##maf version=1 scoring=autoMZ.v1 a score=469763.000000 s hg19.chrUn_gl000245 0 521 + 36651 GATCAGATAGGCTTTTGGCTCATT---GTAATGAGATGTTCCTATAAACCTAATTTGAAAGACAAAGACAGAGTTTGGAGTCTTTAATTCTTGGTAAAAAT--CAG-TAGCTCTATTTAGGGCTATATTTGCAAAATACTATTTCAACTCAAGCATATTTTTATTTACAAGGCACTTCACAAATGTTGACCACAAAGATGTTTCTACCTAGC---AGAAATA---ATTATAGTTACATATAG-TTGTCTAGGAATATCTTAAACATGGGGTATTAAAATAACTTTCAAGA---ACAAGAAGAAATGTTACA--------------------CCAGGCATTTTTGCAACTAGTGCTCTATTTCAGTGCAATATTTGTGGCAA----TTAAAAA-------ACATAAATGGCTTGGATATATAGCTAAGTTATCAAAGGAAAA-ATATGCAAAGGCATGATTAT----------TTTAT------AAATGTGCCACATATGTGACTT---------------GAG-GTACAAATCCTCT------------AAGTTTAAAATTGTCTTTTTAAAAAAGA-----AAT----CAAAACAGACAAGTGGGCAATGAGTTATGGATA s cavPor3.scaffold_34 15803671 497 - 24440124 GATCAAACAAGTCTTTGATTCATT---AAAATGAGATGTTTCTATGAAATGAATTTGAAAACTAAAGATAGATTTGTGAATATTTGATTCTGGGAAAAA-T--TGA-CAGTTA-----------ATATTTGTAGGGTCC---TTCCACTTTATTGTATTTTTGTTTACACTGCATTTGATAGATGTTAACCATGTGAATATTTCTAACTATCAAGAATAATA---ATTGTAGTTTTAAACAA-TTATCCAAGAACAAATTAA--ATGTGA-ATTGAAAGAATTTTCAAGGGTGACAAGAATAAATTTTGTA--------------------TTAGGCATTTCTTTATCTAGTGCTATATATGAGTACT---TTTTTGATAA----TTAAAAATTGTTTCATATATATGGTTTGG--ATATCATTATGATATCAAAAGTGAA-ATATGTAAAAGCATGATTCT----------TTTAT------AAATGCATAGCTTATATAGATC---------------AAA-GTACAGAA-TTCT------------AAGTTTAAAATTTTC--TTTAAAAATAA-----AAT-----------GATAAATGGGCTATGTTTTAGG---- i cavPor3.scaffold_34 N 0 C 0 s rheMac2.chr2 189449919 519 - 189746636 GATCAAATAAGCTTTTGGTTCATT---GTAATGAGATGTTCCTATAAACCAAAGTTAGAAGACAAAGACAGAGTTTGGAGTCTTTAATTCTTGGAAAAA-T--CAG-TAGCTCTATTTAGGGCTCTGTTTCCAAAATACTGTTTCTACTCAAGCATGTTTTTATTTACAAAGCACTTCACAAATGTTGACCACAAAAATGTCTCTACCTAGC---AGAAATA---ATTATAGTTACATCTAA-TTGTCTAGGAATATATTAAACATGGGG-ATTAAAATAACTTTCAAGA---ACAAGAAGAAATGTTGTG--------------------CCAGGCATTTTTGTACCTAATGCTCTATTTGGGTGCGATATTTGTGGCAA----TTGAAAA-------ACATAAATGGCTTGGATATATAGTTAAGATATCAAAGGAAAA-CTATGCAAAGGCATGATTAT----------TTTAT------AAATGTGCCACGTATGTGAATT---------------GAG-GTACAAAACCTCT------------AAGTTTAAAATTGTCTTTTTAAAAAAGA-----AAT----CAAAACGGACAAGTGGGCAATGAGTTATGGATA i rheMac2.chr2 N 0 C 0 s panTro2.chrUn 47396666 519 - 58616431 GATCAGATAGGCTTTTGGCTCATT---GTAATGAGATGTTCCTATAAACCTAATTTGAAAGACAAAGACAGAGTTTGGAGTCTTTAATTCTTGGTAAAA-T--CAG-TAGCTCTATTTAGGGATATATTTGCAAAATACTATTTCTACTCAAGCATATTTTTATTTACAAGGCACTTCACAAATGTTGACCACAAAGATGTTTCTACCTAGC---AGAAATA---ATTATAGTTACATATAG-TTGTCTAGGGATATCTTAAACATGGGGTATTAAAATAACTTTCAAGA---ACAAGAAGAAATGTTATA--------------------CCAGGCATTTTTGCAACTAGTGCTCTATTTCAGTGCAATATTTGTGGCAA----TTAAAAA-------ACATAAATGGCTTGGATATATAGCTAAGATAACAAAGGAAAA-ATATGCAAAGGAATGATTAT----------TTTAT------AAACGTGCCACATATATGACTT---------------GAG-GTACAAATCCTCT------------AAGTTTAAATTTGTCTTTTTAAAAA-GA-----AAT----CAAAACAGACAAGTGGGCAATGAGTTATGGATA i panTro2.chrUn N 0 C 0 s equCab2.chr26 13357203 529 + 41866177 -ATCAAATAGACCCTAGGATCATT---ATAATGAGATATTCCTATGATCCAAAGTTGAAAGTTATAGACAGATTTAGAGATCTTCAATCCGTCGGAAAA-T--GAG-CACTTGTAATTAGGACAATATTTACAGAGAACTCTTTCTACTCAAGCATATTTTCATTCATAATGCATTTTATAAATGTTGACCACACAAATGTTTCTGGCTAAC---AGGAATCGCCATCATACTTATGTACCATTTATCCAGGGATAGATGAAACATGTAG-ATTGAAAGAA--TTTAAGGATCACAAGAATAAATTTCATA---------------------CAGGCATTTCTTGATATAGTGCTATATTTGGGTA-T---CATCTGACAATTTTTTTAAAA-------ACATGAATAGCTTGGATATCTAGTGAAGCTATCACAGGAAAAAATATTCAAAAGAATGATTAT----------TTTAT------AAATAAGCCATATGTGTGAACC---------------AAG-AACATAAGAAAATCAAAAACATAAGACATTTAAAATTTCC--TTAAAGGA---------AT----CAAAATAGACAAGTGGACAGCAGGCTATGGATA i equCab2.chr26 N 0 C 0 s canFam2.chr31 14105605 521 + 42263495 -ATCAAATAGGCCCTTGGCTCATT---TTAACGAAATGTTCCTATGATCCAAAGCTGAATGATACAGACAGCT---GGGAATCTGAATCCTTTGGAAAA-T------CAATTCTAATAAGGGAAATTTCTGTAGAATACTATTTCTACTCAAACATGTTTTTATTTGCAAAACACTTTATCAGTGTTAACCACACAAATGTTTCTGGCTATC---A-AAACAGCCATTATAATTACATACAA-TTACCTGGGGGTGAATTAAATACATGG-ATTGAAATAA--TTCAAGGGTTGTAAGAATAAATATTATATCCAGCATTTCTTTTTTCTTTTAGTCATTTCTTGATACAGTAGTATATTTGGTTATT---TTTCTGACCAAAAAAAAAAAA-------ACATGAATACCATGAATATCT----AAGTTAACAAAGAAAAACACATTCAAAGGCATGAATA-------------TAT------GAATAAGCCATATGTATAAATC---------------AAA-ACCATAAAACCCT------------ACATTTAAAATTGTC--TTTTAAAA----------------AAGAGAAATAATTGGACACCCAATTATGGGCA i canFam2.chr31 N 0 C 0 s oryCun2.chr14 141885530 532 + 163896628 -ATCAAATAGGTCTTTGACTCATTATAATAATAAAATGTTCCTATGAAGCTAAATGGAAAAATAAACAGAGATTTAGGGAACTTCAATCCTTGGGAAAA-TGCTAATTAGACA-----------ATATTTGAAGAATACGATTTCTATGCAAGCCTACTTGTATTTACTATGTACCTTTTATATATTAGCCAAATCAATGTTTCCACATAGC---AGTAATA---ATTGCAGTTATACACAA-CTATTCAGGGAGATATTAAACATACGG-ATTGAAATAATTTTCAAGGGTTACCAG--TGAA-TTTATA--------------------TTAGACATTTCCTGACCTACTGCTATATTTGGACACC--ATTTTTGACCA----TGAAAA--------ACATGAATGGATTCA------TATCAAGTTAACAAATGAAAA-ATATACACAGAAATAATTATCAACATACTATCTATGTGAAGATAGGCATATCTGA-ATAGATCGGCATCTATATGAAGAAG-GCACACAACCTCT------------AACTTTAACATTGTC--TGAAAGAACAA-----AAGGTATTGAAATAGACAAGTGGGCCTTGGGTTATG---- i oryCun2.chr14 N 0 C 0 s loxAfr3.scaffold_13 20600821 514 - 62548349 GATCAAAAAGGCCCTTCTCTCATT---ATAATGAGATCCTCCTATGAACATAAGTTGAAAGATAAACATAGGTTTAGAGATCTTCAATCCTTGG--AAA-T--AGG-CAGTTCTAATTAGAGCAATATTTGAATTATAGTACTTTTACTCAAACATATTTTCATTTACATTGCA-TTTGTATATTCTAATCACACTAGTGTTTTGGACTAGC---AGGAATAGCCCTTAAGGTTATATATAA-TTACTCAGGGATAAGTTAAGTGTGTAG-ATTAAAGAAATTTTCAAAGGTCACAAGAA-------------------------------TCAGGCATTTTTGG-TCTAGTGCTATATTTGGATACAATTTTCCTGAAAA----TTAAAAAAAA----AAATGAATGGCTTTAATATCT---TAAGCTTTCAGAGGAGCT-ATATATAAAGGCATTATTAT----------TTTAT------AAGTGAGTCACATGATTGAATC---------------AAGAGCATAAAATCTCT------------AAGTTTAAAATTGCT--TTAAAGCAAAAATATGAAT----CAAAATAGACAAGCAGGAAAGGGGTTATGAGTA i loxAfr3.scaffold_13 N 0 C 0 a score=50498.000000 s hg19.chrUn_gl000245 521 56 + 36651 CTATTATAGGG-TACCCTGATAAACTAGTAAGAAGACGACTTTTGGTACTGAAAATT s panTro2.chrUn 47397185 56 - 58616431 CTATTATAGGG-TACCCTGATAAACTAGTAAGAAGACGACTTTTGGTACTGAAAATT i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189450438 48 - 189746636 CCATTACAGGG-TACCCTGATAAC--------ACGAAGACTTTTGGTACTGAAAATT i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15804168 51 - 24440124 -----ATAGGT-ACCCTTAAAAGCCTAGAAACCAGAGTAGCTTTGCTACTAAAAACT i cavPor3.scaffold_34 C 0 I 1396 s oryCun2.chr14 141886062 42 + 163896628 -----AGATAT----------AACCTAGTAACAAGGAGACCACAGATATTAAAACTT i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138175929 57 - 161106243 cTGTTATAAGACTATACAGATATTCTAGTAATGAAAGGACTTTTGATACTAAAAAAT i bosTau4.chr1 N 0 C 0 s equCab2.chr26 13357732 57 + 41866177 TTATTATAAGACTACCGTGTTAACCTGATAACAAGACCACCTTTGGTGCTAACAAGC i equCab2.chr26 C 0 C 0 s canFam2.chr31 14106126 57 + 42263495 CTGTGGTAAGAGTACCCTGGTAACCTGGTACCAATAGGGGCTTTGGTACTAAAAAGC i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20601335 53 - 62548349 ---CTGTAGGA-TATCCTGATAATCTAATAACAAGAGAATCTTTGGTTCTAAAATTT i loxAfr3.scaffold_13 C 0 C 0 a score=205177.000000 s hg19.chrUn_gl000245 577 246 + 36651 CCAATTAACCACATGCCCCCATTAAGGCCAT----GATCACTGC---CA---ATTTTTACTCACAAAGGCTGGAGCTAGA--------GTTATATGGAATTCCATATGTATCTAAACCATAGATTTATCAATTATCACTTAAATA-CAACTTGGAAGACACTATCCAGAATTTGTAGGGC--TTGGCCTTATTCTAGAGAAACATACACTGGAATAGGCAGT----------------------------------T-G-------GATTTTA----AATTCAGTCTTAAATCTGTTGAAAATAATGCATTTT s panTro2.chrUn 47397241 246 - 58616431 CCAATTAACCACATGCCCCCATTAAGGCCAT----GATCACTGC---CA---ATTTTTACTCACAAAGGCTGGAGCTAGA--------GTTATATGGAATTCCATATGTATCTAAACCATAGATTTATCAATTATCACTTAAACA-CAACTTGGAGGACACTATCCAGAATTTGTAGGGC--TTGGCCTTATTCTAGAGAAACTTACACTGGAATCGGCTGT----------------------------------T-G-------GATTTTA----AATTCAGTCTTAAATCTGTTGAAAATAATGCATTTT i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189450486 246 - 189746636 CCAATTAGCCACATACCTCCACTAAGGCCAC----GATTACTGC---CA---ATTTTTACTTGCAAAGACTGGAGCTAGA--------GTTATATGGAATTCCATATGTATCTAAACCATAGATCTGTCAATTATCACTTAAACA-CAACTTGGAGGACACTATCCAGAATTTGTGGGGC--TTGGCCTTATTCTGGAGAAACATCCACTGGAATAGGCAGT----------------------------------T-G-------GATTTTA----AATTCAATCTTAAATCTCTTGAAAATGATGCATTTT i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141886104 272 + 163896628 CCAATTATCCACATGC--CCATTACAAACAT----CATTACTGC---CATCTATTTTTATTCACAAAGGC---AGATACA--------GTTATGTGGGATTTCTTATGTATTTAAATAATATATATACCAACTCTCACTTGAAGA-TAACTT--AGCACACTATCTAGGACTTCAAATAT--TTGATC---TTCTGGAGGAACTTCCGTTGTGATAGGCAGTTATAAGACCTCCCTGAAGCCTTAATTTAGTATTCT-G-------GGTTTTA----GGTCCACTCTT-AATGTCTTGGAAATACTGAATATT i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138175986 242 - 161106243 CTAATGAGCCACTTGCC-CCTTGCAGGCCAC----CATTCCTGC-ATCA---TGTTTTACTCACAAAGGCATGTGTTAGAGAGAGAAACTGATGTGGAATGCCATGCATATTTAAACCAGAAATTTACCAA--------------------------ATATCATCTAAAGAGTGAAAGACGGTTCTTT---TTCTGGAGACGCTTCCATTGAGATAGGTAGTTCTAAGGCCACCTTGGAGACTCAATTTACTGTTTGAG-------ATTTTTAAGATAGCTCACTGT-------------------------- i bosTau4.chr1 C 0 I 24 s equCab2.chr26 13357789 290 + 41866177 CTAATTAGCCAC-TGCC-CCATGAAAGCCAG----CATTGCTGCAATCA---ATTTTTACTCACAAAGGCAGATGGGAAAGAGAGAGTGTGATGAGGAATCCCGTGTGTATTTAAACAAGAGATTTACCGATTATTATGTAAAGC-CAACTTGGAAGACACTGTCTAGAGGTTGAAAGAT--TTGAGC---TTCTAGAGAAGCTTCCATTGAGATAGGCCATTCTAAAGCACCTCTGGAGATTTAACTTACTGTTTT-T-------GGTTTGGGGGCAATTCACTCTTAAATCTCTTGGAAATGATACACATT i equCab2.chr26 C 0 C 0 s canFam2.chr31 14106183 282 + 42263495 CTAGTTAGCCACTTGTC-TCATGAAGGTCAGTCATCATTGTTGCCACCA---ATTTTTACTCAAAAAGGCAAGTGGTAGATAAAGA--CTGATGTGGAATCTCATGGGTATTAAAACCAGAGATTCACCAATTCTTACTTAAAGC-TGACTTAGATTATACTATCTAGAGGTTGAAAAGT--TTGGCC---TTCTATAGAAGCTTCCACTAAGATAAGC-------AGGCCCCTCTGGAGACTG---TTATGATTTT-G-------ACATTTAAGGCAGTTTACTCTTAAATATCTTGAAAATGATACACAt- i canFam2.chr31 C 0 I 237 s loxAfr3.scaffold_13 20601388 261 - 62548349 CTAACTATCCATATGC--CCATTAAGGCCAA----AATAATTGCCACCA---ATTTTTGCTCACAAAGTTTTTAGATATAGA------ATTATGTGGAATCACCTATGTATTTAACCAAGAGATTCAGCAATTATCACCCAAAAACCAACTTGAAGGGCACTCTCTCAGGTGTGAAAGAT--TTTACATCCTTCTGTAGAAACTTCCCATGAGATAGGAAATTCTAAGTCCTAGCTAGAGTGTAAATT--------T-GATATTTCGGTTTTAAGACAGTTCACTTT-------------------------- i loxAfr3.scaffold_13 C 0 I 594 e cavPor3.scaffold_34 15804219 1396 - 24440124 I a score=80003.000000 s hg19.chrUn_gl000245 823 93 + 36651 TTTCTCAGAGATGAGATATTGTTCAACTCTTTTGACTTATTTTAGATTTGATAATATACAGTTCAAACACCATGGAGATTTACTAATCTGAAT s panTro2.chrUn 47397487 93 - 58616431 TTTCTCAGAGATGAGATACTGTTCAACTCTTTTGACTTATTTTAGATTTGATATTATACAGTTCGAACACCATGGAGATTTACTAATCTGAAT i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189450732 93 - 189746636 TTTCTGAGAGATGAAAAATTGTCCAACTCTCTTGGCTTATTTTAGATTTGATATTATACAGTTCGAACACCATGGAGATTTACTAATCTGGAT i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141886376 90 + 163896628 CT--TAAAAGATAAAA-ATTATCCAATACTTTGGGATCATACTGGCTTTGATATTACACAATTCAAATGTTACAAGGACTTATGATTCTGGAT i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138176252 47 - 161106243 TTTTTGAGAGAGCAGAAATTCTCAAGCATCCTTGAAC----------------------------------------------TACTCTAGAT i bosTau4.chr1 I 24 I 142 s equCab2.chr26 13358079 91 + 41866177 --CTTGAGAGAGCAGAAAGTATTCAACTCTTTTGGACTATTCTAGATTTGATATTATACAGTTCAAATGCCAAGTAGCTTTATCATTATGGAT i equCab2.chr26 C 0 C 0 s canFam2.chr31 14106702 93 + 42263495 TTCTTGAGAGAGCAGAAATTATCCAATTCTCTTAGACTATTCGAGATTTTATTTTTTACAATTGAAATGCCAAATTACTTTATTATTATGGAT i canFam2.chr31 I 237 C 0 s loxAfr3.scaffold_13 20602243 88 - 62548349 TTCTTGAGAGCTTAGAAATTTACCAACTCTCTTAGGATATCGAAG-----ATATTATGTAGTTCAAACATCAAGTAGATTTATCTTTATGAAT i loxAfr3.scaffold_13 I 594 C 0 e cavPor3.scaffold_34 15804219 1396 - 24440124 I a score=225228.000000 s hg19.chrUn_gl000245 916 193 + 36651 GAACACATACCAAATTTGTCTTTGCTCCAGTCTCGAAATCTGAGATTAATTCTAGCTGCTGAAG-AAATTTTCCAGTGTTAGGAGTATGC-TTCAATGCTGGTGACCGGTACTACTTTCTGGTAAACTATAGATGA---CATGTGTGCTTTCATTGCCTAAACTCACTTTGTAGAACACCATTAAATGAAAATCATCA s panTro2.chrUn 47397580 193 - 58616431 GAACACATACCAAATTAGTCTTTGCTCCAGTCTCAAAATCTGAGATTAATTCTGGCTGCTGAAG-AAATTTTCCAGTGTTAGGAGTATGC-TTCAATGCTGGTGACCGGTACTACTTTCTGGTAAACTATAGATGA---CATGTGCGCTTTCATTGCCTAAACTCACTTTGTAGAAAACCATTAAATGAAAATCATCA i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189450825 193 - 189746636 GAACACATACCAAATTAGTCTTTGCTCCAGTCTCAAAATCTGAGATTAATCCTGGGAGCTGAAG-AAATTTTCCAGGGTTAGGAGTATGC-TTCTACGCTGGTGACCAGTACTACTTTCTGGTAAACTATATATGA---CATGTGCCCTTTCACTGCCTAAACTCACTTTGTAGAACACCATTAAATGAAAATCATCA i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141886466 184 + 163896628 GAACACATGTCAAATTAGCCTTGGTTTCTTTCTTAAAGGTTAGGATTACTTCCTGCCACTGAAG-AAATTGTTCAAGGTTCAGGCTATGC-ATCAG-GTTGGTGATTGG---TGCTCTCTGGTAAATTATAGATAATTTTAAGTGCCCTTTAGCAGACT-AACTCATTTGATGAAACACTACTAAATGAAA------- i oryCun2.chr14 C 0 I 18 s bosTau4.chr1 138176441 188 - 161106243 GAACAAAAACCAAATTAGCTCTTGATCCAACCTCAAAATCTGGGATAACTCCTGGCAACTAGAGAAAATATTCCGTGTTTAGGGATAGACATTCAAGCTTGATGACTGA---AACATTCTAGTGAAATATAGGTGGTGCCATATGCCCTCTCACTGCCTACATTCACTTTATATAACATTTTTAGATGAAA------- i bosTau4.chr1 I 142 C 0 s equCab2.chr26 13358170 186 + 41866177 GAGCACATAGCAAATTAGCCCTTGTTCCAACCTCAAAATTGGAAATAACTCCTGGCAGCTGGAG-AAATATCCCATAGTTAGAGATACGTATTCAAGGTTGATAATTGG---CACTTTCTGGTAAACTATAGATGATGCCATGTACCCTTTCACTGGCTAAACTCACTTTAGAAAACA--GTTAGATGAAAA------ i equCab2.chr26 C 0 I 10 s canFam2.chr31 14106795 191 + 42263495 GAAAATATACCAAATTAGCCTTTGTTCCAATCTCAAAATTTGGGATAACTCCTGGCAGCTGGAG-AATTGTTACATGGTTAGGGATATACATTCAAGTTTGATGATTGT---CAGTTTCTAATAAACTACAGATGATGGCATATACCTGTTTGTCACCTAAACTCACTTTCTAAACCACTGTTAAATGAAAATCA--- i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20602331 185 - 62548349 GAATGCATACCAAATCAGCCCTTGTTTTAACCTCAAAACTTGGAGTGAG----GGCAGCTGGAG-AAATTCTCTAGGGTTAGGAGTATGC-ATTAAGTATGGTGGTTGA---CATTTTCTGATAAACTATACATGA---TACCTACCCTTACATTGCCAAAATT-GCTTCATAAAATATTACTAAATGGAAGTTGTCA i loxAfr3.scaffold_13 C 0 I 15 e cavPor3.scaffold_34 15804219 1396 - 24440124 I a score=71552.000000 s hg19.chrUn_gl000245 1109 293 + 36651 ccagcaatttgggaggctaaggcgggcagatcatttgaggtcaggagtttgagaccagcctggccaacatgatgaaaccccgtctctactgaaaatacaaaaacttatccaggcatggcgggatgcacctggaatcccagctacttgggaggctgaggcaggaaaatcgcctgaacccaggatgtgaaggttgcagtgaacagagatgttgccattgcactccagcctgggcaacagagtgagacttc-atctccaaaaaaaggaaaaaaTGAGAGAGAGAGA--GAAAAAAAATT s panTro2.chrUn 47397773 292 - 58616431 ccagcaatttgggaggctaaggcgggcagatcatttgaggtcaggagtttgagaccagcctggccaacatgatgaaaccccttctctactgaaaatacgaaaacttatccaggcatggcgggatgcacctggaatcccagctacttgggaggctgaggcaggaaaatcgcctgaacccaagatgtgaaggttgcagtgaacagagatgttgccattgcactccatcctgggcaacagagtgagacttcaatctccaaaaaaaggaaaaaa-gagagagagaga---aaAAAAAATT i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189451018 294 - 189746636 ccaacactttgggaggctgaggcgggcagatcatttgagctcaggagatcgagatcagcctggccaacatgatgaaaccccatctctactaaaaatacaaaaacttatccaggcatggtgggatacacctgtaatccctgccactggggaggctgaggcaggagaatcacctgaacccaggatgtggaggttgcagtgaacagagatgttgcccttgcactccagcctgggcaacagagcgagacttc-atctcaaaaaaaaggaaaaaa-aaaaGAGAGAGACAGAAAGAAAATT i rheMac2.chr2 C 0 C 0 e bosTau4.chr1 138176629 0 - 161106243 C e loxAfr3.scaffold_13 20602516 15 - 62548349 I e oryCun2.chr14 141886650 18 + 163896628 I e canFam2.chr31 14106986 0 + 42263495 C e equCab2.chr26 13358356 10 + 41866177 I e cavPor3.scaffold_34 15804219 1396 - 24440124 I a score=-6996.000000 s hg19.chrUn_gl000245 1402 60 + 36651 ATCAGTGTTCAGTGACTCTTTGTTTTTCATGCTGATAAACTATTACGAAGAAAAAGAAAA s rheMac2.chr2 189451312 20 - 189746636 ATCAGTGTTCAGTGACTCTT---------------------------------------- i rheMac2.chr2 C 0 C 0 s panTro2.chrUn 47398065 60 - 58616431 ATCAGTGTTCAGTGACTCTTTTTTTTTCATGCTGATAAACTATTACACAGGAAAAGAAAA i panTro2.chrUn C 0 C 0 s bosTau4.chr1 138176629 21 - 161106243 ACCTGCGTTGAGTGACTTTAT--------------------------------------- i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13358366 6 + 41866177 ------------------------------------------------------AGTAAC i equCab2.chr26 I 10 C 0 s canFam2.chr31 14106986 21 + 42263495 ----------------------------GTGTTGAAAAACTATTTTTAA----------- i canFam2.chr31 C 0 C 0 e loxAfr3.scaffold_13 20602516 15 - 62548349 I e oryCun2.chr14 141886650 18 + 163896628 I e cavPor3.scaffold_34 15804219 1396 - 24440124 I a score=123772.000000 s hg19.chrUn_gl000245 1462 99 + 36651 TTTTCATGCTGATAAACTATTACACAGAAAAAGAAATGTATCCATTATGGACAATTAAAAGGGCTATACAATCTCTCTCATTGTATGATTCTAGTTTTC s panTro2.chrUn 47398125 99 - 58616431 TTTTCATGCTGATAAACTATTACACAGAAAAAGAAATGTATCCATTATGGACAATTAAAAGGGCTATACAATCTCTCTCATAGTATGATTCTGGTTTTC i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189451332 99 - 189746636 TTTCCATGCTGATAAACTATTACATAGAAAAAGAAATGGATCCATTATGGACAATTAAAAGGGCTACACAACCTCTCTCATTGTTTGATTCTGGTTTTC i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141886668 78 + 163896628 TTTTAATGCTAATAAACTGTTACATAGGA----AAATGTATTCATTATGGACACCTGAAAGAG--ACAAAAATTATTTCATCAT--------------- i oryCun2.chr14 I 18 I 3 s bosTau4.chr1 138176650 85 - 161106243 ---------TGACAAACTATTACACTGAAAATGTAATGTATCCATTATGAACACCTGAAAAAAATATATACCCTCTCCCACTATAGGATTCTGG----- i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13358372 99 + 41866177 TGTTTTTAATGACACACTATTACACAGAAAAAGAAATGTATCTATTATGGCCACCTGAAAGGAACATACAACTGCTCTCACTATATAATTCTGGTTTTA i equCab2.chr26 C 0 C 0 s canFam2.chr31 14107007 88 + 42263495 ---------TGACAAACTATTACACAGAAAAAGAAGTGTGTCCATTCTGGACACCTGAAAAGAATATATAACT--TCTTATTATAAAATTTTGGTTTTA i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20602531 94 - 62548349 TTTTAAGACTGATAAACTATCAGACAGAAAAAGAAATGTATTCACTATGGGCACCTGGAAGGAATACACAACTTCTCTCACTATTTGATTCTAG----- i loxAfr3.scaffold_13 I 15 C 0 e cavPor3.scaffold_34 15804219 1396 - 24440124 I a score=4684.000000 s hg19.chrUn_gl000245 1561 36 + 36651 TTTAtttttcttttctt------ttgttcttt--------ttttttttaa