAGTAA-----------------------------A i macEug1.Scaffold81348 C 0 C 0 s monDom5.chr2 304513421 22 - 541556283 GGA-AAAGTTTCACAATGGTAGT-------------------------------- i monDom5.chr2 C 0 C 0 e micMur1.scaffold_89264 1166 3270 + 5251 M a score=-125503.000000 s hg19.chr17_gl000204_random 32925 12 + 81310 AT-----AAAAAA---TAGA s otoGar1.scaffold_94362.1-287808 15911 12 + 287808 AG-----GAAAAA---TTCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tarSyr1.scaffold_131410 4319 13 + 8975 ACA----AAAAAA---TTCC i tarSyr1.scaffold_131410 C 0 C 0 s calJac1.Contig5139 32986 12 + 225949 AT-----TAAAAA---TGGC i calJac1.Contig5139 C 0 C 0 s panTro2.chr17 79462568 12 + 83384210 AT-----AAAAAA---TAGA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 2782 12 - 64270 AT-----AAAAAA---TAGA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16049481 12 + 17838096 AT-----AAAAAA---TAGA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75024039 12 + 78773432 AT-----AAAAAA---TGGA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 31288 12 - 95547 AT-----AAAAAA---TGGA i papHam1.scaffold8336 C 0 C 0 s mm9.chr11 118746781 7 + 121843856 --------GAAGG-----CC i mm9.chr11 I 1 C 0 s cavPor3.scaffold_76 4379855 9 + 7991924 --------AAAAG---TTCC i cavPor3.scaffold_76 I 2 C 0 s speTri1.scaffold_128900 44305 12 + 44573 --------GAAAGAAATTCC i speTri1.scaffold_128900 I 1 C 0 s ochPri2.scaffold_6980 56447 12 + 61692 --------GGGGGTGCTTTC i ochPri2.scaffold_6980 I 7 C 0 s vicPac1.scaffold_234559 26 11 + 1001 --GAAAAAAAAAA------- i vicPac1.scaffold_234559 C 0 I 11 s turTru1.scaffold_106006 117323 6 + 145505 -------AAAATA------- i turTru1.scaffold_106006 C 0 I 11 s bosTau4.chr19 10849285 6 - 65312493 -------AAAATA------- i bosTau4.chr19 C 0 I 12 s equCab2.chr11 58031486 8 - 61308211 -----AAAAGAAA------- i equCab2.chr11 C 0 I 5 s canFam2.chr9 59426338 8 - 64418924 -----AAAAAAAA------- i canFam2.chr9 C 0 I 9 s felCat3.scaffold_206428 3806 8 + 132007 -----aaaaaaaa------- i felCat3.scaffold_206428 C 0 I 14 s pteVam1.scaffold_11245 4991 4 + 48268 ---------AAAA------- i pteVam1.scaffold_11245 C 0 I 14 s loxAfr3.scaffold_49 14419795 12 - 17734757 -----AAAAAAAA---ATCA i loxAfr3.scaffold_49 I 2 C 0 s proCap1.scaffold_29042 4426 12 + 24616 -----AAAAAAAA---TCCC i proCap1.scaffold_29042 I 2 C 0 s dasNov2.scaffold_28617 1690 12 + 20752 -----gaggAAAA---TCTC i dasNov2.scaffold_28617 I 2 C 0 s macEug1.Scaffold81348 5539 4 - 9603 ---------AACC------- i macEug1.Scaffold81348 C 0 C 0 s monDom5.chr2 304513443 8 - 541556283 --------AAAAA---CTC- i monDom5.chr2 C 0 C 0 e myoLuc1.scaffold_4816 4704 14 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e dipOrd1.scaffold_53224 1130 2495 + 10229 I a score=455587.000000 s hg19.chr17_gl000204_random 32937 27 + 81310 TTTGCTG--CTACAGATGCAG-AAACTGGT s otoGar1.scaffold_94362.1-287808 15923 22 + 287808 TTTGCTG--TTAC-----CAG-AAACCGGT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tarSyr1.scaffold_131410 4332 27 + 8975 TTTGCTG--CTGCAGATGCAG-AAACGGGT i tarSyr1.scaffold_131410 C 0 C 0 s calJac1.Contig5139 32998 27 + 225949 TTTGCCG--CTACAGATGCAG-AAACGAGT i calJac1.Contig5139 C 0 C 0 s panTro2.chr17 79462580 27 + 83384210 TTTGCTG--CTACAGATGCAG-AAACTGGT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 2794 27 - 64270 TTTGCTG--CTACAGATGCAG-AAACTGGT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16049493 27 + 17838096 TTTGCTG--CTACAGATGCAG-AAACTGGT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75024051 27 + 78773432 TTTGCTG--CTACAGATGCAG-AAACCGGT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 31300 27 - 95547 TTTGCTG--CTACAGATGCAG-AAACCGGT i papHam1.scaffold8336 C 0 C 0 s mm9.chr11 118746788 27 + 121843856 TTCGCTG--CAGCAGATGCAG-AAGCAGAC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4379864 26 + 7991924 TTTGCTG--CTCCAGACACAG--AGCAGAT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128900 44317 27 + 44573 TTCGCTG--CTGCAGATGCAG-AAACTGGT i speTri1.scaffold_128900 C 0 C 0 s ochPri2.scaffold_6980 56459 29 + 61692 TTTCCAGGCTTGTGGCTGCAA-AAGCTGGA i ochPri2.scaffold_6980 C 0 C 0 s vicPac1.scaffold_234559 48 28 + 1001 TTTGCTG--CTGCAGATGGGAGAAACTTGT i vicPac1.scaffold_234559 I 11 C 0 s turTru1.scaffold_106006 117340 27 + 145505 TTTGCTG--CTGCAGATGGAG-AAACTGGT i turTru1.scaffold_106006 I 11 C 0 s bosTau4.chr19 10849303 28 - 65312493 TTTGCTG--CTGCAGATGGAGAAAACTGGT i bosTau4.chr19 I 12 C 0 s equCab2.chr11 58031499 27 - 61308211 TTGGCTG--CTGCAGATGGAG-AAACTGGT i equCab2.chr11 I 5 C 0 s canFam2.chr9 59426355 27 - 64418924 TTTGCTG--CTGCAGATGGAG-AAGCTGGT i canFam2.chr9 I 9 C 0 s felCat3.scaffold_206428 3828 27 + 132007 TTTGCTG--TTGCAGATGGAA-AAGCTGGC i felCat3.scaffold_206428 I 14 C 0 s myoLuc1.scaffold_4816 4718 26 + 14340 TTTGCTG--CTGCAGATGGAG-AAA-CGGT i myoLuc1.scaffold_4816 I 14 C 0 s pteVam1.scaffold_11245 5009 27 + 48268 TTTGCCG--CTGCAGATGGAG-AAATTGGT i pteVam1.scaffold_11245 I 14 C 0 s loxAfr3.scaffold_49 14419807 27 - 17734757 TTTGCTA--CTGCCGACgcag-gagctggt i loxAfr3.scaffold_49 C 0 I 576 s proCap1.scaffold_29042 4438 27 + 24616 TTTGCTG--CTGCAGACGCAG-GAGCTGGT i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 1702 27 + 20752 TTTGCTA--CTGAGGCTGCAA-GAACTTGT i dasNov2.scaffold_28617 C 0 I 1 s macEug1.Scaffold81348 5543 27 - 9603 TTTTCTG--CAACAGATGCCA-GGGCTGGT i macEug1.Scaffold81348 C 0 C 0 s monDom5.chr2 304513451 27 - 541556283 TTTTCTA--GAGCAGATGCCA-GGGCTGGT i monDom5.chr2 C 0 C 0 e micMur1.scaffold_89264 1166 3270 + 5251 M e dipOrd1.scaffold_53224 1130 2495 + 10229 I a score=256287.000000 s hg19.chr17_gl000204_random 32964 46 + 81310 C---CAAGAAAGACCACTGGAAATTGACTC-AA-------TAACTGG--CCGG----TCCC-AA s otoGar1.scaffold_94362.1-287808 15945 46 + 287808 C---CAAGCAAGACCCTTTGAAATCAACTC-AA-------TGACTGG--TCAG----TCCC-AA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tarSyr1.scaffold_131410 4359 46 + 8975 C---CAAGCAAGACCATTTGAAATTGATGT-AA-------CATCTGG--CTAG----TCCC-AA i tarSyr1.scaffold_131410 C 0 C 0 s calJac1.Contig5139 33025 46 + 225949 C---CGAGCAAGACCACTGGGAATTCACTC-AA-------CAACCGG--TCGG----TCCC-GA i calJac1.Contig5139 C 0 C 0 s panTro2.chr17 79462607 46 + 83384210 C---CAAGAAAGACCATTGGAAATTGACTC-AA-------TAACTGG--CCGG----TCCC-AA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 2821 46 - 64270 C---CAAGAAAGACCATTGGAAATTGACTC-AA-------TAACTGG--CCGG----TCCC-AA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16049520 46 + 17838096 C---TAAGAAAGACCATTGGAAATTGACTC-AG-------TAACTGG--CCGG----TCCC-AA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75024078 46 + 78773432 C---CAAGAAAGATCACTGGAAATCGACTC-AA-------TAACTGT--CCAG----TCCC-AA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 31327 46 - 95547 C---CAAGAAAGATCACTGGAAATCGACTC-AA-------TAACTGT--CCAG----TCCC-AA i papHam1.scaffold8336 C 0 C 0 s mm9.chr11 118746815 49 + 121843856 C--------AAGATTGTTCCAGACAAGCAC-AGGGGTGGGCCAC-----CCCGAAACTCCC-AA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4379890 49 + 7991924 CATTTGAGGAAGAGCATTTGAAATCGATCC-AG--------CAC-----CTGGCCACTTCC-AT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128900 44344 43 + 44573 G---GGGGCAAGGTCGCTTGAAACTGAACC-AA-------CCAT-----CCAG----TCCC-AA i speTri1.scaffold_128900 C 0 N 0 s ochPri2.scaffold_6980 56488 36 + 61692 A---AAGGCAAGACCACTG------GTCTT-AA-------CCA------TCAG----TCTC-AG i ochPri2.scaffold_6980 C 0 C 0 s vicPac1.scaffold_234559 76 47 + 1001 C---TTGGCATGGCCGTTTGAAATCAACTC-AA-------TGACTGG--CCAG----TCCCAAA i vicPac1.scaffold_234559 C 0 C 0 s turTru1.scaffold_106006 117367 46 + 145505 C---CTGGCAAGGCCATTTGAAATTAACTC-AA-------CAACTAG--CCAG----CCCC-AA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10849331 46 - 65312493 C---CTGGCAAGGCCATTTGAAATTAACTA-AA-------CAACTGG--CCAG----CCCC-AA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58031526 46 - 61308211 C---CTGGCAAGGCCGTTTGAAATCAACTC-AA-------CAACTGG--CCAG----ATCC-AA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59426382 46 - 64418924 C---CTGGCAAGGCCATTTGAAATCAACTC-AA-------CAACTGG--CCGG----CCCC-AA i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 3855 47 + 132007 C---CTGGCAAGGCCGTTTGAAACCGACTCAAA-------CAACTGG--CCAG----CCCC-AA i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_4816 4744 46 + 14340 C---CTGGCAAGGCCGTTCGGAATCCACTC-CC-------TGGCAGG--CCAG----GCCC-GG i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 5036 46 + 48268 C---CTGGCAAGGCCGCTGGAAACAAGCTC-AA-------CAACTGG--CCAG----CCGC-AG i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 4465 25 + 24616 -------GTGGTGCAGCGG---------------------CCAGGGGGTGAAG----------- i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 1730 42 + 20752 C---TGGGCGGGGTCACTGGAAATCGTCTC-AA-------CAACTGGGTCAGG----------- i dasNov2.scaffold_28617 I 1 I 10 s oryCun2.chrUn0958 9589 30 + 41507 -------------------GAAACAGACTG-AG-------CCACGGG--TCAG----GCCC-AG i oryCun2.chrUn0958 N 0 C 0 s macEug1.Scaffold81348 5570 47 - 9603 --AGAAGGGCAAACCATTTAAACTTGGCTC-TG-------AAATTGG--TCAA----GCTT-GA i macEug1.Scaffold81348 C 0 C 0 s monDom5.chr2 304513478 47 - 541556283 --AGAAGGGCAAACCATTTAAACTTGGCTC-CA-------AAATTGG--TCAA----GCTT-GA i monDom5.chr2 C 0 C 0 e micMur1.scaffold_89264 1166 3270 + 5251 M e dipOrd1.scaffold_53224 1130 2495 + 10229 I e loxAfr3.scaffold_49 14419834 576 - 17734757 I a score=-43462.000000 s hg19.chr17_gl000204_random 33010 47 + 81310 GAAGTC-----TGTAGCCAGAGTAACTGGT---GGGCGCAA-GGCAGAAAG-G-TGAA s otoGar1.scaffold_94362.1-287808 15991 39 + 287808 AATTTC-----T---------GCCACTGAT---GAGTCCAAGGGCAGAAAG-G-TAGA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tarSyr1.scaffold_131410 4405 42 + 8975 ATATTC-----TGTGGCCAGAGTCGCTGGT---GGGTTCAA-GGCAGG-------GGA i tarSyr1.scaffold_131410 C 0 C 0 s calJac1.Contig5139 33071 47 + 225949 GAATCC-----TGTCGCCAGAGTAACCGGC---AAGGGCAA-GGCAGAAAA-C-TGGA i calJac1.Contig5139 C 0 C 0 s panTro2.chr17 79462653 47 + 83384210 GAAGTC-----TGTAGACAGAGTAACTGGT---GGGCGCAA-GGCAGAAAG-G-TGAA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 2867 47 - 64270 GAAGTC-----TGTAGCCCGAGTAACTGGT---GGGCGCAA-GGCAGAAAG-G-TGAA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16049566 47 + 17838096 GAATTC-----TGTAGCCAGAGTAACTGGT---GGGCGCAA-GGCAGAAAG-G-TGAA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75024124 47 + 78773432 GAATTC-----TGTAGCCAGAGTAACTGGT---GGGTGCAA-GACAGAAAG-G-TGGA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 31373 47 - 95547 GAATTC-----TGTAGCCAGAGTAACTGGT---GCATGCAA-GACAGAAAG-G-TGGA i papHam1.scaffold8336 C 0 C 0 s mm9.chr11 118746864 37 + 121843856 -----------GGTGG---GACTTACTGGT---G-CCTGAA-GGTCAGAAG-G-TTGA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4379939 22 + 7991924 -----------GGCAG----------------------GAA-GGACGGCGG-G-GGGT i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 9619 25 + 41507 CCGGTC-----TGCGG-------------------CCGGA-------GTCG-G-GGGA i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_6980 56524 19 + 61692 ACA--C-----TGTGG-------------------------------GTTG-GTGGAA i ochPri2.scaffold_6980 C 0 C 0 s vicPac1.scaffold_234559 123 38 + 1001 AAATTA-----TGTGG---------CAGGT---GCGTGCAA-GGCAGAAAA-A-TGAA i vicPac1.scaffold_234559 C 0 C 0 s turTru1.scaffold_106006 117413 38 + 145505 AAATTA-----TGTGG---------CAGGT---GTGTGCAA-GGCAGAAAG-A-TGAA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10849377 38 - 65312493 AAATTA-----TGTGG---------CAGGT---GTGTTCAA-GGCAGAGAG-A-TGAA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58031572 38 - 61308211 AAATAC-----TGGAG---------CAGGT---GCGTGCAA-GGCAGAAGG-A-TGGA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59426428 37 - 64418924 AGATTC-----TGTGG---------CAGGT---GCATGCA--AGCAGAAAG-A-CGGA i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 3902 38 + 132007 AAATCC-----CGTGG---------CAGGT---GCATGCAC-GGGAGAACA-A-CAGA i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_4816 4790 41 + 14340 AAAGCC-----TGCGG---------CAGGTGCGGCGTGCGA-GCCAGGAAG-G-CGGA i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 5082 36 + 48268 AAA--C-----TGTGG---------CAGGT---GCACGCGA-GGCAGAACG-C-CCGC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14420410 46 - 17734757 ggagct-----cgtgggggcaggagctggT---GGGCACAA-A-CAGAAAT-G-TGGA i loxAfr3.scaffold_49 I 576 C 0 s proCap1.scaffold_29042 4490 12 + 24616 ---------------------------------------------AAAAATAG-TAGG i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 1782 40 + 20752 ----CTACCTCCACGGCAGGGTGATCTGGT---GGGCGCAG-G---------G-CGGA i dasNov2.scaffold_28617 I 10 C 0 s macEug1.Scaffold81348 5617 47 - 9603 AAATCT-----CATGAGAAGAGTTCATGGT---TGGTAAAa-gtcagaaag-a-agaa i macEug1.Scaffold81348 C 0 I 3367 s monDom5.chr2 304513525 47 - 541556283 AAATCT-----CATGAGAGGAGCTCCTCAT---TGGTAAAA-GTCAGAAAG-G-AGAA i monDom5.chr2 C 0 C 0 e micMur1.scaffold_89264 1166 3270 + 5251 M e dipOrd1.scaffold_53224 1130 2495 + 10229 I a score=99257.000000 s hg19.chr17_gl000204_random 33057 49 + 81310 ---CCAT-TAAGGC--CTAG-----ACCACACACCCTG--TGGT-------G----CCTCCACT---CTC-----CAAGAC s otoGar1.scaffold_94362.1-287808 16030 47 + 287808 ---GGAC-AGAGAC--CCAG-----AACACCCACCCTT--CAGG-------G----CATCGGTC---CTC-----TAAG-- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tarSyr1.scaffold_131410 4447 48 + 8975 ---TGAC-GGAGAC--CCAG-----AACACTCACCTTT--TCAT-------G----CATCAACT---CTC-----CAAGA- i tarSyr1.scaffold_131410 C 0 C 0 s calJac1.Contig5139 33118 49 + 225949 ---TGAT-GGAGGC--CCAG-----ACCACCCACCCTG--TGGT-------G----TTTCCACT---CTC-----CAAGAC i calJac1.Contig5139 C 0 C 0 s panTro2.chr17 79462700 49 + 83384210 ---CCAT-TAAGGC--CTAG-----GCCACCCACCCTG--TGGT-------G----CCTCCACT---CTC-----CAAGAC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 2914 48 - 64270 ---CCAT-TAAGGC--CTAG-----ACCACCCACCCTG--TGGT-------G----CCTCCACT---CTC-----CAAGA- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16049613 49 + 17838096 ---CCAT-TAAGGC--CCAG-----ACCACCCACCCTG--TGGT-------G----CCTCGACT---CTC-----CAAGAC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75024171 53 + 78773432 ---CCAT-GGAGGC--CCAG-----ACCACCCACCCTG--TGGT-------GGTCTCCTCTACT---CTC-----CAAGAT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 31420 53 - 95547 ---CCAT-GGAGGC--CCAG-----ACCACCCACCCTG--TGGT-------GGTCTCCTCGACT---CTC-----CAAGAT i papHam1.scaffold8336 C 0 C 0 s mm9.chr11 118746901 53 + 121843856 ---AGGC-AAAGAC--TCAG-----AAGCTCCAGCCCT--TAGA-------C----TATCCGCT---CTCCAGGACAAAA- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4379961 47 + 7991924 ---GTCC-TGAGAA--CCAC-----CTCCCACCTCCTA--TGGT-------G----CACCTGCT---TC------CACAA- i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 9644 47 + 41507 ---CACC-AGAGAC--CCTG-----CACCCCGCCCCTG--CTGC-------C----CTCCCAGT---GC------CGAGA- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_6980 56543 56 + 61692 ---GGCC-AGAGACCACACA-----CACCCAGCCTCTG--CTGCCAAGACAC----CCCCTAAT---CC------CAAGA- i ochPri2.scaffold_6980 C 0 C 0 s vicPac1.scaffold_234559 161 49 + 1001 ---CAAC-ACAGAC--CCAG-----AACATCCACCTTT--CGGT-------G----CATCAGCT---CTG-----CAAGAC i vicPac1.scaffold_234559 C 0 C 0 s turTru1.scaffold_106006 117451 46 + 145505 ---C----AGAGAC--CCAG-----AACACCCACCCTT--TGGT-------G----CACCAACT---CTG-----CAAGAC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10849415 48 - 65312493 ---CAAT-AGAGGC--CCTG-----AACACCCACCCTT--TGGT-------G----CACCAGCT---CTG-----CAAGA- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58031610 47 - 61308211 ---CACC-AGAGAC--CCCA-----AACACCCCGCCTC--TGGT-------G----CA-CAGCT---CTC-----CAAG-C i equCab2.chr11 C 0 C 0 s canFam2.chr9 59426465 49 - 64418924 ---CAAC-AGAGCC--CCAG-----AACACTCACCCTT--CAGT-------G----CCCCAATT---CCC-----CAAGAC i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 3940 49 + 132007 ---CAAC-AGAGAC--CCAG-----GACACCCACCCTT--TGGC-------G----CATCGATT---TGC-----CAAGAC i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_4816 4831 37 + 14340 ---CA------GGC--CCAG-----CACACCAGCCCG--------------G----CACCACCT---CTC-----CAGG-- i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 5118 26 + 48268 ---CC--------C--CTGG-----CACACCAG-----------------------------CT---CTC-----CAAGGC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14420456 47 - 17734757 ---CAAT--GAGTC--CCGG-----GACATCCACCTCG---GGT-------G----CACCAACT---CCC-----CAAGAC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 4502 46 + 24616 ---CAGT--GAGT---GGGG-----AACACCCACCCTG---GGT-------G----CACCAGCC---CCC-----CGAGAC i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 1822 57 + 20752 ---CAGGCAGAGT---TGGGTTTCTAGCAGCCCCCCTG--TGGT-------G----CACCAACCTCACTC-----TAGGAC i dasNov2.scaffold_28617 C 0 C 0 s monDom5.chr2 304513572 54 - 541556283 AGAAAGC-TTAGCC--CCAG-----AGCATTCATCACTAACAGT-------G----CATCTCCA---CTC-----AAAGGC i monDom5.chr2 C 0 I 3178 e micMur1.scaffold_89264 1166 3270 + 5251 M e macEug1.Scaffold81348 5664 3367 - 9603 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I a score=18000.000000 s hg19.chr17_gl000204_random 33106 22 + 81310 C--CCCC-------GCAACCCTGAGAATAGG s otoGar1.scaffold_94362.1-287808 16077 22 + 287808 T--CCCA-------GCATCCTTGAGAACAGG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tarSyr1.scaffold_131410 4495 22 + 8975 C--CCCT-------GCAACCTCAGTAGCAGG i tarSyr1.scaffold_131410 C 0 C 0 s calJac1.Contig5139 33167 22 + 225949 C--CCCC-------GCAACCCTGAGAACAGG i calJac1.Contig5139 C 0 C 0 s panTro2.chr17 79462749 22 + 83384210 C--CCCC-------GCAACCCTGAGAACAGG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 2962 22 - 64270 C--CCCN-------GCAACCCTGAGAACAGG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16049662 22 + 17838096 C--CCCC-------GCAACCCTGCGAACAGG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75024224 22 + 78773432 G--CCCC-------GCAACCCTGAGAACAGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 31473 22 - 95547 G--CCCC-------GCAACCCTGAGAACAGG i papHam1.scaffold8336 C 0 C 0 s mm9.chr11 118746954 21 + 121843856 ---CCAA-------GATGCACAGCGAAGAGA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4380008 2 + 7991924 ---CC-------------------------- i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 9691 9 + 41507 C--CC--------------------AGCAGA i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_6980 56599 8 + 61692 ---TC--------------------AGCAGA i ochPri2.scaffold_6980 C 0 C 0 s vicPac1.scaffold_234559 210 22 + 1001 C--CCCT-------CCAGCCCCCAGAACGAG i vicPac1.scaffold_234559 C 0 C 0 s turTru1.scaffold_106006 117497 22 + 145505 C--CCCT-------CCAGTCCCCAGAAAAAA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10849463 22 - 65312493 C--CCCT-------CCAGTCAACAAAACAAA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58031657 21 - 61308211 C--CCCT-------CCAGCCC-GAGAACAAG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59426514 29 - 64418924 C--CCCTCCACCCCCCAACCCCGAGAGTGTG i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 3989 22 + 132007 C--CCCT-------CCAGCCCTGAGAATGTG i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_4816 4868 20 + 14340 C--CGCT-------CAG--ACCGAGAACGAG i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 5144 22 + 48268 C--CGCT-------CCGGCGCCGGGCACGAG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14420503 19 - 17734757 C--TCCA----------ACCCCAAAAACAAG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 4548 18 + 24616 C--CCCC----------ACCTCCACAGTCA- i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 1879 21 + 20752 CTTCTCG----------AACTCGAGAATGAG i dasNov2.scaffold_28617 C 0 I 1196 e micMur1.scaffold_89264 1166 3270 + 5251 M e macEug1.Scaffold81348 5664 3367 - 9603 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I a score=-5589.000000 s hg19.chr17_gl000204_random 33128 40 + 81310 AAGGTGGTGTGAGGAGAAGGGAGCATGGCTGGTCACGAGA s otoGar1.scaffold_94362.1-287808 16099 36 + 287808 AAGGACATGTGAGGCAAAGGGA----CACTCTCTATGACA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tarSyr1.scaffold_131410 4517 40 + 8975 AAGACAGCTCGAGGAGAAGGGAACGCTGCTGGTTATGACA i tarSyr1.scaffold_131410 C 0 C 0 s calJac1.Contig5139 33189 40 + 225949 AAGGTGGAGTGAGAAGAAGGGAGCACAGCTGGTCACGAGA i calJac1.Contig5139 C 0 C 0 s panTro2.chr17 79462771 40 + 83384210 AAGGTGGTGTGAGGAGAAGGGAGCATGGCTGGTCACGAGA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 2984 40 - 64270 AAGGTGGTGTGAGGAGAAGGGAGCATGGCTGGTCACGAGA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16049684 40 + 17838096 AAGGTGGTGTGAGGAGAAGGGAGCACGGCTGGTCACGAGA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75024246 40 + 78773432 AAGGTGGTGTGAGGAGAAGGGAGCACGGCTGGTCATGACA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 31495 40 - 95547 AAGGTGGTGTGAGGAGAAGGGAGCACGGCTGGTCATGACA i papHam1.scaffold8336 C 0 C 0 s mm9.chr11 118746975 33 + 121843856 CAGGAGCCCAG------CTGGTGAGCGGC-TGGCACTAGA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4380010 21 + 7991924 ------CCC------------TGCACCCC-CAGAACAAGA i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 9700 31 + 41507 CGGGGGCGG---------GGGGGCACAGGGCCGTGTGACA i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_6980 56607 27 + 61692 T----GCCG---------TGGGGGACAGCTGGGTCTGAGA i ochPri2.scaffold_6980 C 0 C 0 s vicPac1.scaffold_234559 232 37 + 1001 GAGACGGTGTGAGGAGAGGGTGATGCTGG-GGACATCA-- i vicPac1.scaffold_234559 C 0 I 3 s turTru1.scaffold_106006 117519 36 + 145505 CAGACAGTGTGAGAAGAGGGGAACAT-GG-GGACATGA-- i turTru1.scaffold_106006 C 0 I 3 s bosTau4.chr19 10849485 36 - 65312493 GAGACAATGTGGGGAGAGGGGAACAC-GG-GGACATCG-- i bosTau4.chr19 C 0 I 3 s equCab2.chr11 58031678 37 - 61308211 GAGACGGCGTGAGGAGAAGGGAACATTCC-CGAGGTGA-- i equCab2.chr11 C 0 I 9 s canFam2.chr9 59426543 37 - 64418924 GAAGCAGCATGAGGAGAAGAGCATAGTGC-TAACATCA-- i canFam2.chr9 C 0 I 16 s felCat3.scaffold_206428 4011 36 + 132007 GAAACGGCAT-AGGAGGAGGGAACAGTGC-TGACGTCG-- i felCat3.scaffold_206428 C 0 I 10 s myoLuc1.scaffold_4816 4888 36 + 14340 GAGACGGCGCGAGGAGAAGGGCGT-CTGC-CCACGGGA-- i myoLuc1.scaffold_4816 C 0 I 458 s pteVam1.scaffold_11245 5166 31 + 48268 GAGACGGTGTGAGGAGACA------CGGC-CGGCGCGG-- i pteVam1.scaffold_11245 C 0 I 16 s loxAfr3.scaffold_49 14420522 36 - 17734757 GAGTCGGTGTGGGGAGAGGAGAATGCTGA-TGTTGCA--- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 4566 34 + 24616 GAGATGGTGTGGGGAGAGAAGGATGGGGG-TGACG----- i proCap1.scaffold_29042 C 0 C 0 e micMur1.scaffold_89264 1166 3270 + 5251 M e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I a score=-348474.000000 s hg19.chr17_gl000204_random 33168 54 + 81310 GCCCTTT----------TCC--------ACAC---------------TC--G--------GTCAC-TA-TGGTGCTG--------------------GCATCCTTCC------TGTGCAATG-TAA s otoGar1.scaffold_94362.1-287808 16135 57 + 287808 GCCCCTT----------CCC--------ACAC---------------ACATG--------GTCACTTG-TGGTCCTC--------------------AAATCCTTTT------CAGGAGATG-GGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tarSyr1.scaffold_131410 4557 55 + 8975 GTACCTT----------CCC--------ACTC---------------TG--G--------GCCAT-TGATGGTCCAC--------------------AGGTCCTTCC------TGTGCCACA-TGG i tarSyr1.scaffold_131410 C 0 C 0 s calJac1.Contig5139 33229 54 + 225949 GCCCC-T----------TCC--------ACAC---------------TC--G--------GTCACTTG-TAGCACTG--------------------GCATCCTTCC------TGTGCAACG-TAA i calJac1.Contig5139 C 0 C 0 s panTro2.chr17 79462811 54 + 83384210 GCCCCTT----------TCC--------ACAC---------------TC--G--------GTCAC-TG-TGGTGCTG--------------------GCATCCTTCC------TGTGCAATG-TAA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 3024 54 - 64270 GCCCCTT----------TCC--------ACAC---------------TC--G--------GTCAC-TG-TGGTGCTG--------------------GCATCCTTCC------TGTGCAATG-TAA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16049724 54 + 17838096 GCCCCTT----------TCC--------ACAC---------------TC--G--------GTCAC-TG-TGGTGCTG--------------------GCACCCTTCC------TGTGCAATG-TAA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75024286 54 + 78773432 GCCTCTT----------TCC--------ACAC---------------TC--G--------GTCAC-TG-TGGTGCCA--------------------GCATCCTTCC------TGTGCAATG-TAA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 31535 54 - 95547 GCCTctt----------tcc--------acac---------------tt--g--------atcac-tg-tggtgcca--------------------gcatccttcc------tgtgcaatg-taa i papHam1.scaffold8336 C 0 C 0 s mm9.chr11 118747008 74 + 121843856 GTCTGGC----------CCCGGGAAGCTATTT---------------GG--G--------GCCTT--G-TGTTCCAGTGAGGTACACAAGGGCCAGCGTGTCCTTC--------------TGATGA i mm9.chr11 C 0 I 7 s cavPor3.scaffold_76 4380031 45 + 7991924 GACAGCC----------CAC--------ACTG---------------GG--T--------CCCTC--A-TGGTCCTA--------------------GCATCCCTC--------------TG-TGG i cavPor3.scaffold_76 C 0 I 7 s oryCun2.chrUn0958 9731 44 + 41507 GTCCTGG----------GCC--------GCTC---------------GG--G--------GCCACGGG-TGGGCCTC--------------------AGAC---TA--------------TG-GGA i oryCun2.chrUn0958 C 0 I 6 s ochPri2.scaffold_6980 56634 33 + 61692 GCCCCTC----------TCC-----------------------------------------------A-TGGGTCTC--------------------GGTCCTTTC--------------CA-GGA i ochPri2.scaffold_6980 C 0 I 5 s vicPac1.scaffold_234559 272 50 + 1001 GCCACTG----------TAC--------AGCCGGCGCCCCTGCACACAC--A------CTGTCATGCG-TGGTCCTC------------------------------------------------- i vicPac1.scaffold_234559 I 3 C 0 s turTru1.scaffold_106006 117558 42 + 145505 GTCACTG----------TAC--------AGGTGACGCCCCTG--CACAC--A----CTCTGTCATGTG---------------------------------------------------------- i turTru1.scaffold_106006 I 3 C 0 s bosTau4.chr19 10849524 42 - 65312493 GTCACTG----------TAC--------AGCCAGCACCCCT------CC--ACACGCTCTGTCATGTG---------------------------------------------------------- i bosTau4.chr19 I 3 C 0 s equCab2.chr11 58031724 18 - 61308211 -------------------C--------AGGC---------------AC--G--------------TG-CGGTCCTC------------------------------------------------- i equCab2.chr11 I 9 C 0 s canFam2.chr9 59426596 35 - 64418924 GCCCCTG----------CCC--------ACAC---------------AC--A------CGGTTGTCTG-TGGTCCTC------------------------------------------------- i canFam2.chr9 I 16 C 0 s felCat3.scaffold_206428 4057 31 + 132007 --CCCTG------------C--------ACAC---------------TC--A------CCATCATCTG-TGATGCGC------------------------------------------------- i felCat3.scaffold_206428 I 10 C 0 s pteVam1.scaffold_11245 5213 34 + 48268 G-CCCTG----------CGC--------ACAC---------------TC--G------CTCTCGTGTG-TGGTCCTT------------------------------------------------- i pteVam1.scaffold_11245 I 16 C 0 s loxAfr3.scaffold_49 14420558 67 - 17734757 GTCTCCTTCCAGAGCCCCCA--------AGCC---------------AC--T------TTGTTGTTTG-tgaccctc--------------------gcaccacccttggagatgggca------- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 4600 50 + 24616 -----------------TTA--------AGCC---------------TC--T------GTGTTGTTGG-TGACCTTC--------------------AGGTCATCCTCCAAGACGGGCA------- i proCap1.scaffold_29042 C 0 C 0 e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I a score=-150067.000000 s hg19.chr17_gl000204_random 33222 61 + 81310 GGG--GCAGCAGTGGTGC----CCACATTGCACAGG--AGAGGC--------TCCATGGAGCCA---AGGCA---GCATGACC s papHam1.scaffold8336 31589 61 - 95547 agg--gcagcagtggtgc----ccacactgcatggg--agaggc--------tccatggagccc---aggtg---gcatgacc i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75024340 61 + 78773432 GGG--GCAGCAGTGGTGC----CCACACTGCATGGG--AGAGGC--------TCCATGGAGCCC---AGGTG---GCATGACC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16049778 61 + 17838096 GGG--GCAGCAATGGTGC----CCACATTGCATGGG--AGAGGC--------TCCATGGAGCCA---AGGCG---GCGTGACC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 3078 61 - 64270 GGG--GCAGCAGTGGTGC----CCACATTGCACAGG--AGAGGC--------TCCATGGAGCCA---AGGCA---GCATGACC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79462865 61 + 83384210 GGG--GCAGCAGTGGTGC----CCACATTGCACAGG--AGAGGC--------TCCATGGAGCCA---AGGCA---GCATGACC i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 33283 60 + 225949 GGG--GTAGCCGTGGTG-----CCACACTCCACGGG--AGAGGC--------CCCACGGAGCCA---AGGTG---GTGCGACC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 4612 63 + 8975 GGG--GCAGTGTGGGTGC----CTGTGTTGTATGGGTTTGATGC--------TCCAAGAAGCTA---AGGCA---GCGTGATC i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 16192 59 + 287808 AGG--GGCACAGTGGTGC----CTGAGTTCCATG----TGAGGC--------TCCCAGAAGCTG---AGGCG---GTGTGACC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 1640 55 + 15939 GAG--CCAGCGGTGGTGC----CTGCATTCCA-GGG--CGATGA--------TCTGAGGACCTA---CGGCG---GCG----- i tupBel1.scaffold_124459.1-15939 N 0 C 0 s mm9.chr11 118747089 62 + 121843856 TGG--GCCAGTGCAGCAT----CTGTGTTCCAGGGG--AAA--C--------TCCAGGGAGCCACAGAAAAG---GGAAAATT i mm9.chr11 I 7 C 0 s cavPor3.scaffold_76 4380083 51 + 7991924 AGG--ACCA--GCAGGGT----GTCTGCTCCAGGG---------------------TGGGGCTGCAAAGGTG---GGAAGAGG i cavPor3.scaffold_76 I 7 C 0 s oryCun2.chrUn0958 9781 59 + 41507 AGG--CCAGCAGCGGCGT----CTGTGTGCCACGGG--CAAGGC--------TCCAAAGAACCA---AGGTG---GCATGA-- i oryCun2.chrUn0958 I 6 C 0 s ochPri2.scaffold_6980 56672 65 + 61692 AGGGAGCAGGAGCAGCATATCCCTTCCGTCCACGGG--CAAGGC--------TCCATTAGCTCGGGCAGGTG---ACC----- i ochPri2.scaffold_6980 I 5 I 1113 s vicPac1.scaffold_234559 322 28 + 1001 --------------------------------------AAATC--------ATTCTTGTGA------GGGGT---GCAGGGCC i vicPac1.scaffold_234559 C 0 I 4 s turTru1.scaffold_106006 117600 35 + 145505 --------------------------------------TGGTCCTCGTATCATTCTTGTGA------GGGGT---GCAGAAC- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10849566 35 - 65312493 --------------------------------------TGACCCTCATATCATTCTTGTGA------GGGGT---GCAGGAC- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58031742 28 - 61308211 --------------------------------------ATATCA--------CTCTTGTGA------GGGAT---GCAGGGCC i equCab2.chr11 C 0 I 14 s canFam2.chr9 59426631 28 - 64418924 --------------------------------------AGATCA--------TCCTTGTGA------GGGGT---GCAGGGCC i canFam2.chr9 C 0 I 14 s felCat3.scaffold_206428 4088 28 + 132007 --------------------------------------AGAGCA--------TCCTTGTGA------GGGGT---GCAGGACC i felCat3.scaffold_206428 C 0 I 14 s pteVam1.scaffold_11245 5247 28 + 48268 --------------------------------------ATGTCA--------CTCTTGTGA------GGGCT---GCAGGGCC i pteVam1.scaffold_11245 C 0 I 5 s loxAfr3.scaffold_49 14420625 63 - 17734757 ggg--acagaggtg-tgc----ctgcatttcccagg--tgaggt--------tctgaggagcta---agggacacatgtgaca i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 4650 64 + 24616 GGG--ACAGAGATGATGC----CTGTGTTTTGCAGT--TGAGGA--------TCCAAGGAGCTG---AGGGACATGTGTGACA i proCap1.scaffold_29042 C 0 C 0 e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I a score=43969.000000 s hg19.chr17_gl000204_random 33283 33 + 81310 TTAC------------ATAGCATG----TCCACGGCAG-CCTGATCCCAA s papHam1.scaffold8336 31650 33 - 95547 ttac------------acagcacg----tccatggcag-cctgatcccaa i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75024401 33 + 78773432 TTAC------------ACAGCACG----TCCACGGCAG-CCTGATCCCAA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16049839 33 + 17838096 TTAC------------ACAGCACA----TCCACGGCAG-CCTGATCCCAA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 3139 33 - 64270 TTAC------------ATAGCATG----TCCACGGCAG-CCTGATCCCAA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79462926 33 + 83384210 TTAC------------ATAGCATG----TCCACGGCAG-CCTGATCCCGA i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 33343 33 + 225949 TTAC------------ACAACATG----TCCACGGCAG-CCAGATCCCAA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 4675 33 + 8975 TTAT------------ATAGCATG----GGTGTGGCAG-CTGGATCCAAA i tarSyr1.scaffold_131410 C 0 M 1996 s otoGar1.scaffold_94362.1-287808 16251 33 + 287808 ATAC------------ACGGCACG----GCCATGGCAG-CCCGACCCCAA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 1695 30 + 15939 ------------------AGTGTGTTGTTCCATGGCTG-C-TGACCCCAA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118747151 27 + 121843856 CACC------------CTTGCCCG----TGT-CA--AG--CTGACCCT-- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4380134 31 + 7991924 TCAC------------TCAGCAGG----TGC-TGGCGG--TTGATCTCAA i cavPor3.scaffold_76 C 0 I 4 s oryCun2.chrUn0958 9840 5 + 41507 ----------------------------------------TTGAC----- i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_234559 354 22 + 1001 -----------------------G----TCAGGGACAG-CCTGATTTCAA i vicPac1.scaffold_234559 I 4 C 0 s turTru1.scaffold_106006 117635 14 + 145505 -----------------------------------CAG-CCTGACCCCAA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10849601 14 - 65312493 -----------------------------------CAG-ACCGGTCCCCA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58031784 33 - 61308211 CTGC------------ACAGCACA----TCAGAGACAG-CCTGGTCCCAA i equCab2.chr11 I 14 C 0 s canFam2.chr9 59426673 33 - 64418924 CTAC------------ACAGCACG----TCAGTGACAG-CCCAATCCCAA i canFam2.chr9 I 14 C 0 s felCat3.scaffold_206428 4130 45 + 132007 CCCCATGGCATGTCAGATGGCATG----TCAGTGACAG-CCCGATCCCAA i felCat3.scaffold_206428 I 14 C 0 s pteVam1.scaffold_11245 5280 19 + 48268 ------------------------------AGTGACAG-CCTGATCTCAA i pteVam1.scaffold_11245 I 5 C 0 s loxAfr3.scaffold_49 14420688 34 - 17734757 ttat------------gcaggaag----gcagtggcaggcctgatcccat i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 4714 33 + 24616 TTGC------------ACAGGCAG----GCAG-GGCAGGCCTGATCCCGT i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I a score=56479.000000 s hg19.chr17_gl000204_random 33316 23 + 81310 GACCTCCACCTTGCAG-------TCCAGTG s papHam1.scaffold8336 31683 23 - 95547 gacctccaccttacag-------tccagtg i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75024434 23 + 78773432 GACCTCCACCTTACAG-------TCCAGTG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16049872 23 + 17838096 GACCTCTACCTTGCAG-------TCCAGTG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 3172 23 - 64270 GACCTCCACCTTGCAG-------TCCAGTG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79462959 23 + 83384210 GACCTCCACCTTGCAG-------TCCAGTG i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 33376 23 + 225949 GACCTCCATCTTGCAG-------TCCAGTG i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 16284 22 + 287808 GACCTGGGCC-CGCAG-------CCCAGCG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 1725 16 + 15939 GGCCCC-------CAG-------TCGAGTG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118747178 22 + 121843856 GGCTGTGTCCTTGCAG--------CTGGGT i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4380169 22 + 7991924 GACCACCCCCTCGAAG--------CTGGGG i cavPor3.scaffold_76 I 4 C 0 s oryCun2.chrUn0958 9845 22 + 41507 AGCTGGGCAGCGGCAG--------CCAGGC i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_234559 376 15 + 1001 AGCC-CCACTTTGCAG-------------- i vicPac1.scaffold_234559 C 0 C 0 s turTru1.scaffold_106006 117649 16 + 145505 AACCTCCACCTTGCAG-------------- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10849615 16 - 65312493 AACCTCCACCTTGTAG-------------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58031817 16 - 61308211 GACCTCCTCTGTGCAG-------------- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59426706 16 - 64418924 GACCTCTACCCTACAG-------------- i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 4175 23 + 132007 GACCTCTACCCTACAGTTTTGGG------- i felCat3.scaffold_206428 C 0 I 416 s pteVam1.scaffold_11245 5299 16 + 48268 GACCTCCACCTCGGAA-------------- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14420722 23 - 17734757 gacttccacctggaag-------ctccatg i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 4747 22 + 24616 GGCTT-CACCTTGCAG-------GGCCGCG i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I a score=194238.000000 s hg19.chr17_gl000204_random 33339 106 + 81310 T------------CCTTTGCA-GTAGACACCAG----CA----AGGCTAGGGACCCCAGCCCCTGCTGTTTTCATCCTAACTTGGACTTATCT--GTTGTGAT--GGCCA--------GGCCAACC---CTGT---------TTGGGAGAA-- s papHam1.scaffold8336 31706 106 - 95547 t------------cctttgca-GGAGACACCAG----CA----AGGCTGGGGACCCCAGCCCCTGCTGTTTTCATCCTAACTTGGACTTATCT--GTTGTGAT--GGCCA--------GGCCAATC---CTGT---------TTGGGAGAA-- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75024457 106 + 78773432 T------------CCTTTGCA-GGAGACACCAG----CA----AGGCTGGGGACCCCAGCCCCTGCTGTTTTCATCCTAACTTGGACTTATCT--GTTGTGAT--GGCCA--------GGCCAATC---CTGT---------TTGGGAGAA-- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16049895 106 + 17838096 T------------CCTTTGCA-GGAGACACCAG----CA----AGGCTAGGGACCCCAGCCCCTGCTGTTTTCATCCTAACTTGGACTTATCT--GTTGTGAT--GGCCA--------AGCCAATC---CTGT---------TTGGGAGAA-- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 3195 106 - 64270 T------------CCTTTGCA-GTAGACACCAG----CA----AGGCTAGGGACCCCAGCCCCTGCTGTTTTCATCCTAACTTGGACTTATCT--GTTGTGAT--GGCCA--------GGCCAATC---CTGT---------TTGGGAGAA-- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79462982 106 + 83384210 T------------CCTTTGCA-GTAGACACCAG----CA----AGGCTAGGGACCCCAGCCCCTGCTGTTTTCATCCTAACTTGGACTTATCT--GTTGTGAT--GGCCA--------GGCCAATC---CTGT---------TTGGGAGAA-- i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 33399 98 + 225949 T------------CCTTTGCA-GGCGATACCAG----CA----AGGCTGGGGA--CCAGCCCCGGCCATTTTCATCCTA------ACTGATCT--GTTGTGAT--GGCCA--------GGCCAGTC---ATGT---------TCAGGAGAA-- i calJac1.Contig5139 C 0 I 617 s otoGar1.scaffold_94362.1-287808 16306 103 + 287808 T------------TCTCGGCA-GGGGGTACTGG----CA----GGGC--AGGGTCATGGCTCCGGCT-TTTTGATCCTAACTAGGAATCACCT--GTTGTAAT--GGCCA--------GGCCAGTC---CTGC---------CCAAGAGAC-- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 1741 93 + 15939 C------------CCTCTGCA-GGGGGC-CCAG--------------TGGGCACCACA-CTGCAGCCGTTGAACTCCCAGCGTGGCTCCCTCT--GCTGCACT--GGGTG--------GGCCAATC---CTGC---------TCAA------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118747200 108 + 121843856 C------------TCTCTTCG-AGAGGAACAGGGTTACA----GGGGGTGGGGGTGGCACTCCTGTTTCCTCGAG-AGAAGTCCAGACCTTCTAATGTATGACCAAGCCA--------GCCCA--------GC---------TCTGGAGAC-- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4380191 99 + 7991924 T------------TCTGAGTG-AGAGGTCCCAG--TAGA----GGCCATCATTCTGCCGCTGCAGCCT---------GAGCTTGGAACCATCC--TTTGTGAC--AGCTG--------GCCCACTG---CCAC---------CTAGGAGAG-- i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 9867 93 + 41507 CCTGAGACCCTCACCTGGACA-GGAGGCGCCGG----CA----GGAGTGGAGACCACATCTCCCGCTG--------------------CTTCA--CCCGCCAC--GTGGA--------GCCCG--------GC---------TCAGCAGAG-- i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_234559 391 104 + 1001 T------------TCTTTGCC-AGAGGCACCTG----CA----GGGC-------------TTCTGCTGTTTTAATCGTAACTTAGAGTCCTGT--GATGCTCC--AACCACAGTGATGGGCCAATCCTCCTGC---------TCAGGGGTA-- i vicPac1.scaffold_234559 C 0 I 16 s turTru1.scaffold_106006 117665 104 + 145505 T------------TCTTTACA-AGATGCATCTG----CA----GGGG-------------TTCTGCTGTTTTAATCATAATTTAGAGCCCTCT--GATGCTCC--GACCACAATAATGGTGCAATCCTTCTGC---------TCTGGAGTA-- i turTru1.scaffold_106006 C 0 I 14 s bosTau4.chr19 10849631 96 - 65312493 T------------TCTCTGTA-AGATGGACCTG----CA----GGGG-------------TTCTGCTATTTTAATCATAACGTAGAGCCCTCT------------GACCACAATAATGGGGCAACCCTTCTGC---------TCAGGAGTA-- i bosTau4.chr19 C 0 I 14 s equCab2.chr11 58031833 112 - 61308211 --------------CTTTGTGCAGATGCACCTG----CACATTGGGA------CCACAGCTCCTGCTTTTGTAATCCCAACTTGGAGCCACCT--GTGGTAAT--GACCACAGAAATGGGCCAATCCTTCTGC---------TCAGGAG---- i equCab2.chr11 C 0 I 11 s canFam2.chr9 59426722 102 - 64418924 T------------TCTTTGCA-AGAGGCAACTG----CA----GGGG-------------TTCTGCTTTTTTAATCCTAACGTAGAGCCATCT--GATCTACC--GACCGTATTAATGGGCCAATCGTTCTGT---------TTGGGGC---- i canFam2.chr9 C 0 I 5 s pteVam1.scaffold_11245 5315 68 + 48268 T------------TCTTTGCA-AGA-GCCACTG----CA----GGGG-------------CCCAGCCACCGCAGTACTAGGGTGG---------------------------------------TCCTCCTGC---------TGGGGGGTC-- i pteVam1.scaffold_11245 C 0 I 6 s loxAfr3.scaffold_49 14420745 109 - 17734757 -------------tctttgca-GGAGGCACCTG----TG----AGGT-GGGGACCACAGCACCTGCTCTTTGAATCCTGACTTGGAAC-GTCT--GCTGTAAT--GCCCA--------GC-----C---CTGCTCAGGTGAGTGAGGGGTGGA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 4769 103 + 24616 -------------TCTGCGCA-GGAGGCATCCG----CA----GGGT-GGGGACTGT-GCATCTGCTCTTTGGGTCCTGACTCGGATCTGTCT--GCTGCAAT--GATCA--------GC--AGAC---ATGC---------TGTGGGGAGAA i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e felCat3.scaffold_206428 4198 416 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I a score=-63113.000000 s hg19.chr17_gl000204_random 33445 60 + 81310 GGCGGCT----G------GTGA--------G-AAT--AA-AC----AGG-GAA--CACCGGCATCGTCTACAAACCCAGTGGAGCCACT s papHam1.scaffold8336 31812 60 - 95547 GGGGGCT----G------GTGA--------G-AGT--AA-CC----AGG-GGA--CACCAGCATCGCCTACAAACCCAGTAGAACCACT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75024563 60 + 78773432 GGGGGCT----G------GTGA--------G-AGT--AA-CC----AGG-GGA--CACCAGCATCGCCTACAAACCCAGTAGAACCACT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16050001 60 + 17838096 GGCGGCT----G------GTGA--------G-AGT--AA-CC----AGG-GAA--CACCGGCATCGTCTACAAACCCAGTGGAGCCACT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 3301 60 - 64270 GGCGGCT----G------GTGA--------G-AAT--AA-AC----AGG-GAA--CACCGGCATCGTCTACAAACNCAGTGGAGCCACT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79463088 60 + 83384210 GGCGGCT----G------GTGA--------G-AAT--AA-AC----AGG-GAA--CACCGGCATCGCCTACAAACCCAGTGGAGCCACT i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 16409 64 + 287808 AAAGCAC----G------GTGA--------GAAGT--AA-CCACCAAGA-GGA--CGCCAGCATCCTCTGCCACCCCAGTGGAGACAC- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 1834 45 + 15939 --------------------------------------G-GC----AGT-GAGTTCTCCAGAACCATCTGGGGGCCTGTTGGGGCAACC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118747308 41 + 121843856 --AGTAG----G------ATTA--------C-ATC--AT-CC----AGACGAC--AGAGACTAT--TCAGCAA---------------- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4380290 38 + 7991924 --TGAGGAGCAG------ATTG--------A-AGT--AG-CC----AGAAGGA--TG---------CCAGCAA---------------- i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 9960 45 + 41507 --CGGGA----G------GGGG--------C-AGCAGAG-CC----AGGAGGG--TGCCAGCATCATCTGCAA---------------- i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_234559 511 65 + 1001 GGAGAAA----A------GTAACCACAGTGT-CAT--GA-CC-------AGAA--CACCAGCCTTATCTACCAACTC-GTGGGGCTGCC i vicPac1.scaffold_234559 I 16 C 0 s turTru1.scaffold_106006 117783 67 + 145505 AGAGAAA----A------GTAACCCCGATGT-CAT--GA-CC----AGGAGAA--CACTACCCTCATCTACCAACCT-GC-GGGCTGCC i turTru1.scaffold_106006 I 14 C 0 s bosTau4.chr19 10849741 68 - 65312493 GGAGCAA----A------GTAACCATGAAGT-CAT--GA-CC----ACCAGAA--CACCAGCCTCACTTACCAACCT-GTGGGGCTGTC i bosTau4.chr19 I 14 C 0 s equCab2.chr11 58031956 65 - 61308211 GGAGAGA----A------GTAATCGCGG--T-CAT--GA-CC----AGGAGAA--TGCCA-CTGCGCCTACCAAACT-CCTGGGCCACC i equCab2.chr11 I 11 C 0 s canFam2.chr9 59426829 67 - 64418924 GGGGGTT----A------GTCACCGCAGCAT-CAT--GA-CC----AGGAGAA--CACAG-CATCATCCACCAATCT-GCAGGGCTGCC i canFam2.chr9 I 5 C 0 s pteVam1.scaffold_11245 5389 65 + 48268 CGCGGTG----A------GTAACCACAAT-G-CCT--GA-CC----AAAATAA--CAAC--TACTGGCTACCAACCT-GTGAGGCCACC i pteVam1.scaffold_11245 I 6 C 0 s loxAfr3.scaffold_49 14420854 65 - 17734757 ---GAAA----AGCCACTGCAGC-------A-ACT--AGACC----AGAGGGA--TGCTGGCACCATCTACAAGCCTGTGGGGACCAC- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 4872 58 + 24616 ---GAAG----G------GCAAC-------A-ACC--AG-CC----TGGGGGG--TGCTGCCGTCATCTACAAACCTACAGGGACCGC- i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e calJac1.Contig5139 33497 617 + 225949 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e felCat3.scaffold_206428 4198 416 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I a score=-184256.000000 s hg19.chr17_gl000204_random 33505 122 + 81310 CAGCCAGGA-----------------CCCTCAGCCC--CAAGCTGC-CCA-AG---------------TCACTCAG-CCAG----------------------------------GCGAGG------------------------------------------------------TCCCCC-------CACG--------------------GAG---------CAG-----------CAGG--------------------------------CTGGCCAGAAAGC-----------------------------------------------------------------------------------------------------------------------------------------TTCA----GACCACAAGCTTC----GGACCAAG-----------------------------C-------G------------GCACctagga------a-------g s panTro2.chr17 79463148 122 + 83384210 CAGCCAGGA-----------------CCCTCAGCCC--CAAGCTGC-CCA-AG---------------TCACTCAG-CCAG----------------------------------GCGAGG------------------------------------------------------TCCCCC-------CACG--------------------GAG---------AAG-----------CAGG--------------------------------CTGGCCAGAAAGC-----------------------------------------------------------------------------------------------------------------------------------------TTCA----GACTACAAGCTTC----GGACCAAG-----------------------------C-------G------------GCACCTAGGA------A-------G i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 3361 122 - 64270 CAGCCAGGA-----------------CCCTCAGCCC--CAAGCTGC-CCA-AG---------------TCACTCAG-CCAG----------------------------------GCGAGG------------------------------------------------------TCCCCC-------CACG--------------------GAG---------CAG-----------CAGG--------------------------------CTGGCCAGAAAGC-----------------------------------------------------------------------------------------------------------------------------------------TTCA----GACCACAAGCTTC----GGACCAAG-----------------------------C-------G------------GCACCTAGGA------A-------G i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16050061 123 + 17838096 CAGCCAGGA-----------------CCCTCAGCCC--CAAGCTGC-CCG-AG---------------TTACTCAG-CCAG----------------------------------GCGAGG-----------------------------------------------------TTCCCCC-------CACG--------------------GAG---------CAG-----------CAGG--------------------------------CCGGCCAGAAAGC-----------------------------------------------------------------------------------------------------------------------------------------TTCA----GACCACAAGCTTC----AGCCCAGG-----------------------------T-------G------------GCACCTAGGA------A-------G i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75024623 122 + 78773432 CAGCCAGGA-----------------CCCTCAGCCC--CAAGTTGC-CCA-AG---------------TTGCTCAG-CCAG----------------------------------GCGAGG------------------------------------------------------TCCCCC-------CACA--------------------GAG---------CAG-----------CAGG--------------------------------CCAGCCGGAAAGC-----------------------------------------------------------------------------------------------------------------------------------------TTTA----GACCACAAGCTTC----GGACCAGG-----------------------------T-------G------------GCACCTAGGA------A-------G i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 31872 122 - 95547 CAGCCAGGA-----------------CCCTCAGCCC--CAAGTTGC-CCA-AG---------------TCACTCAG-CCAG----------------------------------GTGAGG------------------------------------------------------TCCCCC-------CACA--------------------GAG---------CAG-----------CAGG--------------------------------CCAGCCAGAAAGC-----------------------------------------------------------------------------------------------------------------------------------------TTTA----GACCACAAGCTTC----GGACCAGG-----------------------------T-------G------------GCACctagga------a-------g i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 34114 122 + 225949 CAGCCAGGA-----------------CCCTCAGCCC--CACGCTGC-ACA-AG---------------CCACTCAG-CCAG----------------------------------GCGAGG------------------------------------------------------CCCCCA-------CACA--------------------GAG---------CAG-----------CAGT--------------------------------CTGGCCGGAAAGC-----------------------------------------------------------------------------------------------------------------------------------------TTCA----GACCACAGGCCTC----AGACCAGG-----------------------------T-------G------------GCACCTAGGA------A-------G i calJac1.Contig5139 I 617 C 0 s otoGar1.scaffold_94362.1-287808 16473 132 + 287808 AAGCCATGT-----------------CCCTCAGCCC--AGTGCTGC-GGA-AG---------------TCA-TCAG-TCAG----------------------------------GCCAGG------------------------------------------------------ACCCCA-------TCTG--------------------GAG---------CAG-----------CAGG--------------------------------CTGGCCAGAAGCC-----------------------------------------------------------------------------------------------------------------------------------------TCTCCCATAAACACAGGCCTA----GGACCAGG-----------------------------TACCTGGGG------------ACACCTGGGA------A-------G i otoGar1.scaffold_94362.1-287808 C 0 I 1 s tupBel1.scaffold_124459.1-15939 1879 118 + 15939 CCACCAGGT-----------------CCCTCAGCCC---AGACTGC-AGA-TG---------------TCACCCAG-TCGG----------------------------------GCCAGG------------------------------------------------------TGTTCA-------ACCGA-------------------GAG---------CTA-----------CAGG--------------------------------CCGAC----GCGC-----------------------------------------------------------------------------------------------------------------------------------------CCCAC---AAGCACAGGCCAG----GCGCCAGG-------------------------------------G------------ACACCGCAGA------A-------G i tupBel1.scaffold_124459.1-15939 C 0 I 1 s mm9.chr11 118747349 114 + 121843856 -------TG-----------------CCCCTGGCCC--AGCATGAC-AGA-AG---------------TCACCCAG-TCAA----------------------------------ACAAGA------------------------------------------------------CCCCTA-------CCTG--------------------AAG---------CAG-----------AGGC--------------------------------TCACCCA-AAGCT-----------------------------------------------------------------------------------------------------------------------------------------TCCT----C----TATGCTCG----GTGACAGC-----------------------------T-------G--------AGGGAGTCACAGGA------C-------C i mm9.chr11 C 0 I 1 s cavPor3.scaffold_76 4380328 122 + 7991924 --------------------------CCTCAACACA--CCCATGAG-GGCTAG---------------CCATCCAG-GGAA----------------------------------GCAGGG------------------------------------------------------CTCCCA------GCCTG--------------------GGG---------CAG-----------CAGG--------------------------------CCACCCAGAAGGC-----------------------------------------------------------------------------------------------------------------------------------------TCTG----C----CACAC-CA----AGGACAAG-----------------------------T-------GCCTAGCACAGGAACTCACGGGA------A-------G i cavPor3.scaffold_76 C 0 I 1 s oryCun2.chrUn0958 10005 153 + 41507 -------AG-----------------CCCGGGGCCCTGCCCAGAGC-AGC-AGGCGGCCAGGGGTCTCCCCCGCAG-GCAC----------------------------------CCAGGG------------------------------------------------------AGCCCAGAAGGGGCCAA--------------------GGG---------CAAACCTGCTTGGCCAGG--------------------------------GGACCCATGCACC-----------------------------------------------------------------------------------------------------------------------------------------CCCG----C---TCAGGCTGC----GGGACGGA-----------------------------G-------G------ACATGCAGAGCCGAGA------G-------G i oryCun2.chrUn0958 C 0 I 1 s vicPac1.scaffold_234559 576 104 + 1001 CAGCCAGGT-----------------CCTCCAGCCC--AGGGCTGC-AGA-AG---------------TCACCCAG-CCAA----------------------------------GCAGAG-------------------------------------------------------------------------------------------GGC---------TGA-----------CTTG---------------------------AAAGTCTCTCCCA------------------------------------------------------------------------------------------------------------------------------------------------CA----AGCACC------------GGTCAGG---------------------------GAC-------G------------ACACCTCAGA------A-------G i vicPac1.scaffold_234559 C 0 N 0 s turTru1.scaffold_106006 117850 102 + 145505 --ACCAGGT-----------------CCCGCAGCCC--AGGACTGC-AGA-AG---------------TCGCCCAG-CCAA----------------------------------GCAGAG-------------------------------------------------------------------------------------------GAC---------CAG-----------CTTG---------------------------AAAGCCTCTCCCA------------------------------------------------------------------------------------------------------------------------------------------------CA----AGCACC------------AGCCAAG---------------------------TGC-------A------------ACACCTCAGA------A-------G i turTru1.scaffold_106006 C 0 I 2 s bosTau4.chr19 10849809 262 - 65312493 CAGTAAGAT-----------------CCTGCAGCCC--AGGACTGC-AGA-AG---------------TCACTCAG-CCAA----------------------------------ACAGAG-------------------------------------------------------------------------------------------GCC---------CAG-----------CTTG---------------------------AAAGCCTCTCCCACAAGCACCTCAGAAGCCCACCTGGATGCCACCTAACCCCACCCTCCAGTCTCAATACATGGCATCCTTCAGGACCTTGCAGGGAGCTGGTTTCTACTGACTATGCTGGCCGAGGGTGGAATCTGGCCTGGGAACCTGCCTTTTTCA----AGAAACACAGTGT----GATCCAGG---------------------------AGC-------C------------ACACCTTGGGAAATGCA-------G i bosTau4.chr19 C 0 I 10 s equCab2.chr11 58032021 118 - 61308211 AGAT----------------------CCCCCTGCCC--TGGACTGT-GCA-AG---------------TCACCTGG-TCAG----------------------------------GCCAGG------------------------------------------------------ACCCCA-------CCCT--------------------GGA--------GCAG-----------CGGG--------------------------------CCAGCCCAAAAGC-------------------------------------------------------------------------------------------------------------------------------------CTCTTCCA----CAAGCCCCAG----------GCAGG---------------------------TTC-------G------------ACACCTCAGA------A-------G i equCab2.chr11 C 0 C 0 s canFam2.chr9 59426896 332 - 64418924 GAGCCAGGGCGCCCCCCCCACCCCCACCCCCTGCCC--AGGACTAT-AGA-AA---------------TCACC-AG-TCAGAGGGCCGGTGTGAAACTCTCTTCCACAAGCAGTAGCCAAGTGCAACAGCTCAGAAGCACCCCCAACCCCCCACGCCCCCACCAGAAGCCACCTCACCCCA-------CCCTCCATGCTCAGCTCTGCTTCCGGACCTCCTCCACGG-----------CTGGTGACCTTGgactctattggcccagggtggagtctggcctggaaac----------------------------------------------------------------------------------------------------------------------------tgcatttttttttttca----agaaacacagtgtttcagatgcagggggtccagggac-cacaaccttgaaaaTTT-------G------------TGACCACAGA------A-------G i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 5454 220 + 48268 CAGC-----TGGGCACCCCTTCCCCAACCCCCGCCC--AGGACTGC-AGA-AG---------------TCACCCAG-TCAC----------------------------------GCAAAG-------GGTCAGCCGGAAAGCCTCTTCCACAAGCACTGGCCAGGTGCAAC---ACCTGG-------GC----------------------GGC--------ACAC-----------CTGG--------------------------ATGCGCCTTACCCCAA------------------------------------------------------------------------------------------------------------------------------------TCTTTGGTCTCA----GGGCACACCATGCCTCATTTCCTGGGGAGCCGGTTACACGTGAC--------TCT-------G------------TTGGCCAGGA------ATGGGGggg i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14420919 123 - 17734757 CGGCCAGGT-----------------CCCTCAGCCC--AGGACCGC-AGA-AG---------------CCACCTGG-CCAA----------------------------------GCAGGC------------------------------------------------------CCCCAC-------CCTG--------------------GAG---------CAG-----------CAGG--------------------------------CCGGCTCAAAAGC-----------------------------------------------------------------------------------------------------------------------------------------TTCT----T-CCACAAACAAG----A--CCAGG-------------------------GATCA-------G------------AGGCCCAGGA------A-------C i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 4930 126 + 24616 CAGCCAGGT-----------------CCCT-GGGCC--GGCACAGCAAGA-AG---------------TCACTCAGCCCAA----------------------------------GCAGGT------------------------------------------------------CCCTAC-------CCCA--------------------GAG---------CAG-----------CAGG--------------------------------CCAGCTCCAAAGC-----------------------------------------------------------------------------------------------------------------------------------------TTCT----T-CTACAAACACG----GATCCAGA-------------------------GATCA-------G------------AGGCCCAGAA------A-------C i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e felCat3.scaffold_206428 4198 416 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I a score=-41050.000000 s hg19.chr17_gl000204_random 33627 17 + 81310 ggagcaggtat---gtaacc s panTro2.chr17 79463270 17 + 83384210 GGAGCAGGTGT---GTAACC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 3483 17 - 64270 GGAGCAGGTAT---GTAACC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16050184 17 + 17838096 GGAGCGGGTAT---GTAACC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75024745 17 + 78773432 GGAGGGGGTAT---GTAACC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 31994 17 - 95547 ggagggggtat---gtaacc i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 34236 17 + 225949 GGGGAGGGTAT---GTAGCC i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 16606 13 + 287808 TGAGGGCGTAT---GT---- i otoGar1.scaffold_94362.1-287808 I 1 C 0 s tupBel1.scaffold_124459.1-15939 1998 17 + 15939 TGACAGGGTAC---GGAGCC i tupBel1.scaffold_124459.1-15939 I 1 C 0 s mm9.chr11 118747464 2 + 121843856 TG------------------ i mm9.chr11 I 1 C 0 s cavPor3.scaffold_76 4380451 17 + 7991924 TGGTGGGACAT---GCAGCT i cavPor3.scaffold_76 I 1 C 0 s oryCun2.chrUn0958 10159 13 + 41507 GGGAGGGACGT---GT---- i oryCun2.chrUn0958 I 1 C 0 s turTru1.scaffold_106006 117954 11 + 145505 ------TGCCT---GGATGC i turTru1.scaffold_106006 I 2 I 341 s bosTau4.chr19 10850081 11 - 65312493 ------GGGCT---GGGCAC i bosTau4.chr19 I 10 I 44 s equCab2.chr11 58032139 13 - 61308211 ----CCAGCCT---GGATGC i equCab2.chr11 C 0 I 339 s canFam2.chr9 59427228 13 - 64418924 ----AGAGGCT---CTGCGC i canFam2.chr9 C 0 I 5 s pteVam1.scaffold_11245 5674 10 + 48268 ----cggggat---ctg--- i pteVam1.scaffold_11245 C 0 I 101 s loxAfr3.scaffold_49 14421042 18 - 17734757 --ACCAAGCTGGACACAGTC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 5056 15 + 24616 --GCCAAGCCA---ACAATC i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e felCat3.scaffold_206428 4198 416 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I a score=48733.000000 s hg19.chr17_gl000204_random 33644 75 + 81310 agggaatcacagga-------------ccttgatcgaggtcccactt-------------------------------ggaggcagggggaaaggctgtgggagaatagatgaaggagc s panTro2.chr17 79463287 75 + 83384210 AGGGAATCACAGGA-------------CCTTGATCGAGGTCCCACTT-------------------------------GGAGGCAGGGGGAAAGGCTGTGGGAGAATAGATGAAGGAGC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 3500 75 - 64270 AGGGAATCACAGGA-------------CCTTGATCGAGGTCCCACTT-------------------------------GGAGGCAGGGGGAAAGGCTGTGGGAGAATAGATGAAGGAGC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16050201 75 + 17838096 AGGGGATCACAGGA-------------CCTTGATCCAGGTCCCACTT-------------------------------GGAGGCAGGGGGAAAGGCTGTGGGAGAATAGATGAAGGAGC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75024762 75 + 78773432 AGGGAACCACAGGA-------------CCTTGATCCAGGTCCCACTT-------------------------------GGAAGCAGGGGGAAAGGCTGTGGGAGAATCGATGGAGGAGC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 32011 75 - 95547 agggaaccacagga-------------ccttgatccaggtcccactt-------------------------------ggaagcagggggaaaggctgtgggagaatcgatggaggagc i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 34253 52 + 225949 AG-----------------------------------GGTCCCCCTT-------------------------------GGAGGCA-GGGGAAAGGCTGGGAGAGTAGAGATGAAGGAGC i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 16619 35 + 287808 ------------------------------------------------------------------------------------GGAGAGAGGGGCTGTGGGAGAGGGGGTGAAGGAGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 2015 54 + 15939 AGGGTGTCACA-GA-------------CCCCAGTCCCGGTTCCATCT-------------------------------GGAGGCTAGGAGA-AGGCTGTG------------------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118747466 52 + 121843856 ----------------------------------CCCGGGCCCACAT-------------------------------GGAGGCCAGGGGA--GACTGTGTAAGAACACAGAAAGTATC i mm9.chr11 C 0 I 1 s cavPor3.scaffold_76 4380468 59 + 7991924 AGGGAAA---------------------------TACAGGGCCACCT-------------------------------GGAGgacagggga--agctgtgggaaaacagatgacggagt i cavPor3.scaffold_76 C 0 I 1 s oryCun2.chrUn0958 10172 45 + 41507 ----------------------------------GCTGGGGCTGGGG-------------------------------GCAGGAGTGGGGG--TTCTGGGTGGG-------GAAGGAGC i oryCun2.chrUn0958 C 0 I 1428 s bosTau4.chr19 10850136 78 - 65312493 AGAAAATTATACGA-GCC--------GCCCCAGTCCAGGTCCCACTT-------------------------------GGAGGCAGGG-GAGGGGCTGCAGGAGAACAGATGAAGAAGC i bosTau4.chr19 I 44 I 1 s canFam2.chr9 59427246 61 - 64418924 GAGAAAGAACAGGA--------------------------CCCTCTT-------------------------------GGAggcaggg-caggggctgcgggaaaacagatgaaggtac i canFam2.chr9 I 5 I 1 s pteVam1.scaffold_11245 5785 76 + 48268 GGGGAAGGACGGGAAGTG--------GGGCCAGGGCGGGTCCCGCTT-------------------------------agaggcagg----gaggctgtgggagagcagatgccggagc i pteVam1.scaffold_11245 I 101 I 1 s loxAfr3.scaffold_49 14421060 96 - 17734757 --------------AGTGCCATCCTGCCCCTCCTTCAGCTGGCAGCTCTCTACACACAGCCTATGTCAGGGTCCCCTGGGGAGCTGGTGACCCTGTTGTCCGGGAGTAGA--------- i loxAfr3.scaffold_49 C 0 I 209 s proCap1.scaffold_29042 5071 31 + 24616 --------------AGTGCCATCCCATCCCT-------CCTGCAGCT-------------------------------GGGGG------------------------------------ i proCap1.scaffold_29042 C 0 I 27 e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e turTru1.scaffold_106006 117965 341 + 145505 I e felCat3.scaffold_206428 4198 416 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e equCab2.chr11 58032152 339 - 61308211 I a score=88105.000000 s hg19.chr17_gl000204_random 33719 84 + 81310 -ccacggggaagc--agacggagctacttcacgggaggacggaacatttgagttgggtctt----ttttctttttagagatgggctctcac s panTro2.chr17 79463362 84 + 83384210 -CCACGGGGAAGC--AGACAGAGCTACTTCACGGGAGGACGGAACATTTGAGTTGGGtctt----ttttctttttagagatgggctctcac i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 3575 84 - 64270 -CCATGGGGAAGC--AGATGGAGCTACTTCACGGGAGGACGGAACATTTGAGTTGGGTCTT----TTTTCTTTTTAGAGATGGGCTCTCAC i gorGor1.Supercontig_0007361 C 0 M 446 s ponAbe2.chr17_random 16050276 84 + 17838096 -CCACGGGGAAGC--AGACGGAGCTACTTCACGTGAGGACGGAACATTTGAGTTGGGTCtt----ttttctttttagagatgggctctcac i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75024837 83 + 78773432 -CCG-GGGGAAGC--AGACAGAGCTACTTCACAGGAGGATGGAACATTTGAGTTGGGtctt----ttttctttttacagatgggctctcac i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 32086 84 - 95547 -ccagggggaagc--agacagagctacttcacaggaggatggaacatttgagttgggtctt----ttttctttttagagatgggctctcac i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 34305 84 + 225949 -CCAGGGGGAAGT--GGGCAGAGCTACTTCACAGGAGGATGGAACATTTGAGTAGGGtctt----ctttctttttagagatgggctctcgc i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 16654 46 + 287808 -CTCTGGAG----------GGACCCACTTCATGGGAGAAGGGGACCCTAGAGGAGGG---------------------------------- i otoGar1.scaffold_94362.1-287808 C 0 I 37 s tupBel1.scaffold_124459.1-15939 2069 41 + 15939 -----GGGGGACC--AGGCAGACCTGCTTCTCGGGATGAGGGGACACT------------------------------------------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118747519 44 + 121843856 -CTGGGAGGAATT--TGACAAATTCAC-TCATAGG-TGTGGGAACATTT------------------------------------------ i mm9.chr11 I 1 I 3 s cavPor3.scaffold_76 4380528 55 + 7991924 -cttggagaaatc--cggcta--tcacttcataggaggagggaatatgtgagttgggtct------------------------------- i cavPor3.scaffold_76 I 1 C 0 s bosTau4.chr19 10850215 57 - 65312493 -ACTGCAGCAATCA-GGGCAGGACCACTTCATGGGTGTGTGT------------------G----TGtgtgtgttag----------tcac i bosTau4.chr19 I 1 C 0 s canFam2.chr9 59427308 45 - 64418924 -gctggaggaatcg-gggcaggactgcaccatggaaggaagggacat-------------------------------------------- i canFam2.chr9 I 1 I 1 s pteVam1.scaffold_11245 5862 57 + 48268 -cctggaggagtc--aggcaggactgcaccgtgggagaaggggacatttcatgtgggtct------------------------------- i pteVam1.scaffold_11245 I 1 I 201 s proCap1.scaffold_29042 5129 81 + 24616 CCCCTGAGGAGCTGATGACCTTGTTGTCTGGGGGGTGGAGAGGACAGCC----TGGGCCTTGGAGTCTGCATTTTTCAAATGAGC------ i proCap1.scaffold_29042 I 27 I 156 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e turTru1.scaffold_106006 117965 341 + 145505 I e felCat3.scaffold_206428 4198 416 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e equCab2.chr11 58032152 339 - 61308211 I e loxAfr3.scaffold_49 14421156 209 - 17734757 I a score=51075.000000 s hg19.chr17_gl000204_random 33803 50 + 81310 ccaggctggagtgcagtggcacaa--tca---------tacctcactgcaaccttgaactc s panTro2.chr17 79463446 50 + 83384210 ccaggctggagtgcagtggcacaa--tca---------tagctcactgcaaccttgaactc i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16050360 50 + 17838096 ccaggctggaatgcagtggcacaa--tca---------tagctcactgcaaccttgaactc i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75024920 50 + 78773432 ccaggctggagtgcagtggcacaa--tca---------tagctcactgcaaccttgaactc i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 32170 50 - 95547 ccaggctggagtgcagtggcacaa--tca---------tagctcattgcaaccttgaactc i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 34389 50 + 225949 ccaggcttgagtgcagtgacacaa--tca---------tagctcactgcaaccttgaactc i calJac1.Contig5139 C 0 C 0 s bosTau4.chr19 10850272 51 - 65312493 tcagtcatgtctgactctttgcaa--tcacatggactgtagcctgttaggctc-------- i bosTau4.chr19 C 0 C 0 s felCat3.scaffold_206428 4614 53 + 132007 CTGGGCAGGTGCAATGCCTCGGAAGCCCGCCTGGACACCACCTAACCCCGCCC-------- i felCat3.scaffold_206428 I 416 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5210 156 + 24616 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e gorGor1.Supercontig_0007361 3659 446 - 64270 M e tupBel1.scaffold_124459.1-15939 2110 0 + 15939 C e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e turTru1.scaffold_106006 117965 341 + 145505 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e otoGar1.scaffold_94362.1-287808 16700 37 + 287808 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e canFam2.chr9 59427353 1 - 64418924 I e equCab2.chr11 58032152 339 - 61308211 I e cavPor3.scaffold_76 4380583 0 + 7991924 C e mm9.chr11 118747563 3 + 121843856 I e loxAfr3.scaffold_49 14421156 209 - 17734757 I a score=43314.000000 s hg19.chr17_gl000204_random 33853 21 + 81310 ctgggctcaagcaatgctccc s calJac1.Contig5139 34439 21 + 225949 ctaggcttaagcaatcctccc i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 32220 21 - 95547 ctgggctcaagcaatcctccc i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75024970 21 + 78773432 ctgggctcaagcaatcctccc i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16050410 21 + 17838096 ctgggctcaagcaatcctccc i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 4105 21 - 64270 ctgggctcaagcaatcctccc i gorGor1.Supercontig_0007361 M 446 C 0 s panTro2.chr17 79463496 21 + 83384210 ctgggctcaagcaatcctccc i panTro2.chr17 C 0 C 0 s bosTau4.chr19 10850323 21 - 65312493 ctctgtccatgaaattctcca i bosTau4.chr19 C 0 I 121 s felCat3.scaffold_206428 4667 21 + 132007 TCCAGGCTCAGCACTGCTTCG i felCat3.scaffold_206428 C 0 I 10 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5210 156 + 24616 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e tupBel1.scaffold_124459.1-15939 2110 0 + 15939 C e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e turTru1.scaffold_106006 117965 341 + 145505 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e otoGar1.scaffold_94362.1-287808 16700 37 + 287808 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e canFam2.chr9 59427353 1 - 64418924 I e equCab2.chr11 58032152 339 - 61308211 I e cavPor3.scaffold_76 4380583 0 + 7991924 C e mm9.chr11 118747563 3 + 121843856 I e loxAfr3.scaffold_49 14421156 209 - 17734757 I a score=105076.000000 s hg19.chr17_gl000204_random 33874 64 + 81310 acctcagcttcctgaatagctgg-gac-acag------------aggcatgccaccatgcctg-------gctctttttaaaaaa s calJac1.Contig5139 34460 64 + 225949 acctcagcttcgtgagtagctgg-gacaacag------------aggcatgccaccatacctg-------gctcttttc-aaaaa i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 32241 65 - 95547 ccctcagcttcctgagtagctgg-gacaacag------------gggcatgccaccatgcctg-------gctctttttttaaaa i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75024991 65 + 78773432 ccctcagcttcctgagtagctgg-gacaacag------------gggcatgccaacatgcctg-------gctctttttttaaaa i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16050431 64 + 17838096 actccagcttcctgagtagctgg-gac-acag------------gggcatgccaccatgcctg-------gctctttttaaaaaa i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 4126 64 - 64270 acctcagcttcctgagtagctgg-gac-acag------------aggcatgccaccatgcctg-------gctctttttaaaaaa i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79463517 64 + 83384210 acctcagcttcctgaatagctgg-gac-acag------------aggcatgccaccatgcctg-------gctcttttttaaaaa i panTro2.chr17 C 0 C 0 s felCat3.scaffold_206428 4698 76 + 132007 ---------TCCTCAGCAGCTGGTGACCtcagactctgttggccaagggtggagcctggcctgggaacctgcatttttcaagaaa i felCat3.scaffold_206428 I 10 I 196 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5210 156 + 24616 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e tupBel1.scaffold_124459.1-15939 2110 0 + 15939 C e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e turTru1.scaffold_106006 117965 341 + 145505 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e otoGar1.scaffold_94362.1-287808 16700 37 + 287808 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e canFam2.chr9 59427353 1 - 64418924 I e bosTau4.chr19 10850344 121 - 65312493 I e equCab2.chr11 58032152 339 - 61308211 I e cavPor3.scaffold_76 4380583 0 + 7991924 C e mm9.chr11 118747563 3 + 121843856 I e loxAfr3.scaffold_49 14421156 209 - 17734757 I a score=205158.000000 s hg19.chr17_gl000204_random 33938 117 + 81310 tgtttttgtaaagaa--gggctctcactatatt------gctggacttgaactcttgagctcaatccatcctcccaccttggcctcccaaagtgctgggattgcagtcatgagccaccttacttg s panTro2.chr17 79463581 117 + 83384210 tgtttttgtaaagaa--gggctctcactatatt------gctggtcttgaactcttgagctcaatccatcctcccaccttggcctcccaaagtgctgggattgcagtcatgagccaccttacttg i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 4190 117 - 64270 tgtttttgtaaagaa--ggggtctcactatatt------gctggtcttgaactcttgagctcaatccatcctcccaccttggcctcccaaagtgctgggattgcagtcatgagccaccttacttg i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16050495 117 + 17838096 tgtttttgtaaagaa--ggggtctcactatatt------gctggtcttgaactcttgagctcaatccatcctcccacgttggcctcccaaagtgctgggattgcagtcatgagccaccttactcg i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75025056 119 + 78773432 tgtttgtgtaaagaaggggggtcttgctatatt------gctggtcttgaactcttgagctcaatccatcctcccaccttggcctcccaaagtgctgggactgcagtcgtgagccaccttactcg i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 32306 119 - 95547 tgtttgtgtaaagaaggggggtcttgctatatt------gctggtcttgaactcttgagctcaatccatcctcccaccttggcctcccaaagtgctgggactgcagtcgtgagccaccttactcg i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 34524 123 + 225949 tgtttttgtaaagaa--ggggtctcactatattgcccaggctggtcttgaactcttgagctcaacccacccacccacctcagcctcccaaagttctgggattgcagtcgtgagccacATTACTCA i calJac1.Contig5139 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5210 156 + 24616 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e tupBel1.scaffold_124459.1-15939 2110 0 + 15939 C e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e turTru1.scaffold_106006 117965 341 + 145505 I e felCat3.scaffold_206428 4774 196 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e otoGar1.scaffold_94362.1-287808 16700 37 + 287808 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e canFam2.chr9 59427353 1 - 64418924 I e bosTau4.chr19 10850344 121 - 65312493 I e equCab2.chr11 58032152 339 - 61308211 I e cavPor3.scaffold_76 4380583 0 + 7991924 C e mm9.chr11 118747563 3 + 121843856 I e loxAfr3.scaffold_49 14421156 209 - 17734757 I a score=582375.000000 s hg19.chr17_gl000204_random 34055 139 + 81310 gcctgagttgggtcttgaggcatgcataggagtttccagg--tgg-ga--TGCAGTTGCTGGAGCTGGACCATGCAGATCCAGCTCTGGAGCTCACAG----TAATGTTCATAAACAAATGGTTTTGAGCCTT-ACGTGAGCCAGGCCC s felCat3.scaffold_206428 4970 86 + 132007 -cttgagctgggtcttgaagcacgagtaggagtttgtagg--tggcag--ggctg----tgggga--aggTATCCAGATCTGGCTCTTGAGCCCACA---------------------------------------------------- i felCat3.scaffold_206428 I 196 C 0 s equCab2.chr11 58032491 134 - 61308211 atctgagttgggtcttgaagcatgagtaggagcttccagg--tgg-gg--agtcg----gggggg--gagcatctaggTCTGGCTGTTGAGCCCACAG----TAATGTTCAGAAACAAACGTTTTTCAGCCTTAACGCAGGCCAGGCCC i equCab2.chr11 I 339 C 0 s bosTau4.chr19 10850465 132 - 65312493 -tttgaattgggtcttaaagcatgagtaggagtttccagtgttgg-ggatggcag----gggtga------aTCCAGATCTGGCGCTTGAGCCCACTA----TAATGTTCATAAACAAATGCTTTTT-GCTTTAACGTGGCCCAGGTCC i bosTau4.chr19 I 121 I 89 s turTru1.scaffold_106006 118306 135 + 145505 atttgagttcggtcttaaagcatgagtaggagtttccagggttgg-gg--ggcgg----tggtgatgggccatccagATCTGGCTCTTGAGCCCACTG----TAATGTTCATAAACAAATGCTTTTGAACCTTAACGT---CCCGGCCC i turTru1.scaffold_106006 I 341 C 0 s panTro2.chr17 79463698 139 + 83384210 gccTGAGTTGGGTCTTGAGGCATGCATAGGAGTTTCCAGG--TGG-GA--TGCAGTTGCTGGAGCTGGACCATGCAGATCCAGCTCTGGAGCTCACAG----TAATGTTCATAAACAAATGGTTTTGAGCCTT-ACATGAGCCAGGCCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 4307 139 - 64270 gccTGAGTTGGGTCTTGAGGCATGCATAGGAGTTTCCAGG--TGG-GA--TGCAGTTGCTGGAGCTGGACCATGCAGATCCAGCTCTGGAGCTCACAG----TAATGTTCATAAACAAATGGTTTTGAGCCTT-ACGTGAGCCAGGCCC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16050612 139 + 17838096 gccTGAGTTGGGTCTTGAGGCATGCATAGGAGTTTCCAGG--TGG-GG--TGCAGTTGCTGGAGCTGGACCATGCAGATCCAGCTCTGGAGCTCACAG----TAATGTTCATAAACAAATGGTTTTGAGCCTT-ACGTGAGCCAGGCCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75025175 139 + 78773432 gccTGAGTTGGGTCTTGAGGCATGAATAGGAGTTTCCAGG--TGG-GG--TGCAGTTGCTGGAGCTGGCCCATGCAGATCCAGCTCTGGAGCTCACGG----TAATGTTCATAAACAAATGAGTTTGAGCCTT-ACTTGAGCCAGGCCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 32425 139 - 95547 gcctgagttgggtcttgaggcatgaataggagtttccagg--tgg-GG--TGCAGTTGCTGGAGCTGGCCCATGCAGATCCAGCTCTGGAGCTCACGG----TAATGTTCATAAACAAATGAGTTTGAGCCTT-ACTTGAGCCAGGTCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 34647 139 + 225949 GCCTGAGTTGGGTCTTGAGGCATGCATAGGAGTTTCCAGG--CGG-GG--TGCGGTTGCTGGAGGTGGACCATGCAGCCCCAGCTCTAGAGCTGGCGG----TAATGTTCACAAACAAATGGCTCTGAGCCTT-ATGTGAGCCAGGCCC i calJac1.Contig5139 C 0 C 0 s proCap1.scaffold_29042 5366 119 + 24616 ---tgagttgggttttgatgtacaagcaggagtttccagg--tgg-TG-------------------GGCCCACAAGATCTGGTTCTTAGGTCCACAA----TGATGCCCATAAACAAATGTTTTTGAGCCTTAATACAGGG-AGGTCC i proCap1.scaffold_29042 I 156 C 0 s loxAfr3.scaffold_49 14421365 120 - 17734757 ---tgaattgggtcttgatgtatgagtaggaatttccagg--tgg-TG-------------------GGCCAACAAGATCTGGCTCTTGGTCCCACAA----TGATGTTCATAAACAAATGTTTTTGAGCCTTATTATGGGTCAGGTCC i loxAfr3.scaffold_49 I 209 C 0 s mm9.chr11 118747566 139 + 121843856 ---TGAGTTGGACCTTGAGTCATTTGTAGAAGTTCCTAGG--TGG-GA--GGTGGTCTTGGGCTATGGGTCACTCAAACCTAGCTCTT-AGCTCACTGTTCATAATGTTCATAAACAAATGATTTTGTCCCTT-ACCATGGGCAATACC i mm9.chr11 I 3 I 21 s cavPor3.scaffold_76 4380583 108 + 7991924 ---------------tggagcacatataggagtttctagg--caa-ga--agggATTTTTAGGGGTGGACCATCTAGAACTGGCTATCAAGCTCACAG----TAATGTTGAGAAaaaagttcttgagccctt----------------- i cavPor3.scaffold_76 C 0 C 0 s tupBel1.scaffold_124459.1-15939 2110 113 + 15939 -----AGTTGGGTCGTGAAGCACGTGGAAGCGTTTCCAGA--TGT-G----GCAG--GGCGGGGAAGGACCACGTACACCTGCCTTCAGAGTTCGCAG----TAAGGCTCACGAGCAAACGT------------------GCGAGTCCC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s canFam2.chr9 59427354 87 - 64418924 ---tgagctgggtcttaaggcacgagcgggagtttctaag--tggtgg--ggttg----tgggga--aggcgtcccTATCTGGCCCTTGAGCCCAGG-------------------------------------------------CCC i canFam2.chr9 I 1 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e otoGar1.scaffold_94362.1-287808 16700 37 + 287808 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I a score=181229.000000 s hg19.chr17_gl000204_random 34194 122 + 81310 AAGACTGGGCATTTTCTCATGTGTTTTCTAATGCACTTGATAACTGATC------TTATTCT--CCCCC-G--------------------GGGACTCTG-GG----------TGCAAG--------G-AGACATTCTGGGCTTCATCCCACCATGA-AGACCAAAAA-ACAT s calJac1.Contig5139 34786 121 + 225949 GAGACTGGGCATTTTCTCCCGTGTTTTCTAATGTACTTGGCAACCGATC------TTACTCT--CCCTG-A--------------------GGGACTCCC-AG----------TGTAAG--------G-AGACATTCAGGGCCTCATCCTGCCACTA-AGAT-AAAAA-ACAT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 32564 121 - 95547 AAGACTGGGCATTTTCTCACGTGTTTTTTAATGCACTTGACAATGGATC------TTACTCT--CCCCCTG--------------------GGGACTC---GG----------TGCAAG--------G-AGACATTCTGGGCTTCACCCCACCACGA-AGACCAAAAA-ACAT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75025314 121 + 78773432 AAGACTGGGCATTTTCTCATGTGTTTTTTAACGCACTTGACGACGGATC------TTACTCT--CCCCCTG--------------------GGGACTC---GG----------TGCAAG--------G-AGACATTCTGGGCTTCACCCCACCACGA-AGACGAAAAA-ACAT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16050751 122 + 17838096 AAGACTGGGCATTTTCTCATGTGTTTTCTAATGCACTTGACAACTGATC------TTACTCT--CCCCC-G--------------------GGGACTCTG-GG----------TGCAAG--------G-AGACATTCTGGGCTTCATCCCACCACAA-AGACCAAAAA-ACAT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 4446 122 - 64270 AAGACTGGGCATTTTCTCATGTGTTTTCTAATGCACTTGATAACTGATC------TTACTCT--CCCCC-G--------------------GGGACTCTG-GG----------TGCAAG--------G-AGACATTCTGGGCTTCATCCCACCATGA-AGACCAAAAA-ACAT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79463837 122 + 83384210 AGGACTGGGCATTTTCTCGTGTGTTTTCTAATGTACTTGATAACTGATC------TTACTCT--CCCCC-G--------------------GGGACTCTG-GG----------TGCAAG--------G-AGACATTCTGGGCTTCATCCCACCATGA-ACACCAAAAA-ACAT i panTro2.chr17 C 0 C 0 s tupBel1.scaffold_124459.1-15939 2223 98 + 15939 AA-------------CACATGGGTCTGC-------CTGGGCTCCTGGTC------TGGCCCC--GCCT--G--------------------GGTTCTCTC-TC----------TGC-AG--------A-GGACATTCTGGGCCTCG-CCCGCTGCTC-AGCCCACAGC-A-GT i tupBel1.scaffold_124459.1-15939 C 0 C 0 s cavPor3.scaffold_76 4380691 111 + 7991924 -aacatgggcactttttc------------acccacttaacaatggatctatgcattatatt--ctctc-a--------------------gctgctctg-ga----------tg---g--------t-aggcagtctcaGCCTCATCCTGTTCCTA-AGACCACGGT-CCT- i cavPor3.scaffold_76 C 0 C 0 s turTru1.scaffold_106006 118441 122 + 145505 CACCCTGGGCACTTTCTCACATGCGTTCTTTTCCACTGGGCAACTGATT------GTTTACT--CATCC-TG-------------------GGAGCTCTC-AA----------TGCAAG--------A-AGACCTCCTGGGCTTCATCTCACCGCTC-AGACTGACTTCTT-- i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58032625 119 - 61308211 CACGCTGGGCACTTTCTCACGCTTGCTCTCTTCCACTTGGCAATAGACC------TTCTCCT--CCTCC-T--------------------GGGACTCTT-AC----------TACAGG--------A-AGACCTCCCAGGCTTCATCTCAGGCTTT--GACTGAAGA-CC-- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59427441 143 - 64418924 CATGGCGGGCACTTTCTCCTGGGTGTTCTCCTCCCCTTGGCAACAGGCC------TATGACTCGCCCCC-CACCCCACCCCACGCCCGCCCGGAATGCTC-AC----------TGCAAG--------ATAGACCTCCGAGGCTCCATCCCACCTGCT-GGACTGAAGA-TC-- i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 5056 105 + 132007 ------------------------GTAATGTTCCCCTTGGCGACGGGTC------TTTCACT--CCCCC-CACCTCG--------------GGGGAACTCTAC----------TGCAAG--------A-AGACCTCGGGGGTTTCATCCTGCCACTTGGGACTGGAGACTT-- i felCat3.scaffold_206428 C 0 C 0 s loxAfr3.scaffold_49 14421485 116 - 17734757 CAAATGGGGAAGCGTCCCATGTG-CTTATTgtcc--------------c------ccaagcc--cttcc-a--------------------gcagccact-tggtggtaaccttgcccc--------c-aggtactctggactttatctcaccactt-ggacagaagg-ctt- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 5485 114 + 24616 C-AACGGGGACGCTTCCCAGGTGTTTTATGGTCC--------------T------CCAAGCC--CTTCC-A--------------------GCAGCCACC-TG----------TGCCCCATGTGCCTC-ACACATTCTGGGCTTCATCACCCCACTT-GGATAAGAAA-CTT- i proCap1.scaffold_29042 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e otoGar1.scaffold_94362.1-287808 16700 37 + 287808 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e bosTau4.chr19 10850597 89 - 65312493 I e mm9.chr11 118747705 21 + 121843856 I a score=214600.000000 s hg19.chr17_gl000204_random 34316 96 + 81310 CCTGAGGGC---AGG--CTTGGCATCAAATCCTCCTCCTGCCACTCCAGGAGCCGAGCGCA-GACCTTGCTGCAGCCAGGAAAATAAA-TAATAG----TTGACCAA-- s calJac1.Contig5139 34907 98 + 225949 CCTGAGGCCCTGAAT--GTTGGCTTCAGATCCTCCTTCTTCCACTGCAGAAGCTAAACACA-GACCTTGCTGCAGCCAGGAAAAT-AA-TCAGAG----TTGACCAA-- i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 32685 96 - 95547 TCTAAGGGC---AGG--CTTGGCATCAAATCCTCCTCCTGCCTCTCCAGGAGCCGAGCACA-GACCTTGCTGCAGCCAGGAAAATAAA-TAATAG----TTGACCAA-- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75025435 96 + 78773432 CCTAAGGGC---AGG--CTTGGCATCAAATCCTCCTCCTGCCTCTCCAGGAGCCGAGCACA-GACTTTGCTGCAGCCAGGAAAATAAA-TAATAG----TTGACCAA-- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16050873 96 + 17838096 CCTGAGGGC---AGG--CTTGGCATCGAATCCTCCTCCTGTCACTCCAGGAGCCGAGCATA-GACCTTGCTGCAGCCAGGAAAATAAA-TAATAG----TTGACCAA-- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 4568 96 - 64270 CCTGAGGGC---AGG--CTTGGCATCAAATCCTCCTCCTGCCACTCCAGGAGCCAAGCACA-GACCTTGCTGCAGCCAGGAAAATAAA-TAATAG----TTGACCAA-- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79463959 96 + 83384210 CCTGAGGCC---AGG--CTTGGCATCAAATCCTCCTCCTGCCACTCCAGGAGCCGAGCACA-GACCTTGCTGCAGCCGGGAAAATAAA-TAATAG----TTGACCAA-- i panTro2.chr17 C 0 C 0 s tupBel1.scaffold_124459.1-15939 2321 83 + 15939 CCTGACAGC---GGC--CTTGGCGCGAG----TCCTCGGGCCACTCCAGGAGCCCAGCACAGGGCCCTACT-CGGCCGCAAGAACAA--------------GCCCTG-- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118747726 93 + 121843856 CCTGAGGGC---AGT--CTTGGCATCAAATCCTTCCTA-GCCATGTGAGGAACCCAAACTT-ATCCTTGCTTCAGCCAGAAAA--GAA-TAATAA----TAAACtga-- i mm9.chr11 I 21 I 2632 s cavPor3.scaffold_76 4380802 70 + 7991924 CCTGAAGCC---AGG--CATGTCCACAAATCCTCCTGAGGCCATGCCTGGGGCCAA-----------------GGACAGGAAAATAAG-TAGT---------------- i cavPor3.scaffold_76 C 0 I 975 s turTru1.scaffold_106006 118563 90 + 145505 TGCAAGGGT---G-G--CTTAGTG-----TCCTCCTTAGGCTGCCCCAGATGCCCAGCACA-GGGCCTTCCCCAGGCAGGAAAACAAA-TAACAG----TTGATGGA-- i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58032744 96 - 61308211 CCCACGGGC---AGG--CTTGGTGTGGAGCCCTTCTTAGGCCCCTCCAGGTGCCCGGCACA-GGGCCTTCCTCAGACAGGAAAATGTG-TGGTCG----TTGATGTG-- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59427584 91 - 64418924 CTCCAGGGC---A-G--CTCTGTGCAAAACC---CTCGGGCTGCTCCCAGGGACAAGCACC-AGGCCTTCC-CAGTCAGGAAAATAAG-TAATAG----CTGATGGG-- i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 5161 90 + 132007 CCTGAGGGC---AGG--CTTGGTG---ATCC---TTTGGGCCGCCCCAAGTGACAAGCACA-GGGCCTTCC-CGGTCAGGAAAATAAGTTAATAG----TTGATGGG-- i felCat3.scaffold_206428 C 0 C 0 s loxAfr3.scaffold_49 14421601 80 - 17734757 cctgagggc---agg--aatgctctggatgccacatccttaccctccaggtacccagcaga-gtct----------------aataaa-tagtgg----tcggtgga-- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 5599 66 + 24616 CCTGAAGGC---AGG--GATGCCCTCAGGGCCATGTCATTGCCCTCCAGGTGCCCAGCACA-AAGT----------------CACA-------------------GA-- i proCap1.scaffold_29042 C 0 C 0 s oryLat2.scaffold4784 2549 101 - 5056 CCTCAGAGC---AGAACCCTGACCTCAGAGCAGAACCCTGAC---CTCAGAGCAGAACCCT-GACCTCAGAGTAGAACCCAAACCTGA-GAGTAGAACTTTGACCTGAG i oryLat2.scaffold4784 N 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e otoGar1.scaffold_94362.1-287808 16700 37 + 287808 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e bosTau4.chr19 10850597 89 - 65312493 I a score=145220.000000 s hg19.chr17_gl000204_random 34412 118 + 81310 GGTA-----CTGAC-C----------ACCCTCACCCCA--------GGTTAGGAAG--AACC-TGCAAGC-CAATTTCTCTTTGATGTGTTGAGCTATAGCCC--------ACCCCACACCCCCTTCACTGCTGTTTGCT------TCCCTAAAAATGAA--------------- s proCap1.scaffold_29042 5665 116 + 24616 GGTA-----TTGGC-------------------CCCAACACAAGGCAATTGAAAAGA-AGTC-TGAGAGCTGTGCTGCCATCTCGTCTACTGATCCCC-CCCC--------ACCCCACACCC---TCATGGTGGTTTGTT------CCCCAGGAAATGAA--------------- i proCap1.scaffold_29042 C 0 I 1 s loxAfr3.scaffold_49 14421681 118 - 17734757 tgtA-----CTGGC-------------------CCCGACATAAGCCGAATGGGAAGG-AGTC-TGAGAGCTGCGCTGCTATTTGATCTGTTGATTCATGCCCC--------ACCCCACACCCA--TCATGGCTGTGTGTT------TCCCAAGAAGTGAA--------------- i loxAfr3.scaffold_49 C 0 I 1 s felCat3.scaffold_206428 5251 96 + 132007 ---------CTTAT-C----------AACCGC-CCCTG--------AATCAGAAAGG-AATC-TGCAAGCTAGGTTTCTATTTGGTCTAGTAGGATCTGCCCC--------ACTCCCACCC-------------------------CCACCAGAAGTGAA--------------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59427675 94 - 64418924 ---------TTTAT-C----------AACCGG-CCCTA--------AATTAGGAAGC-CATC-TGCAGGC-------------------------TCTGCTCC--------ACCCCCACTCTGC--TGTTGCTGTTTCATTCGTTTCCCCCAGAAGAGAA--------------- i canFam2.chr9 C 0 C 0 s equCab2.chr11 58032840 109 - 61308211 ---------TTGAT-C----------AACCGG-CCCC----------ATTAGGAAGG-AACC-TGCAAGC-CCCTTACCACCCCGTCT-GTAAGCTATGCCCC--------ACGCCGCCCCCAG--CAGCGCGGTTTGTC------TCCCAAGAAGCAAA--------------- i equCab2.chr11 C 0 C 0 s turTru1.scaffold_106006 118653 113 + 145505 ---------TTGAT-T----------GACAAG-CCCT---------CATTAGGAAGG-AATC-TGCAAGCCAGGTTACTATTTGGTCTAGGAAGCTACACCCC--------ACCCCGACCCCTC--AATATCGTCATCATT-----TCCAGAGAAGTGAA--------------- i turTru1.scaffold_106006 C 0 C 0 s tupBel1.scaffold_124459.1-15939 2404 85 + 15939 TGGG-----CTCACGC----------ACTCTCCC-------------ATCAGGAAG--ACAT-TTGCAGC-GAGCCTGGCATTG--------------------------------GCACC-----CACCGCTGCTGCCA------TTTCTGAGGAAGGG--------------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s panTro2.chr17 79464055 118 + 83384210 GGTA-----CTGAC-C----------ACCCTCACCCCA--------GGTTAGGAAG--AAAC-TGCAAGC-CAATTTCTCTTTGATCTGTTGCGCTATGGCCC--------ACCCCACACCGCCTTCACTGCTGTTTGCT------TCCCTAAAAATGAA--------------- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 4664 119 - 64270 GGTA-----CTGAC-C----------ACCCTCACCCCA--------GGTTAGGAAG--AACCTTGCAAGC-CAATTTCTCTTTGATCTGTTGAGCTATGGCCC--------ACCCCACACCCCCTTCACTGCTGTTTGCT------TCCCTAAAAATGAA--------------- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16050969 118 + 17838096 GGTA-----CTGAC-C----------ACCCTCACCCCA--------GGTTAGGAAG--AACC-TGCAAGC-CAAGTTCTCTTTGATCTGTTGAGCTATGGCCC--------ACCCCACACCCCCTTCACTGCTCTTTGCT------TCCCTAAAAATGAA--------------- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75025531 118 + 78773432 GGTA-----CTGAC-C----------ACCCTCACCCTG--------GGTTAGGAAG--AACC-TGCAAGC-CGATTTCTCTTTGATCTGTTGAGCTATGGCCC--------ACCCCACACCTCCTTCACTGCTGTTTGCT------TCCCTAAAAATGAA--------------- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 32781 118 - 95547 GGTA-----CTGAC-C----------ACCCTCACCCTG--------GGTTAGGAAG--AACC-TGCAAGC-CAATTTCTCTTTGATCTGTTGAGCTATGGCCC--------ACCCCACACCTCCTTCACTGCTGTTTGCT------TCCCTAAAAATGAA--------------- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 35005 115 + 225949 -GTA-----CTGCC-C----------ACCCTC-CCCCA--------GGTCAGGAAG--GACC-CACACGC-CTATTTCTCTTTGATCTGTGGAACGATGGCCC--------A-CCCACACCCACTTTGCTGCTGCTTGCT------TCCCTAAGAATGAA--------------- i calJac1.Contig5139 C 0 C 0 s oryLat2.scaffold4784 2650 154 - 5056 AGTAGAACCCTGAC-CTCAGAGTAAAACCCTGACCTCA--------GAGCAGAACCCTGACC-TCAGAGC-AAAACCCAGACCTAAGAGTAGAACCCTGACCTCAGAGTAGAACCCTGACC----TCAGAGCAGAACCCT------GACCTCAGAGTAGAACCCTGACCTCAGAG i oryLat2.scaffold4784 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e otoGar1.scaffold_94362.1-287808 16700 37 + 287808 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e bosTau4.chr19 10850597 89 - 65312493 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I a score=6569.000000 s hg19.chr17_gl000204_random 34530 23 + 81310 TAGCACTCT------GCAGGTAT-----CCCCAC-- s calJac1.Contig5139 35120 16 + 225949 CA-------------GCAGGTGT-----CCCCAC-- i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 32899 23 - 95547 CAGCACCCT------GCAGGTGT-----CCCCAC-- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75025649 23 + 78773432 CAGCACCCT------GCAGGTGT-----CCCCAC-- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16051087 23 + 17838096 CAACACCCT------GCAGGTGT-----CCCCAC-- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 4783 23 - 64270 CAGCACTCT------GCAGGTGT-----CCCCAC-- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79464173 23 + 83384210 CAGCACTCT------GCAGGTGT-----CCCCAC-- i panTro2.chr17 C 0 C 0 s tupBel1.scaffold_124459.1-15939 2489 23 + 15939 CAGAGCCCT------GCAGGCTC-----TCCCAG-- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s turTru1.scaffold_106006 118766 21 + 145505 GAGTCTG--------CCAGGACT-----GCCGGC-- i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58032949 22 - 61308211 GAGAACCT-------GCAGGACT-----CCCCAC-- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59427769 20 - 64418924 GGGCCTGC-------CCAGGACT-------CTGC-- i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 5347 19 + 132007 -CGCCCGG-------CCAGGACT-------CCAC-- i felCat3.scaffold_206428 C 0 C 0 s loxAfr3.scaffold_49 14421800 28 - 17734757 CAATACCTG------CAAGGAGCACTGGCCCCAC-- i loxAfr3.scaffold_49 I 1 I 22 s proCap1.scaffold_29042 5782 28 + 24616 TCATGCCTG------CCAGGAGCGCCAGCCCCAC-- i proCap1.scaffold_29042 I 1 I 20 s xenTro2.scaffold_1328 5742 23 - 113503 TAGTGTTCT------GTATGGGC-----CCCAGA-- i xenTro2.scaffold_1328 N 0 I 12 s oryLat2.scaffold4784 2804 31 - 5056 CAGAACCCTGACCTCAGAGTAGA-----ACCCAGAC i oryLat2.scaffold4784 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_89264 1166 3270 + 5251 M e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e otoGar1.scaffold_94362.1-287808 16700 37 + 287808 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e bosTau4.chr19 10850597 89 - 65312493 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I a score=-136569.000000 s hg19.chr17_gl000204_random 34553 31 + 81310 -------------------CCTTAAGCAC--------AGCCCTCCCCCAAG-----------------AGACCTG--------- s oryLat2.scaffold4784 2835 40 - 5056 CGGAGAGCAGAACGCTCACCTTAGAGTAG--------AACTTTGACCG------------------------------------ i oryLat2.scaffold4784 C 0 I 13 s xenTro2.scaffold_1328 5777 40 - 113503 -------------------CCTAGTGTCCAGGGTAAGAGCCCAGCCTAGTGTTCTGTAT------------------------- i xenTro2.scaffold_1328 I 12 C 0 s proCap1.scaffold_29042 5830 27 + 24616 -------------------CCTTCACCCC------AGAGTCCTGTGTTGAGC-------------------------------- i proCap1.scaffold_29042 I 20 C 0 s loxAfr3.scaffold_49 14421850 31 - 17734757 -------------------CCTCCAGCCCCCA--AAGAGTCCAGCCCTGAGC-------------------------------- i loxAfr3.scaffold_49 I 22 C 0 s felCat3.scaffold_206428 5366 16 + 132007 -------------------CCTGAAACCC--------AGTCCT----------------------------------------- i felCat3.scaffold_206428 C 0 I 23 s canFam2.chr9 59427789 35 - 64418924 -------------------CCCGAAACCC--------AGGCCTGAGCTTGGTGGCCCCCAAG---------------------- i canFam2.chr9 C 0 I 110 s equCab2.chr11 58032971 38 - 61308211 -------------------CCCAAAGCCC--------AGTGCCGACCCGGGAAATGCCTCCCAGG------------------- i equCab2.chr11 C 0 C 0 s turTru1.scaffold_106006 118787 4 + 145505 -------------------CCCA------------------------------------------------------------- i turTru1.scaffold_106006 C 0 C 0 s tupBel1.scaffold_124459.1-15939 2512 30 + 15939 -------------------CCC---ACAC--------GGCCCTCCTCTGAG--------------CCCAGCCCC---------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s micMur1.scaffold_418 370977 25 - 520352 ----------------------------C--------CTTCTTTTCC-----------------------ACCCAGGAAGTGTC i micMur1.scaffold_418 n 0 C 0 s otoGar1.scaffold_4132.1-50298 45259 36 - 50298 -------------------CCTAAAGCTC--------AGCCTTGACCT---------------------GGCCTGCAAGGTGAG i otoGar1.scaffold_4132.1-50298 n 37 C 0 s calJac1.Contig5139 35136 33 + 225949 -------------------CCTGAAGCA----------GCCCTCCCCGGAA-----------------AGGGTCC-----AAGG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 32922 31 - 95547 -------------------CCTTAAGCAC--------AGCCCTCCCCCGAA-----------------AGACCTG--------- i papHam1.scaffold8336 C 0 I 4 s rheMac2.chr16 75025672 31 + 78773432 -------------------CCTTAAGCAC--------AGCCCTCCCCTGAA-----------------AGAcctg--------- i rheMac2.chr16 C 0 I 4 s ponAbe2.chr17_random 16051110 31 + 17838096 -------------------CCTTAAGCAC--------GGCCCTCCCCCGAA-----------------AGACCTG--------- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 4806 31 - 64270 -------------------CCTTAAGCAC--------GGCCCTCCCCCAGA-----------------AGACCTG--------- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79464196 31 + 83384210 -------------------CCTTAAGCAC--------GGCCCTCCCCGAAA-----------------AGACCTG--------- i panTro2.chr17 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e bosTau4.chr19 10850597 89 - 65312493 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I a score=-13976.000000 s hg19.chr17_gl000204_random 34584 16 + 81310 TCCT------GAGCTTGGACCT s panTro2.chr17 79464227 16 + 83384210 TACT------GAGCTTGGACCT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 4837 16 - 64270 TCCT------GAGCTTGGACCT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16051141 16 + 17838096 TCCT------GAGCTTGGACCT i ponAbe2.chr17_random C 0 C 0 s calJac1.Contig5139 35169 16 + 225949 TCCT------GAGCTTGGACCT i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_4132.1-50298 45295 22 - 50298 TCCTGCGGATCAGCCTTGACCT i otoGar1.scaffold_4132.1-50298 C 0 C 0 s micMur1.scaffold_418 371002 4 - 520352 TCCT------------------ i micMur1.scaffold_418 C 0 C 0 s tupBel1.scaffold_124459.1-15939 2542 3 + 15939 ----------AAG--------- i tupBel1.scaffold_124459.1-15939 C 0 I 80 s equCab2.chr11 58033009 1 - 61308211 -------------C-------- i equCab2.chr11 C 0 I 119 s loxAfr3.scaffold_49 14421881 8 - 17734757 --------------ATGGACCT i loxAfr3.scaffold_49 C 0 I 6 s proCap1.scaffold_29042 5857 8 + 24616 --------------AGGGACCT i proCap1.scaffold_29042 C 0 I 10 s petMar1.Contig50312 2649 16 + 9080 ------TCCTGAGTCCTCGCCT i petMar1.Contig50312 N 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e papHam1.scaffold8336 32953 4 - 95547 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e xenTro2.scaffold_1328 5817 0 - 113503 C e turTru1.scaffold_106006 118791 0 + 145505 C e felCat3.scaffold_206428 5382 23 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e oryLat2.scaffold4784 2875 13 - 5056 I e monDom5.chr2 304513626 3178 - 541556283 I e canFam2.chr9 59427824 110 - 64418924 I e bosTau4.chr19 10850597 89 - 65312493 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e rheMac2.chr16 75025703 4 + 78773432 I a score=111383.000000 s hg19.chr17_gl000204_random 34600 116 + 81310 GGGTGATATAACGAGA-CCCATC-CT--------------GAGCTT---GG-ACCTCGGCAATATAGTGAGACCCCATCCTG-AGCTTGGACCTGGGCCATATAGCGAGATCCCGTCCTGAGCTT---GGA--CCTGGGCCA s panTro2.chr17 79464243 116 + 83384210 GGGTGATATAACGAGA-CCCATC-CT--------------GAGCTT---GG-ACCTCGGCAATATAGTGAGACCCCATCCTG-AGCTTGGACCTGGGCCATATAGCGAGATCCCGTCCTGAGCTT---GGA--CCTGGGCCA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 4853 116 - 64270 GGGTGATATAACGAGA-CCCATC-CT--------------GAGCTT---GG-ACCTCGGCAATATAGTGAGACCCCATCCTG-AGCTTGGACCTGGGCCATATAGCGAGATCCCGTCCTGAGCCT---GGA--CCTGGGCCA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16051157 116 + 17838096 GGGTGATATAACGAGA-CCCATC-CT--------------GAGCTT---GG-ACCTGGGCCATATAGTGAGACCCCATCCCA-AGCTTGGACCTGGGCCGTATAGCGAGACCCCATCCTGAGCTT---GGA--CCTGGGCCA i ponAbe2.chr17_random C 0 C 0 s calJac1.Contig5139 35185 117 + 225949 GGGTGGTATAGTGAGATCCCATC-CT--------------GAGCTT---GG-ACCTGGGTGGTATAGTGAGATCCCATCCTG-AGCTTGGACCTGGGTGGTATAGTGAGATCCCATCCTGAGCTT---GGA--CCTGGGTGG i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_4132.1-50298 45317 112 - 50298 GGCCTGCATGATGAGT-CCTAAAGCT--------------CAGCCT---TG-ACCTGGCCTGCACATTGAG------TCCTGTAGCCTTGACCTGGCCTGCATGGTGAGTCCTGCAGTTCAGCCT---TGA--CCTGGCCTG i otoGar1.scaffold_4132.1-50298 C 0 C 0 s xenTro2.scaffold_1328 5817 130 - 113503 GGGCCCCAGAGTGAGAGCCCAGC-CTAGTGTCCAGGGTAAGAGCCC---AG--CCTAGTGTCCAGGGTAAGAGCTCAGCCTA-GTGTTCTGTATGGGCCCCAGAGTGAGAGCCCGGCCTAGTGTT---CTG--TATGGGCCC i xenTro2.scaffold_1328 C 0 C 0 s oryLat2.scaffold4784 2888 119 - 5056 TGACCTCAGAGTAAAACCCTGAC-CT--------------CAGAGC---AGAACCCTGACCTCAGAGTAGAACCCAAACCTG-AGAGTGGAACCCGGCTGCAGAGCAGAACCCTGACCTGAGAGT---AGAACCCTGACCC- i oryLat2.scaffold4784 I 13 I 19 s petMar1.Contig50312 2665 118 + 9080 -GGT----TAATGAGACTGCATC-CT--------------GACCTCCTGAG-TCCTCGCCTGGTTAATGAGACTGCATCCTG-ACCTGAGTCCTCGCCTGGTTAATGAGACTGCATCCTGACCTCCCGAGT--CCTCGCCTG i petMar1.Contig50312 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5865 10 + 24616 I e papHam1.scaffold8336 32953 4 - 95547 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e tupBel1.scaffold_124459.1-15939 2545 80 + 15939 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371006 0 - 520352 C e turTru1.scaffold_106006 118791 0 + 145505 C e felCat3.scaffold_206428 5382 23 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e canFam2.chr9 59427824 110 - 64418924 I e bosTau4.chr19 10850597 89 - 65312493 I e equCab2.chr11 58033010 119 - 61308211 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e loxAfr3.scaffold_49 14421889 6 - 17734757 I e rheMac2.chr16 75025703 4 + 78773432 I a score=68199.000000 s hg19.chr17_gl000204_random 34716 96 + 81310 TATAGTGAGACCCCATCCTGAACTTC---G-ACCTGGGCAATA-TAGCGAGAT-----------CCCATCCTGAGCT--TGGGCCTGGGCCC-TATAGCGAGACCCCATCCT-GAG s panTro2.chr17 79464359 96 + 83384210 TATAGTGAGACCCCATCCTGAGCTTC---G-ACCTGGGCAATA-TAGCGAGAT-----------CCCATCCTGAGCT--TGGGCCTGGGCCC-TATAGCGAGACCCCATCCT-GAG i panTro2.chr17 C 0 T 111 s gorGor1.Supercontig_0007361 4969 59 - 64270 TATAGTGAGACCCCATCCTAAGCTTC---G-ACCTGGGCAATA-TAGCGAGAC-----------CCCATCCTGAG----------------------------------------- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16051273 96 + 17838096 TATAGTGAGACCCCATCCTGAGCTTT---G-ACCTGGGCAATA-TAGCAAGAT-----------CCCGTCCTGAGCT--TGGGCCTCGGCCC-TATAGCGAGACCCCATCCT-GAG i ponAbe2.chr17_random C 0 C 0 s calJac1.Contig5139 35302 96 + 225949 TATAGTGAGATCCCATCCTGAGCTTG---G-ACCTGGGTGGTA-TAGTGAGAT-----------CCCATCCTGAGCT--TGGACCTGGGTGG-TATAGTGAGATCCCATCCT-GAG i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_418 371006 98 - 520352 TACAATGAGACACCAGCCTGGAATCC---A-GACAGGGCCTTACCAATGAGAC-----------ACCAGCCTGGAAT--CCAGACAGGGCCT-TACAATGAGACACCAGCCTGGAA i micMur1.scaffold_418 C 0 C 0 s otoGar1.scaffold_4132.1-50298 45429 96 - 50298 CACAGTGAG------TCCTGCAGTTC---A-GCCTTGACCTGGCCTGCAAGGTGAGTCCTGCGGATCAGCCTT---------GACCTGGCCTGCATGATGAGTCCTAAAGCT-CAG i otoGar1.scaffold_4132.1-50298 C 0 C 0 s xenTro2.scaffold_1328 5947 96 - 113503 CAGAGTGAGAGCCCAGCCTAGTGTTC---T-GTATGGGCCCCA-GAGTGAGAG-----------CCCAGCCTAGTGT--TCTGTATGGGCCC-CAGAGTGAGAGCCCAGCCT-AGT i xenTro2.scaffold_1328 C 0 C 0 s oryLat2.scaffold4784 3026 97 - 5056 TAGAGTAGAACCCTGACCTCAGAGCA---GAACCCTGACCTCA-GAGTAGAAC-----------CCAAACCTGAGAG--TGGAACCCGGCTG-CAGAGCAGAACCCTGACCT-GAG i oryLat2.scaffold4784 I 19 I 7 s petMar1.Contig50312 2783 102 + 9080 GTTAATGAGACTGCATCCTGACCTCCTGAG-TCCTCGCCTGGT-TAATGAGAC-----------TGCATCCTGACCTCCTGAGTCCTCGCCTGGTTAATGAGACTGCATCCT-GAC i petMar1.Contig50312 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5865 10 + 24616 I e papHam1.scaffold8336 32953 4 - 95547 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e tupBel1.scaffold_124459.1-15939 2545 80 + 15939 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e turTru1.scaffold_106006 118791 0 + 145505 C e felCat3.scaffold_206428 5382 23 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e canFam2.chr9 59427824 110 - 64418924 I e bosTau4.chr19 10850597 89 - 65312493 I e equCab2.chr11 58033010 119 - 61308211 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e loxAfr3.scaffold_49 14421889 6 - 17734757 I e rheMac2.chr16 75025703 4 + 78773432 I a score=24678.000000 s hg19.chr17_gl000204_random 34812 37 + 81310 CTTGGACCTGGG-------------CCATATAGTGAGACCCCGTCCTGCA s panTro2.chr17 79464344 37 + 83384210 CTTGGACCTGGG-------------CCATATAGTGAGACCCCATCCTGAG i panTro2.chr17 T 111 I 74 s gorGor1.Supercontig_0007361 5028 37 - 64270 CTTGGACCTGGG-------------CCATATAGTGAGACCCCATCCTGAG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16051369 37 + 17838096 CTTGGACCTGGG-------------CAATATAGCAAGACCCCATCCTGAG i ponAbe2.chr17_random C 0 C 0 s calJac1.Contig5139 35398 37 + 225949 CTTGGACCTGGG-------------TGGTATAGTGAGATCCCATCCTGAG i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_418 371104 36 - 520352 TCCAGACAGGGC-------------CT-TACAATGAGACACCAGCCTGGA i micMur1.scaffold_418 C 0 I 1 s otoGar1.scaffold_4132.1-50298 45525 31 - 50298 CCTTGACCTGGC-------------CTGCACATTGAG------TCCTGCA i otoGar1.scaffold_4132.1-50298 C 0 I 1 s xenTro2.scaffold_1328 6043 37 - 113503 GTTCTGTATGGG-------------CCCCAGAGTGAGAGCCCGGCCTAGT i xenTro2.scaffold_1328 C 0 C 0 s oryLat2.scaffold4784 3130 50 - 5056 CCCTGACCTGAGAGCAGAACCCTCACCTTAGAGTAGAACCCTGACCTCAG i oryLat2.scaffold4784 I 7 I 1 s petMar1.Contig50312 2885 3 + 9080 CTC----------------------------------------------- i petMar1.Contig50312 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5865 10 + 24616 I e papHam1.scaffold8336 32953 4 - 95547 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e tupBel1.scaffold_124459.1-15939 2545 80 + 15939 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e turTru1.scaffold_106006 118791 0 + 145505 C e felCat3.scaffold_206428 5382 23 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e canFam2.chr9 59427824 110 - 64418924 I e bosTau4.chr19 10850597 89 - 65312493 I e equCab2.chr11 58033010 119 - 61308211 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e loxAfr3.scaffold_49 14421889 6 - 17734757 I e rheMac2.chr16 75025703 4 + 78773432 I a score=30958.000000 s hg19.chr17_gl000204_random 34849 31 + 81310 CTTGGACCTGGGCCATATAGTGAGACCCCAT s panTro2.chr17 79464455 31 + 83384210 CTTAGACCTGGGCCATATAGTGAGACCCCAT i panTro2.chr17 I 74 C 0 s gorGor1.Supercontig_0007361 5065 31 - 64270 CCTGGACCTGGGCCATATAGTGAGACCCCAT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16051406 31 + 17838096 CTTGGCCCTGGGCCATACAGTGAGACCCCAT i ponAbe2.chr17_random C 0 C 0 s calJac1.Contig5139 35435 31 + 225949 CTCGGACCTGGGTGGTATAGTGAGATCCCAT i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_418 371141 30 - 520352 TCCAGACAGGGCCT-TACAATGAGACACCAG i micMur1.scaffold_418 I 1 n 1 s otoGar1.scaffold_4132.1-50298 45557 29 - 50298 CCTTGACCTGGCC--TGCATGGTGAGTCCTG i otoGar1.scaffold_4132.1-50298 I 1 I 2 s xenTro2.scaffold_1328 6080 31 - 113503 GTTCTGTATGGGCCCCAGAGTGAGAGCCCGG i xenTro2.scaffold_1328 C 0 C 0 s oryLat2.scaffold4784 3181 31 - 5056 GCAGAACCCTGACCTCAGAGTAGAACCCAAA i oryLat2.scaffold4784 I 1 C 0 s petMar1.Contig50312 2888 31 + 9080 CTGAGTCCTCGCCTGGTTAATGAGACTGCAT i petMar1.Contig50312 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5865 10 + 24616 I e papHam1.scaffold8336 32953 4 - 95547 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e tupBel1.scaffold_124459.1-15939 2545 80 + 15939 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e turTru1.scaffold_106006 118791 0 + 145505 C e felCat3.scaffold_206428 5382 23 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e canFam2.chr9 59427824 110 - 64418924 I e bosTau4.chr19 10850597 89 - 65312493 I e equCab2.chr11 58033010 119 - 61308211 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e loxAfr3.scaffold_49 14421889 6 - 17734757 I e rheMac2.chr16 75025703 4 + 78773432 I a score=52551.000000 s hg19.chr17_gl000204_random 34880 40 + 81310 CCTGAGCTTG---GACCTGGGCCATATAGTGAGACCCCATCCT s panTro2.chr17 79464486 40 + 83384210 CCTGAGCTTC---GACCTGGGCCATATAGTGAGACCCCATCCT i panTro2.chr17 C 0 T 74 s gorGor1.Supercontig_0007361 5096 40 - 64270 CCTGAGCTTG---GACCTGGGCCATATAGTGAGACCCCATCCT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16051437 40 + 17838096 CCTGAGCTTG---GACCTGGGCCATATAGCGAGATCCCATCTT i ponAbe2.chr17_random C 0 C 0 s calJac1.Contig5139 35466 40 + 225949 CCTGAGCTCG---GACCTGGGTGGTATAGTGAGATCCCATCCT i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_4132.1-50298 45588 34 - 50298 GTTCAGCCTT---GACCTGGCCTGCACAGTGAG------TCCT i otoGar1.scaffold_4132.1-50298 I 2 I 6 s xenTro2.scaffold_1328 6111 40 - 113503 CCTAGTGTTC---TGTATGGGCCCCAGAGTGAGAGCCCGGCCT i xenTro2.scaffold_1328 C 0 I 26 s oryLat2.scaffold4784 3212 40 - 5056 CCTGAGAGTG---GAACCCGGCTGCAGAGCAGAACCCTGACCT i oryLat2.scaffold4784 C 0 I 7 s petMar1.Contig50312 2919 43 + 9080 CCTGACCTCCTGAGTCCTCGCCTGGTTAATGAGACTGCATCCT i petMar1.Contig50312 C 0 T 155 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5865 10 + 24616 I e papHam1.scaffold8336 32953 4 - 95547 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e tupBel1.scaffold_124459.1-15939 2545 80 + 15939 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e turTru1.scaffold_106006 118791 0 + 145505 C e felCat3.scaffold_206428 5382 23 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e canFam2.chr9 59427824 110 - 64418924 I e bosTau4.chr19 10850597 89 - 65312493 I e equCab2.chr11 58033010 119 - 61308211 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e loxAfr3.scaffold_49 14421889 6 - 17734757 I e rheMac2.chr16 75025703 4 + 78773432 I a score=62248.000000 s hg19.chr17_gl000204_random 34920 37 + 81310 GAGCTTGGACCTGGGCCATATAGTGAGA-CC--CCGTCCT s panTro2.chr17 79464452 37 + 83384210 GAGCTTAGACCTGGGCCATATAGTGAGA-CC--CCATCCT i panTro2.chr17 T 74 I 37 s gorGor1.Supercontig_0007361 5136 38 - 64270 GAGCTTGGACCTGGGCCATATAGTGAGACCC--CCATCCT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16051477 29 + 17838096 GAGCTTGGACCTGGGCCATATAGTGAGA-C---------- i ponAbe2.chr17_random C 0 I 230 s rheMac2.chr16 75025707 37 + 78773432 gagcctggacctgggccatatagcgaga-cc--ctgtcct i rheMac2.chr16 I 4 C 0 s papHam1.scaffold8336 32957 37 - 95547 GAGCCTGGACCTGGGCCATATAGCGAGA-CC--CCGTCCT i papHam1.scaffold8336 I 4 C 0 s calJac1.Contig5139 35506 37 + 225949 GAGCTCGGACCTGGGTGGTATAGTGAGA-TC--CCATCCT i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_4132.1-50298 45628 37 - 50298 CAGCCTTGACCTGGCCTGCATGGTGAGT-CCTGCAGTT-- i otoGar1.scaffold_4132.1-50298 I 6 C 0 s xenTro2.scaffold_1328 6177 36 - 113503 GTGTTCTG-TATGGGCCCCAGAGTGAGA-GC--CCAGCCT i xenTro2.scaffold_1328 I 26 I 14 s oryLat2.scaffold4784 3259 31 - 5056 GAACCCTGACCTAGG------AGCAGAA-CC--CTGACCT i oryLat2.scaffold4784 I 7 I 7 s petMar1.Contig50312 2807 35 + 9080 --CCTGAGTCCTCGCCTGGTTAATGAGA-CT--GCATCCT i petMar1.Contig50312 T 155 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5865 10 + 24616 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e tupBel1.scaffold_124459.1-15939 2545 80 + 15939 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e turTru1.scaffold_106006 118791 0 + 145505 C e felCat3.scaffold_206428 5382 23 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e canFam2.chr9 59427824 110 - 64418924 I e bosTau4.chr19 10850597 89 - 65312493 I e equCab2.chr11 58033010 119 - 61308211 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e loxAfr3.scaffold_49 14421889 6 - 17734757 I a score=86117.000000 s hg19.chr17_gl000204_random 34957 61 + 81310 --------GAGCTTGGACC-----------TGGGCCATATAGTGAGACC--CCGTCCT--------------GAGCTTGGACAGTTCTTTCAGGGC- s otoGar1.scaffold_4132.1-50298 45665 44 - 50298 --------CAGCCTTGACC-----------TGGCCTGCACAGTGAGTCCTGCAGCCTT--------------GACCT-------------------- i otoGar1.scaffold_4132.1-50298 C 0 n 0 s calJac1.Contig5139 35543 47 + 225949 --------GAGCTCGGACC-----------TGGGTGGTATAGTGAGATC--CCATCCT--------------GAGCTCGGAC--------------- i calJac1.Contig5139 C 0 I 198 s papHam1.scaffold8336 32994 61 - 95547 --------GAGCCTGGACC-----------TGGGCCATATAGTGAGACC--CCATCCT--------------GAGCTTGGACAAGTCTTTCAGGGC- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75025744 61 + 78773432 --------gagcctggacc-----------tgggccatatagtgagacc--ccgtcct--------------gagcttggacAGGTCTTTCAGGGC- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16051736 61 + 17838096 --------GAGCTTGGACC-----------TGGGCCATATAGCAAGACC--CCGTCCT--------------GAGCTTGGACAGGTCTTTCAGGGC- i ponAbe2.chr17_random I 230 C 0 s gorGor1.Supercontig_0007361 5174 61 - 64270 --------GAGCTTGGACC-----------TGGGCCATATAGTGAGACC--CCGTCCT--------------GAGCTTGGACAGTTCTTTCAGGGC- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79464526 61 + 83384210 --------GAGCTTCGACC-----------TGGGCCATATAGTGAGACC--CCGTCCT--------------GAGCTTGGACAGTTCTTTCAGGGC- i panTro2.chr17 I 37 C 0 s turTru1.scaffold_106006 118791 35 + 145505 -------------------------------------------GAAGCC--CAGTCCT--------------GAGCTTGGACATGCCTCCCAGG--- i turTru1.scaffold_106006 C 0 C 0 s xenTro2.scaffold_1328 6227 70 - 113503 --------GAGCTCAGCCTAGTGTTCTGTATGGGCCCCAGAGTGAGAGC--CCAGCCTAGTGTCCAGGGTAAGAGCTCAG----------------- i xenTro2.scaffold_1328 I 14 C 0 s oryLat2.scaffold4784 3297 56 - 5056 --------GAACCCTGACC-----------TGAG------AGTAGAACC--CTGACCT--------------GAAAGTGGAACGCTGACGTGAGACT i oryLat2.scaffold4784 I 7 C 0 s petMar1.Contig50312 2842 45 + 9080 GACCTCCTGAGTCCTCGCC-----------TGGT-----TAATGAGACT--GCATCCT--------------GACCT-------------------- i petMar1.Contig50312 C 0 N 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5865 10 + 24616 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e tupBel1.scaffold_124459.1-15939 2545 80 + 15939 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e felCat3.scaffold_206428 5382 23 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e canFam2.chr9 59427824 110 - 64418924 I e bosTau4.chr19 10850597 89 - 65312493 I e equCab2.chr11 58033010 119 - 61308211 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e loxAfr3.scaffold_49 14421889 6 - 17734757 I a score=183698.000000 s hg19.chr17_gl000204_random 35018 147 + 81310 ATAGCAGTGCTCAAGGGTGGGGAACTTAAGGAACTGCCTGGGAGGGGGCATTAGAGctggggctaccataacaca-ggactg--ca-cactggcggccacaaacaacagcatgaatcctcttgcgctgcggcaggctgccgtctgagtctg----------- s calJac1.Contig5139 35788 149 + 225949 ACAGCAATGCTCAAGGGTGGGGAACTTAAGGAACTGCCTCAGAGGGGGCATTCACACTGGGGCTGCCCTTACACA-GGACCATGCA-CACTGGCAGCCACAAACAATGGCAGGGACCCCCTCGAACTGCGTGAGGCTGCCACCCGAGTTGG----------- i calJac1.Contig5139 I 198 C 0 s papHam1.scaffold8336 33055 146 - 95547 ACAGCAGTGCTCAAGGGCAGGAAACTTAAGGAA-TGCCTCAGAGGGGGCATCAGCGctggggctaccataacaca-ggacca--ca-cactggcggccacaaacaacagcatagatcctctcgcgctgtggcaggctgctgtctgagtcag----------- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75025805 146 + 78773432 ACAGCAGTGCTCGAGGGCAGGAAACTTAAGGAA-TGCCTCAGAGGGGGCATCAGCGctggggctatcataacaca-ggacca--ca-cactggcggccacaaacaacagcatagatcctctcgcgctgcggcaggctgctgtctgagtcag----------- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16051797 147 + 17838096 ATAGCAGTGCTCAAGGGTGGGGAACATAAGGAACTGCCTGGGAGGGAgcattagtgctggggctaccataacaca-ggacta--ca-caccggcggccacaaacaacagcatggatcctctcgcgttgcggcaggctgccgtctgagtctc----------- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 5235 147 - 64270 ATAGCAGTGCTCAAGGGTGGGGAACTTAAGGAACTGCCTGGGAGGGGgcattagcactggggctaccataacaca-ggacta--ca-cactggcagccacaaacaacagcatggatcctctcatgctgtggcaggctgccgtctgagtctg----------- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79464587 147 + 83384210 ATAGCAGTGCTCAAGGGTGAGGAACTTAAGGAACTGCCTGGGAGGGGgcattagcgctggggctaccataacaca-ggacta--ca-cactggcggccacaaacaacagcatgaatcctcttgcgctgcagcaggctgccgtctgagtctg----------- i panTro2.chr17 C 0 C 0 s turTru1.scaffold_106006 118826 108 + 145505 ----------------------------------TGACTGGGTGagtgtc------ctggggcagccctatcaaa-ggacca--caccatgggtggcttaagacaacaggaatcgatccctcacagtctggaggtgagaagtccaagatca----------- i turTru1.scaffold_106006 C 0 I 5 s xenTro2.scaffold_1328 6297 98 - 113503 ------------------------CCTAGTGTTCTGTATGGGCCCCAGAGTGAGAGCTCAGCCTAGTGTTCTGTATGGGCCC--CA-GAGTGAGAGCC--------CGGC---------CTAGTGTTCTGTATGG-----GCCCCAG--------------- i xenTro2.scaffold_1328 C 0 C 0 s oryLat2.scaffold4784 3353 146 - 5056 ACAACCCTGACCTGAGAGTAGAACCCTGA-------CCTCAGAGTAGAACCCTGACCTGAGAGTAGAAC----CC-TGACCT--CA-GAGTAGAACCCAAACCTAAGAGT-GGAACCCGGCTGCAGAGCAGAACCCTGACCTGAGAGCAGAACCCTGACCTG i oryLat2.scaffold4784 C 0 N 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5865 10 + 24616 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e tupBel1.scaffold_124459.1-15939 2545 80 + 15939 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e felCat3.scaffold_206428 5382 23 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e otoGar1.scaffold_4132.1-50298 45709 0 - 50298 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e canFam2.chr9 59427824 110 - 64418924 I e bosTau4.chr19 10850597 89 - 65312493 I e equCab2.chr11 58033010 119 - 61308211 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e loxAfr3.scaffold_49 14421889 6 - 17734757 I a score=195480.000000 s hg19.chr17_gl000204_random 35165 111 + 81310 ggtgtggactcc-gcaggtgggcttcttctgggggctctgagcgagg----atccgccccagggctc--tcctggctttag-----gtgct--------ctcctgagtgtccgt-ggcctgtggctggctca s calJac1.Contig5139 35937 112 + 225949 GGTGTGGACTACTGCAggtgagctctttctgggggctctgagtgaga----atccgccccaggcctc--tcctggcttcca-----gtgct--------cccctgagtactggg-agcctgtggcccactgg i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 33201 112 - 95547 ggtgtggactccggcaggtgggctccttttgggggctctaagcgaga----atccaccccaggcctc--tcctggctttgg-----gtgct--------cccctgagtgccggt-ggcctgtggctgcctca i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75025951 112 + 78773432 ggtgtggactccggcaggtgggctccttttgggggctctgagcgaga----atccaccccaggcctc--tcctggctttgg-----gagct--------cccctgagtgccggt-ggcctgtggctgcctcg i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16051944 112 + 17838096 ggtgtggactccagcaggtgggctccttttaggggctctgagcaaga----atccaccccaggcctc--tcctggctttgg-----gtgct--------ctcctgagtgtcagc-ggcctgtggctggctcg i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 5382 112 - 64270 ggtgtggactccggcaggtgggcttcttctgggggctctgagcgaga----atccgccccagggctc--tcctggctttag-----gtgct--------ctcctgagtgtccgt-ggcctgtggctggctca i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79464734 112 + 83384210 ggtgtggactccggcaggtgggctttttctgggggctctgagcgaga----atccgccccagggctc--tcctggctttag-----gtgct--------ctcctgagtgtccgt-ggcctgtggctggctca i panTro2.chr17 C 0 C 0 s turTru1.scaffold_106006 118939 120 + 145505 ggcacgtgcgaggctga------ctccttcggaggctgtgagggaggatccatccaccccggacctctgtcctagcttcac-----gtgttgcctgca-accctcagcgtcccttgacaggtagacgcatcc i turTru1.scaffold_106006 I 5 C 0 s equCab2.chr11 58033129 114 - 61308211 ggcgagggcggcgccgg------ttcc-tctgaggctctgaggagg-----agctgccccgggcccctctcctggcctcat-----gtgttgccaagc-atcgtcggtgtccctgggcttacagacgcctca i equCab2.chr11 I 119 C 0 s xenTro2.scaffold_1328 6395 106 - 113503 AGTGAGAGC-CCGGCCAGTG---TTCTGTATGGGCCCCAGAGTGAGA----GCCCGGCCTAGTGTTCTGTATGGGCCCCAGAGTGAGAGCT--------CAGCCTAGTGTCCAG-GGTAAGAG--------- i xenTro2.scaffold_1328 C 0 N 0 s otoGar1.scaffold_94362.1-287808 16737 98 + 287808 --------------------GGTTCCTTCTGGAGGCTCTGACAGAAG----GCCTCACCCCGGCCTC--TGCTGGCTTCT------GTGCTGTGGGCGGCTCCCAGGCACCCCT--GCTAGTGGCCACGTCA i otoGar1.scaffold_94362.1-287808 I 37 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5865 10 + 24616 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e tupBel1.scaffold_124459.1-15939 2545 80 + 15939 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e felCat3.scaffold_206428 5382 23 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e canFam2.chr9 59427824 110 - 64418924 I e bosTau4.chr19 10850597 89 - 65312493 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e loxAfr3.scaffold_49 14421889 6 - 17734757 I a score=56862.000000 s hg19.chr17_gl000204_random 35276 47 + 81310 ccccagc--caagtgctgtcttctccctgtc---tctccacatcaccgtccc s otoGar1.scaffold_94362.1-287808 16835 48 + 287808 CTCCAGCTGCAAG-GCCACCTTCTCCTTGTG---TCTTCACATCATCTTCCA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s calJac1.Contig5139 36049 46 + 225949 ccccagc--catgtggtgtctt-tctctgtc---tctccacatcaccctcct i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 33313 47 - 95547 gcccagc--caagtgctgtcttctccctgtc---tcttcacatcaccctccc i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75026063 47 + 78773432 gcccagc--caagtgctgtcttctccctgtc---tctccacatcaccctccc i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16052056 47 + 17838096 ccccagc--caagtgctgtcttctccctgtc---tctccacatcaccgtccc i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 5494 45 - 64270 ccccagc--caagtgctgtcttctcc--ntc---tctccacatcaccgtccc i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79464846 47 + 83384210 ccccagc--caagtgctgtcttctccctgtc---tctccacatcaccgtccc i panTro2.chr17 C 0 C 0 s turTru1.scaffold_106006 119059 37 + 145505 cttctgt------------cacatggccatc---ttctccctttgtcttcac i turTru1.scaffold_106006 C 0 I 9 s canFam2.chr9 59427934 36 - 64418924 -CCCCCC------------CAAAACACACCc---tccccactctgccctccc i canFam2.chr9 I 110 I 10 s tupBel1.scaffold_124459.1-15939 2625 43 + 15939 ---------CAGGTGCTGAGTGGGGCCTGCCAGGCCTCTGCGTCCGAGTCCC i tupBel1.scaffold_124459.1-15939 I 80 C 0 s equCab2.chr11 58033243 21 - 61308211 --------------------------ctcca---gtccca--cggccgtacc i equCab2.chr11 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5865 10 + 24616 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e felCat3.scaffold_206428 5382 23 + 132007 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e bosTau4.chr19 10850597 89 - 65312493 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e loxAfr3.scaffold_49 14421889 6 - 17734757 I a score=245853.000000 s hg19.chr17_gl000204_random 35323 110 + 81310 ct--gtttgtgcctctgt--gtcctgatttacccttcagataaggaca---ccagtcctgttggattagggcc-----------cccca-----------t-----------------cc------cctctgagaagaccctgtctctaa----ggtcacattctg s tupBel1.scaffold_124459.1-15939 2668 116 + 15939 ACGAGTCTTTCCCTCCGTGGGTCCAAACGTCCTCTTCTCATAGAGACAAGGCCAG----GCTGCATCAGAGCCAGCCGC----ATTCCA-----------C-----------------CCTGACGACTTCAGCAAAGACACTGTCTCCCT--------------TA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s otoGar1.scaffold_94362.1-287808 16883 71 + 287808 CA--AAc--caccctaat--gtccttgtct-----------------------------------------ca-----------tctca-----------c-----------------aa------cttccatgaaga--ctgtctccag-tgaggtcacattctg i otoGar1.scaffold_94362.1-287808 C 0 C 0 s calJac1.Contig5139 36095 129 + 225949 ----gtttgtgcctctgt--gtcctgatttacccttcagatgaggaca---tcagttctgttggattagggtc-----------cccca-----------tgcccttgttctaacttgcc------cctctgaaaagaccctgtctctaaataaagtcacattctg i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 33360 110 - 95547 ct--gtttgtgcctctgt--gtcctgatataccctgcggataaggaca---ccagttctgttggattagggtc-----------cccca-----------t-----------------cc------cctctgagaagaccctgtctctaa----ggtcacattctg i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75026110 108 + 78773432 ----gtttgtgcctctgt--gtcctgatataccctgaggataaggaca---ccagtcctgttggattagggcc-----------cccca-----------t-----------------cc------cctctgagaagaccctgtctctaa----ggtcacattctg i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16052103 108 + 17838096 ct--gtttgtgcctctgt--gtcctgatttacccttcggataa-gaca---ccagtcctgttagattagggcc-----------cccca-----------t-----------------cc------cctctgagcagaccctgtctctaa-----gtcacattctg i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 5539 110 - 64270 ct--gtttgtgcctctgt--gtcctgatttacccttcggataaggaca---ccagtcctgttggattagggcc-----------cccca-----------t-----------------cc------cctctgagaagaccctgtctctaa----ggtcacattctg i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79464893 110 + 83384210 ct--gtttgtgcctctgt--gtcctgatttacccttcggataaggaca---ccagtactgttggattagggcc-----------cccca-----------t-----------------cc------cctctgagaagaccctgtctctaa----ggtcacattctg i panTro2.chr17 C 0 C 0 s turTru1.scaffold_106006 119105 134 + 145505 ct--ctgggcaagtctgc--atccgaatttccccttttcataaggaca---ccagtcctataggattagg-cccaccctaatgacctcattttaacttgat-----------------ta-------ccctgtaaagaccctattttcagataaggttacattttg i turTru1.scaffold_106006 I 9 C 0 s canFam2.chr9 59427980 122 - 64418924 ca--gtatgcatgt-gga--gcccaaatgtccccttctgataaggaca---ccagtcctatcggatggtg----------atgacttcattttagct---g-----------------ca------tccccgtgagcaccctgtttccgaagaaagccacgttctg i canFam2.chr9 I 10 C 0 s felCat3.scaffold_206428 5405 132 + 132007 ct--gtgtgcacgtctgc--ctccgagtgtcccc-tctggtaaggaca---gtggtcatactggatcagggctggtccttatgacctcattttaact---c-----------------ca------tccctgtaaagaccccatttccaaagaaggccaggttctg i felCat3.scaffold_206428 I 23 C 0 s equCab2.chr11 58033264 136 - 61308211 ct--gtgtgcatgtctgt--gtccgaatgtcccctttttatggggaca---ccagtcgtattggatcagagcccaccctaatggcttcaccttaacttgac-----------------ca------cccctgtaaagaccccgtttccaaacgaggccacatgcgg i equCab2.chr11 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5865 10 + 24616 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e bosTau4.chr19 10850597 89 - 65312493 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e loxAfr3.scaffold_49 14421889 6 - 17734757 I a score=78318.000000 s hg19.chr17_gl000204_random 35433 28 + 81310 agg------tcccggaggttaggacgtcaacatg s tupBel1.scaffold_124459.1-15939 2784 19 + 15939 AGG----------AGGGGCCGGGGTGTCG----- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s otoGar1.scaffold_94362.1-287808 16954 27 + 287808 agg-------cctgggggtcaggacttcaacgta i otoGar1.scaffold_94362.1-287808 C 0 C 0 s calJac1.Contig5139 36224 28 + 225949 agg------tcccggggcttaggacgtcagcaca i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 33470 23 - 95547 agg------tcccagaggttaggacatca----- i papHam1.scaffold8336 C 0 I 157 s rheMac2.chr16 75026218 28 + 78773432 agg------tcccagaggttaggacatcaacatg i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16052211 24 + 17838096 agg------tcct-gaggt--aggcgtca-catg i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 5649 28 - 64270 agg------tcccggaggttaggacgtcaacatg i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79465003 28 + 83384210 agg------tcccggaggttaggacgtcagcatg i panTro2.chr17 C 0 C 0 s turTru1.scaffold_106006 119239 34 + 145505 aggtaaacttactggaggttaggacttcaacata i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10850686 28 - 65312493 agg------tactggtgtttatgacttcagcata i bosTau4.chr19 I 89 C 0 s canFam2.chr9 59428102 28 - 64418924 agg------tcctagggcttgggactccatcgcg i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 5537 28 + 132007 acg------tcctgggggttaggattccaaccta i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58033400 27 - 61308211 agg------cactggggc-taggacttcaacgta i equCab2.chr11 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5865 10 + 24616 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e loxAfr3.scaffold_49 14421889 6 - 17734757 I a score=76767.000000 s hg19.chr17_gl000204_random 35461 29 + 81310 gctttttgggaggacatgattcagcccGA s equCab2.chr11 58033427 20 - 61308211 cccttctggggagacacagt--------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 5565 20 + 132007 actttttctggggacacaat--------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59428130 20 - 64418924 actttttgaggggacacaat--------- i canFam2.chr9 C 0 C 0 s bosTau4.chr19 10850714 20 - 65312493 tcttttgggggggacacaat--------- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 119273 20 + 145505 tctttgtggggggacacaTT--------- i turTru1.scaffold_106006 C 0 C 0 s speTri1.scaffold_128901 5 28 + 44242 GCCTCTTTGGAGGACA-AACTCAGCCCCG i speTri1.scaffold_128901 N 0 C 0 s tupBel1.scaffold_124459.1-15939 2803 25 + 15939 ----TTTTGGGAGACACAGGTGGGCCCAC i tupBel1.scaffold_124459.1-15939 C 0 I 1 s otoGar1.scaffold_94362.1-287808 16981 28 + 287808 -ccttttaggaggatgtaattcaacccag i otoGar1.scaffold_94362.1-287808 C 0 I 1 s calJac1.Contig5139 36252 29 + 225949 gctttttgggaggacatgattcagccaga i calJac1.Contig5139 C 0 C 0 s rheMac2.chr16 75026246 29 + 78773432 gctttttgggaggacatgattcagccTGA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16052235 29 + 17838096 gctttttgggaggacataatccagcccGA i ponAbe2.chr17_random C 0 I 361 s gorGor1.Supercontig_0007361 5677 29 - 64270 gctttttgggaggacatgattcagcccGA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79465031 29 + 83384210 gcttttggggaggacatgattcagcccGA i panTro2.chr17 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 5865 10 + 24616 I e papHam1.scaffold8336 33493 157 - 95547 I e tarSyr1.scaffold_131410 4708 1996 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e loxAfr3.scaffold_49 14421889 6 - 17734757 I a score=25052.000000 s hg19.chr17_gl000204_random 35490 51 + 81310 ATGGGTAGCCTCTT-CCCT------CCCAATCTCCTCC---------CTGCTGC-------CTGCCCAGGCTCC s calJac1.Contig5139 36281 51 + 225949 acaGGTAGCCTCTT-CCCT------CCCAGTCACCTCC---------CTGCTGC-------CTGCCCAGGCTCC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 33650 51 - 95547 GCGGATAGCCTCTT-CCCT------CCCAATCCCCTCC---------CTGCTGC-------CTGCCCAGGCTCC i papHam1.scaffold8336 I 157 C 0 s rheMac2.chr16 75026275 51 + 78773432 GCGGATAGCCTCTT-CCCT------CACAATCCCCTCC---------CTGCTGC-------CTGCCCAGGCTCC i rheMac2.chr16 C 0 C 0 s gorGor1.Supercontig_0007361 5706 51 - 64270 ATGAGTAGCCTCTT-CCCT------CCCAATCTCCTCC---------CTGCTGC-------CTGCCCAGGCTCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79465060 51 + 83384210 ATGGGTAGCCTCTT-CCCT------CCCAATCTCCTCC---------CTGCTGC-------CTGCCCAGGCTCC i panTro2.chr17 C 0 M 343 s tarSyr1.scaffold_131410 6723 24 + 8975 ----------------------------------CTCC---------CCACTGC-------CTCTCCAGGCTCC i tarSyr1.scaffold_131410 M 1996 C 0 s otoGar1.scaffold_94362.1-287808 17010 60 + 287808 acaGGCAGCCTCTC-CCCT------CCTGACACCCTCCATCACACTACCCCTGC-------CTCCCCAGGCTCC i otoGar1.scaffold_94362.1-287808 I 1 I 1 s tupBel1.scaffold_124459.1-15939 2829 47 + 15939 TTGGGCGGCCTCCCATTCT------CCCAGC-----CC---------CAGCCTT-------CCCCCAGGGATCC i tupBel1.scaffold_124459.1-15939 I 1 I 1 s speTri1.scaffold_128901 33 51 + 44242 ACAGGCAGTCTTTC-CCTC------CAGACGCTCCCCA---------GGGCCTG-------CTCCCCAGCCTCC i speTri1.scaffold_128901 C 0 I 8 s turTru1.scaffold_106006 119293 23 + 145505 ---------------------------------CCTCC---------CC-CT-T-------GACCCCAGGCTCC i turTru1.scaffold_106006 C 0 I 2 s bosTau4.chr19 10850734 24 - 65312493 ---------------------------------tcTCC---------CCTCT-T-------GCCCTCAGGCTCC i bosTau4.chr19 C 0 I 2 s canFam2.chr9 59428150 21 - 64418924 ---------------------------------tcTTC---------CC----T-------CCGGCCAGGCTCC i canFam2.chr9 C 0 I 2 s felCat3.scaffold_206428 5585 21 + 132007 ---------------------------------tcTTC---------CC----T-------TCCCCCAGGTGCC i felCat3.scaffold_206428 C 0 I 2 s equCab2.chr11 58033447 21 - 61308211 ---------------------------------ccTTC---------CT----C-------CTCCCCAGGTTCC i equCab2.chr11 C 0 I 2 s proCap1.scaffold_29042 5875 40 + 24616 -------------------------CCCACCCACCTCT---------CTGCCATGCGTGCCCTCACTGGGCTGC i proCap1.scaffold_29042 I 10 C 0 s loxAfr3.scaffold_49 14421895 63 - 17734757 AAGGGCGGTTTTCT-CCctcccacccccaccccgctcc---------ccacccc-cttccccgcccTGGGCTGC i loxAfr3.scaffold_49 I 6 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e ponAbe2.chr17_random 16052264 361 + 17838096 I a score=-66278.000000 s hg19.chr17_gl000204_random 35541 44 + 81310 TGGAGCTTCCCTG---GGACGCCCTG----GGGGCTG--------------------TACCAGAAATGCAC s gorGor1.Supercontig_0007361 5757 44 - 64270 TGGAGCTTCCCCG---GGAGGCCCTG----GGGGCTG--------------------TACCAGAAATGCAC i gorGor1.Supercontig_0007361 C 0 C 0 s rheMac2.chr16 75026326 44 + 78773432 TGGAGCTTCCCCG---GGAGGCCCTG----GGCGCTG--------------------TACCAGAAATGCAC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 33701 44 - 95547 TGGAGCTTCCCCG---GGAGGCCCTG----GGCGCTG--------------------TACCAGAAATGCAC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 36332 42 + 225949 TGGAGTGTCCCAG---GGAGG--GTG----GGGGCCA--------------------CACCAGAAATGCAC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 6747 51 + 8975 CAGTGCTGCCTGG---GAGGG--CTG----GGGGCCTG--------CACTCA---CCTACCAGAGCCGCGT i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 17071 52 + 287808 GGGTGCCTCCCAG---GGAGC--CTG----CGGGCTT---------CACACAGCCACCACCAGAAAC-CAT i otoGar1.scaffold_94362.1-287808 I 1 C 0 s tupBel1.scaffold_124459.1-15939 2877 57 + 15939 AGGAGCTCCTCCA---GGAGA--GCT----GGGGCTGGGGAGTCTACACACAGC---AACTAGAGGTCC-- i tupBel1.scaffold_124459.1-15939 I 1 C 0 s speTri1.scaffold_128901 92 48 + 44242 CTGTGC-TCCCAG---GAGGG--CCG----GGGCCTG---------CACACCC----GCCCCAAGGTGCGT i speTri1.scaffold_128901 I 8 C 0 s turTru1.scaffold_106006 119318 34 + 145505 TGTG--TCCCCTG---GGA-GGCAGG----TGGGCCT---------CACACAC------------------ i turTru1.scaffold_106006 I 2 I 14 s bosTau4.chr19 10850760 35 - 65312493 TGTG--CCCCCTG---GGAGGGCAGG----TGGGCTT---------CGCACAC------------------ i bosTau4.chr19 I 2 I 14 s canFam2.chr9 59428173 34 - 64418924 CG---CTCCCCTG---GGAGGGCCCG----CGAGCCA---------CATGCAG------------------ i canFam2.chr9 I 2 I 14 s felCat3.scaffold_206428 5608 31 + 132007 ------TCCCTTA---GGAGGGTGTG----CGAGCCG---------CACACGC------------------ i felCat3.scaffold_206428 I 2 I 14 s equCab2.chr11 58033470 39 - 61308211 TGAGCCTCCCAGGGGCGGGGGGCATG----TGGGCCT---------CGCACA------------------- i equCab2.chr11 I 2 C 0 s proCap1.scaffold_29042 5915 39 + 24616 CGTGGGCTTACCA---GAGGGGCA------GGGGTCC---------TACACAC----CCCT---------- i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14421958 44 - 17734757 TGTGAGTTTCCTG---GGAGGACACGGGAGGGGGGCC---------CACACA-----GCCT---------- i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e pteVam1.scaffold_11245 5919 201 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e panTro2.chr17 79465111 343 + 83384210 M e monDom5.chr2 304513626 3178 - 541556283 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e ponAbe2.chr17_random 16052264 361 + 17838096 I a score=42712.000000 s hg19.chr17_gl000204_random 35585 48 + 81310 GGGGAGGAGCTG-------------G-GA--CCCC----------CTGGAAGGGACCCTGGAGAACGGCAGTGA s gorGor1.Supercontig_0007361 5801 48 - 64270 GGGGAGGAGCTG-------------G-GA--CCCC----------CTGGAAGGGACTCCGGAGAACGGCAGTGA i gorGor1.Supercontig_0007361 C 0 C 0 s rheMac2.chr16 75026370 48 + 78773432 GGGGAGGAGCTG-------------G-GA--CCCC----------CTGGAAGGGGCTCTGGAGAACAGCAGTGA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 33745 48 - 95547 GGGGAGGAGCTG-------------G-GA--CCCC----------CTGGAAGGGGCTCTGGAGAACAGCAGTGA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 36374 48 + 225949 ATCGAGGAGCTG-------------G-GA--CCCC----------CTGGAAGGGGCTCTGGAGAACAGCAGTGA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 6798 45 + 8975 GGGAAGGAGTCG-------------G-GG--CTCA----------CTCGATGGGGTTCTGGAGGACAGAGG--- i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 17123 44 + 287808 GGGAAGGAGCCG-------------GAGA--GCCC----------CTGGAAGG--CTCTGGAGGAGGGCAG--- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 2934 36 + 15939 ---------CTG-------------G-GG--GTCC----------CCAGAAGCGGCTCCAGAGGAAGGCCG--- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s speTri1.scaffold_128901 140 37 + 44242 GGGAAGGAGCCC-------------A-GC--ATCC----------TGCAGAGGGGCTCTGGAG----------- i speTri1.scaffold_128901 C 0 C 0 s turTru1.scaffold_106006 119366 48 + 145505 GGGAAGGAGCAA-------------G-GACCGCCCC---------CCCAAGAGGACTGAGGAAGGTGCTAA--- i turTru1.scaffold_106006 I 14 C 0 s bosTau4.chr19 10850809 57 - 65312493 GGAAAGGAACAA-------------G-AATTGCCCCCTCATCTCACCCAAGAGGCCTGAGGAAGGTGCTCA--- i bosTau4.chr19 I 14 C 0 s equCab2.chr11 58033509 44 - 61308211 --GGAGGAGCTG-------------G-GGACCCTG----------CACAA-GGGCCCGAGGAGGACAGGCG--- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 5653 47 + 132007 CTGGAGGCACCA-------------G-GGATACCC----------CACAAGGGGCCTGAGGAAGGCGGTGG--- i felCat3.scaffold_206428 I 14 C 0 s canFam2.chr9 59428221 47 - 64418924 GGGAAGGAGCCA-------------G-GGATGGCC----------CACAAGGGGCCCGAGGAAGGCAGTGG--- i canFam2.chr9 I 14 C 0 s pteVam1.scaffold_11245 6120 46 + 48268 GGGGAGGAGCCA-------------A-GGGTCCCC----------CACGA-GGGTCTGGGGAAGGCGGTGA--- i pteVam1.scaffold_11245 I 201 C 0 s proCap1.scaffold_29042 5954 23 + 24616 ATCAGAGAGCAG-------------G-GA--CCTC----------CAG----------------A--------- i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14422002 51 - 17734757 ACCGGAGAGCAGGGGAAGGGGCTCTG-GA--CCTG----------CAGCA-GGGGCTCCGGAGAA--------- i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e panTro2.chr17 79465111 343 + 83384210 M e monDom5.chr2 304513626 3178 - 541556283 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I e ponAbe2.chr17_random 16052264 361 + 17838096 I a score=-239595.000000 s hg19.chr17_gl000204_random 35633 35 + 81310 AGAGGGGTC--ACATGCA------CCCCGACACCCT--------------------------------------------------------CCAC-ACA s gorGor1.Supercontig_0007361 5849 35 - 64270 AGAGGGGTC--ACATGCA------CCCTGACACCCT--------------------------------------------------------CCAC-ATA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79465464 36 + 83384210 AGAGGGTTC--ACNTGCA------CNCNGACACCCT--------------------------------------------------------CCACCACA i panTro2.chr17 M 343 C 0 s ponAbe2.chr17_random 16052625 11 + 17838096 --------------------------------CCCT--------------------------------------------------------CCAC-ACA i ponAbe2.chr17_random I 361 C 0 s rheMac2.chr16 75026418 35 + 78773432 AGAGGGGTC--ACACGCA------CCCCAACACCCC--------------------------------------------------------CCGC-GCA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 33793 35 - 95547 AGAGGGGTC--ACACGCA------CCCCAAAACCCC--------------------------------------------------------CCGC-GCA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 36422 91 + 225949 AGAGGGGCC--ACACGTA------CCCCAACACCCTCCATGCACCCCGACATCCCCCACACACCCTGACACCTCACACGCACCCCGACACTCCCAC-GCA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 6843 57 + 8975 GGAGGACTG--ACTCACC------CGATGAGGCTCTGGAGGACGGTGGGGAGGACTAG----------------------------------CCAC-ACA i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 17167 23 + 287808 ------------CATGCA------CCTCGACACCCC--------------------------------------------------------ACAC-A-- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 2970 16 + 15939 --------------------------------------AAGCAGGTG---------------------------------------------GCAA-GTA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s speTri1.scaffold_128901 177 6 + 44242 -----------------------------GGGCCC----------------------------------------------------------------- i speTri1.scaffold_128901 C 0 C 0 s turTru1.scaffold_106006 119414 27 + 145505 GGACAG-----GCCGGCT---------GCATGCCCT--------------------------------------------------------GCTC-A-- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10850866 24 - 65312493 GGACAG-----ACTGGGT------------CACCTC--------------------------------------------------------GCTC-A-- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58033553 29 - 61308211 -GACAGGGCTGACACGCC----------GGCACCCT---------------------------------------------------------CTC-C-- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 5700 41 + 132007 GGATGGATGGGACAGGCTACGGGCACTGGGCGCCCT--------------------------------------------------------GCTC-A-- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59428268 28 - 64418924 ----GGCCCAGACAGGCT------GCTGGG---CCT--------------------------------------------------------GCTC-A-- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 6166 31 + 48268 GGACGGCT---GCACGCG-------CTGGGTTCCCC--------------------------------------------------------GCTC-T-- i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 5977 23 + 24616 -GGAGGCCGGGGATGGCC------TGAGGA---------------------------------------------------------------------- i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14422053 23 - 17734757 -GGCGGCCAGGCCCGGCC------TGTGGA---------------------------------------------------------------------- i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e cavPor3.scaffold_76 4380872 975 + 7991924 I e mm9.chr11 118747819 2632 + 121843856 I a score=-41306.000000 s hg19.chr17_gl000204_random 35668 68 + 81310 CCCCAATACCCCCATGTGGGTTTGGCC---TGCATCGTCC---CACCAT--GGGGGG----------------------------TCTGTCCTTCCAGGT---CT--CG s gorGor1.Supercontig_0007361 5884 69 - 64270 CCCCAATACCCCCACGTGGGTTTGGCC---TGCATCGTCC---CACCACG-GGGGGG----------------------------TCTGTCCTTCCAGGT---CT--CG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79465500 68 + 83384210 CCCCAATACCCCCACGTGGGTTTGGCC---TGCATCGTCC---CACCAT--GGGGGG----------------------------TCTGTCCTTCCAGGT---CT--CG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16052636 68 + 17838096 CCCCAACACCCCCACGTGGGTTTGGCC---TGCATCGTCC---CACCAC--GTGGGG----------------------------TCTGTCCTTCCAGGT---CT--CG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75026453 68 + 78773432 CCCCGACACCCCCACGTGGGTTTGGCC---TGCATCGTCC---CACCAT--GGGGGG----------------------------TCTGTCCTTCCAGGT---CT--CG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 33828 68 - 95547 CCCCGACACCCCCACGTGGGTTTGGCC---TGCATCGTCC---CACCAC--GGGGGG----------------------------TCTGTCCTTCCAGGT---CT--CG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 36513 68 + 225949 CCCCAACACCCCCATGTGAGTTTGGCC---TGCATCGTCC---CACCAC--GGGGGG----------------------------TCTGTCCTTCCAGGT---CT--CA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 6900 68 + 8975 CACTGCACACTCCGCGGGGGGTTGTCC---TGCATTGTCC---CACCAC--AGGGTA----------------------------TCTGTCCTTCCAGGC---CT--CC i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 17190 43 + 287808 -------------------GTTTGTCC---CACGTGGTAC---CACCAC--GGTGG--------------------------------GTCCTTCCAGAC---TT---- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 2986 48 + 15939 CTCGGACATCCCTGTGAGAGTCTGTCC------------------CCGC--GTGG-------------------------------CCGTCCTTGCAGG---------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s speTri1.scaffold_128901 183 52 + 44242 ----------------TGGGTTTGTCC---GGCTTCCTCC---CTCCAC--AGCAGG----------------------------TCTGTCTCTCCAGGC---CT--CC i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4381847 39 + 7991924 --------------------------------cccctttc---cctctg--tgtgtc----------------------------tctgggtcctaaagt---cc--cc i cavPor3.scaffold_76 I 975 C 0 s turTru1.scaffold_106006 119441 67 + 145505 -------------------ATCTGTCC---TGCATC-CCC---CTGCACG-GGGGTG--GGGCTGGGGGGAGGTGGG---------CTGTCCTTCCAGCCTCTCT---- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10850890 79 - 65312493 -------------------ATCCATCC---TGCATCACCC---AAGCACA-GGCATGGAGGACAGAGTGGGGGTGGGGGCTGGCGTTTGTCCTTCCAGCCTCTCT---- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58033582 52 - 61308211 -------------------ATCTGTCC---TGCATCGCCC-GCCCGCACA-GGGGAG----------------------------TCTGTCCTTCCAGGC---CTCT-- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 5741 48 + 132007 -------------------GTC---CC---TGCACAACCCTGCACACACG-AGGGTG----------------------------TCTGCCTTTCCAGGC---CT---- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59428296 44 - 64418924 -------------------GTC---CC---TGCATGACCCTG----CATG-GGAGCG----------------------------GCTACCTTTCCAGGC---CT---- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 6197 45 + 48268 -------------------GTGTGTCC---TGCACGGTCC------CATTCGGGGTG----------------------------TCTGTCCTT-CAGGC---CT---- i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 6000 41 + 24616 CCCCAGCACCCTGGCACGGCTGCACCCTCGTGCAGCTTCT---G----------------------------------------------------------------- i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14422076 41 - 17734757 TCCTGGCACCCTAACGCAGCTGCGTCCATTTCCAGCCTCT---G----------------------------------------------------------------- i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 10217 1428 + 41507 I e ochPri2.scaffold_6980 56737 1113 + 61692 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e macEug1.Scaffold81348 5664 3367 - 9603 I e dasNov2.scaffold_28617 1900 1196 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e mm9.chr11 118747819 2632 + 121843856 I a score=-59604.000000 s hg19.chr17_gl000204_random 35736 22 + 81310 GCAAGGCCCAGG----CA---TGCTG-----------------GGG s dasNov2.scaffold_28617 3096 3 + 20752 -------------------------------------------GGG i dasNov2.scaffold_28617 I 1196 C 0 s loxAfr3.scaffold_49 14422117 24 - 17734757 CCGGGCCCCATG----CC---TGTCTGG---------------GGG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 6041 23 + 24616 CTGGGTCCCACG----CC---TGTCT-G---------------GGG i proCap1.scaffold_29042 C 0 C 0 s pteVam1.scaffold_11245 6242 17 + 48268 --AAGGCCCCGG----------GGTG-----------------GGG i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59428340 21 - 64418924 --GAGG-CCCAG----CGCC-AGGTG-----------------GGG i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 5789 22 + 132007 --AAGGCCCCAG----CACC-CGTGG-----------------GGG i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58033634 27 - 61308211 CGAAGG-CCCGGCTCCCGCC-AGGTG-----------------GGG i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10850969 22 - 65312493 ---AAGCCCCAC----CGCCAGGGTG-----------------GGG i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 119508 22 + 145505 --AAAGCCCCAT----CGCC-TGGTG-----------------GGA i turTru1.scaffold_106006 C 0 C 0 s oryCun2.chrUn0958 11645 21 + 41507 -GTGAGGCCCGG----TG---CCCGG-----------------GGC i oryCun2.chrUn0958 I 1428 C 0 s speTri1.scaffold_128901 235 21 + 44242 -ACAGGGCCCGG----CA---GCTGG-----------------GGG i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4381886 38 + 7991924 -ttttgataagg----at---gctggGTCACGACCAGATCCCTGGG i cavPor3.scaffold_76 C 0 C 0 s tupBel1.scaffold_124459.1-15939 3034 20 + 15939 --GAGGTCAGCG----CC---CAGTG-----------------GCG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s tarSyr1.scaffold_131410 6968 23 + 8975 GTACGGCCCCAG----TG---TGGAGA----------------GGA i tarSyr1.scaffold_131410 C 0 C 0 s calJac1.Contig5139 36581 22 + 225949 GCCAGGCCCGGG----CA---CGCTG-----------------GGG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 33896 22 - 95547 GCAAGGCCCAGG----CA---CGCTG-----------------GGG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75026521 22 + 78773432 GCAAGGCCCGGG----CA---CGCTG-----------------GGG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16052704 21 + 17838096 GCAAGG-CCAGG----CA---TGCTG-----------------GGG i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79465568 22 + 83384210 GCAAGGCCCAGG----CA---TGCTG-----------------GGG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 5953 22 - 64270 GCAAGGCCCGGG----CA---TGCTG-----------------GAG i gorGor1.Supercontig_0007361 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e macEug1.Scaffold81348 5664 3367 - 9603 I e otoGar1.scaffold_94362.1-287808 17233 0 + 287808 C e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304513626 3178 - 541556283 I e mm9.chr11 118747819 2632 + 121843856 I a score=1267429.000000 s hg19.chr17_gl000204_random 35758 123 + 81310 AGG--------GCTGTCAG--TTCAATGGTGGAC----ACCAGCGT-TTGATGTGGAG-ATT-TGGCAGTGAGAACGGATGTGCCTCAGTGCGAGGTTTATATAAAATG-ACAGATTCT--GGAAA-ATGAAGCCCTCAGATTA------ s gorGor1.Supercontig_0007361 5975 123 - 64270 AGG--------GCTGTCAG--TTCAATGGTGGAC----ACCAGCGT-TTGATGTGGAG-ATT-TGGCAGTGAGAACGGATGTGCCTCAGTGCGAGGTTTATATAAAATG-ACAGATTCT--GGAAA-ATGAAGCCCTCAGATTT------ i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79465590 123 + 83384210 AGG--------GCTGTCAG--TTCAATGGTGGAC----ACCAGCGT-TTGATGTGGAG-ATT-TGGCAGTGAGAACGGATGTGCCTCAGTGCGAGGTTTATATAAAATG-ACAGATTCT--GGAAA-ATGAAGCCCTCAGATTA------ i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16052725 123 + 17838096 AGG--------GCTGTCAG--TTCAATGGTGGAC----ACCAGCGT-TTGATGTGGAG-ATT-TGGCAGTGAGAACGGATGTGCCTCAGCGCGAGGTTTATATAAAATG-ACAGCTTCT--GGAAA-ATGAAGCCCTCAGATTA------ i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75026543 123 + 78773432 AGG--------GCTGTCAG--TTCAATGGTGGAC----ACCGGCGT-TTGATGTGGAG-ATT-TGGCAGTGAGAACGGATGTGCCTCCGCGCGAGGTTTATATAAAATG-ACAGCTTCT--GGAAA-ATGAAACCCTCAGATTA------ i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 33918 123 - 95547 AGG--------GCTGTCAG--TTCAATGGTGGAC----ACCAGCGT-TTGATGTGGAG-ATT-TGGCAGTGAGAACGGATGTGCCTCAGCGCGAGGTTTATATAAAATG-ACAGCTTCT--GGAAA-ATGAAACCCTCAGATTA------ i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 36603 123 + 225949 AGG--------ACTGTCAG--TTCAAGGGTGGAC----ACCAGCGT-TTGATGTGGAG-ATT-TGGCAGTGAGAACGGATATGCCTCAGCACGAGGTTTATATAAAATG-ACAGCTTCT--GGAAA-ATGAAGCCCTCAGATTA------ i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 6991 123 + 8975 AGG--------GCTGTCAG--CTCGACGGTGGAC----ACCAGTGT-TTGATGTGGAG-ATT-TGGCAGTGGGAGCGGGTGTGCCTCAGTGAGAGGTTTATGTGAAATG-ACAGCTTCT--GGGAA-ATGAAACCCTCTGATGA------ i tarSyr1.scaffold_131410 C 0 C 0 s tupBel1.scaffold_124459.1-15939 3054 122 + 15939 AGG--------GCTGTCAG--TTCGATGGCGGAC----ACCAGCGT-TTGATACGGAG-ATTCTGGCAGTGAGAATGGATGTGCCTCA-TGAGAGGTTGATGTGAGACG-ACGGCTTCT--GGGAA-ATGAAGCCCTCAGATT------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s cavPor3.scaffold_76 4381924 117 + 7991924 GAA--------GCTGTTAG--CTCCATGGTGGAT----GTCGGCAC-TGGAGATGGAA--TC-TGGCAGGGGATAGG----TGATGTGGTGAGAGGTCTATGCAGA-TGTACAACATCC--GGGGA--CGAAACCTTTGGCCCC------ i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 256 93 + 44242 GGA--------GCCGCCAG--TTCCACGGTGGAC----GCCAGCGT-TCGAGATGGAGACTC-TGGCTGTGCCT----------------------------CAAG-TG-ACAGCATCT--GGAAA---GGAGCCCGCAGCCTG------ i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 11666 92 + 41507 AGG--------GCCGTGGG--CTCAGCACTGGCC----CCCAGTGC-GTGACTCGGAG------GAGTGGGAAG-------------GGTGAGAGGTTTGTGCAAA----GCAAGAT------------GCAGCCCTCAGAT-------- i oryCun2.chrUn0958 C 0 I 1 s turTru1.scaffold_106006 119530 124 + 145505 AGG--------GCTGGCAG--TTCCACAGTGTAT----TCCAGTGT-TTGATATGGAG-ATTCTGGCAGTGAGAATGGATGAGCCTTGGTCAGAGGTTTATGTAAAATG-ACAGCTTCT--GGAGA-ATGAAGCCCTGGGATTA------ i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10850991 126 - 65312493 GGG------TTGCTGTCAG--TTCCACAGTGGAT----GCCTGTGT-TTGATATGGAG-ATTTCGGCAGTGAGAATGCATGTGCCTCGGTCAGAGGTTTATACAAAATG-ACAGCTTCT--GGAGA-AAGAAGCCCTGGGATTA------ i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58033661 114 - 61308211 AGG--------GCCAGCAG---TCCAGGGCCCA-----GCCGGTGT-TTGGGA-GGAG-ATGCTGGCGGTGAGAACGGACG-GCCCCAGTGAGCGGTTAATGTAAAATG-ACAGCTTTC--GGAGA-AGGGAGCCCTC------------ i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 5811 116 + 132007 GCA-------GGCAGTCAG--TTCCAGGGTGGAC----ACCGGTGT-TTGATA----------TGCCAGTGAGAATAGATGTGCTTCACGGAGAGGCTTATGTAAAGTG-ACAGCTTTT--GGAGA-ATGAAGTCCTCAGATTA------ i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59428361 126 - 64418924 ACA--------GCAGTCAG--TTCCATGGAGGAC----GCCAGTGT-TTGATATGGAG-ATTTTGGCAGTAAGAATGGATGTGCCTCAGTGAGAGGTTTATGTAAAATG-ACAGCTTTTGGGGGGA-ATGAAGTCGTCAGATTG------ i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 6259 132 + 48268 GCGTAGGGAGGCCTGTCAG--CTCCCCGGTGGAT----GCCAATGT-TTGATATGGAG-ATTTTGGCAGTGAGAATGGATGCGGCTCAGCCAGAGGTTTATGCAAAGTG-ACAGCTTCT--GAAGA-ATGAAGCCCTCAGATCA------ i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 6064 106 + 24616 ATG--------GTTGTCAGCTCTCTGTG-----C----ACTAGTGC----AGGGTGGG-ACTGTGGCTGA------------GTCCCCTGAAGAAGTTTATATAATGTG-ACAGCTTCT--GGAGT-GTGAAGCTCTGGGAAGG------ i proCap1.scaffold_29042 C 0 I 1 s loxAfr3.scaffold_49 14422141 117 - 17734757 AGG--------GCTGTCAG--CTCTGTG-----C----ACCAGTGT-TTGATGGGGAG-ATTTGGGCTGGAAG--TGGACGTGCCTCCTGCAGAAGTTTACGTAAAATG-ACAGCTTCT--GGAGA-CTGAAGCTTTCAGATGG------ i loxAfr3.scaffold_49 C 0 I 1 s otoGar1.scaffold_94362.1-287808 17233 121 + 287808 -GG--------GCTGTCAG--TTCAATGGTGGAC----ACCAGCGT-TTGATATGGAG-ATT-TGGCAGCGGGAAGGGAAATGCCTCAGTGAGAGGTTTATGTAAAATG-ACAGCTTCT--GGAAA-ATGAAGCCCTCAGATT------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s dasNov2.scaffold_28617 3099 122 + 20752 GCG--------GCTATCGG--CTCAGCAGC--CC----CCGAGCAT-TTGATATTGAG-ATTTTGGCAGCGAGAAGGGATGTGCCTCGGCGAGAGGTTTATGGAAAATG-ACAGCTTCC--GGAGG-ACGAAGTGCTCTGATTC------ i dasNov2.scaffold_28617 C 0 I 1 s macEug1.Scaffold81348 9031 129 - 9603 AGA--------ACTGTCAG--TTCAGTAGCGGTCTGTTACAAGTGTTTTGATATGGAG-ATTCTGGCAGTGGGAATGGATGTACCTCAATGAAACGTTTATGGAAAATG-ACAGCTTCT--GGAAA-ATGATGTAGTcaggttt------ i macEug1.Scaffold81348 I 3367 I 9 s monDom5.chr2 304516804 135 - 541556283 AAA--------ACTGTCAA--TTTGGTAGTGGTCTGTTACAAGTGT-TTGATATGGAG-ATTTTGGCAGTGGGAATGGATGTGCCTCAATAAAATGTTTATGTAAAATG-TCAGTTTAT--GGAAAAATGATATAGTCAGGTTTCAAGCA i monDom5.chr2 I 3178 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e mm9.chr11 118747819 2632 + 121843856 I a score=-18986.000000 s hg19.chr17_gl000204_random 35881 37 + 81310 AAAAAGA-----AGA----AGAAA-AGGAA-------------AGAGGAGGAAGA-G-G-------CAG s gorGor1.Supercontig_0007361 6098 37 - 64270 AAAAAGA-----AGA----AGAAA-AGGAA-------------AGAGGAGGAAGA-G-G-------CAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79465713 37 + 83384210 AAAAAGA-----AGA----AGAAA-AGGAA-------------AGAGGAGGAAGA-G-G-------CAG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16052848 37 + 17838096 AAAAAGA-----AGA----AGAAA-AGGAA-------------AGAGGAGGAAGA-G-G-------CAG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75026666 37 + 78773432 AAAAAGA-----AGA----AGAAA-AGGAA-------------AGAGGAGGAAGA-G-G-------CAG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 34041 37 - 95547 AAAAAGA-----AGA----AGAAA-AGGAA-------------AGAGGAGGAAGA-G-G-------CAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 36726 38 + 225949 AAAAGGA-----AGA----AGAAA-AGGAA-------------AGAGGAGGAAGAGG-G-------CAG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 7114 51 + 8975 AAAAAGG-----AAA----AGAAA-AGGAAGGAGGGAGAGGGGGGAGGAGGAAGAGG-A-------CAC i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 17354 36 + 287808 aaaaaga-----aaa----agaaa-aggac-------------ggaggaggaa-a-g-g-------agg i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 3176 38 + 15939 GAAAAGG-----AAA----AGAAA-AGGAC-------------AGAGAAGGAGGA-GCA-------CGA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118750451 37 + 121843856 aaagagg-----gga----gcatg-gggag-------------gcaggaggaggg-g-a-------CCA i mm9.chr11 I 2632 C 0 s cavPor3.scaffold_76 4382041 32 + 7991924 --AGTGA-----GAA----AGAAG-TGGGG-------------CCCTGAGTGGAG-G-A---------- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 349 34 + 44242 ---GGGA-----GAA----AGGGG-CGGTG-------------GTACGGACAGGC-A-G-------CGG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 11759 34 + 41507 AACGGGA-----GGA----GGAGGAGGGAG-------------GTATGAAGGCGA-A------------ i oryCun2.chrUn0958 I 1 C 0 s turTru1.scaffold_106006 119654 31 + 145505 AAAAAGA-----AAA----GAAAA----AA-------------GGAGGAGGACAA-A-G---------- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10851117 34 - 65312493 AAAAAGA-----AAA----GAAAA-GAGAA-------------GGAGGAGGACAA-A-G---------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58033775 24 - 61308211 -------------------GGAAG-AACAA-------------CAAGGAGGATGA-G-G---------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 5927 40 + 132007 CAAAAAA-----AAAAAAAAAAAG----------------------GAAGGAGGA-G-GAGGAGGGCCA i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59428487 48 - 64418924 GGggaaa-----aaaggaaggaag-aacaa-------------ggaggaagagaa-g-gaaggGGGCCA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 6391 29 + 48268 GAAAAG-------------GAAAG----------------------GAAAGAGGT-G-C---GGTGCAC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14422259 34 - 17734757 AGGACCg-----agg----gggag-aggga-------------gggggaggagga-g-a---------- i loxAfr3.scaffold_49 I 1 C 0 s proCap1.scaffold_29042 6171 33 + 24616 AAGCCTC-----AGG----GGGAG-AGGCT-------------GGAGGAGGA-GA-G-A---------- i proCap1.scaffold_29042 I 1 C 0 s dasNov2.scaffold_28617 3222 24 + 20752 A------------------GAGAG-GGGAC-------------GGGCAGGCA-CA-G-G---------- i dasNov2.scaffold_28617 I 1 C 0 s macEug1.Scaffold81348 9169 41 - 9603 agagaga-----gga----agaaa-aaaga-------------tgacaaggaagg-a-c---agtacaa i macEug1.Scaffold81348 I 9 C 0 s monDom5.chr2 304516939 37 - 541556283 agagggatggtgaga----gggag-aggga-------------gga-aaggaaga-g------------ i monDom5.chr2 C 0 I 504 e ochPri2.scaffold_6980 56737 1113 + 61692 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I a score=-137905.000000 s hg19.chr17_gl000204_random 35918 24 + 81310 CAGGGAA------GGTGCCCTCCA--------------------CCCCCC s gorGor1.Supercontig_0007361 6135 24 - 64270 CAGGGAA------GGTGCCCTCCA--------------------CCCCCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79465750 24 + 83384210 CAGGGAA------GGTGCCCTCCA--------------------CCCCCC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16052885 24 + 17838096 CAGGGAA------GGTGCCCTCCA--------------------CCCCCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75026703 24 + 78773432 CAGGGAA------GGTGCCCTCCA--------------------CCCCCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 34078 24 - 95547 CAGGGAA------GGTGCCCTCCA--------------------CCCCCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 36764 24 + 225949 CGGGGAA------GGTGCCCTCCA--------------------TCCCCC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 7165 24 + 8975 TGGGGAA------GACGCTCAGAG--------------------CTCCCC i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 17390 16 + 287808 aggggag------ggag----------------------------gaCCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 3214 24 + 15939 CAGGAAG------GGACTCCCTCC--------------------TCCCTC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118750488 20 + 121843856 CAGGAAC------AAG----GGGA--------------------CAGGGC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4382073 10 + 7991924 --------------------GGCT--------------------CCTGTC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 383 22 + 44242 TATGGAC------GGG--CAGGGG--------------------CCTCTC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 11793 10 + 41507 --------------------GGCT--------------------CTGTCC i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 119685 42 + 145505 ---AGAAGCCTTGGGCTCCCTCCC-CCTTCTCCCCT----TCCCCTCCTC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10851151 47 - 65312493 ---AGAAGCCTTGGGCTccctcccttcccctcccctcgcctcccctccTC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58033799 28 - 61308211 ---GGAA------GGCCCC-------------GCCGGCTGCCCCCTCCCT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 5967 40 + 132007 CA-GGAA------AGCACCCTCGA--CCCCTAGCCG-GCAACCCCTCCCT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59428535 42 - 64418924 CAGGGAA------AGTGCCTCCCA--CCCCTAGCAGAGCACCCCCTCCCT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 6420 35 + 48268 CAGGGAA------GGCCCCCTCCC--CCC---GCGG----CCCCCCACAC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14422293 30 - 17734757 ---ggga------ggggCCTGCCT-----------TCTGCCCCCTGTGCC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 6204 30 + 24616 ---GAAC------AGGGCCTGCCT-----------TCTGCCCTCCTCCCC i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 3246 13 + 20752 ---GGAG------GGGGCGCGC---------------------------- i dasNov2.scaffold_28617 C 0 C 0 s macEug1.Scaffold81348 9210 24 - 9603 atggaaa------agctcccttct--------------------tccctc i macEug1.Scaffold81348 C 0 N 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304516976 504 - 541556283 I a score=-149865.000000 s hg19.chr17_gl000204_random 35942 97 + 81310 A---------------TGT----AT--TCCCTGGA------G----------G---GCACTG----CAG------GGGCGGTGGGGGACCGGGAGAC-AAATGC-----CCCA-TTTGGGGGTG-------------------CTTCCTGTGCTGCTCAG---------------TGTGC---------CTTAGCTT s gorGor1.Supercontig_0007361 6159 97 - 64270 A---------------TGT----AT--TCCCTGGA------G----------G---GCACTG----CAG------GGGCGGTGGGGGACCGGGAGAC-AAATGC-----CCCA-TTTGGGGGTG-------------------CTTCCTGTGCTGCTCAG---------------TGTGC---------CTTAGCTT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79465774 97 + 83384210 A---------------TGT----AT--TCCCTGGA------G----------G---GCACTG----CAG------GGGCGGTGGGGGACCGGGAGAC-AAATGC-----CCCA-TTTGGGGGTG-------------------CTTCCTGTGCTGCTCAG---------------TGTGC---------CTTAGCTT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16052909 97 + 17838096 A---------------TGT----AT--TCCCTGGA------G----------G---GCACTG----CAG------GGGCCGTGGGGGACCGGGAGAA-AAATGC-----CCCA-TTTGAGGGTG-------------------CTTCCTGTGCTGCTCAG---------------TGTGC---------TTTAGCTT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75026727 97 + 78773432 A---------------CGC----AT--TCCCTGGA------G----------G---GCACTT----CAG------GGGCCATGGGGGCCTGGGAGAC-AAATGC-----CCCA-TTTGGGGGTG-------------------CTTCCTGTGCTGCCCAA---------------TGTGC---------CTTAGCTT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 34102 97 - 95547 A---------------CGC----GT--TCCCTGGA------G----------G---GCACTG----CAG------GGGCCATGGGGGCCTGGGAGAC-AAATGC-----CCCA-TTTGGGGGTG-------------------CTTCCTGTGCTGCCCAA---------------TGTGC---------CTTAGCTT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 36788 85 + 225949 A---------------TGC----AT--TCCCTGGA------G----------G---GCACTG----CAG------GGGCTGTGAGAGACCGGGAAAG-AAATGC-----CCCA-TTTGGAGG-------------------------------TGCCCAG---------------TGCGC---------CTTAGCTT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 7189 98 + 8975 A---------------GGC----AT--TTCCTGGA----GGG----------G---GCACAG----CAG------GGGCTATGAGGGAGCCAGAGAG-AAGTAC-----CCCT-TTTGAGGGAG-------------------CCTCCCTTCCC-CTCCC---------------TGTGC---------CTTATCTT i tarSyr1.scaffold_131410 C 0 M 466 s otoGar1.scaffold_94362.1-287808 17406 74 + 287808 A---------------TGC----AC--TTCCTGGA----GGG----------A---GCACAG----CAG------GGACT---GGGACCCCAGGGAG-AGATGC-----CCCA-AT-----ATG-------------------CCTCCAG----------------------------------------CTAGCT- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 3238 93 + 15939 A---------------CGC----AG--TTCCTGGGGTGGGGG----------G---ACGCAG----CCC------GAGCAGTGGGACACCCAGAAAG-AAATGT-----GCAAGTTTGGGGG---------------------------GTGCTCCTCAG---------------T-TGC---------CT--GCCT i tupBel1.scaffold_124459.1-15939 C 0 I 1 s mm9.chr11 118750508 99 + 121843856 A---------------CAT----GG--TTCCTGGA------A----------G---AATGAAGGG-TTG------GGGCTATGAGGAGCCAAGGGAG-AAGTAT-----GGGC-TT-GGAAGTG-------------------ACTTCTGGTCACTTTAA---------------TTTGT---------CTTACCTT i mm9.chr11 C 0 I 5 s cavPor3.scaffold_76 4382083 108 + 7991924 T---------------TCT----GC--TCCCTGCG------G----------G---GGCCCCAGG-TGT------GGAC--------ACACAGAGAG-AAACGC-----AGGC-TC---AAGTGCTTCTTCATCATTTCATGCACCTCAGTTCACCCCAA---------------TCTGC---------CCCTCCAT i cavPor3.scaffold_76 C 0 I 10 s speTri1.scaffold_128901 405 112 + 44242 C---------------TCCCCAGGC--TTCCTGGA------A----------G---AGCCGCGGACCCA------GGGCCATAGGACACGCAGAGGG-AGATGC-----AGGT-TC--GGGGTG-------------------CTTCCTGGGTACCCCAC---------------TGTGCATGGCTTCTCCCCACCT i speTri1.scaffold_128901 C 0 I 5 s oryCun2.chrUn0958 11803 78 + 41507 A---------------GGC----AC--TTCCTGGA------G----------G---CCAGCAGGA-CCC------CCGC-------------GGGGG-ACATGC-----CGAG-TG-CGGGCTG-------------------TCTGC------CCCCGT---------------GCTGC---------CCT--CCT i oryCun2.chrUn0958 C 0 I 2 s turTru1.scaffold_106006 119727 111 + 145505 A---------------TGC----AT--TTCCTGGA-GGGTTG--------GGG---GCACAG----CAGCTCCTAAGGCTGTGGGAACCCCAGAGAG-AAACCT----GTGCA-TTTGGGGTTG-------------------CTTCCTCTTCACCTCAA---------------TTTGT---------CTCACCTT i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10851198 112 - 65312493 A---------------CGC----CT--TTCCTGGA-AGGGTG--------GGG---GTACAG----CAGCTCCTAAGGCTGTGGGACCCCCAGAGAGAAAATCC----GTGCA-TTTGGGGCTG-------------------CTTCCTCTTCACCTCAA---------------TTTGT---------CTCACCTT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58033827 61 - 61308211 G---------------TGC----GT--TCCCTAGA-GGGCGG----------G---GCACAG----CAG------------------CCCCAGAGAG-AAATCC----------------------------------------------------TCAA---------------TTTGT---------CTCACC-- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 6007 113 + 132007 G---------------GGC----AT--TTCCTGAA-AGATGGGGGCGGGGGGG---GCACAG----CAGC-CCCCAGGCTGTAGGACCTCCAAAGAG-AAACCC----ACGTA-TCTGGGGCTG-------------------CTTCCT-----GTTCTA---------------TCTGC---------CCCCCCTT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59428577 111 - 64418924 G---------------TGC----AA--TGCCTGAA-AGGTGG----GTGGGGG---GCACAG----CAGT-CCCTGGGCTGTGGGGCCCCCAGAGAG--AACCC----CTGCA-TCTGGAGCTG-------------------CTTCCTCCTCCCTTCCA---------------TCTGC---------CCCACC-- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 6455 108 + 48268 A---------------CGC----AT--TTCCCAGG-TGCTGG----------G---GCACAG----AAG--CCCCAGGCTGTGCCCCCGCCCCAGAG-AAACCCTCCCATACA-CTTGGGGCTG-------------------CTTCTTCCTCCC-TCGA---------------TCTCT---------CGCCTC-- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14422323 109 - 17734757 A-----------GGGATGC----AT--GGCCACGG------G----------G-CTGGCCAG----CAT------GGGCTGCAGAGGCT---GGGAG-AAATGC-ACAAAGAA-TTTGGGGCTG-------------------TTTCGCCTTCACCTGAATCTGG----------TCATT---------CTCACCTG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 6234 120 + 24616 ACCCCCAGTAAGGGGACAG----AT--GGCCTAGA------G----------G-CTGGCCAG----CGA------GAGCTACAGAGGCT---GAGAG-AAATGC-AAGAAGCA-TTTGGGGCTG-------------------GTTCTCCCTCACCTGGGCCACA----------TCAGG---------CTCACCTG i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 3259 104 + 20752 ------GGCGGGGGGACGC----CTGCGGCTGCGA------G----------TCCTGGCCGG----C---------AGCTCGGCAGGCC-------------------------CCCGGGGCTG--------------------CTCGGCTTCACCTTGCCCCTGGCCCCCAGCCTCGTT---------CTCCTCTG i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304516976 504 - 541556283 I a score=-91603.000000 s hg19.chr17_gl000204_random 36039 23 + 81310 TGCCCCAA-----CACCG----CCTCC----------------------------CCA-------------------CC s gorGor1.Supercontig_0007361 6256 23 - 64270 TGCCCCAA-----CACCG----CCTCC----------------------------CCA-------------------CC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79465871 23 + 83384210 TGCCCCAA-----CACCG----CCTCC----------------------------CCA-------------------CC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16053006 23 + 17838096 TGCCCCAA-----CAACG----CCTCC----------------------------CCA-------------------CC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75026824 42 + 78773432 TGCCCCAA-----CACCG----CCTCC----------------------------CCACCTCCCCATTCAGACCCCCCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 34199 42 - 95547 TGCCCCAA-----CACCG----CCTCC----------------------------CCACCTGCCCATTCAGACCCCCCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 36873 23 + 225949 TGCCCCAA-----CACCG----CCTCC----------------------------CCC-------------------TC i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 17480 9 + 287808 -----------------------CCCC----------------------------TCA-------------------TA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 3332 22 + 15939 TGCCCCCC-----TAG-G----CTCCT----------------------------CCA-------------------CC i tupBel1.scaffold_124459.1-15939 I 1 C 0 s mm9.chr11 118750612 23 + 121843856 CTCCCC-A-----CAAAG---CCATAC----------------------------CTA-------------------TT i mm9.chr11 I 5 C 0 s cavPor3.scaffold_76 4382201 27 + 7991924 ATCCCCAA-----CACAGGGCCCATCA----------------------------CTC-------------------CT i cavPor3.scaffold_76 I 10 C 0 s speTri1.scaffold_128901 522 32 + 44242 CTCCCCAACCTGCCACAGGCCCTTTCC----------------------------ACT-------------------CC i speTri1.scaffold_128901 I 5 C 0 s oryCun2.chrUn0958 11883 21 + 41507 --CCCC-------CACAGG--CCACGC----------------------------CCA-------------------CC i oryCun2.chrUn0958 I 2 C 0 s turTru1.scaffold_106006 119838 22 + 145505 TGCCCCAA-----CCT-G----CCCCT----------------------------TCC-------------------TC i turTru1.scaffold_106006 C 0 I 26 s bosTau4.chr19 10851310 14 - 65312493 TGCGCCAA-----CA-----------------------------------------CT-------------------TC i bosTau4.chr19 C 0 I 170 s equCab2.chr11 58033888 22 - 61308211 TTCATCCC-----CCC-G----CCCCC----------------------------TCC-------------------CA i equCab2.chr11 C 0 I 23 s felCat3.scaffold_206428 6120 23 + 132007 TGCCCCAA-----CCT-G---CCCCCC----------------------------TCT-------------------AA i felCat3.scaffold_206428 C 0 I 21 s canFam2.chr9 59428688 22 - 64418924 TGCCCCCC-----CCA-G----CCCCG----------------------------TCT-------------------CA i canFam2.chr9 C 0 I 20 s pteVam1.scaffold_11245 6563 21 + 48268 TGCCCCCA-----CC--G----CCCCC----------------------------TCC-------------------TC i pteVam1.scaffold_11245 C 0 I 20 s loxAfr3.scaffold_49 14422432 51 - 17734757 TGTCCCAA-----GTGGC----CCCCTCCCATCTAATCCTCCCTTCCTCCCTTCCCCC-------------------TC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 6354 23 + 24616 AGCCCCAG-----GCGAC----ACCCT----------------------------CCC-------------------CA i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 3363 23 + 20752 CCCGCTGC-----GCGTG----TCCCC----------------------------CCA-------------------CC i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 7287 466 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304516976 504 - 541556283 I a score=-247463.000000 s hg19.chr17_gl000204_random 36062 31 + 81310 CCCCAG--GC-----CACA--C-----------------------------------------ACTTCT---TTACCATCCCCA s gorGor1.Supercontig_0007361 6279 31 - 64270 TCCCAG--GC-----CACA--C-----------------------------------------ACTTCT---TTACCATCCCCA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79465894 31 + 83384210 TCCCAG--GC-----CACA--C-----------------------------------------ACTTCT---TTACCATCCCCA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16053029 31 + 17838096 TCCCAG--GC-----CACA--C-----------------------------------------ACTTCT---TTACTGTCCCCA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75026866 31 + 78773432 TCCCAG--GC-----CACA--C-----------------------------------------ACTTCT---TTACTGTCTCCA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 34241 31 - 95547 TCCCAG--GC-----CACA--C-----------------------------------------ACTTCT---TTACTGTCTCCA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 36896 3 + 225949 CTC--------------------------------------------------------------------------------- i calJac1.Contig5139 C 0 I 31 s otoGar1.scaffold_94362.1-287808 17489 33 + 287808 CAGCAG--GC-----CCCGTCT-----------------------------------------ACCCCT---TAACTGTCCTGC i otoGar1.scaffold_94362.1-287808 C 0 I 1 s tupBel1.scaffold_124459.1-15939 3354 7 + 15939 TCT-----GC-----TA------------------------------------------------------------------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118750635 2 + 121843856 CC---------------------------------------------------------------------------------- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4382228 12 + 7991924 TCATTG--CC-----CTGA----------------------------------------------------------------- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 554 12 + 44242 TCACTG--TC-----CCCA----------------------------------------------------------------- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 11904 9 + 41507 CCTTGA--CC-----C-------------------------------------------------------------------- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 119886 31 + 145505 -CCC----CA-----CACA--C-----------------------------------------ACTCCTCATTTACTGTCCTGA i turTru1.scaffold_106006 I 26 C 0 s bosTau4.chr19 10851494 73 - 65312493 CCCC----AA-----CCTG--CCCCCTCCTTTCTAATTCTCCTCCGCTCTGAACTGTCTCCCAACTCCTCATTTACTGTCCTGA i bosTau4.chr19 I 170 C 0 s equCab2.chr11 58033933 36 - 61308211 CCACAGGTCG-----CACC--C-----------------------------------------ACTCCTCAGTTACCGCCCTTT i equCab2.chr11 I 23 C 0 s felCat3.scaffold_206428 6164 28 + 132007 CCCCAA--CA-----CACA--C-----------------------------------------ATTCCTCAC------TCCTGA i felCat3.scaffold_206428 I 21 C 0 s canFam2.chr9 59428730 34 - 64418924 CCCCAG--CA-----CACA--T-----------------------------------------ACCCCTCACTCACCGTCCTGA i canFam2.chr9 I 20 C 0 s pteVam1.scaffold_11245 6604 32 + 48268 CCTC----CA-----CGCA--C-----------------------------------------ACACCTCACGCACTGTCCTGA i pteVam1.scaffold_11245 I 20 C 0 s loxAfr3.scaffold_49 14422483 31 - 17734757 ---CCA--CAGG---CACA--------------------------------------------TCTCCTCATCTGCTGCCCCA- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 6377 33 + 24616 ---CAG--CAGGCACCACG--------------------------------------------ACACCTC-TCTCCTGCCCCA- i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 3386 27 + 20752 ---CAG--GA-----CAAA--------------------------------------------TCCCCTC--CTCACGCACCG- i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 7287 466 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304516976 504 - 541556283 I a score=-344412.000000 s hg19.chr17_gl000204_random 36093 95 + 81310 TCCGTCCTA---TACCCAG---GATA-AGAACC------CCAGG----GGA-C---AAGGC----CC-TGATA----GGG-GACAG------ACACGCGCCAAGATAGCACG-------CG--GTAAGAGACAAGC-----AATTA s dasNov2.scaffold_28617 3413 60 + 20752 ------------------------------TCCCCGCCTTCCCA----CGC-C---CGGGC----TA-AGACCTGT-GGT-GGCAGGTGACCGCACAGGCGAC-----------------------------------------CC i dasNov2.scaffold_28617 C 0 C 0 s proCap1.scaffold_29042 6410 75 + 24616 ------------------------------TCC------TTCAA----TGC-C---CAGTG----GC-TGGCCAGC-AGC-GACAG------GCACAGGCCACGGCTGCCCG-------CT--ATAAACAACCAGG-----GATCC i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14422514 76 - 17734757 ------------------------------TCC------TTCAA----TGC-C---CAGCG----GC-AGGCCAGCGGGT-GACAG------GCACAGGCCACGTCCACGAG-------CT--ATAAACAACCAAG-----CATCA i loxAfr3.scaffold_49 C 0 C 0 s pteVam1.scaffold_11245 6636 82 + 48268 --CCTCTAA---TGGCCAG---GAGA-AGGACG------TCAGG----TGA-C---CAGGC----CC--AGTCG---GGT-GACAC------G--CACACTAAGA--------------CTCAGTAAACGAC---------AATTT i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59428764 74 - 64418924 --TCCCTGA-----GCCGG---GATG-AGGACC------CCAGG----TGA-C---AGGCC----CC-GGGC-----AGG-GACAG------CCACACACTCAGA--------------CT--GTAAAGGAG-------------- i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 6192 77 + 132007 --TCGCTGACCGAGGCGGG---GAGGAAGGACC------CCAGA----TGA-C---AGGCC----CC--TGT-----GGG-GACAG------C--CACACTCTGA--------------CT--GTAAAGGAG-------------- i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58033969 79 - 61308211 --CTTTCAA---GGCCCAG---GAGG-AGGACC------CCAGA----TGA-C---AGGGC----CC----------AGG-GACAG------G--CAGACAGACG--------------CT--GTAAACAAGGAGC-----AGTCA i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10851567 87 - 65312493 --TCTGTCA--TTGCCCAG---GATA-AGGACC------CCGGA----TGACC---AGGCC----CG--GGTG----GTT-GATAG------ACACACATCACGA--------------CA--GTAAACTATGAGC-----AGTCA i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 119917 92 + 145505 --TCTGTCA--TTGCCCAG---GATA-AGGACC------CCAGAGAGGTGA-C---AGGCC----CC--GGTG----GGT-GACAG------ACACACACGAAGA--------------CATCGTAAACTATGAAC-----AATCA i turTru1.scaffold_106006 C 0 C 0 s oryCun2.chrUn0958 11913 87 + 41507 TGCCCGTCT---CCTCCAGGTTGGC------CC------CGGCG----TGC-----CAGGC--GACC-----------GT-GACGG------ATGCCATCCGAGACTGCGCT---------------GTAGCCGGCAGTCAGGGCT i oryCun2.chrUn0958 C 0 C 0 s speTri1.scaffold_128901 566 91 + 44242 GGGTTTCGA---TGCCCAG---GATA-AGG-AC------GTAGG----CGA-----GGGGCTGGGTG-----------GG-GGCAG------ACACG--CCAAGGCCACATG-------CC--CTAGATGACAAACGG---AGCAG i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4382240 97 + 7991924 TGCTTTTAA---TTCCCAG---GAC------CC------CAAGG----GGA-CGGGGAGAC---ACC-----------AG-GAT-G------GCACA--CTGGGGCTGACCAGCAGCGACT--CTGAGATACCAGTATTACGGGAT i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118750637 85 + 121843856 TGTTCCTCA---GAGCAAG---GGC------CT------ACAGA----AGA-----GAGAC----CC-----------AG-GACAG------ACACA--CCCAGGCTCATCA--------C--TTAGAAGGTAAAGAGGAGAACAG i mm9.chr11 C 0 C 0 s tupBel1.scaffold_124459.1-15939 3361 57 + 15939 -------------------------------CC------CT-----------------GCC----CC-TTGCA----GGGCTGCCG------GCCTGGGCCACGG------G-------CT--GTAAGCAACCAAG-----GGCTG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s otoGar1.scaffold_94362.1-287808 17523 81 + 287808 CCTTTCTTA---AGCCCAG-----TG-AGGACC------CC-------GCA-C---CTGGC----CTGGGATG----GGG-GGGAG----------------GGGTTAGAAG-------TG--GTAAATAGTAAGC-----AGTCG i otoGar1.scaffold_94362.1-287808 I 1 C 0 s gorGor1.Supercontig_0007361 6310 95 - 64270 TCCATCCTA---TACCCAG---GATA-AGAACC------CCAGG----GGA-C---AAGGC----CC-TGATA----GGG-GACAG------ACACGCGCCAAGATAGCACN-------NG--GTAAGAGACAAGC-----AATTA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79465925 95 + 83384210 TCCGTCCTA---TACCCAG---GATA-AGAACC------CCAGG----GGA-C---AAGGC----CC-TGATA----GGG-GACAG------ACACGCGCCAAGATAGCACG-------CG--GTAAGAGACAAGC-----AATTA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16053060 95 + 17838096 TCCATCCTA---TACCCAG---GATA-AGAACC------CCAGG----GGA-C---AAGGC----CC-TGATA----GGG-GACAG------ACATGCGCCAAGATAGCACA-------CG--GTAAAAGACAAGC-----AATTA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75026897 95 + 78773432 TCTGTCCTA---TCCCCAG---GATA-AGAACC------CCAGG----GGA-C---GAGGC----CC-TGGTA----GGG-GACAG------ACACGCGCCAAGATAGCACA-------CG--GTAAAAGACAAGC-----AATTA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 34272 95 - 95547 TCTGTCCTA---TCCCCAG---GATA-AGAACC------CCAGG----GGA-C---GAGGC----CC-TGGTA----GGG-GACAG------ACACGCGCCAAGATAGCACA-------CG--GTAAAAGACAAGC-----AATTA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 36930 95 + 225949 TCCTTCCTG---TGCCCGC---AGTA-AGAACC------CCAGG----GAA-C---GAGGC----CC-TGGCA----GGG-GACAG------ACAAGCGCCAAGACAGCATG-------TG--GTCAGAGACAAGC-----AATTA i calJac1.Contig5139 I 31 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 7287 466 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304516976 504 - 541556283 I a score=925944.000000 s hg19.chr17_gl000204_random 36188 193 + 81310 TTTGGAAACTTTCACATTACTGTCGTTTTAAAAGGGAGGGGGCTA--G-AT-----------------GGAGGCAAAGACTCCAAG-AATCCTTCCTAGGA----AGC------------CCACAAAAGCAAAGATGGATTGCACATAATTGCCC-TTTGTTTAAAAGG-CACATGGATATTCCTGCAGAGCTGGAAACTCATTCTTCACAC------AAAAAAGCTTCCAAAAATTG s calJac1.Contig5139 37025 192 + 225949 TTTGGAAACTTGCACATTACCGACGTTTTAAAAGGGTGGGGGCTA--G-AT-----------------GGAGGCAAAGACTCC-AG-AATCCTTCCCAGGA----ACA------------CCGCAAGAGCCAAGAC-GATCGCACACAATTGCCCTTTTGTTTCAGAGG-CACATGGACATTCCTGCAGAGCTGGAAACTCACTCTTCACAC------AAATAAGCTTCCAAACATTG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 34367 193 - 95547 TTTGGAAACTTTCACATGACTGTCATTTTAAAAGGGAGGGGGCTA--G-AT-----------------GGAGGCAAAGACTCCAAG-AATCCTTCCTAGGA----AGC------------CCACAAAAGCAAAGATGGATTGCACATAATTGCCC-TTTGTTTAAAAGG-CACATGGATATTCCTGCAGAGCTGGAAACTCATTCTTCACAC------AAAAAAGCTTCCAAAAATTG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75026992 193 + 78773432 TTTGGAAACTTTCACATGACTGTCATTTTAAAAGGGAGGGGGCTA--G-AT-----------------GGAGGCAAAGACTCCAAG-AATCCTTCCTAGGA----AGC------------CCACAAAAGCAAAGATGGATTGCACATAATTGCCC-TTTGTTTAAAAGG-CACATGGATATTCCTGCAGAGCTGGAAACTCATTCTTCACAC------AAAAAAGCTTCCAAAAATTG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16053155 193 + 17838096 TTTGGAAACTTTCACATTACTGTCATTTTAAAACGGAGGGGGCTA--G-AT-----------------GGAGGCAAAGACTCCAAG-AATCCTTCCTAGGA----AGC------------CCACAAAAGCAAAGATGGATTGCACATAATTGCCC-TTTGTTTAAAAGG-CACATGGATATTCCTGCAGAGCTGGAAACTCATTCTTCACAC------AAAAAAGCTTCCAAAAATTG i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79466020 193 + 83384210 TTTGGAAACTTTCACATTACTGTCGTTTTAAAAGGGAGGGGGCTA--G-AT-----------------GGAGGCAAAGACTCCAAG-AATCCTTCCTAGGA----AGC------------CCACAAAAGCAAAGATGGATTGCACATAATTGCCC-TTTGTTTAAAAGG-CACATGGATATTCCTGCAGAGCTGGAAACTCATTCTTCACAC------AAAAAAGCTTCCAAAAATTG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 6405 193 - 64270 TTTGGAAACTTTCACATTACTGTCGTTTTAAAAGGGAGGGGGCTA--G-AT-----------------GGAGGCAAAGACTCCAAG-AATCCTTCCTAGGA----AGC------------CCACAAAAGCAAAGATGGATTGNACATAATTGCCC-CTTGTTTAAAAGG-CACATGGATATTCCTGCAGAGCTGGAAACTCATTCTTCACAC------AAAAAATCTTCCAAAAATTG i gorGor1.Supercontig_0007361 C 0 C 0 s otoGar1.scaffold_94362.1-287808 17604 185 + 287808 TCC-AAAACTGTCGTGTTGGTGGCATTTTAGGAGGG--------------T-----------------AGGGGCAAAGGCTGGGAC-AA-CCTTCCTAGGATCTTAGCTT----------CCACAAAAGCAAAGAAGGATT-CGTGTGATTGCCC-TTTGTTTAAGAGT-CAGAGGAATATTCCTGCAGCGCTGGAAACTCATTCTTCACAC------AAAGAAGCTTCCAAAAATTG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 3418 177 + 15939 TCTGGAAACTTCCGCAGCA---GCACTTCAGGAGGGCAG-----------T-----------------GGAGGGGA--GCCCCGCG-TGTGTTCCCAGGGC----AGC--------------GCAGGGGCACAG-CAGAGCGAGTGTCGTCGCCT-TTTGTTTAAGAGG-CAAATGAATATTCCTGCAGCGCTGGAAACGCGGTCTCCACAC------AGATCCGCTTCCAAAAATTG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118750722 155 + 121843856 TTTAGAA----------------------------GCAACACCAG--G-GT-----------------GAAAGGG-----CTGAGC-CGTCCCTCCCGGGG----A--------------CTGTGGGAGCCGGGAGGCTTGGGA--GGACCTCTG-TTTGTTCAGGAGG-CAAATGAATACCTGTGCCAA-------ACCCGCTTTCCACACACACAGAAGTAAGCTTCCAAAATCAG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4382337 183 + 7991924 TTTCGAGGG-----------------------GGTGGGGTGCCAG--G-GTGTCGAAAGAGACCCCAAGAAAGGGT--CTCCTAGG-GATCCTTCTAGGAA----G--------------CCACCGAGACTGAGAAGAGTTGCACGGAATTGTTC-TATGTTTAGGGGG-CACATGAATGTTCCTGCAGGGCTGGGTACTTGCTCTTCACAC------AAAGAAGCTTCCAAAAATTG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 657 175 + 44242 CTTGGGACTT-------------CCCACGACCAGTCAGGTGCCAG--G-GT-----------------GGAGGGAC--ACCCCCGG-GATCCTTTCTGGGA---CG--------------CGAGGGCAGCCCTGAAGGGGTGCCCACCGTGGCCC-TGTGTCTAG--GG-CAAGTGCACATTCCTGCAGAGCTGGGAACTCGCGCCTCACAC------AAACAAGCTTCCAAAAATTG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 12000 175 + 41507 TCTGGAGCTTGTCCC----TCGCCGCGCTGTGAGGGCAGCACTGG--G-GC-----------------GGAGGGGC--GGCCCCAG-GGCTCTCCCCGGGA--------------------------CGCCTGGAATGGCCGAGCCTCGGCCTGC-TTTGCTTAGGAGG-CCGATGAAGA-GCGAGCAGCACCGGGGACTGCGCTCCCACAC------ACACAGGCTTCCCGAAACG- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 120009 191 + 145505 TTCTGAAACTTTCTCGTC-CTATCATGTTAAGAGGATGGGTACTA-GG-GT-----------------GGAGGGACCAACTCCAGA---TCCTTCTTGGGA----AGC------------CGACAAAAGCAGAGAAGGATTGCATATAATTGCCC-TTTGTTTAAGAGG-CAAATGAATATTCCTGCAGAGCTGAAAACTCATTCTTCACAC------AGATAAGCTTCCAAAAATTG i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10851654 191 - 65312493 TTTTGAAACTTTCTCAAC-CTATCGTTCTAAGAGGGTGGAAACTG-GG-GT-----------------GGAGGGACCAACTCCAGA---TCCTTCTTGGGA----AGC------------CAACAAAAGCAGAGAAGGATTGCATATAATTGCCC-TTTGTTTAAGAGG-CAAATGAATATTCCTGCAGAGCTGAAAACTCATTCTTCACAC------AGATAAGCTTCCAAAAATTG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58034048 185 - 61308211 TTCTGGAACTTTCTGGGC-CTGTCCTTTGAAGGGGGTGGGTACCA-GG-GC-----------------GGAGGGACCAACTCCAGC---TCCTTCTC-TGA----AGC------------CGACAAAAGCG---GGGGATTGC-TGTAATTGCCC-TTTGTTTAGGAGG-C-AACGAATATTCCTGCACAGCTGAAAGCTCCTTCTTCGCAC------AGAGAAGCTTCCAAAAATTG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 6269 124 + 132007 ------------------------------------------------------------------------------TCTCCAGTGAGTCCTTCTTGGGA----AGC------------CCACAAAGGCA---CAGGATTGCACATAATTGCCC-TTTGTTTAAGAGG-CAAATGAATATTCCTGCAGAGCA---------TTCTTCACAC------AGATAAGCTTCCAAAAATTG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59428838 123 - 64418924 ------------------------------------------------------------------------------ACTCCACTGAGTCCTTCTTGGGA----AAC------------CCACAAAAGCA---CAGGATTGCACATAATTGCCC-TTTGTTTAAGAGG-CAAATGAATATTCCTGCAGAGCG---------TTCTTC-CAC------AGATAAGCTTCCAAAAATTG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 6718 178 + 48268 ATTTTGAAACTTTCCATC-CTGTCGTTTTCAGAGGCTGGGTACGA-GG-GT-----------------GGAGGGACCCACTCCAGC-------------------AGC------------CGACAAAGCCA-AGAAGGATTGCACATAATTGCCC-TTTGTTTAAGAGG-CAAATGAATATTCCTGCAGAGCTGAAAACTCATTCTTCACAC------AGATAAGCTTCCAAAAATTG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14422590 177 - 17734757 CTTGGAAACTCTTGCCTG-GCTTCAATCGAAGAGGGTGGGGCTCTCGG-GT-----------------GGCGGGA--------AGG-ACT----CCAAGGA----A------------------GAAGGCCAGAAAGGAGGGCTTAGCACTGCCC-TTTGTTTGGGAGGCAAAATGAATATTCCCGCAGAGCTGAGAACTCATTCTTCACAC------AAATAAGCCACCAAAAATTG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 6485 196 + 24616 CTTTGAAACCCTGGCCTG-GCTTCAGCTGAGGAGTGTGGAGCTCTCAGCGT-----------------GGCGGGA------CCAGG-ACCCATGCCAAGGA----ATCGTCTCCGGGAAAGGACAAAAGCAAGGAAGCACGTGTCAGCA---CCC-TTTGTTTGGAAG--CAAGCGAACG-CCCCGCAGAGCCAGGAACGCGCTCTTCACAC------AAATAAGCCACCCCAAACTG i proCap1.scaffold_29042 C 0 I 1648 s dasNov2.scaffold_28617 3473 156 + 20752 TCCTGCGACTTCTGCC---GTGTGGATGTGAGACAGCGGGGC-------GC-----------------GGTGGGG-------CGGG-AC-----------------------------------GAGAGCAAGGGCGGTGGGCACACAACCGCCC---TGTCAGGAGG--CACGTGAATT-TCCTCCAGAGCTAGAAACCCAGTCTTCACAC------AAATACGCTACCAAAGATTG i dasNov2.scaffold_28617 C 0 C 0 s monDom5.chr2 304517480 162 - 541556283 TTTTGGAACTTTTACCTAATATAATTTTTAAGAGAG-----------T-AG-----------------AGGGGGAAAGATACCAACTAATCCTCCTTTGGA----AGC------------TGACAA-AGCA---AAGGATTGTCTGTAATTGTCT-TTTGTTTAAAAAG-TAAATTCATATTCCTGCAGAGAT--AAAGTTATCCTCCCCCC------ATT----------------- i monDom5.chr2 I 504 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e tarSyr1.scaffold_131410 7287 466 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I a score=537422.000000 s hg19.chr17_gl000204_random 36381 174 + 81310 CAACCTATTTGTTGCCAAGTTTGGGACTGTTATTTCCTTCCC-A------GCCCCC-------TTGG---GTTG--------------CTT----TT--TTAT----------------------TTTTTAATG---ACCTGAAATGT-AAATTGCCTT-CCCTG-TGGGTCTCCTGGGGCTGGGATGA----GGTCTAGGGAAGTCC-----------GCCT--C---CCAGGACATCCCAGCTGG----GGC-------------------------TCC----T--CCAGG s calJac1.Contig5139 37217 171 + 225949 CAACCTATTTGTTGCTGAGTTTGGGTCTGTTATTTCCTTCCC-A------GCCCAC-------TTGG---GTCG--------------CTT----TT--T--T----------------------TTTTTTATG---ACCCGAAATGT-AAGTTGCCTT-CCCTA-TGAGTCTCCT-GGGCTCAGACGA----GGTCTCAGGAAGTCT-----------GCCT--C---CCAGGACATCCCAGCTGG----AGC-------------------------TCC----T--CCAGG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 34560 174 - 95547 CAACCTATTTGTTGCCAAGTTTGGGACTGTTATTTCCTTCCC-A------GCCCCC-------TTGG---GTTG--------------CTT----TT--TTAT----------------------TTTTTAATG---ACCTGAAATGT-AAATTGCCTT-CCCTG-TGGGTCCCCTGGGGCTGGGATGA----TGTCTAGGGAAGTCC-----------GCCT--C---CCAGGACATCCCAGCTGG----GGC-------------------------TCC----T--CCAGG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75027185 173 + 78773432 CAACCTATTTGTTGCCAAGTTTGGGACTGTTATTTCCTTCCC-A------GCCCCC-------TTGG---GTTG--------------C-T----TT--TTAT----------------------TTTTTAATG---ACCTGAAATGT-AAATTGCCTT-CCCTG-TGGGTCTCCTGGGGCTGGGATGA----TGTCTAGGGAAGTCC-----------GCCT--C---CCAGGACATCCCAGCTGG----GGC-------------------------TCC----T--CCAGG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16053348 174 + 17838096 CAACCTATTTGTTGCCAAGTTTGGGACTGTTATTTCCTTCCC-A------GCCCCC-------TTGG---GTTG--------------CTT----TT--TTAT----------------------TTTTTAATG---ACCTGAAATGT-AAATTGCCTT-CCCTG-TGGGTCTCCTGGGGCTGGGATGC----GGTCTAGGGAAGTCC-----------GCCA--T---CCAGGACATCCCAGCTGG----GGC-------------------------TCC----T--CCAGG i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79466213 174 + 83384210 CAACCTATTTGTTGCCAAGTTTGGGACTGTTATTTCCTTCCC-A------GCCCCC-------TTGG---GTTG--------------CTT----TT--TTAT----------------------TTTTTAATG---ACCTGAAATGT-AAATTGCCTT-CCCTG-TGGGTCTCCTGGGGCTGGGATGA----GGTCTAGGGAAGTCC-----------GCTT--C---CCAGGACATCCCAGCTGG----GGC-------------------------TCC----T--CCAGG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 6598 174 - 64270 CAACCTATTTGTTGCCAAGTTTGGGACTGTTATTTCCTTCCC-A------GCCCCC-------TTGG---GTTG--------------CTT----TT--TTAT----------------------TTTTTAATG---ACCTGAAATGT-AAATTGCCTT-CCCTG-TGGGTCTCCTGGGGCTGGGATGA----GGTCTAGGGAAGTCC-----------GCCT--C---CCAGGACATCCCAGCTGG----GGC-------------------------TCC----T--CCTGG i gorGor1.Supercontig_0007361 C 0 C 0 s otoGar1.scaffold_94362.1-287808 17789 171 + 287808 CAATCTATTTGTTGCCAAGTTTGGGACTGTTATTTCCTTCCC-A------ACCCCC-------TGAG---GTTG--------------ttt----tt--tctttttttttttttgttttgttttgtttttAATG---GCCTGAAATGC-AGATTGCTCT-CCCAG--GGGTCTCTCAGGGCC----------------------GCCC-----------ACCT--C---ACAAGGCATCCCAGCTG-----------------------------------C----T--CAAGG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 3595 190 + 15939 CAACCTATTTGTTGCCAAGTTTGGGACTGTTATTTCCTTCCA-A------ACCTCC-------TTGG---GTTT--------------TTT----CTGGTTTA----------------------TTTTTAATG---GCCTGAAATGC-AAATTGCTTT-CCCTGGTGGACTTCTCAGGGCTAGGACA------GTTTGGGGAAGCCCTCAGA----AGACCT--C---CTAGGGCACCCCTCCTGG----GCCACAGC-------------------TTCC----TGGCCAGG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118750877 140 + 121843856 TCAT--------TGCCAAGTTGGTGGCTG------CCCTCCC-A------GCCCC----------------------------------------------------------------------------TCA---GCTGGAAAAGT-ACACAGTAGT-ATCTGACAGACAGCTATG----------------GTCCAGGGTTGTCT-----------ACCT--C---GTGGAACCTCCCAGCTAG----TGTGGGACA----------GGAGACTGTTCC----T--CCAGG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4382520 186 + 7991924 CAATCTGCCTGCTGCCAAGTTTGGGGCTGTTATTTCCTTCCC-A------GCCCCC-------TCGG---GT----------------TTT----TT--TTTT----------------------TTTTAATTG---GCCTGAAATGC-AAACTGCTTT-GCCTGATGGGTCCCTCTGTGGCAGGACAC-----GTGCAGGGAATCCC-----------ACCTACC---GCACAGCCTT---GCAAA----GGCCAGGAA----------GGAGACATCTCC----T--CTGAG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 832 202 + 44242 CAGTCCGTCTGCCGCCAAGTTTGGGACTGCTATTTCCTTCCC-A------GCCCCCCGCGCCGTCGT---TTTT--------CTTTTCTTT----TT--TTTT----------------------TTTCAATTG---GCCCAAAATGC-AAATTGCCTG-ACTTGACGGGTCTTTGGATGGTAGGACGT----GGCCCAGGGCAGTCC-----------ACCT--C---ACAGGGCACTCC-CCTAG----GACCAGAAA----------GGAGATGATCCC----T--CCAAG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 12175 107 + 41507 ------------CACCGAGCTCG-GGCTGCT---------------------------------------------------------CTG----TC--TTTG----------------------TTTCAGTGG---GGCCAGAGGTC-CAGGGGCCTG-GCCT------------------------------GCCCAGGGCATCCC-----------AGCT--C---G----------------------GCCAGCCA----------GGAGACGGCTCC----T--CCAGG i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 120200 172 + 145505 CACTCTATTTGTTGCCAAGTTTGGGACTATTATTTCCTTCCC-A------AACCCC-------TCGG--------------------------------ATCT----------------------TTTTTCGTG---GCCTGAAATGC-AAATTGCCTT-CCTTG-GTGGCCCTTTGGGGCTAGAACCTT---GGTCTAAAGAAGTCT-----------ATCT--C--ATCTGGACCTTGGGGAAAGAGATGGC-------------------------TCCC---C--CTAGG i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10851845 175 - 65312493 CAGTCTATTTGTTGCCAAGTTTAGGACGATTATTTCCTTCCC-A------ACCCCC-------TTGG--------------------------------ATAT----------------------TTTTTAATG---CCCTGAAACAC-AAACTGTCTT-CCTTG-GTGGCCCTTTGGGGCTAGAAACGT---GGTCTAAAGAAGTCC-----------ATCT--C--AACTGGACCATGGGAAAAGAGATGGC-------------------------TCCCCCGC--CCCGG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58034233 143 - 61308211 CAGGCTATTTGTGACCACGGTGAGGCCTGTGCCTTCCTCCCC-A------GCCC---------------------------------------------TGGG----------------------GTTTCCACA---GCCCCAGCTGC-AAACTGCCAT-CCCAG-GTGG--CTGCGGGGCTAGAACGCG---GGGCTGAGG-AGGTC-----------ACCT--C-----------------ACAG----GGC-------------------------TGC----C--CCAGG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 6393 171 + 132007 CCGTCTATTTGTTGCCAAGTTTGGGGCTGTTATTTCCTTCCC-A------ACCCCC-------TCGC--------------------------------TATC----------------------TTTTTAATG---GCCTCAAATGC-AAACTGCCTT-CCCTG-GTGATCCTCTGGGGCTAGAACATT---GGCCTGAGGCAGGCC-----------ACCT--C-TCCTGGGGCCACGAGAATGGAGC-GCC-------------------------TCC----C--CCAGG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59428961 159 - 64418924 CCATCAATTTGTTGCCAAGTATGGGACTGTTACTTCCTTCCC-A------ACCCCC-------TCG---------------------------------GATG----------------------TTTTCTGTGCCCGCCTGAACTGC-AAACTGCCTT-CCCTG-GTGGCCCTGTGGGGCTA----------------AGGCAGGCC-----------ACCT--CATCCC---GCCGGGCTAACGGAGCTGGC-------------------------TCC----G--CCAGG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 6896 168 + 48268 CAATCCATTTGCTGCCAAGTTTAGGACTGTTATTTCCTTCCC-A------ACCCCC-------CT----------------------------------TTTT----------------------TTTTTAATG---CCCCAAAATGCAAAACTGCCTT-CCCCG-GTGGCCCTTTGGAGCTA-GACGCC---GGTCTAAGAAAGTCC-----------ACTT--C---ACCGGGCCACGAAAAAGGGAAGGAC-------------------------TCT----T--CCAGG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14422767 216 - 17734757 CCAACCATATGATGCCAAGTTTGGGATTATTATTTCCCTCCA-GCCCCCAACCCCC-------TTGTTGTTTTGTTGTGTGTGTTTTGTTGTTTTTT--TTTT----------------------TTTTTAATG---GCCCGAAATGC-AAACTGCCTTCTCTGG-TGGGCCTTT-------AGGTCAAGAAAGCTATGTGACAGGGC-----------TCCC--T-----AAGACCGACCACCTGG----GACCAAGGCTTCC------CGGCCTGGCTCC----T--CCAGG i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 3629 201 + 20752 CAATCCAGGTGTTGCCACGTTTGGGGCGGTTCTTTTCTTCCC-T-------CTCCC-------CCGGTGTTTTG--GCTTTTGTCTTCTTG----GG--TTTT----------------------TTTTTAAGG---GTCCAA------ATATCGCCTT-TCCGG-CAGGCCTTTCTGAGCCAGGCCTTG---GGTCTGCAGGAGTGC-----------ACCC--T-----GCGGCAG------CGG----GACCTGGGCTGGCGAGAGACGAGGCGGCCCC----T--TCAGG i dasNov2.scaffold_28617 C 0 I 267 s monDom5.chr2 304517642 182 - 541556283 CAATCAAACTGCTGCCAAGTTTAGGATTGTTATTTTCTTCCCTA------ACCACC-------CTGC---------------------TCC--------TATA----------------------TTTTTAATA---GCCTCAAATGC-AATTTGCATT-CCCTGGTAAGAATTTTCTGGCAAGGATGTT---ACTCTAAAGAAGCAACTGGAGTAGAAGGTT--C---CCAGGAGGAAAGAAAGAT----GGT-------------------------TCC----T--ATAGG i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 6681 1648 + 24616 I e tarSyr1.scaffold_131410 7287 466 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I a score=227505.000000 s hg19.chr17_gl000204_random 36555 87 + 81310 AAAGGAGG---CG-------GAAAATCCAGGATACCAATGAAGTTCATTCTGGCCACCTGGCAC-----CGAAAGTGGAGCAAGAGACCAGAC---CTCT-TCCCC s calJac1.Contig5139 37388 88 + 225949 AAAGGAGGCTTCG-------GAAAGTCCGGGAGACCAGTGAAGTTCATTCTGG-TGCCTGGCAC-----CGAAAGTGGAGCAGG-GGCCGGAC---CCCT-TCCCC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 34734 87 - 95547 AAAGGAGG---CG-------GAAAGTCCAGGATACCAATGAAGCTCACTGTGGCCACCTGGCAC-----CGAAAGTGGAGCAGGAGACCAGAC---CTCT-TCCCC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75027358 87 + 78773432 AAAGGAGG---CG-------GAAAGTCTAGGATACCAATGAAGCTCACTCTGGCCACCTGGCAC-----CGAAAGTGGAGCAGGAGACCAGAC---CTCT-TCCCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16053522 87 + 17838096 AAAGGAGG---CA-------GAAAATCCAGGATACCAATGAAGTTCATTCTGGCCACCTGGCAC-----CGAAAGTGGAGCAGGAGACCAGAC---CTCT-TCCCC i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79466387 87 + 83384210 AAAGGAGG---CG-------GAAAATCCAGGATACCAATGAAGTTCATTCTGGCCACCTGGCAC-----CGAAAGTGGAGCAAGAGACCAGAC---CTCT-TCCCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 6772 87 - 64270 AAAGGAGG---CG-------GAAAATCCAGGATACCATTGAAGTTCATTCTCGCCACCTGGCAC-----CGAAAGTGGAGCAAGAGACCAGAC---CTCT-TCCCC i gorGor1.Supercontig_0007361 C 0 C 0 s otoGar1.scaffold_94362.1-287808 17960 38 + 287808 A-----------------------------------------------TCTGG----------C-----TGAATGTGGAGCCAGGA--CAGGC---CTTG-CCACC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 3785 54 + 15939 AAGGGAAG---TC-------GAAGGTC-----------------------------ACAGCCGC-----TGGAAGAGGACGAGG----CGGGC---CTGT-GCACA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118751017 77 + 121843856 AAGGAAGG---CT-------TGAGGTCACGG-------TGAAGGTCACTTGTG--AGGAGGCAC---ACTGCAGGTGGAGCAGGTT--CAGG----CTGT-CCACC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4382706 73 + 7991924 AAACAAGG---TG-------GAAGCTC-------------AGGGACACT--GG--AGCACGCTCCCAGCTGAAAGAGGAGCGCGTG--TAGGT---CTGA-CTACC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 1034 93 + 44242 AACAGAGG---TC-------AAAGGCCAAGGGCACTACTGAAGGTCATTTGGGCCAAGTGGCACTGGGTAGAAGAGGGAGGAGTGA--CAGATGGCCCAC-TCACC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 12282 86 + 41507 AAAGAAGG---CT-------CAAGGCCAAGGATGGCGGCAAAGGTCATTTCCACCAGGACACAC-----TGAAGGCGGGGCAGGGC--CAGG--GCCTGT-CCACC i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 120372 87 + 145505 AAAGAAAG---TT-------GAAGGTCAGGGATACTGATGAAGGTCATTCTGGCCACCTCTCCC-----TGTCAGTGAAGCAGGTAATGAGAC---CTGT-CCTCC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10852020 87 - 65312493 AAAGAAAG---TT-------GAAGGTCAGGGATACTAATAAAGGTCATCTTGGCCATGTCTCCC-----TGTCAGTGAAGCAGGTAAAGAGAT---CTGT-CCTCT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58034376 86 - 61308211 AAAGAAAG---GA-------GAAGGTCAAGGACACTAACGAAGGTCGTCTTGGCCGCGTGGCCC-----CGACAGTGAGGCAGGTGACGGACA---GGTG--CACC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 6564 86 + 132007 AGAGAAAG---CT-------GAAGGTCAAGGACACTGATGAAGGTCATTTCAGGCGCACACCGC-----TCACGGTGAGGCAGGTAATGGCAC---CTGG--CAAA i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59429120 86 - 64418924 AAGGAAAA---GT-------GAAGGTCAAAGATACTGATGAAGGTCACTTCACGCATGCAGCAC-----CCACAGTGAACCAGGTAACAGGAC---CTAG--CACC i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 7064 95 + 48268 ACAGAAGG---GTGAAGGCCGAAGGTCAAGGATGCTAACGAAGGTCATTTCGGCTGCGTGGCGC-----TGGCAGTGAAGCAGGTTAGTGGAA---CCTGTTCACT i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14422983 85 - 17734757 AGAGAAGG---TT-------GGAGGCCAGAGATAGTTCTGAAGGTGACCACAGCCA-ATAGCAC-----TGAAAACCAGGTAGGTAA-GGGGG---CTGT-TCCCC i loxAfr3.scaffold_49 C 0 C 0 s monDom5.chr2 304517824 85 - 541556283 AAGGAGAG---TT-------CCAGGTCAGTAATAATACCCATGATTATG--AACGAATTGACAA-----AGGACACTAAGTAGGAGAAGGGAT---TTGA-AGGCC i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 6681 1648 + 24616 I e tarSyr1.scaffold_131410 7287 466 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dasNov2.scaffold_28617 3830 267 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I a score=-16728.000000 s hg19.chr17_gl000204_random 36642 36 + 81310 --TGCCTTCTCCCTGGATG-------------------CTGCGTGTCCACCTCCTGG----- s calJac1.Contig5139 37476 36 + 225949 --TGCCTTCCCCCTGGATG-------------------CCGTGTGTCTACTCCCTGG----- i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 34821 36 - 95547 --TGCCTTCTCCCTGGATG-------------------CCGCGTGTCCACCCCCTGG----- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75027445 36 + 78773432 --TGCCTTCTCCCTGGATG-------------------CCGCGTGTCCACCCCCTGG----- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16053609 36 + 17838096 --TGCCTTCTCCCTGGATG-------------------CTGCGTGTCCACCTCCTGG----- i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79466474 36 + 83384210 --TGCCTTCTCCCTGGATG-------------------CTGCGTGTCCACCTCCTGG----- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 6859 36 - 64270 --TGCCTTCTCCCTGGATG-------------------CTGCGTGTCCACCTCCTGG----- i gorGor1.Supercontig_0007361 C 0 C 0 s otoGar1.scaffold_94362.1-287808 17998 33 + 287808 --TGTC--CTGCCTAGAC--------------------CTCCATGTCCATCCCCTGG----- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 3839 23 + 15939 --CGCCGCTTGC-----------------------------TGTGTCTGCTCCC-------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118751094 33 + 121843856 --TGTCTCACCA---GATG-------------------CTCTGTGCCTGGCCCTCAG----- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4382779 14 + 7991924 --TGTCTCAGCC---GGGG------------------------------------------- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 1127 33 + 44242 --TGTCCTCCCC---ACTG-------------------CTCCCTGCCTGGCCCTGTG----- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 12368 28 + 41507 --TGTCTCACC------TG-------------------CGCCATGCCAGTTCATG------- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 120459 34 + 145505 --TGTCTCACCT--GGAGG-------------------TTCCACCTCCATTCCCTGG----- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10852107 21 - 65312493 --T------------GAGA-------------------TTCTGCCTCAATTCCT-------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58034462 33 - 61308211 --TGCCTTGCTC--GGATG--------------------CTCAGCTCCTCTCCCTGC----- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 6650 34 + 132007 --TGTCTCGCCT--GGATG-------------------TCCCAACTCCATTCCCTGG----- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59429206 34 - 64418924 --TGTCTCACCT--GGATG-------------------CTTCATCTCTGTTCCTGGG----- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 7159 34 + 48268 --TGTCTCACCC--GGATG-------------------CTCCATCTCCATTCCCCAG----- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14423068 8 - 17734757 -------------------------------------------------TCTCTCAC----- i loxAfr3.scaffold_49 C 0 I 9 s dasNov2.scaffold_28617 4097 55 + 20752 --GGCCCTCCCCACGGACGCGAGGGGCGGCCGAGCCCACCGCGCGTCCAGCTCCCAG----- i dasNov2.scaffold_28617 I 267 I 146 s monDom5.chr2 304517909 43 - 541556283 AATTCTCCCATCTAAGAAC-------------------TCAAGTTTCCACTTCTAAAAATAG i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 6681 1648 + 24616 I e tarSyr1.scaffold_131410 7287 466 + 8975 M e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I a score=61065.000000 s hg19.chr17_gl000204_random 36678 93 + 81310 CGTTCAGATGGCCCCTTTCTCACCAGAAC-------GAAAAGG-AGA-AAGCAAGGAC--ATCAGCTCAGCCCTGGGGTAAGAGTTCTC-ATCACCA-CAAGG--CC--------C s calJac1.Contig5139 37512 89 + 225949 TGTTCAG-TGGCCCCTTTCTCACCAGAAT-------GGAAAGG-----ACTCAGGGTC--ATCAGCTCAGCCCTGGGGGAAGAGTTCTC-ATCTCCA-CAATG--CC--------T i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 34857 95 - 95547 CATTCAGATGGCCCCTTTCTCACCAGAAC-------GAAAAGG-AGA-AAGCAAGGAC--ATCAGCTCAGCCCTAGGGTAAGAGTTCTC-ATCGCCA-CAAGGCCCC--------C i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75027481 95 + 78773432 CATTCAGATGGCCCCTTTCTCACCAGAAC-------GAAAAGG-AGA-AAGCAAGGAC--ATCAGCTCAGCCCTAGGGTAAGAGTTCTC-ATCGCCA-CAAGGCCCC--------C i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16053645 93 + 17838096 CGTTCAGATGGCCCCTTTCTCACCAGAAT-------GAAAAGG-AGA-AAGCAAGGAC--ATCAGCTCAGCCCTGGGGTAAGAGTTCTC-GTCGCCA-CAAGC--CC--------C i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79466510 93 + 83384210 CGTTCAGATGGCCCCTTTCTCACCAGAAC-------GAAAAGG-AGA-AAGCAAGGAC--ATCAGCTCAGCCCTGGGGTAAGAGTTCTC-ATCACCA-CAAGG--CC--------C i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 6895 93 - 64270 CGTTCAGATGGCCCCTTTCTCACCAGAAC-------GAAAAGG-AGA-AAGCAAGGAC--ATCAGCTCAGCCCTGGGGTAAGAGTTCTC-ATCACCA-CAAGG--CC--------C i gorGor1.Supercontig_0007361 C 0 C 0 s otoGar1.scaffold_94362.1-287808 18031 100 + 287808 CATTCAGATGGCCCCTATCTCACCAGAAG-------GCAAAGG-GAG-AAACAGGGAC--ATGGACCCAGCCCTGGGG-AAATGTCCCC-ATTGCCA-TAAGG--CCCATGTCAGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 3862 68 + 15939 CACTCTCAGGGCCCCTCTCCCACCAGAAG-------GAAAAGC-AAG-AAACAGAGAC--TTGGAGGCAGC-----------------------------AGGCGCC--------C i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118751127 87 + 121843856 AGTCCAC--TGATCCTTTCTAACTAGAAG-------AGACGTA-AAA-CACCAGGAAT--ATTGGCACATCCCTGAGAGAAAATGTCTC-TTTGT-----AGA--CC--------A i mm9.chr11 C 0 I 10 s speTri1.scaffold_128901 1160 90 + 44242 CTGAGTG--GGCTCCTTTATCACCAGAAG-------GGGAACA-AGC-AGCAGGGGAC--ATCGGCCTAGCCCTGGACGG-AAGTTCTC-ACTGCGG-TGAGA--CC--------C i speTri1.scaffold_128901 C 0 I 1336 s turTru1.scaffold_106006 120493 86 + 145505 TATTC--------TTTTTCTCAGGGGAAG-------GGGCAGG-GGT-ACACAGGGAC--ATCCCTGCAGCCCTGGGAGAAACCTTCTC-ACTGTGACCCATG--TC--------A i turTru1.scaffold_106006 C 0 I 1 s equCab2.chr11 58034495 77 - 61308211 TGCTC-AGACGCTCCCTTCCCCCTAGAGA-------GGAAGGG-GAG-ACAC-GGGAC--ACGCACAC---------------GTTCTC-ACTGTGACCCACG--TC--------A i equCab2.chr11 C 0 I 1 s felCat3.scaffold_206428 6684 89 + 132007 CGTCC-GGTGGCCCCTTTCTCACCGAAA---------GAAGGA-TGG-ACACAGGGAC--ACCAGGGCAG-CCTGGGAGAGAGGCTCT--AACGTGACCCATG--TC--------A i felCat3.scaffold_206428 C 0 I 1 s canFam2.chr9 59429240 94 - 64418924 CGTCCAGAAGGCCCCTTGCTCACCACAAG-------GGAAAGG-CGG-ACACGGGGAC--ACCCACCCGGCCCTGGGAGAGAGGTTCTC-GCCATGACCCAGG--CC--------A i canFam2.chr9 C 0 I 1 s pteVam1.scaffold_11245 7193 94 + 48268 TGTCCAGATGGCCCCTTTCTAACCAGAAG-------GGCAAGG-GGG-ACACGGGGAC--ATCCATGCGGCCCTGAGACAAGTGTTCTC-GCCGTGACCCACT--TC--------A i pteVam1.scaffold_11245 C 0 I 1 s loxAfr3.scaffold_49 14423085 91 - 17734757 CA-TCCTATGTCCTCTTCCTCACCAGAAG-------GGCAAGA-AGG-ACAGAGGCAC--CCATG--TGGCCCTGAGAGTAGTGTTCTCGGTTGTGA-CGACG--CC--------C i loxAfr3.scaffold_49 I 9 I 7 s dasNov2.scaffold_28617 4298 82 + 20752 CACTTGGGTGTCCCCTTTCTCACCAGAAG-------AGAAAGG-AGGAAAAGAGGGTC--ATCGG--CAGCCCTG------GCACACAC-----CGG-CAAAG--CC--------C i dasNov2.scaffold_28617 I 146 I 6 s bosTau4.chr19 10852128 43 - 65312493 -----------------------------------------------------GGGA---------GCAGCCCTGGGAGAAGCTTTCTC-ACCGTCACCCACG--TC--------A i bosTau4.chr19 C 0 I 1 s oryCun2.chrUn0958 12396 7 + 41507 ---------------------------------------------------CAGGGCC---------------------------------------------------------- i oryCun2.chrUn0958 C 0 C 0 s cavPor3.scaffold_76 4382793 51 + 7991924 ---------------------------------------------------CAGGGAC--ATCATCGCAGCCTTGGGGGATGTGTCCTC-TCTGCCA-TAAGG--CC--------A i cavPor3.scaffold_76 C 0 I 9 s tarSyr1.scaffold_131410 7753 79 + 8975 ----------------------CTAGAAG-------GGAAAGGAAGG-AAACAGGGAA--ATCAACTCAG-CCTGGGGAAAGTGTCCTC-ATCATCA-TAAGG--TCCATGTCAGC i tarSyr1.scaffold_131410 M 466 C 0 s monDom5.chr2 304517952 97 - 541556283 CATAAACACTTGCCCTTCCTCATCAATAAACAGGCTGTaaagt-tgg-a---aggaactagtcaaatctacacctaacaaggaattgtc-at-ataa-tatac--cc--------- i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 6681 1648 + 24616 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I a score=-39980.000000 s hg19.chr17_gl000204_random 36771 36 + 81310 AGGAGGACAATATCAAA-CACAGCCAGC----------------A-----TGGACCCC s gorGor1.Supercontig_0007361 6988 36 - 64270 AGGAGGACAATATCAAA-CACAGCCAGC----------------A-----TGGACCCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79466603 36 + 83384210 AGGAGGACAATATCAAA-CACAGCCAGC----------------A-----TGGACCCC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16053738 36 + 17838096 AGGAGGACGATGTCAAA-CACAGCCAGC----------------A-----TGGACCCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75027576 36 + 78773432 GGGAGGACAATGGCAAA-CACAGCCAAC----------------A-----TGGACCCT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 34952 36 - 95547 GGGAGGACAATGGCAAA-CACAGCCAAC----------------A-----TGGACCCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 37601 36 + 225949 GGGGGGAAAATAGCAAG-CACAGCCAGC----------------G-----TGGACCCC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 7832 36 + 8975 AGGAGAATGATGGCGAA-GACGGGCAGT----------------G-----TGGACCCT i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 18131 41 + 287808 AGGAGAATGATGGTCAG-GACAGCTGGG----------------GACAGCTAGACCCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 3930 15 + 15939 AG--------------------GCTAGG----------------G-----TGGGCC-- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118751224 25 + 121843856 ---AGAGAGAAGGACAT-CAGGGACATG----------------G------------- i mm9.chr11 I 10 C 0 s cavPor3.scaffold_76 4382853 32 + 7991924 ---GGAATGAAGT-CAG-CGAGGGCTAG----------------G-----TGCACCCC i cavPor3.scaffold_76 I 9 C 0 s oryCun2.chrUn0958 12403 16 + 41507 ---AGGAGGACAAACGG-CA-------------------------------------- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 120580 23 + 145505 -------------GGAA-GAGGACTAGC----------------A-----TGGACCCC i turTru1.scaffold_106006 I 1 C 0 s bosTau4.chr19 10852172 23 - 65312493 -------------GAAA-GAAGACTAGA----------------G-----TGGACCCC i bosTau4.chr19 I 1 C 0 s equCab2.chr11 58034573 23 - 61308211 -------------GGGA-GAGAGCCAGC----------------T-----CAACCCCC i equCab2.chr11 I 1 C 0 s felCat3.scaffold_206428 6774 23 + 132007 -------------AGAA-GGGGACTAGT----------------A-----CAGACCCC i felCat3.scaffold_206428 I 1 C 0 s canFam2.chr9 59429335 23 - 64418924 -------------AGAG-GGGGACTAGT----------------A-----CAGACCCC i canFam2.chr9 I 1 C 0 s pteVam1.scaffold_11245 7288 24 + 48268 -------------AGAACAGGGGCTAGA----------------G-----CAGACCCC i pteVam1.scaffold_11245 I 1 C 0 s loxAfr3.scaffold_49 14423183 52 - 17734757 CAGAGGATGGGGGGTGA-GACGGCTGTGCGGATGCCTGTGTAAGG-----CGTGCTCC i loxAfr3.scaffold_49 I 7 C 0 s dasNov2.scaffold_28617 4386 45 + 20752 CAGAGGACACCGTAGAA-GGGGCCAGGCCAGCTGCCC-------A-----CGGGCTCC i dasNov2.scaffold_28617 I 6 C 0 s monDom5.chr2 304518049 31 - 541556283 -----aacaagtgatta-tccaatctgc----------------c-----tgaatctc i monDom5.chr2 C 0 I 8722 e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 6681 1648 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I a score=-277438.000000 s hg19.chr17_gl000204_random 36807 193 + 81310 A----CCCCAAATCT-CAAAGAAATCTTCAATGAAC---CCC------AAGA----AG-----------GGGCCTCA-------------------------------------------------AGAC--TGCAGCCAACTTCTCAGA-------------------------------------------------A--TTCCCCA--------------------------------------AGCATC---------------------------------------------CAGCCTCTCAGGAGCACAAAAGAAGCCTGTGAGCAG-CTTCCCAGC------------------------CCTCGG------A-----GGGAC---------------------------------GAGAAGTT----CCCGTGT---C------TGCCG------GGG------------------------ACCCTGGGA---------------------------------------------GCAGGGAGCTGT-CGCCGCC s gorGor1.Supercontig_0007361 7024 193 - 64270 A----CCCCAAATCT-CAAAGAAATCTTCAATGAAC---CCC------AAGA----AG-----------GGGCCTCA-------------------------------------------------AGAC--TGCAGCCAACTTCTCAGA-------------------------------------------------A--TTCCCCA--------------------------------------AGCATC---------------------------------------------CAACCTCTCGGGAGCACAAAAGAAGCCTGTGAGCAG-CTTCCCAGC------------------------CCTCNG------A-----GGGAC---------------------------------GAGAAGTT----CCCGTGT---C------TGCCG------GGG------------------------ACCCTGGGA---------------------------------------------GCAGGGAGCTGT-CGCTGCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79466639 193 + 83384210 A----CCCCAAATCT-GAAAGAAATCTTCAATGAAC---CCC------AAGA----AG-----------GGGCCTCA-------------------------------------------------AGAC--TGCAGCCAACTTCTCAGA-------------------------------------------------A--TTCCCCA--------------------------------------AGCATC---------------------------------------------CAACCTCTCAGGAGCACAAAAGAAGCCTGTGAGCAG-CTTCCCAGC------------------------CCTCGG------A-----GGGAC---------------------------------GAGAAGTT----CCCATGT---C------TGCCG------GGG------------------------ACCCTGGGA---------------------------------------------GCAGGGAGCTGT-CGCTGCC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16053774 193 + 17838096 A----CCCCAAATCT-CAAAGAAATCTTCAATGAAC---CCC------AAGA----AG-----------GGGCCTCG-------------------------------------------------AGAC--TGCAGCCAACTTCTCAGA-------------------------------------------------A--TTCGCCA--------------------------------------AGCATC---------------------------------------------CAACCTCTCGGGAGCACAAAAGAAGCCTGTGAGCAG-CTTCCCAGC------------------------CCTCGG------A-----GGGAC---------------------------------GAGAAGTT----CCCGTGT---C------TGCTG------GGG------------------------CCCCTGGGA---------------------------------------------GCAGGGAGCTGT-CGCTGCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75027612 192 + 78773432 A----CCCCAAATCT-CAAAGAAATCTTCAATGAAC---CCC------AAGA----AG-----------GGGCCTCG-------------------------------------------------AGAC--TGCAGCCAACTTCTCAGA-------------------------------------------------A--TTCACCA--------------------------------------AGCATC---------------------------------------------CAGCCTCTTGGGAGTGCAAAAGAAGCCTGCAAGCAG-CTTTCCAGC------------------------CCTCGG------A-----GGGAC---------------------------------GAGAAGTT----CCCGTGT---T------TGCTG------GGG-------------------------CCCCGGGA---------------------------------------------GCAGGGAGCTGT-CGCTGCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 34988 237 - 95547 A----CCCCAAATCT-CAAAGAAATCTTCAATGAAC---CCC------AAGA----AG-----------GGGCCTCG-------------------------------------------------AGAC--TGCAGCCAACTTCTCAGA-------------------------------------------------A--TTCACCA--------------------------------------AGCATC---------------------------------------------CAGCCTCTCGGGAGTGCAAAAGAAGCCTGCAAGCAG-CTTTCCAGC------------------------CCTCGG------A-----GGGAG---------------------------------GAGAAGTT----CCCGTGT---C------TGCTG------GGG-------------------------CCCCGGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCTGT-CGCTGCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 37637 193 + 225949 A----CCCCAAATCT-CAAAGAAATCTTCAAAGAAC---CCC------AAGA----AG-----------GGGCTTCA-------------------------------------------------AGAC--TGTAGCCAACTTGTCAGA-------------------------------------------------A--TTCACCA--------------------------------------AACATC---------------------------------------------CAACCTCTCAGGAGTGC-AAAGAGGCCTGTGAGCAGTTTTCCCAGC------------------------CCTCGG------A-----GGGAC---------------------------------GAGCCGTT----CCTGTGT---C------TGCTG------GGG------------------------CCCCTGGGA---------------------------------------------GCAGGGAACTCT-CACCGTC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 7868 200 + 8975 G----TCCTAATCCTAGAAAGAAGCTGTCAGTGAAC---CTC------TAAAAGAGAG-----------GGCCCTCA-------------------------------------------------AGAC--TATGGCTGATTTGTCAGA-------------------------------------------------A--CTCACCA--------------------------------------GAAGTC---------------------------------------------CAGCTTCTTAGCCACG-----------TGCGAGCAG-CTTCCCGGCCCAAGTCA----------------CCTCTG------ACACCCTGGAG---------------------------------GGTGTGAT----CGCATGT---C------TGCTG------GGG-------------------------CCCAGGGA---------------------------------------------ACAGGGAACAGTCCTCTGTC i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 18172 213 + 287808 G----CCCTAAACCT-CCAAGAAATCCTCAGTGAGCC-TCCC------AAGA----AG-----------AGGC------------------------------------------------------GGG--GGCAGGAGACTGTGCCAG-------------------------------------------------A--TTCACCA---------------------------------------GCGTC---------------------------------------------CCACCTCCGGGCACCATAGAGGAGGCCTGTGAGCAG-CTCCTGTGC------------------------CCTCAG------G-----GAGACAGATCACCTCTGACACCCTAGGTG---------GTACACTT----TAGGTGT---C------TGCCA------GGG-------------------------CCCTAGGG---------------------------------------------ACAGAGACCCGTCCTCCATC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 3945 123 + 15939 G----TCCCGAACCT-ACAGGAAGTATTCA-CGCAC---CTCTTCAGAGAAG----AG-----------GGGC------------------------------------------------------------------------TCCGG-------------------------------------------------A--CTGGCCA--------------------------------------GACA--------------------------------------------------------------------------------CAG-ACTC-----------------------------CCACAG------G-----TGTCC-------------------------------------------------------C------CACTG------GGG------------------------CCCCTAGCC---------------------------------------------GCAAGAAGCTGTCCTCCGCC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118751249 240 + 121843856 ------CCCAAATCT-CGGGGCCATCTTTAAAAAGC---CTC--------------TG-----------GGAGCTCA-------------------------------------------------AGGC--CGCAAGTGGCTTGCTAGA-------------------------------------------------C--CCAACTA--------------------------------------GGCATT---------------------------------------------CAGCCTTCCA---CAGCACAGACATTCAGTGAGCAG-CTTGCCTGTGCACGACCCCCATCACCACCTTTCCCTCAC------A-----GACACATATCCCTTCTGATACCTGAGATGGCATCCTTCAAGAATCT----GCCATG----C------TACTG------AGG------------------------CCTGTGGGA---------------------------------------------ACAGGAAGCTGTCCTCTGT- i mm9.chr11 C 0 I 1 s cavPor3.scaffold_76 4382885 234 + 7991924 A----CCCCAATCCT-CAAACCGGCCTTCGAGGAAC---CTC----CACAGG----TA-----------GGGCCTCT-------------------------------------------------AGAT--GGCAGCAGATTCCCCtgg-------------------------------------------------cgtcccacgt--------------------------------------ggcgtc---------------------------------------------ccatgtggcg---tcccacgtggAGAAGATGAGCAG-CCTG---GCCCATGGCCCCTA------------CCTTA-------A-----GGGACAAGTCACTTCTGATAGCTGGGATGGTGTCCTCCAAGTGTCT----TCCATG----T------GCTCA------AGG------------------------CTCTGAAGA---------------------------------------------GCAAGACACTGCCCTCTGT- i cavPor3.scaffold_76 C 0 I 1 s oryCun2.chrUn0958 12419 80 + 41507 ------CCTGATGGT-TGGAG--------AAAGGCC---CTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTGCCTGCAAGTGGCC----------------------------G-----G------------CCTGACACC--GGACGGTACCCTGGGAGTCCCT----------------------------------------------------------------GGGA---------------------------------------------GC------------------ i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 120603 169 + 145505 A-----CCCAAACCT-CAGAGAAATCTTCAATGAAC---CTC-TTAAGAGGA----GA-----------GGGGCTCA-------------------------------------------------AGAC--TGGGACTGACTTGCCAGA-------------------------------------------------A--ATC-CCAG-------------------------------------GGGGTC---------------------------------------------CCACTTCCCA-GAACACAAAATAAGCCTGTGA-CAG-CTTCT----------------------------------------G-----AAGAT---------------------------------ACT--TCT--------------------------------GGG-------------------------CCCTGGAA---------------------------------------------GGAGGGAGCTATCCCTTGT- i turTru1.scaffold_106006 C 0 I 44 s bosTau4.chr19 10852195 169 - 65312493 G-----CCCAAACCT-CAGAGAAATCTTCAATGAAA---CTC-TTATGCAGA----GA-----------GAGGCTCG-------------------------------------------------AGAC--TGAGGCTGACTTGCCAGA-------------------------------------------------G--ATC-CCA--------------------------------------GCGGTC---------------------------------------------CCACTTCCCA-AAGCACAGAACAAGCCTGTAA-TGA-CTTCT----------------------------------------G-----AGGGC---------------------------------AAG--GCT--------------------------------GGG-------------------------CCCTGAAA---------------------------------------------GGAGGGAGCTGTCCCCTGTC i bosTau4.chr19 C 0 I 41 s equCab2.chr11 58034596 167 - 61308211 T----CCCCGAACCT-CAAAGAAATCCTCAGTGGAT---TCT-TGAGAAGAC----GG-----------GG--CTCG-------------------------------------------------AGAC--TGGAGCTGACTTGCCGCA-------------------------------------------------G--TTC-CCA--------------------------------------GGGG-----------------------------------------------CCACTTCCGGGGGGCACAAAGGAGGCCGGTGAGCAG-CCTCT----------------------------------------G-----AAGAC---------------------------------AAGCCCCT-----------------------CTG------AGG-------------------------TCCTGCCG---------------------------------------------GGAGGAGGGGCGCC------ i equCab2.chr11 C 0 I 16 s felCat3.scaffold_206428 6797 214 + 132007 A----CCCCAAACCT-CACGGAAATCTCCAATAAAC---CTC-TTAGGAGCA----GA-----------GGCACTCA-------------------------------------------------AGAC--TGGAGCCAACTTGCCAGA-------------------------------------------------G--ATG-CCG--------------------------------------GGGGTC---------------------------------------------CCGCCCCCCAGGAGCACAAAGTAGGCC-GTGAACAG-CTTCT----------------------------------------G-----AAGAC---------------------------------AAGCCACT-TCCAAAGGCA---C------CGCTG------GGCTTCCAAGGGCACTGCTGTCCCCTGTCCCTTCCA---------------------------------------------CCAGCTGTGTTTTCAGTACA i felCat3.scaffold_206428 C 0 I 27 s canFam2.chr9 59429358 190 - 64418924 A----CCCCAAACTT-CACGGAAATCTCCAGTGAAC---CTC-TGATGAGAA----GA-----------AGTGCTCA-------------------------------------------------AGGC-AGGGGGCCAACTTGCCAGA-------------------------------------------------A--ATC-CCC--------------------------------------GGGGTC---------------------------------------------CCACCTCCCAGAGGCACAATGTAGGCC-TTGGCCAG-CTTCT----------------------------------------G-----AAGAC---------------------------------AAGACACT-TCCAAAGGCA---T------TGCTG------GGC-------------------------TCCTGGAA---------------------------------------------GGAGAGAGGTGTCCTCTGTC i canFam2.chr9 C 0 I 53 s pteVam1.scaffold_11245 7312 191 + 48268 G----CCCCTAGCCT-CAGAGAAACCTTCGATGAAC---CTC-TTCTGAGGA----GA-----------GGGGCTCG-------------------------------------------------AGAC--TGGGGCTCACCTGCTAGA-------------------------------------------------A--ACC-CCA--------------------------------------AGTGTC---------------------------------------------CCCCTTCCCAAGGACGCCGAAAAGGCCTGTAAGCAG-CTTCT----------------------------------------G-----GAAAG---------------------------------AGGGAGCTGTCCCCTGTCC---C------TTCTGCCACATGTT-------------------------TTCAGCTC---------------------------------------------AGAGCAGTGTTGCC------ i pteVam1.scaffold_11245 C 0 I 14 s loxAfr3.scaffold_49 14423235 419 - 17734757 ACCCACTCCAGACCT-CCAAGACATCGTCAGTGGACA--CGT-GAGAGGAGA----GAAgggagccctggtggcacaaccattaagtgtttggctgctaaatgaaaggtcaacagttcaaaccagcagctctgaggggcagctctgagggggaaagacctagcgatctgctcctgtaagactccagcctaggaaacccta--tgcggcagctctattctgtcacgtggagtcactgtgtgttggCTCAACAGCACCCAACAACAACCGCAAAGAGGAGGGGGCAATCAGGACAGGGTATAACTGGTCAGAATCTGCCAGTTTGCCTCTTGACTC-CTAGCCCCT------------------------CCAAGGACAGTCC-----TGGAT---------------------------------GGCGTCTT----GTTACTTATCTGCCCAGTGCCA------AGG------------------------ACCCAGGGC---------------------------------------CCCCAGAAAGAGGGCTGGCCCTTGTT i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 4431 192 + 20752 AGCGTGCCTGAGCCT-CCCAGAAGCCACCGGTGAGCGCTCTT-AAGAGGGGA----GA-----------GCAGCACG-------------------------------------------------AGCT----GGGGCAGCTCACCGGA-------------------------------------------------A--TGCGACAG-------------------------------------ACCAGC---------------------------------------------CAGCTGCTCA----------------CTCGAGGCTC-CCTCCCCTT------------------------CCCAGGG-----G-----TGGAC---------------------------------AAGCCATT----CTGACTC-TCT------TGCTG------AGG------------------------CCCCTGGCC---------------------------------------------AGAGGGGACTGTCCCCAGTC i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_6980 56737 1113 + 61692 I e proCap1.scaffold_29042 6681 1648 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I a score=-5769.000000 s hg19.chr17_gl000204_random 37000 233 + 81310 -----------------------------------------------------------------------------------CCTTCCTC-CCAAGCCTG--CT--CACTGTTCCAGAAACAAGGAGTCCAGGAGAAGAGCCAGGATGGGGGAATAAAGGTT-----T----CCAT---GAGGGGAGAT-CCCAGAGAGGCCCCCT-GAA--CCTGGCAGTCAC-GTGGTCCCGGGGGTCGGCACCCATTGCCATGTGTCCCCCCT--GGCACAGGTGTCGCTGGG---GGCCAAGGCTT--------CAGA----AGTTACTGCTG-----GAATGAGCCCACCTGCCTC--GGGGGCTT s gorGor1.Supercontig_0007361 7217 233 - 64270 -----------------------------------------------------------------------------------CCTTCCTC-CCAAGCCTG--CT--CACTGTTCCAGAAACAAGGAGTCCAGGAGAAGAGCCAGGATGGGGGAATAAAGGTT-----T----CCAC---GAGGGGAGAT-CCCAGAGAGGCCCCCT-GAA--CCTGGCAGTCAC-GTGGTCCCGGGGGTCGGCACCCATTGCCATGTGTCCCCCCT--GGCACANGTGTCACTGGG---GGCCAAGGCTT--------CAGA----AGTCACTGCTG-----GAATGAGCCCACCTGCCTC--GGGGGCGT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79466832 233 + 83384210 -----------------------------------------------------------------------------------CCTTCCTC-CCAAGCCTG--CT--CACTGTTCCAGAAACAAGGAGTCCAGGAGAAGAGCCAGGATGGGGGAATAAAGGTT-----T----CCAC---GAGGGGAGAT-CCCAGAGAGGCCCCCT-GAA--CCTGGCAGTCAC-GTGGTCCCGGGGGTCAGCACCCATTGCCATGTGTCCCCCCT--GGCACAGGTGTCGCTGGG---GGCCAAGGCTT--------CAGA----AGTTACTGCTG-----GAATGAGCCCACCTGCCTC--GGGGGCTT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16053967 234 + 17838096 -----------------------------------------------------------------------------------CCTTCCTC-CCAAGCCTG--CT--CACTGTTCCAGAAACAAGGAGTCCAGGAGAAGAGCCAGGATGGAGG-ATAAAGGTT-----C----CCAC-ATGAGGAGAGAT-CTGAGAGAGGCCTCCT-GAA--CCCGGCAGTCAC-GTGGTCCTGGGGGTCGGCACCCATTGCCATGTGTCCCCCCT--GGCACAGGTGTCGCTGGG---GACCAAGGCTT--------CAGA----AGTCACTGTTG-----GAATGAGCCCACCTGCCTC--GGGGGCTT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75027804 233 + 78773432 -----------------------------------------------------------------------------------CCTTCCTA-CCAAGCCTG--CT--GACTGTTCCAGAAACAAGGAGTCCAGGAGAAAAGCCAGGATGGGGG-ATAAAGGTT-----C----CCAC-ATGAGGGGAGAT-CCCAGAGAGGCCTCCT-GAA--CCTGGCAGTCAC-GTGGTCCTGGGGGTTGGCACCCATCGCCATGTG-CTCCCCC--GGCACAGGTGTCACTGGG---GGCCAAGGCTT--------TGGA----AGTCACTGCTG-----GAATGAGCCCTGCTATCTC--AGGGGCTT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 35225 234 - 95547 -----------------------------------------------------------------------------------CCTTCCTTACAAAGCCTG--CT--CACTGTTCCAGAAACAAGGAGTCCAGGAGAAGAGCCAGGATGGGGG-ATAAAGGTT-----C----CCAC-ATGAGGGGAGAT-CCCAGAGAGGCCTCCT-GAA--CCCAGCAGTCAC-GTGGCCCTGGGGGTCGGCACCCATCGCCATGTG-TCCCCCG--GGCACAGGTGTCACTGGG---GGCCAAGGCTT--------CGGA----AGTCACTGCTG-----GAATGAGCCCTGCTATCTC--AGGGGCTT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 37830 230 + 225949 -----------------------------------------------------------------------------------CCTTCCTC-GCAAGCCTG--CT--TACTATTCCAGAAAC---GAGTCTAGAAGGAGAGCCAGGATGAGGG-ATAAAGGCT-----C----CCAC-AACAGGGGAGAT-CCCAGAGAGGCCCCCT-GAA--CCCGGCAGTCAC-ACAGTTCCGGGGGTCGGCACCCATTGCCATGTATCCCCCGT--GGCACAGGTATTACC-TG---GACCAAGGTTT--------TAGA----AGTCACTGCTG-----CAATGAGCCCACCTGCCTT--GGGGGCTT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 8068 223 + 8975 -----------------------------------------------------------------------------------CCTTCCTC-CTGAG-CTG--CT--TGTTGTTCTGGAAACAAGGAATCTGGGAGAAGAGCCAAGATAGAAG-ACGAAGGCT-----C----CCACCATGAGCG--GAT-CCAAGAGAGATC-CCT-GAG--CTTGGGGGTTGCGGCGGTCCCAGTGGTCAGCATGC---GTCATGTG-TCCCTGT--GGTGCTGGTGTCAC--------AACGTGGTTT--------CAGA----AGTCACTGCTA-----GAATGAAACCACCTGCTCC--AGGGCCTT i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 18385 223 + 287808 -----------------------------------------------------------------------------------CCTTCCAC-CTAAACCTA--CTTACACTTTTCTGGAAACAAGGAATCCAGGAGAAGCAACAGGATGGG---GTAAAGGGT-----C----CCTCCACAAGAGAAGAT-CTGAGAGAGACA-TCT-GAG--CCTG---------GCTGTTCCAGTGGTTGCCACCCATCAGGATATGTCTCCCAT--GG---AGGTGTCACCAGG---GGCTGAGGCTT--------CAGG----AGTCACTGCAG-----GAATAAGCCCATCTGCCCC--GGAGGCTT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 4068 215 + 15939 -----------------------------------------------------------------------------------CCTTCTTC-CCGAGCCTG--CC--CACTGTCCCACAAATGGGGGGCCCAGGAAGAGAGCCAGGTTGGG---GTCGGGGGT-----C----CCACCCCAGGAGCAGGT-CCAAAAGGG--CCCCT-GGG--CCCA---------GTGG-CCTGGCAGTCGGTGCCACCGGC--TGTGCCCACTGT--GGTGCAGGTGAGGCCAGG---GGCCACAA-TG--------TGGA----AACTGCT-CTG-----GAACCAG-CCACCGGCTCC--AGGCGC-- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118751490 192 + 121843856 -------------------------------------------------------------------------------------------------------TT--TCTTGTTCTAGAAGCAAGGCAC------------CCAGGA----------AAGCGACCCCCC----CCCC-ATGAGTGAAGAT-CTGGGAGA--CACCCA-GAGACCCTGGGGGCTG--GATATCCAGTG-------ACACATGCCCCCCCCCCCCCAGA--AGCTCAGGTATATCTAGG---GACCAGGGCTC--------TAGA----AGTCATTGCTG-----GAGTGAGCTCATCT-GTTT--GGGGGCTT i mm9.chr11 I 1 C 0 s cavPor3.scaffold_76 4383120 182 + 7991924 -----------------------------------------------------------------------------------CCTTCCTC-AACAGCCTA--CT--CCCCATCTCAGCAGTAGGGACC-CTGCAGAAGAGCCAGGATGGGAG-GTGAAGGGTCCTGGT----CCCC-ACCA-TGAAGAG-CTGAGAG---CCCTCA-GAG-CGCAGGGATCCC--AATATCCA----------------------------CCACA--A-------------TGAG---GACACGAG-----------TGGA-----------GCCA-----GGGTGACCCCACCT-TCTC--TGGGGCCA i cavPor3.scaffold_76 I 1 C 0 s oryCun2.chrUn0958 12499 146 + 41507 ---------------------------------------------------------------------------------------CTTC-CGTGG------CT--CTATGTTCCAGAAATGAGGAATGCAGGGGACTGGCTGGGA-TGGGG-GCACAGGGT-----C----CCCG-GTGAGCAAAGAC-CCCGGACA--GACCCT-GAG--CCTGGCAGCCC--GCAGCC------------------------------CCACA--G--------------------TGCAGGGC--------------------------GGCT-----GTG---------GC-CTCC--AAA----- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_6980 57850 163 + 61692 -----------------------------------------------------------------------------------CCTTCCTC-TGAGA------TTC-CTCTGTCCCAGAGACAGGGAACCCGAGAGAAGAGCTGGGA-TGCGG-GTGCAGGATCTGCCC----CCCT-CCGAGTGAAAAC-TGTG------GAGCCT-GCA--CCTGGCAGGCC---CAGCCCA----------------------------CCCCA--G--------------------AGCCCGGT--------------------------GGCG-----GGGTG---CCACTC-CTCC--AGAGGCC- i ochPri2.scaffold_6980 I 1113 C 0 s turTru1.scaffold_106006 120816 212 + 145505 -----------------------------------------------------------------------------------CCCACTTC-CCCAG------CT--CGCTGTCCTGG--------------GACACGGATCCAGGACTGAGG-ATGAAGAGT-----C----CCGTCACAAGAGATGCA-CCAAGAGGGACCCCTGAGCA--CCTG----CCCT-GGAGTCCCAAGTGCTGGCATCCATTGCAACATGTCCACC----CAGGGCCAGGTAGCCCCA---GGTTGAGGCTT--------TGTG----AGTCAAGGCTG-----GACTGAGCCCACCTGCACC--AGGGGCTG i turTru1.scaffold_106006 I 44 C 0 s bosTau4.chr19 10852405 207 - 65312493 -----------------------------------------------------------------------------------CCCCCTTC-CGCAT------CT--TGCTGTCCTGG--------------GACACGGATCCCGGACTGAG-------GAGT-----C----CCTCCAGGAGAGGTGCA-TCAAGAGAGACCCCTGAGCA--CCTG---CCCCC-GGGATCCCAGGGGCTGGCATCCATTGCAATGTGTCCATC----CCGGGCCAGGTAGCCTCT---GGCTAATGTTT--------CATG----AGTCAAGGCTG-----GACTGAGCTCACCTTCCCC--AGGGGCTG i bosTau4.chr19 I 41 C 0 s equCab2.chr11 58034779 210 - 61308211 -----------------------------------------------------------------------------------CCCAC-TT-CCCAC------CT--CACTGCCTCAG--------------GGTGCGGAATCA-GATTGGGG-GTGAAGAGT-----C----CCCCCG-GAGAGGAGCA-CTGAGAGAGACCCCTGAGCA--TCTG----CACG-GGGGTCCCGGCGGCTGGCCTCCACAGCTGCATGTCCACT-C--GGGGGCAGGGTGGCCGGG---GCCCGAGGCTC--------TGGG----AGTCACCGCTG-----GGCTGGGCCCACCTGCTCC--GGGGGCTT i equCab2.chr11 I 16 C 0 s felCat3.scaffold_206428 7038 204 + 132007 -----------------------------------------------------------------------------------CCCACCTC-CCCAC------CT--CGCTGTCCCAG--------------GACAAGGATCCAGGACTGGGG-AGGA--AGT-----C----CTGCCATGAAGGGCGCAACCAAGAGAGACACCTG---------------CCC-GGGGGCCCAGGGGCTGACAGCCATGGAGGGATGTCCATCAT--GGGGGCAGGGAAGCCAGG---GGCCAAGGCTT--------TGGG----AGTGCCTGCGG-----GAAGGAACCCACCTGCTCT--GGGGGCTT i felCat3.scaffold_206428 I 27 I 517 s canFam2.chr9 59429601 195 - 64418924 -----------------------------------------------------------------------------------CCCATGCC-CCCAC------TC--TGCTGTCCCAG--------------GACAAGGATCCAGGGCTGGGG-ATGA--AGT-----C----CTACCATGAGTTATGCACCCAAGAGAGACACCTA---------------GCC-GGAGTCCCTGTTGCAGGCAGCCACAGAGGTATGCCCACCAT--GGGGG---------CAGG---GGCCAGGGCTT--------TGGG----AGCTCCTGCTG-----GAATGAGCCCACCTGCTCC--AGGGGCTT i canFam2.chr9 I 53 C 0 s pteVam1.scaffold_11245 7517 207 + 48268 -----------------------------------------------------------------------------------CCCTCTCC-TCCAC------CT--TGCTGTCCAGA--------------AAGCCAGACCCATAATTGGGG-GTGAAGAAT-----C----TCACCACAAGAGGCACACCCAAG---GAGACCCA-GCA--TCTA----CACG-GGGATCCAGGCGGCTGGCATCCATCACCGTGTGTCCCCCAC--AGGGGCAGAGCAGTCCTG---AGCCAAGGCTC--------TAGG----AGTCACTGCTT-----GAATGAGCCCACCTACCTG--TGAG---- i pteVam1.scaffold_11245 I 14 C 0 s loxAfr3.scaffold_49 14423654 285 - 17734757 CCTTCTCCTTAGCCTGGCCTC---TTAAAGGAGCCTTGTGCATTTTAAACTCAA--CCTGGCATTGCCCAGCA-------TAGCTTTCACC-CAT--CCCCCCTT--CACTGTTCCAGGGACACAGACCCCA--AGAGGACCCAGGGTTAAAG-AGGAAGGGA-----CTAGCCCAC-ATGAAGC------CTCTGCCAAGGTCCCA-GGG---------------GGAGGCCATGAGA----------------CATGTCCACGTGA-GGGGCAGGTGTAGGCAG----GACCGAGGCTCTGTGAGCAGAGG----GGGCACTGGCACCACCACAAAGGGCCAGCAGCT----CAGGGCAT i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 4623 282 + 20752 CCCTCAACCCAGGCTTGGCTCCCTTCAAAGG--------GCGTGTTAGCCTCCAGGCCTGGCATTGCTCACCACTGCCACCAGCTCTCAGC-CACAGCCCGTCTG--TGCTGCCCTGGTGACAAGGACAC------GGCATCCAGCTCCCCAG-GGTCAGGGC-----CAAGGCCCC-CCAAAA-----------GTGAGGCATCCA-AGA---------------GAGGCCCCCGAGCCT--------------CCTGCCATCTTGAGGGGGCACACGTGGGCCGGCCTGGCCAGGGCTC--------AAGGCTTTGGGCATCGG-------GCACGGGGACGGGAGCTGCTGGGGGGCAC i dasNov2.scaffold_28617 C 0 C 0 e proCap1.scaffold_29042 6681 1648 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I a score=44851.000000 s hg19.chr17_gl000204_random 37233 110 + 81310 C------CTTCATCTCAAAACTCAGAGTG---------TTGTCACAGCCACGCTGCCACTCTAGAATTCCTGGGGACAGG----AGACACA------CCATGGCCAGGA----C-------CAATCCTGGCACC-AAAAAGGAGAA-C s gorGor1.Supercontig_0007361 7450 110 - 64270 C------CTTCATCTCAAAACTCAGAGTG---------TTGTCACAGCCACGCTGCCACTCTGGAATTCCTGGGGACAGG----AGACACA------CCATGGCCAGGA----C-------CAATCCTGGCACC-AAAAAGGAGAA-C i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79467065 110 + 83384210 C------CTTCATCTCAAAACTCAGAGTG---------TTGTCACAGCCACGCTGCCACTCTGGAATTCCTGGGGACAGG----AGACACA------CCATGGCCAGGA----C-------CAATCCTGGCACC-AAAAAGGAGAA-C i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16054201 111 + 17838096 C------CTTCATCTCAAAACTCAGAGTG---------TTGTTACAGCCACGCTGCCACTCTAGAATTCCTGGGGACAAG----AGACACA------CCATGGCCAGGA----C-------CAATCCTGTCACCAAAAAAGGAGAA-C i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75028037 110 + 78773432 C------CTTCATCTCGAAACTCAGAGTG---------TTGTCACAGCCACGCTGCCACTCTAGAATTCCTGGGGACAGG----AGACACA------CGATGGCCAGGA----C-------CAATCCTGGCACC-AAAAAGGAGAA-C i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 35459 110 - 95547 C------CTTCATCTCGAAACTCAGAGTG---------TTGTCACAGCCACGCTGCCACTCTAGAATTCTTGGGGACAGG----AGACACA------CGATGGCCAGGA----C-------CAATCCTGGCACC-AAAAAGGAGAA-C i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 38060 105 + 225949 C------CTTTGTCTCAAAACTCAGGGTG---------TTATCACAGCCACGCTGCCACTCTAGAATTCCTGGGGACAGG----AGACACA------CCAAGGCCAG-----------------TTCTGGCACCAAAAAAGGAGAA-C i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 8291 117 + 8975 CGTTCCTGTTCATCTCACAACTCAGAGCAT--------TTGTCTCAACCACAATGTCATCCTAGAATTCCTGGGGATGGG----GAATACA------CCATTCCCATGA----C-------GAATCCTGGTACC-AAAGAGAAGAG-C i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 18608 97 + 287808 C------ATTCAACTAGAAATTCGTACAT---------TTGTCATAACCACATCGTCAGTCTGGGATTCTTGGGGAT-GG----GGACACA------CCATG-CCTTGA----C-------TGAGTCTACCTCC-A------------ i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 4283 57 + 15939 -------CCTCATCTCGCAGCTCGGAGTA-----------GCCACGACCACTCTG---------------TAGGAATGGG----AGTCA----------------------------------------GTACC-------------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118751682 100 + 121843856 C------CTCTGGCTTGC----TTGGGTAC------------CACAAGCAATCTGTCAGTGCAGTCCTCTAGAGGACAGA-----AGCACA------CCACCTCCAGGACTGTC-------CCACACTAGACAG-AAGAGC------- i mm9.chr11 C 0 I 147 s cavPor3.scaffold_76 4383302 110 + 7991924 C------ATTCACCTTGCA--TCTGAGTGTCTGTGCCCATTACTCTACTGCTCTGTCACTGCAGACTGCTTGGAGACAGG----CAACGCA------CCACGTCCATGA----C-------CAACTCTGGTGCC-AAAAG-------- i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 12645 65 + 41507 ----------------------------------------------ACCACCCAG-----------TTCTGGAGATCCCG-----GGGACC------CCA--CCCACGA----C-------CAATCCCAGCTCC-AGAATCAGAGC-C i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_6980 58013 69 + 61692 ----------------------------------------------ACTGCCCAG--------GGCGTCTGGAGATCCTG-----GGGCCA------CCAC-CCCATGA----C-------CAATCCCAGCACC-AAAGTAACAGC-C i ochPri2.scaffold_6980 C 0 C 0 s turTru1.scaffold_106006 121028 106 + 145505 ------TACTCTGCTTGCAGCTCAGAGTCT--------TTGTCAC-ACCGCTTTGCACTTCTGGAATTCCCAGGGGT-GG----GGGAC--------ACCTTCCTATGA----C-------CAATCATGGCACC-AAAAGGAAGA--C i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10852612 110 - 65312493 ------CCTTTTATTTGTAACTCAGAATAT--------TGGGCACAACCACTTTGCACTTATGGAATTCCTGGGAGTGGG----GGGAC--------ACCTTCCTATGA----C-------CAATCCTGGCACC-AAAAGCAAGGGCC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58034989 102 - 61308211 ------CACTTTTCCTCCGACTCAGAGCTT--------TGGTCCCGACCACTTTGTTGTCCTAGATTTCGTAGGGGCAAG----G---------------GCACCATGA----C-------CAGTCTTGGCTCC-AACAGTAAGAG-C i equCab2.chr11 C 0 C 0 s canFam2.chr9 59429796 114 - 64418924 ------TGTTTTTCTTCCAACTGGGAGTAT--------CAGTCACAA-CACTTTGTC-TTCTGGAATACTTAGGGATGAG----GTGGGGAGGGATGCCATCCCCATGG----C-------CACTCCTGACACC-AAAAAGAAGA--C i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 7724 80 + 48268 -------------CTCACACCTCAGAGTGC--------TGGTGACAACCCCCACGTCCTTCCG----------------------------------CCCTCCCCATGG----C-------CAATCCTGGCACC-AAAACAAAGAG-C i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14423939 121 - 17734757 ------CGTTTGTCTTGCTGCTCAGAGTGT--------TCTGCA-AACCACATTGTCATTGTGGAACTCCTGGGGCCTGAGGTGGGGGGTA------CACCATTCACAT----CCATAGGACCACCCTAGCTCC-AAAAGCAAGGG-C i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 4905 101 + 20752 ------CATCCGTCTTCCAGGTCAGGGTGTCG------TCGGC--ACCCACCTGACCGCTG-GGAGACCCTGGGGGCTGA----GGGGGCC------CCCCATCCACAC----C----------CCGTGACT-----AAGCCA--G-C i dasNov2.scaffold_28617 C 0 C 0 e proCap1.scaffold_29042 6681 1648 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e felCat3.scaffold_206428 7242 517 + 132007 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I a score=104029.000000 s hg19.chr17_gl000204_random 37343 162 + 81310 CCCCAGCCAGGCTGCGCCCATCC-------GATGGACA-------CCAG-------ACTC---CTTGGTAC---aca----tttattgggcacctactgtg--ttcca-ggcacagcctgaagtgATAAAAGCCAGGC-ACAGCGCCAAAGG--TCCCAGCAGAAG---GTGGCGGCCACC-CCCAACCCCCAG-CCCATCCCC s gorGor1.Supercontig_0007361 7560 161 - 64270 CCCCAGCCAGGCTGCGCCCATCC-------GATGGACA-------CCAG-------ACTC---CTTGGTAC---aca----tttntcgggcacctactgtg--ttcca-ggcacagcctgaagtgataaaagccaggc-acagcgccgaaGG--TCCCAGCAGAAG---GTGGCGGCCA-C-CCCAACCCCCAG-CCCATCCCT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79467175 162 + 83384210 CCCCAGCCAGGCTGCGCCCATCC-------AATGGACA-------CCAG-------ACTC---CTTGGTAC---aca----tttgttgggcacctactgtg--ttcca-ggcacagcctgaagtgataaaagccaggc-aCAGCGCCAAAGG--TCCCAGCAGAAG---GTGGCGGCCACC-CCCAACCCCCAG-CCCATCCCC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16054312 161 + 17838096 CCCCAGCCAGGCTCCGCCCATCC-------GATGGACA-------CCAG-------ACTC---CCTGGTAC---aca----tttattgggca-ctactgtg--ttcca-ggcacagcctgaagtgataaaagccaggc-acagcggcgaaGG--TCCCAGCAGAAG---GTGGAGGCCACC-CCCAGCCCCCAG-CCCATCCCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75028147 162 + 78773432 CCCCAGCCAGGCTCTGCCCATCC-------GACGGACA-------CCAG-------ACTC---tttggtac---aca----tttattgggcacctactgtg--ttcca-ggcacagcctgaagtgataaaagccaggc-acagcagcgaaGG--TCCCAGGAGAAG---GTGGCGGCCGCC-CCCAGCCCCCAG-CCCATCCCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 35569 162 - 95547 CCCCAGCCAGGCTCTGCCCATCC-------GACGGACA-------CCAG-------ACTC---tttggtac---aca----tttattgggcacctactgtg--ttcca-ggcacagcctgaagtgataaaagccaggc-acagcagcgaaGG--TCCCAGGAGAAG---ATGGCGGCCGCC-CCCAGCCCCCAG-CCCATCCCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 38165 167 + 225949 CCCCGGCCAGACTCTGCCCACCCGAACACTGATGGACA-------CCAG-------ACTC---CTTGGTAC---aca----tttattgggcacctactgtg--ttcca-ggcacagtccaaagtgacaaaagc----a-acagtggcaaagg--tcccagcagaag---gtggcagcccccacccagcccccagcccCATCCCT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 8408 178 + 8975 CCTCAGCCAAGCTCTGCCCATCTGAAGATGGATGGACACCAGTGTCCAG-------ACTC---ATCAGCACGaagta----cttattgggcacctactgtg--tgcct-ggcacagcccgaggtcatggAAGCCAACT-GCGGGCTGCAAAG--TCCCAGGGGAAG---GCAGAAGCTGAG-CC--ATCCCCAGCCCCATCACC i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 18705 152 + 287808 ----------------CCCGTCTGAAGACAGACAGACA-------CCAGTGTCCCAGCTT---GTCAGTGT---GCAGAGTCCCactgggcatctactgtg--tgcca-ggcacagccccaagggggacagcccagca-atgttcacagagg--tccttgcAAAAG---AAGGCGGCCTCC-TCT----------CTAATC--- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 4340 111 + 15939 ------------------CACTC-------GGGG-----------CCAA---------------------C---ACG----ATTACTGAGTCCCTCCTGCTGCTGCCA-GGCACAGCC-ACGGGGAGGGAAGCAGTGG-TCTACAACAGTGC--TCC--------------GGAGGCCGTG-CCC--------G-CACGCCGCC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s cavPor3.scaffold_76 4383412 126 + 7991924 ---------------------------------------------CACA-------GCTCTGGGTCCGCAA---ACA----------CCGCACACACCACA--CACCACAGGGAGAATCCACGTAATCACAGCCAGGCGACTGCTGCAATGA--TCCCAAAG-------TCGAAGGCAGTG-GCCAGCCTGTAA-CCAGTCCCC i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 12710 164 + 41507 CC---GCCGGGCCCCGCCCACCCTGAGA---AAGGACGGCG----TCAG-------ACTCttcgtccacaa---ata----cttggtgagcacctactgcg--cgcca-ggcacggccccgagcgAGGAAAGGCGGGC-ACTGCCGCACAGG--CCCCGGG--------AAGAAGGCAGGT-GGCGTCCCCCTG-CCTGTGCCC i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_6980 58082 174 + 61692 CACTGACCAGGCTCTGCCCATCTAGAGAG-CAAGGACAGCAC---CCAG-------ACTC-CCGTCCACAG---ACA-------AGGTAGCACCTGCTGCA--TGCCC--TCCTGACTCGCAGCAAGGAGCGGCAGGAGACTGCTGCAAAGG--TCCCGGGGCAAGGGTGGGGAGGCAGGT-GCCTGCCCATCA-CCTGAGCCC i ochPri2.scaffold_6980 C 0 C 0 s turTru1.scaffold_106006 121134 145 + 145505 CCCCAGCCAGGCTCCACCACCCA-GAGAGGTAAGGGCACC-ATGTCCAG-------actc---atcagtcc---acaaatgttcactgagcacctactgtg--tgcca-gatgcagcccaaagtaata-aagcagcacagttcctataaagg--tcccA------------------CATC-CCA------------------- i turTru1.scaffold_106006 C 0 I 4 s bosTau4.chr19 10852722 145 - 65312493 CCCCAGCCATGGTCCACTGCCTT-GAAAGGCAAGGGCACC-AGGTCCAG-------ACTC---ATCAGCGC---ACAAATCCTCACTGCACACCTCCTGTG--TGCCA-TGCACAGCCCAAAGCAATA-AAGCAACACAGTCCCCAAAGAAG--CCCCA------------------TGTC-CCA------------------- i bosTau4.chr19 C 0 I 604 s equCab2.chr11 58035091 138 - 61308211 CCCGAGCCAGGCTCCACCC--------AGGCGTGCACACCCGTGTCCAG-------actc---atcaggcg---acaggtgtgtattgagcacctgctgtg--tgcca--gCGTGGCCCAGAGTGAGGAAAGCGGCGCCATGGCTGCCAAGG--GCCC-------------------CGTC-CCA------------------- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59429910 128 - 64418924 ACCCAGCCAGGCTCCACCCATCA-GAGAGGCAAGGATACCTGTGTCCAG-------actc---attggccc---acagatatttgttgagcacctactgtg--tg---------agccccaagcaatgAAAGC----CCAcatc--cca------ctc-------------------catc-cca------------------- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 7804 144 + 48268 CCTGAGCCAGGCTCCACCT-TCA-GG-AGGCAAGGACACCCAAGTCCTG-------ACGC---Atcagtcc---gcaaatgtttactgagcacctactgtg--cgcca-ggcagggcgttgacggatg-aagcaacacatttgctgccAAGG--TCCCA------------------CGTC-CCT------------------- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14424060 155 - 17734757 --CTGACCAAGCTCCACC-ACCCGGAAGTGAACGGCCG-------CCAG-------CCTC----CAGGCAC---AC-----CATCCTGAGTGCCTGCTGTG--TGCCA------GGGCAAAAG-GGTGAAAGCATGGCCGCTGCTGCGAAGGCTTCCCTTAAGGAG---CTGGGGCCCATC-------CTCCAG-CCCTCCCCC i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 5006 134 + 20752 --CTCCCCAGGCTCCGCTGACCCacaaacaa---------------------------------------------------ttactaagcacctactgtg--tgccc--acgtgggctgggg-gatggcagcaaagcagttgctacaaagg---tccTGGAGAAA---GGGGGGCATAGC-CA----CCCCGG-CCCTGCCCC i dasNov2.scaffold_28617 C 0 C 0 e proCap1.scaffold_29042 6681 1648 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e felCat3.scaffold_206428 7242 517 + 132007 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e mm9.chr11 118751782 147 + 121843856 I a score=-50549.000000 s hg19.chr17_gl000204_random 37505 43 + 81310 GTCTTTCCTTCC-----TCTTGGGCCTCCTGT----CCCCTCTGGAATTCAG s gorGor1.Supercontig_0007361 7721 43 - 64270 GTCTTTCCTTCC-----TCTTGGGCCTCCTGT----CCCCTCTGGAATTCAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79467337 43 + 83384210 GTCTTTCCTTCC-----TCTTGGGCCTCCTGT----CCCCTCTGGAATTCAG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16054473 43 + 17838096 ATCTTTCCTTAC-----TCTTGGTCCTCCTGT----CCCCTCTGGAACTCAG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75028309 43 + 78773432 ATCTTTCCTTCC-----TCTTGGGCCTCCTGT----CTCCTCTGGATTTCAG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 35731 43 - 95547 ATCTTTCCTTCC-----TCTTGGGCCTCCTGT----CCCCTCTGGATTTCAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 38332 41 + 225949 GTCTT--CTTCC-----TCTTGGGCCGCCTGT----CCCCTCTGGAATTCAG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 8586 37 + 8975 -----TCCTTCC-----TCTGAGGCCTCTTGC----CTGCTCTGGAA-TCAG i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 18857 20 + 287808 ---------------------------CCTGC----CTGCTCTAGAC-TCAG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 4451 24 + 15939 -----------------------GCCTCCTTC----CCACCTCGGAC-TCAG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s cavPor3.scaffold_76 4383538 34 + 7991924 TCTC-------------CCTCAGGACTGCTC-----CATTTCTAGAACCCAG i cavPor3.scaffold_76 C 0 I 103 s oryCun2.chrUn0958 12874 47 + 41507 GCCCCCGCTCCGGGGTTCTGCTGTCCTGCGG-----CCGCTCAGGAGTTCAG i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_6980 58256 24 + 61692 CTCCATCCGCCA-----CCACCGTGCTGC----------------------- i ochPri2.scaffold_6980 C 0 C 0 s turTru1.scaffold_106006 121283 8 + 145505 ------------------------------------ATCGTCCT-------- i turTru1.scaffold_106006 I 4 C 0 s equCab2.chr11 58035229 40 - 61308211 ----CTCCTCCC-----TCCTGGGCCGGCCTCG---CTCCTCCTTAATTCAG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59430038 43 - 64418924 ----ctccatcc-----cactccgtcccactcagtccTGCTCCTGAATCTAG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 7948 20 + 48268 ----CTCC----------------------------GTCCTCCTAAACTCAG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14424215 28 - 17734757 --------------------AAGCCTGCCCTC----CCCCATCTGAACTAGG i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 5140 19 + 20752 --------------------GCGGGGGTCTTC-------------AATTCAG i dasNov2.scaffold_28617 C 0 C 0 e proCap1.scaffold_29042 6681 1648 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e felCat3.scaffold_206428 7242 517 + 132007 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e bosTau4.chr19 10852867 604 - 65312493 I e mm9.chr11 118751782 147 + 121843856 I a score=208251.000000 s hg19.chr17_gl000204_random 37548 54 + 81310 CCCCAAACAGTAT-------CGTGTTTTCTGTTGGGTCAccgcctttgcttggagc---ccctg s gorGor1.Supercontig_0007361 7764 54 - 64270 CCCCAAACAGTAT-------CGTGTTCTCTGTAGGGTCAccgcctttgcttggagc---ccctg i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79467380 54 + 83384210 CCCCAAACAGTAT-------CGTGTTTTCTGTAGGGTCACCGCCTTTGCTTGGAGC---CCCTG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16054516 54 + 17838096 CCCCAAACAGTAT-------CGTGTTCTCTGTAGGGTCAccgcctttgcttggagc---ccctg i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75028352 54 + 78773432 CCCCAAACAGTAG-------CGTGTTCTCTGTAGGGTCACCGCCTTTGCTTGGAGC---CCCTG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 35774 54 - 95547 CCCCAAACAGTAG-------TGTGTTCTCTGTAGGGTCAccgcctttgcttggagc---ccctg i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 38373 54 + 225949 CGCCAAACAGTAG-------TGTGTTCTTTGTCGGGTCActgcctttgcttggagc---ccctg i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 8623 54 + 8975 CCCCATGCAGTAG-------TGTGCTTCCTGTGGAGTCActgccttcgcttgcagc---ccctg i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 18877 52 + 287808 CCCCAGCCAGGGA-------C-TGTTTCCTATGGGGTCTCTGCCTGAATGCAGAG----CCGTG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 4475 48 + 15939 CC----ACAGT-G-------TGTGTCCTGTACAGGGTGGCC-CCTTCACGTGGAGC---CCCTG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s oryCun2.chrUn0958 12921 63 + 41507 -TCCACACAGGAGCTTCCCACGGGGCCCCTGCTCCCTCCTCAGAGCCCCCGAACACACAGCGGG i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_6980 58280 52 + 61692 -CCCACACAGGAG-------TGGGTATCCTGCACACTCCCCACCCTCCCTTGGAGC----CTGG i ochPri2.scaffold_6980 C 0 C 0 s turTru1.scaffold_106006 121291 48 + 145505 -CCTGAACGG-----------ATGTTTCCTGTAG-GTTGCTAGGtcagcttggatc---ccctg i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58035269 54 - 61308211 CCCAGAACACTAA-------CGAGTTTTCTGTGGAGTCCCCGCGTCAGCTTGGAGC---CCCCG i equCab2.chr11 C 0 I 813 s canFam2.chr9 59430081 54 - 64418924 GCCTCAACAGTAC-------TGGGTATTCTGTGCAGTCACTGCGCTAGCTAGGAGC---CCCTG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 7968 49 + 48268 GCCTGAGAAGCTG-------TGCGTTTTCTGT---GTCGCTGCATTGGCTTGGGAT---CCT-- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14424243 53 - 17734757 CCCTGCACCATCG-------CGTATTTGCTGCAGGGTCACCGCCTCAGCTTGGACC----cctg i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 5159 46 + 20752 CTCTGGGCAGACA-------CATGTTTTCTGTG--------GCCTCAGCTCGGACC---ACCTG i dasNov2.scaffold_28617 C 0 C 0 e proCap1.scaffold_29042 6681 1648 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e felCat3.scaffold_206428 7242 517 + 132007 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e bosTau4.chr19 10852867 604 - 65312493 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I a score=282115.000000 s hg19.chr17_gl000204_random 37602 73 + 81310 aaaacagag------cctgggg---------------caagggttggg---gcacagattgctg----gtttgagagcaagtccaggaag-ctggtgtgagg s gorGor1.Supercontig_0007361 7818 73 - 64270 aaaacagag------cctgggg---------------caagggttggg---gcacagattgctg----gtttgagagnaagtccaggaag-ctggtgtgagg i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79467434 73 + 83384210 AAAACAGAC------CTTGGGG---------------CAAGGTTTGGG---GCACAGATTGCTG----GTTTGAGAGCAAGTCCAGGAAG-CTGGTGTGAGG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16054570 73 + 17838096 aaaacagag------cctgggg---------------caagggttggt---gcacagattgctg----gtttgagagcaagtccaggaag-ctggtgtgagg i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75028406 73 + 78773432 AAAACAGAG------TCTGGGG---------------CAAGGGTTGGG---GCACAGATTGCTG----GTTTGAAAGCAAGTCCAGGAAG-CTGACGTGCGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 35828 73 - 95547 aaaacagag------tctgggg---------------caagggttggg---gcacagattgctg----gtttgaaagcaagtccaggaag-ctggcgtgcgg i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 38427 61 + 225949 aaaacagag------cctagg------------------------------acacagattgctg----gtttgagagcaaggccaggaag-ctggtgtgagg i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 8677 73 + 8975 aaaacagag------cctggga---------------caagggtctgc---gtacagatagctt----gtttgagagcaattccagggag-ctggtatgagg i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 18929 70 + 287808 GAAACAG--------CCTGGGA---------------CAAGGGCTGGG---G-ACAGGCTGCTT----GCTTGGGAGCAATTCCAGGTGG-CTGGTAAGGGG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 4523 71 + 15939 AAAACACGG------TCTGGGA---------------C-AGGGTCTGG---GTACAGATCGGTC-----TCAGGGAGTGGGTCCAGGGAG-CTGGCAAGGGG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s oryCun2.chrUn0958 12984 101 + 41507 GACACAGGAGCTTCCCACGGGGCCCCTGCTCCCTCCTCAGAGCCCCCGAACACACAGCGGGGACAGCAGTGGGGGAACAACTCCAGGAAG-CTGGCGTGAGA i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_6980 58332 66 + 61692 CAAACAG--------CCCGGGG---------------CAGAAGTCTAG---GCACAGATGGCTC--------GCGTGCAACTCCAGGAGG-CTGGCCCGAG- i ochPri2.scaffold_6980 C 0 C 0 s turTru1.scaffold_106006 121339 71 + 145505 -acatacag------cctgaga---------------c-agggtgtgg---gtacagattactt----gttagggagtgatcccaggaag-ctggagtgaag i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59430135 58 - 64418924 -AAATACAGC-----CCCGGGA---------------C-AGGGTTTGG---ATCTAAGCGACTT----GTCTGGGACTGA-TCCAGGA-------------- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 8017 65 + 48268 -------GAA-----CCTGAGT---------------C-AGGGTCTGG---GTGCAGGCTACGT----GTCTGGGGGTGA-CCCAGGAAG-CTGGAGCGAAG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14424296 60 - 17734757 aaaacag----------------------------------ggtttgg---atatagattgcat----atttaggagcaattccaggaag-ctggagtgggg i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 5205 74 + 20752 AAAACAGAA------GCTGAGA---------------CAAAGGTGTGG---GCACAGGCTGCTC----ACCTGGGCAGGGTTCCAGGAAGTCCGGAGCGAGG i dasNov2.scaffold_28617 C 0 I 685 e proCap1.scaffold_29042 6681 1648 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e felCat3.scaffold_206428 7242 517 + 132007 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e bosTau4.chr19 10852867 604 - 65312493 I e equCab2.chr11 58035323 813 - 61308211 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I a score=58373.000000 s hg19.chr17_gl000204_random 37675 45 + 81310 ttat-ctgggagcctg--atgaggatg--gaataaaagctatgtgtgcac s gorGor1.Supercontig_0007361 7891 45 - 64270 ttat-ctgggagcctg--atgaggatg--gaataaaagctatgtgtgcac i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79467507 45 + 83384210 TTAT-CTGGGAGCCTG--ATGAGGATG--GAATAAAAGCtatgtgtgcac i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16054643 45 + 17838096 ttat-ctgggagcctg--atgaggatg--gaataaaagctaTGTGTGCAC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75028479 45 + 78773432 TTAT-CCGGGAGCCTG--ACGAGGATG--GAATAAAAGCTATGTGTGCAT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 35901 45 - 95547 ttat-ccgggagcctg--acgaggatg--gaataaaagctaTGTGTGCAC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 38488 45 + 225949 ttat-ccgggagcctg--acgaggaag--aaataaaagcTGTGAGTACAT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_131410 8750 36 + 8975 gc-c-ctgggacccagacacagggatg--aaagaaaagcT---------- i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 18999 39 + 287808 ---T-CTGGGAACCTA--ACACAGGTG--CAAAAAGAGCTGTGCATG--- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 4594 19 + 15939 --GC-CAGGGAGCCTG--GCACAG-------------------------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s oryCun2.chrUn0958 13085 36 + 41507 --GC-CCAGGAGCCTG--ACACAGGCGT-GGAGAACAGCCAC-------- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_6980 58398 37 + 61692 --GA-CCAGGAGCGTG--ACACAGGCGTGGGAGAAGGGGCAC-------- i ochPri2.scaffold_6980 C 0 C 0 s turTru1.scaffold_106006 121410 43 + 145505 --ga-ttgggggcctgagccagggatg--gaagaacagc--cgtgtgtgt i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59430193 29 - 64418924 -----TCAGGGGCCTGAGATGGGGACA--GAAGGGC-------------- i canFam2.chr9 C 0 I 11 s pteVam1.scaffold_11245 8082 44 + 48268 --GCGTCGGCAGCCCGAGACCGAAAGG--GAAGAACAGC--CGTGTGCAC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14424356 35 - 17734757 -gac-ctgggagagtgagacagggatg--gcgggcaggc----------- i loxAfr3.scaffold_49 C 0 C 0 e proCap1.scaffold_29042 6681 1648 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e felCat3.scaffold_206428 7242 517 + 132007 I e dasNov2.scaffold_28617 5279 685 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e bosTau4.chr19 10852867 604 - 65312493 I e equCab2.chr11 58035323 813 - 61308211 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I a score=31735.000000 s hg19.chr17_gl000204_random 37720 34 + 81310 gtatggagggtgtgaggag-----gggtgtgcacgtgtg s panTro2.chr17 79467552 34 + 83384210 gtatggagggtgtgtggag-----gggtgtgcacgtgtg i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16054688 34 + 17838096 GTAtggagggtgtgtggag-----gggtgtgcatgtgtg i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75028524 25 + 78773432 ---------GTGTGTGGAG-----GGGGATGCACGTACA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 35946 25 - 95547 ---------GTGTGTGGAG-----GAGGATGCACGTACA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 38533 34 + 225949 GTGTGGAGGGTGTGCAGAG-----GGGtgtgcatgtgtg i calJac1.Contig5139 C 0 I 392 s tarSyr1.scaffold_131410 8786 26 + 8975 --------GGGGCGGGGAG-----gtatgtgcatgtgtg i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19038 19 + 287808 ---------------GGGG-----CGGGgtgtgtgtgtg i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 4613 30 + 15939 ---------gtgtgtggagtgtgagtgtgtgcacgtgtg i tupBel1.scaffold_124459.1-15939 C 0 C 0 s ochPri2.scaffold_6980 58435 15 + 61692 ------------------------TGAACATCGTCTGTG i ochPri2.scaffold_6980 C 0 C 0 s turTru1.scaffold_106006 121453 17 + 145505 ----------------------gtgtgtgtgtgtgtgtg i turTru1.scaffold_106006 C 0 I 370 s pteVam1.scaffold_11245 8126 17 + 48268 ----------------------ATGTGTGTGCACGTGTG i pteVam1.scaffold_11245 C 0 I 758 e oryCun2.chrUn0958 13121 0 + 41507 C e proCap1.scaffold_29042 6681 1648 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e gorGor1.Supercontig_0007361 7936 0 - 64270 C e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e felCat3.scaffold_206428 7242 517 + 132007 I e dasNov2.scaffold_28617 5279 685 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e canFam2.chr9 59430222 11 - 64418924 I e bosTau4.chr19 10852867 604 - 65312493 I e equCab2.chr11 58035323 813 - 61308211 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I e loxAfr3.scaffold_49 14424391 0 - 17734757 C a score=6130.000000 s hg19.chr17_gl000204_random 37754 37 + 81310 gagggtgtg-------tggaggggtgtgcacgtgtggagggtgt s panTro2.chr17 79467586 37 + 83384210 gagggtgtg-------tggaggggtgtgcacgtgtggagggtgt i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16054722 30 + 17838096 gagggtatg-------tggaggggtgtgcctgtgtgg------- i ponAbe2.chr17_random C 0 I 123 s rheMac2.chr16 75028549 30 + 78773432 GAGGGTGTG-------TGGAGGGgtgtgcatgtgtgg------- i rheMac2.chr16 C 0 I 746 s papHam1.scaffold8336 35971 30 - 95547 GAGGgtgtg-------tggaggggtgtgcatgtgtgg------- i papHam1.scaffold8336 C 0 I 658 s tarSyr1.scaffold_131410 8812 35 + 8975 agtagcatgtgtgtgatgtggatgtgttcatgtgt--------- i tarSyr1.scaffold_131410 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19057 21 + 287808 gagtctgtg-------tg-------acgcatgtgg--------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 4643 36 + 15939 cat-gtgca-------tgtttgtgtgtatatatgaagagggtgt i tupBel1.scaffold_124459.1-15939 C 0 C 0 s ochPri2.scaffold_6980 58450 8 + 61692 TTGGGTGT------------------------------------ i ochPri2.scaffold_6980 C 0 C 0 e oryCun2.chrUn0958 13121 0 + 41507 C e calJac1.Contig5139 38567 392 + 225949 I e proCap1.scaffold_29042 6681 1648 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e gorGor1.Supercontig_0007361 7936 0 - 64270 C e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e turTru1.scaffold_106006 121470 370 + 145505 I e felCat3.scaffold_206428 7242 517 + 132007 I e dasNov2.scaffold_28617 5279 685 + 20752 I e pteVam1.scaffold_11245 8143 758 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e canFam2.chr9 59430222 11 - 64418924 I e bosTau4.chr19 10852867 604 - 65312493 I e equCab2.chr11 58035323 813 - 61308211 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I e loxAfr3.scaffold_49 14424391 0 - 17734757 C a score=6612.000000 s hg19.chr17_gl000204_random 37791 45 + 81310 gtggaggcatgtgcacgtgtggagggt-----gtgtggaggggtgtgcat s panTro2.chr17 79467623 45 + 83384210 gtggaggggtgtgcacgtgtggagggt-----gtgtggaggggtgtgcat i panTro2.chr17 C 0 C 0 s tarSyr1.scaffold_131410 8847 30 + 8975 ---gtgctgtgtgcatgtgt-----at-----atgtg-------gtgtat i tarSyr1.scaffold_131410 C 0 C 0 s oryCun2.chrUn0958 13121 28 + 41507 ----------gtgcatgggt------------gttcacatgggtgtgcgt i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_6980 58458 46 + 61692 ---Agtgtgtgtgcatgtgt-gagtgtgctgggtgtacctgagtgtgtgt i ochPri2.scaffold_6980 C 0 C 0 e calJac1.Contig5139 38567 392 + 225949 I e proCap1.scaffold_29042 6681 1648 + 24616 I e papHam1.scaffold8336 36001 658 - 95547 I e speTri1.scaffold_128901 1250 1336 + 44242 I e gorGor1.Supercontig_0007361 7936 0 - 64270 C e tupBel1.scaffold_124459.1-15939 4679 0 + 15939 C e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e turTru1.scaffold_106006 121470 370 + 145505 I e felCat3.scaffold_206428 7242 517 + 132007 I e dasNov2.scaffold_28617 5279 685 + 20752 I e pteVam1.scaffold_11245 8143 758 + 48268 I e otoGar1.scaffold_94362.1-287808 19078 0 + 287808 C e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e canFam2.chr9 59430222 11 - 64418924 I e bosTau4.chr19 10852867 604 - 65312493 I e equCab2.chr11 58035323 813 - 61308211 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I e loxAfr3.scaffold_49 14424391 0 - 17734757 C e ponAbe2.chr17_random 16054752 123 + 17838096 I e rheMac2.chr16 75028579 746 + 78773432 I a score=19561.000000 s hg19.chr17_gl000204_random 37836 49 + 81310 gtgtggagggtgtgtggaggggtgtgcatgtgttgtgtgtgg---catgtgt s panTro2.chr17 79467668 49 + 83384210 gtgtggagggtgtgtggaggggtgtgcatgtgtggtgtgtgg---catgtgt i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 7936 49 - 64270 atgtggagggtgtgtggaggggtgtgcacgtgtgatgtgtgg---catgtgt i gorGor1.Supercontig_0007361 C 0 C 0 s tarSyr1.scaffold_131410 8877 48 + 8975 atatgtgtgATGTGCACATGTGTATCCACATGT-GTATGTGG---CATGTGT i tarSyr1.scaffold_131410 C 0 N 0 s oryCun2.chrUn0958 13149 22 + 41507 -----------------------------gtgtactgtgtac-ctcatgtgt i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_6980 58504 48 + 61692 ----ggatgtggtgtgtatgagtgcatgggtgtgCTGCGTGCTCACACGTGT i ochPri2.scaffold_6980 C 0 I 3 e calJac1.Contig5139 38567 392 + 225949 I e proCap1.scaffold_29042 6681 1648 + 24616 I e papHam1.scaffold8336 36001 658 - 95547 I e speTri1.scaffold_128901 1250 1336 + 44242 I e tupBel1.scaffold_124459.1-15939 4679 0 + 15939 C e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e turTru1.scaffold_106006 121470 370 + 145505 I e felCat3.scaffold_206428 7242 517 + 132007 I e dasNov2.scaffold_28617 5279 685 + 20752 I e pteVam1.scaffold_11245 8143 758 + 48268 I e otoGar1.scaffold_94362.1-287808 19078 0 + 287808 C e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e canFam2.chr9 59430222 11 - 64418924 I e bosTau4.chr19 10852867 604 - 65312493 I e equCab2.chr11 58035323 813 - 61308211 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I e loxAfr3.scaffold_49 14424391 0 - 17734757 C e ponAbe2.chr17_random 16054752 123 + 17838096 I e rheMac2.chr16 75028579 746 + 78773432 I a score=18314.000000 s hg19.chr17_gl000204_random 37885 75 + 81310 aaacgtgtg--------cacgcatgtggta-----tgtgcagtgtgtg-------tgtgtggagtgtggagtattgtagtgtgtgcacacatgca s panTro2.chr17 79467717 75 + 83384210 aaacgtgtg--------tacatatgtgata-----tgtgcagtgtgtg-------tgtgtggagtgtggagtattgtagtgtgtgcacacatgca i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 7985 75 - 64270 aaacgtgtg--------cacatatgtggta-----tgtgcagtgtgtg-------tgtgtggagtgtgGAGTATTGTAGTGTGTGCACACATGCA i gorGor1.Supercontig_0007361 C 0 C 0 s oryCun2.chrUn0958 13171 31 + 41507 gcacctgtg--------cctgtgtgt---------tgtgcactgtctg----------------------------------------------- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_6980 58555 95 + 61692 GCATGTGTGGTATAGCTGCTGTGTGCGGTGCTCTAGGTGCACTGTGTGGCATGTGTGTACTGGACGTGAAGCTTGGTGCTGCCTGCATGTACACA i ochPri2.scaffold_6980 I 3 M 1409 e calJac1.Contig5139 38567 392 + 225949 I e proCap1.scaffold_29042 6681 1648 + 24616 I e papHam1.scaffold8336 36001 658 - 95547 I e speTri1.scaffold_128901 1250 1336 + 44242 I e tupBel1.scaffold_124459.1-15939 4679 0 + 15939 C e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e turTru1.scaffold_106006 121470 370 + 145505 I e felCat3.scaffold_206428 7242 517 + 132007 I e dasNov2.scaffold_28617 5279 685 + 20752 I e pteVam1.scaffold_11245 8143 758 + 48268 I e otoGar1.scaffold_94362.1-287808 19078 0 + 287808 C e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e canFam2.chr9 59430222 11 - 64418924 I e bosTau4.chr19 10852867 604 - 65312493 I e equCab2.chr11 58035323 813 - 61308211 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I e loxAfr3.scaffold_49 14424391 0 - 17734757 C e ponAbe2.chr17_random 16054752 123 + 17838096 I e rheMac2.chr16 75028579 746 + 78773432 I a score=48600.000000 s hg19.chr17_gl000204_random 37960 188 + 81310 tgtatgtgtatgtgtgtgggtgtgtgcaggggtggagtattttgtgtgcacatatgcatgcatg--tgtgtgtgtgtagtgtgtgtggaatgtgaagtattgtcgtgtgtgcatgcatgcatgtgtgtgtgtctgcagggtgtggagtactgtcgtcgtatgtgcacacatgcatgcatgtgtgtgtggg s panTro2.chr17 79467792 187 + 83384210 tgtatgtgtatgtgtgtgggtgtgtgcaggggtggagtattttgtgtgcacatatgcatgcatgtatgtgtgtgtgtggtgtgtgcggaatgtgaagtattgtcgtgtgtgcatgcatgcatgtgtgtgtgtctgcagggtgtggagtact---gtcgtatgtgcacacatgcatgcatgtgtgtggggg i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 8060 183 - 64270 tgtatgtgtatgtgtgtgggtgtgtgcaggggtggagtattttgtgtgcacgtatgcatgca----tgtgtgtgtgtggtgtgtgtgGGATGTGAAGTATTGTCgtgtgtgcatgcatgcacgtgtgtgtgtctgcagggtgtggagtact---gtcgtatgtgcacanatgcatgcatgtgtgtgtggg i gorGor1.Supercontig_0007361 C 0 C 0 s oryCun2.chrUn0958 13202 93 + 41507 -----atgtgtgcatctggg--------------------cttgtgtgcat---tgtatgtc----ggtgtgtgtgtggtgtg----------------------------------tgcacgcgcgtgt-------gggcgtgGTGCTCT------------GTGCACATGTATACA------------ i oryCun2.chrUn0958 C 0 C 0 e ochPri2.scaffold_6980 58650 1409 + 61692 M e calJac1.Contig5139 38567 392 + 225949 I e proCap1.scaffold_29042 6681 1648 + 24616 I e papHam1.scaffold8336 36001 658 - 95547 I e speTri1.scaffold_128901 1250 1336 + 44242 I e tupBel1.scaffold_124459.1-15939 4679 0 + 15939 C e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e turTru1.scaffold_106006 121470 370 + 145505 I e felCat3.scaffold_206428 7242 517 + 132007 I e dasNov2.scaffold_28617 5279 685 + 20752 I e pteVam1.scaffold_11245 8143 758 + 48268 I e otoGar1.scaffold_94362.1-287808 19078 0 + 287808 C e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e canFam2.chr9 59430222 11 - 64418924 I e bosTau4.chr19 10852867 604 - 65312493 I e equCab2.chr11 58035323 813 - 61308211 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I e loxAfr3.scaffold_49 14424391 0 - 17734757 C e ponAbe2.chr17_random 16054752 123 + 17838096 I e rheMac2.chr16 75028579 746 + 78773432 I a score=126177.000000 s hg19.chr17_gl000204_random 38148 121 + 81310 gtgtggagtattgtcgtctgtggatgcatatatgcatgtgtatgtgggt-gGGGGGTGTGGAATATTGTTGTGTGTGCACATATGCATGCCtgtgtatgtgtgtggtgtgtgaacatgtgca s gorGor1.Supercontig_0007361 8243 117 - 64270 gtgtggagtattgtcntctgtggatgcatatatgcatgtgtatgtgg---ggggggtgtggagtattgttgtgtgtgcacatatgcatgcctgtgta--tgtgtggtgtgtgaacatgtgca i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79467979 122 + 83384210 gtgtggagtattgtcgtctttggatgcatatatgcatgtgtatgtgggtgggggggtgtggagtattgttgtgtgtgcacatatgcatgcctgtgtatgtgtgtggtgtgtgaacatgtgca i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75029325 115 + 78773432 gtgtggagtattgtcgtgtgtgcatgcatgcatgcatgtgtatgtg----tgggggggtggagta---ttgtgtgtgtacatatgcatgcctgagtatgtgtgtggtgtgtgAACATACGCA i rheMac2.chr16 I 746 C 0 s ponAbe2.chr17_random 16054875 115 + 17838096 -----gagtattgtcgtgtgtggatgcatacatgcaggtgtatgtgtgt-gGGGGGTGTGGAGTATTGTTGTGTGTGCACATATGCATGCCtgtgta-gtgtgtggtgtgtgcacatgtgca i ponAbe2.chr17_random I 123 C 0 s papHam1.scaffold8336 36659 118 - 95547 gtgtggagtattgtcatgtgtgcatgcatgcatgcatgtgtatgtg----tgtgGGGGTGGAGTATTGTCGTGTGTGTACATATGCATGCCTGTGTATGTGCGTGGTGTGTGAACATACGCA i papHam1.scaffold8336 I 658 C 0 s oryCun2.chrUn0958 13295 57 + 41507 -------GCGTTGCTGTCTGA-----------------------------TGTGAGTGTGGTGTA------------------TGCATGTGCGTGTA-----------GGTGCACATGGACA i oryCun2.chrUn0958 C 0 C 0 e ochPri2.scaffold_6980 58650 1409 + 61692 M e calJac1.Contig5139 38567 392 + 225949 I e proCap1.scaffold_29042 6681 1648 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e tupBel1.scaffold_124459.1-15939 4679 0 + 15939 C e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e turTru1.scaffold_106006 121470 370 + 145505 I e felCat3.scaffold_206428 7242 517 + 132007 I e dasNov2.scaffold_28617 5279 685 + 20752 I e pteVam1.scaffold_11245 8143 758 + 48268 I e otoGar1.scaffold_94362.1-287808 19078 0 + 287808 C e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e canFam2.chr9 59430222 11 - 64418924 I e bosTau4.chr19 10852867 604 - 65312493 I e equCab2.chr11 58035323 813 - 61308211 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I e loxAfr3.scaffold_49 14424391 0 - 17734757 C a score=88324.000000 s hg19.chr17_gl000204_random 38269 74 + 81310 tatgtaaatgagtgcatgtgtgtggtgtgtgcagtgtgtgatatgtgtggaatgtgtagtatgtgcacacgtgt s otoGar1.scaffold_94362.1-287808 19078 60 + 287808 tgtgtatgtgtgtgcgtatttgtggtgtgtgtAGAGT--------------ATACGCAgtatgtggatgggtgt i otoGar1.scaffold_94362.1-287808 C 0 C 0 s gorGor1.Supercontig_0007361 8360 74 - 64270 tatgtaaatgggtgcatgtgtgtggtgtgtgcagtgtgtgatatgtgtggaatgtgtagtatgtgcacacgtgt i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79468101 74 + 83384210 tatgtaaatgggtgcatgtgtgtggtgtgtgcagtgtgtgatatgtgtggaatgtgtagtatgtgcacacgtgt i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75029440 68 + 78773432 TATGTAAATG------TGTGTGTGGTGTGTCCAAAAAATAATATGTGTGGAATGTGTAGTAAGTGCACACGTGT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16054990 74 + 17838096 tatgtaaatgtgtgcatgtatgtggtgtgtgcagtgtgtgatatgtgtggaatgtgtagtatgtgcacacgtgt i ponAbe2.chr17_random C 0 C 0 s papHam1.scaffold8336 36777 68 - 95547 TATGTAAAtg------tgtgtgtggtgtgtgccgtgtgtaatatgtgtggaatgtgtagtatgtgcacacgtgt i papHam1.scaffold8336 C 0 C 0 s oryCun2.chrUn0958 13352 24 + 41507 -----------CAGAGAGCATGTGGTG---------------------------------------ACCTGTGT i oryCun2.chrUn0958 C 0 C 0 e ochPri2.scaffold_6980 58650 1409 + 61692 M e calJac1.Contig5139 38567 392 + 225949 I e proCap1.scaffold_29042 6681 1648 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e tupBel1.scaffold_124459.1-15939 4679 0 + 15939 C e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e turTru1.scaffold_106006 121470 370 + 145505 I e felCat3.scaffold_206428 7242 517 + 132007 I e dasNov2.scaffold_28617 5279 685 + 20752 I e pteVam1.scaffold_11245 8143 758 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e canFam2.chr9 59430222 11 - 64418924 I e bosTau4.chr19 10852867 604 - 65312493 I e equCab2.chr11 58035323 813 - 61308211 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I e loxAfr3.scaffold_49 14424391 0 - 17734757 C a score=30770.000000 s hg19.chr17_gl000204_random 38343 30 + 81310 gca--------tgtgtggtgcgtgca-tatgtgtgtgga s tupBel1.scaffold_124459.1-15939 4679 31 + 15939 gca--------cgtgctatgtgtgcattgtgtgtgtggt i tupBel1.scaffold_124459.1-15939 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19138 35 + 287808 gtggttttggtggtgtgatgtatgca-catgtg---gag i otoGar1.scaffold_94362.1-287808 C 0 C 0 s gorGor1.Supercontig_0007361 8434 30 - 64270 gca--------tatgtggtgcgtgca-tgtgtgtgtgga i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79468175 30 + 83384210 gca--------tgtgtggtgtgtgca-tatgtgtttgga i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75029508 28 + 78773432 CCA--------TTTGTGGTGAGTGAA-AAAAAG--TGGA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16055064 30 + 17838096 gca--------tgtgtggtgagtgca-tatgtgtgtgga i ponAbe2.chr17_random C 0 C 0 s papHam1.scaffold8336 36845 28 - 95547 gca--------tgtgtggtgagtgca-tgtgtg--tgga i papHam1.scaffold8336 C 0 C 0 e oryCun2.chrUn0958 13376 0 + 41507 C e ochPri2.scaffold_6980 58650 1409 + 61692 M e calJac1.Contig5139 38567 392 + 225949 I e proCap1.scaffold_29042 6681 1648 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e turTru1.scaffold_106006 121470 370 + 145505 I e felCat3.scaffold_206428 7242 517 + 132007 I e dasNov2.scaffold_28617 5279 685 + 20752 I e pteVam1.scaffold_11245 8143 758 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e canFam2.chr9 59430222 11 - 64418924 I e bosTau4.chr19 10852867 604 - 65312493 I e equCab2.chr11 58035323 813 - 61308211 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I e loxAfr3.scaffold_49 14424391 0 - 17734757 C a score=27977.000000 s hg19.chr17_gl000204_random 38373 28 + 81310 cagg---------tgtg-catgtgtgtagtgtgtgcat s papHam1.scaffold8336 36873 28 - 95547 catg---------tgtg-cgtgtgtgtagtgtgagaat i papHam1.scaffold8336 C 0 C 0 s ponAbe2.chr17_random 16055094 28 + 17838096 cagg---------tgtg-catgtgtgtagtgtgtgcat i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75029536 28 + 78773432 CATG---------TGCG-CGTGTATGTAGTGTGAGAAT i rheMac2.chr16 C 0 C 0 s panTro2.chr17 79468205 28 + 83384210 catg---------tgtg-catgtgtgtagtgtgtgcat i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 8464 28 - 64270 cagg---------tgtg-catgtgtgtagtgtgtgcat i gorGor1.Supercontig_0007361 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19173 27 + 287808 tgtg---------tgtgttgtgtgtggagtgtatgt-- i otoGar1.scaffold_94362.1-287808 C 0 I 2 s tupBel1.scaffold_124459.1-15939 4710 22 + 15939 c------------tgta-caca-ggggagtgtgtgt-- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s loxAfr3.scaffold_49 14424391 28 - 17734757 caGGTGTTGTGTGTGTG-CGTGTGTTTAT--------- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 8329 15 + 24616 -------------tgtg-tgtgtgtgtgt--------- i proCap1.scaffold_29042 I 1648 C 0 e oryCun2.chrUn0958 13376 0 + 41507 C e ochPri2.scaffold_6980 58650 1409 + 61692 M e calJac1.Contig5139 38567 392 + 225949 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e micMur1.scaffold_418 371171 1 - 520352 I e turTru1.scaffold_106006 121470 370 + 145505 I e felCat3.scaffold_206428 7242 517 + 