s panTro2.chrUn 47398224 34 - 58616431 TTTCtttttcttttctt------tttttc--t--------ttttttttaa i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189451431 44 - 189746636 TTTCATTTTCTTttctt------ttttttttttttttttgttttttttga i rheMac2.chr2 C 0 C 0 s equCab2.chr26 13358471 37 + 41866177 -----AACACAATTCTTAAATGATTGCTTCTT--------TTATTTTCAA i equCab2.chr26 C 0 C 0 e bosTau4.chr1 138176735 0 - 161106243 C e loxAfr3.scaffold_13 20602625 0 - 62548349 C e oryCun2.chr14 141886746 3 + 163896628 I e canFam2.chr31 14107095 0 + 42263495 C e cavPor3.scaffold_34 15804219 1396 - 24440124 I a score=47190.000000 s hg19.chrUn_gl000245 1597 202 + 36651 tacaggatctcactctctcacccaggctggaatgcagtggctctatcttgactcactgcaacctcagcctcctgggttcaagctattctcctgccttagcctcctgagtagctaggaataaaggcattcaccaccacg-ccagctaatttgtgtattttttttaa--tacaggtggcgttttgccatgttgcccaggctggtctt s panTro2.chrUn 47398258 200 - 58616431 gacaggatctcactctgtcacccaggctggaatgcagtggctctatcttggctcactgcaacctcagcctcccgggttcaagctattctcctgccttagcctcctgagtagctaggaataaaggcattcaccaccaca-ccagctaatttgtgta--ttttttaa--tacaggtggggttttgccatgttgcccaggctggtctt i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189451475 203 - 189746636 gacaggatctcactccgtcacccaggccagagtgcagtggcactgtcttggctcactgcaacctcagcctcccgggttcaagtaattctcctgccttagccttctgagtagctgggactgaagacattcaccaccacgcccagctaatttgtgta--ttttttaaattagaggtgggtttttgccatgttggccaggctggtctc i rheMac2.chr2 C 0 I 310 e bosTau4.chr1 138176735 0 - 161106243 C e loxAfr3.scaffold_13 20602625 0 - 62548349 C e oryCun2.chr14 141886746 3 + 163896628 I e canFam2.chr31 14107095 0 + 42263495 C e equCab2.chr26 13358508 0 + 41866177 C e cavPor3.scaffold_34 15804219 1396 - 24440124 I a score=36223.000000 s hg19.chrUn_gl000245 1799 80 + 36651 gaactcctgacctcaaatgatcctcccgcctcggcctccctaagtgttggcattacaggcataagccaccatgcttggcc s ponAbe2.chr3 159728676 62 - 202140232 ------------------gatcctcctgcctcggcctccctaagggctggcattacaggcataagccaccatgcttggcc i ponAbe2.chr3 N 0 C 0 s rheMac2.chr2 189451988 80 - 189746636 gaactcctgacctcaaatgatcctcccgcctcggcctcccaaagtgctggcattacaggcataagccaccatgcttggcc i rheMac2.chr2 I 310 C 0 s panTro2.chrUn 47398458 80 - 58616431 gaactcctgacctcaaatgatcctcccacctcggcctccctacgtgttggcattacaggcataagccaccatgcttggcc i panTro2.chrUn C 0 C 0 e bosTau4.chr1 138176735 0 - 161106243 C e loxAfr3.scaffold_13 20602625 0 - 62548349 C e oryCun2.chr14 141886746 3 + 163896628 I e canFam2.chr31 14107095 0 + 42263495 C e equCab2.chr26 13358508 0 + 41866177 C e cavPor3.scaffold_34 15804219 1396 - 24440124 I a score=55445.000000 s hg19.chrUn_gl000245 1879 48 + 36651 TGATTCTGTTTTTTAACACAATTCTTA-----TTACTTCTGTTTTAATTTTAC s panTro2.chrUn 47398538 48 - 58616431 TGATTCTGTTTTTTAACACAATTCTTA-----TTACTTCTGTTTTAATTTTAC i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189452068 48 - 189746636 TGATCCTGTTTTTTAACACGATTCTTA-----TTACTTCTCTTTTACTTTTAC i rheMac2.chr2 C 0 C 0 s ponAbe2.chr3 159728738 48 - 202140232 tgattctgttttttaacagaATTCTTA-----TTACTTCTGTTTTAATTTTAC i ponAbe2.chr3 C 0 C 0 s cavPor3.scaffold_34 15805615 48 - 24440124 TAATTGAGTTTTTTAGTTCAACTTTTA-----AATTATCAGTTCTTTCCTGAA i cavPor3.scaffold_34 I 1396 C 0 s oryCun2.chr14 141886749 46 + 163896628 --ATTCTGTTTTTTAATGCAGTTCTTA-----GATTATTTCTTCTATTTTAAC i oryCun2.chr14 I 3 C 0 s loxAfr3.scaffold_13 20602625 44 - 62548349 ---------TTTTTCACACaatttttaaattattatttatcttttattttCAC i loxAfr3.scaffold_13 C 0 C 0 s bosTau4.chr1 138176735 41 - 161106243 ---------TTTTAAACACAATTCTTA---CATTACTTCTCCATTATTTTCAA i bosTau4.chr1 C 0 C 0 s canFam2.chr31 14107095 39 + 42263495 --------------AAAACAATTCTTAAATCATTACTTCTCTTTTATTCTCAA i canFam2.chr31 C 0 C 0 e equCab2.chr26 13358508 0 + 41866177 C a score=706963.000000 s hg19.chrUn_gl000245 1927 402 + 36651 AAAGCCATA-GGTTTTTAATCTGGGAAACCTTTGAGAAAACATCCAGATAAATTTATAAATAGAAAAATAAA------------------------------------------------------------------------------------------TTCAGACAAATATAATTAAGTTTATGATCTAACAAGTGGGTGGCAACCG--AAAACTTTCCAAGTTCCA---TAAACTGAAGTGAAAGGATCACTTTCCTGAAAAT-ATTACAAAGGCTTGATAATTACCTGGATTGTACTAAAACCTACACAATCTAGTATATTC-TATAGCAGCAATTCATAAAGACAGCTTCACTTACCATGTAGAATTTATACATACATTAAATT----TAAGGAATGCGTTACTTGCTATTGGAGTAGGATAATAAACTCCCAGCAGAACTGATTTTCATGAATGCCTATTAAACTATCATTGATGTAGAAATTAAACAATATATTA s panTro2.chrUn 47398586 402 - 58616431 AAAGCCATA-GGTTTTTAATCTGAGCAACCTTTGAGAAAACATCCAGATAAATTTATAAATAGAAAAATAAA------------------------------------------------------------------------------------------TTCAGATACATAGAATTAGGTTTATGATCTAACAAGTGGGTGGCAACTG--AAAACTTTCCAAGTTCCA---TAAACTGAAGTGAAAGGATCACTTTTCTGAAAAT-ATTACAAAGGCTTGATAATTACCTGGATTGTACTAAAACCTACACAATCTAGTATATTC-TATAGCAGCAATTCATAAAGACAGCTTCACTTACCACGTAGAATTTATACGTACACTAAATT----TAAGGAATGCGTTACTTGCTATTGGAGTAGGATAATAAACTCCCAGCAGAACTGATTTGCATGAATGCCTATTAAACTATCATTGATGTAGAAATTAAACAATATATTA i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189452116 401 - 189746636 AAAGCCATA-GGTTTTTAATCTGAGAAACCTTTGAGAAAGTATCCAGATAAATTTATAAATAGAAAAATAAA------------------------------------------------------------------------------------------TTCAGATACATAGAATTAAGTTTATGATCTAACTAGTGGGTGACAACTG--AAAAATTTCCAAGTCCCA---CAAATTGAAGTGAAAGGGTCACTTTCCTGAAAAT-GTTAC-AAGGCTTGATAATTACCTGGATTGTACTAAAACCTACACAATCTAGTATATTC-TATAGCAGCAATTCATAAAGACAGCTTCACTTACCATGTAGAATTTATACCTACACTGAATT----TAAGGAATGCATTACTTGTTATTGGAGTAGGATAATAAACTCCCAGCAGAACTGATTTGCATGAATGCCTATTAAACTATCATCAATGTAGAAATTAAACAATATATTC i rheMac2.chr2 C 0 C 0 s ponAbe2.chr3 159728786 373 - 202140232 AAAGCCATA-GGTTTTTAATCTGGGAAACCTTTGAGAAAGCATCCAGATAAATTTATAAATAGAAAAATAAA------------------------------------------------------------------------------------------TTCAGATACATAGAATTAAGTTTATGATCTAACTAGTGGGTGGCAAATG--AAAAATTTCCAAGTTC-------------------------------CTGAAAAT-ATTAC-CAGGCATGATAATTACCTGGATTGTACTAAAACCTACACAATCTAGTATATTC-CATAACAGCAATTCATAAAGACAGCTTCACTTTCCATGTAGAATTTATACCTACACTAAATT----TAAGGAATGCATTACTTGTTATTGGAGTAGGATAATAAACTCCCAGCAGAACTGATTTGCATGAATGCCTATTAAACTATCATTGATGTAGAAATTAAACAACATATTC i ponAbe2.chr3 C 0 C 0 s cavPor3.scaffold_34 15805663 397 - 24440124 AAAGT-ATA-ATTTTTTAATCTGGGAAGTCTGTGAGAAAGCATCCAGATAATTTCACAAGTAAAAAAATAAA------------------------------------------------------------------------------------------CTTAAGTCTGTCAAATTAAGTTCAT-ATTTAACTGGTAGATAGTAACTG--ATAAGTTTTAAAATCCTACTCTAAAGTAAAATGAAAAGATTTCTTACTTTTAAAATGCTAA-GATATTGGAAAA-TGACTTGGATTATCTGAAATTCATGCAGTCTAGTATCTTCTTAATAAAACAATGTATAAAGTTAATTTCCCATTATGTATGAAATTTATATTTACTCTGTATTTAAATAAGGGATGCATTACTTGCTATTGGATAAGAATAATAGACTTCTACTAGAATCTGTTTGCA----TGCGTGTCATAATAGCAATGGT-TAAAAATTAAACAGTG----- i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141886795 391 + 163896628 AAAGTCATAGATTTTTTAGTTTAGGAGAGTTTTGAGAGA--ATC----TAATGTTATAAATAGTAAAATAGA-------------------------------------------------------------------------------------------TTAGGAATATAGAATTAAATAT-T-TTCTAAATAGCAAATGGCAAATG--ATAAGTTTTAAAGTCTAA---TAAACTAAAATGAAAGGATTACTTTCCAACAAAG-GTTGA-AATATTTGAAAACTACCTTGAATGTCCTAAAATACACACAATTTGATATATTA-TATGGTAGTAATTAGTAAAAGTAACTTCACATGCCATTTGGAGTATATATTAACACTGAATTTCAGTAAGGAATGCACTTTTTACTATTAGAGTTGAAAAATAAACCCTTCACAGAAATGATCTGCGTTATTGTATGTTAAAATACCATCGATGCAGAAATTGAACCAT------ i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138176776 462 - 161106243 AAAGCCATA--------------GAGGGACAC--AGGAAGCATCTAGATAAATTGATAAACAgaaaaacatgtatacctgtggtggattcattctgatatttggcaaaactaatacaactttgtaaagtttaaaaacagaaaaaaaagaaaagaaaaataaaCTCTGGCATGATGAAACAAGCCAGTGTTCCAACTAATAGATGGAAACTTAAACAAGTTTTAAAGTCATA---TAAACTGAAATGAAAGGATCACTTTCCTGAAAAG-GTTCA-AGTGCATGAAAATCACCTGGATTGTCCTAAGACCTGCACAGTCTGGAATATTC-TATAGCTGTAATTCAAAAAGATAACTTTATATACCATCTGGAATTTATCCTTACATTAAATTGAAGTAAGGAATGTA-CACTTGTTACTGGAGGAGAATGACAGACTCCCACC----------TGCATAAATGCCTATTAAAGTATCACTGATGTAGAAATT----ATTT----- i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13358508 380 + 41866177 AAAGCTACA--------------GGAGGGCTTTGAGAAAGCATCTATATAATTTGATAAACAGAAAAATTA-----------------------------------------------------------------------------------------------GGCATGCAGAATTAAACGAGTGATCCAACTAGTAGATGGTAAC----ATAAGTTTTAAAGTCCTA---CAAACTTAAACGAAAGGAACATTTTCCTGAAAAT-GTTAA-AATACTTAAAAATTTCCTTGACTATCCTAAAACTCATACAATCTGGAATATTC-TATAGCAGTAATTCAAGAAGATAGCATTACATACCATATGGTATTTATACTTACACTGAATTTAAGTAAGGAATGTATTGCTTGTTATTGGAGAAGGATAGTAAACTTCCATCAGAACCGATTTGCATGAATGCCTATCAAGATATCACTGACGTTGAAGTTAAACAATA----- i equCab2.chr26 C 0 C 0 s canFam2.chr31 14107134 382 + 42263495 AAAGCCATA--------------GAAGAACTTTGAGAAAACAACTAGATAATTTGATAAGTAGAAAAATAAA---------------------------------------------------------------------------------------------TGTCGGGATGTATTAAGTTAGTAATTTAATTAGTAGGTGGTAACTT--ACAAGTTTTAAAGTCCTA---TAAACTAAAACAAAAGGAATACTTCCCTGAAAAT-TTTTA-AACGCTTGAAAATTATATTGACTATCCTAAAACCCACACAATAAAATATATTC-TATAGTAGTAATTCAAAAAGATAGCTTTACATATCATAAGGAATTTATATTTATATTGAGTTTAAGTAAGGAGTAGATTCCTTGTTATCGGAAGAAGATACTAAACTCACACTAGAACTGATGTGCGTGAAT-CATGTTGGAATAAC-TTGATGTAGAAATTAAACAACA----- i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20602669 397 - 62548349 AAAATCATA-AGTTTTAAACCTGGGAGGGTTTTGAGTATATATACA-ATTATTTTATAAACAGACAAATAA-------------------------------------------------------------------------------------------TGTAGCCATGGAGAATGGAATTAGTGAGTCAACTAGCAGTTGGCAACTT--TTAAGCTTTAAAGACCCA---TAAACTGAAATGAAAAGAACATTTTCCCGAAAAT-CTTGA-AAGGCTTTAAAATTACCTGGAGTGTCCTAGAACCCACACAGGCTGGTATATTA-TATAGAAGTTATTCATAAAGACAGCTTTACATACCATATGGAATTTATACTTACACTGAATTTACATAAGGAATGCATTAATTATTATTGGAAAGAGATAGTTCACTT----CAGAATGTATTTGTATGAATGTCTGTTAAAATATTATTGATGAAGTAATTAAATAATatat-- i loxAfr3.scaffold_13 C 0 I 849 a score=1648457.000000 s hg19.chrUn_gl000245 2329 1029 + 36651 AGCTATTCAGACCCAGAT-TGTGAGAGACAGAGAAAAACTTCAAAAAAGTTCAGCTACCAAATCCCTTC---CTC-AATAGCTCTTTGAGTCTCAAGACAGTTTCAACCA-CAC-AC--ATCCT-CAGAGTCTTATGGTCCAAACAACATTTGACTGCAGCTCTAA------AGTAAGCAAACATTTGAAAAGA---AA-----C--TCAAAGATCTATACCTGTAGTTATGGTCAAGGAGGTCCACCTACTGGTGGGTGAGC--ATGGCAAGGATAGGGACTAAGCCAAATGATGG---GTTTACCAAAACAGAAACAAGAGAAGTCATTGGAAGCAC-------AGTCCAGGTTATAACAGGAGCCCAGGCACTTGATGTGGG----A-ACCCTATTTGTCTCATTCAGCACCTAGA-GTTTTAACGTCCTATGAGG-CACAGCTAA------------------TGC--C----------------CTTCA-----TTAT------TTTTTTGTAATTGACTGCATAGTTTAGAACTATGCCTTGAATTTAATATCTATCTGTTGAATAAATGAATtaataatgatg----aaaatctgtccacaggttatgtgcagtactgaagagtaacttcagctattgaggtatctatcagaagtcttactctccaaaaagcctctggttagttactg--atatacgttgctgataatttcactctcacaatgtaggggaagcaggaatgttatctgacctCTTGGCTCCTCTTCCTTTGCCTTCCACAGATCTCTCTGCT--GGTTCACAGAGGAACACTTTCGTGGCTCTCAGTTCATTTTGCAATTCTGCTAGAATCTCATT-CCATCCTCAGTTGTAACTACCTTGTCCTTCACCCAATGCTTATTT----ACGGAGGGACAGATAGC--AAGAAGAAATCGCACTCTGGATTACAAAG----TGGGAAGACGCACCCCTTGG-CCAGAATGcctgcctcctatgttcatgaaggatatttctaattgatctcggcactct-tttccattgagcccATGTCCCAAATTGGCCGTGAGTTAGGGAGAGGGCTCTAGAGTGGG-AAAGGTGT--ACCCAAA-ACTTCCCTAATCTGACTATCAACCC s panTro2.chrUn 47398988 1032 - 58616431 AGCTATTCAGCCCCAGATGTGTGAGAGACAGAGAAAACCTTCAAAAGAGTTCAGCTACCAAATCCCTTC---CTC-AATAGTTCTTTGAGTCTCAAGACAGTTTCAACCA-CAC-AC--ACCCT-CAGAGTCTTACGGTCCAAACAACATTTGACTGCAGCTCTAA------AGTAAGCAAATATTTGAAAATA---AA-----CAATCAAAGATCTATGCCTGTAGTTATGGTCAAGGAGGTCCACCTACTGGTGGGTGAGC--ATGGCAAGGATAGGGACTAAGCCAAATGATGG---GTTTACCAAAACAGAAACAAGAGAAGTCATTGGAAGCAC-------AGTCCAGGTTATAACAGGAGCCCAGGCACTTGATGTGGG----A-ACCCTATTTGTCTCATTCAGCACCTAGA-GTTTTAACGTCCTATGAGG-CACAGCTAA------------------TGC--C----------------CTTCA-----TTAT------TTTTTTGTAATTGACTGCATAGTTTAGAACTATGCCTTGAATTTAATATCTATCTGTTGAATAAATGAATtaataatgatg----aaaatctgtccacaggttatgtgcagtactgaagagcaacttcagctattgaggtatctatcagaagtcttactctctaaaaagcctctggttagttactg--atatacgttgctgataatttcactctcacaatgtaggtgaagcaggaatgttatctggcctCTTGGCTCCTCTTCCTTTGCCTTCCACAGATCTCTCTGCT--GGTTCACAGAGGAACACTTTCGTGGCTCTCAGTTCATTTTGCAATTCTGCTAGAATCTCTTT-CCATCCTCAGTTGTAACTAGCTTGTCCTTCACCCAACGCTTATTT----ACGGAGGGACAGATAGC--AAGAAGAAATCGCACTCTGGATTACAAAG----TGGGAAGACGCACCCCTTGG-CCAGAATGCCTGcctcctatgttcatgatggatatttctaattgatctcggcactct-tttccattgagcccaTGTCCCAAATTGGCCGTGAGTTAGGGAGAGGGCTCTAGAGTGGG-AAAGGTGT--ACCCAAA-ACTTCCCTAATCTGACTATCAAGAC i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189452517 1009 - 189746636 AGCTATTCAG-CCCAGATGTGTGAGAGACAGAGAAAAATTTCAAAAGAGTTCGGCTACCAAATCCTTTC---C---------TCTTTGAGTCTCAAGACAGCTTCAACCA-CAC-AT--AGCCT---GAGTCTTATGGTCCAAACAACATTTGATTGCAGCTCTAA------AGTAAGCAGACATTTGAAAAGA---AA-----C----AAAGATCTATGCCCATAGCTACAGTCAAGGAGGTCCACCTACAGGTGGGTGACC--ATGGCAATGATAGGGACTAAACCAAATGGTGC---GTTTACCAAAACAGAAACAAGAGAAGCCACTGGAAGCAG-------AGTCCAGGTTATAACAGGAGGCCAGGCACACGATGCGGG----A-ACCCTATTTGTCTCATTTAGCAGCTAGA-GTGTTAACATCCTATGAGG-CAGAACTAA------------------TGC--C----------------CTTCG-----TTATTATTTATTTTTTGTAATTGACAGTATAGTTTAGAACTATGCCTTGAATTTAATATCTATCTGTTGAATAAATG----AATAATGATG----AAAA----TCcacaggttatgtgcagtactaaagagctacttcagcta-cgaggtagctattagaagtcttactctctaaaaagcctctggttaattattg--atacaggttgctgacaatttcactctcactatgtaggggaagcaggaatgtgatctggcctctcgactCCTCTTCCTTTGCCTTCCACAGCAATCTCTGCT--GGTTCACAGAGGGACACCTTCGTGGCTCTCAGTTCATTTTGCAATTCTGCTAGAATCTCGTT-CCATCCTCAACTGTAACCAGCTTGTCCTCTGCTGAACACTTATTT----ATGGAGGGGCAGATAGC--AAGAAGAAATCGCACTCTGGATTACAAAG----TGGGAAGACGCACCCCTTGG-CCAGAATGTCTGcc-ccggtgttcatgatggatatttctcattaatcttggcactct-tttccattgaacccaTGTCCCAAGTTGGCCCTAAGTTAAGGAGAAGACACTAGGGAGGG-AAAGGTTT--ACCCAAA-ACTTCCCTAAT----CTATCAAACC i rheMac2.chr2 C 0 C 0 s ponAbe2.chr3 159729159 1031 - 202140232 AGCTATTCAGCCCCAGATGTGTGAGAGACACAGAAAAATTTCAAAAGAGTTCGGCTACCAAATCCCTTC---CTC-AATAGCTCTTTGAGTCTCAAGACAGTTTCAACCA-CAC-AC--AGCCT-CAGAGTCTGATGGTCCA---AATATTTGACTGCGGCTCTAA------AGTAAGCAAACATTTGAAAAGA---AA-----C----AAAGATCTATGCCTGTAGTTACCATCAAGGAGGTCCACCCACTGGTAGATGACC--ATGGCAAGGATAGGGACTAAGCCAAATGATGG---GTTTACCAAAACAGAAACAAGAGAAGCCATTGGAAGCAG-------AGTCGAGGTTATAACAGGAGTGCAGGCACTTGATGTGGG----A-ACCCTATTTGTCTCATTTAGCAGCTAGA-GTTTTAACATCCTATGTGG-CAGAGCTAA------------------TGC--C----------------CTTCA-----TTATTATTTATTTTTTGTAATTGACTGCATAGTTTAGAACTATGCCTTGAATTTAATATCTGTCTGTTGAATAAATGAATtaataatgatg----aaaatctgtccacaggttatgtgcagcactgaagagcgacttcagctattgaggtatctagcagaagtcttactctctaaaaagcctctcgttaattactg--atataggttgctgacgatttcactctcacaatgtaggggaagcaggaatgttatctggcctCTTGGCTCCTCTTCCTTTGCCTTCCACAGCTCTCTCTGCT--GGTTTACAGAGGGACACTTTTGTGGCTCTCAGTTCATTTTGCAATTCTGCTAGAATCTCATT-CCATCCTCAACTGTAACCAGCTTGTCCTCCACCCAGCGCTTATTT----ATGGAGGGACAGATAGC--AAGAAGAAATCACACTCTGGACTACAAAG----TGGGAAGACGCACCCCTTGG-CCAGAATGCCTGcctcctatgttcgtgatggatatttctaattgatcttggcactct-tttccattgaacccaTGTCCCAAGTTGGCCCTGAGTTAGGGAGAGGACTCTAGAATGGG-AAAGGTGT--ACCCAAA-ATTTCCCTAATCTGACTATCAAGCC i ponAbe2.chr3 C 0 C 0 s cavPor3.scaffold_34 15806060 951 - 24440124 ---CATACAGGCTCTAATATATGAGAGATAGGAAAAA--TTCAAAA----CTGGCCATTAAAATTTCTGTTTTTC-GAAAGGT-TTTGA--CACAAGATAATTGCAGCTAATAA-TA--GGCCT-C--AGTCTGATGATTGAAACCACATTCTACTGCATCT----------------TAGACATTTGAAAAGC---AG-----C----AAAGACCTCAACAGG-TGTTACCGTGAGGAAGGTCTCCCCTCAGATGGGGCAGCCTATGAGAAAGGAAGGGAATTAGCCAAATGAC-----------------AAGTACTAGA-AACATATCAGAAGCAG-------AGATGCAGTTACAACAGGATCATAGGCACATCACCTGGG----A-TCTCTATTTATCTC-----------AGT-ATTTTAGCATCCTAAAAAT-CAGAGGCAG------------------TGATGT----------------TTTTC-----TTCT------ATTTTTCGACTTTCCTGTATAGTTGAGGACTATGCCTTGATTTTTGTATCTACTTGTTGAATAAATTAATAATTGATTGTGACT-AAAACCTGCC--TAAGTCTT--------TCATAgggggactgcagccaggaaggtatctattagaaggctta--ttttaaagagcttctgattaaatattg--ataagtgttgccaacaatctccttcttacaagacagagagagcagtgaggTTAGTTGGCCTCTTAGCTCCT--TCCTTTCTCTTCTACAGCACTCTGGCCT--GGCCCACAGAGTGACACTTCTGGGCCTCTCAATTGATTTTGCACTTT----------CCTCT-TCATCCTCAAGTGTCACAA-GTTTTCTTCTACCCAACACTCATTCTTAAAAAAAAAAAAAAATAGGGAAAGAAGAGATCATATTCTCAATTGCAAAG----GGGAAAGAAACATGGTTTGG-CCAGAA---TTACCACGAG---CCATGGTGCATATTTCTAATTG-TCTTACCACAAT-TTTTCACTGAACCCTTGTTCCAAGTAGGCCCTAAATT----AGAGGATTT-----------TTTTTTTAAATCACAATACCTCCCTAACCTAACTCCCAAACT i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141887186 935 + 163896628 -------TAGCCTCAGATGTGTGATAGATAGAAAAAG--TTCAAAGGTGCTTGACTACCAGGCTCCATG----------------TTGA--ATCAAAACACGGTCAGCCATCACTTA--AGTCT-CAAAGTCTCATGGTCCAAACCATATTCTATTGCCGTTCTAA------GGTAACCAGACATTTGAAAAGA---AA-TAACC----GAAGATCTATACAGGTTGATATGGTGAGGGAAGTCCACCTCCAAGTGAGCGAGCC-ACGGTAGCAGCAGAAAATGAGCCAAATGATGC---ACTGACCAA---AAGAACAAGAGAAGACATTAGAAGCAGTCCCTGATGGTGCA--TGGTACATGTGCATGTACACAGCA--TGGA----G-TTCCTGTTTGTCTCTGTTAGCAGCGAGG-GTGTTGGTGTCCTTTGAGT-CAGAGGCAG------------------TGC--C----------------CTTTG-----TTTT------ATTT----AACTCCCTTCATAGTTTAGGTCTAAGCTTTGAATTT------TATTTGTGGAATACATGAATAATTCATAATATCTAAAAATCTGTC--TAGGTCCTGGGtggtactaaggagggactattg------aagtgtctgttagaagtcttactctctaaaaagcttctgattaattattg--atatgtgttgccgactgtttcactttcccaagac----agagCAGGGAGGTTATCTGGCCTCTTCACTGCT----CTTTGTCTT---------------CT--GGCCCACAGGACAATGCTTTGG---------ATTCATTTTACACTTTTGCTACTATCTCTGT-CCATCCTCAAGTGTGACCATGTTGTCCTCTGCCCAGCAATCATTC----AGAGAGCTACAGACAGG--AGGAAGAAGTCACG--CTAGACTACAGAG----AGGAAAAAGGCAACTTTTGG-CCACCA---CTGCCTC------------TGGGTGTGTCTAGTTGAACCCTGTGCTCT-TTGTCATTGAGCCA-TGTCCCACATTGGCCCTTAGTC----ACAGGACTC-----------ATTGTCT--ATCCAAATGCTTCTCTAATCTAATTACTAAGCC i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138177238 976 - 161106243 ---TTTTCAGCCCCAGATGCATGAAAGACAGA---AAATTTCAAAGCAGTGTGGCTACTAATTTCCTTC---TTT-CACAGGACCTTGA--CTTGAGACAACTTCAGCCATTAC-TT--ATCCT-TA-AATCTCATGTTCCAAACTACACACTATCGTGGCTTTAA------GTTAACTAGAAATTTAAAAACA----------------AGTATCTAGATAGGTAGTTACAGTGAAGGACATGAATCTACAAGTAAGTTGGCC-ATGTGACGGATAGGGAGTGAGCCAAACGACAGGCAAGTT------ACAAGAGCAAGGGAACAGATC-ACCACAG-------AGTTCCAGTTGTAATTAGAGCCCAAGTATATGACATGGG----A-TCCCTATTTTTCT--GTTAGCACCTAGG-ATTTTAATATCCTCAGAGC-CACAGAGAG------------------C---------------------CTTCAATTTTTCTT------TTAAATTTAATTCCCCACATGCTTGAGGACT-----TTGAACTTAATATCCATTTGTTGACTAAATGAATAATTAATGGTGACT-aaaacctgtccacaggtcatgtgtaatactgaggag-gacttcagctattaaagtatctattagtagtcttactttctaaaaagcctctaattaattattgatatatatattgctgacaagttcactctcacaaggtagagaaagcgctgagg-------TTCTCTTGGC----CTTCCTCTGCCTTCCACAGCCCTCTCCCCT--GGTCCATAAAGGGACAGCTTTGTGGCTCTCAGCTCATTTC-CACTCCTGCTAGACCCTCTTTAACATTCTCCAGTATAGCCAGCTTCACTTCTCCCCAACTCTCG-GG----GTGGGGTGAGGGGAAGC--ATGAAGAAATCCCACTCTAGATGACAAAGTTTCAGAAAATAAGCACTATTTGGGCCACCAT-ACTGTCTCCTAAGCTTG-ACCAAGCATT-----------TCAACACTGTTTTTCCATTGAGCCCACATCCCAAATTGGCCCCAAGTTGGACATAGGAATAAAGACTGGAAAATTCCTT--ACCC-AA-ACTTCctt----------------- i bosTau4.chr1 C 0 I 295 s equCab2.chr26 13358888 1027 + 41866177 ---TATTCAGCCCCAGATGTGTGAAGAACAGAGAAAACTTTCAAAGGAGTTTGACTACTAAATTCCTTC---CCC--AACGGTCTTTGA--GTCAAGACAGGTTCAGCCATTAG-TT--ATCTT-CAGAGACTCATGTTCCAAACCACATTCTATTGCAGCTCTAA------AGTAACCAGACATCAAAAAAGAAACAAACAACC----TACAATCTCAGTCGGTAGTTATTGTGAGAAAGTTCCATCCACAGGTGGGCTGGCC-ATGGCAGGCGTAGGGAA-GAACCAAACGAGAGGCAAGTGACCAGAACAAGAATAAGGGAACAGGTCAGCAGCAG-------AGTCCCAGTTATGACTAGAGCCTAGGTTTATGACATAGG----A-TCCCTATTTTTCTTAGTTAGCTGATAGG-ATTTTAATGTCCTATGAGGCCCCGGACTG------------------TGC--CGTTTCGGTACCTAGCGCTTCG-----TCCT------CTAGGTTGAA--------ATAGTTTAGGACTATGCTTTGAACTTAGTACCTATTTGTTGAGT-AATGAATAATtaatagggact-aaaatctgtccacaggtcatgtgaagtactgaggagggacttttgctattaaggtatctattagaagtcttagtttctaaaaagcctctaattaattattg--atatgtattgctgacaattttactctcacaaggtagagaaagcaatgagg--------------gatcctgctttctctgCCATTCACAGCTCTCTCTCCTCGGGTCTATAGAGGAATGCTTCTGTGGCTCTCAATTCATTTTTCACTTCTCTTAGAACCTTTTT-CCATCATCCAGTGTAACCAACTTGTCCTCTGCCCAACATTCACTC----ACAGAGGGACAAACAGT--GAGAAGAAATCACACTCTAGATGACAAAG----GGGAGAGAAGCATCGCTTGGGCCAGAATAACTATCTCCTAGGCTCA-AAGGGATATTTCTGCTGGATCTCAGGACCAT-------TTGAGCCCATGCCCCAAACTGGCCCTGAGTTAGGTAGAGGAATAAAGAGTGGGAAATTGTTT--ATCCAAA-ACTTTCCAAACCACACTATCAAGT- i equCab2.chr26 C 0 C 0 s canFam2.chr31 14107516 1010 + 42263495 ---AATTCAGCCCCAGATGTGTGAAGAATAAAGACAATTTTTA----AGTTTGGCCACTAAGTTCCTCC---CCTAAAAAGGTCTTTGA--GTCCAGACAGTTGCATCCATTAC-TCAGAGCCT-CAGAGCCTCATGTTTCAAAGTACATTTTCTTGCAGTTAT-A------AGTAATCAAATATTAAAAAAGG---AAATAATC----AAAGACCAAAATAGGTAGTTAGGGTGACAGAGTTTCATCCACAGGTGGGTTTACT-CTGACAGAAGTACGGAGTGTGCCAAATGATAG--------CCAGAACAAGAACAAGGAAACTGATC-TCAACAG-------AGTCTCAG-TAGAACCGGAACC-AGGTATA-GACATGGAATCTA-TCCTCATTTTTCTCACTTAGCAGCTAGGTTTTTTAATGTCCTATGAGG-CAGGGAGAG------------------TGC--C----------------CTTCA---TTTCTG------TTTGATTTAATT-CCTGCATAGTTTAAGACTATTCCTTCAACTTAG---CTGTTTGT--------TGAATAATTAATgatgact-aaaatctgtccacaggtcatgtgtagtactgaggagagacttcagctattaaggtatctattagaagtcttaccttttaaaaagcctctaattaattattg--atatgtatcactaacaatttcactctcacaaggtagagaaagcagtgaggTTATTTGGCCTCTTGGCTTCTCTTCCTTTGCCTTCCACAGCCCTCTCTCCT--GGTTCACATATAGGCAATTTTGTGACTTTCAATTTATTTTGCACTTCTGCTAGAACCTCTTT-TCATCCTCCAGTCTAAGCAACTTGTCCTCTGCCCAACATTCACTC----ATAGAAGGACAATCAGC--AAGAAG---TCACACTCTAGATA--TAAG----AAGAAAGAAGCACCACTTGGACTAGAAGGACTATCTCCTATGCTCA-AATGAGTATTTCTGCTGGATCTCAGCACTGT-TTTCCATTGAGCCCATGTACCAAATTGGCTCTGAATTAGGTA---GAATAAAAAATTGGAAATTGTTT--ATCCAAA-AATTCCCTATTCAAACTGCCAACTC i canFam2.chr31 C 0 I 258 s loxAfr3.scaffold_13 20603915 1048 - 62548349 aacaaTTCAGACCCAGATGTGTGAAAGGCAAA--AATTTTTCCAAGGAGTTTGGCTACTAAATTCCTTC---ATC-AAAAGGCCTTCAA--ATCAAGACAGTTTCAGCCATTAC-TT--AGTCTTCAAAGTTTCATGTCCCAAACCACATTATACTGCAGCTGTAAAACATTAGAAAACAAACAAACAAAAAGG---CA---ATC----AACAGTCTAGGCAGGTAGTTATAAT----GAGGTCTATCCACAGGTGGGTAGGC--ATGGTAAGGGCAAGGGACAAGTCAATTTATAGGTAGGTTACCAAAACAAGAACAAGGGGACAGATGAGAAACAG-------AGTCCTGGCTGTAACTGTAGCCCAGGTACAGGATATGGA----GCTTCCAATTTGTGTTAGTTAGCAGCTAGG-GTTTTAAAATCCTGTGAGG-TAGAGAAAGAGTCTGCCCATCCTTTTTTGC--T----------------TTTGT-----TTTT------TTCTTTTTAATTCCCTGCATAGTTTAGGACAGTGCCTTTTGCTTAGTATCTATTTGTTGAATAAATGAATAATGAAGGATGACT-AAAACCCACTAGTGGGTCATGtgtagcagtgaggagtgcctttagctattgaagtatctattacaagtcttactctctaaaaagcttttgattaattattg--atatgggctgctgaaaatttcactctcacaaggcagagaaagcagtgaggttacctggcctcttgacttCTTTTCCT-----TTCTGCAGCCCTCTCCCCT--GGTTCACAGAGGGACAATTTTGTGCTTCTCAATTCATTTTGAACTTCTGCCAAAATATCTTT-CCACCATCAACTGTAACCAATTTGCCCTCTGCCCAACACTCACTT----GCCCAGGGACAGATAGC--GAGTAGAAGTCACACTCTAGATTACAAAG----AGGAAATAAGTATCACCCAA-GCCTGATGGCTGCCTCCTTTGCTCACGATGAATATTTCCCATTGATCTCAGCACTCT-TTTCCATATGGCCCATGTGCCAGATTGGCC--AAGTTAGATAGAGGAATA-AGAGTGGAAAATATGTT--ATCCAAA-ACTTCCCTTGCCTAAACACCAGGCT i loxAfr3.scaffold_13 I 849 C 0 a score=56272.000000 s hg19.chrUn_gl000245 3358 39 + 36651 TAAAAAATTAAACTTTCAATTCAACATCCCTTGTTTCTC s panTro2.chrUn 47400020 39 - 58616431 TAAAAAATTAAACTTTCAATTCAACATCCCTTCTTTCTC i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189453526 39 - 189746636 TAAAAACGTAAACGTTCAATTCGACATCCCCTGTTTCTC i rheMac2.chr2 C 0 C 0 s ponAbe2.chr3 159730190 39 - 202140232 TAAAAAATTAAACTTTCAATTCAACATCCCTTGTTTCTC i ponAbe2.chr3 C 0 C 0 s cavPor3.scaffold_34 15807011 39 - 24440124 GAATAAACAGCACACTCCTGCCAACAGCCCTCATTTCTC i cavPor3.scaffold_34 C 0 I 71 s oryCun2.chr14 141888121 27 + 163896628 AAACAAATCAAACATT-----------CTCTCCTTTCC- i oryCun2.chr14 C 0 C 0 s equCab2.chr26 13359915 39 + 41866177 GAATGAATTAAACGCTCAATTCACCATCCTTTGTTTCTC i equCab2.chr26 C 0 C 0 s canFam2.chr31 14108784 39 + 42263495 AAACAAACTAAATGCTCAACTCACCATCCTTTGTTTCTT i canFam2.chr31 I 258 C 0 s loxAfr3.scaffold_13 20604963 39 - 62548349 GAACAAATTAAATGATGAAATCAACATTCCTTGTTTCTC i loxAfr3.scaffold_13 C 0 C 0 e bosTau4.chr1 138178214 295 - 161106243 I a score=89902.000000 s hg19.chrUn_gl000245 3397 92 + 36651 CAACTTGGAGTGCCTGATGGTGTGGGAAGCCCCTACTC------ATAAAAATTCATAGTTGAAGATTGTTGGTAATTTTGCCCAACCTTCttcttttc s panTro2.chrUn 47400059 90 - 58616431 CAACTTGGAGTGCCTGATGGTGTGGGAAGCCCCTACTC------ATAAAAATTCATAGTTGAAGATTGTTGGTAATTTTGCCCAACCTCCttcttt-- i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189453565 86 - 189746636 CAGTTCAGAGTGCCTGACGGTGTGGGAAGCCTCTACTCACAAAAATAAAAATTCATAGTTGAAGATTGTTGGTAATCTTGCTCAAC------------ i rheMac2.chr2 C 0 C 0 s ponAbe2.chr3 159730229 81 - 202140232 CAGCTCGGAGTGCCTGATGGTGTGGGAAGCCCCTACTC------ATAAAAATTCATCATTGAAGATTGTTGGTAATTTTGCCCAACT----------- i ponAbe2.chr3 C 0 C 0 s oryCun2.chr14 141888148 78 + 163896628 CTAGTAGGAGC-CCTGGTGGTCTTGCAAGCCACTGTTC------ATCAAAACTCATCTTTAAAAACTGTTAGTAAT-TTGCCCAAA------------ i oryCun2.chr14 C 0 C 0 s equCab2.chr26 13359954 75 + 41866177 CATCTTGGGATGCTTGACAGTGTTGGAAG-CTCAACGC------ATAACAACCTATAGTTCAAAGTTGCTAGCAGTTTTGAC---------------- i equCab2.chr26 C 0 C 0 s canFam2.chr31 14108823 78 + 42263495 CATATCAGGATGTTTGATGGTGTTGGAAG-CTTGACTC------AAAACAACTCATAGTTCAAAATTGTTAGCAAC------CAACCTTCT------- i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20605002 92 - 62548349 CATCTCAGAGTGTCTGATGGTGTTGGAAGCCCCTACTC------ACGACGCTTCACAGTTGAAAATTCATAGTAACTCTGCCCAACTTCCTTCTCTGC i loxAfr3.scaffold_13 C 0 C 0 e bosTau4.chr1 138178214 295 - 161106243 I e cavPor3.scaffold_34 15807050 71 - 24440124 I a score=29049.000000 s hg19.chrUn_gl000245 3489 322 + 36651 tttttattctactttaagttctagggtacatgtgcacaacgtgcaggttcattacatatgtatacatgtgacatgttggtgtgttgcacccattaactcgtcatttacattaggtatatcccctaatgcttttcctcccctagcccgtcaccccacaacaggtcccggtgtgtgatgttcccctttctgtgtccatgtgtactcattgtttaattcccacctatgagtgagaacatgtggtgtttgtttttttgtccttgtgatagtttgctgagaatgatggtttccagcttcatccttgtccctacaaaggacatgaact s panTro2.chrUn 47400149 322 - 58616431 tttttattatactttaagttctagggtacatgtgcacaacgtgcaggttcattacatatgtatacatgtgacatgttggtgtgctgcacccattaactcgtcgtttacattaggtatatcccctaatgcttttcctcccctagcccgtcaccccacaacaggcaccagtgtgtgatgttccccttcctgtgtccatgtgtactgattgtttaattcccacctatgagtgagaacatgtggtgtttggttttttgtccttgtgatagtttgctgagaatgatggtttccagcttcatccttgtccctacaaaggacatgaact i panTro2.chrUn C 0 C 0 e ponAbe2.chr3 159730310 0 - 202140232 C e bosTau4.chr1 138178214 295 - 161106243 I e loxAfr3.scaffold_13 20605094 0 - 62548349 C e oryCun2.chr14 141888226 0 + 163896628 C e canFam2.chr31 14108901 0 + 42263495 C e equCab2.chr26 13360029 0 + 41866177 C e rheMac2.chr2 189453651 0 - 189746636 C e cavPor3.scaffold_34 15807050 71 - 24440124 I a score=10842.000000 s hg19.chrUn_gl000245 3811 118 + 36651 catcatttttatggctgcatagtattccatggtgtatatgtgccacattttcttaatccagtctatcattgttggacatttgggtt------------ggttccaagtctttgctattgtcagtagtgcc s panTro2.chrUn 47400471 118 - 58616431 catcatttttatggctgcatagtattccatggtgtatatgtgccacattttcttaatccagtctatcattgttggacatttgggtt------------ggttccaagtctttgctattgtcagtagtgcc i panTro2.chrUn C 0 C 0 s bosTau4.chr1 138178509 92 - 161106243 CATCCTTTTTAT---------TTGTCTCACAGTG-----GTGCCTCAT-------------------GGTGCTGGAAGCTTGACTTATGACAACCCAGAGTTCAAAATCATTGCCATT-TTACCAG---- i bosTau4.chr1 I 295 C 0 e ponAbe2.chr3 159730310 0 - 202140232 C e loxAfr3.scaffold_13 20605094 0 - 62548349 C e oryCun2.chr14 141888226 0 + 163896628 C e canFam2.chr31 14108901 0 + 42263495 C e equCab2.chr26 13360029 0 + 41866177 C e rheMac2.chr2 189453651 0 - 189746636 C e cavPor3.scaffold_34 15807050 71 - 24440124 I a score=482773.000000 s hg19.chrUn_gl000245 3929 329 + 36651 tcaataaa--cTCCTTCTTTCTTTGCCTAGTTACAC--CTCAATGCAACCTGCTGGCAGGCCAGCCTTAAGCCCAGCAGTCCAACCATGCATCTAAGCTGAGTTCTCATCAGAGCCAACTTCAATTATAA-----ACAACTGAGATGATGCCAGAGGCCAGAATCCCTGAGAACCCAATTTGCTGTCATCACCACAGCT-------GAAACAAGGC--------GCTTGGCATCTAGAAAAGCTGATCTGTAGGAAATTTCCAATAG--AGTTCAAGTTTTTCTAAGTT-TAAAGTGTACAATA-TCATCAAGGTGAGACACTCAAGATAAAACTAGGCTTGTGtttaaatataata s oryCun2.chr14 141888226 315 + 163896628 -------------CTACTCTCTCTGCCTAGTTATAC--CTCAGGGCAACCTCTTAGCAGGTAAACCTGAAACCTACCTGTCCAATCAGAGATCTAAACTGGTTCTTCCTCATAGTCAGCTTACATTACAA-----CTAAGCAAGAGCACATGAGCGGCTGTAACCCCAGAAGACCTGACTTGCAGCCCTCATGGTAGCT-------AAAACAAGAA--------CTATAGCAACCAGAAAAGTTGAAATGTAGGCAAAGCCCAATAG--AAATCAATTTTTTGTTTCTT-TAAAATTTGC---A-TGATCAGGATCACACACGTGAGATAAAATTAGACTTATATTTAATTGGGATA i oryCun2.chr14 C 0 C 0 s ponAbe2.chr3 159730310 320 - 202140232 -----------TCCTTCTTTCTTTGCCTAGTTACAC--CTCAAGGCAACCTCCTGGTAGACCAGCCTTAAGCCCAGCAGTCCAACCATGCATCTAAGCTGAGTTCTCATCAGAGCCAACTTCAATTATAA-----ACAACTGAGATGATGCCAGAGGCCAGAATCCCTGAGAACCCACTTTGCTGCCATCACCATGGCT-------AAAACAAGAC--------TATTGGCATCTAGAAAAGCTGATGTGTAGGAAATTTCCAAAAG--AGTTCAATTTTTTCTAAGTT-TAAAGTACACGATA-TCATCAAGGTCAGACACTCGAGATAAAACTAGGCTTGCATTTAAATAGAATA i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189453651 318 - 189746636 ----------CTCCTTCTTTCTTTCCCTAGTTACAT--CTCAAGGCAACCTCCTGGCAGGCCAGCCTTAAGTCCAGCAGTCCAACCATGCATCTAAGCTGAGTTCTCATCAGAGCCAACTTCAATCATAA-----ACAACTGAGATGATGCCAGAGGCCAAAATCCCTGAGAACCCAATTTGTTGTCATCACTGTGGCC-------AAAACAACGT--------GCTTGGCATCTAGAAAAGCTGATCTGTAGGAAATTTTTAATAG--AGTTCAATTTTTTCTAAGTT-TAAAGTGTACAAT----ATGAAGATCAGACACCTGAGATAAAACTAGACTTGCATTTAAATAGAATA i rheMac2.chr2 C 0 C 0 s bosTau4.chr1 138178601 308 - 161106243 -----------GCCTTCTCCTCTTGTCCAGTTACAC--CTCCAGGCAACCTCCCAGCAGGTCAGTTTCAGGCCCATGTTACCCATCATGCATCCTGCCCGAACTCTCATCAC--TCAAATGTAATTAGGA-----CCAATCAAGCCCA-ATCAGAAGGTGGAGTTCCTGACTCCCTGATTTTCTACCATCACAATGACT-------AAAACTACAA--------ATTTGGCATCTAGAGAAA--GATATGTAGACAATGCCCAATAG--AGAT---TTTTATG----TT-TCAGATGTATAATA-TCATCAGGTCTACATACCTGGGGTAAAACCAGTCTCACATTTAAAGAGGCTA i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13360029 319 + 41866177 ----TAAA--CGTGTTCTCTCCTCGTTGAGTTACAT--TTCAAGGCAACCTCTCAGCAGATCAGCCTTAAGCCCAGCTGCCCAATCACACATCTCAGCTGAGCCCCCATCACAGTCAGCTTAAATTATGA-----CCAATCAAGGCCACACCAGAGGTTGGAGTTCCTGACTTCTTGACTTGCTGCCATGATGGTGCT--------ACAAAAAGAA--------ATTTGGCATCTAGAAAAGCTGATATGTATGGCATGCCCAAAAG--AGATACATTTTTTT----TT-TCAAATTTATGATA-TCCTCAGGGCCATGCACCCGGGATGAAACTTGGCTTACTTTTAAGG-GGTTA i equCab2.chr26 C 0 C 0 s canFam2.chr31 14108901 313 + 42263495 ----------------CTCTCCTTGTTGAGTTAGAT--CTCAAGGCAACCTCTGAGCAGGTCACCCTTAAGCCCAAGTGCCCAATCATGCACCTCAGTGGAGCCCTCATCAAAGATAG-----GTTATAA-----TCAATCAAGACCATACCAGAGGCCAGAGTT-CTGACTACCTGACTTGCTGCTATCATGAGGCCttaaaaaaataaaaaaaaataaaGGTATTTAGCATATAAATAAGCTGATATGTAGGCAATGCCCAATAG--AGATCTTTTTTCTTT-AGTT-TCAAATTT---TTA-TCATCAGGGCTACAAAACTGGGATAGAGCTAGACTTACATTTAAA------- i canFam2.chr31 C 0 I 207 s panTro2.chrUn 47400589 329 - 58616431 tcaataaa--cTCCTTCCTTCTTTGCCTAGTTACAT--CTCAATGCAACCTCCTGGCAGGCCAGCCTTAAGCCCAGCAGTCCAACCATGCATCTAAGCTGAGTTTTCATCAGAGCCAACTTCAATCATAA-----ACAACTGAGATGATGCCAGAGGCCAGAATCCCTGAGAACCCAATTTGCTGTCATCACCGCAGCT-------GAAACAAGGC--------GCTTGGCATCTAGAAAAGCTGATCTGTAGGAAATTTCCAAAAG--AGTTCAATTTTTTCTAAGTT-TAAAGTGTACAATA-TCATCAAGGTCAGACACTCGAGATAAAACTAGGCTCGTGtttaaatataata i panTro2.chrUn C 0 C 0 s cavPor3.scaffold_34 15807121 321 - 24440124 TCCATAAATTATCATTTTTCCTATATTTTGTTTTACATCTCAAAGCAGCCTGACAG-AGAGCAGCTTTAACCCTAATTTTTCAATCATGTAATGGAGCCGAGTCCTCTTCAAAGCCAGCTGCATTTAGAAACAATCTGGATGAGACCAAACCAGACACTTCAGTTCCTGAAGACTTGACT-----------------CC-------AATTTAAGAC--------ATCTGGTATCCAGAAAAGTATATATATGAGGAATGCCCAACAGCAAGATCAAATTTTTCTTAGTTCTAAAATTCACTCTA-TCATCAGGGTAACATC--TAGGAAAAAGTTATGCTTATACTCAAATGAGACA i cavPor3.scaffold_34 I 71 C 0 s loxAfr3.scaffold_13 20605094 300 - 62548349 ----------------------TTGCCTAGTTACAC--CTCAGGCGAAACTCCCAGCAGGCCAGTCTTAAGCCTAGCTGTCCTATCATACATCTAA-CTGAGCCCTCATTATAGCCATCTTCAATTACGA-----CCAACTTAGACCATAGCA-----CTGAAGCCCTAAGGACC-AATGTGCTGCCACCATGATGGGT-------AAAGCAAGGA--------ATTTGGC-TCTAGAAAAGTAGATATG-AAGCAATGCCCAACAA--AGGTCC-TTTTTTTTAAGTT-TAAATTTTATGATACCCATCTGAGTCACACATTTTGTATAAAACTAAGGTTATATTTACAGAGAATC i loxAfr3.scaffold_13 C 0 C 0 a score=104668.000000 s hg19.chrUn_gl000245 4258 47 + 36651 ------------------------------------------aaaatatttGAAGAATAGTAAGAGTGGTGACTACTTTTACACAGGAA s panTro2.chrUn 47400918 47 - 58616431 ------------------------------------------aaaatatttGAAGAATAGTAAGAGTGGTGACTACTTTTACACAGGAA i panTro2.chrUn C 0 C 0 s cavPor3.scaffold_34 15807442 47 - 24440124 ------------------------------------------AAGGTATTTAAAGACTAATAAGATGGGTTATTATTTTTCTTCAGGAA i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141888541 44 + 163896628 ------------------------------------------AAAATACTT---GACTAGTAAGAATGGTGACAAATTTTACACAGGAA i oryCun2.chr14 C 0 C 0 s ponAbe2.chr3 159730630 47 - 202140232 ------------------------------------------AAAATACCTGAAGAATAGTAAGAGTGGTGACTACTTTTACACAGGAA i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189453969 47 - 189746636 ------------------------------------------AAAATATTTGAAGAATAGTAAGAGTGGTGACTACTTTTACACAGGAA i rheMac2.chr2 C 0 C 0 s bosTau4.chr1 138178909 43 - 161106243 ------------------------------------------AAAATTTTTGAAGA----CAATAATGGTAACTAATTTTACACAGAAA i bosTau4.chr1 C 0 I 757 s equCab2.chr26 13360348 43 + 41866177 ------------------------------------------AAAATACTTGAAGA----CAGCAGTGGTAACTAATTTTACATAGAAT i equCab2.chr26 C 0 C 0 s canFam2.chr31 14109421 43 + 42263495 ------------------------------------------AAAACATTTGAAGA----CAACAGTGGTAACTAATTTTACGTAGGAA i canFam2.chr31 I 207 C 0 s loxAfr3.scaffold_13 20605394 89 - 62548349 AACTTGACAGCGACTAACAACAACAACATATTTAATGAGGATAAAATATTTGAAGACCAGTAAGAATGGTAACTAATTTTATACAGGAA i loxAfr3.scaffold_13 C 0 I 2 a score=-2292.000000 s hg19.chrUn_gl000245 4305 23 + 36651 T---------GTTTCAAATAAATT--GTTTTTTT s panTro2.chrUn 47400965 23 - 58616431 T---------GTTTCAAATAAATT--GTTTTTTT i panTro2.chrUn C 0 C 0 s cavPor3.scaffold_34 15807489 21 - 24440124 ----------CTTGCAAAACCAT---ATTGTTTT i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141888585 27 + 163896628 CTG-------CTTTCAAACACATTAAGTTTTTTT i oryCun2.chr14 C 0 C 0 s ponAbe2.chr3 159730677 23 - 202140232 T---------GTTTTAAATAAATT--GTTTTTTT i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189454016 23 - 189746636 T---------GCTTTAAATAAATT--GTTTTTTT i rheMac2.chr2 C 0 C 0 s canFam2.chr31 14109464 28 + 42263495 -CTTTTTTT-TTTTTTTTTACCTA--GGTTTC-- i canFam2.chr31 C 0 C 0 s equCab2.chr26 13360391 29 + 41866177 -CTTTTTTTATTTTTTAACACATT--GCTTTC-- i equCab2.chr26 C 0 C 0 s loxAfr3.scaffold_13 20605485 21 - 62548349 ---------TATTTTTAACGTATT--TATTTT-- i loxAfr3.scaffold_13 I 2 C 0 e bosTau4.chr1 138178952 757 - 161106243 I a score=315775.000000 s hg19.chrUn_gl000245 4328 220 + 36651 CTTGTGCCTTTTAAATTTTGTGATTTGTCAATGAGA-TGCTGACATGTTTTTAATGAAG----CATGCCTTGTAAA-ATAATAAGTGAATGAAAACTACACAGTAATATTTACATCAACAAAGCTAGAAGAAGA----C----TGTATGTCTCAAGAGGCTCCATCATCTACCCAGTGGCCACTTCACCAAATTA-AGATCCAAATACCAAAAAG-AAA-----------AGTAATTAAAATTTGTG s panTro2.chrUn 47400988 217 - 58616431 CTTGTGCCTTTTAAATTTTGTGATTTGTCAATGAGA-TGCTGACATATTTTTAATGAAG----CATGACTTGTAAA-ATAATAAGTGAATGAAAACTACACAGTGATATTTACATCAACAAAGCT---AGAAGA----C----TGTATGTCTCAAGAGGCTCCATCATCTACCCAGTGGCCACTTGACCAAATTA-AGATCCAAATACCAAAAAG-AAA-----------AGTAATTAAAATTTGTG i panTro2.chrUn C 0 C 0 s cavPor3.scaffold_34 15807510 166 - 24440124 CCTTTGTTT------AATTTTAGTTTGT---------TGTGTAACACTTTTAAATGAAA----TGTACTTTGTTAA-AT--------CCTGGGAAGTATATTAGATTAGTTACAATGCCAAAGCTGTAGAAAGG----T----TGTATGACCCAAGAGGTCCTGTCATCCCCTTGG----CAGACACTT-----------------------------------------AGCAACTAAAATTAATG i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141888612 200 + 163896628 CCAGTATCTTTTAAAAGCTATAATTTGTAAATTGTACTGTTTATGTGTTCTTAATACTG----TACTCTTTTTAAA-ATAATAAGTGCATATGAAATATACTA---TATTTACAGCAACAAAGCTGTAGGCAGA----TGATCTGTATGTCCCACAAGA-CTTCAAATCCACCAGGTGGCCAGAAAACCAAGTTG-AAAT-CAAATGCCAAAAAg-------------------------------- i oryCun2.chr14 C 0 I 157 s ponAbe2.chr3 159730700 221 - 202140232 CTTGTGCCTTTTAAATTTTGTGATTTGTCAATGTGA-TACTGACATATTTTTCATGAAG----CATGCCTTGTAAA-ATAATAAGTGAATGAAAAATACACAGTAATATTTACATCAACAAAGCTAGAAGAAGA----C----TGCATGTCCCAAGAGGCTCCATCATCTACCCAGTGGCCACTTGACCAAATTA-AGATCCAAATACCAAAAAGAAAA-----------AGTAAATAAAACTTGTG