132007 I e dasNov2.scaffold_28617 5279 685 + 20752 I e pteVam1.scaffold_11245 8143 758 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e canFam2.chr9 59430222 11 - 64418924 I e bosTau4.chr19 10852867 604 - 65312493 I e equCab2.chr11 58035323 813 - 61308211 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I a score=221051.000000 s hg19.chr17_gl000204_random 38401 210 + 81310 gtgtacgtgcgtTTATGCAgtgttattgaacaggtcaccct-gtgggcaactggagctggatcca--tggggacctTCCAGGTCACCCCGTGGACTG--CC---------TG-TCCCTGGGA--------AGGCTGGGG-CAGGG-----------------AGTGG--TTCC---------------CTCCCCACACTCCCA------------------------------------------CCTGCGCTGTGAAC--------ACACTCCCTCCTC---------------------------------------------TCCCA---------------CTGAGTT-----------GAGCCCAGG---------------------------------AC-TGCGGGCTCAGGACA s gorGor1.Supercontig_0007361 8492 210 - 64270 gtgtacgtgcgtTTATGCAGTGTTATTGAACAGGTCACCCT-GTCGGCAACTGGAGCTGGATCCA--TGGGGACCTTCCAGGTCACCCCGTGGACTG--CC---------TG-TCCCTGGGA--------AGGCTGGGG-CAGGG-----------------AGTGG--TTCC---------------CTCCCCACACTCCCA------------------------------------------CCTGCGCTGTGAAC--------ACACTCCCTCCTC---------------------------------------------TCCCA---------------CTGAGTT-----------GAGCCCAGG---------------------------------AC-TGTGGGCTCAGGANG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79468233 210 + 83384210 gtgtacgtgcgtTTATGCAGTGTTATTGAACAGGTCACCCT-GTGGGCAACTGGAGCTGGATCCA--TGGGGACCTTCCAGGTCACCCCGTGGACTG--CC---------TG-TCCCTGGGA--------AGGCTGGGG-CAGGG-----------------AGTGG--TTCC---------------CTCCCCACACTCCCA------------------------------------------CCTGCGCTGTGAAC--------ACACTCCCTCCTC---------------------------------------------TCCCA---------------CTGAGTT-----------GAGCCCAGG---------------------------------AC-TGCGGGCTCAGGACA i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75029564 210 + 78773432 GTGTAAGTGTGTTTATACAGTGTTATTGAACAGGTCACCCT-GTGGGCAACTGGAGCTGGATCCA--TGGGGACCTTCCAGGTCACCCCGTGGGCTG--CC---------TG-TTCCTGGGA--------AGGCT-GGG-TGGGG-----------------AGTGG--TTCC---------------CTTTGCACACTCCCA------------------------------------------CCTGCTCTGTGAAC--------ACACTCCCTCCTC---------------------------------------------TCCCA---------------CTGAGCT-----------GAGCCCAGG---------------------------------ACAAGCAGGTTCAGGACG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16055122 209 + 17838096 gtgtACGCACGTTTATACAgtgttattgaacaggtcaccct-gtgggcaactggagctggatcca--tggggaccttctaggacaccccgtggactg--cC---------TG-TCCCTGGGA--------AGGCC-GGG-CGGGG-----------------AGTGG--TTCC---------------CTCCCCACACTCCCA------------------------------------------CCTGCTCTGTGAAC--------ACACTCCCTCCTC---------------------------------------------TCCCA---------------CTGAGTT-----------GAGCCCAGG---------------------------------AC-TGCGGGCTCAGGACA i ponAbe2.chr17_random C 0 C 0 s papHam1.scaffold8336 36901 210 - 95547 gtgtatgtgtgtTTATACAGTGTTATTGAACAGGTCACCCT-GTGGGCAACTGGAGCTGGGTCCA--TGGGGACCTTCCAGGTCACCCCGTGGACTG--CC---------TG-TCCCTGGTA--------AGGCT-GGG-TGGGG-----------------AGTGG--TTCC---------------CTTTGCACACTCCCA------------------------------------------CCTGCTCTGTGGAC--------ACACTCCCTCCTC---------------------------------------------TCCCA---------------CTGAGCT-----------GAGCCCAGG---------------------------------ACAAGCAGGTTCAGGACG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 38959 204 + 225949 gtgtatgtgtgtTTATACAgtgctattgaatgggtcaccct-gtgggcaactggagcttgatccc--tggggaccttccagggcaccctgtcgactg--cT---------TG-TCCCTGGGA--------AGGCT-GGG-CAGGG-----------------AGTGG--TTCC---------------CTCCCCACACTCCCA------------------------------------------CCTGC-----GAAC--------ACACTCCCTCCTC---------------------------------------------TCCCA---------------CCGAGCT-----------GAGCCCAGG---------------------------------AC-AGTGGGCTCAGGGCA i calJac1.Contig5139 I 392 C 0 s otoGar1.scaffold_94362.1-287808 19202 161 + 287808 gtgg--gtttgtTTA--CAGTATTGTTGAA--------CCT-GTGGGCA--TGGGGCTCCATCCA--CGGGAACCTTCCAGGGAAGC----GGGCAG--CC---------CTGGTCCCAGGA--------AGGCT-GGGATGGGAGC--------------AGGTAG--CCTCAGGGGG------TGGCTCCCCATAC-CCCA------------------------------------------CCAGAT------------------------------------------------------------------------------------------------------------------------C---------------------------------AC-AGCAGCCTGAGCA-- i otoGar1.scaffold_94362.1-287808 I 2 C 0 s micMur1.scaffold_89264 4437 158 + 5251 ------GTTTGTTTA--TCGTGTTGCTGAACTGGCCACCCT-GCGGACA-CTGGGGCTCCACCCG--CAGGGCCTTTCCGGGGACGCTGATGTGCAG--CC---------CT-GTCCCCGGA--------AGGCT-GGG-TGG-------------------GGTGG--CCCCG------------GGCCCCACACAC-TCCA------------------------------------------CCTGCTC-----------------------------------------------------------------------------------------------------------------------C---------------------------------GC-AGCAGCCTGAGCA-- i micMur1.scaffold_89264 M 3270 C 0 s tupBel1.scaffold_124459.1-15939 4732 161 + 15939 gagtgcatgtgtTTACATGGTGTCATTGAACTGGTTACCT---------------GCTCGATCCA--GAGGGCCCTTCCA--------------------------------------------------------GGG-TGGGGGA--------------CAGTGG--CCCCTGGTGGC---CCTAACTCTCC-CGC-CCCA------------------------------------------CCTGCCCTG-------------------CCATCCC---------------------------------------------TCTCA---------------CAGAGCT-----------GAGCCCAGG---------------------------------AC-AG-GGGCTCGGGGCA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s oryCun2.chrUn0958 13376 209 + 41507 -----TGTACACTTACACAGTA--ATTCAACTCGGCACTct-gtgggcaacggggcc--actcca--tggggacgctcctggaaa-cacacagactg--tcctt------tg-tcccctgaaggccggc-aggca-ggG-TGGGGGTGG------------GACTGG--CTGCCAGGGGTGCATCACCCCTCCCCTGCCCTCT------------------------------------------CCCACTCTC-AAGC--------AAGCCCCCGTCTC---------------------------------------------CCCCG------------------------------------------------------------------------------TG-GGACTCAGGGCC i oryCun2.chrUn0958 C 0 C 0 s canFam2.chr9 59430233 310 - 64418924 ------GTGTATTCATGTGGTATTGGTGAACTGTTCACCCT-GCAGGTAACTGGGGCTCAGTCTGT-TGGGGATCTTCTGGGGACACACGAGGATTGACCC---------CA-GCCTTGTGAAGGTGGAGAGGCT-GGG-ACGGG-----------------GGTAGCATTTC---------------CACCCCATGTCCCCAGTGACAGAGCGCTGTCTGGGTGCATTAAGTCTCCACACTGTGGCTGCTCCATTAGCCGCCTGGGCCGCCCCCCACCC---------------------------------------------CCAGA---------------CAAAGCTTGGGGGCAGAGGAGCTCAGGTAGTCAAGGCGGGGGCCACCAGCATGCAGGGGAAC-TGAGCACTCATGGCC i canFam2.chr9 I 11 I 14 s loxAfr3.scaffold_49 14424419 304 - 17734757 -TGTTTGTGTGTTTACc----gttactgaaccggttactcccgtaggcaactggagttcaatccatctggggacccgtgggggaa-catgcaggttg--ctcctctaaatta-cccctcaga--------ggact-tgg-aggatgcggAGGATCGAGGGCAGGTGG--GCCCTGGGTGCAGCAA---CTTCCCACCCTTC--------------------------------------------CTGGCG--GTCAGCAGCTATGCACACTGTCTTCCC-GGGAGGAGCTCAGCACCAGGGAAGCC-GTGCTGGGGCGGGAGCTGTCCACCCAGCACGGAGAGGGAGAGCC-----------GAGCCCAAG------------------------------------GGCCTGCTCAGGGCA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 8344 305 + 24616 gtgtgtgtgtgttttcctaatgtgattgaaccagttaccctggtaagcacctggggctcaatccatccagggacccattgggcaa-catgctgactg--tacctccaaactg-tccctccaa--------agact-ggg-aggctgCGGGCAAGTGAGGGCAGCTGG--AACCTCAGCACGCGAA---CTTCCCGCA--TC--------------------------------------------CCGGCTCCGTTAGCCGCCGCACACGCCCACTGCCCTGGGAGGTGCTCGGCCCCTAGAAAGCAGGTGCT-GGGTGGGAATTGTCCA-----CATGAACACCCAGGGCT-----------GAGCCCAGG------------------------------------GCCTGCCTCAGGGCC i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_6980 58650 1409 + 61692 M e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e turTru1.scaffold_106006 121470 370 + 145505 I e felCat3.scaffold_206428 7242 517 + 132007 I e dasNov2.scaffold_28617 5279 685 + 20752 I e pteVam1.scaffold_11245 8143 758 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e bosTau4.chr19 10852867 604 - 65312493 I e equCab2.chr11 58035323 813 - 61308211 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I a score=116938.000000 s hg19.chr17_gl000204_random 38611 47 + 81310 CCAGGACT-----------CTCCCAGGGACAGCCACTCCCAAGGTGGCCCCAGCAGGC s gorGor1.Supercontig_0007361 8702 47 - 64270 CCAGGACT-----------CTCCCAGGGATAGCCACTCCCAAGGTGGCCCCCGCAGGC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79468443 47 + 83384210 CCAGGACT-----------CTCCCAGGGACAGCCACTCCCAAGGTGGCCCCGGCAGGC i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75029774 47 + 78773432 CCAGGACT-----------CTCCCAGGGACAGCCACTCCCAAGGTGGTCCCGGCAGGC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16055331 47 + 17838096 CCAGGACT-----------CTCCCAGGGACGGCCACTCCCAAGGTGGTCCCGGCAGGC i ponAbe2.chr17_random C 0 C 0 s papHam1.scaffold8336 37111 47 - 95547 CCGGGACT-----------CTCCCAGGGACAGCCACTCCCAAGGTGGTCCCAGCAGGC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 39163 46 + 225949 CTAGGACT-----------CTCCCA-GGATGGCCACTCCCAAGGTGGTCCCGGCAGGC i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19363 23 + 287808 ------------------------------AGCC-CCTTCAAATGAGC----AGAGCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_89264 4595 23 + 5251 ------------------------------AGCCGCCCCCAACTGAG-----GGAGCC i micMur1.scaffold_89264 C 0 C 0 s tupBel1.scaffold_124459.1-15939 4893 41 + 15939 CCAGGGCC-----------CTT----GGTGACACAAGCTCATGGAGGTCCC--CAGGC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s oryCun2.chrUn0958 13585 46 + 41507 CCAGGCCT-----------GTCTCTGAGACATGCTCTCCCAAG-CGGCCCCTGCAGGC i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 121840 35 + 145505 CCAGAGGT-----------CTCCAAGGGACACACACTCCC------------GCAGGC i turTru1.scaffold_106006 I 370 C 0 s canFam2.chr9 59430557 47 - 64418924 CCAGAGGC-----------CTCCAGGGGACACTCGTTCCCAAGGTGGTCCCAGGAGGC i canFam2.chr9 I 14 C 0 s felCat3.scaffold_206428 7759 45 + 132007 CCAGAGGC-----------C-CCAAGGGACAGGCA-TCCCGAGGTGGTCCCAACAGGC i felCat3.scaffold_206428 I 517 C 0 s loxAfr3.scaffold_49 14424723 58 - 17734757 CCAGAAATGTCTCCTCTACCTCCAGGGGACAAGCCCTCCCTGAGTGGCTCTGGCAGGC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 8649 56 + 24616 CCAG-AGTACCTCCCCGACCCCCAGGGGACAAGCCGTCCC-GGGTGACTCTGCTAGCC i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_6980 58650 1409 + 61692 M e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e dasNov2.scaffold_28617 5279 685 + 20752 I e pteVam1.scaffold_11245 8143 758 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e bosTau4.chr19 10852867 604 - 65312493 I e equCab2.chr11 58035323 813 - 61308211 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I a score=-6116.000000 s hg19.chr17_gl000204_random 38658 33 + 81310 CCAAGCCAAGGCTGTCGTC-------------------TGTTT------C-----------------AGACTGGG s gorGor1.Supercontig_0007361 8749 33 - 64270 CCAAACCAAGGCTGTTGTC-------------------TGTTT------C-----------------AGACTGGG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79468490 33 + 83384210 CCAAACCAAGGCTGTCATC-------------------TGTTT------C-----------------AGACTGGG i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75029821 31 + 78773432 CCAAACCAAGGCTGTTGTC-------------------TGTTT------C-----------------AGAC--GG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16055378 33 + 17838096 CCAAACCAAGGCTGTTGTC-------------------TGTTT------C-----------------AGACTGGG i ponAbe2.chr17_random C 0 C 0 s papHam1.scaffold8336 37158 31 - 95547 CCAAACCAAGGCTGTTGTC-------------------TGTTT------C-----------------AGAC--GG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 39209 33 + 225949 CCCAATCAAGGCCATTTTC-------------------TGTTT------C-----------------AGACTGGG i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19386 30 + 287808 CTAGGCCACATCCATCACC----------------------AT------G-----------------AGATTGGT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_89264 4618 29 + 5251 CTGGGCCATGTCCCTC-CC----------------------TT------A-----------------AGACCGGT i micMur1.scaffold_89264 C 0 C 0 s tupBel1.scaffold_124459.1-15939 4934 29 + 15939 CCAAAGCAAAGCTG----C-------------------GGTTT------C-----------------AGAGAGTG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s oryCun2.chrUn0958 13631 30 + 41507 CC----TAAGGCTGCTGTG-------------------TTTCTGGAGAAC-----------------ACA----- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 121875 25 + 145505 CAAAACCAAGGCAGTTGTC-------------------TATTT------C------------------------- i turTru1.scaffold_106006 C 0 I 438 s equCab2.chr11 58036136 23 - 61308211 cccagcctgagctgtt--c-------------------tgtta------c------------------------- i equCab2.chr11 I 813 I 14 s felCat3.scaffold_206428 7804 25 + 132007 CCAAAACAAGGTGGTTGTC-------------------TATTT------C------------------------- i felCat3.scaffold_206428 C 0 I 457 s canFam2.chr9 59430604 25 - 64418924 CCAAAACAAGGTGGTTGCC-------------------TATTT------C------------------------- i canFam2.chr9 C 0 I 463 s loxAfr3.scaffold_49 14424781 75 - 17734757 CCAAGCCCAGAAGGTTGTCCCCCGCCCTTACCCCTCGAGTCTCAGCTTTTCAAACAACCCTAGCCGTAGACTGGA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 8705 25 + 24616 CCCAGCACAGAAGGTCGAC-------------------GACTTA------------------------------- i proCap1.scaffold_29042 C 0 I 72 e ochPri2.scaffold_6980 58650 1409 + 61692 M e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e dasNov2.scaffold_28617 5279 685 + 20752 I e pteVam1.scaffold_11245 8143 758 + 48268 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e bosTau4.chr19 10852867 604 - 65312493 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e mm9.chr11 118751782 147 + 121843856 I a score=-107830.000000 s hg19.chr17_gl000204_random 38691 54 + 81310 CA------CTGC-----------------------------------------GGCATGGGGCCCTTGACAGGGAAATGTACA-GCA--------GTCCTGGCGCATCCC s gorGor1.Supercontig_0007361 8782 54 - 64270 CA------CTGC-----------------------------------------AGCATGGGGCCCTTGACAGGNAAATGTACA-GCA--------GTCCTGGTGCATCCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79468523 54 + 83384210 CA------CTGC-----------------------------------------AGCATGGGGCCCTTGACAGGGAAATGTACA-GCA--------GTCCTGGCGCATCCC i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75029852 55 + 78773432 CA------CTGC-----------------------------------------AGCATGGGACCCTTGACAGGGAAATGTACAGGTG--------GTCCTGGCACATCCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16055411 54 + 17838096 CA------CTGC-----------------------------------------AGCATAGGACCCTTGACAGGGAAATGTACA-GCA--------GTCCTGGTGCATCCC i ponAbe2.chr17_random C 0 C 0 s papHam1.scaffold8336 37189 55 - 95547 CA------CTGC-----------------------------------------AGCATGGGACCCTTGACAGGGAAATGTACAGGTG--------GTCCTGGCTCATCCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 39242 38 + 225949 CA------CTGC-----------------------------------------AGGATGGGACC-----------------CAGGCA--------GTCCTGGCGCATCCC i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19416 55 + 287808 CA------GTAC-----------------------------------------AAGAAGTGAGCCTTGGCAGGGACATGCACTCACA--------GCCCTGACACATCCA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_89264 4647 55 + 5251 CA------CTTG-----------------------------------------GAGAAGAGACGCATGACAGAGACATGCACACACG--------GCCTGGGCACACCCA i micMur1.scaffold_89264 C 0 C 0 s tupBel1.scaffold_124459.1-15939 4963 100 + 15939 CATGCCCTCTGCCCCTCCCACCACACCCTACCCCAAGTCTTCGAGCCTCTCCTACCACGAGACCCTTGACAG--AAAGGCACGTAAG--------GTCTTGACACTTCCA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118751929 47 + 121843856 -----------C-----------------------------------------ACTGAGGAATACCTAGAGAGAG---GCACCCACA--------GCCATGGCACATCTA i mm9.chr11 I 147 C 0 s oryCun2.chrUn0958 13661 32 + 41507 ------------------------------------------------------------AACTCCTGCCCTGAG--------CCCG--------GTCAGGACGCAGC-- i oryCun2.chrUn0958 C 0 C 0 s pteVam1.scaffold_11245 8901 58 + 48268 -----------------------------------------------cgttacggcaCCTGGATCC-----AGACAAGGGGTCCACGAACCGACAGCCTCGGTGTTTCTG i pteVam1.scaffold_11245 I 758 C 0 s equCab2.chr11 58036173 43 - 61308211 ------------------------------------------------actgagacaACGGGC-----------GAAGGTTCCCACG--------GCCTCGCCACATCCA i equCab2.chr11 I 14 C 0 s felCat3.scaffold_206428 8286 25 + 132007 ----------------------------------------------------------------------------AGGTAGATGT---------CCCTCGGCATATCCA i felCat3.scaffold_206428 I 457 C 0 s canFam2.chr9 59431092 10 - 64418924 ----------------------------------------------------------------------------------------------------GATGCACCCC i canFam2.chr9 I 463 C 0 s turTru1.scaffold_106006 122338 33 + 145505 ---------------------------------------------------------------------CAGGTAAATGTACGTGCA--------GCCTTGGCGTATCCA i turTru1.scaffold_106006 I 438 C 0 s bosTau4.chr19 10853471 36 - 65312493 ------------------------------------------------------------------TGATAGGTAAGTGAACCTGCA--------AACTCAGTGTATTCA i bosTau4.chr19 I 604 C 0 s loxAfr3.scaffold_49 14424856 33 - 17734757 -------------------------------------------------------------------CACTACGAGAAGTGACCTTA--------GTGTTCACACTCC-- i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_6980 58650 1409 + 61692 M e proCap1.scaffold_29042 8730 72 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e dasNov2.scaffold_28617 5279 685 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e cavPor3.scaffold_76 4383572 103 + 7991924 I a score=-4632.000000 s hg19.chr17_gl000204_random 38745 36 + 81310 AAATGTT--CTCT----ATGATGGCAGCACCTTAGA--CTTCAT s gorGor1.Supercontig_0007361 8836 36 - 64270 AAATGTT--CTCT----ATGACGGCAGCACCTTAGA--CTTCAT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79468577 36 + 83384210 AAATGTT--CTCT----ATGACGGCAGCACCTTAGA--CTTCAT i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75029907 36 + 78773432 AAATGTT--CTGT----ACGACGGCAGCACCTTAGA--CTTCAT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16055465 36 + 17838096 AAATGTT--CTCT----ATGACAGCAGCACCTTAGA--CTTCAT i ponAbe2.chr17_random C 0 C 0 s papHam1.scaffold8336 37244 36 - 95547 AAATGTT--CTGT----ACGACGGCAGCACCTTAGA--CTTCAT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 39280 24 + 225949 AAATGTT--CTCC----GTGATGGCAG--------------CAT i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19471 28 + 287808 GAATGTT--CTCC----TCCCCAA--------CAGG--GCACTT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_89264 4702 34 + 5251 GAATGTT---TCC----CCCACAACA-CACCTCAGG--GGTAGT i micMur1.scaffold_89264 C 0 C 0 s tupBel1.scaffold_124459.1-15939 5063 38 + 15939 GAAAGTTCTCTCC----ACAACTTCAACACCTTAGC--CTTAGT i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118751976 34 + 121843856 GAATGCT--CTCA----CAGGCAGGA--ACCTTAGA--TGGAAT i mm9.chr11 C 0 C 0 s oryCun2.chrUn0958 13693 27 + 41507 -AGTGAC--CC------CAGGAAGTG--ACCCTGGC--TG---- i oryCun2.chrUn0958 C 0 C 0 s pteVam1.scaffold_11245 8959 40 + 48268 GAACAAT--CTCCTCCACCAACAACCTCACCTGAGG--CCTAAT i pteVam1.scaffold_11245 C 0 I 1 s equCab2.chr11 58036216 40 - 61308211 GAACCTT--CTCCTCCCCTGACAGGATCACTCTGGG--CTCAGT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 8311 40 + 132007 GAACGGT--CTCCTCCACTGACAGCATGGCCTTGGA--ATTAAG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59431102 35 - 64418924 AG-------CTTCTCCACTGGCAGCATCGCCTTGGA--CTTAAT i canFam2.chr9 C 0 C 0 s turTru1.scaffold_106006 122371 38 + 145505 GA-CTAT---TCCTCCACTGACAGCATCACCTTAGG--CTTAAA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10853507 39 - 65312493 GA-CTGT--CTCCTCCACTGACAGCATCACCTTAGG--CTTAAA i bosTau4.chr19 C 0 C 0 s proCap1.scaffold_29042 8802 42 + 24616 GACTGGT--CACTATGAGAAAGGACCTCAGTGTCTATGTTCCAT i proCap1.scaffold_29042 I 72 C 0 s loxAfr3.scaffold_49 14424889 26 - 17734757 ----------------ACCAAGAGCATCACCTTCCA--CTCCAT i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_6980 58650 1409 + 61692 M e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 4924 458 + 14340 I e dasNov2.scaffold_28617 5279 685 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e cavPor3.scaffold_76 4383572 103 + 7991924 I a score=-19034.000000 s hg19.chr17_gl000204_random 38781 81 + 81310 CCCACAGCCA---TGT------GCTC---CCCTGCCCC--------------------------TTCTCCCT-GCCCAGAAGGAACCTGGCACA--------CCCA-CT-----ACCCCACACCCCTGCTTCCA s gorGor1.Supercontig_0007361 8872 81 - 64270 CCCACAGCCG---TGT------GCTC---CCCTGCCCC--------------------------TTCTCCCT-GCCCAGAAGGAACCTGGCACA--------CCCA-CT-----ACCCCACACCCCTGCTTCCA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79468613 81 + 83384210 CCCACAGCCA---TGG------GCTC---CCCTGCCCC--------------------------TTCTCCCT-GCCCAGAAGGAACCTGGCACA--------CCCA-CT-----ACCCCACACCCCTGCTTCCA i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75029943 80 + 78773432 CCCACAGCCA---TGT------GCTC---CCCTGCCCC--------------------------TTCTCACT-ACTCAGAAGGAGcctggcaca--------ctca-cc-----a-cccacacccctgcttcca i rheMac2.chr16 C 0 I 54 s ponAbe2.chr17_random 16055501 81 + 17838096 CCCACAGCCA---TGT------GCTC---CCCTGCCCC--------------------------TTCTCCCT-GCCCAGAAGGAACCTGGCACA--------CCCA-CT-----ACCCCACACCCCTGCATCCA i ponAbe2.chr17_random C 0 C 0 s papHam1.scaffold8336 37280 81 - 95547 CCCACAGCCA---TGT------GCTC---CCCTGCCCC--------------------------TTCTCACT-ACTCAGAAGGAGCCTGGCACA--------CCCA-CC-----ACCCCACACGCCTGCTTCCA i papHam1.scaffold8336 C 0 I 107 s calJac1.Contig5139 39304 81 + 225949 CCCACAGCCA---CGT------GCTC---CCCTGCCCC--------------------------TTCTCCCC-CCTCAGCAGGAGCCTGGCACA--------CCCC-TC-----ACCCGCCACCCCTGCTCCTA i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19499 70 + 287808 CCCACAGC-G---TGT------ACTCTG-CCCCTCCCC--------------------------TGCTCTCA-GCCCAGAGGG--CCAGGCACAC-------CCCA-CT-----ACCATATAC----------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_89264 4736 71 + 5251 CCCACAGCTG---TGT------GCCCTG-CCTCGCCCC--------------------------CACCCCCT-GCCCAGGGGG--ACGGGGACAC-------CCCG-CT-----GCCCCACCC----------- i micMur1.scaffold_89264 C 0 C 0 s tupBel1.scaffold_124459.1-15939 5101 54 + 15939 CCC----------CGG------GATG---CCCTGCC------------------------------------------AAAGAGAACCAGTACA--------CCCAGCC-----ACCCCACAGCTCTG------ i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118752010 75 + 121843856 TAAGCAGCCA---TTC------TGTCTGCTCTCACTCCCGCTACCCTCAA--------------TGCTTCCTGGCTC--------TTGCCTACT--------CTTG-CC------CCCCAT------------- i mm9.chr11 C 0 I 16 s oryCun2.chrUn0958 13720 87 + 41507 -----------------------------CCCCACACCTGACCCCCATGACATGGCCCGGCAGCTGCTCCCT-GCCC--------ACGTGCACC--------CCTG-CCCCGGGACCCCAAACCACAGCCTCCA i oryCun2.chrUn0958 C 0 C 0 s pteVam1.scaffold_11245 9000 75 + 48268 -CCGAGGCTG---CCC------ACCCCG-CCCCTCACC--------------------------TCCGCGCT-GCCCAGAG-GAGCCAGGCGCA--------CCTA-CC-----ACCCCGCACCCCTG------ i pteVam1.scaffold_11245 I 1 C 0 s myoLuc1.scaffold_4816 5382 70 + 14340 -CCGA--CTg---ccccccccgcccccg-ccccccgcc--------------------------TCCTCACT-GCCCGGAGAGAGCCAGGC----------------CC-----AGCCCACATCC--------- i myoLuc1.scaffold_4816 I 458 C 0 s canFam2.chr9 59431137 71 - 64418924 TCCAAGGCTG---TGT------TCTCTG-CCCCTCCCC---------------------------AACCCCT-GCCGGGAAGGAGCCAGGCACAC-------CCCA-CC-----ACCCTGCA------------ i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 8351 89 + 132007 CCCAGGGCCGTGTTGT------TCTCCG-CCCCTCGCC---------------------------CCTCCTT-GCCCAGGAGGAGCCACACACACCC---CACCCA-CC-----ACCCTGCACACCCGCTCC-C i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58036256 89 - 61308211 TCTGAGGCTG---CAT------TCCCTA--AGTTCACC---------------------------CCTCCCT-GCCCAGAGGGAGCCAGGCACGCCCCTGCTCCCC-TG-----ACCCTGTACCCCTGCTCCTC i equCab2.chr11 C 0 C 0 s turTru1.scaffold_106006 122409 32 + 145505 -------------------------------------------------------------------TGCCT-GCCCAGAGGGAGCCAGACACA----------CC-CC-----AC------------------ i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10853546 53 - 65312493 ----------------------TCTCTG-CCACTCACC--------------------------TCTTCCCT-GCCCAGAGGGGGCCAGACACAG-------GCTG-CC-----AC------------------ i bosTau4.chr19 C 0 C 0 s proCap1.scaffold_29042 8844 65 + 24616 --CCCGCCCA---CAC------TCTGCC-TCCTGCCCT----------------------TCACCTCCCCCT-GCCCAGAAGGAGCCAAGCA-C--------ACCG-CC-----A------------------- i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14424915 59 - 17734757 --CACG-------CGC------TCTGCT-GCCTGCCCC----------------------------------------GAAGGAGCCAGGCACC--------CCCG-CC-----CCTTCACTCCCCTGT----- i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_6980 58650 1409 + 61692 M e speTri1.scaffold_128901 1250 1336 + 44242 I e dasNov2.scaffold_28617 5279 685 + 20752 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e cavPor3.scaffold_76 4383572 103 + 7991924 I a score=-123932.000000 s hg19.chr17_gl000204_random 38862 19 + 81310 TGGC-CCCC-----------TG--CACTCCTG--A s equCab2.chr11 58036345 18 - 61308211 CCG--CCCC-----------AG--CACCCCTG--C i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 8440 20 + 132007 AAGTCCCCC-----------CG--CAACCCTG--C i felCat3.scaffold_206428 C 0 C 0 s ochPri2.scaffold_9426 97 16 - 54875 CAAT-GCCC-----------TG--CAATGG----- i ochPri2.scaffold_9426 n 3 I 25 s oryCun2.chrUn0958 13807 18 + 41507 CGGC-AGCC-----------TGACCTCTGG----- i oryCun2.chrUn0958 C 0 I 19 s mm9.chr11 118752101 16 + 121843856 TGCT-CCTC-----------CC--CCAACA----- i mm9.chr11 I 16 I 26 s calJac1.Contig5139 39385 19 + 225949 TGGC-CCCC-----------TG--CACTCCTG--A i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 37468 19 - 95547 TGGC-CCCC-----------TG--CACTCCTG--A i papHam1.scaffold8336 I 107 C 0 s ponAbe2.chr17_random 16055582 19 + 17838096 CAGC-CCCC-----------TG--CACTCCTG--A i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75030077 19 + 78773432 tggc-cccc-----------tg--cactcctg--a i rheMac2.chr16 I 54 C 0 s panTro2.chr17 79468694 19 + 83384210 TGGC-CCCC-----------TG--CACTCCTG--A i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 8953 19 - 64270 TGGC-CCCC-----------TG--CACTCCTG--A i gorGor1.Supercontig_0007361 C 0 C 0 s micMur1.scaffold_89264 4807 5 + 5251 ----------------------------CCTG--C i micMur1.scaffold_89264 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19569 5 + 287808 ----------------------------CCGG--C i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 5155 1 + 15939 ----------------------------------G i tupBel1.scaffold_124459.1-15939 C 0 C 0 s pteVam1.scaffold_11245 9075 17 + 48268 -----CACC-----------CA--CACCCCCACAC i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 5452 11 + 14340 -------CC-----------CA--CACCCT----G i myoLuc1.scaffold_4816 C 0 C 0 s canFam2.chr9 59431208 14 - 64418924 -----CCCT-----------TG--CACCCCTG--- i canFam2.chr9 C 0 C 0 s turTru1.scaffold_106006 122441 15 + 145505 -----CACC-----------CG--CAGCCCTG--C i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10853599 15 - 65312493 -----CATC-----------CA--CAGCCCTG--C i bosTau4.chr19 C 0 C 0 s dasNov2.scaffold_28617 5964 15 + 20752 -----CCCCACCACCCCTGC--------------- i dasNov2.scaffold_28617 I 685 C 0 e proCap1.scaffold_29042 8909 0 + 24616 C e speTri1.scaffold_128901 1250 1336 + 44242 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I e cavPor3.scaffold_76 4383572 103 + 7991924 I e loxAfr3.scaffold_49 14424974 0 - 17734757 C a score=196351.000000 s hg19.chr17_gl000204_random 38881 34 + 81310 CCTGGCAGAC---CCCAAACC-ACAGTCTGCTTAGTGG s gorGor1.Supercontig_0007361 8972 34 - 64270 CCTGGCAGAC---CCCAAACC-ACAGTCTGCTTAGTGG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79468713 34 + 83384210 CCTGGCAGAC---CCCAAACC-ACAGTCTGCTTAGTGG i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75030096 34 + 78773432 cctggcaGGC---CCCAAACC-ACAGACTGCTTAGTGG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16055601 34 + 17838096 CCTGGCAGAC---CCCAAACC-ACAGTCTGCTTAGTGG i ponAbe2.chr17_random C 0 C 0 s papHam1.scaffold8336 37487 34 - 95547 CCTGGCAGGC---CCCAAACC-ACAGACTGCTTAGTGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 39404 34 + 225949 CCTCGCAGAC---CCCAAACC-ACAGACTGCTTAATGA i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_89264 4812 27 + 5251 CTTAGTAGA----CCCAAACC-CCAGCCCGTT------ i micMur1.scaffold_89264 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19574 33 + 287808 TCTGGCAGAC---CCCAAACC-ACAGGCTGCTT-GTGG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 5156 34 + 15939 CTTGGCAGTC---CCCAAACC-ATAGCCCGCTTAGTGA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118752143 35 + 121843856 CCTGAGAGTCCCACCCACAGC-CGGCTCTGC--AGGAG i mm9.chr11 I 26 C 0 s cavPor3.scaffold_76 4383675 35 + 7991924 CCTGGGAGGCACAGCCGCAGC-CTGGTTCCC--AGTAG i cavPor3.scaffold_76 I 103 C 0 s oryCun2.chrUn0958 13844 23 + 41507 CCT------------CACCCC-CGGGTCTGC--AACGG i oryCun2.chrUn0958 I 19 C 0 s ochPri2.scaffold_9426 138 31 - 54875 CCTGTG------ACCCAAGCC-CCAGCCTGCTGGGCGG i ochPri2.scaffold_9426 I 25 C 0 s pteVam1.scaffold_11245 9092 32 + 48268 CCCAGCAGAC---CATAAA-C-ACAGCCCACTTAGTG- i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 5463 33 + 14340 CCTAGTGCAC---CCCAAACC-ACAGCCTGCCCAGTG- i myoLuc1.scaffold_4816 C 0 C 0 s canFam2.chr9 59431222 34 - 64418924 CCACACAGCC---CCCAAACC-ACAGCCTGCTGAGCAG i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 8460 34 + 132007 CCAAGCAGAC---CCCAAAAC-ACGGCCCGCTGAGAGG i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58036363 34 - 61308211 TCTGGCAGAC---TCCAGCCC-ACAGCCTGCTTAGCAG i equCab2.chr11 C 0 C 0 s turTru1.scaffold_106006 122456 23 + 145505 CCTAGCAGAG---CCCAAACC-GCGGC----------- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10853614 23 - 65312493 CCTGGCAGAC---CCTAAACC-ACAGC----------- i bosTau4.chr19 C 0 C 0 s loxAfr3.scaffold_49 14424974 33 - 17734757 CCTGGCAGG----CCTAAACC-ACAGTCTGCGTAGGGA i loxAfr3.scaffold_49 C 0 I 3 s proCap1.scaffold_29042 8909 34 + 24616 CCCAACAGA----CCCCAACCAACAGTCTGCATGTTGG i proCap1.scaffold_29042 C 0 I 315 s dasNov2.scaffold_28617 5979 32 + 20752 CCCCGCAGA----CCAAAGCC-ACAG-CCACGCCGCGG i dasNov2.scaffold_28617 C 0 C 0 e speTri1.scaffold_128901 1250 1336 + 44242 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I a score=-771419.000000 s hg19.chr17_gl000204_random 38915 78 + 81310 CAGCA--ACCAC--------------------CGGGTGAAAAGCCTG--AGTGCTCGGAGG---TGG---------------------------GGGTCAGG---------------------------------GAAGG------CAG-CCCAC--AC-----------------------------------TGG------------------------GCTCTTGCCACT s gorGor1.Supercontig_0007361 9006 78 - 64270 CAGCA--ACCAC--------------------TGGGTGAAAAGCATG--AGTGCTCGGAGG---TGG---------------------------GAATCAGG---------------------------------GAAGG------CAG-CCCAC--AC-----------------------------------TGG------------------------GCTCTTGCCACT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79468747 78 + 83384210 CAGCA--ACCAC--------------------CGGGTGAAAAGCATG--AGTGCTCGGAGG---TGG---------------------------GGGTCAGG---------------------------------GAAGG------CAG-CCCAC--AC-----------------------------------TGG------------------------GCTCTTGCCACT i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75030130 78 + 78773432 CAGCA--ACCAC--------------------CAGGTGAAAAGCATG--AGTGATCGGAGG---TGG---------------------------GGGTCAGG---------------------------------GAAGG------CAG-CCCCC--AC-----------------------------------TGG------------------------GCTCTTGCCACT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16055635 78 + 17838096 CAGCA--ACCAC--------------------CGGGTGAAAAGCATG--AGTGCTCGGAGG---TGG---------------------------GGGTCAGG---------------------------------GAAGG------CAG-CCCAC--AC-----------------------------------TGG------------------------GCTCTTGCCACT i ponAbe2.chr17_random C 0 C 0 s papHam1.scaffold8336 37521 78 - 95547 CAGCA--ACCAC--------------------CAGGTGAAAAGCATG--AGTGATCGGAGG---TGG---------------------------GGGTCAGG---------------------------------GAAGG------CAG-CCTCC--AC-----------------------------------TGG------------------------GCTCTTGCCACT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 39438 76 + 225949 CAGCA--ACCGC----------------------AGAGAGAAGCATG--CATGCTCAGAGG---TAG---------------------------GGGTCAGG---------------------------------GAAGG------CCG-TCCCC--AC-----------------------------------TGG------------------------GCTGTTGCCACT i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_89264 4839 90 + 5251 ------------------------------------------CCGTG-----GCTGGGAGA---GGACAAG----CCCCAAGCCTC--------GGTCCAAA-----TGGCGGTT--------CCCAGGCGTGGGTCAGG------CAG-TCCCC--AC-----------------------------------TGG------------------------GCTGTGGCCACT i micMur1.scaffold_89264 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19607 119 + 287808 TATC---ACCAC--------------------C-GATGAGAACTGTG--AGTGCTTGGAGG---TGGCAGGGAGAAGACAGGCCCC-CAGCCTGGGTCTGGA----CTGTCCATT--------CCCAGGCAC---CCAGG------T-G-CTCCC--AT-----------------------------------TAG------------------------ACTGTTACAGCA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 5190 136 + 15939 CAGTATGACAAG--------------------ACAGCAACAAAGGTG--ACAACTTAGAGA---TGC-AGAGAGAGAATGGTCCCCGCCCCCTCAGGCTAGA---------------------------------ACAGGAGTTCCCAG-GCCAC--AG-----------------------------------GGGCAGGTGTGTCGGGAAGCCCCACCTGCTGTCAAAGCT i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118752178 100 + 121843856 CCACTG-CCTGC--------------------TAAGTTGGACATATA----------GAGA---TGT---------------------------GAACCAGT------GACAGAC--------ACCAGGCCT---TGGGG------TGA-CTCCC--AGACAACCCA----------------------CGTGGAGA------------------------ATCACCATGACT i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4383710 71 + 7991924 CAACT--CCAGC--------------------TAAAAAGGGGGTAAA----------GGGC---TGG---------------------------AAAT----------------------------------------GG------TGG-CTCCC--AGACAA---------------------------GAGGTAG------------------------GTGCTTGTGGGT i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 13867 46 + 41507 CAGCT--CCCAC--------------------GCGGCTGCCAG--------------GGGC---C-----------------------------GCAGCAGT------------------------------------CA------CAG-CCCTC--GG-------------------------------------------------------------------------- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 169 52 - 54875 T-GCA--ACCGC--------------------AGGGGTGGCAG-AGA----------GGGC---CGG---------------------------GCACCAGG------------------------------------GG------AAA-CACCA--GGAC------------------------------------------------------------------------ i ochPri2.scaffold_9426 C 0 C 0 s pteVam1.scaffold_11245 9124 131 + 48268 --------CAAC--------------------CAGAGGAGAAAGGGG--CCGGCTTGGAGG---CTG---------------------------GCGGAGAGGCGGGACCCCCAC--------CACTCCCACCGGAAAGG------TGT-TCCCC--AGCACATGGGAGCAGG----------------CGCGGTAGGTACACAGC---------CGCCTTTGGCGTCACGGC i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 5496 85 + 14340 --------CAGC--------------------CAGATGAGAAGGGG----CGGCTTGGAGA---CTG---------------------------TCAGAGAG-----------------------------------AGG------GGG-ACCCC--AGCCCCTCGGCTCAGC----------------CCCGGTGGGTGCCAAGC--------------------------C i myoLuc1.scaffold_4816 C 0 C 0 s canFam2.chr9 59431256 50 - 64418924 CGCCA--ACAGC--------------------CAGACAGGAGACATA--GCTGC--GGAGC---CTG---------------------------GCAGA--G-----------------------------------AGG------AGG------------------------------------------------------------------------------------ i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 8494 54 + 132007 CAGTA--ACAAC--------------------CACAGAGGAAACATA--ACTGCTTGGAGC---CTG---------------------------GCAGAGGG-----------------------------------AGG------AGG------------------------------------------------------------------------------------ i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58036397 116 - 61308211 CAGCA--ACAAC--------------------CAGAGGAGAAATGTG--ACCACCTGGACA---CCA---------------------------GCAGAGAG-----------------------------------AGG------AGG-CACCC--GGTCCCTCAGCCCAGA-----------------GTGATGGCT-CCTGGCACAGAG-GGAGGACGCGGTACCCGGCC i equCab2.chr11 C 0 C 0 s turTru1.scaffold_106006 122479 125 + 145505 ----A--ACAGC--------------------CAGATAAGACACGTG--ACTGCTTGGGGA---ATG---------------------------GCAGAGAG-----------------------------------AGG------AGGGACCCC--AGCCCCTCAGTCTAGAATGGA-------TACACACGGGGTGCGGGCAGCACACAGCTCCCTTTGGCTGATGCCACC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10853637 121 - 65312493 ----A--ACAGC--------------------CAGATAAGAAACATG--AC--------------TG---------------------------GCAGCAAG-----------------------------------AGG------AGGGACCCC--AGCCACTCAATCTAGAATGACAGCCCCTGACACCCGGGGCTAGGGTGGCACACAGCTCCGTTTGCCTGACGCCGTC i bosTau4.chr19 C 0 C 0 s loxAfr3.scaffold_49 14425010 129 - 17734757 AAAAC--ATGACTACGTGGCGCCTTGGGCAGACAGAGGAATGCTTTCCAGCTTCATGAGAAGCATGA--------------------CTATCT-ACCAAGGG----GTCTCGGACACTCAGGAACCCCTACCCTTGTAGG------TGG-TCTCCTTGCTGTT---------------------------------------------------------------------- i loxAfr3.scaffold_49 I 3 C 0 s dasNov2.scaffold_28617 6011 90 + 20752 CAGCC--ACGAC--------------------CCGATGGGCGGTGTC--GCCGCATGGAGAACTTGG---------------------------GCGGAGGG----GTCCTCGAT---------CCTCCAGCCTAGAACG------GGG-TTCCC--ACCACC---------------------------------------------------------------------- i dasNov2.scaffold_28617 C 0 I 14 e proCap1.scaffold_29042 8943 315 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I a score=-141416.000000 s hg19.chr17_gl000204_random 38993 70 + 81310 CTCGGGGGACAGAAGTGGGTG----------------GCAG----CTGC--TCCA---GGGAGGGGTGC-AG-GTGCAG---AAGAA-----------------A---------CCCCTAAGAGAG s gorGor1.Supercontig_0007361 9084 70 - 64270 CTCGGGGGACAGAAGTGGGTG----------------GCAG----CTGC--TCCA---GGGAGGGGTGC-AG-GTGCAG---AAGAA-----------------A---------CCCCTAAGAGAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79468825 70 + 83384210 CTCGGGGGACAGAAGTGGGTG----------------GCAG----CTGC--TCCA---GGGAGGGGTGC-AG-GTGCAG---AAGAA-----------------A---------CCCCTAAGAGAG i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75030208 70 + 78773432 CTCGGGGGACAGAGGTGGGTG----------------GCAG----CTGC--TCCA---GGGAGGGGTGC-AG-GTGCAG---AGAAA-----------------A---------CCCATGAGAGAA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16055713 70 + 17838096 CTTGGGGGACAGAGGTGGGTG----------------GCAG----CTGC--TCCA---GGGAGGGGTGC-AG-GTGCAG---AAGAA-----------------A---------CCCCTAAGAGAG i ponAbe2.chr17_random C 0 C 0 s papHam1.scaffold8336 37599 70 - 95547 CTCGGGGGACAGAGGTGGGTG----------------GCAG----CTGC--TCCA---GGGAGGGGTGC-AG-GTGCAG---AGAAA-----------------A---------CCCATGAGAGAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 39514 69 + 225949 CTC-GGGGACAGAGGCGGGTG----------------GCAG----CTGC--TCCA---GGGAGGGGCGC-AG-GTGCAG---GGGAA-----------------A---------CTCCTGAGACAG i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_89264 4929 72 + 5251 CTCAGGTGACAGAGGTGGGTG----------------GCAG----CTGC--TCCGGGAGGGAGGGGCGC-AG-GTGCGG---GGGAA-----------------G----------CCCCGAGAGAG i micMur1.scaffold_89264 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19726 80 + 287808 CTCAAGGGACAGAGGTGGGTG----------------GCAG----CTGC--TCCAG--GGAGGGGGCAT-AG-GTGCAG---GGTAA-----------------GAGACAGGAGCTCCAGAGACAG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 5326 74 + 15939 CTCAGGGAACAGAGGTGGGTG----------------GCAG----CTGG--TCT----GGGGTGGGCCC-AG-GCACAA---AGAAC-----------------A----GGCGTCCTTCTGGGGAG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118752278 70 + 121843856 CTCAGATAACAGG---AGGTGG---------------GCAG-----TGC--TCAG---AGGAGGAGCCCAAG-GTTCTGAGTCAGGG-----------------A---------CACTTAAGGAG- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4383781 70 + 7991924 GT-GGGTGACAGA--TGGGTGC---------------GTAG----CTGC--TCCA---GAGAGGAGTAC-AG-GTACAGAA-CGGGG-----------------A---------CCCTAGAGAAGA i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 13913 40 + 41507 -------GACAGAGGTGGGTGG---------------GCAG------------AG---AGGAGGA-----AG-G--------CGGGG-----------------A---------CCC--------- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 221 56 - 54875 -------AACAGAGCAGGGTGGCACCTGTCTACCTGAGCAG------------AG---AGCAGGG-----AGTG--------ACGGG-----------------A---------CCC--------- i ochPri2.scaffold_9426 C 0 C 0 s pteVam1.scaffold_11245 9255 68 + 48268 CTTGGGTGACAGAGGTGGCTGG---------------GCAG----CGGC--TCC----AGGAGAGGCAC-AG-GTGCAG---AAAAA-----CCAGCACGGTA----------------------- i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 5581 53 + 14340 CTCGGGTGGCCCTGG-GGCCGG------------------G----CGGC--TGC----AGGACAGGCGC-AG-GTGCGG---AGAGA--------------------------------------- i myoLuc1.scaffold_4816 C 0 C 0 s equCab2.chr11 58036513 56 - 61308211 CTCAGGGGATGGAGGTGGGTGG---------------GC-A----CTGC--TCC----AGGAGAGGCAC-AG-GTGCGG---AGAGC--------------------------------------- i equCab2.chr11 C 0 C 0 s turTru1.scaffold_106006 122604 69 + 145505 CTCAGGTGACAGAGGTGGGCGG---------------GCAG----CTAC--TCC----GGGAGAGGCAC-GG-GTGCAG---AGAGA-----CCTGCACGGGAG---------------------- i turTru1.scaffold_106006 C 0 M 502 s bosTau4.chr19 10853758 67 - 65312493 CTCAGGTGACAGAGGCAGGGGG---------------GCAG----CTGC--TCC----AGGAGAGGTCT-GG-GTGC-----AGAGA-----CTTCCACAGAAG---------------------- i bosTau4.chr19 C 0 C 0 s loxAfr3.scaffold_49 14425139 67 - 17734757 --TTGGTGACAGAGGAGGGTG----------------GTGG----CTGC--TCT----GGGGGACACCC-AG-GTGCAG---AGAAA-----------------T---------CCATGTGAGGGA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 9258 59 + 24616 CTCTGGTGACAGA-GAGGGTG----------------GTGG----CTGT--TCT----GGGGT-CACCC-CA-GTGCAG---GAAAA-----------------T---------TCAC-------- i proCap1.scaffold_29042 I 315 C 0 s dasNov2.scaffold_28617 6115 67 + 20752 CCCGCGGGGCGGG-AGGGATG----------------GTAGGAGTCACC--TCC----GGGGG-----C-AG-GTGGGC---GGGAA-----------------G---------CCGCTTGCAGGG i dasNov2.scaffold_28617 I 14 C 0 s eriEur1.scaffold_290756 1014 66 - 7602 ---------CACAGG-TGTTGG---------------GAAG----TTGCCTTCA----AGGAGCAATAC-AG-CTACAG---GGATACGCCACCTACACAAGAT---------------------- i eriEur1.scaffold_290756 N 0 I 2 s canFam2.chr9 59431306 9 - 64418924 ----------------------------------------------------------------GGCAT-TG-GC--------------------------------------------------- i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 8548 8 + 132007 ----------------------------------------------------------------GGCAC-AG-G---------------------------------------------------- i felCat3.scaffold_206428 C 0 C 0 e speTri1.scaffold_128901 1250 1336 + 44242 I e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I a score=-485187.000000 s hg19.chr17_gl000204_random 39063 105 + 81310 GAACATGT---------------------------------------------GTGTCCACAGCCC----------ACTCTTGGCAGGC-------------AGACACC-C-------------------------------------CCAGGAGA-CCCCA--------------------------CATCCCA--CC-AGGACGGA--------CACCACCTGCCCT----TCCCT--GGCAGCTCCCAATC--C s gorGor1.Supercontig_0007361 9154 105 - 64270 GAACATGT---------------------------------------------GTGTCCACAGCCC----------ACTCTTGGCAGGC-------------AGACACC-C-------------------------------------CCAGGAGA-CCCCA--------------------------CATCCCA--CC-AGGACGGA--------CACCACCTGCCCT----TCCCT--GGCAGCTCCCAATC--C i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79468895 105 + 83384210 GAACATGT---------------------------------------------GTGTCCACAGCCC----------ACTCTTGGCAGGC-------------AGACACC-C-------------------------------------CCAGGAGA-CCCCA--------------------------CATCCCA--CC-AGGACGGA--------CACCACCTGCCCT----TCCCT--GGCAGCTCCCAATC--C i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75030278 105 + 78773432 GAACACGT---------------------------------------------GTGTCCACAGCCT----------ACTCTCGGCAGGC-------------AGACACC-C-------------------------------------CCAGGAGA-CCCCA--------------------------CATCCCA--CC-AGCACGGA--------CACCACCTGCCCT----TCCCT--GGCAGCTCCCAATC--C i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16055783 105 + 17838096 GAACATGT---------------------------------------------GTGTCCACAGCCC----------ACTCTTGGCAGAC-------------AGACACC-C-------------------------------------CCAGGAGA-CCCCA--------------------------CACCCCA--CC-AGGACGGA--------CACCACCTGCCCT----TCCCT--GGCAGCTCCCAATC--C i ponAbe2.chr17_random C 0 C 0 s papHam1.scaffold8336 37669 105 - 95547 GAACACGT---------------------------------------------GTGTCCACAGCCT----------ACTCTCGGCAGGC-------------AGACACC-C-------------------------------------CCAGGAGA-CCCCA--------------------------CATCCCA--CC-AGGACGGA--------CACCACCTGCCCT----TCCCT--GGCAGCTCCCAATC--C i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 39583 104 + 225949 GAA-ATGT---------------------------------------------ATGTCCACAGCCC----------ACTCTTGGCAGGC-------------AGATGCC-C-------------------------------------CCAGGAGA-CCCCA--------------------------CATCCCA--CC-AAGGCAGA--------CACCATCTGCCCT----TCTCT--GGCAGCTCCTGATC--C i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_89264 5001 102 + 5251 GAGCGCAC---------------------------------------------CTGTCCACAGCC-----------GTTCTTGGCAGGC-------------CA-CGCC-C-------------------------------------ACGGGAGG--CCCA--------------------------CG-ACGG--CAGGGGACAGA--------CACCACCTGCCCT----ACCCT--GGTGGCTCCCGGCT--C i micMur1.scaffold_89264 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19806 105 + 287808 GAGCATGC---------------------------------------------GTGTCCACAGCCT----------GCCTCTGGCAGGC-------------AG-TGCC-T-------------------------------------TTAGGAGG-CCCCA--------------------------TGTGTGG--CTGGGGACAGA--------TGTCACCTGCCCC----ACTCT--GGAGACTCCCCGTC--C i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 5400 116 + 15939 GAGCATGTACCCTCA----------------------------------GCTGGCGAACACCGCCCACC----CCTACCCTCAGCTGGC-------------GGACACCGC-------------------------------------CCAGGAGG-TCGCA--------------------------CGTCAGG--CC-CGGCAGGA--------CACGGCCG--CCT----TCTC---GCAAGCCCCTA------ i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118752348 143 + 121843856 GACCTCAT---------------------------------------------GTGTTGGCAGTAC----------AC-CTTGGCAGGCCCCGCACACTGCTATCCCTG-C-------------------------------------TCCTGGAT-TAACCAGACTGCATAGCCTGCGCTGTTCCTGCCCAAGC--AT-AGGACGAC--------CCCTGCCTGCCCT--GCTACCA--AA--GCTCGCTTTC--T i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4383851 104 + 7991924 GACCTCAA---------------------------------------------ATGTCCTCAGCCC----------TC-CTTGATAGGC-------------AGCCATT-C-------------------------------------CCTGGAAG-TGACC--------------------------CCCTCAG--AC-AGGACAGG--------ACACAACACACCT--ACTCCAG--GG--GCTCTGGTAT--C i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 13953 68 + 41507 --CCCCG-------------------------------------------------------------------------------GGG-------------ACCCTTC-C-------------------------------------CCCGGGCG-GGACC--------------------------CCT-------------------------CCCCTGCACCCCT-CACTCCCG--GGCAGCTCCGGTTC--T i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 277 42 - 54875 --CCTCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCCACACCCCTCCACGCCTG--GACAGCGCCCCTTT--T i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10853825 93 - 65312493 ----------------------------------------------------------------------------------GACAGCCCTCCCCTGGCCGGCAAAACGAC-------------------------------------CCAGGAGGCCCCCG--------------------------CCTGGGG--CCAGGTGCAGGG-------ACACCACCCTCCT----ACCCC---TCTGCCCCAAGC---C i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58036569 116 - 61308211 ------------------------------------------------------------------------------GGGAAGCTGCC-------------CAGGACGACGTGTCATCAACAGCGCACTCCTCGCAGGCAAACGCCGCCGGGAGA-CTCCA--------------------------CGAAGGA--CCGGGG-CAGAG-------TCCCCGCCGTCCC----TCCGT----CTGCCCCGA-----T i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 8556 86 + 132007 ---------------------------------------------------------------------------------------CC-------------CGCGTCCAC-------------------------------------CCAGGAGTTCCCCA--------------------------CATCAGA--CCAGGGACAGAGACGCACCCCCCCCCCATCCT----TCCCC--AGATGCCCACACTTCTC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59431315 80 - 64418924 ---------------------------------------------------------------------------------------CC-------------CGAGGCTAC-------------------------------------CCAGGAGATCCCCA--------------------------CGTCAGG--CCAGGGTCAGAG------TGCCCCCCCACCCT----TCTTT--AGCTGCCCCCACCTCCC i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 5634 61 + 14340 ---------------------------------------------------------------------------------------------------------GGCCAC-------------------------------------CCAGCAGGCCCCCG--------------------------CGTGGGA---CACGGAC--AG-------TCACCCGCGTCCT----GCCC----GCTGCCC--------C i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 9323 103 + 48268 -------------------------------------------------------GGCCGTGGACATGGACGGCCCGCTCCCGGCAGGC-------------CAGCGCCAC-------------------------------------CCAGGAGGTCCTCC--------------------------CATCAGA--CCGTGGACAGAG-------TCATCACGGTCCT----GCCCC--AGCTCCCC--------C i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_290756 1082 96 - 7602 -------------------------------------------------------------GCTCCCATACAGCCCACTCTCAGTGGGC-------------AGACACTAC-------------------------------------CCGGGAGACCCCCA-----------------------------GTAA--CCAGGggcagct-------cccctccctccca----taCCTCCACTAGTCC--------C i eriEur1.scaffold_290756 I 2 C 0 s loxAfr3.scaffold_49 14425206 102 - 17734757 --------AGACGTA----------------------------------------CTCAAGAGTCC----------ACTGGTGGAGGCC-------------AGAGGCTGC-------------------------------------CCGGGAGA-CCCCC--------------------------CGTGTGAAGCA-GGGACAGA-----------GCCTCGTCCT----TCCCT--GATGGCTCCAAATG--A i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 9317 86 + 24616 -------------------------------------------------------------AGCCC----------ACTGCAGGAGGCC-------------AGACAGTGC-------------------------------------CCAGGGAC-TCCCA--------------------------CATGGGA--CA-GGGACAGG-----------GCCGCATCCT----T-CCT--GGCTGCTCCCAGTG--A i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 6182 141 + 20752 --------AGGCGGAGACGCGGAGAGAGAGGAGACCGCGCTCTCGGGGAACGGGCACCAGGGGCCC----------CTCGCGGCAGGCC-------------ACGTGCCCC-------------------------------------CTGGCAAC-CCCGT--------------------------CGTTCGA-----GGGGCAGA--------CGTGGCCCAGCCT----TCCCC--GGCCGCCCACGGTG--G i dasNov2.scaffold_28617 C 0 C 0 e speTri1.scaffold_128901 1250 1336 + 44242 I e turTru1.scaffold_106006 122673 502 + 145505 M e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I a score=-138752.000000 s hg19.chr17_gl000204_random 39168 40 + 81310 TCCCT--CCTTCTCCCA--GCTC----TTTTTTTGTAAAC------TAAGTCT---G------ s dasNov2.scaffold_28617 6323 38 + 20752 CTCGC--CATCCCCCCT--GCTC----CGCTG--GCGAGC------TGAGCGG---C------ i dasNov2.scaffold_28617 C 0 C 0 s proCap1.scaffold_29042 9403 33 + 24616 TTC-C--CGCCCCCTTT--GCTG----TTTT---CTAAAC------T---CTG---C------ i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14425308 33 - 17734757 GTT-C--CGTCCCCTGC--ACTC----TTCT---TTAAAC------T---CAG---C------ i loxAfr3.scaffold_49 C 0 C 0 s eriEur1.scaffold_290756 1178 18 - 7602 TACCC--CGTC----------------ATT------------------GGCCT---C------ i eriEur1.scaffold_290756 C 0 C 0 s pteVam1.scaffold_11245 9426 30 + 48268 GCCCC--AGGC----------------CCTTTTCTTTAAC------TAAGCTG---C------ i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 5695 30 + 14340 CCTTC--CCTC----------------TCTTCCCTGTAAT------TAAGCTC---C------ i myoLuc1.scaffold_4816 C 0 C 0 s canFam2.chr9 59431395 38 - 64418924 TCCCC--CTCCCACCCT--GC------TTTTTTTTTTAAC------TAAGCTT---C------ i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 8642 43 + 132007 TCCTC--CTCCCACTTT--GCT-TTTTTTTTTTTTTTAAC------TAAGCTG---C------ i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58036685 44 - 61308211 TCCCC--CCTCCCCTTT--GCTCTCTTTTTTTCTTTTAAC------CAGGCTT---C------ i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10853918 41 - 65312493 TTCCC--GCTCCCCTTT--GCCCT---TTTTTCTTTTAAC------TAAGCCT---C------ i bosTau4.chr19 C 0 C 0 s ochPri2.scaffold_9426 319 36 - 54875 G------CGACTCGTAC--AGTC----TCTCATTGTGCAA------CAGCCCC---T------ i ochPri2.scaffold_9426 C 0 C 0 s oryCun2.chrUn0958 14021 43 + 41507 GCCCGGTCGCTCTGCACCGAACG----CCTCGTT-TCCTG------AGGCTCC---C------ i oryCun2.chrUn0958 C 0 C 0 s cavPor3.scaffold_76 4383955 35 + 7991924 T------CTCTCCTCTC--ACTC----TTTTGTT-CACAC------CAGGTCC---C------ i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118752491 35 + 121843856 G------CTTCCCCTCC--GCTC----TTTTGTT-CACAC------CAGGTCT---C------ i mm9.chr11 C 0 C 0 s tupBel1.scaffold_124459.1-15939 5516 24 + 15939 -------------CCCA--GCAC----TCTTT-----AAC------CACATCC---C------ i tupBel1.scaffold_124459.1-15939 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19911 36 + 287808 TTCCC--CTTTCCCTCT--TATT----TTTT----TTAAC------TAAGTCT---C------ i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_89264 5103 42 + 5251 TTCCC--TTTCCGCTCG--GGTT----TTTT----TAAACTATTAATAAGTCT---C------ i micMur1.scaffold_89264 C 0 C 0 s calJac1.Contig5139 39687 43 + 225949 TTCCT--CACACCTCTG--GCTC----TTTTTCTGTAAAC------TAAGTCTCCGG------ i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 37774 40 - 95547 TCCCT--CCTTCTCCCA--GCTC----TTTTTTTGTAAAC------TAAGTCT---G------ i papHam1.scaffold8336 C 0 C 0 s ponAbe2.chr17_random 16055888 40 + 17838096 TTCCT--CCTTCTCCCA--GCTC----TTTTTTTGTAAAC------TAAGTCT---G------ i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75030383 40 + 78773432 TCCCT--CCTTCTCCCA--GCTC----TTTTTTTGTAAAC------TAAGTCT---G------ i rheMac2.chr16 C 0 C 0 s panTro2.chr17 79469000 40 + 83384210 TTCCT--CCTTCTCCCA--GCTC----TTTTTTTGTAAAA------TAAGTCT---G------ i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 9259 40 - 64270 TTCCT--CCTTCTCCCA--GCTC----TTTTTTTGTAAAC------TAAGTCT---G------ i gorGor1.Supercontig_0007361 C 0 C 0 s ornAna1.Contig9679 17710 46 + 20910 TCTCT--CTTTTTTTTT--TTTT----TGTCTTTGTTAAA------GAGGTAC---TGGGCTC i ornAna1.Contig9679 N 0 C 0 e speTri1.scaffold_128901 1250 1336 + 44242 I e turTru1.scaffold_106006 122673 502 + 145505 M e dipOrd1.scaffold_53224 1130 2495 + 10229 I e monDom5.chr2 304518080 8722 - 541556283 I a score=557746.000000 s hg19.chr17_gl000204_random 39208 57 + 81310 -TTTC---------TGGAGGGCGCGTCA--TGTGTG----CACGCCTGTACATGCATGCCGAGTTTTTATTCC s gorGor1.Supercontig_0007361 9299 57 - 64270 -TTTC---------TGGAGGGCGCGTCA--TGTGTG----CACGCCTGTACATGCATGCCGAGTTTTTATTCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79469040 57 + 83384210 -TTTC---------TGGAGGGCGCGTCA--TGTGTG----CACGCCTGTACATGCATGCCGAGTTTTTATTCC i panTro2.chr17 C 0 I 396 s rheMac2.chr16 75030423 57 + 78773432 -CTTC---------TGGAGGGCGCGTCA--TGTGTG----CACGCCTGTACACGCATGCCGAGTTTTTATTCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16055928 57 + 17838096 -TTTC---------TGGAGGGCGCGTCA--TGTGTG----CACGCCTGTACATGCATGCCGAGTTTTTATTCC i ponAbe2.chr17_random C 0 C 0 s papHam1.scaffold8336 37814 57 - 95547 -CTTC---------TGGAGGGCGCGTCA--TGTGTG----CACGTCTGTACACGCATGCCGAGTTTTTATTCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 39730 57 + 225949 -TTTC---------TGGAGGGCACGTCA--TGTGTG----CACGCCTATACATGAGTCCCGAGTTTTTATTCC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_89264 5145 63 + 5251 -TTCTGTTGT---GTGAGGGTCCCTTCA--TGTCTG----CGCGCCTGCACATGTGTGTCGAGTTTTTATTCC i micMur1.scaffold_89264 C 0 C 0 s otoGar1.scaffold_94362.1-287808 19947 63 + 287808 -TTTTGTTCC---ATGAGGGCCCCTTCA--TGTGTG----CACGCCTGCACACGTGTGTCGAGTTTTTATTCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 5540 61 + 15939 -TGTCGCTGG----GTGAGAACACGTT---CGTGTG----TGTGCCTGCACATGCGTGTCGGGCTTTTATTCC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118752526 65 + 121843856 -CATTGTTTCTGAACACCGGCTTCTTCA--CGCGTG----CGTGTTCGCACATGCGTGTCAAG-TTTTATTCC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4383990 61 + 7991924 -TATTGTTTC---ACAAGCACTGCTACA--CACGTG----CACATCCACACATGCGTGTCGAG--TTTATCCC i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 14064 43 + 41507 -TGCA-------------------------CGTGTG----CACACCCGCACACGCGTGTCAGGCTTTTATTCC i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 355 43 - 54875 -TCCC-------------------------CATGTG----CACGCCCGCACATGCGTGACGAGCTTTTATTCC i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10853959 63 - 65312493 -TTTTGTTTAG---CGAGGACCCCTTCA--TGTGTG----CACACCCGCACATGCGTGTCAAGTTTTTATTCC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58036729 63 - 61308211 -TTTTGTTTTT---CGAGGATCCCTTCA--TGTGTG----CGCGCCCGCACATGCGTGTCTAGTTTTTATTCC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 8685 63 + 132007 -TTTTGTTTTT---TGAGGATGCCTTCA--TGTGTG----CATGCCCGCACACGCATGTCAAGTTTTTATTCC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59431433 63 - 64418924 -TTTTGTTTTT---TGAGGATCCCTTCA--TGTGTG----CACGCCCGCACATGCATGTCAAGTTTTTATTCC i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 5725 62 + 14340 -TTTTGTTTTC---CGAGGATCCCTCCA--CCCGTG----CTCG-CCGCACATGCGTGTCGAGCCTTTATTCC i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 9456 61 + 48268 -TTTTGTTTTG---CGAGGACCCCTCCG--TGTGTG----CACG--CGCACACGCATGTCACGTTTTCACTCC i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_290756 1196 56 - 7602 -TTCTGCTTTG---CAAGGATGC-------TGCGTG----TACT--CACTCATGCGTGTCAagtcctccttcc i eriEur1.scaffold_290756 C 0 C 0 s loxAfr3.scaffold_49 14425341 65 - 17734757 -TCCTCTATGT---CGCGAGGCTCCCCACATGTGTG----CATGCCTGCACACGCATGTGGAGTTTTTATCCC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 9436 65 + 24616 -TTCTCTGGGC---GGCGAGGCCCCCCACACATGTA----CATGCCTGCACACGTCTGTCGAGCTTTGATCCC i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 6361 59 + 20752 -TTTTGTTTGG---CGCGGAGCCTTCC----GTGGG----CACGC--GCACATGCGTGTCGAGTTTTTATTCC i dasNov2.scaffold_28617 C 0 C 0 s monDom5.chr2 304526802 57 - 541556283 -------TTTG---TGAGGTTTTCTTAA--TGTATA----CATGCGTGCACATGCATTTAATGTTTTTATTCC i monDom5.chr2 I 8722 C 0 s dipOrd1.scaffold_53224 3625 37 + 10229 ------------------------------TGCGTG----CGTG-GCGCACATGCGTGTCGGG-TTTTGCTCT i dipOrd1.scaffold_53224 I 2495 C 0 s ornAna1.Contig9679 17756 67 + 20910 CTTCCGTGTGGC--TCAGGGCTCCTAAA--TGTGGGTCTCTCCTCCCGCACATGCGTTT--GCTTCTCGTTCC i ornAna1.Contig9679 C 0 C 0 e speTri1.scaffold_128901 1250 1336 + 44242 I e turTru1.scaffold_106006 122673 502 + 145505 M a score=789320.000000 s hg19.chr17_gl000204_random 39265 41 + 81310 AATCC----------TTAAATGAGGTCTTTGCTGAGAA-TTTACAATTCCCC s gorGor1.Supercontig_0007361 9356 41 - 64270 AATCC----------TTAAATGAGGTCTTTGCTGAGAA-TTTACAATTCCCC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16055985 35 + 17838096 AATCC----------TTAAATGAGGTCTTTGCTGAGAA-TTTACAA------ i ponAbe2.chr17_random C 0 M 327 s rheMac2.chr16 75030480 41 + 78773432 AATCC----------TTAAATGAGGTCTTTGCTGAGAA-TTTACAATTCCCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 37871 41 - 95547 AATCC----------TTAAATGAGGTCTTTGCTGAGAA-TTTACAATTCCCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 39787 41 + 225949 AATCC----------TTAAATGAGGTCTTTGCTGAGAA-TTTACAATTCCCC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_89264 5208 42 + 5251 AATCC----------CTTTTTTTCTCCTTTGCCGAGAATTTTACAATTCCCC i micMur1.scaffold_89264 C 0 N 0 s otoGar1.scaffold_94362.1-287808 20010 41 + 287808 AATGC----------TTAAATGAGGTCTTTGCTGAGAA-TTTACAATTCCCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 5601 41 + 15939 AATCC----------TTAAACAAGGTCTTTGCTGAGCA-TTTACAATTCCCC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118752591 41 + 121843856 GATCC----------TTAAATGAGGTCTTGGCTGAGAA-TCTACGATTCCCC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 3662 40 + 10229 CGTCC----------TTAAATGAGGTCTTGGCGGAGGT-TCTATCGTT-CCC i dipOrd1.scaffold_53224 C 0 C 0 s cavPor3.scaffold_76 4384051 41 + 7991924 AATCC----------TTAAATGAGGTCTTGGCTGAGAA-TCTACAATTCCCC i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 14107 41 + 41507 GATGC----------TTACGTGAGGTCTGGGCTGAGAA-CGCACGATCCCTC i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 398 41 - 54875 GATCC----------TTAAATGAGGTCTTGGCTGAGAA-TTTACAATTCCCC i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10854022 41 - 65312493 AATCC----------TTAAATGAGGTCTTTGCTGAGAA-TTTACAATTCCCC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58036792 41 - 61308211 AACGC----------TTAAATGAGGTCTTTGCTGAGAA-TTTACAATTCCCC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 8748 41 + 132007 AATCC----------TTCAATGAGGTCTTTGCCGAGAA-TTTACAATTCCCC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59431496 41 - 64418924 AATCC----------TTCAATGAGGTCTTTGCTGAGAA-TTTACAATTCCCC i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 5787 41 + 14340 AAGCC----------TCAAACGAGGCCTTTGCTGAGCG-TTTACAATCCCCC i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 9517 41 + 48268 AACCC----------TTAAACGAGGTCTTTGCTGAGGA-TTTACAATTCCCC i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_290756 1252 41 - 7602 tttcc----------ttcaatgAGGACTTTGCCaagaa-tttaaaattcctg i eriEur1.scaffold_290756 C 0 C 0 s loxAfr3.scaffold_49 14425406 50 - 17734757 ATCCCTTTTTTTTTTTTAGATGAGG-CTTTGCTGAGAA-TTCACAATTCCCC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 9501 41 + 24616 CTCCC---------TTTGGATGAGG-CTAGGCTGAGCG-TCCACCGTTCCCC i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 6420 41 + 20752 GATCC----------CTAAACGAGGTCTTTGCCGAGAA-TTTACAATTCCCC i dasNov2.scaffold_28617 C 0 C 0 s monDom5.chr2 304526859 41 - 541556283 ATTCC----------TTAAATGAGGTTTTTGCTGAGAA-TTTACAATTCCCC i monDom5.chr2 C 0 C 0 s ornAna1.Contig9679 17823 41 + 20910 AGTGC----------TCGGACGAGGCCTTTACGGAGAA-TTTACAATTCCCC i ornAna1.Contig9679 C 0 C 0 e speTri1.scaffold_128901 1250 1336 + 44242 I e turTru1.scaffold_106006 122673 502 + 145505 M e panTro2.chr17 79469097 396 + 83384210 I a score=1600017.000000 s hg19.chr17_gl000204_random 39306 97 + 81310 TGTGGCCTCAATCTTGCAAAGATTGC-TTTTTT-------AACGCTGTTAGGCCTTAATTCTAATAAGCCTCCTCCTTA-----------TTACAG-------AACCAGGTCACATTGCCTTG s gorGor1.Supercontig_0007361 9397 97 - 64270 TGTGGCCTCAATCTTGCAAAGATTGC-TTTTTT-------AACGCTGTTAGGCCTTAATTCTAATAAGCCTCCTCCTTA-----------TTACAG-------AACCAGGTCACATTGCCTTG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79469493 96 + 83384210 TGTGGCCTCA-TCTTGCAAAGATTGC-TTTTTT-------AACGCTGTTAGGCCTTAATTCTAATAAGCCTCCTCCTTA-----------TTACAG-------AACCAGGTCACATTGCCTTG i panTro2.chr17 I 396 C 0 s rheMac2.chr16 75030521 97 + 78773432 TGTGGCCTCAATCTTGCAAAGACTGC-TTTTTT-------AACGCTGTTAGGCCTTCATTCTAATAAGCCTCCTCCTTA-----------TTACAG-------AACCAGGTCACATTGCCTTG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 37912 97 - 95547 TGTGGCCTCAATCTTGCAAAGATTGC-TTTTTT-------AACGCTGTTAGGCCTTCATTCTAATAAGCCTCCTCCTTA-----------TTACAG-------AACCAGGTCACATTGCCTTG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 39828 97 + 225949 TGTGGCCTCAATCTTGCAAAGATTGC-TTTTTT-------AACGCTGTGAGGCCTTAATTCTAATAAGCCTCCTCCTTA-----------TTACAG-------AACCAGGTCACACAGCCTTG i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 20051 96 + 287808 CGTGGCCTCAATCTTGCAAAGATTGC-TTTTTT-------AACGCTGTTAGGCCTTAATTCTAATAAGCCGCCTCCTTA-----------TTACGG-------AACCAGGTCACACTGCCTG- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 5642 94 + 15939 CATGGCCTCAATCTTGCAAAGATTGC-TTTTTT-------AACGCTGTTAGGCCTTAATTCTAATAAGCCT-CTCTTTA-----------TTACAG-------AACCAGGTCACATTGCAG-- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118752632 97 + 121843856 GGTGGCCTCAATCTTGCAGAGATTGC-TTTTTT-------AACGCTGTTAGGCCTTAATTCCAACAGGCTTCTTCTCCA-----------TTACCG-------AACCGGGTCAGTTTGCCCTG i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 3702 95 + 10229 GGTGGC--CAATCTTGCAGAGATTGC-TTTCCT-------AGCACGGCCAGGCCTTCACGCTAATCAGCTTTCTCCCTA-----------GCGTGG-------AAGCCGGACACTTGGCCCTG i dipOrd1.scaffold_53224 C 0 C 0 s cavPor3.scaffold_76 4384092 97 + 7991924 AGTGGCCTCAATCTTGCAAAGATTGC-TTTTTT-------AATGCTGTTAGGCCTTAATTCTAATAAGCTTCCTCTCTA-----------GTACAG-------AACCGGGTCACTCTGCCCTG i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 14148 92 + 41507 CGTGGCCTCAATCTTGCA-AGGTTGC-TTTT-T-------AGGGCCGTTAGGCC-TACTTTTAATAAGCCCTCTCCCCA-----------C--CGG-------AGCCCGGTCACTCCGCCCCA i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 439 95 - 54875 TGTGGCCTCAATCCTGCA-AGATTGC-TTTTGG-------AACACTGTTTGGCC-TCGTTCTAATAAGCCTTCTCCCTG-----------TCACAG-------AACCGGGTCGCTCTGCCCTG i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10854063 97 - 65312493 CGTGGCCTCAATCTTGCAAAGATTGC-TTTTTT-------AACGCTGTTAGGCCTTAATTCTAATAAGCCTCCTCTTTA-----------TTACAG-------AACCAGGTCACATTGCCTTG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58036833 97 - 61308211 TGTGGCCTCAATCTTGCAAAGATTGC-TTTTTT-------AACACTGTTAGGCCTTAATTCTAATAAGCCTCCTCTTTA-----------TTACAG-------AACCAGGTCACATTGCCTTG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 8789 95 + 132007 CGTGGCCTCAATCTTGCAAAGATTGC---TTTT-------AACGCTGTTAGGCCTTAATTCTAATAAGCCTCCTCTTTA-----------TTACAG-------AATCAGGTCACATCTCCTTA i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59431537 96 - 64418924 TGTGGCCTCAATCTTGCAAAGATTGC--TTTTT-------AACGCTGTTAGGCCTTAATTCTAATAAGCCTCCTCTTTA-----------TTACAG-------AACCAGGTCACATTTCCTTG i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 5828 108 + 14340 --GGGGCTCGGTCCTGCAGGGATCGC---TCTC-------AGCGCTGCGAGGCCTTCATTCCAAGGAGGCTCCTCGTCATCCCcagccggttacagccggtcccagccggtcaca---gccgg i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 9558 62 + 48268 CGCGGCCCCGATCTCGCGGAGATCGC-------------------------------------------CTCCTCTTTA-----------TTACAG-------AACCGGGTCACACTGCCTTG i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_290756 1293 97 - 7602 aatgaTCTCAGTCTTGCAAAGATTGC-TTTCTT-------AAAACTGTTAGGCCCTAATCCTAATATGTCTCCTCTTTA-----------TCACAG-------AACCAGGTCACACCGCCTTG i eriEur1.scaffold_290756 C 0 C 0 s loxAfr3.scaffold_49 14425456 97 - 17734757 CGGGGCCTCCATCTTGCTAAGATTGC-CAGTTT-------AACACTGCTAGGCTTTAATTCTAATAAGCTTCCTCTGTG-----------TTACAG-------AACCAGGCCTCCCTGCCCTG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 9542 97 + 24616 TGGGGCCTCTGTCTTGCAAAGATTGC-CTGTTT-------AACACGGCTAGGCCTTGACTCCGATACACTTCCTCACTG-----------TCACAG-------AGCCAGGCCTCCCTGCCCTG i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 6461 98 + 20752 CGCGGCCTCAATCTTGCAGAGACGGCTTTTTTT-------AATGCCGTTAGGCCTTAATTCTAATAAGCCTCCTCTTCA-----------TTACAG-------AACCAGGTCACACGGCCTTG i dasNov2.scaffold_28617 C 0 C 0 s monDom5.chr2 304526900 104 - 541556283 CATGGCTTCAATCTTGCAAAGATTGC-TTTTTTTTTTTTAAACACTGTTTGGCTTTAATTCTAACAAGCTGCCTCTTTA-----------TTATAG-------AACCAGGTCACATTGTCTTG i monDom5.chr2 C 0 C 0 s ornAna1.Contig9679 17864 98 + 20910 TGTGGCCTGAATCTTGCAGAGGCTGCTTTTTTT-------AACGGCGCTGGGCTTTAATTCTAATAAGCCTCCTCTTTA-----------TTACCA-------AATGGGGTCACGTTGCCTTG i ornAna1.Contig9679 C 0 C 0 e speTri1.scaffold_128901 1250 1336 + 44242 I e turTru1.scaffold_106006 122673 502 + 145505 M e ponAbe2.chr17_random 16056020 327 + 17838096 M a score=7205.000000 s hg19.chr17_gl000204_random 39403 80 + 81310 ACACCGCCAGA-AA-A-TCTCTCAT-GGCCACGG------------------G--AGGG--T---GGGCGTGGA---G--------AAA-------GGGGCTGCCAGAGAATGGGG--CAGAGATCTGG s gorGor1.Supercontig_0007361 9494 81 - 64270 ACACCGCCAGA-AA-A-TCTCTCATCGGCCATNG------------------G--AGGG--T---GGGCGTGGA---G--------NAA-------GGGGCTGCCAGAGAATGGGG--CAGAGATCTGG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79469589 81 + 83384210 ACACCGCCAGA-AA-A-TCTCTCATCGGCCACGG------------------G--AGGG--T---GGGCGTGGA---G--------AAA-------GGGGCTGCCAGAGAATGGGG--CAGAGATCTGG i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75030618 81 + 78773432 ACACCGCCAGA-AA-A-TCTCTCATCGGCCGCGG------------------G--AGGG--T---GGGCGTGGA---G--------AGA-------GGGGCTACCAGAGGAAGGGG--CAGAGAGCTGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 38009 81 - 95547 ACACCGCCAGA-AA-A-TCTCTCATCGGCCGCGG------------------G--AGGG--T---GGGCGTGGA---G--------AGA-------GGGGCTACCAGAGGAAGGGG--CAGAGAGCTGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 39925 81 + 225949 ACACTGCCAGA-AA-A-TCTCTCATCGGCCGCTG------------------G--AGGG--T---GGGCGCGGA---G--------AGA-------GGGGCTGCCAGAGGAAGGGG--CAGAGAGCCGG i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_184068 1 76 + 702 ACACTGCCAGGAAA-A-TCTGTCCCCGG---TGG------------------G--GCGG--G---GGGCGAGGG---G--------AG--------CGGACGGCCGGGGAGGGGG----CGGGAGCCGG i micMur1.scaffold_184068 N 0 C 0 s otoGar1.scaffold_94362.1-287808 20147 74 + 287808 ACACTGCCAGG-AA-A-TCTTTCACTGG---TGG------------------G----AG--G---GGGCTGGGA---G--------AGAC-----CTGGAC--CTAGGGACAGGG----AGGGGACCAT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16056348 78 + 17838096 ---CCGCCAGA-AA-A-TCTCTCATCGGTCACGG------------------G--AGGG--T---GGGTGTGGA---G--------AAA-------GGGGCTGCCAGAGAATGGGG--CAGAGATCTGG i ponAbe2.chr17_random M 327 C 0 s tupBel1.scaffold_124459.1-15939 5736 77 + 15939 ACACCGCCAGG-AA-G-TCTTTCTCTGG---CGG------------------A--GGGA--T---GGGCGGGAA---G--------AG--------GGGGCTGTTCGGGGCAGGTG--CAGAGAGTGGG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118752729 63 + 121843856 ACACGGCCAGA-AA-A-TCTCCCATCGA---GCG------------------G--GGAG--A---GGGCCTGGG--AG--------GGA-------AGGCG------------------CGGGAGCTGG i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 3797 47 + 10229 GCACCG-CAGA-CG-A-TCTTCCGTGGG---GTG------------------G------------------------G--------GGA-------AGGGG------------------CGGGAGCTGG i dipOrd1.scaffold_53224 C 0 C 0 s cavPor3.scaffold_76 4384189 77 + 7991924 ACATCACCAGA--A-A-TCTCGCCTGGG---CTG------------------G--AGGG--C---GGGTGGGAA--TG--------GGG-------AGGGGCCCCTCAGGGAAGG---CCCGGAGCCAG i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 14240 58 + 41507 CCAGCACCAGA-AA-A-TCCCGCTCAGG---CAG------------------G--CGGCGAG---GGGCT-------G--------CGA-------GGGGC------------------TGGGAGC--G i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 534 57 - 54875 ACATGGCCAGA-GG-A-TCTTCCCCTCG---GTG------------------G--CAGC--A---GGGTG-------G--------TGA-------GGGAC------------------AGGGAGCT-G i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10854160 82 - 65312493 ACACCGCCAGA-AA-A-TCTTTCATCGG---CAG------------------GGAGGGA--T---GGGCAAGAG---G------AGAGA-------GGGACACCGAGAGGAAGGGG--CAGGGAGACGG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58036930 78 - 61308211 ACATCACCAGA-AA-A-TCTTTCATTGG---CAG------------------GGAGGGG--T---GGGCGAGCA---G----------A-------GGGACGGCGAGAGGAAGGGG--CCGGGAGCCAG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 8884 88 + 132007 ACACCACCAGA-AA-A-TCTTTCATCGG---CCG------------------GTGGGGG--GGC-GGGGGGGCA---GTAAGAGAGAGA-------GGGTCAGAAAGAGGAAGGGG--CAGGGAGAC-- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59431633 89 - 64418924 ACACCGCCAGA-AA-A-TCTTTCATCGG---CCG------------------GGAGGGG--TCCAGGGGGGGCA---G--GCAGAGAGA-------GGGCTAGAAAGAGGAAGGGG--CAGGGAGACAG i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 5936 60 + 14340 GCGCGGCCAGG-GA-GTCCCTCCG--GG---CAG------------------G--AGGG--T---GGGC--------G--------AGA-------GGG-CGGCCGCGGGACGGGG------------- i myoLuc1.scaffold_4816 C 0 I 117 s pteVam1.scaffold_11245 9620 68 + 48268 ACACCGCCAGA-AA-A-CCTTCCGTCGG---CAG------------------GGAGGAG--T---GGGCAAGGA---G--------AGA-------GAG-TGGCAGTGGGGTGGGG------------- i pteVam1.scaffold_11245 C 0 I 17 s eriEur1.scaffold_290756 1390 47 - 7602 CCACAGCCAGG-AT-A-CT------------------------------------GGAG--T---GGCAAGGGA---A--------ACA-------GAG-------AAGACTGGGG------------- i eriEur1.scaffold_290756 C 0 C 0 s loxAfr3.scaffold_49 14425553 87 - 17734757 GCACTGCC-CA-GA-A-TCGCTAGTCAG---CAGGAAGGGTGCCCAAGAAGAG--AGGG--G---CCTCGAGGAGAAG--------AGA-------AGAGGGGTGGGGGGAAGGAC------------- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 9639 68 + 24616 ACACTGCA-CA-GA-A-TGGTCCATCAG---CAG------------------G--AGGG--A---CCCTGAGGAGCCG--------AGA-------GGAGGGGC-AGGGGATGGAG------------- i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 6559 63 + 20752 ACACTGCCGGA-GA-A-TCCTTCACCGG---C--------------------G--GAGG--G---GTGCAAGGAGCGG--------GGA-------GTGG-----GCGGCAGGAGG------------- i dasNov2.scaffold_28617 C 0 C 0 s monDom5.chr2 304527004 76 - 541556283 ACAATGCAAGA-AA-A-TCTTTTATCAG---CAA------------------A--GGGG--G---ATGCATGTG---T--------ATA-------AGAGTGGAAAAGAGAAGGG----AGTAACCCAG i monDom5.chr2 C 0 C 0 s ornAna1.Contig9679 17962 88 + 20910 ACGCTGCCAGA-AAGA-TCTTGCGTCGC---CCA------------------G--GCAG--G---GGGCGGTGG---G--------AGAAACAAGTGGGCAGACCCGCAGTCGGGCAGGCAGGACCTGG i ornAna1.Contig9679 C 0 I 1768 e speTri1.scaffold_128901 1250 1336 + 44242 I e turTru1.scaffold_106006 122673 502 + 145505 M a score=238005.000000 s hg19.chr17_gl000204_random 39483 50 + 81310 GAACACCGA-GGGAGGAATCCTTT--CTTAATTCAA-TGCAATTCTAAAATAAT s gorGor1.Supercontig_0007361 9575 50 - 64270 GAACACCGA-GGGAGGAATCCTTT--CTTAATTCAA-TGAAATTCTAAAATAAT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79469670 50 + 83384210 GAACACCGA-AGGAGGAATCCTTT--CTTAATTCAA-TGCAATTCTAAAATAAT i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75030699 50 + 78773432 GAACACTGA-GGGAGGACTCCTTT--CTTAATTCAA-TGAAACTCTAAAATAAT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 38090 50 - 95547 GAACACTGA-GGGAGGACTCCTTT--CTTAATTCAA-TGAAACTCTAAAATAAT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40006 49 + 225949 GAATGCCG--GGGAGGAATCCTTT--CTTAATTCAA-TGAAATTCTAAAATAAT i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_184068 77 49 + 702 GAAAGCCA--GAGAGGAATCCTCC--CTGAGTGCCA-CCAAACTCTAAAATAAT i micMur1.scaffold_184068 C 0 C 0 s otoGar1.scaffold_94362.1-287808 20221 47 + 287808 GAAA--CA--GAGAGGAATACTCG--CTCCATGTGA-CAAAACTCTAAAATCAT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16056426 50 + 17838096 GAACACCGA-GGGAGGAATCCTTT--CTTAATTGAA-TGAAATTCTAAAATAAT i ponAbe2.chr17_random C 0 C 0 s tupBel1.scaffold_124459.1-15939 5813 45 + 15939 GAACACCAACGGGAGG----CCCC--CTTCAGTCGG-CGAAATTCCAGGA--AC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118752792 50 + 121843856 GAGAGCCGA-GCTCGGAACCCTCC--CTTAATTCGA-TGAGATTCCGGAATGAT i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 3844 48 + 10229 GAAAGCC---GCGAGGAACCCTCC--CTTAATTCAA-TGAAACCCTAAAATAAT i dipOrd1.scaffold_53224 C 0 C 0 s cavPor3.scaffold_76 4384266 50 + 7991924 GGAGGCCCA-GAGACGAATCCTCC--CTTAATTCCT-TGGAATTCCCAAATCAT i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 14298 52 + 41507 CGCAGCTGC-AGTGTGGAACCCCCCTCTTCATTCCA-TGGAATTCTAAAACCAC i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 591 50 - 54875 GGAAGCTGG-CATGCGAATCCTCC--CTTAATTCGA-TCAAATTCTACAATGAT i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10854242 49 - 65312493 GAAC-CAGA-GAGAAGAATCCTCC--CTTAATTTGA-TGGAATTCTAAAATAAT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58037008 49 - 61308211 GAGC-CACA-GAGAGGAACCCTCC--CTTAATTCAG-TGGAATTCTAAAATAAT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 8972 37 + 132007 --------------GGAATCCTCC--CTTAATGTGA-TGGAATTCTAAACTAAT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59431722 45 - 64418924 AAT----CG-GAGAGGAATCCTCC--CTTAATGTGA-TGGAATTCTAAA-TAAT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 9705 48 + 48268 GATC---CT-GAGGGGAACCCCCC-GCTCAGAGCGA-TGAAACCCCACAGCAGC i pteVam1.scaffold_11245 I 17 C 0 s eriEur1.scaffold_290756 1437 35 - 7602 ---------------CAGTGGCCA--CTCAGTTC-A-TGGGGTTCCAGAACCAT i eriEur1.scaffold_290756 C 0 C 0 s loxAfr3.scaffold_49 14425640 40 - 17734757 -----CACA-GAGAGGAAGCCCCC--CTTAATGCCA------GTCTAAAATGAT i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 9707 43 + 24616 -----CACA-GGATAGGAG-CCCC--CTCAAGGCCA--GGCGGCCTCAAACCAT i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 6622 43 + 20752 -----CCCA-G---GGGCGTCCCC--CCCAAATTCGACGAAACGCTGAACGCAT i dasNov2.scaffold_28617 C 0 C 0 s monDom5.chr2 304527080 38 - 541556283 GGAAA--GA-GAGAGTGATGACTC-------------TAAACTCATACAATAAC i monDom5.chr2 C 0 C 0 e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e turTru1.scaffold_106006 122673 502 + 145505 M e ornAna1.Contig9679 18050 1768 + 20910 I a score=308570.000000 s hg19.chr17_gl000204_random 39533 26 + 81310 CTAATTTCTGAGGACCGGAGTGGC--CT s gorGor1.Supercontig_0007361 9625 26 - 64270 CTAATTTCTGAGGACCGGAGCGGC--CT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79469720 26 + 83384210 CTAATTTCTGAGGACCGGAGTGGC--CT i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75030749 24 + 78773432 CTAATTTCTGAGAACCAGAGTGGC---- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 38140 24 - 95547 CTAATTTCTGAGAACCAGAGTGGC---- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40055 24 + 225949 CTAATTTCTGAGAACCAGAGCGGC---- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_184068 126 24 + 702 CTAATTTCTGGGAACCAGCGTGGC---- i micMur1.scaffold_184068 C 0 C 0 s otoGar1.scaffold_94362.1-287808 20268 24 + 287808 CTACTTTCTGGGAACCAGAGTGGC---- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16056476 24 + 17838096 CTAATTTCTGAGAACCAGAGTGGC---- i ponAbe2.chr17_random C 0 C 0 s tupBel1.scaffold_124459.1-15939 5858 24 + 15939 CTAGTTTCTGGGACACCGTGTGGC---- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118752842 24 + 121843856 CTAATTTCTGGGAGCAAGCGTGCC---- i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 3892 24 + 10229 CTAATTTCTGGGAACCCGCGCGGC---- i dipOrd1.scaffold_53224 C 0 C 0 s cavPor3.scaffold_76 4384316 24 + 7991924 CTAATTTCTGGGAACCAGTGTGGC---- i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 14350 24 + 41507 CTCCTTCCCGGGAGGCACAGGGGC---- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 641 24 - 54875 CTCATTTCTAGGGACTAGCGTGGC---- i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 123178 24 + 145505 CTAATTTCTGGGAACCAGAGTGGC---- i turTru1.scaffold_106006 M 502 C 0 s bosTau4.chr19 10854291 24 - 65312493 CTAATTTCTGGGCACCAGAGTGGC---- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58037057 24 - 61308211 CCAATTTCTGGGGACCAGAGTGGC---- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 9009 24 + 132007 CTCATTTCTGGGAACCAGAGAGGC---- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59431767 24 - 64418924 CTAATTTCTGGGAACCAGGGTGGC---- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 9753 24 + 48268 CTCATTCCCGGGAACCCCAGCGGC---- i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_290756 1472 26 - 7602 CTCCTTTCTGGAAGTTGGGGAGGTCT-- i eriEur1.scaffold_290756 C 0 I 1154 s loxAfr3.scaffold_49 14425680 21 - 17734757 CTAATCCTGGGAAGCTGG---AGT---- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 9750 19 + 24616 CTCAT-CTGGGGAGCTAG----GT---- i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 6665 24 + 20752 CTCGTCTCCGGGACCCGGGGTGGC---- i dasNov2.scaffold_28617 C 0 C 0 s monDom5.chr2 304527118 21 - 541556283 TTAATTTTTACAAATAAAAAT------- i monDom5.chr2 C 0 C 0 e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e ornAna1.Contig9679 18050 1768 + 20910 I a score=947509.000000 s hg19.chr17_gl000204_random 39559 166 + 81310 CTGCTCACTTTAGATAACTTTG--TGATGTGGTTGT----GTCTCCTGCAAAT---GTTAGTTTTCTT-TT--------TTGTGTCTTGAT-TTTGAAAACGACAAGAG------GA-GT--CGGGGA--GCGACGG------AACCC-GATGGGCA------CACTGGG-CACCAGTTCAGGCCCTGGCCTCAGGCAGTCGGTCATCTG s monDom5.chr2 304527139 155 - 541556283 -------TTTCAAATGCCTGAGATTAATAAAACAGT----ATCTCCTGGAAAT---GGTA---------TG--------TGTTGTCTAAAA----AAAAAAAACAGGAG------GA-AAGAAGGGAAATGTGACAA------AACTTTGATAGACA------AATTGGGACCAAAGTTCAGCTCCC-TTCCTGCACAGATGGTTGTTAT i monDom5.chr2 C 0 C 0 s dasNov2.scaffold_28617 6689 160 + 20752 CGGATCACTGCAGGAAACTTCA--GGACGCGGTCGG----GTCGCCCACAAGC---GC-GCGTTTCCT-CT--------CAGCGTCTTGAGCTCTTCA-GTGACGGGGG------AAGGC-CAGGGAG--AAAACAC------GCTCC-GGCGGCCG------CGC-GGG-CGCAGGTGCAGGGCCT-GCTCATGACCAACGGTC----- i dasNov2.scaffold_28617 C 0 C 0 s proCap1.scaffold_29042 9769 147 + 24616 CTGTCT--------GAGCCACA--G-----CGCTGG----GTCTCCTGCAAAC---ACCGC-TTTCTT-GC-----------TGTGTGGGT-TTTGAA-ATGGCGTGGG------GA-GC-AAGGGGA--AGACGAA------AAGCC-AACATCCA------CACTGGG-CAGGAA-TCAGGGCCA-GCTCTGGACAGCCGGTCATTGG i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14425701 160 - 17734757 CTGCTCA-TGTTGAGAGCTTTA--T-----GGGTGGCTTCGTCTTCTACAAAT---GCTGCTTTTCTT-TT-----------TGTCTTGCG-TTTTAA-ATAACGAGAG------GA-GG-GAGGGGA--GGAACAG------AAGTC-AATATCCA------CACCAGG-CACAAGCTCAGGGCCA-GCTCTGGACAGCTGGTCATTGG i loxAfr3.scaffold_49 C 0 C 0 s pteVam1.scaffold_11245 9777 165 + 48268 CCAATCACGGCACACAACTCTG--TGACACGACCGA----GTCAGCCACCGGT---GTCAGC-TTCTC-TC---------TGTGCCTTGGT-TTTTAACATGACGAGAG------GA-GGAAGGGGAA--GCAACAG------CACCC-GATGGCCA------CGCCCGG-CACAAGCTCA-GGCCCCGGCCTGGACAGAAGGTCACCGG i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59431791 165 - 64418924 CTGACCGCTTTAGAGAACTCTG--TGATACGACTGC----GTCTCCTACCAGC---GTCAGTTTTCCT-TT---------TGTGTCTTGAT-TTGTCAAGTGACAAGAG------GA-GGGAGGGGCA--GCAACGG------GA-CG-GCTGCCCG------CGCCAGG-CACGCATCCA-GGCTCCGCCCTGGACAGACGGTCATCTG i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 9033 165 + 132007 CTGACTGCTTTAGATAACTCTA--TGATACGACTGC----GTCTCGTACCAGT---GTTCGCTTTATT-TT---------TGTCTCTTGGT-TTGT-AAACGACAAGAG------GA-GGAAGGGGCA--GCGCTAG------GATcc-gcccgccg------cgccggg-cgcgggTCCA-GGCTCCGCCCTGGCCAGCCGGTCATCTG i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58037081 166 - 61308211 CTGATCGCCTTAGATAACTCTA--CAGTGTGACTGT----GCCCCCTCCCGAT---GCCAGTTTTCTT-CT---------TGTGTCTTGAT-TTTTTAAATGATGAGAA------GA-GGAAGGGAAA--GCAACAG------AAGCC-AACAGCCA------CA-CGGG-CACAAGTTCAGGGCCCGGCCCTGGACAGATGGTCATTTG i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10854315 167 - 65312493 CTGATAGCGTTAGATAACTCTG--TGATATGATCGT----GTCTCCTTCCAAT---GTTAGTTTTCTT-TT---------ACTGTCTTGGT-TTCTAAAATGACTAGAG------AG-AGAAGCGGGA--GCAACAG------AACCT-GATGGCTA------CGCCAGG-CACAAGCTCAGGTCCCAGCTCTGGACAGAAGGTCACCAG i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 123202 167 + 145505 CTGATAGCTTTAGATAACTCTG--TGATATGATCAT----GTCTCCTACCAAT---GTTAGTTTTCTT-TT---------TGTGTCTTGGT-TTTTAAAATGACCAGAG------GG-AGAAGGGGAA--GCAACAG------AACCC-GATGGCCA------CGCCGGG-CACAAGTTCAGGTCCCAGCCCTGGAGAGAAGGTCATCTG i turTru1.scaffold_106006 C 0 C 0 s ochPri2.scaffold_9426 665 146 - 54875 CCAACTGCTTTAGATAACTTCA--CGATGCAATCGC----GTCTCCTGCGGAC---CCTCAGCGCCATCCT--------CCGTGGCTCAAT-TTTACA-ATGACGAGAG------GA-GG-AATGGGA--GGTGGAG--------------CGGCCG------TCCCTGG-CACCCATCCAGCCCCCTGCTG--------------CACG i ochPri2.scaffold_9426 C 0 C 0 s oryCun2.chrUn0958 14374 134 + 41507 CCTCCCG------------------GACGCGACTAC----GTCTCCCGCAGAC---ACCCGTCTCCCT-CT--------CCACGCCTTGAC-CGCAAA-ACGGCAGGAG------GA-GG-AAGAGGA--GGCGAGG--------------CTACCGACGGCCACCCTGG-CACCGGCTCAGGCGCC-GCCG--------------TGTG i oryCun2.chrUn0958 C 0 C 0 s cavPor3.scaffold_76 4384340 151 + 7991924 CTGACTGTTATGGCTAACTTTG--AGATGTGACCGT----GTCTCCTATAA---------------TG-TC--------AGGAGTCTTGAT-TTTTAA-ATGACAGGAG------GA-AG-AAAAGGA--AGCACAG------AGCCC---TGGCCA------CACCTGG-CACAGACACAGGGCCC-GCCCTGGACAGACGGTCTCCAG i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_53224 3916 165 + 10229 CTGATTGCTGAAGATAACTTCG--TGATGTGATTGC----GTCTCCTCCAAATCTAAGTTGTTTTTTT-TTTTCCTTTGCTGTGTTTTGAT-TTTAAA--TGAGAAGAA------GA-AG-----GGA--CGTGTAG------GTCTC---TCCTTG---GCTGCCCTGG-CTGGAGTTCAGGGCTCTGCTG--------GGGTCCTGTG i dipOrd1.scaffold_53224 C 0 C 0 s mm9.chr11 118752866 164 + 121843856 CTGATTACTGCGGATAACTTCA--TGATGTGATTCA----GTCTCCGGCAAAC---ACTCGTTTTCTT-TT--------CTGCGTCTGGGT-TTTCAA---GCGACGGG------AT-GG-----GGA--TGGCTGGTACACAGACTC---TCATCG------CACCTGG-CTCAGGTTCAGATCCCGGACGTGAACAGAAGGTCATCTT i mm9.chr11 C 0 C 0 s tupBel1.scaffold_124459.1-15939 5882 144 + 15939 CTGACCGCTT-GGATAACT--A--TGATGCGATGAG----GTCCCAT----------CTAGCACTC-T-TT--------CCATGTCTCAGT-TTTTAAAATGACAAGAG-------------TGGGGA--------G------AACCC-CGTGGCCA------CCCTGGG-CACACGTTCAGGTCCCGGCCT-GGACAGACGGCCTCTTG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s ponAbe2.chr17_random 16056500 166 + 17838096 CTGCTCACTTTAGATAACTTTG--TGATGTGGTTGT----GGCTCCTACAAAT---GTTAGTTTTCTT-TT--------TTGTGTCTTGAT-TTTGAAAACGACAAGAG------GA-GT--CGGGGA--GCGACGG------AACCC-GATGGGCA------CACTGGG-CACCAGTTCAGGCCCTGGCCTCGGGCAGTTGGTCATCTG i ponAbe2.chr17_random C 0 C 0 s otoGar1.scaffold_94362.1-287808 20292 166 + 287808 CTCACGGCTTCAAATAACTTCA--CGATGTGACTGT----GGCCCCTACAAAT---GTTCGTTTTCTT-TT--------TTGTATCTTGAT-TTTGACCATGGCAAGAG------GA-GG--GAGGAA--GTAACAG------AAGCC-CGTGGCCA------CAATGGG-CACAAGTTCAGGCCCCAGCCCTGGGCAGACGGTCATCTG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_184068 150 166 + 702 CCGACAGCTTCAGATGACTCCA--CGGTGTGACTGT----GGTTCCTACAAGC---GTTAGTTTTC--------------TGCGTCTTGAT-TTTGACCACGGTAAGGGATGGGTGG-GG--GGGAGA--GTGACAG------AAGCC-GGTGGCCA------CACTGGG-CACAGGTTCAGG-CCCAGCCCTGGGCAGACGGTCCTCTG i micMur1.scaffold_184068 C 0 C 0 s calJac1.Contig5139 40079 166 + 225949 CTGCTCACTTTGGATAACTTTG--TGAGGCGATTGC----TGCTCCTACAAAC---GTTCATTTTCTT-TT--------TTGTGTCTTGAT-TCTGAAGATGACAAGAG------GA-GC--CGGGGA--GCACCAG------AACCC-GACGGGCA------CCCCCAG-CACCGGTTCAGGCCCCAGCCTCGGGCAGTCGGTCATCTG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 38164 166 - 95547 CTGCTCACTTTAGATAACTTTG--TGATGTGGTTGT----GGCTCCTACACAT---GTTAGTTTTCTT-TT--------CTGTATCTTGAT-TTTGAAAACGACAAGAG------GA-GT--CCGGGA--GCAACAG------AACCC-GATGGGCA------CACTGGG-CACCAGTTCAGGTCCCGGCCTCGGGCAGTCGGTCGTCTG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75030773 166 + 78773432 CTGCTCACTTTAGATAACTTTG--TGATGTGGTTGT----GGCTCCTACACAT---GTTAGTTTTCTT-TT--------CTGTATCTTGAT-TTTGAAAACGACAAGAG------GA-GT--CCGGGA--GCAACAG------AACCC-GATGGGCA------CACTGGG-CACCAGTTCAGGTCCCGGCCTCGGGCAGTCGGTCATCTG i rheMac2.chr16 C 0 C 0 s panTro2.chr17 79469746 166 + 83384210 CTGCTCACTTTAGATAACTTTG--TGATGTGGTTGT----GTCTCCTGCAAAT---GTTAGTTTTCTT-TT--------TTGTGTCTTGAT-TTTGAAAACGACAAGAG------GA-GT--CGGGGA--GCGACGG------AACCC-GATGGGCA------CACTGGG-CACCAGTTCAGGCCCTGGCCTCAGGCAGTCGGTCATCTG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 9651 166 - 64270 CTGCTCACTTTAGATAACTTCG--TGATGTGGTTGT----GTCTCCTGCAAAT---GTTAGTTTTCTT-TT--------TTGTGTCTTGAT-TTTGAAAACGACAAGAG------GA-GT--CGGGGA--GCGACGG------AACCC-GATGGGCA------CACTGGG-CACCAGTTCAGGCCCTGGCCTCAGGCAGTCGGTCATCTG i gorGor1.Supercontig_0007361 C 0 C 0 e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e ornAna1.Contig9679 18050 1768 + 20910 I a score=451220.000000 s hg19.chr17_gl000204_random 39725 63 + 81310 CAGCGGCCCAACGTCTGTTCT---------------------CCCTGCTCCCAAGGGCCAGGAGAGGAAATTGAG-AG---AGTATGG s gorGor1.Supercontig_0007361 9817 63 - 64270 CAGCGGCCCAACGTCTGTTCT---------------------CCCTGCTCCCAAGGGCCAGGAGAGGAAATTGAG-AG---AGTATGG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79469912 63 + 83384210 CAGTGGCCCAACGTCTGTTCT---------------------CCCTGCTCCCAAGGGCCAGGAGAGGAAATTGAG-AG---AGTATGG i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75030939 63 + 78773432 CGGCGGCCCAACGTCTGTTCT---------------------CCCTGCTCCCAAGGGCCAGGAGAGGAAATGGAG-AG---AGTATGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 38330 63 - 95547 CGGCGGCCCAACGTCTGTTCT---------------------CCCTGCTCCCAAGGGCCAGGAGAGGAAATGGAG-AG---AGTATGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40245 62 + 225949 CAGCGACCTAGCATCTGTTCT---------------------TCCTGCCCCC-AGGGCCAGGGGAGGAAATTGAG-GG---AGGATGG i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_184068 316 73 + 702 CCCTGGCC-AGCGTCTG-TCTCCTCGC--AGCCGG-------CCCCGGTCCTGAGGGCCAGGAGAGGAAATTGAG-AG---AGGATGG i micMur1.scaffold_184068 C 0 C 0 s otoGar1.scaffold_94362.1-287808 20458 74 + 287808 CTCTGGCC-AGTGTCTGTTCTCTTCAC--AGTCAG-------CCCCGGTCCTGAGGGCCAGGAGAGGAAATTGAG-AG---AGAATGG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16056666 63 + 17838096 CGGCGGCCCAACGTCTGTTCT---------------------CCCTGCTCCCAAGGGCCAGGAGAGGAAATTGAG-AG---AGTATGT i ponAbe2.chr17_random C 0 C 0 s tupBel1.scaffold_124459.1-15939 6026 71 + 15939 CTCCAGCCCAGCACCTGTTTC-CGCAC--AGCC---------TGCCGGTCCTGAGGGCCAGGAGAGGAAATTG-G-AG---GGGGCAG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118753030 73 + 121843856 TCCTGGCCCGGTGCCTGTCCCACCATGGCAGG-----------TCCGGTCTTGAGGGCCAGGAAAGGAAATTGAG-AG---AGGACAG i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 4081 61 + 10229 CTCCGGCCCAGCACCTGCTCCCCCCCA------------------CAGCCT-----GCCAGGACAGGAAATTGAG-AG---AGGACAG i dipOrd1.scaffold_53224 C 0 C 0 s cavPor3.scaffold_76 4384491 70 + 7991924 CTCTGGCCTGGAGCCTCTGCCCCACGG--AGC-----------CCCAGTCCTGAG-GCCAGGAGAGGAAATTGAG-AG---AGGATGG i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 14508 75 + 41507 CTCTGGCCCCACGCCCGTTCCCCTCAC--AGCCTG-------TCCCGGGCCTGAGGGCCAGGAGAGGAAATTGGA-AGCCCAGGA--- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 811 74 - 54875 CTCTGGCCCCGAGCCAGGTCCCCTCAC--AGCCTG--------CCCGGGCCCCAGGGCCAGGAGAGGAAATTGAA-ACTCCTGGA--- i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 123369 72 + 145505 CTCTGGCCCAGCACGTGTTCTCCTGCC--AGCCTG-------CTCTGGTCCTGAGGGCCAGCAGAGGAAATAGA-------AGAAAGG i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10854482 72 - 65312493 CTCCGGCCCAGCACGTGTTCTCCTGCC--AGCCTA-------CTCCAGTCCTGAGGGCCAGCAGAGGAAATAGA-------AGAAGGG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58037247 72 - 61308211 CTCTGGCCCAGCGCGTGTGCTCCTGCC--AGCCTG-------CTCGAGTCCTGAGGGCCAGCAGAGGAAAGAGA-------AGGACAG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 9198 72 + 132007 CTCTGGCCCAGCACGTGCTCTCCTGCC--AGGCTG-------CTCCGGTCCTGAGGGCCAGCAGAGGAAATAGA-------AGAACGG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59431956 72 - 64418924 CTCTGGCCCAGCACGTGTCCTCCGGCC--AGGCGG-------CTCCGGTCCTGAGGGCCAGCAGAGGAAACAGG-------GGAACAG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 9942 71 + 48268 CTCTGGCCCAGCACGCGT-CTCCCGCC--GGCCTG-------CTCCAGTCCCGAGGGCCAGCGGAGGAAACAGA-------ACAACAG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14425861 76 - 17734757 TGCTGGCCCAGAGCATGTTCTCCTCAT--GGTCAGT------GCCCAGTCCTGAGGGCCAGGAGAGGAAATTGAG-GA---AAGGAGG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 9916 76 + 24616 AACCGGCCCAGAGTGTGTCCTCCTCAC--TGTTAGC------GCCCAGTCCTGAGGGTGAGGATAGGAAATTGAG-GG---AAGTAGG i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 6849 57 + 20752 ------CCCTG--------CTCCTGAC--AGCCAGC------GGCCGGCCC--AGGGCCAGGAGGGGAAAT---G-GG---AGAGCAG i dasNov2.scaffold_28617 C 0 C 0 s monDom5.chr2 304527294 80 - 541556283 TACTGGTCCAGTGCATTTTTTCCTAAT--TGCTTGAGCATAGTCACTGTCCAATGCAGCAGGGAAGGGAAATAGG-AA---GGGAC-- i monDom5.chr2 C 0 C 0 s ornAna1.Contig9679 19818 64 + 20910 CACCGGACCAACGCCGCCTCC---------------------AGGTGCTCCCAAGGAAGAGAGGAGGAGGCGGGGCGG---AGGGTGG i ornAna1.Contig9679 I 1768 N 0 e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I a score=472113.000000 s hg19.chr17_gl000204_random 39788 35 + 81310 CACCAGC-AGG-CTCCAGGACAGAAACCAAAACC----------------CGC s gorGor1.Supercontig_0007361 9880 35 - 64270 CACCAGC-AGG-CTCCAGGACAGAAACCAAAACC----------------CGC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79469975 35 + 83384210 CACCAGC-AGG-CTCCAGGACAGAAACCAAAACC----------------CGC i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75031002 35 + 78773432 CACCAGA-GGG-CTCCAGGACAGAAACCAAAACC----------------TGC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 38393 35 - 95547 CACCAGA-GGG-CTCCAGGACAGAAACCAAAACC----------------TGC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40307 35 + 225949 CACCAGC-AGG-CTCCAGGACAGAAACCCTAACC----------------CAC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_184068 389 35 + 702 CACCAGC-AGG-CTCCAGGACGGAACCCAAAACC----------------CAC i micMur1.scaffold_184068 C 0 C 0 s otoGar1.scaffold_94362.1-287808 20532 35 + 287808 CACCAGC-GGG-CTCCAGGACTGAAACCAAAACC----------------CAC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16056729 35 + 17838096 CACCAGC-AGG-CTCCAGGACAGAAACCAAAACC----------------CGC i ponAbe2.chr17_random C 0 C 0 s tupBel1.scaffold_124459.1-15939 6097 50 + 15939 CGCCA-C-AGG-CTCCAGGACAGAGACCAAAGCCGGCCCCGCCTCCCGGACAC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118753103 35 + 121843856 AAGTAGC-AAG-CTCCCGGACATAAACCAGTTCC----------------CTG i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 4142 35 + 10229 CACTGTG-GGA-ATCCGGGACAAGAACCAAGCCC----------------CAC i dipOrd1.scaffold_53224 C 0 C 0 s cavPor3.scaffold_76 4384561 35 + 7991924 CATCAGC-AGG-CTCCAGGACAGGGACCAAGCCT----------------GAC i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 14583 34 + 41507 -GCCACC-GGG-CCCCAGGACAGGAACCAGAGCC----------------CGC i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 885 35 - 54875 -GCTCCCAGGG-CCCCACAACAGGAACCAAAGCC----------------TGC i ochPri2.scaffold_9426 C 0 I 2104 s turTru1.scaffold_106006 123441 35 + 145505 GACCAGC-AGG-CTCCAGGACAGAAAGCAAAACA----------------TGC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10854554 35 - 65312493 GACCAGC-GGG-CTCTAGGACAGAAACCAAAAAC----------------CAC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58037319 35 - 61308211 GAACGGC-AGG-CCCCAGGACAGAAACCAAAACC----------------CAC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 9270 34 + 132007 GGCCAGC-AGG-CTCCAGGACAGAAACC-AAACC----------------CAC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59432028 34 - 64418924 CACCAGC-AGG-CTCTAGGACAGAAACC-AAACC----------------CAC i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 10013 35 + 48268 GACCCGC-GGG-CTCCAGGGCAGAAACCGAAACC----------------CTC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14425937 35 - 17734757 GACCAGC-AGG-GTCCAGGACGGAAACCAAGCCC----------------CAC i loxAfr3.scaffold_49 C 0 I 1 s proCap1.scaffold_29042 9992 35 + 24616 GACCAGC-AGC-GCCCAGGATGTAAACCAAAGTC----------------CAC i proCap1.scaffold_29042 C 0 I 1 s dasNov2.scaffold_28617 6906 34 + 20752 GAGCAGC-GGG-CTCCAGGAAGCTGACCAAAA-C----------------GGC i dasNov2.scaffold_28617 C 0 I 1 s monDom5.chr2 304527374 27 - 541556283 --CCAGC-AGGACTACAGGATGAGAACTAA----------------------- i monDom5.chr2 C 0 I 602 e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I a score=-82379.000000 s hg19.chr17_gl000204_random 39823 66 + 81310 TGGCACTTGTTGGGGGTGGGAGGCACTTGGACCAAAGGGTTTGGGCACCTG----GGGAAT-----CCATCAGTC s gorGor1.Supercontig_0007361 9915 66 - 64270 TGGCACTTGCTGGGGGTGGGAGGCACTTGGACCAAAGGGTTTGGGCACCTG----GGGAAT-----CCATCAGTC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79470010 66 + 83384210 TGGCACTTGCTGGGGGTGGGAGGCACTTGGACCAAAGGGTTTGGGCACCTG----GGGAAT-----CCATCAGTC i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75031037 64 + 78773432 TGGCACTTGCT-GGGTGGGGAGGCACTTGGACCAAAGGGTTGGGGCACCTG----GGGAAT------CATCAGTC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 38428 65 - 95547 TGGCACTTGCT-GGGTGGGGAGGCACTTGGACCAAAGGGTTGGGGCACCTG----GGGAAT-----CCATCAGTC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40342 64 + 225949 GGGCACCTGCT-GCGGCAGGAGGCACTCGGACCAAAGGGTTTGGGCACCT-----GGGAAT-----CCATCAGTC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_184068 424 36 + 702 TCGTGCTGGCG--------------CCGGGGCCAACGGGGC-------------------------TCGTCACTC i micMur1.scaffold_184068 C 0 C 0 s otoGar1.scaffold_94362.1-287808 20567 47 + 287808 CCACGCCTGCA--------------CCTGGGCGGAAGGGCC-AGGCACCTG--------CT-----TCCCTACTC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16056764 65 + 17838096 TGGCACTTGCT-GGGTTGGGAGGCACTTGGACCAAAGGGTTTGGGCACCTG----GGGAAT-----CCATCAGTC i ponAbe2.chr17_random C 0 C 0 s tupBel1.scaffold_124459.1-15939 6147 55 + 15939 AGGTGCTGGCC--CCTGGGTAGGTGCTACGGCC------CTCAGGCTCTCA----GGG--------CTCTCAGTC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118753138 46 + 121843856 ----------------CAGAA--CCCCAGGGCTCCAAGGCGGAGCAC------CTCAGAAT-----CCATCCATC i mm9.chr11 C 0 I 1 s dipOrd1.scaffold_53224 4177 32 + 10229 ----------------TGG------CCAGG-----AAGGCAGAG-----------GGGTAC-----CCATCCTCC i dipOrd1.scaffold_53224 C 0 I 1 s cavPor3.scaffold_76 4384596 46 + 7991924 -------------------------CCAGG----CAAGGCACAGAGCCCAGGGCTGGGCACCAGGACCGTCAATC i cavPor3.scaffold_76 C 0 I 36 s oryCun2.chrUn0958 14617 39 + 41507 -------------------------------CCGCGGGGGGCAGGTGCGTGGGCGGAGGCT-----CGGTCCACC i oryCun2.chrUn0958 C 0 I 4 s turTru1.scaffold_106006 123476 48 + 145505 -----------TCGGAGAAGAGGCTCACTGG-------ATCAGGATACCTG----GGGAAT-----CCGTCAACG i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10854589 48 - 65312493 -----------TTGCGGAAGAGGCTCACTGG-------ATCTGGATACCTG----GGGAAT-----CCATCAATC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58037354 51 - 61308211 -----------TTGGAGGAGAGGCACACAGGT----GGATTCGGACACCTG----GGGAAT-----CCATCAATC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 9304 50 + 132007 -----------TCAGGGGAGAGGCACACGGGT----GGGTCTGGACCCCC-----GGGAAC-----CCGTCAATC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59432062 50 - 64418924 -----------TCAGAGGAGAGGCACACCGGT----GGGTGTGGATACCT-----GGGAAC-----CCGTCAATC i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 10048 47 + 48268 -----------CTGGAGGACAGGCGCACAGG--------TTTAGACACCTG----GGGAAC-----CTGTCAATC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14425973 47 - 17734757 ------------TAGCAGAGGGGTGCC--GGC----AGACCTGGGCACCT-----GGGACT-----CGGTCCATC i loxAfr3.scaffold_49 I 1 C 0 s proCap1.scaffold_29042 10028 47 + 24616 ------------TAACAGAGAGGCACA--GGC----GGCGTTGGGCACCT-----GGGAAT-----CTGTCCATC i proCap1.scaffold_29042 I 1 C 0 s dasNov2.scaffold_28617 6941 43 + 20752 ------------CGGCCCAGAGACGC---GGC----ATATCGGGGTCCTG-----GGGACC-----C---CCAGT i dasNov2.scaffold_28617 I 1 C 0 e ochPri2.scaffold_9426 920 2104 - 54875 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e monDom5.chr2 304527401 602 - 541556283 I a score=-56385.000000 s hg19.chr17_gl000204_random 39889 17 + 81310 AAACTCGCTCT--------------------------------CCTCCC s gorGor1.Supercontig_0007361 9981 17 - 64270 AAACTCGCTCT--------------------------------CCTCCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79470076 17 + 83384210 AAACTCACTCT--------------------------------CCTCCC i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75031101 17 + 78773432 AAACTCTCTGT--------------------------------CCTCCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 38493 17 - 95547 AAACTCTCTGT--------------------------------CCTCCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40406 16 + 225949 AAACTCTCCCT--------------------------------CC-CCC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_184068 460 9 + 702 CAACACG----------------------------------------CC i micMur1.scaffold_184068 C 0 C 0 s otoGar1.scaffold_94362.1-287808 20614 9 + 287808 AGACCCT----------------------------------------CC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16056829 17 + 17838096 AAACTCTGTCT--------------------------------CCTCCC i ponAbe2.chr17_random C 0 C 0 s tupBel1.scaffold_124459.1-15939 6202 10 + 15939 GGCCCCA---------------------------------------CCC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s dipOrd1.scaffold_53224 4210 5 + 10229 G--------------------------------------------ACCC i dipOrd1.scaffold_53224 I 1 C 0 s mm9.chr11 118753185 4 + 121843856 ---------------------------------------------ACCC i mm9.chr11 I 1 C 0 s oryCun2.chrUn0958 14660 17 + 41507 ACCGCCGGCCC--------------------------------CCACCC i oryCun2.chrUn0958 I 4 C 0 s turTru1.scaffold_106006 123524 19 + 145505 ACACACTCTCCCT------------------------------CCTCCC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10854637 16 - 65312493 CTACCCTCTC---------------------------------CCTCCC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58037405 49 - 61308211 AAActccctccctcctccctctctcctcctcccatccctcctgccccct i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 9354 18 + 132007 AAACTCTCTCTC-------------------------------CCTCCT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59432112 24 - 64418924 AAACCATCCCTCT-------------------------TCCGGCCTCCC i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 10095 18 + 48268 AAACGCCCTCCT-------------------------------CCCTCC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14426020 17 - 17734757 CAACTCCCTCC--------------------------------CTCCCT i loxAfr3.scaffold_49 C 0 I 22 s proCap1.scaffold_29042 10075 11 + 24616 AAACTCCCT--------------------------------------CT i proCap1.scaffold_29042 C 0 I 1067 s dasNov2.scaffold_28617 6984 12 + 20752 -GACTCCCTCC--------------------------------CC---- i dasNov2.scaffold_28617 C 0 I 1 e ochPri2.scaffold_9426 920 2104 - 54875 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e monDom5.chr2 304527401 602 - 541556283 I e cavPor3.scaffold_76 4384642 36 + 7991924 I a score=39866.000000 s hg19.chr17_gl000204_random 39906 33 + 81310 T------------------CTTCC---------------TGA-GATAGCTGTTTTTAGGTTCAAGGG s gorGor1.Supercontig_0007361 9998 33 - 64270 T------------------CTTCC---------------TGA-GATAGCTGTTTTTAGGTTCAAGGG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79470093 33 + 83384210 T------------------CTTCC---------------TGA-GATAGCTGTTTTTAGGTTCAAGGG i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75031118 33 + 78773432 T------------------CTTCC---------------TGA-GATAGCTGTTTTTAGGTTCAAGGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 38510 33 - 95547 T------------------CTTCC---------------TGA-GATAGCTGTTTTTAGGTTCAAGGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40422 33 + 225949 T------------------CTTCC---------------TGA-CGCAGTTGTGTTTAGGTTCAAGGG i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_184068 469 32 + 702 C------------------CCACC---------------CCT-GCTAGCTGTGTTCGGCTTC-AGGG i micMur1.scaffold_184068 C 0 C 0 s otoGar1.scaffold_94362.1-287808 20623 32 + 287808 C------------------CCACC---------------TGA-GTTAgccctttgtaggttc-aagg i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16056846 33 + 17838096 T------------------CTTCC---------------TGA-GATAGCTGTTTTTAGGTTCAAGGG i ponAbe2.chr17_random C 0 C 0 s tupBel1.scaffold_124459.1-15939 6212 31 + 15939 T------------------TCTCC---------------TGT-G--GGCTGCTCGCAGGTACAAGGG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s dipOrd1.scaffold_53224 4215 25 + 10229 C------------------GCCCC---------------TGC-CTCAGCA---TTGGGGG----GG- i dipOrd1.scaffold_53224 C 0 C 0 s mm9.chr11 118753189 32 + 121843856 T------------------CCTCC---------------TTA-GTCAGCAGCTTTGAGGTTCACAG- i mm9.chr11 C 0 C 0 s oryCun2.chrUn0958 14677 23 + 41507 T------------------GCTCC---------------CTCTGTCGGTTGTTCTT----------- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 123543 44 + 145505 T--------------CCTTCCTCC--------CTCTTTCTGA-GTTTGTTGTTTTAAGGTTTAGGGG i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10854653 44 - 65312493 T--------------GCTTCTTCC--------CTCTTCCTGA-GTTAGCTGTTTTAAGGTTTATGGG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58037454 66 - 61308211 cctcccatccctcctgctccctcctcccgtccctcTTCATAA-GTTAGTTGTTTTAAGGTTCAAGGG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 9372 35 + 132007 C---------------CTCCTTCC---------------TGA-GTTAGGAGTGTCAAGGTTTGGGG- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59432136 31 - 64418924 C--------------GCTCCTTCC---------------------CAGGGGGGTTTGGGGCCACGG- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 10113 46 + 48268 C---------------GCCTTTCC-----TCCCTCTACGGAA-ATTAGTTGTTTTAGGGTTCAGAGG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14426059 32 - 17734757 -------------------TCTTC---------------CTG-AGTTAGTGTTTTAGGATTTAAGAT i loxAfr3.scaffold_49 I 22 C 0 s dasNov2.scaffold_28617 6997 32 + 20752 -------------------CCCCC---------------CCA-GGGAGCTGTTCTAAGGTTTAAGGC i dasNov2.scaffold_28617 I 1 C 0 e ochPri2.scaffold_9426 920 2104 - 54875 I e proCap1.scaffold_29042 10086 1067 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e monDom5.chr2 304527401 602 - 541556283 I e cavPor3.scaffold_76 4384642 36 + 7991924 I a score=48228.000000 s hg19.chr17_gl000204_random 39939 28 + 81310 GATACAGAG-------------GAAG-CACGCAATTGAGGAA s gorGor1.Supercontig_0007361 10031 28 - 64270 GATACAGAG-------------GAAG-CACGCAATTGAGGAA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79470126 28 + 83384210 GATACAGAG-------------GAAG-CACGCAATTGAGGAA i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75031151 28 + 78773432 GATACAGAG-------------GAAG-CACGCAATTGAGGAA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 38543 28 - 95547 GATACAGAG-------------GAAG-CACACAATTGAGGAA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40455 28 + 225949 GATACAGAG-------------GAAG-CACACAATGGAGGAA i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_184068 501 28 + 702 GACATGGGG-------------GGAG-GATGTGAGGGAGGAA i micMur1.scaffold_184068 C 0 C 0 s otoGar1.scaffold_94362.1-287808 20655 16 + 287808 gacaca--------------------------gagggaggaa i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16056879 28 + 17838096 GATACAGAG-------------GAAG-CATGCAATTGAGGAA i ponAbe2.chr17_random C 0 C 0 s tupBel1.scaffold_124459.1-15939 6243 24 + 15939 G-TCCTGGG-------------AGAG-CGC---AGTGAGGAA i tupBel1.scaffold_124459.1-15939 C 0 I 968 s cavPor3.scaffold_76 4384678 25 + 7991924 GACATGGAG-------------GATG-TGTG---ACGGGGAA i cavPor3.scaffold_76 I 36 C 0 s dipOrd1.scaffold_53224 4240 30 + 10229 GACACGGGGCTCCAGCTCCTTTGAAC-CTGG----------- i dipOrd1.scaffold_53224 C 0 C 0 s mm9.chr11 118753221 28 + 121843856 GACAGAGAG-------------GAAG-CAGGGGGTGGGGGAA i mm9.chr11 C 0 C 0 s oryCun2.chrUn0958 14700 10 + 41507 --------------------------------GCTGGTGGAA i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 123587 29 + 145505 GATATGCAG-------------GGAGAGATGTTACTGAGGAA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10854697 29 - 65312493 GATATAGAG-------------GGAGAGATGTTACTGAGGAA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58037520 29 - 61308211 AATATGGAG-------------GTAGAGAGGTAACTGAGGAA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 9407 28 + 132007 -CTTTGGAG-------------GGAGAGATGCGGCTTAGGAA i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59432167 28 - 64418924 -CCGGGGGA-------------GGGGGCATACTGCTGAGGAT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 10159 29 + 48268 GATATGGAG-------------GAGGAGATATAACTGTGGAA i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14426091 21 - 17734757 CATG---------------------GAAATATAATTGAGTAA i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 7029 29 + 20752 AATGCAGAG-------------GGAGAGACGCAATTGGGGGA i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_9426 920 2104 - 54875 I e proCap1.scaffold_29042 10086 1067 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e monDom5.chr2 304527401 602 - 541556283 I a score=162055.000000 s hg19.chr17_gl000204_random 39967 43 + 81310 AATGAACCT-GCCTCTGTCTGACTCATCAGGACAGCGC-GACAGT s gorGor1.Supercontig_0007361 10059 43 - 64270 AATGAACCT-GCCTCTGTCTGACTCATCAGGACAGCGC-GACAGT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79470154 43 + 83384210 AATGAACCT-GCCTCTGTCTGACTCATCAGGACAGCGC-GACAGT i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75031179 44 + 78773432 GATAAACAT-ACCTGTGTATGACTCATAGGGACAGAACAAACCGT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 38571 43 - 95547 GATGAACCT-GCCTCTGTCTGACTCATCGGGACAGAGC-AACAGT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40483 43 + 225949 AAGGAACCT-GCCTCTGTCTGACTCGTCAGGAAGGAGC-AACAGT i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_184068 529 43 + 702 AATGCACCT-GTCTCTGTCCGAATCCTCAGTTCAGCAG-GACAGT i micMur1.scaffold_184068 C 0 C 0 s otoGar1.scaffold_94362.1-287808 20671 43 + 287808 aacaaaccc-gtccctgtctgaattctcaggacaacag-gacagt i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16056907 43 + 17838096 AATGAACCT-GCCTCTGTCTGACTCATCAGGACAGCGC-GACAGT i ponAbe2.chr17_random C 0 C 0 s cavPor3.scaffold_76 4384703 39 + 7991924 AAT----CC-GTCTCCATCTGTGTTCTCAGGACTGAAA-AAAGAG i cavPor3.scaffold_76 C 0 I 11 s dipOrd1.scaffold_53224 4270 27 + 10229 ------------CTCTGTCCTCCTTCTTAGGAC------AAATGG i dipOrd1.scaffold_53224 C 0 I 4 s mm9.chr11 118753249 31 + 121843856 AAT--------TCTCTGTTCACATCCCCAGGAC------CAAAGT i mm9.chr11 C 0 I 1 s oryCun2.chrUn0958 14710 35 + 41507 AAC-AAGCA-GCCTCTGTCCACTCGCTCGGGTC------AGCG-- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 123616 40 + 145505 AGTGAAG----TGTCAATCTGCATTTTCAGGACAAAAG-GACAGC i turTru1.scaffold_106006 C 0 I 3 s bosTau4.chr19 10854726 41 - 65312493 AAGGAAGC---TGTCAGTCTGCATTCTCAGGGCAGAAG-GACAGT i bosTau4.chr19 C 0 I 3 s equCab2.chr11 58037549 42 - 61308211 AATGAAGCT-GTCTCTAGCTGCTTTCTCAGG-CAAAAG-GACAGC i equCab2.chr11 C 0 I 3 s felCat3.scaffold_206428 9435 44 + 132007 CACGAGGCTCATTTCTACCTGCATTCTCCGGACAGAAG-GACAGG i felCat3.scaffold_206428 C 0 I 3 s canFam2.chr9 59432195 42 - 64418924 CACCAAGCTTATCTCTACCTGCCTTCTCAGGACAAAAG-GACA-- i canFam2.chr9 C 0 I 221 s pteVam1.scaffold_11245 10188 43 + 48268 AATGAAGCT-GTCTCTATCTGCATTCTCAGGTCAAAAA-TACAGT i pteVam1.scaffold_11245 C 0 I 3 s loxAfr3.scaffold_49 14426112 42 - 17734757 GATGAAGCT-GTCTCCATTGGCATTCTCAGGACA-AAG-CACAGC i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 7058 43 + 20752 AACGTAGCT-GCCTCTACCTACACCCCCGGGACACAAG-GAGAGC i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_9426 920 2104 - 54875 I e proCap1.scaffold_29042 10086 1067 + 24616 I e speTri1.scaffold_128901 1250 1336 + 44242 I e tupBel1.scaffold_124459.1-15939 6267 968 + 15939 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e monDom5.chr2 304527401 602 - 541556283 I a score=67994.000000 s hg19.chr17_gl000204_random 40010 39 + 81310 CCCt-cc------tgcatt--ctcacaacattgattaagcgcc---tactc s gorGor1.Supercontig_0007361 10102 39 - 64270 CCCt-cc------tgcatt--ctcacaacattgattaagctcc---tactc i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79470197 39 + 83384210 CCCt-cc------tgcatt--ctcacaacattgattaagcgcc---tactc i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75031223 24 + 78773432 CCCT-CC------TGCATT--ATCGCAACATTG------------------ i rheMac2.chr16 C 0 I 16 s papHam1.scaffold8336 38614 39 - 95547 CCCT-CC------TGCCTT--CTCGcaacattgattaagcact---tacta i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40526 28 + 225949 CCCT-CC------TG-------------Cactgattaagcacc---tacta i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_184068 572 39 + 702 CCCT-CC------TGCACT--CGTGCACCATTGATGAAGTGCC---CACCG i micMur1.scaffold_184068 C 0 C 0 s otoGar1.scaffold_94362.1-287808 20714 39 + 287808 ccct-ct------tgtact--catgcaGCATTGATTAAGTACC---TACTG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16056950 39 + 17838096 CCCt-cc------tgcatt--ctcacaacattgattaagcacc---tactc i ponAbe2.chr17_random C 0 C 0 s speTri1.scaffold_128901 2586 39 + 44242 CCCT-CA------GGCACC--TCTGCAGATTTGATTAGGCACC---CACTG i speTri1.scaffold_128901 I 1336 C 0 s cavPor3.scaffold_76 4384753 28 + 7991924 CCTT-AG------GGCATT--TATGAA-----------GCACC---CACTA i cavPor3.scaffold_76 I 11 C 0 s dipOrd1.scaffold_53224 4301 31 + 10229 CCCT-CC------CACATC--CCTGCA-----------ACACTGAGTGCCA i dipOrd1.scaffold_53224 I 4 I 1 s mm9.chr11 118753281 31 + 121843856 CCCT-CT------CACATC--CCCGAA-----------ACACAAAACAGCA i mm9.chr11 I 1 C 0 s ochPri2.scaffold_6980 60076 20 + 61692 ----------------------------CGCTGATTAAACTCC---CACTC i ochPri2.scaffold_6980 M 1409 C 0 s oryCun2.chrUn0958 14745 18 + 41507 ------------------------------TTGCCCGAGCACC---TGCCA i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 123659 39 + 145505 CACA-CA------CACACATTCTTTCAATGTTTATTAAACATC---TAC-- i turTru1.scaffold_106006 I 3 C 0 s bosTau4.chr19 10854770 39 - 65312493 CCCC-CA------CACGTA--CTTTaagtgtttattaaacatc---tgcta i bosTau4.chr19 I 3 C 0 s equCab2.chr11 58037594 45 - 61308211 TCCC-CACCCCCCCtcatt--cttgcaacatttattaagcacc---tacta i equCab2.chr11 I 3 C 0 s felCat3.scaffold_206428 9482 39 + 132007 CACC-AA------TGCACT--GCTGCaatgtttatgaagcacc---tacta i felCat3.scaffold_206428 I 3 C 0 s pteVam1.scaffold_11245 10234 39 + 48268 CTCT-CA------GGCTTT--CTTGCaatacttactaagcacc---tacta i pteVam1.scaffold_11245 I 3 C 0 s loxAfr3.scaffold_49 14426154 32 - 17734757 CCCCACA------TGCATT--CTTTCAACATTTATTAAGC----------- i loxAfr3.scaffold_49 C 0 I 592 s dasNov2.scaffold_28617 7101 39 + 20752 CCCT-CG------TGcatg--ctttcaacacttattaagcacc---tactg i dasNov2.scaffold_28617 C 0 C 0 e proCap1.scaffold_29042 10086 1067 + 24616 I e tupBel1.scaffold_124459.1-15939 6267 968 + 15939 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e monDom5.chr2 304527401 602 - 541556283 I e canFam2.chr9 59432237 221 - 64418924 I a score=-77733.000000 s hg19.chr17_gl000204_random 40049 62 + 81310 tgtgccagggagtgg-ag-aGGTGGGTCCTCCTGACCCACCTTCTCC-------------A----------------CTGG-AAGTAGAAGA-AT------- s gorGor1.Supercontig_0007361 10141 62 - 64270 tgtgccagggagtgg-ag-aGGTGGGTCCTCCTGACCCACCTTCTCC-------------A----------------CTGG-AAGTAGAAGA-AT------- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79470236 62 + 83384210 tgtgccagggagtgG-AG-AGGTGGGTCCTCCTGACCCACCTTCTCC-------------A----------------CTGG-AAGTAGAAGA-AT------- i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75031263 61 + 78773432 TGTGCCAGAGAAGGGTAG-AGGTG---TCTCCTGACCCCCCTTCTCC-------------A----------------CCGGAAAGTAGAAGG-GT------- i rheMac2.chr16 I 16 C 0 s papHam1.scaffold8336 38653 60 - 95547 tgtgccagAGAGGGT-GG-AGGTGG--TCTCCTGACCCCCCTTCTCC-------------A----------------CCGG-AAGTAGAAAG-GT------- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40554 59 + 225949 cgtgccaggGAGAGG-AG-AGGCA---TCTCCTGACCCCCCTTCTCT-------------G----------------CCAG-AAGTAGAAGG-AT------- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_184068 611 66 + 702 TGTGCCCAAGGCGCG-AG-AGCCG---TCCCCCGTCCTTTCTCCACC-------------G---------CTTGCCACTGG-GCGTAGAAGG-AG------- i micMur1.scaffold_184068 C 0 C 0 s otoGar1.scaffold_94362.1-287808 20753 59 + 287808 TTTGGCCAAGGGCTG-AG-AGCTG---TGCCCTGTCCTTTCTCCACC-------------A-----------TGCCACTGG-ACATAGA------------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16056989 61 + 17838096 tgtgccaggGAGGGG-AG-A-GTGGGTCCTCCTGACCCACCTTCTCC-------------A----------------CCGG-AAGTAGAAGG-AT------- i ponAbe2.chr17_random C 0 C 0 s speTri1.scaffold_128901 2625 67 + 44242 TGTGCCCGAGAGGTG-AG-AGCGGCCCCGACCCTCCTGTCCTCCCTA-------------G---------CTTGTCCCTGG-AAATGGGAGA---------- i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4384781 65 + 7991924 TGTGCAGAAAGGGGA-G--CAGTGACCCGTCCATCCCACTGTT-----------------G---------TGCCACACTAG-AGATAGGAGGGGT------- i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_53224 4333 82 + 10229 TGTGGACCACAGGGG-TG-AGAGGTCATACTCCCCCTCCCACTCACCCCCACCACCAATGG---------CTTCTCCCTG--GAGTGGAGGGAAT------- i dipOrd1.scaffold_53224 I 1 C 0 s mm9.chr11 118753312 62 + 121843856 GATACAACAGAGAGG-T--CGGGGCCATGGCCCTCTGCCC--------------------G---------CTTCTTGTTGA-GAGTGGAAGGGAT------- i mm9.chr11 C 0 C 0 s ochPri2.scaffold_6980 60096 48 + 61692 --CATCAGGGCAGCG-AGAAGGGTGTCCCACCCTCCCCTCCTGCACA-----------------------------------GAAT---------------- i ochPri2.scaffold_6980 C 0 C 0 s oryCun2.chrUn0958 14763 49 + 41507 CGCGCCAGGGAGGGG-AG-AGCTTGTCCCGCCCTCCCCTCCTCCACA-----------------------------------AAGT---------------- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 123698 61 + 145505 --TGCCAGGGAGGTA-AG-AGGCTGTTCCCCTTTCCTCTAC-------------------G---------CTTGTCACTGG-AAGTAGAA-GAAT------- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10854809 63 - 65312493 tgtgccaggGAGGTG-AG-AGGCTGTGGCCCTTTCCTCTAC-------------------T---------CTTGTTGCTGG-AAGTAGAA-GAAT------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58037639 65 - 61308211 catgccaggGAGGTG-AG-AGGCTGTGCCCCTTTTCTCCACT------------------G---------CTAGTCATTGG-AAGTAGAAGGAAT------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 9521 65 + 132007 ggtgccgggGACACG-AG-CGGCTGTGCCCCTTTCCTCCACT------------------G---------CGTGAGGCCAG-AAGCAGACGGAAT------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59432458 60 - 64418924 TGTGCCATAGCTG-------GGCAAGGTCCCTCCCCACCACT------------------G---------CTTGTCACTGG-GAGTGGAAGGAGT------- i canFam2.chr9 I 221 C 0 s pteVam1.scaffold_11245 10273 63 + 48268 tgcgccagaggcg---ag-agGCTGTGCCCTTTGCCTCCACT------------------G---------CTTGTCACTGG-AAGCAGAAGGAAT------- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14426778 81 - 17734757 TATGCCAGAGAGATG-AG-TGGCTGTCCTTCTTGCCTCCATG------------------GGAAGTACTTCCTGCCATTGG-GAGCAGACGGAATCTAGGAG i loxAfr3.scaffold_49 I 592 I 7 s dasNov2.scaffold_28617 7140 51 + 20752 tgtgccagAGAGGTG-GG-AGGATGCCCCCCCC---------------------------GGCACTGCCTCCGTCCCCAG---------------------- i dasNov2.scaffold_28617 C 0 C 0 e proCap1.scaffold_29042 10086 1067 + 24616 I e tupBel1.scaffold_124459.1-15939 6267 968 + 15939 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e monDom5.chr2 304527401 602 - 541556283 I a score=187519.000000 s hg19.chr17_gl000204_random 40111 43 + 81310 CTCAGAGCTAAGGG-CTGAGACGGTGCTAGAAT--GTTCTT----TAAAA- s gorGor1.Supercontig_0007361 10203 43 - 64270 CTCAGAGCTAAGGG-CTGAGANGGTGCTAGAAT--GTTCTT----TAAAA- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79470298 43 + 83384210 CTCAGAGCTAAGGG-CTGAGACGGTGCTAGAAT--GTTCTT----TAAAA- i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75031324 43 + 78773432 CTCAGAACTAAGGG-TTGAGACGGCGCTGGAAT--GTTCTT----TAAGA- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 38713 43 - 95547 CTCAGAACTAAGGG-CTGAGATGGCGCTGGAAT--GTTCTT----TAAGA- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40613 43 + 225949 CTCACAGCTAATGG-CTGAGATGGTGCCAGAAT--GTTCTT----TAAAA- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_184068 677 25 + 702 CTCAGCGCTGAGGG-CTGAGACGGTG------------------------- i micMur1.scaffold_184068 C 0 N 0 s otoGar1.scaffold_94362.1-287808 20812 30 + 287808 -------------G-CCAAGACAGTGCCAGAAT--GTCCCT----CAAAA- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16057050 43 + 17838096 CTCAGAGCTAAGGG-CTGAGACAGTGCTAGATT--GTTCTT----TAAAA- i ponAbe2.chr17_random C 0 C 0 s speTri1.scaffold_128901 2692 17 + 44242 ---------------------------CAGAGT--GTTCCC----TGGAA- i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4384846 35 + 7991924 CCCAGAGT-------------CAGTGCCAGAAT--GTTCATTCCCTAAAA- i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_53224 4415 43 + 10229 CTCAGAGTTAAAAC-CTGATACAGTGCCAGGGT--GTTCCT----TAAAA- i dipOrd1.scaffold_53224 C 0 I 916 s mm9.chr11 118753374 38 + 121843856 GGTGGAGCCTAAGCACTGAGACCATGCCAGAGC--ATCGt----------- i mm9.chr11 C 0 I 316 s ochPri2.scaffold_6980 60144 45 + 61692 CCCAGAGCTATGGG-CTGAGACAGGACCAGAAAACATTCCT----TAAAA- i ochPri2.scaffold_6980 C 0 C 0 s oryCun2.chrUn0958 14812 42 + 41507 -CCAGAGCTAAGGG-CTGAGACGGTGCCTGAAG--GTTCCT----CAAAG- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 123759 42 + 145505 CCTAGAGCTAAGGG-CTAAGAT-GTTGCAAGAT--GCTCCT----TAAAA- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10854872 42 - 65312493 CCAAGAGCTAAGGG-CTGAGTT-GGTGCGAGAT--GCTCCT----TAAAA- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58037704 34 - 61308211 CCAAGAGCTGACG----------GTGCCAGAAT--GCTCCT----TAAAA- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 9586 41 + 132007 CCAAGAGCTAACAG-CTGAGGT-GTGCCAGAGT--GCTCC-----TAAAG- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59432518 42 - 64418924 CCAAGAGGGAAAGG-CTGACAT-GTGCCAGAACG-GCTCC-----TAAAA- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 10336 42 + 48268 CCAAGAGCTGAGGG-CTGACACGGTGCCAGAAT--GCTCC-----CTAAA- i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 11153 41 + 24616 CTAAGGGCTACGAG-CTCAGACACCACCAGA-C--GCAAC-----TAAAA- i proCap1.scaffold_29042 I 1067 C 0 s loxAfr3.scaffold_49 14426866 42 - 17734757 CTAAGAGCTGTGAG-ATGAGGCACTGCCAGA-T--GTTGC-----TGAAGC i loxAfr3.scaffold_49 I 7 C 0 e tupBel1.scaffold_124459.1-15939 6267 968 + 15939 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dasNov2.scaffold_28617 7191 0 + 20752 C e monDom5.chr2 304527401 602 - 541556283 I a score=-17792.000000 s hg19.chr17_gl000204_random 40154 156 + 81310 CCCTTGGAAACTTTC-GAGACTGA--GGGGTGAGTCCAGAAACAAGGTCTTTC-TTCTAGAAGATTCTGCATATGGA----GCTGTGGAG-------------------ACGGCACTCTGC--------GGGGCAGCAGG----------------------------------------GACAAACAAG------AAGTGGAAGA--CACAG--------------CCCTGA--------------------------------------------------------------------CCCTCTGGA----------GGCA--------------------------CCCAGGC s panTro2.chr17 79470341 156 + 83384210 CCCTTGGAAACTTTC-GAGACTGA--GGGGTGAGTCCAGAAACAAGGTCTTTC-TTCTAGAAGATTCTGCATATGGA----GCTGTGGAG-------------------ACGGCACTCTGC--------GGGGCAGCAGG----------------------------------------GACAAACAAG------AAGTGGAAGA--CACAG--------------CCCTGA--------------------------------------------------------------------CCCTCTGGA----------GGCA--------------------------CCCAGGC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 10246 157 - 64270 CCCTTGGAAACTTTC-GAGACTGA--CGGGTGAGTCCAGAAACAAGGTCTTTC-TTCTAGAAGATTCNGCATATGGA----GCTGTGGAG-------------------ATGGCACTCTGC--------GGGGCAGCAGG----------------------------------------GACAAACAAG------AAGTGGAAGA--CACAG--------------CCCTGA--------------------------------------------------------------------CCCTCTGGAG---------GGCC--------------------------CTCAGGC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16057093 156 + 17838096 CCCTTGGAAGCTTTT-GAGACTGA--GGGGTGAGTCCAGAAACAAGGTCTTTC-TTCTAGAAGATTCTGCATATGGA----GCTGTGGAA-------------------ACGGCACTCTGC--------GGGGCAGCAGG----------------------------------------GGCAAACAAG------AAGGGGAAGA--CACAG--------------CCCTGA--------------------------------------------------------------------CCCTCTGGA----------GGCA--------------------------CCCAGGC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75031367 167 + 78773432 CCCTTGGAAGCTTTT-AAGACTGA-GGGGGTTAGTCCAGAAACAAGGTCTTTC-TTCTAGAAGATTCTGCACATGGA----GCTGTGGAA-------------------ATGGCACTCTGC--------GGGGCAGCAGG----------------------------------------GACAAACAAG------AAGTGGAAGA--CATAG--------------CCCTGA--------------------------------------------------------------------CCCTCTGGAGGCACCTGGAGGCA--------------------------CCCAGGC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 38756 166 - 95547 CCCTTGGAAGCTTTT-AAGACTGA--GGGGTTAGTCCAGAAACAAGGTCTTTC-TTCTAGAAGATTCTGCATATGGA----GCTGTAGAA-------------------ATGGCACTCTGC--------GGGGCAGCAGG----------------------------------------GACAAACAAG------AAGTGGAAGA--CATAG--------------CCCTGA--------------------------------------------------------------------CCCTCTGGAGGCACCTGGAGGCA--------------------------CCCAGGC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40656 157 + 225949 CCCCTGGAAGCGTTC-AAGACTTA-GGGGATGAGTTCAAAAACAAGGTATTTC-TTCTAGAAGGTTCTGCATAGGGA----GCTGTGGAA-------------------ATGACACCCTGC--------AGGGCAGTGGA----------------------------------------GACAGACAAG------AGGCAGAACA--CACAG--------------CCCCGA--------------------------------------------------------------------CCCCCTGGA----------GGCA--------------------------CCCAGGC i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 20842 155 + 287808 CCCTCAGGAGCTCTT-GAAACTGA-AGGGGGGAATCCAGAAACAAGACCTTCC-TTCTAGAAGGTTCTGTGTATGCA----GCTGTGGAG-------------------AGGACACTGTGTGGGCAGTGGGGACAAAGGG----------------------------------------GACAAACAAG------AAGTGGAAGA--TTCAG--------------------------------------------------------------------------------------------TGGGA----------AGCG--------------------------CCCAGGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118753728 305 + 121843856 ACTGTGAGAGCATTA-AAGACTAAAAGAAG-AGACCTAGAGGTAAAACTGACA-TTCTAGAAGGTTCTGCGT--AGA----GCTGTGTAGAGAATAGGATGCAGGCAGCAGGATCCTGGAG--------AGGGCGGAGAGGGAAATAGCCTGTGGGGCCAGCATTTAGTGGGTGAGCCAAGTCGAGCA------------ACCAGG--AGCAG--------GCC---CTCTCATTTTCTGGGTGAGATAGTAAATATTAACCAGGTGTCAAGCAGGTGTTCAGCAGGTGTCAGCCAGGCCCTCTCCCACA----------GGCCAACCTTAACAAGCATCTGTATTAAGCCTCTGAC i mm9.chr11 I 316 C 0 s cavPor3.scaffold_76 4384881 126 + 7991924 --CCCATGGGCAATG-AAGGT--------------------GTGAGTCCTTCA-TTCCAGAAGGTTCTGAAT--TTA----GCTGAGGAG-------------------AGGACTCTGAGT--------AGGTCACAGAG----------------------------------------AATGAGGA------------GTCAGA--GACAG--------------CTCTTG--------------------------------------------------------------------CCTCCCA--------------------------------------AAGCCCCTGGT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 2709 96 + 44242 --------------------------------------------------------CCCACAGGTTCCCAGT--GGA----GCCGTGCAG-------------------AGGA--CAGCAT--------GGGGCAGCAGA----------------------------------------GATGAACG------------GGTGGACCTACAG--------------CCCCTG--------------------------------------------------------------------CCCTGCACG----------GGCA--------------------------CCCGGGC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 14854 158 + 41507 CCAGGAGGCGCCTTC-AAGACCACAGGGTGCAAGTCCA-AACCAGGACCTTCA-TTCTAGAAGGTTCTGCAAACGGC----GCTGTCAAG-------------------AGGACATCGTGC--------AGGGCAGCAGG--------------------------------------------------------------------GACAGAGACAGAAGCCAAACCCCCGCCCCCAC-------------------------------------------------------------CCACCCAGT----------GGCA--------------------------CCCAGGC i oryCun2.chrUn0958 C 0 I 486 s ochPri2.scaffold_6980 60189 125 + 61692 TCTGGATG---------------CAGGCTGCGGGTTCAGAAACAGGGTGTTCA-ATCTAGAAGATTCTGTGTACGGA----ACTGTCCAG-------------------GGCATGCCTTGC--------CTTGCAGTGGA--------------------------------------------------------------------GACAG--------------CCCCTGCACTCAG-------------------------------------------------------------CCCCT----------------CA--------------------------TCCAGGC i ochPri2.scaffold_6980 C 0 C 0 s turTru1.scaffold_106006 123801 108 + 145505 CCTGCCGGAGCTTTCTGAAACTGA-GGATGTGAGT-CAGGAACAAGGCTTTCA-TTCTAGAAGTTTCTGCCTATAAA----GCTGTGGGG------------------CAGTGCCCTGCAG--------AAGCACTCAGA----------------------------------------C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10854914 107 - 65312493 CCTGCAGGAGCTTTCTGGGATTGA-GGATGTGAGT-CAGGAACAA-GCCTTCA-TTCTAGACGGTTCTGCCAAAAAA----GCTATGGGA------------------CAGCACCCTCCAG--------AAGCTCTCAGA----------------------------------------C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58037738 109 - 61308211 CCCATGGGAGCTTTCTGAGACTGA-GGGCTCGAGTCCAGGAACAAGGCCTTCA-TTCTAGAAGGTTCTGCATATGGA----GCCGTGGGG------------------CGGGGCCCTCCAG--------AAGTACCCAGG----------------------------------------C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 9627 103 + 132007 CCTGGGGGGCCTTTTGGAGACTGA-GGGTGTGAGTCCAGGAGCAAGGCCTTCA-TTCTAGAAGGCACCACATGTGGAGCTGGGGGTGGGG------------------GGGAG--CTGCAC--------AAGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59432560 90 - 64418924 CC-----------TCCAAGACTGA-GCATGTGCACCTAGGAATAAGGCCTTCA-CTCTAGAAGGTTCTGCACATGGA---GGACGTGGGG------------------TGGGG-CCTGCGG--------AAGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 10378 109 + 48268 CCCGTGGGACCTTTCTGAGACTGA-GGTTGTGACTACACAAACAAGGCCTTCA-TTCGAGAAGGTTCTGCCTGTGGA----GTTGTGGGA------------------TGGGGCCCCCCAG--------AGGCACGCAGA----------------------------------------T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 11194 157 + 24616 -CCATGGGGGCTTTCCGAGACTGA-GGACTTAAGTCCAGGGACA-GGCCTTCATTTCTAGAGGGCTCTCTGCATGCA----GCTGGGAAA-------------------CAGACACTGTGT--------GGGGCAGCGGG----------------------------------------AGCTCAGTGGGGACATGGGTGGAAGA--CACCA--------------T-------------------------------------------------------------------------CTGCCCAGA----------AGTA---------------------------CCATGC i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14426908 156 - 17734757 -CCATGGGGGCTTTCTGAGACTGA-GGGTGTGAGTCCAGGGACA-GGTCTTCA-TTCTAGAGGGTTCTGTGTGTGCA----GGTGGGGGG-------------------CAGACACCATGC--------AGGGTGGCGGG----------------------------------------GGATCAGTGGGGACACAAGTGGAAGA--CGCAG--------------C-------------------------------------------------------------------------CTACCCAGG----------AGCA---------------------------CCAGGC i loxAfr3.scaffold_49 C 0 C 0 e tupBel1.scaffold_124459.1-15939 6267 968 + 15939 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dasNov2.scaffold_28617 7191 0 + 20752 C e dipOrd1.scaffold_53224 4458 916 + 10229 I e monDom5.chr2 304527401 602 - 541556283 I a score=-57962.000000 s hg19.chr17_gl000204_random 40310 37 + 81310 C------ATAGCAAGG-AA-------------A--GAGATGG-AA-ATGGCTTGCTGTCCC s panTro2.chr17 79470497 37 + 83384210 C------ATAGCAAGG-AA-------------A--GAGATGG-AA-ATGGCTTGCTGTCCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 10403 37 - 64270 C------ATAGCAAAG-AA-------------A--GAGATGG-AA-ACGGCTTGCTGTCCC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16057249 37 + 17838096 C------ATAGCAAGG-AA-------------A--GAGATGG-AA-ACGGCTTGCTGTCCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75031534 37 + 78773432 T------ACAGCAAGG-AG-------------A--GAGACGG-AA-ATAGCTTGCTGTCCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 38922 37 - 95547 C------ACAGCGAGG-AA-------------A--GAGACGG-AA-ATAGCTTGCTGTCCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40813 37 + 225949 C------ACAGCAAGG-AA-------------A--GAGAAGG-AA-ATGCCTTGCTGCCAC i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 20997 34 + 287808 C------ACGGCAAGG-AC-------------A--GAGA-GG-GG-ACAGCT--CAGATCT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118754033 56 + 121843856 TTCCTAAACATCAGTT-ACTGCTACTCAGGACA--GAGAGGG-AA-ACGGCCTGTGGGGCC i mm9.chr11 C 0 I 249 s cavPor3.scaffold_76 4385007 34 + 7991924 T------ATAGGAGTG-ACCG-----------A--GAAAGGATAA-ACAGCC------ACC i cavPor3.scaffold_76 C 0 I 6 s speTri1.scaffold_128901 2805 31 + 44242 C------ACAGGGAGG----------------A--GAGTGGA-GT-CCAGCCTTCAG---- i speTri1.scaffold_128901 C 0 C 0 s ochPri2.scaffold_6980 60314 34 + 61692 --------TATGGGTA----------------C--GACAGGCAGA-GTGGTCTCTAGACCC i ochPri2.scaffold_6980 C 0 I 8 s turTru1.scaffold_106006 123909 37 + 145505 --------TGTGGGAA-AG-------------ACGCAGAAGG-AA-CTAGACCATTGTCTC i turTru1.scaffold_106006 C 0 I 8 s bosTau4.chr19 10855021 35 - 65312493 --------CACGGGAA-AG-------------A--CAGGAGG-AA-CTAGATCGTTGCCTC i bosTau4.chr19 C 0 I 8 s equCab2.chr11 58037847 28 - 61308211 --------C--------AC-------------A--GAGAAGG-AA-ATCAACCATCGTCTC i equCab2.chr11 C 0 I 8 s felCat3.scaffold_206428 9730 19 + 132007 -----------------AC-------------A--GAGAACA-ACTCCAGAT--------- i felCat3.scaffold_206428 C 0 I 3 s canFam2.chr9 59432650 18 - 64418924 -----------------AT-------------G--GAGAATG-AA-ATGGAC--------- i canFam2.chr9 C 0 I 3 s pteVam1.scaffold_11245 10487 36 + 48268 --------CTCAGGAAGGG-------------A--AAGAAGG-GA-ACAGACTATCGTCTC i pteVam1.scaffold_11245 C 0 I 8 s proCap1.scaffold_29042 11351 36 + 24616 -------CGGGGACGG-AC-------------A--AAGCGAG-AA-TGAGACAACTCTCTC i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14427064 36 - 17734757 -------CGGGGAAGG-AC-------------G--GAGAAGG-AA-CGAGACAACTATCTC i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 15012 486 + 41507 I e tupBel1.scaffold_124459.1-15939 6267 968 + 15939 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dasNov2.scaffold_28617 7191 0 + 20752 C e dipOrd1.scaffold_53224 4458 916 + 10229 I e monDom5.chr2 304527401 602 - 541556283 I a score=24164.000000 s hg19.chr17_gl000204_random 40347 58 + 81310 ---------CAGATGCTCC------------TGTTCACACCA-CC-----------------A---GCCA-GCCCC-CTCCAGGCTCT---GCCTC--CCA-----------CATGCT s panTro2.chr17 79470534 58 + 83384210 ---------CAGATGCTCC------------TGTTCACACCA-CC-----------------A---GCCA-GCCCC-CTCCAGGCTCT---GCCTC--CCA-----------CATGCT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 10440 58 - 64270 ---------CAGATGCTCC------------TGTTCACACCA-AC-----------------A---GCCA-GCCCC-CTCCAGGCTCT---GCCTC--CCA-----------CATGCT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16057286 58 + 17838096 ---------CAGATGCTCC------------TGTTCACACCA-CC-----------------A---GCCA-GCCCC-CTCCAGGCTCT---GCCTC--CCA-----------CATGCT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75031571 58 + 78773432 ---------CAGATGCTCC------------TGTTCACACCA-CC-----------------A---GCCA-ACCCC-CTCCAGGCCCT---GCCTC--CCA-----------CATGCT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 38959 58 - 95547 ---------CAGATGCTCC------------TGTTCACACCA-CC-----------------A---GCCA-ACCCC-CTCCAGGCCCT---GCCTC--CCA-----------CATGCT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40850 39 + 225949 ---------CAG--------------------------------C-----------------A---GCCA-GCCCC-GTCCAGGCCCT---GTGTC--CCA-----------CACACT i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 21031 57 + 287808 ---------CAGATGCGCC------------TGTTCAC-CCT-CC-----------------T---GCCA---CCC-CTCCACCCCCG---TCCTCAGCCG-----------CATGCA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s cavPor3.scaffold_76 4385047 45 + 7991924 -----------------------------------CAT-CCTGTA-----------------G---ACCACGCCCT-CGCCAGGGCCC---ACGGC--TTC-----------CCACCA i cavPor3.scaffold_76 I 6 C 0 s speTri1.scaffold_128901 2836 60 + 44242 ---------CAGGCACCTC------------TGTTCACACCAATC-----------------A---GCCAGCCCCT-CTCCGGGCTCT---GTCCC--TCT-----------CCTGCA i speTri1.scaffold_128901 C 0 C 0 s ochPri2.scaffold_6980 60356 83 + 61692 ---------CAGATGTCTCGTG---------CCCTCGCACCAGCCCCGTCCTCCAGGGGTCAG---CCCAGGACAC-CACTGGGCCCCACAGCTGC--TGC-----------TGCCCA i ochPri2.scaffold_6980 I 8 C 0 s turTru1.scaffold_106006 123954 80 + 145505 ---------GAGACATTCTCTGGAAGCATCTTTTCCTCACCA-TC-----------------A---TTCA-GCCCC-CTCCAAGCCCT---GTTTT--TCTTCTCTCCCCA-AAAGTC i turTru1.scaffold_106006 I 8 C 0 s bosTau4.chr19 10855064 81 - 65312493 ---------GAGACATTCTCTGGAAGCATCTTTTCCTCACCA-TC-----------------A---ATCA-GCCCCTCTCCATATCCT---GTTTT--TCTTCTCCCCCTA-CAAGTC i bosTau4.chr19 I 8 C 0 s equCab2.chr11 58037883 82 - 61308211 ---------AAGACGTTCTCTGGAAGCTTCTTTTCCTTGCCA-TT-----------------C---ACCG-GCCCCTCTTCAAGCCCC---ATCCA--TCCTGCTCCCACCACAAGCC i equCab2.chr11 I 8 C 0 s felCat3.scaffold_206428 9752 78 + 132007 ---------AAGATGTTCTCTGGAAGCCTGTTTTCCTTGTCA-TC-----------------AACCACCA-GCCCCTCTCAAAGACCC---ATTCT--CCTCCCT-------CATGTC i felCat3.scaffold_206428 I 3 C 0 s canFam2.chr9 59432671 73 - 64418924 ---------GAGAGGTTCTCTGGAAGCTTCTCTCCCTTGTCA-CC-----------------A---ACCA-GCCCCTCTCCAAGACCT---GTCCC--CCTCA---------CATGTC i canFam2.chr9 I 3 C 0 s pteVam1.scaffold_11245 10531 62 + 48268 ---------AAGACATTCTCTAGAAGCT--TTCTCCTTGTCA-TC-----------------A---GCCA-GCCACTCTCCAAGCTCC---A--------------------CATGCT i pteVam1.scaffold_11245 I 8 I 295 s proCap1.scaffold_29042 11387 84 + 24616 TCAGATCCCAAGCCCACCACTGACCGCTTCTTTCCCTCACCA-AG-----------------C---CCCG-TACCTTCTCCCAGCCCC---ACCCT--CCCATGG-------CAAGTC i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14427100 83 - 17734757 T-GGATCCCAAGACCATCGCTGGCCACTTCTTTTTCTCACCA-AC-----------------A---CCCG-GCCCTTCTCCCAGCCTC---GTCCT--CCCACAA-------CAAGTC i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 15012 486 + 41507 I e tupBel1.scaffold_124459.1-15939 6267 968 + 15939 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dasNov2.scaffold_28617 7191 0 + 20752 C e dipOrd1.scaffold_53224 4458 916 + 10229 I e monDom5.chr2 304527401 602 - 541556283 I e mm9.chr11 118754089 249 + 121843856 I a score=-304543.000000 s hg19.chr17_gl000204_random 40405 96 + 81310 GACT----TCAGAAGC-----------------TGTCCACTCCA---GGGCCAC-CCGGGG-------------CCT----------------AAATCCGGCCGTG-----------------------------------CAGCC-----CGGCCCCT----GCGCAGGG------AGGACTCGAGCCACACAAACC-----CA s panTro2.chr17 79470592 95 + 83384210 GACT----TCAGAAGC-----------------TGTCCACTCCA---GGGCCAC-CCGGG--------------CCT----------------AAATCCGGCTGTG-----------------------------------CAGCC-----CGGCCCCT----GCGCAGGG------AGGACTCAAGCCACACAAACC-----CA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 10498 95 - 64270 GACT----TCAGAAGC-----------------TGTCCACTCCA---GGGCCAC-CCGGG--------------CCT----------------AAATCTGGCTGTG-----------------------------------CAGCC-----CNGCCCCT----GCGCAGGG------AGGACTCGAGCCACACAAACC-----CA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16057344 95 + 17838096 GACT----TCAGAAGC-----------------TGTCCACTCAA---GGGCCAC-CCGGG--------------CCT----------------AAATCCGGCTATG-----------------------------------CAGCC-----CGGCCCCT----GCGCAGGG------AGGACTCGAGCCACACAAACC-----CA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75031629 95 + 78773432 GACT----TCAGAAGC-----------------TGTCCACTCCA---GGGCCAC-CTGGG--------------CCT----------------AAAGCCGGCTGTG-----------------------------------CAGCC-----CAGCCCCT----GCGCAGGG------AGGACTCGAGCCACACAAACC-----CA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 39017 95 - 95547 GACT----TCAGAAGC-----------------TGTCCACTCCA---GGGCCAC-CTGGG--------------CCT----------------AAAGCCGGCTGTG-----------------------------------CAGCC-----CGGGCCCT----GCACAGGG------AGGACTCGAGCCACACAAACC-----CA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 40889 94 + 225949 GACT----CCAGAAGC-----------------TGCCCACTC-A---AGGCCAC-CCGGG--------------CCC----------------AACACCGACTGTG-----------------------------------CGGCC-----CGGCCCCT----GCGCAGGG------AAGACTCCAGCCACACAGATC-----CA i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 21088 37 + 287808 GACT----TGGGA------------------------------------GCCAT-CTGTG--------------CTC-----------------------------------------------------------------------------------------CTGGA------GAAAATAAAG------------------ i otoGar1.scaffold_94362.1-287808 C 0 C 0 s cavPor3.scaffold_76 4385092 97 + 7991924 GTCCCTGTGATGAGCTC--TCAT---------GTGGGTCAGCCA---GGGTCTC-CCAGG--------------CCC-----------------------CTGGTG-----------------------------------CCTCC-----TGACCCTG----GACAC-GA------AAAACACTGGCCATGAAAAGC-----CA i cavPor3.scaffold_76 C 0 I 2 s speTri1.scaffold_128901 2896 70 + 44242 GTCC----ACTGGACT-----------------TGGGTCAGGCACAGATGCCCC-CAGGG--------------TGC-----------------------CTGGTG-----------------------------------------------------------------------GAGAGCCCGGCCTTGAGAAGC-----CA i speTri1.scaffold_128901 C 0 C 0 s ochPri2.scaffold_6980 60439 102 + 61692 GTCCCCAAGCCTGGAG-----------------TGCATGGGCCA--GAGACCCT-CGCAG--------------CTC-----------------------TCACAG-----------------------------------CAGCC-----CCCCGCTGCAGCGTCACGGA------CAGCTGCTTCTCCTCAGTAACACTTGCA i ochPri2.scaffold_6980 C 0 I 2 s turTru1.scaffold_106006 124034 136 + 145505 AACT----TGAGAGCCT--CCATCCCAGTTGGGTATATAAATC----AGGCTCCACA--A--------------CCC----------------TGGACAAGCACAG-----ACACAGTCAGACCACCC--CAGGCCTGCAGCCACC-----CAGCCTCT----GAGCACAG------AGAAGATGCGCCCTGTAGAGC-----CA i turTru1.scaffold_106006 C 0 I 2 s bosTau4.chr19 10855145 129 - 65312493 AACT----CGAGAGCCT--TGATTCTGGTTGGGTATTTAAAGC----AGGCACCGCAGGA--------------CCC----------------TGGACAAGCAGAG-----GCACACACAGAGCCCCC--CAGGCCTGCAGCCACC-----TAGCCCCT----GAGC---------------ATGCACCCTGCACAGC-----CA i bosTau4.chr19 C 0 I 2 s equCab2.chr11 58037965 138 - 61308211 AACT----TGAGAAGCCACTCATTCAGGTTGGGTACTTAAATCA---AGGCACC-CAGGA--------------TCC----------------CGCACCAGCGCAG----CGAGCTCACTGACCACCC--CAGGCGGCAG-CCACC-----TGCCCCTT----GAGCATGG------AGAAGACA--CCCTCCATAGC-----CC i equCab2.chr11 C 0 I 2 s felCat3.scaffold_206428 9830 128 + 132007 AACC----TGGGAAGCCAGTCATTCGTGTGGGGCATTTA-ATCA---AGGCACCACAGGA--------------GCC----------------CGGACAGGCACAG----TGAACACGCAGACCACC--------------CCGGG-----GGGCC-CT----GAGTGTTA------AGGAGACATGCCTCGTGCAGT-----CA i felCat3.scaffold_206428 C 0 I 2 s canFam2.chr9 59432744 120 - 64418924 AGCA-----------------------GTGGGGCGTTTACATCA---AGGCAGCACGGGA--------------CCC----------------CGGGCCACCACGG----TGAACA---AAACCACCC--GAGGCCTGGGGCCGTG-----GGACCTCC----GAACCGTG------GGAAGACACGTCCTGCACAGC-----CA i canFam2.chr9 C 0 I 2 s proCap1.scaffold_29042 11471 157 + 24616 TGCT----TGGGAAGT----CATCCGGG--GGGTGTGTCACTTG---AGGTGTC-CCAGGACACCCCAAAGAG-CCCATTTCCCCAGTCTCACGGGGACGGCTGCGGCAGCAAACACAGTGACCACCCCTTAGGCCTT---CAGCCTTGAACTGTCCCC----AAGCAGGG------GGGAGCCA-------------------- i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14427183 166 - 17734757 TGCT----TGGGAAGT----CGTCTGTGTTGAGTATTTCAGCTG---AGGCATC-CCAGGACACCAGGAGGAGCCCCGCTTTTCCAGCCTCACAGGCAAAGCTGCAGCAGCAAGTAGACTGGCCACCCTCCAGGCCTG---CCACCATGAACTGTCCCC----AAGCATGAGGCCACGGGAGCCA-------------------- i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 15012 486 + 41507 I e tupBel1.scaffold_124459.1-15939 6267 968 + 15939 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dasNov2.scaffold_28617 7191 0 + 20752 C e pteVam1.scaffold_11245 10593 295 + 48268 I e dipOrd1.scaffold_53224 4458 916 + 10229 I e monDom5.chr2 304527401 602 - 541556283 I e mm9.chr11 118754089 249 + 121843856 I a score=280433.000000 s hg19.chr17_gl000204_random 40501 72 + 81310 GCACC-----------TCGAGGT----------TCTTG--TTCCTGTCCC-TGGGACTGCAGGACCCAACAGCACTC--------TTCCTCGAGGGCAGTGTGA s dasNov2.scaffold_28617 7191 65 + 20752 -----------------CGGGGC----------TCCCACTCTCTTG-CCC-CTCGCCCATGGCACCTGGCTGCGCTC----------CCAGAAGGGTGGTGTGA i dasNov2.scaffold_28617 C 0 C 0 s loxAfr3.scaffold_49 14427349 69 - 17734757 GCATC-----------TCAAGGT----------TCCTG--CACCTG-TCC-TGAGTCCAGTGACCCAAAGACAGCTC----------CTGGGAGGGCAATGTGA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 11628 69 + 24616 GAGTC-----------CTGAGGT----------CCCTG--GGCCTG-TCC-TGATCCCAGCAAGCCAACAGCTGCTC----------CTGGGAGGGCGGCGTGA i proCap1.scaffold_29042 C 0 C 0 s canFam2.chr9 59432866 71 - 64418924 AAGCC-----------TGGCGG-----------CCCTC--CTCCTGCCCC-TGAGCCTGTGTGACCCCACGGCGCTC--------CTCTGGGAGGGCAGTGTGA i canFam2.chr9 I 2 C 0 s felCat3.scaffold_206428 9960 72 + 132007 AAGCC-----------TCTCGGC----------CCCTG--CTCCTGTCCC-TGAGCCCGCAGGACCCCACAGTGCTC--------TTCCGGGAGGGCAGCGTGA i felCat3.scaffold_206428 I 2 C 0 s equCab2.chr11 58038105 71 - 61308211 AAGCC-----------TCAAGGT----------CCCTG--CTCCTGGCCC-TGAGTCCGTGGGACCCCACGGTGCTC--------TTCTGGGAGGGCAG-GTGA i equCab2.chr11 I 2 C 0 s bosTau4.chr19 10855276 78 - 65312493 AAGCC-----------TCCCCGC---CCCAAGTCCCTG--GTCCTA-CCC-TGAGTCTGTGTGACTTCACGGTGTTC--------TTCTGGGAGGACAGTGTGA i bosTau4.chr19 I 2 C 0 s turTru1.scaffold_106006 124172 73 + 145505 AAGCC-----------TCCCCGC---CCCTAGTCCCTG--GTCCTA-TCC-TGAGTCTGTGTGACTTCA--GTG-----------TTCTGGGAGGACAGTGTCA i turTru1.scaffold_106006 I 2 C 0 s ochPri2.scaffold_6980 60543 89 + 61692 ---CCATGTCGCGGTGGGGAGGTTGGCCC----TATGG--CTCCAGCT---GAAGCC---AGGAACCAGGAGCCCCTTTTGGGTCTTCCATAGAGGCAGAGAAT i ochPri2.scaffold_6980 I 2 C 0 s speTri1.scaffold_128901 2966 68 + 44242 GGGCC-----------CGGAGGT----------TCTCG---CTCTGTCCC-TGGGCCCCCGGGGCCTGAGAGTCT-----------TCCAGGAGGGCAGTGAGT i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4385191 65 + 7991924 GCCCC--------------AGGT----------TCTGG--TCTCTGCC---TGAGCTTGGAGGACTTGACAGTTCC----------TCTGGGATGGCAGTGGGA i cavPor3.scaffold_76 I 2 C 0 s mm9.chr11 118754338 72 + 121843856 GCACC-----------GGGAGGG----------CCTCG--CTCCAGTCGA-TGAGCCTGTGGGACCTGACAGAGCCT--------TTCTAGGAGGGCAGTGTGA i mm9.chr11 I 249 C 0 s otoGar1.scaffold_94362.1-287808 21125 68 + 287808 ----C-----------TTGTGCT----------TCTTC--CTCCTGTCAC-CGGGCCCAGAGGACTCGGCAGCACTC--------TCCCTCCAGGGTGCTGTAA i otoGar1.scaffold_94362.1-287808 C 0 I 1403 s calJac1.Contig5139 40983 72 + 225949 GCGCC-----------TTCAGGC----------TCTCG--TTCCTGTCCC-TGGACCTGCAGGACCCAGCAGCACTC--------TTCCTCAGGGGCAGTGGGG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 39112 72 - 95547 GCACC-----------TCGAGGT----------TCTTG--TTCCTGTCCC-TGGGACTGCAGGACCCGACAGCACTC--------TTCCTTGAGGGCAGTGTGA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75031724 72 + 78773432 GCACC-----------TCAAGGT----------TCTTG--TTTCTGTCCC-TGGGACCACAGGACCCGACAGTACTC--------TTCCTTGAGGGCAGTGTGA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16057439 72 + 17838096 GCACC-----------TTGAGGT----------TCTTG--TTCCTGCCCC-TGCGACTGCAGGACCCAATAGCACTC--------TTCCTCGAGGGAAGTGTGA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 10593 72 - 64270 GCACC-----------CTGAGGT----------TCTTG--TTCCTGTCCC-TGGGACTGCAGGACCCAACAGCACTC--------TTCCTCGAGGGCAGTGTGA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79470687 72 + 83384210 GCACC-----------TCGAGGT----------TCTTG--TTCCTGTCCC-TGGGACTGTAGGACCCAACAGCACTC--------TTCCTCGAGGGCAGTGTGA i panTro2.chr17 C 0 C 0 s monDom5.chr2 304528003 63 - 541556283 ---------------------GT----------TCTCA--TTTCTATTATATGAGCCAGAGCAGTGTAACTGCACTA--------TTCTGGGAGGGCAGTATGA i monDom5.chr2 I 602 C 0 e oryCun2.chrUn0958 15012 486 + 41507 I e tupBel1.scaffold_124459.1-15939 6267 968 + 15939 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e pteVam1.scaffold_11245 10593 295 + 48268 I e dipOrd1.scaffold_53224 4458 916 + 10229 I a score=457860.000000 s hg19.chr17_gl000204_random 40573 98 + 81310 GCAGAG--------------------CCAATTTTTTAAAT--------ACAGAACTGTACATCAATGTGACGTCTAACATAAGGCACCTTATAAATCAGAGGCCATTTTTTAAAACTTGGATGTGA s panTro2.chr17 79470759 98 + 83384210 GCAGAG--------------------GCAATTTTTTAAAT--------ACAGAACTGTACATCAATGTGACGTCTAACATAAGGCACCTTATAAATCAGAGGCCATTTTTTTAAACTTGGATGTCA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 10665 98 - 64270 GCAGAG--------------------CCAATTTTTTAAAT--------ACAGAACTGTACATCAATGTGACGTCTAACATAAGGCACCTTATAAATCAGAGGCCATTTTTTTAAACTTGGATGTCA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16057511 98 + 17838096 GCAGAG--------------------CCAATTTTTTAAAT--------ACAAAAATGTAAATCAATGTGACGTCTAACATAAGGCACCTTATAAATCAGAGGCCATTTTTTTAAACTTGGATGTCA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75031796 98 + 78773432 GCAGGG--------------------CCAATTTTTTAAAT--------ATAGAGATGTAAATCAATGTGACGTCTAACATAAGGCACCTTACAAATCAGAGGCCATCTTTTTAAACTTGGATGTCA i rheMac2.chr16 C 0 I 20 s papHam1.scaffold8336 39184 98 - 95547 GCAGGG--------------------CCAATTTTTTAAAT--------ATAGAGATGTAAATCAATGTGACGTCTAACATAAGGCACCTTACAAATCAGAGCCCATCTTTTTAAACTTGGATGTCA i papHam1.scaffold8336 C 0 I 20 s calJac1.Contig5139 41055 97 + 225949 GCAGGG--------------------CCAACTTTTTAAAT--------GTAGAATTGTAAATCAATGTGGAGTCTAACATCAGGCGCCTTACAAATCAGAGGCCAT-TTCTAAAACTTGGCTGCCA i calJac1.Contig5139 C 0 I 20 s mm9.chr11 118754410 94 + 121843856 CAGCAG--------------------TCAGTGatttaaat--------ataaaa-tataaatGGATGTGGTATCTAGTGTTGGG-GCTTTAGCCACTGAAGGTCATGCTTTAAGCTTTCAAC--CG i mm9.chr11 C 0 I 20 s cavPor3.scaffold_76 4385256 87 + 7991924 CTAATA--------------------TCAA-GTTTTAAAT--------ACAAAAGTGTAGGTCACTATGGTATCCACAGTCAAGTACCACAGACACCAAAGACCATGTCTGAAG----------CA i cavPor3.scaffold_76 C 0 I 12 s speTri1.scaffold_128901 3034 89 + 44242 CCAGCA--------------------GCAGCATTTTGAGCATC----AATAAAA-TGTGAATCAATGT----------GCCAGGCACCTGAGACACCAGAGGTCATGTTTTAAGCTTTATGC--CA i speTri1.scaffold_128901 C 0 I 20 s ochPri2.scaffold_6980 60632 118 + 61692 TAGCCAATTGAGCCATCATGTTGGCCCCAGAGAAATAAAAATCTCCTTGTAAAA-TGTCAG-CGGCGTAATGTCCAACA-CAAGCTCCTGAGGCATTAACGGT-ATTTTCCAATTTTTCATC---- i ochPri2.scaffold_6980 C 0 I 2 s turTru1.scaffold_106006 124245 91 + 145505 GCTCAG--------------------CCAATTG-TTCAGT--------ATAAAAATTTAAAT-----CAAGGTCTAATGTAAGGGACCTTAGAAATCAAAGGTCA-TTTTTTAAACTTTGGTGCCA i turTru1.scaffold_106006 C 0 I 1 s bosTau4.chr19 10855354 97 - 65312493 GCTCAG--------------------CCAATTG-TTCAAT--------ATAAAACTGTCAATCGATACAAGGTCTAAAGTAAGGCACCTTAGAAATCAAAGGTCATTTTTTTAAACTTTGGTGCCA i bosTau4.chr19 C 0 I 1 s equCab2.chr11 58038176 97 - 61308211 ACACAG--------------------CCAACTGGTTAAAT--------ATAAAAATGTAAATCGATGCAACGTCTGATGTAAGGCACCTTGGAAATGAAAGGGCA-TTTTTTAAACTTTGGTGCCA i equCab2.chr11 C 0 I 1 s felCat3.scaffold_206428 10032 92 + 132007 GTTCGG--------------------CCAATAGCTTAAAT--------AT-AAAATCGAAATCAATACAGTGTCTAATGTAAGGCACCTTAGAAATCAATGGT-C-TTTgggacacctgggcg--- i felCat3.scaffold_206428 C 0 I 226 s canFam2.chr9 59432937 96 - 64418924 GTGCAG--------------------CCAATGGTTTAAAT--------AT-AAAATttaaatcgatacgatgtctcatgtaaggcaccttagaaatcaaaggtat-ttttttaaactttggtgcca i canFam2.chr9 C 0 I 1 s loxAfr3.scaffold_49 14427418 95 - 17734757 GCAGAG--------------------CCAACTGTCTTAAC--------ATAAAAATGCAAATCAATGTGATATATAACTCAAGGTAGCTCAGAAATCAAAGGTCATT---TGTAACTCTGATGCCA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 11697 95 + 24616 GCATCG--------------------CCACCTGTCTTCAT--------GTAAGAATGTAAATCAGTGTGATGTATAATTCAAGGCAGCTCAGAAAGCAAAGGTCATT---TGTAACTCAGGTGCCA i proCap1.scaffold_29042 C 0 I 30 s dasNov2.scaffold_28617 7256 98 + 20752 ACAGAG--------------------GCAACTTGTTAGAT--------AGAAAAATTTAAATTAATGTGATGTATAATTTAAGGCAGCAAAGAAACCAAAGGTCATTTCCTTTCTCTTTGATGCCA i dasNov2.scaffold_28617 C 0 C 0 s monDom5.chr2 304528066 95 - 541556283 CTGTAG--------------------CCAAATTTCTTTTT--------ATAAAAATTTAAATCAATGTGATGTATAATTTAAAGCAGCTCAGAAATCAAGAGTTGTTTTT---AGCTCTGGTGCCA i monDom5.chr2 C 0 C 0 e oryCun2.chrUn0958 15012 486 + 41507 I e tupBel1.scaffold_124459.1-15939 6267 968 + 15939 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e pteVam1.scaffold_11245 10593 295 + 48268 I e otoGar1.scaffold_94362.1-287808 21193 1403 + 287808 I e dipOrd1.scaffold_53224 4458 916 + 10229 I a score=-56367.000000 s hg19.chr17_gl000204_random 40671 43 + 81310 -------AAGGT------TCTGGTGTCCAGGGGCTGAGG--------------GTGTAGGCAGCTGCGAG s calJac1.Contig5139 41172 43 + 225949 -------AAGGT------TCTGACGTCCAGGGGCCAGGG--------------GTGGACACAGCTGTGAG i calJac1.Contig5139 I 20 C 0 s papHam1.scaffold8336 39302 43 - 95547 -------AAGGT------TCTGGCGTCCAGGGTCCAGGG--------------GTGTAGGCAGCTGTGAG i papHam1.scaffold8336 I 20 C 0 s rheMac2.chr16 75031914 43 + 78773432 -------AAGGT------TCTGGCGTCCAGGGTCCAGGG--------------GTGTAGGCAGCCGTGAG i rheMac2.chr16 I 20 C 0 s ponAbe2.chr17_random 16057609 43 + 17838096 -------AAGGT------TCTGGCCTCCAGGGGCCGGGG--------------GTGTAGGCAGCTGCAAG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 10763 43 - 64270 -------AAGGT------TCTGGTGTCCAGGGACTGGGG--------------GTGTAGGCAGCTGCGAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79470857 43 + 83384210 -------AAGGT------TCTGGTGTCCAGGGGCTGGGG--------------GTGTAGGCAGCTGCGAG i panTro2.chr17 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7235 43 + 15939 -------AAGGC------CCTGGATTCCAGGAGGCGTGG--------------GGGCCAGTTGCCACAAG i tupBel1.scaffold_124459.1-15939 I 968 C 0 s mm9.chr11 118754524 42 + 121843856 -------CAGGT------TCTGATGTCCAGAGGCCA-GA--------------GGGACAGTCAGTACCAG i mm9.chr11 I 20 C 0 s cavPor3.scaffold_76 4385355 41 + 7991924 -------GAGGG------TCT-ATGTCATGAGGCAG-GA--------------GTGGACGCAGCTGGGAG i cavPor3.scaffold_76 I 12 C 0 s speTri1.scaffold_128901 3143 29 + 44242 -------TAGGT------CGG-CGGTCGGGAGGT---GA--------------GTGGACC---------- i speTri1.scaffold_128901 I 20 C 0 s ochPri2.scaffold_6980 60752 35 + 61692 -------GAGGT------CCTGATGTCCACA------AA--------------GGGGAAT--CCCAGCGA i ochPri2.scaffold_6980 I 2 C 0 s turTru1.scaffold_106006 124337 17 + 145505 -------AGAGC------ACTGGTGCACAG---------------------------------------- i turTru1.scaffold_106006 I 1 I 80 s bosTau4.chr19 10855452 43 - 65312493 -------AGAGC------ACTGGTGCATAGA--TTGAGATG------------CTGATGGCAGGGGAGAG i bosTau4.chr19 I 1 I 28 s equCab2.chr11 58038274 55 - 61308211 -------AGAGC------ACTCGTGCCCAGA--TTGAGGTGCTCACGTGGGACGTTGGGGCAGCCCTGTG i equCab2.chr11 I 1 C 0 s canFam2.chr9 59433034 24 - 64418924 -------agagc------tcgggtgcccagg--ctgagg------------------------------- i canFam2.chr9 I 1 I 268 s loxAfr3.scaffold_49 14427513 43 - 17734757 -------GAAAG------CGTGGTGCCAAGAGTGAGAAG--------------CTGGTGAGTGGAGGAAG i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 7354 25 + 20752 -------A-------------AGGGCCAAGAGCGAGACG--------------CC-----------AAAG i dasNov2.scaffold_28617 C 0 C 0 s micMur1.scaffold_15893 0 36 + 19765 ----------GT------TCTGACGTCCAGGGGAGGAGG--------------G----GGCAGCCGCGAG i micMur1.scaffold_15893 N 0 C 0 s monDom5.chr2 304528161 42 - 541556283 ATGATCAATGGTATCATGTCTGAGGTACAGGGTGGGTGA--------------GGG-------------- i monDom5.chr2 C 0 I 3081 e oryCun2.chrUn0958 15012 486 + 41507 I e proCap1.scaffold_29042 11792 30 + 24616 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e felCat3.scaffold_206428 10124 226 + 132007 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e pteVam1.scaffold_11245 10593 295 + 48268 I e otoGar1.scaffold_94362.1-287808 21193 1403 + 287808 I e dipOrd1.scaffold_53224 4458 916 + 10229 I a score=-102831.000000 s hg19.chr17_gl000204_random 40714 77 + 81310 GCCTTCCAGGGGCACCCCT---GAACA----TACAAGGAA----GCACCCACTCAGCGCTTCCCCAC-CCTCGGCATGCCCCGGAAGCC s panTro2.chr17 79470900 76 + 83384210 GCCTTCCAGGGGCACCCCT---GAACA----TACAAGGAA----GCACCCACTCAGCGCTTCCCCAC-CCTCGGCATGCCC-GGAAGCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 10806 77 - 64270 GCCTTCCAGGGGCACCCCT---GAACA----TACAAGGAA----GCACCCACTCAGCACTTCCCCAC-CCTCGGCATGCCCCGGAAGCC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16057652 77 + 17838096 GCCTTCCAGGGGCACCCCT---GAATA----TACAAGGAA----GCACCCACTCAGCGCTTCCCCAC-CCTCGGCACGCCCCGGAAGCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75031957 77 + 78773432 GCCTTCCAGGGACACCTCT---GAACA----CGCAAGGAA----GCACCCACCCAGCGCTTCCCCAC-CCTCGGCACACCCCAGAAGCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 39345 77 - 95547 GCCTTCCAGGGACACCTCT---GAACA----CGCAAGGAA----GCACCCACCCAGCGCTTCCCCAC-CCTCGGCACACCCCAGAAGCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41215 68 + 225949 GCCTTCCAGGGTC-CCCCT---GAACG----TGCAAAGAA----GCACCCACCCAGCACTTCCCCAG-CCTCGGCGCACCC-------- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 36 33 + 19765 GC--------------------GAGGA----C------------GCACCCACCGGGCGCTCCCTCGC-CT------------------- i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 22596 60 + 287808 GCC-CCCAGGAACCCCACCACGGAGGA----TGTTATGAG----GCACCCACTCAGCGCTTCCCCAG-TC------------------- i otoGar1.scaffold_94362.1-287808 I 1403 C 0 s tupBel1.scaffold_124459.1-15939 7278 67 + 15939 GCC-ACCAGGGCCCCCGCT---GAGGA----TGCGGGG------GCGGCCCCCGTGC---TGCCCAC-CT--GGTAGACCC--AGAGCC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118754566 60 + 121843856 GTCTT----------CCCG---GGAGACACCAGGAAGATC----TCAGCGCTG----------CCAT-CCTTAGTCCACCTTGACAGC- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4385396 65 + 7991924 GCCTTGTGGG----CCACA---GAAGA----GGGGAGGAT----GCACCCCTG--------CCCCAT-CCTTGGCTCACCGCAGCTGTG i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_6980 60787 64 + 61692 GTCCCCCGCA----CTGGG---GTAGA----AGGATGCAT----GTACCCATT--------GCCGACCCATCAAGACACCCAGAGCC-- i ochPri2.scaffold_6980 C 0 C 0 s equCab2.chr11 58038329 41 - 61308211 GCCTTCCGGGGCCCCCACC---GAAAA----TGCAAGGAC----GCACCCAC------------------------------------- i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14427556 43 - 17734757 ----GCC-------------------------------------GTGGCCTTGAGGC--CTCCCCGC-CCCAAAGGTGCACCTGCAG-- i loxAfr3.scaffold_49 C 0 I 141 s dasNov2.scaffold_28617 7379 34 + 20752 ----TCCA--------------------------GGGACG----GCGGCCTTGGG----------GC-CCCTGGGGG---------GG- i dasNov2.scaffold_28617 C 0 C 0 s proCap1.scaffold_29042 11822 42 + 24616 ----------------------------------GGGGCACACCATGGCCTGCAGGG--CTCCCTGC-CCCCAAAGTG---------C- i proCap1.scaffold_29042 I 30 C 0 s speTri1.scaffold_128901 3172 57 + 44242 ---------------CGTG---GAAGA----TGTGAGGAC----GCACCCCGAGAG-----CTCCACACCTCGGCACAGCCCAGCAGC- i speTri1.scaffold_128901 C 0 I 5 e oryCun2.chrUn0958 15012 486 + 41507 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e turTru1.scaffold_106006 124354 80 + 145505 I e felCat3.scaffold_206428 10124 226 + 132007 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e pteVam1.scaffold_11245 10593 295 + 48268 I e dipOrd1.scaffold_53224 4458 916 + 10229 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59433058 268 - 64418924 I e bosTau4.chr19 10855495 28 - 65312493 I a score=39059.000000 s hg19.chr17_gl000204_random 40791 104 + 81310 ACCCTCAGAAGCCTCCACTGGGAATTTCTGAG-----------TTTTCACGTGTGGTTCCTCT---TATCCT---CCATCCCCTGTGGGTGCCACACAGAGGGCCAGAAGGTTTGCATTTA s panTro2.chr17 79470976 104 + 83384210 ACCCTCAGAAGCCTCCACTGGGAATTTCTGAG-----------TTTTCACGTGTGGTTCCTCT---TATCCT---CCATCCCCTGTGGGTGCTACACAGAGGGCCAGAAGGTTTGCATTTA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 10883 104 - 64270 ACCCTCAGAAGCCTCCACTGGGAATTTCTGAG-----------TTTTCACGTGTGGTTCCTCT---TATCCT---CCATCCCCTGTGNGTGCCACACAGAGGGCCAGAAGGTTTGCATTTA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16057729 104 + 17838096 ACCCTCAGAAGCCTCCACTGGGAATTCCTGAG-----------TTTTCACGTGTGGTTCCTCT---TATCCT---CCATCCCCTGTGAGTGCCACACAGAGGGCCGGAAGGTTTGCATTTA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75032034 104 + 78773432 ACCCTCAGAAGCCTCCACTGGCAATTTCTGAG-----------TTTTCACATGTGGTTCCTCT---TATCCT---CCATCCCCTGTGGGTGCGACACAGAGGGCCAGAAGGTTTGCATTTA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 39422 104 - 95547 ACCCTCAGAAGCCTCCACTGGCAATTTCTGAG-----------TCTTCACATGTGGTTCCTCT---TATCCT---CCATCCCCTGTGGGTGCGACACAGAGGGCCAGAAGGTTTGCTTTTA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41283 97 + 225949 -----CAGAAGCCTCCACTGGGAACTTCTGAG-----------CTATAACATGTGGTTCCTCT---TATCCT---CCCTCCCCTGTGGGTGC--CACAGAGGGCCAGAAGGTTTGCATTTA i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 69 80 + 19765 -------------------GGAAATGTCCGTG-----------TTGTC-CACGTGTTCCCTGT---TATTAT-------TCCCCACGGGTGCCACATGGAAGGCCGGCGTGTGTGCGAGGA i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 22656 87 + 287808 -------------------AGAAATTTCTGCG-----------TTGTC-CACTTGTTATCCCT---TCTTATGACTTAATCCCTGCAGGTGCCACACACAAGACCAAACTGTTTGCACTTA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7345 96 + 15939 AGCCCTAGGAGCCCTCCC-GGCACTCTGTGTG-----------GC-CCACAGATCGCTCCTTTCTGTGTTCT---CTGCTC--------TGTCACGTGGAAG-CCGGAGCATCTGCCTTCA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118754626 99 + 121843856 --CCTCAGAACCACA--CCAGCACCTCCAGGG-----------TTTCCACAAGCCATTCCTTC---TAACCG--TTGATGCCCTGTGGGTTTCACACACTA--CCAGAGGGTTTTTGCTCG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4385461 90 + 7991924 GGCCTGAGAGCCCCAGCTCCGGACCCCTGGGA-----------TGTCCACATACTGTTC-------------------TGTCCCTTGGCTCATCCACAATAGGCCCGAGGATGAGATCTC- i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_6980 60851 90 + 61692 --------AGCCCCA----CGAGCCCCCGGGGGAGGGGGCTGTGACCTGCAGGATGCCC-------------------CTCCCTGCGGGTCTCACACAGAAGGCCACAGGAGGTGCAGTTG i ochPri2.scaffold_6980 C 0 C 0 s equCab2.chr11 58038370 23 - 61308211 ----TCAGCACTCCTCCCTGGGGCACG---------------------------------------------------------------------------------------------- i equCab2.chr11 C 0 C 0 s proCap1.scaffold_29042 11864 81 + 24616 ACCCCCAGAGCCTGG----GGGAGTTGCATCT-----------TTCCAACATGATGCCCCTTC---TGACCC-CTTATTCTCCTTCAGGCAGCA---------------------CCCACT i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 7413 76 + 20752 ATCCTCAGGACC-------------------------------CCCCAGGAT-----TTCTGC---TGGACA-AGCACAGCCCCGCGAGCAGCA-----GAGGCCAGCAGGCTTGCCCGCC i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 15012 486 + 41507 I e speTri1.scaffold_128901 3229 5 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e turTru1.scaffold_106006 124354 80 + 145505 I e felCat3.scaffold_206428 10124 226 + 132007 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e pteVam1.scaffold_11245 10593 295 + 48268 I e dipOrd1.scaffold_53224 4458 916 + 10229 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59433058 268 - 64418924 I e bosTau4.chr19 10855495 28 - 65312493 I e loxAfr3.scaffold_49 14427599 141 - 17734757 I a score=44041.000000 s hg19.chr17_gl000204_random 40895 60 + 81310 CTGGGTCCCCAAAGA----GGAGACCAGACTGGACCATGTT-----TGGCACAAGTGCTGACCAAGAA-C s panTro2.chr17 79471080 60 + 83384210 CTGGGTCCCCAAAGA----GGAGACCAGACTGGACCATGTT-----TGGCACAAGTGCTGACCAAGAA-T i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 10987 60 - 64270 CTGGGTCCCCATAGA----GGAGACCAGACTGGACCACATT-----TGGCACAAGNGCTGACCAAGAA-C i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16057833 60 + 17838096 CTGGGTCCCCAAAGG----GGAGAACAGACTGGACCACATT-----TGGCACAAGTGCTGACCAAGAA-C i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75032138 60 + 78773432 CTGGGTCCTCAAAGA----GGAGACCAGACGGGACCATGTT-----TGGCACAAGTGCTGACCAAGAA-C i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 39526 60 - 95547 CTGGGTCCTCAAAGA----GGAGACCAGACGGGACCACGTT-----TGGCACAAGTGCTGACCAAGAA-C i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41380 59 + 225949 CTGGGTCCCCAAAGA----GGAGACCAGACTGGACCAGGGT-----TGGCACCAATGCTGACCAAGAC-- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 149 59 + 19765 CTGGGGCCCCGAAGA----AGAGACCAGGTCGTGGCGGCGT-----TGGCACGAGTGCCGGCCAAGGC-- i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 22743 59 + 287808 TTGGGTCCCCAGAGA----AGAGACCAGATTAGAGCAGTGT-----TAGCATGAGT-TCAGCCAATAC-T i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7441 58 + 15939 --GTGTCCTCGAACC----GAAGACCAGACCAAACTCGTGT-----GGGCACGCGTACTGAACCAGAT-C i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118754725 52 + 121843856 CTGTGTCCCTGAAGA----AGACACCAGGCTCTATAA-CAT-----CAGCACATGTAATA------AT-- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4385551 56 + 7991924 CTGAGCACTTGAAAA----GGACACT--GCTGCAATA-TGC-----TGGTACATGTGGTAGCCGAGAG-- i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_6980 60941 60 + 61692 TTGCGTCCCCAAAGA----GGACATCAGACTGGATCAGGGC-----CAGCGCACGTGGTTGCAAAGGAC- i ochPri2.scaffold_6980 C 0 n 0 s pteVam1.scaffold_11245 10888 48 + 48268 CTTTGGTCCCAAAGAGTGCGGTGCCCAGACTGAGGTGCTGC-----CAG-GCAG---------------- i pteVam1.scaffold_11245 I 295 C 0 s proCap1.scaffold_29042 11945 58 + 24616 GTG---CCCCAAGGA----GGAGAGCAGCCCCGTACCAGCACCTT-GTGTCCAGCAGCGTGTCCCA---- i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 7489 49 + 20752 CTGCGTCCCCGGGG------------ACCCCAGACCCGACA-----ACGCCCACGTGTGCCCCCGG---- i dasNov2.scaffold_28617 C 0 C 0 s loxAfr3.scaffold_49 14427740 56 - 17734757 ------CCCCGAGGA----GGAGACCAGCCCAGCACAGGCTCGTTGGGGCCCAACAGTGTGTTCTG---- i loxAfr3.scaffold_49 I 141 C 0 s equCab2.chr11 58038393 23 - 61308211 ------CCCCAGA------GGTGAACAGTCAGAGG----------------------------------- i equCab2.chr11 C 0 C 0 e oryCun2.chrUn0958 15012 486 + 41507 I e speTri1.scaffold_128901 3229 5 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e turTru1.scaffold_106006 124354 80 + 145505 I e felCat3.scaffold_206428 10124 226 + 132007 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dipOrd1.scaffold_53224 4458 916 + 10229 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59433058 268 - 64418924 I e bosTau4.chr19 10855495 28 - 65312493 I a score=-25250.000000 s hg19.chr17_gl000204_random 40955 76 + 81310 GGAGCCCT---------------GAGGAC-----ACGCCCTCAGAAGACGCTGATCCC-CTCCCTGGGAT-----GACGCTCCCCATCCCACCCTTAGAGTA s panTro2.chr17 79471140 76 + 83384210 GGAGCCCT---------------GAGGAC-----ATGCCCTCAGAAGACGCTGATCCC-CTCCCTGGGAT-----GACGCTCCCCATCCCACCCTTAGAGTA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 11047 76 - 64270 GGAGCCCT---------------GAGGAC-----ACGCCCTCAGAAGACGCTGATCCC-CTCCCTGGGAT-----GACACTTCCCATCCCACCCTTAGAGTA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16057893 76 + 17838096 GGAGCCCT---------------GAGGAC-----ACATCCTCAGAAGACGCTGATCCC-CTCCCTGGGAT-----GACGCTCCCCATCCCACTCTTAGAGTA i ponAbe2.chr17_random C 0 I 926 s rheMac2.chr16 75032198 77 + 78773432 GGAGTCCT---------------CAGGAC-----ACACCCCCAGGAGACGCTGATCCCACTCCCTGGGAT-----GACGCTCCCCATCTCACCCTTGCAGTA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 39586 77 - 95547 GGAGTCCT---------------CAGGAC-----ACACCCCCAGGAGACGCTGATCCCACTCCCTGGGAT-----GACGCTCCCCATCTCACCCTTGCAGTA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41439 73 + 225949 --AGCCCT---------------GAGGAC-----ACACCCCCAGGAGCCGCTGATCCC-ACCCCT-GGAT-----GACGCTCCCCATCCCACCCTTGGGGTA i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 208 57 + 19765 -GGGTCCTGAGACTCCCACAAAGAAGGAC-----GGGCCCCCGG-AGACGCTGGTGCT-----------------GACACT--------------------- i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 22802 42 + 287808 -GAGTGCTAGTACTCAGGCA---AAGGAC-----AGGCCCCCAG-AGATGGT-------------------------------------------------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7499 60 + 15939 -AAGTCCT---------------GGGAGC-----TTTAGCC----AGGGGCAGGCCAC-----------------CACGCATCACCACCCTGCCTGGGAGCA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118754777 48 + 121843856 -ACATCCC---------------------------ACCCC--------------CTCC-------AGAAT-----AACAACTGCTACTGTTGTCTGGAGGTA i mm9.chr11 C 0 I 8 s cavPor3.scaffold_76 4385607 60 + 7991924 -TTGTCCT-----------------GGAG-----GAGCCCTGGCAAAGGACAGATTCC-------AAGATGTGCCAACAACTCTCCC------------ACA i cavPor3.scaffold_76 C 0 I 8 s pteVam1.scaffold_11245 10936 31 + 48268 ------------------------GGGGC-----GGG-----GGGAGGCGGTGCCTGC-----------------ATCACTC-------------------- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14427796 66 - 17734757 GGAGCCTT------------GGCGAGGGC-----ATGCCCCAAG-GGATGCTGATTGC-----------------GCCACCCC-CACATCACCCTTGTAGTA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 12003 62 + 24616 GGAGTCTC------------GGCAAGGGT-----GTGCCCCAA--AGACGCTGCTGGC-----------------ACCGCACC---CATCCTCTTTG-AATT i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 7538 71 + 20752 GGGCCCCG------------GGCAAAGGCAGTGAGTGTCCCCAG-GAGTGCTGGACCC-----------------GCCGCCCCCCACCCCACCTTTG-AGTG i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 15012 486 + 41507 I e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e turTru1.scaffold_106006 124354 80 + 145505 I e felCat3.scaffold_206428 10124 226 + 132007 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dipOrd1.scaffold_53224 4458 916 + 10229 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59433058 268 - 64418924 I e bosTau4.chr19 10855495 28 - 65312493 I e equCab2.chr11 58038416 0 - 61308211 C a score=-77096.000000 s hg19.chr17_gl000204_random 41031 36 + 81310 ACAG---CAGGAATGACCCCCACCCCCGCC------T-GGAGAGCC s gorGor1.Supercontig_0007361 11123 36 - 64270 ACAG---GAGGAATGACCCCCACCCCCGCC------T-GGAGAGCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79471216 36 + 83384210 ACAG---GAGGAATGACCCCCACCCCCGCC------T-GGAGAGCC i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75032275 36 + 78773432 ACAA---GATGAATGACCCCCACCCCCGCC------T-GGAGAGCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 39663 36 - 95547 ACAA---GATGAATGACCCCCACCCCCGCC------T-GGAGAGCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41512 35 + 225949 ACAG---AAGGAATGACCCCCA-CCCCACC------T-GGAGGGCC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 265 20 + 19765 -------------------CTGCCCCCACC------T-GGGGAGCC i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 22844 13 + 287808 --------------------------CACC------T-GGTGAGCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7559 22 + 15939 ------------------CCAGGCTCTGTC------TCAGGGCTCG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118754833 31 + 121843856 GAAGATAGAAACAGCACCCCCAAAAC---------------AAACA i mm9.chr11 I 8 C 0 s cavPor3.scaffold_76 4385675 35 + 7991924 GAGG---GACGGATGACTCCCAGTCCTG-C------T-GTAGAATC i cavPor3.scaffold_76 I 8 C 0 s pteVam1.scaffold_11245 10967 18 + 48268 ----------------CAGGG--CCCCGC---------GGAGGGG- i pteVam1.scaffold_11245 C 0 C 0 s felCat3.scaffold_206428 10350 25 + 132007 ------------AAAACAGTGGTGCCCAG---------GCTGAGGT i felCat3.scaffold_206428 I 226 C 0 s equCab2.chr11 58038416 14 - 61308211 -----------------------CCCCAT---------GGGGAACT i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14427862 24 - 17734757 ---------------ATGACAGTCCCAGCC------A-GATGAGCC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 12065 24 + 24616 ---------------ATGGCATTCCCAGGC------A-GGTGAGCC i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 7609 30 + 20752 ---------------ACGGTGCCCCCGGCCCAGGCGG-AGAGAGCC i dasNov2.scaffold_28617 C 0 I 510 e oryCun2.chrUn0958 15012 486 + 41507 I e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e turTru1.scaffold_106006 124354 80 + 145505 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dipOrd1.scaffold_53224 4458 916 + 10229 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59433058 268 - 64418924 I e bosTau4.chr19 10855495 28 - 65312493 I e ponAbe2.chr17_random 16057969 926 + 17838096 I a score=-86188.000000 s hg19.chr17_gl000204_random 41067 95 + 81310 ATCGGTATT-GAGAGAA-----A---CGAGCCACTTTCCAGGTGTGCCGAGGCTGACCATAATGG-GGCCACCAAGG---TGCAAG-----------------------------GTCAA-------GCTTGCCAGAAAGAAAC s gorGor1.Supercontig_0007361 11159 95 - 64270 ATCNGTATT-GAGAGAA-----A---GGAGCCACTTTCCAGGTGTGCCGAGGCTGACCATAATGG-GGCCACCAAGG---TGCAAG-----------------------------GTCAA-------GNTTGCCAGAAAGAAAC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79471252 95 + 83384210 ATCGGTATT-GAGAGAA-----A---CGAGCCACTTTCCAGGTGTGCCGAGGCTGACCATAATGG-GGCCACCAAGG---TGCAAG-----------------------------GTCAA-------GCTTGCCAGAAAGAAAC i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75032311 95 + 78773432 ATCGGCATT-GAGAGAA-----A---GGAGCCACTTTCCAGGTGTGCCGAGGCTGACCGTAATGG-GGCCACCAAGG---TGCAAG-----------------------------GTCAA-------GCTCACCAGAAAGAAAC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 39699 95 - 95547 ATGGGCATT-GAGAGAA-----A---GGAGCCACTTTCCAGGTGTGCCGAGGCTGACCGTAATGG-GGCCACCAAGG---TGCAAG-----------------------------GTCAA-------GCTCACCAGAAAGAAAC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41547 86 + 225949 ATCAGTATT-GAGAAAA-----A---GGAGCCACCTTCCA---------AGGCTGACCATGATGG-AGCCACCAAGG---CGCAAG-----------------------------GTCAA-------GCAGGCCACAAAGAAAC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 285 91 + 19765 A-CGGCACA-GGTAGAA-----A---GCACTCACCTCACAGGGGTGCCAAGGCCAGCACCA--GG-AGCCA-CAAGC---TGCAAA-----------------------------GTCAA-------ATCCACCAGAGAGAAGA i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 22857 93 + 287808 A-CTGCATA-GATAGAA-----A---GGGCCTGCCTTGCAGGGTGTGCAAGCCCAGCCCGA--GGTAGCCAGCAAGC---TGCAAA-----------------------------GTCAA-------TTTCACCAGAAAGAAGA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7581 44 + 15939 AGCAGTAGT-GACAG---------------------------------------------------CGCCACTGCGG---TGCAGG---------------------------CAGTCAC------------------AGAGAT i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118754864 74 + 121843856 AACAAAAAC-AGATAAACAAAGA---CTGCCCAAT----------------------------GC-AGCAACCAAGA---GGTAAA-----------------------------CTCAA----CTAGACCGTAAAGATCAAA- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4385710 69 + 7991924 ACCAGCACT-GAATAGA-----A---CCACCCTCT----------------------------------AGCCGCAA---GGCCAG-----------------------------TCCAAGCCTCTGGTCCACCAGAAAGAAAT i cavPor3.scaffold_76 C 0 C 0 s pteVam1.scaffold_11245 10985 30 + 48268 ---------------GC-----GAGAGGGTCCGCG----------------------------TG-----TTCCGGA---CGCAGG---------------------------------------------------------- i pteVam1.scaffold_11245 C 0 C 0 s felCat3.scaffold_206428 10375 73 + 132007 GCTGACGTG-GG--GGT-----G---GGGGCCGCA----------------------------CG-GCCTTCCTGGGTCCCACAGAGGACATGGGATGTGCTGCACGGTCCAG------------------------------- i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58038430 34 - 61308211 TCT------------GC-----G---GTATCCACG----------------------------CA-TCGCTCCAGGG---CACAGA---------------------------------------------------------- i equCab2.chr11 C 0 C 0 s proCap1.scaffold_29042 12089 93 + 24616 -ACTGTGTC-ATGGCAA-----G---GGCCCCACCCCATAAGTGTGCAGAGACTGACTGCCATGG-AGCTCCCA-GG---TGTAAA-----------------------------ATCAA-------GCTCTCTGGGAAGACGT i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14427886 94 - 17734757 -ACAGCATCGATGGAAA-----G---GGCCCCACCCCTTAGGTGTGCAGACACTGAGCACAATGG-ATCCTTCA-GG---TATAAA-----------------------------ATCAA-------GCTCTCTGGGAAGAGGC i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 15012 486 + 41507 I e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e turTru1.scaffold_106006 124354 80 + 145505 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dasNov2.scaffold_28617 7639 510 + 20752 I e dipOrd1.scaffold_53224 4458 916 + 10229 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59433058 268 - 64418924 I e bosTau4.chr19 10855495 28 - 65312493 I e ponAbe2.chr17_random 16057969 926 + 17838096 I a score=-83885.000000 s hg19.chr17_gl000204_random 41162 26 + 81310 ------CGGCACGC------AG--ACACGC-AGCTCCCTGG s gorGor1.Supercontig_0007361 11254 26 - 64270 ------CGGCACGC------AG--ACACGC-AGCTCCCTGG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79471347 26 + 83384210 ------CGGCACGC------AG--ACACGC-AGCTCCCTGG i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75032406 26 + 78773432 ------CGGCGCGC------AG--ACACAC-AGCTCCCTGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 39794 26 - 95547 ------CGGCGCGC------AG--ACACGC-AGCTCCCTGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41633 20 + 225949 ------TGGCGCAC------AG--ACACG-------CCTGG i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 376 17 + 19765 ------CAgcacat------gc--acgtgc-a--------- i micMur1.scaffold_15893 C 0 I 37 s otoGar1.scaffold_94362.1-287808 22950 20 + 287808 ------CGGCACAA------GCCAACACGC----TC----- i otoGar1.scaffold_94362.1-287808 C 0 I 2 s tupBel1.scaffold_124459.1-15939 7625 23 + 15939 ------CAGCACCC------AA--GCACCC-AGCTCCC--- i tupBel1.scaffold_124459.1-15939 C 0 I 2 s mm9.chr11 118754938 21 + 121843856 ---------CACGG------AG--ACATGTGGGCTCCC--- i mm9.chr11 C 0 I 2 s cavPor3.scaffold_76 4385779 21 + 7991924 ------TGGCACCA------TC--ACAT---AGATCCC--- i cavPor3.scaffold_76 C 0 I 2 s turTru1.scaffold_106006 124434 16 + 145505 ------AGACACAC------AC--GCCCCT----------- i turTru1.scaffold_106006 I 80 I 2 s bosTau4.chr19 10855523 16 - 65312493 ------GGAGATGT------GG--GCCCCT----------- i bosTau4.chr19 I 28 I 2 s equCab2.chr11 58038464 12 - 61308211 ---------TACAC-------G--GCTCCT----------- i equCab2.chr11 C 0 I 2 s felCat3.scaffold_206428 10448 21 + 132007 -------GGCACACAGGAGGGG--GCTTGC----------- i felCat3.scaffold_206428 C 0 I 2 s pteVam1.scaffold_11245 11015 10 + 48268 ---------TGCAC------GG--GCT-------------- i pteVam1.scaffold_11245 C 0 I 2 s proCap1.scaffold_29042 12182 22 + 24616 CAGTCACGAGAGAT------AA--GCTCCC----------- i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14427980 22 - 17734757 CGATAGACAGAGAC------AA--ACTCCT----------- i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 15012 486 + 41507 I e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dasNov2.scaffold_28617 7639 510 + 20752 I e dipOrd1.scaffold_53224 4458 916 + 10229 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59433058 268 - 64418924 I e ponAbe2.chr17_random 16057969 926 + 17838096 I a score=-5933.000000 s hg19.chr17_gl000204_random 41188 15 + 81310 --AG-AGCAGACTTG---GGT s gorGor1.Supercontig_0007361 11280 13 - 64270 --AG---CAGACTTG---GGT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79471373 13 + 83384210 --AG---CAGACTTG---GGT i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75032432 16 + 78773432 --AGCAGCAGACCTG---GGT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 39820 16 - 95547 --AGCAGCAGACTTG---GGT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41653 13 + 225949 --AG---CAGACTCA---GGT i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 430 13 + 19765 --AG---CAGGCCCG---GCA i micMur1.scaffold_15893 I 37 C 0 s otoGar1.scaffold_94362.1-287808 22972 13 + 287808 --GG---CAGGCCCA---GCA i otoGar1.scaffold_94362.1-287808 I 2 C 0 s tupBel1.scaffold_124459.1-15939 7650 13 + 15939 --AG---TAGCCCCA---GCT i tupBel1.scaffold_124459.1-15939 I 2 C 0 s mm9.chr11 118754961 12 + 121843856 --AG---CAGA-TCC---ATC i mm9.chr11 I 2 C 0 s cavPor3.scaffold_76 4385802 13 + 7991924 --AG---CAGGCCCC---ACT i cavPor3.scaffold_76 I 2 C 0 s turTru1.scaffold_106006 124452 10 + 145505 --AG---CAGGCCCA------ i turTru1.scaffold_106006 I 2 I 2 s bosTau4.chr19 10855541 10 - 65312493 --AG---CAGGCCCA------ i bosTau4.chr19 I 2 I 2 s equCab2.chr11 58038478 13 - 61308211 --AG---CAGGCCCTGTG--- i equCab2.chr11 I 2 I 1 s felCat3.scaffold_206428 10471 10 + 132007 --GA---TCAGCCCT------ i felCat3.scaffold_206428 I 2 I 1 s pteVam1.scaffold_11245 11027 11 + 48268 --AG---CAGGCCCCG----- i pteVam1.scaffold_11245 I 2 C 0 s proCap1.scaffold_29042 12204 15 + 24616 AGAG---GAGACACA---GGT i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14428002 15 - 17734757 GGAG---GAGACCGA---GGT i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 15012 486 + 41507 I e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e myoLuc1.scaffold_4816 5996 117 + 14340 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dasNov2.scaffold_28617 7639 510 + 20752 I e dipOrd1.scaffold_53224 4458 916 + 10229 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59433058 268 - 64418924 I e ponAbe2.chr17_random 16057969 926 + 17838096 I a score=-31377.000000 s hg19.chr17_gl000204_random 41203 27 + 81310 -CCC-CAGC-CCAGGAACTTGATCCTCCCA s gorGor1.Supercontig_0007361 11293 27 - 64270 -CCC-CAGC-CCAGGAACTCGATCCTCCCA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79471386 27 + 83384210 -CCC-CAGC-CCAGGAACTCGATCCTCCCA i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75032448 27 + 78773432 -CCC-CAGA-CCAGGAACCTGATCCCGCCA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 39836 27 - 95547 -CCC-CAGA-CCAGGAACCCGATCCCGCCA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41666 25 + 225949 -CCC-CAGC-CT-GGAACCCGATCCC-CGA i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 443 25 + 19765 -CCAGCAGC-CCAGGAACC--ATCCCCTG- i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 22985 27 + 287808 -CCAGCAGCTTTGGGAGGC--ATCTCCTGA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7663 24 + 15939 -GCC-CCGG-CCCAGACCCCG---CCCTGA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118754973 23 + 121843856 -CTG-CAGG-CCTGGAGATCGTTTCT---- i mm9.chr11 C 0 I 5 s cavPor3.scaffold_76 4385815 22 + 7991924 -CCC-CTGG-CCCAG-GACCCTTCCA---- i cavPor3.scaffold_76 C 0 C 0 s turTru1.scaffold_106006 124464 27 + 145505 -CAC-CCGC-ACTGGGACCCATGCCCCTAA i turTru1.scaffold_106006 I 2 C 0 s bosTau4.chr19 10855553 27 - 65312493 -CAC-CCGC-ACTGGGGCCCATGCCCCTAA i bosTau4.chr19 I 2 C 0 s equCab2.chr11 58038492 26 - 61308211 -TAC-CCAC-ACAGGAACCC-TTCCCCTCA i equCab2.chr11 I 1 C 0 s felCat3.scaffold_206428 10482 27 + 132007 -CAC-GCGC-ACAGAGGCCTGCTTGCCTCA i felCat3.scaffold_206428 I 1 C 0 s myoLuc1.scaffold_4816 6113 27 + 14340 -CTC-CGGC-ACAGGAACCCAGCCCCCTAA i myoLuc1.scaffold_4816 I 117 C 0 s pteVam1.scaffold_11245 11038 20 + 48268 -CCC-CGCC-CC----ACCCCACCCGC--- i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 12219 25 + 24616 CCAC-TCAC---AGAACATCACTCCTGCA- i proCap1.scaffold_29042 C 0 I 9 s loxAfr3.scaffold_49 14428017 27 - 17734757 CTAC-CTAC-GGAGGACTTCACTCCCCCG- i loxAfr3.scaffold_49 C 0 I 9 e oryCun2.chrUn0958 15012 486 + 41507 I e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dasNov2.scaffold_28617 7639 510 + 20752 I e dipOrd1.scaffold_53224 4458 916 + 10229 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59433058 268 - 64418924 I e ponAbe2.chr17_random 16057969 926 + 17838096 I a score=-139807.000000 s hg19.chr17_gl000204_random 41230 44 + 81310 ---CTGAGG--CCCAC-CGT------GCCCCAGCGAAGAACATGC---tc------------agtca---gcaa--- s gorGor1.Supercontig_0007361 11320 44 - 64270 ---CTGAGC--CCCAC-CGT------GCCCCAGCGAAGAACATGC---tc------------actca---gcaa--- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79471413 44 + 83384210 ---CTGAGC--CCCAC-CGT------GCCCCAGCGAAGAACATGC---tc------------agtca---gcaa--- i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75032475 44 + 78773432 ---CTGAGC--CCCAC-AGC------GCCCCAGCAAAGAACATGC---tc------------agtca---gcaa--- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 39863 44 - 95547 ---CTGAGC--CCCAC-AGC------GCCCCAGCGAAGAACATGC---tc------------agtca---gcaa--- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41691 44 + 225949 ---CTGAGC--CCCAC-AGT------GCCCCAGCAAAGAACATGC---tc------------agtca---gcaa--- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 468 40 + 19765 ------AGC--CTCGC-GCC------GCCCGAGC-CCGAGCCCGC---CC------------ACCCA---GCCT--- i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 23012 36 + 287808 ---CCAAGC--TTCGC-GCC-------------C-CCTAGCCCAC---TC------------ACCCA---GCCT--- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7687 39 + 15939 ---TAGAGC--CTCGC-TGCTGTGGAGCCGCAGC--------------TC------------ACCCC---GCGA--- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s cavPor3.scaffold_76 4385837 31 + 7991924 ----TAAG---------CCT------GGCACGGCCCAGCCCAGAG---CC---------------------CAG--- i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_53224 5374 44 + 10229 ---CTGGAA--CCCAC-CCT------GCCCAACCCCAGAGCCCAC---TC------------ACTCA---GCCA--- i dipOrd1.scaffold_53224 I 916 C 0 s mm9.chr11 118755001 50 + 121843856 ---CTAGG---------CCT------CCCTAACCCTAACCCTAAC---TCTGAGTGTCCCCAACTTG---CTCA--- i mm9.chr11 I 5 C 0 s turTru1.scaffold_106006 124491 27 + 145505 ---CTGAGC--CCC---CAG------Cca---------------c---tc------------accca---gcaa--- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10855580 15 - 65312493 ---CTGAGC--C---------------------------------------------------TCCA---GCAA--- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58038518 35 - 61308211 ---CTGAGT--GTC---CCA------CCCCGAGC----------t---cc------------aaccactcgcaa--- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 10509 34 + 132007 ---CCGGGC--CTC---CCG------TCCCAAGC---------GC---CC------------AGCCATCCAC----- i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_4816 6140 28 + 14340 ---CCAAGC--CCC---CCA------GCTC--------------C---tc------------accca---gcaa--- i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 11058 35 + 48268 ---ACGGGCCGCCC---CGA------GCCCTAGT---------GC---TC------------ACCCG---GCAA--- i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 12253 54 + 24616 ATGAAGAGC--CCCCTGCCA------CCTCAAATCCGCACCCCATGCACT------------GTCCA---tcaatag i proCap1.scaffold_29042 I 9 C 0 s loxAfr3.scaffold_49 14428053 51 - 17734757 ATAGAGAGT--CTTCTGCCT------CCCTGAGCCCGCACCCTGT---CC------------Gtccc---tcaacaa i loxAfr3.scaffold_49 I 9 C 0 e oryCun2.chrUn0958 15012 486 + 41507 I e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dasNov2.scaffold_28617 7639 510 + 20752 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59433058 268 - 64418924 I e ponAbe2.chr17_random 16057969 926 + 17838096 I a score=56914.000000 s hg19.chr17_gl000204_random 41274 25 + 81310 ccg--ctcgctgggcacctgctttg-----------tg s gorGor1.Supercontig_0007361 11364 25 - 64270 ccg--ctcgctgggnacctgctttg-----------tg i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79471457 25 + 83384210 ccg--ctcgctgggcacctgctttg-----------tg i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75032519 25 + 78773432 ccg--ctcgctgggcacctgctttg-----------tg i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 39907 25 - 95547 ccg--ctcgctgggcacctgctttg-----------tg i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41735 25 + 225949 ctg--ctcacagcgcacctgctttg-----------tg i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 508 24 + 19765 CTG--CGTGCCGAGCACTGAC-CGG-----------GT i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 23048 24 + 287808 CTG--TGTCCTGACAACCTGC-GGG-----------GG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7726 20 + 15939 CCG--TGCACGGAGC-----CTCTG-----------GG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s cavPor3.scaffold_76 4385868 25 + 7991924 CAG--CACAAtgagcacctactgtg-----------tg i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_53224 5418 36 + 10229 CTG--TGCACTGAGCACCTGGCAAGCTCCTGTTCCATG i dipOrd1.scaffold_53224 C 0 C 0 s mm9.chr11 118755051 28 + 121843856 CTT--GGCATTGACCATGTACAGAGCAC--------TA i mm9.chr11 C 0 C 0 s turTru1.scaffold_106006 124518 25 + 145505 gtg--tgtcttgagcacctactgtg-----------tg i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10855595 24 - 65312493 GTG--CACGCTGAGCACCTACTGTG-----------T- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58038553 25 - 61308211 gtg--cctattgtgtgcctactgtg-----------tg i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 10543 14 + 132007 -----CCTG--------CAAGTGTG-----------TG i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_4816 6168 25 + 14340 gtg--cggactgagcacctactgtg-----------tg i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 11093 22 + 48268 GCA--GGTACTGAGCACCCAC---G-----------AG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14428104 25 - 17734757 cta--tgtactgagcacccatggtg-----------tg i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 12307 25 + 24616 cta--ggcactgagcacccacggtg-----------tg i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 8149 27 + 20752 CCACCCGCAGCAGGCTCCCGCGACG-----------TG i dasNov2.scaffold_28617 I 510 C 0 e oryCun2.chrUn0958 15012 486 + 41507 I e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59433058 268 - 64418924 I e ponAbe2.chr17_random 16057969 926 + 17838096 I a score=-181925.000000 s hg19.chr17_gl000204_random 41299 67 + 81310 ccaggcactgggc--------taagcactgagaataccagatgaagacgagacagtgca-ccag-gtccACACG--C--TT s gorGor1.Supercontig_0007361 11389 67 - 64270 ccaggcactgggc--------taagcactgagaataccanatgaagatgagacagtgca-ccag-gtccACATG--C--TT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79471482 67 + 83384210 ccaggcactgggc--------taagcactgagaataccagatgaagttgagacagtgca-ccag-gtccACACG--C--TT i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75032544 67 + 78773432 ccaggcactgggc--------taagcactgagaataccagatgaagacaagacagtgca-ccag-gtccACATG--C--TT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 39932 67 - 95547 ccaggcactgggc--------taagcactgagaataccagatgaagacaagacagtgca-ccag-gtccACATG--C--TT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41760 67 + 225949 ccacgcactggct--------tacacactgaggaaaccaggtgaagatgagatagtgca-ccag-gtccACACG--C--TT i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 532 67 + 19765 GCGGGCACGGCGT--------TCGGCGCCGAGAACACAAGAGGAAGACGAGACC-CGCACCCAG-CCCCACACG--T--TC i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 23072 75 + 287808 CCAGGCACCGTGTCACTTTTGTGAACCCTGAGAACAC-AGATGAAGGTGAGACCATGTGCCCAG-CCCTACATG--T--TT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7746 40 + 15939 GCAGGT-----GC--------CAAGCCCTGAAAGCAC-----------------------GCAG-AGCCGCACG--C--CT i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118755079 48 + 121843856 CCAGGC------C--------CAAATACAAGA---------TGAATGCAGGACTACACA-CATT--AATTCAAG------- i mm9.chr11 C 0 I 9 s dipOrd1.scaffold_53224 5454 55 + 10229 CCAGGTGCTCAGC--------TAAGTACTAGG----------GACAGGAGGGTCAGACC-AACTGGAGCACACG------- i dipOrd1.scaffold_53224 C 0 I 176 s cavPor3.scaffold_76 4385893 46 + 7991924 ccaggcccccagt--------ccagtgctga-----------gacagcACGCATCTCCC-CACT---------------GT i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 15498 59 + 41507 CCATGTGCCGGGC--------TCCGCACTGAG-----CAGACGATGCCGAGACCACGCA-CGGC-GTCCCCACG------- i oryCun2.chrUn0958 I 486 C 0 s turTru1.scaffold_106006 124543 45 + 145505 -------------------------ccctgagaatacaagaggaagacaagaca--GTA-T----ATGTGTATGT----TT i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10855619 33 - 65312493 --------------------------CTTGAGAAT-----------ACAAGACA--GTA-T----ATGTATTCGT----TT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58038578 68 - 61308211 ccaggcactgtca--------tgagccccaagaatacacgacgtagacaagagaatgca-c----atgtattcataggttt i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 10557 37 + 132007 ----------------------------------GACACGATGAAGACAGGA-CGTGTG-C----GTCTACTCGTGT---- i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_4816 6193 60 + 14340 ca-ggtcactgcg--------tcagccctgagaacacggGACAAGGAC---ACT--GCA-C----ATGTGTGTGTGT--TT i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 11115 66 + 48268 CATGAGCATAGGC--------TTAAGCCCGAGAACGCGCGATGGAGACCAGACCAGGCA-C----GTGTGCGCACGT--TT i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14428129 53 - 17734757 ccaggcactgtgc--------aaggcaccgggtataccagatga-gccaagacaATGCA-CTA------------------ i loxAfr3.scaffold_49 C 0 I 350 s proCap1.scaffold_29042 12332 67 + 24616 ccagacactgtgc--------aaggcaccaagtacaccagatga-ggcaagacaACGCG-CTTAGATTCACAAG----TTT i proCap1.scaffold_29042 C 0 I 480 s dasNov2.scaffold_28617 8176 48 + 20752 CCAG-------------------------GAGAATTCCGCAAGG-AACAAGACG--GCA-CCTGCGTCCATATG----TCT i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59433058 268 - 64418924 I e ponAbe2.chr17_random 16057969 926 + 17838096 I a score=5518.000000 s hg19.chr17_gl000204_random 41366 47 + 81310 TAGGA--TTAAATCACACTGACGGTTCTGCCGT----CTTTCT--TTTCCACGAA- s gorGor1.Supercontig_0007361 11456 47 - 64270 TAGGA--TTAAATCACCCTGACGGTTCTGCCGT----CTTTCT--TTTCCACGAA- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79471549 47 + 83384210 TAGGA--TTAAATCACACTGACGGTTCTGCCGT----CTTTCT--TTTCCACGAA- i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75032611 47 + 78773432 TAGGA--TTAAATCACACTGACAGCTCTGCCAT----CTTTCC--TTTCCACTAA- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 39999 47 - 95547 TAGGA--TTAAATCACACTGACAGCTCTGCCAT----CTTTCC--TTTCCACTAA- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41827 47 + 225949 TAGGA--TTAAATCGCACTGACGGTCCTGCCAG----CTTTCT--TTTCCACCAC- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 599 48 + 19765 AAAGA--TTAAAACACAC-GACGGTTCCGCAAT----CTCCCCCTTTTCAGTTAA- i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 23147 47 + 287808 AAAGA--TTAAAGTGTAT-GATGCTTCTGCAAT----CTTCCCC-TTGCGGTTAA- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7786 42 + 15939 GTGAG--TCACAGCACACGGCCTGGTCTGCAGT----C-------CTCCCGTCAC- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118755136 36 + 121843856 -------TTAAAGCA-------TGGAGACCACTAAGGCTTCCC--TTT---CATA- i mm9.chr11 I 9 C 0 s cavPor3.scaffold_76 4385939 49 + 7991924 CTGGACGTTAAGACATCCTGGCTGGCGGGCACT----CTTCCC--TTTGCAAGTA- i cavPor3.scaffold_76 C 0 C 0 s turTru1.scaffold_106006 124588 47 + 145505 CCATA--CTAAAGTACACAGATTGTTCTGCCGA----CTTCCC--TTTCCAATTA- i turTru1.scaffold_106006 C 0 I 1 s bosTau4.chr19 10855652 47 - 65312493 CCATA--TTAAAGGACACAGATTGTTCTGCCGA----CTTCCG--TTTCCAGTTA- i bosTau4.chr19 C 0 I 1 s equCab2.chr11 58038646 47 - 61308211 ccata--ttaACATACACAGATTGTTCTGCTGT----CTTCCT--TTCCCAATCA- i equCab2.chr11 C 0 I 1 s felCat3.scaffold_206428 10594 28 + 132007 -------------TACAACGACTGTTC------------CCCT--GTCCCGGCTG- i felCat3.scaffold_206428 C 0 I 1 s myoLuc1.scaffold_4816 6253 33 + 14340 CCATA--TTAAAATACCCAGACTGCTCTGCG--------GCCT------------- i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 11181 28 + 48268 CCCTG--TTTCAGCTC----ACTGTTCCGC---------CTCT------------- i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 12879 40 + 24616 ----A--TTAAAGCAGACA----GTTCCGAAGC----CTTGCT--TTTTCAGCTGA i proCap1.scaffold_29042 I 480 C 0 s loxAfr3.scaffold_49 14428532 46 - 17734757 AAATA--TTAAAACACATA--TTGTTCTGAAGC----CTTCCT--TTTTCAGTAGA i loxAfr3.scaffold_49 I 350 C 0 s dasNov2.scaffold_28617 8224 48 + 20752 AAACA--GGAAAACATGCATATTGTTCGGAAGC----CTTGCT--TTCCCAGCCGA i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 15557 0 + 41507 C e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dipOrd1.scaffold_53224 5509 176 + 10229 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59433058 268 - 64418924 I e ponAbe2.chr17_random 16057969 926 + 17838096 I a score=202289.000000 s hg19.chr17_gl000204_random 41413 56 + 81310 AATG-GACTGTG---GGTC--TCTTTCCACATCCATGGAAAGCAGCTGCCTAAAACCC--AC--CG s gorGor1.Supercontig_0007361 11503 56 - 64270 AATG-GACTGTG---GATC--TCTTTCCACATCCATGGAAAGCAGCTACCTAAAACCC--AC--CG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79471596 56 + 83384210 AATG-GACTGTG---GATC--TCTTTCCACATCCATGGAAAGCAGCTGCCTAAAACCC--AC--CG i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75032658 56 + 78773432 AATG-GACTGTG---GATC--TCTTTCCACATCCATGAAAAGCAGCTGCCTAAAACCC--AC--CG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 40046 56 - 95547 AATG-GACTGTG---GATC--TCTTTCCACATCCATGAAAAGCAGCTGCCTAAAACCC--AC--CG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41874 53 + 225949 AATG-GACTGTG---G-------CTTCCACATCCGTGGACAGCAGCTGCTTGAAACCC--ACTGTG i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 647 56 + 19765 AGCA-TATCGCG---GGGC--TCCCTGCACGCCCCTCCACGGCAGCTGCATACGGCCC--GC--TG i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 23194 56 + 287808 AACG-TATTGTG---GGTC--TCCTTCCACACCCCTCCAGGGCAGCTGCACACAGCCC--AC--TG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7828 45 + 15939 GGCG-GAAGGCGCCCGGAT--GCCTCGCACGTCCGTCTAAAGCAGC------------------CT i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118755172 45 + 121843856 AACG-T----------------CCTTCCACAGCTATCTATAGAAGCTGCACTAAGCCC--AC--CG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4385988 54 + 7991924 AACG-TGTTGCA---GA-C--ATCTTCCACACCCACCCGCGGCAGCTGT-CAGAACCC--AC--TG i cavPor3.scaffold_76 C 0 I 94 s oryCun2.chrUn0958 15557 36 + 41507 -----------------------CTTCCGCATC--CCCGAGGCGACTGC-CCAGCCAC--AG--CA i oryCun2.chrUn0958 C 0 I 7 s pteVam1.scaffold_11245 11209 41 + 48268 ---------------------TCCTTCCACGTCCAGCTGGAACAGTCGCACGAAAGCC--AC--CG i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 6286 41 + 14340 ---------------------TCCCTCCTCGCCCGCCTGAAACGGCTGCGCAGAGCCC--AC--CG i myoLuc1.scaffold_4816 C 0 C 0 s canFam2.chr9 59433326 58 - 64418924 AACA-GACTGCG---GATACATCCTTCCATGCTCGTCTACCGCAACGGCACGACACCC--AC--CG i canFam2.chr9 I 268 C 0 s felCat3.scaffold_206428 10623 58 + 132007 GACG-GGCTGTG---GATACACCCTTCCCTACTCGTCTAAAGCAGCTGCCTAAAACCC--AC--CG i felCat3.scaffold_206428 I 1 C 0 s equCab2.chr11 58038694 55 - 61308211 AACG-CATTGTG---GAT--AGCCTTCCACATCCGTC-AAAACAGCTGCACAAAACCC--AC--TG i equCab2.chr11 I 1 C 0 s bosTau4.chr19 10855700 55 - 65312493 ACTG-CACTGTG---GCTT--TCTTTCCACA-TCATCTAAACCAGCTGCATAAAACTC--AC--TG i bosTau4.chr19 I 1 C 0 s turTru1.scaffold_106006 124636 55 + 145505 ACTG-TATTGCG---GATT--TCCTTCCACA-TCATCTAAAACAGCTGCATAAAACCC--AC--TA i turTru1.scaffold_106006 I 1 C 0 s proCap1.scaffold_29042 12919 56 + 24616 AACA-TACTGTG---CCCC--TCCCTCCACATCTGTCTATGGGGTCCGCATCTGACCT--GC--TG i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14428578 55 - 17734757 AATG-TATTGTG---GCTG--TCCTTCCATACCCATCCAACGCTGCCACACCAGACC---GC--TA i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 8272 59 + 20752 AATGTTTTTGTG---GCTC--CCCTTCCAGGGCCATCTAACTCAGCTGCTTAGAACACAGGC--TA i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dipOrd1.scaffold_53224 5509 176 + 10229 I e monDom5.chr2 304528203 3081 - 541556283 I e ponAbe2.chr17_random 16057969 926 + 17838096 I a score=-104529.000000 s hg19.chr17_gl000204_random 41469 80 + 81310 TGTGTATG--------AATAGGCCATTCT----CTC-TTGAACGC--TTTTAACCAATCCCCTGCTGCAG---GG-AGTGTGT--TAGCAGCGG--GGAGACC s gorGor1.Supercontig_0007361 11559 80 - 64270 TGTGTATG--------AATAGGCCATTCT----CTC-TTGAACGC--TTTTAACCAATCCCCTGCTGCAG---GG-AGTGTGT--TAGCAGCGG--GGAGACC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79471652 80 + 83384210 TGTGTATG--------AATATGCCATTCT----CTC-TTGAACGC--TTTTAACCAATCCCCTGCTGCAG---GG-AGTGTGT--TAGCAGCGG--GGAGACC i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75032714 80 + 78773432 TGTGTATG--------AATAGGCCATTCT----CTC-TTTAACGC--TTTTAACCAATCCCCGGCTGCAG---GG-AGTGTGT--TAGCAGCGG--GGAGACC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 40102 80 - 95547 TGTGTATG--------AATAGGCCATTCT----CTC-TTTAACGC--TTTTAACCAATCCCCGGCTGCAG---GG-AGTGTGT--CAGCAGCGG--GGAGACC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 41927 80 + 225949 TGTGTGTG--------AATAGTTCATTCC----CTC-CTTACCGC--TTCAAACCAATCTCCTGCTGCAT---GG-AGCGTGT--CAGCAGTGG--GGACACC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 703 79 + 19765 CGTGCACA--------GATAGACGGTTCT----TTC-TTTAACGC--TTCCGACCAATCCC---CTGCCG---CA-TCCGTGCGGCAGGGGCGG--GAGGACC i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 23250 78 + 287808 TAAGGATA--------AACAGACCGTTCT----TTC-TTTAACGC--TTTGTACCAACCCC-TACTGCAG---GG-AACGTGT--CAGCGGCAG--G-GGACC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7873 77 + 15939 TACGTGTG--------AACAGACCGCGCG----TTC-TCCGACAC--GCTGACCCACGCCCCTACTGCAG---AG-A--GAGC--GAGCAGCGG--G-CCACC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118755217 71 + 121843856 ----------------TACATACGAGGCCAGCATTC-TGCCATAC--TT----TGAACCCCACCCTATGG---TG-AACATAA--TC-AAGCGG--ACAGACC i mm9.chr11 C 0 I 2 s oryCun2.chrUn0958 15600 72 + 41507 -GTGGACGGACCACTCTACCTGCCACGCC------C-TGCCACAC--GTGGACTGGCCACCGTCCTCC-----------------TC-CAG-GG--CCAGACC i oryCun2.chrUn0958 I 7 I 3 s pteVam1.scaffold_11245 11250 78 + 48268 ----TGCG--------AGAGGACCAACCC----CTC-TCTAAGGG--TCCTAACCAGTCCCCTGCTGCGGGAAGG-GGCGGCG--C--TGGCGGCCGGGGAC- i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 6327 60 + 14340 ----TCTG--------AACAGCCCGGTCT------------------TTTTGACCCGCCCCCTCCCCCAG---GG-GGCGGGG------GGTGG--GGGGGC- i myoLuc1.scaffold_4816 C 0 C 0 s canFam2.chr9 59433384 49 - 64418924 ----TCTG--------GGTAG--------------------------------ACCATCCCCTCGTGCA----GG-GGCTTCT--CAGCAGTGG--GCGGCC- i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 10681 49 + 132007 ----TGTG--------CCCAG--------------------------------CCCACCCCTTTCTGCA----GG-GGTCTGT--TAGCAGTGG--GGGGAC- i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58038749 75 - 61308211 ----TTTG--------AATAGACGATTCT----TTCTTTTAACGG--TTTTAACCAATCCCCTCCCACAG---GG-GGTTTGT--CGGCAGTGG--G-GACC- i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10855755 74 - 65312493 ----TTTG--------AATAAACCATTCT----TTC---TAATCGTTTTTTACACAGT-CCCCGCTACA----GGAGGTTTGT--CAGCAGTAG--GAGACC- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 124691 74 + 145505 ----TTTG--------AATAAACCATTCT----TTC---TAATCGTTTTTTAAACAATCCCCCACTACA----GG-GGTCTGT--CAGCAGCGG--GAGACC- i turTru1.scaffold_106006 C 0 C 0 s proCap1.scaffold_29042 12975 75 + 24616 ------------TGACAATAGACCGTTA----TCAG-TGTAAAGG--TTTCGGCCAAT-CCCTGCTGCAG---GG-AAAGGGC--TAGCAGTGG--GGAGCTC i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14428633 75 - 17734757 ------------GGTGAATAGACCGTTA----TTTC-TTTAAAGG--TTTTAGCCAAT-CCTTACTGCAG---GG-AAATCAC--TAGCAGTGG--GGGACCC i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 8331 41 + 20752 ------------CG--AATAGACCATCG----TTTC-CTTAAGAG--TTTTAG---------------------------------------GG--GCGACCT i dasNov2.scaffold_28617 C 0 C 0 s echTel1.scaffold_194555 762 59 + 11139 --------------------------------TTTC-CTAAGAGG--GTTCAGCCAGTCCCCTCCTGCAG---GG-ACCT-GC--TGGCAGTGA--GGGAGCT i echTel1.scaffold_194555 N 0 C 0 e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dipOrd1.scaffold_53224 5509 176 + 10229 I e monDom5.chr2 304528203 3081 - 541556283 I e cavPor3.scaffold_76 4386042 94 + 7991924 I e ponAbe2.chr17_random 16057969 926 + 17838096 I a score=61643.000000 s hg19.chr17_gl000204_random 41549 30 + 81310 TGTGGGA----------AGTGGC-ATGCCAGCCGCGCAGAG s panTro2.chr17 79471732 30 + 83384210 TGTGGGA----------AGTGGC-ATGCCAGCCGCGCAGAG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 11639 30 - 64270 TGTGGGA----------AGTGGC-ATGCCAGCCGCGCAGAG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16058895 30 + 17838096 TGTGGGA----------AGTGGC-GTGCCAGCCGCGCAGAG i ponAbe2.chr17_random I 926 C 0 s rheMac2.chr16 75032794 30 + 78773432 TGTGGGA----------AGTGGC-ATGCCAGCCGCGCAGAG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 40182 30 - 95547 TGTGGGA----------AGTGGC-ATGCCAGCCGCGCAGAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42007 30 + 225949 TGTGGGA----------GGTGGT-GTGCCAGCCGCGCAGAG i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 782 30 + 19765 GCTGCAG----------AGCGCT-GCGCGGACGGCGCCGTG i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 23328 30 + 287808 TCTACAA----------CCTGGC-GTGCCCACGGCACGGTG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7950 29 + 15939 -TTCGAC----------AGGCGT-GTGCCAGCCGCGTGGCA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118755290 30 + 121843856 TGTGGGA----------GATAGT-GTGCCAACCAGACAGTG i mm9.chr11 I 2 C 0 s oryCun2.chrUn0958 15675 40 + 41507 CGTGGGATGCCCCTGGGAAGGGT-GTGCCGACCGGGCAGCG i oryCun2.chrUn0958 I 3 I 1 s pteVam1.scaffold_11245 11328 23 + 48268 TCTGGGG----------TGGTGT-GTG-------GCCGGGG i pteVam1.scaffold_11245 C 0 I 18 s myoLuc1.scaffold_4816 6387 25 + 14340 TGTGA-------------GGTGT-GTGCCAGC--GCCGGCG i myoLuc1.scaffold_4816 C 0 I 17 s canFam2.chr9 59433433 30 - 64418924 TAGGAGA----------GGCGGC-GTGCCCACCACACGGCG i canFam2.chr9 C 0 I 17 s felCat3.scaffold_206428 10730 30 + 132007 TGGGAGA----------GGCAGT-GTGCCCACCGTGCAGCG i felCat3.scaffold_206428 C 0 I 17 s equCab2.chr11 58038824 30 - 61308211 TTGGAGA----------GGTGGC-GTGCCAATCGGGCAGCG i equCab2.chr11 C 0 I 17 s bosTau4.chr19 10855829 11 - 65312493 TTTGAGA------------------------------GATG i bosTau4.chr19 C 0 I 17 s turTru1.scaffold_106006 124765 11 + 145505 TTTGAGA------------------------------GCTG i turTru1.scaffold_106006 C 0 I 17 s loxAfr3.scaffold_49 14428708 29 - 17734757 --TGGAA----------GAGCCATATGCCCAGCATGCAGTG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 13050 28 + 24616 ---AGAA----------GAGCGGCATGCCCAGCGCACGGAG i proCap1.scaffold_29042 C 0 C 0 s echTel1.scaffold_194555 821 28 + 11139 --TGGAA----------GGGAGG-ATTCCCAGTGTGTGGTG i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 8372 28 + 20752 --TGGGA----------AATTTT-ATTCCGAGCCTGTGGTG i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e dipOrd1.scaffold_53224 5509 176 + 10229 I e monDom5.chr2 304528203 3081 - 541556283 I e cavPor3.scaffold_76 4386042 94 + 7991924 I a score=166759.000000 s hg19.chr17_gl000204_random 41579 29 + 81310 ---------------------GGGAGGA-CGGACCTGGCAT--CTCCCTCTAA s panTro2.chr17 79471762 29 + 83384210 ---------------------GGGAGGA-CGGACCTGGCGT--CTCCCTCTAA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 11669 29 - 64270 ---------------------GGGAGGA-CGGACCTGGCGT--CTCCCTCTAA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16058925 29 + 17838096 ---------------------GGGAGGA-CGGACCTGGCAC--CTCCCTCTAA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75032824 29 + 78773432 ---------------------GGGAGGA-CGGACCTGGCGC--CTCCCTCTAA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 40212 29 - 95547 ---------------------GGGAGGA-CGGACCTGGCGC--CTCCCTCTAA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42037 29 + 225949 ---------------------GGGAGGA-TGGACCTGGCGC--CTCACTCAAA i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 812 29 + 19765 ---------------------GGGAGGA-CGGGCCTGGCGC--CTCACTCCGC i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 23358 29 + 287808 ---------------------GGGAGGA-CGGGCCTGGCGC--CTCACTCTGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 7979 29 + 15939 ---------------------GGAAGGC-GGGGCCTGGCGC--TCCACTCCAA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118755320 9 + 121843856 -----------------------AAGGC---------------------ACGG i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 5685 28 + 10229 ---------------------GGAAAGC-T-GGGTTAGCGC--TTCCCTACGA i dipOrd1.scaffold_53224 I 176 C 0 s oryCun2.chrUn0958 15716 31 + 41507 ---------------------GGAAGGA-TAGGGCTGGCACGGGCACCTCCAC i oryCun2.chrUn0958 I 1 C 0 s pteVam1.scaffold_11245 11369 29 + 48268 ---------------------GGAAGCA-GCGACCGGGCGC--TGTGCTCCGA i pteVam1.scaffold_11245 I 18 C 0 s myoLuc1.scaffold_4816 6429 29 + 14340 ---------------------GGGAGGA-CGGCCCTGGCAC--CGAGCTCTGC i myoLuc1.scaffold_4816 I 17 C 0 s canFam2.chr9 59433480 28 - 64418924 ---------------------GGCGGGA-TGGG-CTGGCAC--TTCACTCTGC i canFam2.chr9 I 17 C 0 s felCat3.scaffold_206428 10777 28 + 132007 ---------------------GGCGGGA-CAGG-CTGGCAC--TTCACTCTGC i felCat3.scaffold_206428 I 17 C 0 s equCab2.chr11 58038871 29 - 61308211 ---------------------GGAAGGA-TGGGCCTGGCGC--TTCACTCGAA i equCab2.chr11 I 17 C 0 s bosTau4.chr19 10855857 29 - 65312493 ---------------------AGTAAGG-ATGGTCTGGCGC--TTCCCTCTGT i bosTau4.chr19 I 17 C 0 s turTru1.scaffold_106006 124793 29 + 145505 ---------------------GGTAAGG-ATGGCCTGGCAC--TTTCCTCTGT i turTru1.scaffold_106006 I 17 C 0 s loxAfr3.scaffold_49 14428737 47 - 17734757 GGGAGAGGGCAGATGCG----GGGAAGGATGGGTCTGGCGC--TTCACTCTAT i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 13078 46 + 24616 GGGGCAGGGCAAACGCG----GGAGCAG-CGGGTCAGGCAC--CTCACTCGAC i proCap1.scaffold_29042 C 0 C 0 s echTel1.scaffold_194555 849 51 + 11139 GGCAGAGGACAGACAAGACAAGAAAATGATGGGTCTGGTGC--TTCACTCTCA i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 8400 45 + 20752 GGGAGAAGACAGGGGAT----GGAAGGG-GGGGCTGGCCAC--ATCCCACGA- i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e eriEur1.scaffold_290756 1498 1154 - 7602 I e monDom5.chr2 304528203 3081 - 541556283 I e cavPor3.scaffold_76 4386042 94 + 7991924 I a score=722871.000000 s hg19.chr17_gl000204_random 41608 65 + 81310 GCCAGCCGCCAAGTCACGAGGGG-CTC----CTATGCATTCCAAAAA-----CCCTCCTAGAGGAAGAGCAAGGT s panTro2.chr17 79471791 65 + 83384210 GCCGGCCGCCAAGTCACGAGGGG-CTC----CTATGCATTCCAAAAA-----CCCTCCTAGAGGAAGAGCAAGGT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 11698 65 - 64270 GCCGGCCGCCAAGTCACGAGGGG-CTC----CTATGCATTCCAAAAA-----CCCTCCTAGAGGAAGAGCAAGGT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16058954 65 + 17838096 GCCGGCCGCCAAGTCACGAGGGG-CTC----CTATGCATTCCAAAAA-----CCCTCCTAGAGGAAGAGCAAGGT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75032853 65 + 78773432 GCCGGCCGCCAAGTCACGAGGGG-CTC----CTATGCTTTCCAAAAA-----CCCTCCTAGAGGAAGAGCAAGGT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 40241 65 - 95547 GCCGGCCGCCAAGTCACGAGGGG-CTC----CTATGCTTTCCAAAAA-----CCCTCCTAGAGGAAGAGCAAGGT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42066 65 + 225949 GCCGGCCGCCAAGTCACGAGGGG-CTC----CTGTGCATTCCAAAAA-----CCCTCCTAGAGGAAGAGCAAGGT i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 841 52 + 19765 GCCGGCCGCCAAGTCACGAGG------------------TCCAAAAG-----CTCTCCTAGAGGGAGAGCAAGGT i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 23387 65 + 287808 GCTGGCCGCCAAGTCACGAGGGG-CTC----TTACGCCTTCCAAAAA-----CTCTCCTAGAGGGAGAGCAAGGT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 8008 49 + 15939 GCCTGCCGCCAAGTCACAAGGGG---------------------AAA-----GTCCCCTGGAGGGAGAGTGAGGG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118755329 62 + 121843856 GCCGGTCCCTCAGT---GCACAC-ATG----CTGTGCATCCTGAAAA-----CCTTCTCGGAGGGAGTGAAAAGC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 5713 62 + 10229 GCTGGCCGCAGAGCTGAGCA-AG-GCG----CCGTGTGTTCC--AAA-----CTCTCCTGGAGGAGACGCGGCGC i dipOrd1.scaffold_53224 C 0 C 0 s oryCun2.chrUn0958 15747 53 + 41507 GCTGGCCGCCGGGTCACACG-GG-CTC----CTGTGTGCCCC----------------GGGAGGGCGGGCAAGGC i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 124822 69 + 145505 GCTGGTGGCCAAGTCACGAGGGG-TTCGAGTGCGTGTGTTCCAACAA-----CTCTCCTGGAAGGACAGCAAGGT i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10855886 69 - 65312493 GCTGGTGGCCAAGTCACGAGGGG-ATCGAGTGCGTGTGTTCCAACAA-----CTCTCCTGGAAGGAGAGCAAGGT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58038900 64 - 61308211 GCTGGCTGCCAAGTCACG-AGGG-CTC----TTGTGCGTTCCAACAA-----CTCCCCTACGGGGAGAGCAAGGT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 10805 64 + 132007 ACTGGCCGCCAAGTCACGCGGGG-TCC----TCGTGTGTTCCAACAA-----CCCTCCTA-GGGGGGAGCAAGGT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59433508 64 - 64418924 ACCTGCCGCCAAGTAACGCGGGG-TCC----TTGTGTGTTCCAACAA-----CCCTCCTA-GGGGGGAGCAAGGT i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 6458 65 + 14340 GCCGGCCGCCAAGTCACGAGGGG-CTC----CCGTGCGTTCCAACAG-----CCCTCCTGGAGGGAGCGCAAGGT i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 11398 69 + 48268 GCAGGCCACCAAGTCACCGGGGG-CTC----TC-CGCGTTCCAGCAACGCTCCGCTCCCAGAGGCAAAGCAAGGT i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_355010 606 62 + 8359 GCTGGCGGCCCAGTCAGGAGCAA-GT-----GAATGGGTCCCA-CAA-----CCCCACTAGATGAATTGT-GGGT i eriEur1.scaffold_355010 n 1154 C 0 s loxAfr3.scaffold_49 14428784 65 - 17734757 GCTGGTCGCCAAATCACCAGGGG-TTC----TCATGCGTTCCAATAA-----CTCTCCTAGAGGGAAGGCAAGGT i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 13124 64 + 24616 ACTGCTCGCCAAAT-AGGTGGGG-TTC----CTGCATGTTCCCGTGA-----CTCTCCTAGCAGGAAGGCACAGT i proCap1.scaffold_29042 C 0 C 0 s echTel1.scaffold_194555 900 64 + 11139 GTTGGCTGCCAAGT-CACACGGG-TTC----TCTTGCGTTCCAATAA-----GTGTCCTGGAGGGAGGGCAAGGT i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 8445 65 + 20752 GCTTGTCGCCAAAT-CACAGGGGTTTC----CCACGCATCCCAACAG-----CTCTCCCAGAGTGACAGCAAGGT i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_6980 61001 0 + 61692 I e speTri1.scaffold_128901 3229 5 + 44242 I e monDom5.chr2 304528203 3081 - 541556283 I e cavPor3.scaffold_76 4386042 94 + 7991924 I a score=1222817.000000 s hg19.chr17_gl000204_random 41673 77 + 81310 GGCAGCCCTTGGCCC-ATGGGCAGCAGATTCTTGGATTCTGCAAAA--C-ATAATTGTGAAGCCCAATCTGCCAG--CGGAGA s panTro2.chr17 79471856 77 + 83384210 GGCAGCCCTTGGCCC-GTGGGCAGCAGATTCTTGGATTCTGCAAAA--C-ATAATTGTGAAGCCCAATCTGCCAG--CGGAGA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 11763 77 - 64270 GGCAGCCCTTGGCCC-GTGGGCAGCAGATTCTTGGATTCTGCAAAA--C-ATAATTGTGAAGCCCAATCTGCCAG--CGGAGA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16059019 77 + 17838096 GGCAGCCCTTGGCCC-ATGGGCAGCAGATTCTTGGATTCTGCAAAA--C-ATAATTGTGAAGCCCAATCTGCCAG--CGGAGA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75032918 77 + 78773432 GGCAGCCCTTGGCCC-GTGGGCAGCAAATTCTTGGATTCTGCAAAA--C-ATAATTGTGAAGCCCAATCTGCCAG--CGGAGA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 40306 77 - 95547 GGCAGCCCTTGGCCC-GTGGGCAGCAAATTCTTGGATTCTGCAAAA--C-ATAATTGTGAAGCCCAATCTGCCAG--CGGAGA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42131 77 + 225949 GGCAGCCCTTGGCCC-GTGGGCAGCAGATTCTTGGATTCTGCAAAA--C-ATAATTGTGAAGCCCAATCTGCCAG--CAGAGA i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 893 77 + 19765 GGCAGCCCTTGGCCC-GTGGGCAGCAGATTCTTGGATTCTGCAAAA--C-CTAATTGCGAAGCCCAATCTGCCAG--CGGAGA i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 23452 76 + 287808 GGCAGCCC-TGGCCC-GTGGGCAGCAGATTTTTGGATTCTGCAAAA--C-ATAATTGTGAAGCCCAATCTGCCAG--CGCAGA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 8057 69 + 15939 GGCGGCCC-TGGCCC--TGGGCCCCAGATCCCTGGGTGGTGCAGAA--C-AGGGCTGTGAAGACCGAGGTGCC--------GC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s dipOrd1.scaffold_53224 5775 69 + 10229 ------CCGTGGCC--GGGGGCAGCAGAGTCCTGACTTCTGTGAAC--A-GTTATCACGAAGACCAACGAAGA-G--TGGAGA i dipOrd1.scaffold_53224 C 0 C 0 s mm9.chr11 118755391 77 + 121843856 TATAGACCCTGGACTGTGGGGCAGCAGCATCTCAAATCATGCAAAA--GCATAATGGTGAAGGCCGACCATTA----CGGAGA i mm9.chr11 C 0 C 0 s speTri1.scaffold_128901 3234 77 + 44242 GGCAGCCCTTGGCCC-ATGGGCAGCAGAGTCTTGGATTCTGCGAAA--C-AAAACCATGAAGACCAACCTGCCTG--CGGGGA i speTri1.scaffold_128901 I 5 C 0 s oryCun2.chrUn0958 15800 67 + 41507 -ACAGGCCTCTGCCG-GTGGGCAGCAGA---------TGCATGAAG--C-AGGACCCCGAGGGCCAGTCTGCCAG--CAGAGA i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 124891 77 + 145505 GGCAGCCCTTGGCCC-ACCGACAGCAGATTCTTGGATTCTGCAAAA--T-ATAATTGTGAAGGCCAATCTGCCAG--CGGAGA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10855955 77 - 65312493 GGCAGCCCTTGGCCC-GACGACAGCAGATTCTTGGATTCTGCAAAA--T-ATGATTGTGAAGGCCAATCTGCCAG--TGGAGA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58038964 77 - 61308211 GGCAGCCCTTGGCCC-GCGGATGGCAGATTCTTGGATTCTGCAAAA--T-ATAATTGTGAAGCCCAACCTGCCAG--CAGAGA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 10869 77 + 132007 GGCAGCCCTTGGCCC-ACGGACAGCAGATTCTTGGATTCCGCAAAA--T-ATAATTGTGAAGACCAATCTGCCAG--CAGAGA i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59433572 77 - 64418924 GGCAGCCCTTGGCCC-GCGGACAGCAGATTCTTGGATTCCACAAAA--T-ATAATTGTGAAGACCAATCTGCCAG--CAGAGA i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 6523 77 + 14340 GGCAGCCCTTGGCCC-GCGGACAGCACATTCTTGGATCCCGCAAAG--T-ATAATTGTGGAGGCCAACCTGCCAG--CGAAGA i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 11467 78 + 48268 -GCAGCCCTCGGCCC-GCGGACCGCGGAGTCTTTGATTCCGCAAAA--C-ATAACGGCAAGGGCCGATCTGCCAGCCCGGAGA i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_355010 668 71 + 8359 TGCAGTCC-AGGCT----GGATGGCTAGCTCTGGGAGCCCAGGGCA--T-GTGGCTGT--ATACTGACCTGccag--cagaga i eriEur1.scaffold_355010 C 0 I 3107 s loxAfr3.scaffold_49 14428849 77 - 17734757 GGCACACCTTGGCCC-ACAGGCAGCAGGTTCTTGGACTCCACAAAA--C-ATAATCGTGAAGGCCAATCTGGCAG--CAGAGA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 13188 76 + 24616 GGCACACCTTGGCCC-ATGAGTCCCAGGTT-TGGGACTCCACAATA--C-ATAATCGCCAAGGCCAATCTGCCAG--CAGAGA i proCap1.scaffold_29042 C 0 C 0 s echTel1.scaffold_194555 964 78 + 11139 GGCA-GTGCTGGCCT-GTGGGCAGCAGGTTCCTGGACGCCACAGAGACC-ATGGTCACAAAGGCCGAGGGGCCAG--CAGAGA i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 8510 76 + 20752 GGCAGTCCCCAGCCC-ATGGGGGGCAGATTCTTGGACTCTGCAAAA--T-ATAACTGCGAAGGCCAATC-GCCAG--CAGAGA i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_6980 61001 0 + 61692 I e monDom5.chr2 304528203 3081 - 541556283 I e cavPor3.scaffold_76 4386042 94 + 7991924 I a score=2713621.000000 s hg19.chr17_gl000204_random 41750 211 + 81310 AATA--------TGCAGCGCATTCACAGGCTAAATATAAATAATATTGATTCATCTGCCATCTTGAATTATCCATTCCACTTCTGTTT-TCCATT-------AGCATCAATAATCACGAGCGTA-CTCCCCTGTGGA-CGGGGTACATTACGCTCCGAAGG---ATGC-AGCTGGCCCCAGGG------TCACACATCTGGAGGAGCCTCAGGATATCTTCCAGAATTATC-TGGCAT--------------------CT s panTro2.chr17 79471933 211 + 83384210 AATA--------TGCAGCGCATTCACAGGCTAAATATAAATAATATTGATTCATCTGCCATCTTGAATTATCCATTCCACTTCTGTTT-TCCATT-------AGCATCAATAATCACGAGCGTA-CTCCCCTGTGGA-CGGGGTACATTACGCTCCGAAGG---ATGC-AGCTGGCCCCAGGG------TCACACATCTGGAGGAGCCTCAGGATATCTTCCAGAATTATC-TGGCAT--------------------CT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 11840 211 - 64270 AATA--------TGCAGCGCATTCACAAGCTAAATATAAATAATATTGATTCATCTGCCATCTTGAATTATCCATTCCACTTCTGTTT-TCCATT-------AGCATCAATAATCACGAGCGTA-CTCCCCTGTGGA-CGGGGTACATTACGCTCCGAAGG---ATGC-AGCTGGCCCCAGGG------TCACACATCTGGAGGAGCCTCAGGATATCTTCCAGAATTATC-TGGCAT--------------------CT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16059096 211 + 17838096 AATA--------TGCAGCGCATTCACAGGCTAAATATAAATAATATTGATTCATCTGCCATCTTGAATTATCTATTCCACTTCTGTTT-TCCATT-------AGCATCAATAATCATGAGCGTA-CTCCCCTGTGGA-TGGGGTACATTATGCTCCGAAGG---ATGC-AGCTGGCCCCAGGG------TCACACATCTGGAGGAGCCTCAGGATATCTTCCAGAATTATC-TGGCAT--------------------CT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75032995 211 + 78773432 AATA--------TGCAGCGCATTCACAGGCTAAATATAAATAATATTGATTCATCTGCCATCTTGAATTATCCATTCCACTTCTGTTT-TCCATT-------AGCATCAATAATCACGAGTGTA-CTCCCCTGTGGA-CGGGGTATATTACGCTCCGAAGG---ATGC-AGCTGGCCCCAGGG------TCACACATCTGGAGGAGTCTCAGGATATCTTCCAGAATTATC-TGGCAT--------------------CT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 40383 211 - 95547 AATA--------TGCAGCGCATTCACAGGCTAAATATAAATAATATTGATTCATCTGCCATCTTGAATTATCCATTCCACTTCTGTTT-TCCATT-------AGCATCAATAATCACGAGTGTA-CTCCCCTGTGGA-CGGGGTACATTACGCTCCGAAGG---ATGC-AGCTGGCCCCAGGG------TCACACATCTGGAGGAGCCTCAGGATATCTTCCAGAATTATC-TGGCAT--------------------CT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42208 211 + 225949 AATA--------TGCAGCGCATTCACAGGCTAAATATAAATAATATCGATTCGTCTGCCATCTTGAATTATCCATTTCACTTCTGCTT-TCCATT-------AGCATCAATAATCGCAAGTGGA-CTCCCCTGTGGA-TGGGGTACATCACGCTCCGAAGG---ATGC-AGCCAGTCCCAGGG------TCACACATCTGGAGGAGCCTCGGGATATCTTCCCAAAATATC-TGGCAT--------------------CT i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 970 209 + 19765 AATA--------TGCAGCACATTCGCGGGCTAAATATAAATACTATCGATTCATCTGCCATCTTGAATTATCCGTCTCACTTCTGCTC-TCCATT-------AGCATCGATAATCGCAGGCTGC-CTCCCCCG-GGG-GTGGCTGCATTACCCTCTGAA-G---ATGC-AGCCAGCCCCACGG------GCATGCACCTCGTGCAGTCTCGGGGCATCTTCCAAAACAGCC-CAGCAC--------------------CT i micMur1.scaffold_15893 C 0 I 222 s otoGar1.scaffold_94362.1-287808 23528 188 + 287808 AATA--------TGCAGCACATTCCCAGGCTAAATATAAATAATATCGATTCATCTGCCATCTTGAATTATCCATCTCACTTCTGCTT-TCCATT-------AGCATCAATAATCACGAGCTGC-CCACCCCGCAGA-GGGGCTGCGTCACCCCGGGAA-G---ACAC-AGCCAGCCC-------------------------GAGTCAC---GCGTCTTCCACAACAGGC-CAGCAT--------------------CT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 8126 178 + 15939 AGTT--------CGCCGCG----CTCAGTCTGGTTATAAATAACACCGACCCACCTGCCATCTCACGTTA-CCATCTCGC-TCTCTTC-CCCATT-------AGCATCCGTGACCACGAGCCAG-C--CTCTGCAGG-TGGGCGGCTTTACGCTCCAGAGA---GGG---GCCGGCCCCAG------------------------GCCCCA----ACCTTCCTGAGCAGCC-GGGCAT--------------------C- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s dipOrd1.scaffold_53224 5844 176 + 10229 CATTCTTGGCTAGTTAGCCCAT-CACGGGCTAAATATGAGCAGAATCGAGTCACCTGCCATCTACAATCCTCGAGTCCACTTCCGCTT-TCCATT-------CGCATC------------------CCCC--------------------------GATGGCCCCTGC-AGCCATCCCCAGGA------ACATGCACGTGGTGTG---TGAGGATAGCTTCCAGCACAGTC-CAGCAT--------------------CT i dipOrd1.scaffold_53224 C 0 C 0 s mm9.chr11 118755468 212 + 121843856 CATC--------AGCAGTACATGCGCAGGCTAAATATAAATAGCATTGATTTGTCTGCCATCTTGAATTAGTCATTCAACTCCTGCAC-TCCGTC-------AGCATCAATAATCATGAGCGAG-TCCCT--GAAGA-AAG---------------GATGG---CTGC-AGTCAGTCCCATGG------GTGTGCACCTAGAAAT---TCTGGAAAGCTTCCAGAACATTCTCAGCATCATCTTGAGCAATCCATAACCC i mm9.chr11 C 0 C 0 s speTri1.scaffold_128901 3311 166 + 44242 AACG--------GGCAGCGCGTTCAGAGGCTAAATATAAATAGTATTGATCGGTGTGCCATCTTGAATTATCCATTCCACGTCGGTTT-TCCGTT-------AGCATC------------------------------------------------GACCG---TCACGAGTGACTCCCTGGG------TTGTGGACCTGGAGAAGTCTCGGGCTAGCTCCCAGGACAGGC-CAGCAT--------------------CT i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 15867 189 + 41507 AGCA--------CGCTGCACAGTCACGGGCTAAATATAAATAACATCGATCCGTCTGCCATCTTGAATTATCC--TCCCGGTCCGTTT-CCCATG-------AGCATCGATAATCACACGCTGA-CTCC---------------------------GAAGG---TCGC-AGGCGGCCCGGGAGTCAGCAGCCGGCACCCGCAGGAGTCTCCGGAGAGCCTCCAGAACAGTC-CGGCAC--------------------CT i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 124968 209 + 145505 AATA--------TGCAGTGCATCCACAAGCTAAATATAAATAATATTGATTAGTCTGCCATCTTGAATTATCCATTTCACTTCTGTTT-TCCATT-------AGCATCAATAATCACGAGCTGA-CTCCCCAGTAGA-TGGGCCACATTGCACTCCACAGG---ATGC-AGCCAGCCC-AGAG------TCACGCATCTA-AGGAGTCTCAGGCTCTCTTCCAGAACAGTC-TGGCAT--------------------CT i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10856032 209 - 65312493 AATA--------TGCAGCACATTCACAAGCTAAATATAAATAATATTGATTCATCTGCCATCTTGAATTATCCATTTCACTTCTGTTT-TCCATT-------AGCATCAATAATCGCGAGATGA-CTCCCCAGTAGA-CGGGCTACATTGCACTCTACAGG---ATGC-AGCCAACCC-AGGG------TCATGCACCTA-AGGAGTCTCAGGCTCTCTTCCAGAATAGTC-TGGCAT--------------------CT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58039041 211 - 61308211 AATA--------TGCAGCACATTCACAAGCTAAATATAAATAATATGGATTCATCTGCCATCTTGAATTATCCACGGCACTTCTGTTT-TCCATT-------AGCATCAATAATCACGAGCTGA-CTCCCCTGGAGA-TGGGCTACCTGACACTCGGAACG---ACGC-AGCCAGCCTGAGCG------CCACACCTCTAGAGGAGCCACAGGCCATCCTCCAGAATAGTC-CAGCAT--------------------CT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 10946 210 + 132007 AATA--------TGCAGCATATTCACAAGCTAAATATAAATAATATTGATTCGTCTGCCATCTTGAATTATCCATTTCACTTCTGTTT-TCCATT-------AGCATCAATAATCACGAGCTGA-CGCCCCTGTGGA-T-GGCTACATTGCCCTCCAAAGG---ACAC-AGCCAGCCCCAGGG------TCATGCACCTAGAGGAGTCGCGGGCTGTCTTCCAGAATAGCC-CGCCGT--------------------CT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59433649 211 - 64418924 AATA--------TGCAGCATATTCACAAGCTAAATATAAATAATATTGATTTGTCTGCCATCTTGAATTATCCATGTCACTTCTTTTT-TCCATT-------AGCATCAATAATCACGAGCTGACCCCCCCTGTGGA-T-GGCCACGTTGCCCTCTGAAGG---ACAC-AGCCAGCCCCAGGG------TCATGCACCGAGAGGAGTCTCAGGCTGCCTTCCAGAATGGCC-TGCCAT--------------------CT i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 6600 198 + 14340 AGTA--------TGCA--------GCACACTACATATGAATAATGTCGATTCATTTGCCATCGCGAGTCACCCG-TCCAC-TCTGCCT--GCATT-------CGCATCAATAACCACAGCGGA--CTCCCCCGTAAACG-GGCTACACTGCACCCTGAA-G---ACGT-AGCCAGCCCCAGGG------CCGGGCATCTAGAGGAGTCTCAGGCTGTCTTCCAGAGCAGTC-CGGCAC--------------------CT i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 11545 199 + 48268 CGTG--------CGCA---CACTCACAGCCTAAATATGAAGAGCAGCGACTC---CGCCATCTCGAGCCACCCGCTTCACTTCTGCCT-CCCACG-------GGCGTTGACGGTCCCAAGCTG--GTGCCCTGCAGG-G-GGACACACTGCCCCCAAAG-G---GTGC-GGCTGGCCCCAGGC------TCACGCGCCC---GGTGACTTCGGCTAGCTTCCAGAACAGTC-CGGCGC--------------------CT i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_290756 2652 209 - 7602 AAGA--------CACAGCGCTTTCACAAGCTAAATATAAATCCTATTGATCCATCTGCCATCTTGAATTATCTGTTCCACTCCTCTTTTTCCATC-------AGCATCGATAATCATGGGCTGC-CGGCTACCTCCA-G-AGCCTCCATAGGCTCTGGG-A---GTGA-GGCTGGCCTCAG-G------TCACACACCCAGAGGCATGTCAAGCAGTCTTTCAGAATGGTC-TAGCAC--------------------CT i eriEur1.scaffold_290756 I 1154 C 0 s ochPri2.scaffold_9426 3024 163 - 54875 -----------------------------CTACACAACAATAACACCGATCCGCCTGCCATCTTGAGTTATCTA-TCCGGGCCTGGTT-CCCATT-------AGCATCAATGATCACAGGCCGA-CTCT---------------------------GAAGG---ACGC-AGCTGGCCCTAGGG------ACCCACGCCTGCACGAGTCTGAGGACGGCTTCTGGAACGCCC-CAGCAT--------------------CT i ochPri2.scaffold_9426 I 2104 C 0 s loxAfr3.scaffold_49 14428926 211 - 17734757 AATA--------TGCAATGCATTCACAAGCTAAATATAAATAATATTGATCTGTCTGCCATTTTGAATTATCCATTTCACTTCTGCTT-TCCACT-------AGCATCGATAATCACGAGCTGA-CTCCCCCGTAGA-TAGGTTGCATTAGACTCAGAAGG---ATGC-AGCCAGCCCCAGGG------TCATGCATTTGGAGGAGTCTCAGGATATCTTCCAGAATAGTT-CAGCGT--------------------CT i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 13264 208 + 24616 AACA--------GGCAACACACTCACAAGCTAAATATAAATTGTATTGATCGATCTGCCATCTTGTATGATCTATTTCACT--TGTTT-TCCACT-------AGCATCAATAATCAACAGCTGA-CTCGCCCATAGG-TGGGTTCCGTCCAACTCAAAAAC---ATGC-AGCCAG-CCCAGGG------TCAAGCATTTGGAGGAGTCGCAGGACACCTTCCAGAACAGTC-CAGCAT--------------------CT i proCap1.scaffold_29042 C 0 C 0 s echTel1.scaffold_194555 1042 208 + 11139 AATA--------TGCAATGCACTCACAAGCCAAATATAAATGCTATCGATCCAGCTGCCACTGTGAATGATCCGTTCCCCTTCTG-TT-TCCATC-------AGCATCAATAATCACACGCTGG-CTCCTGGGGAGA-CAGGCCGCTTCGCACACCCAAGG---CTGC-TGCCAGGCCCAGGA------CCCTGAGACTGGAGGAGTCCTGGGATCTCTTCTAGAACAGTC-CAG--T--------------------CT i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 8586 217 + 20752 AAGA--------GGCAAGGCAGTCACATGCTAAATATAGAAAATATCGATCCGTCGGCCATCCTGAGTTATCCGCTTCACTTCTGTTT-TCCATTATCCACGAGCATCAATAGTCAGTAGCTGA-TCCCTCTCTGGA-TGAACTACACTATAGGCCAAAGG---CTGC-AGCTGG-CCCAAGA------GCCCCACCCCGGATAAGTCTTGGGAAATCTTCCGGACTAGTC-CGGCAT--------------------CT i dasNov2.scaffold_28617 C 0 C 0 e monDom5.chr2 304528203 3081 - 541556283 I e cavPor3.scaffold_76 4386042 94 + 7991924 I a score=1037020.000000 s hg19.chr17_gl000204_random 41961 95 + 81310 TCTAGAGC--------------------AATCCAGAACCTT---------CCTGG-----TACTT---TTTC------CTCCCTCTTATCTACTCCTCATTCCAAGCCCAGGAAAGAGGG------G----TGGCTC-AAAGAGACATC s panTro2.chr17 79472144 95 + 83384210 TCTAGAGC--------------------AATCCAGAACCTT---------CCTGG-----TACTT---TTTC------CTCCCTCTTATCTACTCCTCATTCCAAGCCCAGGAAAGAGGG------G----TGGCTC-AAAGAGACATC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 12051 95 - 64270 TCTAGAGC--------------------AATCCAGAACCTT---------CCTGG-----TACTT---TTTC------CTCCCTCTTATCTACTCCTCATTCCAAGCCCAGGAAAGAGGG------G----TGGCTC-AAAGAGACATC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16059307 95 + 17838096 TCTAGAGC--------------------AATCCAGAACCTT---------CCTGG-----TACTT---TTTC------CTCCCTCTTATCTACTCCTCACTCCAAGCCCAGGAAAGAGGA------G----TGGCTC-AAAGAGACATC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75033206 95 + 78773432 TCTAGAGC--------------------AATCCAGAACCTC---------CCTGG-----TACTT---TTCC------CTCCCTCTCATCTACTCCTCACTCCAAGCCCAGGAAAGAGGG------G----TGGCTC-AAAGAGACATC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 40594 95 - 95547 TCTAGAGC--------------------AATCCAGAACCTC---------CCTGG-----TACTT---CTCC------CTCCCTCTCATCTACTCCTCACTCCAAGCCCAGGAAAGAGGG------G----TGGCTC-AAAGAGACATC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42419 95 + 225949 TCTAGAGC--------------------AATTCAGAACCTT---------CCTGA-----CACTT---TTTC------CTCCCTCCGATCTACTCCTCACTCAAAGCCCAGGGAAGAGGG------G----TGACTC-AAAGAGACATC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 1401 91 + 19765 TCTAGAGC--------------------AATCCAGAAGCTT---------CCTAG-----TACTT---TTTC------CTCCCTTTC-TCTCCTCCTCACTCCAAACCCAGGGAATGG--------C----TGGCTC-GAAA-TCCACC i micMur1.scaffold_15893 I 222 C 0 s otoGar1.scaffold_94362.1-287808 23716 93 + 287808 TCCACAGC--------------------AATCCAGAACCTT---------GCTGG-----TACTA---GTTT------CTCCCTTAC-CGTCCTCCTCACTCCAAGTCCAGGAAAGAGGC------C----TGGCTC-AAAG-GCCCCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 8304 92 + 15939 TCTGGAGC--------------------AATCCAGAACCTT---------CCTGG-----AGCTT---CT-C------CTCCCTGTCATGGACTCCTCACCCCAAGCCAGGGAAGAAG--------G----TGGCCC-CCAGGTGCGTG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s dipOrd1.scaffold_53224 6020 100 + 10229 TCTAGAAC--------------------AATCTGGAACCTC---------CCCAGCATTTTTTTTC--CTCT------TTCCCTTCCACCTACTCCTCACTCCAAACTGGGGGAAAAGGG------T-----GGCTC-AGAAGTAGACC i dipOrd1.scaffold_53224 C 0 I 2 s mm9.chr11 118755680 110 + 121843856 TCTGGAGC--------------------AATCTGGAGCCTTCCAGAGCAACCCGGAACCCTACTAG--CTCC------TCCCTCTCCATCTGCTCCTCACTCCAAACCCAGGAAGGAGAG------C----AAGCTT-ACAGATAGACC i mm9.chr11 C 0 I 2 s speTri1.scaffold_128901 3477 90 + 44242 TCTGGA-C--------------------AGCCCAGAACCTT---------CCTGG-----TACTTC--CTCC------TCCCCTTCAA-CTACTCCTTACT-CAAGCCCGGG--AGCGGG------T-----GGCCC-CAACACAGCCC i speTri1.scaffold_128901 C 0 I 2 s oryCun2.chrUn0958 16056 84 + 41507 TCTGGAGC--------------------AACCCAGAGCCTC---------CCTCG-----TGCCTCAGCTCC------CTCCCTTCCACCT----CTC------AGTCCGGGAAAGGGGG-------------CCTCGTGAAGCCCG-- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 3187 97 - 54875 TCTAGAGC--------------------AACCCAGAACCTC---------CCTCC-----TGCTTCGGCTCG------CTTCTTCCCAGCT----CGCTCCCCAAGCCCAGGAAAGAGGGGGTGACC-----AGCTC-TGAGGCAGG-- i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 125177 94 + 145505 TCTAGAAG--------------------AGTCCAGCACCTT---------CCTAG-----GAACG---TTCC------TTCCCTTTCATCTATTCCTCACTCCAAGCCCAGTAAACAGTG------G-----GGCTC-AAAGACACATC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10856241 94 - 65312493 TCTAGAAG--------------------ACTCCAGCATCTT---------CCTAG-----GAATG---TTCT------TTCCCTTTCATCTACTCCTCACTCCAAGCCCAGCAAAGAATG------G-----GACTG-AGAGACACATC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58039252 95 - 61308211 TCTAGAAC--------------------AGCCCAGCACCTT---------CCTAC-----TACTT---TTTC------CTCCCTCTCACCTACTCCTGACTCACCACCCAGCAAAGAGGA------G----TGGCCC-AAAGACACATC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 11156 95 + 132007 TCTAGAAC--------------------AGTCCAGCACATT---------CTGAG-----GAATT---TTGC------CTCCCTCACATCTGTTCCTCACCCCCAACCCAGCAAAGAGGG------G----CAGCTC-GAAGGCGCATC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59433860 95 - 64418924 TCTAGAAC--------------------AGTCCAGCACCTT---------CCTGG-----GAATG---TTTC------CTCCCCAACAACTACTCCTCACTCCAAGCCCAGCAGTGAGGG------G----CAGCTT-GAAGGCACATC i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 6798 114 + 14340 TCCAGAACATTCCAGCACCTTCCAGAATAGTCCAGCACCCT---------CCTAG-----GCATC---TCCC------CTCCCTTCCATCGACTTCCCACTCTGGGCCCAG-CAGAGAGG------G----TGGCTC-AGGCACGCACC i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 11744 95 + 48268 TCTAGAAC--------------------AGTCCAGCACCTT---------CCTAG-----ACATT---TTCC------CTCCCTTTCATCTACTCCTCACTCCAAGCCCGGCCAGGAGGG------G----CGGCTC-AAGGACGCATC i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_290756 2861 98 - 7602 TCTAGAAC--------------------AGTCCAGAGACTT---------CCTGC-----Caaat---tttc------cttccttctg-ctGCACCTAACTCCAAGCCCAGCAAAAGGTA------GGAGGAAGGCT-AAAGTCAGACC i eriEur1.scaffold_290756 C 0 C 0 s loxAfr3.scaffold_49 14429137 92 - 17734757 TCTAGAAC--------------------AGTCCAGTACTTT---------CCTAC-----TACTT---TGTC------CTCTCCT---TCTACCCCTCACTCCACAACCAGGAAAGAGGT------G----TGGCTG-AAACACATACA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 13472 88 + 24616 TCTGGAAG--------------------AGTCGGGCACTTT---------CCTAC-----TACTC---TGCC------CTC-------TCTACTCCTCACTCCACGCCCAGGAAGGAGGG------G----CGGCTG-GAATGCACATC i proCap1.scaffold_29042 C 0 C 0 s echTel1.scaffold_194555 1250 93 + 11139 TCTAGAAC--------------------CACCCAGCTCATG---------CCCAC-----CACTT---TGCCATGTTGCTCACGC---TCCACTCCTCG---CATGCCCAGGAAGGAATT------G----T--CTG-GCGCACAGCCC i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 8803 94 + 20752 TCTAGAAC--------------------AGTCTGGCACCTT---------CCTAC-----TACCT---TGTT------CTCCCTTTCATCTACTCCATACCTCAAG-CCAGCAAAGAGGC------C----CGGCTC-AGAGGCGCATC i dasNov2.scaffold_28617 C 0 C 0 e monDom5.chr2 304528203 3081 - 541556283 I e cavPor3.scaffold_76 4386042 94 + 7991924 I a score=18073.000000 s hg19.chr17_gl000204_random 42056 28 + 81310 TGAG-A--C-------C--CCC-------CT----TTCAGAGGCAGTCTG--C s panTro2.chr17 79472239 28 + 83384210 TGAG-A--C-------C--CCC-------CT----TTCAGAGGCAGTCTG--C i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 12146 28 - 64270 TGAG-A--C-------C--CCC-------CT----TTCAGAGGCAGTCTG--C i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16059402 28 + 17838096 TGAG-A--C-------C--CCC-------CT----TTCAGAGGCAGTCTG--C i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75033301 28 + 78773432 TGAG-A--C-------C--CCC-------CT----TTCGGAGGCAGTCTG--C i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 40689 28 - 95547 TGAG-A--C-------C--CCC-------CT----TTCGGAGGCAGTCTG--C i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42514 28 + 225949 TGAG-A--C-------C--CCC-------CT----TTCGGAGGCAGTCTG--C i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 1492 30 + 19765 GGAG-ACCC-------C--CCC-------CT----TTCAGAGGCATTCTG--C i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 23809 28 + 287808 TCAG-A--C-------C--CCC-------CT----TCCGGAGGCATTCTG--C i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 8396 25 + 15939 GGTA-A--C-------C--CCC-------C-------CGCAGGCACTCTG--C i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118755792 28 + 121843856 AGAG-G--C-------CCTCCT-------CC----TT-GTAAGTGTTCCG--- i mm9.chr11 I 2 C 0 s dipOrd1.scaffold_53224 6122 21 + 10229 GGGG-A--C-------C--TCT-------CC----TT-TTGGGGG-------- i dipOrd1.scaffold_53224 I 2 C 0 s cavPor3.scaffold_76 4386136 25 + 7991924 AGAA-A--C-------C---CC-------CG----AG-AGAGGTGTTCTG--- i cavPor3.scaffold_76 I 94 C 0 s speTri1.scaffold_128901 3569 31 + 44242 AGGA-A--C-------C--CCT-------CCACCTTC-TGGAGTGTTCTGC-- i speTri1.scaffold_128901 I 2 C 0 s oryCun2.chrUn0958 16140 25 + 41507 -TGA-G--C-------C--CCT-------CC----C--ACAGGCAGCCCA-C- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 3284 27 - 54875 -GGA-G--C-------C--CCA-------CT----TTGGGAGCTGGCCTG-C- i ochPri2.scaffold_9426 C 0 I 449 s turTru1.scaffold_106006 125271 42 + 145505 TGAG-T--CACACACAC--CCGCCCCCCACT----TTTGGAGGCATTCTG--C i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10856335 35 - 65312493 TGAG-G--T-------C--TCCCCACCCACT----TTTGGAGGCATTCTG--C i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58039347 28 - 61308211 GGAG-A--C-------C--CCC-------CT----TTCGGAGGCAGTCTG--C i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 11251 33 + 132007 GGAGCA--C-------C--CCCACCC---CT----TGCAGAGGCATTCTG--C i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59433955 29 - 64418924 TGAG-A--C-------C--CCCA------CT----TTTAGAGGCATTCTG--T i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 6912 26 + 14340 T--G-G--C-------C--CCC-------TT----TTTGGAGGCCTGCTG--C i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 11839 28 + 48268 TGAG-A--C-------C--GCC-------CT----TTTGGAGGCATTCTG--C i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_290756 2959 21 - 7602 AGAG-A--C-------A--ccc-------cc----c-------cATTCTG--G i eriEur1.scaffold_290756 C 0 C 0 s loxAfr3.scaffold_49 14429229 8 - 17734757 --CG-A--G-------A--ACC------------------------------- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 13560 26 + 24616 --TG-A--C-------A--GCC-------CT----CTGGGAGTCATCCTG--C i proCap1.scaffold_29042 C 0 C 0 s echTel1.scaffold_194555 1343 26 + 11139 --CA-G--A-------C--CCC-------CT----CCTGGAAGCAGGCAG--C i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 8897 26 + 20752 --TG-A--G-------A--CTC-------CC----TTTTGGAGGCATCTG--C i dasNov2.scaffold_28617 C 0 C 0 e monDom5.chr2 304528203 3081 - 541556283 I a score=317973.000000 s hg19.chr17_gl000204_random 42084 33 + 81310 TTTATTT-GGCAGCTG--ACTCTGGTTCTGGGAAAC- s panTro2.chr17 79472267 33 + 83384210 TCTATTT-GGCAGCTG--ACTCTGGTTCTGGGAAAC- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 12174 33 - 64270 TCTATTT-GGCAGCTG--ACTCTGGTTCTGGGAAAC- i gorGor1.Supercontig_0007361 C 0 I 45 s ponAbe2.chr17_random 16059430 33 + 17838096 TCTATTT-GGCAGCTG--ACTCTGGTTCTGGGAAAC- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75033329 33 + 78773432 TCTATTT-GGCAGCTG--ACTCTGGTTCTGGGAAAC- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 40717 33 - 95547 TCTATTT-GGCAGCTG--ACTCTGGTTCTGGGAAAC- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42542 33 + 225949 TCTATTT-GGCAGCTG--ACTCTGGTACCGGGAAGC- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 1522 32 + 19765 TCTGTTT-GGCAGCCG--ACGCCGG-CCTGGGAAAA- i micMur1.scaffold_15893 C 0 I 1 s otoGar1.scaffold_94362.1-287808 23837 33 + 287808 TCTATTT-GGCAGCTG--ACACTGGTTCTGGGAAAA- i otoGar1.scaffold_94362.1-287808 C 0 I 2 s tupBel1.scaffold_124459.1-15939 8421 31 + 15939 TCTAGTT-GGCA-CTG---CTCTGGTTCTGGAAAAA- i tupBel1.scaffold_124459.1-15939 C 0 I 1 s mm9.chr11 118755820 32 + 121843856 -CTGTTT-GGCAGCTG--ATCTTGACTCCAGGATGA- i mm9.chr11 C 0 I 1 s dipOrd1.scaffold_53224 6143 13 + 10229 -----------------------GGCTTCAGGAAGA- i dipOrd1.scaffold_53224 C 0 I 1 s cavPor3.scaffold_76 4386161 32 + 7991924 -CTGTTT-GGTAGTCC--ACTCTGGTTCTAGGACGA- i cavPor3.scaffold_76 C 0 I 1 s speTri1.scaffold_128901 3600 32 + 44242 TCTATTT-GGCAGCCA--ACGC-GGCTCAGAGAACA- i speTri1.scaffold_128901 C 0 I 1 s oryCun2.chrUn0958 16165 15 + 41507 ---------------------CCGGCTCTGGGACAA- i oryCun2.chrUn0958 C 0 I 1 s turTru1.scaffold_106006 125313 33 + 145505 TCTCTCT-GGCAGCTG--ACCTTGGTTCTGGGAAAA- i turTru1.scaffold_106006 C 0 I 1 s bosTau4.chr19 10856370 33 - 65312493 TCTCTTT-GGCAGTTG--ACCTTGGTTCTGGGAAAA- i bosTau4.chr19 C 0 I 1 s equCab2.chr11 58039375 32 - 61308211 TCTCTTT-GGCAGCTG--ACTCTGGTTCT-GGGAAA- i equCab2.chr11 C 0 I 1 s felCat3.scaffold_206428 11284 33 + 132007 TCTCTTT-GGCAGCCG--ACCCCGGTTCTAGGGAGG- i felCat3.scaffold_206428 C 0 I 1 s canFam2.chr9 59433984 33 - 64418924 TCTCTCT-GGCAGCCG--CCCTTGCTTCTGGGGAAG- i canFam2.chr9 C 0 I 1 s myoLuc1.scaffold_4816 6938 32 + 14340 TCTCCT--GGCAGCCG--ACCCGGGTTCTGGGAAAG- i myoLuc1.scaffold_4816 C 0 I 1 s pteVam1.scaffold_11245 11867 36 + 48268 TTTCTTTGGGCAGCCGCCCCCCGGGTTCTGGGAAAA- i pteVam1.scaffold_11245 C 0 I 1 s eriEur1.scaffold_290756 2980 32 - 7602 CCTCT---GGCAGCCA-CCCCCCTGTTCCAGGGACC- i eriEur1.scaffold_290756 C 0 I 1 s loxAfr3.scaffold_49 14429237 33 - 17734757 -CCTCTT-GGCAGCCG--ACTCTGGGGCTGGGAGCGC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 13586 32 + 24616 TCTCCTG-GGCAGTTG--GCCT--GGGCTAGGAGCAC i proCap1.scaffold_29042 C 0 C 0 s echTel1.scaffold_194555 1369 34 + 11139 TCTGTTT-GGCTTCCG--GCCCCCAGGCTGGGACCGT i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 8923 34 + 20752 TCTCCTT-GGCAGCAG--GCTCTGGTTCTGGGAACAC i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_9426 3311 449 - 54875 I e monDom5.chr2 304528203 3081 - 541556283 I a score=200110.000000 s hg19.chr17_gl000204_random 42117 83 + 81310 A-ATTGCAC--AC---GCTCCAA-GGTTC---ACTTCC-AAGGAAGG--AGGG-GAAG------AAGCTCCTG-GGGCT-GAT--------GCAGAGCCCAA-CTGAA-CCCTCA s calJac1.Contig5139 42575 84 + 225949 A-GTTGCAC--AT---GCTCCAA-GGTTC---ACTTCC-AGGGAAGGTAAAGG-GAGG------AAGCTCCTG-GGGCG-GAT---------CACAGCCCAG-CTAAA-CCCTCG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 40750 83 - 95547 A-ATCGCAC--AA---GCTCCAA-GGTTC---ACTTCC-AGGGAAGG--AGGG-GAGG------AAGCTCCTG-AGGCT-GAA--------GCACAGCCCCA-CTGAA-CCCGCA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75033362 83 + 78773432 A-ATCGCAC--AA---GCTCCAA-GGTTT---ACTTCC-AGGGAAGG--AGGG-AAGG------AAGCTCCTG-GGGCT-GAT--------GCACAGCCCCA-CTGAA-CCCGCA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16059463 83 + 17838096 A-ATTGCAC--AC---GCTCCAA-GGTTC---ACTTCC-AGGGAAGG--AGGG-GAGG------AAGCTCCTG-GGGCT-GAT--------GCAGAGCCCAA-CTGAA-CCCTCA i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79472300 83 + 83384210 A-ATTGCAC--AT---GCTCCAA-GGTTC---ACTTCC-AAGGAAGG--AGGG-GAAG------AAGCTCCTG-GAGCT-GAT--------GCAGAGCCCAA-CTGAA-CCCTCA i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 1555 50 + 19765 A-GGTGCGC--GC---ACGCCAA-GGTTC---GCTTCC-AGGGAC----------------------------------------------------CCCGA-CCCGA-CCCGCA i micMur1.scaffold_15893 I 1 I 29 s otoGar1.scaffold_94362.1-287808 23872 84 + 287808 A-ATTGCTC--AA---GCGCCAA-GGTTC---ACTTCC-AGGGATGA--AGGG-AAGG------AAGCGTGTG-TGGCTGGAC--------GCACAACCCCA-CAAAA-CCTGCA i otoGar1.scaffold_94362.1-287808 I 2 I 29 s tupBel1.scaffold_124459.1-15939 8453 82 + 15939 G-ATCGCTC--AG---GCTCCCA-GGCTC---CCTTCC-AGGGAC----AGGG-AAGG------CAGCTTCCG-TGGCAGGAT--------GCACTGCACGA-CCAGC-CCCACG i tupBel1.scaffold_124459.1-15939 I 1 I 29 s mm9.chr11 118755853 65 + 121843856 T-TATAAAC--CC---ACTCCCA-AGTTC---TTGTGC-AGGGATGA--CAGC-AAGG------AAGGTTATA-TGG-TGGCT--------GCTC-------------------- i mm9.chr11 I 1 I 19 s dipOrd1.scaffold_53224 6157 77 + 10229 A-GCCACGC--TC---GTTCCCA-GGTTC---C--------AAAAGG--TAGG-AAGG------AAGCTCCCA-TGACTGGAC--------GCTCAGCCCAG-GGAAA-CCCGCA i dipOrd1.scaffold_53224 I 1 I 27 s cavPor3.scaffold_76 4386194 77 + 7991924 ----TGTGT--CC---ATGCCAA-GGTTC---ACTTCC-GCAGGTTG--TGGG-GAGGCCTGCTGAGCTGATA-GAA------------------AGCCCAG-CACAG-CCTACT i cavPor3.scaffold_76 I 1 I 28 s speTri1.scaffold_128901 3633 85 + 44242 C-TACCTGC--CT---GCGCCCAGGGCTC---ACTTCC-AGGGAAGA--GGGG-AAGG------AAGCTCCCA-TGGCTGCCT--------GCACGGCCCAG-TGACA-CCCGCA i speTri1.scaffold_128901 I 1 I 28 s oryCun2.chrUn0958 16181 77 + 41507 C-ACCGCGT--CC---AGGCCAA-GCCTG---GCCCCC-A-GGACGA--GCGG-AAGG------GAGCCTTCG-GGC-AGGAT--------GTGC-----AG-CAAAC-CCCGCG i oryCun2.chrUn0958 I 1 I 16 s turTru1.scaffold_106006 125347 75 + 145505 A-GTGGCAC--AC---AGTCCAA-GGTTC-------------ACTGA--AGGG-AAGG------AAGCTAGCA-TGGCTGGAT--------GCACAGCCCGA-CCACG-CTCACA i turTru1.scaffold_106006 I 1 C 0 s bosTau4.chr19 10856404 86 - 65312493 A-GCGGCAC--AC---AGTGCAA-GTCCCTTCACTTCC-A-GGCTGA--AGGG-GAGG------AAGCTGGTG-TGGCTGGAT--------GCACAGCCCAA-CCAAG-CCCATG i bosTau4.chr19 I 1 C 0 s equCab2.chr11 58039408 83 - 61308211 A-GTGGCAC--AC---AGTCCAA-CGTTC---ACTTCC-A-GGCTGG--AGGG-AAGG------AAGCTGGTA-TGGCTGGAT--------GCACAGCCCAA-CAAAA-CCTGCA i equCab2.chr11 I 1 C 0 s felCat3.scaffold_206428 11318 75 + 132007 A-GTGGCAC--AC---GGTCCAA-GGTTC---ACCGC----CGGCGA--CGGG-AAGG------AAGCTGATA-TAGCTGGAA--------GCACAGCCCAA-CCC-------CA i felCat3.scaffold_206428 I 1 C 0 s canFam2.chr9 59434018 82 - 64418924 AGGTGGCAC--AC---AGTCCAA-GGTTC---ACTCC----GGCTGA--AGGA-AAGG------GAGCTGATA-TGGCTGGAT--------ATGCAGCCCAA-CCAAA-CCCGCG i canFam2.chr9 I 1 C 0 s myoLuc1.scaffold_4816 6971 83 + 14340 A-GTGGCAC--AC---GATCCAG-GGTTC---ACGTCC-A-GGCTGC--CGGG-CAGG------AAGCGGATA-TGGCTGGAC--------ACACAGCCCAG-CTGCA-CCTGCA i myoLuc1.scaffold_4816 I 1 C 0 s pteVam1.scaffold_11245 11904 84 + 48268 A-GTGGCAC--AG---GGTCCGC-AGCTC---ACTTCC-A-GGCTGC--CGGGAAAGG------AAGCCGCCA-CGGCCAGAT--------GCGCAGCCCCA-TGGAA-CCCGCA i pteVam1.scaffold_11245 I 1 C 0 s eriEur1.scaffold_290756 3013 68 - 7602 G-CTGGCTC--ACCATAATCACA-GGATT---A--------GGC--A--TGGA-GAGG------AAGCTCACA-TGGTCCAGT--------GCACAGCC------------TGCA i eriEur1.scaffold_290756 I 1 C 0 s loxAfr3.scaffold_49 14429270 82 - 17734757 -AAGCTCAT--AC---ATGCCAA-GGTTC---TCCTCC-A-GGCTGA--AGGG-AAGA------AAGCATAAA-CAGCTGG-T--------GTGCAGCCCAA-CCAGA-CCTGCA i loxAfr3.scaffold_49 C 0 I 29 s proCap1.scaffold_29042 13618 82 + 24616 -CGTCACAC--AG---ATGCCAA-GGTTC---TCTTCC-A-GGCAGC--AGGA-AAGG------ATACTTAGATTGGCTCA-T--------GTGCAGCCCAATCCAG---CTGCG i proCap1.scaffold_29042 C 0 I 21 s echTel1.scaffold_194555 1403 93 + 11139 -TACCACACATAC---ACACCAA-GGTCC---ACTTCC-A-GGCTGG--CCCG-AAAG------TCACTCCGG-TGGCTGG-TACAGTCTCATGCAGCTCCA-TCACACCCCACA i echTel1.scaffold_194555 C 0 I 28 s dasNov2.scaffold_28617 8957 84 + 20752 -AACTGCTC--GT---GCTCGGA-GGCGC---ACGCCCGG-GGCTGG--CGGG-AAGG------AAGCATGGA-TGGCTGGAT--------GCGCAGCCCGG-CCACA-CGCACG i dasNov2.scaffold_28617 C 0 I 29 e ochPri2.scaffold_9426 3311 449 - 54875 I e gorGor1.Supercontig_0007361 12207 45 - 64270 I e monDom5.chr2 304528203 3081 - 541556283 I a score=28353.000000 s hg19.chr17_gl000204_random 42200 13 + 81310 GGGCA-------------GAACCAGG s panTro2.chr17 79472383 13 + 83384210 GGGCA-------------GAACCAGG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16059546 13 + 17838096 GGGCA-------------GAACCACG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75033445 13 + 78773432 GGGCA-------------GAACCAGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 40833 13 - 95547 GGGCA-------------GAACCAGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42659 13 + 225949 GGGCA-------------GAACCAGG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 67 13 + 1188 GGAGA-------------GAACCAGG i tarSyr1.scaffold_458502 N 0 C 0 s micMur1.scaffold_15893 1634 13 + 19765 AGGTG-------------GAAGCGAG i micMur1.scaffold_15893 I 29 C 0 s otoGar1.scaffold_94362.1-287808 23985 13 + 287808 AGGTA-------------GAACCGAG i otoGar1.scaffold_94362.1-287808 I 29 C 0 s tupBel1.scaffold_124459.1-15939 8564 12 + 15939 AGGCA-------------GAACCA-G i tupBel1.scaffold_124459.1-15939 I 29 C 0 s mm9.chr11 118755937 8 + 121843856 ------------------AGATGCAA i mm9.chr11 I 19 C 0 s dipOrd1.scaffold_53224 6261 13 + 10229 CAGGC-------------AGAACCCA i dipOrd1.scaffold_53224 I 27 C 0 s cavPor3.scaffold_76 4386299 13 + 7991924 GGGCA-------------GAACCAAG i cavPor3.scaffold_76 I 28 C 0 s speTri1.scaffold_128901 3746 13 + 44242 CAGCA-------------GGACCAAG i speTri1.scaffold_128901 I 28 C 0 s oryCun2.chrUn0958 16274 8 + 41507 ------------------GAATCAGG i oryCun2.chrUn0958 I 16 C 0 s turTru1.scaffold_106006 125422 13 + 145505 GGGCA-------------CCACCTCA i turTru1.scaffold_106006 C 0 I 29 s bosTau4.chr19 10856490 13 - 65312493 GGGCA-------------TCGCCTCA i bosTau4.chr19 C 0 I 28 s equCab2.chr11 58039491 13 - 61308211 GGGCG-------------CCACCTTG i equCab2.chr11 C 0 I 29 s felCat3.scaffold_206428 11393 13 + 132007 GGGCA-------------CCGCCTCA i felCat3.scaffold_206428 C 0 I 27 s canFam2.chr9 59434100 13 - 64418924 GGGCA-------------TCGCCTCA i canFam2.chr9 C 0 I 33 s myoLuc1.scaffold_4816 7054 13 + 14340 GGGCA-------------CTGCCTCG i myoLuc1.scaffold_4816 C 0 I 28 s pteVam1.scaffold_11245 11988 13 + 48268 GGGCG-------------CCACCTGA i pteVam1.scaffold_11245 C 0 I 199 s eriEur1.scaffold_290756 3081 26 - 7602 GGGCATGCCTGGTTGTGCCAGCCTGA i eriEur1.scaffold_290756 C 0 I 23 s loxAfr3.scaffold_49 14429381 13 - 17734757 AGGCT-------------GAATCAGG i loxAfr3.scaffold_49 I 29 C 0 s proCap1.scaffold_29042 13721 7 + 24616 GGGCT-------------GA------ i proCap1.scaffold_29042 I 21 C 0 s echTel1.scaffold_194555 1524 7 + 11139 GGCCT-------------GA------ i echTel1.scaffold_194555 I 28 C 0 s dasNov2.scaffold_28617 9070 12 + 20752 GG-CA-------------GAACCAGG i dasNov2.scaffold_28617 I 29 C 0 e ochPri2.scaffold_9426 3311 449 - 54875 I e gorGor1.Supercontig_0007361 12207 45 - 64270 I e monDom5.chr2 304528203 3081 - 541556283 I a score=163217.000000 s hg19.chr17_gl000204_random 42213 21 + 81310 GC-CCATTTCCTCTC----------TGGGCCA s panTro2.chr17 79472396 21 + 83384210 GC-CCATTTCCTCTC----------TGGGCCA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16059559 21 + 17838096 GC-CCATTTCCTCTC----------TGGGCCA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75033458 21 + 78773432 GC-CCATTTCCTCTC----------TGGGCCA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 40846 21 - 95547 GC-CCATTTCCTCTC----------TGGGCCA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42672 21 + 225949 GC-CCATTTCCTCTC----------CAGGCCA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 80 21 + 1188 GC-CCATTTCCTCTC----------TGGACCA i tarSyr1.scaffold_458502 C 0 C 0 s micMur1.scaffold_15893 1647 21 + 19765 GC-CCATTTCCTCTC----------TGGGCCA i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 23998 21 + 287808 GC-TCATTTCCTCTG----------CAGGCCA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 8576 21 + 15939 GC-CCATTTCCTCCC----------CGGGTCA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118755945 2 + 121843856 GG------------------------------ i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 6274 21 + 10229 GGTCCCTTTTCCCTC----------TGGGC-A i dipOrd1.scaffold_53224 C 0 C 0 s cavPor3.scaffold_76 4386312 21 + 7991924 GT-CCATTTCCCCTC----------TGGCCTG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 3759 21 + 44242 GC-CCACTTCCTCTC----------CGGGCCA i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 16282 19 + 41507 GC-CTGCTTCCTCCC----------CGCG--A i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 125464 18 + 145505 GC-CCACTTCTT-------------TGAGCCA i turTru1.scaffold_106006 I 29 C 0 s bosTau4.chr19 10856531 21 - 65312493 GA-CCACTTCTTCTC----------CAAGCCA i bosTau4.chr19 I 28 C 0 s equCab2.chr11 58039533 21 - 61308211 GC-CCATTTCCTCTC----------CAGGCTA i equCab2.chr11 I 29 C 0 s felCat3.scaffold_206428 11433 31 + 132007 GC-CTGCTTCCTCTCCAGGCCTCTGCAGGCCA i felCat3.scaffold_206428 I 27 C 0 s canFam2.chr9 59434146 21 - 64418924 GC-CCGTTTCCCGTC----------CGGGCCA i canFam2.chr9 I 33 C 0 s myoLuc1.scaffold_4816 7095 21 + 14340 GC-CCGCTTCCTCTC----------CGGGCCG i myoLuc1.scaffold_4816 I 28 C 0 s eriEur1.scaffold_290756 3130 20 - 7602 GC-CTGCTTCCTCC-----------CTGACCA i eriEur1.scaffold_290756 I 23 C 0 s loxAfr3.scaffold_49 14429394 20 - 17734757 G--CTGTGTCTTCTC----------AAGGCTG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 13728 4 + 24616 ----------------------------GCCA i proCap1.scaffold_29042 C 0 C 0 s echTel1.scaffold_194555 1531 4 + 11139 ----------------------------GACA i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 9082 21 + 20752 GC-CCGTTTCCTCTC----------GTAGCCA i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_9426 3311 449 - 54875 I e gorGor1.Supercontig_0007361 12207 45 - 64270 I e pteVam1.scaffold_11245 12001 199 + 48268 I e monDom5.chr2 304528203 3081 - 541556283 I a score=22095.000000 s hg19.chr17_gl000204_random 42234 97 + 81310 GAAACCACAGTGGC-TTTCCTGCAGATCAGCGGGGTCCTTG-------------TTCCTCTGACAGCCC--------TCTGCCCCCAGGCC------CTGGGG---------CTCTCTGATCAGCAGGC--------AGAGA s panTro2.chr17 79472417 97 + 83384210 GAAACCACAGTGGC-TTTCCTGCAGATCAGCGGGGTCCTTG-------------TTCCTCTGACAGCCC--------TCTGCCCCCAGGCC------CTGGGG---------CTCTCTGATCAGCAGGC--------AGAGA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0430519 5 97 - 1067 GAAACCACAGTGGC-TTTCCTGCAGATCAGCGGGGTCCTTG-------------TTCCTCTGACAGCCC--------TCTGCCCCCANGCC------CTGGGG---------CTCTCTGATCAGCAGGC--------AGAGA i gorGor1.Supercontig_0430519 n 45 C 0 s ponAbe2.chr17_random 16059580 97 + 17838096 GAAATCACAGTGGC-TTTCCTGCAGATCAGCAGGGTCCTTG-------------TTCCTCTGACAGCCC--------TCTGCCCCCAGGAC------CTGGGG---------CTCTCTGATCAGCAGGC--------AGAGA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75033479 97 + 78773432 GAAACCACAGTGAC-TGTCCTGCAGATCACCAGGGTCCTTG-------------TCCCTCTGACAGCCC--------TGTGCCCCGAGGCC------CTGGGG---------CTCTCTGATTAGCAGGG--------AGAGA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 40867 97 - 95547 GAAACCACAGTGAC-TGTCCTGCAGATCACCAGGGTCCTTG-------------TCCCTCTGACAGCCC--------TCTGCCCCGAGGCC------CTGGGG---------CTCTCTGATTAGCAGGG--------AGAGA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42693 96 + 225949 GAAGCCACAGTGGC-TTTCCTGAAGATCAGCGGGGTCCTTG-------------TCCCTCTGACAGCCC--------TCTGCCCCCAGGCC------TT-GGG---------CTTTCTAATCAGCAGGC--------AGAGA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 101 94 + 1188 GAAACCATGGTGGC-TTTCCTGCAGATCAGCAGAGTCCTTG-------------TCCCTCTGACAGCCC--------CCTACCCCGAGGCC------CGGGG------------CTCTGATCAGCAGGC--------ACAGA i tarSyr1.scaffold_458502 C 0 C 0 s micMur1.scaffold_15893 1668 93 + 19765 GAAACCACGGCGGC-TTTCCGACAGATCAGCGGGGTCCTTG-------------TCCCTCCGACAGCGC--------CCTGCCCCCAGGCC------CCTG-------------CTCCAACCAGCGGGC--------ACAGC i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 24019 92 + 287808 GAAACCTCGGTTGC-TTTCCGACAGGTCAGTGGGGT-CTTA-------------TCCCTCTGACAGCCC--------CCTGCCCCTAGCCC------TGGG-------------CTCTGACCAGCAGTC--------ACAGA i otoGar1.scaffold_94362.1-287808 C 0 I 733 s tupBel1.scaffold_124459.1-15939 8597 75 + 15939 -GAACCACGGTGGG-T-TCCTACAGGTCAGCAGGGTCCTTG-------------TCCCTCCAGCAGCCT--------CCT-CTCCCAGGCC------CCG--------------CTCTGA---------------------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118755947 74 + 121843856 -----------AGC-TTCTGTATAGACCAGCAGGGGCCATG-------------TCTTACAG-----------------------CGGTCC--TTCTCCAGGA---------T-CCATGACCCTTATCA--------GAAAG i mm9.chr11 C 0 I 5 s dipOrd1.scaffold_53224 6295 97 + 10229 GAAACCATGGTGGC-TCTGCTGAAGGTCAGCCTGGTCTCTG-------------TCCCTCTGGCTATTC--------CCT---CCCCGCCC--CACCCCAGCC---------T-TCCTGAGCAGCAGAG--------GTGAC i dipOrd1.scaffold_53224 C 0 I 5 s cavPor3.scaffold_76 4386333 61 + 7991924 GAAACCACAATGGC-TTTCCTACCACTCAGGAGGA--------------------CTCACAG----------------------------------------------------TGCTGATCAGCAGGT--------AAGCG i cavPor3.scaffold_76 C 0 I 5 s speTri1.scaffold_128901 3780 92 + 44242 GAAACCAGAGTGGC-TTTCCTACCGAGCGGCCGGT-CCATG-------------TCCTCCTGGCAGCGT--------CCT---CCCAGGCC------CCAGGG---------C-CTCTGATGAGCAGTC--------AGGAA i speTri1.scaffold_128901 C 0 I 2 s oryCun2.chrUn0958 16301 90 + 41507 GGAGCCGCAGCCAC-TTCCCTCCTG--CAGCAGAG-----G-------------GTCCCTGGCCCGTGC--------CCC---CCCCCCCCGCAGCCCCACAG---------C-CTCCCATGGGCAGGT--------GCA-- i oryCun2.chrUn0958 C 0 I 2 s turTru1.scaffold_106006 125482 82 + 145505 GAAACCAC-ATGGC-TTTCCTACGGACCAGCGGGTTCCTCG-------------TCCCTCTGGCAGCAC--------CCCCGCTCCAGGCC------CCTGGA------CAC-------------AGAG--------T---- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10856552 82 - 65312493 GAAACCAC-AAGGC-TTTCCTACAGACCAGTGGGCCCATGG-------------CCCCTTTGGCAGCAG--------CCCAGCTCCAGGCC------CCTGGA------CAC-------------AGAG--------T---- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58039554 83 - 61308211 GAAACCATAGTGGC-TTTCCTA-TGACCAGCAGGCTCCTCG-------------TCCCTCTGGCAGCGC-------TCCCCTCCCCAGGCC------CTGGGG-------------------CACAGAG--------C---- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 11464 105 + 132007 GGAGCCTCCGAAGCGTTTCCTACAGATCAGCAGGTCCCTCTGGCAGCCGCTGCACCCCCCCCCCGCCCCGCAAACTCCCCACCCCCAGGCC------CTGGGA-------------------CACAGAG--------T---- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59434167 82 - 64418924 AGAACCTCAGTAGC-TATCCTACTGATCAGCAG---------------------CCCCACCACCACCAC-------CACCAGCCCCAGGGC------ACAGCGTGTGCC-------------CACAGCA--------T---- i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 7116 66 + 14340 GACGCCAC-GAGGC-TTTCCGATGGAGCAGCGGGCTCCTCG-------------CCCCTCTGGCAGCAC---------CCCGCCCCAGGC---------------------------------------------------- i myoLuc1.scaffold_4816 C 0 C 0 s eriEur1.scaffold_290756 3150 59 - 7602 GCAACTGTGATGGCTTTTTCTACAGCTCCATGGG--------------------GCCCCCTAgaagcac--------ccccacccca------------------------------------------------------- i eriEur1.scaffold_290756 C 0 C 0 s loxAfr3.scaffold_49 14429414 88 - 17734757 GAAACCAC-GTGGC-TTCCCTCCACGTCAGTGGGTGGCTCA-------------CTCCTCTGGCAGCAC------------ACCCCGTGCT------GG--AC-----------TTCTGACCAGCAGAC--------ACCAA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 13732 70 + 24616 AAAAGCGC-ATG-------------GTCAGC-AGCACCCTG-------------CTCCCCTAGGAGTAC------------ACCCCGGCCT------GA---------------CTCTGAC---CAGAC--------AACAA i proCap1.scaffold_29042 C 0 C 0 s echTel1.scaffold_194555 1535 82 + 11139 GGACCCAT-GTC------CCAACTGGTCAGTGGGTGCTTTG-------------CCAGTCTCATAGCCC------------ACCCCAGGCC------AG---C-----------ATATGGTGAGCAAAG--------ACCAA i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 9103 80 + 20752 CAACCC-C-GAGGT-TTTCCCACTCATTGGTGGACA------------------------------CAC------------CCCCCGGGCC------CGGGGC-----------TTCTGATTGGCAGACGGGGGTGTACCCA i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_9426 3311 449 - 54875 I e pteVam1.scaffold_11245 12001 199 + 48268 I e monDom5.chr2 304528203 3081 - 541556283 I a score=-480836.000000 s hg19.chr17_gl000204_random 42331 74 + 81310 G-TGTGCCC-AGCACCAG--------CCAGGGGT----------GGGCCAGGG---------CCTCCGGCACACCCTCCTACCCCT-----TCTC-------------AGTGGAGCCTCTA s panTro2.chr17 79472514 74 + 83384210 G-TGTGCCC-AGGACCAG--------CCAGGGGT----------GGGCCAGGG---------CCTCCGGCACACCCTCCTACCCCT-----TCTC-------------AGTGGAGCCTCTA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0430519 102 74 - 1067 G-TGTGCCC-AGCACCAG--------CCAGGGGT----------GGGCCAGGG---------CCTCCGGCACACCCTCCTACCCCT-----TCTC-------------AGTGGAGCCTCTA i gorGor1.Supercontig_0430519 C 0 C 0 s ponAbe2.chr17_random 16059677 74 + 17838096 G-TGTGCCC-AGCACCAG--------CCAGGGGT----------GGGCCAGGG---------CCTCTGGCACACCCTCCTACCCCT-----TCTC-------------AGTGGAGCCTCTA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75033576 74 + 78773432 G-TGTGCCT-AGCACCAG--------CCAGGGGT----------GGACCAGGG---------CCTCCGGCACACCCTCCCACCCCT-----TCTC-------------AGTGGAGCCTCTA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 40964 74 - 95547 G-TGTGCCT-AGCACCAG--------CCAGGGGT----------GGACCAGGG---------CCTCCGGCACACCCTCCTACCCCT-----TCTC-------------AGTGGAGCCTCTA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42789 74 + 225949 G-CGTGCCC-AGCACCAG--------CCAGGAGT----------GGGCCAGGG---------ACTCCGGCACACCCTTCCACGCCA-----GGTC-------------AGCGGAGCCTCTA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 195 79 + 1188 G-TGCGCCCTGGCACCAA--------CCAGGAGC----------AGG-CGGTG---------TCTCCTGCACACCCTCCCACATCAGCAGGTTTC-------------AACAGAGCCTTCA i tarSyr1.scaffold_458502 C 0 C 0 s micMur1.scaffold_15893 1761 78 + 19765 G-GGTGACATGGCACCGG--------CCAGGAGT----------TGGCCAGGG---------CCTCC-GCACACCCTCCTTGGCCAGTGG-GTCC-------------AACGCAGCCTCTG i micMur1.scaffold_15893 C 0 C 0 s tupBel1.scaffold_124459.1-15939 8672 52 + 15939 ---------------------------------------------GAGCAGTG---------ACGCC--CGCGCCCTCCCGCCCCCGGGGGTTTC-------------AGCGGGGTCTCTG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118756026 90 + 121843856 G-AATGC---TGTAGCAC--------C------------------AGGCAGGGATCTGAAGTacacacacacacacacacacacCAGTAG-ATCCCCTGAGCCACTGAAATGGGAAGACCA i mm9.chr11 I 5 C 0 s dipOrd1.scaffold_53224 6397 68 + 10229 G-GATGC---GGCTTCCC--------C------------------AGCCCAGG---------GCTCCTGTACCCCCTCCCAGGCCAGTGC-GTCC-------------AAAGGAACTGCTA i dipOrd1.scaffold_53224 I 5 C 0 s cavPor3.scaffold_76 4386399 56 + 7991924 GAAATGG---GGTGG-------------------------------GGCAAGG-------------CTGCACCCCCACCCACA----TGT-CTCC-------------CTTGGGGCCTCTA i cavPor3.scaffold_76 I 5 C 0 s speTri1.scaffold_128901 3874 82 + 44242 G-GCTGC---GGCACCCG--------CCGG---------------GAGCCAGG---------GCTGCTGCAC-CCCTCCCACACCAGCAG-CCCCACAGAGCCTCCGAGACAGAAATGCC- i speTri1.scaffold_128901 I 2 C 0 s oryCun2.chrUn0958 16393 36 + 41507 G-CGAGT---GGCGGCTC--------C-----------------------AGG---------ACCCCTGGA-------------------------------------GGCAGGAA----A i oryCun2.chrUn0958 I 2 C 0 s turTru1.scaffold_106006 125564 76 + 145505 -----------GTGCCCATAACACACCTGGGAGG----------AAGCCCAGG---------CCTCCTGCAAACCCTCC--CACCACCAGGACTC-------------AGCAGGGGTTCGA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10856634 76 - 65312493 -----------AGACCCACAACACACCCAGGAGG----------AGGACCAGG---------CCTCCTGCAAACCCTCC--CACCACCAAGACTC-------------GGCAGGCCTTCCA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58039637 63 - 61308211 -----------GTGC-----------CCACAGCA----------CGGCC-------------CCTCTCATGTACCCTCTCCCCACAGCAGGACCC-------------AGTGGGGCTGCTA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 11569 56 + 132007 -----------GG--------------------------------GGCCCCAG---------CCTCCTGCATAGCTCCCCACACCAGCAAGACTC-------------CACGGGGCCGGTA i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59434249 65 - 64418924 -----------GG-------------CCGGGAGG----------CGGCCCAGG---------CCTCCTGCCTGCCCTCCCTCACCGGCAAGACAC-------------CCCGGGGCTGTTA i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 7182 42 + 14340 --------------------------CCGGCACA----------C-----------------------------CCTCCAACGCCACCATGACGC-------------AGT-GCGCTGCCA i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 12200 75 + 48268 -----------GTGCCTACAGCACAGCCGGGACG----------T-GCCCGGG---------CCTCCTGCGGA-CCCCGCACACCAGCAGGACTC-------------AGC-AGGCTGCTA i pteVam1.scaffold_11245 I 199 C 0 s eriEur1.scaffold_290756 3209 51 - 7602 ---------------------------------------------agccagGG---------TCTTCttcatgcccccc--ccccatacagaCA--------------AGCTGTGCTGCCT i eriEur1.scaffold_290756 C 0 C 0 s loxAfr3.scaffold_49 14429502 61 - 17734757 ---------------------------GAGCACC----------ATAGCCAGG---------ACTCCCACGCACCTTCCATACCGGCAAG-ATCC-------------AGCCAGACCACTG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 13802 57 + 24616 ---------------------------GGGTACC----------ACAGCCGGG---------ACTCCTGCGCACCCCCCAAGGCAGTGAG------------------AACCGGGCCACTG i proCap1.scaffold_29042 C 0 C 0 s echTel1.scaffold_194555 1617 63 + 11139 ---------------------------AGGCACCCAGCCCCAGTGCTGACCAG---------GCCCCCAGGCACCCTCCACACTGGTGGG-------------------TCCAGGCAA--- i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 9183 59 + 20752 ---------------------------CAGCTCC----------AGGACTGCG---------CCCCCTGGGAGATTTTCTCTACCATATA---TC-------------AGTCACACCTTCA i dasNov2.scaffold_28617 C 0 I 805 e ochPri2.scaffold_9426 3311 449 - 54875 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I a score=66080.000000 s hg19.chr17_gl000204_random 42405 44 + 81310 GAGA--CAGAAATAACCAAGGCAC-GGAAACCCAC--------CAGGGCC-ACCCA s panTro2.chr17 79472588 44 + 83384210 GAGA--CAGAAATAACCAAGGCAC-GGAAACCCAC--------CAGGGCC-ACCCA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0430519 176 44 - 1067 GAGA--CAGAAATAACCAAGGCAC-GGAAACCCAC--------CAGGGCC-ACCCA i gorGor1.Supercontig_0430519 C 0 C 0 s ponAbe2.chr17_random 16059751 44 + 17838096 GAGA--CAGAAATAACCAAGGCAC-GGAAACCCAC--------CAGGGCC-ACCCA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75033650 44 + 78773432 GAGG--CAGAAATAACCAAGGCAT-GGAAACCCAC--------CAGGGCC-ACCCA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 41038 44 - 95547 GAGG--CAGAAACAACCAAGGCAC-GGAAACCCAC--------CAGGGCC-ACCCA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42863 44 + 225949 GAGA--CAGAAATAACCAGGGCAC-AGAAACCCAC--------CAGGGCC-ACCTA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 274 44 + 1188 GAGG--CAGAAATAACCAGGGCAC-CGAAACCCAC--------CAGGGCC-ACTCA i tarSyr1.scaffold_458502 C 0 C 0 s micMur1.scaffold_15893 1839 43 + 19765 GAGA--CAGAAGTAGTCAGGGTGC-AGACGCCCA---------CGCGGCC-ACTCA i micMur1.scaffold_15893 C 0 C 0 s tupBel1.scaffold_124459.1-15939 8724 21 + 15939 AGGA--CAAA----------------------CGC--------CAGGGCT-GCC-- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118756116 28 + 121843856 GGGA--CAAGA---------------------CAT----CCCACAGGGCC-ACCTG i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 6465 32 + 10229 GAGA--CAGAA---------------------GTTTACCCACACATGACC-ACCCA i dipOrd1.scaffold_53224 C 0 C 0 s cavPor3.scaffold_76 4386455 26 + 7991924 GAGCCTCAGAG---------------------CAT--------GGAAGCC-ACCAG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 3956 15 + 44242 ------CAGGG---------------------CGT--------GGAAGCC------ i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 16429 25 + 41507 GGAA--CAGGG---------------------CAC--------GGAAGCCCACCCA i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 125640 43 + 145505 GCGA--CAGAAAGGACCAAGGCAC-GGAAACCCAC---------CAGGCC-CCTCA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10856710 39 - 65312493 GTGA--CAGA----ACCAAGGCAC-AGAAACCCCT---------CAGGCC-CCTCA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58039700 29 - 61308211 GCGA--CA---------------C-GGAAACCCAC--------ATGGGCC-ACTCA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 11625 45 + 132007 GCGA--CAGAAAGCACAGGGGCCCAGAAACCCTCC--------CTGGGCC-TCTCG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59434314 42 - 64418924 GCAA--CAGAAAGAACAGGG---CATGGAACCCAC--------ACAGGCC-GCTCG i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 7224 38 + 14340 GCGA--CG----CAATCAGGGCTC-GGTAA--CCC--------CCGGGCC-CCGCA i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 12275 40 + 48268 GTGA--CA----GAACCAGGACAC-GGAAAGCCAC--------ACGGGCC-CCTCA i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_290756 3260 40 - 7602 GAAA--CTGAAGGCAC-AGCACAC-AGACACCTGC---------CAGGCT-ACT-- i eriEur1.scaffold_290756 C 0 C 0 s loxAfr3.scaffold_49 14429563 43 - 17734757 GAGA--CGGACAAGG-CAGGGCAT-GGAGACCCCC--------ATAGGTC-ACTCA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 13859 41 + 24616 GAGG--CGGAAAGGA-CATGGCAC-AGAAACACCC----------AGGTC-ATTCA i proCap1.scaffold_29042 C 0 C 0 s echTel1.scaffold_194555 1680 42 + 11139 GAGA--CAGGAACG--CAGGATGT-GGGAAGCCCT--------ACAAGTC-ACTCA i echTel1.scaffold_194555 C 0 I 843 e ochPri2.scaffold_9426 3311 449 - 54875 I e dasNov2.scaffold_28617 9242 805 + 20752 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I a score=-186671.000000 s hg19.chr17_gl000204_random 42449 50 + 81310 CC------------GTGGGCCCAGCCA-------GGCCAC-AGAGCT-AATGAGCCACAAAGTCC-------C-------CTGCC s panTro2.chr17 79472632 50 + 83384210 CC------------GTGGGCCCAGCCA-------GGCCAC-AGAGCT-AATGAGCCACAAAGGCC-------C-------CTGCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0430519 220 50 - 1067 CC------------GTGGGCCCAGCCA-------GGCCAC-AGAGCT-AATGAGCCACAAAGGCC-------C-------CTGCC i gorGor1.Supercontig_0430519 C 0 C 0 s ponAbe2.chr17_random 16059795 50 + 17838096 CC------------GTGGGCCCAGCCA-------GGCCAC-AGAGCT-AATGAGCCACAAAGGTC-------C-------CTGGC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75033694 50 + 78773432 CC------------GTGGGCCCAGCCT-------GGCCAC-AGAGCT-AATGAGCCACAAAGACC-------C-------CTGCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 41082 50 - 95547 CC------------GTGGGCCCAGCCT-------GGCCAC-AGAGCT-AATGAGCCACAAAGACC-------C-------CTGCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42907 50 + 225949 TC------------GTGGGCCCAGCCA-------GGCCAC-AGAGCT-AATGAGGCACAAAGGCC-------C-------CTGCC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 318 50 + 1188 CC------------ATGGACCTAGCCA-------GGCCAG-AGAGCT-AATGAGACAAAGCAGCC-------C-------CTGCG i tarSyr1.scaffold_458502 C 0 C 0 s micMur1.scaffold_15893 1882 52 + 19765 CC------------GGGGGCCTGGCCC-------GCCCAGAAGAGCTGAAGGGGGCACAAAAGGG-------C-------CTCTT i micMur1.scaffold_15893 C 0 C 0 s tupBel1.scaffold_124459.1-15939 8745 40 + 15939 ----------------------------------GCACAG-CAAGCT-AATGAAGCACAGAGGTCCTGCA--C-------CTGGG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118756144 43 + 121843856 CC------------AGAGAGCCAGATA-------GT--TC-AGAGTT-CAGAGGCCACAAATGGT-------C------------ i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 6497 52 + 10229 GCCTGCTGCACCTTGGAGGGCCGGCCA-------TG--AC-ACAGC----GGGGCCCCCAACCCC-------A------------ i dipOrd1.scaffold_53224 C 0 C 0 s cavPor3.scaffold_76 4386481 48 + 7991924 CTGTGCC-------CGAGGCCTGGTCA-------AG--AC-AGAGCA-CCTGAGGCACAAGGGCC-------C------------ i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 3971 51 + 44242 --------------AGAGGCCCCG--A-------GG--AC-AGAGTG-CGAGAGGCACAGAGGCC-------CTGTCCCACCCTC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 16454 12 + 41507 GG------------GGAGGGCCAG------------------------------------------------------------- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 125683 53 + 145505 -CA-----------GCCGGCCCAGCCA-------GGATGG-AGGGCT-AACAAGACACAAGGCCCACG----T-------CCACC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10856749 60 - 65312493 GCT-----------GCTGGCCCAGCTGACCCAGTGGATGG-AGGGC--AACAGGATACCAGGCCCGCT----T-------CCACA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58039729 55 - 61308211 CCA-----------GCCGGCCCAGCCA-------GGGCAG-AGGGCT-AACGAGGCACACGGCCCCTTC---C-------CCATC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 11670 42 + 132007 CCA-----------GCCGGCCCGGCCA-------GGATGG-AGGGC--TCAAAGGCGCCAGG----------------------A i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59434356 43 - 64418924 CCA-----------GCCAGCCCAGCCA-------GGATGC-AGGGTG-CCCAGGGCACGTGG----------------------C i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 7262 44 + 14340 CCG-----------GCC---------A-------GGACG---GGGCT-AGCACAGCACAAAGCCCACTC---C-------CCACC i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 12315 54 + 48268 CCA-----------GCCTG-CCAGCTG-------GGACGA-AGGGCT-CACGAGGCAGGAGGCCCACTC---C-------CCACC i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_290756 3300 38 - 7602 ----------------------ATCTG-------GGGTGC-AACCTG-GCAGGGGCATGAGGC---------C-------ATGCC i eriEur1.scaffold_290756 C 0 C 0 s loxAfr3.scaffold_49 14429606 53 - 17734757 ----------CCAGGGGGGTCCAGTCA-------GGACAG-AGGGCT-AATGCAGCCGAAAGGCCCCTtgtc------------- i loxAfr3.scaffold_49 C 0 I 505 s proCap1.scaffold_29042 13900 28 + 24616 ----------CCAGAGAGGCCCAGTCA-------GGACAC-AGGGC--------------------------------------- i proCap1.scaffold_29042 C 0 I 801 e ochPri2.scaffold_9426 3311 449 - 54875 I e dasNov2.scaffold_28617 9242 805 + 20752 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I a score=81132.000000 s hg19.chr17_gl000204_random 42499 18 + 81310 CC----CC---A----------------------ACCAGCTCTCAGA--- s panTro2.chr17 79472682 18 + 83384210 CC----CC---A----------------------ACCGGCTGTCAGA--- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0430519 270 18 - 1067 CC----CC---A----------------------ACCAGCTGTCAGA--- i gorGor1.Supercontig_0430519 C 0 C 0 s ponAbe2.chr17_random 16059845 18 + 17838096 CC----CC---A----------------------GCCAGCTGTCAGA--- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75033744 18 + 78773432 CC----CC---A----------------------GCCAGCTGTCAGA--- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 41132 18 - 95547 CC----CC---A----------------------GCCAGCTGTCAGA--- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42957 18 + 225949 CC----CC---A----------------------GCCAGCTGTCAGA--- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 368 29 + 1188 CC----CC---ACTGC-----------TACCTTGGCCAGCTGTCAGA--- i tarSyr1.scaffold_458502 C 0 C 0 s micMur1.scaffold_15893 1934 7 + 19765 CC----CC---A----------------------AC-------------- i micMur1.scaffold_15893 C 0 I 1647 s tupBel1.scaffold_124459.1-15939 8785 40 + 15939 CC----CC---ACGCCCCACTCCTCCACACCCCTGCCAGCTTTCAGA--- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118756187 16 + 121843856 ------TC---A----------------------TTCGGCTCCCAGA--- i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 6549 19 + 10229 ------CCAGAA----------------------GCCAGTTCTGGGG--- i dipOrd1.scaffold_53224 C 0 C 0 s cavPor3.scaffold_76 4386529 14 + 7991924 -----------A----------------------CCCGGCTCTCAGc--- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 4022 21 + 44242 AC----CC---A----------------------GTCAGCTCTCAGAGGG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 16466 13 + 41507 -----------A----------------------GGC-GCTCTTGGA--- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 125736 21 + 145505 CCACC-CC---A----------------------GCCAGCTGTCAGA--- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10856809 22 - 65312493 CCTCCACC---A----------------------GCTAGCTGTCAAA--- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58039784 21 - 61308211 CCAGC-CC---A----------------------GGCAGCTATCAGA--- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 11712 21 + 132007 CCACC-CC---C----------------------GCCAGCTGTCAGA--- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59434399 21 - 64418924 CCACC-CC---G----------------------GCCAGATGTCAGA--- i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 7306 17 + 14340 ----G-CC---C----------------------ACCAGCTGCCGGC--- i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 12369 21 + 48268 CCCAC-CC---C----------------------GCCAGCTGTCAGA--- i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_290756 3338 21 - 7602 CCCTC-CA---T----------------------GCCAGCTATCAGA--- i eriEur1.scaffold_290756 C 0 C 0 e ochPri2.scaffold_9426 3311 449 - 54875 I e proCap1.scaffold_29042 13928 801 + 24616 I e dasNov2.scaffold_28617 9242 805 + 20752 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I e loxAfr3.scaffold_49 14429659 505 - 17734757 I a score=-49208.000000 s hg19.chr17_gl000204_random 42517 55 + 81310 at-------tcaacaaatgttga---ttgagaa---tggactatgagcagacagccatgctaggtgct s panTro2.chr17 79472700 55 + 83384210 at-------tcaacaaatgttga---ttgagaa---tggactacgagcagacagccatgctaggtgct i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0430519 288 55 - 1067 at-------tcaacaaatgttga---ttgagaa---tggactatgagcagacagccatgctaggtgct i gorGor1.Supercontig_0430519 C 0 C 0 s ponAbe2.chr17_random 16059863 55 + 17838096 at-------tcaacaaatgttga---ttaagaa---tggactatgagcagagagccatgctgggtgct i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75033762 55 + 78773432 at-------tcaacaaatgttga---cggagaa---cggactatgagcggagagtcatgctgggtgct i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 41150 55 - 95547 at-------tcaacacatgttga---cggagaa---cggaccatgagcggagagccacgctgggtgct i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 42975 55 + 225949 at-------tcagcaaacgtcga---ttgagaa---tggactgtaagtggacagcctcactaggtggt i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 397 37 + 1188 at-------gcagcaaatattaa---ttgagga---------------------ccatcctaggtact i tarSyr1.scaffold_458502 C 0 C 0 s tupBel1.scaffold_124459.1-15939 8825 56 + 15939 AC------GTCCACGAATGCTGG---CCGCGAC---CCTCTTATGAGTGGGGAGTCACGCCAGGTGCT i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118756203 36 + 121843856 AT-------CTCACTAACACTGA---CTGTAGA---CC------------TTTG-------AAGGGCT i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 6568 44 + 10229 AT-------CCCACAAGTGTTGA-----GAAAA---CCAGCCTTGGG--GGTGG-------GGGGGAA i dipOrd1.scaffold_53224 C 0 C 0 s cavPor3.scaffold_76 4386543 47 + 7991924 acacacacacacacacacacTCATACCCATATA---TT-----------GACAG-------GAGCCTT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 4043 34 + 44242 AC-------CTTCTGTGCGACCA-------GAA---CC------------TTTG-----CTAGGTGCT i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 16479 35 + 41507 AT------GTCCGTGAACGCTGA---TGGCCAG---CC------------CCGA-------GGAGG-- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 125757 56 + 145505 AC------CCCCacaaacagtga---ctgaaaa---catacagtgagtacaggagcagcctacacgcg i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10856831 55 - 65312493 AC------CCCCacaaacagtga---ctaagaa---catactgcgagtagagaggcatcc-acaagct i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58039805 54 - 61308211 AT------CCCCAGATACA--GA---CTGAGAA---TCCAGGGTGAGTGGAGAAACATCCCACGTATT i equCab2.chr11 C 0 I 1 s felCat3.scaffold_206428 11733 56 + 132007 AT------GCCCACAAACATGGA---CTGAAAA---CCTACCGTGAGTAGACAGCCATCCTATGTGCT i felCat3.scaffold_206428 C 0 I 719 s canFam2.chr9 59434420 56 - 64418924 AA------GCCCACAAACACCGA---CCGAGAA---CCTACCGCGAGGAGATAACTGTCCCGTGTGCT i canFam2.chr9 C 0 I 1 s myoLuc1.scaffold_4816 7323 49 + 14340 GT--------CC-GCAGTGCTGA---CCGGGAC---CCCCGTGGGTAGAG----GCGTCCTCCGTGTT i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 12390 50 + 48268 AT------ACCC-CAAATACTGA---CTGGAAA---CCTGCTGCAAGTGG----CCATCCTACGCG-T i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_290756 3359 35 - 7602 GT------ACCCACAAATACAGA---TGGG------------------------GTGTCCTATATGTC i eriEur1.scaffold_290756 C 0 C 0 s loxAfr3.scaffold_49 14430164 58 - 17734757 at-------ttaacacataacca---tcaagaactgcctactgtgagtagggagccattctaggtact i loxAfr3.scaffold_49 I 505 C 0 s dasNov2.scaffold_28617 10047 48 + 20752 -------------CAACTGTTTC---TTGAGAA---GCTCCTGGGAGAAGGGAGCC-TTCTGGGTACT i dasNov2.scaffold_28617 I 805 C 0 e ochPri2.scaffold_9426 3311 449 - 54875 I e proCap1.scaffold_29042 13928 801 + 24616 I e micMur1.scaffold_15893 1941 1647 + 19765 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I a score=224766.000000 s hg19.chr17_gl000204_random 42572 145 + 81310 ctgg-gaaga--catg---gatcagctgcagcccctgcccg---cgaagcacttgcagccc----------------aatacgggagatggagctgc-agac--GCCCATCAGG----ATCTGTGATTTTTTGCTCTT-CCTTCTCAGTGCTGATTACAGCTCCC-A-GAAAG-TGCTATG-- s panTro2.chr17 79472755 145 + 83384210 ctgg-gaaga--catg---gatcagctgcagcccctgcccg---cgaagcacttgcagccc----------------aatacgggagatggagctgc-agac--GCCCACCAGG----ATCTGTGATTTTTTGCTCTT-CCTTCTCAGTGCTGATTACAGCTCCC-A-GAAAG-TGCTATG-- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0430519 343 145 - 1067 ctgg-gaaga--catg---gatcagctgcagcccctgccng---cgaagcacttacagccc----------------aatacgggagatggaGCTGC-AGAC--GCCCACCAGG----ATCTGTGATTTTTTGCTCTT-CCTTCTCAGTGCTGATTACAGCTCCC-A-GAAAG-TGCTATG-- i gorGor1.Supercontig_0430519 C 0 C 0 s ponAbe2.chr17_random 16059918 145 + 17838096 ctgg-gaaga--catg---gatcagctgcagcccctgcccg---cgaagcacttacagccc----------------aatacgggagacggaGCTGC-AGAC--GCCCACCAGG----ATCTGTGATTTTTTGCTCTT-CCTTCTCAGTGCTGATTACAGCTCCC-A-GAAAG-TGCTATG-- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75033817 145 + 78773432 ctgg-ggaga--tgtg---gatcagctgcagcccctgcccg---caaagcacttacagccc----------------aacacgggagacggagctgc-agac--GCCCACCAGG----ATCTGTGATTTTTTGCTCTT-CCTTCTCAGTGCTGATTACAGCTCCC-A-GAAAG-TGCTATG-- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 41205 145 - 95547 ctgg-ggaga--tgtg---gatcagctgcagcccctgcccg---caaagcacttacagccc----------------aacacgggagacggagctgc-agac--GCCCACCAGG----ATCTGTGATTTTTTGCTCTT-CCTTCTCAGTGCTGATTACAGCTCCC-A-GAAAG-TGCTATG-- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 43030 144 + 225949 ctca-ggagg--cgtg---gatcagcggcagtccctgccca---cgaagcacttacagccc----------------agtacgggagacagagctgc-agac--GCCCACCAGG----ATCTGTGA-TTTTTGTTCTT-CCTTCTCAGTGCTGATTCCAGCTCCA-A-AAAAG-TGCTACG-- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 434 147 + 1188 ctggaggaaa--taag---gaccagctttggtccctgtctt---cgaaacacttgcaatcc----------------aatacaggagacagatatgc-aaac--aCCCACCAGG----ATCCACCATTTTTCATTCTT-CCCCATTAGTGCTGATTGCAGCTCCCAA-GAAAG-TGCCATG-- i tarSyr1.scaffold_458502 C 0 C 0 s tupBel1.scaffold_124459.1-15939 8881 133 + 15939 CTAG-GGAGAAGCAAG---GTTGGGCCAGGGCTGCGGTCTT---CAAAGCACTCATGACCC----------------GATGCAGGAGACGGAGGTGC-AGAC--ACT--GCGGG----TTCCACGACTCCCGGCTCCT-CCCACCAGGTGCTGATCACCGCTCTC---------------G-- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118756239 130 + 121843856 CTGA-AGATC--CG-----------CCATGGTTCCTGCCTGCTTGCTGCCTGCTAACA-------------------AGCTAAAGAGACAGGTGCAC-AAAC--ACCCACCC-A----ATCTGTCACCTTCCATTTTT-CCCCACCAGTGCTGAATTCGGCTCCC-A-GAAAA-------G-- i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_53224 6612 119 + 10229 GCAG-AGGTC--AG------------CGTGGTTTGGGGAAGTACGGAGGAGGAGGAGGAGC----------------AGCAGCAGCAGCAGGTGTGC-AAAC--ACCCACCC-G----AGCTGTCACGCCCCACCCTT-CGTCACCCATACGGCCTACA------------------------ i dipOrd1.scaffold_53224 C 0 N 0 s cavPor3.scaffold_76 4386590 96 + 7991924 CCAG-ATGTA--AG------------------------------GCTGGCTG-------------------------AGCAGGA--------------AGAC--TCGACCCT-C----GTGTGTCATCTTCTGGGCTC-CCATATCTGTGCTGACCATAGCTTCC-A-GAAAAA---TATG-- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 4077 143 + 44242 CTGG-GGGAC--AGGG---A--TCCCGATGGTTCCTGCCTT---GGAGGCACTAAGGATCT----------------GGTGTCGGAGACAGGTGTCC-CAAC--ACCTCCCA-G----ATCTGTCATCTCCCACTCTT-CCTTATCAGTGCTGATTGCAGCCCCC-A-GAAAAGTGCTGTG-- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 16514 154 + 41507 --GG-AGGAG--AGCG---CCTTGCTAAGTGTTCCGGC------GCTGGCCTCGGAGCTCTGTCAGCTCCCCCAGAAAGCGCGGGAGATGGG-GTGC-AAAC--ACCTGCCA-G----GCCTGCCCTCCCCCA-TCTG-CCCCCCTGGTGCTGGCAACGGCCCCC-A-GAGATGTACAGTG-- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 125813 140 + 145505 ------------ctgg---gggaaaacagggtccctgcttt---caaagcctttacactct----------------gatacaggagacgggtgtgc-aaac--aTCTAGAAGGATCTATCTATCAGTTTTCATTCTT-CCTTAGGAGTGCTAATTACCGCTCCC-A-GAAAG-TGCTGCG-- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10856886 135 - 65312493 ------------ct-g---gggaaaacagggtccctgccat---caaagcctttccaatct----------------gacacagcagacagatgtgc-aaac--aCCTACCAGG----ATCTATCACTTTTCATTCTT-CCTTATGAGTGCTAATTACCGCTCCC-A-GAAAG-TGCTGCG-- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58039860 116 - 61308211 --------------TG---GGGGAGACAGGTCCCCTGCCTT---CGATACA--------------------------------GGAGACAGGTGTGC-CAAC--ACCTACCAGG----ATCCATCATTTTTCATTCTT-CCTTATCCGTGCTAATTACGGCTCCC-ACGAAAG-TGTG----- i equCab2.chr11 I 1 C 0 s canFam2.chr9 59434477 135 - 64418924 --------------TG---CAGGagacggggtccctgcctt---cgaagcatttacgatcg----------------acgg-gggagacagatgtgc-aaacTTACCTACCGGG----ACCTGTCATTTCTCATTCTT-CCTCATCGGGGCT-GTTATAACTCCC-AGAGAAG-TGCCATG-- i canFam2.chr9 I 1 I 183 s myoLuc1.scaffold_4816 7372 115 + 14340 ---------------C---CAGGAAGCAGAGGCCCCGCCTT---CGAAGCATCTACAACCG----------------AAT---GCACACCAGTGCG-----C--ACCCACCAGG----A--CGCGGCTTCTCGTGCCT-CCTCGTCAG-GCTG---GTGCGGCTC-CGGGGAG-C-------- i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 12440 122 + 48268 ---------------C---TGGGGAACAG-GTCCCCGCCTG---C----CATC-----CGG----------------TAT---GGAGACCGATGTGC-CAAC--ACCCACCAGC----ATCCGTGGGTTCCCATCCGTCCCTCATCAGTGCTGATTATGGGTCCC-CGGAAAG-TGCTGAG-- i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_290756 3394 123 - 7602 -------------------------CAAGGGTCTCTGCCTT---GGAAGTGTGTGCAGACT----------------GAC---AGAGACAGGTATGTGGAAC--ACATACT--G----CCCCCTGAGCTGTCATCTGC-CCCCATCAGTATTTATTACACCTTTC-TGTGAAG-TTGGGGT-- i eriEur1.scaffold_290756 C 0 I 15 s loxAfr3.scaffold_49 14430222 122 - 17734757 gtgg-ggaca--agag-------------AGCTCCCGCCTT---GGAAGCACTTACCATCT----------------GACACGGGAGGCAGATGTGC-AAGC--AGCCACCAGG----ATCTGTGACGCCCCATTCTT-CCTCGTAAGTGCTAATGACCACTCCC------------------ i loxAfr3.scaffold_49 C 0 I 4 s dasNov2.scaffold_28617 10095 142 + 20752 CTGG-GGACA--CGAGGGGGGCCGGCCTCAGCACCTACCCT---CGGAGCCCTTCCAGTGT----------------GATACGGT-GACAGATGTTC-AAAC--TGATGCCAGG----A--TGTCACATTGCGTTCCT-CCTTGTGGTTCCCA---GCCGCTCCC----AGAG-CGCACGGCT i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_9426 3311 449 - 54875 I e proCap1.scaffold_29042 13928 801 + 24616 I e micMur1.scaffold_15893 1941 1647 + 19765 I e felCat3.scaffold_206428 11789 719 + 132007 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I a score=-48509.000000 s hg19.chr17_gl000204_random 42717 41 + 81310 -GGAAG------CAGGTGCTGACATCAGGCCCAGAGGGAGGCTTTGTG s panTro2.chr17 79472900 41 + 83384210 -GGAAG------CAGGTGCTGACATCAGGCCCAGAGGGAGGCTTTGTG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0430519 488 41 - 1067 -GGAAG------CAGGTGCTGACATCAGGCCCAGAGGGAGGCTTTGTG i gorGor1.Supercontig_0430519 C 0 C 0 s ponAbe2.chr17_random 16060063 41 + 17838096 -GGAAG------CAGGTGCTGACTTCAGGCCCAGAGGGAGGCTTTGTG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75033962 41 + 78773432 -GAAAG------CAGGTGCTGACTTCAGGCCCAGAGGAAGGCTTTGTG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 41350 41 - 95547 -GAAAG------CAGGTGCTGACTTCAGGCCCAGAGGAAGGCTTTGTG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 43174 28 + 225949 -GAAAG------CAGGTGCTG-----AGGCCCAGAGGGAG-------- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 581 41 + 1188 -AAAAG------CAGGTGCTGCTTTCAAGCCCAGAAGGAAGCTCTGTG i tarSyr1.scaffold_458502 C 0 C 0 s tupBel1.scaffold_124459.1-15939 9014 40 + 15939 -ACACG------CAGCTGCCGACTCCAAACCC-GAGGGAGGCTTCGGA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118756369 37 + 121843856 -AGTGC------TGAGGACAGTC----ACCCATAAGGAAGGCCCTGTG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4386686 33 + 7991924 -AAAGA------CGAGGTGGGGC----TGC----AGAACGGCTTTGCA i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 4220 31 + 44242 -ACAGA------TGGGG----------GCCTGTGGGGATGGCTCTGCA i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 16668 23 + 41507 -CAGGC------CCAG------------------AGGGAGCCCGTGTG i oryCun2.chrUn0958 C 0 I 31 s turTru1.scaffold_106006 125953 39 + 145505 -AAAGA------CAGGG--TGCTGTCAGGCCTGGAAGAAGCCATGAGG i turTru1.scaffold_106006 C 0 I 14 s bosTau4.chr19 10857021 39 - 65312493 -AAATA------GAGGG--TGCTGTCAGGCCCAGAGGGAGCCACGAGA i bosTau4.chr19 C 0 I 14 s equCab2.chr11 58039976 42 - 61308211 -AAAGATGGGTGCTG-----ACTGTCAGGCCCAGAGGGAGCCAGGAGC i equCab2.chr11 C 0 I 13 s canFam2.chr9 59434795 28 - 64418924 -AAAGA-------------------CAGGGACGGACGGAGCCATAAGG i canFam2.chr9 I 183 I 13 s myoLuc1.scaffold_4816 7487 27 + 14340 ------------CGG-----GCTGTCAGGC-CCCAGGAGGCCG---GG i myoLuc1.scaffold_4816 C 0 I 13 s pteVam1.scaffold_11245 12562 36 + 48268 -AAAGA------CGGGG--TGCTGTCGGGG-CGGAGAAAGCCAT--GG i pteVam1.scaffold_11245 C 0 I 13 s eriEur1.scaffold_290756 3532 11 - 7602 ------------------------------------GGAAGCATG-AA i eriEur1.scaffold_290756 I 15 I 13 s dasNov2.scaffold_28617 10237 34 + 20752 CGGGAC------TGGGG--------CACACCCTGCCGGGGGCTCTGGG i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_9426 3311 449 - 54875 I e proCap1.scaffold_29042 13928 801 + 24616 I e micMur1.scaffold_15893 1941 1647 + 19765 I e felCat3.scaffold_206428 11789 719 + 132007 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I e loxAfr3.scaffold_49 14430344 4 - 17734757 I a score=144751.000000 s hg19.chr17_gl000204_random 42758 169 + 81310 -GATG-CTTCTC--------------ATGTCC-TCTGCGTGCCTGTCTACGTCAG-----TACGTCCCACTTGCTCACC-GCCT---TAG---ATACACCCAGTGATAACCTATGGCTTCGCTATGTTCCGTG------------TTGATAGAAGGATCCA-AAACCT-TCCCGTTGGCCTTCACCGTC------TACTTAACGAGCCACGCCCCTCC s panTro2.chr17 79472941 169 + 83384210 -GATG-CTTCTC--------------ATGTCC-TCTGCGTGCCTGTCTACGTCAG-----TACGTCCCACTTGCTCACC-GCCT---TAG---ATACACCCAGTGATAACCTATGGCTTCGCTATGTTCCGTG------------TTGATAGAAGGATCCA-AAACCT-TCCCGTTGGCCTTCACCGTC------TACTTAATGAGCCACGCCCCTCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0430519 529 169 - 1067 -GATG-CTTCTC--------------ATGTCC-TCTGCGTGCCTGTCTACGTCAG-----TACGTCCCACTTGCTCACC-GCCT---TAG---ATACACCCAGTGATAACCTATGGCTTNGCTATGTTCCGTG------------TTGATAGAAGGATCCA-AAACCT-TCCCGTTGGCCTTCACCGTC------TACTTAACGAGCCACGCCCCTCC i gorGor1.Supercontig_0430519 C 0 C 0 s ponAbe2.chr17_random 16060104 169 + 17838096 -GATG-CTTCTC--------------ATGTCC-TCTGCGTGCCTGTCTACGTCAG-----TACGTCCCACTTGCTCACC-GCCT---TAG---ATACGCCCAATGATAACCTATGGCTTCGCTATGTTCCGTG------------TTGATAGAAGAATCCA-AAACCT-TCCCATTGGCCTTCACCATC------TACTTAATGAGCCACGCCCCTCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75034003 167 + 78773432 -GATG-CTTCTC--------------ATGTCC-TCT--GTGCCTGTCTACGTCAG-----TACGTCCCACTTGCTCACC-GCCT---TAG---ATACACCCAATGATAACCTATGGCTTCGCTATGTCCCGTG------------TTGATAGAAGGATCCA-AAACCT-TCCCATCGGCCTTCACCATC------TACTTAATGAGCCAAGCCACTCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 41391 169 - 95547 -GATG-CTTCTC--------------ATGTCC-TCTGTGTGCCTGTCTACGTCAG-----TACGTCCCACTTGCTCACC-GCTT---TAG---ATACACCCAGTGATAACCTATGGCTTCGCTATGTCCCGTG------------TTGATAGAAGGATCCA-AAACCT-TCCCATCGGCCTTCACCATC------TACTTAATGAGCCAAGCCACTCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 43202 166 + 225949 ----G-CTTCTC--------------ATGTCC-TCTACGTGCCTGTCTACATCAG-----TACACCCCACTGGCTCACC-GCCT---TAG---ATACATCCAGCGATAACCTATGACCTCGCTATGTCCCATG------------TTGATAGAAGGATCTA-GAACCT-TTCTTCTAGCCTTAACCATC------TACTTAATGAGCCACACCACTCC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 622 160 + 1188 -GATG-CTTTTT--------------GTGTCC-TTTGTGTG-ATGTGTGTGGCAG-----TTCATCCCACATGACCACT-GCCT---TAG---ATACAGCCACTGATAATGTATGTTCTTACAA--------G------------TTATTAGAAGGATCCA-GAACCT-TCCTTTTGACCTTCACCATC------TATTTAACTGGCCAAGCAGCTCC i tarSyr1.scaffold_458502 C 0 C 0 s tupBel1.scaffold_124459.1-15939 9054 144 + 15939 -GACG---------------------------------AGGGCAGACCACGCAAG-----CAT-TTCCATGCGCCCACT-CTCC---T------TACAGCCACGGGTAACT----GCCTCGCCGTGCCCCATG------------TT-TCGGAAGGTTCCA-GAGCCTGTCCCGTCAGCCTCCACCATC------TACTTAGCCAGCCAGGAAGCTCC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s speTri1.scaffold_128901 4251 123 + 44242 ---TG-TCCCTC--------------CT------AGGCATGCACGTC-------------CACGTGGCACCTGCCC-CA-GACGGCACGG---ATGGCACATG------------GCCTCTCTGTGCC-------------------------GGGGTCCA-GTACCC-TCCCCTTTGCCTTCTCCATC------TACTTAGCC--------AGTTCC i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4386719 123 + 7991924 ---GG-TCCTTC--------------GTGCAA-CAGGCATGCACA---------------CACAGTCCCTGTGCCC-CT-GACT---TAG---ATGCAGCCCT------------GGCCTTCTGT------------------------------GCTCTGTGCAGTC-TTCCGCAGGCCTGTGCCG-T------CACTAGGCCAGCCA---AGGTAC i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118756406 118 + 121843856 ---TG-TCCTTC--------------CTGCAG-ATGTCCTACATG---------------------------GCTA-CT-GCTG---TGC---ATACAGCCAC------------AAGTCACTGTA---------------------------GAAGTCCAGACCTCC-TTCCCGTTGCTATTGTCACT------TACTTAGCATAACAAGCAGCTCC i mm9.chr11 C 0 C 0 s turTru1.scaffold_106006 126006 161 + 145505 -ACAG-CTTCTC--------------ATGTCC-TTTGTGTGA-GGTGTGCAAG-------TAAGTTCCAAATGCCCACCCGCCT---TAG---ATCCGGCCACAGGTG----------CAGCTCTGCCCCAGG------------TTTGTGGAAGGATCTA-GGACCT-CCCCATTTGTCTTCACCATCTACCCATACC-CACTGGCCAACTACTCC- i turTru1.scaffold_106006 I 14 C 0 s bosTau4.chr19 10857074 143 - 65312493 -ATGG-CTTCTC--------------CTGTCC-TTTGTGTGA-GGAGCACAAGT------TAAGTTCCAGTTGCCCACCAGCCT---TAG---ATAT-----------------------GCCCTGTCCCATG------------CTTGTGAAAGAATCTA-GAATGT-CCCCATTTGTCTTCACCATC------TACC-CACTGGCCAACCATTCC- i bosTau4.chr19 I 14 C 0 s equCab2.chr11 58040031 156 - 61308211 -CAGG-CTTTCC--------------ACGTCC-TCTGCGTGCACATGTGCAGA-------GATCTTCCAAATGCCCACCTACCT---TAG---GTACGGCCATGATT-----------CAGCTCTGCCCTGGG-------------CTGTGGAAGGATCCA-GAACCT-CCCCACTTGCCTTTGCCATC------TACCTGACTGGCTGAGCTGCTCC i equCab2.chr11 I 13 C 0 s canFam2.chr9 59434836 158 - 64418924 -ATGG-CTCTTC--------------ATGTCT-TCTGTGTGAAA--GTACACC-------AACATTCCCGATGCCCACCCACCC---TGG---ACACGGCTGTAGCTG----------CAGCTCTGCCTCGAG-----------GCTTGTGGAAGGATCCA-GAAGCTCCCCCATTTGCCTTCACCATC------TACCTCGCCAGCCAAGCAGGGCA i canFam2.chr9 I 13 I 12 s myoLuc1.scaffold_4816 7527 125 + 14340 -ACGGCTCCCGC--------------GT-----CCTGTGTGACCGTGT------------------------GGCCG-----------------TGCGGCCACGCACG----------CTGCTCTGCCCAGGA-------------CCCTGGAAGGACCCA-GCGCCT-GCCCATTGGCCTTCCCCACC------GCCCTCGC-GGCCAAACCGTCCC i myoLuc1.scaffold_4816 I 13 I 86 s pteVam1.scaffold_11245 12611 150 + 48268 -TGGGGCTCTTC--------------ATGGCC-TTTGTGTGGCAGTGTGCACA-------TATGCTCCATACGGCCGCC-ACCC---T-----ATACAGTCACAGATG----------CTGCTCTGCTC-TGA-------------CTGTGGAAGGATCTA-GAGCCT-T----TTCGCTTTCACTATC------TATCTAACTGGCCAAGTAGCTCC i pteVam1.scaffold_11245 I 13 C 0 s eriEur1.scaffold_290756 3556 184 - 7602 -GTGC-CATtgctacagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg-------tgtgttccaa--agCCATGCACCC---AGGAAAACATGGCCATAGATG----------AACACTGGTCTTGTGTcccccccACCTTTCAAGGAAGGCTCCA-GATCAT-GCATTTCCACCTGAGCTGTC------CACT-AACTAGTCAGCAGCCCC- i eriEur1.scaffold_290756 I 13 C 0 s dasNov2.scaffold_28617 10271 143 + 20752 GGCAG-CTTCCC--------------TTGTTT-TCTGTGCGAATGTCTGCGAGAGGCTCCCAAATGGCAGGGATCGGCC-GCCC---TCG---CTCCACCC------------------------------TG------------TTTGCAGAAGGGCCCT-GAGCCT-CCCCTTTG--CTTCACCATC------TGCTAAACAAGCCGACCCCCTGT i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 16691 31 + 41507 I e ochPri2.scaffold_9426 3311 449 - 54875 I e proCap1.scaffold_29042 13928 801 + 24616 I e micMur1.scaffold_15893 1941 1647 + 19765 I e felCat3.scaffold_206428 11789 719 + 132007 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I e loxAfr3.scaffold_49 14430344 4 - 17734757 I a score=124106.000000 s hg19.chr17_gl000204_random 42927 70 + 81310 TAGG-ACACCGCAAGAGAAATGCTGGGGTCACCCCTGGCCGAGGCCTCCCTCCTGCTG--GCCACAC----GTAA---GA s panTro2.chr17 79473110 70 + 83384210 TAGG-ACACTGCAAGAGAAATGCTGGGGTCACCCCTGGCCAAGGCCTCCCTCCTGCTG--GCCACAC----GTAA---GA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0430519 698 70 - 1067 TAGG-ACACTGCAAGAGAAATGCTGGGGTCACCCCTGGCCAAGGCCTCCCTCCTGCTG--GCCACAC----GTAA---GA i gorGor1.Supercontig_0430519 C 0 C 0 s ponAbe2.chr17_random 16060273 68 + 17838096 TAGG---ACTGCAAGAGAAATGCTGGGGTCACCCCTGGCCTCGGCCTCCCTCCTGCTG--GCCACAC----GTAA---GA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75034170 70 + 78773432 TAGG-ACTCTGCAAGAGAAATGCTGGGGTCACCCCTGGCCTCGGCCTCCCTCCTGCTG--GCCACAC----ATAA---GA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 41560 70 - 95547 TAGG-ACTCTGCAAGAGAAATGCTGGGGTCACCCCTGGCCTCGGCCTCCCTCCTGCTG--GCCACAC----ATAA---GA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 43368 70 + 225949 TAGG-ATTCTGCAAGAGAAATGCCGGGGTCACCCCTGGCCTCAGCCTCCCTCCTGCTG--GCCACAT----GTAA---GA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 782 68 + 1188 TAGATTCTCTGGAAGAAAAGT---TGGGTCACCCTTGGCCTCAGTCTCCCTACTGCCA--GCCACAC----ATAG---GA i tarSyr1.scaffold_458502 C 0 C 0 s tupBel1.scaffold_124459.1-15939 9198 67 + 15939 TAGT-ATTCTCCAGGAGGAACGCT--AGTCACCC-TGGCCTTGGCCTCCCTCCTGCTG--GCCCCAC----GCCT---GA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s speTri1.scaffold_128901 4374 72 + 44242 TTGG-ATGCTTCAGGAGAAACGCCTGGACAT-CCCTGGCCTCAGCCTCCCTCCTGCCA--GCCACTC----CTATGACCA i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4386842 56 + 7991924 TGGG-AAGCTCTGGGAG--------GAACCA-CCTCAGCCTCGCTCACACCCCCTGCA--CACCCG------------GA i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118756524 62 + 121843856 CATG-ATGCTCCGTGAGAGGTGTACAAGCCAGCTTGGGCCTCACTCTCCTACCTTCCA--GCCAC--------------- i mm9.chr11 C 0 C 0 s turTru1.scaffold_106006 126167 64 + 145505 CAAG-ATTCTCTAGGAGAAATGC--AGGTCACCCCCAGCCTCAGCATCCC-ACTGCCCACTCCACAT----A-------- i turTru1.scaffold_106006 C 0 I 3 s bosTau4.chr19 10857217 61 - 65312493 TAAG-ATCCTATAGGAGAAATCC--AGGCCACCCCTGGCCTCAGCACCCC-ACTGTCTG-TCAAAA-------------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58040187 65 - 61308211 TAGG-ATTCTCCAGGAGAAACGG--AGTCC-CCTTGGGCCTCAGCGTCCC-ACTGCCG--GCCACACGTTAA-------- i equCab2.chr11 C 0 I 2 s pteVam1.scaffold_11245 12761 61 + 48268 TACA-AGTCTCCAGGAGAAATGC--AAGTA-ACCCTGGCCTCGACGTCCC-GCTGCCA--TCCACGT----A-------- i pteVam1.scaffold_11245 C 0 I 2 s eriEur1.scaffold_290756 3740 33 - 7602 ------------AGAAAAAATGG--GGTCA-GCTCTGGCCTCAGC-------CTG------------------------- i eriEur1.scaffold_290756 C 0 C 0 s dasNov2.scaffold_28617 10414 66 + 20752 TAGC-TTTCTCCAGGGGGGACGCTGGG----CCCCCAGCCCTGGCCTCGCAGGGACGC--GCAACAC----GGAT---GA i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 16691 31 + 41507 I e ochPri2.scaffold_9426 3311 449 - 54875 I e proCap1.scaffold_29042 13928 801 + 24616 I e myoLuc1.scaffold_4816 7652 86 + 14340 I e micMur1.scaffold_15893 1941 1647 + 19765 I e felCat3.scaffold_206428 11789 719 + 132007 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59434994 12 - 64418924 I e loxAfr3.scaffold_49 14430344 4 - 17734757 I a score=418277.000000 s hg19.chr17_gl000204_random 42997 150 + 81310 AAGGACTTCACAAGGGAGACCTCCGTGGCTG---CCACACACATTCA-CCCCAAATGCTTCCTGGAGAAAG-CA-CATGCCCTCACACTGTGAGCTCGTGAGTTTGCCAAAAAGGAGATGC----------------AGGAGCCTGA-GATCACC---TCCTGTCTTGCTGCTAAA s panTro2.chr17 79473180 150 + 83384210 AAGGACTTCACAAGGGAGACCTCCGTGGCTG---CCACACACATTCA-CCCCAAATGCTTCCTGGAGAAAG-CA-CCTGCCCTCACACTGCGAGCTCATGAGTTTGCCAAAAAGGAGATGC----------------AGGAGCCTGA-GATCACC---TCCTGTCTTGCTGCTAAA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0430519 768 150 - 1067 AAGGACTTCACAAGGGAGACCTCCGTGGCTG---CCACACACATTCA-CCTGAAATGCTTCCTGGAGAAAG-CA-CCTGCCCTCACACTGCGAGCTCGTGAGTTTGCCAAAAAGGAGATGC----------------AGGAGCCTGA-GATCACC---TCCTGTCTTGCTGCTAAA i gorGor1.Supercontig_0430519 C 0 C 0 s ponAbe2.chr17_random 16060341 150 + 17838096 AAGGACTTCATGAGGGAGACCTCCGTGGCTG---CCACACACATTCA-CCCCAAATGCTTCCTGGAGAAAG-CA-CCTGCCCTCACACTGCGAGCTCATGAGTTTGCCAAAAAGGCGATAC----------------AGGAGCCTGA-GATCACC---TCCTGTCTTGCTGCTAAA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75034240 150 + 78773432 AAGGACTTCATGAGGGAGACCCCCCTGGCTG---CCGCACACAGTCA-CCCCAAATGCTTCCTGGAGAAAG-CA-CCTGTCCTCACACTGCGAGCTCATGAGTTTGCCAAAAAGGCAATGC----------------AGGAGCCTGA-GATCACC---TCCTGTCTTGCTGCTAAA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 41630 150 - 95547 AAGGACTTCATGAGGGAGACCCCCCTGGCTG---CCGCACACATTCA-CCCCAAATGCTTCCTGGAGAAAG-CA-CCTGTCCTCACACTGCGAGCTCATGAGTTTGCCAAAAAGGCAATGC----------------AGGAGCCTGA-GATCACC---TCCTGTCTTGCTGCTAAA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 43438 150 + 225949 AAGGACTTCACGAGGGGGACCCCCGTGGCTG---CCACCTACATTCA-CCCCAGATGCTTCCTGGAGAAGG-CA-CCTGCCCTCACACTGCCAGCTCAGGAATCTGCCAAAAAGACGATGC----------------AGGAGCCTGA-CATCACC---TCCTGTCTTGCTGCTAAA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 850 149 + 1188 AAGGATTTCATGAGCGAGACCCTCATGGCTG-----GGCTGCATCAA-TCCCAAATGCTTCCTCAAGAAAT-CACCCTGCCCTCACACTGCAGGCTCCAGAATTTGCCAAAAAGATAAAGC----------------AAGAGTCTGA-GATCACC---TCTCATCTTACTGCTAAA i tarSyr1.scaffold_458502 C 0 C 0 s tupBel1.scaffold_124459.1-15939 9265 141 + 15939 GAGGACAGCAAGAGGGAGACCCACGC--CTG---CCGCACACCTGCAGCCCCAAACATTCCCCCAGGGAAG-TG-CCTGCCCTTCTACCACAGGCTCGCGAATTGGCC---GAGGCCATGA----------------ACAGTACGGA-GA--GCC---TCTTCTCTCGCTG---AG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s speTri1.scaffold_128901 4446 150 + 44242 CGGGACTCCGTGAGAGGG--CACGGCGGCTG---CTGCACATACCCAGCCCCAAATGTTCTCCTGAGAAAGCCC-CCTGCCCTTACACCACAGGCTCCCACACGTGCCAGAAGATTGATGC----------------AAGAGCTTGC-AGTCACC---GCCCATCTTGCTGCTAAA i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4386898 128 + 7991924 AGGGACCCAGGCAG-----------------------CACTTCCTCAGCCCCACCTGTTTCCCC--GCACTGCC-CTGGCCCCACCACCACCGGCTCCCGCATTTGTCCAGAAGCCCACAC----------------GAGTCA--GC-ACTCGCT---GCCTAGCGCACTGTTCAA i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118756586 92 + 121843856 -AGGACCTATACAA-----------------------------------CCCAATTGTTTCC----------TT-CAGAAAATGCTGCCACCA----------------AGATGGTGACAC----------------AAGAGAGTGT-GTTCGCC---ACCT-GCTTGCTGCTGAG i mm9.chr11 C 0 C 0 s turTru1.scaffold_106006 126234 111 + 145505 AAGGACGTCATGAG-GAGACACCAG----------------GGCTC-----C---TGGTTCCTCAAGAAAA-CA-CCTGCCCTTAAACCAGGGGTTCATGAATTGGCCAAAAACACAATGC----------------CAGAGTCTGA-GATCACA--------------------- i turTru1.scaffold_106006 I 3 C 0 s equCab2.chr11 58040254 111 - 61308211 AAGGACTTCCGGAG-GAGACCTC------------------CGCCC-----CAAACGTCTCCTTGAGAAAA-CA-CTCACCCTCAAACCACAGGCTTATGAATTGGCCGAAGGGGAGATGC----------------CAGAG-TTGA-GATCACC--------------------- i equCab2.chr11 I 2 C 0 s pteVam1.scaffold_11245 12824 133 + 48268 AAGGACGTCATGAG-AAGACCCCAA-GGCCC---CTGGGCTCGCTCA-ACACGGATGTCCCCTCAAAGAAT-CA--------------CACAGGCTTGTGAACCGGCCACAAGGGTGGTGAACCAGCCACAAGGGCGCAGAGCCCAA-GGTCACC--------------------- i pteVam1.scaffold_11245 I 2 C 0 s eriEur1.scaffold_290756 3773 133 - 7602 GAGGACTTCATAAG-GAGACCCCAA-GGCTT---GTGGGTTCATTCA-CCTCAAATGTTTCTTCCAGAAA--CA-CCTGCCCATAAGCCATGGGAGCACAGACTGACCAAATAGACAGTGT----------------CAATGTCCAAGGGCCACCTTC------------------ i eriEur1.scaffold_290756 C 0 I 634 s dasNov2.scaffold_28617 10480 153 + 20752 AGGGGCTTCACCAG-GAGACCCTTGTGGCTCCGTCTGGGCTCATTCACCCCCAAACGCTGCCTCGAGAAAC-CA-CCTGCTCTTAAACTACAGACTCATGAAGTCACCGAAAAGGGGGTGC----------------AAGTGTCTGC-GCCCACC---TGCCATCTCGCTGCTAAA i dasNov2.scaffold_28617 C 0 I 226 e oryCun2.chrUn0958 16691 31 + 41507 I e ochPri2.scaffold_9426 3311 449 - 54875 I e proCap1.scaffold_29042 13928 801 + 24616 I e myoLuc1.scaffold_4816 7652 86 + 14340 I e micMur1.scaffold_15893 1941 1647 + 19765 I e felCat3.scaffold_206428 11789 719 + 132007 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59434994 12 - 64418924 I e bosTau4.chr19 10857278 0 - 65312493 C e loxAfr3.scaffold_49 14430344 4 - 17734757 I a score=162219.000000 s hg19.chr17_gl000204_random 43147 115 + 81310 ATATCCCAGCCGT-----GGAAAAGCAAGGCTGGC------CTCAAATTGGGGAATCTGGT-----------CTTGC----------------CAGCCCAGCTGTGCTCCAGGGACTCCGGTTTGCA-TTGGGAATG----AGAGAG---TGTTGGC-CGGG s panTro2.chr17 79473330 115 + 83384210 ATATCCCAGCCGT-----GGAAAAGCAAGGCTGGC------CTCAAATTGGGGAATCTGGT-----------CTTGC----------------CAGCCCAGCTGTGCTCCAGGGACTCCGGTTTGCA-TTGGGAATG----AGAGAG---TGTTGGC-CGGG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0430519 918 115 - 1067 ATATCCCAGCCNT-----GGAAAAGCAAGGCTGGC------CTCAAATTGGGGAATCTGGT-----------CTTGC----------------CAGCCCAGCTGTGCTCCAGGGACTCCGGTTTGCA-TTGGGAATG----AGAGAG---TGTTGGC-CGGG i gorGor1.Supercontig_0430519 C 0 C 0 s ponAbe2.chr17_random 16060491 115 + 17838096 ATATCCCAGCCGT-----GGAAAAGCAAGGCTGGC------CTCAAATTGGAGAATCTGGT-----------CTTGC----------------CAGCCCAGCTGTGCTCCAGGGACTCCGGTTTGCA-TTGGGAATG----AGAGAG---GGTTGGC-CGGG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75034390 115 + 78773432 ATATCCCAGCCAT-----GGAAAAGCAAGACTGGC------CTCAAATTGGGGAATCTGGT-----------CTTGC----------------CAGCCCAGCTGTGCTCCAGGGACTCCGGTTTGCA-TTGGGAATG----AGAGAG---GGCTGGC-CGGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 41780 115 - 95547 ATATCCCGGCCAT-----GGAAAAGCAAGACTGGC------CTCAAATTGGGGAATCTGGT-----------CTTGC----------------CAGCCCAGCTGTGCTCCAGGGACTCCGGTTTGCA-TTGGGAATG----AGAGAG---GGCTGGC-CGGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 43588 112 + 225949 ATATCCCTGCAAT-----GGAAAAGCAAGACTGGC------C-CAAACTGGGTGATCTGGT-----------CTTGA----------------CAGCCCCGCTGAGCTCCAGGGACTCTGGTTTGCA-CTGGGAAT------GAGAC---GGCTGGC-CGGG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 999 107 + 1188 ATATCCTAGCCAT-----GGAAAAGCAAGACTGGC------CTCAAGATAGGAAATCTGGCCCTGCTAGGTGCTTGC----------------CAGCCCAGCTGTGCCCA--------------------GGGAATG----AGAGAG---AGCTGGC-CGGG i tarSyr1.scaffold_458502 C 0 C 0 s tupBel1.scaffold_124459.1-15939 9406 113 + 15939 ACGCCCCTGCCAG-----GG--GAGTGAGGCTGG------------------GGACCTGGC-----------CCTCAGAGAC----CCT---GCAGCCCAGCTGTGCCCAGGGAACATGGTTGCAAA-TTGGTTTTG----AGCTAGTACGGCTGCC-AGGC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118756678 97 + 121843856 GTGTCCCTGCTGA-----GGAGAAACAAGGCCAGC------CCAAGGC--GTAA--------------------------------------------CAGGAGCCTGCTGGTACCTCAAGTTTGTG-CTAGCAATG----AGTGAG---GGCTGGCTATTG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4387026 119 + 7991924 ATGTCCCTGCCAC-----AGCAAAACAA-GCTGGC------CTAGGGT--GGGAATGTGGT-----------TCTGGCACAT----TCT----GGG-CCAGCAGTGCCCAGGGACCTGAGGTCTGCA-TTTGGAATG----AGTGAA---GGCTGTC-AGAG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 4596 117 + 44242 ATGCCCCTGCCGT-----GGAAAGGCAAGACTGGC------CCAGGGC--GGGGACCCAGT-----------CCTGCCAGGA----GCT---CCAG-CCTGGGAAGCCCAGGGACTC--AGGCTGC--CTTGGAATG----CAAGA----GTCTGGC-CGGG i speTri1.scaffold_128901 C 0 C 0 s ochPri2.scaffold_9426 3760 101 - 54875 ATCTCCCCACTGT-----GGGGA------GCTGGG------CCCTGCA--GGGAGCCCGC---------------------------------AAG-CCCAGCATGCCCAGGGACACCAGGTTTGTACCTGGCTTTG----GGTGTA---ACCAGTC-CGAG i ochPri2.scaffold_9426 I 449 C 0 s turTru1.scaffold_106006 126345 78 + 145505 ---CCCCATCCAT-----GGAATAGTGAGACTGGC------ATGAAGTTGGGGAAT-TGGC-----------TCCAGTTGGG--------------------------------------------------GAATG----AGCGAG---GACCAGC-TGTG i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58040365 131 - 61308211 ---TCCCACGCAGAAACAGAAAAAGTGAGACTGGC------GTGAAGATAGGAGCC-AGGT-----------CCCGCGAGGG----GCTCCACCAG-CCAGTCAGGCGGAAGGAATGCAGCTTACCA-CGTGGAGCGAGCAAGCGGG---GACCGGC-CGGG i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_11245 12957 110 + 48268 ---CCCCATCTGT-----GAAAAAATGCAGCCTGCGAGTCGGTGAAGAAGGG------GGT-----------GCCGTGGAGGCCGAGCTGGGCCAG-ACACAGGGGC-----------------CTA-TTTAGAAGG----CGTGAG---GACTGGC-CGGG i pteVam1.scaffold_11245 C 0 I 8 e oryCun2.chrUn0958 16691 31 + 41507 I e proCap1.scaffold_29042 13928 801 + 24616 I e myoLuc1.scaffold_4816 7652 86 + 14340 I e micMur1.scaffold_15893 1941 1647 + 19765 I e felCat3.scaffold_206428 11789 719 + 132007 I e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59434994 12 - 64418924 I e bosTau4.chr19 10857278 0 - 65312493 C e loxAfr3.scaffold_49 14430344 4 - 17734757 I a score=69906.000000 s hg19.chr17_gl000204_random 43262 35 + 81310 TAAGATGGCAAGACAGACACAGTCCTCCTACAGAC s panTro2.chr17 79473445 35 + 83384210 TAAGATGGCAAGACAGACACAGTCCTCCTACAGAC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0430519 1033 32 - 1067 TAAGATGGCAAGACAGACACAGTCCTCCTACA--- i gorGor1.Supercontig_0430519 C 0 n 0 s ponAbe2.chr17_random 16060606 35 + 17838096 TAAGATGGCAAGACAGACACAGTCCTCCTACAGAC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75034505 35 + 78773432 TAAGATGGCAAGACAGACACAGTCCTCCTACAGAC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 41895 35 - 95547 TAAGATGGCAAGACAGACACAGTCCTCCTACAGAC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 43700 33 + 225949 TAAGATGGCAAG--AGACACAGTCCTCCCACGGGC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 1106 35 + 1188 TACTCAGGTGAGAGTGACACAGTTCCCATACAGAC i tarSyr1.scaffold_458502 C 0 C 0 s tupBel1.scaffold_124459.1-15939 9519 18 + 15939 CAAGCCTAGAAGGTGGGT----------------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118756775 33 + 121843856 --AGCAGATGAGAGGTATACGGGTCTTCAGCAGAC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4387145 33 + 7991924 --AGAAGGCAAGAAAACCTCGGTCCTCCTACAGAC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 4713 29 + 44242 --CGAGGAGGAGCAGA----GACCCCTGCGCAGGC i speTri1.scaffold_128901 C 0 C 0 s ochPri2.scaffold_9426 3861 33 - 54875 --GGGAGGGGAGGTGGACGCCTTCCTCCTACTGAC i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 126423 31 + 145505 GGAGAAGGGGAGAGATAGGC----CTCCTATGGAG i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58040496 32 - 61308211 AGAGAAGGGGAAGATGAGGCG---CTCGGACGGAG i equCab2.chr11 C 0 C 0 e oryCun2.chrUn0958 16691 31 + 41507 I e proCap1.scaffold_29042 13928 801 + 24616 I e myoLuc1.scaffold_4816 7652 86 + 14340 I e micMur1.scaffold_15893 1941 1647 + 19765 I e felCat3.scaffold_206428 11789 719 + 132007 I e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I e pteVam1.scaffold_11245 13067 8 + 48268 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59434994 12 - 64418924 I e bosTau4.chr19 10857278 0 - 65312493 C e loxAfr3.scaffold_49 14430344 4 - 17734757 I a score=55812.000000 s hg19.chr17_gl000204_random 43297 21 + 81310 TTGTAGAAGGGCTTTCTGCCC s panTro2.chr17 79473480 21 + 83384210 TTGTAGAAGGGCTTTCTGCCC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16060641 21 + 17838096 TTGTAGAAGGGCTTTCTGCCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75034540 21 + 78773432 TTGTAAAAGGGCTTTCTGCCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 41930 21 - 95547 TTGTAGAAGGGCTTTCTGCCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 43733 21 + 225949 TTGTGGAGGAGCTCTCTGCCC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_458502 1141 21 + 1188 TTGCAGAAAGGTTTTCTGCTC i tarSyr1.scaffold_458502 C 0 N 0 s mm9.chr11 118756808 20 + 121843856 TGGAGAAG-GCTTTCGGTACC i mm9.chr11 C 0 I 2 s cavPor3.scaffold_76 4387178 20 + 7991924 TTCCAGTG-GCTTTTCCAACC i cavPor3.scaffold_76 C 0 I 3 s speTri1.scaffold_128901 4742 20 + 44242 TTGCAGAG-GGCTTTCTGCTC i speTri1.scaffold_128901 C 0 I 2 s ochPri2.scaffold_9426 3894 8 - 54875 TTTCAGGA------------- i ochPri2.scaffold_9426 C 0 I 1082 s turTru1.scaffold_106006 126454 20 + 145505 GTGCAG-CGGGTTTTCTGCTC i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58040528 21 - 61308211 TCGCAGAGGGGTTTTCTGCTC i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_11245 13075 21 + 48268 CTGCGGGAGGGCTTTCTGCTC i pteVam1.scaffold_11245 I 8 C 0 e oryCun2.chrUn0958 16691 31 + 41507 I e proCap1.scaffold_29042 13928 801 + 24616 I e gorGor1.Supercontig_0430519 1065 0 - 1067 I e tupBel1.scaffold_124459.1-15939 9537 0 + 15939 C e myoLuc1.scaffold_4816 7652 86 + 14340 I e micMur1.scaffold_15893 1941 1647 + 19765 I e felCat3.scaffold_206428 11789 719 + 132007 I e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59434994 12 - 64418924 I e bosTau4.chr19 10857278 0 - 65312493 C e loxAfr3.scaffold_49 14430344 4 - 17734757 I a score=147175.000000 s hg19.chr17_gl000204_random 43318 112 + 81310 GCCCCCACCCAGGGCAGAAAGAGGAGGCACAGGGG-AAAACAACAAGAGCC-----C---TGGCCAAGAAT--GAGCCCTCTG-CCGTCGTC-CTGT-GTGT----GGCCTTGTGGCCCAGCACCAGCGC s calJac1.Contig5139 43754 109 + 225949 ACCCCCAACCGGGACAGAAAGAGGGGGTGCAAGGG-AAAACAACAAGAGCC-----C----GGCCAAGAAT--AAGCCC-CTG-CTGTCG-C-CTGT-GTGT----GGCCTTGTAGCCCAGCACCAGGGC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 41951 109 - 95547 GCCCCCACCCGGGGCAGAAAGAGGAGGCACGAGGG-AA---AACAAGAGCC-----C---TGGCCAAGAAT--GAGCCCTCTG-CCGTCATC-CTGT-GTGT----GGCCCTGTGGCCCAGCACCAGCGC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75034561 109 + 78773432 GCCCCCACCCGGGGCAGAAAGAGGAGGCACGAGGG-AA---AACAAGAGCC-----C---TGGCCAAGAAT--GAGCCCTCTG-CTGTCATC-CTGT-GTGT----GGCCCTGTGGCCCAGCACCAGCAC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16060662 112 + 17838096 ACCCCCACCCAGGGCAGAAAGAGGAGGCACAAGGG-AAAACAACAAGAGCC-----C---TGGCCAAGAAT--GAGCCCTCTG-CCTTCATC-CTGT-GTGT----GGCCTTGTGGCCCAGCACCAGCGC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 12252 112 - 64270 GCCTCCACCCAGGGCAGAAAGAGGAGGCACAAGGG-AAAACAACAAGAGCC-----C---TGGCCAAGAAT--GAGCCCTCTG-CCGTCGTC-CTGT-GTGT----GGCCTTGTGGCCCAGCACGAGCGC i gorGor1.Supercontig_0007361 I 45 C 0 s panTro2.chr17 79473501 112 + 83384210 GCCCCCACCCAGGGCAGAAAGAGGAGGCACAAGGG-AAAACAACAAGAGCC-----C---TGGCCAAGAAT--GAGCCCTCTG-CCGTCGTC-CTGT-GTGT----GGCCTTGTGGCCCAGCACCAGTGC i panTro2.chr17 C 0 C 0 s speTri1.scaffold_128901 4764 78 + 44242 G-------------------------GCCTAAGGG-GAGA-AACAGAGATC-----CAGTCAGACCTGAGC--TCCTGCCATGGCCGCCGCG-CTGC---AC----GGC-------CTCGCCAGCAG--- i speTri1.scaffold_128901 I 2 C 0 s cavPor3.scaffold_76 4387201 92 + 7991924 GCCC---------------------AGCTCTAGGG-AAAA-AGTAATAACC-----A---TAGCCACAAGG--GCACACTCTGTCCTCACTG-CTGCCACAG----GGCTTTGAGGCCCGGCACCAGGGC i cavPor3.scaffold_76 I 3 C 0 s mm9.chr11 118756830 92 + 121843856 GCCC---------------------TGCTCAGGGGTCAGA-AACAAGAGTC-----A---CA-CCCCAAAC--CCCTCTGCAGTCCCCCATG-TTACTGAGT----GGCCTCAAAGCTCGGCATCAGCCC i mm9.chr11 I 2 I 1 s turTru1.scaffold_106006 126474 101 + 145505 --------------TTGG----CGGGGCTCAAAGG-AAGGAAACCAGAGCT-----C---TGGCCAAAAATGGGGGCCCTATG-GGGTCCCCACTGT-CCATCCTTGGCCACATGGTCCAGCACTAAGGC i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58040549 102 - 61308211 --------------TCGGCTGGCCAGGCACTAGGG-AAGGAAACCAGATCCCTGTCC---CAGCCGAAAAT--GAGCC--CTG-AGGTCCCC-CTGC-GAACGCCCAGCCTCGTGGTCCAGTGCCAG--- i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_11245 13096 64 + 48268 --------------TTGG--------------------------------------C---CAGCCAAAAAT--GAGCCCTCTG-GGGTCCCCACTGC-TAAT-CCTGACCACGTGGTCCAGCAC------ i pteVam1.scaffold_11245 C 0 C 0 e oryCun2.chrUn0958 16691 31 + 41507 I e ochPri2.scaffold_9426 3902 1082 - 54875 I e proCap1.scaffold_29042 13928 801 + 24616 I e tupBel1.scaffold_124459.1-15939 9537 0 + 15939 C e myoLuc1.scaffold_4816 7652 86 + 14340 I e micMur1.scaffold_15893 1941 1647 + 19765 I e felCat3.scaffold_206428 11789 719 + 132007 I e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59434994 12 - 64418924 I e bosTau4.chr19 10857278 0 - 65312493 C e loxAfr3.scaffold_49 14430344 4 - 17734757 I a score=79092.000000 s hg19.chr17_gl000204_random 43430 79 + 81310 TGGGGGGCACTTTGCCCTGCCTGACAG----GAGGAAGGGATGCCCTAGTGAGGT-GGGAAA----CAGAGGGAGAGGTTGAGACCAC s calJac1.Contig5139 43863 79 + 225949 TTGGG-GCAGTTCACCCTGCCTGACAG----GAGGAAGGGATGCCCCAGTGAGGTGGGGAAG----CAGAGGCAGAGGTTGAAACCAC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 42060 78 - 95547 TGGGGAGCAGTTCTCCCCGCCTGACAG----GAGGAAGGGATGGCCTAGTGAGGC-GGGAAA----CAGAGGGA-AAGTTGAGACCAC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75034670 79 + 78773432 TGGGGAGCAGTTCTCCCGGCCTGACAG----GAGGAAGGGATGGCCTAGTGAGGC-GGGAAA----CAGAGGGAAAAGTTGAGACCAC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16060774 79 + 17838096 TGGGGCGCACTTTGCCGTGCCTGACAG----TAGGAGGGGATGCCCTAGTCAGGT-GGGAAA----CAGAGGGAGAGGTTGAGACCAC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 12364 79 - 64270 TGGGGGGCACTTTGCCCTGCCTGACAG----GAGGAAGGGATGCCCTAGTGAGGT-GGGAAA----CAGAGGGAGAGGTTGAGACCAC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79473613 79 + 83384210 TGGGGGGCACTTTGCCATGCCTGACAG----GAGGAAGGGATGCCCTAGTGAGGT-GGGAAA----CAGAGGGAGAGGTTGAGACCAC i panTro2.chr17 C 0 C 0 s speTri1.scaffold_128901 4842 76 + 44242 CGAGGGGAGCT-----CTCCCCACCAGGCGAGAGGAAGGGAGGCCCCAGCGAGGT-GGACAG----GGAGGGGACAAACAGAGACT-- i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4387293 62 + 7991924 TGGGGAGAGCTCAT--TCCCACAATAG----GAAGAAGGGGTACCCTGGTGAGGA-GGGGAT----ATAGGAG--------------- i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118756923 69 + 121843856 TGAGGAGGGATGAG-ATGCCCCAGCAG----TGGTGTGGAGTAGAAAGACTAGAA-GGTTCTTTGCACAGGAGAC------------- i mm9.chr11 I 1 C 0 s pteVam1.scaffold_11245 13160 4 + 48268 -----------------------------------------------------GT-GG------------------------------ i pteVam1.scaffold_11245 C 0 C 0 e oryCun2.chrUn0958 16691 31 + 41507 I e ochPri2.scaffold_9426 3902 1082 - 54875 I e proCap1.scaffold_29042 13928 801 + 24616 I e tupBel1.scaffold_124459.1-15939 9537 0 + 15939 C e myoLuc1.scaffold_4816 7652 86 + 14340 I e micMur1.scaffold_15893 1941 1647 + 19765 I e turTru1.scaffold_106006 126575 0 + 145505 C e felCat3.scaffold_206428 11789 719 + 132007 I e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59434994 12 - 64418924 I e bosTau4.chr19 10857278 0 - 65312493 C e equCab2.chr11 58040651 0 - 61308211 C e loxAfr3.scaffold_49 14430344 4 - 17734757 I a score=118273.000000 s hg19.chr17_gl000204_random 43509 79 + 81310 CTTGGACAAGAAGGGCCAGGGAAGGCCCTCCT---CACCTGTCACTACAG--CCCGAC-ACTTAGAAGGTACCGCCTGATTTCAG s pteVam1.scaffold_11245 13164 42 + 48268 ----------------------------CTCT---CATCGGTCATTGTCATCCCCAAC-ATCCAGAATTTACTA----------- i pteVam1.scaffold_11245 C 0 C 0 s equCab2.chr11 58040651 54 - 61308211 -----------------------GG---CCCT---CCTCTGTCACTGCCATCCCCAAC-ACCC-GAATTGACTGCCCACTTCCAG i equCab2.chr11 C 0 C 0 s turTru1.scaffold_106006 126575 52 + 145505 --------------------------------CTTCACCTGTCACTGCTGTCCCCAAA-AACTGGAATTTACTGCCCAGAGTCAG i turTru1.scaffold_106006 C 0 C 0 s calJac1.Contig5139 43942 75 + 225949 TTTGGACAAGAAGGGCCGTGGAAGG---TCCT---CACCTGTCACTACAG--CTCGAC-ACTTGGAAGGTACCA-CTGATTTCAG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 42138 79 - 95547 TTGGGACAAGAAGGGTCTGGGAAGGCCCTCCT---CACCGGTCACTACAG--CCTGAC-ACTTAGAAGGTACCACCTGATTTCAG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75034749 79 + 78773432 TTGGGACAAGAAGGGTCTGGGAAGGCCCTCCT---CACCGGTCACTACAG--CCTGAC-ACTTAGAAGGTACCACCTGATTTCAG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16060853 78 + 17838096 TTTGGACAAGAAGGG-CAGGGAAGGCCCTCCT---CACCTGTCACTACAG--CCCGAC-ACTTAGAAGGTACTGCCTGATTTCAG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 12443 79 - 64270 CTTGGACAAGAAGGGCCAGGGAAGGCCCTCCT---CACCTGTCACTACAG--CCCGAC-ACTTAGAAGGTACTGCCTGATTTCAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79473692 79 + 83384210 CTTGGACAAGAAGGGCCAGGGAAGGCCTTTCT---CACCTGTCACTACAG--CTCGAC-ACTTAGAAGGTACCGCCTGATTTCAG i panTro2.chr17 C 0 C 0 s mm9.chr11 118756992 62 + 121843856 ---------------CCCAGGAAGG---CCCT---CATTTGTCACCTAAG--TCCCCCTACCTGGAATGTGTCCCCTGGCTCCAC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4387355 50 + 7991924 -----------------CAGCAAGA-------------TTGTCGCCGAAG--TCCCCA-AACTGGACAGTACCCCTGGATT--AA i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 4918 62 + 44242 --------------GCTACGTACGG---CACT---CATCTATCACCAAAG--TCCTCG-ACCTGGAACGTGTCTCCTGATGCCAG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 16722 76 + 41507 CTAAGACAAAGAGGGCCTTGCCCAG---TCCT---CACCTGTCGCCACTG--TCCCCACCCCCGGGGCG-ACCACCTGGTCCCAG i oryCun2.chrUn0958 I 31 C 0 e ochPri2.scaffold_9426 3902 1082 - 54875 I e proCap1.scaffold_29042 13928 801 + 24616 I e tupBel1.scaffold_124459.1-15939 9537 0 + 15939 C e myoLuc1.scaffold_4816 7652 86 + 14340 I e micMur1.scaffold_15893 1941 1647 + 19765 I e felCat3.scaffold_206428 11789 719 + 132007 I e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59434994 12 - 64418924 I e bosTau4.chr19 10857278 0 - 65312493 C e loxAfr3.scaffold_49 14430344 4 - 17734757 I a score=124176.000000 s hg19.chr17_gl000204_random 43588 44 + 81310 CCTCTGCATCCACGGTCA------CCTACTTAGTAC-CCCC-CATAG-----------GTAGG s oryCun2.chrUn0958 16798 54 + 41507 CTCCTGCACCCACAGTC-------CCCAATGAATGC-CCTG-TGCAGGCGGAGGAGGGGCGGG i oryCun2.chrUn0958 C 0 C 0 s speTri1.scaffold_128901 4980 37 + 44242 CCTCTAGGCCCACTGCCA------CCTGCTAAGTGC-CC-------------------ACAGA i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4387405 37 + 7991924 TTCCTGTAGCCACCATCA------CCTGCTAAGCAT-CC-------------------ACATA i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118757054 44 + 121843856 CTGGTGCGCCCACTATCACACCACCCTGCTGAGTGTCCC-------------------ACATG i mm9.chr11 C 0 C 0 s panTro2.chr17 79473771 44 + 83384210 CCTCTGTATCCACGGTCA------CCTACTAAGTAC-CCCC-CATAG-----------GCAGG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 12522 44 - 64270 CCTCTGCATCCACGGTCA------CCTACTAAGTAC-CCCC-CATAG-----------GCAGG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16060931 44 + 17838096 CCTCTGCATCCACGGTCA------CCTACTAAGTAC-CCCC-CATAG-----------GCAGG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75034828 44 + 78773432 CCTCTGCATCCACAGTCA------CCTACTAAGTGC-CCCC-TGTAG-----------GCAGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 42217 44 - 95547 CCTCTGCATCCACAGTCA------CCTACTAAGTGC-CCCC-TGTAG-----------GCAGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 44017 43 + 225949 CCCCTGCATCCACGGCCA------CCTACTAAGTGC-CTCC-CATGG-----------GCA-G i calJac1.Contig5139 C 0 C 0 s turTru1.scaffold_106006 126627 44 + 145505 TCCCTGCCTCCACCATCA------CTTGCTGAGTGC-CCCC-ACATG-----------GCCCA i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58040705 41 - 61308211 TCCCTGCATCCACTCTCA------CTTGCTGAG----CCCC-ACACA-----------GCCCA i equCab2.chr11 C 0 I 1 s pteVam1.scaffold_11245 13206 35 + 48268 ---------CCACCGTGA------CTTGCTGAGTGC-CCAC-ACACA-----------GCCTG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14430348 36 - 17734757 ---------CCACAGTCA------CTTGCTAAGTGC-CTACACACAG-----------GCCCA i loxAfr3.scaffold_49 I 4 C 0 s proCap1.scaffold_29042 14729 44 + 24616 CCTCTTCA-CCACGGTCA------CTTGCTACAGGT-CTGCACTCAG-----------GCCTG i proCap1.scaffold_29042 I 801 C 0 e ochPri2.scaffold_9426 3902 1082 - 54875 I e tupBel1.scaffold_124459.1-15939 9537 0 + 15939 C e myoLuc1.scaffold_4816 7652 86 + 14340 I e micMur1.scaffold_15893 1941 1647 + 19765 I e felCat3.scaffold_206428 11789 719 + 132007 I e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59434994 12 - 64418924 I e bosTau4.chr19 10857278 0 - 65312493 C a score=238669.000000 s hg19.chr17_gl000204_random 43632 102 + 81310 GGTTGGCTCCTGCCTTTC-CCAG----GAGG------GAGGA----CAGACTCACCCTGTGGCCAGCAGGGAGCAGACACCCCCAAAAGCCACTGGGGCTGCAGGGCCCCCAAAGTG s calJac1.Contig5139 44060 104 + 225949 GGTTGGCTCCTGCC-TTC-CCAGGAGAAAGG------GAGGA----CAGCCTCA-CCTGGGGCCAGCAGGGAGCAGACACCCCCAAAAGCCGCTGGGGCTGTAAAGCCCCCCAAAGT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 42261 105 - 95547 GGTTGGCTCCTGCC-TTC-CCAGGAGAGAGG------GAGGA----CAGCTTCTCCCTGTGGCCAGCAGGGAGCAGACACCCCCAAAAGCCACTGGGGCTGCAGGGCCCCCAAAGTG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75034872 105 + 78773432 GGTTGGCTCCTGCC-TTC-CCAGGAGAGAGG------GAGGA----CAGCTTCTCCCTGTGGCCAGCAGGAAGCAGACACCCCCAAAAGCCACTGGGGCTGCAGGGCCCCCAAAGTG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16060975 101 + 17838096 GGTTGGCTCCTGCC-TTC-CCAG----GAGG------GAGGA----CAGACTCACCCCGTGGCCAGCAGGGAGCAGACACCCCCAAAAGCCACTTGGGCTGCAGGGCCCTCAAAGTG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 12566 102 - 64270 GGTTGGCTCCTGCCTTTC-CCAG----GAGG------GAGGA----CAGACTCACCCTGTGGCCAGCAGGGAGCAGACACCCCCAAAAGCCACTGGGGCTGCAGGGCCCCCAAAGTG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79473815 102 + 83384210 GGTTGGCTCCTGCCTTTC-CCAG----GAGG------GAGGA----CAGACTCACCCTGTGGCCAGCAGGGAGCAGACACCCCCAAAAGTCACTGGGGCTGCAGGGCCCCCAAAGTG i panTro2.chr17 C 0 C 0 s mm9.chr11 118757098 83 + 121843856 GG-------------------------CTGG------AAAGAAAATCAGCTTCACCAAGTGGTCAACAGGAAAC--CCCACCACCACCGCCA-CGAAACTACAGAGTCCCCAGTCCA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4387442 65 + 7991924 GG-------------------------CCAG------GAAGA----------CAGCAAGGAGTGGACA---------CATCCATGAGCTTT--TGGCGCCACAGGGCCTCCAATGCT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 5017 78 + 44242 GG-------------------------CAGG------GAGGG----GACCCTCACCATATGGTCCATAAGGAGCAGACACCCACAAGCCCC--TGGAACTGCAAGG-CCCTGATGC- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 16852 72 + 41507 GG-------------------------CAGG------AAGGA----TGACCTCACACTGTGGCCAGCGGGGAGCAGTCACCCT----------TGGGGCCGTGGGGCCCCTTCCACG i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 126671 101 + 145505 AGTTGGCTCCTGCCTTTC-TGGG----GAAA------GAGAA----CAGCTTCACCCTGCAATAAGCAGGGAGCAGACACCCC-ACAAGTCACTGAGGCCTCAAGGCCCCCAACACA i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58040747 84 - 61308211 --GCGGCTCCCGCCTTCC-AGGG----GGAG------GA------------------GAAGAAGAGCAGGGAGCAGACACCCC-ACAAGTCGTT-GGGCCTGAGGGCCCCCGACACA i equCab2.chr11 I 1 C 0 s felCat3.scaffold_206428 12508 68 + 132007 GGCTGCCTCCCGCCTTCC---TG----GGAG------AA------------------CACGGCCGGCAGGGAGCAGA------------------GGGCCCCAGGGCCCCCAGCACA i felCat3.scaffold_206428 I 719 C 0 s pteVam1.scaffold_11245 13241 101 + 48268 GGCTGGCTCCTGCCTTCC-CAAG----GGAA------GAAAA----CAGCTTCACCCCACGACCAGCAGAAAGCAGACGCCCG-ACACATCGCCGGAGTCCCAGGGCCCCAGACACA i pteVam1.scaffold_11245 C 0 C 0 s bosTau4.chr19 10857278 63 - 65312493 -------------------------------------GAGGA----CAGCTTCACCTTGCAATCAGCATGGAGGAGACACCCT-ACAGGTCACAGGAGCCCTGAG------------ i bosTau4.chr19 C 0 C 0 s loxAfr3.scaffold_49 14430384 105 - 17734757 GGCTGGCCTCTGCCCTCTGCAGG----GAAGACAAG-AAGAG----TGGCCTGACCCCATGGACACCAGGGAGCAGAGACCCC--CAAGTCAGAGGGGCTGCAGG-CCCCCATCACA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 14773 103 + 24616 GGCTGGCCTCTGCCCCCC---AG----GAGGACACGCAGGAG----CAGCTTCCCCCTGTGGGCAGCAGGGAGCAGAGACCCC--CAAGTCACAGAGGCTACAGA-TTTCCCTCACA i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_9426 3902 1082 - 54875 I e tupBel1.scaffold_124459.1-15939 9537 0 + 15939 C e myoLuc1.scaffold_4816 7652 86 + 14340 I e micMur1.scaffold_15893 1941 1647 + 19765 I e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I e echTel1.scaffold_194555 1722 843 + 11139 I e otoGar1.scaffold_94362.1-287808 24111 733 + 287808 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59434994 12 - 64418924 I a score=60448.000000 s hg19.chr17_gl000204_random 43734 76 + 81310 GAAATG--ACCTGCCACTCTGTCCATCCCA--TGGGGGAGAAACAATCA-GACCCTA-GGCAGGGGGCA-TTTAGGGCA-AACA s panTro2.chr17 79473917 76 + 83384210 GAAATG--ACCTGCCACTCTGTCCATCCCA--TGGGGGAGAAACAATCA-GACCCTA-GGCAGGGGGCA-TTTAGGGCA-AACA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 12668 76 - 64270 GAAATG--ACCTGCCACTCTGTCCATCCCA--TGGGGGAGAAACAATCA-GACCCTA-GGCAGGGGGCA-TTTAGGGCA-AACA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16061076 76 + 17838096 GAAATG--ACCTGCCACTCTGTCCATCCCA--TGGGGGAGAAACAATCA-GACCCCA-GGCAGGGGGCA-TTTAGGGCA-AACA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75034977 76 + 78773432 GAAATG--ACCTGCCAGTCTGTCCATCCCA--TGGGGGAGAAACAATGG-GACCCCA-GGCAGGGGGCA-TTTAGGGCA-AACC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 42366 76 - 95547 GAAATG--ACCTGCCAGTCTGTCCATCCCA--TGGGGGAGAAACAATCG-GACCCCA-GGCAGGGGGCA-TTTAGGGCA-AACC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 44164 75 + 225949 GAAATG--AACTGCCACTCTGTCCACCCCA--TGGGAGAGAAACCGTCA-GACCTGA-GGCAGGGGGCA-TTCAGGGC--AACA i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 24844 76 + 287808 GAAACG--CTCAGCTGTTCTGTTCAGTCTA--TGGGGGAGGAACAGTCA-GACCCAA-GGCAGGTAGCA-TTGAGGGCA-AGCA i otoGar1.scaffold_94362.1-287808 I 733 I 260 s mm9.chr11 118757181 69 + 121843856 AAAGTG--ACCAGCCACTCAGCCTTTC-----AGGGGAATAGGCAACCT-GACTCCA--TGACATGGCA-CATGGGTGA-A--- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4387507 62 + 7991924 GAAACA--GTCAGCCACTCTTCC--TC-----AGGTGAAGTGGTGGTCA-CACCCCA---AAAGTGGCA-CTCAGG-------- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 5095 58 + 44242 AAAGCA--GCCGGCCACCCTGCCCATC-----AG-----TGGGCACCCA-CAAGGCA--------GGCA-TGTGGGGCA-A--- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 16924 72 + 41507 GGAACACCACGGGCCACACCATCCATCCCAAGAGAAGAACAGGAAGCCACCAGGCCA--------CCCT-CGCGGGGGGCA--- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 126772 65 + 145505 AAAATA--GCCAGACA----------CCCA--TGCGAGAAAAGTAGCCG-GACCCCACGGCAGGTGGTGA--CAAGGCA-GT-T i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58040831 64 - 61308211 GAAA--------------CCATCCACCCCA--CGGGAGAAACGCAGTCA-GACCCCCAGGAAGGTGGCA--ACAGGGCA-GACA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 12576 74 + 132007 CAAGCA--GATGGCCATTCCATCCGTCCCA--GGGGAGAAAGGCGGCCA-GACCCCAAGGTGCGCGATG--TCAGGGCG-A--T i felCat3.scaffold_206428 C 0 C 0 s pteVam1.scaffold_11245 13342 74 + 48268 AAAACA--GCCAGCCTTCCTGTCCATCC----ATGTAGAAGGTCAGTCG-AGCCCCGAAGCAGGCGGTG--ACAGGGCA-CACT i pteVam1.scaffold_11245 C 0 C 0 s bosTau4.chr19 10857341 58 - 65312493 --------GCCAGATG----------CCCA--CGGGAGAAAAGCAGTCA-GACTCTAGGGCAGGTGGTGA--CAAGGCA-GT-- i bosTau4.chr19 C 0 C 0 s loxAfr3.scaffold_49 14430489 76 - 17734757 AAGCCC--ACCAACCACTCCTTCAATT-CA--TGTGAGAAAAACCATCA-AACCACATGGTGGACAGTG-AACAGACCA-GACA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 14876 76 + 24616 GAGCCC--GCTAACCAATCCTTCAGTG-CA--TGTGAGAGAAACCGTCA-GAGCACAAGGTGGGCAGTG-CATAGACGG-GACA i proCap1.scaffold_29042 C 0 C 0 s echTel1.scaffold_194555 2565 44 + 11139 ----------------------------CA--AGGGGCAGAGACC-CCG-AGGCATGGGGTTG-CAGGC-CGCAGGCC------ i echTel1.scaffold_194555 I 843 C 0 e ochPri2.scaffold_9426 3902 1082 - 54875 I e tupBel1.scaffold_124459.1-15939 9537 0 + 15939 C e myoLuc1.scaffold_4816 7652 86 + 14340 I e micMur1.scaffold_15893 1941 1647 + 19765 I e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I e monDom5.chr2 304528203 3081 - 541556283 I e canFam2.chr9 59434994 12 - 64418924 I a score=58697.000000 s hg19.chr17_gl000204_random 43810 50 + 81310 GCTGGCCCACAGCACGGACT------CTCCTCTTTGCAGCTAATT----------------TTTGGACTGC---------------------------A s otoGar1.scaffold_94362.1-287808 25180 48 + 287808 gctgg-tctcaaactAG--T------CTTCTCTCCTTAGCAGAGTA---------------TTTTGGCCTC---------------------------A i otoGar1.scaffold_94362.1-287808 I 260 C 0 s micMur1.scaffold_15893 3588 50 + 19765 gctgg-tctcagactGGTCT------CTCCTTTTCTTTGCTTATTG---------------TTTTGGCTGC---------------------------A i micMur1.scaffold_15893 I 1647 C 0 s calJac1.Contig5139 44239 49 + 225949 GCTGG-CCGCAGCACGGACT------CTCCTCTCTGCAGCTAAGT----------------TTTGGGCTGC---------------------------A i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 42442 50 - 95547 GCTGGCCCACAGCATGGACT------CTCCTCTTTGCAGCTAATT----------------TTTGGGCTGC---------------------------A i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75035053 50 + 78773432 GCTGGCCCACAGCATGAACT------CTCCTCTTTGCAGCTAATT----------------TTTGGGCTGC---------------------------A i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16061152 50 + 17838096 GCTGGCCCACAGCACGGACT------CTCCTCTTTGCAGCTAATT----------------TTTGGACTGC---------------------------G i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 12744 50 - 64270 GCTGGCCCACAGCACGGACT------CTCCTCTTTGCAGCTAATT----------------TTTGGACTGC---------------------------A i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79473993 50 + 83384210 GCTGGCCCATAGCACGGACT------CTCCTCTTTGCAGCTAATT----------------TTTGGACTGC---------------------------A i panTro2.chr17 C 0 C 0 s mm9.chr11 118757250 92 + 121843856 GACTG-TCTGTACCTGGCCT------CTTCTCCATGTGGCTGGTCACATAGGTATTGTGTGTGATATATGAGCATATATAGGAATATGCTTACACAATA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4387569 50 + 7991924 --------TGCCCCTGGCCT------CTTCTCTTTCTGGCTGTCCA---------------TTCTACCTGTGCACACA--------------------G i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 5153 54 + 44242 ACACT-GCCACGTCTGGCCT------CTT-----TCTGGCTAATCA---------------TGATAGCTGTCCACTTACA------------------G i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 16996 64 + 41507 AACAG-CCGGCCCCTGGCCTGGGCTGCTCCTCTGAGCGGGTGGTG----------------TGGCCACAGGGGATGGACT------------------G i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 126837 50 + 145505 GGTGGCCCGCAGCCTGGTCT------CTTCACTTTTTAGCTGATG----------------TTTTAGCAAC---------------------------A i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10857399 48 - 65312493 --TGGCCAACCACCTGGTCT------CCTCTTTTTTTAGCTAATG----------------TTCCAGCTAC---------------------------A i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58040895 50 - 61308211 GCTGGCCCTCAGCCTGGTCT------CTTCCCTTTTTAGCTGGTG----------------TCGGAGCCAC---------------------------A i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 12650 50 + 132007 GTTCAGCTACAGCCTGGTCT------CCTTCCTATCTTGCTGGTG----------------TTCTGGACAC---------------------------G i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59435006 50 - 64418924 CTTCGCCTACAGCCTGGGCC------CTGCCCTTTTCTGCTGGTG----------------TTCTGGACAC---------------------------A i canFam2.chr9 I 12 C 0 s pteVam1.scaffold_11245 13416 49 + 48268 GTTGGCCCACGGCCTGGTCT------CCTCTTTTTTTAGCTGCT-----------------TTCTGGCCAC---------------------------A i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 14952 50 + 24616 ACTGCTCAGTGTCCCGGACT------CTGATCATT-GAGCTGGCTG---------------TCCTGGCAGT---------------------------G i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14430565 51 - 17734757 ACTGGTCAACATCCTGAACC------CTGCTCTTTGGAGCCAGCTG---------------TCTTGGCAGT---------------------------G i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_194555 2609 47 + 11139 -CCCATCAA-ACACTGGACA------CTACCTGTG-CTACCAGTTG----------------CTTGCCAGC---------------------------G i echTel1.scaffold_194555 C 0 C 0 e ochPri2.scaffold_9426 3902 1082 - 54875 I e tupBel1.scaffold_124459.1-15939 9537 0 + 15939 C e myoLuc1.scaffold_4816 7652 86 + 14340 I e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I e monDom5.chr2 304528203 3081 - 541556283 I a score=-376498.000000 s hg19.chr17_gl000204_random 43860 69 + 81310 TGGGCCACATC-------TGGGC------------CCTGG--------GACTTCCCATGGAGCCGCGGCAG-----GTAGAAGG-ATG-------------------GAACCCC-----------ACAATCT---------------- s echTel1.scaffold_194555 2656 80 + 11139 TCCAGCAAGCC-------TGGGCAGCGGGCA----CCTGG--------GCCTCCGCCCAAC-CT-AAGCAG-----ACAGGAAGTACC----CACTCCCCCATACAAGGG-------------------------------------- i echTel1.scaffold_194555 C 0 C 0 s loxAfr3.scaffold_49 14430616 90 - 17734757 TTGGCCAAGCC-------TGGGCTGTGGGCA----CCAGG--------GACACTTACAGAGGCC-AGGCAG-----CCAGGAAGTACC------CCTCCCCACGTGAGGGCCCA-----------GCTCTTC---------------- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 15002 52 + 24616 CTGGC---------------------------------------------------------CC-CGACAG-----ACCAGATGTACC------CCTCCCCGTCTGAGGGGCCT-----------GCGCTTT---------------- i proCap1.scaffold_29042 C 0 C 0 s tupBel1.scaffold_124459.1-15939 9537 68 + 15939 ---------------------GC------------CCTGG--------CGCTCCCCACAGAGCCCCAGGAG-----GTAAGAGA-ATA----CCCTATCTGTTCC--AAGGCCC-----------TCTCTCT---------------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s pteVam1.scaffold_11245 13465 95 + 48268 CAGGCCAAGCC-------CG---AACGTAGGTGTGCAGGG--------GGG-TCCCCAGGAGCC-CAGCAG-----ACAGCAGG-GTGACAACTCGACCCATCCTGAGGACCCC-----------GCTCTCT---------------- i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 7738 84 + 14340 tgggccaagcc-------tg---gACCCAGCGCTGCCTGG--------A----CCCCA----CC-CAGC--------CCGAAAG-ATGACCCCTCGACCCAGCCTGAGGGCCCT-----------CCCTCC----------------- i myoLuc1.scaffold_4816 I 86 C 0 s canFam2.chr9 59435056 60 - 64418924 GAGGCTGAGCC-------TG------------------------------------------------CAG-----ATAGGAGA-AAGGTGCCTCTGCCCATTCCGAGGGCCCC-----------GCTCTCT---------------- i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 12700 60 + 132007 CAGGCTGAGCC-------GG------------------------------------------------CGG-----GTAGCAGA-ACGGTGCCTCTCCCCACGCTGAGGGCCCT-----------TCTCTCA---------------- i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58040945 94 - 61308211 CAGGCAGAGCC-------TGG--ACCGTGGATACCTCGGG--------GGT-CCCCCCAAAGCC-TGACGG-----AGAACAGA-ATGACACCCCTACCCACTCTGAGGGCC-------------TGTCTCT---------------- i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10857447 94 - 65312493 AAGGCTGAGCT-------TGG--ACCGTGGGTACCCAGGG--------GGC-CCCTTGAGAGCC-CA-TAG-----ACAGCTGA-ATG-TGCCTCGACTCATTCTGTGGGCTCT-----------GCTCTCT---------------- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 126887 96 + 145505 AAGGCAGAGCT-------TGG--ACCATGGGTACCCTGGG--------GGCTCCCTTCGGAGCC-CAGCAG-----ATAGCAGA-ATG-CGCCTCTACCTGTTCCGAGGGCTCC-----------GCTCTCT---------------- i turTru1.scaffold_106006 C 0 C 0 s oryCun2.chrUn0958 17060 87 + 41507 CGGGC----------------TC------------CCCAG--------GGCTCCCCATGGAGCC-TGGCAGGGCCGGGGGGGGG-ACG-----------------------CCCCTCCTCCACGAGGGTCCTGCTCCGGGTGCAGGGG i oryCun2.chrUn0958 C 0 C 0 s speTri1.scaffold_128901 5207 53 + 44242 TGGGC----------------AC------------CCTGAGGGGACACAGCCCCA------------GCAG-----ACAGAAGG-AGG-----------------------CCC----------AACACCTT---------------- i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4387619 30 + 7991924 TGGGT----------------AC------------CCTGA--------GGCTCCC------------TAAG------------------------------------------------------AGGCTTT---------------- i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118757342 29 + 121843856 TAAAT----------------AT------------CCTG---------GGCTCCC------------GCAC------------------------------------------------------TGAACTT---------------- i mm9.chr11 C 0 C 0 s panTro2.chr17 79474043 69 + 83384210 TGGGCCACATC-------TGGGC------------CCTGG--------GACTTCCCATGGAGCCGCGGCAG-----GTAGGAGG-ATG-------------------GAACCCC-----------ACAATCT---------------- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 12794 69 - 64270 TGGGCCACATC-------TGGGT------------CCTGG--------GACTTCCCATGGAGCCACGGCAG-----GTAGGAGG-ATG-------------------GAACCCC-----------ACAATCT---------------- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16061202 69 + 17838096 TGGGCCACATC-------TGGGC------------CCTGG--------GACTTCCCATGGAGCCATGGCAG-----GTAGAAGG-ATG-------------------GAACCCC-----------ACAATCT---------------- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75035103 69 + 78773432 TGGGCCACATC-------TGGGC------------CCTGG--------GACTCCCCACGGAGCCATGGCAG-----GTAGGAGG-ATG-------------------GAACCCC-----------ACAGTCT---------------- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 42492 69 - 95547 TGGGCCACATC-------TGGGC------------CCTGG--------GACTCCCCATGGAGCCATGGCAG-----GTAGGAGG-ATG-------------------GAACCCC-----------ACAGTCT---------------- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 44288 69 + 225949 TGGGCCACGTC-------TGGGC------------CCTGG--------GACTCCCCATGGATCCATGGCAG-----GTAGGAGG-ATG-------------------GAACCCC-----------ACTCTCT---------------- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 3638 76 + 19765 GGGGCCAAGCCCACACTGTGGACA-----------CCTGG--------AGCTCTCCATGGAGCCCCGGCGG-----GTGGGAGA-GTG-------------------CCACCCC------------CACACT---------------- i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 25228 74 + 287808 AGGGCCAAGTCCAGACCATGGGCA-----------CCTGG--------AGCTCCCTACGGAGCCCTGACAG-----ATGGGAGA-GCG---------------------ACACC------------CACTCT---------------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 e ochPri2.scaffold_9426 3902 1082 - 54875 I e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I e monDom5.chr2 304528203 3081 - 541556283 I a score=-277659.000000 s hg19.chr17_gl000204_random 43929 280 + 81310 GAAGAGCAG---------AGA-GG----------------------AGCCTGATCAGAAGGAGTCT-----TG----GCTTCTTTA--TTCCTCCTTGACCCACCCTCTTGC--CACCATCC-CTCA--------------CTA--GCAATTC-TCC------CCAAAATCCTGCTGCAGA--AATCT-GCCTTCCAATAACATTGCC--------TGGGCAGAAGCCACA-----GGAGCAGG-AGCGCTGCCTGCTGGAGGGTGACCAACAGGTGCA-GGG------GC-----------CTCAGG-T-GCCACTGCCTT---TACACACGTGGCCAGT--ACAAA-----AGAGCACTCCAGGAGG-A-------------AGGTGGTGGCAATGCAGAGATGACCG s otoGar1.scaffold_94362.1-287808 25302 242 + 287808 GAGGAGGAG---------CGA-GG----------------------AGTCAG-----GAGGGATGG-----CG----GCATCTTTA--TTCCTCCTTGGTGAA-CCATTTCC--CACTGGCC-TTCA--------------CTA--CCAAGCCTTCC------C--AAATCCCCCTGCACA--AATCT-GCCACCGGTGAGCACACCC--------TGGA-------------------------CACGGCCCAT-----------GGCAGCAGGGGCG-GGG------CT-----------CTGGGC-T-G-C-CTGCCCGTCTTGAGAGTGCGGCCAGGG-AC--A-----GACGCTCTCGGAGAAG-G-------------AGCCAGTGTGAATGCAGAGACAACC- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 3714 256 + 19765 GAGGGGCAG---------CAA-GA----------------------GTCCAG--CCAGAGGGACTG-----TG----GCTTCTCTA--GTCCTCCTTGGTCCT-CCTCTTCC--CACCTCCC-TTCG--------------CTA--CCAAGAC-TCC------C--GAACCCCTCTGCAGA--AACCC-GCCACCACAGAGCATGGCC--------TGGA-------------------------AGCGCCACCTGCTGCTGGCCAGCCCACGGGTGTG-GGG------GC-----------TTGGGC-T-GTC-CCGCCGG---TGCATGCATGGCCAGGA-ACGAA-----CACGCTCTCTGAGAAG-C-------------AGCCGCTGCAAGTGCAGAGACAGCCT i micMur1.scaffold_15893 C 0 C 0 s calJac1.Contig5139 44357 262 + 225949 GAAGAGCAG---------AGA-GA----------------------AGTCCGGCCAGAAGGAGCCT-----TA----GTTTCTTTA--TTCCTCCTTGACCCACCCTCTTCC--CACCATCC-CTCA--------------CTA--GCAATTC-TCC------CCAAAATCCCCCTGCAGA--AATCT-GCCCTCCAAGAGCATCGCC--------CAGGCACAAGCCATA-----GGAGCAGGAAGGGCTGCCTGCTGGAGGCTGGCCAA--------------------------------------T-GCCACTGCCTT---TACACACATGGCCAGT--ACAAA-----AATGCACTCGGAGAGG-A-------------AGCTGGTGGCAATGCAGAGACAACca i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 42561 279 - 95547 GAAGAGCAG---------AGA-GG----------------------AGCCTGGTCAGAAGGAGTCT-----TG----GCTTCTTTA--TTCCTCCTTGACCCACCCTCTTTC----CCATCC-CTCA--------------CTA--GCAATTC-TCC------CCAAAATCCCCCTGCAGA--TATCT-GCACCTCAGTAGCATTGCC--------TGGGCACAAGCCACA-----GGAGCAGGAAGCACTGTCTGCTGGAGGCCGGCCAACAGGTACA-GGG------GC-----------CTCAGC-T-GCCACTGCCTT---TACACACGTGGCCAGT--ACAAA-----AGAGCACTCCAGGAGG-A-------------AGTTGGTGGCAATGCAGAGACGACCA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75035172 279 + 78773432 GAAGAGCAC---------AGA-GG----------------------AGCCTGGTCAGAAGGAGTCT-----TG----GTTTCTTTA--TTCCTCCTTGACCCACCCTCTTTC----CCATCC-CTCA--------------CTA--GCAATTC-TCC------CCAAAACCCCCCTGCAGA--TATCT-GCACCTCAGTAGCATTGCC--------TGGGCACAAGCCACA-----GGAGCAGGAAGCACTGCCTGCTGGAGGCCGGCCAACAGGTGCA-GGG------GC-----------CTCAGC-T-GCCACTGCCTT---TACACACGTGGCCAGT--ACAAA-----AGAGCACTCCAGGAGG-A-------------AGTTGGTGGCAATGCAGAGACGACCA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16061271 281 + 17838096 GAAGAGCAG---------AGA-GG----------------------AGTCTGGTCAGAAGGAGTCT-----TG----GCTTCTTTA--TTCGTCCTTGACCCACCCTCTTTC--CACCATCC-CTCA--------------CTA--GCAATTC-TCC------CCAAAATCCTGCTGCAGA--AATCT-GCCTTCCAATAGCATTGCC--------TGGGCACAAGCCACA-----GGAGCAGGAAGCGCTGCCTGCTGGAGGGTGACCAACAGGTGCA-GGG------GC-----------CTCAGG-T-GCCACTGCCTT---TACACACGTGGCCAGT--ACAAA-----AGAGCACTCCAGGAGG-A-------------AGGTGGTGGCAGTGCAGAGACGACca i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 12863 280 - 64270 GAAGAGCAG---------AGA-GG----------------------AGCCTGATCAGAAGGAGTCT-----TG----GCTTCTTTA--TTCCTCCTTGACCCACCCTCTTTC--CACCATCC-CTCA--------------CTA--GCAATTC-TCC------CCAAAATCCTGCTGCAGA--AATCT-GCCTTCCAATAGCGTTGCC--------TGGGCACAAGCCACA-----GAAGCAGG-AGCGCTGCCTGCTGGAGGGTGACCAACAGGTGCA-GGG------GC-----------CTCAGG-T-GCCACTGCCTT---TACACACGTGGCCAGT--ACAAA-----AGAGCACTCCAGGAGG-A-------------AGGTGGTGGCAATGCAGAGACGACTG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79474112 280 + 83384210 GAAGAGCAG---------AGA-GG----------------------AGCCTGATCAGAAGGAGTCT-----TG----GCTTCTTTA--TTCCTCCTTGACCCACCCTCTTTC--AACCATCC-CTCA--------------CTA--GCAATTC-TCC------CCAAAATCCTGCTGCAGA--AATCT-GCCTTCCAATAGCATTGCC--------TGGACACAAGCCACA-----GGAGCAGG-AGCGCTGCCTGCTGGAGGGTGACCAACAGGTGCA-GGG------GC-----------CTCAGG-T-GCCACTGCCTT---TATACACGTGGCCAGT--ACAAA-----AGAGCACTCCAGGAGG-A-------------AGGTGGTGGCAATGCAGAGACGACCG i panTro2.chr17 C 0 C 0 s mm9.chr11 118757371 233 + 121843856 CAGCAG------------AGA-GG----------------------ATCATGGTG----------------AA----ATCTCATGCAGGAAGAAGCCAAGCCA-----------AAGGGGTC-CTGG--------------TTGGCTTCCTGT-TC--------------TGCCC--CGGA--AAGGC-CTTGTCAAAGAGCACTGGC--------TCAGCACAGCT-GCA------TAGCAGG--------CCTG-CTGGAGCGAGCCAACAGGTGTG-GGG-T----GC-----------CTCGGG-T-ACTATTGCCCC---AGCAGGTATAATCAGGT-GCCAGCAAGCGGAGTACTGAGGTACA-A-------------AGCCAACAGAG--------------- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4387649 229 + 7991924 AGGCAGCCC---------AAA-GG----------------------CCCCTGGTC----------------CT----GCTTT-------------CCAAGCCACTCTCTTCT--CACTGTCC-CTCA--------------TTA--TCAATGT-TCT------CCAAAGGTGCCCTGCAGA--AAGTC-GCCATCAGGTAGCATCGCC--------TACACCCACCTCACA------TAGC----------------TAGAGGCTGGCCAGTAGG-GTA-GGG-A----GG-----------CTCAGG-TGGCTGATGCCCC---CATAGGAATAGCTGGGT-GCCAA-----AGTGCACCCAGAGAAG-A-------------AGCCAGTGGCA--------------- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 5260 283 + 44242 CAGTGGGCCCTGCTCTATAGA-GGAGGAAGGGCCCAGTCATCAAGCATCCTGATC----------------CA----GCTTCTTCTCAGCCCTCCTTGACCCATCCTCTTAC--CACCATCC-CTCA--------------CTG--TCCAGGC-CC--------CCAAGTCCCCC--CAGATGAAGTC-ACCATCAAATGGCATGGCC--------TGGGCACAACA-----------AGCAGGAAGTGCTACCTG-CTGCAGGTAGTCAACAGGTGTGAGGA-T----GC-----------TTCAGG-TGGCCACCACCCA---GGCAGGTGTGACCAGGT-CCAAA-----AGAGTGCTGGGAGAAG-G-------------TGCCAGCGCCA--------------- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 17147 197 + 41507 CGGCAGCCA---------GGA-GG----------------------GACCTGCCC----------------TG----GCTTCATAC---------CCTCCTCATCCTGTCGTTGCCCAGCCC-CCGG--------------CCA---CAATGC-TCC------CCAAATTCCCCCTGCAGA--AAACC-ACCTCCAAGAGCCCCCG-----------GGGCACGGCA------------------------------CAGGGGAGAGGCCGCCCGTCAG-GGA---------------------CAGA-CGACGCTCGGCCA---AGCAGCCAGCACGGGG------------CGAACCCCACGG--------------------------------------------- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 126983 203 + 145505 ---GACTAG---------AAA-GA----------------------AGTCTGGCCAGGAGGAATCTCGGTCTG----GCTTCTTTC--TCC-----------------------------------------------------------------C------CCAAGG-CCCCCCGCAGA--AACT--CATATCCCATAGCATGGCC--------TGGGCACATGCTCTG---------------------------------CAGCCGACAGGTGTA-GGGGC---TAC-----------CGCAGG-TTGT-GCTGTCCT---TACACGTATAGCCAGGT-ACAGG-----TAAGTGCTCCTTGAAG-C-------------AGCCAGGGAATAAGCCA--------- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10857541 202 - 65312493 ---GAGTAG---------AGA-GA----------------------AGTCTGGCTGGAAGGAATCTTGGTCTG----GCATCCTTC--TCC-----------------------------------------------------------------C------CCAAAG-CCTCCTGCAGA--AATT--TATATCCCATAGCATGGTC--------TGGATACACGCTATA---------------------------------CAGCCGACAGGTGCA-GGGAC----GT-----------GGCAGG-TCGTGGCTGCCCT---TACATGTATAGCCGGAT-ACATA-----CAAGTGCTCCTTGAAG---------------AACCAGGGAATAAGGCA--------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58041039 253 - 61308211 GAGGAGTAG---------AGA-GA----------------------AGTCTGGCCAGAAGACCTCTTGGTCTG----GCTTCTGTC--TCCCACCTTGATCCATCATTTTCC--CACCATCC-------------------CTA--TCCATTC-TCT------CCAAAACCCACCAGCAGA--AATTC-CCCATCCGATGGCATGGCC--------TGGGCGCACCCTATC---------------------------------CAGCCAACAGGTGTG-AGGAC----AC-----------TTCAGG-CAAC-GTTGCTCT---TGCACACACGGCCGGGT-ACAAG-----CAAGTGCTTTTCAAAG-A-------------AGCCAGCGCC-AGGCAGGGACTG--- i equCab2.chr11 C 0 I 3 s felCat3.scaffold_206428 12760 240 + 132007 GA-GGGCAC---------ATG-AG----------------------TGCCTGGCCAGAGGGAATCTT-GCCTG----GCGTCTTTC--CCCCACTTTGATCCACCCTTTCCC--CACCTTCC-------------------CTA--TCAGTTC-TCC------CCAAAAACCCCCTGCAGA--AATT--------------CACCGTC--------TGTGCATGTGCTATC---------------------------------CAAGCAACAGGTGCA-GGGGT----GC-----------TTCAGG-TTATGGCTGCCCT---TACACACATGGCCAGGC-ACACG-----TGTGTGCTCCTCGAAG-A-------------AGCCAGAGCCTATGCAGGGGCTG--- i felCat3.scaffold_206428 C 0 I 3 s canFam2.chr9 59435116 249 - 64418924 GAGGGGCAG---------ACGAAG----------------------AATCTGGCCGGAAGGAATCCCGGCCTG----ACTTCTTTC--TCCTACCTGGGTCCACTCTTATCC--CACCTTCC-------------------CTA--TTGGTTC-T-C------AAAACAATCCCCTGCAGA--AATT-------CTGATAGCATGGTC--------TGGGCATGTGCCATG---------------------------------CAGGCAACAGGTGCG-GGGAT----GC-----------TCGGGG-TTGCGGCTGTTCT---CACACGCCTGGCCAGGC-GCACG-----TGTGTGCTCCCCAAAG-A-------------AGCCAGAGCCTATGCAGGAGCTG--- i canFam2.chr9 C 0 I 3 s myoLuc1.scaffold_4816 7822 225 + 14340 ---GTGCGG---------AG--AG----------------------CAGTCGGACAGAAGGAATCGTGGTCTG----GCTTCTTTC--TCCTGCCTTGACC---CCCTTTCC--CACCATCC-------------------CTA--CAGATTC-TCC------CCAAAA---CCCTGCGGA--GATTC-ACCACCCGATGGTGCGGTG--------TGGGCACATGCTCTC---------------------------------TGGGCTGCGGCCGCC-CTCAC----ACGCGTGGCCAGGTGCTGG-CTGTGGCCGCCCT---CACACGCGTGGCCAGG-------------------TGCTGGCCG-T-------------GGCCG--------------------- i myoLuc1.scaffold_4816 C 0 I 4 s pteVam1.scaffold_11245 13560 244 + 48268 AGGGAGCAA---------AC--AG----------------------GATCTGGCCAG--GGAACCTGGGTCTG----G---CTTTC--TCCTGCCTTGGCCCA-CTCTTTCC--CACCATCT-------------------CTG--TCAATT--TTC------CCAAAA---CCCTGCAGA--AATTC-ACCATCCCATAGGGTGGTC--------TGGGCACACGCTCTC---------------------------------CAGCCAACAGGTGCA-GGGAC----AC-----------CTCCAG-TTGTGGCTGCCCT---TACACACGTCGCCAGGG-ACAAA-----CAAGTGCTCCTGGAGG-A-------------AGCCAGCACCGACACAGGGACCG--- i pteVam1.scaffold_11245 C 0 C 0 s tupBel1.scaffold_124459.1-15939 9605 272 + 15939 G-GGAATGC---------AGA-GG----------------------AGTCCAGCCAGGAGGGATCT-----CGGTTCGCTTCTCTG---TCCCCCTTAATCTGCCCTCGTCC--CACCACCC-CTCA--------------CTA--TGGGTTC-TTG------CCCAAGTCCCCC-GCAGA--AGTCC-GCCTTC-GACACCGTGGCC--------TGGC--CCAGCGGCA-----GCAGCAGGAAGCACTCCCTGCTGGAGGCCGGCCCAGAGGGGCA-GGGAT----GC-----------TTCGGGAC-CTCACTGCCC----TGCACACCTAGCCGGG----CAG-----AGTGCAT-----GGAG-A-------------AGCCAGCGCCGATG-AGAGACGCCC- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s proCap1.scaffold_29042 15054 268 + 24616 GAGCAGTGG---------AGA-GG----------------------ACC--AGCCCGAGGAATCCTGGGTCGG----GCGTCCTCA--TCTGTCCTGGCTCTG-CCGTCTGA--CGCCGTCCATCCACGATCTTACACCATCCA--TCTGTCC-CCC------CACGGG-CCTTGTGCAGT--TCTGT-GCCT-------------------------GGCACAGTGCCCA------GGGAAGGAGACGCTACCTACTGGACGGCAACCCACAGGTGTG-GGGGT-----T-----------CTCAGG-AGGTGCTGGTGCT---TAGAGATATGGCCAGGCAGCAGG-----GGCGTGCTCGGGGAACTG-------------AACAcacaca---------------- i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14430706 267 - 17734757 GAGGAGCGG---------AGA-GG----------------------AAC--AA-TGGAGGAATCCTTGGCCTG----GCTTCTTTA--CCTGTCCTGGATCTG-CCATCTCC--CACCATCTGACCA--------------CCA--TCTATCC-TCC------CCAGGT-CCCTGTGCTGT--CCAGT-ACCT-------------------------GGCACAACCCACA------GTACAGGAGGCATTACCTGCTGGAGGGCAACCCACAGGTGTG-GGGGT----GC-----------CTCAGG-TAGTACTGGTACT---TATAGATATGGCCAGGCAGCTGG-----AGCGCTCTCTGGGGAGCGCTCTCTGGGGAGAAGCCAGCAGG---------------- i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_194555 2736 201 + 11139 -------------------GA-GG----------------------GGC--AACCCGAGGGGTCCTTGGTCTG----ACTTCTTCA--ACCATGCTGGAACC--TCGTCTCC--CACCA-CCATTCA--------------CCA--CCTGTCC-ATC------CCAGGC-CTCTGCGCTGC--CAGGT-ACGC-------------------------AGCACA-CCCACA------GTGCAGGTGGCCCTGCCAGCTGGAGGGCGGCCCACAGGTG------------------------------------------ACC---TGTCG-TAGGACCAGGGAGCAAG-----AG---------------G-------------AGCCAGCATG---------------- i echTel1.scaffold_194555 C 0 C 0 s monDom5.chr2 304531284 271 - 541556283 GAAGAATAT---------AGACTG----------------------AGGCAAATCAGAAGGAGT-------AA----AATAATGTA--TTTGTCTCTTAGTATTTTCCTTTC--CATATCCT-CACC--------------CTT--TCTGATC-CCCACATGGCAAAAATTTTCTTATAGA--AATTCAGTCTGTTAAATTTATTGTTCAGCTGAATGAGCACATAACATCCAGCTGCACCAGAGGTTCATAACTGCTGCAGATTAGCTAACAGATTTG-TTGCTAACCAA-----------TCCAAG-G-GTAAAAGGCAG---TCTA--------------TTAGT-----CAAGTGCTTGATGAAT-C-------------AAT----------------------- i monDom5.chr2 I 3081 C 0 e ochPri2.scaffold_9426 3902 1082 - 54875 I e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I a score=45641.000000 s hg19.chr17_gl000204_random 44209 21 + 81310 TGcaca---tgcacacat-gcacac s panTro2.chr17 79474392 21 + 83384210 TGCACT---TGcacacat-gcacac i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 13143 21 - 64270 TGcaca---ngcacacat-gcacac i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16061552 21 + 17838096 tgcaca---tgcacacat-gcacac i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75035451 21 + 78773432 TGcaca---cgcatacat-gcacac i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 42840 21 - 95547 TGcaca---cgcatacat-gcacac i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 44619 21 + 225949 tacaca---cacgcacat-gcacac i calJac1.Contig5139 C 0 I 344 s micMur1.scaffold_15893 3970 2 + 19765 CG----------------------- i micMur1.scaffold_15893 C 0 C 0 s turTru1.scaffold_106006 127186 21 + 145505 TGTGCG---TGCGTGcac-acacac i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10857743 21 - 65312493 TGCGCG---TGcacgcat-gcacac i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58041295 16 - 61308211 TGCACA---CACGCACAC-A----- i equCab2.chr11 I 3 C 0 s felCat3.scaffold_206428 13003 21 + 132007 CGCGCG---cacacacac-acacac i felCat3.scaffold_206428 I 3 C 0 s canFam2.chr9 59435368 21 - 64418924 CACGCA---CGCGCACAC-TCTCTC i canFam2.chr9 I 3 C 0 s myoLuc1.scaffold_4816 8051 21 + 14340 CACACG---CGTGGCCAG-GTACAA i myoLuc1.scaffold_4816 I 4 C 0 s proCap1.scaffold_29042 15322 19 + 24616 tgcatg---tatgcacac---acat i proCap1.scaffold_29042 C 0 I 2 s loxAfr3.scaffold_49 14430973 22 - 17734757 TGCAGG---TGTAGGGACTGGacac i loxAfr3.scaffold_49 C 0 I 2 s echTel1.scaffold_194555 2937 24 + 11139 TGCAGGGGCTGcacacac-gcatat i echTel1.scaffold_194555 C 0 I 2 s monDom5.chr2 304531555 21 - 541556283 TGCATC---CGATTGTCA-TTAAAT i monDom5.chr2 C 0 C 0 e oryCun2.chrUn0958 17344 0 + 41507 C e ochPri2.scaffold_9426 3902 1082 - 54875 I e speTri1.scaffold_128901 5543 0 + 44242 C e tupBel1.scaffold_124459.1-15939 9877 0 + 15939 C e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I e pteVam1.scaffold_11245 13804 0 + 48268 C e otoGar1.scaffold_94362.1-287808 25544 0 + 287808 C e cavPor3.scaffold_76 4387878 0 + 7991924 C e mm9.chr11 118757604 0 + 121843856 C a score=-26448.000000 s hg19.chr17_gl000204_random 44230 24 + 81310 gtgcacacatgca----cacacacactc s papHam1.scaffold8336 42861 28 - 95547 acacacacatgcacacgcacacacgctc i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75035472 28 + 78773432 acacacacatgcacacgcacacacgctc i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16061573 24 + 17838096 gcacacacatgca----cacacacgctc i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 13164 24 - 64270 gcacacacatgca----cacacacactc i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79474413 24 + 83384210 gcacacacatgca----cacacacgctc i panTro2.chr17 C 0 C 0 s tupBel1.scaffold_124459.1-15939 9877 8 + 15939 -cacacaca------------------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s speTri1.scaffold_128901 5543 18 + 44242 ------ACAGGCA----Gccgcccgccc i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4387878 15 + 7991924 ------Acaggca----cacaccca--- i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118757604 9 + 121843856 ------ACAGCCT----CA--------- i mm9.chr11 C 0 C 0 s turTru1.scaffold_106006 127207 22 + 145505 acacacacacaca----cacacacac-- i turTru1.scaffold_106006 C 0 M 749 s felCat3.scaffold_206428 13024 22 + 132007 acacacacacaca----cacacacac-- i felCat3.scaffold_206428 C 0 M 17456 s canFam2.chr9 59435389 2 - 64418924 TC-------------------------- i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 8072 10 + 14340 TCAAGCGCCC------------------ i myoLuc1.scaffold_4816 C 0 I 38 s proCap1.scaffold_29042 15343 19 + 24616 acatgcacgtgca----aa-atgc---- i proCap1.scaffold_29042 I 2 I 4 s loxAfr3.scaffold_49 14430997 15 - 17734757 gcacacacgtgca----ca--------- i loxAfr3.scaffold_49 I 2 I 1 s echTel1.scaffold_194555 2963 20 + 11139 gctcacatgtgcc----cacaccc---- i echTel1.scaffold_194555 I 2 I 10 s monDom5.chr2 304531576 11 - 541556283 TTACATATATG----------------- i monDom5.chr2 C 0 C 0 e oryCun2.chrUn0958 17344 0 + 41507 C e ochPri2.scaffold_9426 3902 1082 - 54875 I e calJac1.Contig5139 44640 344 + 225949 I e micMur1.scaffold_15893 3972 0 + 19765 C e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I e pteVam1.scaffold_11245 13804 0 + 48268 C e otoGar1.scaffold_94362.1-287808 25544 0 + 287808 C e bosTau4.chr19 10857764 0 - 65312493 C e equCab2.chr11 58041311 0 - 61308211 C a score=-22997.000000 s hg19.chr17_gl000204_random 44254 50 + 81310 atgcacatgcacacacata--------------------c-atgcacacatgtgcacacatacatgcacat s papHam1.scaffold8336 42889 40 - 95547 atgcacacacatacgcaca--------------------c-acgtacacacacacgcacat---------- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75035500 48 + 78773432 atgcacacacatacatgtg--------------------c-gcgcacacacgtacacacac--acgcacat i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16061597 25 + 17838096 atgcacatgcacacacata--------------------c-atgca------------------------- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 13188 36 - 64270 atgcacatg----cacata--------------------c-atgcacacatgtgcacacat---------- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79474437 50 + 83384210 atgcacatgcacacacata--------------------c-atgcacacatgtgcacacatacatgcacat i panTro2.chr17 C 0 C 0 s speTri1.scaffold_128901 5561 28 + 44242 gcccgcccgcacgcacgca--------------------c-gcGCACAC---------------------- i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4387893 29 + 7991924 ------caatatgcatgca--------------------t-gtgcacgcgcgtgca--------------- i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118757613 11 + 121843856 -----------------CA--------------------T-AGGCACGT---------------------- i mm9.chr11 C 0 C 0 s canFam2.chr9 59435391 8 - 64418924 --------------TCTca--------------------c-at---------------------------- i canFam2.chr9 C 0 C 0 s proCap1.scaffold_29042 15366 46 + 24616 gcacacacatgcgtgtgca--------------------c-atatacgtgtgtgtacatctgcgtgt---- i proCap1.scaffold_29042 I 4 C 0 s loxAfr3.scaffold_49 14431013 47 - 17734757 gtacacacatgcatgcata--------------------caatgcacttgcatgtgcacatgtacac---- i loxAfr3.scaffold_49 I 1 C 0 s echTel1.scaffold_194555 2993 41 + 11139 acacacacgtgcacacacg--------------------c-acactctcacatgt-----tgcacat---- i echTel1.scaffold_194555 I 10 C 0 s monDom5.chr2 304531587 46 - 541556283 --GCAAAGGCACTCAGATAGCTCTCCTGGGAAAAGACAGC-ATACTCCC---------------------- i monDom5.chr2 C 0 C 0 e oryCun2.chrUn0958 17344 0 + 41507 C e ochPri2.scaffold_9426 3902 1082 - 54875 I e calJac1.Contig5139 44640 344 + 225949 I e tupBel1.scaffold_124459.1-15939 9885 0 + 15939 C e myoLuc1.scaffold_4816 8082 38 + 14340 I e micMur1.scaffold_15893 3972 0 + 19765 C e turTru1.scaffold_106006 127229 749 + 145505 M e felCat3.scaffold_206428 13046 17456 + 132007 M e eriEur1.scaffold_290756 3906 634 - 7602 I e dasNov2.scaffold_28617 10633 226 + 20752 I e pteVam1.scaffold_11245 13804 0 + 48268 C e otoGar1.scaffold_94362.1-287808 25544 0 + 287808 C e bosTau4.chr19 10857764 0 - 65312493 C e equCab2.chr11 58041311 0 - 61308211 C a score=-32674.000000 s hg19.chr17_gl000204_random 44304 21 + 81310 -gtgcgcgcacacacacacatg s papHam1.scaffold8336 42929 21 - 95547 -gcgcatacactcacacacatg i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75035548 21 + 78773432 -gcgcatacactcacacacatg i rheMac2.chr16 C 0 C 0 s gorGor1.Supercontig_0007361 13224 13 - 64270 ---------gcgcacacacatg i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79474487 21 + 83384210 -gtgtgtgcacacacacatatg i panTro2.chr17 C 0 C 0 s canFam2.chr9 59435399 13 - 64418924 -------a--cacacacacaca i canFam2.chr9 C 0 C 0 s eriEur1.scaffold_290756 4540 18 - 7602 -GTGCGTg--cgcatgcacat- i eriEur1.scaffold_290756 I 634 C 0 s pteVam1.scaffold_11245 13804 3 + 48268 -------------------AGG i pteVam1.scaffold_11245 C 0 C 0 s bosTau4.chr19 10857764 11 - 65312493 -----------acacacacaca i bosTau4.chr19 C 0 C 0 s tupBel1.scaffold_124459.1-15939 9885 12 + 15939 ----------cacacacacatg i tupBel1.scaffold_124459.1-15939 C 0 C 0 s otoGar1.scaffold_94362.1-287808 25544 5 + 287808 ---------------ACACA-- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 3972 2 + 19765 --------------------TG i micMur1.scaffold_15893 C 0 C 0 s calJac1.Contig5139 44984 12 + 225949 ----------cacacacacatg i calJac1.Contig5139 I 344 C 0 s proCap1.scaffold_29042 15412 21 + 24616 -gtgcgcgcatgtgtacatATG i proCap1.scaffold_29042 C 0 I 6 s loxAfr3.scaffold_49 14431060 21 - 17734757 -gtgtgcgcacacacacatgtg i loxAfr3.scaffold_49 C 0 I 6 s echTel1.scaffold_194555 3034 8 + 11139 -gcacccac------------- i echTel1.scaffold_194555 C 0 I 901 s monDom5.chr2 304531633 22 - 541556283 CTTCTTCCCCCCAGCATATATG i monDom5.chr2 C 0 C 0 e oryCun2.chrUn0958 17344 0 + 41507 C e ochPri2.scaffold_9426 3902 1082 - 54875 I e speTri1.scaffold_128901 5589 0 + 44242 C e myoLuc1.scaffold_4816 8082 38 + 14340 I e turTru1.scaffold_106006 127229 749 + 145505 M e felCat3.scaffold_206428 13046 17456 + 132007 M e dasNov2.scaffold_28617 10633 226 + 20752 I e equCab2.chr11 58041311 0 - 61308211 C e cavPor3.scaffold_76 4387922 0 + 7991924 C e mm9.chr11 118757624 0 + 121843856 C e ponAbe2.chr17_random 16061622 0 + 17838096 C a score=1971003.000000 s hg19.chr17_gl000204_random 44325 173 + 81310 cacacgcgcacacacCC-----------------TCCT--CGTT---GTTAAGGACCTTAACTTAGAATGATGTATTCTCTGTTCTCCTGGCTATAATTATTTTAGCGTGGGAGACAAATTCTG---TCTCCAGCATCTCCGAAGTGCAATGTTGGAAAATCACATCCCATGGTCCTGG-AAGA-----TCCCTACCTTCTCCA s dasNov2.scaffold_28617 10859 168 + 20752 CACACACGCGCACACCC-----------------TCCT--CGTT---GTTAAGGA-CTCAACGTGGAATGGTGCAGGCTCCCT--TCCTGGCTATAATTATTTGAGCGTGGGAGAGAAATTCTG---TCTCCGATATCTCAAAAGTGCTACATTAGAATATCACATTCGAGGG-CCTGCAAAAA-----TCACTGCATCCCA-- i dasNov2.scaffold_28617 I 226 C 0 s loxAfr3.scaffold_49 14431087 188 - 17734757 cacacacatacacacTCTTCTCGTTGACACACTCTTCT--CGTT---GTCAAGGACCTTGACTTAGAATGATGCAGTCTCTGTTCTCCTGGCTATAATTATTTTAGCGTGGGAGAGAAATTCTG---TCTCCGATATCTCAAAAGTGCTACGTGAGAATGGCACATAGCACGGCCCTGC-AAAG-----TCTCTCCCTCATG-- i loxAfr3.scaffold_49 I 6 C 0 s proCap1.scaffold_29042 15439 185 + 24616 tgcacacacacacacac-acacaGAAGCATGCTGTCCT--CGTC---GTTAAGGACCTTAACTCAAAATGAGGCAGCCTCTGTTCTCCTGGCTATAATTATTTTCGCGTGGGAGAGAAATTCTG---TCTCTCATCTCTCCCAAGTGCTGCACGAGAATGGCTCCTTCCACGG-CCTGC-AAAG-----TCTCTCCCTCGT--- i proCap1.scaffold_29042 I 6 C 0 s calJac1.Contig5139 44996 165 + 225949 cacacgtgcacacacCC-----------------TCCT--CGTT---GTTAAGGACCTTAACTTAGAACCATATATTCTCTGTTCTCCTGGCTATAATTATTTTAGCGTGGGAGACAAATTCTG---TCTCCAGCATCTCAGAAGTGCAACGTTGAAAAATCATA--------TCCTGG-AAGA-----TCCCTACCTTCTCCA i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 3974 173 + 19765 CACGCGCGCACACACCC-----------------TCCT--CGTT---GTTAAGGACCTTAACTTAGAACGGCGTATTCTCTGTTCTCCTGGCTATAATTATTTTAGCGTGGGAGACAAATTCTG---TCTCCAGCATCTCAGAAGCGCGACGTTAAAATTTCGCATCCTGTGGTCCGGG-AAGC-----TCTCTGCCGTCTCCA i micMur1.scaffold_15893 C 0 C 0 s ponAbe2.chr17_random 16061622 173 + 17838096 catgcgcgcacacacCC-----------------TCCT--CGTT---GTTAAGGACCTTAACTTAGAATGATGTATTCTCTGTTCTCCTGGCTATAATTATTTTAGCGTGGGAGACAAATTCTG---TCTCCAGCATCTCAGAAGTGCAATGTTGGAAAATCACATCCCGTGGTCCTGG-AAGA-----TCCCTACCTTCTCCA i ponAbe2.chr17_random C 0 C 0 s tupBel1.scaffold_124459.1-15939 9897 156 + 15939 cacacacgcacacG---------------------CCT--CGTT---GTTAAGGCCCTTAACTTAGAATGATGTATTCCCTGTTCTCCT-GCTATAATTACTTCAGCGTGGGAGAC--ATTCTG---TCT-CAGGGTCTCCAGAGCACCACGTTGGGCTGTGCAAAC---TGCTCCTGG-ACGC-----------CTGGCCCTG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s bosTau4.chr19 10857775 167 - 65312493 cacacacacacacacac-----------------TCCT--CACC---GTTAAGGGCCT------GGAATGATGTCTTCTCTGTTCTCCCGGCTATAATTATTTTAGCGTGGGAGACAAATTCTG---TCTCCAGAGTCTCAGTAGCGCTACATTAGAATATCATGCACTATGGTCCTGC-AAAA-----TCTCTACTGTAGCCT i bosTau4.chr19 C 0 I 1 s pteVam1.scaffold_11245 13807 167 + 48268 CGCGCGCTCACACCCCC-----------------TCCT--CGCT---GTTAAGGACCT------GGAGTGATGTATTTTCTGTTCTCCCGGCTATAATTACTTTAGCGTGGGAGACAAATTCTG---TCTCCAGCATCTCAGAAGCGCTACACTAGAACACCACATTCCACGGTCCTGG-ACAG-----CCGCGGCGGTGCCCC i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59435412 167 - 64418924 cacacacacacacacac-----------------TCCT--CGCT---GTTAAGGACCC------AGAATGATGTATTCTCTGTTCTCCCAGCTATAATTATTTTAGCGTGGGAGACAAATTCTG---TCTCCAGTAACTCAGAAGCGCTACATTAGAATATCACATTCTGTGGTCTTGG-AAAA-----TCTGTATAGTATCCC i canFam2.chr9 C 0 C 0 s panTro2.chr17 79474508 173 + 83384210 cacatgcgcacacacCC-----------------TCCT--CGTT---GTTAAGGACCTTAACTTAGAATGATGTATTCTCTGTTCTCCTGGCTATAATTATTTTAGCGTGGGAGACAAATTCTG---TCTCCAGCATCTCCGAAGTGCAATGTTGGAAAATCACATCCCATGGTCCTGG-AAGA-----TCCCTACCTTCTCCA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 13237 173 - 64270 cacacgcgcacacacCC-----------------TCCT--CGTT---GTTAAGGACCTTAACTTAGAATGATGTATTCTCTGTTCTCCTGGCTATAATTATTTTAGCGTGGGAGACAAATTCTG---TCTCCAGCATCTCCGAAGTGCNATGTTGGAAAATCACATCCCATGGTCCTGG-AAGA-----TCCCTACCTTCTCCA i gorGor1.Supercontig_0007361 C 0 C 0 s rheMac2.chr16 75035569 173 + 78773432 cacacgcgcacacacCC-----------------TCCT--CGTT---GTTAAGGACCTTAACTTAGAATGATGTATTCTCTGTTCTCCTGGCTATAATTATTTTAGCGTGGGAGACAAATTCCG---TCTCCAGCATCTCAGAAGTGCAATGTTGGAAAATCACATCCCATGGTCCTGG-AAGA-----TCCCTACCTTCTCCA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 42950 173 - 95547 cactcgcgcacacacCC-----------------TCCT--CGTT---GTTAAGGACCTTAACTTAGAATGATGTATTCTCTGTTCTCCTGGCTATAATTACTTTAGCGTGGGAGACAAATTCCG---TCTCCAGCATCTCAGAAGTGCAATGTTGGAAAATCACATCCCATGGTCCTGG-AAGA-----TCCCTACCTTCTCCA i papHam1.scaffold8336 C 0 C 0 s macEug1.Scaffold297525 387 172 + 996 -atatgcacacatacac-----------------tccT--TGTT---GTTAAGGACCTTAACTTAGAATACTGGATTATCTGTTCTCCTGGCTAAAATTATTTTAGCGTGGGAGAAAAATTCAGCCCTCTCCAATATCTCAAAAGTACTACCTTAGAATATCACTTTCCAAGGTCTAGA-AAAA-GTAGTCATCACA------- i macEug1.Scaffold297525 N 0 C 0 s otoGar1.scaffold_94362.1-287808 25549 171 + 287808 --TACACACACACACCC-----------------TCCT--CGTT---GTTAAGGACCTTAACTTAGAACGATGTATTCTCTGTTCTCCTGGCTATAATTATTTTAGCGTGGGAGACAAACTCTG---TCTCCACCATCTCAGAAGCGCGACATTAGAATATCACACCCTGTGGTCCGGG-AAGG-----TCTCTGCCACCCCCA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s cavPor3.scaffold_76 4387922 167 + 7991924 --cacacgca------c-----------------gcTCTGTGTT---GTTAAGGACCTTAACTTAGAATGATGTATTCTCTGTTCTCCTGACTATAATTATTTCAGCGTGGGAGACCAATCCTG---TCTCCAGTGTCTCAGAAGCTCGACATGAGAATCTCACATTCCAGGGCCCTGG-AAAA-----TCCCCACGGTCTTCA i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 17344 91 + 41507 --------------CCC-----------------TCCC--CGTTCGCGTCAGGGGCCTTGGTGCG------------------------GGCAGGGTCGGCGTCGGCATGGGAGGCGGGCCCTG---CCCCC----------------------------------CCTCCGGCAGCGG-------------------CATGCA i oryCun2.chrUn0958 C 0 C 0 s speTri1.scaffold_128901 5589 153 + 44242 ----------------C-----------------TCCT--CGCT---GTTAGGGACCTTGACTTGGAATGATGTATTCTCTGTTCTCCTGGCTATAATTATTTTAGCGTGGGAGACCAGCTCTG---TCTCCAGCGTCTCCGAAGGGCGGGTCCAGAACCTGGCATCCCCCAGCTCTGG-AAAA-----TCCCA----TCTCCA i speTri1.scaffold_128901 C 0 C 0 s mm9.chr11 118757624 117 + 121843856 ----------------C-----------------GCCC--TCTT---GTTAAAGGCCTTAACTTA----------------GTTCTCCTGGCTATAATTATTTTAGCGTGGGAGATCAGTTCTG---TCTCC----------------------AGAATCTCACACTCCAAGGTCCTGG-AAAA-----TCCCCAT--TCTCCA i mm9.chr11 C 0 C 0 s myoLuc1.scaffold_4816 8120 162 + 14340 -CTGTGCACACGCAGCC-----------------GCCT--CGCT---GT--GGGGCCG------GGAGTGACGTAGTCCCTGTTCTTC--GCTATAATTATTTTCGTGTGGGAGACAGAATCTG---TCTCCCGTTTCTCCTAGCTTCTACCCTGGACCATCGCATCGCAAGGGCCCAG-GAAA-----CCTCCCGGGTTCCCC i myoLuc1.scaffold_4816 I 38 C 0 s equCab2.chr11 58041311 159 - 61308211 --------CACACACCC-----------------TCCT--GGCT---GTTAAGGACCT------GGAGTGATGTATTCTCTGTTCTCCCGGCTATAATTATTTTAGCGTGGGAGACAGATTCTG---TCTCCAGGATCTGAGAAACGCGACACGAGAATACCACACTCCACGGTCCTGG-ACAA-----TCTCTGCCCCGGCCC i equCab2.chr11 C 0 I 1 s eriEur1.scaffold_290756 4558 161 - 7602 ---acacacacaactcT-----------------GCCT--GCCT---GCCAAGGTCCA------GGAGTGATGTATT--CTATTCTCC-AGCTATAATTATTTTCAAGTGGGAGATGGAGTCTA---TCTCCAGGGCCTTGCAGGCGTCATATGAGAAGATGCCACCCAAGGGTCCTGC-AGAT-----TCCCAGGGCAGCCCT i eriEur1.scaffold_290756 C 0 C 0 s monDom5.chr2 304531655 165 - 541556283 ------CACACATATAC-----------------TCCT-----T---GTTAAGGACCTTAACTTAGAATGCTGGATTATCTGTTCTTCTGGCTATAATTATTTTAGCATGGGAGAGAAATTCAGACATTTCTAATATCTCAAAAGTCCTACCTTAGAATATCACTTTCCAAGATCTGGA-AAAAAATAATCATCACA------- i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_9426 3902 1082 - 54875 I e turTru1.scaffold_106006 127229 749 + 145505 M e felCat3.scaffold_206428 13046 17456 + 132007 M e echTel1.scaffold_194555 3042 901 + 11139 I a score=-43189.000000 s hg19.chr17_gl000204_random 44498 84 + 81310 GCTCTTTTCCTCCAC--AGAGGAGCATAAACAGACCCTT----------------CC---AA----GGGGTGAACC-T------------------------TGG------------------------------A---------GGCTTTAATTCCTCCTCCAAGCAGCTCC s panTro2.chr17 79474681 84 + 83384210 GCTCTTTTCCTCCAC--AGAGGAGCATAAACAGACCCTT----------------CC---AA----GGGGTGAACC-T------------------------TGG------------------------------A---------GGCTTTAATTCCTCCTCCAAGAAGCTCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 13410 84 - 64270 GCTCTTTTCCTCCAC--AGAGGAGCATAAACAGACCCTT----------------CC---AA----GGGGTGAACC-T------------------------TGG------------------------------A---------GGCTTTAATTCCTCCTCCAAGCAGCTCC i gorGor1.Supercontig_0007361 C 0 C 0 s rheMac2.chr16 75035742 84 + 78773432 GCTCTTTTCCTCCAC--ACAGGAGCACAAACAGGCCCTT----------------CC---AA----GGGGTGAACC-C------------------------TGG------------------------------A---------GGTTTTAATTCCTCCTCCAAGCAGCTCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 43123 84 - 95547 GCTCTTTTCCTCCAC--ACAGGAGCACAAACAGGCCCTT----------------CC---AA----GGGGTGAACC-C------------------------TGG------------------------------A---------GGTTTTAATTCCTCCTCCAAGCAGCTCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 45161 83 + 225949 GCTCTTTTCCTCCCT--ACCAGAGCACAAACAGG-CCTT----------------CT---AA----GGGGTGAAGC-T------------------------CAG------------------------------A---------GGCTTTCATTTCTCCTCCGAGCAGCTCC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 4147 101 + 19765 GCTCTGTTCCTGCTC--TCCGGAGCACAGCCAGGCCTTCCAGAGGGGGGACATACCT---TG----GGGGCCTGCAGC------------------------AGA------------------------------G---------GGTTTTAATTCCCACTCCTGGCGGCTCC i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 25720 77 + 287808 GCACATTTC-----C--TCCAGAGC----CGGGGCCCTCCA--------------CC---TG----GGGACCTGCA-C------------------------TGA------------------------------G---------GGTCCTAATTCCTACTCCAAGTGCCTCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16061795 84 + 17838096 GCTCTTCTCCTCCAC--AGAGGAGCATAAACAGACCCTT----------------CC---AA----GGGGTGAAGC-T------------------------CGG------------------------------A---------GGCTTTCATTCCTCCTCCAAGCAGCTGC i ponAbe2.chr17_random C 0 C 0 s tupBel1.scaffold_124459.1-15939 10053 86 + 15939 GTTCCTTTCCTCCAC--GGA-GAGCACAGA-AAGCCCTC----------------CC---AGCGATGGACGGGACC-C------------------------AGC------------------------------G---------AGTCTCAGCTTCAACTCCAAGCAGCGCC i tupBel1.scaffold_124459.1-15939 C 0 I 1462 s cavPor3.scaffold_76 4388089 104 + 7991924 GTGCCTCCCTCCTGGAAGCAGAAGTACC-ACAGGGCTTT----------------CA---GA----CGAACGGCAC-CATCG--------------AGAGGGTGC------------------------------ATCACCGGTTGGGTTTAATTCCCACTCCAAGAGCCTCT i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 17435 71 + 41507 GCCGACTCCC-------GCA----------CAGGGG-------------------AG---CA----CGCGGAGCCC-CGCCA-------------------CCGA------------------------------G---------GATCTTCACTCCTACTCCAAGCGGCTCC i oryCun2.chrUn0958 C 0 C 0 s speTri1.scaffold_128901 5742 106 + 44242 GATCCTTCCGTCCAT--GCAGAAGCACC--CGGGCCCTT----------------CA---GA----TGGGCAGGCC-CCCCGCTGCCCTGGGAGGCCAGGGTCAA------------------------------A---------GGGTTTCATTCCTACTCCAAGCAGCTCT i speTri1.scaffold_128901 C 0 C 0 s mm9.chr11 118757741 83 + 121843856 GTTCCTTCCCTCCGT--GCAAGAGCTGA-GCAGGGA-------------------CA---GA----TGAAGGGGGC-C--------------------TGGATGA------------------------------A---------AGGCTTAATTCCTAC-CCGATGGCTTCC i mm9.chr11 C 0 C 0 s bosTau4.chr19 10857943 101 - 65312493 ACTCTTTCCCTCCAT--GCCAGAGCACAAACGGGCTCCT----------------CA---GA----TGGGCGGACA-CACCG--------------------TGG---------------AAGCCCCGCAC--CAA---------GGGTTTAATGCCTGCTCTGAGCCGCTCC i bosTau4.chr19 I 1 C 0 s equCab2.chr11 58041471 99 - 61308211 GCTCTTTCCCTGCAC--CCCGGAGCACAAAC-GGCTCTC----------------CA---TA----AGGGCGGACA-CGCCG--------------------CCG---------------AGGCCGGCTGG--AGG---------GTTGTGGAGGCCTGCTCC-CGCCGCTCC i equCab2.chr11 I 1 C 0 s felCat3.scaffold_206428 30830 101 + 132007 GCTCCCTCCCTCCAT--CCAGGGACACTCACAGCCTCTT----------------CA---GA----TGGGTGAACA-CACCA--------------------CAA---------------AGGCCCAGCAC--GGA---------GGCTTTGGTGCGTGCTCCAAGCCGATCC i felCat3.scaffold_206428 M 17456 C 0 s canFam2.chr9 59435579 101 - 64418924 AGCCCCTTCCTCCAT--CCTGGGGCACAAAGAGGCTCTT----------------CA---GA----TGGGTGAACA-CACCA--------------------CGG---------------AGGCCCAGCAC--AGA---------GGGCTTCACGCCTGCTCCAAGCCGATCT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 13974 114 + 48268 -GGCTGCCCCCCCAC--ACCGC-GCGCCAACGGGCTCAC----------------GGGCGGG----CAGGCGAGCA-CG-CA--------------------TCGCACACGCACCGCCCCGGGCCTGCGCC----G---------GGGCTTAACGCCTGCTCCAGGCCGCCCC i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 8282 83 + 14340 -GCCCTTCCCTCCAC--GGAGG-GCACCGCCCAGGCCAC----------------GG----------------CCA-CG-CA--------------------TGG---------------AGGGCTG--------A---------GGGCTGAGTGCCTGCCCCAAGCCGCCCC i myoLuc1.scaffold_4816 C 0 C 0 s eriEur1.scaffold_290756 4719 96 - 7602 --GCTCTGTCCTCCC--TATGGAACACAAATGGAGTCTC----------------CC----A----CAACAAGGCA-GAAAG--------------------CCA---------------AGCCCAGGCAT--CCA---------GGGCTCA--GCAAGACCCCAGGCTGTGT i eriEur1.scaffold_290756 C 0 C 0 s proCap1.scaffold_29042 15624 100 + 24616 GCCCTCCTTCTACAG--GCAGGAGCACG-GCAGGCTCTT----------------CA---GC----AGGGGGAGCA-GACCA--------------------CAG---------------CGGCCCGGAAC-TCGG---------GGCTCCAAGTCCTGCT-TGGGGTGCTCT i proCap1.scaffold_29042 C 0 I 1 s loxAfr3.scaffold_49 14431275 102 - 17734757 GCCCTTCTCCTCCAA--GCAGGAGCACGAGCAGGCTTTG----------------CA---GA----TGGGGAAACA-GACCT--------------------TGG---------------ATGCTGGGAAC-GCAG---------GGCTTTAATTCCTACTCCGAGCTGCTTT i loxAfr3.scaffold_49 C 0 I 1 s dasNov2.scaffold_28617 11027 97 + 20752 GCTCTGTTCCTCCGC--CCAGGAGCACCCCCAGGCT-------------------CG---GA----TGGGGGAGCA-GACCA--------------------CGG---------------AGGCCCAGGAA-CCGG---------GGGTTC-GTTCCCACT-CGCAGAGGCCG i dasNov2.scaffold_28617 C 0 I 1 s macEug1.Scaffold297525 559 90 + 996 GCTCTTTTATCCCAC--ACAAGAGCACAAA-------------------------CA---GG----TGAGCATACA-TGCCA--------------------CAG---------------ATGCTCTAAAAGTGCA---------GGTTTTCACTCATCCTGCTAACAC---- i macEug1.Scaffold297525 C 0 C 0 s monDom5.chr2 304531820 94 - 541556283 GTTCTTTTATCCTAC--ACAAGAGAACAAA-------------------------CA---GG----TGAGCATACA-TGCCA--------------------CAG---------------ATGCTCTAAAAGTACA---------GATTTTCGCTCATCCTGCTAACACTTAC i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_9426 3902 1082 - 54875 I e turTru1.scaffold_106006 127229 749 + 145505 M e echTel1.scaffold_194555 3042 901 + 11139 I a score=987646.000000 s hg19.chr17_gl000204_random 44582 90 + 81310 ACGTAGAGCAACAGAGACGC-A-GGGA---------CCGTGCAAGTAACCATGGCAAC-TCCAGGAAGTTT-----AAAAA------------AAT---AAGTTTTTGAGTTGTTGAGTTGT s panTro2.chr17 79474765 90 + 83384210 ACGTAGAGCAACAGAGATGC-A-GTGA---------CCGTGCAAGTAACCATGGCAAC-TCCAGGAAGTTT-----AAAAA------------AAT---AAGTTTTTGAGTTGTTGAGTTGT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 13494 90 - 64270 ACGTAGAGCAACAGAGACGC-A-GGGA---------CCATGCAAGTAACCATGGCAAC-TCCAGGAAGTTT-----AAAAA------------AAT---AAGTTTTTGAGTTGTTGAGTTGT i gorGor1.Supercontig_0007361 C 0 C 0 s rheMac2.chr16 75035826 87 + 78773432 ACGTAGAGCAACAGAGACGC-A-AGGA---------CCGTGCAAGTAACCATGGCAAC-TCAAGGAAGTTT-----AAAAA------------AAT---AAGTTTTTGAGTTGTTGA---GT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 43207 90 - 95547 ACGTAGAGCAACAGAGACGC-A-AGGA---------CCGTGCAAGTAACCATGGCAAC-TCAAGGAAGTTT-----AAAAA------------AAT---AAGTTTTTGAGTTGTTGAGTTGT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 45244 90 + 225949 ACGTAGAGCAACAGAGACGC-G-AGGA---------CCGTGCAAGTAACCATGGCAAC-TCCAAGAAGTTA-----AAAAA------------AAT---AAGTTTGTGAGTTGTTGAGTTGT i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 4248 104 + 19765 GCTTAGAGCAACAGAGACCC-A-AGGACCACCCATGCCATGCGAGTAACCATGGCAAC-CTCGGGAACTTTAAAAAAAAAA------------AAT---AAGTTTGTGAGTTGTTGGGCTGT i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 25797 101 + 287808 ACTCAGAGCAACAGAGAGCC-A-AGGACCACCCGCACCATACAAGTAACCATGGCAAC-TGCGGGAAGTTT---AAAAAAA------------AAT---AAGTTTGTGAGTTGCCGGGCTGT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16061879 90 + 17838096 ACGTAGAGCAACAGAGACGC-A-GGGA---------CCGTGCAAGTAACCATGGCAAC-TCCAGGAAGTTT-----AAAAA------------AAT---AAGTTTTTGAGTTGTTGAGTTGT i ponAbe2.chr17_random C 0 C 0 s mm9.chr11 118757824 94 + 121843856 -CTCAGAGCAGGAGAGACCC-G-GCCGCTGCACGGGCCTTTCGAGTAACCATGGTAAC-TTGGGGGAGCTT-----AAAAC------------AAT---AAGTTTCTGAG----TTTGGGGT i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4388193 100 + 7991924 GCCTGGAGCCACAGAGACAC-A-GGCACCGCGCATGCTTGGCAAGTAACCATGGCAACTTTGAGGAAGTTT-----CAAAC------------AAC---CAGTTTGTGGATTGTTTTATGGC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 5848 95 + 44242 GC---GAGCAGCAGAGAC-C-A-GGCACCACGCATGCCT-CCTCGTAACCATGGCAACTTCAGGGAAGTTT-----CCAAC------------AGT---AAGTTTGTGAGTTGTGGAGCTGT i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 17506 102 + 41507 ACGCACCGCAACAGAGACCC-A-GGGACCGCGAGGACCTCG-ATGTAACCATGGCAACTTTGGGGAAGTTT-----ACAAA------------AAAAATAAGTTTGCGACTTGTGGAGCTGT i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 4984 100 - 54875 ACTTAGCACAACGGAGACCC-A-GGGACCACATGTGCCTGGCACGTAACCATGGCAACTTCAAGGAAGTTT-----AAAAA------------AAA---AAGTTTGCGATCTGTGCAGTTGT i ochPri2.scaffold_9426 I 1082 C 0 s bosTau4.chr19 10858044 92 - 65312493 ACTTAGAGCAA--GAGAGCC-A-GGAACCAC-----GCATGCGGGTAACCATGGCAACTTCAGGGAAGTTT-----AAAAA------------AAT---AAGTTTGTGAGTTGCTG-GTTGT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58041570 91 - 61308211 ACTTAGAGGA---GAGA-CG-C-GGGACCGC-----GCATGCGGGTAACCATGGCAACTTCAGGGAAGTTT-----AAAAAA-----------AAT---AAGTTTGCGAGTTGCTG-GTTGT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 30931 94 + 132007 ACTTAGAGCGG--GAGACCT-G-GGAACCAC-----GCACGCAGGTAACCATGGCAACTTTGGGGAAGTTA-----AAAAAAA----------AAA---AAGTTTGTGAGTTGTTG-GTTGT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59435680 92 - 64418924 ACTTA--------GAGACCT-C-GGAACCAC-----ACATGCAGGTAACCATGGCAACTTTGGGGAAGTTA-----AAAAAAA------TAATAAT---AAGTTTGTGAGTTGTTG-GTTGT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 14088 91 + 48268 TTAGACCAA----GACACCG-GGGGAACTGC-----GCATGCGAGTAACCATGGCAACTTCGGGGCAGTTT-----AAAAA------------AAT---AAGTTTGTGAGCTGTTG-GTTGT i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 8365 90 + 14340 ACTTACAGG----GAGGCCG-CGGGAACCAC-----GCATGCGGGTAACCATGGCAACTTCCAGA-AGTTA-----AAAAA------------AAT---AAGTTTGTGAGTTGTTG-GTTGC i myoLuc1.scaffold_4816 C 0 C 0 s eriEur1.scaffold_290756 4815 103 - 7602 ACCCAGCCT----TACACCC-A-GCAACCAA-----GCAGGCAGGTAACCATGGCAACTCagggaaatttg-----aaaaaaaaaaaaagaagaag---aagtttgtGAGTTGTTGAGTTGT i eriEur1.scaffold_290756 C 0 n 0 s proCap1.scaffold_29042 15725 87 + 24616 ---TGCTCCCAC---GAG---T-GGAACTAC-----ATGTGCAGGTAACCATGGCAACCTCAGGGAAGTTT-----GAAAA------------AAT---AAGTTTGTGGGTTGTTGGGTTGC i proCap1.scaffold_29042 I 1 C 0 s loxAfr3.scaffold_49 14431378 93 - 17734757 ---AGCTACAGCAGTGAGACCT-GGGACTGT-----GTGTGCGGGTAACCAAGGCAACCTCAGGGAAGTTT-----AAAAA------------AAT---AAGTTTATGAGTTGTTGGGTTGC i loxAfr3.scaffold_49 I 1 C 0 s dasNov2.scaffold_28617 11125 91 + 20752 ---AAGCACAGGGGAGAGGA-A-GGAAGCGC-----GCATGCGCGTAACCATGGCAACGTC-GGAAAGTTC-----AAAAA------------AAT---GAGTTTGCAACTAGCAGAGTTGT i dasNov2.scaffold_28617 I 1 C 0 s macEug1.Scaffold297525 649 93 + 996 ACTTATGGGAACAGAGCCTT-A-GAAACCAT-----GCCTGGGAGTAACCATGACAAC-Ttctagaagtta-----aaaaa------------aa----aagtttgtgggTTGTTGGATTGC i macEug1.Scaffold297525 C 0 I 16 s monDom5.chr2 304531914 92 - 541556283 ACTTACAGGAACAGAGCCTT-A-GAAACCAT-----GCCTGTGAGTAACCATGACAAC-TTCTAGAAGTTA-----AAAAA------------A-----AAGTTTGTGGGTTGTTGGATTGC i monDom5.chr2 C 0 C 0 e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e turTru1.scaffold_106006 127229 749 + 145505 M e echTel1.scaffold_194555 3042 901 + 11139 I a score=130760.000000 s hg19.chr17_gl000204_random 44672 42 + 81310 ----------------TATTTGGTGC-TT-A-G--TGGGT-TGGACTCT-TGC---------CTTCCTTTTTGA- s panTro2.chr17 79474855 42 + 83384210 ----------------TATTTGGTGC-TT-A-G--TGGGT-TGGACTCT-TGC---------CTTCCGTTTTGA- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 13584 42 - 64270 ----------------TATTTGGTGC-TT-A-G--TGGGT-TGGACTCT-TGC---------CTTCCTTTTTGA- i gorGor1.Supercontig_0007361 C 0 C 0 s rheMac2.chr16 75035913 43 + 78773432 ----------------TATTTGGTGC-TT-AGG--TGGGT-TGGACTCT-TGC---------CTTCCTTTTGGA- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 43297 43 - 95547 ----------------TATTTGGTGC-TT-AGG--TGGGT-TGGACTCT-TGC---------CTTCCTTTTGGA- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 45334 42 + 225949 ----------------TATTTGGTGC-TA-G-G--TGGGT-TGGACCCT-TGC---------CTTCCTCTTTGA- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 4352 41 + 19765 ----------------TATTTGGCGC-TT-G-G---GGGT-TGGGTTCC-TGC---------CTTCCTTTCCAA- i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 25898 44 + 287808 ----------------TAGTTGGTGC-CT-G-GGGTGGGT-GGGGGCCT-TGC---------CTTCCTTTATAA- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16061969 42 + 17838096 ----------------TATTTGGTGC-TT-A-G--GGGGT-TAGACTCT-TGC---------CTTCCTTTTTGA- i ponAbe2.chr17_random C 0 C 0 s mm9.chr11 118757918 39 + 121843856 ----------------TATCCAGTGC-TTCC-G--TGGCT-AGGT-GCC--AG---------CTTTCCT--TAA- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4388293 42 + 7991924 ----------------TATGCGGTGC-TCCA-A--AGGGTCAGGTCATT--GC---------CTCTCCTC-TAC- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 5943 41 + 44242 ----------------TATGTGGTGT-CTGG-G--TGGGT-TGGCTCCT--GC---------CTTCTTTT-TAG- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 17608 39 + 41507 ----------------CACGTGGCGC-TT-G-G--TGGCT-TGGGCCCT--GC---------CTCCCTT--TGC- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 5084 28 - 54875 ----------------CACGTGGCTC-TG-G-G--TGGCT-TGGGCCTTT------------------------- i ochPri2.scaffold_9426 C 0 I 263 s bosTau4.chr19 10858136 34 - 65312493 ----------------TATTTGGTGC-TTGG-G--T----------TCT-TTC---------CTTCTTTTTTAA- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58041661 51 - 61308211 ----------------TA-TTGGTGC-TTGG-G--TGGGC-TGGGTTCT-GTTGGGTTCTGACTTCTTTTTTCA- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 31025 43 + 132007 ----------------TATTTGGTGC-TGAG-G--TGGGG-TGGCTTCT-TTC---------CTTCTTCTTCGA- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59435772 43 - 64418924 ----------------TATTTGGTGC-CTAG-G--TGGGT-TGGGTTCT-CTC---------CTTCTTTTTAAA- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 14179 42 + 48268 ----------------TATTTGGTGC-TTGA-G--T-GGC-CAGGTTCT-TTC---------CCTCCTTTTTAA- i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 8455 43 + 14340 ----------------TATTCGGTGC-TTGA-G--TGGGT-TTGGTTCT-CTC---------TTTCCTTTTTAG- i myoLuc1.scaffold_4816 C 0 C 0 s proCap1.scaffold_29042 15812 42 + 24616 ----------------TATTTGGTGCTTT-C-A--TGGAT-TGAG-TTT-TTC---------CTTGTTTTTTAG- i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14431471 42 - 17734757 ----------------TATTTGGTGC-TT-C-G--TGGGT-TGGGTTTT-TTC---------CTTCTTTTTTAG- i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 11216 33 + 20752 ----------------TCTGTGGCGC-TT-C------------GG-TTT-TCT---------TCTCTGTTTTGA- i dasNov2.scaffold_28617 C 0 C 0 s macEug1.Scaffold297525 758 39 + 996 ----------------GCTTTAGTGG-TG-T-G--TGGgg-ggaatttt-taa---------att---ttttaa- i macEug1.Scaffold297525 I 16 I 1 s monDom5.chr2 304532006 56 - 541556283 TGTTGGGGATTTATGTGCTTTAGTGG-TG-T-G--TGGGG-GGAATTTT-------------TTAATTTTTTAAA i monDom5.chr2 C 0 C 0 e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e turTru1.scaffold_106006 127229 749 + 145505 M e eriEur1.scaffold_290756 4918 0 - 7602 I e echTel1.scaffold_194555 3042 901 + 11139 I a score=262164.000000 s hg19.chr17_gl000204_random 44714 77 + 81310 GATAACGAGG-CCTCTGAATGGTGCTTTTAA-TGAGCTTTGTGGGTACCGTATGGAAGGCAGCCCGTGTCCCCAGA--ATC s panTro2.chr17 79474897 77 + 83384210 GATAACAAGG-CCTCTGAATGGTGCTTTTAA-TGAGCTTTGTGGGTACCGTATGGAAGGCAGCCCGTGTACCCAGA--ATC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 13626 77 - 64270 GATAACAAGG-CCTCTGAATGGTGCTTTTAA-TGAGCTTTGTGGGTACCGTATGGAAGGCAGCCCGTGTCCCCAGA--ATC i gorGor1.Supercontig_0007361 C 0 C 0 s rheMac2.chr16 75035956 74 + 78773432 GATA---AGG-CCTCTGAATGGTGCTTTTAA-TGAGCTTTGTGGGCACCATATGGAAGGCAGCCTGTGCCCCCAGA--ATC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 43340 74 - 95547 GATA---AGG-CCTCTGAATGGTGCTTTTAA-TGAGCTTTGTGGGCACCATATGGAAGGCAGCCTGTGCCCCCAGA--ATC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 45376 78 + 225949 GATGACAAGG-CCTCTGAGCGGTGCTTTTCA-TCAGCATTGTGGGTATCGTGTGGAAGGCAGCCCCTCCCACCAGAC-ATC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 4393 75 + 19765 GATAACGAGG-CCTCTGCACGAGG---TTTA-TGGGCTTTGCTGGTTCAGGGTCCCAGACAGCAGCTGCCCCCAGAC-TCC i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 25942 76 + 287808 AGTAACATGG-TCTCTGAATAGTGC-CTTGG-CAGGCTCTGCAGGTT-GGGGTCCAAGGCAGCAGCTGCCTCCTGGC-TCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16062011 77 + 17838096 GATAACAAGG-CCTCTGAATGGTGCTTTTAA-TGAGCTTTGTGGGTAACGTATGGAAGGCAGCCCGTGTCCCCAGA--ATC i ponAbe2.chr17_random C 0 C 0 s mm9.chr11 118757957 73 + 121843856 GATAACAGAGCCCCCCAAGTAACAC-TTTCG-GGAGCACCGAGGGGACAGTATACAAGGAA----CAGCCTCTAC-C-TGC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4388335 70 + 7991924 AATACCAAGA--CCCTGAATGACAC-TGTTA-GGC-CACTGCAGGGCTGGTGTCCCA-GAG----CAGCCTCCACAC-TGC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 5984 71 + 44242 GGTAACAGGA-TCCCAGCCTCACAC-TTCCA-TGAGCTCTGTGGG--CAGTGTCCAGGGAG----CTGCCTCCAGAC-TCC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 17647 23 + 41507 ACACACGGGG------------------------------------------------GAG------GCCACCGG-C-T-- i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_218698 52 77 + 1062 GATAACAAGG-TCCCTGAATAACAC-TTCCG-TGAGGTTTTTGGGTACAGCGTCCAAAGCAGCAGCTGCCTCCAGAC-TTC i vicPac1.scaffold_218698 N 0 C 0 s bosTau4.chr19 10858170 77 - 65312493 GATAACAAGG-TCCCTGAATAACAC-TTTTA-TGAGTTTTTTGGGTACTGCATCCGAGGCAGTGGCTGTCTCCAGAC-TTG i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 127987 49 + 145505 -------------------------------ATGAGTTTTTCAGGTACAGCATCCAAAGTAGAGGCTGCCTCCAGAC-TTC i turTru1.scaffold_106006 M 749 C 0 s equCab2.chr11 58041712 76 - 61308211 GATAACAAGG-TCCCTGAATAA-GT-TTTTA-TGAGGTTTCCGGGTCCAGCGTCCGAGGCAGCGGCGGCCTGCAGAC-GCG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 31068 76 + 132007 GATAACAAGG-TCCCTGAATAACAC-TTTTA-TGAATGTTTTGGGT-AAGCGTCCAAGGCAGGAGCTGCCTCCAGAC-ATT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59435815 76 - 64418924 GATAACAAGG-TCCCTGAATCACAC-TTCTC-TGAGTGTTTTGGGT-AAGCGTCCAAGGCAGCAGCTGCCTCCAGAC-GTT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 14221 72 + 48268 GATAACAAGG-TCCCTGAGTGATGC-TTTTA-CGAG-GTTTTGGGTGCAGTGTGCAAGGCACC----GCCTGCAGAC-TCC i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 8498 68 + 14340 GATA--AGGT-TCCCTGCGCAAC-C-CTCTA-CGA--GTTTGGGGTTCGGGGTCCCAGGCTGT----GCCCCTCGAC-CTC i myoLuc1.scaffold_4816 C 0 C 0 s proCap1.scaffold_29042 15854 75 + 24616 GGTAACAAGG-TCCCCAAATAGCAC--GCTC-TGAGCATTGCTGGCCCAGCGTTCAAGGCAGCAGCTGCCTCCAGAC-TC- i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14431513 76 - 17734757 GATAACAAGG-TCCCCAAATAGCGC--TCTA-TGAGAGTGGTTGGCCCGGCGTTCAAGGCAGCAGCTGCCTCCAGACTTC- i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 11249 69 + 20752 GATAAGGGGG-TCCGTGAGCAGCTC-----C-TGGG---GGTTGGCCCAGCGTGCAAGGCAGCAGGTGCCTCCAGAC-TC- i dasNov2.scaffold_28617 C 0 I 545 s macEug1.Scaffold297525 798 71 + 996 gataata----tcCTTAAATAACAT----TA-TAGGCTATGTTGGAACAAAGTCCAATACTGTAGCTGTCTCCTAAC-TTC i macEug1.Scaffold297525 I 1 C 0 s monDom5.chr2 304532062 71 - 541556283 GATAATA----TCCTTAAATAACAT----TA-TAGGCTGTGTTGGAACAAAGTCCAATACTGTAGCTGTCTCCTAAC-TTC i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_9426 5112 263 - 54875 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e eriEur1.scaffold_290756 4918 0 - 7602 I e echTel1.scaffold_194555 3042 901 + 11139 I a score=45940.000000 s hg19.chr17_gl000204_random 44791 33 + 81310 T-CATGACCTTTGAAGGGGGAAG-CAAGTGTCTC-A s panTro2.chr17 79474974 33 + 83384210 T-CATGACCTTTGAAGGGGGAAG-CAAGTGTCTC-A i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 13703 33 - 64270 T-CATGACCTTGGAAGGGGGAAG-CAAGTGTCTC-C i gorGor1.Supercontig_0007361 C 0 C 0 s rheMac2.chr16 75036030 33 + 78773432 T-CACGACCTTTGAAGGGGGAAG-CAAGTGTCTC-A i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 43414 33 - 95547 T-CACGACCTTTGAAGGGGGAAG-CAAGTGTCTC-A i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 45454 33 + 225949 T-CATGACCTTGGAAGCTGGAAG-CAAGTGTCTC-A i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 4468 33 + 19765 T-AATTACCTTTGACGGGAGAAG-CAGGTGTCTC-A i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 26018 22 + 287808 T-AAC-----------GGAAGAG-CGAGTGTCTC-C i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16062088 33 + 17838096 T-CCTGACCTTTGAAGGGGGAAG-CAGGTGTCTC-C i ponAbe2.chr17_random C 0 C 0 s mm9.chr11 118758030 28 + 121843856 T-CCCCACCATGCCTTCAG------CAGTGTCTT-A i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4388405 23 + 7991924 T-GGCTACCTTTGCTC-----------ACGTCTC-A i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 6055 23 + 44242 C-GGCCACCTGGGCCA-----------GCATCTC-A i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 17670 28 + 41507 -----CACCTTGGCCGTGG-AGC-CCCACGCCCC-A i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_218698 129 26 + 1062 T-CATTACTTTCCGAGGGGGAGG-CGC--G------ i vicPac1.scaffold_218698 C 0 C 0 s bosTau4.chr19 10858247 31 - 65312493 C-AATTACCTTCCAAGGGGGAGG-CAC--GTCTT-G i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 128036 31 + 145505 T-AATTACCTTCAAATGGGGCGG-CGC--ATCTC-G i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58041788 30 - 61308211 G-AATCACGCTCCAAGCGGAG----GCGCATCTT-C i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 31144 33 + 132007 C-AATTACCTTCCGAGGGGAAAG-CACGCATCAC-G i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59435891 33 - 64418924 T-AATTACCTTCTGAGGGGGAAG-CACGTGTCAC-G i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 14293 32 + 48268 T-AATTACCTCCCGAGGGGGAGG-AGC-TATCTC-G i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 8566 31 + 14340 TAAACTACCTTCCGAGGGGGCGG-GG---GTCCG-G i myoLuc1.scaffold_4816 C 0 C 0 s loxAfr3.scaffold_49 14431589 34 - 17734757 T-AATTACCTCCGGGGGTGGAGG-GGTGTGTGTCTG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 15929 34 + 24616 T-AATTACCCCTGGGGGCGGAGG-GGCACGTGTCTG i proCap1.scaffold_29042 C 0 C 0 s macEug1.Scaffold297525 869 34 + 996 T-AATTACCTTTGAAGTGGGAGGATATATGTCTT-A i macEug1.Scaffold297525 C 0 N 0 s monDom5.chr2 304532133 34 - 541556283 T-AATTACCTTTGAAGTGGGAGGATGTGTGTCTT-A i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_9426 5112 263 - 54875 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e eriEur1.scaffold_290756 4918 0 - 7602 I e dasNov2.scaffold_28617 11318 545 + 20752 I e echTel1.scaffold_194555 3042 901 + 11139 I a score=-155136.000000 s hg19.chr17_gl000204_random 44824 37 + 81310 TCTCAGTTCCACAGAGTCCCAGG---CAGGTCTGT----------CCT----CA s panTro2.chr17 79475007 37 + 83384210 TCTCAGTTCCACAGAGTCCCAGG---CAGGTCTGT----------CCT----CA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 13736 37 - 64270 TCTCAGTTCCACAGAGTCCCAGG---CAGGTCTGT----------CCT----CA i gorGor1.Supercontig_0007361 C 0 C 0 s rheMac2.chr16 75036063 35 + 78773432 TCTCAGTCC--CAGAGTCCCGGG---CAGGTCTGT----------CCT----CA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 43447 35 - 95547 TCTCAGTCC--CAGAGTCCCGGG---CAGGTCTGT----------CCT----CA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 45487 37 + 225949 TGTCAGTCCCACAGAGTCCCAGT---CAGGTCTGT----------CCT----CA i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 4501 40 + 19765 TGTCAGGCCCACAGCGTCTCCAGTCCCGGTTCTGT----------CCT----TG i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 26040 40 + 287808 TCTCAGTCCCACAGCGTCACGGGTCCCAGTGCTGG----------CCT----TG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16062121 37 + 17838096 TCTCAGTTCCACAGAGTCCCAGG---CAGGTCTGT----------CCT----CA i ponAbe2.chr17_random C 0 C 0 s mm9.chr11 118758058 25 + 121843856 CCTTGAGTacacacacacacaca---ca-------------------------- i mm9.chr11 C 0 I 306 s cavPor3.scaffold_76 4388428 23 + 7991924 CCTCAGTCACAGTCCT------------GGTCTGT------------------- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 6078 29 + 44242 CTTCAGTCCCAGAGGG----TCA---CAAGTCCCTG------------------ i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 17698 12 + 41507 CCGCCGTCTTCA------------------------------------------ i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_218698 155 33 + 1062 ----AGCACCACCATCACCAGTT--TGGGTTCTGT----------CCT----T- i vicPac1.scaffold_218698 C 0 C 0 s bosTau4.chr19 10858278 36 - 65312493 TCCAAGCACCACCGTCACAAGTC--CAGTTTCTG-----------CTC----T- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 128067 37 + 145505 TCCAAGCACCACTGTCACATATC--CAGGTTCTGT----------CCT----T- i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58041818 41 - 61308211 TCGGAGCAGCTCCCTCCCAAGTC---CGGCGGCGT----------CCTGGGGCC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 31177 38 + 132007 TCTGAGCACCA--GTCACCAGTCAGTGGGCTCTGT----------CCT----TG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59435924 38 - 64418924 TCTGAGCACCACTGTCACAAGTC--TGGGTTCTGT----------CCT----CA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 14325 37 + 48268 TCTGAGCACCACAGGCAGAAGGC---CGAGCTCAT----------TCT----CC i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 8597 36 + 14340 TCTGAGCATCCTCCGCA-CAGGC---CGGCTCTGT----------CCT----CC i myoLuc1.scaffold_4816 C 0 C 0 s loxAfr3.scaffold_49 14431623 38 - 17734757 TCTCCGCACCAGAGTCACAGGTG--CTGGTTTTGT----------CCC----CA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 15963 38 + 24616 TCTCCACCCCAGAGTCACAGGTG--CAGGCTTTGT----------CCC----CA i proCap1.scaffold_29042 C 0 C 0 s monDom5.chr2 304532167 23 - 541556283 ---------------------------TGGTTTGTAAAGTAgaatcct----ta i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_9426 5112 263 - 54875 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e eriEur1.scaffold_290756 4918 0 - 7602 I e dasNov2.scaffold_28617 11318 545 + 20752 I e echTel1.scaffold_194555 3042 901 + 11139 I a score=257541.000000 s hg19.chr17_gl000204_random 44861 37 + 81310 GATTA---GGTT----GCTCCCT-GTGGGGTGATCTTGAGCCAGT s panTro2.chr17 79475044 37 + 83384210 GATTA---GGTT----GCTCCCT-GTGGGATGACCTTGAGCCAGT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 13773 37 - 64270 GATTA---GGTT----GCTCCCT-GTGGGGTGACCTTGAGCCAGT i gorGor1.Supercontig_0007361 C 0 C 0 s rheMac2.chr16 75036098 37 + 78773432 GATCA---GGTT----GCTCCCC-GTGGGGTGACCTTGAGCCAGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 43482 37 - 95547 GATCA---GGTT----GCTCCCC-GTGGGGTGACCTTGAGCCAGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 45524 37 + 225949 GATCA---GGTT----GGTCTCC-GTGGGATGACCTTGAGCCAGT i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 4541 37 + 19765 AGTCA---GGCT----GTTCACT-GTGGGGTGACCTTGAGCCAGC i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 26080 37 + 287808 AGTCA---GGCT----GTTCCCT-ACAGGGTGACCTTGAGTCAAC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16062158 37 + 17838096 GATCA---GGTT----GCTCCCT-GTGGGGTGACCTTGAGCCAGT i ponAbe2.chr17_random C 0 C 0 s dipOrd1.scaffold_56485 1430 39 + 7959 GAGCAGGTTACT----GCTCCTA-CAG-AGTAACTACAAACTTGG i dipOrd1.scaffold_56485 N 0 C 0 s cavPor3.scaffold_76 4388451 35 + 7991924 GATCA---TGCT----GTGCCTG-CTG--GTGACCATGGGCCAGT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 6107 35 + 44242 GGTTG---AGCT----GTCCCCT-CAG--ATGACCTGGAGTTAGC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 17710 31 + 41507 GACCA---GGCT----CTCGCC-------CTGCCTGTGAGCCCCA i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_218698 188 35 + 1062 -GGGC---AGCG----GTTCACT-GT-GGGTGACCTTGAGCCAGT i vicPac1.scaffold_218698 C 0 C 0 s bosTau4.chr19 10858314 36 - 65312493 -GGGT---GGCT----GTTCTCT-GTGGGGTAACCTGGAGCCAGT i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 128104 36 + 145505 -GGGT---GGCT----GTTCTGC-GTGGGGTGACCTTGAGTCAGT i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58041859 37 - 61308211 GGGAG---GGCT----GTCCTCC-GTGGGGTCACCTTGGGTCAGC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 31215 37 + 132007 GGAAG---GGTT----GCTCTCC-ATGGGGTGACCTCGAGCCAGC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59435962 38 - 64418924 GGGCG---GGTT----GTTCTCCAATGGGGTGACCTTGGGCCAGC i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 14362 36 + 48268 AGGAG---GGCC----ACTCTCT-GTGGGGTGACCT-GAGCCGGG i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 8633 27 + 14340 GTGGG---GGCT----GTTCTCC-GCGGGAG----------CAGT i myoLuc1.scaffold_4816 C 0 C 0 s loxAfr3.scaffold_49 14431661 32 - 17734757 GAGAG---GGCT----GTTCTAC------GTGACCTTGAACCTGG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 16001 36 + 24616 GAGAG---GGCT----GTTCTCC--TGGGATGACCCTGAACCTGG i proCap1.scaffold_29042 C 0 C 0 s monDom5.chr2 304532190 38 - 541556283 gattc---tgttattggttcact-at---gtgaacttgagtaaat i monDom5.chr2 C 0 I 436 e ochPri2.scaffold_9426 5112 263 - 54875 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e eriEur1.scaffold_290756 4918 0 - 7602 I e dasNov2.scaffold_28617 11318 545 + 20752 I e echTel1.scaffold_194555 3042 901 + 11139 I e mm9.chr11 118758083 306 + 121843856 I a score=-78942.000000 s hg19.chr17_gl000204_random 44898 154 + 81310 GTGG---------------------CCCCT-------------------CCCCAACCTTCCACCCACCCACAGAAGTGAGAAGTGCTCCATGCCTCCCCCT--CCC----CAGGAGACCCAACATTTACAGG-----------A---ACT---CTTACAGTGCCCAG-CTACTCTGCAATCCAGATCCACCAGGAT-------CCCAAATATTCATCCCAAGACA s panTro2.chr17 79475081 154 + 83384210 GTGG---------------------CCCCT-------------------CCCCAACCTTCCACCCACCAACAGAAGTGAGAAGTGCTCCATGCCTCCCCCT--CCC----CAGGAGACCCAACATTTACAGG-----------A---ACT---CTTACAGTGCCCAG-CTACTCTGCAATCCAGATCCACCAGGAT-------CCCAAATATTCATCCCAAGACA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 13810 154 - 64270 GTGG---------------------CCCCT-------------------CCCCAACCTTCCACCCACCCACAGAAGTGAGAAGTGCTCCATGCCTCCCCCT--CCC----CAGGAGACCCAACATTTACAGG-----------A---ACT---CTTACAGTGCCCAG-CTACTCTGCAATCCAGATCCACCAGGAT-------CCCCAATATTCATCCCAAGACA i gorGor1.Supercontig_0007361 C 0 C 0 s rheMac2.chr16 75036135 147 + 78773432 GTGG---------------------CCCCT-------------------CCTCAACCTTCCACCCACCCAC-------AGAAGTGCTGCATGCCTCCCCCT--CCC----CAAGAGACCCGACATTTAGAGG-----------A---ACT---CTTACAGTACCCAG-TTACTCTGCAATCCAGACCCCCCAGGAC-------CCCAAATATTCATCCCAAGACA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 43519 147 - 95547 GTGG---------------------CCCCT-------------------CCTTAACCTTCCACCCACCCAC-------AGAAGTGCTGCATGCCTCCCCCT--CCC----CAAGAGCCCCGACATTTAGAGG-----------A---ACT---CTTACAGTACCCAG-TTACTCTGCAATCCAGACCCCCCAGGAC-------CCCAAATATTCATCCCAAGACA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 45561 147 + 225949 GTGG---------------------CCCCT-------------------TCCCAACCTTCCACCCACCCAC-------AGAAGTGCTCCATTCCTCCGGGA--CCC----CAGGAGACCTGACATTTACAGG-----------A---ACT---CATACAGTTCCTGC-CTACTCCACAATCCAGACCCCCCAGGAT-------CCCAAATATTCATCCCAAGACA i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 4578 146 + 19765 GT-GCCCCCACATGTGTTGGAGTGCCCCCT-------------------CCCCAGTCTCCCACCCACCCTC---------------------------------CC----CTGGAGTCCTAGCGTATACAGG-----------A-CTCCA---CCCACAACTTCCCGTCTACTGCACAGTCCAGAGCCCTCGGGGC-------CCCAAACGTGCAGCCCAAGTCA i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 26117 154 + 287808 ATGGCCCCCACATGTGTTGGGGTG-CCCCT-------------------CCCCAATCTCCCACCTACCCAC-------AGAGGTGCCCCATACCTCTCCCT--GCC----CAGGAACCCTGACATA-ACAGG-----------AGGGCCA---CCCACTACTGCCGG----------------GATCCCTCAGGAC-------CCCAAACATTTAGCCCAGCACA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s ponAbe2.chr17_random 16062195 154 + 17838096 GTGG---------------------CCCCT-------------------CCCCGACCTTCCACCCACCCACAGAAGTGAGAAGTGCTCCATGCCTCCCCCT--CCC----CAGGAGACCCAGCATTTACAGG-----------A---ACT---CTTACAGTGCCCAG-CTACTCTGCAATCCAGATCCCCCAGGAT-------CCCAAATATTCATCCCAAGACA i ponAbe2.chr17_random C 0 C 0 s dipOrd1.scaffold_56485 1469 123 + 7959 GT-G---------------------CCCTT-------------------CCCCAA--TCTCTCTCAG---------------------AGCCCCCCAGGGT--CCT------GGCAGTCTTGGGAATGTTGT-----------A--------------GGTACCCGT-CCACTCTACAATCCACATCCCTCAGACCTCAGACGCCCACAT----ATCCTAAAATA i dipOrd1.scaffold_56485 C 0 C 0 s cavPor3.scaffold_76 4388486 131 + 7991924 GC-A---------------------CTCCTGT------------CTCCCCCCAGG--TCCCACCCATCCAG-------AGAA-TTCTCAGTACCCAGGAGT--CCCAG--GAGGTGGCCTTGGAGA-ACTGC-----------A--------------TGCACCTAC-CTACTCTGCAATCCAGACCCCATGGGAT-------------------TTCTAGAATG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 6142 166 + 44242 AT-A---------------------CCCCCATGAAAGTGGGGTGTTCCTCCCCAGTCTCCCGCCCACCCAC-------AGAAGCGCTCAGTACCTCCCCTC--CCC------AGGAGTCTGGCAGGTGCAATGTGGTGCCCAGA--------------GGTGCCTAT-CTACCCTGCAGTGTGGATCCTTCAGAAT-------CCCACACCTTGGTCCCAAGACA i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 17741 108 + 41507 CC-G---------------------CGCCC-------------------CTCAGG--ACGCCCCCTTCCCC-------AGAG------AGCGCCCCACGCG--CCCCTCCCGCGAGAGCTGGCAGGTGCGGG-----------A--------------ACTCCCTCT-CCAACACACGCTAAGCCCCTCCCA--------------------------------- i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_218698 223 94 + 1062 ---G---------------------CACAT-------------------CCCACACATGT-------------------------CTTGGCACCTTCCCCT--CCC----CAGGAGTCCTGA---------G-----------A-------------------CTGT---------CACTCCAGACCCCTGGGGAC-------CCCAGCCAG--GCCCCACAACA i vicPac1.scaffold_218698 C 0 C 0 s bosTau4.chr19 10858350 92 - 65312493 ---G---------------------CACCT-------------------CCCACAC--AT-------------------------CTCCATGCCTCCTCCT--CCC----TAGGAGTCCAGA---------G-----------A-------------------TTGT---------CAAACCAGACCCCTGGGGAT-------CCCAACCAG--GTCCCACAACA i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 128140 94 + 145505 ---G---------------------CACCT-------------------CCCACACGTGT-------------------------CTCCATGCCTCCCCCT--CTT----CAGGAGTCCCGA---------G-----------A-------------------CTGT---------CAATCCATACCCCTGGGGAT-------CACAACCAA--GTCCCACGACA i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58041896 105 - 61308211 ---G---------------------CACCT-------------------CCCACCTGTGTCGCAGTGCCCG--------------TCTCCTGCCTCACCCT--CCC----CGGGAGTCCTGA---------G-----------A-------------------TTGG---------CAGTCCAGACCCCTCGGGAT-------CCCAGCCAG--GTCCCAAGACA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 31252 104 + 132007 ---A---------------------CCTCC-------------------CTTG--TGTATTGCAATGCCCC--------------CCCTGCACCTGCCCCTCCCCC----CAGGAGTCTTGA---------C-----------A-------------------CTGG---------CCATCCAG-TCCCTCTGGGT-------CCCCATCGG--GCCCCAGGACA i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59436000 92 - 64418924 ---G---------------------TGCCT-------------------CCCG--AGTGTCACAGTGCCCC--------------TCTCAGCACTGCTCCT--CCC----TAGAAGTCTGGA---------G-----------A-------------------CTAG---------CAATCCAGTTCCCTCTGGGT--------------------CCCAGGATA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 14398 98 + 48268 ---G---------------------CGCCT-------------------CCCACCCCTAC-------CCCT--------------CTCGGCCCCTCATCCT--CCC----GAGGAGTCTTGG---------G-----------A-------------------CTGG---------CCATCCAGACCCCTCGGGAT-------CCCAACCAA--GTCCCAAGAAA i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 8660 70 + 14340 ---G---------------------CGCCT-------------------CCC----------------------------------------------CCT--CCG----CAGGAGCCCTGA---------C-----------A-------------------GAGG---------CGATCC---CCAACCTGAGT-------CCCACCCAG--GGGCAAAGACA i myoLuc1.scaffold_4816 C 0 C 0 s loxAfr3.scaffold_49 14431693 129 - 17734757 ---C---------------------CACCT-------------------CCCACCTGCTCCAGGTA----------------------TGCCCCTCCCCAC---CC----CAGGTATTCAGAAAGGCACAGA-----------G---ACTCGACCCTGACATCCTGG---TCTCAGCAACCTAGACCCCTCAAGGA-------CCCCAACATCCATCCCAGCCAC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 16037 128 + 24616 ---C---------------------CACTT-------------------TCCATCTCTAGAAGG------------------------TGCTTTACCCCAC--TCC----CAGGGGTTCTCAGAGGCACAGA-----------A---ACTGAACCCCGACATCCTGG---TCTCTTCAATCCTGATCCCTCAGGGA-------AGCCAACATCCAACCCAGCCCC i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_9426 5112 263 - 54875 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e eriEur1.scaffold_290756 4918 0 - 7602 I e dasNov2.scaffold_28617 11318 545 + 20752 I e echTel1.scaffold_194555 3042 901 + 11139 I e monDom5.chr2 304532228 436 - 541556283 I e mm9.chr11 118758083 306 + 121843856 I a score=-105594.000000 s hg19.chr17_gl000204_random 45052 67 + 81310 CCCACGGGGG-----CAAGTTTCCACGCACG-CATC----TCCTAAGTGGGGGAAGAG---GGTCAGGC-TACCCCTGCGA s panTro2.chr17 79475235 67 + 83384210 CCCACGGGGG-----CAAGTTTCCATGCACG-CATC----TCCTAAGTGGGGGAAGAG---GGTCAGGC-TACCCCTGCGA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 13964 67 - 64270 CCCACGGGGG-----CAAGTTTCCACGCACA-CATC----TCCTAAGTGGGGGAAGAG---GGTCAGGC-TACCCCTGCGA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16062349 63 + 17838096 CCCACGGGGG-----CAAGTTTCCACGCACG-CATC----TCCTAAGTGGGGGAAGAG---GGT----C-TACCCCTGCGA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75036282 67 + 78773432 CCCACAGGGG-----CAAGTTTCCATGCATA-CATC----TCCTAAGTGGAGGAAGAG---GGTCAGGC-TACCCCTGCGA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 43666 66 - 95547 CCCACAGGGG-----CAAGTTTCCATGCATA-CAT-----TCCTAAGTGGAGGAAGAG---GGTCAGGC-GACCCCTGCGA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 45708 66 + 225949 CCCACAGGGG-----CAAGTTCCCATGCATG-CATC----TCTTAAGTCGGGG-AGAG---GGTCAGGC-TAACCCTGGGA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 0 55 + 9575 CCCATGGGGA-----TAAGTTTTCACTCACATCATC----TCCCAAGTTGAGGAAAAG---TGTCAG-------------- i tarSyr1.scaffold_143701 N 0 C 0 s otoGar1.scaffold_94362.1-287808 26271 21 + 287808 -CCCATGGGG-----CAG------------------------------------------------------CCCCTGCCA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 4724 63 + 19765 -CCCCGGGGG-----CGAGTTCCCACGTGTG-CGCC----CCCCGAGTGGGGG-AGAG---GGCCAGGC---CGCCTGCAA i micMur1.scaffold_15893 C 0 C 0 s dipOrd1.scaffold_56485 1592 64 + 7959 -CACGTGGTGCATGCCAGCTCTCCACC-----CGGC----TCCAAGTGGGGGAGGGGT---G---GGGC-TGCCCACGCGA i dipOrd1.scaffold_56485 C 0 I 16 s cavPor3.scaffold_76 4388617 48 + 7991924 ------GGTG-------GTCCCACACA-----CAGC----TCCCACAGTGGGGAGGCT---G--CTGGC-TGCCCT----- i cavPor3.scaffold_76 C 0 I 12 s speTri1.scaffold_128901 6308 59 + 44242 -CCCCGGGTA-----TGAGTTCACACA-----CATC----TGTGAAGCTGGGGAGCAG---G-TCAAGC-TGCCCACGC-- i speTri1.scaffold_128901 C 0 I 21 s vicPac1.scaffold_218698 317 50 + 1062 ----------------------CCACTCACA-CATC----TCCCAGTTTGGGG-AGAG---GCTCCGGTGATCTCCTGCAA i vicPac1.scaffold_218698 C 0 I 13 s bosTau4.chr19 10858442 46 - 65312493 ----------------------CCACTCA------------CCCAATCTGGGG-AGAGTCAGGCAATCTCCTCCAAAATCA i bosTau4.chr19 C 0 I 10 s turTru1.scaffold_106006 128234 50 + 145505 ----------------------CCACTCACA-CATC----TCCCAATTTAGGG-AGAG---GGTCAGGTGATCCCCTACAA i turTru1.scaffold_106006 C 0 I 13 s equCab2.chr11 58042001 48 - 61308211 ----------------------CCACTCACA-CATC----TCTCAAAGCGGGG-AGGG---GGTCAGG--CAACACCGCAA i equCab2.chr11 C 0 I 12 s felCat3.scaffold_206428 31356 49 + 132007 ----------------------CCATTCACA-CACG----TCCCACTGTGGGG-AGAG---GGTGAGGC-CACCCGCGCAA i felCat3.scaffold_206428 C 0 I 12 s canFam2.chr9 59436092 39 - 64418924 ----------------------TCACTCACA-CATT----GTCCTCTGTGGGG-AG--------------CCCCCCCACCA i canFam2.chr9 C 0 I 13 s pteVam1.scaffold_11245 14496 49 + 48268 ----------------------CCATTCACA-CGTC----TCCCAAGGTAGGG-CGAG---GGCCAGGC-ACGCCCTGCAA i pteVam1.scaffold_11245 C 0 I 13 s myoLuc1.scaffold_4816 8730 40 + 14340 ----------------------CCGTTCACA-CGCC----C---------GGG-AGAG---GGTCAGGC-AGCCCCTACAA i myoLuc1.scaffold_4816 C 0 I 13 s loxAfr3.scaffold_49 14431822 68 - 17734757 CCTGTAGGAGGGGCCAGACTATCCCTGCAAG-CATCATGACCCCCACTTGCAG--------AGTCA----CGTCCACACAC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 16165 59 + 24616 CCTGCAGGAGGGGCCAGGCTGCCCTGGCTGG-CAACAGGAGCCC-----------------AGTCA----CATCCCCACAT i proCap1.scaffold_29042 C 0 C 0 e oryCun2.chrUn0958 17849 0 + 41507 C e ochPri2.scaffold_9426 5112 263 - 54875 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e eriEur1.scaffold_290756 4918 0 - 7602 I e dasNov2.scaffold_28617 11318 545 + 20752 I e echTel1.scaffold_194555 3042 901 + 11139 I e monDom5.chr2 304532228 436 - 541556283 I e mm9.chr11 118758083 306 + 121843856 I a score=-355901.000000 s hg19.chr17_gl000204_random 45119 69 + 81310 ACATACTAATATGCT-------------------------GGCCAGCA--CGCA-T---GTGTAG-GTGCACAGGAGACC-CGTGCAA-----------CTCCACCCCCGC---AC s panTro2.chr17 79475302 69 + 83384210 ACATACTAATATGCT-------------------------GGCCAGCA--CGCG-T---GTGTAG-GTGCACAGGAGACC-CATGCAA-----------CTCCACCCCCGC---AT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 14031 69 - 64270 ACATACTAATATGCT-------------------------GGCCAGCA--TGCG-T---GTGTAG-GTGCACAGGAGACC-CGTGCAA-----------CTCCACCCCNGC---AC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16062412 69 + 17838096 ACATACTAATATGCT-------------------------GGCCAGCA--TGCA-T---GTGTAG-GTGCACAGGAGACC-CGTGCAA-----------CTCCACCCCCGC---AC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75036349 63 + 78773432 GCATACGAATATGCT-------------------------GGCCAGCG--TGCG-T---GTGT-------GCAGGAGACC-AGTGCAA-----------CTCCATCCCCAC---AT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 43732 63 - 95547 GCATACGAATATGCT-------------------------GGCCAGCG--TGCG-T---GTGT-------GCAGGAGACC-AGTGCAA-----------CCCCATCCCCAC---AT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 45774 67 + 225949 GTGTCCTGATATGCC-------------------------AGCCAGCA--TGCG-T---GTGTGC-GTGTAGAAGAGACC-GGTACAA-------------CCACCCACAC---AC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 55 59 + 9575 ------------GCT-------------------------GGCCTGCA--TGGGTT---ATGTGC-ATGTAAATATGACCAAATGCAA-----------TTCCATCTCCAC---AT i tarSyr1.scaffold_143701 C 0 C 0 s otoGar1.scaffold_94362.1-287808 26292 96 + 287808 GCCTGCTGTGACAACATGCTACATGTAGGACCACACAGAGGGCCAGCA--TGTG-GTGTACACCC-ATGGAAATGTGTCC-ACAGCCA-----------CTCAG-GCCCAC---AC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 4787 88 + 19765 GCGTGCTGATACGCC--GGCACATGTGCG--CGCACGAGCAGCCAGCA--CGCA-G---GCGTGC-AGGTGAAGGTGACC-AGAGCGA-----------CTCA--TCCCAC---AC i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118758389 14 + 121843856 ---------------------------------------------gca--tact-t---atatac--------------------------------------------------- i mm9.chr11 I 306 C 0 s dipOrd1.scaffold_56485 1672 53 + 7959 GGAGTCATGCACATA-------------------------CATCTGCA--TGCA-T---GTGTGCCTCAGGCATGTG--C-A--------------------------CCC---AC i dipOrd1.scaffold_56485 I 16 I 631 s cavPor3.scaffold_76 4388677 65 + 7991924 GCGTGCACACACACA-------------------------CAGGAGCC--TGTA-T---GTGTGC-ACATGAAGTTA--C-AGGGTGG-----------CTCCAG--CCCC---AC i cavPor3.scaffold_76 I 12 I 2 s speTri1.scaffold_128901 6388 34 + 44242 GCATGCACACACACG-------------------------CAGGCCTG--TACC-T---GTGCGT--------------------------------------------------- i speTri1.scaffold_128901 I 21 C 0 s oryCun2.chrUn0958 17849 53 + 41507 --------------G-------------------------TGCCACCA--CGCG-T---GTGTGC--CGTGATGGTGGCC-AGCACGA-----------CTTCAT-CCCCC---AC i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_218698 380 75 + 1062 ACACGCAGAGT--CA-------------------------CACACACT--CACC-C---ACATG---TGGATGGAAGGCC-AGCATGT-GTTGAGTAAACTACATCCCCCC---AC i vicPac1.scaffold_218698 I 13 C 0 s bosTau4.chr19 10858498 79 - 65312493 ACAGGCAGAGTTGCA-------------------------CACACACT--CACA-C---ACGTGC-ATACACAAGGGGCC-AGCACAA-GCCATGTAAACTACGTTCTCCC---AC i bosTau4.chr19 I 10 C 0 s turTru1.scaffold_106006 128297 79 + 145505 ACATGCAGAGCTGTG-------------------------CACACACT--CACA-C---ACATGC-ATGCACAAAGAGCC-ACCATGA-GTCGTGTAAACTACATTCCCCC---AC i turTru1.scaffold_106006 I 13 C 0 s equCab2.chr11 58042061 76 - 61308211 ACACGCAGAGA--CG-------------------------CACACACATTCACA-C---ACGTGC-GTGCAAGAAGGGCG-AGCA----TGCGTGTAAACTACATCCCCCA---CA i equCab2.chr11 I 12 C 0 s felCat3.scaffold_206428 31417 80 + 132007 GCTCGCAATC---CA-------------------------CACGCACG--CATG-C---ACACGC-GTGCACAAAGGGCC-AGCGTGCCTGCGTGTAAACACCATTCTCCCTAAAA i felCat3.scaffold_206428 I 12 C 0 s canFam2.chr9 59436144 78 - 64418924 GCACACAATCA--CC-------------------------CCCCAACA--CACA-C---ACGGGT-GTGCACAGAGGGCC-AGCAGGCCTGTGCATAAACTCCAGTCCCCC---AA i canFam2.chr9 I 13 C 0 s pteVam1.scaffold_11245 14558 35 + 48268 ATGCGCAGTCA--CG-------------------------CACAAACT--CACA-C---ACA---------------------------------------------CCCA---CA i pteVam1.scaffold_11245 I 13 C 0 s myoLuc1.scaffold_4816 8783 55 + 14340 GCGCGCAGT----CG-------------------------CACACACT--CACA-C---ACACGC-G----------------------TGCGGGTAAACTACACCCCCCA---CC i myoLuc1.scaffold_4816 I 13 C 0 s loxAfr3.scaffold_49 14431890 66 - 17734757 GCACACACACACACA-------------------------GGAGGGCC--AGCA-T---GTGTGC-ACAC--AGCTGAGC-GCTGTGA------------TACATCCCCAC---AG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 16224 64 + 24616 GCAC---TGTACACA-------------------------GAAGGGCC--CGCA-C---ATGTGC-ACACG-AGGGGAGC-GGCGTGG------------TACGTTCCTGC---GG i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_9426 5112 263 - 54875 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e eriEur1.scaffold_290756 4918 0 - 7602 I e dasNov2.scaffold_28617 11318 545 + 20752 I e echTel1.scaffold_194555 3042 901 + 11139 I e monDom5.chr2 304532228 436 - 541556283 I a score=-248054.000000 s hg19.chr17_gl000204_random 45188 48 + 81310 GACA--CGACCCCAC--TGCCCACGCTCGGAGATTCTCAGGGTC--------CCTTG-AAG s proCap1.scaffold_29042 16288 46 + 24616 GAAG--CAGCATTCCAGGGCCCATCCTCGGGATCCC----TGTC--------ATCTC-TGG i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14431956 45 - 17734757 AAAG--CAGCATCCCAGCACCCACCCTCAGGAT-CC----TGCT--------GCCCT-TGG i loxAfr3.scaffold_49 C 0 C 0 s myoLuc1.scaffold_4816 8838 41 + 14340 --AA--CGAAGT-CC--TGCCCA-ACTCGGAACCGCCC---CCC--------GCCCC-ACG i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 14593 45 + 48268 --AA--CGGCGT-CC--TGCTCACACTCGGGCACGCCCGCTGCC--------GCTCG-AAG i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59436222 45 - 64418924 --AA--CCATATCCC--TCCCTACACTCAGAAACACCAGGTGCC---------CTCA-AAG i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 31497 45 + 132007 --AA--GCACATGCT--CGCCCACGCTCAGAAACGCCGGGTGCC---------CTCC-ACG i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58042137 33 - 61308211 --GA--ACAT---CC--CGCCCACACTCGG---CGC------CC---------CTCC-GAG i equCab2.chr11 C 0 C 0 s turTru1.scaffold_106006 128376 28 + 145505 --AAAACAACAT-CC--CACCTAA----------------------------ACTCGGAAA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10858577 5 - 65312493 --AA------------------------------------------------------AAA i bosTau4.chr19 C 0 C 0 s vicPac1.scaffold_218698 455 31 + 1062 --AAAATGATGT-CC--CGCCCAG----------------TGCC--------TCTCA-AAG i vicPac1.scaffold_218698 C 0 C 0 s oryCun2.chrUn0958 17902 35 + 41507 ---------------------AACACCACAGCAGCACCCCTCCCCACCCCCGCCCC----- i oryCun2.chrUn0958 C 0 C 0 s speTri1.scaffold_128901 6422 29 + 44242 ---------------------------GTATCGGTGACCCTGTCT----CTGCCTAG-AGC i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4388744 26 + 7991924 ---------------------------GCAGGAGTCCGCAGGTCT-------CCTCA-AAG i cavPor3.scaffold_76 I 2 C 0 s mm9.chr11 118758403 30 + 121843856 ----------------------ataTTAAAAGATTCAAGAGGTC--------ACTGG-AAG i mm9.chr11 C 0 C 0 s micMur1.scaffold_15893 4875 46 + 19765 AAGA--CGGCATCAC--CACCCACACCTGGAAATTC-CA-GGCC--------CCTCA-GAT i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 26388 47 + 287808 GAAA--CAGCATTGC--CACCCACATGGGGAAACTC-CAGGGTC--------CCTCA-AAT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tarSyr1.scaffold_143701 114 47 + 9575 AACA--C-ACATCTC--CATCCACACTCGGACATTTCCGGGGCC--------TCTCA-CAG i tarSyr1.scaffold_143701 C 0 C 0 s calJac1.Contig5139 45841 48 + 225949 AACA--CAACCCTGC--CACCCACACTCCAAAATTCCCAGGGCC--------CCTTG-AAG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 43795 48 - 95547 GACA--TGACCCCAC--GGCCCACACTCGGAAATTCCCAGGGCC--------CCGTG-AAG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75036412 48 + 78773432 GACA--TGACCCCAC--GGCCCACACTCGGAAATTCCCAGGGCC--------CCGTG-AAG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16062481 48 + 17838096 GACA--CAACCCCAC--TGCCCACACTCGGAAATTCTCAGGGTC--------CCTTG-AAG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 14100 48 - 64270 GACA--TGACCCCAC--NGCCCACACTCAGAGATTCTCAGGGTC--------CCTTG-AAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79475371 48 + 83384210 GACA--CGACCCGAC--TGCCCACACTCGGAGATCCTCAGGGTC--------CCTTG-AAG i panTro2.chr17 C 0 C 0 e ochPri2.scaffold_9426 5112 263 - 54875 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e eriEur1.scaffold_290756 4918 0 - 7602 I e dasNov2.scaffold_28617 11318 545 + 20752 I e echTel1.scaffold_194555 3042 901 + 11139 I e dipOrd1.scaffold_56485 1725 631 + 7959 I e monDom5.chr2 304532228 436 - 541556283 I a score=171934.000000 s hg19.chr17_gl000204_random 45236 19 + 81310 GGTCCAG--------------------CTGGCCTTGGT-G s panTro2.chr17 79475419 19 + 83384210 AGTCCAG--------------------CTGGCCTTGGT-G i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 14148 19 - 64270 GGTCCAG--------------------CTGGCCTTGGT-G i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16062529 19 + 17838096 GATCCAG--------------------CTGGCCTTGGC-G i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75036460 19 + 78773432 GGTCCAG--------------------CTGGCCTTGAT-G i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 43843 19 - 95547 GGTCCAG--------------------CTGGCCTTGAT-G i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 45889 19 + 225949 GACCCAG--------------------CTGGCCTTGGT-G i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 161 19 + 9575 AGCTAAG--------------------GTGGCCTCATT-G i tarSyr1.scaffold_143701 C 0 C 0 s otoGar1.scaffold_94362.1-287808 26435 19 + 287808 GGCCCAG--------------------GTGGCCTCCGG-G i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 4921 19 + 19765 GGCCCAG--------------------GTGGCCTCAGG-G i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118758433 19 + 121843856 TGTTCAA--------------------GTGGGCTCAGT-G i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4388770 19 + 7991924 GGCTGAA--------------------GAGGCCTCCAT-G i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 6451 39 + 44242 CATCCAGGCCCACACTGGGGACCGCCCGCAGCCTCAGT-G i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 17937 12 + 41507 ---------------------------GGGGGCTCAGG-G i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_218698 486 19 + 1062 GGCTGAG--------------------ATAGCCTCAGC-G i vicPac1.scaffold_218698 C 0 C 0 s bosTau4.chr19 10858582 19 - 65312493 TGCCCGA--------------------GTGGCCTCTGT-G i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 128404 19 + 145505 TGCCCAG--------------------GTGGCCTCCAC-G i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58042170 18 - 61308211 GGTCCAG--------------------GTGGCCTTACC-- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 31542 20 + 132007 GGCCCAG--------------------CTGGCCTCAGCAG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59436267 17 - 64418924 GGCCCGG---------------------TGGCCTCAGT-- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 14638 19 + 48268 GGCCCAG--------------------GCGGCCTCGGT-G i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 8879 19 + 14340 GGCCCAG--------------------GTGGCCTCGGT-G i myoLuc1.scaffold_4816 C 0 C 0 s loxAfr3.scaffold_49 14432001 19 - 17734757 GCCCCAG--------------------GCAGCCTCGGT-G i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 16334 16 + 24616 TCCCCGG-----------------------GTCCCAGT-G i proCap1.scaffold_29042 C 0 C 0 s monDom5.chr2 304532664 19 - 541556283 GGCTCTA--------------------TTGGCCTCAGT-G i monDom5.chr2 I 436 C 0 e ochPri2.scaffold_9426 5112 263 - 54875 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e eriEur1.scaffold_290756 4918 0 - 7602 I e dasNov2.scaffold_28617 11318 545 + 20752 I e echTel1.scaffold_194555 3042 901 + 11139 I e dipOrd1.scaffold_56485 1725 631 + 7959 I a score=161706.000000 s hg19.chr17_gl000204_random 45255 136 + 81310 GAGGCGAA--TG-----GGAGCCGCTGTCCTG-GGG---TCAG----CCCTTCTC-TGTGCAGGCCACAGCAGCA-------GGTGTTCTGTGCCAAAGGTCATCCTCGCGTGTGCCGATGGGG-----TGTACA------TGTGCT--CA----CACAG--------GCAC------AAAAGC-ACGCAC s panTro2.chr17 79475438 136 + 83384210 GAGGCGAA--TG-----GGAGCCGCTGTCCTG-GGG---TCAG----CCCTTCTC-TGTGCAGGCCACAGCAGCA-------GGTGTTCTGTGCCAAAGGTCATCCTCGCGTGTGCCGATGGGG-----TGTGCA------TGTGCT--CA----CACAG--------GCAC------AAAAGC-ACGCAT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 14167 136 - 64270 GAGGCGAA--TG-----GGAGCCGCTGTCCTG-GGG---TCAG----CCCTTCTC-TGTGCAGGCCACAGCAGCA-------GGTGTTCTGTGCCAAACGTCATCCTCGCGTGTGCCGATGGGG-----TGTGCA------TGTGCT--CA----CACAG--------GCAC------AAAAGC-ACGCAT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16062548 136 + 17838096 GAGGCGAA--TG-----GGAGCCACTGTCCTG-GAG---TCAG----CCCTTCTC-TATGCAGGCCACAGCAGCA-------GGTGTTCTGTGCCAAAGGTCATCCTCGCGTGTGCCGATGGGG-----TGTGCA------TGTGCT--CA----CACAG--------GCAC------AAAAGC-ACGCAT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75036479 136 + 78773432 GAGGCGAA--TG-----GGAGCCGCTGTCCTG-GGG---TCAG----CCCTTCTC-TGTGCAGGCCACAGCAGCA-------GGTGTGCTGTGCCAAAGGTCATCCTCGCGTGTGCCGATGGGG-----TGTGTG------TGTGCT--CA----CACAG--------GCAC------AAAAGC-ACGCAT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 43862 136 - 95547 GAGGCGAA--TG-----GGAGCCGCTGTCCTG-GGG---TCAG----CCCTTTTC-TGTGCAGGCCACAGCAGCA-------GGTGTGCTGTGCCAAAGGTCATCCTCCCGTGTGCCGATGGGG-----TGTGTG------TGTGCT--CA----CACAG--------GCAC------AAAAGC-ACGCAT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 45908 136 + 225949 GAGGCAAA--TG-----GGAGCTGCTGTCCTG-GGG---CTAG----CCCTTCTC-TATGCAGGCAACAGCAGCA-------GGTGTTCGATGCCAAGGGTCATCCTCATGCATACCAGTGGGG-----TATGCA------TGTGCT--CA----CACAG--------GCAC------AAAAGC-ATGCAT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 180 138 + 9575 GAGCTAAA--GA-----GGAGCCACTGTCTTA-AGG---CCAA----CGCTTCTT-TGCACAAGCCACAGCAACA-------GGCTTTCAATGCCAAGGGACATCCTCATGTGTGTCAATAGGG-----TGTGAG------TGTGCTCACA----CACAT--------GCAT------GAAAAC-ACATAT i tarSyr1.scaffold_143701 C 0 C 0 s otoGar1.scaffold_94362.1-287808 26454 131 + 287808 CTGGTGAA--TG-----GGAGCC-CTGTCT-A-GGG---CCCG----CCCTTCTC-TGTACAGG-AACCGCAACA-------AGCTTTCAACGCTAAAGGACATGCTCAGGTGTGTCGAT-GGG-----TGTGCA------TCCACT--CAGA--CATAC--------ACAC------AGAAAC-ACA--- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 4940 136 + 19765 -GGGTGAG--CG-----GCAGCC-CTGTCC-G-GGG---ACAG----CCCTTCCC-TGTGCAGGCAACAGCAGCA-------AGCTCCCAGTGCCAAGGGACATCCTCACGTGCGTTCATGGGG-----TGTGCG------TGCGCT--CACACTCACAC--------GCAC------AAAAAC-ACGAA- i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118758452 125 + 121843856 ACATCAG---TG-----TGAGCCACTGTCCCA-GGA---CCAC----CC----TC-TTTG--------AGCAGGGGAC----AAC-AGTAA----GAAGGACACCCTCCCTCCCGCCTGTGGC------TGGCTA------CACCTC--CC----AAGGC---CACATACCC------GTAAGT-GTGCAC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4388789 147 + 7991924 GAGACAGA--TG-----GCAGCCCGTGGCCTT-TGG---CCACCAACCCCG--TC-TGTGTAGGGCACAGCAGGAGGC----AGCTTTGGATGT-CAAGGACAGCGTCGCAGGTATCGATCAA------TGGGTA------TGTGCT--CA----CACGCACTCCCACACCT------GTAAAC-ATGCAC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 6490 135 + 44242 GAGGTGGG--TG-----GGAGCC-GCATCCTG-GGG---ATGG----CCCT--TC-TGTGCAGGGGACAGAGGAACACAGGAAGCGTCCGAAGG-TGAGGACGTCCTCACACATGCTAATGGT---------GCA------CGCACA--CA----CAGGT--------GCAC------ACAAAC-ACGAAC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 17949 96 + 41507 CAGGCGGA---G-----GGAGCCGCTGTCCTG-CGG---CCAG-----------C-TGTGCA--------------------AGCG---------CCGGTACACCC----GTGTGTTCACGGG-------GCGAG------TGCGTT--CC----CGGGT------------------GTGCAA-ACACGC i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_218698 505 109 + 1062 GAGGCGAA--CG-----GGAGC-----CCCGG-GCA---CCGA----CC-GTCTC-CGTGAAGGCAGCGGAAGCA-------GGCTCTCGATGCCGAGAGACCTCCTCTCATGT-----------------------------------CG----ATGGG--------GCAC------ACACGCCATGCAC i vicPac1.scaffold_218698 C 0 C 0 s bosTau4.chr19 10858601 115 - 65312493 GGAGCAAA--TG-----GGAGCCACAGCCCTG-ACA---CTGA----CCTTTCTC-CACGAAGGCAGCAGGAGCA-------GCCTCTCCATGCTGAGGGACATGCTCACGTGT-----------------------------------CA----ACAGG--------GCAC------ACCCGCCATGCAC i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 128423 115 + 145505 GAGGCAAA--TG-----GGAGCCGCACCCCTG-ACA---CTGA----CCCTTTTC-CGTGAAGGCAGCAGGAACA-------GGCTCTCAATGCTGAGGGACATGCTCACGTGT-----------------------------------TG----ACGGG--------GCAC------ACATGCCACACAC i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58042188 125 - 61308211 TCGGCAGA--GGTGAACGGGGCCGCTGCCCTGGGCC---CCGA----CCCTTGTC-CCCGAA-CCGATGGGAGCA-------GGCCTTCGATGCCAAGGGACAGCCGCACGTGT---------------------------GCTGAC--CG----GGTGC--------ACGC------ACACGC-CCGCAT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 31562 121 + 132007 GGGGCAAA--GG-----GGAACCACTGCCCTGGGCA---CCAG----CCCTTCCC-CACGAAGCCAACGGGAGCA-------GGCTTTCGATGCCGAGGGACGTCCTCACGTGT---------------------------CACGCC--TG----CACAC--------GCAC------ACACGC-ACGCAC i felCat3.scaffold_206428 C 0 C 0 s pteVam1.scaffold_11245 14657 124 + 48268 GGGGCGAA--TG-----GGAGCCGCTGCCCTGAACA---CCGA----CCCCTCTC-CCGGAGGCCGACGAGGGCG-------GGCCTTCGATGCCCGGGAACACGCCCACGTGCG--CACGGGG-----CG------------------CG----CGCAC--------GCGC------ACACGC--CGTCC i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 8898 140 + 14340 GATGCCCC--TG-----GGAGCCCCAGCCCTGGGCA---CGGA-----CCTTCCC-TGTGAAGCTGACAGGAGCA-------GGCTCTCCACGCCAGGGGACACGCTCACGCATG--GGTGGGG-----TGTgcacgcacgctcgct--cg----cgcgc--------gcgc------acacac-acacac i myoLuc1.scaffold_4816 C 0 C 0 s proCap1.scaffold_29042 16350 124 + 24616 -GAG----TACA-----AGAGTTGTC----------------G----TCCTGTTT-TGTGACTTCGGCAGCGGCA-------GGCTTTCTATGCCAAGGGGCG-CCACACGTGGGCTGATGCAG-AGCACGtgtg------tgcaca--ca----tgtgt--------gcac------acatgc-gcgtac i proCap1.scaffold_29042 C 0 I 808 s loxAfr3.scaffold_49 14432020 138 - 17734757 -GAGCAGATACA-----GAAGTTGCT-----C-AGC---TGGG----CCCTTTTTGTGTGACTTTAGCATCACTG-------GGCTTTCCATGCCAAGGGACA-CCACACACAGGCTGATGTAG-Tacacatgta------cgcaca--cg----tgtgt--------gcgc----atacacac-gggtac i loxAfr3.scaffold_49 C 0 I 90 s dasNov2.scaffold_28617 11863 130 + 20752 GGGGCA--CACG-----CGCGTCACCCTCC-C-GGC---ACGG----GCGCTTCC-CAGGGGTGCGGCGGCAGCA-------GGCTGTCCTCGCGCGGTTGGG-CTGCCCGTGg---------------tgtgtg------cgcgca--cg----tgcgc--------gcacccgtggacacac-gcgtgc i dasNov2.scaffold_28617 I 545 I 39 s canFam2.chr9 59436284 114 - 64418924 -----------------GGGACCACTGGCCTGGGCA---CCAG----TCTTTCCC-CATGAAGCCAACA-----A-------GATTTTCGATGCCAAGAAACACCCTCACGTGG----ACGGGG-----CA----------TGTGCA--CA----TGCAT--------GCAT------CCACGC-ATGCAC i canFam2.chr9 C 0 C 0 s dipOrd1.scaffold_56485 2356 114 + 7959 ----------TG-----GGACCC----TCCAA-GGG---CCAAGAAGCC----TC-TGTG---------GAGGTGAAT----AGCTCGTGATGTCGCAGGACATCC-----CGTACGTGTGGC------TGGGCG------TGTGTT--CA----CAGGC---C---CACGT------GTACAC-ATACAC i dipOrd1.scaffold_56485 I 631 C 0 s monDom5.chr2 304532683 134 - 541556283 ---GAGAA--AA-----GATGGTGAGTTCTTT-GAACACCCAG----CAATCCTC-TGTAAA------AGGAGAA-------TGCCTTCATTGCTAAGAGAGGCCCTTA-ATATATTGTTGATGTAATGCGTaca------catgca--aa----cacac--------acac------acacac-acacac i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_9426 5112 263 - 54875 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e eriEur1.scaffold_290756 4918 0 - 7602 I e echTel1.scaffold_194555 3042 901 + 11139 I a score=-402530.000000 s hg19.chr17_gl000204_random 45391 95 + 81310 ----------------------------GCTGCTATTCGTGCCGTGACC----------------------GTGA-----------------------AGCCACCGCAGCAGGCC--ACGTCCTGCGGCT--C---CCAAGGGCAGGCTGCCTTGACCACCCACTGAGCACCTCC s panTro2.chr17 79475574 95 + 83384210 ----------------------------GCTGCTATTCGTGCTGTGACC----------------------GTGA-----------------------AGCCGCCGCAGCAGGCC--ACGTCCTGCGGCT--C---CCAAGGTCAGGCTGCCTTGACCACCCGCTGAGCACCTCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 14303 95 - 64270 ----------------------------GCTGCTATTCGTGCCGTGACC----------------------GTGA-----------------------AGCTGCCGCAGCAGGCC--ACATCCTGCGGCT--C---CCAAGGGCAGGCTGCCTTGACCACCCGCTGAGCACCTCC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16062684 95 + 17838096 ----------------------------GCTGCTATTCGTGCTGTGACC----------------------ATGA-----------------------AGCCGCCGCAGCAGGCC--ATGTCCTGTGGCT--C---CCAAAGGCAGGCTGCCTTGACCACCCGCTGAGCACCTCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75036615 95 + 78773432 ----------------------------GCTGCTATTCACACCGTGACC----------------------GTGA-----------------------AGCCGCCACAGCAGGCC--ACATCCTGTGGCT--C---CCAAGGGCAGGCTGCCTTGACCACCTGCTGCACACCTCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 43998 95 - 95547 ----------------------------GCTGCTATTCACACCGTGACC----------------------GTGA-----------------------AGCCGCCACAGCAGGCC--ACATCCTGTGGCT--C---CCAAGGGCAGGCTGCCTTGACCACCTGCTGCACACCTCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 46044 94 + 225949 ----------------------------G-GACCATCCGTGCCGTGACT----------------------GTGA-----------------------AGCCACCACAGCAGGCC--ATGTCCTGTGGCT--C---CCAAGGGCAGGCTGCCTTGACCGCCCGCTGAGCACCTCT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 318 92 + 9575 ----------------------------GCCACCGTTAGTTTTGTGGCC----------------------AGGA-----------------------CATCACCACA-CAGGCA--GAGCCACACCGCT--C---C--AGAGTAGGCTGCCTCAGTCACCTGCAAAGCACCTCA i tarSyr1.scaffold_143701 C 0 C 0 s otoGar1.scaffold_94362.1-287808 26585 62 + 287808 ---------------------------------CATTCGTCCCCTGGCT----------------------GCGA-----------------------AATC----------------------------------CCTGGGGCAGGCGGCCACAA-CACCCACAAGCCACCCTG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 5076 95 + 19765 ----------------------------ACCGCCATGAGTTCCCCAGCT----------------------GCTA-----------------------AATCACCGTGGCAGGCA--GTGCCGCACCGCC--G---CACGGGGCAGGCTGCCGCGGTCGCCGGCAAAGCGCCTCG i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118758577 84 + 121843856 ----------------------------ACTGCCATCTG-TCACAAGAG-------------------------A-----------------------AACTGTCAGAGCAGGCA--GCACT-----GCA--C---ACTGAAGTACGACCTCCTCAGTGGCTGTGGTGTCCGT-- i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 2470 70 + 7959 ----------------------------ACAGCCTTCTG------------------------------------------------------------GCTGGCGGCGGA-GCA--GCCCC-----ACT--C---ACAG----GCTCCGGCCTGGGTAGCTGTGGGGCACCTCA i dipOrd1.scaffold_56485 C 0 C 0 s cavPor3.scaffold_76 4388936 84 + 7991924 ----------------------------ACTGTCCTCTG-CCGGTGGCC-------------------------A-----------------------AGCAGCAGCAGCAGACA--GTGCC-----GCTGGC---ACTG----CAGACTTTCGGGGCAGCTGCACCCCCACAGA i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 6625 70 + 44242 ----------------------------ACTGGCATCAA-CGCTATGCC-------------------------A-----------------------AGCCGTGGAGG---GTG--GCACC-----CCC--C---CCAG---------GGCCCAGGACGCCTTGCTGCCC---- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 18045 50 + 41507 ----------------------------ACCTCCATGGGTCCCGTGGCT-------------------------A-----------------------AGTCCCTGATG---GCA--GCAGA-----GCC--C---CCAG----------------------------------G i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_218698 614 100 + 1062 ----------------------------ACCGCCATCGGTTCAGTGGCC-----CCAGCTCTGCCAGCA--GTGA-----------------------AGTCACTGCAGCAGGCCGCAGATT-----CCT--C---CCA---GCTCGTCGCCCCCA----CTGCAAAGCACCTCC i vicPac1.scaffold_218698 C 0 I 1 s bosTau4.chr19 10858716 104 - 65312493 ----------------------------ACGGCCATCGGTTCAGTGGCC-----CTGGCTGTGCCAAAA--GTTA-----------------------AGTCACCGCAGCAGGAAGCACACT-----CCT--C---CAG---GCCTGCAGTACCAATAGTCTGCAAAGCACCTCC i bosTau4.chr19 C 0 I 1 s turTru1.scaffold_106006 128538 104 + 145505 ----------------------------ATAGCCATTGGTTCAGTGGCC-----CTGGCTGTGCCAGCA--GTTA-----------------------AGTCACCATGGCAGGAAGCACACT-----CCT--C---CAG---GCCCGATGCCCCGATTGTCTGCAAAGCACCTCC i turTru1.scaffold_106006 C 0 I 1 s equCab2.chr11 58042313 111 - 61308211 ----------------------------GGGCCCAGGGGATCTGAGGCC--CTCGAGGACTGCCCGGCGC-GGTA-----------------------AGTCACTGC-GCAGGCGCCGCACG-----CCG--CAGGCAAA--GCACGCGCGCCGCAGTGGGAGCCCGTGCGCCCG i equCab2.chr11 C 0 I 1 s felCat3.scaffold_206428 31683 101 + 132007 ----------------------------ACCTCTGCTGGTTCAGGGGCC--------GCTGCGCCGGCGT-GGTA-----------------------AGTCACGGCGGGAGGCG--GTGCG-----GCT--CCGCCAG-----AAGCCGCCCTGATTGCGGGCACAGCCCCTCG i felCat3.scaffold_206428 C 0 I 1 s canFam2.chr9 59436398 101 - 64418924 ----------------------------ACCTCCACTGGTTCAGTGGCCCGCTCGTGGCCATGCCGGCAC-GCTA-----------------------AGTCAGGGTGGGAGG-------------------CCACCAA---GCACGCTGCCTTGATTGTGTGCAGAGCACCTCG i canFam2.chr9 C 0 I 1 s pteVam1.scaffold_11245 14781 74 + 48268 ----------------------------GCG----------CAGGGGCC---------------CGCTG------------------------------GCCGCGGC-GCAGGCA--GCTCT-----GCT--C---CCG-----ACGCCCGCCGGGCTGTCTGCGAAGCGCCTGC i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 9038 82 + 14340 ----------------------------aca----------cacTGTTC---------------TTCCGT-GGGA-----------------------AGTCAC-GC-ACAGGCA--GTGCG-----GCT--C---CCAT--GCACGCTGCCCCCGTTGTCCGCAGAGCACCCCC i myoLuc1.scaffold_4816 C 0 I 91 s loxAfr3.scaffold_49 14432248 114 - 17734757 ----------------------------acacacacacacatacagacT---------------CGCTGCTGCAG-----GTTCGCCGGCTTGCTTGCGGCA-CTGTAGCAGGCA--GTGCC-----ACC--C---CGTAGGGCACGCTGCCTTGATTGTCTGCACGGCACCTCA i loxAfr3.scaffold_49 I 90 I 1 s dasNov2.scaffold_28617 12032 106 + 20752 -------------------------------CGCGCAGGCGCCTTGACT---------------CGTTGC-GCGGGCGGCGCCCTCCATCGCGATCGCAGCCTCCGCCGTCTGCA--CGGCC-----CCC--C---AGCAAGA-Aggccgcc-------cctgccgcgcccct-- i dasNov2.scaffold_28617 I 39 C 0 s monDom5.chr2 304532817 131 - 541556283 acacacacacacacaGAGTCTCACACACTCAACCATTCATTCTGTTCTT-----TCTACTATAATGCTGC-TTTA-----------------------ACTTACTGCAGCAGGCA-----CT-----GTT--C---TGTAATGCAGATTACCTTTATTGTCTGCAAAATACCTCA i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_9426 5112 263 - 54875 I e proCap1.scaffold_29042 16474 808 + 24616 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e eriEur1.scaffold_290756 4918 0 - 7602 I e echTel1.scaffold_194555 3042 901 + 11139 I a score=-67862.000000 s hg19.chr17_gl000204_random 45486 42 + 81310 -GA-CAGAACCATGGCGG--AGCCGCAGCCC---C----C--CA--------ACAA----------GAG----TT-------------TG---- s panTro2.chr17 79475669 42 + 83384210 -GA-CAGAACCATGGAGG--AGCCGCAGCCC---C----C--CA--------ACAA----------GAG----TT-------------TG---- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 14398 37 - 64270 -GA-CAGAACCATGGAGG--AGCCACAGCCC---C----C--C-----------------------GAG----TT-------------TG---- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16062779 42 + 17838096 -GA-CAGAACCATGGCGG--AGCCGCAGCCC---C----C--CA--------ACAA----------GAG----TT-------------TG---- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75036710 42 + 78773432 -GA-CAGAACCATGGCAG--AGCCCCAGCCC---C----C--CA--------GCAA----------GAG----TT-------------TG---- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 44093 42 - 95547 -GA-CAGAACCATGGCAG--AGCCCCAGCCC---C----C--CA--------GCAA----------GAG----TT-------------TG---- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 46138 42 + 225949 -GG-CAGAACAATAGTGG--AGGCCCAGCCC---C----C--CA--------ACAA----------GAG----TT-------------TG---- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 410 59 + 9575 -GAGCAGAACAATGGTGG--A--CCCAGCCC---C----C--CACACTGTATGCAGCTGGAACATTGTA----TG-------------TG---- i tarSyr1.scaffold_143701 C 0 C 0 s otoGar1.scaffold_94362.1-287808 26647 43 + 287808 -GAGCAGAACCATGGCAG--ATCCCCTCGAC---A----C--TG--------TCTG----------CAG----TC-------------TG---- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 5171 58 + 19765 -CCGAGGAACAATGGCGGCCGGCGCCCGCAG---G----C--TG--------TCCG----------CGG----TCAGAACGCTGTGTTTG---- i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118758661 42 + 121843856 -GG-CTGGACAATGGCAG--GCCCAGCCCAC---C----C--CG--------TCTG----------CGC----CC-------------TG---- i mm9.chr11 C 0 I 16 s dipOrd1.scaffold_56485 2540 42 + 7959 -GG-CAGAACAAAGGCAG-CGTCCAGAGCCC---G----C--CT--------GCTG----------CGC----CC--------------G---- i dipOrd1.scaffold_56485 C 0 I 13 s cavPor3.scaffold_76 4389020 45 + 7991924 -GG-CAGAACAGTGGTGG--CCCAGGCCCAC-TGC----C--TA--------CCTG----------AGC----CCA------------CG---- i cavPor3.scaffold_76 C 0 I 15 s speTri1.scaffold_128901 6695 38 + 44242 -------AGCAGAGGCAG--CGCCAGCCCAC---C----CGGGG--------CCTG----------GGC----CT--------------G---- i speTri1.scaffold_128901 C 0 I 14 s oryCun2.chrUn0958 18095 45 + 41507 -AG-CAGGACAATGGCAG--CGCCCGCCCACCCGC----C--CG--------TCTG----------CAG----CT-------------CG---- i oryCun2.chrUn0958 C 0 I 7 s pteVam1.scaffold_11245 14855 43 + 48268 --A-CAGAACACGGACGG---GCCGCACCCC---C-GCAA--GG--------TCTG----------CAG----TC-------------CC---- i pteVam1.scaffold_11245 C 0 I 11 s canFam2.chr9 59436500 46 - 64418924 -AG-CCGAACAATGGTGG--AGCCCCGCCCA---CGGCGC--CG--------GCTG----------GAG----TT-------------TG---- i canFam2.chr9 I 1 I 11 s felCat3.scaffold_206428 31785 46 + 132007 -AG-CGGAACAGAGGTGC--AGCCCCGCCCG---GGGCAC--GG--------GCCG----------TAG----CT-------------CG---- i felCat3.scaffold_206428 I 1 I 11 s equCab2.chr11 58042425 46 - 61308211 -AG-CAGAAGGACGGCGG--GGCCGCCCACC---CCGCAC--CG--------CCCA----------CGG----CT-------------CC---- i equCab2.chr11 I 1 I 11 s turTru1.scaffold_106006 128643 46 + 145505 -GG-CAGAACAATGGTGG--GGCCCCGCCTA---CCCTGC--TG--------CCCA----------CTG----TG-------------CC---- i turTru1.scaffold_106006 I 1 I 10 s bosTau4.chr19 10858821 46 - 65312493 -GG-CAGAACAATGGTGG--GGCCCCGCCCA---CCCTGC--TG--------CCCA----------CTG----TG-------------CC---- i bosTau4.chr19 I 1 I 10 s vicPac1.scaffold_218698 715 46 + 1062 -GG-CAGAACAAAGGTGG--GGCCCGCCCCC---TCCCAC--TG--------CCCA----------CTG----TG-------------CC---- i vicPac1.scaffold_218698 I 1 I 10 s loxAfr3.scaffold_49 14432363 46 - 17734757 -AA-CAGAACAATGGAGC--AGCCCCCGCCC---G----G--CC--------CTCA----------CAGCTGTCT-------------CC---- i loxAfr3.scaffold_49 I 1 I 18 s dasNov2.scaffold_28617 12138 28 + 20752 ----------------gc--cgcacccctgc---c----g--cc--------cccg----------ccg----cc-------------cc---- i dasNov2.scaffold_28617 C 0 I 16 s monDom5.chr2 304532948 47 - 541556283 ATG-CAGAACAATGGTTC--AATCCCTTCCC---A----C--CA--------AATT----------GGT----TT-------------TCTAAA i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_9426 5112 263 - 54875 I e proCap1.scaffold_29042 16474 808 + 24616 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e myoLuc1.scaffold_4816 9120 91 + 14340 I e eriEur1.scaffold_290756 4918 0 - 7602 I e echTel1.scaffold_194555 3042 901 + 11139 I a score=-417776.000000 s hg19.chr17_gl000204_random 45528 37 + 81310 ----------TTGCA----GGTTGGT-G---CCGGGAGAGCTGAGGAGT----------------------------------------G--CTTGG s panTro2.chr17 79475711 37 + 83384210 ----------TTGCA----GGTTGGT-G---CCGGGAGAGCTGAGGAGT----------------------------------------G--CTTGG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 14435 37 - 64270 ----------TTGCA----GGTTGGT-G---CCGGGAGAGCTGAGGAGT----------------------------------------G--CTTGG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16062821 37 + 17838096 ----------TTGCA----GGTTGGT-G---CCGGGAGAGCTGAGGAGT----------------------------------------G--CTTGG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75036752 55 + 78773432 ----------TTGCA----GGTCGGT-G---CCAGGAGAGCTGAGAAGC------------------GCTTG----GGGCCAGCACACAG--CTTGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 44135 55 - 95547 ----------TTGCA----GGTCGGT-G---CCAGGAGAGCTGAGAAGC------------------GCTTG----GGGCCAGCACACGG--CTTGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 46180 55 + 225949 ----------TTGCA----GGTGGGT-G---CCAGGAAAGCTGAGGAGC------------------ACTTG----GGGCCAGCGCACCA--CTTGG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 469 54 + 9575 ----------TTGCA----GATTGGA-G---CCAGGAGAGCAGACTAGC-------------------ACTG----GGGCTGGTGCAAGG--CCCGG i tarSyr1.scaffold_143701 C 0 C 0 s otoGar1.scaffold_94362.1-287808 26690 55 + 287808 ----------TAGCA----GGTTGGA-G---CTGAGAGAGCCAAAGCCT------------------GCCTG----GGGCCAGCACAAAG--AGCAG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 5229 52 + 19765 ----------TCGCA----GGTCGG--G---CCGGGAGAGCCGAGG-GT------------------GCGT-----GGGCCGGTGCAAGG--CCCTG i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118758719 34 + 121843856 ----------TTGCA----CACC-AA-C--CTTAGGA------GACAGA-------------------------------------ACAG--CCTGT i mm9.chr11 I 16 C 0 s dipOrd1.scaffold_56485 2595 46 + 7959 ----------TGGCA----GACCGGA-G--CTTGGGAG--CGGGGCAGA------------------GCC------------CCGGGCGG--CCTCT i dipOrd1.scaffold_56485 I 13 C 0 s cavPor3.scaffold_76 4389080 54 + 7991924 ----------CTGCG----GGTCAGA-G----TGGGAGTTCGGGACAGT------------------GCCT------GGCAGCCAGAAAGGCCCTGT i cavPor3.scaffold_76 I 15 C 0 s speTri1.scaffold_128901 6747 31 + 44242 ----------CAGCA----GAGCG----------------CTGGGCAG----------------------------------CCAGCGAG--GCCAT i speTri1.scaffold_128901 I 14 C 0 s oryCun2.chrUn0958 18147 59 + 41507 ----------TGGCACTGCTGACGGG-A--GCCAGCAGGGCTGGGCAGC------------------GCCT------GGCGGCCAGCGAGGCCCC-G i oryCun2.chrUn0958 I 7 C 0 s ochPri2.scaffold_9426 5375 55 - 54875 ----------TTGCA----TGCTGGG-A--ACC-GCAGGGCTGGACGGT------------------GTAT------GGCAGCCAACAGGGCCCCAA i ochPri2.scaffold_9426 I 263 C 0 s pteVam1.scaffold_11245 14909 33 + 48268 ----------TCTGA----C--CCAG-G---ATGGGCCCGCTCAAGAGC------------------GCCT-------------------------- i pteVam1.scaffold_11245 I 11 I 18 s canFam2.chr9 59436557 37 - 64418924 ----------TCACA----CACGGAA-G---ACGGGCGCACTGGAGAGC------------------TCTTG----A-------------------- i canFam2.chr9 I 11 I 20 s felCat3.scaffold_206428 31842 37 + 132007 ----------TTACA----CGCGCAA-G---ACAGGCGCGCTGAAGGGC------------------TCTTG----A-------------------- i felCat3.scaffold_206428 I 11 I 20 s equCab2.chr11 58042482 34 - 61308211 ----------TCACA----CATCCGG-A---GCCAGC---CTGAAGAGT------------------GCTTG----A-------------------- i equCab2.chr11 I 11 I 20 s turTru1.scaffold_106006 128699 36 + 145505 ----------TTAGG-----GTCAGA-G---TCAGGAGTGTCGAGGAGC------------------GCTTG----A-------------------- i turTru1.scaffold_106006 I 10 I 19 s bosTau4.chr19 10858877 36 - 65312493 ----------TTAGG-----GTCGGG-G---TCAGGAGCACCGAGGACT------------------GCTTG----A-------------------- i bosTau4.chr19 I 10 I 19 s vicPac1.scaffold_218698 771 36 + 1062 ----------TTAGG-----GGCGGA-G---TCGGGAGCTGGGAGGAAT------------------GCTTG----A-------------------- i vicPac1.scaffold_218698 I 10 I 19 s loxAfr3.scaffold_49 14432427 29 - 17734757 ----------CTACA----G-------A---CCGAGAG--CTGGCAAGC------------------GCCTG----G-------------------- i loxAfr3.scaffold_49 I 18 I 20 s dasNov2.scaffold_28617 12182 40 + 20752 ----------TCACA----GCCCAGACA---CCGCGAG--CTCCGGAGC------------------GCCTGACGCG-------------------- i dasNov2.scaffold_28617 I 16 I 20 s monDom5.chr2 304532995 68 - 541556283 TTTTGAATTATTACA----TATATTA-TTATCTACCAGAGTTAAAGAGCCAAGCCACATTGACAGCTGCCTG----A-------------------- i monDom5.chr2 C 0 C 0 e proCap1.scaffold_29042 16474 808 + 24616 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e myoLuc1.scaffold_4816 9120 91 + 14340 I e eriEur1.scaffold_290756 4918 0 - 7602 I e echTel1.scaffold_194555 3042 901 + 11139 I a score=1841867.000000 s hg19.chr17_gl000204_random 45565 171 + 81310 --------GCCACAGCTG---CAGAGGCAAA-GG----------GCTG---------------GGCTACCTGGCTGG-----GGAAAAAGG-----AATAT--TTTCTTA---------------AAGGG-AG----AAAAATCCTAAAT-GGCCC-TCGCAGTCTCTTGG-CACACATAATTGTAGTATCCAAGTTAATGAAAGGCCTGGCACATGGGCT----GAGTCACAGCAAATGCCTGGCC s panTro2.chr17 79475748 171 + 83384210 --------GCCACAGCTG---CAGAGGCAAA-GG----------GCTG---------------GGCTACCTGGCTGG-----GGAAAAAGG-----AATAT--TTTCTTA---------------AAGGG-AG----AAAAATCCTAAAT-GGCCC-TCGCAGTCTCTTGG-CACTCATAATTGTAGTATCCAAGTTAATGAAAGGCCTGGCACATGGGCT----GAGTCACAGCAAATGCCTGGCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 14472 171 - 64270 --------GCCACAGCCN---CAGAGGCAAA-GG----------GCTG---------------GGCTACCTGGCTGG-----GGAAAAAGG-----AATAT--TTTCTTA---------------AAGGG-AG----AAAAATCCTAAAT-GGCCC-TCGCAGTCTCTTGG-CACACATAATTGTAGTATCCAAGTTAATGAAAGGCCTGGCACATGGGCT----GAGTCACAGCAAATGCCTGGCC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16062858 171 + 17838096 --------GCCACAGCTG---CAGAGGCAAA-GG----------GCTG---------------GGCTACCTGGCTGG-----GGAAAAAGG-----AATAT--TTTCTTA---------------AAGGG-AG----AAAAATCCTAAAT-GGCCC-TCGCAGTCTCTTGG-CACACATAATTGTAGTATCCAAGTTAATGAAAGGCCTGGCACATGGGCT----GAGTCACAGCAAATGCCTGGCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75036807 171 + 78773432 --------GCCACAGCTG---CAGAGGCAAA-GG----------GCTG---------------GGCTACCTGGCTGG-----GGAAAAAGG-----AATAT--TTTCTTA---------------AAGGG-AG----AAAAATCCTAAAT-GGCCC-TCGCAGTCTCTTGG-CGCACATAATTGTAGTATCCAAGTTAATGAAAGGCCTGGCACATGGGCT----GAGTCACAGCAAACGCCCAGCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 44190 171 - 95547 --------GCCACAGCTG---CAGAGGCAAA-GG----------GCTG---------------GGCTACCTGGCTGG-----GGAAAAAGG-----AATAT--TTTCTTA---------------AAGGG-AG----AAAAATCCTAAAT-GGCCC-TCGCAGTCTCTTGG-CGCACATAATTGTAGTATCCAAGTTAATGAAAGGCCTGGCACATGGGCT----GAGTCACAGCAAACGCCCAGCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 46235 170 + 225949 --------GCCACAGCTA---CAGAGGCAAA-GG----------GCTG---------------GGCTATCTGGCTGG-----GGAAAAAGT-----AATCT--TTTCTTA---------------AAGGG-AG----AAAAATCCTAAAT-GGCCC-TCACAGCCTCTCGG-CACACGTAACTGTAGTATCCAGGTTAATGAAAGGCCTGGCACATGGGCT----GAGTAATAGCAAACACC-GGCC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 523 168 + 9575 --------GTCACAGCTG---CTATGGCAAA-GG----------GCTG---------------GACCACATGGCTGT-----GAAAAGACG-----AATAT--TTTCTTA---------------AAGGG-AG----AAAAATCCTAAAT-GG-CC-TCTCAGCCTCCTGG-CGCACATAATTGTAGTATCCAAGTTAATGAAAGGCCTGGCACGCAGGCT----GAGTAGC-GCTCACGCCCAG-C i tarSyr1.scaffold_143701 C 0 C 0 s otoGar1.scaffold_94362.1-287808 26745 148 + 287808 --------GTCACAGCTG---C-----------------------------------------------ATGGCTCT-----GAGAAAGGA-----AATGT--TTTCTTG---------------CAGGG-AG----AAAAATCCCAAAC-AGCCC-TCTCAGCCTTCCTG-TGCACATAATTGCAGTATCCAAGTTCACGATAGGCCTGGCACACAGCC------GGTAACAGCCACCGCCCAGGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 5281 153 + 19765 --------GTCACAGCTG---CGGTGGCAA---------------------------------------AAGGCGGG-----AAGAAGGGG-----AACGT--TTTCTCA---------------AAGGC-AG----GAAAACCCCAAAT-GGTGC-TCTCGGCCTTTCAG-CGCGCAGAATCGTGGCACCCAAGTGCACGGCA-GCCCGGCACTCGGGCT----GGGTCAGCGCCGCCGCCC---- i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118758753 172 + 121843856 --------GTCATGGCTGCTTCGATGGCCAA--G----------GCTG---------------G-------GGCTGT-----GAAAAGCGG---AAGGATT--TTTTTTC---------------AGGGA-AG----AAAAATCCTACAT-GGCCC-TTTCAGCCTTTCGG-CGCACATAATTGTAGTATCCAAGTTAATGAAAGGCCTGGCCTGCTGGCTGGCTGAATAAGCACTAATGCCACGGC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 2641 181 + 7959 --------GGCACAGCTG---TGGCGGCAGA--G----------GCTG---------------AGCCGCTTGGCTGT-----GAAAAGAGGAATAAAAAAA--TGTTTTA---------------AGGGA-GGGGAAAAAAATCCTAAAT-AGCCC-TTTCAA--TTTTGG-CGCACGTAATTGTAGTATCCAAGTTAATGAAAGACCTGGCCTGCTGGCTGGCTGAATTACCACTAATGCGGACGC i dipOrd1.scaffold_56485 C 0 C 0 s cavPor3.scaffold_76 4389134 172 + 7991924 --------GTCACAGCCG---TGGTGGCAAA--G----------GCTA---------------GGCTACATGGCTGT-----GAAAAGAGG------AATC--ATTTTTA---------------AAGGA-AA----AAGAACCTTAAAT-GGTCC-TTTCAG-TCTACGG-CGCACATAATTGTAGTATCCAAGCTAATGAAAGGCCTGGCGTGCTGGCTAGCTGAATGAGGGCTAATGCCACAGC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 6778 173 + 44242 --------GTCACAGCCG---CAGTGGCAAA--G----------GCTG---------------GGCTGCACGGCTGT-----GCAGGGAGG-----AATCA--TTTTTTA---------------AGGGG-AG----AAAAATCCTAAAT-GGCCC-TTTCAGCCTTTCGG-CGCAAGTAATTGTAGTATCC-AGTTAATGAAAGGCCTGGCGTGCTGGCTGGCTGAATGGCGGCCAAAGCCGCGGC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 18206 168 + 41507 --------GTCACAGCTG---CGGAGG------------------CCG---------------CGCTGCATGGCTGT-----GACAAGGGA--AAGATTTT--TTTTCAA---------------AAGGG-AG----AAAAATCCTAACT-GGCCC-TCGCAGCC-CTCGG-CACACATAATTGTAGTATCGGAGCTCACGCGCG-CCCGGCGTGCGGGCT-GCTGAGTGACGGCTGCCGCCACGGC i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 5430 149 - 54875 --------GCCACCATTG---CCAAGGC-AA--G----------TCTA---------------AGCTGTATCACTAT-----GAAAAGG-------------------------------------------A----AAAAATCTTAAAC-GGCCC-CTTCAGCCTCGCAG-CACACATAATTGTAGTATCCGAGCTTGCGCCAG-CCTGGCATGCGGGCC-GCTGAGTGACGGCTGGCGCCCCG-- i ochPri2.scaffold_9426 C 0 C 0 s vicPac1.scaffold_218698 826 166 + 1062 --------GTCACAGCTG---TGGCGCCAAA-GG----------GCTG---------------GGC-ACAGGGCTGT-----GCAAAAAGG-----AA-----TCTTTTT---------------AAGGC-AG----AAAAATCCTAAAT-GGCCC-TTTCAGCCTTTCGG-CGCACATAATTGTAGTATCCGAGTTAATGAGAGGCCCGGCGTGCCGGCTGGCTGAACAcc-gcgcccgccg---- i vicPac1.scaffold_218698 I 19 I 4 s bosTau4.chr19 10858932 171 - 65312493 --------GTCACAGCTG---TGGCCCCAGA-GG----------GCTG---------------GGC-AGATGGCTGT-----GAAAAAAGG-----AATATATTTTTTTT---------------TAAGC-AG----AAAAATCCTAAAT-GGCCC-TTTCAGCCTTTCGG-CGCACATAATTGTAGTATCCGAGTTAATGAAAGGCCTGGCGTGCTGGCTGGCTGAATACC-GCTAACGCCG---- i bosTau4.chr19 I 19 I 4 s turTru1.scaffold_106006 128754 171 + 145505 --------GTCACAGCTG---TGGCGCCAAA-GG----------GCTG---------------GGC-AGATGGCTGT-----GAAAAAAGG-----AATATTTTTTTTTT---------------AAAGC-AG----AAAAATCCTAAAT-GGCCC-TTTCAGCCTTTCAG-CGCACATAATTGTAGTATCCGAGTTAATGAAAGGCCTGGCGTGCTGGCTGGCTGAATACC-CCTAACGCCG---- i turTru1.scaffold_106006 I 19 I 4 s equCab2.chr11 58042536 162 - 61308211 --------GTCACCGCTG---C-GTGACGAA-GG----------GCTG---------------GGC-ACGTGGCTAT-----G-AAAAAGG-----ACTATT-TTTTTTA---------------AAGGC-AG----AAAAATCCTAAAT-GGCCC-TTTCAGCCTCTCCG-CGCACATAATTGTAGTATCCAAGTTAATGAGAGGCCT-ACGTGCCGGCCGGCTGCACCCC------AGCTA---- i equCab2.chr11 I 20 I 10 s felCat3.scaffold_206428 31899 165 + 132007 --------GTCACAGCCG---TGGTGCCGAC-GG----------GCTG---------------GGC-ACACGGCTGT-----GAAAAAAAG-----GAGAAG-TTTTTTA---------------AAGGC-AG----AAAAATCCCACAT-GGCCC-TCTCAGCGTTTCGG-TGCGCATAATTGTAGTATCCGAGTTAACGAAAGGCCCGGCGTGCTGGCCGGCTGAATACC------CACTA---- i felCat3.scaffold_206428 I 20 I 10 s canFam2.chr9 59436614 166 - 64418924 --------GTCACAGCTG---TGGTGCCAAT-GG----------GCTG---------------GGC-ACACGGCTGC-----GAAAAAAGG-----AATTAT-TTTTTTT---------------AAGGC-AG----AAAAATCCTAAAT-GGCCCTTTTCAGCATTTCTG-TGCACATAATTGTAGTATCCAAGTTAATGAAAGGCCTGGCATGCTGGCGGACTGAATACC------CGCTA---- i canFam2.chr9 I 20 I 10 s pteVam1.scaffold_11245 14960 161 + 48268 --------GTCACAGCTG---TGGTGCCGAA-GG----------GCTG---------------GGC-ACATGGCTGT-----GGAAAAGGG-----AACA---CTTTTAA---------------AAGGC-AG----AAAATCCCTAAC--GGCCC-TTTCAGCCT-TCAG-CGCACATAATTGTAGTATCCACGTTAACGAGAGGCCTGGC-TGCTGGCTGGCTGAATACC-----ACGATC---- i pteVam1.scaffold_11245 I 18 I 8 s eriEur1.scaffold_355010 3846 168 + 8359 --------GTCACAGCTG---TGGTACCAAA-GA----------GCCA---------------GAC-ATATGACTGG-----CAAAGAAAg-----acgcttgtttttttttttttttttcccccaaagg-aa----GAAAGTCCTAAAT-GGCCC-TTGCAGTCC-------ACACATAATTATAGTATCCAAGTTTGCAAAGGGCCTGGCAAGCTGGCTAGCCCAGCC----------------- i eriEur1.scaffold_355010 I 3107 C 0 s dasNov2.scaffold_28617 12242 143 + 20752 -----------------------------GC-CGCCGTGCTGGCGCCG---------------GCCCACGTGGCTGG-----GAGGCAGGG-----ACT----TGTTTCG--------------AAAGGG-AG----AAAAGCCCTAAGT-GCGCC-CCTCGGGCCTTCGG-CGCCCCTAACTGTGGCATGGGAGTCCGCTAGCAGCCG-GCGCGCTGACTGGAA---------------------- i dasNov2.scaffold_28617 I 20 C 0 s echTel1.scaffold_194555 3943 131 + 11139 -----------------------GTTACAGA-AGCCGGGCT---GCAG---------------GGCTGCGGGGCTCA-----GGAAAGGCA-----ACA----CGCTTTG---------------CAGGG-AG----AGCAGCCCCCAA--GGCTC-TGGCGG--------------GTAATTGCAGGATCTAAGTTAATGAAAGGCCT-GCGTGCTGGCTGCCT---------------------- i echTel1.scaffold_194555 I 901 C 0 s loxAfr3.scaffold_49 14432476 161 - 17734757 -----------------------GTTGCAGA-GG----------GCTG---------------GGCCACACGGCTGT-----GAAAAGGGA-----GTA----TTTCTTA---------------AAGGG-AG----AAAAATCCTAAAT-GGCCC-TTTCAGCCTTTCAG-CAGACATAATTGTAGTATCCGAGTTAATGAAAGGCCTGGTGTGCTGGCTGGCTGAATACCAGCTAATACCACGCA i loxAfr3.scaffold_49 I 20 C 0 s myoLuc1.scaffold_4816 9211 154 + 14340 ------------------------------A-GG----------GCTGTGCTGCGCACGGGCCAGC-GCATGGCTGT-----GAATAAAGG-----GACC---TTTTTTT---------------AAGGC-AG----AAAAACTCTAAATGGGCCC-CTCCAGGCT-TGCG--GCGCGTAATTGTAGTGTGCGAGCTAATGAAAGGCCCGG---GCCAGCT-ACTGAACACC------CGCTC---- i myoLuc1.scaffold_4816 I 91 I 140 s monDom5.chr2 304533063 193 - 541556283 GAGTTCCTTTCCCAACCA---CAGGGTCAAAAGG----------ATCA---------------TGTTACATTGCTGTTTAAAAAAAAAAGT-----AATATAGTTTTTTA---------------AAGGCTAA----GAAAACCCTAAAC-AGCCT-TTTCAGCCTTTTGATTTCCTGTAATTGTAGTATCTTAGCTAATGCAAAGCCTGGCATGATGACTGGCTGAATTACATCTAATGTCAGTCC i monDom5.chr2 C 0 C 0 e proCap1.scaffold_29042 16474 808 + 24616 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I a score=106067.000000 s hg19.chr17_gl000204_random 45736 52 + 81310 CTGC-ACCT--------CACATG-C---AGCA------------------------------GCTC------------------------------GTAGAAATCAGACG-AT--G-----GCGGGCAGGGG--G s panTro2.chr17 79475919 52 + 83384210 CTGC-ACCT--------CACGTG-C---AGCA------------------------------GCTC------------------------------GTAGAAATCAGACG-AT--G-----GCAGGCAGGGG--G i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 14643 52 - 64270 CTGC-ACCT--------CACGTG-C---AGCA------------------------------GCTC------------------------------GTAGAAATCAGACG-AT--G-----GCGGGCAGGGG--G i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16063029 52 + 17838096 CTGT-ACCT--------CACATG-C---AGCA------------------------------GCTC------------------------------GTAGAAATCAGACG-AT--G-----GCGGGCAGGGG--G i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75036978 52 + 78773432 CTGC-ACCT--------CACATG-C---AGCA------------------------------GCTC------------------------------GTAGAAATCAGACG-AT--G-----GCGGGCAGGGG--G i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 44361 52 - 95547 CTGC-ACCT--------CACGTG-C---AGCA------------------------------GCTC------------------------------GTAGAAATCAGACG-AT--G-----GCGGGCAGGGG--G i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 46405 52 + 225949 CTGC-GCCT--------CACGTG-C---AGCA------------------------------GCTC------------------------------CTAGAAATCAGACC-AC--G-----GCGGGCAGGGG--C i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 691 60 + 9575 CGGC-ACCT--------CACGTG-G---CATG------------------------------GCTCCATTGC----CAC----------------TGTGGAAATCAGACC-AC---------TGGACTGGGG--G i tarSyr1.scaffold_143701 C 0 C 0 s otoGar1.scaffold_94362.1-287808 26893 53 + 287808 CCGC-ACCT--------CACGCA-G---AGCA------------------------------GCTCCATCGC----CAC----------------CGTGGAAATCAGACC-AC--G-----GGG----------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 5434 18 + 19765 --------------------------------------------------------------------------------------------------TGCAATCAGACC-TC--G-----GGG----------- i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118758925 61 + 121843856 CCGG-GCCT--------CACGGG-G---AGCA------------------------------GTTCCATCTC----CG-----------------AGTGGAAATCAGACC-AC--A-----GTGGGGTGGTG--G i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 2822 62 + 7959 AGAA-GCCT--------CACGTG-G---AGCG------------------------------GCTCCATCGC----CAC----------------CGCGCACACCAGACC-TC--G-----GTGGGGAGGAG--C i dipOrd1.scaffold_56485 C 0 C 0 s cavPor3.scaffold_76 4389306 64 + 7991924 CTGC-AGCT--------CATGTG-G---CGAG------------------------------GCTCCATCAC----CGG----------------CATGGAAGACAGATC-AG--T-----TTAGGGAGGTGGAC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 6951 60 + 44242 C-GC-ACCT--------CACGTG-G---CGCG------------------------------GCTCCACCGC----CC-----------------CGTGCAAGTCCCACC-GC--G-----CTGGGGAGGTG--G i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 18374 58 + 41507 CCCACGCCT--------CACGTG-G---CACC------------------------------ACTCCATCCC----CAT----------------CACCGCAATCAGACC-C------------GAGGGGTG--G i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 5579 58 - 54875 -----GCTT--------CACGGG-G---CACC------------------------------ACTCCACCAC----AAT----------------CATGCGAACCAGACC-AC--A-----GTGGGGAGGTG--G i ochPri2.scaffold_9426 C 0 C 0 s vicPac1.scaffold_218698 996 62 + 1062 ccgc-cgcg--------cACGTG-G---AGGG------------------------------GCTCCGCCGC----CGC----------------CGTGGAAAGCAGACC-CC--A-----GTGGGGAGGCG--G i vicPac1.scaffold_218698 I 4 N 0 s bosTau4.chr19 10859107 62 - 65312493 CTGC-GGCT--------CATGTG-G---AGTG------------------------------GCTCCACCAC----CAT----------------CGTGGAAAGCCGACC-CC--A-----GTGGGGAGGCA--G i bosTau4.chr19 I 4 I 6 s turTru1.scaffold_106006 128929 62 + 145505 CCGC-AGCG--------CACGTG-G---AGTG------------------------------GCTCCACTGC----CAC----------------CAGGGAAAGCAGACC-AC--A-----GTGGGGAGGTG--G i turTru1.scaffold_106006 I 4 I 7 s equCab2.chr11 58042708 66 - 61308211 CGGC-GCCT--------CACGTG-G---AGCG------------------------------GCTCCATCACCCATCCT----------------CGTGGAAATCAGACC-CC--A-----GTGGGGAGGGG--G i equCab2.chr11 I 10 I 4 s felCat3.scaffold_206428 32074 62 + 132007 CCGC-GTCT--------CACGCC-G---AGCG------------------------------GCTCCGGCAC----CGG----------------CTTGGAAAGCAGACC-CC--G-----GTGGGGAGGCG--G i felCat3.scaffold_206428 I 10 I 7 s canFam2.chr9 59436790 62 - 64418924 CCGT-GCCT--------CACGTG-G---AGCG------------------------------GCTCCAGCAC----CGT----------------CGTGGAAATCAGACC-CC--A-----GTGGGGAGGTG--G i canFam2.chr9 I 10 I 7 s myoLuc1.scaffold_4816 9505 101 + 14340 CAAC-ACTTATAATACATACATA-T---AATGACAGACAAGACAAAAAACAATAGCAAGAAAACTCCACAG------------------------CGAGAGAACCAGAGC-AC--ACAAATGGGAGAAGATA--G i myoLuc1.scaffold_4816 I 140 I 7 s pteVam1.scaffold_11245 15129 60 + 48268 CGCT-GCCT--------CACGTG-G---AGCG------------------------------GCCCCATCGC------T----------------CGTGGAAACCAGACC-CC--A-----GTGGGGAGGAG--G i pteVam1.scaffold_11245 I 8 I 7 s eriEur1.scaffold_355010 4014 57 + 8359 ----------------CCACAGG-GCCTAGAG------------------------------GATCTCCTGC----AGG----------------CTGGAAAAGCAGACC-CT--------gtggggaggtg--g i eriEur1.scaffold_355010 C 0 I 7 s loxAfr3.scaffold_49 14432637 63 - 17734757 CCGC-ACCC--------CACACG-G---AACG------------------------------GCGCCTTCAC----CCG----------------CGTGGGAGTCAGCCCACA--C-----GTGGGGAGGTG--G i loxAfr3.scaffold_49 C 0 I 9 s echTel1.scaffold_194555 4074 55 + 11139 ------CCT--------GGGAGG-G---GGTG------------------------------GTGTCAGCAC----T------------------AGTGGGCGTCAGCTC-CG--A-----GTGAGGAGGTG--G i echTel1.scaffold_194555 C 0 I 8 s dasNov2.scaffold_28617 12385 79 + 20752 -GGC-GCCT--------AAGGCGCA---GGCC------------------------------GTGGTCACGC----CCAGACGCCCCTTTGCCATCGCAGGAACCAGCCCAGC--A-----GCGGGGAGGCG--G i dasNov2.scaffold_28617 C 0 I 8 s monDom5.chr2 304533256 64 - 541556283 CACC-ACCA--------CATATT-G---AGCC------------------------------TCTTCATAGC----CAT----------------CAAGGAATTAAAAAC-CCTAA-----GTGAGAAAGGG--A i monDom5.chr2 C 0 C 0 e proCap1.scaffold_29042 16474 808 + 24616 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I a score=659521.000000 s hg19.chr17_gl000204_random 45788 65 + 81310 CA-GGG---GG--GGCC-----------------------CAGGAAATAAAGAGCATTTCCAGGAATGGCAAGTCTCCCA--------CGCGGGATCATATC s panTro2.chr17 79475971 65 + 83384210 CC-GGG---GG--GGCC-----------------------CAGGAAATAAAGAGCGTTTCCAGGAATGGCAAGTCTCCCA--------CGCGGGATCATATC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 14695 66 - 64270 CTGGGG---GG--GGCC-----------------------CAGGAAATAAAGAGCGTTTCCAGGAATGGCAAGTCTCCCA--------CGCGGGATCGTATC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16063081 64 + 17838096 C--GGG---GG--GGCC-----------------------CACGAAATAAAGAGCGTTTCCAGGAATGGCAAGTCTCCCA--------CGCGGGATCATATC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75037030 64 + 78773432 C--GGG---GG--GGCC-----------------------CACGAAATAAAGAGCATTTCCAGGAATGGCAAGTCTCCCA--------CGCGGGATCATATC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 44413 64 - 95547 C--GGG---GG--GGCC-----------------------CACGAAATAAAGAGCATTTCCAGGAATGGCAAGTCTCCCA--------CGCGGGATCATATC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 46457 66 + 225949 T--GGG---GGCAGGGG-----------------------CAGGAAATAAAGAGCGTTTCCAGGAATGGCAAGTCTCCCA--------CGCAGGATCATATC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 751 63 + 9575 ---TGG---GG--GGCA-----------------------CAAGAAATAAAGAGTGTTTCCAGGAATGACAAGTCTCCCA--------TGCAGGATCATATC i tarSyr1.scaffold_143701 C 0 C 0 s otoGar1.scaffold_94362.1-287808 26946 63 + 287808 ---TGG---GG--GCCC-----------------------CATGAAATAAAGAGCGTTTCCAGGAATGACAAGTCTCCCA--------CGCAGGATCATAGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 5452 63 + 19765 ---GTG---GG--GCCG-----------------------CGTGAAATCGGGAGCGCTTCCAGGAATGACAAGTCTCCCA--------CGCGGGATCAGATC i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118758986 84 + 121843856 C--GGG---AG--GGGCGGT-G--GAAGAGGAGGGAAACACACGGAATAAAGAGCTCTTCCAGGAACGACAAGTCTCCCA--------CGCGGGATCATATT i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 2884 85 + 7959 G--GGG---TG--GGGAGGG-A--GGAGGGGAG-------CACGGAAGAAAGAGCCCGTCCAGGAATGACAAGTCTCCCACGCAGGATCGCAGGATCGTATC i dipOrd1.scaffold_56485 C 0 C 0 s cavPor3.scaffold_76 4389370 77 + 7991924 A--AGG---CG--GGAAGGA-G--GTGGAAAAA-------CAGGAAACAAAGGGCGCCTCTGGGAATGACACATCTCCCA--------CTTGGGATCACATC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 7011 72 + 44242 G--GGG---CG--GGGAGGG-G--GGAGCG----------CGCGCAGCCCAGAG--CTTCCAGGAACGGCAGGTCTCCCA--------CGCGGGATCACATC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 18432 68 + 41507 G--GGC---GG--CGGAGGC-G--GCAGACG---------CATGGGACGCGGCGCGCTTGCAGGAACGTCGCGTCCCCCG--------C-------AGGCTC i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 5637 74 - 54875 G--GAC---GG--AGGCGGA-G--GGAGCCA---------CACAGAACACAGCGTACTTGCAGGACCCT-ACGTCCCCCA--------CCGGGGAAAGACCT i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 128998 76 + 145505 --TGGG---GA--AGGAGGTGG--GGAAACG---------CAGGAAATAAAGAGCGTTTCCAAGAATGACAAGGCTCCCA--------CACGGGATCACATC i turTru1.scaffold_106006 I 7 C 0 s bosTau4.chr19 10859175 76 - 65312493 --CGGG---GA--AGGAGGTGG--GGAAACG---------CAGGAAATAAAGAGCGTTTCCAGGAATGACAAGGCTCCCA--------TGCGGGATCACATC i bosTau4.chr19 I 6 C 0 s equCab2.chr11 58042778 76 - 61308211 --CGGG---GG--AGGAGGTGG--GGAAAAG---------CACGAAATAAAGAGCGTTTCCAGGAATGACAAGGCTCCTA--------CGCGGGATCATATC i equCab2.chr11 I 4 C 0 s felCat3.scaffold_206428 32143 62 + 132007 --CGGG---C------------------AAG---------CACGGAATAAAGCACGCTTCTAGGAGTGACGGGGCTCCCA--------CGCGGGACCGTATC i felCat3.scaffold_206428 I 7 C 0 s canFam2.chr9 59436859 75 - 64418924 --CGGG---CA--GGGAGGT-G--GGAAAAG---------CGTGCAATAAAGAGCGTTTCTAGGAATGACAGGACTCCCA--------CGCGGGATCATATC i canFam2.chr9 I 7 C 0 s myoLuc1.scaffold_4816 9613 77 + 14340 --CAGG---GA--AGGAGGAGGGTAGAGACG---------CAGGAGATAAAGCACGTTTCCAGGAATGCCAACGCTCCCA--------CGC-GGATCCGATC i myoLuc1.scaffold_4816 I 7 C 0 s pteVam1.scaffold_11245 15196 76 + 48268 --CGGG---GA--AGGGGGCGG--AGAAACA---------CATGAAATAAAGAGTGTTTCCAGGAATGACAGGGCTCCCA--------CGCGGGATCATATC i pteVam1.scaffold_11245 I 7 C 0 s eriEur1.scaffold_355010 4078 75 + 8359 --tggg---ct--aGGAGGT-G--AGTAGCG---------CAGGTGCTAAGGAGCAGTTCTAGGAAGGACAGGACTCCCA--------CATGGGATCACAGC i eriEur1.scaffold_355010 I 7 C 0 s loxAfr3.scaffold_49 14432709 75 - 17734757 --TGTGGACGG--AGGC----A--GGAAAGA---------CACAGAATAAAGCCTACTTCCAGGAACCACAAGCCTCCCA--------CACGGGACCACATC i loxAfr3.scaffold_49 I 9 C 0 s echTel1.scaffold_194555 4137 72 + 11139 --TGGGGATGG--AGGC----G--GGAAAGA---------CG-AGGGCAATGC--ATTTCCAAAACCCATCAGCCTCCCT--------GCGGGGACCACATC i echTel1.scaffold_194555 I 8 I 322 s dasNov2.scaffold_28617 12472 72 + 20752 --CGGG---GG--GAGT----G--GGGAGGG---------CGCGGAAGAAAGAGCGTTTCCAGGCACGACGGGGCTCCCA--------CGGGGGCTCCTGTC i dasNov2.scaffold_28617 I 8 C 0 s monDom5.chr2 304533320 73 - 541556283 ----GG---GG--TGTAGTGAA--GAAAAAA---------CATCAAATAAAGAAAGTTACCAGGAACTACAAGTCTCCTA--------CAT-GAATCCTATC i monDom5.chr2 C 0 C 0 e proCap1.scaffold_29042 16474 808 + 24616 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I a score=1387490.000000 s hg19.chr17_gl000204_random 45853 78 + 81310 ATCAATTAGCCAGTGGGAGGGCCGAGGAGTGC--------TGGCATCTCATTTCCACAAAGACAAAGTTTCCTTGAGGAAATTGCC s panTro2.chr17 79476036 78 + 83384210 ATCAATTAGCCAGTGGGAGGGCCGAGGAGTGC--------TGGCATCTCGTTTCCACAAAGACAAAGTTTCCTTGAGGAAATTGCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 14761 78 - 64270 ATCAATTAGCCAGTGGGAGGGCCGAGGAGTGC--------TGGCATCTCATTTCCACAAAGACAAAGTTTCCTTGAGGAAATTGCC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16063145 78 + 17838096 ATCAATTAGCCAGTGGGAGGGCCGAGGAGTGC--------TGGCATCTCATTTCCACAAAGACAAAGTTTCCTTGAGGAAATTGCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75037094 78 + 78773432 ATCAATTAGCCAGTGGGAGGGCCGAGGAGTGC--------TGGCATCTCATTTCCACAAAGACAAAGTTTCCTTGAGGAAATTGCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 44477 78 - 95547 ATCAATTAGCCAGTGGGAGGGCCGAGGAGTGC--------TGGCATCTCATTTCCACAAAGACAAAGTTTCCTTGAGGAAATTGCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 46523 78 + 225949 ATCAATTAGCCAGTGGGAGGGCCGAGGAGCAC--------TGGCATCTCATTTCCACAAAGACAAAGTTTCCTTGAGGAAATTGCC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 814 77 + 9575 ATCAATTAGCCAGTGGGAGGGCCGGGGAGTGC--------TGGCATCTTGCTTCTACAAAGACAAAG-TTCCTTGAGGAAATTGCC i tarSyr1.scaffold_143701 C 0 C 0 s otoGar1.scaffold_94362.1-287808 27009 78 + 287808 ATCAATTAGCCAGTGGGAGGGCCGAGGAGCGC--------TGGCATCTCACTTCTACAAAGACAAAGTTTCCTTGAGGAAATTGCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 5515 78 + 19765 ATCAATCGGCCAGTGGGAGGGCCCAGGAGCGC--------CGGCTCCTCGTTTCCACAAAGACAAAGTTTCCTTGAGGAGACTGCC i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118759070 78 + 121843856 GGTAATTAGCCAGTGGGAGGCCCGCAGAGTGC--------TGGCATCTCCTCACCACAAAGACAAAGTTTCCTTGAGGAACCTGCC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 2969 78 + 7959 AGCAATTAGCCGGTGGGAGGCCCGGGGAGTGC--------TGGCGTCTCATTTCTACAAAGACAAAGTTTCCTTGAGGAAACTGCC i dipOrd1.scaffold_56485 C 0 C 0 s cavPor3.scaffold_76 4389447 76 + 7991924 ACCCATT-GCCGGCAGGCGG-CCACGGAGTGC--------TGGCATCTCGTTTCTGCTCAGGCTAAGTTTCCTTCATGAAACAGTC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 7083 76 + 44242 GCCAATGAGCCAGTGGGAGGGCCGC--CGCGC--------TGGCATCTCGCTTCCACAAAGACAAAGTTTCCTTGAGGAAATTGCC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 18500 72 + 41507 GGCGAGTGGCCGTGGGGGGG-CCGCCG-GTGC--------CAGCCTCCC-GCCCCACAGATGCCACGCTGTCCTGGGGCAACG--- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 5711 46 - 54875 GGCTGCTGGCCAGAGGGAGG------------------------------GCTCCACAAAGGCCACACTTCCCTGG---------- i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 129074 79 + 145505 ATCAATTAGCCAGTAGGAGGGCTGGGGAGTGCT-------TGGCATCTCATTTCCACAAAGACAAAGTTTCCTTGAGGAAACTGCC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10859251 79 - 65312493 ATCAATTAGCCGGTAGGAGGGCCGAGGAATGCT-------TGGCATCTTATTTCCACAAAGACAAAGTTTCCTTGAGGAAACTGCC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58042854 79 - 61308211 ATCAATTAGCCAGTAGGAGGGCCGAGGAGCACT-------TGGCATCTCATTTCCACAAAGACAAAGTTTCCTTGACGAAACTGCC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 32205 79 + 132007 AGCAATTAGCCAGGAGGAGGGCCGAGCAGCCCT-------TGGCACCTCATTTCCACAGAGACAAAGTTTCCTTGAGGAAACTGCC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59436934 79 - 64418924 ATCAATTAGCCAGTGGGAGGGCCGAGCAGCCCT-------TGGCATCTCATTTCCACAAAGACAAAGTTTCCTTGAGGAAACTGCC i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 9690 66 + 14340 GTCAATTAGCC-GCAGGAGGGCCCAGGAGCGCC-------TGGCATCTCATCCC------------GTCTCCTTGAGGAGCCTGCC i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 15272 79 + 48268 ATCAATTAGCCAGTAGGAGGGCTGAGGAGCACT-------TGGCACCTCGTTTCCACAAAGACAAAGTTTCCTTGAGGAGCCTGCC i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_355010 4153 78 + 8359 ACCAATTAGCCAGTGGGAGGGCCAGGGAGCACT-------TGGCTTCTC-CTGCCACAAAGACCACATTTCCCTGAGCAAATGGCC i eriEur1.scaffold_355010 C 0 C 0 s loxAfr3.scaffold_49 14432784 79 - 17734757 ACCAATTAGCCAGCAAGAGGGCCTCAGAGCGCT-------CTGCATCTCATTTCTGCAAAGACAAAGTTTCCTTGAGGAAATTGCC i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 12544 77 + 20752 TCCCACTCGCCGGTAGGAGGGCCCGGGCGCGCC-------CT--CTCTCATTTCTGCAAAGACCAAGTTTCCTGGTGGAAAGTGCC i dasNov2.scaffold_28617 C 0 C 0 s monDom5.chr2 304533393 82 - 541556283 ATTAATTAGACAGCAGAAGGGCCAAAGGGTATCTCCTAGATCTCAACTTTTTACTGTAAAGATAA----TCCAGGAGTATATTTCC i monDom5.chr2 C 0 I 4348 e proCap1.scaffold_29042 16474 808 + 24616 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e echTel1.scaffold_194555 4209 322 + 11139 I a score=546042.000000 s hg19.chr17_gl000204_random 45931 54 + 81310 -AGAGTCTTCA---AGGTACTGAAAT---AACACACAGAACAAATGAAG-AAGGACGGCCGC s panTro2.chr17 79476114 54 + 83384210 -AGAGTCTTCA---AGGTACTGAAAT---AACACACAGAACAAATGAAG-AAGGACGGCCGC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 14839 54 - 64270 -GGAGTCTTCA---AGGTACTGAAAT---AACACACAGAACAAATGAAG-AAGGACGGCCGC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16063223 54 + 17838096 -AGAGTCTTCA---AGGTACTGAAAT---AACACACAGAACAAATGAAG-AAGGACGGCCGC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75037172 54 + 78773432 -AGAGTCTTCA---AGGTACTGAAAT---AACACACAGAACAAATGAAG-AAGGACGGCCGC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 44555 54 - 95547 -AGAGTCTTCA---AGGTACTGAAAT---AACACACAGAACAAATGAAG-AAGGACGGCCGC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 46601 54 + 225949 -AGTGTCTTCG---AGGTACTGAAAT---AACACACAGAACAAATGAGG-AAGGAGGGCTGC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 891 55 + 9575 -AGAGTCTTCA---GGCCACTGATAT---ATCTCTCCGATCAAATGAAGAAAGGACAACCAC i tarSyr1.scaffold_143701 C 0 M 2384 s otoGar1.scaffold_94362.1-287808 27087 56 + 287808 -AGGGTCTTCG---AGGTACTGAAATAACAACACACAGAACAAGTGAAG-GAGGACAACCG- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 5593 53 + 19765 -A-GGTCCTCA---AGGTACCGAAAT---AACACGCAGAACAAATGAAG-GAGGACGACCGC i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118759148 54 + 121843856 -AGCATCTTCA---AGGTACTGAAAT---AACACACAGAACAAATGGAG-AAGAATGACTAT i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 3047 55 + 7959 -AGAGTCTTCAAGGAGGCACCAAAAT---AACACGCAGAACAAATGAAG-AAGGATGAGC-- i dipOrd1.scaffold_56485 C 0 C 0 s cavPor3.scaffold_76 4389523 47 + 7991924 -TGGCTTTGCA---TGGAACTGAAAT---AATACCCAGAACGAATGAAG-AAGGA------- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 7159 52 + 44242 -AGAGTCTTCA---AGGCTCTGAAAT---AACA--CAGAACAAATGAAG-AAGGACGGCCGC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 18572 27 + 41507 -------TGCA------------------------GACAGCA---GGTG-GGGGGCGGCCCC i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 5757 23 - 54875 --------GCA------------------------CACCAC------TG-GAGAACACGCTT i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 129153 54 + 145505 -AGAGTCTCCA---AGGCACTGAAGT---CAGACACAGAACAAATGAAG-AGGGACGATGGC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10859330 54 - 65312493 -AGAGTCTCCA---AGGCACTGAAGT---CAGACACAGAACAAATGAAG-AGGGACGATGGC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58042933 54 - 61308211 -AGGGTCTTCA---AGGCATTGACAT---GAGACGCACAGCAAATGAAG-AAGGACCACGGC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 32284 54 + 132007 -AGAGTCTCGG---AGGCGCTGAAGT---AAGACACAGAACAAATGAAG-GAGGACGGCCGC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59437013 53 - 64418924 -AGGGTCTTCA---AGGCGCTGAAAT---AAGACACAGAACAAATGAAG-AAGGCCGG-AGC i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 9756 47 + 14340 ---CGGCTCCC---GGGCACCAA--C---AGGACGCAGAGCAAATGAGG-GAGGACGG---C i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 15351 50 + 48268 -AGCGTCTTCA---AGGCTCGGAACT---CAGACGCAGAACAAATGGAG-GAGGAGGA---- i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_355010 4231 34 + 8359 -AAG--------------------------AGGAGCAGGACAGGTAGAG-AAGGGCACATGC i eriEur1.scaffold_355010 C 0 C 0 s loxAfr3.scaffold_49 14432863 55 - 17734757 AAGAGCCTTTA---AGGTGCTGAATG---AAGGCCTAGAGCAAACGAAG-AGGGAGGGCCAC i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 12621 54 + 20752 -AGAGTCTTCG---GGGGACTGAAAT---AACACGGAGTACAAATGAAG-AAGGACCCCCAC i dasNov2.scaffold_28617 C 0 C 0 e proCap1.scaffold_29042 16474 808 + 24616 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e echTel1.scaffold_194555 4209 322 + 11139 I e monDom5.chr2 304533475 4348 - 541556283 I a score=249319.000000 s hg19.chr17_gl000204_random 45985 38 + 81310 AGGGCTTGGTGGATGCTCAGAAGCCCAGCTCCCGGCAG s panTro2.chr17 79476168 38 + 83384210 AGGGCTTGGCGGATGCTCAGAAGCCCAGCTCCCGGCAG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 14893 38 - 64270 AGGGCTTGGCGGATGCTCAGAAGCCCAGCTCCCGGCAG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16063277 38 + 17838096 AGGGCTTGGCGGATGCTCAGAAGCCCAGCTCCCGGCAG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75037226 38 + 78773432 AGGGCTTGGCGGATGCTCAGAAGCCCAGCTCCCGGCAG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 44609 38 - 95547 AGGGCTTGGCGGATGCTCAGAAGCCCAGCTCCCGGCAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 46655 38 + 225949 AGGGCTTGGCTGATGCTCAGAAGCCCAGTTCCTGGCGG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_507768 106 38 + 1063 AGGACTTGGCTGGTGCTCTGAAGCCCTGCTCCTGGCAC i tarSyr1.scaffold_507768 n 0 C 0 s otoGar1.scaffold_94362.1-287808 27143 34 + 287808 GAGACCTGGC---CGCTCA-CAGCCCAGCTCCCGGCAG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 5646 38 + 19765 GGGGCTTGGCCGGCGCTCAGAAGCCCAGCTCCTGGCAG i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118759202 38 + 121843856 AGGGTTTGGTGGCTGCTTAGAAGGCTGGCGGCTGGCGG i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 3102 37 + 7959 -GGGCTCGGCCCGTGCTCCGAAGCCTGGCTCCTGGCAG i dipOrd1.scaffold_56485 C 0 C 0 s cavPor3.scaffold_76 4389570 27 + 7991924 -GGCCTTGCT-----CCTAGAGGCCTGGC-----ACGA i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 7211 37 + 44242 AGGGCCTGGC-CAGGCTCGGAAGCCCCGCCCCCGCCGC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 18599 35 + 41507 AGGGCCTGGC-CACGCTGGGAAAC--AGCTCCCGGCGG i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 5780 19 - 54875 GGGACCTG-------------------GCTCCTGGCGG i ochPri2.scaffold_9426 C 0 I 131 s turTru1.scaffold_106006 129207 37 + 145505 CGGGCTTGGCTGTCGCTCAGACACCCGCC-CCAGGCAG i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10859384 37 - 65312493 TGGGCTTGGCCGTTGCTCAGACACCCGCC-CCAGGCAG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58042987 35 - 61308211 GGGGCTCGGCCAG-GCTCT-GCGCCGGCT-CCTGGCAG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 32338 36 + 132007 TGGGCTTggccggcccccc-gcgcccggg-ccTGGCAG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59437066 37 - 64418924 AGGGCCTGGCCAGTACTCAGGCGCCCAGC-CCTGGCAC i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 9803 34 + 14340 AGGGCTCGGCGGG-GCTCAGAGGCCCGG---CCCGCCG i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 15401 18 + 48268 ------CGGCAGG-GCTC-------------CTGGCAG i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_355010 4265 35 + 8359 AGGGCTTGCCTGAGGCCC--GGCACTGGC-CCTGGCAG i eriEur1.scaffold_355010 C 0 C 0 s loxAfr3.scaffold_49 14432918 37 - 17734757 -AGGTGTGGACGACGCTCAGACACCTGTGCCCCAGCCA i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 12675 34 + 20752 -GGGGTGGGGCGGCGCCCAGACCCGT---CCCCTGAAG i dasNov2.scaffold_28617 C 0 C 0 e proCap1.scaffold_29042 16474 808 + 24616 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e echTel1.scaffold_194555 4209 322 + 11139 I e monDom5.chr2 304533475 4348 - 541556283 I a score=311842.000000 s hg19.chr17_gl000204_random 46023 63 + 81310 CCT-T-GCAGAGGGGCGTGTGTGTTTAAAGACACAAGTGGAG----C-CTGCGA-T---GTCCAAGAGGCAAGC s panTro2.chr17 79476206 63 + 83384210 CCT-T-GCAGAGGGGCGTGTGTGTTTAAAGACACAAGTGGAG----C-CTGCGA-T---GTCCAAGAGGCAAGC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 14931 63 - 64270 CCT-T-GCAGAGGGGCGTGTGTGTTTAAAGACACAAGTGGAG----C-CTGCGA-T---GTCCAAGAGGCAAGC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16063315 63 + 17838096 CCT-T-GCAGAGGGGCATGTGTGTTTAAAGACACAAGTGGGG----C-CTGTGA-T---GTCCAAGAGGCAAGC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75037264 62 + 78773432 CCT-T-GCAGA-GGGTGTGTGTGTTTAAAGACACAAGTGGAG----C-CTGCGA-T---GTCCAAGAGGCAAGC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 44647 63 - 95547 CCT-T-GCAGAGGGGTGTGTGTGTTTAAAGACACAAGTGGAG----C-CTGCGA-T---GTCCAAGAGGCAAGC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 46693 63 + 225949 CCT-T-GCAGAGGTGCGTGTGGGTTTAAAGACACAAGAGGAG----C-CTGCGA-T---GCCCAAGAGGCAAGC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_507768 144 63 + 1063 CCT-T-GCAGAGGGGCACGTGGCTTTAAAGACACAAGTGAAG----C-CTGTGA-G---TATCAAGAGGTGAGT i tarSyr1.scaffold_507768 C 0 C 0 s otoGar1.scaffold_94362.1-287808 27177 63 + 287808 CCT-T-GCAGA-GGGCGCGTGGGTCTGAAGACAAACGCGGGG----C-CTGTGAGC---GTCCAAGAAGCAATC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 5684 63 + 19765 CCG-T-GCAGAGGGGCACGTGGGTCTAAAGACACG-GTGCAG----C-CTGCGAGT---GTCCAAGAATCGAGC i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118759240 50 + 121843856 -GC-T-CACGGAAGGCC---------AGACACGCA-GAGAGG----T-CAAAGG-G---GCCCAAGAGATGG-- i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 3139 64 + 7959 -CC-T-CTGCGAGGACCTGAGGGCTGAGAGGCGCA-GAGGAG----T-CTGGAT-GCATCTCCAAGCAACGTCC i dipOrd1.scaffold_56485 C 0 C 0 s cavPor3.scaffold_76 4389597 53 + 7991924 -GA-G-CTGCCAGGTAC---------AGGGACATA-AGGGAGCTTTT-CTGG-------GTCCAAACAGCAAGC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 7248 55 + 44242 -CT-C-GCGGGGGGAGCCGTGGGCTCCGAGGCGCC-ACGGGG----C-CTGCTA-GT--GCTcacac------- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 18634 50 + 41507 GGG-C-ACGCGGGGTCCC--------AGAGGCA------GAG----C-TTGGGA-GT--GTCTCAGAGGAGAGC i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 129244 64 + 145505 -CCTG-GCAGAGGGTTGTGTGGGTTTAGAGACACAAGTGGAG----C-CTGCGCGT---GTCCAGGAGATGAGc i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10859421 64 - 65312493 -TCTG-GCAGCGGGCTGTGTGGGTTTAGAGACACAAGTGCAG----C-CTGCAGGT---GTCCAGGAGGTGAGA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58043022 64 - 61308211 -CC-TGGCAGAAAGGTGTGTGGGTTTAAAGACACAAGCGGGG----C-CTGCAGGT---GTCCAAGAGGTGAGC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 32374 58 + 132007 -CC-T-GCAAGGGGCTGTGTGGGCTGGAAGACAGGCGTGGGG----C-CCGCCGGT---GTCCTTGATG----- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59437103 62 - 64418924 -CC-A-GCAGGGGCCCGCGTGGGCT-GAAGACATGTGTGGAA----C-CCCCCAGT---GCCTGAGAGGTGAGC i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 9837 56 + 14340 -CC-G-GCAGGGGG--GTGTGCTTTCCTAC-----AGGGGAG----C-CTGGGAGT---GTCCAGGAGCTAAGc i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 15419 64 + 48268 -CCTG-GCAGAGGGCTGTGTGGGTTCAAGCACACGAGCAGAG----C-CTGGGAGC---GTCCACGAGGTGAGc i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_355010 4300 58 + 8359 -CT-T-TCAGGAGGCCATGTGGGTTTAAAGACA-----GGAG----C-TGGTGTAC---ACATGAGGGATGAGC i eriEur1.scaffold_355010 C 0 C 0 s loxAfr3.scaffold_49 14432955 63 - 17734757 CCA-A-GCACAGGG-TGTGT-GGTTTAAAGACACAAGCGGGG----CTCtgcaagc---attcaagaggcaagc i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 12709 63 + 20752 GCC-C-GCAGAGGGCTGTGCAGGCCTGAAGTCAC-CGTGGAG----C-CCGCGAGC---GTTCAAGAGGCGAGC i dasNov2.scaffold_28617 C 0 I 887 e ochPri2.scaffold_9426 5799 131 - 54875 I e proCap1.scaffold_29042 16474 808 + 24616 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e echTel1.scaffold_194555 4209 322 + 11139 I e monDom5.chr2 304533475 4348 - 541556283 I a score=-805276.000000 s hg19.chr17_gl000204_random 46086 135 + 81310 ACCAGTACCAATACAT---Gaca----ca----------c---acatgtgctcaca-cat-gta------cg------acacacatatgctc-atgcacgc-----acacagg-tacat---gtgggtacaca----a--------------------------------------------------------atgcaga--------------aacac----actt-gtgca---------------------tgtg-caca-----------------------ta-------catgcacacacatg s panTro2.chr17 79476269 139 + 83384210 CCCAGTACCCATACAT---Gaca----ca----------c---acatgtgctcaca-cat-gta------cg------acacacatatgctc-atgcacac-----acacagg-tacat---gtgggtacacacacca--------------------------------------------------------atgcaga--------------aacac----actt-gtgca---------------------cgtt-caca-----------------------ta-------catgcacacacatg i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 14994 141 - 64270 ACCAGTACCCATACAT---Gaca----ca----------c---acatgtgctcaca-cat-gta------ng----acacacacatatgctc-atgcatgc-----acacagg-tacat---gtgggtacacacacca--------------------------------------------------------atgcaga--------------aacac----actt-gtgca---------------------cgtg-caca-----------------------ta-------catgcacacacatg i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16063378 127 + 17838096 ACCAGTACCCATACAT---Gaca-----------------------------caca-cat-gta------cg------acacacatatgctc-atgcattc-----acacagg-tacat---gtgggtacacatacaa--------------------------------------------------------atgcaga--------------cacac----actt-gtgca---------------------cgtg-caca-----------------------ta-------catgcacacacatg i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75037326 139 + 78773432 ACTAGTACCcacacac---gaca----ca----------c---acatgtgctcaca-cat-gta------cg------gcacacatatgctc-atgcatgc-----acacagg-tacat---gtgggtacacatacaa--------------------------------------------------------atgtaga--------------aacac----actt-gtgca---------------------tgtg-caca-----------------------ta-------catgcacgcacatg i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 44710 139 - 95547 ACTAGTACCcacacac---gaca----ca----------c---acatgtgctcaca-cat-gta------cg------gcacacatatgctc-atgcatgc-----acacagg-tacat---gtgggtacacatacaa--------------------------------------------------------atgcaga--------------aacac----actt-gtgca---------------------tgtg-caca-----------------------ta-------catgcacacacatg i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 46756 133 + 225949 ACCAacacccacacac---gaca----------------c---acatgtgctcacg-cat-gca------ct------gcacacatatgctc-atgcatgc-----acacatg-taca-----tgagtgcacatacaa--------------------------------------------------------atgcgga--------------aacac----actt-gtgca---------------------tgtg-caca-----------------------tg-------tgtgcatgcac--g i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_507768 207 138 + 1063 ----GTGAacacgcat---gaca----ca----------c---acatgtgcgcaca-cat-gcc------cg-------tgcccccatgcac-acatgtgc-----acacacg-tacat---atgggcacacgtgtga--------------------------------------------------------atgcagg--------------aacacgtgtgctt-gtgtg---------------------catg-tgga-----------------------ta-------catgcgtgcgtgca i tarSyr1.scaffold_507768 C 0 C 0 s otoGar1.scaffold_94362.1-287808 27240 84 + 287808 ATGAACATGCACA--------------------------------GTGTGGgcaca-cat-gca------tg-------------------------------------cggg-aacac---atgtgtgcaca----------------------------------------------------------------tgtg--------------tgcag----atgt-gtg-------------------------------------------------------ta-------catgcatgcacatg i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 5747 92 + 19765 ATGAAcatgcacgcgc---aaca---------------------catgtgtgcaca-cac-gca------tg-------------------------------------catg-cacat---acatgtgcgtg----------------------------------------------------------------cagg--------------aacac----acat-ttg-------------------------------------------------------ag-------cttgtgcacagatg i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118759290 94 + 121843856 ----------------------ACTGCCA----------C---ATATATGGACACA-CACGATA------TG---------------------ATGTATGT-----GCACACA-TGCGG---------------------------------------------------------------------------GTGCAGG--------------AACGC----ACAA-GAGAT---------------------CGTA-AACATG---------------------CA-------CATGTGCGG---TG i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 3203 195 + 7959 -------TCGGTG-------ACACCCGCG----------C---ACACGTGAGTGCT-CACCATG------TGTGCACATGCAGGAGCAGAGCAATGCATGTGAAACGCACACG-TGTGG------TGCACACCTGCCTCCTGGCACTGTCTTCCACCAACACCCGTGTACACACAAGCGCCCACACATGTGTATGTGCAGG--------------AACAC----ACTA-ATGCA---------------------TGCA-AGCA-----------------------CG-------CAGGTGCAG---TA i dipOrd1.scaffold_56485 C 0 C 0 s cavPor3.scaffold_76 4389650 121 + 7991924 ACAAG--CCTGTG-------ACA----CA----------C---ACATGCACATACA-CACGGCA------CA----CAGGGGACACAAGCACTATGCAGGT-----GGTCACA-CGCA----------------------------------------------------------------------------GAGTAGG--------------AACAC----ATTC-GCATA---------------------CGTA-CTCATG---------------------CA-------CAGG-GCAGGCATG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 7303 98 + 44242 ----------------------acactca----------c---acatgcgtgcaca-cac-aca------ca-------GAGGCACTTGTGC-CTGCACAC-----TTACCCA-AGCAC---------------------------------------------------------------------------AGGCAGG--------------AACAC----GCT--GTGCA---------------------TGTG-AGCATG---------------------TG-------CC----------TA i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 18684 107 + 41507 ----------GTGC------ACACGCTCA----------CATGacacacgtgtgca-cat-gca------tg---------agcaggactgc-atgcacac-----atgcatg-tacat------gct------------------------------------------------------------------gcgcagg--------------aacac----act--gctca---------------------catacaaca-----------------------ca-------catg---------- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 129308 91 + 145505 ----------acacac---aaca----------------c---acatgtgcatgca-cac-ata------ca------------------tc-atgcacac-----gcatgc---acac---gcatgtgcatg----------------------------------------------------------------------------------cacac----gtgt-gtgca---------------------cacg-catg-----------------------ca-------cacg---------- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10859485 65 - 65312493 ----------ACACAC---AACA----TC----------T---ATGTGTGcacaca-cac-aca------ca------------------cc-gtgcacac-----acatgcc-aacac---tca------------------------------------------------------------------------------------------------------------------------------------------------------------------ca-------cctg---------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58043086 119 - 61308211 ----------ACACAC---AGCA----CAAATGTgcacgc---acacgtgcacaca-tac-acg------at------------------gc-atgcacac-----ctacagg-cacat---gtgtgcacatgtgcc----------------------------------------------------------tgca-----cacaca-----cacgt----gc-----------------------------catg-caca-----------------------cacatatgctgtg---------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 32432 22 + 132007 ---------------------------------------C---GCGTGGGCA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CG-CGTG-----------------------CA-------TCCG---------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59437165 50 - 64418924 ----------ACGTAC---AACA----CA----------C---GCACGGGCAGGTA-TGC-----------------------------------------------------------------------------------------------------------------------------------------------------------CACAT----GC-----------------------------TCCG-CACA-----------------------CA-------TGTG---------- i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 9893 133 + 14340 ----------acacac---aaca----------------c---acacgtgcacgca-----cct------gc------------------ac-gcgcacac-----acacatg-aacat---gggtgcacacatgcc---------------------------------------------------------atgtgcacagcgtgca-----cacgt----atat-gcaca---------------------tatg-tgcactgcacccttgcacacacacaagca-------catg---------- i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 15483 96 + 48268 --------------------aca----------------c---acatgtgcacacagaac-act------ac------------------gc-atgcacac-----acataca-tgcag---gtgtgtgcacatgcc---------------------------------------------------------gtgtg----------------catgt----gcag-gtaca---------------------catg-cgca-----------------------ca-------cgcg---------- i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_355010 4358 160 + 8359 ----------ACACACCCAGGCA----------------C---ACACGTGCATACA-TAC-CCAGGCTCCCT------------------CC-ATGCACAC-----ACAGGTGTTATAT---AGGTGCAGACCTCCCTGCATAGAGAC----------------------------------------------ATTTAGCAGGCAGGCATctagcatgt----gtgt-gtgcatctgtgaATGCAGGATCAGATTATG-CACA-----------------------GC-------TCCA---------- i eriEur1.scaffold_355010 C 0 C 0 s loxAfr3.scaffold_49 14433018 93 - 17734757 ------------------------------------------------------------------------------------acacacgt-gtgcatgt-----acatagg-tgcatgtagtatgcacacatgaat--------------------------------------------------------gtgcctg--------------cacac----atgtggcgtg---------------------cgtg-caca-----------------------ta-------catgcatacacgtg i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 5799 131 - 54875 I e proCap1.scaffold_29042 16474 808 + 24616 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e dasNov2.scaffold_28617 12772 887 + 20752 I e echTel1.scaffold_194555 4209 322 + 11139 I e monDom5.chr2 304533475 4348 - 541556283 I a score=-594457.000000 s hg19.chr17_gl000204_random 46221 47 + 81310 caca--cat-acaggatgcacatgcatgcc-------tgtgtgca-----------cac-tctacacac--------------------- s panTro2.chr17 79476408 47 + 83384210 caca--cat-acaggatgcacatgcatgcc-------tgcgtgca-----------cac-tctacccac--------------------- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 15135 47 - 64270 caca--cat-acaggatgcacatgcatgcc-------tgtgtaca-----------cac-tctacccac--------------------- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16063505 46 + 17838096 caca--cat-acaggatgcacatgcatgcc-------t-tgtgca-----------cac-tctacacac--------------------- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75037465 47 + 78773432 gaca--cat-acaggatgcacatgcatgcc-------tgtgtgca-----------cac-tctacacac--------------------- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 44849 47 - 95547 gaca--cat-acaggatgcacatgcatgcc-------tgtgtgca-----------cac-tctacacac--------------------- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 46889 47 + 225949 caca--cat-acaggatgcacacacatgcc-------tgtgtgca-----------cac-tctacacac--------------------- i calJac1.Contig5139 C 0 I 76 s tarSyr1.scaffold_507768 345 48 + 1063 cacaggcac-acaggtggtgcgtgcatgca-------tatgtgca-----------catgtgtactt----------------------- i tarSyr1.scaffold_507768 C 0 C 0 s otoGar1.scaffold_94362.1-287808 27324 46 + 287808 caca--cat-ccaggaagcccatgcatgca-------cacgtgt------------cac-tcaacacac--------------------- i otoGar1.scaffold_94362.1-287808 C 0 I 2 s micMur1.scaffold_15893 5839 24 + 19765 caca--cat-----------------------------gcgtg-------------cac-tccacacac--------------------- i micMur1.scaffold_15893 C 0 I 2 s mm9.chr11 118759384 23 + 121843856 C---------CCCCACAAGCAGGATGCATG-------TC--------------------------------------------------- i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 3398 41 + 7959 CACA--TCTGCCTGGAAGACTAGACACACA-------CCTGTGCACGCTG---------------------------------------- i dipOrd1.scaffold_56485 C 0 C 0 s cavPor3.scaffold_76 4389771 36 + 7991924 TACA--TGCATCTGCACACCCTCACATGCA-------CCTGTGTa--------------------------------------------- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 7401 42 + 44242 CACA--CACACC------ACGGGACACACAGGCACGGTCTGTGCACACAC---------------------------------------- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 18791 31 + 41507 tgca--caggatt-cacacgtg----tgca-------tttgtgca--------------------------------------------- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 5930 47 - 54875 CACA--CATGACTGCACACGTGGGCCTGCA-------TGTGCGTGCCCAGACACAC---------------------------------- i ochPri2.scaffold_9426 I 131 C 0 s loxAfr3.scaffold_49 14433111 36 - 17734757 ----tgcacccatggatgc----------------------------------------------acctcacacgtgcatg----cacct i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 17282 20 + 24616 -----------------------------------------------------------------ACATC-CACGTGTGTG----TGCAT i proCap1.scaffold_29042 I 808 C 0 s echTel1.scaffold_194555 4531 9 + 11139 ---------------------------------------------------------------------------------CACGTGCAC i echTel1.scaffold_194555 I 322 C 0 s eriEur1.scaffold_355010 4518 9 + 8359 ------------------------------------------------------------TGAATACAC--------------------- i eriEur1.scaffold_355010 C 0 I 27 s pteVam1.scaffold_11245 15579 8 + 48268 ------------------------------------------------------------tacacaca---------------------- i pteVam1.scaffold_11245 C 0 I 6 s myoLuc1.scaffold_4816 10026 9 + 14340 ------------------------------------------------------------tacacgcat--------------------- i myoLuc1.scaffold_4816 C 0 I 19 s canFam2.chr9 59437215 9 - 64418924 ------------------------------------------------------------TGTGCACAC--------------------- i canFam2.chr9 C 0 I 1 s felCat3.scaffold_206428 32454 9 + 132007 ------------------------------------------------------------TGCACACAC--------------------- i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58043205 9 - 61308211 ------------------------------------------------------------tgcacgcac--------------------- i equCab2.chr11 C 0 I 9 s bosTau4.chr19 10859550 9 - 65312493 ------------------------------------------------------------tgcacacac--------------------- i bosTau4.chr19 C 0 I 1 s turTru1.scaffold_106006 129399 9 + 145505 ------------------------------------------------------------tgtgcacac--------------------- i turTru1.scaffold_106006 C 0 I 1 e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e dasNov2.scaffold_28617 12772 887 + 20752 I e monDom5.chr2 304533475 4348 - 541556283 I a score=-747363.000000 s hg19.chr17_gl000204_random 46268 72 + 81310 agg-----------------------cacatgcatgtacaatc------------------------ta--c----acgtgtg--catgtgtgcactga---------------ta------tgcacgcacctg---tgcacacataca--tg s panTro2.chr17 79476455 74 + 83384210 agg-----------------------cacatgcatgtacaatc------------------------ta--c----acatgtgcacatgtgtgcactga---------------ta------tgcacgcacctg---tgcacacataca--tg i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 15182 74 - 64270 agg-----------------------cacatgcatgtacaatc------------------------ta--c----acatgtgcacatgtgtgcactga---------------ta------tgcacgcacctg---tgcacacataca--tg i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16063551 74 + 17838096 agg-----------------------cacatgcatgtacaatc------------------------ta--c----acatgtgcacatgtgtgcactga---------------ta------tgcacatacctg---tgcacacataca--tg i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75037512 32 + 78773432 agg-----------------------cacatgcatgtacaatc------------------------ta--c----acatgtgca-------------------------------------------------------------------- i rheMac2.chr16 C 0 I 47 s papHam1.scaffold8336 44896 74 - 95547 agg-----------------------cacatgcatgtacaatc------------------------ta--c----acatgtgcacacgtgtgcactaa---------------ta------tgcacacacctg---tgcacacatata--tg i papHam1.scaffold8336 C 0 C 0 s tarSyr1.scaffold_507768 393 80 + 1063 gtg-----------------------tgcatgtgtgcacaatc------------------------tatgc----acgtgtgtgcatgcatgcactca---------------catacatttgcacacatcc-----atgcacacata--tg i tarSyr1.scaffold_507768 C 0 C 0 s otoGar1.scaffold_94362.1-287808 27372 54 + 287808 gag-----------------------catgtgtgtgtacaatc------------------------tg--c----gtgtgtgcaca--catgT---------------------------------------G---GGTGCACACGCC--TG i otoGar1.scaffold_94362.1-287808 I 2 C 0 s micMur1.scaffold_15893 5865 56 + 19765 gtg-----------------------cacacacgcgtgcagtc------------------------tg--t----gcgtgtgcacatgcatgt---------------------------------------a---ctcataaacaca--tg i micMur1.scaffold_15893 I 2 C 0 s mm9.chr11 118759407 62 + 121843856 --------------------------CTCACATCTGCACA---------------------------CA--C----ACACACACATATGTGTGCCTT-------------------------TACACACCT--AGC-CACACACATATA---- i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 3439 73 + 7959 --------TGTGCTGGCAT-AGcacgctcatacatgcacg---------------------------ct--c----acacatacacagat----cct-------------------------tgcacacgc--a---cacacacacaca---- i dipOrd1.scaffold_56485 C 0 C 0 s cavPor3.scaffold_76 4389807 63 + 7991924 --------------------------cacacacacacaca---------------------------ca--c----acacacacacGACTGTGCACC-------------------------CACACCCAC--ATCATGCACACATACA---- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 7443 59 + 44242 --------------------------CTCCTGCGTGTGCG---------------------------CA--C----ACCCATGCACACTCATGTATG-------------------------CCCATATCT--G---TGCACACAT-CA---- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 18822 51 + 41507 --------------------agcgc-cacacaagtgtgca---------------------------aa--c----acgtgcaca---------------------------------------cacgcat--g---tgcaggcatgca---- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 5977 68 - 54875 ---TCATGTGCATTTGCACAAGCTC-CACACACCTGCCGa---------------------------ca--c----acacgcaca---------------------------------------cacacgc--a---cacacacgcgca---- i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 129409 26 + 145505 -------------------------------------------------------------------ca--c----atacatatcc--------------------------------------------------atgtgcacgcaca---- i turTru1.scaffold_106006 I 1 C 0 s bosTau4.chr19 10859560 26 - 65312493 -------------------------------------------------------------------cg--c----acacaTATCC--------------------------------------------------ATGGACACGCACA---- i bosTau4.chr19 I 1 C 0 s equCab2.chr11 58043223 54 - 61308211 --------------------------------ttcgcacat-----gcatgcaggt-gtgcacact-ca--c----atatccatgc--------------------------------------------------acgcacacacAAA---- i equCab2.chr11 I 9 C 0 s felCat3.scaffold_206428 32463 26 + 132007 -------------------------------------------------------------------CG--G----CTGTGCGTAC--------------------------------------------------ACGCACACACGCA---- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59437225 34 - 64418924 ----------------------------------------------------------TGCATCCA-CA--G----ACACACATGT--------------------------------------------------GTGTGCACATATC---- i canFam2.chr9 I 1 C 0 s myoLuc1.scaffold_4816 10054 66 + 14340 -----------------------------GAGCATGCACATACAATGCACACACGT-GTGTGTGAA-CA--GGTGCACACACAAGC--------------------------------------------------ACACACTTGCACA---- i myoLuc1.scaffold_4816 I 19 C 0 s pteVam1.scaffold_11245 15593 44 + 48268 --------------------------------cctgcacacatgcagaaaacacgt-gtgcatacg-ca--g---------------------------------------------------------------------catgcaCA---- i pteVam1.scaffold_11245 I 6 C 0 s eriEur1.scaffold_355010 4554 66 + 8359 -----------------------------GTGTTCGTTCATGCATGAAGCATacctcatgaacacagaa--t----gcacctctct--------------------------------------------------gtgcacacacacatg-- i eriEur1.scaffold_355010 I 27 I 3093 s echTel1.scaffold_194555 4540 50 + 11139 -----------------------------AGGCGTGTGCAGTGCCA---------------------CG--T----GTGTGTGCACGTGTGAGCCGCAT--------ACATAGC--------------------------------------- i echTel1.scaffold_194555 C 0 C 0 s loxAfr3.scaffold_49 14433147 17 - 17734757 -----------------------------ggg---------------------------------------t----gtatatacacatg---------------------------------------------------------------- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 17302 53 + 24616 -----------------------------AGGCACATGCAG--------------------------CA--T----GTGTGTACATATGTGCGCCCCATGTGCACACACGCAGC--------------------------------------- i proCap1.scaffold_29042 C 0 C 0 e calJac1.Contig5139 46936 76 + 225949 I e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e dasNov2.scaffold_28617 12772 887 + 20752 I e monDom5.chr2 304533475 4348 - 541556283 I a score=1153108.000000 s hg19.chr17_gl000204_random 46340 243 + 81310 TGCACAA--------------------------G--CTC-TGCTTGCAGGTGGG--GGTCCACTATCCTGACTTCC--AAACATTCAGGTTTGAGG-----CTCTTGCAAATGCCAGATACC-ATGGAGA--CAAAACGCCCTCTAAACACATTATCCAGAATTT----TCCCT----TAA---TTCCCTACAGCACAT-GCCCCATTTGTGAGGAGAC----CCCCGGGGTCTTCAGGCTCTG--------ACTCTGATGGAGCTC-AGAGTAT----GTCAAACCCTTGAACAGTCCATTCAGGAACCTTC s micMur1.scaffold_15893 5921 191 + 19765 tgtg--------------------------------------------------------cacTGCCCTGAC-CCC--AGACATTCAAGTTTGTGG-----CCTTCACAGCTGCCAGCTGCC-ATGGGGA--CAAAACGCCCTGCAAATGTGTCACCTGGAACTT----C-------------------------------CCCTAATAGTGA-GAGAC----CCCCA-GGTCCTCAGGCCCCG--------GCTCTAATGGAGCTC--GAGCAC----GTCAGACCCTTGCACAGTCCATCCTGGAACCTTG i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 27426 194 + 287808 GGGG-------------------------------------------------------CCACTATTCTGGC-CCC--AAACATTCACATCTGCAG-----CCCTCACAGCTGCCAGAGGCT-ATGGAGA--CAAAA-GACCTGCACATGTGTCATCTGGAATGT----C-------------------------------CCTCAATTGTGAGGAGGC----CCCCATGGTCCTCAGGGCCTG--------ACTCTGATGGAGCTC-AGAGCAT----GTCAGAGCCTTGAACAGCCCATTCTAGAACCTTC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tarSyr1.scaffold_507768 473 241 + 1063 tgcacaagcatacataaacacacgcactcgcata--cTT-TACTTGCAGGTAGG--GGTTCATTGTCCTGACCCCC--AACCATTCAGATTTGTGA-----CTCTCACAGCTGCCA----------GAGG--CAAAATGCCCTGCAAATGCATTATCT-GAATTT----CCCCC----TAA---TTCCCTACAGCACAT-CCCCCATTT----------------------TCTTCAGTACCTG--------ACGCTGATGGAGCTC-AGAGTAT----GTCAAACCCTTGAACAGTCCATTCTGGAACCTTC i tarSyr1.scaffold_507768 C 0 C 0 s rheMac2.chr16 75037591 244 + 78773432 -------------------------GTGCACACG--CTC-TGCTTGCAGGTGGG--GGTCCACTATCCTGACTCCC--AAACATTCAGGTTTGAGA-----CTCTTGCAGATGCCAGGTACC-CTGGAAA--CAAAATGCCCTCTAAACACATTATCCAGAATTT----TCCCT----TAA---TTCCCTACAGCACAC-GCCCCATTTGTGAGGAGAC----CCCCAGGGTCTTCAGGCTCTG--------ACTCTGATGGAGCTC-AGAGTAT----GCCAAACCTTTGAACAGCCCATTCTGGAACCTTC i rheMac2.chr16 I 47 C 0 s calJac1.Contig5139 47012 235 + 225949 ------------------------------------cTC-TGCTTGCAAGTGGG--GGTCCACCATCCTGACTCCC--AAATGTTTAGGTTTGAAG-----CTCTTGCAGAGGCCAGATGCC-ATGGAGA--CAAAACACCCTCTAAACACATTACCCAGAATTT----TCCCT----TCA---TTCCCTACAGCACAT-GCCCCATTTGTGAGGAGAC----CCCCAGGGTCTTCAGGCTCTG--------ACTCTGATGGAGCTC-AGAGTGT----GTCAAACCCTTGAACAGTCCATTCCGGAACCTTC i calJac1.Contig5139 I 76 C 0 s papHam1.scaffold8336 44970 269 - 95547 tgcacaagcatacacaagcacatgcgtgcacacg--tTC-TGCTTGCAGGTGGG--GGTCCACTATCCTGACTCCC--AAACATTCAGGTTTGAGA-----CTCTTGCAGATGCCAGGTACC-CTGGAGA--CAAAATGCCCTCTAAACACATTATCCAGAATTT----TCCCT----TAA---TTCCCTACAGCACAC-GCCCCATTTGTGAGGAGAC----CCCCAGGGTCTTCAGGCTCTG--------ACTCTGATGGAGCTC-AGAGTAT----GCCAAACCTTTGAACAGCCCATTCCGGAACCTTC i papHam1.scaffold8336 C 0 C 0 s panTro2.chr17 79476529 259 + 83384210 tgcacaa----------gcacatgtgtgcaCACG--CTC-TGCTTGCAGGTGGG--GGTCCACTATCCTGACTTCC--AAACATTCAGGTTTGAGG-----CTCTTGCAGATGCCAGGTACC-ATGGAGA--CAAAACGCCCTCTAAACACATTATCCAGAATTT----TCCCT----TAA---TTCCCTACAGCACAT-GCCCCATTTGTGAGGAGAC----CCCCGGGGTCTTCAGGCTCTG--------ACTCTGATGGAGCTC-AGAGTAT----GTCAAACCCTTGAACAGTCCATTCAGGAACCTTC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 15256 259 - 64270 tgcacaa----------gcacatgtgtgcaCANG--CTC-TGCTTGCAGGTGGG--GGTCCACTATCCTGACTTCC--AAACATTCAGGTTTGAGG-----CTCTTGCAGATGCCAGATACC-ATGGAGA--CAAAATGCCCTCTAAACACATTATCCAGAATTT----TCCCT----TAA---TTCCCTACAGCACAT-GCCCCATTTGTGAGGAGAC----CCCTGGGGTCTTCAGGCTCTG--------ACTCTGATGGAGCTC-AGAGTAT----GTCAAACCCTTGAACAGTCCATTCAGGAACCTTC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16063625 269 + 17838096 tgcacaagcatacacaAGCACATGCGTGCACACG--CTC-TGCTTGCGGG-GGG--GGTCCACTATCCTGACTTCC--AAACATTCAGGTTTGAGG-----TTCTTGCAGATGCCGGATACC-ACGGAGA--CAAAACGCCCTCTAAACACATTATCCAGAATTT----TCCCT----TAA---TTCCCTACAGCACAT-GCCCCATTTGTGAGGAGAC----CCCCAGGGTCTTCAGGCTCTG--------ACTCTGATGGAGCTCAAGAGTAT----GTCAAACCCTTGAATAGTCCATTCCGGAACCTTC i ponAbe2.chr17_random C 0 C 0 s mm9.chr11 118759469 165 + 121843856 ------------------------------------CCC-TG-------------------------------------G--------AGTTGTGG-----TTTCG-TATTGGCCAGGTGCA-GAGA---------------------------ATCCTGGAAAT----CTCCC----TGA---GTCCG-CCAGCGTGA-ACCATATTAGTAAGAAGAC------ACGGGATCTCCAGGCCCCG--------ACTCTGGTAGAGTTC-AGAGCAT----GACAGCTTCCCTCACAGTCTCTTCTGGAATCTTC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 3512 198 + 7959 ------------------------------------cTG-TG-------------------------------------AATAGGTGCAGTTGGGC-----TCCTG-GGTCTCCCATGTTCC-CATAGGAACAAAACAGCCGTTCAGGAGTGTCAGCCAGGATCT----CCTCC----TCC---CTCCC-ACTGAATGA-GCTCCATTTGGGAGGAGAC------ACTGGGTATTTAGGCCTTG--------TCTCTAGGAGAGCTT-GTGGCAT----GTCAGATTCC--TGTAGTCTCTTCCAGAACCTTC i dipOrd1.scaffold_56485 C 0 I 4014 s cavPor3.scaffold_76 4389870 184 + 7991924 ---------------------------------G--CCC-CG-------------------------------------AGCATTCAGCTCTATGG-----CTCTGCTGGCAGCCACACGCT-AAGGGGA--CAAAAAGTCCTGCAAATGTGCTACCTGGAATTT----CTCCC----CTC---CTT---ACAATATGA-GCTCCATTCTTGAGGAGAC-------CTGATGGTTTAG---------------CTCT-----AGCTC-TGAGCAT----G-CAGACCCTTGCACAGTCCATTCCAGAGCCTTC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 7502 212 + 44242 ------------------------------------CCC-TGCTTGCAAGTTGG--GGGCCACTGTGCTGACCCTT--AAACACGCAGGTCTGTAG-----CTCTCACAGTGGCCACACT----AGAGGA--CAAAGCGCCCTGCAGATCTGCTCTCTGGAATTT----TCCCC----TCA---CTCC--ACAGCGAGA-ACTCCATCTGAGAGGAGCC------------TCCACCGTCTTCT--------GACCTGGTAGAGCT---------------CAGACCCTCGCACAGTCCATTCTGGAAGCTTC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 18873 214 + 41507 ------------------------------------cTC-TGCGTGCA-GGATG--GAGTCTCCGTTCTGACCCTC--AAACATTCAGCTTTGTGG-----CTCCA-GGGCTTCCAGA---C-CAGGGGA--CAAAACCGCGTGCAAATGTGCCGTCTGCAGAGT----CCCTG----CCC---CTCC-------------CCCCATCGTGGGGGGGCA-----CCCAGGGTCTTCAGGCCCTG--------GCTCCCACGGGGCTC-ACGTGAG----C-CAGGCCTT--GGCAGTCCACCCTGGAACCTTC i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 6045 223 - 54875 ------------------------------------TCA-GACTTGTA--TATT--GTGACACAGTTCTGACTCCCCAAAACATTCAGCTTTGT--------------GGCTTCCAGATGCT-AAGGGGA--CAAAACTGCTTGCAAACGAGGCGTCTGCAATCTCCCGCCCTG----CCCGTTCCTC-------------CCCTATTGCCGCGGGGCGTGTCTTCCAGCGCCTGCAGGCCCCA--------GCTCTGA-GGGGCTC-ATGAAGG----T-CAGGCTTCCACACAGTCCATACCCGAAGCTTC i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 129435 229 + 145505 ------------------------------------cTC-TATTAGCAGGTTAG--GGTCCACCATTCTGACCCAC--AAACATTCCAGTTTGTGG-----CTCTCTCGCCTGCCAGGTACT-AAGGAGA--TAACAC-----ACAGATGTGTTATTCAGAACTT----CTGCA----GAA---GACCCTGCAGCACAT-CCCCCATCTGTGAGGAGA-----CCCTGGGGTCTTCAGCCCTGG--------CCTCGGATGGAGCTC-AGAGTAT----GTCAGATCCTTCAACAGTCCATTCTGGAGCCTTC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10859586 229 - 65312493 ------------------------------------CTC-TACTGCCAGGTTGG--GGTCCACTATTCTGACCCAC--AAACATTCCAGTTTGTGG-----CTCTTTCGCCCACCAGCTGCT-CAAGAGA--CAAAAC-----ACAAATGCGTTACTCAGAACTT----GCGCG----GAA---GACCCTGCAGCACAT-CCCTCATCTGTGAGGAGA-----CACTGGGGTCTTCAGGTCCGG--------TCTCAGATGGAGCCC-AGAGCAT----GTCAGATCCTTTAATCGTCCATTGCAGAGCCTTC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58043277 212 - 61308211 ------------------------------------CTC-CACTTGATGGTTGG--GGTCCACTATT--------------CATTGCAGTTTGTGG-----CTCCCACAGCTGCCAGGTGCT-AAGGAGA--CGGA------------TGTGTTACCCAGAACTT----CGCCC----TAA---GGCCCTACAGCTCATCCCCCCAGGGGTGGAAAGAC----TCCTGGGGCCTTCAGGCCCCA--------ACTCTGTTGGAGCTC-AGAGTAT----GTCAGACCCTTCAACAGCCCACTCTGGAGCCTTC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 32489 232 + 132007 ------------------------------------CTC-TGCCTTCAGGTTGG--CGTCCGCTACTCCGA---CG--GAACATTCCAGTCTGCGG-----CTCTCACGGGTGCCGGCTGCT-GAGGGGA--CAAACA-GCCTGCAAGCGTGTCACCCAGAATCA----GCCCC----TGG---GGCCCCCCGGCACACCCCCCCATCTGGGAGAAGAC----CCCTGGGATCCTGGGGACCCA--------AATGCTATGGTGCTC-GGAGCAC----GTCAGATCCCTCAACGGCCCGTCCTGGAGCCTTC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59437259 239 - 64418924 ------------------------------------CTC-TGCTGTCAGGTCGG--GGTCCTCTAGTCTGACCCCC--ATACATTCTAGTCTGTGG-----CTTTCCC-AGTGCCAGGTGCT-AAGGAGA--CAAACG-CCCTGCAAATGTGTTCTCTAGATTTT----GCCCCAAAGTAA---GGCCTGACAGCACATCCCCC-------AAGTAGAC----CCCTCGGGTCTTCAGGCCCCAATTCCCCCAACCCCTCGGTGCTC-ACAGTAT----GTCAGATCCTCCAACAGTCCATTCTGGAGCCTTC i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 10120 222 + 14340 ------------------------------------CTC-TAATCTCAGGCGGGGTCA-----TA-TCTGACACAC--AAACATCCCACTTTGTGG-----CTCTCAC-GGTGCCGGGTGCT-CAGGAGA--CAAACC-CCCTTCAAATGTGTGACCCAGAACTT----GCCCG-----CG---GGCCCCACCGCTCA--CCCCCACCTGTGAGGAGA------CCCAGGGTCTCCAGGCCCC---------ACCCCGATGGCGCTC-AGAGTCC----GCCAGACCCCTCAACAGGCCACTCCGGAGCCT-- i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 15637 233 + 48268 ------------------------------------C-------CTCAGGTTGG--CATCCACTG-TCTGGCCTAC--AGACAGTCCGC-CTGTAG-----CTCTCGTGGGTGCCAGGTGATGTAGGAGG--TAAAACGGCCTGCAAATGTGTCATCTGGAGCTT----GCCCG------G---GGCCCTGCAGATCCT-CCTCCTTCTATGAGGAGAT----CCCCGGGGTCTTGAGGCCCCC-TACTGGGACTAGGATGGAGCTC-AGAGCAT----ATCAGACCTTTCAAGAGTCTATTCTGGAGCCTTC i pteVam1.scaffold_11245 C 0 C 0 s echTel1.scaffold_194555 4590 207 + 11139 TGTACAGGCATAGG----------------------AGCACACACACAGG-TGA--GCCCCACTATTCTGATGCGC---------CAAGTGGGCAGGAGTAGGCTCTGAGCCGCACAAGGCT-AGAGAGA--CAGAGCGTCGTGCAAAGCTTCCTG--GGGGTTC----AGCCC----GAG---GGCCCCAG----------------------------------CGTGGTCCCCAGGC----------------TGATGGAGCTC-AGAAGAT----GGCCGA-CCCTGAGCAGCTGATTCCAGCACCTTC i echTel1.scaffold_194555 C 0 C 0 s loxAfr3.scaffold_49 14433164 231 - 17734757 ------------------------------------TGC-TACGTGCAGGTTGG--AGTCCCCTACTCTGACCCAC--------TCCGGTTGGTGG-----CTCTCAGAGCAGCAAGATGCT-AAAGAAA--CAAAGCACCTTGCAAATGCTTTGAAGGGAATTT----CACCC----TAA---TGCCCCAAAGCACAG-CCCCCATTTGTGAGGAG------CCCCAAGGTCTCCAGGCCCTG--------ACTCTGATGGGGCTC-AGAGTATGTCAGTCAGATCCTTGAGCAGTTGATTCCGGAGCCTTC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 17355 250 + 24616 TGCCCAGGCATGTGTATCCTTGTGTGCACACAGGCCTGC-TGTCTGCAGACTGG--GGCCCCCTATTCTGGCCCAT--------TCAGGTTGGTGG------TCTCAGAGCAGCAAGATACT-AAAGAAA--CAAAGTGCTTCTCA------------GGAACTC----TGTCC----CAA---CGCCCTAAGGCACAG-CGTCCATTAGGAAGGAG------CCCCGAGGTCTCTGGGCCCCA--------ACTTCGAGGAGGCTC-AGAAGAT----GTCAAATCCTTAAGCAGCTGATTCCAGAGCCTTC i proCap1.scaffold_29042 C 0 C 0 e tupBel1.scaffold_124459.1-15939 10139 1462 + 15939 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e dasNov2.scaffold_28617 12772 887 + 20752 I e monDom5.chr2 304533475 4348 - 541556283 I a score=217890.000000 s hg19.chr17_gl000204_random 46583 25 + 81310 AAAGC-----------------CACACCCCAGGGGGCTCCCA s proCap1.scaffold_29042 17605 23 + 24616 AAGTC-----------------CACCCCC--AGGGGTTCCTG i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14433395 24 - 17734757 AAATC-----------------CACCCCC-AAGGGGTTCACG i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_194555 4797 41 + 11139 TGTGCCCGCTCTGCCACCCCCACACCCCC-GGGGGACTGGCG i echTel1.scaffold_194555 C 0 C 0 s pteVam1.scaffold_11245 15870 25 + 48268 GAACC-----------------CACATCCAAGGGGCCTCCTG i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 10342 8 + 14340 ----------------------CACACCCA------------ i myoLuc1.scaffold_4816 C 0 C 0 s canFam2.chr9 59437498 25 - 64418924 AAACC-----------------TACAACCAAGGGGGCTCCCA i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 32721 25 + 132007 AAACC-----------------CACCCCCGAGGGGGCTCCCA i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58043489 25 - 61308211 AGACC-----------------CACACCCAAGGGGGCTCCCT i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10859815 24 - 65312493 AAACC-----------------CACACCCAAGGGA-CTCCTG i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 129664 24 + 145505 AAACC-----------------CACACCCAAGGGG-CTCCCG i turTru1.scaffold_106006 C 0 C 0 s ochPri2.scaffold_9426 6268 15 - 54875 AAGCC-----------------CACACCTGCA---------- i ochPri2.scaffold_9426 C 0 C 0 s oryCun2.chrUn0958 19087 15 + 41507 AAGCC-----------------CGCACCCGAG---------- i oryCun2.chrUn0958 C 0 C 0 s speTri1.scaffold_128901 7714 25 + 44242 TTACC-----------------AACACCCAAGGGGGTCCCTG i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4390054 25 + 7991924 TAACC-----------------CACGCCCAAGGGGGTTCCTG i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118759634 25 + 121843856 CACCC-----------------CATGCCAATGGAGGATCCTG i mm9.chr11 C 0 C 0 s tupBel1.scaffold_124459.1-15939 11601 25 + 15939 AAACC-----------------CACAGCAAAGGGAGTTTTCA i tupBel1.scaffold_124459.1-15939 I 1462 C 0 s micMur1.scaffold_15893 6112 25 + 19765 AAGCC-----------------CACACCCAAGGGGGCTCCTG i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 27620 25 + 287808 AAACC-----------------CACACCCAAGGGGGCTCCTG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tarSyr1.scaffold_507768 714 25 + 1063 AAGCC-----------------CACACCCAAGGGGGTTCCTG i tarSyr1.scaffold_507768 C 0 C 0 s rheMac2.chr16 75037835 15 + 78773432 AAATC-----------------CACACCCCAG---------- i rheMac2.chr16 C 0 C 0 s calJac1.Contig5139 47247 25 + 225949 AAATC-----------------CACACCCAAGGGGGCTCCCG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 45239 15 - 95547 AAATC-----------------CACACCCCAG---------- i papHam1.scaffold8336 C 0 C 0 s panTro2.chr17 79476788 25 + 83384210 AAATC-----------------CACACCCCAGGGGGCTCCCA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 15515 25 - 64270 AAATC-----------------CACACCCCAGGGGGCTCCCA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16063894 25 + 17838096 AAATC-----------------CACACCCCAGGGGACTCCCC i ponAbe2.chr17_random C 0 C 0 e eriEur1.scaffold_355010 4620 3093 + 8359 I e dasNov2.scaffold_28617 12772 887 + 20752 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304533475 4348 - 541556283 I a score=3949123.000000 s hg19.chr17_gl000204_random 46608 277 + 81310 CCTCGAAGGCCCGGGGAAGCAGTCTAGCTCAGCCGTCT-AAGTGGAGGTGACTGA-TTTATTCTGACCATCCTGACTCTTCACGACACTGCTCTCCTCCAACCATGCACGGCTTTAATTGTCCATCAAGCAGGGCAGGGAG-----GAACCGTAAATCTTTCCTCCCG-CTGCTCC--GAGCTGAGC-CTGCTTGACCTGCAAT-T--GCCAG-CCCC------TCGCCTGCGTGCAGCCTGGAGAAGTCCGCTGGCTCTGAAG-GTG--AAGG-AGGGGAGTGAGGAAG-GGGAACGCAGGA s ponAbe2.chr17_random 16063919 277 + 17838096 CCTCGAAGGCCTGGGGAAGCAGTCTAGCTCAGCCGTCT-AAGTGGAGGTGACTGA-TTTCTTCTGACCATCCTGACTCGTCACGACACTGCTCTCCTCCAACCGTGCGCGGCTTTAATTGTCCACCAAGCAGGGCAGGGAG-----GAACCGTAAATCTTTCCTCCCG-CTGCTCC--GAGCTGAGC-CTGCTTGACCTCCAAT-T--GCCAG-CCCC------TTGCCTGCGTGCAGCCTGGAGAAGTCCGCTGGCTCTGAAG-GTG--AAGG-AGGGGAGTGAGGAAG-GGGAACGCAGGA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 15540 277 - 64270 CCTCGAAGGCCCCGGGAAGCAGTCTAGCTCAGCCNTCT-AAGTGGAGGTGACTGA-TTTATTCTGACCATCCTGACTCTTCACGACACTGCTCTCCTCCAACCGTGCACGGCTTTAATTGTCCATCAAGCAGGGCAGGGAG-----GAACCGTAAATCTTTCCTCCCA-CTGCTCC--GAGCTGAGC-CTGCTTGACCTGCAAT-T--GCCAG-CCCC------TCGCCTGNGTGCAGCCTGGAGAAGTCCGCTGGCTCTGAAG-GTG--AAGG-AGGGGAGTGAGGAAG-GGGAACGCAGGA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79476813 277 + 83384210 CCTCGAAGGCCCAGGGAAGCAGTCTAGCTCAGCCGTCT-AAGTGGAGGTGACTGA-TTTATTCTGACCATCCTGACTCTTCACGACACTGCTCTCCTCCAACCGTGCACGGCTTTAATTGTCCATCAAGCAGGGCAGGGAG-----GAACCGTAAATCTTTCCTCCCG-CTGCTCC--GAGCTGAGC-CTGCTTGACCTGCAAT-T--GCCAG-CCCC------TCGCCTGCGTGCAGCCTGGAGAAGTCCGCTGGCTCTGAAG-GTG--AAGG-AGGGGAGTGAGGAAG-GGGAACGCAGGA i panTro2.chr17 C 0 C 0 s papHam1.scaffold8336 45254 263 - 95547 -------------GGGAAGCAGTCTAGCTCAGCCGTCT-AAGTGGAGGTGACTGA-TTTATTCTGACCATCCTGACTCTTCACGACACTGCTCTCCTCCAACCGTGCACAGCTTTAATTGTCCATCAAGCCGGGCAGGGAG-----G-ACCGTAAATCTTTCCTCCCG-CTGCTCC--AAGCTCAGC-CTGCTTGACCTCCAAT-T--GCCAG-CCCC------TTGCCTACGTGCAGCCTGGAGAAGTCCGCTAGCTCTGAAG-GTG--AAAG-AGGGGAGTGAGGAAG-GGGAACGCAGGA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 47272 277 + 225949 CCTCGAAGGCCCGGGGAAGCAGTCTAGCTCAACCGTCT-AAGTGGAGGTGACTGA-TTTATTCTGACCATCCTGACTCTTAACGACACTGCTCTCCTCCAACCGTGCACGGCTTTAATTGTCCATCAAGCAGGGCAGGGAG-----GAACCGTAAATCTTTCCTCCTG-CTGCTCT--GAGCTCAGC-CTGCTTGACCTCCAAT-T--GCCAG-CCCC------TTGCCTGCAAGCCGCCTAGAGAAGTCCGCTGGCTCTGAAG-GTG--AAGG-AGGGGAGTGAGGAAG-GGGAACACAGGA i calJac1.Contig5139 C 0 C 0 s rheMac2.chr16 75037850 263 + 78773432 -------------GGGAAGCAGTCTAGCTCAGCCGTCT-AAGTGGAGGTGACTGA-TTTATTCTGACCATCCTGACTCTTCACGACACTGCTCTCCTCCAACCGTGTGTGGCTTTAATTGTCCATCAAGCCGGGCAGGGAG-----G-ACCGTAAATCTTTCCTCCCG-CTGCTCC--GAGCTCAGC-CTGCTTGACCTCCAAT-T--GCCAG-CCCC------TCGCCTACATGCAGCCTGGAGAAGTCCGCTAGCTCTGAAG-GTG--AAAG-AGGGGAGTGAGGAAG-GGGAACGCAGGA i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_507768 739 277 + 1063 CCCTGAAGGCCCCAGGAAGCAGTCTCGCTCAGCCATCT-AAGTGGAGGTGACTGA-TTTATCCTGACCATCCTGACTCTTAACGACACCGCTCTCCTCTAGCCATGCACGGCTTTAATTGTCCATCAAGCAGGGCAGGGAG-----GAACCGTAAATCTTTCCTCCCG-CTGCTCT--GAGCTCAGC-CTGCTTGACCTCCAAC-T--GCCAGCCCCC------TCACCTGCATCCCGCCTGGCGAAGTCTACTGGCTTTGAAG-GTG--AAGG-AGGGAAAC-AGGAAG-GGAAAACAAGAG i tarSyr1.scaffold_507768 C 0 C 0 s otoGar1.scaffold_94362.1-287808 27645 255 + 287808 CCTTAAAGGCCCCAGGAAGCA-TCTAGCTCAGCCGTCT-AAGTGGAGGTGACTGA-TTTATTCTGACCATCCTGACTCTTAATGACA-CGCTCTCCTCCAGCCGTGCGCAGCTTTAATTGTCCATCAAGCAGGGCAGGGAG-----GAA-CGTAAATCTTTCCTCCTG-CTGCTCC--AGGCGCAG--CTGTCTGACCTCCAA--C--TGCGG-CCCC------TCCCC--ACCCCAGCCTGGCCAGACCTGCT-GCTCTGAAG-GTG--AAGGACGGGACAAC----------------GGG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 6137 272 + 19765 CCTTAGAGGCCCCGGGAAGCAGTCTAGCTCGGCCGTCT-AAGTGGAGGTGACTGA-TTTATTCTGACCATCCTGACTCTTAACGACACCACTCTCCTCCAGCCGTGAGCAGCTTTAATTGTCCATCAAGCAGGGCAGGGAG-----GAACCGTAAATCTTCCCTCCCG-CTGCTCC--GGGCACAGC-CTGCCTGACCTCCAGT-C--TCCGG-CCCC------TCCC----GCACAGCCAGGAGAGGCCTGCT-GCTTTGAAG-GTG--AAGG-CGGAATGACAGGGAG-AGGGATGCGGGA i micMur1.scaffold_15893 C 0 C 0 s tupBel1.scaffold_124459.1-15939 11626 261 + 15939 -GTCACAGGCCACAGAAGGCAGCCTGGATCAGCCGTCGAAAGTGAGGGTGACTGACTTTTCCCTGTCCATCCTGACTCGTAGCGACACCGCTCCCCCCCGACTGTGTGCGGCTTTAATT-TTCATCCAGCAGGGCAGGGAG-----GGGCCATCAGTCTTCCCTGTGG-CCGCTCT--AGCTCGCTG-CAGCCCGACCTCCGAC-T--GCCAG-CCCC------TCACCTGCATCCCGCCTGGACAAGACCGCTGGCTTTGA----TG--GAGG-AGGGAGCTGG--------------AGGG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118759659 250 + 121843856 CTTAAAGGCCCT-GGGATGCAGTCTAGCAGGGCTGTCT-AAGTGGAGGTGACGGA-TTTATTCCAACCGTCCTGCCTCTTAACAACCTCTCTCTCCTCCAAGCCTGCACAGCTTTAATTGTCCATCAGGCAGGTCAGAGCA-----GAGCTGTAAATCTTTCCTCCCG-------------------GCTGCTTGACCTCCAAC-G--GCC-G-CCCC------TCACCA-GATCTCACCTGGAAA-----GCTGGCTTCGAAGCACA--GAGA--AGGAAATGGAGAGG-AGG----CTTCA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4390079 258 + 7991924 CCTTCAAGACCT-GGGAACCAAGCCGGCTCCTCCATCT-ACGTGAAGGTGACTGA-TTTATTCTGACCATCCTGACTCTTAATGACACAGCTCTCCTCCAAGCCTGCGCAGCTGTAATTGTCCATCATGCAGGG-AGGGCAGGCAGGGACTGTAAATCCTTCCTCCCAGCTGCGCA--GAGCTCCATGCTGCCTGACCTCTGGC-T--ACTGG-CCCC------TCATCGCCCTCCCACC---ATC-----ACCAGCTTTCAAG------GAGC--AGGA----GGGAAG-CAG----C---- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 7739 255 + 44242 CCTTCAAGGCAT--GGACGAAGTCCAGCTCCGCCATCT-AAGTGGAGGTGACTGA-TTTATTCTGACCGTCCTGACTCTTGGCGACACCACTCTCCTCCGAGTCTGCGCAGCATTAATTGTCCATCAGGCGGGGCAGGGAG-----GAACCGTAAATCTTCCCTTCCCACTGCTGG--GAGCTCCGCACTGCTTGACCTCCAGT-T--GCCAG-CCCC------TCACAG-GCATCCGCCTGGAGAGCTCTGCTGGCTTTGATG------AAGG--GGGGAACGG------------------ i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 19102 212 + 41507 --------------GGGAGCGGCCCGGCTCGGCCGCCT-GAGTGGAGGGGACTGA-TTTATTCCCACCGTCCTCTCTCCTAACGA---------------------CGCGGCTTTAATTGTCCATCAGACAGGGCAGGGAG-----GAGCCGTAAA--TCTTCCCCTGGCTGCTCC--GGGCCCAGCTCTGCTTGACT----------GCCAG-CCCC------TCACCG-CTT-----------------CCCGGCTCTGAGG-GTG--AAGG--GGGTGGCGGGGAGG-GGG----CGCGG i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 6283 239 - 54875 --------------GGGACCTGCCCAGCCCGGCCGC-------GGAGGGCACTGA-TTTATTCTGGCCGTCCTCACTGCTAACGACCCGGCTCTCCCCCAGCCGTGCGCGGCTTTAATTGTCCATCAAGCAGGGCAGGGAG-----CAGCCGTATATCTCTCCTCCCGGCTGCTCC--AGGCTCAGTGCAGCTTGACCTCCACA-GTGGCCAG-CCCC------TCACCG-CCA-----------------GCCAGCTCTGAAG-GTG--AAGG-CGGGAAACGGGGAGC-AAG----CAAAG i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 129688 276 + 145505 CCCTAAAGGCCCCAGGAAGCAGCCTAGCTCGGCCATCT-AAGTGGAGGTGACTGA-TTTATTCTGACCGTCCTGCCTCTTAACGACAT-GCTCTCCTCCAGCCATGCAAGGCTTTAATTGTCCATCCAGCAGGGCAGGGAG-----GAACCGTAAATCTTTCCTCCCAGCTGCTCA--GAGCTCAGCACTGCTTGACCTGCCGT-T--GCCAG-CCCC------TCGCTTGCATCCCCC-TGGAGCAGTCTGCTGGCTTTGAAG-GTG--GAAG-AGGGGAGTGGGAAAGCGGGAG--CAGAA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10859839 270 - 65312493 CCCTATAGGCCCCAGGAAGCAGCCTAGCTCAGCCGTCT-AAGTGGAGGTGACTGA-TTTATTCTGACCGTCCTGACTCTTAACGACCC-GCTCTCCTCCAGCCGTGCAAGGCTTTAATTGTCCATCCAGCAGGGCAGGGAG-----GAACCGTAAATCTTTCCTCCCGGCTGCTCT--GAGCTCAGCGCTGCTTGACCTGCCAT-T--GCCAG-CCCC------TCGCCTGCATCCCGC-TGGAGCAGTCTGCTGGCTTTGAAG-GTG--AAGG-CGGGGACTgg------gggag--gggga i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58043514 276 - 61308211 CCTTAAAGGCCCCAGGAAGCGGTCCAGCTCAGCCGCCT-AAGTGGAGGTGACTGA-TTTATTCTGACCGTCCTGACTTTTAACGACACCGCTCTCCTCCAGCCGTGAGCGGCTTTAATTGTCCATCCAGCAGGGTGCGGAG-----GAGCAGTAAATCTTTCCTCCCAGCGGCTCT--GAGCTTAGCGCTGCCTGACCTGCCCC-G--CCCAG-CCCC------TCACCTGCATCCCGC-TGGAGAAGTCTGCTGGTTTTGAAG-GTG--AAGG-AGTGAAATGGGGAAG-GGGGG--CAGAG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 32746 283 + 132007 CCGTAAAGGCCCCAGCAAGCAGTCCAGCCCAGCCATCT-GACTGGAGGTGACTGA-TTTATTCTGACCGTCCTGACTCTTAATGACACCGCTCTCCTCCAGCCGTGCGTGGCTTTAATTGTCCCTCCAGCAGGGCAGGGAG-----GAACCGTAAATCTTTCCTCACGGCTGCTGT--GAGCTCAGCGCCGCTGGACCTGCCGTAC--GACAC-CCCCCCCCCGCCCCCCACATCCCAC-CGGAGAAGCCTGCTAGCTCTgaag-gtg--gagg-ggggcaggaggcagg-gggag--cagga i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59437523 278 - 64418924 CCTCAAAGGCCCCGGGAAGCAGTCCAGCTCAGCCATCT-AAGTAGAGGTGACTGA-TTTATTCTGACCGTCCTGACTCTTAACGACACTGCTCTCCTCCAGCCGTGCATGGCTTTAATTGTCCATCCAGCAGGGCAGGGAG-----GAACCGTAAATCTTTCCTCGCGGCTTCTCT--GAGCTCAGCGCTGCTTGACCTGCCAT-T--GCCAG-CCCC------TCCCCTGCATCCCGC-TGGAGAAGTCTGCAGGCTTTgaag-gagaagaag-ggaggaagggggaag-gggag--cagga i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 10350 235 + 14340 -CCCCAGGGGCCCCGGAGGCA-TCCAGCCCG--CGTCT-GAGGGAAGGTGACTGA-CTCATCCCCACCGTCCTGACCC---CTGGCACAGC-CTCTTCCAGCCGCGC--GGCTGTAACTGTCCA-TCAGCAGGGC-AGGAG-----GGACCGTAAATCTTTCCTCCC-GTGGCTCT--GTGCTCGG-G--GCACGGCC-GCC-C-T--GCCAG-CGCC------AAGCCCTCGCCACTC--------------------TGAAG-GTG--ACAG-AGGG----GGAGGGG-AGGGG--CAGGA i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 15895 241 + 48268 CCTCCCAGGTCCCAGGAAGCAGTCTGGCTCGGCTGTCT-AAGTGAAGGTGAC-GA-TTTATGCTGACCGTCCTGACGCGTACCGACCCCGCTCTCCTCCAGCCCTGC--GGCTTTAGCTGTCCACCCAGCGGGGCAAGGAG-----GAACCGGAAATCTTCCCTCCCAGCTGCTCT--GAGCTCAGCG--GCTTGACCTGCCAC-T--GCCAG-CGCC------TGGCCTGCACCCTGC--------------------TGGAG-GAA--GCAG------------GGCG-GGGGT--CAGGA i pteVam1.scaffold_11245 C 0 C 0 s echTel1.scaffold_194555 4838 262 + 11139 CTCCCGGGCCC---AGGAGCG-TCTGGCTCAGCCGGCC-GAGTCGAGGTGACTGA-TTTATTCCTGCCATCCTGACTCCTAACGACCTTGCTTTCCTCTGGCCGGGCTGGACTTAAATTGTCCATCAAGTGGAGCAGGAAC-----AAGCTGCAGAGCCCGCCTCCCG-G-CCTCC--CAGCTCAGCACAGCCTGGCCTCCAAT-T--GCCTG-GCTG------CTGCCCGTACCC-ACCTGGACA-GCCCACTGGCTCCGAAA-G-G--GATG---------GGGAGCT-TGGAGCATGAGG i echTel1.scaffold_194555 C 0 C 0 s loxAfr3.scaffold_49 14433419 262 - 17734757 GTTTAAGGCCCC-GGGAAGCC-TCTGGCTC-ACCGTCT-AAGTAGAGGTGACTGA-TTTATTCTGACCATCCTGACTCCTAACGACCTCGCTCTCCTCCAGTCGTGCAGAACTTTAATTGTCCATCAAGTGAAGCAGGGAA-----GAGCTGTAAAT-----CTTCCA-GCCCTCC--CGGCTCAGCACTGCTTGACCTCCAAT-T--GCCAG-CCTA------CCACCTGCACCCTGCCTGGAGGGGCCTGCTGGCTCTGAAG-GTG--AAGG---------GGGAAGG-TGAGGTGCAAGA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 17628 263 + 24616 CTTTACAGCCCC-AGGAAGCA-TCTGGCTG-GCCGTCT-GAGCAGAGGTGACTGA-TTTATTGTGACCGTTCTGACTCCTGACGACCTCGCTCTCTGCCAGCCAGGCAGGACTTTAATTGTCCATCAAGCGAAGCAGGCAA-----GAGCCGTAAATCCTCCCTCCCA-GCCCTCC--CGGA-CAACACGGCTCGACCTCCAAT-T--TCCAG-C---------CCGCGTGCACCCCGCCCAGAGAGGCCTGCCTGCTCTGAGA-GTG--AAGG---------GGGCAGG-TGGGGTGCAGGA i proCap1.scaffold_29042 C 0 C 0 s macEug1.Scaffold23956 1646 268 - 25324 CTTTAAAGTCCCCTGAAAGCAGTCCAGTTCAGACCTTT-AAGCGAAGGTGACTGA-TTTATTCTGACTATTCCGACTCTGAACGACATTGCTCTCTTCCAAGCGTGCAGCACTTTAATTGTCCATCAAGTGGAGCAGGGAG-----GAACTGTAAATCTTCCCTCCCG--TGCTTCTGGAGCTAAACACTGCTTGACCTCCGCT-T--ACCAG-CCTCA-----TCACCTGCATCCAGACTGGAGTaa-----------tgaag-ggg--aggg--gaaaaacttggaag-gggaagaaagaa i macEug1.Scaffold23956 N 0 I 110 s monDom5.chr2 304537823 266 - 541556283 CTTTAAAGTCCCCAGAAAATAGTCCAGCTCAGACCTTT-AAGTGAAGGTGACTGA-TTTATTCTAACTATTCTGACTCTTAACGACATTGCTCTCTTCCAACCGTGCAGCACTTTAATTGTCCATCAAGTGGAGCAGGGAG-----GAACTGTAAATCTTCCCTCCTG--TGCTTCTGGAGCTAAACACTGCTTGACCTCCGCT-T--GCCAG-CCCCA-----TCACCTGCATCCAGGCTGGAATAA-----------TGAGG-GGG--AGGG--GAGAAACTTGAAGG-GGAAG--CAAGA i monDom5.chr2 I 4348 C 0 e eriEur1.scaffold_355010 4620 3093 + 8359 I e dasNov2.scaffold_28617 12772 887 + 20752 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=-191590.000000 s hg19.chr17_gl000204_random 46885 31 + 81310 GAGGC---------AGA---------AG------------------------------------------GGGG--TCAGGAGGGGAACAGAG s ponAbe2.chr17_random 16064196 35 + 17838096 GAGGC---------AGA---------GG-----------------------------------CTC---CGGGG--TCAGAAGGGGAACAGAG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 15817 31 - 64270 GAGGC---------AGA---------AG------------------------------------------GGGG--TCAGGAGGGGAACAGAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79477090 31 + 83384210 GAGGC---------AGA---------AG------------------------------------------GGGT--TCAGGAGGGGAACAGAG i panTro2.chr17 C 0 C 0 s papHam1.scaffold8336 45517 35 - 95547 GAGGC---------AGA---------GG-----------------------------------CTC---AGGGG--TCAGGAGGGGAACAGAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 47549 34 + 225949 GAGGC---------AGA---------GG-----------------------------------CTC----GGGG--TCAGGAGGGGAACAGAG i calJac1.Contig5139 C 0 C 0 s rheMac2.chr16 75038113 35 + 78773432 GAGGC---------AGA---------GG-----------------------------------CTC---AGGGG--TCAGGAGGGGAACAGAG i rheMac2.chr16 C 0 C 0 s tarSyr1.scaffold_507768 1016 34 + 1063 GAGCA---------AGA---------GG-----------------------------------CTG----GAGG--TCGGGAGAGGAACAGAG i tarSyr1.scaffold_507768 C 0 n 0 s otoGar1.scaffold_94362.1-287808 27900 27 + 287808 GGAGG---------AGG---------GA------------------------------------------GAGG--CCGGGTGGG---CAGG- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 6409 28 + 19765 GGAGG---------AGG---------CT------------------------------------------GGGG--TCGGAGGAG---CAGGG i micMur1.scaffold_15893 C 0 I 3 s tupBel1.scaffold_124459.1-15939 11887 38 + 15939 GGAGC---------AGA---------GT-----------------------------------TCTGCTAGTAG--GCTGGGAGGGCCCAAAG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118759909 39 + 121843856 GAGGTCACAGACCGGGG---------CA------------------------------------------GGGG--TCACAGATGGGG-GGAG i mm9.chr11 C 0 I 1 s cavPor3.scaffold_76 4390337 26 + 7991924 --------------GGA---------AA------------------------------------------GGGG--TGGCTGATGGAGCAGAA i cavPor3.scaffold_76 C 0 I 1 s speTri1.scaffold_128901 7994 24 + 44242 --------------GGA---------AA------------------------------------------GGGG--CATCAAGAGGAG--GAA i speTri1.scaffold_128901 C 0 I 1 s oryCun2.chrUn0958 19314 31 + 41507 GAGCC---------GGA---------GA------------------------------------------CAGG--CTGGGGAGGGGGACAGA i oryCun2.chrUn0958 C 0 I 1 s ochPri2.scaffold_9426 6522 39 - 54875 GAGAC---------AAA---------GAG-----------------------GCTG-------CTG----GGGG--GTGGGGGGCGAGCCAGT i ochPri2.scaffold_9426 C 0 I 1 s turTru1.scaffold_106006 129964 39 + 145505 GCAGG---------AGAAAGAGGCTGGT------------------------------------------GGGC--TCAGGGAGGGG-GATAG i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10860109 39 - 65312493 gcagg---------agaaagaggctggt------------------------------------------gggg--tcggggaggga-gacag i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58043790 31 - 61308211 GAGGG---------A-------GCT-GG------------------------------------------TGGG--GTGGGGGTGGG-GAGAG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 33029 38 + 132007 ggaag---------agaaagaggct-gt------------------------------------------gggg--tcagggagggg-gagag i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59437801 38 - 64418924 gaaag---------agaaccaggct-at------------------------------------------gggg--tcagggagggg-gagag i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 10585 35 + 14340 GGGGG---------C-----AGGCTGGT------------------------------------------GGGG--TCAGAGAGGAGGCAGAG i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 16136 17 + 48268 --------------------------GC------------------------------------------AGGG--CCAGGTGGGAG------ i pteVam1.scaffold_11245 C 0 C 0 s echTel1.scaffold_194555 5100 23 + 11139 GGTGC---------AGG---------AT------------------------------------------GCAG---------GAGG-CAACT i echTel1.scaffold_194555 C 0 C 0 s loxAfr3.scaffold_49 14433681 32 - 17734757 GAAAC---------AGG---------CT------------------------------------------GGGGTGTCAGGGAGGGG-CACAG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 17891 32 + 24616 GAAAG---------AGG---------AT------------------------------------------GGGGTGTCAGAGAGGGG-TGGAG i proCap1.scaffold_29042 C 0 C 0 s monDom5.chr2 304538089 51 - 541556283 ----------------------------AAGCTCACTGCAAATAGATCTCCAGCTGCTTCTAACCC----CAGG--TCATCTGAG-------- i monDom5.chr2 C 0 C 0 e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 1914 110 - 25324 I e dasNov2.scaffold_28617 12772 887 + 20752 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=-869477.000000 s hg19.chr17_gl000204_random 46916 95 + 81310 AG--AGCCAG-----GCA----GCAGGAGAAAG----CAAG---CAGCCGACATGGCCATGCTC--CCGCTGCT----------CCCGC--------C------------CCGGGGCCCCTGCGGAGGAA--TGAATGCCTCAG---------CC-------------------------C s proCap1.scaffold_29042 17923 80 + 24616 ---------------------------AGCATG----CAGA-----GCAGAC---CGCAGGCAC--CAGCTACC-------CTGCAGAG--------G------------CAGCTGTCGACCAGGGCACA--TGAAGGCCACAG------CGCTG-------------------------G i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14433713 89 - 17734757 ---------------------------AGCATG----CAGA---GTGCAGAA---CGCAGGTGC--CGGCCACCCTGGGAACTGCAGAG--------G------------CAGCTGGTGCCCAGGAAACA--CCAAGGCCACGG------TGCTG-------------------------G i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_194555 5123 32 + 11139 ---------------------------GGTCCC----CAGG---ATGT------------GTGC--CGGCC----------------AG--------G------------CAC----------------------------------------TG-------------------------G i echTel1.scaffold_194555 C 0 C 0 s pteVam1.scaffold_11245 16153 41 + 48268 -------------------------------------------------------------CTC--CTGCTG----------------------------------------CTGCACACTGCGGAGGGC--TCCCCGCTGCGG----------C-------------------------T i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 10620 72 + 14340 CG--AGCGGG------------GC-GGAGAGCA----GGGA-----GCCA-------TGGCCGC--GTGCTG--------------------------------------GACTGCACAC-GCAGAGGCC--TCTCT-CTGCAA---------CC-------------------------T i myoLuc1.scaffold_4816 C 0 C 0 s canFam2.chr9 59437839 85 - 64418924 ag--ggatgg------------gcaggaggaCA----CATG---TGGCCA-------CGTGCTC--TGGCTG-------------CTAA--------TGGGGG---------CGGGGCACTGCAGAGGAC--TCACCGCTGCAG---------CC-------------------------T i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 33067 86 + 132007 ag--ggatgg------------gcagaagaaCA----CGTA---AGGCCA-------CGTGCTC--TGCCTGCG----------CCTAA--------GGGGG-----------GGAGCACTGCAGAAGAC--TCACCCCGACCG---------CC-------------------------A i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58043821 97 - 61308211 AGCCAGCAGG------------GCAGGAGAGCA----TGTG---TGGCCA-------CGTGCTT--TGGCTGCT----------CCTAA--------GGGGTGGGGGTGGGAGGGGGCACTTCGGAGGA----TGTCACTGCAG---------CT-------------------------T i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10860148 76 - 65312493 ag--gggtgg---------------------------agCA---CGGCCA-------TGTGCCCTGTGTCTGCT----------CCTAA--------C------------CCCAGGGTACTGAAGAGGAG--TCTTCACTGCAG---------CT-------------------------T i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 130003 73 + 145505 AG--GGATGG---------------------------TGCA---TGGCCA-------TGTGCTC--AGTCTGCT----------CCTAA---------------------CCCGGGGCACTGCAGAGGAG--TCCTCACTGCAG---------CT-------------------------T i turTru1.scaffold_106006 C 0 C 0 s ochPri2.scaffold_9426 6562 100 - 54875 GC--TGCAGGTGTCTGGG----GCAGAGGAAGGGGAAGGGA---GAGCCTGC---AGCTGCCTA--AAGCTGTT----------CCAAC--------A------------CCCAG--CACT-CAGAGGAGGAAGGAAGCCACAG---------CC-------------------------C i ochPri2.scaffold_9426 I 1 C 0 s oryCun2.chrUn0958 19346 88 + 41507 AC--AGCAGA-----GGG----GTCCAGCAGGG----AGGA---GAGCCCCC---ACCCCGCTT--ACGCTGCT----------CCAGC---------------------CCGGG--CGCTGCGGGGGAGGCAGAAGGCCGCAG------------------------------------- i oryCun2.chrUn0958 I 1 C 0 s speTri1.scaffold_128901 8019 99 + 44242 AG--GCCAGAGGGCCAGG------AGGGACAGG----GAGGGCAGGAGCACT---GGCCACCTT--TGGCTGCT----------CTGAC-------TA------------CAAGG--CGCTGCAGAGCAGTGGTGCCCCTGGAG---------TC-------------------------T i speTri1.scaffold_128901 I 1 C 0 s cavPor3.scaffold_76 4390364 89 + 7991924 GC--GGCAAGAGGTCAGG----GCAGGTGCA-G----AGGG---GGAGTGTG---GCCTGCATC--CTGCTGCG----------CAGAC-------AC------------CGAGG--TGCTGCAGAGTGA--------CTGCTG---------CC-------------------------T i cavPor3.scaffold_76 I 1 C 0 s mm9.chr11 118759949 89 + 121843856 AC--AGCAGGGGG--GGG----TCACAGGCAGG----AAGG---GGACTTAA---GGCTGAGCT--CTGCTGCT----------GTAAC--------T------------TAAGA--TGCTGCAGAGCAA------CTCTGCAG---------CT-------------------------G i mm9.chr11 I 1 C 0 s tupBel1.scaffold_124459.1-15939 11925 106 + 15939 ------------------GCAGGCGGGAGAAAG----CATG---TGCCCAGCACGGTCA---------GGCGCT----------CTAAC--------C------------TGGGGCCCGCAGAGGTGTGC--TGCAGCCCGGAG---------CTGTGGCCACACACACACACACACGTAT i tupBel1.scaffold_124459.1-15939 C 0 C 0 s micMur1.scaffold_15893 6440 77 + 19765 AG--AGCCAG------------CCAGGAGAAAG----CGTG---CAGCC-------------------GCTGCT----------TGAAC--------C------------C---GGGCACCGTGGAG------GAATGCCTCAGCGGAGTCACCC-------------------------T i micMur1.scaffold_15893 I 3 C 0 s otoGar1.scaffold_94362.1-287808 27927 41 + 287808 -----------------------CAGGGGA-------CGTA---TGGCTG------------------GCTGCC----------TCA--------------------------------------------------GCCTCAG----ACAGCCA-------------------------T i otoGar1.scaffold_94362.1-287808 C 0 C 0 s rheMac2.chr16 75038148 97 + 78773432 AG--AGCCAG-----GCA----GCAGGAGAAAG----CATG---CGGCCACCACAGCCATGCTC--CGGCTGCT--------CCCCCAC--------C------------CCAGGACCACTGCGGAGGAA--TGAATGCCTCAG---------CC-------------------------T i rheMac2.chr16 C 0 C 0 s calJac1.Contig5139 47583 96 + 225949 AG--AGCCAG-----GCAGGCGGCAGGAGAAAG----CAAG---CGGCCAGCC--ACCATCCTC--CAGCTGCT-----------CCAC--------C------------CCTGGGCCGCTGCAGAGGAA--TGAATGCCTCAG---------CC-------------------------G i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 45552 97 - 95547 AG--AGCCAG-----GCA----GCAGGAGAAAG----CATG---CGGCCGCCACAGCCGTGCCC--CGGCTGCT--------CCCCCAC--------C------------CCGGGGCCACTGTGGAGGAA--TGAATGCCTCAG---------CC-------------------------T i papHam1.scaffold8336 C 0 C 0 s panTro2.chr17 79477121 95 + 83384210 AG--AGCCAG-----GCA----GCAGGAGAAAG----CATG---CAGCCGACATGGCCATGCTC--CCGCTGCT----------CCCGC--------C------------CCGGGGCCCCTGCGGAGGAA--TGAATGCCTCAG---------CC-------------------------C i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 15848 95 - 64270 AG--AGCCAG-----GCA----GCAGGAGAAAG----CAGG---CAGCCGACATGGCCATGCTC--CCGCTACT----------CCCGC--------C------------CCGGGGCCCCTGCAGAGGAA--TGAATGCCTCAG---------CC-------------------------C i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16064231 95 + 17838096 AG--AGCCAG-----GCG----GCAGGAGAAAG----CATG---CGGCCGCCATGGCCACGCTC--CGGCTGCT----------CCAGC--------C------------CTGGGGCTCCTGCGGAGGAA--TGAATGCCTCAG---------CC-------------------------C i ponAbe2.chr17_random C 0 C 0 s monDom5.chr2 304538140 61 - 541556283 ------------------------------------------------------------AGAA--ATGCAGTA----------CCAATAAGATTTAT------------CAATGCAGACCTTAGAAAGG--AGAAGGCTCCCA---------TA-------------------------A i monDom5.chr2 C 0 C 0 e tarSyr1.scaffold_507768 1050 0 + 1063 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 1914 110 - 25324 I e dasNov2.scaffold_28617 12772 887 + 20752 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=-667823.000000 s hg19.chr17_gl000204_random 47011 93 + 81310 GA----CTGCAGCC-------TCGAG--GGGCCCC------------------GGCT--------------GGG------GCGT------CTACACACCTC---------------------GCCTCCCAGGCTCCTGCTCTCAAGCAGCGGGA--CC----C-TGATAAAGTGA---------GCC s ponAbe2.chr17_random 16064326 93 + 17838096 GA----CTGCAGCC-------TCCAG--AGGCCCC------------------GGCT--------------GGG------GCGT------CTACACACCTC---------------------ACCTTCCAGGCTCCTGCTCTCAAGCAGCAGGA--CC----C-TGATAAAGTGA---------GCC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 15943 93 - 64270 GA----CTGCAGCC-------TCGAG--GGGCCCC------------------GGCT--------------GGG------GNGT------CTACACACCTC---------------------GCCTCCCAGGCTCCTGCTCTCAAGCAGCAGGA--CC----C-TGATAAAGTGA---------GCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79477216 93 + 83384210 GA----CTGCAGCC-------TCGAG--GGGCCCC------------------GGCT--------------GGG------GCGT------CTACACACCTC---------------------GCCTCCCAGGCTCCTGCTCTCAAGCAGCGGGA--CC----C-TGATAAAGTGA---------GCC i panTro2.chr17 C 0 C 0 s papHam1.scaffold8336 45649 93 - 95547 GA----CTGCAGCC-------TCCAG--GGGCCAC------------------GTCT--------------AGG------GCAT------CTACACACCTC---------------------GCCTCCCAGGCTCCCGCTCTCAAGCAGCAGGA--CC----C-TGATAAAGTGA---------GCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 47679 93 + 225949 GA----CTGCAGCT-------TCGAG--GGGCAGC------------------AGCT--------------GGA------GCGT------CTACACACCTC---------------------GCCTCCCAGGCTCCGCCTGTCCAGCAGCGGGA--CC----C-TGATAAAGTGA---------GCC i calJac1.Contig5139 C 0 C 0 s rheMac2.chr16 75038245 93 + 78773432 GA----CTGCAGCC-------TCCAG--GGGCCAC------------------GTCT--------------GGG------GCAT------CTACACACCTC---------------------GTCTCCCAGGCTCCCGCTCTCAAGCAGCAGGA--CC----C-TGATAAAGTGA---------GCC i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94362.1-287808 27968 84 + 287808 CA----CTGCAGGT-------TGAGG--GGA--GC------------------CGCA--------------GGG------GCAG------TG--ACACCTT---------------------GTCCCCAGGATTCTGTCTCT-----AGCATGA--CT----C-TGGTCAAGTGG---------GCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 6517 85 + 19765 CG----CTGCAGGT-------TGAGG--GAG--GT------------------GGCA--------------GGA------GCGG------CT--ACACCAC---------------------ACCCCCAGGG-CCCGTCTCT---ACAGTGAGA--CT----C-CAGTAAAGTGG---------GCC i micMur1.scaffold_15893 C 0 C 0 s tupBel1.scaffold_124459.1-15939 12031 88 + 15939 GG----CCGCAGCT-------CGGGG--GAG--GC------------------GGAT--------------GGG------G--T------TCACATACCTC---------------------GCCTCGCAGGCCCC-GCTCTCAAGCAGCGTGA--CT----C-CATCAAAGTGG---------GCC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118760038 68 + 121843856 ----------------------------GAGTC--------------------TGTC--------------GGG------ACCT------CT------------------------------GCTTCCAGGGC-ACTGGCTGGATACGGCTGGT--GCAG--T-GCCCTTCGAAC---------AGT i mm9.chr11 C 0 I 12 s cavPor3.scaffold_76 4390453 69 + 7991924 ----------------------------GAGTCAC--AGCAGCTT--------TGAA--------------GGG------GGCA------CT-------------------------------CCTCCAGGGC--TAGGCGCCACATAGTT-----------C-ACCCTCTGGGT---------GCC i cavPor3.scaffold_76 C 0 I 11 s speTri1.scaffold_128901 8118 82 + 44242 ----------------------------GAGCCACGTGGCAGCTTCCAAGGGCTGTG--------------GAG------GCCATGCAGGCT------------------------------CCTTCCCAGCC--TGCCCCGCACGC---------------C-ACACTGCAGGC---------TGC i speTri1.scaffold_128901 C 0 I 13 s oryCun2.chrUn0958 19434 69 + 41507 ------------------------AG--GAGCCGC-------------------------------------AG------GCAC------CT------------------------------GCCTCCCAGGC-CCGGTTCTCAGGCAGACAAA--GCGGCCC-GGCCAGAGGGA---------GCC i oryCun2.chrUn0958 C 0 I 568 s ochPri2.scaffold_9426 6662 53 - 54875 ------------------------AGCCAGGCCAC-------------------------------------AG------GCAT------CC------------------------------GC----------------CGAAGCCAACCAGG--GTGACCC-CAGCACTGGAC------------ i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 130076 124 + 145505 AAAGGGGAGGCGGC-------GGGAA--G-GTAGT------------------GTGCAC-----------AGGGTGCCCTGGGC-------TACACCCTCCCGGGCCAGTGTCTACACACCTGCCTCACCGGGCCCAGCTCTCAAGCAGCCTGA--CT----C-ATATGAAGT-G---------GGC i turTru1.scaffold_106006 C 0 I 1 s bosTau4.chr19 10860224 125 - 65312493 GGAGGGGAGGCGGC-------AGTAG--GCACAGT------------------GTGCAT-----------GGGGTACCCTGGGC-------TACGCCCTCCTGAGCCAGCGTCTACACACTGGCCTCACAGAGCCCAGCTCTCAAGCAGCCTGA--CT----C-CTATGAAGT-G---------GGC i bosTau4.chr19 C 0 I 1 s equCab2.chr11 58043918 119 - 61308211 CGAGGGGAGGGGGC-------TGTAG--GTGCCGT------------------ACGCAC-----------GGGG------GTGCCCTGGGCCACGCCCTCCCAGGCTGT-GTCTCCACATCTGCCT------CACCAGCTCTCAAGCAGCCTGA--CT----C-CAATAAAGC-G---------GGC i equCab2.chr11 C 0 I 1 s felCat3.scaffold_206428 33153 83 + 132007 TA----------------------AG--GTGCGGT------------------GTGCAT-----------GGGG------GTGCCCCGGGCCACGCCCTCCCG-----------------------------CCCCAGCTCTCAGGCAGCCCGA--CT----C-CACTAAAGCGG---------GGC i felCat3.scaffold_206428 C 0 I 1 s canFam2.chr9 59437924 81 - 64418924 CG----------------------AG--ATGCAAC------------------GTGCAT------------GGG------GTG-CAGGGACCGCGCCCTCCGG-----------------------------CCCTAGCTCTCAAGCAGCCCGA--CT----C-CAGTAAAGCAG---------GGC i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 10692 76 + 14340 CAAGGGGAGGTGGC-------CGAGG--GTGCGGT------------------GTGT-----------------------------------------------------------------GC-----GGGCCCCAGCTCGCAGGCAGCCCGAGTCT----C-CGATAAAGCCA---------GGC