i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189454039 216 - 189746636 CT----CCTTTAAAATTTTGTGATTTGTCAATGTGA-TGCTGACATATTTTTAATGAAG----TATGCCTCATAAA-ATAATAAGTGAATGAAAAATATACAGTAATATTTACATCAACAAAGCTAGAAGAAGA----C----TGTATGTCCCAAGAGGCTCCATCATCTACCCAGTGGCCACTTAACCAAATTA-AGATCCAAATACCAAAAAG-AAA-----------AGCAAATACAATTTGTG i rheMac2.chr2 C 0 C 0 s bosTau4.chr1 138179709 232 - 161106243 CTTGTGCC--TTAAATTTTGTGAGTTGCTGATATGA-TGTTATCTTTTTTTAAATGAAA----TATCCTTTTTTAA-ATAAAAAGAGAATGGAGAATATACTATAGTGTTTATATCATCAAAGCTGTAGGAAGGCTATC----TGTATGTT-CATAAGGCTCCATCACACACCTGTTGGCCATTTACCCAAGTTA-AAATTCAAATACCAAAAAA-AAAGAAAAAAACCCAGTAAGCAAAATTTGTG i bosTau4.chr1 I 757 C 0 s equCab2.chr26 13360420 215 + 41866177 CTTGTGTCTTTTAAATTTTAAGCTTTGTCGATATAA-TGCTATC--TTTTTTCATGAAG----TGTGCTTTTTTAA-ATAAAAAGGGAATGGAAAATATACTATAATATTTACATTATCCAAGTGGTAGGAAGA----C----TATATGTCCCACAAGCCTCTATTATATTCCAGGTGGCCATTTGCCCAGGTTG-AAATTCAAATACCAAAAA---------------CAGTAAATAAAATTTATA i equCab2.chr26 C 0 C 0 s canFam2.chr31 14109492 215 + 42263495 TTTGTGGCTTTTAAATTTTATGATTTGTTGATATAA-TGCTCTC--TTTTTAAATGAAGGTTTTTTGTTTTTTTTA-ATAAAAAGAGAATGGAAAATAC-------TACTGTCATCATCAAAAGTGTGGGGAAGCCATC----TGTATGTTCCACAAGCCTCCATCATCCACCCGGTAGCCATTTACCCAAATTA-AAATCCAAATGGGGAAAA----------------AGTAAATAATATTTGTG i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20605506 217 - 62548349 CTTGTACATTTTAAATGTCATGATTAGTCGATGTGA-TGCTTATCTGTTTTTAATGAAG----TGTGCTTTTTTTACCTAATAATTTAACGGAAAATATAC-----TATTTACATTGTCAAAACTATAGGAAAACTATC----TGTATAGCCCACAAGGTTCTACCATTTACCTGGTGGCCATTTACCAAAAAAAGAAATACAAATACAAAAAA----------------AGGAAATAAAATTGGTG i loxAfr3.scaffold_13 C 0 C 0 a score=491499.000000 s hg19.chrUn_gl000245 4548 190 + 36651 TTGTAT--GCC-TTATA--------AGACCAAA-CCTATAAAATGAGGGGAAACTTCACAATTACTTGTAATTTGCTCTGTGGAATTGTAACAGATGGATTATAAAGATGATTCCATGATAAACATGTAAATGTGGTTACTACCTTCTGTGCTTTCTTGGTTCATATTTTTATTGTTTTTTT-----CTTTATAAACAGAT----------------------------------------------------------AATTTA--------------------- s panTro2.chrUn 47401205 190 - 58616431 TTGTAT--GCC-TTATA--------AGACGAAA-CCTATAAAATGAGGGGAAACTTCACAATTACTTGTAATTTGCTCTGTGGAATTGTAACAGATGGATTATAAAGATGATTCCATGATAAACATCTAAATGTGGTTACTACCTTCTGTGCTTTCTTGGTTCATATTTTTATTGTTTTTTT-----CTTTATAAACAGAT----------------------------------------------------------AATTCA--------------------- i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189454255 190 - 189746636 TCATAT--GCT-TTACA--------AGACCAAA-CCCATGAAATGAGGGGAAACTTCACAATTACTTGTAATTTGCTCTGTGGAATTGTGACAGATGGATTGTAAAGATGATTCCATGATAAACATCTAAATGTGGTTACTACCTTCTGTGCTTTCTTGGTTCATATTTTTAACGTTTTCTT-----CTTTATAAACAGAT----------------------------------------------------------AATTCA--------------------- i rheMac2.chr2 C 0 C 0 s ponAbe2.chr3 159730921 192 - 202140232 TTGTAT--GCCTTTACA--------AGATCAAACCCTATAAAATGAGGGGAAACTTCACAATTACTTGTAATTTGCACTGTGGAATCGTAACAGATGGATTATAAAGATGATTCCATGATAAATATCTAAATGTGGTTATTACCTTCTGTGCTTTCTTGGTTCATATTTTTATTCTTTTTTT-----CTTTATAAACAGAT----------------------------------------------------------AATTCA--------------------- i ponAbe2.chr3 C 0 C 0 s cavPor3.scaffold_34 15807676 191 - 24440124 TTATAC--GCC-TTACA--------AATGGAAA-TCTGTAAAATAAGAAGAAACTTACTGATTACTCCTACTCTATTCTGTGGAATTGTAGCAGATGGATTATAATGATCATTCCATGATAAACATCTAAATGTGGTTTCTACCTTCTGTGCTTTCTTGATTCATACTTTTATTGAGTTTTT-----TCTTATAAACACACA---------------------------------------------------------AAAATT--------------------- i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141888969 189 + 163896628 TGGTAT--GCC--TAAG--------AGCCTAAA-TTTATAAAATGAGAAGAAACTTCCCAATTACTCCTAATTTTGTCTGTGGAATTGTAACAGATGGATTATAAAGATGATTCCATGATAAACATCTAAATGTGGTTTCTACCTTCTGTGCTTT-TGGGTTCATATTTTTTATTTTTTCTT-----CCTTATAAACAGACA---------------------------------------------------------AAACTT--------------------- i oryCun2.chr14 I 157 C 0 s bosTau4.chr1 138179941 199 - 161106243 TTGTCTTGACT-TTACAAGCTTCCAAGCCCAAA-TCTATAAAAT---GAGAAACTTTCTAATTACTCAC-ACTTGCTCTGTGAAATCAAAACAGATGGATTATAAAGATGATTCCATGATAAACAACTAAATGTGATCACTACCTTCTGTGCTTTCTTGGTTTATGTTTTTACTGTTTTTTTTCCCCCCTTTTAAGAAGAT----------------------------------------------------------AATG----------------------- i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13360635 203 + 41866177 TTGTACTGGCC-TAAAAAGTTTCCAAGCCCAAA-TCTATAAAATGAAGAGAAACTTCCTAATTACTCGTAATTTGCTCTGTGGAATTGAAACAGATGGATTATAAAGATGATTCCGTGATAAACAACTAAATGTGGTTACTACCTTCTGTGCTTTCTTGGTTCATAATTTTATTGTTTTTTT--AATCTTTATAAGCACAT----------------------------------------------------------AATGCC--------------------- i equCab2.chr26 C 0 C 0 s canFam2.chr31 14109707 201 + 42263495 TTGTACTTGCC-TTACAAGCTTCACAGCCCAAA-TCTATAAAATGAGGAGAAACTTCCTAATTATTCATAATTTGCTCTGTGGAGTTGAAACAGATGGATTATAAAGATGATTCCATGATAAACAACTAAATGTGGTTACTACCTTCTGTGCTTTCTTGGTTCATATTTTTATTGTTTTTTT----TCTTCATAAGCAGAT----------------------------------------------------------AATACT--------------------- i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20605723 280 - 62548349 TTGTACTAGCC-TTACA----TGCAAATTGAAG-ACTATAAAATAAGGAGAAACTTCCCAATTACTAGTCATTTGTTCTGTGGAATCATAACAGATGGATTATAAAGATGATTCCATGATAAACATCTAAATATGGTTACTACCTTCTGTGCTTTCTTGGTTTATACTTTTATTGTTTTATATGTATATATAGAAACAGACATACTTGAACATTGTGCTCTCTTAAGATCTATCTATATAAGATCAAACTGACTATAGCAACTCAAAAGATTAGATAGAAAACTTA i loxAfr3.scaffold_13 C 0 I 198 a score=522408.000000 s hg19.chrUn_gl000245 4738 290 + 36651 TTCTTATCTATGGCAATGCAAACTTTTCAGATGTATTGAATATGTCATAG-TGTTTTTCT-------ATTGTAGGCATCTCT-AAA-AAAGTTATAGAAAACAAACAGAGAAAAGTCTGGTGTTGGAAAG--GAGAGAGAAATAAAGCTTGTAAAGGAATGAAGATTAGAGCTTTCTGGAGATAAAAAT-TCTTAGAAGATACAAAAGCTAGTTACTGAATTAGATGAAGGTTCTTTTTCAGTTTTTCCCAGTTGTTCACCTCTTAGAAGG--------CACATA----------------TTCACAGCAGAA----------AAG-AAAAA-TGTGTT s panTro2.chrUn 47401395 292 - 58616431 TTCTTATCTATGGCAATGCAAACTTTTCAGATGTATTGAATATGTCATAG-ATTTTTTCT-------ATTGTAGGCATCTCTAAAA-AAAGGTATAGAAAACAAACAGAGAAAAGTCTGGTGTTGGAAAG--GAGAGAGAAATAAAGCTTGAAAAGGAATGAAGATTAGAGCTTTCTGGAGATAAAAAT-TCTTAGAAGATACAAAAGCTAGTTACTGAATTAGATGAAGGTTCTTTTTCAGTTTTTCCCAGTTGTTCACCTCTTAGAAGG--------CACATA----------------TTCACAGCAGAA----------AAGAAAAAA-AGCGTT i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189454445 288 - 189746636 TTCTTATCTACGGCAATGTAAAATTTTCAGATGTTTTGAATATGTCATAC-TTTTTTTCT-------ATTGTAGGCGTCTCTGTAA-AAAGGTGGAGAAAACAAACAAGGAAAAGTCTGGGGTTGGAAAG--GAGAAAGAAATAAAACTTGTAATGGAATGAAAATTAGAGCTTTTTGGAGACAAAAAT-TCTTAGAAGATACAAAAACTAGTTACTGAATTGGATGAAGGTCCTTTTTCAGTTTTTCCCACTTGTTCATCTCTTAGAAGG--------CACTTA----------------TTCACAGCAGAA----------AAG----AA-AGGGTC i rheMac2.chr2 C 0 C 0 s ponAbe2.chr3 159731113 290 - 202140232 TTCTTATCTATGGCAATGCAAAATTTTCAGATGTATTGAATATGTCATAG-TTTTTTTCT-------ATTGTAGGTATCTCT-AAA-AAAGTTAGAG-AAACAAACAGAGCAAAGTCTGGTGTTGGAAAG--GAGAGAGAAATAAATCTTGTAAAGGAATGAAAATTAGAGCTTTCTGGAGACAAAAAT-TCTTAGAGGACACAAAAGGTAGTTACTGAATTAGATGAAGGTTCTTTTTCAGTTTTTCCCATTTGTTCATGTCTTAGAAGT--------CACTTA----------------TTCACCGCAGAA----------AATAAAGAA-AGGGTT i ponAbe2.chr3 C 0 C 0 s cavPor3.scaffold_34 15807867 259 - 24440124 TCCTTTTTTGTAGCAATGACAAATGTACAACTAGACTGAATATGCCACAG-TTATTATTT---CTTTGTAATAGGT---TCTCTAA-AAAGACAGAGAA---------------------------------AGGGAAAAAATAAAACTTGAAAAGAAAT-AAAATGAGAGTGATTTAGGGACAAATACATCTTAGGAGAT-AGGGAACTGGTTCCTTAATTAAATCCAGGTTCTTTTCTAGTTTTGCTCACTTGTTAATCTTTTC-AAGG--------CATTCA----------------TTGGTAGTGAGA----------AAG-AATAA-AGTGTT i cavPor3.scaffold_34 C 0 I 133 s oryCun2.chr14 141889158 298 + 163896628 TTTTTCCCTATAGCAACGCAAAATTTGCAGCTGCATT-AATATGTCACAG-TTGTTTTTT--CCTTTATTGTAGGTGTCTCTTTTA-AGAGATAAAGAAAACAAACAGTGGAAAGTCTGATGTTGGAAAGGGAAGAGAAAAAGACAGCTTGAACAGAAATAAAAATGAGAGCTATTTGGAGACCAAAATGTCCTAGGAAATGGGGGAGCTAGTTGTTTAATTTGATTGAGGACCTTGACCAATTTTTTCTGCATGTTCTTCTATGAGAAGG--------CACTTA----------------GTGAAAGCAGGA----------AAG-ATCAA-AGGGTT i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138180140 316 - 161106243 --CTTTTCTGTAGCCGTGTAAAATTTGCAGCTGCATTGGAAATGCC--AGTATATTTTTT--TCTTTACTGTAGGTGTCTTTTCA--AAAGGTATAGAAGACAAATG--GGAAAGTCTGGTGTTGGAAAGGATAAAGAAAAACAAAACTTGAAAAAAAGGAAAATT---AGTCATTTGAAAACAAAAGT-TCTTGAGATAG--GGGAGCTAATTACT----TAGATTAATGTTCTGTTCCTATTTTCACTGCTTGCT--CCTCTCAGGAGATTTTTCTCTTTTTAAACCTTTCTTTTTTGTCTGCTATCAATAATTGTCTCTTAGG-AGAGACAAGGTT i bosTau4.chr1 C 0 I 1 s equCab2.chr26 13360838 293 + 41866177 TTCTTTTCTGTAGCCGTGCAGAATTTGCAGCTGCATTGGAAATGTCATAG-TTATTTTTT--TCTTTACTGTAGGTGTTTCTTTAT-AAAGGTAGAGAAAACAAACA--GGAAAGTCTGAAGTTGGAAAGGGTAAAGAAATATAAAGCTTGGAAAGGAAGAGGAATGAGAATTATTAGAAAACAAAAAT-TCTTAAGAGAA--GGGGACTAGTTACTTAATTAGATTAAGGTTCTTTTCTAGTTTTTCCTGCTTTTTTACCTCTTAGAAGA---------ACTTA----------------CTGATAGCAGAA----------AAG-AAAGA-AGGGTT i equCab2.chr26 C 0 I 1 s canFam2.chr31 14109908 291 + 42263495 TTCTTTTCTGTAGC--TACAAAATTTGTAGCTGCATTGGAAATGTCACAGTTTTTTTTTT--TCTTTACTGTAGGTGTCTATTTTTAAAAGGTAGAGAAAACAAACA--GGAAAGTCTGGTGTGGGAAAGGGTAAAGAAAAATAAAGCTTGAAGAGGAAG-----TGAGAATTATTTGAAAACAAAAAT-TCGTAAGAGAGACAGGAGCTAGTTACTTAACTAGACTAAGGTTCTTTTCTAGGTTTTCCTGTTTGTTCATCTCTTGGAAGA--------CATTTA----------------TTGATAGCAGAA----------AAG-AAAGA-GGGGTT i canFam2.chr31 C 0 I 1 s loxAfr3.scaffold_13 20606201 297 - 62548349 TTCTCTTCTGTGGCAATACAAAATCTGCATCTTCATTGAAAATGTCAGGT-TTTTTTTTTTTTCTTTATTGTAAGTGTCTCTTTAA-AAAGGTAAAGAAAGAAAACAGGAGAAAGTCTGGTGTTGGAAAGAGCAGAGAAAAATAAAACTTGAAAAGGAAAGAAAATGATAGTTATTTGGAAACAAAGAA-CAGCAGGAGACAAGGAAGCTGGTTGCTTAATTAGATTAAGGTTCTTTTCCAGTTTTTCCTTCTTGTTCATCTACTAGAAAG--------TAATCA----------------AGAACAGCAGAA----------AAG----AA-AGGTTT i loxAfr3.scaffold_13 I 198 C 0 a score=350188.000000 s hg19.chrUn_gl000245 5028 201 + 36651 AAAAAGAAAAT-ACCTCGGTGTAGTGAGACTG-TAATTTCATGAGGGCATT-ACTGAAGACTCA-CTTTTTCCAGCATCACTCAGCATGGTATTATGCATGTGTGTAATGTAAAGGAAAGTGA-ATACGCATTCTTGGATGGGTGATCAAATCGTAA------TTCCAGAATAT-AATCAGAA---GCTGATTCATTATCCTCTTGAGATTTCACA s panTro2.chrUn 47401687 201 - 58616431 AAAAAGAAAAT-ACCTCAGTGTAGTGAGACTG-TAATTTCATGAGGGCATT-ACTGAAGACTCA-CTTTTTCCAGCATCACTCAGCATGGTATTATGCATGTGTGTAATGTAAAGGAAAGTGA-ATACGCATTCTTGGATGGGTGACCAAATCGTAA------TTCCAGAATAT-AATCAGAA---GCTGATTCATTATCCTCTTGAGATTTCACA i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189454733 197 - 189746636 AGAAAGGAAAT-ACCTCGGTGCAGTGAGACTG-TAGTTTCATGAAGGCATT-GCTGAAGGCTCA-CCTCTTCTAGCACCACTCAGCATGGTATTAAGAATGC----AACGTAAAGAAAAGTGA-ATACACATTCTTGGATGGGTGATCAAATCGTGA------CTCCAGAATAT-AATCAGAT---GCTGATTCATTATCCTCTTGAGATTTCATA i rheMac2.chr2 C 0 C 0 s ponAbe2.chr3 159731403 200 - 202140232 AAAAAGAAAAT-ACATCAGTGTAGTGAGACTG-TAATTTCATGAAGGCATT-ACTGAAGACTCA-CCTTTTCCAGCATCACTCAGCATGGTATTATGCATGCATGTAATGTAAAGGAAAGTGA-ATACTCATTCTTGGATGGGTGATCAAATCATGA------TTCCAGAATAT--ATCAGAA---GCTGATTCATTATCCTCTTGAGATTTTACA i ponAbe2.chr3 C 0 C 0 s cavPor3.scaffold_34 15808259 180 - 24440124 gaaaagaAGAT-GCTTAGGTTTATATAA-CTGATAACTTCAAAAAGGCATT-ATTGAACATTCA-CTTCATATTATATATG------------TGTGCAA--------TGTGGAGGAATAGTA-ATACATATTGTTGCAGTGATGATCAAATGATGATGATGATTCTAGAAATGCAATCTGAT-----------GTTTTTCTCTTGAGATTCCATA i cavPor3.scaffold_34 I 133 C 0 s oryCun2.chr14 141889456 204 + 163896628 TAAAAGAAAATGGCTAAGGTGTACTGAGTCTGATAATCTCACAAAGTCATTCACTGGGACTTCA-CCTTTTCCAACATTTGTCAGCATGGTCTTATGCAAGTACAT-CCATGAAAGAAACTTA-ACACACATCGCCACATAGATGATCAAATTATGAT-----TCCCAGAAGAG-AATCAGAC---ACTGATCAATTTTCCTcctgaaattccaca i oryCun2.chr14 C 0 I 402 s bosTau4.chr1 138180457 163 - 161106243 AAAAAGAAAAT-ACCAGGGTGTAATGAGATTGGTAATTTCATAAACATGTT-GCAAAAGATGCA-CTTTTTCTAACAGTACTCAGTGTAATATTACATACATGTACAATGTAGAGAAGAGTTC-ACACACATTGTTGAATGGGTAATC------------------------AG-AATCA------------------------TAAGATTCCATA i bosTau4.chr1 I 1 C 0 s equCab2.chr26 13361132 205 + 41866177 AAGAAGAAAAC-ATCTAGGCGTAGTGAGATTGACAATTTCAT-AAGACATT-CCTGAAGATGCA-CCTTTTCCAGCATTAGTCAACATGGTATTTTGTATGTGTGCAATGTGAAGGAAAGTAC-ACACACATTGTTGGATGGGTGATCAAATCACGAT-----TCCAAGAATAG-AATCAGACTATTCTGATTCATTTTCTTCTTGAAATTCTATA i equCab2.chr26 I 1 C 0 s canFam2.chr31 14110200 204 + 42263495 AAAAATAAAAT-ACTTAGGTGTGATGAGACTGACCATTTCATGAAGATGTT-CCTGAAGATGCACCCTTTTCTAGCACTACTTAACCTGGCATTATGTATGTGTGCAATGTGAAGGAAAATTA-ACACACATTGTTGGACGGATGATCAGATCGTGAT-----TCCCAGAATAG-AATCAGAC---ACTGATTCATTTTTCTCTTGAGATCCCATA i canFam2.chr31 I 1 C 0 s loxAfr3.scaffold_13 20606498 202 - 62548349 AAAAGAAAAAT-GTCTTGATGTAGTGAGACTAATTATTTCATGAAGGCATT-ATCGATAATGCA-CCTTTTCCAA-GCTAGTTAGAATAGCACTGTGCATGTGTGCAACTTGAGGGAAAGTTAGACACATAGCATTGGATGGGTGACCAAATTGTGAT-----TCCCAGAATGG-AATTAGGC---ACT-ATTCATTTTCCTCTTGAGGTTACATA i loxAfr3.scaffold_13 C 0 C 0 a score=83599.000000 s hg19.chrUn_gl000245 5229 66 + 36651 ATCTTTTCATCAGGAATT-AAAATTCAGAAGAGGGTAAATGT--------ATCTA-----ATCAGTTGAAAGTTAAAAAT s panTro2.chrUn 47401888 66 - 58616431 ATGTTTCCATCAGGAATT-AAAATTCAGAAGAGGGTAAATGT--------ATCTA-----ATCTTTTGAAAGTTAAAAAT i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189454930 64 - 189746636 ATCTTTGCATCAGGAATT-AAAATTCAGAAGAGGGCGAATGT--------ATCTA-----ATCTTTTGAAAGTTAAAA-- i rheMac2.chr2 C 0 I 1 s ponAbe2.chr3 159731603 66 - 202140232 ATCTTTCCATCAGGAATT-AAAATTCAGAAGAGAGTGAATGT--------ATCCA-----GTCTTTTGAAAGTTAAAAAT i ponAbe2.chr3 C 0 C 0 s cavPor3.scaffold_34 15808439 65 - 24440124 ATATTTACATAAAGAATT-AAAATGCAGAGGAAGTTCACTAT--------ATCTA-----ATCATTCTAAGTTTAAAAA- i cavPor3.scaffold_34 C 0 I 14 s bosTau4.chr1 138180620 68 - 161106243 ATCTTAATATCAAAAGCTGAAAATTCAGAAGAGGTTGAATATATTCATGCATATA-----ATCTTTGTAAAAT------- i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13361337 60 + 41866177 ATCTTAGTCTCAAAAATGGAAAATTCAGAGGAGCTTTAATAT--------ATATA-----ATCCTTCCAAAAT------- i equCab2.chr26 C 0 C 0 s canFam2.chr31 14110404 65 + 42263495 ATCTTAGTATCTAAAATTGAAAATTCAAAGGAAGTTTAAGAT--------ATA-A-----TTTTGCCCCAAATTAAAAA- i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20606700 72 - 62548349 ATCTTTGTATCCGGAGTTGAAAATTCAAAGGAGGTTGaatat--------atatatatatatttttGCAAAGTTAAAAAT i loxAfr3.scaffold_13 C 0 I 18 e oryCun2.chr14 141889660 402 + 163896628 I a score=289160.000000 s hg19.chrUn_gl000245 5295 1166 + 36651 TAgaggatggaggcaacatggccgaataggaacagctccagtctacagctgccagcgtgagtgatgcagaagacaggtgatatctgcatttccaactgaggtaccaggttcatctcactggggagtgct--------------ggacagtgggtgcagcgcaccatgcatgagccaaagcagggaaaggcatcacctcacctgggaagcagaatgggtcagagaattccctttcctagtcaaagaaaggggtgacagatggcacctggaaaatcaggtcactcccaccctaatactgcgcttttccaacaggcttatcaaatggcacaccaggagattgtatccagcacctggcttggaggatcctacacccacggagcctcgctgtttgctagcacagcagtctgagatcaaactgcaaggttacagtggggctgggggaggggcgcccgccattgctcaggcttgagtaagtaaacaaagcagccaggaagttcgaactgggtggagcctaacacagctcaaggaggccagcctgcctctgtaggctccacctctgggggcaggacacagacaaacaaaagacagcaataccctctgcagacttaaatatccctgtctgacagctttgaagagagtagtggttctcccagcatgcagcttgagatctgagaacgggcagacagcctcctcaagtgggttcctgacccctgagtagcctaactgggaggcaccccccagtagaggcagactgacatctcacatgcccgggtacccctctgagtcaaaactttcagaggaacgatcaggcagcagcatttgcagttcaccaatatccactgttctgcagccaccgctgctgatacccaggcaaatagtgtctggagtagacctccagtaaactccaacagacctgcagctgagggccctgactgttagaaggaaaactaacaaacagaaaggacatccacaccaaaaccccatctgtatgtcaccatcatcaaggaccaaaggaagataaaaccacaaagat-gggaaaaaacagagtagaaaacctggaaactctaaaaatcagagtgcctctcctcctgcaaaggaatgcagctcctcaccagcaatggaacaaagctggacggagtatgactttgacgagttgagagagaaaggcttcagaagatcaa s panTro2.chrUn 47401954 1166 - 58616431 TAgaggatggaggcaacatggccgaatagaaacagctccagtctacagctcccagcttgagtgatgcagaagacaggtgatatctgcttttccaactgaggtaccaggttcatctcactggggagtgct--------------ggacagtgggtgcagcgcaccatgcatgagccaaagcagggcaaggcatcacctcacctgggaagcacaatgggtcagggaattccctttcctagtcaaagaaaggggtgacagatggcacctggaaaatcaggtcactcccatcctaatactgcacttttccaacaggcttatcaaatggcacaccaggagattatatccagcacatggcttggaggatcctacacccacggagcctcaccgtttgctagcacagcagtctgagatcaaactgcaaggttacagtggggctgggggaggggcgcccaccattgctcaggcttgagtaagtaaacaaagcagccaggaagttcgaactgggtggagactgccacagctcaaggaggccagcctgcctctgtaggctccacctctgggggcagggcacagacaaacaaaagacagcaataacctctgcagacttaaatgcccctgtctgacagttttgaagagagtagtggttctcccagcatgcagcttgagatctgagaacgggcagacagcctcctcaagtgggttcctgacccctgagtagcttaactgggaggcaccccccagtaggggcagactgacatctcacatgaccgggtaccactctgagtcaaaacttccagaggaacgatcaggtagcagcatttgcagttcaccaatatccactgttctgcagccaccgctgctgatacccagggaaatagtgtctggagtagacctccagtaaactccaacagacctgcagctgagggtcctgactgttagaaggaaaactaacaaacagaaaggacatccacaccaaaaccccatctgtatgtcaccatcatcaaggaccaaaggaagataaaaccacaaagat-gggaaaaaacagagcagaaaaactggaaactctaaaaatcagagtgtctctcctcctgcaaaggaaggcagctcctcaccagcaatggaacaaagctggacggagtatgactttgacgagttgagagaggaaggcttcagaagatcaa i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159731669 1180 - 202140232 TAGAGGGTGGAGAcaagatggccgaataggaacagctctagtctacagctcccagcgtgagcgacacagaagatgggtgatttctgcatttccaactgaggtaccaggttcatctcactagggagtgccagacagtgggtgcaggacagtgggtgcagtgcaccatgcatgagccaaagcagggcaaggcattgcctcacctgggaagcacaagcggtcagggaattccctttcctagtcaaagaaaggggtgacagatggcacctggaaaaccgggtcacgcccaccctaatactgtgcttttccaacaggcttatcagacggcacgccaggagattatatcctgcacctggcttggagggtcctacgcccacggagcctcgctcattgcaaacacagcagtctgagatcaaactgcaagctagaagcaaggctgggggaggggcgcccaccattgctcaggcttgagtacctaaacaaagcggccaggaagcttgaactccgtggatcccgccacagctcaaggaggcctgcctgcctcattaggctccacctctgggggcagggcacagacaatcaaaagacagcaataacctctacagacttaaatgtccctgtctgacagctttgaagagagtagtggttctcccagcacacagcttgatatctgagaagaggcaggctgcctcctcaagtgggtccctgacccccgagtagcctaactgggaggcaccacccagtaagcacggactgacacctcacaaagccgggtactcctctgagacaaaacttccagaggaacgatcaggcagcagcatttgcagttcaccaatatccactgttctgcagcctctgctgctgatacccaggaaaacagggtctggagtggacctccagtaaactccaacagacctgcagctgagggacctgactgttagaagaaaaactaacaaacagaaaggacatccataccaaaaccccatgtgtatgtcaccatcatcaaagaccaaaggtagataaaactacaaagatggggagaaaacagagcagaaaaaccagaaactctaaaaatcagagtgcctctcctcctccaaagaaatgcagctcctcaccagcaacggaacaaagctggatggagaatgacattgacgagttcagagaagaa-gcttcagaagatcaa