i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 16194 124 + 48268 CCGTGGGCGCTGGC-------AGGAG--TTGCAGC------------------GTGT-----------------------------TGGGCCACGCCCTCCCAGACCCCAACCAACACATGGGCCCCCGGGGCCCCAGCTCTCAAGCAGTCTAA--CT----C-CAAGAAAGCGGGTGGAACACGGG i pteVam1.scaffold_11245 C 0 C 0 s echTel1.scaffold_194555 5155 92 + 11139 GAGGG-------------------------GCCAT------------------GTGCACCGCCCTGGGGAGCAG------GTAT------CT--ACACCTG---------------------GCCTCAACAACTCCACCTCTGGGCCAG-GGGA--CA----C-CCACAAAGTGG---------GTC i echTel1.scaffold_194555 C 0 C 0 s loxAfr3.scaffold_49 14433802 112 - 17734757 GAGGGACGGCTGCTG-----GCACAG--GTGCCCT------------------GTATGCTGCCCTCCCAGGGAG------GCGT------CTACACACCTG---------------------GCCTCACCAACCCCATCTCTGGAGCAGCAGAG--CT----C-CTATAAGT-GG---------GTC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 18003 111 + 24616 GGGGCGGGGCAGCT------GCAGAG--GTGCCCT------------------GTGTGCTGCCCTCCTGGGCAG------GTGT------CTACACACCAG---------------------GCCCC-CCAACCCTGTCTCTGGGGCAGCAGGG--CC----C-CTACAAACAGG---------GTC i proCap1.scaffold_29042 C 0 C 0 s macEug1.Scaffold23956 2024 98 - 25324 ----AGCTGCAGTGTTC---TTCCAA--AAGTGGC------------------TGCT--------------GGC------TGAT------AGACACACCTT---------------------CCTTTTTGAACCCATTCTCCAAACCATTGTGA--CT----CTCAATGAAGGGG---------GTC i macEug1.Scaffold23956 I 110 C 0 s monDom5.chr2 304538201 97 - 541556283 -----GCTGCAGTGTTCTTTCAAAAG--TGGTCAC------------------AGAC--------------AGG------TGGC---------CACACCTT---------------------CCCTTTGGAACCCAGTCCACAAACCAGTGTGG--CT----CTCAATACAGTGG---------CTC i monDom5.chr2 C 0 C 0 e tarSyr1.scaffold_507768 1050 0 + 1063 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e dasNov2.scaffold_28617 12772 887 + 20752 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=138158.000000 s hg19.chr17_gl000204_random 47104 59 + 81310 AGACCCTCAGGG--------AGTCTTGGCATT-CC-CTTGCC-AGGCTAT-AAAAC---ATCACAGCCCCAAA-A s ponAbe2.chr17_random 16064419 59 + 17838096 AGATCCTCAGGG--------AGTCTTGGCATT-CC-CTTGCC-AGGCTAT-AAAAC---ATCACAGCCCCTAA-A i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 16036 59 - 64270 AGACCCTCAGGG--------AGTCTTGGCATT-CC-CTTGCC-AGGCTAT-AAAAC---ATCACAGCCCCAAA-A i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79477309 59 + 83384210 AGACCCTCAGGG--------AGTCTTGGCATT-CC-CTTGCC-AGGCTAT-AAAAC---ATCACAGCCCCAAA-A i panTro2.chr17 C 0 C 0 s papHam1.scaffold8336 45742 59 - 95547 AGGCCCTCAGGG--------AGTCTTGGCATT-CC-CTTGCC-AGGCTAT-AAAAC---ATCACAGCCCCAGA-A i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 47772 58 + 225949 -GCCCCTCAGGG--------AGTCTTGTCATT-CC-CTTGCC-AGGCTAT-AAAAC---ATAACAGCCCCAAA-A i calJac1.Contig5139 C 0 C 0 s rheMac2.chr16 75038338 59 + 78773432 AGGCCCTTAGGG--------AGTCTTGGCATT-CC-CTTGCC-AGGCTAT-AAAAC---ATCACAGCCCCAGA-A i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94362.1-287808 28052 53 + 287808 AACACCCGGGGG--------AGTCTGCGCCCC-CCTCCCGCC-TTGGAAC-ATG---------CAGCTCGAA--A i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 6602 60 + 19765 AGACCCTGGGGG--------AGTCCCCGCACT-CC-CTCGCC-TGGCTGC-AGGAC---AGCACAGCTCCGAGCA i micMur1.scaffold_15893 C 0 C 0 s tupBel1.scaffold_124459.1-15939 12119 59 + 15939 AGACCCTCAGGG--------AGTCTTGGCATC-CC-ATGGCC-TGGCTAT-AAAAC---AGCACCGCCCTGGG-A i tupBel1.scaffold_124459.1-15939 C 0 I 375 s mm9.chr11 118760118 57 + 121843856 -GGGCCTTGGGG--------CACCCCA-AGTT-CC-CTTGGC-TAGCTGC-AAAGC---TGAACAGTCTAGAA-G i mm9.chr11 I 12 C 0 s cavPor3.scaffold_76 4390533 60 + 7991924 -AGGCCTTGGGA--------GCCACAG-CATT-CT-CTGGAC-TGACATC-CAAACACACAGACAACCTTCCA-A i cavPor3.scaffold_76 I 11 C 0 s speTri1.scaffold_128901 8213 51 + 44242 -GGGCCCTGGGG--------CGTCTGGACACT-GC-CTTGCC-TGGCCTG-AAAGG--------AACCCCC---A i speTri1.scaffold_128901 I 13 C 0 s ochPri2.scaffold_9426 6715 55 - 54875 ACAGCACGGGGGAGGGCCACCACCTTG-CTTC-CT-CCTGCC-T-GCGTC-ATCAC---------GCCCA----- i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 130201 59 + 145505 AGACCCCGGGGG--------AGTCTCAGCATT-CC-CTTGCT-TTGCTGA-AAAAC---AGCACAGCCCTGAA-A i turTru1.scaffold_106006 I 1 C 0 s bosTau4.chr19 10860350 58 - 65312493 AGACCCCGGGGG--------AGTCTTGGCATT-CC-CCTGCC-TT-CTGA-AAAAC---AGCACAGCCCTGAA-A i bosTau4.chr19 I 1 C 0 s equCab2.chr11 58044038 59 - 61308211 AGACCCTGGGGG--------AGTCTCAGCATT-CT-CTTGCC-TTACTGG-AAAAC---AGCACCAGCCTGAA-A i equCab2.chr11 I 1 C 0 s felCat3.scaffold_206428 33237 59 + 132007 AGAAGCTGGGGA--------AGTCTCCGCGTT-CG-CACCCC-TTGCTGG-AAAAC---AGCACAGCCCTGAA-A i felCat3.scaffold_206428 I 1 C 0 s canFam2.chr9 59438005 42 - 64418924 -------------------------CTGCATC-CC-TTCGCC-TTGCTGG-AAAAC---AGCACAGCCCTGAA-A i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 10768 55 + 14340 ----CCTGGGGG--------CCTCTCGGCAAC-CC-CTCTCC-TCGCTGG-ATCCC---CACACAGCCCCGAG-C i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 16318 53 + 48268 ----GCGAGGGG--------AGTCTCGGCATC-AC---CCCC-TCACTGG-AAAAC---AGCACAGCTCTGAA-A i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 18114 61 + 24616 AGCCAATGCAGG--------AACCCCTACACC-CT-CTCAACATGGCTAAGGAAAC---ACCACCACCCTGAC-A i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14433914 59 - 17734757 AGCCAAGGGAGG--------AGCCCCCGTACC-CT-CCTGAC-TGGCTAA-GAAAT---AGCACCGACGTGAA-A i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_194555 5247 27 + 11139 AGC---------------------------CC-CT----------------GAAGG---ACCCCCACCCTGAA-A i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 13659 50 + 20752 AGCC-CTGGAGG--------AGGCCGGGCATT-CC-CCAGCCTCG----------T---ACAGTCGCCCCAAA-A i dasNov2.scaffold_28617 I 887 C 0 s macEug1.Scaffold23956 2122 58 - 25324 -AAGAATCAGAA--------AAGCTCTTCATT-TC-TATCAC-TTACTAG-ACATC---AATGTCATATTTGA-A i macEug1.Scaffold23956 C 0 C 0 s monDom5.chr2 304538298 51 - 541556283 ---------AAA--------ATTTTTTTCATTACT-ATCACT-TAAGGAC-ACATC---AGCATCCTATTGAA-A i monDom5.chr2 C 0 C 0 e oryCun2.chrUn0958 19503 568 + 41507 I e tarSyr1.scaffold_507768 1050 0 + 1063 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=-127672.000000 s hg19.chr17_gl000204_random 47163 49 + 81310 GGAG-CCCGCTG-----------CGGGGGATACTGA--------------------TTCTCCATCCCACATTCACGGTGTC-- s ponAbe2.chr17_random 16064478 49 + 17838096 GGAG-CCCGCCG-----------CGGGGGATACTGC--------------------TTCTCCATCCCGCATTCACGGTGTC-- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 16095 49 - 64270 GGAG-CCCGCTG-----------CAGGGGGTACTGC--------------------TTCTCCATCCCGCATTCACGGTGTC-- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79477368 49 + 83384210 GGAG-CCCGCTG-----------CGGGGGATACTGC--------------------TTCTCCATCCCGCATTCACGGTGTC-- i panTro2.chr17 C 0 C 0 s papHam1.scaffold8336 45801 49 - 95547 GGAG-CCCGCTG-----------CGGGGCATACTGC--------------------TTCTCCATCCAGCCTTCACGGTGTC-- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 47830 34 + 225949 GGAG-TCCCCTG-----------TCGGGGATACTGC--------------------TTCTCCATCC----------------- i calJac1.Contig5139 C 0 I 5 s rheMac2.chr16 75038397 49 + 78773432 GGAG-CCCGCTG-----------CGGGGGATACTGC--------------------TTCTCCATCCAGCCTTCATGGTGTC-- i rheMac2.chr16 C 0 C 0 s otoGar1.scaffold_94362.1-287808 28105 49 + 287808 GGAG-CCATCAA-----------GGGAGGGTAAATA--------------------ATCACCATCCAGTCCGTATGGTGCC-- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 6662 50 + 19765 GAGC-CCACCAG----------CGGGATGACATTCA--------------------TTCTCCATCCGGTCCTCGCGGCGCG-- i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118760175 33 + 121843856 -------------------------GGAAATGCTGGCAAAGGAG------------CTTTCCCTGCGCTC------------- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4390593 52 + 7991924 -------------------------GCGAGGCCTGGAGAGGAAGGAATGATGCTCATTCTCCTTGCAGTCTACACAG------ i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 8264 44 + 44242 -------------------------GTGAGGACCAGCAAAATCC------------TTCTCCCTCTGAACTCAAGAGTGCC-- i speTri1.scaffold_128901 C 0 C 0 s ochPri2.scaffold_9426 6770 11 - 54875 --------------------------------------------------------GTTCCCCAGCG---------------- i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 130260 48 + 145505 GGAA-CCCACTG---------GGGAGGAAATACTAT---------------------CCTCCATCCAACCCTCAC--TGTG-- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10860408 50 - 65312493 GGAA-CCCACTG---------GGGAGGAAATACTAT---------------------CCTCCATCCAACCTTCATTGTGTG-- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58044097 51 - 61308211 GGAG-CCCACGG---------GGGAGGAAACAACAC--------------------TCCTCCATCCAATCCTCATTGTGTC-- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 33296 51 + 132007 GGAA-CCCACTG---------GGGCGGGAATTCTAT--------------------TTCTCTCTTCCATCTGCACCGTGTG-- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59438047 51 - 64418924 GGAA-CCCACTG---------GAGAGGAAATAATAT--------------------TTCTCTATCCCATCTGCATTGTGTA-- i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 10823 49 + 14340 AAGG-CCC-GTG---------GGGAGGGAAGAACAT---------------------CCTCCATCCGGGCCTCACTGTGCA-- i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 16371 50 + 48268 GGAC-ACC-CCA---------GGGAGGAAAGGGGAC--------------------GTCTTCACCCAGCCCTCGCCATGGA-- i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 18175 56 + 24616 GGAG-CCCACTGGCGCC----AGCGAAGAATAATAA--------------------GTCCTCTTCAGGAGTCCTTCTCATC-- i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14433973 47 - 17734757 GGAG-CCCAGTGGGGTG----GGCA------AATAA--------------------GTCCCTGTCAAG---CCTCCATGTT-- i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_194555 5274 56 + 11139 AGAA-CCTGCTGAGACT----GGGGAAGAGGGACAC--------------------GCATCCATCACAGCTCCTTTAGGCC-- i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 13709 55 + 20752 GGAGTCCCACTGGGG------AGGAAATCATCATAA--------------------TTCTCCATCACGCCTCGGCTCTGCC-- i dasNov2.scaffold_28617 C 0 C 0 s macEug1.Scaffold23956 2180 60 - 25324 GGAA-CCAACTGGAAGGATGAGGGAGAGGCTAATAA--------------------TCTAATTTCAAGTCTATATTTTGTG-- i macEug1.Scaffold23956 C 0 I 2 s monDom5.chr2 304538349 62 - 541556283 TGAA-TCAACTGGAAGGGTGAAGGAGGGGATAATAA--------------------TTCAATATCAAGTCTATGTTTTGTGTT i monDom5.chr2 C 0 C 0 e oryCun2.chrUn0958 19503 568 + 41507 I e tarSyr1.scaffold_507768 1050 0 + 1063 I e tupBel1.scaffold_124459.1-15939 12178 375 + 15939 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=-345767.000000 s hg19.chr17_gl000204_random 47212 80 + 81310 TGCAACTGG---------ACCCCAGCTA-GGGGCACAGGATC---CTCTCTTAGG--GTGGGTGTCTCTGT------GAGGGC-------A-GG-------GACAGGCCAGGGGCC s calJac1.Contig5139 47869 79 + 225949 TGCAGTTGG---------GCCCCAGCTA-GGGGCACAGAAGC---CCCTCTCAGG--GCAGGTGACTCCAC------AAGGGC-------A-GG-------GACA-ACCAGGGGCC i calJac1.Contig5139 I 5 C 0 s papHam1.scaffold8336 45850 80 - 95547 TGCAACTGG---------GCCCCAGCTA-GGGCCACAGGATC---CTCTCTTAGG--GCGCGTGTCTCTGT------GAGGGC-------A-GG-------GACGGGCCAGGGGCC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75038446 80 + 78773432 TGCAACTGG---------GCCCCAGCTA-GGGCCACAGGATC---CTCTCTTAGG--GCAGGTGTCTCTGT------GAGGGC-------A-GG-------GACGGGCCAGGGGCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16064527 80 + 17838096 TGCAACTGG---------ACCCCAGCTA-GGGGCACAGGAGC---CTCTCTTAGG--GCGGGTGTCTCTGT------GAGGGC-------A-GG-------GACAGGCCAGGGGCC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 16144 80 - 64270 TGCAACTGG---------ACCCCAGCTA-GGGGCACAGGATC---CTCGCTTAGG--GTGGGTGTCTCTGT------GAGGGC-------A-GG-------GACAGGCCAGGGGNC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79477417 80 + 83384210 TGCAACTGG---------ACCCCAGCTA-GGGGCACAGGATC---CTCTCTTAGG--GTGGGTGTCTCTGT------GAGGGC-------A-GG-------GACAGGCCAGGGGCC i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 28154 84 + 287808 TGCAACT-G---------GCCCAAGCT--GGGGCACAGGGAC---CTCTCTGAGG--GCGTGTGTTGCTGTAGAACAGGGGGT-------T-GG-------GGCAGGCCACAGCCC i otoGar1.scaffold_94362.1-287808 C 0 I 10 s micMur1.scaffold_15893 6712 82 + 19765 TGGAACTGG---------GCCCAGGCTG-GGGGCACAGGGACCG-CGCTCTTAGG--GCTTGTGTTGCTAT------GAGAGC-------A-GG-------GCAAGGCCATGGGCC i micMur1.scaffold_15893 C 0 I 2607 s mm9.chr11 118760208 56 + 121843856 ----------------------CTGGTG-TGG-------------------TGGG--GCCTGACACGATCC------AAGGACCTTTC--G-GG-------TGTGTCTAGAGAGCC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4390645 56 + 7991924 ---------------------TCCTCCA-TGGC------------TCTTACTGGA--GCCTG----------------GGGACTTCTCTGG-GG-------GGTGGAGGGTCGGCC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 8308 79 + 44242 -GGAACAGG---------GCCTCTCCCA-GGGCC---TGCCT---CCCCGTGGGA--GTCTGGACCAGGCC------CAGGGCCAC----A-GG-------GCTAGGCAGCGGCCT i speTri1.scaffold_128901 C 0 C 0 s ochPri2.scaffold_9426 6781 49 - 54875 ---------------------------------------------------TGGG--TCTTGGTGACAGTT------CGGGGCAGACCGTG-GT-------GTTGGACTCTGGCCC i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 130308 67 + 145505 TGTGACTGG----------TCCCGGCTG-GGGGCACAGGGAC---CTCTCTGTA-----------------------AGAGAT-------G-GT---GGGGGGTAGGCCACAGGC- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10860458 70 - 65312493 TGTGACTGG----------TCCCAGCTG-AGAGCACAGGGAC---CTCTCTGTA-----------------------AGAGAT-------G-GGGGAGGGGGGTAAGCCACGGGC- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58044148 62 - 61308211 GGCAGTGGG----------ACCCGGCTA-GGGGCACAGGGAC---CTCTCTCTA----------------C------CGGGGC-------A----------GGCAGGCCACAGGT- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 33347 63 + 132007 TGCAACTGA----------CCCTGGCCG-GGGGCACAGGGGC---CTCCCCATA-----------------------AGAGAC-------G-GG-------GGCAGGCCACAGGC- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59438098 64 - 64418924 TGCAACCGA---------GCCCCATCTG-GGGGCACAGGGAC---CTGCCCATA-----------------------AGAGAC-------A-GG-------GGCGGGCCACAGGT- i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 10872 36 + 14340 --CAGCTGG---------GCGCCGGC-------------GAC---CT-CCCGTA-----------------------TGAGGC-------G---------------------GGC- i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 16421 24 + 48268 TGCAACGGG---------ACCCTGGC------------------------------------------------------TGG-------G---------------------GGC- i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 18231 78 + 24616 -ACAGCGTC---------CCCCATGCTA-GAGGAACGGGGAG---CCCCCCAG----GTGTGTGTCTCTGT------AAAAGC-------CAGG-------GGCCGTCTGGGAGCA i proCap1.scaffold_29042 C 0 I 4 s loxAfr3.scaffold_49 14434020 75 - 17734757 -GTAGCTGC---------CCCCTGGCTG-GGGGAACGGGGA----TCCTCCAG------ATGTGTCTCTGT------AAGAGC-------CAGG-------GGTGGGCTGGGAGTG i loxAfr3.scaffold_49 C 0 I 4 s echTel1.scaffold_194555 5330 72 + 11139 --CAGCTGCCCCACCCCACCCCAAACTG-GGGGAGTAATGAGAGAGCCTCCAG----GTGTGTGTCTCTG----------------------GG-------AGCCGGC-------- i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 13764 82 + 20752 GGCGGCTGA---------ACCCCTGCGG-CAGGCGCAGGCCT---TGCTCCGAGGACGCGCGCCTCTTTGT------CAGGGA-------C-CG-------CGTGGCCTGGGCGGC i dasNov2.scaffold_28617 C 0 I 4 s macEug1.Scaffold23956 2242 89 - 25324 TATGAAAGA---------ATCCCtgctgtcagaggcaggact---ctcAATTAGAGTGATAATGTCTTCTCATAAGAGATGAC-------A-GC-------TGCACTCCTGAAGCC i macEug1.Scaffold23956 I 2 I 1 s monDom5.chr2 304538411 89 - 541556283 TATGAAAGA---------ATCCCTACTGTCAGGGGCAGGGCT---CTCAATTAGAATAATAATGTCATCTCATAAAAGATGAC-------A-GC-------TGCACTCCTGAAGAC i monDom5.chr2 C 0 C 0 e oryCun2.chrUn0958 19503 568 + 41507 I e tarSyr1.scaffold_507768 1050 0 + 1063 I e tupBel1.scaffold_124459.1-15939 12178 375 + 15939 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=27448.000000 s hg19.chr17_gl000204_random 47292 96 + 81310 ACATAGCCCCAGCTGTGGCCGGGAGAACAGAGCTGGTCCAGGAGGTTTAGCCA---CAAGCTCCAAAGCACG---C--CCCCTTCCCC-TG--CAGCAGACTTAATA s otoGar1.scaffold_94362.1-287808 28248 54 + 287808 TGATAGCTCCAG----------------AGAGCCGCTTCATG---------CA---C----------GCACA---C--CCCCTCCT---------GCAGACTC-ATA i otoGar1.scaffold_94362.1-287808 I 10 C 0 s panTro2.chr17 79477497 96 + 83384210 ACATAGCCCCAGCTGTGGCCGGGAGAATAGAGCTGGTCCAGGAGGTTTAGCCA---CAAGCTCCAAAGCACG---C--CCCCTTCCCC-TG--CAGCAGACTTAATA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 16224 96 - 64270 ACATAGCCCCAGCTGTGGCCCGGAGAACAGAGCTGGTCCAGGAGGTTTAGCCA---CAAGCTCCAAAGCACG---C--CCCCTTCCCC-TG--CAGCAGACTTAATA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16064607 96 + 17838096 ACATAGCCCCAGCTGTGGCCCGGAGAACAGAGCTGGTCCAGGAGGTTTAGCCA---CAAGCTCCAAAGCACG---C--CCCCTTCCCC-TG--CAGCAGACTTAATA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75038526 96 + 78773432 ACATAGCCCCAGCTGTGGCCTGGAGAACCGAGCTGGTCCAGGAGGTTTAGCCA---CAAGCTCCAAAGCACG---C--CCCCTTCCCC-TG--CAGCAGACTTAATA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 45930 96 - 95547 ACAGAGCCCCAGCTGTGGCCGGGAGAACCGAGCTGGTCCAGGAGGTTTAGCCA---CAAGCTCCAAGGCACG---C--CCCCTTCCCC-TG--CAGCAGACTTAATA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 47948 96 + 225949 ACATAGCCCCAGCCGTGGCCCAGGGAACCGAGCTGGTCCAGGAGGTTTAGCCA---CAAGCTACAAAGCATG---C--CCCCTCCCCC-TG--CAGCAGACTTAATA i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118760264 66 + 121843856 GAGCACC--------------------------------TGGAAGCTCAGCCAACGCAGAGTCTGACGCTCG---C--CTCTCTCC-C-TC--CAACAGCCCAGATA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4390701 93 + 7991924 GTGCGCCCACAGCAGCAGCAGCACGGGCTGTACCGCTT-CAGAGGCTCAGCCACCTC----CTCCAGGCTGG---C--CTCCTTCT-C-TG--CAGAGGACTGGCCT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 8387 70 + 44242 GGAAAGCCAAGGTC-------------------------CAGAGGCCCAGCCA---CAGGCTCCAGAGCAGG---A--CTCCCAGC-C-TC--CAGCCGCCGGAACC i speTri1.scaffold_128901 C 0 C 0 s ochPri2.scaffold_9426 6830 55 - 54875 ---------------------------------------CCGAGGCTCCGCTGAAGC----CAGCAGGTGCA---G--TTCCCACC-C-CA--TGGCGGACCTGGCA i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 130375 61 + 145505 ACA-----------------------------------TAGAAAG-TCAGCCT---CAGGCTCCAAAGCAGG---C--TTCCTTTCCCCTC--CAAAAGACTTAATA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10860528 61 - 65312493 ACA-----------------------------------CAGGAGG-TTGGCCT---CAGGCTCCAAAGCAGG---C--CTCCTTCCCCCTC--CAGCAGACTTCATA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58044210 84 - 61308211 GCAGAGGCCTGAAAGCAAC------------GCCAATCCAGAAGGCTCGGCCT---CAAGCTCCAGAGCACA---C--CTCCTTCCCC-TC--CAGCCAACTTAATA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 33410 83 + 132007 TCAGAGCCCCAGAGGCGGC------------GTGGGGACAGAAGACCTGGCC----TGGGGCCCAGAGCACA---C--TTCCTTCCCCTTC--CAGCAGACTTAAT- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59438162 84 - 64418924 GCAGAGCCCCAGACGTGGT------------GCTGGTACAAAAGGCCCAGCCG---CAGGCCCCAAAGCACA---C--CTCCTCCCCCTTC--CAGCAGGCTTAAT- i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 10908 87 + 14340 ACAGAGCCCCGGGGATGGC------------GCTGGCCCAGGAGGCGGGGCCT---CGGGCTCCAAAGCCTGCCCC--CTCCCTCCCC-TC--CAACAGACCCAGTG i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 16445 82 + 48268 ACGGAGCCCCGAAACTGGC------------GCTGGCCCAGAAGGCTGGGCC----CAGGCTCC-CAGCACG---C--CTCCTTCCCC-TC--CAGCAGACCCGACA i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 18313 72 + 24616 ACACAGCCACAGCCCCA-------------------TGCCAGGAGT------------GGGTCCACAGCATG---TAGCCCCAGGCTG-TAAGCACGCAACTTAATA i proCap1.scaffold_29042 I 4 C 0 s loxAfr3.scaffold_49 14434099 59 - 17734757 ACACA--------------------------------GCCCAGAGC------------AGGTCCACAGCATG---TAGCTCCAGGCTC-CCAGCACACGACTTAATA i loxAfr3.scaffold_49 I 4 C 0 s echTel1.scaffold_194555 5402 48 + 11139 -------------------------------------GTGGGGGGC------------AGGTCCAGGGAGTC---CCACTCCAGCCTC-TGGGC------CTTAACA i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 13850 78 + 20752 CCACAAGCCTGGCGGGT--------------------CCCCGGAGCTCAGTGG---CAGGGTCCAGAGCACG---T--CCGCACCCCC-TCTTCAGCAGACTTAATA i dasNov2.scaffold_28617 I 4 C 0 s macEug1.Scaffold23956 2332 88 - 25324 AGAAGACACCTGAGGTCCTTTGGTACAAAAAACCAGCACTGGaa------------aaaaaCTCATTCctgg---t--ttttttcctctcc--cagtGGACTTAATA i macEug1.Scaffold23956 I 1 C 0 s monDom5.chr2 304538500 77 - 541556283 ----------------------AAGAAGACCCTTGATGCAAAGGGTCAGTACAGGATAAAAATCCACCTTGA---T--TTTTTCCCCC-TC--CAGTGGACTTGATA i monDom5.chr2 C 0 C 0 e oryCun2.chrUn0958 19503 568 + 41507 I e tarSyr1.scaffold_507768 1050 0 + 1063 I e tupBel1.scaffold_124459.1-15939 12178 375 + 15939 I e micMur1.scaffold_15893 6794 2607 + 19765 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=1149364.000000 s hg19.chr17_gl000204_random 47388 86 + 81310 TTTTCTGTAATTTTAGTATATAT----TAATGCACTTCAAAGTGGTGAACATTATAGT-TATGATTATTACCTAAAGACTTCCTTTATAGC s calJac1.Contig5139 48044 86 + 225949 TTTTCTGTAATTTTCGTATATAT----TAATGCATTTCAAAGTGGCGAACATTATAGT-TATGATTATTACCTAAACACTTCCTTTATAGC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 46026 86 - 95547 TTTTCTGTAATTTTAGTATATAT----TAATGCACTTCAAAGTGATGAACATTATAGT-TACGATTATTACCTAAAGACTTCCTTTATAGC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75038622 86 + 78773432 TTTTCTGTAATTTTAGTATATAT----TAATGCACTTCAAAGTGATGAACATTATAGT-TACGATTATTACCTAAAGACTTCCTTTATAGC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16064703 86 + 17838096 TTTTCTGTAATTTTAGTATATAT----TAATGCACTTCAAAGTGGTGAACATTATAGT-TATGATTATTACCTAAAGACTTCCTTTATAGC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 16320 86 - 64270 TTTTCTGTAATTTTAGTATATAT----TAATGCACTTCAAAGTGGTGAACATTATAGT-TATGATTATTACCTAAAGACTTCCTTTATAGC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79477593 86 + 83384210 TTTTCTGTAATTTTAGTATATAT----TAATGCACTTCAAAGTGGTGAACATTATAGT-TATGATTATTACCTAAAGACTTCCTTTATAGC i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 28302 86 + 287808 TTTCCTATAATTTTAATCCATAT----TAATGCATTTCAAAGAGGCGACCATTATAGT-TAGGATTATTACCTAAAGACTTCCTTTCTAGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 12553 86 + 15939 CTCACGGCGATGTTAGCCGATAA----TGACGCATCTCGGAGTGACGCAGGTAATAGT-TGTGATTGTTACCTAAAGACTTCCTTTGGCGC i tupBel1.scaffold_124459.1-15939 I 375 C 0 s mm9.chr11 118760330 76 + 121843856 TCTTCTGTAATTCCAATATACGT----TAATGTGTCTCAACGTGCTGAGCTGTG--------GATGACTACCCAGA---CTCACTTCTCGA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4390794 86 + 7991924 TTTTCTGTGATTTTAGTGTACAA----TAACATTTCTCAAAGTGGCAGGCATTACACT-TATGATTATTACCTAAAGACTTCCTTTATAGC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 8457 84 + 44242 TTTTCTGCAATTTTAGTATATAT----TAATGCATCTCAAAGCGGCGGACATTATAGT-TACGATTATTACCCAAAGACTTCCC--ACAGC i speTri1.scaffold_128901 C 0 C 0 s ochPri2.scaffold_9426 6885 72 - 54875 TTGTCTGTCAGCTCAGCACACAC----ACTCATGCACTCAGGTGGTGGACGGTGCACTGTGCCTGGACTGCCCAGC--------------- i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 130436 83 + 145505 TTTTCTGTAATTTTAGTCTATAT----TAATGCATTTCAAAGTGGTGAACATTATAGT-TATG---ATTACCTAAAGACTTCCTTTATAGC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10860589 86 - 65312493 TTTTCTGTAATTTTAGTCTATAT----TAATGCATTTCAAAGTGGTGAACATTATAGT-TATGATTATTACCTAAAGACTTCCTTTATAGC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58044294 86 - 61308211 CTTTCTGTAATTTCAGTATATAT----TAATGCATTTCAAAGTGGTGCCCATTACAGT-TATGATTATTACCTAAAGACTTCCTTTATAGC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 33493 86 + 132007 TCTTCTGTAATTCTGGTGTGTAT----TAAAGCATCTCAAGGCAGTGCACATCACAGT-TACGATTATTACCCAAAGACTTCCCTTACAGC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59438246 86 - 64418924 TTTTCTGTAATGTTGGTGTATAT----TAATGCATTTCGAGGTAGTGCACATCACAGT-TATGATTATTACCTAAAGACTTCCTTTACAGC i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 10995 85 + 14340 CCTTCTGGAAT-CTGGGGTACAT----CAATGCCTTCCAAAGCGGCCAGCGTCACAGC-TATGATTATGACCGACACGCTTCCTCTGCAGC i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 16527 65 + 48268 CCCTCTGTGGT--TCCAGCCCATCATACACTGTGCTGCGAAGTGGCGAACGTCACGGT-CGTGACGAT----------------------- i pteVam1.scaffold_11245 C 0 M 472 s proCap1.scaffold_29042 18385 86 + 24616 TTTTCTGTAATTTTCATCTGTAT----TAATGCTTTTCAAAGTGGCGCACATTGCAGT-TATGATTATTACCTAAAGACTTCCTTTATAGG i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14434158 86 - 17734757 TATTCTGTAATATTCGTGTACAT----TAACGCTTTTCAAAGTGGCACATATTACAGT-CATCATTATTACCTAAAGACTTCCTTTATAGG i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_194555 5450 59 + 11139 CTGCCTGTGCTGT-----------------------------TGGTGCCCACGGGAGA-CGTGGACATGACCTGAAGGTTG--TTTGTGGC i echTel1.scaffold_194555 C 0 C 0 s dasNov2.scaffold_28617 13928 86 + 20752 TTTTCTGTAATTTCAGTATATAT----TAATGCATTTCAAAGTGGCGAACATTATAGC-TATGATTATTACCTAAAGACTTCCTTTATAAC i dasNov2.scaffold_28617 C 0 C 0 s macEug1.Scaffold23956 2420 85 - 25324 TTTTACACCATTTTAGTATATAT----TAATACA-TTCAAAGTGGCAAACATTATAGT-TATGATCATTACTTAAAGACTTCCTTTATAAC i macEug1.Scaffold23956 C 0 C 0 s monDom5.chr2 304538577 69 - 541556283 TTTTACACAATTTTAGTACATAT----AAATGCATTC--AAATAGCAAATAT-ATATC-T--------------AAAACTTCCTTTATAGT i monDom5.chr2 C 0 C 0 e oryCun2.chrUn0958 19503 568 + 41507 I e tarSyr1.scaffold_507768 1050 0 + 1063 I e micMur1.scaffold_15893 6794 2607 + 19765 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=1438136.000000 s hg19.chr17_gl000204_random 47474 178 + 81310 CCTCATTTTCCAGTGC-TC---ATT-ACTTTCTGAAAAATTATCCT-TGGGGGCTGAAATTTTCCTAGTCTGGTCTTGTGAGTTTT-CTTCTTAGGTTTTAAGCAAAAC-ATATC-------------CGG-AA--------------------G-GGG---GAGAAA----TTACTTCTCCCAAAGTCAGTCTCCTTGGTGACTTCTG-----------------CCAAGGAAAGA--ACCCCA--TG s calJac1.Contig5139 48130 178 + 225949 CCTCATTTTCTAGTGC-TC---ATT-ACTTTCTGAAAAATTATGCT-TGGAGCCTGAAATTTCCCCAGTCTGGTCTTGTGAGTTTT-CTTCTTAGGTTTTGAGCAAAAC-ATATC-------------CAG-GA--------------------G-CAG---GAGAAA----TGACTTCTCCCTACATCAGTCTCCTTGGTGACTTCTG-----------------CCAAGGAAAGA--ATCCCA--TG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 46112 178 - 95547 CCTCATTTTCTAGTGC-TC---ATT-ACTTTCTGAAAAATTATCCT-TGGGGGCTGAAATTTTCCTAGTCTGGTCTTGTGAGTTTT-CTTCTTAGGTTTTGAGCAAAAC-ATACC-------------CAG-AA--------------------G-GGG---GAGAAA----TTACTTCTCCCAAAGTCAGTCTCCTGGGTGACTTGTA-----------------CCAAGGAAAGA--ACCCCG--TG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75038708 178 + 78773432 CCTCATTTTCTAGTGC-TC---ATT-ACTTTCTGAAAAATTATCCT-TGGGGGCTGAAATTTTCCTAGTCTGGTCTTGTGAGTTTT-CTTCTTAGATTTTGAGCAAAAC-ATACC-------------CGG-AA--------------------C-GGG---GAGAAA----TTACTTCTCCCAAAGTCAGTCTCCTGGGTGACTTGTA-----------------CCAAGGAAAGA--ACCCCG--TG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16064789 177 + 17838096 CCTCATTTTCTAGTGC-TC---ATT-ACTTTCTAAAAAATTATCCT-TGGGGGCTGAAATTTTCCTAGTCTGGTCTTGTGAGTTTT-CTTCTTAGGTTTTGAGCAAAAC-ATATC-------------CGG-AA--------------------G-GGG---GAGAAA----TTACTTCTCCCAAAGTCA-TCTCCTTGGTGACTTCTG-----------------CCAAGGAAAGA--ACCCCA--CG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 16406 178 - 64270 CCTCATTTTCCAGTGC-TC---ATT-ACTTTCTGAAAAATTATCCT-TGGGGGCTGAAATTTTCCTAGTCTGGTCTTGTGAGTTTT-CTTCTTAGGTTTTAAGCAAAAC-ATATC-------------CNG-AA--------------------G-NGG---GAGAAA----TTACTTCTCCCAAAGTCAGCCTCCTTGGTGACTTCTG-----------------CCAAGGAAAGA--ACCCCA--TG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79477679 178 + 83384210 CCTCATTTTCCAGTGC-TC---ATT-ACTTTCTGAAAAATTATCCT-TGGGGGCTGAAATTTTCCTAGTCTGGTCTTGTGAGTTTT-CTTCTTAGGTTTTAAGCAAAAC-ATATC-------------CGG-AA--------------------G-GGG---GAGAAA----TTACTTCTCCCAAAGTCAGTCTCCTTGGTGACTTCTG-----------------CCAAGGAAAGA--ACCCCA--TG i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 28388 179 + 287808 CCTCATTTTCTAGTAT-GC---ATT-ACTTTCCAAAAAATTATCCT-TAGAGGCTGAAATTTTCCAAGTCTAGTCTGGTGAGTTTC-CTTCTTAGAATCTGAGCAAACC-AAATG-------------TGGAAA--------------------A-GGG---GAGAGA----TGGGTTCTCCCAAAGTCAGCCTCTTTTTTACTTCTTC-----------------TTTGAGAGAAG--ACCTCC--TG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 12639 185 + 15939 CCTCATCTTCCAGTGC-TC---GCT-ACTTTCCGAGAAGTTATCCA-TGGGAGCTGAAATTTCCCAAGTCTGGTCTTGTGAGTTTT-TTCCTTAGGATTTGAGCAAAGC-ATACT-------------GGG-AAAGAGGT--------------G-GAG---GGGGGA----TTAG-TCTCCTGAAATTAGCCTTTCCGAAGACTTCTG-----------------ACAATGAAAACTTAACTCC--TA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118760406 170 + 121843856 CTTCATTTTCTAGCAC-TG---ATTCAGTTTACGGAAAACCATCCT-TGGGGCTTGCGG-TTTCCAAGGTAGATCTTGTGTGTCTC-CTTCATGGGATTTGAGGGAAAC-ATACC-------------AAG-GAA-------------------T-GGG---GAGAGA----TTTGTTTCCTGGAAGACGGGCAGGCTGATG--------------------------GAGAATGGA--AATCAG--CC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4390880 176 + 7991924 CTTCATTTGCCAATGC-TC---ATT-ACTTCCTGAAAAATTATCCT-TGGGAACTGAAATTTTCCAAGACTGGTCTTGTGAGTTTT-TT---TAGGATCTGGGCAAAAC-ATATT-------------TGG-GAA-------------------G-GAG---GTGAAA----TCAGTGCTCCTGAAGTCAGTCTCCTTGGTGACTTCTG-----------------ACAGGAAAGAG--AAACCT--CT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 8541 177 + 44242 CTTCATCTTCCAGTGC-TC---ATT-ACTTTCTGAAAAATTATCCT-TGGGGACTGAATTTGTCCAAGGCTG-TCTTGTGGGGGTT-TTTCGTAGGATTTGGGCAACAC-GCATT-------------TGG-GAA-------------------G-AGG---GAGGAA----TTAGC-CTCCTGAAGTCAGTCTCCTTGGTGACATCTG-----------------ACAAGGAGAGA--ATGCCA--TC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 20071 151 + 41507 CCTCGTTTTCCTGCGC-------TC-GTCACCTGAGGATCCACCCT-CGGG--CCGAAGCCTTCCAGGTCCGCTCCTGCGAGTTTT-CTCCTTGGGATTTCGGTGGAACGATGCA-------------GAG-AG-----------------------------------------GTCGGGACACAGCCCGTCCCCGTGGCGACTC---------------------------GTGG--ACATGT--CT i oryCun2.chrUn0958 I 568 C 0 s ochPri2.scaffold_9426 6957 143 - 54875 ------TGCCCAGAGC-GT---ACC-ACCTCCTGAAAAATTACCTTCCGGG--CTGACATTTGCCCAGTCCACG--TGAGAGCTTT----CCTAGGATTTCTGCAAGGC-ACCCT-------------CAG-AA-----------------------------------------GCTCCCCCGAGGCCTGCCTCCTTGGTGACTC---------------------------AAGG--CAGCCT--CT i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 130519 194 + 145505 CCTCATTTTCTAGCGT-TC---ATT-ACTTTCTGAAAAATTATCCT-TGGGGGCGGAAGTTTTCCAAGTCTGGTCTTGTGAGTTTT-CTTCTTAGGATCTGAGCAAAAC-ATACTATTGTGTCCATGACGG-GA--------------------AGGGG---GGCAGATGGCTTAGCTCTCCCCAAGTCAGTCTCCGTGGTGACTTCTG-----------------ACAAGGAAAGA--ATAACG---- i turTru1.scaffold_106006 C 0 I 13 s bosTau4.chr19 10860675 190 - 65312493 CCTCATTTTCTAGCGT-TC---ATT-ACTTTCTGAAAAATTATCCT-TGGGGCCCGAAATTTTCCAAGTCTGGTCTTGTGGGTTTTCCTTCTTAGGATCTGAGCAAAAC-ATACGATTGTGTCCATGATGG-GC--------------------A-GGG---GGCAGGTGGTTTAGCGCTCCC----TCAGTCTCCGTGGTGACTTCTG-----------------ACGAGGAAAGA--ATGGTG---- i bosTau4.chr19 C 0 I 6 s equCab2.chr11 58044380 190 - 61308211 CCTCATTTTCCAGTGC-TC---ATT-ACTTTCTGAAAAATTATCCT-TGGGGGCTG-AATTTTCCAAGTCTGGTCTTGTGAGTTTT-TTCCTTAGGACTTGAGCAAAAC-ATATTATTGTGTCTGTGATGG-GC--------------------G-GGG---AGGGGA----TGCGTGCTCCCTAAGTCGGTCTGCGTGGTGCCTTCTG-----------------ACAAGGAAAGA--ACAACGTC-- i equCab2.chr11 C 0 I 28 s felCat3.scaffold_206428 33579 204 + 132007 CCTCA-TTTCCAGCGC-TT---ATT-ACTTTCGGAAAAATCATCCT-CGGGGGCCCAAATTTCCCAAGTCTGGTCTTGGGAGTTTT-CGTCTTAGGATCTGAGAAAAAC-A--TTATTGTGTCCGTGATGG-GGGAGAGAATACGGCGGGGGTTG-GGG---GGGGG------GGATCCTTCCTTAGCTGATCTGGATGTCGACACACA-----------------GCCAAGAAAGA--ATAACA---- i felCat3.scaffold_206428 C 0 I 10 s canFam2.chr9 59438332 188 - 64418924 CCTCA-TTTCTAGCGC-TC---ATT-ACTTTCTGAAAAATTATCCT-CGGGGGCCGAAATTTTCCAAGTCTGGTCTTGTGAGTTTT-CTTCTTAGGATCCAAGCAAAAC-ATGTTATTGTGTCCATGATGG-GA--------------------A-GGG---GGAGG------GGGCTCTTCCTTAGTTGGTCTCCGTGGTGACACAGA-----------------GCCAAGAAAGA--ATAACATG-- i canFam2.chr9 C 0 I 36 s myoLuc1.scaffold_4816 11080 186 + 14340 CTCGT-TTTCCAGCGCTTC---GTT-GCTTCCTGAGAAATCACCCT---GGGGTTCGATGTTCCCCAGTCTGGTCTTAGGCGTGTT-CTTCTTAGGATCTGAGCAAAAC-ATACGCTCACGTCCACGGCAG-GA--------------------A-GGG---GGGTGA-----TTATTCTCCCT--GTCAGTCTCCGTGGTGACGTGTC-----------------ACGAGGACAGAGGACACCA---- i myoLuc1.scaffold_4816 C 0 C 0 s proCap1.scaffold_29042 18471 196 + 24616 CCTCATTTTCCAGTGC-TC---ATT-ACTCTGGGAGAAATTCTCCT-CGGGGGCTAGAATTTTCCAAGTCAGGTCTTGAGAGTCGG-CTTCTCAGGATTTGAGCCAAAT-ACATTACTGCATCTGTGATGG-GGGGT-----------------G-GGGGCAGAGGGA----GGAGGTCTCCCTCGGTAAGTCTCCGCGGTGACTCCCA-----------------ACAAGGAAAG---ATCACA--TT i proCap1.scaffold_29042 C 0 I 13 s loxAfr3.scaffold_49 14434244 194 - 17734757 CCTCATTTTCCAGTGC-GC---ATT-ACTCTCAGAGAAATTTTCCT-CAGGGGCTGGAATTTCTCAAGTCAGGTCTTGAGAATTTG-CGTCTCAGGATTTGAGCCAAAT-CTATTACTGAGTTCATGACGG-GG--------------------A-GGGGATGAGGAA----TGCAGTCTCCCTAAGTAAGTCTCCGTGGTGACTTCCG-----------------ACAATGACAGA--ATCATG--TT i loxAfr3.scaffold_49 C 0 I 13 s echTel1.scaffold_194555 5509 170 + 11139 CCTCCCTCTCAGGGGT-CCCGAATC-ACAC-----GGAATTGCCCT-CAGGGGCCGG-TTCTTCCAGGGTAGGTGGGGAGAACCTG-TTTCT-GGCATCTGAGCTTCAG-CTCCAACCCAGTCCAGGATGG-GG--------------------C-GGGATCGAGGGG----------CTCTCTCAGCC--TCCCTGCAG-GAC--CCA-----------------GGAGGAGCAG------------- i echTel1.scaffold_194555 C 0 I 9 s dasNov2.scaffold_28617 14014 191 + 20752 CCTCATTTTCTAGAGC-TC---ATT-ACTTGCCAAAAAATTATCCT-TGGGGACCGAGATTTTTCAAAGCTGGTCTCGAGGGTTTC-CTTCTTAGGATTGGAGCAAAAT-ATACTTTTGCAGTCATGATGG-GA--------------------A-AAG---GGGAAA----TTAGTTCTCCCTAAGTAAGTCTCCACAAGGGTTGCTG-----------------AAAACTAAAGT--AAAACA--TT i dasNov2.scaffold_28617 C 0 I 14 s macEug1.Scaffold23956 2505 188 - 25324 CCTCATTTTCAAATGC-TC---ATTTGCTTTCTGAAGGAATATCCT--------TTAAATTTTCCATGTTCAGTC----AAGTTTT-CTTCTCAGGAAAAGAGCAAGCT-AAATTGATGT--------TTG-GA--------------------A-GGG---GAGT------CTAGTTATCGTTGACTAAGTCTCCTTGTTGACTTCTGAATGCTATagttatggaaaaataaaaga--atcaaa--ta i macEug1.Scaffold23956 C 0 C 0 s monDom5.chr2 304538646 180 - 541556283 ACTCATTTTCAAATGT-TT---GTTTACTTTCTGAAAAATTATCCT-TTGAAACTGAAATTTTCCATATCCAATC----AAGTATT-CTTCTCAAGAATTGAGCAAACT-AAACTGTTGT--------TTG-GA--------------------A-GGA---GAGT------CTAGTTATTATTTACTAAGTTTTCTTGGAGACTTTTGAAAACTAAAG-------GTAAGGAAAAG------------ i monDom5.chr2 C 0 C 0 e tarSyr1.scaffold_507768 1050 0 + 1063 I e micMur1.scaffold_15893 6794 2607 + 19765 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e pteVam1.scaffold_11245 16592 472 + 48268 M e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=-76828.000000 s hg19.chr17_gl000204_random 47652 10 + 81310 GGAAG-GGGGC s calJac1.Contig5139 48308 10 + 225949 GGAAG-GGGGC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 46290 11 - 95547 GGAAATGGGGC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75038886 11 + 78773432 GGAAATGAGGC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16064966 9 + 17838096 GGAA--GGGGC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 16584 10 - 64270 GGAAG-GGGGC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79477857 10 + 83384210 GGAAG-GGGGC i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 28567 9 + 287808 CGGA--GGGCA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 12824 9 + 15939 AGCA--GGGAG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118760576 7 + 121843856 TGAAG-GA--- i mm9.chr11 C 0 I 1 s cavPor3.scaffold_76 4391056 10 + 7991924 TAAAG-GGGGT i cavPor3.scaffold_76 C 0 I 1 s speTri1.scaffold_128901 8718 10 + 44242 AGAGC-GGGGA i speTri1.scaffold_128901 C 0 I 1 s oryCun2.chrUn0958 20222 7 + 41507 AAAGG-GA--- i oryCun2.chrUn0958 C 0 I 4 s ochPri2.scaffold_9426 7100 7 - 54875 AACGG-GA--- i ochPri2.scaffold_9426 C 0 I 2802 s turTru1.scaffold_106006 130726 10 + 145505 GGGCA-GGACT i turTru1.scaffold_106006 I 13 I 2 s bosTau4.chr19 10860871 10 - 65312493 GGGCA-GGACT i bosTau4.chr19 I 6 I 2 s equCab2.chr11 58044598 10 - 61308211 GGCAG-AGAGC i equCab2.chr11 I 28 I 2 s felCat3.scaffold_206428 33793 10 + 132007 GGCAG-AGACC i felCat3.scaffold_206428 I 10 I 2 s canFam2.chr9 59438556 10 - 64418924 GGCAG-AGACC i canFam2.chr9 I 36 I 2 s myoLuc1.scaffold_4816 11266 3 + 14340 ------GGG-- i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 17071 8 + 48268 GGTAG-AGG-- i pteVam1.scaffold_11245 M 472 C 0 s proCap1.scaffold_29042 18680 10 + 24616 GGACA-GAGCC i proCap1.scaffold_29042 I 13 I 2 s loxAfr3.scaffold_49 14434451 10 - 17734757 GGGCA-GAGAC i loxAfr3.scaffold_49 I 13 I 3 s echTel1.scaffold_194555 5688 8 + 11139 GGG---GAAGC i echTel1.scaffold_194555 I 9 I 3 s dasNov2.scaffold_28617 14219 10 + 20752 GGGCG-GAGAG i dasNov2.scaffold_28617 I 14 I 3 s macEug1.Scaffold23956 2693 4 - 25324 aaca------- i macEug1.Scaffold23956 C 0 C 0 s monDom5.chr2 304538826 10 - 541556283 TAAAA-GAGCC i monDom5.chr2 C 0 C 0 e tarSyr1.scaffold_507768 1050 0 + 1063 I e micMur1.scaffold_15893 6794 2607 + 19765 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=283806.000000 s hg19.chr17_gl000204_random 47662 73 + 81310 --GGGCTGTGTCTTTAGCATGTAGATA-CTGAT--ACTGTTATCAGTGATCTGGCCTTAGTTGTGCCCGTCTGTTCTG s calJac1.Contig5139 48318 73 + 225949 --AGCCTGTGTCTTTAGCATGTAGATA-CTGAT--ACTGGTATCAGTGACCTGGCCTGAGGTGCGCCTGTCTGTTCTG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 46301 71 - 95547 --GAGCTGTGTCTT-AGCATGTAGATA-CTGAT--ACTATTATCAGTGACCT-GTCTTAGTTGTGCCCGTCTGTTCTG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75038897 72 + 78773432 --GAGCTGTGTCTTTAGCATGTAGATA-CTGAT--ACTGTTATCAGTGACCT-GTCTTAGTTGTGCCCGTCTGTTCTG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16064975 73 + 17838096 --GGGCCGTGTCTTTAGCATGTAGATA-CTGAT--ACTGTTATCAGTGATCTGGCCTTAGTTGTGCCCGTCTGTTCTG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 16594 73 - 64270 --GGGCTGCGTCTTNAGCATGTAGATA-CTGAT--ACTGTTATCAGTGACCTGGCCTTAGTTGTGCCCGTCTGTTCTG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79477867 73 + 83384210 --GGGCTGTGTCTTTAGCATGTAGATA-CTGAT--ACTGTTATCAGTGATCTGGCCTTAGTTGTGCCCGTCTGTTCTG i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 28576 67 + 287808 --GGGCCGCACCTTCAGCACCGAAAGA-CCCAC---CCGCTGGCGGGGAGCTGGTCTCA-CTGTGCCCGGCTAT---- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 12833 53 + 15939 --GGGCTGCCTCTTTAACATGTGAGGC-CCGGCCCACGGTTA----------------------GCCTGGCTGTTCTC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118760584 53 + 121843856 --GGGC---ACCTTCAACGTACAAAAC-CCGAT--CTCACCG-------CTTAGCCCT----------GTCTGCTCTG i mm9.chr11 I 1 C 0 s cavPor3.scaffold_76 4391067 55 + 7991924 --GGGCTGAGTCTTTAACATGCAAATG-AAGAT--TCCTTTA-------TTTGGTTTT----------GTCTG-TTGG i cavPor3.scaffold_76 I 1 C 0 s speTri1.scaffold_128901 8729 56 + 44242 --AGGCCGCGTCGTCACTGTGCAGACC-CCGGT--TCCATTA-------TTCAGTTCT----------GTCTACTGTG i speTri1.scaffold_128901 I 1 C 0 s oryCun2.chrUn0958 20233 49 + 41507 --GGGCTG-CCCCTCGGCACAGAAACA-CCACT--GCCATTA-------CCC--CCGT----------GTCCC----G i oryCun2.chrUn0958 I 4 C 0 s turTru1.scaffold_106006 130738 66 + 145505 --GAGCTGCAC-TTTAACATGTCAGCA-CTGAT--A------TCTATGACCTGGTTTTGGTTTTGCCCATCTGTTCTG i turTru1.scaffold_106006 I 2 C 0 s bosTau4.chr19 10860883 67 - 65312493 --GCGCTGCACTTTTAACATGTCAGCA-CTGAT--A------TCGATGACCTGGTTTTGGTTTTGCCCATCTGTTCTG i bosTau4.chr19 I 2 C 0 s equCab2.chr11 58044610 69 - 61308211 -----CTGCGTTTCTCGCGTGGAAATA-CTGAT--ACTCTTAGCAAGGACCCGCTTCTAGTTTTG-CCGTCTGTTCCG i equCab2.chr11 I 2 C 0 s felCat3.scaffold_206428 33805 73 + 132007 --GTGCTGCATTTTTAACACATAAATA-CAGAT--ACTATTGTCAATGACCTGGTTTTATTTGTACCCATCTGTTCTG i felCat3.scaffold_206428 I 2 C 0 s canFam2.chr9 59438568 73 - 64418924 --ACGCTACAGTTCCAACACATAAATA-CAGAC--ACTGTTATCAATGACCTGGTTTCAGTTTTACCCATCTGTTCTG i canFam2.chr9 I 2 C 0 s myoLuc1.scaffold_4816 11269 58 + 14340 -----CCGCCCTGT--GAGCGTAAACG-CCGCC--ACCCT--------CCCCGGGGGCAGCTCTGCCCGTCTG--CGC i myoLuc1.scaffold_4816 C 0 I 355 s pteVam1.scaffold_11245 17079 70 + 48268 -----CGGGACTGTCGACACGCGAACA-CCGAT--ACCCTGAACGGTGACCCGGTTTCAGGCTTGCCCATCTGTTCGC i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_29042 18692 72 + 24616 --ATGCTATATTTTTCAAATGTAAATA-CAGAT--ACCGTTATCAATGACCTAGTTTCGCATTTG-CTGTCTGCTCTG i proCap1.scaffold_29042 I 2 C 0 s loxAfr3.scaffold_49 14434464 72 - 17734757 --GTGCGGTATTTTTAACATGTAAATA-CAGCT--GCCATTATCAATGACCTAGTTTTAGATCCG-CCGTCTGTTCTA i loxAfr3.scaffold_49 I 3 C 0 s echTel1.scaffold_194555 5699 60 + 11139 --G--------TTTTAACATGTAAATA-CGCA-----CGTTATCAATGACCTAGTTTGGGA-AGG-CCCTCCGCTCCA i echTel1.scaffold_194555 I 3 C 0 s dasNov2.scaffold_28617 14232 73 + 20752 --GTGTTGTATTTTTAACATGTAAGTA-CAGAT--ACCACTCACAACGACCTAGTTTGGGTTGTGCCCGTCTGTTCTC i dasNov2.scaffold_28617 I 3 C 0 s macEug1.Scaffold23956 2697 64 - 25324 --------tattttt-gcaTGCAAATATCTGAT--A---TTATCAGTAGCCTAGGCTTTATTTTGCATGCCTCTTCCA i macEug1.Scaffold23956 C 0 I 3 s monDom5.chr2 304538836 75 - 541556283 ACATAATGTATTTTT-GCATATAAATACCTGAC--AGCATTAAGAATAAACTGAGTTTTATTTTGCTTGTCTGTTCCA i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_507768 1050 0 + 1063 I e micMur1.scaffold_15893 6794 2607 + 19765 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=-98231.000000 s hg19.chr17_gl000204_random 47735 33 + 81310 G-AGAGACGGCTCT---ATTTTAA--AAGT----------CCAAGA----GGC s calJac1.Contig5139 48391 25 + 225949 G-AGAGATGGCTCT---ATTTTTA--AAGT----------C------------ i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 46372 33 - 95547 G-AGAGATGGCTCT---ATTTTAA--AAGT----------CTAAGA----GGC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75038969 33 + 78773432 G-AGAGATGGCTCT---ATTTTAA--AAGT----------CTAAGA----GGC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16065048 33 + 17838096 G-AGAGACGGCTCT---ATTTTGA--AAGT----------CCAAGA----GGC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 16667 33 - 64270 G-AGAGACGGCTCT---ATTTTAA--AAGT----------CCAAGA----GGC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79477940 33 + 83384210 G-AGAGACGGCTCT---ATTTTAA--AAGT----------CCAAGA----GGC i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 43 44 + 4992 CAAGAGACAGCTCG---GTCTCTG--AAACAAGAGCCCACCCCGAG----TGG i micMur1.scaffold_72647 n 2607 C 0 s otoGar1.scaffold_94362.1-287808 28643 41 + 287808 --GGAGACTGATCT---GTTTCTA--GAGTTAGAGTCTG-ACGGAA----AGG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 12886 35 + 15939 C-AGAGGTGGCTGG---AGTTTTAGCGGGT----------TCAGTC----TAG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118760637 39 + 121843856 A-GGAGA---TCTC---AATTTCA--AAGTGGAAG-----TTGGTCTTTAGGG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4391122 38 + 7991924 A-GGAGACAGCCCT---ATTTTTA--CAGTGAAAG-----CTCAAC----GGG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 8785 38 + 44242 A-GGTGACAGTCCT---ATCTTAA--AAGTGAGAG-----CTCAGT----GGG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 20282 36 + 41507 A-CGAGCCGGCTCT---------C--CGGCAAGAG-----CTCAGTCCCCGCG i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 130804 29 + 145505 -TCCAGACAGTGCA---ACTTCTG--AAATGGGAT------------------ i turTru1.scaffold_106006 C 0 I 14 s bosTau4.chr19 10860950 29 - 65312493 -TCCAGACAGTTCT---ACTTCTG--AAATGGGAT------------------ i bosTau4.chr19 C 0 I 14 s equCab2.chr11 58044679 29 - 61308211 -TACAGACAGTTCT---ACTTTTA--AAATGAGAT------------------ i equCab2.chr11 C 0 I 18 s felCat3.scaffold_206428 33878 29 + 132007 -TGCAGACACTTCT---ACTTTTA--AAATGAGAT------------------ i felCat3.scaffold_206428 C 0 I 32 s canFam2.chr9 59438641 29 - 64418924 -TGCAGACACTTCT---ACTTTTA--AAATGAGAT------------------ i canFam2.chr9 C 0 I 14 s pteVam1.scaffold_11245 17149 29 + 48268 -TACAGACAGTTCT---ACTTTTA--AAACGAGAC------------------ i pteVam1.scaffold_11245 C 0 I 15 s proCap1.scaffold_29042 18764 42 + 24616 -TAGAGATGGTTCT---ATTTTTA--AAATGAGAT-----TTCACTCTAAAAG i proCap1.scaffold_29042 C 0 I 1 s loxAfr3.scaffold_49 14434536 42 - 17734757 -TAGAGATGGTTCT---ATTTTTA--CAATGAGAT-----TTCACTCTGAATG i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_194555 5759 42 + 11139 -CTGAGATGCTTCT---ATTTTTA--AAAGGAGAG-----TTCGTGCTCAGTG i echTel1.scaffold_194555 C 0 I 9 s dasNov2.scaffold_28617 14305 41 + 20752 -CAGAGACAGGTCT---ATTTTTA---AATGAGAT-----TTCAATCTAAATG i dasNov2.scaffold_28617 C 0 I 1 s macEug1.Scaffold23956 2764 38 - 25324 -GAacaattctttt---atttgaa--aaaggAGAT-----CCTAAG----TGC i macEug1.Scaffold23956 I 3 C 0 s monDom5.chr2 304538911 41 - 541556283 -TTGGGATAATTCTTTTATTTTAT--AAGCAAGGA-----GTTAAG----TGC i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_507768 1050 0 + 1063 I e myoLuc1.scaffold_4816 11327 355 + 14340 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=-424868.000000 s hg19.chr17_gl000204_random 47768 39 + 81310 GGGGA-GG----TA----CCCATGC---GACACTC---------------AT---CT--TG----CATGCTGCAG s calJac1.Contig5139 48416 34 + 225949 ------------TC----TCCACAC---GACATTC---------------AT---CTTGTG----TATGCCGAAG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 46405 39 - 95547 GGGGA-GG----TA----CCTGTGC---AACACTC---------------AT---CT--TG----CATGCTGCAG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75039002 39 + 78773432 GGGGA-GG----TA----CCCATGC---AACACTC---------------AT---CT--TG----CATGCTGCAG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16065081 39 + 17838096 GGGGA-GG----TA----CCCATGC---GACACTC---------------AT---CT--TG----CCTGCTGCGG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 16700 39 - 64270 GGGGA-GG----TA----CCCATGC---TACACTC---------------AT---CT--TG----CATGCTGCAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79477973 39 + 83384210 GGGGA-GG----TA----CCCATGC---GACACTC---------------AT---CT--TG----CATGCTGCAG i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 87 38 + 4992 GGAGA-GG----TG----CCCGTGC---AACCT-C---------------GG---CT--TG----CCCGTTTAAG i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 28684 39 + 287808 AGGGA-AA----TA----CCTGTGC---TACGTCC---------------AC---CT--CG----CATGCTTGAA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 12921 38 + 15939 GTGGG-GA----CA----CCTACAC---G-CAATC---------------GC---TT--GG----CATGCTTCGG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118760676 32 + 121843856 CTGGT-G-----------CCCCTGT---GACATCC---------------CT---AC--TG--------CTGAAG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4391160 35 + 7991924 GGAAG-A-----------CCTCTAC---AGCACTC---------------CTTTGGT--AG--------CTGAAG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 8823 42 + 44242 GTGGA-GG----GGGCACTCCCTGC---CATGGTC---------------ATCGTGC--AG--------CTGAAG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 20318 33 + 41507 GCAGA-AA----CA----CGCATGC---CACGAGC---------------AT---GT--TGCGTG---------- i oryCun2.chrUn0958 C 0 I 1124 s turTru1.scaffold_106006 130847 39 + 145505 GGGAA-AG----CA----CCCATGC---ACCATTCATTTTACAAG------------------------CTTAAG i turTru1.scaffold_106006 I 14 C 0 s bosTau4.chr19 10860993 39 - 65312493 GGGAA-AG----CA----CCCATGC---ACCATTCGTTTTACAAG------------------------CTTAAG i bosTau4.chr19 I 14 C 0 s equCab2.chr11 58044726 20 - 61308211 AGAGC-AA----CA----TTCACTC----------------------------------------------TACA i equCab2.chr11 I 18 C 0 s felCat3.scaffold_206428 33939 40 + 132007 GGGGGTAG----AA----CCCACGCCACATTGGTT---TTACATG------------------------CTTAAG i felCat3.scaffold_206428 I 32 C 0 s canFam2.chr9 59438684 22 - 64418924 AGGGA-AG----CA----CCCATGC--------------------------------------------ATTTAG i canFam2.chr9 I 14 C 0 s myoLuc1.scaffold_4816 11682 37 + 14340 GGGGA-AG----CC----CCCGCGG---ACAGTCCG--TGTCCTG------------------------CTGACG i myoLuc1.scaffold_4816 I 355 C 0 s pteVam1.scaffold_11245 17193 20 + 48268 ---AA-AG----CA----CCCACGC---GTAAGCA---------------------------------------- i pteVam1.scaffold_11245 I 15 C 0 s proCap1.scaffold_29042 18807 39 + 24616 GGGGA-AG----TA----CCCAAGC---CATCCTCATCTGACGTG------------------------CCAGAG i proCap1.scaffold_29042 I 1 I 1037 s loxAfr3.scaffold_49 14434578 38 - 17734757 GTGGA-AG----TA----CCCATG----CATGCTCATTTGACATG------------------------CCTAAG i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_194555 5810 24 + 11139 GGAGG-GG----AG----CCCATGC---AACACTCA--------------------------------------- i echTel1.scaffold_194555 I 9 I 1715 s dasNov2.scaffold_28617 14347 38 + 20752 GGAAG-AG----TT----CCCGTGC---AACATTCATTTTACATG------------------------CTAAA- i dasNov2.scaffold_28617 I 1 C 0 s macEug1.Scaffold23956 2802 42 - 25324 -AAAA-AGCTCTTA----CCAATGA---AACATTAGTATTACATATTAAAA------------------------ i macEug1.Scaffold23956 C 0 C 0 s monDom5.chr2 304538952 42 - 541556283 -AAAA-AGACCTTA----TCAATGA---AACATTAATATTACATAATATAA------------------------ i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_507768 1050 0 + 1063 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=406950.000000 s hg19.chr17_gl000204_random 47807 103 + 81310 CCTGGGCAAGTCAGGAAAG-TGAAT--GCTGGTTA------TGGCAATGCTGCCGAC------GCACACACAC------AAGCAGACGT--A-T-TTTCCAACACA------AA--GTGCAGATCTGCAGAAAGTC s calJac1.Contig5139 48450 100 + 225949 CATGGGCGAGTCGGGACAC-TGAAC--GCTGCTTA------TTGCCATGCTGCTGAT------G--CACACGC------AGGCAGACGT--A-T-TTTCCAACATG------AG--GGG-AGATCTGCAGAAAGGC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 46444 101 - 95547 CCTGGGC-AGTCAGGAAAG-TGAAT--GCTGGTTA------TGGCAACGCTGCCAAC------GCACACACAC------AGGCAGAT-T--A-T-TTTCAAACACA------AA--GGGCAGATCTGCAGAAAGCC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75039041 103 + 78773432 CCTGGGCAAGTCAGGAAAG-CGAAT--GCTGGTTA------TGGCAACGCTGCCAAC------GCACACACAC------AGGCAGATGT--A-T-TTTCAAACACA------AA--GGGCAGATCTGCAGAAAGCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16065120 103 + 17838096 CCTGAGCAAGTCAGGAAAG-TGAAT--GCTGGTTA------TGGCAATGCTGCCGAC------GCACACACAC------AAGGAGATGT--A-T-TTTCCAACACA------AA--GGGCAGATCTGCAGAAAGTC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 16739 103 - 64270 CCTGGGCAAGTCAGGAAAG-TGAAT--GCTGGTTA------TGGCAATGCTGCCGAT------GCACACACAC------AAGCAGACGT--A-T-TTTCCAACACA------AA--GTGCAGATCTGCAGAAAGTC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79478012 103 + 83384210 CCTGGGCAAGTCAGGAAAG-TGAAT--GCTGGTTA------TGGCAATGCTGCCGAC------GCACACACAC------AAGCAGACGT--A-T-TTTCCAACACA------AA--GTGCAGATCTGCAGAAAGTC i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 125 104 + 4992 CACGGACTCGTCAGGAGAG-CAAAG--GCCGGTCA------TTGCCAGACTGTCGAC------GCGCACGCAC------AGGTGGACATGCC-C-TTTCCGAGGCG------AG--G-GCAAACGTGCAGGTGGTC i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 28723 102 + 287808 CACAGACAAGACAGAAAAG-CAAAC--ACTGGCCA------CTGTGATGCTGTCGAC------CCCCA--CAC------AGGAGGATGTGCA-C-ATTCCAGGACA------CA--A-GCAAACCTGAGGAGAGGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 12959 105 + 15939 CGGGGAC-CGTCGGG-GAG-CAGAG--GCTGGT-G------CTACAGCACTGTCGA--------CACACATAT------GGCCAGACGT--G-TATTTCCTACACGTTTTCTAA--GGGCAAACTTGCAGGACGTC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118760708 88 + 121843856 TACGGATGGGGCAGGAAAG-CTAAG--GCCAGCCA------T----------------------CACAGAGAT----GAAACTAGACCTGCA-T-TTTCTAATTTA------AG--G---CAACTAGTCTGAAGTC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4391195 104 + 7991924 CACGGACAAGTCAGGAAAG-CAAAT--GCCAATTA------CTGGAATACTGTGGAT------GCACAAAAAT------AGCTAGACATGTA-T-TTTCCAACGCA------AG--G-GCAAACTTGCAGAAAGTC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 8865 92 + 44242 TGCAGGCCCGTCAGGGATG-CCGAGAAGGTGACCA------C--------------A------GCACGGGAAG------GGCTGGACATGTA-T-TTTGCAAAGCA------AA--G-GCAGACTTTCAGAAAGTC i speTri1.scaffold_128901 C 0 C 0 s turTru1.scaffold_106006 130886 104 + 145505 CACAGACAAGTCAGGACTG-CAAGT--GCTAATCA------CTGCAATACTGTCAAT------GCATGGATAC------AGCTGGACACTTA-T-TTTCCAACACA------AA--G-GCAACCTTGGGGAGAGAG i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10861032 104 - 65312493 CACAGACAAGTCAGGACAG-CCAGC--ACTAATCA------CTGCAATATTGTCAGT------GAACCGATAC------AGCTGGACACGTA-T-TTTCGAAAACA------AA--G-GCAACCTTAGGGAGCGAT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58044746 104 - 61308211 CGCAGACAAGTCAGGACGG-CAAAT--GCTCGTCA------CTGCCGCACTGTCCAC------GCGTGGACAC------AATAGGACACGGA-T-TTTGTAACACA------AT--G-GCAAACCTGCAGAAAGAT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 33979 104 + 132007 CACGGCCAAGTCAGGAAAG-CAAAT--GCTGATCA------CTGCAACACTGTCAAC------GCCCATACAG------CACCAGACATGCA-T-TTTCCAACTCA------AG--G-GAGAACTTGTAGAAAGAT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59438706 104 - 64418924 CACAGACAAGTCAGGAAAG-CAAAC--ACTCATCA------TTGCAACATTGTCAAT------GCACATTCAG------AGTTGCACACATA-T-CATCCAACTCA------AG--G-GCAAACTTGCAGAAAGAT i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 11719 96 + 14340 CGTGGGCCAGCCAGG---G-A-CGC--GGCGCTCT------TTGCGATATGGTCAG---------ATGTACAC------GTGCGGCCGTGCA-C-TTTCCAAC---------AGCAG-GCAAAGGTGCGCGGAGTC i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 17213 97 + 48268 ---GGGCCAGCCAGGACAG-C-CGT--GCCGGTCA------CGGCGATGCCGACAGC------GCACGTGCAC------GGCTGGACACGCA-C-CTTCCACC---------AG--G-ACGGACGTGTGGAAAGAT i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14434616 106 - 17734757 ---------GACAGAGAAGCCAAAT--GCTGACAATTACGCTGATAATTGCAACAGTATCCGTGCACGTGTGC------CTACACACGT--G-T-TTTCCAACACA------CG--G-GCAACCCTGCAGAAAGTC i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 14385 99 + 20752 CACAGGCTAGACGGAAAAG-CACAT--TCGGACGA------CGCCAATCCCACCA--------ACGCGTGGAC------AGGTTCACGT--ATT-TTTCCAACACA-------G--G-GCAAGCTGGCAGGAGG-C i dasNov2.scaffold_28617 C 0 C 0 s macEug1.Scaffold23956 2844 102 - 25324 TACAAGtaaataaggaaaa-acaaa--a------g------ttacagtattgtctat------atacatatatgtaagaaaCAAAAGGC--A-T-TTACTAACATG------AG--G-GTATATTTATAATAAGCC i macEug1.Scaffold23956 C 0 I 17402 s monDom5.chr2 304538994 71 - 541556283 TACAGGTAAATAAGGGGAA-ATAAA--A------G------TTACAATATTGACAAT------ACACACATAA------AGC---------A-T-TTACCAACACA------AG--G------------------- i monDom5.chr2 C 0 I 11756 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 18846 1037 + 24616 I e tarSyr1.scaffold_507768 1050 0 + 1063 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e echTel1.scaffold_194555 5834 1715 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I a score=193424.000000 s hg19.chr17_gl000204_random 47910 61 + 81310 TCCTGTCTGTGGCCTGGGGA-TGCCGATAGAGT-------TAAAAGCATGCAGA------------TTCTA------------GGTG-TATC-C-T s calJac1.Contig5139 48550 58 + 225949 C-CCGTCCGTGGCCTGGGGG-TGCTGGCAGAGT-------TAAAAGCATGCAGA------------TTCTA------------GGAG-TATC---- i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 46545 61 - 95547 CCCCGTCCGTGGCCCAAGGA-TGCTGTTAGAGT-------TAAAAGCAGGCAGA------------TTCTA------------GGTG-TATC-G-T i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75039144 61 + 78773432 CCCCGTCCATGGCCCAAGGA-TGCTGTTAGAGT-------TAAAAGCAGGCAGA------------TTCTA------------GGTG-TATC-G-T i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16065223 60 + 17838096 T-CTGTCCGTGGCCTGGGGA-TGCCGATAGAGT-------TAAAAGCATGCAGA------------TTCTA------------GGTG-TACC-C-T i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 16842 61 - 64270 TCCTGTCCGTGGCCCGGGGA-TGCCGACAGAGT-------TAAAAGCATGCAGA------------TTCTA------------GGTA-TATC-C-T i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79478115 61 + 83384210 TCCTGTCCGTGGCCCGGGGA-TGCCGATAGAGT-------TAAAAGCATGCAGA------------TTCTA------------GGTG-TATC-C-T i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 229 61 + 4992 CCCCGGCCGCAGCCAGGAGG-TGCTGGCAGAGT-------TAAAAGAATGCAGA------------TTCTG------------CGGG-CATC-C-T i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 28825 56 + 287808 CCCTACCCAAGGCCAGGAGC-TGCTGGCAGGAT-------TAGAAGACCACCAA------------TTCTG------------CGTG--------T i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 13064 54 + 15939 --CCGTCCGTGGCCCGGGAG-TACTGGCAGAGT---------GAAGACTGCAGA------------GTGCA------------TGCG-AG-----T i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118760796 75 + 121843856 CCT--------GCCAAGGTG-TGGT-ACACAGT-------CAAAAGGATGTAGGGTCCCTGTTTGTTCTTGATTTTAAAAAAATGTG-TATC-t-- i mm9.chr11 C 0 I 298 s cavPor3.scaffold_76 4391299 53 + 7991924 ---------------AGACGTTGGC-AGATGCTGGCGGAGCAATAGAACGCAAG------------TTTTG------------TGTG-CATC-CT- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 8957 61 + 44242 CCCTGAGCGTGGCCAGGGTG-TGCTGACACAAC-------CCAAAGAACACAGG------------TGCCC------------TGTGCCAGC-T-- i speTri1.scaffold_128901 C 0 C 0 s turTru1.scaffold_106006 130990 60 + 145505 C-CCAGTCATGGCCAAGGGG-TGCTGGAAGGGT-------CAAAAGAATGCAGA------------TTCTG------------TGTG-CATT-C-T i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10861136 60 - 65312493 C-CCAGTCTTGGCCAGCGGA-TGTTGGAAGGGT-------CAAAAGAATGTAGA------------TTCTG------------TGTG-CATT-C-T i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58044850 60 - 61308211 C-CCAGTCATGGCCAGAGGA-TGCTGGAAGAGG-------CAACAGAAGGCAGA------------TTCTA------------GGTG-CATT-C-T i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 34083 59 + 132007 C-CCAGCCGTGGTCATGGAG-TGCCGGAAGAGT-------CCAAAGAATAAGGA------------TTCTA------------CGGG--GCT-C-T i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59438810 59 - 64418924 C-CCAGTCATAGCCA-GGAG-ACACTGAAGAGT-------CAAAAGAATAAGGA------------TTCTA------------TGTG-CATT-C-C i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 11815 55 + 14340 C-CAG-CCACGGCCA-GGGC-CGCAGGGCGAG--------GCTGAGAACGCAGG------------CTC--------------GGCG-AGGT-C-T i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 17310 49 + 48268 C-CTG-----------GGGA-CACTGGAAGAGC-------AAAGAGAATGCAGA------------TTCTA------------GATG-CATT-G-T i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14434722 61 - 17734757 TCTTGTTCATGACCAAAGGG-TTGAGAAACAGG-------CAAAAGAAAGCACA------------GTCTA------------GGTG-CATTGC-- i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 14484 60 + 20752 CCCCGTCCATGGCCAGGGGG-TGCTGGAATAGT-------TAAAAGAATGCAGA------------TCCTA------------CATG-TGTC-C-- i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 18846 1037 + 24616 I e tarSyr1.scaffold_507768 1050 0 + 1063 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 5834 1715 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=338096.000000 s hg19.chr17_gl000204_random 47971 49 + 81310 TCTCAGC-TGTCC---------TA--GATGAGATCTGCCGGTGAG--------------AAAGAAAAATGTACCC s calJac1.Contig5139 48608 47 + 225949 -TTCAAC-TGCCC---------TAG-GATGAGATCTGCCAGTGAG----------------AGGAAAATGTACCC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 46606 50 - 95547 TCTCAAC-TGTCC---------TAG-GATGAGATCTGCTGGTGAG--------------AAAGAAAAATGTACCC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75039205 50 + 78773432 TCTCAAC-TGTCC---------TAG-GATGAGATCTGCCGGTGAG--------------AAAGAAAAATGTATCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16065283 50 + 17838096 TCTCAGC-TGTCC---------TAG-GACGAGATCTGCCAGTGAG--------------AAAGAAAAATGTACCC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 16903 50 - 64270 TCTCAGC-TGTCC---------TAG-GATGAGATCTGCCAGTGAG--------------AAAGAAAAATGTACCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79478176 50 + 83384210 TCTCAGC-TGTCC---------TAG-GATGAGATCTGCCAGTGAG--------------AAAGAAAAATGTACCC i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 290 50 + 4992 TCTCCAC-CGCTC---------TGG-GAAAGGATCTGCCGGGGAG--------------GAAGAAAAATGTATCT i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 28881 35 + 287808 TCTTCA--------------------------ACCTTCTGGCGAG--------------AATGAGATGTGGGCCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 13118 49 + 15939 TCGTAAT-TGTCC---------TAG-GAAGAGACCTGCTGGTGAG--------------AAAGGAA-ACATACAT i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118761169 49 + 121843856 TCCTAGG-TGTCC---------TAG-GATGAGGTGCGGAG-TGAG--------------AAAGAGAAGTAGACAC i mm9.chr11 I 298 C 0 s cavPor3.scaffold_76 4391352 50 + 7991924 TCTCCCC-TGCCC---------TAG-GAAGAGGCCTGCTGTTGAG--------------AAAGAAAAGGGTACAC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 9018 50 + 44242 TCTCAAC-TGTCC---------CCC-CAGCAGATCTGCTGGTGGG--------------AAAGAAAACCGTGCCC i speTri1.scaffold_128901 C 0 C 0 s tarSyr1.scaffold_143701 3332 45 + 9575 ------C-TGTCC---------TAGAGAGGAGATCTGCTGGTGAG--------------AAAGAAGAATGTACCC i tarSyr1.scaffold_143701 M 2384 C 0 s turTru1.scaffold_106006 131050 45 + 145505 TCTCAAC-TGTCC---------TAG-GA-GAGA----TCTATGAG--------------AAAAAAAAAAGGACAT i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10861196 63 - 65312493 TTTCAAC-TGTTC---------TAG-GA-GAGATCAGTCTGTGAGGGGAAAAAAACAAAAACAAAAAAAAGACAT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58044910 35 - 61308211 TCTTAAT-TGTCC---------TAG-GA-GAGATCTG-CTGGGAG--------------G-------------TT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 34142 48 + 132007 ACTTAAC-TGTCC---------TAG-GA-GAGGTCTG-TGGCGGG--------------AAAGAAAAATGCACTC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59438869 46 - 64418924 TCTTAAT-TGTCC---------TAG-GA-GAGATCTG-CGGTGAG--------------AA--AAAAATGTACTT i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 11870 48 + 14340 CCCTCAT-CGG-C---------GGG-GG-CAGGCCTGCCCGCGAG--------------AGAGAAAAACGCGCTC i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 17359 49 + 48268 CCTTAAC-TGTCC---------CAG-GG-GAGACCTGCCCGGGGA--------------AAAGAAAAATGTGGTC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14434783 59 - 17734757 TTTTAAC-TGTCCTACTGGGTATAA-GCAGAGATCTGCTTGCAAG--------------GAAGGAAAATGTGCTA i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 14544 51 + 20752 TCTAAGCGTGTCC---------TAA-GACGAGATCTGTTGATGAA--------------AAAGAAAAATAGACAA i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 18846 1037 + 24616 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 5834 1715 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=19934.000000 s hg19.chr17_gl000204_random 48020 28 + 81310 GCTGGAAGACGGC------CT-T---TAATCATCCTAT s calJac1.Contig5139 48655 27 + 225949 GCTGGAAGATGGC------CT-T---TAATC-TCCCAT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 46656 28 - 95547 GCTGGAAGATGGC------CT-T---TAATCATCCCGT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75039255 28 + 78773432 ACTGGAAGATGGC------CT-T---TAATCATCCCGT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16065333 28 + 17838096 GCTGGAAGATGGC------CT-T---TAATTGTCCCAT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 16953 28 - 64270 GCTGGAAGACGGC------CT-T---TAATCGTCCCAT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79478226 28 + 83384210 GCTGGAAGACGGC------CT-T---TAATCATCCTAT i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 340 28 + 4992 TCTGGAAGATCGC------CT-T---TAATCACCCTAC i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 28916 9 + 287808 ACTAGAAGA----------------------------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 13167 28 + 15939 GCTGGAGAACTGC------CT-C---TGATCATCCCGT i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118761218 20 + 121843856 GCTGGCAGACAGC------CC-T-----------CTTG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4391402 28 + 7991924 ACAGGAAGATGGC------CT-T---TCATCCTCCTAG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 9068 27 + 44242 -CTGGAAGATGAC------CC-C---TTGTGGGCCTGT i speTri1.scaffold_128901 C 0 C 0 s tarSyr1.scaffold_143701 3377 28 + 9575 ACTGGAAGATGGT------CT-G---TAATCATCCTCT i tarSyr1.scaffold_143701 C 0 C 0 s turTru1.scaffold_106006 131095 28 + 145505 GCTGGTAAGCTGC------CT-T---TTGTCCTGTTGT i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10861259 23 - 65312493 GCTGGTAAGCTGC------CT-T---TCATCCT----- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58044945 17 - 61308211 GCCT------------------C---TAATCGAGCCGT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 34190 17 + 132007 GCTT------------------C---CAGTCACGCTGG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59438915 17 - 64418924 GCTG------------------G---TAGTCATGCTGG i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 11918 25 + 14340 ACCAG-AGCCGGC------C--T---TAGTCACGCTG- i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 17408 28 + 48268 GCTGG-GAGGTGC------CTTT---TCGTCATGCTGT i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14434842 28 - 17734757 GCTGGTAGATTTC------CT-T---TAATCTTCCTGT i loxAfr3.scaffold_49 C 0 I 484 s proCap1.scaffold_294600 234 27 + 1002 GTTGGGGGACAGCAGCCAACA-C---CAACC------- i proCap1.scaffold_294600 n 1037 C 0 s dasNov2.scaffold_28617 14595 31 + 20752 GCCGGGAGCACGC------TT-TGCACGATCCACCTGT i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 5834 1715 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=320448.000000 s hg19.chr17_gl000204_random 48048 97 + 81310 AAAGTTGTCCCAGACAACGTCAC-AA-GGCTTT-AATGGTAA-GGAAAAGGGTAAC----AGGCTCCCCCATCAAACACA-GGC-----CATCG-TCCACCTGCTCTCCCT---------C s calJac1.Contig5139 48682 97 + 225949 AAAGTGGTCCCAGACACCATCAC-GA-GCCTTT-AATAGTGA-GGAAAAGGGAAGC----TGGCTCCCCCATCAAACACA-GGC-----CATCA-TCCACCTGCTCTCCCT---------C i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 46684 97 - 95547 AAAGTTGTCCCAGACACCATCAC-AA-GGCTTT-AACAGTGA-GGAAAAGGGTAAC----AGGCTCCCCCATCAAACACA-GGC-----CATCG-TCCACCTGCTCTCCCT---------C i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75039283 97 + 78773432 AAAGTTGTCCCAGACACCATCAC-AA-GGCTTT-AACAGTGA-GGAAAAGGGTAAC----AGGCTCCCCTATCAAACACA-GGC-----CATCG-TCCACCTGCTCTCCCT---------C i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16065361 97 + 17838096 ATAGTTGTCCCAGACAACGTCAC-AA-GGCTTT-AATAGTGA-GGAAAAGGGTAAT----AGGCTCCCCCATCAAACACA-GGC-----CATCG-TCCACCTGCTCTCCCT---------C i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 16981 97 - 64270 AAAGTTGTCCCAGACAACGTCAC-AA-GGCTTT-AATGGTAA-GGAAAAGGGTAAC----AGGCTCCCCCATCAAACACA-GGC-----CATCN-TCCACCTGCTCTCCCT---------C i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79478254 97 + 83384210 AAAGTTGTCCCAGACAACGTCAC-AA-GGCTTT-AATGGTAA-GGAAAAGGGTAAC----AGGCTCCCCCATCAAACACA-GGC-----CATCG-TCTACCTGCTCTCCCT---------C i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 368 79 + 4992 AAAGTTGTCCCAGACATCATCCC--G-GGCTTT-AACGGTCA-GGAAAAGGGCCC------------------------------------TTG-TCCAGCTTCTCCCCCTAGCCCCACCC i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 28925 94 + 287808 ----TGGGCCCAAACACCAGCCC-AG-AGCTTT-AGTGGTTA-GGAAAAGGGTCCC----AGACTTCCCCATCAAACAAAAGGT-----CATCA-TCCATCTTCTCTTTTT---------C i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 13195 95 + 15939 GAGATCACTCCAGACACC--CTC-AG-GGCTGT-GGAGGGGA-GGACAAGGATAAC----GGGC-CCCCCATCGAACACGGGGT-----CATCA-TCCAGCTTCCCTCCTG---------C i tupBel1.scaffold_124459.1-15939 C 0 I 1863 s mm9.chr11 118761238 91 + 121843856 ACAGTCGTCTCAGACCCAGAAAC-CG-GAGCTT-TATAGATC-AGGGA--AAGAAC----AGTG-CCCCCACCA-ACAAACA-------CATCG-TCCGTCGGCAC-CGTC---------C i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4391430 73 + 7991924 AACGGTATCTCCACTCCCGTAGC-CA-TAGCAG-TCTGAATC-AGAAG--GGTAAC----AGGC-TTCTCTCC----------------------TCCTT-----C-CCCT---------T i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 9095 95 + 44242 AGAACTGCCCCAGACCCCGTCTC-CA-GGGCGG-GGTGGCCA-GGGAA--GGCAAG----GGGC-CCCCTTTCAGACAAAGAGG-----CTCCG-TCCAGCGTCCCACCCT---------C i speTri1.scaffold_128901 C 0 C 0 s tarSyr1.scaffold_143701 3405 99 + 9575 AAAGTTGCCCCAGACATAATCAC-AAGGGCTTC-AATGGTGA-GGAAAAGGGTAAC----TGGCTCCCCCATCAAAGGCAGGGT-----CATCG-TCCACCTTCTCTCCTT---------C i tarSyr1.scaffold_143701 C 0 C 0 s turTru1.scaffold_106006 131123 96 + 145505 AAAGTTGTCCCAGACACCAATCCCAG-GGCTTT-CGAGGTTA-GGATAAGGGCAGT----GGGGTCCCCCATCAAACAAA-GGT-----TATCC-TCTAGCTTCTGTA--T---------C i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10861282 94 - 65312493 ---GTTGTCCCAGACACCAACCTCAG-GGCTTC-CGAGGTTA-GGACAAGGA-AAT----GGAGCCCCTCACCAAACAAA-GGC-----CATCC-TCCGGCTTCTCTATCT---------C i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58044962 94 - 61308211 AAAGTTGTCCCAGACACCAACACAAG-GGCTTT-TGTGGTCA-GGATCAGGCTAAT----GGGCTCCCCGATCAGACGAG-GGT-----CATTG-TCTAGCCTCT--C--T---------C i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 34207 89 + 132007 AAAGTCGTCCCTGACACCTGCAGAAG-GGCTTT-CGCGGTAA-CG---------------GGCCGCCCC-ACCAAACAAA-GGTCAGGCCACTG-TCCAGCTTCCGTG--T---------C i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59438932 98 - 64418924 AAAGTTGTCCCAGACACC-ACAGAAG-GGCTTT-CGTGGTGA-GGGCAAGGGTAACTAGCGGGCTCCCC-ACCAAACAAA-GGT-----CATCA-TCCAGCCTCTGAC--T---------C i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 11943 91 + 14340 GAGGTTCCCCCAGATTCCAACAC-GA-GGCCCA-CGCAGTTA-GCACAAGGGCGAC----AGCTTCCCC-ATCGAACAA--GAT-----CACCC-T-GAGCTTC-CTG--T---------C i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 17436 76 + 48268 AAAGTTGTCCCAGACACAGACAC-AG-GGCTTC-CCCAGTTAGGCACAGG-----------------------TAACGA--GAC-----CAGCC-TCCAGCTTCTCCA--T---------C i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_294600 261 91 + 1002 AACACTGTAACAGACCCCATCGT-GA-GCCCT--AAGGGTCG-AGAAAGGGG--AC----CAGGCCCCCCATCAAACACAGCAC-----CATTG-CCAGGCTTCTCTC------------- i proCap1.scaffold_294600 C 0 I 4 s loxAfr3.scaffold_49 14435354 92 - 17734757 aAAGTTGTAACAGA-CCCACCAT-GA-GCCCT--AAGGGTCA-AGAAAAGGG-TAC----CAGGCCTCCCTGCAAACAGAGGGT-----CACTGTCCAGGTTTCTCTC------------- i loxAfr3.scaffold_49 I 484 I 4 s dasNov2.scaffold_28617 14626 94 + 20752 -AAATGGTGCCAAGCACCGTGGC-GA-GGGCTTGAAGGGTTA-AGAAAAGAGAAAG----CGGCGCCGGCGTCAAACCGAGGGT-----CATCG-CCCGGTTTCTCTC------------- i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 5834 1715 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=1811765.000000 s hg19.chr17_gl000204_random 48145 233 + 81310 CCGCCC-TTT-GGCCATCA-------------------GCTGAAGGTTCCCAGCTGTCAAGAT-ATCAAACAGAC-TTCTGG-ACGATAAAGCTCGACACAGCGTTGGCTGTCTGGGAGTGTTGATTATAATGTTACGCC-ACTGACAACAGTAATTCTCACCTT---AAATTT---------------CTTC-TCTTTTCTGCTAAGATTCCAAAATACTTGAATAATGTACCCTTGGA-TAGCACCCCTGCGA--G--GAACACAACCAACCACTGTC--GG s calJac1.Contig5139 48779 230 + 225949 CCACCT-TTT-GGCCATCA-------------------GCTAAAGGTTCCCAGCTGTCAAGAT-ATCAAACAGAC-TTCTGG-ATGATAAAGCCCGACACAGCGTTGGCTGTCTGGGAGTGTTG---ATGATGTTACGCC-ACTGACAACAGTAATTCTCACTTT---AAATTT---------------CTTC-TCTTTTCTGCTAAGATTCCAAAATACTTGAATAACGTACCCTTGGA-TAGCACCCCTGTGA--G--GTACACAATCAACCACTATG--GG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 46781 233 - 95547 CCACCC-TTT-GGCCATCA-------------------GCTAAAGGTTCCCAGCTGTCAAGAT-ATCAAACAGAC-TTCTGG-ACGATAAAGCTCAACACAGCATTGGCTCTCTGGGAGTGTTGATTATAATGTTACGCC-ACTGACAACAGTAATTCTCACCTT---AAATTT---------------CTTC-TCTTTTCTGCCAAGATTCCAAAATACTTGAATAATGTACCCTTGGA-TAGCACCCCTGAGA--G--GAACACAATCAACCACTGTT--GG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75039380 233 + 78773432 CCACCC-TTT-GGCCATCA-------------------GCTAAAGGTTCCCAGCTGTCAAGAT-ATCAAACAGAC-TTCTGG-ACGATAAAGCTCAACACAGCATTGGCTCTCTGGGAGTGTTGATTATAATGTTACGCC-ACTGACAACAGTAATTCTCACCTT---AAATTT---------------CTTC-TCTTTTCTGCCAAGATTCCAAAATACTTGAATAATGTACCCTTGGA-TAGCACCCCTGAGA--G--GAACACAATCAACCACTGTT--GG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16065458 233 + 17838096 CCGCCC-TTT-GGCCATCA-------------------GCTGAAGGTTCCCAGCTGTCAAGAT-ATCAAACAGAC-TTCTGG-ACGATAAAGCTCAACACAGCGTTGGCTGTCTGGGAGTGTTGATTATAATGTTACGCC-ACTGACAACAGTAATTCTCACCTT---AAATTT---------------CTTC-TCTTTTCTGCTAAGATTCCAAAATACTTGAATAATGTACCCTTGGA-TAGCACCCCTGCGA--G--GAACACAATCAACCACTGTC--GG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 17078 233 - 64270 CCGCCC-TTT-GGCCATCA-------------------GCTGAAGGTTCCCAGCTGTCAAGAT-ATCAAACAGAC-TTCTGG-ACGATAAAGCTCGACACAGCNTTGGCTGTCTGGGAGTGTTGATTATAATGTTACGCC-ACTGACAACAGTAATTCTCACCTT---AAATTT---------------CTTC-TCTTTTCTGCTAAGATTCCAAAATACTTGAATAATGTACCCTTGGA-TAGCACCCCTGCGA--G--GAACACAATCAACCACTGTC--GG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79478351 233 + 83384210 CCGCCC-TCT-GGCCATCA-------------------GCTGAAGGTTCCCAGCTGTCAAGAT-ATCAAACAGAC-TTCTGG-ACGATAAAGCTCGACACAGCGTTGGCTGTCTGGGAGTGTTGATTATAATGTTACGCC-AGTGGCAACAGTAATTCTCACCTT---AAATTT---------------CTTC-TCTTTTCTGCTAAGATTCCAAAATACTTGAATAATGTACCCTTGGA-TAGCACCCCTGCGA--G--GAACACAATCAACCACTGTC--GG i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 447 222 + 4992 CCACCC-TTTGGGGCACCA-------------------GTTAGGGGTTCACGGCTGTCAAGAT-ATCAAACGGGC-CTCCGGCACGACAAAAGTCGAGTCCGCCTTGGCTATCT-GCAGTGTCGATTACAATGTGGCACC-ACTG---ATGACAATTCTCACCTT---AAATTT-------CTTCAGCACATC-TCTTTTCTGCTAATATTCCAAAGCATTTGGCTGCTGTACCCCTGGGCGGGCACCGCTGTGA--G--TAGC-------------------- i micMur1.scaffold_72647 C 0 I 14 s otoGar1.scaffold_94362.1-287808 29019 222 + 287808 CCGCCG-TTC---GCATCA-------------------GTTAGAGGTTCCCAGCTGTCAAG--------ACAGAC-CTCTGGCCTGATAAAGCCCCATGTAAGGTTGGCTATGT-GAGGCGTTGATTAGAATGTTACACC-ACAG---ACAGTAATTCACACCTT---AAATTTTAAGGTGCTTAAA------------TCTGCTAAGATCCCAAAGTATTTGACTGAGGCACCCTTGGG-GAGCACCGCTGTGG--GGTGAGCGCAAGTG--CATCGC----- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118761329 213 + 121843856 GG-----------CTTTCGTCCCTCTCTCCCGGGCACCACTGAAGGCATGCAGCTGTCTCGGT-ATC----------------------AAGCGAGCTGCCTTGTGGGCTGTCAAGGAGTGTTGATTGCAATACTGTGCC-GATGACAACCATAATTCTCACCTT---AAGTTC-------CTCTGGTACTTC-TCTTTCCTGCTAAGATTCCAAAGTGCTTGACTAATGTACCCTCGGA-TAGCACCGCCTCGA--G--GCCC-------------------- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4391503 227 + 7991924 GG-----------CTTTCA-------------------GCTAAAGGCACAAAGCTGTCAACAT-AGC----AGAC-TCCTGC-CCTGCAAAGCTCACTGTAATGCCGGCTGTCTGGGAGTGTTGATTATAATACTACACT-GCTGACAACAATAATTCTCACCTT---AAGTTT-------CTCCAGCACTTC-TCCTTTCTGCTAAGATTCCAAAATACTTGCCTAATGTACCTGCGCA-GAGCAACACTCTGA--A--GCCCACAG-CAAGCACTACC--AG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 9190 215 + 44242 AG-----------CCCTCA-------------------GTTAAAGGCGTGCAGCTGTGGACAT-GTCCAACAGAC-CTCTGT-GCCCC-AAGCGCAGCGCAGTG-GTGCTGTGCGCGAGTGCTGATGGCATTATTAGTCC-GCTGACA------------ACCTG---AAGTTT-------CCCCAGCACTTC-TCTTTTCTGCTAAGGTTCCAAAATACTTGACTAGCGGGCCCTCAGA-CG----CACGCTGATCA--GCAAGCCA-CAAGCACTCTG--GT i speTri1.scaffold_128901 C 0 C 0 s tarSyr1.scaffold_143701 3504 239 + 9575 CCACCT-TTT-GGGCATCA-------------------GTTAAAGGTTCCCAGCTGTCTAGAT-ATCAAACAGAC-TTCTGG-ACGATAAAACTTGATGCTGCGTTGGCTGTCAGGAAGTGTTGATTATAATGTTACACC-ACTGACAACAATAATTCTCACCTT---AAATCT-------CTTCAGCACTTC-TCTTTGCTGCTAAGACTCCAAAATACTTGACTAATGTACCCTTGGA-TAGCACCCCTGCAA--G--GTA-AAAAGCAAGCACTGTC--A- i tarSyr1.scaffold_143701 C 0 C 0 s turTru1.scaffold_106006 131219 241 + 145505 CCTCCC-TTT-GGTCATCA-------------------GTTAAAGGTTCACAGCTGACAACAT-ATCAAAAAGAC-TTCTGGTATGATAATACTCAATACAGCGTTGGCTGTCTAGGAGTGTTGATTATAATATTACACC-ACTGAAaacaataattctcatctt---aaattc-------ctccagcacttc-tcttttctgcgaacatttcaaaatagttgactaatgtactcataga-cagcacccctaaga--g--gtaggcag-caggcactatc--ag i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10861376 241 - 65312493 CTTCCC-TTT-GGTCAGCA-------------------ATTAAAGGTTCACAGCTGGCAACGT-AGCGAACAGAC-TTCTGGAATGATGATACTTGATA-GGCGCTGGCTGTTTGGGAGTGTTGATTATAATATTACACCAACCCAAAACAATAATTCTCACCTT---AAATTC-------CTCCAGCACCTC-TCTTTTCTGTGAACATTTCAAAATACTTGACTAATGTACCCGTGGA-TAGCACTCCTAAGA--G--GTATGCTG-CAGGCACTATC--AG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58045056 240 - 61308211 AATCCC-TTT-GGCCGTCA-------------------GTTACAGGGTCACAGCTGTCAACGT-ATCAAACAGAC-TC-CAGTGCGATAATGCTCCGTATAGCGCTGGCTGTCTGGGAGTGTTGATTATAATATTACACC-CCTGAAAATAATAATTCTCACCTC---AAATTT-------CTCCAGCACTTCTTTTTTTCTGCTAAGATTCCAAAATACTTGACTAATGTAGCTGTGGA-AGGCGCCCCTGAGA--G--GAAGGCGG-TAAGCACTAGC---A i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 34296 209 + 132007 CCTCCC-TTC-AGCCAAGA--------------------------------------------------GCAGAC-TCGCGG-----TAATACGCACCCTGGCATCGGCTGACTGCGAGTGCCGCTTATAATATTACAGC-GCTGAAAATATTAATTCTCACCTTGTGAGTTTT-------CCCCAGCTCTTC-TCTTTTCTGCTAAGATTCCAAAACACTTGACTAATGTGCCCACGGA-TGGCACCCCTACGG--G--GCAGGCAG-CGAGTGCTATC--CA i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59439030 211 - 64418924 CCTGCC-CTC-GGCCAGGA-------------------G------------------------------GCTGAC-TTGCGGCACGCTAACACTCGATGTGACGTGGGTTGTCCACGAGCACTGC-TACAATATTACACC-ACTGAAAATCCTAATCTTCACCTT---AGATTT-------CTCCAGCTCTTC-CCTTTTCTGCTAAGATTCCAAAACACTTGACTAATGTACCCGTGGA-TGGCACCCCTATGA--G--GCAGGCAG-CGAGCGCTATC--AA i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 12034 217 + 14340 CCTC---------CCGTGG-------------------GTCCAA-GTTCACGGCTGTCAATGT-ATCAGGCAGACGTC-TGG-GCGCTAAGACTGGATACACCA--GGCTGTCTGG--GTGCCGATGACAA-GTCACTCC-CCTGAAAACAATAATCCGCACCGT---CCACGT-------CCCCGCCGCTTC-TCTGTCCTGCGAAGATCCCCCATC-TTAGCGGAAAGT-GCCCTGGC-CAGCACCC------------CCAGAGG-TGGGCACACGC--AC i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 17512 235 + 48268 CCTCCC-TGC-GGCCGTCA-------------------GTTAAAGGTTCGCAGCTGTCAGCGT-GTCGAAGGGAC-TC-CGG-TAGGTAAGAGCGGATATAGTGTTAGCTGTCTGGCAGTGCTGATTATAGCATTACACC-CCCGAAAATAATAATTCTCACC-----CCGAAT-------TTCCAGCACGTC-TCTTTTCTGCTAAGATTCCACAAC-CTTGACTAGTGT-CCCATGGA-CAGCGCCCCTGAGG--G--GCCAGCAG-CGAGCACTCTC--CG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14435450 235 - 17734757 -CTGCC-TTG-GGCCA-CA-------------------GTTAAACAAACACAGCTGTCAGCAC-CTCAAATAGAC-TTCCGGAACAAGAAGATGTGATATAGCTTTGGCAG-CTGTGAGTGTTGATTATAATATGACACC-ACTGACGACAATAATTCTCACCTT---AAATTT-------CTCCTCCATTTC-TCTTTTCTGCTAAGATTCCAAAACACTTGGCTAATGGACTCCTGAA-TGGCCCCCCTGCGA--G--GAAGAAG--CCGGCACTGCT---- i loxAfr3.scaffold_49 I 4 C 0 s proCap1.scaffold_294600 356 238 + 1002 -CTTCCGGGG-GGCCA-CT-------------------GTCAGACGCACAT-GCTCTCAGTGC-CTCACAGAGGC-GTCCAGAATGAGAAGACGTGACACAGCTTTGGCGGCCTGTGAGGGTTGATCATAATATCACACC-ACAGACGATAGTAACGCTCACCTT---CAATTC-------CCGCGGCACTTC-TCTCAGCTGCTAAGATTCGGAAGCCCTTGGCTAATGGACTCTCAAA-CAGGCCCCCTGCGC--G--GAAGAAG--CAGGCACTGCTGG-- i proCap1.scaffold_294600 I 4 C 0 s echTel1.scaffold_194555 7549 235 + 11139 CCAGTC-CTG-GGCCA-CC-------------------GCTTGGGGCTCTGAGCCGCCAGG---CTCAGATAGAT-TCCTGGGATGTGGAGATGGGCTGCCGCTCCTGCTGTCTGGGAGTGTTGATTATCATATTACAGC-ACTGACAACAATAATTCTCACCTT---GAATTT-------CC-CGGCACTTC-TCTCCTCCGCTAAGATTCCAAAGCACTTGACTAATGGACTCTCAGA-TCGGCCCCCTGCGA--G--GAGGAAG--CAGGCACTTCG-G-- i echTel1.scaffold_194555 I 1715 C 0 s dasNov2.scaffold_28617 14720 216 + 20752 CCTCCC-TCT-GGCCATCA-------------------GCCGAAGGTTCCCGGCTTTCGGTGTAGCCAGTCCACT-TCCCGGGACGACGAGATTTGACACGGCTTTGGCTGTCT--GGCTGTTGATTATAATATTACACC-ACTGGCAGCAA-AACTGTCACCTT---AAATGC-------CTCCAGAGCTT------TGCTGCTAAGACTCTGAAATGCTTGACTGCCGTCCTCTTGGG-TAGCTCCCCTGTGT--G-------------------TCT---- i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=371729.000000 s hg19.chr17_gl000204_random 48378 151 + 81310 TCTTCTCCCCAG--CAGC----T-GGGGGCACGCAGCCAGG---ATGGCCGGTGAACCACACGCCCCGTCCCAG-GTCTAT--AAGGAGCCTGTGGAAGCAACCCCTCGGGT-C--TCTAGTTCCACTTCACCTGTCCCTGCCATGA-----GG-CCCCC---A-----GCTGTGCCTAAT s panTro2.chr17 79478584 151 + 83384210 TCTTCTCCCCAG--CAGC----T-GGGGGCACGCAGCCAGG---GAGGCCAGTGAACCACACGCCCCGTCCCAG-GTCTAT--AAGGAGCCTGTGGAAGCAACCCCTCGGGT-C--TCTAGTTCCACTTCACCTGTCCCTGCCATGA-----GG-CCCCC---A-----GCTGTGCCTAAT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 17311 151 - 64270 TCTTCTCCCCAG--CAGC----T-GGGGGCACGCAGCCAGG---GAGGCCGGTGAACCACATGCCCCGTCCCAG-GTCTAC--AAGGAGCCTGTGGAAGCAACCCCTCGGGT-C--TCTAGTTCCACTTCACCTGTCCCTGCCNTGG-----GG-CCCCC---A-----GCTGTGCCTAAT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16065691 151 + 17838096 CCTTCTCCCCAG--CAGC----T-GGGGGCATGCAGCCAGG---GAGGCCAGTGAATCACATGCCCCGTCCCAG-GTCTAC--AAGGAGCCTGTGGAAGAAACCCCTTGGGT-C--TCTAGTTCCACTTCACCTGTCCCTGCCGTGG-----GG-CCCCC---A-----GCTGTGCCTAAT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75039613 150 + 78773432 TCTCCTCCCCAG--CAGC----T-GGGGGCACGCAGCCAGG---GACACCGGTGAACCACATGCCCCGTCCCAG-GTCTAC--AAGGAGCCTGTGGAAGAAGCCCCTC-AGT-C--TCTGGTTCCACTTCACCCGTCCCTGCCGTGG-----GG-CCCCC---A-----GCTGTGCCTAAT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 47014 151 - 95547 TCTCCTCCCCAG--CAGC----T-GGGGGCACGCAGCCAGG---GACACCGGTGAACCACATGCCCCGTCCCAG-GTCTAC--AAGGAGCCTGTGGAAGAAGCCCCTCAGGT-C--TCTGGTTCCACTTCACCCGTCCCTGCCGTAG-----GG-CCCCC---A-----GCTGTGCCTAAT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 49009 144 + 225949 TCTCCTTCACAG--CAGC----T-GGGAGCACCTGACCAGG---GAGGTGGGTGCACCACATCCTCTGTCCCAG-GCCTAC--GAGGAGCCTGTGG------TCCCTCGGGT-C--TCCAGTTCCACCTCACCTGACCCTGCCGTG------GG-CCCCC---G-----GCTGTGCCCGAC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 3743 142 + 9575 ---TCTCCTTAG--TAGCATTTT-GGGGACATGTCATC-GG---GAAGTGGGTGAACTGGTTGCCCCACCCCCA-GTCTAC--AAGTAG---------GAAACCCTTTGGGC-C--T-TGGTTCCACCTCACCTGTCCCTGCAGCAG-----GGCCCCCC---A-----CCTGCATCTAAT i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_72647 683 133 + 4992 TCTTCCCGCCAG--CAGC-------------------CGGG---GACGCAGGCGAGCCGCGAGCCCCA-CCCCG-GTCCGC--CAGGAGCCTGTGTTAGAAACCCCCGTGGG-C--CTTGGTTCCAGCTCACCTGTCCCTGCAGCGG-----G----CCC---A-----GCCGAGCCTAAT i micMur1.scaffold_72647 I 14 C 0 s otoGar1.scaffold_94362.1-287808 29241 130 + 287808 --TCTTTACCAG--CAGC----T--------------TAGG---GAAGGAGGTGATTC-----CCCCACCCCCG-GTCTGT--GAGGAG-CTGTGTAAGAAACCGCTGTGGG-C--CTTGGTTCCACCTCACCTGTCCCAGGCGTGG-----GG-GCCCC---A-----GCCGTGCCTAAT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118761542 151 + 121843856 ---CATTACAGG--CCCT----TAGAGGGAATGCAG--GAG---GAAGCCTGAGATCC--CGTGCCCACCCGCC-GTGCAC--CAACAGCCTGTGTAGGCAACCCCTGTGGG-C--C-TGCTTCCCCCTCGCCTGTCCCTGCATTAGCCATCC--CCCCGCCCA-----GCTGAGCTTAAT i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4391730 145 + 7991924 CTGTGTTATGAG--CTGC----GTGAGAAAAGGCAGCCGGG---AAGGGCATGGATGC--TGCGTCCACCCGCA-GTCTA---CAGAAGCCTGAGCAGG-AACCCCTG-GGC-C--C-TGGCTTCTCCCTGCCTGTCCCTGCATTAG-----G--CCCCG---A-----GCCATCCTTAAT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 9405 125 + 44242 TCCCACTGTGAG--CGGC----TCCAGGAAGCGCAGCCGAG----------------------GCCCA-CTGGG-GCCTGT--GAGGAGCCCATGGGGGAAAGCCCTGCAGG-C--C-CGACCTCC-----ACTGTCCCTGCCGTAG-----G--CCCCG---A-----GCCGTGCCTAGT i speTri1.scaffold_128901 C 0 C 0 s turTru1.scaffold_106006 131460 149 + 145505 tcccattacgag--cagc----c-tgggggacacag-cggg---gaagtCGGTGAATCACG-GCCCCCACCCCCGGTCTGT--GAGAAGCCTGGGTAAGAAGGCCCTTGGGC-C--C-TAGTTCCACTTCGCCTGTCCCTGCAGCGG-----GG-GCCCC---A-----GCTGTGCCTAAT i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10861617 148 - 65312493 TCCCACGATGAG--TAGC----T-TGGGGGACACAT-GAGG---GAAGTTGGTGAATCACA-GCCCCCACCCCC-ATCGAC--GAGGAGCCTGGGTAAGAAGGCCCTTAGGC-C--C-TGGTTCCACCTCACCAGTCCCTGCAGTGG-----GG-GCCCC---A-----GCTGTGCCTGAT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58045296 135 - 61308211 GGCCATTGTGAG--CTG--------AGGAA--------GGG---GATGCTGGCAAAGCACC-GCCCGG--CCCG-GCCCACGAGGGGAGCCTGTGGAGGAAGCCCCTTGGGC-C--C-TGGTTCCACCTCGCCTGTCCCTGCAGCAG-----G----CGC---A-----GCCGTGCCTAAT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 34505 148 + 132007 GTCCATTATGAG--CAGC----T-CAGGGAGCGCAG-CGGG---GAAGTCGGTGAACCGCA-GCCCCGTCCCCG-GTCTAC--AGGAGGCCTGTGTAAGCAGCCCCCTGGGC-C--C-CGGCTCCGCCTCGACTGTCCCTGCGGTGG-----GG-GCCCC---A-----GCCATGCCTAAT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59439241 148 - 64418924 GTCCATTATGAG--CAGC----T-CGGGGAGCGCAG-CGGC---GACGTTGGTGAACCACA-GCCCCATCCCTA-GTCTAC--AAGAAGCCTGTGTAAGCAGCCCCTGGAGC-C--C-CGGTTCCACCTCACCTGTCCCTGCAGTGG-----GG-GCCCC---A-----GCGGTGCCTAAC i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 12251 63 + 14340 ----------------------------------------------------------------------CCCA-GTCTCC--CAGGGGCCTG--GGGAGAGTCC--------------------------CTTGTCCCTGACGCGG-----GA----CC---C-----GCCAGGCCTGAC i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 17747 88 + 48268 ----------------------------------------------------------------------CCAC-GCCCCC--T----GCCTGTAAGAGCAGTCCCCTGTGC-CTTC-TGGTTCCACCCCGCCTGTCCCTGCAGTGG-----GG-ACCCC---A-----GCCAGGCCTAAT i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14435685 137 - 17734757 --------TCAG-GTAAC----TCTA----------TCGGGTATGGGGGGAGTGAACCCATGTTCCTCGCACCC-ATCTGC--TTAGAGCCAGGTGAAGAAATCCCTTTGGC-C--C-TGGTCCC-CTTGGCCGGCCCCAAGGGTGG-----GTCCCTCT---A-----GCCGTACCTGAT i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_294600 594 150 + 1002 ---TCCCCTCAGAGTAGC----TTCAGG----GTATTTGGCCAGGGGCTAGATGAACCCACAATCCTTCGCTGT-TCCTGT--GCAGAGCTAGCTGCACAAACCCCTTTGGCTC--C-AGGTCCC-CAGGGCCTCCCCGAAATGTGG-----GTACCGCT---A-----GCTGTTCCTAAT i proCap1.scaffold_294600 C 0 n 0 s echTel1.scaffold_194555 7784 145 + 11139 ---CCCCATTAGACTGGC----TTCGGGAAGTGCGGTCGGGTGAGCAGGGAGCCAGCCCATGTTCCCACTCTCC--TCTGT--GCAGGCCAAG------AAACCCCTCTAGC-C--C-TGAGCTC------CCGCCCCCCACTGCCC-----AGACCACC---ACCACCACCATGCCTAA- i echTel1.scaffold_194555 C 0 I 1421 s dasNov2.scaffold_28617 14936 130 + 20752 --------CCAG----GT----CCCATG--------GCGGGAGCTGGGGGAGGGCGGCCTCGGCCCCCACCCCG-GCCTGT--GCGGAGTCGGTGCAGGAAGCCCCTCTGGG----------CCC-CCTCGCCTGCCCCTGGGGTGG-----GCCCCTCC---AGCACCGCCTTCC----- i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=573945.000000 s hg19.chr17_gl000204_random 48529 94 + 81310 GGCATGACA---------TCAATGAT----AGTCAATACTCCAGAAAGAATAAAAGCACACACTT-TG---------TTTTTTTTTTCTAATGGGCTTTGCAAAGCTGTGCTTCGGT s panTro2.chr17 79478735 95 + 83384210 GGCATGACA---------TCAATGAT----AGTCAATACTCTAGAAAGAATAAAAGCACACACTT-TG--------TTTTTTTTTTTCTAATGGGCTTTGCAAAGCTGTGCTTCGGT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 17462 96 - 64270 GGCGTGACA---------TCAATGAT----AGTCAGTACTCCAGAAAGAATAAAAGCACACACTT-TGT-------TTTTTTTTTTTCTAATGGGCTTTGCAAAGCTGTGCTTCGGT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16065842 91 + 17838096 GGCATCACA---------TCAATGAT----AGTCAATATTCCAGAAAGAATAAAAGCACACACT-------------GGTTTTTTTTCTAATGGGCTTTGCAAAGCTGTGCTTCGGT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75039763 92 + 78773432 GGCCTCACA---------TCAATGAT----AGGCAATATTCCAGAAAGAATAAAAGCACACACTT-TG-----------TTTTTTTTCTAATGGGCTTTGCAAAGCTGTGCTTCAGT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 47165 92 - 95547 GGCCTCACA---------TCAATGAT----AGGCAATATTCCAGAAAGAATAAAAGCACACACTT-TG-----------TTTTTTTTCTAATGGGCTTTGCAAAGCTGTGCTTCGGT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 49153 89 + 225949 AGCATCACG---------TGGCTGAT--AGAGTCACTATTCCAGAAAG----ACAGCATGCACGT-CA------------TTTCTTCCTAATGGGCTTTGCAAAACTGTACTTTGGT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 3885 99 + 9575 GGCATCCCA---------TCAACAAT----CGTCAATATTCCAGAAAG----ACAACTCATGCTT-TATTTATTTCCCTTTTTTTCCCTAATGGGCTTTGCAGCACTGTGCTTCAGT i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_72647 816 94 + 4992 GGCATCTCC---------TCAATGACAGAGAGTCAGTTCTCCAGAAAG----ACGGCGCTCGCTTACG---------GGCTTTTTCCCTAAT-GGCTCTGCCACGCTGTGCTTCAGG i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 29371 91 + 287808 GGCATCACA---------TCAATGAC--AGAGTCAATATTCCAGAAAG----ACAGTG-TCGCTT-TA---------TGTCTTCCCCCTAATGGGCTTTGCAAAGCTGTGCTTCGGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118761693 92 + 121843856 GGTATCTTC---------TCAGTGAGGGAGAGTCAATAACTTAGAGAG----GC-GGGCAGGCTC-TC----------TGTTTATTTCTAATGGGTCTCTCAGAGCTACGCCTTGCT i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4391875 87 + 7991924 GGCAACACA---------TCGGTGAGTG------GATATTCCAAAGAA----GCAGGGCAGGCTT-TC----------TGTGTGTTCCTAATGGGCCTCGCAAAGTGGCGCTCTGGT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 9530 92 + 44242 GGCATCGCA---------TCAGAGAGGCACAGTCAATATTCCAGAATG----ATGGCGCGGGCTT-TC----------TGTCGACTTCCAGT-GGTCTTACAGAGCCGCATTTCAGC i speTri1.scaffold_128901 C 0 C 0 s turTru1.scaffold_106006 131609 101 + 145505 GGCATCACAGTGGTCCCTTCAATGAGGGAGAGTCAATATTCCAGAAAG----GCA-TGCACACTT-TA----------TGTTTATTTCTAATGGGTTTTGCAAAACTGGGTTTCGGT i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10861765 101 - 65312493 GGCATCACAGTGGTCCCTTCAATGAGGGAGAGTCAATATTCCAGAAAG----GCA-TGTACACTT-TA----------TGTTTATTTCTAATGGGTTTTGCAAAACTGAGTTTCGGT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58045431 101 - 61308211 GGCATCACAGTGGTCCCCTCAATGACGGAGAGTCAATATTCCAGAAAG----ACAGCACACACTT-TG----------TGTTTATTTCTAATGGGTTTTGCAAAACT-CGTTTCGGT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 34653 101 + 132007 GGCACCACTGTGGTCCCTTCAATGAGGAAGAGTCAAGATTCCAGAAAG----ACA-AGCACACTT-TA----------TGTTTACTGCTAATGGTTTCTGCAACACCATGTTTCGGT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59439389 101 - 64418924 AGCACCGCTGTGGTCCCTTCAATGAGGAAGAGTCAATATTCCAGAAAG----ACA-CACACACTT-CA----------TGTTTATTGCTAATGGTTTCCCCAAAACTATGTTTTGGT i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 12314 97 + 14340 GGCATCAC-GTGGTCCCTCCAATGA---GGAGTCAGTACTCCTGGGAG----ACA-CGCACACTT-CA----------TGCTCACTGCTCATGGGTTTTGCAAAGTCGTGTCTCGGT i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 17835 99 + 48268 GGCATCACAGCAGTCTCTCCAATGAAGGAGAGCTTGCATTCTAGAAAG----ACA-GCTGCACTT-A------------GTTTATTTCTAATGCGTTTCGCAAAACCGTGTTTCGGT i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14435822 102 - 17734757 CACTTTCCTGTGGTCCCTTTAAAGATGGAGAGCTAATAGTCTAGGAAG----GCAATGTACCCTT-CA----------TGTGTATTTCTCGTGGGTTTTGCAAAACCATGGATTTGT i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 15066 75 + 20752 ---------------------AGGAC--AGAGTGGGTGGCC--GGCGT----GACGCGTGCTCTC-C------------GTTTGTTTCTCAAGGGTTTTGCAGATCCACGCATCGGT i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_294600 744 0 + 1002 I e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 7929 1421 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=309827.000000 s hg19.chr17_gl000204_random 48623 97 + 81310 TTTTCATGGGTTGAGAACTGAGATCCAA-AAA-----CATATATCCACACGGAA----GGCAGGG-GTGAG--CTGGAATCCCTCAGCCTGCGCGG------------TAAGCGATGTGGC---------------A----------------------------------------------------------------------- s panTro2.chr17 79478830 95 + 83384210 TTTTCATGGGTTGAGAACTGAGATCCAA-AAA-----C--ATATCCACACGGAA----GGCAGGG-GTGAG--CTGGAATCCCTCAGCCTGCGCGG------------TAAGCGATGTGGC---------------A----------------------------------------------------------------------- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 17558 95 - 64270 TTTTCATGGGTTGAGAACTGAGATCCAA-AAA-----C--ATATCCACACGGAA----GGCAGGG-GTGAG--CCGGAATCCCTCAGCCTGCGCGG------------TAAGCAATGTGGC---------------A----------------------------------------------------------------------- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16065933 95 + 17838096 TTTTCATGGGTTGAGAACTGAGATCCAA-AAA-----C--GTATCCACACAGAA----GGCAGGG-GTGGG--CTGGAATCCCTCAGCCTGCGCGG------------TAAGCGATGTGGC---------------A----------------------------------------------------------------------- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75039855 95 + 78773432 TTTTCATGCATTGAGACCTGAGATCCAA-AAA-----C--ATATCCACACGAAA----GGCAGGG-GTGGG--CTGGAATCCCTCAGCCTGCACGG------------TAAGCAATGTGGC---------------T----------------------------------------------------------------------- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 47257 95 - 95547 TTTTCATGCATTGAGACCTGAGATCCAA-AAA-----C--ATAGCCACACGGAA----GGCAGGG-GTGGG--CTGGAATCCCTCAGCCTGCACGG------------TAAGCGATGTGGC---------------T----------------------------------------------------------------------- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 49242 90 + 225949 TTCTCA-----TGAGACCTGAAATCCAA-AAA-----C--ACCTCCACGTGGAA----GGCAGGG-GTGGG--CTGGAATCGCTCAGCCTGCCCGG------------TAAGCGATGTGGC---------------A----------------------------------------------------------------------- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 3984 90 + 9575 TTCTCCTGCATTCGGTCCTGAGCTCCAA-AAT-----C--ATCCCCATGCAGAA----GGCAGGA-ATGGG--CTGGAA----TCAGCCAGAGTGG------------TTGG-ACTATGAT---------------G----------------------------------------------------------------------- i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_72647 910 95 + 4992 TTTTCATGCATTCAGGCCTAAGATCCAA-AAA-----C--ACCCCCAAGCTGAA----GCCAGGG-GCGAG--CTGGAACCACCCAGCCTGGGAGG------------GGGGTGCCAGGGT---------------G----------------------------------------------------------------------- i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 29462 93 + 287808 TTTTCATGCAGCAAGTCCTGAGATCCAA-AAA-----C--ATCCCCAAGCTGAA----GGCA-GG-GTGGG--CTGGGGTGGCTCAGCCTGAGAGG------------TGGGCACCA-GGT---------------G----------------------------------------------------------------------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118761785 94 + 121843856 TTTTCATGGGCTGAGTCCTGAGACCCTGAAAA-----C--ATCTCCATGCTGTG----GGAGGGG-GGAAG---TGGATTCCCTC-GGCTTGGGAG------------GAAATGTCTTAGC---------------A----------------------------------------------------------------------- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4391962 92 + 7991924 GTTTTGTGCACTGAGTCCCAAGACCCAG-AAA-----C--ATCCCCATGCTGAA----AGCAGAT-GGGAG----GGAGCCACTG-GCCTGAGTGA------------GAAGGGCCAGAGC---------------A----------------------------------------------------------------------- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 9622 94 + 44242 TTTTCATGTGTTGAGTCCTGAGACCCCA-AAA-----C--ATCTCCATGCTGAA----GGTGGGGCAGCAG----GAAATCCCTGAGCCTGAGAGG------------GAGGCACCATGGT---------------G----------------------------------------------------------------------- i speTri1.scaffold_128901 C 0 C 0 s turTru1.scaffold_106006 131710 90 + 145505 TTGTCACACATTGAGCCCTGAGAACCAA-AAA-----C--ATCTCCCTGCTGAA----GGCAGGG-GTGGG--ATAGAACCACTGAGTCTGA-----------------AAGTGCCACGGT---------------G----------------------------------------------------------------------- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10861866 95 - 65312493 TTGTCACACTTTGGGTCCTGGGAATCAA-AAA-----C--ATCTCCTTGCTGAA----TGCAGAG-GTGGG--ATAGAATCCTTCAGTCTGAGCGT------------TAAGTGCCATAGT---------------G----------------------------------------------------------------------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58045532 80 - 61308211 TTTTCGCACATTAAGTCCTGAGAAGCAA-GAA-----C--ATCTCCACACTGGA----GGCAGGG-ACGGG--ATAGAGTCACTC---------------------------GGCCACAGT---------------G----------------------------------------------------------------------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 34754 70 + 132007 TT-TCAC------------------------T-----C--ATCTCCACACCGAA----CGCAGAG-AAGGA--AGAGAATCCCTCTGTCTGAGAGT-------------AAGTGCCACGGT---------------G----------------------------------------------------------------------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59439490 73 - 64418924 TTGTCAC------------------------T-----C--ATCTCGGTACTGAA----AGCAGAG-GTGGGACAGAGAATCTCTCTGGCTGAGAGT-------------AAATGCCATGGT---------------G----------------------------------------------------------------------- i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 12411 90 + 14340 GGGCCACGCACTGAG---CGAGAAGCAG-ACA-----C--GTCCTCGCACCGAATGGTGGCCGGG-C--GG--GCAGAGTCGCC--GTCTGAGAGC--------------CGTGCCATGCG---------------G----------------------------------------------------------------------- i myoLuc1.scaffold_4816 C 0 I 30 s pteVam1.scaffold_11245 17934 92 + 48268 TTGTCACAC-CCGAGATCTGAGAACCAA-A-G-----T--GTCCCCATACTGAA----AGCGGGG-CTGGG--ACAGAGTTGCTTGGCCCGAGAGT-------------GCGTGGCATGGC---------------G----------------------------------------------------------------------- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14435924 193 - 17734757 TTTGCAGGCATTGGGTTCTGAGAGTCAA-AAATCTTCC--CTATCTGTG---AA----GGCAGGG-CTGGG--ATGGAACCCCTCAGGCTGAGAGAGAACCCACCCATGAAG--GCAGGGCTGGGGTAGAACCCCTCAGTCTGAGAACAAACCCACTCGTGATGGCAGGGCTGGGGTGGAGGTGCTCAGTCTGAGAGAAAGCATGGCC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 19883 101 + 24616 TTTTCAGGCATTAGGATCTGACAGCCAG-AGATCT--C--CCGTCTGTG----A----GACAGGG-CTGGG--CTGGAAGCCCTCAGCATGAGAGA------------GAAG--ACGTGGC---------------CAGTTTG----------CAC---------------------------------------------------- i proCap1.scaffold_29042 I 1037 C 0 s dasNov2.scaffold_28617 15141 79 + 20752 CTTTCCCCCATTGAGTCCTAAGAAGCAA-A-------C--CTTCCTAGG---------GGGAGCG-TCATG--GTGGCAATCTAC------AGCGC------------AGAG------------------------GAGTCTG----------------------------------------------------------------- i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 7929 1421 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=465347.000000 s hg19.chr17_gl000204_random 48720 134 + 81310 GCAAACTATAGGCTCAGAGGAGCCCGGGAAG-------G---GCTGGGG-G---AG-GGAGGCCATGA--TCCTGCTTCCTT--TCCTCTCCCTCATGGGAAATCCAACTGGCATGG-TCT--GGAGCCTCATCTCTGATGATCCA-ATGCCACTCC s panTro2.chr17 79478925 134 + 83384210 GCAAACTATAGGCTCAGAGGAGCCCGGGAAG-------G---GCTGGGG-G---AG-GGAGGCCATGA--TCCTGCTTCCTT--TCCTCTCCCTCATGGGAAATCCAACTGGCATGG-TCT--GGAGCCTCATCTCTGATGATCCA-ATGCCACTCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 17653 133 - 64270 GCAAACTATAGGCTCAGAGGAGCCCGGGAAG-------G---GCTGGGG-G---A--GGAGGCCATGA--TCCTGCTTCCTT--TCCTCTCCCTCATGGGAAATCCAGCTGGCATGG-TCT--GGAGCTTCATCTCTGATGATCCA-ATGCCACTCC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16066028 135 + 17838096 GCAAACTATAGGCTTAGAGGAGCCCGGGAAG-------G---GCTGGGG-G---AG-GGAGGCCATGA--TCCTCCTTCCTT--TCCTCTCCCTCGTGGAAAATCCAGCTGGCATGGTTCT--GGAGCCTCATCTCTGATGATCCA-ATGCCACTCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75039950 134 + 78773432 GCAAACTGTAGGCTCAAAGGAGCCCGGGAAG-------G---GCTGGGG-G---AG-GGAGGCCATGA--TCCTCCTTCCTT--TCCTCTCCCTCAGGGGAAATTCAACTGGCATGG-TTT--GGAGCCTCGTCCCTGATGATCCA-ATGCCACTCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 47352 134 - 95547 GCAAACTGTAGGCTCAAAGGAGCCCGGGAAG-------G---GCTGGGG-G---AG-GGAGGCCATGA--TCCTCCTTCCTT--TCCTCTCCCTCATGGGAAATTCAACTGGCATGG-TTT--GGAGCCTTGTCCCTGATGATCCA-ATGCCACTCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 49332 132 + 225949 GCAAACTACAGGCTCAGAGGAG-CCGGGAAG-------G---GCTGGGG-A---AG-GGAGGCCATGA--TCCTTCTTCCTT--TCCTA-CCCTCATGAGAAATCCAGCTGGCATGG-TCT--GGAGCCTCATCTCTGATCGTCCA-ACGCCACACC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 4074 135 + 9575 GCCACTGACAGGCTCAGAGGATTATGGGATG-------G---GCTGGGG-A---AGTGGGGGTCATGA--TTCTCCTTCCTT--TCTTCACCCTCATGAGAAATCCAACTGGCACTG-ATC--AGGGCCCCATCCCTTACGATCCA-AGGCCACTCC i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_72647 1005 123 + 4992 AT-GATCACAG-AGCAGAGGAACCAGGGAAC-------GCTTGGGGGGG-G------TGAGGTCCCCA--TTCTCCTTCCTT--TC--CTCCCACGTGGGAAGTCCAACTGGCGGAG-----------CCCTTCGTTTATAATCCA-AGGCCATTTG i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 29555 107 + 287808 GT-ATCCACAGTCTCGGGGGAGCCCGGGAAG-------A---GCCGGGG-C------TGAGGGTCACC--ATCTCCTCCCAT--CCCTCTCCCTCATGGGAAATCCACC---------------------------TTATAATCCA-AGGCCACTTG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118761879 91 + 121843856 GCGACTCATGGGCTC--AGGAGTCCAAGATG-------A------TGGG-G---AT-AGTGGCC---A--TACTCTATCTTTCTCCCATCTCGCCATG---------ACCGGCAGCA-CCC--T-------TTCT---------------------- i mm9.chr11 C 0 I 37 s cavPor3.scaffold_76 4392054 125 + 7991924 GCCGCCCACGGGCACAGAGGGATCAGGAAGG-------G------TGGGCG---AA-GGAGGCT--------CATGATTCTTATTCCTCTTCATCGTGGAAAAT-CAGCTGGCATCA-GCC--TGGTCCACCTCT--CCTAACCCA-AGACCACGTC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 9716 114 + 44242 GCCATCCACAGGCTGAGAGGCCTCCAGGAAG-------A------AGGG-GGGCAC-AAGGGTCAGGA--TTCGCCTCCCATCCCCCACTCTGCACTGGACACT-CTGCTGGTGCTG-ACC--TGGTCCCTCTCT---------------------- i speTri1.scaffold_128901 C 0 I 17 s turTru1.scaffold_106006 131800 127 + 145505 GCGATCTACAGGTTCAGAGGAGTCTGGGAGG----------------AG-A---GG-GGACGTCACGA-----TTCTTCTCT--TCCTCCTCCTCATGGAAAATCCAGCTGGCACTG-ACCTAGGGCCCCGACCTCTTAGAATCCA-AAGCCACTCC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10861961 126 - 65312493 GCGATCTTCAGATTCAGAGACGTCCGGGAAG-----------------G-G---GA-GGAGGTCACGA-----TTCTTCTTT--TCTTCCTCCTCGTGGAGAATCCAGCTGACATTG-AGCTAGGGCCCCCATCTCTTAGAATCCA-AAGCCACTCC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58045612 143 - 61308211 GCTGCCTACAGGTTCAGAGGAGGCCGGGAAGGGGTGGGG---GGGGGGG-G---CG-TGGTGTCACAA--TTCTTCTTCCTT--TCCTCCTCCTCCTGGAAAATCCAGCTTGCATTG-ACCTAGGGCCCCCAACTCTCAGAATCCA-AGGTCACTCC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 34824 128 + 132007 GCAACCTACAGGTTCAGAGGGCTC-------------TG---GTGGCGG-G---GG-CGAGGCCAAGG--TTCTTCTTCTTT--CCCACCCCG-CATGG-AAACCCAGCTGGCAATG-ACCTAGGCCCCCCCAGCCCAGCAATCCA-AGGCCATTCC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59439563 137 - 64418924 G-GATCCACAGGTCCAGAGGAGGCTGGGAAG----GGTG---GTGGTGG-G---AG-TG-GGTCATGA--TGCTTCTTCCTT--TCAGCACCACCATGGAAAACCCAGCTGGCAATG-ACCTAGGGCCCTCAACTCTGAGAATCCA-AGGCCACTCT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 18026 105 + 48268 GCAACCTACGGGCTCCGAGGAGCCCAGGCAG-----------GCCTGGG-G---TG-TGGGGTCGCAATCTTCTCGCTCTGT--CCCGCCCCCTCACGGGAAATCCGACTGGCACTG-ACCCAG--------------------------------- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14436117 132 - 17734757 ACAGTGCACAATGTAAACGACATCCGGGAAG-------G-------GCA-G---GA-GGGGGTCATGA--TTCTTCTTCTTG--TCCCACCCCTCATGAAAAACCCAGCTGGCATTC-ACATGAGGGCCCAAACTCTTACAATCCA-AGGCCACTCC i loxAfr3.scaffold_49 C 0 I 23 s proCap1.scaffold_29042 19984 101 + 24616 -----------TGTAAAGGATACCCAGGAAG-------G-------GTG-G---GG-TGG--------------------TG--TCCTCCCTCTCTCAGAAAACCCAGCCGTCACTG-ACTTGGGCCCCTG---TCTCATAATCCATAGGCCTCCCC i proCap1.scaffold_29042 C 0 C 0 s dasNov2.scaffold_28617 15220 114 + 20752 ------------GGAAAGGGCGCGGAGGGGG-------G-------CGG-A---GG-TGAGGGTGTGA--GTCTTC----AT--TTCCTCCCTGCATGGAAAGTGCAGCCGGCACGG-ACCTG-GACCCCGAGCTCTCACAATTCC-AGGCCGCCC- i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 7929 1421 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=52239.000000 s hg19.chr17_gl000204_random 48854 55 + 81310 CTTTGCAAAAGCAA---GAGGACCTGCTGCAGTG--CTCCTCT--------C--TCCTTGAGCTACCCtt s panTro2.chr17 79479059 53 + 83384210 CTTTGCAAAAGCAA---GAGGACCTGCTGCAGTG--CCCCTCT--------C--TCCTTGAGCTACtc-- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 17786 53 - 64270 CTTTGCAAAAGCAA---GAGGACCTGCTGCAGTG--CCCCTCT--------C--TCCTTGTGCTACtc-- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16066163 57 + 17838096 CTTTGCAAAAGCAA---GAGGACCTGCTGCAGTGCCCCCCTCT--------C--TCCTTGTGGTACtctt i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75040084 55 + 78773432 CTTTGCAAAAGCAA---GAGGACCTGCTGCAGTG--CCCCTCT--------C--TCCTTGTGGTACTCtt i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 47486 55 - 95547 CTTTGCAAAAGCAA---GAGGACCTGCTGCAGTG--CCCCTCT--------C--TCCTTGTGGTACtctt i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 49464 54 + 225949 CTTTGTAAAAGCAA---GAGGACCAGCTGCAGC---CCCCTCT--------C--TCCTTGTGATACTCTt i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 4209 53 + 9575 CTTTGCAAAAGCAA---AGGGATCTGCTGCAGTG---TTCTTT--------T--TCCTTGTGGTACTCT- i tarSyr1.scaffold_143701 C 0 M 1361 s micMur1.scaffold_72647 1128 47 + 4992 CTTTGCAAAAGCAAAGGAGGGACCTGCTGCCCTG--CCCCTCT--------G--TCCCT----------- i micMur1.scaffold_72647 C 0 I 10 s otoGar1.scaffold_94362.1-287808 29662 45 + 287808 CTTTGCAAAAGCAA---AGCGGCCTGGTGCAGTG--TCCCTCT--------C--TCCCTG---------- i otoGar1.scaffold_94362.1-287808 C 0 I 53 s cavPor3.scaffold_76 4392179 54 + 7991924 CCCTGCAAAGGCAC---AGGCACTTGCTGCCAAC--CCCCTCA--------C--GCTGTGGGTCCCCGT- i cavPor3.scaffold_76 C 0 I 76 s speTri1.scaffold_128901 9847 35 + 44242 TTTTGCTCAAGCAC---TGGC-------GGCAAT--GCCCCCA--------T--CTC------------- i speTri1.scaffold_128901 I 17 C 0 s turTru1.scaffold_106006 131927 34 + 145505 ---TGC-AAAGCAA---AGTGCCCAGCACTCCCC--CCTCCTT--------------------------- i turTru1.scaffold_106006 C 0 I 35 s bosTau4.chr19 10862087 35 - 65312493 ---TGCGAAAGTAA---AGCACCCAGCACTTCCC--CCTCCTT--------------------------- i bosTau4.chr19 C 0 I 2 s equCab2.chr11 58045755 38 - 61308211 ---TGCAAAGGCAT---AGAGCCCAGAAACAGCG--TCCCTCT---CCT--------------------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 34952 35 + 132007 ---TGCAAAAGCAA---AGAGCCCAGGTGCCGCA--CCCCCCC--------------------------- i felCat3.scaffold_206428 C 0 I 49 s canFam2.chr9 59439700 43 - 64418924 ---TACAAAAGCAA---AGAGCCCAGCTGCAGTA--CCCCCCTAACTGTGG------------------- i canFam2.chr9 C 0 C 0 s proCap1.scaffold_29042 20085 33 + 24616 -----GCAAGGCCC---AGGAGTC-ATTGCAGAA--CCCCTGT--------C------------------ i proCap1.scaffold_29042 C 0 I 30 s dasNov2.scaffold_28617 15334 38 + 20752 ---TGGAACGGC-------------------AAA--CGTCTTC--------CTCTCCTTGAGGTTCTCTT i dasNov2.scaffold_28617 C 0 I 1362 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e pteVam1.scaffold_11245 18131 0 + 48268 C e echTel1.scaffold_194555 7929 1421 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118761970 37 + 121843856 I e loxAfr3.scaffold_49 14436249 23 - 17734757 I a score=181255.000000 s hg19.chr17_gl000204_random 48909 147 + 81310 t----------------------tttttttttttttttttagggggagtcttgctctgttgcccagactggagtgcagcggtatgatcttggctcactgcgacctccacctcccaggttcaagtgattctcctgcctcagcctcctgagtagctgggattataggcgtg s calJac1.Contig5139 49518 164 + 225949 t----ttttcttcttttttttcttttttcttttttttttgagacagagtcttgctctgttgcccagactggaatgcaggggtgtgatcttgcctcactgtaacctagacctaccggattcgagggattctcctgcctcagcctcccaagtggc-aggattacaggcgtg i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 47541 164 - 95547 t-----ttttttcttttcttttcttttttttttttttttgagatggagtcttgctctgttgcccagactggagtgcagtggtgtgatcttggctcactgcaacctccacctcccagattcaagtgattctcctgcctcagcctcctgagtagctgggattataggtgtg i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75040139 169 + 78773432 tttttttcttttcttttttttttttttttttttttttttgaaatggagtcttgctctgttgcccaaactggagtgcagtggtgtgatcttggctcactgcaacctccacctcccagattcaagtggttctcctgcctcagcctcctgagtagctgggattataggcgtg i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16066220 155 + 17838096 t--------------gttttttgttttttttttttttccgagacagagtcttgctctgttgcccagactggagtgcaatggtgtgatcttggctcactgcaacctccacttcccagattcaagtgattctcctgcctcagcctcctgagtagctgggattataggcatg i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 17839 147 - 64270 t----------------------tttttttttttttttttagacggagtcttgctctgttgcccagactggagtgcagcggtatgatcttggctcactgcaacctacacctcccaggttcaagtgattctcctgcctcagcctcctgagcagctgggattataggtgtg i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79479112 146 + 83384210 -----------------------tttttttttttttttttagggggagtcttgctctgttgcccagactggagtgcagcagtatgatcttggctcactgcaacctccacctcccaggttcaagtgattctcctgcctcagcctcctgaatagctgggattataggtgtg i panTro2.chr17 C 0 C 0 s bosTau4.chr19 10862124 35 - 65312493 ---------------------------------------------GTGTC----------------------------------------------------CCTTGAC-------ATTCAA------------------------------CCGGGAGTAGAGGCATG i bosTau4.chr19 I 2 I 16 s pteVam1.scaffold_11245 18131 18 + 48268 -----------------------------------------GCCCGGGTC----------------------------------------------------CCT--------------------------------------------------AGAGTG-------- i pteVam1.scaffold_11245 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 20118 30 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e speTri1.scaffold_128901 9882 0 + 44242 C e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e micMur1.scaffold_72647 1175 10 + 4992 I e turTru1.scaffold_106006 131961 35 + 145505 I e felCat3.scaffold_206428 34987 49 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e otoGar1.scaffold_94362.1-287808 29707 53 + 287808 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I e canFam2.chr9 59439743 0 - 64418924 C e equCab2.chr11 58045793 0 - 61308211 C e cavPor3.scaffold_76 4392233 76 + 7991924 I e mm9.chr11 118761970 37 + 121843856 I e loxAfr3.scaffold_49 14436249 23 - 17734757 I a score=59628.000000 s hg19.chr17_gl000204_random 49056 41 + 81310 caccatcatacccagcgaattttttgtacttttagtataga s calJac1.Contig5139 49682 41 + 225949 caccatcatgcctggctaactttttgtactcttagtagaaa i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 47705 41 - 95547 caccatcatacccaactaattttttgtactcttagtataga i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75040308 41 + 78773432 caccatcatacccaactaattttttgtactcttagtataga i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16066375 41 + 17838096 caccatcatacccagctaatttcttgtacttttagtataga i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 17986 41 - 64270 caccatcatacccagcgagttttttgtacttttagtataga i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79479258 41 + 83384210 caccatcatacccagtgaattttttgtacttttagtataga i panTro2.chr17 C 0 C 0 s pteVam1.scaffold_11245 18149 3 + 48268 CAC-------------------------------------- i pteVam1.scaffold_11245 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 20118 30 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e speTri1.scaffold_128901 9882 0 + 44242 C e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e micMur1.scaffold_72647 1175 10 + 4992 I e turTru1.scaffold_106006 131961 35 + 145505 I e felCat3.scaffold_206428 34987 49 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e otoGar1.scaffold_94362.1-287808 29707 53 + 287808 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I e canFam2.chr9 59439743 0 - 64418924 C e bosTau4.chr19 10862159 16 - 65312493 I e equCab2.chr11 58045793 0 - 61308211 C e cavPor3.scaffold_76 4392233 76 + 7991924 I e mm9.chr11 118761970 37 + 121843856 I e loxAfr3.scaffold_49 14436249 23 - 17734757 I a score=59376.000000 s hg19.chr17_gl000204_random 49097 40 + 81310 tggggtttcaccatgttgaccaggctggtgttgagctcct s calJac1.Contig5139 49723 40 + 225949 tagggtttcaccatgttggccagactggtcttgaactact i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 47746 40 - 95547 cggggtttcaccatgttgaccagactggtcttgagctcct i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75040349 40 + 78773432 cggggtttcaccatgttgactagactggtcttgagctcct i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16066416 40 + 17838096 cggggtttcaccatgttgaccaggctggtcttgagctcct i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 18027 40 - 64270 cggggtttcaccatgttgaccaggctgggcttgagctcct i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79479299 40 + 83384210 tggggtttcaccatgttgaccaggctggtcttgagctcct i panTro2.chr17 C 0 C 0 s equCab2.chr11 58045793 12 - 61308211 --------------------TGGGGTCCTCTT-------- i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_11245 18152 16 + 48268 ----------------------GGCTGCTGCTGAGCCC-- i pteVam1.scaffold_11245 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 20118 30 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e speTri1.scaffold_128901 9882 0 + 44242 C e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e micMur1.scaffold_72647 1175 10 + 4992 I e turTru1.scaffold_106006 131961 35 + 145505 I e felCat3.scaffold_206428 34987 49 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e otoGar1.scaffold_94362.1-287808 29707 53 + 287808 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I e canFam2.chr9 59439743 0 - 64418924 C e bosTau4.chr19 10862159 16 - 65312493 I e cavPor3.scaffold_76 4392233 76 + 7991924 I e mm9.chr11 118761970 37 + 121843856 I e loxAfr3.scaffold_49 14436249 23 - 17734757 I a score=79473.000000 s hg19.chr17_gl000204_random 49137 72 + 81310 gacctcaggtgat-tccctgcctcggcctcccaaagtgctgggattacaggcgtgagacaccctgccctggcc s pteVam1.scaffold_11245 18168 20 + 48268 ------------------GGCTACG-----------------------------GAGCGACCCCGCC------ i pteVam1.scaffold_11245 C 0 C 0 s felCat3.scaffold_206428 35036 39 + 132007 GGCCCGAGGCAAT-CCACCGCCAGC-----------------------------AGGCGAGCCTCCCCT---- i felCat3.scaffold_206428 I 49 C 0 s equCab2.chr11 58045805 19 - 61308211 -------GACATT-CCCCGGGCATG-----------------------------GA----------------- i equCab2.chr11 C 0 C 0 s panTro2.chr17 79479339 72 + 83384210 gacctcaggtgat-tccctgcctcggcctcccaaagtgctgggattacaggcgtgagacaccctgccctggcc i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 18067 72 - 64270 gacctcaggtgat-tccctgcctcggcctcccaaagtgctgggattatagacgtgagacaccctgccctggcc i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16066456 72 + 17838096 gacctcaggtgat-tccctgcctcagcctcccaaagtgctgggattacgggcgtgagccaccctgcccTGGCT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75040389 72 + 78773432 gacctcagttgat-tccctgccttggcctcccaaaatgctgggattacaggtgtgagccaccctgccccggcc i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 47786 72 - 95547 gacctcaggtgat-tccctgccttagcctccaaaaatgctgggattacaggtgtgagccaccctgccctggcc i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 49763 72 + 225949 gacctcaagtgatctgccctcctcggcctcccaaagtgctgggattacaggtgtgagccaccatgccc-agcc i calJac1.Contig5139 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 20118 30 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e speTri1.scaffold_128901 9882 0 + 44242 C e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e micMur1.scaffold_72647 1175 10 + 4992 I e turTru1.scaffold_106006 131961 35 + 145505 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e otoGar1.scaffold_94362.1-287808 29707 53 + 287808 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I e canFam2.chr9 59439743 0 - 64418924 C e bosTau4.chr19 10862159 16 - 65312493 I e cavPor3.scaffold_76 4392233 76 + 7991924 I e mm9.chr11 118761970 37 + 121843856 I e loxAfr3.scaffold_49 14436249 23 - 17734757 I a score=41682.000000 s hg19.chr17_gl000204_random 49209 27 + 81310 TCCTT--------GTGGTACTCTTGACACCCCGCT s mm9.chr11 118762007 26 + 121843856 CAAAG--------GTGGTTTTCTTGAT-CCCCATC i mm9.chr11 I 37 C 0 s calJac1.Contig5139 49835 27 + 225949 CCCTG--------GTGGTACTCTTGACACCCCGCT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 47858 27 - 95547 TCCTT--------GTGGTACTCTTGACACCCCGCT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75040461 27 + 78773432 TCCCT--------GTGGTACTCTTGACACCCCGCT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16066528 27 + 17838096 TCCTT--------GTGGTACTCCTGACACCCCGCT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 18139 27 - 64270 TCTTT--------GTGGTACTCTTGACACCCCGCT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79479411 27 + 83384210 TCCTT--------GTGGTACTCTTGACACCCCGCT i panTro2.chr17 C 0 C 0 s canFam2.chr9 59439743 29 - 64418924 --TTTGTGAAATTGTGGCCACCCCCA----CCCCG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 18188 22 + 48268 -------------GTGGTTCCCTTGACAGTCCGCC i pteVam1.scaffold_11245 C 0 C 0 s speTri1.scaffold_128901 9882 20 + 44242 -------------AGGGCTCTCTTGAC-TCCTG-C i speTri1.scaffold_128901 C 0 C 0 s micMur1.scaffold_72647 1185 12 + 4992 -----------------------GGACATCCCGCT i micMur1.scaffold_72647 I 10 C 0 s loxAfr3.scaffold_49 14436272 20 - 17734757 ---------------GGGTCGCCTGACATTCGGCC i loxAfr3.scaffold_49 I 23 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 20118 30 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e turTru1.scaffold_106006 131961 35 + 145505 I e felCat3.scaffold_206428 35075 0 + 132007 C e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e otoGar1.scaffold_94362.1-287808 29707 53 + 287808 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I e bosTau4.chr19 10862159 16 - 65312493 I e equCab2.chr11 58045824 0 - 61308211 C e cavPor3.scaffold_76 4392233 76 + 7991924 I a score=61955.000000 s hg19.chr17_gl000204_random 49236 23 + 81310 GGCAGTGGAGGCA-TGGGGAGAGC- s panTro2.chr17 79479438 23 + 83384210 GGCAGTGGAGGCA-TGGGGAGAGC- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 18166 23 - 64270 GGCAGTGGAGGCA-TGGGGAGAGC- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16066555 24 + 17838096 AGCAGTGGAGGTATTGGGGAGAGC- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75040488 23 + 78773432 GGCAGTGGAGGCA-TGGGGAGAGC- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 47885 23 - 95547 GGCAGTGGAGGCA-TGGGGAGAGC- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 49862 23 + 225949 GGCAGTGGAGGCA-CAGGGAGAGG- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_72647 1197 22 + 4992 GGGAGTGGAGGCG-TGGGGTGGG-- i micMur1.scaffold_72647 C 0 C 0 s mm9.chr11 118762033 15 + 121843856 AGGAGTAGAGACC-TG--------- i mm9.chr11 C 0 I 8 s speTri1.scaffold_128901 9902 22 + 44242 AGGAATGGACACA-TGAAGAGGG-- i speTri1.scaffold_128901 C 0 C 0 s turTru1.scaffold_106006 131996 15 + 145505 AATGGGGAGGGCG-TG--------- i turTru1.scaffold_106006 I 35 C 0 s equCab2.chr11 58045824 13 - 61308211 ---------GGCA-TGGGGAGGG-- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59439772 22 - 64418924 GGGAGCAGAAGCA-TGAGGAAGG-- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 18210 21 + 48268 TGCAGTGGAGGCG-CG-GGACGA-- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14436292 24 - 17734757 GGGAGTGCAGGCA-CGGGGAGGAGG i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 20118 30 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35075 0 + 132007 C e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e otoGar1.scaffold_94362.1-287808 29707 53 + 287808 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I e bosTau4.chr19 10862159 16 - 65312493 I e cavPor3.scaffold_76 4392233 76 + 7991924 I a score=3268.000000 s hg19.chr17_gl000204_random 49259 24 + 81310 ----------ACACCGGGCCC-----------ATTGAGG---GGACAC s panTro2.chr17 79479461 24 + 83384210 ----------ACACCGGGCCC-----------ATTGAGG---GGACAC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 18189 24 - 64270 ----------ACACTGGGCCC-----------ACTGAGG---GGACAC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16066579 24 + 17838096 ----------ACAGTGGGCCC-----------ATTGAGG---GGACAC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75040511 24 + 78773432 ----------ACAGTGGGCCC-----------ATTGCGG---GGGCAC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 47908 24 - 95547 ----------ACAGTGGGCCC-----------ATTGCGC---GGGCAC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 49885 23 + 225949 ----------GCAGCGAG-AC-----------ATCAAGG---GGACAC i calJac1.Contig5139 C 0 C 0 s speTri1.scaffold_128901 9924 22 + 44242 ----------GCTGTGGGCCT-----------GTCCAGG---GGAC-- i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4392309 8 + 7991924 -------------------AT-----------ACCC-GG--------- i cavPor3.scaffold_76 I 76 C 0 s mm9.chr11 118762056 18 + 121843856 ----------CCAGAGGACAT-----------ACCAGGG--------- i mm9.chr11 I 8 C 0 s bosTau4.chr19 10862175 15 - 65312493 -------------------GC-----------ATCAGTG---GGGCAC i bosTau4.chr19 I 16 C 0 s turTru1.scaffold_106006 132011 21 + 145505 -------------TATGGCGC-----------ATCAATG---GGGCAC i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58045837 24 - 61308211 ----------GGTGGCAGCCC-----------ATCGAGG---GGACAT i equCab2.chr11 C 0 C 0 s canFam2.chr9 59439794 27 - 64418924 ----------ACAGGTGGCCC-----------ATTGAGGCAACAACAT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 18231 24 + 48268 ----------GGCGGTGGCCC-----------ATTCAGG---TGACAC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14436316 45 - 17734757 ACACCCCAGCCCTTGGGGCCCTGGCCAGTGGGATCACAA---GGCCAC i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 20118 30 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e micMur1.scaffold_72647 1219 0 + 4992 C e felCat3.scaffold_206428 35075 0 + 132007 C e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e otoGar1.scaffold_94362.1-287808 29707 53 + 287808 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=-16456.000000 s hg19.chr17_gl000204_random 49283 46 + 81310 AGC----ACAGGCAGGAGCCCTGTTATCCCCTGG-----ATGGCCTGACCCGGGT s panTro2.chr17 79479485 46 + 83384210 AGC----ACAGGCAGGAGCCCTGTTATCCCCTGG-----ATGGCCTGACCAGGGT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 18213 46 - 64270 AGC----ACAGGCAGGAGCCCCGTTATCCCCTGG-----ATGGCCTGACCAGGGT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16066603 46 + 17838096 AGC----ACAGGCAGGAGCCCCATTATCCCCTGG-----ATGGCCTGACCAGGGT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75040535 46 + 78773432 AGC----ACAGGCAGGAGCCCTGTTGCCCCCTGG-----ATGGCCTGACCAGGGT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 47932 21 - 95547 AGC----ACAGGCAGGAGCCCTGTT------------------------------ i papHam1.scaffold8336 C 0 I 69 s calJac1.Contig5139 49908 11 + 225949 A----------GCAGGAGCCC---------------------------------- i calJac1.Contig5139 C 0 I 27 s micMur1.scaffold_72647 1219 40 + 4992 ---------GGTCGGGGAGCCTGCCATCCCCTGC-----AT-GCCTGGCCAGGGC i micMur1.scaffold_72647 C 0 C 0 s speTri1.scaffold_128901 9946 16 + 44242 -------TCAGAGGGGAGCCT--------------------------------GC i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4392317 7 + 7991924 -------CCAGG-----------------------------------------GT i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118762074 40 + 121843856 -------TCAGGCAGGAGCCT---AACCTCTTGG-----GCAGCATGTCCAAAGT i mm9.chr11 C 0 C 0 s bosTau4.chr19 10862190 50 - 65312493 ACCTCGAGAGGCCAGAAGCCCCTTCACCCTCTGG-----AGGCCATGAACAGGGT i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132032 50 + 145505 ACCAAGAGCAGGCAGAAGCCCCTCCACTCTCCAG-----ATGTCCTGGACAAGGC i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58045861 50 - 61308211 ACCATGGGCAGCTAAGAGCCCCTCCACCCTCTGG-----ATGCCCTGGTCAGAGC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 35075 22 + 132007 ----------------------------CTCCCA-----GCGCCCTGGCGACGGT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59439821 49 - 64418924 ACCATGAGGAAGCAAGAG-CCCTCCATTCTCCCA-----GTGCCCTGGTCAGAGT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 18255 48 + 48268 ACCACAGGCGGGCAGGAGCCTATCCA--CCCTGG-----ATGCCTGGGTCCAGGT i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14436361 28 - 17734757 ---------------------------GACCCCGCAGACAGGCCCTGGTCAGCAG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 20148 46 + 24616 AGC----ACGGGGAGAAGCCGAGCCTAGCCCCCG-----GGGCCCCGGTCAGAAC i proCap1.scaffold_29042 I 30 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e otoGar1.scaffold_94362.1-287808 29707 53 + 287808 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=282442.000000 s hg19.chr17_gl000204_random 49329 89 + 81310 AACAACTGAGT--CCACGGCCCCACAGACAGGACC----TTACTTCTTTCTGCCTGGCTTCGGGGTG-TTCCTAAGGACATGAGCTGCTGGGG-GCT s rheMac2.chr16 75040581 89 + 78773432 AACCACCTAGT--CCATGGCCCCACAGACAGGACC----TCACTTCCTTCTGCCTGGCTTCAGGGTG-TTCCTAAGGACATGAGCTGCTGGGG-GCT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16066649 89 + 17838096 AACAACCGAGT--CCATGGCCCCACAGACAGGACC----TCACTTCCTTCTGCCTGGCTTCAGGGTG-TTCCTAAGGACTTGAGCTGCTGGGG-GCT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 18259 89 - 64270 AACAACCGAGT--CCACGGCCCCACAGACAGGACC----TCACTTCTTTCTGCCTGGCTTCGGGGTG-TTCCTAAGGACATGAGCTGCTGGGG-GCT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79479531 89 + 83384210 AACAACCGAGT--CCACGGCCCCACAGACAGGACC----TTACTTCTTTCTGCCTGGCTTCGGGGTG-TTCCTAAGGACATGAGCTGCTGGGG-GCT i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 49946 89 + 225949 AACGTCTGAGT--CCGC-GCCCCACAGACAGGGCCT---TCACTTCCTTCTGCCTAGCTGGAGGGTG-CTCCTGAGGACATTGGCTGCTGGGG-GCC i calJac1.Contig5139 I 27 C 0 s micMur1.scaffold_72647 1259 71 + 4992 --CACCCTCGCAAACACAGCCCGATAGACCGGGCC-------------------TGGCCACAGGGTG-TCCCTAAGAGCCTGAGGTGCTGGCT---- i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 29760 48 + 287808 -------------CCACAGTCCCACAG--------------------------------ACAAGGTG-TTCCTTAGAAGCTGAGCTGCTGGGCT--- i otoGar1.scaffold_94362.1-287808 I 53 C 0 s speTri1.scaffold_128901 9962 78 + 44242 -CACCCACTGG--ATGC-----CCCGACCAGGGCA----CAGCCCCCTCCTGCT-GTTCATGGCGAG-TGTCTGAG-ATGTGAGCTGCT-GGC-T-- i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4392324 86 + 7991924 -GACCCCGCGC--CCACAGCTGCCCAGTCGGGACC----TCACACCTTCCTGCTAGGCCACAGGGTG-GTCTTGAGAATGGCAGGTGCTGGGC-T-- i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118762114 83 + 121843856 -GACCCTTAAT--GCGCAGGTCTTCGGACGGGACC----TCATATC-TCCTGCCCAGCCACAGGGTG-CTCCTGAGTATG--AGCTGCTAGGC-T-- i mm9.chr11 C 0 C 0 s bosTau4.chr19 10862240 90 - 65312493 GACCGCTGGGA--CCACAGCCCCACAGACAGACCCTCACTCATGTCTTTCTGCCTGGCCATA-AGTG-TTCCTGAGAACATGAGCTGCCAGGT-T-- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132082 89 + 145505 GACCCCTGGGT--CCACAGCCCCACAGACAGGACCTCACTCACATCTTTCTGCCTGGCCGT--GGTG-TTCCTGAGAACATGAGCTTCCAGGT-T-- i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58045911 88 - 61308211 AACCCCTGGGT--CCACA-CCCCACATACGGGACCTCACTCAGGT-CCTCTGCCTGGCCCTAGGGTG-GTCCTAAGAACAGGAGCTGCCTGTC---- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 35097 72 + 132007 GATCCCTGGGT--CCACAGCCCCACCGACAGGA-------------CCTCCGCCTGGCC------TG-CTCCTGACGACATGAGCTGCCCGGC-T-- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59439870 84 - 64418924 GACCCCT-GGT--CCACAGCCCCATGGACAGGACCTGGCTCACGTCCCTCTGCCTGGCC------TG-GCTCTGAAAACCTGGGCAGCTGGGC-T-- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 18303 90 + 48268 GACATCTGGGT--CCCCAGCCCCCCAGACAGGCCCTCGCTCACATCCTTCTGCCTGGCCATACGGTG-CTCCTGAGAACAGGAGCTGC-GGGC-T-- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14436389 87 - 17734757 -GATCACAAGT--CCCCAGCCCCGCAGACAGGCCC----ACCTGCTCTTCTGCCAGGCTAGACTGTGTTTCCTGAGAACAGGAGCTGCTGGTC-T-- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 20194 68 + 24616 -GATCACACGT--CCGCAGCCCCACAGACAGG-AC----GCCTGCTCTTCTGTCAGG------------------AAGCACGAGCTACTGGTC-A-- i proCap1.scaffold_29042 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e papHam1.scaffold8336 47953 69 - 95547 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=99978.000000 s hg19.chr17_gl000204_random 49418 54 + 81310 GCTCCAGGGAGCC-------CTTCCAGGCCACCCAAGGGAGT--GAGGGTCCCCTCA-GA-CCCC s panTro2.chr17 79479620 54 + 83384210 GCTCCAGGGAGCC-------CTTCCAGGCCGCCCAAGGGAGT--GAGGGTCCCCTCA-GA-CCCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 18348 54 - 64270 GCTCCAGGGAGCC-------CTTCCAGGCCACCCAAGAGAGT--GAGGATCCCCTCA-GA-CCCC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16066738 54 + 17838096 GCTCCAGGGAGCC-------CTTCCAGGCCACCCAAGGGAGT--GAGGGTCCCCTCA-GA-CCCT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75040670 53 + 78773432 GCTCCAGGGAGCC-------CTTCCAGG---CCCGAGGGAGTGGGGGGGTCTCCTCA-GA-CCCC i rheMac2.chr16 C 0 C 0 s papHam1.Contig132331 0 52 - 1174 GCTCCAGGGAGCC-------CTTCCAGG---CCCGAGGGAGT-GGGGGGTCTCCTCA-CA-CCCC i papHam1.Contig132331 n 69 C 0 s calJac1.Contig5139 50035 37 + 225949 CCTCCAGGGAGCC-------CTTCCAGG-------------T-------TCTCCTCATGA-CCCC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_72647 1330 34 + 4992 ----------------------------CCTCCCGACTGAGT--GAGGGTCGCCTGG-CATCCCC i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 29808 55 + 287808 TCTCCTGGGGGCC-------CTTCCAGGCCTCCCAGCTGAGT--GAAGATCTCCTGG-CATCCCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s speTri1.scaffold_128901 10040 51 + 44242 CCTGCTTGCAGCC-------TTCCCAGGCCCCGAGTGGGAGA--A--GGTC-CCCAG-CA-TCCC i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4392410 52 + 7991924 GCCCCTTGGAGAC-------CTTCCAGGTTCCCAGATTCATG--A--GGTTCCCTTG-TT-TCCC i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118762197 61 + 121843856 CGAACCTGGAGACACCCACACCCTTAGATCACCAGAACAAGG--AAGGGTCGCCCAA-CA-TCTC i mm9.chr11 C 0 C 0 s bosTau4.chr19 10862330 50 - 65312493 CCTCCTGGGGACC-------CTCATCAGCCCCCTGAGCACGT--AAGGATATCCTCA-CC----- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132171 49 + 145505 CCTCCTGGGGGCC-------CTCCTAGGCCCCC-GAGCAAGT--AAGGACCTCCTCA-CC----- i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58045999 49 - 61308211 CCTCCTGGGGGCC-------CTTCCAGGCCACCCGAGTGGGG--AGGATC-TCCTCA-CT----- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 35169 41 + 132007 CCTCCGGGGGGCC-------CCTCCTGGCCGCCCAAGCAAGA--AATGAC--------------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59439954 41 - 64418924 GCTCCTGGGGATG-------CCTCCAGCCCACCCAAGTAAGA--AATGCT--------------- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 18393 45 + 48268 CCTCCCGGGGGCC-------CTTCCAGGCCGCCGAGCTAAGG--AGCCCT-----CA-CC----- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14436476 54 - 17734757 ACCTCCTAGGGCG-------CTTCTAGGCCACCTGAGTGAAC--AAGGAGCTCCTCA-CA-TCCC i loxAfr3.scaffold_49 C 0 I 619 s proCap1.scaffold_29042 20262 54 + 24616 ACCTCCGAGGGCC-------CTTCCATGGCACGTGGGTGACG--GGGGAGCCCCTCA-TG-CCCC i proCap1.scaffold_29042 C 0 I 645 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=152193.000000 s hg19.chr17_gl000204_random 49472 75 + 81310 AACCTCTCT-ATAGAGACATGCTAAGGGTTGTT--------------------TCCA-----------------TCCTTACAT-------CTGCAAGT------TTATCTTTTAAAGC-GAGCTCTA s panTro2.chr17 79479674 75 + 83384210 AACCTCTCT-ATAGAGACATGCTAAGGGTTGTT--------------------TCCA-----------------TCCTTGCAT-------CTGCAAGT------TTATCTTTTAAAGC-GAGCTCTA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 18402 76 - 64270 AACCTCTCT-ATAGAGANATGCTAAGGGTTGTT--------------------TCCA-----------------TCCTTGCAT-------CTGCAAGT------TTATCTTTTAAAGCAGAGCTCTA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16066792 96 + 17838096 AACCTCTCT-ATAGAGACATGCTAAGGGTTGTTTCCATCCTTACATCTGCAAGTCCA-----------------TCCTTGCAT-------CTGCAAGT------TTATCTTTTAAAGCAGAGCTCTC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75040723 68 + 78773432 TCCCTCTCT-TTAGAGACATGCTAAGGGTTGTT--------------------TCCA-----------------TCCTAGCAT-------CTGCAAGT------TTATC------AG--GAGCTCTT i rheMac2.chr16 C 0 C 0 s papHam1.Contig132331 52 68 - 1174 TCCCTCTCT-TTAGAGACATGCTAAGGGTTGTT--------------------TCCA-----------------TCCTAGCAT-------CTGCAAGT------TTATC------AG--GAGCTCTT i papHam1.Contig132331 C 0 n 0 s calJac1.Contig5139 50072 68 + 225949 ACCCTCTCC-ATAGAGACATGCCAAGAGTTGTT--------------------TCCA-----------------TCCTGGTAT-------CTGCGGGT------TGATC------AG--AAACTCTT i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_72647 1364 62 + 4992 GCCGTACCC-AGAGAGACATGCTAAGGCTTGTT--------------------TCCA-----------------TCCTG-------------GAAACT------TCATC------AG--GAGCCGTT i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 29863 68 + 287808 ACCCTACCT-AGAGAGACATGCTAAGGGCTGTT--------------------TCCA-----------------TTCCGACTT-------CTGCAGCT------TCACC------AG--GAGCCATT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s speTri1.scaffold_128901 10091 75 + 44242 CACCTCACCTGCAGAGAGATGC--GGGGTGGTT--------------------TCCA----------------TCCCCTGCATGAAGCACCTGCAGCT------TCCCT------AG--AAGCCAGT i speTri1.scaffold_128901 C 0 I 4 s cavPor3.scaffold_76 4392462 86 + 7991924 CATCTTGCT-GCAGAGAAATGC--AGCG----G--------------------TCCACTGCAGGGACAGTGGTCTCCTAGCACTCTGGCCCAGCAGCT------TCCCC------TG--GAGCCATC i cavPor3.scaffold_76 C 0 I 4 s mm9.chr11 118762258 65 + 121843856 CACCTCACC--------------------------------------------TATACCGTAA----------CTCCGAGCATCCTATGCGAGCACCTGGAAGGTCACC------CG--GAGCTACT i mm9.chr11 C 0 I 4 s bosTau4.chr19 10862380 60 - 65312493 --------T-ATACAGGAATGCTAAGACTTGTT--------------------TCTG-----------------TCCTAGCAT-------CTGCGACT------TTATC------TG--GAAACATT i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132220 60 + 145505 --------T-ATACAGAAATGCTGAGACTTGTT--------------------TCCA-----------------TCTTGGCAC-------CTGCAACT------CTATC------TG--GAACCATT i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58046048 60 - 61308211 --------T-AGAGAGAAATGCTAAGACTCGCT--------------------TCCA-----------------TCTTGGCAC-------CTGCGACT------TTATC------TG--GAACCATT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 35210 58 + 132007 -----------CAGAGAGACGCCAAGCCTCATT--------------------TCCA-----------------CCCTGGCAC-------CTGCAACC------CTACC------TG--GAACCATT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59439995 41 - 64418924 ----------ATAGAGAGATGCTCAGCCTCAT-------------------------------------------CTTGGC-------------------------ACC------TG--GAACCATT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 18438 57 + 48268 --------C-ACAGA---CTGCGGAGGCTTGTT--------------------TCTC-----------------TCTCGGCAC-------CTGCGATT------TTACC------TG--GAACCATT i pteVam1.scaffold_11245 C 0 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 20316 645 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I e loxAfr3.scaffold_49 14436530 619 - 17734757 I a score=91850.000000 s hg19.chr17_gl000204_random 49547 24 + 81310 TTAAAGC---------AGCCTCATA--ATTATACC s pteVam1.scaffold_11245 18495 26 + 48268 TTAAAAC---------AGCGTCATCTCCTTGTGGA i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59440036 26 - 64418924 TCAAAAC---------CATGTCATCTCCTTGTGGC i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 35268 26 + 132007 TTAAAAC---------CATGTCGTCTCCTCACGGC i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58046108 26 - 61308211 TTAAAAC---------AACGTCCTGTCCTTGTGGC i equCab2.chr11 C 0 C 0 s turTru1.scaffold_106006 132280 26 + 145505 TTAAAAC---------AGCATCATCTCCTTGTGGC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10862440 26 - 65312493 TTAAAAC---------AGCATCATCTCCTTGTGGC i bosTau4.chr19 C 0 C 0 s otoGar1.scaffold_94362.1-287808 29931 26 + 287808 TTAAAAC---------AGCCTCGTCTTCTCGTAGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_72647 1426 26 + 4992 TTAAAAT---------AGCATCATCTCCTTGGAGC i micMur1.scaffold_72647 C 0 C 0 s calJac1.Contig5139 50140 23 + 225949 TTAAAGC---------AGCATTAT---ATTGTAGC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 48022 24 - 95547 TTAAAGC---------AGCATCATA--ATTGTGCC i papHam1.scaffold8336 I 69 C 0 s rheMac2.chr16 75040791 24 + 78773432 TTAAAGC---------AGCATCATA--ATTGTGCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16066888 24 + 17838096 TTAAGGC---------AGCATCATA--ATTATACC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 18478 24 - 64270 TTAAAGC---------AGCATCATA--ATTATACT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79479749 24 + 83384210 TTAAAGC---------AGCATCATA--ATTATACC i panTro2.chr17 C 0 C 0 s loxAfr3.scaffold_49 14437149 34 - 17734757 -TGAAGCAGTTTTAAAAGTTTCATCTTCTTGTTGT i loxAfr3.scaffold_49 I 619 C 0 s mm9.chr11 118762327 19 + 121843856 ----AAC---------AGCCTCAT---CTTGTAAT i mm9.chr11 I 4 C 0 s cavPor3.scaffold_76 4392552 21 + 7991924 --GTGAC---------ATTATCTA---CTTGCAGC i cavPor3.scaffold_76 I 4 C 0 s speTri1.scaffold_128901 10170 8 + 44242 ---------------------------ATGGTAGC i speTri1.scaffold_128901 I 4 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 20316 645 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=85467.000000 s hg19.chr17_gl000204_random 49571 51 + 81310 CACAGGGAACAGTTTGGAATCC-----------------A-TTCCTT-----------------AACCCTGACCCTTCCGAACCCT s panTro2.chr17 79479773 51 + 83384210 CACAGGGAACAGTTTGGAATCC-----------------A-TTCCTT-----------------AACCCTGACCCTTCCTAACCCT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 18502 50 - 64270 CACAGGGAACAGTTTGG-ATCC-----------------A-CTCCTT-----------------AACCCTGACCCTTCCTAACCCT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16066912 51 + 17838096 CACAGGGAACAGTTCGGAATCC-----------------A-TTCCTT-----------------AACCCTGACCCTTCCTAACCCT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75040815 51 + 78773432 CACAGGGAACAGTTCGGAATCC-----------------A-TTCCTT-----------------AACCCTGACCCTTCCTAACCCT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 48046 51 - 95547 CACAGGGAAGAGTTCGGAATCC-----------------A-TTCCTT-----------------AACCCTGACCCTTCCTAACCCT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 50163 36 + 225949 CACAGGAAACAG-TCAGAATCC-----------------A-TTCCTT-----------------AACCCTGA-------------- i calJac1.Contig5139 C 0 I 6 s micMur1.scaffold_72647 1452 68 + 4992 TACACGCAACAGTTCGGAACCC-----------------A-TTTCCTGAACCGCGATCCTTGCTAACCCCGATTCCTACTAACCCT i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 29957 52 + 287808 CACAGGCAACGGTTCAGAACCC-----------------A-TTTCCTG----------------AGCCCCCGTTTGTGCTAATGCA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s speTri1.scaffold_128901 10178 49 + 44242 --CATG-AACAGTTCAG-AGCCTGTGTCCTCAACCCTGAC---------------------------------CTTCACCAGCCCT i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4392573 27 + 7991924 --CATGAAACAGTTCAG-AGCC-----------------A---------------------------------CCTCCCC------ i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118762346 32 + 121843856 --CAGGAAATAACTCTGAAGCC-----------------A---------------------------------CTCCTTCATCC-- i mm9.chr11 C 0 C 0 s bosTau4.chr19 10862466 39 - 65312493 AAAAGGACACAGTGCAGAATCC-----------------ACTTCCTT-----------------AACTCTGAC------------- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132306 39 + 145505 CACAGGAAACAGTGCAGAATCC-----------------ATTTCCTT-----------------AACTCTGAC------------- i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58046134 38 - 61308211 G-TAGGAAACAGTGCAGAATCT-----------------ATTCCCTT-----------------AACGCTGAC------------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 35294 33 + 132007 GACAGGAAACAGTGCA-----------------------GTGTCCTT-----------------GACCCGGAC------------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59440062 39 - 64418924 CATAGGAGACAATGCAGAGTCT-----------------GCGTCCTT-----------------AACTCAGAC------------- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 18521 39 + 48268 CGTAGCAAACAGTGTAGCATCC-----------------AATTCCTT-----------------AGCTCTGAC------------- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14437183 49 - 17734757 CATAGGAAACAGTTCAGAGTCC-----------------TGTTCCTT-----------------AACCCTAATCCTTAACCCC--- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 20961 49 + 24616 CATAGGAGACTGCTCTGAATTC-----------------TTTCCTTT-----------------AACCTTGACCTTTGACCCC--- i proCap1.scaffold_29042 I 645 C 0 e oryCun2.chrUn0958 20351 1124 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=-24701.000000 s hg19.chr17_gl000204_random 49622 87 + 81310 AGCAACATGCTCGTTCC--------TCTACTAGGTGGATAGCCC---CAGGGAA---G-GGTCCCACTCA-----------CCA---------------------CATCAGCGGCTTTACATAG----ATCGCCTGAT-- s calJac1.Contig5139 50205 97 + 225949 AGCGACGTGCTCGTTCC--------TCTACCAGGTGGATAGCCC---CA-GGAA---G-AGTCCCACTCAGCAGCACTGCTGCA---------------------CGTCAGTAGCTTTACagag----atcacctagt-- i calJac1.Contig5139 I 6 C 0 s papHam1.scaffold8336 48097 87 - 95547 AGCAACGTGCTCTTCCC--------TCTACCAGGTGGATAGCCC---CAGGGAA---G-GGTCCCATTTA-----------CCA---------------------CGTCAGCAGCTTTACATAG----ATCCCCTGAT-- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75040866 87 + 78773432 AGCAACGTGCTCTTCCC--------TCTACCAGGTGGATAGCCC---CAGGGAA---G-GGTCCCATTTA-----------CCA---------------------CATCAGCAGCTTTACATAG----ATCCCCTGAT-- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16066963 87 + 17838096 AGCAACATGCTCGTTCC--------TCTACTAGGTGAATAGCCC---CAGGGAA---G-GGTCCCACTCA-----------CCA---------------------TGTCAGCGGCTTTACCTAG----ATCGCCTGAT-- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 18552 87 - 64270 AGCAACATGCTTGTTCC--------TCTACTAGGTGGATAGCCC---CAGGGAA---G-GGTCCCACTCA-----------CCA---------------------CATCAGCGGCTTTACATAG----ATTGCCTGAT-- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79479824 87 + 83384210 AGCAACATGCTCGTTCC--------TCTACTAGGTGGATAGCCC---CAGGGAA---G-GGTCCCGCTCA-----------CCA---------------------CATCAGCGGCTTTACATAG----ATCGCCTGAT-- i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 1520 98 + 4992 AGCAACGTGCTCCTCCT--------TCTAACAGGTGGGTGGCAC---CAGAGGA---G-GGTCACAGTCGGCACCACTGCTGTG---------------------TTCCACCTACTTTCCAAAG----ATCGCCTGAT-- i micMur1.scaffold_72647 C 0 M 2454 s otoGar1.scaffold_94362.1-287808 30009 98 + 287808 AGCCATGAGCTAGTTCC--------CTTAACAGGTGGATAGCAC---TAGAGGA---G-GGTCACAGTCAACACCACTGCTACA---------------------TGCCAACTACTGTCCACAG----GTCACCCAGT-- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118762378 94 + 121843856 CTCATGAGGCCTGGCTCTTCTGTCTCCACAAAAGCAGGCGCCTCCTGCACAGAG---GTGGGTGGTGACGCCAGT------CTA---------------------CACCCATGGTCCTGCTGCG---------------- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4392600 80 + 7991924 ------AGGCCTGACCC-----TCACCCCACTGACAAGTGGCCACACCAAGGAA---G-GGGCACTGTCCCCA--------CCA---------------------TGCCAGGCACCTGGCTGTG---------------- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 10227 90 + 44242 CTCAACCGGCCCGGCCC--------TCTCACATGCAGCTGGCTC---CAAAGCA---G-GGTCACTATCCCTATT------CC------------------------CCTGGGTACCCACTGAGCTACTTCACAT----- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 21475 84 + 41507 -----CCGTCCTAACTC-------TAGCGACAGACAGAAGGCA----CAGGGGA---A-GGCTCACGGCCACACC------TCC---------------------AGCGTGCGTCCCTACCACA----CGCAGAT----- i oryCun2.chrUn0958 I 1124 C 0 s bosTau4.chr19 10862505 72 - 65312493 ----ATTTGCTCATTCC--------TCCAACATGCGGATGGCAC---CAGGGAA---G-GTCTGTGCTCA-----------CCA-----------------------CCAGCTGTTGCAGGCCT----A----------- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132345 73 + 145505 ---GAGATGCTCATTCC--------TCCACCAGGCAGATGACAC---CGAGGAA---G-GCTCATGCTCA-----------CCA-----------------------CCAGTTGCTGTGCGCCT----A----------- i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58046172 76 - 61308211 ---AGGATGCTCATTCC--------TCTAATGGGTGGACGGCAC---CAGGGACGGTG-GTTCACATGCG-----------CCA-----------------------CCGGCTGTTGTGTGCCT----A----------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 35327 72 + 132007 ---AAGACACTCGCTCC--------TGTAACAGGCCGGCGGCAC---CAGAAA----G-GCCCGCGCTCG-----------CCA-----------------------CCGGCTGCTGTGTGCCT----A----------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59440101 71 - 64418924 ---AAGATGTTCATCCC--------TCTAGTAGG-CAGCTGGAC---CAGAAA----A-GGCCACGCTCA-----------CTA-----------------------CAGGCTGCTGTGAGCCT----A----------- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 18560 50 + 48268 ---AAGATGCCTCCTCC--------TTCGACAGACAGCCGGCAC---C-------------------------------------------------------------GACTGCCGTGTGCCT----C----------- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14437232 110 - 17734757 AGCCACATGCTCTTCCC--------TCTAAGGAGTGGCTGGCAC---TGGGGAA---G-GCAAGCCATCA-----------CCCAGGTGTTGTGTGACTACTAAGTGCCATCGACTTTGCATGT----ACGGCCTCCTGG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 21010 96 + 24616 AGCCACACACTCAGTCC--------TCTAACAAGTGGCTGGCAG---CAGGGAA---G-GTGAGAGGCCA-----------CCCAGGTGTCACA--------------CACCTACACTGTACGT----CTTCCCTCCAAT i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=257627.000000 s hg19.chr17_gl000204_random 49709 111 + 81310 CCACGC---AGCAG-------------------TC--CCTGCTTCTCAGCAGGGT-AAACTG--AGGTTCCAGA-GCCTGCCC-TGGGTGGCAAGGCTGGGAAGGGTGCACGCCCTCCCCAGCGGTATGCTGCAGGCAAC s calJac1.Contig5139 50302 109 + 225949 ccacac---aaccg-------------------tc--cctgcttctcagctgggt-aaactg--aggttccaga-gCCTGCCC-TGGCTGACAAGGCTGGGAAGGGTGCATG-CCTCCCTAGCGGTATGCTGCAGGC-AC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 48184 91 - 95547 CCACGC---AGCAG-------------------TC--CCTGCTTCTCAGCTGGCT-AAACTG--AGGTTCCAGA-GCCTGCCC-TGGGTGACAAGGCTGGGAA--------------------GGTCTGCTGCAGGCAAC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75040953 111 + 78773432 CCAGGC---AGCAG-------------------TC--CCTGCTTCTCAGCTGGCT-AAACTG--AGGTTCCAGA-GCCTGCCC-TGGGTGACAAGGCTGGGAAGGGTGCACGCCCTCTCCAGCGGTCTGCTGCAGGCAAC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16067050 110 + 17838096 CCACGC---AGCAG--------------------C--CCTGCTTCTCAGCTGGGT-AAACTG--AGGTTCCAGA-GCCTGCCC-TGGGTGACAAGGCTGGGAAGGGTGCACGCCCTCCCCAGCGGTATGCTGCAGGCAAC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 18639 111 - 64270 CCACGC---AGCAG-------------------TC--CCTGCTTCTCAGCAGGGT-AAACTG--AGGTTCCAGA-GCCTGCCC-TGGGTGACAAGGCTGGGAAGGGTGCACGCCCTCCCCAGCGGTATGCTGCAGGCAAC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79479911 111 + 83384210 CCACGC---AGCAG-------------------TC--CCTGCTTCTCAGCAGGGT-AAACTG--AGGTTCCAGA-GCCTGCCC-TGGGTGGCAAGGCTGGGAAGGGTGCACGCCCTCCCCAGCGGTATGCTGCAGGCAAC i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 30107 111 + 287808 CTCCAC---AGCAG-------------------TG--CCCACTGCTCAGCTGGGT-AAACTG--AGATTTCAGA-GCCTGCCC-TGGGAGACAAGCTTGGGAAGTCCTCATCCCTGCCACAAAAGCACACTGTGGGGAAC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118762472 76 + 121843856 ----GG--------------------------------CCATGTCTCAGCTGAGC-ACCAGT---GGCCTCAGA-GATTACCA-TGTGTAATGTGGTTGATAATCTTGTGTCCCCTCC---------------------- i mm9.chr11 C 0 I 1042 s cavPor3.scaffold_76 4392680 109 + 7991924 ----GAGGGCACAG-------------------TC--TCTGTGTCCCAGCGGAGC-AAAGAC--AGGTCTCAGC-ACCCGCCC-TGGATGACAGAGTTGGAAGGTCTGTGTCCCTTCT-CCACCCCATGCCACAGGCAAT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 10317 101 + 44242 CTATGA--------------------------------CCAAATTCTTGCTCAGC-ACCCTCTGAGGGTTCAG--ACTGGCCC-TGGGCAGCGAGGCCAGGACATCCGCGTACCCTTC--CCCAGCACGCTGCAGCCAA- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 21559 94 + 41507 CTGTGA--------------------------------GCCGATCC--GCAGAGC-AGCCCC--ACAGCCCGGCTGCATGCGC-CGTGTGAGGTGGCCGGGA-GTCCGCACCCCCTCGCCCACAGTGTGTCCT------- i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10862577 132 - 65312493 CTGTGC---ACCAGTTCCTTTACGTGTATCACTTCGCCCCTCTTCTCAGCTGAGC-AAGCTA--GGCTTCACAA-GCTTGACC-CAGGACACAGGGTTGGGAAGTCTACATGCTCTCCCCTCCGGCATATTGCAGTCAGT i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132418 131 + 145505 CTATGT---GCCAGCTCCTTTACATGTGT-GTATCG-CCCTCTTCACAGCTGAGT-AAACGA--GAGTTCAAGA-GCTTGCCCGCAGGCCACAGGGTTGGGAAATCTGCGTGCCCTCCCCCACTGCATGCTGCAGTCAGC i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58046248 122 - 61308211 CTATGT---GCCAGCTCCGGTCTTTGTGGTATCTC--CCTTCTTCTCAGCTGAGT-AAAC---------TGAGA-GCTTGCC--CCAGGTACAGGGTTGGGGAGTCTGCATTCCCTCCCCCAGAGCATGCAGCAGGCAGC i equCab2.chr11 C 0 I 2 s felCat3.scaffold_206428 35399 125 + 132007 CTAAGT---GCCAGCTGGTTG-TACGTCGCACCTC--CCCGCTGCTCGGCTGAGT-AAACT----GGTGTGAGG-ACCTGCC--CCACCCGCAGGGGGGAGAAGGCCGTATGCCCT-CCCCACGGCACGCCGCGGTCAGC i felCat3.scaffold_206428 C 0 I 2 s canFam2.chr9 59440172 127 - 64418924 CTAAGT---GCCAGCTCCTTGCTATGTGCTGCCTC--CCCAGCGCTCAGCTGAGTAAAACG----GGTTTGAGA-GCTTGCT--CCGGCCACGGGGTTGGGAAGTCTGCATTCCCT-CCCGAGAACACGCTGCGGTCAGC i canFam2.chr9 C 0 I 2 s pteVam1.scaffold_11245 18610 125 + 48268 CTGTGC---ACCGGCCCTTCG-CGGGTGTTCTCTC--CCCATTTCTCAGCTGAAT-AGACTG--AGGGCTAAGT-GCCCGCC--TGGGTCACAGGCCTGGG-AGTCTGCGC-CCCT-GCCCACGGCATGCTGCAGTCAGC i pteVam1.scaffold_11245 C 0 I 721 s loxAfr3.scaffold_49 14437342 101 - 17734757 CCTCAC---TGCCG-------------------TC--CCT---TCTCAGCTGAGA-CAACAG--AGGT-CCAGA-GCTCGCC--TGTGTTCCTGGGCTGGGCAGTCAGCATTCCCTCCTCCACACCACGCTGCAG----- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 21106 91 + 24616 CCTCAC---TGCCC-------------------TC--CCCACATCTCAGCTGAGA-CCACGG--AGGT-TCAGA-GCTCACC--TGTGTCACT-GGCTGGGACGTCTGCAACCCCTC------------CCATGG----- i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e micMur1.scaffold_72647 1618 2454 + 4992 M e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e echTel1.scaffold_194555 7929 1421 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I a score=15252.000000 s hg19.chr17_gl000204_random 49820 69 + 81310 CCTGCCACCATCAGAGGTCAGCTCCGGCCTCAGGCT-----GTCCCTGCACAGAGCC---CGCCCAC------CAGCCAGCAG s calJac1.Contig5139 50411 69 + 225949 ACTGCCATCATCAGAAGTCAGCTCTGGCCTCAGGCT-----GTCCCTGCACAGAGCC---CTCCCAG------CAGCCAGCAG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 48275 69 - 95547 CCTGCCACCATCAGAAGTCAGCTCTGGCCTCAGGCT-----GTCCCTGCCCAGAGCC---CTCACAC------CAGCCAGCAG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75041064 69 + 78773432 CCTGCCACCATCAGAAGTCAGCTCTGGCCTCAGGCT-----GTCCCTGCCCAGAGCC---CTCACAC------CAGCCAGCAG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16067160 69 + 17838096 CCTGCCACCATCAGAAGTCAGCTCTGGCCTCAGGCT-----GTCCCGGCACAGAGCC---CTCCCAC------CAGCCAGCAG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 18750 69 - 64270 CCTGCCACCATCAGAGGTCAGCTCTGGCCTCAGGCT-----GTCCCTGCACAGAGCC---CGCCCAC------CAGCCAGCAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79480022 69 + 83384210 CCTGCCACCATCAGAGGTCAGCTCTGGCCTCAGGCT-----GTCCCTGCACAGAGCC---CGCCCAG------CAGCCAGCAG i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 30218 67 + 287808 CACACCTCCACCAGCAGTCAGCTCTG--CTCACACT-----GGCCCTGTACAGCGCC---CTCCTGC------CAGAACTCAG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s cavPor3.scaffold_76 4392789 50 + 7991924 CCTGCCACTCCCCAGAGCCTGGCC-----TCATGCT-----GGCCCTGCC-----------------------CGGCCCACAA i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 10418 52 + 44242 CCTGCCACCTCCCGAAGCCAGCTCTG---TCCTCCC-----CTCCCTACA-----------------------CAGACCGCAG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 21653 31 + 41507 GCTGCAGCCACCAGCGGCCAGCT----------------------------------------------------GGCCTCAA i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10862709 73 - 65312493 CCCACCGTCCTGGAAGTCAGAACCTGGCCTCACACCTTACATCCCCTGCACACAGCC---TCCCGCTACATCTCAG------- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132549 73 + 145505 CCCACCACTCAGGAAGTCAGAGCCTGGCCTCACACCTCACGTCCCCTGCACACAGAC---TCCCTCTGTATCTCAG------- i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58046372 37 - 61308211 CCGGC-------------------------CTCGCC--CCGTCCCCTGCACAGGGCC---CGCC---------TGG------- i equCab2.chr11 I 2 I 8 s felCat3.scaffold_206428 35526 43 + 132007 CCCGCC----------------CCACGCTGCCCACC--CCCCCCCGC---CCGTGCC---GGCC---------CTG------- i felCat3.scaffold_206428 I 2 I 679 s canFam2.chr9 59440301 20 - 64418924 CCC---------------------------CCCACC--AAGCCCCA---------------------------GTG------- i canFam2.chr9 I 2 I 7 s loxAfr3.scaffold_49 14437443 63 - 17734757 -------TCACCGGAAGTCACTTCCGGCCTCATGCT----GTCCCCTACACAGAGCC---TTCCCTC------CAGGTCACAG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 21197 66 + 24616 -------TCACCGGAAGCCACTTCCAGTCCCACACG----GTCCCCAGCACAAGGCCCAGCCCCTGC------CAGCTCACGG i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e micMur1.scaffold_72647 1618 2454 + 4992 M e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e pteVam1.scaffold_11245 18735 721 + 48268 I e echTel1.scaffold_194555 7929 1421 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118762548 1042 + 121843856 I a score=188861.000000 s hg19.chr17_gl000204_random 49889 97 + 81310 GTGCAGGCCG---AATCCACTCACCACACCCACAGGTTGTGCGGCCGGCCCTGATGGGCTTTAAGAG--CTCAT-GAAAGGTAACT-GACATACCGCCTTGCTC s calJac1.Contig5139 50480 97 + 225949 GTGCAGGCTG---AGTCCACTCACCACACCCACAGGTTGTGTGGCCAGTCCTGATGGGCTGTGAGGT--CTCAT-GCAAGGTAATG-TATGTACTGCCTTGCAC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 48344 97 - 95547 GTGCAGGCCG---AATCCACTCACTACACCCACAGGTTGTGCGGCCAGCCCTGACGGGCTTTAAGGC--CTCAT-GAAAGGTAACT-GACATACTGCCTTGCTC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75041133 97 + 78773432 GTGCAGGCCG---AATCCACTCACCACACCCACAGGTTGTGCGGCCAGCCCTGACGGGCTTTAAGGT--CTCAT-GAAAAGTAACT-GACATACTGCCTTGCTC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16067229 97 + 17838096 GTGCAGGCCG---AGTCCACTCACCACACCCACAGGTTGTGCAGCCGGCCCTGATGGGCTTTAAGGT--CCCAT-GAAAGGTAACT-GACATACCGCCTTGCTC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 18819 96 - 64270 GTGCAGGCCG---AATCCACTCACCACACCCACAGGTTGTGCGGCCAGCCCTGATGGGCTTTAAGAG--CTCA--GAAAGGTAACT-GACATACCGCCTTGCTC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79480091 97 + 83384210 GTGCAGGCCG---AATCCACTCACCACAGCCACAGGTTGTGCGGCCGGCCCTGATGGGCTTTAAGAG--CTCAT-GAAAGGCAACT-GACATACCTCCTTGCTC i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 30285 93 + 287808 --GCAGGGCT---GGTCCACCCACTGCAGTGA-GTGTTGTGCAGCTGTCCCTGATGAGCTTCCAGGT--CTCAG-AAAAGGTGATT-AAC-TACAATCTTGTTC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s cavPor3.scaffold_76 4392839 89 + 7991924 AAGT-GGCTG---GGTCCACTCATGGCACTGACAGGTAAAATGTCTATCCCT--------CTGGGAG--CTCGT-GAAAGGTAACTAAATGCTGAGCGTTGTTC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 10470 95 + 44242 ACGT-GACTG---AGGCCACTCAC-ACACTGACCGGCTACGCAGCTCTCCCTGCCG---CCTGCGAGGCCTCACGGAAAGGTAATT-AATGTTCCAACCTGTTC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 21684 60 + 41507 ------GCCG---TCGCCACTG---GCACCTACAGGCTGGG------TCCTC--------CCGGGCA--CTCAC----ACACAGCT------------CGGGTC i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10862782 77 - 65312493 GCGAGTGCC--------------------AGATCGGCT-CCTTGCA-CCCTTAATGGGC-TTGAGGT--CTCAA-GTAAGGTAATT-AACTCACAGCTCTGTCC i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132622 77 + 145505 GCATGTGCC--------------------AGAACTGCT-CCCTGCT-CCCCTAATGGGC-TTGGGGT--CTCGA-GTAAGGTAATC-AGCTCACAGCTTTGTCC i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59440328 95 - 64418924 GCGCTTGCCT---CCTCCATGCACTGGGCTGATCAGCAGAGCCGCT-GCTCCAGTGGGC-TCAAGGT--CTCCA-GAAAGGTAAGA-AAGCTACAGCTTTGTTC i canFam2.chr9 I 7 C 0 s equCab2.chr11 58046417 81 - 61308211 GCGTCTGCT------------CACTGCGAGGACAGGCTGCGTGACT-GCCCTAATGGGC-TTGAGGT--CCCGA-GAAAGGTAATT-AACTTACAGCTT----- i equCab2.chr11 I 8 C 0 s loxAfr3.scaffold_49 14437506 94 - 17734757 -----GGCCTGTGGAACCAGCTCCCCTGCTGACAAGCTGTGCTGCCATCGCTGACAGGCCTTGAGGT--CTCAT-GAAAGGTGATT-AA-TTGCAGCCTTGTTC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 21263 93 + 24616 -----AGCCTGC-ACCCCAGCTCCTCTGCCTACAAGCTGTACTGTCGCAGCTGATGGGTTCTGAGGC--CTCGT-G-CGGGTAACG-AAGTTGCAGCCTCCGCC i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e micMur1.scaffold_72647 1618 2454 + 4992 M e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e pteVam1.scaffold_11245 18735 721 + 48268 I e echTel1.scaffold_194555 7929 1421 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118762548 1042 + 121843856 I a score=199102.000000 s hg19.chr17_gl000204_random 49986 33 + 81310 AGAAGTCA-CTTCCATTTCAATGTGCATGTAACT s calJac1.Contig5139 50577 33 + 225949 AGAAGTCA-CTTCCATTTCAATGCATGTGTAACT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 48441 33 - 95547 AGAAGTCG-CTTCCATTTCAATGTGCATGTAACT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75041230 33 + 78773432 AGAAGTCG-CTTCCATTTCAATGTGCATGTAACT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16067326 33 + 17838096 AGAAGTCA-ATTCCATTTCAATGTGCATGTAACT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 18915 33 - 64270 AGAAGTCA-CTTCCATTTCAATGTGCATGTAACT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79480188 33 + 83384210 AGAAGTCA-CTTCCATTTCAATGTGCATGTAACT i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 9401 33 + 19765 agaaGTTG-CTTCCACTTAAATGTGCGTGTAAAT i micMur1.scaffold_15893 I 2607 C 0 s otoGar1.scaffold_94362.1-287808 30378 33 + 287808 TGAAGTGG-CTTAAATTCAAATGTGCATCTAAAT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s cavPor3.scaffold_76 4392928 34 + 7991924 AAAAGCTGTGTCCCATCTAAGTACGCATGTAAAA i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 10565 33 + 44242 AGAAGTTGTGTTCCATTTAAGT-TACATCTAAAT i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 21744 33 + 41507 TGCAGCAG-GCTCCATTTCAACGTGTGTCCAGAT i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10862859 34 - 65312493 AGAAGTTACATTCCATTTAAATGTGCATCTAAAT i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132699 34 + 145505 AGAAGTTACATTCCATTTAAATGTGCATCTAAAT i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59440423 34 - 64418924 AAAAGTTGCATAGCATTTCAACATGCATCTAAAT i canFam2.chr9 C 0 C 0 s equCab2.chr11 58046498 27 - 61308211 --GAGTT-----CCATTTAAATGTGCGTCTAAAT i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14437600 34 - 17734757 AGAAGTTGTGCTACATTTCAACATACATCTAAAT i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 21356 32 + 24616 AGAAGCTGTGCT--GTTTCGGTGTGTGTCCACGT i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e pteVam1.scaffold_11245 18735 721 + 48268 I e echTel1.scaffold_194555 7929 1421 + 11139 I e dipOrd1.scaffold_56485 3710 4014 + 7959 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118762548 1042 + 121843856 I a score=151043.000000 s hg19.chr17_gl000204_random 50019 53 + 81310 GTGTGTGCCC------ACGGGCAAAGG----GTGATTCTTGTAAG--AAT--CAGC-TGATGGGAGTG s calJac1.Contig5139 50610 53 + 225949 GTGTGGGCCC------CAGGGCAAAGG----GTGATTCTTATAAG--AAT--CAGC-TGATGGGAGTG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 48474 54 - 95547 GTGTGTGCCCT-----GGGGGCAAAGG----GTGAGTCTTATAAG--AAT--GAGC-TGATGGGATTG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75041263 54 + 78773432 GTGTGTGCCCT-----GGGGGCAAAGG----GTGAGTCTTATAAG--AAT--GAGC-TGATGGGATTG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16067359 54 + 17838096 GTGTGTGCCCT-----GGGGGCAAAGG----GTGACTCTCATAAG--AAT--CAGC-TGATGGGAGTG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 18948 54 - 64270 GTGTGTGCCC------ATGGGCAAAGG----GTGATTCTTGTAAG--AAT--CAGCTTGATGGGAGTG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79480221 53 + 83384210 GTGTGTGCCC------ATGGGCAAAGG----GTGATTCTTGTAAG--AAT--CAGC-TGATGGGAGTG i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 9434 51 + 19765 GCATGCGTCCT-----GGGGGTGACGG----GCGGCTCTTACAAG--AAC--CAGC-TGGGGGTG--- i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 30411 53 + 287808 GTGTGTGTCCT-----GGGGGTGAAGG----GTGGCTCTTATAAG--AACCACACC-CAGGGGAG--- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s dipOrd1.scaffold_43980 65 52 + 11404 GTGCGTGTC-------AGGAGGCAAGGC---CTGGTTCCTAAGAG--AGC--TGG--TGGAGCGCGCA i dipOrd1.scaffold_43980 n 4014 C 0 s cavPor3.scaffold_76 4392962 62 + 7991924 GTGGCTGTCCTGGGCGGGGTGGGGAGAC--GGTGGTTCTTAAAAGCCATC--CAT--GGAGAGGCAGG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 10598 53 + 44242 GCACATGTCCT-----GGGGGTGAAGG----ATGGCTCTTAGAGC--ACC--CAG--TGAGGGGCGTG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 21777 53 + 41507 GCCTGCGTTGT-----GGGGGTGATGGCGGGGTGCTTCTTACCAT--GAC--TGT--GGA----TGGA i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10862893 37 - 65312493 GTGTGTGTCCC-----AGGGGTGAAGG----GTGGTTCTTACAAG--A-------------------- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132733 50 + 145505 GTGTGTGTCCC-----AGGGGTGAAGG----CTGGTTCTTACAAG--AAT--CAGC-TGACAGG---- i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59440457 47 - 64418924 GTGC--GTCCT-----GGAGGTGAAGG----GTGCTTCTTCTAC---AAT--CAGC-CCATGGG---- i canFam2.chr9 C 0 C 0 s equCab2.chr11 58046525 48 - 61308211 GTGCGTGTCCT-----GGGGGTCAAGG----GTAGTTCTTAGAAG--AAT--CAGC-TGAC--G---- i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14437634 50 - 17734757 GTGTGTGTCTT-----GGGAGTGGAGC----GAGGTTCCCAGAAG--AAT--CAGC-TGGCCAG---- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 21388 50 + 24616 GTCTGTGTCAT-----GGGGCCAGCAG----GAGTCTCACAGGAC--AAT--CGGC-CGGCTGG---- i proCap1.scaffold_29042 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e pteVam1.scaffold_11245 18735 721 + 48268 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118762548 1042 + 121843856 I a score=157319.000000 s hg19.chr17_gl000204_random 50072 27 + 81310 GGGAGCTGCCAAGA---------TGTACAACCTCAG s calJac1.Contig5139 50663 27 + 225949 GGGAGCTGCCAAGA---------TGTACAACCTCAG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 48528 27 - 95547 GGGAGTTGCCAAGA---------TGTACAACCTCAG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75041317 27 + 78773432 GGGAGTTGCCAAGA---------TGTACAACCTCAG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16067413 27 + 17838096 GTGAGCTGCCAAGA---------TGTACAACCTCAG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 19002 27 - 64270 GGGAGCTGCCAAGA---------TGTACAACCTCAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79480274 27 + 83384210 GGGAGCTGCCAAGA---------TGTACAACCTCAG i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 30464 26 + 287808 -GGAGCAGCCAGGA---------TGTACAATGTCAG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s dipOrd1.scaffold_43980 117 36 + 11404 GGGAATGGCCAAGAGCTCCGGTCTGTGGGAAGCAAG i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4393024 25 + 7991924 GGGAAGGGCTGAGA-----------CACAATGTTAG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 10651 26 + 44242 GGG-AGGGCCAAGA---------CGCTTCATCTCAG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 21830 19 + 41507 GGG-GTGGCCGAGA----------------CGCCAG i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10862930 27 - 65312493 AGGAACGGCCACAA---------CGCACAATCTCAG i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132783 27 + 145505 AGGAACGGCCACGA---------TGTACAATCTCAG i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59440504 27 - 64418924 AGGAACGCCCGGGA---------TGGGCCATCTCAG i canFam2.chr9 C 0 C 0 s equCab2.chr11 58046573 27 - 61308211 AGGAACAGCCAAGC---------TGTGGGATCTCAG i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14437684 27 - 17734757 GGGAGCAGCCAAAT---------GGTACTATCTCAG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 21438 27 + 24616 TGGAGTGGCCAGGT---------GGCACTATCTCAG i proCap1.scaffold_29042 C 0 I 1065 e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e micMur1.scaffold_15893 9485 0 + 19765 C e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e pteVam1.scaffold_11245 18735 721 + 48268 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118762548 1042 + 121843856 I a score=-57436.000000 s hg19.chr17_gl000204_random 50099 31 + 81310 A--ACCT----CCCATG--AATAAGGA----AACTAACTGAGT s calJac1.Contig5139 50690 31 + 225949 A--GCCT----CCAACA--AGTAAGGA----AACTAACAGGGC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 48555 31 - 95547 A--ACCT----CCCATG--AATACGAA----AACTAACCAAGT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75041344 31 + 78773432 A--ACCT----CCCATG--AATACGAA----AACTAACCAGGT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16067440 31 + 17838096 A--ACCT----CCCATG--AATAAGGA----AACTAACTGGGT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 19029 35 - 64270 A--ACCT----CCCATG--AATAAGGAAACTAACTAACTGAGT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79480301 31 + 83384210 A--ACCT----CCCATG--AATAAGGA----AACTAACTGAGT i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 30490 33 + 287808 G--GGCA----CACCTGTTGATGAGAA----GCCTGGCAGGGG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s dipOrd1.scaffold_43980 153 17 + 11404 GGAAGC------CTGTT--GAGTGT------------------ i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4393049 26 + 7991924 GGAAGCT----GCCCTT--GACAGTCA----CCTCC------- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 10677 19 + 44242 GG-AGCT----GCCACA--AACAGT----------C------- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 21849 33 + 41507 GGAGCCC----AGTACT--CACAGGGA----CACGCGGAGAAG i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10862957 37 - 65312493 GGAAGCCAGTGCCGGTT--AATAAGGA----GACGAACTGAAT i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132810 37 + 145505 GGAAGCCAGCACCCGTT--AACAAGGA----AACTAACTGAGT i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59440531 32 - 64418924 GGAATC-----CCTGTT--AACAAGGG----GACTGACTAACC i canFam2.chr9 C 0 C 0 s equCab2.chr11 58046600 32 - 61308211 GGAAGC-----TCCTTT--ACTAAGGA----GAGTAACTGAAT i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14437711 22 - 17734757 -----------------GGAACaaaaa----aaataaataaat i loxAfr3.scaffold_49 C 0 I 308 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e micMur1.scaffold_15893 9485 0 + 19765 C e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e pteVam1.scaffold_11245 18735 721 + 48268 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118762548 1042 + 121843856 I a score=329287.000000 s hg19.chr17_gl000204_random 50130 143 + 81310 GAAGACTCAG-CCACA----------------CCTCC-------AGGGTGAAGGGCAGGTGTCAA------------CACCAAGTCATT--AGGCTTT-GCA----GAGCCCAT-------CAGGAGCCTGTGCA----------------TGGACCCAGTTTAAAGCAT-ATTCTGGGTTTCCTTTTTTTGCTCGGATCTCAAGGTGAC s calJac1.Contig5139 50721 135 + 225949 AGAGACTCGG-CC-------------------------------CTGGTGAAGGGCAGGTGTCGG------------GAGCAAGTCAGT--AGTCTTC-CCA----GAGCCCAT-------CAGGAGCCTGTGCA----------------TGGACCCAGCTTAAGGCAT-ATTCTGGGTTTCCTTTTTTTGCTTGGATCTCAAGGTGAC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 48586 143 - 95547 GAAGACTCAG-CCACA----------------CCTCC-------AGGGTGAAGGGCAGGTGTCAA------------GAGCAGGTCAGT--AGGCTTT-GCA----GAGCCCAT-------CGGGAGCCTATGCA----------------CGGACCCAGTTTAAAGCAT-ATTCTGGGTTTCCTTTTTTTACGCGGCTCTCAAGGTGAC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75041375 150 + 78773432 GAAGACTCAG-CCACA----------------CCTCCAGGGTGAAGGGTGAAGGGCAAGTGTCAA------------GAGCAGGTCAGT--AGGCTTT-GCA----GAGCCCAT-------CGGGAGCCTATGCA----------------CGGACCCAGTTTAAAGCAT-ATTCTGGGTTTCCTTTTTTTACGCGGATCTCAAGGTGAC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16067471 143 + 17838096 GAAGACTCAG-CCACA----------------CCTCC-------AGGTTGAAGGGCAGGTGTCAA------------CACCAAGTCATT--AGGCTTT-GCA----GAGCCCAT-------CAGGAGCCTGTGCA----------------CGGAACCAGCTTAAAGCAT-ATTCTGGGTTTCCTTTTTTTGCTCGGATCTCAAGGTGAT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 19064 143 - 64270 GAAGACTCAG-CCACA----------------CCTCC-------AGGGTGAAGGGCAGGTGTCAA------------CACCAAGTCATT--AGGCTTT-GCA----GAGCCCAC-------CAGGAGCCTGTGCA----------------CGCACCCAGTTTAAAGCAT-ATTCTGGGTTTCCTTTTTTTGCTCGGATCTCAAGGTGAT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79480332 143 + 83384210 GAAGACTCAG-CCACA----------------CCTCC-------AGGGTGAAGGGCAGGTGTCAA------------CACCAAGTCATT--AGGCTTT-GCA----GAGCCCAT-------CAGGAGCCTGTGCA----------------CGGACCCAGTTTAAAGCAT-ATTCTGGGTTTCCTTTTTTTGCTCGGATCTCAAGGTGAC i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 30523 139 + 287808 AAAGGATCAG-AGGCA----------------CCTCC-------AGGGAAGAAGGTGGG---CGA------------GGTCAGGTTGGT--AGTCTTT-TCC----GATCCCTG-------CAGGAGCCTGC-TG----------------TGGCTCTAGTTTGAAGTGTCACCCTGATTTTCCTTTTCTTTTTC-GATCTCAAGGTGAC i otoGar1.scaffold_94362.1-287808 C 0 I 12 s dipOrd1.scaffold_43980 170 140 + 11404 --AGGCTGGGACCCGG----------------CCTTC-------GGGGA---GGGTGGGCGGTGA------------CAGGAACGTGGCCAGGGCCTCTGTG----GAGGCCCTGTGCAGGAAGGAGCC----CA---------------CAGGAACCAGCTGAAGACTCCA-------TTTCCTTTTTCTCCTTGGAGCTCAAGGAACT i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4393075 146 + 7991924 CAAAGCT--AACTAGG----------------TGTCA-------CGTCACATGGTTGGACATCAA------------GGCCAAATGGGTTGGTGTCTC-GTG----GAGGCCAT-------CAAGAGCC----TATCCATGCCCACCCTGCCAAAGCAAGGTTCAGAGTC-----------TCCTTTTATCTCTGGGATGGAAAATCGAG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 10696 137 + 44242 AAAGATTGAGACCAGA----------------CCCCG-------GGGCAA--GGGTGGACGC--A------------CGGGTGAGTGGCTCCGATCTG-GTG----GAGGACAT-------CAGCTGCT----CA------------------GACCCAGCTGAAAGCATCATTGTGATTTTCCCCTTTCTCCCTGGACCTCGGGCTGAT i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 21882 138 + 41507 GACGGCTGAGACCAGA----------------CCTCC-------CAGCGCAAGGGAAGGCACCGA--------------------GGGCGTCGGCCCA-GTGCCCAGGGGCCAG-------CAGGCGCC-ATGCA----------------CTGCACCAGCTGCCACCATGACGGACGGT----TCTTTCTTCTCTGAACTCAAGGTGAC i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10862994 142 - 65312493 GAAGATTCAGAGTAGA----------------TCTCC-------AGGGAAAAGAAAGGATGGGAG------------AGTGAGTCAGGA--GAGG----GTG----GAACCCAA-------CAGGAACCTGTGTG----------------CAGACCCAGCTTGAAGCATCATTCTGATTTTCCTTTTGCTTCTTGCATCTCAAGGTGAC i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132847 142 + 145505 GAAGATTCAGACTAGA----------------CCTCC-------ACGGAGAAGAGAGGATGGGAG------------GGCAAGTCAGGA--AAGG----GTG----GGGCCCAA-------CAGGAAACTGTGTG----------------CAGACCCAGCCTGAAGCATCATTCTGATTTTCCTCTTTCTTCTAGGATCTCAAGGTGAT i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59440563 130 - 64418924 AAGGGTTCAGACTAGA----------------CCTCC-------AGGGACAGGCCAGGCTGTGAG------------GATGAATCAGCA--CGTGCTG-CTG----GAGTCTGG-------CAGGAGCCACAACA----------------CAA--------------CCCATTCTGATTTTCCTTCCTCTCCTCGGGTC-CAAGGTAAT i canFam2.chr9 C 0 C 0 s equCab2.chr11 58046632 173 - 61308211 GGAGATGCAGACTAAATGGAGATGCAGACTAGCCCTC-------GGGGAGAGGAGAGGACGTGAGGGGAGTGGGGCAGGGGAGTGGGGC--AGTGCCC-GTG----GGGCCCCG-------GAGCAGCCAGTGTG----------------CAGACCCAGGGTGAAGCCTCATTCTGAGCTTCCTTTTTCCTCTTGGATCTCAAGGTGAT i equCab2.chr11 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e micMur1.scaffold_15893 9485 0 + 19765 C e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e pteVam1.scaffold_11245 18735 721 + 48268 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118762548 1042 + 121843856 I e loxAfr3.scaffold_49 14437733 308 - 17734757 I a score=43526.000000 s hg19.chr17_gl000204_random 50273 35 + 81310 GGGTAAT----------GTCGGGACATACCG--GTGTGTGCGGCTCT s calJac1.Contig5139 50856 35 + 225949 AGGTAAC----------ATCGGGACATAACG--GTGTGTGTGGCTCT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 48729 35 - 95547 AGGTAAT----------GTCGGGACATACTG--GTGTGTGTGGCTCT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75041525 35 + 78773432 AGGTAAT----------GTCGGGACATACTG--GTGTGTGTGGCTCT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16067614 35 + 17838096 GGGTAAA----------GTCGGGACATACCG--GTGTGTGTGGCTCT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 19207 35 - 64270 GGGTAAN----------GTCGGGACATACCG--GTGTGTGTGGCTCT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79480475 35 + 83384210 GGGTAAT----------GTCGGGACATACCG--GTGTGTGCGGCTCT i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 9485 32 + 19765 GGGAACA----------GCTGGGACGCA-CA--GTGT--GGGGGAAT i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 30674 44 + 287808 GGACACAATGGTGTGATATTGGGACACAGTG--GTGTG-GGGGGAAT i otoGar1.scaffold_94362.1-287808 I 12 C 0 s dipOrd1.scaffold_43980 310 34 + 11404 GGTCG-C----------GTGGAGACACGGAG--GCCTGTGTGGCAAC i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4393221 36 + 7991924 GGGCA-C----------TCGGGGACACAAAGGTGCAGAAGCAGCAAG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 10833 25 + 44242 GGGCA--------------------ACATGG--GCACATGTGCTGAC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 22020 16 + 41507 GGCTGGC----------GTAGGGACA--------------------- i oryCun2.chrUn0958 C 0 I 1478 s bosTau4.chr19 10863136 35 - 65312493 GAGAAAA----------GTAGGGAAACCGTG--GTATGTGCGGCGAT i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 132989 35 + 145505 GGGAAAC----------ATAGGGAAACCACG--GTGTGTGCGGTGAT i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59440693 32 - 64418924 GGGACAC------------AGGAAAAC-CTG--GTGTGTGTGGCCAT i canFam2.chr9 C 0 C 0 s equCab2.chr11 58046805 33 - 61308211 GGGAAAC------------AAGGAAGCAATG--GTGTGAGCCACGAT i equCab2.chr11 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 15372 1362 + 20752 I e pteVam1.scaffold_11245 18735 721 + 48268 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118762548 1042 + 121843856 I e loxAfr3.scaffold_49 14437733 308 - 17734757 I a score=146657.000000 s hg19.chr17_gl000204_random 50308 50 + 81310 CCCAGGTGATACATTAAAAAGTCATCCTCACACCTCGCTGCTGAAAACAA s calJac1.Contig5139 50891 50 + 225949 CTCATGTGATACATTAAAAAGTCATCCTCATATCTCACTGCTGAAAACAA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 48764 50 - 95547 CCCATGTGATGCACTAGAAAGTCATCCTCATACCTCGTTGCTGAAAACAA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75041560 50 + 78773432 CCCATGTGATGCACTAGAAAGTCATCCTCATACCTCGTTGCTGAAAACAA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16067649 50 + 17838096 CCCATGTGACGCATTAAAAAGTCATACTCATACCTCGCTGCTGAAAACAA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 19242 50 - 64270 CCCAGGTGATACATTAAGAAGTCATCCTCACACCTCGCTGCTGAAAACAA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79480510 50 + 83384210 CCCAGGTGATACATTAAAAAGTCATCCTCACACCTCGCTGCTGAAAACAA i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 9517 49 + 19765 CTCACGTGAAGCACAAAACCT-CATCCTAATACGTCTCTGCTGAGAACAG i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 30718 44 + 287808 CTCATGGGAAGTATTAACCCTGCAAAGTGTTAAATAC------AGAACAA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s dipOrd1.scaffold_43980 344 39 + 11404 CCCA-----------CAGGAGGCGTCCTGACGCCTCTGTGCTGGAAACAG i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4393257 45 + 7991924 CTCAGATG-----TTCTGAAGTCATTTCAGTAGCTCCCTGCTGAAAACAG i cavPor3.scaffold_76 C 0 I 209 s speTri1.scaffold_128901 10858 35 + 44242 C--------------CAGAGATTAGCTAGCCCTCTGGATGCTGAGAACA- i speTri1.scaffold_128901 C 0 C 0 s bosTau4.chr19 10863171 48 - 65312493 CTCAC-TGAAGTATTAAAAATTCATCTTAACACCTC-TTGCTGAAAACAG i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 133024 48 + 145505 TTCAC-TGAAGTAGTAAAAATTCATCTTAACACCTC-TTGATGAAAACAG i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59440725 48 - 64418924 CTCGCGCAAACTACTGGGAAATCATCTTCACACCTC-CTGCTGAAAACA- i canFam2.chr9 C 0 C 0 s equCab2.chr11 58046838 44 - 61308211 CTCATGTGAAGTGTTACAAAGTCATCTTAATACCTC-TGGCAGAC----- i equCab2.chr11 C 0 C 0 s dasNov2.scaffold_28617 16734 47 + 20752 CTCGTGGGACGCATTCACGAG-CATCTTAATACTCC-CCGCTTAG-ACAG i dasNov2.scaffold_28617 I 1362 C 0 e oryCun2.chrUn0958 22036 1478 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e pteVam1.scaffold_11245 18735 721 + 48268 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118762548 1042 + 121843856 I e loxAfr3.scaffold_49 14437733 308 - 17734757 I a score=88418.000000 s hg19.chr17_gl000204_random 50358 41 + 81310 AA--------AGCTACAAAGC--CCTTCTTGCCATTGCT-------------------TTTTAAAAAgtg s calJac1.Contig5139 50941 49 + 225949 AAAGCTTTTTAGCTCTTTAGC--CCTTCTTGTGATTGCT-------------------TTTTAAAAAgtg i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 48814 41 - 95547 AA--------AGCTAAAAACC--CCTTCTTGCCATTGCT-------------------TTTTCAAAAgtg i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75041610 41 + 78773432 AA--------GGCTAAAAACC--CCTTCTTGCCATTGCT-------------------TTTTCAAAAgtg i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16067699 41 + 17838096 AA--------AGCTAAAAAGC--CCTTCTTACCATTGCT-------------------TTTTAAAAAgtg i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 19292 41 - 64270 AA--------AGCTACAAAGC--CCTTCTTGCCATTGCT-------------------TTTTAAAAAgtg i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79480560 41 + 83384210 AA--------AGCTACAAAGC--CCTTCTTGCCATTGCT-------------------TTTTAAAAAgtg i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 9566 37 + 19765 AG--------AGTTAAAGAGC--CCTTTTGGCTGTTGC-----------------------AAAAAAAAA i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 30762 37 + 287808 AA--------GGTTAAAAAGC--TCTTCTTGCTAGTGC-----------------------CAAAAAACC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s dipOrd1.scaffold_43980 383 41 + 11404 AA--------GGTTTGCAAGCCTTCGCCTTGCCAGGAC---------------------ACCAACAGGCG i dipOrd1.scaffold_43980 C 0 C 0 s speTri1.scaffold_128901 10893 9 + 44242 -----------------------TCG--------------------------------------AAGGAG i speTri1.scaffold_128901 C 0 C 0 s bosTau4.chr19 10863219 36 - 65312493 AA--------GGTTAAAAAGC--CCTTCTTGCTATTGCC------------------------AAAAGAA i bosTau4.chr19 C 0 I 2 s turTru1.scaffold_106006 133072 36 + 145505 AA--------GGTTAAAAAGC--CCTGCTTGCTATTGCC------------------------AAAAGAA i turTru1.scaffold_106006 C 0 I 2 s canFam2.chr9 59440773 41 - 64418924 AG--------AGCTACATGGC--CCTTCTTGCCACTGCC-------------------AACAGCAAAGAA i canFam2.chr9 C 0 I 2 s equCab2.chr11 58046882 56 - 61308211 ----------CGTTACAAAGC--CTTTCTTGCTGTTGCCCCCCACCCACCCACCCCCGCCCCGCAAAG-- i equCab2.chr11 C 0 I 2 s dasNov2.scaffold_28617 16781 38 + 20752 AG--------GGCTCAAGACC--CCTTCTTGCTGTTGCC----------------------AAACCAGTG i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 22036 1478 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e pteVam1.scaffold_11245 18735 721 + 48268 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e cavPor3.scaffold_76 4393302 209 + 7991924 I e mm9.chr11 118762548 1042 + 121843856 I e loxAfr3.scaffold_49 14437733 308 - 17734757 I a score=-57480.000000 s hg19.chr17_gl000204_random 50399 10 + 81310 ---gggtgggc------------------------tg s calJac1.Contig5139 50990 10 + 225949 ---gggtggag------------------------tg i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 48855 10 - 95547 ---gggtgggg------------------------tg i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75041651 10 + 78773432 ---gggtgggg------------------------tg i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16067740 10 + 17838096 ---gggtgggc------------------------tg i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 19333 10 - 64270 ---gggtgngc------------------------tg i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79480601 10 + 83384210 ---gggtgggc------------------------tg i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 9603 9 + 19765 ---AAAAAATG-------------------------G i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 30799 5 + 287808 ---CAGCA----------------------------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s dipOrd1.scaffold_43980 424 2 + 11404 -----------------------------------TG i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4393511 34 + 7991924 ---gggtgttttgtcgtggtgatgagaacagtgactg i cavPor3.scaffold_76 I 209 C 0 s bosTau4.chr19 10863257 8 - 65312493 ---AGGGATAG-------------------------- i bosTau4.chr19 I 2 C 0 s turTru1.scaffold_106006 133110 8 + 145505 ---AGGTGTGG-------------------------- i turTru1.scaffold_106006 I 2 C 0 s canFam2.chr9 59440816 4 - 64418924 ---AAAT------------------------------ i canFam2.chr9 I 2 C 0 s equCab2.chr11 58046940 4 - 61308211 ---AGGT------------------------------ i equCab2.chr11 I 2 C 0 s dasNov2.scaffold_28617 16819 10 + 20752 GGGAGGCCAA--------------------------- i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 22036 1478 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e speTri1.scaffold_128901 10902 0 + 44242 C e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e pteVam1.scaffold_11245 18735 721 + 48268 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118762548 1042 + 121843856 I e loxAfr3.scaffold_49 14437733 308 - 17734757 I a score=342045.000000 s hg19.chr17_gl000204_random 50409 92 + 81310 gggtggg-gtggggAAGAAGAGGTCAC----------CAGCAGGTGC---TTGATTCCAAGGTGCCCAGAAGCTCTTAGGAACAGACCCTGGAGCTTCAGCCAGCC s calJac1.Contig5139 51000 92 + 225949 ggctggg-gtggggtAAAAGGAGTTAT----------CACTCGGTGC---TTGATTCCAAGGTGCCCAGAAGCTCTTAGGAACAGACCCTGCAGCTTCAGCCAGCC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 48865 95 - 95547 ggctggg-gtggggAAGAAGAAGTCACC-------ATCATCAGGTGC---TTGATTCCAAGGTGCCCAGAAGCTCTTAGGAACAGACCCTGGAGCTTCAGCCAGCC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75041661 95 + 78773432 ggctggg-gtggggAAGAAGAGGTCACC-------ATCATCAGGTGC---TTGATTCCAAGGTGCCCAGAAGCTCTTAGGAACAGACCCTGGAGCTTCAGCCAGCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16067750 92 + 17838096 gggtggg-gtggggAAGAAGAGGTCAC----------CCGCAGGTGC---TTGATTCCAAGGTGCCCAGAAGCTCTTAGGAACAGACCCTGGAGCTTCAGCCAGCC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 19343 92 - 64270 gggtggg-gtggggAAGAAGAGGTCAC----------CAGCAGGTGC---TTGATTCCAAGGTGCCCAGAAGCTCTTAGGAACAGACCCTGGAGCTTCAGCCAGCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79480611 92 + 83384210 gggtggg-gtggggAAGAAGAGGTCAC----------CAGCAGGTGC---TTGATTCCAAGGTGCCCAGAAGCTCTTAGGAACAGACCCTGGAGCTTCAGCCAGCC i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 9612 60 + 19765 GGTGGGG-GTGGCG---GAGAAGTCAC----------CAGCAGGTGC--TTTGATGCCAAGGT------------------------------GCTTTACCCGGCA i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 30804 88 + 287808 GGTTTGG-GTAGC-----AGAAGTCAC----------CAGCAGGTGC--AATGATTCCAAGGCACCCAGCAGTTCTTATTAACAGACCTTGGGGCTTTACCTGGTA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s dipOrd1.scaffold_43980 426 85 + 11404 GGGCGGG-CGGGGCAGGAAGGAGACAC----------CAGCAGGATA--TTTGACTCCAAGGTGCCGGAAAGCTC---CGAGCTCCC-----AGCTCAGCTCAAAC i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4393545 94 + 7991924 aaacaGGTCAGACTGGGAAGAAGTCAG----------CACCAGAAGC--TTTGATGCCAAGATGCCCAGCAGCTCTCACGGACACACCCCAGAGCTGTGCCCTGCA i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 10902 64 + 44242 GGACCCG-CAGGGTGGGGTGG------------------GCAGGAGC--TTGGATTCCAAGGTGCCCACCTG--------------------AGCTGGGC-CTAAA i speTri1.scaffold_128901 C 0 C 0 s bosTau4.chr19 10863265 85 - 65312493 -----GG-GTGGGG---GAGAAATCAT----------CAGCAGAAGC--TTTGATTTCAAGTGGCCCAGAAGCTTTTATGTACACACCCTGGAGCATTGCCCTGCA i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 133118 85 + 145505 -----GC-GTGGGG---GAGAAGTCAC----------CAGCAGGAGA--TTTGATTTCAGGGGGCCCAGAGGCTCTTATGTACAGACTCTGGAGCATTGCCCTGCA i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58046944 87 - 61308211 --GTGGA-GTAGGG---GAGAAGTCAG----------CAGCAGGAGC--TTTGATTTCAAGGTGCCCAGAAGCTCTTCTGTACAGACCCTGGAGCCCTGCCCTGC- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59440820 85 - 64418924 --ATGGG-GTTGGG---AAGAAGAGAC----------CAGCAGGAGC--TGTG--CTGAAGGTGCCCGGCTGCTCCTACATA-AGACCCGGGAGCGGCGTCTTATA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 19456 79 + 48268 -GAGGGG-GCAGGG---GAAGAGCCAC----------CAGCAGGAGC--TCTGATTTCAAGGTGCCCAGAAGCTCGCATGACCAGACCGTGGAGCA---------- i pteVam1.scaffold_11245 I 721 C 0 s dasNov2.scaffold_28617 16829 95 + 20752 ---------GGAGCAAAGAGAAGTCGCCTCTGCTTCTCAGAAGGACGCTTCTGCCTGCAAGGTGCCTGG-AGCACTTAGGGGTAAGCTCTG-AGCTCTGCCTTGCG i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 22036 1478 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e tarSyr1.scaffold_143701 4262 1361 + 9575 M e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118762548 1042 + 121843856 I e loxAfr3.scaffold_49 14437733 308 - 17734757 I a score=119397.000000 s hg19.chr17_gl000204_random 50501 25 + 81310 CCCAG-CCCTC------AAAAGTTCCAG---AAAA- s panTro2.chr17 79480703 25 + 83384210 CCCAG-CCCTC------AAAAGTTCCAG---AAAA- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 19435 26 - 64270 CCCAGCCCCTC------AAAAGTTCCAG---AAAA- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16067842 25 + 17838096 CCCAG-CCCTC------AAAAGTTCCAG---AAAA- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75041756 27 + 78773432 CCCTG-CCCTC------AAAAGTTCCAG-AAAAAA- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 48960 27 - 95547 CCCTG-ACCTC------AAAAGTTCCAG-AAAAAA- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 51092 26 + 225949 CCCAG-CCCTC------AAAACTTCCAA--AAAAA- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 5624 28 + 9575 CCCAG-TCCTC------AAAAGTTTCAGAAAAAAA- i tarSyr1.scaffold_143701 M 1361 C 0 s micMur1.scaffold_15893 9672 31 + 19765 CTCAA-TCCTT-ACAAGAAAAGTTCCAG--AAAAA- i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 30892 30 + 287808 CTGAA-TCCTT-AAAAGAAAATTTCCAG---AAAA- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s dipOrd1.scaffold_43980 511 31 + 11404 TCGAA-TTTTCAAGAGAAAAAGTTCCAA---GAGA- i dipOrd1.scaffold_43980 C 0 I 2 s cavPor3.scaffold_76 4393639 29 + 7991924 CCTGA-TCCTC--TGGACAAAGCTCCAG---GAAG- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 10966 28 + 44242 CCTGG-CCTTC---GATAAAAGTTCCAG---AAAA- i speTri1.scaffold_128901 C 0 I 1 s bosTau4.chr19 10863350 30 - 65312493 CCCAG-CCCTT-AAAAGAGAAGTTCTAG---GAAA- i bosTau4.chr19 C 0 I 1 s turTru1.scaffold_106006 133203 25 + 145505 CCCAA-TCCTT-AA-----AAGTTCCAG---AAAA- i turTru1.scaffold_106006 C 0 I 1 s equCab2.chr11 58047031 30 - 61308211 CCTGC-TCCTT-AAAAGAAAACTTGTAG---AAAA- i equCab2.chr11 C 0 I 1 s canFam2.chr9 59440905 30 - 64418924 CCCGA-GTCTC-AGAAGAAAAGTTCCAG---AAGA- i canFam2.chr9 C 0 I 1 s pteVam1.scaffold_11245 19535 25 + 48268 CCCCA-TCTTT-GAAAG-----TTCCAG---AAAA- i pteVam1.scaffold_11245 C 0 I 1 s dasNov2.scaffold_28617 16924 31 + 20752 CCCAA-CCCTG-CAAAGAGCAGTTCTGG---ATCAA i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 22036 1478 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118762548 1042 + 121843856 I e loxAfr3.scaffold_49 14437733 308 - 17734757 I a score=734195.000000 s hg19.chr17_gl000204_random 50526 91 + 81310 ATAGGAGTTGTTT--TTGATGTAATCCAGGAGAG-AAACCTCTAATTTGCAT----TAAGAGTTTGGAGCT-ATGAAAGTTTAGTGAGAAATGATTTCT s panTro2.chr17 79480728 91 + 83384210 ATAGGAGTCGTTT--TTGATGTAATCCAGGAGAG-AAACCTCTAATTTGCAT----TAAGAGTTTGGAGCT-ATGAAAGTTTAGTGAGAAATGATTTCT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 19461 91 - 64270 ATAGGAGTTGTTT--TTGATGTAATCCAGGAGAG-AAACCTCTAATTTGCAT----TAAGAGTTTGGAGCT-ATGAAAGTTTAGTGAGAAATGATTTCT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16067867 91 + 17838096 ATAGGAGTTGTTT--TTGATGTAATCCAGGAGAG-AAACCTCTAATTTGCAT----TAAGAGTTTGGAGCT-ATGAAAGTTTAGTGAGAAATGATTTCT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75041783 95 + 78773432 ATAGGAGTTGTTT--TTGATGTAATCCAGGAGAG-AAACCTCTAATTTGCATTGAGTAAGAGTTTGGAGTT-ATGAAAGTTTAGTGAGAAATGATTTCT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 48987 95 - 95547 ATAGGAGTTGTTT--TTGATGTAATCCAGGAGAG-AAACCTCTAATTTGCATTGAGTAAGAGTTTGGAGTT-ATGAAAGTTTAGTGAGAAATGATTTCT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 51118 95 + 225949 AAAGGAGTTATTT--TTTATGTAATCCAGGAGAG-AAACCTCTAATTTGCATTGAGTGAGAGTTTGGAGCT-CTGAAAGTTTAGCGAGAAATGATTTCT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 5652 95 + 9575 TTAGAAATTATTG--TATATTGAAATCAGCAGAG-AAACCTCTAATTTGTATTTAGTAAGAGTTTCGGGCT-ATGAAAGTTTCGTGACAAATCATTTCT i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_15893 9703 91 + 19765 ATAGGAGTTATTT--TCTATTTTATCCAGTGGAG-AAGTCTCTAATCTGCAT----TGAGGATTTCGAGCC-ATGAGAGTTTAGTGAGGAATTATCTCT i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 30922 92 + 287808 ATGGGCGTTCTTT--TCTATTTAATACACTAGAG-AAATCTCTAATTTGCAT----TAAGGATCCTGAGCTAATGAAAGTTTAGTGAGAAATTATTTCT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118763590 97 + 121843856 GAATTTCTTCCTCCCCCTCTTTAATATAGTGAGC-AAACCGCCTATCTGAACTCAGTAAGGATTTTAAATT-ATTAAAGTTTAGTGAGAAAATATTTGt i mm9.chr11 I 1042 I 207 s dipOrd1.scaffold_43980 544 93 + 11404 AAACTGTACCTTTTCCCTCTCCA----AGAAGAG-AAATGTTTTATTTGTATTCAGGAAAGACTTCAAACT-AGTAAAGCTTAGTGAGAAATTCTTTCT i dipOrd1.scaffold_43980 I 2 C 0 s cavPor3.scaffold_76 4393668 91 + 7991924 -GACTGGTTATTT--CCTACTTAGACCATTAAGG-AAATGTTGCATTTGTATTCGGGAAGGATTTTGAGCT-ATTAATGTTTAGTGA-CAATTATCT-- i cavPor3.scaffold_76 C 0 I 4 s speTri1.scaffold_128901 10995 92 + 44242 AACGTAGTTGTTT--TTGATTGA---CAGTAGAG-AAACCTCCCGTTTGCATTCAGCCTGGGCTTCAAACT-ATGAAAGTTGAGTGAGAGATCATTTCT i speTri1.scaffold_128901 I 1 C 0 s bosTau4.chr19 10863381 95 - 65312493 TTAGGAGTTATTT--TCTTTTGGATCCTATAGTG-AAGCATCTCATTTGGATTCAGGAAGGATCTTGAGCT-ATTAAAGTTTAGTGAGAAATTACTCCT i bosTau4.chr19 I 1 C 0 s turTru1.scaffold_106006 133229 94 + 145505 TTAGGAACTATTT--TCTTTTTAATCCTGTAGAG-AAACCTCTCATTTAGATTCAGGAAGGAT-TTGAACT-GTCAAAGTTTAGTGAGAAATTATTTCT i turTru1.scaffold_106006 I 1 C 0 s equCab2.chr11 58047062 95 - 61308211 TTAGGAGTTATTT--TCTGTTTAATCTAGTAGAG-AAACCTCTCCTTTATATTCAGTATGGATTTCAAACA-ATAAGAGTCTAGTGAGAAATTATTTCT i equCab2.chr11 I 1 C 0 s canFam2.chr9 59440936 93 - 64418924 CTAGGAGTTATTT--CCTGTTTAATCCAGTAGAG-AAACTTCTCATTTATACTCAGTAGGGATTTTAAAC---TACTAGTTCAGCGAGAGATTATTTCC i canFam2.chr9 I 1 C 0 s pteVam1.scaffold_11245 19561 95 + 48268 ACAGGCGTTACTT--TCTATCTAATCCAGTAGAG-AAACCTCTAATTTATATTCGGTAAGGATTCTGAACT-ACTAAAGTTTAGTCAGAAACCATTTCT i pteVam1.scaffold_11245 I 1 C 0 s dasNov2.scaffold_28617 16955 96 + 20752 CTAGGAATTATTT--TCTAGTCAACCCGCCAGAGAAAAAATCTAATTTACCTTCAGTAAGGATCTCAAAGC-ACGAGAGTTTTGTGAGAAATTATTTCT i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 22036 1478 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e loxAfr3.scaffold_49 14437733 308 - 17734757 I a score=178822.000000 s hg19.chr17_gl000204_random 50617 47 + 81310 -----------------------------------------AAAGGTACC---------------------------AGGGTGTTTGT----ACTTGCTTTAAATCT----TTCTCCAAATTG s panTro2.chr17 79480819 47 + 83384210 -----------------------------------------AAAGGTACC---------------------------AGGGTGTTTGT----ACTTGCTTTAAATCT----TTCTCCAAATTG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 19552 47 - 64270 -----------------------------------------AAAGGTACC---------------------------AGGGTGTTTGT----ACTTGCTTTAAATCT----TTCTCCAAATTG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16067958 41 + 17838096 -----------------------------------------AAAGGTACC---------------------------AGGGTGT----------TTGCTTTAAATCT----TTCTCCAAATTG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75041878 46 + 78773432 -----------------------------------------AAAGGCACC---------------------------AGGGCGTTTGT----A-CTGCTTTAAATCT----TTCTCCAAATTG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 49082 46 - 95547 -----------------------------------------AAAGGCACC---------------------------AGGGTGTTTGT----A-CTGCTTTAAATCT----TTCTCCAAACTG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 51213 46 + 225949 -----------------------------------------AAGGGCACC---------------------------AGGATGTTTGT----A-CTTCTTTAAATCC----TTCTCCAAATTG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 5747 42 + 9575 -----------------------------------------AAATGTACC---------------------------CAGGTGTTTGC----A-TCTTTTTAA--------CTCTCCAATTGG i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_15893 9794 43 + 19765 -----------------------------------------AAACGCACC------------------------------GTGTTTGC----A-CCGCTTTAAATCT----TTGTCCCAACTG i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 31014 43 + 287808 -----------------------------------------AACTGCACC------------------------------CTGTTTGC----A-CCTCTTTAAATCT----TGGTCCAAACTG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118763894 36 + 121843856 -----------------------------------------GAAAGCATT---------------------------TCTA--AGTGC-------------AAATCT----TGTCTCAAAATG i mm9.chr11 I 207 I 228 s dipOrd1.scaffold_43980 637 45 + 11404 -----------------------------------------GAATGTACC---------------------------TAGAT-TGTGC----A-CCTCTTTAAATCT----TCCTACAAATAG i dipOrd1.scaffold_43980 C 0 I 265 s cavPor3.scaffold_76 4393763 36 + 7991924 -----------------------------------------CGAGGTA-----------------------------------TGTAC----A-CCTCCTTAAAGCT----CTGTCTACAC-- i cavPor3.scaffold_76 I 4 C 0 s speTri1.scaffold_128901 11087 46 + 44242 -----------------------------------------AAATGTCCC---------------------------TAGATGGGTGC----A-CCTCTTTAAATCC----TTCTCCAAATTC i speTri1.scaffold_128901 C 0 I 2 s bosTau4.chr19 10863476 46 - 65312493 -----------------------------------------AAATGTACC---------------------------TAGGTATTCAT----A-CCTCTTTAAATCT----TTCTCCAAGTTG i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 133323 44 + 145505 -----------------------------------------AAATGTGCC---------------------------TAGGTGTTTGT----G-CCTC--TAAATCT----TTCTCCAAGTTA i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58047157 46 - 61308211 -----------------------------------------AAATGTACC---------------------------TAGGTGTTTGC----A-CCTCTTAAAGTCT----TTCTCCAAATTA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59441029 47 - 64418924 -----------------------------------------AAATGTACC---------------------------TGGGTGTGTGCTCGTT-CCTCTTTA---CC----TCCCCAGAGATA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 19656 46 + 48268 -----------------------------------------AAATACAGC---------------------------CAGGTATTTGC----A-TCTCTTTACATCT----TTCCCCAAACCG i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_28617 17051 118 + 20752 AAATAATAGATTGCTTATTTAGGACTTCCCAAATTTTTTAAAAATGTAATTCATAATCATTTAATTTGGTAACTTAATAAATCTTTGA----A-TTTCTAATAATTTACACTTCTTGAAACCA i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 22036 1478 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e loxAfr3.scaffold_49 14437733 308 - 17734757 I a score=365637.000000 s hg19.chr17_gl000204_random 50664 95 + 81310 -------------TGG----------------------------------------------------------------------AC-CTTCCT----AATACAAGGAAACCCTATGTCCTTTGGCTCCAAAAGAGG--TTCCCAT---TTTTCCATCAA-A--AATC-TCATTGCTGAGGA-TAGCCTGCT- s panTro2.chr17 79480866 90 + 83384210 -------------TGG----------------------------------------------------------------------AC-CTTCCT----AATACAAGGAAACCCTATG-----TGGCTCCAAAAGAGG--TTCCCAT---TTTTCCATCAA-A--AATC-TCATTGCTGAGGA-TAGCCTGCT- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 19599 95 - 64270 -------------TGG----------------------------------------------------------------------AC-CTTCCT----AATACAAGGAAACCCTATGTCCTTTGGCTCCAAAAGAGG--TTCCCAT---TTTTCCATCAA-A--AATC-TCATTGCTGAGGA-TAGCCTGCT- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16067999 95 + 17838096 -------------TGG----------------------------------------------------------------------AC-CTTCCT----AATACAAGGAAACCCTATGTCCTTTGGCTCCAAAAGAGG--TTCCCAT---TTTTCCATCAA-A--AATC-TCATTGCTGAGGA-TAGCCTGCT- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75041924 95 + 78773432 -------------TGG----------------------------------------------------------------------AC-CTTCCT----AATACAAGGAAACTCTATGTCCTTTGGTTCCAACGGAGG--TTCCCAT---TTTTCCATTAA-A--AATC-TCATTGCTGAGGA-CAGCCTGCT- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 49128 95 - 95547 -------------TGG----------------------------------------------------------------------AC-CTTCCT----AATACAAGGAAACTCTATGTCCTTTGGTTCCAAAGGAGG--TTCCCAT---TTTTCCATTAA-A--AATC-TCATTGCTGAGGA-CAGCCTGCT- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 51259 95 + 225949 -------------TGG----------------------------------------------------------------------TC-CTTTCT----AATACAAGGAAACTCTATGTCCTTTGGCCTCAAAAGAGG--TTCCTAT---TTTTCCATGAA-A--AATC-TCATTGCTGAGAA-CAGCCTGCT- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 5789 80 + 9575 -------------TAT--------------------------------------------------------------------CCAC-CCTTTT----AATACAAATAAACTTC------------------TGATG--CTCCCAT---TTTAATGTAAA-A--ATTCTTCATGACTGAGAA-CAGCCTGCT- i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_15893 9837 97 + 19765 -------------TAT--------------------------------------------------------------------CCAC-CTTTTT----AATACAAGTAAACTTTGCGTCCCTT-----CAACAGAGGGCCCCCCAC-CCCGTTACACAAACA--GGCT-TCCCCGCTGAGAG-CAGCCCGCG- i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 31057 89 + 287808 -------------TAT--------------------------------------------------------------------CCAT-CATTTT----CATACAAGTAAACTTTGTGCTCTC-------------GGCCTGCCCATGTTTACTATATAAG-A--GCCT-TCCTTGCTGAGAA-CAGCGGGCT- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s speTri1.scaffold_128901 11135 90 + 44242 -----------------------------------------------------------------------------------TCCTC-CTTTTT----AATACAAGTAAACTCCATGTCTTTTGGCTTCAACAGAAG--------G---TTTTATATAAA-A--AGCCCTCGTTGCTGAGAA-CAGCCTGCT- i speTri1.scaffold_128901 I 2 C 0 s cavPor3.scaffold_76 4393799 94 + 7991924 -------------TGA-----------------------------------------------------------------A-TCTTC-CCGTTT----GATGCAAGTACACTTCATGTCTTTGGGCTCCGACGGATG--------G---TTTTATATAAA-A--AGCCTTCACTGCCGAGAA-CAGCCTGCT- i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118764158 86 + 121843856 ------------------------------------------------------------------------------------CTGT-CCTTCTTAAAAACACATGTGAAGCTCATGTCTTTGGGCTTCAGTGGG----------------TTTTATAGA-G--AGCC-TCAT--CTGAAGAGCAGCCAGCT- i mm9.chr11 I 228 C 0 s oryCun2.chrUn0958 23514 85 + 41507 ------------------------------------------------------------------------------------------TTTTT----AACACAAGTAAGCTCA--GTCCTTTGGCGTCGACTGAGG--TCTCCAT---CTTCACACAAA-A--AGCC-CCAGCGCCAAGAA-CAGC--GCT- i oryCun2.chrUn0958 I 1478 C 0 s dipOrd1.scaffold_43980 947 78 + 11404 ---------------------------------------------------------------------------------------------------AACACGAGTAAAGTTTATATCTTTTGGCTTCAAAGGGAC--------A---CATTAGATTAA-A--AGCT-TCATTGCCGAGGA-CAGTCTGCT- i dipOrd1.scaffold_43980 I 265 C 0 s bosTau4.chr19 10863522 100 - 65312493 ---------------------------------------------------------------------------------TATCCAG-TTTTTT----AATACAAGTAAACTTTATGTTCTTTGGCTTCAACAGAGT--TTCACAT---TTTTACATAAA-AAGAGCCTTCATTGCCGAGAA-CAATGTGCC- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 133367 98 + 145505 ---------------------------------------------------------------------------------TACCCAC-CTTTTT----AATACAAGTAAACTTTATGTTCTTTGGCTTCAACAGAGC--TTCCCAT---TTTTACATAAA-A--AGTCTTCATTGCTGAGAA-CAATGTGCT- i turTru1.scaffold_106006 C 0 C 0 s equCab2.chr11 58047203 97 - 61308211 ---------------------------------------------------------------------------------TCTCCAC-CTTTTT----AATACAAGTAAACTTCATGTTCTTTGCCTTCAATAGACA--TGCCAAT---GCGT-CATAAA-A--CGGTTTCATTGCCACGAA-CAATGCGCT- i equCab2.chr11 C 0 M 917 s canFam2.chr9 59441076 98 - 64418924 ---------------------------------------------------------------------------------TCCATGCACTTTTT----AATAGAACTAAACTTGATGTTCCTTGGCCTTCACAGAGG--TTCCCCT---TTCTGCACACA-G--AGGCTTCAGTGCTGAGAA-CGGTGTCT-- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 19702 84 + 48268 ---------------------------------------------------------------------------------TCTCCAC-CTTCAC----GATCC--------------TTCCTTCGCTTCAGTAGAGG--TTCCCAA---TTCTACATAAA-A--CGCCTTCGCTGCCGAGCC-CGACGTGCT- i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_28617 17169 177 + 20752 TAATCATTTAATTTGGCTGTTTAATTAATAAATCTTTTAATTTCTAATAATTTGCCCTTCTTAAATCCTTTATCAAAATCATATCCAC-CTTTTT-----ATACCAGTAAACTTCCTGTTCTTTGGCTTCAACAGAGC--CTCCCAT---TTGCACGTAAA-A--TGCCTTCAGTGCCACGGC-CA--CTGCCT i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e loxAfr3.scaffold_49 14437733 308 - 17734757 I a score=250146.000000 s hg19.chr17_gl000204_random 50759 36 + 81310 CCTC-CATGTTCTCATG-----ACCGTTGCCTAAAA-GCAAAC s panTro2.chr17 79480956 36 + 83384210 CCTC-CATGTTCTCATG-----ACCGTTGCCTAAAA-GCAAAC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 19694 36 - 64270 CCTC-CATGTTCTCATG-----ACCGTTGCCTAAAA-GCAAAC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16068094 36 + 17838096 CCTC-CATGTTCTCATG-----ACTGTTGCCTAAAA-GCAAAC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75042019 36 + 78773432 CCTC-CATGTTCTCATG-----ACCATTGCCTAAAA-GCAAAC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 49223 36 - 95547 CCTC-CATGTTCTCATG-----ACCATTGCCTAAAA-GCAAAC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 51354 36 + 225949 TCTC-CGTGTTCTCACG-----ACCTTTGCCTAAAA-GAAAAC i calJac1.Contig5139 C 0 I 300 s tarSyr1.scaffold_143701 5869 34 + 9575 CCTC---TGTTCTCATT-----ACCTTTGCCTAAAA-GAAAAT i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_15893 9934 41 + 19765 CTTCTTGTGTTCTCGCCATCCCATCCGTGCCC-GGA-GAACAC i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 31146 33 + 287808 CTGCATCTGCTTT---------GTCCTTGTCTAAAA-GAGAAC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s speTri1.scaffold_128901 11225 36 + 44242 TCTC-TGTGTTCTCATT-----ACCCTCGCCTAAAA-GAAAAC i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4393893 36 + 7991924 TCTC-TGTGTTCTCATC-----ATCTCTGCCTACAA-GAAAAC i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118764244 34 + 121843856 TGTC-TGTCCTCATTTC-------CCTTGCCTGAGA-GAAAAT i mm9.chr11 C 0 C 0 s oryCun2.chrUn0958 23599 31 + 41507 TCTC-TGTGGTCTCACG----------AGCCTGAAA-CACAAC i oryCun2.chrUn0958 C 0 C 0 s dipOrd1.scaffold_43980 1025 35 + 11404 TCTC-TGTGTTCTCATC-------CTCTGCCTAAAACAAAAAC i dipOrd1.scaffold_43980 C 0 C 0 s bosTau4.chr19 10863622 36 - 65312493 TCTC-TGTGTTCTCATT-----ATCCCTACCTAAAA-GGAAAC i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 133465 36 + 145505 TCTC-TGTGTTCTCATT-----ATCCTTGCCTAAAA-GAAAAC i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59441174 36 - 64418924 TCTC-TGTGCTCTCATT-----ATCCTGGCCTACAA-GAAAGC i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 19786 31 + 48268 --TC-TGTG---TTATC-----ATCCTTGTCTAAAT-GAAAAC i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_28617 17346 35 + 20752 TCTC-TGGGTTCTCACT-----GTCCTTGCTTAAAG-AAAGT- i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e equCab2.chr11 58047300 917 - 61308211 M e loxAfr3.scaffold_49 14437733 308 - 17734757 I a score=349407.000000 s hg19.chr17_gl000204_random 50795 173 + 81310 GATCCGGAGACA-TGA-GC-CTGGCCCAGGAATCGGCATTTGCTT---GGTGTCCA-AGGATGTGAACTGCAGGATGAGAGCAAGGG----CAGGAGAAGCACCTGGACTCCAG-GGA-----------------C---ACCATT-CCTGCCATCTTCAT----CCCTGGGTCTCACCTGGTGT-C-ATAGACAAGGAGACGTGGATGAG----AA s otoGar1.scaffold_94362.1-287808 31179 157 + 287808 AGCCTGGAGACA-TGA-GGTCCAGCCTAGG----------------------TCTA-AAAATGTGAACAGCAGG------GCTGGGGGTGAGGGGAGAAGCCCCCCAACTCAGG-AGGGC---------------C---ACCTTT-CCTGCTGTCTTCAT----CCCTCAGTCTCACCGAGGGT-T-GCAGACAAGGAGACT--GGTTAGCAGACG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 9975 136 + 19765 AGCCCTGGGACG-TGA-GG-CCAGCCCAGG----------------------------------GACCACC---------GCTTGTG----GGAAAGAAGCACCCAGGCTCCGGAAGGGC---------------C---ACCTGT-CCTGCCATCACCAT----TCCTCGATCTCATCTGCCGT-CAACAGACAAGGAGACC--GGGGAG----CG i micMur1.scaffold_15893 C 0 C 0 s tarSyr1.scaffold_143701 5903 175 + 9575 GATCCTGAGACA-CGAGGC-CCAATTCAGGAAACATT-TCTGCCT---GGTGTCCA-AAGATGTGAATTGCAGGGCTGCAAGGGAAG----CAGAGGAAGCACCTAGATGCCAG-AGGGC---------------C---ACCTTT-CCTGCCATCTTCAT----CTCTCAGTCTCATCTGGTGT-C-ACAGGCAAGGAGACATGGGCGAG----TA i tarSyr1.scaffold_143701 C 0 C 0 s calJac1.Contig5139 51690 188 + 225949 GATCCAGAGATA-TGA-GC-CTGG-CCAGGAATCGCTATCTGTCT---GGTGTCCA-AGCATGTGAACTGCAGGATGCGAGCAGGGA----CAGGACAAGCACCCGGACTCCGG-AAG-CTTCTCCTACAGGAAGC---ACCGTT-CCTGCCATCCTCAT----CCCTGGGTCTCACCTGGTGT-C-ACAGACAAGGAGCCGTGGGTGAG----AA i calJac1.Contig5139 I 300 C 0 s papHam1.scaffold8336 49259 174 - 95547 AATTCGGAGACA-TGA-GC-CTGACCCAGGAATGGGCATTTGCTT---GGTGTCCA-AGGATGTGAACTGCAGGATGAGAGCAAGGG----CAGGAGAAGCACCTGGACTCTGG-GGG-C---------------C---ACCGTT-CCTGCCATCTTCAT----CCCTGGGTCTCATCTGGTGT-C-ATAGACGAGGAGACGTGGGTGAG----AA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75042055 174 + 78773432 GATTCGGAGACA-TGA-GC-CTGACCCGGGAATGGGCATTTGCTT---GGTGTCCA-AGGATGCGAACCGCAGGATGAGAGCAAGGG----CAGGAGAAGCACCTGGACTCTGG-GGG-C---------------C---ACCGTT-CCTGCCATCTTCAT----CCCTGGGTCTCATCTGGTGT-C-ACAGACGAGGAGACGTGGGTGAG----AA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16068130 174 + 17838096 GATCCGGAGACA-CGA-GC-CTGGCCCAGGAATCGGCATTTGCTT---GGTGTCCA-AGGATGTGAACTGCAGGATGAGAGCGAGGG----CAGGAGAAGCACCTGGACTCCGG-GGA-C---------------C---ACCATT-CCTGCCATCTTCGT----CCCTGGGTCTCACCTGGTGT-C-ATAGACAAGGAGACGTGGATGAG----AA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 19730 173 - 64270 GATCCGNAGACA-TGA-GC-CTGGCCCAGGAATCGGCATTTGCTT---GGTGTCCA-AGGATGTGAACTGCAGGATGAGAGCAAGGG----CAGGAGAAGCACCTGGATTCCAG-GGA-----------------C---ACCATT-CCTGCCATCTTCAT----CCCTGGGTCTCACCTGGTGT-C-ATAGACAAGGAGACGTGGATGAG----AA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79480992 173 + 83384210 GATCCGGAGACA-TGA-GC-CTGGCCCAGGAATCGGCATTTGCTT---GGTGTCCA-AGGATGTGAACTGCAGGATGAGAGCAAGGG----CAGGAGAAGCACCTCGACTCCAG-GGA-----------------C---ACCATT-CCTGCCATCTTCAT----CCCTGGGTCTCACCTGGTGT-C-ATAGACAAGGAGACGTGGATGAG----AA i panTro2.chr17 C 0 C 0 s speTri1.scaffold_128901 11261 158 + 44242 TATTCTGCCACACACG-GC-CCAGCCCGGGGTCCACCATTTGCCT---GGTGTCCA-AGGATGTAAA-----------------TTT----CAGGGGAGGCACCCAGATCCTGG-AGGGC---------------C---AGCCCT-CCCACCACCTTCA-----CCCTCCATCTCATTTTGTGT-C-ACGGACAAGGAGACCTGGTTGAG----CA i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4393929 146 + 7991924 TCTTCTGCCATGTAAG-GC-CCAGCCCAGTAGCTATCAGATGCCTGGAGAATTTTG-GGGAAGAG-------------------GAG----CAGGAAAGGCACCTA------------GA---------------CTCAAG------ACACCATCTTCGT----CCCTCCACCTCATTTGGGGT-C-ACAGACAAGGGACCATGGG-GAA----CA i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118764278 132 + 121843856 GCTTCTGGTTC--AAG-GC-CCAGTGCATGAAGCACTATTTTCCC----AGTACTT-AAGATGTG-------------------CAT----TCTGAAAGCAGTGGG------------GA---------------C---AGC----TACCCCTGCTGC-------------CTTCATCCTGGTAAC-AGGGACAGGGGGACATCAGTGAG----CA i mm9.chr11 C 0 C 0 s oryCun2.chrUn0958 23630 128 + 41507 AC-----------AAG-AC-CTG-----------ACCTCTGGCCT---GACGTCCATGGGGTGGG-------------------GAG----CAGAAGG---ACCCAGACCCCAG-AGAGC---------------C---CC------CCCCTGGCCACGCCCAACCCTCGACCTCAACTGGCAT-C-----ACAAAGAGGCGCTGGTGAG----CA i oryCun2.chrUn0958 C 0 C 0 s dipOrd1.scaffold_43980 1060 141 + 11404 TCTTCTACCACA-AAA-GG-CCAGGCTAGGAACCATCGCCTGCCT---GAGGTCCA-AAGATGGGAATC---------------CAT----CACGGAGGTGGCGGGAG---AGA-GGAGG---------------C---AG------ACGCCGGCAGAG------------CCTCGTCCCG----C-AGAGATAAGGAGACGTGGGCGAC----CA i dipOrd1.scaffold_43980 C 0 C 0 s bosTau4.chr19 10863658 127 - 65312493 TATCCTGAGAC----------------------------------------------AGGGCGCAAATTTCAGGG---------GTG----CAGGGGAAGTACCTAGACTCTGG-GGGAC---------------C---ACACTT-CTTGTCACCACCAT----CCCTCTGTTTCATTTGGTGT-C-ACAGACAAGGAGACAGTAATAAG----CA i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 133501 148 + 145505 CACCCTGAGATG-TGACGC-CCAG------------------CCT---GGTGCCCA-AAGACGCAAATTTCAAGG---------GTG----CAGGGGAAGTACCCAGACTCTGG-AAGGC---------------C---ACCTTT-CCTGCCATCACCAT----CCCTCAGTTTCATTTGGTGT-C-ACAGACAAGGAGA-ACTGATGAG----CA i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59441210 106 - 64418924 TCTCCTGAGACA-TGATAC-CCAGCCCAGGAATCACCAGTCACCT---G--------------------------------------------------GGGCACGGAT---------------------------------------------CGTCAT----CCCTCGGTCTCATTTGCTGT-C-ACAGACAAGGAGACATCGGTGAG----CA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 19817 165 + 48268 TATCCTGAGATA-CGACAC-CCAGCTCAGTAATCGTCAGCTGCCT---GGTACCCA-AAGACACACACTGCGGGG---------GGC----C---GGGAGGGTCCAGACTCCGG-AGGGC---------------C---ACGCTTCCCTGCCAGCGTCAT----TCCTTGGTGTCACTGGGTGT-C-AAAGCCAAGGAGACACCGGTAAG----CG i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_28617 17381 143 + 20752 AACCCAGAGAGG-TGA-GG--GAGGCCAGGAATCACCACTGGCT----GGCATCCA-GAAACGTG----------------------------------GCATCCAGACTCCAG-AGAGC---------------C---ACCTGT-CCTGCCGTCCCCAT----CCCTGGGCGTCGTTTGGTGT-C-CCACGCAAGGAGACACGGGCGAG----CA i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e tupBel1.scaffold_124459.1-15939 13290 1863 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e equCab2.chr11 58047300 917 - 61308211 M e loxAfr3.scaffold_49 14437733 308 - 17734757 I a score=78414.000000 s hg19.chr17_gl000204_random 50968 50 + 81310 GGACTGCAGTCCATGGTGT-TCG--GGCTGCTC-A--AGGGCAGAACTCTGAAT---GC s panTro2.chr17 79481165 50 + 83384210 GGACTGCAGTCCATGGTGT-TCG--GGCTGCTC-A--AGGGCAGAACTCTGAAT---GT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 19903 50 - 64270 GGACTGCAGTCCATGGTGT-TCG--GGCTGCTC-A--AGGGCAGAACTCTGAAT---GN i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16068304 50 + 17838096 GGACCGCAGTCCATGGTGT-TCA--GGCTGCTC-A--CGGGCAGAACTCTGAAT---GT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75042229 50 + 78773432 GGACTGCAGTCCGTGGTGT-TCG--GGCTGCTC-A--TGGGCAGAACTCTGAAA---GT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 49433 50 - 95547 GGACTGCAGTCCGTGGTGT-TCG--GGCTGCTC-A--CGGGCAGAACTCTGCAA---GT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 51878 52 + 225949 GGACTGCAGTCCATGGTGT-GTGCCAGCTGCGC-A--CAGGCAGAACTCTGAAT---GT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 6078 29 + 9575 AG-----------------------TAGAGCTC-A--GAGGTAG-ACTCtgaat---gt i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_15893 10111 42 + 19765 GGGTTGCAG--------GC-TCA--GGCTGTGC-A--CAGGCAGGCCCCTGCCC---GT i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 31336 32 + 287808 GGGCAGGAT--------AC-TCA--GCC--TAC-T--CAGGGAAG--------T---GG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 15153 53 + 15939 GGGCTGCAGTCCCCAGCGTCCCG--GGCTGCTC-AGCTGTGCAGTACTCTGAGT---GC i tupBel1.scaffold_124459.1-15939 I 1863 I 19 s speTri1.scaffold_128901 11419 52 + 44242 GGGCTGCAGCCCTCAG-GT-TCA--GGTTGCAC-A--TAGCTAGAAGTCAGTCCCCAGG i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4394075 50 + 7991924 GGACTGCAGCCCTTGCTGA-TTT--GTCTGTTC-A--CAGCTGGAgatgtggct---gt i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118764410 50 + 121843856 GAGCCACAGCCCTTGGTAT-CTG--AGGTGCTC-A--CAGTCAGAAATCTGAAT---GG i mm9.chr11 C 0 C 0 s oryCun2.chrUn0958 23758 20 + 41507 GGGCG------------------------------------CGGAACTCTGACC---GT i oryCun2.chrUn0958 C 0 C 0 s dipOrd1.scaffold_43980 1201 46 + 11404 GGGCGGCAGCCCTCAGCAT-CTA--CACTACTC-A--CAACTCAAAATCTTA------- i dipOrd1.scaffold_43980 C 0 C 0 s bosTau4.chr19 10863785 43 - 65312493 GGGTGGCAGC-------TC-TCC--ACCTATTC-G--CACACAGAGCTCTGAAC---AG i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 133649 43 + 145505 GAGCTGCAAC-------GT-TCT--ACCTATTC-C--CAGATAGAGCTCtgaat---gg i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59441316 43 - 64418924 GGGCTGCAGT-------GT-TCC--AGATATTC-A--AAGGGAGACCTCCGAAT---GT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 19982 42 + 48268 TGGCTGCAGT-------GT-TCC--AACTACTC-A--CAGGCAGAACGCGGAGC---G- i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_28617 17524 51 + 20752 GGGCCACGGCCCAGGCTGC-ACG--GCCTTTTCTG--CAGGTGGAGCTGTGGTT---GT i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e equCab2.chr11 58047300 917 - 61308211 M e loxAfr3.scaffold_49 14437733 308 - 17734757 I a score=202995.000000 s hg19.chr17_gl000204_random 51018 40 + 81310 GCCCTTGGTTTGCGTGGCACACTGC-----CTCCACTACTGTATT s otoGar1.scaffold_94362.1-287808 31368 39 + 287808 GTCCTCagc-ggttcagtgcacacc-----ctctacaactgtaca i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 10153 39 + 19765 GCCCTCGGT-TGGGCGGTGCACTGC-----CTCTACAACTGTATC i micMur1.scaffold_15893 C 0 C 0 s tarSyr1.scaffold_143701 6107 40 + 9575 gtcctcagcttgtgcagtgcactgc-----ctccacaaccatact i tarSyr1.scaffold_143701 C 0 C 0 s calJac1.Contig5139 51930 39 + 225949 GCCCTCAGTTTGCCTGGTACTCTGC-----CTCCACTAC-GTATT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 49483 40 - 95547 GCCCTTGGTTTGCCTGGTACGCTGC-----CTCCACTACAGTATG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75042279 40 + 78773432 GCCCTTGGTTTGCCTGGTACGCTGC-----CTCCACTACAGTATT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16068354 40 + 17838096 GCCCTTGGTTTGCGTGGTGCACTGC-----CTCCACTACTGTATT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 19953 40 - 64270 GCCCTTGGTTTGCGTGGTACACTGC-----CTCCGCTACTGTATT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79481215 40 + 83384210 GCCCTTGGTTTGCGTGGCACACTGC-----CTCCACTACTGTATT i panTro2.chr17 C 0 C 0 s speTri1.scaffold_128901 11471 40 + 44242 GTCTTAGGCCTGGGCTGCCCACTGC-----CCCCACAGCTGTATC i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4394125 40 + 7991924 gccctaggcttgtgcagtccacagc-----ctctaccactgtatc i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118764460 26 + 121843856 ATCTTGGGTCTGCGT-------------------GCAACTGTCTC i mm9.chr11 C 0 C 0 s oryCun2.chrUn0958 23778 40 + 41507 GCCCTAGGTCTAGGCAGTGCGCGAC-----CCCCACAACGGTATC i oryCun2.chrUn0958 C 0 C 0 s dipOrd1.scaffold_43980 1247 23 + 11404 GTCCTGGGCCTGAGC----------------------AATGCCCT i dipOrd1.scaffold_43980 C 0 C 0 s bosTau4.chr19 10863828 45 - 65312493 TCCCTAGGTTTGTGCAGGGCACTACTGGTACATCGTAGTTGTAAT i bosTau4.chr19 C 0 I 5 s turTru1.scaffold_106006 133692 39 + 145505 tccctaggtttctgcagtgca-tgc-----cagcgcagctgtaat i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59441359 40 - 64418924 GCCCTAGGCTTGTGTACTACGCTGC-----CCACACAACTGTAAT i canFam2.chr9 C 0 I 1 s pteVam1.scaffold_11245 20024 21 + 48268 -------------------CGCCGC-----CTGCGCAGCTGTATC i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_28617 17575 40 + 20752 GCCccaggcttgtgcagtgcacagc-----ctctacaactgtctc i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e tupBel1.scaffold_124459.1-15939 15206 19 + 15939 I e myoLuc1.scaffold_4816 12501 30 + 14340 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e echTel1.scaffold_194555 7929 1421 + 11139 I e monDom5.chr2 304539065 11756 - 541556283 I e equCab2.chr11 58047300 917 - 61308211 M e loxAfr3.scaffold_49 14437733 308 - 17734757 I a score=355586.000000 s hg19.chr17_gl000204_random 51058 97 + 81310 GGTGGCCCTGCAGAAGAGAATCTGAT-CTGG-AGGTCCGGGTT----A-C-CTT-----T-GTTTGTTTGTTTTGATGGAGGGAGAA------TTTTGGAGCAAGAC-AAGATGCCTT s otoGar1.scaffold_94362.1-287808 31407 94 + 287808 ggcaaccctgCAGGACAGAATCTGAT-GTGA-GGGTCTGGGTT----A-C-TTT-----T----TGTCTGTTTCAGTGGAGGGATAA------ACTAGTTGCAAGAC-AAGATGCCTT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 10192 94 + 19765 CACAAGCCTACGGGAGAGAATCCGAT-TTGG-GCCTCTGCGTT----A-C-TTT-----T----TGCTTATTTTGGTGGAGTGGGAA------TTTTAAAGCAAGAC-GAGATGCCTT i micMur1.scaffold_15893 C 0 C 0 s tarSyr1.scaffold_143701 6147 98 + 9575 agcagccctgCAGGAGAGAATCTGAT-TTGG-TGATCTGGGTC----AGT-TTT-----T-GTTTGTTTGTTTCAGTGGAGGGAGAA------TTTTGAAGCAAGAC-AAAATGCCTT i tarSyr1.scaffold_143701 C 0 C 0 s calJac1.Contig5139 51969 92 + 225949 GGTGGCCCTGCAGAAAAGAATCTGAT-CTGG-ATGTCTGGGTT----A-C-TTT-----T-GTTTGTTTGTTTTGATGGAGGGAGAA------TTTTGAAGCAGGAC-AAGA-----T i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 49523 98 - 95547 GGTGGCCCTGCAGAAGAGAATCTGAT-CTGG-AGGTCCGGGTT----A-C-TTT-----T-GTTTGTTTGTTTTGATGGAGGGAGAAT-----TTTTGAAGCAAGAC-AAGAGGCCTT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75042319 98 + 78773432 GGTGGCCCTGCAGAAGAGAATCCGAT-CTGG-AGGTCCGGGTT----A-C-TTT-----T-GTGTGTTTGTTTTGATGGAGGGAGAAT-----TTTTGAAGCAAGAC-GAGAGGCCTT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16068394 97 + 17838096 GGTGGCCCTGCAGAAAAGAATCTGAT-CTGG-AGGTCCGGGTT----A-C-CTT-----T-GTTTGTTTGTTTTGATGGAGGGAGAA------GTTTGAAGCAAGAC-AAGATGCCTT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 19993 97 - 64270 GGTGGCCCTGCAGAAGAGAATCTGAT-CTGG-ACGTCNGGGTT----A-C-CTT-----T-GTTTGTTTGTTTTGATGGAGGGAGAA------TTTTGNAGCAAGAC-NAGATGCCTT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79481255 97 + 83384210 GGTGGCCCTGCAGAAGAGAATCTGAT-CTGG-AGGTCTGGGTT----A-C-CTT-----T-GTTTGTTTGTTTTGATGGAGGGAGAA------TTTTGGAGCAAGAC-AAGATGCCTT i panTro2.chr17 C 0 C 0 s speTri1.scaffold_128901 11511 92 + 44242 AGCAGCC--GCAGAGGAGAACCTGGG-TTGG-GGGTTACCGTT----T-C-TTT--------GTTGTTTGTTTTGGTGGAGGCAAA-------TTTTGCAGCAAGAT-AAGAGGCCTT i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4394165 102 + 7991924 ggtggccctACATGAAAGAATTTGAT-TTTGAGGGCCTGGGTC----A-C-ATTTTGTTT-GCATATTTGTTTTGGTGGAGGCAAA-------GTTTGAAGCAAGAC-AAGATGCCTT i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118764486 79 + 121843856 ATATGCCCAGCAGTGAGAAACCTAGT-TTGCTAGTGTGAGGTC----A-C-ACA------------------------TAGGGAGA-------TTTTAAAGTGAGAC-CAGGTGCCTT i mm9.chr11 C 0 C 0 s oryCun2.chrUn0958 23818 64 + 41507 GGCAGCCCCACGGGACAGAAGCCAGC-CTGG-ACAGCTGGCCT----G-C-TTT------------------------GTGTCTGC-------TTTGAGAA---------------TT i oryCun2.chrUn0958 C 0 C 0 s dipOrd1.scaffold_43980 1270 49 + 11404 CCCTGCACAGC--------------T-CGACTCGGGTTCCCTT----A-C-ACC------------------------GGATGACA-------TCTTGGAG----------------- i dipOrd1.scaffold_43980 C 0 C 0 s bosTau4.chr19 10863878 87 - 65312493 GGCAGCCCTGTGCGGGAG---------CGGG-GGGCCTGGCTG----A-C-TTC-----TGGCTTGTTTGATTTGGTGGAAGAA---------TTTTGGTGTCAGAC-AAGACGCCTT i bosTau4.chr19 I 5 C 0 s turTru1.scaffold_106006 133731 105 + 145505 ggcagccctgTGACAGAGGATCTTTT-TGGT-GGGCTTGGGTT----A-CTTTT-----TTGCTTGTTTGATTTGGCGGAGGGAGATATTTTTTTTTGACATAAGAC-AAGATGCCTT i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59441400 100 - 64418924 ACCTGCCCTGTGAGAAGGGATTTTTTTGGAG-GGGACTGTGTT----A-C-TTT-----TAGCTTATTTGTTTCAGTAGAAGGACAA------TTTTGAACTGAAACTAAGATGTCTC i canFam2.chr9 I 1 C 0 s myoLuc1.scaffold_4816 12531 93 + 14340 GAGGAGCCGCCGGGGAGGAGCTCATC----G-GGGCCTGGCT-------C-CTC-----CTGGGCGCTGGTTTTGGAGGAGAGGGAA------TGCTGAGGGGAGAC-CAGAGGCCTG i myoLuc1.scaffold_4816 I 30 C 0 s pteVam1.scaffold_11245 20045 97 + 48268 AGCGGCCCGGCAGGAAGGGTCTTATCT--AG-CGGTTTGAGTT----G-C-TTT-----TTGCTCATTCGTTTTGGCGAAGGGAGAA------TTCTGAAGTGAGTC-AAGATGCCCC i pteVam1.scaffold_11245 C 0 C 0 s tupBel1.scaffold_124459.1-15939 15225 80 + 15939 -----------GAGAGAGAACCTGCT-GCGG-CGGGGGGAGGG----G-G-TAT-----T-GT-GGTTTGTTTTGAGGGACTGAGAA------TCCTGACGCCAGAC-A-----CCTC i tupBel1.scaffold_124459.1-15939 I 19 C 0 s dasNov2.scaffold_28617 17615 94 + 20752 agcggccctgCGGGAAAGAATCTAAC-TTGG-GGGGTTAGGTT----G-C-TAT-----T----TGTTTGCTTAGGTAGAGGGAGAA------TTTTGAAGCAAGAG-ACAGTGCCTC i dasNov2.scaffold_28617 C 0 I 11 s echTel1.scaffold_194555 9350 53 + 11139 -----------------------------------------------T-C-TGT-----C----TGTCCGTTCTAATGAAGAGCGAG------TTCTGAAAGCAGAA-AAGCTGCCTT i echTel1.scaffold_194555 I 1421 I 11 s loxAfr3.scaffold_49 14438041 72 - 17734757 -------------------------T-CTTG-GAGTTTGAGTTGCATT-T-TGT-----T----TGTTTGTTTTGGTGGAGGG-GGG------TCTTGAAGGAAGGA-AAGGTGCCTT i loxAfr3.scaffold_49 I 308 I 11 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I e equCab2.chr11 58047300 917 - 61308211 M a score=451049.000000 s hg19.chr17_gl000204_random 51155 154 + 81310 GG-----------CACAC-AGGA--------TTCTCCGCTC--TGGC-ACAA--AAGATACATGTTATGATCTCAACTG----------GGCCCC------CAA---ACAAGGA---CTT----G-AAACTGTTCAGGGGCTGGCTGGTGGCAGCTTT-CTATGCTCAGGCAGTTTCCTTGCCTGCAAATGGGATTATTTTCTAAAA s otoGar1.scaffold_94362.1-287808 31501 167 + 287808 GGAGAAATAAAAGTAGAT-AACA--------GCTTCCACTCTTCGGT-ATAA--AAGATACTTGTTATGATTTCAACT-----------AGCTTC------CAA---AGCAGGA---CTTA-ACG-ACAATAGGCAGGGTCCAGCTGGTAGCAGTTGT-CTGTGCCTGTGCAGTTGCCTCACCTGCAAAT-GGACTGTCTTCT-AGA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_15893 10286 164 + 19765 GGAGAAATAAAAGCACGC-AGGA--------GTCTCCTCTCTTTGCT-GTAA--AAGATGCATGTCATGACCTCAACT-----------GGCCTC------CAA---AACGGCA---CGTG-ATG-ATGCTGGGCCGGGTCT-GCTGGTAGCAGTAGC-CTGTGCCCAGGCAGTTTCCTCCCCTGCAAATGGGACTGCTTCCT---- i micMur1.scaffold_15893 C 0 C 0 s tarSyr1.scaffold_143701 6245 170 + 9575 GGAGAAAAAAAGGCACCC-AGAA--------GTCTCCTCTCTTTGGT-ACCA--AAGATACATGTTATGATCTCAACTT----------GACCCC------CAC---AAAAGGA---CTTG-AGG-AAACTGTGCGGGGTCTGGCTGGTAGCAGTTGT-CTGTGCCCAGACAGTTTCCACAGCTGTAAATGGGATTGTTTTCAAAAA i tarSyr1.scaffold_143701 C 0 C 0 s calJac1.Contig5139 52061 153 + 225949 GGAGAAATAAAGGCACAC-AGGA--------TTCTCCTCTC--TGTT-ACAA--AA------------GATCTCCACCA----------GGCCTC------CAA---ACAAGGA---CAT----G-AAACTGTTCAGGGTCTGGCTGGTGGCAGTTTT-CTACGCTCAGGCAGTTTCCTCGCCAGCAAATGGGATTATTTTCTCAAA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 49621 165 - 95547 GGAGATATAAAGGCACAC-AGGA--------TCCTCCTCTC--TAGT-ACAA--AAGATACATGTTATGATCTCAACCG----------GGCCCC------CAA---ACAAGGA---CTT----G-AAACTGTTCAGGGGCTGGCTGGTGGCAGCTTT-CTATGCTCGGGCAGTTTCCTTGCCCGCAAATGGGATTATTTTCTAAAA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75042417 165 + 78773432 GGAGATATAAAGGCACAC-AGGA--------TCCTCCTCTC--TAGT-ACAA--AAGATACATGTTATGATCTCAACCG----------GGCCCC------CAA---ACAAGGA---CTT----G-AAACTGTTCAGGGGCTGGCTGGTGGCAGCTTT-CTATGCTCGGGCAATTTCCTCGCCTGCAAATGGGATTATTTTCTAAAA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16068491 165 + 17838096 GGAGAAATAAAGACACAC-AGGA--------TTCTCCTCTC--TAGC-ACAA--AAGATACATGTTATGATCTCAACCG----------GGCCCC------CAA---ACAAGGA---CTT----G-AAACTGTTCAGGGGTTGGCTGGTGGCAGCTTT-CTGTGCTCAGGCAGTTTCCTCGCCTGCAAATGGGATTATTTTCTAAAA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 20090 154 - 64270 GG-----------CACAC-AGGA--------TTCTTCTCTC--TGGC-ACAA--AAGATACATGTTATGATCTCAACCG----------GGCCCC------CAA---ACAAGGA---CTT----G-AAACTGTTCAGGGGCTGGCTGGTGGCAGCTTT-CTATGCTCAGGCAGTTTCCTTGCCTGCAAATGGGATTATTTTCTAAAA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79481352 154 + 83384210 GG-----------CACAC-AGGA--------TTCTCCTCTC--TGGC-ACAA--AAGATACATGTTATGATCTCAACTG----------GGCCCC------CAC---ACAAGGA---CTT----G-AAACTGTTCAGGGGCTGGCTGGTGGCAGCTCT-CTATGCTCAGGCAGTTTCCTTGCCTGCAAATGGGATTATTTTCTAAAA i panTro2.chr17 C 0 C 0 s speTri1.scaffold_128901 11603 76 + 44242 GGAGAAATAAAGTCATTC-GGGA--------TTCTCCTCTT--TGGT-ACA----------------------------------------------------------AAAG--------------------------------------------------------ATAAATTTTAGATGTG-----AGTACTGGTTTCTTAAA i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4394267 130 + 7991924 AGC-CAATAAAGG--CCC-AGGCCAT----TCACCTCTCTT--CGGT-GCAC--ACA-------------TTATATCCA----------GGAAAC------T-----GCAGAG----TCTG-GTG-GCAGCAGA-------TGCCTGG-CCTAG---------------GCAATTTCAGCATCTG-AAACAGAACTGGTCTCTAAAA i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118764565 128 + 121843856 TGA-AAAAAAAGGCACCC-AGGT--------CAGTTCCCCA--TCCC-CCA-------------------CCGTATCAA----------GGGAAT------CC----ACAGAGA---GATG-GAG-GTAGCGCC-------TGTCTGGACGCAG---------------GCAGTTTCTTTACCTGTAAACAGGACTGGTTTCTAAGA i mm9.chr11 C 0 I 311 s oryCun2.chrUn0958 23882 172 + 41507 GAG-AACTAAAGGCCCAG-AGGACAGAGGATCGTCCTTGCC--TGGT-ACAA--AAGACACGCG-CGTGGTCTCATCCC----------AGCCCC------C-----GAGAAGA---CACGCGAG-GAACCCCGCAGGATCTGTGGGGACGCAGGTGT-CCGTGCACAGGCAGAGCGCTGGCCTGCAAGCCG-ACTGCTTTCTAGAG i oryCun2.chrUn0958 C 0 C 0 s dipOrd1.scaffold_43980 1319 152 + 11404 ----AAACAAAGGCACGC-AGGG---------ATCTCTCCT--TGGG-GCAG--AAGAT-----------GTGTGTCAG----------GATCTT------CTAATAAAAAAGA---CCTG-GTG-GAATCACAC-GGCCGTGCCGGGACCCGGA-GA-TTACACCCACGCAGTTCCTTCATCTATAAATGGGA-TGGTTTCTACAA i dipOrd1.scaffold_43980 C 0 C 0 s bosTau4.chr19 10863965 165 - 65312493 GGAGAAATAGAGGCACAC-AGAA--------TTCTCTTCTC--TTCC-ATACAGAAGACTTCTGTTACATTTCCACTTG----------GCCCTC------CA----AAAGGAA---TGTG-ATG-AAGCTGTGCAGGGGCCGGCTGGGAGCGAGTGT----GCCCCAGGCAG-TTCCTCCCCTGCAAGCAGGACTATTTTCTTGAA i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 133836 169 + 145505 GGAGAAATAGAGGCACAT-GGGA--------GTCTCTTCTC--TTCC-ATACAAAAAACACGTGTTACAATTTCACCTG----------GCCCTC------CA----AAAGGAA---CTTG-ATG-AAACTGTGCAGGGTCCGGCTGGTAGCAAGTGT-CTGTCCCCAGGCAGTTTCCTCACCCGCAAGTAGGACTGTTTTCTTGAA i turTru1.scaffold_106006 C 0 C 0 s canFam2.chr9 59441500 180 - 64418924 AGAGAAATCAAGGCACAC--AGA--------TTCTCCTGTT--ATGT-AGAG--AAGATAGAAGTTATGATCTTGTCTGCCTGCACCCCGCCCCCCACCGCCA----AAAGGAA---CCTG-ATG-TAACTGTGCAGAGCCTGGCTGCTAGCAGGTGC-CTGCCCC--AGCAGTTCCCTCACCTGCAAGTGGGACTCTTTTCTAAAA i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 12624 147 + 14340 GGACAGATGGAGGCGCAC-GGGC--------CTCGCCCCTC--CCTC-AGAC---AAACCCCCGCTG-GACGGCATCGA----------GGCCTC------------------G---CCCG-GAA-GGAGCGGGCGG---CCAGCCGGCGGCAGGTGT-CTGTCCCCAGGCCGTGCGCGCCTCTGCAAGC-GGATGGCTTT------ i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 20142 164 + 48268 GGAGAGATAAAGGCACACAGGGA--------TTCTCCTCCC--TTGC-ATAC--AAAATATATGTTATGGTCTCATCTA----------GCCCCT------CA----AAAGGAA---CTTG-ATA-AAAGTGTGCAGGGTCTGGCTGGTAACAGGTGT-CTGTCCCCAGGC----ACCTCATCTGTGAGTGGGACTGTTTTCTCAAA i pteVam1.scaffold_11245 C 0 C 0 s tupBel1.scaffold_124459.1-15939 15305 149 + 15939 GGAGAAATAA---------GGGA--------CTGTCCTCTTCTTGGT-ACAG--AAGACACCCGTCATGGTCTCAGTCT----------GGTCCC------CAA---A--GGGA---CTT----G-AACCTGTGCGG--------TGGCAGCTGGTGT-CTGTGCCCAGGCAGCTTCCTCACCTGCAAAGGGAACTGTTTCCTACAA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s loxAfr3.scaffold_49 14438124 154 - 17734757 -----------GGCACAC-CG-A--------CTCTCCTCTC--CTTG-CTAA--CGGACACCTGCTGTGATCTCACC-T----------GTCCCC------C-----AGAAGAAGGACGA----G-ACCCTGTGCAGGGTCCAGCTGGTAGCAGGTGTTCTGTCCCCAGGCAGCTTCCAGGCTTGCAAATGGGATTGTTTTCTACAA i loxAfr3.scaffold_49 I 11 C 0 s echTel1.scaffold_194555 9414 135 + 11139 -----------GACGCCT-CA---------------CTGTC--CCTG--------------TGGTTGAGAGCAGGCC-T----------GTTCTG------A-----AGGAGGTGG-CAT----G-AGGCGGCGCGGGG-CTGACTGGTACCAGGTGTCCCATCTCCCGGCAGCATCCGGGCTTGCAAATGGGATTGCTTCCTGCCA i echTel1.scaffold_194555 I 11 C 0 s dasNov2.scaffold_28617 17720 154 + 20752 -----------GATGCTG-AGGA--------TTTTCATCTC--TTGGTGCAG--AAGATGCCCATGAGGTTCTCACCTT----------GGCCCT------T-----ACTAGGA---CTT----GCTGACACTGCAGGGTCGGCCTGGTAGCAGGTGT-CCGTCTCCACGCAGGTTCCTTGCCTGCACATGGGACTGTTTTCTAAAG i dasNov2.scaffold_28617 I 11 C 0 s choHof1.scaffold_149147 333 149 + 9388 -----------GACACAC-AGGA--------GTCTCCTCTC--TTTG-GTAC--AAGATACCC-TGAGGAGCTCACCCT----------GGCCCA------T-----AAAAGAG---CTT----G-GGACCCTGCAGGGTCTGGCTGGTGGCAGATG--CAGCCCCCAGGCA-GTTCCTTGCCTGCACATGGGATTGTTTTCTAAAG i choHof1.scaffold_149147 N 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I e equCab2.chr11 58047300 917 - 61308211 M a score=349028.000000 s hg19.chr17_gl000204_random 51309 60 + 81310 GGGCT-AAAATAGACATACCCGGCCACCTT-CCTCGCCAGCTGGCTTCCACTCACAGCC---------------------------------------------------------------------------------------------------------CAG s panTro2.chr17 79481506 60 + 83384210 GGGCT-AAAATAGACATACCCGGCCACCTT-CCTCGCCAGCTGGCTTCCACTCACAGCC---------------------------------------------------------------------------------------------------------CAG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 20244 60 - 64270 GGGCT-AAAATAGACATACCCGGCCACCTT-CCTCGCCAGCTGGCTTCCACTCACAGCC---------------------------------------------------------------------------------------------------------CAG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16068656 60 + 17838096 GGGCT-AAAATAGACATACCCGGCCACCTT-CCTCGCCAGCTGGCTTCCACTCACAGCC---------------------------------------------------------------------------------------------------------CAG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75042582 60 + 78773432 GGGCT-AAAACAGACATACCCGGCCACCTT-CCTCGCCAGCTGGCTTCCACTCACAGCC---------------------------------------------------------------------------------------------------------CAG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 49786 60 - 95547 GGGCT-AAAACAGACATACCCGGCCACCTT-CCTCGCCAGCTGGCTTCCACTCACAGCC---------------------------------------------------------------------------------------------------------CAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 52214 58 + 225949 GGGCT-AAAATAGACATACCCGGCCACCTT-CGTCGCCAGCTGGTTTCCACT--CAGCC---------------------------------------------------------------------------------------------------------CAG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 6415 60 + 9575 GGGGT-GAAATAGACATGCCTGACCACCTG-CTTCTCCAACTGGCTTCTAGTCACAGTC---------------------------------------------------------------------------------------------------------TAG i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_15893 10450 51 + 19765 --------AACAGACGTGCGCGACCACCTG-CCTCCCCAACGAGCTGCCGGTC--AGCC---------------------------------------------------------------------------------------------------------CGG i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 31668 48 + 287808 GGGCT-AAAAGAGACCTACGTG---ACCTG-CCTCTCCAGCTGGCTGCCAGTC------------------------------------------------------------------------------------------------------------------ i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 15454 60 + 15939 GGGCT-AAAATAGACATACCTGGCCACCTG-CTTCTCCACCTGGCTCCCAGGCACAGCC---------------------------------------------------------------------------------------------------------CCA i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118765004 52 + 121843856 ----A-GGTTGCAGCAGAGATGGCCTACCA-ACTCAT-GAGGTGGTGGCATTCCCATCC------------------------------------------------------------------------------------------------------------ i mm9.chr11 I 311 C 0 s dipOrd1.scaffold_43980 1471 60 + 11404 GGGCA-AAAGGAGACAGACCTGGCCTTCTG-AGTCTTCCAAGGGCCTCCAGCCACCTCCTAG--------------------------------------------------------------------------------------------------------- i dipOrd1.scaffold_43980 C 0 I 1005 s cavPor3.scaffold_76 4394397 57 + 7991924 GGGCT-AAATTAGGCAAACCTGACCATCAG-CCTCCTCCCCAGGTTCCTGGGCACTGCC------------------------------------------------------------------------------------------------------------ i cavPor3.scaffold_76 C 0 I 3 s speTri1.scaffold_128901 11679 120 + 44242 -----------------------------------------AGGCTAAAATGCACAGAC---CNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG--- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 24054 48 + 41507 GGGCC-AAGGCAGTCTCCCCTGCCCACCTG-CCCCTCC-----GACCCGGCCCAC---------------------------------------------------------------------------------------------------------------- i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10864130 62 - 65312493 GGGCCAAAAAAAGACAAACCTGACCACCTGCCCTCTCCTCCTGGTTTCCAGGCATAGTC---------------------------------------------------------------------------------------------------------CGA i bosTau4.chr19 C 0 I 7 s turTru1.scaffold_106006 134005 60 + 145505 GGGCC-AAAAGAGACATACATGACCACCTG-CCTCTCATCCTGGTTTCCAGCCACAGCC---------------------------------------------------------------------------------------------------------CAG i turTru1.scaffold_106006 C 0 I 7 s canFam2.chr9 59441680 60 - 64418924 GGGCT-GAAGTAGACATACCTGAGCACCTG-CCTCTCCTCCTGGTTGCTAATCACTGTC---------------------------------------------------------------------------------------------------------CAG i canFam2.chr9 C 0 I 7 s myoLuc1.scaffold_4816 12771 56 + 14340 ---CT-ACAACAGGCATCCCTGACC-CCCG-CCTCTCCTCCTGGTCCCCAGGCTCAGCC---------------------------------------------------------------------------------------------------------CAG i myoLuc1.scaffold_4816 C 0 I 7 s pteVam1.scaffold_11245 20306 60 + 48268 GGGCT-AAAAAAGACATACCTGACCACCTG-CCTCTCCTCCTGGTTTCCAGTCGCAGCC---------------------------------------------------------------------------------------------------------CAG i pteVam1.scaffold_11245 C 0 I 7 s loxAfr3.scaffold_49 14438278 60 - 17734757 GGGCT-AAAACAGACATACCTACCCACCTG-TCTCTCCTCCTGGTTTCTAGGCGCATCC---------------------------------------------------------------------------------------------------------TAG i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_194555 9549 58 + 11139 GGGCT-GGAACAGGTACACCTGCCCACTTC-CCTCACCTCCTGGATCCCGGGCGCATCC---------------------------------------------------------------------------------------------------------C-- i echTel1.scaffold_194555 C 0 N 0 s dasNov2.scaffold_28617 17874 57 + 20752 GGGCA-AAAATAG--ACGCTTGTCCACCTG-CCTCTATTCCTGATCTCCA-TCAGATCC---------------------------------------------------------------------------------------------------------CAG i dasNov2.scaffold_28617 C 0 C 0 s choHof1.scaffold_149147 482 59 + 9388 GGGCA-GAAATAGACACACCTGTCCACCTG-CTGCGCTGCCGGGTTTCCA-TCAGATCC---------------------------------------------------------------------------------------------------------CAG i choHof1.scaffold_149147 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I e equCab2.chr11 58047300 917 - 61308211 M a score=-124549.000000 s hg19.chr17_gl000204_random 51369 91 + 81310 -------CGTTCAAGGCAGGGTGGGCTCACCTC---CC--CAAATATGGAGCAGCCAGCCAAGCAG---------------AGACC-------TG----CGCATAC------AGAG---CTGATGACCAG--CGGTGGGT s panTro2.chr17 79481566 91 + 83384210 -------TGTTCAAGGAAGGGTGGGCTCACCTC---CC--CAAATATGGAGCAGCCAGCCAAGCAG---------------GGACC-------TG----CGCATAC------AGAG---CTGATGACCAG--CGGTGGGT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 20304 91 - 64270 -------CGTTCAAGGAAGGGTGGGCTCACCTC---CC--CAAATATGGAGCAGCTAGCCAAGCAG---------------AGACC-------TG----CGCATAC------AGAG---CTGATGACCAG--CGGTAGGT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16068716 91 + 17838096 -------CGCTCAAAGAAGGGTGGGCTCACCTC---CC--CAAATATGGAGCAGCCAGCCAAGCAG---------------AGACC-------TG----TGCATAC------GGAG---CTGATGACCAG--CGGTGGGT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75042642 91 + 78773432 -------CGCTCAAGGAAGGGTGGGCTCACCTT---CC--CAAGTATGGAGCAGCCAGCCAAGCAG---------------AGACC-------TG----TGCCTAC------GGAG---CTGATGGCCAG--TGGTGGGT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 49846 91 - 95547 -------CGCTCAAGGAAGGGTGGGCTCACCTT---CC--CAAGTATGGAGCAGCCAGCCAAGCAG---------------AGACC-------TG----TGCATAC------GGAG---CTGATGGCCAG--TGGTGGGT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 52272 89 + 225949 -------CACTCCAGGAAGGGTGGGCT--CTTC---CC--CAGGGAAGCAGCAGCCAGCCCAGTGG---------------AGGCC-------TG----TGCACAT------GGAG---CTGACGGCCAG--CAGTGGGT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 6475 39 + 9575 ----------------------------------------------------------------GC---------------AGACC-------CA----GGCACAG------AGAG---CTGATGACCAG--GAGTGGAC i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_15893 10501 94 + 19765 -------GGCTGCCAGAAGGGCGGGCTCGCCTC---cc--cgg----------cccggcccggccc---------------ggcctggcccggcA----CAGACCTCACGCCGGGG---CTGCCGGCCAG--CAGTGGGT i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 31716 63 + 287808 -------------------------CTTCCTTC---CC--CAG----------GCCTGCCCGCCTG---------------AGGCT-------TA----TGAACAT------GGAG---CTGATGCCCAG--GAGAGGGT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 15514 90 + 15939 -------CCCTGCTGGGACAACCGAGTCGCTTG---CC--TGG-TCCAGAGCAGGCAGACCAGCTG---------------GGACC-------TG----CGTGTGC------GGAGGCCCTGAGGGCTGG----GTGGG- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118765056 43 + 121843856 -------------------------------------------------AGGCAGCAGACTAACTG---------------CCAAC-------CG-----------------AGAC---CAAACACACAG------GAGC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 7724 75 + 7959 -------CA---CCAGAGAGGCCGGCCTGTCTC---CC--TGG-----GTGGTGGCAGGCCGCCGG---------------TGATC-------TG--------TCC------GGAG---CCGATTCCCAG------GAGG i dipOrd1.scaffold_56485 I 4014 C 0 s cavPor3.scaffold_76 4394457 89 + 7991924 -------CAGTGCCAGAAGGGTGGTCCAGCCTCTGATC--AGG-----GAACAAGCATCCTGGGTG---------------AGGGC-------TGGGATTGCATGG------AGCC---CTGGAAAGCAG------GAGG i cavPor3.scaffold_76 I 3 C 0 s speTri1.scaffold_128901 11799 70 + 44242 -----------------------------TCTT---CC--GGG---TAGGAGCAGCAGTCCGCACGGCAGTCCCGTGCACTGGAGC-------TG-----------------CCAG---CTGCTGCCTGG------AGGG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 24102 53 + 41507 ------------------------------------CC--TGC---TGCAGGGAGCAGACGGCTGGGCA------------AGAGC-------TC----------C------GCAC---ACGACGCCCAT--------GG i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10864199 73 - 65312493 -------AGAGACCAGAAGGGGTGG-----CTT---CC--CTG----------AGCAAC--AGCTG---------------AGACC-------TG-----ACACAC------GGGG---TTGATGATCAG--GAGGAGAT i bosTau4.chr19 I 7 C 0 s turTru1.scaffold_106006 134072 77 + 145505 -------AGAGACCAGAAGGGTTGGCCCA-CTT---CC--CTG----------AGCATC--AGCTG---------------AGACC-------TG-----GCACAC------AGAG---TTGATGACCAA--GAGTAGGT i turTru1.scaffold_106006 I 7 C 0 s canFam2.chr9 59441747 90 - 64418924 -------CTGGACCAGAAGAGCTAGCCAC--TC---CCTGCAG-CACTCAGCAGACACC-TGGCGG---------------ACACC-------TG----CACACACA-----AGTA---CTGATGACCAT--GACAGGAT i canFam2.chr9 I 7 C 0 s myoLuc1.scaffold_4816 12834 76 + 14340 -------CTGGACCCAAAGGGCCGGCTGA--TC---CC--CGG----------AGCGTC-GGGCAG---------------GGACC-------CG----CGCACA--------GCG---CCGATGGCCGG--GCATGGAT i myoLuc1.scaffold_4816 I 7 C 0 s pteVam1.scaffold_11245 20373 90 + 48268 -------CTGGACCGGAAGAGCTGGCTCACTTC---CC--CAG-CACCCGGCAGACACC-TGGCAG---------------AGACC-------TG----CGCACAC------GGAG---CTG-CGGCCAGGTGTGTGGGT i pteVam1.scaffold_11245 I 7 C 0 s loxAfr3.scaffold_49 14438338 98 - 17734757 CACTAACCTAGACCAGAAGGTGTGGCTCACTGC---CC--CAAGCCCCTAGCAAACAGCCAAGAAG---------------GGACC-------CG----TGATCAC------AGAG---CTGACGACAGC--GAGTGGGC i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 17931 78 + 20752 GGCAAGGAGGGA--------------------T---CC--CGAAGTGCCAACAGGCAACCAGGCCA---------------AGACC-------CA----CACACGC------AGGG---CTGGCGAAGGG--GAGTGGGC i dasNov2.scaffold_28617 C 0 C 0 s choHof1.scaffold_149147 541 85 + 9388 CGCTGGGCGGGACCAGAA-----GGCTCAGCCC---CC--CGAGCTGCCAGCCGGCG--------G---------------AGACC-------TG----CACACGC------GGGG---CTGATGAGGGC--GCGTGGGC i choHof1.scaffold_149147 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I e equCab2.chr11 58047300 917 - 61308211 M a score=-171435.000000 s hg19.chr17_gl000204_random 51460 28 + 81310 CCAGTAGGGAGAC-------GGCCAGGTA------CAGAGC s panTro2.chr17 79481657 28 + 83384210 CCAGTAGGGAGAC-------GGCCAGGTA------CAGAGC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 20395 28 - 64270 CCAGTAGGGAGAC-------GGCCAGGTA------CAGAGC i gorGor1.Supercontig_0007361 C 0 I 21 s ponAbe2.chr17_random 16068807 28 + 17838096 CCAGCAGGGACAT-------GGCCAGGTA------CAGAGC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75042733 28 + 78773432 CCAGGAGGGAGAT-------GGCCAGGTA------CAGTGC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 49937 28 - 95547 CCAGGAGGGAGAT-------GGCCAGGTA------CAGTGC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 52361 28 + 225949 CCAGGAGGGAGGT-------GGCCAGGTC------CAGTGC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 6514 27 + 9575 CCAAG-GGGAGGT-------GGCTAAGTA------TACCAC i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_15893 10595 23 + 19765 CTGGGCGGGAGCT-------GGCTGGGCA------C----- i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 31779 3 + 287808 CTG-------------------------------------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 15604 11 + 15939 --------------------AGCGGGGTT------CA---- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118765099 18 + 121843856 GTGTAGTGAGAAA-------AGCCG---------------- i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 7799 27 + 7959 GTTGGGAGGACAG-------GGCCTGGCC-CAGGG------ i dipOrd1.scaffold_56485 C 0 C 0 s cavPor3.scaffold_76 4394546 21 + 7991924 G-AGGGAGGAGGC-------AGCCAGGCT------------ i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 11869 28 + 44242 ACAGGGAGGGCGG-------AGCCTGCTCCCGGGG------ i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 24155 22 + 41507 CTGGGCACAGAGC-------AGCCGCCTC------------ i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_196076 0 28 + 1154 CTGGGAGGGAGA--GGAAA-AACTAGATA------CA---- i vicPac1.scaffold_196076 N 0 I 4 s turTru1.scaffold_106006 134149 29 + 145505 CTGAGAGGGAGCT-GGCAT-GGCTAGATA------CA---- i turTru1.scaffold_106006 C 0 I 4 s bosTau4.chr19 10864272 33 - 65312493 CTGGGAGGGAACC-GTTGT-GGTAAGGCA------TAGGGC i bosTau4.chr19 C 0 I 4 s canFam2.chr9 59441837 34 - 64418924 CTCAGAAGGAGCCTGGCAT-GGCCAGGTA------CAACAG i canFam2.chr9 C 0 I 3 s myoLuc1.scaffold_4816 12910 31 + 14340 GCGGGAGGGCGCCTGGCAGCTGCCTTGCC------CA---- i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 20463 30 + 48268 CCGGGAGGGAGCCTGGCGG-GGCCGGGCA------CA---- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14438436 18 - 17734757 TTGGGGGCAGCCT-------GATGT---------------- i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 18009 18 + 20752 GGGGAGGGGCCCT-------AACCC---------------- i dasNov2.scaffold_28617 C 0 C 0 s choHof1.scaffold_149147 626 18 + 9388 CTGGGAGGGTCAT-------AACGC---------------- i choHof1.scaffold_149147 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I e equCab2.chr11 58047300 917 - 61308211 M a score=454440.000000 s hg19.chr17_gl000204_random 51488 89 + 81310 GGTTGCTCC---GCC-TAGGCCTCTGTTCTTCTGGAGTCTTGGGAGA--AAGCTCTCAGCACAGC--CGCTAACCAA---AGCAATAA--GCAAGTAA---ATTC s panTro2.chr17 79481685 89 + 83384210 GGTTGCTCC---GCC-TAGGCCTCTGTTCTTCTGGAGTCTTGGGAGA--AAGCTCTCAGCACAGC--CGCTAACCAA---AGCAATAA--GCAAGTAA---ATTC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16068835 89 + 17838096 GGTTGCTCT---GCC-TAGGCCTCTGTTCTTCTGGAATCTTGGGAGA--AAGCTCTCAGCACAGC--CGCTAACCAA---AGCAATAA--GCAAGTAA---ACTC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75042761 89 + 78773432 AGTTGCTCC---GCC-TAGGCCTCTGTTCTTCTGGAATCTTGGGAGA--AAGCTCTCAGCACAGC--CGCTAACCAA---AGCAACAA--GCAAGTAA---ACTC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 49965 89 - 95547 AGTTGCTCC---ACC-TAGGCCTCTGTTCTTCTGGAATCTTGGGAGA--AAGCTCTCAGCACAGC--CGCTAACCAA---AGCAACAA--GCAAGTAA---ACTC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 52389 89 + 225949 AGTGGCTTC---ACC-CAGGCCGCTGTTCTTCTAGAAACTTGGGAGA--AAACTCTCAGCACAGC--TGCTAAGCAA---AGCCATAA--GCAAGTAA---ACTC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 6541 86 + 9575 AGCTGCTGA---ACC-AAAGCCTCTG---TTCTAGAATCTTGGGAGA--AAGCTCTCCACACAGC--CACTAACCAA---AGCAATAA--GTGGGCAA---AATT i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_15893 10618 90 + 19765 GGCCACTTC---ACCCGGGGCCTCTTTCCTCCTAGAATCTGGGGAGA--AAGCTCTCGGTACAGC--CACTAACCAA---AGCAGTAC--ATGGGTAA---AATT i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 31782 77 + 287808 ----------------GGAGATTCTGTTCTTCTAGAATCTTGGGAGC--AAGCTCTCAGCACAGC--CACTAACCAG---AGTAGTAA--GTGGGTAA---AATT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 15615 79 + 15939 ------GTT---ACC----GCCTCTGCCCTTCCAAAGCCTTGGGAGA--CAGCTCTC---ATAAC--CACCAAGCGA---AGCAGTAAGTGTGGGTAA---AACT i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118765117 85 + 121843856 ---CTATCC---ACC---GTGCTCCTGTCCCTGAGACCCCGGTGAAA----GGTCTCAGTCCGTA--CAAGGAGCAA---AGCCGTAA--GTGGGCAAAACAGTT i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_56485 7826 75 + 7959 AACCTCTCC---ACC-T-GGACTCGGCTCTTCTGGAATTTGGGGAGAGGGTGGTCTCAGCACACAGCCACGGAGCCA---AGC---------------------- i dipOrd1.scaffold_56485 C 0 n 0 s cavPor3.scaffold_76 4394567 74 + 7991924 ---CTCTGC---AGC------------TCTCCTGGAATCGTGGGAGA--ACCCTCTCAGTACAGC--CCCTGAGCGA---AGTGGTAA--GTGGGTA----AGTT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 11897 75 + 44242 AGCTGCTCC---AGC----AGCTC---TGCTGTGGGATCTTGGGAGA--AAGCTCTCAGCACAGC--CACTGAGCAA---AG---------TGGGCA----AAAT i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 24177 79 + 41507 ---CCCGGC---GTC-T-GTCCCC---CGTCCCAAGTCCTGGGGAGA---TGCGCTCAGAGCAGC--CACTGCACAC---AAC--ACC--ATGGGCAG---TGTC i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_196076 32 82 + 1154 -AGTTCTTC----CC-CAGGCCTCGCCACC----GAACTTCAGGAGG--AAGCTCTCAGGACAGC--CACTAACCAA---AGC---AATACGTGGTAA---AATT i vicPac1.scaffold_196076 I 4 C 0 s turTru1.scaffold_106006 134182 87 + 145505 -AGTTCTCC---ACG-CATGCCTCTGCTCTTCTAGAATCTTGGGAGG--AATCTCTCGGGACAGC--CATTAACCAA---AGC---AATCCGTGGTAA---AATT i turTru1.scaffold_106006 I 4 C 0 s bosTau4.chr19 10864309 87 - 65312493 -AGTTCTTC---ACT-CATGCCTCTGTTCTTCTAGAATCTTAGGAAG--AAGCTCTTTGGACAGC--CATGAACCAA---AGA---AATATTTTATAA---AATT i bosTau4.chr19 I 4 C 0 s canFam2.chr9 59441874 84 - 64418924 -----CTTC---ACC-CATGCCCCTGTTTTTGTAGAACCTTGGGAGG--AAGATCTCAGTAGAGC--CACTAACCAACGCAGT---AA--GTGGATGA---AGTT i canFam2.chr9 I 3 C 0 s myoLuc1.scaffold_4816 12941 72 + 14340 ------------------CGCCGCTGTTATTCTAGAAACTTGGGAGG--AAGCGCTTAGTACAAC--CACTAACCAA---AGC---CA--CGCAGGAA---AATT i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 20493 65 + 48268 -----------------------GTGCCCTTCTGCAACCTC--GAAG--GAGCTTTCAGTGCAGC--CACCAACCAA---AGC---AA--CGTGCTGA---GGTT i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14438454 92 - 17734757 AGGGGGTTCTATGCA-GTTGCCTCTGCCCTTCTAGAACCTTGGCAGA--ATGCTCTTAGTACTGC--CAACACCCTG---AGAAATAA--ATGGGTAA---AATT i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 18027 88 + 20752 AGCTGCTTC---ACC-TATGCCTCTGCCCTTCTGGAATCTTGAAAGG--AAGTGCTCAGCTCAGC--C-CTAACTAA---AGTAATAA--GTGCATAA---GATT i dasNov2.scaffold_28617 C 0 C 0 s choHof1.scaffold_149147 644 87 + 9388 AACTGCTTC---ACC-AACGC--CCGTTCTTCTAGAATCTTGAGAGA--AAGCACTCAGTACAGC--CACTGACCAA---AGCAACAA--CCGCATAA---AATT i choHof1.scaffold_149147 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e gorGor1.Supercontig_0007361 20423 21 - 64270 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I e equCab2.chr11 58047300 917 - 61308211 M a score=376938.000000 s hg19.chr17_gl000204_random 51577 86 + 81310 CT-GCTA-AA------AATACA---TATAT--TCTTC-CTCTTTC-TTTTTTCT-----GCTGGG--A--ATATGTTCTGAGCACAAAT-AATTAAACC--T-TAAAAGA---AAAC---- s panTro2.chr17 79481774 86 + 83384210 CT-GCTA-AA------AATACA---GATAT--TCTTC-CTCTTTC-TTTTTTCT-----GCTGGG--A--ATATGTTCTGAGCACAAAT-AATTAAACC--T-TAAAAGA---AAAC---- i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16068924 86 + 17838096 CT-GCTA-AA------AATATA---TATAT--TCTTC-CTCTTTC-TTTTTTCT-----GCTGGG--A--ATATGTTCTGAGCACAAAT-AATTAAACC--T-TAAAAGA---AAAC---- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75042850 86 + 78773432 CT-TCTA-AA------AATATA---TATAT--TCTCC-CTCTTTC-TTTTTTCT-----GCTGGG--A--ATATGTTCTGAGCACAAAT-AATTAAACC--T-TAAAAGA---AAAC---- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 50054 86 - 95547 CT-TCTA-AA------AATATA---TAAAT--TCTCC-CTCTTTC-TTTTTTCT-----GCTGGG--A--ATATGTTCTGAGCAGAAAT-AATTAAACC--T-TAAAAGA---AAAC---- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 52478 86 + 225949 CT-GCTG-AA------AATATG---TATAT--TCTCG-GTGTTTC-TTTTTTCT-----GCTGGG--A--ATATGTTACGAGCACAAAT-AATTAAACC--T-CAAAAGA---ATAC---- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 6627 84 + 9575 CA-GCCA-AA------AACATG---CATAT--TTTCC---TCTTA-ATTTTTCT-----GCTGAG--A--ATATCTTCTGACCTTAAAT-AATTAAACT--T-AAAAAGA---AAAC---- i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_15893 10708 85 + 19765 CT-GCTA-AG------AATATG---TATAT--TCTCC-CTCTTTA-TCTC-TCT-----GCTGGG--A--ATATGCCCTGACCTTAAAT-GATTAAATC--C-TAAAAGA---AAAC---- i micMur1.scaffold_15893 C 0 C 0 s otoGar1.scaffold_94362.1-287808 31859 91 + 287808 CT-GCTACAA------CCTATGTATTATGT--TCTCC-TTCTTTC-TTTCATCT-----GCTGGG--A--ATACGTACTGACCTTAAAT-AATTGAAGC--CTTAAAATA---AAGC---- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 15694 77 + 15939 CT-GCTA-GA------AATCCG---AATCT--TTC-----CTTGC-TTATTTCT-----GCTGGGGTA--CAGGGTTCTGGCCTTAGAT-AATGAAGCC--G-TAAG-------------- i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118765202 72 + 121843856 ----CTA-GA------AATGTG---CA--------------CTGG-ATACTTCG-----GCTAGG--A--ATGTGCCCTGACCTGAGAT-AATGGGATC--T-GGAAGAA---GAAC---- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4394641 84 + 7991924 CT-GCTA-AA------AATATC---CACTT--TCCCCTCCTTCCT-GCTCTTCT-----G---GG--A--CTGCGTGCCAGCCTTCAGT-GATTGAACC--T-TAAAAGA---AAAC---- i cavPor3.scaffold_76 C 0 I 3 s speTri1.scaffold_128901 11972 82 + 44242 CT-GCTA-AA------AATACG---CA------TGTCCCCCCTCC-TTCTTTCT-----GCTGGG--A--GTAGCTTCTGGCCTTAAAT-AACTGAACC--T--AAAAGA---GAAC---- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 24256 74 + 41507 CA-GCTG-GG------GACG-----------------------TG-ACTCTCCG-----GCTGGG--GTCGCGTGTGCCAGCCCTAAAT-GACGAAGCC--T-CAACAGATACGGAG---- i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_196076 114 98 + 1154 CC-ACTC-AAAGGGCGAGTATG---TATAC--TCTCC-CTTTTTTTTTTTTTTTTCCGAGCTGGG--A--GTATGCTCTGACTTTAAAC-AATTAAACC--T-AAAAAAA---AAAA---- i vicPac1.scaffold_196076 C 0 I 7 s turTru1.scaffold_106006 134269 85 + 145505 CT-GGTC-AA------AACATG---TATAC--TCTCC-CTCCTTC-TTTTTTCT-----GCTGGA--A--ATTCACTCTGACTTTAAACAAATTAAGCC--T-TCCAAAA---AA------ i turTru1.scaffold_106006 C 0 I 1 s bosTau4.chr19 10864396 84 - 65312493 CT-GCTC-AA------AATATG---TATAT--TCTCC-CCCCTCCTTTTTTTCT-----GCTAGG--A--ATTCTCTCTGGCTTTAAAC-AATTAGACC--T-TTC-AAA---AA------ i bosTau4.chr19 C 0 I 1 s equCab2.chr11 58048217 86 - 61308211 CT-GCTA-AA------AATATG---TATAT--TCTCT-CTCCTTC-TTTTTTCT-----ACTGAG--A--ATATGCTCCGACTTTAAAC-AATTAAACC--T-TAAAAAA---AAAA---- i equCab2.chr11 M 917 I 4 s canFam2.chr9 59441958 85 - 64418924 CT-GCTA-AA------AACACA---TATATCCTCCCC-CTCCCAT-TTTTTTCT-----GCTAAG--A--CTATGCTCTGGCTTTAGAC--ACTAAACC--T-TAAAATA---TA------ i canFam2.chr9 C 0 I 191 s myoLuc1.scaffold_4816 13013 83 + 14340 CC-GCTA-AA------ATGATG---TATAG--TCTCC-CTC---T-TTTTTGCT-----GCTAGG--A--AGATGATCTGACTTTAAAC-AATTAAACC--T-TCAAAAA---AAAA---- i myoLuc1.scaffold_4816 C 0 I 4 s pteVam1.scaffold_11245 20558 16 + 48268 CT-ACTC-AA------A--ATG---TATG-------------------------------------------------------------------------------------------- i pteVam1.scaffold_11245 C 0 C 0 s dipOrd1.scaffold_43980 2536 71 + 11404 ---------------------------TAT--TCCCCTCCCTTCT-TTTCTCCT-----GTCGGG--A--ATAAGTTCCAACCTTGAAT-AAGTGAACC--T-TGAAAGA---AAAC---- i dipOrd1.scaffold_43980 I 1005 C 0 s loxAfr3.scaffold_49 14438546 88 - 17734757 CTGTTTA-AA------AATATG---TGTAT--TCTCC-TTC---C-TTTTTCCT-----GCTGGG--C--ACATCCTCTGACCTTGAAC-AACTTAACC--T-TAAAAAA---AAAAATAC i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 18115 85 + 20752 CT-TTTA-AA------AGTAAG---TATAT--TCTCT-GTCCTTC-TTTTGCCT-----GCTAGG--A--ATATGCTCTGATCTTCAAC-AATTTAACCTTT-TGAAAGA---A------- i dasNov2.scaffold_28617 C 0 C 0 s choHof1.scaffold_149147 731 74 + 9388 CC-ATTA-AA------TACACG---TATAT--TCTCC-CTCTCTC-CTTTTCAT-----GCTAGG--A--CTATGCTCTGATCTTGAAC-AATTTAACC---------------------- i choHof1.scaffold_149147 C 0 M 1005 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e gorGor1.Supercontig_0007361 20423 21 - 64270 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I a score=273504.000000 s hg19.chr17_gl000204_random 51663 41 + 81310 TTGCAGTAGCAAGTGCTTGGCTCTTGG-TCCTAAGAGGAAAC s panTro2.chr17 79481860 41 + 83384210 TTGCAGTAGCAAGTGCTTGGCTCTTGG-TCCTAAGAGGATAC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16069010 41 + 17838096 TTGCAGTAGCAAGTGCTTGGCTCTTGG-TCCTAAGTGGAAAC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75042936 41 + 78773432 TTGCAATACCAAGTGCTTGGCTCTTGG-TCCTAAGAGGAAAC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 50140 41 - 95547 TTGCAATACCAAGTGCTTGGCTCTTGG-TCCTAAGAGGAAAC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 52564 41 + 225949 TTGCAATACCAACTGCTTGGCTCTTGG-TGGAAAGAAGAAAC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 6711 41 + 9575 TTGCCATGAGAACTGCTTTGTTCTTAG-TCTTAAGAGGAAAC i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_15893 10793 27 + 19765 TTGCAATAAGAACTGCTTTGCTGTCGG--------------- i micMur1.scaffold_15893 C 0 I 3214 s otoGar1.scaffold_94362.1-287808 31950 30 + 287808 CTGCAATAAGAACTGTTTTGCTCT------------GGACAC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 15771 29 + 15939 ----------AACCACTTTGCTCGG---AGCTAAAAGGAAAC i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118765274 40 + 121843856 TGGGAAT-AAGACTCTTTTGCTTCCTG-GCCTAACAGGAAAC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 2607 24 + 11404 TTGCCATGAGGACGTCTCTGCT------------------GC i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4394728 41 + 7991924 TGATCATCTGGACCTCTCTGCTCTTTG-TCCTCAGAGGAAAC i cavPor3.scaffold_76 I 3 C 0 s speTri1.scaffold_128901 12054 41 + 44242 TTGCAACAGGGACCACCATGCTCTTGG-TCCTGTGAAGAAAT i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 24330 22 + 41507 CGGTGACGAGACAGCGCCCACT-------------------- i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_196076 219 41 + 1154 TTGCAAAAAGAACCATTTTTCTCCCAG-TTCTCAAAGAAAAC i vicPac1.scaffold_196076 I 7 C 0 s turTru1.scaffold_106006 134355 41 + 145505 TTGCAACTAGGACTGCTTTGTTCTAGG-TCCTCAGAGGAAAC i turTru1.scaffold_106006 I 1 C 0 s bosTau4.chr19 10864481 40 - 65312493 TTGCAACCA-AACTGCTTTGTTCTTGG-TCCTCAGAGGAAAC i bosTau4.chr19 I 1 C 0 s equCab2.chr11 58048307 41 - 61308211 TTGCAACAAGAACTGCCTTGCCCTTGG-TCCTCAGAGGAAAC i equCab2.chr11 I 4 C 0 s canFam2.chr9 59442234 41 - 64418924 TTTCAACAAGAACTGCTTTGCTCTTGA-TCCTCAGAGAACAC i canFam2.chr9 I 191 C 0 s myoLuc1.scaffold_4816 13100 41 + 14340 TCCCAAAAGGAACTGCTCTGCTCTTGG-TCCTCAGAGGAAGC i myoLuc1.scaffold_4816 I 4 C 0 s pteVam1.scaffold_11245 20574 38 + 48268 ---CAATAAGCACTGCTTTGCACTTGG-ACCTCAAAAGAAAC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14438634 42 - 17734757 TTGCAACCAGAACTGCTTTGCTCTTAGCCCCTGAGAGGAAAC i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 18200 41 + 20752 TTGCAGCAAGAACTGATATGCTCTGGG-CTCTAGGAGGAAAC i dasNov2.scaffold_28617 C 0 I 1805 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e gorGor1.Supercontig_0007361 20423 21 - 64270 I e choHof1.scaffold_149147 805 1005 + 9388 M e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I a score=-31258.000000 s hg19.chr17_gl000204_random 51704 26 + 81310 CACGGAGGCTGAGGACCCC------------CAACT-CA s panTro2.chr17 79481901 26 + 83384210 CACGGAGGCTGAGGACCCC------------CAACT-CA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16069051 26 + 17838096 CACAGAGGCTGAGGACGCC------------CAACT-CA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75042977 26 + 78773432 CATGGAGGCTGAGGACCCC------------CAACT-CA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 50181 26 - 95547 TATGGAGGCTGAGGACCCC------------CAACT-CA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 52605 26 + 225949 CACAGAGGCTGAGGACCCA------------CAACT-CA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 6752 23 + 9575 CACAGACTC---AAACCCC------------CAACG-TG i tarSyr1.scaffold_143701 C 0 C 0 s otoGar1.scaffold_94362.1-287808 31980 26 + 287808 CACCAACTCTGAAGACCCC------------CAACT-GG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 15800 25 + 15939 CAGAGGCTCTG-GAGCCCC------------CATCT-TG i tupBel1.scaffold_124459.1-15939 C 0 C 0 s mm9.chr11 118765314 31 + 121843856 TGAAGAC-------ACCCCCCCCCCACTCAGTGAGT-TG i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 2631 18 + 11404 TGAAGCC-------GGGC-------------TGGGC-TG i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4394769 25 + 7991924 TGTGGACCCTGAAGACCC-------------CAGTG-TG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 12095 25 + 44242 CACAGACCCCATAGAATC-------------CCACG-AG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 24352 17 + 41507 ---AGGC-----AGCCCC-------------CAGCG-TG i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_196076 260 34 + 1154 CATAAACTCTGAAGACCCCGCCATATC----CAACA-CA i vicPac1.scaffold_196076 C 0 C 0 s turTru1.scaffold_106006 134396 34 + 145505 CACAGACTCTGAAGACCCCACCCCATC----CAACA-CA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10864521 33 - 65312493 TATA-ACTCTGAAGACCCCACCCCATC----CCACA-CA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58048348 31 - 61308211 CATGGCCTCTGAAGACC---CCCCACC----CAACA-GG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59442275 35 - 64418924 CACAGACTCTAAAGACCCCACCTCCCC----TAACATGA i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 13141 32 + 14340 CACAGAGTCCAGCCCCCCATGCAGCCC----GAGCT--- i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 20612 31 + 48268 GACAGACCCGGACGACCCAT-CCCCTC----TACCT--- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14438676 34 - 17734757 CAGTGACCCTGAAGCCCTCACCCTATC----CAAGG-CA i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 21465 1065 + 24616 I e gorGor1.Supercontig_0007361 20423 21 - 64270 I e choHof1.scaffold_149147 805 1005 + 9388 M e micMur1.scaffold_15893 10820 3214 + 19765 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 18241 1805 + 20752 I e monDom5.chr2 304539065 11756 - 541556283 I a score=117974.000000 s hg19.chr17_gl000204_random 51730 114 + 81310 AGTTGACGCCAGCAAGTTACAA----CCCAC---------CTCTCAG--GTGGAA---CCCACGAGCCCTGGCCCC-AACCTACACGGAAGGAGTGGAGA-----C-GGA--TCCAAGGGA-------AGAC----------------TGATTTTCACTTCTAA s panTro2.chr17 79481927 114 + 83384210 AGTTGACGCCAGCAAGTTACAA----CCCAC---------CTCTCAG--GTGGAA---CCCACGAGACCTGGCCCC-AACCTACACGGAAGGAGTGGAGA-----C-GGA--TCCAAGGGA-------AGAC----------------TGATTTTCACTTCTAA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16069077 114 + 17838096 AGTTGACGCCAGCAAGTTACAA----CCCAC---------CTCTCAG--ACGGAA---CCCGCAAGACCTGGCCCC-AACCTACACAGAAGGAGTGGAGA-----C-GGA--TCCAAGGGA-------AGAC----------------TGATTTTCACTTCTAA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75043003 114 + 78773432 AGTTGACACCAGCAAGTTACAA----CCCAC---------TTCTCAG--GTGGAA---CCCGCAGGACCTGGCCCC-GACCTACACGGAAGGAGTGGAGA-----T-GGA--TCCAAGGGA-------AGAC----------------TGATTTTCACTTCTAA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 50207 114 - 95547 AGTTGACACCAGCAAGTTACAA----CCCAC---------TTCTCAG--GTGGAA---CCCGCAGGACCTGGCCCC-GACCTACATGGAAGGAGTGGAGA-----C-GGA--TCCAAGGGA-------AGAC----------------TGATTGTCACTTCTAA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 52631 115 + 225949 GGCTGACGCCGGCAAATTATAA----CCCAC---------CTCTCCG--GTGAAA---TCTGTGGGGCCTGGCCCC-GACCTACACGGAAGGAGTGGAGA-----CTGGA--TCCAAAGGA-------AGGC----------------TGATTTTCACTTCTAC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 6775 115 + 9575 AGTTGATGCCAACAAGTTACAA----GCCAC---------CTCTCGG--GTGGAA---CCAGCAGGAGCTGGCCCT-GAGCTGCACAGAAGGAGTGAAGA-----CCAGA--TCCAAGGGA-------AAAT----------------TGTTTTTTACTTCTAA i tarSyr1.scaffold_143701 C 0 C 0 s otoGar1.scaffold_94362.1-287808 32006 111 + 287808 AGCTGACGCCAATAAGCGCCAA----CCC-C---------CTCTCAG--GTGGAG---TCAGCGGGAATGG--CCT-GAACTACACAGAGGGAGTCAGAT-----G-AGA--TCCACGGGA-------AGGC----------------TGTTTCTTACTTCTAA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_124459.1-15939 15825 113 + 15939 AACTGCCACTAACAAGGTACAA----GCC------------CCTCAG--G-GCAG---TCAGCAGGGCCTGGCCCTGGAACTGGCAGGTGGGAATGGGGG-----A-AGGACTCTGAGGGA-------AGAT----------------ATTTCCTGGCTCCTAA i tupBel1.scaffold_124459.1-15939 C 0 N 0 s mm9.chr11 118765345 126 + 121843856 GTGTAACA----AGGGATAGCA-GAAGCCTCTCTCTCTCTCTCTCTG--ACAGAG---GAGGTAGAAGCAGGCTGT-GGACTGTAC---AGGACTGGAGA-----CTGGA--TACAAGAGA-------AGGTTTATGTCC----------ATTTTTACTTGTAA i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 2649 54 + 11404 G-------------------------GCCCC------------------------------GCAGGGACCAGTCCT-GTGCCGCGC---AGGGGAGCAGC-----CCGGA--T-----GGG-------AGGT-------------------------------- i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4394794 110 + 7991924 GGGTGACA----CAAGTCACAA----GCCCC---------CTCTTGG--CCAGGGTCATCAGCAAGAGCTGGGCCC-TGGCCACAC---AGGAGTGGAGATGAGGCTAGA--C-----ACG-------GTGT-----TTC----------GTTTTAACTTCC-- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 12120 118 + 44242 GCTTGACA------AGTCACGA----GCCCC----------TCCCAG--CTGGGG---TCAGCAGGAGCTGGCCAC-T--CCAGGC---AGG-GTGAAGA-----CTAGA--CCAAGGGAA-------GGGTTTGAGCTCTTGGCTGGGGGTTTTGGCTTCTCG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 24369 74 + 41507 GGCTGAGGTC--ACGGTCACGGCTCAGCCCT----------CCGTGG--GC-------TCAGCCAGAACCCCACCC-ACGCTGCAC---AGG--------------------------AGG-------GGGC-------------------------------- i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_196076 294 97 + 1154 AACTGATGCCAACGAGTTACAA----ACCAC---------TCCCCAG--GAGGAG---T---CAGAGCCCAGCCCT-GAGCTACACAGGAAGGGTAGAGA-----CCAGA--TCCAAAGGA--GAGGT------------------------------------ i vicPac1.scaffold_196076 C 0 C 0 s turTru1.scaffold_106006 134430 82 + 145505 AACTGATGCCAACGAGTTACAA----CCCAC---------TTCCCGG--GTGGAA---TTAGTAGGACCCAGCCCA-GAGCTACACAGAATAGGTAGAGA-----C---------------------------------------------------------- i turTru1.scaffold_106006 C 0 I 12 s bosTau4.chr19 10864554 97 - 65312493 AATTGATGCCACCAAGTTATAG----CCCAC---------TCCCCAG--GTGGAA---TCAGCAGTACCCAGCCCC-GAGCTACACAGAAAGGGTGAAGA-----CTAGA--TCCAAAGGA--GG--------------------------------------- i bosTau4.chr19 C 0 I 3 s equCab2.chr11 58048379 93 - 61308211 AGTTGATGCCAACAAGTTACAA----CCCAG---------CCCCCAG--GTGGAA---TC-GCAGGCACC-GCCCT-GAGCTGCACAAAGACAGTGGAGA-----CCAGA--TCCAGAGGA------------------------------------------- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59442310 97 - 64418924 AATTGATGCTAACAAGTTACAA----CCCAC---------CTCCCAG--GTGAAA---TCAGCAGGAACCAGCCCT-GAGCTACACAGGAAGAGTGGATA-----CTAGA--TCCAGAGGAAG----------------------------------------- i canFam2.chr9 C 0 I 5 s myoLuc1.scaffold_4816 13173 62 + 14340 AACCAGTG---AGAGCCCCCCA----CCCCC--------ACCCCCAG--GCGGAG---CA-GCCGGCACC-GGCCT-GAGCGACA------------------------------------------------------------------------------- i myoLuc1.scaffold_4816 C 0 I 102 s pteVam1.scaffold_11245 20643 79 + 48268 ---CAGTG---AAAAGTTATCA----TCTGC---------CTCCCAG--GTGGAA---C---------CA-GCCCT-GGGCCACACAGAAAGAGTGGAGG-----CTAGA--TCTAAAAGA------------------------------------------- i pteVam1.scaffold_11245 C 0 I 4 s proCap1.scaffold_29042 22530 112 + 24616 AGTGGATGCCAGTACGCCACAA----CCCAC---------CTGGCAGGTGTGTGA---CAAGCATGAACTGACCCT-GCAGGGCACAGGAA-GGCAGAAA-----CCAGA--TCCA----A-------AGCC----------------CGTTCTTTACTTACAG i proCap1.scaffold_29042 I 1065 C 0 s loxAfr3.scaffold_49 14438710 115 - 17734757 AGCTGATGCCAATAAGCCACAA----TCCAC---------CTGGCAG--GTGGAA---TCAGCATGACCCATCCCT-GAACTACACAGAAAGGGTGGAGA-----CTAGA--TTCAAAGGA-------AGAC----------------CTTTCTTTGCTTATAA i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e gorGor1.Supercontig_0007361 20423 21 - 64270 I e choHof1.scaffold_149147 805 1005 + 9388 M e micMur1.scaffold_15893 10820 3214 + 19765 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 18241 1805 + 20752 I e monDom5.chr2 304539065 11756 - 541556283 I a score=21195.000000 s hg19.chr17_gl000204_random 51844 26 + 81310 AAAGCTTCCC-CAAG-CCGCAGCTT----TCT--- s oryCun2.chrUn0958 24443 9 + 41507 -GCGGCTTCT------------------------- i oryCun2.chrUn0958 C 0 C 0 s speTri1.scaffold_128901 12238 27 + 44242 GGAGCCTCCC-AGAGCCCACCTCTG----GCT--- i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4394904 27 + 7991924 AGAGATTCCCCAGAACTCACAGCTT-----GC--- i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_43980 2703 27 + 11404 GGAGGTTTCT-----TCCGCCCCCTGTGGGCC--- i dipOrd1.scaffold_43980 C 0 C 0 s mm9.chr11 118765471 26 + 121843856 GGAGGTTTCT-GGAATCCACAGCTC-----CC--- i mm9.chr11 C 0 C 0 s otoGar1.scaffold_94362.1-287808 32117 27 + 287808 AGTGCCTCCC-TGAGCCCACAGCTG----GCT--- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tarSyr1.scaffold_143701 6890 27 + 9575 GGAGCCTCCC-AGAGCCCACAGCTT----CCT--- i tarSyr1.scaffold_143701 C 0 C 0 s calJac1.Contig5139 52746 26 + 225949 ACAGCCTCCC-CAGG-CCGCAGCTT----GCT--- i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 50321 26 - 95547 AAAGCCTCCC-CAAG-CCGCAGCTT----ACT--- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75043117 26 + 78773432 AAAGCCTCCC-CAAG-CTGTAGCTT----ACT--- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16069191 26 + 17838096 AAAGCTTCCC-CAAG-CCGCAGCTT----TCT--- i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79482041 26 + 83384210 AAAGCTTCCC-CAAG-CCGCAGCTT----TCT--- i panTro2.chr17 C 0 C 0 s proCap1.scaffold_29042 22642 29 + 24616 AGAGCCTGTC-AGAGACC-CTGCCT----GATGCC i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14438825 30 - 17734757 AGAGCCTCCC-AAAGCCCACAGCTT----GACGCC i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e gorGor1.Supercontig_0007361 20423 21 - 64270 I e vicPac1.scaffold_196076 391 0 + 1154 C e choHof1.scaffold_149147 805 1005 + 9388 M e myoLuc1.scaffold_4816 13235 102 + 14340 I e micMur1.scaffold_15893 10820 3214 + 19765 I e turTru1.scaffold_106006 134512 12 + 145505 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 18241 1805 + 20752 I e pteVam1.scaffold_11245 20722 4 + 48268 I e monDom5.chr2 304539065 11756 - 541556283 I e canFam2.chr9 59442407 5 - 64418924 I e bosTau4.chr19 10864651 3 - 65312493 I e equCab2.chr11 58048472 0 - 61308211 C a score=1536.000000 s hg19.chr17_gl000204_random 51870 151 + 81310 CTACCCACAAGGGGAA-----CACTCC------CCACAGAGG-AGAGCACC-CCATCC--CT-----------TGTTCTTCT-------------------------G-CC-CCCTATCCCCTGA----CTGCAGAGCCTTC--GATACCACAG---TCTTGTCAA-TG-----TTTCGAGTGCAGTGAG---TTGGCAGG-GGCAGCAGCAGTGAG---AAGGGA s panTro2.chr17 79482067 151 + 83384210 CTACCCACAAGAGGAA-----CACTCC------CCACAGAGG-AGAGCACC-CCATCC--CT-----------TGTTCTTCT-------------------------G-CC-CCCTTTCCCCTGA----CTGCAGAGCCTTC--GATACCACAG---TCTTGTCAA-TG-----TTTCGAGTGCAGTGAG---TTGGCAGG-GGCAGCAGCAGTGAG---GAGGGA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16069217 150 + 17838096 CTACCCACAAGAGGAA-----CA--CC------CCACAGAGG-AGAGCACC-CCATCC--CT-----------TGTTCTTCT-------------------------GCCC-CCCTTTCCCCTGA----CTGCAGAGCCTTC--GATGCCACAG---TCTTGTCAA-TG-----TTTCGAGTGCAGACAG---TTGGCAGG-GGCAGCAGCAGTGAC---GAGGGA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75043143 151 + 78773432 CTACCCACAAGGGGAA-----CACTCC------CCATAGAGG-AGACCACC-CCATCC--CT-----------TGTTCTTCT-------------------------G-CC-CCCTTTCCCCTGA----CTGCAGAGCCTTC--AGTACCATTG---TCTTGTCAA-TG-----TTTCGAGTGCAGAGAG---TTGGCAGG-GGCAGCAGCAGTGAG---GAGAGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 50347 151 - 95547 CTACCCACAAGGGGAA-----CACTCC------CCATAGAGG-AGAGCACC-CCATCC--CT-----------TGTTCTTCT-------------------------G-CC-CCCTTTCCCCTGA----CTGCAGAGCCTTC--AGTACCATTG---TCTTGTCAA-TG-----TTTCAAGTGCAGAGAG---TTTGCAGG-GGCAGCAGCAATGAG---GAGAGA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 52772 151 + 225949 CAACCCACAAGGGGAG-----CACTCC------CCACAGAGG-AGACCACC-CCATCC--CT-----------TGTTCTTCT-------------------------G-TC-ACCTTTCCTCCGA----CTGCAGAGCCTTC--GATGTCACAG---TCTTGTCAA-TG-----TTTCGAGTACAGACAA---TTGGCAGG-AGCAGCAGCAGTGAG---GAGGGA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 6917 154 + 9575 CTGCCCCCGTGGGGGA-----AACTCC------CCACAGGGGCAGACCACC-TCATCC--CT-----------TGTTCTTCC-------------------------G-CC-ACCTTCTCTCTGA----CTTCAAAGCCTTT--GATATCGCAGTCTTCTTGTCAA-TG-----TTTCAAGAGTAGAGAG---TTGGCAGG-GGACGTAACAGTGAG---G-GGAA i tarSyr1.scaffold_143701 C 0 C 0 s otoGar1.scaffold_94362.1-287808 32144 141 + 287808 CTACACACAAGGGGGA------ACTCT------CCACAGGGG-CAGACCCC-AAGGCC--CT-----------TGTTCTCCT-------------------------G-CC-ACCTTCTCTCTGA----CAGCACAGCCTTT--GATGTCACAT---TC------------------CAAGTGCAGAAGA---GTTGGGGG-GGGAGTAGGGGTAGGAGTGAGGAG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118765497 142 + 121843856 TTCCTTGA-GGGGGGG--------TGGGAGGGACTGACAAGG-AAACTGCC-CAGCTCGTCC-----------TTTCTTTCT-------------------------T-CCACCCTCTGCCTT-----------TTAGCCTC--TGTGTCACAGCCTCCCTGCCAA-----------GCAGTCAAGAGAG---ATGGCCAA-TG--GAAGCTG-GAG---GGTA-- i mm9.chr11 C 0 I 741 s dipOrd1.scaffold_43980 2730 134 + 11404 TTCCACAC-GCGGTCA--------TCT------CTCACAGGG----------CAGCCAGGTC-----------TGTCTGCCG-------------------------T-CT-TCCTCTACCAC-----------TCGCCTTG--AATAGCTCAGCCTCCTCCACAGATA-----TTTGGAGTGAAGAGCG---TCGGAGGG-CA--GTAGCAGTGAG---GGGA-- i dipOrd1.scaffold_43980 C 0 I 1 s cavPor3.scaffold_76 4394931 137 + 7991924 TGCCCTGCTGGTGGGA--------CCT------TCCGCGGGC-AGTCCACCTCCCTCGGGTT-----------TGGCTGTCT-------------------------C-CT-TCCTGATTCTT-----------TCAGAGTG--AG-------GCCTCCATTGCCAGTG-----TTTCGGGCAAAATGAG---CTGGCTGG-GT--GGAGCAGTACA---AGAA-- i cavPor3.scaffold_76 C 0 I 1 s speTri1.scaffold_128901 12265 129 + 44242 CTCCCCACAAGCGGCA--------ACT------CCACAGGGC-GAACCGCC-CCGTCC--CT-----------TGTTCTGCC-------------------------T-CC-TTCTCTCTGAC-----------TCGCCTTT--GATTCCGGGGCCTCCTTGCCAG-TG-----TTTGTGGTGAAGAGGG---TGGGCAGG-AA--GGAA---------------- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 24452 94 + 41507 ---------------------------------GTTCTGGGG-CTGCCTCC-CCCCTCACAG-----------CCTCTGACG-------------------------T-CA-CCGTC------------------------------------GACTCC----CAG-TG-----TTT-CAGTGGAAGGCG----GGGTGGG-AG--GGGGCCTGGCA---GGGA-- i oryCun2.chrUn0958 C 0 I 8 s myoLuc1.scaffold_4816 13337 135 + 14340 ------------------------CCG------TCCCCAGGG-TGGCCACC-TGGCTC--CTGAGAGATCAGCCGTTCTCCC-------------------------G-CC-CCCCCACCCCCGAC--TCTGCGACACCGTCCAAAGAGCAAGG---TACAGACCG-CGAGCGCTTTCAAATAAAGTGACAGCCCGGCCGG-G----------------------- i myoLuc1.scaffold_4816 I 102 C 0 s proCap1.scaffold_29042 22671 183 + 24616 CTGCCCACAGGGAGGGACCCTCCCTCT------CCATTCAGG-GGACCATC-TCATCC--CT-----------TGCTTCTGACCACCCCTCACCCGCCCCTCACGGCC-CC-CTGACTTCTCACACCTTCTTCAGAGCCTTT--GATTTCT--GTCTTCTTGT----CA-----TTTTAAGTGTGGGGTG---GGGGCAGG-GGCTGCCACAGGGAA---GAGAAG i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14438855 161 - 17734757 CTGCCCGCAAACAGGGAAGCTCCTTCT------CCATCCAGGTGGACCTTC-TCACCC--CT-----------TGCTTCTCA-------------------------C-CC-CCGAATTTTTCCACCTTGTTCAGAGCC--T--GATTTCC--ATCTTCTTGTCAA-CA-----TTTCAAGTGAAGAGTG---TTGGCAGGAGGCTGCCGCAGGGAG---GGGAAA i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e gorGor1.Supercontig_0007361 20423 21 - 64270 I e vicPac1.scaffold_196076 391 0 + 1154 C e choHof1.scaffold_149147 805 1005 + 9388 M e micMur1.scaffold_15893 10820 3214 + 19765 I e turTru1.scaffold_106006 134512 12 + 145505 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 18241 1805 + 20752 I e pteVam1.scaffold_11245 20722 4 + 48268 I e monDom5.chr2 304539065 11756 - 541556283 I e canFam2.chr9 59442407 5 - 64418924 I e bosTau4.chr19 10864651 3 - 65312493 I e equCab2.chr11 58048472 0 - 61308211 C a score=8970.000000 s hg19.chr17_gl000204_random 52021 90 + 81310 GAGGAGGGGCAAGGAGACCACCTCAAGCTGCTGGTCTGT------CT-AGAGACCAGG------AAGAAACCA--GAA-GGACG------------------CCTGGGCCTGACCAGAACAGT-C s panTro2.chr17 79482218 90 + 83384210 GAGGAGGGGCAAGGAGACCACCTCTAGCTGCTGGTCTGT------CT-AGAGACCAGG------AAGAAACCA--GAA-GGACG------------------CCTGGGCCTGACCAGAACAGT-C i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16069367 84 + 17838096 GAGGAAAGGCAAGGAGACTACCTCTAGCTGCTGGTCTGT------CT-AGACACCAGG------AAGAAACCA--GAA-GGACA------------------TCTGG------CCAGAACAGT-C i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75043294 84 + 78773432 GAGGAGGGGCAAGGAGACCATCTCTAGCTGCTGGTCTGT------CT-AGAGACCAGG------AAGAAACCA--GAA-GGATG------------------CCTGG------CCAGAACAGT-C i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 50498 84 - 95547 GAGGAGGGGCAAGGAGACCATCTCTAGCTGCTGGTCTGT------CT-AGAGACCAGG------AAGAAACCA--GAA-GGATG------------------CCTGG------CCAGAACAGT-C i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 52923 90 + 225949 GAGGACAGGCAGAGAGACCACCTCGAGCTGCTGGTCTGTCAAAACCT-AGAGACCAGG------AAGAAACCA--GAA-GGACA------------------CCCAG------CCACGACAGT-C i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 7071 90 + 9575 GGAGAGGGGCA-GGAGACCACCTTTAGCTGCTGGCCTAT------CA-AGACCTCAAGCACCCCAAGAAACCA--CCA-TGACA------------------CCTGC------CCAGGTGGGTCC i tarSyr1.scaffold_143701 C 0 C 0 s otoGar1.scaffold_94362.1-287808 32285 79 + 287808 AAGCAGGGGCGAGGACATCACCATTAGCTA----------ACAACCC-AGAAGACAGA------AGGAAACCA--GGA-CGACA-------------------CTGC------CCAGGGGAGC-G i otoGar1.scaffold_94362.1-287808 C 0 I 1 s dipOrd1.scaffold_43980 2865 82 + 11404 ------------GGGGAGAGTCCCTTAGAACCCATCCAGCTAGACCTGAGATCATGGG------AGGGAGCAG--GGC-AC-CAACCG--------------CCTGG------AGAAGCTTGG-A i dipOrd1.scaffold_43980 I 1 C 0 s cavPor3.scaffold_76 4395069 103 + 7991924 --AACGGAGGACAGGGAGGGT-GCTCAGAGTTTGCTCACCAAGACCT-AGAGAATGGG------AACGTCCAGCTGAC-ACACAGCAGTTAA----------CCTGGTTCACACGGAGCACAC-A i cavPor3.scaffold_76 I 1 C 0 s speTri1.scaffold_128901 12394 113 + 44242 --AGTGGGAGGGCAGGAGAGCCCCTTGCAGCTTGCCTGGTAAGACCT-AGAGACTGGC------AGAG-CCAGCTGAA-AGATGGCCAAGAGGACAGAGGCCCCCGGGCCTCACAGGGAAGGC-A i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 24554 100 + 41507 CAGGCGGAGGTTGGGATCCACCTTCCCCCACTGGCCTTCCAGGATCC-AGAGAACGGG------AAAAGCCAG--GAG-GGGTCTCCT--------------CCCGGGGAGGGCGAGGACGAG-A i oryCun2.chrUn0958 I 8 C 0 s gorGor1.Supercontig_0007361 20444 61 - 64270 ------------------------------CTGGTCTGT------CT-AGAGACCAGG------AAGAAACCA--GAAGGGACG------------------CCTGGGCCTGACCAGAACAGT-C i gorGor1.Supercontig_0007361 I 21 C 0 s myoLuc1.scaffold_4816 13472 50 + 14340 ---GCGGCTCAGGGGCTGAGCCTCGAC------------------CT-AGGAACCAGG------AGGTCACGG--TTC-GA-------------------------------------------- i myoLuc1.scaffold_4816 C 0 C 0 s proCap1.scaffold_29042 22854 86 + 24616 