i ponAbe2.chr3 C 0 I 6617 e bosTau4.chr1 138180688 0 - 161106243 C e loxAfr3.scaffold_13 20606772 18 - 62548349 I e oryCun2.chr14 141889660 402 + 163896628 I e canFam2.chr31 14110469 0 + 42263495 C e equCab2.chr26 13361397 0 + 41866177 C e rheMac2.chr2 189454994 1 - 189746636 I e cavPor3.scaffold_34 15808504 14 - 24440124 I a score=438202.000000 s hg19.chrUn_gl000245 6461 4959 + 36651 agtactccgagctaaaggaggaagttcgaaccagtggcaaagaagttaaaaactttg-aaaaaaaattagacgaatggataactagaataacaaatgcagagaagtccttaaaggacctgatggagctgaaaaccatggcacaagaactacatgacaaatgcataagcctcagtaaccgatgtgatcaactggaagaaagagtatcagcgatggaaaacgaaatgaatgaaataaagcatgaagagaagtttagaggaaaaggaatagaagaaatgaacaaagcctccaagaaatatgggactatgtgaaaagaccaaatgtatgtctaattggtgtacctgaaagtgacggggagaatggaaccaagttggaaaacactctgcaggatattatccaggagaacttccccaatctagtaaggcaggccaacatacaaattcaggaaatacagagaatgccacaaagatactcctcgagaagaacaactccaagacacataattgtcagattcaccaaagttgaaatgaatgaaaaaattttaaaggctgcca-agagaaaggtcaggttacccacaaaaggaagcccatcagacaatctgctgatctctcctcagaaactctacaagccagaagagagtgggggccaatattcaacattcttaaagaaaagaattttcaacccagaatttcatattcagctaaactaggcttcataagtgaaggagaaataatatactccacagacaagcaaatgctgagagattttgtcaccaccaggcctgccctaaaagagctcctgaaggaagcactaaacatggaaaggaacaactggtaccagccactgcaaaaacatgccaaattgtaaagaccatcaaggctaggaagaaactgcatcaactaacgaggaaaataaccagctaacatcataatgacaggatcaaattcacacataacaatactaagcttaaatgtaaatgggttaaatgctccaattaaaaggcacagactggcaaattggataaagagtcaagacccatcagtgtgctgtattcaggaaacccttctcacctgcagagacacacataggctcaaaataaagggatggaggaagatctaccaagcaaatggaaaac-aaaaaaaggcaggggttgcaatcctagtctctgataaaacagactttaaaccaccaaagatcaaaagagacaaagaaggccattacataatggtaaagggatcaattcaacaagaactaactatcctaaatatatatgcacacaatacagaagcacccagattcataaagcaagtccttagtgatctccaaagtgacttagacgcccacaaaataataatgggagactttaacaccccactgtcaacattagacagatcaacgagacagaaagttaacaaggatatacaggaattgaactcagctctgcaccaagcaggcctaatagacatctacagaactctctatcccaaatcaatggaatatgtattcttttcagcaccacaccacacctattccaaaattgaccacatacttggaagtaaagcactcctcagcaaatgtaaaagaacagaaagtataataaactgtctctcagaccacagtgcaatcaaactacaactcaggattaagaaactcactcgaaaccactcaactacatggaaactgaacaacctgctcctgaatgactactgggtacataaggaaatgaaggcagaaataaagatgttctttgaaaccaacaagaacaaagacacaacataccggaacctctgggacacattcaaagcagtgtgaagagggaaatttacagcactaaatgcccacaagagaaagcaggaaagaaataaaattgacatcttaacatcacaataaaaagaactagagaagcaagagcaaacacattcaaaagctagcagaaggcaagaagtaactaagatcagagcagaactgaaggaaatagagacacaaaaaacccttcaaaaaatcaatgaatacagaagctg-ttttttgaaaagatcaacaaaattgacagaccactagcaagaccaataaagaagaaaagagagaagaatcaaatagatgcaataaaaattgacaaaggggatatcaccaccaattccacagaaatacaaactacaatcagagaatactattaacacctctacacaaataaactagaaaatctagaagaaatggataaattccttgacacatatactctcccaagactaaaccaggaagaagttgaacctctgaatagacaaataacactctctgaaattgaggcaataattaatagcttaccaaccaaaaaaagtccaggaccagatggattcaaagccgaattctaccagtggtacaaggaggaactggtacaattccttctgaaactattccaatcaatagaaaaagaaggaatcctccctaactcattttatgaggccagcatcatcctgataccaaagcctggcagagacaaaac-aaaaaaaggagaattttaaaccaatatccttgatgaacattgatgcaaaaatcctcaataaaatactggcaaaccaaatccagcaacacataaaaaagcttatccaccatgatcaagcgggtttcatccctgggatgcaaggctggttcaacatatgaaaatcggtcaatgtaatccagcgtataaacaggaccaaagacaaaaaacacatgattatctcaatagatgcagaaaaggcctttgacaaaattcagcaaaccttcatgctaaaaactctcaataaattagggattgataggatgtatctcaaaataataagagctatctatgacaaacccacagccaatatcatactgaatgggcaaaaactggaagcattccctttgaaaactggcacaagatagggatgccctctctcaccactcctattcaacatagtgttggaagttctggccagggcaatcaggaaggagaaggaaataaagggcattcaattaggaaaagaggaagtcaaattgtccctgtttgcagatgacatgactgtgtatgtggaaaaccccatcgtctcagcccaaaatctccttaagctaataagcaacttcagcaatgtctcaggatacaaaatcaatgtgcaaaaatcacaagcattcttatacaccaataacagacaaacagggagccaaatcatgagtgaactcccattcacaattgcttcaaagaaaataaaatacctaggaataccacttacaagggaagtgaaggatctcttcaaggagaactacaaacaactgcttaatgaaataaaaaaggatacaaacaaatggaagaacatgccatgctcatgggtaggaagaatcaatatcgtgaaaatggccatactgcccaaggtaatttatagattcaattccatctccatcaagctaccaatgactttcttcacagaattggaaaaaaactactttaaagttcatatggaac-caaaaagagcccacattgccaagtcaatcctaagccaaaagaacaaaggtggaggcatcatgctacctgacttcaaactatactacaaggctacagtaaccaaaacagcatagtactagtaccaaaacagagatatagacgaatggaacaggacagagccctcaaaaataatgccacatatctacaactatctgatctttgacaaacctgacaaaaacaagaactagggaaaggataccctatttaataaatggtgctgggaaaactggctagccatatgtagaaagctgaaactggatcccttccttacaccttatacagaaattaattcacgatggattaaagacttacttgttagacctaaaaccataaaaaccctagaagaaaaaccaggcaataccattcaggacataggcatgggcagagacttcatgtctaaaacaccaaaagcaatggcaacaaaagccaaaattgacaaatgggatctaattaaactaaggaggttctgcacagcaaaagaaaccaccatcagagtgaacaggccacctacagtatgggagaaaagttttgcgacctccttatctgacaaagggctaatatccagaatctacaatgaactcaaacaaattcacaagaaaaaaacaaacaaccccatcaaaatgtgggcaaaggaaatgaacagacacttctcaaaagaagacattttgcagccaaaagacacatgaaaaaatgctcatcatcactggccatcagagaaatgcatatcaaaaccacaatgagataccatctcacaccagttagaatggccatcattaaaaagtcaggaaacaacaggtgctggagaggatgtggagaaataggaacacttttacactgttggtgggactgtaaactagttcaaccattgtggaactcggtgtggtgattcctcagggatctagaactagaaataccatttgacccagccatcccattgctgggtatatacccaaaggatta-aaatcatgctgctataaagacacaagcacatgtatgtttattgtggcactattcacaatagcaaagacttggagccaacacaaatgtccaacaatgatacattggattaagaaaacgtggcacatataaaacatggaataccatgcagccataaaaaatgttgagttcatgtcccttgtagggacatggatgaagctagaaaccatcattctcagcaaactattgcaaggaaaaaaaccaaacaccacatgttctcactcataggtgggaattgaacaatgagaaaacatggatgcaggaaggggaacatcacacactggggacagttgtggggtgggggaaggggggaaggatagcattaggagatatacctaatgttaaatgacgagttaatgggtacagcacaccaacatggcccatgtatacatatctaacaaacctgcacattgtgcacatgtaccctaaaacttaaaatataataataa s panTro2.chrUn 47403120 4957 - 58616431 agtactccgagctaaaggaggaagttcgaaccaatggcaaagaagttaaaaactttgaaaaaaaaattagacgaatggataactacaataacaaatgcagagaagtccttaaaggacctgatggagctgaaaaccatgtcacaagaactacatgacaaatgcataagcctcagtaactgatgtgatcaactggaagaaagagtatcagcgatggaagatgaaatgaatgaaataaagcatgaagagaagtttagagaaaaaggaatagaagaaatgaacaaagcctccaagaaatatgggactatgtgaaaagaccaaatatatgtctaattggtgtaactgaaagtgacggggagaatggaactaagttggaaaacactctgcaggatattatccaggagaacttccccaatctagtaaggcaggccaacatacaaattcaggaaatacagagaatgccacaaagatactcctcgagaagagcaaccccaagagacataactgtcagattcaccaaagttgaaatgaatg-aaaaattttaaagtcaaccagagagaaaggtcaggttacccacaaaaggaagcccatcagactaactgctgatttcctctcagaaactctataagccagaagagagtgggggccaatattcaacattcttaaagaaaagaattttcaacccagattttcatatccagccaaacgaagcttcataagtgaaggagaaataatatactccacagacaagcaaatgctgagagattttgtcaccaccaggcctgccctaaaagagctcctgaaggaagccctaaacatggaaagcaaaaaccagtaccagccactgcaaaaacatgccaaactgtaaagaccgtcaaggctaggaagaaactgtatcaactaacgaggaaaataaccagctaacatcataatgacaggatcaaattcacacataacaatactaaccttaaatgtaaatgggttaaatgctccaattaaaaggcacagactggcaaattgaataaagagtcaagacccatcagtgtgctgtattcaggaaaccctactcacctgcagagacacacataggctcaaaataaagggatggaggaagatataccaagcaaatggaaaacaaaaaaaaggcaggggttgcaatcctagtctctgataaaacagacttcaaaccaacaaagatcaaaagagacaaagaaggccattacataatggtaaaaggatcaattcaacaagaactaactatcctaaatatatatgcacacaatacagaagcacccagattcttaaagcaagtccttagtgatctacaaagtgacttagacgcccacaaaataataatgggagactttaacaccccactgtcaacattagacagatcaacgagac--aaagttaacaaggatatacaggaattgaactcagctctgcaccaagcagacctaatagacatctacagaactctctatcccaaatcaacggaatgtgtattcttttcagcactacaccacacctattccaaaattgaccacatagttggaagtaaagcactcctcagcaaatgtaaaagaacagaaagtataacaaactgtctctcagaccacagtgcaatcaagctacaactcaggattaagaaactcactcaaaaccactcaactacatggaaactgaacaacctgctcctgaacgactactgggtacataaggaaatgaaggcagaaataaagatgttctttgaaaccaacaagaacaaagacacaacataccggaatctctgggacacattcaaagcagtgtgaagagggaaatttacagcaccaaatgcccagaagagaaagcaggtaagaaataaaattgacatcttaacatcacaattaaaagacctagagaagcaagagcaaacacattcaaaagctagcagaagacaagaagtaactaagatcagagcagaactgaaggaaatagagacacaaaaaacccttc-aaaaatcaatggatccagaagctgtttttttgaaaagatcaacaaaattgacagaccactagcaagaccaataaagaagaaaagagagaagaatcaaatagatgcaataaaaattgacaaaggggatatcacccccgatcccacagaaatacaaactacaattagagaatactataaacacctctatgc-aataaactagaaaatctagaagaaatggataaattccttgacacatatactctcccaagactaaaccaggaagaagttgaacctctgaatagacaaataacacgctctgaaattgaggcaataattaatagcttaccaaccaaaaaaagtcctggaccagatggattcacagccgaattctaccagtggtacaaggaggaactggtaccattccttctgaaactattccaatcaatagaaaaacagggaatcctccctaactcattttatgaggccagcatcatcctgataccaaagcctggcagagacaaaacaaaaaaaaagagaattttagaccaatatccttgatgaacattgatgcaaaaatcctcaataaaatactggcaaacctaatccagcaacacatcaaaaagcttatccaccatgatcaagcgggtttcatccctgggatgcaaggctggttcaacatctgaaaatcagtaaacgtaatccagcatataaacaggaccaaagacaaaaaccacatgattatctcaatagatgcagaaaaggcctttgacaaaattcagcaaaccttcatgctaaaaactctcaataaattagggattgataggacgtatctcaaaataataagagctatctatgacaaacccacagccaatatcatactgaatggacaaaaactggaagcattccctttgaaaactggcacaagacagggatgccctctctcaccactcctattcaacatagtgttggaagttctggccagggcaatcaggaaggagaaggaaataaagggcattcaattaggaaaagaggaagtcaaattgtccctgtttgcagatgacatgactgtgtatgtggaaaaccccatcgtctcagcccaaaatctccttaagctaataaacaacttcagcaaagtctcaggatacaaaatcaatgtgcaaaaatcacaagcactcttatacatcaataacagacaaacagagagccaaatcatgagcaaactcccattcacaattgcttcaaacagaataaaatacctaggaataccacttacaagggaagtgaaggacctcttcaaggagaactacaaactactgctcaatgaaataaaaaaggatacaaacaaatggaagaacatgccatgctcaagggtaggaagaatcaatatcgtgaaaatggctgtactgcccaaggtaatttatagattcaattccatctccatcaagctaccaatgactttcttcacagaattgg-aaaaaactactttaaagttcatatggaacaaaaaaagagcccacattgccaagtcaatcctaagccaaaagaacaaagctggaggcattatgctacctgacttcaaactatactacaaggctacagtaaccaaaatagcatagtactagtaccaaaacagagatatacaccaatggaacaggacagagctctcagaaataatgccacatatatacaactatctgatctttgacaaacctgacaaaaacaagaactagggaaaggattccctatttaataaatggtgctgggaaaactggctagccatatgtagaaagctgaaactggatcccttccttacaccttatacagaaattaattcacgatggattaaagacttacatgttagacctaaaaccataaaaaccctagaagaaaaaccaggcaataccattcaggacataggcatgggcagggacttcatgtctaaaacaccaaaagcaatggcaacaaaagataaaattgacaaatgggatctaattaaactaaggagcttctgcacagcaaaagaaaccactatcagagtgaacaggcatcctacagtatgggagaaaagttttgcgacctcctcatctgacaaagggctaatatccagaatctacaatgaactcaaacaaattcaaaagaaaaaaacaaacaaccccatcaaaatgtgggcaaaggaaatgaacagacacttctcaaaagaagacattttgcagccaaaggacacacgaaaaaaggctcatcatcactggccatcagagaaatgcatatcaaaaccacaatgagataccatctcacaccagttagaatggcgatcattaaaaaatcaggaaacaacaggtgctggagaggatgtggagaaataggaacacttttacactgttggtgggaatgtaaactagttcaaccattgtggaactcggtgtgttgattcctcagggatccagaactagaaataccatttgacccagccatcccattactgagtatatacccaaaggattataaatcatgctgctataaagacacaagcacatgtatgtttattgtggcactattcacaatagcaaagacttggagccaacacaaatgtccaacaatgatagacgggattaagaaaacgtggcacatatacaccatggaataccatgcagccataaaaaatgttgagttcatgtcctttgtagggacacggatgaagctagaaaccatcattctcagcaaactattgcaaggaaaaaaaccaaacaccacatgttctcactcataggtgggaactgaacaatgagaaaacatggatacaggaaggggaacatcacacactggggacagttgtggggtggggggaggggggaaggatagcattaggagatatacctaatgttaaatgacgagttaatgggtgcagcacaccaacatggcccatgtatacatatctaacaaacctgcacgttgtgcacatgtaccctaaaacttaaaat---ataataa i panTro2.chrUn C 0 C 0 e ponAbe2.chr3 159732849 6617 - 202140232 I e bosTau4.chr1 138180688 0 - 161106243 C e loxAfr3.scaffold_13 20606772 18 - 62548349 I e oryCun2.chr14 141889660 402 + 163896628 I e canFam2.chr31 14110469 0 + 42263495 C e equCab2.chr26 13361397 0 + 41866177 C e rheMac2.chr2 189454994 1 - 189746636 I e cavPor3.scaffold_34 15808504 14 - 24440124 I a score=19953.000000 s hg19.chrUn_gl000245 11420 55 + 36651 aaaaaaTTAACAGGAGACTTTTAT-ACAGATAAATTTGCTTTGCATCATGATCAGC------ s rheMac2.chr2 189454995 33 - 189746636 ------TTAACAGGAGCCTTTTAT-ACAGATAAATTTGCT---------------------- i rheMac2.chr2 I 1 I 1 s cavPor3.scaffold_34 15808518 33 - 24440124 ----------------------AT-ACAATTCAACTTGTTTTCCAGCACGGTCAAC------ i cavPor3.scaffold_34 I 14 C 0 s canFam2.chr31 14110469 50 + 42263495 ------CCAACAAGAGTCCATTATTACAGATAAATGTGTTTTGTTTTATCCTCAAT------ i canFam2.chr31 C 0 C 0 s equCab2.chr26 13361397 55 + 41866177 -AATAATCAACAGGAGCCTCTTATTACAGATAAATATGTTTTGCTTCATGGTCTAT------ i equCab2.chr26 C 0 C 0 s bosTau4.chr1 138180688 44 - 161106243 GAAAAATCAATAG------------CCAGATAAATGTGTTTTGTTTCACAATCGAT------ i bosTau4.chr1 C 0 C 0 s panTro2.chrUn 47408077 55 - 58616431 aaaaGATTAACAGGAGACTTTTAT-ACAGATAAATTTGCTTTGCATCATGATCAGC------ i panTro2.chrUn C 0 C 0 s loxAfr3.scaffold_13 20606790 33 - 62548349 -----------------------------ACAAATTTGTTTTCCTTCATGATCGTGATCAAC i loxAfr3.scaffold_13 I 18 C 0 e ponAbe2.chr3 159732849 6617 - 202140232 I e oryCun2.chr14 141889660 402 + 163896628 I a score=105838.000000 s hg19.chrUn_gl000245 11475 107 + 36651 ACTAAAGAGCATCATAGATTTAAACCATATTTTCACAGTTAAAACAATGTAACCAAATATGCAATA-TATTATGTAACATTCTACAAGAT-GTTTTCAAACATGCAAA-C s panTro2.chrUn 47408132 107 - 58616431 ACTAAAGAGCATCATAGATTTAAACCATATTTACACAGTTAAAACAAGGTAACCAAATATGCAATA-TATTATGTAACATTCTACAAGAT-GCTTTCAAACATGCAAA-C i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189455029 108 - 189746636 ACTAAAGAACATCATAGATTGAAACCATATTTACATAGTTAAAACAATATAATCAAATATGCAACA-TATTGTGTAACATTGTACAAGATGGTTTTCAAACATACAAA-C i rheMac2.chr2 I 1 C 0 s cavPor3.scaffold_34 15808551 100 - 24440124 ACTAAAG---GCCATAGATTT-GATAGTATTTACGTAATTAAAATAATATACTCAAATATTGGATA-CA---TGCAAC-TTGTACATAATACTTTTCAGATCAGGTAA-T i cavPor3.scaffold_34 C 0 C 0 s bosTau4.chr1 138180732 95 - 161106243 ACTTAAGAACATCATAGATTTAAAC----TATGTATAGC-----TAATATAATCCAATATTGGGTG-TATAACGTGACA---TATAAAACGTTTTATAAACATGCAAA-- i bosTau4.chr1 C 0 I 1 s canFam2.chr31 14110519 104 + 42263495 ACTAAAGAACATCATAGATTTAAACAGTATTTACATAGT-----TAATATAATCTAATATTGGATGTTATAGTGTGATGCTGTACAAAATGTTTTTCTGACATTCAAAT- i canFam2.chr31 C 0 C 0 s equCab2.chr26 13361452 107 + 41866177 AGTAACGAACATCATAGATTTAAATAGTATTTACATGGTTAAGGTAATATAATCAAATATTGGTTA-TATAATGTGACACTGTATGAAATGCTTTTCAAACATGCAAA-- i equCab2.chr26 C 0 I 255 s loxAfr3.scaffold_13 20606823 103 - 62548349 ACTAGACAGAATCATAGCTTTCAACTGTATTCACATAGT-----TAGATCAATCAAATGTTGAATG-TATAATGAGACATTGTGTAAAGCACTTTTCAAACATGCAAA-A i loxAfr3.scaffold_13 C 0 C 0 e ponAbe2.chr3 159732849 6617 - 202140232 I e oryCun2.chr14 141889660 402 + 163896628 I a score=31692.000000 s hg19.chrUn_gl000245 11582 29 + 36651 TGACCTTTAAAACAATTTTGCATAA----------AATA s panTro2.chrUn 47408239 29 - 58616431 TGACCTTTAAAACAATTTTGCATAA----------AATA i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189455137 29 - 189746636 TGATCTTTAAAACAATTTTTCATAA----------AATA i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15808651 29 - 24440124 TGACTTGTGAGCAAATTTTTCATGG----------AATA i cavPor3.scaffold_34 C 0 C 0 s bosTau4.chr1 138180828 38 - 161106243 TGATTGTTAAAGCTATTGT-CATGGTAATTTTGCAGGTA i bosTau4.chr1 I 1 I 5 s equCab2.chr26 13361814 28 + 41866177 TGATCTTTAAAGCAATTAT-CGTGG----------GATA i equCab2.chr26 I 255 C 0 s canFam2.chr31 14110623 28 + 42263495 TGATCTTTAAAGCAATTAT-CATGG----------GATA i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20606926 29 - 62548349 TGACCTTTAAACCAATTTACAGTGG----------GATA i loxAfr3.scaffold_13 C 0 C 0 e ponAbe2.chr3 159732849 6617 - 202140232 I e oryCun2.chr14 141889660 402 + 163896628 I a score=31338.000000 s hg19.chrUn_gl000245 11611 48 + 36651 ACATTTCTAGGTAAGAGAAAATACAGACATGTGGTTAGGGCAAAATAT s panTro2.chrUn 47408268 48 - 58616431 ACATTTCTAGGTAAGAGAAAAGACAGACATGTGGTTAGGGCAAAATAT i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189455166 46 - 189746636 TCATTTTTAGGTAAGAGAAAAGACAGAC--GTGGTTAGGGCAAAGTAT i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15808680 42 - 24440124 AT-TTTACAGGTAAAACAAAAGACA-----GTGTTTAAAGTAAAATAT i cavPor3.scaffold_34 C 0 C 0 s equCab2.chr26 13361842 45 + 41866177 -ATTTTTTAGGTAAAAGAAATGACATTG--TTGGTTAAGGCAGAATGT i equCab2.chr26 C 0 I 2 s canFam2.chr31 14110651 45 + 42263495 -AATTTGCACATAAAAGAAATGATATTA--TGAGTTAAGGCAAATTTt i canFam2.chr31 C 0 I 184 s loxAfr3.scaffold_13 20606955 44 - 62548349 -GTTTTGCAGGTAAAAAAATAAATAAA---TGGGTTACAGCGAAATAT i loxAfr3.scaffold_13 C 0 I 2 e ponAbe2.chr3 159732849 6617 - 202140232 I e bosTau4.chr1 138180866 5 - 161106243 I e oryCun2.chr14 141889660 402 + 163896628 I a score=29128.000000 s hg19.chrUn_gl000245 11659 34 + 36651 TTCTGT--TCAAATTACAAAATACTGAATGACAAAT s panTro2.chrUn 47408316 34 - 58616431 TTCTGT--TCAAATTACAAAATACTGAATGACAAAT i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189455212 34 - 189746636 TTCTGT--TCAAATTACAAAATCCTGAATGACAAAT i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15808722 34 - 24440124 GTTTGTGCTTAAATTAC-AGATCCTCTTTGCTAAA- i cavPor3.scaffold_34 C 0 C 0 s equCab2.chr26 13361889 32 + 41866177 TTCTGT--TCAAATTAAATGATCCTGAACA--AAAT i equCab2.chr26 I 2 C 0 s canFam2.chr31 14110880 32 + 42263495 TTCTGT--TCAAATTATATGACCCTGaatg--aaat i canFam2.chr31 I 184 C 0 s loxAfr3.scaffold_13 20607001 34 - 62548349 TTCTGT--TCAAATCACATAATCCTACATGGCAAGt i loxAfr3.scaffold_13 I 2 I 192 e ponAbe2.chr3 159732849 6617 - 202140232 I e bosTau4.chr1 138180866 5 - 161106243 I e oryCun2.chr14 141889660 402 + 163896628 I a score=-6949.000000 s hg19.chrUn_gl000245 11693 29 + 36651 -----CACAGGATAGAAAAGAAT-TATATTGTACC s panTro2.chrUn 47408350 29 - 58616431 -----CACAGGATAGAAAAAAAT-TATATTGTACC i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189455246 28 - 189746636 -----CACAGTATAGAAAA-AAT-TATATTGTACC i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15808756 15 - 24440124 --------------------AATACGTATTTTATC i cavPor3.scaffold_34 C 0 C 0 s equCab2.chr26 13361921 26 + 41866177 -----CAT--TATCTCAAAGAAA-TAT-CTGTACC i equCab2.chr26 C 0 I 5 s canFam2.chr31 14110912 2 + 42263495 -----ca---------------------------- i canFam2.chr31 C 0 I 337 s loxAfr3.scaffold_13 20607227 34 - 62548349 TGCAGGACAGAAGGAAAAAAAAA-ATTATTGCCCC i loxAfr3.scaffold_13 I 192 C 0 e ponAbe2.chr3 159732849 6617 - 202140232 I e bosTau4.chr1 138180866 5 - 161106243 I e oryCun2.chr14 141889660 402 + 