CAGGACGGGCAATGAGAGCACTTCCAGCTGCTTGCCTAGGCGGATTG-AGAGCACACA------GGTCAACCA--GAG-AGACA------------------CCGGG------AGAGGCA----- i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14439016 86 - 17734757 GAAGAAAGGCAATGAGACCACCTTTAGCCACTTGCCTATCAAGACTG-AGAAAACACG------GATAAATCA--GAA-TGACG------------------CCAGG------ATAGGAA----- i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e vicPac1.scaffold_196076 391 0 + 1154 C e choHof1.scaffold_149147 805 1005 + 9388 M e micMur1.scaffold_15893 10820 3214 + 19765 I e turTru1.scaffold_106006 134512 12 + 145505 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 18241 1805 + 20752 I e pteVam1.scaffold_11245 20722 4 + 48268 I e monDom5.chr2 304539065 11756 - 541556283 I e canFam2.chr9 59442407 5 - 64418924 I e bosTau4.chr19 10864651 3 - 65312493 I e equCab2.chr11 58048472 0 - 61308211 C e mm9.chr11 118765639 741 + 121843856 I a score=41407.000000 s hg19.chr17_gl000204_random 52111 35 + 81310 A--AGGCC-CCCACGTGTCTTACAGGTAAGGGCCAGGA s panTro2.chr17 79482308 35 + 83384210 A--AGGCC-CCCACGTGTCTTACAGGTAAGGGCCAGGA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 20505 35 - 64270 A--AGGCC-CCCACGTGTCTTACAGGTAAGGGCCAGGA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16069451 35 + 17838096 A--AGGCC-CTCACGTGTCTTACAGGTAAGGGCCAGGA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75043378 35 + 78773432 A--AGGCC-CCCACGTGTCTTACAGGTAAGGGCCAGGA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 50582 35 - 95547 A--AGGCC-CCCGTGTGTCTTACAGGTAAGGGCCAGGA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 53013 35 + 225949 A--AGGCC-TCCACGTGTCTTATAGGTAAGGGCCAGGA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 7161 35 + 9575 G--AGACC-CCTTGGTTGCTTACAGGGAAGAGCAGGGG i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_72647 4079 35 + 4992 A--AGGCA-CCTGTGTCCCTTAGGGGTCAGTCCAAGGG i micMur1.scaffold_72647 M 2454 C 0 s otoGar1.scaffold_94362.1-287808 32365 35 + 287808 A--AGGCA-CCTGCGCTTCCCACAGCTAGGGGCACGGG i otoGar1.scaffold_94362.1-287808 I 1 C 0 s dipOrd1.scaffold_43980 2947 7 + 11404 G--AAGCC-T---------------------------- i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4395172 17 + 7991924 A--AGGTC-C------------------AAGAACTAGA i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 12507 11 + 44242 A--GGGTC-C------------------------TGGG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 24654 19 + 41507 GCCGGGCT-C------------------TGGCTCCCAG i oryCun2.chrUn0958 C 0 C 0 s myoLuc1.scaffold_4816 13522 13 + 14340 -------------------TTCCCGGTCAGGG------ i myoLuc1.scaffold_4816 C 0 C 0 s proCap1.scaffold_29042 22940 36 + 24616 A--AGGCCACCTGCGTCTCTCACAGGCCAGAGACCAGG i proCap1.scaffold_29042 C 0 C 0 s loxAfr3.scaffold_49 14439102 36 - 17734757 A--AGGCTGTCTGGATCTCTCGCAGGCCAGAGTCTAGG i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e vicPac1.scaffold_196076 391 0 + 1154 C e choHof1.scaffold_149147 805 1005 + 9388 M e turTru1.scaffold_106006 134512 12 + 145505 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 18241 1805 + 20752 I e pteVam1.scaffold_11245 20722 4 + 48268 I e monDom5.chr2 304539065 11756 - 541556283 I e canFam2.chr9 59442407 5 - 64418924 I e bosTau4.chr19 10864651 3 - 65312493 I e equCab2.chr11 58048472 0 - 61308211 C e mm9.chr11 118765639 741 + 121843856 I a score=-42287.000000 s hg19.chr17_gl000204_random 52146 58 + 81310 TCAGAGGCCT-----GA-TGAC--ACCAAGCTC-CC------------TGC-------ACCCAAGAGGTGGCCTTTGCTTTGGGAG s panTro2.chr17 79482343 58 + 83384210 TCAGAGGCCT-----GA-TGAC--ACCAAGCTC-CC------------TGC-------ACCCATGAGGTGGCCTTTGCTTTGGGAG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 20540 58 - 64270 TCAGAGGCCT-----GA-TGAC--ACCAAGCTC-CC------------TGC-------ACCCAAGAGGTGGCCTTTGCTTTGGGAG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16069486 58 + 17838096 TCAGAGGCCT-----GA-TGAC--ACCAAGCTC-CC------------TGC-------GCCCGAGAGTTGGCCTTTGCTTTGGGAG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75043413 58 + 78773432 TCAGAGGCCT-----GA-TGAC--ACCAAGCTC-CC------------TGC-------ACCCGAGAGTTGGCCTTTGCTTTGGGAG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 50617 58 - 95547 TCAGAGGCCT-----GA-TGAC--ACCAAGCTC-CC------------TGT-------ACTCGAGAGTTGGCCTTTGCTTTGGGAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 53048 58 + 225949 CCAGAGGCCT-----GA-TGAC--ACCGAGCTT-CC------------CGC-------ACCCAAGAGTTGTCCTTTGCTTTGGGAG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 7196 60 + 9575 AAAAAGTTCTGCC--GA-AGAA--GCCTGGATC-CC------------CA--------ACCCCAGTGTTCATCTTTGCTTTTGGAG i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_72647 4114 63 + 4992 TCAG-GGCCC-----TA-GGAAGGAGCCTGCTG-CC------------TAC---CCCCCCCCCAGAGTTCGTGTTTGCTCCTGGAG i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 32400 57 + 287808 TCAGAGGCCT-----GA-TGAAGAAGCCTGCCA-CC------------TGC-CACCACACCCCATAGCTCATGCTTT--------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s dipOrd1.scaffold_43980 2954 32 + 11404 -GGTACACCT-----GA-------GCCTCCTCC-CC------------TCC----------------------------CTGTGAA i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4395189 33 + 7991924 GAGGATGCCT-----AA-------CTCTTCTTT-GC------------TCC----------------------------TGGAGAA i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 12518 45 + 44242 GCAGGTGCCT-----GA-------CTTTCCCCC-CCACAGGGCCGTCTTTC----------------------------TGAAGGG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 24673 27 + 41507 CACCGCACTC-----AC-------CCTGTGCTC-TC------------TGCT---------------------------------- i oryCun2.chrUn0958 C 0 I 79 s myoLuc1.scaffold_4816 13535 39 + 14340 -CACAGGCCC-----GGCTGCA--GGCTCGATC-CC------------CAC----------TGGGGGGCG---------------- i myoLuc1.scaffold_4816 C 0 I 3 s loxAfr3.scaffold_49 14439138 45 - 17734757 ---------------GA-AGAA--ACCCAGCTCTCA------------GAA-------AGCCTCTCGGTTT----TGTTTTCGAAA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 22976 48 + 24616 ---------------AG-AGAG--ACCCAGCTC-CA------------CAC-------AGATTCTGGGTTTTCTCTGCTTTGGGAG i proCap1.scaffold_29042 C 0 I 935 s choHof1.scaffold_149147 1833 64 + 9388 TCAGGGGTCCAGATGAA-GAAA--GCCCAGCTCTCG------------GGA-------GGCCCACGAGTTTTCCTTGCCTTGGGAG i choHof1.scaffold_149147 M 1005 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e vicPac1.scaffold_196076 391 0 + 1154 C e turTru1.scaffold_106006 134512 12 + 145505 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 18241 1805 + 20752 I e pteVam1.scaffold_11245 20722 4 + 48268 I e monDom5.chr2 304539065 11756 - 541556283 I e canFam2.chr9 59442407 5 - 64418924 I e bosTau4.chr19 10864651 3 - 65312493 I e equCab2.chr11 58048472 0 - 61308211 C e mm9.chr11 118765639 741 + 121843856 I a score=43073.000000 s hg19.chr17_gl000204_random 52204 37 + 81310 AAAACATACT-TGTCCACTTAGCACTTGTAATTTCTA---------------T s speTri1.scaffold_128901 12563 36 + 44242 CAGAGATGCT--GACACCCCGGCGTTCATGGTCTCTG---------------G i speTri1.scaffold_128901 C 0 I 15 s cavPor3.scaffold_76 4395222 34 + 7991924 GAAATATTCC----CACCTCAGCCTCAGTAATCGTGG---------------T i cavPor3.scaffold_76 C 0 I 15 s dipOrd1.scaffold_43980 2986 2 + 11404 CA--------------------------------------------------- i dipOrd1.scaffold_43980 C 0 C 0 s otoGar1.scaffold_94362.1-287808 32457 24 + 287808 ----TGCAC----------TAGCATTTGTCATTTCTG---------------T i otoGar1.scaffold_94362.1-287808 C 0 I 8 s micMur1.scaffold_72647 4177 38 + 4992 GGCATGCACCCCTGCGCCTTCGCATTTGTAACTTCAG---------------T i micMur1.scaffold_72647 C 0 I 15 s tarSyr1.scaffold_143701 7256 53 + 9575 AAAATACACTCCGACACCTCAGCATTTGTAATGTGTGGGGGTGACATGGACAC i tarSyr1.scaffold_143701 C 0 C 0 s calJac1.Contig5139 53106 37 + 225949 AAAACATACT-TGTCCCCTTAGCACTTGTAATTTCCG---------------T i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 50675 37 - 95547 AAAACATGCT-TGTCCACTTAGCACTTGTAATTTCCG---------------T i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75043471 37 + 78773432 AAAACATGCT-TGTCCACTCAGCACTTGTAATTTCCG---------------T i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16069544 37 + 17838096 AAAACATACT-TGTCCACCTAGCACTTGTCATTTCTG---------------T i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 20598 37 - 64270 AAAACATACT-TGTCCACTTAGCACTTGTAATTTCTG---------------T i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79482401 37 + 83384210 AAAACATACT-TGTCCACTTAGCACTTGTAATTTCTG---------------T i panTro2.chr17 C 0 C 0 s loxAfr3.scaffold_49 14439183 37 - 17734757 GCAATACAGTTTTATGCCTTA-TATTAGTAATTTCTG---------------T i loxAfr3.scaffold_49 C 0 I 389 s choHof1.scaffold_149147 1897 36 + 9388 --GGTACAGTTCTACGTTTTAGGATTTGCAATTTCAT---------------T i choHof1.scaffold_149147 C 0 C 0 e oryCun2.chrUn0958 24700 79 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 23024 935 + 24616 I e vicPac1.scaffold_196076 391 0 + 1154 C e myoLuc1.scaffold_4816 13574 3 + 14340 I e turTru1.scaffold_106006 134512 12 + 145505 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 18241 1805 + 20752 I e pteVam1.scaffold_11245 20722 4 + 48268 I e monDom5.chr2 304539065 11756 - 541556283 I e canFam2.chr9 59442407 5 - 64418924 I e bosTau4.chr19 10864651 3 - 65312493 I e equCab2.chr11 58048472 0 - 61308211 C e mm9.chr11 118765639 741 + 121843856 I a score=19346.000000 s hg19.chr17_gl000204_random 52241 20 + 81310 ---------------AGGAGTCCT-ATCACACAGTG s panTro2.chr17 79482438 20 + 83384210 ---------------AGGAGTCCT-ATCACACAGTG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 20635 20 - 64270 ---------------AGGAGTCCT-ATCACACAGTG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16069581 20 + 17838096 ---------------GTGAGTCCT-ATCACACAGTG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75043508 20 + 78773432 ---------------ACGAGTCCT-ATCACACAGTG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 50712 20 - 95547 ---------------ACGAGTCCT-ATCACACAGTG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 53143 20 + 225949 ---------------ACAAGTCCT-ATCACACAGTG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 7309 20 + 9575 ---------------AAGAGTCAC-ATCACACAGTG i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_72647 4230 21 + 4992 ---------------AAGAGTCCTCGTTACACGGTT i micMur1.scaffold_72647 I 15 C 0 s otoGar1.scaffold_94362.1-287808 32489 21 + 287808 ---------------CAGAGTCCCCATGAATCAGTT i otoGar1.scaffold_94362.1-287808 I 8 C 0 s dipOrd1.scaffold_43980 2988 11 + 11404 -----------------GAGTTCT--------AGTG i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4395271 20 + 7991924 ---------------AGGAGTCCT-GTTCCGCAGGG i cavPor3.scaffold_76 I 15 C 0 s speTri1.scaffold_128901 12614 10 + 44242 ---------------AAGTGCCCC-----------A i speTri1.scaffold_128901 I 15 C 0 s turTru1.scaffold_106006 134524 20 + 145505 ---------------AGAGGTCCCTGTCACACAGT- i turTru1.scaffold_106006 I 12 C 0 s myoLuc1.scaffold_4816 13577 6 + 14340 ---------------AGGAGG--------------- i myoLuc1.scaffold_4816 I 3 C 0 s pteVam1.scaffold_11245 20726 14 + 48268 ----------------------CCTGTCACACAACT i pteVam1.scaffold_11245 I 4 C 0 s canFam2.chr9 59442412 14 - 64418924 ----------------------CCTATCACACAGTG i canFam2.chr9 I 5 C 0 s equCab2.chr11 58048472 21 - 61308211 ---------------AGGTGTCCTTGTCACACAGTT i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10864654 14 - 65312493 ---------------------CCCTGTCGCACGGT- i bosTau4.chr19 I 3 C 0 s choHof1.scaffold_149147 1933 36 + 9388 AGTCGAAAGGAAGCCGAAAGCCCCTGCCACACAGTT i choHof1.scaffold_149147 C 0 C 0 e oryCun2.chrUn0958 24700 79 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e proCap1.scaffold_29042 23024 935 + 24616 I e vicPac1.scaffold_196076 391 0 + 1154 C e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e dasNov2.scaffold_28617 18241 1805 + 20752 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118765639 741 + 121843856 I e loxAfr3.scaffold_49 14439220 389 - 17734757 I a score=91092.000000 s hg19.chr17_gl000204_random 52261 36 + 81310 G----AGCACATCCCTAGGCCCCTAAATT--AAAGAT--GGTGG------ s panTro2.chr17 79482458 36 + 83384210 G----AGCACATCCCTACGCCCCTAAATT--AAAGAT--GGTGG------ i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 20655 36 - 64270 G----AGCACATCCCTAGGCCCCTAAATT--AAAGAT--GGTGG------ i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16069601 36 + 17838096 G----AGCACATCCCTAGGCCCCTAAATT--AAAGAT--GGTGG------ i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75043528 36 + 78773432 G----AGCACATCCCTAAGCCCCTAAATT--AAAGAT--GATGG------ i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 50732 40 - 95547 GTGATCGCACATCCCTAAGCCCCTAAATT--AAAGAT--GATGG------ i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 53163 25 + 225949 G----AG-------------CCCTAAGTTTAAAAGAT--GATTG------ i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 7329 37 + 9575 G----AGCAAAACTGTA-GCCCCTAAATT--TAAAATCAGATTG------ i tarSyr1.scaffold_143701 C 0 M 1528 s micMur1.scaffold_72647 4251 21 + 4992 G----AGCACATCTCTGGGCCCCTA------------------------- i micMur1.scaffold_72647 C 0 I 212 s otoGar1.scaffold_94362.1-287808 32510 14 + 287808 G----A-CACACCTCCAGG------------------------------- i otoGar1.scaffold_94362.1-287808 C 0 I 17 s dipOrd1.scaffold_43980 2999 36 + 11404 C----AGCATACCCTGAGACTCTAAAGGC--TAAGAT--GGAAT------ i dipOrd1.scaffold_43980 C 0 I 2 s cavPor3.scaffold_76 4395291 36 + 7991924 C----AGCACAGCTTGAGAACCCTAAGTC--TCTGCT--AAGGT------ i cavPor3.scaffold_76 C 0 I 2 s speTri1.scaffold_128901 12624 33 + 44242 T----GACACATCTTTAGGCCT---AAGT--TGGACT--AAGAT------ i speTri1.scaffold_128901 C 0 I 2 s turTru1.scaffold_106006 134544 36 + 145505 G----AGGGTATCTTTAGGCCCCAGAATT--TAAAAT--GAAAT------ i turTru1.scaffold_106006 C 0 I 2 s myoLuc1.scaffold_4816 13583 1 + 14340 -------------------------------------------C------ i myoLuc1.scaffold_4816 C 0 I 2 s pteVam1.scaffold_11245 20740 36 + 48268 G----AGCACATCTTTAGGCCCCTAAATT--AAAAAT--AAAAC------ i pteVam1.scaffold_11245 C 0 I 2 s canFam2.chr9 59442426 35 - 64418924 G----AGCACATCTTTAAGCCTCT-AATT--TAAAAT--AAAAT------ i canFam2.chr9 C 0 I 2 s equCab2.chr11 58048493 36 - 61308211 T----AGCACATCTTTAGGCCCCTAAATT--TAAAAT--GAAAT------ i equCab2.chr11 C 0 I 2 s vicPac1.scaffold_196076 391 36 + 1154 G----AGCACATCTTCAGGCCCTTGAATT--TAAAAT--AAAAT------ i vicPac1.scaffold_196076 C 0 I 2 s bosTau4.chr19 10864668 36 - 65312493 G----AGCACATCTCTAGGTCCCTGGAGC--CTAAAT--AAAAT------ i bosTau4.chr19 C 0 I 2 s loxAfr3.scaffold_49 14439609 42 - 17734757 G----AGCACGTCCTTAGGCGCCTAAATT--TAAAAT--GAAATTAATGG i loxAfr3.scaffold_49 I 389 C 0 s proCap1.scaffold_29042 23959 38 + 24616 --------ACATCCCTAGGTGCCTAAATT--TATAAG--GAAATTGCTGG i proCap1.scaffold_29042 I 935 C 0 s choHof1.scaffold_149147 1969 42 + 9388 G----AGCACATCCTTAGGCCCCTAAATT--TAAAAT--AAAACTGACAG i choHof1.scaffold_149147 C 0 C 0 s dasNov2.scaffold_28617 20046 31 + 20752 ---------------TAGGCCTCTAAATT--TAAAAT--AAAATTGACGG i dasNov2.scaffold_28617 I 1805 C 0 e oryCun2.chrUn0958 24700 79 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I e mm9.chr11 118765639 741 + 121843856 I a score=41056.000000 s hg19.chr17_gl000204_random 52297 22 + 81310 ATGGTCCTTTCCCAGGCCA--AGA s panTro2.chr17 79482494 22 + 83384210 ATGGTCCTTTCCCAGGCCA--AGA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 20691 22 - 64270 ATGGTCCTTTCCCAGGCCA--AGA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16069637 22 + 17838096 ATGGTCCTTTCCCAGGCCA--AGA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75043564 22 + 78773432 ACGGTCCTTTCCCAGACCA--AGA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 50772 22 - 95547 ACGGTCCTTTCCCAGGCCA--AGA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 53188 22 + 225949 ATGGTCTATTCCCAGGCCA--AGA i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118766380 22 + 121843856 ATAGTCCTTTCCTAAGCCA--TGA i mm9.chr11 I 741 I 34 s dipOrd1.scaffold_43980 3037 22 + 11404 ACAATTCTTTCCCAGGCCC--CTA i dipOrd1.scaffold_43980 I 2 I 30 s cavPor3.scaffold_76 4395329 22 + 7991924 ACTGTCCTTCCCCAGGTCT--TGA i cavPor3.scaffold_76 I 2 I 31 s speTri1.scaffold_128901 12659 22 + 44242 AAAGTGCTTTCCCAGGCCT--TGA i speTri1.scaffold_128901 I 2 I 38 s otoGar1.scaffold_94362.1-287808 32541 9 + 287808 -------------CGCCCC--TTG i otoGar1.scaffold_94362.1-287808 I 17 C 0 s micMur1.scaffold_72647 4484 9 + 4992 -------------CGTCCC--TCA i micMur1.scaffold_72647 I 212 C 0 s turTru1.scaffold_106006 134582 19 + 145505 GCAGTCCTTTCCCAGGCCC----- i turTru1.scaffold_106006 I 2 I 28 s myoLuc1.scaffold_4816 13586 19 + 14340 CCGGTCCATGATCCTCTCT----- i myoLuc1.scaffold_4816 I 2 I 6 s pteVam1.scaffold_11245 20778 20 + 48268 ACAGTCCTTGCTCTGGCCTA---- i pteVam1.scaffold_11245 I 2 I 11 s canFam2.chr9 59442463 19 - 64418924 --AGTCTTTCCTAGGCCTGGC--- i canFam2.chr9 I 2 I 14 s equCab2.chr11 58048531 21 - 61308211 ACAGCCCTCCCCATGCCCCGA--- i equCab2.chr11 I 2 I 27 s vicPac1.scaffold_196076 429 19 + 1154 GCGGTCCTTTCCCAGGCCC----- i vicPac1.scaffold_196076 I 2 I 21 s bosTau4.chr19 10864706 10 - 65312493 GCAGTCTTTT-------------- i bosTau4.chr19 I 2 I 26 s loxAfr3.scaffold_49 14439651 20 - 17734757 --ATCTTTTTCCTGGGTCA--CAA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 23997 20 + 24616 --ATCTTTTTCCTGGGCCA--CAG i proCap1.scaffold_29042 C 0 C 0 s choHof1.scaffold_149147 2011 20 + 9388 --ATCTTTTTCCCAGGCCA--CAA i choHof1.scaffold_149147 C 0 C 0 s dasNov2.scaffold_28617 20077 20 + 20752 --ATCTTTTTCCTGGGCCA--TGA i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 24700 79 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e felCat3.scaffold_206428 35569 679 + 132007 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I a score=-118715.000000 s hg19.chr17_gl000204_random 52319 39 + 81310 --------------------------GGGGGACTCCCGTGG-------TACCCGG-----------------------------GCA-------AGACGCATCCAGAA s panTro2.chr17 79482516 39 + 83384210 --------------------------GGGGGACTCCCGTGG-------TACCTGG-----------------------------GCA-------AGACGCATCCAGAA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 20713 39 - 64270 --------------------------GGGGGACTCCCGTGG-------TACCCAG-----------------------------GCA-------AGACGCATCCAGAA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16069659 68 + 17838096 --------------------------GGGGGACTCCCGTGG-------TACCCAGGCCAAGAGGGGGACTCCCGTGGTACCCAAGCA-------AGATGCATCCAGAA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75043586 39 + 78773432 --------------------------GGGTGACTCACGTGG-------CACCCAA-----------------------------GCA-------AGATGCATCCAGAA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 50794 39 - 95547 --------------------------GGGTGACTCACGTGG-------CACCCAA-----------------------------GCA-------AGATGCATCCAGAA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 53210 39 + 225949 --------------------------GGATGACTCCCCTGG-------CACCCGA-----------------------------GCA-------AGAAGTCTCCAGAA i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 32550 39 + 287808 --------------------------TGGCAGCCTCCCTGG-------CTCCAGA-----------------------------GAG-------GGAAGCCTTCAGTT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_72647 4493 38 + 4992 --------------------------CGGCAGCTGCCCTGG-------TGCCCGA-----------------------------G-T-------GGAAGCATTCAGCG i micMur1.scaffold_72647 C 0 C 0 s pteVam1.scaffold_11245 20809 27 + 48268 --------------------------GGCTGGCTGTCCCTCAAAGTGGCTCCT------------------------------------------------------- i pteVam1.scaffold_11245 I 11 C 0 s myoLuc1.scaffold_4816 13611 20 + 14340 --------------------------TGATGATTCTATCTC-------CCTCT------------------------------------------------------- i myoLuc1.scaffold_4816 I 6 C 0 s canFam2.chr9 59442496 34 - 64418924 ---------------------------GGTGGCCTGTCTTG-------CTCCTGA-----------------------------AGA-------GGA-GCATTCG--- i canFam2.chr9 I 14 C 0 s felCat3.scaffold_206428 36248 34 + 132007 ---------------------------GGTGGCCTACCCTG-------CTCCTGA-----------------------------GTG-------AGA-GCATACG--- i felCat3.scaffold_206428 I 679 C 0 s equCab2.chr11 58048579 34 - 61308211 ---------------------------GGTGTCTCTCCCTG-------CTCCTGA-----------------------------GTG-------ACA-GCATTCA--- i equCab2.chr11 I 27 C 0 s turTru1.scaffold_106006 134629 35 + 145505 --------------------------ACGTGGCTCCCCTGG-------CTCCTGA-----------------------------GCC-------AGA-GCGTTCA--- i turTru1.scaffold_106006 I 28 C 0 s bosTau4.chr19 10864742 35 - 65312493 --------------------------GTGGGGCTCCCCTGG-------CTCCTGG-----------------------------GCC-------ATA-GCATTCA--- i bosTau4.chr19 I 26 C 0 s vicPac1.scaffold_196076 469 16 + 1154 ---------------------------------------GG-------CCCCTG------------------------------------------A-ACATTCA--- i vicPac1.scaffold_196076 I 21 C 0 s mm9.chr11 118766436 36 + 121843856 -----------------------------CCTTTGCCGTGG-------CTCCTGA-----------------------------GTT-------GGGGGCAGCTAGTT i mm9.chr11 I 34 I 38 s dipOrd1.scaffold_43980 3089 43 + 11404 -----------------------------CCCCTGCCCAGA-------CTCCCGG-----------------------------CTCCCACCTGAGAGGCATCCAGTT i dipOrd1.scaffold_43980 I 30 I 2 s cavPor3.scaffold_76 4395382 32 + 7991924 ---------------------------------CGCCCTGG-------CTCCTGC-----------------------------AGG-------AAAGGTGCTCAGTC i cavPor3.scaffold_76 I 31 I 6 s loxAfr3.scaffold_49 14439671 65 - 17734757 GAATCGTGCTCGCTGGCTGTTCCTTTTGGTGACTTCCCTCA-------CTGCTGA-----------------------------GCT-------AGAAGCACTCAGTA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 24017 65 + 24616 GAACCCTGCTCCCTGGCAGTCCCTTACAGTGGCTTCCCTGA-------CTCCTGA-----------------------------GCC-------AGAAGCATTCCCTA i proCap1.scaffold_29042 C 0 C 0 s choHof1.scaffold_149147 2031 64 + 9388 GGGTAGTGCCTGTTGACTGTCCCTCATGGCGGCTCTGCTTG-------CTCCCGA-----------------------------GCT-------AGAA-CATTCCGTA i choHof1.scaffold_149147 C 0 C 0 s dasNov2.scaffold_28617 20097 65 + 20752 GGGTCCTGTGTGCCAGGCGTCCCTGCTGGCGGCTCTGCTTG-------CCCCCGA-----------------------------GCT-------GGAAGCAGCTGGCA i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 24700 79 + 41507 I e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e speTri1.scaffold_128901 12681 38 + 44242 I e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I a score=345058.000000 s hg19.chr17_gl000204_random 52358 107 + 81310 TGACTCCTTCCACCTAGACCCTGGCCACAC-----TTTTCAAAATGCA-ACTG---ATAGA-----CTGA--------------GC-TCGCC--------------------CCGAG---------CTAC----------------AAATAAACTAACAGA-C--------TTTATACT------CTTTA--------TTAT-TC- s calJac1.Contig5139 53249 109 + 225949 CGGCTCCTTCCACCTAGACCCTGGCCACGA-----TTTCCAAAATGCA-ACTG---ACAGA---CTATGA--------------GC-TTGCC--------------------CCGAG---------CTAC----------------AAATAAAGTCACGCA-C--------TTGATGCT------GTTTA--------TGAT-TC- i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 50833 109 - 95547 CGGCTCCTTCCACCTAGAACCTGACCACAC-----TTTTCAAAATGCA-ACTG---ATAGA---CTGTGA--------------GC-TTGCC--------------------CCAAG---------CTAC----------------AAATAAAGTAACAGA-C--------TTTATACT------CTTTA--------TTAT-TC- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75043625 109 + 78773432 CGGCTCCTTCCACCTAGAACCTGACCACAC-----TTTTCAAAATGCA-ACTG---ATAGA---CTGTGA--------------GC-TTGCC--------------------CCAAG---------CTAC----------------AAATAAAGTAACAGA-C--------TTTATACT------CTTTA--------TTAT-TC- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16069727 108 + 17838096 CGGCTCCTTCCACCTAGCCCCTGGTCACAC-----TTTTCAAAATGCA-ACTG---ATAGA---CTGTGA--------------GC-TCGCC--------------------CCCAG---------CTAC----------------AAATAAA-TAACAGA-C--------TTTATACT------CTTCG--------TTAT-TC- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 20752 109 - 64270 CGANTCCTTCCACCTAGACCCTGGCCACAC-----TTTTCAAAATGCA-ACTG---ATAGA---CTGTGA--------------GC-TCGCC--------------------CTGAG---------CTAC----------------AAATAAACTAACAGA-C--------TTTATACT------CTTTA--------TTAT-TC- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79482555 109 + 83384210 CGACTCCTTCCACCTAGACCCTGGCCACAC-----TTTTCAAAATGCA-ACTG---ATAGA---ATGTGA--------------GC-TCGCC--------------------CCGAG---------CTAC----------------AAATAAACTAACAGA-C--------TTTATACT------CTTTA--------TTAT-TC- i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 4531 119 + 4992 CTGCTCCGTCCCCCGAGACTCTGGCCACAC-----GCGCCAGAATACA-GTTT---ACAGA---CCGCGA--------------GC-TCGCT--------------------GCTGGGGGACTCGCTTTC----------------AAATAAAGCAACAAA-C--------TCTATACT------CATTA--------TTATCTC- i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 32589 119 + 287808 CTACTCCTTCCACCGGGACTCAGGCCACAG-----TTTTCAAAAAGCA-ATTT---ATAGA---CCACAG--------------GC-TTGCT--------------------GCTGGAGGAAACGCTTTC----------------AAACAGAGTAACAAA-C--------CTTCTACT------CTTGA--------TTATCTC- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s speTri1.scaffold_128901 12719 125 + 44242 TTGCTCCTCCTACCGGGACTCCAGCAACAC-----TTCGTAAAATGTA-ATTT---ATATA---CTGTGA--------------GC-TTGCC--------------------CTGGG---------CTACCGGAGAAAACACTTTCAAATAAAGTAACAGA-T--------TTTATTCT------CTTTA--------TTAT-CT- i speTri1.scaffold_128901 I 38 I 1 s mm9.chr11 118766510 129 + 121843856 ctctctctctctct-----ctcCCCATTGCAACCTCTGTGCAGGTGCA-ATGT---GTGTGTGCACTTGA--------------GC-CTGCC--------------------CCAGG---------CTGCCAGAGGCAACATTCTCACATGCAGTAACAGA-TC-------TTAATACT------CTTCA--------TTAT-CT- i mm9.chr11 I 38 I 1 s oryCun2.chrUn0958 24779 64 + 41507 ----GGCTCCCCCTG----CCCCGCACTTC--------------------------GCCAA-ACGCCAGG--------------GC-GGGCC--------------------CCGGG---------CTGCCGGAGCAGACGCT--------------------------------------------------------------- i oryCun2.chrUn0958 I 79 I 113 s cavPor3.scaffold_76 4395420 118 + 7991924 -----CTTCCCTCCAGA--CTCCCCACTAC-----TTTGAAAAGAGCA-ATTTACAGTCTA------TGA--------------GC-CTGCC--------------------TGGGG---------CTGCCAGACAGAACACTTTTGAATAAAGTAACAGA-T--------TTTATGCT------CTTTA--------TTAT-CT- i cavPor3.scaffold_76 I 6 I 1 s dipOrd1.scaffold_43980 3134 114 + 11404 -----CCTCCATCC-----AGCAGCATTAC----------CAGATGTG-ATGT---GTGCA-----CTGT--------------GC-TCATC--------------------CTGGC---------CTGCCAGAGGGAAC----------GAGGCAACAGG-CCCAGGGATTTCACCTT------TTTCAGCAGCTCCTCAC-CC- i dipOrd1.scaffold_43980 I 2 I 1 s pteVam1.scaffold_11245 20836 127 + 48268 -----TGCTCCAACTAGGACCTGGCAACAC-----TTTCCAAAATGCA-ATTT---ATACC---CTATGGGCTTGGC-------CC-ACCCC--------------------ACCCC---------CCATCCGGGGAAACACTTTCAAATAAAGTAACAGA-T--------TTTATGCT------CTTTA--------TTAT-CT- i pteVam1.scaffold_11245 C 0 I 1 s myoLuc1.scaffold_4816 13631 77 + 14340 -----CCCTTCCTCT-----CTGAAATCaa-----t----aaaatagatattt---a------------------------------------------------------------------------------aaaataat----aataaaGTGACGGG-C--------TTTGGGCT------CTTTA--------TTAT-CT- i myoLuc1.scaffold_4816 C 0 I 1 s canFam2.chr9 59442530 136 - 64418924 -GATCTGCTCCACCTAAA--CTGGCAACAC-----TTTCCAAAAGGCC-ATTT---GTATA---CTGTGTACTGTGAGCTTCACTC-CTCCC--------------------CCCCC---------TTATTAAAGGAAACACTTTCAAATAAAGTAACAGA-T--------TGTATGCT------CTTTA--------TTAT-CT- i canFam2.chr9 C 0 I 1 s felCat3.scaffold_206428 36282 121 + 132007 -GTTCTGCT-CACCTAGA--CAGGCAGTGC-----TTTCCAAAACGCA-ATTT---GGATG---CTGAGT--------------TC-CCTCC--------------------GCCCC---------TCACTGAAGGAAACACTTTCAAATAAAGTAACACG-T--------TTTATGTC------CTTTA--------ACAT-CT- i felCat3.scaffold_206428 C 0 I 1 s equCab2.chr11 58048613 128 - 61308211 -GTCCTGCTCCACTTAGACCCTGGCAACAC-----TTTTCAAAATGTA-ACTT---ACATA---CTGTGAGCTT----------GC-CCCAC--------------------CCCCT---------ACCCTGACAGAAACACTTGCAAATAAAGTAACAGA-T--------TTTATGCT------CTTTA--------TTAC-CT- i equCab2.chr11 C 0 I 1 s vicPac1.scaffold_196076 485 112 + 1154 -GCTCTGCTCCACCTGGGCTCTGGCAACAC-----TTTTCAAAATGCA-AATT---ATATA---CTGTGA--------------GA-TCTGC--------------------CC-----------------AGAGGAAACGCTTCTAAATGAAGTAACGGA-T--------TCTACAC----------TG--------TTAC-CT- i vicPac1.scaffold_196076 C 0 I 1 s turTru1.scaffold_106006 134664 125 + 145505 -GTTCTGCTTCACCTGGACTCTGGCAACAC-----TTTCCAAAATGCA-ATTC---ATATA---CTGTGA--------------GC-TTTCC--------------------CCAAG---------CTACTAAAGGAAACACTTTCAAATGAAGTAACAGATT--------TTTATGCT------CTTTA--------TTAT-CT- i turTru1.scaffold_106006 C 0 I 1 s bosTau4.chr19 10864777 124 - 65312493 -GTTTTGCTTCACCTGCTCCCTGGCAACAC-----TTTCCAAAATGCA-ATGT---ATATA---CTGGGA--------------GC-TTTCC--------------------CCAGG---------CTACTAGAGGAAATGCTTTCAAATGAAGTAGCAGA-T--------TTTATGCT------CTTTA--------TTAT-CT- i bosTau4.chr19 C 0 I 1 s loxAfr3.scaffold_49 14439736 132 - 17734757 ----CGGGGCCACCTGTGCTCTGATAACA------TTCTCAAAACATA-ATTT---AGATA---CTGTGA--------------GCTTGCCC-----TTGG-----GGTTGGCGGGG---------CGGGTGGAGGAAACACTTACAAATAAAGTAACAGG-T--------TTTGTACT------CTTTA--------TTAT-CTC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 24082 140 + 24616 ----CAGCTCCA-CTAGACACAGGCAAAG------TTCCCAAAACATC-ACTG---ACGTA---CTGTGA--------------GC-TGCACGGGAGTTGGGGGCAGGTGGAGGGGG---------CTGTTGGAGGAAAAATGTTCCAATAAAGTCACAGG-T--------TTTCCACT------CTTTA--------TGAT-CTC i proCap1.scaffold_29042 C 0 C 0 s choHof1.scaffold_149147 2095 126 + 9388 ----CTGTTCCACCGATATGCTGGCCACA------CTTTTGAAACACG-ATTT---CTATA---CT-CGA--------------GC-TGCCC--------------------CAGGA---------GTACCAAAGGAAACACTTTCGAATAAAGTCACACA-T--------ATTCTTCTTCTTCTCTTTA--------TTAT-CTC i choHof1.scaffold_149147 C 0 C 0 s dasNov2.scaffold_28617 20162 121 + 20752 ----CTGTAGCACCCATACTCTGTCCACA------TTTTCAAAATGCA-ATTT---CTGTA---CTGCGA--------------GC-TGGCC--------------------TGGGG---------CTACTGAAGGAAACACTTTCAAGT-AAGTCACACA-T--------TTTATACT-----CTTTTA--------TTAT-CTC i dasNov2.scaffold_28617 C 0 C 0 e ochPri2.scaffold_9426 7107 2802 - 54875 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I a score=622018.000000 s hg19.chr17_gl000204_random 52465 37 + 81310 CAGCCTCCCTC-TAAGGCGTGTTTTGGTGTCAGTCTAT s calJac1.Contig5139 53358 37 + 225949 TGGTCTCCTTC-TAAGGCGTGTTTTGGTGTCAGTTTAT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 50942 37 - 95547 TAGTCTCCCTC-TAAGGCGTGTTTTGGTGTCAGTTTAT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75043734 37 + 78773432 CAGTCTCCCTC-TAAGGCGTGTTTTGGTGTCAGTTTAT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16069835 37 + 17838096 CAGTCTCCCCC-TAAGGCGTGTTTTGGTGTCAGTCTAT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 20861 37 - 64270 CAGCCTCCCTC-TAAGGCATGTTTTGGTGTCAGTCTAT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79482664 37 + 83384210 CAGCCTCCCTC-TAAGGCGTGTTTTGGTGTCAGTCTAT i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 4650 37 + 4992 TAGTCCCCTTC-TAAGGCATGTTTTGGTGTCAGCTTAT i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 32708 37 + 287808 CAGTCTCTTTC-TAAGGCGTGTTTTGGTATCAGCTTAT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118766640 36 + 121843856 AAGTCACCTTC-TGAGGCATGTTTTGGTGTCAA-GTGA i mm9.chr11 I 1 C 0 s dipOrd1.scaffold_43980 3249 35 + 11404 AGG--GCCTCC-TCAGCTATATTGTGATGTCAGCTTGG i dipOrd1.scaffold_43980 I 1 C 0 s cavPor3.scaffold_76 4395539 38 + 7991924 AAGCCACCTTCTTAAGGCTTGTTTTGATGCCAGCTTAA i cavPor3.scaffold_76 I 1 C 0 s speTri1.scaffold_128901 12845 37 + 44242 AAGTCACCTTC-TAAGGCATGTTTTGGTGTCAGCTTAA i speTri1.scaffold_128901 I 1 C 0 s ochPri2.scaffold_9426 9909 36 - 54875 CAGCCACCTCC-CAGGGCAGGCTTCAGCA-CAGCTCCC i ochPri2.scaffold_9426 I 2802 C 0 s pteVam1.scaffold_11245 20964 37 + 48268 AAGTCACCTTC-TAAGGCATGTTTCGGTGTTAACTCAT i pteVam1.scaffold_11245 I 1 C 0 s myoLuc1.scaffold_4816 13709 35 + 14340 --GTCACCTTC-CACGGCATATTCCCGCGTCAGCTCAT i myoLuc1.scaffold_4816 I 1 C 0 s canFam2.chr9 59442667 37 - 64418924 AACTCACCTTC-TAAGGCATGATTTGGTGGCAGCTCAA i canFam2.chr9 I 1 C 0 s felCat3.scaffold_206428 36404 37 + 132007 AAGTCACCTCC-TAAGGCACGATTTGGTGGCGGCTCAT i felCat3.scaffold_206428 I 1 C 0 s equCab2.chr11 58048742 37 - 61308211 CAGTCACCTTC-TTAGGCATGTTTTGGTGTCAGCTCAT i equCab2.chr11 I 1 C 0 s vicPac1.scaffold_196076 598 31 + 1154 A--TCAC---C-TAAGACATG-TTTGGTGTCAGTTCAT i vicPac1.scaffold_196076 I 1 C 0 s turTru1.scaffold_106006 134790 37 + 145505 AAGTCACCTTC-TAAGGCATGTTTTGGTGTCAGCTCAT i turTru1.scaffold_106006 I 1 C 0 s bosTau4.chr19 10864902 37 - 65312493 AAGTCACCTTC-TAAGGCATGTTTTGGTGTCAGCTCAC i bosTau4.chr19 I 1 C 0 s loxAfr3.scaffold_49 14439868 37 - 17734757 AAGTCACCTTC-AAAGGCATGTTTTGGTATCAGCTTAT i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_29042 24222 37 + 24616 AAGTCACCTCC-AAAGGCATGTTTGGGTCTCAGCAAAC i proCap1.scaffold_29042 C 0 C 0 s choHof1.scaffold_149147 2221 37 + 9388 AAGTCACCTTC-TGAGGCATGTTTTGGTATCAGCTTAT i choHof1.scaffold_149147 C 0 C 0 s dasNov2.scaffold_28617 20283 37 + 20752 GAGTCACCTTC-TAAGGCATGTTTTGGTATCAGCTTAT i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 24843 113 + 41507 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e eriEur1.scaffold_355010 4620 3093 + 8359 I e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I a score=1164787.000000 s hg19.chr17_gl000204_random 52502 118 + 81310 GTGTTGGAG-AAACTGTGATAG---CAAACTAATT------------------------TACTAAGTGCATTGC-AC-TT--------AAAAATGTC--TA---TTTTATA-CACC---AAATCAGTCTGTGTCACGTGGTATT-TCTT------GAAGGGAGG-----TGAC---T---CGT s calJac1.Contig5139 53395 118 + 225949 GTGTTGGAG-AAACTGTGGTAG---CAAACTAATT------------------------TACTAAGTGCACTGC-AC-TT--------CAAAACATC--TA---TTTTATA-CACC---AGATCAGTCTGCGTCATGTGGTATT-TCTT------GAAGGGAGG-----TGAC---T---CAT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 50979 120 - 95547 GTGTTGGAG-AAACTGTGATAG---CAAACTAATT------------------------TACTAAGTGCATTGC-AC-TT--------AAAAATGTCTATA---TTTTATA-CACC---AAATCAGTCTGTGTCACGTGGTATT-TCTT------GAAGGGAGG-----TGAC---T---CGT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75043771 120 + 78773432 GTGTTGGAG-AAACTGTGATAG---CAAACTAATT------------------------TACTAAGTGCATTGC-AC-TT--------AAAAATGTCTATA---TTTTATA-CACC---AAATCAGTCTGTGTCACGTGGTATT-TCTT------GAAGGGAGG-----TGAC---T---CGT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16069872 118 + 17838096 GTGTTGGAG-AAACTGTGATAG---CAAACTAATT------------------------TACTAAGTGCATTGC-AC-TT--------AAAAATGTC--TA---TTTTATA-CACC---AAATCAGTCTGTGTCACGTGGTATT-TCTT------GAAGGGCGG-----TGAC---T---CGT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 20898 118 - 64270 GTGTTGGAG-AAACTGTGATAG---CAAACTAATT------------------------TACTAAGTGCATTNC-AC-TT--------AAAAATGTC--TA---TTTTATA-CACC---AAATCAGTCTGTGTCACGTGGTATT-TCTT------GAAGGGAGG-----TGAC---T---CGT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79482701 118 + 83384210 GTGTTGGAG-AAACTGTGATAG---CAAACTAATT------------------------TACTAAGTGCATTGC-AC-TT--------AAAAATGTC--TA---TTTTATA-CACC---AAATCAGTCTGTGTCACGTGGTATT-TCTT------GAAGGGAGG-----TGAC---T---CGT i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 4687 118 + 4992 GTGTTGGAG-AAACTGTGACAG---CAAACTAATT------------------------CACTAAGTGCATCGC-AC-TC--------GAAAACGTG--CG---TTCTATA-CATC---AGATCAGGCCGTGTCGCGAGGTATT-TCTT------AAAGGGAGG-----GAAC---C---CAG i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 32745 121 + 287808 GTGTTGGAG-AAACTGTGATAG---CAAACTAATT------------------------TACTAAGTGCGCCAC-AC-TG--------AGAGACGTG--CA---TCGTATG-CGCC---AGACCTGGCTGTATGTCCAGGTAAT-TCTC------TAAAGCAGG-----GTACTCTT---CCT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118766676 103 + 121843856 GTGTTGTGG-AAGCTGTGATAA---CACAGTAATT------------------------TACTAAGAGCCTTGC-TC-TG--------AAGAGCGTG--------ATTATC-GGGT---GCATC-GGATGGGTCCCCAGGCACC-CATG------TCAGAG---------------------- i mm9.chr11 C 0 I 2 s dipOrd1.scaffold_43980 3284 132 + 11404 GTGTTGAGGAAAACTGTGATAA---CACACTAATTGCTAAGTGCAATTAGTGCGCTAACTACTAAGGGCGTTGC-CT-GG--------A--AACGTG--------TCTACC-TGATACCACATCTGTCTGAGTCGCAAGGCCGC-CCCT------TTAAggaa-------------------- i dipOrd1.scaffold_43980 C 0 I 279 s cavPor3.scaffold_76 4395577 118 + 7991924 GTGTTGGAG-AAACTGTAATAATAGCACACTAATT------------------------TACTAAGTGTGCTATACC-AG--------AAAGGTGTG--------TCATTC--------ACATCAGGACAGGCCACGAGGTTCT-TTTTGTCTTTTGCAAGTTG-----TTTT---T------ i cavPor3.scaffold_76 C 0 I 267 s speTri1.scaffold_128901 12882 117 + 44242 GTGTTGGGG-AAACTGTGATAG---CACACTAATT------------------------TACTAAGTGCATTAC-GC-TG--------AAAAGTGTA--TA---TTTTATC-AGCC---ACATC-AGCTGGGCCACCAGGCGTT-TCCT------TGAGGGAGG-----ATGC---TCAA--- i speTri1.scaffold_128901 C 0 I 4 s ochPri2.scaffold_9426 9945 113 - 54875 AAGCAGGAG--AGGTGTGATCG---CAAGCTACTG------------------------TGCTAAGTGCCTCAC-CC-TC--------AAGAGCACC---C---CTCTGCC-AACC---GAGTTGGTCTGGGTGATGAGGGTTT-CCCT------GGCGAGGGG-----TACT---C------ i ochPri2.scaffold_9426 C 0 I 5 s bosTau4.chr19 10864939 125 - 65312493 GTGTTGGAG-AAACTGCGACAG---CAAACTCATT------------------------TACTAAGTGCGCTGC-GCTTT--------AAAAATGTA--CA---TTTTATATTAAT---AAACCAGTCCACATCACAAGGTATT-TCTT------TAAGTGAGGTATTTCTAC---T---CAT i bosTau4.chr19 C 0 I 4 s turTru1.scaffold_106006 134827 116 + 145505 GTGTTGGAG-AAACTGCGACAG---CAAACTAATT------------------------TACTAAGTGCATTGC-AC-TT--------AAAAACATG--CA---TTTTATA-AATC---AAACCAGTCTGC--CACAAGGTATT-TCTT------TAAGCAAGG-----ATAC---T---CAT i turTru1.scaffold_106006 C 0 I 4 s vicPac1.scaffold_196076 629 118 + 1154 GTGTTGGAG-AAGCTGCAATAG---CAAACTAAGT------------------------CACTAAGTGCATTGC-AC-TT--------AAAAATTTA--CA---TTTCATA-AGCC---AAACTAGTCCGTGCCATGAGGTATT-TCCT------GAAGTGAGG-----ATAC---T---CAT i vicPac1.scaffold_196076 C 0 I 4 s equCab2.chr11 58048779 119 - 61308211 GTGTTGGAG-AAACTGTAATAG---CAAACAAATT------------------------CACTAAGTGCATTGC-AC-TT-------AAAAAATACA--TA---TTTTATA-AACC---AAATAAGTTCACGCCATGAGGTACT-TCTT------TAAGAGAGG-----ATGC---C---CAT i equCab2.chr11 C 0 I 4 s felCat3.scaffold_206428 36441 100 + 132007 GTGTT-GAG-AAGCTGCCACAG---CAGAGTCGTT------------------------CACGCGGTGCACTGC-TC-TC--------TGAAATGTC--TG---TTTTTTA-AGCC---AAAGCAGTTCTTGGCGCGAGGT-----------------------------TGT---T---CAT i felCat3.scaffold_206428 C 0 I 4 s canFam2.chr9 59442704 111 - 64418924 GTGTTGGAG-AAACTGCCATAG---CAAATTAAT---------------------------CTTAGTGCACTGC-AC-TT--------TAAAATGTA--TA---TTTTATA-AACT---AAATCAGTTCTTGTCGTGAGGTA-----TT------TACGCAAGG-----ACAC---T---CAT i canFam2.chr9 C 0 I 3 s myoLuc1.scaffold_4816 13744 117 + 14340 GTGTTGGAG-AAACTGTGATTC---CAAATTAACG------------------------GCCTAAGTGCCCGGC-AC-TT--------ACAAAGATG--CA---TTTTGTG-AGCC---AACTCCATCCACGTCTCGAGGTGTT-TCTT------TAAGCG-AG-----ATTC---T---CAC i myoLuc1.scaffold_4816 C 0 I 4 s pteVam1.scaffold_11245 21001 121 + 48268 GTGCTGGAG-AAACTGTGACAA---CAAGCTAATT------------------------TACTAAGTGCATTGC-AC-TT--------AAAAAAATG--TGCATTTTTACA-AACC---GAATCAGTCCAGGTCACGAGGTACT-TCAT------TCAGCGAAG-----ATAC---T---CAT i pteVam1.scaffold_11245 C 0 I 4 s eriEur1.scaffold_125414 21 124 - 877 GTGTTGCAG-AAACTGCGACA----CAAGCTAATT------------------------GACTAAGTGCattcc-cc-ttaaaaaaaaaaaaaagtg--tg---ttttaTA-AACC---AAGCCAGTCCAT--TGTGGTGTATTCTACC------AAAATGAGG-----CAAC---T---CAT i eriEur1.scaffold_125414 n 3093 I 4 s loxAfr3.scaffold_49 14439905 117 - 17734757 GTGTTGGAG-AAACTGTGACAG---AGAAAGAATT------------------------TGCTAAGTGCATTGC-AC-TT--------AAGAATGTA--TA---TTTTATA-AACC---AAATCAGTGCATGTCACAAGGTAGT-TCCT------TACCTGTGG-----CTAC---T---CA- i loxAfr3.scaffold_49 C 0 I 437 s proCap1.scaffold_29042 24259 112 + 24616 ATGCTGGGG-AAACTGTGACCA---AGAAGGAACT------------------------TGCTAAGTGCATTGC-AC-TT--------CAGAGAGTG--CA---TTTTATC-ACTC---AAAC-----CGTGTCAC-AGACACG-TCCT------CAAGGGTGG-----CTGC---T---CAC i proCap1.scaffold_29042 C 0 N 0 s choHof1.scaffold_149147 2258 117 + 9388 GTGTTGGGG-AAACTGTGACAG---TAAACTAACT------------------------TACTGAATGCATTGC-AC-TT--------AAAAATGTA--TA---TTTTATA-AAAC---AATG-AGTACATGTCACAAGGTATT-TCCT------TAAATGAGA-----AAAG---C---CAT i choHof1.scaffold_149147 C 0 I 7 s dasNov2.scaffold_28617 20320 116 + 20752 GTGTTGGAA-AAACTGTCATAG---TAAAGTAGTT------------------------TGCTGAACACGTCGC-AC-TT---------AAAACGTA--TA---TTTTATA-AACC---AATG-AGCGCATATCGCGAGGGATT-TCCT------TAAATGAGG-----AAAC---A---CCT i dasNov2.scaffold_28617 C 0 C 0 e oryCun2.chrUn0958 24843 113 + 41507 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I a score=131792.000000 s hg19.chr17_gl000204_random 52620 46 + 81310 CT----GTCTGTGGGTCCCC-AAC-CCAGAACA-GGCCCCGCCGGGTATGCAC s calJac1.Contig5139 53513 33 + 225949 CT----GTCTGCGGGTCCCC-AA-------------CCCTGCCGTGTA--CAC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 51099 46 - 95547 CT----GTCTATGAGTCCTC-AAC-CCAGAGCA-GGCCCCGCTGTGTATGCAC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75043891 46 + 78773432 CT----GTCTGTGAGTCCTC-AAC-CCAGAGCA-GGCCCCGCTGTGTATGCAC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16069990 45 + 17838096 CT----GCCTGTGGGTCCCC-AAC-TCAGAACA-GGCCC-GCTGTGTATGCAC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 21016 46 - 64270 CT----GTCTGTGGGTCCCC-AAC-CCAGAACA-GGCCCCGCCGGGTATGCAC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79482819 46 + 83384210 CT----GTCTGTGGGTCCCC-AAC-CCAGAACA-GGCCCAGCCGGGTATGCAC i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 4805 50 + 4992 CTTCCGGTCCGTGACTCCCC-GGC-CCAGAGCA-GGTCCCCAACGGGATACTC i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 32866 43 + 287808 CTTTCCATCACTGGGTCCCT-AGC-ACAGAGCA-GGCCCCCAAGAG------- i otoGar1.scaffold_94362.1-287808 C 0 I 17 s dipOrd1.scaffold_43980 3695 42 + 11404 CT----GTCTGTGGATCCTC-AAC-ACAGAGCA-GGCCCCACTTGA----AAC i dipOrd1.scaffold_43980 I 279 I 4 s mm9.chr11 118766781 36 + 121843856 CT----GT-------TCCTCTAGC-ACGGAGCA-GGCCCCGCTACG----CAC i mm9.chr11 I 2 I 4 s speTri1.scaffold_128901 13003 41 + 44242 CC----GTCTGTGGATCCC--AGC-ACAGAGCA-GGCCCCACTGCG----CAC i speTri1.scaffold_128901 I 4 I 221 s ochPri2.scaffold_9426 10063 27 - 54875 CT----CC-CTGGGCTCCCC-AGC-CCAGAACC-A------------------ i ochPri2.scaffold_9426 I 5 C 0 s bosTau4.chr19 10865068 44 - 65312493 CT----GTCTGCA-GTCCTC-CAC-AAAGAAAA-GACCTCACCATGTACTCA- i bosTau4.chr19 I 4 C 0 s turTru1.scaffold_106006 134947 45 + 145505 CT----GTCTGTA-ATCCTC-CACAAAAAAAAA-GACCTCACTGTGTACTCA- i turTru1.scaffold_106006 I 4 C 0 s vicPac1.scaffold_196076 751 39 + 1154 CC----GGCTGTG-ATCCCC-CAC-AAAGAACA-GACCT----GTGTCCTC-- i vicPac1.scaffold_196076 I 4 C 0 s equCab2.chr11 58048902 45 - 61308211 CC----ATCTGGGGATTGCC-AAC-ACAGAACA-GACCCCACTGTGTACCCA- i equCab2.chr11 I 4 C 0 s felCat3.scaffold_206428 36545 45 + 132007 CC----GTCTGCGGGTCCCC-CAC-AAAGAACA-GACCGCACCACGGACTCA- i felCat3.scaffold_206428 I 4 C 0 s canFam2.chr9 59442818 45 - 64418924 CT----GTCTGCAGATCCCC-CAC-AAAGAACA-GACCCTACTGTGTACTCA- i canFam2.chr9 I 3 C 0 s myoLuc1.scaffold_4816 13865 45 + 14340 CT----GCCTGGGGGTCCCC-AGC-ACAGAACGAGACCCCACCGCATGCTC-- i myoLuc1.scaffold_4816 I 4 C 0 s pteVam1.scaffold_11245 21126 45 + 48268 CG----GCCTGTGCATCCCC-AAC-ACAGAATG-GACCCCACTGTGCGCTTG- i pteVam1.scaffold_11245 I 4 C 0 s eriEur1.scaffold_125414 149 44 - 877 CT----GTCCGTG-Atccca-aac-acaaagca-gaccTCACTGTGTGTCCA- i eriEur1.scaffold_125414 I 4 C 0 s dasNov2.scaffold_28617 20436 32 + 20752 CT----G-CTTTGGCTCACC-AAC-ACAGGAGA-GGCCCC------------- i dasNov2.scaffold_28617 C 0 C 0 s choHof1.scaffold_149147 2382 30 + 9388 -------TCTGTAGATCACT-CAC-CCAGAAGA-GGTCTC------------- i choHof1.scaffold_149147 I 7 C 0 s loxAfr3.scaffold_49 14440459 30 - 17734757 -------TCTGTAGATTGCC-CAC-ACAGAAGA-GGTCCC------------- i loxAfr3.scaffold_49 I 437 C 0 s oryCun2.chrUn0958 24956 22 + 41507 ----------GGGGCTCCCC-AGC-CCACAACT-G------------------ i oryCun2.chrUn0958 I 113 C 0 e tarSyr1.scaffold_143701 7366 1528 + 9575 M e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I e cavPor3.scaffold_76 4395695 267 + 7991924 I a score=-153722.000000 s hg19.chr17_gl000204_random 52666 36 + 81310 AGCATATGTATGTGTGCAATGCTCCTTGCATGC---CCG s calJac1.Contig5139 53546 11 + 225949 AGC-------------------------CATGC---CCG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 51145 36 - 95547 AGCGTATGTATGTATGCAATGCTCCTTGCATGC---TCA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75043937 36 + 78773432 AGCGTATGTATGTATGCAATGCTCCTTGCATGC---TCA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16070035 36 + 17838096 AGCATATGTATGTATGCAATGCTCCTTGCATGG---CCA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 21062 36 - 64270 AGCATATGTACGTGTGCAATGCTCCTTGCATGC---CCG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79482865 36 + 83384210 AGCATATGTATGTGTGCAATGCTCCTTGCATGC---CCG i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 4855 11 + 4992 AGC-------------------------TGTTG---CCA i micMur1.scaffold_72647 C 0 C 0 s dipOrd1.scaffold_43980 3741 6 + 11404 ---------------------------CTATGT------ i dipOrd1.scaffold_43980 I 4 C 0 s mm9.chr11 118766821 6 + 121843856 ---------------------------AGATCA------ i mm9.chr11 I 4 C 0 s oryCun2.chrUn0958 24978 17 + 41507 ----------------------CACCCCCATTACACGCA i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 10090 17 - 54875 ----------------------CGTCCCAATCGTATCTG i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10865112 7 - 65312493 -----------------------------GTTA---CTC i bosTau4.chr19 C 0 I 1 s turTru1.scaffold_106006 134992 7 + 145505 -----------------------------ATTA---CTA i turTru1.scaffold_106006 C 0 I 1 s vicPac1.scaffold_196076 790 4 + 1154 --------------------------------A---CTA i vicPac1.scaffold_196076 C 0 I 1 s equCab2.chr11 58048947 7 - 61308211 -----------------------------ATTA---CTA i equCab2.chr11 C 0 I 3 s felCat3.scaffold_206428 36590 7 + 132007 -----------------------------ATCA---TTA i felCat3.scaffold_206428 C 0 I 3 s canFam2.chr9 59442863 7 - 64418924 -----------------------------ATTA---TTA i canFam2.chr9 C 0 I 3 s myoLuc1.scaffold_4816 13910 7 + 14340 -----------------------------AGTA---CCA i myoLuc1.scaffold_4816 C 0 I 3 s pteVam1.scaffold_11245 21171 7 + 48268 -----------------------------AGCT---CCA i pteVam1.scaffold_11245 C 0 I 3 s eriEur1.scaffold_125414 193 7 - 877 -----------------------------ATTA---TTA i eriEur1.scaffold_125414 C 0 I 3 s loxAfr3.scaffold_49 14440489 9 - 17734757 ---------------------------CAGTAA---CCA i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 20468 18 + 20752 -----------------TGTGAGGTCTCA-TCA---CTG i dasNov2.scaffold_28617 C 0 C 0 s choHof1.scaffold_149147 2412 19 + 9388 -----------------TGTGCAGACTCAGTTA---TTG i choHof1.scaffold_149147 C 0 C 0 e tarSyr1.scaffold_143701 7366 1528 + 9575 M e speTri1.scaffold_128901 13044 221 + 44242 I e macEug1.Scaffold23956 2946 17402 - 25324 I e otoGar1.scaffold_94362.1-287808 32909 17 + 287808 I e monDom5.chr2 304539065 11756 - 541556283 I e cavPor3.scaffold_76 4395695 267 + 7991924 I a score=79858.000000 s hg19.chr17_gl000204_random 52702 52 + 81310 CC-ATGCAACTGTTAACCA--AGA-GCCG----TCCTCAA--CCCTCACAG---GTCACACAAGG s calJac1.Contig5139 53557 52 + 225949 CC-ACGCAACCAATAACCA--AGA-GCCA----TCCTCAA--TGCTCATGG---GCTGTGTAAGG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 51181 52 - 95547 CC-ATGCAACCATTAACCA--AGA-GCCA----TCCTCAA--CCCTCACAA---GTTATGCAAGG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75043973 52 + 78773432 CC-ATGCAACCATTAACCA--AGA-GCCA----TCCTCAA--CCCTCACAA---GTTATGCAAGG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16070071 52 + 17838096 CC-ATGCAACTGTTAACCA--ATA-GCCG----TCCTCAA--CCCTCACAG---GTCACACAAGG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 21098 52 - 64270 CC-ATGCAACTGTTAACCA--AGA-GCNG----TCCTCAA--CCCTCACGG---GTCACATAAGC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79482901 52 + 83384210 CC-ATGCAACTGTTAACCA--AGA-GCCG----TCCTCAA--CCCTCACGG---GTCACATAAGG i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 4866 52 + 4992 CC-ACCCAACTGTGACCCG--AGA-GCCG----CCCGCAA--CTCTCACAG---GTGGCCGGAGG i micMur1.scaffold_72647 C 0 C 0 s otoGar1.scaffold_94362.1-287808 32926 42 + 287808 CC-ATCCAACCAGCAATTG--AGA-GTCA----------------TCTCAG---GTAACTTGAGG i otoGar1.scaffold_94362.1-287808 I 17 C 0 s cavPor3.scaffold_76 4395962 44 + 7991924 CC-ACCTGGCAA----TCA--AGG-GCTG----TCCTCTA--GTCCCACAG---GTACTAT---- i cavPor3.scaffold_76 I 267 C 0 s dipOrd1.scaffold_43980 3747 54 + 11404 CC-ACCAACCAACAGTTCA--TGG-ACAG----CCATCCT--CCACCATGGCCTGTACCACAGC- i dipOrd1.scaffold_43980 C 0 C 0 s mm9.chr11 118766827 49 + 121843856 CC-TCCCTTCCA----TCA--CTG-GCAG----CGACCCTGACTCTCAGAG---GTAGCATGGC- i mm9.chr11 C 0 C 0 s oryCun2.chrUn0958 24995 42 + 41507 TC-ACCCCACGGTGCTCCG--AGA-GCCG----GCCCCAA--GGCGCACAG---G---------- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 10107 42 - 54875 TC-ACCCAGCTGCAAACAG--CGC-ACCA----CCTCCCG--CACACACAG---C---------- i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10865120 52 - 65312493 CC-ATCCCACCTGTAGATG--CGA-GCTG----TCCTCAA--TTCTCATAC---GTAATTCAAAG i bosTau4.chr19 I 1 C 0 s turTru1.scaffold_106006 135000 52 + 145505 CC-ATCCAACTAGTAGATG--AGA-GCTG----TCCTCAA--CTCTCATAT---GTAATTCAAAG i turTru1.scaffold_106006 I 1 C 0 s vicPac1.scaffold_196076 795 52 + 1154 CC-ATCCAACTAGTACATG--AGA-GCTG----TCCTCAA--CTCTCACAC---GTAATTCAAGG i vicPac1.scaffold_196076 I 1 C 0 s equCab2.chr11 58048957 50 - 61308211 CC-AACCAACGATTAATTG--AGA-GCTG----TTCTCAA----CTCAGAG---GTAACACAAGG i equCab2.chr11 I 3 C 0 s felCat3.scaffold_206428 36600 52 + 132007 CC-ATCCAGCTGCTGATGG--AAA-GCTG----TCCTCGA--CTCTCACAG---GTAATGCCAGG i felCat3.scaffold_206428 I 3 C 0 s canFam2.chr9 59442873 52 - 64418924 CT-ATCCAACTGTTCATTG--AAA-GCTG----TCCTCAA--CTCTCCTAG---CTAATGCAAGC i canFam2.chr9 I 3 C 0 s myoLuc1.scaffold_4816 13920 43 + 14340 CC-GTCCAGGGACGCCCTG--AGG-GCCA-----CCCCAC--CTCGAACAG---GTG-------- i myoLuc1.scaffold_4816 I 3 C 0 s pteVam1.scaffold_11245 21181 46 + 48268 CCAACCCCACTACGAGCTG--ATGCGCTG----TCCTCAA--CTGTCACAG---ATG-------- i pteVam1.scaffold_11245 I 3 C 0 s eriEur1.scaffold_125414 203 53 - 877 GC-TCCCCTCCCTCAACTGTTAGG-GTTC----TTCATGG--TTCTTATCA---GTGACA-AGGG i eriEur1.scaffold_125414 I 3 C 0 s loxAfr3.scaffold_49 14440498 35 - 17734757 TC-----------CCACTG--AGA-GCCC----TCCTCAA--CT--CTCAG---AC-----AAGC i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_28617 20486 55 + 20752 TC-ACC-ATGTACCCATTA--ACT-GCATGAGAGCCTCGC--CTGCCACAG---GTGATAGAAGC i dasNov2.scaffold_28617 C 0 C 0 s choHof1.scaffold_149147 2431 48 + 9388 CC-AGC--CACATCCACGA--ATG-GCAT------CTCAA--CTGCCACGG---ACAACGAAAGC i choHof1.scaffold_149147 C 0 C 0 e tarSyr1.scaffold_143701 7366 1528 + 9575 M e speTri1.scaffold_128901 13044 221 + 44242 I e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I a score=-46247.000000 s hg19.chr17_gl000204_random 52754 59 + 81310 AG-GCAATCACACACTAAGCATCCGCGCCACTCAG--AAAGCAC---AGG---------------------------AG----------GAAAAAA-----------------------GAGT-----------TG s choHof1.scaffold_149147 2479 59 + 9388 CG-AGAATCACATGCTAAGTGTCCACAGAGCTCAG--AAAGTAC---AGG---------------------------GG---------AAAAGGGG-----------------------GGCA------------G i choHof1.scaffold_149147 C 0 C 0 s dasNov2.scaffold_28617 20541 45 + 20752 AG-AGGA--------------CCCACAGGGCTCCA--AAAGTAC---AGG---------------------------GA---------GAAAAGGG-----------------------GGGG------------G i dasNov2.scaffold_28617 C 0 C 0 s loxAfr3.scaffold_49 14440533 62 - 17734757 AG-AGAACCACGTCCTAAGTACACACACAGCTCAG--AAAGTACACAAGA---------------------------GG---------AAAAAACA-----------------------GGGA------------G i loxAfr3.scaffold_49 C 0 C 0 s eriEur1.scaffold_125414 256 59 - 877 AT-ACACTCACACCCCATGTGTCCATGCCACTCAG--ACAGCCA---GTG---------------------------GA---------GTAAATga-----------------------gctg------------a i eriEur1.scaffold_125414 C 0 C 0 s pteVam1.scaffold_11245 21227 48 + 48268 -------------TCTAAGTGCCCACACCGCTCAG--AAGGTAG---AGG---------------------------GG--------GAAGGGACA-----------------------GAAG------------G i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_4816 13963 36 + 14340 ---------------------------CCACTCAGACAAGACAG---GGG---------------------------TG--------GGGGGGAGA-----------------------CACG------------G i myoLuc1.scaffold_4816 C 0 C 0 s canFam2.chr9 59442925 59 - 64418924 AG-AAAGTCACATATGAAGTGCCCGCATCCCTCAG--AAAGTAC---AAG---------------------------AG---------GAAAAACA-----------------------GACG------------T i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 36652 67 + 132007 AG-AAAGTCACTTATG-AGTGCCTGCACCAGTCAG--AAAGTAC---GGG---------------------------GGTGGGGGGGAGAAACAAA-----------------------GACG------------T i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58049007 61 - 61308211 AG-AAAGTCACACGCTAAGTGCCCACACCACTCAGA-AAAGTTC---AGG---------------------------GG--------GAAAAAAAA-----------------------GACA------------T i equCab2.chr11 C 0 C 0 s vicPac1.scaffold_196076 847 55 + 1154 AG-AAAGACACATACCAAGTG-CCACACCA-TCAG--AAAGTAC---AGG---------------------------GG---------GAGA--AA-----------------------GACA------------T i vicPac1.scaffold_196076 C 0 C 0 s turTru1.scaffold_106006 135052 59 + 145505 AG-AAAGTCACATACCAAGTGTCCATACCACTCAG--AAAGTAT---AGG---------------------------GA---------GAAAAAAA-----------------------GACA------------T i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10865172 59 - 65312493 AG-AAAGTCATATACCAAGTGCCTGCACCACTCAG--AATGAAA---AGG---------------------------GA---------GAAAAGAA-----------------------GACA------------T i bosTau4.chr19 C 0 C 0 s ochPri2.scaffold_9426 10149 60 - 54875 CA-AGACCAGCAGA-GGAGTGCCC-TGGCTCTCAG--CAGGTGG---AGG---------------------------------------------G-----------------------GTCGGGGTCGGGGGCAG i ochPri2.scaffold_9426 C 0 C 0 s oryCun2.chrUn0958 25037 50 + 41507 AG-GAGCCCACAGACTCGGCACCCACACCTCTCAT--CAGGTGG---AGG---------------------------------------------A-----------------------GACG------------G i oryCun2.chrUn0958 C 0 C 0 s speTri1.scaffold_128901 13265 46 + 44242 AG-GAAGCCACAGA---AGTACCCCCATCACCCAT--AAAGTGT---GGA---------------------------------------------------------------------CAGG------------A i speTri1.scaffold_128901 I 221 C 0 s cavPor3.scaffold_76 4396006 35 + 7991924 AG-GAAATAGCACA---CGAATCCA-------CAG--AAGAAAG---AGA-------------------------------------------------------------------------------------G i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_43980 3801 81 + 11404 AG-GAAAGCCTTCA---AGT-CCCACGGCGCCCAG--GATATAT---Ggggaggaggggaggagagcccggagatgggg----------agggaga-----------------------gatg------------g i dipOrd1.scaffold_43980 C 0 C 0 s mm9.chr11 118766876 41 + 121843856 AG-GAAACCCCAAA---AGCATCCACCCAGCCCAG--AAAGCAC---AGG-------------------------------------------------------------------------------------- i mm9.chr11 C 0 C 0 s otoGar1.scaffold_94362.1-287808 32968 55 + 287808 AGAAAAATCGTATACTAGCATCCTGCA-CACTCCC--AGTATAG---GAG---------------------------GA----------AAAG--------------------------GGGC------------A i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_72647 4918 54 + 4992 AGAAAAATCACACACCGGGGCCGCGCT-CACTCAG--AGGGTAC---GGG---------------------------GG----------AAA---------------------------GGGC------------G i micMur1.scaffold_72647 C 0 C 0 s panTro2.chr17 79482953 59 + 83384210 AG-GCAATCACACACTAAGCATCCGCGCCACTCAG--AAAGCAC---AGG---------------------------AG----------GAAAAAA-----------------------GAGT-----------CG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 21150 59 - 64270 AG-GCAATCACACACTAAGCATCTGCACCACTCAG--AAAGCAC---AGG---------------------------AG----------AAAAAAA-----------------------GAGT-----------CG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16070123 58 + 17838096 AG-GCAATCACACACTAAGCATCTGCGCCACTCAG--AAAGCAC---AGg---------------------------ag----------aaaaaaa-----------------------gagt------------g i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75044025 60 + 78773432 AG-GAAATCACACAGTAAGCACCTGCACCACTCAG--AAAGCAC---AGg---------------------------ag----------aaaaaaa-----------------------gagt----------gag i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 51233 60 - 95547 AG-GAAATCACACAGTAAGCATCTGCACCACTCAG--AAAGCAC---AGg---------------------------ag----------aaaaaaa-----------------------gagt----------gag i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 53609 82 + 225949 AG-GAAACCACACACCGAGCATCCATGCCACACAC--AGAGCAC---AGg---------------------------ag----------gaaaaaaaggagtgagggagaggaaaaaaggagt-----------gc i calJac1.Contig5139 C 0 C 0 e tarSyr1.scaffold_143701 7366 1528 + 9575 M e macEug1.Scaffold23956 2946 17402 - 25324 I e monDom5.chr2 304539065 11756 - 541556283 I a score=-211722.000000 s hg19.chr17_gl000204_random 52813 22 + 81310 GGG---AGAGGAAGAG--A-TAG-----ACGGA s calJac1.Contig5139 53691 22 + 225949 ggg---agaggaagag--a-cag-----acgga i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 51293 22 - 95547 ggg---agaggaagag--a-cag-----acgga i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75044085 22 + 78773432 ggg---agaggaagag--a-cag-----acgga i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16070181 22 + 17838096 ggg---agaggaagag--a-tag-----acaga i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 21209 22 - 64270 GGG---AGAGGAAGAG--A-TAG-----ACGGA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79483012 22 + 83384210 GGG---AGAGGAAGAG--A-CAG-----ACGGA i panTro2.chr17 C 0 C 0 s micMur1.scaffold_72647 4972 20 + 4992 GGG---AGAGGA--AG--A-CAG-----GCGGA i micMur1.scaffold_72647 C 0 n 0 s otoGar1.scaffold_94362.1-287808 33023 25 + 287808 AGA---AAAGGA--AG--A-CGACTCCTACGGA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118766917 3 + 121843856 ---------GTG--------------------- i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 3882 9 + 11404 ggg---ggagag--------------------- i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4396041 9 + 7991924 AGA---GGTAGA--------------------- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 13311 9 + 44242 AGA---GACAGA--------------------- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 25087 9 + 41507 CGG---GGAGGG--------------------- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 10209 9 - 54875 CGG---GGTGGG--------------------- i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10865231 22 - 65312493 AAA---AGGGGAGgag--a-aag-----agaca i bosTau4.chr19 C 0 I 14 s turTru1.scaffold_106006 135111 22 + 145505 GAA---AGGGGAGGAG--A-GAG-----ACACA i turTru1.scaffold_106006 C 0 I 36 s vicPac1.scaffold_196076 902 20 + 1154 GAA---AGgagaggag--a-gag-------aca i vicPac1.scaffold_196076 C 0 I 14 s equCab2.chr11 58049068 22 - 61308211 AAA---AGGAGGAGag--a-cag-----acaga i equCab2.chr11 C 0 I 14 s felCat3.scaffold_206428 36719 25 + 132007 GAAAAGGGGAGGAGAG--A-CAG-----ACAGA i felCat3.scaffold_206428 C 0 I 14 s canFam2.chr9 59442984 17 - 64418924 GAA--------GGGAG--G-CAG-----ACACA i canFam2.chr9 C 0 I 9 s myoLuc1.scaffold_4816 13999 10 + 14340 ACA-----GCCGGGG------------------ i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 21275 20 + 48268 GAA-----GAAGAGGG--A-CAG-----ATCGT i pteVam1.scaffold_11245 C 0 I 6 s eriEur1.scaffold_125414 315 22 - 877 gag---agagaaggag--a-cag-----actat i eriEur1.scaffold_125414 C 0 I 8 s loxAfr3.scaffold_49 14440595 10 - 17734757 G-----------------A-CAG-----GAAGA i loxAfr3.scaffold_49 C 0 I 1 s dasNov2.scaffold_28617 20586 24 + 20752 GGG---GGCGGGAGAGGAA-GAG-----AAAGA i dasNov2.scaffold_28617 C 0 I 3 s choHof1.scaffold_149147 2538 22 + 9388 GGG---AGAGGAGGAG--A-CAG-----ACAGA i choHof1.scaffold_149147 C 0 I 3 s monDom5.chr2 304550821 23 - 541556283 GAA---AGAGAAAAGG--ATTAG-----AATTA i monDom5.chr2 I 11756 C 0 e tarSyr1.scaffold_143701 7366 1528 + 9575 M e macEug1.Scaffold23956 2946 17402 - 25324 I a score=1066618.000000 s hg19.chr17_gl000204_random 52835 157 + 81310 CAGGGA------GACAGGGAGATAGACCC------------------------AGGACGTTA----TAGA-----------GGACAGGGATGGCTCAGGGAG-C-AACCTTCTTCAGA-GA----GGCAGCAGAAAG-TAAGATGTTGAGGCTG-CCTGAA-TGTTTCATGAGCCTGTGAAAATACCGCGCTGCTTTATGAAAG-AGC-GTGGA s choHof1.scaffold_149147 2563 165 + 9388 GAGAGA------GAGAAAGAAATGGAACC------------------------AGAACATTA----TAAAT---AAAAAAGAGACAGTGATGGCTCGGAGAC-A-AGCCTACTTCAGA-GA----GGCAGCAGAAAA-CAAGATGTTTCGGTTG-CCCGAA-TGTTTCCTGGACCTGTGAAAATTACGTGCCGCTTTATAAAAG-AAG-GTGGA i choHof1.scaffold_149147 I 3 C 0 s dasNov2.scaffold_28617 20613 139 + 20752 GAGACA------GAGAAAGTGACGGGACC------------------------AGAGCGTGA----CAAAT---AAGAAAGAGACCGAGAGCGCTCAGTGA-----------------------------GAGCAGA-CCAGGTGCTCGGGCCC-CCTGAGCTACCCCAGGGACCTGTGAAAAGCACGTGCAGCTTTAGAAGGA-ACG------ i dasNov2.scaffold_28617 I 3 N 0 s loxAfr3.scaffold_49 14440606 147 - 17734757 ---ACA------GCCAGTGAGATGGAACC------------------------AGAATGTTA----TAAAT---A--AAAGAGACGGAGAAGGC---------------AGCTTCAGA-GT----GGTTGCCGGAAA-CACGATGTCGAGGCCG-CCTGAA-TGTTTCATGAACCTGTGAGAACAACATGCTGCTTCATAAAAG-GACG-TGGG i loxAfr3.scaffold_49 I 1 C 0 s felCat3.scaffold_206428 36758 162 + 132007 AAAAG-------GCGGGGGAGATGGAACC------------------------GAAACGTTA----TCAA-----TAAAAGAGGCAGCGACGGTTCAGAGAG-A-AACCCACTTCAGA-GA----GGCTGCAGAAAA-TAAGATGTTTCGGTTG-CCTGCG-TGTTTCACGCAGCTGTGAAAATAGTGAGCTGCTTCATAAAAG-AAC-GTGGG i felCat3.scaffold_206428 I 14 C 0 s equCab2.chr11 58049104 158 - 61308211 ga----------GAGGAGGACCAGGAACC------------------------AGAACGTCA----TAAAT---GAGAAAGAGACATC-ATGGCCCAGGGAG----ACCCACCTGAGA-GA----GGCAGCAGCAAA-TAAGATGTTTAGGCTG-CCTGCA-TGTTTCATGAGCCTGTGGACACAACATGCTTCTTCATAAAAG-AAC-GTGGG i equCab2.chr11 I 14 C 0 s vicPac1.scaffold_196076 936 164 + 1154 gagaga------gagagggagaaggagCC------------------------AGAGCGCCA----TAAAT---AAAAAGGAGACAGTGATGGCTCAGAGAG-A-AACCTACTTCAGA-GA----GGCAGCAAAAAA-TAAGATGTTTAGGCTG-TCTGAA-TG-TTCATGAACCTGTGAAAATAACGTGCTGCTTTATAAAAG-AAC-GTGGG i vicPac1.scaffold_196076 I 14 C 0 s turTru1.scaffold_106006 135169 165 + 145505 gagaga------gagagagagaTGGAACC------------------------AGAATGTTA----TAAAT---AAAAAGGAGACAGTGATGGCTCGGAGAGAA-AACCTACTTCAGA-GA----GGCAGCAAAAAA-TAAGATGTTTAGGCTG-TCTGAA-TGTTTCACGAACCTGTGAAAATAA-GTGCTGCTTTATAAAAG-AAT-GTGGG i turTru1.scaffold_106006 I 36 C 0 s bosTau4.chr19 10865267 165 - 65312493 gagaga------gagagagagaTGGAACC------------------------AGAACGTTA----TAAAT---AAAAAGGAGACAGTGATGGCTCAGAGAG-A-AACCTACTTCAGA-GA----GGCAGCAAAAAA-TAAGATGTTTAGGCTG-TCTGAA-TGTTTCATGAACCTGTGAAAATAACGTGCTGCTTTATGAAAG-AAC-GTGGG i bosTau4.chr19 I 14 C 0 s ochPri2.scaffold_9426 10218 97 - 54875 ---GAA------AACAGATGAACAG---C------------------------CGAACCTCA----TGAAC---ATGA---------------------------CACAAACAGCAGG-GAGAAGGGCAGCAG----------------------ACTG----------GGGTGCTG-------GCCTCTTCACGGTAGGACAG-------GGG i ochPri2.scaffold_9426 C 0 C 0 s oryCun2.chrUn0958 25096 129 + 41507 ---GAG------GAGACACGGGTGG---A------------------------CGCGCCTCG----GGGGG---CTGCAGCAG-----------CTAGAAGT-T-CACAAACACCAGG-AGGC--GGCGGCAG----------------------ACTGGG-CGTTTC-GGGGGCCGGGGAAGAGCCCCGCGGCGCTGGGAGAG-AAC-GTGGG i oryCun2.chrUn0958 C 0 C 0 s speTri1.scaffold_128901 13320 160 + 44242 GCTGGA------GAGAGA-AGGAAC---C------------------------AGAACGTTA----TAAAT---AAAAAAGAGACAGCCGTGGCTCAGAGAG-C-AACCAGCTTCCGA-GA----GGCA-CAGAAAA-TAAGAGGTTTAGGCTG-CCTGAA-TGTTTCATGAGTCTGTGAAAATAACGTGCTGCTTTACAAAAG-AAT-GAGGG i speTri1.scaffold_128901 C 0 C 0 s cavPor3.scaffold_76 4396050 148 + 7991924 CGCTAA------GAGGATGCGGAAC---C------------------------AAAATATCA----CAAAT---AAGAAAGAAACCACAATGACTCCAAAAG-C-CACCAACTCCAGA-GA----GGCAGCAGAAAA-TAAGATGTTTGGGCCG-CCTGAA-TGTCCCAGGAGGCTGTGAAAACA--------------TAAAA-GAC-AGGAG i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_43980 3891 156 + 11404 cccggagatggggagggagaTGTAA---C------------------------AGAACATGA----TAAAT---AAAGAAGAGACGTTGATGGCTCGGACGG-CAAACCAACTTCAGAGAA----GGCAGCAGCGAA-GACG----TTAGGCTG-CCTGAA-TGTTTCATGAGCTTGTGAAAATA-------ACCTCAGAAGAG-GCC----GG i dipOrd1.scaffold_43980 C 0 C 0 s mm9.chr11 118766920 163 + 121843856 CTCAGA------GAAGGAGACGAAG---C------------------------AGAACATAA----AAATT---AAACAGGAGACCCTGCTGCCTCAAATGG-C-AGCTGACTTCAGA-AA----GGCAGCAGAAAA-CAAGATGTTTAGGCTGCCCTGAA-TGTTTCATGAACCTGTGAAAATGCTGGGCTGCTTCAGGAGAG-AAT-AAGGG i mm9.chr11 C 0 C 0 s otoGar1.scaffold_94362.1-287808 33048 159 + 287808 -CAGAG------GAGAGCGACATGGGACT------------------------GGACGGTTACACTTAAA-----------GGACAGTGATGGCTCCCAGAG-C-AGCCTACTGCAGA-GA----AG-AGCAGAAAA-TAAGCTGTTTAGGCTG-CCTGAG-TGTCTCATGAGCCTGTGAAAATAATGTGCCGCTTTATAAAAG-CAC-GTGGG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s panTro2.chr17 79483034 157 + 83384210 CAGGGA------GACAGGGAGATAGACCC------------------------AGGACGTTA----TAGA-----------GGACAGGGATGGCTCAGGGAG-C-AGCCTGCTTCAGA-GA----GGCAGCAGAAAG-TAAGATGTTGAGGCTG-CCTGAA-TGTTTCATGAGCCTGTGAAAATACCACGCTGCTTTATGAAAG-AGC-GTGGA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 21231 150 - 64270 CAGGGA------GACAGGGAGATAGACCC------------------------AGGACGTTA----TAGA-----------GGACAGGGATGGCTCAGGGAG-C-AGCCTGCTGCAGA-GA----GGCAGCAGAAAG-TAAGATGTTGAGGCTG-CCTGAA-TGTTTCATGAGCCTGTGAAAATACCGCGCTGCTTTATGAAA---------GA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16070203 157 + 17838096 caggga------gagagggagatagaCCC------------------------AGGATGTTA----TAGA-----------GGACAGGGATGGCTCAGGGAG-C-AGCCTGCTTCAGA-GA----GGCAGCAGAAAG-TAAGATGTTGAGGCTG-CCTGAA-TGTTTCATGAGCCTGTGAAAATACCGCGCTGCTTCATGAAAG-AGC-GTGGA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75044107 158 + 78773432 caggaa------gagagggagatagaCCC------------------------AGGATGTTA----TAGA-----------GGACAGGGATGGCTCAGACAG-C-AGCCTACTTCAGA-GA----GCCAGCAGAAAGTTAAGATGTTGAGGCTG-TCTGAA-TGTTTCATGAGCCTGTGAAAATGCCGTGCTGCTTTATGAAAG-AGC-GTGGA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 51315 157 - 95547 caggaa------gagagggagatagaCCC------------------------AGGATGTTA----TAGA-----------GGACAGGGATGGCTCAGACAG-C-AGCCTACTTCAGA-CA----GCCAGCAGAAAG-TAAGATGTTGAGGCTG-TCTGAA-TGTTTCATGAGCCTGTGAAAATGCCGTGCTGCTTTATGAAAG-AGC-GTGGA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 53713 139 + 225949 caggga------gagagggagatagGCCC------------------------AGAATGTTC----CAGA-----------GGACAG--------------------CCTACTTCAGA-GA----GGCAGCAGAAAG-TAAGATGTTGAGGCTG-CTTGAA-TGTTTCATGAGCCTGAGAAAATACCTCGCTGGTTTAGAAAAG-AAC-GTGGA i calJac1.Contig5139 C 0 C 0 s macEug1.Scaffold385251 443 153 + 1704 -----A------GGCAGGGATATAAAACC------------------------AAgac---a----taaat---aaaatggaaacaatgatgTAACAGAAAG-A-ATCCTACTTcaca-ga----gg---gagagac-acacaTGTTTAGGCTA-CATGAA-AGTTTCATGAACTTGCAAAAAGAGTATAATGTTGtataaaat-aaa-gggg- i macEug1.Scaffold385251 n 17402 C 0 s eriEur1.scaffold_125414 345 160 - 877 ------------gagaaagagg-ggaacc------------------------AAAAGGCTG----TAGATTAAAAAACAGAAGCCATGATGgctcagagag-a-cacctacttcaGA-GA----GGCAGCAAG--C-TCAGCTGTTTCGGCTG-CCTGAA-TGTTTCATGAACCTGTGAAAATAGCACGCAGCTTCATGAAAGAAAT-GTGGA i eriEur1.scaffold_125414 I 8 C 0 s pteVam1.scaffold_11245 21301 140 + 48268 ------------CAGAGAGCGACAGAACC------------------------AGAACGTTA----GCAAT---AAAAGAGAGACCGCGAAGGCTCAGAGAG-G-ACGC--------------------GCCAA-----AAGATGGTCGGGCTG-CGCGGA-CGCCGCGCGAAGCCGCGGAAACGACGCGCCGCTCTCCAGACA-GAC-GTGGG i pteVam1.scaffold_11245 I 6 C 0 s myoLuc1.scaffold_4816 14009 130 + 14340 ------------CAGAGGGGGATGGGGC--------------------------AGCCGTTA----TAAAT---AAATAAGATGAGGCGGCGGCTTCGAGGG-G-AAGCT-----------------CTGCAGA-----GAGAAAGGCTGGCTG-CG-GGA-TGTTTCATGAGCCCACGGAGATAGCGTGTCGCTCT------------GTGAA i myoLuc1.scaffold_4816 C 0 C 0 s canFam2.chr9 59443010 181 - 64418924 ------------GTGGGGGAGATGCAAACCCCCCCCCTTAAATTCTTATTTAAGAATTTATT----TCTT-----AAAAAGAAGCCGCAATGGTTCAGAGAC-A-AACCTACTTCAGA-GA----GGCTGCAGAAAA-TAAGATGTTTCGGTTG-CCTGAA-TGTTTCATGAACCTGTGAAAATAACGTGCTGCTTTATAAAAG-AAC-TTGGG i canFam2.chr9 I 9 C 0 s monDom5.chr2 304550844 158 - 541556283 GGTGCA------GACAAGGATAGAGAACC------------------------AAGAC---A----TAAAT---AAAATGGAGACTGTGATATACCAGAAAG-A-ATCCTACTTCTCA-GA----GGCAGAGGCATA-C---ATGTTTAGACTT-CATGAA-TGTTTCATGAGCTTGTGAAAA-AGTGAAATACTGTTTAAAAC-AAA-GGGGA i monDom5.chr2 C 0 C 0 e tarSyr1.scaffold_143701 7366 1528 + 9575 M e micMur1.scaffold_72647 4992 0 + 4992 I a score=358748.000000 s hg19.chr17_gl000204_random 52992 55 + 81310 GAGATG-CTGCAGCTTATC-AAA-GGGTGGAGGTACAAACGG-GAT-GTGTTTATAAAGC s calJac1.Contig5139 53852 54 + 225949 GAGAGG-CTGCCACTCACC-AAA-GGGTGGAGGAGCAAATGG-GG--GTATTCATAGGGC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 51472 55 - 95547 GAGATG-CTGCAGCTTATC-CAA-GGGTGGAGGTGCAAACGG-GAT-GTGTTTACGAAGC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75044265 55 + 78773432 GAGATG-CTGCAGCTTATC-CAA-GGGTGGAGGTGCAAACGG-GAT-GTGTTTACGAAGC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16070360 55 + 17838096 GAGATG-CTGCAGCTTATC-AAA-GGGTGGAGGTACAAATGG-GAT-GTGTTTATAAAGC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 21381 55 - 64270 GAGATG-CTGCAGCTTATC-AAA-GGGTGGAGGTACAAACGG-GAT-GTGTTTATAAAGC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79483191 55 + 83384210 GAGATG-CTGCAGCTTATC-AAA-GGGTGGAGGTACAAACGG-GAT-GTGTTTATAAAGC i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 33207 56 + 287808 GAGACA-CTGCAGCTTATCAAAA-AGATGTAGGTGCAAATGG-GAT-GTGTTTACAAACC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118767083 55 + 121843856 GAGGCA--GGCAGCTAATCAAAA-AGATGTTGATACAAATGG-GAG-GTGTCTGCGAAGC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 4047 53 + 11404 GTGCC----GCAGCTAATCGCAG-AGGTGGAGGCACAGATGG-ACG-AGGTTAGCAAAGG i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4396198 48 + 7991924 GAACT----GCAGCTAGTCCAAA-AGAT-TAGGTACAAATGG-AAC-GTGTCC----AGT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 13480 56 + 44242 GAGGCA-CTGCAGCTAATCAAAA-AGATGTAGGTGCAAATGG-GAT-GTGTTTATAAAGC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 25225 8 + 41507 GAGACCCC---------------------------------------------------- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 10315 19 - 54875 GAGACCCCTACCTCTAATC----------------------------------------- i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10865432 56 - 65312493 GAGACA-TTGCAGCTAATCAAAA-AGATGTAGGTGCAAATGG-GAT-GTGTTTATAAAGC i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 135334 56 + 145505 GAGATA-TTGCAGCTAATCAAAA-AGATGCAGGTGCAAATGG-GAT-GTGTTTATAAAGC i turTru1.scaffold_106006 C 0 C 0 s vicPac1.scaffold_196076 1100 54 + 1154 GAGATA-CTGCAGCTAATCAAAA-AGATGTA-GTGCAAAT-G-GAT-GTGTTTATGAAGC i vicPac1.scaffold_196076 C 0 N 0 s equCab2.chr11 58049262 55 - 61308211 GAGATG-GTGCAGCTAATCGAAA-CACTGTAGGTGCAAATGG--AT-ATGTTTATACAGC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 36920 56 + 132007 GAGATA-TTGCAGCTAATCAAAA-AGACAGAGGTGCAAATGG-AAT-GTGTTCATAAAGC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59443191 56 - 64418924 GAGACA-TTGCAGCTCATCGAAA-AGATGTAGGTGCAAATGG-GAT-GTGTTCATCAAGC i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 14139 46 + 14340 A----G-CCGGGGGGCGGGGGGC-AGCCA-----GTGAAAGAGGCT-GCGTTTGGA--GC i myoLuc1.scaffold_4816 C 0 C 0 s pteVam1.scaffold_11245 21441 52 + 48268 G----G-CCGCAGCCCACCGTGC-AGACGCACGCGCGAGGGA-GCT-GTGTTTGTGCCGC i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_125414 505 55 - 877 GGGACA-CTGCCACCCATCAAAAGAGATGTGGGTGTCAATCC-ACT-ATGTTTCTGGA-- i eriEur1.scaffold_125414 C 0 C 0 s loxAfr3.scaffold_49 14440753 56 - 17734757 GAGAGA-CTGCAGGTAATCAAAG-AGAGGTAGGTGCAAATGA-GAT-ATCTCTATAAAGT i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_56828 11 55 + 1587 GAGAGG-CTGCAGCCGATCACAG--GGGGTGGGTCCCAATGA-GAT-GTCATGACATGCT i echTel1.scaffold_56828 N 0 C 0 s choHof1.scaffold_149147 2728 55 + 9388 GAGAGA--TGCAGCTTATCAAAA-AGATGTAGGTGCAAATGG-GAT-GCGATTATAATGT i choHof1.scaffold_149147 C 0 C 0 s macEug1.Scaffold385251 596 57 + 1704 gaaaTA-TTATACCTTATAAAAA-AGATTTGGATACAAATGG-GATCTTGTTTACAAAGC i macEug1.Scaffold385251 C 0 C 0 s monDom5.chr2 304551002 55 - 541556283 -AAATA--TATACCTAATGAAAA-AGATGTGGATGCAAATGG-GATCTTGTTTATAAAGT i monDom5.chr2 C 0 C 0 e tarSyr1.scaffold_143701 7366 1528 + 9575 M e micMur1.scaffold_72647 4992 0 + 4992 I a score=1728888.000000 s hg19.chr17_gl000204_random 53047 180 + 81310 CGGTGCCTTGTGCCAGG--AGCA--GGGGCCTGTGGC----------AG-GCAGGGATTTAGGGAATGGTAGGTTCCCTACCAACCAACA-AACGGG-----TCTCTGTTGA------AG---G-----G--GGAGA-----------------------AAGTTTCAAGATGG--CTTCTTCCCCTTCACTTGTTTAAAAAT---------------A-----AAAAATTCCTCAC----CAAATGTCAGCTGCGTGTCAGGTTC s calJac1.Contig5139 53906 171 + 225949 CAGTGCC-TGTGCCGGC--AGCA--GAGGCCTGTGGC----------AG-GCAGGGATTTAGGGGATGGCAGTTTCC-------CCAGGA-AAAGGG-----TCCCTG-GGG------TG---G-----G--TGGGT-----------------------GGGTTTCAAGATGG--CTTTTTCCCCTTCACTTGTTTAAAAAT---------------A-----AAAAATTCCTCAC----CAAATGTCAGCTGCGTGTCGGGTTC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 51527 172 - 95547 CAGTGCCTTGTGCCAGG--AGCA--GGGGCCAGTGGC----------AG-GCAGGGATTTAGGGGATGGTAGGTTCC-------CGAGG--AACGGG-----TCTCTGTTGA------AG---G-----G--GGAGA-----------------------AAGTTTCAAGATGG--CTTTTCCCCCTTCACTTGTTTAAAAAT---------------A-----AAAAATTCCTCAC----CAAATGTCAGCCGCGTGTCAGGTTC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75044320 172 + 78773432 CAGTGCCTTGTGCCAGG--AGCA--GGGGCCAGTGGC----------AG-GCAGGGATTTAGGGGATGGTAGGTTCC-------CGAGG--AACGGG-----TCTCTGTTGA------AG---G-----G--GAAGA-----------------------AAGTTTCAAGATGG--CTTTTCCCCCTTCACTTGTTTAAAAAT---------------A-----AAAAATTCCTCAC----CAAATGTCAGCCGCGTGTCAGGTTC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16070415 173 + 17838096 CGGTGCCTTGTGCCAGG--AGCA--GGGGCCTGTGGC----------AG-GCAGGGATTTAGGGAATGGTAGGTTCC-------CGAGGA-AACGGG-----TCTCTGTTGA------AG---G-----G--GGAGA-----------------------AAGTTTCAAGATGG--CTTTTTCCCCTTCACTTGTTTAAAAAT---------------A-----AAAAATTCCTCAC----CAAATGTCAGCTGTGTGTCAGGTTC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 21436 168 - 64270 NGGTGCCTTGTGCCAGG--AGCA--GGGGCCTGTGGC----------AG-GCAGGGATTTAGGGAATGGTAGGTTCC-------TGAGGA-AACGGG-----TCTCTGTTAA---------------------GAGA-----------------------AAGTTTCAAGATGG--CTTTTTCCCCTTCACTTGTTTAAAAAT---------------A-----AAAAATTCCTCAC----CAAATGTCAGCTGCGTGTCAGGTTC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79483246 173 + 83384210 CGGTGCCTTGTGCCAGG--AGCA--GGGGCCTGTGGC----------AG-GCAGGGATTTAGGGAATGGTAGGTTCC-------TGAGGA-AACGGG-----TCTCTGTTGA------AG---G-----G--GGAGA-----------------------AAGTTTCAAGATGG--CTTTTTCCCCTTCACTTGTTTAAAAAT---------------A-----AAAAATTCCTCAC----CAAATGTCAGCTGCGTGTCAGGTTC i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 33263 168 + 287808 TGGTGCCTCGTGCCAGG--AGCT--AAGGCCCGTTGC----------AGTGGGGAGACTTAGGGAATGGCAGGTTCC-------CAAGGA-GAAGTG-----TTTCGG-----------A---G-----G--GGGGG-----------------------GTGTTTCAAGATGG---TTTTTCCCCTTCACTTGTTTAAAAAT---------------A-----AAGAATTCCTCAC----CAAACGTCAGCTGTGTGTCAGGTTC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118767138 172 + 121843856 C-----G-GGGCCCACGCAGGCAGGAAGGCCTGCTGC----------AG-GCGAGGATGCGGGGAGAGGCGGGCTCC-------CCAGCA-GAAACA-----GCTCCACGGA-----------A-----G--GGGGA-----------------------AACTTTCTAGATGG---TTTCTCCCCCTCACTTGTTCAAAAAT---------------A-----AAAAATTCCTCACCGCACGCACGTCAGCTGCGTGCCAGGCTC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 4100 184 + 11404 CCCTGTA-GGGGCCACG--AGCA--AAGTCCTGCCACGGAAGGGCCTAG-CCCAGGACCGGGAGAGAGGC-GGCTCC-------CGGGGG-GCGACC------CTCTGTGGG-----------GGTGTCG--GGGGA-----------------------GACTTTCAAGATGG-GTTTTTTCCCCTTCACTTGTTTAAAAAT---------------A-----AAAAATTCCTCAC----CGCGTGTCAGCTGTGTGTCAGGTTC i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4396246 168 + 7991924 CCCTGCC-TCGGCCAGG--AGCA--CAG-CCTGTTGC----------AA-GCGAGGATCTGGGGAGGGACAGGCTCC-------CTGGGA-GCAGCA-----TCTGCGTGGA-----------A-----G--GCGGA-----------------------AACTTTCAAGATGG---TTTTTCCCCTTCACTTGTTTAAAAAT---------------A-----AAAAATTCCTCAC----TGCATGTCAGCTGCGTGTCAGGTTC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 13536 167 + 44242 T-GAGCC-GGTGCCAGA--GCCA--AGGCCCGCTTGC----------AG-GCAAGGATATGGGGAGAGGC-AGCTCC-------CCGGGA-GAAGCA-----TCTCCATGGA-----------A-----G--GGGGA-----------------------AAGTTTCAAGATGG---TTTTTCCCCTTCACTTGTTTAAAAAT---------------A-----AAAAATTCCTCAC----TGCGTGTCAGCTGCGTGTCAGGTTC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 25233 150 + 41507 ------------GCAGG--GCCA--GGG-CCAGCTGC----------AG-GCGGGG-ACTGGGGCGAGGC-AGCCCC-------CAGGAGCACCACT-----GCTGCG---------------G-----G--GGGGG-----------------------GGGGTTCATCATGG----CTTTCCCCTTCACTCGTTTGAAAAC---------------A-----CAGACTCCCTGGC----C-CACGTCACCTGCGAGTCAGGTTC i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 10334 152 - 54875 ---------TTGAAACC--ACTG--GCG-CCTGCTGC----------AG-CCAGGGCAGTGCAGGTAGGA-GACCCC-------TGGGAA-GCCATG-----GTTGC----------------A-----A--GGGGA-----------------------AACTTTCAAGCTGG-----TTTCCCTTCCACT-GTTTAAAAAC---------------ATCCCTCAG---TCCCGTC----T-CCCATCTCCTGCGTGGCAGGTCC i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 135390 173 + 145505 CAGTATCTCGTG-CAGA--AG-A--AAGGCCTGCTGC----------AG-GTGGGGATTTAGGGAAAGACAGGTGCC-------CACGGA-GGAGCATAGCATCTCTGCTCA-----------A-----G--GGAGG-----------------------AAGTTTCAGGATGG---TTTTTCCCCTTCACTTGTTTAAAAAC---------------A-----AAAAATTCCTCAC----CAAATGTCAGCTGCGAGTCAGGTTC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10865488 174 - 65312493 CGGCATCGCTTG-CAGA--AGAA--AAAGCCTGCAGC----------AG-GCGGGGATTTAGGGAAAGGCAGGTGCC-------CACAGA-GGAGCATAGCATCTCTGTTCA-----------A-----G--GCAGG-----------------------AAGTTTCAGGATGG---TTTTTCCCCTTCACTTGTTTAAAAAC---------------A-----AAAAATTCCTCAC----CAAATGTCAGCTGTGAGTCAGGTTC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58049317 170 - 61308211 CGGCACCCTGTG-CTCA--AGGA--AA-GCCTGCTGC----------CG-GCGGGCCTTTGGGGAGAGGCCGGTGCC-------CACGGG-GGAGCG-----TCTTCCTTCA-----------CA----G--GGGGA-----------------------AAGTTTCAAGACGG--TTTTTTCCCCTTCACTTGTTTAAAAAT---------------A-----AAAAATTCCTCAC----CAAATGTCAGCTGCGTGTCAGGTTC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 36976 154 + 132007 CGGCACCTTGTG-CGGA--AGAA--AA--------------------------GGGATTTAGGGAAAGGCAGGTGCC-------CAGGAA-GGAGCA-----TCTCTGTTCA-----------A-----G--GGGGA-----------------------AAGTTTCAAGATGG---TTTTTCCCCTTCACTTGTTTAAAAAC---------------A-----AAAAATTCCTCAC----CAAATGCCAGCTGTGTGTCAGGTTC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59443247 173 - 64418924 TGGTCTGTTCTG-CGGC--AGGA--AAGGCCTGTGGC----------GG-GTGGGGATTTGGGGAAAGGCAGGTACC-------CGATGA-GGAGCA-----TCTCTGTTCA-----------AG----G--GGGGA-----------------------AAGTTTCAAGATGGTTTTTTTTCCCCTTCACTTGTTTAAAAAT---------------A-----AAAAATTTCTCAC----CAAATGTCAGCTGTGTGTCAGGTTC i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_4816 14185 155 + 14340 CGGTGCCT---------------------GGTGCTGC----------AG-GCGGGGAGGTGGGGAGAGCCAGGTGCC-------C---AT-GGGGCG------CCCCGTCCC-----------AATGCAGGAGGGAG-----------------------AAGCTGCGAGATGG---CTGTTCCCCTTCACTTGCTTAAAAAT---------------A-----AAAAATCCCTCAC----CC-GTGTCAGCCGCGCGTCAGCTTC i myoLuc1.scaffold_4816 C 0 N 0 s pteVam1.scaffold_11245 21493 173 + 48268 GGGTACCTCGTG-CAGA--ATTA--AAGGGCTGCCGC----------AG-GTGGGGGTGCAGGGAAAGGAGGGGGCC-------CCAGGA-GGAGCG-----ACTCCGTTCG-----------GGGGCCG--AGGAG-----------------------GAGTTTCAAGATGG---TTTTTCCCCTTCACTTGTTTAAAAAT---------------A-----AAAAATTCCTCAC----CCAATGTCAGCTGCGTGTCAGTCC- i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_125414 560 171 - 877 -----CCTGGGC-CTGC--AGCA--CAGGCCAGCTGA----------GG-GCAGGGGT--------AGGAAGCTGTT-------CCATGT-AGAGTG------GGCAGGGCG-----------GG----C--GGGGT-----------------------GGATCTCAGGCTGT---ATGTTCCCTTTCactcttttaaaaacataaataaataaataa-----ataaatccctcca----CACACGTCAGCTGCGTGTCAAGTTC i eriEur1.scaffold_125414 C 0 C 0 s loxAfr3.scaffold_49 14440809 160 - 17734757 TGGTCCCTTGTGCGGGA--AGAA--AAGGCCTGCTGT----------AG-ACAGGGGCTCAGGG-AAGCACGGTTCC-------CAAGGG-TGAGCA-----GCTCCGTGCA------AC---G-----G--CGGAG-----------------------AAGTTTCAAGATGG--TTTTTTCTCCTTCACTTGTTCAAAAAT---------------A-----AAAAATTCCTCAC----TA-ATGT-----------CGGGCTC i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_56828 66 200 + 1587 TGCCCCCCTGCGCCGGA--AGCT--CAGGCCCCCTGC----------CC-ACGGGGGTTCAGGG-AAGCCAGGGGTC-------CAAGGA-TGAGCA-----GCTCTGAGCACTGGGCAG---G-----G--CGGGGGCGGGGCTGGGGGGGGGAGGGGCAAGTCTCAAGATGG--GTTTTTCCCCTTCACTTGCTCAAAAAT---------------A-----AAAAATCCCTCAC----CG-ACGTCAGCCCTGTGGCAGGCTC i echTel1.scaffold_56828 C 0 C 0 s choHof1.scaffold_149147 2783 171 + 9388 CAGTACCCTGCACCAGA--AGAA--AAGGCCTGCTAC----------AG-ACAGGAATTTAGGGAAAGTCAGGTTCC-------CAAGGA-TAAGCG-----GCTCTGTTCC------AA---G-----G--GGGTG-CGGGGGTG--------------GAGTTTCAAGACA------------CTTCACTTGTTTAAAAAT---------------A-----AAAAATCCCTCAC----CGAATGTCAGCTGCGTGTCAGGTTC i choHof1.scaffold_149147 C 0 C 0 s macEug1.Scaffold385251 653 169 + 1704 CAGTGCCttgtg----g--aaaa--gaaaatagatgc----------ag--TAGGGATTTGAGGAAATCCAGGTTTC-------T-AGGA-TGAGTC-----TTTGTTTTCA------AGgtag-----a--aaaaa-----------------------aagttacaatATGG---CTTTTCTCCTTcacatgtttaaaaat---------------a-----aaaaattcctcaC----CAAATGACAGCTCTATGTCAGGTTC i macEug1.Scaffold385251 C 0 C 0 s monDom5.chr2 304551057 170 - 541556283 CAGTGCCTTGTG---GA--AAAG--AAAATATGTAGT-------------ATAGGGATTTGGGGAAATCCAGGTTTC-------TAAGGA-TGAGTC-----TCTGTTTTCA------AGGT-A-----G--AAAAA-----------------------AAGTTACAATATGG---CTTTTCCCCTTCACATGTTTAAAAAT--------------AA-----AAAAATTCCTCAC----CAAATGACAGCTCTATGTCAGGTTC i monDom5.chr2 C 0 C 0 e tarSyr1.scaffold_143701 7366 1528 + 9575 M e micMur1.scaffold_72647 4992 0 + 4992 I a score=1196252.000000 s hg19.chr17_gl000204_random 53227 59 + 81310 CATTTGTCTTTATAACAGAGTATCAAGCAGGA----GCGTG-GAAATAAATAAACACAGGGAGA s calJac1.Contig5139 54077 55 + 225949 CATTTTTCTTTATAACAGAGTATCAAGCAGGA----GTGTG-G----AAATAAACACAGGGAGA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 51699 59 - 95547 CATTTGTCTTTATAACAGAGTATCAAGCAGGA----GTGTG-GAGATAAATAAACACAGGGAGA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75044492 59 + 78773432 CATTTGTCTTTATAACAGAGTATCAAGCAGGA----GTGTG-GAGATAAATAAACACAGGAAGA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16070588 59 + 17838096 CATTTGTCTTTATAACAGAGTATCAAGCAGGA----GTGTG-GAAATAAATAAACACAGGGAGA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 21604 59 - 64270 CATTTGTCTTTATAACAGAGTATCAAGCAGGA----GTGTG-GAAATAAATAAACACAGGGAGA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79483419 59 + 83384210 CATTTGTCTTTATAACAGAGTATCAAGCAGGA----GTGTG-GAAATAAATAAACACAGGGAGA i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 33431 62 + 287808 CATTTGTCTTTATAACAGAGTATAGAGCAGAATTCTGCGTG-GGAATGAA-GAGCACACAGCGA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118767310 60 + 121843856 CATTTGTCTTTATAACAGAGTATCAGGCAGGA----GTGAAGGAGATAAATAAACAGAGAGAGA i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 4284 57 + 11404 CATTTGTCTTTATAACAGAGTAGAGAGCAGCA----GAGAA-GAAATAAATAAAC--ACGGAGA i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4396414 59 + 7991924 CATTTGTCTTTATAACAGAGTATAGAGCAGGA----GTGAG-GAAATAAATAAACACAGAGAGA i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 13703 59 + 44242 CATTTGTCTTTATAACAGAGTATCAAGCAGGA----GTGAG-GAAATAAATAAACAAAGAGAGA i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 25383 51 + 41507 CATTTGTTTTCATAACAGAGCATCAGGCAGGA----GGGTG-GAGACAA--------CGCGAGT i oryCun2.chrUn0958 C 0 I 2 s ochPri2.scaffold_9426 10486 55 - 54875 CATCTGTCTGCCTAACACAGCACCAGGCAGGA----GCATG-GAAATAA----ACTCCGAGAGA i ochPri2.scaffold_9426 C 0 I 484 s turTru1.scaffold_106006 135563 55 + 145505 CATTTGTCTTTATAACAAACTATCAAGCAGGA----GTGTG-G----AAATAAACACAGAGAGA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10865662 59 - 65312493 CATTTGTCTTTATAACAAAGTATCAAGCAGGA----GTGTG-GAAATAAATAAACACAGAGAGA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58049487 59 - 61308211 CATTTGTCTTTATAACAGAGTATCAAGCAGGA----GTGTG-GAAATAAATAAACACAGAGAGA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 37130 59 + 132007 CATTTGTCTTTATAACAGAGTATCAAGAAGGA----GTGTG-GAAATAAATAAATACAGAGAGA i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59443420 55 - 64418924 CATTTGTCTTTATAACAGAGTATCAAGAAGGA----GTGTG-G----AAATAAGCACAGAGAGA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 21666 57 + 48268 CATTTGTCTTGAT-ACAGAGTATCAAGCAAGA----GTGTG-A-AATTAATAAACACAGAGAGA i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_125414 731 59 - 877 CATTTGTCTTTCAAAGGGAGGCTCTGGCAAGA----gtgtg-gaaataaataaacacagggAGA i eriEur1.scaffold_125414 C 0 C 0 s loxAfr3.scaffold_49 14440969 57 - 17734757 CATTTGTCTTTATAACAGAGTATCGGGCAAAA----GTATG-GAAATAAATAA--ACAGAGAGA i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_56828 266 57 + 1587 CATTTGTCTTCATGACAGAGTATTGGGCAGGC----GTATG-GAAATAAATAA--ACAGAGAGA i echTel1.scaffold_56828 C 0 C 0 s choHof1.scaffold_149147 2954 59 + 9388 CATTTGTCTTTATACCAGAGTATCAAGCAAGA----GTGTG-GAAATAAATAAACACAGGGAGA i choHof1.scaffold_149147 C 0 C 0 s macEug1.Scaffold385251 822 59 + 1704 CATTTGTCTTCATAACAGAGTATCAAGCAGGA----GCGAG-GAAATAAATAAACACTGAAAGA i macEug1.Scaffold385251 C 0 C 0 s monDom5.chr2 304551227 59 - 541556283 CATTTGTCTTCATAACAGAGTATCAAGCAGGA----GCGAG-GAAATAAATAAACACTGAAAGA i monDom5.chr2 C 0 C 0 e tarSyr1.scaffold_143701 7366 1528 + 9575 M e micMur1.scaffold_72647 4992 0 + 4992 I a score=368224.000000 s hg19.chr17_gl000204_random 53286 110 + 81310 CAA-CCG--ACCA--------AAACTTGCAGGCT-----CTGGGCT-----GG-----------------------------GCTG---GGCTAGAGGAGGGAAGCCCCACCCTGCAAGGGCTGAAAA-----------ATAATATTGCAGTTTCGCGTTCAGCACT-----GT-GGCTC s calJac1.Contig5139 54132 115 + 225949 CAA-CCG--ACCA--------GAACTTGTAGGCT-----CTGGGCTGGGACGG-----------------------------GCTG---GGCTGGAGGAGGGAAGCCCCACCCTGCATGGGCTGAAAA-----------ACAAGGTTACAATTTCGCATTCAGCACT-----GG-GGCTG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 51758 110 - 95547 CAA-CCG--ACCA--------AACCTTGCAGGCT-----CTGGGCT-----GG-----------------------------GCTG---GGCTAGAGGAGGGAAGCCCCACCCTGCAAGGGCTGAAAA-----------ATAATGTTGCAGTTTCGCATTCAGCGCT-----GT-GGCTC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75044551 110 + 78773432 CAA-CCG--ACCA--------AACCTTGCAGGCT-----CTGGGCT-----GG-----------------------------GCTG---GGCTAGAGGAGGGAAGCCCCACCCTGCAAGGGCTGAAAA-----------ATAATGTTGCAGTTTCGCATTCAGCACT-----GT-GGCTC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16070647 115 + 17838096 CAA-CCG--ACCA--------AAACTTGCAGGCTctgggctgggct-----gg-----------------------------gctg---ggctggAGGAGGGAAGCCCCACCCTGCAAGGGCTGAAAA-----------ATAATATTGCAGGTTCGAATTCAGCACT-----GT-GGCTC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 21663 110 - 64270 CAA-CCG--ACCA--------AAACTTGCAGGCT-----CTGGGCT-----GG-----------------------------GCTG---GGCTAGAGGAGGGAAGCCCCACCCTGCAAGGGCTGAAAA-----------ATAATATTGCAGTTTCGCATTCAGCACT-----GT-GGCTC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79483478 110 + 83384210 CAA-CCG--ACCA--------AAACTTGCAGGCT-----CTGGGCT-----GG-----------------------------GCTG---GGCTAGAGGAGGGAAGCCCCACCCTGCAAGGGCTGAAGA-----------ATAATATTGCAGTTTCGCATTCAGCACT-----GT-GGCTC i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 33493 101 + 287808 CAC-CCA--ACCA--------AAATCT-CAGGCA-----CTGGGAC-------------------------------------------GGCCGGAGGAGGTGAGCCCCACACCTCAGTCGCTAAGAA-----------GAAACATTTCAATCTCGATTTTGTCA-------GT-GGCTC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118767370 88 + 121843856 CAA-CCG--ACCG--------AACCTCACGAGCT-----CCGGACT---------------------------------------G---ACTGGGGGGAGGTGAGCCTCGTGCCGCAGTCACTAAGAA-----------ATAACATTTCAATCTT-----------------GA------ i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 4341 102 + 11404 CAA-CCC--ACCA--------AAGATTGCAGGCC-----CGGGGAG---------------------------------------A---GGCTGAAGCAGGTACCCCCAACGCC-CGCCCCCTGGAAG-----------ATAACAAGTCAATCTCCTGTGTGGCC-A-----GA-GGCT- i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4396473 101 + 7991924 CAA-CCG--ACCA--------CAGATTGCAGGCA-----CGCGGAT---------------------------------------G---G-CTGGTGGAGGTGAGCCCCACGCCACGGTCACTGAGAT--------------ACATTTCAATTCCACAAGCAGCA-T-----AATGGCCC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 13762 104 + 44242 CAA-CCG--ACCA--------AAAACTGCAGGCA-----CGCGGAC---------------------------------------A---GGACGGAGGAGGCAAGCCCCATGCCACAGCCGCTGAAAA-----------ATAACACTTCAGTTCTGTGGGCAGCA-A-----GC-CACTC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 25436 69 + 41507 CAC-CCA----CG--------GACACTGCAGGGG-----CATCGCG---------------------------------------G---GCCC--AGGAGG-AAGGCCCACACCGCAGC----------------------------------------GCGGCC-T-----GG-CACT- i oryCun2.chrUn0958 I 2 C 0 s turTru1.scaffold_106006 135618 102 + 145505 CAA-CCA--ACCA--------AAAACTGCAGGCA-----CACGGAT-----GG-------------------------------------GCTGGAGGAGGTAAACCCCACACTACAACCGCTGAAAA-----------ATAACATTTCAATTTCATG-TT--CACT-----GT-TGCTC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10865721 111 - 65312493 CAG-CTAGGACCAAAAAGACCAAAATTGCAGGCA-----CATGGAT-----GG-------------------------------------GCTAGATGAGGT-AACCCCACACCACAACCGCTGCAAA-----------AGAGTGTTTCAATTCCGTG-TT--CACT-----GT-CACTC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58049546 138 - 61308211 CAA-CCA--AGCA--------AAAATTGCAGGCG-----CCCGTCC-----GGGATGTCGGAGGGAAGCCCCACACTGCCCGTCCG---GGATGTCGGAGGGAAGCCCCACACTGCAACGGCTGAAAA-----------ATAACGTTTCAATTGCGTG-TCGGCCCT-----GT-CACTC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 37189 109 + 132007 TGA-CTG--ACCA--------AAAATTGCAGGCA-----GGCGGAC-----AG------------------------------CCG---GGCTGGAGGAGGTGAGCCCCACGTTGCAACTGCTGAAAA-----------ATAACATTTCAGTTTCGAGCTCGGCACT-----GT-CACTC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59443475 93 - 64418924 CAA-CTG--ACCA--------CAGACTGCAGGTG-----CATGAAC-----AG------------------------------CCG---GGCTGGAGGAAGG---------GCTGTAATCCCTGGGAA-----------ATAACATTCTAGGGTGGAGTTTGGCTC-------------C i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 21723 98 + 48268 CAC-C----ACCA--------C--ACCGCAGATG-------CAGAC-----AG------------------------------CCG---GGCTGGAGGCGGTGAGCCCCCCACCCACTCCACTGCAA--------------AACATTTCAGTTTCCAG-GCGGTACT-----G--CGCTC i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_125414 790 87 - 877 CAA-GCC--ACTG--------AAAACTGAAGGTG-------CAGGA-----GG------------------------------CTGGGAGGCTGGGGGAGGCGGGCCTC---CTGCAGCTGCTGAAAA-----------ACATCATTTCAATTT-------------------------- i eriEur1.scaffold_125414 C 0 n 0 s loxAfr3.scaffold_49 14441026 94 - 17734757 CAACCCA--ACCA--------AAGACTACAGGCA-----CTAGGTG---------------------------------------G---GCTA-GAAGAGGTAAGCCCTGCACTGC-AGCGGCCAAGA-----------ATAACGTTTCCATTTTGC---------------AT-CACTG i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_56828 323 110 + 1587 CAG-CCA--ACCA--------CAGTCCACAGGCA----GGGAGGCG---------------------------------------G---GGGAGGGAGAGGGGAGCCATGTGCTGT-AGCACCATTAA-----------GTAACATTTCAATTTCACCCTGGGGCCCTGGTGGC-CACCa i echTel1.scaffold_56828 C 0 C 0 s choHof1.scaffold_149147 3013 105 + 9388 CAA-CCG--ACCA--------GAAATCGCAGGCA-----CAAGGAT---------------------------------------G---GCCCAGTGGAGGTAAGCCCCACGCTGTAAACGCTGAAAA-----------ATAACATTTCAATTTGGCATTCGGCGCT-----GT-CACTC i choHof1.scaffold_149147 C 0 C 0 s macEug1.Scaffold385251 881 109 + 1704 CAA-CCA--ACCA--------AAAACTGAAGACA-----TATGAGA---------------------------------------G----------AAAGGTAATCCCCATACTGCaaacattgaaaacaaaaacaatgatgaCATTTCAATTTAGCTTTTGCCCCT-----GC-TGCTC i macEug1.Scaffold385251 C 0 n 0 s monDom5.chr2 304551286 109 - 541556283 CAA-CCA--ACCA--------AAAACTGAAGACA-----TATGAGA---------------------------------------G----------AAAGGTAATCCCCATACTGCAACCATTGAAAACAAAAACAACAATGACATTTCAATTTAGCTTTTGCCCCT-----GC-TACTC i monDom5.chr2 C 0 I 4976 e ochPri2.scaffold_9426 10541 484 - 54875 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e micMur1.scaffold_72647 4992 0 + 4992 I a score=-221107.000000 s hg19.chr17_gl000204_random 53396 23 + 81310 TG---G----------CCCACTG-------------ACAT--GTTTT----CC--------TC s calJac1.Contig5139 54247 23 + 225949 TG---G----------CCCACGG-------------AGAT--GCTGT----CC--------TG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 51868 23 - 95547 CG---G----------CCCACTG-------------ACAT--GTTTT----CC--------TC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75044661 23 + 78773432 TG---G----------CCCACTG-------------ACAT--GTTTT----CC--------TC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16070762 23 + 17838096 TG---G----------CCCACTG-------------ACAT--GTTTT----CC--------TC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 21773 23 - 64270 TG---G----------CCCACTG-------------ACAT--GTTTT----CC--------TC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79483588 23 + 83384210 TG---G----------CCCACTG-------------ACAT--GTTTT----CC--------TC i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 33594 24 + 287808 CAC--A----------CCCACTG-------------GGAC--CCTGT----CT--------TC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118767458 20 + 121843856 ----------------CCCATGG-------------ACAG--ATTCA----CC--------TC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 4443 24 + 11404 ----------------CCCACAG-------------ACCA--GCGCAATGTCC--------GC i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4396574 24 + 7991924 TGT--G----------TCCACGG-------------AGAC--GTTCT----CC--------TC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 13866 23 + 44242 TGT--G----------CCC-CTG-------------ACAC--CTTCT----CC--------TC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 25505 7 + 41507 ----------------CCC--------------------------------GG--------TC i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 135720 32 + 145505 CAT--G----------CTCACTG-------------AGAT--GTTTC----CCCCTGCGTGAC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10865832 32 - 65312493 CAG--G----------CTCAATC-------------AGAC--GCTTC----TCCCTGCATGGC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58049684 31 - 61308211 CGT--G----------CTCTCAG-------------AGA---CGGCT----CCCCTGCATGGT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 37298 33 + 132007 CAT--G----------GTCACAG-------------AGACACCCCTG----CCCCCGCAC-GC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59443568 21 - 64418924 CAC--G------------------------------------TCTCC----CTCCTGCGTGGT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 21821 28 + 48268 CGG--G----------CCCTCGG-------------A-----CAAGC----CACCCGCCT-GC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14441120 13 - 17734757 AGTCGG----------CTCCCTT---------------------------------------- i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_56828 433 23 + 1587 ggtcagcagttcaaaccccccag---------------------------------------- i echTel1.scaffold_56828 C 0 C 0 s choHof1.scaffold_149147 3118 24 + 9388 TGT--G----------CTCCCTGAGACGTGTGCCTC--------------------------- i choHof1.scaffold_149147 C 0 I 1766 e ochPri2.scaffold_9426 10541 484 - 54875 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e micMur1.scaffold_72647 4992 0 + 4992 I e eriEur1.scaffold_125414 877 0 - 877 I e macEug1.Scaffold385251 990 0 + 1704 I e monDom5.chr2 304551395 4976 - 541556283 I a score=78164.000000 s hg19.chr17_gl000204_random 53419 380 + 81310 ----------------------TCT-TTACTGC----CCCCCA-----CCCCCT-A------CCACCACCACTCTG------GCGCTTCTGGGAG---GGATAG-------------------------------------GAGCGTG----A-------------CTTATGCATTCCTTCCTTCCGAATTGCAC------AGGCATC----------------------------ATGGGTCAGAACA-CCATCTGCGTATATG--GGGGAGGG--GGCAGA--------TAAACCAAGCAGGGCC----CCTGCCCTC-AGCAGCAAGGCACC--TCCAACTGCCACACAT--CGGTATGA-AGGCGCCTT-----AGGCCAGG-GCTGAATGTGGCTGGGA--------GAG--AGGTG-------TCAAAGAAGGCTGCA-----------GGGGAGAG--GCAA--------------------C---AGGGCTG-----AACCAG----CCAGGGAA-----G-----------ATG------------GCATT----------TTCTCT--GGCCACTACAGTGTCTAGTTCATCCCTAGACACCAAAGAGC-CCGATAA------TCTCTCCAT-TTCACCGA-----------TGCG s calJac1.Contig5139 54270 371 + 225949 ----------------------TCT-TTACTGC----CCCA-------CCCCCC-A------CCGCCACCACTCCA------GCACTTCTGGGTG---GGAAAG-------------------------------------GAGCGTG----A-------------CTTGTGCA----CTCCTCCCAAATTGCAC------AGGCATC----------------------------ATGGGTCAGACCA-TGCTCTGCATATAT---GGGGAGGG--GGCAGA--------T-AACTGAGCAGAGCT----CCTGCCCTC-GGCAGCAAGGCACC--CCCAACTGCCACATAA--CAGCGTGA-AGTTGCCTT-----AGGCCAGG-GCTGAATGTGGCTAGGA--------GAG--AGGTG-------TCAAAGAAGGCTGCA-----------GGGGAGAG--GCAG--------------------C---AGGGCTG-----AACCAG----CCAGGGAA-----G-----------ACA------------GCA-T----------TTCTCT--GGCCACTACCGTGCTTGGTGCATCCCCAGACACCAAAGAGC-CGGATAA------TCTCTCCAT-TTCACTGA-----------TGCG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 51891 357 - 95547 ----------------------TCT-TTACTGC---------------GTCCCC-A------CCACCACCACTCTG------GCACTTCTGAGTA---GGAGAG-------------------------------------GAGCATG----A-------------CTGACGCATTCCTTCCTTCCTAATCGCAC------AGGTGCC----------------------------ATGGGTCAGACCA-CCATCTGCATATAAC--GGGGAGGG--GGCAGA--------TAAACCAAGCAGGGCC----CCCGCCCTC-AGCAGCAAGGCACC--TCCAATTGCCACACAT--TAGTGTGA-AGGCGCCTT-----AGGCCAGG-GCTGACTGTGGCTGGGA--------GAG--AGGTG-------GCAAAGAAGGCTGCA-----------GGGGAGAG--GCAG--------------------C---AGGACTG-----AACCAG----CCAGGGAA-----G-----------ATG------------GCATT----------TTCTCT--GGC-----------------CATCCCCAGACACCAAAGAGC-CCGATAA------TCTTTCCAT-TTCAGCGA-----------TGCG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75044684 377 + 78773432 ----------------------TCT-TTACTGC----GTC--------CCCCCC-A------CCACCACCACTCTG------GCACTTCTGAGTA---GGAGAG-------------------------------------GAGCGTC----A-------------CTTACGCATTCCTTCCTTCCTAATCGCAC------AGGCGCC----------------------------ATGGGTCAGACCA-CCATCTGCATATACG--GGGGAGGG--GGCAGA--------TAAACCAAGCAGGGCC----CCCGCCCTC-AGCAGCAAGGCACC--TCCAACTGCCACACAT--TAGTGTGA-AGGCGCCTT-----AGGCCAGG-GCTGGCTGTGGCTGGGA--------GAG--AGGTG-------TCAAAGAAGGCTGCA-----------GGGGAGAG--GCAG--------------------C---AGGGCTG-----AACCAG----CCAGGGAA-----G-----------ATG------------GCATT----------TTCTCT--GGCCACTACCGTGCTTAGTTCATCCCCAGACACCAAAGAGC-CTGATAA------TCTTTCCAT-TTCAGCGA-----------TGCG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16070785 375 + 17838096 ----------------------TCG-TTACTGC----C----------CCCCCC-A------CCACCACCACTCTG------GCACTTCTGGGTG---GGATAG-------------------------------------GAGCGTG----A-------------CTTATGCATTCTTTCCTTCCGAATTGCAC------AGGCACC----------------------------ATGGGGCAGACTA-CCATCTGCGTATATG--GGGGAGGG--GGCAGA--------TAAAGCAAGCAGGGCC----ACCACCCTC-AGCAGCAAGGCACC--TCCAACAGCCACACAT--CAGTATGA-AGGCGCCTT-----AGGCCAGG-GCTGAATGTGGCTGGGA--------GAG--AGGTG-------TCAAAGAAGGCTGCA-----------GGGGAGAG--GCAG--------------------C---AGGGCTG-----AACCAG----CCAGGGAA-----G-----------ATG------------GCATT----------TTCTCT--GGCCACTACAGCGCTTAGTTCATCCCCAGACACCAAAGAGC-CCGATAA------TCTCTCCAT-TTCACCGA-----------TGCA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 21796 380 - 64270 ----------------------TCT-TTACTGC----CCCCCA-----CCCCCC-A------CCACCACCACTCTG------GCGCTTCTGGGAG---GGATAG-------------------------------------GAGCGTG----A-------------CTTATGCCTTCCTTCCTTCCGAATTGCAC------AGGCATC----------------------------ATGGGTCAGACCA-CCATCTGCGTATATG--GGGGAGGG--GGCAGA--------TAAACCAAGCAGGGCC----CCTGCCCTC-AGCAGCAAGGCACC--TCCAACTGCCACACAT--CGGTATGA-AGGCGCCTT-----AGGCCAGG-GCTGAATGTGGCTGGGA--------GAG--AGGTG-------TCAAAGAAGGCTGCA-----------GGGGAGAG--GCAA--------------------C---AGGGCTG-----AACCAG----CCAGGGAA-----G-----------ATG------------GCATT----------TTCTCT--GGCCACTACAGTGCTTAGTTCATCCCTAGACACCAAAGAGC-CCGATAA------TCTCTCCAT-TTCACCGA-----------TGCG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79483611 380 + 83384210 ----------------------TCT-TTACTGC----CCCCCA-----CCCCCC-A------CCACCACCACTCTG------GCGCTTCTGGGAG---GGATAG-------------------------------------GAGCGTG----A-------------CTTATGCATTCCTTCCTTCCGAATTGCAC------AGGCATC----------------------------ATGGGTCAGACCA-TCATCTGCGTATATG--GGGGAGGG--GGCAGA--------TAAACCAAGCAGGGCC----CCTGTCCTC-AGCAGCAAGGCACC--TCCAACTGCCACACAT--CGGTATGA-AGGCGCCTT-----AGGCCAGG-GCTGAATGTGGCTGGGA--------GAG--AGCTG-------TCAAAGAAGGCTGCA-----------GGGGAGAG--GCAA--------------------C---AGGGCTG-----AACCAG----CCAGGGAA-----G-----------ATG------------GCATT----------TTCTCT--GGCCACTACAGTGCTTAGTTCATCCCTAGACACCAAAGAGC-CCGATAA------TCTCTCCAT-TTCACCGA-----------TGCG i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 33618 366 + 287808 ----------------------TTT-GTACCAG---------------CCTCCC-C------TGACCACCACCCT-------GCACTTCC-ACTG---CGACAG-------------------------------------GAG--------------------------TGCCATCCCTCCCTGCCCATCCCAC------G----------------------------------ATGGGTCAAATAA-TC-TCTGCATATATA--GGGTAGGGGAGGCAGA--------TGAACCTAGCAGGGTC----CCTGCCCTC-AGGAGT-GTATGCC--CCTAACTTCTGCAT---------TGA-AGCCACCTC-----AAGCCC-T-GTTCAATGGTGCTGGGG--------GTG--GCATG-------GGGGTG-GGACTGCA-----------GTGGACAGCAGCAC--------------------A---GGAGCTG-----AACCAGGCCAGCAGGGAG-----GCCCAGCCGGAAATG------------GCATC----------TTCTCT--GGTCACCACCTTGCTTAGTTCATCCCCAGATACCAAAGGGC-TGAATTA------TCTCTTTCTATTCACGGA-----------TGCG i otoGar1.scaffold_94362.1-287808 C 0 I 6958 s mm9.chr11 118767478 358 + 121843856 ----------------------TCC-TCACTGC----CCCAGATGAT-CCCCGC-C------ACCCCCCCCCCCTCGAATTGGCACTTCTGGATA---TGACAG-------------------------------------ATGTTCT----A-------------GTGGTCCAAGCCTTCCTGTTTAACCCCCA------CAGTCCA---------------------------TCCAGGTCCAAAAGATGTTCTGCAC-TGTG--GGGGAGGG--GTGGG---------CAAAACAACCAGACTC----T-TGCCCTG-AGGAGCAGGGCCCC--TCTAGCTTCTACACAG--CAAG-------------------------GGAGCAGGCAGGTACCAGGATGCCAGC-TAG--AAGGG-------CGCACAATGGAGACCAGACC------CTGTTGAG--CCAG--------------------C---TCAGCTA-----AGACCA----GGCACTAC-----G----------AATT------------GCATC----------TTCTCT---GCCAGCCT-------AGTCCATCTCCACACACCAAATAGC---------------CCTTCCAT-CT--------------------- i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 4467 370 + 11404 ----------------------TCC-TTGCTGC---------------CCCCAC-C------TGTCCCTAGCCCTTGGCGGGGGACCTGGGGGAACACTGGAAC-------------------------------------GTACTTT----------------------------CCTTCCGGCCTAGCCCCAG------AAGCA------------------------------GCAGCTCCGTAAG-TGCTCAGTGC-TTTG--GGGAAGGG--CTGGGAAGA-----TAAACCAGCCAGACTC----T-TGCCCC------------TCCC--TCAGACTTCCACACAC--CACGGCGA-AGGGGTCCT-----AGGCTAGGTGCGAAGAGATTCAGGGATG------GAG--AAAGG-------TGAGAGAAAGCTACTGGACAGATGCGACGTGGTG--TCTG--------------------C---TTAACCG-----AGGCCT----GGAACCAA-----G-----------GTG------------GCCTT----------TTCTCTCTGACTACTCTA-TGTTGAGTTTATCCTCAGATACCCAAGGGCTCCA--GA------TCCTTCCAT-TTGACCCA--------------- i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4396598 372 + 7991924 ----------------------CCCTTCACCGC---------------CCCCAC-C------ACACGGCCTCCCCT-----GGCACCTCTGGGTG---GGACGG-------------------------------------GAGCACT------------------ACTGTGTACGCCACCCCTTCTGATCCCAC------AG---------------------------------GCGACTCAGACAA-TGCTCTCT---TCTG--GGGCAGGT--GCAGGAAAGGGATCTAAATCAACCAGGATC----C-TGCCCAT-GGGAGCAGGGTACC--TTCGAGTTCTACA-GT--CAGGGCAA-TGCTAGGCTGGGGAAGGCCAGGCAAGGGAGGCTTCAGGG---------GAG--AAGAG----------GCAACGGC---------------ACGTTGAA--CCAG--------------------C---GTGGCCA-----AGGTCA----GGACCAAACCTGGG----------GATG------------GCACT----------TTCTCT--GATCACACCC-TTGTTAGCTCATCCCTACATAAC-AAGAACTCCATTTC------TCTCTCCAT-CTCGCCGA--------------- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 13889 274 + 44242 ----------------------CCC-----TGG---------------CCCTGT----------GCCCCTCCCCCT------GCACTTGAAGGTG---GGACAG-------------------------------------GAGCCCT------------------CTTGTACATGCCTTCCTCCCTGATCTCAC------AAGC-------------------------------ATGGCTCACATAA-GGCTCTGT---CTTG--GAGTGGGG--GCTGGG--------TAAATCAGCCAA--------------------GAGCAAGGAGCC--TCCAACTTCTACACAT--CAGAGCAA-AGTTGCCTT-----CGGTGAGGGGCAGAGGG----AGGGCTG------GGG--CAGAG--------------------------------------------------------------------------GCTA-----AGGCCT----GGAGTTAG-----G-----------TTG------------GACAG----------CTCCCA------AGCTT-------AGCTCATCTCCAGAGAGCAGAGAGC----------------------------------------------- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 25512 354 + 41507 ----------------------CCC----ACGG---------------CCCCGC-C------AGGCACCGCCCCTG------GCAC-TCCAGGTG---GGACAG-------------------------------------GCGCCCC-----------------------AGACGCACATCCCCCTGATCCCAC------AAGC-------------------------------ACGAGGCAAAGGC-CGCTGGGT---GCAG--GCAGAGGG--GGAGGGG-------CAAACCCACCAGGCTC----TGGGGCCTT-GGGCACGAGGCACC--TCTGCCCGGTACC-AG--CAC--------------------AGGAAAGGAGCTGGAGGGGGCGCGGGTGCTGGCTCGG--GAGAGCCGCCTGCAGGGAGCGGC---------------AGACAGAG--CCAA--------------------CAAGGTGGCCA-----GGATGG----CCAGGTAG-----G----------GATG------------GCCTT----------GTCTCC--CACCACTGTC-TGCTTCCCCCTCGCCCAGA-ACCAGCGAGC-GCAAAGA------TCCGGCCGC-TTCACCCC--------------- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 135752 399 + 145505 ----------------------TCC-TCCAGGC----CCCTTATACTGCCCCCC-A-CAAACACACCACCATTCTG------ACACTTCTGGGTG---GGATAG-------------------------------------CAGCTCCCTTCA-------------CTTGTACATTCCTTCACTCCTAATTCCAC------AAGC-------------------------------ATGCATCAAATAA-CAC--TGCGTGTACA--GGAGGAGA--TGGGGA--------TAAATCAACCAGCATC----TCTGCCCTT-AGGAGCAAGGTGCC--TCCAACTTCTACACATCACAGAACGA-ACGGGTCTC-----GGACCATG-GTTGAATGGGG-GTGGG--------GGG--ATACT-------GTAAAGAAGACTGTA-----------GGGTAGAG--GCAG---------------------------CAAG-----GATCCA----GAACCAGG-----G-----------ATG------------GCATT----------TTCTAT--GGCCAATACCAGGCCTAGTTCATTCCCCAATACTAAAGAAC-TCCATAATT----TCTCTCCAT-TTCTCTGATGCTATTTCTTTGAG i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10865864 331 - 65312493 ----------------------TCC--CCAGGC----TCCTTACATTGCCCCCC-ACCCCACACACCACCACTCTG------ACATGTACGGG-G---GGAGAG-------------------------------------GTGCTTCCTTCA-------------CCTTTACATTCCTTTACTCCTAATTCTAC------AAGC-------------------------------AGGCATCAAATAA-TGC--CACGTGCCCA--GGAGGAAG--TGGGGA--------TAAATCAACCAGTATC----TCTGCCCTT-AGGAGTAAGGTGC----------TGTACCCAAGCTGGACCAG-GCTGGCCAA-----GGAGCA--------------------------------------------------------------------------------------------------------------------------ATCCA----GACTTGGG-----G-----------CTG------------GCATT----------TTCTCT--GGCCAATACCATGCCCAGTCCA-CCCCAAATACCAAAGAGC-TCCATAATT----TCTCTCCAA-TTCTTGGAAGCCATTTCTTTAAG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58049715 399 - 61308211 ----------------------TCC-TCCA-------CTCGTGCCCCCTCCCAC-A------TCCCCACC-ACCTG------ACACTTCTGGGTG---GGACAG-------------------------------------GAGCTTCCTTCG-------------CTTGAACACTGGTTCACTCCTAACCCCACAAGCATAAGC-------------------------------ATGCATCAAATAA-CACTCTACGTAGACA--GGAGGAGG--TGGGGA--------CAAATCAAGCAGGATT----CCTGCCCTT-AGGAACAAGGT-CC--TCCAACTTCTACACATGACAGAATAC-GGGGGCCTC-----AGGCCGTG-GTT----------GAAC--------AGG--GAACT-------GGAAAGACAGCTGCT-----------GGGCAGAG--GCGGTGTCCCAGC--TGGACCAGGC---TGGCGAG-----AATCCA----GAGCTGGG-----G-----------AGG------------GCATT----------TTCTCT--GGCCACTACCATGCCTAGTTCATCCCCAGATACCAAAGAGC-TCCATAATT----TCTCTCCAT-TTTTCCAA-----------TGAG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 37331 393 + 132007 ----------------------TCC-TCCAGGC----CCGTTACACTGTCCCCC-C------GCCGCAC--CCCCG------ATACTTCTGGGTG---GGATAG-------------------------------------GAGCTGCCTTCA-------------TTCGTACACTCCTTCGCTGCTGGGTCCAC------GAGC-------------------------------AGGCACCCAATAG-CAC---GCACGTAAA--GGAGGAGG--TGGGGA--------TACATCAACCACGGTC----A-GAACTGT-AAAAG-------------CAACTTGTACACATCACAGAATAA-AGGAGCCTC-----GGGCCATG-GTTG---GGGG-GGGAG--------GGG--GCTCT-------GGAAAGAAGTCTGCA-----------AGGGAGAG--ACAG-GCCTGAGCTCTATACCAGGC---TGGCAAG-----GATCCA----CAACTGGG--------------------------------ATACAATTTTTTTTTTTTTCT--GGCTGCTGCCATATCTTGTATAT-CCCAGATAGCAAAGAGC-TCTATCATT----TCTCTCCTT-TTCTCCCA-----------CAAG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59443589 379 - 64418924 ----------------------TCC-TCTAGGC----CCCATATACGCCCCCCCTC------ACCCCACCACCCTG------ACGCGTCTGAGTG---GGATAG-------------------------------------GAGGAGC--------------------------TCCCTTCACTGAT---TCCAC------AAGC-------------------------------ATACACTGAATAG-CAT---GCATGTGCA--GGAGGAGG--TGGGCA--------TAAATCAGCCAGGATC----CTTGCCCAT-AAGAGCAAGGTGCC--TCCAACCTGTACACGTCAAAGAATGA-AGGAGCCTC-----AGGTCATG-GTT----------GAAG--------GGG--GCTCT-------GGGAAGAAGTCTGC------------TGAGTGGA--ACAG-GCCTGAGCTATGTACCAGGC---TGGC-AG-----CATCCA----CAACTAGG-----G-----------CTA------------GCACA----------TATTCT--GGCCGCTGCCACATTTCATGTATCCCCAGATATCAAAGAGC-TCCATAATT----TCTCTCCAT-TTCTCCCA-----------CAAG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 21849 374 + 48268 ----------------------TCC-GCCAAGCCAGACCCCTCTTCCTTCCCCC-G------CCACTGCCACCCTG------ACACTTTCAGGTG---GGACAG-------------------------------------GAGCTTCCTTCC-------------TGCGAACATGCCTTCACTCCTGACTCCAC------AGGC-------------------------------ATGCGGCAAACCA-CAC----TGGGTGTG--TGTGGAGG--TGGG-A--------CAGGCCCACTGGGACC----CCCGCCGTT-AGGAGCCGG---CC--TCCAACTTCCACACACCACAGAATAA-CGGGGCCTC-----GGCTTGCG-GCT----------GAGT--------CGG--GGCTG-------TCAGAGAAGGCTGT---------------------------GCCCATGG--TGGACCCGGC---TGGCGAG-----GAGCCA----GACCTGGA-----G-----------ATG------------GCACG----------TTCTTG--GGCCACTACCAT-CCCGGCTAATTCCTGGATAT----GATG-TCCACGACA----CCTCTCCA--CGCTCTGA-----------GGAG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14441133 353 - 17734757 CCTTTCCT--------------GAC-TTGCTGC----C----------TCCCTG-G------CCACCACCAGCCTC------A----------------------------------------------------------CGGCCTG----A-----------------------------CATTTTATCCCAC------AAGCACC-------------------------------AGTCAGGTGC-TGTCCTGCGTGGACA--GGGGCAGG--TGGGGA--------TGAACCAACCAAGATC----CCTGCCCCTAAAAAGCCAGACACT--GCCACCTCCTACAAATCACAGAAGGGAAGGAGTCTT-----AAGTCATG-GCTGAATTGGG-AGGTG--------GGGGTGGGTG-------TCAAACAGGGCTACA-----------GGGTAGAA--TCAG--------------------CCCCAGAGCTG-----GGCCAG----GCTGGAAG-----G-----------ATC-----------------------------CTCT--GACCACTGCTTTGTGTAACTCATCCCCAGATATGGAAGGGG-TTGGGTTGTCTCCCCTCTAGGT-TTCACCCA-----------TGAG i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_56828 456 485 + 1587 ctgctccgagggacagagatgagac-tttctgc----t----------cccata-a------agagcttcagcctc------agacacccaaggg---gggcagctctactctgtcctacagggtcacaatgagtcagaatgggcctg----gtggcagtgAGGCCCCTGCTTCCCTGTCTCCTTGACCTCCCCC------AGGCTCCCCACTCAGACCCCTTACTTCCAAATAGGCTTAACCAGGTGT-TAGCCTGCCTCAATATTAGGGGAGG--CAGGGG--------CACACCAG-TGAGACCCACACACACCCCTAAAGAGCCAGGCACTCCCCCACCTCAAGCCCATCTCAGGAGAG-AGGACTCTG-----CAGCCA---------------AGATG--------GAG--------------------ACCCCTTCC-----------AGGTGGGG--TCAG--------------------CCACAGGGCTGGACTTGGCTGG----GCTGGAAG-----G-----------ATCCAGAAGTGTGATGC-TC----------CTCTCT--GGCCACTGCCTTACCTAAGCCACCCCCAGGTACCAGAAGGC-TGGGTGATCCTCCCCTCCCCCT-TCCAGTCA-----------TCAG i echTel1.scaffold_56828 C 0 C 0 e ochPri2.scaffold_9426 10541 484 - 54875 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e choHof1.scaffold_149147 3142 1766 + 9388 I e micMur1.scaffold_72647 4992 0 + 4992 I e eriEur1.scaffold_125414 877 0 - 877 I e macEug1.Scaffold385251 990 0 + 1704 I e monDom5.chr2 304551395 4976 - 541556283 I a score=298917.000000 s hg19.chr17_gl000204_random 53799 73 + 81310 CCATCAGCCACGCTCCAAGTTGAGTAAGT-GACAGGCGCAGGACAGAAGGCC-----CACT--------CTGGAATGGTACCCA----GGA s panTro2.chr17 79483991 73 + 83384210 CCATCAGCCACGCTCCAAGTTGAGTAAGT-GACAGGCGCAGGACAGAAGGCC-----CACT--------CTGGAATGGTACCCA----GGA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 22176 73 - 64270 CCATCAGCCATGCTCCAAGTTGAGTAAGT-GACAGGCGCAGGACAGAAGGCC-----CACT--------CTGGAATGGTACCCA----GGA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16071160 73 + 17838096 CCATCAGCCACGCTCCAAGTTGAGTAAGT-GACAGGCGCAGGACAGAAGGCC-----CACT--------CTGGAATGGTACCCA----GGA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75045061 73 + 78773432 CCATCAGCCACGCTCCAAGTTGAGTAAGT-GACAGGCACAGGACAGAAGGCC-----CACT--------CTGGAATGGTACCCA----GGA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 52248 73 - 95547 CCATCAGCCATGCTCCAAGTTGAGTAAGT-GACAGGCACAGGACAGAAGGCC-----CACT--------CTGGAATGGTACCCA----GGA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 54641 71 + 225949 CCATCA--CATGCTCCAAGTTGAGTAAGT-GACAGGCACAGGACAGAAGGCA-----CACT--------CTGGAATGGCACCCA----GGA i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118767836 49 + 121843856 -----------CTCTTGCGT----------GGCTGCCACAAGACCACACACT-----------------GGGGAATGATGCCCA----AGA i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 4837 72 + 11404 ----------CGGCCTGCGTCGAGGGATTGGGGGGCTAGGGGACGAAGGGCTT------TTGAGGGAGGAGGGAGTGGTACCCA---CAGG i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4396970 60 + 7991924 -----------ATTCAGGGTTGAGAGT---GGCAGGAGCAGGACAGAAGGCCTGCTTCCTC-------------ATGGGACCCA----GGA i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 14163 50 + 44242 -------------------ATGAGGA----GGTGGCAGGCAGACAGAAGGCC-----CTTT--------CCAGAGTGGTACCCA-----GG i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 25866 51 + 41507 ----------TGCTCAGGGCTGAGGG----AGCCGCAG--GGAC--CAGACC----------------------GTGGAACCTGCCCCGGA i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 136151 73 + 145505 CCATTGGTAATGCTCAAAGTTTAGTAAGT-GGCAGGAACATAACATAAGGTC-----CACT--------CTGGAATAGTACCCA----GGA i turTru1.scaffold_106006 C 0 I 11 s bosTau4.chr19 10866195 72 - 65312493 CCGTTGGTAGAGCTCAAAGCTTAGCAAGT-AGCAGGAACATAACA-GAGGCC-----CACT--------CTAGAGTGGTACCCA----AGA i bosTau4.chr19 C 0 I 11 s equCab2.chr11 58050114 73 - 61308211 CGATCGGCAATGCTCAAAGTCGAGGAAGT-GGCAGGAACGCGACAGAAGGCC-----CATT--------CTGGGACCGCACCCA----GCA i equCab2.chr11 C 0 I 11 s felCat3.scaffold_206428 37724 72 + 132007 CCATTGGCAACGCTTCAAGTTGAGTAAGT-GGCAGGAACACCACAGAA-GCC-----CACT--------CTGGAATGGCACCCA----GGA i felCat3.scaffold_206428 C 0 I 7125 s canFam2.chr9 59443968 73 - 64418924 CCGTTGGCAAGGCTCAAAGTTAAAGAAGT-GGCAGGAACACCACAGAAGGCC-----CACT--------CTGGAATGGCACCCA----GGA i canFam2.chr9 C 0 I 11 s pteVam1.scaffold_11245 22223 72 + 48268 CCATCGCCAGTGCTCGGGGCTGAGGAGCT-GGCA-GAACATGACTGAAGGTC-----CGCT--------CTGGAACAGTATCTA----TCC i pteVam1.scaffold_11245 C 0 I 4 s loxAfr3.scaffold_49 14441486 72 - 17734757 TCATTAGAGGGGCTGAAAGTTAAGTAGGT-GGCAGGAAGCCGACA-GACACC-----CACT--------CTGGAATAGTACCCC----GGA i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_56828 941 46 + 1587 CCAT-------GCT---------GTCAGT-GGTAGGAA-TGGGCA-CAGGTC-----CCTT--------CCG---------CCT----GGA i echTel1.scaffold_56828 C 0 C 0 e ochPri2.scaffold_9426 10541 484 - 54875 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e choHof1.scaffold_149147 3142 1766 + 9388 I e micMur1.scaffold_72647 4992 0 + 4992 I e eriEur1.scaffold_125414 877 0 - 877 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304551395 4976 - 541556283 I a score=143024.000000 s hg19.chr17_gl000204_random 53872 24 + 81310 GGCCTCCTTGCTGTAATTACCTCT s panTro2.chr17 79484064 24 + 83384210 GGCCTCCTTGCTGTAATTACCTCT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 22249 24 - 64270 GGCCTCCTTGCTGTAATTACCTCT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16071233 24 + 17838096 GGCCTCCTTGCTGTAATTACCTCT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75045134 24 + 78773432 GGCCTCCTTGCTGTAATTACCTCT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 52321 24 - 95547 GGCCTCCTTGCTGTAATTACCTCT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 54712 24 + 225949 GGCCTCCTGGCTGTAATTACCTCT i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118767885 24 + 121843856 GACCTCCTTACTGTAATTACCTCT i mm9.chr11 C 0 I 1 s dipOrd1.scaffold_43980 4909 24 + 11404 GTCTCCCctgctgctgctgctgct i dipOrd1.scaffold_43980 C 0 I 280 s cavPor3.scaffold_76 4397030 24 + 7991924 GACCTCCTCGCTGTAATTACCTTT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 14213 24 + 44242 CACCTCCTGGATGCAATTATGTCT i speTri1.scaffold_128901 C 0 I 1 s oryCun2.chrUn0958 25917 24 + 41507 GGCCTCCTTGCAGTGGTCACCTGC i oryCun2.chrUn0958 C 0 I 5 s turTru1.scaffold_106006 136235 24 + 145505 TGCCTCCTTCTTAAATCTGCCTCT i turTru1.scaffold_106006 I 11 C 0 s bosTau4.chr19 10866278 24 - 65312493 TGCCTCCTTCCTAAATCTGCCTCT i bosTau4.chr19 I 11 C 0 s equCab2.chr11 58050198 24 - 61308211 GGCCTCCCTCCTGATTCTGCCTCT i equCab2.chr11 I 11 C 0 s canFam2.chr9 59444052 24 - 64418924 TGCTTCCTTCCTAAATTTGCCTCT i canFam2.chr9 I 11 C 0 s pteVam1.scaffold_11245 22299 18 + 48268 GTCTTCCCACC------AGCCTGT i pteVam1.scaffold_11245 I 4 C 0 s loxAfr3.scaffold_49 14441558 19 - 17734757 GTCCCACCTCC-----CTGCCTCC i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_56828 987 19 + 1587 GTCCCACGTCT-----CTGCTTCT i echTel1.scaffold_56828 C 0 C 0 e ochPri2.scaffold_9426 10541 484 - 54875 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e choHof1.scaffold_149147 3142 1766 + 9388 I e micMur1.scaffold_72647 4992 0 + 4992 I e felCat3.scaffold_206428 37796 7125 + 132007 I e eriEur1.scaffold_125414 877 0 - 877 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304551395 4976 - 541556283 I a score=270056.000000 s hg19.chr17_gl000204_random 53896 103 + 81310 TCGCAGGCCCTGG-----GCTTTTCTGGCTCTTGAATGAGCCTCGGGAGCCCTCCCCATGT-------------CCTC--AGCAGCCTGAGGGCGG--------CCGCC------CGCAGCGCCTCCAGCGGCCCTG s panTro2.chr17 79484088 103 + 83384210 TCGCAGGCCCTGG-----GCTTTTCTGGCTCTTGAATGAGCCTCGGGAGCCCTCCCCATGT-------------CCTC--AGCAGCCTGAGGGCGG--------CCGCC------CGCAGCGCCTCCAGCGGCCCTG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 22273 103 - 64270 TCGCAGGCCCTGG-----GCTTTTCTGGCTCTTGAATGAGCCTCGGGAGCCCTCCCCATAT-------------CCTC--AGCAGCCTGAGGGCGG--------CCGCC------CGCAGCGCCTCCAGCGGCCCTG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16071257 102 + 17838096 TCGCAGGCCCTGC-----GCTTTTCTGGCTCTTGAATGAGCCTCGGGAGCCCTCCCCATGT-------------CCTC--AGCAGCCTGAGGGCGG---------GGCC------CGCAGAGCCTCCAGCGGCCCTG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75045158 102 + 78773432 TCGCAGGCCCTGG-----GCTTTTCTGGCTCTTGAATGAGCCT-GGGAGCCCTCCCCATGT-------------CCTC--AGCAGCCTGAGGGCCG--------GTGCC------CGCAGCGCCTCCAGCGGCCCTG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 52345 102 - 95547 TCGCAGGCCCTGG-----GCTTTTCTGGCTCTTGAATGAGCCT-GGGAGCCCTCCCCATGT-------------CCTC--AGCAGCCTGAGGGCCG--------GTGCC------CGCAGCGCCTCCAGCGGCCCTG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 54736 103 + 225949 TAGAAGACCCTGT-----GCTTTGCTGGCTCTTGAATGAGCCTCGGGAGCCCTCCCCAAGT-------------CTTC--AGCAGCCTGAGGGCAG--------GTGCC------CCCAGCGCCTCTAGCGGCCCCA i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118767910 105 + 121843856 CT-CTGG-CCTGG-----ACCTCCCTGACCCTGT---TGGCAT-GGGGACTCCTCCTGTAC-------------CTTCCAAGCAGGATGAAGACTA-AT---AAGCCCCGGAT--CTCAGTGTCCACA--GGACACA i mm9.chr11 I 1 C 0 s cavPor3.scaffold_76 4397054 61 + 7991924 CTGCTGG-CCCTG-----GGCTGCCTGCCTCTGG---------------------CTGTAC-------------CTCC--AGC---------------------GCCCTG-----CCCTTCCCCCAC--------CA i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 14238 102 + 44242 CC-CGAG-ACTGG-----GGTTTCCTGGCTCTGA-ACCGGCCT-CGGAGCTTC--CCCCTC-------------CCCC--AGCAGGGTGAGGGCAACATCTGACACCCC------CACACTATCCGA---GGTTCCA i speTri1.scaffold_128901 I 1 C 0 s oryCun2.chrUn0958 25946 82 + 41507 CCGCTGGCCCTGG-----GCCTCCCTGGCGCGGAGGGCGCCCC-GGGAGC-----CCTCGC-------------CTTC-------------------------CTCCCC------CGCAGCGCCCCCAGCGGCCCCA i oryCun2.chrUn0958 I 5 C 0 s turTru1.scaffold_106006 136259 71 + 145505 TTGCTGGCCTCGG-----GCT--------------------------AACCCTT-----CC-------------CCCC--AGCAGGGTGAGG-TGA--------GCCAC------AGCAGCGCCCCCAGCGGCCCCA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10866302 78 - 65312493 TGGCTGGCATTGG-----GTT--------------------------AACCCTTC----CC-------------CCCC--AGCAGGGTGAAG-AGA--------GCCACCGCCGAGGCAGCGCCCCCAGCGGCCCCA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58050222 102 - 61308211 TCGCTGGCTCTGG-----GCCCCCCTAGCTCTGC-ATGGGCCTCAGGAGCCCTTTCCTTCC-------------TCCA--AGCAGGATGAGGGAGA--------GCGCC------CGCAGCGCCCCCAGCGGCCCCA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59444076 102 - 64418924 TCACTGGCCCTGG-----GCTCCCCTGGCTCTGC-GTGCACCTCAGCAGCCCTCCCCTTCC-------------CCCT--AGCAGGGTGAGGGCGA--------GCGCC------GGCAGCGCCCCCAGCGGCCCCA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 22317 99 + 48268 CTGCTGGCCCTGG-----GCACCCCAG--CGGGC-ATGGGCCTGGGGAACCCTTCCCTTCC-------------CCC---AGCAGGTTGAGGCCAG--------GCCCC------GACAGCGCCCCCAGCAGCCCCA i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14441577 100 - 17734757 -TCCTGGCCCTGG-----GCCTCCCTGGCTCTGA-AAGGACTCCAGGAGCCATCCCCTTCC-------------CCTC---TCAGGGTAACAGCGA--------GTGCC------CACAGCGCCCCCAGCGGCCCCA i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_56828 1006 117 + 1587 -TTCTGTCCCCCGCGCCCACCCCACACACCCCCA-ACTACCACCACCA-CCACCCACCTCCCTCGTGGTCCTCTCCTC---TCAGTGTGAGAGCAA--------GCGCC------CGCAGCGCCCCCAGCGGCCCTG i echTel1.scaffold_56828 C 0 C 0 e ochPri2.scaffold_9426 10541 484 - 54875 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e choHof1.scaffold_149147 3142 1766 + 9388 I e micMur1.scaffold_72647 4992 0 + 4992 I e felCat3.scaffold_206428 37796 7125 + 132007 I e eriEur1.scaffold_125414 877 0 - 877 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 4933 280 + 11404 I e monDom5.chr2 304551395 4976 - 541556283 I a score=523825.000000 s hg19.chr17_gl000204_random 53999 189 + 81310 GGACCGTGTCAGAGGAGG----GAGGGCGAGG----AGGGCAGGCTGTGGAGG----CCCCGGCCCTGTCCTTGGTGCTGGCGCCCGCT-----------GAGT----GCCTGCTGAGCCACTCAGAGGCA-GGGGCCGCCCATG----CCGCC------------ACCTTCCCTC-GACATCCGC----CTCTGGT-CCCTGCGGAAGGGCAGTGAATACTCCCA-GCCCCGCTGTGGC s calJac1.Contig5139 54839 189 + 225949 AGACCTTGTCAGAGGAGG----GAGGGTGATG----AGGGCAGGCGGTGGAGC----CCCCAGCCCTGTCCTCAGTGCTGGTGCCCGCC-----------GTGA----GCCCGCTGAGCCACTCAGAGGCA-GGGGTAACCCATG----CCGCC------------ACCTTCCCTC-CAGCCCAGC----TTCTGGT-CCCTGCGGAAATGTAGTGAATACTCCCA-GCCCTGCTGTGGC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 52447 190 - 95547 GGACCATGT-AGAGGAGG----GAGGACGAGG----AGGGCAAGTTGTGGAGG----CCTCGGCCCTGTCCTTGGTGCTGGCGCCCGCT-----------AAGT----GCCTGCTGAGCCACT--GAGGCA-GGGGCCGCCCATGCCGCCCGCC------------ACCTTCCCTC-CAGCTCAGC----CTCTAGT-CCCTGCCGAAGGGCAGTCAATACTCCCA-GCCCCACTGTGGC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75045260 186 + 78773432 GGACCATGT-AGAGGAGG----GAAGACGAGG----AGGGCAAGTTGTGGAGG----CCTCGGCCCTGTCCTTGGTGCTGGCGCCCGCT-----------AAGT----GCCTGCTGAGCCACT--GAGGCA-GGGGCCGCCCATG----CTGCC------------ACCTTCCCTC-CAGCTCAGC----CTCTAGT-CCCTGCCGAAGGGCAGTCAATACTCCCA-GCCCCACTGTGGC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16071359 189 + 17838096 GGACCGTGTCAGAGGAGG----GAGGGCGAGG----AGGGCAGGCTGTGGAGG----CACTGGCCCTGTCCTTGGTGCTGGCGCCCTCT-----------GAGT----GCCTGCAGAGCCACTCAGAGGCA-GGGGCCGCCTATG----CCGCC------------ACCTTCCTTC-AACATCCGC----CTCTGGT-CCCTGCGGAAGGGCAGTGAATACTCCTA-GCCCCGCTGCGGC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 22376 189 - 64270 GGACCNTGTCAGAGGAGG----GAGGGCGAGG----AGGGCAGGCTGTGGAGG----CCCCGGCCCTGTCCTTGGTGCTGGCGCCCGCT-----------GAGT----GCCTGCTGAGCCACTCAGAGGCA-GGGGCCGCCCAAG----CCGCC------------ACCTTCCCTC-GACATCCGC----CTCTGGT-CCCTGCGGAAGGGCAGTGAATACTCCCA-GCCCCGCTGTGGC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79484191 189 + 83384210 GGACCGTGTCAGAGGAGG----GAGGGCGAGG----AGGGCAGGCTGTGGAGG----CCCCGGCCCTGTCCTTGGTGCTGGCGCCCGCT-----------GAGT----GCCTGCTGAGCCACTCAGAGGCA-GGGGCCGCCCATG----CCGCC------------ACCTTCCCTC-GACATCCGC----CTCTGGT-CCCTGCGGAAGGGCAGTGAATACTCCCA-GCCCCGCTGTGGC i panTro2.chr17 C 0 C 0 s tupBel1.scaffold_124460.1-4080 2 141 + 4080 GGACCGCGGCAGAGGCGA----GCGGCTG--G----GGGGCAGGGTGCGCA-------CCCGGCCCTGTCCTTGGTGCTGACGCCCGCT-----------GCGC----------------------------AGGCCTGCCCAGG----CTGC--------------------------------C----CTCTGGT-CCGTGCAGAAGGGCACCTAGTAC-CAGG-GCCCCACTGCAGC i tupBel1.scaffold_124460.1-4080 N 0 C 0 s mm9.chr11 118768015 166 + 121843856 -----------AGACAGGCAGAGGTGGCAGAA----GAGTGAAACGCTGCAGCTCGGCCCTAGCCCTGTCCTTGGTGCTGCCGCCCTCT-----------GTGC---------------GGCTGCGTGGCA-GGT--------------CAGC---------------CTTTGCTC-CTGACCAGCGTCTGTCTGGT-CCCTGCTGAAGGGCAGTAAATTCACCCA-GGCCTGCTGCGGC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4397115 143 + 7991924 -----------GGACAAG-------------A----GTTTAGGTCTCTGGAGCGCGCTCCTGGCCCTGTCCTTGGTGCTG--GCCGACT-----------GCGC----------------GCCAAGTGGCA-GGC--------------CCGT---------------CTTT-TTC-CAGCCTGGC----CTCTGGT-CTCTGTAGAAGGACAGTGAAG--ACAGG-AGCCCGCGACCGC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 14340 155 + 44242 -----------GGGGAGG----GTTGGCGGGA------------------AGCGCG-CCCAGGCCCTGTCCTTGGTGCTGCCGCCCGCT-----------GTGCTCCCGCCAGCT--ATGCCAAGGCGGCA-GGA--------------GCCG---------------CTTCCTTC-CAATCCGGC----CTCTGGT-CCCTGTGGAAGGGCAGTAAAC--ACTGTCAGCCCCGTGTGGC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 26028 95 + 41507 -----------GGACCGT--------GCGGGA----------GGCGCCGGGGTCGGCCCCCAGCCCTGG-CTGACTGCTGCCGCCC-CC-----------GCCC------------------------GAG-GGT--------------CCGC---------------CATC-------------C-----------------------------------GCCGG-GCCCCGCCGCGGC i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 136330 175 + 145505 GGACAATGTCAAAGGC------GAGAGT--GG-GCCAGGGCAGGCTGCGCG------CCCTGGCCCTGTCCTTGGTGCTGCCGCCAGCT-----------GCAC----------------CCCCTGTGGCAGGGGGCCTACCAGG----ACGCA------------GCCTTCCCTC-CAGCCCAGC----CTCTGGT-CCCTGCGGAAGGGCCATGAATACACCCG-GATCAGCTGCAAC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10866380 176 - 65312493 GGACAACCTCCTCAGG------GAGGAT--GGCACCAGAGCAGGCTGCGGG------CCCTGGCCCTGTCCTTGGTGCTGCCGCCAGCT-----------GCGC----------------CCCCTGTGGCA-GGGGCCGTCCAGG----ACTCA------------GCCTTCCGTC-CCGCCTGGC----CTCTGGGACCCTGCGGAAAGGCCATGAATACACCCG-GACCAGCTTCGAC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58050324 184 - 61308211 GGACAATGTCAGAGGCGG----GAGGGCG-GG----AGCGCAGGCTGCGCGC-----CCCTGGCCCTGTCCTTGGTGCTgccgccggctgcgggcccgctgcgc----------------ccccggtggcagggggccgcccagg----ccgcc------------gccTTCCCTC-CAGCCCGAC----CTCTGCT-CCCTGCGGAAGGGCAGTGCACACACCCG-GCT---CTGTGGC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59444178 198 - 64418924 GTACAATGTCGGAGGCGG----GAGGGC--GG----AGCGCGGGCAGCGCGC-----CCCTGGCCCTGTCCTTGGTGCTGCTCCGGGCTGCCCGCTCAAGGAGC----------------CCTAGGTGGCAGGGGGCCGCCCAGG----CCGCCgccttccctccagccttccctc-cagcctGGC----CTCTGGC-CCTTGCTGAAGGGCAGTGAGCACACCCA-GCTCTGCTGCTGC i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 22416 117 + 48268 GGACAAGGTAGGAGGC------AAGGGC-------------AGGCTGCACAC-----CCCGGGCCCTGTCCTTGGTGCTGCT------------------GCGC----------------CC----------------------G----CTGCA------------CCCTTCCCTC-C--CCCGCC----CCCTCCC-ACCTCCA------------------CCG-GCTCTGCTAAGGC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14441677 179 - 17734757 GGATGGTGTCAGAGGCTG----GGGGATG-AG----AGCGCAGGCTGGGG-------CCCTGGCCCTGTCCTTGGTGCTGCCAGCTGCC-----------GCGC----CCCTGCTGCACCGCCCCAGGGCAAGGGCCCA--CCGG----CCGCG------------TCCTTTTCACGCTCCCTGGC----ATCGGGT-GCCTGCAGAAGGGTAGTGAATACATCCA-GCCTATC------ i loxAfr3.scaffold_49 C 0 C 0 s echTel1.scaffold_56828 1123 186 + 1587 GACTGG-GTCAGAGGCTG----GAGGGCG-GG----CGCTCAAGCTGCGC-------CTCTGGCCCTGTCCTTGGTGCTGCCCGCGGCC-----------GCGC----GCCCTCTGTGCTGCCCAGAGGCCAGGGCCCACCCCGG----CCCCC------------GCCGCCTCCAGCCGCCCTAT----TCAGGGT-CCCTGCGGAAGGGCTGTGAGTACACCGG-GCCCCGCTGCAGC i echTel1.scaffold_56828 C 0 N 0 e ochPri2.scaffold_9426 10541 484 - 54875 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e choHof1.scaffold_149147 3142 1766 + 9388 I e micMur1.scaffold_72647 4992 0 + 4992 I e felCat3.scaffold_206428 37796 7125 + 132007 I e eriEur1.scaffold_125414 877 0 - 877 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 4933 280 + 11404 I e monDom5.chr2 304551395 4976 - 541556283 I a score=231558.000000 s hg19.chr17_gl000204_random 54188 69 + 81310 TCCCAACCGAGGTCACTGGGT----GCGGAGCATTTGCCGC------AAAGG-CCCATCCGAGTAAGGGGCGGAGCCTAG s calJac1.Contig5139 55028 70 + 225949 TCCCGAGCTAGGTCCCGGTGT----ATAGAGCATCTGCAGC------AAAGGCCCCATCTGAGAAAGGGGCTGAGCCTCG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 52637 69 - 95547 TCCCGACCGAGGTCACTGGGT----GAGGAGCGTTTGCAGC------AAAGG-CCCATCCGAGTAAGGGGCGGAGCCTAG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75045446 69 + 78773432 TCCCGACCGAGGTCACTGGGT----GAGGAGCGTTTGCAGC------AAAGG-CCCATCCGAGTAAGGGGCGGAGCCTAG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16071548 69 + 17838096 TCCCCACCGAGGTCACTGGGT----GCGGAGCATTTGCAGC------AAAGG-CCCATCCGAGTAAGGGGCGGAGCCTAG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 22565 69 - 64270 TCCCAACCGAGGTCACTGGGA----GCGGAGCATTTGCCGC------AAAGG-CCCATCCGAGTAAGGGGCGGAGCCTAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79484380 69 + 83384210 TCCCAACCGAGGTCACTGGGT----GCGGAGCATTTGCCGC------AAAGG-CCCATCCGAGTAAGGGGCGGAGCCTAG i panTro2.chr17 C 0 C 0 s tupBel1.scaffold_124460.1-4080 143 56 + 4080 T-CTGCCCGAGGTCACTGGGC----GAGGAGTGTTTACAGC------GAAGG-CCCATCCCGGTGAG------------G i tupBel1.scaffold_124460.1-4080 C 0 C 0 s mm9.chr11 118768181 67 + 121843856 T-CTGCCTGAGGTCGT-----------GGAGCCTTTGCAGCGAAGGTGAAGG-CACAGCATTGCTAGAGGCCCGATCTAT i mm9.chr11 C 0 I 2 s cavPor3.scaffold_76 4397258 66 + 7991924 T-CTACCCTAGGTCATCGCAC------AGCGCGTTAGCAGC------GAGGG-CTCAGCAGCGTCGGAGCCAGAGCCTAA i cavPor3.scaffold_76 C 0 I 2 s speTri1.scaffold_128901 14495 71 + 44242 T-CTGTCGGAGGCCACTGAAT----GAGGAGTGTTTGCAGCGCG---GACGG-TGCAGCGCCGTCAGAGACCGATCCTAA i speTri1.scaffold_128901 C 0 I 2 s oryCun2.chrUn0958 26123 58 + 41507 T-CCAGCGGCGCTCACTGGGCCGGCGGGGAGCGCTGGAGGC------CAAGG-CCCAGCGAAGTGA-------------- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 136505 68 + 145505 TCCTATCCCAGGGCACTGGAC----CAGAGGCATTTGCAGT------GAAGG-CCCAGCATAGTCAGA-GCCTGGCCTGC i turTru1.scaffold_106006 C 0 I 2 s bosTau4.chr19 10866556 68 - 65312493 TCCTTTCCCAGGGCACTGGAC----AGGAGACATTTTCAAT------GAAGG-CCCAGCATAGCCAGA-TCCTGGCCTAT i bosTau4.chr19 C 0 I 2 s equCab2.chr11 58050508 69 - 61308211 TTCTGTCCGAGGGCGCTGAAC----GACGGACGTTTGCAAC------GAAGG-CCCAGCATAGTGAGAGGCTGGGCCTGC i equCab2.chr11 C 0 I 2 s canFam2.chr9 59444376 57 - 64418924 TCCTGTTGGAGGGCACTGGGC----GAGGGGCATTCAGAAT------G-------------AGCCAGAGGCCAGGCTGGG i canFam2.chr9 C 0 I 2 s pteVam1.scaffold_11245 22533 59 + 48268 TCCCGTCCCAGGGCGCTGGGC----GAGCGGCATTTGCAAC------GAA-----------GGCCAGGGGCCAGGGCTGC i pteVam1.scaffold_11245 C 0 I 2 s loxAfr3.scaffold_49 14441856 62 - 17734757 -------CCTCGGCAGGGGAC----AAGTGTCATTTGCAGC------GAAGT-CCCAGCACAATCAGAGACCGGGTGTGG i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 10541 484 - 54875 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e choHof1.scaffold_149147 3142 1766 + 9388 I e micMur1.scaffold_72647 4992 0 + 4992 I e felCat3.scaffold_206428 37796 7125 + 132007 I e eriEur1.scaffold_125414 877 0 - 877 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 4933 280 + 11404 I e monDom5.chr2 304551395 4976 - 541556283 I a score=220927.000000 s hg19.chr17_gl000204_random 54257 40 + 81310 GGACT-----------TCCCTGGACTCCTGGCTCCTCC---TGGCACCCAGAGG s calJac1.Contig5139 55098 40 + 225949 GGACT-----------TCCCTGGACTCCTGGCTCTTCC---TGGCAACCCGAGG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 52706 40 - 95547 GGACT-----------TCCCTGGACTCCTGGCTCCTCC---TGGCAACCCGAGG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75045515 40 + 78773432 GGACT-----------TCCCTGGACTCCTGGCTCCTCC---TGGCAACCCGAGG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16071617 40 + 17838096 GGACT-----------TCCCTGGACTCCTGGCTCCTCC---TGGCAACCAGAGG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 22634 40 - 64270 GGACT-----------TCCCTGGACTCCTGGCTCCTCC---TGGCAACCAGAGG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79484449 40 + 83384210 GGACT-----------TCCCTGGACTCCTGGCTCCTCC---TGGCACCCAGAGG i panTro2.chr17 C 0 C 0 s tupBel1.scaffold_124460.1-4080 199 39 + 4080 GAACT-----------TCCCTGGACGCCT-GCTCCCCC---TGGCGACTTGAGG i tupBel1.scaffold_124460.1-4080 C 0 C 0 s mm9.chr11 118768250 33 + 121843856 GGACT-----------TTCCTAGACTCTGGGCTCTTCC---TATAGA------- i mm9.chr11 I 2 C 0 s dipOrd1.scaffold_43980 5213 40 + 11404 NGACT-----------TTCCCAGACTGCGGGTCCCTCC---TGGAGACCTGCGG i dipOrd1.scaffold_43980 I 280 C 0 s cavPor3.scaffold_76 4397326 39 + 7991924 GGTCT-----------TTCCCGGACTCTGGGTTTCTCC----AGAGGCCCCTGA i cavPor3.scaffold_76 I 2 C 0 s speTri1.scaffold_128901 14568 40 + 44242 GGACT-----------TTTCTGAATTCTGGATTCCTCC---TGGCGACCTGAGG i speTri1.scaffold_128901 I 2 C 0 s oryCun2.chrUn0958 26181 30 + 41507 ---------------------GGACCCCCAGCTCCTGC---AGGCGACCCACCG i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 136575 39 + 145505 GGACT-----------TTCCTGGACTCC-AGCTTCTCC---AGGTGACCTGAGG i turTru1.scaffold_106006 I 2 C 0 s bosTau4.chr19 10866626 39 - 65312493 GGACT-----------TTCCTGGACTCC-AGCTTCCCC---AGGTGACCTGAGG i bosTau4.chr19 I 2 C 0 s equCab2.chr11 58050579 40 - 61308211 GGACA-----------TTCCTAGACTCCCCGCTTCTCT---GCGCGACCTGAGG i equCab2.chr11 I 2 C 0 s canFam2.chr9 59444435 51 - 64418924 GGGAAGGGGAGGGGGCTTCCGAGATTCCCAGCTTCTCC---CAGCATCCTAAGA i canFam2.chr9 I 2 C 0 s pteVam1.scaffold_11245 22594 42 + 48268 GGACT-----------TTCCTGGACTCCTGGCTACTCTG-GGGGAGACCTAGGG i pteVam1.scaffold_11245 I 2 I 2 s loxAfr3.scaffold_49 14441918 16 - 17734757 --------------------------------------AAGGGACGACCTGAGA i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 10541 484 - 54875 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e choHof1.scaffold_149147 3142 1766 + 9388 I e micMur1.scaffold_72647 4992 0 + 4992 I e felCat3.scaffold_206428 37796 7125 + 132007 I e eriEur1.scaffold_125414 877 0 - 877 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304551395 4976 - 541556283 I a score=68476.000000 s hg19.chr17_gl000204_random 54297 30 + 81310 CGACCCGAGGTCCCCGG--GGTGGGCACGGGT s calJac1.Contig5139 55138 30 + 225949 TGACCTGAGGTCCCTGG--CGTGGGCACGGGT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 52746 30 - 95547 CGACCCGAGGTCCCCGG--GCTGGGCACGGGT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75045555 30 + 78773432 CGACCCGAGGTCCCCGG--GCTGGGCACGGGT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16071657 30 + 17838096 CGACCCGAGGTCCCCGG--GGTGGGCACAGGT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 22674 30 - 64270 CGACCCGAGGTCCCCGG--GGTGGGCACGGGT i gorGor1.Supercontig_0007361 C 0 M 2602 s panTro2.chr17 79484489 30 + 83384210 CGACCCGAGGTCCCCGG--GGTGGGCACGGGT i panTro2.chr17 C 0 C 0 s tupBel1.scaffold_124460.1-4080 238 30 + 4080 CTACCGAAACCCCAGGA--GATGGCCATGCGT i tupBel1.scaffold_124460.1-4080 C 0 C 0 s mm9.chr11 118768283 16 + 121843856 ---CCCAAGACTAT-------------CTGGT i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 5253 18 + 11404 GGCCCCAGGTCCCT-------------CTGG- i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4397365 14 + 7991924 GGCCGCAGGGTCCC------------------ i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 14608 29 + 44242 CGACCCAAGGCCCA-GG--GTTAGACACAGGT i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 26211 16 + 41507 ---CCCGGGGCGGA-------------CCGGA i oryCun2.chrUn0958 C 0 C 0 s pteVam1.scaffold_11245 22638 29 + 48268 CCCCCCGAGGCCTGCGG--GGTAGACACAGG- i pteVam1.scaffold_11245 I 2 C 0 s canFam2.chr9 59444486 31 - 64418924 CAACATAAGGCCCA-GGGAGGTGGACAGAGGT i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 44921 29 + 132007 CAACCCAAGGCCCA-GG--AGTGAATGGAGGT i felCat3.scaffold_206428 I 7125 C 0 s equCab2.chr11 58050619 29 - 61308211 CGACCCAAAGCCCG-GG--GGTGGACGCAGGT i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10866665 29 - 65312493 CTACCCAAGGCCCA-AG--GATGGACTCAGTT i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 136614 29 + 145505 CTACCCGAGGCCCA-AG--TGTGGACACAGGT i turTru1.scaffold_106006 C 0 C 0 s loxAfr3.scaffold_49 14441934 28 - 17734757 GGACCAGAGGTTG--GG--GGCGGACGCACAT i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 10541 484 - 54875 I e tarSyr1.scaffold_143701 7366 1528 + 9575 M e choHof1.scaffold_149147 3142 1766 + 9388 I e micMur1.scaffold_72647 4992 0 + 4992 I e eriEur1.scaffold_125414 877 0 - 877 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304551395 4976 - 541556283 I a score=416792.000000 s hg19.chr17_gl000204_random 54327 130 + 81310 CTCTCTAGGCCCCAGGCCCCTGA-GGAAGGTGGATCAAAGCAATCACCCAGGTTCCCTTTTTT----------------CTTTGG--GGG---GAGGAG--GGTGGATAGCTG-CTAGAAATGGACA-ACTCACCCCAGAAAA--CCCCGGCCGTGCA s panTro2.chr17 79484519 130 + 83384210 CTCTCTAGGCCCCAGGCCCCTGA-GGAAGGTGGATCAAAGCAATCACCCAGGTTCCCTTTTTT----------------CTTTGG--GGG---GAGAAG--GGTGGATAGCTG-CTAGAAATGGACA-ACTCACCCCAGAAAA--CCCCAGCCGTGCA i panTro2.chr17 C 0 I 128 s ponAbe2.chr17_random 16071687 130 + 17838096 CTCTCTAGGCCCCAGGCCCCTGA-GGAAGGTGGATCAAAGCAATCACCCAGGTTCCCTTTTTT----------------CTTTTG--GGG---GAGGGG--GGTGAATAGCTG-CTAGAAATGGACA-ACTCACGCCAGAAAA--CCCCAGCCGTGCA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75045585 130 + 78773432 CTCTCTAGGCCCCAGGCACCTGA-GGAAGGTGGATCAAAGCAATCATCCAGGTTCCCTTTTTC----------------CTTTGG--GGG---GAGGGG--AGTAGATAGCTG-CTAGAAATGGACA-ACTCACGCCCGAAAA--CCCCAGCCATGCA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 52776 130 - 95547 CTCTCTAGGCCCCAGGCACCTGA-GGAAGGTGGATCAAAGCAATCATCCAGGTTCCCTTTTTC----------------CTTTGG--GGG---GAGGGG--AGTAGATAGCTG-CTAGAAATGGACA-ACTCACACCCGAAAA--CCCCAGCCATGCA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 55168 133 + 225949 CTCTCTAGACTCCAGGCCCCTAAGGGAAGGTGGATCAAAGCCATGATCCAGGTTCCCTTTTGT----------------TTGGGG--TGG---GCGGGGGAGGGGGGCAGCTG-ATAGAAATAGGCA-ACTCACGCCAGAAAA--CCTCAGCCGTGCA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 8926 116 + 9575 -TCTCTA-----TAGGCCCCTGG-GGAGGGCGGACCAGAACAATCATCTAGGTTCCCCTTTTT----------------AT---G--GGG---GAGGGG-------ATAGCTG-TTAGAAATGGGCA-ATTCGTGCCAGAAAA--TCCCAGCGGCTCC i tarSyr1.scaffold_143701 M 1528 C 0 s tupBel1.scaffold_124460.1-4080 268 113 + 4080 CTGACTAGGTCCCAGAC-CCTGA-GGGAGGGAGAGCAGAGGGGTTATCTAGGTTCTCTTTCTG----------------T----G--TGG---GAGGGA-------CTAGCT--TTGTAAATGGGCA-------GCCTGAAAA--CCCCAGGGGCTCC i tupBel1.scaffold_124460.1-4080 C 0 C 0 s mm9.chr11 118768299 120 + 121843856 TGTT--TGGGC------CTCCGA-GAAGGATGGTACAGAGTAATTGTCAGGGTTCTCTTTCAT----------------TAGTGA--GAG---TGGGAG--GGCGGGCAGACAGTTGGAAACGTTGA-TCT-ATACCAGAAAT--CCTCAG--GGCTT i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 5271 95 + 11404 --------------------AGG-GCAGGGCAGGGCAGAGCGGCCATCTGCCGTCTCTTTTCA----------------TGGTGG--AGG---AGAGAG--CTC----------CTGGAAACAAGG-------CACCAGAGAA--CCCCAGCAGCTCC i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4397379 117 + 7991924 --------------------TGG-GGAAGGTGGACCAGAGCAATTGTCTG--TTCTCCTTCTACGTCGAGGGGTGTGTGTGTTTG--GGG---TGGGGG--TGCTGTTAGAAA-CGGGAAACTCGG--------GCCAGGAAA--CCCTGGCGGCTCC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 14637 114 + 44242 CTCTCCTGGGCCCTAGTCTCTGA-GGAGGGCAATTCAGAGCCACCATCTAGGTTCTCTTTTTA----------------TAGCGG--AGG---GGAGAG--CTA----------TTAGAGACCCGCA-ACTCCTGCCAGAAAA--CCCCAG------- i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 26227 97 + 41507 CTCTGCAGGCC------CCCTGC-GGAGGGCGGGTCACAGCGGTC--------------CCCA----------------CGGTGG--ACG---GTACAG--CTG----------TTAGCACTGAGCA-ACT----CCGGAGAA--CGCCAGCTGCTTG i oryCun2.chrUn0958 C 0 C 0 s pteVam1.scaffold_11245 22667 105 + 48268 ---TCTAAGACCCTGACCCCTAG-G--GAGTGAACGGGAGCAGTGATTTAAGTGCTCCTTTTA----------------T----G--GGG---GAGGGG-------ATCACTG-TTGGA---------ACTGGTGCCAGAAA---CCCCACC--CCCA i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59444517 119 - 64418924 CTCTCTAGGCCCCAGATCCCCGG-A--GGGTGGGTCAGATAAATCGTTTAAGTCCTCTTTTCA----------------T----G--GGG---GAAGAA-------ATCGCTG-TTGGAAATGGGCA-ACTCATGCCAGCAAA--CCCCAGCGGCTCC i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 44950 126 + 132007 CTATCTAAGCCCCAGGCCTTCTG-GCCGGAGGGATCAGATAAATCATTTAAGTCATCTTTTTA----------------T----GCAGGG---AAGGGA-------ATCGCTG-TTGGAAAGGGGCGCCCTCGTGCCCAGAAAGTCCCAAACAGCTCC i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58050648 122 - 61308211 GTTTCTAGGCCCCAGGCCCCTGG-A--CGGTGGATCAGAGTAATCATTTAAGTCCTCTTTTTA----------------T----G--GGGGGTGGGGGG-------ATTGCTG-TAGGAAAAGGGCA-GCTTGTGCCAGAAAA--CCCCAGCGGCTCC i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10866694 119 - 65312493 CTCTCT-AAGCTCAGGCCCCTAG-A-GGGGGGAATCTGAGCAATCATTCGAGTCCTCTTTTAA----------------T----G--GAG---GAGGGG-------ATTGCTG-TTGGAAATGGGCA-AGTGGTGCCAAAAAA--GCCCAGCAGCTCC i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 136643 120 + 145505 CTCTCTAAAGCTCAGGCCCCTGG-A-GGGGGGAATCAGAGCAATCATTCAAGTCCTCTTTTAA----------------T----G--GAG---GAGGGA-------ATTGCTC-TTGGAAATAGGCA-ACTTGTGCCAGAAAA--CCCCAGCAGCTCC i turTru1.scaffold_106006 C 0 C 0 s loxAfr3.scaffold_49 14441962 103 - 17734757 CCCTCTGCGCCCCAGACTCCTGG-G--TTGTGAGTCAGAGC-----CCTAGGCCGACTTTTAT---------------------G--GGG---GAGGGG-------GTAGCTG-TTTGAAATGGGTA-CCTCACGCGAGAAAA--CTC---------- i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 10541 484 - 54875 I e gorGor1.Supercontig_0007361 22704 2602 - 64270 M e choHof1.scaffold_149147 3142 1766 + 9388 I e micMur1.scaffold_72647 4992 0 + 4992 I e eriEur1.scaffold_125414 877 0 - 877 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304551395 4976 - 541556283 I a score=92576.000000 s hg19.chr17_gl000204_random 54457 22 + 81310 AGCGCAAACAGCCCA-GCA------------------CCAG s tarSyr1.scaffold_143701 9042 23 + 9575 AGCGCAAACAGCTCACGAG------------------CCAC i tarSyr1.scaffold_143701 C 0 C 0 s calJac1.Contig5139 55301 22 + 225949 AGTGCAAACAGCCCA-GAA------------------CCAG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 52906 19 - 95547 ---ACAAACAGCCCA-GCA------------------CCAG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75045715 19 + 78773432 ---ACAAACAGCCCA-GCA------------------CCAG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16071817 22 + 17838096 AGCGCAAACAGCCCA-ACA------------------CCAG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0468881 9 22 + 1088 AGCGCAAACAGCCCA-GCA------------------CCAG i gorGor1.Supercontig_0468881 n 0 C 0 s tupBel1.scaffold_124460.1-4080 381 23 + 4080 AGCGCCAACAGCCCACGCA------------------CTCC i tupBel1.scaffold_124460.1-4080 C 0 C 0 s mm9.chr11 118768419 22 + 121843856 GGGGCAAACAGCCTGTATG-------------------ACC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 5366 41 + 11404 AGCTCAAACAGCCcacgcacgcacgcacgcgcacacgcacg i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4397496 23 + 7991924 AGCGCAAACAGCCCACGCG------------------CCAC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 14751 21 + 44242 --AGCAAACAGCCCACGAG------------------ACGC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 26324 23 + 41507 TGCGCCAGCAGCCCTCGGG------------------CCCC i oryCun2.chrUn0958 C 0 I 1 s pteVam1.scaffold_11245 22772 22 + 48268 AGTGCAACCAGCCCACACG-------------------CAC i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59444636 23 - 64418924 AACGCAAACAGCCTACAGG------------------CCAC i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 45076 22 + 132007 AACGCAAA-AGCCTATACA------------------CCGC i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58050770 22 - 61308211 AGCGCAAACAGCCCACA-G------------------CCAC i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10866813 23 - 65312493 AGCACAGACAGCCCACGTG------------------ACTC i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 136763 23 + 145505 AAGACAAACAGCCCACATG------------------ACCC i turTru1.scaffold_106006 C 0 C 0 s loxAfr3.scaffold_49 14442065 10 - 17734757 -----AAACAACCCA-------------------------- i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 10541 484 - 54875 I e choHof1.scaffold_149147 3142 1766 + 9388 I e micMur1.scaffold_72647 4992 0 + 4992 I e eriEur1.scaffold_125414 877 0 - 877 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e panTro2.chr17 79484649 128 + 83384210 I e monDom5.chr2 304551395 4976 - 541556283 I a score=-2225.000000 s hg19.chr17_gl000204_random 54479 72 + 81310 TGG-C-AACCCCT-------GC----CGC---ACGCAC----GCA-GCCACCTCGCC------------AGGCCCA-----GGCTGTCTCGGCTTG-----------GGTGC-GTCC----CT----TCA s tarSyr1.scaffold_143701 9065 72 + 9575 TGG-C-AAACCCT-------TT----TCC---GCGCAC----GCA-GCAGCCTCCCC------------AGGCCGT-----GGCTGTCTCGGCCCG-----------AACGC-GCCC----CT----TCG i tarSyr1.scaffold_143701 C 0 C 0 s calJac1.Contig5139 55323 78 + 225949 TGG-C-AACCCCC-------AC----CGC---GGGCAC----GCA-GCTATCTCGCC------------AGGCCCA-----GGCCTTCTCGGCTGG-----AGTGCAGGTGC-GCCC----CT----TCA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 52925 72 - 95547 TGG-C-AACCCCT-------GC----CGC---ACGCAG----GCA-GCCAACTCGCC------------AGGCCCA-----GGCTGTCTCGGCTTG-----------GGTGC-GTCC----CT----TCA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75045734 76 + 78773432 TGG-C-AACCCCT-------GCCGCACGC---ACGCAC----GCA-GCCAACTCGCC------------AGGCCCA-----GGCTGTCTCGGCTTG-----------GGTGC-GTCC----CT----TCA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16071839 72 + 17838096 TGG-C-AACCCCT-------GC----CGC---ACGCAC----GCA-GCCACCTCGCC------------AGGCCCA-----GGCTGTCTCGGCTTG-----------GGTGC-GTCC----CT----TCA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0468881 31 72 + 1088 TGG-C-AACCCCT-------GC----CGC---ACGCAC----GCA-GCCACCTCGCC------------AGGCCCA-----GGCTGTCTCGGCTTG-----------GGTGC-GTCC----CT----TCA i gorGor1.Supercontig_0468881 C 0 C 0 s tupBel1.scaffold_124460.1-4080 404 72 + 4080 TGC-CGAGCCTCT-------CC----CCC---TCCCACCACGGCA-GCTCTCTCCCC------------AGGCAGA-----AGCTGTT---GCCTG-----------AGTGT-GCCC----TC----C-- i tupBel1.scaffold_124460.1-4080 C 0 C 0 s mm9.chr11 118768441 76 + 121843856 TGG-C-CAACCCT-------CC----CCT----GGCAC----TCA-GCTGCCTCCCT---------------------------AGGAGCATCTAATGGGGTCTGATGCGCC-CCGC----TTCAGCTCT i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 5407 74 + 11404 cTG-T-CAGCCCT-------GC----CCC----GGAGC----CCA-GCTGCCTCCCTCAGC-------------CA-----GGCAGCCCCACCTCA-----------GCGTG-CCCC----CTCTGCTCC i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4397519 64 + 7991924 TAG-C-AAGCCCT-------CT----CCT----GGCAC----GCA-GTTGCCTGCTA------------------------AGCCAGACTGTCTCG-----------GCGGG-TTTT----TT----TTT i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 14772 57 + 44242 TGG-C-CATCCCT-------CC----CCT----GGCAC----GCA-GCTGCCTCCCA------------------------GGCCGAGCTGTCTTG-------------------TC----CC----TCT i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 26348 84 + 41507 -CG-C-AAGCCCT-------GG----CCT---CAGTCC----GCG-TTCGTCATCTCTGACAGCTGTCTATACTCC-----GGTGGTCCTGCTCCG-----------CTTCCAGTCT----CG----CCG i oryCun2.chrUn0958 I 1 C 0 s ochPri2.scaffold_9426 11025 81 - 54875 TGG-C-AAACTTC-------TG----CGCGAACCGCCC----GCG-GCCCCTGCGCCCAGCACC------AACCCC-----GGCCGGCCGGTCCCG-----------CCGCC-GCCT----CC----CCG i ochPri2.scaffold_9426 I 484 C 0 s pteVam1.scaffold_11245 22794 53 + 48268 TGG-C-AAACCCT-------CC----CCC---TCACAC----GCA-GCTGCCTCTCT------------G------------------------CA-----------AGTGC-GCCC----CT----CAA i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59444659 71 - 64418924 TGGCC-AGCCGT--------CC----CCC---TTACAC----ACC-GCTGCCTCACC------------AGGCCCA-----GACTGGCT-GGCCTG-----------AGTAC-GCCC----CT----GTC i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 45098 62 + 132007 TGG-C-AGACCT--------CC----CCC---TCACAC----GCA-GCTGCCTCACC------------AGGCCCA--------------GGCCTG-----------GGTGC-ACCC----CG----TTC i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58050792 78 - 61308211 TGG-C-AAACCCCCGCCCCACC----CCC---CCGCAC----GTA-GCTGATTCGCC------------AGGCCCA-----GGCCCTCT-CGGCCG-----------GGTGG-GCCC----CT----CAC i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10866836 60 - 65312493 TGG-C-AAACCCC-------TT----CCT---TGGTTT----CCA-GCTGCCTCACC------------AGGCCCC--------------------------------AAGC-ACCAGAAACT----CCA i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 136786 59 + 145505 TGG-C-AAACCCT-------CC----CCT---TCGCTG----GCA-GCTGTCTCACC------------AGGCCCA--------------------------------GTGT-ACCA-CCACT----CAG i turTru1.scaffold_106006 C 0 C 0 s loxAfr3.scaffold_49 14442075 70 - 17734757 ----------CGT-------GC----CAC---TAGCCC----ACATGCCACCTCCCA------------TCGGCCAGTGGAGCCTGTCCCGGCCTG-----------AGTGC-ACCT----CT----CAA i loxAfr3.scaffold_49 C 0 C 0 e choHof1.scaffold_149147 3142 1766 + 9388 I e micMur1.scaffold_72647 4992 0 + 4992 I e eriEur1.scaffold_125414 877 0 - 877 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e panTro2.chr17 79484649 128 + 83384210 I e monDom5.chr2 304551395 4976 - 541556283 I a score=45445.000000 s hg19.chr17_gl000204_random 54551 76 + 81310 ACCGT-GCTTCTTGCTCCTTAAC-CCCTTCAGTGGTCCCCAC--------------GTCACCC-----------------GCTCTGT--CTCCCTCCTGGGGACAGCCTTG s gorGor1.Supercontig_0468881 103 76 + 1088 ACCGT-GCTTCTTGCTCCTTAAT-CCCTTCAGTGGTCCCCAC--------------GTCACCC-----------------GCTCTGT--CTCCCTCCTGGGGACAGCCTTG i gorGor1.Supercontig_0468881 C 0 C 0 s ponAbe2.chr17_random 16071911 75 + 17838096 ACCGT-GCTTC-TGCTCCTTAAC-CCCTTCAGGGGTCCCCAC--------------ATCACCC-----------------GCTCTGT--CTCCCTCCTGGGGACAGCCTTG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75045810 75 + 78773432 ACCGT-GCTTC-TGCTCCTTAAC-CCCTTCAGGGGTTCCCAC--------------GTCACCC-----------------ACTCTGT--CGCCCTCCTGGGGACAGCCTTG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 52997 75 - 95547 ACCGT-GCTTC-TGCTCCTTAAC-CCCTTCAGGGGTTCCCAC--------------GTCACCC-----------------ACTCTGT--CGCCCTCCTGGGGACAGCCTTG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 55401 75 + 225949 ACAGT-GCTTC-TGCTCCTTAAC-CCCTTCGGTAGTCCCCAC--------------GTCACCC-----------------ACTCTGT--CGCCCTCCTTGGGACAGCCTTG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 9137 75 + 9575 ACTCT-GCCTC-TGCTCCCTAAT-CCCTTCAGGGTTCCCCAC--------------CTCGCCC-----------------ACTCTGT--CGCCCTCCTGGGGGCGGCTCTG i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_15893 14034 71 + 19765 ACTCT-GCCTC-TGCCCCCTGTC-CCCCTAAGCGCTCCCCAC---------------TCGCCC-----------------ACTCTGT--GTC---CCTGAGGACGACCCTG i micMur1.scaffold_15893 I 3214 C 0 s tupBel1.scaffold_124460.1-4080 476 61 + 4080 ---------------ACCCTGCC-CCGGTAGGGCTCCCCCAC--------------CTCGCCT-----------------ACCATGT--CGCCCTCC-GGGGTGGCCCCTG i tupBel1.scaffold_124460.1-4080 C 0 C 0 s mm9.chr11 118768517 54 + 121843856 ------GCCTC-ACCTCCCTAGC-CTCCTATGGGTTC-------------------CCCCATC-----------------TTCC--------CCTCTACAG-----CCCAG i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 5481 73 + 11404 ------ACCTC-CCGTCCCAAGC-CTCTGGGGGGATCCCCACCTCCCCTACGGTCACCCCCTT-----------------GCCC--------CCTCCCTGG-----TCCAG i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4397583 64 + 7991924 ------CCCTC-TGCTCCTTAAC-CTCTTTGGGGTTCCCTAC--------------CTCACCC-----------------ACTC--------CCTCCCAGGAACACCCCAG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 14829 70 + 44242 ------GCCTC-TGCTGCCTAAC-CTCTTTGGGGTTCCCCGC--------------CTCGCCC-----------------ACTCCGC--CGGCCTTCCAGGGACAGCCCGC i speTri1.scaffold_128901 C 0 C 0 s oryCun2.chrUn0958 26432 47 + 41507 ------GCGAC-CCGCCCTCAAC-CCGTCCGGCCGTCCTTGC--------------CGGATCG-----------------TCCTTG------------------------- i oryCun2.chrUn0958 C 0 I 1096 s ochPri2.scaffold_9426 11106 58 - 54875 ------ACAGC-TCCCTC----C-CCTTTAGGCGGCCC--GC--------------CTCACCG-----------------GCTTCGG--TG-CCCTCCAGG-----GCTGG i ochPri2.scaffold_9426 C 0 I 1 s pteVam1.scaffold_11245 22847 63 + 48268 -CTCA-GCCTC-TGCTCCCTAACCCTT--CTGGGTGTCCCGC--------------CTCACCC-----------------ACACTGGGGGCCGCTCTGC------------ i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59444730 57 - 64418924 ACTCT-GCCTC-TGCTCCCAAAATCCC--CAGGGTTTCCCAC--------------CTCACCC-----------------ACATTGT-------TACTA------------ i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 45160 53 + 132007 GCTTC-ACCTC-TGCTCCCTAAA-CCC--CAGGGTTTCCCAC--------------GTCACCC-----------------ACGCTGT----------CG------------ i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58050870 52 - 61308211 -CTCC-GCCTC-TGCTCCTAACT-CCT--CAGGGTTTCCCGC--------------CTCACCC-----------------ACGCCCG----------CC------------ i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10866896 61 - 65312493 -CTCTAGCTTC-TGCTTCCTAAC-CCC--CAGACCTTCTCAC--------------CTCATTCTCCAGG-----------GCTCTGC--------TCTA------------ i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 136845 72 + 145505 -CTCT-GCCTC-TGCTCCCTAAC-CCC-TCAGAGTTTCCCAC--------------CTCACTCTCCAGTTTTCTCCTCACTCTCTGC--------TCTA------------ i turTru1.scaffold_106006 C 0 C 0 s loxAfr3.scaffold_49 14442145 71 - 17734757 -----AGCAGCCTGCTCCCCAGA-CCCTTTAGACGCTCCC-C--------------ACCACCC-----------------TCTCCCA--GGCCCCCGCCAGGAGGACTCTA i loxAfr3.scaffold_49 C 0 C 0 e choHof1.scaffold_149147 3142 1766 + 9388 I e eriEur1.scaffold_125414 877 0 - 877 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e panTro2.chr17 79484649 128 + 83384210 I e monDom5.chr2 304551395 4976 - 541556283 I a score=1105498.000000 s hg19.chr17_gl000204_random 54627 205 + 81310 CCCTCCCAGAAGCT-----GTCAGCCAGGAAATGAAGGGTT--AAGCGTTGCTTCCAG--GAG--TGTG---------C------GGTGAGCGGTGAGCGAGG-------CGCCCACGCAGGAA-GGCCTCCAGTC-CT-GGGGGAGGGGC-G-GGGGG--GCCAGCC---------TC--GGTC-CTCG--GC-C--------------AA--------AGGGAGCTCCTCGCCCGCA---GGAGGCGG--AGAAG--G-AAGG--------CGCGC-CGGGATGG----------T-TC-TAAGAAGGC s gorGor1.Supercontig_0468881 179 198 + 1088 CCCTCCCAGAAGCT-----GTCAGCCAGGAAATGAAGGGTT--AAGCGTTGCTTCCAG--GAG--TGTG---------C------GGTGAGCG-------AGG-------CGCCCACGCAGGAA-GGCCTCCAGTC-CT-GGGGGAGGGGC-G-GGGGG--GCCAGCC---------TC--GGTC-CTCG--GC-C--------------AA--------AGGGAGCTCCTCGCCCGCA---GGAGGCGG--AGAAG--G-AAGG--------CGCGC-CGGGATGG----------T-TC-TAAGAAGGC i gorGor1.Supercontig_0468881 C 0 C 0 s ponAbe2.chr17_random 16071986 199 + 17838096 CCGTCCCAGAAGCT-----GTCAGCCAGGAAATGAGGGGTT--AAGCGTTGCTTCCAG--GAG--TGTG---------C------GGTGAGCG-------AGG-------CGCCCACGCAGAAA-GGCCTCCAGTC-CT-GGGGGAGGGGCGG-GGGGG--GCCAGCC---------TC--TGTC-CTCG--GC-C--------------AA--------AGGGAGCTCCTCGCCCGCA---GGAGGCGG--AGAAG--G-AAGG--------CGCGC-CGGGATGG----------T-TC-TAAGAAGGC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75045885 202 + 78773432 CCCTCCCAGAAGCT-----GTCAGCCAGGAAATGAGGGGTT--AAGCGTTGCTTCCAG--GAG--TGTG---------C------GGTGAGCG---AGCGAGG-------CGCCCACGCAGGAA-GGCCTCCAGTC-CT-GGGGGAGGGGC-G-GGGGG--GCCAGCC---------TC--GGTC-CTCG--GC-C--------------AA--------AGGGAGCTCCTCGCCCGCA---GGAGGCGG--AGAAG--G-AAGG--------CAAGC-CGGGATGG----------T-TC-TAAGAAGGC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 53072 198 - 95547 CCCTCCCAGAAGCT-----GTCAGCCAGGAAATGAGGGGTT--AAGCGTTGCTTCCAG--GAG--TGTG---------C------GGTGAGCG-------AGG-------CGCCCACGCAGGAA-GGCCTCCAGTC-CT-GGGGGAGGGGC-G-GGGGG--GCCAGCC---------TC--GGTC-CTCG--GC-C--------------AA--------AGGGAGCTCCTCGCCCGCA---GGAGGCGG--AGAAG--G-AAGG--------CAAGC-CGGGATGG----------T-TC-TAAGAAGGC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 55476 205 + 225949 CCCTCCCAGAAGCT-----ATTAGCCAGGAAATGAGGGGTT--CAGCGTCGGTTCCAG--GAG--TGTG---------C------GCTGAGTG-------CGG-------CGCCCCCGCAGGAA-GGCCTCCAGCC-CCAGGGGGAAGGGC-G-GGGGT--GGCAGCC---------TC--GGTC-CTGG--GC-C--------------GA--------AGGGAGCTCCTTGCCCGCA---GGAGGCAG--AG--G--G-AAGGCGTGCGCCCGAGC-CTGGATAG----------T-TC-CAAGAAGCC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 9212 198 + 9575 CCCTCCCAGAAGCT-----CCCAGTCAGGAGAGGAGGGGTT--AAGCGCTGCTTCCAG--GAG--TGTG---------C------GGTGAGCC-------CCG-------CGCCCACGCAGGGA-GGCCTCCAGTC-CC-CGGAGAGGGGC-G-GGGGC--GGCCGCC---------TC--GGTC-CTCAGCGC-C--------------GA--------AGGGAGCTCCTAGCCAGCA---CGCGGCAG--AGAAG--G-GA----------CGCGC-CGGGCGGA----------G-TC-CAAGGAGCC i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_15893 14105 196 + 19765 CCCTCCCAGAAGCT-----CCCAGCCAGGAAATGAGGGGTT--AAG-GCTGCTGCCAG--AGG--CGTG---------T------GTGGAGCC-------CAG-------CGCCCACGCAGGGA-GGCCTCCAGTCGCC-GGGGGAGCGGC-G-GGGGT--GGCAGGC---------TC--GGTC-CTCA--GCAC--------------CG--------AGGGAGCGCCGCGCC-GCA---GGGGGCGG--AG--G--G-AGGG--------CCCAC-TGGGCTGG----------T-CC-TCAGGGGGT i micMur1.scaffold_15893 C 0 C 0 s tupBel1.scaffold_124460.1-4080 537 177 + 4080 CCCTCCCAGGAGCT-----CTCGGCAGAGGAATAAAGGGGTTAAAACCTGGCTTTCCA--GAGACTGTG---------T------GGGGGAGC-------TCG-------TGCCCACTCAGGAA-GGC---------CC-AGGAG--------------------GCC---------CC--GGT--GTAA--GC-A--------------GA--------AGGGAGCTCTTTGCCCACC---AGGAGCAG--GGAAG--G-GGC---------TTTGC-CTGGCTGG----------TGCC-TGAGCAGGC i tupBel1.scaffold_124460.1-4080 C 0 I 2422 s mm9.chr11 118768571 191 + 121843856 TGTTCCCAG-AGCTCCAAGCCCAGCCGGGAAAGTAGGGGTT--AAGCGCTGCTTCCCC--GAG--TGTG---------C------AGTGCGCT-------TAG-------CTCCCACGCAGGGA-GGCCTCTGGT--CC-CCGGGGAGGGC-G-GAGGC--GGCAGCT------CGATC--CTCC-CTCT--GG-G------------CCCA--------GGGGAGCTCCTCGCCCGC---------------------G-GGGG--------ACGA--GGGGCTGG----------C-TC-TGAGAAGGC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 5554 185 + 11404 CATTCCCAGAAGCT-----CCCAGCCGGGAAGTGAGGGGTT--AAGCACTGCTTACAG--CAG--AGTG---------T------GGTAAGCG------------------GCCCACGCATGGA-GGCCATCAGT---C-CTGCGGAGGGA-G-GGGCCCTGGCGGCC---------TC--CATC-CTCC--GG-C------------CTCC--------AG---CCTCCCTCCCTGCA---GAAA-------------G-GAGG--------CAGAATGGGGCTGG----------C-AG-TACGGAGGG i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4397647 203 + 7991924 CATTCCCAGACTCT-----CCCAGCCGAGAAATGAGGGGTT--AAGCGTGGCTTCCAG--GAG--TGCG---------C------AGAGAGTC-------CAG-------CGCCCACGCAGGGA-GGCCTCCAGTC-CC-TCGGGAGGGGC-G-GGGGT--GGCAGCCT-----CTGTT--CTCC-CTTC--GC-A------------CGCACCCGCCGGAGGGAGCTCCTGGCTCACA---GGGG------------CG-GGGG--------CGGG--GTAGGCGG----------T-CC-TCAGAAGGC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_128901 14899 191 + 44242 CATTCCCAGGAGCT-----CCCACCCGGGAAATGAGGAGTT--AAAC-CTGCTTCCAG--GAG--TGTT---------G------GGTGAGCC-------CAG-------CGCCCACGCAGGGAGGGCCTCCAGTC-CC-CAGGGAGGGGT-G-GGGGT--GGCAGCCTTTGGCCCTTC--CTTC-CTCT--GA-A------------------------AGGGAGCTCCTGGCCTCA---------------------G-CAGG--------CGAAG-AGGGCTGG----------C-CC-TAAAAAGGC i speTri1.scaffold_128901 C 0 C 0 s ochPri2.scaffold_9426 11165 222 - 54875 ---TCCTCGGAGCT-----CCCGGCCGGGACTGGAGGGGTT--AAGCGCTGCTCGCAG--GAG--CGCGCGGCGGCGAC------GGCGAGTC-------GGG-------CGCCCACGCAGGGA-GGCCTCCAGTC-CC-CGGGAAGCGGC-G-GGGGT--GGCAGCC------TCGTC--CTCCACTCC--GG-C-----------GCGCA--------AAGGAGCGCCTCGCCGACG---CGGGGCTC--GGGGTGGG-AAGG--------CGGT--GCGCCCGGCCCGCCGGGTC-CC-TGGGCAGGC i ochPri2.scaffold_9426 I 1 C 0 s pteVam1.scaffold_11245 22910 178 + 48268 CCCTCCCCGAAGCT-----CCCAGCTGTGGAATGAGGGGTT--AAGCATTGCTT-CAG--GAG--TGTG---------A------GGTGCACC-------CCG-------GGCCCACCCTGGGA-GGCCTGCAGTC-CC-TGGGGAGGGAC-T-AGGGT--GGCAGCC---------TT--GGTC-CTCA--GC-G------------C-CA--------AAGCAGCTCCCCACTCACACCTGGAGACAG--GGAGG--G-AGG--------------------------------------------GGC i pteVam1.scaffold_11245 C 0 I 14 s canFam2.chr9 59444787 193 - 64418924 CCCTCCCTGAAACT-----CCTGGCAGGGAAATGAGGGGTT--AAGCGTCGCTTCCAG--GAG--TGTG---------CGGT---GGCGAGCC-------T-G-------TGCCCACGCAGAGA-GGCCTCCAGTC-CC-CAGGGAGGGAT-G-AGGGT--GGCAGCC---------TCGAGGTC-CTC-------------------------------------CT---CGTTCACCAGTGGAGGCGGGAAGGGA--G-GGGG--------TGCACATTGGCTGG----------T-GC-TTAGGAGGC i canFam2.chr9 C 0 I 12 s felCat3.scaffold_206428 45213 202 + 132007 CCCTCCCAGAATCT-----CCCAGCAGGAGAACGAGGGGTT--AAGCGTCGCTCCCAG--GAG--TGTG---------C------CGCGAGTC-------G-G-------TGCCCACGCAGGGA-GGCCTCCAGTC-CC-CGGGGACGAAC-G-GGGGC--GGCAGCC---------TT--GGTC-CTCG--GC-T------------CTGG--------AGGCAGCTAAACGCTCCCTGGTGGAGGCGG--AGAGA--G-CGGG--------TTCGC-CTAACTGG----------T-GC-TCAGAAGGC i felCat3.scaffold_206428 C 0 I 16 s equCab2.chr11 58050922 205 - 61308211 TCCTCCCAGAAGCT-----CCGGGTCGGGGAATGAGAGGTT--AAGCGTTGTTTCCAG--GAG--TGTG---------C-------GCGAGCC-------TCG-------TGCCCACGCAGGGA-GGCCTCCAGTC-CC-CGGGGAGGGAG-ACGGGGT--GGCAGCC---------TTG-GGTC-CTCA--GC-G------------CGCA--------AGGGAGCTTCATGTCTGCAGGCGGAGGAGG--GGAGG--G-AGGG--------ACCGCGACGTCTGG----------T-GC-TCAGAAGGC i equCab2.chr11 C 0 I 17 s bosTau4.chr19 10866957 204 - 65312493 CCCTCTCAGAAGCT-----CCCGGTTGGGAAATCA---GTT--AAGCACTGCTTCCAGGAGAG--TGTG---------C--C---TGTGAGCC-------CAG-------TGCCCACCCAGAGA-GGCCTCCAGTC-TC-TGGGGAGGGAC-G-GGGGT--GGCAACC---------TC--CAAC-CTCA--GG-G------------CATA--------ATGGAGCTCTGAGCCCCAAGGTGGAGACGG--GGACT--G-TGGG--------ACAAGCCCGCCTAA----------T-GC-TCAGAAGGA i bosTau4.chr19 C 0 I 12 s turTru1.scaffold_106006 136917 206 + 145505 CCCTCTCAGAAGCT-----CCCAGTTGGGAAATGAGGGGTT--AAACGTTGCTTTCAG--GAG--TGTG---------C--C---AGCGAGCC-------CCGAGCCCCATGCCCATTCAGGGA-GGCCTCCAATC-TC-GGGGGAGGGTC-A-AGG---------CC---------TC--CATC-CTCA--GC-G------------CAGA--------GGGGAGCTCTGAGCCCGAAGGTGGAGGCAG--GGACC--GAGGGG--------GCCCGCCAGGCTGG----------C-TC-TCAGAAGGC i turTru1.scaffold_106006 C 0 I 20 s loxAfr3.scaffold_49 14442216 218 - 17734757 CTCTCCCAGCAGC------CCCAGCCGGAAAAGGCGGGGTT--AAGCCTTGCTTCCAG--GAG--AGGC---------C--CCCAGGGGAGCC-------GGG-------TGCCCACGCAGGGA-GGCCTGTGGTC-CC-CTGGGAGGCGCCG-GAGGT--GGCAGCT---------TG--GCTT-CTCA--GA-GCTGGCGCAGGCTCAGA--------TGGGAGCTACGTGCCTCCAGGTGGAGGCGA--CAGGA--G-GGGG--------CGAGA---GGTTGG----------T-CCGTGGCAAGGC i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 26479 1096 + 41507 I e choHof1.scaffold_149147 3142 1766 + 9388 I e eriEur1.scaffold_125414 877 0 - 877 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e panTro2.chr17 79484649 128 + 83384210 I e monDom5.chr2 304551395 4976 - 541556283 I a score=-349336.000000 s hg19.chr17_gl000204_random 54832 36 + 81310 TCCCC--TC------------CTCC-------GCCCCCGCCATGCCGC-----------CCCCACGCC s gorGor1.Supercontig_0468881 377 36 + 1088 TCCCC--TC------------CTCC-------GCCCCCNNNNNNNNNN-----------NNNNNNNNN i gorGor1.Supercontig_0468881 C 0 C 0 s ponAbe2.chr17_random 16072185 36 + 17838096 TCCCC--TC------------CTCC-------GCCCCAGCCATGCCGC-----------CCCCACGCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75046087 23 + 78773432 TCCCC--TC------------CTCC-------GCCCCCGCCATG------------------------ i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 53270 23 - 95547 TCCCC--TC------------CTCC-------GCCCCCGCCATG------------------------ i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 55681 14 + 225949 TTCTC--TC------------CTCC-------GCC--------------------------------- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 9410 27 + 9575 CCGCCGACC------------CGAT-------GCCTCCCCTAAGCC---------------------- i tarSyr1.scaffold_143701 C 0 C 0 s micMur1.scaffold_15893 14301 34 + 19765 GCCTC--TCTGCCCCCACACACACC-------GCCCCCAAACT------------------------- i micMur1.scaffold_15893 C 0 C 0 s turTru1.scaffold_106006 137143 16 + 145505 CGCCC--CC------------CAAA-------ACCCC------------------------------- i turTru1.scaffold_106006 I 20 C 0 s bosTau4.chr19 10867173 16 - 65312493 CGCCC--TC------------CCCA-------AACCC------------------------------- i bosTau4.chr19 I 12 C 0 s equCab2.chr11 58051144 14 - 61308211 AGCGG--CC------------CGGA---------GCC------------------------------- i equCab2.chr11 I 17 C 0 s felCat3.scaffold_206428 45431 16 + 132007 CGCTG--CC------------CCCG-------AAGCC------------------------------- i felCat3.scaffold_206428 I 16 C 0 s canFam2.chr9 59444992 14 - 64418924 CCCTG--CC------------CTGG---------GCC------------------------------- i canFam2.chr9 I 12 C 0 s pteVam1.scaffold_11245 23102 16 + 48268 CAGGG--CC------------CCTG-------AAGCC------------------------------- i pteVam1.scaffold_11245 I 14 C 0 s eriEur1.scaffold_355010 7713 23 + 8359 GGGTG--TC------------CCACCTCGCCCACGCC------------------------------- i eriEur1.scaffold_355010 I 3093 C 0 s loxAfr3.scaffold_49 14442434 29 - 17734757 --CTT--TC-CGCCAGCGCCCCGCT-------GCCCCAGCG--------------------------- i loxAfr3.scaffold_49 C 0 C 0 s choHof1.scaffold_149147 4908 19 + 9388 ----------CGC-----CCCCGAA-------ATCCCCAcg--------------------------- i choHof1.scaffold_149147 I 1766 C 0 s ochPri2.scaffold_9426 11387 11 - 54875 --------------------------------AC-------------------------CCCCAGATC i ochPri2.scaffold_9426 C 0 C 0 s speTri1.scaffold_128901 15090 23 + 44242 --------------------------------GCCGCCCCAGCT----CCCCAGACCGC--------- i speTri1.scaffold_128901 C 0 N 0 s cavPor3.scaffold_76 4397850 29 + 7991924 --------------------------------GCCCCTCCAC-------CCCATGCCTCCCCCGGACC i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_43980 5739 24 + 11404 --------------------------------ACCCCTCCAA------------ACCCTCCCCCCAGG i dipOrd1.scaffold_43980 C 0 C 0 s mm9.chr11 118768762 17 + 121843856 --------------------------------GCCC-------------------CCTGCCCCACATG i mm9.chr11 C 0 C 0 e oryCun2.chrUn0958 26479 1096 + 41507 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e panTro2.chr17 79484649 128 + 83384210 I e monDom5.chr2 304551395 4976 - 541556283 I a score=844396.000000 s hg19.chr17_gl000204_random 54868 142 + 81310 CCCACCCCGCCGGCG--------CTCAGTGA---------------CC---------TGGGG---------CGC-CCCTGCAAGAGG--------CCCATACCCGGC-----TTTCATCAG--GCAGCGCCTTC-TCGACAACTT-----TTCTCCCTCTC-TCCCCTCA-CAATTTTTGCTCACCTGGagggtcggtttttaatta s panTro2.chr17 79484777 142 + 83384210 CCCACCCCGCCGGCG--------CTCAGTGA---------------CC---------TGGGG---------CGC-CCCTGCAAGAGG--------CCCATACCCGGC-----TTTCATCAG--GCAGCGCCTTC-TCGACAACTT-----TTCTCCCTCTC-TCCCTTCA-CAATTTTCGCTCACCTGGAGGGTCTGGTTTTAATTA i panTro2.chr17 I 128 C 0 s gorGor1.Supercontig_0468881 413 142 + 1088 NNCACCCCGCCGGCG--------CTCAGTGA---------------CC---------TGGGG---------CGC-CCCTGCAAGAGG--------CCCATACCCGGC-----TTTCATCAG--GCAGCGCCTTC-TCGACAACTT-----TTCTCCCTCTC-TCCCTTCA-CAATTTTCGCTCACCTGGagggtctggttttaatta i gorGor1.Supercontig_0468881 C 0 C 0 s ponAbe2.chr17_random 16072221 142 + 17838096 CCCACCCCGCCAGCG--------CTCAGTGA---------------CC---------TGGGG---------CGC-CCCTGTAAGAGG--------CCCATACCCGGC-----TTTCATCAG--GCAGCGCCTTC-TCGACAACTT-----TTCTCCCTCTC-TCCCTTCA-CAATTTTCGCTCACCTGGAGGGTCTGGTTTTAATTA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75046110 136 + 78773432 ------CTGCTGGCG--------CTCAGTGA---------------CC---------TGGGG---------CGC-CCCCCAAAGAGG--------CCCATACTCAGC-----TTTCATCAG--GGAGCGCCTTC-TCGACAACTT-----TTCTCCCTCCC-TCCCTTCA-CAATTTTCGCTCACCTGGAGGGTCTGGTTTTAATTA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 53293 136 - 95547 ------CTGCTGGCG--------CTCAGTGA---------------CC---------TGGGG---------CGC-CCCCCAAAGAGG--------CCCATACTCGGC-----TTTCATCAG--GGAGCGCCTTC-TCGACAACTT-----TTCTCCCTCTC-TCCGTTCA-CAATCTTCGCTCACCTGGagggtctggttttaatta i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 55695 150 + 225949 CCCACCCCTCCGGCG--------CTCAGCGG---------------CC---------TGGGGTGAACTACCCAC-CCCCCTCAGCAG--------CCCATACCCTGC-----TTTCATCAG--GCAGGGCCTTC-TTGGCAACTT-----TTCT-TCTCTT-TCCCTTCA-CAATTTTCGCTCACCTGGAGGGTCTGGTTTTAATTA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_143701 9437 138 + 9575 CCCACCCCGCCAGAG--------CTCCGCGG---------------CC---------TGGGG---------CGC-CCCCG---GCCA--------CCCGCATCCCAC-----TTTCATCAG--GCTGAGCCTTC-TCTCCAACTT-----TTCTCCCTCTC-TCCCTTCA-CAATA-TCGCTCACCTGAAGGGTCTGGTTTTAATTA i tarSyr1.scaffold_143701 C 0 N 0 s micMur1.scaffold_15893 14335 104 + 19765 ----cccc---------------------------------------------------------------cgc-cccc-------g--------ccc---ccccgc-----TGTCACCAG--GCAGTGCTCTC-ACTGCAACTT-----TTCT--CTGTC-TCCCTTCG-AAATTCTCGCTCACCTGGagggtctggttttaatta i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118768779 117 + 121843856 -CCCACCCTACAGCG--------------GC---------------CC---------TGAC----------CAC-CTC--------G--------CCAGCGCCTCTC-----TTCCACCAG--CAGGCGCCTTC-TCTACAACTT------TCTCCCTTCC----------CAGTAGTCGCTCACCTGGAGGGTCTGGTTTTAATTA i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 5763 127 + 11404 --ACACCCTCCGG---------------------------------CC---------TGCA----------GGC-CTC--------C--------CCCAGCCTCCGC-----CTTCATCAG--CTGGAGCCTTCTTCTACAACTTCCCCTCTCTCCCTCCC-TCCTTCTA-CAGTTCTCTCTCACCTGGagggtctggttttaatta i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4397879 130 + 7991924 --CCACCTGCCAGCA--------CCCAGCGG---------------CC---------TCCT----------CGC-GCC--------A--------CCAGCCCCCAGC-----TCTCATCAG--CCAGCGCCTTT-TCTACAACTT------TCTCCCCCTC-TCGCGTCA-CAATTCTCGCTCACCTGGagggtctggttttaatta i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 11398 110 - 54875 --CCACCC--CGG---------------------------------------------------------------GC--------G--------TCCGCACCCCGC-----TTTCCTCAG--GCAGCTCTTTC-TCCACAACTT------TCTCCCTCTCCTCCCGCCGCCACTTCCGGCTCACCTGGagggtctggttttaatta i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 137159 139 + 145505 -CCGGTGCCAGCGCT--------CTTGCGGT---------------CT---------GAGGG---------AGG-CCCACACCTG----------CCCGCATGCCGC-----TTTCATCAG--GCGGCGCTTTC-ACTGCAACTT-----TTCTCCCTCTC-TCCCTTCA-CAATTTTCGCTCACCTGGagggtctggttttaattg i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10867189 140 - 65312493 -CCCGTCCCAGTGCT--------CTTCGGTC---------------CT---------CAGAG---------AGGCCCCCCACTTG----------CCTGCCTCCCGC-----TTCCATCAG--GCTGCGCTTCC-ATTGCAACTT-----TTCTCCCTCTC-TCCCTTCA-CAATCTTCCCTCACCTGGagggtctggttttaatta i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58051158 139 - 61308211 -CCCACCCCTGGGCG--------------CC---------------CTGTAGCC--TGGGGG---------AGG-TCCCCAGCTGC---------CCGGCACCCCGC-----TTTCATGAG--GCGACGCTTTC-A-TGCAACTT-----TCTTCC-TCCC-TCCCTTCA-CAATTTTCGCTCACCTGGagggtctggttttaatta i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 45447 123 + 132007 -CCCACC--------------------------------------------------GGGGG---------CAC-TCCCCCTATCCG--------CAGGCACCCTGC-----TTTCATCGGCAGCAGCGCTCTC-AGTGCAACTT-----TTCTCC--CTC-TCCCTCCA-CAATTTTCGCTCACCTGGAGGGTCTAGTTTTAATTA i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59445006 124 - 64418924 -CCCACT--------------------------------------------------GGAGG---------AGT-GGCCCCCCTACG-----TTACATGCACCCCAC-----TTTCATCAG--GGGGTGCTTTT-GCTGCAACTT-----TTCTCT--CTC-TCCCTTCA-CAGTTTTTGCTCACCTGGAAGGTCTGGTTTTAATTA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 23118 135 + 48268 -CCCGCCCCCAGGCA--------CTC---CC---------------CTAT-------GGGGG---------AGG-CCTTCAGCCG----------CCTGCACCCCGC-----TTGCATCAG--GCGGTGCTTTC-GCGGCAACTT-----TTCCC---CTC-TCCCCTCG-CAATTTTCACTCACCTGGagggtctggttttaatta i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_355010 7736 155 + 8359 -TACaccccaaagggaaaaaaatctcccagc---------------cagaaactgaggggtT---------AAG-CCCCCGAAGGTGGCCTGTGATAGGCCCCATGCGGGGTTTCCACCAG--ACAGTGCTTTC-C-CGCAACTT-----TCCTC---CAC-CCCCTAC---------CCCTCCC----AGGCTCTGGCTTTAATTA i eriEur1.scaffold_355010 C 0 C 0 s loxAfr3.scaffold_49 14442463 150 - 17734757 ----CCCCGCCAGCC--------CTCCCTGCAGCAGTCGCTGTAGCCT---------CGGGG---------CGC-CCCCCACCCT----------CCTGCGCCCCGT-----TTTTATCCG--GCAGAGCTTTC-TCTGCAACTT-----TTCTCCCTCTC-TCCCCGCA-C-AATTTCGCTCACCTGGagggtctagttttaatta i loxAfr3.scaffold_49 C 0 C 0 s choHof1.scaffold_149147 4927 128 + 9388 --------gccgccc--------cccaccgc----------------------------ggg---------cgc-ccgcagcccg----------ccggcgccccgc-----TTCCATCCG--GCGGAGCTTTC-ACGGCAACTT-----TTCTCCCTTTC-TCCCGTCA-CGAGGTTCGCTCACCTGGagggtctggttttaatta i choHof1.scaffold_149147 C 0 C 0 e oryCun2.chrUn0958 26479 1096 + 41507 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304551395 4976 - 541556283 I a score=1310739.000000 s hg19.chr17_gl000204_random 55010 106 + 81310 gtgtaatatccccgtgaacaacgcagcctaattaagacatccgtcccgaatccgcgatgcacac-ttaatgagcaggttcTGCCGCAATGTTTATAC---TTTTTTTTTC------ s panTro2.chr17 79484919 106 + 83384210 GTGTAATATCCCCGTGATCAACGCAGCCTAATTAAGACATCCGTCCCGAATCCGCGATGCACAC-TTAATGAGCAGGTTCTGCCGCAATGTTTATAC---TTTTTTTTTC------ i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0468881 555 109 + 1088 gtgtaatatccccgtgaacaacgcagcctaattaagacatccgtcccgaatccgcgatgcacac-ttaatgAGCAGGTTCTGCCGCAATGTTTATACTTTTTTTTTTTTC------ i gorGor1.Supercontig_0468881 C 0 C 0 s ponAbe2.chr17_random 16072363 108 + 17838096 GTGTAATATCCCCGTGAACAACGCAGCCTAATTAAGACATCCGTCCCGAATCCGCGATGCACAC-TTAATGAGCAGGTTCTGCCGCAATGTTTATAC-TTTTTTTTTTTC------ i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75046246 105 + 78773432 GTGTAATATCCCCGTGAACAACGCAGCCTAATTAAGACATCCGCCCCGAATCCGCGATGCACAC-TTAATGAGCAGGTTCTGCCGCAATGTTTATAC----TTTTTTTTT------ i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 53429 105 - 95547 gtgtaatatccccgtgaacaacgcagcctaattaagacatccgccccgaatccgcgatgcacac-ttaatgagcaggttcTGCCGCAATGTTTATAC----TTTTTTTTC------ i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 55845 106 + 225949 GTGTAATATCCCCGTGAACAACGCAGCCTAATTAAGACATCCG-CCCGAATCCGCGATGCACAC-TTAATGAGCAGGTTCTGCCGCAATGTTTACAC--TTTTATTTTTT------ i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 14439 100 + 19765 gtgtaatatccccgctaacaacgcagcctaattaagacatccg--CCTGAGCCGCCATGCACAC-TTAATGGGCAGGTTCTGCCGCAATGTTTACAC-------TCTTTT------ i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118768896 105 + 121843856 GTGTAATATCCCCGTTACCAGCGCAGCCTGATTAAGACATCCGCCCTGA-TCCGCGATGCGCAC-TTAATGAGCTCAGTCTGCCATAATGTTTGTAC---TTTTTTTTTT------ i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 5890 105 + 11404 gtgtaatatccccgttaactgcgcagcctaattaagacatccgCCCCAA-TCCACCATGCACAC-TTAATAAGCACGTTCTGTCGCAATGTTTATAC---TTTCCCCCCC------ i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4398009 103 + 7991924 gtgtaatatccccgttaa---cgcagcctaattaagacatccgccccaagcccgcgattcacac-ttaatgAGCACGCTTTGCCGCAATGTTTATAC---TTTTTTTTTT------ i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 11508 106 - 54875 gtgtaatatccccgttaacaacgcagcctaattaagacatccgCGCCGCAGCCGCGCAACGCAC-TTAATGAGCTGCTTCTGCCGCAACGTGAAGAC---TTTCTCTGTC------ i ochPri2.scaffold_9426 C 0 I 23 s turTru1.scaffold_106006 137298 99 + 145505 gtgtaatatccccgttaacaacgcagcctaattaagacatccg-cccaattccgcgatgcacac-ttaatgaacaggttcTGTCGCAGTGTTTATAC---------TTTT------ i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10867329 99 - 65312493 gtgcaatatacccgttaacaacgcagcctaattaagacatccg-cccaattccgagatgcacac-ttaatgagcaggttcTGCTACAATGTTTATAC---------TTTT------ i bosTau4.chr19 C 0 I 6 s equCab2.chr11 58051297 99 - 61308211 gtgtaatatcgcctttaacaacgcagcctaattaagacatccg-cccaaatccgCGAGGCACCC-TTAATGAGCAGGAGCTGCTGCAATGTTTAGAC---------TTTT------ i equCab2.chr11 C 0 I 4 s felCat3.scaffold_206428 45570 99 + 132007 GTGTAATATCCCCATTAACAACGCCGCCTAATTAAGACATCCG-CCCAGATCCACTATGCACAC-TTAATGAGCAGGTACTGCTGTCAtgtttatac---------ttct------ i felCat3.scaffold_206428 C 0 I 23 s canFam2.chr9 59445130 99 - 64418924 GTGTAATATCCCCGTTAATAATGCAGCCTAATTAAGACATCCG-CCCAAATCCACTATGCACAA-TTAACAAGCAGGTTCTGTGGCGATGTTTATAC---------Tttt------ i canFam2.chr9 C 0 I 27 s pteVam1.scaffold_11245 23253 99 + 48268 gtgtaatatccccgttaacaacgcagcctaattaagacatccg-cccaaatccacgatgcacac-ttaacgagcaggttccgtcgaaatgtttatac---------tttt------ i pteVam1.scaffold_11245 C 0 I 7 s eriEur1.scaffold_355010 7891 78 + 8359 GTGTAATATCCCCACAAACAATGCAG-CTAATAAAGACATC---CCCGAATCT-------------------GCAGGTTCTGCCGCAATGTGTCTAC---------TTCT------ i eriEur1.scaffold_355010 C 0 I 33 s loxAfr3.scaffold_49 14442613 109 - 17734757 gtgtaatatcacggttaacaacgcagcctaattaagacatccACCCCGAATCCACCTTGCACAC-CTAATGAGCAGGTTCTGCCGCAATGTTTATAC------TTTTTTTTTCTCT i loxAfr3.scaffold_49 C 0 C 0 s choHof1.scaffold_149147 5055 105 + 9388 gtgtaatatccttgttaacagcgcagactaattaagacatccgCCCCGGAGCCGCGGTGCACGCTTTAATGAGCAGCTTCTGCCGCAATGTTTATAC------TTATTTT-----T i choHof1.scaffold_149147 C 0 C 0 e oryCun2.chrUn0958 26479 1096 + 41507 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304551395 4976 - 541556283 I a score=515582.000000 s hg19.chr17_gl000204_random 55116 46 + 81310 CATTAT---GTTTTGCAGACCAGTAAAA-CCGAAGCCGGCTTCCGGCTGA s panTro2.chr17 79485025 46 + 83384210 CATTAT---GTTTTGCAGACCAGTAAAA-CCGAAGCCGGCTTCCGGCTGA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0468881 664 46 + 1088 CATTAT---GTTTTGCAGACCAGTAAAA-CCGAAGCCGGCTTCCGGCTGA i gorGor1.Supercontig_0468881 C 0 C 0 s ponAbe2.chr17_random 16072471 46 + 17838096 CATTAT---TTTTTGCAGACCAGTAAAA-CCGAAGCCGGCTTCCGGCTGA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75046351 46 + 78773432 CATTAT---TTTTTGCAGACCAGTAAAA-CCGAAGCCAGCTTCCGGCTCT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 53534 46 - 95547 CATTAT---TTTTTGCAGACCAGTAAAA-CCGAAGCCAGCTTCCGGCTGA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 55951 46 + 225949 CATTAT---TTTTTGCAGACCAGTAAAA-CCGAAGCCGACTTCCGGCTGA i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 14539 46 + 19765 CGTTAT---TTTTTGCAGACCAGTAAAA-CCAAAGCCAGCTTCCGGCTGA i micMur1.scaffold_15893 C 0 C 0 s cavPor3.scaffold_76 4398112 46 + 7991924 CATTAT---TTTTTGCAGACTAGTAAAA-CCAAAGCCGGCTTCTGGCTAA i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_43980 5995 42 + 11404 -----T---TTTTTGCAGACCAGTCAGATCCAAAGCCGGCTTCTGGCTGA i dipOrd1.scaffold_43980 C 0 C 0 s mm9.chr11 118769001 45 + 121843856 CATTAT---TTTTTGCAGACCAGTAAAA-CCAAAGCTGATTTCT-GCTGA i mm9.chr11 C 0 C 0 s turTru1.scaffold_106006 137397 42 + 145505 ----AT---TATTTGCAGACCAGTAAAA-CCAAAGCCGGTTTCTGCCTTA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10867434 42 - 65312493 ----AT---TATTTGCAGACCACTAAAA-CCAAAGCCGGCTTCCGGCTGA i bosTau4.chr19 I 6 C 0 s equCab2.chr11 58051400 46 - 61308211 AACTAT---TTTTTGCAGACCAGTAAAA-CCCAAGCCAGCTTCCTGCTGA i equCab2.chr11 I 4 C 0 s felCat3.scaffold_206428 45692 46 + 132007 atttat---tttttGCAGGCCAATAAAA-CCAAAGCTGTCTTCCGACTGA i felCat3.scaffold_206428 I 23 C 0 s canFam2.chr9 59445256 46 - 64418924 atttat---CTTTTGCAGACCGGTAAAA-CCAAAGCTGTCTTCTGACTGA i canFam2.chr9 I 27 C 0 s pteVam1.scaffold_11245 23359 46 + 48268 aTTATT---TTTTTGCAGACCAGTAAAT-CCAAAGCCGGCTACCGGCCGA i pteVam1.scaffold_11245 I 7 C 0 s eriEur1.scaffold_355010 8002 44 + 8359 atgtatgcatttttGATGACCTGTGA------AAGCTGGCTTCCGGGGAG i eriEur1.scaffold_355010 I 33 C 0 s loxAfr3.scaffold_49 14442722 46 - 17734757 CATTAT---TTCTTGCAGACCAGTAAAG-CCAAAGCCAGTTTCCAGCTGA i loxAfr3.scaffold_49 C 0 C 0 s choHof1.scaffold_149147 5160 45 + 9388 CATTAT---ATTTTGCAGACCAGTATAA-CC-AAGCGGGCTTCAAGCTGA i choHof1.scaffold_149147 C 0 C 0 e oryCun2.chrUn0958 26479 1096 + 41507 I e ochPri2.scaffold_9426 11614 23 - 54875 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304551395 4976 - 541556283 I a score=999809.000000 s hg19.chr17_gl000204_random 55162 177 + 81310 AAGACCTCA-TTACGGGCGACCCCACTC-CATTAGCCTCCTACCTGCTCCACGCTAAGTGCCCGGGGCGCCCGGGTGCAT--GCCCAAGGCGT-CCCC-GAGTCCAACCTGCGTTTGGAGCAGGAAATT-AGCAACCTGC-GC-GCC-CGAGAAGCG-----ACTTCACCA--CCAGCTGGGGCAGGAAGGGG--G s panTro2.chr17 79485071 177 + 83384210 AAGACCTCA-TTACGGGCGACCCCACTC-CATTAGCCTCCTACCTGCTCCACGCTAAGTGCCCCGGGCGCCCGGGTGCAT--GCCCAAGGCGT-CCCC-GAGTCCAGCCTGCATTTGGAGCAGGAAATT-AGCAACCTGG-CC-GCC-CGAGAAGCG-----ACTTCACCT--CCAGCTGGGGCAGGAAGGGG--G i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0468881 710 177 + 1088 AAGACCTCA-TTACGGGCGACCCCACTC-CATTAGCCTCCTACCTGCTCCACGCTAAGTGCCCGGGGCGCCCGGGTGCAT--GCCCAAGGCGT-CCCC-GAGTCCAGCCTGCGTTTGGAGCAGGAAATT-AGCAACCTGC-GC-GCC-CGAGAAGCG-----ACTTCACCT--CCAGCTGGGGCAGGAAGGGG--G i gorGor1.Supercontig_0468881 C 0 C 0 s ponAbe2.chr17_random 16072517 177 + 17838096 AAGACCTCA-TTACGGGCGACCCCACTC-CATTAGCCTCCTACCTGCTCCACGCTAAGTGCCCGGGGCGCCCGGGTGCGT--GCCCAAGGCGT-CCCC-GAGTCCAGCCTGCGTTTTGAGCAGGAAATT-AGTAACCTGC-GC-GCC-CGAGAAGCG-----ACTTCTCTT--CGAGCTGGGGCAGGAAGGGG--G i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75046397 176 + 78773432 AAGACCTCA-TTACGGGCGACCCCACTC-CATTAGCCTCCTACCTGCTCCACGCTAAGTGCCCGGGGCGCCCGGGTGCGT--ACCCGAAGTGT-CCCC-GAGTCCAGCCTGCGTTTTCAGCAGGAAATT-AGCGACCAGGAGC-GCC-CAAGAAGCG-----ACTTCACCT--C--GCTGGGGCAGGAAGGGG--G i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 53580 176 - 95547 AAGACCTCA-TTACGGGCGACCCCACTC-CATTAGCCTCCTACCTGCTCCACGCTAAGTGCCCGGGGCGCCCGGGTGCGT--ACCCGAAGTGT-CCCC-GAGTCCAGCCTGCGTTTTCAGCAGGAAATT-AGCGACCAGGAGC-GCC-CGAGAAGCG-----ACTTCACCT--C--GCTGGGGCAGGAAGGGG--G i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 55997 176 + 225949 AAGACCTCA-TTACGGA-GACCCCACTC-CATTAGCCTCCTACCTGCTCCACGCTAAGTGCCAGGGGCGCCCGGGTGCGC--GCCCAAGGCGT-CCCC-GAGTCCAGCCTGCGTTTTCAGCAGGAAATT-AGCCACCGCC-GC-GCC-CGAGAAGCG-----ACTTCGCCT--CGAGCTGGGGCAGGAGGGGG--A i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 14585 171 + 19765 AAGACCTCA-TTACGCGCGACCCCGCTC-CATTAGCCTCCTACCTGCTCTGAGCTAAGTGCCCCGGGC-TCCGGGCGCGC--GCCC-AGGCGT-CCCC-GCGCTGAGCCTGCGTCTTCGGCAGGAAATT-AGCGACCCAGTGC-G-C-CGAGGAGCG-----ACTTCGCCT--GGAGCTG----CGGGAGGGG--G i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118769046 169 + 121843856 AAGACCTCA-TTACCCGAGACCCTACTC-CATTAGCCCCGTACCTGCTCTGGAC-------CCTAGACTCCCCGATGCGC--TCCCGAGGCGT-CCCC-A-GCTTAGCCGGCGTTTGTGACAGAAAATT-AACGACCCTGCGC-GCA-CCAGAAGGC-----ACTTCACCT--CCAGCCGGAGGAGGAAGGGA--- i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 6037 136 + 11404 AGGGTCT-------CCGAG------------------CAGGACTATCTGTGGGC-----------GCCTGCCCACTGGGTTGTCCCCAGG-GT-CCCC-A---------GGGAGCCGTGACAGGAAATA-AACGACCCTAGACAGCAGCCAGGGGCG-----ACTTCGCCT--CCAGCTGG-GGAGAGAGCGA--- i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4398158 175 + 7991924 AAGACCTCA-TTACAGGAGACCCCACTC-CATTCGCCCCGTAGCTGCTGGGCGCTAAGTGCCCTGGGCTCCCGGGTGCGC--GCCTAGGGCGT-CCCT-A--CCAAGTCTGCGTTATAGGCAAGAAATT-AACAACCTGGCGCTCCA--GGGAAGTG-----ACTTCACCT--CGAGCTGCCGGAGGAAGGGA--- i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 11637 157 - 54875 AAAACCTCAGCCCCGCAACCCCCCGCTCTCAGGAGCCTCCCACCTGCTCGGCGG--CGCGCGGAGGGGCTCCAGGTGCGC--GCCCAGGGCGT-CCCC-G----CACCCGGCG-----GGCAGGAAGTC-GCCGAGACGCCCCCGCA-CCGGAGGCG-----CAGTGGACC--CTGGCTGG--------------- i ochPri2.scaffold_9426 I 23 C 0 s turTru1.scaffold_106006 137439 170 + 145505 AAGACCTCA-T-ACGGGCGACCCCACTC-TATTAGCTTCGTACCTGCTCGGTGCTAAGTGCCCTGGACTTCCTAGTGTGC--GCCCAGGGCGT-CCCA-GCGCCGAGCGGGTGTTT-CAGCGGGAAATT-AGCCGCCGGGCGC-GCG-GGAAAAGCG-----ACTTCACCT--CCAGCTGGGGTGGA--------G i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10867476 171 - 65312493 TAGACCTCA-T-ACCGGCGACCCCACTC-CATTAGCCTCCTACCTGCTCTGTACTAAGTGCCCCGGGCTCCCGGGCGCGC--GCCCAGGGCGTCCCCC-GAGCCGAGCGGGTGTTT-CAGCTGGAAATT-AGCGGCCGGGCGC-GAG-GGAGAAGCG-----ACTTCACCC--CCAGCTGAGGTGTA--------G i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58051446 174 - 61308211 AAGACCTCA-TTACGGGCGACCCCACTC-CATTAGCTTCGTACCTGCTCGGTGCTAAGTGCCCCGGGCTCTCGGGTGCGC--GCCCAGGGCGG-CCCT-GGGCCCAGCCGGTGTCT-CAGCAGGAAATC-AACGACCCGGCGC-GCG-GGAGAAGTG-----ACTTCACCT--CGAGCTGGGGGAGGGAC-----G i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 45738 180 + 132007 AAGACCTCA-TTACGTTCGACCTGACTC-CATGAGCCTGGTACCTGCTCGGTGCTAAGTGCCCTGGGCTCCCCGGTGGGC--GCCCAGGGCGT-CCCT-GAGCCAAGCGGGTGTCT-CAACAGGAAATT-AGCAACCTGGCGC-AGGCAGAGGCCGG-----ACTTCACCC--CTAGGTGAGGAGGGGACAAGGAG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59445302 163 - 64418924 AAGACCTCA-TGAAGGGCGA---------------CCTGGAATCTGCTAGGCGCTGAGTGCCCGGGGCAACTGGGGGTGC--ACCCAGGGCGT-TCCT-GAGCAGGGAGGGTGTTT-CAGCAGGAACTT-CGTGACCCTGCGC-GTGCAGATCCCTGACTTCACTTCACCT--CTAGCTCGGGGTGG--------G i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 23405 169 + 48268 AAGACCTCA-TTACCGGCAGCCCCCCTC-CACTGGCCC-GTCCCTGCTCGGCGCCTAGTGCCCCGCTCCCGCGTGCGCGC--GCCCAGGGCGT-CCCT-GAGCCGAGCT-GTATTT-CAGCAGGAAATT-GGCGACCTGGCG--GAACCGAGGAGCG-----GCTTCATCT--GGGGTGGGGGTGGG--------G i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_355010 8046 137 + 8359 AAGCCCTCC-CGGTGGGCCACCCCGCTC-CACCAGCCCCTTGACCACCCCA-GCTCAGCGCCGCAGGAT--------------CCGAGGGCGC-TC----AGCCTTGCCAGGGT--------GTAAATA-CAT---------------GGAGGAGCA-----ATTTCCCCCAAGAAGCTGAGGTGGG--------G i eriEur1.scaffold_355010 C 0 C 0 s loxAfr3.scaffold_49 14442768 130 - 17734757 AAGATGTCA-TTATAGGCGGCCCCACTC-CATTAGCCTTGTAACTGCTTGGCGCTAAAT-----------------------GCCCCGGGCGT-CTCC-GAGCCCAACCCGCATTTCCAGCAGGACATT------------------------AGCG-----ACTTCACGC--CGGGCCGGAGGGAGG-------- i loxAfr3.scaffold_49 C 0 I 1 s choHof1.scaffold_149147 5205 173 + 9388 AAGGCACGA-TTATGGGTGACTCCGCTC-CATTAGCCTCGTACTTGCCCGGTGCTAAGTGCCCGGGGCTCCCCGATGCGC--GCCCGGGGCGT-CCCCGGAGCCAAGCCCCGGCTTTCAGCAGGAAAATTAGCGACCCGGCAC-GGG--GAGCAGCG-----ACTTCACCT--Cggggtggaggtggg-------- i choHof1.scaffold_149147 C 0 I 3095 e oryCun2.chrUn0958 26479 1096 + 41507 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304551395 4976 - 541556283 I a score=512368.000000 s hg19.chr17_gl000204_random 55339 151 + 81310 ACTTAAACCCAGGG-----ATGGATCCCT------------TGGGTCTCTGTCCTTAGCCTCCACCGTGGG-GTGTCTCGCGCGTCGGGACTAGCGGCTCCGCGGGACTCCTTTTT-AAAAGTGATCATT--A---AATAAATCAGGT-----ACCTCGCCAAAGCTGGAACGGAAAGGG s panTro2.chr17 79485248 151 + 83384210 ACTTAAACCCAGGG-----ATGGATCCCT------------TGAGTCTCTGTCCTTAGCCTCCACCGCGGG-GTGTCTCGCGCGTCGGGACTAGCGGCTCCGCGGGACTCCTTTTT-AAAAGTGATCATT--A---AATAAATCAGGT-----ACCTCGCCAAAGCTGGAACGGAAAGGG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0468881 887 151 + 1088 ACTTAAACCCAGGG-----ATGGATCCCT------------TGGGTCTCTGTCCTTAGCCTCCACCGCGGG-GTGTCTCGCTCGTCGGGACTAGCGGCTCCGCGGGACTCCTTTTT-AAAAGTGATCATT--A---AATAAATCAGGT-----ACCTCGCCAAAGCTGGAACGGAAAGGG i gorGor1.Supercontig_0468881 C 0 C 0 s ponAbe2.chr17_random 16072694 151 + 17838096 ACCTAAACCCAGGG-----ATGGATCCCT------------TGGGTCTCTGTCCTTAGCCTCCACCGCGGT-GTGTCTCGCGCGTCGGGACTAGCGGCTCCGCGGGAGTCCTTTTT-AAAAGTGATCATT--A---AATAAACCAGGT-----CCCTCGCTAAAGCTGGAACGGAAAGGG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75046573 151 + 78773432 ACCTAAACCCACGG-----ATGGATCCCT------------TGGGTTTCTGTCCTTAGCCTCCACCGCGGG-GTGTCTCGCGCGTCGGGACTAGCGGCTCCACTGGAGTCCTTTTT-AAAAGTGATCATT--A---AATAAATCAGCT-----CCCTCGCCAAAGCTGGAACGCAAAGGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 53756 151 - 95547 ACCTAAACCCACGG-----ATGGATCCCT------------TGGGTTTCTGTCCTTAGCCTCCACCGCGGG-GTGTCTGGCGCGTCGGGACTAGCGGCTCCACTGGAGTCCTTTTA-AAAAGTGATCATT--A---AATAAATCAGCT-----CCCTCGCCAAAGCTGGAACGCAAAGGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 56173 152 + 225949 ACCTAAGCCCAGGG-----ATGGATCCCT------------TGGGTCTCTGTCCTTAGCCTCCACTGCGGG-GTGTCTCGCGCTTCGGGACCAGAGGCTCCGCAGGAGTCCTTTTTAAAAAGTGATCATT--A---AATAAATCAGGT-----CCCCTGCCAAAGCCGGAACGGAAAGGG i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 14756 152 + 19765 ACTC-GGCTAAGGA-----ATGGATCCCG------------CAGGTCCCTGTCCTTTGCCTCCGCCA-GGG-GTGTCTTGCGCATCAGGATTAGTGGCGCCTCGGGAGTCCTTCTT-AAAAGTGACCATT--AAATAATAAATCGAGT-----CCCTCCCAAAAGCTAGAACGGAAAGGG i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118769215 153 + 121843856 -CTT--GCCCAGAAGAAGAAAGGATCCCT------------C-AGTCCCTGTCCATAGCTCCCACTGTGGGTGTCTCGCACATCGAGAGACTACTGGCGCCACCGGCGTCCTTTTT-AAAAGTGACCATT--A---AATAATTAGAGT-----GCGTCTGAAAAGCAGAATCCAAAAGGG i mm9.chr11 C 0 I 2 s dipOrd1.scaffold_43980 6173 148 + 11404 ---------GAGAGGACCAGAGCATCCTC------------T-GCGCCCCTCCT---GCCCCCAATCCCTGCCTCCCTGCCAACCTG-GGCTACCAGCACCCCAAAGATGGTTTCT-CAAGACTACCAAA--C---AATAAATAATCTCCCCGTCACCCACAAAGCAAGGACGGAGAGGG i dipOrd1.scaffold_43980 C 0 I 2064 s cavPor3.scaffold_76 4398333 142 + 7991924 -CTC--TCCCAGGG-----ACGGATCCCT------------C-CGCCCCAGCCCTTGGCCTGCACCGCCTG-GTGTCTGGCGCCCCGGGGCTA--GGGCCCAGCGGGAGTCCATTT-AAAAGTAACCTTT--A---AATAACAGAACC--------TCCGGAAAGCAGGAGCAGACCGGG i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 11794 36 - 54875 --------CCAGGG-----------------------------AGACCCAGCCA--AGCCCCC----------------------------------TGCCAGTGCCAG----------------------------------------------------------------------- i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 137609 131 + 145505 GGC-----------------TGGGTCCCT------------C-CGTCCCTGTCCTTTTCTTCCACCGCGGG-ATGTCTCATGCGTCAGCATGAGCAGAACCGCGGGTGTTCTTTTT--AAAGTGACCATT--AAAAAATAAATCTAGT-----CCCTCCCCAAAGCTGGAG--------- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10867647 131 - 65312493 GGC-----------------TGAGTCCCT------------C-CGTACCCGTCCTTTTCCTCCACCGCGGA-ATGTCTCGTGCATCAGCGTGAGCTGCACCGCGGGCGTCCTTTTT--AAAGTGACCATT--AAAGAATAAATCCAGT-----CCCTACCCAAAGCTGGAG--------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58051620 156 - 61308211 GCCTCGCCCGACGG-----ATGGATCCCACCCCGCCGGACCC-CGTCCTTGTCCTATGCCTCCGTCGCGGG-GTCTCTCGCACACCAGGATGAGCGGCGCCGCCGGAGTCCTTTTT-AGAAGTGACCATC--AAAAAATAAATCTAGT-----CCCTCCCCAAAGCTAGCA--------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 45918 144 + 132007 GTCTCTCCTGGGGG-----ATGGTTCCTT------------C-GGCCCCTTTCCTTTGCCTCCGCTGCCAG-GTGTTTCGCGCGTCAGTAAGTGCGGCGCCGCGGGAGTCCTTTTT-AAAAGTGGCCATT--AAAAAATAAACCTAGT-----CCCTCGGAAAGGCTGGAA--------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59445465 141 - 64418924 GGTTCGCCTGGGAG-----ATGGATCCTG--------------GGTCCCTGTCCTTCACCTCCACCACCGG-GTG-TTCACA-GGCAGGAAGAGCGGCGCCCCAGGAGTCCTTTTT-TAAAGTGACCACT--AAAAAATAAACCCAGT-----CCCTTGGAAAAGCTGGAA--------- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 23574 152 + 48268 GTCTCGCCCAAGGG-----ATGGAGCACC-CCCGCCCCCGCG-CGTCCCTA---TTTGCCCCCACCTCCGG-GCGTCCTACGCATCATGATGAGCAGCGCAGCGGGAGTCCTTTTT-TAAAGTGACCAGT--AAAAAATAAATCTAGA-----GCCTACCAAAAGCTGAGA--------- i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_355010 8183 108 + 8359 GTG-ACCCCAAGGG-----AAGAACCCCT------------C-TGT------------CCTCCACGGCGAG-GTA----------------GAG---------AGATATTCTTTTT-CAAAacgaccattaaaaaaaattaatcctgT-----TTTTCTCTAAAGCTGGAA--------- i eriEur1.scaffold_355010 C 0 N 0 s loxAfr3.scaffold_49 14442899 149 - 17734757 GCGCTGGCCCTAGC-----ACTGCTCCCT------------AGAGTCTCTGCCCTCCGCCCCCACCGCAGG-GGGTCGCGCAT-----CATTACAGCTGCCGCGGCACCCGTTTTT-AAAAGGGCCCATC--TCGTAACAAATCTCGT-----CCTTTCCAAATGCAGGAAAGGAAAGGG i loxAfr3.scaffold_49 I 1 C 0 e oryCun2.chrUn0958 26479 1096 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304551395 4976 - 541556283 I a score=136868.000000 s hg19.chr17_gl000204_random 55490 41 + 81310 GAGGGGGAGGCAG---------CTC--------TGTTGTCCAGGAGTTTCTCCCCACC s panTro2.chr17 79485399 41 + 83384210 GAGGGGGAGGCAG---------CTC--------TGTTGTCCAGGAGTTCCTCCCCACC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0468881 1038 41 + 1088 GAGGGGGAGGCAG---------CTC--------TGTTGTCCAGGAGTTTCTCCCCACC i gorGor1.Supercontig_0468881 C 0 n 0 s ponAbe2.chr17_random 16072845 41 + 17838096 GAGGGGGAGGCAG---------CTC--------TGTTGTCCAGGAGTTTCTCCCCACT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75046724 41 + 78773432 GACGGGGAGGCAG---------CTC--------TGTCATCCAGGAGTTTCTCCCCACC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 53907 41 - 95547 GACGGGGAGGCAG---------CTC--------TGTCATCCAGGAGTTTCTCCCCACC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 56325 41 + 225949 GAGGGGGAGGCAG---------CTC--------TGTCATCCAGGAGTTTCTCCCCACC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 14908 38 + 19765 GA--GGCAGGCGG---------CTC--------TGTCACCCAGGAGTTTCTTCTCCC- i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118769370 39 + 121843856 AGCGGGGATGTGG---------CTC--------GGCCATCCTGGACCCTC--CTCACC i mm9.chr11 I 2 C 0 s cavPor3.scaffold_76 4398475 33 + 7991924 --------GTCAG---------CTC--------AGTCATCCAGGAGTTTTGACCCATC i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 11830 10 - 54875 ----------------------------------------------CCCC--CACAAC i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 137740 30 + 145505 -----------AG---------CTT--------CGCCAGGAAGGAGTTTCTCCTCATC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10867778 30 - 65312493 -----------AG---------CTC--------CGTCAGGAAGGAGTTTTTCCTCACC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58051776 30 - 61308211 -----------AG---------CTC--------TATCACCCAGAAGTTTCTCCCCACC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 46062 28 + 132007 -----------AG---------CTG----------TCACGGAGGAGTTTCTCCCCACC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59445606 27 - 64418924 -----------AG---------CTC----------TCACGGAGGAGTTTC-CCTCACT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 23726 37 + 48268 -----------CAGATGAGTTTCTG----------TCACCCAGGAGTTTCTCCCCACC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14443048 44 - 17734757 ---AAGCAGGCAG---------CTCCGTCACCCTGTCACCAAGAAGTTTCTCCCCC-- i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 26479 1096 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e monDom5.chr2 304551395 4976 - 541556283 I a score=350595.000000 s hg19.chr17_gl000204_random 55531 128 + 81310 TCG-CTGGGCCC-----CCGCCCCCACCAGTGGAC-----------------TCCGGGAA-------------CAT---CCCACCC-CCACCC-TACGTGATACCAGGGATCCCAGGGCCGCTTGGG-GACCCGACAGGTTCCCAATGCCCCTCCACG--CGGGGCGCCGCG s panTro2.chr17 79485440 128 + 83384210 TCG-CTGGGCCC-----CCGCCCCCACCAGTGGAC-----------------TCCGGGAA-------------CAT---CCCACCC-CCACCC-TACGTGAGACCAGGGATCCCAGGGCCGCTTGGG-GACCCGACAGGTTCCCAATGCCCCTCCACG--CGGGGCGCCGCG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16072886 128 + 17838096 TCG-CTGGGCCC-----CCGCCCCCGCCAGTGGAC-----------------TCCGGGAA-------------CAT---CCCGCCC-CCACCC-CACGTGAGACCAGGGATCCCAGGGCCGCTTGGG-GACCCGACAGGTTCCCAATGCCCCTCCACG--CGGGGCGCCGCG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75046765 127 + 78773432 TCG-CTGGGCCC-----CCGCCCCCGCCAGTGGAC-----------------TCCGGGAA-------------CAT---CCCA-CC-CCACCC-CACGTGAGACCAGGGATCCCAGGGCCGCTAGGG-GACCCGACAGGTTCCCAATGCCCCTCCACG--CTGGGCGCCGCG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 53948 127 - 95547 TCG-CTGGGCCC-----CCGCCCCCGCCAGTGGAC-----------------TCCGGGAA-------------CAT---CCCA-CC-CCACCC-CACGTGAGACCAGGGATCCCAGGGCCGCTAGGG-GACCCGACAGGTTCCCAATGCCCCTCCACG--CTGGGCGCCGCG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 56366 127 + 225949 TCG-CTGGGCCC-----CCG-CCCCGCCAGTGGAC-----------------TCCAGGGA-------------CAT---CTCACCC-CCACCC-CACGTGAGACTAGGGATCCCAGGGCCCTTTGGG-GACCCAACGGGTTCCCGAAGCCCCTCCACT--CGGGGCGCCGCG i calJac1.Contig5139 C 0 I 326 s micMur1.scaffold_15893 14946 118 + 19765 ACG-CCAAGCCC-----CCGCCCCTGCCAGTGGGC-----------------TCCGGGAA-------------TAT---CCCGCCCACCACCC-CACGTGAGACTTGGCGCCCC-GGGCCGCTCTGG-GACCCGACAGGTTCCCTGTGCCCCTACCCG--CG---------- i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118769409 140 + 121843856 TCG-CAGCCCAC-----ACACACTAGCCGACG--------------------TCAGTGAGCTTCGTGAACAGCCAA---CCAACCC-CCAATCTCATGCAAGACCCAAGATCCTGGGTCTGTTCCAGCTGTCTAATAGGGTCTCAATGCCCCCCCCCC--GTGCTGGTCGCG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4398508 89 + 7991924 TCG-CTGGGCCC-----CCGCCCCTGCCGGAA--------------------TCCGGAAA-------------CAT---CCCACCC-CCACTC-CACGTGAG------------------GTGCTGACTGTTTAGGA-------------------CG--ATGGTGGCCACA i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 11840 123 - 54875 ACA-CAAGCCGCCGCCGCCGCCCCTGCCAGGGCTC-----------------TCCAGGCG-------------CAG---CTGCCCC-CGCTTC-CACGGGGGTCCTGGAATGCCAGTTCCGCTCCGG-----------GGCCTCGATGCCCAGCTACG--CGGGACGCCGCG i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 137770 139 + 145505 CCC-CTGGACCC------CGT-GCCGCTGGCGGGG--CTGCAGTCCTGGACTCCAAGGAA-------------CAT---CC--CTC-CTGCCC-CACGTAAGACCCCGCATCCTGGCGCCGCTCTGG-AATGGGATGGGGTCCCCTTGTCCCTCCACG--CCCGGGGCCGCA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10867808 140 - 65312493 CTCGCCGGACCC------CGCGGCCGCTGGAGGAG--CTGAAATCCTGGACTCCCAGTAA--------------AT---CC--CTC-CTACCC-TATGTCAGACCTCGGATCCTGGGGCCGCTCTGG-GACGGGATGGGGTCCCAATGTTCCTCCACG--CCCCGCGCCGCG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58051806 140 - 61308211 CCG-CTGGACCC------CACGCCCGCTGGCGGGG-GCCAGAGTTCGGGACTCCCAGGAA-------------GAT---CC--TCC-CCACAC-A-CGTAAGACCCCGGATCCCGGGGCCGCTCTGG-GACGGGACGGAATCCCAATGTCCCTCCACG--CCGGGCGCTGCG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 46090 137 + 132007 CCG-CAGGACCC------CGCGCTAGCTGGCGGGG--CCGGAGTTCCAGACTCCCAGAGA-------------CAC-------CCT-CCACCC-CACGTGACACTCTGGATCCCAGGGCCACTCTGG-GAC-GGACGGGGTCCCAACGTCCCTCCGCG--CCAGGCGCCGCT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59445633 132 - 64418924 CGG-CAGGACCC------TGTGCCCTGTGGCGGGA---GGGAGCTCCAGACTCCCAGGAA-------------CACCGCCA--CCC-CCACCC-C-CAGGAGACTGTGGATCCGGGGGCTGCGCTGG-GGC-GCACAGG--------GTCGGTCCTCG--GCAGGCGCCGCT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 23763 141 + 48268 CCG-CTAGACTC------CTTGCACTGGGGTGGGGGGACAGAGCTCTGGGCTCCCAGGAA-------------CAC--------CC-CCATCC-CACGGGAAACCCCGGATCCCCGGGCCACTCGGG-GACAGGACTGGGTCCTAGTGTCCCCGCTGGGACTGGGTGAGGGC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14443092 130 - 17734757 CAA-CTGGGCTC-----CTGCGCCCGCCAGCTGTT-GCCTGAGTTCTGGAC-TCCAGGAC-------------CTT--------CC--------CCCGTGGGGCTTCGGATACCTGGGTCGCTCCGG-GGA-GGGCGGGGTACCAAGGCATCTCCGCG--CCGGGTGGCCA- i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 26479 1096 + 41507 I e gorGor1.Supercontig_0468881 1079 0 + 1088 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e monDom5.chr2 304551395 4976 - 541556283 I a score=-119307.000000 s hg19.chr17_gl000204_random 55659 166 + 81310 TCTCGGTCCCCGCACCGA------------------------------------------------CACTGCAGGGCTGCG-CGCCAGGGGAGG---CTCCGCGTCCCGGGGAGGGAGGCTGCGACCCC------CAGCACCAAAATGACC---ACTGGCCT-----CGCGCC--ACCCCGAGACGC------CACAGAAGACCACCTTCCCGA------GCGT--------------------GCGAGCCCAACACGCCCCGGGC s papHam1.scaffold8336 54075 166 - 95547 TCTGGGTCCCCGCACCAA------------------------------------------------CACTGCAGGGCTGCG-CGCCAGGGGAGG---CTCCGCGTTCGGGGAAGGGAGGCTGCGACTCG------CAGCATCAAAATGACC---ACCGGCCT-----CGCGCC--ACCCCGAGACGC------CACAGGAGACCACCTTCCCGA------GGGT--------------------GCGAGCCCCAGACGCCTGGGGC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75046892 166 + 78773432 TCTCGGTCCCCGCACCAA------------------------------------------------CACTGCAGGGCTGCG-CGCCAGGGGAGG---CTCCGCGTTCGGGGAAGGGAGGCTGCGACCCG------CAGCATCAAAATGACC---ACCGGCCT-----CGCGCC--ACCCAGAGACGC------CACAGGAGACCACCTTCCCGA------GGGT--------------------GCGAGCCCCAGACGCCTGGGGC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16073014 166 + 17838096 TCTCGGTCCCCGCACCGA------------------------------------------------CAGTGCAGGGCTGCG-CGCCAGGGGAGG---CTCCGCGTCCGGGGGAGGGAGGCTGCAACCCA------CAGCACCAAAATGACC---ACTGGCCT-----CGCGCC--ACCCCGAGACGC------CACAGAAGACCACCTTCCCGA------GGGT--------------------GCAAGCCCCAGACGCCCCAGGC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0460956 22 186 + 1444 TCTCGGTCCCCGCACCGA------------------------------------------------CACTGCAGGGCTGCG-CGCCAGGGGAGG---CTCCGCGTCCGGGGGAGGGAGGCTGCGACCCC------CAGCACCAAAATGACC---ACTGGCCT-----CGCGCC--ACCCCGAGACGC------CACAGAAGACCACCTTCCCGA------GGGTGCGAGCCCCAGACGCCCCGGGCGAGCCCCAGACGCCCCGGGC i gorGor1.Supercontig_0460956 n 0 C 0 s panTro2.chr17 79485568 166 + 83384210 TCTCGGTCCCCGCACCGA------------------------------------------------CACTGCAGGGCTGCG-CGCCAGGGGAGG---CTCCGCGTCCGGGGGAGGGAGGCTGCGACCCC------CAGCACCAAAATGACC---ACTGGCCT-----CGCGCC--ACCCCGAGACGC------CACAGAAGACCACCTTCCCGA------GGGT--------------------GCGAGCCCCAGACGCCCCGGGC i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 15064 162 + 19765 CCTCTGT-CCGGCACCGACAGG-----GTGCGG----G--CTG-CGCGGCC-------GGCCGGGGCACTGCGGGGCGGTG-CGCCAGGGGAGGTTCCTCCGCGCT-----GGGGGAGGCTGCCACC--------------------AACC---GCC-------------------CCCTGAGACGC------CACAGGAGACCAGCCACCCGA------------------------------AGGAGCCTCAGACGCCCCCTGT i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118769549 161 + 121843856 TCTTGCTCCGGGTACAGACTGG-----GTGCGG----GACCTG-GGTGGCCA------GGA-----CACTGAAGGGCTGCA-TGCCAATGGA----------------------TAGGGGCGAAGCTTCATCAGGGAGCTCCCAGAGGACC---GCCGGCCTGAAGCCACC-----CCCTGACACCTTTCTCCTGAAGAAGACAGC----CCCA------GGA------------------------------------------- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4398597 164 + 7991924 TCTCTGT-CGCACACAGACTGG-----GTGAGG----GCCCGG-GTCGGCC-------GAG-----CACTGCGGAGCCACG-CGCCAGGGGAGG---CTCCGCGCC--GCAGTGTAAGGTTGAGGCGACCC----GAGCCCCAAAACGACC----CCAGCCT-----CATG-----CCCTGAGACAT------CGCGGGAGACTGCCGTTCCGA------GGG------------------------------------------- i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 11963 98 - 54875 CTTCCTC-CTTCCGTCCACTGG-----GGGCGG----GCCCCG-GGCGACGAGG----GGC-----CACTGCGGGG---------------------------------------AAGCTCGGCGCCCCA-----GGGCACCCAGATGCCCTCCGCAGGGCT-------------------------------------------------------------------------------------------------------- i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 137909 165 + 145505 TCCTCGTCCCCGCGCGTACTGT-----AAGAGG----GCCCCC-TGCGGG--GATGCGGGG-----CACTGCGGGGATGCA-CGCCTGGGGAGG---CTCCGCACC-----GAGGGAGGCTGC------------------------GACC---TACGGCCT-----CGTGCC--ACCCCTAGGTTC------CTCGAGAGACAGCCCTCCCGA------GGGG--------------------GCGACC---------CCCGGAC i turTru1.scaffold_106006 C 0 I 10 s bosTau4.chr19 10867948 146 - 65312493 TCCTCGTCCCCGCGTGTACCCG-----GTGAGG----GCCCCC-GGCAGC--GC----GGG-----CACTGCGGGGATGCA-AACCCGGAGAGG---CTCCGCGCC-----GGGGGAGGCTGC-----------------------------------------------GTC--ACCCCGAGGTGC------CGCCAGAGACAGCCCTCCCGA------GGGG--------------------GCGAGC---------CCTGGAC i bosTau4.chr19 C 0 I 18 s equCab2.chr11 58051946 137 - 61308211 CCCTCGTTCGCGCGCAGCCCGGGCACTGTGGGGATGCGCGCCT-------------------------------------------GGGGGAGA---CTCCGCGCCC----GGGTGAGACTGC------------------------GACC---GCCGTCCT-----CGCGCTG-CCCCGGAGGCGCCTT---CGGG-TAGACACCCCTTCCCT-----AGGGG--------------------GCGAG----------------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 46227 150 + 132007 CCCTCGTCCTCTCTCCGACTGG-----GTGAGG----GCCCCT-GTC-----AGCGC-GCG-----TACTGCGGAGATG------CCGGGGAGG---CTCCGCGCCC----GGCAGTGGATGC------------------------GACC---TTGGGCCT-----CGGGCCG-CGTCCGGGGCCC------CGCG-GAGACAACCCTCCCAA-----AGGGA--------------------G-GAGC---------------- i felCat3.scaffold_206428 C 0 T 8110 s canFam2.chr9 59445765 119 - 64418924 CCCTCGATCTCACACGGACAGG-----ATGAGG----GTCCCG-------------------------------------------CAGGGAGG---CTCCGCGCCC----GGAGGAGGAGAG------------------------GACC---TCAGGCCC-----TGTGCC--TGCCGGGGGCAC------CGCG-GAGGCAGCCGCCCGAA-----------------------------------------------GGGAC i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 23904 139 + 48268 CCCAGCATCCC---CGGCCCCG-----AAGGGGATGAGCGCC--------------------------------------------AGGAAAGG---CTCTGCCTTG----GGAGAAGGCTGC------------------------TACC----CAAGCCT-----CGCTCAGCCGCCGAAGGCAA------CGCGAGAGACAGCCCTGGGGAGGGGGAGGGG--------------------GCGAAC---------TCGGGAC i pteVam1.scaffold_11245 C 0 I 5 s loxAfr3.scaffold_49 14443222 161 - 17734757 GCTCTCTCCCCGCGCCGGCTGG-----GTGCGC----ACCCCCAGGCAGCCC------GGG-----CCCTGCGAGGCTGCGTTACACGGAAAGG---CTTCGCGCCCCGGGGAGT--------------------------------GTCC---ATC----------CACAGC--ACCC--AGGCGC------CGCGGGAGACAGCCCTTGCCA------GGGA--------------------ACGAACCCCGGACGCCCCCGC- i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 26479 1096 + 41507 I e calJac1.Contig5139 56493 326 + 225949 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e monDom5.chr2 304551395 4976 - 541556283 I a score=421126.000000 s hg19.chr17_gl000204_random 55825 68 + 81310 GAGCCCCACC---------ACCGCCCGGGGCCACCAGGGCAGAAAGTTTGGGCCAGGGGCG-TGCCCGGC-TTTCCCAG----- s papHam1.scaffold8336 54241 67 - 95547 GAGCCCC-CC---------ACCGCCCGGGGCCACCGGGGCAGAAAGTTTGGGCCAGGGGCG-TGCCCGGC-TTCCCCAG----- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75047058 67 + 78773432 GAGCCCC-CC---------ACCGCCCGGGGCCACCGGGGCAGAAAGTTTGGGCCAGGGGCG-TGCCTGGC-TTCCCCAG----- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16073180 68 + 17838096 GAGCCCCACC---------ACCGCCCGGGGCCACCAGGGCAGAAAGTTTAGGCCAGGGGCG-TGCCCGGC-TTCCCCAG----- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0460956 208 68 + 1444 GAGCCCCACC---------ACCGCCCGGGGCCACCAGGGCAGAAAGTTTGGGCCAGGGGCG-TGCCCGGC-TTCCCCAG----- i gorGor1.Supercontig_0460956 C 0 C 0 s panTro2.chr17 79485734 68 + 83384210 GAGCCCCACC---------ACCGCCCGGGGCCACCAGGGCAGAAAGTTTGGGCCAGGGACG-TGCCCGGC-TTCCCCAG----- i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 15226 68 + 19765 GAGCCCCGCC---------GCCTCCTGGGGCCACCGGGGCAGAAAGTTTGAGCCAGGGGCG-TGCCTGGC-CGCCCTGG----- i micMur1.scaffold_15893 C 0 I 10 s mm9.chr11 118769710 66 + 121843856 GAATCCCACC---------ACCTCCCGGGGCCACA-AGTCAGAAAGTTTGGGCTAGGGTTG-TGCA-GGC-CACCTTAG----- i mm9.chr11 C 0 I 9 s cavPor3.scaffold_76 4398761 67 + 7991924 CAAGCTCGAG---------GCTTTCTGAGGCATCA-GGGCAGAAAGTTTGGGCCAGGGGTG-TGCC-AACGCGCCCTGG----- i cavPor3.scaffold_76 C 0 I 8 s oryCun2.chrUn0958 27575 67 + 41507 GAACCTGGAC---------GCCTCCCCGGACCACAGGGGCAGAAAGTTAGGGCCAGGGCTG-TGCCCGGC-CACCC-GG----- i oryCun2.chrUn0958 I 1096 I 9 s ochPri2.scaffold_9426 12061 68 - 54875 GACCCTTGCT---------GCCTCCCGGGACCTCAGGGGCAGAAAGTTTGGGCCAAGAGTG-GGCCTGGC-CTCCCTGA----- i ochPri2.scaffold_9426 C 0 I 7 s calJac1.Contig5139 56819 59 + 225949 ---------C---------ACCGACCGGGGCCACCGGGGCAGAAAGTTTGGGCCAGGGGCG-TGCCCGGT-TTCCCAAG----- i calJac1.Contig5139 I 326 C 0 s turTru1.scaffold_106006 138084 74 + 145505 GAGTCTCGCCGCCTCCGGGGCC-TCTGGGGCCTCCGGGGCAGAAACTTTGGGCCGGGTGTG---CCCAGC-CGCCTTGG----- i turTru1.scaffold_106006 I 10 I 15 s bosTau4.chr19 10868112 65 - 65312493 GAGTCTCACC---------ACC-TCTGAGACCACCGGGATAGAAAGTTTGGACTGGGTGTG---CCTGAC-CGCCTTCG----- i bosTau4.chr19 I 18 I 18 s equCab2.chr11 58052083 66 - 61308211 --GCCCCGCC---------ACC-ACCGTGGGCACAGGAACAAACAACTTGCGCACAGTGTATTGCCCGGC-CGCCCTAG----- i equCab2.chr11 C 0 I 1497 s canFam2.chr9 59445884 57 - 64418924 GAGCGCCACC---------GCCTCCCGGGGCCGCTGGGGCAGAAAGTTTGGGCCAGGGGTG----------CGCCC-------- i canFam2.chr9 C 0 I 23 s pteVam1.scaffold_11245 24048 67 + 48268 GATCCCCACC---------GCCTGCCGGGGCCACCGGGCCAAA-AGTTTAGGCCAAGGGTG-TGCCCGGC-CGCCCTCG----- i pteVam1.scaffold_11245 I 5 I 15 s loxAfr3.scaffold_49 14443383 65 - 17734757 -----------------AAGCCTCCCAGGGCAGCCAGGGCAGAAAGTTTGGGCCAGGGGTG-TGCCCGGC-CCCACGGCGCCAG i loxAfr3.scaffold_49 C 0 C 0 e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e felCat3.scaffold_206428 46377 8110 + 132007 T e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e monDom5.chr2 304551395 4976 - 541556283 I a score=238957.000000 s hg19.chr17_gl000204_random 55893 77 + 81310 ----CCCGGCCGCGCTG-CTCGAGGCCCT-----GGGGGTGGC--CGAGGCTTCAGAGAG-GCAGCCTCTGCTCCCGTTCCAGCCTTCCT s papHam1.scaffold8336 54308 77 - 95547 ----CCCGGCCGCGCTG-CTCTAGCCCCT-----GGGGGCAGC--CAAGGCTTAGGAGAG-GCAGCCTCTGCTCCGGCTCGAGCCTCCCT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75047125 77 + 78773432 ----CCCGGCCGCGCTG-CTCTAGCCCCT-----GGGGGCAGC--CAAGGCTTAGGAGAG-GCAGCCTCTGCTCCGGCTCGAGCCTCCCT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16073248 77 + 17838096 ----CCCGGCCGCGCTG-CTCGAGGCCCT-----GGGGGTGGC--CGAGGCTTCAGAGAG-GCAGCCTCTGCTCCCGCTCGAGCCTTCCT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0460956 276 77 + 1444 ----CCCGGCCGCGCTG-CTCGAGGCCCT-----GGGGGTGGC--CGAGGCTTCAGAGAG-GCAGCCTCTGCTCCCGCTCCAGCCTTCCT i gorGor1.Supercontig_0460956 C 0 C 0 s panTro2.chr17 79485802 77 + 83384210 ----CCCGGCCGCGCTG-CTCGAGGCCCT-----GGGGGTGGC--CGAGGCTTCAGAGAG-GCAGCCTCTGCTCCCGCTCCAGCCTTCCT i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 15304 67 + 19765 ----CCCAGCAGGACTG-CAAGGGCCCGT------GGGGCAGC--GGAGGCTTTGGAGAA-GCTGCC---------GCCAGAGCCACCCT i micMur1.scaffold_15893 I 10 C 0 s mm9.chr11 118769785 63 + 121843856 ----CCCAGCCGGGCTG-TCCCA--GCCC-----TGTAGCTGTGCCAAAGC----GAGCA-GTAACCT----------CCGATCCTTGCT i mm9.chr11 I 9 C 0 s cavPor3.scaffold_76 4398836 75 + 7991924 ----CCTGGACGGGCTA-CACCA--GCAT-----GGGGGCAGT--CGAAGCTTGGGGAAG-GCATCCTGGGCGCGCGCCGGAGCCTAGCT i cavPor3.scaffold_76 I 8 C 0 s oryCun2.chrUn0958 27651 53 + 41507 ----CCCGGCCGGGCTG-GGCCT--CCCT-----GGGGGCGGC--CAAAGCTCCGAAGAA-GCAGCCG---------------------- i oryCun2.chrUn0958 I 9 C 0 s ochPri2.scaffold_9426 12136 56 - 54875 ----TCCGGCCGGGCTGAGGCCT--CCCC----GGGGGGCGGC--CGAGGCTCCGGGGGATGCAGCCC---------------------- i ochPri2.scaffold_9426 I 7 C 0 s calJac1.Contig5139 56878 75 + 225949 ----CTGACCAGCG--G-CTCGAGCCCCT-----GGGGGCTGC--CAAGGCTTCGGAGAG-GCAGCCTCCTCTCCCGCTGGAGCCTTCCT i calJac1.Contig5139 C 0 C 0 s turTru1.scaffold_106006 138173 71 + 145505 ---------CCGCGCTG-CGCCGGTCCCT-----GGGGGCGGC--CGAGAC-TCGGAGAA-GCAGCCTGGGTTCACGCCCGAGCCTCCCT i turTru1.scaffold_106006 I 15 C 0 s bosTau4.chr19 10868195 71 - 65312493 ---------CCGGGCTG-CGCCAGCCCCT-----GGGGGCGGC--CGAAGC-TCGGAGAA-GCAGCCTGGGTTCACGCCAGAGCCTCTCT i bosTau4.chr19 I 18 C 0 s canFam2.chr9 59445964 66 - 64418924 ---------GGGGGGCG-TGTTGGCCCCT-----GGAG-CGGC--CACAGC-GGGGAGCA-GCAGACCCGGCTCGGGCTGGAGACT---- i canFam2.chr9 I 23 C 0 s pteVam1.scaffold_11245 24130 70 + 48268 ---------CAGGGCTG-CGCTGGCCCCT-----GGAGTTGGC--CGAAGC--TCCAGAA-GCAGTACGGGTTCCCGCGGGAGCCTTCCT i pteVam1.scaffold_11245 I 15 C 0 s loxAfr3.scaffold_49 14443448 85 - 17734757 CTTCTCCAGCCGGGAGG-CCCGAGTCTCTGGGGGGGGGGCCGT--CGCGGCCCCCAAGAA-GCAGCCTCCGCTCCTGC-GTAGCTTTCCT i loxAfr3.scaffold_49 C 0 I 1343 e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e felCat3.scaffold_206428 46377 8110 + 132007 T e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e monDom5.chr2 304551395 4976 - 541556283 I e equCab2.chr11 58052149 1497 - 61308211 I a score=592066.000000 s hg19.chr17_gl000204_random 55970 189 + 81310 ATCGT----GCT---TGGGGACTCGGCCC---GGAGCG-CCCCCAGCCCGCCCCCT---G--TAGGGCC-----------------------------------------------CTGCGCGCCGCT-----CG----CCCCTCGCTGCTCG-G-C---CCCCGC-GCACACCGCGGTG-CTGCGGGCCCCGCTCCTATTTGGGGAGCT--GTGGCAGCCCCTTCCTC-------CCCACAACTCCTTTGGGTCATCAA-----CCTCT-----CAGCGACCCTCC s papHam1.scaffold8336 54385 236 - 95547 AACGC----GCT---TGGGGACTCGGCCC---GGAGCG-CCCCCAGCCCGCCCCCT---G--TAGGGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGCGCCGCT-----CG----CCCCTCGCCGCTCA-GCC---CCCCGC-GCACACCGCGGTG-CTGCGGGCC-GGCTCCTATTTGGGGAGCT--GTGGCAGCCCCTTCCTC-------CCCATAACTCCTTTGGGTCATCAA-----CCTCT-----CCGCGATCCTCC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75047202 189 + 78773432 AACGC----GCT---TGGGGACTCGGCCC---GGAGCG-CCCCCAGCCCGCCCCCT---G--TAGGGCC-----------------------------------------------CTGCGCGCCGCT-----CT----CCCCTCGCCGCTCA-G-C---CCCCGC-GCACACCGCGGTG-CTGCGGGCCGGGCTCCTATTTGGGGAGCT--GTGGCAGCCCCTTCCTC-------CCCATAACTCCTTTGGGTCATCAA-----CCTCT-----CCGCGATCCTCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16073325 189 + 17838096 ATCGT----GCT---TGGGGACTCAGCCC---GGAGCG-CCCCCAGCCCGCCCCCT---G--TAGGGCC-----------------------------------------------CTACGCGCTGCT-----CG----CCCCTCGCTGCTCG-G-C---CCCCGC-TCACACCGCGGTG-CTGCGGGCCCCGCTCCTATTTGGGGAGCT--GGGGCAGCCCCTTCCTC-------CCCACAACTCCTTTGGGTCATCAA-----CCTCT-----CAGCGACCCTCC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0460956 353 189 + 1444 ATCGC----GCT---TGGGGACTCGGCCC---GGAGCG-CCCCCAGCCCGCCCCCT---G--TAGGGCC-----------------------------------------------CTGCGCGCCGCT-----CG----CCCCTCGCTGCTCG-G-C---CCCCGC-GCACACCGCGGTG-CTGCGGGCTCCGCTCCTATTTGGGGAGCT--GTGGCAGCCCCTTCCTC-------CCCACGACTCCTTTGGGTCATCAA-----CCTGT-----CAGCGACCCTCC i gorGor1.Supercontig_0460956 C 0 C 0 s panTro2.chr17 79485879 189 + 83384210 ATCGC----GCT---TGGGGACTCGGCCC---GGAGCG-CCCCCAGCCCGCCCCCT---G--TAGGGCC-----------------------------------------------CTGCGCGCCGCT-----CG----CCCCTCGCTGCTCG-G-C---CCCCGC-GCACACCGCGGTG-CTGCGGGCCCCGCTCCTATTTGGGGAGCT--GTGGCAGCCCCTTCCTC-------CCCACAACTCCTTTGGGTCATCAA-----CCTCT-----CAGCGACCCTCC i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 15371 170 + 19765 AACGC----AC----CGCGGACTCGGCCA---GGAGCG-CCCCCTGCCCGCCCCCT---G--GAGGTCC-----------------------------------------------CTGCGCGCCTCT-----CT---------------------G---CCCCTT-GCACACCACGGCG-CTGCGGGCCCTGGTCCT-CTTGAGGAGTC--GTGGGAGGCCCTTCCTC-------CC---AACTCCTTTAGGTCATCAA-----CCCCTC----CAGCCACCCTCT i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118769848 189 + 121843856 CA-CG----CCTCTGGGAAGACTCGGCCC---CGAGCGCCCCCCAGCTCGCGGACT---A--GAGAGCC-----------------------------------------------CTGTGCG---CC-----AC------CCGCGCCTGT----------TCCAC-GCGTGCCGCTATG-CTGAGGGCTCTGGTCCTCCCGAGAGAGCCGAG-GAGGACCTCAGTCCT-------CCCACAACTCCTTGAGGTCATCAGTCAGTCCCCTCGG--C--CGGCTCTCC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4398911 192 + 7991924 CAGCC----ACTCCCGGTCTCCGCGGCCG---GGTGCACCCCTCCCCCGGCGCCCC---ACGGAGGGCG-----------------------------------------------CTGCGCGAGACC-----GC------CCCCGCCACTCT-G-C---CCCCGC-GCACTCCGCGGCG-CC-CGGGCCCTGGTCCTCCTGGAGGACCC--G-GAGACCCCATGCCTT-------CCCACAGCTCCTTAGAGCCTTC-------CACCTTTG--CAGTGACTCTCC i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 27704 147 + 41507 ---CT----GCT---------------------------CCCTC--CCGGGCCTCTCCAA--CAACGCT-----------------------------------------------CCGAG-Acggcc-----gg------gggcgcccccgg-g-agggccccgc-gcacgccccggcA----------CTGC------------------GTGGGAGCCCCTTCCTC-------CCAGCAACTCCTTGGGGTCTTCAACC---CCTCCCTC--CAGCGGCCCTCC i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 12192 150 - 54875 ---CC----ACG---------------------------CCCCCAGCCAGCCCCCT---G--GAGGGTC-----------------------------------------------CTGCGCACAGCC-----TG------CTCCGCCCCCGC-T-C---CCCCGC-GTTCGCCTCGGCAGCCGCGCGCCCTGCTTCTCTACGGAGAGTG--GCGGGAGCCCCTTGCTC-------CCGACAACTCCTTCGGGTCTG-------------------------CCACC i ochPri2.scaffold_9426 C 0 C 0 s calJac1.Contig5139 56953 197 + 225949 AACGCGCTAGCT---CGGAGACTCGGCCG---GGAGCG-CCCCCAGCCCGCCCCCT---G--GAGGGCC-----------------------------------------------CTGCGCGCCGCT-----CGCTCACCCCTAGCCGCTCG-G-C---CCACGC-GCATGCTGCTGCG-CCGCGGGCCCAGCTCCTATCTAGGGAGCT--GTGGCAGCCCCTTCCTC-------CCCACAACTCCTTTGGGTCATCAA-----CCTCT-----CAGCGATCCTCC i calJac1.Contig5139 C 0 C 0 s turTru1.scaffold_106006 138244 193 + 145505 AATGC--AGCTC---CCGAGACTTTGCGG---GGAGCG-CCCTCAGTCCGCCCCCT---G--TTGGGCC-----------------------------------------------CTGCGCGCGGCT-----CG----ACCCCTGCCGCTTT-A-C---ACTCGC-GCACAGCGCTGCG-CTGAGGGCCCGGGGCCTCTCTAGAAGACC--GTGGGAGACCCTTCCTC-------CCCAAAACTCCTTTGGGTCATCAA-----CTCCTCT---AGTGAACCATTC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10868266 188 - 65312493 GA-------CTC---CCGAGACTCTGCGG---GGAGCG-CCCCCAGCCCGCCGCCT---G--GAGGGCC-----------------------------------------------CTGCTAGCGGCT-----CG----CCCCCTGCCGCTTC-A-C---ACCGGC-GCACAGCGCGACG-CTCCGGGCCCGGGGCCTCTCTAGGGAACC--GTGGGAGACCCTTCCTC-------CCCACAACTCTTTTGGGTTATCAA-----CTCCTCC---GGTGAACCCTTC i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59446030 182 - 64418924 -CCGC--TG-----------------------GGAGCG-CCCCCAG-CCGCCCCCC---G--GAGGGCC-----------------------------------------------CCGC--GCTGCTAGCCACC----CCCACCGCGGCGCCTA-C---CCTCGC-GCACGGTGCAACG--CGCGGCCCCGGGGCT-CTTCAGGGAGCC--GTGGGAGCCCCTTCCTCCCTTCCACCCACAACTCCTTTGCGTCCTCCA-----CTCCTC----GCGGGAGCCTCC i canFam2.chr9 C 0 M 622 s pteVam1.scaffold_11245 24200 195 + 48268 GCCGC--CGCTC---CGGGGACTCGCTCGGCCGCAGTG-CCCCCAGCCCACCCGCT---G--GAGGACC-----------------------------------------------CTGC--GCGGCTGCTCACG----CCCCCCGCCGCTCC-A-C---CCACACAGCACGGAGC------TGCGG--CCAGGGCC-CCCTAGGGAGCC--GTGGGAGCCCCTTCCTC-------CCCACAACTCCTTTGGGTCATCGA-----CTCCTCCATGAACGAAGCCTCC i pteVam1.scaffold_11245 C 0 C 0 e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e felCat3.scaffold_206428 46377 8110 + 132007 T e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e monDom5.chr2 304551395 4976 - 541556283 I e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I a score=172199.000000 s hg19.chr17_gl000204_random 56159 82 + 81310 TTTCAGAGGACCCCGG-CAGGGCTCTCTCCGGGCCTGGGTGCCGCGACAGACGC------ACGTTGCACCACCGCCG--------GGTCGCC-AG-CCT s pteVam1.scaffold_11245 24395 70 + 48268 TCCCGGGGGACCTGGG-CACGG------------CTGAGTGCCAGAAGGGAAGC------GCACTGCATC-CCGCGG--------GGCCGCCAAC-CCC i pteVam1.scaffold_11245 C 0 C 0 s bosTau4.chr19 10868454 47 - 65312493 TCCTCGAGGACTTAGG-CAGGGTTCCC--GGGGACTGGGTGCCCAGGGG-------------------------------------------------T i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 138437 85 + 145505 TCCTCGAGGACCCAGG-CAGGGGTCCC--GGGGACTGGGTGCCTAGCGGGAAGC------GCA-TGCATC-CCGTGGAGATCGCTGACCGTC--C-CCC i turTru1.scaffold_106006 C 0 C 0 s calJac1.Contig5139 57150 81 + 225949 TTCCAGAGGA-CCCGG-CAGGGCTCTCTCGGGGCCTGGGGACCGCTACAGAAGC------ACGTTGCACCACCGCCG--------GGTCGCC-AG-CCC i calJac1.Contig5139 C 0 C 0 s ochPri2.scaffold_9426 12342 80 - 54875 CCTCAGAGGACCCGG--CAGGGCTCCAGT--GGCCTGGATGCTGCGAGGGATGCGGGGCGACGCGA----ACTGCGG--------GCTC-CC-GG-CCT i ochPri2.scaffold_9426 C 0 C 0 s oryCun2.chrUn0958 27851 79 + 41507 CCTCAAAGAGCCCCG--CAGGGCGTCTTT--GGCCTGGATGCCTCGCGGGAAGC------ACGCGACACCACTGCGG--------GGTc-cc-ggcccc i oryCun2.chrUn0958 C 0 C 0 s cavPor3.scaffold_76 4399103 34 + 7991924 TAAAGGAGGACTCCTGTCAGGACTCCC---------------------------------------------------------------CC-GG-GCC i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118770037 79 + 121843856 TCCTCCTGGACCCCAG-CAGCCCTCCCG---AGCCTGAGGATGGCGAGAGTCGC------ACGCCGTAGCGCATCAG--------GGTCGCC-AG-CCG i mm9.chr11 C 0 C 0 s micMur1.scaffold_15893 15541 77 + 19765 TTCCAGAGGACTCC-G-CAGGG--CTCCCAGGGCCT-GGTGCCGTGACAGAAGC------ATGTTGCACTA-CGGCG--------GGTCGAC-AG-CCC i micMur1.scaffold_15893 C 0 C 0 s panTro2.chr17 79486068 83 + 83384210 TTTCAGAGGACCCCGG-CAGGGCTCTCTCCGGGCCTGGGTGCCGCGACAGACGC------ACGTTGCACCACCGCCG--------GGTCGCCAAG-CCT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0460956 542 82 + 1444 TTTCAGAGGACCCCGG-CAGGGCTCTCTCCGGGCCTGGGTGCCGCGACAGACGC------ACGTTGCACCACCGCCG--------GGTCGCC-AG-CCT i gorGor1.Supercontig_0460956 C 0 C 0 s ponAbe2.chr17_random 16073514 82 + 17838096 TTTCAGAGGACCCCGG-CAGGGCTCTCTCGGGGCCTGGGTGCCGCGACAGACGC------ACGTTGCACCACCGCCG--------GGTCGCC-AG-CCT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75047391 82 + 78773432 TTTCAGAGGACCCCGG-CAGGGCTCTCTCCGGGCCTGGGTGCCGCGACAGACGC------ACGTTGCACCACCGCCG--------GGTCGCC-AG-CCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 54621 82 - 95547 TTTCAGAGGACCCCGG-CAGGGCTCTCTCCGGGCCTGGGTGCCGCGACAGACGC------ACGTTGCACCACCGCCG--------GGTCGCC-AG-CCC i papHam1.scaffold8336 C 0 C 0 e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e felCat3.scaffold_206428 46377 8110 + 132007 T e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e monDom5.chr2 304551395 4976 - 541556283 I e canFam2.chr9 59446212 622 - 64418924 M e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I a score=686662.000000 s hg19.chr17_gl000204_random 56241 166 + 81310 CTCT--CCCACCCGCGCGGGCTCCGGCTGCCTG-CTCGGACGCGCCCCGCGGGGCCGGGATCTCCGC----GCGCC-----TCTGCCTCCCCCC--GCCGGGGAGTTCCCC--GCGCC----------GGGCAT---TGT------------gccgccgccgccgccgccacagccaccaccaccgccaccgccaccgccactgcca s papHam1.scaffold8336 54703 160 - 95547 CTCT--CTCACCCGCGCGGGCTCCGGCTGCCTC-CCTGGACGCGCCCCGCGGGGCCGGGATCTCCGC----GCGCC-----TCTGCCTCCCCCC--GCCGGGGAGTTCCCC--GCGCC----------GGGCAT---TGT------------gccgccgccgccgccgccaccgccaccaccaccgccaccgccactgcca------ i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75047473 153 + 78773432 CTCT--CTCACCCGCGCGGGCTCCGGCTGCCTC-CCTGGACGCGCCCCGCGGGGCCGGGATCTCCGC----GCGCC-----TCTGCCTCCCCCC--GCCGGGGAGTTCCCC--GCGCC----------GGGCAT---TGT------------gccgccgccgccgccgccaccgccaccaccaccgccaccgcc------------- i rheMac2.chr16 C 0 M 1133 s ponAbe2.chr17_random 16073596 160 + 17838096 CTCT--CCCACCCGCGCGGGCTCCGGCTGCCTC-CTCGGACGCGCCCCGCGGGGCCGGGATCTCCGC----GCGCC-----TCTGCCTCCCCCC--GCCGGGGAGTTCCCC--GCGCC----------GGGCAT---TGT------------gccgccgccgccgccgccacagccaccaccaccgccacagccactgcca------ i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0460956 624 166 + 1444 CTCT--CCCACCCGCGCGGGCTCCGGCTGCCTG-CTCGGACGCGCCCCGCGGGGCCGGGATCTCCGC----GCGCC-----TCTGCCTTCCCCC--GCCGGGGAGTTCCCC--GCGCC----------GGGCAT---TGT------------gccgccgccgccgccgccacagccaccaccaccgccaccgccaccgccactgcca i gorGor1.Supercontig_0460956 C 0 C 0 s panTro2.chr17 79486151 139 + 83384210 CTCT--CCCACCCGCGCGGGCTCCGGCTGCCTG-CTCGGACGCGCCCCGCGGGGCCGGGATCTCCGC----GCGCC-----TCTGCCTCCCCCC--GCCGGGGAGTTCCCC--GCGCC----------GGGCAT---TGT------------GCCGCCGCCGCCGCCGCCACAGCCACCA--------------------------- i panTro2.chr17 C 0 I 825 s micMur1.scaffold_15893 15618 131 + 19765 AGCT--CCCACCCGCAC-AGCTCTGGCTGATTC-CCAGGACAAGCCCCGCGG-GCCAGGATCTCCAC----GCGCC-----TTGTACTTCCCCC--GCCAGGGAGTTCCCC--GCGCC----------GGGCAT---TGT------------gccgccgccgccgccaccgcca--------------------------------- i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118770116 142 + 121843856 TGCT-TCCAGCCC-TGCGGGTTGGGGCCGCCTC-CCT-GATGCGCCCCGCGG-GCCGGGATCTCCGT----GCGCC-----ACGGCTTCCCCCCAATCCTGGGAGTTCCCA--GAGCC----------GGGCAT---TGTgccgccgccgccgccgccgccgccgccgccA------------------------------------ i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4399137 119 + 7991924 TGCC-TGCAGCCT----------GGGCCGCCTC-CCCGGACCCGACCCGCGG-GCCGGGATCTCCTT----GCGCC-----TTGGCCTCCCCC---GCCGGGGAGTTCCCC--GAGCC----------GGGCAT---TGT------------GCCTCCGCCGCTGCACACA------------------------------------ i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 27930 111 + 41507 cgcgctgccgcccgcgcgggcTCCGGACGCCTC-CCC-------------------GGGATCTCCGC----CCGCC-----TCGGCCTCCCCC---GCC-GGGAGTTCCCC--GCGCC----------GGGCAT---TGT------------GCCGCCGCCGCCGCCGCCA------------------------------------ i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 12422 93 - 54875 CGCG---------GCGCGGGCTCCGGCCGCTTC-CCC--------------------GGACCTCCG------CGCC-----TCGGCCCTCCCC---GCC-GGGAGTTCCCG--GCGCC----------GGGCAT---TGT------------------GCCGCCGCCGCCA------------------------------------ i ochPri2.scaffold_9426 C 0 C 0 s calJac1.Contig5139 57231 143 + 225949 CTCT--CCCACCCGCTCGGGCTCCGGCTGCCTC-CCCGGACGCGCCCCGCGGAGCCGGGATCTCCGC----GCGCC-----TCGGCCTCCCCCC--GCCAGGGAGTTCCCC--GCGCC----------GGGCAT---TGT------------gccgccgccaccaccgccaccgccaccgccAC----------------------- i calJac1.Contig5139 C 0 I 7 s turTru1.scaffold_106006 138522 142 + 145505 CACT--CCCACCTGCGCGAGCTCCAGCCGCGTA-CCCGGACGCACCCCGCAGGGCCGGGATCTCCTC----GCGC------TCGGCCTCCCCCC--GCCAGGGAGTTCCCC--GCGCC----------GGGCAT---TGT------------gccgccgccgccgccaccaccgccgccgccgc----------------------- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10868501 148 - 65312493 CGCT--CCCACCCGCGCAGGTTCCAGCTCCGTACCCCGGACGCGCCCCGCGGAGACGGGATCTCCTC----CCGC------TCAGCCTCCCCCC--GCCAGGGAGTTCCCC--ACGCC----------GGGCAC---TGT------------Gccgccaccgccgccaccaccaccgccgccacgatca------------------ i bosTau4.chr19 C 0 C 0 s pteVam1.scaffold_11245 24465 128 + 48268 TGCT--CCCACCCGCGTGGGCTCAGGC--CGGCCCCCCGATGCGCCCTGC-GGGCCGGGATCTCCTC----GCGCG-----TCGGCGGCCCCCC--GCCAGGGAGTTCCCCCGGCGCC----------GGGTAT---TGT------------GCCGCCGCCGCCACCAC-------------------------------------- i pteVam1.scaffold_11245 C 0 C 0 s monDom5.chr2 304556371 150 - 541556283 CCCC--CCAACCCTTCAGGGC----GCTGTCCT-CTCGAATCTGCGATGC----------TCTCCCCTTCAGCACCTATCATCTGTTCCCCGCT--ACCTAGGAGCTCTCC--AACCCTTAGACCTCAGCGAATCCATTT------------AGCATCTCTGGTCCCTCAATTCCCCCACACA------------------------ i monDom5.chr2 I 4976 C 0 e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e felCat3.scaffold_206428 46377 8110 + 132007 T e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e canFam2.chr9 59446212 622 - 64418924 M e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I a score=1011787.000000 s hg19.chr17_gl000204_random 56407 257 + 81310 ccgccacGCAGCGCGCGGGACTCTCTGGCGTCTCCATGGAGCCCG-----------ACCCCCGGGCCTTCCCATTCACAAAATCGCCCCTCT-G-GCCCACGGCCGGACAGAGCGT--CCA-------GACCCCAGCCCCGGAGGGA--CCC-AGGG-ACCCCGACCCCG--CGCAGGGACCCCTGA-CCCCGAGGGCGCCACCC-CACCCCACGCGCCCTCGGGTC--------------AGCC----CCGGCCGCGCTCAG-----------------CAGC-CCG----------------CCTCCCACTGCGGGGTCC-CATGCGCCCCTCCGCG-G s pteVam1.scaffold_11245 24593 259 + 48268 -CACCAAGCAGCGCACGGGACTACCCTGCGTCTCCATGGAGCCCG-----------ACCCCAGGGCCCTTCCATTCACAAAATCGCCCCTCC-ATGCCCCCGGCTAGGCCACGTGT--CCC-------AACCCCAGCCCGGGAAAGA---CT-GGGA-GCTCCCACCCTG--TGCAGAGACCCCTGA-CCCCGAGGGCGCCACCC-TTCCCCATGCGCCCTCGGGTT-------------GGTCC----CCAGCCATGCTGCG-----------------CAGCCCCG----------------CCTTCCCCTGCGGGGTGC-CGTGCTCCCCTCCCCAGG i pteVam1.scaffold_11245 C 0 C 0 s bosTau4.chr19 10868649 280 - 65312493 acaccacG-AGTGCGCGGGACTCCCTGGCTTCTCCATGGAGCCCG-----------ACCCCGGGGCCTTCCCATTCACAAAACCGCCCCTCC-G-GCCGCGGGCTGGACCACGTGCCGCGC-------GACCCGAGCCCAGGAGGGAACCCA-GAGA-GCCCCGACCCCG--CGGGGAGACCCCTGA-CCCCGAGGAAGCCACCC-CTCCCCGAGCGCCCTCGGGTG-------------GGTCC----GCGTCCGCGCTCTGCAACCCCGCGCCCCCACCAGCCCCG----------------CCTCCCCCTGCGGGGTCC-GGTGCGCCCCTCCCCGGG i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_106006 138664 256 + 145505 -cgccAAGCAGTGCGCGGGACTCCCCGGCGTCTCCATGGAG-CCG-----------ACCCCGGAGCCTTCCCATTCACAAAACCGCCCCTCC-G-GCCGTAGGCTGGACCACGTGC--CCC-------GACCCGAGCCCAGGAGGGA-------------------------CACGGAGAGCCCCGA-CCTCGAGGGCGCCACCC-CTCCCCGCGCGTCCTCGGGTC-------------GGTCC----CTGACCGCGCTCTGCAGCCCCGCGCCCCCGCCAGCCCCG----------------CCTCCCCCTGCGGGGTCC-TGTGCGCCCCTCCCTGGG i turTru1.scaffold_106006 C 0 C 0 s ochPri2.scaffold_9426 12515 214 - 54875 CGGCCACGCAGCGCGCGGGACTCCCTGGCATCTCCAAGGAGCCTG-----------AT-CCGGGGCCTCCCCATTCACAGAACC---------G-GACCTCGGCGGGATCACGCGC--CCC-------GGCTGCAGACCCGGAGGAG--CTG-GGGG-GGCCCGACCCCT--CCTGGAGCGCCCGCA-GCTCGG------------------------------------------------TCC----CCAGCCGCGCGCTG-----------------CAGCACCG----------------CCTCCCACTGCGGGGTCC-CGTGCGCCAACCCCC--- i ochPri2.scaffold_9426 C 0 C 0 s oryCun2.chrUn0958 28041 207 + 41507 CGGCCACGCAGCGCGCGGGACTCCCCGGCGTCTCCAAGGAGCCGG-----------ATCCCGGGGCCTTCCCACTCACAAGATC---------G-GACCCCGTC---------------------------------CCCGGAGGAG--CTACGGGA-ACCCCGACCCCG--CGAGGGGATCCCTGA-CCCCGAGGGCGCCGCCC------------------------------------CTCC----CCGAGCGCCCTCGC-----------------CAGCCCCG----------------CCTCCCGCCGCGGGGTCC-CAGGCGCCCCTCCTCGGG i oryCun2.chrUn0958 C 0 C 0 s cavPor3.scaffold_76 4399256 263 + 7991924 CGGTCACGC--CGCGCGGGACTCCCCGGCGTCTCCATAGAGCCTG-----------AC-CCCGGGCCTTTCCATTCACAAAATCGCCTCCC--G-GTCCCTTGCGGTGACACGCGC--CCG-------GACCCCAGCCCCGGAGGAA--ACT-GGAA-A-----ACCCCG--CGCCAGAACCTCTGA-CCCCAAGGGCACCACCC--TCCCAGCGCGACCTCTGCTCTATCCCGGTCCCAGGTCC----CTGCCCGCCGTCTG-----------------CAGCCCCG----------------CCTCCCGCCGCGGGGTCT-TAAGCGCCCCTCCCGGGC i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118770258 286 + 121843856 CGGGCACGCAGCGCGCGGGACTCCCCGGTGTCTCCATGGAGCCTG-----------AC-CCCGGGCCTTCCCATTTACAAAATCTCCCCTCTGG-TTTCCCAGGGGAGCCCGGAGC--CCGGAGCCACGACCCCAGCCCCCGCACAA--CTC-GGGA-ACCCCGACCTCG--CGCGCAGACCCCTGACCCCCAAGGGCGCCACCCCATCCTCGCGCGACCTCAGGTCTGTCCCCAGCCACGCTCCGCAGCCCCGCGTCCTCGC-----------------CGGCCCCG----------------CCTCCCACTGCGGGGTCC-CGTGCGCCCCTCCCCGGG i mm9.chr11 C 0 C 0 s micMur1.scaffold_15893 15749 273 + 19765 ccgccACGCAGTGCTCGGGACTCCCTGGCGTCTCCATGGAGCCTG-----------ACCCCCGGGCCCTCCCATTCACAAAATCGCCCCTCT-G-ACCCACTGCCGGACCAAGGGT--CCC-------GATCCCAGCTCCTGAAGGA--CCC-GGGGAACCCAGACCCCG--CGCTGGGACCCCTGA-CCCGGA-GGCG-CACCC-CTCCCCACGCACCCTCGGGTC--------------AGTC----CCGGCCACGCTCTG-----------------CAGC-CCTGCGCCCTCGCCAGCCCCTCCTCCCTGCGGGGTCT-CATGCGCCCCTCCCCACG i micMur1.scaffold_15893 C 0 C 0 s calJac1.Contig5139 57381 243 + 225949 ------------GCGCGGGACTCCCCGGCGTCTCCATGGAGCCCG-----------ACCCCCGGGCCTTCCCGTTCACAAAATCTCCCCTCT-G-GGCTACGGCGGGACAGAGCGT--CCG-------GACCCCAGCCCCGCAGGGA--CCC-AGGG-AC-CGGACCCCA--CGCAGGGACCCCTAA-CCCCGAGGGCGCCACCC-CTCCCCACGCGCCCTCAGGTC--------------AGCC----CCGGCAGCGCTCCG-----------------CGTT-CCG----------------CCTCCCGCCGCAGGGTCC-CGTGCGCCCCTCC-CG-A i calJac1.Contig5139 I 7 C 0 s panTro2.chr17 79487115 257 + 83384210 CCGCCACGCAGCGCGCGGGACTCCCTGGCGTCTCCATGGAGCCCG-----------ACCCCCGGGCCTTCCCATTCACAAAATCGCCCCTCT-G-GCCCACGGCCGGACAGAGCGT--CCA-------GACCCCAGCCCCGGAGGGA--CCC-AGGG-ACCCCGACCCCG--CGCAGGGACCCCTGA-CCCCGAGGGCGCCACCC-CACCCCACGCGCCCTCGGGTC--------------AGCC----CCGGCCGCGCTCAG-----------------CAGC-CCG----------------CCTCCCACTGCGGGGTCC-CATGCGCCCCTCCGCG-G i panTro2.chr17 I 825 C 0 s gorGor1.Supercontig_0460956 790 257 + 1444 ccgccacGCAGCGCGCGGGACTCCCTGGCGTCTCCATGGAGCCCG-----------ACCCCCGGGCCTTCCCATTCACAAAATCGCCCCTCT-G-GCCCACGGCNNNNNNNNNNNN--NNN-------NACCCCAGCCCCGGAGGGG--CCC-AGGG-ACCCCGACCCCG--CGCAGGGACCCCTGA-CCCCGAGGGCGCCACCC-CACCCCACGCGCCCTCGGGTC--------------AGCC----CCGGCCGCTCTCAG-----------------CAGC-CCG----------------CCTCCCACTGCGGGGTCC-CATGCGCCCCTCCGCG-G i gorGor1.Supercontig_0460956 C 0 C 0 s ponAbe2.chr17_random 16073756 256 + 17838096 ccgccACGCAGCGCGCGGGACTCCCCGGCGTCTCCATGGAG-CCG-----------ACCCCCGGGCCTTCCCATTCACAAAATCGCCCCTCT-G-GCCCACGGCCGGACAGAGCGT--CCG-------GACCCCAGCCCCGGAGGGA--CCC-AGGG-ACTCCGACCCCG--CGCAGGGACCCCTGA-CCCCGAGGGCGCCACCC-CACCCCACGCGCCCTCGGGTC--------------AGCC----CCGGCCGCGCTCCG-----------------CAGC-CCG----------------CCTCCCATTGCGGGGTCC-CATGCGCCCCTCCGCG-G i ponAbe2.chr17_random C 0 C 0 s papHam1.scaffold8336 54863 257 - 95547 ccgccacGCAGCGCGCGGGACTCCCCGGCGTCTCCATGGAGCCCG-----------ACCCCCGGGCCTTCCCATTCACAAAATCTCCCCTCT-G-GCCCACGGCCGAACAGAGCGT--ACG-------GACCCCAGCCCCGGTGGGA--CCC-AGGG-ACCCCGACCCCG--CGCAGGGACCCCTGA-CCCCGAGGGCGCCACCC-CACCCCACGCGCCCTCGGGTC--------------AGCC----CGGGCCGCGCTCCG-----------------CAGC-CCG----------------CCTCCCACTGCGGGGTCC-CACGCGCCCCTCCCCG-G i papHam1.scaffold8336 C 0 C 0 s monDom5.chr2 304556521 249 - 541556283 CCCCCCCATCACTTCCTGCATTCGCTTCCCTTTATGTAATGCCCACCCCCATTTATACCCCTAG---TGCTCAGTCTCCAATCCCCACCCCC-G-GTCT---------CTTCGTCT--CTG-------GTCTTCCTCTCCAAAG-----CCA-CAGT-AGTCCATTCTCGATTTCCTAGtcttcctc-ctcctctttctcctcct-cctcttccttctcctccACTC--------------ACCC----CCATCCCT-----------------------CGGT-GCA----------------TCTCCTACCCCAGGTTCCATATTTTCCCTTCTCTT-- i monDom5.chr2 C 0 C 0 e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e felCat3.scaffold_206428 46377 8110 + 132007 T e macEug1.Scaffold385251 990 0 + 1704 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e canFam2.chr9 59446212 622 - 64418924 M e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I e rheMac2.chr16 75047626 1133 + 78773432 M a score=190510.000000 s hg19.chr17_gl000204_random 56664 88 + 81310 CCATGT--CCCCCTCC----CC----------CAGCTCAGCCC----GATGGGAATGACCGCCGCA------------GAGCGAGGCG--GGCG-ACGAGG------CCAGGCTACTCACGGGCTCAGC s papHam1.scaffold8336 55120 89 - 95547 CCATGC--CCCCCTCC----CC----------CAGCTCAACCC----GATGGGAATGACCGCCGCA------------GGGCGAGGCG--GGCG-ACGAGGG-----CCGGGCTACTCACGGGCTCAGC i papHam1.scaffold8336 C 0 C 0 s ponAbe2.chr17_random 16074012 89 + 17838096 CCATGC--CCCCCTCC----CC----------CAGCTCAGCCC----GATGGGAATGACCGCCGCA------------GGGCGAGGCG--GGCG-ACGAGGA-----CCGGGCTACTCACGGGCTCAGC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0460956 1047 88 + 1444 CCATGC--CCCCCTCC----CC----------CAGCTCAGCCC----GATGGGAATGACCGCCGCA------------GAGCGAGGCG--GGCG-ACGAGG------CCAGGCTACTCANNNNCTCAGC i gorGor1.Supercontig_0460956 C 0 C 0 s panTro2.chr17 79487372 88 + 83384210 CCATGC--CCCCCTCC----CC----------CAGCTCAGCCC----GATGGGAATGACCGCCGCA------------GAGCGAGGCG--GGCG-ACGAGG------CCAGGCTACTCACGGGCTCAGC i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 57624 88 + 225949 CAGTGA--CCCCCTCC----CC----------CAGCTCAGCCC----GCCGGTAATGACCGCCACA------------GGGCTAGGCG--GGCG-ACGAGG------GCCGACTACTCACGGGCTCAGC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 16022 89 + 19765 CTGTGC--CCCCCCCA----AC----------CCGCCCATCCC----GATGGTAATGACCGCCACA------------GGGCGAGGCG--GGCA-ACGAGGG-----CCAGGCTACTCACAGGCTCAGC i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118770544 82 + 121843856 CCGTGC--CCACAGTCCCA-GC----------CGGCCCCTCGC----GATGGTCGTGACCGAGGTG------------GAAG-------------CCCAGGG-----TCTGGCTACTCACGGGTTCAGC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4399519 92 + 7991924 CCGAGC--CCCCACCATCG-GC----------TCACGCGTCGC----GATGGTGATGAGCGCCGCA------------GGGGCGAGGC--GCCC-CGCAGGT-----CGGGACTACTCACAGGCTCCAC i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 28248 90 + 41507 CCGTGC--CCTCCACCTCTAAC----------CGGCTCCCGGC----CGTGTTAATCCATACCACA------------GGCACTGGCG--GTCG---CGAGC-----TGGGG-TACTCACTGTCTCGGC i oryCun2.chrUn0958 C 0 I 941 s ochPri2.scaffold_9426 12729 76 - 54875 --------------------AC----------CCGCTCGCCGC----CGTGGCACGTACGGCCGCA------------GGGAGAGGCG--GGCGGCCAGAGA-----TAGGGTTACTCACGTGCTCAGC i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 138920 92 + 145505 ACGTGC--CCACCCCCACC-CC------------GCTCAACAC----GAATGTAATGACCGCCGCA------------GGGCGAAGCGCTGGCG-GCGAGGA-----CCCAGCTACTCACGGGCTCAGC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10868929 105 - 65312493 ACGTGC--CCACCCCCACC-CCCGAGCCCAGCCGGCTCCACGG----GAAGGTAATGACCACCGCA-----------GGGGTGAAGCGCGGGCG-GCGGGGG-----CTAGGTTACTCACGGGCTCAGC i bosTau4.chr19 C 0 C 0 s pteVam1.scaffold_11245 24852 78 + 48268 CCATGCCACCACTCCCACG-GC----CCCAGCCGGCTCATGAC----GATGGTAATGACTGCCGCA-------------GACGAAGCGCGGGTG-GTGAGG---------------------------- i pteVam1.scaffold_11245 C 0 I 119 s macEug1.Scaffold23956 20348 112 - 25324 Ccatgttttcccttct----ct----------tctctcacccCCAAAGATAATAATAACCAATAAAATAGGAATCCGGAGCCGAAGCG--GCTG-GCCGGGGGGCGCTGCTGTTACTCACGGTCTCAGC i macEug1.Scaffold23956 I 17402 C 0 s monDom5.chr2 304556770 93 - 541556283 ---------------------------------CTTTCACCCCCAAATATCATAATAACCAATAAAATAGGAACCCGGAGCCGAAGTG--GCTG-GCCGGGGGGCGCCGCTGTTACTTACGGTCTCAGC i monDom5.chr2 C 0 C 0 e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e canFam2.chr9 59446212 622 - 64418924 M e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I e rheMac2.chr16 75047626 1133 + 78773432 M a score=491435.000000 s hg19.chr17_gl000204_random 56752 97 + 81310 GCTCCCCGCGGCAGGTGACTGGGGGCCGGCGGCCATGCCCCGGCTGCA-TCCCGGCC----GCCGAGCGGGCAGCGGCGTCCTGGGGCCGCAC--------AGGCA-CCGG-------------------- s papHam1.scaffold8336 55209 97 - 95547 GCTCCCCGCGGCAGGTGACTGGGGGCCGGCGGCCATGCCCCGGCTGCA-TCCCGGCC----GCCGAGCGGGCAGCGGCGTCCCGGGGCCGCAC--------AGGCA-CCGG-------------------- i papHam1.scaffold8336 C 0 C 0 s ponAbe2.chr17_random 16074101 97 + 17838096 GCTCCCCGCGGCAGGTGACTGGGGGCCGGCGGCCATGCCCCGGCTGCA-TCCCGGCC----GCCGAGCGGGCAGCGGCGTCATGGGGCCGCAC--------AGGCA-CCGG-------------------- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0460956 1135 97 + 1444 GCTCCCCGCGGCAGGTGACTGGGGGCCGGCGGCCATGCCCCGGCTGCA-TCCCGGCC----GCCGAGCGGGCAGCGGCGTCCTGGGGCCGCAC--------AGGCA-CCGG-------------------- i gorGor1.Supercontig_0460956 C 0 C 0 s panTro2.chr17 79487460 97 + 83384210 GCTCCCCGCGGCAGGTGACTGGGGGCCGGCGGCCATGCCCCGGCTGCA-TCCCGGCC----GCCGAGCGGGCAGCGGCGTCCTGGGGCCGCAC--------AGGCA-CCGG-------------------- i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 57712 101 + 225949 GCTCCCCGCGGCAGGTGACGGGGGGCCGGCGGCCATGCCCCGGCTGCA-TCCCGGCCGCTGGCTGAGCGGGCAGCGGAGTCCCGGGGCCGCAC--------AGGCA-CCCG-------------------- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 16111 96 + 19765 GCTCCCCGCGGCAGGTGACGGGGGCCCGGCGCCCATGCCCCGGCTGCA-TCCTGGCC----GCCGAGCGGGCAGCCGCGTCCC-GGGCCGCAC--------GGGCA-CCCG-------------------- i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118770626 63 + 121843856 GTTCCCCACGGCAGGTGACGGGGCCCTGGCGGCCATGCCCCGGCTGCA-TCCCGGCC----GCC-------------------------------------------CCGG-------------------- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4399611 63 + 7991924 GCTCCCCGCGGTAGGTGATGGGGCACCGGCGGCCATGCCCCGGCTGCA-TTCCGGCC----GCA-------------------------------------------CTGG-------------------- i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 12805 97 - 54875 GCTCCCCGCGGCAGGGGACGGAGACTCGGCGGCCATGCCCCGGCTGCA-TCCCGGCC----GCCGAGTTGA-AGAGGTGTCCCGGGTCCGTAC--------GGGCAACCTA-------------------- i ochPri2.scaffold_9426 C 0 C 0 s turTru1.scaffold_106006 139012 97 + 145505 GCTCCCCGCGGCAAGTGACAGGGGCCCAGCGGCCATGCCCCGGCTGCA-TCCCGGCC----GCCGAGCTGGCAGCGGCGTCCCGGGGACGCGC--------GGGCA-CCGG-------------------- i turTru1.scaffold_106006 C 0 I 1621 s bosTau4.chr19 10869034 97 - 65312493 GCTCCCCGCGGCAGGTGACAGGGGCCCGGCGGCCATGCCCCGGCTGCA-Tcccggcc----gccgagcgggcagcggcgtcccggggccgcgc--------gggca-ccgg-------------------- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59446852 71 - 64418924 GCTCCCCGCGGCAGGTGACCGGTGCCCGGCGGCCATGCCCCGGCTGCA-Tcccggcc-----ccgagcgggcagcgg------------------------------------------------------ i canFam2.chr9 M 622 C 0 s macEug1.Scaffold23956 20460 99 - 25324 GTTCCCAACGGCAGGTGAGGGGAGACGCACTGCCATCCCCTAGCTGCATTCCCCACC----CCC-------TCAAAGTGTCCGGAGAAGGCACCCCCTCAGAGGGA-CTGG-------------------- i macEug1.Scaffold23956 C 0 I 6 s monDom5.chr2 304556863 119 - 541556283 GTTCCCAACGGCAGGTGAGGGGAGACGCACTGCCATCCCCTAGCTGCATTCCCCACC----CCC-------TCAAAGTGTCCGGAGAAGGCACCCCTTCTGGGGGA-CTGGGAGAGCCCTGCCGGCCGCAg i monDom5.chr2 C 0 C 0 e oryCun2.chrUn0958 28338 941 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e felCat3.scaffold_206428 46377 8110 + 132007 T e pteVam1.scaffold_11245 24930 119 + 48268 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I e rheMac2.chr16 75047626 1133 + 78773432 M a score=155399.000000 s hg19.chr17_gl000204_random 56849 32 + 81310 CGAGCCGGCG-GCAAGGGGCGCGCG-AGGCCGGG-- s papHam1.scaffold8336 55306 32 - 95547 CGAGCCGGCG-GCAAGGGGCGCGCG-AGGCCGGG-- i papHam1.scaffold8336 C 0 C 0 s ponAbe2.chr17_random 16074198 32 + 17838096 CGAGCCGGCG-GCAAGGGGCGCGCG-AGGCCGGG-- i ponAbe2.chr17_random C 0 I 504 s gorGor1.Supercontig_0460956 1232 32 + 1444 CGAGCCGGCG-GCAAGGGGCGCGCG-AGGCCGGG-- i gorGor1.Supercontig_0460956 C 0 C 0 s panTro2.chr17 79487557 32 + 83384210 CGAGCCGGCG-GCAAGGGGCGCGCG-AGGCCGGG-- i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 57813 32 + 225949 CGAGCCGGCG-GCAAGGGGCGCGCG-AGGCCGGG-- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 16207 32 + 19765 CGAGCC-GCG-GCAAGGGGCGCGCGAAGGCTGGG-- i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118770689 32 + 121843856 CGAGCCGGCG-GCAAGGGGCGCGAG-AGGCCGGG-- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4399674 32 + 7991924 CGAgccggcg-gcgaggggcgcgcg-aggccggg-- i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 12902 33 - 54875 CGAGCCGGCACGTGAGTGGGGTGCG-AGGCCGGG-- i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10869131 32 - 65312493 cgagccggcg-gcgAGGAGATCGCG-GGGCCGGG-- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59446923 27 - 64418924 --agcgggcg-gcgagggg--cgc--gggccggg-- i canFam2.chr9 C 0 C 0 s macEug1.Scaffold23956 20565 32 - 25324 CTGGCCGGCC-GCAGGAAGCGGAGG-AGGAGGCG-- i macEug1.Scaffold23956 I 6 I 4 s monDom5.chr2 304556982 34 - 541556283 gaagcggagg-aggaggcgaaggcg-aaggcggagg i monDom5.chr2 C 0 C 0 e oryCun2.chrUn0958 28338 941 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e pteVam1.scaffold_11245 24930 119 + 48268 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I e rheMac2.chr16 75047626 1133 + 78773432 M a score=40397.000000 s hg19.chr17_gl000204_random 56881 36 + 81310 CTCGGGCGGCAGCTGTGGCAGCTGCTT-CTC-----CTCC-GA------ s panTro2.chr17 79487589 36 + 83384210 CTCGGGCGGCAGCTGTGGCAGCTGCTT-CTC-----CTCC-GA------ i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0460956 1264 36 + 1444 CTCGGGCGGCAGCTGTGGCAGCTGCTT-CTC-----CTCC-GA------ i gorGor1.Supercontig_0460956 C 0 C 0 s papHam1.scaffold8336 55338 36 - 95547 CTCGCGCGGCAGCGGTGGCAGCTGCTT-CTC-----CTCC-GA------ i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 57845 36 + 225949 CTCTGGCGGCCGCGGTGGCAGCTGCTT-CTC-----CTCC-GA------ i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 16239 36 + 19765 CTTGGGCAGCCGCGGC-GCAGCTGCTTCCTC-----TTCC-GA------ i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118770721 34 + 121843856 -TTGGAG--CGGCGGTGGCTGCCGCGG-CGT-----CTCCGGA------ i mm9.chr11 C 0 I 2 s cavPor3.scaffold_76 4399706 28 + 7991924 -ctggg-------ggcggcggccgcgg-cgT-----CTCC-AA------ i cavPor3.scaffold_76 C 0 I 2 s ochPri2.scaffold_9426 12935 39 - 54875 -GTACAGGTAGACGAGAAAAGCCGC-A-CGTTCTCACTCC-GA------ i ochPri2.scaffold_9426 C 0 I 406 s bosTau4.chr19 10869163 33 - 65312493 CTCAGG---CGGCGGCGGCGACCGCGT-CTC-----CTCC-GA------ i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59446950 29 - 64418924 ct-------cggcggcggcggccgcgT-GTC-----CTCC-GA------ i canFam2.chr9 C 0 C 0 s macEug1.Scaffold23956 20601 37 - 25324 ---CGGAGGCGGCAGAGGCTGCAGCGG-ATCTCGG-CTCT-GT------ i macEug1.Scaffold23956 I 4 I 226 s monDom5.chr2 304557016 43 - 541556283 ---cggaggcggcagaggctgcagcgg-ATCTCGG-CTCT-GTAGCCTA i monDom5.chr2 C 0 C 0 e oryCun2.chrUn0958 28338 941 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e pteVam1.scaffold_11245 24930 119 + 48268 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I e ponAbe2.chr17_random 16074230 504 + 17838096 I e rheMac2.chr16 75047626 1133 + 78773432 M a score=82466.000000 s hg19.chr17_gl000204_random 56917 35 + 81310 CCACGCGA-GC----------TG-CTGGGGC--CC--GGCTG-GGGCCGC-TG s panTro2.chr17 79487625 35 + 83384210 CCACGCGA-GC----------TG-CTGGGGC--CC--GGCTG-GGGCCGC-TG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0460956 1300 35 + 1444 CCACGCGA-GC----------TG-CTGGGGC--CC--GGCTG-GGGCCGC-TG i gorGor1.Supercontig_0460956 C 0 C 0 s papHam1.scaffold8336 55374 35 - 95547 CCACGCGA-GC----------TG-CTGGGGC--CC--GGCTG-GGGCCGC-TG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 57881 35 + 225949 CCACGCAA-GC----------TG-CTGAGGC--CC--GGCTG-GGGCCGC-TG i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 16275 36 + 19765 CCACACGA-AC----------TG-CTGGGGC--CC--GGCCG-GGGCCGCTTG i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118770757 35 + 121843856 CCACGCGA-GC----------TG-CTGGGGC--AG--GCGCC-CGACTGC-TG i mm9.chr11 I 2 C 0 s cavPor3.scaffold_76 4399736 33 + 7991924 CCACGCGA-GC----------TG-CCGGGCC------GCGCC-GCGCCGC-TG i cavPor3.scaffold_76 I 2 C 0 s ochPri2.scaffold_9426 13380 38 - 54875 CCACACAA-GC----------TGACTGGGGCCCCG--GAGCG-GGGCGGC-TG i ochPri2.scaffold_9426 I 406 C 0 s bosTau4.chr19 10869196 35 - 65312493 CCACGCGA-GC----------GG-CTGGGAC--CG--CGGAG-GGGCCGC-TG i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59446979 48 - 64418924 GCGGGCGG-GCGCTGGAGCGggg-ccgggcc--gggccggggcgggcGGC-TG i canFam2.chr9 C 0 C 0 s monDom5.chr2 304557059 36 - 541556283 CCACGCGACTC----------AG-CTCGTGT--GC--AGCGT-GTGCAGC-GG i monDom5.chr2 C 0 I 184 e oryCun2.chrUn0958 28338 941 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e macEug1.Scaffold23956 20638 226 - 25324 I e pteVam1.scaffold_11245 24930 119 + 48268 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I e ponAbe2.chr17_random 16074230 504 + 17838096 I e rheMac2.chr16 75047626 1133 + 78773432 M a score=25516.000000 s hg19.chr17_gl000204_random 56952 34 + 81310 -TCCGAGGAGG-TTCTGCT--GGCTTCGGAGCAGCCCC--------------- s panTro2.chr17 79487660 34 + 83384210 -TCCTAGGAGG-TTCTGCT--GGCTTCGGAGCAGCCCC--------------- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0460956 1335 34 + 1444 -TCCGAGGAGG-TTCTGCT--GGCTTCGGAGCAGCCCC--------------- i gorGor1.Supercontig_0460956 C 0 C 0 s papHam1.scaffold8336 55409 34 - 95547 -TCCCAGGAGG-TTCTGCT--GGCTTCGGAGCAGCCCC--------------- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 57916 34 + 225949 -TCCTAGGAGG-TTCTGCT--AGCTCCGGAGCAGCCCC--------------- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 16311 36 + 19765 -TCCGAGGCGC-TTCTTGCAGGGCTTCGAAGCAAGCCC--------------- i micMur1.scaffold_15893 C 0 I 2687 s mm9.chr11 118770792 35 + 121843856 -TCCGAGGAGGTTTCCGCC--GGTTCCGGAGCAACGGC--------------- i mm9.chr11 C 0 I 9 s cavPor3.scaffold_76 4399769 25 + 7991924 TTCCTGGGAGGGTT----C--GGCGCTGGCG---------------------- i cavPor3.scaffold_76 C 0 I 4 s ochPri2.scaffold_9426 13418 33 - 54875 -TCGAAGGAGCCTGCC--G--GGCTCCGGGAGCAGGCC--------------- i ochPri2.scaffold_9426 C 0 I 9 s bosTau4.chr19 10869231 14 - 65312493 -TCCTAGGAG--------------------------------------GCTCG i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59447027 47 - 64418924 -TCCGAGGAGG-CTCC--C--GGCTCCGGAGCTGCCCCGCGGCTCGGCGCTCC i canFam2.chr9 C 0 C 0 e oryCun2.chrUn0958 28338 941 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e macEug1.Scaffold23956 20638 226 - 25324 I e pteVam1.scaffold_11245 24930 119 + 48268 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e monDom5.chr2 304557095 184 - 541556283 I e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I e ponAbe2.chr17_random 16074230 504 + 17838096 I e rheMac2.chr16 75047626 1133 + 78773432 M a score=13810.000000 s hg19.chr17_gl000204_random 56986 63 + 81310 GCGCTCGCTCTTC--------CCT---CGCCTCct-ctctctctct----------------------------ctctcctccctcctctctccgccctcctc s canFam2.chr9 59447074 43 - 64418924 GCGCTCGCTCCTG---------CT---CGCCGCCG-CCTcctctcc------------------------------------------ctctgctccc----- i canFam2.chr9 C 0 C 0 s bosTau4.chr19 10869245 38 - 65312493 GCGCTCGCTCTTG--------CCT---CGCTGCCG-CCctctctct------------------------------------------ctct----------- i bosTau4.chr19 C 0 C 0 s ochPri2.scaffold_9426 13460 37 - 54875 GCGCTC-CGCTCTGGCTGTCCCCT---CGCCGCCTGCTCGC-------------------------------------------------------------- i ochPri2.scaffold_9426 I 9 C 0 s cavPor3.scaffold_76 4399798 28 + 7991924 CCTCTT-CCTTTT--------CCG---TGCCGGTT-CCGGC-------------------------------------------------------------- i cavPor3.scaffold_76 I 4 C 0 s mm9.chr11 118770836 28 + 121843856 CCGCTC-CGCTTG--------CCT---CGCCGAct-ctctc-------------------------------------------------------------- i mm9.chr11 I 9 C 0 s calJac1.Contig5139 57950 80 + 225949 GCGCTCGCTCTTC--------CCTCGCCGCCTCCC-Ttctcttctc--------------ctctctctttctcccccccctccctcctctctccgccctcctc i calJac1.Contig5139 C 0 I 147 s papHam1.scaffold8336 55443 93 - 95547 GCGCTCGCTCTTC--------CCTCGCCGCCTCct-ctctctctctctctctctctctcgctctctctctctctctctcctccctcctctctccgccctcct- i papHam1.scaffold8336 C 0 C 0 s gorGor1.Supercontig_0460956 1369 64 + 1444 GCGCTCGCTCTTC--------CCT---CGCCTCct-ctctctctct--------------------------ctctctcctccctcctctctccgccctcct- i gorGor1.Supercontig_0460956 C 0 C 0 s panTro2.chr17 79487694 51 + 83384210 GCGCTCGCTCTTC--------CCT---CGCCTCct-ctctctctct----------------------------------------ctctctcctccctcctc i panTro2.chr17 C 0 C 0 e oryCun2.chrUn0958 28338 941 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e micMur1.scaffold_15893 16347 2687 + 19765 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e macEug1.Scaffold23956 20638 226 - 25324 I e pteVam1.scaffold_11245 24930 119 + 48268 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e monDom5.chr2 304557095 184 - 541556283 I e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I e ponAbe2.chr17_random 16074230 504 + 17838096 I e rheMac2.chr16 75047626 1133 + 78773432 M a score=5027.000000 s hg19.chr17_gl000204_random 57049 32 + 81310 ----tctctctctctctctctctctctctctc--tctc s macEug1.Scaffold23956 20864 32 - 25324 Tggctccctccctctttctctctcgttctctc------ i macEug1.Scaffold23956 I 226 I 2 s panTro2.chr17 79487745 12 + 83384210 ----tctctctccttc---------------------- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0460956 1433 10 + 1444 ----tctctctctc------------------------ i gorGor1.Supercontig_0460956 C 0 n 0 s papHam1.scaffold8336 55536 34 - 95547 ----tctctctctctctctctctctctctctctctctc i papHam1.scaffold8336 C 0 I 70 s calJac1.Contig5139 58177 32 + 225949 ----tctctctctctctctctaactctctctctctc-- i calJac1.Contig5139 I 147 C 0 s mm9.chr11 118770864 32 + 121843856 ----tctctctctctctctctctctctctctctctc-- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4399826 32 + 7991924 ----TCCGATTCTTTTTCGTTTCTTCTTCTTCTTGA-- i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 13497 32 - 54875 ----TCCGAGTGTCTGTACCCCCTCTCCGTTCGTAT-- i ochPri2.scaffold_9426 C 0 C 0 s monDom5.chr2 304557279 25 - 541556283 -------CTGGctccctctctctttctctcat------ i monDom5.chr2 I 184 C 0 e oryCun2.chrUn0958 28338 941 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e micMur1.scaffold_15893 16347 2687 + 19765 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e pteVam1.scaffold_11245 24930 119 + 48268 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e canFam2.chr9 59447117 0 - 64418924 C e bosTau4.chr19 10869283 0 - 65312493 C e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I e ponAbe2.chr17_random 16074230 504 + 17838096 I e rheMac2.chr16 75047626 1133 + 78773432 M a score=39962.000000 s hg19.chr17_gl000204_random 57081 33 + 81310 --tctctctctctc-----tctctctctctctctctctcg s gorGor1.Supercontig_0007361 25310 33 - 64270 --tctctctctctc-----tctctctctctctctctctct i gorGor1.Supercontig_0007361 M 2602 C 0 s ponAbe2.chr17_random 16074734 29 + 17838096 ------tctctctc-----tctctctctctctctctctct i ponAbe2.chr17_random I 504 C 0 s calJac1.Contig5139 58209 33 + 225949 --tctctctctctc-----tctctctctctctctctctcn i calJac1.Contig5139 C 0 I 9 s mm9.chr11 118770896 32 + 121843856 --tctctctctctc-----tctctctctctctctGCCAC- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4399858 37 + 7991924 --GCTTCTCTTCTAGGGGGTCTCGTTCCCCACCCCCCTT- i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 13529 26 - 54875 --tctctctctctc-----tctctctctAGCTC------- i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10869283 18 - 65312493 -----ctttctctc-----g-----------cctctctc- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59447117 29 - 64418924 -----ctccctccc-----gccctccttctccctctctc- i canFam2.chr9 C 0 C 0 s macEug1.Scaffold23956 20898 31 - 25324 --tctttccccctc-----tccctccctgtatCTTTCG-- i macEug1.Scaffold23956 I 2 C 0 s monDom5.chr2 304557304 33 - 541556283 tccctctctctttc-----tgtctctctctctctctct-- i monDom5.chr2 C 0 C 0 e oryCun2.chrUn0958 28338 941 + 41507 I e papHam1.scaffold8336 55570 70 - 95547 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e micMur1.scaffold_15893 16347 2687 + 19765 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e pteVam1.scaffold_11245 24930 119 + 48268 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e panTro2.chr17 79487757 0 + 83384210 C e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I e rheMac2.chr16 75047626 1133 + 78773432 M a score=406096.000000 s hg19.chr17_gl000204_random 57114 207 + 81310 ctctccgccctcct--------tctctctctct--ctctctctctctctctcGTTCCTC-TGGC--TCGTT-CGGCTGGAGCGAggcggc-agc-aggagcac------------gcggcggcggcgcgggcggcggtggcagcTCGAGCG--GAGCGCGCAGCGCGCGG-CATGGGAGG-------------------------------------------------------------------------------------------------GGGCTCTGG------------------CTGTCGCGCGGCCGGGGAGGGCGGCGGAGCGGGGAGAGCCATGACCGGG s calJac1.Contig5139 58251 218 + 225949 ctctctctctctc---------tctctctctct--ctctctctctctctctcGTTCCTC-TGGC--TCGCT-CGGCTGGAGCGAGGCGGC-AGC-AGGAGCACgcggcggcggcggcggcggcggcggcggcggcggcggcggctccggcg--gAGCGCGCAGCGCGCTGCCAAGGGAGG-------------------------------------------------------------------------------------------------GGGCTCCGG------------------AGACCGCGAGGCCAGGGAGGGCAG-GGAGCGGGGAGAGACATGGCCGGG i calJac1.Contig5139 I 9 C 0 s papHam1.scaffold8336 55640 224 - 95547 ctctccgccctccttctctctctctctctctct--ctctctctctctctctcGTTCCTC-TGGC--TCGCT-CGGCTGGAGCGAGGCGGC-AGC-AGGAGCAC---gcggcggcggcggcggcggcggcggcggcggtggcagctccggcg--gcgCGCGTAGCGCGCGG-CATGGGAGG-------------------------------------------------------------------------------------------------GGGCTCGGG------------------CGGTCGCGCGGCCGGGGAGGGCGGCGGAGCGGGGAGAGCCATGGCCGGG i papHam1.scaffold8336 I 70 C 0 s gorGor1.Supercontig_0007361 25343 198 - 64270 ctctc-----------------tctctctctct--ctctctctctctctctcGTTCCTC-TGGC--TCGTT-CGGCTGGAGCGAggcggc-agc-aggagcac------------gcggcggcggcgcgggcggcggtggcagctcgggcg--gagcgcgcagcgcgcgg-catgggagg-------------------------------------------------------------------------------------------------gggctctgg------------------ctgtcgcgcggccggggagggcggcggAGCGGGGAGAGTCATGACCGGG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16074763 201 + 17838096 ctctc-----------------tctctctctct--ctctctctctctctctcGTTCCTC-TGGC--TCGCT-CGGCTGGAGCGAGGCGGC-AGC-AGGAGCAC---------gcggcggcggcggcgcgggcggcggtggcagcTCGGGCG--GAGCGCGGAGCGCGCGG-CATGGGAGG-------------------------------------------------------------------------------------------------GGGCTCTGG------------------CTGTCGCGCGGCCGGGGAGGGCGGCGGAGCGGGGAGAGCCATGACCGGG i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79487757 193 + 83384210 ----------------------tctctctctct--ctctctctctctctctcGTTCCTC-TGGC--TCGTT-CGGCTGGAGCGAggcggc-agc-aggagcac------------gcggcggcggcgcgggcggcggtggcagctcgggcg--gagcgcgcagcgcgcgg-catgggagg-------------------------------------------------------------------------------------------------gggctctgg------------------ctgtcgcgcggccggggagggcggcggAGCGGGGAGAGCCATGACCGGG i panTro2.chr17 C 0 C 0 s mm9.chr11 118770928 179 + 121843856 -------------------------------------------CCCCCCCTCGTTCCTC-TGGC--TGGCT-CGGCTGAAGCGAGAAggc-agc-aggagcac---------gcggcggcggtggcggtggtggtggcggctgcacgggcg--gAGCGCGCAG--CTCGG-CGAGGGAGG---------------------------------------------------------------------------------------------GAGGGGGCTCCGG------------------CGGTCGCGCGGCCAGGGAGGGCGGCGAGGCAGGGAGGGCCGCGAGCCAG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4399895 234 + 7991924 -------------------------------------------TTCTCTCCCGGTCCTCTTGGC--TGGCTCCAACTGGAACAAAAAGGCTAGC-GGCAGCAC---------TC-----------------------CCGTCGGACTAGGG--AACCGC------TACCG-CATGCTAGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTccgg----------------------cgcggcgccgggggtgg----------gggaggctcgggggcggg i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 13555 134 - 54875 --------------------------------------------GCTCGCTCGTTCCTC-TGGC--TCGCT-CGGCTGGAGCGAGGAGGC-AGCTGGGAGCAC---------GCGGCGGG----------------------GCTCGGGCA--GAGCGCGCTGTCCGCGG-CGAGGGAGG-------------------------------------------------------------------------------------------------------GGG----------------------CGCGG---CGGGGAGGGCTGC------TCGAGGCCCACGGGCT-- i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10869301 180 - 65312493 -----------------------ctcccccttt--ctctctccctctcGCCGGCTCCTC-TGGC--TCGCT-CGGCTGGAGCGAAGAGAC-AGC-AGGAGCAC------------gcggcggcggcg------------gcggccctggcg--gagcgcgcagcgcgctg-caagggagg-------------------------------------------------------------------------------------------------gggctcggg------------------cggccgcgcggccgggaagggcggcggggcggggagggccgcggcgggg i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59447146 177 - 64418924 -----------------------ctccccctttcgctctctccctctcccCGGCTCCTC-CGGC--TCGCT-CGGCTGGAGCGAGGAGAC-AGC-GGGAGCAC---------gcggcggcggcggcg------------gcggcTCGGGCG--GAGCGCGCAGCGCG--G-CGAGG--GG-------------------------------------------------------------------------------------------------GGGCTCggg------------------cgg-agcg-ggccggggacggcggcggggcggggcggg--gcggggGGG i canFam2.chr9 C 0 C 0 s macEug1.Scaffold23956 20929 167 - 25324 ---------------------------------------------------------------------CT-TTGCTGAGGAGGGGAAAG-AGC-AGGAGCac------------gcagcagtggcagcagcagcacccGC-GCGAGTGTA--GCGCGCGCACCGCCCAA-CGAGGGAGG-------------------------------------------------------------------------------------------------GGTCCCGGGGTTAGGGAGGGTAAGGGAAGACCGTGCaggagagga-ggcggaggagagggagcggccagtcccagg i macEug1.Scaffold23956 C 0 N 0 s monDom5.chr2 304557337 175 - 541556283 -----------------------------------ctctccccctctccctc---cctc-tatctttcGCT-TCGCAGAGGAGAAGGagc-aga-agaagcac---------gcagcagtagcagtagcagcagcagcTCCCGCGCAAGTGTAGCGCGCGCACCGCCCAA-CGAGGGAGG-------------------------------------------------------------------------------------------------GGTCCCGGG------------------GTTAGGGAGGGTAGGGGAAGACCGTGTAGGAAAGAGGG----------- i monDom5.chr2 C 0 I 13025 e oryCun2.chrUn0958 28338 941 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e micMur1.scaffold_15893 16347 2687 + 19765 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e pteVam1.scaffold_11245 24930 119 + 48268 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I e rheMac2.chr16 75047626 1133 + 78773432 M a score=32150.000000 s hg19.chr17_gl000204_random 57321 54 + 81310 TGGGCTTCGGCGGTCAGCACCCT-GCAGCCTTCAGCGCCAACTC--CTCGGGGCAGG s calJac1.Contig5139 58469 53 + 225949 TGGGCTTAGGCCGTCGGCACTCT-GCAGCCTTCAGCACCATC-C--CTCGGGGCAGG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 55864 54 - 95547 TGGGCTTAGGCGGTCAGCACCCT-GCGGCCTTCAGCACCAACCC--CTCAGGGCAGG i papHam1.scaffold8336 C 0 C 0 s gorGor1.Supercontig_0007361 25541 54 - 64270 TGGGCTTCGGCGGTCAGCACCCT-GCAGCCTTCAGCACCAACTC--CTCGGGGCAGG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16074964 54 + 17838096 TGGGCTTCGGCGGTCAGCACCCT-GCGGCCTTCATCGCCAACTC--CTCGGGGCAGG i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79487950 54 + 83384210 TGGGCTTCGGCGGTCAGCACCCT-GCAGCCTTCAGCGCCAACTC--CTCGGGGCAGG i panTro2.chr17 C 0 C 0 s mm9.chr11 118771107 53 + 121843856 CTGAATGTGGCCACAGGAGCCCT-GGAGTC-CCAGCTCCAGCCT--TGGAGAACGGG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4400129 49 + 7991924 ccgAGTGGGGACAC----GCTCT-GCAGGT-TCCCTGTCAGTCC--AGTGGAGCAAG i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 13689 21 - 54875 -------CGGGCAG----GCTCT-----------------GCCC--TGGTG------ i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10869481 52 - 65312493 acagcgCAGGCCCGACGCACCCTTGTGGCCCGAAGCTCCGGCCCGG-----AGCAGA i bosTau4.chr19 C 0 I 3 s canFam2.chr9 59447323 33 - 64418924 ---------------CGCACCCTGGCGG-CCGCAGCGCTGGCCC--------GCGGA i canFam2.chr9 C 0 I 5 e oryCun2.chrUn0958 28338 941 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e micMur1.scaffold_15893 16347 2687 + 19765 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e pteVam1.scaffold_11245 24930 119 + 48268 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 6321 2064 + 11404 I e monDom5.chr2 304557512 13025 - 541556283 I e equCab2.chr11 58052149 1497 - 61308211 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I e rheMac2.chr16 75047626 1133 + 78773432 M a score=89232.000000 s hg19.chr17_gl000204_random 57375 53 + 81310 GGCACAGAAGAGGTGGG--GTACACACGGAAGATCCCAGAACCCA----GTGCT--GC---CCT s calJac1.Contig5139 58522 52 + 225949 AGCTTGGAAGAGGTGG---GTACACAGCGAGGATCTCAGAACCCA----GTGGT--GC---CCT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 55918 53 - 95547 GGCACAGAAGAGGTGGA--GTACACACGGGAGATCCCAGAACCCA----GTGCT--GC---CCT i papHam1.scaffold8336 C 0 C 0 s gorGor1.Supercontig_0007361 25595 53 - 64270 GGCACAGAAGAGGTGGG--GTACACACGGAAGATCCCAGAACCCA----GTGCT--GC---CCT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16075018 53 + 17838096 GGCACAGAAAAGGTGGG--GTACACACGGGAGATCCCAGAACCCA----GTGCT--GC---CCT i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79488004 53 + 83384210 GGCACAGAAGAGGTGGG--GTACACACGGAAGATCCCAGAACCCA----GTGCT--GC---CCT i panTro2.chr17 C 0 C 0 s mm9.chr11 118771160 61 + 121843856 GATG-CGTAG--GCTGGTGAGACTTGTAGGGCACCCTAGAGCTCAGAAGGAGCTGGGCTCCTCC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 8385 45 + 11404 GGTG-TGGAG-----GGCGGGAC-------GCACCCTGGTGCGCA----CAGCC--GCAGCTCT i dipOrd1.scaffold_43980 I 2064 C 0 s cavPor3.scaffold_76 4400178 50 + 7991924 GGCG-TAAAGTGATGGGCAACACGCGCAGGGCACCC-AGAGCCCA----GTGCT--GC------ i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 13710 35 - 54875 -------AAGTGATGGGCGC----------TGACCCTGGAGCCTG----GTGCT--GC------ i ochPri2.scaffold_9426 C 0 C 0 s rheMac2.chr16 75048759 22 + 78773432 ---------------------------------TCCCAGAACCCA----GTGCT--GC---CCT i rheMac2.chr16 M 1133 C 0 s micMur1.scaffold_145100 0 49 + 1040 ----CGGAAGGGGTGGG--CCACGCGCTGGGGCCCCCAGAACCCA----GTGCT--GC---CGG i micMur1.scaffold_145100 n 2687 C 0 s bosTau4.chr19 10869536 53 - 65312493 TGCACGAGAGAGGTGGG--CGAGGCGCGGAGGACCCCAAAGCCCG----GGGCT--GC---CCA i bosTau4.chr19 I 3 C 0 s canFam2.chr9 59447361 52 - 64418924 GGCGGGGGAGGAGTGAG--CGAAGCGCAGGGGTCCCCAGGGCCCG----GAGCA--GC---CC- i canFam2.chr9 I 5 C 0 s equCab2.chr11 58053646 53 - 61308211 GGCACGAGAGAGGCGGG--CGAGGCGCGGGGGACCCCAGACCCCG----GAGCT--GC---CCA i equCab2.chr11 I 1497 C 0 e oryCun2.chrUn0958 28338 941 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e pteVam1.scaffold_11245 24930 119 + 48268 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I a score=148861.000000 s hg19.chr17_gl000204_random 57428 140 + 81310 GGTCCCTTCAAGGGCAGCCCC------------AAGCCCG--------CTGCCCCTCCCCACCTCCAAG--------CTATC--TTGGGGGCGGATCAACCCAGGTGACCCTTAACAGGACCCCTGCCCT----TGTGCCTC---GCTGTCCCTGG--------GGGCCATTTTTCTTTGCCAGG s pteVam1.scaffold_11245 25049 124 + 48268 GGGTCCCGCGAGCGCAG-CCTCCGATCCA----GAGCCCG---------CCTCCCTCCCTCCCGCCCCG--------CGATC---TGGGGG----------CCAGCAGCCCCTATCAGGACCCCTGCCCT----CCCACC---------GCCCTGGCCGAGAAAGGACAACA------------- i pteVam1.scaffold_11245 I 119 C 0 s canFam2.chr9 59447413 136 - 64418924 GGTCCCCGCAAGCGCCGCCCTCCAGCCCT----GGCCCCGCCTCTCCTCCCTCCCTCCCTCCCGCCTGCCCCCGGGGCGATC--GTGGG------------CCGGCAGCTCCTCGGAGGACCCCTGCCCT----CCCACCTC---CCGGGCTCTGGCCCTG------------------------ i canFam2.chr9 C 0 C 0 s equCab2.chr11 58053699 142 - 61308211 GGTCCCCGCGAGCGCCGCCCTCCGGCCCCG---GGCTCCGCCTCccctccctccctccctccctcccGC--------TGATG--GTGGGAA----------CAGGCAGCCTCTATCAGGACCCCTGCCCT----CCCGCCCC---CCTGGGCCTGGCCCAGAAAGGACAAAA------------- i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10869589 148 - 65312493 GTTTCCCTCGAGCGCCGCCCTCCGGTCCC----GGACCCGCTTCCCCTCGCTTCCTCCCTCCCTCACTC-CCTGCAGCGATC--CTGAGGC----------CGGGCAGCCCCTACCAAGACCCTTACCCT----CCTGCCAC---CCTGGCCCTGGCCAAGAAAGAACAACA------------- i bosTau4.chr19 C 0 C 0 s micMur1.scaffold_145100 49 137 + 1040 GACCCCTTCTAGTGCCGCCCT------------GGGCCC---------CGCCTACCCGCCCCCTCCAGG--------G-ATC--TTGGGGGCTGTCCAGGTGAAACGACCCTTACCAGGGACCCTGCCCT----CCTGCTTC---CCTGTCCCTGG--------GGGCTGTTTCCCTTT-CCTGG i micMur1.scaffold_145100 C 0 C 0 s rheMac2.chr16 75048781 140 + 78773432 GGTCCCTTCAAGGGCAGTCCC------------AAGCCCG--------CTGCCCCTCCCCACCTCAAGG--------CTATC--TTGGGGGCGGTTCAGCCCAGGTGACCCTTAACAGGACCCCTGCCCT----TGTGCCTC---CTTGTCCCTGG--------GGGCCATTTTTCTTTCCCAGG i rheMac2.chr16 C 0 C 0 s ochPri2.scaffold_9426 13745 77 - 54875 ---------------------------------C--------------------------------------------------TTGGGGACCGGCCAACGCAGCGGACCCTTATGTAGACCCTGGCC------TGTGTCTG---CCTGTCCCTAG--------GGGGCATCCTGGT-------- i ochPri2.scaffold_9426 C 0 C 0 s cavPor3.scaffold_76 4400228 150 + 7991924 ---CCGGTCAGCTCAAGCACCGCCCAGGGTC--CCGCCTC--------TCCTCCCCGCCCCCACTCGGA--------TGGCT--CTTGGGACGAGCCAGTCCAGGCAGTCCTTAACAGTACCCCCTCCCCACTATACTCCTG---CCTATCTCTGG--------GAAACATCTCGCCGC-CACTC i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_43980 8430 116 + 11404 GAGCCCTGGAGCAGGGACCCCTCGGAG------CCTCCTA--------GGATGCCCCCCTACCCCCAGG--------GAGCTACCTCGGGGCTGG---------------------GGGACCCCGGCGCCCCC-TCCTCCTTGTCCCTGCCCC-----------------CCCAG--------GG i dipOrd1.scaffold_43980 C 0 C 0 s mm9.chr11 118771221 145 + 121843856 GAGCTCACCACCACCACCACCGCTGTGGTCTCACCTCCCC--------TTCCTCCCTCCCTTCTTCTGG----------GCGACCTCAGTGTAAGTCATCACTAGCAACACTTAGCAGGACCCCTGCACCCTCGTTCCACTGGGACCGGTTTC-----------------TCTCGCT-----CTG i mm9.chr11 C 0 C 0 s panTro2.chr17 79488057 135 + 83384210 GGTCCCTTCAAGGGCAGCCCC------------AAGCCCG--------CTGCCCCTCCCCACCTCCAAG--------GTATC--TTGGGGGCGGATCAGCCCAGGTGACCCTTAACAGGAACCCTGCCCT----TGTGCCTC---GCTGTCCCTGG--------GGGCCATTTTTCTTTG----- i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16075071 140 + 17838096 GGTCCCTTCAAGGGCAGCCCC------------AAGCCTG--------CTGCCCCTCCCCACCTCCAGG--------CTATC--TTGGGGGCGGATCACCCCAGGTGACCCTTAACAGGACCCCTGCCCT----TGTGCCTC---GCTGTCCCTGG--------GGGCCATTTTTCTCTGCCAGG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 25648 140 - 64270 GGTCCCTTCAAGGGCAGCCCC------------AAGCCCG--------CTGCCCCTCCCCACCTCCAAG--------CTATC--TTGGGGGCGGATCAGCCCAGGTGACCCTTAACAGGACCCCTGCCCT----TGTGCCTC---GCTGTCCCTGG--------GGGCCATTTTTCTTTGCCAGG i gorGor1.Supercontig_0007361 C 0 C 0 s papHam1.scaffold8336 55971 140 - 95547 GGTCCCTTCAAGGGCAGTCCC------------AAGCCCG--------CTGCCCCTCCCCACCTCAAGG--------CTATC--TTGGGGGCGGTTCAGCCCAGGTGACCCTTAACAGGACCCCTGCCCT----TGTGCCTC---CTTGTCCCTGG--------GGGCCATTTTTCTTTCCCAGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 58574 140 + 225949 GGCCCCCTCAAGGGCAGCTCC------------GAGCCTG--------CAGCTTCTTTCCACCTCCAGA--------TTATC--TTGGGGGCTGTCCAGCCCGGGTGACCCCTACCAGGACCCCTACCCT----GGTGACTC---ACTGTCCCTAA--------GGGCCATTTTTCTGTCCCAGG i calJac1.Contig5139 C 0 C 0 e oryCun2.chrUn0958 28338 941 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e loxAfr3.scaffold_49 14443533 1343 - 17734757 I a score=159869.000000 s hg19.chr17_gl000204_random 57568 63 + 81310 CCCAGGGATCCCCAGCAATGGGACGTGGTCACCAA-------------G--CATCAGGGACGAATG-CCACCCCA--C-CCC-------- s calJac1.Contig5139 58714 63 + 225949 CCCAGGGATCCCCAGCAATGGGACGTGGTCACTGA-------------G--CATCAGGGGCCAATG-CCACCCCA--C-CCC-------- i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 56111 54 - 95547 CCCAGGGATCCCCAGCAATGGGACATGGTCACCAA-------------G--CATCAGGGACGAATG-CCA-------------------- i papHam1.scaffold8336 C 0 I 42 s gorGor1.Supercontig_0007361 25788 63 - 64270 CCCAGGGATCCCCAGCAATGGGACGTGGTCACCAA-------------G--CATCAGGGACGAATG-CCACCCCA--C-CCC-------- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16075211 63 + 17838096 CCCAGGGATCCCCAGCAATGGGACGTGGTCACCAA-------------G--CATCAGGGACGAATG-CCACCCCA--C-CCC-------- i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79488192 62 + 83384210 -CCAGGGATCCCCAGCAATGGGACGTGGTCACCAA-------------G--CATCAGGGACGAATG-CCACCCCA--C-CCC-------- i panTro2.chr17 C 0 C 0 s mm9.chr11 118771366 60 + 121843856 CCCAGGGGTCCCTAGAAA---GACTTGGTCGCTGA-------------A--TGGCAGGAATGGATG-TCCCCTCC--C-CCA-------- i mm9.chr11 C 0 I 1 s dipOrd1.scaffold_43980 8546 63 + 11404 CTCAAGGGCCCCCGGAGATGGGACTTGGTCACAGA-------------G--CAGCAAGGATGGACA-GCTCCTCC--C-GCA-------- i dipOrd1.scaffold_43980 C 0 I 1 s cavPor3.scaffold_76 4400378 63 + 7991924 CCCCCCCCCCCCCGCAAACGGGACTTCATCACAGA-------------G--CAA-AAGGATGGATG-TCCCTTCC--CAGCT-------- i cavPor3.scaffold_76 C 0 I 1 s ochPri2.scaffold_9426 13822 31 - 54875 -------------------------------CAGG-------------G--GAG-AGGGGTCCTCC-CTCCCTCC--A-CCG-------- i ochPri2.scaffold_9426 C 0 I 1 s rheMac2.chr16 75048921 63 + 78773432 CCCAGGGATCCCCAGCAATGGGACATGGTCACCAA-------------G--CATCAGGGACGAATG-CCACCCCA--C-CCC-------- i rheMac2.chr16 C 0 C 0 s micMur1.scaffold_145100 186 62 + 1040 CCCAGGGAT-TCTGGAAATGGGACTTGGTCGCCTA-------------G--CAGAAGGGACGAATG-CCCCCCTA--C-CCC-------- i micMur1.scaffold_145100 C 0 C 0 s bosTau4.chr19 10869737 75 - 65312493 -CTGGGGATCCCTAGGAATGGGACTCGGGCCCCAAGAATGGGACTCGGG--CATCGAGGGCGAATG-CTCCCCAA--C-CTC-------- i bosTau4.chr19 C 0 I 12 s equCab2.chr11 58053841 54 - 61308211 -CCCAGGATGTCCAGAAATGGGACTCGGG----------------------CAGCGGGGGTGAATG-CCCCCACA----CTC-------- i equCab2.chr11 C 0 I 13 s canFam2.chr9 59447549 42 - 64418924 ---------GGCCTGCGGTGGAACTCAGGC------------------A--CAGCGGGAGTGAATG-CCCCC------------------ i canFam2.chr9 C 0 I 2 s pteVam1.scaffold_11245 25173 58 + 48268 --CTGCGATCCCCAGAAATGGGGCTCAGG-------------------G--CAGGGAGGCTGAATGACCCCCATACTC-CTC-------- i pteVam1.scaffold_11245 C 0 I 14 s loxAfr3.scaffold_49 14444876 68 - 17734757 CCCCAGAATCCCCAGAGATGGGA----GCAGCCGA-------------GGACAGCAAGG-CGAAAG-CCCCCACA--C-TCCACCACCCG i loxAfr3.scaffold_49 I 1343 C 0 e oryCun2.chrUn0958 28338 941 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=-75729.000000 s hg19.chr17_gl000204_random 57631 17 + 81310 GCA-TGCCATGCCATG------------CC s gorGor1.Supercontig_0007361 25851 17 - 64270 GCA-TGCCATGCCATG------------CC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16075274 22 + 17838096 GCA-TGCCATGCCATGCCATC-------CC i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79488254 17 + 83384210 GCA-TGCCATGCCATG------------CC i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75048984 8 + 78773432 GCA-TGCCA--------------------- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 56207 29 - 95547 GCA-TGCCATGAGTTGCCCACCCCGCATGC i papHam1.scaffold8336 I 42 C 0 s calJac1.Contig5139 58777 17 + 225949 GCA-TGCCATGCCATG------------CC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_145100 248 18 + 1040 GCACTGCCATGCCTCC------------TC i micMur1.scaffold_145100 C 0 C 0 s mm9.chr11 118771427 12 + 121843856 GCC-TCTCCAGCT----------------- i mm9.chr11 I 1 I 2 s dipOrd1.scaffold_43980 8610 12 + 11404 GCC-GCCCATGCC----------------- i dipOrd1.scaffold_43980 I 1 I 669 s cavPor3.scaffold_76 4400442 12 + 7991924 ACA-TTCATAGCC----------------- i cavPor3.scaffold_76 I 1 I 5 s ochPri2.scaffold_9426 13854 3 - 54875 GCA--------------------------- i ochPri2.scaffold_9426 I 1 C 0 s bosTau4.chr19 10869824 5 - 65312493 GCA-CC------------------------ i bosTau4.chr19 I 12 I 14 s equCab2.chr11 58053908 5 - 61308211 GCA-CT------------------------ i equCab2.chr11 I 13 I 14 s canFam2.chr9 59447593 5 - 64418924 ACA-CT------------------------ i canFam2.chr9 I 2 I 5 s pteVam1.scaffold_11245 25245 5 + 48268 GCG-CC------------------------ i pteVam1.scaffold_11245 I 14 I 6 s loxAfr3.scaffold_49 14444944 23 - 17734757 ------CCCTGCCGCACAGTGGTTCCTCC- i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 28338 941 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=52130.000000 s hg19.chr17_gl000204_random 57648 146 + 81310 TTTGAGTT-GCCCACATA---CCCCAAACC-----------CCC-TCACTAGGCCCAG-------GTGCCCTGACTTCCTG-------GAGGACCACTGGAAAGG-AAGGG------ATCGGG-C-----CCACTCCGTGCTGT-------------------TA-------GTCCAGATTGGCCAACCCAA-C---------CCATTTAA--ACATTTCCACCTGT s gorGor1.Supercontig_0007361 25868 146 - 64270 