163896628 I a score=241595.000000 s hg19.chrUn_gl000245 11722 649 + 36651 TGGAATTTGAA---GTCTTCAAATTTATTTAGGTATATGTATCT-----------------------------ATA--------------TGTATT-------AATAGAGACATAT-----------------TTAACTGATTATAAGTTTAGAACATTTATATTTTAAAGATGTCATTCTTT-A-------AAAATTATTAATATCTACAGGATT---------GATACAGATATTTTAATTT-----------------------------TAAA--CAAATATT---TTTCACTAA--TGTGACCAGCATTTATGTCCTATTTCATTAAACAGACATTTCAAGATT--TTTTAGAGTTAATTTTTAAAAATTAAGTATCACAAATATTTCTGAAGTACTA-CCTTAAAAAA----------TAAA---ACTCTTTCCTAGCTTTTCATATAGTTaaacattttcataatgactaaaaagataaaaataaattagcaaccataattaaattagaattctac--tttttatatcagatgaaatactacataaaatgtccagaaaatctagtgttaatgaggctgtgcagcctggacatttgatgtctcatctgtgggaatgtgaactaacccaacc---attctgaataattattgactctgtgtgttaacagtctagagtcc--tgaaacaaggatcttaattctaaaataaaatcctattctaagaatataccaagggttgataatcaaggaagtttcaaagttatagagaagaaccttcatcctagcatta s panTro2.chrUn 47408379 650 - 58616431 TGGAATTTGAA---GTCTTCAAATTTATTTAGATATATGTATCT-----------------------------ATA--------------TGTATT-------AATAGAGACATAT-----------------TTAACTGATTATAAGTTTAGAACATTTATATTTTGAAGATGTCATTCTTT-A-------AAAATTATTAATATCTACAGGATT---------GCTGCAGATATTTTAATTT-----------------------------TAAA--CAAATATT---TTTCATTAA--TGTGACCAGTATTTATGTCCTATTTCATTAAACAGACATTTCAAGATT-CTTTTAGAGTTAATTTTTAAAAATTAAGTATCACAAATATTTCTGAAGTACTA-CCTTAAAAAA----------TAAA---ACCCTTTCCTAGCTTTTCATATAGTTAAACATTTTCATAATGACTAAAAAGATAAAAATAAATTAACAACCATAATTAAATTAGAATTCTAC--TTTTTATATAAGATGAAATACTATATAAAATGTCCAGAAAATCTTGTGTTAATGAGGCTGTGCAGCCTGGACATTTGATGTCTCATCTGTGGGAATGTGAACTAACCCAACC---ATTCTGAATAATTATTGGCTCTGCGTATTAACAGTCTAGAGTCC--TGAAACAAGGATCTTAATTCTAAAATAAAATCCTATTCTAAGAATATACCAAGGGTTGATAATCAAGGAAGTTTCAAAGTTATAGAGAAGAACCTTCATCCTAGCATTA i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189455274 656 - 189746636 TGGAATTTGAA---GTCTTCAAATTTATTTAGATCTATGTATGC----------------------------------------------TATTTT-------AATAGAGGCATAT-----------------TTAACCGATTATAAGTTTATAACATTTATATTTTGAAGATGTCattatttaa-------aaaaatattaatatttataGGATT---------GCTGCAGAGATTTTAATTT-----------------------------TAAA--CACGTATT---TTTCACTAA--CGTGATCAGCATTTATGTTCTATTTCATTAAAGAGACATTTCAAGAGC-CTTCTAGAATGAATTTTTAGAAATTAAGTATCACAAATATTTCTGAAGTACTA-CCTAAAAAAAAAAAAAAAACAAAA---ACGCTTTCCTGGTTTTTCATGTAGTTAAACATTTTCATAATGACTAAGAAAGTAAAAATAAATTAATGACCACTACTAAATTAGAATTCTAC--TTTTTATACCAGATGAAATACTGTATAAATCATCCAGAAAATCTAGCATTAATGAGGCTGTGCAGCCGGGACATTTCATGTCCC--TTGTGGGAATGTAAACTAACCTGACC---ATTCTGAATAATTATTGGCTCTGTGTGTTAACGGACTAGAGTCC--TGAAACAAGGATCCTAATTCTAAAATAAAATCCTATTCTAAGAATATGCCAAGGGTTGATAATCAAGGAAGTTTCAAAGTTATAGGGAAGAACCTTCATCCTAGCATTA i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15808771 647 - 24440124 TAGAATGTGAATTTGTCTAGATGTTCCTTTAGGTGTATTTATCTTAATAA-------------AGCTATTCAAATAT-------------TGTTTTTACACAAAATTAAAATATGTGATGA---AAATATTCCTTAATTGATTAGAATTTCACAAC-TTTATATTTTAGAGATGCCAGCTTTT-A---GCTTAAAATCACTAAAGTCTACAATATT---------GCTGAAGACATTTTAATTG-----------------------------AAAATCCATGTATTATATTCCATGAAATTGTAAGGATTATTTATGTCATGTTTCATTAAAGAGATATCTCAGGAATGGTTTCATAATT-TTTTTAAAAAATCAAATATCACAAACTTTTCTAAAGCAGAAGTATTAAAATA-------------------CCCTTTGAAGCTGTATGTATA---------TTTTTTAAAAACAAAAATACCAAAAATACAT------------ACAAATTTGATTT------TGTTCATACTAGCTTAAATATTTCAAAACATGCCCATAAAATCTAGTGCTGTTGAAGTTATACAACTTAGACTATTGATGTCCCATTTGTGGAAAT------CAACCCAGACAAAATTCTGAAGAATTACTGAGGGTGCTTAATAATAGCCTACTGTCCTTTGAAACCAGAGTCCTACTTCCAAAATATGAAC-------------------AGGATTGATAACCAGGAAAGTTTCAGAAGTACAAATAATAGCATTTATCCCA----TA i cavPor3.scaffold_34 C 0 C 0 s loxAfr3.scaffold_13 20607261 724 - 62548349 TCAAACTTGAGTTTGTCTTTA----TACGTAGGCATATTTATTTCATTAAAGAAAATAAGTACAGAGATTAAAATATTGGGGGAATTGAGTGCTTTTCCAC--AGTTAAAATATTAAGTAACACAAATATTTTTTAACTGATTATGAGTTAACGACATCCATATTTTGGATATGTTATTTTGA-AACAGTGTAACATTGCTAGTATTGACAGGATTCCCACTTCAGATACTGAGATTCTAATTGAAATTAAATAGAGATTTGTTTCTCTTCCATAAA--CTGATATT---TTACACTAA--TGAGACTGCCATTTGCGTCCTCCTTCATTAAAGGGACTTTT-----TT-TTTTTAAAGTAAATCAAAATAAATCAAGTATCAAAAATTTTTCTGAAATA----CTTTAGAACA--------ACTAAAAGTATACTTTTCTGACTTTTGATATAGTTTAA-GTTTTCATAGTGATGAAAAAATT---GATAGAC------------TTACATTAGAATTTTACCTTTATCCTACCAGGGGGTAAATTATATCAAGTGTTTACAAAATTCATTGTAAGGAAGGTTGTACATCCTGGACATTTGATATCACATTTGCGGGAATGTGAATTAACCCAGCC---CTTCCAGAGAAGTGTTGG-TATGTTTATTAACACACTACATTCCATTAAAACAGGAATCTCAATTCTGA------------------GAATGTACCCAGGGTTGGTAACCAAG-AATTTTCAGCCACCTAGAGAAGGACAATCATCCTATCATCA i loxAfr3.scaffold_13 C 0 I 2496 e ponAbe2.chr3 159732849 6617 - 202140232 I e bosTau4.chr1 138180866 5 - 161106243 I e oryCun2.chr14 141889660 402 + 163896628 I e canFam2.chr31 14110914 337 + 42263495 I e equCab2.chr26 13361947 5 + 41866177 I a score=66004.000000 s hg19.chrUn_gl000245 12371 196 + 36651 tatatGTAATCAT--------------------------CCATATAAACCACATAGTGTTGAATGAAATTACAGAAAAACAAAGAGCCTACAGAATATGTTTCTCTTTGTGTACAACAGTAAATGTACACATCTATCCATGTAAAATTTTACATCTCAGGAAGATAGGTACCAACATGTTAAC-ATG---CTATATCTATAAGATAAGAAATTTTACTTTCCTACA s panTro2.chrUn 47409029 196 - 58616431 TATATGTAATCAT--------------------------CCATATAAACCAGATAGTGTTGAATGAAACTGCAGAAAAACAAAGAGCCTACAGAATATGTTTCTCTTTGTGTACAACTGTAAATGTACACATCTATCCATGTAAAATTTTACATCTCAGGAGGATAGGTACCAACATGTTAAC-ATG---CTATATCTATAAGATAAGAAATTTTACTTTCCTACA i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189455930 197 - 189746636 TATATGTAATCAT--------------------------CCATATAAACCAGATAGTGTTGAATGAAACTGCAGAAAAACAAAGAGCCTACAGAATATGTTTCTCTTTGTGTACACCTGTAAATGTACACATCTATCCATGTAAAATTTTACATCTCAGAAGAATAGGCACCAACATGTTAACAATG---TTATATCTACAAGATAAGAAATTTTACTTTCCTACA i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15809418 213 - 24440124 TATATGTGTATATAGATGTATGTGGGTACATAAATCTCACCATGTAAACCTGATAATTTTGAGTGAAACAGTAAAATAACAAAAAGCATATAAA------TTACCTTTGTGTGAAACTAAAAGTATGCACTT------ATGCAAAATTTTATATCTTATAAAGATTTGCACAAAATAATTTAA-ATGTGCTTAAATGTAGAAAATATGAAATTTTACTCCTGTATA i cavPor3.scaffold_34 C 0 I 54 e ponAbe2.chr3 159732849 6617 - 202140232 I e bosTau4.chr1 138180866 5 - 161106243 I e loxAfr3.scaffold_13 20607985 2496 - 62548349 I e oryCun2.chr14 141889660 402 + 163896628 I e canFam2.chr31 14110914 337 + 42263495 I e equCab2.chr26 13361947 5 + 41866177 I a score=106469.000000 s hg19.chrUn_gl000245 12567 462 + 36651 ATTTcat----acacacacacacacacacactctcaaacatacatacccacacacCGAGGatatatacacacacaaatatatatataaacatacatgtttatataggtac----------acacacacatacatatacacagatggtcaacaaattataatggttcaatttatga---tttatttactttatgatgaagcaaaagtgatagctttgaatagaatataaccattctgcttttcactttcagtacaatattcaacaaattacataaaatatccaaaactttattataaagtgggttttgtattcaatgattttgcccaattgtcagctgatgtaagtgttctgagcacattaaaggtatgccaggctaagctgtgatattcagtaagttagg--tattaaatacatttttaacttactgtattttcaatttataatcagcttatcaagacttaaccccattgtacattgaaaa s panTro2.chrUn 47409225 469 - 58616431 ATTTcatacacacacacacacacacacacactctcaaacacacatacacacacacCGAGGatatatacgcacacaaatatatatataaacatacatgtttatgtaggtac----------acacacacatacatatacacagatggtcaacaacttataatggttcaatttatgattttttttttactttatgatgaagcaaaagtgatagctttgaatagaatataaccattctgcttttcactttcagtacaatattcaacaaattacataaaatatccaatactttattataaagtgggttttgtattcaatgattttgcccaattgtcagctgaagtaagtgttctgatcacattaaaggtatgccaggctaagctgtgatattcagtaagttagg--tattaaatacatttttaacttactgtattttcaacttataatcagcttatcaagacttaaccccattgtacattgaaaa i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189456127 450 - 189746636 ATTTCAT--------ACACACACACACTCTCTCTCA------------CACACACAGAGGatatatatgcacacaa--atatatataaacatacatatttatatagatacacacacatatacacacacatacatataCAcagatggtcaccaacttataatggttcaatttatga---tttttttactttatgatgaagcaaaagtgatagctttcaatagaatataactattctgcttttcactttcagtataatattcaacaaattacataaaatatacaatactttattataaaatgggttttgtattcaatgattttgcccaactgtcagctgatgtaagtattctgagcacattaaaggtatgccaggcta-----tgatattcagtatgtcaggtatattaaatacatttttaacttacagtatttt-aatttatgatcagtttatcaagacttaaccccattgtacattgaaaa i rheMac2.chr2 C 0 C 0 e ponAbe2.chr3 159732849 6617 - 202140232 I e bosTau4.chr1 138180866 5 - 161106243 I e loxAfr3.scaffold_13 20607985 2496 - 62548349 I e oryCun2.chr14 141889660 402 + 163896628 I e canFam2.chr31 14110914 337 + 42263495 I e equCab2.chr26 13361947 5 + 41866177 I e cavPor3.scaffold_34 15809631 54 - 24440124 I a score=8538.000000 s hg19.chrUn_gl000245 13029 33 + 36651 gcatttgTATTGCATTAAACATGTTATAT-ATAT-- s rheMac2.chr2 189456577 34 - 189746636 gcatttgTATCGCATTAAGCATGTTATATAATAT-- i rheMac2.chr2 C 0 C 0 s panTro2.chrUn 47409694 34 - 58616431 gcatttgTATTGCATTAAACATGTTATATAATAT-- i panTro2.chrUn C 0 C 0 s loxAfr3.scaffold_13 20610481 32 - 62548349 gtGTTTGTAT----TTGAGCACGTATAATAATAGTT i loxAfr3.scaffold_13 I 2496 C 0 e ponAbe2.chr3 159732849 6617 - 202140232 I e bosTau4.chr1 138180866 5 - 161106243 I e oryCun2.chr14 141889660 402 + 163896628 I e canFam2.chr31 14110914 337 + 42263495 I e equCab2.chr26 13361947 5 + 41866177 I e cavPor3.scaffold_34 15809631 54 - 24440124 I a score=38218.000000 s hg19.chrUn_gl000245 13062 77 + 36651 TTTT---AATTGAAATTACTGGCAACTTTTGAAAAAATGTAATGAAATAATGTGCTTTGCTATTGGTTAAAATGTTTTTG s panTro2.chrUn 47409728 77 - 58616431 TTTT---AATTGAAATTACTGGCAATTTTTGAAAAAATGTAACGAAATAATGTGCTTTGCTATTGGTTAAAATATTTTTG i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189456611 77 - 189746636 TTTT---AATTGAAATTACTGGCAACTTTTGAAAAAATGAAATGAAATAATGTGTTTTGCTATTGGTTAAAATGTTTTTg i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15809685 76 - 24440124 TTTT---AATAGGAATGATTTACAACTTTC-AAAAAATGAAATTAATTAAGGTCTTTTGTCATTGGTTATGATGATTTCG i cavPor3.scaffold_34 I 54 I 1072 s loxAfr3.scaffold_13 20610513 72 - 62548349 TTTTAAAAATTGAAGGTTTTTGCTACTTTTAAGAGAATGAAACAAAGTGAAGTCTTTTGTTATTGCTTAAGA-------- i loxAfr3.scaffold_13 C 0 I 3 e ponAbe2.chr3 159732849 6617 - 202140232 I e bosTau4.chr1 138180866 5 - 161106243 I e oryCun2.chr14 141889660 402 + 163896628 I e canFam2.chr31 14110914 337 + 42263495 I e equCab2.chr26 13361947 5 + 41866177 I a score=26883.000000 s hg19.chrUn_gl000245 13139 119 + 36651 ggcagggtcagtggcttacacctgtaatcccagcactttggtaggctgaggtgggcagatcgcttgaggtcaggagtttgagaccaacctggcaaacagggtgaaaccccatctctact s panTro2.chrUn 47409805 119 - 58616431 ggccgggtcagtggcttacacctgtaatcccagcactttggtaggctgaggtgggcagatcacttgaggtcaggagtttgagaccagcctggcaaacatggtgaaaccccatctctact i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189456688 119 - 189746636 gccaggggcagtggctcatgcctgtaatcccagaactttgggaggccaaggcggctgcatcagttgaggtcaggagtttgagaccagcctggaaaacatggtaaaacctcatctctact i rheMac2.chr2 C 0 C 0 e ponAbe2.chr3 159732849 6617 - 202140232 I e bosTau4.chr1 138180866 5 - 161106243 I e loxAfr3.scaffold_13 20610585 3 - 62548349 I e oryCun2.chr14 141889660 402 + 163896628 I e canFam2.chr31 14110914 337 + 42263495 I e equCab2.chr26 13361947 5 + 41866177 I e cavPor3.scaffold_34 15809761 1072 - 24440124 I a score=82860.000000 s hg19.chrUn_gl000245 13258 200 + 36651 aaaaatacaaaaatcatctgagtgtggtggcatgtgcctgtaatcccagctactagggaggctgaggtgtgagaattgcttgaactaggcaagcagaggttgcagtgagccaagatcatgccactgcactccagcctgggcaactgagtaagattctgtcaaaaaaaaaaa-------------aaaaaagaaggaaagaaaaG-AAAAAAAGT s panTro2.chrUn 47409924 203 - 58616431 aaaaatacaaaaattatctgagtgtggtggcatgtgcctgtaatcccagctactagggaggctgaggtgtgagaattgcttgaactaggcaagcagaggttgcagtgagccaagatcatgccattgcactccagcctgggcaacagagtaaggttctgtcaaaaaaaaaaa-----------agaaaaaagaaagaaagaaaaGAAAAAAAAGT i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159739466 213 - 202140232 aaaaatacaaaaattatccgagtgtggtggtg-gtgcctgtaattccagctacttgggaggctgaggtgggagaattgcttgaaccaagcaagcagaggttgcagtgaaccaaaatcatgccattgcactccagcctgggcaacagagtaagactctgtcaaaaaaagaaaaaaaaaagaaaaaagaaaagaaagaaagaaaagaaaaaaaaAG i ponAbe2.chr3 I 6617 C 0 s rheMac2.chr2 189456807 174 - 189746636 aaaaatacaaaaattaccttagtgtggtggcgtgtgcctgtagtcccagctacttgggaggctgaggtgggaggattgcttgaaccaggcaagcagagattgcagtgagccgagatcatgccatttcacttcagcct--gcaacagagtaagactctgtcaaaaagaaaaa--------------------------------------CAAGT i rheMac2.chr2 C 0 C 0 e bosTau4.chr1 138180866 5 - 161106243 I e loxAfr3.scaffold_13 20610585 3 - 62548349 I e oryCun2.chr14 141889660 402 + 163896628 I e canFam2.chr31 14110914 337 + 42263495 I e equCab2.chr26 13361947 5 + 41866177 I e cavPor3.scaffold_34 15809761 1072 - 24440124 I a score=183631.000000 s hg19.chrUn_gl000245 13458 284 + 36651 TTTCAGCTTCAAGTAACAGAATAGTCAACTAATTAAAG-AAAAAAACAAGGAGCAACTTTT-----ACCAAATCGCACAACAAATAGATGGTATCAATGCTTACTTAATTCAACATGATCCA---CTTTGTGATTCTCTTATCTTTCTACCTATGTTTTCAAGATGGCTATGGCATTCCC-AGCCTTACAACTTCATGTGACAAAATCCAATGGCAGGAAATAATAAGTGACGGCATTTTGGAACTTTAAGGAAAAACTTTAAGGATTGGAAAAcagggatgccatatgtccag s rheMac2.chr2 189456981 287 - 189746636 TTTTAGCTTCAAGCAACAGAATAGTCAACTAATCGTAGAAAAAAAATAAGGAGCAACTTTT-----ACCAAATTGGACAACAAATAGAT-GTATCAATGGTTAGTTAACTCAACATGATCCACTTCTTTGTGATTCTCTTATCTTTCTACCTATGTTTTCAAGATGGCTATGGCATTCCC-AGCCTTACAACTTAATGTGACAAAATCCCATGGCAGGAAAGGATAAGTGAGGATGTTTGGGAACTTTGAGGAAGAACTTTAAGGACTGGAAAAcagggctgccaaatgtccag i rheMac2.chr2 C 0 C 0 s ponAbe2.chr3 159739679 287 - 202140232 TTTTAGCTTCAAGTAACAGAATAGTCAACTAATTGTAG-AAAAAAACTAGGAGCAACTTTT-----ACCAAATCACACAGCAAATAGATGGTATCAATGGTTAGTTAATTCAACATGATCCACTTCTTTGTGATTCTCTTATCTTTCTACCTATGTTTTCAAGATGACTATGGCATTCCC-AGCCTTACAACTTCATGTGACAAAATTCAATGGCAGGAAAGAATAAGTGAAGGCATTTTGGAACTTTAAGGAAGAACTTTAAGGATTGGAAAAcagggatgccaaatgtccag i ponAbe2.chr3 C 0 C 0 s panTro2.chrUn 47410127 287 - 58616431 TTTTAGCTTCAAGTAACAGAATAGTCAACTAATTGAAG-AAAAAAACAAGGAGCAACTTTT-----ACCAAATTGCACAACAAATAGATGGTGTCAATGCTTAGTTAATTCAACATGATCCACTTCTTTATGATTCTCTTATCTTTCTACCTATGTTTTCAATATGGCTATGGCATTCCC-AGCCTTACAACTTCATGTGACAAAATCCAATGGCAGGAAATAATAAGTGACGGCATTTTGGAACTTTAAGGAAAAACTTTAAGGATTGGAAAAcagggatgccgtatgtccag i panTro2.chrUn C 0 C 0 s loxAfr3.scaffold_13 20610588 277 - 62548349 TTTTGATTTCAAGTAACAGTATACTTAACAAACAATAG-AGAAAAACAA--AGTAATTTTTTTTAAATCAAATTACACAACAAGCAAGGCGTTTCCAGGGTTGTTTAGTCCAACGTGGTTCACTTGTC--TGATTCTCTTGCCTTTC-ACCTATGTTTACAAAATGGCTACAGCAGACCCAAACCTTACAACTTCACATGACAACACCACTTGAC-----------AGTGGGAGTATTTTAGAACTTTGTGGAAGAATtttaatagatggaaaccagggatgctaaacgtccag i loxAfr3.scaffold_13 I 3 C 0 e bosTau4.chr1 138180866 5 - 161106243 I e oryCun2.chr14 141889660 402 + 163896628 I e canFam2.chr31 14110914 337 + 42263495 I e equCab2.chr26 13361947 5 + 41866177 I e cavPor3.scaffold_34 15809761 1072 - 24440124 I a score=152106.000000 s hg19.chrUn_gl000245 13742 226 + 36651 taacatgggatagccgttcctaattaaggattgctgtatgtcctgaatgactttctaatgtaatgaaggtgaataacctgctttgtttaattatacaatcccaaa-tgtaact---gcctaagtgccaag-------------------tacttttgcatggttttaatatgccatgaattttgcaagaatgaaactactatgtatatgagaaaagatggtagattttttcattt--------------agaTACTCATTTCA------- s cavPor3.scaffold_34 15810833 213 - 24440124 TGACAAGGTAAAATCTATCCCATTAAAGGATTTCCGTCTGTCTTGAA----TTTCCAATATACTAAGAGTGAATAACTTGGTTT---TATTTTTAACAATCTGAA-T---AAT---ATATAAGTGCCAGG-------------------TGTTTTTGCTTGGTCTTAACATAGTATGAATTTTTCAGGTACAAAACTATT--------------GGGTGATAGAATTTTTCACTTAAAGTTTTGC---AAAATATAAATTGCA------- i cavPor3.scaffold_34 I 1072 C 0 s rheMac2.chr2 189457268 225 - 189746636 taacatgggataaccactcctaatcaaggattgctgtatgtcctgaatgactttctaatgtaatgaaggtgaataacccattttgtttaattatacaaacccaaa-tgtaact---gcctaagtgccaag-------------------tacttttgcatggttttaatatgccatgaattttccaggaatgaaactactatgtacatgagaaaagatggtaGA-TTTTTCATAT--------------AGATACTCATTTCA------- i rheMac2.chr2 C 0 C 0 s ponAbe2.chr3 159739966 223 - 202140232 taacatgggatagccgctcctaatcaaggattgctacatgtcatgaatgactttctaacataatgaaggcgaataacctgccttgtctaattatacaaacccaaa-tgtaact---gcctaagtgccaag-------------------tacttttgcatggttttaatattccatgaattttgcaggaatgaa---actatgtacattagaaaagatggtagattttttcgttt--------------agaTACTCATTTCA------- i ponAbe2.chr3 C 0 C 0 s panTro2.chrUn 47410414 226 - 58616431 taacatgggatagccgcgactaattaaggattgctgtatgtcctgaatgactttctaatgtaatgaagatgaataacctgctttgtttaattatacaatcccaaa-tgtaact---gcctaagtgccaag-------------------tacttttgcatggttttaatatgccatgaattttgcaagaatgaaactactatgtatatgagaaaagacggtagattttttcattt--------------agaTACTCATTTCA------- i panTro2.chrUn C 0 C 0 s loxAfr3.scaffold_13 20610865 266 - 62548349 caaatgagcctaatcaaccctaataaaggattatcacacagcctgagagactccataatgtcatgaaggtgaatgacttgtcttttttaattatctgaatccagactctaactccaattaacatatcaaggtttttttttttcttttttcttttttttgtggttttaatatgtgatgcattttccaggaatgaaacaattatg----tgaagaaagatggtagtttatttcctttggatatttgccaaaggctattcacTGTATCTGTTA i loxAfr3.scaffold_13 C 0 C 0 e bosTau4.chr1 138180866 5 - 161106243 I e oryCun2.chr14 141889660 402 + 163896628 I e canFam2.chr31 14110914 337 + 42263495 I e equCab2.chr26 13361947 5 + 41866177 I a score=59847.000000 s hg19.chrUn_gl000245 13968 77 + 36651 GA------------GTCTCAATAGGAAAAAT-----------------------AGAACA---------------CACACAAACT-----------------AAGATAATTTAACATGGG----TTTATTTCCAAAGA-----GACTACTTAC s panTro2.chrUn 47410640 77 - 58616431 GA------------GTCTCAATAGGAAAAAT-----------------------AGAACA---------------CACACAAACT-----------------AAGATAATTTAACATGGG----TTTATTTCCAAAGA-----GACTACTTAC i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159740189 77 - 202140232 CA------------GTCTCAATAGGAAAAAG-----------------------AGAACA---------------CATCCCAACT-----------------AAGATAATTTAACATGGG----TTTATTTCCAAAGA-----GACTACTTAC i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189457493 77 - 189746636 GA------------GTCTCAATAGGACAAAG-----------------------ACAACA---------------CACTGAAACT-----------------AAGATAATTTAACATGGG----TTTATTTCCAAAGA-----GACTACTTAC i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15811046 145 - 24440124 AAAACATTGCAAGTGTTTCATCTGGaaaaaaaacaaaacaaaacaaaacaaaacaaaacaaaaAAA--------CCACTCCAACTCCAAATGTCCAAAGATCAAGATAAATGATCAAAAGATCATTTATTTTCTAAGATTTTTTTTTTTTTAT i cavPor3.scaffold_34 C 0 C 0 s canFam2.chr31 14111251 58 + 42263495 -------------------------aaaaaT-----------------------GAAATA---------------TCCTCA---------------------AAGATAATTTAAC-AAGG----TTTATTTACAAA-A-----GACTACTTAC i canFam2.chr31 I 337 C 0 s equCab2.chr26 13361952 77 + 41866177 GA------------GTACAAAAACAAAGAAA-----------------------AAAGCA---------------TTCTCAAAGT-----------------AAGATAACTTAACAAAGG----TTTAATTATAAAGA-----GATCACTTAC i equCab2.chr26 I 5 C 0 s loxAfr3.scaffold_13 20611131 92 - 62548349 AA------------GTCCCATAGGAAAAACA-----------------------ATGGCATACTCGATTTTTTTTTACTCAAATT-----------------AAGATAATTTAACAAGGG----TTTATTTACAAAGA-----GACTACTGGC i loxAfr3.scaffold_13 C 0 C 0 e bosTau4.chr1 138180866 5 - 161106243 I e oryCun2.chr14 141889660 402 + 163896628 I a score=627547.000000 s hg19.chrUn_gl000245 14045 491 + 36651 GAAAATGTCAGCGGAGAAG----GGTGAAGGAATCACAGAAATCACACCCCACAATAACTCTGG--GTTAGTAGCAGCAGGC-AGAGTTCTGGGGA-GTAAACTTCCCTGATCATGCAAGGAAACACTAATTT-TCTTATGAAAA----AGATT----GGTCAAGGAGACCTAGCAGAGAGGGAGTTTAGGCAA-----------------TAACCCCCAATC-CCATTTCCTCCTTCCCTTTAATCTCATGAACATGCATAGAAGGCAATGAGCAAGGGAA--CAGATTG---AGATATTCAATATGGA---------CCATTCCACTTGGACAAAAGCCA-GTAAATAGGGGAGTATAACAGGGGACAAGGGCCAAACAGAAAGTATCTATTACAtttaccaatgcagatcaatcatgtcaaaaacagaaatggcagttttggcatttg-gttattcaatgaaact-------------atatttgtagctttttatttacaatgtttcaaggtatgggcgaagatatgaaaatttcattatgttctatttta s panTro2.chrUn 47410717 491 - 58616431 GAAAATGTCAGGGGAGAAG----GGTGAAGGAATCACAGAAATCACACCCCACAATAACTCTGG--GTTAGTAGCAGCAGGC-AGAGTTCTGGGGA-GTAAACTGCCCTGATCACACAAGGAAACACTAATTT-TCTTATGAAAA----AGATT----GGTCAAGGAGACCTAGCAGAGAGGGAATTTAGGCAA-----------------TAACCCCCAATC-GCATTTCCTCCTTCCCTTTAATCTCATGAACATGCATAGAAGGCAATGAGCAAGGGAA--CCGATTG---AGATATTCAATATGGA---------CCATTCCACTTGGACAAAAGCCA-GTAAATAGGGGAGTATAACAGGGGACAAGGGCCAAACAGAAAGTATCTATTACAtttaccaatgcagatcaatcgtgtcaacaatagaaatggcagttttggcatttg-gttattcaatgaaact-------------atatctgtagctttttatttacaatgtttcaaggtatgggcgaagatatgaaaatttcattatgttctattgta i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159740266 491 - 202140232 GAAAATGTCAGGGGAGAAG----GTTGAAGGAATCACAGAAATCACACCCCACAATAACTCTGG--GTTAGTAGCAGCAGGC-AGAGTTCTGGGGA-GTAAACTGCCCTAATCACACAAGGAAACACTGATTT-TCTTATGAAAA----AGATT----GGTCAAGGAGGCCTAGCAGAGAGGGAGTTCAGGCAA-----------------TAACCCTCAATC-CCATTTCCTCCTTCCCTTTAATCTCATGAACATGCATAGAAGGCAATGAGCAAGGGAA--CCTATTG---ACATATTCAATATGGA---------CCATTCCACTTGGACAAAAGCCA-GTAAATAGGGGAGTGTAACAGGGGACAAGGGGCAAGCAGGAAGTATCTATTACATTTGCCAGTGCAGATCaatcatgtcaacaatagaaatggcagttttggcatttg-gctattcaatgaaact-------------atatttgtagctttatatttacaatgtttcaaggtatgggtgaagatatgaaaatttcatcatgttctattgta i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189457570 485 - 189746636 AAAAATGTCAGGAAAG-AG----GGTGAAGGAACCACAGAAATCACACCCAACAATAACTCTGG--GTTAGTAGCA----GC-AGAGTTCTGGGGA-GCAAACTGCCCTGATCACATAAGGAAACACTGATTT-TCTTATGAAAA----AGAGA----GGTCAAGGAGACCTAGCAGAGTGGGAGTTTAGGCAA-----------------TAATCCCCAGTC-CCCTTTCCTCCTTCCCTTTAATCTCATGAACACGCATAGAAGGCAATGAGCAAGGGAA--GCTATTG---AGATATTCAATATGGA---------CCACCCCACTCGGAC-AAAGCCA-GTAAATAGGGTAGTATAACTGGGGACAAGGGGCGAACAGAAAGTATCCATCGCATTGACCAGTGCAAATCAATCATGTCAACAATAGAAATGGCAGATTTGGCATTTA-GTTTTTCAATGAAAct-------------gtatttgtagccgtttatttacaatgtttcaaggtatgggcgcagatatgaaaatttcatcatgttccactgta i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15811191 465 - 24440124 GAAGTTGGGGAAGGAGA-------GTAGAGGAACCTTA----------------GTAACTCTGG--GTTGGTAGCATCAG---AAAGTTGT-GGCT-ACAAACCACCTTGTTTATACAAG--------TATTT-TCTTATGAGAA----ACACA------TCAAGACCATTCAGTAAGAATGGATCCTGTAACA----------------CTACACCATA-TC-TCATTTCTACCTTCTCTTGAA--CCTTAAATACACCCAGAAACCAAAGAACAGGACAGCCTATCCTgttcacacagttcacacagttcacacagttcaTTCAATCCAAACAAACTC-----AGGTAAAGAGA---AAAGTATAACAGGGAAAGAAGTGAGGATATTTGTGACATTTTCCACTTCATGTCAGTCATATCAACAATGGGAATGGCAGTTTTGGTATTTG-GTTAGGAAATGAAACAGAAACACATGATAGTATTTGTAGCTTTGTGTCTGTAATCATGCAAAATAGAATTCAGCCATAAAATA-TTCATTAT----------- i cavPor3.scaffold_34 C 0 C 0 s bosTau4.chr1 138180871 471 - 161106243 GAAGGTGTGGGAAGATAGG----AGAAGATGCACCACAGTAG-----------TATAACTCTGACTTTTACTCACAGCAGAG---TATCCTGGGGA-AGAAGCCACCTTGAGACAGAAAGGGAACA-GGACCT-TC--ATAGCAGACACAGATT----GGCCAAGGAGACCTAGCAGGCAGAGAGCTTGTGG-A-----------------TAACCCCTGACCATTCTCTCTTCCTTCTCACTGATGTCTTGAACACATATAAAAGTCAAAGAGCAAGGGAG--CTCACTG---ATATATTCAATACAGG---------TCATTCTACTTGGATGGAAATGGAGTAGAGTGTGAAGTACAACTCAGAATA-AGGA-GCACATAGAATATCT--CACAGGTACCAGTCCAGATCAGTCATGTCAAAAATACAGATGGAAATTTCGGTTTTTGAGTTCTCCAGTGAAACTTAGATGCATCACTATATTGTA----TTGCATTCACAGGGATTCCAGATATGGGTATAGGCCGAAGAC-TGC---------------- i bosTau4.chr1 I 5 I 266 s equCab2.chr26 13362029 500 + 41866177 AAAGGTGTGGGGGGATGGG----AATAGAGGAACCACAATAAGTAGC----ACCATAATTCTGG--GTTAGGAACAACAGAG-AGAATCATGGGTATAGAAACCACCTTGAGAGGAGAACGGAACACCCACCT-TCTTATGAGAGA---AGATT----AG-CAAGGAgaccttgtagggagggagcctgtggaa-----------------ttatccctgactgctctttctaacttccttccaatctcttgaacacaaacagaaatgaaagagcgaggga---gctactg---atatatttagtacagg---------tcatt---cttggacaaaagcagcgtagcgggtggagaacaactagggatgaaggatggacagaagatatctatcaTGTGTTCCAATCCAGATCAGtcatgtcaacaatgagaatggcagtttcagtgtttgagttctccagtgaaactcatatgcattactgtatttgtctctttgcgtttacgatgactcaacatctgggtgcagacatgaaaattttattgcctttcattgta i equCab2.chr26 C 0 I 1 s canFam2.chr31 14111309 499 + 42263495 AAAGGTA-AGGGGGATGAG----ACTGGAGGAACCACAGTGAGTAGC----A-CATA-----GG--GTTAGTAGCAGCAGAGAAAAATCATTGGGA-AGAAACCATCTTAAGAGGAGAAAGAAACACTGAATT-TCTTATGAGAGGCACAGGTT----GGCCAAATAGAccaagtagggagggagattgggaaa-----------------tatcccctgaccactctctactccctccctctaatctcttaaacataaacagaagccaaagggcaagggag--gctactg---atatattcaatatagg---------tcattctacttggacaaaagtgaggtaaactgtgcggtaccacttgggatg-gggatgaacaaaagatatctaCGGCATTTGCCGGTCCAGATCaatcatgtcaacaatgagaatggcagcatcaatatttgaattgtccaataaaactcacacgcattaccatattatagtttttgcatatataatgatataagatacaagtgcacacataaaaa-tgtattatcttccatagta i canFam2.chr31 C 0 I 1 s oryCun2.chr14 141890062 506 + 163896628 --AAGTGTGAAAAGAGAAG----GGAGGAGGAATCACAAGAATTAGA----ATTGTAACTCTGG--GT---TAGCATTAG---AGAGTCATAAGGA-ACAAACTACATTTGTTACACAAGGGA----TCATTTGTCTTAGGAGAG----ACAGAGAGAAGTCAAGAAACCCTATTagggagggagcctttggaataattcctagttccatctcccccacagtt-tcatttccctcttccgtctaatttcttgaatacacccagaagcctaagagtgaaggag--tgtcttg---atatatccaatacaggtcac-----tcattctccttggacaaaatc-----agacagagtagCATACAATGAGACAAGGATAAAGCAGAAGATATGCATCACATTTGCCAATTCAGATCAACCACATCAAT-ATGAGAATGATATTTTAGATATTTG-ATCATCCATTGAACCTCATACGCTTCACCATATTGGTAACTTTGTATTCATAATTATCCAAGAAATAGTTATAGATAAGAACA-TTTTTTATATTCTATT--- i oryCun2.chr14 I 402 I 391 s loxAfr3.scaffold_13 20611223 481 - 62548349 AAAGGGGTAGGCGGCCACGTGGTTGTAGAGCAATCACTGGGGATAGC----GTCATAACTCTGG--GTTAGCAGCAGCAGAG-AGAGTTGTGGGGA-AAAAACTACCTTGAG---AGAAGGGAACACTGACAT-TTTTATGAGAC----AGAGA----GGCTGAAGAAACCTAAAAGGGGAGAAGCCTGTGAAA-----------------CAACCCCTGACTTCTTTCTTCTCCTTCTCTCCAGTTTCTAGAGCCCAGAGAGAAGCTAAAGAACCAAAAAG--CATAGTG---ATTTAGTCAATATGGG---------TGATTCTACTTGGACAAAAGCAT-GAAAAAGGTGGAGCACAAGGCAGGACAAGAGGCAAACA----------------------AGTTCAGATCAATGGCTTCGACAACAGGAAGGGCAGTTTGggtattttaggcatccaacgaaactcacacatatcaatatatttgtagctttacattcagagtgacttaagatgtgtgcggataccttgcgacttcattatgttctatggca i loxAfr3.scaffold_13 C 0 C 0 a score=254770.000000 s hg19.chrUn_gl000245 14536 186 + 36651 -tttgatatgtaaatgttctggcacaattata-tacattttggatcatatattgacagtaaattatttct--ccttt--gttagcttcagcataacattaatattttcaacaacttgaatgcatacattgtg-ttctcactaatagtttagaatagtgaaggggtctttgaagaatttcttatgaagtagagg s panTro2.chrUn 47411208 186 - 58616431 -ttagatatgtaaatgttctggcacaattata-tacattttggattatatattgacagtaaattatttct--ccttt--gttagcttcagcataacattaatattttcaacaacttgaatgcatacattgtg-ttctcactaatagtttagaatagtgaaggggtctttgaagaatttcttatgaagtagagg i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159740757 186 - 202140232 -ttttatatgtaaatgttctggcacaattata-tacattttggattatatattgacagtaaattatttct--ccttt--gttagctgcagcataacattaatattttcaacaacttgaatgcatacattgtg-ttctcactaatagtttagaatagtgaaggggtctttgaagaatttcttatgaagtagagg i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189458055 185 - 189746636 -tttgatatat-aatgttctggcacaattata-cacactttggattctatattgacggtaaattatttct--ccttt--gttagctgcagtataacattaatattttcaacaacgcaaatgtatacattgtg-ttctcactaatagtttagaatagcgaaggggtctttgaagaatttcttatgaagtagagg i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15811656 171 - 24440124 --TAAACATGCAAATGCTTTGATATAAATATATAACCTTT--GATAACAAATTGAGCTTGAG---TGTTT--TTTTT--TATAA-TGTGACATTATGTTG--ATTTCTAATAAATTGAACACATATG-------TTTCACTAGCATTTTAGAATAGTGAAAGGTCCATTCATGAATTTGTT-CTAAATAGAAG i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141890959 184 + 163896628 -TTAAATATATAAATGTTCTTGCATAACTATA-AGCATTTCAGATGATCAATTGATTTTGAGCTATGTCTCATTTGT--GTTAA-TCTTGCAAAGTGTT---ATTTTTAATGATTTGAATGCATACAttata-tttttattaacattttagaatagaataaggggcattcaataatttgttacaaagtagagg i oryCun2.chr14 I 391 C 0 s canFam2.chr31 14111809 183 + 42263495 -ttaaatatgtaaatactttggcacaattat---acagtatttactataaattgatttcaaatcatttct--cctttacataacttgtggc---atatttat-ttcttaaggactcaaaaacatacattatgtttttcactaacatttcagtatagtgaagtgaccattcaagaatgtgttatgatttagagg i canFam2.chr31 I 1 C 0 s equCab2.chr26 13362530 186 + 41866177 -ttaaatatgtaaatgctttggaacaactaca-aacattttttattataatttgatttcaaattatttct--tctttatattagttacagcattatattaat-tttttaatggcttcaatatatatgttatg-ttttcactaacatctttgagtagtgaaggggccactcaagaatttgttctgagtga-agg i equCab2.chr26 I 1 C 0 s loxAfr3.scaffold_13 20611704 181 - 62548349 ttaatacatgtaaatgctcacatacaactaca-------ttttatcataaattgagctcaaattatttct--catttatatcatttgggacattatgtta--aattttaatgatgtgaatacataggttgta-ttatcactagcattttagattagtggatgggccgtccaaaaatttgttataaagtagagg i loxAfr3.scaffold_13 C 0 C 0 e bosTau4.chr1 138181342 266 - 161106243 I a score=622804.000000 s hg19.chrUn_gl000245 14722 455 + 36651 cattgggtcagacagagccgaaaaccattg---gctta---gattaatcactatt--tatcctagggctga---agagggcc------aattgaa---g-acaca------a------at--------gtccaat---ccct---------------------ttatgaccttg----------gagttctatg--aaccagagaaataga-gactggttcttaaggaggtaaTAAG--------------------------------TGTGCCTTCTATGGTTTATAATAATATGCATTGTCTTA-------AC-------AATCGAATACTT-AAAAGTTAATGCCCTC----------------ATAATATGCAAAAT-TTTTAATAAGCACATTG--------------GTCCCTGTGTTCAAGTAGTTGGTAATCAAATTAGCGAAGT---AT---GGTAAGTcttttg-aagagcattaaacagcagagaatgtaagaaatttgtctctataatagtgtggg---------ccttctgtgtttcct---aagggcacattcat--atgatctaa----taactga----gcagagagaagCCTAAGGGATAGTTTTTGGTTTCATTT--------GTTTG-T s panTro2.chrUn 47411394 452 - 58616431 cattgggtcagacagacccgaaaaccattg---gctta---gattaatcactatt--tatcctagggctga---agagggcc------aattgaa---g-acaca------a------at--------gtccaat---ccct---------------------ctatgaccttg----------gagatctatg--aatcagagaaataga-gactggttcttaaggaggtaataag--------------------------------tgtgccttctaTGGTTTATAATAATATGCATTGTCTT-----------------AATCGAATACTT-AAAAGTTAATGCCCTC----------------ATAATATGCAAAAT-TTTTATTAAGCACATTG--------------GTCCCTGTGTTCAAGTAGTTGGTAATCAAATTAGTGAAGT---AT---GGTAAGTcttttg-aagagcattaaacagcagagaatgtaagaaatttgtctctataatagtgtggg---------ccttctgtgtttcct---aaggacacattcat--atgacctaa----taactga----gcagAGAGAAGCCTAAAGGATAGTTTATGGTTTCATTT--------GTTTG-T i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159740943 455 - 202140232 cactgggtcagacagagctgaaaaccgttg---gctta---gattaatcactatt--tatcctagggctga---agagggcc------aattgaa---g-acaca------a------at--------gtccaat---ccct---------------------ctaggacctgg----------gagttctatg--aaccagagaaataga-gactggttcttaaggaggtaaTAAG--------------------------------TGTGCCTTCTATGGTTTATAATAATATGCATTGTCTTA-------AC-------AACTGAATACTT-AAAAGTTAATGCCCTC----------------ATAATGTGCAAAAT-TTTTAATAAGTACTTTG--------------GTCCCTGTGTTCAAGTAGTTGGCAATCAAATTGCTGAAGT---AT---GGTAAGTcttttg-aagagcattaaacagcagagaatgtaagaaatttgtgtctataatagtgtggg---------ccttctgtgtttcct---aaggacacattcat--atgatctaa----taactgg----gcagaaagaagcCTAAAGGATAGTTTATGGTTTCATTT--------GTTTG-T i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189458240 454 - 189746636 cattgggtcagacagagctgaaaaccactg---gctta---gattaattattctt--tatcctagggttga---agagggcc------aattgaa---c-acaca------g------at--------gtctaat---ccct---------------------c-atgaactgg----------gagttctatg--aaccagagaaatagaggactggttcttaaggaggtaataag--------------------------------tgtgccttccataGTTCATAATAATATTCATTGTCTTA-------AC-------AATCGAATACTC-AAACATTAATGCCCTC----------------ATGATATGCACAAT-TTTTAATGAGTACTTTG--------------GTCCCTGTGTTCAAGTAGTTGGTAATCAAACCAGTGAAGT---AT---CGTAAGTCTTTTG-AAGAGCATTAAACAGCAGAGAATGTAAGAAATCTGT-TCTATAATAGTGTGGG---------ACTTCCGTGTTTCCT---AAGGGCACATTCGT--ATGATCTAA----TAACTAA----GCATAGAGAAGCCTAAAGGATAGTTTATGGTTTCATTT--------GCTTG-T i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15811827 423 - 24440124 CATTTGATCCAATA----TGAAAGCT-------GCTTATTTGACTAATCACCATT--CTTCCT-------------GGGGTC------CACTGAA---GCACACA------G------AT--------TTCTATT---ATCA---------------------GTATATACCGA----------GAGATTGATT--AACCAGAGAAATAGA-GATTGGCC----GGGAGGTGACAAC--------------------------------TATGTCTTCTATGGTTGGTTAGAATATGTGCTAACTTA-------TC------------AACAATT-GAATGTTAATGCTCCCTATAATGAAACAAAATATAATCCCTAAT----TTCAAGAATGACTTTT--------------TTTTC-----------CTTT-----TTTCTTCTATAAGGT---AA------------GCTG-AAGACCATTAAA-AACAGAGAATATAAGAAATTCATCtttttaacagtgtttgcagtgtagcgctgctgaatttcctgttaaggtcatattcat--ttaatttaa----aaactga----gcagagagcagcctagaggatcacttatgaTTTAG-----------------C i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141891143 460 + 163896628 cactgcatcagatagagctaaaaaccatag---gctta---gattaatcaccgtt--catcctagggctga---ggagggcc------cattgag---gaacaca------a------aa--------gtctaac---acct---------------------gtatg-aatga----------gagttctatt--agctattgaaataga-gaatgactcttgagtaggcagcaa---------------------------------tgtgtcttctaTGACTTGTAACAATGTGCATGGTCTTA-------TTACttaataataaaataatt-aaaaGTTAATGCTCTC----------------ATAATTTGTAAGAC-ATTTGATAGGTACTTTG--------------AGACC-----------AGTTGGCAATCTAATTGACGAGGT---ACCGTAATAAGTCTGTTG-GAGAGCATTAAACAGCAGAGAAGGTAAGAAATTTGTCTCTGTAATGGTATGTGCAGTGTG--ACTTCTGCGTTACCTGACAAGGGCACAGATATGATCTAATTAC----AAACTGA----GCAGA-AGCAGCCCATGGAGTCAGTCATGATTTTGT------------TCA-T i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138181608 555 - 161106243 catggggtcacaaagagtcagacatgactgagcaatta---aGCAAAGCACAGCCGGTATTCTTgggcttccctggtagctcagacggtaatgaatctgcctgcactatgggagatccag--------gttcaat---ccctaggtcaggaagatcccctggagaagggaatgactatccacatcagtattctt--atctggagaattccatggacagtccatg---ggatcacagagtcagagaagactgacagctaatacTTTCACTTTCATCCTCTATGACTTATCACCT-ATGCA-TGTCTA--------AT-------AACCAAATAATT-AAAAGTTAGAG-CCTC----------------ATAACATGAAAGAC-ATTTAATAAGTACTTTGAAACAAAAAATATAGTCTGTGTTTTGAAGTAATTGGCAGTCTGATTGCTGAAGCAAAAT---AACAGATCTCTTG-ACAAACAGTAATCAGAAGAGAATGTAAGAAAATCTTCTCTGT----TTGTCTGCCATCTGAACTTTTTGC-TTCC-TGTTA-AGGCACATTTAT--ATGATCTA-----TAAC--A----GCATAGAACAGCTTCA-----AGTTTATTATTGTATTT--------ATTTG-- i bosTau4.chr1 I 266 C 0 s equCab2.chr26 13362716 491 + 41866177 tattgggtcagacagagctgagaacaattg---gctta---gatttatcaccatt--cattctagggctga---ggaaggcc------cactgaa---gcacgca-----gg------gt--------gtccagt---tcct---------------------gtatgaaatgg----------gagtcctatt--gaccagagaaataga-gaatgactctta---aggtaacAAG--------------------------------TGCTTCTTCTATGGTTTATAACATGATGCCCTGTCTTATTAATT-AC-------AATAGAATCATT-AAAAGTTAAGGCCCCC----------------ATAATGTAAAAGAC-ATTTGAGAAGCACTTTGAGAGAACAAATATGGTCCCTGTTTTCATGTAGTTGGCAGTCTGATTGTTGAAGTAAGAC---AATAGGTCTTTTC-AAGAACATTAAACAGAAAACAATGTAAGAAAGTTATCTCTATAATAGTGTCT---------GCTCTCTGTGTTCC-TACTAAGGGCACATTCAT--AGGATCCAACAGTTAACTGA----GCATAGAGCAGCCTAAAGGATAGTTTATGATTTTATTTTATCATTTATTTAC- i equCab2.chr26 C 0 I 11 s canFam2.chr31 14111992 488 + 42263495 ctttaggtcatatagagctgaaaaccattg---gctta---gatttatcactatt--cattctagggctga---ggagggcc------tattgaa---gcataca-------------gt--------gtccaat---tcct---------------------gtatgaaatga----------gagtttcatt--agcctgaaaaattga-gaatgtctcatg--taagtaacaag--------------------------------tgtgtcttctaTGATTTATAACATTATGCATTGTCTTATTAATTAAC-------AATTGAATAATTAAAAAGCTACAGCCCCC----------------ATAATGTGAAAAAC-ACTTGACAAGTACCTTGAGACAAAAAATATAGTCCCTGTTTTCAAGTAATTGGCAGTCAAATTACTGAGAT--GAT---AACAGATCTTCTG-AAGGACATTAAACAAAGGAGAAAGGAAGAAAGTCATCtctttaatagtgtctgcagtatgggctttctgtgctccttgttagaggcaca-tcgt--atgatctaataattaattaactacgcatatggcagTCTAAAGG-TAGTGTATGGTTTTATTT--------------- i canFam2.chr31 C 0 I 368 s loxAfr3.scaffold_13 20611885 491 - 62548349 cattggatttgatggagttgagagccCttg---actta---gattaatcaacatt--catcctaggattga---agaggggc------cattgaa---gcacaca------g------gtcccaatggttccaatgggccct---------------------gtatgaaataa----------gaattctatttgaaccaggaaaatagg-gaatggtt-ttagggaagtcaCAAA--------------------------------TGTACCTTCTGGGGTTTGTAACACTATGCACTATCTTA-------TT-------AATT-AATAACT-AAAAGTTAAAGCCTCT----------------ATAACGTGCCAAACAATTTGGCAAGTACTTTGAGACAGAAAATACGGTCCTTGTTTTCCAGTAGTTTACAGCCTCATCA-TGAAATAAGAT----GTAGGTcttttgaaagagtaataaatatcacagaatgtaagag--tagactctataataaagtttgcagcatgagtcttctgctcttcctattaagggcacattcat--atgatctaataacaaactga----gcagagagcagcctaaaggatcatttatgataatttt---------------- i loxAfr3.scaffold_13 C 0 C 0 a score=278479.000000 s hg19.chrUn_gl000245 15177 192 + 36651 TTTT-CCAATTAACATACATTTCTAGATT--AA---AGGTCAACTATCTTTTCCTTGGGAGTCAACTATAGGAGAAGATA-GTGAAGAGGCAAGGAA-AATTACAGCAGC-TCAA--CAGCTTTACCCTGGAAATATCTGTATTGTGTACCGCTATAGCCTACCTT----TATCAGTCAGATAACAATGTCAAAGAGGCAag-cttgg s panTro2.chrUn 47411846 193 - 58616431 TTTTGCCAATTAACATACATTTCTAGATT--AA---AAGTCAACTATCTTTTCCTTGGGAGTCAACTATAGGAGAAGATA-GTGAAGAGGCAAGGAA-AATTACAGCACC-TCAA--CAGCTTTACCCTGGAAATATCTGTATTGTGTACCACTATAGCCTACCTT----TATCAGTCAGATaacaaggtcaaagaggcaag-cttgg