TTTGAGTT-GCCCACACA---CCCCAAACC-----------CCC-TCACTAGGCCCAG-------GTGCCCTGACTTCCTG-------GAGGACCACTGGAAAGGAAAGGA------ATCGGG-C-----CCACTCCGTGCTGT-------------------TT-------GTCCAGATTGGCCAACCCAA-C---------CCATTTAA--ACA-TTCCACCTGT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16075296 146 + 17838096 TTTGAGTT-GCCCACACG---CCCCAAACC-----------CCC-TTACTAGGCCCAG-------GTGCCCTGACTTCCCG-------GGGGGCCACTGGAAAGG-AAGCG------ATCGGG-C-----CCACTCCGTGCTGT-------------------TA-------GTCCAGACTGGCCAACCCAA-C---------CCATTTAA--ACATTTCCACCTGT i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79488271 146 + 83384210 TTTGAGTT-GCCCACACA---CTCCAAACC-----------CCC-TCACTAGGCCCGG-------GTGCCCTGACTTCCTG-------GAGGACCACTGGAAAGG-AAGGG------ATCGGG-C-----CCACTCCGTGCAGT-------------------TA-------GTCCAGATTGGCCAACCCAA-C---------CCATTTAA--ACATTTCCACCTGT i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75048992 144 + 78773432 --TGAGTT-GCCCACACG---CCCCAAACG-----------CCC-TTACTAAGCCCAG-------GTGCCCTGACTTCCTG-------GGGGATCACTGGAGAGA-AAGCC------ACTGGG-C-----CCACTCCAGGCTGT-------------------TA-------GTCCAGATTGGCCAACCCAA-C---------CCATTTAA--ACGTTTCCACCTGC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 56236 146 - 95547 CATGAGTT-GCCCACACG---CCCCAAACG-----------CCC-TCACTAAGCCCAG-------GTGCCCTGACTTCCTG-------GGGGATCACTGGAGAGA-AAGCC------ACTGGG-C-----CCACTCCAGGGTGT-------------------TA-------GTCCAGATTGGCCAACCCAA-C---------CCATTTAA--ACGTTTCCACCTGC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 58794 140 + 225949 TTCGAGTG-GCCCGCATG---CCCCATAC------------CCC-TTACCAAGCCCAG-------GTGCCCTGACTT-CTG-------GGGGATCACCGGAGAGG-ATGCG------ATAGGG-C-----CCACTCCAGATTGT-------------------TA-------GTCCAGACTGGCCAACCAAA-C------------TTCCA--AC-TGTCCACCTGC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_145100 266 154 + 1040 TTCCACTTCCCCCAGGCG---CCCTGGAT------------GCC-TTAATAGGCCTGGA-ATTCCATGCCCTGCCCTCC---------GGGGATAATCGGAG----GAGCG------ATCAGG-C-----CTGCCCTGTCCAGC-------------------TGGGCGCCTGTCCAGGTTGGCCAGCCCAA-C---------CCCGTGAG--ACATTTCCCCTGGG i micMur1.scaffold_145100 C 0 C 0 s mm9.chr11 118771441 181 + 121843856 TCTGCAGC-GCCCGCGCC---TAACTGGCCACTGGGGAAGACCC-TTAATAGGCCTGGA-GTTCCATGCCTTGCCTTCCTGAGAATCACAGAGCAGGCGGGGAGG-CAG----------GAGG-C-----CTAC-CCTGGAACAGGACACAGGGAGGACACACTT-------GTCCCCGCTGATAATCCT-A-T---------GGCCTTAA--ATATTTCCATCC-- i mm9.chr11 I 2 I 2 s cavPor3.scaffold_76 4400459 122 + 7991924 -TTTCAGT-ATCCACG-----------------------------TTAATGG-------------------TGTCTTCCTGCCCCTC------CGAATGGAGTGA-CC------------AGG-T-----CCACTCCAAGACCCGGCCACAGCA---------TT-------GTCCAATTTGGTCAACCTGA-T---------CTCCCTCA--GTGTTTCCACCC-- i cavPor3.scaffold_76 I 5 I 2 s ochPri2.scaffold_9426 13857 92 - 54875 --------------------------------------------------GGGTTGCGC-CTTCCCTCCCCTTCCCTTCTTCCTGTCCCAGCATCAACAGAGGGA-CGGAG------CTGAGA-CTTTGGCCACCCCTGGACCTAGG----------------TT-------GG----------------------------------------------------- i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10869843 150 - 65312493 TCCAATTT-GCCCACACA------CCTACT------------CC-TTACTGGGGCTTGAAATTCCCTGCCTTGCGTTCCTG-------GGAATCCAAGAGTGAAT--AATCAGCCACACAGAG-T-----CACCACTGGGGTGT-------------------AG-------GTCCACACTGACCAACCACA-C---------GGATTCAA--ACATTTCCAC---- i bosTau4.chr19 I 14 C 0 s equCab2.chr11 58053927 153 - 61308211 TTCACTTT-ACCCACTCG---CC-CCTACC-----------CCC-TTACTAGGGCCTGAGGTGCAAGGCCTTGCCTTCCTG-------AGGATCACAGAGGGAGC-GAACCCCCACCGCAGGG-T-----TGTTGCTGGGGCCT-------------------TT-------GTCCAGACC-GCCACCCCAA-C---------AGATTTAC--ACATTTCCAC---- i equCab2.chr11 I 14 C 0 s canFam2.chr9 59447603 150 - 64418924 TCCACTTG-GTCCACAGG---CCTCCCACT-----------CCC-TTACCTAGGCCTGAAATTCAGTGCCTTGCCTTCCT------------CCAGATGGAGAGT-GAAGGGGCCACACAGGG-C-----CACTGCTGGGGTGG-------------------TT-------CTCCAGATTGGCGAAGGTAA-C---------CTATGTAA--ACATCCCTGC---- i canFam2.chr9 I 5 C 0 s pteVam1.scaffold_11245 25256 144 + 48268 TCCAGTCT-G--------------CCCATC-----------CCC-TTACTAGGGCCTGAAACTGGGTGCCTTGCCTTCCTG-------AGGAGGGGAGAGGGCGT-GAGCCAGCAGCGCAGGGCC-----CACTGCCCTGGCGT-------------------CT-------GTCCAGACT-GCCAACCCAACC---------CGATTTAA--ACGTTTCCA----- i pteVam1.scaffold_11245 I 6 C 0 s loxAfr3.scaffold_49 14444967 133 - 17734757 TCCACTCT-GCCCGCAGGGGGCCACACACC-----------CCCTTTACTAGGGCCTG---------------GATTCC---------------------------GGGCC------TTAAGG-C-----CAACGCCGAG-CGT-------------------TT-------GTCCAGCTCAGCCAACCCAA-CCAACGACAGCCATTTCACTCCATTTCCACCCGG i loxAfr3.scaffold_49 C 0 I 5 e oryCun2.chrUn0958 28338 941 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 8622 669 + 11404 I e monDom5.chr2 304557512 13025 - 541556283 I a score=50511.000000 s hg19.chr17_gl000204_random 57794 29 + 81310 GCCT---GGCTGGAG--AGGAAGGAC-------TGTGGGAG s gorGor1.Supercontig_0007361 26014 29 - 64270 GCCT---GGCTGGAG--AGGAAGGAC-------TGTGGGAG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16075442 29 + 17838096 GCCT---GGCTGGAG--ATGAAGGAC-------TGTGGAAG i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79488417 29 + 83384210 GCCT---GGCTGGAG--AGGAAGGAC-------TGTGGGCA i panTro2.chr17 C 0 I 493 s rheMac2.chr16 75049136 29 + 78773432 GCCT---GGGTGGAG--AGGAAGGAC-------TGTGGGAG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 56382 29 - 95547 GCCT---GGGTGGAG--AGGAAGGAC-------TGTGGGAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 58934 28 + 225949 TCGT---GGCTAGAG--AGGAAAGGC-------TGTGGGG- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_145100 420 28 + 1040 GCCT---GGCTGGGG--AGAAGGGGC-------TGGGGAG- i micMur1.scaffold_145100 C 0 C 0 s mm9.chr11 118771624 25 + 121843856 GTCA---GTTAGGAG--AACCTAAAA-------CC----AG i mm9.chr11 I 2 C 0 s cavPor3.scaffold_76 4400583 27 + 7991924 GTCG---GCTCAGGATTTGCCTACAA-------TC----AG i cavPor3.scaffold_76 I 2 C 0 s oryCun2.chrUn0958 29279 29 + 41507 GCCA---GGCCGGAG--AGCAGGGGC-------GGTGGGAG i oryCun2.chrUn0958 I 941 C 0 s ochPri2.scaffold_9426 13949 29 - 54875 GACT---GGCTGGAG--AGGCTGGGC-------TCTGGGAG i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10869993 35 - 65312493 -CTT---GGCCGCGG--AAGAGGGGCTGTCACTTGTAGGAG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58054080 34 - 61308211 -CCT---GGCTCCAG--AAGGGGGGCTGTAGA-TGTCGGAG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59447753 33 - 64418924 -CCT---GGC-CTAG--ATGTGGGGCTGTCAC-TGTGGGAG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 25400 33 + 48268 -CCT---GGT-GGGA--GAAAGGGGCTGTCAC-TATCAGGG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14445105 32 - 17734757 GCCTCGCGGCTGGAC--GGAAAAGGC-------TGTCCCAG i loxAfr3.scaffold_49 I 5 C 0 e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 714 2422 + 4080 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 8622 669 + 11404 I e monDom5.chr2 304557512 13025 - 541556283 I a score=258305.000000 s hg19.chr17_gl000204_random 57823 93 + 81310 GTCAGCTTAGGATTTCCCTAAAATCAAAAGATCAGGTAGCTCCTGTCCCCAGTCCCAGCCTCCCCCAGCATCTAGAGTAAGGG--GCCTGGTGTG s micMur1.scaffold_145100 448 85 + 1040 GTCAGTTTAGGATTTACCTAAAATCAGAAAAGCAGGTAGTCCCCGTCCCTGCTCTCAGCCTCCCC--------AGACCAGGGC--CCCTAGTGTA i micMur1.scaffold_145100 C 0 C 0 s calJac1.Contig5139 58962 89 + 225949 GTCAGCTCAGGATTT-GCTAAAATC---AGATCAGGCAGCTCCTGTCCCCAGTCCCAGCCTTCCCCAGCCTCTCGGGTAAGGG--GCCTGGTGTG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 56411 93 - 95547 GTCAGCTTAGGATTTCCCTAAAATCAGAAGATCAGGCAGCTCCTGTCCCCAGTCCCAGCCTCCCCCAGCCTGTAGGATAAGGG--GCCTGGTGTG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75049165 93 + 78773432 GTCAGCTTAGGATTTCCCTAAAATCAGAAGATCAGGCAGCTCCTGCCCCCAGTCCCAGCCTCCCCCAGCCTGTAGGGTAAGGG--GCCTGGTGTG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16075471 93 + 17838096 GTCAGCTTAGGATTTCCCTAAAATCAAAAGATCAGGTAGCTCCTGTCCCCAGTCCCAGCCTCCCCCAGCATCTAGGGTAAGGG--GCCTGGTGTG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 26043 93 - 64270 GTCAGCTTAGGATTTCCCTAAAATCAAAAGATCAGGTAGTTCCTGTCCCCAGTCCCAGCCTCCCCCAGCATCTAGGGTAACAG--GCCTGGTGTG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79488939 93 + 83384210 GTCAGCTTAGGATTTCCCTAAAATCAAAAGATCAGGTAGCTCCTGTCCCCAGTCCCAGCCTCCCCCAGCATCTAGGGTAAGGG--GCCTGGTGTG i panTro2.chr17 I 493 C 0 s tupBel1.scaffold_124460.1-4080 3136 64 + 4080 --------------------------AAAGAATCGGTATTCCCTGTCGCT-GTCCCAGCGTGCTCAGCCATGT--GTTAAGGG--TTACTGTGCA i tupBel1.scaffold_124460.1-4080 I 2422 C 0 s mm9.chr11 118771649 46 + 121843856 AAGAGTTCCA----------------------------------------------GCCTCCCCCTAACCC--AGGGAAAGGG-AGTCTAGCGTG i mm9.chr11 C 0 I 6 s cavPor3.scaffold_76 4400610 48 + 7991924 --GAGCTCGGGGA------------------------------------------CGCCCTGTCCCAGTCC--AGACTAAAGG-ATCCTGCTGTG i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 29308 70 + 41507 AGGAGCTTAGCCATGGTGTGG----------------------TGTGGCCACTGCCAGCATCCTCCAGCCT--GGGGCACGGG-AGCCCGCTGTG i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 13978 92 - 54875 GTGAGCCTGGGGGTTGTGTGATGTCACCACAGCAGGTGGCTCCTGTGCCCACTCCCAGCATCCCCTTACCC--AAGGCAAGGG-ACACTGCTGTG i ochPri2.scaffold_9426 C 0 C 0 s bosTau4.chr19 10870028 91 - 65312493 GTCAGCTAAGAATTTGCCTAAAGTCAGAAAAGCAAGTATTCCCTGTCCCCACTCCCAGC-TCCCCCACCCT--AGGGGAAGGG-ACCCTGATGTA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58054114 69 - 61308211 ATCAGCTTGGGATTTGCCTAAAATCAGAAGAGCAGGCAGT-----------------------GCCAACCT--AGGGGCCGGG-GCCCTGCTGTA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59447786 90 - 64418924 GTC-GCCTAGGATTTGCCTCAAATCAGGAGAGCAGGTTGTCCCTGTTCTTACTCCATCC-TCCCCCAACCT--GGGGGAAGAG-GCCCTGGTTTA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 25433 86 + 48268 GCTTACTAAGGGTTTGCCGAAAATCAGAAAAGCAGGTAGTCTCCCCACTTCCAGGATCT----CCCAACCC--AGGGGAAGGG---CCCGGTGTA i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14445137 93 - 17734757 GTCTGGAGAGGGTGCCCCAAAACTAAGAGGAACCGGTAGCTCCTGTCCCGGGTTCCAGCCTCCCCCGACCT--AGGATCAGCCAACCCCGGTTTC i loxAfr3.scaffold_49 C 0 C 0 e choHof1.scaffold_149147 5378 3095 + 9388 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 8622 669 + 11404 I e monDom5.chr2 304557512 13025 - 541556283 I a score=49596.000000 s hg19.chr17_gl000204_random 57916 91 + 81310 -AGTTCTGGGAGGG-------TCT-CTATCC----------------TTGGTGCA--------GAGGG-AGCAGGAGAGCAGAGGCT-------GAGGACACAGTGGAGT-GG---GGACCCTCTGGAA--AGGCAGG s micMur1.scaffold_145100 533 88 + 1040 -GG-TATGGGAGGG-------TGT---ATCC----------------TTGGGGGA--------GGGGG-AGAAGTCAAGCCCAAGCT-------GAGGACCCAGTGGACT-GG---GGACACCTTGAAT--GGACAGA i micMur1.scaffold_145100 C 0 C 0 s calJac1.Contig5139 59051 91 + 225949 -GGGTCTGGGAAGG-------TCT-CTATCC----------------TTGGTGCA--------GCGAG-AGCAGGAGAGCAGAGGCT-------GAGAACACGGTGGAGT-GG---GGACCCTCTGGAC--AGGCAGG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 56504 75 - 95547 -GATTCTGGGAGGG-------TCT-CCATCC----------------TTGGTGCA--------GAGGG-AGC-----------------------AGGACACAGTGGAGT-GG---GGACCTTCGGGAA--AGGCAGG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75049258 75 + 78773432 -GATTCTGGGAGGC-------TCT-CCATCC----------------TTGGTGCA--------GAGGG-AGC-----------------------AGGACACAGTGGAGT-GG---GGACCTTCTGGAA--AGGCAGG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16075564 91 + 17838096 -AGTTCTGGGAGGG-------TCT-CTATCC----------------TTGGTGCA--------GAGGG-AGCAGGAGAGCAGAGGCT-------GAGGACACAGTGGAGT-GG---GGACCCTCTGGAA--AGGCAGG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 26136 91 - 64270 -AGTTCTGGGAGGG-------TCT-CTATCC----------------TTGGTGCA--------GAGGG-AGCAGGAGAGCAGAGGCT-------GAGGACACAGTGGAGT-GG---GGACCCTCTGGAA--AGGCAGG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79489032 91 + 83384210 -AGTTCTGGGAGGG-------TCT-CTATCC----------------TTGGTGCA--------GAGGG-AGCAGGAGAGCAGAGGCT-------GAGGACACAGTGGAGT-GG---GGACCCTCTGGAA--AGGCAGG i panTro2.chr17 C 0 C 0 s tupBel1.scaffold_124460.1-4080 3200 91 + 4080 -GCTTCTGGGATGG-------TGTCCCAACC----------------TTGG-GAA--------AGGAA-AGCAGTAGTGTCTATCCT-------GATGGGCCAGAGGGAT-GG---TGTCTCTCTCAAG--GGCCGGG i tupBel1.scaffold_124460.1-4080 C 0 I 306 s mm9.chr11 118771701 68 + 121843856 -GGTCCG----GCA-------TCT-CTAGTC----------------TTGGGAAA--------AGAAA---------------------------GGGGTTGGGAGGCAG-GC---ATTGCCTCTGAGC--TGTCAAG i mm9.chr11 I 6 C 0 s dipOrd1.scaffold_43980 9291 74 + 11404 -GGAGCT----GTG-------CCA-TAGGTC----------------CTGGGAGA--------CGGAG-----------CTGAGGCC--------GAGGCTGGGAGT--G-GC---GGCCTCTCCGAGC--CTGCAGG i dipOrd1.scaffold_43980 I 669 C 0 s cavPor3.scaffold_76 4400658 67 + 7991924 -----------GGG-------TCT-CTAGGC----------------TTGGGACA--------GGGTG-----------CT--------------GAGACTGGGAAGAAG-ACTAGGGGTGTTTTGGGC--TGGCAGG i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 29378 79 + 41507 -GGGGCTGAGAGGG-------TCT-CTCTTC----------------TTGCGTGAAGGACAAGAGGAG-----GGGGTCCTGGGCCT-------GGAGACTCAGGGGGCG-GT---GGGG------------------ i oryCun2.chrUn0958 C 0 I 488 s ochPri2.scaffold_9426 14070 56 - 54875 -GGGCCTGAGAG---------------------------------------GTGA--------GGGAG-----GGATGTCTGGGCTT-------GAAGACCGGCAGGGCA-GT---GGGT------------------ i ochPri2.scaffold_9426 C 0 I 30 s bosTau4.chr19 10870119 91 - 65312493 -GGTTCTGAGACGG-------TCT-CTATCC----------------TCCGGAGG--------GGGAGCAGAAGGAAAGCAGAAGCT-------AAGGGC-CAGAGGAGT-AG---GGATCATCTGGGC--TGGCAGG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58054183 91 - 61308211 -GGATCCGGGAGGG-------TCT-CCAGCC----------------TCGGGAGC--------TGGAGCAGAAGGAAAGCGGAGGCT-------CAGGGC-CAGCGGAGT-GG---GGACCCTCAGGGA--GCACAGG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59447876 70 - 64418924 -GGGGCTGGGGAGG-----------------------------------------------------GGAGAAGGAAAGCCAAAGGT-------AAGGGT-GGGTGGAGT-GG---GGACCCTGTGGGC--TGGTGGG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 25519 108 + 48268 -GGGTCTGGGGCAG-------TTT-CTAGCCTTGCGGGGGGGGGGGGTCGAGGGG--------GGGAGCAGAAAGAACGCTGAGGCC-------AAGGGC-TTGTGGAGTCGG---GGACTCTCTGGGC--TGGCGGG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14445230 108 - 17734757 CGGTCTTGGAGGGGAGATATGGTT-CTAGCC----------------GGGGGAGG--------GGAAGCAGAACGGAAGCCCCGGCTGGTTGGCGGGGGGCCAGGGCTGT-G----GGACCCTCTGGGCTTGGGCGTG i loxAfr3.scaffold_49 C 0 C 0 e choHof1.scaffold_149147 5378 3095 + 9388 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=-60291.000000 s hg19.chr17_gl000204_random 58007 22 + 81310 A----GA----GATCTATTGC--TGGGGTCAG s micMur1.scaffold_145100 621 23 + 1040 AT---GA----GACCTGCCAG--TCGGGTCAG i micMur1.scaffold_145100 C 0 C 0 s calJac1.Contig5139 59142 22 + 225949 A----GA----GATCTACCGC--TGGGGTCAG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 56579 22 - 95547 A----GA----GATCGGCTGC--TGGGGTCAG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75049333 22 + 78773432 A----GA----GATCGGCTGC--TGGGGTCAG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16075655 22 + 17838096 A----GA----GATCTATTGC--TGGGGTCAG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 26227 22 - 64270 A----GA----GATCTATTGC--TGGGGTCAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79489123 22 + 83384210 A----GA----GATCTATTGC--TGGGGTCGG i panTro2.chr17 C 0 C 0 s mm9.chr11 118771769 29 + 121843856 -ATGAGACCCAGGTACAACAG--TGGGGCTAG i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 9365 28 + 11404 -ATG-GACGCAGGGACAGCTG--CGGGGCCAA i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4400725 28 + 7991924 -ATGAGACCC-GGGAGGGGAG--TGGACTCAG i cavPor3.scaffold_76 C 0 C 0 s ochPri2.scaffold_9426 14156 27 - 54875 -GCC-GACC--AGCATGGTGG-TTGGGGTCAG i ochPri2.scaffold_9426 I 30 I 4444 s bosTau4.chr19 10870210 10 - 65312493 ----------------------ATGAGACCCA i bosTau4.chr19 C 0 I 6 s equCab2.chr11 58054274 10 - 61308211 ----------------------ATGAGACCCA i equCab2.chr11 C 0 I 20 s canFam2.chr9 59447946 10 - 64418924 ----------------------ATGAGACCCA i canFam2.chr9 C 0 I 6 s pteVam1.scaffold_11245 25627 10 + 48268 ----------------------ATGAGACCCA i pteVam1.scaffold_11245 C 0 I 11 s loxAfr3.scaffold_49 14445338 28 - 17734757 ----AGAGCCCGAGGGAGCACAGTGAGGCCAG i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 29457 488 + 41507 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 3291 306 + 4080 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=260295.000000 s hg19.chr17_gl000204_random 58029 125 + 81310 CCCACCACTGGCAC-ACAACACCAGAAGTGGGCAAGAAGGTCTGGACGGTCCCAAACA--------GGTTTAGGCAGGAGGCTGAGTAATCATTTC-C-----------AAAACAAAAGACA-TTCTGGTGCAGCAACCAGGCTGGA---------- s micMur1.scaffold_145100 644 116 + 1040 CCAGCCACTGTCAT-ACAGCACCAGAGGTAACCAAGAAGGCCTGGAC--CTCCGCACA--------GGTTTGGGCAGGC--CAG----ACTGTTTC-T-----------AAAACAAAAGACT-TTCAAATGCAGCA-CCGGGCTGGG---------- i micMur1.scaffold_145100 C 0 C 0 s calJac1.Contig5139 59164 122 + 225949 CCCACCACTGGCAC-ACTGCACCAGAGGTGGGAGAGGTGGGCAAGAAGG-CCCAAACA--------GGTTTGTGCAGGC--CTGAGCAATCGTTTC-C-----------AAAACAAAAGACA-TTCCGGTGCAGCACCCGGGCTGGA---------- i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 56601 123 - 95547 CCCACCCCTGGCAC-ACAGCACCAGAGGTGGGCGAGAAGGCCTGGACGGTCCCAAACA--------GGTTTGGGCAGGC--CTGAGCAATCATTTC-C-----------AAAACAAAAGACC-TTCTGGTGCAGCACTCGGGCTGGA---------- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75049355 123 + 78773432 CCCACCACTGGCAC-ACAGCACCAGAGGTGGGCGAGAAGGCCTAGACGGTCCCAAACA--------GGTTTGGGCAGGC--CTGAGCAATCATTTC-C-----------AAAACAAAAGACC-TTCTGGTGCAGCACCCGGGCTGGA---------- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16075677 125 + 17838096 CCCACCACTGGCAC-ACAACACCAGAAGTGGGCAAGAAGGTCTGGACGGTCCCAAACA--------GGTTTAGGCAGGAGGCTGAGTAATCATTTC-C-----------AAAACAAAAGACA-TTCTGGTGCAGCACCCAGGCTGGA---------- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 26249 125 - 64270 CCCACCACTGGCAC-ACAACACCAGAAGTGGGCAAGAAGGTCTGGATGGTCCCAAACA--------GGTTTAGGCAGGAGGCTGAGTAATCATTTC-C-----------AAAACAAAAGACA-TTCTGGTGCAGCAACCAGGCTGGA---------- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79489145 125 + 83384210 CCCACCACTGGCAC-ACAACACCAGAAGTGGGCAAGAAGGTCTGGACGGTCCCAAACA--------GGTTTAGGCAGGAGGCTGAGTAATCATTTC-C-----------AAAACAAAAGACA-TTCTGGTGCAGCAATCAGGCTGGA---------- i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4400753 97 + 7991924 ----GCCTTGGTAT-TCAACACCAGAGGTGGACAAGG-GACCTGGA---TCCCAAACA--------GGGTTGGGCAGGC--CCCAGAGACTGTTCT-------------AAAACTAGAGACA-TCAC--------------ACT------------- i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_43980 9393 113 + 11404 ----C--CCAACTC-TCAGCATCAGAGGTAGGCAAGG-GGCCTGGATGGTCTCACACA--------AGCTTGGGCCAGA--CCTACCTCTTGTTTC-------------TAAATAAAGACCACACTCCTCCAACCGGAAGGACT------------- i dipOrd1.scaffold_43980 C 0 C 0 s mm9.chr11 118771798 130 + 121843856 ----TTACTGGCAT-TCAGCCCCAGAAGTGAGCAAAG-AGGCTAGATGATACCCAAAG--------GCTTTAAACTGGA--TCCAGATACTGTTCT-ATATGAAAGACGAAAATAAAAGACAATCACCATGCAGTGCCTGGACTCTG---------- i mm9.chr11 C 0 C 0 s bosTau4.chr19 10870226 117 - 65312493 ------GCAGTGAGGTCA-CACCAAAGGCAGGCA-GGAGGCCTTGACTGTCCCAAACAGAACCACGGAATTAGGCAAAG--CCTTGCTCCTGATTC-T-----------ACA-CAAAAGACA-ATCGGATGCAG-GCCTGGA--------------- i bosTau4.chr19 I 6 I 30 s equCab2.chr11 58054304 122 - 61308211 CCAGCAGCTGGCAT-TCAGCACTGCAGGCAA----GAGGGCCTGGACTGTCCCAAACAGATCTGCGGGAGTGGGCAGGG--CCCGGCTCCTGTTTC-T-----------AAGACAAAAGACA-GACGGAAGCAGTGCCCGGA--------------- i equCab2.chr11 I 20 I 16 s canFam2.chr9 59447962 111 - 64418924 ------GCAGGAATGTCAGCACCAAAGGCAG----GAGGACCTGGACTGTCCCAAGCAGAACCACAGGATCAGGCA-GA--CCTTACTTCTGTTTC-T-----------AAG-CAAAACACA-GAT----GCTGTGCCCAGA--------------- i canFam2.chr9 I 6 I 16 s pteVam1.scaffold_11245 25648 115 + 48268 CCGGTGGCTGGCAT-TCAGCACCAAAGGCAGGCCAGAGGGCCTGGACTGTCCCAAACCCAACTGCAGG-TTGGGCA-GA--GCTCCATCCTGTTTC-T-----------AAG-CAAAAGAC---------CCAGTGCACAGA--------------- i pteVam1.scaffold_11245 I 11 I 28 s loxAfr3.scaffold_49 14445366 135 - 17734757 GGCTCTGCTGGCAT-TCAGCTCCAGAGG----CCACAGGGCCAGCACTGTCCCCAGCAGATCTC--GGCTTGGGCAGGC--CCCACCACCTTCCTTGT-----------AGGATGATGGGTG-CTGGGAGCTGGGAGG-AGGCCGGAAGCAGCGGAG i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 29457 488 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e choHof1.scaffold_149147 5378 3095 + 9388 I e tupBel1.scaffold_124460.1-4080 3291 306 + 4080 I e turTru1.scaffold_106006 139109 1621 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=929408.000000 s hg19.chr17_gl000204_random 58154 202 + 81310 GAAAC-GAGCCTGCACCATCGAAGGACATT--TCCAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAC------ACACAAACAGATC----CAAACCCGTCCCCATGTC-------------------------------AC-TTTTG------CTCCTGAAGGCTGCTCCTGGAACAATTAGCCTCC---TC-----CTCGCACCTGACTGTCCTGCTTTTCTGTGTGAGGTGAAAAGCACATCATGGAA---TCTGGGGT---TTGGTAGG-----GGCCTGGAAGACCCAGAGGC s micMur1.scaffold_145100 760 169 + 1040 GGAATGGGGCCTGCAACCTCAAAGGACATC--TCCAAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAA------AAACAAATGGA-------AAACCCGTCCCCAGGTT-------------------------------GC-CTTTA------CTTC----------------------------------C-----TTTGCACCTGACTATCCTGCTTTTCTGGGTGAGGGGGAAAAAACGTCATGGAA---TCTGAGGT---TTGGTAGG-----GGCCTGGAAGATTCGGAGAC i micMur1.scaffold_145100 C 0 C 0 s calJac1.Contig5139 59286 186 + 225949 GGAAC-TGGCCTGCACCCTCAAAGGACATT--TCCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATC----TAAACCCATCCCCGGGTT-------------------------------GC-TTTTG------CTCCTGAAGGCTGCTCCTGGAACAATTAGCCTCC---TC-----CTTGCACCTGACTGTCCTGCTTTTCCGTGTGAGGCAAAAAGCATGTCATGGAA---TCTCGGGT---TTGGTAGG-----GGTCTGGAAGACCTGGAGGC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 56724 202 - 95547 GGAAT-GAGCCTGCACTGTCAAAGGACATT--TCCAAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAC------ACACAAACAGATC----CAAACCTGTCCCCACGTT-------------------------------GC-TTTTG------CTCCTGAAGGCTGCTCCTGGAACAATTAGCCTCC---TC-----CTGGCACCTGACTGTCCTGCTTTTCTGTGTGAGGTGAAAAGCACATCATGGAG---TCTGGGGT---TTGGTAGA-----GGCCTGGAAGACCCGGAGGC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75049478 202 + 78773432 GGAAT-GAGCCTGCACTGTCAAAGGACATT--TCCAAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAC------ACACAAACAGATC----CAAACCCGTCCCCATGTT-------------------------------GC-TTTTG------CTCCTGAAGGCTGCTCCTGGAACAATTAGCCTCC---TC-----CTGGCACCTGACTGTCCTGCTTTTCTGTGTGAGGTGAAAAGCACATCATGGAA---TCTGGGGT---TTGGTAGA-----GGCCTGGAAGACCCGGAGGC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16075802 202 + 17838096 GAAAC-CAGCCTGCACCATCGAAGGACATT--TCCAAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAC------ACACAAACAGATC----CAAACCCGTCCCCATGTT-------------------------------GC-TTTTG------CTCCTGAAGGCTGCTTCTGGAACAATTAGCCTCC---TC-----CTCGCACCTGACTGTCCTGCTTTTCTGTGTGAGGTGAAAAGCACATCATGGAA---TCTGGGGT---TTGGTAGG-----GGCCTGGAAGACCCGGAGGC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 26374 202 - 64270 GAAAC-GAGCCTGCACCATTGAAGGACATT--TCCAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAC------ACACAAACAGATC----CAAACCCGTCCCCATGTC-------------------------------AC-TTTTG------CTCCTGAAGGCTGCTCCTGGAACAATTAGCCTCC---TC-----CTCACACCTGACTGTCCTGCTTTTCTGTGTGAGGTGAAAAGCACATCATGGAA---TCTGGGGT---TTGGTAGG-----GGCCTGGAAGACCCAGAGGC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79489270 202 + 83384210 GAAAC-GAGCCTGCACCATCGAAGGACATT--TCCAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAC------ACACAAACAGATC----CAAACCCGTCCCCGTGTC-------------------------------AC-TTTTG------TTCCTGAAGGCTGCTCCTGGAACAATTAGCCTCC---TC-----CTCGCACCTGACTGTCCTGCTTTTCTGTGTGAGGTGAAAAGCACATCATGGAA---TCTGGGGT---TTGGTAGG-----GGCCTGGAAGACCCAGAGGC i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4400850 193 + 7991924 ------TGGGTGGCACCCTCTGAAGACCTT--CCCGGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAG------A-ACAAATGG-------AAAACCTGTCCCCAGGTG-------------------------------GC-CCTGA------CTCCTG--CGCTGCTTCTGGAA-CATCAGATGCC---TC-----CGTGTACCTGACCGTACTGCTTTACAGCGTGAGGCA-AAAAGAGAAGCTGGGG---TTCAGGGCGAACCTGAGGGATTCAGAGCCCTAAGGCAAGG---- i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_43980 9506 166 + 11404 ------GGGCCTGCCTCCTCCCAGCACCTCGGTGTTAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT--------------------------------------------------------------------------TG-CCTTA----------TGGGTGCTGCCTGGGGAACCATCAGATTCC---TCCAGGACCTGGACCTGACCAGG-TGCTCTTCAGTGGGAGGCATAAAGCAGGTCATGGAGACCCCATGGGG---TCTGTAAG----AGGCCTAGAGGACACGG---- i dipOrd1.scaffold_43980 C 0 C 0 s mm9.chr11 118771928 215 + 121843856 ------GGACCTGCACTCTCAAAGGACATT--TGCAAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTaa------a-aaacaaaa-------aacaacaacaacaaaacaaacaacaacaacaaaacaTGATTAAAAAACAAG-CCTGATACACGTTGCTGGATGCTGTTTGTAAAACCATCAGCTT------------CTTGCACCTAACTAAG----CTTCCAGTGTGAGGCA-----CATACCACGGAG---CCTGGGGC---CCTGTGGG---TAGGGCAGCTAGACAGAG---- i mm9.chr11 C 0 C 0 s vicPac1.scaffold_56870 89 171 + 4541 -GAAA-TGCGCCACACCCTCAAAG-ACATT--CACAG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTA------AAGCGAATGA-------CAAGCCTGTC-CCAGGTT-------------------------------G--TTTTA------CCTCCGGGTGCTGGTTCCGGAACACTTGGATTCC---TC-----CTTGCTCCTGACTGCCCTG-----------------------ACGTCATGGAA---TCTGGGGT---TTCTTAGG-----GGCCTGGAGGATTCAGAGCC i vicPac1.scaffold_56870 N 0 C 0 s turTru1.scaffold_106006 140730 188 + 145505 -GAAG-TGAGCTGCACC-TCAAAG-ACATT--CTCAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAA------AAGCAAATGA-------AAAACCTGTG--CAGGTT-------------------------------GC-TTTTA------CTTCTCGATGCTGC-ACTGGAACA----GATTCC---TC-----CTTATACCTGACTGTCCTGCTTTTCTGTGTGAGGCAAAAAGCATGTCATGGAA---TCTGGGGT---TTGTTAGG-----GGCCTGGAGGATTCAGAGAC i turTru1.scaffold_106006 I 1621 C 0 s bosTau4.chr19 10870373 398 - 65312493 -GAAG-TGAGCTGAACCATCAAAG-ACATT--CTCAACCTAAGTGAAGTGAAagtcgctcagttgtgtccaactctttgcgactccaagaactatacagtccatggaattctctaggtcagaatactggagtgggtagccttttccttctccaggggatcttcccaacccagggatcgaactcaggtctcccgtattgcaggcagattctttaccagctgagccacaagggaagccctCTCAAGCTAA------AAGCAAATGA-------AAAACCTGTG-TCAGGTT-------------------------------GC-TTTTA------CTTCTGGATGCTGCTTCTAGAACA----GATTTC---TT-----CTTGTACCTGACTGTTCTGCTTTTCTGTGTGAGGCAAAGACCATGTCATGGAG---TCTGGAGT---TTGTTAGG-----AGCTTGTAGGACTCAGAGAC i bosTau4.chr19 I 30 C 0 s equCab2.chr11 58054442 199 - 61308211 -GGGG-TGAGCTGCGCCCTCAAAG-ACATT--CTCAAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGATAAAACAGAGAAATGA-------AAACCT-GTG-CCAGGCT-------------------------------GC-TTTTA------CCTCTGGATGCTGTTTCTGG-ACAATCGGAGTCC---TC-----CTTGTACCAGACTGTCCTTCTTTTCCATGTGAGGCAAAAAGTCGGCCGTGGAA---TCTGGGGT---TTGGCA-G-----GGCCTGGACGATTCTGAGGC i equCab2.chr11 I 16 C 0 s canFam2.chr9 59448089 196 - 64418924 -GGGG-TGAGCTGTAACCTCAAAG-ACGTT--CTCAAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAA------AAACAAACGA-------AAAACC-ATC-CCAGGTT-------------------------------GCTTTTTA------CTTCTGGATGATGCTTCTGGAACCCTAGGATTCC---TC-----TCTGTACCTGACTGTCCTGCTTTTCTGCGTGAGGCAAAAAGCATGTCATGGAA---TCTGGGGT---TTGTTAGG-----GGCCTAGAAGAATCAGAGGC i canFam2.chr9 I 16 C 0 s pteVam1.scaffold_11245 25791 195 + 48268 -AGGG-GGGGCTGCACCCTCCAAA-ACATT--CTCAAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGA------AAACAAATGA-------AAAACTGGTC-CCAGGTC-------------------------------GA-TTTTA------CATCTGGACGCTGCTTCTGGAACAATTAAATTCC---TC-----CTTGTACCTGCTAGTCCTGCTTTTCCGTGTAAGGCAAAAAGCATGCCATGGAA---TGT-GAGT---TTGGCAGG-----GGCCTGGAAGGTTCAGAGGC i pteVam1.scaffold_11245 I 28 C 0 s tupBel1.scaffold_124460.1-4080 3597 183 + 4080 ---------------CCCTGGAAGGACATT--TCCAGT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTA---------AGAAGCAGCTCACGAAAAGCCTGTCCTCAGGTG-------------------------------GT-GTTCC------CTCCTGGACACTACTTCTGGAGCAATTAGACCCT---TC-----CTTG-----GCTTGGCCTGCGTTTCTGTGTGAGGAAGAAGGCACATCCTGGGG---TCTGGGGC---TCAG-ACG-----GCCTTGAGAGTTTTGGTGGT i tupBel1.scaffold_124460.1-4080 I 306 C 0 s loxAfr3.scaffold_49 14445501 200 - 17734757 GAAGG-TGGGCTGGACATGCAAAAGCCATC--TCCGAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTAA------GAGTAAACACATGG---GAAACCGG--CCCAGGTT-------------------------------GC-TTTGA------GTTCTGGGGGCTGCTCCCCAAATGATTAGA-GTA---CC-----CCTGCATGGGACTGTGCTGCTTTCCTGTGTGAGGCAAAAAGAGCATCATGGAG---TCTAGGGC---TCGGCTGG-----GGCCTGCAAGATTCCAAGGC i loxAfr3.scaffold_49 C 0 I 29 s choHof1.scaffold_149147 8473 205 + 9388 GGAGT-TGACTTGCACCCTCATAGGACACT--TCCAAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTA------AAACCAACAAATGA---AAAACCTGTCCCCAGGTT-------------------------------GC-TTTTA------GTTCTGGAAGCTGCTTCTGAAATGACGAGATGCATCTTC-----CTTGCATCTGCCTGTCCTGCTTTTCTGTGCAAGGCAAAAAGTACGTCATGGAA---TCTGGTGT---TTGGTT-G-----GGCCTGGAAGATTCTGAGCA i choHof1.scaffold_149147 I 3095 C 0 e oryCun2.chrUn0958 29457 488 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=-15377.000000 s hg19.chr17_gl000204_random 58356 38 + 81310 CAGGAAGAGGGGAG-TATGGATT----------T--GGAGCTTCT-----CGGTAG s micMur1.scaffold_145100 929 38 + 1040 AGTGAAGGGAGGGG-CGTGAACT----------C--AGAGCTCCT-----CCAAGC i micMur1.scaffold_145100 C 0 C 0 s calJac1.Contig5139 59472 38 + 225949 TGGTAAGGGTGGGG-CATGGACT----------T--GGAGCTTCT-----CCGTGC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 56926 38 - 95547 CAGGAAGGGAGGGG-CCTGGATT----------T--GGAGCTTCT-----CCATGC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75049680 38 + 78773432 CAGGAAGGGAGGGG-CCTGGATT----------T--GGAGCTTCT-----CCATGC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16076004 38 + 17838096 CAGGAAGGGAGGGG-TATGGATT----------T--GGAGCTTTT-----CGGTAC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 26576 38 - 64270 CAGGAAGGGAGGAG-TATGGATT----------T--GGAGCTTCT-----CAGTAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79489472 38 + 83384210 CAGGAAGGGAGGAG-TATGGATT----------T--GGAGCTTCT-----CGGTAG i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4401043 27 + 7991924 --GGTTTGTGGTTC-CGTG---C----------T--GCAGCCCCA----------- i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_43980 9672 30 + 11404 --GGGAAGGGGGAG-GGTAGACA----------C--ACAAACTCC----------- i dipOrd1.scaffold_43980 C 0 C 0 s mm9.chr11 118772143 34 + 121843856 TAGAGAAGAGGGAG-AATA---A----------G--AGAGGCCCTGAGGT------ i mm9.chr11 C 0 C 0 s vicPac1.scaffold_56870 260 36 + 4541 AGTGACGGGAAGGA-TGTAAACT----------C--AGCTCCTG-------CGTGC i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_106006 140918 36 + 145505 AGTGAAGGGAGGGA-CGTAAACT----------C--AGTTCCTA-------CGTGC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10870771 36 - 65312493 AGTGAAGGGAGGGA-TATAAACT----------C--AGCTCCTC-------TGTGC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58054641 36 - 61308211 AGTGAAGGGAAGGA-CGTGAACT----------C--AGGTCCTG-------CGAGC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59448285 38 - 64418924 AGCGGAGGGAGGCG-TGTGGGCT----------CTGCGTTCCTG-------CATGC i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 25986 35 + 48268 AGCGAAGGG-GGCG-CGTACACC----------C--AGGCCCTG-------GGTGT i pteVam1.scaffold_11245 C 0 C 0 s tupBel1.scaffold_124460.1-4080 3780 36 + 4080 GGGGGAGGGGGGGG-CGAGAAGG----------A--GGGAGCTCC-----CGCT-- i tupBel1.scaffold_124460.1-4080 C 0 C 0 s choHof1.scaffold_149147 8678 43 + 9388 -GTGAAGGGAGGGGCCATGAACTGCCTGACCACC--CCTTCCT--------CAT-- i choHof1.scaffold_149147 C 0 C 0 e oryCun2.chrUn0958 29457 488 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e loxAfr3.scaffold_49 14445701 29 - 17734757 I a score=375502.000000 s hg19.chr17_gl000204_random 58394 68 + 81310 TAGGGGCTCTG----------GGCT---GCTGGCTGCCC----CCCCTGCAG-GGCAGCAGAGACGGTGGCCAAGAC------------AGTGGCCGC s panTro2.chr17 79489510 80 + 83384210 TAGGGGCTCTG----------GGCT---GCTGGCTGCCC----CCCCTGCAG-GGCAGCAaagacggtggccaagacggtggccaagGCAGTGGCCGC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 26614 68 - 64270 TAGGGGCTCTG----------GGCT---GCTGGCTGCCC----CCCCTGCAG-GGCAGCAGAGACGGNGGCCAAGAC------------AGTGGCCGC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16076042 68 + 17838096 TAGGGGGTCTG----------GGCT---GCTGGCTGCCC----CCGCTGCAG-GGCAGCAGAGACGGTGGCCAAGAC------------AGTGGCTGC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75049718 51 + 78773432 TGGGGGCTCTG----------GGCT---GCT----------------------GGCAGCAGAGACGGTGGCCAAGAC------------AGTGGCCAC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 56964 51 - 95547 TGGGGGCTCTG----------GGCT---GCT----------------------GGCAGCAGAGACGGTGGCCAAGAC------------AGTGGCCAC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 59510 68 + 225949 TAGGGGCTCTG----------GGCT---GCTGGCTGCCC----GCCCTGCAG-GGCAGCAGAGATGGTGGCCAAGAC------------AGTGGCTGC i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_145100 967 73 + 1040 C-TGGATTCTG----------GGCT---GCTGGCTGCCTCCCGCCCCTGCAGAGCCTGGAGAGACAGTGTCCAAGATG-----------AGTGGCTGC i micMur1.scaffold_145100 C 0 n 0 s tupBel1.scaffold_124460.1-4080 3816 68 + 4080 --TGGGCTCTG----------GGCT---GCT-GCTGCCA----GCCCTGCAGAGCCCGGACAGGCAACGCCCAAAAACA----------AGTGGCTGC i tupBel1.scaffold_124460.1-4080 C 0 C 0 s mm9.chr11 118772177 75 + 121843856 -----GCTCTCTGGCTTGCTGGGCT---GCACACTGCCT----TCCCTACAGAGTGAGGGCAGACGGTGTCCAGGCTG-----------AGTGACTGT i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 9702 47 + 11404 ---------------------AGTC---GCAGGCTG---------------GAGCAAGGATTGGAGGTGTCAATGCTG-----------GG-GGCGGC i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4401070 59 + 7991924 ---------------------GGCT---ACTGGCTGCCT----TCCCTGCAGAGAAAGGAGAGGCAGTGCCCAAGACA-----------AGTGGCTGC i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 29945 71 + 41507 ---GGGGGCAGGGGCCC----AGCG---GCCGGCTGTCT----GCCCTGCAGAGCGAGAGCAG--AGTGTCCAAGACA-----------AGTGGCTGC i oryCun2.chrUn0958 I 488 C 0 s vicPac1.scaffold_56870 296 70 + 4541 CTGGGGCTCTG----------CACT---GGTGGCTGCCT----TCCCTGCAGAGCGAGGACAGACAGTGTCCAAGACA-----------AGTGGCTAC i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_106006 140954 70 + 145505 CTAGAGCTCTG----------CACT---GCTGGCTGCCT----TCCCTGCAGAGCAAGGACAGACAGTATCCACGACA-----------AGTGGCTAC i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10870807 70 - 65312493 CCAGGGCTCTG----------CACT---GCCAGCTGCCT----TCCCAGCAGAGCAAGGACAGATAGTGTCCACAACA-----------GGTGGCTAC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58054677 69 - 61308211 CGGGGGCTCC-----------TGCT---GCTAGCCGCCT----TCCCTGCAGAGCGAGGGTAGACAGTGTCCAAGACA-----------AGTGGCTAC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59448323 70 - 64418924 CTGGGGCGCCG----------TGCT---GCCGGCTGCCT----TCCCTGCAGGGTGAGAATAGACAGTGTCCAAGACA-----------AGTGGCTAC i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 26021 70 + 48268 CTGGGGCTCCA----------CACA---GCGGGCGGCCT----TCTCTGCAGAGCAAGGACAGACGGTGCTCGAGACA-----------AGTGGCTAC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14445730 50 - 17734757 CCAGGGCCGTG----------GGCTT--TCTGGTTGCCC----TCCC-------TGAGAAG--------------GTC-----------AGTGCCTGC i loxAfr3.scaffold_49 I 29 C 0 s choHof1.scaffold_149147 8721 67 + 9388 -----GCCCTG----------GGCTTGGGTTGGCTGCCC----CCCT-GCACAGTGAGGAGAGACAGTGTCCCAAGTA-----------AGTGGTCGC i choHof1.scaffold_149147 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=1711079.000000 s hg19.chr17_gl000204_random 58462 201 + 81310 TGCCC---ACTTATGAGCGTCATGCTTTTAATTTCTGGCCCTCCAGCCCGTCTGGGTCATTGATCTGTCTTGGCCGGTGGGAATCGTGTTATACAATTCCAAGCATACAGCTAAACAGCCCCACAGCTAACCACCAGATAAATGCCGTGTCTACGAGCAAG--GCAGCCGCCTGGTTGACTGAACTTTCCCCTGCCACCGGATTTG s panTro2.chr17 79489590 201 + 83384210 TGCCC---ACTTATGAGTGTCATGCTTTTAATTTCTGGCCCTCCAGCCTGTCTGGGTCATTGATCTGTCTTGGCCGGTGGGAATCGTGTTATACAATTCCAAGCATACAGCTAAACAGCCCCACAGCTAACCACCAGATAAATGCCGTGTCTACGAGCAAG--GCAGCTGCCTGGTTGACTGAACTTTCCCCTGCCACCGGATTTG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 26682 201 - 64270 TGCCC---ACTTATGAGCATCATGCTTTTAATTTCTGGCCCTCCATCCTGTCTNGGTCATTGATCTGTCTTGGCCGGTGGGAATCGTGTTATACAATTCCAAGCATACAGCTAAACAGCCCCACAGCTAACCACCAGATAAATGCCGTCTCTACGAGCAAG--GCAGCTGCCTGGTTGACTGAACTTTCCCCTGCCACCGGATTTG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16076110 201 + 17838096 TGCCC---GCTTATGAGTGTCATGCTTTTAATTTCTGGCCCTCCAGCCTGCCTGGGTCATTGATCTGTCTTGGCCGGTGGGAATCGTGTTATACAATTCCAAGCATACAGCTAAACAGCCCTACAGCTAACCACCAGATAAATGCCATGTCTATGAGCAAG--GCAGCTGCCTGGTTGACTGAACTTTCCCCTGCCACCGGATTTG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75049769 201 + 78773432 TGCCC---ACTTATGAGCTTCATGCTTTTAATTTCTGGCCCTCCAGCCTGTCTGGGTCATTGATCTGTCTTGGCCGGTGGGAATCGTGTTATACAATTCCAAGCATACAGCTAAACAGCCCTACAGCTAACCACCAAATAAATGCCATGTCTATGAGCAAG--GCAGCTGCCTGGTTGACTGAACTTTCCCCAGCCCCGGGATTTG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 57015 201 - 95547 TGCCC---ACTTATGAGCTTCATGCTTTTAATTGCTGGCCCTCCAGCCTGTCTGGGTCATTGATCTGTCTTGGCCGGTGGGAATCGTGTTATACAATTCCAAGCATAGAGCTAAACAGTCCTACAGCTAACCACCAAATAAATGCCATGTCTATGAGCAAG--GCAGCTGCCTGGTTGACTGAACTTTCCCCAGCCCCCGGATTTG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 59578 200 + 225949 TGCCC---TCTTACGATCTTCATGTTTTGAATTTGTGGCCCTCTAGCCTGTCTGTGTCACTGATCTGTCTTGGCTGGTGGGAATCGTGTTATACAATTCCAAGCACACAGCTAAACA-CCCTACAGCTAACCAGCAGATAAACGCCTTGTCTACGAGCAAG--GCAGCTGCCTGGTTGACTGAACCTTCCCCAGCCCCCGGATTTG i calJac1.Contig5139 C 0 C 0 s tupBel1.scaffold_124460.1-4080 3884 196 + 4080 TGCCC---ACTCACCAGGCTAATGCTTTTAATT-CTGGGCCTGCGGCCTGTCTGGGTCATTGATCTGTCTTGGTCAGTGGGAATCGTGCTATACAATTCCCAGC---CAGCT-GCCTGCCCTGCAGCTACAAGCCCGATGAATGCCTTGTCTG-GAGCAAGCAGCCACAGCATGCCTGGCTGAACCTG-CCTGGCCCTCGTATTTG i tupBel1.scaffold_124460.1-4080 C 0 N 0 s mm9.chr11 118772252 179 + 121843856 TGCCT---TCTCAGGA-------GCTTTTAATTCT-GCTCCTTCGGCCTGTCTGGGCCATCGATCTGTCTTGCCCAGTGGGAATCACGTGCTTTAGAG-CACGT---AAGCAGTCGAGTCCTGCAGCCGA-----ATATAAATGCCTTGTCTCTGGCACAG--TCGCAAGGGTCCCTGAAGCG----GCCCTAGCCCC-AAATTTG i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 9749 195 + 11404 TGCCTGAGCCCCAGCAG---AATGCTTATCATTTTGGGTCCTTCAGCCTGCTTGGGTCATTGATCCGTCTTGGCCCGTGGAAATCGTGCGCTACAGTT-CAAGT---AAGCCCCGCAGCCCCACAGCTAA-CGCCAGCTAGACACCTAGTCTGTGCTGCGG--GCAGCTGTGTGGCTGATGAACCTCACCCCAGCCCT-GGATTCA i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4401129 197 + 7991924 TGCCC---ACTCAGGAGCTTAATGCTTTTAATTTCTGGCCCTTGGGCCTGTGTGAGCCATTGATCTGTCGTGGCCCGTGGGAATCGTGCTCCGCAGTTCCAAGT---CAGCTGCTTGGCTCTGCAGCTAAACACCAGATAAATGCCTTGTCTTCAAGGGAA--GCAGCTGCTTGGTTGAATGAACTTTCCCCAGCCCC-AGATTTG i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 30016 162 + 41507 CGCCC---TCTTACTCGCTTCCCGCCTCTCATTTCTGGCCCTTGGGCCTGTCTGGG---TTGTCCTGTCTTGGCCGGTGGGACTC--------------CAGGT---AAGCCGCCCGGCCCTGGAGCTGAACGCCGGATAAACGCCTTGTCACCGAGAGCC--ACAGCTGCTCAGCC----------TCCCCGGCCC--------- i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 366 198 + 4541 TGTTC---ACTTAAGACCTTAATGCTTTTAATTTCTAGCCCTCCAGCCAGTCTGGGTCATTGATCTGTCCTGGTCAGTGGGAGTCATTCTATACACTTTACAGT---TAGCTTCTGCGCCCTACAGCTAAACCCCGGATAAATGCCTTGTCTACCAGTGAG--ACAGCTGTGTGGTTGACTGAACTTTCCCCAGCCCCCGTGTTTG i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_106006 141024 198 + 145505 TGTCC---GCTTACGAGCTTAACGCTTTTAATTTCTGGCCCTTTGGCCTGTCTGGGTCATTGATCTTTCTTGGTCAGTGGGAGTCATGCTATACAATTTCGAGT---TAGCTTCTTGGCCCTACAGCTAAACACTGGATAAATGCCTTGTCTACCAGCAAG--GCAGCTGCTTGGTTGATTGAACTTTCCCCAGCCCCCGTATTTG i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10870877 198 - 65312493 TGTCC---ACTCACGAGCTTGATGTTTTTAATTTCTGGCCCTTTTCCCTGTCTGGGTCACTGATCTGTCTTGGTCAGTGGGAGTCATGCTACACAATTTCGAGT---TAGCTTCTTGGCCCTACAACTAAACACTGGATATATGCCTTGTCCACCAGCAAG--GCAGCTGCTTGGTTGATTGAACTCTCCCCAGCCCCCATATTTG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58054746 198 - 61308211 TGTCC---ACTGACGAGCTGAATGCTTTTAATTTCTGGCCCTCCGGCCTCTCCAGCTCATTGATCTGTCTTGGCCAGTGGGAATCGTGCTACGCAATTTCGAGT---TAGCGGCTCGGCCCTACAGCTGAACAGCGGATAAATGCCTTGTCCACGAGCGAG--GCAGCTGCTAGTTTGATTAAACTTCCCCCGGCCCCCGAATTTG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59448393 197 - 64418924 TGTCC---ACTTACGAGCTTAATGCTTTTAATTTCTGGCCCTCCAGCCTGTCTGGATCATTGATCTGTCTTGGCCAGGGGGAATCGTGCTATACAATTTCAAGT---AAGCTGCTCGG-CCTACAGCTAAACACCGGATAAATGCCTTGTCTACCAGCAAG--GCAGCTGCTTGGATGATTGAACTTTCCCCAGCCCCCATATTTA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 26091 198 + 48268 TGTCC---ACTTACGAGCTTAATGCTTTTCATTTCTGGCCCTCTGGCCTGTCCGGGTCACTGATCTGTCCTGGCCAGTGGGAGTCATGCGATACAATTTCAGGT---TAGCTGCTCGGCCCCGAAGCCACACAGCGATTAAACGCCTCATCTCTGAGCAAG--GCAGCCGCTTGGCTGACTGCGCTTTCTGCAGCCCCCGTATTTG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14445780 172 - 17734757 TGCCC---AACCACGAGCTTCATGTTGTTCATTTCAGGCCCTCT-GCCTGTCAGGGTCCGTGCTCTGCCTCAGCCAGTGGGGACCGTGAGCAGCAATTCCACAG---GAGCTGCTCGACCATACAG-TGAACACCAGATGAAAGCCTAATCTAAGGGCAAC--CAAggagc---cctggtggcac--------------------- i loxAfr3.scaffold_49 C 0 I 109 s choHof1.scaffold_149147 8788 197 + 9388 TGCCC---ATTCACGAGCCTCACACTCCCCATTTCCGGCCTTCCGGCCAGCCTGGGTCACTGCTCGGTCTCGGCCAGCGGGAATTGCACTCTCGGATCCTGCGT---GAGCTGCCCGGCCGCACAGCTGAACGCCGGATAAATGCCTTGTCTGCAGGCAAG--GCAGCTGCATGCCTGATTGAAC-TGTCCCAGCCCTGGTACTTG i choHof1.scaffold_149147 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e micMur1.scaffold_145100 1040 0 + 1040 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=803511.000000 s hg19.chr17_gl000204_random 58663 170 + 81310 AAATGGCGCATTCCAGCTCTAAAGCCCTAATTGG--GCCTCTTGGTTCTCTGCTGTCAGATGGTCCAGGCTTTCGTGGCCTCCAACT-CCCGGCTGGGCCCAGCCACTGCCTGGCAGGCACCTGTCTCCC--TGCAGGCAGGGCTCTTGCCTCGCTGTGCCGGCAGCGCCCCCTG s panTro2.chr17 79489791 170 + 83384210 AAATGGCGCATTCCAGCTCTAAAGCCCTAATTGG--GCCTCTGGGTTCTCTGCTGTCAGATGGTCCAGGCTTTCGTGGCCTCCAACT-CCCGGCTGGGCCCAGCCACTGCCTGGCAGGCACCTGTCTCCC--TGCAGGCAGGGCTCTTGCCTCGCTGTGCCGGCAGCGCCCCCTG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 26883 170 - 64270 AAATGGCACATTCCAGCTCAAAAGCCCTAATTGG--GCCTCTCGGTTCTCTGCTGTCAGATGGTCCAGGCTTTCGTGGCCTCCAACT-CCCGGCTGGGCCCAGCGACTGCCTGGCAGGCACCTGTCTCCC--TGCAGGCAGGGCTCTTGCCTCGCTGTGCCAGCAGCGCCCCCTG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16076311 170 + 17838096 AAATGGCGCATTCCAGCTCAAAAACCCTAATTGG--GCCTCTCGGTTCTCTGCTGTCAGATGGTCCAGGCTTTCGTGGCCTCCAACT-CCCGGCCGGGCCCAGCCACTGCCTGGCAGGCACCTGTCTCCC--TGCAGGCAGGGCTCTTGCCTCGCTGTGCCGCCAGCGCCCCCTG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75049970 170 + 78773432 AAATGGCGCATTCCAGCTCAAAAGCCCTAATTGG--GCCTCTCCGTTCTCTGCTGTCAGATGGTCCAGACTTTCATGGCCTCCAACT-CCCGGCTGGGCCCAGCCACTGCCTGGCAGGCACCTGTCTCCC--TGCAGGCAGAGCTCTTGCCTCGCTGTGCCGGCAGCGCCCCCTG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 57216 170 - 95547 AAATGGCGCATTCCAGCTCAAAAGCCCTAATTGG--GCCTCTCCGTTCTCTGCTGTCAGATGGTCCAGACTTTCGTGGCCTCCAATT-CCCGGCTGGGCCCAGCCACTGCCTGGCAGGCACCTGTCTCCC--TGCAGGCAGAGCTCTTGCCTCGCTGTGCCGGCAGCGCCCCCTG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 59778 159 + 225949 AAATGGCGCATCCCAGCTCAAAAGCCCTAATTGG--GCCTCTCGGTTCTCTGCTGTCAGATGGTCCAGGCTTCC-TGGCCTCCAACTCCCCGGCTGGGCCCAGTTACTGCCTGGCCGGCACCGGTCTCCC--TGCAGGCAGG-----------GCTGTGCCAGCAGCGCCCCCTG i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118772431 146 + 121843856 AGATGGCACAGTTCTGCCCCCATGGACCAACTGT--TTCTCTCTG-----TGTGGCCTGGTGATCCAAGCTTTCATGGCATGGGACT-GCTGGCTAGGCCCATCCA------------CACCAATCTC------TAGGCTG---TCTTGCCTCTCTGGGCCAACGGTGAGTCCCT i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 9944 130 + 11404 GAA--------------------GACCTAATTGG--CTGTCTCTG-----TGCTGCCAGATGGCCCAGGCTTTCACGGCCTGTGACT-GGTCGCCGGAACCCGCCA----------CTCACCTGTCTCCC-TCACAGGCAG---GCTT---TTTGTGTGCTACGGGCACACCCCG i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4401326 166 + 7991924 AAATGGCACATCCCTATTCAAAAAACCTAATTG---CTCTCTCTGCCCTCTGCTGTCAGATGGTCCAGGCTTTCAGGGCCTGTGAGT-AGTGGCTGAGCCCACCCACACCCCATCACTCACCTGTCTGCTGTGGCATGCC----TCTTGCTTCTCTTTGCTGC-AGTGCCTCCTC i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 30178 126 + 41507 --------------TGCTCCACAGCCCTGA------CGCCCTCGG-----TCCCTCTAG-----CCTGGCCTCCCC--------CCC-AGCGGCGGGACCCACCTG-------CCGCTCACCTGCCTCCCTGTGCCGACAG---CACCGCCTGTCGCTCCTGCTTGTGCTGGGCC i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 564 143 + 4541 AAATGGCAAGTCCCTGCTCAAAAGACCTAATTGGCTCTCTCTCTGTCCTCTGCTGTCAGATGGTCCA---------GGCCTCCAACT-TGTGGGCAGGCCCACCCACTCCCCATCACCCACCTGTCTCCC--TGTGGGCACGTCTTTCACTTCAC-------------------- i vicPac1.scaffold_56870 C 0 I 2222 s turTru1.scaffold_106006 141222 126 + 145505 AAACGGCACATCCCTGCTCAAAAGACCTAATTGG--CTCTCTCCATCCTCTGCTGTCAGATGGTCCA---------GGCCTCCAACT-CGTGGCTGGGCCCACCCACTCCTCGTCATC----------CC--TATAGGCAGGTCTTTTGC------------------------- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10871075 128 - 65312493 AAATAGAACGTCCCTGCTCAAAAGACCTAATTGG--CTTTCTCTGCCCTCTGCTGTCAGATGGTCCA---------GGCCTCCAACT-TGTGGCTGGGCCCACTCACTCCTCATCACCCGCCTGTCTTCT--TATAGGCAGG--------------------------------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58054944 148 - 61308211 AAATGGAACGTCCCCACTCTAAAGACCTAATTGG--CTCTCCCTGTCCTCTGCTGTCAGATGG-CCGGGCTTCCGTGGCCTCGGACT-TGTGGCTGGGCCCACCCACTCCCCATCGCTCACCTGTCTCTC--CACAGGCAGGCCTCTTGCTTCA--------------------- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59448590 152 - 64418924 AAATGGCACATCCCTGCTCAGAAGACCTAATTGG--CTTTCTCTGTCCTCCACTGTCAGATGGTCCAGGCTTCTGTGGCCTCCAACT-CGTGGCTGGGCCCACCCACTACCCATCACCCAACTGTATCCC--TACAGGCAGGCCTCTTCCTTCACAG------------------ i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 26289 149 + 48268 AAATGGCACATCCCTGCTC---AGACCTAACTGG--TTCTCTCTGTCCTCGGCTGTCAGATGGTCCAAGTGTTCATGGCCCTGAACG-CGTGGCTGGGCCCACCCACTCGCTGTCACCCACCTGTCTCCA--TCTAGACAGGCCTCCTGCTTCACAG------------------ i pteVam1.scaffold_11245 C 0 I 19 s choHof1.scaffold_149147 8985 148 + 9388 AAATGACATGTCCCTGCTCAGAGGACCTCATTGG----CTCTATGTCCTCTGCTGTCAGGCGGCCCCGGC--------------ATT-CG----TGGGCCCACCCACTCACCATCACTCACCTGCCTCAC--TGTGGGGAGGCCTCTTGCCTCAGGTGCCCAAGATCTCCCTG-- i choHof1.scaffold_149147 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e micMur1.scaffold_145100 1040 0 + 1040 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e loxAfr3.scaffold_49 14445952 109 - 17734757 I a score=43367.000000 s hg19.chr17_gl000204_random 58833 73 + 81310 TCGGTCCCGCTTGTCCCTTGCCCACATTTCTTCTCCCTGGGGAG--------CCTTTTC--------------------------------------------------------------CTCTCTGGTCCAGACCCTACTG s panTro2.chr17 79489961 73 + 83384210 TCGGTCCCGCTTGTCCCTTGCCCACATTTCTTCTCCCTGGGGAG--------TCTTTTC--------------------------------------------------------------CTCTCTGGTCCAGACCCTACTG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 27053 73 - 64270 TCGGTCCCGCTTGTCCCTTGCCCACATTTCTTCTCCCTGGGGAG--------TCTTTTC--------------------------------------------------------------CTCTCTGGTCCAGACCCTACTG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16076481 73 + 17838096 TTGGTCCCGCTTGTCCCTTGCCCACATTTCTCCTCCCTGAGGAG--------TCTTTTC--------------------------------------------------------------CTCTCTGGTCCAGACCCTACTG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75050140 115 + 78773432 TCGGTCCCGCTTGTCCCTTGCCCAGATTTCTTCTCCCTGGGGAG--------TCCTTTCctccctccctctctct--------------------ctctctctctctctctctctctctctctctctGGTCCAGACCCTACTG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 57386 135 - 95547 TCGGTCCCACTTGTCCCTTGCCCAGATTTCTTCTCCCTGGGGAG--------TCCTTTCctctctctctctctctctctctctctctccctctctctctctctctctctctctctctctctctttctGGTCCAGACCCTACTG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 59937 73 + 225949 TCGGTCCCGCCTGTCCCCTGACCACATTTCTTCTCCCCTGGGAG--------TCCTTTC--------------------------------------------------------------CTCCCTGGTCCAGACCCTACTG i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118772577 50 + 121843856 CCTG----------------------GTTCTTCTGTCCTGAGAG--------CCCTTCC---------------------------------------------------------------CGTCTGGTCCAGTTCCCACTG i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 10074 37 + 11404 CC-----------------------------TCTGCCCTGCTAG--------CCTTTCT---------------------------------------------------------------------GCGAAGTCTCCAACG i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4401492 71 + 7991924 CCCGCCACCCCGTCCCCATCATCCATGGTCTTCCTGCCTGGGGG--------TCCTTTC---------------------------------------------------------------TCTCT-GTCCAGGTCTCCTTG i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 30304 54 + 41507 AC------------------------ATGTGTTCTCCCGGGGGGAGGGGGGTTGCTTTC---------------------------------------------------------------TCTGTGGTCCATGCTC--TTG i oryCun2.chrUn0958 C 0 C 0 s equCab2.chr11 58055092 5 - 61308211 -----------------------------------------------------------------------------------------------------------------------------------CAGGC------- i equCab2.chr11 C 0 C 0 s choHof1.scaffold_149147 9133 50 + 9388 ----------CCGCCCCTCACTCCCACATTTCCTCAC------A--------CCCTTCC-----------------------------------------------------------------CCTGGTCCAGAT----GTG i choHof1.scaffold_149147 C 0 I 5 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e micMur1.scaffold_145100 1040 0 + 1040 I e turTru1.scaffold_106006 141348 0 + 145505 C e felCat3.scaffold_206428 46377 8110 + 132007 T e pteVam1.scaffold_11245 26438 19 + 48268 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e canFam2.chr9 59448742 0 - 64418924 C e bosTau4.chr19 10871203 0 - 65312493 C e loxAfr3.scaffold_49 14445952 109 - 17734757 I a score=-5645.000000 s hg19.chr17_gl000204_random 58906 43 + 81310 CCCTTTGGAGCCTCCTCGCAGAAACCTCT--CGAAGAGTGGGATT s oryCun2.chrUn0958 30358 12 + 41507 CC-----------------AGTTCTGTGT---------------- i oryCun2.chrUn0958 C 0 C 0 s cavPor3.scaffold_76 4401563 27 + 7991924 CTCTGCAGAGC---CAAAGAGAGAGGTCT--C------------- i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_43980 10111 23 + 11404 ACCCACACAGC------AGTGTGCCGCCT---------------- i dipOrd1.scaffold_43980 C 0 C 0 s mm9.chr11 118772627 17 + 121843856 CCCTTC-------------TGATCCCTCT--C------------- i mm9.chr11 C 0 C 0 s calJac1.Contig5139 60010 43 + 225949 CCCTTCGGAGCCTCCTCACAGAAGCCTCT--CAAAGAATGAGGCT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 57521 41 - 95547 CCCTTTGGAGCCTCCTCGCAGAAACCTCT--C--AGAGTGGGGTT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75050255 41 + 78773432 CCCTTTGGAGCCTCCTCGCAGAAACCTCT--C--AGAGTGGGGTT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16076554 43 + 17838096 CCCTTTCCAGCCTCCTCACAGAAACCTCT--CAAAGAGTGCGGTT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 27126 45 - 64270 CCCTTTGGAGCCTCCTCACAGAAACCTCTCACAAAGAGTGGGATT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79490034 43 + 83384210 CCCTTTGGAGCCTCCTCGCAGAAACCTCT--CAAAGAGTGGGGTT i panTro2.chr17 C 0 C 0 s loxAfr3.scaffold_49 14446061 16 - 17734757 ccctctggagcagttc----------------------------- i loxAfr3.scaffold_49 I 109 C 0 s choHof1.scaffold_149147 9188 16 + 9388 TCCTCCCGTGCAGGTT----------------------------- i choHof1.scaffold_149147 I 5 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e micMur1.scaffold_145100 1040 0 + 1040 I e turTru1.scaffold_106006 141348 0 + 145505 C e felCat3.scaffold_206428 46377 8110 + 132007 T e pteVam1.scaffold_11245 26438 19 + 48268 I e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e canFam2.chr9 59448742 0 - 64418924 C e bosTau4.chr19 10871203 0 - 65312493 C e equCab2.chr11 58055097 0 - 61308211 C a score=-28812.000000 s hg19.chr17_gl000204_random 58949 106 + 81310 CGAGCCCATCTCCGTCTCCCTTCAGCTCCCCATGCGAGTTCTGCA--TGTGCCTGTGA--AGTG---GGGACACATTGACCTG---------GCAG-AGCTGTGTGC-CCGAGTGGAAGAGGGG------------------- s panTro2.chr17 79490077 106 + 83384210 GGAGCCCATCTCTGTCTCCCTTCAGCTCCCCACGCGAGTTCTGCA--TGTGCCTGTGA--AGTG---GGGACACATTTACCTG---------GCAG-AGCTGTGTGC-CCGAGTGGAAGAGGGG------------------- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 27171 106 - 64270 CGAGCCCATCTCTGTCTCCCTTCAGCTCCCCGCGTGAGTTCTGCA--TGTGCCTGTGA--AGTG---GGGACACATTTACCTG---------GCAG-AGCTGTGTGC-CCGAGTGGAAGAGGGG------------------- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16076597 106 + 17838096 TGAGCCCATCTCTGTCTGCCTTCAGCTCCGCACGCGAGTTCTGCA--TGTGTCTGTGA--AGTG---GGGACGCATTTACCTG---------GCAG-AGCTGTGTGC-CCGAGTGGAAAACGGG------------------- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75050296 105 + 78773432 CAAGCCCATCTCTGTCTCCCTTCAGCTCCCCACACGAGTTCTGCA--TGTGCCTGCGA--AGTG---GGGACA-ATTTACCTG---------GCAG-AACTGTGTGC-CCGAGTGGAAAAGGGG------------------- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 57562 105 - 95547 CAAGCCCATCTCTGTCTCCCTTCAGCTCCCCACGCGAGTTCTGCA--TGTGCCTGCGA--AGTG---GGGACA-ATTTACCTG---------GCAG-AACTGTGTGC-CCGAGTGGAAAAGCGG------------------- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 60053 106 + 225949 CGAGCCCACCTCTGTCTCCCTTCAGCTCCCCATGCAAGTTCTGCC--TGTGTCTGTGA--AGTG---GGGACACATTTACCTG---------GCAG-AGCTGTGTGC-CCGAGTGGAAAAGGTG------------------- i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118772644 77 + 121843856 -------------------TTAGAACCCTCCCAGAG------------------------ACCA---AGG-TCTGCTTCCCCATACTGCACTGCACAAGCTGTGAGCTTCAAGTGGAAGGGCTC------------------- i mm9.chr11 C 0 I 1 s dipOrd1.scaffold_43980 10134 65 + 11404 ----------------------GTGCCGCCGTGGGG------------------------AACA---GGGCTGTGTTTTCCTA---------GCAC-AGCTGTGAGCCCTGCGTGGAGGAGGGG------------------- i dipOrd1.scaffold_43980 C 0 I 1 s cavPor3.scaffold_76 4401590 79 + 7991924 ----------------------AAGCCACCCACGTG----CTGCA--TGTGCTAGGAAGTGGCA---GGA-CACGTGCATCTG---------ATGC-AGCTGCAAGC---AGGTGCAAGAGGAG------------------- i cavPor3.scaffold_76 C 0 I 42 s oryCun2.chrUn0958 30370 56 + 41507 ----------------------GTGCCGGTGATGTT--------------------------CG---GGG--ACGCTTGCCTG---------GCCG-AGCCGTGAGCACCGAGGAGAAA------------------------ i oryCun2.chrUn0958 C 0 C 0 s pteVam1.scaffold_11245 26457 16 + 48268 CGAGC-----------------------------CACTGTCTTGG-------------------------------------------------------------------------------------------------- i pteVam1.scaffold_11245 I 19 C 0 s bosTau4.chr19 10871203 29 - 65312493 ------------------CCTTTTGCTTCCCAGGCAAGATCTTTACT------------------------------------------------------------------------------------------------ i bosTau4.chr19 C 0 C 0 s loxAfr3.scaffold_49 14446077 64 - 17734757 t-------gctctgacactcacggg-----------------------gtcaccatga--gttg--------gggttgacttg---------gcggcaACTGGTGGTGGT------------------------------GGG i loxAfr3.scaffold_49 C 0 C 0 s choHof1.scaffold_149147 9204 129 + 9388 TGAGCCCGGCTCTGCCTCCCTCCAGCTCCACACGTGAGCTCAGCC--AGTCTCCATGG--GGTGCCAGGGATGTATTTACTTC---------ACAG-AGCTGTGAGGGCTGAGTGGAAAAAGTGGACACTCCAGCCCCCGGGG i choHof1.scaffold_149147 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e micMur1.scaffold_145100 1040 0 + 1040 I e turTru1.scaffold_106006 141348 0 + 145505 C e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e canFam2.chr9 59448742 0 - 64418924 C e equCab2.chr11 58055097 0 - 61308211 C a score=27997.000000 s hg19.chr17_gl000204_random 59055 43 + 81310 TCCCTGCAAAGCATAGG-GCCCGGTA-AATCATTCCTTGG--GGACG s oryCun2.chrUn0958 30426 42 + 41507 -CACGGCCAAGTGTAGG-CCCTTGGG-CTTCACTGCCCTG--CGTGG i oryCun2.chrUn0958 C 0 C 0 s mm9.chr11 118772722 39 + 121843856 GGACTG--AAACTCTAG-TCACACAC-CCAC----CTCTGGAGGCCA i mm9.chr11 I 1 C 0 s dipOrd1.scaffold_43980 10200 39 + 11404 GAAACGCAAAGCTCAGG-TCCCAGAG-TCCC----CTGTG--GGTCA i dipOrd1.scaffold_43980 I 1 C 0 s calJac1.Contig5139 60159 43 + 225949 TCCCTGCAAAGCACAGG-ACCCCATA-AGTCACTCCTCAG--GGACG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 57667 42 - 95547 T-CCTGCAAAGCATAGG-GCCTTGTA-ACTCACTCCTTGG--GGACG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75050401 42 + 78773432 T-CCTGCAAAGCATAGG-GCCTTGTA-ACTCACTCCTTGG--GGACG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16076703 43 + 17838096 TCCCTGCAAAGCATAGG-GTCTGGTA-AATCATTCCTTGG--GGACG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 27277 43 - 64270 TCCCTGCAAAGCATAGG-GCCCGGTA-AATCATTCCTTGG--GGACG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79490183 43 + 83384210 TCCCTGCAAAGCATAGG-ACCCGGTA-AATCATTCCTTGG--GGACG i panTro2.chr17 C 0 C 0 s pteVam1.scaffold_11245 26473 3 + 48268 --------------------------------------------TCA i pteVam1.scaffold_11245 C 0 C 0 s equCab2.chr11 58055097 35 - 61308211 --------AAGTACAAG-TCCTCATG-AGTCACTCCTCTG--CACCA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59448742 38 - 64418924 -----GCA-AGTAATAGCTCCTTATA-GGTCACTCTTCTA--GATCA i canFam2.chr9 C 0 C 0 s bosTau4.chr19 10871232 18 - 65312493 ---------------------------AGTCACTCCTCTG--GATCA i bosTau4.chr19 C 0 C 0 s loxAfr3.scaffold_49 14446141 43 - 17734757 CAGCTGCAAAGCTCAGG-TCCCTGCA-AGTCATCCCTCTG--GGTCA i loxAfr3.scaffold_49 C 0 C 0 s choHof1.scaffold_149147 9333 43 + 9388 CATCTGC-AAGCTCAGG-CCCCTGTACAAACACTCCCTGG--GGTCG i choHof1.scaffold_149147 C 0 N 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e micMur1.scaffold_145100 1040 0 + 1040 I e turTru1.scaffold_106006 141348 0 + 145505 C e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e cavPor3.scaffold_76 4401669 42 + 7991924 I a score=174759.000000 s hg19.chr17_gl000204_random 59098 67 + 81310 TTCTGGAA-gagctctctgaagacagcaccaaatcttgttc--------caagt-tccaccagt------------------------------------------------------cccag--cccaggac- s panTro2.chr17 79490226 67 + 83384210 TTCTAGAA-GAGCTCTCTGAAGACAGCACCAAATCTTGTTC--------CAAGT-TCCACCAGT------------------------------------------------------CCCAG--CCCAGGAC- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 27320 67 - 64270 TTCTAGAA-GAGCTCTCTGAAGACAGCACCAAATCTTGTTC--------CAAGT-TCCACCAGT------------------------------------------------------CCCAG--CCCAGGAC- i gorGor1.Supercontig_0007361 C 0 I 169 s ponAbe2.chr17_random 16076746 67 + 17838096 TTCTAGAA-GCGCTCTCTGAAGACAGCACCAAATCTTATTC--------CAAGT-TCCACCAGT------------------------------------------------------CCCAG--CCCAGGAC- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75050443 42 + 78773432 TTCTAGAA-GAGCTCTCTGAAGACAGCACCAAATCTTGTTC--------CA----------------------------------------------------------------------------------- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 57709 42 - 95547 TTCTAGAA-GAGCTCTCTGAAGACAGCACCAAATCTTGTTC--------CA----------------------------------------------------------------------------------- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 60202 67 + 225949 TTCTAGAA-GAGCTCTCTGAAAACAGCACCAAATCTTATTC--------CAAGC-GCCACTGGG------------------------------------------------------CCCAG--CCCCATAC- i calJac1.Contig5139 C 0 C 0 s dipOrd1.scaffold_43980 10239 65 + 11404 TTCTGGAA-AGA--TTCTTGGGATGACACCAGGCCTTGTTC--------CAAGCTCCCCCCAGG------------------------------------------------------CCCGG--CCCAGCA-- i dipOrd1.scaffold_43980 C 0 C 0 s mm9.chr11 118772761 66 + 121843856 TTCCCAAA-AAG--GTCTGCAGGTGGCACCAAGCCTTCTTC--------CAGTCTCCAGACAGGT-----------------------------------------------------TCCAG--CCAAACA-- i mm9.chr11 C 0 C 0 s oryCun2.chrUn0958 30468 129 + 41507 TTCTGGGA-GAG-CCCTGGAGGGCAGCACCACGTCTGATTCGCACACAGCAGGC-CCACCCATATGCCCTGCGTGCGCACCCACAGTGTGTCTGAGGTAGGGAGTGGGGGGGCTATGCCCCGGACCCCAGCA-- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 141348 67 + 145505 TTCCAGGA-GAGCTCTCTGAAGACAGCACCAAATCTTGTTC-------CCAAGC-TCCACCAGA------------------------------------------------------CCCAG--CCAGCAC-- i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10871250 67 - 65312493 TTCCAGAG-AAGCTCTCGGAAGACAGCACCAAATCTTGTTC-------CCAAGC-TCCACCAGA------------------------------------------------------CCCAG--CCAGGGC-- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59448780 67 - 64418924 TTCCAGAA-AATCTCTCTGAAGACAGCACCAAATCCTGTTC-------CCAAGC-TCCATCAGA------------------------------------------------------CCCAG--CGGGCAC-- i canFam2.chr9 C 0 C 0 s equCab2.chr11 58055132 67 - 61308211 TTCCAGAC-AAGTTCTCTGAATTCAGCACCAAATCTTGTGC-------CCGGGT-TGCATCCAA------------------------------------------------------CCCAG--CCAGAGC-- i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_11245 26476 68 + 48268 TTCCGGCCAAAGCTCCCTGAAGACAGCACCAGGTCTTGTGC-------CCAAAC-TCCATGGGG------------------------------------------------------ATCGG--CCAGCGC-- i pteVam1.scaffold_11245 C 0 C 0 s cavPor3.scaffold_76 4401711 53 + 7991924 ------------TTCTTTGAAGACAACACTATG--TTCTGC--------CCATC-CCATCCAGA------------------------------------------------------GCAGG--GCAGGGC-- i cavPor3.scaffold_76 I 42 C 0 s loxAfr3.scaffold_49 14446184 68 - 17734757 CTCCGGAA-AAGCTGCTTGAAGACAATGCCAAACCCTGCTC-------TGAATC-TCCACCAGT------------------------------------------------------CCCAG--CGCAGTG-C i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e micMur1.scaffold_145100 1040 0 + 1040 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=30927.000000 s hg19.chr17_gl000204_random 59165 83 + 81310 tcaggacacggtgggcct---------gctcagACGCCCG---------------------------------GGTG-GTAAACTGAAATTGGCC-TCT-------------------------GTGGTT--------------GGGACTGGCCACAGGGCCTGCG s ponAbe2.chr17_random 16076813 83 + 17838096 TCAGGACACGGTGGGCCT---------GCTCAGACGCCCA---------------------------------GGTG-GTAAACTGAAATTGGCC-TCT-------------------------GTGGTT--------------CGGACTGGCCACAGGGCCTGCG i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79490293 83 + 83384210 TCAGGACATGGTGGGCCT---------GCTCAGACGCCCA---------------------------------GGTG-GTAAACTGAAATTGGCC-TCT-------------------------GTGGTT--------------GGGACTGGCCACAGGGCCTGCA i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 60269 83 + 225949 TCGGGACACAGTGGCCCT---------GCTGAGACACCCA---------------------------------GGTG-GCAAATTGAAATTGCCC-TCT-------------------------GTGGTT--------------TGGACTGGCCACAGGGCCTGCG i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118772827 78 + 121843856 -----GCACAGTCAGCC----------ACTCAGAAAGCCT---------------------------------GGTA-CTAAAATGAAGCAGGCA-CCT-------------------------GTAGCC-------------AAGGGGCAGCCATGTGGCCTGTC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_43980 10304 86 + 11404 -----GC-----CGGCC----------ACTCAACCAGCC----------------------------------AGTG-GTGAATTCAAGCTGGCATCCT-------------------------GCAGCTGGCATCTTGAGGGAAGGGTGGGCTGTGAGGCCGGGC i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4401764 74 + 7991924 -----ATGGAGTCAGCC----------CTCGAGGACAGC----------------------------------AGAT-GGGAATTGAAGTTGGCA-CCT-------------------------GCAGTA-------------AAA---CCGCTGGGGCACCTGCC i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 30597 150 + 41507 -----GCCG---CGGCCTGGGGCTCTGGCTGGGAAAGACTGCCAGGGACACGGTGCAGGTCCACGGAGCTCCAGGGG-GTGCATCTGAGTGAAtt-cttttttaagattttatttatttcagaggcagag------ttacagagagagagagagaggtcttccatt i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 141415 83 + 145505 TCAGCATGCAGTAGGTCT---------GCTCAGACACCTG---------------------------------AGCCTGTGAATTGAAGTTGGCA-TCT-------------------------GTGGCA---------------GGATCAGCCACAGGACCTGCA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10871317 83 - 65312493 TCAGCATGCTGTAGGTCC---------ATGCAGACACCTG---------------------------------AGCGCATGGATTGAAGTTGGTG-TCG-------------------------GTGGCA---------------GGATCAGCCCCAGGATATGCA i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59448847 80 - 64418924 TCAGCA--CCACAGACCC---------ATG-GTGCTCCTG---------------------------------TGTGGGTGGGCTGAAGTTGGCA-GCT-------------------------GTGGCA---------------GCTTGAGCCACAGGACCTGCA i canFam2.chr9 C 0 C 0 s equCab2.chr11 58055199 83 - 61308211 CCAGCATGCAGTAGGCCC---------GCACGGACGCCCG---------------------------------TGTGGGTGGATGGAAGTTGTCC-TCT-------------------------ATGACC---------------GAATCAGCTGTGGGACCCGCA i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_11245 26544 82 + 48268 TCGGTACACAGCAGGTCA---------CCCCAGACGCC-A---------------------------------CGCGGGTGGGCGGAAGCCGGTA-TCC-------------------------ATGGCC---------------CCATCAGCTTCAGGACCTGCA i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14446252 83 - 17734757 TAAGCACATAGTAGGCCT---------GCTCAGACACCGT---------------------------------GCCA-GTGGATCGAAATTCGTA-TTC-------------------------GTAACA--------------AGGATCAGCCACAGGGCGTCTG i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e papHam1.scaffold8336 57751 0 - 95547 C e gorGor1.Supercontig_0007361 27387 169 - 64270 I e vicPac1.scaffold_56870 707 2222 + 4541 I e micMur1.scaffold_145100 1040 0 + 1040 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e rheMac2.chr16 75050485 0 + 78773432 C a score=246423.000000 s hg19.chr17_gl000204_random 59248 132 + 81310 CG------------TGAGGAC-ACCCCTTGGGAACAGGCCCCAGCC-AGGCC--GGCCTCATTACCAGCCCCAGAGAGTTTGCCCTTCGTGCTCA-GCTGTCGTAGACAGG----------------------GATCTGGCCGGAAGAGAGTAAGTGTCAGGGCCAGCAGG s panTro2.chr17 79490376 132 + 83384210 CG------------TGAGGAC-ACCCCTTGGGAACAGGCCCCAGCC-AGGCC--GGCCTCATTACCAGCCCCAGAGAGTTTGCCCTTCACGCTCA-GCTGTCGTAGACAGG----------------------GATCTGGCCGGAAGAGAGTAAGTGTCAGGGCCAGCAGG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16076896 132 + 17838096 CG------------TGAGGAC-ACCCCTTGGGAACAGGCCCCAGCC-AGGCC--GGCCTCATTACCAGCCCCAGAGAGTTTGCCCTTCACGCTCA-GCTGTCGTAGACAGG----------------------GATCTGGCCAGAAGAGAGTAAGTGTCAGGGCCAGCAGG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75050485 132 + 78773432 CG------------TGAGGAC-GCCCCTTGGGGACAGGCCCCAGCC-AGGCC--GGCCTCATTACCAGCCCCAGAGAGTTTGCCCTTCACGCTCA-GCTGTTGTCGACAGG----------------------GATCTGGCCGGAAGAGAGTAAGTGTCAGGGCCGGCAGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 57751 132 - 95547 CG------------TGAGGAC-GCCCCTTGGGGACAGGCCCCAGCC-AGGCC--GGCCTCATTACCAGCCCCAGAGAGTTTGCCCTTCACGCTCA-GCTGTTGTTGACAGG----------------------GATCTGGCCGGAAGAGAGTAAGTGTCAGGGCCGGCAGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 60352 129 + 225949 CG------------TGAGGAC-GCCCCCTGGGGACAGGCCCCTGCC-AGGCC--GGCTTCATTGCCAGCCCCAGAGAGTTTGCCCTTCACGCTCG-GCTGTCATAGAC--G----------------------GATCTGGCCGGAAGAGAGCGCGTGTC-GGGCCTGCAGG i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118772905 95 + 121843856 TA------------GTAGGTT-ATCCCTCGAGAACAGAGCC------------------------------CAGGGCATATGTCCCGTGGACTCA-GAGGTCATCAAAGGG------------------------TCTGCCCAGAAAAGGAT----GGCAGGGC----CTG i mm9.chr11 C 0 I 259 s dipOrd1.scaffold_43980 10390 99 + 11404 CG------------TCAGGAG-GTCCCT-GGGAACAGGCCC------------------------------CGGGGAGTTGACTCTTCTGGTCCA-GCTGTCCACCAATAG---------------------AAATCTG-CCAGAAGAAAGT----GTCAGGGC-AGTCTG i dipOrd1.scaffold_43980 C 0 I 9 s cavPor3.scaffold_76 4401838 106 + 7991924 TACC------CTTCGCAGGTG-TTCACT-GGGGACAGGCCC------------------------------CAGGGGGCTTGCCCTTCAGGCCTA-GCTGCTGTCCATAGG----------------------GCTCTGCCCAGAGGAGGCT----GCTGAGGCCAGTCTG i cavPor3.scaffold_76 C 0 I 7 s oryCun2.chrUn0958 30747 136 + 41507 cactggttcactccccaaata-gccaca-atggccagagctgcgcc-ga-------------tgcaaa--gccaggagccaggtctgggggcc------gtcatccactgcttccccaggcgcgtgggcaggaagctggatcagaagaggagca--gccagg--------- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 141498 130 + 145505 CA------------TCAGAAT-CCCTGTCAGGGACAGGCCCTGGCA-AGGTT--AGCCTCGTTACAAGCCCCATGGAATTTGCCCTTCCAGCACCAGCTGCCGTGGAATGG---------------------GGATCTGGCCAGAAAAGGGG----GTCAGGACCAATCTG i turTru1.scaffold_106006 C 0 I 7 s bosTau4.chr19 10871400 132 - 65312493 CA------------TTGGGAT-CACCATCAGGGAGAGGCCCTGGCA-AGGCTAGAGCCTCATGACAAGCCTCAGAGACTTTGGCCTCTCAGCACCAGTTGCTGTGGAATGA---------------------GGATCTGCCCAGGAAAGGGG----CTCAGGGCCAAACTG i bosTau4.chr19 C 0 I 7 s canFam2.chr9 59448927 130 - 64418924 CA------------ATGGGATCCCCCCTTGGAGACAGGCCCCAGCA-AGGCT--GGCCTCACGGCGAGCCCTAGGGAATGTGCCCTTCCAGCTGCAGCTGCTGTCCACTAG---------------------GGATCTGGCCAGAAAAGGGC----A-CAGGACCAAACTG i canFam2.chr9 C 0 I 7 s equCab2.chr11 58055282 114 - 61308211 CG------------TCAGGAT-CCTCCTCGGGGACAGG-CCCAGCA-GGGCT--GGCTTCATCACAGGCCCCAGGGAATTT---------------GCGGCAGTAGAACAG---------------------GCCTCTGGCCAGAAAAGGGT----GTCACGGCCAGTCCA i equCab2.chr11 C 0 I 7 s pteVam1.scaffold_11245 26626 98 + 48268 TG------------TCA-CAT-CCCCCCAGAGGACAGGCCCCTGCA-GTGCT--GGCCTCATGACAAGCCCCAGGGAACAC---------------GC-----------------------------------CCTGTGGCCAGAAGCGGGG------TTGGGGCGGTCTG i pteVam1.scaffold_11245 C 0 I 7 s loxAfr3.scaffold_49 14446335 130 - 17734757 CA------------TCAGGTT-TCCCCT-GGTGACAGGCCCCAGCCAAGGCT--GGCTGTGGTACCAGCACCAGGGAGTCTGGCCTTCTGGCTCCAGCTGCTGTAAACTAG---------------------GGATTTGGCCAGAAAAGGGT----GTCAGGGCCAGTCTG i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e gorGor1.Supercontig_0007361 27387 169 - 64270 I e vicPac1.scaffold_56870 707 2222 + 4541 I e micMur1.scaffold_145100 1040 0 + 1040 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=47320.000000 s hg19.chr17_gl000204_random 59380 34 + 81310 -------ACATACCAGCACTAAC-------CGGGAGAT-TTTCCAT----TTG s panTro2.chr17 79490508 34 + 83384210 -------ACATACCAGCACTAAC-------CGGGAGAT-TTTCCAT----TTG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16077028 34 + 17838096 -------ACATACCGGCACTAAC-------CAGGAGGT-TTTCCAT----TTG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75050617 34 + 78773432 -------ACATACCAGCACTCAC-------CAGGAGGT-TTTCCTT----TCA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 57883 34 - 95547 -------ACATACCAGCACTCAC-------CAGGAGGT-TTTCCTT----TCA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 60481 34 + 225949 -------ATACAGCAGCACTAAC-------CAGGAGCG-TTTCCAT----TTG i calJac1.Contig5139 C 0 C 0 s dipOrd1.scaffold_43980 10498 30 + 11404 ---------ACACGGGAG-TGGC-------CAGGAGGT-CGCTCCT----TG- i dipOrd1.scaffold_43980 I 9 C 0 s cavPor3.scaffold_76 4401951 33 + 7991924 -------TCACACTGGGGCCAGC-------CAGGGTGC-CTTCCCT----TG- i cavPor3.scaffold_76 I 7 C 0 s oryCun2.chrUn0958 30883 40 + 41507 -----------actctaaccagcacccatgtgggatgc-ccacgctgcgacg- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 141635 34 + 145505 -------TCGTACTAGGATCAGC-------CAGGGGGG-TTTCTAT----CTT i turTru1.scaffold_106006 I 7 C 0 s bosTau4.chr19 10871539 35 - 65312493 -------TCATATTAGTATCAGC-------CAGGGGGGATTCCTGT----CTT i bosTau4.chr19 I 7 C 0 s canFam2.chr9 59449064 34 - 64418924 -------TCATACCAGGAACACC-------CAGGAGAT-TGTCCAT----CTT i canFam2.chr9 I 7 C 0 s equCab2.chr11 58055403 34 - 61308211 -------TCATCTCAGGACCAAC-------CAGGAGCT-TTTTCAT----CTT i equCab2.chr11 I 7 C 0 s pteVam1.scaffold_11245 26731 30 + 48268 -------TCGCA----GTCCAAC-------CAGGAGGC-TCTCCAT----CTT i pteVam1.scaffold_11245 I 7 C 0 s loxAfr3.scaffold_49 14446465 41 - 17734757 TCTGTCCTCCTCTGAGGACAAAG-------CAGGAGGT-TTTCCAT----CTT i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e gorGor1.Supercontig_0007361 27387 169 - 64270 I e vicPac1.scaffold_56870 707 2222 + 4541 I e micMur1.scaffold_145100 1040 0 + 1040 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118773000 259 + 121843856 I a score=199315.000000 s hg19.chr17_gl000204_random 59414 36 + 81310 GGGAC-----------------------GTCA-TCTAAGAGAATTTTTAAAACCTCTGAT s calJac1.Contig5139 60515 36 + 225949 GGGAT-----------------------ATCA-CCTAAGAGAAGTTTTTAAACCTCTGAT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 57917 36 - 95547 GGGAT-----------------------ATCA-TCTAAGAGAATTTTTAAAACCTCTGAT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75050651 36 + 78773432 GGGAT-----------------------ATCA-TCTAAGAGAATTTTTAAAACCTCTGAT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16077062 36 + 17838096 GGGAT-----------------------GTCA-TCTAAGAGAATTTTTAAAACCTCTGAT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 27556 36 - 64270 GGGAC-----------------------GTCA-TCTAAGATAATTTTTAAAACCTCTGAT i gorGor1.Supercontig_0007361 I 169 C 0 s panTro2.chr17 79490542 36 + 83384210 GGGAC-----------------------GTCA-TCTAAGAGAATTTTTAAAACCTCTGAT i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 19034 25 + 19765 -----------------------------------TAAGAGAATTTTTAAAACCTCTGAT i micMur1.scaffold_15893 I 2687 C 0 s dipOrd1.scaffold_43980 10528 34 + 11404 GGGGT-------------------------CA-TCTAAGAGAATTCTCGGAACCTGTGAT i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4401984 36 + 7991924 GGGGT-----------------------GCCA-CCTCCAAGAATCTTTGAAACCTCTAAT i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 30923 59 + 41507 gaggctcagccaatacgtcacagcgccggccC-CCGGGGCAGCCTTTTAAAACCTCTGAC i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_106006 141669 36 + 145505 GGGAT-----------------------ATCA-TTGAAAAGAATTTTACAAACCTCTGAT i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10871574 36 - 65312493 GGGAT-----------------------ATGA-CTGAACAGAATTTTACAAACCTCTGAC i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59449098 36 - 64418924 GGGAT-----------------------AGCA-TAAAAGAATATTTTATACACCTCTGAC i canFam2.chr9 C 0 C 0 s equCab2.chr11 58055437 35 - 61308211 GGGAT-----------------------ATCACTGAAAGA--ATTTTACAAACCTCTGAT i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_11245 26761 34 + 48268 GAGAC-----------------------GGCA-CCAAAGAGAATTTCACAAAC--CTGAT i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14446506 36 - 17734757 GGGAG-----------------------AGCA-TCTAAGGGAATATTACAAACCTCTGAT i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118773000 259 + 121843856 I a score=364511.000000 s hg19.chr17_gl000204_random 59450 100 + 81310 TTGGAAACTTTA-------------------------ATT-----------TTTAAAAAGTGA--GCACAT--GGGGAGGACTGGGGA--GTCCTTGGTAA---TAATCATTAGGAGAGAAACACAGGGAGACTGGGCTTGGGGC- s calJac1.Contig5139 60551 100 + 225949 TTGGAAACTTTA-------------------------ATT-----------TTTAAAGAATGA--GCACAC--GGGGAGGACTGGAGC--GTCCTTGGCAA---TACTCACGAGGAGAGAAACACAGGGAGGCTGGGCTTGGGGC- i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 57953 100 - 95547 TTGGAAACTTCA-------------------------ATT-----------TTTAAAAAGTGA--GCACAT--GGGGAGGACTGGGGA--GTCCTTGGCAA---TAATCATTAGGAGAGAAACACAGAGAGACTGGGCTTGGGGC- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75050687 100 + 78773432 TTGGAAACTTCA-------------------------ATT-----------TTTAAAAAGTGA--GCACAT--GGGGAGGACTGGGGA--GTCCTTGGCAA---TAATCATTAGGAGAGAAACACAGAGAGACTGGGCTTGGGGC- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16077098 100 + 17838096 TTGGAAACTTTA-------------------------ATT-----------TTTAAAAAGTGA--GCACAT--GGGGAGGACTGGGGA--GTCCTTGGCAA---TAATCATTAGGAGAGAAACACAGAGAGACTGGGCTTGGGGC- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 27592 100 - 64270 TTGGAAACTTTA-------------------------ATT-----------TTTAAAAAGTGA--GCACAT--GGGGAGGACTGGGGA--GTCCTTGGTAA---TAATCATTAGGAGAGAAACACAGGGAGACTGGGCTTGGGGC- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79490578 100 + 83384210 TTGGAAACTTTA-------------------------ATT-----------TTTAAAAAGTGA--GCACAT--GGGGAGGACTGGGGA--GTCCTTGGTAA---TAATCATTAGGAGAGAAACACAGGGAGACTGGGCTTGGGGC- i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 19059 103 + 19765 TTGGAAACTTT--------------------------ATG-----------CTTGAAAAGCAA--GCGCGT--GGGAAGAAATGGGGAC-GTCCTTTGCAACCGTAAATATTAAGAGAGAAAGAAAGGGAGATTAAGCCTGGGGC- i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118773259 83 + 121843856 ACAGAAACTTCG-------------------------TTT-----------TTAAGAATATGA--GGATG---TAGAAGCGCCAAGAACAACCCCCTGCAG---TAGCAACTAGGAAAGAAGCAAAG------------------- i mm9.chr11 I 259 I 4 s dipOrd1.scaffold_43980 10562 80 + 11404 TTGGAAACTTTA-------------------------TTT-----------GAAA-------A--GTGCG---GGGCAGCATCTAGGAGCATCCTTTGCGG---TGGTAATTAGG---GAAACAAAGG-----------GAGAGT- i dipOrd1.scaffold_43980 C 0 I 6 s cavPor3.scaffold_76 4402020 91 + 7991924 TTGGAAACTTTA-------------------------TTT-----------TTAAAGACATGACTGGCTA---GGGCGGAACTGGAAATAGGCCTTTGCAG---TA-CGTTTAGAAAAGAAACAAAGG-----------GAGGTT- i cavPor3.scaffold_76 C 0 I 4 s oryCun2.chrUn0958 30982 99 + 41507 TTGGAAACTTCT-------------------------CTT-----------TAAA--ATTGGT--AGCCA---GGGAGGAACTGGGAACAGCCCATCGCGA---TGAGCACTAGGAACGGAACAAAGGCGGACGTGGCTGGGGGC- i oryCun2.chrUn0958 C 0 I 964 s turTru1.scaffold_106006 141705 107 + 145505 TTGGAAACTTCA-------------------------TT--------TAAAAAAAAAAAGTGA--GACCATGAAGAAGGAACCAGGAACGGTCCTTTGCAA---TAATGATTAGCATAGAAGCAAAAGGAGATTTAGCTCGGAGC- i turTru1.scaffold_106006 C 0 I 1 s bosTau4.chr19 10871610 111 - 65312493 TTGGAAGCTTCA-------------------------TTaaaaaaaaaaaaaaaaaaaaaTGA--GACCATGAAGGAGGAACCAGGAACAGCCCTTTGCAA---C----ACTAAGAAAGAAGCAAAAGGAGATTTAGCTCAGAGC- i bosTau4.chr19 C 0 I 1 s canFam2.chr9 59449134 120 - 64418924 TTGGAAACTTTGTTGGTTTTCGTGTTTTCTTGTTTGTTTT------------------AGTGA--GAACAGGGAGGAGAAGCTGAGAATGGTACTTTGCAC---TGATAATTAGGGA--CAAAACGAGGAGATTTACCTCAGAAA- i canFam2.chr9 C 0 I 1 s equCab2.chr11 58055472 110 - 61308211 TTGGAACCTTTA-------------------------TTTAA-----AAAAAAGAAAAAGTGA--GAACATGGAGAAGGAAGTGGGAACGGTCCTTTGCAG---CAATAATCAGGAAAGCAACAAAAGGAGGTTTAGCTCAGGGG- i equCab2.chr11 C 0 I 1 s pteVam1.scaffold_11245 26795 94 + 48268 TTGGAACTTTTT-------------------------TTA------------------AGTGA---AATATGGAGAAGAAACTGAGAACGGTCCTTTATGA---TAATAATTAGGAA--AGAAATAAAAAGATTTAGCTCAGGgg- i pteVam1.scaffold_11245 C 0 I 1 s loxAfr3.scaffold_49 14446542 96 - 17734757 TTGGAAACTTTA---------------------------------------AAGAAAAAGTGA--GTTTGTGGGGGAGGAACTGGGAATGGTCCGTTGTAA---TGAT------AAAAGAAACGAAAGGAGATACAACTCGGGggc i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=243349.000000 s hg19.chr17_gl000204_random 59550 84 + 81310 CAACAGGACgactgaa---ggcacagagctaatttcgtgccctctgaaaaatcccactaa-aactacaaagagaaaa-tttt--------aaaaagg s calJac1.Contig5139 60651 83 + 225949 CAACAGGACAactgaa---cacacagagctcattccgt-ccctctgaaaaatcccactaa-aactacgaagagaaca-tttg--------tgaaagg i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 58053 85 - 95547 CAACAGGACAactgaa---cacacagagctaatttcgtgccctctgaaaaatcccactaa-aactacaaagagaaaattttt--------aaaaagg i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75050787 85 + 78773432 CAACAGGACAactgaa---cacacagagctaatttcgtgccctctgaaaaatcccactaa-aactacaaagagaaaattttt--------aaaaagg i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16077198 84 + 17838096 CAACAGGACgactgaa---cacacagagctaatttcgtgccctctgaaaaatcccactaa-aagtacaaagagaaaa-tttt--------aaaaagg i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 27692 84 - 64270 CAACAGGACgactgaa---ggcacagagctaatttcgtgccctctgaaaaatcccactaa-aactacgaagagaaaa-tttt--------aaaaagg i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79490678 84 + 83384210 CAACAGGACgactgaa---ggcacagagctaatttcgtgccctctgaaaaatcccactaa-aactacaaagagaaaa-tttt--------aaaaagg i panTro2.chr17 C 0 C 0 s micMur1.scaffold_15893 19162 73 + 19765 TAAAAGGACAactgaa---cccaccgggctgattttgtcctctctg--agatcccacc---gactacaaaaggacat-tttt--------------- i micMur1.scaffold_15893 C 0 C 0 s mm9.chr11 118773346 73 + 121843856 CACTCTAGCTATTACA--------AGGCC--ACAGCTCACCCTCAG-AAAGATACAGCAA----AGCACAGAAAAGA-CTCT--------AAGAGGA i mm9.chr11 I 4 I 752 s dipOrd1.scaffold_43980 10648 85 + 11404 CAGGCTACTGACCACACTGAACACAGGCT--ACCTTGCTCCTTCTG-AACCCCCCCCCAATGGCTGCAAAAAGAGGT-CTTT--------TATAAAA i dipOrd1.scaffold_43980 I 6 C 0 s cavPor3.scaffold_76 4402115 73 + 7991924 CAGGCTGACAGCtgag---cgcacagacc--actttgctgtctgtg-aaaacctcactaa-aactacaaaaagagat-ttt---------------- i cavPor3.scaffold_76 I 4 C 0 s turTru1.scaffold_106006 141813 82 + 145505 Taaaatgacaactgaa---cacacatagctaattttactccccctg-aaaaccccactaa-aactattgaaaga--g-atttttttaaag------- i turTru1.scaffold_106006 I 1 I 2493 s bosTau4.chr19 10871722 75 - 65312493 Taaaatgacaactgaa---cacacatagctaattttactctctctg-aaaaccccactaa-aactaccaaaaga--g-atttc-------------- i bosTau4.chr19 I 1 C 0 s canFam2.chr9 59449255 64 - 64418924 ATTTTAGTCAAGGGca---cac----aactaattttgttccctcta-aaa-ccccactaa-aactaccaaaaga----------------------- i canFam2.chr9 I 1 I 2 s equCab2.chr11 58055583 76 - 61308211 TAAAACGACTACGgga---cacccatagctaattttgctccctctg-aaacccccactaa-aactcccaaaagagat-tttt--------------- i equCab2.chr11 I 1 C 0 s pteVam1.scaffold_11245 26890 63 + 48268 taaaataacaactgaa---cacacacagctaattctgctccctctg-aaa--------------caccaaaagagaa-gttt--------------- i pteVam1.scaffold_11245 I 1 C 0 s loxAfr3.scaffold_49 14446638 79 - 17734757 taaaatgtcgaataaa---cacacatgtctaattttgcttcctc---aaaactccagtaa-aactccagaaagagat-gttt--------aaaga-- i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 31081 964 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=24629.000000 s hg19.chr17_gl000204_random 59634 47 + 81310 ggctgggcatggtggctcaagcctgtaatcccagcactttgggaggc s calJac1.Contig5139 60734 47 + 225949 ggctggacaaggtggctcacgcctgtaatcccagcactttgggaggc i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 58138 47 - 95547 ggccaggagcggtggctcacgcctataatcccagcactttgggaggc i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75050872 47 + 78773432 ggccaggcgtggtggctcacgcctataatcccagcactttgggaggc i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16077282 47 + 17838096 ggccgggcgtggtggctcaagcctgtaatcccagcactttgggaggc i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 27776 47 - 64270 ggctgggcgtggtggctcaagcctgtaatcccagcactttgggaggc i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79490762 47 + 83384210 ggctgggcgtggtagctcaagcctgtaatcccagcactttgggaggc i panTro2.chr17 C 0 C 0 s dipOrd1.scaffold_43980 10733 24 + 11404 -------------------AGGTCTAAACCTCCAAGCACCTGG---- i dipOrd1.scaffold_43980 C 0 C 0 s cavPor3.scaffold_76 4402188 35 + 7991924 ------------ttttttaaggtaaaaatccccgcatactggaaagc i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10871797 11 - 65312493 ----------------ctgaagatgaa-------------------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58055659 12 - 61308211 ---------------tttaaagatata-------------------- i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_11245 26953 11 + 48268 ---------------tttaaagctat--------------------- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14446717 9 - 17734757 -----------------------tataaaccc--------------- i loxAfr3.scaffold_49 C 0 I 13 e oryCun2.chrUn0958 31081 964 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e micMur1.scaffold_15893 19235 0 + 19765 C e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e canFam2.chr9 59449319 2 - 64418924 I e mm9.chr11 118773419 752 + 121843856 I a score=46620.000000 s hg19.chr17_gl000204_random 59681 33 + 81310 tgaggtgggtggatcacctgaggtcaggagttc s micMur1.scaffold_15893 19235 15 + 19765 ------------------taaggtctaaagccc i micMur1.scaffold_15893 C 0 C 0 s panTro2.chr17 79490809 33 + 83384210 tgaggtgggtggatcacctgaggtcaggagttc i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 27823 33 - 64270 tgaggtgggtggatcacctgaggtcaggagttc i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16077329 33 + 17838096 tgaggtgggtggatcacctgaggtcaggagttc i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75050919 33 + 78773432 caaggtgggcggatcacctgaggtcaggagttc i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 58185 33 - 95547 caaggtgggcggatcacctgaggtcaggagttc i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 60781 33 + 225949 caaggcgggtggatcacttgaagttaggagttc i calJac1.Contig5139 C 0 C 0 s bosTau4.chr19 10871808 12 - 65312493 -----------aacctcccaagg---------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58055671 12 - 61308211 -----------aaccccccaggg---------- i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_11245 26964 12 + 48268 -----------gatcccccaagg---------- i pteVam1.scaffold_11245 C 0 C 0 e oryCun2.chrUn0958 31081 964 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e dipOrd1.scaffold_43980 10757 0 + 11404 C e monDom5.chr2 304557512 13025 - 541556283 I e canFam2.chr9 59449319 2 - 64418924 I e cavPor3.scaffold_76 4402223 0 + 7991924 C e mm9.chr11 118773419 752 + 121843856 I e loxAfr3.scaffold_49 14446726 13 - 17734757 I a score=193260.000000 s hg19.chr17_gl000204_random 59714 142 + 81310 gagaccagcctggccaacatg-gtgaaacgccgtctctactaaaaa-tagcaaaactagccaggtgtggttgtgggtgcctgtaatcccaattacttgggaggctgaggcaggagaatcacttgaatccggga-ggtggaggttg s pteVam1.scaffold_11245 26976 92 + 48268 -------acctggacaacagg-gaaaggaa-----------aacga-cagtgaaa---------------tgtgggc-----------------ccaggaaggcagagacacaagccgcacctggcCCCTCAG-AGCAAATCCTC i pteVam1.scaffold_11245 C 0 C 0 s equCab2.chr11 58055683 93 - 61308211 -------acctggcaaacaggagaagagac-----------gacaa-caataaaa---------------tgtgggc-----------------agaggacagccaagggacaagcaatgcctgacctTGGGG-GCTGCATCCTA i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10871820 95 - 65312493 -------agctggtgaacaga-gaaaagac-----------aaccaccagcaaag---------------tgtgggag----------------gcaggaaggcaaatggacaagaggtgcttggccttgcagagctgagtcctg i bosTau4.chr19 C 0 C 0 s dipOrd1.scaffold_43980 10757 60 + 11404 ------AGTCTAGCTGA------------------------AAAGA-CAACAAA---------------CTGTGAG---CTGT-----------------------AGGAAAGAAAA------------GGAA-AGTGGAGAGCA i dipOrd1.scaffold_43980 C 0 I 2 s panTro2.chr17 79490842 142 + 83384210 gagaccagcctggccaacatg-gtgaaacgccgtctctactaaaaa-tagcaaaactagccaggtgtggttgtgggtgcctgtaatcccaattacttgggaggctgaggcaggagaatcactcgaatccggga-ggtggaggttg i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 27856 142 - 64270 gagaccagcctggccaacata-gtgaaacgccgtctctactaaaaa-tagcaaaactagccaggtgtggttgtgggtgcctgtaatcccaattacttgggaggctgaggcaggagaatcacttgaatccggga-ggtggaggttg i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16077362 142 + 17838096 gagaccagcctggccaacatg-gtgaaatgctgtctctactaaaaa-taccaaaactagccaggtgtggttgagggtggctgtaatcccaattacttgggaggctgaggcaggagagtcacttgaacccggga-ggtggaggtta i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75050952 142 + 78773432 aagaccagcctggccaacatg-gtgaaaccctgtctctactaaaaa-taccaaaattagccaggtgtgcttgtgggtgcctgtaatcccagctacttgggaggctgaggcaggagaatcacttgaacccagga-ggtggaggttg i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 58218 142 - 95547 gagaccagcctggccaacatg-gtgaaaccccgtctctactaaaaa-taccaaaattagccaggtgtgcttgtgggtgcctgtaatcccagctacttgggaggctgaggcaggagaatcacttgaacccagga-ggcggaagttg i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 60814 142 + 225949 aagaccagcctggctaacatg-gcaaaaccccatctctactaaaaa-tacaaaaattagctgggcgcagttgtgggcacctgtaatcccagctcctcgggaggcaaaagcaagagaattgttttaacccagga-ggcggaggttg i calJac1.Contig5139 C 0 C 0 e oryCun2.chrUn0958 31081 964 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e micMur1.scaffold_15893 19250 0 + 19765 C e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e canFam2.chr9 59449319 2 - 64418924 I e cavPor3.scaffold_76 4402223 0 + 7991924 C e mm9.chr11 118773419 752 + 121843856 I e loxAfr3.scaffold_49 14446726 13 - 17734757 I a score=58050.000000 s hg19.chr17_gl000204_random 59856 77 + 81310 cagagagccgagatcgcgccactgtactactccagcctggacaacaagagtgagacttccatctcaaataagaataa s panTro2.chr17 79490984 77 + 83384210 cagtgagctgagatcgcgccactgtactactccagcctggacaacaagagtgagacttccatctcaaataagaataa i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 27998 77 - 64270 cagtgagccgagattgcgccactgtactactccagcctggacaacaagagtgagaattccatctcgaataagaataa i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16077504 77 + 17838096 cagtgagccgagattgcgccactgtactactccagcctggacaacaagagcgagacttccgtctcaaataagaataa i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75051094 69 + 78773432 cagtgagccgagatcgtgccactg---taccccaccctgggcaacaagagtgagacttccgtcccaaaaaaa----- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 58360 73 - 95547 cagtgagccaagatcgtgccactg---taccccaccctgggcaacaagagtgagacttccgtctcaaaaaaaaaaa- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 60956 73 + 225949 cagtgagccaatattgcaccactg---cactctagcctgggcaataagagcaagac-tctgtctcaaaaaaaaagaa i calJac1.Contig5139 C 0 C 0 s dipOrd1.scaffold_43980 10819 23 + 11404 CAGGGAGCTGAG------------------TCCAGCACGGG------------------------------------ i dipOrd1.scaffold_43980 I 2 C 0 s bosTau4.chr19 10871915 18 - 65312493 ----------------------------accccatcatggggaggg------------------------------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58055776 28 - 61308211 ----------------------------GTGCCCCAGGGGAGCGGGGCGGGAGGGA--------------------- i equCab2.chr11 C 0 I 2 e oryCun2.chrUn0958 31081 964 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e micMur1.scaffold_15893 19250 0 + 19765 C e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e pteVam1.scaffold_11245 27068 0 + 48268 C e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e canFam2.chr9 59449319 2 - 64418924 I e cavPor3.scaffold_76 4402223 0 + 7991924 C e mm9.chr11 118773419 752 + 121843856 I e loxAfr3.scaffold_49 14446726 13 - 17734757 I a score=31453.000000 s hg19.chr17_gl000204_random 59933 31 + 81310 ctttaaaaaggcataaa-ccccaacgacctgg s pteVam1.scaffold_11245 27068 15 + 48268 ----------------A-TCCCACTATGGGGG i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59449321 31 - 64418924 ttttataaagatataaa-caccaaagagctgg i canFam2.chr9 I 2 C 0 s equCab2.chr11 58055806 27 - 61308211 ----CTGAAAAACGGAG-CCTCAGAGGCTCGG i equCab2.chr11 I 2 C 0 s bosTau4.chr19 10871933 27 - 65312493 ----ctaagaaacagaa-cctccaaaggctta i bosTau4.chr19 C 0 C 0 s dipOrd1.scaffold_43980 10842 10 + 11404 ----------------------AAGGATCCGG i dipOrd1.scaffold_43980 C 0 I 1 s micMur1.scaffold_15893 19250 11 + 19765 ---------------------caaagacctgg i micMur1.scaffold_15893 C 0 C 0 s calJac1.Contig5139 61029 32 + 225949 aaaaaaaaaggcataaacccccaaagacctgg i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 58433 28 - 95547 ----aaaaaggcataaacccccaatgacctgg i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75051163 28 + 78773432 ----aaaaaggcataaacccccaatgacctgg i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16077581 31 + 17838096 ctttaaaaaggcataaa-ccccaatgacctgg i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 28075 31 - 64270 ctttaaaaaggcataaa-ccccaatgacctgg i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79491061 31 + 83384210 ctttaaaaaggcataaa-ccccaacgacctgg i panTro2.chr17 C 0 C 0 e oryCun2.chrUn0958 31081 964 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e cavPor3.scaffold_76 4402223 0 + 7991924 C e mm9.chr11 118773419 752 + 121843856 I e loxAfr3.scaffold_49 14446726 13 - 17734757 I a score=188661.000000 s hg19.chr17_gl000204_random 59964 272 + 81310 agaataggagaaaagagaacagta----gccggctgtgggcagcggggaggcacaggag-aagtggcggcccgccctcacggagctgagt------ctcggcccagaggcagggaaggctgacaat-------------------ggaatcccccgaaggctcagaaGGCGTGGGGCCCAAGACCC-----------------------------------GGGG---------------------------------------------------AAGC-------------------------CTGGAGATCCTCGGATA---------GCCCCTctggaggtttattccctgagg----acactgaagcagc--ctctgtggcctgggggccgccagacactgcggacagaggggcgtcct-gcac-- s panTro2.chr17 79491092 272 + 83384210 agaataggagaaaagagaacagta----gccggctgtgggcagcggagaggcacaggag-aagtggcggcccgccctcacggagctgagt------ctcagcccagaggcagggaaggctgacaat-------------------ggaatcccccgaaggctcagaaggcgtggggcccaagacct-----------------------------------gggg---------------------------------------------------aagc-------------------------ctggagatCCTCCGATA---------GCCCCTctggaggtttattccctgggg----acactgaagcagc--ctctgtggcctgggggccgccagacactgcggacagaggggcatcCT-GCAC-- i panTro2.chr17 C 0 I 436 s gorGor1.Supercontig_0007361 28106 270 - 64270 agaataggagaaaagagaacacta----gcnggctgtgggcagcggggaggcacaggag-aagtggcagcccaccctcatggagctgagt------ctcagcccagaggcagggaaggctgacaat-------------------ggaatcccccaaaggctcagaaGGCGTGGGGCCCAAGACCT-----------------------------------GGGG---------------------------------------------------AAGC-------------------------CTGGAGATCCTCGGACA---------GCCCCTctggaggtttattccctgggg----acactgaagcagc--ctctgtggcctgggggccgccagacactgcggac--aggggcttcct-gcac-- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16077612 272 + 17838096 agaacaggagaaaagagaacagta----gccggctgtgggcagcggggaggcacaggag-aagtggtggcctgccctcacagagctgagt------ctgggcccagcagcagggaagactgacaac-------------------ggaatcccccgaaggctcagaagccatggggcccaagacct-----------------------------------gggg---------------------------------------------------aagc-------------------------ctggagatCCTCGGATA---------GCCCCTctggaggtttattctctgggg----acactgaagcagc--ctctgtggcctgggggccaccacacactgcggacagaggggcatcct-gcac-- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75051191 272 + 78773432 agaacaggaggaaagagaacagta----gccggctgtgggcagtggggaggcacaggag-aagtggtggccagccctcacggagctgagt------ctcggcccagcggcagggaaggctgacaat-------------------ggaatcccccgaaggctcagaagcagtggggcccaagacct-----------------------------------gggg---------------------------------------------------aagc-------------------------ctggagatCCTTGGATG---------GCCCCTctggaggtttattccctgggg----acgcggaagcagt--ctctgtggcttgggggccgccacacactgcggacagagcggcgtcct-gcac-- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 58461 272 - 95547 agaacaggaggaaagagaacagta----gccggctgtgggcagtggggaggcacaggag-aagtggtggccggccctcacggagctgagt------ctcggcccagcagcagggaaggctgacaat-------------------ggaatcccccgaaggctcagaagcagtggggcccaagacct-----------------------------------gggg---------------------------------------------------aagc-------------------------ctggagatCCTTGGATG---------GCCCCTctggaggtttattccctgggg----acgctgaagcagt--ctctgtggcttgggggccaccacacactgtggacagagcagcgtcct-gcac-- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 61061 257 + 225949 agaacaggagaaaagagaatcgta----gctggctgtgggcagcggggaggcacaggat-aagtggcagccggccctcatggagctgagt------cttggcacagtggcagggaaggctgacaaa-------------------ggaatctcccaaaggctcaggaccagcgggacccaaggcct-----------------------------------gggg---------------------------------------------------aagC-------------------------CTGG------------------------CCCTctggagatttattccctggtg----atgctgaagcaac--ctctgtggcctggtagccaccacacactgtggaccgaggggcatcct-gcac-- i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 19261 257 + 19765 aggacaggag----gagagCGGCA----G-TGGCCATGGGCAGCAGGTACGCACA-GAG-AAG----------------CGGAGCTGGGT------CCCAACCCAGGCGCAGGGACACCGGAGACT-------------------GGCATC-CCAGCAGTCTTGGAGCA---GGGGCCAGAGGCCT-----------------------------------AGGG---------------------------------------------------AAGC-------------------------CCGGAGGTGCTTGGACG---CCCCACGCCCACCCCAGGCTTCATTCCCCAGGGAATAAAGCTGAAGTCGC-ACTCTGTGGCCTGGGGGCCGGCACGCACCAGGGACAGAGGGGCAGCCT-GCAC-- i micMur1.scaffold_15893 C 0 C 0 s bosTau4.chr19 10871960 214 - 65312493 gagccatgggacagg----------------------------------------------------------------taactgtgggcaaaaaaaaaaaaaaaaaggcagctaggagtggtgat---------------------------------gatctg-tttaaagagcct-cagatcc-----------------------------------tgga---------------------------------------------------tggt-------------------tgcccactccagatcactggatg-----gctggtcaccatggaagggtattcttcgagg----agggtgaagcaggggctctgtggcctgggggactccatgcat-ggtgacagaggggtGTCTT-TCAC-- i bosTau4.chr19 C 0 I 9 s equCab2.chr11 58055833 206 - 61308211 AACCAGTGGGGCTGGAC--------------------------------------------------GCCTG-------TGGAGGTGGGG---------------AAAGCAGCCAGGAGCCGGGGA---------------------------------GATCTG-TTTAAGGAGCCCACAGGTCC-----------------------------------TAGG---------------------------------------------------TGGC-------------------TGCCCGCTCCAGATCACTGGATG-----GCCAGTCCCCCTG-GAGGGTGTTCCCTGGGG----AGGGAGAAGCAGGGGCTCTGTCGCCCCGGGGACTTCATGCAC-AGTGACAGGGGGGTCCTCT-GCAC-- i equCab2.chr11 C 0 I 9 s canFam2.chr9 59449352 316 - 64418924 agaacgggaggaaagacaaGAAAA----A---------------------TGATA-GAG-CAGTGGTGTCTGGCC----TGGCCATGCTG---ACTCCTAACCCCACAGCAGAGGGAAGCTGAGAA-------------------ACCACCTCC--AAGGCTCCG-ACCAGTAAGGCCAGGGACCCGTGGAGA----------------------------TAGGGAAGGCAGCTCAGAGCAGCAGGATCTTTTTGAGAAGCCCACAGACCCTTGCTGGC-------------------TACCTGCTCCAGACCCCCAGATG-----GCCAGCCACAAGGAGGGGGTGTTCCCTGGGG----AGAATGAAGCAGGGGCTCTGTGGCTGGAGGGACTTCTTGCACGGGTGGCAGAGAGGTATGTT-GTCC-- i canFam2.chr9 C 0 I 9 s pteVam1.scaffold_11245 27083 203 + 48268 AGGCAG-GAAACAGAACTTCCACA----G---------------------GCTCA-GAA-CTGGGGAGCCAGGTCCTTGTAGAGGTGGGG--------------CAGAGCAGCAGA-------------------------------------------GATCTGTTTTAAGGAGCCCACAGACTC-----------------------------------TAGA---------------------------------------------------TGGC-------------------------ACCCAGATCACTGTATG-----GCCCGTCACCCTG-GAAGGTGC--------------------AGCATGGGCTCT-TGGCCTGA-GGACTTCATAAAT-AGTGACAGAGCGGTACCCT-GCAT-- i pteVam1.scaffold_11245 C 0 I 9 s loxAfr3.scaffold_49 14446739 343 - 17734757 aaaatggaagaaaaagcagcagca----gcagg-tatggacagcaggaaagcagaagagcaagtggtgactggcc-tcgcagacctgagt------gctaatccagcggcagggagg-ctgacgagcggacacaatttacaccacggaatcctcccagccctcaggactg--ggggccagacacctggaaaggaggggcatgcagctgaaatctgttcaatgagg---------------------------------------------------aagccgttggatacctagatccctgtctactccggaccactgggcg---------gctgccctggaggt-tactccaagcac----agggggaaacagaggctctggggc-------acttcacatatagtagacgggagggtatcct-tccctc i loxAfr3.scaffold_49 I 13 C 0 s cavPor3.scaffold_76 4402223 209 + 7991924 -----agaagaaaagacaccaata----aAGGGCTGTCAGCTGCATGAAA--CCCGAGG-CTGGGGGTGC-----------------AGT------C------------CATGGAGG--TGACAAA-------------------CAAAACCCTCGAAGGCTTAGAACCAGCAGG-CCCGGCACCTGT---------------------------------GGAG---------------------------------------------------AGGA-------------------------AGCCAGAGGGCTGGACAGGGCTGGATGGCCCTGGG----TGCTTTTTCTGGGG----A-GTCAAAGCAAG---------------------------------GAGAGAAGGGCACTTTGGCAG-- i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_43980 10853 150 + 11404 -----AGTATGAGGGCTCCCCACAGCAGAGGGGCCGGCTCCTGCA----------GAgg-gaggggagg-------------------------------------------ggagg--cgg---------------------------------ggaggc------------------------------------------------------------gggg---------------------------------------------------aggt-------------------------agggaggggagggga-----------ggCCCTGGGAAGCCTCTATTCCTGGAG----A-GCTGGGCCAGG---------------------------------AAAAGAGGCACGTGGTTGCAA-- i dipOrd1.scaffold_43980 I 1 I 16 e oryCun2.chrUn0958 31081 964 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118773419 752 + 121843856 I a score=250201.000000 s hg19.chr17_gl000204_random 60236 140 + 81310 ggagagccc---ccctttt-ccctcacggcacctgtcagcatcctgacctccaccctcctggcaggaggccggaagaatct--cctctg---ggg-aatctcaccagcacccagaggggaaacctgaagatagagctttgctgcttccaa s panTro2.chr17 79491800 141 + 83384210 Ggagagccc---ccctttttccctcacagcacctgtcagcatcctgacctccaccctcctggcaggaggccggaagaatct--cctctg---ggg-aatctcaccagcacccagaggggaaacctgaagatagagctttgctgcttccaa i panTro2.chr17 I 436 C 0 s gorGor1.Supercontig_0007361 28376 140 - 64270 ggagagccc---ccctttt-ccctcacagcacctatcagcatcctgacctccaccctcctggcaggaggccggaagaatct--cctctg---ggg-aatctcaccagcacccagagggnaaacctgaagatagagctttgctgcttccaa i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16077884 140 + 17838096 ggagagctc---ccctttt-ctctcacagcacctgtcagcatcctgacctccaccctcctggcaggaggccggaagaatcg--cctctg---ggg-aatctcaccagcacccagaggggaaacctgaagatagagctttgctgcttccaa i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75051463 139 + 78773432 ggagagc-c---ccctttt-ccctcacagcacctgtcagcatcctgacctccaccctcctggcaggaggccagaagaatct--cctctg---ggg-agtctcaccagcacctagaggggaaacctgaagatagagctttgctgcttccca i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 58733 139 - 95547 ggagagc-c---ccctttt-ccctcacagcacctgtcagcatcctgacctccaccctcctggcaggaggccagaagaatct--cctctg---ggg-agtctcaccagcacctagaggggaaacctgaagatagagctttgctgcttccca i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 61318 123 + 225949 agagaac-C---CCCTTCC-CCCCAACAGCATTTGTCAGGATCCTGACCTCCAGCCCCC---------------agaatct--cctctg---gggaaatctgatcagcacccagaggggaaacccgaagac--aGCTTTGCTGCTTCCCA i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 19518 129 + 19765 -CAGAGC-C---CCCT----AGCCCACGGCACCGAT----GTCCTGGCCTTCACCCTCA-GGCAAGAGGCCAGAAGCGACG--CCCCTG---GGG-GAATCGCCCAGCACCCAGAGGAG-AACCTGAAGCTGGAGCCTTGCTATTTCCCA i micMur1.scaffold_15893 C 0 C 0 s dipOrd1.scaffold_43980 11019 111 + 11404 AG----------------------CATAACACC----AGCCTCGTGC------CCTTCGCTCCAGGGAGCCAGGAAGAGGT--CATGCG---AGG-ATTCAGGCCAGCACCAAGAGGAAAAGCCTGAAGACTTCACTCTGCTG-TTCCCA i dipOrd1.scaffold_43980 I 16 C 0 s mm9.chr11 118774171 118 + 121843856 --AGAGTC-----CCACTA-GTGCCACAGCCCA----GTTATCCTGa------ccctctagatcaggagcctgg---------cctgctctcagg-actctgaccagc-cgtagggagaaaccct--acacctacctttagga-ttccct i mm9.chr11 I 752 C 0 s cavPor3.scaffold_76 4402432 133 + 7991924 --AGAGCCT---TCTCCCT-GCcccacagcact----gacacctggc-cttcaccctccaaaccagcagccagaggagtgtcccctggg----ga-aaactgcccagc-actaagaggaaatcttaaaaagacagctttgccatttctca i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10872183 118 - 65312493 TAAAAGccc---cacccag-cccccatagcacc----------------aacatcctccaggcaagaagctagaaaagtct--cttccc---cct---cctgcagatttta----ggagaaacctatggatataattttattgtttccaa i bosTau4.chr19 I 9 I 40 s equCab2.chr11 58056048 121 - 61308211 CGAGGGccc---cgctcag-cccccacagcacc----------------gatgtcctccaggccagaggctggaagattct--cctctg---ggagcatctgcccagcacc----cagggagaaatgagatggacctttgctgcttccca i equCab2.chr11 I 9 I 38 s canFam2.chr9 59449677 101 - 64418924 TGAGAGCCC---CCATCAG-CCCCCAGAGGACC-----------------ATGCCCTTCAGG-CAAAGCCCAGGAGAGTCC--C--------------TCTCTCCTCCTGC----AGGTAAGACATAACCTGG-------CTATTTCCCA i canFam2.chr9 I 9 I 38 s pteVam1.scaffold_11245 27295 110 + 48268 TGA--GTcc---cactcag-cccctgtagcact----------------gacatcttccagc-aagagacgagaagggtct--ccttcc---------tctgcccgttgca----ggagaagcctaaagatgtgactg--ctgttttcca i pteVam1.scaffold_11245 I 9 I 39 s loxAfr3.scaffold_49 14447082 137 - 17734757 tgaaggctcacgcccacca-gctccacagcgct----gacaagcaggcctttaccctct-ggtaagaggctgtaagagtct--cctttg---ggg-gaactgaccagc-ccaagaggagaaacctagtagtatgactttgctgtttccga i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 31081 964 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=127366.000000 s hg19.chr17_gl000204_random 60376 123 + 81310 -----------------------------------------gcaca---------------ggccccactccc--tgctcgg-agctgccaacc-----agc-tttg--cagcccccc----ctaaggtgagtaaaaagccaaggatgaccagacacctgcgg-----aaagccttc------------atgagaaggagccg-----ccaaaa-------ca s panTro2.chr17 79491941 122 + 83384210 -----------------------------------------gcaca---------------ggccccactccc--tgctcgg-agctgccaacc-----agc-tttg--cagcccccc-----taaggtgagcaaaaagccaaggatgaccagacacctgcag-----aaagccttc------------atgagaaagagccg-----ccaaaa-------ca i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 28516 122 - 64270 -----------------------------------------gcaca---------------ggccccactccc--tgctcgg-agctgccaacc-----agc-tttg--cagcccccc-----taaggtgagtaaaaagccaaggatgaccagacacctgcgg-----aaagccttc------------atgagaaagagccg-----ccaaaa-------ca i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16078024 124 + 17838096 -----------------------------------------gcata---------------ggccccactccc--tgctcag-agctgccaacc-----agcttttg--cagcccccc----taaaggtgagtagaaagccaaggatgaccagacacctgcgg-----aaagccttc------------atgagaaagagccg-----ccacaa-------ca i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75051602 130 + 78773432 -----------------------------------------gcaca---------------gaccccaatccc--tgcttag-agctgccaacc-----agt-tttg--cagcccccc----taaaggtgagtaaaaagccaaggatgaccagacatctgcgg-----aaagccttc------------atgagaaacagctg-----ccaaagaccgagctc i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 58872 130 - 95547 -----------------------------------------gcaca---------------ggccccaatccc--tgctcag-agctgccaacc-----agt-tttg--cagcccccc----taaaggtgagtaaaaagccaaggatgaccagacatctgcgg-----aaagccttc------------atgagaaacagctg-----ccaaagaccgagctc i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 61441 121 + 225949 -----------------------------------------GTGca---------------ggccccactccc--tgctcgg-agctgccaacc-----agc-tttg--cagccccc------taaggtgagcagaaagccaaagaggaccaaatgcctgcgg-----aaagccttc------------ccgagaaagagccg-----ccaaaa-------ca i calJac1.Contig5139 C 0 C 0 s micMur1.scaffold_15893 19647 116 + 19765 -----------------------------------------GCCAG---------------GGCCCCG----C--TGCTCAG-AGCT----CCC-----CGC-TTTGGCTGGCCCTGG----TAGAGGTGGGGAGGCAG-CGAGGGTGACCAGCCGCCTGCAG-----AAGGCCTTT------------CAGAGAAAAAGCTG-----CCAAAA-------CA i micMur1.scaffold_15893 C 0 N 0 s mm9.chr11 118774289 129 + 121843856 -----------------------------------------gccagaagtagcaggacagaagcccca---------cttag-cactgaaggtc-----agc-tctg--caggcctccccct--aacgctggtagc---ctaaa-----------ctc--agc-----agagctgtaaacacaggctctgaaagagggagcca-----ctaaac-------aa i mm9.chr11 C 0 I 7 s dipOrd1.scaffold_43980 11130 109 + 11404 -----------------------------------------GCCAG---------------AGTCCCA--------------------AAGGTCTTCTGAGC-TCTA--CAGGCCCCTCTCTTAAAGGTGAGTAGC---CAGAG-----------CTCTGAGG-----ACAGCCagagagagaga----gagagagagagaga-----gCGCAC-------AA i dipOrd1.scaffold_43980 C 0 I 5 s cavPor3.scaffold_76 4402565 126 + 7991924 -----------------------------------------gccag---------------gtcctca---------gttggtctctccagaga-----gga-cctc--caggcacgaccct-------gcccagc---ctggagctgccc--tcctctgaggctcctggagcccttcagacagccctggggaggaaacccaa-----caagac-------aa i cavPor3.scaffold_76 C 0 I 5 s oryCun2.chrUn0958 32045 115 + 41507 -----------------------------------------gcccg---------------ggccccgcccac--tgcttggagcctgcagtcc------ac-tccc--caggccctcaccttccaagtgagcagac-gccaag-----------ccctgagg-----ccagcctgt------------aagaggtgggccac-----cagaac-------ga i oryCun2.chrUn0958 I 964 I 5 s bosTau4.chr19 10872341 121 - 65312493 -----------------------------------------ggata---------------ag-cccactcaa--tcctcag-a-cctttgggt-----agc-tctg--caatcccttcccctaaatgtgagtagacaacccaggattaccagacattggggg-----aaagctttt------------gagagaaagagcca----ccca------------ i bosTau4.chr19 I 40 C 0 s equCab2.chr11 58056207 119 - 61308211 -----------------------------------------ggaca---------------ag-cccactcag--ccctcag-agcctctgggc-----tgc--ctg--cagacccctcccctaaacctgagcagaca---ctggggttcctgacctct--gg-----gacgcctgt------------aagagaaagagccg-tgagcca------------ i equCab2.chr11 I 38 C 0 s canFam2.chr9 59449816 125 - 64418924 -----------------------------------------gggca---------------ag-cccacccagtcctc--ag-agcctccagtc-----agc-tctg--caggccactccccaaaatgtgagtggacatccccaaatttccagacatctgagg-----aaagccttt------------caga-agagagccaccaaacta------------ i canFam2.chr9 I 38 C 0 s pteVam1.scaffold_11245 27444 119 + 48268 -----------------------------------------ggaca---------------ag--ccacccag--cccacag-agcctccggtc-----agc-tctg--caggatccccaggccaaagtgagtaaacc-acctggattagcagacatctgagg-----aatgccttt------------tagagaaagagtcc-----cta------------ i pteVam1.scaffold_11245 I 39 C 0 s loxAfr3.scaffold_49 14447219 167 - 17734757 gccaagaacccagccaatcaccctacagggaagctccaaggggata---------------agccccactcac--cactcag-agctgccagtc-----agc-cttg--cagcccctc-ccttaaatgtgagtagacaaacaagaattaccagacatctcaag-----aaagccttt------------aagagacagagcca-----ctgaaa-------ca i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=194293.000000 s hg19.chr17_gl000204_random 60499 65 + 81310 cgcaacag------agc-------------------------------------------------ggggc-------cgacttcgaggaaacagatattaggcagggaggagaaaacatcagaaat s panTro2.chr17 79492063 65 + 83384210 tgcaacag------agc-------------------------------------------------ggggc-------cgacttcgaggaaacagatattaggcagggaggagaaaacatcagaaat i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 28638 65 - 64270 cgcaacag------agc-------------------------------------------------ggggc-------cgacttcgaggaaacagntattaggcagggaggagaaaacatcagaaat i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16078148 65 + 17838096 cgcaacag------agc-------------------------------------------------ggggc-------cgacttcgaggaaacagacattaggcagggaggagaaaatatcagaaat i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75051732 69 + 78773432 tgcaacag------agc----------------------------------------gagt-----ggggc-------cgacttcgaggaaacagacattaggtagggaggagaaaatatcagaaat i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 59002 69 - 95547 tgcaacag------agt----------------------------------------gagt-----ggggc-------cgacttcgaggaaacagacattaggtagggaggagaaaatatcagaaat i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 61562 64 + 225949 c-ccacag------cgc-------------------------------------------------ggggc-------ctacttcgtggaaacagccgttaggcagggaggagaaaatatcagaaat i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118774425 67 + 121843856 tgggggag------gga------------------------------------------cc-----gaggg-------tggcctggaggagacaggcattgggcagggaggagaaaatatcagaaat i mm9.chr11 I 7 C 0 s dipOrd1.scaffold_43980 11244 64 + 11404 TGGTACAG------GGA-------------------------------------------------GAGGG--------Gacttggaggagtcagatattaggcagggaagagaacatatcagaaat i dipOrd1.scaffold_43980 I 5 C 0 s cavPor3.scaffold_76 4402696 68 + 7991924 agggtgggtcaggtggg------------------------------------------tg-----gggag--------agctttgaagaaacagac-ttaggcacggagg---aaatatcagaaat i cavPor3.scaffold_76 I 5 C 0 s oryCun2.chrUn0958 32165 58 + 41507 cgga----------gga-------------------------------------------------gcggg--------aactc--aggagtgaggcctcgggcaggaaggagaagtgaccagaaat i oryCun2.chrUn0958 I 5 C 0 s bosTau4.chr19 10872462 64 - 65312493 ---ggtgg------gga--------------------------------cctaggggtgtg-----gtgca-------caacttcaaagaaatagacattagacagggagg----------agaaat i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58056326 64 - 61308211 ---cttgg------ggc------------------------------------------ca-----ggggg-------caactttgagggaaccgacacgaggcagagagcccgaagcaccagaaat i equCab2.chr11 C 0 C 0 s canFam2.chr9 59449941 86 - 64418924 ---cccag------ggc-ggtggtggctgggggggtggggggg--------tgggggggtg-----gagag-------gaactttgaggaaacgaagacgag-----------agggtatcatcaac i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 27563 111 + 48268 ---cacag------ggcagggggcttctgggggagagggagagggtaacgctgaggaagtgtgggtggggg-------gaatgctgaggaagcagaccttaggcagggaggaggaaatatcagagag i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14447386 79 - 17734757 ---aacat------ggc----------------------------------ggtgggggcg-----ggggaagggttgcaactgtgaggaaacaggtattaagcaaagaggagaaaatatcaaaaat i loxAfr3.scaffold_49 C 0 I 225 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=656976.000000 s hg19.chr17_gl000204_random 60564 96 + 81310 agcagtatttaatatcctcccagagatcagaggagataccgcat-ccatgaaccaagagcagggtgctattttaaggagaacatttagagaac-a-------aaa s panTro2.chr17 79492128 96 + 83384210 agcagtatttaatatcctcccagagatcagaggagataccgcat-ccatgaaccaagagcagggtgctattttaaggagaacatttagagaac-a-------aaa i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 28703 96 - 64270 agcagtatttaatatcctcccagagatcagaggagataccgcat-ccatgaaccaagagcggggtgctattttaaggagaacatttagagaac-a-------aaa i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16078213 96 + 17838096 agccgtatttaatatcctcccagagatcagaggagataccgcat-ccatgaaccaagagcagggtgctattttaaggagaacatttagagaac-a-------aaa i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75051801 96 + 78773432 agccgtatttaatatcctcccagagatcagaggagataccgcat-ccatgaaacaggagcagggtgctattttaaggagaacatttagagaac-a-------aaa i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 59071 96 - 95547 agccgtatttaatatcctcccagagatcagaggagataccgcat-ccatgaaacaagagcagggtgctattttaaggagaacatttagagaac-a-------aaa i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 61626 94 + 225949 agtcatacttaatatcctcccagagatcagaggacataccgcat-ccatgaaccaagagcagggtgctattttaagg---acatttagagaacaa-------aaa i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118774492 92 + 121843856 agacatatttaatatcctcaaagagatcagaggagatattgcaa-cca-gaaccaggagcaggatgctatttta---agaacatttagagaac-a-------aaa i mm9.chr11 C 0 I 2 s dipOrd1.scaffold_43980 11308 96 + 11404 agccatatttaatatcctcaaaaagatcagaggagataccacagccca-gaaccacgagctggatgctattttaaggagaacatttagagagg-a-------aaa i dipOrd1.scaffold_43980 C 0 N 0 s cavPor3.scaffold_76 4402764 96 + 7991924 agccatatttaatatcctcgaagagatcagaggagatattgcatccca-gaaccaagagcaggatgctattttaaggagaacatttagagaac-a-------aaa i cavPor3.scaffold_76 C 0 I 1 s oryCun2.chrUn0958 32223 92 + 41507 agccgcgtttaatcccctccgc-agatcacagg-ggcacggcgt-cca--aaccgcgggcaggatgctattttagggagagcgtccagagaac-a-------aaa i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10872526 94 - 65312493 agaca--tttaatatcctcaaagacagcagataagatattgcat-ttaggaaccaagagcaggatgctattttaaggagaacatttagagaac-a-------aaa i bosTau4.chr19 C 0 I 2 s equCab2.chr11 58056390 103 - 61308211 agccattttcaatatcctcaaagacagcagagaagacactgcat-ccataaaccaggagtgggatgctattttaagaagcacgtttaaagaac-aacaaaaaaaa i equCab2.chr11 C 0 I 2 s canFam2.chr9 59450027 93 - 64418924 agtccctttcaatgtctcaaaaggcagcagagaagatactgcat-ctacgcatcaagaacaggacgctctttgaaagaaaacactgagagaac-c---------- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 27674 93 + 48268 agtcgcctttaacatcctcagagacagcagagaagattctgcct-ccatgaaacaagagcaggatgctattttaaga---acatttagagaac-a-------aaa i pteVam1.scaffold_11245 C 0 I 2 s loxAfr3.scaffold_49 14447690 96 - 17734757 AGCCatttttaatatcttcagctagatcagggaagatattgtat-ccatgaaccaagagtaggctagtcttttaaatagaacatttagagaac-g-------aaa i loxAfr3.scaffold_49 I 225 I 2 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=388194.000000 s hg19.chr17_gl000204_random 60660 91 + 81310 aagctgggaagttaaaagcatgagagcagaa-------acaaaacat-----------ctcaacagacaggctg--gaagagaaaagtaagggaatgccccagaaggcaaa s panTro2.chr17 79492224 91 + 83384210 aagctgggaagttaaaagcatgagagcagaa-------acaaaacat-----------ctcaacagacaggctg--gaagagaaaagtaagggaatgccccagaaggcaaa i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 28799 91 - 64270 aagctgggaagttaaaagcatgagagcagaa-------acaaaacat-----------ctcaacagacaggctg--gaagagaaaagtaagggaatgccccagaaggcaaa i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16078309 91 + 17838096 aagctgggaagttaaaagcataagagcagaa-------acaaaacat-----------ctcaacagacaggcta--gaagagaaaagtaagggaatgccccagaaggcaaa i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75051897 91 + 78773432 aagctgggaagttaaaagcatgagagcagaa-------acaaaacat-----------ctcaacagacaggcta--gaagagaaaagtaagggaatgccccagaaggcaaa i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 59167 91 - 95547 aagctgggaagttaaaagcatgagagcagaa-------acaaaacat-----------ctcaacagacaggcta--gaagagaaaagtaagggaatgccccagaaggcaaa i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 61720 86 + 225949 aagctgggaagtt-aaagcatgagcgcagaa-------acaaaacat-----------ctcaacagactggcca--gaagagaaaagtaaggggatgccgcagaagg---- i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118774586 91 + 121843856 gggccggggaattaaaagcatgcaagccgaa-------acaaaaaaa-----------ctcagcagactggttg--gaagataaaagtaagggaatgttccagaaggcaaa i mm9.chr11 I 2 C 0 s cavPor3.scaffold_76 4402861 102 + 7991924 gggctgggaaattaaaagcatgagaaccgaa-------acaaaaaggaaaaaaaagccctcaacagactggttg--gaagataaaagtacgcaaatgtcccagaaggcaca i cavPor3.scaffold_76 I 1 C 0 s oryCun2.chrUn0958 32315 84 + 41507 -gactgggaaattaaaagcaggagaacggaatttttttacgaagaat-----------ctcagcagac--------------aaaagtgagggcagggctgagaggg-gga i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10872622 90 - 65312493 ggactggaaaattaaacgtgtgagaacagaa-------acaaaa-cc-----------ctcaacagacaggttg--gaagatggaagggaggagctatcccagaatgcaaa i bosTau4.chr19 I 2 C 0 s equCab2.chr11 58056495 89 - 61308211 gggttgggaaattaaaagcatgagaagagaa-------gcaaaa-ac-----------ctcaacagccaggtca--gaagatagaagggaggg-gcatcccagaacgggag i equCab2.chr11 I 2 C 0 s canFam2.chr9 59450120 12 - 64418924 ------------------------aaaacag-------gcaaa-------------------------------------------------------------------- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 27769 86 + 48268 gggctgcaagattaaaagcatgagaacagaa-------acaaaa-ac-----------ctcaacagacagttt------ggtggaagtgagggaatatcccagaatgcaaa i pteVam1.scaffold_11245 I 2 C 0 s loxAfr3.scaffold_49 14447788 89 - 17734757 gggctgggaaattaaaa-cacgagagcaaaa-------ccaaaata------------ctcaacagacaggttg--gaaggcaaaggtaaggaaacctcccagaaggcaaa i loxAfr3.scaffold_49 I 2 C 0 s dasNov2.scaffold_171027 146 83 + 4838 --------aaattaaaa-aataaataaataa-------ataaataa------------ataaataaataaataaataaataaaAAAGCAAGTGaatcttcaaggaaacaaa i dasNov2.scaffold_171027 N 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=193690.000000 s hg19.chr17_gl000204_random 60751 83 + 81310 gcaaaaaggcaaagaggagaaaaagaagaaagaggggatgaaaaaaaactagatgatcaattcacgagg------ctcaacacaaaagg s panTro2.chr17 79492315 83 + 83384210 gcaaaaaggcaaagaggagaaaaagaagaaagaggggatgaaaaaaaactagatgatcaattcacgagg------ctcaacacaaaagg i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 28890 80 - 64270 gcaaaaaggcaaagaggagaaaaggaagaa--aggggatg-aaaaaaaccagatgatcaattcatgagg------ctcaacacaaaagg i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16078400 82 + 17838096 gcaaaaaggcaaagaggagaaaaagaagaaaagggggatg-aaaaaaactagatgatcaattcacaagg------ctcaacacaaaagg i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75051988 81 + 78773432 gcaaaaagacaaagaggagaaaaagaagaaagaggggatg--aaaaaactagatgatcaatttacgagg------ctcaacacaaaagg i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 59258 81 - 95547 gcaaaaagacaaagaggagaaaaagaagaaagaggggatg--aaaaaactagatgatcaattcacgagg------ctcaacacaaaagg i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 61806 71 + 225949 ---------caaagaggagaaaaagaagaaacaggggatg---aaaaactagatggtcaattcgtgcag------ctcaacgcaaaagg i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118774677 73 + 121843856 gcaaaaagacaaagagggggagaatagaa----aaggaGG---AGAAATGAGATGGCACACTCATGAGA------GCCGGCGCCTG--- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4402963 76 + 7991924 gcaaaaagacaaagaggaaaaaataagaaa-ggaaggagg---aaaaattagatgccatgttcatgaaa------gtctgcgttca--- i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 32399 56 + 41507 gcaaggaggcggaaggagggGGATGAGCC------------------------CGGCAGCCTCGCCAGG------GCCCCCTCCCC--- i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10872712 83 - 65312493 gcaaaaagacaaagaggagaaaaataagaaaggatgaaag------aattagatgaccagttcaggcggcctaGGACCCATACAAAAGC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58056584 72 - 61308211 gcaaaaagacaa--tggggaaaaacaggaaagaa--------------ttcaatgatgagttcatgagg-ctgacatccacacaaaagg i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_11245 27855 46 + 48268 gcaaaaaga--------agaaagaaaggataaaa-----------------------gagTTTctcag------------cacaagggg i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14447877 86 - 17734757 gcaaaaagaaaaagaggagg-aaataagaaagtaggggtg--agaaaattagacaatcaattcatgaggtccaatatctacataaaaag i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 229 83 + 4838 gcaaaaagaccaagtggaggaaaataagaaaata----tg--agaaaatttgatggccagttcatgaggcccagcatccacatatatag i dasNov2.scaffold_171027 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e canFam2.chr9 59450132 0 - 64418924 C a score=12449.000000 s hg19.chr17_gl000204_random 60834 29 + 81310 aattctaacccc----------gaccc------------------c--catagggcccc s panTro2.chr17 79492398 29 + 83384210 aattctaacccc----------caccc------------------c--catagggcccc i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 28970 29 - 64270 aattctaACCCC----------CACCC------------------C--CATAGGGCCCC i gorGor1.Supercontig_0007361 C 0 M 25 s ponAbe2.chr17_random 16078482 29 + 17838096 aattctaacccc----------caccc------------------c--catagggcccc i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75052069 28 + 78773432 aatcctaacccc-----------actc------------------c--cgtaggacccc i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 59339 28 - 95547 aatcctaacccc-----------actc------------------c--cataggacccc i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 61877 57 + 225949 aatcttggcccctcccccaccccaccccgcggggccccccccccac--catagagcctc i calJac1.Contig5139 C 0 C 0 s bosTau4.chr19 10872795 25 - 65312493 AACCCTTCTTTC----------CATTC------------------CATCCTGC------ i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58056656 22 - 61308211 -atcctcccctc----------cagcc------------------a--cctgc------ i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14447963 13 - 17734757 aatctt--cccc----------cac---------------------------------- i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 32455 0 + 41507 C e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 707 2222 + 4541 I e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e dasNov2.scaffold_171027 312 0 + 4838 C e pteVam1.scaffold_11245 27901 0 + 48268 C e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e canFam2.chr9 59450132 0 - 64418924 C e cavPor3.scaffold_76 4403039 0 + 7991924 C e mm9.chr11 118774750 0 + 121843856 C a score=-4467.000000 s hg19.chr17_gl000204_random 60863 23 + 81310 cagagagaaggaggagg--------aggaga s panTro2.chr17 79492427 23 + 83384210 cagagagaaggaggagg--------aggaga i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16078511 23 + 17838096 cagagagaaggaggagg--------agaaga i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75052097 23 + 78773432 cagatagaaggaggagg--------aggaaa i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 59367 23 - 95547 cagatagaaggaggagg--------aggaaa i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 61934 20 + 225949 cagag---aggagcagg--------aggaaa i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118774750 11 + 121843856 ---------CGGAAAGG-----------GAG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4403039 22 + 7991924 ---------cacaaaggagtcctccatagag i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 32455 14 + 41507 ---------CACGTGGG--------GGAGGG i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10872820 2 - 65312493 CT----------------------------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58056678 17 - 61308211 ctgagagagaaaagagg-------------- i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14447976 23 - 17734757 caaaaaaaaaagagaaa--------aggggc i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 312 20 + 4838 ---aaagaacaagaaag--------agggag i dasNov2.scaffold_171027 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e gorGor1.Supercontig_0007361 28999 25 - 64270 M e vicPac1.scaffold_56870 707 2222 + 4541 I e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e pteVam1.scaffold_11245 27901 0 + 48268 C e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e canFam2.chr9 59450132 0 - 64418924 C a score=-20423.000000 s hg19.chr17_gl000204_random 60886 30 + 81310 aga-a---agg---aa----atca-----tcaattactta-----agaat-t s panTro2.chr17 79492450 33 + 83384210 aga-agaaagg---aa----atca-----tcaatgactta-----agaaa-t i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16078534 33 + 17838096 aga-ggaaagg---aa----atca-----tcaattattta-----agaaa-t i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75052120 33 + 78773432 aga-agaaagg---aa----atca-----tcaattattta-----agaaa-a i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 59390 33 - 95547 aaa-agaaagg---aa----atca-----tcaattattta-----agaaa-a i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 61954 30 + 225949 aga-agaaaga---aa----atca-----tc----attta-----agaatct i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118774761 34 + 121843856 GGA-AGAGGGG---GC----ATCG-----CTAATCATTTAACTC-AAG---- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4403061 38 + 7991924 agacagacaga---ca----atca-----caaattatttaattc-aagaa-g i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 32469 41 + 41507 AGA-CGAGGGG---GTTGCGATCC-----CTGGCTACTTGATTC-AGGAA-A i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 2929 32 + 4541 ----AGAGAGA---GA----ATTATATATTTCA--ACTCA-----ACACA-- i vicPac1.scaffold_56870 I 2222 C 0 s bosTau4.chr19 10872822 24 - 65312493 -------GAAA---GA----GTTA-----TTTA--ATTCT-----ATAAA-- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58056695 26 - 61308211 -----gctaat---ca----atta-----tgca--gttca-----agaaa-- i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14447999 37 - 17734757 ----agagggtgaggg----gtca-----tcaatgatttaatttaagaaa-- i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 332 34 + 4838 ----ggagggt---gt----acca-----acaatggtttaattcaagaat-- i dasNov2.scaffold_171027 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e gorGor1.Supercontig_0007361 28999 25 - 64270 M e turTru1.scaffold_106006 141895 2493 + 145505 I e felCat3.scaffold_206428 46377 8110 + 132007 T e pteVam1.scaffold_11245 27901 0 + 48268 C e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I e canFam2.chr9 59450132 0 - 64418924 C a score=186481.000000 s hg19.chr17_gl000204_random 60916 40 + 81310 tttttccag------aaataagtttccaaattg--------tccacaaaatcga s panTro2.chr17 79492483 40 + 83384210 attttccag------aaataagtttccaaattg--------tccacaaaatcaa i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16078567 40 + 17838096 tttttccag------aaataagtttccaaattg--------tccacaaaatcga i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75052153 40 + 78773432 tttttccag------aaataagtttccaaattg--------tccacaaaatcga i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 59423 40 - 95547 tttttccag------aaataagtttccaaattg--------tccacaaaatcga i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 61984 40 + 225949 tttttccag------aaataagtttccaaattg--------tcaacaaaatcaa i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118774795 19 + 121843856 ---------------------------AAATTC--------TCCACACAATGGA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4403099 46 + 7991924 ttttcccaggaatgaaaatgaatcttcaaattc--------tacacacaatggg i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 32510 40 + 41507 TTTTCCTAG------AAACTGGTTTCCAAATTC--------TCCACACCGTGGG i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 2961 48 + 4541 TCTTACCAg------aaatgagtttcctaattctcatcacatcagcacaccgga i vicPac1.scaffold_56870 C 0 C 0 s bosTau4.chr19 10872846 39 - 65312493 TTTCC-CAG------AAATGAGTTTCCAAGTTC--------TCAGTAGAGCAGA i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59450132 40 - 64418924 ttgccctag------aaatgagtttcctggttc--------tcagcacaatgga i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 38267 40 + 132007 TTTCCCTAG------AGAAGAGTTTccgagttc--------ttagcacagcgga i felCat3.scaffold_206428 T 8110 C 0 s equCab2.chr11 58056721 40 - 61308211 tttccccaa------aaatgaacttccgagttc--------tcagcacaatgga i equCab2.chr11 C 0 C 0 s turTru1.scaffold_106006 144388 29 + 145505 ------CAG------AAATGAGTTTc--aagtc--------tcagca---cagt i turTru1.scaffold_106006 I 2493 C 0 s loxAfr3.scaffold_49 14448036 34 - 17734757 ttttcttag------aagtgagtttccaAGTCC--------CCCACGC------ i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 366 40 + 4838 ttttcccag------aaatgagtttccaagttC--------CTCACACTAAGGA i dasNov2.scaffold_171027 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e gorGor1.Supercontig_0007361 28999 25 - 64270 M e pteVam1.scaffold_11245 27901 0 + 48268 C e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=288128.000000 s hg19.chr17_gl000204_random 60956 58 + 81310 tggaaa-tga-ttcatatcaaggca---------cattatcttgaaaagtaaatcactgaagaaaaaaa s panTro2.chr17 79492523 58 + 83384210 tggaaa-gga-ttcatatcaaggca---------cattatcttgaaaagtaaatcactgaagaaaaaaa i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16078607 59 + 17838096 tggaaattga-ttcctatcaaggca---------tattatcttgaaaagtaaatcattgaagacaaaaa i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75052193 59 + 78773432 tggaaattga-ttcatatcaaggca---------tattatcttgaaaagtaaatcactgaggacaacaa i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 59463 59 - 95547 tggaaattga-ttcatatcaaggca---------tattatcttgaaaagtaaatcactgaggacaacaa i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 62024 59 + 225949 tggaaattga-cccatatcaaggca---------tattatcttgaaaagcaaatcactgggaataaaaa i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118774814 56 + 121843856 TAAGAATTGA-CCCACATCAGAGCA---------TATTCTCAC-AAATACAAAACACTAAAG--AGGGA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4403145 40 + 7991924 tggagattga-cccacatcaaggca-------------ctcac----tacagaaacct----------- i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 32550 34 + 41507 TGGCAATTAA-TCCACGTTA-------------------TCAG----GACAAAAAGTT----------- i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 3009 59 + 4541 tggaaggtgt-cccacatgaaggca---------tattatcattaaaagcaaaacactgaagacaaaaa i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_106006 144417 59 + 145505 gggaaattgaccccacatcaaggca---------ta-tatcatgaaaagcaaaacactgaagagaaaga i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10872885 59 - 65312493 TGGAAATTGA-CCCATATCAAGGCA---------TATTATCACACAAAGcaaagcactgaagaaaaaaa i bosTau4.chr19 C 0 I 202 s equCab2.chr11 58056761 59 - 61308211 cggaaactga-ccaacatcaaggca---------tattatcatgaaaagcaaaatgctgaagacaaaga i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 38307 59 + 132007 tggaaactga-cccacaggaaggcc---------tatgaacgcggaaagcacagccctaaggacaaaga i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59450172 54 - 64418924 tggaaactga-cccacatcaaagta---------tactgacataccaaaca-----ctgaggccaaaaa i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 27901 68 + 48268 tggaaactga-cccacatcaaggcatcaaggttttgttatcatggaagacaaaacactgaggacaaaca i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14448070 50 - 17734757 ---------A-ATcacttcaaggca---------tattatcatgaaaagcagaacactgaggtcaaaga i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 406 57 + 4838 TGGAAATCAA-CCCATGTTAAGGCA---------TATAACCACGCAGTGcataacac--aggacaaaga i dasNov2.scaffold_171027 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e gorGor1.Supercontig_0007361 28999 25 - 64270 M e otoGar1.scaffold_94362.1-287808 33984 6958 + 287808 I e monDom5.chr2 304557512 13025 - 541556283 I a score=311809.000000 s hg19.chr17_gl000204_random 61014 70 + 81310 aaaaatgtttccccaagtttccag-gtgccataaaaaagagcaggaacgagaat-agctccaga-attctcaa s panTro2.chr17 79492581 68 + 83384210 aag--tgtttccccaagtttccag-gtgccataaaaaagagcaggaatgagaat-agctccaga-attctcaa i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16078666 70 + 17838096 aaaaatgtttcccgaagtttccag-gtgccataaaaaagagcaggaatgagaat-agctccaga-attctcaa i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75052252 70 + 78773432 aaaaatatttccccaagtttccag-gtaccataagaaagagcaggaatgagaat-agctctaga-attctcaa i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 59522 70 - 95547 aaaaatatttccccaagtttccag-gtgccataagaaagagcaggaatgagaat-agctccaga-attctcaa i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 62083 70 + 225949 aaaacagtttccccaagtttccag-gcaccataaaaaagagcagaaacgagaat-agcttcaga-attctcaa i calJac1.Contig5139 C 0 C 0 s mm9.chr11 118774870 68 + 121843856 AAGAAAAATAAATCTTCAGTTTAAGGTTCTGTGAAAAA---CAAGAATGAGTGT-GGCTCCAAG-AGTCTCAA i mm9.chr11 C 0 I 446 s cavPor3.scaffold_76 4403185 67 + 7991924 aagcaagctccctctggtgtccga-gtaccatgacaaagagcagggatgag----aactcctga-attttcag i cavPor3.scaffold_76 C 0 I 4 s oryCun2.chrUn0958 32584 27 + 41507 -------------------------GTCC----ATAAA---C-------------GGCTCCAGG-GGTCCCAG i oryCun2.chrUn0958 C 0 I 1 s vicPac1.scaffold_56870 3068 68 + 4541 ---atagtttccacgagtttccag-gttccataaaaacgagcaggaataagaacaagcttcaga-agccttaa i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_106006 144476 67 + 145505 ---aaagtttccacaagcttc-ag-gttccacagaaaagagcaggaatgagactgtgcttcaga-agtctcaa i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10873146 67 - 65312493 AAAAAGGCCTCCACAAGTTTCTGG-GCTTCATAGAAAAGAGCAGAGGT----CTTTTCTtcaga-ggtctcaa i bosTau4.chr19 I 202 C 0 s equCab2.chr11 58056820 61 - 61308211 ---aaagtttccacaagtttctgg-gtcccataaaaag-------agcaggaacgggcttcaga-agtctcag i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 38366 69 + 132007 ---cacacccccccaagtctccag-gtcccgtagaaaggagcccagacgagaaggggcctcagcgggtctcaa i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59450226 67 - 64418924 ----aagttcccacaagtttccag-gtcccataaaaaagagcccaaatgagaatgggcattagc-catctcta i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 27969 66 + 48268 ----aagttaccacacgtttccag-gt-ccataaaaaagagctggaatgagaatgggcctcaaa-agtctcaa i pteVam1.scaffold_11245 C 0 C 0 s otoGar1.scaffold_27969.1-945 0 38 - 945 --------------------------------Aaaaaaaaacaaaaagacaaac-agctctaga-a-tctcaa i otoGar1.scaffold_27969.1-945 n 6958 C 0 s gorGor1.Supercontig_0007361 29024 43 - 64270 ----------------------------Ccataaaaaagagcaggaatgagaat-agctccaga-gttctcaa i gorGor1.Supercontig_0007361 M 25 C 0 s loxAfr3.scaffold_49 14448120 67 - 17734757 ---gaattttccacaagcttccag-gttccatacaaaggaatgggaataagaat-gacttcagg-ctttgtaa i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 463 66 + 4838 ---aaagttcccatgagtttccag-gtcctataaaatagggc-agagtaagaat-ggctctaga-ctttccaa i dasNov2.scaffold_171027 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e monDom5.chr2 304557512 13025 - 541556283 I a score=1549154.000000 s hg19.chr17_gl000204_random 61084 222 + 81310 cacaaagaggg---c-agctaaccaatcacaaagc-gtgccttcaaaa-gc-tgatggcaagtgatttctggcctggaatcccttacttcacaaaattaacaatc-aaacgtgagat-----------taaaacaaagacattt-gc--acatgcgagatctc-------gacaaaat---------------------------tatttc----ccacacaccatctctca----gctaccagaggacgtgctctaacaaaacaagggtgtaaagcat-gaaa----gag s calJac1.Contig5139 62153 219 + 225949 aac----aggg---caagctaactagtcatgaagt-gtgccttcagaa-gc-tgacagaaaatgatttcaggactggaattcctcgctttgcaaaattaacgatc-aaatgtgagat-----------taaaataaagacattt-gc--acatgcaaggtctc-------aacaaaat---------------------------tatttc----ccacactccctctctca----gctaccagaggatgtgctccaacaaaaccagggtgtaaagcgc-gaaa----gag i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 59592 223 - 95547 cacaaagaagg---caagctaaccaatcacagagc-gtgcctccaaaa-gc-tgacaaaaagtgctatctggcctggaatccctcacttcacaacattaacaatc-aaatgtgagat-----------taaaacaaagacgttt-gc--acaggcaacgtctc-------aacaaaat---------------------------tatttc----ctacacaccatccctca----gctaccagaggatgtgctccaacaaaacaagggtgtaaaacat-gaag----gag i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75052322 223 + 78773432 cacaaagaggg---caagctaaccaatcacagagc-atgcctccaaaa-gc-tgacaaaaactgctatctggcctggaatccctcacttcacaacattaacaatc-aaatgtgagat-----------taaaacaaagacgttt-gc--acatgcaacgtctc-------aacaaaat---------------------------tatttc----ctacacaccatccctca----gctaccagaggatgtgctccaacaaaacaagggtgtaaagcat-gaag----gag i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16078736 223 + 17838096 cacaaagaggg---caagctaaccaatcacagagc-atgccttcaaaa-gc-tgacggaaagtgatttctggcctggaatccctcacttcacaaaattaacaatc-aaatgtgagat-----------taaaacaaagacgttt-gc--acatgcaagatctc-------gacaaaat---------------------------tatttc----ccacacaccatctctca----gctaccagaggatgtgttccaacaaaacaagggcgtaaagcat-gaaa----gag i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 29067 221 - 64270 cacaaagaggg---c-agctaaccaatcacaaagc-gtgccttcaaaa-gc-tgatggcaagtgatttctggcctggaatcccttacttcacaaaattaacaatc-aaacgtgagat-----------taaaacaaagacattt-gc--acatgcgaggtctc-------aac-aaat---------------------------tatttc----ccacacaccatctctca----gctaccagaggacgtgctccaacaaaacaagggtgtaaagcat-gaaa----gag i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79492649 222 + 83384210 cacaaagaggg---c-agctaaccaatcacaaagc-gtgccttcaaaa-gc-tgatggcaagtgatttctggcctggaatccctcacttcacaaaattaacaatc-aaatgtgagat-----------taaaacaaagacattt-gc--acatgcgagatctc-------gacaaaat---------------------------tatttc----ccacacaccatctctca----gctaccagaggacgtgctccaacaaaacaagggtgtaaagcat-gaaa----gag i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_27969.1-945 38 221 - 945 cagcagtaaag---caagctaataagtaatggaacagtgccttcaaaaggc-agaagagaaatgattcctggcctagaatcctttgctcagccacattaa----c-aaacatgagat-----------taaaataaagacattt-gc--acattcgaggtctc-------aaaaaatg---------------------------tatttc----ccatgctccatttctca----cttactaggggatgtgctccaacaaaataagggagtaaagtgt-gaaa----gaa i otoGar1.scaffold_27969.1-945 C 0 C 0 s cavPor3.scaffold_76 4403256 223 + 7991924 tgc-agcaggg---caagctagcaaatgacagag--acgccttcaaaa-caccaacagggagggatgtccagcctagaatcttctacttaactaacatggcaata-aaaagtgaatt------------aaaataaagacattt-ga--ataggtaaggtgtc-------agaaacaa---------------------------tatctc----ctgtgtgccatcttcca----gctactgcaggatgtgctccaacaaaacaatgagggagagcat-gaaa--gTGAG i cavPor3.scaffold_76 I 4 C 0 s oryCun2.chrUn0958 32612 227 + 41507 CGC-AGCAGA----------------------------GCCTCCGAAA-CA-CAGAGGCAAGCGGCTTCCGGCCGAGGCCCT--CACTTGGCCCAAATCACAGCC-CTGTGTGAGCT-----------GAGAACAGAGACGCTT-GC--TTGGACAGGGTCTC-------AAAAACAGAGAAGAGAATAGAATAGAAAACCCCGCTGTTtc----ccatgcaccgtttctca----gccgcttcaggatgcgttccagcaaaacaagggagtaaaacat-gaaaCCATGAC i oryCun2.chrUn0958 I 1 C 0 s vicPac1.scaffold_56870 3136 234 + 4541 ---caacagca---gaagataacagacaaggaagcagagctttcagagcac-ttacggaaaatatcttttggcgcagaatgcattatttagccaaattaacaatg-taatgtgagac-----------ccaaataaagacattc-ac--tcatgaaaggtctcaaaaaaaaaaaaaaa--------------------------gcacctc----ccacgaatcatttctcaggaaggtactagaggatgtgttccaacaaaacaaaggagtaaagcat-gaaa----agg i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_106006 144543 227 + 145505 ---caacagca---gaagctaatagataatggagcagtgccctcaaagtgc-tgaaggaaaatattttctggcctagaatccattacttagccaaatgagcaatc-taatgtgagat-----------taaaataaagatgttt-gc--atgtgcaaggtctc-------aaacaaat--------------------------ttaccac----ccatgtaccatttttcaggaagctactagaggatgtgctccaacaaaacaagggagtaaagcct-gaaa----gag i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10873213 227 - 65312493 ---caacagca---gaagctaatagataatggagcagtgccttcaaagtgt-tgaaggaaaatattttctggcctagaatccattatgtagccaaatgaacaatc-taatgtgaaat-----------taaaataaatatgttt-gc--atgtgcaaggtctc-------agacaaat--------------------------ttaccca----ccatgtgccatttctcaggaagctattagaggatgtgctacaataaaacaagggagtaaagcat-gaaa----gag i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58056881 227 - 61308211 ---caacagca---gaagctaatatataatggatcggtgctttcaaagtgc-tgaaggaaagtatttcctggcctagaatcctttacttagccaaattaacaatc-aaatgtgagat-----------taaaataaagacatttggc--acgtacgaggtctc-------aaaaaaat--------------------------ttttttc----c-atgcaccatttctcaggaagctactagaggatgtgctccaacaaaacaagagtgtaaagcat-gaaa----gag i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 38435 211 + 132007 ---gagca------gaagctgacagatgagg--------------cggtgc-caacgggaaagccctcctggcctaggatcccttcctcagccagattaacaaccaaaccgtgagat-----------taaaataaagacgctt-ac--gcacgcaaggtctc-------aaacacgt--------------------------ttattcc----ctacgcgccgtttctcaggaagctactagagggtgtgctccaacaaaacaggggaggaaagcct-gaaa----gcg i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59450293 239 - 64418924 ---gaacaacagtgagagccaggagataaggg--tggtgccttcaaagtgc-caaaggaaaatctttcctggcctagaatccctaacttagccaaattaacaatc-agctgtgagattaaaattaaaataaaataaaaaccttt-gc--acatgcaaggtttc-------aaaaacct--------------------------ttatttc----ctatgcactgcttctcaggaagccactagaggatgtgctccaacaaaacaagggagtaaatcgt-gaaa----aca i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 28035 217 + 48268 ---cagtgacagcagaagctaaaagacaaca--------------aagtgc-tgaaaaaaatggttttctggcct-gaattgcacactgagccaaattaacaatc-aaatctgagat-----------taaaat-aagacactt-gc--acatgcgaggtctc-------aaaaaatt--------------------------tcactccggagccacgtaccacttctca-gaagctactgaaggatgtgctccaacaaaacaagagggtaaagcac-gaaa----aag i pteVam1.scaffold_11245 C 0 M 584 s loxAfr3.scaffold_49 14448187 219 - 17734757 aaactacaggg---gaagctaat-------------gagccttcaaaatgc-tgaaggaaaaatatttctggcctaaaatcccttacttattcaaattaacaatc-taatgtgagat-----------tagaataaagacattt-gcagacatgcgaggcctc-------acaagaat--------------------------ttacttc----ccctgcaccatttcccaggaagctactagaggatgtgctctaacaaaacaaaggagtaaaccac-gaaa----gag i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 529 233 + 4838 cagccatggag---gaagggaacagataacggatcagtgccttcaaaatgc-tggatgaaaatgatttctggcctagaattccttacttagtcaaagtaacagtc-aaatgtgatat-----------tagattgaagatattt-gcagatatgcatgttctc-------aaaaattt--------------------------tcatctt----ccatgcatcttttctcaggaaattactggaggatgtgctccaataaaacaaggaagtaaaccataaaaa----aag i dasNov2.scaffold_171027 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118774938 446 + 121843856 I a score=481425.000000 s hg19.chr17_gl000204_random 61306 144 + 81310 ggcaatg-agggatggaag-aaac----agaggatctagtaagcg-ggcaggga----------tccacatagtgggagaggagggag----ggc--aggagggcagctgtgtaccgggcaagaggttgccagtccagatgagagcaggG----------------TGGTGGCA--------------------------------------TGTCCAGCT s calJac1.Contig5139 62372 135 + 225949 gtcaatg-agagagggaag-aaac----agaggatctagtaagtg-gggaggGA----------TCCAT-------------------------------AGGGCAGCTGTGTACCGGGCAAGAGGTTGCCAGTCCAGATGACAGCAAGGTGGTAGCATGTCCAGATGGTGGCA--------------------------------------TGTCCAGCT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 59815 144 - 95547 gacaacg-agggatggaag-aaac----agaagatctagtaagtg-gggaggga----------tccacatagagggagaggagggat----ggc--aggagggcagctgtgtatcaggcaagaggttgccagtccggatgagagcaggG----------------TGGTGGCA--------------------------------------TGTCCAGCT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75052545 144 + 78773432 aacaaca-agggatggaag-aaac----agaagatctagtaagtg-gggaagga----------tccacatagagggagaggagggat----ggc--aggagggcagctgtgtatcaggcaagaggttgccagtccggatgagagcaggG----------------TGGTGGCA--------------------------------------TGTCCAGCT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16078959 144 + 17838096 ggcaatg-agggatggaag-aaac----agaggatctagtaagtg-ggcaggga----------tccacatagtgggagaggagggat----ggc--aggagggcagctgtgtaccgggcaagaggttgccagtccagatgacagcaggG----------------TGTTGGCA--------------------------------------TGTCCAGCT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 29288 144 - 64270 ggcaatg-agggatggaag-aaac----agaggatctaataagtg-ggcaggga----------tccacatagtgggagaggagggat----ggc--aggagggcagctgtgtaccgggcaagaggttgccagtccagatgagagcaggG----------------TGGTGGCA--------------------------------------TGTCCAGCT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79492871 144 + 83384210 ggcaatg-agggatggaag-aaac----agaggatctagtaagtg-ggcaggga----------tccacatagtgggagaggagggat----ggc--aggagggcagctgtgtaccgggcaagaggttgccagtccagatgagagcaggG----------------TGGTGGCA--------------------------------------TGTCCAGCT i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_27969.1-945 259 121 - 945 ggca--g-agggctgggcg-aaacccctagggggtccagccagag-agcgagg----------------------------------C----AGC--AGGAGGGCTGACATGCACCAGGGAAGAGGGCGCCAGTCCAGACTAGAGC-GAG----------------TGGGGGCA--------------------------------------CATCCAACT i otoGar1.scaffold_27969.1-945 C 0 C 0 s cavPor3.scaffold_76 4403479 148 + 7991924 GGTAATG-AGGAAGAGATG-ACCTC---CGAGCCTCCGCTAAGAA-AACAAGAA----------GCCAGGTGTGCAGGACAGAGAAGGCATTGGC--AGGAGAGCAGCTGTACACTAGGCAAGAGGCC-CTCGTCCAAAGTGGCGTGTGG----------------AAGCCACA--------------------------------------CCGCCAGCT i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 32839 126 + 41507 GGGGATG-G--------------------GCGCCACAGCCAGGAA----GAGCC----------GCAGGGTGGGAAAGACGGGAAATG----GGA--GGGTGGGGCGCCGTGTGGCCAGCAAGAGGTCACGGGACCAGATTCCAGCAGGG----------------TGGCCACA--------------------------------------CGTCCAGCT i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 3370 133 + 4541 gatgaca-agggacagatg-aaac----agtggatccagtaagagagggagagaggaagggga-gccagaggatgggagagaagggag----ctctcaggaggacagctgt-----------------------ccaGATTAGAGCAGGA----------------TGGTGACA--------------------------------------CGTCCAACT i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_106006 144770 134 + 145505 gatgaca-agggatagatg-caac----agtggatccagtaagagagggagagacgaggggaattccacaggatgggagagaagggag----atcacaggagggtggctgt-----------------------CCGGATTAGAGCAGGG----------------TGTCAACA--------------------------------------CATCCAACT i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10873440 122 - 65312493 gatgaca-gtgggtagatg-aaac----aatggatccagtaagagagggagagaggaagggaattccacagaatcagagagaagggag----atc-----------tctgt-----------------------ctagatgagagca-tg----------------tgGTGACA--------------------------------------CATTCAACT i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59450532 130 - 64418924 tatgaca-agggatgcatg-aaat----agtgcatccagtaagag-gggggagaagaggggag-tccacaggatgggagagaaggCAG----ACCGTGTAGGGGAAGCCAT------------------------CA-ATTAGAGCAGGG----------------TGGTGACA--------------------------------------CATCCAACT i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 38646 166 + 132007 gatggggtgggggcagatg-agcc----aacggctccag-aaaaa-gggagagaggagggCCG-TGTACAGGA---GAGACGAGGAAG----GTCGTGGGAGGGGAGCCGT------------------------CAGAGTAGAGCAGGG----------------TGGTGGCGGTCCAAATGGAAGCAACACACACGTCGAGGGCTGTGCTCACCAAAAC i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58057108 133 - 61308211 gatgata-agggatagatg-aaac----agtggatccagtaagagagggagagagaaggggaa-tccacaggatgagagagaaaggca----atcacacgagggcagctgt-----------------------ccaGATTAAAACAGGG----------------TGGTGACA--------------------------------------GGTCCAACT i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14448406 154 - 17734757 gaagaca-agggctagatg-aaat----agtggatccaacaagag-agcaagagaggaggtaa-aacataggatgggaagcaagggag----atggcaggagggcagctgtgcaccaggcaagaggccacca-tcaagatgagagcagaa----------------TGGTGACA--------------------------------------CATCCAACT i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 762 156 + 4838 aaagacc-agggattcatgaaaag----agtggattcagtaaaag-aacaaaagaggaggaaa-atccacaaagaagaaagaagggag----ctctcaggagagcagcggtacaccaggcaagaggtcaacagtccagacaacagcgggG----------------TGGCGATA--------------------------------------TGTCCAGCT i dasNov2.scaffold_171027 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e pteVam1.scaffold_11245 28252 584 + 48268 M e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118774938 446 + 121843856 I a score=151707.000000 s hg19.chr17_gl000204_random 61450 25 + 81310 GCCT---------------------AGGGCTCAGACATGTAGAGGG s calJac1.Contig5139 62507 25 + 225949 GTCT---------------------AGGGCTCAGACATGTGGAGTG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 59959 25 - 95547 GCCT---------------------AGGGCTCATACATGTGGTGGG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75052689 25 + 78773432 GCCT---------------------AGGGCTCATACATGTGGTGGG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079103 25 + 17838096 GCCT---------------------AGGGCTCAGACATGTGGAGGG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 29432 25 - 64270 GCCT---------------------AGGGCTCAGACATGTAGAGGG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493015 25 + 83384210 GCCT---------------------AGGGCTCAGACATGTAGAGGG i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_27969.1-945 380 23 - 945 GGCC---------------------GGTGCCCAG-CCTGT-TAGGG i otoGar1.scaffold_27969.1-945 C 0 C 0 s cavPor3.scaffold_76 4403627 25 + 7991924 ACCC---------------------AGTACACAGACACATTGAGGG i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 32965 25 + 41507 GCCC---------------------AGTGTGCAGATGTGCTGAGGG i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 3503 25 + 4541 GTCC---------------------AGTGCACAGACCTGCTGATGG i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_106006 144904 25 + 145505 GCCC---------------------AGTACACAGACCTGCTGAGGG i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10873562 25 - 65312493 GTCC---------------------GATATATAGACCTGCTGAGAG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58057241 25 - 61308211 GTCC---------------------AGTCCACAGCCATGTTGAGGA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 38812 45 + 132007 GTCTCTGGACGCGTgaggcgcctggggggctcagtcg-gttgagag i felCat3.scaffold_206428 C 0 I 117 s canFam2.chr9 59450662 25 - 64418924 GTCT---------------------AGTACACAGACATGTTGAGGG i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_9058 3007 25 + 10968 GCTC---------------------AGGAGACAGGCATGTTGAGGG i myoLuc1.scaffold_9058 N 0 C 0 s loxAfr3.scaffold_49 14448560 25 - 17734757 GTCC---------------------AGTACACAGATATGTTGAGGG i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 918 23 + 4838 GTCC---------------------AGT--AATGACATGTTGAGGA i dasNov2.scaffold_171027 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e pteVam1.scaffold_11245 28252 584 + 48268 M e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118774938 446 + 121843856 I a score=193900.000000 s hg19.chr17_gl000204_random 61475 41 + 81310 C-----------------TGTCACTACC-----------------------------AAGATGCCTCCTGCCATTGTACCACCCTTT s calJac1.Contig5139 62532 41 + 225949 C-----------------TGTCATTACC-----------------------------AAGATGCCTCCTGCCATTGTACCAGCGCTT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 59984 41 - 95547 C-----------------TGTCATTACC-----------------------------AAGATGCCTCCTGCCATTGTGCCACCTTTT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75052714 41 + 78773432 C-----------------TGTCATTACC-----------------------------AAGATGCCTCCTGCCATTGTGCCACCTTTT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079128 41 + 17838096 C-----------------TGTCATTACC-----------------------------AAGATGCCTCCTGCCATTGTACCACCCTTT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 29457 41 - 64270 C-----------------TGTCATTACC-----------------------------AAGATGCCTCCTGCCATTGTACCACCCTTT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493040 41 + 83384210 C-----------------TGTCATTACC-----------------------------AAGATGCCTCCTGCCATTGTACCACCCTTT i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_27969.1-945 403 41 - 945 C-----------------TGTCATCACC-----------------------------AGCATGACTTCTGCCATCGTAACACCCTTT i otoGar1.scaffold_27969.1-945 C 0 C 0 s cavPor3.scaffold_76 4403652 31 + 7991924 C-----------------TGTCATCACT-----------------------------AAAATGTC-CGAGACACGGTA--------- i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 32990 31 + 41507 C-----------------TGTCGTCACC-----------------------------GAAATATC-CCTGCCGTCACA--------- i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 3528 41 + 4541 C-----------------TGTCACCACT-----------------------------AAAATACCTCCCGGTATTGCACTGCCCTTT i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_106006 144929 43 + 145505 T-----------------TGTCATCACT---------------------------AATATATACCTTCTGACATTGTACTGCCCTTT i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10873587 41 - 65312493 C-----------------TATCATCACT-----------------------------CAAATGCCTTCTGACATCATACCACCCTTT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58057266 41 - 61308211 C-----------------TGACATCACC-----------------------------AAAATGCTCTCTGCCATCATAGGACCCTCT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 38974 86 + 132007 ctgcccctccccaatttgcaccctctctctccctctctcaaaagaataaacattttaaaaaTGC-CTCTAGCATCATGCTGCCCGTT i felCat3.scaffold_206428 I 117 C 0 s canFam2.chr9 59450687 39 - 64418924 ------------------CGTCATCACC-----------------------------AAAACAC-CTCTGGCAGCCTAGTGACAGAT i canFam2.chr9 C 0 C 0 s myoLuc1.scaffold_9058 3032 41 + 10968 -----------------CTGTCAACGCC-----------------------------AAGATGCCTTCTGCCCTCGTACTGTCGTCT i myoLuc1.scaffold_9058 C 0 N 0 s loxAfr3.scaffold_49 14448585 35 - 17734757 C-----------------TGTCATCCAC-----------------------------AAGATGCC-TCTGCCT-----TGGCCTTTT i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 941 40 + 4838 C-----------------TGTCATCACC-----------------------------AAGCAGCC-TTCACCTCTGTACTGCCCTTT i dasNov2.scaffold_171027 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e pteVam1.scaffold_11245 28252 584 + 48268 M e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118774938 446 + 121843856 I a score=69170.000000 s hg19.chr17_gl000204_random 61516 31 + 81310 --------CAGTG-CCAGGTGAGCCTGGCCCCTGCTCCCC s calJac1.Contig5139 62573 30 + 225949 --------CAATG-CCAGGCGAGCCCAG-CCCTGCTCCCC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 60025 31 - 95547 --------CAGTG-CCAGGTGAGCCTGGCCCCCGCCCCAC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75052755 31 + 78773432 --------CAGTG-CCAGGTGAGCCTGGCCCCCGCCCCAC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079169 31 + 17838096 --------CAGTG-CCAGGTGAGCCTGGCCCCTGCTCCCC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 29498 31 - 64270 --------CAGTG-CCAGGTGAGCCTGGCCCCTGCTCCCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493081 31 + 83384210 --------CAGTG-CCAGGTGAGCCTGGCCCCTGCTCCCC i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_27969.1-945 444 22 - 945 --------CAAGG-CCGGGTGAACCTAGCCA--------- i otoGar1.scaffold_27969.1-945 C 0 C 0 s cavPor3.scaffold_76 4403683 12 + 7991924 -------------------TGAACCTGGCCC--------- i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 33021 7 + 41507 -------------------GGGCCCC-------------- i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 3569 31 + 4541 --------TAATG-CCAGGAGCACCTGGCCCAGGTGCTTA i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_106006 144972 29 + 145505 --------TAATG-CCAGATGCACCTG--CCAGGTTCTTA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10873628 29 - 65312493 --------TAATG-CCAGTTGCACCTG--CCAGGTTCTTA i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59450726 31 - 64418924 --------TAACG-CCAGACAAACCTGGCCCAGGTTGTAA i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 39060 31 + 132007 --------TAACT-CCAAACGCTCCCCGCCCAGGTTCAGG i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58057307 31 - 61308211 --------TAACA-CCAGATGAACCAGGCCCAGACTCTTG i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14448620 40 - 17734757 TAACCTGTCATTGCCCATATGAACCTGGCCCAGATTCTTA i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 981 40 + 4838 CAGCCTGTCATTGTTCAGATGAACCTGGCCCAGATTCTTC i dasNov2.scaffold_171027 C 0 I 439 e ochPri2.scaffold_9426 14183 4444 - 54875 I e pteVam1.scaffold_11245 28252 584 + 48268 M e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118774938 446 + 121843856 I a score=184436.000000 s hg19.chr17_gl000204_random 61547 53 + 81310 TCTG----TGCCCGGCCGGCTCGGG-CCATGTTGCAGTGGAGTGCCTGTTTTCCTTTC s calJac1.Contig5139 62603 52 + 225949 TGTG----AGCCCGGC-AGCTCAGG-CCATGTTGCAGTGGAGTGCCTGTTTGCGTCTC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 60056 53 - 95547 TCTA----TGCCTGGCCGGCTCGGG-CCATGTTGCAGTGGAGTGCCTGTTTTCTTCCC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75052786 46 + 78773432 TCTA----TGCCTGGCTGGCTCGGG-CCATGTTGCA-------GCCTGTTTTCTTCCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079200 53 + 17838096 TCTG----TGCCTGGCCGGGTTGGG-CCATGTTGCAGTAGAGTGCCTATTTTCTTCTC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 29529 53 - 64270 TCTG----TGCCCGGCCGGCTCGGG-CCATGTTGCAGTGGAGTGCCTGTTTTCCTTTC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493112 53 + 83384210 TCTG----TGCCCGGCCGGCTCGGG-CCATGTTGCAGTGGAGTGCCTGTTTTCCTTTC i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_27969.1-945 466 19 - 945 -----------------GGCTC--------------------TGTCTGTT--CCCCTA i otoGar1.scaffold_27969.1-945 C 0 C 0 s cavPor3.scaffold_76 4403695 30 + 7991924 ----------------------------AGGCTGAGATGGAGTTCCCACTCCCCTGTC i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 33028 16 + 41507 ------------------------------------------TTCCTGCATTCCTCTC i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 3600 37 + 4541 TCTG----TACTCGGCCTCCTTGGG-CCAGGTCCTGATGGAG---------------- i vicPac1.scaffold_56870 C 0 I 8 s turTru1.scaffold_106006 145001 53 + 145505 TCTG----TACTTGGCCTGCTTGGG-CCAGGTCCTGATGGAGTTCCAGCTCTCCTCTG i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10873657 54 - 65312493 TCCG----TACTTGGCCTGTACAGGTCCAGGTCCTGATAGAGTTTCAGCTCTCCTCTG i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59450757 57 - 64418924 TCTGTACCTTCCTGGCCTGCGTGGG-CCAAGTCCTGATGGAGTGCCTCCTTTCTTCTC i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 39091 53 + 132007 TCTG----TCCCTGGCCTGCCTGGG-CCAGGTCCTGATGGGGCCCCTGCTCTCCTGTC i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58057338 53 - 61308211 CCTG----TACTTGGTCTGCTCAGC-CCAGGTTCTGATGGAGTTCCTGCTCTCCTCTC i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14448660 53 - 17734757 TCTT----TACCTGGCCTTCTTGGG-CCAGATTCTGATGGATTTCTTGCTCTCTTCTC i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 1460 53 + 4838 TCTG----TGCTTGGCCTGTTCAGC-CCAGGTTCTGATGGACTTCCTGCTCTCTTCCC i dasNov2.scaffold_171027 I 439 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e pteVam1.scaffold_11245 28252 584 + 48268 M e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118774938 446 + 121843856 I a score=431033.000000 s hg19.chr17_gl000204_random 61600 155 + 81310 CACGCACT-GC-CACCTGTGTA----AGCTGAAGACCCTCATTTCGCCCCATGGAAGCATTT-ACTT----TGATCCACTCTTA-GCATCAGGA-GGTG----------GCCACA-GGGAACAAAGAAACAGAAAACACACATCAGC-------------------CCACCAA--CCT--GCAA--------GAAGCCCCAGCCAAGGAG s calJac1.Contig5139 62655 155 + 225949 CACGCACT-GC-CACCTGTGTA----AGCTAAAGACCCTCATTTCATGCCACAGAAGCACCT-ACTT----TGATCTACTCTTA-GCAACAGGA-GGCA----------GTCATG-GAGAGCAAAGAGACAGAAAACACACGTGAGC-------------------CCACCAA--CCC--GCCA--------GATGTCCCAGGCAAGGAG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 60109 155 - 95547 CATGCACT-GC-CACCTGTGCA----AGCTGAAGACCCTCATTTCGCCCCACAGAAGCATTT-ACTT----TGATCTATTCTTA-GCAACAGGA-AGTG----------GCCACT-GGGAGCAAAGAAGCAGAAAACATCCATCAGC-------------------CCACCAA--CCG--GCCA--------GAAGCCCCAGCCGAGGAG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75052832 165 + 78773432 CATGCACT-GC-CACCTGTGTA----AGCTGAAGACCCTCATTTCGCCCCACAGAAGCATTT-ACTT----TGATCTACTCTTA-GCAGCAGGA-AGTGGCCACTGGGAGCCACC-GGGAGCAAAGAAGCAGAAAACATCCATCAGC-------------------CCACCAA--CCG--GCCA--------GAAGCCCCAGCCGAGGAG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079253 155 + 17838096 CACGCACT-GC-CACCTGTGTA----AGCTGAAGACCCTCATTTCGTCTCCCAGAAGCATTT-ACTT----TGATCTAGTCTTA-GCAACAGGA-GGTG----------GCCACA-GAGAAGAAAGAAATAGAAAACACACATCAGC-------------------CCACCAA--CCT--GCCA--------GAAGCCCCAGCCAAGGAG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 29582 155 - 64270 CACACACT-GC-CACCTGTGTA----AGCTGAAGACCCTCATTTCGCCCCACAGAAGCATTT-ACTT----TGATCTACTCTTA-GCAACAGGA-GGTG----------GCCACA-GGGAACAAAGAAACAGAAAACACACATCAGC-------------------CCACCAA--CCT--GCAA--------GAAGCCCCAGCCGAGGAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493165 155 + 83384210 CACGCACT-GC-CACCTGTGTA----AGCTGAAGACCCTCATTTCGCCCCACAGAAGCATTT-ACTT----TGATCTACTCTTA-GCAACAGGA-GGTG----------GCCACA-GGGAACAAAGAAACAGAAAACACACATCAGC-------------------CCACCAA--CCT--GCAA--------GAAGCCCCAGCCGAGGAG i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_27969.1-945 485 156 - 945 CAGGCATC-AC-CACTCGTGCA----CACTGAAGACACTGGCGTCACCCCTCAGAAGGGTCCAACTT----TGACCTACTCTTAGGTAACAGGAGGGTG----------GCCATG-GGGCACTCA-AAACAGAAAACAGAAGTCTGC-------------------AC-CCAG--CCT--GCCC--------CACCTCCCAGCCAAGAAG i otoGar1.scaffold_27969.1-945 C 0 n 0 s cavPor3.scaffold_76 4403725 154 + 7991924 TG----CA-GCACCACGGGATA----AGCTA--AACATGCATTTCAGCCCTTGGAATTATCTTACCT----TACTCTAATCATA-G-AAAGGGA-AGGA----------GCTCCC-TGTGACTGGGAACTAAAAGACAG--ATCAGC-------------------TGCTCAC--TCC--ATCACCAGACTGGACACCCTGGCTGGGG-- i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 33044 106 + 41507 TGGGTACA-GC-CACCGGTACA----GGCTG-CAGCCCTCGTCCCACCCCTCAGAAGTGT-------------------------------------------------GCTTTC-T------------TAGAAGGCTG--ATGGGT-------------------CAAACAA--GCC--ACCA--------GGCACCCCGGCTGGGG-- i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10873711 167 - 65312493 CAAGCA-T-GG-CACCAGTATA----AGCTGAAGACATTCATTTCCCCCATCAGAAGTGTGC---TA----TTTTGTTTTCTTA-GAAATAGAAGGATG----------GCCATG-GTTAGCTAAGAAACATAAAATTCAGATCCGTCTATTTCTCCATCC-----CCACCAA--TCT--ACCA--------GACATCCCAGCTGGGGAT i bosTau4.chr19 C 0 I 1 s turTru1.scaffold_106006 145054 168 + 145505 CATGCACT-GG-CACCTGTATA----AGCTGAAGACACTCATTTTCCCCATCAGAAGTGTCC---TA----TTTTGTTTTCTTA-GAAACAGGAGGATG----------GCCATA-GTGAGCTAAGAAACAGACAATTCAGATAGGTCTATTCCCCCACCC-----CCACCAA--CCT--GCCA--------GACATCCCAGCTGGGGAT i turTru1.scaffold_106006 C 0 I 1 s equCab2.chr11 58057391 151 - 61308211 CCTGTGCT-GC-CACCTGGATA-----------AGCGCTCATTTGACCCTTAGAA--CTGCC---CTCCTTTGTTCTACTCCCA-GACATGGGAGGGTG----------GCCATG-GTGAACTCCGAAACAGAAAAGGCACATCAGCCTACAC-------------------A--CCCAAGGCA--------GACATCTTAGCTGGGGGA i equCab2.chr11 C 0 I 1 s felCat3.scaffold_206428 39144 147 + 132007 CAAGCTCT-GC-CACCTGTATG----AGCTGAAGGCACTCGTTTCATCCCTCGG-----------------TAGTGACCTCTTA-GAAACAGGAGGGTG----------GCCCCG-GT-------GAGGCAGAAAATGCAGATCAGCCTATCCTCCC---------CCTCCAA--CCT--GCTG--------GACACCCCATCTGGGGTG i felCat3.scaffold_206428 C 0 I 1 s canFam2.chr9 59450814 105 - 64418924 CATGCACT-GC-CACCTGTATGTATAAGCTGAAGACACTCATTTCCCCCCTCAGA--CAAC----------ACATGTCCTCTTA-GGAACAGGAGGGCG----------GCC-------------------------------CAGCC------------------------A--CCT--GCCA--------GACAT------------- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 28838 168 + 48268 CGTGTGCT-GC-CACCTAGGTA----AGCTGAAGACACGCATTTCACTCTTCCGAGGTATC----------CTTTGTCCTCTTA---AACAGGAAGATG----------GCCATG-CAGAGCTGAGAAGCAGAAAATGCAAGTCGGCCTACTCCCCCAACCACCCACCACCAC--CCT--ACCA--------GGCGTCTCTGATGGGGTA i pteVam1.scaffold_11245 M 584 I 1 s loxAfr3.scaffold_49 14448713 158 - 17734757 CATACACT-TC-CACTTGGTTA----CACTAAAGACGCTTATTTCACCCCTCAGAAGTGTTCTACCT----TGATATCCTTTTA-GAAACAGGACAGTG----------GCCATG-GTGAGCTAAGAAGCAGAAAATACAGATCAGCCTGCT--------------CCCTCATGACCT--GCT---------GATGCCCCACAAG----- i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 1513 139 + 4838 CAC-CACTGTC-CCCTGGGATA--------------GCCTGTTTCACCCATGGGAAGTGTTCAACTT----TCATCTACTCTTA-GAGACAAGAGCATG----------GCCATGTGGAAGCTAGAAAACAGAAGATA-AGATCAGTCCACT--------------CTCCCAT--CCT--A----------------TCCAACGG----- i dasNov2.scaffold_171027 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 3637 8 + 4541 I e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118774938 446 + 121843856 I a score=165730.000000 s hg19.chr17_gl000204_random 61755 53 + 81310 GCCCTTGGTT-CCCCAGG-A-CCCCTCATGCCTTGCCCAA-GAACTCCCTAAAAGAG s calJac1.Contig5139 62810 53 + 225949 GCCCTTGGCT-CCCTAGG-A-GCCCTCATGCCTTGCTCAC-GAGCTCCCTAAAAGAG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 60264 54 - 95547 GCCCTCGGTT-CCCCAGGCA-CCCCTCATGCCTTGCCCAT-GAGCTCCCTAAAAGAG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75052997 54 + 78773432 GCCCTTGGTT-CCCCAGGCA-CCCCTCATGCCTTGCCCAT-GAGCTCCCTAAAAGAG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079408 53 + 17838096 GCCGTTGGTT-CCCCAGG-T-CCCCTCATGCCTTGCCCAC-GAACTCCCTAAAAGAG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 29737 53 - 64270 GCCCTTGGTT-CCCCAGG-A-CCCCTCATGCCTTGCCCAC-GAACTCCCTAAAAGAG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493320 51 + 83384210 GCCCTTGGTT-CCCCAGG-A-CCCCTCATGCCTTGCCCAC-GAACTCCCTAAAGG-- i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4403879 46 + 7991924 --TCTCTTTT-CCCCAGG-T-CCCCTCATGCCCTGCTTAC-----TCCCAAAAGG-G i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 33150 49 + 41507 --CCGTCCAT-CCCCAGG-GACACCCTGTGCCTTGCTCAT-TG--TCCCTCCAAG-G i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10873879 51 - 65312493 GACCT--GTT-TCCCAGGCA-GC-CCCATGACCTTGCCAA-GAGCTTTCTAGAACAG i bosTau4.chr19 I 1 I 49 s turTru1.scaffold_106006 145223 54 + 145505 GCCCTCAGTT-CCCCAGGAA-ATGTCCATGGCCTTGCCAA-GAGCCTCTTAGAACAG i turTru1.scaffold_106006 I 1 I 49 s equCab2.chr11 58057543 54 - 61308211 ATCCTCAGGC-CCCCAGGAA-GCCCTCGAGGTCTGGCCAA-GAGCCTGGTAGAACAG i equCab2.chr11 I 1 I 58 s felCat3.scaffold_206428 39292 54 + 132007 GCCCTCCGTC-CCCCGGGAA-GCCCTCGCGGCCTTGCCAA-GAGCCTCCTAGAACAG i felCat3.scaffold_206428 I 1 I 34 s canFam2.chr9 59450919 54 - 64418924 -CCCTCTGTTAACACAGGAA-GCTCTTGTGGCCTCGCCAA-GAGCCTCCCAGACCAG i canFam2.chr9 C 0 I 49 s pteVam1.scaffold_11245 29007 54 + 48268 GTCCCCGGTT-CCCCAGGGA-GCCCTCACGGCCTTGCTAA-GAGCCTCCTAGAACAG i pteVam1.scaffold_11245 I 1 I 47 s loxAfr3.scaffold_49 14448871 39 - 17734757 GCCCTCAGTTCCCCCAGAAA-CTTCTCATGGCCTTGCCTA----------------- i loxAfr3.scaffold_49 C 0 I 435 s dasNov2.scaffold_171027 1652 45 + 4838 CCCATCAGC--------GGA-TCTCTCATAGTCATGTCACTGGAGTCCCTAAAA--- i dasNov2.scaffold_171027 C 0 M 1984 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 3637 8 + 4541 I e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118774938 446 + 121843856 I a score=57071.000000 s hg19.chr17_gl000204_random 61808 27 + 81310 GCTCTTGTAAAGCGTGG---GGCAGCTGCG s calJac1.Contig5139 62863 27 + 225949 GCTCTTGTAAAGTGTGG---GGCAGCTGTG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 60318 27 - 95547 GCTCTTGTAAAGCGTGG---GGCAGCTGCA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75053051 27 + 78773432 GCTTTTGTAAAGCGTGG---GGCAGCTGCA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079461 27 + 17838096 GCTCTTGTAAAGCGTGG---GGCAGCTGCG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 29790 27 - 64270 GCTCTTGTAAAGCGTGG---GGCAGCTGTG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493371 27 + 83384210 GCTCTTGTAAAGCGTGG---GGCAGCTGCG i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4403925 27 + 7991924 ATTCTTGAAAATTGCTA---AGCAACTGAG i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 33199 26 + 41507 GCTCTC----ATTGCTGTCTGTCCGCCGAG i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10873979 27 - 65312493 GCTCGAGTAAACTCCCA---GGCAGCTGAG i bosTau4.chr19 I 49 I 13 s turTru1.scaffold_106006 145326 26 + 145505 ACTCTAGTAAACTCTCA----GCAGCTGAC i turTru1.scaffold_106006 I 49 I 12 s canFam2.chr9 59451022 16 - 64418924 GCTCTTATAAGCT--CA----G-------- i canFam2.chr9 I 49 I 7 s felCat3.scaffold_206428 39380 22 + 132007 GCTCTTATAAACT--CA----GC--CCGAG i felCat3.scaffold_206428 I 34 I 12 s pteVam1.scaffold_11245 29108 23 + 48268 GCTCTCGTAAACTC-CA----GA--CTGAG i pteVam1.scaffold_11245 I 47 I 12 s loxAfr3.scaffold_49 14449345 27 - 17734757 TCTCTTGTAAACTCTTG---GGCAGCTGAA i loxAfr3.scaffold_49 I 435 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 3637 8 + 4541 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e equCab2.chr11 58057597 58 - 61308211 I e mm9.chr11 118774938 446 + 121843856 I a score=95037.000000 s hg19.chr17_gl000204_random 61835 43 + 81310 -----------GTTCCAGA--GT---TTCACATTCTCTT-----CTCCCAGGCTCCTCCGTCTA s calJac1.Contig5139 62890 43 + 225949 -----------GTCCCAGA--CT---TTCACCTTCTCTT-----CTCCCAGGCTCCTCCATCTA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 60345 43 - 95547 -----------GTTCCAGA--CT---TTTGCCTTCTCTC-----CTCCCAGGCTCCTCTGTCTA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75053078 43 + 78773432 -----------GTTCCAGA--CT---TTTGCGTTCTCTT-----CTCCCAGGCTCCTCCGTCTA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079488 43 + 17838096 -----------GTTCCAGA--CT---TTCACATTCTCTT-----CTCCCAGGCTCCTCCGTCTA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 29817 43 - 64270 -----------GTTCCAGA--GT---TTCACATTCTCTT-----CTCCCAGGCTCCTCCGTCTA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493398 43 + 83384210 -----------GTTCCAGA--GT---TTCACATTCTTTT-----CTCCCAGGCTCCTCCGTCTA i panTro2.chr17 C 0 C 0 s mm9.chr11 118775384 45 + 121843856 -----------GCCCCAGATCTT---TCCTTCCTGTCTT-----CTACCAGGCTTCTCCATCAA i mm9.chr11 I 446 C 0 s cavPor3.scaffold_76 4403952 34 + 7991924 -----------GCCTGAGA-CTT---TCCCCTTTGTCCC-----CTCCCAGGCC---------- i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 33225 23 + 41507 ---------------------GT---CCATGGCTGCCTC-----CATCTGAG------------ i oryCun2.chrUn0958 C 0 C 0 s bosTau4.chr19 10874019 39 - 65312493 -----------CCCCAAGA--CT--CTT-CTCTTCTCTT-----CTCCCAGGCTTCTGTG---- i bosTau4.chr19 I 13 C 0 s turTru1.scaffold_106006 145364 44 + 145505 -----------CCCCAAGA--CT--ATTCCTCTTCTCTT-----CTCCCAGGCTCTTCCATCTA i turTru1.scaffold_106006 I 12 C 0 s canFam2.chr9 59451045 48 - 64418924 -----------CCCCAAAA--CT--ATTTAACTTGTCTTCCCTTCTCCTAGAC-CCTCCATCCG i canFam2.chr9 I 7 C 0 s felCat3.scaffold_206428 39414 47 + 132007 -----------CCCCCAAA--CC--ACTCCCCTTGTCTT-CTTTCTCCCCGAC-CCTCCATCCC i felCat3.scaffold_206428 I 12 C 0 s pteVam1.scaffold_11245 29143 43 + 48268 -----------CACCGAGA--CC--ACCCACCCTGTCAT-----CCCCAGGGT-CCTCTAGCCA i pteVam1.scaffold_11245 I 12 C 0 s loxAfr3.scaffold_49 14449372 57 - 17734757 GCCAGGCCGTGACTGGAGA--CTCTGTCCACCTTGTCTT-----CTTTCAGGCTCCTCCATCTC i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 3637 8 + 4541 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e equCab2.chr11 58057597 58 - 61308211 I a score=114179.000000 s hg19.chr17_gl000204_random 61878 57 + 81310 AGGGTAGCAGACCCAAATCATCACAGACAGAAAGGACATCATGGCC---CCA---------------CTTTCATA s calJac1.Contig5139 62933 51 + 225949 AGGGTAGCAGCCCCAAATCATCACGGACAGA------ATCGTGGCC---CCA---------------CTTTCATA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 60388 57 - 95547 AGGGTAGCAGCCCCAAATCATCACAGACAGAAAGGACATCATGGCC---CCA---------------CTTTCATA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75053121 57 + 78773432 AGGGTAGCAGCCCCAAATCATCACAGACAGAAAGGACATCATGGCC---CCA---------------CTTTCATA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079531 57 + 17838096 AGGGTAGCAGACCCAAATCATCACAGACAGAAAGGACATCATGGCC---CCA---------------CTTTCATA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 29860 57 - 64270 AGGGTAGCAGACCCAAATCATCACAGACAGAAAGGACATCATGGCC---CCA---------------CTTTCATA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493441 57 + 83384210 AGGGTAGCAGACCCAAATCATCACAGACAGAAAGGACATCATGGCC---CCA---------------CTTTCATA i panTro2.chr17 C 0 C 0 s mm9.chr11 118775429 40 + 121843856 TGAGTAGCAGCTCAAAGGGGT--------GC---------GTGGCT---CCA---------------TTTTTACA i mm9.chr11 C 0 I 584 s cavPor3.scaffold_76 4403986 28 + 7991924 --AGAAGGACACCGGAGGA------------------------------CCA---------------TTTCTGTG i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 33248 59 + 41507 --AGCCGTAGCCCAAAGCAACCCCGGACAGA---------AAGACC---CCAGCCCCCAGCCCGGGTTTTCTC-- i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 3645 57 + 4541 AGAGCAGCAGCCCAAAGGAGCCACGGACAGGGAGGATCCCGTGGCT---AGC---------------TCTTCACA i vicPac1.scaffold_56870 I 8 C 0 s turTru1.scaffold_106006 145408 54 + 145505 -CAGTAGCAACCCAAAGTAG-CACAAACAGAAAGGATACCAT-GCT---AGT---------------TCTCTATA i turTru1.scaffold_106006 C 0 C 0 s bosTau4.chr19 10874058 55 - 65312493 --AGTAGCAGCCCAAAGTGGCCCCAAACAGAAAGGATGTCATGGCT---AGC---------------TCTCTATG i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59451093 54 - 64418924 AGATGAGCAG-CCTGAAAAGCCACAG-CAGAAAGG-CACCGTGGCT---AGG---------------TCTTTATG i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 39461 51 + 132007 AGACCAACAG-CTGAAGCGGCCACGG-CAGAAAGGACACCGTGGC----------------------CCTTTAGA i felCat3.scaffold_206428 C 0 C 0 s pteVam1.scaffold_11245 29186 46 + 48268 AGCCCCACA--------CAGCCACAG--ACAGAGGACGCTGCGGCT---GGC---------------TCTTCAC- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14449429 58 - 17734757 AGGGTGGCAG-CCAAATTAGCCAC-GACAGGAAGGACACCACAGCCTCTCAG---------------CTCTTAGA i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e equCab2.chr11 58057597 58 - 61308211 I a score=89315.000000 s hg19.chr17_gl000204_random 61935 54 + 81310 TTCAGCACTGGACACATCCACAGATAGAAAGG-AGGTGAAGATGCAACTGTAGA---A s calJac1.Contig5139 62984 54 + 225949 TTCAGCACTGGACACGTCCACGGATAGGAAGG-AGGTGAAGGTCCAGCTGCAGA---A i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 60445 54 - 95547 CTCAGCACTGGACACATCCACGGATAGGAAGG-AGGTGAAGATGCAGCTGTAGA---A i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75053178 54 + 78773432 TTCAGCACTGGACACATCCACGGATAGGAAGG-AGGTGAAGATGCAGCTGTAGA---A i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079588 54 + 17838096 TTCAGCACTGGACACATCCACAGATAGAAAGG-AGGTGAAGATGCAACTGTAGA---A i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 29917 54 - 64270 TTCAGCACTGGACACATCCACAGATAGAAAGG-AGGTGAAGATGCAACTGTAGA---A i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493498 54 + 83384210 TTCAGCACTGGACACATCCACAGATAGAAAGG-AGGTGAAGATGCAACTGTAGA---A i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4404014 51 + 7991924 TCCATCACCTTGCACATTCACTCCTAGG--GA-AGTCAGTGGTG----TATAGAAGTA i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 33307 47 + 41507 TTAGCCACTGCGCTCCTGCGCTTGTGTG--GA-AGTTGATGATG-----ACAAA---A i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 3702 43 + 4541 CTCGTCACCTTGTACA-----------TGAGT-AGATGATGATCCAACATTACG---A i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_106006 145462 42 + 145505 TT-ATCACCTTGCACA-----------TAAGT-AGATGATGATAAAACAATAAA---A i turTru1.scaffold_106006 C 0 N 0 s bosTau4.chr19 10874113 40 - 65312493 TTAATCAGCTTGCACA-----------TA----AGACGACGCTAAAACAGTAAT---A i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59451147 42 - 64418924 GTGAGCATCTTGCAC------------TAAGG-AGGTGCTCACACAACAGCGAA---A i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 39512 28 + 132007 GCGACCACTTCGCACG-----------GAAGG-AGG---------------GAA---G i felCat3.scaffold_206428 C 0 C 0 s pteVam1.scaffold_11245 29232 41 + 48268 -CGGTCACCCTGCAC------------GTAGG-CAATGACGACGCAACGATGAA---A i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14449487 54 - 17734757 -GCATCACCTTGCGTGTCCACTTATATAAAGGTAGATGGTGATACAACAGAAAA---A i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e equCab2.chr11 58057597 58 - 61308211 I e mm9.chr11 118775469 584 + 121843856 I a score=690.000000 s hg19.chr17_gl000204_random 61989 54 + 81310 GGATC------------------GAGGAAA-GCAAGAGATCAGGGGCCT-----GCTTTTTCCTT-------GCTGGTCTTTGAC s calJac1.Contig5139 63038 45 + 225949 GAGTC------------------GAAGAAA-GC---------GGGGCCT-----GCTTTTCCCTT-------GCTGGACGTGGGT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 60499 54 - 95547 GGATC------------------GAGGAAA-GCAAGAGATCAGGGGCCT-----GCTTTTTCCTT-------GCTGGTCTTTGAT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75053232 54 + 78773432 GGATC------------------GAGGAAA-GCAAGAGATCAGGGGCCT-----GCTTTTTCCTT-------GCTGGTCTTTGAT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079642 54 + 17838096 GGATC------------------GAGGAAA-GCAAGAGATCAGGGGCCT-----GCTTTTTCCTT-------GCTGGTCTTTGAT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 29971 54 - 64270 GGATC------------------GAGGAAA-GCAAGAGATCAGGGGCCT-----GCTTTTTCCTT-------GCTGGTCTTTGAC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493552 54 + 83384210 GGATC------------------GAGGAAA-GCAAGAGATCAGGGGCCT-----GCTTTTTCCTT-------GCTGGTCTTTGAC i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4404065 69 + 7991924 GGATCTCCAGCAATATAGTG-TTAAGGAAA-ACCCAATCTAAGGGGC-------ATCTTTCCCAT-------CATCAGCTTTCAA i cavPor3.scaffold_76 C 0 I 1 s oryCun2.chrUn0958 33354 25 + 41507 TGCTCTCC-----------------------------------------------CCATGTCCAT-------CCTGAGT------ i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 3745 41 + 4541 ------------------TGTTTGAGGAAA-ACACGGTCTGAAGGGACT-----TCTTTGTCCTT-------------------- i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_98008 4850 41 + 223990 ------------------TGTTTGAGGAAA-ACACAATCTAAGGGGCCT-----TCTTTGTCCTT-------------------- i turTru1.scaffold_98008 N 0 C 0 s bosTau4.chr19 10874153 40 - 65312493 ------------------TGTTTGAAGAAA-ACACAGTCCAAGGGA-CT-----TCTTTGTCCCT-------------------- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59451189 47 - 64418924 ------------------TGTGGGAGAAAAGACAGAA----GAGGA-CT--TTCTGCGTGCCCTTTCTCCAT------------- i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 39540 52 + 132007 ------------------GGTGGGAGGAAA-ACAGGGTGTCGGGGA-CTTCTTTTCCTTGTCGGTCTTTCAT------------- i felCat3.scaffold_206428 C 0 C 0 s pteVam1.scaffold_11245 29273 39 + 48268 ------------------TG-AGGAGGAAA-ACAAGTCATCCGGGA-CT-----TTCCTGTCCTT-------------------- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14449541 53 - 17734757 ------------------TATTTGAGGAAA-ACAAGATGCAGAGAA-CT-----TCTTTTTCCCT-------GTCAACCCTTAAT i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e equCab2.chr11 58057597 58 - 61308211 I e mm9.chr11 118775469 584 + 121843856 I a score=174347.000000 s hg19.chr17_gl000204_random 62043 91 + 81310 GTTCTTGTGAGGTCCACAGATGGCCAGCACCGACGGCCCGTTGGAGAGCTGATGTCACCGC-------------------CATTG----GCTGCCTTG-------CTTGCTCTCTCAGTCC s calJac1.Contig5139 63083 90 + 225949 GTTCTTGTGAGGTCCACACACAGCCGGCACTGACGGCCTGTTGGAGAGCCGATGTCACC-C-------------------CATCA----GCGGCTTCG-------CTTGCTCTCTCAGCCC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 60553 91 - 95547 GTTCTTGTGAGGTCCGCAGATGGCCAGCACTGACGGCGTGTTGGAGAGCTGATGTCACTGC-------------------CATTG----GCTGCCTCA-------TTTGCTCTCTCAGTCC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75053286 91 + 78773432 GTTCTTGTGAGGTCCGCAGATGGCCAGCACTGACGGCGTGTTGGAGAGCTGATGTCACTGC-------------------CATTG----GCTGCCTCA-------TTTGCTCTCTCAGTCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079696 91 + 17838096 GTTCTTGTGAGGTCCACAGATGGCCAGCACCAACGGCCCATTGGAGAGCTGATGTCACTGC-------------------CATTG----GCTGCCTTG-------CTTGCTCTCTCAGTCC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 30025 91 - 64270 GTTCTTGTGAGGTCCACAGATGGCCAGCACCGACGGCCCGTTGGAGAGCTGATGTCACCGC-------------------CATTG----GCTGCCTTG-------CTTGCTCTCTCAGTCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493606 91 + 83384210 GTTCTTGTGAGGTCCACAGATGGCCAGCACCGACGGCCCGTTGGAGAGCTGATGTCACCGC-------------------CATTG----GCTGCCTTG-------CTTGCTCTCTCAGTCC i panTro2.chr17 C 0 C 0 s mm9.chr11 118776053 92 + 121843856 GCCTTTATTAGGCTCATAGGTGTTCTGCACTCCAGGCT-------GAGCTTATGCTACAGCATGGCGCCCAACAG-----CCTCG----GCTGCCTTG------------TCATCCAGCA- i mm9.chr11 I 584 C 0 s cavPor3.scaffold_76 4404135 102 + 7991924 ------GTTAGGGTCAGTAGT-------ACTGCAGGCT-ACTGCAGAGTCGATGTTATA-CCTGGTACTCAGttggtttattttg----tttgatttgatttgatttgatttTTGCAGTAC i cavPor3.scaffold_76 I 1 C 0 s oryCun2.chrUn0958 33379 80 + 41507 GCCCTGGTTAGCCCCATAGATGACCAGTCCTATGGGCT----TTGGAGGCCTTGT-----CTTAGTGCCCG--------------------TGCCTGG------------TCTTTGAACCC i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 3786 74 + 4541 ------GTCAGTCTTCC---TGACCAGC--TGGT--------GGAGAGCATACTTTACAGC-------------------CATTACC--GCTTCCCTG-------TTTGGTCTTTCAATCC i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_98008 4891 85 + 223990 ------GTCAGTCTTTC--ATGACCAGC--TGGTGGACTGTTGGAGAGTGTACTTTACACC-------------------CATTGCTGGGCTTCTTTG-------TTTGGTCTTTTAATCC i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10874193 85 - 65312493 ------GTCGGTCTTTT--ATGACCAGC--TGGTGGGCTATGGGAGAGTGTACTTTACATC-------------------TATTAGCAGGCTTCCTTG-------TCTGGTCATTTAATCC i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59451236 92 - 64418924 GATCCTGTTAGGTCCACAGATGACCAGC--AGGTGTACCGGTGGGAAGTGCATTTTACA-T-------------------GGTTACCGGGCCTCCTTG-------TTTGGTCTCTCAATCC i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 39592 80 + 132007 GACCTTGTCAGAGCCGCAGATGACCAGC--TGGCGTGCTGGTGGAGCCT--------------------------------GTCACCGGGCTTCCTGG-------GTGAGTCTTTTCATCC i felCat3.scaffold_206428 C 0 C 0 s pteVam1.scaffold_11245 29312 88 + 48268 --TCAGGCGAGGTCCAC--ACGGCCAGC---GGTGGGCTCCCAGGGAGCGTATCTGACACT-------------------CATTACTGGGCTTCTTCG-------TTTGATCTTTTAACCC i pteVam1.scaffold_11245 C 0 I 370 s loxAfr3.scaffold_49 14449594 93 - 17734757 GTTCTTGTCAGGTCCCTAGATGACAAG-ACTGATGAGCT-CTGGAGGGCTTATTTCATGCC-------------------CACGACTGGACTGCCCTG-------TGTAGTCTCCTAATCC i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e equCab2.chr11 58057597 58 - 61308211 I a score=182003.000000 s hg19.chr17_gl000204_random 62134 31 + 81310 AACAGAGTAAATTATAAGGTTACTCTATGTA s calJac1.Contig5139 63173 31 + 225949 AACAGAGTCAATTATAAGGTTACTCAATACA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 60644 31 - 95547 AAGAGAGTAAATTATAAGGTTATTAAATGCA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75053377 31 + 78773432 AAGAGGGTAAATTATAAGGTTATTCAATGCA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079787 31 + 17838096 AACAGAGTAAATTATAAGGTTACTCTATGCA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 30116 31 - 64270 AACAGAGTAAATTATAAGGTTACTCTATGTA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493697 31 + 83384210 AACAGAGAAAATTATAAGGTTACTCTATGTA i panTro2.chr17 C 0 C 0 s mm9.chr11 118776145 27 + 121843856 --GAGAGCAGTC--CAAAGTTGCTTGACACA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4404237 30 + 7991924 TGGGGATTAAAC-ACAGGACTATCTCACCTA i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 33459 31 + 41507 AAAGGAGTGAATTATAGGATGACCTAATGCA i oryCun2.chrUn0958 C 0 C 0 s vicPac1.scaffold_56870 3860 31 + 4541 AACAGAGTAAATTATAAAATTACTTAGGGCA i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_98008 4976 31 + 223990 AACAGAGTAAATTAGAAGGTTACTCAATGCA i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10874278 23 - 65312493 AACAG--------AGAAGGTTACTTAATGCA i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59451328 31 - 64418924 AATAGAGTAAATTCTAAGGCTACTTAATGCA i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 39672 31 + 132007 AGCGGAGCAAATGGTAAGGCCACTTAAGGCA i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58057655 31 - 61308211 AACAGAGTAAATTACAAGTTTACTTAATGCA i equCab2.chr11 I 58 C 0 s loxAfr3.scaffold_49 14449687 31 - 17734757 AGCAGAGTAAATTATAAACTTACTTAATAAA i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e pteVam1.scaffold_11245 29400 370 + 48268 I e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I a score=71388.000000 s hg19.chr17_gl000204_random 62165 62 + 81310 GTCGTAACCTCCTTGTTAAGAATGGATCTCTCggccgggcacggtggctcacacctgtattc s calJac1.Contig5139 63204 62 + 225949 GCTGCAACCTCCTTGTTAAGACTGGATCACTTggccaggctcggttgctcacgcctgtaatc i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 60675 62 - 95547 ATCGTAACCTCCTTGTTAAGAATGGATCTCTTggccaggcacggtggctcatgcctgtaatc i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75053408 62 + 78773432 ATCGTAACCTCCTTGTTAAGAATGGATCTCTTggccaggcacggtggctcatgcctgtaatc i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079818 62 + 17838096 GTCGTAACCTCCTTGTTAAGAACAGATCTCTCagccgggcacggtggctcacacctgtattc i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 30147 38 - 64270 GTCGTAACCTCCTTGTTAAGAATGGATCTCTCGGCCgg------------------------ i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493728 62 + 83384210 GTCGTAACCTCCTTGTTAAAAATGGATCTCTCggccgggcacggtggctcatgcctgtattc i panTro2.chr17 C 0 C 0 s mm9.chr11 118776172 33 + 121843856 GTTATAAACTCAGAGAGGCGAATGGACCCCTAG----------------------------- i mm9.chr11 C 0 I 1 s cavPor3.scaffold_76 4404267 5 + 7991924 GCTGT--------------------------------------------------------- i cavPor3.scaffold_76 C 0 I 198 s oryCun2.chrUn0958 33490 10 + 41507 GTCATAATCT---------------------------------------------------- i oryCun2.chrUn0958 C 0 I 978 s vicPac1.scaffold_56870 3891 20 + 4541 GTGAGAACCTCCTTGCCAGG------------------------------------------ i vicPac1.scaffold_56870 C 0 I 10 s turTru1.scaffold_98008 5007 32 + 223990 GTCATAACCTCCTTGCTAAGAATGGATCTTTC------------------------------ i turTru1.scaffold_98008 C 0 I 3 s bosTau4.chr19 10874301 32 - 65312493 GTCATAACCTCCTTGCTAAGAATAAATATTTC------------------------------ i bosTau4.chr19 C 0 I 692 s equCab2.chr11 58057686 16 - 61308211 -TCATAACCTCCCTGCT--------------------------------------------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 39703 18 + 132007 ACGATAACTTCCTTGCTA-------------------------------------------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59451359 29 - 64418924 GTCCTAACTTCCTTGTTAA-AATGACTCTT-------------------------------- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 29770 30 + 48268 GTCACAACCTCCTTGTCAAGAATGGATGTC-------------------------------- i pteVam1.scaffold_11245 I 370 I 73 s loxAfr3.scaffold_49 14449718 34 - 17734757 GCTCTAACCTCCTAGTTAAGGATGGATCTCTCTG---------------------------- i loxAfr3.scaffold_49 C 0 I 278 e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I a score=113874.000000 s hg19.chr17_gl000204_random 62227 87 + 81310 ctagcactttgggaggccgaggcaggtggaccacctgaggtcaggagctcaagaccagcctggccaacatggcgaaaccccctctct s panTro2.chr17 79493790 87 + 83384210 ctagcactttgggaggccgaggcaggtggaccacctgaggtcaggagctcaagaccagcctggccaacatggcgaaaccccctctct i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 30185 41 - 64270 ----------------------------------------------gctcaagaccagcctggccaacatggcgaaaccccctctct i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16079880 87 + 17838096 ctagcactttgggaggccgaggcgggcagcccacctgaggtcaggagctcaagaccagcctggccaacatggtgaaaccccctctct i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75053470 87 + 78773432 ctagcacttggggaggccaaggcaggtggatcacctgaggtcaggagttcaagaccagcctggtcaacatggcgaaaccccctctct i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 60737 87 - 95547 ctagcacttcgggaggccaaggcaggtggatcacctgaggtcaggagttcaagatcagcctggtcaacatggcgaaaccccctctct i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 63266 86 + 225949 acagcaatttgggaggccgaggcaggcagatcatctgaggtcaggagttcaagaccagcctggccaacataacgaaa-cccctctct i calJac1.Contig5139 C 0 C 0 s felCat3.scaffold_206428 39721 18 + 132007 ----------GGGAGGCC-----------------------------------------------------------CCTCCTCCCT i felCat3.scaffold_206428 C 0 C 0 e oryCun2.chrUn0958 33500 978 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 3911 10 + 4541 I e turTru1.scaffold_98008 5039 3 + 223990 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e pteVam1.scaffold_11245 29800 73 + 48268 I e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e canFam2.chr9 59451388 0 - 64418924 C e bosTau4.chr19 10874333 692 - 65312493 I e equCab2.chr11 58057702 0 - 61308211 C e cavPor3.scaffold_76 4404272 198 + 7991924 I e mm9.chr11 118776205 1 + 121843856 I e loxAfr3.scaffold_49 14449752 278 - 17734757 I a score=271265.000000 s hg19.chr17_gl000204_random 62314 156 + 81310 actaaaaatacaaaaattagccgggcgaagtggagggcacctataatcccagctactcaggaggctgaggcaggagagtcacttgaacccgggaggtggagat---tgcagtgagccaagatcacaccactgcactccggcttgggcgac-agagcaaga s calJac1.Contig5139 63352 160 + 225949 actaaaaatacaaaaattagcctggtgaagtggcaggcacctgtaatcccagctactcaggaggctgaggcaggggaatcccctgaacctgagaggcagagatgaatgcagtgagccgagattgtgccattgcactccagcctgggcaacaagaacaaga i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 60824 156 - 95547 actaaaaatacaaaaattagccaggcaaagtggagggcacctataatcccaactgctcaggaggctgaggcaggagaatcacttgaactcaggaggtggagat---tgcagtgagccaagatcgtaccactgcactccagccagggcgac-agagcaaga i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75053557 156 + 78773432 actaaaaatacaaaaattagccaggcaaagtggagggcacctataatcccaactgctcaggagactgaggcaggagaatcacttgaactcgggaggtggagat---tgcagtgagccaagatcgcaccactgcactccagccagggcgac-agagcaaga i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16079967 156 + 17838096 actaaaaatacaaaaattagccgggcgaggtggagggcacctataatcccagctactcaggaggctgaggcaggagagtcacttgaacccaggaggtggagat---tgcagtgagccaagatcacaccactgcactccagcttgggtgac-agagcaaga i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 30226 156 - 64270 actaaaaatacaaaaattagccgggcgaagtggagggcacctataatcccagctactcaggaggctgaggcaggagagtcacttgaacccgggaggtggagat---tgcagtgagccaagatcacaccactgcactccggcttgggtgac-agagnaaga i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79493877 156 + 83384210 actaaaaatacaaaaattagccgggcgaagtggagggcacctataatcccagctactcaggaggctgaggcaggagagtcacttgaacccgggaggtggagat---tgcagtgagccaagatcacactactgcactccagcttgggtgac-agagcaaga i panTro2.chr17 C 0 C 0 e oryCun2.chrUn0958 33500 978 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e vicPac1.scaffold_56870 3911 10 + 4541 I e turTru1.scaffold_98008 5039 3 + 223990 I e felCat3.scaffold_206428 39739 0 + 132007 C e dasNov2.scaffold_171027 1697 1984 + 4838 M e pteVam1.scaffold_11245 29800 73 + 48268 I e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e canFam2.chr9 59451388 0 - 64418924 C e bosTau4.chr19 10874333 692 - 65312493 I e equCab2.chr11 58057702 0 - 61308211 C e cavPor3.scaffold_76 4404272 198 + 7991924 I e mm9.chr11 118776205 1 + 121843856 I e loxAfr3.scaffold_49 14449752 278 - 17734757 I a score=-27163.000000 s hg19.chr17_gl000204_random 62470 42 + 81310 ctccatctcaag----aaaaaaaaaaaaaagaaTGGATCTCTCTGT s panTro2.chr17 79494033 45 + 83384210 ctccatctcaag-aaaaaaaaaaaaaaaaagaaTGGATCTCTCTGT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 30382 41 - 64270 ctccatctcaag-----aaaaaaaaaaaaagaaTTGATCTCTCTGT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16080123 46 + 17838096 ctccatctcaaaaaaaaaaaaaaaaaaaaagaaTGGATCTGTCTGT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75053713 37 + 78773432 ctccatctcaaa---------aaaaaaaaaaaaTTGATCACTCTGT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 60980 41 - 95547 ctccatctcaaa-----aaaaaaaaaaaaaaaaTGGATCACTCTGT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 63512 35 + 225949 ctttgtctcata----taataataataaaaGGATGGATC------- i calJac1.Contig5139 C 0 C 0 s vicPac1.scaffold_56870 3921 10 + 4541 ctctgtctc------------------------------------t i vicPac1.scaffold_56870 I 10 C 0 s felCat3.scaffold_206428 39739 7 + 132007 ------CTCC---------------------------------TCT i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58057702 12 - 61308211 ----------A------------------AGAAAGGA------TCT i equCab2.chr11 C 0 C 0 s cavPor3.scaffold_76 4404470 17 + 7991924 -----------------------------AGCCTAGACCTCCTGGT i cavPor3.scaffold_76 I 198 C 0 s canFam2.chr9 59451388 5 - 64418924 --------------------------------------C---CTCC i canFam2.chr9 C 0 C 0 s turTru1.scaffold_98008 5042 6 + 223990 ----------------------------------------CTCTGT i turTru1.scaffold_98008 I 3 C 0 e oryCun2.chrUn0958 33500 978 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e pteVam1.scaffold_11245 29800 73 + 48268 I e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e bosTau4.chr19 10874333 692 - 65312493 I e mm9.chr11 118776205 1 + 121843856 I e loxAfr3.scaffold_49 14449752 278 - 17734757 I a score=31368.000000 s hg19.chr17_gl000204_random 62512 23 + 81310 CTCTCTCTAT------acaaa---cacacaca-- s calJac1.Contig5139 63547 22 + 225949 -TCTCTCTac------ataca---cacacaca-- i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 61021 23 - 95547 CTCTCTCTAT------ACAAA---CACACACA-- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75053750 23 + 78773432 CTCTCTCTCT------acaca---cacacaca-- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16080169 23 + 17838096 CTCTCTCTAT------ACAAA---CACACACA-- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 30423 23 - 64270 TTCTCTCTAT------acaaa---cacacaca-- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79494078 23 + 83384210 CTCTCTCTAT------acaaa---cacacaca-- i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4404487 8 + 7991924 CACTCCGT-------------------------- i cavPor3.scaffold_76 C 0 C 0 s equCab2.chr11 58057714 26 - 61308211 CTCTCTCTAC------ACACACACCCCCAATA-- i equCab2.chr11 C 0 I 7 s canFam2.chr9 59451393 20 - 64418924 CTCCTCCTCC------CCACA------CCAAT-- i canFam2.chr9 C 0 I 7 s felCat3.scaffold_206428 39746 19 + 132007 CTCC-CCTCT------CCACA------CCATA-- i felCat3.scaffold_206428 C 0 I 7 s turTru1.scaffold_98008 5048 29 + 223990 CTCTCTCTACACACAGACACA---CCCCAATA-- i turTru1.scaffold_98008 C 0 I 7 s vicPac1.scaffold_56870 3931 23 + 4541 ctctctctAC------ACACA---CATCAATA-- i vicPac1.scaffold_56870 C 0 I 7 s loxAfr3.scaffold_49 14450030 22 - 17734757 ctcacacaac------acaca------ccacact i loxAfr3.scaffold_49 I 278 C 0 e oryCun2.chrUn0958 33500 978 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e pteVam1.scaffold_11245 29800 73 + 48268 I e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e bosTau4.chr19 10874333 692 - 65312493 I e mm9.chr11 118776205 1 + 121843856 I a score=8009.000000 s hg19.chr17_gl000204_random 62535 40 + 81310 cacacaca-cacacac---------acacacacGTGTTACTACT----TCCCCA s calJac1.Contig5139 63569 40 + 225949 cacacaca-cacacac---------acacacacacGTTTCAACT----TCCCCA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 61044 21 - 95547 CACACACA-CAAA----------------------------ACT----TCCCTA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75053773 39 + 78773432 cacacaca-cacacac-acaca--cacacacaAA-------ACT----TCCCTA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16080192 24 + 17838096 CACACAC--------------------------GTGTTACTACT----TCCCCA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 30446 46 - 64270 cacacaca-cacacac-acaca--cacacacacGTGTTACTACT----TCCCCA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79494101 30 + 83384210 cacacaca-cacacac-------------------GTTACTACT----TCCCCA i panTro2.chr17 C 0 C 0 s mm9.chr11 118776206 32 + 121843856 CAGGCAAA-CCCACAT-----------------GCATCTGAGTC----TCCCTA i mm9.chr11 I 1 C 0 s cavPor3.scaffold_76 4404495 30 + 7991924 ------CA-CACACAC-----------------AGATTTGTATCGCTGCCCCTC i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_56870 3961 34 + 4541 TACATGTA-AATATAT---------------AAACATTTCCATT----TCTCCA i vicPac1.scaffold_56870 I 7 C 0 s turTru1.scaffold_98008 5084 34 + 223990 TACatata-aatatat---------------aaattttttCATT----TCCTCA i turTru1.scaffold_98008 I 7 C 0 s felCat3.scaffold_206428 39772 33 + 132007 TACCTATA-AATACAC----------------AGTGCTTCCGTT----TCCCCA i felCat3.scaffold_206428 I 7 C 0 s equCab2.chr11 58057747 34 - 61308211 TACACACA-GAAATAT---------------AAATACCTCCATT----TCCCCA i equCab2.chr11 I 7 C 0 s canFam2.chr9 59451420 33 - 64418924 CACATGTT-AACACAC----------------AGGCATGTCCAT----GTCCTA i canFam2.chr9 I 7 C 0 s loxAfr3.scaffold_49 14450052 50 - 17734757 cacatacaccacatatcacatggtcacacaaacaTGTCTCTACC----CCCCCC i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 33500 978 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e pteVam1.scaffold_11245 29800 73 + 48268 I e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e bosTau4.chr19 10874333 692 - 65312493 I a score=284261.000000 s hg19.chr17_gl000204_random 62575 165 + 81310 CTACTG-C-CAGGCCTGCT-ACCGCTGTTGTATGTGTC----------GGATCTCCCCTTCAGGCCACCA----TCCA----AGC-ACGCTGTGGGACCCTGTGCAG--------TCCTGCATCAA----TAAATACCACTTAGGGAGAGCCCCACACGACCTGAGGGAATGTATGATCAAAACGCCCCACTACTGTTT s calJac1.Contig5139 63609 166 + 225949 CTACTG-C-CAGGCCTGCTGACCGCTGTTGTATGCATC----------AGGTCTCCCCTTCGGGCCACCA----TCCA----GGC-GCCCTGTGGGACCCTGTGCAG--------CCCCCCATCAA----TAACTCCCACTTAGGGAGAGCCCCACACACCCTGAGGGAATGTATGATCAACACACCCCACTACTGTTT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 61065 165 - 95547 CTACTG-C-CAGGCCTGCT-ACCGCTGTTGTATGTGTT----------GGATCTCTCCTTTGGGCCACCA----TCCA----AGC-ACCCTGTGGGATCCTGTGCAG--------CCCCGCATCAG----TAACTCCCACTTAGGGAGAGCCCCACACAACCTGAGGGAATGTATGATCAAAACACCCCACTAGTGTTT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75053812 165 + 78773432 CTACTG-C-CAGGCCTGCT-ACCGCTGTTGTATGTGTT----------GGATCTCTCCTTTGGGCCACCA----TCCA----AGC-ACCCTGTGGGACCCTGTGCAG--------TCCCGCATCAA----TAACTCCCACTTAGGGAGAGCCCCACACAACCTGAGGGAATGTATGATCAAAACACCCCACCAGTGTTT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16080216 165 + 17838096 GTACTG-C-CAGGCCTGCT-ACCAGTGTTGTATGTGTC----------GGATCTCCCCTTTGGGCCACTG----TCCA----AGC-ACCCTGTGGGACCCTGTGCAG--------CCCTGCATCAG----TAACTCCCACTTAGGGAGAGCCCCACACGACCTGAGGGAATGTATGATCAAAATGCCCCACTACTGTTT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 30492 165 - 64270 CTACTG-C-CAGGCCTGCT-ACCGCTGTTGTATGTGTC----------GGATCTCCCCTTCAGGCCACCA----TCCA----AGC-ACGCTGTGGGACCCTGTGCAG--------TCCTGCATCAA----TAAATACCACTTAGGGAGAGCCCCACACGACCTGAGGGAATGTATGATCAAAACGCCCCACTACTGTTT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79494131 164 + 83384210 CTACTG-C-CAGGCCTGCT-ACCACTGTTGTATGTGTC----------GGATCTCCCCTTCGGGCCACCA----TCCA----AGC-ACGCTGTGGGACCCTGTGCAG--------TCCTGCATCAA----TAAATACCACTTAGGGAGAGCCCCACACGACCTGAGGGAACGTATGATC-AAACCCCCCACTACTGTTT i panTro2.chr17 C 0 C 0 s mm9.chr11 118776238 128 + 121843856 CTCCCATC-CGGGCCCTCT-AACA---------GTTCCTTTGTCTTCAGGGTCTCCTCTTTGGGCTGTCA----TTAA----TGG-GGTTGGGG-------GTGCAG--------GTGCC------------------------------------ATGACCTGAAGGAATGTAATAATAAAGCGACCCACGAATGCTC i mm9.chr11 C 0 I 629 s cavPor3.scaffold_76 4404525 157 + 7991924 CCCCAATC-CAGGCTTACT-GACATCATCACAGATGCCTCTCTCCTC-TGGTCTGCCATCTGGGCACTAAGGACTCAT----GGA-GACTTGTC-------GTGAGG--------GTTCCCACCTG----T--------------GCAAGACGCAGGCAACCTGATGGAATGGATTCCTGAGGC-CTCCACTAATGTTC i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_56870 3995 163 + 4541 CCACCA-C--------------CACTGCTGGATATTTG----------CGCTTTCCACTTTGG-CCGTGC----TCCG----GGC-CTTTGGTAGGACGCCGCAGAGAAGTG-CTACCTATCTTAACGACTGACTACCTCACAGGGACAGCCCCACAGGGCCTGAGGGAACCTATTATTCAAATAACCCATTAACATTC i vicPac1.scaffold_56870 C 0 I 3 s turTru1.scaffold_98008 5118 154 + 223990 CCACCA-T--------------TGTT----GGTATTTG----------GGCTTTCCCGTTCGG-CCACAG----TCCA----GGC-C-GTGCTAGGACACTGTGGAGAAGTG-CCCCCTATCTTAG----TGACTTCCCCATAGGGACAGCCCCACAGGGCCTGAGGGAACCTGTTATTCAAACGACACATCAACATTC i turTru1.scaffold_98008 C 0 I 3 s equCab2.chr11 58057781 157 - 61308211 CCACCG-CCCAGGCTTGCTGACCATGGCTGGATCTGCA----------GGG--TCCCCTTCGGGCCGCAG----TCTG----AGC-ACGCTG---------CGGGAGACA-------CTGTGTTCA----TGATTTCCACGTAGCGACAGTCCTGCAGAGCCTGAGGTCACGTATTATTGAAACAACCCACTAACGTTC i equCab2.chr11 C 0 I 3 s canFam2.chr9 59451453 151 - 64418924 CCCCTG-CCCTGTCCTGTTGGCCACTGCTGGCTACCGC----------GAGTTTCCCTTTCAGGCCGCGG----TCTG----AGC-GCACCATAGGTCA--CTGGACAGGTGCCTGCCAGTGTTCA----TGACTTCCCTGTAAGGACAGCCCCACAGG--------------------GAAACCACCCACTGACGG-- i canFam2.chr9 C 0 I 2 s felCat3.scaffold_206428 39805 135 + 132007 CCCCCG-CACC----------CCACTGCTGGCTACGCA----------GGGTTTCCCATCTGGGCCACGG----TCTG----AGCAGCGCTGTGGATC---CTGAAGAAGTGTCTGCCTGAATTCA----TGGCCGGCCCACAGGG--------GCTGG--------------------GAAACAACCCACTAACATTC i felCat3.scaffold_206428 C 0 I 3 s pteVam1.scaffold_11245 29873 153 + 48268 CCACCG-C-CAGACTTGCTGGACG-------------A----------GGGTTTCCTCTTCGG---CCAG----TCTT----GGC-TCGCTGCAGGACAGGGCGGAGAAGTGCCTGCCTACACTGG----GGACC-CCACGTAGGCACAGCCCCAGGGG-CCTGGGGGAACACATGACTGAA---ACCCACTCACGTTC i pteVam1.scaffold_11245 I 73 I 3 s loxAfr3.scaffold_49 14450102 172 - 17734757 CCACCA-CACAGGTTTGCT---GACTGGTTGCAAGGTA----------GGGTCTCCTTATTGGACAGTCT----TGCACACCTGT-ACACCGTCGGGCACTCTGATGGACTGCTTACCTGTACGGA----TGACTCCCACCTTG-GAGAGCCC-AGGTGGCCTGAAGG-ACATGTTGTTGGA-CAGCCCACCGGCGTTC i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 33500 978 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e bosTau4.chr19 10874333 692 - 65312493 I a score=490831.000000 s hg19.chr17_gl000204_random 62740 130 + 81310 CACGAAACACGCGGGGCAGATGTGCAAACATTTATACTGTG-TGGGCTCT------------CAGGGG----TTGTGCACCTGTCCGGGCTCCATGGAATGTAGGTCACAAGGAGACCTTGGAGGTCAGAGACGCCAACCAGCTAAC s calJac1.Contig5139 63775 129 + 225949 CAC-AAACACAC-GGGCAGACAGGCAAACACTGACACTCTGTTGGGCTCT------------TGGGGG----TTATGCGCCTGTCTGGGCTCTGTGGAATGTAGGTCACAAGGAGACGCTGGAGGTCAGAGATGCTGGCCAGCTAAC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 61230 131 - 95547 CACGACACACACGGGGCAGACGTGCAAACATTTATTCTCTGTTGGGCTCT------------CAGGGG----TTGTGCACCTGTCCGGGTTCCATGGAATGCAGGTCACAAGGAGACCTTGGAGGTCAGAGACACCAACCAGCTAAC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75053977 131 + 78773432 CATGACACACACGGGGCCGACGTGCAAACATTTATTCTCTGTTGGGCTCT------------CAGGGG----TTGTGCACCTGTCCGGGTTCCATGGAATGTAGGTCACAAGGAGACCTTGGAGGTCAGAGACACCAACCAGCTAAC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16080381 130 + 17838096 CACAAAACACGCGGGGCAGACGTGCAAACATTTATACTCTG-TGAGCTCT------------CGGGGG----TTGTGCACCTGTCCGGGCTCCATGGAATGTAGGTCACAAGAAGACCTTGGAGCTCAGAGACGCCAACCAGCTAAC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 30657 130 - 64270 CACGAAACACGCGGGGCAGATGTGCAAACATTTATACTGTG-TGGGCTCT------------CAGGGG----TTGTGCACCTGTCCGGGCTCCATGGAATGTAGGTCACAAGGAGACTTTGGAGGTCAGAGACGCCAACCAGCTAAC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79494295 130 + 83384210 CACGAAACACGCGGGGCAGATGTGCAAACATTTATACTCTG-TGGGCTCT------------CAGGGG----TTGTGCACCTGTCCGGGCTCCATGGAATGTAGGTCACAAGGAGACCTTGGAGGTCAGAGACGCCAACCAGCTAAC i panTro2.chr17 C 0 C 0 s vicPac1.scaffold_56870 4161 101 + 4541 CACACAAAATGCAGAGCAGCTGTGCAAAAGCTTATATTCCG-CAGGACTC------------CGGGGG----CTGCATCTC--TCCGG---------------------------ACCCTCGAGGTCAGAGGCACCAGCCAGCAAAC i vicPac1.scaffold_56870 I 3 C 0 s turTru1.scaffold_98008 5275 128 + 223990 CGCACAAAATGCAGGGCAGCCATGAAAAAGCTTATATTCTC-TAGGGCTC------------CAGGGG----TTGTATCTC--TCTGGATCTTGTGAGATATAGGTCCCAATGAAACCTCGGAGGTCAGAGGCACCAACCTGATTAA i turTru1.scaffold_98008 I 3 C 0 s bosTau4.chr19 10875025 128 - 65312493 cacacaaaaTGCGGGGCAGCCGTGCAAGAGCTTCTAGTCTG-TAGGGCTC------------CGGGGC----TTGTATCTC--TCTGGATCCTGTGAAATATAGGTCACAATGAAACCTTGGAGGTCAGAGACACCAATCCAAGAAC i bosTau4.chr19 I 692 C 0 s equCab2.chr11 58057941 140 - 61308211 CACGAGAAACGCGGGGCAGCCGTGCAAAAGCTTCTATTCCG-TAGGGCTCCGTGTGGGGGGAGGGGGG----GTGTGTCTC--TCCGGACCCCGTGAAATATAGATCACAATGAAACCTTGGAGGTCGGAGGCTCTGACTCGCCAGT i equCab2.chr11 I 3 C 0 s canFam2.chr9 59451606 120 - 64418924 C-------GTGCGGAGCAGATGTGCGGAAGCATATACTCTG-TAGGGCTCC-----------AGGGGC----TTGTGTCTC---TCAGACCCCATGAAACCCAGATCACGATGAAACCT-GGCAGTCAGAGGCTCCAACCCACTGAC i canFam2.chr9 I 2 C 0 s felCat3.scaffold_206428 39943 121 + 132007 C-------GTGCGGGGCAGACGTGCAAAAGCTTATGTTCTG-TGGGGCTCCG----------GGGGGG----TTGTGTCTC---CCAGGCCCCAGGAAATCTAGATCACGGTGAAACCTGGGGGGTCAGAGGCTCCAA-GTACTGAC i felCat3.scaffold_206428 I 3 C 0 s pteVam1.scaffold_11245 30029 125 + 48268 CATGCGGAACACGGGGCAGATGTGTCAAG---TTCATCTGG-TAGGGCTT------------GGGGGG----CTGTGTCTC--CCCAGACCCGGTGAAATACAGATCAATAGGAAACCTCGCAGTTCAGAGGCACCAACCCGCTCAC i pteVam1.scaffold_11245 I 3 M 100 s cavPor3.scaffold_76 4404682 95 + 7991924 --------------------TGCGTAGAAGCTTTCACCCCT-CAGGGCTT------------GTGGCA----TCCTGTGTCCCTCTGGGCCCCATGGAATATG---CAGTGGGCCACCTTGGAACTCAG------------GCTGAC i cavPor3.scaffold_76 C 0 C 0 s loxAfr3.scaffold_49 14450274 114 - 17734757 -----------------TTGCACACAGAAGCACGCGTTCTG-TAGGGCTC------------TCGGGGAGGCTGACGTTGC--TCTAGGCTCCATGGAACACGCGTCATGATAAGGCCTTGGAGCGCCGATGCTATGACCCGCAAC- i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 33500 978 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118776366 629 + 121843856 I a score=165539.000000 s hg19.chr17_gl000204_random 62870 95 + 81310 TTAAATGAAGACGTCACAG-GG-CCGG-GCTGT-----GCTCTGTCC------CATAGCTGGAAGAGAGGTGTTCGGCCCTCA-------CACACC------CAGCCTCAGCCTCAGCTGTG s calJac1.Contig5139 63904 88 + 225949 TTCAACAATGACATCACGG-GG-CCGG-GCCGC-----ACTCTGTCC------AGCAGCTGGAGGAGAGGCG-------CTCA-------CACACC------CAGCCTCAGCCTCAGCTGTG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 61361 101 - 95547 TTAAATAATGACGTCACTG-GG-CCGG-GCTGT-----GCTCTGTCC------CACAGCTGGAGGAGAGGTGCTCGGCCCTCA-------CACGCCCAGCCTCAGCCTCAGCCTCAGCTGTG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75054108 101 + 78773432 TTAAATAATGACGTCACTG-GG-CCGG-GCTGT-----GCTCTGTCC------CACAGCTGGAGGAGAGGTGCTCGACCCTCA-------CACGCCCAGCCTCAGCCTCAGCCTCAGCTGTG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16080511 95 + 17838096 TTAAACGATGATGTCGCGG-GG-CCGG-GCTGT-----GCTCTGTCC------CATAGCTGGAGGAGAGGTGTTCGGCCCTCA-------CACACC------CAGCCTCAGCCTCAGCTGTG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 30787 95 - 64270 TTAAATGAAGACGTCACGG-GG-CCGG-GCTGT-----GCTCTGTCC------CATAGCTGGAAGAGAGGTGTTCGGCCCTCA-------CACACC------CAGCCTCAGCCTCAGCTGTG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79494425 95 + 83384210 TTAAATGATGACGTCACGG-GG-CCGG-GCTGT-----GCTCTGTCC------CATAGCTGGAAGAGAGGTGTTCGGCCCTCA-------CACACC------CAGCCTCAGCCTCAGCTGTG i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4404777 50 + 7991924 --AGACACTCCCCTTACAA-GGTCTGG-GCTG--------------------------------------------------------------CC------AGGCAGGAGCTCTAGCTATG i cavPor3.scaffold_76 C 0 I 49 s vicPac1.scaffold_56870 4262 98 + 4541 TCAGCGAGTGACACTGTGGGTG-CCCA-GCCAGCCCGGGCCCTGGCCTCTGCTCACAGCTGGCGGG--GGCGCCCAGTGC-----------ACACC------CAGCCGCGGCAGCGGCC--- i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_98008 5403 102 + 223990 TTAACAAGTGACACTGTGGAGG--CTG-GCCGGCTCAGGCCCACACCTCTACTCACAGCTGGTGGAGAGGCACCCAGCCT-----------GCGCC------CAGCCTCAGCAGGGGCCACA i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10875153 102 - 65312493 TTAACAAGAGACAACGTGGAGG--TTG-ACTGGCTCAGGCCCACGCCTCTGCTCACAGCCAGTGGGGAGGCACCCAACAC-----------GCGCC------CAGCCTCGACAGGGGCCCCA i bosTau4.chr19 C 0 C 0 s felCat3.scaffold_206428 40064 93 + 132007 TTAACCAGTGAAGTCACAGAGG-CCAG-----------ATCCTGGCCTCTGGCCGCAGGGGGTGGAGAGGCCCTCATCCC-----------ACGTG------GAGCCACAGCACCGGCCACG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59451726 101 - 64418924 TTACCCAGTGAAGCCACGGAGG-CCCGCGCCAGCCCA-GCCCTCACCTCCGGTCACAGCTGGCGCAGAGACCCTCCTCCC------------TGCA------CTGCCTCAGCACCAGCTG-G i canFam2.chr9 C 0 C 0 s equCab2.chr11 58058081 102 - 61308211 TTAACCAGTGAAGTCTCGGAGG-CCGG-GCTGGCGCT-GCCCTCGCCTCCGGCCGCAGCTACAGGACAAGTCCTCATCAC-----------ACGCC------GTGCCTCAGCACCCGCTGCC i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14450388 111 - 17734757 TTAACCGGTGAAGCCTTGGAGG-CCCG-GCTGGTCCA-GAACTTGCCTCCGGCCACA-CCGCTGGGGAGAGGCCCCACCCCTACCCTGAGCACACC-------TGCCTCGGCACCATCTGGG i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 33500 978 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e pteVam1.scaffold_11245 30154 100 + 48268 M e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118776366 629 + 121843856 I a score=91303.000000 s hg19.chr17_gl000204_random 62965 74 + 81310 ----TCCGCCGGCTGGCTCTC-----CGCTCTTCACTTCAG--------TCCCAAGGTTTA----TCATCCCTCTTTCTCCTGACCCTTTTTTCC s panTro2.chr17 79494520 74 + 83384210 ----TCCGCCGGCTGGCTCTC-----CGCTCTTCACTTCAG--------TCCCAAGGTTTA----TCATCCCTCTTTCTCCTGACCCTTTTTTCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 30882 74 - 64270 ----TCCGCCGGCTGGCTCTC-----CGCTCTTCACTTCAG--------TCCCAAGGTTTA----TCATCCCTCTTTCTCCTGACCCTTTTTTCC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16080606 74 + 17838096 ----TCCGCTGGCTGGCTCTC-----CACTCTTCACTTCAG--------TCCCAAGGTTTA----TCATCCCTCATTCTCCTGACCCTTTTTTCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75054209 74 + 78773432 ----TCTGCCGGCTGGCTCTC-----CACTCTTCACTTCAG--------TCCCAAGGTTTA----TCATCCCTCGTTCTCCTGACCCTTTTTTCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 61462 73 - 95547 ----TCTGCCGGCTGGCTCTC-----CACTCTTCACTT-AG--------TCCCAAGGTTTA----TCATCCCTCGTTCTCCTGACCCTTTTTTCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 63992 73 + 225949 ----TCCGCCGGCTGGCTCTC-----CGCTCTTCACTTTGG--------TCCCAGGATTTG----TTATCCCTCATTCTCCTGACCC-TTTTTCC i calJac1.Contig5139 C 0 C 0 s vicPac1.scaffold_56870 4360 83 + 4541 -------GCTGGGCTGGCTTCCCCGTCTTCCTCCACACCTGAAAAACC-TTCCAGACTTTGC---CCACCCCCGGCCCTCCCGACCCCAGTTCC- i vicPac1.scaffold_56870 C 0 C 0 s turTru1.scaffold_98008 5505 87 + 223990 ----GCGGCTGGGCTGGCTTCCCAGTCTTCCCTCATACCTGAGTAACAGTCCCAAACTTTGC---CCACTCCTGGTCCTCCGGACCCTGGTTGC- i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10875255 87 - 65312493 ----ACAGCTGGACCGGCCTCCCAGTCTTCCCTCACACCTGAACAACGGTCCCAAACTTTGC---CCACTCCCGGTGCTCTGGACCCTGATTCC- i bosTau4.chr19 C 0 C 0 s felCat3.scaffold_206428 40157 50 + 132007 ----CCAGCTGGG-------------CCGGCTGCACACCTGAGCCACCACCCG---------------------------CCCACCCTTGCTCC- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59451827 59 - 64418924 ----CCAGCTGGGTGGGCTGC-----CCGACTACACACCCGAGCCACCATGTGA--------------------------CCCCCCCTTACTCC- i canFam2.chr9 C 0 C 0 s equCab2.chr11 58058183 81 - 61308211 ----ACAGCCAGACCAGCTTC-----TTCCCTTCAC-CCCGAGCAACCGTCCCAACCTTTGC---CCATCCCACCTTCTCCTGCCCCCTGATCC- i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14450499 74 - 17734757 CGGCGCCACCAGCTCTTCCTT-----CTCCTCTTCCACCTTAGCAGCT-GTCCACGCTTTGCCTGTCATCTCGTTTCCCC--------------- i loxAfr3.scaffold_49 C 0 C 0 e oryCun2.chrUn0958 33500 978 + 41507 I e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e pteVam1.scaffold_11245 30154 100 + 48268 M e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e cavPor3.scaffold_76 4404827 49 + 7991924 I e mm9.chr11 118776366 629 + 121843856 I a score=145529.000000 s hg19.chr17_gl000204_random 63039 98 + 81310 -----TGG----CAGATG-----GTGGC-ACAG----TTTCA-CCTTGAAGCTAGAGCCTTCAG-TGGGAGCAGCTTTCTCCCTGCACGCCTCCT-TCTAGTTTCATCTTGTCTTCCTGC s calJac1.Contig5139 64065 99 + 225949 -----TGG----CAGATG-----GTGGC-ACAG----TTTCA-CCTGGAAGCTAGAGCCTTCCGATGGGAGCAGctttctccctgcatgccttct-tccagcttcatctcaccttcctcc i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 61535 99 - 95547 -----TGG----CAGATG-----GTGGC-ACAG----TTTCA-CCTCGAAGCTAGAGCCTTCAGATGGGAGCAGCTTTCTCCCTGCACGCCTCCT-TCTAGTTTCATCTTGCCTTCCTGC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75054283 99 + 78773432 -----TGG----CAGATG-----GTGGC-ACAG----TTTCA-CCTCGAAGCTAGAGCCTTCAGATGGGAGCAGCTTTCTGCCTGCATGCCTCCT-TCTAGTTTCATCTTGCCTTCCTGC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16080680 99 + 17838096 -----TGG----CAGATG-----GTGGC-ACAG----TTTCA-CCTCGAAGCTAGAGCCTTCAGATGGGAGCAGCTTTCTCCCTGCACGCCTCCT-TCTAGTTTCATCTTGCCTTCCTGC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 30956 99 - 64270 -----TGG----CAGATG-----GTGGC-ACAG----TTTCA-CCTCGAAGCTAGAGCCTTCAGATGGGAGCAGCTTTCTCCCTGCACGCCTCCT-TCTAGTTTCATCTTGTTGTCCTGC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79494594 99 + 83384210 -----TGG----CAGATG-----GTGGC-ACAG----TTTCA-CCTCGAAGCTAGAGCCTTCAGATGGGAGCAGCTTTCTCCCTGCACGCCTCCT-TCTAGTTTCATCTTGTCTTCCTGC i panTro2.chr17 C 0 C 0 s oryCun2.chrUn0958 34478 87 + 41507 -----TGG----CTGGTG-----GTCTC--CCG----TTTCC-CCCGGAAGCCGGCGTCTTCC--TCGGAGCAGCTCCCCGCCGGCACAGCTCC----------CAGCCCGCTCTCCCCC i oryCun2.chrUn0958 I 978 I 6 s cavPor3.scaffold_76 4404876 61 + 7991924 -------------------------------------TTCAC-CTCGGGGGACAGCTTTGTGC--CCCAAGTCACCTGCCCCTGTCACCTATGC-------------------CTCCTCC i cavPor3.scaffold_76 I 49 C 0 s vicPac1.scaffold_56870 4443 98 + 4541 -----TGA----CAGACA-----AGGGC-GCTGTCTTCTTCA-CAGGGAAGGGA-GGC--TCAGACGTGAGCACCTTTCTTCCCTCACATCTCTC--TCGTGTTCATCT-CTCTTCCCGC i vicPac1.scaffold_56870 C 0 N 0 s turTru1.scaffold_98008 5592 107 + 223990 -----TGG----CAGACAGACAGACAGC-GCTGTCTTCTTTG-CCGAGAAGGGAGGGC--TCAGATTTGAGCAGCTTTCTTCCCTCTCCCCCACCGTCTGTGTCCATCTCCTCTTCCTGC i turTru1.scaffold_98008 C 0 I 5 s bosTau4.chr19 10875342 107 - 65312493 -----TGG----CAGACAGACAGACAGG-GTTCTCTTTTTCT-CCAAGAAGGGAGGGC--TCAGATTTAAGCAGCTTTCTTTCCTCTCATCTTCCATCCGTGCTCAACTCCTCCTGCTGC i bosTau4.chr19 C 0 I 5 s felCat3.scaffold_206428 40207 60 + 132007 -----TGG----CGGTCG-----ACCGC-ACCGTCTTTGTCC-CTGGGCAGGGAGAGC--TCAGA-------------------------CTTCC-TCC----------------CCTTC i felCat3.scaffold_206428 C 0 I 5 s canFam2.chr9 59451886 61 - 64418924 -----TGG----CAGATG-----ACTAC-ACCATGGGTTTCCACTAGGAAGGGAGAGC--TCAGA-------------------------CTTCC-TCC----------------CCATC i canFam2.chr9 C 0 I 5 s equCab2.chr11 58058264 100 - 61308211 -----TGG----CAGATG-----ACCAC-GTTGTCTTTTTCA-CCAGGAAGAGACAGC--TCAGATTCGAGCAGCTTTC-TCCTTCTCATCTCCC-TCCGTATTCATCTCTGCCTCCCGC i equCab2.chr11 C 0 I 5 s loxAfr3.scaffold_49 14450573 78 - 17734757 AGCCCTGGCTCTCAGCTG-----ATGACTGTAG----TGTCT-CATGGAGG------------------------------TCTTCGCTGATCGC-TCTGAACTCACCACTTCT-CCTGC i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e pteVam1.scaffold_11245 30154 100 + 48268 M e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118776366 629 + 121843856 I a score=280212.000000 s hg19.chr17_gl000204_random 63137 139 + 81310 TCCCTTTCAAATTCTTCTTCCGTTTTCTCCCTCCATCCAGCCCTCTCTTGCTCTATCCTCTTCTGTCTTTCCTGCTCTGGGGAT-GGGGGGGTCTTAGCCTACCAGCCTAAAAACCTTAT-CTGGTCTTCCCCATCCTTCC s calJac1.Contig5139 64164 132 + 225949 tccctttcaaattctccttccattttctccctccatccagccctctcttgctccatcctcttctgtctctcctgctc--------TGGGGGGTGTTAGCCCACAAGCCTAAAAACCTTAT-CTGGCCTTCCCCATCCTTCA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 61634 136 - 95547 TCCCTTTCAAA---TGCTTCTGTTTTCTCCCTCCATCCAGCCCTCTCTTGCTCCATCTTCTTCTGTCTTTCCTGCTGTGGGGGT-GGAGGGGTCTTAGCCTACCAGCCTAAAAACCTTAT-CTGGTCTTCCCTGTCCTTCC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75054382 136 + 78773432 TCCCTTTCAAA---TGCTTCCGTTTTCTCCCTCCATCCAGCCCTCTCTTGCTCCATCCTCTTCTGTCTTTCCTGCTCTGGGGGT-GGAGGGGTCTTAGCCTACCAGCCTCAAAACCTTAT-CTGGTCTTCCCCATCCTTCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16080779 139 + 17838096 TCCCTTTCAAATTCTTCTTCCATTTTCTCCCTCCATCCAGCCCTCTCTTGCTCCATCCTCTTCTGTCTTTCCCGCACTGGGGAT-GGGGGGGTCTTAGCCTACCAGCCTAAAAACTTTAT-CTGGTCTTCCCCATCCTTCC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 31055 139 - 64270 TCCCTTTCAAATTCTTCTTCCGTTTTCTCCCTCCATCCAGCCCTCTCTTGCTCTATCCTCTTCTGTCTTTCCTGCTCTGGGGAT-GGGGGGGTCTTAGCCTACCAGCCTAAAAACCTTAT-CTGGTCTTCCCCATCCTTCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79494693 140 + 83384210 TCCCTTTCAAATTCTTCTTCCGAATTCTCCCACCATCCAGCTCTCTCTTGCTCCATCCTCTTCTGTCTTTCCTGCTCTGGGGATGGGGGGGGTCTTAGCCTACCAGCCTAAAAACCTTAT-CTGGACTTCCCCATCCTTCC i panTro2.chr17 C 0 C 0 s mm9.chr11 118776995 93 + 121843856 TCCTCTCCAAGccctcccctcccctcctctctcctctcctctttctctctcc-tctcctctcctcacctctctctcc-------------------------ccttccc----------t-c---ccctcccc-------- i mm9.chr11 I 629 C 0 s cavPor3.scaffold_76 4404937 84 + 7991924 --------------TCCCTTGTCCTGATCTCCCCTCATGTCCTGAATCCTCC-CAGCCTGGCCTCTTTTATTTCTCC-------------------------TGTGCTT----------T-CAGGACATCCCAAG------ i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 34571 104 + 41507 -TGCCATCAAACCCTCCCCCGACTT-CTGTCTCCACCCAGCACCCGCTCGCCGCCTCCTCGCCCGTCTTTCTGCTCC----------GGGAGTCCCAGCC-ACCTGCTT----------T-AGGGACT------------- i oryCun2.chrUn0958 I 6 C 0 s turTru1.scaffold_98008 5704 125 + 223990 TCCCATTCAAATCCTCCCC-------CTGCCCCCATCCAGCCCCCTTGGGCTTCCTCCTCTTCCACCTTCCCTGCTC--------TGGGGGGTTCTAGCCCACCAGCCTAAAAGCATAGT-CAGTCTTTACCCATCCTTTA i turTru1.scaffold_98008 I 5 C 0 s bosTau4.chr19 10875454 117 - 65312493 TTCCTTTCAAATCCTCTCC-------CCATACTGGTCTAGCCCCCTTGGGCTTCCTCCTCTTCCACTTTCCCTGCTC--------TGAGGAGCTCT--------AGCCTAAAAGCGTGGT-CAATCCACACCCATCCTTTG i bosTau4.chr19 I 5 C 0 s felCat3.scaffold_206428 40272 125 + 132007 TTCCTCCCAGAGCCCCTCC-----TGCTTTCTCTGTCCAGCCCTCTCGTGCCTCCGCCTCTCCCATCTTTCCTGCTC--------TAGGG-GCCTTCACCCACCGGCCTGAACGCA-GAT-CAGGTCCCACCCGGGCTGTG i felCat3.scaffold_206428 I 5 C 0 s canFam2.chr9 59451952 125 - 64418924 TTCCCTCCAAATGCCCTCC-----TGCTTCCTCTGTCCAGCCATGTCGGGCCTCCCCGACTCCAATCCCTCCTGCCC--------TGGGG-GCCCTGGCCCA-CAGTCTGAAAGCG-GGTGGGGGTCTCACCCTTGCTGTG i canFam2.chr9 I 5 C 0 s equCab2.chr11 58058369 105 - 61308211 CTCCTTGCAAATCCTCCTCCCA-TTTCTCTCTCAGTCCAGCCCCCTCATGCCTCCTCCCCTTCCAG---GCCAGCTC--------TGGG--------CCCCA---------------GGT-CAGGCCTCACCTGTCTTGGA i equCab2.chr11 I 5 C 0 s loxAfr3.scaffold_49 14450651 126 - 17734757 --TCTTTCAAAGTCTCCTCACCTTT-CCCCTTTGGTCCAGCAGCTTTAGCCTTC--CCTCTCCCATCTGTCGTGCTC--------CGGGC-TTCCTAGCCCACCAGCCCAAAAGCATGAG-TGGGCCTCCCCCGCCCTTGC i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e pteVam1.scaffold_11245 30154 100 + 48268 M e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I a score=93349.000000 s hg19.chr17_gl000204_random 63276 35 + 81310 AGAAGCACCCCTAGATG-CTCTTCTCTC-CCCTCGTT s calJac1.Contig5139 64296 34 + 225949 AGAAGCGTCCCTAGATG-CTCC-CTCTC-CCCTCGTC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 61770 35 - 95547 AGAAGCACCCCTAGATG-CTCCTCTCTC-CCCTTGTT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75054518 35 + 78773432 AGAAGCACCCCTAGATG-CTCCTCTCTC-CCCTCGTT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16080918 36 + 17838096 AGAAGCACCCCTAGATGCCTCCTCTCTC-CCCTCGTT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 31194 35 - 64270 AGAAGCACCCCTAGATG-CTCCTCTCTC-CCCTCGTT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79494833 35 + 83384210 AGAAGCACCCGTAGATG-CTCCTCTCAC-CCCTCGTT i panTro2.chr17 C 0 C 0 s mm9.chr11 118777088 29 + 121843856 ------tcccctccccc-ctctcctctc-cccactct i mm9.chr11 C 0 I 14 s cavPor3.scaffold_76 4405021 28 + 7991924 ------TCCCTAGGCCA-CCTTCCCCTC-CCTGTTC- i cavPor3.scaffold_76 C 0 I 4 s oryCun2.chrUn0958 34675 26 + 41507 ------GGCCCTGGGTG-CTGCTCCTGC-CCCAC--- i oryCun2.chrUn0958 C 0 C 0 s turTru1.scaffold_98008 5829 34 + 223990 AGAACAGACCTTAGA-G-CTGCTCCCCT-CCCGTCTC i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10875571 34 - 65312493 AGAACAAACCCTAGT-G-ATGCTCTCCT-GCCATTGC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58058474 35 - 61308211 GGAACCATCCCTAGACG-CTGCTCTCGC-CCCACGTC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59452077 35 - 64418924 AGAGCCGCTTGTAGACA-CTGCTCTCTC-CCCAAGGA i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 40397 35 + 132007 AGCGCCATCCAGAGACG-CTGCTCTCTC-CCCACGGC i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_125911 355 36 + 4959 AGAACTGTCCCTCGACG-CTGCGCCCCCTCCCCCAGC i myoLuc1.scaffold_125911 N 0 C 0 s loxAfr3.scaffold_49 14450777 30 - 17734757 AGAACCATCTCTAGACT-CTGGG---GC-CCCAAG-- i loxAfr3.scaffold_49 C 0 C 0 e ochPri2.scaffold_9426 14183 4444 - 54875 I e dasNov2.scaffold_171027 1697 1984 + 4838 M e pteVam1.scaffold_11245 30154 100 + 48268 M e otoGar1.scaffold_27969.1-945 641 0 - 945 I e monDom5.chr2 304557512 13025 - 541556283 I a score=-20928.000000 s hg19.chr17_gl000204_random 63311 58 + 81310 CCCCTTCCA-TCCTCGCCTTCCCTCGATCAC------AAGCA-TCCCTACCTCCAC-GTCCACACCC s calJac1.Contig5139 64330 58 + 225949 CCCCTGCCA-TCCTTGCCTTCCCTTGATGAC------AAGCA-CCCCCACCTCCAC-GCCCACACCC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 61805 52 - 95547 CCCCTGCCA-TCCTTGCCTTCCCTCGATCAC------AAGC-------ACCCCCAC-GTCCACACCC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75054553 52 + 78773432 CCCCTGCCA-TCCTTGCCTTCCCTCGATCAC------AAGC-------ACCCCCAC-GTCCACACCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16080954 58 + 17838096 CCCCTGCCA-TCCTCGCCTTCCCCCGATCAC------AAGCA-CCCCCACCTCCAC-GTCCACACCC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 31229 58 - 64270 CCCCTTCCA-TCCTCGCCTTCCCTCGATCAC------AAGCA-TCCCCACCTCCAC-GTCCACACCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79494868 58 + 83384210 CCCCTTCCA-TCCTCGCCTTCCCTCGATGAC------AAGCA-TCACCACCTCCAC-TTCCACACCC i panTro2.chr17 C 0 C 0 s mm9.chr11 118777131 46 + 121843856 ctctcctct-cctctctcctccc-ccctctc----------t-ctccccctcccct-ccc------- i mm9.chr11 I 14 I 80 s oryCun2.chrUn0958 34701 49 + 41507 ----------TCCCTGCCTTCCC-CAGTCAC-----AAAGCG-CTCCCACCTCCAC-AGCAACACGT i oryCun2.chrUn0958 C 0 I 11 s ochPri2.scaffold_9426 18627 63 - 54875 CCCCCTCCT-TCTCTGCCTTCCC-CCGTTCCCTTCTCAAGGG-CTCCCACCTCCAC-AGCAACACCT i ochPri2.scaffold_9426 I 4444 I 10 s otoGar1.scaffold_94362.1-287808 40942 36 + 287808 -----------------------TCACTCAC------TACCA-CTCAGGCAGTCAC-ACCAACACCC i otoGar1.scaffold_94362.1-287808 I 6958 C 0 s turTru1.scaffold_98008 5863 34 + 223990 -CTTC----------------CCTTTATCAC------AAGTGGTCCCCATCTCCTTT---------- i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10875605 35 - 65312493 -CTTC---------------TCTTTTATCAC------AAGTGGTCCCCACCTCCTCT---------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58058509 48 - 61308211 -CCCTGCCA-TCATCTTCTTCCCTTTATCAC------CAACAGTCCCCATCTCCTC----------- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59452112 29 - 64418924 -CCC--------------------TTATCGC------TGACACTTCCCATCTGCCC----------- i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 40432 45 + 132007 -TCCCGC----CACCCTCTCCCCGTTATGGA------TGACAGTTCCCACCTGCTC----------- i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_125911 391 26 + 4959 -CTCTGCCA-TCATC----------------------------TCCCCGCCTCCTC----------- i myoLuc1.scaffold_125911 C 0 C 0 s loxAfr3.scaffold_49 14450807 54 - 17734757 CTCCTACCAGCTCTCCCCCTCCCTTTATCAT------GCCCAGCCCCCACACCCTC-CCCG------ i loxAfr3.scaffold_49 C 0 C 0 e dasNov2.scaffold_171027 1697 1984 + 4838 M e pteVam1.scaffold_11245 30154 100 + 48268 M e monDom5.chr2 304557512 13025 - 541556283 I e cavPor3.scaffold_76 4405049 4 + 7991924 I a score=39285.000000 s hg19.chr17_gl000204_random 63369 72 + 81310 ----------------ACGGACA-CCCCAGGGAAATGGC-TC--------TCTCGGGTCACCA------GGGAA-GGCTGAATCA--CAAACAGCCAGGCCTGCACT s panTro2.chr17 79494926 72 + 83384210 ----------------ACGGACA-CCCCAGGGAAATGGC-TC--------TCTGGGGTCACCG------GGGAA-GGTTGAATCA--AAAACAGCCAGGCCTGCACT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 31287 72 - 64270 ----------------ACGGACA-CCCCAGGGAAATGGC-TC--------TCTGGGGTCACCA------GGGAA-GGCTGAATCA--CAAACAGCCAGGCCTGCACT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16081012 71 + 17838096 ----------------ACGGACA-CCCCA-GGAAATGGC-TC--------TCTGGGGTCACCA------AGGAA-GGCTGAATCA--CAAACAGCCAGGTCTGCACT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75054605 72 + 78773432 ----------------ACCGACA-CCCCAGGGAAATGGC-TC--------TCTGGGGTCACCA------GGGAA-GGCCGAATCA--CAAACAGCTGGGCCTGCACT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 61857 72 - 95547 ----------------ACCAACA-CCCCAGGGAAATGGC-TC--------TCTGGGGCCACCA------GGGAA-GGCCGAATCA--CAAACAGCTGGGCCTGCACT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 64388 72 + 225949 ----------------ACTGACA-CCCCAGGGAAGCGGC-TC--------TCTGGGGTCACCA------GGGAA-GGTCCAATCA-GCAAACAG-GAGGCCTGCGCT i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 40978 73 + 287808 ----------------TTCGTAT-ACTCATAGAATTGGCACC--------TCTGGAATCACCG------GGGGATGGCCTAGTCACCCAAACAGACCAGCCTG---T i otoGar1.scaffold_94362.1-287808 C 0 C 0 s cavPor3.scaffold_76 4405053 61 + 7991924 ----------------ACGTAGA-T------------GC-CA--------GTTTAGGGGAACA------GGAGC-AGCCCCACCT-CCAAGCAGCCCAGCCCATGCT i cavPor3.scaffold_76 I 4 C 0 s oryCun2.chrUn0958 34761 44 + 41507 ----------------ACGGACA-C------------GC-TC--------CCCGGGGTCACCA------CGAGC-AGCCCCACC--------------GCCCA---- i oryCun2.chrUn0958 I 11 C 0 s ochPri2.scaffold_9426 18700 61 - 54875 ----------------ACAGACA-C------------AT-TCAACAGTCACCCCCAGTCACCAGCCTGGCTGGC-GCCCCCTCCT-----------CAGCACA---- i ochPri2.scaffold_9426 I 10 C 0 s turTru1.scaffold_98008 5897 58 + 223990 -----------------CCAACAACCCCTTGGAAATGGC-CC-------TGCCGGGGTCCCTG------GTGAC-CA-----------------ACTAGCCTGTGCG i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10875640 58 - 65312493 -----------------CCAACATCCCCCTGGAAATGGC-TC-------TGCTGGCGTCCCTA------GAGAC-CA-----------------ACTGGCCTGTGCC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58058557 71 - 61308211 -----------------TCAGTG-CCCCATGGAAATGGC-TT-------TCCTGGGGTCACTG------GGAAC-AG--GAGTCA-CCAGACAAACTAGCCTGTGCT i equCab2.chr11 C 0 C 0 s canFam2.chr9 59452141 65 - 64418924 -----------------CCAACA-CCCCACAG-AATGGC-CC-------TCCTGGGGTCTCCA------GGGAT--G--GAGTCA-CCAA----ACTAGCCTGCACT i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 40477 66 + 132007 -----------------CCAGCA-CCCCACAG-AATGCC-TC-------TCCCAGGGCCACCA------GGGAT-GG--GAGTCC-CCAG----ACCAGCCCGCGCT i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_125911 417 57 + 4959 -----------------CCCACA-CCCCACGGGAAC------------------GGGTCACCA------GG-----G--GAGTCG-CCGGGCAAACTAGCCTGTGGC i myoLuc1.scaffold_125911 C 0 C 0 s loxAfr3.scaffold_49 14450861 90 - 17734757 GTGTGGGCAGCTCCCTCCCAGCA-CCCCATGGAAATGGC-TC-------TCCCGGGGCCACCA------GGAAC-ACCCTAGTCC-CCCGACAAGCTGGCTTGTAAC i loxAfr3.scaffold_49 C 0 C 0 e dasNov2.scaffold_171027 1697 1984 + 4838 M e pteVam1.scaffold_11245 30154 100 + 48268 M e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118777177 80 + 121843856 I a score=30487.000000 s hg19.chr17_gl000204_random 63441 49 + 81310 CCCTCCTT-GGTTTACTTGATCCTTTACTG---------CAGG-------------------TGG--CCCCGTGGCCAAG- s panTro2.chr17 79494998 49 + 83384210 CCCTCCTT-GGTTAACTTGATCCTTTACTG---------CAGG-------------------TGG--CCCCGTGGCCAAG- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 31359 36 - 64270 CCCTCCTT-GGTTTACTTGATCCTTTGCTG---------CAGG-------------------TGG---------------- i gorGor1.Supercontig_0007361 C 0 M 8539 s ponAbe2.chr17_random 16081083 45 + 17838096 CCGTCCTT-GGTT-ACTTGATCCTTTACTG---------CA-G-------------------TG---CCCCGTGGCC-AG- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75054677 49 + 78773432 CCCTCCTT-GGTTTACTTGATCCTTTACCG---------CAGG-------------------TGG--CCCCGTGGCCAAG- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 61929 49 - 95547 CCCTCCTT-GGTTTACTTGATCCCTTACCG---------CAGG-------------------TGG--CCCCGTGGCCAAG- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 64460 49 + 225949 CCCTCCTG-GGTTTACTTGATTCTTTACAG---------CAGG-------------------TAC--CGCTGCAACTGAG- i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 41051 52 + 287808 CCCTCCTCAGGTGTACTTGACACTTCAGTA---------CAGG-------------------GGGATCCTACCACCCATG- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s cavPor3.scaffold_76 4405114 37 + 7991924 C---CTTC-GGTTCCCATGG---------G---------CAGG-------------------TGG--CCCTGTGGCCAAC- i cavPor3.scaffold_76 C 0 I 24 s oryCun2.chrUn0958 34805 11 + 41507 ------AC-AGCCCCCA--------------------------------------------------------------C- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 18761 34 - 54875 ------CT-AGGTCATTTAA---------G---------GTGG-------------------TGG--CCCTACTGCCCAC- i ochPri2.scaffold_9426 C 0 C 0 s pteVam1.scaffold_11245 30256 44 + 48268 CCCTCTT---GTGCACTGGATCATTT-AAG---------CGGG-------------------TGG--CCCGGC--TCTAC- i pteVam1.scaffold_11245 M 100 C 0 s myoLuc1.scaffold_125911 474 49 + 4959 CCCTCCTC-CATGCACTTGATCATTTCACG---------CAGG-------------------TGG--CCCTGCCGTCCGC- i myoLuc1.scaffold_125911 C 0 C 0 s felCat3.scaffold_206428 40543 49 + 132007 CCACCCTG-AGTGCGCTTGATCATTCAAGG---------CAGG-------------------TGG--CCCTGCTGTCCAC- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59452206 49 - 64418924 CCACCCTC-GGTGCACTTGATCATTTAAGG---------TAGG-------------------TGG--CCCTGCTATCCAC- i canFam2.chr9 C 0 C 0 s equCab2.chr11 58058628 49 - 61308211 CCCTACAT-GGTGCCCTTGATCATTTAAGG---------CAGC-------------------TGG--CCCTGCTAGCCAC- i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10875698 76 - 65312493 CCTTCCTC-CACACAGTGAATCATTCAAGGGGTTGCCCCCAAGCGGACCACAGCATCTGTTCTGG---GAGGCTCTTGGC- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 5955 48 + 223990 CCCTCCTC-CGTGCACTGGATCTTTCAAGG---------CAGG-------------------TGG---CATGCTCTCCAC- i turTru1.scaffold_98008 C 0 C 0 s eriEur1.scaffold_157372 140 21 + 3406 -----------------------------G---------CAGG-------------------TGG--CCTCAATCCCCAC- i eriEur1.scaffold_157372 N 0 C 0 s loxAfr3.scaffold_49 14450951 50 - 17734757 CATTCCTC-GGTGGGCTTGATGGTGTGAGG---------CCAG-------------------TGG--CCCTGCTGACCACC i loxAfr3.scaffold_49 C 0 C 0 e dasNov2.scaffold_171027 1697 1984 + 4838 M e monDom5.chr2 304557512 13025 - 541556283 I e mm9.chr11 118777177 80 + 121843856 I a score=-18809.000000 s hg19.chr17_gl000204_random 63490 27 + 81310 T-------CCCTTTCTA---------------------GAAAC-----------------------------------------------C--TCG-----ACT-TCATC- s panTro2.chr17 79495047 27 + 83384210 T-------CCCTTTCTA---------------------GAAAC-----------------------------------------------C--TCC-----ACT-TTATC- i panTro2.chr17 C 0 M 785 s ponAbe2.chr17_random 16081128 15 + 17838096 T-------CCCTTTCTA---------------------GAAAC-------------------------------------------------------------------- i ponAbe2.chr17_random C 0 I 801 s rheMac2.chr16 75054726 27 + 78773432 T-------CCCTTTCTA---------------------GAAAC-----------------------------------------------C--TCT-----TCT-TTACC- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 61978 27 - 95547 T-------CCCTTTCTA---------------------GAAAC-----------------------------------------------C--TCT-----TCT-TTACC- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 64509 27 + 225949 T-------CCCTTTCTA---------------------GAACC-----------------------------------------------C--TCA-----TCT-TTATC- i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 41103 28 + 287808 T-------CCCTTTCCA---------------------GAAAT-----------------------------------------------T--TCA-----TTTCTTACC- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118777257 20 + 121843856 c-------cctcccct------------------------ccc-----------------------------------------------c--tcc---cctc-------- i mm9.chr11 I 80 C 0 s cavPor3.scaffold_76 4405175 26 + 7991924 G-------Cctcctctg---------------------tggcc-----------------------------------------------c--tctggggctc-------- i cavPor3.scaffold_76 I 24 C 0 s oryCun2.chrUn0958 34816 21 + 41507 T-------CCCTTCCTA---------------------GGAGC-----------------------------------------------T--TGT-----TC-------- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 18795 21 - 54875 T-------CCCTTTCTA---------------------GAAGT-----------------------------------------------T--TCT-----TC-------- i ochPri2.scaffold_9426 C 0 C 0 s pteVam1.scaffold_11245 30300 26 + 48268 T-------CCCTTTCTA---------------------GAAAC-----------------------------------------------G--TCT-----TCC-CGC-C- i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_125911 523 27 + 4959 T-------CCGTTTCTA---------------------GAAAG-----------------------------------------------T--TCT-----TCC-TTCTC- i myoLuc1.scaffold_125911 C 0 C 0 s felCat3.scaffold_206428 40592 27 + 132007 T-------CCCTTTCTG---------------------GAAAC-----------------------------------------------T--TCC-----TCC-TCATC- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59452255 27 - 64418924 T-------CCCTTTCTG---------------------GAAAC-----------------------------------------------T--TCT-----TCC-TGATT- i canFam2.chr9 C 0 C 0 s equCab2.chr11 58058677 27 - 61308211 T-------CCCTTTCTA---------------------GAAAC-----------------------------------------------T--TCT-----TCC-TCATC- i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10875774 102 - 65312493 TCTGTCACCCCTTGTTATGAAAGTTGGATGGTGCCTGGGAACCCTCTGCTGGCTCCTCGGCCTTCTCAGCAGGGAACAAGGCAGGTGGCAT--GTT-----CTC-CACTC- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 6003 27 + 223990 T-------CCCTTTCTA---------------------GAACC-----------------------------------------------T--GCT-----CCC-TTATC- i turTru1.scaffold_98008 C 0 C 0 s eriEur1.scaffold_157372 161 29 + 3406 T-------CCTCTTCTA---------------------GAAAC-----------------------------------------------TTGTCT-----TCC-TTGCC- i eriEur1.scaffold_157372 C 0 C 0 s loxAfr3.scaffold_49 14451001 28 - 17734757 -------ACTGGGTCTT---------------------GAGAC-----------------------------------------------C--CTC-----TCC-CTCCTT i loxAfr3.scaffold_49 C 0 C 0 e gorGor1.Supercontig_0007361 31395 8539 - 64270 M e dasNov2.scaffold_171027 1697 1984 + 4838 M e monDom5.chr2 304557512 13025 - 541556283 I a score=-217946.000000 s hg19.chr17_gl000204_random 63517 60 + 81310 CTCCA-----CCACAGCACCGTCT-----CCC-----ACTCTTCTCTCCC------------GAGGT-------------TGCACGTCAGCATC-------TCCAC--C s rheMac2.chr16 75054753 60 + 78773432 CTCCA-----CCACAGCACCGTCT-----CCT-----ACTCTTCTTTCCC------------AAGGT-------------TGCACGTCAGCATC-------TCCAC--C i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 62005 60 - 95547 CTCCA-----CCACAGCACCGTCT-----CCT-----ACTCTTCTTTCCC------------AAGGT-------------TGCACGTCAGCATC-------TCCAC--C i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 64536 59 + 225949 CTCCA-----CCGCTGTGCTATCT-----CCC-----ACTCCTCTCTCCC------------GAGG--------------TGCACGGCCGGATC-------TCCAC--C i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 41131 35 + 287808 CTCCAG----GGACAGCAC-------------------------------------------------------------TAGGCTTCAGCACT-------GCCAT--C i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118777277 44 + 121843856 --------------------ctct-----cct------ctcctctcccTC------------AGGGC-------------TCTGGATTGGGCTTC------TCCAT--- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4405201 56 + 7991924 --------------------ctctggggccctctgtggctcctctgtCCT------------GAGCC-------------TGCTGTCCAGACTCC------TCCAT--C i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 34837 50 + 41507 --------------------CTTG-----CCC------TCCCTCTG---T------------ATGGG-------------CGCCGTCCCGCACCCGTCGTGTCCAAGGC i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 18816 39 - 54875 --------------------CTCA-----CCC------TCCC--------------------AAGGC-------------CATGGCTCTGAGGCC------TCCATGGC i ochPri2.scaffold_9426 C 0 C 0 s pteVam1.scaffold_11245 30326 36 + 48268 CTCCG-----TCGCGGCACTCC-------GCT-----GCTC--CTCTG---------------------------------------------C-------ACTCC--C i pteVam1.scaffold_11245 C 0 I 2 s myoLuc1.scaffold_125911 550 42 + 4959 CTTCA-----CCTCAGCACTGCCCCGGAGGCT-----GCT---CTCTG---------------------------------------------C-------ACCTT--C i myoLuc1.scaffold_125911 C 0 I 2 s felCat3.scaffold_206428 40619 40 + 132007 CCGCG-----CGACAGCAAGCTCT-----CCT-----GCTCTTCCCTC---------------------------------------------C-------TCCTT--C i felCat3.scaffold_206428 C 0 I 7 s canFam2.chr9 59452282 40 - 64418924 CTGCA-----TGACAGCCTGGTCT-----TCC-----ACTCGTCCTTC---------------------------------------------C-------TCCTT--C i canFam2.chr9 C 0 I 4 s equCab2.chr11 58058704 49 - 61308211 CTCCA-----TGACAGCATTCTGT-----GCC-----GCTCCCCTCTCCC------------GAGG------------------------CAGC-------TCCCG--C i equCab2.chr11 C 0 I 11 s bosTau4.chr19 10875876 48 - 65312493 CCTTT-----CTAGAACTTTCTCT------CT-----GTTCTTCCCTCCC------------GAGG------------------------CAGC-------TCCCT--C i bosTau4.chr19 C 0 I 11 s turTru1.scaffold_98008 6030 48 + 223990 CTCTA-----TAACAGCACTCTCT------CT-----GCTCTTCCCTCCT------------GAGG------------------------CAGC-------TCCCT--C i turTru1.scaffold_98008 C 0 I 11 s eriEur1.scaffold_157372 190 21 + 3406 CT---------------------------CCT-----GGTCTTCCT-----------------------------------------------C-------TCCAT--C i eriEur1.scaffold_157372 C 0 C 0 s loxAfr3.scaffold_49 14451029 90 - 17734757 -----GTCTTCCACATCACTCTCTTTGCCTCC-----GTTTGTTTTTCCCTGATGTTGTTGTTAGGtgccatccagccgatctgactcagcaac-------cccat--g i loxAfr3.scaffold_49 C 0 I 35 e gorGor1.Supercontig_0007361 31395 8539 - 64270 M e dasNov2.scaffold_171027 1697 1984 + 4838 M e panTro2.chr17 79495074 785 + 83384210 M e monDom5.chr2 304557512 13025 - 541556283 I e ponAbe2.chr17_random 16081143 801 + 17838096 I a score=-31818.000000 s hg19.chr17_gl000204_random 63577 11 + 81310 TGTC--------------TTTCTCT- s rheMac2.chr16 75054813 11 + 78773432 TGTC--------------TTTCTCT- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 62065 11 - 95547 TGTC--------------TTTCTCT- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 64595 11 + 225949 TGTC--------------TTTCTCT- i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 41166 10 + 287808 TGT---------------TTTCCCC- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118777321 2 + 121843856 -----------------------CT- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4405257 11 + 7991924 TGTC--------------TCTCCCT- i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 34887 11 + 41507 CAGC--------------ACTCGAC- i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 18855 3 - 54875 C----------------------TT- i ochPri2.scaffold_9426 C 0 C 0 s pteVam1.scaffold_11245 30364 11 + 48268 CGGC--------------TTCCTCC- i pteVam1.scaffold_11245 I 2 C 0 s myoLuc1.scaffold_125911 594 8 + 4959 TTGC--------------TTCC---- i myoLuc1.scaffold_125911 I 2 C 0 s felCat3.scaffold_206428 40666 11 + 132007 TTGC--------------TTCCCTC- i felCat3.scaffold_206428 I 7 C 0 s canFam2.chr9 59452326 11 - 64418924 TTGC--------------TTCCCTC- i canFam2.chr9 I 4 C 0 s equCab2.chr11 58058764 11 - 61308211 TTGT--------------TTCTCCT- i equCab2.chr11 I 11 C 0 s bosTau4.chr19 10875935 11 - 65312493 TTGG--------------TTCCCTT- i bosTau4.chr19 I 11 C 0 s turTru1.scaffold_98008 6089 11 + 223990 TTGG--------------TTCCCCT- i turTru1.scaffold_98008 I 11 C 0 s loxAfr3.scaffold_49 14451154 25 - 17734757 -tgcagcaggtcgccaggtctttctc i loxAfr3.scaffold_49 I 35 I 317 s choHof1.scaffold_410167 26 11 + 1023 -TGC--------------TCTTCCCT i choHof1.scaffold_410167 N 0 C 0 e gorGor1.Supercontig_0007361 31395 8539 - 64270 M e eriEur1.scaffold_157372 211 0 + 3406 C e dasNov2.scaffold_171027 1697 1984 + 4838 M e panTro2.chr17 79495074 785 + 83384210 M e monDom5.chr2 304557512 13025 - 541556283 I e ponAbe2.chr17_random 16081143 801 + 17838096 I a score=-219594.000000 s hg19.chr17_gl000204_random 63588 70 + 81310 GCTTCTCCC--TAAACACCAGCGTC-CCA-----------------------------------------------------------------TTTT-CCCAGGTG-----------ATCCTAT---TTTTCTCCCCAA---------------TGAGCTCATC-CCT s rheMac2.chr16 75054824 70 + 78773432 GCTTCTCCC--TAAACACCAGCTTC-CCA-----------------------------------------------------------------TCTC-CCCAGGTG-----------TTCCTAT---TTTTCTCCCCAG---------------TGAGCTCATC-CCT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 62076 70 - 95547 GCTTCTCCC--TAAACACCAGCTTC-CCA-----------------------------------------------------------------TCTC-CCCAGGTG-----------TTCCTAT---TTTTCTCCCCAG---------------TGAGCTCATC-CCT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 64606 71 + 225949 GCTTCTCCC--TAACCACCAGCTTC-TCC-----------------------------------------------------------------TTTCTCCCAGGTG-----------TTTCTAT---TTTTTCTCCCAG---------------TGAGCTCCTC-CCT i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 41176 72 + 287808 ACATCTCCCCGTGAGCACCAACTGC-TCC-----------------------------------------------------------------AAGA-CTCAGGGG-----------TTCCCAT---TCTTCTCCATGA---------------CCAACTCATC-CAT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118777323 97 + 121843856 GCTTGTCCT--TGCACACCAGCTTC-CCAATCCGAGCAGAGCA-GAGTGCGGGGAAGGCTTG--------------------------------CCAG-CTCAGCTGC------CCCCCCCCCAA---C--------------------------TGATGTCATCCACT i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4405268 152 + 7991924 GCTGCTCCC--TGCATGACAGCTTG-CCA----GAGGCATGCACCAGGCCTCGTTCTGCTTGctcctcctcttcctcctcctcctcttcttcctcctc-ctcctcttc------ctcctcctcct---cctcttcctcctcctccttctcctcTGTGATGTCATCTGCT i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 34898 83 + 41507 GC-----------CTCCATTGCTCC-GCG----GCCTGGGACTCCAGCGC--------------------------------------------CAGC-CTCGCCCCA------CCCCTTCCCGA---TCTCCTCCTTG----------------TGTTCTCATCCCCC i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 18858 57 - 54875 GC-----------CACCAGGG-------------------GGTCCAGGGT--------------------------------------------CCGC-CTCACCCCG------CCCCTCCGCAT---CCCCCTCCTC----------------------------CCG i ochPri2.scaffold_9426 C 0 C 0 s pteVam1.scaffold_11245 30375 79 + 48268 ACTGCTCCG--TGAAGTCCAGCTGT-CCC-----------------------------------------------------------------GAGC-CGCCATCGTC---GGCCCTTTCTCAT---TCTCTCCCTCCA---------------CGATCTCACCCTGT i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_125911 602 6 + 4959 ------------------------------------------------------------------------------------------------------------------CCCTTT------------------------------------------------- i myoLuc1.scaffold_125911 C 0 C 0 s felCat3.scaffold_206428 40677 76 + 132007 ACTGCTCCC--CAAATGCCAGCTTT-CCC--------------------C--------------------------------------------GAGA-CTCAATCT-------CCAGTTCACGT---TATTTTCCTCCA---------------CGATCTTACCCCTT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59452337 76 - 64418924 ACTTCCTCC--CAAATGCCAGCTTT-CCC--------------------T--------------------------------------------GAGA-CTCAATCT-------CCAGTTTACAT---TATTTTCCTCCA---------------CCATCTTACTCCTT i canFam2.chr9 C 0 C 0 s equCab2.chr11 58058775 79 - 61308211 GCTTCTCCC--TAAATGCCAGCTTT-CCC--------------------A--------------------------------------------GAGA-CTCCATCA-------CCCGTCCTTGTGACTGTTTTCCTGTC---------------TGATCTCACCCCCT i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10875946 80 - 65312493 GCTCCTCCT--TAAATGCCCGCTTT-CCC--------------------T--------------------------------------------GAGA-CTCCACTGTC---AGTCCCTTCATGT---TATTTTCCTTGA---------------TGATCTCATCCCCT i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 6100 81 + 223990 GCTTCTCCC--TAAATGCCAGCTTTCCCC--------------------C--------------------------------------------GAGA-CTCCATTGCC---AGTCCCTTCACAT---TATTTTCCTCGA---------------TGATCTCACCCCCT i turTru1.scaffold_98008 C 0 C 0 s eriEur1.scaffold_157372 211 41 + 3406 -------CC--CAAATGCCAGCTGC-----------------------------------------------------------------------------------------CCTTGGCCTAT---ggttttcc---------------------------ccccac i eriEur1.scaffold_157372 C 0 C 0 s choHof1.scaffold_410167 37 88 + 1023 -CCTTCTCC--TTAATGTGATCTTT-CCC--------------AGACTTC--------------------------------------------CCTC-TTCCATTGTCTCAACTGCGGTCACAC---GACATTCCTCGG---------------AAATCCCACCCACT i choHof1.scaffold_410167 C 0 C 0 e gorGor1.Supercontig_0007361 31395 8539 - 64270 M e dasNov2.scaffold_171027 1697 1984 + 4838 M e panTro2.chr17 79495074 785 + 83384210 M e monDom5.chr2 304557512 13025 - 541556283 I e loxAfr3.scaffold_49 14451179 317 - 17734757 I e ponAbe2.chr17_random 16081143 801 + 17838096 I a score=-13940.000000 s hg19.chr17_gl000204_random 63658 71 + 81310 CCAGTGGTCTC--ACTGTCGTGGAAGTCATCCCCGCATTTT-gagctgaaag--ca---acttc-------------agaggtcatgttgca s rheMac2.chr16 75054894 71 + 78773432 CCAGTGGTCTC--ACTGTCGTAGAAGTCATCCCCACATTTT-gagctggaag--ca---acttc-------------agaggtcgtgttgta i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 62146 71 - 95547 CCAGTGGTCTC--ACTGTCGTGGAAGTCATCCCCACATTTT-gagctggaag--ca---acttc-------------agaggtcgtgttgta i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 64677 71 + 225949 CCAGTGGTCTC--ACTGTTGTGGAAGTCATCTCTGCATTTT-gagctggaag--tg---acttc-------------agagatcatgttgca i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 41248 70 + 287808 TTCATGGTCTC--TC-GCCACAGAag-catcctggcctttcagagccagaag--ca---acttc-------------agaggctgcactgtg i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118777420 66 + 121843856 CCC-CACAGTC--CCTGGGACAGAAGTCACCA----------GGGCTGAATG--CATCCACCCCAG-----------AGCAGCCCCTTTGTG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4405420 61 + 7991924 CCTGTGGTTTC--ACTGtcaaaggattcgtca----------tagctgggag--ta---acttctg--------------agtcatttcatg i cavPor3.scaffold_76 C 0 C 0 s oryCun2.chrUn0958 34981 67 + 41507 CCCCGCCCCGC--CCTGGG--------CTACA----------GGGCCGGGCA--CC---ATCCCCGGGCAGCAGCTAAGAGGTCGCGTGGCG i oryCun2.chrUn0958 C 0 C 0 s ochPri2.scaffold_9426 18915 54 - 54875 CCTGATTCCAT--TCTGCC--------TCCCA----------GCGGGGGAGG--TC---ACTCC-------------GGAGGGTGTGCCGTA i ochPri2.scaffold_9426 C 0 C 0 s pteVam1.scaffold_11245 30454 45 + 48268 CCCCTGGTTTC----------------------------Acagagctggaag--ca---actc--------------agaggtccctttgta i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_125911 608 35 + 4959 ----------------------------------------CAGAGCCGGGGGGCGA---GGCC--------------AGGGGTCCTCTGGTA i myoLuc1.scaffold_125911 C 0 C 0 s felCat3.scaffold_206428 40753 69 + 132007 CCCC-GGCTTC---CTGTCCCAGATGTCTtcatggcatttccga-ctggaag--ca---gctct-------------agaggtcatttcgta i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59452413 68 - 64418924 CGTT-GGCTTC---CTGTCCCAGACGTCatcatggcatttccga-atggaag--cg---gctc--------------agaggtcattctgaa i canFam2.chr9 C 0 C 0 s equCab2.chr11 58058854 69 - 61308211 CCCCTGGCTTC--ACTGTGGCAGACGTCatcttggtatctcagagctggaag--ca---acccc-------------agggttcgt---gac i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10876026 56 - 65312493 CCCTTGGTGTC--ACTGTCGCGGGCATCATCCCGGCATTTCAGAGCTGGAGG--CA---ACTC----------------------------- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 6181 56 + 223990 CCCCTGGTTTC--ACCATCGCAGACGTCATCCCAACATTTCAGAGCTGGAAG--CA---ACTC----------------------------- i turTru1.scaffold_98008 C 0 C 0 s eriEur1.scaffold_157372 252 52 + 3406 ccccag---tc--attATCCCAGGTGCCAACTCAGCCTTTCAAA-CCAGAAG--CT---GCTG----------------------------- i eriEur1.scaffold_157372 C 0 C 0 s loxAfr3.scaffold_49 14451496 72 - 17734757 TCGGTGAGCTCATCCTGCCATGGAAGTCACCATGGCCCTGa-gagctgggag--cc---acctc-------------agaagtcgctttgt- i loxAfr3.scaffold_49 I 317 C 0 s choHof1.scaffold_410167 125 71 + 1023 CCTGTGGCTTC--CCTGCCAGAGAAGGGATTCTGGCCTCTT-GAGCCAGAAG--CA---GCCTC-------------AGACGTTGCTCTGTA i choHof1.scaffold_410167 C 0 I 1 e gorGor1.Supercontig_0007361 31395 8539 - 64270 M e dasNov2.scaffold_171027 1697 1984 + 4838 M e panTro2.chr17 79495074 785 + 83384210 M e monDom5.chr2 304557512 13025 - 541556283 I e ponAbe2.chr17_random 16081143 801 + 17838096 I a score=-156632.000000 s hg19.chr17_gl000204_random 63729 198 + 81310 cagtccgcccatatcacagatgagaacactgaggcccagaatgtccc--gtggctcgc---------------------cAGCAGCTCTGGGTCC------TGGC-CTG------GGA---TGCTGCCTACTGCG------CCA-------GCCCCA----CTGCCCCGCCGCCT-----------CTTGTGTCACATG-------C----------------AGGGAGCA-GCAAGCGCATCTGCGATGT----CACATGTGC--ACCT----CCAGGCTTGAT----------ATTTTATTTAAGAG s choHof1.scaffold_410167 197 186 + 1023 CATT-GCCTCATTCCTCGGATGAGAACACCAAGGCCCGGAGTGGCC---ATCGCCTGC-----------------------------TTTGAGCC------CGGC-CTC------GGACTCCACTGCAGCTGGGA------CCC-----------------CCTGCCACCATCCC-----------CTCACTTCCCACA-------C----------------AGTGAGCAGGTGGGTCTACCTGCTACGT----CACATGCCC--ACTT----TCAGGCTTGAC----------ATTTTATTGAAGTG i choHof1.scaffold_410167 I 1 C 0 s loxAfr3.scaffold_49 14451568 196 - 17734757 cagt-cctgcatttcacagatgagcaaacacaggcccaaagCTGCC---CTGGCCTT-----------------------------------ACC------AGGC-CCCCAGAGAGGGAGGGGCAGCCCCAGGCG------AAC-----------------CCCGCCTCTGGCTCTGCAGACAGGGCTGACACCTGGCT-------C----------------TGCAGACAGGTCGGTGGCTCTGCGGTGT----CCAAGGCAT--ACCT----TCAGAGCGGAT-----------CTTCACTGACGAG i loxAfr3.scaffold_49 C 0 C 0 s eriEur1.scaffold_157372 304 170 + 3406 CAGTGAAGGGCCTATGCAGAAGGGGGAATTAAGGC-TGGAACTGCCAA-A-------------------------GAGATAGCATCT-TGGACCCTGACC-CCAC-TCC------AGG----ACTGCAAG------------CC----------TCC----GAGCCAC---ATCC-----------TCTGTGTCACATT-------TA---------------TGGGAGC-----------TCTGT---------CACTC-CAA--TCTT----GCAGATGCAAC----------ATTTTATTTCAGGC i eriEur1.scaffold_157372 C 0 C 0 s turTru1.scaffold_98008 6237 218 + 223990 CAG------------AAAGATGAGAAAACTGAGGC-CAGCATGTCCAG-GTGCACTGCCGGGGCCTCCCAGCACATGGGCAGCAACTCCAGACCTTGAACGCAAC-CTC------CGA---CTCTGCCAGCAGCGCTGCCCCCA----------CCC----CTGCCATGGTGCCT-----------CTTATTTCACATG-------CA---------------GGGGAGCAGGTGGGTGCATCTGCAATGT----CACACACAC--ACTT----CCAGACTTGAT----------ATTTTATTTAAGAG i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10876082 232 - 65312493 CAG------------AAAGATGAGACAACTGAGGT-CAGCGTGTCCAG-GTGCCCTGCGGGGGCCTCCCAATGCCTGGGTAGCAGCTCTGGACCCTGAACCCCGC-CTC------TGG---CTCCGCCAGTAGTCCTGCCCCCACCCCCCCCGCCCC----CCACCACACTGCCT-----------CTTATTTCACATG-------CA---------------GGGGAGCTGGTGGGTGCATCTGCAATGTCACACACACACAC--ACTT----CCAGACTTGAT----------ATTTTATTTAAGAG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58058923 218 - 61308211 cagtccc--catgctacagatgagaaaagcaagccccagagcatccag-gtgccctgccagggtctcccggcGCTCGAGAAGTGACTCGGGACCTTGAAC-CAGC-CTC------GGA---CTCTGCGA-------------CA----------GCC----CTGCCACACGGCCT-----------CTTATTTCACAGG-------CA---------------GGGGAGCAGGCAGGGGC-CCTGCACTGT--CACACACACACGTGCTG----CCAGACTTGAT----------ATTTTATTTAAGAG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59452481 197 - 64418924 cagtcccctcctattacagctgaggaaactgaggctcagagT------------------------------GCCTGAACAGCAGCCCTAGACCCTGACC-CCAG-GTC------TGA---GTCTGCAAGCAGGA------CCA----------CCC----CCGCCATGCCGCCT-----------CCTACTTCACATG-------CA---------------GGGGAGCAGACAGGTGCATCTGCAATGT--CACACACACAC--ACTT----CCAGACTTGAT----------ATTTTATTTAAGAG i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 40822 217 + 132007 cagtcccctcctgtcacgttggaggaaactgaggctcagagCAGCCAG-G----CTGTCGG--------GGAACCTGCGCGGAAGCCCTGGACCCTCAAC-CCGGCCTC------GGA---GTCTGGGAGCAGGG------CTA----------CCCCCCGCCCCCACCGCACCT-----------CCCACATCACATG-------CA---------------GGGGAGCAGGTAGGTGTATCTCCAATGT----CACACACAC--ACTT----CCAGACTTGAT----------ATTTTATTTAAGAG i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_125911 643 176 + 4959 CAG-CC---CATACTACAGGCGAGAAAACCGAGGC-CAGCGACCTCGC-CTGCGG-------GTCTCC-TGCGCAGGGGCAGCCCCTCCAGGCCGCGACC-CCGC-CCC------TG-----CACGCCCGCATCG------CCC----------ACC----GGGG----------------------AGATGTCACGCGTCTGCCCTG---------------T---------------------------------CACACAC--AAGC----CCAGACGTGAT----------CTTTGATTGAAGAG i myoLuc1.scaffold_125911 C 0 C 0 s pteVam1.scaffold_11245 30499 227 + 48268 cagtcc---cctattacagataaggaaactgaggctcagagagtccag-gtgcgt-gccggcgtctccaagcgcgcgggcagcacctccagacctcggcc-ccgc-ccc------tg-----tctgCAGGCAGCGCGG--CCCC----------ACC----CGGGCACTCGGCCT-----------CGTATGTCACGTATCTCACGTG---------------TGGGGGCAGGAAGGTGCCTCTGCAGT------CACACACAC--ACTT----CCAGACATGAT----------ATTTTATTTAAGAG i pteVam1.scaffold_11245 C 0 C 0 s ochPri2.scaffold_9426 18969 125 - 54875 CAGC------------------------------CCCAGGACA-------------------------------------------------------------C-TCC------AGA---TGCTGCCCACAGAG------CC-------------------------GTCACCT-----------CACCCTGACCGTG------------------------AGGAAGCTGGCAGGTGTGTCAGCCACAC----CATGCACGC--ACGCACTGCCCAGGTCGAT----------GCTCGCCT-CGGAG i ochPri2.scaffold_9426 C 0 C 0 s oryCun2.chrUn0958 35048 206 + 41507 CAGTGCCCCCACACCACAG-TGACAAAACCGAGACCCGGGACATTGCAGGCCTTTGGCTGTGG----------------CTCCAGCCGGGGGAGC------CAGC-CTC------AGA---TGCTGCCCGCGGAG------CCT---GCTGGGCCTA----CCGG-GTGCCCTCT-----------CA-CCTGCACGCA------------------------GGGCGGCCGGCAGGTGCAGCAGCGGCGC----AGCGCACGC--CTGC----CCCGGCTCGAG----------GCTTCCTTCCAGAG i oryCun2.chrUn0958 C 0 C 0 s cavPor3.scaffold_76 4405481 179 + 7991924 tggt-ctccaacaggacagatgaggagactgaggccctagcat----ggaggacttgcTGGAC---------------ACTCCAGACATGGCACT------CAGC-CTT------GGA---CGCTGCCCC-AG-----------------------------------------T-----------CACTGGGCACATA------------------------GGGGAGCAGGC-GGCATGTCTGCAAGGC----CATGTGAAT--CCTC----------TTGGCTGGACAGCTTGTTTTATTTAAGAG i cavPor3.scaffold_76 C 0 I 343 s mm9.chr11 118777486 125 + 121843856 T--------------------------------GCCACAGTCA----GGGTGTCCTGCAG-------------------CTACAGACATGG-ACT------CTGC-CTC------AGA---TGCTGTCAAGGG-----------------------------------------T-----------CACTCCAAAGAAG------------------------GGGAGGAAGTT-GGTAT-----CA--------CAAACAAAC--CTGT----------CTGAC----------ATCTTATTCAAGAG i mm9.chr11 C 0 C 0 s otoGar1.scaffold_94362.1-287808 41318 186 + 287808 cagcc-cctcacagtgcagatgaacacacggaggcccagaACGTCCC------------------------------------AGTACCTGGCCT------TGGA-CCG------AG----TGTTACCCA----A------CCC-------------------GTCCTGTTACCC-----------CACCTGTC-CCTG-------CCCTGGCTCCAGACTCAAGGGAGCCGGCCAGTATAGTTGCAATGT----CACAGTTGC--ACTT----CCAGGCCTGAT----------GCTT-ATTTCCGAG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s calJac1.Contig5139 64748 197 + 225949 cagcctccccatattacagatgagaagactgaggcccagcatgtccca-gtggcttgc---------------------cAGCAGCTCTGGGCCC------TGGC-CTG------GGA---TGCTGCCGACTGCG------CCG--------GCCCG----CTGCCCCGCCACCT-----------CT--TGTCACATG-------C----------------GGGGAGCAGGCAGGCACATCTGCAATGT----CACATGTGC--GCTT----CCAGGCTTGAT----------ATTTCATTTAAGAG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 62217 191 - 95547 cagtcaccccatattacaggtgagaacactgaggcccagaatgtccc--atggcttgc---------------------cAGCAGCTCTGCATCC------CGGC-CTG------AGA---TGCTGCCAACTGCA------CCA-------------------GCCCTGCTGCCT-----------CTTGTGTCACATG-------C----------------AGGGAGCAGGCAGGCGCATCTGCGATGT----CACGTGTGC--ACCT----CCAGGCTTGAT----------ATTTTATTTAAGAG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75054965 191 + 78773432 cagtcaccccatattacaggtgagaacactgaggcccagaatgtccc--atggcttgc---------------------cAGCAGCTCTGCATCC------CGGC-CTG------AGA---TGCTGCCAACTGCG------CCA-------------------GCCCCGCTGCCT-----------CTTGTGTCACATG-------C----------------AGGGAGCAGGCAGGCGCATCTGCGATGT----CACGTGTGC--ACCT----CCAGGCTTGAT----------ATTTTATTTAAGAG i rheMac2.chr16 C 0 C 0 s gorGor1.Supercontig_0270811 0 198 - 780 cagtccccccatatcacagatgagaacactgaggcccagaatgtccc--gtggctcgc---------------------cAGCAGCTCTGGGTCC------CGGC-CTG------GGA---TGCTGCCTACTGCG------CCA-------GCCCCA----CTGCCCCGCCGCCT-----------CTTGTGTCACATG-------C----------------AGGGAGCA-GCAGGCGCATCTGCGATGT----CACATGTGC--ACCT----CCGGGCTTGAT----------ATTTTATTTAAGAG i gorGor1.Supercontig_0270811 n 0 C 0 e dasNov2.scaffold_171027 1697 1984 + 4838 M e panTro2.chr17 79495074 785 + 83384210 M e monDom5.chr2 304557512 13025 - 541556283 I e ponAbe2.chr17_random 16081143 801 + 17838096 I a score=918817.000000 s hg19.chr17_gl000204_random 63927 148 + 81310 TGTGCGACTCCATATCAGTGCCCAGTGGCTTTCAGTTCTGACATTTATCTTCTCCAGAGGAGGATGAACCA----CTTGCACGCCGT-CCGTC----TCTCCTCCC--ACGTGGATGGGAA----AT-GTCAGAGGG----------AAGTCCAGGTAGT--TC-----------AGGGTCCCACGT s gorGor1.Supercontig_0270811 198 148 - 780 TGTGCGACTCCATATCAGTGCCCGGTGGCTTTCGGTTCTGACATTTATCTTCTCCAGAGGAGGATGAACCA----CTTGCACGCCGT-CCGTC----TCTCCTCCC--ACGTGGATGGGAA----AT-GTCAGAGGG----------AAGTCCAGGTAGT--TT-----------GGGGTCCCACGT i gorGor1.Supercontig_0270811 C 0 C 0 s rheMac2.chr16 75055156 148 + 78773432 TGTGCGACTCCATATCAGTGCCCAGTGGCTTTCAGTTCTGACATTTATCTTCTCGAGAGGAGGATGAACCA----CTTGCACGCCGT-CCGTC----TCTCCTCCC--ACGTGGATGGGAA----AT-GTCAGAAGG----------AAGTCCAGGCAGT--TC-----------GGGGTCCTACGT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 62408 148 - 95547 TGTGCGACTCCATATCAGTGCCCAGTGGCTTTCAGTTCTGACATTTATCTTCTCGAGAGGAGGATGAACCA----CTTGCACGCCGT-CCGTC----TCTCCTCCC--ACGTGGATGGGAA----AT-GTCAGAAGG----------AAGTCCAGGCAGT--TC-----------GGGGTCCTACGT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 64945 148 + 225949 CGTGCGGCTCCATATCAGTGCCCAGTGGCTTTCAGTTCTGACATTTATCTTCTTGAGAGGAGGATGAGCCA----CTTGCACATCGC-CCGTC----TCTCCTCCC--ACGTGGCTGGGAA----AT-GTCAGAGGG----------AGGTCCAGGCAGC--CT-----------GGGGTCCCACAT i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 41504 132 + 287808 GGTGCACCCCTATGTCAGCGCCCAGCTGCTCTCCGTCCTGACACTGATC-CCTCCAGAGGAGGATGAGTCA----CTTGCTCATCATCCCACC----TCTCCTCCC--ACATGGGTGAGAA----AT-GCCGGAGGG----------A-----------------------------GGTCCCATGT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118777611 138 + 121843856 ------CTCCCCAGATGGA-CCTAGCTGCTTTTAGACCTAATACCCAACTTCTCCAAAAGAGGGTGAACCA----CTGGCAAACTGT-CC-TG----TCTCCCCTA--AGATGGATGGAAG----AA-GTCAGAAGG------------GAACAGGCAGC--TC-----------GAGGCTCCGGGC i mm9.chr11 C 0 C 0 s oryCun2.chrUn0958 35254 79 + 41507 --------CGCATCTCGGT-CTCGGC----------TCTGACATTTA----------CAgcgg----------------cccgtcgc-cc-cc----ccccccccc--ccggggAGGAGGA----CA-AGCAGGGGG-------------------------------------------------- i oryCun2.chrUn0958 C 0 N 0 s ochPri2.scaffold_9426 19094 142 - 54875 --------CGTGTGGCTGT-GCGGGC-------AGTTCTGACACTTAGCTCT-----CTGAGGATGAGCCA----C--ACTCACCGC-AT-CCCGGTCTCCCTTCC--GTGAGGATGGGAAATGTCA-GCCAGGAGTCAGAGGTCGGAGGTCGAGACATC--TC-----------AGGGTCCAGGTC i ochPri2.scaffold_9426 C 0 C 0 s pteVam1.scaffold_11245 30726 145 + 48268 CGTGCAGCTCTACATCAGTACCCAGTTGCTTTCAGTTCTGACATTTATCTT---GAGAGGAGGGGGAACCA----CTTGCAGATCGTCCCGTC----T-CCCTCCC--ATGTGGCTGGGGA----AGTGGCAGAGGG----------AGA-CCAGGCCGC--TC-----------AGGGGCCCACGT i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_125911 819 150 + 4959 CGAGCAGCTCTGTGTCGGT-CCCGGTCGCTTGCCGTCCTGACATTTATCTCCTGGAGGGGAGGGTGAACTAAGGGCTCGCAAAGCGTCCCCTG----TCCCCTCCC--GTGAGGATGGGAA----AG-GTCAGCGGG----------AGAGCCGGGCAGC--GC-----------GGGG--CCGCAG i myoLuc1.scaffold_125911 C 0 C 0 s felCat3.scaffold_206428 41039 149 + 132007 TGTGCAGCTCTATATCAGTACCCGGTTGCTTGCAGTTCTGACATTTATCTTCTCGAGAGGAGGGCGAACCC----CTTGCAAATCATGCCATG----TCTCCTCCC--ACGTGGATGGGAA----AT-GTCAGAGGG----------AGATCCAGACAGC--TC-----------AGGGTCCTGTGT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59452678 148 - 64418924 TGTGCAGCTCTATATCAGTACCCGCTTGCTTTCAGTTCTGACATTTATCTTCTCGAGAGGAGGGTGAACCC----CTTGCAAATCAT-CCATA----TCTCCTCCC--ACGTGGACGGGAA----AT-GTCAGGGGG----------AGATCCAGGCAGC--TC-----------AGGGTCCCGTGT i canFam2.chr9 C 0 C 0 s equCab2.chr11 58059141 159 - 61308211 CGTGCAGCTCTATATCAGGACCCAGTTGCTTTCGGTTCTGACATTTATCTTCTCGAGAGGCGGGTGAACCA----TTTGC-CATCGTCCTGTC----TCTCCTCCC--ACGTGGACAGGAA----AT-GTCAGAGGG----------AGATCCAGGAAGA--TCCAGAGGGAGATCAGGTCCCGTGT i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10876314 149 - 65312493 CAGGCAGCTCTATATCAGTACCCAGTTGCTTTCAGTTCTGACATTTATCTTCTCCAAAGGAGGGTGAGCCA----CTTGCAAATCGTCCCATC----TCTCCTCCC--ACGTGGCTGGGAA----AT-GTCAGAGGG----------AGATCCAGGCAGC--TC-----------AGGATCCCTGGC i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 6455 149 + 223990 CATGCAGCTCTATATCAGTACCCAGTTGCTTTCAGTTCTGACATTTATCTTCTCCAAAGGAGGGTGAGCCA----CTTGCAGATCGTCCCATC----TCTCCTCCC--ACGTGGCTGGGAA----AT-GTCAGAGGG----------AGATCCAGGCAGC--TC-----------AGGGTCCCTTGC i turTru1.scaffold_98008 C 0 C 0 s eriEur1.scaffold_157372 474 147 + 3406 TGTGCTGCTCGGTAGCAGTCCCCAGTTGCTTCTAGTTTTGACATTTATCTTCTGGGGAGGAGAGTGAACCA----CCTGCAAACTGTCCCACC----ACTCCTCCC--ACGTGGAT-GAAA----AT-GTCAGAGGG----------AACGCCAGGTGGC--AC-----------AGGGTCCCA-GC i eriEur1.scaffold_157372 C 0 C 0 s loxAfr3.scaffold_49 14451764 145 - 17734757 TGGGCAGCTCAACATCCATCCCCAGCTGCCTGCAGTTCTGACATTCATCTTCTGCAGGGAGGGG-GAACCA----CTTGTAAACTGTCCCATC----TCACCTCCC--ACGTGGAT-GGAA----AT-GTCAGAGAG--------------AGATGCGGCTTAT-----------GGGGTCCCCTGA i loxAfr3.scaffold_49 C 0 C 0 s choHof1.scaffold_410167 383 142 + 1023 TATCAGTATCTGTATCAGTGCCTGCTTGCTTTCAGCTTTGACATTTATCTTCTCGAGAGGAGGG-GGATCC----CTGGCAGGCTGTCCCACC----TCTCCTCCC---CGTGGGT-GGAG----AT-GTCAGCAGA--------------TCAGATAGC--AT-----------GGGGTCCCACGT i choHof1.scaffold_410167 C 0 C 0 s monDom5.chr2 304570537 140 - 541556283 TATACAAATTAATCTTGGTGCTTATTTGCTTTCAGTTCTGACATTTATTTAT-----------ATGTGTCA----CTTGCAAATTTTTGCATC----TCTTCTCCTATACATGAATGAGAA----AT-GTAGGAGGG----------AAAGCCAGCCAGC--AT-----------AGGATCCTATAT i monDom5.chr2 I 13025 C 0 e dasNov2.scaffold_171027 1697 1984 + 4838 M e panTro2.chr17 79495074 785 + 83384210 M e cavPor3.scaffold_76 4405660 343 + 7991924 I e ponAbe2.chr17_random 16081143 801 + 17838096 I a score=-30568.000000 s hg19.chr17_gl000204_random 64075 89 + 81310 CCACACCACA-AGGATTTA---CTGTTTT-TGTGCTGC------TTGATG-ACACAGCTG------TGTTTGGGGA-GCGGCGAT------------AGCCTAAAAAA-CACACAAGTGGA--------------- s gorGor1.Supercontig_0270811 346 89 - 780 CCACACCACA-AGGATTTA---CTCTTTT-TGTGCTGC------TTGATG-ACACAGCTG------TGTTTGGGGA-GCCGCGAT------------AGCCTAAAAAA-CGCACAAGTGGA--------------- i gorGor1.Supercontig_0270811 C 0 C 0 s rheMac2.chr16 75055304 88 + 78773432 CCACACCACG-AGGATTTG---CTCTTTT-TGTGCTGC------TTGATG-GCACAGCTG------CGTTTGGGGA-GCGGCGAT------------AGCCT-AAAAA-CGCACAAGTGGA--------------- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 62556 88 - 95547 CCACACCACG-AGGATTTG---CTCTTTT-TGTGCTGC------TTGATG-GCACAGCTG------CGTTTGGGGA-GCGGCGAT------------AGCCT-AAAAA-CGCACAAGTGGA--------------- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 65093 89 + 225949 CCACACCACG-AGGATTCT---CTTTTTT-TGTGCTGC------TTCATG-ACACAGCTG------CATTTGGGGA-GCGGCGAT------------AGCCTGAGAAA-CGCACAGGTGGA--------------- i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 41636 63 + 287808 CCACACCCCA-AGTGTTTA---TCCTTTTATGGGCCGT------GTGATG-ACTCAGCTG------CTTCTGGAGA-GCAG------------------------------------------------------- i otoGar1.scaffold_94362.1-287808 C 0 I 2195 s mm9.chr11 118777749 49 + 121843856 -CATGGCTGGTATGGTTCA---ATCT-----------------------------------------CTGTAGGGGAGCAGCTGT------------GGCCT---------------TGAA--------------- i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_149396 782 58 + 1524 CCACACCTCACGGGGTTCA---CTCTTCT-TGGGACAT------TTGGTA-ACGAGCC--------ACTTTGGGAGA----------------------------------------------------------- i dipOrd1.scaffold_149396 N 0 I 32 s ochPri2.scaffold_9426 19236 55 - 54875 -----------CTGCCCCA---CACT----------GC------TGGGTA-AGGCGCCTGAGTCGGCCCTCAGGC--------GA------------GGCGC---------------TGGG--------------- i ochPri2.scaffold_9426 C 0 I 7 s pteVam1.scaffold_11245 30871 91 + 48268 CCACACTGTGCATGTTTCA---GTCCCTC-CAGGCTGC------CTGATTATCGCTGCTG------CTCTGGGAGA-ACAGAGAG------------GACCTGCTGGC-TGTGTGAGGGGA--------------- i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_125911 969 84 + 4959 CCGCAGGGC-CGCACTTCA---CTCCCCT-TGGGCCGC------GGGACC-CCACAGCGG------CC----GAGA-GCCTGGGC------------GGCCTG--GGCAGGTGTGAGCGGA--------------- i myoLuc1.scaffold_125911 C 0 C 0 s felCat3.scaffold_206428 41188 88 + 132007 CCACATTGCACATACTT-----CTCTCGT-CACCCTGC------TTGATA-ACACAGCTG------CTTCTGGAGA-GCCGAGAT------------GGCCTGGGGAC-TGTGCGAGGGGC--------------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59452826 94 - 64418924 CCACATCGCACACTCTT-----CTCTCTT-CGCTTTGCTTAATATTAATA-ACCCGGCTG------CTTCTGGAGA-ACCGGGAT------------GGCATGGGGAA-TGTGACAGGGGT--------------- i canFam2.chr9 C 0 C 0 s equCab2.chr11 58059300 90 - 61308211 CCACATGGCGCATATTTCA---CTCTCTT-TGGACTGC------TTGATA-ACGCAGCTG------CTCGTGGAGA-GCAGAGAC------------GGCCTGGGAGA-CGCATGAAGGGA--------------- i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10876463 89 - 65312493 CCACATCGAGCACATTT-----CACTCTT-TGGGCTGC------TTGGTA-ACCCGGCTG------CTTTGGGAGA-GCTGAGAA------------GGCCTGGGAAATTGCATGAGAGGA--------------- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 6604 86 + 223990 CCACATTGCACACATTT-----CAGTCAT-TGGGCTGC------TTGGTA-ACCCAGCTG------CTTT-GGAGA-GCTGAGAC-------------GCCTGCGAAA-TGCATGAGGGGA--------------- i turTru1.scaffold_98008 C 0 C 0 s eriEur1.scaffold_157372 621 71 + 3406 CTGCTCCATGCAGATTTCACTCCTCTCCA-CAGACTCC------AGGAGG----------------------GAGA-ACC---AT------------GTGCTGGGAGC-----CAAGGGTA--------------- i eriEur1.scaffold_157372 C 0 C 0 s loxAfr3.scaffold_49 14451909 90 - 17734757 TCACACCACGCGTAGTCCG---TGCTTTC-TGCGCCAC------TCGACA-GCACAGCTG------CTTTTGGAGA-GCTGCGCT------------GGCTTGGGACG-CGTGTGCGGGGA--------------- i loxAfr3.scaffold_49 C 0 C 0 s choHof1.scaffold_410167 525 75 + 1023 CCACATCACACACATTTCA---CTCTTGC-T---------------------TGCAGCTG------CCCTTGGAGA-GCCAAGCT------------GGCCTGAAA-A-TGTGTGAGGGGT--------------- i choHof1.scaffold_410167 C 0 C 0 s monDom5.chr2 304570677 116 - 541556283 CAACATCACATTTATTTCA---TTCCCTT-TATGCTTC------TTGACA-ACATGGA-G------ACTTTGGAGT-GCCATGATGGCAGGACTGAAGGCATGGGAAA-TGAGTGTGGGAAGACTGTTCAACTTTT i monDom5.chr2 C 0 C 0 e dasNov2.scaffold_171027 1697 1984 + 4838 M e panTro2.chr17 79495074 785 + 83384210 M e cavPor3.scaffold_76 4405660 343 + 7991924 I e ponAbe2.chr17_random 16081143 801 + 17838096 I a score=-10131.000000 s hg19.chr17_gl000204_random 64164 39 + 81310 AAT-AGCAAA------GGTTTTCTGAGGCACCGT-CAAT--TTCTGCAG s gorGor1.Supercontig_0270811 435 39 - 780 AAT-AGCAAA------GGTTTTCTGAGGCACCGT-CAAT--TTCTGCAG i gorGor1.Supercontig_0270811 C 0 C 0 s rheMac2.chr16 75055392 39 + 78773432 AAT-AGCAAA------GGTTTTCTGAGGCACCAT-CAAT--TTCTGTAG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 62644 39 - 95547 AAT-AGCAAG------GGTTTTCTGAGGCACCGT-CAAT--GTCTGCAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 65182 39 + 225949 AAC-AGCAAA------GGTTTTCTGAGGCACTGC-CAAC--TTCTGCAG i calJac1.Contig5139 C 0 C 0 s dipOrd1.scaffold_149396 872 17 + 1524 GAC-AACAGG------GGTTTTCC------------------------- i dipOrd1.scaffold_149396 I 32 I 7 s mm9.chr11 118777798 39 + 121843856 AGG-AAGGAG------GGTTTTCTAAGGTTCCAT-TCAA--CTTTGAAA i mm9.chr11 C 0 I 9 s ochPri2.scaffold_9426 19298 13 - 54875 GGG-AACTGG------GGTG----------------------------- i ochPri2.scaffold_9426 I 7 I 1 s tarSyr1.scaffold_41848 188 19 + 21754 ---------------------------GCTCTGT-CAAC--TTTTACAA i tarSyr1.scaffold_41848 N 0 C 0 s panTro2.chr17 79495859 28 + 83384210 ------------------TTTTCTGAGGCACCGT-CAAT--TTCTGCAG i panTro2.chr17 M 785 C 0 s pteVam1.scaffold_11245 30962 39 + 48268 GTG-AATGGA------GCATCCCC-AGGCACCTTCCAGC--TCCTGCAG i pteVam1.scaffold_11245 C 0 I 15 s myoLuc1.scaffold_125911 1053 28 + 4959 CGG-AGCAGA------GGGTCC------------CCGGC--GCCTCCTA i myoLuc1.scaffold_125911 C 0 I 4 s felCat3.scaffold_206428 41276 40 + 132007 ACAGGGCACA------GCGACCCC-AGGTGCCACCCAAC--TTTCATAA i felCat3.scaffold_206428 C 0 I 7 s canFam2.chr9 59452920 39 - 64418924 GCA-GGCAGA------GGGTCCCC-AGGTGCCACACAAC--TTTCACAA i canFam2.chr9 C 0 I 7 s equCab2.chr11 58059390 38 - 61308211 GCG-AGCAGA------GGGTTTCT-AGGCACCGC-CAAC--TTCTACAA i equCab2.chr11 C 0 I 8 s bosTau4.chr19 10876552 39 - 65312493 GCC-AGCAGA------GGGTTCCC-AGGCACCATCCAAC--TTTCATAA i bosTau4.chr19 C 0 I 8 s turTru1.scaffold_98008 6690 39 + 223990 GCC-AGCAGA------GGGTTCCC-AGGCACTGTCCAAC--TTTCATAA i turTru1.scaffold_98008 C 0 I 8 s eriEur1.scaffold_157372 692 45 + 3406 GCT-GGCAGACAGTGGCAGTGCCC-AGGCCCCATCCAGC--TTCCACAG i eriEur1.scaffold_157372 C 0 I 7 s loxAfr3.scaffold_49 14451999 39 - 17734757 GCA-AGCCGA------GGGCGCCC-AGGTACCAGCCAAC--TTTTACGG i loxAfr3.scaffold_49 C 0 I 8 s choHof1.scaffold_410167 600 39 + 1023 GCA-AGCAGA------GGGTTCCC-AGGCACCATTGAAG--TTTTGCAA i choHof1.scaffold_410167 C 0 I 7 s monDom5.chr2 304570793 40 - 541556283 AAT-AACAGA------GAAGTTAT-TGCAACagt-cagtcattcaacag i monDom5.chr2 C 0 I 26 e dasNov2.scaffold_171027 1697 1984 + 4838 M e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e cavPor3.scaffold_76 4405660 343 + 7991924 I e ponAbe2.chr17_random 16081143 801 + 17838096 I a score=1013831.000000 s hg19.chr17_gl000204_random 64203 160 + 81310 CCGGGG---------CAGTGGCCAGTGT---CT----CCG-----------------GGAACAGG---------------CGC-CGCAGTCCACTCAGGGGCCCACAGG-TTCTTC---CCCG--TC--TTCC---ATCTCCTT--GTCTTGAGTGGGACGTGAGCCGTATCTCTGAGCTCAGCC----TGTGATTGCACAATAATA-C---CACCCAG-AAAACAAATTA s choHof1.scaffold_410167 646 161 + 1023 TATGAC---------CAAAGCCAAGAAC---CT----TCT-----------------AGAACAGA---------------GAC-TACGGTCCATTCAAGGGCCTGTGGC-CTCTT----CCCA--TC--TTTTTGGATCTCCTC--ACTTTGCATGGGACACATGCTCTATCTTTGAGCTGTGCC----TGTGATTGC-AAGTCATATC---CACCCAG-AAAACTAA-TA i choHof1.scaffold_410167 I 7 C 0 s dasNov2.scaffold_171027 3730 161 + 4838 ---GAC---------CGGAGTCCGCAGC---CT----CCG-----------------GAAACAGA---------------GGC-CACCGTCCCCTCGATGGCCCACTGCGCTCTT----CCCA--TC--CTCTTGGGCCTCCTT--GCTTCGAGTGGGACACATGCCCTACCTTTGAGCTCTGCC----TGCAATTGCAAAGTAATACC---CACCCAG-AAAACAAATTA i dasNov2.scaffold_171027 M 1984 C 0 s loxAfr3.scaffold_49 14452046 154 - 17734757 TGTGGC---------CAAAGCCA----------------------------------AGAACAGA---------------TGC-CGCCATCCACTGGCAGGCCAGCGGG-TTCTTC---CCCA--TC--TTCCCAGATCCTCTT--GTGGTCAATGGGACACAGACCACATCTTTGAGCTGAGCC----TGTGATTGCAAAATGATACC---TACCCGG-AAAACAAATTA i loxAfr3.scaffold_49 I 8 C 0 s eriEur1.scaffold_157372 744 163 + 3406 --CTGG---------CTGAGCCAAGGACGCTAC----CCC-----------------AGGGAAGA---------------CAG-CTGGGCTCCTGTGGTGGGGGAATGG-GCCTCC---CGCA--CCATTGCTGGGCCCTGCTT--GCTTAAA-----------GCCAGATCTTTGAGCTTTCCTCAAATGCAGTTGCACAATTATACCCCTCCTccag-aaaacaaatta i eriEur1.scaffold_157372 I 7 C 0 s turTru1.scaffold_98008 6737 163 + 223990 GACAGC---------CAGGGCCAAGAGC---CT----CCC-----------------AG-ACAGA---------------TGC-CACGGTCCACTCAGGGGCAGGTGTG-TCCTTC---CCCA--TC--TTCTCAGATCTCCTT--GTTTTGAGTGGGACCCACGCCATGGCTTAGAGCTCTGCC----TGCGATTGCACAATAATACC---CACCCAG-AAAACAAATTA i turTru1.scaffold_98008 I 8 C 0 s bosTau4.chr19 10876599 164 - 65312493 GGCAGT---------CAGAGCCAAGAGC---CT----CCC-----------------AGAACAGA---------------TGC-CGTGGCCCGCTCGGGGGCAGCTGGG-TCCTTC---CCGA--TC--TTCTCAGATCTGCTT--GTTTTGAGTGGGACCCATGCCACGTCTTAGAGCTCTGCC----TGTGATTGCACAATAATACC---CACCCAG-AAAACAAATTA i bosTau4.chr19 I 8 C 0 s equCab2.chr11 58059436 164 - 61308211 GCCGGC---------CGGAGCCAAGAGC---CT----CCT-----------------AGAGCAGA---------------TGC-CACGGCCCATTTGGGGGCCGGTGGG-TTCTTC---CCCA--TC--TTCTCAGACCTGCTT--GTTTTGAGTGGGGCCCACGCCATATCTTTGAGCTCAGCC----TGTGATTGCACAATAATACC---CACTCAG-AAAACAAATTA i equCab2.chr11 I 8 C 0 s canFam2.chr9 59452966 148 - 64418924 GACGGC---------CAGAG----------------------------------------ACAGA---------------TGC-TGAGGCCCCTTCGAGGACCTGTGGG-CTCCTC---CCCA--TC--TTCCTGGACCTACTT--GTTTCGAGTGGGACCCATGCCATATCTTTGAGCTCAGCC----TACGACTGCACAATAATACC---CACCCAG-AAAACAAATTA i canFam2.chr9 I 7 C 0 s felCat3.scaffold_206428 41323 164 + 132007 GGCGGC---------TGGAGCGGAGAGC---CT----CCT-----------------AGAACAGA---------------TGC-CGAAGTCCGTTTGAGGACCAGTCGG-TTCCTC---CCCA--TC--TTCCTAGACCGACTC--GTTTCGAGTGGGACGCACGCCATATCTTTGAGCTCAGCC----TGTGATCGCACAATAATACC---CACCCAG-AAAACAAATTA i felCat3.scaffold_206428 I 7 C 0 s myoLuc1.scaffold_125911 1085 138 + 4959 AGACGC---------CGCGGTCCGGTCC---AT----CC---------------------------------------------------------GGGGCCCGGTGGG-T--CCC---CCCT--CC--TTCTCGGCCCTACTT--GCTCCGATTGGGACGCACGCCATATCTTTGAGCTCAGCC----TGTGCTCGCACAATAATACC---CGCCCAG-AAAACAAATTA i myoLuc1.scaffold_125911 I 4 C 0 s pteVam1.scaffold_11245 31016 162 + 48268 GGCGGC---------TGCAGCCCAGAGC---CT----CCC-----------------AGCACAGA---------------TGAGGGAAGAACGCAGCAGGGCCGGTGGG-CTGTTC---CCCG--CC--TTCTCAGACCTACTT--GTTTTGAGTGGGACCCATGCCATATCTTTGAGCTCGGCC----TGTG---ACTCCACAATATA---CACCCAG-AAAACAAATTA i pteVam1.scaffold_11245 I 15 C 0 s ochPri2.scaffold_9426 19312 150 - 54875 GGGGGC---------TGGAGCCAGGGGT---CT----CC------------------AAGACAGG---------------AGC-CTTGTC---CCCCACAGTCATCGCT-CCATCCTCTTGA---------CTCAGCCCCATTTCGGCGTGAAATGTGGCCGGGTGCCGGCAGCTCAGCTGTGAC----TGCTC---------AGCACC---CGCTCAG-AACGCAAACC- i ochPri2.scaffold_9426 I 1 C 0 s mm9.chr11 118777846 163 + 121843856 TATGGC---------CAGCTCCAAGAGC---CT----CCTGGGACAG----------AGGACAGG---------------ATC-CCCA--------CAGGGGCTCCGCA-CTGCTC---TGCA--GT--CTCTGACGGCCACTT--GCCTCAAGCGGGACACACACCATATCTTCCAGCTCAGCC----CATGATTATACAATAATACC---CACCCAG-AAAACAAATTA i mm9.chr11 I 9 C 0 s dipOrd1.scaffold_149396 896 159 + 1524 ---------------------CCAGGGC---CTgcggcggggggggg----------gggggggg---------------cgc-ggcg--------TGGCGGCTGGGCT-CCGTTCCCTCGGG--AC--CTCTCAGATCTCCTT--GTTTTGAGGGGGGCTCACTGCGTGTCACTGAGCTGGGCC----TGCGATTGCACAATAATACC---CACCCAGAAAAACAAATTA i dipOrd1.scaffold_149396 I 7 C 0 s cavPor3.scaffold_76 4406003 115 + 7991924 CTCGGC---------CAGAACCCAGAAC---TC----CC------------------GGGACAGG---------------TTC-CGCAG----CCCTGGGGGCAGCACA-TTCCTC---TGCA--AC--CTGGTAGATCCACT----------------------------------GTTGATTC----CG------------AGTGCC---CACCCAG-TACACAAATTA i cavPor3.scaffold_76 I 343 C 0 s tarSyr1.scaffold_41848 207 172 + 21754 CCAGGGGCCTACAGCCAGAGCCGTGAGT---CT----CGT-----------------AGAACAGG---------------TGC-TGAGGTCCACTTGGGGGCCAGTGGG-TTCTTG---CTCA--TC--TTCTTAGATCGACTT--GCTTTGAGTAGGACATGAGCCATATCTTGGAGCTCAGCC----TGTGATTACACCATAACA-C---CACCCAG-AAAACAAAATA i tarSyr1.scaffold_41848 C 0 C 0 s panTro2.chr17 79495887 160 + 83384210 CCGGGG---------CAGTGGCCAGTGT---CT----CCG-----------------GGAACAGG---------------CGC-CGCAGTCCACTCAGGGGCCCACAGG-TTCTTC---CCCG--TC--TTCC---ATCTCCTT--GTCTTGAGTGGGACGTGAGCCGTATCTCTGAGCTCAGCC----TGTGATTGCACAATAATA-C---CACCCAG-AAAACAAATTA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0270811 474 160 - 780 CCGGGG---------CAGTGGCCAGTGT---CT----CCG-----------------GGAACAGG---------------TGC-CGCAGTCCACTCAGGGGCCTACAGG-TTCTTC---CCCG--TC--TTCC---ATCTCCTT--GTCTTGAGTGGGACGTGAGCCGTATCTCTGAGCTCAGCC----TGTGATTGCACAATAATA-C---CACCCAG-AAAACAAATTA i gorGor1.Supercontig_0270811 C 0 C 0 s rheMac2.chr16 75055431 160 + 78773432 CCGGGG---------CAGTGGCCAGTGT---CA----CCT-----------------GGAACAGG---------------CGC-CACAGTCCACTCAGGGGCCTACGGG-TTCTTC---CCCG--TC--TTCC---ATCTCCTT--GTCTTGAGTGGGACATGAGCCGTATCTCTGAGCTCAGCC----TGTGATTGCACAATAATA-C---CACCCAG-AAAACAAATTA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 62683 160 - 95547 CCGGGG---------CAGTGGCCAGTGT---CA----CCT-----------------GGAACAGG---------------CCC-CACAGTCCACTCAGGGGCCTAAGGG-TTCTTC---CCCG--TC--TTCC---ATCTCCTT--GTCTTGAGTGGGACATGAGCCGTATCTCTGAGCTCAGCC----TGTGATTGCACAATAATA-C---CACCCAG-AAAACAAATTA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 65221 160 + 225949 CCGGGA---------CAGAGGCCAGTGT---CA----CCT-----------------GGAACTGG---------------TGC-CGAAGTCCACTCGGGGGCCCACGGG-TTCTGC---CTCA--TC--TTCC---ATCTCCTT--GTCTTGAGTGGGACATGAGCCGTATCTCTGAGCTCAGCC----TGTGATTGCACAATAATA-C---CACCCAG-AAAACAAATTA i calJac1.Contig5139 C 0 C 0 s monDom5.chr2 304570859 196 - 541556283 --ccgg---------caaaatactaagt---gt----tgggggataaaaaaaaaggcaaaaCAGGGAAACAGCTGTTGAATGT-TGCAGTCAATTCAGTAGTGTGTGGA-TTCTTC---TCTATGTT--TTCTTATATCTACTT--GTTTTGAACTGGGCATGTGCCATATTCTTGAGCTAAGCC----TGTGATTGCAAAATAATACC---CATCCAG-AAAACAAATTA i monDom5.chr2 I 26 C 0 e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e ponAbe2.chr17_random 16081143 801 + 17838096 I a score=2187457.000000 s hg19.chr17_gl000204_random 64363 146 + 81310 AAAATAGGAAAAATCCATCCAAGCC----GTGTGTCT---GCTCA-GGCAG---AATAGTGTCAGATTGCTAGGCAACTCCAGGCAGTCCTGGGGGAAGGAGGGCCGT------GCTCAG-------CTTGTTCTGCAGAAGTAGAGTCCTTGT-CCCTTTTGTGTGGATG s calJac1.Contig5139 65381 146 + 225949 AAAATAGGAAAAATCCATCCAAGCC----GTGTGTCT---GCTCA-GGCAG---AATAGTGTCAGATTGCTAGGCAACTCCAGGCAGTCCTGGGGGAAGGAGGGCCGT------GCTCAG-------CTTGTTCTGCAGAAGTAGAGTCCTTGT-CCCTTTTGTGTGGATG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 62843 146 - 95547 AAAATAGGAAAAATCCATCCAAGCC----GTGTGCCT---GCTCA-GGCAG---AATGGTGTCAGATTGCTAGGCAACTCCAGGCAGTCCTGGGGGAAGGAGGGCCGT------GCTCAG-------CTTGTTCTGCAGAAGTAGAATCCTTGT-CCCTTTTGTGTGGATG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75055591 146 + 78773432 AAAATAGGAAAAATCCATCCAAGCC----GTGTGCCT---GCTCA-GGCAG---AATGGTGTCAGATTGCTAGGCAACTCCAGGCAGTCCTGGGGGAAGGAGGGCCGT------GCTCAG-------CTTGTTCTGCAGAAGTAGAATCCTTGT-CCCTTTTGTGTGGATG i rheMac2.chr16 C 0 C 0 s gorGor1.Supercontig_0270811 634 146 - 780 AAAATAGGAAAAATCCATCCAAGCC----GTGTGTCT---GCTCA-GGCAG---AATAGTGTCAGATTGCTAGGCAACTCCAGGCAGTCCTGGGGGAAGGAGGGCCGT------GCTCAG-------CTTGTTCTGCAGAAGTAGAGTCCTTGT-CCCTTTTGTGTGGATG i gorGor1.Supercontig_0270811 C 0 n 0 s panTro2.chr17 79496047 146 + 83384210 AAAATAGGAAAAATCCATCCAAGCC----GTGTGTCT---GCTCA-GGCAG---AATAGTGTCAGATTGCTAGGCAACTCCAGGCAGTCCTGGGGGAAGGAGGGCCGT------GCTCAG-------CTTGTTCTGCAGAAGTAGAGTCCTTGT-CCCTTTTGTGTGGATG i panTro2.chr17 C 0 C 0 s tarSyr1.scaffold_41848 379 146 + 21754 AAAATAGGAAAAATCCATCCAAGGC----ATGTGTCT---GCTGA-GGCAG---AGTAGTGTCAGATTGCTAGGCAACCCCAGGCAATCCTGTGGGAAGGAGGGCTGC------GCCGAG-------CATGTTCCGCAGAAGTAGGGCTCTTGT-CCCTTTTGTGTGGATG i tarSyr1.scaffold_41848 C 0 C 0 s cavPor3.scaffold_76 4406118 148 + 7991924 AAAACAGAAAAACTCCACCTAAGCT----ATGGGTCT---GCAGC-AGCGGCCTGGTGGTGTCGGATTGCTAGGCAACCCCAGGCAATCCTGGGAGAAGAAAGTCGC-------GCAGAG-------CCAGCTCCACAGAGGCAGTGCTCCTGG-TGCTTTTGTGCAAATG i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_149396 1055 160 + 1524 AAAATAGGAGAAACGCATCGGAGGCGTGGGTGGGTCT---GCGGCTGGCAG---GGTGGCGTCAGATTGCTAGGCAACCCCGGGCAGTCCTGC--GAAGGAGGTCTGCGGCGCTCGGGAGCTCGGTCCCCGTTCCACAGACG-CGCACCGCTGT-CCCTTCTGCATAGAC- i dipOrd1.scaffold_149396 C 0 C 0 s mm9.chr11 118778009 145 + 121843856 AAAATAGGAAAAATCCATCGGAGCC----GTGGGTCT---GCTGC-GGCGG---GGTGGTGTCGGATTGCTAGGCAACCCCAGGCAATCCTGCAGGAAGGAGGTCTG-------TGTGAG-------CCGCTTGCACAGAAGAAGGGCTCTTGT-CCCTTTTGTGTGGATG i mm9.chr11 C 0 C 0 s ochPri2.scaffold_9426 19462 127 - 54875 -GAACAGCAGGCTCTCGTCCCAGCC----TTCCGCGT---GCA---GGCCT---AGCCGGGGTGGATTGCTAGGCAACCTGGGGGGCCACTGGGGGAAGGGGGC----------TGTGCC-------CCCGCCCAGCGCA------GCTCTTGT-CCCTGTTGTG------ i ochPri2.scaffold_9426 C 0 C 0 s pteVam1.scaffold_11245 31178 144 + 48268 AAAATAGG-AAAATCCATCGGAGTC----GTGTGTCT---GCCGA-GGCAG---AGTGCTGTCAGATTGCTAGGCAACCCCAGGCAATCCTGTGGGAAGAAGGCCTGT------GCCAGG-------CTCGTTCCACAGAAGTCACACTCTTGT-CCC-TTTGTGTGGATG i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_125911 1223 138 + 4959 AAAATAGGAAAAATCCATCCCAGCC----G-GT-TCT---GCCGA-GGCAG---AGTGCTGTCGGATTGCTAGGCAACCCC--GCAATCCTGTGGGAAGAGGCCTCGT--------CGAG-------CTCGCTGCGCGGAAATGGCGCTCTGGG-CCC--GGGTGCGGATG i myoLuc1.scaffold_125911 C 0 C 0 s felCat3.scaffold_206428 41487 146 + 132007 AAAATAGGAAAAATCCATCCGAGTC----GTGTGTCT---GCCGA-GGCAG---AGTGCTGTCAGATTGCTAGGCAACCCCAGGCAATCCTGTGGGAAGAAGGTCTGT------GCTAAG-------CTTGTTCCACAGAAGTAGCACTCTTGT-CCCTTTTGTGTGGATG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59453114 146 - 64418924 AAAATAGGAAAAATCCATCCAAGTC----GTGTGTCT---GCTGA-GGCAG---AGTGCTGTCAGATTGCTAGGCAACCCCAGGCAATCCTGTGGGAAGAAGGTCTGT------GCTAAG-------CTTGTTCTACAGAAGTAGCACTCTTGT-CCCTTTTGTGTGGATG i canFam2.chr9 C 0 C 0 s equCab2.chr11 58059600 146 - 61308211 AAAATAGGAAAAATCCATCCAAGCC----GTGTGTCT---GCCGA-GGCAG---AGCGCTGTCGGATTGCTAGGCAACCCCAGGCAGTCCTGCGGGAAGAAGGGCTGT------GCTAAG-------CTTGTTCCACAGAAGCAGCCCTCTTGT-CCCTTTTGTGTGGATG i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10876763 143 - 65312493 AAAATAGGAAAAATCCATCCGAGGC----GTGTGTCT---GCTGA-GGCAG---AGTGCTGTCAGATTGCTAGGCAACCCCGGGCGATCCTGTGGGAA---GGTCTGT------GCTAAG-------CTTGTTCCACAGAAGTAGCACTCTTGT-CCCTGTTGTGTGGATG i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 6900 143 + 223990 AAAATAGGAAAAATCCATCCAAGGC----GTGTGTCT---GCTGA-GGCAG---AGTGCTGTCAGATTGCTAGGCAACCCCAGGCGATCCTGTGGGAA---GGTCTGT------GCTAAG-------CTTGTTCCACAGAAGTAGCACTCTTGT-CCCTGTTGTGTAGATG i turTru1.scaffold_98008 C 0 C 0 s eriEur1.scaffold_157372 907 148 + 3406 aaaataggaaaaatccaTCCCAGGC----GTGTGTCTGTGGCAGA-GGCAG---AGTGCTGCCCGATTGCTAGGCAACCCCGCGCCAGCCTGTGGTAAGCTGGGCTG-------GCAGAG-------CTCATTCCACAGAAGTAGCGCTCTTGT-CCCTTTTGTGTGGATG i eriEur1.scaffold_157372 C 0 C 0 s loxAfr3.scaffold_49 14452200 144 - 17734757 AAAATAGGAGAACGCCATTTGAGGT----GCCTGTCT---GCTGT-GGCAG---AGTGGTGTCGGATTGCTAGGCAACCCC-GGCAATCCTGTGGGAAGAGGG-CTGT------GCCAAG-------CGTGTTCCACAGAAGTGGAGCTCTTGT-CCCTTTTGTGTGAATG i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 3891 146 + 4838 AAAATAGGAGAAATCCATCCAAGCC----GCCTGTGA---GCTGC-GGCAG---AGTGGCCTCCGATTGCTAGGCAACCCCAGGCAATCCTGTGGGAAGAAGGCCTGC------GCTGAG-------CTTGCTCTGCAGAAGTAGAGCTCTCGT-CCCCTTTGTGAGAACG i dasNov2.scaffold_171027 C 0 C 0 s choHof1.scaffold_410167 807 147 + 1023 AATATAGGAGAAATCCATCCAGTCT----GCATGCGG---GCTGT-AGCAG---AGCAGTGTTGGATTGCTAGGCAACTCCAGGCAATCCTGCGGGAAGGAGATCTGC------ACTCGG-------CTTGTTCTGCAGAAATAGAGCTCTTGTCCCCCTTTGTGGGAATG i choHof1.scaffold_410167 C 0 C 0 s macEug1.Scaffold273400 0 147 + 1010 AAAATAGG-AAAATCCATCCAAGTA----GTATGTCT---GCTGT-AGCAG-AGAGTGGTGTCAGATTGCTAGGCAACCCCAGGCAATATTGTAGGAAGGAGGTCTAT------ACTAAG-------CTGGTAGCACAGAAGTGGAGCTCTTGT-CCTTTCTGTGTGAATG i macEug1.Scaffold273400 N 0 C 0 s monDom5.chr2 304571055 148 - 541556283 AAAATAGGAAAAATCCATCCAAGTA----GTATGTCG---GCTGT-AGCAG-AGAGTGGTGTCAGATTGCTAGGCAACCCCAGGCAATATTGTGGGAAGGAGGTCTAT------ACTAAG-------CTGGTAGCACAGAAGTGGAGCTCTTGT-CCCTTCTGTGTGAATG i monDom5.chr2 C 0 C 0 e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e ponAbe2.chr17_random 16081143 801 + 17838096 I a score=239002.000000 s hg19.chr17_gl000204_random 64509 45 + 81310 TGCTCAGCCGAATCTCAGCAAAAGTCATGAACAGAAAGGAGAGGC s panTro2.chr17 79496193 45 + 83384210 TGCTCAGCCGAATCTCAGCAAAAGTCATGAACAGAAAGGAGAGGT i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75055737 45 + 78773432 TGCTCAGCCGAATCTCAGCAAAAGTCATGAACAGAAAGGAGAGGC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 62989 45 - 95547 TGCTCAGCCGAATCTCAGCAAAAGTCATGAAGAGAAAGGAGAGGC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 65527 45 + 225949 TAGTCAGCCGAATCTCGGCAAAAGTCATGAACAGAAAGGAGAGGC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 525 41 + 21754 AGCTCAGCCGCATCTGAGC-AAAGTCATGAACAGAA---AGACAC i tarSyr1.scaffold_41848 C 0 C 0 s cavPor3.scaffold_76 4406266 44 + 7991924 TGCTCGGCCACATCTGAGCAGAAGTCAT-AGGAGGACAGAGATGC i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_149396 1215 45 + 1524 CCCTCGGCCCGATGGGAGCAAAAGGCAGGAGCAGAAGGGAGGTGT i dipOrd1.scaffold_149396 C 0 C 0 s mm9.chr11 118778154 45 + 121843856 TACTCAGCCAGATCTGAACAGAGGTCCTGAACAGGGAGGAGGTGC i mm9.chr11 C 0 C 0 s ochPri2.scaffold_9426 19589 24 - 54875 TGTGCGGCCG-------------------GGGCGGGGGGAGGC-- i ochPri2.scaffold_9426 C 0 C 0 s pteVam1.scaffold_11245 31322 39 + 48268 TGCTCAGCCGA--CTGAGCAAA-GCCATGAACAGAGGGACGC--- i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_125911 1361 21 + 4959 CTCCGGG---------------------GAACAGGGGCAGGC--- i myoLuc1.scaffold_125911 C 0 C 0 s felCat3.scaffold_206428 41633 42 + 132007 TGCTCAGCCGAATCTGAGCAGA---CACGAACAGAGGGAAGGCGC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59453260 39 - 64418924 TGCTCAGCCGAATCTGAGCAGA---CGTGAGTGGAGGGAAGG--- i canFam2.chr9 C 0 C 0 s equCab2.chr11 58059746 44 - 61308211 TGCTCAGCCGAATCTGAGCAAA-GTCGTGAACAGAGGGAAGACGC i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10876906 44 - 65312493 TGCTCAGCTGAATCTGAGCAAG-GTCATGGACAGAGGGAAGGCAC i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 7043 44 + 223990 TGCTCAGCCGAATCTGAGCAAG-GTCATGAACAGAGGGAAGGCAC i turTru1.scaffold_98008 C 0 C 0 s eriEur1.scaffold_157372 1055 36 + 3406 TgctcagccagagcagagcaggagtCATGCACACAG--------- i eriEur1.scaffold_157372 C 0 C 0 s loxAfr3.scaffold_49 14452344 31 - 17734757 TGTTCAGCCGAACC-------------TGAGCAGGA-GAGAGAGC i loxAfr3.scaffold_49 C 0 I 1 s dasNov2.scaffold_171027 4037 44 + 4838 AGCTCAGCCAGGCCCCGGCACTAGACGTGAACAGAA-GACGACGC i dasNov2.scaffold_171027 C 0 C 0 s choHof1.scaffold_410167 954 45 + 1023 TGCTCAGGCCGAGCCCATCATCAGCCACAAACAGAATGATGACGC i choHof1.scaffold_410167 C 0 N 0 s macEug1.Scaffold273400 147 45 + 1010 TACTCAGCTGAATCCAAGCAAAAGTCATACACAAAAGAAAGATAC i macEug1.Scaffold273400 C 0 C 0 s monDom5.chr2 304571203 45 - 541556283 TACTCATCTGAATCCAAGCCTAAGTCATACACAAAAGAAAGATAC i monDom5.chr2 C 0 C 0 e gorGor1.Supercontig_0270811 780 0 - 780 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e ponAbe2.chr17_random 16081143 801 + 17838096 I a score=884569.000000 s hg19.chr17_gl000204_random 64554 171 + 81310 GGGCTGCATAAGCCGGCGGAGTGCACAT--------CC---------------------GT----------CTGGACAAATGGATTTTCCGGAGGATGGAGAAGA---GAC-GG-GGGTGTCCAC----------GTGATGAGAAACATCTGGATACGCGCTGGA-AAAATCAA-TCTGATT-TCTCTGTGCTTCCCAAGATCCAGGTGTT---TACAATT-GTGTAGGC----AA s panTro2.chr17 79496238 171 + 83384210 GGGCTGCAGAAGCCGGCGGAGTGCACAT--------CC---------------------GT----------CTGGACAAATGGATTTTCCGGAGGATGGAGAAGA---GAC-GG-GGGTGTCCAC----------GTGATGAGAAACATCTGGATGCGCGCTGGA-AAAATCAA-TCTGATT-TCTCTGTGCTTCCCAAGATCCAGGTGTT---TACAATT-GTGTAGGC----AA i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75055782 171 + 78773432 GGGCTGCATAAGCCGGCGGAGTGCACAT--------CC---------------------GT----------CTGGACAAATGGATTTTCCGGAGGATGGAGAAGA---GAT-GG-GGGTGTCCAC----------GTGATGAGAAACATCTGGATATGCGCTGGA-AAAATCAA-TCTGATT-TCTCTGTGCTTCCCAAGATCCAGGTGTT---TACAATT-GTGTGGAC----AA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 63034 171 - 95547 GGGCTGCATAAGCCGGCGGAGTGCACAT--------CC---------------------GT----------CTGGACAAATGGATTTTCCGGAGGATGGAGAAGA---GAT-GG-GGGTGTCCAC----------GTGATGAGAAACATCTGGATATGCGCTGGA-AAAATCAA-TCTGATT-TCTCTGTGCTTCCCAAGATCCAGGTGTT---TACAATT-GTGTGGAC----AA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 65572 171 + 225949 AGGCTGCACAGGCTGGCGGAGCGCACAT--------CC---------------------GT----------CTGGACAAATGGATTTTCCGGAGGACAGAGAAGA---GAC-AG-GGGCGTCCAC----------GTGATGAGAAACATCTGGAGACGCACTGGA-AAAATCAA-TCTGATT-TCTCCGTGCTTCCCGAGATCCAGGTGTT---CATAATC-ATGTAGGC----AA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 566 169 + 21754 AGGCCGCGGGAGCCAGCGGAGCGCACAT--------CC---------------------GT----------CTGGACAAATGAATTTTCCAGAGGACGGAGAAGA---GAC--G-GGGCATCCAC----------GTGATGAGAAACATCTGGATACATACT-GA-AAAATCAA-TCTGATT-TCTCCGTGTTTCCCATGATCCAGGTGTT---TAAAATC-ATGTAGGC----AA i tarSyr1.scaffold_41848 C 0 C 0 s cavPor3.scaffold_76 4406310 164 + 7991924 AGGCTGCGTCCGCTGGCGGAGCACGCGT--------CC----------------------T----------TTGGACAAATGGATTTTCTGGAGGATGGAAAAGA---GT---G-GGGTGCCCAC----------GTGATGAGAAACATCTGGAAACACATTGGA--AAATCAG-TCTGATTCTC----TGTTTCTCCAAGTCCAGGTGTT---TAGAATC-GTGCAGGC----AA i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_149396 1260 164 + 1524 GGCCGCAGGC------CACCGCGCCAGT--------CCGCAAG--------------TCCT----------TCGGACCAGTGGACGGTCTGGAAGACGAGCAA-----CA---G-AGGTGCCCAT----------GTGATGAGAAACATCTGGAAATGGACTGGGAAAAAGCAG-ACAGGTT-TC----TGTCTCCCAAGGCCCATGTGCT---TGGAACT-GTGTAGG-----CA i dipOrd1.scaffold_149396 C 0 C 0 s mm9.chr11 118778199 173 + 121843856 CGGCTCTGGCGGATGGCACAGCTCACGT--------CC-------------------TTCT----------TTGGACAATTGGATTTTCAGGAGGATGACAGAGAAGGGA---G-GGGTGGCCAT----------GTGATGACTAACATCTGGAGCTACACTGGG--AAATCAG-CCTGATT-TC----TGCTTCCCGAGGCCCAGGTGTT---TGGAACT-GTGCAGGCAAAACA i mm9.chr11 C 0 C 0 s ochPri2.scaffold_9426 19613 139 - 54875 ----------------CACACCACAAGC--------AC---------------------------------------AGAGGGATTCTGCGGATGACGGAGAAGC---GC---C-AGGTGCCCAC----------GTGACTGAAAACATCTGGAAGTGT-CTGGA--AAATCAA-TCTGAGC-TC----GGTTTCCCAAGACCCAGGTGTT---TGAAATT-GTGTGGGT----GA i ochPri2.scaffold_9426 C 0 I 30 s pteVam1.scaffold_11245 31361 160 + 48268 --------CTAGCTGAAGGCGTGTGCGC--------CC---------------------GC----------CCGGAAGGGTGAATTATCTGGAGAACAGAGAAGA---TGC-CG-GGGTGTCCAC----------AGGGTGAGGGACATCTGGACACATACTGGG--ATAGCCA-TCTGACT-TCT-CATG-TCCCCAGCCTCCAGGTGTT---TAGAATC-GTGCAGGC----AA i pteVam1.scaffold_11245 C 0 C 0 s myoLuc1.scaffold_125911 1382 153 + 4959 -------GCCGCCTGAAGGGACGTGCG---------CC---------------------AC----------CAGGACCGACGGACAG--CAGAGGACAGAGAATG---CGC-T--GGGTGT-CAC----------GGGATGA--GACAGCTGGACACACA--GGA--AAATGCA-CCCCGTT-TCTCCGTG-TTTCCAACATCCAGGTGTT---CCGAACT-TCGCGGGC----CA i myoLuc1.scaffold_125911 C 0 C 0 s felCat3.scaffold_206428 41675 169 + 132007 GAGCTGCCCAAGCTGAAGGCGCACGCGT--------CC---------------------GC----------CTGGACAGACAGATTCTCCGGGGGACAGAGAAGA---CGC-CA--GGTGTCCAC----------AGGACGCGAGACACCTGGACGCACCCTGGA--AAATCAA-TCTGATT-TCCCCGTGTTCCCCAAGAGCCACGTGTG---TAGCACT-GTGTAGGC----AA i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59453299 147 - 64418924 -----------------------CGCAT--------CC---------------------GC----------CTGGACAGACAGATTCTCCAGAGGACAGAGAAGA---CAC-CG-TGGTGTCCAC----------GGGATGACAGACATCTGGATACACACTGGA--AAATCAA-TCTGATT-TCTCCGGGTTTCCCAAGAGCCAGGTGTG---TAGCACT-GTGAAGGC----AA i canFam2.chr9 C 0 C 0 s equCab2.chr11 58059790 169 - 61308211 AGGCCGCCTGAGCCGGAGGAGAGTGCAG--------CT---------------------GC----------CTGGACAAACGGATCCTTCAGAGGACAGAGAAGA---CAC-AGGGGGTGTCCAC----------AGGACAAGACGCACCTGGAGACACACTGGA--AAATC---TCCTCGT-TCCCCGCGTTTCCCGAGATCCAGGtgtt---tggaatg-gtgtaggc----aa i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10876950 169 - 65312493 AGGCTGCCTGAGCCGAAGACGTGCCCAT--------CC---------------------GC----------TTGGACAGATGGATTTTCCAGAGGACAGAGAAGA---GGC-CGAGGGTGTCTGC----------AGGATAAGAGGCATCTGGGAGCATGCTGGA--AAATCTA-TCTAGTT-T-CCCATGTTCCCCAA-ATCCAGGTGCT---TAGAATT-GTGTAGGC----AA i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 7087 171 + 223990 AGGCTGCCTGAACTGAAGACGTGCCCAT--------CT---------------------GC----------CTGGACAAAGGCATTTTCCGGAGGACGGAGAAGA---GGC-CGAGGGTGTCCGC----------AGGATGAGAGGCATCTGGACGCACGCTGGA--AAATCTA-TCTGGTT-TCCCCATGTTCCCCAAGATACAGGTGTT---TAGAACT-GTGTAGGC----AA i turTru1.scaffold_98008 C 0 C 0 s eriEur1.scaffold_157372 1091 178 + 3406 ------CCCGtgtcagaagtgtgtgtgtggggggtgtt---------------------gc----------CTGGACACCCTGCTCCTTCTG------GAGGAGG---CAA-TTGAGGTGTTTACCTGGGGGTGTGGGAGGGGAGACATCTGGACACATGCTGGA--GAATCAGTTCTGCTC-TCCCCTTAACTCCCCCAAACTGAAGGCC---TGAGACT-GTGGAGAC----CA i eriEur1.scaffold_157372 C 0 C 0 s loxAfr3.scaffold_49 14452376 166 - 17734757 -----------GTGATACAAGGCCCCAG--------TC---------------------GCTCACATCCCTGTGGACGGGTGGATGTTCT-GAGGACAGAGAAGA---GGTGGG-GGGTGTCTAT----------GGAGT---ACACATCTGGATAAACCCAGGA--AAACCAA-TCAGATA-TCTCCGTGCTTCCCAAGATCCAGATGTT---TAGAATT-GTGCAGAC----AA i loxAfr3.scaffold_49 I 1 C 0 s dasNov2.scaffold_171027 4081 161 + 4838 ----------GGGGCCAAGAGCCCCCAG--------CC---------------------GC----------GTGGACAAGTGGCTTTTCCAGAGGACAGGGAAGA---GAC-GG-GGGTGCCTAC----------GTGGTCAGGAATATCTGGATGCTCACCGGA--AAATCCA-TCAGATT-TCTCCATGGTTCCCAAGATCTAGATGTT---TAGAATTCCCTTAGAC----AC i dasNov2.scaffold_171027 C 0 C 0 s macEug1.Scaffold273400 192 186 + 1010 AAAATACATAAGCTG----AGTGCACAT--------CTGgatgcatacatgtatgcaaCGG----------GTGAATGGACAGATTTTCGAAAGAACTGAAAAGA---TTCAAA-CTATGTCTAG----------AAGATGCTAAATATCAAAATGAAACCTGAA--AAGTCTG-TTAATTA-TCTGGATGTTTCCTAAAATTCAGATATTGGACATAATT-AAGTA--------- i macEug1.Scaffold273400 C 0 N 0 s monDom5.chr2 304571248 178 - 541556283 AAAATACATATGCTG----AGTGCACAT--------TTGGATGGATGCATGTATGCAATAG----------GTGAATGGACAGATTTTTGGAAGAAATGAAAAGA---TTCAAA-CTGTGTCTAG----------AGGATGCTGAATATGAAAATGAAACCTGAA--AAGTCTG-TCAATTA-TCTGGATGTTTCCTGAGA---------T---TCAGATT-CAATAGGC----A- i monDom5.chr2 C 0 C 0 e gorGor1.Supercontig_0270811 780 0 - 780 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e ponAbe2.chr17_random 16081143 801 + 17838096 I a score=12566.000000 s hg19.chr17_gl000204_random 64725 37 + 81310 AGCGTCTGAATGTTAATGAAGTCTT--TC-CTCTCA--ATAT s panTro2.chr17 79496409 37 + 83384210 AGCGTCTGAATGTTAATGAAGTCTT--TC-CTCTCA--ATAT i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75055953 37 + 78773432 AGCGTCTGAATGTTAATGAAGTCTT--TC-CTCTCA--ATAT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 63205 37 - 95547 AGCGTCTGAATGTTAATGAAGTATT--TC-CCCTCA--ATAT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 65743 37 + 225949 AGCGTCCGAATGCTAATGAAGCCTT--TC-CTCCCA--ATAT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 735 36 + 21754 AACAAGTGATTG-TAATGAATTCTT--TC-CCCCCA--GTTT i tarSyr1.scaffold_41848 C 0 C 0 s mm9.chr11 118778372 32 + 121843856 AACGTCAGGATGCTAATGG-----C--TC-TTCCTG--GTTC i mm9.chr11 C 0 C 0 s dipOrd1.scaffold_149396 1424 37 + 1524 AATGTGCGAATGTGAATGAGATCTT--TC-TTCCCA--GTCT i dipOrd1.scaffold_149396 C 0 C 0 s cavPor3.scaffold_76 4406474 35 + 7991924 AACGTCTGAATTTTAATGGGTT--C--TT-TCCCTG--GGTT i cavPor3.scaffold_76 C 0 C 0 s pteVam1.scaffold_11245 31521 34 + 48268 AACGCCTAAGTTTTAGCTGATT-----TT-CTCCCC--GGGT i pteVam1.scaffold_11245 C 0 I 2 s myoLuc1.scaffold_125911 1535 39 + 4959 AACGCCTGGATTTTCTCGGTTCCCCCGCT-CCCTCC--CAGT i myoLuc1.scaffold_125911 C 0 I 1 s felCat3.scaffold_206428 41844 34 + 132007 AACACCTGAATTTTATCGGACA-----CC-CCCCCC--ATGT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59453446 35 - 64418924 AACACCTGAATTTTAACTGATT-----TTGCCCCCC--ATGC i canFam2.chr9 C 0 C 0 s equCab2.chr11 58059959 34 - 61308211 accgcctgaattttaactgatt-----tt-ccccca--gttt i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10877119 34 - 65312493 CATGCTTGAATCTTAACTGACT-----TA-CCCATT--CCGC i bosTau4.chr19 C 0 I 2 s turTru1.scaffold_98008 7258 33 + 223990 AATGCCTGAATCTTAACTGATT-----T--TCCATC--CAGC i turTru1.scaffold_98008 C 0 I 2 s eriEur1.scaffold_157372 1269 33 + 3406 GA-GTCTTAGTGTGAACTGACT-----CC-CAGCCC--CTGC i eriEur1.scaffold_157372 C 0 I 8 s loxAfr3.scaffold_49 14452542 38 - 17734757 AACGCCTTAATGTTAACTGATTTAT--TT-CCCCCGGACTG- i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 4242 35 + 4838 AACGTC-TGATTTTAACTGATTTTT--TT-TCACAG--CTT- i dasNov2.scaffold_171027 C 0 C 0 s monDom5.chr2 304571426 16 - 541556283 ----TCTGAATTCTTAAAAA---------------------- i monDom5.chr2 C 0 C 0 e ochPri2.scaffold_9426 19752 30 - 54875 I e gorGor1.Supercontig_0270811 780 0 - 780 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e ponAbe2.chr17_random 16081143 801 + 17838096 I a score=130141.000000 s hg19.chr17_gl000204_random 64762 33 + 81310 CCTGCATCTCCCTC----AGCAAGAG-----GCAAATGAAAA s panTro2.chr17 79496446 33 + 83384210 CCTGCATCTCCCTC----AGCAAGAG-----GCAAATGAAAA i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75055990 33 + 78773432 CCTGCATCTCCTTC----AGCAAGAG-----GCAAATGTAAA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 63242 33 - 95547 CCTGCATCTCCTTC----AGCAAGAG-----GCAAATGTAAA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 65780 32 + 225949 CCTGCGTCTCCTTC----A-CAAGAG-----GCAAATGTAAA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 771 30 + 21754 CCTGTGTCACCTT-------CAAGAG-----ACAAACGTAAA i tarSyr1.scaffold_41848 C 0 C 0 s cavPor3.scaffold_76 4406509 33 + 7991924 CCCGCATCACCTTC----AGCAAGAA-----GCAAATGTAAA i cavPor3.scaffold_76 C 0 C 0 s dipOrd1.scaffold_149396 1461 26 + 1524 CCTGTCTC-CCCTT----CT-----------GCAAATATAAA i dipOrd1.scaffold_149396 C 0 C 0 s mm9.chr11 118778404 32 + 121843856 CCAGAATC-CTTTC----AGCAGGAA-----GCAGATGTAGG i mm9.chr11 C 0 C 0 s ochPri2.scaffold_9426 19782 32 - 54875 CCCCACTT-GCTGC----AACCAGAA-----GCAGGTGTAAG i ochPri2.scaffold_9426 I 30 C 0 s speTri1.scaffold_86778 0 18 + 8487 -------------------GCAAGAA-----GCACATGCACA i speTri1.scaffold_86778 N 0 C 0 s pteVam1.scaffold_11245 31557 33 + 48268 TCTTCATCATCTTC----AGCAAGAG-----GGAAATGACAG i pteVam1.scaffold_11245 I 2 C 0 s myoLuc1.scaffold_125911 1575 33 + 4959 TCTTCATCATCTTC----AAGGAGAG-----GCGACTGAGAG i myoLuc1.scaffold_125911 I 1 C 0 s felCat3.scaffold_206428 41878 33 + 132007 TCTTCATCACCTCC----AGCAAGAG-----GTGAAGGGAAG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59453481 33 - 64418924 TCCTCACCCCCTTT----GGCGCAAG-----GTGAGTGCAAA i canFam2.chr9 C 0 C 0 s equCab2.chr11 58059993 33 - 61308211 ccttcatcaccatg----agcaagag-----gtgaacgtggg i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10877155 32 - 65312493 TCTTCATCACCTTC----AGTCAGAG-----GTGAAT-TAAG i bosTau4.chr19 I 2 C 0 s turTru1.scaffold_98008 7293 32 + 223990 TCTTCATCACCTTC----AGCCAGAG-----GTGAAT-TAAG i turTru1.scaffold_98008 I 2 C 0 s eriEur1.scaffold_157372 1310 42 + 3406 CCTCCATGGTTTCCCGGTAGCCTGGGCTCCAGCAAGTGCCAG i eriEur1.scaffold_157372 I 8 C 0 s loxAfr3.scaffold_49 14452580 29 - 17734757 TCTTCATCACCTTC----AGCAAGAG-----GCTagaa---- i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 4277 33 + 4838 TCTTCCCCGCCTCC----AGCCAGAG-----GCCAATATAAG i dasNov2.scaffold_171027 C 0 C 0 s monDom5.chr2 304571442 32 - 541556283 -CATTTATATATAT----AGCATGAT-----GCAGACAACAA i monDom5.chr2 C 0 C 0 e gorGor1.Supercontig_0270811 780 0 - 780 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e ponAbe2.chr17_random 16081143 801 + 17838096 I a score=-171218.000000 s hg19.chr17_gl000204_random 64795 45 + 81310 CTAG--GCT---------CAGCAGGCCT--GGG--AGAGACG-GGGAG---CAG---G--A---GGAGGAAC s panTro2.chr17 79496479 45 + 83384210 CTAG--GCT---------CAGCAGGCCT--GGG--AGAGACG-GGGAG---CAG---G--A---GGAGGAAC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16081944 44 + 17838096 CTAG--GCT---------CAGCAGGCCT--GGG--AGAGCCG-GGGAG---CAG---G--A---GGAGGAA- i ponAbe2.chr17_random I 801 I 10 s rheMac2.chr16 75056023 45 + 78773432 CTAG--GCT---------CAGCAGGCCT--GGG--AGAGACG-GGGAG---CAG---A--A---GGAGGAAC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 63275 45 - 95547 CTAG--GCT---------CAGCAGGCCT--GGG--AGAGATG-GGGAG---CAG---A--A---GGAGGAAC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 65812 45 + 225949 CTAG--GCT---------CAGCAGGCCT--GGG--AGAGACA-GGGAG---CAG---G--A---GGAGGAGC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 801 50 + 21754 CTAG--GTT---------CAGAAGGCTG--GAGACAGAGAGG-AGGAG---GAA---G--AAGTGGAGAAAT i tarSyr1.scaffold_41848 C 0 C 0 s cavPor3.scaffold_76 4406542 37 + 7991924 CTGG--GTT---------TAGGATCCTG--GAG--AGAGACA----------AG---G--A---GGAGGA-- i cavPor3.scaffold_76 C 0 I 5 s dipOrd1.scaffold_149396 1487 34 + 1524 CTAG--CTT---------CCAAAGCCAG--GAG--GAGG-------------AG---G--A---GGAGGA-- i dipOrd1.scaffold_149396 C 0 N 0 s mm9.chr11 118778436 39 + 121843856 CTAG--GTT---------TGGAAGGCTG--GAG--AGAGCCA----------AG---G--G---GGAGGAAT i mm9.chr11 C 0 C 0 s ochPri2.scaffold_9426 19814 44 - 54875 GGGGGAGGT---------GAAGAGCTGG--GAG--GCTGGAG----------AGCTTG--G---AGAGGAGC i ochPri2.scaffold_9426 C 0 N 0 s speTri1.scaffold_86778 18 45 + 8487 CTCG--GTT---------CAGAAGCTGG--AGA--GCAGTCA-TGGAG---CAG---G--A---GGAGGAGT i speTri1.scaffold_86778 C 0 C 0 s pteVam1.scaffold_11245 31590 33 + 48268 -CAA--GGTC--------CGCGAGGCTG--GGG--ACGG----AGGAG---------G--A---GG------ i pteVam1.scaffold_11245 C 0 I 16 s myoLuc1.scaffold_125911 1608 27 + 4959 -CAG--GTT-----------------TG--GGA--GCGG----AGAAG---TGA---G--A---GG------ i myoLuc1.scaffold_125911 C 0 I 390 s felCat3.scaffold_206428 41911 31 + 132007 -CAA--GTT---------CAGGAGGCTG--GAG--GCAG--------A---TGA---A--A---GA------ i felCat3.scaffold_206428 C 0 I 10 s canFam2.chr9 59453514 39 - 64418924 -CAA--GTT---------CAGGAGGCTG--GAG--ACAGGAGGAGATA---TGA---G--A---GA------ i canFam2.chr9 C 0 I 10 s equCab2.chr11 58060026 42 - 61308211 -caag-gct---------gcaaaggctGGAGAG--ACAGGAGGAGAAA---GGG---G--A---GG------ i equCab2.chr11 C 0 I 10 s bosTau4.chr19 10877187 32 - 65312493 -CAG--GTT----------CAGAGGCTG--GAG--AC------AGGAG---GAG---G--A---GA------ i bosTau4.chr19 C 0 I 19 s turTru1.scaffold_98008 7325 34 + 223990 -CAG--GTT----------CAGAGGCTG--AAG--ACAG----AGGAG---GAG---G--A---GA------ i turTru1.scaffold_98008 C 0 I 19 s eriEur1.scaffold_157372 1352 39 + 3406 -CAG--GTGC--------AGAGGGGCTA--GAG--AGAA----AAAAGCTCCAT---G--A---GA------ i eriEur1.scaffold_157372 C 0 I 12 s loxAfr3.scaffold_49 14452609 23 - 17734757 ------------------------------aga--ggaggaagaggag---gag---gaat----------- i loxAfr3.scaffold_49 C 0 I 15 s dasNov2.scaffold_171027 4310 37 + 4838 ---------CA---Agggtcagaggctg--gaa--ggaggcaggggcg---gag---g--c----------- i dasNov2.scaffold_171027 C 0 I 14 s monDom5.chr2 304571474 46 - 541556283 ----------CTATATGATCAAAGGTTA--GAG--GAAGATA-GGAGA---AAA---A--A---GAAATAAC i monDom5.chr2 C 0 C 0 e gorGor1.Supercontig_0270811 780 0 - 780 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I a score=4780.000000 s hg19.chr17_gl000204_random 64840 172 + 81310 T-------------AGAGAGACCC------AGGCAGAG-GAAGCCGGG--AAATG---GAACTGGGAGATCA---CA----CTCGCCCA-----GTCGGGGTTTCTGCTCCC--AGGAAGGAGATGGAGG-CAACAG------------------GGC---AAGAAA---GACAC--GTGCA---TTTTTC--ACAGT-TCAGTCGAAACCATAATCATATTAATATG-TTTGTGGATGCTAAGA s panTro2.chr17 79496524 171 + 83384210 T-------------AGAGAGACCC------AGGCAGAG-GAAGCCGGG--AAATG---GAACTGGGAGATCA---CA----CTCGCCCA-----GTCGGGGTTTCTGCTCCC--AGGAAGGAG-TGGAGG-CAACAG------------------GGC---AAGAAA---GACAC--GTGCA---TTTTTC--ACAGT-TCAGTCGAAACCATAATCATATTAATATG-TTTGTGGATGCTAAGA i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75056068 159 + 78773432 T-------------AGAGAGGCCC------AGGCAGAG-GAGGCCGGG--AA----------------ATCA---CA----ACGGCCCA-----GTCAGGGTTTCTGCTCCC--AGGAAGGAGATGGAGG-CAACAA------------------GGC---AAGAAA---GACAC--GTGCG---TTTTTC--ACAGT-TCAGTCGAAACCATCATCACATTAATATG-TTTGTGGATGCTAAGA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 63320 159 - 95547 T-------------AGAGAGGCCC------AGGCAGAG-GAGGCCGGG--AA----------------ATCA---CA----ACGGCCCA-----GTCAGGGTTTCTGCTCCC--AGGAAGGAGATGGAGG-CAACAA------------------GGC---AAGAAA---GACAC--GTGCG---TTTTTC--ACAGT-TCAGTCGAAACCATCATCACATTAATATG-TTTGTGGATGCTAAGA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 65857 171 + 225949 G-------------AGAGAGACCT------GGGCAGGG-GAAGCCGGG--AAATG---GAACTGGGAGATCA---CA----CGGGCCCA-----GTCGGGGTTTCTGCTCCC--AGGAAGGAGATGGAGG-CAGCAA------------------GGC---AAGAAA---GACAC--GTGCA----TTTCC--ACTGT-TCAGTCGGAATCATAATCACGTCAACATG-TTAGTGGGTGCTAAGA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 851 167 + 21754 A-------------AAAGAGACC-------AGACAGAG-GGAGAGGGG--AGATG---GAGCTGGCAGATCA---TG----AGAACCCA----TAGCTGGCTTGGTGCTCCC--AGAAGGGAGACAGAAG-CA----------------------------AGGAAT---TGCAT--GTGTG---TTCTTCTTATAGT-TTGATCTTGATCTTAATCACGTTACAATG-TTTGTGGGTGTTAAGA i tarSyr1.scaffold_41848 C 0 C 0 s mm9.chr11 118778475 164 + 121843856 G-------------GAAGAGACCC------TGGGGGGC-CAGACAGGA--AAATG---GATCCAGAAAATAA---TG----AGGACCCA----CGGCTGGATTTGTGCTCCC--AAGAGCAAAATGGA---------------------------AGC---AAGAA-------GCCTGCACG---CTTCTT--TCAGAGCCCAGTCAAGCCTTAATCTCATTAAAACA-TTTGTGGATGTGGAAA i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4406584 166 + 7991924 G-------------AAAGAGACCC------TGGGGGAG-GGTGCAGGG--ACATT---GAGCC-GAAGATAA---TG----AGGGCCCA----CGTCTGGCTCTGTGCTCCC--GGGAGCGAGACAGA---------------------------GGC---AAGAAA---CGCACTGGCATC---CTCCTT--ACAGC-TCCGGCCAAGCCCTAATCTCATTAAAATG-TGCACAGATGTTAAAA i cavPor3.scaffold_76 I 5 C 0 s speTri1.scaffold_86778 63 164 + 8487 G-------------GAAGAGACCC------TGGGGGAG-GATGCAGAG--AGATG---GAGCCGGGAAATAA---TG----AGGGCCCA----CGTCTGGCTCCACACTCCC--AAGAGCGAGATGGA----------------------------GC---AGGAAA---CGCAC--ACGTT---CTCTTC--GCATT-TCCATCCAAGCCTTAATCTCATTCAAACG-TTTGTGGATGTTAAAA i speTri1.scaffold_86778 C 0 C 0 s ponAbe2.chr17_random 16081998 163 + 17838096 ------------------------------AGGCAGAG-GAAGCCGGG--AAACG---GAACTGGGCGATCCCTTCA----AAGAAACA-----GTCGGGGTTTCTGCTCCC--AGGAAGGAGATGGAGG-CAATA-------------------GGC---AAGAAA---GACAC--GTGCG---TTTTTC--ACAGT-TCGGTTGAAACCATAATCACATTAATATG-TTTGTGGATGTTAAGA i ponAbe2.chr17_random I 10 C 0 s turTru1.scaffold_98008 7378 159 + 223990 G-------------CCAGAGCCC---------GTGGAG-GAGCAGGGAGGAAGCA---GAGCTGG--GAGCA---CC----CAGGCACCGCCATTCTGGGCTTTGTGCTCCC--AAGGCCGAGATGGA-------------------------------------AG---AGCAT--GCTTT---CTTTTT--ACAGT-TCCATTCAAACCATAATCACGATAACATC-TTTGTGGATGTTACAA i turTru1.scaffold_98008 I 19 C 0 s bosTau4.chr19 10877238 159 - 65312493 G-------------CCAGAGCTG---------GTGGAG-GAGCAGGGAGGAAGCA---GAGCTGG--GAGCA---CC----CAGGCACTGCTGTGCTTGGCTTTGTGCTCCC--AAGGCCAAGACGGA-------------------------------------AG---CACAT--GCTCT---CTCTTT--ACAGT-TTCATCCAAACCGCACTCACAATAACATG-TTTGTGGATGGTACAA i bosTau4.chr19 I 19 C 0 s equCab2.chr11 58060078 134 - 61308211 A-------------CCAGAG--------------GACCAGAGACGGTG-------------------GAGGA---GC----AGGGAGGGAGCACAGA-------GGGGTCCC--GAGGCCGAGATGGA-------------------------------------CA---CACGT--GCCTT---CCCTTT--GCAGT-TCTTTCCAAACCGTAACCATATTTACATG-TTCATGGATGTTAAAA i equCab2.chr11 I 10 C 0 s canFam2.chr9 59453563 137 - 64418924 G-------------CCAGAGGCC-----------AGCTGGAGAAAGGG-------------------AAACA---GT----GGGGCGCAGGCACGCCCGGCTCTGGGCTCCC--AAGGCCGCGATGGA-------------------------------------AG---CACGT--GCTCT---CTCTGT--ACGCT-G-----CAAACAGTAACCACATCACAGAG---CGCGGGTGTTAGAA i canFam2.chr9 I 10 C 0 s felCat3.scaffold_206428 41952 139 + 132007 G-------------CAGGAGACG-----------GGCT-GAGAAGGGG--AGCCA---GGGCTGG-AAAACA---CT----GAGTCATGGGCACATCCGGCTCTGTGCTCCC--AAGGCTCCG------------------------------------------------------GCACT---CTTCCC--ACAGC-A-----CGAACAGCAATCACGTTGCGGGG-TTCGTGGGTGTTGAAA i felCat3.scaffold_206428 I 10 C 0 s pteVam1.scaffold_11245 31639 150 + 48268 G-------------CAAGAGGCC-----------AGTA-GAGGAGGGATAAGAGC---GAGCTGG--AACCC---CC----AAGGCCCAGGCTCGGCAGGCACTGCGCT-GC--GAGGCTCAGGTGGA-------------------------------------CG---CAA----CGCCG---CTTCCT--GCGGT-TCAGGCCACACCGCGATCACATGACGATG-----TGGACATTAAAA i pteVam1.scaffold_11245 I 16 C 0 s eriEur1.scaffold_157372 1403 145 + 3406 GCCAT---------CCAGGGCAC-----------AGAG-GAGCCTGGG--AACAC---AGCCCAG--GATCA---CCTCCACAGCCCCCTCCAC-CCAAGCTCTGTGCTCCC--AGGG--------GA-------------------------------------CA---CAC----ACCAT---ACTCAT--ACAGT-TCCCTCCGAACTGTGATCAGTTTCACCTG--------AAACTGAGA i eriEur1.scaffold_157372 I 12 C 0 s loxAfr3.scaffold_49 14452647 170 - 17734757 g-------------gaaggaggc--------aggtgga-ggagtaggg--agaCGCCAGAGAAGGAAAATGA---CC----GGAGCTGA-----GCCTGGTGTCGTGCTCCCGAGAGAGGCAGGGGGA---------------------------AGC---AAGAAAACACAAAT--GCTTG---CTTTAC--GCAGT-TCCCTGGGAACCTTAAGAACATCAAGACG-TTTGGGGAAGTTAAAA i loxAfr3.scaffold_49 I 15 C 0 s dasNov2.scaffold_171027 4361 164 + 4838 g-------------caggggagc--------gggggca-gaagcaggg--aagtg---gagaaggggaaggg---CA----TGTGCTGC-----CCCTGGCTCTGGACGTCC--GGGAGGCAGAGGGA---------------------------AGC---AAGAAGAGCCAAAC--ACGTT---CTCTGT--ACGGT-TCAGGCCAGGCCTTAGTAGCATTAAAGTG--TTGTGAATGTTAAAA i dasNov2.scaffold_171027 I 14 C 0 s monDom5.chr2 304571520 201 - 541556283 --AATAATAAATGAGTAGCAACCACAGATGGAAAGGAG-GAAGAGAGG--AAAGA---AAATTAATAGACTA---TA----A------------TCCAGCTTTTATGTAACT--TCGGCTGTGATAGAAGTCAGCAAATACAAAAGAGAAGATTTAGCCCTAATAAA---GATAA--ACCTTGGCATTTCT--AAATT-TGTTTTACAACCTTGGTAATATTGTAGTGTTTTGTGAAT------- i monDom5.chr2 C 0 I 52790 e gorGor1.Supercontig_0270811 780 0 - 780 I e myoLuc1.scaffold_125911 1635 390 + 4959 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I a score=645971.000000 s hg19.chr17_gl000204_random 65012 112 + 81310 CGTTGGCTATAAGCATCAAATACTTT-----TCAAAGGAAGAGG-CAGGGGAC------GTGGCATCGTGAAA--AATAGCACCAATTTTCCATTTGATTGTAAGCTCTT-TAGCACTCCA---GGAGGG--- s panTro2.chr17 79496695 112 + 83384210 CGTTGGCTGTAAGCATCAAATACTTT-----TCAAAGGAAGAGG-CAGGGGAC------GTGGCATCGTGAAA--AATAGCACCAATTTTCCATTTGATTGTAAGCTCTT-TAGCACTCCA---GGAGGG--- i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75056227 112 + 78773432 CGTTGGCTATAAGCATCATATACTTT-----TCAAAGAAAGAGG-CAGGGGAT------GTGGCATCGTGAAA--CATAGCACGAATTTTCCATTTGATTGTAAGCTCTT-TAGGACTCCA---GGAGGG--- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 63479 112 - 95547 CGTTGGCTATAAGCATCATATACTTT-----TCAAAGAAAGAGG-CAGGGGAT------GTGGCATCATGAAA--CATAGCACGAATTTTCCATTTGATTGTAAGCTCTT-TAGGACTCCG---GGAGGG--- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 66028 112 + 225949 CATTGGCTATAAGCATCAAATACTTT-----TCAAAGAGGGAGG-CAGGGGAC------GTGGCATCGTGAAA--AACAGCACGAATTTTCCAGTGGATTGTAAGCTCTT-TGGAACACCC---GGAGAA--- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 1018 114 + 21754 TGTTGACTATGAGCATCAAATACTTT-----TAAAAGAAAATGG-T-TGGGAC------ATGGCATTGTGAAA--AATAGCAGGAGTTTTCCGTTTGATTTGCAGGTCTT-TAGAACAACATGGAGAGAA--- i tarSyr1.scaffold_41848 C 0 C 0 s mm9.chr11 118778639 100 + 121843856 TATTGACTAGAAGCGTCAAATGCTT-----------AAAAGGGG-TGGG-----------CAGCATCATGAAA---ACAGCAGAAATCTTCCATTTGATTTGAAGTTCTACCAGA-CACTT---AGAGGG--- i mm9.chr11 C 0 I 1362 s cavPor3.scaffold_76 4406750 104 + 7991924 TAT-------GAGCATCAAATAGTTT-----TAAAAGAAAAAGG-TGGG-GAT------ATAGCATTGTGAAAAACACAGCAGAAATTTCCCATTTCATTTGAAGTTCTG-CAGA--GGTG---AGAGGG--- i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_86778 227 110 + 8487 TTTTGACGATGAGCATCAAATACTTT-----TAAAAGAAAAAGG-TGGGGGAC------ATGGCATCACGAAA--CACAACAAAAATTTCCCATTTGATTTCCAGGTCTG-TAGA--CTCT---GCAGGA--- i speTri1.scaffold_86778 C 0 I 1 s ponAbe2.chr17_random 16082161 112 + 17838096 CGTTGGCTATAAGCATCAAATACTTT-----TCAAAGAAAGAGG-TAGGGGAC------GTGGCATCGTGAAA--AATAGCACAAATTTTCCGTTTGATTGTAAGCTCTT-TAGCACTCCA---GGAGGG--- i ponAbe2.chr17_random C 0 C 0 s turTru1.scaffold_98008 7537 107 + 223990 TGTTGGCCATGAGCATAAAATACTTT-----TAAAAGGAAAAGG-CAGGGGAT------GCGGCATCATGAAA--AATAACGAGAATTTTCATTTAGACTTGAAGATCTT-TAAAACA--------AGGG--- i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10877397 107 - 65312493 CGTTGGTTGTGAGCATAAAATACTTT-----TAAAAGGAAAAGG-TGGGGGAT------GCGGCATCATGAAA--AATAACAAGAATTTTCCATTAGACTTGAAGGTCTT-TAAAACA--------ATGA--- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58060212 103 - 61308211 CGTTGACTGTGGCCATGAAATGCTTT-----CAAAAGAAAAAGG-CAGGGGAT------GTGGCATCGTGAAA--AATAATAAGAATTTTCCGTTTGACTTTAAGGTCTT-TAGAACA--------------- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59453700 116 - 64418924 TGTTCACTAGGCACGTGCAATACTTTATTTAAAAAAAAAAAAAG-CAGGAAAT------GTGGCATTGTGAAA--AATGACAAGGATTTTCCATTTGACTCTAAAGTCTT-CAGAGCAG-G---AGAAGG--- i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 42091 111 + 132007 CGTTGACTGGGCGTGTAAAACACTTT-----CAACAGAAAAAGG-CGGGAAAC------GTGGCATCGTGAAA--AATGACAAGGCTTTCCCATTTGATGCTGAAGTCTC-CAGAGCAG-G---AGAGGG--- i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_125911 2025 110 + 4959 CATTGACTATGACCACGAAACGCTTT-----TCAAAGGAAAAGG-CGGGGGGC------GTTGCATCATTAAA--AATAACGAGAATTTTCCATTTGACTTTAGGGTCCT-CCG-AAGC-G---AGAGGG--- i myoLuc1.scaffold_125911 I 390 C 0 s pteVam1.scaffold_11245 31789 106 + 48268 CACTGACTACGAGTGTGAAGTGCTTC-----TCAAAGGAAGAGG-C-AGAGAC------GTCGCACTGTGAAA--AGT----ATAATTTTCCGTATGACTCTAAGGTCTT-TAGCGCGG-G---AGAGAC--- i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_157372 1548 118 + 3406 TGTCAACAGTACTTGTTAAATACTTG-----GGAAAGGGGGAGGTCAAGGGACAGAGGGGCAATAGAGGGAAA--AAATACATGAATTTTCAATCTCATTTCCAGATCTT-GACAACAC-A---AGAAAG--- i eriEur1.scaffold_157372 C 0 N 0 s loxAfr3.scaffold_49 14452817 110 - 17734757 TGTTGACTA-GACCATAAAGTACTTT-----TGAAAGGAAAAGG-CGGGGGAA------ACGGCGTCGTGTAA--AACAGGGAGGATTTTTCCTTAGACTTGGAGGTCTT-TAG----GTG---ACCGGGGTG i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_171027 4525 102 + 4838 CCTTGACC--TACCAT-AAGTACTTT-----TAAAAGAAAAAAG-CGGGGGAG------CCGCC--CATGAAA--AATAACCAGACAATTCC------GTTTAAGGCCTT-TAGAACAGAG---AGCGGGG-- i dasNov2.scaffold_171027 C 0 C 0 e gorGor1.Supercontig_0270811 780 0 - 780 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I a score=118334.000000 s hg19.chr17_gl000204_random 65124 61 + 81310 TAGAACCTCGACAGCGTCTTCTCTT-TTAGGAGG---TGCAGAGACTGCCCAG--GGCCAGCACAAA s panTro2.chr17 79496807 61 + 83384210 TAGAACCTCGACAGCGTCTTCTCTT-TTAGGAGG---TGCAGAGACTGCCCAG--GGCCAGCACAAA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16082273 61 + 17838096 TAGAACCTCGACAGTGTCTTCTCTT-TCAGGAGG---TGCAGAGGCTGCCCAG--GGCCAGCACAAA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75056339 61 + 78773432 TAGAACCTCGACAGCATGTTCTCTT-TTAGGAGG---TGCAGAGACTGCCCAG--GGCCAGCACAAA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 63591 61 - 95547 TAGAACCTCGACAGCATGTTCTCTT-TTAGGAGG---TGCAGAGACTGCCCAG--GGCCAGCACAAA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 66140 60 + 225949 TAGCGCCTTGACAGCGTCTTCCCAT-TTAGGAGG---TGCAGAGA-TGCCTAG--GGCCAACACAAA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 1132 61 + 21754 TAAAGCCAAGAGAGCCTCTACCTGT-ATGTGAGG---TGCAGAGACTGCCCAG--GGCCAAAGCAGA i tarSyr1.scaffold_41848 C 0 C 0 s cavPor3.scaffold_76 4406854 61 + 7991924 TAAAACCTAGAGAGCTT-TGCATCTACAACCAGG---CGCACAGACTGCCTGG--GGCAGGGGCAGG i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_86778 338 57 + 8487 --GAAGCCAGAGACCTTATGCCTGT-TGGTGGGG---TGCAGAGATCACCCAG--GCCA--TGCAGA i speTri1.scaffold_86778 I 1 C 0 s turTru1.scaffold_98008 7644 64 + 223990 TGAAGCCAAGAGAGCTTCTTCCCTT-TTACGATGCTGCACAGAGACTGCCCAG--GGCGAAGGCAAA i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10877504 64 - 65312493 TGAAGTCAAGAGAGCTTCTTCCCTT-TTCCGAGGCTCCACAGAGACAACCCAG--GGTGAAAGCAAA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58060315 18 - 61308211 ---------------------C------------------------TGCCCAG--AACC--GGCAAA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59453816 61 - 64418924 CAAAGCAGAGGAAGCACCTTCCCTT-TCGTGCCA---CACAGGGAACGCCCGG--GGCCGGGGCAGC i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 42202 60 + 132007 CGGGACTGAGGGAGTGTCCT-CCTT-GCGTGACA---CGCGGGGAGTGCCCCG--GGCCTCAGCAGC i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_125911 2135 48 + 4959 GGGAGCCG--AGAGCCCCTTGCCCT-CTGCGATG---TGCAG-------------GGCACCGGCACC i myoLuc1.scaffold_125911 C 0 C 0 s pteVam1.scaffold_11245 31895 59 + 48268 TGAAGCCAACAGAGCTTCTT-CCCT-GTGGGATG---TGCAGAGA-CCTCCCA--GGCCAAGGTGAC i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14452927 59 - 17734757 CAGAGGCCCGGAGCTGCTCCTCTTT-ATA--ACA---TGCAGAGAATGCCCGG--GGCTGAGGCGAA i loxAfr3.scaffold_49 C 0 I 2029 s dasNov2.scaffold_171027 4627 55 + 4838 --GAAGCGGAAGAGCGCCCGGCCGC-CTA--ACG---GGCAGGGAGCGCCCGGCCTCCCCAGG---- i dasNov2.scaffold_171027 C 0 C 0 e gorGor1.Supercontig_0270811 780 0 - 780 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e mm9.chr11 118778739 1362 + 121843856 I a score=62882.000000 s hg19.chr17_gl000204_random 65185 27 + 81310 AGCATGGATTCAGG----tcct-------------------------------------------------------ggggctgcc s panTro2.chr17 79496868 27 + 83384210 AGCATGGATTCAGG----tcct-------------------------------------------------------ggggctgcc i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16082334 27 + 17838096 AGCTtgtattcagg----tcct-------------------------------------------------------ggggctgcc i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75056400 27 + 78773432 AGCGTGGATTCAGG----tcct-------------------------------------------------------ggggctgcc i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 63652 27 - 95547 AGGGTGGATTCAGG----tcct-------------------------------------------------------ggggctgcc i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 66200 27 + 225949 AGCATGGACTTACG----tcct-------------------------------------------------------cgggctgcc i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 1193 27 + 21754 AGGAtggattcatg----tccc-------------------------------------------------------ggggctgcc i tarSyr1.scaffold_41848 C 0 C 0 s cavPor3.scaffold_76 4406915 82 + 7991924 AGAGTAGATCAGGG----TCCTGTGACTGCCACAACAAAGCTTTGATGAAATTGATGGTTtaatcccagcactctgggaggctgat i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_86778 395 26 + 8487 AGGATGGGCTAGGG----Tct--------------------------------------------------------ggagctgct i speTri1.scaffold_86778 C 0 C 0 s turTru1.scaffold_98008 7708 27 + 223990 AGGGtgtgttagct----tcct-------------------------------------------------------ggggctccc i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10877568 27 - 65312493 AGGGtgtgtcagct----tccc-------------------------------------------------------ggggctccc i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58060333 27 - 61308211 AGGAtgttctcatt----tccc-------------------------------------------------------ggggctgct i equCab2.chr11 C 0 C 0 s canFam2.chr9 59453877 26 - 64418924 AGG-TGATTCCACt----ccct-------------------------------------------------------agggcttct i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 42262 23 + 132007 AG--------CGCCAGGGTCCC-------------------------------------------------------Ggggctgcc i felCat3.scaffold_206428 C 0 C 0 s myoLuc1.scaffold_125911 2183 27 + 4959 AGGATGCCCGCGTT----CCCC-------------------------------------------------------GGGGCTGCC i myoLuc1.scaffold_125911 C 0 N 0 s pteVam1.scaffold_11245 31954 26 + 48268 AGGA-GCCGTCCTT----CCCC-------------------------------------------------------GGGGCCGCC i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_171027 4682 27 + 4838 CGCGGCAGCCGTGG----ACTC-------------------------------------------------------GAGGCCCTC i dasNov2.scaffold_171027 C 0 C 0 e gorGor1.Supercontig_0270811 780 0 - 780 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e mm9.chr11 118778739 1362 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=241225.000000 s hg19.chr17_gl000204_random 65212 163 + 81310 acaacaaag------------------------------------------------tcccacaaaac------caga---------------------------------------------------------ggctga-aaac-------acagaaacttattctctcacagttctggaggccaggtgtttgaaatcaaggtgtcag---tggggc-----caggctctct-caaaaggct-cca-gggggactccctcccgtgcttccctcctcgctcctgggggc--cag s panTro2.chr17 79496895 163 + 83384210 acaacaaag------------------------------------------------tcccacaaaac------caga---------------------------------------------------------ggctgg-aaac-------acagaaacttattctctcaccgttctggaggccaggtgtttgaaatcaaggtgtcag---cggggc-----cgggctctct-caaaaggct-cca-gggggactccctcccgtgcttccctcctcgttcctgggggc--cag i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16082361 164 + 17838096 ccaacaaag------------------------------------------------tcccacaaaag------caga---------------------------------------------------------ggctga-aaac-------acagaaacttattctctcacagttctggaggccaggattttgaaatcaaggtgtcag---cggggc-----tgggctctct-caaaaggct-ccaggggggactccctcccgtgcttccctcctcgctcctgggggc--cat i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75056427 163 + 78773432 acaaccaag------------------------------------------------tcccacaaaac------caga---------------------------------------------------------ggcaga-aaac-------gcagaaacttactctctcaccgttctggaggccaggagtttggaatcaaggtgtcgg---tggggc-----caggctctct-caaaaggct-cca-gggggattccctcctgtgcttccctcctcgctcctgggggc--cac i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 63679 163 - 95547 acaaccaag------------------------------------------------tcccacaaaac------caga---------------------------------------------------------ggcaga-aaac-------gcagaaacttactctctcaccgttctggaggccaggagtttgggatcaaggtgtcgg---cggggc-----caggctctct-caaagggct-cca-gggggattcccccctgtgcttccctcctcgctcctgggggc--cac i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 66227 163 + 225949 acaacaaag------------------------------------------------tcccacaaaat------ccga---------------------------------------------------------ggctga-aaac-------acagaaacatattctctcacagttctggaggccagaagtttgaaatcaaggtgtcag---cggggc-----cagggtctct-caaaaggct-cca-gagggactccctaatgtgtgtccctcctctcccctgagagc--cgt i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 1220 135 + 21754 acagtaaag------------------------------------------------taccacaaaac------caga---------------------------------------------------------ggttta-aagc-------acagaaatgtgttttctcacagttctggagatcagaagtctgaaatcaggttgtcag---c-----------------------aaagatc-cct--------------ccaagcctctctcctcgttcctggtggctgccc i tarSyr1.scaffold_41848 C 0 C 0 s cavPor3.scaffold_76 4406997 246 + 7991924 gcaggaggatctcaaattctagcccagcttgggcaacttagtgagttagcaataccctgtctcaaaattttaaagggttggagaTATAGCCCGGTGCAAAGACTCTGAGTTCAATCCCCAGGACCATGAAGCAAAGAATCA-AAAC-------Ccagaaaggtatttccttgacgtcctggaggtcagaagtccaaaatgaaggtgtcag---cagggc-----caggctccctgcaaaggtgg-cca-gagagaccctat-------------------------------cgc i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_86778 421 110 + 8487 gcagcaggg------------------------------------------------tgccacaaaat------gggt---------------------------------------------------------ggctta-aaa---------cagaaatgctgtccctcga------ggaggtcagaagt-----------GAGCAAGACCCATGCC-----CTGCCTCCCTCCCA--GCTT-CCA-GTGGG--------------------------------------CAC i speTri1.scaffold_86778 C 0 C 0 s turTru1.scaffold_98008 7735 149 + 223990 --------a------------------------------------------------tcacacaaaac------ccgg---------------------------------------------------------ggcttt-aaac------aacagaaatgtattctctcacagtcctgaaggtcagaagttggaaat--------------caaggtgtcagcctgctgcct-c-ggaagct-cca-gggagaaaccacgccaggcctccctcctggcttctggccac--tgc i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10877595 138 - 65312493 --------a------------------------------------------------tcacacaaaac------cacc---------------------------------------------------------ggctgcaaaac------aacagagatgtattctctcacagtactgaaggtgaa--------------------------aaggtatcagcctgctgtct-c-aaaggct-cca-gggagaaatcatgccaggcctcccttctggcttctggttgc--ggc i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58060360 139 - 61308211 --------g------------------------------------------------aaacacagggt------cggg---------------------------------------------------------ggctca-aaat------agcagaaatgcatttcctctcagtcctggaggccagagg-ccgacat--------------cacggtgtc-gttcgctgctt-ctgaaggctgcag-gggaccgtccgtcccaggcctcccgccccacttc------------ i equCab2.chr11 C 0 C 0 s canFam2.chr9 59453903 145 - 64418924 --------g------------------------------------------------gaacccaaaat------cggg---------------------------------------------------------ggctta-agac------aagagaaatatcttttctcacagtcctgaaggccagatgtcccaaat--------------caaggc-----atctccacct-ccgaggact-ctg-gtcagaaaccatcccaggcccctctcctggcttctgggggt--tgc i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 42285 155 + 132007 --------a------------------------------------------------gaacccaacgt------cagg---------------------------------------------------------ggcata-agac------cacagagacgtcttctctcacagccctggaggccagaagtcccaaatctgcgtgtcag---cagggc-----cgcaccatct-ctcagggct-ctg-gtgagaggccgtcccaggccac-ctcccagcttcgggggcc--tgc i felCat3.scaffold_206428 C 0 C 0 s pteVam1.scaffold_11245 31980 150 + 48268 --------A------------------------------------------------CAACGCAAAAC------C------------------------------------------------------------gactta-aagc------aatggaaa----tttactctcagtcctagaggcgggaagtccaaaatcggggtgtcag---caggac-----cacactgcct-ccacagtctccag-tggagaacctgcccatggcccttgccctggcttctggtggc--tcc i pteVam1.scaffold_11245 C 0 I 135 s dasNov2.scaffold_171027 4709 125 + 4838 CCGACCAGG------------------------------------------------AGCCCGGAGAG------CATG---------------------------------------------------------GGCTGC-AGCCCGTCCCCACGGGAACTTCTCTTGCCACGTCCC-----GCCAGGG-----------------------CGTGGC-----CCCGCT--CT-CAGCAG----CCA-CGGAGACA-----GGGCGCCGCCCTCCCCGCTCC------------ i dasNov2.scaffold_171027 C 0 N 0 e gorGor1.Supercontig_0270811 780 0 - 780 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e mm9.chr11 118778739 1362 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=114198.000000 s hg19.chr17_gl000204_random 65375 107 + 81310 gggcaa--------------------------------tcccaggt--actccggggcttgtggctgcgtctctctgacctccgcctct---gtcttcatg------cagccttctcctctg--------cccttc----tttgtacaagggcagcagtcgt s panTro2.chr17 79497058 107 + 83384210 gggcaa--------------------------------tcccaggt--actctggggcttgtggctgcgtctctctgacatccgcctct---gtcttcacg------cagccttctcctctg--------cccttc----tttgtacaagggcagcagtcgt i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16082525 104 + 17838096 gggcaa--------------------------------tcccaggt--actccggggcttgtggctgcgtcactcggacctccacctct---gtcttcgtg------gaacattctcctatgt------ccctttc----tttgtacaaGGGAAGCA----- i ponAbe2.chr17_random C 0 I 92 s rheMac2.chr16 75056590 109 + 78773432 aggcaa--------------------------------tcccaggt--accccggggcttgtggctacctttctctgacctccgcctct---gtcttcatg------tggccttctcctctgt------ccttttc----tttgtacaagggcggcagtcgt i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 63842 109 - 95547 aggcaa--------------------------------tcccaggt--accccggggcttgtggctacctttctctgacctccgcctct---gtcttcatg------tggccttctcctctgt------ccttttc----tttgtacaagggcggcagtcgt i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 66390 102 + 225949 ggaaaa--------------------------------ttccagat--gcccctgggcctgtggctgcgtccctc------cagcctct---gcctttatg------tggccttctcctccgt------ccttttg----ttt-tacaagagcagcagttag i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 1355 121 + 21754 cagcaa--------------------------------tccatggt--gctcctgggcttgtggccacgttactccagtctctacctcc---acccttacatggtcttggccttctcctctgtgtgtcctcttcac----tctatacaaggacactagtcat i tarSyr1.scaffold_41848 C 0 C 0 s cavPor3.scaffold_76 4407243 90 + 7991924 c-ttct--------------------------------tccccgctaagctcccagtgctgtggctccc--------accttggcccca---gtcttcatg------tggcctctgtctgtgc----------------------acagggacatcagccac i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_86778 531 73 + 8487 T-GCAA--------------------------------CCCCTGGT--GGTCCCAGGCTTGTGGCATCCT------GGCTGCAACCCCACCTGTCTTCACA------TGGGTTCTTTGTG------------------------------------------ i speTri1.scaffold_86778 C 0 C 0 s turTru1.scaffold_98008 7884 112 + 223990 caatgg--------------------------------tccttggc--g-tcctcggcttgcggcagcatcactccagtctctgcctct---gtctccaca------tggccttgt-ctctgt-----gtcctcttcccttccttataaggaccccagtctt i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10877733 112 - 65312493 cgatgg--------------------------------tgcttggc--a-tccttggcttgtggcagcattgctccagtctctgcctct---gtctccatg------tgggtttgt-ctctgc-----atcctcttccctttcttataaggatctcagtcat i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58060499 59 - 61308211 ----------------------------------------ctcggc--attgctctgctcgtggtggcatcacccc-gaccctgcctcc---ctctccatg------t---------------------------------------------------cgt i equCab2.chr11 C 0 C 0 s canFam2.chr9 59454048 104 - 64418924 tggcaa--------------------------------tccttggg--cttccttggcttgtggcaacatcacttt-acctctgcctct---gtctccaca------tggcctccc-ccatgc-----attccctc------cttctaaggg--caaatcac i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 42440 105 + 132007 tggcca--------------------------------ctctcggg--gctccttggcttgtggcaacatcacctc-ccctctgcctct---gtctccacg------tggcctcct-ctgtgc-----gccccccc-----tcttacaaggg--catgacat i felCat3.scaffold_206428 C 0 C 0 s pteVam1.scaffold_11245 32265 144 + 48268 tggcgatccctggctggcccctggcgatccctggctggtccttggc--gatccctgcctggcagacacgtcgctcc-ggcctcagctct---gtctcctc-------tatccgcat-ctgtgtccacagttgcctc----ttcctacgaggaccccagctgt i pteVam1.scaffold_11245 I 135 C 0 e gorGor1.Supercontig_0270811 780 0 - 780 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e mm9.chr11 118778739 1362 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=502823.000000 s hg19.chr17_gl000204_random 65482 182 + 81310 tggacttagggcca--c-cctg-atcctgtatgacttcatcttatc-------taactatacctgcaaaggtactgtgtccaaataagg-caggctctgaagttctaggtggacatgaacaggggatggggg-gcagctcaacccact-acaAAGGGCTTGTGAAGGGACTCAGGCAGGCTCCGGGGCAGGTGGAC s panTro2.chr17 79497165 182 + 83384210 tggacttagggcca--c-cctg-atcctgtatgacttcatcttaac-------taactatacctgcaaaggtactgtgtccaaataagg-caggctctgaagttctaggtggacatgaacaggggatggggg-gcagctcaacccact-acaAAGGGCTTGTGAAGGGACTCAGGCAGGCTCCAGGGCAGGTGGAC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16082721 178 + 17838096 tggac-tagggccc--a-cctg-atcctgtatgacttcatc-taac-------taactata-ctgcaaaggtactgtgtcc-aataagg-caggctctgaagttctaggtggacatgaacaggggatggggg-gcagctcaacccTCT-ACAAGGGGCTTCTGAAGGGACTCAGGCAGGCTCCGGGGCAGGTGGAC i ponAbe2.chr17_random I 92 C 0 s rheMac2.chr16 75056699 182 + 78773432 tggacttagggccc--c-cccg-atcctgtatgacttcatcttaac-------taactatacctgcaaaggtactgtgcccaaataagg-caggctctgaagttctaggtggacatgaacaggggatggggg-gcagctcaacctact-acaAGGGGCTTGTGAAGGGACTCAGGCAGGCTCCAGGGCAGGTGGAC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 63951 182 - 95547 tggacttagggccc--c-cccg-atcctgtatgacttcatcttaac-------taactatacctgcaaaggtactgtgcccaaataagg-taggctctgaagttctaggtggacatgaacaggggatggggg-gcagctcaacctact-acaAGGGGCTTATGAAGGGACTCAGGCAGGCTCCAGGGCAGGTGGAC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 66492 182 + 225949 tggacttgggaccca-c-cctg-attctgtatgactccatcgtaac-------taaccatacctgcaaaggtactctatccacagaagA-CAGGCTGTGACGTTCTCGGTGGGCATGAACAGGTGATGGAGA-GCGGCTCAGCCCACT-ACAA-GGACTTGTTAAGAGACTCAGGCAGGCCTCGGGGCAGGTGGAC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 1476 183 + 21754 tgaacttatggcccacc-tctg-accttgtatgacttcctctcaac-------taatgacacctgcactgatactgcttccaaataaggccagattctaaagctctgggtgaacttgaatttgg--tggtgacactatctaacccact-acaACAGAC-TGCTAATGGACTCAAATGTGCTTCGAGGCAGGTAGAC i tarSyr1.scaffold_41848 C 0 C 0 s cavPor3.scaffold_76 4407333 174 + 7991924 tgggc----agtcc--c-cctg-ctcccatgggactccatcttcac-------cacttaggcttgccccaaccttacttccaaataaggccatatttcgaggttccagg--AACATGAATCGAG-ACACACA-GTATTCCA--TCGCT-GCAAGCATTTTTTTAATGGACACAGACAAGCTTCAGAACAGGGTGGC i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_86778 604 112 + 8487 Tgggt----ctttc--a-ccca-acccagtatgacttcatcttgac-------ca-ttacctttgcaaaaaccctgctcctaaataaggccacattcccaggttgcagg---------------------------------------------------------------ggACAAACACTGGGGCGGG----- i speTri1.scaffold_86778 C 0 C 0 s turTru1.scaffold_98008 7996 181 + 223990 tggactgagggccc--acccta-atccagcacgacctcatcttaac-------taattgcatctgcaaagaccctatttccaaataaggtcccattctgaggttctgggtgggcatgaatttgg--ggggac-attattcaatccaCT-CCAGGGGGATTGATAATGAAATAAGATGAGC-TCAGAGCAGGGAGGC i turTru1.scaffold_98008 C 0 I 1218 s bosTau4.chr19 10877845 189 - 65312493 cggattgagggcgc--actcaa-actcagcacaacttcatcttaactattcaataattgcatctgcaaagacactgtttccaaataaggacctattctgcgg-tctgggtgggcatgaatttgg--ggggac-attattcaacccaCTCCCAGGGGAATTAATAATGAAATCAGACGAGCTTCAGAGCAGACAGGT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58060558 182 - 61308211 tggatttggggccc--acccca-gtccagcacggtctcatcttaat-------taaccccatctgcaaaggccctatttccaaataagttcactgtttgaacttctgggcggacacgaatttca--gggggc-actattcaacccaCT-ACGAGGGGATCGATAatgaaagcagatgagcttcagagcaggtgggc i equCab2.chr11 C 0 C 0 s canFam2.chr9 59454152 170 - 64418924 tgaattcagatccc--a-ccta-atccagcaggacctgatcttaac-------caattacatcctcaaagaccctatttctaaggaagacc----actgggattccaagtggacacaaattttg--agggat-actattcaacacaca-TCGAAGGGATCAATAATGAAATCAGATGAGCTTCAGAGCA------- i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 42545 171 + 132007 tgagtttaggcccc--a-ccta-atccagaacga-ctcatcctaac-------cagctatgtcctcgaaaaccctacttcctgggaaggccccctcctgaggtgctgggCGACCAAGAATTTTG--ACAGAC-AC---------CATG-TCCAGGGGATCAATAATGAAACGAGACAAGCTTCCGAGCAGGCAGGC i felCat3.scaffold_206428 C 0 C 0 s pteVam1.scaffold_11245 32409 166 + 48268 tggctctggggccc--a-cctgcagccagcgtgacc---tcctaac-------taatcacatctgcaaaggcctcagtccccaacaaggccccatcctgagggtctgggCGGATGTGACTCTGG--AGGAAC-ACTACCC--------------GGGACAGACAatggcatcagacaagcttcagagcaggctggg i pteVam1.scaffold_11245 C 0 C 0 e gorGor1.Supercontig_0270811 780 0 - 780 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e mm9.chr11 118778739 1362 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=186438.000000 s hg19.chr17_gl000204_random 65664 200 + 81310 TCCAGCAATCCTCTGATCT--------CCTCC-------A-CGTC-----CCCGA------CGG-------ACAGGGTGTCACCCAGG-------AAGCA-CTCCAGGGACAAGCCATTCACCATCTCCC-----------CTCCTCCA--------G--CCC-----TGGGGG--AGCCTCCT-CTACTGGAAAACATCCTTTTCAACAGCAACC-AAATTCTCCT----CT-GGCCGTCGTCCAGGTTGGAGTTCAGAC------CTACCTTCTGGAGTAA s panTro2.chr17 79497347 200 + 83384210 TCCAGCAATCCTCTGATCT--------CCTCC-------A-CGTC-----CCGGA------CGG-------ACAGGGTGTCACCCAGG-------GAGCA-CTCCAGGGACAAGCCATTCACCATCTCCC-----------CTCCTCCA--------G--CCC-----TGGGGG--AGCCTCCT-CTACTGGAAAACATCCTTTTCAACAGCAACC-AAATTCTCCT----CT-GGCCGTCATCCAGGTTGGAGTTCAGAC------CTACCTTCTGGAGTAA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16082899 197 + 17838096 TCCAGCAATCCTCTGAT-----------CTCC-------A-TGTC-----CCCGA------CGG-------ACAGAGTGTCACCCAGG-------GAGCA-CTCCAGGGACAAGCCATTCACCATCTCCC-----------CTCCTCCA--------G--CCC-----TGGGGG--AGCCTCCT-CTACTGGAAAATATCCTTTTCAACAGCAACC-AAATTCTCCT----CT-GGCCGTGGTGCAAGAAAGAGTTCAGAC------CTACCTTCTGGAGTAA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75056881 200 + 78773432 TCCAGCAATCCTCTGATCT--------CCTCC-------A-AGTC-----CCCGA------CAG-------ACAGGGTGTCACCCAGG-------GAGCA-CTCCAGGGATAAGCCATTCACCATCTCCC-----------CTCCCCCA--------G--CGC-----TGGGGG--AGCCCCCT-CTACTGGAAAACGTCGTTTTCAATAGCAACC-AAATTCTCCT----CT-GGCAGTCGTCCAGGTTGGAGTTCAGAC------CTACCTTCCGGAGTAA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 64133 200 - 95547 TCCAGCAATCCTCTGATCT--------CCTCC-------A-AGTC-----CCCGA------CAG-------ACAGGGTGTCACCCAGG-------GAGCA-CTCCAGGGATAAGCCATTCACCATCTCCC-----------CTCCCCCA--------G--CGC-----TGGGGG--AGCCCCCT-CTACTGGAAAACGTCCTTTTCAATAGCAACC-AAATTCTCCT----CT-GGCAGTCGTCCAGGTTGGAGTTCAGAC------CTACCTTCTGGAGTAA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 66674 200 + 225949 TCCAGCGATCCTCTCATCT--------CCTCC------AA-CGTC-----CCTGA------TGG-------ACAGGGTGTTACCCAGG-------GAGCA-CTACAGGGACAAGCCATCCACCACCTCCC-----------CTCCCCCA--------G--CCC-----TGGGGG--AGCC-CCA-CTGCTGAAAAACGTCCTTTTCAACAGAAACC-AAAGTCTCCC----CT-GACTGTCTTCCAGTTTGTAGTTCAGAC------CTACCTTCTGTAGTAA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 1659 213 + 21754 TCAGGTGGTCATCTGATCT--------CTTCC-------ATCATC-----ACCAA------CAG-------ACAGGGTGTCACTCAGG-------GAGCA-CCACC-GGACACAGCACTGACCACCTCCCACAACAGCCTTCTCCCCCA--------ATCCCC-----AGGGAG--AGCCCACA-TGGCTGGAAAATGTCCTTTTCAACAATGACC-AAAATCTGCT----CT-GGCCATTGTCCAGTTTGGAGTCCAGGC------CTACCTTCTGAAGTGA i tarSyr1.scaffold_41848 C 0 C 0 s cavPor3.scaffold_76 4407507 172 + 7991924 -CTGGTGACCCTCTGGTCC--------TGCTC-------A-TCAC-----TCCCAGCCACCTCC-------ACAGAACATTGCCCAGG-------GTCTG-CTCTAAAGGGAGA-CGTTTACTACCTCCC-------------TTGGCA--------G--CCC---ACTGTGGA--GACCTGCA-TAGTTGGAAAGTGCCACCCCC--CAGTGACT------------------GGCC-TGGTT-----------------------CTGGCTTTTGGGGGGA i cavPor3.scaffold_76 C 0 C 0 s speTri1.scaffold_86778 716 201 + 8487 -----------TTTGGCTC--------TTC-C-------A-CCAC-----TACGAGTGTCACAC-------AGAGGGTGTCACCCAGA-------GACCA-CTGCAGTGCTGGG-CACTCACCACCCCCT-------------GAGACA--------A--CCCTTTCCTGGGGAAGAGCCCGCA-GAGCTGAAAAAGTCCCTCCCC--TAGTGACC-CAA-CCTCCT----CTGGGCCATGGTCCA-CCCAGAGTGCAGAGTGCAGACCATCTTCTGGAGCAA i speTri1.scaffold_86778 C 0 N 0 s bosTau4.chr19 10878034 195 - 65312493 GTTGGCCATCATCTGGCCCGGCCTGTCTCTCT----------CTCTC---TGTTA------CAGCACCCAGATATAGCATC-CCCAGCTCTGCCTGGGCA-CTGCCATGGCGGTGCGCTCCCCACCTCGC---ATGACGGCCTCCCC----------A--TTA-----GAGGAG--AGCCTGCA-CTGCAGGGAAACCTTCCT-CTCAAGAGGACGCGGACTCTGCT----GC-GGTCATGGTCC-------------------------------------- i bosTau4.chr19 C 0 I 7 s equCab2.chr11 58060740 214 - 61308211 gctgaccgtcgcctgatccagcctgtccctctcgagggaa-cctc-----cctta------caacctccctgtccgggatggccctgctccgcctgcgtg-ctaccgtgacagggcgccccccacctccc---acgacagccttctcc---------t--cc-------gggag--agcctgca-ctgctggaaaacattctcgccaacgttgacctgaaatctgct----gt-ggtcgtcatccagct-ggatttc-------------------------- i equCab2.chr11 C 0 I 1 s canFam2.chr9 59454322 239 - 64418924 GCTGGCCAtcacctgatccagcgtgt-cctct-gtgggaa-cctttcctacctta------caaccctcc-gcacggcaccacccagctctgcccgagcaaccacggtggcagggtgctccccacgtccc---ccgacagactttccc---------t--caa-----ggggaa--gacctgca-ctgctgggaaacattctt-ccaacgttgatcccagacctgct----gt-gctcgtcatccagttgggaattc------gcttctgccttctggagtga i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 42716 234 + 132007 GCCGGCCATCATCTGATCCAGCCCCTCCCTCT-GTGGGAA-ACTCTCTTACCTTA------CAACCCTCCAACAGGGTGTCACCTCGCTCGGCCTGAGCA---------------------CCACCTCCC---AGGACGGACTCCCCCCTCCCCCTGC--CGA-----GGGGAG--GACCTGTACCTACTGGAAAATATTCTT-CCAATGCTGACCTCAGACCCACTGCGCGT-GCTCGCTGTCTGGCTGGGGGTTC------ACCTCTGCCTCCTGGAGCGA i felCat3.scaffold_206428 C 0 C 0 s pteVam1.scaffold_11245 32575 166 + 48268 gctggccgccctctgacccagcctgtccctccagagggaa-cctc-----tgtta------cagcccctg-acaaggtatcgcccagcttGGCA-GGGCG------------GGGCGCCT-CGGCCTCCC---ATGA--------------------C--CTT-----GGAGAG--AGCCAGCG-CTTCTG--------CTTC-CTGGCATCGGCC-AAAATCGCCC----AT-GGTCCTC------------------------------------------ i pteVam1.scaffold_11245 C 0 I 1959 e gorGor1.Supercontig_0270811 780 0 - 780 I e turTru1.scaffold_98008 8177 1218 + 223990 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e mm9.chr11 118778739 1362 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=150614.000000 s hg19.chr17_gl000204_random 65864 94 + 81310 CGAA-AAATAACAAAAACAGCAA-TCGTGGCTGCTTCCCGCACCCTGGAGCCCAAGCCAACcacacgcgcacacacgcacatgcacacacatgcac s panTro2.chr17 79497547 92 + 83384210 CGAA-AAATAACAAAAACAGCAA-TCGTGGCTGCTTCCCGCACCCTGGAGCCCAAGCCAACcacacgcgcacacacgcacatgcacacaca--cac i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16083096 94 + 17838096 CAAA-AAATAACAAAAACAGCAA-TCAAGGATGCTTCCCGCACCATGGAGCCCAAGCCAACcacacgctcacacacacacatgcacacatacgcac i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75057081 94 + 78773432 CAAA-AAATAACAAAAACAGCAA-TCATGGCTCCTTCCCGCACCATGGAGCCCAAGCCAACcacacaggcacacacgcacatgcacacacacgcat i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 64333 94 - 95547 CAAA-AAATAACAAAAACAGCAA-TCATGGCTCCTTCCCGCACCATGGAGCCCAAGCCAACcacacaggcacacacgcacatgcacacacacgcat i papHam1.scaffold8336 C 0 I 15 s calJac1.Contig5139 66874 90 + 225949 CAAA-AAGTAACAAAAACAGCGA-TCATGGCTCCTTCCTGCACCATGGAGCCCAAGCCAACcacacacacacacacgcacacacacatgcac---- i calJac1.Contig5139 C 0 I 2 s tarSyr1.scaffold_41848 1872 89 + 21754 C--A-GAGTAAAGAAAACCACCA-GCATGGCTCCTTTCCACACCACCGAGCTCCCACCAACCACACGCTCACACACTTGTGTACATATACGTG--- i tarSyr1.scaffold_41848 C 0 C 0 s mm9.chr11 118780101 88 + 121843856 TGGA-GAATAAGGAAAGCAGTGT-CCATGGCTCCCTACTGAACCA-CAGGCC-AGGGCAGCCACAGGGGTGAGCCCGTGCCTATACACACAT---- i mm9.chr11 I 1362 I 2 s cavPor3.scaffold_76 4407679 79 + 7991924 TGCAGGAGGAAGGAGAACAGGGGACCACGACTCCTTCTTGCACCACCAGGCT--------TCAC-----TAAGCTCAGGCACACACACATAC---- i cavPor3.scaffold_76 C 0 I 2 s felCat3.scaffold_206428 42950 76 + 132007 CGAG-GAACAGGGAAGA--GTGA-TCATGACTCCTTCCTACACTGTCAAGCCCAG------CGCACAGGTgtgcacacaggtgcac---------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59454561 73 - 64418924 tgag-gaataagGAAGA--GTGA-CCGTGGCTCCTTCCTGCACCATCAAGCCCAG------CACACAG--ATGCCCACAGGTGTG----------- i canFam2.chr9 C 0 C 0 e gorGor1.Supercontig_0270811 780 0 - 780 I e turTru1.scaffold_98008 8177 1218 + 223990 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10878229 7 - 65312493 I e equCab2.chr11 58060954 1 - 61308211 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=-16706.000000 s hg19.chr17_gl000204_random 65958 41 + 81310 -----------atgcacaca------cacacgt--------------gcacacatgcatatg--cacacacgca s panTro2.chr17 79497639 31 + 83384210 -----------gtgcacaca------------t--------------acgcatatgca------cacacacgca i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16083190 43 + 17838096 -----------atgcacata------cacgcgc--------------acacacacggacatgcacacacacgga i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75057175 45 + 78773432 -----------atgcacaca--tgcacacacat--------------gcacacacacacatg--cacacacaca i rheMac2.chr16 C 0 C 0 s calJac1.Contig5139 66966 26 + 225949 -----------atgcacata--------cacat--------------gcacacacgcat--------------- i calJac1.Contig5139 I 2 I 114 s mm9.chr11 118780191 36 + 121843856 -----------ATGCACACG--------CTCCT--------------ACAGCTGTTCTTATG--GAC---CAGG i mm9.chr11 I 2 I 1 s cavPor3.scaffold_76 4407760 50 + 7991924 -----------ATACCCACA--------TTCTTGGCTATGCACAAACACACATACGAGTATG--CAC---CGCA i cavPor3.scaffold_76 I 2 I 6 s felCat3.scaffold_206428 43026 40 + 132007 acaccacacagatgcccacaggtgcacacaagt--------------acacaca-------------------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59454634 33 - 64418924 ----CATAGAGATCCCCACAGGTacaaaca-----------------acacaca-------------------- i canFam2.chr9 C 0 C 0 e papHam1.scaffold8336 64427 15 - 95547 I e tarSyr1.scaffold_41848 1961 0 + 21754 C e gorGor1.Supercontig_0270811 780 0 - 780 I e turTru1.scaffold_98008 8177 1218 + 223990 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10878229 7 - 65312493 I e equCab2.chr11 58060954 1 - 61308211 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=2562.000000 s hg19.chr17_gl000204_random 65999 46 + 81310 catgcacacatatgtacatg--cacacatgcacacaagc--acatgcaca s panTro2.chr17 79497670 50 + 83384210 catgcacacatatgtacatgcacacacacgcacacacacagacatgcaca i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16083233 31 + 17838096 catacacacacatgcacata--cacacatgcac----------------- i ponAbe2.chr17_random C 0 I 60 s rheMac2.chr16 75057220 46 + 78773432 tatgcacacatgcacacacg--cacacatgcac--acacgggcatgcaca i rheMac2.chr16 C 0 C 0 s mm9.chr11 118780228 32 + 121843856 CAGCCACAGATGTGTGCATGACTATACACACA------------------ i mm9.chr11 I 1 I 502 s felCat3.scaffold_206428 43066 30 + 132007 gatgcacacaggcattcaca--caggtacaca------------------ i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59454667 13 - 64418924 gatgcccacagat------------------------------------- i canFam2.chr9 C 0 C 0 e calJac1.Contig5139 66992 114 + 225949 I e papHam1.scaffold8336 64427 15 - 95547 I e tarSyr1.scaffold_41848 1961 0 + 21754 C e gorGor1.Supercontig_0270811 780 0 - 780 I e turTru1.scaffold_98008 8177 1218 + 223990 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10878229 7 - 65312493 I e equCab2.chr11 58060954 1 - 61308211 I e cavPor3.scaffold_76 4407810 6 + 7991924 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=30860.000000 s hg19.chr17_gl000204_random 66045 388 + 81310 catgtgtgcatgcacgcatatg--------cacacatacacacatgcacacgcgcacacacaTGCACGCGCGGacatgcacacacacatgcacaca--catgtgcac--atgcacacacgtgcacatgcacacacagggacatgcacacacgcacatgcacacatacgcacatgcacacacacgtgcacacatacgcatatgcgcacacac--gcacacacgcacatgcacaaatatgtacatacacgcacgcaca--cagacatgcacacacacggacatgga----cacacacggacatacacacacatgcacacatgcccacatgcacacacacggacatgcacaca--cgcacgtgcacacatg----cacatgcacacatgcgcacacacatgcacacgtgcacacac--g s panTro2.chr17 79497720 404 + 83384210 cacacggacatgcacacacacggacatacacgcacatgcgcacatgcacacgcgcacacatgcacacacacggacatgcacacacgcgtgcacacacgcacatgcac--atacacacatgagcacacgcacacacatgcacacatggacatgcacacacgcacatacacacacgcacacaca--tgcacacacacggacatgcacacacgcgtgcacacacgcacatgcacacatacgcacatgcacacacgcacacgcacacatgcacacgcacacatatgtacatgcacacacgcacacacacggacatgcaca------cacacggacatacacgcacatgcacacatgcgcacatgcacacgtgcacacacatgcacacacacggacatgcacacacgcatgcacacac--g i panTro2.chr17 C 0 C 0 s felCat3.scaffold_206428 43096 330 + 132007 --------caggtgcacacaga--------tgcccacaggtacacgcagacgcacacacagatgacc------acaggtgcacacagatgcttacaggtgcacacag--atacacacaggtg----tgaacaccagaacacaaacag---------cacacagatgcccacaggtgcacacagatgcacacaggcacacacaggcatacacgggtgcacaaaggcatgcacacaggtgcaca----------------aaggtgtgcatactgaca------------cacaca-------gcacacagatgcacc------caggatcccacaggtggacataggcacc--cacaggtgcacacata------tatgcacacaggtggacacagacatgcacaggtgcacacggg i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59454680 206 - 64418924 -----------gcacacacaag--------tgcccaaaggcacaaacag-----cacacagatgcat------acaggtgcacacagatgcccacaggtgcgcaaaggcatacacacaggtg------------------cacgtag---------cacacacatacccacacgtgcgcac----------------------------------------aggcattcacacaggtg--------------------------------------------------cacata-------gcacacaGATG------------------------------------CC--CACAGGTGTGCAAAGG------CATACACTCGGGTG----------TGTACAGGCATACAC--A i canFam2.chr9 C 0 C 0 e calJac1.Contig5139 66992 114 + 225949 I e papHam1.scaffold8336 64427 15 - 95547 I e tarSyr1.scaffold_41848 1961 0 + 21754 C e gorGor1.Supercontig_0270811 780 0 - 780 I e turTru1.scaffold_98008 8177 1218 + 223990 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10878229 7 - 65312493 I e equCab2.chr11 58060954 1 - 61308211 I e cavPor3.scaffold_76 4407810 6 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I e ponAbe2.chr17_random 16083264 60 + 17838096 I e rheMac2.chr16 75057266 0 + 78773432 C a score=9392.000000 s hg19.chr17_gl000204_random 66433 80 + 81310 cacgtgcacacacgcgcacacacatgcgcatacg--tgcacatgcatacgcgc--acatgcacacacg--catgcacacatg----tgca s gorGor1.Supercontig_0191203 5705 86 + 8483 cacatgcacacacgcgcacacacatgcacacaca--cggacatgcacacacgg--acatncacacacggacatgcacacacggacatgca i gorGor1.Supercontig_0191203 n 0 C 0 s panTro2.chr17 79498124 84 + 83384210 cacatgcacaca----tacacacatgtgcacacgcacacacatgcacacacacggacatgcacacaca--cgtgcacacacgcacatgca i panTro2.chr17 C 0 C 0 s felCat3.scaffold_206428 43426 40 + 132007 ----------------------catgtgcacaga------gatgcacacaagc------------------atacacacagg----tgca i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59454886 35 - 64418924 ----------------------CAGGTGCACATG---------GCACACAG--------------------ATGCCCACAGG----TGCA i canFam2.chr9 C 0 C 0 e calJac1.Contig5139 66992 114 + 225949 I e papHam1.scaffold8336 64427 15 - 95547 I e tarSyr1.scaffold_41848 1961 0 + 21754 C e turTru1.scaffold_98008 8177 1218 + 223990 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10878229 7 - 65312493 I e equCab2.chr11 58060954 1 - 61308211 I e cavPor3.scaffold_76 4407810 6 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I e ponAbe2.chr17_random 16083264 60 + 17838096 I e rheMac2.chr16 75057266 0 + 78773432 C a score=8810.000000 s hg19.chr17_gl000204_random 66513 32 + 81310 cac--ccgcgcgtgcacaca--cgcacgcacgcacg s papHam1.scaffold8336 64442 32 - 95547 cac--gcacacatgcacaca--catgggcatgcaca i papHam1.scaffold8336 I 15 C 0 s gorGor1.Supercontig_0191203 5791 32 + 8483 cac----gcacatgcacacacgcacatgcacacacg i gorGor1.Supercontig_0191203 C 0 C 0 s panTro2.chr17 79498208 36 + 83384210 cacatacgcacatgcacacatgcacacgcacacacg i panTro2.chr17 C 0 C 0 e calJac1.Contig5139 66992 114 + 225949 I e tarSyr1.scaffold_41848 1961 0 + 21754 C e turTru1.scaffold_98008 8177 1218 + 223990 I e felCat3.scaffold_206428 43466 0 + 132007 C e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59454921 0 - 64418924 C e bosTau4.chr19 10878229 7 - 65312493 I e equCab2.chr11 58060954 1 - 61308211 I e cavPor3.scaffold_76 4407810 6 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I e ponAbe2.chr17_random 16083264 60 + 17838096 I e rheMac2.chr16 75057266 0 + 78773432 C a score=20906.000000 s hg19.chr17_gl000204_random 66545 57 + 81310 cacacatgcacacacgcacatgcacacacgcacatgcacacacacgcacac------acacgg s gorGor1.Supercontig_0191203 5823 55 + 8483 cacgtgcacacatacgnacangcacacacacatgtgcacatgcacacac--------acacGG i gorGor1.Supercontig_0191203 C 0 C 0 s panTro2.chr17 79498244 63 + 83384210 catacatgcacacactgacatgcacacacgcacatgcacacacatgtgcacatacatacacgg i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75057266 53 + 78773432 cacacatgcacacacggacatgcatacacacacagagacatgcatacac--------acgc-- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 64474 53 - 95547 cacacatgcacacacggacatgcatacacacacaGAGACatgcatacac--------acgc-- i papHam1.scaffold8336 C 0 C 0 s canFam2.chr9 59454921 11 - 64418924 ------------------------TACACACACAG---------------------------- i canFam2.chr9 C 0 C 0 e calJac1.Contig5139 66992 114 + 225949 I e tarSyr1.scaffold_41848 1961 0 + 21754 C e turTru1.scaffold_98008 8177 1218 + 223990 I e felCat3.scaffold_206428 43466 0 + 132007 C e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10878229 7 - 65312493 I e equCab2.chr11 58060954 1 - 61308211 I e cavPor3.scaffold_76 4407810 6 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I e ponAbe2.chr17_random 16083264 60 + 17838096 I a score=54950.000000 s hg19.chr17_gl000204_random 66602 37 + 81310 acatgcacacacgcacaTGCACACATGTGCCCATGCC s calJac1.Contig5139 67106 31 + 225949 ------ACACACGCACATGCACACATGTGTACACACC i calJac1.Contig5139 I 114 C 0 s panTro2.chr17 79498307 37 + 83384210 acatgcacacacgcacatgcacacaTGTGCACCTGCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0191203 5878 37 + 8483 ACATGCACACACGCACATGCACACATGTGCACATGCC i gorGor1.Supercontig_0191203 C 0 C 0 s ponAbe2.chr17_random 16083324 37 + 17838096 acatgcacacacacacacgcacacatgtgcacatgcC i ponAbe2.chr17_random I 60 C 0 s rheMac2.chr16 75057319 37 + 78773432 acatgcacacatacacatgcacacatgcacacaCGCT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 64527 37 - 95547 acatgtacacatacacatgcacacatgcgcacaCGCT i papHam1.scaffold8336 C 0 C 0 s canFam2.chr9 59454932 13 - 64418924 AGGTGCA------------------------CGTGCA i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 43466 24 + 132007 -------------cacatgcaaagaggtacgcacgcG i felCat3.scaffold_206428 C 0 C 0 e tarSyr1.scaffold_41848 1961 0 + 21754 C e turTru1.scaffold_98008 8177 1218 + 223990 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10878229 7 - 65312493 I e equCab2.chr11 58060954 1 - 61308211 I e cavPor3.scaffold_76 4407810 6 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=122546.000000 s hg19.chr17_gl000204_random 66639 49 + 81310 GTCCTGTAGGTATTTCTCAGGCGACCCCCTCCACACCCTGATGCCCTCC s papHam1.scaffold8336 64564 44 - 95547 GTCCTGTAGGTATTTCTCAAATGACCCCCT-----CCTGGACGCCCTCC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75057356 44 + 78773432 GTCCTGTAGGTATTTCTCAAATGACCCCCT-----CCTGGACGCCCTCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16083361 49 + 17838096 GTCCTGTAGGTATTTCTCAAATGACCCCCTCCACACCCTGACGCCCTCC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0191203 5915 49 + 8483 GTCCTGTAGGTATTTCTCAGGTGACCCCCTCCACACCCTGATGCCCTCC i gorGor1.Supercontig_0191203 C 0 C 0 s panTro2.chr17 79498344 49 + 83384210 GTCCTGTAGGTATTTCTCAGGTGACCCCCTCCACACCCTGATGCCCTCC i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 67137 48 + 225949 ATCCTGTAGGTATTTA-CAAATGACCCCGTTCACACGCTGATGCCCTCC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 1961 49 + 21754 GTCCTGCAGGCATTTCTCAGGTGACTACCACCCTACCCTGATGCCCTCC i tarSyr1.scaffold_41848 C 0 C 0 s cavPor3.scaffold_76 4407816 46 + 7991924 GTCCTGCAGGTGTCTCTCAGGCAACCCCTGCCA--GCTCAGTG-CCTCC i cavPor3.scaffold_76 I 6 C 0 s canFam2.chr9 59454945 49 - 64418924 GTCCCACAGCTACTTTGCAAACAACCTGTCCTCATCCTAACTGCCATCC i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 43490 49 + 132007 GTCCCACAGCTGCTTTTCAAATGACCTCTCCCCACCCTAACTACCACCC i felCat3.scaffold_206428 C 0 C 0 e turTru1.scaffold_98008 8177 1218 + 223990 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10878229 7 - 65312493 I e equCab2.chr11 58060954 1 - 61308211 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=480736.000000 s hg19.chr17_gl000204_random 66688 249 + 81310 TGGAACCCCACATGATTCTCTGGGGGTTCCTCAATGGTCCCAGAACCTGGCTCCACCCTCCACAGCAGGGCAAACGGCAGAGAAGGGTTATCATTCCTGCCCTTGGGACCCAGGCTGTCCACTGTGACGTCCTT---AGCTGCCACATCACACCCGATCTCATTTCAGGCTG--GTTTCTTCTACGCCGTTCCTGGGG----ACATCCAGACAT-CAGTGGG-GTA---CTTCTCTTACTCCTGTTAAAGTTAATC---C---AACttc s papHam1.scaffold8336 64608 236 - 95547 TGGAACCCCACACGATTCTCTGGCAGTTCCTCAATGGTCCCAGAACCTGGCTCCCCCCTCCATAGCAG----------------GGGTTATCATTCCTGCCCTTGAGACCCAGGCTTTCCACTGTGACGTCCTT---TGCTGCCACATCACACCCGATCTCATTTCAGGCTG--GTTTCTTCTACACCACTCCTGGGG----ACATCCAGACAC-CAATGGG-GCACTTCTTCTCTTACTCCTGTTAAAGTTAGTC---C---AACttc i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75057400 236 + 78773432 TGGAACTCCACACGATTCTCTGGCGGTTCCTCAATGGTCCCAGAACCTGGCTCCACCCTCCACAGCAG----------------GGGTTATCATTCCTGCCCTTGAGACCCAGGCTTTCCACTGTGACGTCCTT---TGCTGCCACATCACACCCGATCTCATTTCAGGCTG--GTTTCTTCTACACCACTCCTGGGG----ACATCCAGACAC-CAATGGG-GCACTTCTTCTCTTACTCCTGTTAAAGTTAGTC---C---AACttc i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16083410 249 + 17838096 TGGAACCCCACACAATTCTCTGGGGGTTCCTCAATGGTCCCAGAACCTGGCTCCACCCTCCACAGCAGGGCAAACGGCAGAGAAGGGTTATCAGTCCTGCCCTTGAGACCCAGGCTGTCCACTGTGACGTCCTT---AGCTGCCACATCACACCCGATCTCATTTCAGGCTG--GTTTCTTCTACACCGTTCCTGGGG----ACATCCAGACAT-CAATGGA-GTA---CTTCTCTTACTCCTGTTAAAGTTAATC---C---AACttc i ponAbe2.chr17_random C 0 I 12 s gorGor1.Supercontig_0191203 5964 249 + 8483 TGGAACCCCACATGATTCTCTGGGGGTTCCTCAATGGTCCCAGAACCTGGCTCCACCCTCCACAGCAGGGCAAACGGCAGAGAAGGGTTATCATTCCTGCCCTTGGGACCCAGGCTGTCCACTGTGACGTCCTT---AGCTGCCACATCACACCCGATCTCATTTCAGGCTG--GTTTCTTCTACGCCGTTCCTGTAG----ACATCCAGACAT-CAATGGG-GTA---CTTCTCTTACTCCTGTTAAAGTTAATC---C---AACttn i gorGor1.Supercontig_0191203 C 0 n 0 s panTro2.chr17 79498393 249 + 83384210 TGGAACCCCACATGATTCTCTGGGGGTTCCTCAATGGTCCCAGAACCTGGCTCCACCCTCCACAGCAGGGCAAACGGCAGAGAAGGGTTATCATTCCTGCCCTTGGGACCCAGGCTGTCCACTGTGACGTCCTT---AGCTGCCACATCACACCCGATCTCATTTCAGGCTG--GTTTCTTCTATGCCGTTCCTGGGG----ACATCCAGACAT-CAACGGG-GTA---CTTCTCTTACTCTTGCTAAAGTTAATC---C---AACttc i panTro2.chr17 C 0 I 7 s calJac1.Contig5139 67185 249 + 225949 TGGAACCCCACACGATTCTCTGGCAGTTCCTCAATGGACCCAG-ACCTGGCTCCACCCTCCACAGCAGGGCAAATGGCAGCGGGGGACCATCATTCCTGCCCTTCAGACCCAGGCTTTCCACTGTGATGTCCTC---AAAGACCACATCACATCCAATATCATTTCAGGCTG--GTTTCTTCTACACCATTCCTGGGC----ACATCCAGATAT-CAAAGCG-GTGCTTATTCACTTACTCCTGTTAAAGTTAATC---C---AACT-- i calJac1.Contig5139 C 0 I 33 s tarSyr1.scaffold_41848 2010 250 + 21754 TGGAATCACACACAATTCTCAAGAGGCCCCTCACCGTGCCCTAACCGGGGCTCCACCCTCCA-AACAGGTCCAACAGCCCAAAGGGGTGAGAACC----CCCTCCAGACAGGTGCTTTCCATTCAGACATCCTTCCCAGTGGCCGCATCACACCCTGCCTCATTTCAAGTTG--GTTTTTTCCACCCTGCTTCCGTGCATTTATGTCCAGACAT-AAGCGGG-G-ACTTTTTCACCCACTCCTGTTCAATTGAATC---T---AAC--- i tarSyr1.scaffold_41848 C 0 I 37 s cavPor3.scaffold_76 4407862 215 + 7991924 TAAAATTGCATGAGCTCCTCGGAGGA--CCCCAGTGTGGCTGGGACAGG--------CCCAACAGCAA-----------------------CAGTGCCCTCCTTAATGCGCTTTCTGCTCACT-----GTCCTC---CAC--CCCAGCCACCTGCAGCCTCATCTCTAGCTGCTGCTTCTGC-ACACATGTCCAGAGT----GGGTGCAGGTGT-GGGTGTG-GGGCT-CTTCTCCCTCTCCTGGGAAGTTTAAAC---CTGGAGCTTC i cavPor3.scaffold_76 C 0 I 1006 s canFam2.chr9 59454994 247 - 64418924 TGGAATTCTGCACAAGTGTCTGGAGG-CCCAGAATGTGCCCAGAACCTGGCTCCAG-GCTCACAGCAG-TCCAATGGCAAAGAGCTAAGAGAACTCCCTCCA-TCACACCTGGGGTGTCCACCAAGACACTCCTAACAGTAGCTGCA--ATAGGCTG-CTTGTTTTAAGCCC--ATTTCTTCTGCACTATTTCTGTAAATCTATGTCCAAACATGGCATGGGTGAGCTCTCTTCCTTACCCCTGTTAAATGTAATC------------- i canFam2.chr9 C 0 I 42 s felCat3.scaffold_206428 43539 179 + 132007 TGGAATTTTGCACGAGCGTCTGGAGGCCCCAGAACATACCCAGAACCCAGATCTAG-CCCCACAGCAG-TTGAATGGCAAAGAG-------------------------------------GCGACACGTTCCTAATAGTTGCTGCA--ATGGGCCATCTCATTTGAAGCCC--ATTTCTTCTGCCCTGTTGCTCTGTACATACGTTCAAAC---GTATGCG-GAg------------------------------------------- i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58060955 242 - 61308211 tggaatctcgcacaagtccccagaggcccctcagagtgcctcgaagcctgctccag--cacgcggccg-tcaaatggcagggaggcgatatcattccctcccttcagacacgggctttcctccaagacttccccaatggtccctaca--acacgcggcctcatttctagccg--a-ttcttccacaccgtttctgggcgtacatctccaaacatgGGGGGGG-AGG-----TCACTTACACCTGTTAAATTTAACC------------- i equCab2.chr11 I 1 C 0 s bosTau4.chr19 10878236 225 - 65312493 ------------------TCTCGGGACTT-------TGCACAAGTCCCGGCATCAG-TCCCACCACAG-CTGGGTGGCAAAGAGGACATGTAATTCCCCGCT-TTAGACATGGAGTTTCCACTGAGATG-TCCTAACCGTCGCTACAGCACAGGCTGCCTCGTTCCCAGTCT--GTTTCTTCTGCGTGGTTTCTGTGCG--TATGCCCAAACAGGTGAGGGT-GGGGGTTTCGACTTATTTCTGTTAAATTGAATCCAA---------- i bosTau4.chr19 I 7 I 96 e turTru1.scaffold_98008 8177 1218 + 223990 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=35791.000000 s hg19.chr17_gl000204_random 66937 60 + 81310 ttttttttttttttgagatggagtctcattctgttgcccaggtgggagtgcagtg----gcaca s panTro2.chr17 79498649 60 + 83384210 ttttttttttttttgagatggagtctcattctgttgcccaggcgggagtgcagtg----gcaca i panTro2.chr17 I 7 C 0 s ponAbe2.chr17_random 16083671 60 + 17838096 ttttttttttttttgagatggagtctcattctgttgcccaggctggagtgcagtg----gcaca i ponAbe2.chr17_random I 12 C 0 s rheMac2.chr16 75057636 60 + 78773432 ttttttatttttttgagatggagtctcattctgttgcccaggctggactgcagtg----gcaca i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 64844 60 - 95547 ttttttatttttttgagatggagtctcattctgttgcccaggctgaatctcggtg----gcaca i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 67467 40 + 225949 --------------------gtgtgtacatgtgtTgcccaggtgggagtgcagtg----gcatg i calJac1.Contig5139 I 33 C 0 s equCab2.chr11 58061197 40 - 61308211 ---------------CGACTGG---TCATCTT------CTGTTTGGATTCTGTCATCTGACACA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 43718 25 + 132007 -------------cggggcggg-----------------ggggggggcggtggcg--------- i felCat3.scaffold_206428 C 0 I 71 e tarSyr1.scaffold_41848 2260 37 + 21754 I e gorGor1.Supercontig_0191203 6213 0 + 8483 I e turTru1.scaffold_98008 8177 1218 + 223990 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59455241 42 - 64418924 I e bosTau4.chr19 10878461 96 - 65312493 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=283357.000000 s hg19.chr17_gl000204_random 66997 230 + 81310 atctcagctcactgcaagctccacctcccaggttcaagtgactctcctgcctcagcctcccaagtagctgggactacaggcacgtgccaccacgcccggcttatttttctatttttagtagagatgtggtttcaccatgctggccaggcgggtctcgaactcctgacctcaggtgatccgcccgcctcggcctcccaaagtgctggaattacaggtgtgagccaccacgc s calJac1.Contig5139 67507 229 + 225949 atcttggcttactgcaacctctgcctcctgggttcaagcaattctcccgcctcagcctcccaagtagctgggacaacaagcacgtaccaccactcctggcccattttcctatttttagtagagacagggtttcaccatgctggccaggctcatctcgaactcctgacctcaggtgatctgcccacctcagcctcccaaagtgctgggattacaggtgtgag-caccacac i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 64904 230 - 95547 atctcggctcactgcaacctccgcctcccagattcaagcgattcttctgcttcagcctcgcaagtagctgggactacaggcacgtaccaccacgcctggcttatttttctatttttagtagagatggggtttcaccatgcaggccaggctggtctcgaactcctgacctcagatgatctgcctgcctcggcctcccaaagtgctggtattacaggtgtgagccaccatgc i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75057696 230 + 78773432 atctcggctcacggcaacctccgcctcccagattcaagcgatccttctgcttcagcctcgcaagtagctgggactacaggcacgtaccaccacgcctggcttatttttctatttatagtagagatggggtttcaccatgcaggccaggctggtctcgaactcctgacctcagatgatctgcctgcctcggcctcccaaagtgctggtattacaggtgtgagccaccatgc i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16083731 230 + 17838096 atctcagctcactgcaacctccacctcccaggttcaagtgattctcctgcctcagcctcccaagtagctgggactacaggcacgtgccaccacgcccagcttatttttctatttttagtagagatgtggtttcaccatgctggccaggctggtctcgaactcctgacctcaggtgatccacccgcctcagcctcccaaagtgctggaattacaggtgtgagccaccacgc i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79498709 230 + 83384210 atctcagctcactgcaacctccacctcctaggttcaagtgactctcctgcctcagcctcccaagtagctgggactacaggcacgtgccaccacacccggcttatttttctatttttagtagagatgttgtttcaccatgctggccaggtgggtctcgaactcctgacctcaggtgatccgcccgcctcggcctcccaaagtgctggaattacaggtgtgagccaccacgc i panTro2.chr17 C 0 C 0 e tarSyr1.scaffold_41848 2260 37 + 21754 I e gorGor1.Supercontig_0191203 6213 0 + 8483 I e turTru1.scaffold_98008 8177 1218 + 223990 I e felCat3.scaffold_206428 43743 71 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59455241 42 - 64418924 I e bosTau4.chr19 10878461 96 - 65312493 I e equCab2.chr11 58061237 0 - 61308211 C e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=496957.000000 s hg19.chr17_gl000204_random 67227 241 + 81310 ccagccTGTCCTTCACTTTGTATTATCCCAAAGTTGAAACCCAGCACCG-AAGGGCTTGATCCAAGCTGGGGGAAACCGTTGAGCAGGAATGGAGCCCTGAGCAACCCTGCAAAGCCAACGATACCCAGC----------GAGGGGGCCATCCTGAATCTACACATTTTCAAGGTGCAGATATTAAATAACCATAGTAAAAGCACGTCTCTACCA--ACAGGCAGAAGTGAGACTTCACTGAATCATGTTG----------GTC s panTro2.chr17 79498939 251 + 83384210 ccagccTGTCCTTCACTTTGTATTATCCCAAAGTTGAAACCCAGCACCG-AAGGGCTTGATCCAAGCTGGGGGAAACCGTTGAGCAGGAATGGAGCCCTGAGCAACCCTGCAAAGCCAACGATACCCAGC----------GAGGGGGCCATCCTGAATCTACACATTTTCAAGGTGCAGATATTAAATAACCATAGTAAAAGCACGTCTCTACCA--ACAGGCAGAAGTGAGACTTCACTGAATCACGTTGGGTGGCTTTTGTT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16083961 251 + 17838096 ccACCCTGTCCTTCACTTTGTATTATCCCAAAGTTGAAACCCAGCACCG-AAGGGCTTGATCCAAGCTGGGGGAAACCGTTGAGCAGGAATGGAGCCCTGAGCAACCCTGCAAAGCCAGTGATACCCAGC----------GAGGGGGCCATCCTGAATCTACACATTTTAAAGGTGCAGCTATTAAATAACCATAGTAAAAGCACGTCTCTACCA--ACAGGCAGAAGTGAGACTTAACTGAACCAAGTTGGATGGCTTTTGTT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75057926 250 + 78773432 ccagccTGTCCTTCACTTTGTATCATCCCAAAGTTGAAACCCAGTACTG-AAGGGTTTGATCCAAGCTGGGGGAAACCGTTGAGCAGGAATGGAGCCCTAAGCAACCCTACAAAGCCAATGATACCCAGC-----------AAGGGGCCATCAGGAATCTACACACTTTAAAGGTACAGCTCTTAAATAACCACAGTAAAAGCACGTCTCTACCA--ATAGGCAGAAGCGAGGCTTAACTGAATCATGTTGGATGGCTTTTGTC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 65134 251 - 95547 ccagccTGTCCTTCACTTTGTATCATCCCAAAGTTGAAACCCAGTACTGAAAGGGTTTGATCCAAGCTGGGGGAAACCGTTGAGCAGGAATGGAGCCCTGAGCAACCCTGCAAAGCCAATGATACCCAGC-----------AAGGGGCCATCAGGAATCTACACACTTTAAAGGTACAGCTCTTAAATAACCACAGTAAAAGCACGTCTCTACCA--ATAGGCAGAAGCGAGGCTTAACTGAATCATGTTGGATGGCTTTTGTC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 67736 250 + 225949 ctggccTGTCCTTCACTTTGTATCATCCCAAAGTTGAAACCCAGCACTG-AAGGGTTCAAAGTGAGCCGGGGGAAACTGTTGAGCAGGAATGAAGCCCTGAGCAACCCTGCAAAGCCAGTGATACCCAGC-----------GGGGAGTCATTGTGAATCTATACATTTTAAAGGTACAGCTATTAAATAACCATGGTAAAAGCACGTCTCTACCA--ATAGGCAGAAGTGAGGCTTCACTGAATAGCATTGGATGGCTTTTGTC i calJac1.Contig5139 C 0 C 0 s felCat3.scaffold_206428 43814 205 + 132007 TCAGCCTGTCCATCAGTTCACATCATCCCTGGGTTGAAAGCAGG-AAGG-AAGAGCCTGACCGAGGCTGGCGAGAAACGCTGGG---GGAGGGGGGT----------GAGCAGAGC------------------------CGGTGGGTGGCCATGGCTCTGTACTTTTTAAGGGTACAGCTATTA---AATCGTAGCAG----------CGAAC---GTAGAAAGAAA----GCTTCACTAAATCATTCCGGATGGCTTTTATC i felCat3.scaffold_206428 I 71 C 0 s equCab2.chr11 58061237 230 - 61308211 TCAGCCTGTCCTTTGGTCTATATCGTCCCCAGGTTGAAGGCACG-ATTG-AAGAGCTGGACCCAGGCCGGTGAGCAGC--TGCA------GCGGGCC----------CAGCAGAGCCCAGAGCCTCCACGGTGGGCTGAGGGGTGGGCTGCCTCGACTGTGTACATTTCAAGGGCACAGCTATTAAATAATCCTAGTAA----------CTAAT---ATAGTCAGAAAGAG-GCTTCACTAAACCACTTTGAATGGCTTTCATC i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10878557 208 - 65312493 ---------CCTTCAGTCTGCATCATCCCTGGGTTGAAAGCATG-ATAG-GAAAGCCTGGTCCAGACCCGTGAGTAACTGAATA------CAGTGCCCTC--CCACACGCCTGAGT------------------------GGGTAGCTTGCCGTAAGGATGTACATTTTCAGGGTACCGCTATTAAATAATCTAAGTAA----------CTAAC---ATAGTTAGAAAGAACACTTCACTGAATCACTTTGGATGGCTTTTATC i bosTau4.chr19 I 96 C 0 s canFam2.chr9 59455283 192 - 64418924 ------TGTCCCTCAGTTCGCATCACTCCAGGGTTCAAAGCACG-ACTG-AAGAGCTTGACCCAGACCAGCAAGAAACAGTGTG------CAGAGCC----------CAGCAGAGT------------------------GGGTGAGTGGTCATGGCTCTATACTTTTTAAGGGTATAGCTATTA---AATCATTGTAA----------CTAAC-------ACAGAGA----GCTTCACAGAGTCATTCTGGATGGCTTTTATC i canFam2.chr9 I 42 C 0 s tarSyr1.scaffold_41848 2297 249 + 21754 -CAGCTTGTCCTTCAGCTTGCATTATCCTGGAGTTGAAACTTCACACTG-AAGGGCTTGATCTGAGCCATGGGAAAC--TTCAGCAGGAATGGAGCCCAGAGCCATCCTGCAAAG-TAGTGACACCAAGT----------GAGTGGGCCATCAAGAATCTGTACATTTGGGAGATACAGCTATTAGGTAATCCTAATAAAAGcacatctctaccaatatagtcagaagctgtgcttcactaagtcACTTTAGATGGATTTTATC i tarSyr1.scaffold_41848 I 37 C 0 e gorGor1.Supercontig_0191203 6213 0 + 8483 I e turTru1.scaffold_98008 8177 1218 + 223990 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=178590.000000 s hg19.chr17_gl000204_random 67468 56 + 81310 GTTAGAGTTTGCAATACACTGAGTGCCTGGGTGGCAAATTCTGACCTGTACAAGT-G s panTro2.chr17 79499190 56 + 83384210 GTTAGAGTTTGCAATACACTGAGTGCCTGGATGGCAAATTCTGACCTGTACGCGT-G i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0472850 35 56 - 730 GTTAGAGTTTGCAATACACTGAGTGCCTGGATGGCAAATTCTGACCTGTACAAGT-G i gorGor1.Supercontig_0472850 n 0 C 0 s ponAbe2.chr17_random 16084212 56 + 17838096 GTTAGAGTCTGCAATACACTGAGTGCCTCGATGGCAAATTCTGACCTGTACAAGT-G i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75058176 56 + 78773432 ATTAGAGTCTGCAATACACTGAGTGCCTCGATGGAAAATTCTGACCTGTACTAGT-G i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 65385 56 - 95547 ATTAGAGTCTGCAATACACTGAGTGCCTCGATGGAAAATTCTGACCTGTACTAGT-G i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 67986 56 + 225949 ATTAGAGCTTGCAATACACCGAGTGCATCAATAGAAAATTCCAACCCGTACAAGT-G i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 2546 56 + 21754 ATTAAAGTTTGTAGTATATTGAGTTCCTGAATGGAAAATTCGGACCGGTACTGGT-G i tarSyr1.scaffold_41848 C 0 C 0 s canFam2.chr9 59455475 46 - 64418924 CTTCAAGTTTAGAAGATACTGAATTCCTTAATGGAAAATTCAGACC----------- i canFam2.chr9 C 0 I 189 s felCat3.scaffold_206428 44019 56 + 132007 CTTCAAGTTTAGAATATAACAAACTCCTTAATGGAAAATTCAGACCTTTGCTACTC- i felCat3.scaffold_206428 C 0 I 174 s equCab2.chr11 58061467 54 - 61308211 GTTAAAATTTGGAACGTACTGAGTGCCATAA-GGAAAATTCAGACCTTTACAGTT-- i equCab2.chr11 C 0 I 182 s bosTau4.chr19 10878765 55 - 65312493 ATTAAAGTTTGGAATCTACTGAGTGCCTTAATGGAAAATTCAGACCTTTACTATT-- i bosTau4.chr19 C 0 I 267 e turTru1.scaffold_98008 8177 1218 + 223990 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=91829.000000 s hg19.chr17_gl000204_random 67524 31 + 81310 TCCATGAACTTCTCAGTGATGACTGTCGGGT s panTro2.chr17 79499246 31 + 83384210 TCCATGAACTTCTCAGTGATGACTGTCGGGT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0472850 91 31 - 730 TCCACGAACTTCTCANTGATGACTGTCNGGT i gorGor1.Supercontig_0472850 C 0 C 0 s ponAbe2.chr17_random 16084268 31 + 17838096 TCCATGAACTTCTCAGTGATGACTGTCAGAT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75058232 31 + 78773432 TCCATGAACTTCTCAGTGATGACTGTCAGGT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 65441 31 - 95547 TCCATGAACTTCTCAGTGATGACTGTCAGGT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 68042 30 + 225949 TCCGTAAACTTCTCAGTGATGAC-GCTGGGT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 2602 31 + 21754 TCCACTGAGTTCTCAGTGACAGCTGTCGGGT i tarSyr1.scaffold_41848 C 0 I 21 s felCat3.scaffold_206428 44249 30 + 132007 TCCGAGAATTTCTCAGCGGCAGCTGT-GGGT i felCat3.scaffold_206428 I 174 I 28 s canFam2.chr9 59455710 30 - 64418924 TCCAAGAACTTCTCA-TGGCAGCCATGGGGC i canFam2.chr9 I 189 I 26 s equCab2.chr11 58061703 27 - 61308211 ----TGAACATCTCAGTGACCGCTGTGGGGT i equCab2.chr11 I 182 I 21 e turTru1.scaffold_98008 8177 1218 + 223990 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10878820 267 - 65312493 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=310505.000000 s hg19.chr17_gl000204_random 67555 121 + 81310 CAATGTCAGTTTCATCGGGGCATAACC---CAGTGTCCTTCAGAAACCAAGTGCGGGAGTCGTGCAT-------GTCACTAAATG---TTCATGCGTGCCTGCAGGACTCAGGGGCACGTGGCTGTGTGGGATG s panTro2.chr17 79499277 121 + 83384210 CAATGTCAGTTTCATCGGGGCATAACC---CAGTGTCCTTCAGAAACCAAGTGCGGGAGTCGTGCAT-------GTCACTAAATG---TTCATGTGTGCCTGCAGGACTCAGGGGCACGTGGCTATGTGGGATG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0472850 122 121 - 730 CAATGTCAGTTTCATCGGGGCATAACC---CAGTGTCCTTCAGAAACCAAGTGCGGGAGTCGTGCAT-------GTCACTAAATG---TTCGTGTGTGCCTGCAGGACTCAGGGGCACGTGGCTGTGTGGGATG i gorGor1.Supercontig_0472850 C 0 C 0 s ponAbe2.chr17_random 16084299 121 + 17838096 CAATGTCAGTTTCATCGGGGCATAACC---CAGTGTTCTTCAGAAACCAAGTGCAGGAGTCGTGCAT-------GTCACTAAATG---TTCATGTGTGCCTGCAGGACTCAGGGGCAGGTGGCTGTGTGGGATG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75058263 121 + 78773432 CAGTGTCAGTTTCATTGGGGCATAACC---CAGCGTCCTTCAGAAACCAAGTGTGGGAGTCGTGCAT-------GTCACTAAAAG---CTCGTGTGTGCCTGCAGGACTCAGGGGCACGTGGCTGTGTGGGATG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 65472 121 - 95547 CAGTGTCAGTTTCATTGGGGCATAACC---CAGCGTCCTTCAGAAACCAAGTGTGGGAGTCGTGCAC-------GTCACTAAAAG---CTCGTGTGTGCCTGCAGGACTCAGGGGCACGTGGCTGTGTGGGATG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 68072 109 + 225949 CAATGTCAGTTTCATCCAGGCATAACC---CAGTGTTCTTCAGAAACCAAGTTCAGGACTCATGCAT-------GCCACTAAATG---CTCACATGTGAATGCAGGGCTCAAGGGGACATGG------------ i calJac1.Contig5139 C 0 I 17 s tarSyr1.scaffold_41848 2654 108 + 21754 CGGTGTTGGTTGCATTAGGGCATGA------AATGC--------AACCAAATGCAGA--CCCCACAG-------GTCCCTAAAGG---CTCATGCGTACATGCAGGAGTCGGGGGTACGTGATCGTGTGTGAAG i tarSyr1.scaffold_41848 I 21 C 0 s turTru1.scaffold_98008 9395 124 + 223990 CGACATCAGCTTCACTGGGACGTGACCGATTGATGTCCTCTAGAAACCAAGGACAG--CCCTCCCCT-----CAGTCACCGAAAG---CTCACGTACGCAGGAAGGGCTGAGGGACACATGGTTGTGTGCGAAG i turTru1.scaffold_98008 I 1218 C 0 s felCat3.scaffold_206428 44307 115 + 132007 CAGGGTCAGTTTCACTGGGGCACGACC---CAGTGTCCTGTTGAGGCCAAGTGCAG--CCCACGTCC---CCCGGTCATGATGCG---CTCCCGTGCGTACAAAG--------CATGGGTGGCTGTGTGCCGTG i felCat3.scaffold_206428 I 28 C 0 s canFam2.chr9 59455766 113 - 64418924 CAGGGTCAGTTTCGCTGGCGCATGACT---CGGTGTCCCTTCTAGGCCAGCTGCAG--CCCGCACCC--TCCCAGTCACTAAATG---CTCTCACGCGCAC---G--------GACACGTGGATGTGTGCCCTG i canFam2.chr9 I 26 C 0 s equCab2.chr11 58061751 129 - 61308211 TGGTGCCACTTTCACGGGGGCATCACC---CAATG-CCGTTGGAAAACAAGGGCAGTCCCCACGCCCAAGCCCCGTCATTAAATAAATCTCAGGTATGCGTGAAGGGCTG-GTGACAGGGGGCTGTGTGCATTA i equCab2.chr11 I 21 C 0 e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10878820 267 - 65312493 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=86613.000000 s hg19.chr17_gl000204_random 67676 35 + 81310 CAGCCTCTAT-GGGAAGCTTGCTGCTAGCACTGCTA s panTro2.chr17 79499398 35 + 83384210 CAGCCTCTAC-GGGCAGCTTGCTGCTAGCACTGCTA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0472850 243 35 - 730 CAGCCTCNAC-AGGCAGCTTGCTGCTAGCACTGCTA i gorGor1.Supercontig_0472850 C 0 C 0 s ponAbe2.chr17_random 16084420 35 + 17838096 CAGCCTCTAT-GGGCAGCTTGCTGCTAGCACTGCTA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75058384 30 + 78773432 CAGCCCCTAT-GGGCAGCTTGCTGCTAGCAC----- i rheMac2.chr16 C 0 I 282 s papHam1.scaffold8336 65593 30 - 95547 CAGCCCCTAT-GGGCAGCTTGCTGCTAGCAC----- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 68198 30 + 225949 CAGCCCCTGT-GGGCAGCCTGCTGCTAGCAC----- i calJac1.Contig5139 I 17 I 4 s tarSyr1.scaffold_41848 2762 31 + 21754 CAGCCCCTGCGGGGTGGCTCGCTGCTGTCAC----- i tarSyr1.scaffold_41848 C 0 C 0 s turTru1.scaffold_98008 9519 30 + 223990 CAGCCCCCAT-GGGGTGCTGGCTGCTGTCTC----- i turTru1.scaffold_98008 C 0 C 0 s felCat3.scaffold_206428 44422 29 + 132007 CCGCTCCCGT-GG-GCGCCCGCTGCTGCCAC----- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59455879 29 - 64418924 CGGCTCCCGT-GG-GTACTTGCTGCTGCCAC----- i canFam2.chr9 C 0 C 0 s equCab2.chr11 58061880 30 - 61308211 CGTCCCCCAC-GGCGTGCGTGCTGCTGTCTC----- i equCab2.chr11 C 0 C 0 e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10878820 267 - 65312493 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=55949.000000 s hg19.chr17_gl000204_random 67711 62 + 81310 GCACGTGTTACTAGGTGTACACAGGCTAACCCAGTCACCACCCACAAAGGCAGCAGCTGCTG s rheMac2.chr16 75058696 62 + 78773432 GCACATGTTACTAGGTGTACGCAGGCTAACCCAGTCACCACCCACAAAGGCAGCAGCTGCTG i rheMac2.chr16 I 282 T 344 s ponAbe2.chr17_random 16084455 62 + 17838096 GCACATGTTACTAGGTGTACACAGGCTAACCCAGTCACCACCCACAAAGGCAGCAGCTGCTG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0472850 278 62 - 730 GCACATGTTACTAGGTGTACACAGGCTAACCCAGTCACCACCCACAAAGGCAGCAGCTGCTG i gorGor1.Supercontig_0472850 C 0 C 0 s panTro2.chr17 79499433 62 + 83384210 GCACATGTTACTAGGTGTACACAGGCTAACCCAGTCACCACCCACAAAGGCAGCAGCTGCTG i panTro2.chr17 C 0 C 0 s bosTau4.chr19 10879087 28 - 65312493 -----------------------------CCCAGTCACTG-----AAAGCTCACATAGGCAG i bosTau4.chr19 I 267 I 39 e calJac1.Contig5139 68228 4 + 225949 I e papHam1.scaffold8336 65623 0 - 95547 C e tarSyr1.scaffold_41848 2793 0 + 21754 C e turTru1.scaffold_98008 9549 0 + 223990 C e felCat3.scaffold_206428 44451 0 + 132007 C e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59455908 0 - 64418924 C e equCab2.chr11 58061910 0 - 61308211 C e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=629921.000000 s hg19.chr17_gl000204_random 67773 250 + 81310 GTGGCTGCTCTCA--CCCGTGTGAAGACACACACATCATACAAGATCGAGCGTGTGTTCATGACA--CCGCTTAAGAGACACCCGAATCCGGGGAGAAGGATA--------AGGGACAGGCTGCAGAGAAGA-----CCGCAAGCTAATCTCAGACCTCTCAGACCCTGAACTGTGCGTGTCTTTGAATTCACCCTTAATGTAAATTTCATT-CTCCTTAGTTCAAGATCTT-TCAA-AAGTAGGGCTTTTCTAAGGTGTCCTTTCATTC s papHam1.scaffold8336 65623 250 - 95547 GTGGCTACTCTCA--CCCATGTGAAGACACATACATCACACAAGACCGAGCGTGTGTTCATGACA--CCGCTTAAGAGACACCTGAATCTGTGGAGAACGATA--------CGAGACAGGCCGTAGAGAAGA-----CAGCAGGCTAATCTCAGACCTCTCAGACCCTGAACTGTGCGTGTCTTTGAATTCACCCTTAATGTAAATTTCATC-CTCCTTAGTTCAAGATCTT-TCCA-AAGTAGGGATTTTCTAAGGTATCCCTTCGTTC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75058414 239 + 78773432 GTGGCTACTCTCA--CCCATGTGAAGACACATACGTCATACAAGACCGAGCGTGTGTTCATGACA--CCGCTTAAGAGACACCTGAATCTGTGGAGAAGGATA--------CGAGACAGGCCGTAGAGAAGA-----CAGCAGGCTAATCTCAGACCTCTCAGACCCTGAACTGTGCGTGTCTTTGA-----------ATGTAAATTTCATC-CTCCTTAGTTCAAGATCTT-TCCA-AAGTAGGGATTTTCTAAGGTATCCTTTCGTTC i rheMac2.chr16 T 344 C 0 s ponAbe2.chr17_random 16084517 250 + 17838096 GTGGCCGCTGTCA--TCCGTGTGAAGACACACACATCATACAAGATCGAGCGTGTATTCATGACA--CCGCTTAAGAGACACCCGAATCCGGGAAGAAGGATA--------AGGGACAGGCCATAGAGAAGA-----CGGCAGGCTAATCTCAGACCTCTCAGACCCTGAACTGTGCATGTCTTTGAATTCACCCTTCATGTAAATTTCATT-CTCCTTAGTTCAAGATCTT-TCAA-AAGTAGGGATTTTCTAAGGTGTCTTTTCATTC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0472850 340 250 - 730 GTGGCTGCTCTCA--CCCGTGTGAAGACACACACATCATACAAGATCGAGCGTGTGTTCATGACA--CCGCTTAAGAGACACCCGAATCCGGGGAGAAGGATA--------AGGGACAGGCTGTAGGGAAGA-----CGGCAAGCTAATCTCAGACCTTTCAGACCCTGAACTGTGCGTGTCTTTGAATTCACCCTTAATGTAAATTTCATT-CTCCTTAGTTCAAGATCTT-TCAA-AAGTAGGGATTTTCTAAGGTGTCCTTTCATTC i gorGor1.Supercontig_0472850 C 0 C 0 s panTro2.chr17 79499495 241 + 83384210 GTGGCTGCTCTCA--CCCGTGTGAAGACACACACATCATACAAGATCGAGCGTGTGTTCATGACA--CCGCTTAAGAGACACCCGAATCCGGGGAGAAGGATA--------AGGGACAGGCTGTAGAGAAGA-----CAGCAAGCTAA---------TCTCAGACCCTGAACTGTGCGTGTCTTTGAATTCACCCTTAATGTAAATTTCATT-CTCCTTAGTTCAAGATCTT-TCGA-AAGTAGGGATTTTCTAAGGTGTCCTTTCATTC i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 68232 230 + 225949 -------CTCTCA--CCCGTGTGAAGGCACATACATCATACAAGATGGAGTATGTGTTCATGAC---CCACTTAAGAGACACCCAAATCCGGGGA-AAGGATG--------AGGGACAGGCAGTAGAGAAGC------------CTACTCTCAGACCTCTCAGACCCTGAATGGTGAGTGTCTTTGAATTCACCCTTAACATAAATTTC----CTTCTTAGTTCAAGATCTT-TCCA-AAGTAGGCATTTTCTAAGGTGTC-TTTCATGC i calJac1.Contig5139 I 4 C 0 s tarSyr1.scaffold_41848 2793 250 + 21754 GTGACTAATCTCT--CCCATGTGAAGACACATACGTCATACAAGACACAGCGTGTGTCAATGACA--CCACTTAGGAGCCACCCAAAAGGAGGGA-GAGGGTG--------AAGGGCAGGCGGTAGAGAAAA-----CTGCAGGTTGATCTCAGAACTCTTAGACCCTGAGCTGTTCGTGTCTTTGAATTCATGCTTCATTTAAATTTTATT-CTCCTTATTTTAAGTTCTT-TCCAGAAGAAGACATATTTTTAATTGTTCTTTCATTT i tarSyr1.scaffold_41848 C 0 C 0 s turTru1.scaffold_98008 9549 245 + 223990 GTGGCTTCTGGCA--CCCATGTGATGGTACCTACATCCTACAGGACAGGGTGTGTGGTAATGACA--TGGCTTGGGAGCCA-CCCGAAGGAGGCAGGGGAATA--------AATGACAGA--GGGGAGAAAA-----CTGTAGGTGGGTTCCAGGCCTCTTAGAACCTGAGCTGTTGCTGTCTTTGAATTCATCCTTATTTTGAATTTCATT---CTCTGTTTTAAGATCTTCCCCA-AAGAAGACA-TCTTTACGTTGTGGCTTCATTT i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10879154 175 - 65312493 ATGGCTTCTGGCA--AATATGTGATGGCACATACATCCTACAGGTCAGGGCATGTGTTAATGACG--TGGCTTGGGAGTCACCCCGAAGGAGGCAGAAGAATA--------AATAACAGA--GGAAAGAAAA-----CTTCAGGTGGATCGTAGGCCGCTTAGAACCT---------------------------------------------------------------------------GACA-TTTTTACACTGTGGCTTAATTT i bosTau4.chr19 I 39 C 0 s felCat3.scaffold_206428 44451 187 + 132007 GTGGCTTCCCACA--CCCACACAAGACTATCTTCATCCTACAAGACAGGACA---------------TGGCCCAGGAGCTGCCC---------------------------GAGGGCACA--G-GGAGGAGA-------------------------------AGACGGAACCATTCTTGCCTTTGAATCCATGCTTACTTTGAACTTCATT-CTCCCTGGTTGGAGATCTT-CCAC-AAGAAGACA--GCTTACACTGTGGCCTCACTG i felCat3.scaffold_206428 C 0 I 2 s canFam2.chr9 59455908 186 - 64418924 GTGGCTTCCCACA--CCCACACAACAGCACCTTCATCCTACAAGATGGGACA---------------CGGCCCCAAAGCCACCC---------------------------AAGGGGGTA--GAGGAGGAGA-------------------------------AAACTAAACCATTTTTGCCTTTGAATTCATTATTAC-TTGGATTTCATTGCCCCCCGGTTTAAGATCTT-CCAA-AAGACGATA----CTGTGTTGCTACTTCATTG i canFam2.chr9 C 0 I 2 s equCab2.chr11 58061910 259 - 61308211 CTGACTTCCTGCAGCCCCCCCCGACGGCGCACTCATCCTACAAGGCGGGGCGTGTGTTAACTAACGTCGGCTTGGGAGCCACCCCGAGGGAGGCTGAGGAACGACCGGAAGACGGGGGGG--GGGGGGGAGAGAGAGCTACAGGCTGAT--CAGGCCCCTGAGAGCCTGAGGGGTTCCTGTCTTTGGATTCATCCTTATCTTGAATTTCATC-----CTGTTTTAAGATCTTGCCAA-AAGAAGACACTTTTTAAGTTGTCG-TTCATTC i equCab2.chr11 C 0 I 2325 e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=123381.000000 s hg19.chr17_gl000204_random 68023 76 + 81310 TCATTC-TCCTCCTGGAGACTCTCTGTG-GGTTTCT-----CTTC--------AGCCATGCACATGTTACTAGGTATACACAGGCTAACCC s papHam1.scaffold8336 65873 75 - 95547 TCATTC-TCCTCCTGGAGACTCTCTGT--GGCTTCT-----CTTC--------AGCCGTGCACATGTTACTAGGTGTACACAGGCTAACCC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75058653 75 + 78773432 TCATTC-TCCTCCTGGAGACTCTCTGT--GGCTTCT-----CTTC--------AGCCGTGCACATGTTACTAGGTGTACGCAGGCTAACCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16084767 76 + 17838096 TCATTC-TCCTCCTGGAGACTCTCTGTG-GGTTTCT-----CTTC--------AGCCATGCACATGTTACTAGGTATACACAGGCTAACCC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0472850 590 76 - 730 TCATTC-TCCTCCTGGAGACTCTCTGTG-GGTTTCT-----CTTC--------AGCCATGCACATGTTACTAGGTATACACAGGCTAACCC i gorGor1.Supercontig_0472850 C 0 C 0 s panTro2.chr17 79499736 76 + 83384210 TCATTC-TCCTCCTGGAGACTCTCTGTG-GGTTTCT-----CTTC--------AGCCATGCACATGTTACTAGGTATACACAGGCTAACCC i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 68462 72 + 225949 TCA----TCCTCCTGGAGACTCTGTGCG-GGCTTCT-----CTTC--------AGCCATACACATGTTTCTAGGTG-ACACAGGCTAACCC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 3043 79 + 21754 GCATACTTCCTTCCAGAGACTCTGAGAC-ATTTTCTACAGGCTTC--------AG---TGTGCACACTCCCATACGTACACAACCTAACCC i tarSyr1.scaffold_41848 C 0 M 1004 s turTru1.scaffold_98008 9794 82 + 223990 -CATACTTCCTCCCAGAGAC-CTCGGAG-CACTGCG-----TTATCTATGGGCTCCCATACACACAGTCCTGTACGAATATA-CCTGATCA i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10879329 82 - 65312493 CCATGCTTCCTCCCAGAGAC-CTCAGGG-CACCGTG-----TTATCTCCGTG-TCCCGTACACATGGTCCTGTACAAACACG-CCTGATCG i bosTau4.chr19 C 0 C 0 s felCat3.scaffold_206428 44640 54 + 132007 --GCACTTCATCC----------------CACTGCA-----CTGT--------TCCCAGGC------TCCTCTGCGAACACGACCCCATCA i felCat3.scaffold_206428 I 2 C 0 s canFam2.chr9 59456096 69 - 64418924 --GCACTTCCTCCCAGAGAC-CCCTGAGGCACGGTC-----TTGT--------TCCCAGGC------TCCTGTGCAAACACGACCTAATCA i canFam2.chr9 I 2 C 0 e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=201640.000000 s hg19.chr17_gl000204_random 68099 83 + 81310 AGTCACCACCCACA--AAGGCAGCAGCTGCTGGCCACCACCGCCAGCCAGACTCACATCTTGGCACACCTTCAGACCGCCTGCCC s papHam1.scaffold8336 65948 83 - 95547 AGTCACCACCCACA--AAGGCAGCAGCTGCTGGTCACCACCGCCAGCCAGACTCACGTCTTGGCACAGCTTCAGACCGCCTGCCC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75058728 83 + 78773432 AGTCACCACCCACA--AAGGCAGCAGCTGCTGGTCACCACCGCCAGCCAGACTCACGTCTTGGCACAGCTTCAGACCGCCTGCCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16084843 83 + 17838096 AGTCACCACCCACA--AAGGCAGCAGCTGCTGGTCACCACCGCCAGCCAGACTCATGTCTTGGCACACCTTCAGACCGCCTGCCC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0472850 666 59 - 730 AGTCACCACCCACA--AAGGCAGCAGCTGCTGGTCACCACCGCCAGCCAGACTCACATCTT------------------------ i gorGor1.Supercontig_0472850 C 0 n 0 s panTro2.chr17 79499812 83 + 83384210 AGTCACCACCCACA--AAGGCAGCAGCTGCTGGTCACCACCGCCAGCCAGACTCACATCTTGGCACACCTTCAGACCGCCTGCCC i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 68534 83 + 225949 AGCCACCACCCACA--AAGGCAGCAGCTGCTGGTCACCACTGCCAGCCAGACTCACATCTTGGCACACCTCTGGACTACCTGCCC i calJac1.Contig5139 C 0 C 0 s turTru1.scaffold_98008 9876 69 + 223990 TGTCCCCAACAACA--AAGGCAG----TGCCAGTCACCACCACCAGCCGGACTCACAGCTC--CAAGG-------CCCTCTGTC- i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10879411 69 - 65312493 CGTCCCCAACAACA--AAGGCGA----TGCCGGTCACCACCACCAGCCAGATTCCCAGTTC--CGAGG-------CCTTCTGCC- i bosTau4.chr19 C 0 C 0 s felCat3.scaffold_206428 44694 73 + 132007 CGTCACCAGC------AAGGTGGCAGCCGCTGGGCACCCTCGCCAGCCAGGCTCTCGGCTC--CGCAGCCT----CCGTCTGCCT i felCat3.scaffold_206428 C 0 I 1753 s canFam2.chr9 59456165 74 - 64418924 TGTCACCACCAATAAGAAGGTAGCAGCCACCGG----CCTTGCCAGTCAGACTCACAGCTT--GGCGGGC-----CTGTCTGCCT i canFam2.chr9 C 0 I 4 e tarSyr1.scaffold_41848 3122 1004 + 21754 M e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=121228.000000 s hg19.chr17_gl000204_random 68182 105 + 81310 GTGGAGCCTGATGGGGTGGGGGGTGGCAGGAC-CGAGCCCCCTCCTTCCAGTTCCAACCTGCTCTTGGAGAAG-CATCTGTCACGGGGAGTGGCAGCCCCGTACCCT s panTro2.chr17 79499895 105 + 83384210 GTGGAGCCTGATGGGGTGGGGGGTGGCAGGAC-CGAGCCCCCTCCTTCCAGTTCCAACCTGCTCTTGGAGAAG-CATCTGTCACGGGGAGTGGCAGCCCTGTACCCT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16084926 105 + 17838096 GTGGAGCCTGATTGGGTAGGGGGTGGCAGGAC-CGAGCCCCCTCCTTCCAGTTCCAACCTGCTCTTGGAGAAG-CATCTGTCACGGGGAGTGGCAGCCCTGTACCCT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75058811 104 + 78773432 GTGGAGCCTGAT-GGGTGGGGGGTGGCGGGAC-TGAGCCCCCTCCTTCCAGTTCCAACCTGCTGTTGGAGAAG-CATCTGTCATGGGGAGTGGTAGCACTGCACCCT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 66031 104 - 95547 GTGGAGCCTGAT-GAGTGGGGGGTGGCGGGAC-TGAGCCCCCTCCTTCCAGTTCCAACCTGCTGTTGGAGAAG-CATCTGTCATGGGGAGTGGTAGCACTGCACCCT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 68617 104 + 225949 ATGGAGCCTGATGGGGTGGGGGGTGGCAGTAC-TGAG-CCCCTCCTTCCAGTTCCAACCTGCTCTTGGAGAAA-CGTCTGTCATGTGGAGTAGCAGCCCTGCACCCT i calJac1.Contig5139 C 0 C 0 s turTru1.scaffold_98008 9945 61 + 223990 --------TGAC---CAAGGCAATAGCAGAACAGGAGATGCCTCCCTCCAGCTCCAGCTGACTC-TGGAGAAG---------------------------------- i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10879480 61 - 65312493 --------TGAC---CAGAGCAACAGCAGGATGCAAGCCGCCTCCCTCCAGCTCCAGGGGACTC-CGGACAAG---------------------------------- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59456243 82 - 64418924 --------------------GGGTGGTGGGGCTGGAGCTGCCTCACCGTGG---CGGTGGACTC-TGGAGAAGACATCCATC-TGGGGAGTGCCTGCCTGGCATGTT i canFam2.chr9 I 4 I 44 e tarSyr1.scaffold_41848 3122 1004 + 21754 M e gorGor1.Supercontig_0472850 725 0 - 730 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=208145.000000 s hg19.chr17_gl000204_random 68287 184 + 81310 GCACCCTCCCCGGGCTCTCCCTGCCTCCCCGAGACTCAGCCAGAGGAGGTGGGG-CTGGGAGGTGGCCTCTCCCTCTCACAGGGCCAGACCACCACTGCTCTCCCTCCCCCAGgtctgagttggctcaggccaccgtctcagaggaccgcagactgtggatgtaaacattcattctcccgcagat s panTro2.chr17 79500000 185 + 83384210 GCACCCTCCCCGGGCTCTCCTTGCCTCCCCGAGACTCAGCCAGAGGAGGTGGGGNCTGGGAGGTGGCCTCTCCCTCTCACAGGGCCAGACCACCACTGCTCTCCCTCCCCCAGgtctgagttggctcangccaccgtctcagaggaccgcagactgtggatgtaaacattcattctcccgcagat i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16085031 184 + 17838096 GCACCCTCCCCAGGCTCTCCCTGCCTCCCCGAGACTCAGCCAGAGGAGATGGGG-CTGGGAGGTGGCCTCTCCCTCTCACAGGGCCAGACCACCACTGCTCTCCTTCCCCCAGgtctgagttggctcaggccgccttctcagaggaccacagactgtggatgtaaacattcattctcccgcagat i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75058915 181 + 78773432 GTGCCCTCCCCGGGCTTTCCCTGCCTCCCGGAGACTCAGCCAGAGGAGGTGGGG-CTGGGAGGTGGCCTCTGCCTCTCACAGGGCCAGACCACC---GCTCTCCTTCCCCCAGgtctgagttggctcaggccgctgtctcagaggaccacagactgtgggcgtaaccattcattctcccgcagat i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 66135 181 - 95547 GTGCCCTCCCTGGGCTTTCCCTGCCTCCTGGAGACTCAGCCAGAGGAGGTGGGG-CTGGGAGGTGGCCTCTCCCTCTCACAGGGCCAGACCACC---GCTCTCCTTCCCCCAGgtctgagttggctcaggccgccgtctcagaggaccacagactgtgggcgtaaccattcattctcccgcagat i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 68721 184 + 225949 GCAGCCTCCCTGGGCTCTTCCTGCCTCCCCAAGACTCAGCCAGAGGAGGTGGGG-CTGGGAGAGGGCCTCTCCCTCTCCCAGGACCAGACCACCACCGCTCCCCTTCCCCCAtgtctgagttggtgcaggccagcgttgtagaggacctcagactgtgggtgtaaacattcattctcccgcagat i calJac1.Contig5139 C 0 C 0 s bosTau4.chr19 10879541 82 - 65312493 GCACCCACCCTGGG------------------------------------AGGG-CTG-------------------------------CCCACATTGCGCTCCT-CCCT---GTGTTAGTGGCCCTGGTTCTCCAAAATAAAGCAGC-------------------------------GCAGAC i bosTau4.chr19 C 0 I 1 s turTru1.scaffold_98008 10006 104 + 223990 GCGCCCATTGTGGG-----------------------------------TAGGG-CTA-------------------------------CCCACATTGCATTCCTGCCCt---gtgttagtgtccccgggccaccaaaacaaagcagcacaggctggtagcctaaaca-----------acagac i turTru1.scaffold_98008 C 0 I 1 e tarSyr1.scaffold_41848 3122 1004 + 21754 M e gorGor1.Supercontig_0472850 725 0 - 730 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59456325 44 - 64418924 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=66270.000000 s hg19.chr17_gl000204_random 68471 36 + 81310 cttgaggccagacgtccaagatggagatgtcagc-ag s panTro2.chr17 79500185 36 + 83384210 cttgaggccagacgtccaagatggagatgtcagc-ag i panTro2.chr17 C 0 M 716 s ponAbe2.chr17_random 16085215 36 + 17838096 cttgaggccagacgtccaagatggagatgtcagc-ag i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75059096 36 + 78773432 cttgaggctggacgtccaagatggagatgtcagc-ag i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 66316 36 - 95547 cttgaggctggacgtccaagatggagatgtcagc-ag i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 68905 34 + 225949 cttgaggc-ggatgtccaggatggagatgtcagc-g- i calJac1.Contig5139 C 0 C 0 s turTru1.scaffold_98008 10111 36 + 223990 ctggaggccaggaggccaagatcagggtgttggc-ag i turTru1.scaffold_98008 I 1 C 0 s bosTau4.chr19 10879624 35 - 65312493 CTGCAGGCC-GCAGGCCAAGATCAAGGTGTTGAC-GG i bosTau4.chr19 I 1 C 0 s canFam2.chr9 59456369 37 - 64418924 ctccaggctggaggtctgggatgaaggtgccagtggg i canFam2.chr9 I 44 C 0 e tarSyr1.scaffold_41848 3122 1004 + 21754 M e gorGor1.Supercontig_0472850 725 0 - 730 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=233102.000000 s hg19.chr17_gl000204_random 68507 272 + 81310 gacggcttccttcggaggcctctctcct-----tgctctcagctggccgtcccctccctgtgtcctc-cacagccgtccc--------catgtggcctgcattctacattccctcttccactgaggacaccagtc--aggttggattggggcccatcc-caccacctc-atttcacctgaatcacctcttcaaagatcctctctccaaacacggtcacacgcagaggtcctgggagttaggacggcaccatatagattttgaggggCCCATGATATACCTGTTTCTTCTA s ponAbe2.chr17_random 16085251 245 + 17838096 gatggcttccttcagaggcgtctctcct-----tgctctcagctggccg-----tccctg------------------------------tgtggcctgcattctgcattccctcttccactgagg-caccagtcaaaaaatggattggggcccatcc-caccacctc-atttcacctgaatcacctcttcaaagatcctctctcc-aacacagtcacacgcagaggtcctgggagttaggacggcaccatatggattttgaggggCCCATGATATA-CTGTTCCTTCTA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75059132 265 + 78773432 gacagtttccctcggaggcctctctcct-----tgctctcagctgaccatctcctccctgtgtcctc-caccgccgtccc--------tgtgtggcctg-------cattccctcttccactgaagacaccagtc--aggttggattggggcccatcc-caccacctc-atttcacctgaatcacctcttcaaagatcctctctccaaacatggtcacacgcagaagtcctgggagttaggacggcaccatgtggactttgaggggcccatactatacctGTTCCTTCTA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 66352 265 - 95547 gacggtttccctcggaggcccctctcct-----tgctgtcagctgaccgtcccctccctgtgtcctc-caccaccgtccc--------tgtgtggcctg-------cattccctcttccactgaagataccagtc--aggttggattggggcccatcc-caccacctc-atttcacctgaatcacctcttcaaagatcctctctccaaacatggtcgcacgcagaagtcctgggagttaggacggcaccatgtggactttgaggggCCCATACTATACCTGTTCCTTCTA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 68939 263 + 225949 gacagcttccttcggaggcctctctcc------tgctggcaggtggctgtccccttgtcgtgtcctc-cacagccatccc--------tgtgtggcctg-------cattccctcttccactgtggacaccaggg--aggttggattagggcccctcc-caccacccc-atttcacctgactcacctcttcaaagatcctctcttcaaatgcggtcgcatgctgaggtccgggggctgaggacagcaccatatgga-tttGAAGCGTCCGTAACACACCTGCTCCTTCTA i calJac1.Contig5139 C 0 C 0 s turTru1.scaffold_98008 10147 261 + 223990 -ggtggtgc--------------ctcctgggcctgaggacaga----cgtcttctccctgtgtcctcacgtgatcgtccctctgtgtgtctgtgtccta--------acctcctcttctcataaggacaccagtc--atgttggattaggacccacccacatgacctcagcttaacctaattgccctctctaaaggccctgcccccgaatacaggcacatcctgaggtgttgggggttagggcttcaacatgtgaatctgggggacagttcagcccacaTGCCCTGTTGA i turTru1.scaffold_98008 C 0 I 64 s bosTau4.chr19 10879659 222 - 65312493 -GCTGCTTC-----------------------------------------cttctccctgtttcctcccgtgatcgttct--------tctgtgcccta--------a---ccttttccgataaggacaccagtc--atgttggattagggcccatccatatgaactcagtttaacctaactg-cctctctaaagatcccacctccaaatacaggcatgtcctgaggtgctaggggttaggacttcaacatgtgaatctgggggacagttcagcccacaCACCCTG---- i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59456406 231 - 64418924 -gctggttc-ttctgaggcctctctcctgggctggtagacgaatgaccatcttccccctaaacccacaggcgtccctcca--tgtatgtctgtgtcctg--------atgcccgct------------------------CTGGATTGGGGCTAACCCACATGGCCGC-GTGTAACCTAACTG-CCTCTCCCGAGGCCCCACCTCTGGATACAGGTGCATCCTGAAGTGCT-GGGGTTAGGGCTTCAAC--------------------TCAACGCACAGATTCCCTCCA i canFam2.chr9 C 0 I 8 e tarSyr1.scaffold_41848 3122 1004 + 21754 M e gorGor1.Supercontig_0472850 725 0 - 730 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e panTro2.chr17 79500221 716 + 83384210 M e monDom5.chr2 304571721 52790 - 541556283 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=56881.000000 s hg19.chr17_gl000204_random 68779 81 + 81310 CTAATGTCTTTATTCCAAC--ACAGCCACAGTGGTTCCTGTTCTGCAAACGTGGCAGAGCCTCCG---CTCCTCCCCTTCCCCAGC s ponAbe2.chr17_random 16085496 79 + 17838096 CTAATGTC--TGTTCCAAC--ACAGCCACAATGGTTCCTGTTCTGCAAACCCGGCAGAGCCTCCG---CTCCTCCCCTTCCCCAGC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75059397 81 + 78773432 CTAATGTCTTTATTCCAAC--ACAACCACAATGGTTCCTGTTCTGCAAACTCAGCAGAGCCTCTG---CTCCTCCCCCTCCCCAGT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 66617 81 - 95547 CTAATGTCTTTATTCCAAC--ACAGCCACAGTGGTTTCTGTTCTGCAAACTCAGCAGAGCCTCTG---CTCCTCCCCCTCCCCAGC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 69202 83 + 225949 TGCACATCTCTATTCCACC--ACAGCCACAGTGATTCCTGTTCTGCAAAAG-GGCGGAGACGCCAATCCTCCTTCCCCTCTCTAGC i calJac1.Contig5139 C 0 C 0 s bosTau4.chr19 10879881 79 - 65312493 TTGATGTCCCTATCTCTCCTAACAGTCAGAGT--TCCCAGTCCTG-AAATTCAGCCATACCTCT----CACTCCTCCTTCCCCTCC i bosTau4.chr19 C 0 I 1 s canFam2.chr9 59456645 60 - 64418924 -CAACCTGCTTCTCCCTAC--ACAGCCGGCTT--TCCCAG-----------------CACCTGT----CTCCTCCCCTCCCCCACG i canFam2.chr9 I 8 I 2 e tarSyr1.scaffold_41848 3122 1004 + 21754 M e gorGor1.Supercontig_0472850 725 0 - 730 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e panTro2.chr17 79500221 716 + 83384210 M e monDom5.chr2 304571721 52790 - 541556283 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=52387.000000 s hg19.chr17_gl000204_random 68860 81 + 81310 TGCCACTCCCCATCAGCCACAGGCCCCATCTCTACCACGCCCTGTCCTCAGTGCCCTCCTGGCCTCCCCACTGCCCTGCCT- s ponAbe2.chr17_random 16085575 81 + 17838096 TGCCACTCCCCATCAGCCACAGGTCCCATCTCTACCACGCCCTGTCCTCGGTGCCCTTCTGGCCTCCCCACTGCCCTGCCC- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75059478 81 + 78773432 GGCCCCTCCCCATCAGCCGCAGGCCTCATCTCTACCACGCCCTGTCCTCTGTGCCCTCTTGGCCTCCCTACTGCCCTGCCC- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 66698 81 - 95547 GGCCCCTCCCCAACAGCCACAGGCCTCGTCTCTACCACGCGCTGTCCTCTGTGCCCTCTTGGCCTCCCTACTGCCCTGCCC- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 69285 60 + 225949 TGCCATTCCCCGTCAGCCGCGGGCCCCGTATCTACCACGCCCTGTCCTCTGTGC----------------CTGCCC------ i calJac1.Contig5139 C 0 C 0 s canFam2.chr9 59456707 61 - 64418924 -ACCCCCACCCCACAGCCAC-----------------CCCTCTGGGCTTTGGGCACCAC---CCCACCCCCTGCCCTGGCCA i canFam2.chr9 I 2 C 0 e tarSyr1.scaffold_41848 3122 1004 + 21754 M e gorGor1.Supercontig_0472850 725 0 - 730 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e panTro2.chr17 79500221 716 + 83384210 M e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=63960.000000 s hg19.chr17_gl000204_random 68941 44 + 81310 CAGCCCAGACCCTCAGCTCCCTCCCCTACACTCAT------GTACACCTG s panTro2.chr17 79500937 44 + 83384210 CAGCCCAGACCTTCAGCTCCCTCCCCTACACTCAT------GCACGCGTG i panTro2.chr17 M 716 C 0 s ponAbe2.chr17_random 16085656 44 + 17838096 CAGCCCAGACCCTCAGCTCCCTCCCCTACACTCAT------GCATACCTG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75059559 44 + 78773432 CAGCCCAGACCCTCAGCTCCCTCCCCTACACCCAT------GAACACCTG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 66779 44 - 95547 CAGCCCAGACCCTCAGCTCCCTCCCCTACACCCAT------AAACACCTG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 69345 50 + 225949 CAGCCCAGACCCTCAGCTCCCTGCCCCACACCGATGTTCGAGCACACCTG i calJac1.Contig5139 C 0 C 0 s canFam2.chr9 59456768 44 - 64418924 CACTCTGGGCCCTCAGCTCCCTCGCCTTCATTCCT------GCACACGTG i canFam2.chr9 C 0 I 1595 e tarSyr1.scaffold_41848 3122 1004 + 21754 M e gorGor1.Supercontig_0472850 725 0 - 730 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=86100.000000 s hg19.chr17_gl000204_random 68985 86 + 81310 ACCGGGGAGCCAGAAACGTGCCCCAGCCCTGTTACTGCCCCAGCAGAATCCTTCCCAGCTGAAGAAGAGACTGCCTCCACTCAGGA s panTro2.chr17 79500981 86 + 83384210 ACCGGGGAGCCAGAAACATGCCCCAGCCCTGTTACTGCCCCAGCAGAATCCTTCCCGGCTGAAGAAGGGACTGCCTCCACTCAGGA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16085700 85 + 17838096 AGCAGGGAGCCAGAAACTTG-CCCGGCCCTGTTACTGCCCCAGCAGAATCCTTCCCGGCTGAAGAGGAGACTGCCTCCACTCAGGA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75059603 86 + 78773432 ACTGAGGAGCCAGAAACGTGCCCCGGCCCTATTACTGCCCCAGCAGAATCCCTCCCGGCTGAAGAGGAGGCCGCCTCCGCTCAGGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 66823 86 - 95547 ACTGAGGAGCCAGAAACGTGCCCCGGCCCTATTACTGCCCCAGCAGAATCCCTCCCGGCTGAAGAGGAGACCGCCTCCGCTCAGGA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 69395 67 + 225949 CCAGAGGAGCCA-------------------TTACCTCCCCCGCAGAATCCTTCCAGGCTGGAGAGGAAACCACCTCTGCTCAGGG i calJac1.Contig5139 C 0 C 0 e tarSyr1.scaffold_41848 3122 1004 + 21754 M e gorGor1.Supercontig_0472850 725 0 - 730 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59456812 1595 - 64418924 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=66904.000000 s hg19.chr17_gl000204_random 69071 42 + 81310 TCCTTCCCTGACCTCTgcaggtgtgctcatccccatctacag s calJac1.Contig5139 69462 41 + 225949 TCCTTCCCTGGCCTCTGCAGCGGCGCCCATCCCC-TCTACAG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 66909 42 - 95547 TCCCTCCCTGGCCTCTTcaggtgtactcatccccatctacgg i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75059689 42 + 78773432 TCCCtccctggcctcttcaggtgtactcatccctatctacag i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16085785 42 + 17838096 TCCTTCCCTGACTTCCgcaggtatgctcatccccatctacag i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0240964 1 42 - 2202 TCCTTCCCTGACCTCTgcaggtgtgctcatccccatctacag i gorGor1.Supercontig_0240964 n 0 C 0 s panTro2.chr17 79501067 42 + 83384210 TCCTtccttgacctctgcaggtgtgctcatccccatctacag i panTro2.chr17 C 0 C 0 e tarSyr1.scaffold_41848 3122 1004 + 21754 M e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59456812 1595 - 64418924 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=955524.000000 s hg19.chr17_gl000204_random 69113 524 + 81310 atgaagaaactgaggACTTGATAGACGCAGA-GCAAGGTATGGGG--TCAAGGCTGAACTTCTAGAAGCAA---CCAAAACTAC-CAAAAAACTGGTTCAAGAACACCACCATGCCCACTGCTGCCCACAGCCTGGGCGCTGAGTTTGAGATACCCCACAGGAgggaggtagaatactgg-ccccaaaatgtccacgtcctaacccctggaacctgtgactatcttaggttacacagcaaggaggaaggaaggttccagatgggattggggttgctcactgg-tgaccttgagatgggaggtgatcctggatgatccaggtggcccaacgtaaccacagggtccttaaaagtggaagaggagactgggcgcagtggctcagacctgtaatcccagcactttgggaggccaaggcggggtggattgcttgaggtcaggagtttgagaccagcctggccaacatggtgaaacgctgtctctactaaaaaataaataaataaaaaattagccaggcatggtggcccacacctgcaa s panTro2.chr17 79501109 524 + 83384210 atgaagaaactgaggACTTGATAGACGCAGA-GCAAGGTATGGGG--TCAAGGCTGAACTTCTAGAAGCAA---CCAAAACTAC-CAAAAAACTGGTTCAAGAACACCACCATGCCCACTGCTGCCCATAGCCTGGGCGCTAAGTTTGAGATACCCCACAGGAgggaggtagaatactag-ccccaaaatgtccacgtcctaacccctggaacctgtgactatgttaggttacacggcaaggaggaaggaaggttccagatgggattggggttgctcattgg-tgaccttgagatgggaggtgatcctggatgatccaggtggcccaacgtaaccacagggtccttaaaagtggaagaggagactgggcgcagtggctcagacctgtaatcccagcactttgggaggccaaggcggggtggattactggaggtcaggagtttgagaccagcctggccaacatggtgaaacgccgtctctactaaaaaataagttaattaaaaattagccaggcatggtggcccacacctgcaa i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0240964 43 524 - 2202 atgaagaaactgaggACTTGATAGACGCAGA-GCAAGGTATGGGG--TCAAGGCTGAACTTCTAGAAGCAA---CCAAAACTAC-CAAAAAACTGGTTCAAGAACACCACCATGCCCACTGCTGCCCACAGCCTGGGCGCTGAGTTTGAGATACCCCACAGGACGGaggtagaatactgg-ccccaaaatgtccacgtcctaacccctggaacctgtgactatgttaggttacacggcaaggaggaaggaaggttccagatgggactggggttgctcattgg-tgaccttgagatgggaggtgatcctggatgatccaggtggcccaacgtaaccacagggtcctnaaaagtggaagaggagactgggcgcagtggctcagacctgtaatcccagcactttgggaggccaaggcggggtggattacttgaggtcaggagtttgagaccagcctggccaacatggtgaaacgccgtctctactaaaaaataaataaataaaaaattagccaggcatggtggcccacacctgcaa i gorGor1.Supercontig_0240964 C 0 n 0 s ponAbe2.chr17_random 16085827 521 + 17838096 atgaagaaactgaagACTTGATAGATGCAGA-GCAGGGTGTGGAG--TCAAGGCTGAATTTCTAGAAGCAA---CCAAAACTAC-TGAAAAACTGGTTCAAGAACACCACCATGCCCACTGCTGCCTGCAGCCTGGGTGCTGAGTTTGAGATACCCCACCGGAgggaggtagaacactgg-ccccaaaatgcccacgtcctaagccctggaacctgtgactatgttagcttacatggcaaggaggaaggaaggttccagatgggattgggattgctcattgg-tgaccttgagatgggaggtgatcctggatgatccaggtggcccaatgtaaccacagggtccttaaaagtggaagaggagactgggcgcagtggctgacgcctgtaatcccaacactttgggaggccaaggcggggtggattacttgaggtcagcagtttgagacaagcctgaccaacatggtg-aatgctgtctctactaaaaactaaa--aataaaaaattagccaggcatggtggcacacacctgcaa i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75059731 491 + 78773432 atgaagaaactgaggGCTTGATAGACGCAGA-GCAGGGTGTGGGG--ACAAGGCTGAACTTCTAGAAGCAA---CCAAACCTAC-TGAAAAACTGGTTCAAGAACACCACCATGCTCACTGCTGCCCGGAGCCTGGGCGCTGAGTTTGAGATACCCCACAGGAgggaggtagaatactggcccccaaaacgcccacgtcctaacccctggaacctgtgactatgttaagttacatggcaaggaggaaggaaggttccagatgggaatggg-ttgctccttgg-tgatcttgagatgggaggtgatcctgaatgatccag-------------------------------gtggaaggggagaccgggcgcagtggctcacgcctgtaatcccagcactttgggaggccgaggc-gagtggatcacttgaggtcaagagtttgagaccagcctggccaacatggtgaaacgccatctctactaaaaaaaata-aaattaaaaaatagccaggcatggtggcgcatgcctgcaa i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 66951 491 - 95547 atgaagaaactgaggGCTTGATAGACGCAGA-GCAGGGTGTGGGG--ACAAGGCTGAACTTCTAGAAGCAA---CCAAACCTAC-CGAAAAACTGGTTCGAGAACACCGCCATGCTCACTGCTGCCCGGAGCCTGGGCGCTGAGTTTGAGATACCCCACAGGAgggaagtagaatactggcccccaaaacgcccacatcctaacccctggaacctgtgactatgttaagttacatggcaaggaggaaggaaggttccggatgggaatggg-ttgctcattgg-tgatcttgagatgggaggtgatcctggatgatccag-------------------------------gtggaagaggagaccgggcgcagtggctcacgcctgtaatcccagcactttgggaggccgaggc-gagtggatcagttgaggtcaagagtttgagaccagcctggccaacatggtgaaatgccatctctactaaaaaaaata-aaattaaaaaatagccaggcatggtggtgcatgcctgcaa i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 69503 514 + 225949 ATTAAGACACTGAGGACTTGATAGTCACAGA-GTGGGGTGTGGGG--TCAAGACTGGGCTTCTAGAAGCAA---CCAAAACTAC-CGAAAACCTGGTTCAAGAACACCGCCATGCCCACTGCTGCCCTGGGCCTGGGCGCTGAGTTGGAGATA-CCCACAGGAgggaggtggaatactggcccccaaaatgcccacttcctaacccctggcacctgtgactatgtgaggttacatggcaaggaggaaggagggctgcagatgggactgg--ctgctcactgg-tgacctcgagatgggggatgaccctggatgatccggggcacccagtatagccatagcgtccttcaaagtggaggaggagaccgggcaaggtggctcacgcctgtaatcccaacactttgggaggccgagg--gggt--ataacttgaggtcaggagttcaagactagcttgaccaacatggtgaaactctgtctctacaaaaaaaaaaa----aaaaaaattagttgggccaggtggcacatgcctatag i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 4153 504 + 21754 ATGAAGAAACTGAGAACTTGAGAGAACTGGAGGTGAGGAACAGAGGTTCAAGGTTCAACTTCTAGAAGCAATACTCAAAACCATGCTAAAAACTGGTTTGAGGACATCGCCATCCACATCACTGCACTGAGCATAGGTGCTGACTTTGGGACATACCACCtgaggtaggcaaaatactgg-cccc-aaacgcctttgtgctaacccc-gaaacctgaggacatattaggttttatgtccagggggaatga--------------attaaggttgctcatcagctgaccttgagatgagagatgattctggattatccag-caggtcaatgtaatcccagggtctttaaaagtggaggag--ggctggtggcaatgactcacacctgcaatcccagcactttgggcggcagaatc-aggaaaattgcctgaacccaggggtttgagaccagtctgggcaacttggcaagacctcatctctataataaatcaaa--------aaattagccagccatggtggcgcacacctgtag i tarSyr1.scaffold_41848 M 1004 C 0 e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59456812 1595 - 64418924 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=273211.000000 s hg19.chr17_gl000204_random 69637 219 + 81310 tcccagctacttaggaggctgaggcaggagaatcgcttgaacccaggaga-tggggattgcagtcagccaagactgcaccactgcactccagcctgagcaacaagagctaaactctgtctctaaaaaaaaaaaaaaaaaaa--------------gtgga-ggaggcaagagagtcggtgtcagaga--caatgtgatgatggaggtgggtcggagagagctgtgctgctggctccg s panTro2.chr17 79501633 233 + 83384210 tcccagctacttaggaggctgaggcaggagaatcgcttgaacccaggaga-tggggattgcagtcagccgagactgcaccactgcactccagcctgagcaacaagagctaaactctgtctctaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagtgga-ggaggcaggagagtcggtgtcagaga--caatgtgatgatggaggtgggtcggagagagctgtgctgctggctccg i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16086348 221 + 17838096 tcccagctacctgggaggctaaggcaggagaatcgcttgaacccgggagg-tgggggttgcagtcagccgagactgcaccactgcactccagccagggcaacaagagctaaactctgtctttaaaaaaaaaaaaaaagaaa------------aagtgga-ggaggcaggagagtctgtgtcagaga--caatgtgatgaaggaggcgggtctgagagagctgtgctgctggctccg i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75060222 218 + 78773432 tcccagctacttgggaggctgaggcaagagaatcgcttgaacccgggagagtgggggttgcagtcagccaagattgcaccactgcactccagcctgagcaacaagagcaaaacgctg----taaaaaaaaaaataaaaaag------------tggagga-ggaggcaggagagtcggtgtcagaga--caatgtgatgatggaggcgggtccgagagagctgtgctgctggctccg i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 67442 216 - 95547 tcccagctacttgggaggctgaggcaagagaatcgcttgaacccgggagagtgggggttgcagtcagccaagattgcaccactgcactccagcctgagcaacaagagcaaaacgctgt------aaaaaaaaataaaaaag------------tggagga-ggaggcaggagagtcggtgtcagaga--caatgtgatgatggaggcgggtccgagagagctgtgctcctggctcca i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 70017 195 + 225949 tcccagcttcttgggaggctgaggcaggagaatcacttgaacctgggagg-t-gggcttgcagtgagccgagatcgagtcaccgcactccagcctgagcaacaagagcaaaactccatctt--------aaaaaaaaaaag------------tggagag-ggaggcaggagagtcggcatcccag-----atgtgatgatggaggtgggtctgggagagctg-------------- i calJac1.Contig5139 C 0 I 9 s tarSyr1.scaffold_41848 4657 214 + 21754 ttccagctacttggaaggctgaggtggaaggattgcgtgagcccagcagg-tcgaggctgcgat-agccatgatcatgtaactgtactccagcttgggtgat-agagtgagactctgactc---aagaaagaagaaaaaag------------tagaggagggaggcaggagagtcagagtcagagaagagacacggtaactgaggcaggtcgagaggtgctgtgctactgg----- i tarSyr1.scaffold_41848 C 0 C 0 e gorGor1.Supercontig_0240964 567 0 - 2202 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59456812 1595 - 64418924 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14452986 2029 - 17734757 I a score=472232.000000 s hg19.chr17_gl000204_random 69856 317 + 81310 cagggtgagggcttccatcttgaagaaggaa-gagggagctgggagccaaggagcgcaagcagcctccagagactagaagaggcccggaaacaga--ccgcacctttgacactccagaagggaatgcagcc------tt-------tctgcattttagcccagagaggccagtgtcggacttctgacctccagaacggcaagataatgaacttctg-tgttttaagccactaggtttgttgcagtttgt----tacggtagtcctagaaaactTAATCTACCACTTCTACACCAAGAAGGGTGACGCTTCAACCAC-CCCAG-TACAGCTTCC----TAGAGAG s tarSyr1.scaffold_41848 4871 308 + 21754 ------------------cttgaaggtggag-aaaggtgccatgatccaaggagtgcaggtagcctctagagaccagaaaagatgaggaaacaga--ttctcccttggagacccgagcatggcatgcagctgactaact-------tttg-attttagcccagaga-gcctgtgtcagacttctgatctccaaaacatcaagatcatgaatttctgttgttttaaaccactaggtttgtggacatttgttccctatgccagtcctagaaaactTAGCACACCACTTCTGCACCATG-AGTGTGACACTTCAACCACACCCAC-TATAGATTTC----CCCAGAG i tarSyr1.scaffold_41848 C 0 I 6 s calJac1.Contig5139 70221 310 + 225949 aagggtgagggcttccgtcctgaagaaggaa-gagggagctgggagcgaaggagaacaagcagcctctggagaccagaaaaggcaca-aaacaga--ccgcaccttagacactccagaagggcacacagcc------tt-------tctgcattttagcc-----------acattggacttctgacctccagaacagcaagataatgaacttgtg-tgttttaagccactaggtttgtctccatttgt----tacagtggtcctagaaaactTAATCTACCACTTCTGCAGCAAGAAGGGTGACCCTTCAACCAC-CCccgctacaacctccccaacatagag i calJac1.Contig5139 I 9 C 0 s papHam1.scaffold8336 67658 317 - 95547 ctgggtgaggacttccatcttgaagaaggaa-gagggagctgggagccaaagagcacaaacagcctccagagactagaaaaggcacagaaacaga--ccgcagcttcgacgccccagaggggaatgcagcc------tt-------tctgcatttcaggccagggaggccagtgtcgaacttctgacctccagtacggcaagataatgaacttctg-tgttttaagccactaggtttgttgcagtttgt----tatggtagtcctagaaaactTAATCTACCACTTCTGCACCAAGAAGGGTGATGCTTCAACCAA-CCCAA-TACGGCTTCC----CAGAGAG i papHam1.scaffold8336 C 0 I 128 s rheMac2.chr16 75060440 317 + 78773432 ctgggtgaggccttccatcttgaagaaggaa-gagggagctgggagccaaagagcacaaacagcctccagagactagaaaaggcacagaaacaga--ccgcaccttcgacaccccagaagggaatgcagcc------tt-------tctgcgtttcagcccagggaggccagtgtcgaacttctgacctccagaacggcaagacaatgaacttctg-tgttttaagccactaggtttgttgcggtttgt----tacggtagtcctagaaaactTAATCTACCACTTCTGCACCAAGAAGGGTGACACTTCAACCAC-CCCAA-Aacagcttcc----cagagag i rheMac2.chr16 C 0 I 113 s ponAbe2.chr17_random 16086569 317 + 17838096 cagggtgagggcttccatcttgaagaaggaa-gagggagctgggagccaaggagtgcaagcagcctccagagactagaagaggcacggaaacaga--ccgcaccttcgacactccagaagggaatgcagcc------tg-------tctgcattatagcccagagaggccagtgtctgacttctgaactccagaacagcaagataatgaacttctg-tgttttaagccactaggtttgttgcagtttgt----tacggtagtcctagaaaacttaatccaCCACTTCTACACCAAGAAGGGTGACGCTTCAACCGC-CCCAA-TACAGCTTCC----CAGAGAG i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79501866 317 + 83384210 cagggtgagggcttccatcttgaagaaggaaagagggagctgggggccaaggagcgcaagcagcctccagagactagaagaggcccggaaacaga--ccgcacctttgacactccagaagggaatgcagcc------tt-------tctgcattttagcccagagaggccagtgtcggacttctgacctccagaacggcaagataatgaacgtctg-tgttttaagccactaggtttgttgcagtttgt----tacggt-gtcctagaaaactTAATCTACCACTTCTACACCAAGAAGGGTGACGCTTCAACCAC-CCCAG-TACAGCTTCC----TAGAGAG i panTro2.chr17 C 0 C 0 s loxAfr3.scaffold_49 14455015 238 - 17734757 --------------------tgaagatggag-aaagg--------gccaaggagtgtgggcagcctctggaagttggcaaaggcaagaaaacagattctgtcccctagagattccaggaaagaccatagcc------ctgccaacaccttgactttagcccag-----------------ttctcacccccagaaccataagattgtgc--------tgttttaagccactaggtttgtggtaatttgt----tatgacagaaatacaa-------------aCGTCCACAGAGAGAAGG-------------CAC-CCCAT-CTC---TTCC----------- i loxAfr3.scaffold_49 I 2029 C 0 e gorGor1.Supercontig_0240964 567 0 - 2202 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59456812 1595 - 64418924 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I a score=25125.000000 s hg19.chr17_gl000204_random 70173 29 + 81310 G----GGAGGCCTCATCTCC-TTCCCCGAGACCC s panTro2.chr17 79502183 29 + 83384210 G----GGAGGCCTCATCTCC-TTCCCCGAGACCC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16086886 33 + 17838096 ACAGCGGAGGCCTCATCTCC-TTCCCCGAGACCC i ponAbe2.chr17_random C 0 I 19 s rheMac2.chr16 75060870 29 + 78773432 g----ggaggcctcatctcc-ttccctgagaccT i rheMac2.chr16 I 113 C 0 s papHam1.scaffold8336 68103 14 - 95547 -------------------C-TTCCCTGAGACCT i papHam1.scaffold8336 I 128 C 0 s calJac1.Contig5139 70531 29 + 225949 ----gggatgcctcgtctcc-ttccctgagaccc i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 5185 30 + 21754 ----GGGATGCCTCATCTCCTTTCCCCATGGCCc i tarSyr1.scaffold_41848 I 6 C 0 s loxAfr3.scaffold_49 14455253 15 - 17734757 ----------CCCCACCAcc-ttacc-------- i loxAfr3.scaffold_49 C 0 C 0 e gorGor1.Supercontig_0240964 567 0 - 2202 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59456812 1595 - 64418924 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I a score=166905.000000 s hg19.chr17_gl000204_random 70202 173 + 81310 GTCagctcccggatcagggtctgccatggacacacctgcctggccaagtccgggccacatggctggccttagctgcaggggaggctggggaagggagGGAGGCTGGGGAAGGGAGGGAGGCAGCCCTCACCCTACTAAGTTCCATCATTCCAGAAAGTCCTCCATCACAGAGA s panTro2.chr17 79502212 173 + 83384210 GTCagctcccggatcagggtctgccatggacacacctgcctggccaagtccgggccacatggctggccttagctgcaggggaggctggggaagggagGGAGGCTGGGGAAGGGAGGGAGGCAGCCCTCACCCTACTAAGTTCCATCATTCCAGAAAGTCCTCCATCACAGAGA i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75060899 155 + 78773432 GTCagcttccggatcagggtctgccatggacacacccgcctggccaagtccaggctgcatggctggccctagctgcag------------------gggaggctggggaagggagggagacagccctcaccctgctaaggtccatcattccagaaagtcctccatcacagaca i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 68117 155 - 95547 GTCagctcccggatcagggtctgccatggacacacccgcctgaccaagtccaggctgcatggctggccctagctgcag------------------gggaggctggggaagggagggagacagccctcaccctgctaaggtccatcattccagaaagtcctccatcacagaca i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 70560 155 + 225949 atcagctcctggatcgaggtctgccatggacacacctgctgagccaagtccgggccacatggctggccctagctgcag------------------gggaggctgaggaagtgagggagccagccctcaccctacgaaggtccatcattccagaaagtcccgtatcatggaga i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 5215 111 + 21754 accggctcctgggtcaaaatctactgtggatatatctgcttggcagagcccaggtcacatgactgagcctagctgcaa------------------ggaaagctgggaacgaaagtG--------------------------------------------CCGTCTCAGAGA i tarSyr1.scaffold_41848 C 0 I 19 s loxAfr3.scaffold_49 14455268 140 - 17734757 attagctcctgggtcaaagtctgccatggacatatctgtttggcaaagcctggctcacatg--ttgacctagccacaa------------------aggaagcttgggaagcaagaa-------tctaacgtttttcagtgcc----tgcaagaagat--tctagcatggaga i loxAfr3.scaffold_49 C 0 C 0 e gorGor1.Supercontig_0240964 567 0 - 2202 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59456812 1595 - 64418924 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e ponAbe2.chr17_random 16086919 19 + 17838096 I a score=81834.000000 s hg19.chr17_gl000204_random 70375 97 + 81310 GGCCTCCAGTTGCCAGGCAGCCAGAAAGACAGGGAGGAGCTCCAGGGCAGGGGGTT-TGGTGGAATCTGG-------------------AGACTCAAGTCCAACAGCGACCACAGA-G s calJac1.Contig5139 70715 98 + 225949 ggcctccagttagcaggcagccagaaagaCGGGGAGGAGCCCCTCAGCAGGGGATT-TGGTGGAGTCTGA-------------------AGACTCAAGTCCAGTAGGAGTCACAGGCG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 68272 97 - 95547 ggcctccagttgccaggcagccagaaagaTGGGGAGGAGCTCCGGGGCAGGGGGTT-TGGTGGAATCTGG-------------------AGACTCAAGTCCAACAGTGACTGCAGA-G i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75061054 97 + 78773432 ggcctccagttgccaggcagccagaaagaTGGGGAGGAGCTCTGGGGCAGGGGGTT-TGGTGGAATCTGG-------------------AGACTCAAGTCCAACAGTGACCGCAGA-G i rheMac2.chr16 C 0 C 0 s panTro2.chr17 79502385 97 + 83384210 GGCCTCCAGTTGCCAGGCAGCCAGAAAGACAGGGAGGAGCTCCAGGGCAGGGGGTT-TGGTAGAATCTGG-------------------AGACTCAAGTCCAACAGCGACCACAGA-G i panTro2.chr17 C 0 C 0 s loxAfr3.scaffold_49 14455408 115 - 17734757 -tgccccaatcacagggaggCCA-CATGATGGCCAGGAGCTCCTTCAGGGAGGGTTGTGGTAGACACAGATGCAAATTTCTCACTCAATAGACCAAAGTCCAATGGCAGTGACAGG-T i loxAfr3.scaffold_49 C 0 C 0 e tarSyr1.scaffold_41848 5326 19 + 21754 I e gorGor1.Supercontig_0240964 567 0 - 2202 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59456812 1595 - 64418924 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e ponAbe2.chr17_random 16086919 19 + 17838096 I a score=52878.000000 s hg19.chr17_gl000204_random 70472 74 + 81310 -CCCTCTCAGAGA-------------CCAGCAAGTCCGAACTAAATCCAGAGCCGAGCGAAGGGAGCAGCTCA-------------------------------------------------------------CCCTGGTGCCTAGCA s panTro2.chr17 79502482 74 + 83384210 -CCCTCTCAGAGA-------------CCAGCAAGTCCGAACTAAATCCAGAGCCGAGCGAAGGGAGCAGCTCA-------------------------------------------------------------CCCTGGTGCCTAGCA i panTro2.chr17 C 0 C 0 s rheMac2.chr16 75061151 74 + 78773432 -CCCTCTCAGAGA-------------CCAGCAAGTCCAGACTAAATCCAGAGCCGAGCAAAGGGAGCAGCTCA-------------------------------------------------------------CCTCGGTGCCTGGCG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 68369 74 - 95547 -CCCTCTCAGAGA-------------CCAGTAAGTCCAAACTAAATCCAGAGCCGAGCAAAGGGAGCAGCTCA-------------------------------------------------------------CCTCGGTGCCTGGCG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 70813 135 + 225949 -CCCTCTCAGAGA-------------CCAGCAAGTCCGAACTCAATCCAGGGCCAGGCGAAGGGGGCAGCTCACCTCTAGTGCCTGGAGCCACCTCGGTCCTCTGTCCAGAGCTGGGTGAAGGGGGCAGCTCACCCCTGGTACCTGGCA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 5345 69 + 21754 -CCCTGTCATGG-------------------CAGTCTCCTCTAAATCCAGAGCTGAACTGAGGGACTGACTCA------------------------------------------------------------TACCCAGTCCCTTATA i tarSyr1.scaffold_41848 I 19 I 13 s loxAfr3.scaffold_49 14455523 75 - 17734757 GCTATTTGGGGGATGGCAGACCCACCCCACCCCGTCTCAA--AAATCAAGAGCTAGATCAAGAG------------------------------------------------------------------------CTGGGGCCTGGTA i loxAfr3.scaffold_49 C 0 C 0 e gorGor1.Supercontig_0240964 567 0 - 2202 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59456812 1595 - 64418924 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e ponAbe2.chr17_random 16086919 19 + 17838096 I a score=75806.000000 s hg19.chr17_gl000204_random 70546 64 + 81310 CCACCTCAGTCCTC---TGTCTCTGTTGAGG-----------ATTTTCTCGGGACCTGCT-TCTCTTGTGTCCAGGATG s tarSyr1.scaffold_41848 5427 60 + 21754 CTGTGCTGGTTCTC---TGTCTCTTTTTCAG-----------GTTTTTCCTTGACCTTCTCTGTTGAGTGTTCA----- i tarSyr1.scaffold_41848 I 13 C 0 s calJac1.Contig5139 70948 65 + 225949 CCACCTCGGTCCTC---TGTCTCCATTGAGG-----------ATTTTCTTGTCACCTGCTCTCCCTTGTGTTCATGACG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 68443 64 - 95547 CCACCTCAGTCCTC---TGTCTCCGTCAAGG-----------ATTTTCTCGGGACCTGCT-TCCCTTGTGTTCAGGATG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75061225 64 + 78773432 CCACCTCAGTCCTC---TGTCTCCGTCGAGG-----------ATTTTCTCGGGACCTGCT-TCCCTTGTGTTCAGGATG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16086938 64 + 17838096 CCACCTCAGTCCTC---TGTCTCCGTTGAGG-----------ATTTTCTCGGGACCTGCT-TCCCTTGAGTTCAGGATG i ponAbe2.chr17_random I 19 C 0 s panTro2.chr17 79502556 64 + 83384210 CCACCTCAGTCCTC---TGTCTCTGCTGAGG-----------ATTTTCTCGGGACCTGCT-TCTCTTGTGTCCAGGATG i panTro2.chr17 C 0 C 0 s loxAfr3.scaffold_49 14455598 77 - 17734757 CCATCTTGGCCCCTTCGTGTTGGTTCTTAGGTTCACACTCACGTTGTCAGCTGACCTACTTTGGTGTTTGCCTCGGA-- i loxAfr3.scaffold_49 C 0 C 0 e gorGor1.Supercontig_0240964 567 0 - 2202 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 41699 2195 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59456812 1595 - 64418924 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I a score=141164.000000 s hg19.chr17_gl000204_random 70610 84 + 81310 GCCAAGGTGCTTCGG--CACTTCTGGAAGTAAGGGCCCTGCCGACCCTCCACTCACAGGCAGCCCTTGGAGCCTGCAGACGCCTCT s panTro2.chr17 79502620 84 + 83384210 GCCAAGGTGCTTCGG--CACTTCTGGAAGTAAGGGCCCTGCCGACCCTCCACTCACAGGCAGCCCTCGGTGCCTGCAGACGTCTCT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16087002 84 + 17838096 GCCAAGGTGCTTTGG--CACTTCTGGAAGTAAGGGCCCTACCGACCCTCCACTCACAGGCAGTCCTTGATGCCTGCAGATGCCTCT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75061289 84 + 78773432 GCCAAGGGGCTACGG--CCCTTCTGGAAGTAAGGGCCCTGCAGACCCTCCACTCACAGGCAGCCCTTGGTGCCTGCAGACGCCTCT i rheMac2.chr16 C 0 M 343 s papHam1.scaffold8336 68507 84 - 95547 GCCAAGCGGCTACGG--CCCTTCTGGAAGTAAGGGCCCTGCAGACCCTCCACTCACAGGCAGCCCTTGGTGCCTGCAGACGCCTCT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 71013 84 + 225949 GCCAAGGTGCTTTGG--CACTTTTGGAAGTGAGAACCCTGCCAACCCTCCACACACAGACAGCCTTTGGTGCCTGCAGATACCTCC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 5487 70 + 21754 ---------CTT------ACTTTTGGAAGTAAGTGTCCTGTCGG-CCTCAACTCATGGGCAGCCCTTTGTTCCTGCCAACTTGTCA i tarSyr1.scaffold_41848 C 0 C 0 s otoGar1.scaffold_94362.1-287808 43894 83 + 287808 GCGAAGATGCCTCAG-TCTCTTTCGGGAGTCAAGGCCATGCCCACCCCTAACTCACAGGCAGACCCTGGCTCC--ATGACTTATCT i otoGar1.scaffold_94362.1-287808 I 2195 C 0 s loxAfr3.scaffold_49 14455675 83 - 17734757 ---AAGACGCTCCCACTCCTTTTTGGAAGTAAGGCACCTGCATCTCCTAAACTCACGGGTAGCCATTTGTTCTGGCCCACTTGTGT i loxAfr3.scaffold_49 C 0 C 0 e gorGor1.Supercontig_0240964 567 0 - 2202 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59456812 1595 - 64418924 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I a score=152409.000000 s hg19.chr17_gl000204_random 70694 168 + 81310 CCCATGTCAC--TGAGGTTCTCCCACCTCTGAACTCACCCTTAGAAGGCAcccccgccccccgccccccgccccATCCCTCAAGGAGAACCATCCGGAGCTCCCACTTTGGGCACACTCACT-GCCAGCCAAGCTCA--AGGAAGGGGT---CCCCACCACGAAGCGCCCCAAGGG s ponAbe2.chr17_random 16087086 158 + 17838096 CCCATGTCAC--TGTGATTCTCCCACCTCTGAACTCACCCTTAGAAGGTGCC----CCCCCCGCCCC-------ATCCCTCAAGGAGAACCATCCGGAGCTCCCACTTTGGGCACACTCACT-GCCAGCCAAGCTCA--AGGTTGGGGGG--GCCCACCACAAAGCACCCCAAGGG i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79502704 162 + 83384210 CCCATGTCAC--TGAGGTTCTCCCACCTCTGAACTCACCCTTAGAAGGCAGCCCCGCCCCCCGCCCC-------ATCCCTCGAGGAGAACCATCTGGAGCTCCCACTTTGGGCACACTCACT-GCCAGCCAAGCTCA--AGGAGGGGGGG--CCCCACCACGAAGCGCCCCAAGGG i panTro2.chr17 C 0 C 0 s papHam1.scaffold8336 68591 158 - 95547 CCCATGTCAC--TGTGGTTCTCCCACCTCTGGACTCACCCTGAGAAGGCG------CCCCACCCCCA-------ATCCCTCAAGGAGAACCATCCGGAGCTCCCACTTTGGGCACACTCACT-GCCAGCCAAGCCCA--AGGCTGGGGGGGTCCCCACCACGAAGCACCTCAAGGA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 71097 152 + 225949 CCCATGTCAC--TGGCAGTTCTCCACCTCTGAACTCACCCTTAGAAGGCG------CCCCCCTC----------ATCCCTCAAGGAGAACCGTCCGGAGCTCCCACTTTGGGCATACTCACT-GCTGGCCAAGCCCA--AGGTGGGGGG---CTCCACCACAAAGCAACCCAAGGG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 5557 158 + 21754 TCAATTTCACA-GGTAGTTCTCCCACCTCTGGACTCACCCT---AGGGTGCCCAAACCCACTTCCTC-------ATCCCTCCAGGAGAATCATCCAGGGCTCCCTTCCTAGGCTCACTCATT-GCCTATCAAGCTCT--GGACAGTGAG---TCACATCCCAGGCTGTCCTGTGG- i tarSyr1.scaffold_41848 C 0 I 2120 s otoGar1.scaffold_94362.1-287808 43977 125 + 287808 CCTGTTTCTGG-CGCAGCTCTCCTGCCTCTGGGG----------------------------------------GTGCCCTCAGGAGAACACCCTGGAGCCCTC---CTTGGTAGACTTGCT-GCCTGCCAAGCTCA--GGTCAGTGAG----CCCACCACACATGTCCCTGAGTG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s loxAfr3.scaffold_49 14455758 146 - 17734757 TCCACTTCCTGAGGGGGCACTTTCACCTCGGGATTCGCCTC---AGGCTGCCCAGGCCCACTTCCTT-------GTCTGTCAGGGAGAAAGATCTGGAGCTCCCTTTCTGGGCATGCTGGCTGGGCTGCCAAGTTCAGGAGGTCACGCT---CCCCACC----------------- i loxAfr3.scaffold_49 C 0 I 466 e gorGor1.Supercontig_0240964 567 0 - 2202 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59456812 1595 - 64418924 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e rheMac2.chr16 75061373 343 + 78773432 M a score=50497.000000 s hg19.chr17_gl000204_random 70862 57 + 81310 CAGGACTCCTGCCCTGTGTACTCAGAGACTGGGGAAGGCAGCATGTGTGTGTGttta s panTro2.chr17 79502866 57 + 83384210 CAGGACTCCTGCCCTGTGTACTCAGGGACTGGGGAAGGCAGCATGTGTGTGTGTTTA i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16087244 57 + 17838096 CAGGGCTCCTGCCCCGTGGACTCAGGGACTGGGGAAGGCAGCATGTGTGTGTGttta i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75061716 55 + 78773432 CAGGGCTACTGCCCCGTGGACGCAGGGACTGGGGCAGGCAGCATGTGTGTGT--TTA i rheMac2.chr16 M 343 C 0 s gorGor1.Supercontig_0326658 2 30 + 1079 --------------------------GACTGGGGAAGGCAGCATGTGTGTGTG-TTA i gorGor1.Supercontig_0326658 n 0 C 0 s papHam1.scaffold8336 68749 55 - 95547 CAGGGCTACTGCCCCGTGGACACAGGGACTGGGGCAGGCAGCATGTGTGTGt--tta i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 71249 30 + 225949 CAGGACTCCTGCTCCATGGACTCAGGGACT--------------------------- i calJac1.Contig5139 C 0 I 41 s otoGar1.scaffold_94362.1-287808 44102 43 + 287808 -GAGGCTCCCACATCATGTTCTCAGGGGAT-------ACAATGTGttttta------ i otoGar1.scaffold_94362.1-287808 C 0 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59456812 1595 - 64418924 I e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58062169 2325 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I e loxAfr3.scaffold_49 14455904 466 - 17734757 I a score=362661.000000 s hg19.chr17_gl000204_random 70919 170 + 81310 aagggcgtgattgaggtgtgactggcatatggcacacctcccatggttaaagggtacagtttatgcgcta--tgacatgcagatatgcccgtgaaaccatcaccaccatcaggatagggaacatatccgtcacccccaag-gtttcctcctgc--cctgatgtgccctcctcctc s equCab2.chr11 58064494 160 - 61308211 ---------atcaaggtgtcattgacgtacaacacactgcacgtgtttaaagggcgcagtttataagttg--tgacgtagggatatgcctgtgacaccattaccgcaatccagatagtgaaggtagccatcgcctcaaaa-ctttcctcctgaatctttcaatct---ctccccc i equCab2.chr11 I 2325 I 2 s otoGar1.scaffold_94362.1-287808 44145 148 + 287808 aagagcgttactgagacacaacagccacacaacacactgcccacgtttaaaggggacagtccacttcttg--tgacacagaggtttgcccctaaaaccatcacca-cagtggagcaggca----atgccccacccccaga-ga--cctcctgt-------tgtgg---------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s calJac1.Contig5139 71320 164 + 225949 gtgtgCATGattgctgtatgactggcatacagtgcaccacccatggttaaagcatacagtttatatgctg--tggcacgcaga-atgcctgtgaaagcatcaccaccatcaggatagggaacacacccatcacccccaaa-gcttcctcctgc--cctgatgtgc-----tctcc i calJac1.Contig5139 I 41 C 0 s papHam1.scaffold8336 68804 167 - 95547 aagggcgtgattgaggtgtgactggcatacagcgcaccgcccatggttaaagggtacagtttatacgctg--tgacacgcagacatgccggtgaaaccatcactaccatcaggatagggaacatatccgtcacgcccaaa-gtttcctcctgc--cctgatgtgc---cctcccc i papHam1.scaffold8336 C 0 C 0 s gorGor1.Supercontig_0326658 32 170 + 1079 AAGGGCGTGattgaggtgtgactggcatatggcgcaactcccatggttaaagggtacagtttatgcgcta--tgacatgcagatatgcccgtgaaaccatcaccaccatcaggatagggaacatatccgtcacccccaaa-gtttcctcctgc--cctgatgtgccctcctcctc i gorGor1.Supercontig_0326658 C 0 C 0 s rheMac2.chr16 75061771 167 + 78773432 AAGGGCGTGattgaggtgtgactggcatacggcgcaccacccatggttaaagggtacagtttatacgctg--tgacacgcagacatgccggtgaaaccatcactaccatcaggatagggaacatatccgtcatgcccaaa-gtttcctcctgc--cctgacgtgc---cctcccc i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16087301 169 + 17838096 aagggcatgattgaggtgtgactggcatatggcgcactgcccatggttaaagggtatagtttatgtaaaacgtgatatgcagatatgcccgtgaaaccttcaccaccatcaggatagggaacatatccgtcacccccaaa-gtttcctcctgc--cctgatgtgc---cctcccc i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79502923 170 + 83384210 AAGGGCGTGattgaggtgtgactggcatatggcgcacctcccatggttaaagggtacagtttatgcgcta--tgacatgcagatatgcccgtgaaaccatcaccaccatcaggatagggaacatatccatgacccccaaa-gtttcctcctgc--cctgatgagccctcctcctc i panTro2.chr17 C 0 C 0 s loxAfr3.scaffold_49 14456370 141 - 17734757 --------------------attggcatacagcaaaccacacatgtttaatgtgttcaatttataaattt--tgacgtatgtgtgcacccgtgaaaccatcaccaccatcacggtagtgaatgtatccatcacccccagatgtcttctcccgt--cccgttgtaa---------- i loxAfr3.scaffold_49 I 466 C 0 s canFam2.chr9 59458407 124 - 64418924 --------------------------ACACAGCAAAGCACACAGGATTAAA-GGTGGAGTTCGTAAGTTC--TGAGGTGTGGACGTGC--------------CCCCGGTCC--ACAGCGAACGCAGCTACCCCCAGAAAG-C--TCCTCCCGCACCCTGAGATCt---ccctcct i canFam2.chr9 I 1595 I 2 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10879960 1 - 65312493 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118780260 502 + 121843856 I a score=645490.000000 s hg19.chr17_gl000204_random 71089 296 + 81310 ctcctccctctccctgtattccccacccccgggcaaccactgccttgct-gtctgtc---cctgtaca-------tgagtttgccttttctggag--tttatataagtgaaatgacacagtacatacttctttgtt-gcctggctgccttccctcagcaccgttccccagagatgcggccatgcccttgcctgcaccaaaggttcactccttttcattgctgagtagtattccatcgcatggatgtgctacaatttgcttagctgctgttggtgtacat-------------------------------------ttatctccaggttaggggtatcgtaaatcaa s panTro2.chr17 79503093 296 + 83384210 ctcctccctctccctgtattccccacccccaggcaaccactgccttgct-gtctgtc---cctgtaca-------tgagtttgccttttctggag--tttatataagtgaaatgacacagtacatacttctctgtt-gcctggctgccttccctcagcaccgttccccagagatgcagccatgcccttgcctgcaccaaaggttcactccttttcattgctgagtagtattccatcgcgtggatgtgctacaatttgcttagctgctgttggtgtacat-------------------------------------ttatctccaggttaggggtatcgtaaatcaa i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16087470 295 + 17838096 ctcctccctctccctgtattccccacccccaggcaaccactgccttgct-gtctgtc---cctgtaca-------tgagtttgcc-tttctggag--tttacataagcgaaatgacacagtacatacttctttgct-gcctggctgccttccctcagcaccattccccagagatgcggccatgctttttcctgcaccaatggttcactccttttcattgctgagtagtagtccattgcatggatgtgctataatttgcttagctgttgttggtgtacat-------------------------------------ttatttctgggtgagggctattgtaaatcaa i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75061938 302 + 78773432 ctcctccctctccctgtatcccccacccccaggcaactactgccctgctcctctgtc---cctgtaca-------tgagtttgccttttcgggag--tttacataagtgaaatgacacagtacatgcttcttttct-gtctggctgccttccgttagcaccattccccagagatgcagccatgcccttgcctgcaccaatggctcactccttttcattgctgagtagtattccatcgcatggatgtgctacagtttgcttagctgttgttggtgtacat--------------------------------ttgacttatttccaggttagggctattgtaaatcaa i rheMac2.chr16 C 0 C 0 s gorGor1.Supercontig_0326658 202 296 + 1079 ctcctccctctccctatattccccacccccaggcaaccactgccttgct-gtctgtc---cctgtaca-------tgagtttgccttttctggag--tttatataagtgaaatgacacagtacatacttctttgtt-gcctggctgccttccctcagcaccgttccccanagatgcggccatgcccttgcctgcacaaaaggttcactccttttcattgctgagtagtattccatcgcatagatgtgctacaatttgcttagctgctgttggtgtacat-------------------------------------ttatctccaggttaggggtatcgtaaatcaa i gorGor1.Supercontig_0326658 C 0 C 0 s papHam1.scaffold8336 68971 302 - 95547 ctcctccctctccctgtatcccccacccccaggcaactactgccctgctcctctgtc---cctgtaca-------tgagtttgccttttcgggag--tttacataagtgaaatgacacagtacatacttcttttct-gtctggctgccttcccttagcaccattccccagagatgcagccacgcccttgcctgcaccaatggctcactccttttcattgctgagtagtattccatcgcatggatgtgctacagtttgcttagctgttgttcgtgtacat--------------------------------ttgagttatttccaggttagggctattgtaaatcaa i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 71484 280 + 225949 ctgcctccgtctcctatatcctcca-ccccaggcaaccactgctctgct-----gtc---actgcaca-------tgagtttgccttttctggag--tttacataagtgaaatgacacagtgcatgcttcttttct-gcctggctcccttctct---------------gagatgcag-cacgcccttgcctgcaccaaaggttcactccttttcattgctgagtagtattccatcacacagatgtgctacaatttgcctctctgttgttggtgcacat--------------------------------ttgagttatttccaagttagggctactgtaaatcaa i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 44293 245 + 287808 ------actctccctgtgtcccca--ccccagaaaaccacggatctgct-gtctgtc---actacacg--------------------tctggaa-ctttacattaatgga---------------------------------taacttcactgggtacc-tttcccagagatgca--cctgccatttcctgtgtcag-ggttggtcccccttccctgctgagtaatgtcccacttcatgagtgggccacagtgtgttcatccatcctctgtgcacgt--------------------------------ttgcattatttccagtttggggctgttacaaatcaa i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118780762 317 + 121843856 ccccccccaccccctg----ccctgcgcccagccaccca----tctgct-tcctgcctaatctgcataacacaggtaagcctaaattttctgtac--tttatatacataaaatgaca-ggcatctgctactcttct-g-----------tcactcaacacaat--cccaaaaaagggtctgtacagccgcgtgcatcaaagacgcgctccttttcactaaggggtaatatt-caccatgtggataggttgtcacttgcttacctg---tttgtgtatatttcagttattttatttatggaatcagtatgcattgagttgtttctggtttgggggtatttcagcgcaa i mm9.chr11 I 502 C 0 s equCab2.chr11 58064656 236 - 61308211 cc-------cacacacag--ccccacccccacaccgccattgatctgtt-ttctgtc---tctataaa-------tcactttgcattttctggca-ctttatataaatgagcttattcagcaagtactcttttttt-gtctggctttcctcgctcagcgtgattccccagagatgcacgcatgc----------atcggtcctttgtccctcttcatcgatgggggg-------gcgttccg-----------------------------gcgggtgg--------------------------------ct------ccaccaccattgg-----ctcccccatg i equCab2.chr11 I 2 C 0 s canFam2.chr9 59458533 247 - 64418924 cccttcctgcacccactgccccccgcctcgagccaaccactgatctg--------------------------------------ttctatggaa-ttttacataagtaacattattcagcacagaccctcttcttggtccggctccttgcacgtagcgtcattccccagagaggcgagcacgctgccgagcgtatccgagcctcactccttgttactgctgagcggcactcccgcgcatgg-----------------------------GCggacgt--------------------------------ctgagtgatctccagcgtggggctatcaccagtgca i canFam2.chr9 I 2 C 0 s loxAfr3.scaffold_49 14456511 296 - 17734757 -tcctccccctctctgcatctccca-tcccatgcaaccactgacctgtt-tttggtc---actataga-------ttagtttgcattttctggaatttttccataaatgaaatgatagggca----cttctttttt-gcctggatcctttcatttggcacaattcgctagagcttcgcccatgttgtagcat-tatcagaacttcattcctatctactgcggagtagtactccatagcatagacctaccacggtttgcttatccatcctcgatggacat--------------------------------ttgagttgtttccggcttgggactattacagataga i loxAfr3.scaffold_49 C 0 I 41 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10879960 1 - 65312493 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I a score=83628.000000 s hg19.chr17_gl000204_random 71385 63 + 81310 ggcactatcaacatttggatggacatgtgcttttatttttAAAAATAAGTGAGTTTGGggcca s panTro2.chr17 79503389 63 + 83384210 ggcactatcaacacttggatggacatgtgcttttatttttAAAAATAAGTGAGTTTGGggcca i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16087765 63 + 17838096 ggcactatcaacatttggatggacatgtgcttttatttttAAAAATAAATGAGTTTGGgacca i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75062240 63 + 78773432 ggcactatcaacatttggatggacgtgtgcttttatttttAAAAATAAATGAGTTTGGagcca i rheMac2.chr16 C 0 C 0 s gorGor1.Supercontig_0326658 498 63 + 1079 ggcactatcaacatttggatggacatgtgcttttatttttAAAAATAAGTGAGTTTGGggcca i gorGor1.Supercontig_0326658 C 0 C 0 s papHam1.scaffold8336 69273 63 - 95547 ggcactatcaacatttggatggacatgtgcttttatttttAAAAATAAATGAGTTTGGAgcca i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 71764 62 + 225949 agtactatgaacatttgaatgaacatgtgcttttatttttAAAAATAAATGAG-TTGGggcca i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 44538 8 + 287808 ggcactat------------------------------------------------------- i otoGar1.scaffold_94362.1-287808 C 0 I 35 s mm9.chr11 118781079 36 + 121843856 cctactgtgaacattcatgtggacaaacctctttat--------------------------- i mm9.chr11 C 0 I 122 s equCab2.chr11 58064892 37 - 61308211 gttgatgtatatttgagt---------tatttccag-tttgg----------------ggcca i equCab2.chr11 C 0 I 35 s canFam2.chr9 59458780 53 - 64418924 gctgctgtgaacgttcgtCTGGACACGTGCTTTCAT-TTTATAAGCA----AGGTGGG----- i canFam2.chr9 C 0 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10879960 1 - 65312493 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e loxAfr3.scaffold_49 14456807 41 - 17734757 I a score=449452.000000 s hg19.chr17_gl000204_random 71448 264 + 81310 ggcgtggtggctcacacctgtaatcccagcattttgggaggctgagtgggggcggatcacctgaggtcaggaattcgagaccagcctggccaacatggtgaaatcccatctctactaaaaatacaaaaatcacctgggcatggcactaggtgcccataatcccagctactcaggaggctgaggcaggagaattgcttga----acccgggaggtggaagttgcagtgagccgaaatcgagccattgcactccagcctgagcaacaaga s panTro2.chr17 79503452 264 + 83384210 ggcgtggtggctcacacctgtaatcccagcactttgggaggctgagtgggggcggatcacctgaggtcaggaattcgagaccagcctggccaacatggtgaaatcccatctctaccaaaaatacaaaaattacctgggcatggcgccaggtgcccataatcccagctactcaggaggctgaggcaggagaattgcttga----acccgggaggtggaagttgcagtgagccgagatcgagccattgcactgcagcctgggcaacaaga i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16087828 263 + 17838096 ggcgtggtggctcacacctgtaatcccagcactttgagaggccgag-gtgggtggatcacctgaggtcaggaattcgagaccaacctggccaacatggtgaaatcccatctctactaaaaatacaaaaattacccgggcatggtaccgggtgcccataatcccagctactcaggaggctgaggcaggagaattgcttga----acccgggaggtggaggttgcagtgagccgagatcgagccattgcactccagcctgggcaacaaga i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75062303 263 + 78773432 ggcgtggtggctcacgcctgtaatcccagcactttaggaggctgag-gggggcagatcacctgaagtcaggaattccagaccagcctggccaacatggtgaagtcccatctctactaaaaatacaaaaattacctgaacgtggtaccaggtgcccataatcccagctactcaggaggctgagacaggagaattgcttga----acctgggaggtggaggttgcagtgagctgagatcgagccattgcactccagcctgggacacaaga i rheMac2.chr16 C 0 C 0 s gorGor1.Supercontig_0326658 561 264 + 1079 ggcgtggtggctcacacctgtaatcccagcactttgggaggctgagtgggggcggatcacctgaggtcaggaattcgagaccagcctggccaacatggtgaaatcccatctctactaaaaatacaaaaattacctgggcatggcgctaggtgcccataattccagctactcaggaggctgaggcaggagaattgcttga----acccgggaggtggaagttgcagtgagccgaaatcgagccattgcactccagcctgggcaacaaga i gorGor1.Supercontig_0326658 C 0 C 0 s papHam1.scaffold8336 69336 263 - 95547 ggcgtggtggctcatgcctgtaatcccagcactttaggaggctgag-gggggcagataacctgaagtcaggaattccagaccagcctggccaacatggtgaagtcccatctctactaaaaatacaaaaattacctgaacgtggtaccaggtgcccataatcccagctattcaggaggctgagacaggagaattgcttga----acctaggaggcggaggttgcagtgagctgagatcgagccattgcactccagcctgggaaacaaga i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 71826 266 + 225949 ggcacagtggttaatatctgtaatcccagcacttt-ggaggctgag-gtgggaggatcacctgaggtcaggagttcaagaccaacctggccaacatggtgaaaccctgtctctactaaaactacaaaaattagccaggcgtggtggcaggtacctgtaatcccagctactcaggaggctgaggcaggagaataacttgaacccacccaggaggtggaggctgcagtgagccgagatagatccattgcactccagcttgggcaagaaga i calJac1.Contig5139 C 0 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e pteVam1.scaffold_11245 32741 1959 + 48268 I e otoGar1.scaffold_94362.1-287808 44546 35 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59458833 0 - 64418924 C e bosTau4.chr19 10879960 1 - 65312493 I e equCab2.chr11 58064929 35 - 61308211 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118781115 122 + 121843856 I e loxAfr3.scaffold_49 14456807 41 - 17734757 I a score=15949.000000 s hg19.chr17_gl000204_random 71712 25 + 81310 gcaaaactccgtctcaaaa------------------------ataaat s pteVam1.scaffold_11245 34700 1 + 48268 -------------------------------------------A----- i pteVam1.scaffold_11245 I 1959 C 0 s equCab2.chr11 58064964 20 - 61308211 acacgcttccatttTAAAAA----------------------------- i equCab2.chr11 I 35 C 0 s panTro2.chr17 79503716 25 + 83384210 gcaaaactccgtctcaaaa------------------------ataaat i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16088091 25 + 17838096 gcaaaactccgtctcaaaa------------------------ataaat i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75062566 21 + 78773432 gcaaaactccgtctcaa----------------------------aaat i rheMac2.chr16 C 0 C 0 s gorGor1.Supercontig_0326658 825 25 + 1079 gcaaaactccgtctcaaaa------------------------ataaat i gorGor1.Supercontig_0326658 C 0 C 0 s papHam1.scaffold8336 69599 21 - 95547 gcaaaactccgtctcaa----------------------------aaat i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 72092 49 + 225949 gcaaaactccatctcaaaaatacatacatacatagatgcatgcatacat i calJac1.Contig5139 C 0 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e otoGar1.scaffold_94362.1-287808 44546 35 + 287808 I e monDom5.chr2 304571721 52790 - 541556283 I e canFam2.chr9 59458833 0 - 64418924 C e bosTau4.chr19 10879960 1 - 65312493 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118781115 122 + 121843856 I e loxAfr3.scaffold_49 14456807 41 - 17734757 I a score=188007.000000 s hg19.chr17_gl000204_random 71737 77 + 81310 aaataaaTGAGTTGGGTAAAGGTG-GGCATGTG-----GCCCACTCTCACC-CGCCCACAC--ACGTG----CGCAGACGGGGGTGGCTG s otoGar1.scaffold_94362.1-287808 44581 74 + 287808 -agtaagtgagttgggtaaaGGCA-GG--TGTG-----GCCGGATGCTGCT-CACCCACAT--GCATG----TGCAGTCCGGAGCAGCTG i otoGar1.scaffold_94362.1-287808 I 35 C 0 s equCab2.chr11 58064984 77 - 61308211 --GTAAACGGGTTGGGTATAGACT-GGCATGTG-----GCTGGCTCTCACT-CACCCACACACAAGTG----CACAGACGGCTGCAGGTG i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_11245 34701 77 + 48268 -AATAAATCACTTGGGTAAAGCCAGGGCATGTG-----GCTTGCTCTCACC-CACCCACAC--GAGGG----CACAGGTGGCGCCAGCTG i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59458833 56 - 64418924 ----------------------CA-GGCAGGCG-----GGGGGCTTGCTCT-TACCCACACAAACGTG----CAAAGACGG-GATAGCTG i canFam2.chr9 C 0 C 0 s loxAfr3.scaffold_49 14456848 69 - 17734757 -AATGAACGAGCTGGGAAGAA--A-GGCTTGGGGCCACTCTCACTCCCACCAGCCCCCCAC--CGGTG--------------GGCAAT-G i loxAfr3.scaffold_49 I 41 C 0 s dasNov2.scaffold_85717 166 79 + 6675 AACTGAACGAGTTGGGTAGAGTCA-GGCGTGGG-----CCTCACCCTCAC--GTCCCACCC--AGGTGAGGCCACAGGCCT-GGCAGTCG i dasNov2.scaffold_85717 N 0 C 0 s panTro2.chr17 79503741 77 + 83384210 aaataaaTGAGTTGGGTAAAGGTG-GGCATGTG-----GCCCACTCTTACC-CGCCCACAC--ACGTG----CGCAGACTGGGGTGGCTG i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16088116 77 + 17838096 aaataaaTGAGTTGGGTAAAGGTG-GGCATGTG-----ACCCACTCTTACC-CACCCACAC--ACGTG----CGCAGACTGGGGCGGCTG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75062587 77 + 78773432 aaataaaTGAGTTGGATAAAGGTG-GGCATGTG-----GCCCACTCTTACC-CACCCACAC--ATGTG----CGTAGACTGGGGCAGCTG i rheMac2.chr16 C 0 C 0 s gorGor1.Supercontig_0326658 850 77 + 1079 aaataaaTGAGTTNGGTAAAAGTG-GGCATGTG-----GCCCACTCTTACC-CGCCCACAC--ACGTG----CGCAGACTAGGGTGGCTG i gorGor1.Supercontig_0326658 C 0 C 0 s papHam1.scaffold8336 69620 77 - 95547 aaataaaTGAATTGGATAAAGGTG-GGCATGTG-----GTCCACTCTTATC-TGCCCACAC--ACGTG----CATAGACTGGGGCAGCTG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 72141 71 + 225949 acatacaCGAGTCGGGTAAACGTG-A----GTG-----GCCCACTCTCACC-CGCCCACAC--ACAT------ATAGAGTGGGGCAGCCA i calJac1.Contig5139 C 0 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e monDom5.chr2 304571721 52790 - 541556283 I e bosTau4.chr19 10879960 1 - 65312493 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118781115 122 + 121843856 I a score=180029.000000 s hg19.chr17_gl000204_random 71814 47 + 81310 CGGCCGCTAGGGCATGGGAGGCAGCACCCCTTACCACCAGCGGAAGC s calJac1.Contig5139 72212 47 + 225949 CGGCCGCTAGGGCACGGGACGCAGCGCCCCTGACTGTCAGCAGAAGC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 69697 46 - 95547 CGGCCGCTAGGGCAT-GGAGACAGCGCCCCTTACCACCAGCAGAAAA i papHam1.scaffold8336 C 0 C 0 s gorGor1.Supercontig_0326658 927 47 + 1079 CGGCCGCTGGGGCATGGGAGGCAGCGCCCCTTACCACCAGCGGAAGC i gorGor1.Supercontig_0326658 C 0 C 0 s rheMac2.chr16 75062664 47 + 78773432 CTGCCGCTAGGGCACGGGAGACAGCGCCCCTTACCACCAGCAGAAAA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16088193 47 + 17838096 TGGCCGCTAGGGCATGGGAGGCGGCGCCCCTTACCACCAGCAGAAGA i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79503818 47 + 83384210 CAGCCGCTAGGGCATGGGAGGCAGCGCCCCTTACCACCAGCGGAAGC i panTro2.chr17 C 0 C 0 s dasNov2.scaffold_85717 245 47 + 6675 TGGTCTCCGGGGTGTTGGGGAAAGCATCCCATACTGCCGGCAGAACA i dasNov2.scaffold_85717 C 0 I 1 s loxAfr3.scaffold_49 14456917 47 - 17734757 TGGCCTCCAGGGCGGGGTAGAGAGCGTCCCTTATTGTCAGCAGAAAA i loxAfr3.scaffold_49 C 0 I 1 s canFam2.chr9 59458889 46 - 64418924 TGGCCTCT-GGGCATGGCAGAGAGCATCCATTACCACCAGCAGAAAA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 34778 45 + 48268 TGGCCTGTGGGCTGTGGGAGAGAGCCTCCATCA-CAGCAGCAG-AAA i pteVam1.scaffold_11245 C 0 C 0 s equCab2.chr11 58065061 47 - 61308211 TGGGCTCCGGGGTGTGGGAGAGAGCGTCCGTTACCAGCAGCAGAAAA i equCab2.chr11 C 0 C 0 s otoGar1.scaffold_94362.1-287808 44655 46 + 287808 TGGCTGCTAGGGTGT-GGGGACAGCATCCCTCACCACCCGCAGAAAA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s monDom5.chr2 304624511 33 - 541556283 CTGCTACAAGAGTACGGGAGA--------------ACAATCAGAAAG i monDom5.chr2 I 52790 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e bosTau4.chr19 10879960 1 - 65312493 I e cavPor3.scaffold_76 4408077 1006 + 7991924 I e mm9.chr11 118781115 122 + 121843856 I a score=392131.000000 s hg19.chr17_gl000204_random 71861 105 + 81310 CCCAACTTTGA-GAGCGAGGGGGTTT--GGGGGGACGAGGTGCTGTTTATG---------GTTTTG-CA--GTTGCTCCAGGGGAAAGGCGGGCTAATGAACAGTT-AGTGGGAAAT-AGTT s panTro2.chr17 79503865 105 + 83384210 CCCAACTTTGA-GAGCGAGGGGGCTT--GGGGGGACGAGGTGCTGTTTATG---------GTTTTG-CA--GTTGCTCCAGAGGAAAGGCGAGCTAATGAAGAGTT-GGCAGGAAAT-AGTT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16088240 105 + 17838096 CCCAACTTTGA-GAGCAAGGGGGTTT--AGGGGGACGAGGTGCTGTTTATG---------GTTTTG-CA--GTTGCTCCAGGGGAAAGGCGAGCTAATGAACAGTT-AGTGGGAAAT-AGTT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75062711 105 + 78773432 CCCAACTTTGG-GAGCGAGGGGGTTT--GGGGGGACGGGGTGCTGTTTATG---------GTTTCG-CA--GTTGCTCCAGGGGAAAGGCAAGCTAATGAACAGTT-AGTGGGAAAT-AGTT i rheMac2.chr16 C 0 C 0 s gorGor1.Supercontig_0326658 974 105 + 1079 CCCAACTTTGA-GAGCGAGGGGGTTT--GGGGGGACGAGGTGCTGTTTATG---------GTTTTG-CA--GTTGCTCCAGGGGAAAGGCGAGCTAATGAACAGTT-AGTGGGAAAT-AGTT i gorGor1.Supercontig_0326658 C 0 n 0 s papHam1.scaffold8336 69743 105 - 95547 CCCAACTTTGG-GAGCGAGGGGGTTT--GGGGGGACGAGGTGCTGTTTATG---------GTTTCG-CA--ATTGCTCTAGGGGAAAGGCAAGCTAATGAACAGTT-AGTGGGAAAT-AGTT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 72259 103 + 225949 CCCAGCTTTGG-GAGTGAGGGGTTTT---GGGGTACCAGGCGCTGTTTACA---------GTTT-G-CA--GTCACTGCAGGGGAAAGGCGAGCTAATGACCAGTT-AGTGGGAAAT-AGTT i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 44701 104 + 287808 CTTAGCCTTGG-GAGTGAGGTGTCTT--GGCGGGACGTGGCACTGGTTACA---------CCTTTG-TG--ACTGTTCCAG-GGAAAGGCAAGCAAGTGACCAGGT-GGTGGGAAGT-GGCT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118781237 85 + 121843856 CACAGCCTGGG-----------------AGGAGAGTGGGGAGCTC-CTAT-------------CTG-TG--GCTGCTCT-GGAGAAAGATGCGCTAATGAATAATT-GATGGGAAAT-TGCT i mm9.chr11 I 122 C 0 s cavPor3.scaffold_76 4409083 95 + 7991924 ------------GGGAGACGGGCTTTGGTGGGGAGTGAGAAGCTTGTTATA---------CTCCTG-AG--GTTGCTCCAGGAGAAAGGCATGTT-ATGAACAGTT-CGTGGAACAT-ACCT i cavPor3.scaffold_76 I 1006 C 0 s equCab2.chr11 58065108 97 - 61308211 CCCAACTCTGGGGAGCAGAGGGGTGG--TGAGGG---------TGCTTACA---------CCTTTT-CA--GTCGTTCCGGGGGAAGGGCAAGCTAATGAATCCTG-AGCGGGAAAT-AGTT i equCab2.chr11 C 0 C 0 s canFam2.chr9 59458935 108 - 64418924 CCCAACTTTGGGGAGCAGGGGAGCTC--GGGGGG---------GGGTTACAAACTGCCTGCATTCT-CATGGTTGTTGCAGGCAGAAAGCAAGCTAACGAACTGTT-AGTGGGAAAT-AGTT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 34823 98 + 48268 CCCAAATTTGGGGAGCAGGGTGTTTT--GGGAAC---------TGCTTACA---------CTCTCTGTA--GCTGTTCCAGGGGAAAGGCAAGCTGATGGACTGTC-AGTGGGAAAT-AGTT i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_85717 293 86 + 6675 CC--TCTTTGGGGAGCAAAG--------------------AGCTGTTCGCA---------TTTTTA-AG--CTTCTTCCAG-GGAAAGGCAAGGTGATGCCTTGTG-AGCAGGAAATCAGCT i dasNov2.scaffold_85717 I 1 C 0 s loxAfr3.scaffold_49 14456965 106 - 17734757 TCAAACTTTGGGGAGCAGGGGGACGT--TTGGGGGCAAGAAGCTGTTTACA---------TTTTTA-TG--GTTGTTCCAGTGGAGAGGAAAGCTGATGAGTCATT-AATGGGAACT-AGCT i loxAfr3.scaffold_49 I 1 C 0 s monDom5.chr2 304624544 102 - 541556283 CATAACTTGGAAGGGTGAAGGGGGTG--GGAGGAGTAA---GCTATTTGTC---------TACTTT-----GTTGTTCCAGAGGAAGGGCAAACTAATGAATTGTTCAACAGGAACC-AGTT i monDom5.chr2 C 0 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e bosTau4.chr19 10879960 1 - 65312493 I a score=175523.000000 s hg19.chr17_gl000204_random 71966 63 + 81310 TATTGAAGTGAACAGAA---CAAGAATACATTAAAATTATTAAGACTGTGGCCTGGGGCAGTAAGC s panTro2.chr17 79503970 63 + 83384210 TATTGAAGTGAACAGAA---CAAGAACACACTAAAATTATTAAGACTGTGGCCGGGGGCAGTAAGC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16088345 63 + 17838096 TATTGAAGGGAACAGAA---CAAGAACACATTAAAATTATTAAGATTGTGGCCCGGGGCGGTGAGC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75062816 63 + 78773432 TATTGAAGTGAACAGAA---CAAGAACACATTAAAATTATTAAGATTGTGGCCTGGGGCGATGAGC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 69848 63 - 95547 TATTGAAGTGAACAGAA---CAAGAACACATTTAAATTATTAAGATTGTGGCCTGGGGCGATGAGC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 72362 63 + 225949 TATTGAAGTGAACAGAA---CAAGAGCACATTAAAATTATTCAGATTGTGGCCCAGGGCGGTGAGC i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 44805 63 + 287808 CGCTGGAGTGAACAGAA---TGAGAACGCATGAAGATTACTCAGACGGCAGCCTGGGGTGGTGCAC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118781322 55 + 121843856 CATT-ATGTAAACAGAA---CAGGAACACGCTACAGTTGTGGAGACAGT-------GATGACAATC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4409178 31 + 7991924 CAAT------AGCATGA---CAGGAACAAG--------------------------AGTGACAATC i cavPor3.scaffold_76 C 0 C 0 s equCab2.chr11 58065205 62 - 61308211 CA-TGAAGTGAACGGAA---CCAGAGCACAGCCCAATTATTAAAATCGTCGCCTGGGGCAACATGC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59459043 63 - 64418924 CACTGAAGTGAACAGAA---CAAGAATGCCACAGAATTATTAAAATCATGGCCTGGAGGACCATGT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 34921 61 + 48268 CGTTGACATGGACAGAG-----AGAGCACAGTGAAACTGTTCAAGTCGTGGCGTGGGGCCCCACGT i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_85717 379 55 + 6675 CATTGATGCGAGCGG------AGCAGCACGTTACAATTGTCACAGT-----CCTTCTGCGGGATAC i dasNov2.scaffold_85717 C 0 I 2 s loxAfr3.scaffold_49 14457071 59 - 17734757 CACTGAAGTGAACAGAA---AAACAGCACATTAAAATTATTAAAACCGT-GCCTGCTGTGGCA--- i loxAfr3.scaffold_49 C 0 I 2 s monDom5.chr2 304624646 65 - 541556283 CATTGAACCAAATGGAATTTCAAAACCTCATTAAAATTATTAAAAGTAT-GCCTGAGGCAACAAGA i monDom5.chr2 C 0 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e gorGor1.Supercontig_0326658 1079 0 + 1079 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e bosTau4.chr19 10879960 1 - 65312493 I a score=80398.000000 s hg19.chr17_gl000204_random 72029 49 + 81310 GGCATCC-------T--GTT-T-----TCTCATAGTTTAC----------ATGACAGTGGGAGAACACAGG-AAG s panTro2.chr17 79504033 49 + 83384210 GGCATCC-------T--GTT-T-----TCTCATAGTTTAG----------ATGACAGTGGGAGAACACAGG-AAG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 39934 49 - 64270 GGCATCC-------T--GTT-T-----TCTCATAGTTTAG----------ATCAGAGTGGGAGAACACAGG-AAG i gorGor1.Supercontig_0007361 M 8539 C 0 s ponAbe2.chr17_random 16088408 49 + 17838096 GGCATCC-------T--GTT-T-----TCTCATAGTTTAG----------ATGACAGTGGGAGAGCACAGG-AAG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75062879 49 + 78773432 AGCATCC-------T--GTT-T-----TCTCATAGTTTAG----------ATGAGAGTGGGAGAGCACAGG-AGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 69911 49 - 95547 AGCATCC-------T--GTT-T-----TCTCATAGTTTAG----------ATGAGAGTGGGAGAGCACAGG-AGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 72425 47 + 225949 AGCATCC-------T--GTT-T-----TCTCATAGTTTAG----------ATGAGA--GGGAGAGTGCAGG-AGG i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 44868 40 + 287808 AGCTGAC-------T--GTG-T-------TCATGGTTTAG----------AGGCCAGGGGGCGAGCA-------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118781377 48 + 121843856 TACATCCGGGGCAAT--ATG-T---------GGCATCTGC----------ATGAGACCAGACAG----AGG-ATG i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4409209 43 + 7991924 T-------------T--ATG-T-----CTTCATAGTTCGG----------GTGAGAGTAAAAAAGCCCAGG-GAG i cavPor3.scaffold_76 C 0 C 0 s equCab2.chr11 58065267 51 - 61308211 GTTGTCC-------T--ATTGT-----TTCCACAGTTCAG----------ACTAGAGTGAGAGGCCACGGGCAGG i equCab2.chr11 C 0 C 0 s canFam2.chr9 59459106 33 - 64418924 GGCATTC-------T--ACAGC-----TTT--CAATTCAG--------------------------ATGAGCATG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 34982 50 + 48268 GGCCTCC-------T--CCTAG-----TCTCACAGCTCAG----------AGGAGGGTGAGAGACCGTGGA-AGG i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_85717 436 51 + 6675 GGCATCC-------CATTTT-T-----TTTCAGCGTTTGG----------ATGAAAACGAAAGAACGTGGA-AGA i dasNov2.scaffold_85717 I 2 C 0 s loxAfr3.scaffold_49 14457132 37 - 17734757 AGCATCC-------C--TTT-T-----CTTCATACTTTAG----------ATGAAAA------------AA-AAA i loxAfr3.scaffold_49 I 2 C 0 s monDom5.chr2 304624711 64 - 541556283 AACAGCT-------T--ATT-TCTTTCTTTCATAGTTTAAACTGCCTAAAATAAAAGGGGGAGGAGACAAA-AGG i monDom5.chr2 C 0 I 9630 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e bosTau4.chr19 10879960 1 - 65312493 I a score=378080.000000 s hg19.chr17_gl000204_random 72078 211 + 81310 TGG-GGGGAGGATGCTGG-GGGCAAGGAGATGCAGGGAGGCCTCTGCCAAGGGTCAGGTGGACCAGAAACTTCCCTGGA----CTCATCCTCCAAAAGTTAGCATC-TTCTAGCAGACCCTCCAACCTTTGCACCTCCCACCCCATCCCATTCCGTCCAC-AGCAGTGCC-T-CCT-AGCCACTTCTCT-TTGCTTACTAACAAAAGAAAAGGGGGAAAGCCT s panTro2.chr17 79504082 211 + 83384210 TGG-GGGGAGGATGCTGG-GGGCAAGGAGACGCAGGGAGGCCTCTGCCAAGGGTCAGGTGGACCAGAAACTTCCCTGGA----CTCATCCTCCAAAAGTTAGCATC-TTCTAGCAGACCCTCCAACCTTTGCACCTCCCACCCCATCCCATTCCATCCAC-AGCAGTGCC-T-CCT-AGCCACTTCTCT-TTGCTTATTAACAAAAGAAAAGGGGGAAAGCCT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 39983 211 - 64270 TGG-GGGGAGGATGCTGG-GGGCAAGGAGACGCAGGGAGGCCTCTGCCAAGGGTCAGGTGGACCAGAAACTTCCCTGGA----CTCATCCTCCAAAAGTTAGCATC-TTCTAGCAGACCCTCCAACCTTTGTACCTCCCACCCCATCCCATTCCATCCAC-AGCAGTGCC-T-CCT-AGCCACTTCTCT-TCGCTTNTTAACANAAGAAAAGGGGGAAAGCCT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16088457 210 + 17838096 TGG-GGGGAGGATGCTGG-GGGCAAGAAGACGCAGGGAGGCCTCGGCCAGGGGTCAGGTGGACCAGAAACTTGCCTGGA----CTCATCCTCCAAAAGTGAGCATC-TTCTAGCAGACCCTCCAACCTTTGCACCTCCCACCCCATCCCACTCTGGCCAC-AGCAGTGCC-T-CCT-AGCCACTTCTCT-TTGCTTATTAACAAAAG-AAAGGGGGAAAGCCT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75062928 211 + 78773432 TTGCGGGGAGGATGCTGG-GGGCAAGGAGATGCAAGGAGGCCTCAGCCAGGGGTCAGGTGGACCAGAAACTTCCCTGGA----CTCATCCTCCAAAAGTGAACATC-TTCTAGCAGACCCTCCAACCTTTGCACCTCCCACCCCATCCCACTCTGGCCGC-AGCAGTGCC-T-CCT-AGTCACTTCTCT-TTGCTTATTAACGAAAG-AAAGGGGGAAAGCCT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 69960 211 - 95547 TTGCGGGGAGGATGCTGG-GGGCAAGGAGATGCAAGGAGGCCTCAGCCAGGGGTCAGGCGGACCAGAAACTTCCCTGGA----CTCATCCTCCAAAAGTGAACATC-TTCTAGCAGACCCTCCAACCTTTGCACCTCCCACCCCATCCCACTCTGGCCGC-AGCACTGCC-T-CCT-AGTCACTTCTCT-TTGCTTATTAACGAAAG-AAAGGGGGAAAGCCT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 72472 197 + 225949 TG--GGGGAGCAGGCTGG-GGGGAAGGAGATGCAGGGAGGCCTCAGCCAGGGGTCAGGAGGACCAGAAGCT----------------TCCTCCGAAGGTGAGCATC-TTCTAACAGACCCTCCAACCTTTGCACCTCCCACCCCATCGCACTCTGGCCAC-AACAGTTCC-T-CCT-AGCCACCTGTCT-TTGCTTATTAACAGAAG-AAAAGGGGAAAGCCT i calJac1.Contig5139 C 0 C 0 s otoGar1.scaffold_94362.1-287808 44908 163 + 287808 ----G-------------------AGGAGACGCAGAGAGGCC-CTGCC-GGGGCTAGGCGGACCTGATGCTTCCTTGGC----CTCACCCTC--AGGTTGAGCACCTTTCTAACACACCCC-------------------ACCCACCCCAGTCTGGCCAC-AGCAGAGTT-C-CCT-GTCCAGTTC-CT-GTGACTATT-ACAAA---GAAACAGGAAAGCCT i otoGar1.scaffold_94362.1-287808 C 0 I 1301 s mm9.chr11 118781425 128 + 121843856 TGG-AGGGTGGAAGC----------------ACAGAGAGGCCTTGGCCAGGGGTGAAGGGGACAAGAAGCTTCCCTGGG----CTGGTCC-----------------TTCATACAAGTA-------------AC-TGTCCCCCTACCCCAACCCAGTCAG-AG--ATACT-TCCCT-GTCTAGTG-------------------------------------- i mm9.chr11 C 0 I 11 s cavPor3.scaffold_76 4409252 161 + 7991924 TCA-GGGGTAAAAG------------------------GACCACTGCCAGAGGTCAAATGGATGAGGACTTCCCTTCAGGAACTTGCCCC-----------------TTCTAACAGCCC-------------ACACACACTCCCCTCCCAGCCTGGACAATAG--ATACT-T-CCT-GTCCAGTGCATA-GTGCATGTTAGCAAATA-ACAGGAGGATGGCCT i cavPor3.scaffold_76 C 0 I 13 s equCab2.chr11 58065318 205 - 61308211 GAG-GCGGAGGATGTAGGCAGAGAAGGAGACACAGAGAGGCCTCGGCCAGGGGTCAGGTGGACCAGAAGCTTCCCTGGA----TTCACCCTCCAGGGATGAGCATC--TCCACCAGACCCCC-AGCTCCTGCAT---CCCACCCATCCCGCCTCAGCTGT-GGTGGTGCT-C-CCT-GTTCAGTTCTCC-TTGCTTCGTAGCAACAG-AAAGAGGGAAGCAC- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59459139 189 - 64418924 CTG-GGGTAGGATGTGGG-GGGCACGGAGACGGGGTGGGG--GCAGCCAGGGGTCAGGTGGATCAGAAGC-CCCCTGGA----TCCATTCTCTGCAAACGAGCATC--TCTACCAAGCCCCCTCGCTCCTGCAT------GCCCACCCCGCCC---------ACAGGGCC-C-CCTAATCCAGCT---G-TTGCTTATTATCGACGA-AAGCAGGGACCCCT- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 35032 163 + 48268 CAG-GGGTAGGGTGTGGG---GCAGGGGAGCCGAGGAGGGCCGCAGC--AGGGCCCGGGG----------------GGG----TTTATCCT-TGCAAGCGAGCTTC--TCCAGCAGACCGCC--------GCGG-------------CCGCCGCAGCCAA-AGCAGCGCT-C-GCT-GTCCAGTT---C-TTGCTGCTCATCCGCAG-GAGAGGTCAGCGTC- i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_85717 487 194 + 6675 GTC-TTTGGGGACAGGGG-GGCAGAGAAGGG---GAGGTG---CAGAGAGCGCCT--CCGAGCGAGACGCTGCCCTGGA----GCCATCCTCTGGGATGGAGGGTC-TTCTAATGGGCCCCTCGcctcacacccaccccctccc-ccactccctgtcc----------catc-tcc-gtctccgtctccGTTGCTTGTTCTCAAATG-AAAGAGGGGAAGCGC i dasNov2.scaffold_85717 C 0 C 0 s loxAfr3.scaffold_49 14457169 201 - 17734757 ATT-TTTTCAGATGAGAG-GACAGGGGAGGGGCAGGGAAG---CAGGCAGGGGTTAGATGGGGGAGAAGATTCCCTGGA----CCCCTCTTCCAGGAT-GAGCATC-TTCTAACAGACCCCCAACCCCACACCCACCCCCGTCC-TTCTGCTGTGGCCAC-AG--GAACA-C-CCT-GCCCACTTCTCC-TTGCTTGTGTCCAAA---AAAGGGGAAAAGCAT i loxAfr3.scaffold_49 C 0 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e monDom5.chr2 304624775 9630 - 541556283 I e bosTau4.chr19 10879960 1 - 65312493 I a score=126903.000000 s hg19.chr17_gl000204_random 72289 128 + 81310 TCCTT-CCCAGCTAGGGCAGGATGCT--G-TCTCATCA-----------CCTGTCTC-AGCGG--GCCACGCCAGTAAGCAGGAAGCGG-CCACTGTC--GCTTCTGCAGG-GAAGGAATGGGCTTCCCGGT--GTCTCCGGGGC------------------TTAATAC s calJac1.Contig5139 72669 132 + 225949 TTCTT-CCCAGCCAGGGCTGGACACT--G-TCTCACCA-----------CCTGTCTC-AGCAG--GCCAGCCCTGTAAGCAGGAAGCGG-CCACTGTG--CCTTCTACAGG-GGAGGAGTGGGCCTCCTGGT--GTCCCCGGGGCT--T-----------G-TTTAATAC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 70171 133 - 95547 TCCTT-CCCAGCTAGCGCTGGATGCT--G-TCTCACCA-----------CCTGTCTCAAGGAG--ACCACCCCCATAAGCAGAAAGCAG-CCACTGTC--CCTTCTGCAGG-GAAGGAGTGGGCTTCCCGGT--GTCCCCGGGGCT--T-----------G-TTTAATAC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75063139 133 + 78773432 TCCTT-CCCAGCTAGCGCTGGATGCT--G-TCTCACCA-----------CCTGTCTCAAGGAG--ACCACCCCCATAAGCAGAAAGCAG-CCACTGTC--CCTTCTGCAGG-GAAGGAGTGGGCTTCCCGGT--GTCCCCGGGGCT--T-----------G-TTTAATAC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16088667 126 + 17838096 TCCTT-CCCAGCT------GGATGCT--T-TCTCATCA-----------CCTGTCTC-AGTGG--GCCACGCCAGTAAGCAGGAAGCGG-CCACTGTT--GCTTCTGCAGG-GAAGAAATGGGCTTCCGGGT--GTCCCCGGGGCT--T-----------A-ATTAATAC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 40194 128 - 64270 TCCTT-CCCAGCCAGGGCAGGATGCT--G-TCTCATCA-----------CCTGTCTC-AGCGG--GCCACGCCAGTAAGCAGGAAGCGG-CCACTGTC--GCTTCTGCAGG-GAAGGAATGGGCTTCCCGGT--GTCCCCGGGGC------------------TTAATAC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79504293 128 + 83384210 TCCTT-CCCAGCCAGGGCAGGATGCT--G-TCTCATCA-----------CCTGTCTC-AGCGG--GCCATGCCAGTAAGCAGGAAGCGG-CTACTGTC--GCTTCTGCAGG-GAAGGAATGGGCTTCCCGGT--GTCCCCGGGGC------------------TTAATAC i panTro2.chr17 C 0 C 0 s mm9.chr11 118781564 136 + 121843856 TCTCC-CTCAGCCAGGGTTGGATTCACAG--ATCATCT----------TTCTGGCCT-GGCCA--ACACACCATGTGAGCTAAAAACA--TCTCTGTC--TCTTCTGCTAG-AGAGCATGTGGCTCCCCAGT--CGCCTCAGGACTACT-----------GCTCTGGTAT i mm9.chr11 I 11 C 0 s cavPor3.scaffold_76 4409426 123 + 7991924 TCCTC-CCCACCCAGGACTGGACACTCAA-TATCCTTG----------CCCTGCTTA-GGCTG--ACAAGCCTCATAAGCT-----------TTTG-C--TCCTCTGCCAG-GGAATTAGCAGGCCTCCAATGATGCTGCAGG-----T-----------G-TTTAATAT i cavPor3.scaffold_76 I 13 C 0 s equCab2.chr11 58065523 130 - 61308211 CCTTC-CACAACCAGGGCCTGACACTCGG-TGTCACCA----------CCCTCTCCC-CACAG--ACCCGCCAAGCAAGCAGGAAGCAGCCCCCTGCC--CCTTCTGCGGG-GAGGGAGTGGA---CCCAGC-GGACCCCAGAGCT--T-----------A-TTTA---- i equCab2.chr11 C 0 I 20 s canFam2.chr9 59459328 102 - 64418924 CCCTT-CTAAACCAGAGCCTGA------------------------------------AGCAG--ACCAGCCAAGTAAGCAGGAAGCAG-CCCCTGCC--ACTTCTGCACA-GCGGGCCC------CCGGGC-AGCCTCCAGGGCC--T-----------A-CTTA---- i canFam2.chr9 C 0 I 18 s pteVam1.scaffold_11245 35195 103 + 48268 CCTTC-CACAACCAGCGCCTGACGCTCAG-TCTCACTC----------CTTT------CCCAGCCACTAGCCCAGGAAGCAGGACACAG-CCCCGCCG--GCT-----------------------CCCGGC-AGCCCCCAGGGCT--T-----------A--------- i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_85717 681 129 + 6675 -CCCCTCCCACGCAGGGC-GAA-GCTCCGGCCTCAGCACCTCACTC--CCCCGCCCC-GGCCG--GCCAGC-TGGCGAGCAGGAGGGAC-CCTCGTCCTTCCACCGGGTGG-G-------------CACAGC--CTCCCCTGGTCC--CCAGAGCTC------------- i dasNov2.scaffold_85717 C 0 I 55 s loxAfr3.scaffold_49 14457370 124 - 17734757 -CCTC-CCCAAGCAGGGT-GGATGCTCAG--CTCACCTCCATGCTCCACCCTGCCTC-AACCA--ACCAGCAAGGTGAGAAGGAAGCAG-CCCCTGCC--CCACCTGCTGGAG-------------CCCAGG--AGCCCCAGGACC--T--------GTT---------- i loxAfr3.scaffold_49 C 0 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e felCat3.scaffold_206428 44767 1753 + 132007 I e otoGar1.scaffold_94362.1-287808 45071 1301 + 287808 I e monDom5.chr2 304624775 9630 - 541556283 I e bosTau4.chr19 10879960 1 - 65312493 I a score=32249.000000 s hg19.chr17_gl000204_random 72417 38 + 81310 TAAA-----ATC----ATCATCCCCC------GTCTGGAACCAGGATTC-TCAC s calJac1.Contig5139 72801 38 + 225949 TAAA-----ATT----ATCATCTCCC------TTCTGGAACCAGGATTC-TCTC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 70304 38 - 95547 TAAA-----ATC----ATCATCCCCC------GTCTGGGACCAGGATTC-TCAT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75063272 38 + 78773432 TAAA-----ATC----ATCATCCCCC------GTCTGGGACCAGGATTC-TCAT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16088793 38 + 17838096 TGAA-----ATC----ATCATCCCCC------ATCTGGGACCAGGATTC-TCAT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 40322 38 - 64270 TAAA-----ATC----ATCATCCCCC------ATCTGGAACCAGGATTC-TCAC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79504421 38 + 83384210 TAAA-----ATC----ATCATCCCCC------GTCTGGACCCAGGATTC-TCAC i panTro2.chr17 C 0 C 0 s mm9.chr11 118781700 37 + 121843856 TAAATCAGTATT----AAGACCCTCG------GTGCAG----GGGACTC-Tc-- i mm9.chr11 C 0 I 129 s cavPor3.scaffold_76 4409549 38 + 7991924 TAAA-----GTC----AACAACAACA------GTGCAGACTAGGAACTT-CTTC i cavPor3.scaffold_76 C 0 I 23 s canFam2.chr9 59459448 31 - 64418924 TAGA-----ATC----ATCGTCCTCC------AGTAAAATTTAGAA-------- i canFam2.chr9 I 18 I 31 s felCat3.scaffold_206428 46520 36 + 132007 TAGG-----ATC----ACCACCCTCC------GGGAGGGCTTAGGA--G-ACGT i felCat3.scaffold_206428 I 1753 C 0 s equCab2.chr11 58065673 31 - 61308211 TAGA-----ATC----ATCATCATCC------AGTAGAGCCTAGGG-------- i equCab2.chr11 I 20 I 33 s loxAfr3.scaffold_49 14457494 40 - 17734757 TAGT-----ATCATAATGCACCTTCCTCCACAACCATTATCA--------TCA- i loxAfr3.scaffold_49 C 0 I 123 s dasNov2.scaffold_85717 865 32 + 6675 ----------------AGCATCTCCC------ACCTGTGGCAGGGGCTGCTCAC i dasNov2.scaffold_85717 I 55 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e pteVam1.scaffold_11245 35298 0 + 48268 C e otoGar1.scaffold_94362.1-287808 45071 1301 + 287808 I e monDom5.chr2 304624775 9630 - 541556283 I e bosTau4.chr19 10879960 1 - 65312493 I a score=14195.000000 s hg19.chr17_gl000204_random 72455 23 + 81310 GGccccatctgc--------attctcc-tttt s calJac1.Contig5139 72839 23 + 225949 AGCCCCACCTGC--------ATtcccc-tttc i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 70342 23 - 95547 GGCCCCatctgc--------attctcc-tttt i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75063310 24 + 78773432 GGccccatctgc--------attctccttttt i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16088831 23 + 17838096 GGCCCCatctgc--------attctcc-tttt i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 40360 23 - 64270 GGccccatctgc--------attctcc-tttt i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79504459 23 + 83384210 GGCCCCatctgc--------attctcc-tttt i panTro2.chr17 C 0 C 0 s mm9.chr11 118781866 21 + 121843856 GGCCCCAAGGGCTATA----ACGCT------- i mm9.chr11 I 129 C 0 s cavPor3.scaffold_76 4409610 24 + 7991924 ------AACCGCTGTA-TTCAGGCTcc-tttc i cavPor3.scaffold_76 I 23 C 0 s equCab2.chr11 58065737 23 - 61308211 gtccccaca--------cctgttctcc-tttc i equCab2.chr11 I 33 C 0 s felCat3.scaffold_206428 46556 31 + 132007 CTCCCCCCATGCAACAGCAGGTGCTCA-TGTC i felCat3.scaffold_206428 C 0 C 0 s pteVam1.scaffold_11245 35298 4 + 48268 ----------------------------TTTA i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_85717 897 22 + 6675 -GGCCCCCCGTC--------ATCCTCC-TTCT i dasNov2.scaffold_85717 C 0 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e otoGar1.scaffold_94362.1-287808 45071 1301 + 287808 I e monDom5.chr2 304624775 9630 - 541556283 I e canFam2.chr9 59459479 31 - 64418924 I e bosTau4.chr19 10879960 1 - 65312493 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=31441.000000 s hg19.chr17_gl000204_random 72478 44 + 81310 ttgtgccaatagcaggat----tctcgatattcagctgggcacctcat s calJac1.Contig5139 72862 41 + 225949 atgt---aatagcagaat----tcttggtattcagctgggcacctcat i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 70365 40 - 95547 ttgtg----taatagaat----tcttgatattcagctgggcacctcat i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75063334 40 + 78773432 ttgtg----taatagaat----tcttgatattcagctgggcacctcat i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16088854 43 + 17838096 tagtgc-aatagcaggat----tctcgatattcagctgggcacctcat i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 40383 44 - 64270 ttgtgccaatagcaggat----tctcgatattcagctgggcacctgat i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79504482 44 + 83384210 tcgtgctaatagcaggat----tctcgatattcagctgggcacctcat i panTro2.chr17 C 0 C 0 s mm9.chr11 118781887 37 + 121843856 -------AGCAGCAACAA----CCCTGACAATGAAGCTGGTCCCTCTC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4409634 44 + 7991924 ttg----aatactaataagactccccaattgtgagcctggcatttcat i cavPor3.scaffold_76 C 0 C 0 s pteVam1.scaffold_11245 35302 31 + 48268 ATGTGAAAATGGACGGT-----CCTTGGCAATCATC------------ i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59459510 30 - 64418924 ATGTCA-GATAACTGGA-----ccccgacatttagc------------ i canFam2.chr9 I 31 C 0 s felCat3.scaffold_206428 46587 35 + 132007 ATGTGA-------TGGG-----CCCTGATATTTAAC-GGGTTCACTAG i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58065760 38 - 61308211 ---tca-tataacagaa-----ccctggtatttagc-tggcgcaccat i equCab2.chr11 C 0 C 0 s dasNov2.scaffold_85717 919 41 + 6675 ---TCACCATAAGAGAGC----TGCTGAGGGTTACATGGGGACCTCAT i dasNov2.scaffold_85717 C 0 I 313 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e otoGar1.scaffold_94362.1-287808 45071 1301 + 287808 I e monDom5.chr2 304624775 9630 - 541556283 I e bosTau4.chr19 10879960 1 - 65312493 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=659473.000000 s hg19.chr17_gl000204_random 72522 302 + 81310 cgtccaggataaagaccac--gcctccc-----------gggctggg-tgtgagtctgtgactactctcccaccgatggg--------atatacaca-gaagtgacagctccagctcccgggtcacacactgaag------gg--ggcatcccc------ccatc--------------------tcta------cc-gcatgtttgcaatgcggtg-aattgtgagccttcttgggccaagcatgtgg-gccgacacccttaggatggggagtcccgagagagaaggtgctcgagcctccggtgacCTCCCGGGGCTCAGCCACCTGCCTCCAGATGGTCACTTCTGAGAAAATTAACTTCTGATCT s calJac1.Contig5139 72903 301 + 225949 -gtccagggtaacgaccac--gcctccc-----------aggctggg-tgtgattccgtcattacactcccaccaatggg--------atataaacg-gaagcgacagctccagctcccaggTCACACACTAAAG------GG--GGCATCCTT------CCATC--------------------TCCA------CC-GCAGGTTCGGAACATGGTG-AATTTCGAGCCTTCTTGGGCTAAGCATGTGG-GTCGGCACCCTCAGGACAGGAAGTTCCAAGAGAGAAGGTCCCCAAGCCTCCGGTGACCTCCCAGGGCTCAGCCACCTGCCTCCGGATGGTCACTTCAGAGAAAATTAACTTCCAACGT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 70405 300 - 95547 cgtccaggataatgaccac--gcctccc-----------gggctggg-tgtgagtctgtgactacactcctgctgatggg--------atataaatg-gaagtgacagctccagctcccgggTCACACACTGAAG------GG--GGCATCCCC------CCATC--------------------TCTA------CT-GCAGGTTTGGAACGTGGTG-AATTGTGAA--TTATTGAGCCAAGCATGTGG-GCCAACACCCTCAGGATGGGGAGTCCCAAGACAGAAGGTGCCCAACCCTCCGGTGACCTCCCGGGGCTCAGTCACCTGCCTCTGGACGGTCACTTCCGAGAAAACTAGCTTCTGACCT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75063374 300 + 78773432 cgtccaggataatgaccac--gcctccc-----------gggctggg-tgtgagtctgtgactacactcccactgatggg--------atataaatg-gaagtgacagctccagctcccgggTCACACACTGAAG------GG--GGCATCCCC------CCATC--------------------TCTA------CT-GCAGGTTTGGAACATGGTG-AATTGTGAA--TTATTGAGCCAAGCATGTGG-GCCAACACCCTCAGGATGGGGAGTCCCAAGACAGAAGGTGCCCAACCCTCCGGTGACCTCCCGGGGCTCAGTCACCTGCCTCTGGATGGTCACTTCCGAGAAAACTAGCTTCTGACCT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16088897 302 + 17838096 cgtccaggataatgaccac--gcctccc-----------gagctggg-tgtgagtctgtgactactctcccaccgatggg--------atatacacg-gaagtgacagctccagctcccgggTCACACACTGAAG------GG--GGCATCCCC------CCATC--------------------TCTA------CC-GCACGTTTGCAACGTGGCG-AATTGTGAGCCTTCTTGGGCCAAGCATGTGG-GCCGACACCCTCAGGATGGGGAGTCCCAAGAGAGAAGGTGCTCAAGCCTCTGGTGACCTCCCGGGGCTCAGCCACCTGCCTCCAGATGGTCACTTCCGAGAAAATTAACTTCTGATCT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 40427 302 - 64270 cgtccaggataaagaccac--gcctccc-----------gggctggg-tgtgagtctgtgactactctcccaccgatggg--------atatacaca-gaagtgacagctccagctcccgggtcacacactgaag------gg--ggcatcccc------ccatc--------------------tcta------cc-gcatgtttgcaatgcggtg-aattgtgagccttcttgggccaagcatgtgg-gccgacacccttaggatggggagtcccgagagagaaggtgcttgagcctccggtgacCTCCCGGGGCTCAGCCACCTGCCTCCAGATGGTCACTTCTGAGAAAATTAACTTCTGATCT i gorGor1.Supercontig_0007361 C 0 M 14 s panTro2.chr17 79504526 302 + 83384210 cgtccaggataaagaccac--gcctccc-----------gggctggg-tgtgagtctgtgactactctcccaccgatggg--------atatacaca-gaagtgacagctccagctcccgggTCACACACTGAAG------GA--GGCATCCCC------CCATC--------------------TCTA------CC-ACATGTTTGCAATGTGGGG-AATTGTGAGCCTTCTTGGGCCAAGCATGTGG-GCCAACACCCTTAGGATGAGGAGTCCTGAGAGAGAAGGTGCTCGAGCCTCCGGTGACCTCCCGGGGCTCAGCCACCTGCCTCCAGATGGTCACTTCTGAGAAAATTAACTTCTGATCT i panTro2.chr17 C 0 C 0 s mm9.chr11 118781924 279 + 121843856 TGTCTCAGACCACACTCAG----GGTGg-----------cagctggg-tgtattcctgtggtt---------gtattgtg--------acagaaaag-gaaatggcgtggcaa-cctccaggtcctttgctaaag------ggacaggacactctctatatcttc--------------------tccc------ctaagaggtttg--------tg-aattgaaaaccattttagaccaa--atgtggaaataacatccaaaggatgaggaacc---ataggagagaatgctggcagccacgtgaccctgtggaactcagccacttgactt-gaactgtcaattcaaag-aaattcacttc------ i mm9.chr11 C 0 I 908 s cavPor3.scaffold_76 4409678 303 + 7991924 tgcccaagattatacacagcttcctttg-----------cagctaggttatgatcacatgatt---------ctgtttggtcaataatacgaaaagg-gaagtaacatctaca-agcccagttcatgt-ctgcag------ggaaagca-actc---agactttc--------------------ttcc------cc-agtggcttggaacacaagg-aatcttgagtcatcttggactaaagatgtgaaggcagcaccttaagggtggggaacactgagaggggaggaccctgtcctctggaggaccttctggagGTTGGCTCCCTGCCTC----CAGTCACTTCAGGGAAAATTCATTTCTCACCC i cavPor3.scaffold_76 C 0 I 1 s pteVam1.scaffold_11245 35333 176 + 48268 ---------------------------------------------------------------------------------------------------------------------------------ATTA----------------TCCCC-AGACACCAAC----CTCGCCTCCCACTTCCTCCA------CT-GGTCGTTTGGAGCGCAGACGAATGGTGAACCTCCTGAGACCAAGCATG----------------AGGATGCGGACCCT---AAGGGAGGAGCCTAGGTCCCCAGGTGACCTCCTGGAGCTCAGCCACCTGCCTCTGGACAGTCAC----------------TTTGGACAC i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59459540 312 - 64418924 tgtgcaagataagggccat--acctcctggcctccctggcagccagg-tatgatcacgtgactacactgtggccaatggg--------atgtaaAAC--AAGGGGCACCTACAGCTTGTCGGTCATGCCATCA--------GG--GGAGACCCC-TGAGCTCACC----CTCACCTCTCATTTCCTCCA------CC-AGAGGCTTGGAATGTGAAC-AAAGGAGGACCCTCTGAGACCAAGCATGTGGAGGCAGCACTCTGAGGACAGGAACCCC---AGAAGGAGAGCCTGGGTCTCCAGGTGACCTCCTTGAGCGCAGCCACCTCCCTCTGGACAGTCCC-----------------TCTGACTT i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 46622 321 + 132007 TGTCTGAGAC-AGGGACAA--ACCtcccagcctcccttgcagctagg-cctgatcacatgactacatgtgggccaatggg--------atgtaaaaa-gaagtggtacctacagcttgtgggtcaggaccttaagggaggggg--GGAGACCCC-CAACCCCGCT----CTCACCTCCCAATCCCTCTA------CC-AGAGGCTTGGGACACAAAC-AAAGGGGAGCCCTCTGAGACCAAGCGTGTGAAGGCAGCACCCTAAGGGCGGGGACCCC---AAGAGAAGAGACTGGGTCTCCAGGTGACCTCCGGGAACTCGGCCACCTCCCTCTGGACAGTCCC----------------TTCTAACCT i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58065798 329 - 61308211 cgtccaagacaaggactgc--agctccc-gcttcctttacagctagg-tgtgatcacgtgactacgctctggccgatggg--------acgtaaaaaggaagtgacacccaccgcttgtgggtcaagcacttaagggga--gg--gatgtgccc-CGACCCCACCCTCACTCACCTCCCAATTCCTCCATCCCATCC-GGAGGTTTGGAACATGGATGAAAGGCGAATCATCTTAGACCATGCATGTGGGGGCAGCTCCCCGAGGA-GGGGACCCC---AAG-GGAGAGCCCGGTTCTCCAGGTGACGTCCTGGACCTCTGCCGCCTGACTCTGAACAGTCAC----------------TTCCAACCC i equCab2.chr11 C 0 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e turTru1.scaffold_98008 10408 64 + 223990 I e dasNov2.scaffold_85717 960 313 + 6675 I e otoGar1.scaffold_94362.1-287808 45071 1301 + 287808 I e monDom5.chr2 304624775 9630 - 541556283 I e bosTau4.chr19 10879960 1 - 65312493 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=32919.000000 s hg19.chr17_gl000204_random 72824 31 + 81310 -GTGGAAGACCCATGGAAGCCTGGAGCCTCGG s calJac1.Contig5139 73204 31 + 225949 -ATGGAAGGCCCACAGAAGCCTGGAGCCTCCG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 70705 31 - 95547 -GTGGAAGGCCCGTGGGAGCCTGGAGCCTCCG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75063674 31 + 78773432 -GTGGAAGGCCTGTGGGAGCCTGGAGCCTCCG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16089199 31 + 17838096 -GTGGAAGACCCATGGAAGCCTGGAGCCTCCG i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79504828 31 + 83384210 -GTAGAAGACCCATGGAAGTCTGGAGTCTCCG i panTro2.chr17 C 0 C 0 s micMur1.scaffold_51043 29 26 - 5707 -TAGGAGGTCCCGT-----CTCAGACTCCCCG i micMur1.scaffold_51043 N 0 C 0 s cavPor3.scaffold_76 4409982 27 + 7991924 -CTGGACACCCCAT----TCTTAGTGTTGGCC i cavPor3.scaffold_76 I 1 C 0 s pteVam1.scaffold_11245 35509 28 + 48268 CCTGAAGGCTCTGT----GCTTGGAGTCCCCA i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59459852 21 - 64418924 CCTGAGGGCTCTG------CTTAGAGT----- i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 46943 21 + 132007 CGTGAAGGCTCTG------TTTGGAGC----- i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58066127 28 - 61308211 CTTGAAGGCGCTGT----CCCTGAAGTCCCTG i equCab2.chr11 C 0 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e gorGor1.Supercontig_0007361 40729 14 - 64270 M e turTru1.scaffold_98008 10408 64 + 223990 I e dasNov2.scaffold_85717 960 313 + 6675 I e otoGar1.scaffold_94362.1-287808 45071 1301 + 287808 I e monDom5.chr2 304624775 9630 - 541556283 I e bosTau4.chr19 10879960 1 - 65312493 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=101337.000000 s hg19.chr17_gl000204_random 72855 37 + 81310 TCATGCTCAGCCTCATGTATGTCTTAACGGAAACACC s calJac1.Contig5139 73235 37 + 225949 TCATGCTCAGCCTCGTGTATGTCTTAATGGAAATAGC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 70736 37 - 95547 TCATGCTCAGCCTCATGTATGTCTTCACGGAAACGCT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75063705 37 + 78773432 TCATGCTCAGCCTCATGTATGTCTTCACGGAAACGCT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16089230 37 + 17838096 TCATACTCAGCCTCATGTATGTCTTAACGGAAACACC i ponAbe2.chr17_random C 0 C 0 s panTro2.chr17 79504859 37 + 83384210 TCACTCTCAGCCTCATGTATGTCTTAACGGAAACATC i panTro2.chr17 C 0 C 0 s micMur1.scaffold_51043 55 36 - 5707 CCGTGC-CGGTCTCCTTCACGTGCTCAGCGCAACGGT i micMur1.scaffold_51043 C 0 C 0 s cavPor3.scaffold_76 4410009 37 + 7991924 GTGTGTTCAGCCGCATTTATATCCTTGCCAAAATGAC i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10879961 34 - 65312493 ---TGCTCAGCCCCATCTACATCCTAACTAAAGCTGC i bosTau4.chr19 I 1 C 0 s turTru1.scaffold_98008 10472 37 + 223990 TCCCACTCAGCCCCGTCTACATCCTAACTAAAACTAC i turTru1.scaffold_98008 I 64 C 0 s equCab2.chr11 58066155 36 - 61308211 TTGCGCTCAG-CCCGTCTCTGTCCTGACTACAGCtac i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 46964 26 + 132007 -----------CCTGTCCACATCCTAACTAGCACCGC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59459873 26 - 64418924 -----------CCTGTGCACATCCTAACTAGAACTAT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 35537 37 + 48268 CTACGCTCAGCCCCGCCTACGCCCTAACCAAAACCAC i pteVam1.scaffold_11245 C 0 C 0 e tarSyr1.scaffold_41848 5715 2120 + 21754 I e gorGor1.Supercontig_0007361 40729 14 - 64270 M e dasNov2.scaffold_85717 960 313 + 6675 I e otoGar1.scaffold_94362.1-287808 45071 1301 + 287808 I e monDom5.chr2 304624775 9630 - 541556283 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=149311.000000 s hg19.chr17_gl000204_random 72892 39 + 81310 ATTTCTATCTCAA-----------TTCAGCCtcgagcctcagaatgaaa-c s panTro2.chr17 79504896 39 + 83384210 ATTTCTATCTCAA-----------TTCAGCCTCGAACCTCAGAATGAAA-C i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16089267 39 + 17838096 ATTTCTATCTCAA-----------TTCAGCCTCGAACCTCAGAATGAAA-C i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75063742 39 + 78773432 ATTTCTATCTCAA-----------TTCAGCCTCGAACCTCAGAATGAAA-C i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 70773 39 - 95547 ATTTCTATCTCAA-----------TTCAGCCTCGAACCTCAGAATGAAA-C i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 73272 50 + 225949 ATTTCTATCTCAAGTCTATCTCACTTCAGCCTCCGAcctcagaatgaac-c i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 7835 39 + 21754 ATTTCCATTTTAA-----------GTCAGCACTGAACCTCAGAGTGAAG-T i tarSyr1.scaffold_41848 I 2120 C 0 s micMur1.scaffold_51043 91 39 - 5707 GCTGCTAACTCGG-----------TTCAGTGTCGAACCTCAGAACGGAA-C i micMur1.scaffold_51043 C 0 I 5 s cavPor3.scaffold_76 4410046 25 + 7991924 TTTTCCACCTGGC-----------TGCAGCTTGGAG--------------- i cavPor3.scaffold_76 C 0 I 145 s bosTau4.chr19 10879995 39 - 65312493 ATTTTTGTCTCCA-----------TCCAGCACTGAATCTCCAAGTGAAG-T i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 10509 39 + 223990 ATTTCTGTCTCGA-----------TCCAGCATCGAACCTCCATGTGAAG-C i turTru1.scaffold_98008 C 0 C 0 s equCab2.chr11 58066191 39 - 61308211 atttctaccttga-----------gccaacactgaacctccgtgtgagg-c i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 46990 39 + 132007 GTTTCTGCCTCGT-----------CCCAGCATCGAGCCTCTGCCCGGAG-C i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59459899 39 - 64418924 GTTTCTGTCTCAT-----------CCTAGCATTGAACCTCTGCACAGAG-C i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 35574 40 + 48268 GTCTCCATGTCAT-----------TCCAGCACCGAACTGCCAACAGGAGAC i pteVam1.scaffold_11245 C 0 C 0 e gorGor1.Supercontig_0007361 40729 14 - 64270 M e dasNov2.scaffold_85717 960 313 + 6675 I e otoGar1.scaffold_94362.1-287808 45071 1301 + 287808 I e monDom5.chr2 304624775 9630 - 541556283 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=720783.000000 s hg19.chr17_gl000204_random 72931 301 + 81310 aggaagatgcacccagc-aaa------taatacttttggcatgttactaataaaataaggaaagga--aaaacctggggctcagac-ggtcatctgatttgccaacagccacacacggaggt-gtgaccaggctggggact---------------------gcaggagccct----------------------------------ggccct-------tccctgtcca-gggaatgtgccctctgaggagcctggtctg-ttattctgTTTCCAGCAGTAGTAATCAAGGACCCTGGGCTCCCAGGTGACTTTGAC-----CAGT-GCCTCCACCTGATGCCACCTTCCC-CCCAGG-TGCATCTTCAACATAGCTTCCCCC s panTro2.chr17 79504935 301 + 83384210 AGGAAGATGCAGCCAGC-AAA------TAATACTTTTGGCATGTTACTAATAAAATAAGGAAAGGA--AAAACCTGGGGCTCAGAC-GGTCATCTGATTTGCCAACAGCCACACACGGAGGT-GTGACCAGGCTGGGGACT---------------------GTAGCAGCCCT----------------------------------GGCCCT-------TCCCTGTCCA-GGGAATGTGCCCTCTGAGGAGCCTGGTCTG-TTATTCTGTTTCCAGCAGTAGTAATCAAGGACCCTGGGCTCCCAGGTGACTTTGAC-----CAGT-GCCTCCACCTGATGCCACCTTCCC-CCCAGG-TGCATCTTCAACATAGCTTCCCCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 40743 301 - 64270 AGGAAGATGCACCCAGC-AAA------TAATACTTCTGGCATGTTACTAATAAAATAAGGAAAGGA--AAAACCTGGGGCTCAGAT-GGTCATCTGATTTGCCAACAGCCACACACGGAGGT-GTGACCAGGCTGGGGACT---------------------GTAGCAGCCCT----------------------------------GGCCCT-------TCCCTGTCCA-GGGAATGTGCCCTCTGAGGAGCCTGGTCTG-TTATTCTGTTTCCAGCAGTAGTAATCAAGGACCCTGGGCTTCCAGGTGACTTTGAC-----CAGT-GCCTCCACCTGACGCCACCTTCCC-CCCAGG-TGCATCTTCAACATAGCTTCCCCC i gorGor1.Supercontig_0007361 M 14 C 0 s ponAbe2.chr17_random 16089306 300 + 17838096 AGGAAAATGCACCTAGC-AAA------TAATACTTTT-GCATGTTACTAATAAAATAAGGAAagga--aatacctggggctcagat-ggtcatctgatttgccaacagccacacacagaggt-gtgaccaggctggggact---------------------gcagcaggcct----------------------------------ggccct-------tccttgtcca-gggaacgtgccctgtGAGGAGCCTGGTCTG-TTATTCTGTTTCCAGCAGTAGTAATCAAGGACCCTGGGCTCCCAGGTGACTTTGAC-----CAGT-GCCTCCACCTGATGCCACCTTCCC-CCCAGG-TGCATCTTCAAAATAGCTTCCCCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75063781 301 + 78773432 AGGAAGATGCACCCAGC-AAA------TAATACTTTTGACATGTTACTAACAAAATAAGGaaatga--aaaatctggggctcaggc-agtcatctgatttgccaagagccacaaacag-ggt-gtgacaaggctggagact---------------------gtaacagccct----------------------------------ggccct-------cccctgtcca-gggaatgtgccctctGAGGAGCCTGGTCTG-TTACTCTGTTCCCAGCAGTAGTAATCAACGACCCCGGGCTCCCAGGTGACTTTGAC-----CGGT-ACCTCCACCTGATGCCACCTTCCC-CCCAAGCTGCATCTTCAAGATAGCAGCCCCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 70812 300 - 95547 AGGAAGATGCACCCAGC-AAA------TAATACTTTTGACATGTTACTAATAAAATAAGGaaatga--aaaatctggggctcaggc-ggtcatctgatttgccaagagccatacacgg-ggt-gtgacaaggctggagact---------------------gtaacagcccc----------------------------------ggccct-------cccctgtcca-gggaacgtgccctctgaggagcctggtctg-ttactctgTTTCCAGCAGTAGTAATCAACGACCCTGGGCTCCCAGGTGACTTTGAC-----CAGT-ACCTCCACCTGATGCCACCTGCCT-CCCAGC-TGCATCTTCAAGATAGCAGCCCCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 73322 292 + 225949 aggaagatgcacctggc-aaa------taatacttttgacatgtgactaataaaataaggaaagga--aaaacctggggctccgat-ggtcacctgatttgccaagagccacacatggagat-gtgacaaggctggggact---------------------gtggcagccct----------------------------------ggccct--------ccctgtcca-agGAGTATGCCCTCTGAGGAGGCAGGTCTG-TGACTCTATTTCCAGAAGTAGTGATAAAGGACCCTGGGCTCCCAGGTTACTTTGG---------------CCACCTGATGTCACCTTCCCTCCCAGG-TGCATCTTCAAGATAGCTGCCCCT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 7874 298 + 21754 GAGgagacaagctgggc-agg------tattcgttttgacattttactgataaaacaaagaaaaaaacaaaacctgaggctcagat-gattatctgacttgtccaggatcattcacagAGATCTTAACAAGACTGGGGACT---------CATA-TCCCCACCCAGTAGAGCT----------------------------------GGGTCT-------TTCTCGTCCA-AGAAATAC-CTCTTTGTAGAGTTGGGTCTG-CTATCCTG-TCCTAGCAATAACACCAAAAGGTCCTGGGCTCCCAGGTGATTTGTGC-----CATC-ATCTCCCTCT---------------CCCAGG-TGCATCTTCAAGATCACTGTCCC- i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_51043 135 322 - 5707 GAGGGGCTGGGCTGGGC-AGGGGTTATTAGTACTTTTGACATTTTGCTGATGAAACAAAGAGATAAACAAAACCCGAGGCTCCGAC-AGTCATCTGGTTTGCCCGGGGCCACACACAG-----GTGGGACGGCTGGGGTCTCCGCAGGTGCACAGGTCCTGCCCAGCTGGCCT----------------------------------GGCACCCCTGCACCCCCTGTGCA-GGTAACACACCCTTTG--------GGTCTG-TTGTTCTGTCCCCAGCAGTAGCAATAAGTGACCCTGAGCTCCCAGGTCATTTGGGT-----CAGTGGCCCCCATC----GCTCCCTCTCC-TGCAGG-TGCCTCTTCAAGGTAGCTTCCCCC i micMur1.scaffold_51043 I 5 C 0 s bosTau4.chr19 10880034 232 - 65312493 TGAGAGGTGGACTGGGC-AGA------TGTCACTTTTGACACCTTTGTGAGGCGTG---------G--CAACCCTGGGGCC---ACAGGTCTTC-------------------CACTGCTGC-CCAGCAGACCTGG-----------------------------------------------------------------------TCTCCT-------GGCCCATCCAGGGGAGCACCCCCGCTGCCAGGCTGGGCCTC-CTGTTTTGTTCCCAACAGTGGCAATAAATGGCCCAATGTACCCAAA-TCGTTGGAC-----CAGG-GCC----CCCAGTG---------------TG-TGCATATTCAGGACAGTCA----- i bosTau4.chr19 C 0 I 64 s turTru1.scaffold_98008 10548 242 + 223990 TGGGAGGTGGGCTGGGC-AGG------TGGCACTTTTCACATATTTGTGAGGTGTG---------G--CAGCGCTGGGGTC---GCAGGTCTTC-------------------CACCCCTGC-CCAGCAGACCTGG-----------------------------------------------------------------------TCCCTT-------GG-CCATCCAGGGGAGCACCCCCTCTGCCAAGCTGGGTGTC-TTGTTTTGTCCCCAGCAGTGGCAATAAATGACTCAGAGCACACAGA-TCCTTGGAC-----CAGG-GCCTCCACCCAGTG-------CCC-CCTATA-TGCATCTTCAAAGCAGCCA----- i turTru1.scaffold_98008 C 0 I 65 s equCab2.chr11 58066230 314 - 61308211 tgccacatgggctgggc-aga------tatcac-tttgacatattacagataaaaa---gacaaag--aaaacctaaggatggggagggtcatctgatgtgct---gggctcacactgagac-actgcaaaggtggggtcg-----------------------ggcaggtcttc-----cA-CCTGGCCCAGGGGACTGGTCCCCACCCTGG-------GGCCCATCCAGGGAAACACTCCCCTTGCTGTGCTGGGTCTC-TTG-TTTGTCCCCGGCAGTGGCAATAAATGACCCTGAGCCCCCAGGTTCTTTGGAC-----CAGC-ACCCCCACCCAGCA-------CTC-CCCACG-TGCATCTTCAAGATAGCTGGTCCC i equCab2.chr11 C 0 I 53 s felCat3.scaffold_206428 47029 254 + 132007 TGCAGGACAGGCTGGGGCGGG------GAGCAC---CGATGTACCATGGACAAAAC--------AG--AACACCTACGGCCAGGACAGGCCATCTGACTGCCC---AGCCGCGCAACGAGGC-CGGGCCAAGCAGACG------------------------------------------------------------------CCCCACCAG-------CGGCTGTGC--GGGGGCACTCCCTCTGCCATGCTGGGTCTC-T---TTTGTCCCCAT-----------GGTGGCCCTGAGCTCCCAGGTTCTCTGGAC-----CAGT-GCCCCCTCC--GTG-------TCC-CCCACA-TGCATCTTCAAGGCAGCTGGCCCC i felCat3.scaffold_206428 C 0 I 60 s canFam2.chr9 59459938 288 - 64418924 TGCACCACAGGCTACAG-GAT------CACTGC---TGATATACTTTGGGGAAAAC--AAAGAAag--gaaacctaaggccaggacaggccatcagactgcca---ggccacacagtgaggcacgcacaaagctggggttg-----------------------gatggatct------------------------------cctgCACCAG-------GGCCTGGGCAGGGGAGCGTGCCCTTTCCCATGCTGGGTCTTGT---TTTGTCCCCAGCAGTGGCAATAAGTGACCCTAAGCTCCCAGGCTCTTTGGAC-----CAGT-GCCCCTCCC-AGTA-------TCC-CCCATG-TGCATCTTTAAGACAGCTGCCCCA i canFam2.chr9 C 0 I 322 s pteVam1.scaffold_11245 35614 307 + 48268 TGGGAGACGGGCTGGGC-AGG------CATCGCCTTGGACATATCATGGCTAAAAA-AATAGGAAG--AAACCTTAGGGCC-----GGGTCATCTGCTCTGCC---GGCCACAC----AGAT-GGGGCAAAGCCGATGTCG-----------------------GGCAGGTCTTCACCCGCACCCCCGCCCAGTGG--------ATACCCCCG-------GGCCTGTCCAGGGGAGCACACCCTTCGCCATGATAGGTCTC-TCGTTCTGTTCCCAGCAGTGGCAATAAATGACCCTAAGCCCGCAGGTTCCTCGGACCAGGGCAGT-GCACCCCCC-AG-----------C-CCCCTC-TTAATCTTCAGAACAGCTGGTCCC i pteVam1.scaffold_11245 C 0 I 9 e dasNov2.scaffold_85717 960 313 + 6675 I e otoGar1.scaffold_94362.1-287808 45071 1301 + 287808 I e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=-6799.000000 s hg19.chr17_gl000204_random 73232 34 + 81310 A--C--C-CTCTGGAGTGTCCAGCTG------------------GGCAC-------------AA--CCAGGC s panTro2.chr17 79505236 34 + 83384210 A--C--C-CCCTGGAGTGTCCAGCTA------------------GGCCC-------------AA--CCAGGC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 41044 34 - 64270 A--C--C-CCCTGGAGTGTCCAGCTG------------------GGCCC-------------AA--CCAGGC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16089606 35 + 17838096 AC-C--C-CCCTGGAGTGTCCAACCA------------------GGTCC-------------AA--CCAGGC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75064082 34 + 78773432 A--C--C-CCCTGGAGTGTCCAGCCA------------------GGCCC-------------AA--CCAGGC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 71112 34 - 95547 A--C--C-CCCTGGAGTGTCCAGCCA------------------GGCCC-------------AA--CCAGGC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 73614 33 + 225949 A--C--C-CCC-GGAGTGTCCAGGCC------------------GGACC-------------AG--CTGGGG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 8172 47 + 21754 A--C--C-CCTTTGAGTTTCCAGCCT------------------GGCCCCTGCCTGGGTCAGCC--CCAGGT i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_51043 457 37 - 5707 A--C--CTTCCTCGACCGTCCGACCT------------------GGCCC-------------CAGCCTGGGC i micMur1.scaffold_51043 C 0 C 0 s bosTau4.chr19 10880330 31 - 65312493 -ACTCCC-CCGGGGACTGTTCA-CTG------------------AGCCT-------------GG--C----- i bosTau4.chr19 I 64 I 22 s turTru1.scaffold_98008 10855 29 + 223990 -ACT--C-CTGGAGACTGTTCA-CCA------------------AGCGT-------------GG--C----- i turTru1.scaffold_98008 I 65 I 22 s equCab2.chr11 58066597 27 - 61308211 -ACT--C-TCCAGGACTGTACA-CCC--------------------CCT-------------CG--C----- i equCab2.chr11 I 53 I 5 s felCat3.scaffold_206428 47343 29 + 132007 -ACT--T-ACAGGGACTGTTCA-CCA------------------AGCAC-------------AG--C----- i felCat3.scaffold_206428 I 60 I 14 s pteVam1.scaffold_11245 35930 47 + 48268 -GCC--C-ACAATGGATTTCCT-CCATGATAAAAACATGATAAAAACAC-------------TG--C----- i pteVam1.scaffold_11245 I 9 I 20 e dasNov2.scaffold_85717 960 313 + 6675 I e otoGar1.scaffold_94362.1-287808 45071 1301 + 287808 I e monDom5.chr2 304624775 9630 - 541556283 I e canFam2.chr9 59460226 322 - 64418924 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=1347441.000000 s hg19.chr17_gl000204_random 73266 526 + 81310 CCC------ATGGCACCTGA-----GAAAT-----AGGAACACAGCCTCCC--------CGGTGAAGTA--GAGGAGAGT------TTAAGCCAGGACTTTGCCTGTGCC------------------GAGGGCCTGGGA-GCCGGGCTCAGCT---CTGCCTGCCTGCCAGGGATGGGAC-----------CAGGGCTCGGCTTTCTCCTCTGCTAACA-----GGAAAGACCCCATAAGCCCTCAGGCCTGACTCCAGGAGTGAGA-CCTGTGATTCTATGTGAAACAGCCCCAGGCTGCCCACAGCAAGCCAAAGAATAAGAGCCCGCGCCTCTCCAAGGATCCGAGACCCAAGCAGCCTGGTGCCTTCTGCAAAACC---------------------TCTTCCTGCTTCTCTTCTGCAGGGAGCAGCGGCGTAGGTGGCTGGGGTGGTAGGGAGGAGAGGTGAGCTGCTTATTGCTGGAGATGACTTTCCTCT----CTCCTCCTCCTTCTCTGGGCAGCTCGTT--TTTTCCAAAATAACTCTTCTTCCTCCCTCCCCAGGTTGCTAGTTTCTGTCTCTCCTCCAGGCTTCC----AAGTGCCCCCT-------G--CAAGGGCAGCCGGC s panTro2.chr17 79505270 522 + 83384210 CCC------ACGGCACCTGA-----GAAAT-----AGGAACACAGCCTCCC--------CGGTGAAGTA--GAGGAGAGT------TTAAGCCAGGACTTTGTCTGTGCC------------------GAGGGCCTGGGA-GCCGGGCTCAGCT---CTGCCTGCCTGCCAGGGATGGGAC-----------CAGGACTCAGCTTTCTCCTCTGCTAAAA-----GGAAAGACCCCATAAGCCCTCAGGCCTGACTCCAGGAGTGAGA-CCTGTGATTCCATGTGAAACAGCCCCAGGCTGCCCACGGCAAGCCAAAGAATAACAGCCCACGCCTCTCCAAGGATCCGAGACCCAAGCAGCCTGGTGCCTTCTGCAAAACC---------------------TCTTCCTGCTTCTCTTCTGCAGGGAGCAGCGGCGTAGGTGGCTGGGGTGGTAGGGAGGAGAGGTGAGCTGCTTATTGCTGGAGATGACTTTCCTCT----CTCCTCCT---TCTCTGGGCAGCTCGTTC-TTTTCCAAAATAACTCTTCTTCCTCACTCCCCAGGTTGCTAGTTTCTGTCTC--CTCCAGGCTTCC----AAGTGCCCCCT-------G--CAAGGGCAGCCGGC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 41078 525 - 64270 CCC------GGGGCACCTGA-----GAAAT-----AGGAACACAGCCTCCC--------CGGTGAAGTA--GAGGAGAGT------TTAAGCCAGGACTTTGCCTGTGCC------------------GAGGGCCTGGGA-GCCGGGCTCAGCT---CTGCCTGCCTGCCAGGGATGGGAC-----------CAGGGCTCGGCTTTCTCCTCTGCTAACA-----GGAAAGACCCCATAAGCCCTCAGGCCTGACTCCAGGAGTGAGA-CCTGTGATTCCATGTGAAACAGCCCCAGGCTGCCCACAACAAGCCAAAGAATAACAGCCTGCGCCTCTCCAAGGATCCGAGACCCAAGCAGCCTGGTGCCTTCTGCAAAACC---------------------TCTTCCTGCTTCTCTTCTGCAGGGAGCAGCGGCGTAGGTGGCTGGGGTGGTAGGGAGGAGAGGTGAGCTGCTTATTGCTGGAGATGACTTTCCTCT----CTCCTCCTCCTTCTCTGGGCAGCTCGTTC-TTTTCCAAAATAACTCTTCTTCCTCCCTCCCCAGGTTGCTAGTTTCTGTCTC--CTCCAGGCTTCC----AAGTGCCCCCT-------G--CAAGGGCAGCCGGC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16089641 524 + 17838096 CCC------ACGGCACCTGA-----GAAAT-----AGGAACACAGCCTCCC--------CGGTGAAGTA--GAGGGGAGT------TTAAGCCAGGACTTTGCCTGTGCC------------------GAGGGCCTGGCA-GCCGGGCTCAGCT---CTGCCTGCCTGCCGGGGATGGGAC-----------CAGGGCTCGGCTTTCTCCTCTGCTAACA-----GGAAAGACCCCACAAGCCCTCAGGCCTGACTCCAGGAGTGAGA-CCTGTGATTCCATGTGAAACAGCCCCAGGCTGCCCACAACAAGCCAAAGAATAACAGCCCGTGCCTCTCCAAGGATCCGAGACCCAAGCAGCCTGGTGCCTTCTGCAAAACC---------------------TCTTCCTGCTTCTCTTCTGCAGGGAGCGGCGGCGTAGGTGGCTGGGGCGGTAGGGAGGAGAGGTGAGCTGCTTATTG-TGGAGATGACTTTCCTCT----CTCCTCCTCCTTCTCCGGGCAGCTCATTC-TTTTCCAAAATAACTCTTCTGCCTCCCTCCCCAGGTTGCTAGTTTCTCCCTC--CTCCAGGCTTCC----AAGTGCCCCCT-------G--CAAGGACAGCCGGC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75064116 525 + 78773432 CCC------ACGGCACCTGA-----GAAAT-----AGGAACACAGCCTCCC--------TGGTGAAGTA--GAGGAGAGT------CTAAGCCAGGACTTAGCCTGTGCC------------------GAGGGCCTGGGA-GCCAGGTTCAGCT---CTGTCTGCCCGCCGGGGATGGGAC-----------CAGGGCTCGGCTTTCTCCTCTGCTAATG-----GGAAAGACCCCACAAGCCCTCAGGCCTGACTCCAGGAGCGAGA-CCTGTGATTCCATGTGAAACAACCCTAGGCTGCCCACCACAAACCAAAGAATAACAGCCCCCACCTCTCCAAGGCTCTGAGACCCAAGCAGCCTGGTGCCTTCTGCAAAACC---------------------TCTTCCTGCTTCTCTCCTGCAGGGAGTGGCGGTGTAGGTGGCTGGGGCGGTAGCGAGGAGAGGTGAGGTGCTTATTGTTGGAGATGACTTTCCTCT----CTCCTCCTCCTTCTCTGGGCAGCTCGTTC-TTTTCCAAAATAACTCTTCTGCCTCCCTCCCCAGGTTGCTAGTTTCTCTCTC--CTCCTGGCTTCC----AAGTGCCCCCT-------G--CAAGGGCAGCCGGT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 71146 525 - 95547 CCC------ACGGCACCTGA-----GAAAT-----AGGAACACAGCCTCCC--------CGGTGAAGTA--GAGGAGAGT------CTAAGCCAGGACTTAGCCTGTGCC------------------GAGGGCCTGGGA-GCCAGGTTCAGCT---CTGTCTGCCCGCCGGGGATGGGAC-----------CAGGGCTCGGCTTTCTCCTCTGCTAACG-----GGAAAGACCCCACAAGCCCTCAGGCCTGACTCCAGGAGCGAGA-CCTGTGATTCCATGTGAAATAGCCCTAGGCTGCCCACCACAAGCCAAAGAATAACAGCCCCCACCTCTCCAAGGCTCCGAGACCCAAGCAGCCTGGTGCCTTCTGCAAAACC---------------------TCTTCCTGCTTCTCTCCTGCAGGGAGTGGCGGCGTAGGAGGCTGGGGCGGTAGCGAGGAGAGGTGAGGTGCTTATTGTTGGAGATGACTTTCCTCT----CTCCTCCTCCTTCTCTGGGCAGCTCGTTC-TTTTCCAAAATAACTCTTCTGCCTCCCTCCCCAGGTTGCTAGTTTCTCTCTC--CTCCTGGCTTCC----AAGTGCCCCCT-------G--CAAGGGCAGCCGGT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 73647 522 + 225949 CCC------ACAGCACCTGA-----GAAAC-----AG--AGACAGCCTCCA--------GGGTGAAGCA--GAGGAGAGT------CTAAGCTAGGACTCAGCCTGCGCC------------------GAGGGCCTGGGAGGCCGGGCTCAGCT---CCGCCTGCCTGCCGGGGATGGGAC-----------CAGGGCTCAGCTTTCTCCTCTGCTAAGG-----GGAAAGACCCCACAAGCCCTTAGGCCTGACTCCAGGAGTGAGA-CCTGTGATTCCATCTGCAACAGCCCGAGGCTGCCCACAAC-AGCCAAAGAATAACAGCCCATGCCTCTCCAAGGCTCTGACACCTATGCAGCCTGGTGCCTTCTGCAAAACC---------------------TCTTGCTGCTTCTCTCCT-CAGGGAGTGGCAGCGGAGGTGGCTGGGGCGGTAGGGAGGAGGGATGAGGTGCGTTTTGTTGGAGAAGCCCTTCCTCT----CCCCTCCTCCTTCTCTGGGCAGCTCGTTC-TTTTCCAAAATAACTCCTCTGCCTCCCTCCCCTGGTTGCTAGTTTCTGTCTC--CTCCAGGCTTCC----AAGTGCCCCCT-------G--CAAGGGCAGCTGGC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 8219 488 + 21754 CCC------ATGGCACTGGA-----GAAAT-----AGGAAGACAGCTTCCC--------CAGTAATATG--GAATAGAAT------CTAAGCTGGGACTTAGGCTGGGGC------------------AAGGACCTGGGA-G----------------------------AGAGATGGGGA-----------CAGGGCTCTGTCTTCTCCTCTGCTAAGG-----GGACAGACCCTATTAACCCTCAGGCCCATCTCCAGGATGGAGA-CCTATGATTCTATCTGAAACAGCTTTTGGCTGCCCAAGACAAATCAAAGAATGATGGCCAGTGCCTCTCCAAG-----AAGACCTAGCCAGCCCAGCACCTTCTGCAAAGCC---------------------TCTTCCTGCTTCTACCCTGCAGGGAACAACTGCGTAGGAAGCTGGGGGTGGAAGAAGAAAAGTGAGGGTACGTGTTGTTCGAGGTGACTGTCCTTT----CTCTACCCCCTACCC---------------TTCTCTAAAATAGCTCTTCTACCTCCTCTGCCAAGTTGCTAGTTTCCCTCCC--CTCTGACCTTAC----AAACCTCACCTAGCCAGGA--CAAGAGAAGGAGGT i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_51043 494 455 - 5707 CCC------ATGGCACTTGGCTCCCGAGAA-----TAGTACACAGCCTCCC--------TGGGGGAGT-------GGAGT------GTCAGCCGGG---------------------------------------------GCGCAGGCCAGCT---CTGCCCGAGAGCCGGGGACGGGGA-----------CAGGGCTTCACCTT---CTCTGCTGAGT-----GGACAGGC--------CCCTTAGACCTGTCTCCAGAAGTGAGA-CCTAAGACTCCGACCGAATCAGCCCTCTGCTGCC----------CCAAGGACGACAGCTGGAGCCTCTTCCA-----------CCAGCCAGCCCAGCACC-TCCACTGAGcctctccccccccgccccccccgtcttccccctccaccccTGCAGGCGG-------GCAGG------------------GGAGGGGGGAGCTGCTTGTTC----AGGTGTCTCCTCTCTCCACCCTCCCCTCCTTCTCTGGGCAGCCCCATC-TTTTCCAAACTAGCTCCTCTGCCGCCTTGCCCAGGCTCCCAGTTTCTCTCTC--CTCC-GGCCTCC----AAACACCCCCC---------------CCCCCCAGC i micMur1.scaffold_51043 C 0 C 0 s bosTau4.chr19 10880383 448 - 65312493 CCCCCTTGACCGGTTCTTGA-----GAAAT-----GAGATGGTGGGCTCCCATCTCGTTTGGTGGGGAG-----GACAAT------CCAAGACCAGA--------GGACA------------------GAGGGCCTGGGT-GCCCAGCTCAGCCTGGCCTCCCGTGTGATGGGGACCTTCTGTGGGCATCTTCAGGGCTTGGTTTGCTTCTATGCTAATGTACAGGGACAGACCTCATGA-CCCTCAG-TCCATCTCCAGGGCTGGGAGCCTACAGTTCTCTCTGAAGCAGC--CTGGCTGCCCCAGACCAAATCAGCAG---------------------------------------------------------------------------------------------TGCCAGTGCTCAAAG-----------GAGACGTGGGGG--CAGGAAGAGAGGTGAGCTGCCTATTGTTTCAAGAGATCTCCCTCC----TTCTACCTCCCCCTCT-GGAAGCTCATTC-TTTTCCAAAATAGCTCTTGTGCCTCCTTCCC------------TCCTGTCTC--CTCCCTGCTTCC----GGGAGCTTCAT-------GGCCAAGTCCCACCTGG i bosTau4.chr19 I 22 I 20 s turTru1.scaffold_98008 10906 439 + 223990 CCCACTTGGCCAGTTCCTGA-----GAAAC-----AGGAAAGTAGCCTCCC-------CTGTTGAGGAG-----GACAAT------CCAAGGTGGGA--------GGACA------------------GAGGGCCTGGGT-GCCTGGCCCAGCCTGGCTGCCTGGATGATGGGGACCTACCATTGGCATCTTTAGGGCTTGGTTTTCTCCTGTGCTAATGGTCAGGGATGGACCTCATGA-CCCTCAG-TCCATCTCCAGGAGTGGGAGCCTACAGTTCTGTCTGAAGCAGC--CTGGCTGCCCCAAACCAGCCCAGCAG---------------------------------------------------------------------------------------------TGCCAGTGCCCGAAG-----------GAGACATGGGGG--CAGGAGGAGAGGTGAGCTGCCTGTTGTTCC---AGATCTTCCTCC----TTCTACCTCCTCCTCCGGGAAGCTCATCC-TTTTCCAAAATAGCTCCTCTGCCTCCTTCCC------------TCCTCTCTC--CTCCCTGCTTCC----GGGAGCTCCAT-------GGCCAAGTCCCACCTGG i turTru1.scaffold_98008 I 22 I 20 s equCab2.chr11 58066629 471 - 61308211 CCT------CCGGTGCCCAA-----GAAAC-----AGGAAGGCGGCCTCCC-------CTGGTGAAGGA----GGACAGT------CTCAGGCCCAA--------GGACAGTCTCCAGCCCAgggagggagcacctgggt-acctgg-ccagcctggccacctgcgtgacggggacaagccattcgcatcttcggagcttggttttctcttctgctacggggtgaggatggacctcatgactgctcgg-tccgtctccaggagggagatcccacaattctatCTGAAGCAGC-CCTGCGGGCCCCAAACAAACAGTGGAT---------------------------------------GCTGAG--CC--------ACCG---------------------CCTCGCTGCTCCTCCCCTGCAGGAAGCAGCCGCGTAGGAGACGCGGGGG--CGGGAGGAGAGGTGAGCTGCTTATTGTTCCAGGTGATTTTCCTCT----CTCCA---CCTCCTCCGGGAAGTTCATTC-TTTTCCAAAATAGCTCCTCTGCCTCCATCCCCAGTTTGTCAGTTCGTCTCTC--CTCCCCGCTTCC--------------------------------------- i equCab2.chr11 I 5 C 0 s felCat3.scaffold_206428 47386 397 + 132007 CCCACGCGGCCAGCTTCCAG-----GAAAT-----CAGAAGGTGACCTCCC-------AGGGAGAGAGC-----GACAGT------CCAAGGCGGGG--------GGACA------------------GAGGGCCTGGGT-ACCCAGCCCAGCCTAGACACCTGCGGGGCAGGATCATGACCTTCACACCTTCAGGACTCCACTTTCTCCTCTGCTGAGGGTTGGGGACAGACCCCACAAGCCCCCAG-CCCGTCTCCAGGAGGCAGACCCCA--------------------------------------------------------------------------------------------------------------------------------------------CAGCTCTGTGTGATACA-------CTGACCCTCGGGG-----------CA-GTGGGAGGAG---------AGGTGAGCTGCCTCC----CTGCA-CTCCTCCTACAGGAAGTCCACTC-TCCTCCAGACTAGCT-CTCTGCCTCGTTCTCCAGTCAGCTAGTCTGCGTCTC--CTCCCTACTTCCTTCCAGGAGTTCCAC-------TGCCAAGTCCTGCTGGG i felCat3.scaffold_206428 I 14 I 30 s canFam2.chr9 59460548 423 - 64418924 CCCATGAGGCCAGTTCCCAA-----GAAAT-----CAGAAGGTGACCTCCC--------TGGAGAGGGCAGGCGGGCAGT------CCAAggcggga--------ggaca------------------gagggcttgggt-acctggcccagcacagccacctgtacgacagggacacaccattcacatctccaggactccactttctcctctgctaagggtgggggacaaaccccatggccccccag-cacatctccagGACA-AGATCCCAC--------CTGAAGC-----------------------CATAGGAT---------------------------------------------------------------------------------------------CGGCACTGCAGGGAGCAGCTATGTCAGACACTGGGGG-----------CACGTGAGCTGCATATTGTTTCTGGGGATTTCCCTCT----CTCCA-CTCCTCCCACAGGAAATCCACTCTTTTTCCAAACTAGCTCCTCAGCCTTGTTCCCCAGTTTGCTAGTTT--------------TGTCTGCTTCCAGGAGCTCCAT-------TGTCACGTCTTGCAGGG i canFam2.chr9 I 322 I 19 s pteVam1.scaffold_11245 35997 448 + 48268 CTCATGGGGACTGTTCACCA-----AGCACAGCCACAGGCGCTAACCTCCC--------TAGAGACAG------GACAGTGCCGCCCCTGGACGGCA--------GCCCA-------------------AGGCCCTGGG-------ACAGAGAGCAACTGCCTGCATGGAGGAGACACGCCAT---CACATTTGAGACTCGGCTGTTTCCTCTGCT--------------------ACAACCCCTCGG-CCCATCTCCAGGAGTCAGAGCCTGCCATTCCAGCTGAAGCAGC-ACCCCCCGCCCCAAACAAGCGCCGCAA---------------------------------------GGCGGGGACA--------GGCA---------------------GCCTGGTGCT-TCTCCCTGCAGGGAG-AGCTGTGTGGGAGCTGGGGCG----GGGGGGCGGGGAGGGCTGCT-GTTGCTGCAGGTGCTTGTCCGCC----TTCCG-------------GAAGTTCATTC-TTTTACAAAAGAGCCCCTCCGCCTCGCTCCCCAGTTTGCTAGCTC---TGCT--CTCCCTGCTTCC-----AGAGCTCTGT-------CA-CGAGTCCCACCTGG i pteVam1.scaffold_11245 I 20 I 4 e dasNov2.scaffold_85717 960 313 + 6675 I e otoGar1.scaffold_94362.1-287808 45071 1301 + 287808 I e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=209350.000000 s hg19.chr17_gl000204_random 73792 83 + 81310 GGAGGGAGCAGGGGA-G---GGCTTACGTTCTCAAGATGCAGAAGTACAAGCGTAGACAAAAGAGACCCCCACGGTCCC--CGTCAACC- s panTro2.chr17 79505792 83 + 83384210 GGAGGGAGCAGGGGA-G---GGCTTACGTTCTCAAGATGCAAAAGTACAAGCGTAGACAAAAGAGACCCCCATGGTCCC--CCTCAACC- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 41603 83 - 64270 AGAGGGAGCAGGGGA-G---GGCTTACGTTCTCAAGATGCAAAAGTACAAGCGTAGACAAAAGAGACCCCCATGGTCCC--CCTCAACC- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16090165 82 + 17838096 GGAGGGAGCAGGGGA-G---GGCTTATGTTCTCTAGATGCAAAAGTACAAGGGTAGAC-AAGGAGACCCCCATGGTCCC--CCTCAACC- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75064641 82 + 78773432 GGAGGGAGCAGGGGA-G---GGCTTATGTCCTCAAGATGCAAAAGCACAAGTGTAGAC-AAGGAGACCCCCATGGTCCC--CCTCAACC- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 71671 82 - 95547 GGAGGGAGCAGGGGA-G---GGCTTATGTCCTCAAGATGCAAAAGCACAAGTGTAGAC-AAGGAGACCCCCATGGTTCC--CCTCAAAC- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 74169 81 + 225949 AGAGGGAGCTGGGGA-----GACCAATGTTCTCAAGATGCAAAAGTGCAAGGGTAGAC-AAGGAGATCCCCACGGTCCC--CCTCAGCC- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 8707 81 + 21754 TGAGGAGGGAGGGAG-GTGAGGCTGATGTCCTCAAACTGCAAAAGTGCAAAGTCagcc-agg------ctcggtgtctcagcctgtaat- i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_51043 949 74 - 5707 AGGGGTAGGACGAGACA---GGATGATGTGCTCAAGCTGCAAAACTGCAA----AGTC-AAAGAGCCCTC----GTCCT--CC-CAACC- i micMur1.scaffold_51043 C 0 C 0 s vicPac1.scaffold_72280 22 71 + 3962 GGAGGGAGGGAGGTG-T---GGCT------CTCTAGCTGCAAAAATTCAAGGTCAAAC-AAAGAGCCCT-CAG-----C--TCCCAATCT i vicPac1.scaffold_72280 N 0 C 0 s turTru1.scaffold_98008 11365 69 + 223990 GGAGGGAG---GGTA-T---GGCT------CTCAAGCTGCAAAATTTCAAGGTCAAAC-GATGACCCCTCCAT-----C--CCTCAACCT i turTru1.scaffold_98008 I 20 C 0 s bosTau4.chr19 10880851 69 - 65312493 GGAGGAAG---GGTA-T---GGCT------CTCAAGCTGCAAAATTTCAAAATCAAAC-AATGACCCCTCCAT-----C--CCTCAATTA i bosTau4.chr19 I 20 C 0 s equCab2.chr11 58067100 64 - 61308211 ---GGGAG---GGCA-T---GGCT------CTCAACCAGCAAAAATTCAAGGTTAAAC-AAAGAGCCCTGG-------C--CCCCAAACC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 47813 69 + 132007 ggagggag---ggTA-T---GGCT------CGCAAGCTACAAACTTTCGAAGTCGAAC-CTGGGGCCCTGGGG-----C--CCTGAAACC i felCat3.scaffold_206428 I 30 C 0 s canFam2.chr9 59460990 69 - 64418924 GCAGGAAG---TGTA-T---GATG------CCCAAGCTGCAGAAATTCGGAGTCACAC-CAGGAGCCCTGGGT-----C--CCCCAAAAC i canFam2.chr9 I 19 C 0 s pteVam1.scaffold_11245 36449 69 + 48268 AGAGGGAG---GGGT-C---GGCT------CTCCAGCTGCAAAAACTCAAGGTCACGC-AAAGAGCCCTCCAT-----C--TCCAACCAT i pteVam1.scaffold_11245 I 4 C 0 e dasNov2.scaffold_85717 960 313 + 6675 I e otoGar1.scaffold_94362.1-287808 45071 1301 + 287808 I e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=-52266.000000 s hg19.chr17_gl000204_random 73875 69 + 81310 CCCTCACCT---------------------CTGTTTGAG-CC------CCCATCAC--TCCCCTG---GGCTGCCTCTCTC--TGCTGGCGGCAGAACAACTGC s panTro2.chr17 79505875 69 + 83384210 CCCTCACGT---------------------CTGTTTGAG-CC------CCCATCAC--TCCCCTG---GGCTGCCTCTCTC--TGCTGGCGGCAGACCAACTGC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 41686 69 - 64270 CCCTCACCT---------------------CTGTTTGAG-CC------CCCATCAC--TCCCCTG---GGCTGCCTCTCTC--TGCTGGCGGCAGAACAACTGC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16090247 69 + 17838096 CCCTCACCT---------------------CTGTTTGAG-CC------CCCATCAC--TCCCCTG---GGCTGCCTCTCTC--TGCTGGCGGCAGACCAACTGG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75064723 69 + 78773432 CCCTCACCT---------------------CTGGTTGAG-CC------CCCATCAC--TCCCCTG---GGCTGCCTCTCTC--TGCTGGCAGCAGACCAACTGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 71753 69 - 95547 CCCTCACCT---------------------CTGGTTGAG-CC------CCCATCAC--TCCCCTG---GGCTGCCTCTCTC--TGCTGGCGGCAGACCAACTGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 74250 67 + 225949 CC--CACCT---------------------CTGGGTGAG-CC------CCCATCAT--CCCCCTG---GGCTGCCTCTCTC--TCCTGGCGGCAGACCACCTGG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 8788 69 + 21754 cccgcaccttgggaggccgaggtgagtgaattgcccgag-cctgagggttcaagac---cccctg---ggcaactt---------------------------- i tarSyr1.scaffold_41848 C 0 I 362 s micMur1.scaffold_51043 1023 57 - 5707 CCCTCGCGC---------------------CCAGGTGGG-CC------CCCAC---------------GGGGGTTTCTCTC--TACTGGCG--TGACCCACGGT i micMur1.scaffold_51043 C 0 C 0 s otoGar1.scaffold_94362.1-287808 46372 67 + 287808 CCCTC-CTT---------------------CCAGGCGGGTCC------CCCACAGC--T--TCTG---GGCAGTTTCTCAC--TGCTGGCAGCTGACCCACAAT i otoGar1.scaffold_94362.1-287808 I 1301 C 0 s vicPac1.scaffold_72280 93 56 + 3962 CCCTCCCTC---------------------CC-GGTCAG-GC------TCCACATC--CCCC------GGCCGTTCTCCCC----------CAAGACCAATAC- i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 11434 51 + 223990 CCCTCCCCT---------------------CCAGGTCAG-CC------TCCATCAT--CCCCACAGCTGGC----------------------AGACCAATAG- i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10880920 27 - 65312493 ACCACCCCC---------------------TCAGG---------------------------------AGC----------------------AGACTAATAT- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58067164 47 - 61308211 TTTCCCCTC---------------------CTGC--TGG-GC------TCCAGCGGCACCCC-CG---GGCCATTCCTCCC----------------------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 47882 51 + 132007 CCGGCCCCT---------------------CTAG--TTG-GC------TTCACCATTACCCCTCA---GGCAGTTTCTCCC-------------------TGG- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59461059 72 - 64418924 CCTGCCCCT---------------------CCAGGTTGG-GC------TTCACCATAACCCCTTA---GAACATTTTTCCCCCCAGAGCTGGTGGAGCAATGG- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 36518 44 + 48268 CCTCTCC----------------------------------C------TTCCCCCGCACCCC-------------CCCCCC----GGGTTGGCAGAGC--AGA- i pteVam1.scaffold_11245 C 0 C 0 e dasNov2.scaffold_85717 960 313 + 6675 I e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=318034.000000 s hg19.chr17_gl000204_random 73944 87 + 81310 ACAGAGGCTC-TGCTCAGGCCTGCT-CCCCGCCCAAGGGTCCTCACAGCATCCCAGGCCTCAGAGAAAGCGGCTGCTTTAAGCATTTAA s panTro2.chr17 79505944 87 + 83384210 ACAGAGGCTC-TGCTCAGGCCTGCT-CCCGGCCCAGGGGTCCTCACAGCATCCCAGGCCTCAGGGAAAGCGGCTGCTTTAAGCATTTAA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 41755 87 - 64270 ACAGAGGCTC-TGCTCAGGCCTGCT-CCCGGCCCGAGGGTCCTCACAGCATCCCAGGCCTCAGAGAAAGCGGCTGCTTTAAGCATTTAA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16090316 87 + 17838096 ACAGAGGCTC-TGCTCAGGCCTGCT-CCCAGCCCAAGGGTCCTCACAGCATCCCAGGCCTCAGAGAAAGTGGCTGCTTTAAGCATTTAG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75064792 75 + 78773432 ACAGAGGCTC-TGCTCAGGCCTCCT-CCAGG------------CAAAGCATCCCAAGCCTCAGAGAAAGGGGCTGCTTTAAGCATTTAG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 71822 76 - 95547 ACAGAAGCTC-TGCTCAGGCCAGCT-CCAGGC-----------CAAAGCATCCCAGGCCTCAGAGAAAGGGGTTGCTTTAAGCATTTAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 74317 86 + 225949 ACAGAGGCTC-TGCTCAGGCCTGCT-CCCTGCCCAAGGGTCCCCACAGCATCCCAGGGCTCAGGGAAAGGGGCTAC-TTGAGCATTCAG i calJac1.Contig5139 C 0 I 288 s tarSyr1.scaffold_41848 9219 86 + 21754 ACAGAGCCTG-CAATCAGGCTTACT-CCCTGGCTCAAGGGACTCACATCATCCCAGACCACAGAGAAAAAGGTTGC-TTAAGCATTTAG i tarSyr1.scaffold_41848 I 362 C 0 s micMur1.scaffold_51043 1080 75 - 5707 --GGAGCTCTGTGCT-GGGCCTGCT-CCCTGCTCAAGGG--------GCA-CCCAGGCCCCAGAGACAGGGGCTGC-CTGAGCGTCGAC i micMur1.scaffold_51043 C 0 C 0 s otoGar1.scaffold_94362.1-287808 46439 68 + 287808 --AGAGCCTGGTGCTCAGGCCTGCT-GTCTGCTCTAGGGTCCCCACAGTA-CCCAGGCCTCAGAGACAGGGG----------------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s vicPac1.scaffold_72280 149 73 + 3962 CAAG------------AGGCCAGCT-CCCTGCTCCAGGGCCCTCGCAGAG-CCCAGTCCCCA-GAGAAAGGGTCAC-TTGAGCATTTAG i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 11485 86 + 223990 AAGGAGGCTTGTTCTCAGGCCAGTTCCCCTGTTCCATGGTCCTCACAGTG-CCCAGTCCCCA-GAAGAAGGGTCAC-TTGAGCATTTAG i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10880947 86 - 65312493 AAGAAGCCTTGTTCTCAGGCCAGCTCCCCTGCTCCAGGGTCCTCACAGTG-CCCAGTACCGA-GGAAAGGGATCAT-CTGAGCATTTAG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58067211 77 - 61308211 --------TTGTCCTCAGGCCTGTTCCCCTGCTTAAGGGTCCTTGCAGCA-CCCAACCACGG-AGAA-AGGGTTGC-TTGAGCATTCAG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 47933 84 + 132007 AGAGAACCTTGTTCTCGGGCCTG--CCCCTGCCCCAGGGTCCCGGCTGTA-CCCAGTCCCCA-AGAACCGGGGAAT-TTGAGCATTTAG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59461131 81 - 64418924 AGACAATCTTGTTCTCAGATCTG--CCCCTGCTCAAGGGTCCTTGCTGTG-CCCCGTCCCC----AACAGGGCTGC-TTGAGCAACTAG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 36562 85 + 48268 GGACAGCCTCGTTCTCAGGCCTGCTGCCCTGCTCAAGGGACCCTGAGGCA-CCCAGTCCCCGCAGAACTGGGCTG---TGAGCATGCAG i pteVam1.scaffold_11245 C 0 C 0 e dasNov2.scaffold_85717 960 313 + 6675 I e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=290324.000000 s hg19.chr17_gl000204_random 74031 85 + 81310 AAG-CTC-CTACAGGCTCAACTCCCCCTCCTCTG--TTCCAGGACCCCCAACTCCAAACAAACAGGTGTGCTGATCTATGCTTGAC-------CAG s panTro2.chr17 79506031 85 + 83384210 AAG-CTC-CTACAGGCTCAACTCCCCCTCCTCTG--TTCCAGGACCCCCAACTCCAAACAAACAGGTGTGCTGATCTATGCTTGAC-------CAG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 41842 85 - 64270 AAG-CTC-CTACAGGCTCAACTCCNCCTCCTCTN--TTCCAGGACCCCCAACTCCAAACAAACAGGTGTGCTGATCTATGCTTGAC-------CAG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16090403 85 + 17838096 AAG-CTC-CTACAGGCCCAACTCCCCCTCCTCTG--TTCCAGGACCCCCAACTCCAAACAAACAGGTGCGCTGATCTATGCTTGAC-------CAG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75064867 84 + 78773432 AAG-CTC-CAACAGGTTCAACTCCCCCTCCTCTG---TCCAGGACCCCCAACTGCAAACAAACAGGTGTGCTGACCTATGCTTGAC-------CAG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 71898 84 - 95547 AAG-CTC-CAACAGGCTCAACTCCCCCTCCTCTG---TCCAGGACCCCCAACTGCAAACAAACAGGTGTGCTGACCTATGCTTGAC-------CAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 74691 85 + 225949 AAG-CCC-CTACAGGGTCAACTCCCCCTCCTCTG--CTCCAGGACCCCCAGCTTCAAACAAACAGGTGTGCTGACCTACGCTTGAG-------CAG i calJac1.Contig5139 I 288 C 0 s tarSyr1.scaffold_41848 9305 84 + 21754 AAG-CCC-CTGCAGGCTCAACTCCCCCTTCTCTG--TTCAAGGTCCCCCA-CTCCAAAGGGACAGGTGCACTGACTCATGCTTGAC-------CAG i tarSyr1.scaffold_41848 C 0 I 5 s micMur1.scaffold_51043 1155 84 - 5707 AGGCCCC-CCCCAGACTCACCT-CCCCTGCTCTG--CTCCGGGGCCCCT-GCTCCACGAGGTCAGGTGCACTGAGCTTTGCTCGAC-------CGG i micMur1.scaffold_51043 C 0 C 0 s otoGar1.scaffold_94362.1-287808 46507 71 + 287808 ----ACC-CGGTGGGCTCAGC--CCCCAGCTCTG--CTCCA---------GTTCCACATGATTGGGTGTGCTGAACTTCTCCTGAC-------CAG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s vicPac1.scaffold_72280 222 84 + 3962 AAG-CCC-CTGCAGACCTGCCTCCTCCAGCCCTGCTCCTCTGGGAGCCAGACTCCAAACAG---AGGGAGCTGATCTCTCCTTCGC-------CAG i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 11571 77 + 223990 AAG-CTC-CTACAGACTTGCCTCCCCCTGCCCTG--GCTTGGGAAGCCCAACTCCAAATGA---AGT--GCTGACCTTCCT---GG-------CAG i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10881033 79 - 65312493 AAG-CCC-ATACACACTTGCCTCTTCCTGCTCT---GCTGGGGGAGCCCGACTCCAAATGG---AGT--GTTGACCTTTCCTTGGC-------CAG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58067288 81 - 61308211 AAG-CCCACAGACTCCCTCCCGCCGTCCT-------GCTCAGGGAGCCCCGCTCCAAACGGACAAACATGCTGGCCTTTCCCTGTC-------CAG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 48017 67 + 132007 AAG-CCCCCTGCAGATGTACCTCCCCCT-----------------GCCCAGCTCCAAAAAG---AAC-TAGTGACCTTTCCTTGGC-------CAG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59461212 75 - 64418924 AAG-CCCCCAGCAGACCTCCCTCCCTCT-----------------GACCAGCTCAAAATAG---AACACATCGACCTCTCCTTGGCTGGGTGGCAG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 36647 75 + 48268 AAG-CCC-CTGCGGACTTGCCT------------------GGGGAGCCGGACTCCAAAAGGAGGGATGTGCTGACCTTTCCTTGGCCATGTG-TGG i pteVam1.scaffold_11245 C 0 C 0 e dasNov2.scaffold_85717 960 313 + 6675 I e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=44858.000000 s hg19.chr17_gl000204_random 74116 79 + 81310 GCCGGAGCCCTGGTCCCCAGCTGCCCTTGGCTCAAGTCACCCTCCCAGCCTAGCACATCCTTCTG----TTCC--CCACC-------------CCAAA s calJac1.Contig5139 74776 78 + 225949 GCCAAAGCCCTGGTCCCCAGCTGCCCTTGGCTCAAGCCAGCC-CTCAGCCAGGCACATCCTCCTG----TTCC--CCACC-------------CCAAA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 71982 79 - 95547 GCCGGAGCCCAGGTCCCCAACTGCCCGTGGCTCAAGGCACCCTCCCAGCCTCACACATCCTCCTG----TTCC--CCACC-------------CCAAA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75064951 79 + 78773432 GCCGGAGCCCAGGTCCCCAACTGCCCGTGGCTCAAGGCACCCTCCCAGCCTCACACATCCTCCTG----TTCC--CCACC-------------CCAAA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16090488 79 + 17838096 GCCGGAGCCCTGGTCCCCAACTGCCCTTGGCTCAAGTCACCCTTCCAGCCTGGCACATCCTTCTG----TTCC--CCACC-------------CCAAA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 41927 79 - 64270 GCCGGAGCCCTGGCCCCCAGCTGCCCTTGGCTCAAGTCACCCTCCCAGCCTAGCACATCCTTCTG----TTCC--CCACC-------------CCAAA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79506116 79 + 83384210 GCCGGAGCCCTGGTCCCCAGCTGCCCTTGGCCCAAGTCACCCTCCCAGCCTAGCACATCCTTCTG----TTCC--CCACC-------------CCAAA i panTro2.chr17 C 0 C 0 s micMur1.scaffold_51043 1239 58 - 5707 GCCGTGGTCC------------------TGCTCCAGCCACTC--CCAGCCCGGCGTGTCCTCCTG----TGCC--C-ACC-------------CTGGA i micMur1.scaffold_51043 C 0 C 0 s otoGar1.scaffold_94362.1-287808 46578 74 + 287808 GCCGTGGTCCTGCACCCCAACCTGCCCTTGCTCCAGCCATCC--CCAGCCT-GTGTGTCCTCCTG----TGCC--T--CC-------------CTGGA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s vicPac1.scaffold_72280 306 47 + 3962 ------GCCGAGGCC-C-------------------------TGCCCACCCAGAGGCCTCACCTC----TGCCCGCCCCC-------------CTC-- i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 11648 46 + 223990 ------GCTGTGGCCCC-------------------------TGCCCACCCAGAGGGTCCTCCTC----TGCC--CCCCA-------------CCA-- i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10881112 44 - 65312493 ------GCTGTGGCCGC-------------------------TCCCAACCTGGAGGGTCCTCCTC----TG----CCCCA-------------ACA-- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58067369 51 - 61308211 ------GCCCTGTCCCC---------------------ATCCTGCCCACC-AGAGGGTCCTCCTC--TGCATC--CCCCT-------------GGA-- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 48084 46 + 132007 ------CCCCCGTCCCC---------------------GTCCCACCCACCAGGAGGGTCCT------GGTGGC--CCCA---------------GA-- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59461287 55 - 64418924 ------TCCCCGTCCCCA--------------------GCCCCCCCCACCTAGAACCCCCCCCCCCAAGGAGC--CCCAC-------------CCC-- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 36722 63 + 48268 ------TCTCCATGCCC---------------------ATCCCACCCACCTGGAGAGTCCACCTC----TGTC--CCCACTCCCCTCCTATAAGAA-- i pteVam1.scaffold_11245 C 0 C 0 e tarSyr1.scaffold_41848 9389 5 + 21754 I e dasNov2.scaffold_85717 960 313 + 6675 I e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=373816.000000 s hg19.chr17_gl000204_random 74195 62 + 81310 CAAGGACAGACCTA-GGGATG----ACCAACCCCGGCC---------------------------TGGCCCCAATGCGCCTCCTGCTCAGACCT s panTro2.chr17 79506195 62 + 83384210 CAAGGACAGACCTA-GGGATG----ACCAACCCCGGCC---------------------------TGGCCCCAATGCGCCTCCTGCTCAGACCT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 42006 62 - 64270 CAAGGACAGACCTA-GGGATG----ACCAACCCCGGCC---------------------------TGGCCCCAATGCACCTCCTGCTCAGACCT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16090567 62 + 17838096 CAAGGACAGACCTA-GGGATG----ACCAACCCCGGCC---------------------------TGGCCCCAGTGCGCCTGCTGCTCAGACCT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75065030 62 + 78773432 CAAGAACAGACCTA-GGGATG----ACCAGCCCCGGCC---------------------------TGGCCCTGATGCGCCTCCTGCTCAGACCT i rheMac2.chr16 C 0 M 214 s papHam1.scaffold8336 72061 62 - 95547 CAAGAACAGACCTA-GGGATG----ACCAGCCCCGGCC---------------------------TGGCCCTGATGCGCCTCCTGCTCAGACCT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 74854 62 + 225949 GAAGGACAGGCCTA-GGGGTG----ACCAACCCCAGCC---------------------------TGGCCCTGATGCGCCTCCTGCTCAGACCT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 9394 61 + 21754 CAAGGACAGGCCTA-GGGATG----ACAAACCACA-CC---------------------------TGGCTCTGATGCACCTTCTGCTCAGCTAC i tarSyr1.scaffold_41848 I 5 C 0 s micMur1.scaffold_51043 1297 59 - 5707 CACGAA-GGGCCCA-GGGATG----ATCTGCCCTGGCC---------------------------TGGCCCTGACGCACCTCCTGCTCAGCT-- i micMur1.scaffold_51043 C 0 C 0 s otoGar1.scaffold_94362.1-287808 46652 58 + 287808 CAGGAATGGGCCTG-AGGCCG----ACCCACCTGAGGT---------------------------C--CCCGGATGAGCCACCTGCTCAGCT-- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s vicPac1.scaffold_72280 353 86 + 3962 CAAGGCCAGGCCTA-GGAATGGTCAACCAACACTGGCCAAGTACTTTGGACCCCACAC-------GGACCCTGACGTGCCCTTTGCTCAGCTTT i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 11694 87 + 223990 CAAGGACAGGCCTAGGGGATAGTCAACCAACCTGGGCCAAGCACTTTGGACCCCACAC-------TGACGCAGATGTGCCCTCTGCTCAGCTTT i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10881156 93 - 65312493 CAAGATCAGGCCTA-CGGATGGTCAACCAACCTTGGCCAATTACTTTGGACCCCACACTGACCCTTGACCCAGATGCGCCCTCTGTTCAGCTTT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58067420 88 - 61308211 CAATGACAAGCTGA-GGGATG----ATCAACCCTGGCCGAGTGCTTCAGACCCCATGCTG-CCCCTGGCGCAGACACACCTTCTGGTCATCTTC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 48130 89 + 132007 CAAGGACAGGCTGA-GGGACT----ACCGACCCTGGCCGAGCACTTTGGACCCCATACTGACAACCGGCCCAGATGTGGCCCCTGCTCAGCTTT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59461342 89 - 64418924 CAAAGACAGGCCAA-GGGATG----ACGGACCCTGGACGAGCACTGTGGACCACGTGCTGACCCCTGGCCTAGATGTGCCCTCTGCTCAGCCTT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 36785 88 + 48268 CAAAGACAGGCCTA-GGGATG----ACCAACCC-GGCCAATCACTTTGGACCCCACGCTGACTGCTGGCCCAGATGTGCCCTCTGCTCAGCTTT i pteVam1.scaffold_11245 C 0 C 0 e dasNov2.scaffold_85717 960 313 + 6675 I e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=548718.000000 s hg19.chr17_gl000204_random 74257 185 + 81310 CTGCAAAC-CTGAT--CGTTTCC-C--------CCTCGAAGACTCCCCTGGATTGTGGGACACCAGTTCTGATCTGAGATCTTAGGGCTAACACAGGAAATTAGGGGATGGGTGCATAGATGCAA-TCC-----CTGCTTCATCACAAGGCCGCAGAGTCCTTGTCTGCCATGACGTGCCCGGGTTTAGA--CTGA----AGAGGCAGG- s ponAbe2.chr17_random 16090629 185 + 17838096 CTGCAAAC-CAGCT--CGTTTCC-C--------CCTCGAAGGCTCCCCTGGACTGAGGGACACCAGTTCTGATCTGAGATCTTAGGGCTAACACAGGAAATTAGGGGATGGGTGCACAGATGCAA-TCC-----CTGCTTCATCACACGGCCACAGAGTCCTTGTCTGCCATGACGTGCCCGCGTTTAGA--CTGA----AGAGGCAGG- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 42068 185 - 64270 CTGCAAAC-CGGCT--CGTTTCC-C--------CCTCGAAGACTCCCCTGGACTGTGGGACACCAGTTCTGATCTGAGATCTTAGGGCNAACACAGGAAATTAGGGGATGGGTGCATAGATGCAA-TCC-----CTGCTTCATCACACGGCNGCAGAGTCCTTGTCTGCCATGACGTGCCTGGGTTTAGA--CTGA----AGAGGCAGG- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79506257 185 + 83384210 CTGCAAAC-CAGCT--CGTTTCC-C--------CCTCGAAGACTCCCCTGGACTGTGGGACACCAGTTCTGATCTGAGATCTTAGGGCTAACACAGGAAATTAGGGGATGGGTGCATAGATGCAA-TCC-----CTGCTTCATCACACGGCCGCAGAGTCCTTGTCTGCCATGACGTGCCCGGGTTTAGA--CTGA----AGAGGCAGG- i panTro2.chr17 C 0 C 0 s papHam1.scaffold8336 72123 185 - 95547 CTGCAAAC-CAGCT--CACTTCC-C--------CCTCGAAGACTCCCCTGGACTGTGGGACCCCAGTTCTGATCTGAGATCTCAGGGCTAACACAGGAAATTAGGGGATGGGTGCATAGATGCAA-TCC-----CTGCTTCATCACACGGCCACAGAGTCCTTGTCTGCCACGACGTGCTCGGGTTTGGA--CTGA----AGAGGCAGG- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 74916 182 + 225949 CTGCAAAC-CAGCT--CATTTCT-C--------CGTCAAAGACTCCCCTGGACTGTGGGACCCCAGCTCTGATCTGAGCTCTCAGGGCTGACACAGGAAATTA-GGGATGGGTG---AGATGCAA--CC-----CTGGTTCATCCCATGGCAACAGAGTCCTTGTCTGCCATGACATGCCGGGGGTTAGACTCTGA----AGGGGCAGG- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 9455 189 + 21754 CTACAAAC-CAACTGGCTTTCCC-C--------CTTCACAGACTCTTCCAGACTCTTGGATCCCACTTTTGATCTGGGACCTCAGGGCTAGCACAGCAAATTAAGAGCTAGGTACATGGGTACAA-TCC-----TTGCTTCGCCACACGTGGACAGAGTCCTTTTCTTTCGTGACATGCCACAGACCAGATTCTGA----AGGGACAGG- i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_51043 1356 177 - 5707 CTGAAAAC-CAGCC--GG-------------------GCAGACTCCCCCAGACTGGGGGACCCCACTTCTGCTCTGGGACCTCAGGGGCGACACAGGAAGTCAGGGGCTAGGGACGCGGGTGCTA-TTC-----TTGCTTCGTCACTTGCCAGCAGAGTCCTTGGCTGTCACGAGAGGCCCCGGAACAGCCTCTGA----AGCAGCAGG- i micMur1.scaffold_51043 C 0 C 0 s otoGar1.scaffold_94362.1-287808 46710 154 + 287808 CTGCAAA--CAGCT--GGTTTCC-C--------CA--GCAGACT-TCTTAGATCATGAAACTCCTACTCTGACCTGGGAT-----------------------GGGGT-----ATATGGGTGTGA-CCC-----CTGCTTAATCTCCTGCCAGCAGAGTCCTCGGCAG-CAGGAAACACCCTAGAACAGTCTCTGA----AGCTGCAGC- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s vicPac1.scaffold_72280 439 187 + 3962 CTGCAAGCTCACCT--CATTCCC-CACCCCAC-CCCCGCAAACTCCCTTGGACAGTGAGACCC--ATTCTGACCTGTGACATCAGGGCTAATACAGCAAGCCAGGGGCCGGGTGCACC-ATGCAACTTC-----CACTCCC-TCGCAAGTCGGCAGAGATCTTGCAGGTCACGACACATCACAT----GA--CTGG----ACTGGCCAAG i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 11781 186 + 223990 GTGCAAACCCAGCT--CATCTCC-CCCCCCACCCCCTGCAAACTCCCA-GGACAGTGAGACCC--TTTCTAAT------CTTCAAGGCTAACAAAGCAAACCAGGGGCCCGGTACACCAATGCAATTTC-----CTGCTCC-ATGCAAGTCAGCAGAGTCCTTGGCAGTCATGACACACCACATATCAGG--CTGA----AGTGGCCAGG i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10881249 178 - 65312493 CTGCAAACCCAGCT--CACTCCC-CACTCATCTCTCCGCCAACTCCCCTGGACAGTGAGACTC--ATTCTGATCTGTGACTTCAGGGCTAACACAACAAACCAACGGCCCAGTGCACCAATGCAATTTC-----CT----------------GCAGAATCTTTGGCAGTCGTGACACACCACATATCAGG--CTGA----AGTGGCCGGG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58067508 185 - 61308211 CTGCGATCCCAGCT--CATTTTGTC--------CCCTGCAAACTCCACTCAACAGTGGGACCT--GTTCTGA-CTGGGACCGGCGGGCTAACAAAGGAAGCCAGGGCC-ACGTGCACGGATGCAATTCC-----AGGCTCCATCGCAAGTGGGCAGAGGCCTTGGCAGTCCTGACACACCACATGTCAGC--CTGA----AGTGGCCGGG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 48219 169 + 132007 CGGCAGACCCAGCT--TGTCCTG-C--------CCCCATACGCTCCCCTGGACAGTGGGGCCG--GGGCTGACCCGTGACCTCAGGGCAGACACAGCAGCCTGGACGT-GGGTGC---------GTCCCCCACTCTGCTGCGTCGCAGGCGG-CAGAGTCCCAGGCAGTGATGAC-----------CAGG--CTGA----AGTGGCTGGC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59461431 174 - 64418924 CTACAGACCCAGC---TGTGCTG-C--------TGCTGCAGACTCCCCTGGACAGAGGAGCCC--GTGCTGATCCGCGACCTCAGGGCTGACACAGCAAGCCAGAAGC--GGTGC---------GTTCC-----CTGCTCCATCGCAAGCTGCCGGAGCCCCAGGCAGTCATGACACACAACACATCAGG--CTGA----AGTGGCTGGG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 36873 159 + 48268 CTGCAAACCCAGC---ATTCCCG-C--------CCCCGCAAACTCCCCTGGG-AGGGGGATCC--CATTTGATCTGTGAGCTTAGGG----------AGCCAGGGGCC-AGGCACACGGATCCAGTTCC-----CAGCTCCTTCGCAGGTCA---------CACGCA--CCTGACACAT-------CAGA--CTGAATGCAGCGACCAGG i pteVam1.scaffold_11245 C 0 C 0 e dasNov2.scaffold_85717 960 313 + 6675 I e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I e rheMac2.chr16 75065092 214 + 78773432 M a score=569832.000000 s hg19.chr17_gl000204_random 74442 102 + 81310 AGCTGGGGCCAGCGAGGGGAG--CCCTGAA------C------TCCATTCCttttaattgaggcgaaatttatataacataaaagtagcca----------------tttaaagtgtg--------------------------------caattg----aggggcac s pteVam1.scaffold_11245 37032 85 + 48268 AGCAGGGGCCAGCGAGGCGAA--CCTTCTG------C----------Cttttttaaattgaggtgaaattcccataac--agattgaacgg---------------ctttcaagtggc----------------------------------ac-------------- i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59461605 106 - 64418924 AGC-AGGGCCAGCAAGGACAG--CCTTGTG------C--TGCTTTTTTtttttttaattgaggtgaaatttgcacaacatagaattaacca---------------ttttaaagtgca--------------------------------tgactc----agtagcat i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 48388 159 + 132007 AGC-AGGGCCAGCGAGGACAG--CCCTGTC------CCTTTTTTTTTTtttttttaattgaggtgaaattcacataacatagaattagccatttgatgttttatttttttaatgtgtatttatttttgacagagagacggagacagagcctgacctgaggaggggcac i felCat3.scaffold_206428 C 0 I 287 s equCab2.chr11 58067693 108 - 61308211 AGCAAGGGCCAGCCAGGAGAA--CCTTGTG------C-TTTTTTTCTCtttttttaattgagatgaagttcccataacacagaattaacca---------------ttttaaagtgtg--------------------------------caattc----ggtgccat i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10881427 100 - 65312493 AGCAGGGAACAGCCAGGAAAA--CCTTGTG------C---------CTttttttaaactaagatgaaattcacataacctagaattaacca---------------ttttaaagtgtg--------------------------------cagttc----agtgctat i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 11967 102 + 223990 AGCAGGGGCCAGCCAGGAGGA--CCTTGTG------C-------TTTTtttttttaattgagatgaaattcacataacataaaattaacca---------------ttttaaagtgcg--------------------------------caattc----agtgccgt i turTru1.scaffold_98008 C 0 C 0 s vicPac1.scaffold_72280 626 100 + 3962 AGCAGCGGCCAGCCAGGAGAA--GCTTGCG------t---------ttttcaaaaacttaagatgaaattctcgtaacatagaattaacca---------------ttttaaagtgtg--------------------------------cgagtc----agtgccat i vicPac1.scaffold_72280 C 0 C 0 s panTro2.chr17 79506442 102 + 83384210 AGCTGGGGCCAGCGAGGGGAG--CCCTGAA------C------TCCATTCCTTTTaattgaggtgaaatttatataacataaaagtagcca----------------tttaaagtgtg--------------------------------caattg----aggggcac i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 42253 102 - 64270 AGCCGGGGCCAGCAAGGGGAG--CCCTGAA------C------TCCATTCCttttaattgaggtgaaatttatataacataaaagtagcca----------------tttaaagtgtg--------------------------------caattg----aggggcac i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16090814 102 + 17838096 AGCTGGGGCCAGCGAGGGGAG--CCCTGAA------C------TCCGTTCCttttaattgaggtgaaatttatataacgtaaaagtagtca----------------tttaaagtgtg--------------------------------caactg----aggggcac i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75065306 102 + 78773432 AGCTGGGGCCAGTGAGGGGAG--CCCTGCG------C------TCCCTTCCTTGTaattgaggtgaaatttatataacataaaagtaacca----------------tttaaagtgtg--------------------------------caatgc----agtggcac i rheMac2.chr16 M 214 C 0 s papHam1.scaffold8336 72308 102 - 95547 AGCTGGGGCCAGTGAGGGGAG--CCCTGCA------C------TCCCTTCCTTGTaattgaggtgaaatttatataacataaaagtaacca----------------tttaaagtgtg--------------------------------caattc----agtggcac i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 75098 100 + 225949 AGCTGGGGCCAGCAAGGGGAG--CCCTGCA------C------T--GTttcttttcatggaggtaaaatttatattacataaaagcagcca----------------tttaaagtgtg--------------------------------caattc----accggcac i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 9644 108 + 21754 AACAGGGGCCAGCAAGGAAAG--CCCTGCAGATTTGT------TTTGTttttttaaattgaggtggaatttatataacatggagctggcca----------------tgtaaagtgtg--------------------------------caattc----agtggcac i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_51043 1533 101 - 5707 AACAGCGGCT-GCGAGGGGAGCCCCCTGC-------C------CGGGttt-ttctaactggggtgaaatttacataacataaaattgccca----------------tttaaagagca--------------------------------ggattc----ggaggcac i micMur1.scaffold_51043 C 0 C 0 s otoGar1.scaffold_94362.1-287808 46864 100 + 287808 AACAGTGGCC-GCAAGGAGAG--CCCTGCA------C------TGAGttt-ttttaactggtgtgaaattcatatagcatggaagtaccca----------------tttaaagagtg--------------------------------ccattc----cgaggcac i otoGar1.scaffold_94362.1-287808 C 0 C 0 s dasNov2.scaffold_85717 1273 85 + 6675 -----------------GGAG--CTCTGTG------C------TTCTCTTTTATTCAC-GACCtaaaactctcataacataaaactggccc---------------ttttgcagggta--------------------------------caattc----ggcgtcat i dasNov2.scaffold_85717 I 313 C 0 e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=502794.000000 s hg19.chr17_gl000204_random 74544 209 + 81310 tcggtgcattcacaatgttttgtagccagcacctctatcttgctgca----ccttccatcat---cccagaaggaaagaccttacccatgaggcagcaattccctgt--ctc--ccACCACTGG-ACTTTGTGTTTTCTTGGAAAGCTTTTGATCCGAGTGCCAATCTGCCCTCCAGAAAGGCAGATTGTCTATTTGATGATAAATAGAC-AAAAGGCAACT s otoGar1.scaffold_94362.1-287808 46964 153 + 287808 tcagcacgctccccacatcacacagccgtcatcttcaccaagctccaaagcatctccatcac---cccaaaaggaaactctgtccccacgaagcagcccctccctg---cct--ccacctcTGT-GCTTC-TGTT----------------------------------------------------------TTTGATATTAAATAAAC-AAAACACGATT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_51043 1634 156 - 5707 tcagtacaggcacagcgtcccacagctgtctcctctatctagctccagagcgtctccaccac---cccaaaagcaaaccctgtacccactaagcagccactccctgtccccc--TCACCACTAT-GCTTT-TGGT----------------------------------------------------------TTTGATATAAAATAAAT-AAAATGCCATT i micMur1.scaffold_51043 C 0 C 0 s tarSyr1.scaffold_41848 9752 157 + 21754 ccaatacattcaccatgttgtgcaactgtcacctctatcttgttccaaagcatttccatcat---cccaagagaaaaccctgtccccattaagctgccactccctgt--cccctccaccagcGT-GCTTTTTGTT----------------------------------------------------------TTTGATGAGACATAGAT-AAAATGCAACT i tarSyr1.scaffold_41848 C 0 C 0 s calJac1.Contig5139 75198 151 + 225949 tcggggccttgaccatggtgtgcagccagcacctccatcttcctgca----ccttccatcat---ccccgaaggaaagaccccacctatgaggcagccattccctgc--ctc--ccACCACTGG-GCTGTTTGTT----------------------------------------------------------CGTGATGATACATAGAC-AGAAGGCAACC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 72410 151 - 95547 tcggtgcatgcacagtgttgtggagctagcacctctatcttgctgca----ccttccatcat---cccagaaggaaagacctgactcatgaggcagcaactccctgt--ctc--ccACCACCGA-ACTTTTTGTT----------------------------------------------------------TTTGATGATAAATAGAC-AAAAGGCAACA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75065408 151 + 78773432 tcggtgcatgcacagtgttgtggagctagcacctctatcttgctgca----ccttccatcat---cccagaaggaaagacctgactcatgaggcagcaactccctgt--ctc--ccACCACCGA-GCTTTTTGTT----------------------------------------------------------TTTGATGATAAATAGAC-AAAAGGCAACA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16090916 209 + 17838096 tcggtgcattcacaatgttgtgtagccagcacctctatcttgctgca----ccttccatcat---cccagaaggaaagaccttacccatgaggcagcaattccctgt--ctc--ccACCACTGG-ACTTTATGTTTTTTTGGAAAGCTTTTGATCCGAGTGCCAATCTGCCCTCCAGAAAGGCAGATTGTCTATTTGATGATAAATAGAC-AAAAGGCAACC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 42355 209 - 64270 tcggtgcattcacaatgttttgtagccagcacctctatcttgctgca----ccgtccatcat---cccagaaggaaagaccttgcccatgaggcagcaattccctgt--ctc--ccACCCCTGG-ACTTNGTGTTTTCTTGGAAAGCTTTTGATCCGAGTGCCAATCTGCCCTCCAGAAAGGCAGATTGTCTATTTGATGATAAATAGAC-AAAAGGCAACT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79506544 209 + 83384210 tcggtgcattcacaatgttttgtagccagcacctctatcttgctgca----ccttccatcat---cccagaaggaaagaccttacccatgaggcagcaattccctgt--ctc--ccACCACTGG-ACTTTGTGTTTTCTTGGAAAGCTTTTGATCCGAGTGCCAATCTGCCCTCCAGAAAGGCAGATTGTCTATTTGATGATAAACAGAC-AAAAGGCAACT i panTro2.chr17 C 0 C 0 s vicPac1.scaffold_72280 726 128 + 3962 ttagcacgttcacagtatagtgcgactgtcaccactgcct--------aacgtttccat--------caaaaggagaccctgtgcccaccaagcagcc-------tag-ccc--ccaACCCTGTGGTTT----------------------------------------------------------------TTTGATAGTAAATGAGTAAAAATGC---- i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 12069 150 + 223990 ttagcacattcacaatattgtacaaccatcaccactatctagttccaaaacgtttccatcat---cccaaaaggagaccctgtacccaccaagcagccactccctact-ccc--ccAGCCCTGT-GCTT----------------------------------------------------------------TTTGATGTTAAATGAAT-AAAATGCAAAT i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10881527 150 - 65312493 ttagcacattcacaatattgtgcaaaaataacccctatctagttccaaaacatttccatcac---cccaaaaggagaccctgtgcccacccagcagccacttcttttt-ccc--ccAACCCTGT-GCTT----------------------------------------------------------------TTTGATGCTAAATGAAT-AAAATGCAAAT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58067801 147 - 61308211 tcagtacattcacaggactgtgccaccatcactactatctagttccaaaccat---tgtcattaccccaaagggagaccctgtgcccactgaggag---ccctctatt-gcc--cTCACCGGGT-GCTT----------------------------------------------------------------TTTGACGTCAAACGAAT-TAAATGCAATT i equCab2.chr11 C 0 C 0 s canFam2.chr9 59461711 147 - 64418924 ctagaaccttcacaagattgtgcaaccatcacc-ctatctggttccaagacatctctgtcat----ccaaaaggagacgttgtacccactaggcagacactccctgtt-ccc--cGACTCCTGT-GCTT----------------------------------------------------------------TTTGATG-CAGGTGAAT-AAAATACAATT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 37117 113 + 48268 ttggcgcgttgacgttactgcataaccat--ccactatctgattccgaaacacccccagcgc----ccgtgaaggggccccacgcc--ccgagcag-------ccact-ccc--cGCCCCATGC-CACT----------------------------------------------------------------ACT-------------------------- i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_85717 1358 147 + 6675 tcaacgcattcgccacgttcatgccccatcaccgccacctagttccaca--tcgtccgccct---cccag-agtggacctcacgctcaccgggcagtcgccgtcccct-cct--ccGGTCCTTT-GCTT----------------------------------------------------------------TTGGATGTGAAGGGACT-AAAACTCAGGC i dasNov2.scaffold_85717 C 0 C 0 e felCat3.scaffold_206428 48547 287 + 132007 I e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=142711.000000 s hg19.chr17_gl000204_random 74753 40 + 81310 TTCTCCTATTATTCTTGC-TTC--ACAGCACCGG-CCC--TT-TGGA s otoGar1.scaffold_94362.1-287808 47117 42 + 287808 TGCCACTATTATTCTTGC-TCC--AAAGCCTCGG-CCCCTTT-TTGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_51043 1790 40 - 5707 CACTCCCATCG-TCTTGC-TTC--AAAGCCTCAG-CCCC-TT-TTGC i micMur1.scaffold_51043 C 0 C 0 s tarSyr1.scaffold_41848 9909 40 + 21754 TGCTCCT-TTTTTTTTGC-TTC--AAAACACCAGTTCC--TT-TTGA i tarSyr1.scaffold_41848 C 0 C 0 s calJac1.Contig5139 75349 40 + 225949 TTCCCCTATTATTCTTGC-TTC--ACAGCACCAG-CTC--CT-TGGA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 72561 40 - 95547 TTCTCCCATCATTCTTGC-TTC--ACAGCACCAG-CCC--TT-TGCA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75065559 40 + 78773432 TTCTCCTATCATTCTTGC-TTC--ACAGCATCAG-CCC--TT-TGCA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16091125 40 + 17838096 TTCTCCTATTATTCTTGC-TTC--ACAGCACCAG-CCC--TT-TGGA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 42564 40 - 64270 TTCTCCTATTATTCTTGC-TTC--ACAGCACCGG-CCC--TT-TGGA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79506753 40 + 83384210 TTCTCCTATTATTCTTGC-TTC--ACAGCACCGG-CCC--TT-TGGA i panTro2.chr17 C 0 C 0 s vicPac1.scaffold_72280 854 34 + 3962 ----------ACTTTTGC-TCCCAAAAGCACTGG-TGCT-TTCCTGA i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 12219 41 + 223990 TGCTTCTACTATTCTTGC-TCC--AAAGCACTGG-TGCT-TT-TTGA i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10881677 41 - 65312493 TTTTCCTACTATTCTTGC-TCC--AAAGCATTGG-CGCT-TT-TTGA i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58067948 40 - 61308211 TGTTCCTGTTATTGTTGC-TCC---AAGTACCAG-GCCT-TT-CCAA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 48834 42 + 132007 tccccTCATGCTTTTTATGTCA--GGAGCACGAG-TGCT-TT-CAGA i felCat3.scaffold_206428 I 287 C 0 s canFam2.chr9 59461858 39 - 64418924 --TGCTCATTGTTCTTGC-TCC--AAAGCACCAG-CACT-CT-TTGA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 37230 14 + 48268 ----CTC------------TCC--AAGGCACG--------------- i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_85717 1505 38 + 6675 ATCTCCTACTCTTCTTGC-TCC--AAAGCACCAG-CCC--TT-CG-- i dasNov2.scaffold_85717 C 0 C 0 e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I e loxAfr3.scaffold_49 14457534 123 - 17734757 I a score=310077.000000 s hg19.chr17_gl000204_random 74793 47 + 81310 ATAGGAGCA-TCACACTGCCC-TTGTCCCCTGGGCTTGACCAC----TG---C-CCC- s otoGar1.scaffold_94362.1-287808 47159 48 + 287808 AAAGGACTG-TCACGCTGTCCTTTGTCTTCCCAGCCTGAGCAC----TG---C-CCC- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_51043 1830 47 - 5707 ACAGGACTGCCCCCACCGCCC--TGCATCCTCAGCCTGAACAC----TG---C-GCC- i micMur1.scaffold_51043 C 0 C 0 s tarSyr1.scaffold_41848 9949 47 + 21754 ACAGGACTG-TCACTCTGTCC-TTGTCTCCTTGACCTGACCAC----TG---C-CCC- i tarSyr1.scaffold_41848 C 0 C 0 s calJac1.Contig5139 75389 47 + 225949 ATAGGAGCA-TCACACTGTCC-TTGTCCCCTGGGCTTGACCAC----TG---C-CCC- i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 72601 46 - 95547 AT-GGGGCA-TCACACCGTCC-TCATCCCCTGGGCTTGACCAC----TG---C-CCC- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75065599 46 + 78773432 AT-GGGGCA-TCACACCGTCC-TCATCCCCTGGGCTTGACCAC----TG---C-CCC- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16091165 47 + 17838096 ATAGGAGCA-TCACACCGTCC-TTGTCCCCTGGGCTTGACCAC----TG---C-CCC- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 42604 47 - 64270 ATAGGAGCA-TCACACCGTCC-TTGTCCCCTGGGCTTGACCAC----TG---C-CCC- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79506793 47 + 83384210 ATAGGAGCA-TCACACAGCCC-TTGTCCCCTGGGCTTGACCAC----TG---C-CCC- i panTro2.chr17 C 0 C 0 s vicPac1.scaffold_72280 888 47 + 3962 ACAGGACCG-TCACATCGTCC-TCATCTCCCTGGCTTGCCCAC----TT---T-CTC- i vicPac1.scaffold_72280 C 0 M 1824 s turTru1.scaffold_98008 12260 50 + 223990 ATAGGACTG-TCACACCGTCC-TCATCTTCTTGGCCTGCCCAC----TTAACA-CTC- i turTru1.scaffold_98008 C 0 I 15 s bosTau4.chr19 10881718 50 - 65312493 ATAGGACTG-TCATACTGTCC-TCATCTTCTTGGCTTGCCCAC----TTAACA-CTC- i bosTau4.chr19 C 0 I 15 s equCab2.chr11 58067988 46 - 61308211 TC-GGTCCG-TCACGCCGTCC-TCATCTTCTTGGCTTGCCCAC----TT---T-CCC- i equCab2.chr11 C 0 I 21 s felCat3.scaffold_206428 48876 47 + 132007 ACGGGATTG-TCACACTGTCC-TTGTGCTCTTGGTTTCGCCAC----TT---A-CCC- i felCat3.scaffold_206428 C 0 I 27 s canFam2.chr9 59461897 47 - 64418924 TCAGGACTG-TCACACAGTCC-TTGTGTTCCTGGCTTGACCAC----TT---A-CCC- i canFam2.chr9 C 0 I 23 s pteVam1.scaffold_11245 37244 45 + 48268 ---GGACTG-TCGCACCATCT-TTGTCTTCTTGGCTTGGTCAC----TC---ATCCC- i pteVam1.scaffold_11245 C 0 I 26 s loxAfr3.scaffold_49 14457657 46 - 17734757 ATAGCATCA-CCATGTCATCC-TTGTCTT--TGGCTCAGCTGC----TT---A-CCCT i loxAfr3.scaffold_49 I 123 C 0 s dasNov2.scaffold_85717 1543 47 + 6675 ATAGGACTG-TCACACCGTCC-TTGGCTT-----CCTGGCCGCACATGT---G-CCCT i dasNov2.scaffold_85717 C 0 C 0 e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I a score=-22688.000000 s hg19.chr17_gl000204_random 74840 18 + 81310 --------------AAGCAAC------------ACGAGGGG----------------G---CA--- s otoGar1.scaffold_94362.1-287808 47207 33 + 287808 --------------GTCCACCCTAAGCTCCCTTCTAAGGGT----------------GTCACA--- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_51043 1877 21 - 5707 --------------CTCCGCA------------CCGAGAAT----------------GTCCAG--- i micMur1.scaffold_51043 C 0 C 0 s tarSyr1.scaffold_41848 9996 34 + 21754 --------------CATCAAT------------ACAAGGGGAACTTCTAGGAGTGTCA---CA--- i tarSyr1.scaffold_41848 C 0 C 0 s calJac1.Contig5139 75436 18 + 225949 --------------AAGCAAC------------ACCATGGG----------------G---CG--- i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 72647 18 - 95547 --------------AAGTAAC------------ACGAGGGG----------------G---CG--- i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75065645 18 + 78773432 --------------AAGTAAC------------ACGAGGGG----------------G---CG--- i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16091212 18 + 17838096 --------------AAGCAAC------------ACGACGGG----------------G---CC--- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 42651 18 - 64270 --------------AAGCAAC------------ACGAGGGG----------------G---CA--- i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79506840 18 + 83384210 --------------AGGCAAC------------ACGAGGGG----------------G---CA--- i panTro2.chr17 C 0 C 0 s turTru1.scaffold_98008 12325 18 + 223990 --------------TTGTCAC------------ATGAAGGG----------------A---CA--- i turTru1.scaffold_98008 I 15 C 0 s bosTau4.chr19 10881783 18 - 65312493 --------------GTGTCAC------------ATGAAGGG----------------A---CA--- i bosTau4.chr19 I 15 C 0 s equCab2.chr11 58068055 18 - 61308211 --------------GTGCCCC------------ATGAAGGG----------------A---CA--- i equCab2.chr11 I 21 C 0 s felCat3.scaffold_206428 48950 18 + 132007 --------------GTGTCGC------------TTGAAGGA----------------A---CG--- i felCat3.scaffold_206428 I 27 C 0 s pteVam1.scaffold_11245 37315 18 + 48268 --------------GTGTCCC------------ATGAAGGG----------------A---TG--- i pteVam1.scaffold_11245 I 26 C 0 s loxAfr3.scaffold_49 14457703 35 - 17734757 TGTCAAGGCAGAAGGAACTTT------------CTAGGAGG----------------G---TCACA i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_85717 1590 33 + 6675 CGGCCACACGGA--GGACCCT------------GTAAGAGC----------------G---TCCCA i dasNov2.scaffold_85717 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e monDom5.chr2 304624775 9630 - 541556283 I e canFam2.chr9 59461944 23 - 64418924 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e mm9.chr11 118782203 908 + 121843856 I a score=-42671.000000 s hg19.chr17_gl000204_random 74858 16 + 81310 TGAAGACCACAGCA------------------------------------------------------------------------------------------------------------GT s panTro2.chr17 79506858 16 + 83384210 TGAAGACCACAGCA------------------------------------------------------------------------------------------------------------GT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 42669 16 - 64270 TGAAGACCACAGCA------------------------------------------------------------------------------------------------------------GT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16091230 16 + 17838096 TGAAGACCACAGCA------------------------------------------------------------------------------------------------------------GT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75065663 16 + 78773432 CGAAGACCACGGCA------------------------------------------------------------------------------------------------------------AT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 72665 16 - 95547 TGAAGACCACGGCA------------------------------------------------------------------------------------------------------------AT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 75454 16 + 225949 TGAAGACCACAGCA------------------------------------------------------------------------------------------------------------AT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 10030 15 + 21754 TGAAGA-CAGAGGA------------------------------------------------------------------------------------------------------------CA i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_51043 1898 15 - 5707 CGACCACCAGGGCA------------------------------------------------------------------------------------------------------------A- i micMur1.scaffold_51043 C 0 C 0 s otoGar1.scaffold_94362.1-287808 47240 15 + 287808 TGAAGACAAGGGCA------------------------------------------------------------------------------------------------------------A- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118783111 16 + 121843856 TGTAAACAGGAATA------------------------------------------------------------------------------------------------------------AA i mm9.chr11 I 908 C 0 s turTru1.scaffold_98008 12343 112 + 223990 ----------GGCAGTCttttttttttttttttttttttttttttttgcggtacgcgggcctctcactgttgtggcctctcccgttgcggagcacaggctccggacgcgcaggctcagcggc-- i turTru1.scaffold_98008 C 0 I 126 s bosTau4.chr19 10881801 4 - 65312493 ----------GGCA-------------------------------------------------------------------------------------------------------------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58068073 6 - 61308211 ----------GGCA------------------------------------------------------------------------------------------------------------AA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 48968 6 + 132007 ----------GGCA------------------------------------------------------------------------------------------------------------AA i felCat3.scaffold_206428 C 0 C 0 s pteVam1.scaffold_11245 37333 6 + 48268 ----------AACA------------------------------------------------------------------------------------------------------------AA i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14457738 16 - 17734757 TGAAGGGCAGAACA------------------------------------------------------------------------------------------------------------AT i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_85717 1623 16 + 6675 TGAAGAGCAGGGCC------------------------------------------------------------------------------------------------------------CT i dasNov2.scaffold_85717 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e monDom5.chr2 304624775 9630 - 541556283 I e canFam2.chr9 59461944 23 - 64418924 I e cavPor3.scaffold_76 4410071 145 + 7991924 I a score=278713.000000 s hg19.chr17_gl000204_random 74874 63 + 81310 GTCCTGAG------------CTGCCTTCCTGATCGACT---TTGCTATTTGCCCAAAGAAAGGAGTAGCTCATGCAGG s panTro2.chr17 79506874 63 + 83384210 GTCCTGAG------------CTGCCTTCGTGATCGACT---TTGCTATTTGCCCAAAGAAAGGAGTAGCTCATGCAGG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 42685 63 - 64270 GTCCTGAG------------CTGCCTTCGTGATCGACT---TTGCTATTTGCCCAAAGAAAGGAGTAGCTCATGCAGG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16091246 63 + 17838096 GTCCTCAG------------CTGCCTTCGTGATCGACT---TTGCTATTTTCCCAAAGAAAGGAGTAGCTCATGCAGG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75065679 63 + 78773432 GTCCTGAA------------CTGGCTTCATGATCGACT---TTGCTATTTGCCTGAAGAAAGGAGTAGCTCATGCAGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 72681 63 - 95547 GTCCTGAA------------CTGGCTTCGTGATCGACT---TTGCTATTAGCCCGAAGAAAGGAGTAGCTCATGCAGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 75470 63 + 225949 GTCCTGAG------------CTGCCTTTGAGATCAATT---TTACCATTTGCCCAAAGAAAGGAGAAGCTCATGCGGG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 10045 62 + 21754 ATCCTCAG------------CTGCCTTTGTGA-AGATC---TTGCCATTTGCCCAAGGAAAGTAGCAGCTTGTGCAGG i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_51043 1913 60 - 5707 GTCCTAAG------------CTGCCT--GGGAGCACCC---TGGCCA-TTGCCCCAAGAAGGTAGCAGCTCACGCGGG i micMur1.scaffold_51043 C 0 N 0 s otoGar1.scaffold_94362.1-287808 47255 62 + 287808 GTCCTCAG------------GGACCTG-GGGAACAACT---TGGTCATTTGCCCAAAGAAAGTGGCCGCCTATTCAGG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118783127 64 + 121843856 GTCCT-AG------------ATGCCTTGGGGAGCAACTAACTCTCCTTTTGCCCAGAAAAAGCAGAGGCCCTGGGAG- i mm9.chr11 C 0 C 0 s turTru1.scaffold_98008 12581 51 + 223990 GTCTTAAG------------CTGCCTTCGTGAACAACT---TTGCCATTTGCCCAAAGACAGTAAT------------ i turTru1.scaffold_98008 I 126 C 0 s bosTau4.chr19 10881805 51 - 65312493 GTCTTAAG------------CTGCCTTCATGAACAACT---TTGCCATTTACCCAAAGACAGTAAT------------ i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58068079 62 - 61308211 GACCTTAG------------CCGCCTCTGTGAACAACT---TTGCCA-TTGCCCAAAGAAAGCAATTCCTCGCGCAGG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 48974 41 + 132007 ATCCTAAG------------CTGCCTT---------------------CTACCCCAAGA----AATTCCCCACGTGGG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59461967 40 - 64418924 -----CAA------------CTGCCTT---------------------CTACCCAAAGGAAGTAATTCCTCATGCAGG i canFam2.chr9 I 23 C 0 s pteVam1.scaffold_11245 37339 57 + 48268 GTCCTAAAACGCAAACGACTCTGCCAT---------------------CTGCCCCAGGAAAGTCAATGCGGGCGCAGG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14457754 63 - 17734757 GTCCTCAG------------CTGCCTTCGTGAACAATA---TTGCCATTTGCCCAAAGGAAGTAGAAGCTCAGGCAGG i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_85717 1639 45 + 6675 ATCTC------------------------------ATG---CCACCATCCGCTCCCGGAAAGCGCACGCTCCCGCGGG i dasNov2.scaffold_85717 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I a score=184695.000000 s hg19.chr17_gl000204_random 74937 38 + 81310 GCCTTTGTTCattcattgattcaacaactattctttg---c s panTro2.chr17 79506937 38 + 83384210 GCCTTTGTTCattcattgattcaacaactattctttg---c i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 42748 38 - 64270 GCCTTTGTTCattcattgattcaacaactattctttg---c i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16091309 38 + 17838096 GCCTTTGTTCattcattgactcaacaactattctttg---c i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75065742 38 + 78773432 GCCTTTGTTCattcattgactcaacaactattctttg---g i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 72744 38 - 95547 GCCTTTGTTCattcattgactcaacaactattctttg---g i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 75533 38 + 225949 GCCTTCGTTCattcattgactcaacaactattctttg---g i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 10107 38 + 21754 GTCTTCATTCattcattgattcaacaaatattctttg---a i tarSyr1.scaffold_41848 C 0 C 0 s otoGar1.scaffold_94362.1-287808 47317 39 + 287808 CTCGTCACTCattcactgattcaacaaatatgcttgg--ag i otoGar1.scaffold_94362.1-287808 C 0 C 0 s mm9.chr11 118783191 32 + 121843856 GCCTCT-----TCCACTGAGTCACAAGCTGTCTTTAG---- i mm9.chr11 C 0 C 0 s turTru1.scaffold_98008 12632 38 + 223990 -TCCTCATGCattcatttacccaaaaaatattctttg--ag i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10881856 38 - 65312493 -TCCTCATGCattcatttatccaacatatattctttg--ag i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58068141 38 - 61308211 -TCTTCGTTCatccatttctccctcaaatatcctttg--ag i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 49015 39 + 132007 GTCCTCATTCatccatgtattgaacaagtacccctcg--ag i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59462007 39 - 64418924 ATCTCCattcattcgtggattcaacaagtatttctca--gg i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 37396 39 + 48268 GTCTTCGTTCattctctcattcaccaaacggtccccg--ag i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14457817 37 - 17734757 TTCTTCATTCATTTGCTTATTCAGCACATTTCCTTTG---- i loxAfr3.scaffold_49 C 0 I 462 s dasNov2.scaffold_85717 1684 21 + 6675 ATCTTCCTTC------------------CCTCCCTTGGT-- i dasNov2.scaffold_85717 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I a score=97267.000000 s hg19.chr17_gl000204_random 74975 46 + 81310 cacctttg-----aagtgaccggctctggggcaggcagaggggccca------cagg s panTro2.chr17 79506975 46 + 83384210 cacctttg-----aagtgaccggctctggggcaggcagaggggtcca------cagg i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 42786 46 - 64270 cacctttg-----aagtgaccggctctggggcaggcagaggggccca------cagg i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16091347 46 + 17838096 caccttca-----aagtgaccggctctggggcaggcagaggggccca------cagg i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75065780 46 + 78773432 cacctttg-----aagtgcccggctctggggcaggtagaggggccca------cagg i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 72782 46 - 95547 cacctttg-----aagcgcccggctctggggcaggtagaggggccca------cagg i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 75571 43 + 225949 catcttcg-----aagcacccggctctggggcaggt---ggggccca------cagg i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 10145 45 + 21754 cactgtct-----aagtgcccggctctgggtcagccag-taagttca------cagg i tarSyr1.scaffold_41848 C 0 C 0 s otoGar1.scaffold_94362.1-287808 47356 47 + 287808 ccccttct-----aagtgccctgctctgggtgggggaGTGGCCCCCAG-----CATA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s turTru1.scaffold_98008 12670 44 + 223990 caccttct-----acgtgcccagctctaggtcagtcggcgg--ctca------caag i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10881894 44 - 65312493 caccttcc-----tagggcccagctctcggtcagtcagtgg--ctca------cagg i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58068179 43 - 61308211 cacattct-----aagtgcccagctgggggtcaggcagtg---ccca------cagg i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 49054 44 + 132007 caccttcc-----cagtgtccagctctgggtcaggcagtga--caca------cggg i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59462046 44 - 64418924 cacgttct-----aagtgtccagctttgggtcaggcagtga--ccca------cagg i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 37435 43 + 48268 cacctgct-----aagtgcccagctct-ggccagacagtgg--cctg------cggc i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_52062 148 39 + 16741 CACCTGTA-----AGGG--CCCACACAGGGTCAGGCCCTGGGACCA----------- i proCap1.scaffold_52062 N 0 C 0 s dasNov2.scaffold_85717 1705 44 + 6675 CACCCCTAGACTTGGGG--TGCCTTCCAGGCGCCGCCCTGAGTCCA----------- i dasNov2.scaffold_85717 C 0 C 0 s mm9.chr11 118783223 14 + 121843856 -------------------------------------GAGAGGACTG------CAGG i mm9.chr11 C 0 C 0 s tupBel1.scaffold_71658.1-10116 228 10 - 10116 -----------------------------------------GGGCCA------CAGA i tupBel1.scaffold_71658.1-10116 N 0 C 0 s micMur1.scaffold_38207 14 37 + 5481 -------------------CCCGCTGTGGGT-CAGGAGTGGCCCCCCTCCCCCCAGG i micMur1.scaffold_38207 N 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e monDom5.chr2 304624775 9630 - 541556283 I e cavPor3.scaffold_76 4410071 145 + 7991924 I e loxAfr3.scaffold_49 14457854 462 - 17734757 I a score=698884.000000 s hg19.chr17_gl000204_random 75021 121 + 81310 cacg---agcaagatgc--aa-tcctgccccc-gtgccctggg--tgtggagttgggga--gacaggt--gggtgaacagccagataacaagtccacctggt-aagtgctctgaGAAAAACCTGAAGA-------AATAATC s otoGar1.scaffold_94362.1-287808 47403 119 + 287808 GATG---GATAAATCCC--AG--CCAGCCCCA-CGCCCCCGGCATGGTGGAAC-TGGGA--GGCAGGT---AGCTAATCATCCAACAGCAAAGCCGCCTGGT-GAGTGTTCTG-GGAGAACGGGAAGA-------AAGGCTG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_38207 51 115 + 5481 CACA---GATAAGATCC--AG--CCTGTCCCA--GACCCCGAGGCTGTGGAACGGGGGA--GGCAGGC---GGTGAA-CACCGAGTGGCAAGGCCACCAGGC-AAGTGCGCTG-GGAAAACGTGAACA-------A---CTC i micMur1.scaffold_38207 C 0 C 0 s tarSyr1.scaffold_41848 10190 121 + 21754 ccta---cacaagatcc--aa-tcctgccccc-aggcgccggt--tgtggagttggaga--gacagat--gggtaaacagccgaatgacaaggccaccttgt-aagtgctctgaggaaaacaagaagg-------aatactC i tarSyr1.scaffold_41848 C 0 C 0 s calJac1.Contig5139 75614 120 + 225949 catg---agcaagatgc--ag-tcctgcctcc-acatgctggg--tgtggagctgagga--gacagat--gggtgaacag-tggataacaagaccacctggt-aagtgctctgagaagaacatgaaGA-------AATACTC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 72828 121 - 95547 catg---agcaagatgc--aa-tcctgccccc-atgtgctgga--tgtggaactgggga--gacagat--gggtgaacagccagataacaaggccacctggt-aagtgctctgagaaaaacatgaaGA-------AATACTC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75065826 121 + 78773432 catg---agcaagatgc--aa-tcctgccccc-acgtgctgga--tgtggaattgggga--gacagat--gggtgaacagccagataacaaggccacctggt-aagtgctctgagaaaaacatgaagA-------AATACTC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16091393 123 + 17838096 catg---agcaagacgc--aa-tcctgccccc-acacgctggg--tgtggagttgggga--gacaggtgggggtgaacagccagataacaaggccacctggt-aagtgctctgaGAAAAACCTGAAGA-------AATAATC i ponAbe2.chr17_random C 0 I 345 s gorGor1.Supercontig_0007361 42832 121 - 64270 catg---agcaagatgc--aa-tcctgccccc-gcnccctggg--tgtggagttgggga--gacaggt--gggtgaacagccagataacaaggccacctggt-aagtgctCTGAGAAAAACCTGAAGA-------AATAATC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79507021 121 + 83384210 catg---agcaagatgc--aa-tcctgccccc-gcgccctggg--tgtggagttgggga--gacaggt--gggtgaacagccagataacaaggccacgtggt-aagtgctctgagaaaaaCCTGAAGA-------AATAATC i panTro2.chr17 C 0 C 0 s tupBel1.scaffold_71658.1-10116 238 103 - 10116 CA-G---AGCGAGAGCC--AGAGCCTG--------GCACTGGG--CATGCAGGTGGAGA--GGTGG----GGGGGGGCAGCTGAGTTCC----TCCCAGGGG-AGGTGCACTGAGAGGA---TGA--G-------AATGCTC i tupBel1.scaffold_71658.1-10116 C 0 C 0 s mm9.chr11 118783237 116 + 121843856 CAGA---GAGAAGGTGG---------GTGCTC----CCCTGGG--CATGGATGCTAAGCCTGGCAGAT--GGGAAG--CACTCAGTGACCA---CACAAGGC-GAGAGCTTCCAGCAAAATGTAGGAAGCCCGCCACCCACC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4410216 122 + 7991924 CATG---TGCAAGCCGATCCA-CCCTGCCCTC----ACCCACG--GAAGGTGGCAGGGAAAGGCAGAT--GGGGAGACAGCTCGCTGACCATGCCACATGGC-AAGCGCTCTAAGAAAAACACAAGGA-------AACACTC i cavPor3.scaffold_76 I 145 C 0 s turTru1.scaffold_98008 12714 122 + 223990 catg---aaaaggatcc--aa-tcctgccgtccaggctctggg--tgctgagttgggga--agcagat--gggtaaacagctaaatgacaaggccacatggc-aagtgctttgagaaaaacatgaaGA-------AATACTC i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10881938 123 - 65312493 catg---aaaaggatct--ga-tgcggccctccaggcactggg--tgctaagtttggga--ggcagaa--gggtaaacagcacaatgacaatGTCACATGGTAAAGCGATTGGAGAAAAACATGAAGA-------AACACTC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58068222 121 - 61308211 catg----aaaagaccc--ag-tcctgccccccaggcgctggg--tactgctttttgga--agcagac--gggtaaacagctaaatggtaacaccacatggt-acgtgctTCGAGAAAAACAGGAAGA-------AATACTC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 49098 121 + 132007 catg----aaaaggttc--aa-cccggACACCCGGGAGCTGGG--TGATGAGCTGGAAA--TGCAGAG--GAGAAAACAGCTAAATGACAACGCCACGTGCT-AAGCACTTTGAGAAGAACGTGAAGA-------AATATTC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59462090 123 - 64418924 cctg---caaagggtcc--aa-tcctgccatccaggcgctggg--tgccaagctggagg--agcagat--gggtaaacagctaaaggacaatgccacatggtaaagcactttgagagaaacatgaagA-------AATATTC i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 37478 117 + 48268 catg----aaaaggtcc--ag-tcct-ccctccaggcgctggg--tgccaagccgggga--tgcagat--ggggaaacagctaaatgacaaGGCCACACGGC-ACGTGCTC---GGAAGACAGGAAGC-------AACACTC i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_52062 187 120 + 16741 TTCGATAAGTGAGGTCC--AG-TCCTGCCAACAAGGCTCTGGG--TGTCGAGCTGGGAG--AGCAGAT--GGGTAAAACACCCA-----AATGCCACACGGT-AAGTGCTTGGAGAGAACCACAGGGA-------ACTTGTC i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 1749 114 + 6675 CACCC----CGTGGTCC--TG-TCATCC------GCCATGGGG--CGTGGAGCTGGGGA--AGCAGGT--GGGGAAACAGCCAAATGACAGCGCCAGCCGCC-AAGTGCTTGGAGAAAACCGTGAAGT-------AG-ATTT i dasNov2.scaffold_85717 C 0 C 0 s loxAfr3.scaffold_49 14458316 96 - 17734757 -------AATAAGATCC--AG-TCCTGCCCGTGAGGCTCTGGG--TGTTGAGCCGGATG--AGCAG------------------------ATGCCTCATGGT-TAGCACATTGAGAGAAACACAAAGA-------AACACTC i loxAfr3.scaffold_49 I 462 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e monDom5.chr2 304624775 9630 - 541556283 I a score=251542.000000 s hg19.chr17_gl000204_random 75142 40 + 81310 AAC-------CTATAGGGTGGCTTTGCCATCTTCTCCAAATATTGTC s panTro2.chr17 79507142 40 + 83384210 AAC-------CTATAGGGTGGCTTTGCCATCTTCTCCAAATATTGTC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 42953 40 - 64270 AAC-------CTATAGGGTGGCTTTGCCATCTTCTCCAAATATTGTC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16091861 40 + 17838096 AAC-------CTATAGGGTGGCTTTGCCATCTTCTCCAAATATTGTC i ponAbe2.chr17_random I 345 C 0 s rheMac2.chr16 75065947 40 + 78773432 AAC-------CTATGGGGTAGCTTTGCCATCTTCTCCAAATATTGTT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 72949 40 - 95547 AAC-------CTATGGGGTAGCTTTGCCATCTTCTCCAAATATTGTT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 75734 39 + 225949 CAC-------CTACGGGGC-GCTCCACCATCTTCTCCCAATATTGTT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 10311 40 + 21754 CAC-------CCAAGGCAAGGCTCTGCTGTCCTCTCTCAATATTGTT i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 166 37 + 5481 CACCCACGGGCCACGGCGTGGCCC-GCCCTCTCCTGTC--------- i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 47522 40 + 287808 CAC-------CCACAGTGTGGCCTGGCCGTCTCCTCTCAGTATTTTC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 341 34 - 10116 AAC-------CC------CAGGCCCCACACCCACCGTCAGTATTTTC i tupBel1.scaffold_71658.1-10116 C 0 C 0 s mm9.chr11 118783353 39 + 121843856 CAC-------CCACGGAGGAGCCCTGACATC-TCTATCAATATTTTC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4410338 40 + 7991924 TGC-------CCACGGAGAAGCCTTGCCATCGTCTATCAATATTTTC i cavPor3.scaffold_76 C 0 C 0 s turTru1.scaffold_98008 12836 40 + 223990 CAC-------CCACAGAGCAGCCTCACCGCCCTCTATCAATATTTTT i turTru1.scaffold_98008 C 0 I 8 s bosTau4.chr19 10882061 40 - 65312493 CAC-------CCACGGAGTGGCCTTGCCATCCTCTATCAGTATTTTC i bosTau4.chr19 C 0 I 8 s equCab2.chr11 58068343 40 - 61308211 CAC-------CCACGGAGTGGCCTTGCCGGCCTCTGTCAATATTTTC i equCab2.chr11 C 0 I 8 s felCat3.scaffold_206428 49219 40 + 132007 CAC-------CCACGGAGTGGCCCTGCCACCCTCCACGAGCATTTCC i felCat3.scaffold_206428 C 0 I 249 s canFam2.chr9 59462213 40 - 64418924 CAC-------CCACAGAGTAGCCCTGCCATCCTCCACGAGCATTTCC i canFam2.chr9 C 0 I 8 s pteVam1.scaffold_11245 37595 39 + 48268 CAC-------CCACAGAGAGGCCCCGCC-CCCTGCATCGCTATTCCC i pteVam1.scaffold_11245 C 0 I 6 s loxAfr3.scaffold_49 14458412 39 - 17734757 --------CACCATGAGGCGACCTTGCTGTCCCCTCCCCATGTTTTC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_52062 307 39 + 16741 --------CACCACCGGGCAGCCTGGCTGTGCCCTCCCTGTATTATT i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 1863 38 + 6675 --------CACTCCCAGAGAGGCTGGCCGCCCCCGTCA-GTATTTCC i dasNov2.scaffold_85717 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e monDom5.chr2 304624775 9630 - 541556283 I a score=-23402.000000 s hg19.chr17_gl000204_random 75182 14 + 81310 ---------CTCCA-AATTTC---------ATG s panTro2.chr17 79507182 14 + 83384210 ---------CTCCA-AATTTC---------ATG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 42993 14 - 64270 ---------CTCCA-AATTTC---------ATG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16091901 14 + 17838096 ---------GTCCA-AATTTC---------ATG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75065987 14 + 78773432 ---------GTCCA-AATTTC---------ATG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 72989 14 - 95547 ---------GTCCA-AATTTC---------ATG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 75773 14 + 225949 ---------GTCCA-GATTTC---------ATG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 10351 23 + 21754 ---------GTCCA-GAATCCCACATGTTAACA i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 203 9 + 5481 ---------------AATCCC---------ACG i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 47562 15 + 287808 ---------ATCCATAATCGC---------ACA i otoGar1.scaffold_94362.1-287808 C 0 I 8 s tupBel1.scaffold_71658.1-10116 375 15 - 10116 ---------ATCCATGATCCC---------ACA i tupBel1.scaffold_71658.1-10116 C 0 I 8 s mm9.chr11 118783392 15 + 121843856 ---------GTCCACAGTCCC---------ACA i mm9.chr11 C 0 I 8 s cavPor3.scaffold_76 4410378 15 + 7991924 ---------ATCCATAGGCCC---------ACA i cavPor3.scaffold_76 C 0 I 8 s turTru1.scaffold_98008 12884 15 + 223990 ---------TCCCACATGCTA---------ACA i turTru1.scaffold_98008 I 8 C 0 s bosTau4.chr19 10882109 15 - 65312493 ---------TCCCACATGTTA---------ACA i bosTau4.chr19 I 8 C 0 s equCab2.chr11 58068391 15 - 61308211 ---------TCCCACACGCTA---------ACA i equCab2.chr11 I 8 C 0 s canFam2.chr9 59462261 13 - 64418924 ---------GCC--CACGCCA---------GCA i canFam2.chr9 I 8 C 0 s pteVam1.scaffold_11245 37640 14 + 48268 ---------ACCC-CACGTGG---------ACG i pteVam1.scaffold_11245 I 6 I 20 s loxAfr3.scaffold_49 14458451 23 - 17734757 ATC-CACAATCCCACATGCTC---------ACA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_52062 346 24 + 16741 TTCTCACAGTCCCCCATGCTC---------ATG i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 1901 23 + 6675 ATC-CGCCGCCCCGCACGCTC---------ACG i dasNov2.scaffold_85717 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e felCat3.scaffold_206428 49259 249 + 132007 I e monDom5.chr2 304624775 9630 - 541556283 I a score=933763.000000 s hg19.chr17_gl000204_random 75196 116 + 81310 CAGCCATCTTCACCTCCCAGGCCATCTTTAACTACCAAAGCCAGGGC-CA-CACATGCTGGGTGACACCTCAGCATGCAGGgacttgaagagg-----ccactcacaaaagaa-gactgagaaa s panTro2.chr17 79507196 116 + 83384210 CAGCCATCTTCACCTCCCAGGCCATCTTTAACTACCAAAGCCAGGGC-CA-CCCATGCTGGGTGACACCTCAGCATGCagggacttgaagagg-----ccactcgcaaaagaa-gactgagaaa i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 43007 116 - 64270 CAGCCATCTTCATCTCCCAGGCCATCTTTAACTACCAAAGCCAGGGC-CA-CATATACTGGGTGACACCTCAGCATGCAGGGACTTGAAGAGG-----CCGCTCGCAAAAGAA-GACTGAGAAA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16091915 116 + 17838096 CAGACATCTTCACCTCCCAGGCCATCTTTAACTACCAAAGCCAGGGC-CA-CACATGCTGGGTGACACCTCAGCACACAGGgacttgaagaga-----ccactcgcaaaagaa-gactgagaag i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75066001 116 + 78773432 CAGCCATCTTCACCTCCCAGGCCATCTTTAACTACCAAAGCCAGGGC-CA-CACATGCTGGGGGACACCTCAGCACACagggacttgaagagg-----ccactcgcaaaagaa-gactgagaaa i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 73003 116 - 95547 CAGCCATCTTCACCTCCCAGGCCATCTTTAACTACCAAAGCCAGGGC-CA-CACATGCTGGGGGACACCTCAGCACGCAGGgacttgaaaagg-----ccactcgcaaaagca-gactgagaaa i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 75787 116 + 225949 CAGCCATCTTCCCCTCCCCAGCAGTCTTTAAATACCTGCCCCAGGGC-CA-CATATGCCAGGTGGCATCTCAGCACGCAGGgacttgaagagg-----ccacccgccaaagaa-gactgagaaa i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 10374 118 + 21754 TGGTTATCCTCACTCCCAAGTTCATCTTTAAATACCAAAGACGGTGCACACCACATGCTagatgacaccccaacaggcagggacttgaagagg-----ccactcacaaaagaa-gactgaaaaa i tarSyr1.scaffold_41848 C 0 C 0 s otoGar1.scaffold_94362.1-287808 47585 113 + 287808 AGGCCACCTTCACGTTCAAGGCCACCTTTGAACACTAAGGGTGAGGG-CA-CATATGCTTGAGGGGACCCCTGCAGGCAGGGGCTCCAAGAGG-----CAACTCACGCA---A-GACTGAAGGG i otoGar1.scaffold_94362.1-287808 I 8 C 0 s tupBel1.scaffold_71658.1-10116 398 109 - 10116 TGGCCTCCTGCAC--CCCAGGGCACCTCTGAACACCAAAGATGGGG--CA-CACGTGCCGGCAGA---CTGCGCAGGCAAGGGCTGAACAAGG-----CCACTCAGGAAGGCA-GGCTGTAAA- i tupBel1.scaffold_71658.1-10116 I 8 C 0 s mm9.chr11 118783415 113 + 121843856 CAACCATCCTCTCCTCCAACTCCATCTTTAAATGCCAAAGACGGG---CG-CATATGTTGGAGGACACCATCACAGGCA-AGGCTGGAAGAGG-----CAATCCACAGAGAAA-GACTTAAAAA i mm9.chr11 I 8 C 0 s cavPor3.scaffold_76 4410401 112 + 7991924 CGGCCATCGTCTCCTCCAACGCCATCTTTAAATACCAAAGATGGG---CA-CATATGCTGAAAGGGACCA--GCAGGCAGGGGCTtgaagagg-----caacgtacacaagaa-gactgaaaaa i cavPor3.scaffold_76 I 8 C 0 s turTru1.scaffold_98008 12899 115 + 223990 TGGCCGTCTTCACCTCCAACACCATCTTTAAACACCAAAGATGGGGA-CA-CATATGCTGGATGAGACCACaacaggcaggggcttaaagagg-----caactcac-aaagaa-gacttcaaaa i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10882124 115 - 65312493 TGGCTGTCTTCACCTCCAACACCATCTTTAAACACCAAAGATGGGGA-CA-CATATGCTGGATGAGACTGCAACAGGAGGGGGCTtgaagagg-----caactcac-aaagaa-gacttaaaaa i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58068406 117 - 61308211 TGGCCATCCTCACCTCCAACGCCATCTTTAAGCACCAAAGACAGGGA-CA-CATATGCCGGATGAGACCACAACAGGCGGCgacttgaagagg-----caactcacaaaagaaggacttgaaaa i equCab2.chr11 C 0 C 0 s canFam2.chr9 59462274 100 - 64418924 CGGCCACCTTCATCGCCAGCGCCATCTTTACATGCCTGAGACAGGGA-CA-CGTGTGCAGGACAAGACCACAGC----------------CGG-----CAACtcacaaaagaa-gactttaaaa i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 37674 94 + 48268 --------------------ACCACCCTGAAACACCAAAGAC-GGGG-CA-CATGTGCC-GACAAGACCCCAAGAGGCGGGGTCTtgaagagg-----caactcacaaaagaa-gactttcaaa i pteVam1.scaffold_11245 I 20 C 0 s felCat3.scaffold_206428 49508 80 + 132007 --------------------GCCATCTGTACACGCCTAAGACAGGGA-CA-CGTGTGCAGGACGAGACCAAAGC----------------CAG-----caactcacaaaagac-gactttaaga i felCat3.scaffold_206428 I 249 C 0 s loxAfr3.scaffold_49 14458474 121 - 17734757 TGGCTCTCCTCGCCTCCAATGCCATCTGTAAATACCAAATACGGGGC-TG-CAAATGCTGGACAAGACCACAGCAGTCAGCAAGTCAAAGAGCCAACACAACACATCAAAGAA-GAACGAAAAA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_52062 370 116 + 16741 TGGCCATCCACACCGCCAACGCCATCTTTAAATACCAAACACAGGGC-CA-TGCATGCTGGATACGACCACAGCAGGTAGCCATTTCAGAAGC-----CAACACTTCAAAGAA-GACCAAAAAA i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 1924 107 + 6675 TGGTCAACCTCACCCCCAACGCCGTTTTTAAATA---------AAGA-CA-CATATGCCAGAGGCGCCTGCAGCAGGCAGGGGCAGGAAAAGG-----CAGCTCCCAACAGAA-GACTTTCCAC i dasNov2.scaffold_85717 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e micMur1.scaffold_38207 212 0 + 5481 C e monDom5.chr2 304624775 9630 - 541556283 I a score=694580.000000 s hg19.chr17_gl000204_random 75312 84 + 81310 tgactccaaagcaggg-acag--tgtcgaa--ccccaccagtcaccaaagcaaagcaaatcaaaac---aaaagcccacttccattttt-tc--c s panTro2.chr17 79507312 84 + 83384210 tgactccaaagcaggg-acag--tgtcgaa--tcccaccagtcaccaaagcaaagcaaatcaaaac---aaaagcccacttccattttt-tc--c i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 43123 84 - 64270 TGACTCCAAAGCAGGG-ACAG--TGTCGAA--TCCCACCAGTCACCAAAGCAAAGCNAATCAAAAC---AAAAGCCCACTTCCATTTTT-TC--C i gorGor1.Supercontig_0007361 C 0 M 157 s ponAbe2.chr17_random 16092031 84 + 17838096 tgactccaaagcaggg-acag--tgtcgaa--tcccaccagtcaccaaagcaaagcaaatcaaaac---aaaaccccacttccattttt-tc--c i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75066117 84 + 78773432 tgactccaaagcaggg-acaa--tgtcaaa--tcccaccagacacgaaggcaaagcaaatcaaaac---aaaagcccacttccattttt-tc--c i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 73119 84 - 95547 tgactccaaagcaggg-acaa--tgtcaaa--tcccaccagacacgaaggcaaagcaaatcaaaac---aaaagcccacttccattttt-tc--c i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 75903 87 + 225949 tgaccccaaagcaggg-acaa--tgatgaa--tcccacccatcaccaaagcaatgcaaatctaaacaaaaaaagcccactgccattttt-tc--c i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 10492 83 + 21754 tcatgccgaa-tgggg-agaa--tgtgaaa--tcctaccagtcaccaaagcaacacaaatcaaaac---aaaaactcacttccattttt-tt--c i tarSyr1.scaffold_41848 C 0 I 1 s micMur1.scaffold_38207 212 85 + 5481 TGACCCCATGGCGGggaaaaa--tgtggaa--ccccaccagtcaccaaagcaatgcaaatcaaaac---aaaaacacgcttccctttct-cc--c i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 47698 84 + 287808 TCACCCCACAGTGGGG-aaaa--cgtcaaa--ccccaccagtcacagaagcaacgcaaatcaaaac---ataaacatgcttccattttt-tc--t i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 507 80 - 10116 TGA-TCCAAGGCAGGG-AGAA--C-TCGAA--GCCCCGCAGTCACCAGAGCAAGGCAAGTCAAACC---CAGA-CACTCCTCCGTGTCT-CC--- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s mm9.chr11 118783528 71 + 121843856 TGACCC---------A-AAGC--AGTTGGA--CCTTACCACTCACCAAGCCAATGAAAACCAAGAC---TAAAAACATCCCCAACT-----G--C i mm9.chr11 C 0 I 4 s cavPor3.scaffold_76 4410513 83 + 7991924 tgacctcgctgcggaa-aaag--tgtagca--tcttaccagtcataaag-caatgtgaatccaaac---aaaaacccttccatactctc-cc--c i cavPor3.scaffold_76 C 0 I 4 s turTru1.scaffold_98008 13014 83 + 223990 gggccccaaagtacag-aaag--tgtctca--tctcaccagccatcaaagcaatataaatcaaaac---aaaaacacacttccacttt--tc--c i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10882239 83 - 65312493 ggaccccaaagcaccg-aaag--tgtctaa--tctcaccagccaccaaagcaacgctaatcaaaac---acaaacagacttccgcttc--tc--c i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58068523 85 - 61308211 ggaactcgaagta-gg-gaagatagtctaa--tctcaacagtcaccaaagcaatgcaaatcgaaac---ggaaacacacgtgcatctgt-tc--c i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 49588 83 + 132007 ggaccccaaggta-gc-aaag--tgtctca--tctcaccagtcaccaaagcaatgcgaatctaaac---aaaaacacacttccgttttt-tc--c i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59462374 84 - 64418924 ggaccccaaagtg-gg-aagg--tgtctga--tctcaccagccaccaaagcaatgcacatctaaac---aaaaacacacttccatttttctc--c i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 37768 83 + 48268 ggaccccaaagta-gg-aaaa-ccatctaa--tctcaccagtcaccaagacaatgcaaatccaaac---aaaaacacgcttccgtttt--tc--c i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14458595 85 - 17734757 TGACCCCACAACAAGG-AAAA--CGCCTGATCTCCCACCAGTCACCAAAGCAACGCAAATCCAAAC---AAAG-CGCACTTCCATTTTT-CC--C i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_52062 486 72 + 16741 TGATCTCCCAACAA-G-CACA--CGTCCAA--GCCCACCAG-CTCCCAGGCAACACAAACACAA------------CACTT-CATTTCT-CC--C i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 2031 85 + 6675 CGACCCCCAAGGCGGC-GAGG--CATCTAA--TCCCACCAGGTTCCAAAGCAACACAAATCAAACA---AAAA-CACGCTTCTACTTTC-CCTGC i dasNov2.scaffold_85717 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e monDom5.chr2 304624775 9630 - 541556283 I a score=355600.000000 s hg19.chr17_gl000204_random 75396 102 + 81310 acctgccagattttgaaaatgcccat----tgc---acccagtgcttca--gggggt----g-----cgg-------ggaaatga-cctc-t--cattcgct-----t---gct----gg-tgggattcgga----gtcagtgtaatc s panTro2.chr17 79507396 102 + 83384210 acctgccagattttgagaatgcccat----tcc---acccagtgcttca--aggggt----g-----tgg-------ggaaatga-cctc-t--cattcgct-----t---gct----gg-tgggattcgga----gtcagtgtaatc i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16092115 102 + 17838096 acctgccagattttgaaaatgccagt----tcc---acccagtgcttcg--gggggt----g-----cgg-------ggaaatga-cctc-t--cattcgct-----t---gct----gg-tgggattcgga----gtcagtgtaatc i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75066201 102 + 78773432 acctgccagattttgaaaatgccagt----tcc---acccagtgcttcg--cggggt----g-----cgg-------agaaatga-cctc-t--ccttcgct-----t---gct----gg-tgggattcgga----gtcagtgtaatc i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 73203 102 - 95547 acctgccagattttgaaaatgccagt----tcc---acccagtgcttcg--gggggt----g-----cgg-------agaaatga-cctc-t--ccttggct-----t---gct----gg-tgggattcgga----gtcagtgtaatc i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 75990 101 + 225949 acctgccagattttgaaaatgccaat----tcc---acccagtgctctg--gggggt----g-----cgg--------gagatga-cctc-t--cattcgct-----t---gct----gg-tgggattcaga----gtcagtgcagtc i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 10576 102 + 21754 atctgccagatgtttaaactactgat----tac---accaagtgcttct--gggggt----g-----ctg-------ggaaatgaccccc-t--cattcgct-----t---gct----gg-tgggatt-gaa----gtcagcataatc i tarSyr1.scaffold_41848 I 1 C 0 s micMur1.scaffold_38207 297 105 + 5481 acctgccagattttgaaactgctgattatatat---accccgtgctcct--gggggg----a-----cgggagggcagggaatgt-ccct-c--tccttccttcgggt---gct----gg-tgggc-----------------taagc i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 47782 103 + 287808 gcttgctagattttgaaaacgctgat----tac---accccgcgcttct--gcggga----g-----ctg-------ggaaatga-ccctgt--tccttgct-----t---gct----gg-tgggatcccaa----gccagcgtaatc i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 587 88 - 10116 ACCTGCCAG-TTTGGGGGAAGCTGGC----CAC---TTCT------------GGGGT----G-----CAG--------GGAATGA-CCCT-G--CCTT---T-----T---GCC----AGCCAGGGCtgcac----atctgcataatc i tupBel1.scaffold_71658.1-10116 C 0 C 0 s mm9.chr11 118783603 109 + 121843856 CTTTGACAGACC-------TGCTTGT----GACGGGGGCTGGTGCATGC--ACAAGT----GAGGCACAG-------GGACCTGA-CCCC-C--CCCCCA-------T---GCTCTCCCG-TGAGACCTACACTTGCTTACCTTCGTC i mm9.chr11 I 4 C 0 s cavPor3.scaffold_76 4410600 100 + 7991924 ccttgccagtct-ggaaaacgctgat----tac----ccttggggagtc--atgggt----g----gctg-------agaggtga-cctc-t--cccacaca----gt---gct-------ggggatccaaa----gtcaccctcatc i cavPor3.scaffold_76 I 4 C 0 s turTru1.scaffold_98008 13097 93 + 223990 acccgccagattttgaaactgctgat----tgc---agccagagctt--------cc----a-----ctg-------ggaagtga-ccct-c-tcccgcact-----a---gat----gg-tgggg-tcgaa----gctggc---atc i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10882322 93 - 65312493 acccgcccgattctgaaactgctgat----tgc---attccgtgctt--------ct----g-----ctg-------ggaagtga-ccct-c-tcctgcact-----a---gct----gg-tgggg-tcgaa----gggggc---atc i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58068608 96 - 61308211 acccgccggattttgaaaccactgat----tgc---atccaggactt--------cc----g-----ctg-------ggaaacga-ccct-c-tcacgcgcc-----t---gct----gg-tgggc-tcgcg----gctggcataatc i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 49671 97 + 132007 accagctggattttgaagctgctgat----tgc---atccagccctt--------ct----g-----ctg-------ggaaatga-ccct-cttcgcacgct-----g---gct----gg-tggga-tccga----agctgggtaatc i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59462458 96 - 64418924 accagctggattctgaaaccgctgat----tgc---atccagtgctt--------ct----g-----ctg-------ggaaatga-ccct-c-tcgcgcgct-----t---gct----gg-tggga-tccga----agctgcgtaatc i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 37851 94 + 48268 acctgcgg----ttgagactgctgac----tgc---atccagtgcttct--ggggct----g-----ccg-------caaagtga-cgtc-c--agtacg-----------gct----gg-tggga-tccgg----gctggcgtgata i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14458680 103 - 17734757 ATCTGCCCGCTTT-GAAGATGCCAAT----TAC---TTTCCCTGTTTCT--GTGGGGAGCTG-----CTA-------AGGGAT---CCCC-T--TGGGGGCT-----t---gct----gg-tgggattccaa----ggtggtataatc i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_52062 558 106 + 16741 ACCCACCCACTTTGGAGGATGCTGAC----GAC---TGTCAGTGTTTCTTGgggggtggttg-----tgg-------aaggat---cccc-t--catcagct-----t---act----ag-tggggttccaa----gacggcagaatc i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 2116 103 + 6675 ACCTGCCAGATTCTGATAAAGCTGAT----TTC---ACCCAGTGTTTCC--GGGAGG----G-----CTG-------GGGGAT---CAGC-T--CTCGAACA-----TGCGGCG----GG-TGGGATTCAGA----GTCCGCATCATC i dasNov2.scaffold_85717 C 0 M 316 e gorGor1.Supercontig_0007361 43207 157 - 64270 M e vicPac1.scaffold_72280 935 1824 + 3962 M e monDom5.chr2 304624775 9630 - 541556283 I a score=452992.000000 s hg19.chr17_gl000204_random 75498 35 + 81310 tttctggagggcagattggcactcggatcaaaagc s panTro2.chr17 79507498 35 + 83384210 tttctggagggcagattggcacttggatcaaaagc i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16092217 35 + 17838096 tttctggagggcagattggcactcggatcaaaagc i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75066303 35 + 78773432 tttctggagggcagattggcactcggatcaaaagc i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 73305 35 - 95547 tttctggagggcagattggcactcggatcaaaagc i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 76091 35 + 225949 tttctggagggcagattggcactcggatcaaaagc i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 10678 35 + 21754 tttctggagggcagattggcactcggatcaaaagc i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 402 35 + 5481 tttctagagggcgggttggcacccgcatcaaaagc i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 47885 35 + 287808 tttccggaggacagattggcactcggatcaaaagc i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 675 35 - 10116 tttcaggaggactgactagcactcggatcaaaagc i tupBel1.scaffold_71658.1-10116 C 0 C 0 s mm9.chr11 118783712 35 + 121843856 TTTCTGGCAAGCAGAGCCGTGTGCCCGTCAAACGC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4410700 35 + 7991924 tatctggtgggcggactggtgcgcagatcaaaagc i cavPor3.scaffold_76 C 0 C 0 s turTru1.scaffold_98008 13190 35 + 223990 tgtctggagggccgagtagcacttggatcaaaagc i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10882415 35 - 65312493 tgtctggagggcagattggtacttggatcaaaagc i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58068704 35 - 61308211 ttcctggagggccgatgggcacctggatcaaaagc i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 49768 35 + 132007 ctcctggagggcagactggcgcttggatcaaaagc i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59462554 35 - 64418924 ctcctggagggcagattggcactcggatcaaaagc i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 37945 35 + 48268 ctcccagacggcagattggcacttggatcaaaagc i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_52062 664 35 + 16741 ttcccagagggcaaattggcacttggatcaaaaac i proCap1.scaffold_52062 C 0 C 0 s loxAfr3.scaffold_49 14458783 35 - 17734757 ttcccagagggcaggttggcacttggattaaaagc i loxAfr3.scaffold_49 C 0 C 0 e gorGor1.Supercontig_0007361 43207 157 - 64270 M e vicPac1.scaffold_72280 935 1824 + 3962 M e dasNov2.scaffold_85717 2219 316 + 6675 M e monDom5.chr2 304624775 9630 - 541556283 I a score=2708568.000000 s hg19.chr17_gl000204_random 75533 201 + 81310 tttccaaatgtgtttaacctttaactcggcaattccacttataggaatttaccctaaggagaaactcaggaacaa--acacaaagacttatctggaaagatttatgtactagaatatttgcaccattgctcataacatcaaaagattgaaaa-caaactaaa-tgtccaactccagggtgcttggtaaataatttgtgcactcat s panTro2.chr17 79507533 201 + 83384210 tttccaaatgtgtttaacctttaactcggcaattccacttatgggaatttaccctaaggagaaactcaggaacaa--acacaaagacttatctggaaagatttatgtactagaatatttgcaccattgctcataacatcaaaagattgaaaa-caaactaaa-tgtccaactccagggtgcttggtaaataatttgtgcactcat i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 43364 201 - 64270 TTTCCaaatgtgtttaacctttaactcggcaattccacttataggaatttaccctaaggagaaactcaggaacaa--acacaaagacttatctggaaagatttatgtactagaatatttgcaccattgctcataacatcaaaagattgaaaa-caaactaaa-tgtccaactccagggtgcttggtaaatagtttgtgcactcat i gorGor1.Supercontig_0007361 M 157 C 0 s ponAbe2.chr17_random 16092252 201 + 17838096 tttccaaatgtgtttaacctttaactcggcaattccacttataggaatttaccctaaggagaaactcaggaacaa--acacaaagacttatctggaaagatttatgtactagaatatttgcaccattgcttataacatcaaaagattgaaaa-caaactaag-tgtccaactccagggtgcttggtaaataatttgtgcactcat i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75066338 201 + 78773432 tttccaaatgtgtttaacctttaactcggcaattccacttataggaatttaccctaaggagaaactcaggaacaa--acacagagacttatctggaaagatttatgtactagaatatttgcaccattgcttataacatcaaaagattgaaaa-caaactaaa-tgtccaactccagggtgcttggtaaataatttgcgcactcat i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 73340 201 - 95547 tttccaaatgtgtttaacctttaactcggcaattccacttataggaatttaccctaaggagaaactcaggaacaa--acacagagacttatctggaaagatttatgtactagaatatttgcaccattgcttataacatcaaaagattgaaaa-caaactaaa-tgtccaactccagggtgcttggtaaataatttgcgcactcat i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 76126 199 + 225949 ttcccaaatgtgtttaacctttaactcggcaattccacttataggaatttaccctacggagaaactcaggaacaa--acgc--agactgagctgggaagatttatgtactagaatacttgcgccattgcttatgccatcaaaagattgaaaa-cgagctcca-tgtccagctccagggtgcttggtaaataatttgtgcactcat i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 10713 201 + 21754 tttcaaaatgtgtttaacctttaactcggcaattccacttataggaatttaccctaaggagaaactcaggaacaa--acacagagatttatctcgaaagatttatgtactagcatatttgcaccattgcttataacatcaaaagattgaaaa-gaaactaaa-tgttcaacaccagggtgcttggtaaataatttgtgCACTCAT i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 437 203 + 5481 tctcgaaatgtgtttaacatttaactcggcaatcccacgtataggaatttaccctcaggagaaactcgggagcaagggaacaaaggtttatctcaaaagatgtgtgcgctgcaatattggcaccactgcttacgacatcaaaagaccgaaaa-caaactaaa-tgtccaaccgcagggtgcttagtaaataatttgtgCACTCAT i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 47920 201 + 287808 tttcaaaatgtgtttaacctttaactcggcaattccacttataggaatttaccctaaggagaaactcaggcacaa--acacaaagatttatctcgaaagatttatgaactagaatatttgcaccgttgcttataacatcaaaagactgaaaa-caaacaaaa-tgtccaactccagggtgcttagtaaataatttgtgCACTCAT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 710 197 - 10116 tttggaaacgtgtttaacctctaacgcagcagttccacttgtaggaattcaccccaaggagaaa--cgggaacaa--acgccgagatctatctccacagacgtaggcactagaacgttcgcagcagtgcttacaacttcaaacggcagaaaa-caaaccaga-cgt-cgactgcagggtgctcggtaaataa-TCGCGCACTCAT i tupBel1.scaffold_71658.1-10116 C 0 C 0 s mm9.chr11 118783747 199 + 121843856 TTTCGACACGCAGCTAAGCTCTAGCTGGGAAATTGCACCTGTAGGATTCACCCC--AGGAGAAGCTCATAAACAA--ATGTGCAGTTTTGCTTAGGAAGACTTATGCGCCCGAATAGCCTCGGCATCGCAGCTAACATCAAAAGACAGAAAA-CAAACCAAG-CGTCCAGCTCGGGGGTGCTCGGTAAATAGCTGGTGCATTCAT i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4410735 200 + 7991924 tttcaaaatgtgtttaacctttcactcagcaattccacttgtaggaatttgccc--taaggagattgttgggaac--atgtgaagatttatcttgaaagattaatgtgctagaatatttgcaacattgcttataacatcaaaagattgaaaa-caaactaaaccggccaactctagggtactcggtaaataatttgtgCACTCAT i cavPor3.scaffold_76 C 0 C 0 s turTru1.scaffold_98008 13225 199 + 223990 ttccaaaatgtgtttaacctttaactcagcaattccacttgtaggaattcaccctaaggagaaactcaggaacaa--acgc--agatttatctcgaaagacttatgtactagaatatttgcagcattgcttatgacatcaagagactgaaaa-caaactgaa-tgtgcaactcctgggtgcttggtaaataatttgggcactcat i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10882450 201 - 65312493 ttccaaaatgtgtttaacctttaactcagcaattcaactcgtaggaattcaccctaaggagaaactcgggaacga--acgcaaaggtttatcttggaagatttatgtaccagaacatttgcagcattgcttatgacatcaaaagactgaaaa-caaactgca-catgcaactcctgggtgcttggtaaataacttgtgcactcat i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58068739 201 - 61308211 tttcaaaatgtatttaacctttaacccggctattccacttataggaatttaccctaaggagaatctcaggaacaa--acacggagacttatctcgaaagatttatgtgctggaatatgtgcagcattgctgatgacatcaaaagactgaaaa-caaactaaa-tgtccaacaccagggtgcttggtaaataattcgtgCGCTCAT i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 49803 195 + 132007 tttcaaattgtgtttaacctttaactcagcaattccacttgtaggaatttaccctaaggagaaactcaggagcaa--acgcaaagatttatctccaaagatttatgtactagaatatttgca-----gcttatggcatcaaaagactgataa-caggctgaa-tgtccagctccaggg-ggtcagtaaataatttgtgcactcat i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59462589 194 - 64418924 tttcaaattgtgtttaacctttaactcagcaattccacttgtaggaatttaccctaaggagaaagtcaggaacaa--atgcaaagatttatctccaaagatttatgtactagaatatttgca-----gcttatggcttc-aaagactgagga-caagctaaa-tgtccagctgcaggt-gcatggtaaataatttgtgcactcat i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 37980 202 + 48268 tttcgaaacgtgtttaacctttaactcggcaattccgcttgtaggaatttgccctaaggagatgctcagggacaa--gcgcgaagatttatctcaaaagatttatgtactagaatgtttgcagcaacgcttacgacatcgaaagaccgaaaagcgagccgaa-tgcccaacTCCGCGGTGCCCAGTAAACAACCTGCGCACTCAT i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_52062 699 201 + 16741 tctcaaagtgtatttaacctttaacgcaacaatttcacttgtagaaatgtaccctaaggagaaagtcagagacaa--atgggaagatttctctacaaagatttctgcactagaatattggcaggattgcttatgatatcaaaagaccgcaaa-caaactaaT-CACTCAGCTCCAGGGTGCTCAGTAAATAATCTGTATGCTCAT i proCap1.scaffold_52062 C 0 C 0 s loxAfr3.scaffold_49 14458818 193 - 17734757 tctcaatgt-tgtttaacctttaacacaacaattccac--ataggaatttatcctaaggagaaactcagagacaa--atgcaaagatttctctagaaagatttctgaactagaatatttgcagcattgcttaagatgtcaaa-----gaaaa-caaactaat-cgtccaactccagggtgcttggtaaataatttgtgCACTCAT i loxAfr3.scaffold_49 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e dasNov2.scaffold_85717 2219 316 + 6675 M e monDom5.chr2 304624775 9630 - 541556283 I a score=1201360.000000 s hg19.chr17_gl000204_random 75734 205 + 81310 taaaaatcctattgtagaagaatattgaatgccattgcaaagtgtt--tataaaccat----taaatgaaaagatttat--aaaacagaa-tgtgcaaagcaatccc-a-TTATACT-CCCCAGGCCTCCGAAGCaggctggaaggacac--actcctg-g-------gcctggcagcggtttc-ctctgtgtaag--tggacgacgggctattt---tgt---at--tttct-ttttt s panTro2.chr17 79507734 205 + 83384210 taaaaatcctattgtagaagaatattgaatgccgttgcaaagtgtt--tataaaccat----taaatgaaaagatttat--aaaacagaa-tgtgcaaagcaatccc-a-TTATACT-CCCCAGGCCTCCGAAGCaggctggaaggacac--actcctg-g-------gcctagcagcggtttc-ctctgtgtaag--tggacgacgggctattt---tgt---at--tttct-ttttt i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 43565 205 - 64270 taaaaatcctattgtagaagaatattgaatgccattgcaaagtgtt--tataaaccat----taaatgaaaagatttat--aaaacagaa-tgtgcaaagcaatccc-a-TTATACT-CCCCAGGCCTCCGAAGCaggctggaaggacac--actcctg-g-------gcctggcagcggtttc-ctctgtgtaac--tggacgacgggctattt---tgt---at--tttct-ttttt i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16092453 205 + 17838096 taaaaatcctattgtagaagaatattgaataccattgcaaagtgtt--tataaaccat----taaatgaaaagatttat--aaaacagaa-tgtgcaaagcaatccc-a-TTATACT-CCCCAGGCCTCCGAAGCaggctggaaggacac--actcctg-g-------gcctggcagcggtttc-ctctgtgtaag--tggacgatgggctattt---tgt---at--tttct-ttttt i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75066539 205 + 78773432 taaaaatcctattgtggaagaatattgaatgtcattgcaaagtgtt--tataaaccat----taaatgaaaagatttat--aaaacagaa-tgtgcaaagcaatccc-a-TTATACT-CCCCAGGCCTCCaaagcaggctggaaggacac--actcctg-g-------gcctgctggcggtttc-ctctgtgtaag--tggacgacgggctattt---tgt---at--tttct-ttttt i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 73541 205 - 95547 taaaaatcctattgtggaagaatattgaatgtcattgcaaagtgtt--tataaaccat----taaatgaaaagatttat--aaaacagaa-tgtgcaaagcaatccc-a-TTATACT-CCCCAGGCCTCCaaagcaggctggaaggacac--actcctg-g-------gcctggcggcggtttc-ctctgtgtaag--tggacgacgggctattt---tgt---at--tttct-ttttt i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 76325 204 + 225949 taaaaatcctattgtagaagaatattgaatgccattgcaaagcgttcgtataaaccat----taaacg-aaagatttct--aaaac--aa-tgtgcagtgcaatccc-a-TTAGGCG-CCCCAAGCCTCCAAAGCAGGCTGGAGGGACAC--GCTCCCG-G-------GCCTGGTGgcggttgc-cactgcgtgag--cggatgacgggcaatgt---tgt---at--tttct-ttttt i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 10914 201 + 21754 TAAAAACCCTATTGCAGAAGAATGTTGAATGCCATTGCAAAGAGTT--TATAAACCAT----CGAGTAAAAAGATATGC--AAAACAGAA-TGTTCAACACAATCCC-A-TTACACT----CAGGCTTCCaaagcaggctggaaggacac--ccttcca-g-------gactggcagcgatttc-ctctctgtaag--tggacgat-ggtaactt---tgt---at--tttct-ttttt i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 640 216 + 5481 TAAAAATCCTCCCGTAGAAGGATAGGGAAGGCC-ATTGCGAGTGCG--TGCAAACCAT----CGGATGAGAAGTTTTGT--GAAACGGAAATGCGCAGCGCAATCCG-G-CTGTGCTTCCCCGGGTCCCCAGGGCAGGCTGGCAGGACACCGCCCCCCC-ACGCACAGGGCCGGcagtgagctc-ctccgggtaag--tgtgccacgggcgattt---tgc---gt--tttctgttttt i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 48121 192 + 287808 TAAAAATCCC----------AATGCGGAAGATC-TTGCAAAGTGCT--TATAAACCAT----CTAAGGAGACGGTTTAT--GGAGCAGAACTGTGCAGGGCGACCCA-G-TTACAC--ACCCTGGCCTCCAGGGCAGGCTGGAAGGAC----CCTCCCC-A-------GGGCAGCAGCGACCTC-CTCTAGGGAAG--AGGGTGACCGGCAATTT---TGT---AT--TTTCC-TTTTT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 907 179 - 10116 TAAA---CCTACTGTGG---AATATTGCACACC-GCGCCGAGTGCT--CATAAACCAT----CAGACGAGAAGGC-TAC--ACCACAGAA-CGCA-AGTGCGATCCCGA-CTGCCCT-CCCCA-GTCCCGAAAACAGGCTGGAAGGACAG----------------------GGCGGCGGCTCC-CTCCATGCGAG--CGGACAAC-GGCGAT-------T---GT--TTCCT-TGTTT i tupBel1.scaffold_71658.1-10116 C 0 C 0 s mm9.chr11 118783946 153 + 121843856 TAAAAATCCTACCACAGAAAAAAAC------CTTTGG-----------------GTGT----CA---------------------------------------CTGC-A-GTGTGTT--CATAAGC--CACAGGAGGGTTGGAAGGAGGA--ACTGCAG-G-GTGGAAGGGCAGTGACACCAAG-TCCTTTGCAAATTTGGACAACGGGTGACTT---TGT---GT--tttct-ctctt i mm9.chr11 C 0 I 2168 s cavPor3.scaffold_76 4410935 177 + 7991924 TAAAACCGCTATTGTAGAAGAATAC-GAATACTGTAGCAAGGAGCT--TATAAAGTGT----TAAATGAAA--------------------T-----------CCCA-A-ATATACT--CATAGGCCTCTCAACACGGCCGGAAGGACTT--GCTCCCG-G-------GGCCAGCAGCTATTGC-CTCTGTGCCAG--CGGACAACGGGTGATTTGGGTGT---GT--TCTTT-TTTT- i cavPor3.scaffold_76 C 0 C 0 s turTru1.scaffold_98008 13424 198 + 223990 taaaaaccctaccatagaagaatattcaataccactgcaaagtgtt--cat-agcctt----caaatgggaaggtttat--aaaacagag-tgtgcaatacaatgcc-atttATAC--TCCCCAGGCCCTGAAACAGGATGGAGGGACAC--AGTCTCT-T-------GGCCGGCAGTGATTCC-CTCTGTACAGG--TGAACAATGGGTAATTT-------------TTCTT-TTTG- i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10882651 204 - 65312493 taaaagtccttctgtagaagaatattcggtgccatcgcaaagtgct--cataaGGCTT----TGAATGGAAAGATTTCT--AAAAC--AG-TGTGCAGTGCAATGCC-ACTTACAC--TCTCCAGGCCCTGGAACAGGCTGCAGGGACAC--ACTCTCT-T-------GGCTGGAAGTGATTCC-CTCCATACAGA--TGAACAATGGGTAATTT---TTT---ATTGTTCTT-TTTT- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58068940 182 - 61308211 TAACAATCCTGTTGTAGGAGGATATTGAATGCCATTGCAGAGTGTT--TAT------------------------------ACAACAGAA-TGCGCGGTGCAAAGCC-GTTTCTACT-CCCCGAGTCTCTGaaacaggctggagggacgc--gctcgccag-------ggccagcagccattcc-ctcagcggagg--tgaatgacaggcaattt---tta---tt--ttctt-tttt- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 49998 204 + 132007 taaaaatcctattgtggaagaatattgaatgccgtggcgaagtgtt--cgtaaaccat----caaatgaaaaGGTCTAT--AAACCCGAC-TGTGCCATACAGGGCC-AATTATATG-CCTTCAGCCTCCagaacaggctagaaggactc--accctccag-------ggctggcagcgattcc-ctctgc--aga--tgggcgctgggtgattt---tgt---ta--tttgt-tctt- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59462783 204 - 64418924 taaaaatcctattgtagtagaacattgaatgccactgcaaagtgtt--cataaGCCAT----CAAATGAAGAGGTTTATAAAAACCAGAA-TGTGCAGTA-AGTGCC-AATTCCATG-CCTCCAGCGTCCAG-ACAGGATGGAAGGATGC--AGCCTCCAG-------GGCTGGCAGCAACTCC-CTCTGT--AGA--TGGACATCGGGTGGTTT---ATT---CA--TTCAT-CTTT- i canFam2.chr9 C 0 I 4 s pteVam1.scaffold_11245 38182 188 + 48268 TAAAGCCC----TCCCGGAGAACAATGAA-GCCGCTGCAAAGGGTT--TGCGAGCCAGGGAACAAACGAACAGGTTTCT--AAGACTAAA-CGCACCTTGCGACGTA-AACGACACG-GCCGCTGCAGCCAG--------------ACAC--GCCCTCC-G-------GGCCAGCAGCCATTCC-CTCCGTGCAGG--TGGACAGCCGGCAATTC---TTT---C----TCGT-TTTT- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14459011 207 - 17734757 TAAAAATCCTATCCTAGGGAAATATCGACTGCCTTTGCAAAGTGTT--TATAAACCAT----CAAATGACAAGGTTTAC--AAAACAGAG-CATGCTAGGCAACCCC-AGTGATCCT-CCACAGGCCTAAAATCCAGGCTGGAAGA-CAG--ACTCTCCAG-------GCTCAGCTGTCATTCC-CTCTCTGTAGA--CAGGTAACAGGTAATAG---TCTT--AT--TTTCT-TTTTT i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_52062 900 205 + 16741 TAAAAATCTTATCCTAGGGAAATACTGAATGCCTTCGCAAAGCATT--TATAAACCAC----CATGTGACGAGG-TCAC--CAAACTGAG-CACATGATACACATCC-AAATGTCCC-CCGCA-GCCTGGACTTCAGGCTGAAAAA-CAA--GCCCTCCGG-------GGTCCGCAGCCATTTC-CTCTCTGGGAG--TGGGTAACAGGTAATAG---TCTT--AT--TTTCT-GTTCT i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 2535 211 + 6675 TAAAAATCCCATTGTGGAAGAATATCGGATGCCACTGCAAAGTGTT--TATAAACCAT----CAGACGCAAAGGTTTAT--AGAACAGAA-TGTACAAAACCTTCCC-AATTATTCT-CCACTGGGCTCTCAAGCCAGCTGCAAGAGCGC--CTTCTCTGG-------GGTGGGCCGTGACTTCGCTGTGTGTGGG--TGGACAATGGGAGATTT---TTTTCAAT--GTTCC-TTTTT i dasNov2.scaffold_85717 M 316 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e monDom5.chr2 304624775 9630 - 541556283 I a score=518851.000000 s hg19.chr17_gl000204_random 75939 52 + 81310 gaattttatgattatattctaaattttctacattggatctgaatcgtatttg s panTro2.chr17 79507939 52 + 83384210 gaattttatgattatattctaaattttctacgttggatctgaattgtatttg i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 43770 52 - 64270 gaattttatgattaaattctaaattttctacattggatctgaattgtatttg i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16092658 52 + 17838096 gaattctatgattatattctaaattttctacattggatctgaattgtatttg i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75066744 52 + 78773432 gaattgtgtgattatattctaaattttctacattggacctgaattgtatttg i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 73746 52 - 95547 gaattttatgattatattctaaattttctactttggacctgaattgtattta i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 76529 51 + 225949 gaattttatgattatattccaaa-tttctacattgggcctgaattgtatttg i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 11115 51 + 21754 gaattgtattg-tatattctaaaatatctacattggacctgaattgtatttg i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 856 51 + 5481 ggattttatta-tatattctaaattttatacgttggacctgattggtattta i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 48313 51 + 287808 GAATTTTATTG-CATGTTCTAGGCTTTCTACATTGGATCTGATTTGTATTTA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 1086 50 - 10116 GCGTTTTATG--TGCATACTGAATTTTTCACATGGAAACTGAAGTGTATTAG i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4411112 51 + 7991924 AAATTTTATTG-CATATTCTACATTTATTATGTTGGCTCCGAGTTGCATTTG i cavPor3.scaffold_76 C 0 C 0 s turTru1.scaffold_98008 13622 51 + 223990 AAATTTTATTT-TATATTCTAAGTTTTCTACGTTGGATCTCAACTGCATTTG i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10882855 51 - 65312493 GAACTTCATTG-TATATTCTAAGTTTTCTATGTTGGATCTCAATCATATTTG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58069122 51 - 61308211 gaattttgttg-tgtagtccaagttttctacattgaacctgaattgcattgg i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 50202 51 + 132007 gaactttcctg-tctacactaagtctcccaccttggatctgaattgtgtttg i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59462991 48 - 64418924 GAATTTTATTG-TCTACCCTAAGTTTTCTAAAGGGGACCTAAACTA---TTG i canFam2.chr9 I 4 C 0 s pteVam1.scaffold_11245 38370 51 + 48268 GAATTTTCTCG-TGTAGTCCAAGTTTTCTATATTGGACCTGAATTGTATTTG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14459218 51 - 17734757 GAATTCTATTG-TCTATTCCAGACTTTTTGCATTGGACTTAGACTATATTTG i loxAfr3.scaffold_49 C 0 I 418 s proCap1.scaffold_52062 1105 51 + 16741 GAATTTTATTG-TCTAGTCTAGACTTCCCACATTGAATTTCAGTTACATTTG i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 2746 51 + 6675 GAATTTCATTG-TCTATTCTAAATTTCCTACATTGACCCCGAATTACAGTTG i dasNov2.scaffold_85717 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e monDom5.chr2 304624775 9630 - 541556283 I e mm9.chr11 118784099 2168 + 121843856 I a score=231247.000000 s hg19.chr17_gl000204_random 75991 54 + 81310 taa------tta-agaaaaCTATAAGGAAAAA-TTT----TTTAACTTGGTAAGGCATGTCATGG-A s panTro2.chr17 79507991 54 + 83384210 taa------tta-agaaaaCTATAAGGAAAAA-TTT----TTTAACTTGGTAAGGCATGTCATGG-A i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 43822 54 - 64270 caa------tca-agaaaaCTATAAGGAAAAA-TTT----TTTAACTTGGTAAGGCATGTCATGG-A i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16092710 55 + 17838096 taa------tca-agaaaaCTATAAGGAAAAATTTT----TTTAACTTGGTTAGGCACGTCACGG-A i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75066796 56 + 78773432 tca------tca-agaaaaCTATAAGGAAAAAATGG----TTAAACTTGGTTAGGCATGTCATGGAA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 73798 55 - 95547 tca------tca-agaaaaCTATAAGGAAAAAATGG----TTAAACTTGGTTAGGCACGTCATGG-A i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 76580 55 + 225949 tca------tca-ggaaaaCCATAAGGGAAATGTTT----TTAAACTTGATTAGACATGTCATGG-A i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 11166 54 + 21754 taa------tca-gaaaaaaTATAAGGAGTAT-TTT----TACAATTCAAATAGAAATGGTATAG-G i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 907 54 + 5481 taa------tca-ggaaaaTTATAAGGAATTT-TTT----AAAAATCCTATTAGCAGTGTTGGAG-A i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 48364 60 + 287808 GAAAATTATACA-GGAAAATTATAAGGAATAT-TTT----AAAAATTCAATTAGAAATGTTAAAG-A i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 1136 48 - 10116 TGA------TGA-GGGAA--TAGAAGAAGTGC-CTT----TTACACATG----GATGCGTTACAG-A i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4411163 54 + 7991924 TAA------TCA-GGAAAAACATGAGAAAGTT-TTG----AAACATTTGATCAGAAACAGTACAG-A i cavPor3.scaffold_76 C 0 C 0 s turTru1.scaffold_98008 13673 53 + 223990 TAA------CCA-GGCAAAATATAAGGAGTGT------CGTTTAATACAATTAGAAATGTTACAG-A i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10882906 54 - 65312493 TAA------CCA-GGAAAAATATAAGGAGTAT-TTTTACGTTT----TGATGAGAAATGTTACAG-A i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58069173 52 - 61308211 taa------tca-ggaaaaaTATAAGGAGTAT-TT-----TTTAATTTGATTGGG-ATGTTACTG-A i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 50253 54 + 132007 taa------tca-agaaaaaCATAAGGAGCGT-TTT----TCTAATTCGATTAGACACGTTACAG-A i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59463039 56 - 64418924 TAA------TCA-AGAAAAATACAAGGAGTGT-TTT--TATTTAACTCGATTAGAAATGTTACAG-A i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 38421 53 + 48268 TCA------TCA-GGAAAAACGTAAGGGAGTT-CT-----TTAAATTCAATCACAAACGTTCCAG-A i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14459687 49 - 17734757 TAA------TTACTAAAA------AGGATCAC-TTT----TTGAGTTCAATTAAAAACGTTATAC-C i loxAfr3.scaffold_49 I 418 I 2 s proCap1.scaffold_52062 1156 29 + 16741 TAA------TCA-GGAAA------ATGataat-ttt----ttaaatt-------------------- i proCap1.scaffold_52062 C 0 I 477 s dasNov2.scaffold_85717 2797 50 + 6675 TAG------TCA-GGAAAA-TATGAGGATGAC-TTT----TTACCTTCAATTAGG---GTTTTAC-C i dasNov2.scaffold_85717 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e monDom5.chr2 304624775 9630 - 541556283 I e mm9.chr11 118784099 2168 + 121843856 I a score=92753.000000 s hg19.chr17_gl000204_random 76045 29 + 81310 TCCAGTTTCTCCCCCAAGGT-ACCAG-CTCA s panTro2.chr17 79508045 29 + 83384210 TCCAGTTTCTCCCCCAAGGT-ACCAG-CTTA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 43876 29 - 64270 TCCAGTTTCTCCCCCANGGT-ACCAG-CTCA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16092765 29 + 17838096 TCCAGTTTCTCCCCCAGGGT-ACCAG-CTCA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75066852 29 + 78773432 TCCAGTTTCTCCTCCAAGGT-ACCAG-CTCG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 73853 29 - 95547 TCCAGTTTCTCCTCCAAGGT-ACCCG-CTCG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 76635 16 + 225949 GCCAGTTTCTCCCCCA--------------- i calJac1.Contig5139 C 0 I 362 s tarSyr1.scaffold_41848 11220 28 + 21754 ATTCGTTTATCCTCCTATGT-GGCAG-CTC- i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 961 28 + 5481 GGCCGCTTATCCTCCA-GGT-ACCTG-CTCG i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 48424 28 + 287808 GCCCCTTTATCCTCCA-AGT-ACAGG-CTCA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 1184 29 - 10116 GGCAGCCTGTGCCCCAGCGT-GGCGT-CTCA i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4411217 14 + 7991924 GTC----------CCAAGGG-AAGG------ i cavPor3.scaffold_76 C 0 C 0 s turTru1.scaffold_98008 13726 29 + 223990 GGTAGTTTATCTGCCAGCAC-ACCAG-CTCG i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10882960 29 - 65312493 GGCAGTTTATCTGCCAGTGC-ACCAG-CTCG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58069225 29 - 61308211 GGCCGTTTATCCTCCAATGC-ACCAG-CTTG i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 50307 18 + 132007 G-----------GCCGGAGC-GCCAG-CTTG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59463095 29 - 64418924 GTTGATTTACCCTCCAGGGG-ACGAG-CTTG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 38474 28 + 48268 GGCAGCTTGTCCTCCAGTGC-ACTGG-CCT- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14459738 29 - 17734757 CCAAGTTTACCCTCCAAGAT-ACTAG-CTTG i loxAfr3.scaffold_49 I 2 C 0 s proCap1.scaffold_52062 1662 31 + 16741 TCGAGTTTGCCCTCCAAGGTAACCAGCCTTG i proCap1.scaffold_52062 I 477 C 0 s dasNov2.scaffold_85717 2847 29 + 6675 TGCAGTTTACCCTCCAAGGT-ACGAG-TCTG i dasNov2.scaffold_85717 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e monDom5.chr2 304624775 9630 - 541556283 I e mm9.chr11 118784099 2168 + 121843856 I a score=150737.000000 s hg19.chr17_gl000204_random 76074 91 + 81310 CAGGGGAA---------------GGAAGACTAAAGGACTGCTCCCTGATGAACGTGGGG---ATCCGCCT-GTAGGGTTTCCACGATGCTCGAGAACCCCGCAGAGTCTC s dasNov2.scaffold_85717 2876 70 + 6675 CAAGGGGA---------------AAAAG-GGAGAAGGTT-----CTGTTGCATGTGGAC---ATTCAT-T-GTAGGGCTCTTGGCCGCCT--------------TCTCCT i dasNov2.scaffold_85717 C 0 C 0 s proCap1.scaffold_52062 1693 73 + 16741 CCAGGTAA---------------GGAAGCACCGAAAGCTGTCC-CAGAGACAC---AGG---ATTGGTGG-GCAGAGTTTTCACACTGCA--------------GCTCTC i proCap1.scaffold_52062 C 0 C 0 s loxAfr3.scaffold_49 14459767 77 - 17734757 CAGGGGAA---------------GGAAGAGAAGAAGGCTGTTG-CCGAGACACGTGGGG---ATTCACAT-GCACGGTTTGTAAACTGCA-------------GGCTCCT i loxAfr3.scaffold_49 C 0 C 0 s pteVam1.scaffold_11245 38502 54 + 48268 -----------------------GCAGAAT-CGAAGATGCCTG-CCGATAAATGCGGG-----CCCCCCA-GCAGGGTCT--------------------GAAGG----- i pteVam1.scaffold_11245 C 0 C 0 s canFam2.chr9 59463124 83 - 64418924 ATGGGGGGGGGGGTGGGAGGGACGGAGGAT-GGAAGGCA-TCC-CTGATGAATGTGGGG---AGCCACCT-GCAGGGTTT--------------------GAAGGTTCTC i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 50325 68 + 132007 CAGGAGGA---------------GGAAGAA-TGAAAGCA-GCC-CTGATAAATGCGGGG---AGCCGCCT-GCAGGGTCG--------------------GAAGGTTCTC i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58069254 70 - 61308211 CAGGGTGA---------------GAAAGAACAGAAAACACTTC-CTGGTGAGCGTGGGG---ATGCCCCT-GTTGGGTGG--------------------GAAGGCTCTC i equCab2.chr11 C 0 C 0 s bosTau4.chr19 10882989 69 - 65312493 AAGCAGGA---------------GGAAGAA-TCAGGACAGTTC-CTGATAAAGGCAAGG---CTCTACCT-GCGGGGGTG--------------------AAAGGTCCCC i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 13755 69 + 223990 CAGGGGGA---------------GGAAGAA-TCTGGACAGTTC-CTGATAAACACAGGG---CCCCACCT-GCAGGGGTG--------------------AAAGGTTCCC i turTru1.scaffold_98008 C 0 C 0 s cavPor3.scaffold_76 4411231 91 + 7991924 -AAGGGAA---------------GGAGAAATAGAAGCTGGCTT-CCAGCAAACATGGGGATCATCTACCCAGTAGGGTTT--ACGGGACTCAGAACGTGGGCGGGGCCTC i cavPor3.scaffold_76 C 0 C 0 s tupBel1.scaffold_71658.1-10116 1213 87 - 10116 CAGGG-GA---------------AAAAGGATAGGAGACGGCTC-CTGGCAAATGCAGGG----TCCACC--ACAGGCCGCCTCGGGTGCTCAGGAACTCTGCGGTTTCCC i tupBel1.scaffold_71658.1-10116 C 0 C 0 s otoGar1.scaffold_94362.1-287808 48452 88 + 287808 CAGGG-AA---------------GGAAGACAAGGAGACCACTC-CCACCCAGCGTAGGG----GCCTCCT-TCAGGGTTCCCACAATGCTCAAGGACCCTGCAGTCTCCT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_38207 989 88 + 5481 CAGGG-GA---------------AGGAGGCCGAGAAGACAGTG-CCACTCAGCGTGGGT----GTCGCCT-GCAGGGTGTCAACTACGCACGAGGACCCTGCAGGCTCCT i micMur1.scaffold_38207 C 0 C 0 s tarSyr1.scaffold_41848 11248 89 + 21754 CAGGGGAA---------------GGAAGACTATAAGACCTCTC-CTGACCAATGTGGGG----TCCGCCT-GCAGGGTTCTCAGGATGCTTGAGAACCCTGTAGAGTCTC i tarSyr1.scaffold_41848 C 0 C 0 s calJac1.Contig5139 77013 88 + 225949 CAGGGGAA---------------GGAAGACTAGAAGGCTGCTCCCTGATCAACATAGGG----TCCGCCT-GTAGGGTTTCCACGATTCTCCAGAACCCCACAG--TCTC i calJac1.Contig5139 I 362 C 0 s papHam1.scaffold8336 73882 74 - 95547 CAGGG--------------------------------CTGCTCACTGATCAATGTGGGG---GTCCGCCT-GTAGGGTTTCCACGATGCTAGAGAACCCCACAGAGTCTC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75066881 74 + 78773432 CAGGG--------------------------------CTGCTCCCTGATCCATGTGGGG---GTCCGCCT-GTAGGGTTTCCACGATGCTAGAGAACCCCACAGAGTCTC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16092794 91 + 17838096 CAGGGGAA---------------GGAAGACTAAAGGACTGCTCCCTGATCAACGTGGGG---GTCTGCCT-GTAGGGTTTCCACGATGCTCGAGAACCCCGCAGAATCTC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 43905 91 - 64270 CAGGGGAA---------------GGAAGACTAAAGGACTGCTCCCTGATGAACGTGGGG---GTCCGCCT-GTAGGGTTTCCACGATGCTCGAGAACCCCGCAGAGTCTC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79508074 91 + 83384210 CAGGGGAA---------------GGAAGACTAAAGGACTGCTCCCTGATGAACGTGGGG---GTCGGCCT-GTAGGGTTTCCACGATGCTCGAGAACCCCGCAGAGTCTC i panTro2.chr17 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e monDom5.chr2 304624775 9630 - 541556283 I e mm9.chr11 118784099 2168 + 121843856 I a score=102306.000000 s hg19.chr17_gl000204_random 76165 43 + 81310 AGGCCTTTGACCAAGAAGACTCC---AGAGTGAGCGCCTT-AGGGAA s panTro2.chr17 79508165 43 + 83384210 AGGCCTTTGACCAAGAAGACTCC---AGAGTGAGCGCCTT-AGGGAA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 43996 43 - 64270 AGGCCTTTGACCAAGAAGACTCC---AGAGCGAGCGCCTT-AGGGAA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16092885 43 + 17838096 AGGCCTTTGACCAAGAAGACTCC---AGAACGAGCGCCTT-AGGGAA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75066955 41 + 78773432 AGGCCTTTG--CAAGAAGACTCC---AGAGTGAGCGCCTC-AAGGAA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 73956 43 - 95547 AGGCCTTTGACCAAGAAGACTCC---AGAGTGAGCGCCTT-AGGGAA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 77101 43 + 225949 AGGCCTTTGACCAAGAAGACTCC---AGAGCAAGCACCTT-AGGGAA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 11337 33 + 21754 AGGTCTTTGACCAAGAA-------------TCAGCGCCTT-ACGGAA i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 1077 46 + 5481 GAGCCTTGGAGCTCAGAGGCCCATGGAGAGTCTGAGCCCT-GGGGAA i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 48540 35 + 287808 --GCCTTTGACCAAGAAAGAC-----AGAGT----GCCCC-AGGGAG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 1300 28 - 10116 AGGCCT--GGCCAAGAAGCTCAC---AGAATGA-------------- i tupBel1.scaffold_71658.1-10116 C 0 I 247 s cavPor3.scaffold_76 4411322 38 + 7991924 GTGCCTACAACTGGGGAG-CCCC---AGAG----CGCCTT-AGAAAG i cavPor3.scaffold_76 C 0 C 0 s turTru1.scaffold_98008 13824 39 + 223990 ATGCCTTTGACCAAGAAGCTGAG---GGA----GTGCAGT-AGTCAA i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10883058 27 - 65312493 GTGCCTTTGACCAAGAAGCTGAG---GGA----A------------- i bosTau4.chr19 C 0 I 4 s equCab2.chr11 58069324 38 - 61308211 GTGCCTTTGA-CAAGAAGCTGAT---GGA----GCGCCCT-GGTAGA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 50393 40 + 132007 CTGCCTCTGACCGGGAAGCTGAC---GGA----GCGCCCCGGGGAGC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59463207 39 - 64418924 ATGCCTTTGACCAAGAAGCTGAC---AGA----GCGCCTC-GGGAGA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 38556 38 + 48268 -GACCGGCGACCGAGAAGCTGGA---AGA----GCACCTC-AGGACA i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14459844 39 - 17734757 GTGTCTTTGACCAACACATGTAG---ACA----GCGCCTC-AGGAAG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_52062 1766 36 + 16741 GTGG-TTTGACCAACACATCTAG---ACA----GCGCCTC-AG--AA i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 2946 36 + 6675 GC---TTTGACCAAGGAGCCCGC---GGA----GCACCTT-AGGAAA i dasNov2.scaffold_85717 C 0 C 0 s monDom5.chr2 304634405 38 - 541556283 AAGCCTTTGACTTGAAAATCTGC---AGT----ATATGCT-GAGAA- i monDom5.chr2 I 9630 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e mm9.chr11 118784099 2168 + 121843856 I a score=370063.000000 s hg19.chr17_gl000204_random 76208 123 + 81310 ACACGGTCGGCCAAGCAT-----------------------------------------------------------GC--AGCACCTCCGT-GCCCAGACTGGATAC-GGCACTAATGATGC---------------------------------------------------------------------------------------------------------------------AAACAAGTCATC-GCTC---AGTCAGGGAGATG--GGTCATTGTTGCTGTTGTTTTTA--TTTGTTGTTCA s panTro2.chr17 79508208 123 + 83384210 ACACGGTCGGCCAAGCAT-----------------------------------------------------------GC--AGCACCTCCGT-GCCCAGAATGGATAC-AGCACTAATGATGC---------------------------------------------------------------------------------------------------------------------AAACAAGTCATC-GCTC---AGTCAGGGAGATG--GGTCATTGTTGCTGTTGTTTTTA--TTTGCTGTTCA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 44039 123 - 64270 ACATGGTCGGCCAAGCGT-----------------------------------------------------------GC--AGCACCTCCGT-GCCCAGACTGGATAC-AGCACTAATGATGC---------------------------------------------------------------------------------------------------------------------AAACAAGTCATC-GCTC---AGTCAGGGAGATG--GGTCATTGTTGCTGTTGTTTTTA--TTTGTTGTTCA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16092928 123 + 17838096 ACACGGTCGGCCAAGCGT-----------------------------------------------------------GC--AGCACCTCCGT-GCCCAGACTGGATAC-AGCACTAATGATGC---------------------------------------------------------------------------------------------------------------------AAACAAGTCATC-ACTC---AGTCAGGGAGATG--GGTCATTGTTGCTTTTGTTTTTA--TTTGTTGTTCA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75066996 123 + 78773432 ACACGGTTGGCCAAGCGT-----------------------------------------------------------GC--AGCACCTCCAT-GTCCAGACTGGATAC-AGCACTAATGATGC---------------------------------------------------------------------------------------------------------------------AAACAAGTCATC-GCTC---AGTCAAGGAGATG--GGTCATTGTTGCTGTTGTTTTTA--TTTGTTGCTCA i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 73999 123 - 95547 ACACGGTCGGCCAAGCGT-----------------------------------------------------------GC--AGCACCTCCAT-GTCCAGACTGGATAC-AGCACTAATGATGC---------------------------------------------------------------------------------------------------------------------AAACAAGTCATC-GCTC---AGTCAAGGAGATG--GGTCATTGTTGCTGTTGTTTTTA--TTTGTTGCTCA i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 77144 122 + 225949 ACGCGGTTGGCCAAGCGT-----------------------------------------------------------G---AGCACCCCTGT-GCCCCGACTGGCTAC-GGCACTAATGATGC---------------------------------------------------------------------------------------------------------------------AAAGGAGTCGTC-GCTC---AGTCAGGGGGATT--GGGCCTCGTTGCTGTGGCTTTTG--TTTGTTTTTCA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 11370 117 + 21754 ACATGGTGGACCAGGTAT-----------------------------------------------------------GT--AGCACCTTCAT-TCAC------GTTGC-AGCACTGATTGTGT---------------------------------------------------------------------------------------------------------------------AAACAAATCATT-GCCC---AGTCAAGGAGGTT--TGTTGTTGGTGCTGTTGTTTTTG--TTTGTTGATCT i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 1123 102 + 5481 ACG------GCCAGCCAG-----------------------------------------------------------GC--TGCAGCACCCC-GGGCTGACTCCACGT-GGCACTAATTATGC---------------------------------------------------------------------------------------------------------------------AAATGAGTCGTC-CCATCAGGGTCAGGGAGATG--GGTCGCTACTGCTGTT-------------------- i micMur1.scaffold_38207 C 0 I 492 s otoGar1.scaffold_94362.1-287808 48575 114 + 287808 ACGCAG-CAGCCAAGCAG-----------------------------------------------------------GC--AGCA-CCCCCC-ATCCACACTCAGTAC-AGTGCTGATTATGC-------------------------------------------------------------------------------------------------------------------TGAAACGAATTGTC-ACCC---GGTCAGGGAGATT--GGTGGCT---------GTTTCTG--TTTGTTGGTCA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 1575 180 - 10116 GCACGGGCCACTGGGCATCGCCGTGGAACACACAGGCCCCTGAGTGACACCGTGGGAATGCACAGGCCCCTGAATGCAT--GGTATCTCCGT-GCACCAGCTGGAGAC-AGCCCAAACCGTGC---------------------------------------------------------------------------------------------------------------------GGCTAAGTCACT-GTCC----CCCAGGGAGAGC--TGCTG-TGTTGCTGTGGCTTTTG--CTCGTTGCTCA i tupBel1.scaffold_71658.1-10116 I 247 C 0 s cavPor3.scaffold_76 4411360 237 + 7991924 AGG-GGTCAGCAGAACAC-----------------------------------------------------------GG--AGCCACTCCA--ATGCAGACTGGACCC-AGTACTAATTATGAAAATTAATCACggggctgggggtttagctcagcggcataagcacctgccttgaaagcaggcagtcgtgagttcgatccctggtaccgataaaaaggAAAAAGACAAAAAAAAAAAGAAAATGAATCACT-GCCC---ATTC-GGGAGCCC--TCTTGTTGCTGCTGTGGTTTTTA--TTTGTCTCTCA i cavPor3.scaffold_76 C 0 C 0 s turTru1.scaffold_98008 13863 63 + 223990 -------------------------------------------------------------------------------------CCTCTT--GACCTCCCTTTTCA--------------------------------------------------------------------------------------------------------------------------------------------------GATT---AAG------------TGTTTtttttgtttttgtttttgtttttgtggtaca i turTru1.scaffold_98008 C 0 I 255 s equCab2.chr11 58069362 114 - 61308211 ACTCAGTCAGCCAAGCGT-----------------------------------------------------------GA--CGCACCTTGAC-GCACGGACTTGACAC-AGTGCTAATTATGC---------------------------------------------------------------------------------------------------------------------AAATAAATCATT-GGCT---GATCGGGGACAT-----------TTGCAGTTGTTTTTA--TTTGTTGCTCA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 50433 122 + 132007 ACAC-GCCGGCT--GCCA-----------------------------------------------------------GC--CGCACCTCGCCTGAGCTGGCTTGACCC-GGCGCTGATTATGC---------------------------------------------------------------------------------------------------------------------AAATCCATCACTGGGCT---AATCAGGGAGATG--TGTCTTTGCTGCCGTTGTTTTTA--TTTGTTGCTTG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59463246 120 - 64418924 ACACGGTCGGCT--GCGC-----------------------------------------------------------GC--TGCACCTCGC--GAGCTGACTTGACAC-AGCGCTGATTATGC---------------------------------------------------------------------------------------------------------------------AAATCAATCACT-GGCT---AATCAGGGAGATG--TGTCTTTGCTGCTGTTGTTTTTA--TTTGTTGCTCG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 38594 122 + 48268 GCGCTGTCGGCC--AAGC-----------------------------------------------------------GC--CACACCCCAC--GCACTGATCGGACGC-AGTGCCGATGTCGC---------------------------------------------------------------------------------------------------------------------AAACAGGTCGCT-GGCT---AATCGGGGAGGGGGCTGCTGCTGGGGCTGGGGTTCTTA--TTTCCCACTCA i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14459883 122 - 17734757 AAGTGGTCAGCCAAGCAT-----------------------------------------------------------GC--AGGGCCCA-AC-ACAGGGACTTGATAC-AGCCCTAATTATGC---------------------------------------------------------------------------------------------------------------------AAGTCAGTCACT-GGCT---AATCAGGGAGACT--TGTCATTAGTGCTGTAGCTCTTA--TTTTTTGTTCA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_52062 1802 116 + 16741 AAGTGGCCAGCC-AGCAT-----------------------------------------------------------GC--AGG--CCA-AT-GCAGAGACTTGATAC-AGCCT--AATATGC---------------------------------------------------------------------------------------------------------------------AA-TCAATCATG-GGCT---AATCAGAGAGATT--TGTTGCTAGTGCTGGTTTTCTTA--GTTTTTGCTGA i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 2982 121 + 6675 GCATGCTCGGCCAAGCGT-----------------------------------------------------------GC--AGCTCCTGCAT-GCACGGACCTGACAC-TACACTAATTATGC---------------------------------------------------------------------------------------------------------------------AAATAAATCACT-GGCT---AATCAGGGAGATT--TGTTGTTGCAGTTGTTTTAATT----TTTTTACTCA i dasNov2.scaffold_85717 C 0 C 0 s monDom5.chr2 304634443 96 - 541556283 ATTTTTTCAGCAATTCAT-----------------------------------------------------------ACTTAGTACATTGAT-GTACTGATTGTACATGGGCAATAATTATGC---------------------------------------------------------------------------------------------------------------------AA-----TCATT-GACA---AGTTACATAGCTC--TTTTTTTCC--------------------------- i monDom5.chr2 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e bosTau4.chr19 10883085 4 - 65312493 I e mm9.chr11 118784099 2168 + 121843856 I a score=20245.000000 s hg19.chr17_gl000204_random 76331 25 + 81310 GTGGCCA---------GATGCAAAC-G---T-GTTGCAT s panTro2.chr17 79508331 25 + 83384210 GTGGCCA---------GACGCAAAC-G---T-GTTGCAT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 44162 25 - 64270 GTGGCCA---------GACGCAAAC-G---T-GTTGCAT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16093051 25 + 17838096 GTGGCCA---------GGCACAAAC-A---T-GTTGCAT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75067119 25 + 78773432 GTGGCCA---------GACGCAAAC-G---C-GTTGCAT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 74122 25 - 95547 GTGGCCA---------GACGCAAAC-G---T-GTTGCAT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 77266 25 + 225949 GTGGCCA---------GACGCAAAC-G---T-GTTACAT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 11487 23 + 21754 GCGGTCA---------GTCTCAAAC-G---T-GTTGC-- i tarSyr1.scaffold_41848 C 0 I 195 s otoGar1.scaffold_94362.1-287808 48689 25 + 287808 GTGGCCA---------GACTCAAAC-A---T-GTTGCAT i otoGar1.scaffold_94362.1-287808 C 0 I 354 s tupBel1.scaffold_71658.1-10116 1755 6 - 10116 GTGGCC--------------------------------- i tupBel1.scaffold_71658.1-10116 C 0 I 869 s cavPor3.scaffold_76 4411597 26 + 7991924 GAGGCCA---------GAGTCAAACTG---T-GCTGCAA i cavPor3.scaffold_76 C 0 C 0 s bosTau4.chr19 10883089 7 - 65312493 ATGGTCA-------------------------------- i bosTau4.chr19 I 4 C 0 s equCab2.chr11 58069476 26 - 61308211 GTAGCCA---------GACTCAAAACA---T-ACCGCAC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 50555 27 + 132007 GTAGCCA---------GACTCAAAACA---TCACTGCAG i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59463366 26 - 64418924 GTAGCCA---------GACTCAAAACA---T-ACCGCAG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 38716 26 + 48268 GGAGCCA---------GTCTCAAAACA---C-AGTGCAG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14460005 30 - 17734757 GTGGCCA--------GGCCTGAAAAAAAACA-GTTGCAT i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_52062 1918 28 + 16741 GTGGCCA--------AGACCAAAAACAA--A-GCAGCAC i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 3103 26 + 6675 ATGGCCA---------GACTGAAAAAG---T-GTTGCAT i dasNov2.scaffold_85717 C 0 C 0 s monDom5.chr2 304634539 20 - 541556283 ----CCACAGGCTGAAGATTAAAT--------------- i monDom5.chr2 C 0 C 0 e vicPac1.scaffold_72280 935 1824 + 3962 M e micMur1.scaffold_38207 1225 492 + 5481 I e turTru1.scaffold_98008 13926 255 + 223990 I e mm9.chr11 118784099 2168 + 121843856 I a score=211476.000000 s hg19.chr17_gl000204_random 76356 67 + 81310 AAGAGCCACCCAGAGGCGGCTTGAGCTCTTCTCGGAGGAAATGTGG-GTACTGTGTTGCTTGATCCTG s otoGar1.scaffold_94362.1-287808 49068 62 + 287808 aaGAATAACCACAAAGAGACTTTGTATATTCTAGAAGGGTCTGTCC-T-----GGTCTCAGGGCGCTG i otoGar1.scaffold_94362.1-287808 I 354 C 0 s micMur1.scaffold_38207 1717 67 + 5481 AGGCGTGGCCACGAGGCGGCTTCATTCATTCTGGGAGTGGACGTCC-CTCACGGGTCGTGTGACCCTG i micMur1.scaffold_38207 I 492 C 0 s tarSyr1.scaffold_41848 11705 66 + 21754 AAGAGTGACCAAGAGGAAGCTTTAGTTATTCTGGGAGGA-ATGTCA-GTACCATGTTGCACAATCCTG i tarSyr1.scaffold_41848 I 195 C 0 s calJac1.Contig5139 77291 67 + 225949 AAGAGCCACCCAGAGGCGGCCTGCGCTATTCTCGGAGGAAGTGTGG-GTACTGAGTCACTCCATCCTC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 74147 67 - 95547 AAAAGCCACCCAGAGGCGGCTTGAGCTCTTCTTGGACGAAATGTGG-GTACCATTTCATTCTATCCTG i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75067144 66 + 78773432 AAGAGCCACCCAGAGGCGGCTTGAGCTCTTCTCGGAGGAAATGTGG-GTAC-GTTTCACTCTATCCTG i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16093076 67 + 17838096 AAGAGCCACCCAGAGGCAGCTTGAGCTCTTCTCGGAGGAAATGTGG-GTACTGTGTTGCTCGATTCTG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 44187 67 - 64270 AAGAGCCACCCAGAGGCGGCTTGAGCTCTTCTCAGNGGAAATGTGG-GTACTGTGTTGCTCGATCCTG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79508356 67 + 83384210 AAGAGCCACCCAGAGGCGGCTTGAGCTCTTCTCGGAGGACATGTGG-GTACTGTGTTGCTCGATCCTG i panTro2.chr17 C 0 C 0 s cavPor3.scaffold_76 4411623 67 + 7991924 AGGAAAGGCTGAGAGACAGCTTTGCTCATACTAGGAGGAAACACCC-ATCACGTGTGGCCCCATCTGA i cavPor3.scaffold_76 C 0 C 0 s equCab2.chr11 58069502 68 - 61308211 AAGCGTGGCCAGAAGGCGACCTCCTTCATTCCAGGAGGAAACGTCCGGTAACGCATCCCATGATCCAA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 50582 67 + 132007 AGGAGCGACCGAGGGACAGCTTTCTTTATTCTCGAAGGAAACGTCCGGCGATGTCCCGCA-GATCCAA i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59463392 66 - 64418924 AGGAGGGACCAAGACGTGTTTTTCTTTATTCTAGGAGGAAATGTCC-ATGACATGCCGCC-GATCCAA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 38742 68 + 48268 GACAGCGCCCAGGAGGTGGCTTGCTTTCTTCCAGGAGGGAAGGTCTGGCTGCGAATTGCGAGACCCGC i pteVam1.scaffold_11245 C 0 C 0 s bosTau4.chr19 10883096 1 - 65312493 -------------------------------------------------------------------A i bosTau4.chr19 C 0 C 0 s vicPac1.scaffold_72280 2815 59 + 3962 ---------CCAGAGGCAGTTTTATTCATTCTGGGGAGAAACGTCCAGTCATTTGTCGCACGATCCAA i vicPac1.scaffold_72280 M 1824 C 0 s loxAfr3.scaffold_49 14460035 68 - 17734757 GAAAGAGTCCAAGAGACGGCTTTGTTTATCCTGGGAGGAAATGTCTGGTAACGTGTTCCATGGTCCAA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_52062 1946 67 + 16741 GAAAGAGACCTA-AGCCAGCTCTGCTTATCCTAGGAGGACAGGCCAGCTGACACTGCCCAGGGTCCAG i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 3129 67 + 6675 CAAAGAGACCAGGAGGAAGCTTT-TTTATTCTAGAAAGGAATAGCCAGGAACGTGGCACATGATGCAA i dasNov2.scaffold_85717 C 0 C 0 s monDom5.chr2 304634559 67 - 541556283 AACTGTTGGGTAAAGGTTGCTTTATTTATTCTAGTAGAAAATGTTTGGTAACATGTTGAA-AATCCAC i monDom5.chr2 C 0 C 0 e tupBel1.scaffold_71658.1-10116 1761 869 - 10116 I e turTru1.scaffold_98008 13926 255 + 223990 I e mm9.chr11 118784099 2168 + 121843856 I a score=379627.000000 s hg19.chr17_gl000204_random 76423 46 + 81310 CCT-CTTGA-CAGTCCTTT-CCAGATTCAAGTTTAAATGGGTTTGCCGG s panTro2.chr17 79508423 46 + 83384210 CCT-CTTGA-CAGTCCTTT-CCAGATTCAAGTTTAAATGGGTTTGCCGG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 44254 46 - 64270 CCT-CTTGA-CAGTCCTTT-CCAGATTCAAGTTTAAATGGGTTTGCCGG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16093143 46 + 17838096 CCT-CTTGA-CGGTCCTTT-CCAGATTCAAGTTTAAATGGGTTTGCTTG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75067210 46 + 78773432 CCT-CTTGA-CAGTCCTTT-CCAGATTCCAGTTTAAATGGGTTTGCCAG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 74214 46 - 95547 CCT-CTTGA-CAGTCCTTT-CCAGATTCAAGTTTAAATGGGTTTGCCAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 77358 46 + 225949 CCT-CTTGA-CAGTCCTTT-CCAGGTTCAAGTTTAAATGGGTTTGCTGG i calJac1.Contig5139 C 0 I 329 s tarSyr1.scaffold_41848 11771 46 + 21754 CCT-CTCGA-CAGCCCTTT-CCAGATTCAAGTTTAAACTGATTTGTTGG i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 1784 46 + 5481 CCC-CTCGC-CCGTCCCTT-CCAGGCGAAGGTTGGAACGGATCTGCCGC i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 49130 46 + 287808 CCT-TCTGC-TGGTCCTTT-CCAGATGAAGGTCTGAATTGATTTGCTGG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 2630 46 - 10116 CCT-CCTGA-CTTTCCTTT-TCAAATCCTGTTTGACACTGACTTGCTGG i tupBel1.scaffold_71658.1-10116 I 869 C 0 s cavPor3.scaffold_76 4411690 45 + 7991924 CCT-CTTGACCACTTTCTT-TCAGGTT--GTTTTAAATTGCTTAGCTGG i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_72280 2874 46 + 3962 CCT-CCCGG-CGTTCTTTTC-CGGATTAAGGTTTGAGTTGATTTGCTGG i vicPac1.scaffold_72280 C 0 C 0 s bosTau4.chr19 10883097 45 - 65312493 CCT-CTTGA-CTTTCCTTTT--CAATTAAGTTTTGAGTTGACTTGCTGG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58069570 45 - 61308211 TCT-CTTGA-GGTTCCTTT--CAGATTAAGTTTTAAATTGACTTGCCTC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 50649 46 + 132007 CTTCCCCCA-CGTTCCTTT--CAGATCAGGCTTGAAATTGATTTGCTGC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59463458 45 - 64418924 CCT-GCTGA-TGCTCCTTT--CAGACCAGGCTGTACGTTGATTTGCCTG i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 38810 45 + 48268 CCT-GCTGA-TGCTCCTTT--CGGGTTACAGTTTAAGTTGATTTGCTGG i pteVam1.scaffold_11245 C 0 C 0 s turTru1.scaffold_98008 14181 28 + 223990 ---------------------CAGATTAAAGTTTGAGTTGATTTGCTGG i turTru1.scaffold_98008 I 255 C 0 s loxAfr3.scaffold_49 14460103 46 - 17734757 CCT-CTTGG-CCCTCCTTT-TCAGATTATGTTTTAAATTGAACTGGTAG i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_52062 2013 46 + 16741 CTT-CCTGG-TCCCCCTTG-TCAGGTGATATTTTACACTGAGATGGTGC i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 3196 46 + 6675 CCT-CTTAA-CGTCCCTTT-TCAGATTAAGTTCTAAATTGATTTGCTGG i dasNov2.scaffold_85717 C 0 C 0 s monDom5.chr2 304634626 45 - 541556283 CCT-CTATG-TATTCCTTT-TCAGATTAAGTTTTAAATTTATTTGCTA- i monDom5.chr2 C 0 C 0 e mm9.chr11 118784099 2168 + 121843856 I a score=24074.000000 s hg19.chr17_gl000204_random 76469 76 + 81310 TATCAGGATGTTAGGGGCTCTCCAAATGCCAGTGGAGCAAATGGC---------------------------CC----ATTGC---AGACAC-ATTTCCAA------CCCTCA-TCAG s panTro2.chr17 79508469 76 + 83384210 TATCAGGATGTTAGGGGCTCTCCAAATGCCAGTGGAGCAAATGGC---------------------------CC----ATTGC---AGACAC-ATTTCCAA------CCCTCG-TCAG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 44300 76 - 64270 TATCAGGATGTTAGGGGCTCTCCAAATGCCAGTGGAGCAAATGGC---------------------------CC----ATTGC---AGACAC-ATTTCCAA------CCCTCA-TCAG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16093189 76 + 17838096 TATCAGGATGTTAGGGGCTCTCCAAATGCCAGTGGAGCAAATGGC---------------------------CC----ATTGC---AGACAT-ATTTCCAA------CCCTCA-TCAG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75067256 76 + 78773432 TATCAGGATGTTAGGGGCTCTCCAAATGCCAGTGGAGCAAATGGC---------------------------CA----ATTGC---AGACAC-ATTTCTAA------CCCTCA-TCAG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 74260 76 - 95547 TATCAGGATGTTAGGGGCTCTCCAAATGCCAGTGGAGCAAATGGC---------------------------CA----ATTGC---AAACAC-ATTTCTAA------CCCTCA-TCAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 77733 84 + 225949 TATCAGGCTGTTAGGGGCTCTCCAAATGCTGGTGAAGCAAATGGT---------------------------CC----ATTGC-AGAGACAC-GTTTCTAATGTGGCTTCTCA-TCAG i calJac1.Contig5139 I 329 C 0 s tarSyr1.scaffold_41848 11817 79 + 21754 TATCTGAATGTGATAGGTTCTCCATATGCGCTTGGAGCAGATGGA---------------------------CC----ATTGT-AGAGACAC-ATTTCTAAG-----CTTCCA-CTTG i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 1830 75 + 5481 CATGAGCCCGTGGGGAGCGCACCGCGAGTC--TCAG--AGCTGGC---------------------------GG----ACCAC-GGAGACGG-GTCTCCAA------CACCCCGTCAA i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 49176 72 + 287808 CGTCAGGCCATCAGGGGCACTCCCTACAGC--TCGGGCAGGTGGA---------------------------CC----ACCAC-AGAGACAA-GTCTCTAA------CCCTCC----- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 2676 74 - 10116 CTCCATGCTGTCAGGAGCCCTCCGAATGTCA-CGGAGCTAATGGC---------------------------CC----ATCGC---AGACAC--TCCTCGC------CCTCCG-CCAG i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4411735 58 + 7991924 CCTTACCCAGCAAGGCACTTTCCCCA------------------C---------------------------CC----GGTGA---GGATAC-GTGTCACC------CTCCCA-TCTG i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_72280 2920 75 + 3962 CGTCCTGCTGTCAGGAGCTCCCGGTGTGTCCCCGGGGCTCACCGG---------------------------CT----GTCTC---AGCGACACACACTAA------CC--TC-CCCC i vicPac1.scaffold_72280 C 0 I 1 s turTru1.scaffold_98008 14209 77 + 223990 TATCATGCCATCAGGAGCTCCACATGTGTCCTTGGAGCTCATGGA---------------------------CC----ATCTT---GGCAACACGTTCTAA------CCCTCT-CTCT i turTru1.scaffold_98008 C 0 I 1 s bosTau4.chr19 10883142 77 - 65312493 TATCAAGCCGTCAGGAGTTCCCCATGTCTCTTTGAAGCTCACGGA---------------------------CC----ATCTT---GGCAATACAGTCTAG------CCCTTT-CTCT i bosTau4.chr19 C 0 I 1 s equCab2.chr11 58069615 80 - 61308211 TGTCGAGTTGCTGGGAGCTC-CCGTGTGCCGTTGAAGCTCGTGGA---------------------------CCACCCACGGC---GGCAACACCTTCGAA------CTCCCC-GTAC i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 50695 76 + 132007 TGCCACGCCGCGGGGAGCTCTCTGTGTGCCCTCAGGGCTCAGGGA---------------------------CC----ATCAC---GGCCCT-CCTTGGGG------CTCTTT-TCAG i felCat3.scaffold_206428 C 0 I 126 s canFam2.chr9 59463503 75 - 64418924 TGCCACG----GCAGGGCTCTCCAAGTGTCATCGGGGCTCACAGA---------------------------CC-CCTGCCAC---GGCCAc-actctggc------cctccc-tcag i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 38855 47 + 48268 CATCGAG---------------------CCGTCGGGAC----------------------------------------GTCGC---GGGCACACCTCCCAA------CCCTCC-CACG i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14460149 47 - 17734757 TATC---------AGAGTCCTCTTTATGCCTTTGGGGCTAATGGA-----------------------CCCCCC----ATCGG----------------------------------- i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_52062 2059 46 + 16741 TGTC---------GGAACTCTCTGTCTGCCACTGGGGCTAGTGGA------------------------ACTCC----ATCAG----------------------------------- i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 3242 78 + 6675 TATCATACCGTCAGGAGCTCTCGACATGTCCTTGGACCTAATGGGCCATTGCAGCAGCACGGCCGCAACCTCCC----ATCA------------------------------------ i dasNov2.scaffold_85717 C 0 C 0 s monDom5.chr2 304634671 77 - 541556283 TATCATACCATTAGGAGTTCTTAATATGTCAGTGGAGCTAATGAA---------------------------CC----ATTGCCAGTGACAC-ATTTATAA--------TCTA-TCAG i monDom5.chr2 C 0 C 0 e mm9.chr11 118784099 2168 + 121843856 I a score=481460.000000 s hg19.chr17_gl000204_random 76545 78 + 81310 GGGC----TTCTCAGGAAAA------------GG---C-CCAG-----------------CCC--------------------------------------------------------------------GTGTTAATTATTATTTGAACACAAGTTCTGGAAGTTTCA-TCCTTACAAAATA s panTro2.chr17 79508545 78 + 83384210 GGGC----TTCTCAGGAAAA------------GG---C-CCAG-----------------CCC--------------------------------------------------------------------GTGTTAATTATTATTTGAACGCAAGTTCTGGAAGTTTCA-TCCTTACAAAATA i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 44376 78 - 64270 GGGC----TTCTCAGGAAAA------------GG---C-CCAG-----------------CCC--------------------------------------------------------------------NTATTAATTATTATTTGAANGCAAGTTCTGGAAGTTTCA-TCCTTACAAAATA i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16093265 78 + 17838096 GGGC----TTCTCAGGAAAA------------GT---C-CCAG-----------------CCC--------------------------------------------------------------------ATGTCAATTATTATTTGAACGCAAGTTCTGGAAGTTTCA-TCCTTACAAAATA i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75067332 78 + 78773432 GGGC----TTCTCAGGAAAA------------GG---C-CCAG-----------------CCC--------------------------------------------------------------------ATGTTAATTATTATTTGAATGCAAGTTCTGGAAGTTTCA-TCCTCACACAATG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 74336 78 - 95547 GGGC----TTCTCAGGAAAA------------GG---C-CCAG-----------------CCC--------------------------------------------------------------------ATGTTAATTATTATTTGAATGCAAGTTCTGGAAGTTTCA-TCCTCACAAAATG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 77817 75 + 225949 TGGC----TTCTCGGGAAAA------------GG---C-CCAA-----------------CCC--------------------------------------------------------------------A---CAATTATTATTTGAACACAAGTTCTAGAAGTTTTG-TCATTACGAAATA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 11896 78 + 21754 GAGG----TTCTTAGGATAA------------GG---C-CCTA-----------------CCC--------------------------------------------------------------------AGATTAATTATTATTTGAACCAAAGTTCTAGAAGTTTTA-TCATCACAAAATA i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 1905 64 + 5481 GCCC----ACGTCGGGAGAA------------GG---CTCCAG------------------CC--------------------------------------------------------------------AGACTCATTACTAT--------------TTGAGGTTTCA-TCGTTAAGAAATA i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 49248 78 + 287808 -CTT----CTTGGGGGAAAA------------GG---CCCCTG-----------------CCC--------------------------------------------------------------------AGGCTGATTCCCATTGGAACCTAAGATCTGGAAGCCTTG-TTATTACAAAGTA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 2750 78 - 10116 CCGC----CTCTCAGGCGCA------------GG---C-CCCC-----------------ACC--------------------------------------------------------------------GGGTTAATTACTGTTTGAACCGGAGTCCCAGACGGTTCA-TCATCACAGAACA i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4411793 72 + 7991924 ACTC----TTT----GAGGA------------GC---C-CCTA-----------------CCC--------------------------------------------------------------------AG--CAACTGTTATTTGAACCCAAGTTCTAGAAATTTCA-CTATTCTTAAATA i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_72280 2996 76 + 3962 GCTC----CTCTCACGAGAA------------GG---C-CCCT-----------------CCC--------------------------------------------------------------------AGGTTTATTATC--ATGAGCTGAAGTTCTGGAAGTTTCA-CCGTTACAAAATA i vicPac1.scaffold_72280 I 1 C 0 s turTru1.scaffold_98008 14287 76 + 223990 GCTC----CTTTCAGGAGAA------------GG---C-CCCT-----------------CAC--------------------------------------------------------------------GGGTTTATTATT--TTGAGCTGAAGTTCTGGAAGTTTCA-TCATTACAAAATA i turTru1.scaffold_98008 I 1 C 0 s bosTau4.chr19 10883220 76 - 65312493 GGTC----CTCTCAGGAGGA------------GC---T-CCCT-----------------CTT--------------------------------------------------------------------GGGTTTATTATT--TTGAACTGAAGTTCTGGAAGTTTCA-TCATTACACAATA i bosTau4.chr19 I 1 C 0 s equCab2.chr11 58069695 77 - 61308211 GCTC----TTCTCAGAAGAA------------GG---C-CCCT-------------G---CCC--------------------------------------------------------------------GGGCGGGTTATT--TTGAACTGAAGTTCTGGAAGTTTCA-TGATTACAAAATA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 50897 159 + 132007 gctccgagctgtcagcacagcgcccgacgcgggg---c-tcga-------------a---cccacaaaccgtgagatcatgacctgagccaaagtcggatgctgaacccactgagccacccaggtgccccAAGGGTTATTATT--CTGAACTAAAGTTCTGGAAGTTTCA-TCCCCA--AAATA i felCat3.scaffold_206428 I 126 C 0 s canFam2.chr9 59463578 73 - 64418924 cctc----ttctcagaa---------------gg---c-ccac-------------a---ccc--------------------------------------------------------------------agggtgatcatt---tgaaCTGTAGTTCTGGAAGTTTCA-CCATTATGAAATA i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 38902 76 + 48268 -----GGGCTTTTAGGAGAA------------GG---C-CCCT-------------G---CTC--------------------------------------------------------------------GGGTTTGTTATT--TTGAACTGAAGTTCTGGAAATTTCT-TCCTTACAAAATA i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14460196 92 - 17734757 GCTC----TTCTGGGAAGAT------------GT---C-CCCTCCACCCCACCCCCA---CCC--------------------------------------------------------------------GGCTTTATGATTACTTGAACTGAAGTTCTGGAAGCTTCA-TCGTTACAAAGTA i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_52062 2105 89 + 16741 GCTT----TCCTGGGAAGGC------------AT---C-CCCT-GGCCCCACTCCCA----CT--------------------------------------------------------------------GGCTTTGCGATCACCTGAACTG-AGTTCTGGAAGCTTCC-CTGTTACAAAGTA i proCap1.scaffold_52062 C 0 C 0 s dasNov2.scaffold_85717 3320 87 + 6675 GCTC----TGCT---------------------T---C-TCCGCCACCCCCACCCCAGGCCCA--------------------------------------------------------------------GGTTTTATTACCATTTGAACTGAGCTTCTGGAAGTTTCCATCGTTGCGAAATA i dasNov2.scaffold_85717 C 0 C 0 s monDom5.chr2 304634748 80 - 541556283 -----CCATTCTGAAGAGAA------------AGATTT-TCCT-----------------CCT--------------------------------------------------------------------TGGTTTATTTTTATTTGTGCTGAAGTTATGAAAGATTAA-TTATGACCAAACA i monDom5.chr2 C 0 I 21374 e mm9.chr11 118784099 2168 + 121843856 I a score=286443.000000 s hg19.chr17_gl000204_random 76623 31 + 81310 -----TTTTTAACGCTCGTGGTTCAGGAGAGGAA--GG s panTro2.chr17 79508623 35 + 83384210 AA-TATTTTTAACGCTCGTGGTTCAGGAGAGGAA--GG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 44454 35 - 64270 AA-TATTTTTAACGCTCGTGGTTCAGGAGAGGAA--GG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16093343 35 + 17838096 AA-TATTTTTAACGCTCGTGGTTCGGGAGAGGAA--GG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75067410 36 + 78773432 AATTATTTTTAACGCTCGTGGTTCGGGAGAGGAA--GG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 74414 36 - 95547 AATTATTTTTAACGCTCGTGGTTCGGGAGAGGAG--GG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 77892 32 + 225949 AA-TATTTTTAAAGCTGATGGTTCAGGAGAGGA----- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 11974 35 + 21754 AG-TAATTTTAAGGCTCATGGCTCAGGAGAGGAA--CA i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 1969 35 + 5481 AG-CGTTCTCAAAGCTCCAGGCTCGGGAGAGCGA--GG i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 49326 30 + 287808 CG-TATTTCTAAAGCTCATGGTTCAGGAGAA------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 2828 33 - 10116 AG---AGTCTAAAGCTCGTGGCTCACAGGAGAAA--CA i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4411865 35 + 7991924 AA-TGTTTTTAAAGGTTATGAATCAGGAGACAAC--TT i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_72280 3072 35 + 3962 AA-TATTTTTCAAGCTCATGATTCATGAGAAAAA--TG i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 14363 35 + 223990 AA-TATTTTTGAAGCTCATGATTCATGAGAGCAA--TA i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10883296 35 - 65312493 AA-TATTTTTGAAGCTCATGATTCATGAGCGCaa--ta i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58069772 35 - 61308211 AA-TATTTTTAAGGCTCATGATTTTTGAGAGGAA--TA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 51056 35 + 132007 TG-TATTTTTAAAGCTTGTGATTCGTGAGAGAAA--GA i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59463651 34 - 64418924 TG-TATTTTTAAGGC-TATGACTCGTGAGAGGaa--ta i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 38978 35 + 48268 GA-TATTTTTAAAACTCATGATTCATGAGAGGAC--TA i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14460288 33 - 17734757 AA-TATTATTAAAGCTCATGGTTCATGAGAGGAA---- i loxAfr3.scaffold_49 C 0 I 3395 s proCap1.scaffold_52062 2194 35 + 16741 AA-CGTCAGCAAAGCTCACAGTTCATGAGAGGAAGG-- i proCap1.scaffold_52062 C 0 I 13555 s dasNov2.scaffold_85717 3407 33 + 6675 AA-TATTTTTCAGGTTTGCGGTTCATTAGAGGAG---- i dasNov2.scaffold_85717 C 0 I 2 e monDom5.chr2 304634828 21374 - 541556283 I e mm9.chr11 118784099 2168 + 121843856 I a score=-4802.000000 s hg19.chr17_gl000204_random 76654 23 + 81310 GAGAGAAG---------TGAGTaacacttact s panTro2.chr17 79508658 32 + 83384210 GAGAGAAGGGAGAGAAGTGAGTaacacttact i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 44489 32 - 64270 GAGAGAAGGGAGAGAAGTGAGTaacacttact i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16093378 23 + 17838096 GAGGGAAG---------TGAGTaacacttgct i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75067446 23 + 78773432 GAGGGAAG---------TGAGTAACACTTACT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 74450 23 - 95547 GAGGGAAG---------CGAGTAACACCTACT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 77924 22 + 225949 -AGAGAAG---------TAAGtaacatttatt i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 12009 23 + 21754 AAGGGAAG---------TAAGtaatatctctt i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 2004 16 + 5481 GAATCCAG-------CGTGCACT--------- i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 49356 5 + 287808 ------------------GAGCA--------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 2861 22 - 10116 GGAGGAAG----------CAATGCTGTGTACT i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4411900 16 + 7991924 G----------------TCAGTGGTGTTTATT i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_72280 3107 19 + 3962 GAAGAAAA---------TAAA----TGATATC i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 14398 21 + 223990 AAAGAAAA---------TTAAT--TTtttatt i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10883331 20 - 65312493 aaagaaaa---------ttaa---tttttatt i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58069807 23 - 61308211 GAAGAAaa---------taaacaatatttatt i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 51091 23 + 132007 Gaatgaaa---------taaataatacttatc i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59463685 19 - 64418924 gaaca-------------aaatgacatttact i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 39013 18 + 48268 Gaat--------------aaataatatttaca i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_85717 3442 23 + 6675 GAGGGAAA---------TAAATAATAGTGATT i dasNov2.scaffold_85717 I 2 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e monDom5.chr2 304634828 21374 - 541556283 I e mm9.chr11 118784099 2168 + 121843856 I e loxAfr3.scaffold_49 14460321 3395 - 17734757 I a score=386818.000000 s hg19.chr17_gl000204_random 76677 62 + 81310 gactccctactatgcactaggcacctaacgt--------------gt-------atttt-ctcgtttaaccctc--aaaataatgc s ponAbe2.chr17_random 16093401 62 + 17838096 gactccctactgtgcactaggcacctaacat--------------gt-------atttt-ctcgtttaaccctc--aaaataatgc i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 44521 62 - 64270 gactacctactgtgcactaggcacctaacgt--------------gt-------atttt-ctcgtttaaccctc--aaaataatgc i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79508690 62 + 83384210 gactccctactgtgcactaggcacctaacgt--------------gt-------atttt-ctcgtttaaccctc--gaaataatgc i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 77946 62 + 225949 gactccctactatgcactagacatctaactt--------------gt-------gtttt-ctcatttaaccccc--aaaataatgc i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 12032 61 + 21754 aaatctttattatgagctgggcagctagcat--------------gt-------atttt-ctcaattagccctc---aaataacac i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 2020 62 + 5481 GACGCCCTGCCGGGCGCCGGGCGCCTGCCGC--------------GC-------ATTTC-CTCGCTTAACCCTC--GGAATGACGA i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 49361 72 + 287808 GACACCCTGC----CACCAGCTGGCTGCCACCTGACTTTATTCCAGA-------CTTTA-TTCACTCATCCCTC--AAAATAACAC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 2883 62 - 10116 GACTCCCAGCAAGGGCCTAGGCTCCTAACTT--------------GC-------ATTTT-CTCATTAAACCCTC--CAAGTAATGC i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4411916 61 + 7991924 -GGTGCCTTTTCTGAGCTGGGCACCTAATGG--------------GT-------GTTTT-CCCATTTAACTCTC--AGAGTAATAT i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_72280 3126 61 + 3962 GCATTCCTactgt-ggcgaggcacccaacat--------------gc-------atttt-ctcatttaaccttt--gaaataatgc i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 14419 62 + 223990 gaattcctactgtgggttacacacctaacat--------------gc-------aattt-ctcatttaaccttt--gaaataatgc i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10883351 63 - 65312493 gaatttctactgtgggctacacacccaacat--------------gc-------aatttcctcatttaaccttt--gaaataatga i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58069830 62 - 61308211 cagttcctactatgggctagacacctagtgt--------------gc-------atttt-cactttcgaccttc--aaaataatgg i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 51114 64 + 132007 aaattcctacttcgtgctaggcaccaaacgt--------------gc-------atttt-ctcatttaatcttcaaaaaataatgc i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59463704 64 - 64418924 gaattcctaccatgtgtgaggcacctaacat--------------gc-------atttt-ctcatttaatcttcaaaaaacaatgc i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 39031 61 + 48268 gaatccctactatgggct-ggcacctaagat--------------gc-------gtttt-ctcatttagccttc--aaaataaggc i pteVam1.scaffold_11245 C 0 C 0 s dasNov2.scaffold_85717 3465 69 + 6675 GGACCCTTACTATGCCCTGGATGCCCAACAT--------------GTGTCTTGAATTTT-CTCATTTAGCTGTC--GAAGTAGCAC i dasNov2.scaffold_85717 C 0 I 1496 e proCap1.scaffold_52062 2229 13555 + 16741 I e papHam1.scaffold8336 74473 0 - 95547 C e monDom5.chr2 304634828 21374 - 541556283 I e mm9.chr11 118784099 2168 + 121843856 I e loxAfr3.scaffold_49 14460321 3395 - 17734757 I e rheMac2.chr16 75067469 0 + 78773432 C a score=248991.000000 s hg19.chr17_gl000204_random 76739 106 + 81310 agc-gggtctgc--attattgaccccagtttacagttgtggaaactgagtctctgagagtc-----------------------------------taagtgacCCAGACCTGCAAGGTTTgctcagcacccagtagcaggctt s ponAbe2.chr17_random 16093463 106 + 17838096 agt-gggtctgc--attattgaccccagtttacagttgtggaaactgagtctctgagagtc-----------------------------------taagtgacCCAGACCTGCAAGGTTTgctcagcacccagtagcagtctt i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 44583 108 - 64270 agc-gggtctgcatattattgaccccagtttacagttgtggaaactgagtctctgagagtc-----------------------------------taagtgacCCAGACCTGCAAGGTTTgctcagcacccagtagcaggctt i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79508752 106 + 83384210 agc-gggtctgc--attattgaccccagtttacagttgtggaaactgagtctctgagagtc-----------------------------------taagtgacCCAGACCTGCAAGGTTTGCTGAGCACCCAGTAGCAGGCTT i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 78008 89 + 225949 tgcggggtctgt--gtgaccaatcccagtttacagatgtggaaac-----------------------------------------------------agtgacccagaCCTGCCAGCTTTGCTCAGCACCTGACTGCAGGCTT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 12093 107 + 21754 catggggtcagt--gttattgctcccagtttacaaataaagaaactgagtctctgagagtc-----------------------------------taaataacCCAGAAccacagagcttgcttggcatatggcagcgggctt i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 2082 69 + 5481 CGG---------------------CCAGCTCGCAC-GGAGGAGACTGAGCCC---------------------------------------------------CCCAGACCTGC-AGGCCTGCCCGG-GCGCAGCAGCCGGCCT i micMur1.scaffold_38207 C 0 I 1002 s otoGar1.scaffold_94362.1-287808 49433 68 + 287808 ------------------------CCCGCGTTCAG-TAAGGAAACTGAGCCT---------------------------------------------------CTGACACCTGCTGGGCCTGCTCTGCATGCAGCTGCAGGGGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 2945 70 - 10116 CGT-GGGTCAGC--TTTATGGCCC-------------------------------AGAGTC-----------------------------------TAAATAACC-AGACCCTCAGGGCTTGCTC---ACTCAGCAGAGGGCT- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4411977 62 + 7991924 TATGGGGTCAGC--TTTCTTGTCC-------------AAGGAAACTAAGTGTCCAAGA--------------------------------------TAAGCAATTCA------TGGGGCTT----------------------- i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_72280 3187 105 + 3962 tttgaggtcaga--gttactgtccccaacttacagataaagaaactgaatctc--agagTT-----------------------------------CAAATAATCCAGACGCAGAGCGCTGGCTCAGGACTCAGCTGCTGGCTT i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 14481 97 + 223990 cttgaggtcagt--gttattgcccccgaattacagataaggaaaatgagtctc---------------------------------------------aATAACCCAGACACAGAAAGCTGGCCTAGGACTCAGAagctggctt i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10883414 97 - 65312493 cttgaggttggt--gttactgcccccaaattacagataaggaaaatgagtctc---------------------------------------------aATAACCCAGACTCAGAAAACTGGCCTTGGTCTCAGAagctggctt i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58069892 107 - 61308211 catgaggtcagt--gtcattgcttccagcttacaggcaaagaaaccgagtctctgagagtc-----------------------------------taaacaacCCAGACCTGAACGGCTGGCCTGGGGCTCggcggctgcctt i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 51178 107 + 132007 tgtgaggttggc--atcgttgcccccagcttgcagataaggaaacggagtctctgagagtc-----------------------------------taaataacccaggccttcagggctggCTCCAGACGTGGCAGGGGGCTT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59463768 142 - 64418924 tgtgaggtcaac--atgattgtccccagcttacagataaggaaactgagtctctgagggTCttttttaattttttatttttttttttttGAGAATATAAATAACCCACACTTTTGGGGCTGGctcaggacttggcagctggctt i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 39092 72 + 48268 tgtgaggccagc--gttactgccctcagcttacagatcaggaaactgagtgtctgaggggc----------------------------------------------------------------------tggcagctggcct i pteVam1.scaffold_11245 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e papHam1.scaffold8336 74473 0 - 95547 C e dasNov2.scaffold_85717 3534 1496 + 6675 I e monDom5.chr2 304634828 21374 - 541556283 I e mm9.chr11 118784099 2168 + 121843856 I e loxAfr3.scaffold_49 14460321 3395 - 17734757 I e rheMac2.chr16 75067469 0 + 78773432 C a score=138323.000000 s hg19.chr17_gl000204_random 76845 67 + 81310 cccccagagcaagcaacccggaaaagcacgacagcccccgcc---c-ca-cgaggtggaggccacagtctct s ponAbe2.chr17_random 16093569 67 + 17838096 cccccagagcaagcaacccgggaaagcacgacagcccccgcc---c-ca-caaggtagaggctacagtctct i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 44691 67 - 64270 cccccagagcaagcaacccagaaaagcacgacagcccccacc---c-ca-caaggtggaggccacagtctct i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79508858 67 + 83384210 CCCCCAGAGCAAGCAACCCGGAAAAGCACAACAGCCCCCGCC---C-CA-CAAGGTGGAGGCCACAGTCTCT i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 78097 67 + 225949 CCACTAAAGCAAGCAACCCAGACAAGCACAAAAGCCCCCGCC---C-CC-CAAGGTAGAGGCTGCAGTCTCT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 12200 67 + 21754 cc-ccagagcaagcgatctagaagagcaagaaagacccccca---c-caccaagatggaggccccgttcttt i tarSyr1.scaffold_41848 C 0 C 0 s otoGar1.scaffold_94362.1-287808 49501 63 + 287808 CCCCCAGACCAGGCGATCT-------CACAAGAACCCCCCCCTTGT-CC-TCAGGTAGAGGCCACAGTCATT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 3015 65 - 10116 -CCCCAGAGCGAGCAGTCAAGGCGGGCCAGAGTCTCCCCTCC---CACC-CCAAGTGGAGGC--CAGTCTTT i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4412039 37 + 7991924 --TCTGGGGAAAGAGG-----------------------------C----CAGGATGGAGGCCACGGTCTTC i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_72280 3292 49 + 3962 CCCCCGGAGCCCGTGACCTGAG----------------GAAG---C-CT-CGAGATGCGGGCCCCAGTC--T i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 14578 63 + 223990 cccccagagcacctgatcgaagagagccagagag----aaag---t-cc-caagatgggggccacaatcttt i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10883511 64 - 65312493 ctcccagagcgtctgatctaag-gagccagagaga--aaaag---c-cc-caaggtgggggccacggtcttt i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58069999 59 - 61308211 cccccagagctggccgtctgagagag--tgag------agag---g-cc-ctagatggaggccacagtgttt i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 51285 60 + 132007 CCCCCAGCCTGAGCCATCTGAGAGAACACGAG------CGAG---T--C-CAGGATGGAGACCACAGGCTGT i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59463910 61 - 64418924 cccccaaaacaagccatctgagagagcacgag------agag---t-cc-caggaaagaggccgcaggcttt i canFam2.chr9 C 0 I 46 s pteVam1.scaffold_11245 39164 57 + 48268 cccccagagtgagccccctgagagggcgtggg------agag---g--c-caagacagaggcc-cgatct-- i pteVam1.scaffold_11245 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e papHam1.scaffold8336 74473 0 - 95547 C e micMur1.scaffold_38207 2151 1002 + 5481 I e dasNov2.scaffold_85717 3534 1496 + 6675 I e monDom5.chr2 304634828 21374 - 541556283 I e mm9.chr11 118784099 2168 + 121843856 I e loxAfr3.scaffold_49 14460321 3395 - 17734757 I e rheMac2.chr16 75067469 0 + 78773432 C a score=-29077.000000 s hg19.chr17_gl000204_random 76912 78 + 81310 tcagaa-----cctcatGGCCAGGGACGGCCGT-CAGAGCCAGAGTCCACTCAGAC--------------------------------------------------------------------------AGCAAAGCAAG-----------------------------------------TCGTCTCTCCA--CTAC--CT s ponAbe2.chr17_random 16093636 78 + 17838096 tcagaa-----cctCACGGCCAGGGACGGCCAT-CGGAGCCAGAGTCCACTCAAAC--------------------------------------------------------------------------AGCAAAGCAAG-----------------------------------------TCTTCTCTCCA--CTAC--CT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 44758 78 - 64270 tcagaa-----cctcatGGCCAGGGACGGCCAT-CGGAGCCAGAGTCCACTCAGAC--------------------------------------------------------------------------AGCAAAGCAAG-----------------------------------------TCATCTCTCCA--CTAC--CT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79508925 78 + 83384210 TCAGAA-----CCTCATGGCCAGGGACGGCCGT-CGGAGCCAGAGTCCACTCAGAC--------------------------------------------------------------------------AGCAAAGCAAG-----------------------------------------TCGTCTCTCCA--CTAC--CT i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 78164 77 + 225949 TCATAA-----CCTCATGGCCGGGGACAGCCAT-CAGAGCCAGCATCCACTCAGAC--------------------------------------------------------------------------AGGAAAGCAAG-----------------------------------------TCTTCTCCCCA---TGC--CC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 12267 80 + 21754 ctataa-----cttCACAGCCAGGAGGGTGCTA-GGAAACCAGACTCCAGTCAGAC--------------------------------------------------------------------------CCCAAAGCAAG-----------------------------------------TGCTCTCTCTTTTTTCA--CT i tarSyr1.scaffold_41848 C 0 C 0 s otoGar1.scaffold_94362.1-287808 49564 80 + 287808 TTGTGA-----CCTCTCAGCCAGCAAGGGTGAC-AGGGAACCAGCTCCATTCAGAC--------------------------------------------------------------------------TCCAGAGCAAG-----------------------------------------AGCTCTCTCTA--CTCCTACT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 3080 194 - 10116 TCATAA-----CCTCACCACCAGCGAGGGCAGTGGGGAACCCAACTTCACGCGGACCAGCTAGCCTGGGAGATTTCTTTTTATTTTCTTTGTATTAGGTTTTTCCATAGGGTGAATACAGTCTCTAGAGAGACAGAGAGAGGGGAAGTGAGAAATCCCCCCGGGGAGATGGCCGCGCCACAATCCCTTCTCCT--CTAC--TT i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4412076 21 + 7991924 T----------------------------------------------------AAC------------------------------------------------------------------------------------------------------------------------------TGCGGTCTCTG--CTGT--TG i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_72280 3341 50 + 3962 TTACAG-----CCTCCCAGCCCGTGAGGACTAGAGGAACCCAAACTTCTCCCAGG---------------------------------------------------------------------------------------------------------------------------------------------------- i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 14641 62 + 223990 ttgtaa-----cctCACAGCCAATAAGGGCTATAGGAACCCAGACTCCACTTGGAC--------------------------------------------------------------------------CCCAAAGTAAG-------------------------------------------------------------- i turTru1.scaffold_98008 C 0 I 4 s bosTau4.chr19 10883575 50 - 65312493 ttataa-----cctCACAACCAGTAAGGGCTTTTGGTACCCAAACTTCACTTGGA---------------------------------------------------------------------------------------------------------------------------------------------------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58070058 63 - 61308211 ttgcaa-----ccGCACAGCCAGCGAGGGCCCTAGGGACCCAAACTCCACCTGGAC--------------------------------------------------------------------------ACCAAAGGAAGT------------------------------------------------------------- i equCab2.chr11 C 0 I 4 s felCat3.scaffold_206428 51345 55 + 132007 CTGTGACCCCCCCCCCCAGCCCACAAGGGCCC-AAGGAACCAAACTCCGCTTAGAC--------------------------------------------------------------------------------------------------------------------------------------------------- i felCat3.scaffold_206428 C 0 C 0 s pteVam1.scaffold_11245 39221 81 + 48268 ttgtga-----cttcacagccagtgAGGGCCAGAGGGCCCCAAACTCCACTCAGAC--------------------------------------------------------------------------CTCAAAGTGCTTGCCATCCCCCCACTTCCT------------------------------------------- i pteVam1.scaffold_11245 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e papHam1.scaffold8336 74473 0 - 95547 C e micMur1.scaffold_38207 2151 1002 + 5481 I e dasNov2.scaffold_85717 3534 1496 + 6675 I e monDom5.chr2 304634828 21374 - 541556283 I e canFam2.chr9 59463971 46 - 64418924 I e mm9.chr11 118784099 2168 + 121843856 I e loxAfr3.scaffold_49 14460321 3395 - 17734757 I e rheMac2.chr16 75067469 0 + 78773432 C a score=92962.000000 s hg19.chr17_gl000204_random 76990 83 + 81310 CACGCCAGTGCCTCTTG----------------catttggattaa---------------------------------------------------------------------------------------ccagggtgatttctaaatctggacgtccatcctgcagcccacacagggtgcagt s ponAbe2.chr17_random 16093714 83 + 17838096 CATGCCCGTGGCTCTTG----------------catttggattaa---------------------------------------------------------------------------------------ccagggtgatttctaaatctggacgtccatgctgcagcccacacagggtgcagt i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 44836 83 - 64270 CACGCCAGtggctctcg----------------catttggattaa---------------------------------------------------------------------------------------ccagggtgatttctaaatctggacgtccatcctgcagcccacacagggtgcagt i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79509003 83 + 83384210 CACGCCAGTGCCTCTTG----------------catttggattaa---------------------------------------------------------------------------------------ccagggtgatttctaaatctggacgtccatcctgcagcccacacagggtgcagt i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 78241 83 + 225949 CGTACCAGTGGCTCTCG----------------CATTTGGATGAA---------------------------------------------------------------------------------------CCAGGGCGATTTCTAAGTCTGGACGTCCAACCTGCAGCCCACACAGTGTGCGGT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 12347 83 + 21754 TATACTAGAGACTCTTG----------------CATTTGGATTGA---------------------------------------------------------------------------------------CCAGGGAGATTTTCAAATCTGGATGTCCAAGCTACAGCCCACACCAAGTAGTGT i tarSyr1.scaffold_41848 C 0 I 715 s otoGar1.scaffold_94362.1-287808 49644 62 + 287808 TAGACCAGGGTTTGT--------------------TTGGAATTAA---------------------------------------------------------------------------------------CTA-----------------GGAGATCCAGGCTGCAGCCCACACAGAGCACAGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 3274 185 - 10116 TCCTCCTGGGATCTTGGGCACACTACATGCACACACCTGGAGTGATTTTCAAGTCACCAGGTCTGGGACTCAAACCACGGTCCCCCATGTGGGAGTCCAGCGCCTTAAGCTCTACACCACCTGCTAGCCCTGCCTGGGAGATTTCTTAGTCTGTATGTCCAA-CAGTGACTCCCAGCAAGTACAGC i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4412097 82 + 7991924 CTGATATGTGTCGCCTG----------------CATCCAGATTTA---------------------------------------------------------------------------------------CCTGGGAGATATCCAAAG-TGGATGTCCAGACAGCAGCCAGCACCAAGCCCAGC i cavPor3.scaffold_76 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e papHam1.scaffold8336 74473 0 - 95547 C e vicPac1.scaffold_72280 3391 0 + 3962 C e micMur1.scaffold_38207 2151 1002 + 5481 I e turTru1.scaffold_98008 14703 4 + 223990 I e felCat3.scaffold_206428 51400 0 + 132007 C e dasNov2.scaffold_85717 3534 1496 + 6675 I e pteVam1.scaffold_11245 39302 0 + 48268 C e monDom5.chr2 304634828 21374 - 541556283 I e canFam2.chr9 59463971 46 - 64418924 I e bosTau4.chr19 10883625 0 - 65312493 C e equCab2.chr11 58070121 4 - 61308211 I e mm9.chr11 118784099 2168 + 121843856 I e loxAfr3.scaffold_49 14460321 3395 - 17734757 I e rheMac2.chr16 75067469 0 + 78773432 C a score=201365.000000 s hg19.chr17_gl000204_random 77073 153 + 81310 caaccctctggggtggga--ctcgcatcaggacgttgaaacctcccccg------------gcggctccagt-----------gtg-agaaccactgCAGATGT-GGGAAGG-----AACCCTCCAGCCTTCAAATCACCACATCATCTGCCTCGGCCATCTCAAGAAATTCATCAGGAAGTGTG s ponAbe2.chr17_random 16093797 151 + 17838096 caaccctctggggtggga--ctcacatcaggacgttgaaacctccccag------------gcggctccagc-----------gtg-agaaccactgCAGGTGTGGGGAAGG-----AACCCTCCAGCCTTCGAATCACCA---CATCTGCCTCGGCCATCTCAAGAAATTCATCAGGAAGTGTG i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 44919 150 - 64270 caaccctctggggtggga--ctcgcatcaggatgttgaaacctccccag------------gcggctccagt-----------gtg-agaaccactgCAGATGT-GGGAAGG-----AACCCTCCAGCCTTCAAATCACCA---CATCTGCCTCGGCCATCTCAAGAAATTCATCAGGAAGTGTG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79509086 153 + 83384210 caaccctctggggtggga--ctcgcatcaggacgttgaaacctccccag------------gcggctccagt-----------gtg-agaaccactgCAGGTGT-GGGAAGG-----AACCCTCCAGCCTTTAAATCACCACATCATCTGCCTCGGCCATCTCAAGAAATTCATCAGGAAGTGTG i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 78324 152 + 225949 CAAGCCCCAGGGTGGGGAGGCTCACATCAGGACACTGAAACCTCCCCAG------------GCGGCTCTGGT-----------GTG-AAACCCACTGCAGGTGG-CGGAAGG-----AACCCTCCAGTCTCCCAGTCACCA---CACATGCCTTAGCCCTTTCAAGAAACTCATCAGGAAGTGTG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 13145 158 + 21754 CAAGCctctggg-tgggg--cttacaccaggatgtttaaaccttcccag------------gcagctccaatgtgcaccctgggtg-agaaccaTGGCATCAGTGGGGAAGG-----AACCCTCAAGTCTTCAGTTCATCA---CATGAACCTTGGCCATTTTAAGAAAC---TCAGGACATGTG i tarSyr1.scaffold_41848 I 715 C 0 s otoGar1.scaffold_94362.1-287808 49706 148 + 287808 AGACCTCCTGGGGCAGAGCCCTGACATTGGGACACCTAAACCTCCTT--------------GCAGCT--GGG-----------CTG-AGAGCCACTGCAGGTGC-AAGAGTC-----AGCCCTCGAGTCTCCAAAGCTCCG---TGTGCACCTCAGCCATTCAGAGAACCTGTTCAGGATTTGTG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 3459 152 - 10116 CAACCTTCTGGGAGAAGGCTCTGACGTCAGGCCATC--AAGCCTCCCAG------------GTGACACCAGAACGCACCCCAGGTG-AGGG---GTGCAGGTGT-GGGGACA-----ATCC-------CTGCGTGCCATCGC--TGTGGGCCTTGGTCATTTCAGGAAGTTGTTCAGGATTCACG i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4412179 168 + 7991924 -TGCCCATCAGAATGGGACTCTGAGATCAGGACA-TGGAGCCTCCCCAGGGACGCCAGCATGCAGCTCCACT-----------GGGCAGCTCCACTGCACGTGT-GGAGAAGTAACTAACTCTCATGTCTTTGCATCACCA---CACATGCCCTGGACTTTTCAAGAAACAGTGTGGTATTTGTG i cavPor3.scaffold_76 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e papHam1.scaffold8336 74473 0 - 95547 C e vicPac1.scaffold_72280 3391 0 + 3962 C e micMur1.scaffold_38207 2151 1002 + 5481 I e turTru1.scaffold_98008 14703 4 + 223990 I e felCat3.scaffold_206428 51400 0 + 132007 C e dasNov2.scaffold_85717 3534 1496 + 6675 I e pteVam1.scaffold_11245 39302 0 + 48268 C e monDom5.chr2 304634828 21374 - 541556283 I e canFam2.chr9 59463971 46 - 64418924 I e bosTau4.chr19 10883625 0 - 65312493 C e equCab2.chr11 58070121 4 - 61308211 I e mm9.chr11 118784099 2168 + 121843856 I e loxAfr3.scaffold_49 14460321 3395 - 17734757 I e rheMac2.chr16 75067469 0 + 78773432 C a score=148216.000000 s hg19.chr17_gl000204_random 77226 101 + 81310 GGTCTAAACACTCTATAGATGCCCCCAGGGTCAAGAAGGAGACACGGGC-AGTGAGAGTGATTCCAGGAAGAAA----GTC-GTTG-ACTGCAATTC-ACACGGTGCAC s cavPor3.scaffold_76 4412347 101 + 7991924 GATCTAAAGAGTTCTGGAGCATCGCCTTGGGCATGAACATGATGTGGGC-AGTGAAGAGACCCCGAGAAGAAAA----GCA-GTTGTTCTTCAGTGC--TGTATGGATG i cavPor3.scaffold_76 C 0 C 0 s tupBel1.scaffold_71658.1-10116 3611 99 - 10116 GGTCCGGACACTCCGC--ACGTCCCAGTGGGCAAGAACAAGACGT-GGC-AACGAGAGAAGCTC-AGGAAGAAA----GCCAGCTGCCCTGCGGGTC-ACACCGCGAAG i tupBel1.scaffold_71658.1-10116 C 0 C 0 s otoGar1.scaffold_94362.1-287808 49854 94 + 287808 -GTCTAAACGCTCTTTAAATGTGTCCAGGGGCAAGAAGG-GGCAAGAGCAGGAGGGGGCACGTCCAGGAGGGAA----GCTGGTGGTTGTGCAGTTC-ACG-------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_38207 3153 102 + 5481 GGTCTAAACACTCTTTAAATGCCCCCAGGGTCAAGAAGGCGGCCTTGGC-GGCGAGAGCACCTCCGGGAGGGAA----GCC-GCGGTCCTGCGATGC-ACGGAACGGCC i micMur1.scaffold_38207 I 1002 C 0 s tarSyr1.scaffold_41848 13303 101 + 21754 TGTCTAAACACTCTTTGAATGCCCCCAGGGGCAAAAATGAGACATGGGC-AGTAAGGGTACTTCTAGGAAGAAAACGGGTT-GCT---CTGCCATTCAACATGATG--- i tarSyr1.scaffold_41848 C 0 C 0 s calJac1.Contig5139 78476 100 + 225949 GG-CTCAACATTCTATAGATACCTCCAGGGTCAAGAAGGAGACCTGGGC-CGTGAGAGTGCTTCCAGGAAGAAA----GCT-GTGG-ACTGCAATTC-ACACAGCGCAG i calJac1.Contig5139 C 0 C 0 s panTro2.chr17 79509239 101 + 83384210 GGTCTAAACACTCTATAGATGCCCCCAGGGTCAAGAAGGAGACACGGGC-AGCGAGAGTGATTCCAGGAAGAAA----GTC-GTTG-ACTGCAATTC-ACACGGTGCAC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 45069 101 - 64270 GGTCTGAACACTCTATAGATGCCCCCAGGGTCAAGAAGGAGACACAGGC-AGTGAGAGTGATTCCAGGAAGAAA----GTC-GTTG-ACTGCAATTC-ACACGGTGCAC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16093948 101 + 17838096 GGTCTAAACACTCTGTAGATGGCCCCAGGGTCAAGAAGGAGACACGGGC-AGTGAGAGCGATTCTAGGAAGAAA----GTC-GTTG-ACCATAATTC-ACACCGTGCAG i ponAbe2.chr17_random C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e papHam1.scaffold8336 74473 0 - 95547 C e vicPac1.scaffold_72280 3391 0 + 3962 C e turTru1.scaffold_98008 14703 4 + 223990 I e felCat3.scaffold_206428 51400 0 + 132007 C e dasNov2.scaffold_85717 3534 1496 + 6675 I e pteVam1.scaffold_11245 39302 0 + 48268 C e monDom5.chr2 304634828 21374 - 541556283 I e canFam2.chr9 59463971 46 - 64418924 I e bosTau4.chr19 10883625 0 - 65312493 C e equCab2.chr11 58070121 4 - 61308211 I e mm9.chr11 118784099 2168 + 121843856 I e loxAfr3.scaffold_49 14460321 3395 - 17734757 I e rheMac2.chr16 75067469 0 + 78773432 C a score=51253.000000 s hg19.chr17_gl000204_random 77327 55 + 81310 GGGCCT-ATTTGG-AGGCTTAGGGAGGACCCAGATGTGAATTTACAAGCCAGTGTCA s ponAbe2.chr17_random 16094049 55 + 17838096 GGGCCC-ATTTGG-AGGCTTAGTGAGGACCCAGATGTGAATTTATAAGCCAGTGTCA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 45170 55 - 64270 GGGCCT-ATTTGG-AGGCTTAGGGAGGACCCAGATGTGAATTTANAAGCCAGTGTCA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79509340 55 + 83384210 GGGCCT-ATTTGG-AGGCTTAAGGAGGACCCAGATATGAATTTACAAGCCAGTGTCA i panTro2.chr17 C 0 C 0 s calJac1.Contig5139 78576 53 + 225949 GGGGCT-ATTTGG-AGGCTTAGT--GGACCCAGATGTGAATTTACAAGCCAGTGTCA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 13404 56 + 21754 GGGCCT-ACCTGGTAGACTTCCTGAGGACCCGGATGTGAATTCACAAGCCAATGTCA i tarSyr1.scaffold_41848 C 0 I 4 s micMur1.scaffold_38207 3255 54 + 5481 CGGCCT-GTTTGG-AGACGTCCTG-GGGCCCAGGCGTGAACTTCCAAGCCCGTGTGA i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 49948 3 + 287808 -------------------------------------------CCA----------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 3710 28 - 10116 GGGCC---------AT---------GGGTTCAGGTGCTAAG---------AGTGC-- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4412448 55 + 7991924 GAGCCA-ACTTTG-GAGGTGGCCAAGGATCCAGATTTGGACTTCCAGGCTGAGGTTG i cavPor3.scaffold_76 C 0 C 0 s dasNov2.scaffold_85717 5030 56 + 6675 GGGCCTGATTTGG-AGACTTCCTCGGGACTCGGACGTGAACTTTTAAACGCGTAGCT i dasNov2.scaffold_85717 I 1496 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e papHam1.scaffold8336 74473 0 - 95547 C e vicPac1.scaffold_72280 3391 0 + 3962 C e turTru1.scaffold_98008 14703 4 + 223990 I e felCat3.scaffold_206428 51400 0 + 132007 C e pteVam1.scaffold_11245 39302 0 + 48268 C e monDom5.chr2 304634828 21374 - 541556283 I e canFam2.chr9 59463971 46 - 64418924 I e bosTau4.chr19 10883625 0 - 65312493 C e equCab2.chr11 58070121 4 - 61308211 I e mm9.chr11 118784099 2168 + 121843856 I e loxAfr3.scaffold_49 14460321 3395 - 17734757 I e rheMac2.chr16 75067469 0 + 78773432 C a score=43472.000000 s hg19.chr17_gl000204_random 77382 37 + 81310 GACA--------------------CCAGC----TTGTACACTCATCTGC---CTTTCAGGGACT s panTro2.chr17 79509395 37 + 83384210 GACA--------------------CCAGG----TTGTACACTCATCTGC---CTTTCAGGGACT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 45225 37 - 64270 GACA--------------------CCAGC----TTGTACACTCATCTGC---CTTTCAGGGACT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16094104 37 + 17838096 GACA--------------------CCAGG----TCATACACTCATCTGC---CTTTCAGGGACT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75067469 37 + 78773432 GACA--------------------CCAGG----TCATACACTCATCTGC---CTTTCAGGGACT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 74473 36 - 95547 GACA--------------------CCAGG----TCATACACTCATCT-C---CTTTCAGGGACT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 78629 37 + 225949 GATG--------------------GCAGG----TCACACACCCATCTGC---CTTTCAGGGACC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 13464 42 + 21754 GACAGACT---------------CTCCAG----TAGTGTGTCCGCCTGC---CTTTCAGAGGCT i tarSyr1.scaffold_41848 I 4 C 0 s micMur1.scaffold_38207 3309 53 + 5481 ----GGTGCCGGGAGGACATGCTCCCCAG----TAGTGCGTCCACCTGC---CCTTCGGAGACT i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 49951 27 + 287808 -----------------------TCCCAA----T--TGCATCCATCTGC---CCTCAGA----- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 3738 39 - 10116 -AGA--------------------CCAGC----CTGGCCAAGCATCTGTCCACCCTCGGGGACC i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4412503 52 + 7991924 ----GGATCCGGGAGGGTGCATCACCCCT----CAGTGC-TTCACCTGC---CCTTCCCAGCCC i cavPor3.scaffold_76 C 0 C 0 s dasNov2.scaffold_85717 5086 36 + 6675 GACA--------------------CCAGGGACATTCCGGGTTCCTCCGC---CTGTCCG----- i dasNov2.scaffold_85717 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e vicPac1.scaffold_72280 3391 0 + 3962 C e turTru1.scaffold_98008 14703 4 + 223990 I e felCat3.scaffold_206428 51400 0 + 132007 C e pteVam1.scaffold_11245 39302 0 + 48268 C e monDom5.chr2 304634828 21374 - 541556283 I e canFam2.chr9 59463971 46 - 64418924 I e bosTau4.chr19 10883625 0 - 65312493 C e equCab2.chr11 58070121 4 - 61308211 I e mm9.chr11 118784099 2168 + 121843856 I e loxAfr3.scaffold_49 14460321 3395 - 17734757 I a score=137971.000000 s hg19.chr17_gl000204_random 77419 113 + 81310 AGG---TCCTCCCAGACCAGGA----AGAC----ATCCACCT----TCAGCGTCCAGACTG----GGGTCCATGAGGGACCGGCCAGG-GCTGACCACACGGGGCCTGGGAGGC--ACCACCTTCCCCACCATTT s panTro2.chr17 79509432 113 + 83384210 AGG---TCCTCCCAGACCAGGA----AGAC----ATCCACCT----TCTGCGTCCAGACTG----GGGCCCATGAGGGACCGGCCAGG-GCTGACCACACAGGGCCTGGGAGGC--ACCACCTTCCCCACCATTT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 45262 113 - 64270 AGG---TCCTCCCAGACCAGGA----AGAC----ATCCACCT----TCCGCGTCCAGACTG----GGGTCNATGAGGGACNGGCCAGG-GCTGACCACACAGGGCCTGGGAGGC--ACCACCTTCCCCACCATTT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16094141 113 + 17838096 AGG---TCCTCCCAGACTAGGA----AGAC----ATCCACCT----TCCGCGTCCAGACTG----GGGTCCGTGAGAGACTGGCCAGG-GCTGAGCACACAGGGCCTGGGAAGC--ACCACCTTCCCCACTATTT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75067506 111 + 78773432 AGG---TCCTCCCAGACCAGGA----AGGC----ATCCACCT----TCCGCATCCAGAC------GGATCCATAAGGGACCGGCCAAG-GCTGACCACACAGGGTCTGGGAAGC--ACCACCTTCCCCACCATTT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 74509 111 - 95547 AGG---TCCTCCCAGACCAGGA----AGAC----ATCCACCT----TCCGCATCCAGAC------GGATCCATGAGGGACCGGCCAAG-GCTGACCACACAGGGTCTGGGAAGC--ACCACCTTCCCCACCATTT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 78666 110 + 225949 AGG---ACCTCCCAGACCAAGA----AGGA----ATCCACCT----TTCACACCCAGACCG----GGGTCCCTGAGGGGCCGG-CAGA-GTTGACCTCACAAG--CTGGGAAGC--ACCCCCCTCCCTGTTGTTT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 13506 97 + 21754 AGG---ATCTCCCAGACCAGGAGGCTGGGC----ATCTACTTACTCTCAGCTTCCAATGTG----GGGCAAAAGAGGGATGAACCAAG-GCTGACCACATGGG--------------------------CCATTT i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 3362 93 + 5481 GGG---ACCTCCCGGACCGCCC----GG------------CT-----------------CG----GGGCAGGTGGGGGATGAGCCGAG-GCCGACCGCACAGGGCTGGGGAGGCA-AAGACCTCCTCCGCTGCCC i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 49978 72 + 287808 --------------------------GG------------CT-----------------TG----GGGCAGATGAGGGACAGGCTGAG-GCTGACTGCAGGGACCCAGG--ATCC-AACCCTGTCTCTGCCATAT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 3777 97 - 10116 AGGGACCCCACCCAGCAAGGCT----GAGC----GTCCACTC----TCAGCACCCGGTC------GGGGAGATGAGG-------CCAG-GCTGGGTG---AGGGCGCGGGCTGA-----GCCTTCCACACT---- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4412555 88 + 7991924 AGG---ACCTTCCAGCCCAGGG----AGGCCAGGAATGGTTC----TCAGTA-CCAGTCGG----GGGCAGAAGA---------CAGA-GGAGGGACCAAAGGACCCAGGCAGC--------------------- i cavPor3.scaffold_76 C 0 C 0 s loxAfr3.scaffold_49 14463716 118 - 17734757 agg---gcctcccgggccaggt----gagg----cctggccT----TCATTCTCAGCACCGTTTCTGACAGACAAGGGAAGAGCGACA-GCTGGTCACACAGAGCC-GGAAGGCATGGCTGTTTCCTTACGTTTT i loxAfr3.scaffold_49 I 3395 C 0 s dasNov2.scaffold_85717 5122 97 + 6675 -------CCTGTCTGTCCA------------------GGCCC----TC-----CCACACTG----GGGCAGGCGAGGTAAGAGCCCGAGGCTGGCCCTGCGGAGCTGGGGAAGCCAGGCCCTTCCTGCGCCATGT i dasNov2.scaffold_85717 C 0 I 55 e proCap1.scaffold_52062 2229 13555 + 16741 I e vicPac1.scaffold_72280 3391 0 + 3962 C e turTru1.scaffold_98008 14703 4 + 223990 I e felCat3.scaffold_206428 51400 0 + 132007 C e pteVam1.scaffold_11245 39302 0 + 48268 C e monDom5.chr2 304634828 21374 - 541556283 I e canFam2.chr9 59463971 46 - 64418924 I e bosTau4.chr19 10883625 0 - 65312493 C e equCab2.chr11 58070121 4 - 61308211 I e mm9.chr11 118784099 2168 + 121843856 I a score=116726.000000 s hg19.chr17_gl000204_random 77532 57 + 81310 CTCATGGT---ATTGACCTTTGA----TTATGTTCTCAAGGCACC-GAGGAAGTGTCT-TCTCACC s panTro2.chr17 79509545 57 + 83384210 CTCATGGT---ATTGACCTTTGA----TTATGTTCTCAAGGCACC-GAGGAAGTGTCT-TCTCACT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 45375 57 - 64270 CTCATGGT---ATTGACCTTTGA----TTANGTTCTCAAGGCACC-GAGGAAGTGTCT-TCTCACC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16094254 61 + 17838096 TTCACGGC---ATTGACCTTTGATTGTTTATGTTCTCAAGGCACC-AAGGAAGTGTCT-TCTCACT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75067617 61 + 78773432 CTCATGGC---ATTGACCTTCGATTGTTTATATCCTCGAGGCACC-AAGGAAGTTTCT-TCTCACT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 74620 61 - 95547 CTCATGGC---ATTGACCTTCGATTGTTTATATCCTCGAGGCACC-AAGGAAGTTTCT-TCTCACT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 78776 61 + 225949 CTCATGGC---ACTGACCTCTGATGGTTTATTTCCTCAAGTCACC-GAGGAAGTTTCT-TCTCACC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 13603 57 + 21754 CTCACTAT---GTTGAACTTTTT----TTGTTTCCTTGGGATGCT-AAGGAGATTCCT-TCCCGTT i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 3455 54 + 5481 CTCACAG----GCTAACCGTG------TTTAATCCTCAAGGTGCT-AAGGAAGTTCCT-TCCCTTC i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 50050 56 + 287808 CTCACTGC--ATTTGACCTTG------CTTCTTTCTTAACAAGCC-AAGGAAGTTTCT-TCCCACC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 3874 54 - 10116 -TCACAGCGGGACTGGC----------TGGTTTCTTGGAGGCCCT-GAGGGAGTTTCTGGCCCAAA i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4412643 36 + 7991924 --TAGGGA---ACCACGCTTT------CTCT------------------GAAGCTTTG-TCCCATC i cavPor3.scaffold_76 C 0 C 0 s loxAfr3.scaffold_49 14463834 56 - 17734757 CCTGCAGC---ATCTGGCGTC------TGGTTTCCTCAAGGCTCTAAAAGAAGTTTCT-TCCCATC i loxAfr3.scaffold_49 C 0 I 3 e proCap1.scaffold_52062 2229 13555 + 16741 I e vicPac1.scaffold_72280 3391 0 + 3962 C e turTru1.scaffold_98008 14703 4 + 223990 I e felCat3.scaffold_206428 51400 0 + 132007 C e dasNov2.scaffold_85717 5219 55 + 6675 I e pteVam1.scaffold_11245 39302 0 + 48268 C e monDom5.chr2 304634828 21374 - 541556283 I e canFam2.chr9 59463971 46 - 64418924 I e bosTau4.chr19 10883625 0 - 65312493 C e equCab2.chr11 58070121 4 - 61308211 I e mm9.chr11 118784099 2168 + 121843856 I a score=11132.000000 s hg19.chr17_gl000204_random 77589 44 + 81310 GC--AGT--GTCTCAGGAA--------------TTCCCTGCA-------------------A---CCCTCCC-CA--------GTGGCTCAC-C---- s panTro2.chr17 79509602 44 + 83384210 GC--AGT--GTCTCAGGAA--------------TTCCCTGCA-------------------A---CCCTCCC-CA--------GTGGCTCAC-C---- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 45432 44 - 64270 GC--AGT--GTCTCAGGAA--------------TTCCCTGCA-------------------A---CCCTCCC-CA--------GTGGCTCAC-C---- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16094315 44 + 17838096 GC--AGT--GTCTCAGGAA--------------TTCCCTGCA-------------------A---CCCTCCC-CA--------GTGGCTCAC-C---- i ponAbe2.chr17_random C 0 I 5 s rheMac2.chr16 75067678 44 + 78773432 GC--AGT--GTCTCAGTAA--------------TTCCCTGCA-------------------G---CCCTCCC-CA--------GTGGCTCAC-C---- i rheMac2.chr16 C 0 I 5 s papHam1.scaffold8336 74681 44 - 95547 GC--AGT--GTCTCAGGAA--------------TTCCCTGCA-------------------A---CCCTCCC-CA--------GTGGCTCAC-C---- i papHam1.scaffold8336 C 0 I 5 s calJac1.Contig5139 78837 44 + 225949 GA--AGT--GTCTCAGGAA--------------TCCCCAGCA-------------------A---CCCTCCC-CA--------GTGGCTGAC-C---- i calJac1.Contig5139 C 0 I 5 s tarSyr1.scaffold_41848 13660 58 + 21754 GCCTCAG--GTCTTAGGAATGGGTTTCTG----TGCCCTGGA-------------------AGTTCTCTCCC-CA--------G-GGCTGAT-T---- i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 3509 53 + 5481 GC--AGCAGGTCTCGGGAGTGGGTGG-------TGCACTGTG-------------------G---CCTTGCC-CC--------GAGGCGCAC-G---- i micMur1.scaffold_38207 C 0 I 5 s otoGar1.scaffold_94362.1-287808 50106 72 + 287808 AT--GGCAGGTCTAGGGGGCGGGCAG-------TGTGCTGCGCA--------GTTCCCTGCA---CCCTGCC-CCATACCCCTGTGGCCCAC-T---- i otoGar1.scaffold_94362.1-287808 C 0 I 5 s tupBel1.scaffold_71658.1-10116 3928 66 - 10116 AC--GGG--ATC-CAGGAGCCAGCGCCGGTGCCTGTCCTGGGTG--------GCCGGGTGTG---GTCTGCC-CA--------GTG--CTGC-T---- i tupBel1.scaffold_71658.1-10116 C 0 I 5 s cavPor3.scaffold_76 4412679 64 + 7991924 AC--AGCAGTTCCTAGGAG--------------T-CACTGCACATGTCTGACAATGTTTGTG---ACCTCTC-CA--------GTGAGCCAC-T---- i cavPor3.scaffold_76 C 0 I 24 s loxAfr3.scaffold_49 14463893 48 - 17734757 GC--GGA--GCCTCTGCAT--------------TTCTGTCTG-------------------T---GACCCCA-CA--------ATGAGTCAG-TCACA i loxAfr3.scaffold_49 I 3 C 0 s dasNov2.scaffold_85717 5274 50 + 6675 GT--GGG--GTCCCTGAGC--------------ACACCTCAG-------------------C---GCCCGCGCCG--------GCGAGTCGTCCCCCA i dasNov2.scaffold_85717 I 55 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e vicPac1.scaffold_72280 3391 0 + 3962 C e turTru1.scaffold_98008 14703 4 + 223990 I e felCat3.scaffold_206428 51400 0 + 132007 C e pteVam1.scaffold_11245 39302 0 + 48268 C e monDom5.chr2 304634828 21374 - 541556283 I e canFam2.chr9 59463971 46 - 64418924 I e bosTau4.chr19 10883625 0 - 65312493 C e equCab2.chr11 58070121 4 - 61308211 I e mm9.chr11 118784099 2168 + 121843856 I a score=56123.000000 s hg19.chr17_gl000204_random 77633 60 + 81310 TCTCAGGAGG-------------------AGC------TGCC-----------------CACACTTCCCTAGAGCGGGGGCCAGAAGATGGAGAAATG--------A-TGG s mm9.chr11 118786267 57 + 121843856 TCCCAGAAGG---------------ATATACC------AACT-----------------CACAGAGCCCCA---------------GGTGGAAAATGGCCTGACCAA-CAG i mm9.chr11 I 2168 C 0 s cavPor3.scaffold_76 4412767 64 + 7991924 CACCACAAGG---------------CTGCTGC------AGCT-----------------CCCAGAGCCTCAGA--------CAGAGGGTGGAGAGAAGAATGCTGAA-TGG i cavPor3.scaffold_76 I 24 C 0 s tupBel1.scaffold_71658.1-10116 3999 52 - 10116 TCCAAGGCTG-------------------CCC------GACC-----------------GTCAGGCCCTCAG---------CAGAGAACCGCGGAGTG--------ACTGG i tupBel1.scaffold_71658.1-10116 I 5 C 0 s otoGar1.scaffold_94362.1-287808 50183 55 + 287808 TCTCAGGAGGGGACATCAACGCATCACACAGC------TGCT-----------------CCTGCTTCCCCAGAAGCTG--------------------------------- i otoGar1.scaffold_94362.1-287808 I 5 C 0 s micMur1.scaffold_38207 3567 66 + 5481 TCCCAGGAGGGGACTCCAACTCCCCACGAGGC------TGCT-----------------CCTGCTTCCCCAGAGCCGGGGACAG-------------G--------G-CGA i micMur1.scaffold_38207 I 5 C 0 s tarSyr1.scaffold_41848 13718 49 + 21754 -------------------------------T------TACT-----------------AACTCTTTCCCAGAGTTGGTGGCAGGAGATGATGAAATG-------AA-CTG i tarSyr1.scaffold_41848 C 0 C 0 s calJac1.Contig5139 78886 60 + 225949 TCTCAGGAGG-------------------AGA------TGCC-----------------CACACCTCCCTAGAGCTGGGAGCAGAAGACGGAGAGATG--------A-TGG i calJac1.Contig5139 I 5 C 0 s papHam1.scaffold8336 74730 60 - 95547 TCTCTGGACG-------------------AGC------TGCC-----------------CACACTTCCCTAGACCTGGGACCAGAAGATGGAGAAATG--------A-TGG i papHam1.scaffold8336 I 5 C 0 s rheMac2.chr16 75067727 60 + 78773432 TCTCTGGACG-------------------ACC------TGCC-----------------CACACTTCCCTAGAGCTGGGACCAGAAGATGGAGAAATG--------A-TGG i rheMac2.chr16 I 5 C 0 s ponAbe2.chr17_random 16094364 60 + 17838096 TCTCAGGAGG-------------------AGC------TGCC-----------------CACACTTCCCTAGAGCTAGGGCCAGAAGATGGAGAAATG--------A-TGG i ponAbe2.chr17_random I 5 C 0 s gorGor1.Supercontig_0007361 45476 60 - 64270 TCTCAGGAGG-------------------AGC------TGCC-----------------CACACTTCCCTAGAGCGGGGGCCAGAAGATGGAGAAATG--------A-TGG i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79509646 60 + 83384210 TCTCAGGAGG-------------------AGC------TGCC-----------------CACACTTCCCTAGAGCGGGGGCCAGAAGATGGAGAAATG--------A-TGG i panTro2.chr17 C 0 C 0 s loxAfr3.scaffold_49 14463941 73 - 17734757 TTTCAGGATG-------------------AGA------CGCC----ACCTCATCAGAGGGCTGCTTGCTCAGGTCCTCAGGCAGAAGATGGTGAAATT--------G-ATG i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_85717 5324 80 + 6675 TCTCGGGGTG-------------------AGAGCTGCCTGCCTGGGACCTCCTCAGGGGGCTGCTTCCCTAGA---TCAGGCAGAGCCCGGTGAAACG--------A-GCG i dasNov2.scaffold_85717 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e vicPac1.scaffold_72280 3391 0 + 3962 C e turTru1.scaffold_98008 14703 4 + 223990 I e felCat3.scaffold_206428 51400 0 + 132007 C e pteVam1.scaffold_11245 39302 0 + 48268 C e monDom5.chr2 304634828 21374 - 541556283 I e canFam2.chr9 59463971 46 - 64418924 I e bosTau4.chr19 10883625 0 - 65312493 C e equCab2.chr11 58070121 4 - 61308211 I a score=243130.000000 s hg19.chr17_gl000204_random 77693 155 + 81310 AGACCCATCTTCACG---GGCCTAGCTCCAGGACACA---------------------------------GGCAGACCCAGC--------CACCCTC---AGGCTGCTCCCCC-TGGAAG-----------------------------AAGGATGCCAG-------------------CTCTGTGGGGTCCCTGGAGTGTCG-------------------TTTATAA-----------------------------------------TTG--CCCTTGCACA----------------------------------------GCACC--CTGAC------GGA-------GG-------GTACCCAGCAGAT s panTro2.chr17 79509706 155 + 83384210 AGACCCATCTTCACA---GGCCTAGCTCCAGGACACG---------------------------------GGCAGACCCAGC--------CACCCTC---AGGCTGCTCCCGC-TGGAAG-----------------------------AAGGATGCCAG-------------------CTCTGTGGGGACCCTGGAGTGTCG-------------------TTTATAA-----------------------------------------TTG--CCCTTGCACA----------------------------------------GCACC--CTGAC------GGA-------GG-------GTACCCAGCAGAT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 45536 157 - 64270 AGACCCATCTTCACA---GGCCTAGCTCCAGGACATG---------------------------------GGCAGACCCAGC--------NACCCTC-AGAGGCTGCTCCCGC-TGGAAG-----------------------------AAGGATGCCAG-------------------CTCTGTGGGGTCCCTGGAGTGTCG-------------------TTTATAA-----------------------------------------TTG--NCCTTGTGCA----------------------------------------GCACC--CTGAC------GGA-------GG-------GTACCCAGCAGAT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16094424 155 + 17838096 AGACCCATCTGCACA---GGCCTAGTTCCAGGACATG---------------------------------GGCAGACCCAGC--------CACCCTC---AGGCTGCTCCCAC-TGAAAG-----------------------------AAGGATGCCAG-------------------CTCTGTGGGGTCCCTGAAGTGTTG-------------------TTTATAA-----------------------------------------TTG--CCCTTGCATG----------------------------------------GCACC--CTGAC------GGA-------GG-------GTACCCAGCAGAT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75067787 152 + 78773432 AGACCCATCTTCACA---GGCCTAGTTCCAGGACGTG---------------------------------GGCAGACCCAGC--------CACCCTC---AGGCCGCTCCCAC-TG---G-----------------------------AAGGACGCCAG-------------------CTCTGTGGGGTCCCTGGAGGGTCG-------------------TTTATAA-----------------------------------------TTG--CCCTTGCATG----------------------------------------GCACC--CTGAC------GGA-------GG-------GTACCCAGCAGAG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 74790 152 - 95547 AGACGCATCTTCACA---GGCCTAGTTCCAGGACGTG---------------------------------GGCAGACCCAGC--------CACCCTC---AGGCCGCTCCCAC-TG---G-----------------------------AAGGACGCCAG-------------------CTCTGTGGGGTCCCTGGAGTGTCG-------------------CTTATAA-----------------------------------------TTG--CCCTTGCATG----------------------------------------GCACC--CTGAC------GGA-------GG-------GTACCCAGCAGAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 78946 154 + 225949 AGACCCATCTTCACA---GGTCTAGTTCCAGGACACA---------------------------------GGCAGGCCAAGC--------CACCCTC---AGGCTGCTCTCAC-TGGAGG-----------------------------AAGGACGCCAG-------------------CTCTGT-GGGTCCCTGGAGTGTCG-------------------TTTATAA-----------------------------------------TTG--CCCTTGCATG----------------------------------------GCGCC--CTGAT------GGA-------GG-------GTACCCAGCAGTT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 13767 159 + 21754 GGACCCATTTTCACT---GGTCTGGTTCCAGGACACT---------------------------------GGCAGGGTGAGC--------CACCCTC-TCTGTGTGCTGCCACATGGGGG-----------------------------AAGGATGCCAG-------------------CTCTTCGGGGTCCA-GGAGTGTCC-------------------TATATAAA---------------------------------------CTTT--CCCTTGCCCG----------------------------------------GCACC--CTGAG------GGA-------GG-------GTACCCAGCAAAC i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 3633 90 + 5481 G-----------------------------------------------------------------------------------------CACCCTC---CGTCTGCTCCC----AGGGG-----------------------------AAGGGTGCCAG-------------------CCCCTCACGCTCCCAGGAGTGTCA-------------------TTTATAGA------------------------------------------------------------------------------------------------------CTGAC------GGA-------GT-------GTACGCAGCGGAC i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 50238 109 + 287808 --------------------------------------------------------------------------------------------CGCTC---TGTCTGCTCCCTC-TAGAGG-----------------------------AGGGGTGCCAG-------------------CTCTTTGGGGTTCCAGGAGTGCCA-------------------TTTTTAGA---------------------------------------GTCC--CTCTTGCATG----------------------------------------GCACC--CTGAC------AGA-------GG-------GTGCCCAGTGGTC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 4051 340 - 10116 GAACCCATCTGTATG---GG--TGGTTCCAGGACGGGCAGGCATCCTATCTCTATGGGTGGGAGGGACACGGCAGGTGCAGCAGATGCAGTGCCCTG-TGAGGCTGAACCATT-GGGGAGGTTCCGGGTTCATACCCAGAGACCTCCCTGAGCGCACCAG-------------------GCCTGCGGGGGCTGGGGAGGATTGCAGCAGCCCTCGCTCGCTCTCAACAAATAAGTCAACTCGAGGAAAGACGAAGATGGGGTAATGAGCGTTGGCCCTTTGCATGGGGTTAGCTCCAGGGCACAGGCAGGGACAAGCCTCTGTCTGCTCT--CTGGCGTCCCGGGA-------GGCCCTGTCGTGCCCAGCAGAC i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4412831 152 + 7991924 AGATTGAT-ATCACA---GCTCTCGTTACAGGACGTG---------------------------------GAGGGGT-------------TACCCTC-----TCTTCTCCTGC-CAGAGA-----------------------------GAGAATGGCAG-------------------CTTCCTGGAGTTCCAGGACTGTCC-------------------CTTATAACC---------------------------------------TGC--CCTTTGT-TG----------------------------------------GTACT--C--AC------TGGACCTCTCAG-------GTTTTCA-CTGCC i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118786324 155 + 121843856 GGATGTATCATCATG---ACGCAAGGGACAAGACAAG---------------------------------GGCAGGT-------------GAGCCCCCATGTTCTGTTCCTAC-TGCAGG-----------------------------AAAGATGTCAG-------------------CCCTTTGGCATCTTGGAAGTACCA-------------------TGTATAAAC---------------------------------------TGC--TCCTTGCGTG----------------------------------------ACACC--CTGAC------AGA-------AG-------GTACTCATCCGAC i mm9.chr11 C 0 C 0 s eriEur1.scaffold_319784 10393 151 - 15705 AGGCCTGTTTCCATG---GGTCTAGTTCTAGGAAGCA---------------------------------GACATGG--ggt--------cacctct-gtcttcccctcaccc-caAGAA-----------------------------AAAGATATCCA-------------------CATCTTGGGGTCT--GGGATGCCT-------------------TTTGTAAA----------------------------------------TAG--TCCCT---TG----------------------------------------GTCCCAGCTGAT------GGA-------AG-------GCATCAAAGGA-- i eriEur1.scaffold_319784 N 0 C 0 s loxAfr3.scaffold_49 14464014 146 - 17734757 GGGACCATTGCCGTG---GGTCTAGTTCCCAGACTTA---------------------------------GGCAGCTTGAGT--------CAGC------------CTCTGTT-TGCAAA-----------------------------GAAAGTGCTGG---------------------CCTCGAGGCTCCACCGGGGTCA-------------------TTTGTAAAT---------------------------------------TGC--CCCTTGCCTT----------------------------------------GCACT--GTGAT------GGG-------TG-------CTACCCAGGGGAC i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_85717 5404 162 + 6675 GGACCC----CCGTGCCTGGTGGAGGTCCAGAACATA---------------------------------GAGAG---GAGC--------ATGCTCT---------CTCCCTC-TGCCAA-----------------------------GAAAGTACTTGTGCTGGGGGGACATGCCAGCTCTTTGGGGCCCCAGGGGCGCCC-------------------CTTGCCAAC---------------------------------------TTC--CCCTTGCCTT----------------------------------------GCACC--CCTAC------AAA-------CG-------GCACCCAGA---- i dasNov2.scaffold_85717 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e vicPac1.scaffold_72280 3391 0 + 3962 C e turTru1.scaffold_98008 14703 4 + 223990 I e felCat3.scaffold_206428 51400 0 + 132007 C e pteVam1.scaffold_11245 39302 0 + 48268 C e monDom5.chr2 304634828 21374 - 541556283 I e canFam2.chr9 59463971 46 - 64418924 I e bosTau4.chr19 10883625 0 - 65312493 C e equCab2.chr11 58070121 4 - 61308211 I a score=-119298.000000 s hg19.chr17_gl000204_random 77848 79 + 81310 CCCTCAAGGTTCTCCCTG-------CCC--CC--------------AGAGAATGA-----------ACAGCTCACGGACAGC----AGAGCTCCGTGTCAT---CCGCC--T---------CCTG-CCAG--G-G s panTro2.chr17 79509861 79 + 83384210 CCCTCAAGGTTCTCCCTG-------CCC--CC--------------AGAGAATGA-----------ACGGCTCACAGACAGC----AGAGCTCCGTGTCAT---CCACC--T---------CCTG-CCAG--G-G i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 45693 90 - 64270 CCCTCAAGGTTCTCCCTG-------CCC--CC--------------AGAGAATGAACAGCTCATGNACAGCTCATGGACAGC----AGAGCTCCGTGTCAT---CCACC--T---------CCTG-CCAG--G-G i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16094579 79 + 17838096 CCCTCAAGGTTCTCCCTG-------CCC--CC--------------AGAGAATGA-----------ACAGCTCACGGATGGC----AGACCTCCGGGTCAT---CCACC--T---------CCTG-CCAG--G-G i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75067939 79 + 78773432 CCCTCAACGTTCTCCCTG-------CCC--CC--------------AGAGAATGA-----------ACGGCTCACGGATGGC----AGAGCTCCGCATCAT---CCACC--T---------CCTG-CCAG--G-G i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 74942 79 - 95547 CCCTCAATGTTCTCCCTG-------CCC--CC--------------AGAGAATGA-----------ACGGCTCACGGATGGC----AGAGCTCCGCATCAT---CCACC--T---------CCTG-CCAG--G-G i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 79100 81 + 225949 CCCTAAAGGTTCTTGCTG-------CCC--CC--------------AGAGAATGA-----------ACGGCTCAGCGATGGC----AGAGCT-CGTGTCAC---ACGCC--T-GCC-----CCTG-TCAG--G-G i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 13926 46 + 21754 CCCTAAAGACCCTTGCTGTTGCCCACCC--CC--------------AAAGAATGC------------------------------------------------------------------CCTG-CCA------ i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 3723 89 + 5481 CCCTAAAGATTCTCGCTGCCCACCACCC--CC--------------AGAGAATAG-----------CTGGCTCAGGGACGGC----GGGGCTCTGTGTCAC---CTGGT--C-TGC-----TCCA-CCAG--G-A i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 50347 94 + 287808 CCCTAAAGAGTCTTGCTGTCCCTCACCT--CC--------------AGAAAGTGG-----------ATGGCTCGTGGACAGC----AGAGCTCTATGTCAC---CCAGT--C-ACCCACCTCCCA-CCAG--G-A i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 4391 78 - 10116 CCC--AAGGTCCTTGCTG-------CCCTACC--------------TCAGAACAG-----------ATGGCTCCCGGAGGGC----AGGGCTTGGTGTCTC---CCGGT--C-GCC-----CCCG-CC------- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4412983 62 + 7991924 CCT----------------------CAT--CC--------------CAAGAATGC-----------ATGGAC----GACTTC----AGAGCTCTATGTCCCTGCCCTCC--T---------CCC--CCAG--G-G i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118786479 51 + 121843856 CAC----------------------CTT--CT--------------CAA---------------------------GACAAT----AGAGCTCTGTGTCCCTTGCCACC--T---------CCCA-CCAG--G-G i mm9.chr11 C 0 C 0 s felCat3.scaffold_206428 51400 84 + 132007 CCCCGTAAGTGCTTGCTG--------CC--CC-------GCTTT-------GCGG-----------ACAGCCATCAGAGGACGGATAGAGCTCCGTGTCAC---CTGGC--C-ACT-----CCCA-CCCA--G-- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59464017 74 - 64418924 -------------------------CCC--CCAGTAAGTGCTTC-------ACAG-----------ACAGACCTCGGAGGACAGACGGAGCTCTGCGTCAC---CCGAC--C-AAC-----CCCG-CCTG--G-- i canFam2.chr9 I 46 C 0 s equCab2.chr11 58070125 75 - 61308211 --------------GCTG--------TC--CT-------TCTTCCTAGAGAATGG-----------ATGGCTCTCGGAGGAC----GGGGCTCTGTGCCCC---CTGCCCTC-GCC-----CACG-CCCA--G-- i equCab2.chr11 I 4 C 0 s bosTau4.chr19 10883625 56 - 65312493 ---------------------------C--CC-----CTTCTT---AGAGAATGG-----------ACGGCCTGCAGAGGAC----AATGCT-TGTGTCT----------------------CCA-CCCA--GC- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 14707 77 + 223990 ---------TGATGTCCA--------CC--CT-------TCCT---AGAGAATGG-----------ACAACTCGCAGAGAAT----GGTGCTCTGTGTCTC---CTGGC--CACAC-----CCCA-CTCA--GC- i turTru1.scaffold_98008 I 4 C 0 s vicPac1.scaffold_279233 501 77 + 797 -------CTTGCTATCTA--------CC--CT-------TCCT---AGGGAACGC-----------ACGGCGAGCAGAGGAC----AGCAC--TGTGTCAC---CTGGC--CACCC-----CCCA-CCCA--GG- i vicPac1.scaffold_279233 n 0 n 0 s eriEur1.scaffold_319784 10544 72 - 15705 CCCCAGAGTTTCCTGATG--------TT--CTC----------------------------------TTTCTTGGAGAGGG-----ATGGCCCCATGTCA----CTGGC--TGCCC-----CTCA-CCCCAGG-- i eriEur1.scaffold_319784 C 0 C 0 s pteVam1.scaffold_11245 39302 59 + 48268 ----------------------------------------------AGAGAATGA-----------ATGG--CTCAGAGGGC----AGAGCTCTGTGTCAC---CTGGC--CGACT-----CCCG-CCCAAGG-- i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14464160 85 - 17734757 CTCTAAAGATGCTGGGGG-----TCCCA--CC--------------AGAGAAAGG-----------GTGGCTCACAGGAGGT----GGAGCTCTATCTCAC---CTGGC--CCCCT-----CCTGCCCCG--G-- i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_85717 5566 76 + 6675 ---TGGAGACTCTTGCCG-----ACCTC--CC--------------TGAGAACGG-----------GTGGCTCACGGAGGGT----GCAGCTCTGCCCC--------GG--CCCCT-----CCCG-CCGG--G-- i dasNov2.scaffold_85717 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e monDom5.chr2 304634828 21374 - 541556283 I a score=48106.000000 s hg19.chr17_gl000204_random 77927 39 + 81310 CACAGGGGATC-CTGG-CAGCCGATGTGCCGT---GGTGCCTGC s dasNov2.scaffold_85717 5642 38 + 6675 CACAGGGGG-C-CCCG-GCCCCGAGGAGACGG---GGAGTCTGC i dasNov2.scaffold_85717 C 0 C 0 s loxAfr3.scaffold_49 14464245 32 - 17734757 CACAGA------TCAG-CGGCTGATGAGATGG---GGG--CCAC i loxAfr3.scaffold_49 C 0 C 0 s eriEur1.scaffold_319784 10616 25 - 15705 CAGGGGGAACC-CCCA-CAGCTGATGG----------------- i eriEur1.scaffold_319784 C 0 C 0 s pteVam1.scaffold_11245 39361 24 + 48268 AACAGGGA--C-ACAGATAGCTGATGA----------------- i pteVam1.scaffold_11245 C 0 C 0 s equCab2.chr11 58070200 39 - 61308211 CACAGAGGCCC-CCGG-CGGCTGACGATCCAG---GGCTCCCGC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59464091 23 - 64418924 CACAGGGA--C-CCAG-CAGCTGAAGA----------------- i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 51484 23 + 132007 CACAGGGA--C-CCAG-CGGCTGAAGA----------------- i felCat3.scaffold_206428 C 0 C 0 s bosTau4.chr19 10883681 37 - 65312493 CACAGGGA--T-GTGG-CAGCTGATGAACTAG---GATGCCCGC i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 14784 37 + 223990 CACAGGGA--C-CCGG-CAGCTGATGAACTGG---GGCACCTGC i turTru1.scaffold_98008 C 0 C 0 s vicPac1.scaffold_72280 3391 37 + 3962 CACAGGGG--C-CCCG-CAGCTGACAAACTGG---GGTGCCTGC i vicPac1.scaffold_72280 C 0 C 0 s mm9.chr11 118786530 38 + 121843856 CCCTAGGCAC--CCTA-CAACTGATGAGCTGA---ATACTTAAC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4413045 18 + 7991924 CCCTGGACAC--TGGG-CACC----------------------- i cavPor3.scaffold_76 C 0 C 0 s tupBel1.scaffold_71658.1-10116 4469 36 - 10116 --CAGGACACC-CCAG-CAGCTGAAGC-CTGG---GGCGCCTGG i tupBel1.scaffold_71658.1-10116 C 0 C 0 s otoGar1.scaffold_94362.1-287808 50441 39 + 287808 CAAAGGGGTCAGCCGG-C-ACTGATGCGCCTG---GGTGCCCGC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_38207 3812 41 + 5481 CACGGGGGACC-CCGG-C-GCTGACACGCCAGGGCGGCGCCCGC i micMur1.scaffold_38207 C 0 C 0 s tarSyr1.scaffold_41848 13972 7 + 21754 -------------------------------------TGCCTGC i tarSyr1.scaffold_41848 C 0 C 0 s calJac1.Contig5139 79181 39 + 225949 CACGAGAGATC-CTGG-CAGCTGATGCACTGT---GGTGCCTGC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 75021 39 - 95547 CACAGGGGATC-CTGG-CAGCCGATGTGCCGT---GGTGCCTGC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75068018 39 + 78773432 CACAGGGGATC-CTGG-CAGCCGATGTGCCGT---GGTGCCTGC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16094658 39 + 17838096 CACAGGGGATC-CTGG-CAGCCGATGTGCCGT---GGTGCCTGC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 45783 39 - 64270 CACAGGGGATC-CTGG-CAGCCGATGTGCCGT---GGTGCCTGC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79509940 39 + 83384210 CACAGGGGATC-CTGG-CAGCCGATGTGCCGT---GGTGCCTGC i panTro2.chr17 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e monDom5.chr2 304634828 21374 - 541556283 I a score=75201.000000 s hg19.chr17_gl000204_random 77966 55 + 81310 GGCAGG-GCAGGCTGCGCAGGGAGACA-GCGAG-CCCT------------C----CGCGCTGCAGGA-ATGTGGG------- s panTro2.chr17 79509979 55 + 83384210 AGCAGG-GCAGGCTGCGCAGGGAGACA-GCGAG-CCCT------------C----CGCGCTGCAGGA-ATGTGGG------- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 45822 55 - 64270 AGCAGG-GCAGGCTGCGCAGGGAGACA-GCGAG-CCCT------------C----CGCNCTGCAGGA-ATGTGGG------- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16094697 55 + 17838096 AGCAGG-GCAGGCTGCACAGGGAGACA-GTGAG-CCCT------------C----CGTGCTGCAGGA-ATGTGGG------- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75068057 55 + 78773432 AGCAGG-GCAGGCTGTGCAGGGAGACG-GTGAG-CCCT------------C----CGTGCCGCAGGA-GTGTGGG------- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 75060 55 - 95547 AGCAGG-GCAGGCTGTGCAGGGAGACA-GTGAG-CCCT------------C----CGTGCCGCAGGA-GTGTGGG------- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 79220 67 + 225949 AGCAGG-GCAGGCTGCCCAGGGAGACA-GGGAC-CCCCGCCCCTGACACAC----TGCGCTACAGGA-ATGAAGT------- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 13979 54 + 21754 AACCAT-AGAGGCTG--CCAGGAGACAGGCCAG-CCCC------------A----CACACCACAGGA-ATGTGAG------- i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 3853 55 + 5481 AGCGGA-GGCGGCCGCCGAGGGAGCCG-GGCCG-GTGC------------G----CACGCCACGGGA-GAGGGAG------- i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 50480 54 + 287808 AGC-GA-GGAGGCCGCTGGGGAAGATG-ACCCA-GCCC------------T----GGAGGGCTCGGA-GCAGGAG------- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 4505 42 - 10116 GGCTGA-GCAGCCCG-------------TCCGG-CCCC------------A----CGC-CCACAGGA-ATGCGAG------- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4413063 45 + 7991924 ----------GGCAGCCATGGGAGGCA-GTCCA-CCCC------------A----CACACCAC-CAG-CACTCCG------- i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118786568 54 + 121843856 AGCTAG---AGGCTGTGGAGGAAGATG-GCCCAGCCTC------------G----AACACTACATGG-CTGTGAG------- i mm9.chr11 C 0 C 0 s vicPac1.scaffold_72280 3428 56 + 3962 GGCTGA-GGGGGCTGTCGGAGGAGACCGTCCAG-CCAC------------G----CACACTGCAGGG-ATCTGAG------- i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 14821 56 + 223990 AGCTGA-GGGGACTATCGGGGGAGACTATCCAG-CCAC------------G----CACACTGCAGGG-ATCTGAG------- i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10883718 57 - 65312493 CTCTGAGGGGGGCTGTCGGGGGAGACTGTCCAG-CCGT------------G----CGCACTGCCAGA-ATCTGAG------- i bosTau4.chr19 C 0 C 0 s felCat3.scaffold_206428 51507 56 + 132007 CGCCCA-AGGGGCCGTCGGGGGAGACAGTGCAG-CTGC------------G----CAGAGCACAGGA-GTCTGAG------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59464114 42 - 64418924 AGCAC---------------GGTGCCAGTCCAG-CTGT------------G----CACACCACAGGA-GTCTGAG------- i canFam2.chr9 C 0 C 0 s equCab2.chr11 58070239 56 - 61308211 AGCCGA-GGGGGCTGGCGAGGGAGACGGTGCAG-CCCC------------G----CGCCCCGCAGGA-ATCGGAG------- i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_11245 39385 41 + 48268 AGTGG---------------GGCGACCGCTCAG-CCAC------------G----CACACCACAGGA--TCCGAG------- i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_319784 10641 37 - 15705 ----------------CTGGGGAG----TTCCC-CCAC------------T----CACACCAAAGGA-ATCTGAG------- i eriEur1.scaffold_319784 C 0 C 0 s loxAfr3.scaffold_49 14464277 58 - 17734757 AGCTGGGGGAGGCTATCGAGGGAGCCG-GTC---CCAC------------TGCGCTACACCGCAGGA-GTGCACA------- i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_85717 5680 51 + 6675 AGCCCGGGGCGGC---CAAGGGGGCAG-GCCAG-CCAC------------C------CACAGCCGGG-GCCCGGA------- i dasNov2.scaffold_85717 C 0 I 1 s monDom5.chr2 304656202 64 - 541556283 GATATG-TCAGGCTGTCATAGGAGACAATCCAG-ACAT------------T----TGCAGTACTTAACATAGGAGCTGTCTT i monDom5.chr2 I 21374 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I a score=2250463.000000 s hg19.chr17_gl000204_random 78021 104 + 81310 CCTCCTTCCTTGAGAATGCAACA----TTTCAGCAACCAAGAGACAACTCTATTGGGAGAACAAGAGCTAATTAAATTTACTGGGATCACTGAAGATGAAATTATTTA s dasNov2.scaffold_85717 5732 104 + 6675 CCCGCGTCCCCGCGCATGCTCCG----TTTCAGAAACCCAGAGACAACTCTGTTGGGAGAACAAGAGCTAATTAAATTTACTGGGATCATTGAAGAGGAAATTATTTA i dasNov2.scaffold_85717 I 1 C 0 s loxAfr3.scaffold_49 14464335 103 - 17734757 CCTCCTTCCTCATGAATGCAACA-----CTCAGAAGCCAAGAGACAACTCTATCGGGAGAACAAGAGCTAATTAAATTTACTGGGATCATTGAAGAGGAAATTATTTA i loxAfr3.scaffold_49 C 0 C 0 s eriEur1.scaffold_319784 10678 103 - 15705 CCTCCTTTCTCGTGAT-GCAGCA----TTGCAGAAGCCAGGAGACAACTCTATTGGGAGAACAAGCTCTAATTAAATTTACCAGGCTCATTGGAGAGGAAATTATTTA i eriEur1.scaffold_319784 C 0 C 0 s pteVam1.scaffold_11245 39426 103 + 48268 CCTCCTTCCCCATGAATGCAGCA----CCTCGGAGCCCAGCGGAC-ACTCTACTGGGAGCAGCAGCACTAATTAAACTTACTGGGATCCCTGAAGACGAAGTTATTTA i pteVam1.scaffold_11245 C 0 C 0 s equCab2.chr11 58070295 104 - 61308211 GCTCCTTCCTTGTGACTGCAACG----TCTCAGAAACCGGGAGACAACTCTGTTGGGAGGACAAGCACTAATTAAGTTTACTGGGATCACTGAAGAGGAAATTATTTA i equCab2.chr11 C 0 C 0 s canFam2.chr9 59464156 102 - 64418924 CCCCCTTCCTTGTGAA-GCAACA----TTTCAGAAACCAGGAGACAACTCTATTGGGAGAAG-AGCACTAATTAAATTTACTGGGATCATTGAAGAGGAAATTATTTA i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 51563 106 + 132007 CCCCCTTCCTCGTGAA-GCCAGGAGGTTTTCAGAAGCCAGGAGACAACTCTATTGGGAGAAC-AGCACTAATTAAATTTACTGGAATCATTGAAGAGGAAATTATTTA i felCat3.scaffold_206428 C 0 C 0 s bosTau4.chr19 10883775 104 - 65312493 CCCCCATACTCGTGACTGCAACA----TCTCTGAAACCAGGAGACAACTCTATTGGGAGAACAAGCACTAATTAAATTTACTGGGATCATTGAAGAGGAAATTATTTA i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 14877 104 + 223990 CCTCCTTCCTTGTGACTGCAACA----TCTCTGAAATGAAGAGACAACTCTATTGGGAGAACAAGTGCTAATTAAATTTCCTGGGATCATTGAAGAGGAAATTACTTA i turTru1.scaffold_98008 C 0 C 0 s vicPac1.scaffold_72280 3484 104 + 3962 CCTCCTTCCTCGTGACTGCAACA----TCTCTGAAACCAGGAGACAACTCTATTGGGAGAACAAGCGCTAATTAAATTTACTGGGATCACTGAAGAGGAAATTATTTA i vicPac1.scaffold_72280 C 0 C 0 s ochPri2.scaffold_6980 15081 104 - 61692 CCACCTTAATCCAGAGTGAAATG----TTTTAGCAATGGTGGGCTGATTCCATCAGGAGAACAAGAGCTAATTAAATTCCCCCTGACCATCAACCAGTCAATTATTTA i ochPri2.scaffold_6980 N 0 N 0 s cavPor3.scaffold_76 4413108 104 + 7991924 CCTCCTTCCCCATGAACACAACA----TTTCAGAAACCAAGAGACAACTCTATTGGGAGAACAAGAGCTAATTAAATTTACTGGGATCACTGAAGAGGAAATTATTTA i cavPor3.scaffold_76 C 0 C 0 s mm9.chr11 118786622 102 + 121843856 CCTCCTTCTTCATGA--ACAGCA----TTTCAGAAACCAAACGACAGCTCTATTGGGAGAACAAGAGCTAATTAAATTTACTGGGATCATTGAAGGGGAAACTACTTA i mm9.chr11 C 0 C 0 s tupBel1.scaffold_71658.1-10116 4547 100 - 10116 CCTCCTT----GGGAATGCAACA----TTTCCGAATCCGAGAGACAGCTCTATTGGGAGGATAAGAGCTAATTAAATTTTCTGGGATCATTGAGGAGGAAATTATTTA i tupBel1.scaffold_71658.1-10116 C 0 C 0 s otoGar1.scaffold_94362.1-287808 50534 104 + 287808 CCTCCTTCCACACAAACGCAACA----TGGCAGAAACCAGCAGAGAACTCTATTGGGAGAACAAGAGCTAATTAAATTTACTGGGATCATTGAAGAGGAAATTATTTA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_38207 3908 104 + 5481 CCTCCTTCTTCGAGAACGCAACA----TTGCAGCAACCCAGAGACAACTCTATTGGGAGAACAAGAGCTAATTAAATTTACTGGGATCACTGAAGAGGAAATTATTTA i micMur1.scaffold_38207 C 0 C 0 s tarSyr1.scaffold_41848 14033 104 + 21754 CCGCCTTCCTCGTGAATGCAACA----TTTCAGCAACCAAGAGACAACTCTATCGGGAGAACAAGAGCTAATTAAATTTACTGGGATCACTGAAGAGGAAATTATTTA i tarSyr1.scaffold_41848 C 0 C 0 s calJac1.Contig5139 79287 104 + 225949 CCCCCTTCCTGGAGAATGCAACG----TTTCAGCAACCAAGAGACAACTCTATTGGGAGAACAAGAGCTAATTAAATTTACTGGGATCACTGAAGAGGAAATTATTTA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 75115 104 - 95547 CCTTCTTCCTTGAGAACGCAGCA----TTTCAGCAACCAAGAGACAACTCTATTGGGAGAACAAGAGCTAATTAAATTTACTGGGATCACTGAAGAGGAAATTATTTA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75068112 104 + 78773432 CCTTCTTCCTTGAGAATGCAGCA----TTTCAGCAACCAAGAGACAACTCTATTGGGAGAACAAGAGCTAATTAAATTTACTGGGATCACTGAAGAGGAAATTATTTA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16094752 104 + 17838096 CCTCCTTCCTTGAGAATGCAACA----TTTCAGCAACCAAGAGACAACTCTATTGGGAGAACAAGAGCTAATTAAATTTACTGGGATCACTGAAGAGGAAATTATTTA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 45877 104 - 64270 CCTCCTTCCTTGAGAATGCAACA----TTTCAGCAACCAAGAGACAACTCTATTGGGAGAACAAGAGCTAATTAAATTTACTGGGATCACTGAAGATGAAATTATTTA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79510034 104 + 83384210 CCTCCTTCCTTGAGAATGCAACA----TTTCAGCAACCAAGAGACAACTCTATTGGGAGAACAAGAGCTAATTAAATTTACTGGGATCACTGAAGATGAAATTATTTA i panTro2.chr17 C 0 C 0 s macEug1.Scaffold3360 45619 103 - 57943 -CCCCTTTGCTCTGAATGTGGCA----TTTCAGAAAGCAAGAGACAACTCTATCGGGAGAACAAGAGCTAATTAAATTTACTGGGATCATTGAAGAGGAAATTATTTA i macEug1.Scaffold3360 N 0 C 0 s monDom5.chr2 304656266 104 - 541556283 TCCCCTTTGTTCTGAATACAGCA----TTTCAGAAAGCAAGAGACAACTCTATCGGGAGAACAAGAGCTAATTAAATTTACTGGGATCATTGAAGAGGAAATTATTTA i monDom5.chr2 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I a score=1300483.000000 s hg19.chr17_gl000204_random 78125 83 + 81310 ATATTCTGAACAGAATTTAATATTTGAAAGCACGAACAGCCTTGGTTCGTTGTAGACGGGTTTTCCATCA--CCTGGGTCTGCAT s panTro2.chr17 79510138 83 + 83384210 ATATTCTGAACAGAATTTAATATTTGAAAGCACGAACAGCCTTGGTTCGTTGTAGACGGGTTTTCCATCA--CCTGGGTCTGCAT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 45981 83 - 64270 ATATTCTGAACAGAATTTAATATTTGAAAGCACGAACAGCCTTGGTTCGTTGTAGACGGGTTTTCCACCA--CCTGGGTCTGCAT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16094856 83 + 17838096 ATATTCTGAACAGAATTTAATATTTGAAAGCATGAACAGCCTTGGTTCGTTGTAGACGGGTTTTCCACCA--CCTGGGTCTGCAT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75068216 83 + 78773432 ATATTCTGAACAGAATTTAATGTTTGAAAGCATGAACAGCCTTGGTTCGTTGTAGACGGGTTTTCCGCCA--TCTGGGTCTGCAT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 75219 83 - 95547 ATATTCTGAACAGAATTTAATATTTGAAAGCATGAACAGCCTTGGTTCGTTGTAGACGGGTTTTCCACCA--TCTGGGTCTGCAT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 79391 81 + 225949 ATATTCTGAGCGGAATGTAATATTTGAAAGCATGA--AGCCTCGGTCCGTTGTAGACGGGTTTCCCATCA--CTAGGGTCTGCAC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 14137 83 + 21754 ATATTCTGAACAGAATTTAATATTGGAAAGCATGAACAGCCTTGGTTCGGTATAGATGAGTTTTCTACCA--TTCAGGACTACGT i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 4012 83 + 5481 ATATTCTGAACAGAATTTAATATTTGGAGGCATGAACAGCCGTGGTTCGCCGTGGATGGGTTTCCTACCA--CCGGGGTCTGCAG i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 50638 82 + 287808 ATATTCCAAACAGAATTTAATATTTGGAAGCGTGAACAGCCTTGCTTCGTTGTAGATGGGTTT-TTACCG--CCCTGGTCTACAC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 4647 74 - 10116 ATATTCCGAACAGAATTTAATATT-GGAAGCATGAACAGCCTGGGTCCCTTGTATTTGGGTCTTCTAGCA--TC--------CAG i tupBel1.scaffold_71658.1-10116 C 0 C 0 s mm9.chr11 118786724 81 + 121843856 ACATTCTGAATAGAATTTAATCTTTAGAAGCACGAGCAGCCTTGATTCATCGTAAAGG-GTTTTCTACCA--TCTGGGTTCACA- i mm9.chr11 C 0 I 1556 s cavPor3.scaffold_76 4413212 85 + 7991924 ATATTCTGAACAGAATTTAATATTTGAAAGCATGAACAGTCTGGATTCGTCATAGAGGAGTTCTCTACCACTCCAGGGGTCACAT i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_72280 3588 81 + 3962 ATATTCTGAACAG-ATTTAATATTTGAAAGCATGGACGGCCTTGATTCGCCGTGGATGGGTTCTCTGCCA--TCG-GGCTTACAT i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 14981 81 + 223990 ATATTCTGAACAG-ATTTAATATTTGAAAGCATGGACGGCCTTGATTTGTCGTGCATGGGTTCTCTGCCA--TCG-GGCTTACAT i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10883879 81 - 65312493 ATATTCTGAACAG-ATTTAATATTTGAAAGCATGGATGGCCTTGATTCGTCGTGGACGGGTTCTTTGCCA--CGG-GGCTTACAT i bosTau4.chr19 C 0 C 0 s felCat3.scaffold_206428 51669 82 + 132007 ATATTCCGAACAG-ATTTAATATTTGAAAGCATGGATGGCCTTGATCCGTCGTGGGTGGGCTCTCTGTCA--CGGGGGCCCATGC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59464258 82 - 64418924 ATATTCTGAACAG-ATTTAATATTTGAAAGCATGGACGGCCCCGATCTATTGTGGGTGGGTTCTCTGCCA--CATGGGCCCACAC i canFam2.chr9 C 0 C 0 s equCab2.chr11 58070399 81 - 61308211 ATATTCTGGACAG-ATTTAATATTTGAAAGTGTGGACGGCCTTGATTCGTCGTGGATGGGTTCTCCGCCA--TCC-GGCTTACGT i equCab2.chr11 C 0 C 0 s pteVam1.scaffold_11245 39529 82 + 48268 ATGCTCTGAACAG-ATTTAACATGAGAAAGCGTGGCCGGCCTTGATTCGTCACGGACGGACTCCCTGCCA--TCCGGGGCTACGT i pteVam1.scaffold_11245 C 0 C 0 s eriEur1.scaffold_319784 10781 81 - 15705 ATATTCTGAACAG-ATTTGATATTTGAGAGCATGGATGGCCCTGATTCATCACAGTTGG-CTCTCTGTGA--TCTGGGTTCATAC i eriEur1.scaffold_319784 C 0 C 0 s loxAfr3.scaffold_49 14464438 83 - 17734757 ATATTCTGAGCAGAATTTAATATTTGAAAGCATGAGTGGCCTCGGTTCACTGTGGGTGGACTCTCCACCA--TCTGGGTCTGCAT i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_85717 5836 82 + 6675 ATATTCTGAGCAGAATTTAATATCTGGAAGCATGAATGGACTTGCTCCACCGTGGACGGCCTCTCTGCC---CCTGGGTTCACGT i dasNov2.scaffold_85717 C 0 C 0 s macEug1.Scaffold3360 45722 83 - 57943 ATATTCTGTGTGGAATTTAATATTTGAGAGCATGAATGGCCTTGTTTCACTGTCACTAGTTTCCCTACCA--TCTgagtttacat i macEug1.Scaffold3360 C 0 N 0 s monDom5.chr2 304656370 83 - 541556283 ATATTCTGTGTGGAATTTAATATTTGAGAGCATGAATGGCCTTGTTTCATTGTCACTAGTTTCCCTACCA--TCTGAGTTTACAT i monDom5.chr2 C 0 I 9698 e proCap1.scaffold_52062 2229 13555 + 16741 I a score=-50058.000000 s hg19.chr17_gl000204_random 78208 40 + 81310 TAGG-AGGATCCGTATACAGAT-G-A-------------G-G--------------------GGT----------GGGGCCGG--GGAT s panTro2.chr17 79510221 40 + 83384210 TAGG-AGGATCCGTATACAGAT-G-A-------------G-G--------------------GCT----------GGGGCCGG--GGAT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 46064 41 - 64270 TAGGCAGGATCCGTATACAGAT-G-A-------------G-G--------------------GGT----------GGGGCCGG--GGAT i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16094939 41 + 17838096 TAGGCAGGATCCGTATACAGAT-G-A-------------G-G--------------------GGT----------GGGGCCAG--GGAT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75068299 41 + 78773432 TAGGCAGGATATGTATACAGAT-G-A-------------G-G--------------------GGC----------GGGGCCGA--GGAT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 75302 41 - 95547 TAGGCAGGATATGTATACAGAT-G-A-------------G-G--------------------GGC----------GGGGCCGA--GGAT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 79472 41 + 225949 CAGGCAGGGTCGGTGTACAGAT-G-A-------------G-G--------------------GGC----------AGGGCTGG--GGAT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 14220 53 + 21754 CAGGTAGGAT-GGCGTACAAAT-T-A-------------G-GGTGAAGAGACC-------GAGGT----------AGAGAGAA--GAAG i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 4095 53 + 5481 TCAGCAGGGC-TGTGCACAGAT-T-AAGGTGGGGAGCCCG-G--------------------GAT----------GCAGAGAG--GGAC i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 50720 35 + 287808 TTAGCAGGG-----GTACAAAT-G-A---------------G--------------------GGG----------GCAGAGAG--GGAC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 4721 63 - 10116 TTAGCAGGCTGCATACCCAAAT-T-A-------------G-GGTGTAGAGACCCTAAGCGAGGGC----------GGAGACGGCCAGCC i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4413297 44 + 7991924 CTAGCAGGATCCACGTGCCAATCC-A-------------G-G--------------------TGT----------GGGGGCTGCAAGAA i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_72280 3669 42 + 3962 TTGG-GGGATCCATATACAAGC-TGG-------------GGG--------------------GGA----------GGGGACTG--AGGT i vicPac1.scaffold_72280 C 0 I 11 s turTru1.scaffold_98008 15062 40 + 223990 TTGATGGGATCC--ACACAAGC-T-A-------------GGA--------------------GGA----------GGGGATGG--AGGT i turTru1.scaffold_98008 C 0 I 11 s bosTau4.chr19 10883960 40 - 65312493 TTGATGGGATCC--ACACAAGC-T-A-------------GGA--------------------GGA----------GGGGATGG--AGGT i bosTau4.chr19 C 0 I 11 s felCat3.scaffold_206428 51751 42 + 132007 GAGCTGGGGTCCGTGTCCCAGC-C-C-------------GTG--------------------GGA----------GGAAATGG--AGCC i felCat3.scaffold_206428 C 0 I 10 s canFam2.chr9 59464340 42 - 64418924 TGGGTGGGGTCCAGGTGCAAGC-C-C-------------ATG--------------------GGA----------GGAGACTG--AACC i canFam2.chr9 C 0 I 7 s equCab2.chr11 58070480 41 - 61308211 TTGGTTGGATCCACACACAAGC-T-A-------------G-G--------------------GGA----------GGGGACCG--AGGT i equCab2.chr11 C 0 I 11 s pteVam1.scaffold_11245 39611 34 + 48268 TTGGTGGGGTCCGTGTGCAAGC-C-C-------------G-G--------------------CTT----------GGGGC--------- i pteVam1.scaffold_11245 C 0 I 9 s eriEur1.scaffold_319784 10862 29 - 15705 TTGAGGGGCGCCCCCAACAAGC-A-T-------------GGA--------------------GC------------------------- i eriEur1.scaffold_319784 C 0 N 0 s loxAfr3.scaffold_49 14464521 41 - 17734757 TCCACAGGGTCCATATGCAAAT-G-A-------------G-G--------------------GGT--CATTCCTAGGAG---------- i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_85717 5918 43 + 6675 GGAGCAGGAGCCACGGGCCCGT-C-G-------------G-G--------------------GGTGGCCTTACCGGGCG---------- i dasNov2.scaffold_85717 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e monDom5.chr2 304656453 9698 - 541556283 I e mm9.chr11 118786805 1556 + 121843856 I a score=38164.000000 s hg19.chr17_gl000204_random 78248 22 + 81310 --GTGCT----GCTTCT--------GGAAACCAGAG s panTro2.chr17 79510261 22 + 83384210 --GTGCT----GCTTCT--------GGAAACCAGAG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 46105 22 - 64270 --GTGCT----GCTTCT--------GGAAACCAGAG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16094980 22 + 17838096 --GTGCT----GCTTCT--------GGAAACCAGAG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75068340 22 + 78773432 --GTGCT----GCTTCT--------AGAAACCAGAG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 75343 22 - 95547 --GTGCT----GCTTCT--------AGAAACCAGAG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 79513 22 + 225949 --GTGCT----GCTTCT--------GAAAACTGGAG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 14273 22 + 21754 --ATGCT----GTTTCT--------GGAAACCAGAG i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 4148 7 + 5481 --GTGCC---------------------------AG i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 50755 7 + 287808 --GAGCC---------------------------TG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 4784 17 - 10116 --GTGCT----GACCCT--------GAGACC----- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4413341 26 + 7991924 --GGGCTGGGTGTTCCT--------GGAACCACAGG i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_72280 3722 22 + 3962 --ATGCT----GTCCCT--------GGAAGCCAGAG i vicPac1.scaffold_72280 I 11 C 0 s turTru1.scaffold_98008 15113 22 + 223990 --GTGAT----GTCCCT--------GGAAGCCAGAG i turTru1.scaffold_98008 I 11 C 0 s bosTau4.chr19 10884011 22 - 65312493 --ATGTT----GTCCCT--------GGAAGCCAGAG i bosTau4.chr19 I 11 C 0 s felCat3.scaffold_206428 51803 20 + 132007 --GTGCT-----GCTAC--------GGAAG-CAGAG i felCat3.scaffold_206428 I 10 C 0 s canFam2.chr9 59464389 10 - 64418924 -------------------------GGACA-CAGAA i canFam2.chr9 I 7 C 0 s equCab2.chr11 58070532 22 - 61308211 --GTGCT----GGCCGT--------GGAAGCCCGAG i equCab2.chr11 I 11 C 0 s loxAfr3.scaffold_49 14464562 29 - 17734757 AGA---T----GACCAGTGGAGGAAGGGAGCCAGGG i loxAfr3.scaffold_49 C 0 C 0 s dasNov2.scaffold_85717 5961 22 + 6675 AGGCTCT----GGCC----------GGACACCAGAG i dasNov2.scaffold_85717 C 0 N 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e pteVam1.scaffold_11245 39645 9 + 48268 I e monDom5.chr2 304656453 9698 - 541556283 I e mm9.chr11 118786805 1556 + 121843856 I a score=189301.000000 s hg19.chr17_gl000204_random 78270 44 + 81310 -GAGATGGGAGAGGAA----------CTGGAAATGGG---------CAGGAGGACAAAGTCCTC s panTro2.chr17 79510283 44 + 83384210 -GAGATGGGAGAGGAA----------CTGGAAATGGG---------CAGGAGGGCAAAGTCCTC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 46127 44 - 64270 -GANATGGGAGAGGAA----------CTGGAAATGGG---------CAGGAGGGCAAAGTCCTC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16095002 44 + 17838096 -GAGATGGGAGAGGAA----------CTGGAAATGGG---------CAGGAGGGCAAAGTCCTC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75068362 44 + 78773432 -GAGATGGGAGAGGAA----------CTGGAAATGGG---------CAGGAGGGCAAAGTCCTC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 75365 44 - 95547 -GAGATGGGAGAGGAA----------CTGGAAATGGG---------CAGGAGGGCAAAGTCCTC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 79535 43 + 225949 -GAGATGGGAG-GGAA----------CTGGAAATGGG---------CAGGAGGGCAAAGTCCTC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 14295 42 + 21754 -GAATTGGAAG-GAAG----------CTGGGAATGGG---------CAGGAGAGCCAGAT-CTC i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 4155 38 + 5481 -G-----GGAGAGGGAAT--------CGGGGCGTGGG----------CGGTGGGC--AGTCCCC i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 50762 61 + 287808 -GACTGCAGAGTGGACATGTTGTCCCCGAAGCCTGGGGAGACGGCACAGGTGGGC--AGTCCTA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 4801 36 - 10116 ---------AGACGAG----------GCAGAAAGGGA---------GGGAGGGGCAAAGTCCCC i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4413367 43 + 7991924 -AAAGTGACAGAGAAG----------CTTGGCCTGGG---------TGAGAGGTT-GAGTCCCC i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_72280 3744 43 + 3962 -GACAG-GGAGAGAAG----------CTGGGCACGGG---------CCAGAGGGCGAGGTCCTG i vicPac1.scaffold_72280 C 0 C 0 s turTru1.scaffold_98008 15135 42 + 223990 -GAGAG-GGAGAGAAA----------CTGGGCAT-GG---------CCAGAGGGCAAGGTCCTC i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10884033 42 - 65312493 -GAGAG-GGAGAGAAG----------CTGGGCAT-GG---------TCGGAGGGTGAGGTCCTT i bosTau4.chr19 C 0 C 0 s felCat3.scaffold_206428 51823 43 + 132007 -GGAAT-GGAGAGGAG----------CCAGGAGTGGG---------TCGAGGGGCGAGATGCTC i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59464399 43 - 64418924 -GGCTC-GGGGAGGAG----------CTGGGAGCAGG---------CCGAGGGGCAAGGTCCTC i canFam2.chr9 C 0 C 0 s equCab2.chr11 58070554 43 - 61308211 -GAGAC-GGACAGAGG----------CTGGGTGTGCG---------CCGGAGCACGAAGTCCTC i equCab2.chr11 C 0 C 0 s loxAfr3.scaffold_49 14464591 44 - 17734757 AACGTGGAAAGAGGGG----------CTAGGGGT-GG---------CAAGGGGGCGCTGTCCTC i loxAfr3.scaffold_49 C 0 I 1115 e proCap1.scaffold_52062 2229 13555 + 16741 I e pteVam1.scaffold_11245 39645 9 + 48268 I e monDom5.chr2 304656453 9698 - 541556283 I e mm9.chr11 118786805 1556 + 121843856 I a score=427021.000000 s hg19.chr17_gl000204_random 78314 241 + 81310 TTCAGGATCCTGGAT-----------GATTCTGCTCC--ACGTTTCCAGAGGG-----------------ACCCCTGTTGGTG-CCTCTAAAGTGA-TGGAAAATC-----ACAGTTGT-GGTG-CCAGGACCCCATGTCTG-GGGTCT-CTGACCACTGCCTGCCTCCGCTCCACCTA----TCTCTAACCCAGGGTCA-TTGCTGGCCAAGTCACATGGTGAAGTCAG-AGGATCCGG----AAGCCAGTGCTCTTCCCTGGCATGCACGAGTCCCCGGCCACACGCTCC s panTro2.chr17 79510327 241 + 83384210 TTCGGGATCCTGGAT-----------GATTCTGCTCC--ACGTTTCCAGAGGG-----------------ACCCCTGTTGGTG-CCTCTAAAGTGA-TGGAAAATC-----ATAGTTGT-GGTG-CCAGGACCCCATGTCTG-GGGTCT-CTGACCGCTGCCTGCCTCCGCTCCACCTA----TCTCTAACCCAGGGTCA-TTGCTGGCCTAGTCACATGGTGAAGTCAG-AGGATCCGG----AAGCCGGTGCTCTTCCCTGGCATGCACGAGTCCCCAGCCACACGCTCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 46171 241 - 64270 TTCGGGATCCTGGAT-----------GATTCTGCTCC--ACATTTCCAGAGGG-----------------ACCCCTGTTGGTG-CCTCTAAAGTGA-TGGAAAATC-----ATAGTTGT-GGTG-CCAGGACCCCATGTCTG-GGGTCT-CTGACCGCTGCCTGCCTCCGCTCCACCTA----TCTCTAACCCAGGGTCA-TTGCTGGCCAAGCCACATGGTGAAGTCAG-AGGATCCGG----AAGCCAGTGCTCTTCCCTGGCATGCACGAGTCCCCGGCCACACGCTCC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16095046 241 + 17838096 TTTGGGATCCTGGAT-----------GATTCTGCTCC--ACGTTTCCAGAGGG-----------------ACCCCTGTTGGTG-CCTCTAAAGTGA-TGGAAAATC-----ATAGTTGT-GATG-CCAGGACCCCATATTTG-GGGTCT-CTGACCACTGCCTGCCTCTGCTCCACCTA----TCTCTAACCCAGGGTCA-TTGCTGGCCAAGTCACATGGTGAAGTCAG-AGGATCCGG----AAGCCAGTGCTCTTCCCTGGCATGCATGAGTCCCCGGCTACATGCTCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75068406 254 + 78773432 TTTGGGATCCTGGACGATTCCTGGAAGATTCTGCTCC--ACGTTTCCAGAGGG-----------------ACCCCTGTTGGTG-CCTCTAAAGTGA-TGGGAAATC-----ATAGTAGT-AGTG-CCGGGACCCCATGTTTG-GGGTCT-CTGACTGCTGCCTGCCTCCGCTCCACCTG----TCTCTAACCCAGGGTCA-TTGCTGGCCAAGTCACATAGTGAAATCAG-AGGATCTAGAAGCAAGCCAATGTTCTTCCCTGGCACGCACGAGTCCCTGGCCACA--CTCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 75409 250 - 95547 TTTGGGATCCTGGACGATTCCTGGACGATTCTGCTCC--ACGTTTCCAGAGGG-----------------ACCCCTGTTGGTG-CCTCTAAAGTGA-TGGGAAATC-----ATAGTAGT-AGTG-CCGGGACCCCATGTTTG-GGGTCT-CTAACTGCTGCCTGCCTCCGCTCCACCTG----TCTCTATCCCAGGGTCA-TTGCTGGCCAAGTCACATAGTGAAATCAG-AGGATCTGG----AAGCCAATGTTCTTCCCTGGCACGCACGGGTCCCTGGCCACA--CTCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 79578 239 + 225949 TTC-TCATCCTGGAC-----------AATCCTGCTCC--GCATTTCCAGTGGG-----------------GCCCCC-TTTGTG-TCTCTAAAGTGA-TAGAAAATC-----ACAGATGT-GGTT-CCGGGACCCCACGTTTG-GGGTCT-CTGACCGCTGCCTGCCTTCGCTCCACCTA----TCTGTCACCCAGGGTCA-TTGCTGGCCAAGTCACATGGCGAAGTCAG-AGGATCTGG----AAGCAAATGCTCTTCCCTGGCAGGCATGAGTCCCTGGCCACGCACTCC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 14337 239 + 21754 CTCGTCATCTTGGAT-----------GATTCTGCTCCGAATCTTCCCAGAGGGCAGGGGTGGGTACGGGTATGGTTGTTGGGG-CCTCTACAGTGA-----AAGTC-----ATATTCAT-GGTC-TCTGTGGCCCTCATTTG-AGGCCC-CTGACCTTGGTCTGCATTCTTTCCACCTG----TTCATAACCCAAGGTCA-TTTGTGGCCAAGTCACACCTCTAAGTGAA-AAGATCAGG----AAGCTAATGCTATTCCTTGGAACACATGAGT----------------- i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 4193 223 + 5481 CGTGTAATCCTGGAC-----------GATTCTGCCCC--G-AGTCCCGAGGGT-----------------CCTCTC--CGGCA-CCTCTGCGGTGAATCGAAAGCC-----AAATCCGTGGGCT-CTGAGGCCCCACGTTCA-AGGTCT-CTCGTCTCAGCCTGCATTTGCACC-CCTG----CCTGTGACCCCGGCTCG--TGTTGGCCAAGGCACAGGTGCAGGAGGACAGGAGCAGG----AAGCCGACGCCATTCCTCGGGATGCGCAAGT-C--------------- i micMur1.scaffold_38207 C 0 I 1 s otoGar1.scaffold_94362.1-287808 50823 224 + 287808 ---GTAGTCCCTGGC-----------AATGCTGCTCT--G-GATCCTAAGGGG-----------------CCTCCCGTGGGTG-CCTCTGCCATGAACTGAAGGTC-----TTGTCCATGGGTT-CCATGGCCCCAAATTTT-GGGTCT-CTAATCCCTGCCCACACTCTGATC-CCTGACCCCCTGGAGTCGTGGGTCA--TGTTGGCCCAGTCACACGTCCAGGTGGG-AGGAGCAGG----GCA-CATCACCATTCCTTAGAAAGCATGTGT-C--------------- i otoGar1.scaffold_94362.1-287808 C 0 I 21 s tupBel1.scaffold_71658.1-10116 4837 180 - 10116 --CATCCTCCTGGAA-----------GACTCTACTCC--A-GTCT----GAGG-----------------GCCCCTGGTGGTT-CCTGCAGGTTCC--------------------TGT-GGTG-CCAGGA------ATTTG-GGGGCTCCTGGCCTCGGCCCACATCCGTCATAATCA----GGGCCA--CCAGGGCCA-CAGCTGCCCA---CAGA----------AG-AGGCCTGGG----AAGCTGCTGCTTGTCCT--------------------CCAAACACTTC i tupBel1.scaffold_71658.1-10116 C 0 C 0 s cavPor3.scaffold_76 4413410 191 + 7991924 --CAGAACGCTGAAC-----------AGTCCT---CT--GGGTCCCCAAGAGG-----------------------GTTGGTT-TCTCCA--GTGAATATAAAGTC--------------ACTC-CC-----------TGTG-GGGCCT-CTGATCTCTGCCTTCATTGTTTGCTGCTG----TATGTCTCCCAGGGCCA-CTGCTGGCCAAGTGA-GCATCTGAATGAG-A-GACCAGA----GGACCAGTGCCC-TCCTTGGGATACATGCATC---------------- i cavPor3.scaffold_76 C 0 I 1087 s vicPac1.scaffold_72280 3787 160 + 3962 GTAGCAGCCCT----------------------------------CCGCAGGG-----------------ACCTG-GCTGGCA-CCGCTACAA-GGTCTGGAGGTC-----ATAGTCAG-GGTCTCTGTGGCCCTGTGCCTGTGGG--C-CTGACGTCGACCTGCATTTGCCC--CCT------------------GCTC-CTGCTGGCCGAGCTGCACACCAG-GTGAG-AGGGTCCAG----AGGCTA------------------------------------------ i vicPac1.scaffold_72280 C 0 N 0 s turTru1.scaffold_98008 15177 193 + 223990 GTAACAGCCCT----------------------------------CCACAGGA-----------------ACCC---CAGGCA-CTGCTACAGCGAGCTGAAAGTC-----ATATTCAT-GGTCTCTGAAGCCCCACGTCTGTAGGTCC-CTGACATCTGCCTGCATTCACCCCACCTT----TCTGTAACTCAGGACTC-TTGTTGGCCAAGGTAGCCAACTGAGTGAG-AGG----AA----GGTCTTGTA---TTCCTTGGAATGCACG-------------------- i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10884075 203 - 65312493 GTAACAACCCT----------------------------------CCACAGGG-----------------ACCC---TGGGCA-CTGCTATAGCAAGCTGGAAGTCTTGCTATATTCAC-AGTTTCTGTGGCCCCATATCTGTGGGTCC-CTAACATCTGCCTGCATTTGCCCTACCTT----TCTGTAACCCAGAGCCC-TTGTTGGCCAAGGTACCCACCTGAGTGAG-AGGGTTCAG----AGTCTTGTA---CCCCTTGGAACACATGA------------------- i bosTau4.chr19 C 0 I 261 s felCat3.scaffold_206428 51866 180 + 132007 CTCATAATCCTGAGC-----------GGCTCTGCTCC--CACCTTCCACAGGT-----------------CCCC--GCGGCCACCCCTTACAGCGACAT-GAAGCC-----CTACCCAT-GACC--------------CCTGTGGGTCC-CCAGCGTCTGCCCTCCTGCGCCCC-CCTT----CCTGTAA-CCAGTGTCA-TCGCTGGCCAAGCCACACGTCAT-GCAGG-AGGGTCCGG----AAG--------------------------------------------- i felCat3.scaffold_206428 C 0 I 3265 s canFam2.chr9 59464442 207 - 64418924 ATTGTAACCCTGTAT-----------GGCTCTGC-CC--CAGCCTCCACAGGC-----------------CCCT--GTTGCCA-CCCGTATAGCAAGAC-GAAGTC-----TTACCCAT-GAGC--------------CTTGTGGGTCC-CTGGCATTTACCCACATGCACCCC-TCTT----CCTGCAACCCAGTGTCATTTGTTAACCAAGTTACACACAAG-GTGAG-ATGGTCTAG----AAGGCAATG-GACTCCTTAGAATG-----------------ATGATCT i canFam2.chr9 C 0 C 0 s equCab2.chr11 58070597 197 - 61308211 GTTAGAACCCCATGT-----------GCCTCTGGTCC--AAA-----AAGGGC-----------------CCCC--ACTGGCA-CCCCTACAGCGGGTTGGAAGTC-----ATATTCGC-CATCTCTGTGGCCCCGTGCCTGTGGGTCC-GTGACATCTGCCTGCATTTGCTCCACCTT----TCTGTAACCCAGGGTCA-TTGCTGGCCAAGTTACGCGTCCA-GGTGA-GGGGTCTGG----AAGGCAATG--------------------------------------- i equCab2.chr11 C 0 I 21 e proCap1.scaffold_52062 2229 13555 + 16741 I e pteVam1.scaffold_11245 39645 9 + 48268 I e monDom5.chr2 304656453 9698 - 541556283 I e mm9.chr11 118786805 1556 + 121843856 I e loxAfr3.scaffold_49 14464635 1115 - 17734757 I a score=186995.000000 s hg19.chr17_gl000204_random 78555 121 + 81310 TGTggcggagtacagtggctcacacctgtaatcccagcacttccggaggctgaggcaggcagatcctttgagcccaggagtctgagaccagcctgggcaacatagcaagaccacgtatcta s calJac1.Contig5139 79817 119 + 225949 TGTGGTGgggggcagtggctcacacctgtaatcccagcactttgggaagctaagacaggcagattgtttgagcccaggagtctaagaccagcc-aggcaacatggcaagaccacgtat-ta i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 75659 121 - 95547 TGTggcagagtgcagtggctcacacctgtaatcccagcactttgggaggctaaggcaggaggatcatttgagcccaggagtccgagaccagcctgggcaacaaagcaagaccacgtatcta i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75068660 121 + 78773432 TGTggcagagtgcagtggctcacacctgtaatcccagcactttgggaacctgaggcaggtggatcatttgagcccaggagtccaagaccagcctgggcaacatagcaagaccacatatcta i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16095287 121 + 17838096 TGTggcggagtgcagtggctcacacctgtaatcccagcactttgggaggccgaggcaggcagatcatttgagcccaggagtctgagaccagcctgggcaacatagcaagaccacgtatcta i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 46412 121 - 64270 TGTggcggagtacagtggttcacacctgtaatcccagcacttcgggaggctgaggcaggcagatcctttgagcccaggagtctgagaccagcctgggcaacatagcaagaccacgtatcta i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79510568 121 + 83384210 TGTggcggagtacagtggctcacacctgtaatcccagcacttcgggaggctgaggcaggcagatcctttgagcccaggagtctgagaccagcctgggcaacatagcaagaccacatatcta i panTro2.chr17 C 0 C 0 s tupBel1.scaffold_71658.1-10116 5017 18 - 10116 TCTG---------------------------TCTCAG-------------------GGGCAGAT--------------------------------------------------------- i tupBel1.scaffold_71658.1-10116 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e tarSyr1.scaffold_41848 14576 0 + 21754 C e micMur1.scaffold_38207 4416 1 + 5481 I e turTru1.scaffold_98008 15370 0 + 223990 C e felCat3.scaffold_206428 52046 3265 + 132007 I e pteVam1.scaffold_11245 39645 9 + 48268 I e otoGar1.scaffold_94362.1-287808 51047 21 + 287808 I e monDom5.chr2 304656453 9698 - 541556283 I e canFam2.chr9 59464649 0 - 64418924 C e bosTau4.chr19 10884278 261 - 65312493 I e equCab2.chr11 58070794 21 - 61308211 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I e loxAfr3.scaffold_49 14464635 1115 - 17734757 I a score=125709.000000 s hg19.chr17_gl000204_random 78676 103 + 81310 ctaaaaaaaaaaaaaaaaaaaa-------------gttagcaaggcctgatggtgcacacctgtggttccagctacttaggaggctaagtaaggcaggaggatggcttgggcctgg s tupBel1.scaffold_71658.1-10116 5035 53 - 10116 --GGGAAGAGAAAGGACA-----------------CTTTGAATGGCC----------------------------CCCAGGGTAC----TCAAG------------TTGGGCCCGG i tupBel1.scaffold_71658.1-10116 C 0 C 0 s panTro2.chr17 79510689 116 + 83384210 ctaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaggttagcaaggcctgatggtgcacacctgtggttccagctacttaggaggctaagtaaggcaggaggatggcttgggcctgg i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 46533 109 - 64270 ctaaaaaaaaaaaaaaaaaaaaaaaaaa-------gttagcaaggcctgatggtgcacacctgtggttccagctacttaggaggctaagtaaggcaggaggatggcttgggcctgg i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16095408 102 + 17838096 ctaaaaaaaaaaaaaaaaaaaaaaa----------gttagcaaggcctgatggtgcacacctgtggttccagctacttaggaggc----taaggcaggaggatggcttgggcctgg i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75068781 90 + 78773432 ctaaaaaaaacaa----------------------gttagcatggcctgatggtgcacacctgtggttccagctactcaggaggc----taaggcaggaggatggcttgggcctgg i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 75780 90 - 95547 ctaaaaaaaaaaa----------------------gttagcaaggcctgatggtgcatacctgtggttccagctactcagaaggc----taaggcaggaggatggcttgggcttgg i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 79936 98 + 225949 ctaaaaaaagaaaattaaaaa--------------gttagccaggcctgatggtgcacacctgtggtcccagctacccaggagcc----tagggcgagtggacggcttgggcctgg i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 14576 30 + 21754 ----------------------------------------------CTAA----ACACGCCTGAATCTCCAG-----GGGGAGGC------------------------------- i tarSyr1.scaffold_41848 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e micMur1.scaffold_38207 4416 1 + 5481 I e turTru1.scaffold_98008 15370 0 + 223990 C e felCat3.scaffold_206428 52046 3265 + 132007 I e pteVam1.scaffold_11245 39645 9 + 48268 I e otoGar1.scaffold_94362.1-287808 51047 21 + 287808 I e monDom5.chr2 304656453 9698 - 541556283 I e canFam2.chr9 59464649 0 - 64418924 C e bosTau4.chr19 10884278 261 - 65312493 I e equCab2.chr11 58070794 21 - 61308211 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I e loxAfr3.scaffold_49 14464635 1115 - 17734757 I a score=119755.000000 s hg19.chr17_gl000204_random 78779 82 + 81310 aggtcaaggcta----------------cagtgagc-----tgtgatcacaaca------ctgtactccagcc---tgggcaa---cagagcaagaccctgccttgaaaaaT-------TTC s calJac1.Contig5139 80034 88 + 225949 aggtcgaggcta----------------cagtgagc-----tatgttcacacca------tggcactccagcc---tgggcga---caaagcaaga-cctgcctcaaacaaTTAATTAATTA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 75870 82 - 95547 aggtggaggcta----------------cagtgggc-----tgtgatcacaacc------ctgcactccagcc---tgggcaa---caaagcaagaccctgccttgaaaaaT-------TTA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75068871 82 + 78773432 aggtggaggcta----------------cagtgggc-----tgtgatcacaacc------ctgcgctccagcc---tgggcaa---caaagcaagaccctgccttgaaaaaT-------TTA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16095510 82 + 17838096 aggtcaaggcta----------------cagagagc-----tgtgatcaaaaca------ctgtactccagcc---tgggcca---cagagcaagaccctgccttgaaaaaT-------TTC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 46642 82 - 64270 aggtcaaggcta----------------cagtgagc-----tgtgatcacaaca------ctgtactccgacc---tcggcaa---cagagcaagaccctgccttgaaaaaT-------TTC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79510805 82 + 83384210 aggtcaaggcta----------------cagagagc-----tgtgatcacaaca------ctgtactccagcc---tgggcaa---aagagcaagaccctgccttgaaaaaT-------TTC i panTro2.chr17 C 0 C 0 s bosTau4.chr19 10884539 115 - 65312493 GAGCCCAGGCTAGGAGTCAGTCACTGCCCAGCAGACAAGCTCAGGGTCACATCCCGTAGGCTGTGCTGCATCCATGGGGGCAACTGCAGGCCAGGAGACCAGCTCAGCCAAC-------CCA i bosTau4.chr19 I 261 I 7 e proCap1.scaffold_52062 2229 13555 + 16741 I e tarSyr1.scaffold_41848 14606 0 + 21754 C e tupBel1.scaffold_71658.1-10116 5088 0 - 10116 C e micMur1.scaffold_38207 4416 1 + 5481 I e turTru1.scaffold_98008 15370 0 + 223990 C e felCat3.scaffold_206428 52046 3265 + 132007 I e pteVam1.scaffold_11245 39645 9 + 48268 I e otoGar1.scaffold_94362.1-287808 51047 21 + 287808 I e monDom5.chr2 304656453 9698 - 541556283 I e canFam2.chr9 59464649 0 - 64418924 C e equCab2.chr11 58070794 21 - 61308211 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I e loxAfr3.scaffold_49 14464635 1115 - 17734757 I a score=74700.000000 s hg19.chr17_gl000204_random 78861 45 + 81310 ATTTA--AAACACTCCTGTATTCCACAGGGGACACTGAAAGAGAGAT s calJac1.Contig5139 80122 45 + 225949 ATTAA--AAACACTCCTGTATCCCACGGGGGACATTGAAAAAGAAAT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 75952 45 - 95547 ATTTA--AAACACTCCTATATTCCACAAAGGACATTGAAAGAGAAAC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75068953 45 + 78773432 ATTTA--AAACACTTCTATATTCCCCAAGGGACATTGAAAGAGAAAC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16095592 45 + 17838096 ATTTA--AAACACTCCTGTATTCCACAGGGGACACTGAAAGAGAAAT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 46724 45 - 64270 ATTTA--AAACACTCCTGTATTCCACAGGGGACACTGAAAGAGAGAT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79510887 45 + 83384210 ATTTA--AAACACTCCTGTATTCCACAGGGGACACTGAAAGAGAGAT i panTro2.chr17 C 0 C 0 s bosTau4.chr19 10884661 43 - 65312493 GCCTGCAGGA----CCCTTGAAGCCCTGAGAAGGGGAGGGGATGAGG i bosTau4.chr19 I 7 C 0 s turTru1.scaffold_98008 15370 42 + 223990 ATCTA-AATA----CCCGTGTCTCTTGGCGGAAGTGGGAAGAAAAAC i turTru1.scaffold_98008 C 0 C 0 s tarSyr1.scaffold_41848 14606 17 + 21754 ---------------------------GGGGAAA---AAAGAGAAAT i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 4417 39 + 5481 -------AAACAGCACCATGTCTCGC-GGGGAGATAGGAGGAGAAAT i micMur1.scaffold_38207 I 1 I 4 s equCab2.chr11 58070815 33 - 61308211 --------------CCCGTGTCTCACGGGGGAAGTGGGAAGAGAAAG i equCab2.chr11 I 21 C 0 s canFam2.chr9 59464649 38 - 64418924 -------AAACACCCTTGAGTCCCATGGGGAACATGGG--GGCAGGT i canFam2.chr9 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e tupBel1.scaffold_71658.1-10116 5088 0 - 10116 C e felCat3.scaffold_206428 52046 3265 + 132007 I e pteVam1.scaffold_11245 39645 9 + 48268 I e otoGar1.scaffold_94362.1-287808 51047 21 + 287808 I e monDom5.chr2 304656453 9698 - 541556283 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I e loxAfr3.scaffold_49 14464635 1115 - 17734757 I a score=98294.000000 s hg19.chr17_gl000204_random 78906 43 + 81310 GGG--------------CACTTTTACCAAG-----------------TCCCTG------------------------------AGATACCCAAGTTTGGACCCA s otoGar1.scaffold_94362.1-287808 51068 40 + 287808 GGA--------------CACTTTGACCAAG-----------------GC-TGG------------------------------AGGTAACCAAGCTTGGCCC-- i otoGar1.scaffold_94362.1-287808 I 21 C 0 s micMur1.scaffold_38207 4460 27 + 5481 GGG--------------CGCTTT-------------------------------------------------------------AGGAACCCAGTGTGTCCC-- i micMur1.scaffold_38207 I 4 C 0 s tarSyr1.scaffold_41848 14623 43 + 21754 GGGA-------------CGGTTTTACCAAG-----------------TC-CTG------------------------------AGATACCCATGTTTGGGCCCA i tarSyr1.scaffold_41848 C 0 C 0 s calJac1.Contig5139 80167 43 + 225949 GGG--------------CACTTTTACCAAG-----------------TCTCTA------------------------------AGACGCCCACGTTTAAACCCA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 75997 43 - 95547 GGG--------------CACTTTTACCAAG-----------------TCCCTG------------------------------AGATACCCAAGTTTGGACCCA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75068998 43 + 78773432 GGG--------------CACTTTTACCAAG-----------------TCCCTG------------------------------AGATACCCAAGTTTGGACCCA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16095637 41 + 17838096 GGG--------------CACTTTTACCAAG-----------------TCCCTG------------------------------AGATACCCAAGTTTGGACC-- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 46769 43 - 64270 GGG--------------CACTTTTACCAAG-----------------TCCCTG------------------------------AGATACCCAAGTTTGGACCCA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79510932 43 + 83384210 GGG--------------CACTTTCACCAAG-----------------TCCCTG------------------------------AGATACCCAAGTTTGGACCCA i panTro2.chr17 C 0 C 0 s bosTau4.chr19 10884704 103 - 65312493 AAGAGGTGGGTGAGCCCAACTTATTCCCTGATGGGGAGAAAATAGTTTCCCAATGGGAACCAGTGAGGTGGGGAGTGGGGTGCAGAAACTCCAGGTAAGAGCT- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 15412 42 + 223990 AAA--------------CACTTTTACCACA-----------------TCCCTA------------------------------AGATACACAAGTTTGGACCT- i turTru1.scaffold_98008 C 0 C 0 s equCab2.chr11 58070848 42 - 61308211 GAG--------------GACTCTTACCACG-----------------CCCCCC------------------------------AGACCCACGAGTCTGGACCT- i equCab2.chr11 C 0 C 0 s canFam2.chr9 59464687 41 - 64418924 GAG--------------CACCTTCACCAAG-----------------TCCCCG------------------------------AGATAC-CAAGTCTGGACCT- i canFam2.chr9 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e tupBel1.scaffold_71658.1-10116 5088 0 - 10116 C e felCat3.scaffold_206428 52046 3265 + 132007 I e pteVam1.scaffold_11245 39645 9 + 48268 I e monDom5.chr2 304656453 9698 - 541556283 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I e loxAfr3.scaffold_49 14464635 1115 - 17734757 I a score=60344.000000 s hg19.chr17_gl000204_random 78949 26 + 81310 GTCAGGAATTT---------------CTCAGCCATTTTTCC s panTro2.chr17 79510975 26 + 83384210 GTCAGGAATTT---------------CTCAGCCATTTTTCC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 46812 26 - 64270 GTCAGGAATTT---------------CTCAGCCATTTTTCC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16095678 26 + 17838096 GTCAGGAATTT---------------CTCAGCCATTGTTCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75069041 26 + 78773432 GTCAGGAGTTT---------------CTCAGCCGTTTTTCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 76040 26 - 95547 GTCAGGAGTTT---------------CTCAGCTGTTTTTCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 80210 26 + 225949 GTCAGGATTTG---------------CTCAGCCATCTTTCC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 14666 26 + 21754 GTCAGGAGTTG---------------CTCAGCTATATTTCC i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_38207 4487 26 + 5481 GTCAGGAGTCA---------------CTCAGCCTTATTTCC i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 51108 25 + 287808 GTCAGGAGTCA---------------CTCA-CCTTATTTCC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 5088 17 - 10116 GTCAGGAGCT------------------------TTCATCC i tupBel1.scaffold_71658.1-10116 C 0 C 0 s bosTau4.chr19 10884807 41 - 65312493 TGGGCTAGCCATGGAGATGAGGAATTCCCACCCACTCCTCA i bosTau4.chr19 C 0 I 220 s turTru1.scaffold_98008 15454 24 + 223990 TTCGGGAGCCG---------------CTCAGC--CTCGTCA i turTru1.scaffold_98008 C 0 I 3 s equCab2.chr11 58070890 24 - 61308211 TCTGGCAGCTG---------------CTCAGC--TTCATGA i equCab2.chr11 C 0 I 3 s canFam2.chr9 59464728 24 - 64418924 TTGGGATGCTG---------------CTCAAT--CTCATCA i canFam2.chr9 C 0 I 3 e proCap1.scaffold_52062 2229 13555 + 16741 I e felCat3.scaffold_206428 52046 3265 + 132007 I e pteVam1.scaffold_11245 39645 9 + 48268 I e monDom5.chr2 304656453 9698 - 541556283 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I e loxAfr3.scaffold_49 14464635 1115 - 17734757 I a score=185638.000000 s hg19.chr17_gl000204_random 78975 74 + 81310 TAAAG----TCACTCTGCAGACCATCCACGAAGTTCCTCAAGGAGAGTTTCTCCTAAAGGAGCT-GTC-GGCCCATGTTG s panTro2.chr17 79511001 71 + 83384210 TAACG----TCACTCTGCAGACCATCCATGAAGT---TCAAGGAGAGTTTCTCCTAAAAGAGCT-GTC-GGCCCATGTTG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 46838 74 - 64270 TAACG----TCACTCTGCAGACCATCCACGAAGTTCCTCAAGGAGAGTTTCTCCTAAAGGAGCT-GTC-GGCCCATGTTG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16095704 74 + 17838096 TAACG----TCACTCTGCAGACCATCCACGAAGTTCCTCAAGGAGAGTTTCTCCTAAAGGAGCT-GTC-AGCCCATGTTG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75069067 74 + 78773432 TCACG----TCACTCTGCAGACCATCCATGACGTTCCTCAAGGAGAATTTCTCCTAAAGGAGCT-GTC-GGCCCACGTTG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 76066 74 - 95547 TCACG----TCACTCTGCAGACCATCCATGACGTTCCTCAAGGAGAATTTCTCCTAAAGGAGCT-GTC-AGCCCACGTTG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 80236 74 + 225949 TAATG----TCACTCCGCAGACCCTCCATGACGTCCTTCAAGGAGAATTTCTCCGAAAGGAGCT-GTC-AGCCCATGTTG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 14692 75 + 21754 TAATG----CTGCTTCAGAGACCGTCCACGAAGTTCCTCAAGGAGACTTGCTCCTAAAGGAGCT-GTCTGGTCCATGCTG i tarSyr1.scaffold_41848 C 0 M 1758 s micMur1.scaffold_38207 4513 68 + 5481 TGA-G----CCACCCC-AGGACCGTCCTCAAAGCTCCTCGCGGAGAAATGCTCCC----GAGCT-GCC-CGCCCGTGTCG i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 51133 74 + 287808 TAA-G----CACCCCTGGGGACCATCCTGGAAGTTTCTCCAGGACAATAGCTCTCAAAGGAGCTCACT-GGCCAGTGATA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 5105 68 - 10116 TAATA----CCACCCTG-AGACCA--CTCGAAGTTCCTCCAAGAGAATGT-TCCCGAAGGAGCT-GCC-AGGCTGTCT-- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s turTru1.scaffold_98008 15481 58 + 223990 TCATG----CCACCCAG-GGACCAGCCACAAG-TTCCTCTGAG--AGCTGTTTCTGGAGGAGTC-GC------------- i turTru1.scaffold_98008 I 3 C 0 s canFam2.chr9 59464755 58 - 64418924 CGATG----CCACCCAA-AGACCATCATGAGG--TCCTCTGAGA-AACCATTCCTGCAGGAGCT-CC------------- i canFam2.chr9 I 3 C 0 s equCab2.chr11 58070917 63 - 61308211 TCATGCTGCCCACCCAG-AGACCATCCACAAG--TTCTCTGAGAGAGCTGTCCCCGAAGGAGCC-AC------------- i equCab2.chr11 I 3 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e felCat3.scaffold_206428 52046 3265 + 132007 I e pteVam1.scaffold_11245 39645 9 + 48268 I e monDom5.chr2 304656453 9698 - 541556283 I e bosTau4.chr19 10884848 220 - 65312493 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I e loxAfr3.scaffold_49 14464635 1115 - 17734757 I a score=87590.000000 s hg19.chr17_gl000204_random 79049 84 + 81310 GC--AACGCCCCACAGTGTTCACGG---GGCCATGACT-----CGGCCTCCAGAGTCCGGGGCTCGGTTTCCCCAGATAC-CCTGGAAAAACTGT s calJac1.Contig5139 80310 84 + 225949 GC--CACGCCCCACGGCGCTCACAG---GGTCACGACT-----CAGCTTCCAAATTCCGGGGCTCGGTTTCCTCAGATAC-CCTGGAGAAACTGT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 76140 83 - 95547 GC--AA-GGCCCACAGTGCTCACGG---GGCCACGACT-----CGGCCTCCAGAGTCTGGGGCTCAGTTTCCCCAGATAC-CCTGGAAAAACTGT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75069141 83 + 78773432 GC--AA-GGCCCACAGTGCTCACGG---GGCCACGACT-----CGGCCTCCAGAGTCTGGGGCTCGGTTTCCCCGGATAC-CCTGGAAAAACTGT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16095778 84 + 17838096 AC--AACGCCCCACAGTGTTCACGG---GGCCACTACT-----TGGCCTCCAGAGTCCAGAGGTCAGTTTCCTCAGATAC-CCTGGAAAAACTGT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 46912 84 - 64270 GC--AACGCCCCACAGTGTTCACGG---GGCCACGACT-----CGGCCTCCAGAGTCCGGGGCTCGGTTTCCCCAGATAC-CCTGGAAAAACTGT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79511072 84 + 83384210 GC--AACGCCCCACAGTGTCCACGG---GGCCACGACT-----CGGCCTCCAGAGTCCGGCGCTCAGTTTCCCCAGATAC-CCTGGAAAAACTGT i panTro2.chr17 C 0 C 0 s micMur1.scaffold_38207 4581 53 + 5481 GCAACACCCTATACAGCGCT----------------CA-----TGGCCTCCAGA-----GAT-------------GACAC-CCTGGGAAA--TGC i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 51207 73 + 287808 GC--CACTCCATACTGCACTCATGGGCTGGCCGTGACA-----TGGCCTCCAGAGTCCTGAG-------------GAGATGCCTGGGAAA--CGT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 5173 49 - 10116 GC--GATGCCCTGCAGAGCCTTCAG-------------------GCCCTCCAGGGCCCAGAGCT-----------GAGAC--------------T i tupBel1.scaffold_71658.1-10116 C 0 C 0 s turTru1.scaffold_98008 15539 45 + 223990 -----ACCCCACAAGCTCATCCAGG---TGCCAGGACG-----TGGTCTCCAGACCCT------------------------------------- i turTru1.scaffold_98008 C 0 C 0 s canFam2.chr9 59464813 69 - 64418924 -----ACCCTGCACGTGTGTCTGGT---CACCAGGACAGGACGTGTCCTCCAGAGCCCTGAGCA-----GCAGCTGACAC-CC------------ i canFam2.chr9 C 0 C 0 s equCab2.chr11 58070980 58 - 61308211 -----ACGCTCCTC------CAGGT---CGCCAGGACA-----CGGCCTCCAGAGCCCTGGCCA-----GCGGCAGAGAC-CT------------ i equCab2.chr11 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e tarSyr1.scaffold_41848 14767 1758 + 21754 M e felCat3.scaffold_206428 52046 3265 + 132007 I e pteVam1.scaffold_11245 39645 9 + 48268 I e monDom5.chr2 304656453 9698 - 541556283 I e bosTau4.chr19 10884848 220 - 65312493 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I e loxAfr3.scaffold_49 14464635 1115 - 17734757 I a score=27272.000000 s hg19.chr17_gl000204_random 79133 104 + 81310 GAGTACAGAGC-----CCAGGAGCCACAGCTAAGACTC------AGCCACCTGGGGCTCCTGCATGGGCAAAGTGGCCGCCAGAAGACTCCCT-------------------------------------------------------------------------GGAGAGCTT-----GACTGTGGGGCCC s calJac1.Contig5139 80394 100 + 225949 GAGTACAGAGC-----CCCGGAGCCACAGCTCAGACTC------A----CCTAGGGCTCCTGCACTGGCAAAGTGGCCTCTGGGATCATCCCT-------------------------------------------------------------------------GGGGAGCTT-----GCCCGTGGGGCCC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 76223 104 - 95547 GAGTATAGAAC-----CCAGGAGCCACAGCTAAGACTC------AACCGCCTGGGGCTCCTGCATGGGCAAAGTGGCTGTCAGAAGACCCCCT-------------------------------------------------------------------------GGAGAGCTT-----GCCTGTGGGGCCC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75069224 104 + 78773432 GAGTATAGAAC-----CCACGAGCCACAGCTAAGACTC------AGCCGCCTGGGCCTCCTGCATGGGCAAAGTGGCTGTCAGAAGATCCCCT-------------------------------------------------------------------------GGAGAGCTT-----GCCTGTGGGGCCC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16095862 104 + 17838096 GAGTACAGAGC-----CCAGGAGCCACGGCTAAGACTC------AGCCGCCTGGGGCTCCTGCACGGGCAAAGTGGCCGCCAGAAGACTCCCT-------------------------------------------------------------------------GGAGAGCTT-----GTCTGTGGGGCCC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 46996 104 - 64270 GAGTACAGAGC-----CCAGGAGCCACAGCTAAGACTC------AGCCACCTGGGGCTCCTGCATGGGCAAAGTGGCCACCAGAAGACTCCCT-------------------------------------------------------------------------GGAGAGCTT-----GCCTGTGGGGCCC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79511156 104 + 83384210 GAGTACAGAGC-----CCAGGAGCCACAGCTAAGACTC------AGCCACCTGGGGCTCCTACATGGGCAAAGTGGCCGCCAGAAGACTCCCT-------------------------------------------------------------------------GGAGAGCTT-----GACTGTGGGGCCC i panTro2.chr17 C 0 C 0 s micMur1.scaffold_38207 4634 45 + 5481 --------------------GAGCCGTGGCCGGGACCC--------------------------------------------------TGCCC-------------------------------------------------------------------------GGAGAGCTC-----GCCAGCCGGGTCC i micMur1.scaffold_38207 C 0 C 0 s otoGar1.scaffold_94362.1-287808 51280 60 + 287808 GAGCTCAGCAC-----CCAGGAGCCATGGCCAAGACCC--------------------------------------------------TCCTC-------------------------------------------------------------------------AGAGAGCTC-----ATAGGTAGGGTCT i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 5222 84 - 10116 GGGCACTGAGCGGGAACCTGGTGCAGTGGCTGGGAGGT------GGT--GCTGGGGCTCCT---------------CTGCTGGGGGGCTGCCC-------------------------------------------------------------------------AGAGACCTG-----GCCGG-------- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s turTru1.scaffold_98008 15584 65 + 223990 -------GAGC----------AGCAGCTGA---GACCT------GGCCACTG------------------------------GGGGCCCCACC--------------------------------------------------------------TT---------GGAG-GCTGGCAGGGGCTGTGGGGGCC i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10885068 81 - 65312493 GAGGACAGAGC-----CCA-TGGCTGCTGC----ACAT------GGGGGCTT------------------------------AGAGCCTCCCA--------------------------------------------------------GTTGAGTG---------GGAG-GCTGCCCCCATCTGTGTCCCCC i bosTau4.chr19 I 220 C 0 s canFam2.chr9 59464882 155 - 64418924 ---------------------AGCCCCCAG----GCCTCTCCTCGGAGGCTTG------CTGGAAGGGCCCCAGGCTGAGAGTCAGCCTCCCTCATCGTGAGCAGACGAGCCTGGGGTCACAGCATTCAGGGAGCGCCATGGCACTCCAGGTGCGTCACAAATACGGGAG-CAAG-----AGCAGAGGGAAC- i canFam2.chr9 C 0 I 19 s equCab2.chr11 58071038 41 - 61308211 ----------------------GCCACCA---------------GGAGGCCT-----------------------------------TTCCCT-------------------------------------------------------------------------GGAG-GCCG-----ACCAATGGGCCC- i equCab2.chr11 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e tarSyr1.scaffold_41848 14767 1758 + 21754 M e felCat3.scaffold_206428 52046 3265 + 132007 I e pteVam1.scaffold_11245 39645 9 + 48268 I e monDom5.chr2 304656453 9698 - 541556283 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I e loxAfr3.scaffold_49 14464635 1115 - 17734757 I a score=-15261.000000 s hg19.chr17_gl000204_random 79237 42 + 81310 CAGGCC-A-GAG----CCACTGTCAGTGC-----------------C--AGC----GGGCAAGGCCACCAC s calJac1.Contig5139 80494 42 + 225949 CAGACT-G-GAG----CCACTGTCAGCGC-----------------C--AGC----AAGCAGAGCCACCAC i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 76327 42 - 95547 CAGGCC-A-GAG----CCACTGTCAGTGC-----------------C--AGC----AGGCAGGGCCACCGC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75069328 42 + 78773432 CAGGCC-A-GAG----CCACTGTCAGTGC-----------------C--AGC----GGGCAGGGCCACCAC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16095966 42 + 17838096 CAGGCC-A-GAG----CCACTGTCAGTGC-----------------C--AGC----AGGCAGGGCCACCAC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 47100 42 - 64270 CAGGCC-A-GAG----CCACTGTCAGTGC-----------------C--AGC----GGGCANGGCCACCAC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79511260 42 + 83384210 CAGGCC-A-GAG----CCACTGTCAGTGC-----------------C--AGC----GGGCAAGGCCACCAC i panTro2.chr17 C 0 C 0 s micMur1.scaffold_38207 4679 39 + 5481 CAAGCC-AGGAG----TCGCCGTCGGTGC-----------------C--C-C----AAACTAGGCCAC--- i micMur1.scaffold_38207 C 0 N 0 s otoGar1.scaffold_94362.1-287808 51340 43 + 287808 CCAAAT-AGGTG----TTACCTGCAGCAC-----------------C--TGC----AGGCCGGGCCCTCAC i otoGar1.scaffold_94362.1-287808 C 0 I 698 s tupBel1.scaffold_71658.1-10116 5306 10 - 10116 ---------GAG----CCCCTGC------------------------------------------------ i tupBel1.scaffold_71658.1-10116 C 0 C 0 s turTru1.scaffold_98008 15649 41 + 223990 CAGGCTGG-GAG----TCACCCTCAGTTA-----------------C--TGCCAAGCAGACAAGC------ i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10885149 44 - 65312493 AGGACACA-GAGCACATCTTCCCCCATCT-----------------C--TGCT---CAGGGAAGCCA---- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58071079 31 - 61308211 CAGGCT---GTG----TCACCCTCAGCCA-----------------C--CGCC---AAG-------C---- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 55311 52 + 132007 CAGATC-A-GGG----CCACTGAGTGTCA--GTGACTGCAGCCTCTC--GGCC---AAG--CGGCCC---- i felCat3.scaffold_206428 I 3265 C 0 s canFam2.chr9 59465056 58 - 64418924 TGGGCT-G-GGG----CCACCACCAGCCAGGGGGACTGGGCTCTGCCAAGGCT---AAGGCCAGCCA---- i canFam2.chr9 I 19 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e tarSyr1.scaffold_41848 14767 1758 + 21754 M e pteVam1.scaffold_11245 39645 9 + 48268 I e monDom5.chr2 304656453 9698 - 541556283 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I e loxAfr3.scaffold_49 14464635 1115 - 17734757 I a score=-7694.000000 s hg19.chr17_gl000204_random 79279 151 + 81310 CAACCGGAGAAGCT-------------------------CTGG-------------------------------GCT------CAGGTCATTCCGGGT---G----------------C------ACCCCCTCCCCGG-----GGCGGCAGCTGCAGGGAGAACACAGAACGCG----TGT-CCACCGTAGGGA--------------GGT--GGGCT---------------------------------------------------------------GGGTGGGCA-GGCCCCAGTGTG----------------------AGCCCTGC--------------AGGGCCCTGGTCTC----------------ATG s panTro2.chr17 79511302 151 + 83384210 CAACCAGAGAAGCT-------------------------CTGG-------------------------------GCT------CAGGTCATTCCGGGT---G----------------C------ACCCCCTCCCCGG-----GGCGGCAGCCGCAGGGAGAACACAGAACGCG----TGT-CCACCGTAGGGA--------------GGT--GGGCT---------------------------------------------------------------GGGCGGGCA-GGCCCCAGTGTG----------------------AGCCCTGC--------------AGGGCCCTGGTCTC----------------ACG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 47142 151 - 64270 CAACCGGAGAAGCT-------------------------CTGG-------------------------------GCT------CAGGTCATTCCGGGT---G----------------C------ACCCCCTCCCCGG-----GGCGGCAGCCGCAGGGAGAACACAGAACGCG----TGT-CCACCGTAGGGA--------------GGT--GGGCT---------------------------------------------------------------GGGCGGGCA-GGCCCCAGTGTG----------------------AGCCCTGC--------------AGGGCCCTGGTCTC----------------ACG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16096008 152 + 17838096 CAACCAGAGAAGCT-------------------------CTGG-------------------------------GCT------CAGGTCATTCTGGGT---G----------------C------ACCCCCTCCCCGG-----GGCGGCAGCTGCAGAGAGAACACAGAACGCG----TGT-CCACTGTAGGAA--------------GGT-GGGGCT---------------------------------------------------------------GGGCGGGCA-GGCCCCACTGTG----------------------AGCCCTGC--------------AGGGCCCTGGTCTC----------------ACG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75069370 152 + 78773432 CAACCGGAGAAGCT-------------------------CTGG-------------------------------GCT------CAGGTCATGCTGGGT---A----------------C------ATCCCCTCCCCAG-----GGCGGCAGCTGCGGAGAGAACACAGAATGCA----TGT-CCACCGCAGGGA--------------GGT-GGGGCT---------------------------------------------------------------GGAGGGGCA-GGCCCCAGTGTG----------------------AGCCCTGC--------------AGGGCCCTGGTCTC----------------ACG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 76369 152 - 95547 CAACCGGATAAGCT-------------------------CTGG-------------------------------GCT------CAGGTCATGCTGGGT---A----------------C------ATCCGCTCCCCAG-----GGCGGCAGCTGCGGAGAGAACACAGAATGCG----TGT-CCACCGCAGGGA--------------GGT-GGGGCT---------------------------------------------------------------GGGGGGACA-GGCCCCATTGTG----------------------AGCCCTGC--------------AGGGCCCTGGTCTC----------------ACG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 80536 161 + 225949 CAACTGGGGCAGGT-------------------------CTGG-------------------------------GCT------CAGATCACTCTAAGT---G----------------T------ACCCCCTCCCCAGGAGGCGGGGACAGCTGCAGAGAGAACACAGAATGTGTGTCTGT-CCACTGTAGGGA--------------GGT-GGGGCT---------------------------------------------------------------GGGCGGGCC-AGTCCCAGCGTG----------------------AGCCCTGC--------------AGGGCCCTGGTCTC----------------ATG i calJac1.Contig5139 C 0 C 0 s tupBel1.scaffold_71658.1-10116 5316 238 - 10116 TACACAGAGAGGCT-------------------------CTGG---------------------------------T------CACATCATGCTGGGG---A----------------T------CACCCC------G-----GGGAACAGCTGCAAATA--------AGCAGG----TGT-CCACTGTGAGGAAAGCGAGGCCCAAGGCT-GGGGCTCAGCAGACCAGATGACACCCAGAGCCCTGGAGTCCCTTGGGAAAGGGAGACGGGAGGGGCGAGGGCTGGGCA-GTCCCCAGCAGGGGGGACAGGCAGAGGCTGCAGCAGCACTGCC-----------TTGGGTACCTGGCCCT----------------ACA i tupBel1.scaffold_71658.1-10116 C 0 C 0 s turTru1.scaffold_98008 15690 98 + 223990 ---------------------------------------TCAG-------------------------------GGT------CACATCACTCTGGCT---G----------------T------GCTGCACCCACGG-----GGGCAAT---------------------TGC----TAG------GCCAG--------------------GGGACA---------------------------------------------------------------AGCTCAGCC-AACCCCAAGGCA----------------------AGCCCTGC--------------AGGCTCCT------------------------- i turTru1.scaffold_98008 C 0 I 996 s bosTau4.chr19 10885193 156 - 65312493 -------------CAGTGAAGGATACGGATCTTCTCGAATCAG-------------------------------TGTGGCCCATCCAACACCATGGCC---GCCCTGAGAGGGGGGCAC------ACTGCACCTGTGG-----AGTGAAG---------------------GGA----CAT------GCAGGCC--------------ATGTGGATCA---------------------------------------------------------------AGGCAGGCA-GAGACCACAGCA----------------------GCTCCAGCCC----------AAGGGTGCCT------------------------- i bosTau4.chr19 C 0 I 8 s equCab2.chr11 58071110 133 - 61308211 -------------T-------------------------CTGG-------------------------------GGT------CACGTCACTCTGG-----G----------------T------GCACTGCCTATGG-----CAGAGAG---------------------AAT----TGTGTCACTGTGAGGA--------------GGGTGGGCTG---------------------------------------------------------------GGGCGGCCACCAGGCCAGGGTACCA-------------------GGTTCAGCCAACCCCAAGGCCAGCATGCAGGGCCCT------------------- i equCab2.chr11 C 0 I 661 s felCat3.scaffold_206428 55363 123 + 132007 -------------C-------------------------CCGG--------------------------CACACAGA------CAGCATCCGCCGGCCCTGG----------------T------AAGCCACCTCGAA-----GGAAGCA---------------------GAC----TGT------GTGGACT--------------GGG------G---------------------------------------------------------------GGATAGGCA-GAGGCCACAGCA----------------------GCTCCCGCCC----------CGGGGTGCCCAGTCTT-------AGACAC------ i felCat3.scaffold_206428 C 0 I 53 s canFam2.chr9 59465114 198 - 64418924 -------------C-------------------------CCAGGAAACTCCACGCTTCTCTCTCCCTCACGCACGTA------CACCCCTCTCTGGTCCTCG----------------TCACCACGACCTAACTCTCC-----CGGGGCA--------------------CGAG----TGT--CGTCGTGCGCT--------------GGTGCAGGCG---------------------------------------------------------------GCAAGGACA-GAGCCCATGGCACAGAGTATCCGC----------GCTGCAGCCCCTCCACCCAGCGGCCTCCCCAGCCCCTGCAGGAAGCCTCAGT--- i canFam2.chr9 C 0 I 81 e proCap1.scaffold_52062 2229 13555 + 16741 I e tarSyr1.scaffold_41848 14767 1758 + 21754 M e pteVam1.scaffold_11245 39645 9 + 48268 I e otoGar1.scaffold_94362.1-287808 51383 698 + 287808 I e monDom5.chr2 304656453 9698 - 541556283 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I e loxAfr3.scaffold_49 14464635 1115 - 17734757 I a score=40182.000000 s hg19.chr17_gl000204_random 79430 27 + 81310 GATGCACAGGTGAGCCA-CCTCCTC-------------------------ACT s equCab2.chr11 58071904 26 - 61308211 GGTGCTCAGGGGAGGCACCTGGTCC-------------------------A-- i equCab2.chr11 I 661 C 0 s felCat3.scaffold_206428 55539 25 + 132007 GGAGCACAAAGGAGGCA-CCAGATC-------------------------A-- i felCat3.scaffold_206428 I 53 C 0 s canFam2.chr9 59465393 26 - 64418924 GAGACGCACAGAGGGC--TCAGCCA-------------------------AGA i canFam2.chr9 I 81 C 0 s bosTau4.chr19 10885357 21 - 65312493 -ATGCCCAGTGA------GCAGCCC-------------------------ATG i bosTau4.chr19 I 8 C 0 s tupBel1.scaffold_71658.1-10116 5554 52 - 10116 TAGGCACAGGCAAGCCA-TCACCACGACCTGAAGGCCACCAGCAGAGAGGACT i tupBel1.scaffold_71658.1-10116 C 0 C 0 s calJac1.Contig5139 80697 27 + 225949 GATGCACAGGTGAGCCA-CCTCCTC-------------------------ACT i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 76521 27 - 95547 GATGCACAGGTGAGCCA-CCTCCTC-------------------------ACT i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75069522 27 + 78773432 GATGCACAGGTGAGCCA-CCTCCTC-------------------------ACT i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16096160 27 + 17838096 GATGCACAGGTGAGCCA-CTTCCTC-------------------------ACT i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 47293 27 - 64270 GATGCACAGGTGAGCCA-CCTCCTC-------------------------ACT i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79511453 27 + 83384210 GATGCACAGGTGAGCCA-CCTCCTC-------------------------ACT i panTro2.chr17 C 0 C 0 e proCap1.scaffold_52062 2229 13555 + 16741 I e tarSyr1.scaffold_41848 14767 1758 + 21754 M e turTru1.scaffold_98008 15788 996 + 223990 I e pteVam1.scaffold_11245 39645 9 + 48268 I e otoGar1.scaffold_94362.1-287808 51383 698 + 287808 I e monDom5.chr2 304656453 9698 - 541556283 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I e loxAfr3.scaffold_49 14464635 1115 - 17734757 I a score=56499.000000 s hg19.chr17_gl000204_random 79457 62 + 81310 GC--------------------CTGATCA--------------------------AACCCCAGATG-GGCAG----ATGCCTCCGCAGGCCCCCAGT--------GGG---A--CTTGGT-----GCCAGC s panTro2.chr17 79511480 62 + 83384210 GC--------------------CTGATCA--------------------------AACCCCAGATG-GGCAG----ATGCCTCCGCAGGCCCCCAGT--------GGG---A--CTTGGT-----GCCAGC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 47320 62 - 64270 GC--------------------CTGATCA--------------------------AACCCCAGATG-GGCAG----ATGCCTCCGCAGGCCCCCAGT--------GGG---A--CTTGGT-----GCCAGC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16096187 62 + 17838096 GC--------------------CTGATCA--------------------------AACCCCAGATG-GGCAG----ATGCCACACCAGGCCCCCAGT--------GGG---A--CTTGGT-----GCCAGC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75069549 62 + 78773432 GC--------------------CTGATCA--------------------------AATCCCAGATG-GGCAG----ATGCCACGGCAGGTCCCCAGC--------AGC---A--CTTGGT-----GCCAGC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 76548 62 - 95547 GC--------------------CTGATCA--------------------------AATCCCAGATG-GGCAG----ATGCCACCGCAGGTCCCCAGC--------AGC---A--CTTGGT-----GCCAGC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 80724 61 + 225949 GC--------------------CTGACCA--------------------------AACCCCAGATG-GGCAG----ATGCCATGGCAGG-CCCCAGC--------AAG---A--CTTGGT-----GCCAAC i calJac1.Contig5139 C 0 C 0 s tupBel1.scaffold_71658.1-10116 5606 78 - 10116 GCCACAACACAGGTGCTCGGAGCTGGCCA--------------------------CGTCCCCGTCC-TGCAG----ACGCCACCCCAG----CCAGC--------AGGGCCA--CTTGGT-----GCC--- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s bosTau4.chr19 10885378 107 - 65312493 GCTG------------------CGTGGCACCAGAGCCACCAGCCAAGAAGTTTGGAGGCCAAAACC-CGCAACATGGAGCTCAGAGGAGGCACCTGGTCAAATTCCAG---A--CCAGGCAAATGCTAGCA i bosTau4.chr19 C 0 C 0 s canFam2.chr9 59465419 83 - 64418924 GGCG------------------CGGAGCA-CAGAAGGACGTGCCGGGA-----GGAATCCAGGCCC-GAAGA----GTGCTACCACCAGCC-TCAGG--------GAG---A--CCTGGC-----CTCCCT i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 55564 55 + 132007 -------------------------------------------------------AATGCAGGCCC-AGCAA----GTACTACAACCAGCCTTCAGG--------GAG---AGCCCTGGC-----CTCAAT i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58071930 53 - 61308211 -------------------------------------------------------AGTCCAGACCT-GGCAG----ACACTGCGACCAGCCTTCAGC--------CTG---A--CTGGGC-----GTCGCT i equCab2.chr11 C 0 C 0 s proCap1.scaffold_52062 15784 63 + 16741 GC--------------------CTGATTA--------------------------AACCCCAGACCCCGTCC----GCGCCGCAGCCAGCCTGCAGC--------GGA---A--CTCGGT-----GTCAGG i proCap1.scaffold_52062 I 13555 C 0 s loxAfr3.scaffold_49 14465750 57 - 17734757 -C--------------------CTGACTA--------------------------AACCCCAGACCTTGTAA----ATGCAATAGCCAGCCTTCAGC--------GGG---A--TTC-GT-----GT---- i loxAfr3.scaffold_49 I 1115 C 0 e tarSyr1.scaffold_41848 14767 1758 + 21754 M e turTru1.scaffold_98008 15788 996 + 223990 I e pteVam1.scaffold_11245 39645 9 + 48268 I e otoGar1.scaffold_94362.1-287808 51383 698 + 287808 I e monDom5.chr2 304656453 9698 - 541556283 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I a score=48775.000000 s hg19.chr17_gl000204_random 79519 30 + 81310 CAGACTCCAG---CGGCTG---------TTTTTTTTTTTAA----C s calJac1.Contig5139 80785 26 + 225949 CAGACTCCGG---CAGCTG-------------TTTTTCTAA----C i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 76610 27 - 95547 CAGACTCCAG---CGGCTG------------TTTTTTCTAA----C i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75069611 27 + 78773432 CAGACTCCAG---CGGCTG------------TTTTTTCTAA----C i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16096249 29 + 17838096 CAGACTCCAG---CAGCTG----------TTTTTTTTTAAA----C i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 47382 30 - 64270 CAGACTCCAG---CGGCTG---------TTTTTTTTTTTAA----C i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79511542 30 + 83384210 CAGACTCCAG---CGGCTG---------GTTTTTTTTTTAA----C i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 52081 37 + 287808 CAGACTCCAGACCCAGCTG---------TCACTATCTGTCACGTGC i otoGar1.scaffold_94362.1-287808 I 698 C 0 s tupBel1.scaffold_71658.1-10116 5684 25 - 10116 CAGCCCACAC---GGGCTA-------------ATTTTCTAA----- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s bosTau4.chr19 10885485 27 - 65312493 CCCGCCTTCA---GAGTGA------------TTGTTTTTAA----A i bosTau4.chr19 C 0 I 2 s canFam2.chr9 59465502 27 - 64418924 CATACCTCAG---CAGAGA------------CTTTGGTTTT----T i canFam2.chr9 C 0 I 1 s felCat3.scaffold_206428 55619 27 + 132007 GAAACTTCGG---CAGTGA------------tgtgtgtgtg----t i felCat3.scaffold_206428 C 0 I 7 s equCab2.chr11 58071983 27 - 61308211 CAGGTTTCAG---CAGCGA------------TTTTTTTTTT----T i equCab2.chr11 C 0 I 7 s proCap1.scaffold_52062 15847 39 + 16741 CAGAGTTCAG---CGGCTGTTGTGTTGTGTTTTTTTTTTAA----C i proCap1.scaffold_52062 C 0 C 0 s loxAfr3.scaffold_49 14465807 39 - 17734757 CAGAGTTCAG---TGGCTGGTTTTTGGTTTTTTTTTTTTAA----C i loxAfr3.scaffold_49 C 0 C 0 e tarSyr1.scaffold_41848 14767 1758 + 21754 M e turTru1.scaffold_98008 15788 996 + 223990 I e pteVam1.scaffold_11245 39645 9 + 48268 I e monDom5.chr2 304656453 9698 - 541556283 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I a score=133081.000000 s hg19.chr17_gl000204_random 79549 26 + 81310 T----------------------GTAACGGATTCTGTGTGCTCCACAC s loxAfr3.scaffold_49 14465846 26 - 17734757 T----------------------GTAAGTGAATCTGTACGCCTCACTC i loxAfr3.scaffold_49 C 0 C 0 s proCap1.scaffold_52062 15886 26 + 16741 T----------------------GTAAGTGAATCTGCACGCCTCACAC i proCap1.scaffold_52062 C 0 C 0 s equCab2.chr11 58072017 26 - 61308211 T----------------------GTAAGTGATTCTGTCTGCTTCACAC i equCab2.chr11 I 7 C 0 s felCat3.scaffold_206428 55653 46 + 132007 tgtgtgtgtACATACACATATATGTAAGTGA--CTGTCTGCCTCACAC i felCat3.scaffold_206428 I 7 C 0 s canFam2.chr9 59465530 23 - 64418924 -----------------------GTAAGTGA--TTGTCTGCTTCATGC i canFam2.chr9 I 1 C 0 s turTru1.scaffold_98008 16784 26 + 223990 T----------------------ATAAGTGATTCTGTCTGCTTCACAC i turTru1.scaffold_98008 I 996 C 0 s bosTau4.chr19 10885514 26 - 65312493 T----------------------GTCGGTGATTCTATCTGCTTCACAT i bosTau4.chr19 I 2 C 0 s tupBel1.scaffold_71658.1-10116 5709 24 - 10116 G----------------------GTAAGTGACTCCG--TGCTCCACGC i tupBel1.scaffold_71658.1-10116 C 0 C 0 s otoGar1.scaffold_94362.1-287808 52118 24 + 287808 T----------------------GTAACTGACTCTGCCTCTTC--CCG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s panTro2.chr17 79511572 26 + 83384210 T----------------------GTAATGGATTCTGTGTGCTCCACAC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 47412 26 - 64270 T----------------------GTAATGGATTCTGTGTGCTCCACAC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16096278 26 + 17838096 T----------------------GTAATGGATTCTGTGTGCTCCACAC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75069638 26 + 78773432 C----------------------GTAATGGATTCTGTGTGCTCCACAC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 76637 26 - 95547 C----------------------GTAATGGATTCTGTGTGCTCCACAC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 80811 26 + 225949 T----------------------GTAAGGGATTCTGTGTGCTCCACAC i calJac1.Contig5139 C 0 C 0 e tarSyr1.scaffold_41848 14767 1758 + 21754 M e pteVam1.scaffold_11245 39645 9 + 48268 I e monDom5.chr2 304656453 9698 - 541556283 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I a score=179014.000000 s hg19.chr17_gl000204_random 79575 29 + 81310 CCTGAGGGCCTGGAGACTGGACA--TGCTTT s calJac1.Contig5139 80837 29 + 225949 CCTGGGGGCCTGGAGATCCGACA--TGCCTG i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 76663 29 - 95547 CCTGAGGGCCTGGAGACTGGACA--TGCTTC i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75069664 29 + 78773432 CCTGAGGGCCTGGAGACTGGACA--TGCTTC i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16096304 29 + 17838096 CCTGTGGGCCTGGAGACTGGACA--TGCTTC i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 47438 29 - 64270 CCTGATGGCCTGGAGATTGGACA--TGCTTC i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79511598 29 + 83384210 CCTGAGGGCCTGGAGACTGGACA--TGCTTC i panTro2.chr17 C 0 C 0 s otoGar1.scaffold_94362.1-287808 52142 28 + 287808 CCTGAGGGCC-GGAGATTGGCCA--TGCTTC i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 5733 27 - 10116 CCCAGGGG-CTGGAGGTTGGGCT--TGCTT- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s bosTau4.chr19 10885540 28 - 65312493 GTCAGGGG-CTAGAGTTTGGACA--TGCttt i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 16810 28 + 223990 TTCAAGGA-CTGGAGATTGGACA--TGCTTT i turTru1.scaffold_98008 C 0 C 0 s canFam2.chr9 59465553 28 - 64418924 TCCAGGGG-CTGGAGATTGGCCA--TGCGTT i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 55699 30 + 132007 TCCAGGGG-CTGGAGACCAGGCACGTGCTTT i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58072043 27 - 61308211 TCTGGGGG-CTGGA-ATTGGACA--TGCTTT i equCab2.chr11 C 0 C 0 s proCap1.scaffold_52062 15912 29 + 16741 CCCGGGGACCTGGAGATTGGGCA--TGCTTT i proCap1.scaffold_52062 C 0 C 0 s loxAfr3.scaffold_49 14465872 29 - 17734757 CCTGGGGACCTGGAGATTGGGCA--TGCTTT i loxAfr3.scaffold_49 C 0 C 0 s monDom5.chr2 304666151 29 - 541556283 CCTAGGAATATGGATAATGGGTT--TATTTA i monDom5.chr2 I 9698 C 0 e tarSyr1.scaffold_41848 14767 1758 + 21754 M e pteVam1.scaffold_11245 39645 9 + 48268 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I a score=254489.000000 s hg19.chr17_gl000204_random 79604 37 + 81310 GTAACTGAAATTAGAAGTCAATAAACCGAGGGCCAGG------ s tupBel1.scaffold_71658.1-10116 5760 36 - 10116 -CAACAGTAATTAAAAGTCAATAAACGGAGCACCATG------ i tupBel1.scaffold_71658.1-10116 C 0 C 0 s otoGar1.scaffold_94362.1-287808 52170 37 + 287808 ATAAGCGTGATTAAAAGTCAACAGACCAAACGCCAGG------ i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_81340 1551 35 + 2222 ------GTGTTTGAAAA-CACTAGTCTAAA-ACTAGGAAAATA i micMur1.scaffold_81340 N 0 C 0 s panTro2.chr17 79511627 37 + 83384210 GTAACTGAAATTAGAAGTCAATAAACCGAGGGCCAGG------ i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 47467 37 - 64270 GTAACTGAAATTAGAAGTCAGTAAACCGAGGGCCAGG------ i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16096333 37 + 17838096 GTAACTGAAATTAGAAGTCAATAAACGGAGAGCCAGG------ i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75069693 37 + 78773432 GTAACTGAAATTAGAAGTCAATAAACCGAGGGCCAGG------ i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 76692 37 - 95547 GTAACTGAAATTAGAAGTCAATAAACCGAGGGCCAGG------ i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 80866 37 + 225949 GTAACTGAAATTAGAAGTCAATAAACTGAAGGCCAGG------ i calJac1.Contig5139 C 0 C 0 s bosTau4.chr19 10885568 32 - 65312493 ataattataattaa-----aataaaCCAAGTGCCAGG------ i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 16838 32 + 223990 ATAATTGTAATTAA-----AATAAACCAAGCGCCAGG------ i turTru1.scaffold_98008 C 0 C 0 s canFam2.chr9 59465581 37 - 64418924 ATAACTGTGATTAGAAGCCAATAAACCCAACGCCAGG------ i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 55729 37 + 132007 ATAACTCTAATTAAAAGTCAATAAACCGAATGCCAGG------ i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58072070 37 - 61308211 ATAACTGGAATTAAAAGTCAATAAACTGAACACCTGG------ i equCab2.chr11 C 0 C 0 s proCap1.scaffold_52062 15941 37 + 16741 ATAACTGTAATTAAAAGTCAACACACCAAACGCCAGG------ i proCap1.scaffold_52062 C 0 C 0 s loxAfr3.scaffold_49 14465901 37 - 17734757 ATAACTGTAATTAAAAGTCAATACTCCAAACTCCAGG------ i loxAfr3.scaffold_49 C 0 C 0 s monDom5.chr2 304666180 26 - 541556283 ATCACTGTAATTTTAGGTCAATAAAC----------------- i monDom5.chr2 C 0 I 2354 e tarSyr1.scaffold_41848 14767 1758 + 21754 M e pteVam1.scaffold_11245 39645 9 + 48268 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I a score=187515.000000 s hg19.chr17_gl000204_random 79641 47 + 81310 TGGGT-CAG-----TAGAAT-TTCCATCGTGAGGCATCGGA----GGCTGCTCTCGGC s tupBel1.scaffold_71658.1-10116 5796 34 - 10116 T---T-CCG-----TGGGGA-----------AGGCGTCGGA----AGCAGCTCTCAGG i tupBel1.scaffold_71658.1-10116 C 0 C 0 s otoGar1.scaffold_94362.1-287808 52207 47 + 287808 TGGGT-TAG-----TAGAATTTTCCACCGTGAGGCATCAGA----AGCTG-CTCTGGG i otoGar1.scaffold_94362.1-287808 C 0 C 0 s micMur1.scaffold_81340 1586 53 + 2222 TATGT-CAGTCCCCTAGAGTCCCCTACAATGAGACATCAGC----AGCTGTCCCAGGG i micMur1.scaffold_81340 C 0 C 0 s panTro2.chr17 79511664 47 + 83384210 TGGGT-CAG-----TAGAAT-TTCCATCGTGAGGCATCGGA----GGCTGCTCTCGGC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 47504 47 - 64270 TGGGT-CAG-----TAGAAT-TTGCATCGTGAGGCATCGGA----GGCTGCTCTCGGC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16096370 47 + 17838096 TGGGT-CAG-----GAGAAT-TTCCATCGTGAGGCATCGGA----GGCTGCTCTCGGT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75069730 48 + 78773432 TGGGT-CAA-----TAGAATCTTCTATCATGAGGCATCGGA----GGCTGCTCTAGGC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 76729 48 - 95547 TGGGT-CAA-----TAGAATCTTCTATCATGAGGCATCGGA----GGCTGCTCTAGGC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 80903 48 + 225949 GAGGT-CAG-----TAGAATATTCCACCATGAGGCCTCAGA----GGCTGCTCTCGGC i calJac1.Contig5139 C 0 C 0 s bosTau4.chr19 10885600 25 - 65312493 AGGGT-CAG-----TAGGATTTTACATCGTG--------------------------- i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 16870 25 + 223990 AGGGT-CAG-----TAGGATTTTACATTGAG--------------------------- i turTru1.scaffold_98008 C 0 C 0 s canFam2.chr9 59465618 47 - 64418924 TGGGT-CAG-----TCGGATTTTCCATTGTGAACCATCAGA----AGT-GCTCTCGGG i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 55766 46 + 132007 TGAGTCCAA-----TTGAGGTTTCCATTCTG---CATCAGA----ATCAGCTCTCGGG i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58072107 48 - 61308211 TGGGT-CAG-----TAGAGTTTCCTGTCAGGAGGCGTCAGA----AGCCGCTCTCGGG i equCab2.chr11 C 0 C 0 s proCap1.scaffold_52062 15978 48 + 16741 TAGGT-CAG-----TGAAATTTTCCATCCTGAAGCTTCAGA----AGCTCTTCTTGGG i proCap1.scaffold_52062 C 0 C 0 s loxAfr3.scaffold_49 14465938 48 - 17734757 TAGGT-CAG-----TGAAATTTTCCATCCTGAAGCTTCAGA----AGCTGTTCTCGGG i loxAfr3.scaffold_49 C 0 C 0 s monDom5.chr2 304668560 52 - 541556283 TGGGT-CAG-----TAACAAATTCCATCATTAAATATTAAATTTGACTTGTTTTCCCC i monDom5.chr2 I 2354 C 0 e tarSyr1.scaffold_41848 14767 1758 + 21754 M e pteVam1.scaffold_11245 39645 9 + 48268 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I e mm9.chr11 118786805 1556 + 121843856 I a score=1172611.000000 s hg19.chr17_gl000204_random 79688 230 + 81310 --ACATCAGCCCTGGCTCCTTCTCTCATCCT-----T-CCAACCCTTCACCCCA-GTGAGTGGGAGTTT-CTAAG-AGCCCCG----TGTCCTGATGTGCCACCCTTGGAAGAAC-AAAACCCTGAGAC-AAACTCGTATTTTGCTTTTTTT-AATTGTCTCTCCCACTTTGCTTCCTGTTCAAACAGATTATCATGCACATCTGTAATCC-CCACTTAAGCACCTAAGACCCCC---TCTAAAATAACCCA s calJac1.Contig5139 80951 228 + 225949 --GTG-CGATCCTGGCTCCTTCTCT-GTCCT-----T-CCAACCCTGCACCCCG-ATGAGCGGGAGTTT-CCAAG-AGCCCCG----TGTCCTGATGTGCCACCCTTGGAAGAAC-AAAACCCTGAGAC-AAGCTCGTATTTTGCTTTTTAT-AATTGTCTCTCCCACTTTGCTTCCTGTTCAAACAGATTATCATACACATCTGTAATCC-CCACTTAAGCACCTAAGACCCCC---TCTAAAATAACCTA i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 76777 230 - 95547 --GCATCAGCCCTGGCTCCTTCTCTCATCCT-----T-CCAACCCTTCACCCCA-GTGAGCGGGAGTTT-CCAAG-AGCCCTG----TGTTCTGATATGCCACCCTTGGAAGAAC-AAAACCCTGAGAC-AAACTCGTATTTTGCTTTTTTT-AATTGTCTCTCCCGCTTTGCTTCCTGTTCAAACAGATTATCATGCACGTCTGTAATCC-CCACTTAAGCACCTAAGACCCCC---TCTAAAATAACCCA i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75069778 230 + 78773432 --GCATCAGCCCTGGCTCCTTCTCTCATCCT-----T-CCAACCCTTCACCCCA-GTGAGCGGGAGTTT-CCAAG-AGCCCCG----TGTTCTGATATGCCACCCTTGGAAGAAC-AAAACCCTGAGAC-AAACTCGTATTTTGCTTTTTTT-AATTGTCTCTCCCACTTTGCTTCCTGTTCAAACAGATTATCATGCACGTCTGTAATCC-CCACTTAAGCACCTAAGACCCCC---TCTAAAATAACCCA i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16096417 230 + 17838096 --GCATCAGCCCTGGCTCCTTCTCTCATCCT-----T-CCAACCCTTCACCCCA-GTGAGCGGAAGTTT-CTAAG-AGCCCCG----TGTCCTGATGTGCCACCCTTGGAAGAAC-AAAACCCTGAGAC-AAACTCGTATTCTGCTTTTTTT-AATTGTCTCTCCCACTTTGCTTCCTGTTCAAACAGATTATCGTGCATGTCTATAATCC-CCACTTAAGCACCTAAGACCCCC---CCTAAAATAACCCA i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 47551 230 - 64270 --GCATCAGCCCTGGCTCCTTCTCTCATCCT-----T-CCAACCCTTCACCCCA-GTGAGCGGGAGTTT-CTAAG-AGCCCCG----TGTCCTGATGTGCCACCCTTGGAAGAAC-AAAACCCTGAGAC-AAACTCGTATTTTGCTTTTTTT-AATTGTCTCTCCCGCTTTGCTTCCTGTTCAAACAGATTATCATGCACCTCTGTAATCC-CCACTTAAGCACCTAAGACCCCC---TCTAAAATAACCCA i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79511711 230 + 83384210 --GCATCAGCCCTGGCTCCTTCTCTCATCCT-----T-CCAACCCTTTACCCCA-GTGAGCGGGAGTTT-CTAAG-AGCCCCG----TGTCCTGATGTGCCACCCTTGGAAGAAC-AAAACCCTGAGAC-AAACTCGTATTTTGCTTTTTTT-AATTGTCTCTCCCACTTTGCTTCCTGTTCAAACAGATTATCATGCACGTCTGTAATCC-CCACTTAAGCACCTAAGACCCCC---TCTAAAATAACCCA i panTro2.chr17 C 0 C 0 s micMur1.scaffold_81340 1639 232 + 2222 --ACGTCAGTTCTGGCTCCTTCTCCCATCCT-----T-CCAACCCCTCACCCCA-CCACGCGGGAGCTT-CCGAG-AG-CCAG----GGCCCCCATGTGCCACCCCTGG-AGAAC-AAAGCCCTGAGACTCAGCTTGTATTTTGCTTCTTTT-AATTGTCTTTCTCACTCAGCTTCCTATTCAAACAGATTATCAGGCAAGTCTATAATCC-CTGTTTAAGCACCTAACCCCCCCCCTTCTAAAATAACCTA i micMur1.scaffold_81340 C 0 C 0 s otoGar1.scaffold_94362.1-287808 52254 208 + 287808 --GCAGTAGTCCTGGCCTGTTCTCCTGTCCT-----T-CCGACCCTTCGCACCA-ATGCACTGGG---------------TGG----TGC---------CCACCCCTGGAAGAAC-AAAGTCCTGAGAC-CAGCTTATATTTTGCTTTTTTT-AATTGTCTTTCCCACTTAGCCTCTTATTCAAACAGATTATCATGAAAGTCCGTAATCC-CCATTTAAGCACCAAAACCCCCC---TCTAAAATAACCTA i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 5830 197 - 10116 --CCACCTGCTCCGGCTCCTCG----GGCCT-----C-CAAACCTGTCCTCCTG-ACCCACAGGAGTTT-CCCAA-GGTCCCG-----------------------CAGGGGAAC-GAAGCCCTGAAAC-AAGCTGGTGTCTCGCTT-TGCT-AATTGT-TCTCCCACTTAGTGTCCTGTT----CAGATCGCCGTGTGTGCCTGTAATCC-CCTTCCAAG--CTTAAA--CCCC---TGGAAAGTAACCTA i tupBel1.scaffold_71658.1-10116 C 0 C 0 s mm9.chr11 118788361 189 + 121843856 --GCACCAGCTCTGTCTCCTCCCATCACTCC-----C-TCAACA-------------AAACAGGG--------------CTTG----TAACCCAGGGTGCCACTCTCCAAAGGTC-AG---TCCAAGAT-GAGTCTGCATCTCCCTC---CC-AATCGTACCTCCCACTCAGCTTCCTGTTCAAATGGATAACCATGTCAGCCTCCAGTCC-CC----AAGTTCCTAAAGCCGTC---TGCAACA------- i mm9.chr11 I 1556 C 0 s bosTau4.chr19 10885625 204 - 65312493 ------------AGG---CTCCTCTCATCCT-----T-CTGACCCTT----CCG-ACTG--GAAGTTTC-CCAGA-GCCGGTG----TCCCCTGACATGCTACTCTTGGAAGAAA-AGAACCC-----T-AAGTCTGCAATTTTCTTTTTTT-CATTGTCTCTCCCACTTAGTTCCCTGTTAAAACAGATCCCCATACCAGTCTGGAACCC-CTATTCAAGCACCTAAACCTTCA-----TAAAATAACCCA i bosTau4.chr19 C 0 C 0 s turTru1.scaffold_98008 16895 216 + 223990 ------------AGGTTCCTTCTTCCATCTT-----T-CTTACCCTTCTGACCG-ACTG--GGAGTTCC-CCAGA-GCCAGTG----TCCCCTGATATACAACACTTGGAAGAAC-AGAGCTCCGAAAT-AAGTCTGTAATTTTGTTTTTTT-AATTGTCTCTCCTACTTAGTTTCCTGTTCAAACAGATCCCCATGCCAGTCTGTAATCC-CTGTTTAAGTACCTAAACCTCCA-----TAAAATAACCCA i turTru1.scaffold_98008 C 0 C 0 s canFam2.chr9 59465665 218 - 64418924 ---GCTCGGCTGAGCCTCCCCGTCCCGTCC------T-TGGACACCTCACCTCG-ACTCT-GGGAGTCT-CCGGA-GCTGGCG-----CCCCCGACGTGCCAGCCCTGGACACAC-AGAACCC--AGAT-GAGGACT----TCAGTTTGTCT-AACTGCCTCTCCCACCTAGTCCCCTACTCGAGCTGAGGTCAATGTAAGTCTGTAGCCC-CCATTCCAGCACCTAGAACCCCA-----TGAAATAACCTC i canFam2.chr9 C 0 C 0 s felCat3.scaffold_206428 55812 223 + 132007 ---GTTCAGCTGAGGCTCCCTCTCCCGTCT------T-CTGACCCTCCACCTGG-ACACA-AGGAGTTT-CCTGATGGTGGC------CCCCCAAACCACCCCCCTTAGACGAAC-AGAACCCTGAGAC-AGGTATTT-TGTTGTTTTCTTT-CATCGTCTCTCCCACTTAGCTTCCCGTTCACACTAAAGACGAGGCAGGTCTGTAGCCC-CCATCCAAGCTCCTAAAACCCCA-----CGAAATAACCCT i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58072155 224 - 61308211 ---GTCCAGCTGTGGCTCCTTCTTTTGTCCT-----T-CCAACCGTTCTCCCGG-ACAC--GGGGTTTC-CCAGA-GCCGGTA----TCCCCTCACGTGCCGCCCTTGGAACGAC-AGAGCCCCGAGAC-CAGTTTGC-ATTTTGTTTTGTT-AATCGTCTCTCCTGCTTGGTTTCCTGTTCAAACAGATCCCCTTGTGGGTCTGTGCCCC-CCATCCAAGCACCTAAAACCCCC-----ATAAGGCGCCCT i equCab2.chr11 C 0 C 0 s proCap1.scaffold_52062 16026 223 + 16741 --GCCTTGGCTGTGACTCCTTCT---GTCCT-----C-CCCACTCTTCACCTGG-ACAT--GTGACCTT-CCTGA-GCCCACA----TTCCCACACATGCCTCCCTTGGAAGAAC-AAAGACCTAGGAT-GAACGCGTGTTTCGGATTTTTTAAATTATCTCTTCTACTTAGTTTCCTGTTCCAACAGATTATCACACACATAGGTAATCCTCCATTTACGTGTCTAAAA-CCCC---TGTAAAA---CCCA i proCap1.scaffold_52062 C 0 C 0 s loxAfr3.scaffold_49 14465986 228 - 17734757 --GCTTTGACTGTGGCTCCTCCT---GCCCTCCACCC-CCTGCCCTGCATCCTG-ACAC--GCAACCTTCCCTGA-GCCCATG----TCTCCGTACACGTTGCCCTCGGAAGAAC-AGAGGCCTGGGAT-GAATGTGTATTTTGTGTTTTTT-AATTGTCTCTTCTACTTAGTTTCCTGTTCAAACAGATTATCATGCACGTCTGTAATCC-CCATTTAAGTACCTAAAACCCCC---TATAAAA---CGCA i loxAfr3.scaffold_49 C 0 C 0 s monDom5.chr2 304668612 233 - 541556283 AAACTGTGGTCTTAGTTCATTCTTTTTCCTT-----TGGTAGCTCCTCGCCTTGAATATAACTGTGTTT-CCAAG-GATAAGGAATTCTTCCTTACACTGAGCTCTTAAAAGAATGAAAGACCTTTAAA-AAATGAATGCTTTCATTTTTCA-GATCA---CTTCTATTTGTTTTCCTGTTCAAATAGATTATCATGCAAGTGTGTAATCC-GTATTTAAGTATCTAAAATGAAC---TATAAAA---TCCA i monDom5.chr2 C 0 C 0 e tarSyr1.scaffold_41848 14767 1758 + 21754 M e pteVam1.scaffold_11245 39645 9 + 48268 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I a score=320062.000000 s hg19.chr17_gl000204_random 79918 123 + 81310 TTAATC----CATTCCCACTCCTGTCTGCTGCT------ATTAACATGTTTGTCTTCGAC-GCCTTTG-------------GCAGCTCATCCCCT--TCCTC-ACCGGGCTTATCTGC-CTTGC-CCGGCATTGGGCATCCCATCCAGAGGT- s panTro2.chr17 79511941 123 + 83384210 TTAATC----CATTCCCACTCCTGTCTGCTGCT------ATTAACATGTTTGTCTTCGAT-GCCTTTG-------------GCAGCTCATCCCCT--TCCTC-ACCGGGCTTATCTGG-CTTGC-CCGGCATTGGGCATCCCATCCAGAGGT- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 47781 123 - 64270 TTAATC----CATTCCCACTCCTGTCTGCTGCT------ATTAACGTGTTTGTCTTCGAC-GCCTTTG-------------GCAGCTCTTCCCCT--TCCTC-ACCGGGCTTATCTGC-CTTGC-CCGGCATTGGGCATCCCATCCAGAGGT- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16096647 123 + 17838096 TTAATC----CATTCCCACTTCTGTCTGCTGCC------ATTAACGTGTTTGTCTTCGAT-GCCTTTG-------------GCAGCTCATCCCCT--TCCTC-ACCGGGCTTATCTGG-CTTGC-CCGGCATTGGGCATCCCAGCCAGAGGT- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75070008 123 + 78773432 TTAATC----CATTCCCACTCCTGTCTGCTGCT------ATTAACGTGTTTGTCTCCGAT-GCCTTTG-------------GCAGCTCATCCCCT--TCCTC-ACCAGGCTTATCTGG-CTTGC-CTGGCACTGGGCATCCCATCCAGAGGT- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 77007 123 - 95547 TTAATC----CATTCCCACTCCTGTCTGCTGCT------ATTAACGTGTTTGTCTCTGAT-GCCTTTG-------------GCAGCTCATCCCCT--TCCTC-ACCAGGCTTATCTGG-CTTGC-CTGGCACTGGGCATCCCATCCAGAGGT- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 81179 123 + 225949 TTAATC----GATTCCCACTCCTGTCTGCTGCT------ATTAATGTGTTTGTCTTTGAT-GCCTTTG-------------GCGGCTCATCCCCT--TCCTC-GCCGAGCTTATCTGG-CTTGC-CCGGCATTGGGCATCCCATCCAGGGGC- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 16565 82 + 21754 TCAATC----AATTCCCACTTCTGTCCGTTGCT------ATTAACCTGTTTGTCTTCAGT-GTCTCTG-------------GCAGCTTAACCTCT--TCGAA-ACGGGG-------------------------------------------- i tarSyr1.scaffold_41848 M 1758 C 0 s micMur1.scaffold_81340 1871 118 + 2222 TTAATC----AATTCCCACTTCCGCCTGTTGCC------ATTAGCCTGTTTGTATTCGGT-GTCTTCG-------------GCGGCTCATCTC----TCGTC-ACTGACCTCACCTGG-CTTGC-TGCG---CTGGTGTCCAGTCCAGAGGC- i micMur1.scaffold_81340 C 0 C 0 s otoGar1.scaffold_94362.1-287808 52462 119 + 287808 TTAATC----AATTCCCACTTCTGTCTGTTGCT------GTTAACCTGTTTGTCTTCAGC-GTCACTG-------------GCGGCTCATCTC----TCTTC-ACTAAGCTCATCTGG-CTGGC-AGTGC--CCACCTTCTTGTCCAGAGGC- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 6027 108 - 10116 TCAACC----AATCCCCACTCCTGCCCATGGCT------CTTA----GCCTGCCTTCCAC-GTCCTCG-------------GTTCTTCACGCTGG--CCGTC-AC-AAGCTCACCTGGTCCTCC-CGGGCTTTGGGCACC-----------T- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s mm9.chr11 118788550 116 + 121843856 -GGAGG----AAGGCCCGCTTCTGTCCATGGTT------CTGAACCTGTGCCTCATCA---GCCTACA-------------GGGGATCATTCCTTAATCTCC-A----GCTTCTCT---CACGC-CTAGCTTTGAGCATCCTGCCTGGAGAG- i mm9.chr11 C 0 C 0 s bosTau4.chr19 10885829 115 - 65312493 -AAGGC----CAGTTCCA--GCTTACTGATGCT------CTTA----ACCTATCTCCCATAGTCTTTG-------------GTGGCTCAGCTTAT--TCGAT-GTGGAGCTTACGTAG-CTTTC-CTGGCTTCAGGTAT-CCATT-GGAGGC- i bosTau4.chr19 C 0 I 1 s turTru1.scaffold_98008 17111 109 + 223990 -CAGAC----CACTCCCA--TCTTCCTGCTGCT------CTTA----ACCTGTCTCCCATAGTCTTTG-------------GTTGCTCAGCCTCT--TTGAC-ACTAAGCTTATCTGG-CTCAC-CTGGCTTCGGGCAT-CCAT-------C- i turTru1.scaffold_98008 C 0 I 1 s canFam2.chr9 59465883 81 - 64418924 -TGTGC-------------------------------------------------TCGGTGGTCTCCG-------------GGAGCTCAGCCTCT--GCGGC-ACTAAGCTCACCTGG-CCCG--CCGACCCCGGGAAT-CGGTC-AGAGGC- i canFam2.chr9 C 0 I 1 s felCat3.scaffold_206428 56035 101 + 132007 -TGAGC-----------------------------------CA----ATTTCTCTCTGTTAGCCTTCGCCCATCTGCCTTCGGGGCTCAGCCTCT--GCGGC-ACCAAGCCCACCCGG-CTAG--CCGCCTTCGGGCAT-CGGTC-AGA---- i felCat3.scaffold_206428 C 0 C 0 s equCab2.chr11 58072379 118 - 61308211 -GGACCGATTCACATCCG--TCCTGCTCTT--C------ACCA----GTTTGTCTTCAGTGGCCCTTG-------------GTGGCTCAGCCTCT--CTGGC-AATAAGCTTATCTGG-TGTGC-CCGGCCTTGGGCATCCCGTC-GGAGGC- i equCab2.chr11 C 0 I 1 s proCap1.scaffold_52062 16249 113 + 16741 TTAAAT----GATTCCCAGTCTCACTCATTGCA------CTGAACTGGTG-----------GTCTTGG-------------ATGGTGTGTCCTCT--TTGTC-ACCAAG-TTTTCTGG-CTCTCTTGGGCTTTGGGCATCCTGTCCAAAGGC- i proCap1.scaffold_52062 C 0 C 0 s loxAfr3.scaffold_49 14466214 114 - 17734757 TTAACT----GATTCCCACTTCTGTCCATTGCA------CTTAACCGGTG-----------GTCTTTG-------------ATGGCACGTCCTCC--TTGTCAACTGCG-TTGTCTGG-CTGTCTCTGGTTTGGGGCATCCTGTCTAAAGGC- i loxAfr3.scaffold_49 C 0 C 0 s monDom5.chr2 304668845 114 - 541556283 TTAACT----AATTCCCACTTCTGCCCATCACTTCCTCCCTCCACCAGTTTGTTA------GTCATAT----------------GCTGACACATT--ATTCC-AACAGGAT--------GCTAT-TTGGACTTTAGCACCCTGGT-GGAGGCA i monDom5.chr2 C 0 C 0 e pteVam1.scaffold_11245 39645 9 + 48268 I e cavPor3.scaffold_76 4413601 1087 + 7991924 I a score=117388.000000 s hg19.chr17_gl000204_random 80041 47 + 81310 GG-G-AG---GG----GTGGCAGCCTGGAGC-----CCTGGAGGCCAGGGCCACCTCCACA-- s panTro2.chr17 79512064 47 + 83384210 GG-G-AG---GG----ATGGCAGCCTGGAGC-----CCTGGAGGCCAGGGCCACCTCCACA-- i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 47904 47 - 64270 GG-G-AG---GG----ATGGCAGCCTGGAGC-----CCTGGAAGCCAGGGCCACCTCCACA-- i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16096770 47 + 17838096 GG-G-AG---GG----ATGGCAGCCTGGAGC-----CCTGGAGGCCAGGGCCACCTCCACA-- i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75070131 47 + 78773432 GG-G-AG---GG----ATGGCAGCCTGGAGC-----TCTGGAGGCCAGGGCCACCTCCACA-- i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 77130 47 - 95547 GG-G-AG---GG----ATGGCAGCCTGGAGC-----TCTGGAGGCCAGGGCCACCTCCACA-- i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 81302 46 + 225949 AG-G-AG---GG----GCAGCCGCCTGCAGC------CTGGAGGGCAGGGCCACCTCCACA-- i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 16647 47 + 21754 GG-A-AG---GG----TGGACAGCCTGGAGC-----CCCAGAGGACAGGGCCACTTCCATG-- i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_81340 1989 49 + 2222 GG-G-GGAATGG----GCAGAGGCCTGGAG------CTAGGAGGACAGAGCCACCTCCAAG-- i micMur1.scaffold_81340 C 0 C 0 s otoGar1.scaffold_94362.1-287808 52581 49 + 287808 AG-G-GCAG-GG----GCAAGGGTCTGGAGC-----CCAGGAGGACAGAGCCACCTCTGCA-- i otoGar1.scaffold_94362.1-287808 C 0 C 0 s tupBel1.scaffold_71658.1-10116 6135 51 - 10116 GT-G-AG---GG----GGCGGGGCATGGAGGGGGCAGCTGGAGGCT-GAGCTGCCTCCGCA-- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s mm9.chr11 118788666 32 + 121843856 GG-GCAA---GT----GTGACATCCTCAAAC------CTGAAGT---------------CA-- i mm9.chr11 C 0 C 0 s bosTau4.chr19 10885945 41 - 65312493 GG-G-AA---GA----CTGACCACG-GGAGT-----CCCAGAGTCCAGAACAAATG------- i bosTau4.chr19 I 1 C 0 s turTru1.scaffold_98008 17221 41 + 223990 GG-G-AG---GA----GGGGCTGCT-GGAGC-----CCCAGAGTCCAGAACAAATG------- i turTru1.scaffold_98008 I 1 C 0 s equCab2.chr11 58072498 47 - 61308211 GG-G-AG---GG----GCCCCAGCCTGGAGT-----CCCAGGGTCCCCGACAACCGCTGTG-- i equCab2.chr11 I 1 C 0 s felCat3.scaffold_206428 56136 30 + 132007 --------------------------GGAGC-----CCCTGAATCCAGAAGGACCGCCATG-- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59465965 39 - 64418924 GG-G-AG---GA----GTGACCACCTGGAGC-----CCCTGAGTCCAGAGGGG---------- i canFam2.chr9 I 1 C 0 s pteVam1.scaffold_11245 39654 41 + 48268 GA-A-AG---GG----GGAGCAACC-GCATC-----CCCGGAGTCCACAGCGACCG------- i pteVam1.scaffold_11245 I 9 C 0 s proCap1.scaffold_52062 16362 47 + 16741 AGAG-AG---AT----GCTACAGCCTGGAGC------TCAGAGTGCAAAGCCTCTTCTGTG-- i proCap1.scaffold_52062 C 0 C 0 s loxAfr3.scaffold_49 14466328 46 - 17734757 AG-G-AG---GA----GCTACAGCCTGGAGC------TCAGAGCACAAAGCTCCCTCTGTG-- i loxAfr3.scaffold_49 C 0 C 0 s monDom5.chr2 304668959 58 - 541556283 GG-G-AG---GGCTATGTTACAGCCTAAAGCACCAACATAAAAAAAAAAGTGACTGCTCTGGG i monDom5.chr2 C 0 C 0 e cavPor3.scaffold_76 4413601 1087 + 7991924 I a score=379622.000000 s hg19.chr17_gl000204_random 80088 151 + 81310 CCTCTCCCATGCT-TCCCAGA-CGCCACCCTCACACTCTGCTTTCTGTACTGGTGAAGGAGACAGGTAAGAA-----CTGCAGATCCACCTGCCCTTGGCCA--TGGGTCAGC-CCTGC------CCACCTCAC------CGCCAG---AGCCACTGGTGA-GCAG--GAAAGGCT-GGG s panTro2.chr17 79512111 152 + 83384210 CCTCTCCCATGCT-TCCCAGA-TGCCACCCTCACACTCTGCTTTCTGTACTGGTGGAGGAGACAGGTAAGAA-----CTGCAGATCCACCTGCCCTTGGCCA--TGGGTCAGC-CCTGC------CCACCTCAC------CCCCAG---AGCCACTGGTGA-GCAG--GAAAGGCTGGGG i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 47951 151 - 64270 CCTCTCCCATGCT-TCCCAGA-TGCCACCCTCACACTCTGCTTTCTGTACTAGTGGAGGAGACAGGTAAGAA-----CTGTAGATCCACCTGCCCTTGGCCA--TGGGTCAGC-CCTGC------CCACCTCAC------CCCCAG---AGCCACTGGTGA-GCAG--GAAAGGCT-GGG i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16096817 152 + 17838096 CCTCTCCCATGCT-TCCCAGA-TGCCACCCTCACACTCTGCTTTCTGTACTGGTGGAGGAGATAGGTAAGAA-----CTGCAGATCCACCTGCCCTTGGCCA--TGGGTCAGC-CCTGC------CCACCTCGC------TCTCAG---AGCCACTGGTGA-GCAG--GAAAGGCTGGGG i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75070178 151 + 78773432 CCTCTCCCATGCT-TCCCGGA-CACCACCCTCACACTCTGCTTTCTGTGCTGGTGGAGGAGACAGGTCAGAA-----CTGCAGATCTAGCTGCTCCTGGCCA--TGGGCCAGC-CCTGC------CCACCTCAC------TCTCAG---AGCCACT-GTGA-GCGG--GAAAGGCTGGGG i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 77177 151 - 95547 CCTCTCCCATGCT-TCCCGGA-CACCACCCTCACATTCTGCTTTCTGTGCTGGTGGAGGAGACAGGTAAGAA-----CTGCAGATCTAGCTGCTCCTGGCCA--TGGGCCAGC-CCTGC------CCACCTCAC------TCTCAG---AGCCACT-GTGA-GCGG--GAAAGGCTGGGG i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 81348 148 + 225949 CCTCTCCCGTGCT-TCGCAGA-TGCCACCTGCACACTCTGCTTTCTGTACTGGT---GGAGATCGGTAAGAA-----CTGCAGATCCACCTGCCGGTGGCCA--TGCGTCAGC-CCTG-------TCACCTCAC------TATCAG---AGCCACTGGTGA-GCCG--GAAAAGCTGGGG i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 16694 152 + 21754 CCTCTCCTATGCT-TCCTGGA-TGCTGCC-TCACACTCTGTTTTCTGTGCTGGTGGAAGAGACCAGTGAGGA-----CTACAGATCTACCTGCCCTTGGCCT--TAGGTTAGCTCCTGC------CCACCTCAC------CAGCAG---AGCCAGTGGTGA-GCAG--GAAAGGCTGGTA i tarSyr1.scaffold_41848 C 0 C 0 s micMur1.scaffold_81340 2038 139 + 2222 CAACCCCTGTGCT-TCCTGGA-GGTGGCCCTGGCAC-------------CTGGCAGAGGAGACAGGCGAGAC-----CTGCAGACCCACCTCCGCCTGGCCC--CAGGGCAGCCCCCGC------CC-CCCCAC------AC-CAGTGTGGCCGCAGCTGA-GCAG--GAAAGGTGGG-- i micMur1.scaffold_81340 C 0 N 0 s otoGar1.scaffold_94362.1-287808 52630 134 + 287808 CCTCTCCTGTGCT-TCCTGGG-TGTGGCCCTCACA--------------CTGGTA---GAGACCGGCGAGAA-----CTGTGGGTCCACCTGCACCTGCCCA--GGGGTCAGCCCCTGC------CCACCTCAC------CA-CAG---AGCCACGGACAA-GCAG--GACAGTCTGAG- i otoGar1.scaffold_94362.1-287808 C 0 N 0 s tupBel1.scaffold_71658.1-10116 6186 73 - 10116 CCTCTCCGGAG----------------TCCTCACGCTTTC-------------------------GGGAGAC-----CTGTGG-------------TGGCCT--CCA--CGGC-TCTGC------C--ACTCGC------CCTCAG---AGCCA-------------------------- i tupBel1.scaffold_71658.1-10116 C 0 C 0 s mm9.chr11 118788698 115 + 121843856 TATGTCCTGTGCC-------------------------------CTGTTCAGGAGGAGGAAGTTGGGGGCGGGGCCCCTCAGGCTCCACCCACACCTG--CC--TGACTAAGC-CCTGC------CCACTTAAC------T--CAG---AGCCTCTGCTGA-ATGG--GGG--------- i mm9.chr11 C 0 C 0 s vicPac1.scaffold_107852 39269 114 + 39997 CCTCTCCCGTGCT-TCCCAAA-CACTGCCCTCGAGCTCTGTTTTTGGTG------------------AAGAA-----CTGTAGA-CACTCTGCACTTGACCG--TGGGTCAGCCCCTGC------CCAC-CTGC------CATCGA---AGCCAGTG-----A----------------- i vicPac1.scaffold_107852 N 0 C 0 s turTru1.scaffold_98008 17262 120 + 223990 CCTCTCCTATGCT-TTCCGAA-CACTACCCTCAAGCTCCATTTTCAGTG------------------AAGAA-----CTGCAGA-TCCCCTGCACTTGACCA--TGAGTCAGCCAC--------------CTGC------CATCAC---AGCCACTG-----GC----GAGTGGCTGGGA i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10885986 114 - 65312493 CCTCTCCTGTGTT-TTCGGAA-CACTGACCT---------------GTG------------------AAGAA-----CCACAGATTCCCCTGTACTTGACCA--TGGCTCAGCCCCTGC------CCGCTTTGT------CATCAA---AACCACTG-----GC----AAGTGGCTGGGG i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58072545 115 - 61308211 CCTCCTGCGCCCT-CCTGAGG--GCTGCCCTCACATCCTGTTTTCCATG------------------GAGAA----------------------CCTGACGG--CGGGTCATCCCCCAC------CCGCCT-GC------CGTGGG---AGCCCCCG-TGA-GCAG--GAAAGGCTGGGA i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 56166 133 + 132007 CCTCTCCCGCATC-CCCAGAAATGCTGCTTTGA-GCTCTGTCTTCAGTG------------------GGGAA-----CCACAGACCCCCTTGCACGTGACCG--TGGATCAGCCCCTGC------CCAGCTCAC------CCCCGG---GGCCACAG-CAG-GAAG--GAAAGGT-GGGA i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59466004 119 - 64418924 --------------CCTGGGAATGCGGCCTTCATACTCCATTTTCCATG------------------AAGAA----TTTACAGATCCCCCTGCACTTGCCTA--TGGGTCAGCCCCTGC------CCACCGCAC------CTTCAG---AGCCCCTG-TGGAGCAG--GAGAGAT----- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 39695 110 + 48268 -------CGCACC-TCCAGTG-TTTTCCCCTCACGCTCTGTCTTCCGTG------------------AAGGA-----------------CTGCACTTGACCG--GGGATCAGCCCCTGT------CCGCCACAA------CGAAGG---GGC-------GG-GCGGTTGCCAGGG-GGGA i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_52062 16409 143 + 16741 CCTCCTCCATGCTTTCCTGGA-CACTGTCTCCACCTTCCAGTTTCCAGATTAGCAGGGGAGCTGGA-GAGAG-----CTAGTGGGCTG-CTGTCCTTGCCTA--TGGGTCAACCTCTGC------CCATCTCAC------CACCTG---A--------CAA-GCAG--GAAAGTCTGGG- i proCap1.scaffold_52062 C 0 I 1 s loxAfr3.scaffold_49 14466374 143 - 17734757 CCTCTGCCATGCTTTCCTGAA-CACTGCCCTCACCTTCCAGTTTCTGGATTGGCAGGGGAGTCCCA-GAGAA-----CTACCAGACCA-CTGCACTTGACCG--TGGGTCAGCCTCTGC------CCATCTCAT------CATCTG---A--------TGA-GCAG--GAAAGGCTGGG- i loxAfr3.scaffold_49 C 0 I 1 s monDom5.chr2 304669017 151 - 541556283 CCCCTGATTTGCTTTACAATG-TAGCACTCTATCTCTCAATTTTTCGTGCT-----------TTGGAAACAA-----CCACAAA---ATCCTCACTTAACCATTTGTATTAACTTCTCTTACATACAGCCTCACTTTAGTCATCAG---AGCTACTAATGA-ACAG--TGCAAACTG--- i monDom5.chr2 C 0 N 0 e cavPor3.scaffold_76 4413601 1087 + 7991924 I a score=1021.000000 s hg19.chr17_gl000204_random 80239 54 + 81310 GCACCTCCCCTCGTCTACCAGTAGG------------------------AAAAG--AGTGA-ATCCCACTTCCA--CC-CACAC s panTro2.chr17 79512263 54 + 83384210 GCACCTCCCCTCGTCTACCAGTAGG------------------------AAAAG--AGTGA-ATCCCACTTCCA--CC-CACAC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 48102 54 - 64270 GCACCTCCCCTCGTCTGCCAGTAGG------------------------AAAAG--AGTGA-ATCCCACTTCCA--AC-CACAC i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16096969 54 + 17838096 GCACCTCCCCTCATCTACCAGTAAG------------------------AAAAG--GGTGA-ATCCCACTTCCA--CC-CACAC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75070329 54 + 78773432 GCACCTCCCCTCCTCTCCCAGTAGG------------------------AAAAG--AGTGA-ATCCCACTTCCA--CC-CACAC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 77328 54 - 95547 GCACCTCCCCTCCTCTCCCAGTAGG------------------------AAAAG--AGTGA-ATCCCACTTCCA--CC-CACAC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 81496 52 + 225949 ACACCTCCCCTCATTTCCCGATAGG--------------------------AAG--AGTGA-ATCCCACTTCCA--CC-TACAA i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 16846 49 + 21754 GTACCTCTCCTCACTTCCCTGT-----------------------------AAG--AGTGA-CCTCCACTCCCA--CC-CACAC i tarSyr1.scaffold_41848 C 0 C 0 s tupBel1.scaffold_71658.1-10116 6259 48 - 10116 -------CCTTCATTTCCCAGTAAG------------------------A-AAG--AGTGACCCCCCACTTCCA--CCACTCAC i tupBel1.scaffold_71658.1-10116 C 0 C 0 s mm9.chr11 118788813 16 + 121843856 GGGGCTCTCCTTATCT-------------------------------------------------------------------- i mm9.chr11 C 0 C 0 s vicPac1.scaffold_107852 39383 59 + 39997 ---------CCTTCCACCCTGTAGGTCCTCCAGAGC---------CAGTATCAG--AGTGA-ACCCCACTCCCA--CC-TGTA- i vicPac1.scaffold_107852 C 0 I 4 s turTru1.scaffold_98008 17382 69 + 223990 GTGCTGCCCCTCCCCTCCCTGCAGGTCCTCAAGAGC---------CCGTAGCAG--AGTGA-ATCCTACTCCCA--CCTTGTA- i turTru1.scaffold_98008 C 0 I 3 s bosTau4.chr19 10886100 69 - 65312493 GTGCTGTCCCACCCCTCCCTGCAGGTCCTCAAGAGC---------CAGTAGCAG--AGTGA-ACCCTACTTCTA--TCTTGTA- i bosTau4.chr19 C 0 I 4 s equCab2.chr11 58072660 29 - 61308211 GTG-----CCCCCCTTCCTCACACGTCCTCGAG----------------------------------------A---------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 56299 57 + 132007 GTG-----CCCCGGCTCCCTGCGGGTGCTCACGGGC---------CGGCAGCAG--AGCGA-ACCCCACTCCCA---------- i felCat3.scaffold_206428 C 0 C 0 s canFam2.chr9 59466123 62 - 64418924 ---------CCCCTCTCCCTGCAGGTCCTCAAGGGC---------CAGCAGCAA--AGCGA-ACCCCACTCCCACCCCATATG- i canFam2.chr9 C 0 I 1 s pteVam1.scaffold_11245 39805 68 + 48268 GTGCCG-CCCTCCCCTCCTTGCAGGTCCTCAAGAGC---------CAGTAGCAG--GGCAA-ACCCAACTCCTG--CCCCATA- i pteVam1.scaffold_11245 C 0 I 1 s proCap1.scaffold_52062 16553 69 + 16741 GTACCTCTCCTCTGTTCCCTGCAGG-CCCCAGGGACAGCAAGGACCCATAAGAA--AGTGC-ACCCCCTCAAT----------- i proCap1.scaffold_52062 I 1 C 0 s loxAfr3.scaffold_49 14466518 71 - 17734757 GTGCCTCCCCTCTGTTCCCCACAGGTCCTCAGGAACAGTGAGGA-CCATCGGAAAGAGTGC-ACCCCCACAAC----------- i loxAfr3.scaffold_49 I 1 C 0 e cavPor3.scaffold_76 4413601 1087 + 7991924 I a score=311491.000000 s hg19.chr17_gl000204_random 80293 44 + 81310 CCTCTATTCCATTCCAGGGGATCCAAAGGCCTTCCGCCCCTGCT s panTro2.chr17 79512317 44 + 83384210 CCTCTATGCCATTCCAGGGGATCCAAAGGCCTTCCGCCCCTGCT i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 48156 44 - 64270 CCTCTATTCCATTCCAGGGGATCCAAAGGCCTTCCGCCCCTGCT i gorGor1.Supercontig_0007361 C 0 I 10 s ponAbe2.chr17_random 16097023 44 + 17838096 CCTCTGTTCCATTCCAGGGGATCCAAAGGCCTTCCGCCCCTGCT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75070383 44 + 78773432 CCTCTATTCCATTCCAGGGGATCCAAAGGCCTTCCGCCCCTGCT i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 77382 44 - 95547 CCTCTATTCCATTCCAGGGGATCCAAAGGCCTTCCGCCCCTGCT i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 81548 44 + 225949 CCCCTATTCCATTCCAGGGGATCCAAAGGCCTTTCACCCCTGCT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 16895 44 + 21754 CATTCATTACATTTCAGAGGACTCAAAGGCCTTCCACCCCTTCT i tarSyr1.scaffold_41848 C 0 C 0 s tupBel1.scaffold_71658.1-10116 6307 39 - 10116 CCTCC---TCCCTCTAGGAGCCTCGAAG--CCTCCACCCCAGCT i tupBel1.scaffold_71658.1-10116 C 0 I 1 s mm9.chr11 118788829 39 + 121843856 ----CGTGCCATTACAGGAGACCCCAAAACCTTTCACCTTGCT- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4414688 43 + 7991924 CTCCCATTCCATCTCAGGGGACTCAAAAGCCTTCCACCCCACC- i cavPor3.scaffold_76 I 1087 C 0 s vicPac1.scaffold_107852 39446 44 + 39997 GACATGTTCCATTCCAGGGGACCTGAAGGCCTTCTACCCCTGCT i vicPac1.scaffold_107852 I 4 C 0 s turTru1.scaffold_98008 17454 44 + 223990 CTCGTGATCCATTCCAGGGGACCTGGAGGCCTTCTGCCCCTGCT i turTru1.scaffold_98008 I 3 C 0 s bosTau4.chr19 10886173 44 - 65312493 CCTGTGTTCCATTTCAGAGGACCTGCAGTCTGTCTGCCATTGCT i bosTau4.chr19 I 4 C 0 s canFam2.chr9 59466186 42 - 64418924 -CCGTGTTCCATTCCAAGGGACCTGAAGGCCTTCTGCC-CTGCT i canFam2.chr9 I 1 C 0 s pteVam1.scaffold_11245 39874 37 + 48268 -CCGTGTCCCATTCCAGGAGCCTTCAGCCCCTGCTGTC------ i pteVam1.scaffold_11245 I 1 C 0 s proCap1.scaffold_52062 16622 44 + 16741 CCAGCATTCCACTCCAGGGAACCTGAAGGCCTTCTGCCCCTGCT i proCap1.scaffold_52062 C 0 C 0 s loxAfr3.scaffold_49 14466589 44 - 17734757 CCTGCATTCCACTCCAGGGGACCTGAAGGCCTCCTCCCCCTGCT i loxAfr3.scaffold_49 C 0 C 0 e felCat3.scaffold_206428 56356 0 + 132007 C e equCab2.chr11 58072689 0 - 61308211 C a score=224498.000000 s hg19.chr17_gl000204_random 80337 87 + 81310 -GT-CCTCAAGACAGG-------CTAAA--ACC-----CACACCCAAAGTGGGCTTTCTGGGCCAACCAAC-TATGGACACAGTACATAG--C-CTGCAAAGCC-----TCC s panTro2.chr17 79512361 87 + 83384210 -GT-CCTCAAGACAGG-------CTCAA--ACC-----CACACCCAAAGCGGGCTTTCTGGGCCAACCAAC-TATGGACACAGTACATAG--C-CTGCAAAGCC-----TCC i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16097067 87 + 17838096 -AT-CCTCAAGACAGG-------CTCAA--ACC-----CACACCCAAAGTGGGCTTTCTGGGCCAACCAAC-TATGGACGCAGTGCATAG--C-CTGCAAAGCC-----TCC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75070427 87 + 78773432 -AT-TCCCAAGACAGG-------CTCAA--ACC-----CACACCCAAAGTGGGCTTTCTGGGCCAACCAAG-CATGGACACAGTGCATAC--C-CTGCAAAGCC-----TCC i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 77426 87 - 95547 -AT-TCCCAAGACAGG-------CTCAA--ACC-----CACACCCAAAGTGGGCTTTCTGGGCCAACCAAG-CATGGACACAGTGCATAG--C-CTGCAAAGCC-----TCC i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 81592 87 + 225949 -GT-CCCCAAGACAGG-------CTCAA--ACC-----CACTCCCAAAGTGGGCTTTCTGGGCCAACCAGC-CATGGACGCAGTGTGCAG--C-CTGCAAAGCC-----TCC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 16939 94 + 21754 -GT-CCCCAAGACAGGCTCAAACCTCAA--ACC-----CAAATCTAAAATGGGCTTTCGGGCCCCACTAAC-AGTGAACACAGTACACAG--C-CTGCAGAACC-----TCT i tarSyr1.scaffold_41848 C 0 C 0 s tupBel1.scaffold_71658.1-10116 6347 57 - 10116 -CT-CCCCGAGACAGG-------CTCAA--ACC-----TACACCCAGAGCGG-------------------------CCGCAGCACAGGG--CACTGCAA------------ i tupBel1.scaffold_71658.1-10116 I 1 C 0 s mm9.chr11 118788868 69 + 121843856 -GT-TCTCA----AGG-------CTCAA--ACC-----CACATCCACAGTGGGTTGAT--GACCAC-----------AGACAGCATACAA----CACTGAAG-C-----TAC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4414731 81 + 7991924 -GT-TC--------AG-------CACAG--ACTCCACACATGTCCAAAGTGGACTTCCTGGGCCTCCTGCG----AGGGACGGCGTTCAA--C-CGTTGAATCC-----TGC i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_107852 39490 84 + 39997 -GTTCCCCAAGACAGG-------CTCAA--ACA-----CACCTCCAAAGTGGACCTTCTGGGCGCACTGAGCTGTGGACACAGTGCTCAG--C-CTGCAAAG---------- i vicPac1.scaffold_107852 C 0 C 0 s turTru1.scaffold_98008 17498 83 + 223990 -GTTCCCCGAAATAGG-------CTCAA--AT------CACATCCAAAGTGGACCTTCTGGGTACACTGAGCTGTGGACACAGTGCCCAT--C-CTGCAAAG---------- i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10886217 83 - 65312493 -CTTCCCTAAGACAGG-------CTCAA--ATC-----CATGTCCAAAGTGGACTTTCTGGGCACACTGAGCTGTGGACACTTTTCCCAG--C-CTACAAA----------- i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58072689 63 - 61308211 ----GCCAGTAGCAGA-------GTGAA--CCC-----CACTCCCGCCGAGC--------------------TGTGGACACGGTGCCCAG--C-CTGCAAAGCC-------- i equCab2.chr11 C 0 C 0 s felCat3.scaffold_206428 56356 79 + 132007 ----CCCCAAGGCAGA-------CTCAA--ACT-----CACGTCCAATGTGG--CTTCTAGGCTCAC-------TGGACCCAGCCCCGAGGGT-TCACAAAGCACCC----- i felCat3.scaffold_206428 C 0 I 174 s canFam2.chr9 59466228 85 - 64418924 -ATTCCCCAAGTCAGG-------CTCAA--ACC-----TGCATCCAACGAGGGCCTTCTGGGCTATCAGAACTGTGGACACAGTGCCCGG----CTGCAAAGCT-------- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 39911 71 + 48268 ----CCCCAAG----------------------------ACATCCGAAGCGGACTTCCTGGGCACGCTGTACCATGGACACAGCACCCAG--C-CTGCGAAGCC---AT--- i pteVam1.scaffold_11245 C 0 C 0 s proCap1.scaffold_52062 16666 70 + 16741 AGT-ACCAAGGACAGG-------CTCAAACACA-----CAGGTCCAAAGTAGACACTCTGGCCTCACTGAGCCATAGACACAG----------------------------- i proCap1.scaffold_52062 C 0 N 0 s loxAfr3.scaffold_49 14466633 81 - 17734757 GTT-CCCCAGGACAGG-------CTCAA--ACC-----CAGGTCCAAAGTGGACGTTCTGGGTTCACCGAGCCATAAACTCTGCACAGGA--G-CCACC------------- i loxAfr3.scaffold_49 C 0 C 0 e gorGor1.Supercontig_0007361 48200 10 - 64270 I a score=16710.000000 s hg19.chr17_gl000204_random 80424 104 + 81310 TTGGACATCAGAGCTG---CCCCAGAACCCCGGCGTTCCCATAGACCCGCAAATGGGG----TTCTATAGAGCACCCACTGCATGTCCGACTC-TGTCTAAAGACC-GTGG-GT s panTro2.chr17 79512448 104 + 83384210 TTGGACATCAGAGCTG---CCCCAGAACCCCGGCGTTCACATAGACCCGCAAATGGGG----GTCTATAGAGCACCCACTGCATGTCCGGCTC-TGTCTAAAGACC-GTGG-GT i panTro2.chr17 C 0 C 0 s ponAbe2.chr17_random 16097154 104 + 17838096 TTGGACATCAGAGCTG---CCCCAGAACCCCGGCGTTCCCATAGACCCGCAAATGGGG----GTCTATAGAGCACCCACTGCATGTCCGGCTC-TGTCTAAAGACC-GTGG-GT i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75070514 104 + 78773432 TCGGACCTCAGAGCTG---CCCCAGAACCCCGGCCTTCCCATAGACCCACAAATGGGG----ATCTATAGagcacccactgcatgtccggctc-tgcctaaagact-gtgg-gt i rheMac2.chr16 C 0 I 49 s papHam1.scaffold8336 77513 104 - 95547 TCGGACCTCAGAGCTG---CCCCAGAACCCCGGCCTTCCCATAGACCCACAAATGGGG----ATCTATAGAGCACCCACTGCATGTCCGGCTC-TGCCTAAAGACT-GTGG-GT i papHam1.scaffold8336 C 0 I 49 s calJac1.Contig5139 81679 103 + 225949 TCGGACCTCAGAGCTG---CCCC-GAACCCCAGCATTCCCACAGACCCACAAATGGGG----GTCTATGGAGCACCCACTGCATGGGCAGCTC-TGCCTAAAGACT-TTGG-GT i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 17033 103 + 21754 TTGGACCCCAGCGCTC---ACCCAGGACCCCAGTGTTCCCACTGACCCATAGACAGAG----GTTTATAAAGCA-CCACTGCATGTCCAGTTC-TGTCTAATGATT-TCAG-GT i tarSyr1.scaffold_41848 C 0 C 0 s tupBel1.scaffold_71658.1-10116 6404 96 - 10116 --TGAGCCCGGGGCTGGGACTGCAGGATCCCGG--TTCCCGG-----CACTGTCCGAG----GGCCTTAAAGCACCCCCTGCGTGTCTAGCT----TCTCGCCACCAGCAG-GT i tupBel1.scaffold_71658.1-10116 C 0 C 0 s mm9.chr11 118788937 93 + 121843856 CTCACCCTCAGAACTG---TCCGA-------GGAGTCCCTTGCAGCACATCCATGACA----ATTTGTGAGGCTCCT----TGCAGAGAGCCAGTGTATGATCGCC-ATGGT-- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4414812 98 + 7991924 TTGGTGCTCAGTTCTG---CCCCAAGACCACAGAAACCCCCACAGCCATTCCA--AAG----GATCGCAAAGCTCCTACC-TACTTTCAGCTCTTCTCT--TCACC-ACTG--- i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_107852 39574 66 + 39997 --------------------------------------ACACTGGGCCACCCCCAGG-----GTTCATAAAGCACCCACTGCAT--TCAGCTC-TGTCTAATGAGT-GTGG-GT i vicPac1.scaffold_107852 C 0 C 0 s turTru1.scaffold_98008 17581 66 + 223990 --------------------------------------ACAATGACCCACCCGTAGGA----GTTCA-AAAGCACCCACTGCCA--TCAGCTC-TGTCTAATGAGC-ATGG-AT i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10886300 63 - 65312493 -------------------------------------------GACTCATCCCCAGGG----GTTCATAAAGCACCCACTACCA-TTCATCTC-CGTCTAATGAGC-ATGG-GT i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58072752 45 - 61308211 ----------------------------------------AGCGACCCGTCCACAGGG----G-TCATAAAGCACC--------------CAC-TGTGT--------TCAG-CT i equCab2.chr11 C 0 C 0 s canFam2.chr9 59466313 53 - 64418924 ----------------------------------------GATGACCCAGCCCCAGGG----GTTCATAAAGCACC--------------CAC-TGTGTGTTCCAA-TCAG-GT i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 39982 56 + 48268 -------------------------------------------GGCCCGTCCAC--GG----GTTCATAAAGCACC----GTAT--GCAGCTC-AGCCCGATCCGT-TCGG-GT i pteVam1.scaffold_11245 C 0 C 0 s loxAfr3.scaffold_49 14466714 83 - 17734757 TTGTGTCTCACAGCTG---CTGCAGGACACCAGGGTCcacaacaacctatcaacagagtcatttttgtcaagtatacatggtatat---------------------------- i loxAfr3.scaffold_49 C 0 N 0 e gorGor1.Supercontig_0007361 48200 10 - 64270 I e felCat3.scaffold_206428 56435 174 + 132007 I a score=181192.000000 s hg19.chr17_gl000204_random 80528 42 + 81310 AACACAGAAGCATGAGGCACAG-AGGGTCCTCAGGGAGCC-TTC s panTro2.chr17 79512552 42 + 83384210 AACACAGAAGCATGAGGCACAG-AGGGTCCTCAGGGAGCC-TTC i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 48210 42 - 64270 AACACAGAAGCATGAGGCACAG-AGGGTCCTCAGGGAGCC-TTC i gorGor1.Supercontig_0007361 I 10 C 0 s ponAbe2.chr17_random 16097258 42 + 17838096 AACACAGAAGCATGAGGCACAG-AGGGTCCTCAGGGAGCC-TTC i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75070667 42 + 78773432 aacacagaagcaTGAGGCACAG-AGGGTCCTCAGGGAGCC-TTC i rheMac2.chr16 I 49 C 0 s papHam1.scaffold8336 77666 42 - 95547 AACACAGAAGCATGAGGCACAG-AGGGTCCTCAGGGAGCC-TTC i papHam1.scaffold8336 I 49 C 0 s calJac1.Contig5139 81782 42 + 225949 AACACAGGAGCATGAGGTACAG-AGGGTCCTCAGGGAGCC-TTC i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 17136 42 + 21754 GACACAGACGCATGAGGCACAG-ACCATCCTCGAGGAGCC-TTC i tarSyr1.scaffold_41848 C 0 C 0 s tupBel1.scaffold_71658.1-10116 6500 28 - 10116 AACGCGAAACC---------------GTCCCCAGGGAGCT-TTC i tupBel1.scaffold_71658.1-10116 C 0 N 0 s mm9.chr11 118789030 40 + 121843856 AACATAGAAGCAGA-GGCAA-G-ATCATCTACAGGGAGAC-TTC i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4414910 42 + 7991924 GGCGCAGACACAGGTGGCAC-A-GGCATCTCTGGGGAATCATCC i cavPor3.scaffold_76 C 0 C 0 s vicPac1.scaffold_107852 39640 33 + 39997 AA--------CAGGAGGCCCAGCACGG--CCTAAGGAGCC-TTC i vicPac1.scaffold_107852 C 0 C 0 s turTru1.scaffold_98008 17647 42 + 223990 GATA-AGCTGCAGGAGGCCCAGGAGCATCCTTGGGGAGCC-TTC i turTru1.scaffold_98008 C 0 C 0 s bosTau4.chr19 10886363 42 - 65312493 GATA-CGCTGCAGGATGCCCAGGAGCATCCTTGGGGAGCC-TTC i bosTau4.chr19 C 0 C 0 s equCab2.chr11 58072797 36 - 61308211 ------GTCTCAGACGGCACTG-GCCGGCCTCCGGGAGCC-TTC i equCab2.chr11 C 0 C 0 s canFam2.chr9 59466366 41 - 64418924 AATA-AGCAGCAGGAGGGACAG-ACCATCTTCGGGGAGCT-GTC i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 40038 41 + 48268 AGCA-AGCAGCAGTGGGCACAG-ACCATCCTCAGGGAGTC-CCC i pteVam1.scaffold_11245 C 0 C 0 e felCat3.scaffold_206428 56435 174 + 132007 I a score=314195.000000 s hg19.chr17_gl000204_random 80570 149 + 81310 AGGGTAATTGACCAACTCACCCCTAAGACAACGGGAGGGAGCACATGGGCTGTGA--GTGTCTTG-GCTGCACACAGAGAGGCCTA-------------CTG-TTCTGCCATTTCCCATCCTCATGTC-CTG-----------GAACTTTCcttccatttcctcaattataaaactg-g s panTro2.chr17 79512594 149 + 83384210 AGGGTAATTGACCAACTCACCCCTAAGACAACGGGAGGGAGCACATGGGCTGTGA--GTGTCTTG-GCTGGACACAGAGAGGCCTA-------------CTG-TTCTGCCATTTCCCATCCTCATGTC-CTG-----------GAACTTTCCTTCCATTTCCTCAATTATAAAACTG-g i panTro2.chr17 C 0 C 0 s gorGor1.Supercontig_0007361 48252 149 - 64270 AGGGTAATTGACCAACTCACCCCTAAGACAACGGGAGGGAGCAAACGGACTGTGA--GTGTCTTG-GCTGGACACAGAGAGGCCTA-------------CTG-TTCTGCCATTTCCCATCCTCATGTC-CTG-----------GAACTTTCcttccatttcctcaattataaaactg-g i gorGor1.Supercontig_0007361 C 0 C 0 s ponAbe2.chr17_random 16097300 148 + 17838096 AGGGTAATTGACCAACTCACCCCTAAGACAACAGGAGGGAGCACATGGGCTGTGA--GTGTCTTG-GCCGGACACAGAGAGGCCTC-------------CTG-TTCTGCCATTTCCCATCCATATGTC-CTG-----------GAACTTTCcttccatttcctcaattataaaa-tg-g i ponAbe2.chr17_random C 0 C 0 s rheMac2.chr16 75070709 149 + 78773432 AGAGTAATTAACCAACTCAGCCCTGAGACAACGGGAGGGAGCACATGAGCTGTGA--GTGTCTTG-GCTAGACACAGAGAGGCCTC-------------CTG-TTCTGCCATTTCCCATCCTCATGTC-CTG-----------GAACTTTCcttctatttcctcaactataaaactg-g i rheMac2.chr16 C 0 C 0 s papHam1.scaffold8336 77708 149 - 95547 AGAGTAATTAACCAACTCAGCCCTGAGACAATGGGAGGGAGCACATGGGCTGTGA--GTGTCTTG-GCTGGACACAGAGAGGCCTC-------------CTG-TTCTGCCATTTCCCATCCTCATGTC-CTG-----------GAACTTTCcttctatttcctcaactataaaactg-g i papHam1.scaffold8336 C 0 C 0 s calJac1.Contig5139 81824 146 + 225949 AGGGTAATTGACGAAGTTACCCCAAAGACAACGGGAGGGAGCACATGGTCTGTAA--GTGGCTTG-GTTGAACACAGAGAGGCCTC-----------------TTCTGCCATTTTCCATCCTCACATC-CTG-----------AAACTTTCcttccatttcctcaattataaagctg-g i calJac1.Contig5139 C 0 C 0 s tarSyr1.scaffold_41848 17178 121 + 21754 AGGGCAATTGACCAACTCGCCCAGAAGACAA--AAAGGGAGGAGAGGGGCTGTGC--GGGAGTTG-GCTGGGCACAGAGAGGTCTC-------------TCG--TCTGCTAGTTACTGTCAATACgtc-ctt-----------gaactctcct-------------------------- i tarSyr1.scaffold_41848 C 0 I 8 s mm9.chr11 118789070 117 + 121843856 AGGACAACTAACCAACTCAGCCCCAAGCTAA----AGAGAAGCTGGGGGGTCTGA--CTGGGCTG-GCTGGGCACAAGAAGAC-------------------------------CCAGCATCCGTATCCCTG-----------GAAC------ACCATCTCCTCTGCTGTAA------- i mm9.chr11 C 0 C 0 s cavPor3.scaffold_76 4414952 153 + 7991924 AGGGCCACTGACTAGCTCTACCAGAAGCCAA----AGAGGGGCTTGGGTAGTAGG--GGAGGTTG-GCTGCGTTCAACAAGACCTT-------------CAGACTCCTAGACCTCCCGCCTACCTGTCACTGTCTGTGGTCTTGAACTTTACTTCTATTGCCTTGACTGTAAA------ i cavPor3.scaffold_76 C 0 N 0 s vicPac1.scaffold_107852 39673 130 + 39997 CTGGAAACTGACTc---------------------agag-ggacgtgagctgtga--agggtcagcactgagtccaaagagacctggcatctaggcctccta-gcctgtcatttgctgtc--catatc-ctt-----------a------actt--gtttctctgactataaaactg-- i vicPac1.scaffold_107852 C 0 N 0 s turTru1.scaffold_98008 17689 138 + 223990 AAGGAAACTGACTc---------------------agagaggacgtgagctgtga--ggggccagtgctgggtccaaagagacctggcatctaggcctccca-gcctatcacttactgtccacacatc-ctt-----------g-actttactt--gtttctctgactataaaattg-- i turTru1.scaffold_98008 C 0 I 36 s bosTau4.chr19 10886405 122 - 65312493 AAGGAAACTGATTC---------------------AGAGATGATGCGAGTGGCGA--GGGGTCAGCGCTTGGTCCAAAGGGACCTG-----------------GCCTGTCACTTACTATCAAcacatc-ctt-----------g-acttcactt--gtttctctgactataaaattg-- i bosTau4.chr19 C 0 N 0 s equCab2.chr11 58072833 132 - 61308211 AGGGGACTTGACTC---------------------TGAGAGGACGAGAGCTGTGACAGGGGTCAGCACTGGGTAGAAGGGGACCTGGTGTCAAGGCCTCTGA--CCTGCTGTTTACTGTCTACGCATC-CTT-----------GAACTTTCTTT--GCTCCCTTAACTA---------- i equCab2.chr11 C 0 I 12 s canFam2.chr9 59466407 136 - 64418924 AGGGCAGCTGACTC---------------------AGAGAGGACATGAGCCATGAGAGGGGACAGCGCTGGCCACA--GAGACGCAGCACCCAGGCCTCCCA-CCCCGCCATCTGCCGTCTACACTTC-CTT-----------T-ACTTCACCT--GTTTCCTTgactagaaaac---- i canFam2.chr9 C 0 C 0 s pteVam1.scaffold_11245 40079 128 + 48268 AGAA-AACTGACTC---------------------AGAGGGGACACGAGCTGTGAG-GGGGTCAGCACTGGGTACA--GAGACCTGGCGTCTAGGCTTCCCG-TCCTGCCGTGTGCTGTCTACGCACC-CTT-----------G-ACCT-----------CTTCGACTATAAAGCTGA- i pteVam1.scaffold_11245 C 0 C 0 e felCat3.scaffold_206428 56435 174 + 132007 I a score=464705.000000 s hg19.chr17_gl000204_random 80719 268 + 81310 -----ggagcaatggctcacacctgtaatcccagcactttgggaggccgaggcgggtagatcacttgaggtcaggagttcgagaccaccctggccaacatgatgaaactctgtctctactaaaattacaaaaattagccaggtgtggtggcatgcacctgtaatcccagctactcaggaggttgaggcaggagaattgcttgaacccaggaggcagaggttgcagcaagccgagatcaccccactgcattccagcttgggcaataaagcgaga s calJac1.Contig5139 81970 273 + 225949 ggccaggcacagtggctcacacctatgatcccagcactttcaaaggccaaggcgagcagattgcttgaggtcaggagttcaaaaccagactggccaacgtgacaaaactccatgtctactaaaattacaaaaattacccaggcatagtggcatgcacctgtaatcccagctacttaggaggctgaggcaggagaattgcttgaacccagaaggcagaggttgtagtgagctgagatcaccccactacattccagcttgggtgacaaagtgaga i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 77857 267 - 95547 -----ggcgcagtggctcatatctgtaatcccagtcctttgggaggccaaggcgggcggatcacttgaggtcaggagttcaagaccaccctggccaatatgatgaaactctgtctctactaaaattacaaaaattagccaagtgtgatggtgtgcacctgtaatcccagctactcaagaggctgaggcaggagaattgcttgaacccaggaggcagaggttgcggtgagcctagatcaccccattgca-tccagcttgggcaacaaagtgaga i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75070858 268 + 78773432 -----ggcgcagtggctcatatctgtaatcccggtcctttgggagaccaaggcaggcggatcacttgaggtcaggagttcaagaccaccctggccaatatgatgaaactctgtctctactaaaattacaaaaattagccaagtgtgatggtgtgcacctgtaatcccagctactcaggaggctgaggcaggagaattgcttgaatccaggaggcagaggttgcggtgagcctagatcaccccattgcattccagcttgggcaacaaagtgaga i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16097448 268 + 17838096 -----ggagcaatggctcacacctgtaatcccagcactttgggaggccgaggcgggcagatcacttgaggtcaggagtttgacaccaccctggccaacatgatgaaactctgtctctactaaaattacaaaaattagccaggtgtggtgacatgcacctgtaatcccagctgctcaggaggttgaggcaggagaattgcttgaaccctggaggcagaggttgcagcaagccgagatcaccccactgcattccagcttgggcaacaaagcgaga i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 48401 268 - 64270 -----ggagcaatggctcacacctataatcccagcattttgggaggccgaggcgggcagatcacttgaggtcaggagttcgagaccaccctggccaacatgatgaaaccctgtctctactaaaatcacaaaaattagccaggtgtggtggcatgcacctgtaatcccagctactcaggaggttgaggcaggagaattgcttgaacccaggaggcagaggttgcagcaagccgagatcaccccactgcattccagcttgggcaacaaagcgaga i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79512743 268 + 83384210 -----ggagcaatggctcacacctgtaatcccagcactttgggaggccgaggcgggcagatcacttgaggtcaggagttcgaggccaccctggccaacatgatgaaactctgtctctactaaaattacaaaaattagccaggtgtggtggcatgcacctgtaatcccagctactcaggaggttgaggcaggagaattgcttgaacccaggaggcagaggttgcagcaagccgagatcaccccactgcattccagcttgggcaacaaagcgaga i panTro2.chr17 C 0 C 0 e tarSyr1.scaffold_41848 17299 8 + 21754 I e turTru1.scaffold_98008 17827 36 + 223990 I e felCat3.scaffold_206428 56435 174 + 132007 I e pteVam1.scaffold_11245 40207 0 + 48268 C e canFam2.chr9 59466543 0 - 64418924 C e equCab2.chr11 58072965 12 - 61308211 I e mm9.chr11 118789187 0 + 121843856 C a score=19692.000000 s hg19.chr17_gl000204_random 80987 41 + 81310 ctccatctcaaaaaaaaaaaaaaaaaaaa---------aaaaaaaaaaac s tarSyr1.scaffold_41848 17307 13 + 21754 ctcgactttaaaa------------------------------------- i tarSyr1.scaffold_41848 I 8 C 0 s calJac1.Contig5139 82243 24 + 225949 ctccatctcaaaaca-----------------------aacaaaaaa--- i calJac1.Contig5139 C 0 C 0 s papHam1.scaffold8336 78124 44 - 95547 ctccatgtcaaaaaaaaaaaaaaaaaaaaaaa------aaaaaaaaaaac i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75071126 31 + 78773432 ctccatgtcaaaaagaaaa-------------------aaaaaaaaaaac i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16097716 20 + 17838096 ctccatctcaaaaaa-----------------------aaaaa------- i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 48669 27 - 64270 ctccatctcaaaaaa-----------------------aaaaaaaaaaac i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79513011 50 + 83384210 ctccatctcaaaaaaaaaaaaacaaaaaacaaacaaaCAAACAAAaaaac i panTro2.chr17 C 0 C 0 e turTru1.scaffold_98008 17827 36 + 223990 I e felCat3.scaffold_206428 56435 174 + 132007 I e pteVam1.scaffold_11245 40207 0 + 48268 C e canFam2.chr9 59466543 0 - 64418924 C e equCab2.chr11 58072965 12 - 61308211 I e mm9.chr11 118789187 0 + 121843856 C a score=106625.000000 s hg19.chr17_gl000204_random 81028 40 + 81310 gttggcactgacatagatgatatctaaggttccttctggc s mm9.chr11 118789187 40 + 121843856 GTTGGCATTGACCTGGGTAAGCACACCAGGTTCTCCAGGG i mm9.chr11 C 0 C 0 s tarSyr1.scaffold_41848 17320 38 + 21754 -ttggcactgacat-gatgatctctaaggtttctcccagc i tarSyr1.scaffold_41848 C 0 C 0 s papHam1.scaffold8336 78168 40 - 95547 tttgtcactgaaatagatgatatctaaggttccttctggt i papHam1.scaffold8336 C 0 C 0 s rheMac2.chr16 75071157 40 + 78773432 tttgtcactgaaatagatgatatctaaggttccttctggt i rheMac2.chr16 C 0 C 0 s ponAbe2.chr17_random 16097736 40 + 17838096 gttggcactgacatagatgatacctaaggttccttctggc i ponAbe2.chr17_random C 0 C 0 s gorGor1.Supercontig_0007361 48696 40 - 64270 gttggcactgacatagatgatatctaaggttccttctggc i gorGor1.Supercontig_0007361 C 0 C 0 s panTro2.chr17 79513061 40 + 83384210 gttggcactgacatagatgatatctaaggttgcttctggc i panTro2.chr17 C 0 C 0 s felCat3.scaffold_206428 56609 35 + 132007 --TGACACCGACACAGGTGATCTGCAGGGGTCTCCCC--- i felCat3.scaffold_206428 I 174 C 0 s pteVam1.scaffold_11245 40207 33 + 48268 ------ACggacacagatgacctctggggtctctccg-gc i pteVam1.scaffold_11245 C 0 C 0 s equCab2.chr11 58072977 32 - 61308211 -------CTGACATCCATGAGCGCTAGGATTTCCCCA-GC i equCab2.chr11 I 12 C 0 s canFam2.chr9 59466543 23 - 64418924 -----------------tgatctcaagggctcctcctggc i canFam2.chr9 C 0 C 0 s calJac1.Contig5139 82267 38 + 225949 --tggcactgatatagatgatatctaaggttccttctggc i calJac1.Contig5139 C 0 C 0 e turTru1.scaffold_98008 17827 36 + 223990 I a score=834271.000000 s hg19.chr17_gl000204_random 81068 242 + 81310 tctcaaattgtctgcttctgtaattcAGATCTGAGTGGTGAGGCATGGGTAAGACACT--CCCAGAGTCTCAG------GGATGCCTGGTTAAGGGCTGGAGGGGGCATGGAAGGCTTCCTGGCATCACCAGGATGCAGCCC-------------AGATACTCATGGGCCCTGGCACCTGGAACCATCTGCTCAAAGGCATC-ACGTGGCAACCTGATCG--TCCCATCAT-----CTTCCAAAGCCTCAGAAGAGCAGCTGAGAAGGATC s panTro2.chr17 79513101 242 + 83384210 tctcaaattgtctgcttctgtaattcAGATCTGAGCGGTGAGGCATGGGTAAGACACC--CCCAGAGTCTCAG------GGATGCCTGGTTAAGGGCTGGAGGGGACATGGAAGGCTTCCTGGCATCACCAGGATGCAGCCC-------------AGATGCTCATGGGCCCTGGCACCTGGAACCATCTGCTCAAAGGCATC-ACGTGGCAACCTGATCA--TCCCATCAT-----CTTCCAAAACCTCAGAAGAGCAGCTGAGAAGGATC i panTro2.chr17 C 0 N 0 s gorGor1.Supercontig_0007361 48736 242 - 64270 tctcaaattgtctgcttctgtaattcAGATCTGAGTGGTGAGGCATGGGTAAGACACC--CCCAGAGTCTCAG------GGATGCCTGGTTAAGGGCTGGAGGGGGCATGGAAGGCTTCCTGGCATCACCAGGATGCAGCCC-------------AGATGCTCATGGGCCCTGGCACCTGGAACCATCTGCTCAAAGGCATC-ACGTGGCAACCTGATCG--TCCCATCAT-----CTTCCAAAGCCTCAGAAGAGCAGCTGAGAAGGATC i gorGor1.Supercontig_0007361 C 0 N 0 s ponAbe2.chr17_random 16097776 242 + 17838096 tctcaaattgtctgcttctgtaattcAGATCTGAGCAGTGAGGCATGGGTAAGACACC--CCCAGAGTCTCAG------GGATGCCTGGTTAAGGGCTGGAGGGGACATGGAAGGCTTCCTGGCATCACCAGGATGCAGCCC-------------AGATGCTCATGGGCCCTGGCACCTGGAACCATCTGCTCAAAGGTATC-ACGTGGCAACCTGATTG--TCCCATCAT-----CTTCCAAAGCCTCAGAAGAGCAGCTGAGAAGGATC i ponAbe2.chr17_random C 0 N 0 s rheMac2.chr16 75071197 242 + 78773432 tctcaaattgtctgcttctgtaattcACATCTGAGCGGTGAGGCATGGGTAAGACACC--CCCAGAGTCTCGG------GGGTGCCTGGTTAAGGGCTGGAGGGGGCAGGGAAGGCTTCCTGGCATCACCAGGATGCAGTCC-------------AGATGCTCACAAGCCCCGGTACCCGGAACCATCTGCTCAAAGGCATC-ACGTGGCAGTCTGATCG--TCCCATCCT-----CTTCCAAAGCCTCAGAAGAGCAGCTAAGAAGAATC i rheMac2.chr16 C 0 N 0 s papHam1.scaffold8336 78208 242 - 95547 tctcaaattgtctgcttctgtaattcACATCTGAGCGGTGAGGCATGGGTAAGACACC--CCCAGAGTCTCAG------GGGTGCCTGGTTAAGGGCTGGAGGGGGCAGGGAAGGCTTCCTGGCATCACCAGGATGCAGTCC-------------AGATGCTCACAAGCCCCGGTACCCGGAACCATCTGCTCAAAGGCATC-ACGTGGCAGTCTGATCG--TCCCATCCT-----CTTCCAAAGCCTCCGAAGAGCAGCTAAGAAGAATC i papHam1.scaffold8336 C 0 N 0 s calJac1.Contig5139 82305 228 + 225949 tctcaaattgtctgcttctgtaattc-------AGCTGTGAAGCATGGGTAAGATATC--CCCAGAGTCTCAG------TGGTGCCTGGTTAAGGGCTGGAGGGGGCAGGGAAAACTTCCTGGCATCACCAAGATGCAGCCC-------------AGATGCTCACAGGCCCTGGCACCTGGAACCATTTGCTCAAAGGCATC-ACGTGGCAACCTGACTG--TCTTGTCCT-----CTCCCAAAGCCTCAGAAGAGCAGCTGAG------- i calJac1.Contig5139 C 0 N 0 s tarSyr1.scaffold_41848 17358 242 + 21754 tctaaaattgtctgcttctataattcAGGTCAAAACTACAAGGTATGGATATGACAGA--CCTAGAGGCTCAG------GGGTTCCTGGTTAAAGGCAAAAGGGAGCAGGAAAAGCTTCCTGGCATCACCAAGACTTAACCT-------------ACACACACAGGGGCCATGGCACAAGGGACCATTGGTTCAAAGGCATT-ATGGGATGACTTGACTGTTTTTTATTCT-----CTCCTGGAACCTCAAGAAAGCAGCTGAGAAGGA-- i tarSyr1.scaffold_41848 C 0 N 0 s mm9.chr11 118789227 210 + 121843856 TCTAAAGGTGTCTACTTCTATAACTCAGGAACGAG-GTCAAGGCTCTGATGATACACAGGCCCCAAGGCTCAG------AA------GGGTAAGGACTGAA--------GAAGAACTTCCTGGTATCACCAGCCCTTAGCCT-------------GAATGCTCAAG---CCCAGCA---GGA-----------GAGGACTCC-ATGTAGCAATCTTATTG--TCTGTCCCTGGAGGCTTCCCTGGCATCTTAGGAGCCAGTGAG------- i mm9.chr11 C 0 N 0 s turTru1.scaffold_98008 17863 233 + 223990 tctaaaattgtctgcttctgtaattcAGGAATAAACTGTGAAACATGGATGAGACAGG--CCCAGAG-CTCAG------AGGGTTACGGTCAACGGTTGTAGAGTTCAGGGGAGGCTTCCTGGCATCCCCGAGACTCAGCCT-------------GCA----CACAGGCCCTGGCACGTGG-GCCATTT-CTTGAAGGTACC-ACATGGCAACCTGAACG--TTCTGACCC-----CTTTGAGAGGCTGGAAAGAGTGGCTGTGAAGGA-- i turTru1.scaffold_98008 I 36 N 0 s felCat3.scaffold_206428 56644 232 + 132007 ----AAATTCTCTG---CTGTAATTCAGGTGTAAACTGTGAGGCGGGGATGAGACAAG--CCCGGAG-CTCGGGG-GCGGGGGCCGCGGTCAAGGGTTGGAGGGCTCCAGGAAGGCTTCCTGGGGGCCCTGAGGCTCGGCCC-------------GCACG--CACAGGCCCTGGAACGAGAAGCCAGTC-CTCAAAGGCACCAACATGGC-ACCTGCAGG--TTCTG--CC-----CTCTTGGAGGCTGGAGACGGTGGCTGGAAAGGA-- i felCat3.scaffold_206428 C 0 N 0 s pteVam1.scaffold_11245 40240 234 + 48268 tcccaagttctctgcttctataattcAGGTCTAAACAG-GAGGCAGGGATGAGACAAG--CCCAGAG-CTTGGGGACTGGGGGTCATGGTCAACAGTCGGAGGGTTCCAAGACAGGTTCCTGGCATCCCCGAGA--CAGCCC-------------GCACA--CACGGG-CCTGGCATGAGGCACCATTT-CTCAAAGGCACC-ACATGGCAACCTGGAAG--TTAA---TG-----CTTCTGGAGCCTGGACAGCATGGCCATGAAGG--- i pteVam1.scaffold_11245 C 0 N 0 s equCab2.chr11 58073009 227 - 61308211 TCTACAATTCTCTGCTTCCATAGGTCAGGTCTAAGCCGTGAGGCGTGGATGGGACAGG--CCT----------------GGGGTCATGGTCAAGGGTTGGGGGATTCGGGGAAGGCTGCCTGGTGTCCCCGAGACTCAGCCT-------------GCACT--CACAGGACCTGGCACCAGGGGCCGTTT-CTCAAAGACGCC-ACGTGGCAAACCAAACA--TTCCGACCC-----CTCTTAGTGGCTGGAGGGAGCAGCCGTGACAGA-- i equCab2.chr11 C 0 N 0 s canFam2.chr9 59466566 222 - 64418924 tataaaactctctgctcctgtaattcAGGTCTACACTGTGAGGCATGGATGAGACAAG--CTTGGAG-CTCAGGGTGGGGGGGTCACAGCCAAGGGTCGGAGGGCTCCAGGATGGCTTCCTGGCAA--CTGAGGCTCAGCCCCACCCCTGCCCCTGCCC---CATAAGCCCGGGAACAAGGGGTGATTT-CTCAACACCACC-ATGTGGCAATCTGAATG--TTCTG--TC-----CTCTT------------------------------ i canFam2.chr9 C 0 N 0