i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159741398 193 - 202140232 TTTTGCCAGTTAACATACATTTCTAGATT--AA---AAGTCAACTATCTTTTCCTTGGGAGTCGACTATAGGAGAAGATA-GCGAAGAGGCAAGGAA-AATTACAGCAGC-TCAA--CAGCTTTACCCTGGAAAGAGCTGTATTGTATACCGCTATAGCCTACCTT----TATCAGTCAGATAACAATGTCAAAGAGGCAag-cttgg i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189458694 194 - 189746636 TTTTGCCAATTAACATACATTTCTAGATT--AA---ATGTCAACTATATTTTCCTCAGGGGTCAGCTATAGGAGAAGCTA-GTGAAGAGGAAAGGAA-AATTATAGCAGC-TCAA--TAGCTTTACCCTGGAAATATCCGTATCGTgtactgccgtggcctacctt----tatcagtccgataacaatgtcaaagaggcaaaccttgg i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15812250 169 - 24440124 TTTTG-CAAAAAACATAAATCTCTCAAGC--AATCTAGG----CCATTCTTGGTTAAAGGGTAAGCT--------AGTGT-AGGGACAAGGAACAAA------CTGCACA-GTAA--TGACTTCAGCCTGAAAATATCTATACCGCCTGAA------GTCTACCTT----TATCAAA---ATACCAACATCAAGGTAGTATG-CTTGG i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141891603 193 + 163896628 TTTTGCCAACCAACATATATTTCTTGATC--AA---AGGTCAACCATTCTTTCCCCAGGAATCAGTTTTAGGGGAAGTTT-GGGCACAGGAAAGAAA-ATTGTATTCCCC-AAAA--TAGCTTTAGCCTAGAAATATCTATATTGCCTGAACCTAAGGCGTTCGTT----TCTCCAACAGctatcaatgtaaaagaggtaag-cttgg i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138182163 198 - 161106243 -----CCTACCAACATAGATTTCTAGATCAAAA---AAGTCAACTATTCTTTCCTCAGAAATCAGCTCTA-GAGAAGCTATGGACAGGGGCAGAAGGCAATTGCAGCCTATCTAACTTAACTTTACTCTGAAAATATTCAGGCTGTCAATATCTAAAGTCTACCTTTTTCTATCAGTCAGGTAGTGATgaaaatgaggtaag-cttgg i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13363218 197 + 41866177 -ATAACCGACTAACACAAATTTCTAGATC--AC---AAATCAACCATCCTTTCCTCAAGAATCAGCCCTAGGAGAAGTTGCATGCAGAGGTGAAGGGCAATCGTAGCCCC-ACAA--TAACTTTACCCTGGAAACATCCAGATTGTCTATGTCT-AAGCCTATGTTTATCTAACAGTCAAGTAAAAATGTCATAGAGGTGag-cttgg i equCab2.chr26 I 11 C 0 s canFam2.chr31 28150548 191 - 42263495 -TTTCCCAACCAACATAAATGTCTAGATC--AC---AAGGCAACCATCCTTTCCTCAGGAATCCTCCCTGGGAGAAGCTGTAGGCAGAGGCAAAGGGCAATGGTAGCTCCAATAG--TAACTCTACTCTGGAAATATCCAGATTGTCTATGTCTAAAGCCTACTTTTTTCTATCAGTCAGGTCTGAATCACTTAGtgac--------- i canFam2.chr31 n 368 n 368 s loxAfr3.scaffold_13 20612376 185 - 62548349 -tttgctaaccaatataaatgcctggatc--at---ag--------tccattcctcgggaatcggccctaggagaagctgtgagcagaTGCAAAGGGTGATTGTGGCCTC-ACAA--TAATTTTAGCCTGGAAA-ATTTCCGATGTCTGTGCCTGAAGCACACCTT----TATCAGTCGATTAACAATGTCGAAGAGGTAag-tttgg i loxAfr3.scaffold_13 C 0 C 0 a score=694008.000000 s hg19.chrUn_gl000245 15369 344 + 36651 caccattg-ctcttagtgaatccctgctgccagccttttatc-ctaagtgctctccaaaga--------cccatttaa--tggaccttcctg-aaattgtgctcaggatcaatatgag----------gctcattgatacagcatt----------------------tttggaactcaccatttgcttatttattaaaCCTGGGATAGTT-GCCCGAC--------TTCTATCATCTGAAATCCTCTCCATG--ACTTTCAAAGTTACCAACATTGGTTCCAACATCATTCCTAGAAAACATTTCAGTGGAGTA--TATTTATCTGACATTTGACTGTATTTATAGCAGTAAGAATCTATGGTGATTCCTCCC---AAAATAA----TCCCACAATTACACATTTTGG s panTro2.chrUn 47412039 344 - 58616431 caccattg-ctcttagtgaatccctgctgccagccttttatc-ctaagtgctctccaaaga--------cccatttaa--tggatcttcctg-aaattgtgctcaggatcaatatgag----------gctcattgatacagcatt----------------------tttggaactcaccatttgcttatttattaaacctgggatagtt-gcccgac--------ttctatcatctgaaatcctctccatg--actttcaaaattaccaacattgcttccaacatcattcctagaaaacatttcagtggagta--tatttatctgacatttgactgtatttatAGCAGTAAGAATCTATGATGATTCCTCCC---AAAATAA----TCCCACAATTACCCATTTTGG i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159741591 344 - 202140232 caccaatg-ctcttagtgaatccctgctgccagccttttatc-ctaagtgctctcaaaaga--------cccatttaa--tggaccttcctg-aaattgtgctcaggatcaatataag----------gctcattgatacagcatt----------------------tttggaactcaccatttgcttatttattaaaCCTGGGATAGTT-GCCAGAC--------TTCTATCATCTGAAATCCTCTCCATG--ACTTTCAAAATTACCAACATTGGTTCCAACATCATTCCTAGAAAACATTTCAGTGGAGTA--TATTTATCTGACATTTGACTGTGTTTATAACAGTAAGAATCTATGATGATTCCTCCC---AAAATAA----TCTCACAATTACCCATTTTGG i ponAbe2.chr3 C 0 I 938 s rheMac2.chr2 189458888 344 - 189746636 cactattg-ctcttagtgaatccctgctgccagccttttatc-ctaagtgctctccaaaga--------cccacttaa--tggaccttcctg-aaatcgtgctcaggatcaatacaag----------gctcattgatacagcatt----------------------tttggaattcaccatttgcttatttattaaacctgggatagtt-gcccgac--------ttctaacatctgaaatcctctccatg--actttcaaaattaccaacattggttcCAACATCATTCCTAGAAAACATTTCAGTGGAGTA--TATTTATCTGACATTTGACCTTATTTACAGCAGTAAGAATCTATGATGATTCCTCCC---AAAATAA----TCCCACAATTACCCATTTTGG i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15812419 343 - 24440124 CAAGATAG-CTTTtagtaaatttctgcttccagcctctt-----taagtgctctgaaaaca--------ctcatttaa--tggaccttcctg-aaattgtgctcaggatcaatataag----------gtccattgatacagcatt----------------------tttggaatccagcat---atcctttattaaaCCTTGGATATCT-GCCTAAT-TTCAGGGTTCTGTCATCTCCAACTCTTTCTG----TTTCTCAAAATCACCAAAGT-CATTTCAATGGCATTCTTAGAAGACTTTTCAATGGAGTT-TGTTTTTTGTCATATATGATCTTATTCATAGCTATACTAATCCGCCATTCTCCCCCCA--CAAAACAG----ACTCATAATTACAAATTTTAA i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141891796 346 + 163896628 cacaattg-cgcttagtcaaactctgctgccagttttttagc-ctaagtgcgctctaaaca--------ttcatttaa--tggaccttcctg-aaatcgtgtccaggatcaatgtaag----------gttcattgatacagcatt----------------------ttcgggattcaccatttgcttctttattaaatctgggataact-gcccaac-ttcagggttctggcatctcataccctctccacgactctttcaaaACCAGCAACATGTATTCTAACACCGTGCCTAGAAGGTTTTTCAATGGAATGATTTTTTACTTGACTCTTGAACTCCTTTACAGCAAT----TTCTACCAT-----CTCCA---AAATGAA----ACTCGAAATTACTTATTTTGG i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138182361 354 - 161106243 cgtgactcactcttagtgaatctctgctgctagctttttatc-ataagtgctcgcaaaaca--------cctatttaa--tggaccttcctg-aaattgcactcacaatcaatatgaa----------gtttactgatagagcatt----------------------tttggaattcaccatttgcttcttcattaaaCCTGGGATACTTAACATATC-TTCAGGGTTCTAATAGCCTAAACCCTCTCCTTGAGTCTCTCAAAATCGCCAACACTTTTTCCAGTATGATTCTTAGAAGATGTCTTGAT--AATG--TATTTATCTTCTATTTGAATTATTTTATAGCAAGGAAGATAGAACACTATCTTTCCC--CAACCTAA----ATTCACAATTACACAGTTTGT i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13363415 349 + 41866177 cactactcacccttggtaaatctctgccaccagctttttacc--taagttctctcagaaca--------cccatttaa--tggaccttcctg-aaactgggctcaggatcaatatgaa----------gctcagtgatacagcatt----------------------tttgggattcaccatttgcttctttattaaacctggggtggtt-acccacc-ttcaaggttctagcatctcaatccctcttcatgattctctcaaaATCACCAAGATTGATTCCAACACCATTCCTAGAACACTTGTTGAT----TG--TGTTTATCTGACACTTGAACTCTTTTATAGCAATGAGAATCTAACACTATCTCCCCC--CAACCTAA----ACTCTCAATTACA-ATTTTGG i equCab2.chr26 C 0 C 0 s canFam2.chr31 14112848 392 + 42263495 TACCATTGCCCTTTG-----CCTCTGCCTACAGCTTCTCCCAGGGAGGATTCCTGAGGAAAGGATGGTTGCCTTGTGATCTAGACATTTATGTTGGTTGGGAAATACATAAATAGGGATGCCTGAGTGGCTCAGTGGTTGAGCCTTTAGCTGATAACTTCAATTGACATTTGgaattcaccatttgcttcttttttcaagctcgaatagtt-acctttc-ttctgggttctaacatctcaacccctctccatggctctctcaaaatcaccaacattgttttcactatcatttctagaagactttttgatccagta--tatttatctgagacctgaa--cttttatagcaATAAGAATCTAATGCTATCTCCCTG--CAACTAAA----ACTCACAATTACACATTTTAG i canFam2.chr31 I 368 C 0 s loxAfr3.scaffold_13 20612561 355 - 62548349 catgactcactctcagtgaatctctgctgccagtcttttatc-ctaagtgctctcaaaaca--------ctcatttaa--tggcccttcctt-aaatggtgaccggaatcaatatgag----------gctcattgatagagcatt----------------------tttggaattcaccgtttccttctttattaaaCCTGGGAGAGCT-GCATTATGTTCAGGGTTCTGTCAACACTGTCCCTCTCCATGACTCTTCCAAAATCACCAACATTTGTTCCAGCAACAT-CCTCGAAGATTTCC------AACA--TTCGTATCTGATCCTTGTGCTCATTTATAGCACTGAGAATCTCCCATTATCCCCCACCTCAACCTAAGCTCTCTCACAATAACACATTTTAG i loxAfr3.scaffold_13 C 0 C 0 a score=34308.000000 s hg19.chrUn_gl000245 15713 38 + 36651 GTCACC-TTGAGGGTCTTATCCTTAATATCAGAGATCTG s panTro2.chrUn 47412383 39 - 58616431 GTCACCTTTGAGGGTCTTACCCTTAATATCAGAGATTTG i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189459232 39 - 189746636 GTCACCTTTGAGGGTCTTATCCTTAATATCAGAAATCTG i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15812762 39 - 24440124 GTCAAATTTTATAGTTTTATTCTTAATACAAGAGTTCTC i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141892142 36 + 163896628 GTCATAGTTTATGTTT---TCCTTAAAACCATAGAATGC i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138182715 25 - 161106243 ATCATCATTGAGGACCT--------ATCCTAAA------ i bosTau4.chr1 C 0 I 322 s equCab2.chr26 13363764 39 + 41866177 ATCGTCTTTGAGGGCTTTGCCCTTAATACTGAAGATCTC i equCab2.chr26 C 0 I 3 s canFam2.chr31 14113240 39 + 42263495 ATCACTTTTAAGGTCCTTATCCTTAATACTAGAGATCTC i canFam2.chr31 C 0 I 3 s loxAfr3.scaffold_13 20612916 37 - 62548349 GTCAC--TTTGAAGCCTTATTTTTAATACCAGTGATCGG i loxAfr3.scaffold_13 C 0 I 3 e ponAbe2.chr3 159741935 938 - 202140232 I a score=167398.000000 s hg19.chrUn_gl000245 15751 135 + 36651 TTCTATACATTTGAGTCTTAGAAATAAT---TACTAGCTTCTCTCTGAATTTAACTGAGGT------TCCTTACTTTTATTCAGCCTGTTACCTAAATTACATA---------------ATGTAT-TGAAGGCTATAAACTGTCCAAATTTCTGATTACA s panTro2.chrUn 47412422 135 - 58616431 TTCTATACATTTGAGTCTTAGAAATAAT---TACTAGCTTCTCTCTGAATTTAACTGAAGT------TCCTTACTTTTATTCAGCCTGTTACCCAAATTACATA---------------ATGTAT-TGAAGGCTAAAAACTGTCCAAATTTCTGATTACA i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189459271 133 - 189746636 TTCTATACATTTGAGTCTTAGAAACAAT---TACTAGCT--TCTCTGAATTTAACTGAAGT------TCCTTACTTTTATTCAGTCTATTATCCAAATTACATA---------------ATGTAT-TGAAGGCTAAAAACTGTCCAAATTTCTGACTACA i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15812801 114 - 24440124 TTCTATACATTTTAATTTAAAAA------------------TTTCTGAATTCCACTGAAAT------TTGTTACTTTTTTCT-GTGTATTATCC-AATTTCATA---------------ATATAT-AGAAGCC--AAAAATGTTTAAATTTCTTATTA-- i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141892178 134 + 163896628 -TCTATACATTTCAGTTTTAGAAACAATTTCTACTAGCTTTTCTTTAGCTTTGATTGAAAT------TCATTACTTTTTTT---CTTATTACCCAAAGTACATA---------------ATATAC-TGGAGACTAAATACTGCCCAAATTTCTGATCGAA i oryCun2.chr14 C 0 I 327 s bosTau4.chr1 138183062 146 - 161106243 TTTTATAAAATTTAGTCTTGTAAATAATTT---CTGGCTTCTCTATGAATTTAATCAAAATCCTTTACCTTTACTTGTATTCTGC-TATTACGAGAATTATATATATAT---------TATATGT-CAAAGACTAAAACCTGCCAAATCTTCTGATTTGA i bosTau4.chr1 I 322 C 0 s equCab2.chr26 13363806 137 + 41866177 TTTGATAATTTCTAGTCTTAGAAATAATTTCTACTAGCTTCTGTATGAATTTAACCTAAAT------CCTTTACTTGTATTCTGC-TATTACCAGCATTACATA---------------ACATAT-TGAAGGCTAAAAACGGCCCAGTTTTCTGATTAGA i equCab2.chr26 I 3 C 0 s canFam2.chr31 14113282 131 + 42263495 TTTTATAAATTTTATTCCTA-AAATTATTTCCACTTGCTTCTCTATGAAGTTAGCTGAAAT------TTTTTACTTGTATTCTAT-GATTTCTAGAATTACATA---------------ATATAT-TGAAGGCT-----CCCTCCAATTTTCTGATTAGA i canFam2.chr31 I 3 C 0 s loxAfr3.scaffold_13 20612956 150 - 62548349 TTCTATAAATTTTAGTCTTGGGAACAATTTCTATTAAT---TCTATGAATTTAACTGATAT------CCCCTATTTATATTCGGT-GATAACCAGAATtgtctgtgtgtgtgtgtgtgtgtgtgtgtgtAGGCTAAAAACTATACTAATTTCTGATTAGA i loxAfr3.scaffold_13 I 3 C 0 e ponAbe2.chr3 159741935 938 - 202140232 I a score=78153.000000 s hg19.chrUn_gl000245 15886 73 + 36651 TTGAGTTAAAAATGGGAATATGAC--TTTCTTTTTCTAACTTGGCAAAGATTATGTTTTTTT-CATG---AAGAAATAT s panTro2.chrUn 47412557 76 - 58616431 TTTAGTTAAAAATGGGAATATGACTTTTTCTTTTTCTAACTTGGCAAAGATTATGTTTTTTTCCACG---AAGAAATAT i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189459404 72 - 189746636 TTTAGCTAAAAATGGGAATATGAC--TTTCTTTTTCTAACTTGGCAAAGCTTATGGTTTTT--CATG---AAGAAATAT i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15812915 68 - 24440124 ---ATATGGAAATGGGAATA------TGTCTTCTCCTAAATTAACAAAGATCCTTATTTCT--CAAGAAAAAAAATTGT i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141892639 64 + 163896628 TTAATTTATAAATGGAAA----------TTTTTTCAGGACTCTGCAAAGATCTTGGTTTCT--CAAT---TTGAATTGT i oryCun2.chr14 I 327 C 0 s bosTau4.chr1 138183208 74 - 161106243 TTAATTTGAGAATAGAATTTTTTTTTTCTTTTCTCATAACTAGCCGAAGATCCTGATTTTT--CATG---CAAAAATCC i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13363943 74 + 41866177 TTAATTTGGAAATGGCAATATGTTTCTTTCTTTTCTTGATGAGGCAAAGATCCTGATTTCT--TATG---CAAAAATAT i equCab2.chr26 C 0 I 210 s canFam2.chr31 14113413 73 + 42263495 TTAAGTTGGAAATGGGAATATGTTTTTTTCTTTTCCTAACTAGGCAAAGATCCTGATTTTT--TATG---C-AAACTAT i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20613106 73 - 62548349 CTAATTTGGAAATTACAATACAGATTTTTCAGGTCCTAGCTCAGCAAAGAATTTG-TTTCT--CAGG---CAGAAACTT i loxAfr3.scaffold_13 C 0 C 0 e ponAbe2.chr3 159741935 938 - 202140232 I a score=81898.000000 s hg19.chrUn_gl000245 15959 87 + 36651 A-GGCAT----ATTTAAACACTCAGGATCTGAGAATTTGAAATACATGAAACTTAGCAAGTGGTCTT----TAAGTAGTTTTCATTTCTAA-----ATTAT s panTro2.chrUn 47412633 87 - 58616431 A-GGCTT----GTTTAAACACTCAGGATCTGAGAATTTGAAATACATGAAACTTGGCAAGTGGTCTT----TAAGTAGTTTTCATTTCTAA-----ATTAT i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189459476 87 - 189746636 A-GGCAT----ATTTAAACACTCAGGGTCTGAGAATCCAAAATATATGAAACTTAACAAGCGGTCTC----TAAGTAGTTTTCGTTTCTAA-----ATTAT i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15812983 91 - 24440124 ACAGTGTACAAACATAGGCATTCATGCTC-AAGATGTTAAGATAC-TAAAACTTAAAAAGTGGGCTT--------AGTTGGATGTCTTAAAGTTTTATTAT i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141892703 83 + 163896628 A-AGTTT----ATTTAAGCATTCAAACTCTGAGATTCTGAGATACTTGAGATTTAACAAGTCACCTT--------TATCCATAGTTTCTAA-----ATAAT i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138183282 78 - 161106243 A-GGCAT----ACTCAATCATTCA-------AGATCCTAAGAAACTTGCTGC--AACAAGTTGGCTT----TGAGTAGTTCTAGTTTCTAA-----AGTAT i bosTau4.chr1 C 0 I 286 s equCab2.chr26 13364227 89 + 41866177 A-GGCAG----ATGCAAGCAGTCAGGATGTGAAATTCTGAGAGATTTGATAA--AACAAGTGGACTTTATCTGAGTAGTTCCAGTTTCTAA-----AATAT i equCab2.chr26 I 210 C 0 s canFam2.chr31 14113486 86 + 42263495 A-GGCAG----ATTAAAACACTGACGTTCTGAGATTCTGAGAAACTTTAC-----ACAAGTGGATTTTATCTGAGTAGTTCCAGTTTCTAA-----AGTAG i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20613179 91 - 62548349 A-GGGAT----ATTCAAGTTTTCAGGCCCTGGGATTTTTAGAGACTTTGAACTTAACAAGTGGACTTTTTCTGGATTGTTCCAGTTTCTAA-----ATTTT i loxAfr3.scaffold_13 C 0 C 0 e ponAbe2.chr3 159741935 938 - 202140232 I a score=49971.000000 s hg19.chrUn_gl000245 16046 74 + 36651 AGTACATACCATTGAATGCTACAGAAGGAAAGACAATGAGGGATTACTC-ATAAACATTGCCTTTATGATATCCT s panTro2.chrUn 47412720 74 - 58616431 AGTACATACCATTGAATGCTACAGAAGGAAAGACAATGAGGGATTACTC-ATAAACATTGCCTTTATGATATCCT i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189459563 74 - 189746636 AGTACATACCATTGAATGCTACAGAAGAAAAGACAATGAGGGATTACTC-ATAAACATTGCCTTTAAGATATCCT i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15813074 70 - 24440124 AATGCAGATACCTGAACATTACCGTAGTTAAGATAACTACTGATTATCT-CCATTCATTGCTTTTGCGCTA---- i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141892786 66 + 163896628 AATACAGGCATATGCATGTAACGGGGGAAAAGTCAGTGACGACTTAT-----GAACATTGCCTTTGGGATG---- i oryCun2.chr14 C 0 C 0 s canFam2.chr31 14113572 66 + 42263495 GATATAGTCATGTCAACAAAAT--GGGGGAAATCAAC---TGATTACTTGGTAAACATTGCCTTTGTGATA---- i canFam2.chr31 C 0 C 0 s equCab2.chr26 13364316 68 + 41866177 AATACAGACACGTGAACATAACAGGGGGAAAATCAAC---TGGTTACTTGGTAAACATTGTCTTTGTGATA---- i equCab2.chr26 C 0 C 0 s loxAfr3.scaffold_13 20613270 73 - 62548349 AATACAGATATGTGAACAGTCCA-TAGGAAAAAAAACTAGTGATTATTCTGCAAACTTTGTTTTTAAGATATCC- i loxAfr3.scaffold_13 C 0 C 0 e ponAbe2.chr3 159741935 938 - 202140232 I e bosTau4.chr1 138183360 286 - 161106243 I a score=99957.000000 s hg19.chrUn_gl000245 16120 129 + 36651 TCCAAAGAAAACCAAGTGTCCCTGTGCTTGGACTCATAAAGCAGAAATGCTTACCTTGC-TTTTATGTCACTAACAAAC---A------------------------------------------------------------------------------------------------ATT--GTGCCTAGTCATTTAATTC------------------------------------------------------------------------TAACGCATTTAAGCCATCTA------------------------------------------------------------------------------------------GAGAGTGG s panTro2.chrUn 47412794 129 - 58616431 TCCAAAGAAAACCAAATGTCCCTGTGCTTGGACTCATAAAGCAGAAATGCTTACCTTGC-TTTTATGTCACTAACAAAC---A------------------------------------------------------------------------------------------------ATT--GTGCCTAGTCATTTCATTC------------------------------------------------------------------------TAATGCATTTAAGCCATCTT------------------------------------------------------------------------------------------GAGAGTGG i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189459637 128 - 189746636 TCCATAGGAAACC-AGTGTCCCTGTGCTTGGACTCACAGAGCAGGAATGTTTACCTTGC-TTTGATATCACCAACAAAC---A------------------------------------------------------------------------------------------------CTT--GTGACTAGTCATTGAATTC------------------------------------------------------------------------TAATGTATTTAAGCCATCTT------------------------------------------------------------------------------------------GAGAGTAG i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15813144 131 - 24440124 TTCAGTGGAAATCAAGTGTCCTTATCCTTGGATTCACAAATCAAGAACACTTAGTATGC-TTTGATATCACAAATGAAA---A------------------------------------------------------------------------------------------------CTTTGGTAATTATTCAGGGAATTC------------------------------------------------------------------------TAATGTATTTAAGATCTCTT------------------------------------------------------------------------------------------GAGAGTAG i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141892852 104 + 163896628 TCCAAAAGAAATCAGATGTCCTTGTACTTGGAGTCACAGAAAAAGAATGTTTTGTTTGCTTTTTCTATAACTAATGAAG---A------------------------------------------------------------------------------------------------TTTT-GTGGCTATTCA-AGAATTC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AC i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138183646 223 - 161106243 TCCAAGGGAAACTATGTGTCCATGTGCTTGGGCTCACAAAGCAAGAG-ATTTCTTTAGC-TAGGATGTCACTAATGAAGTTTT------------------------------------------------------------------------------------------------TTTTTGTAACTATTCATAGGATTT------------------------------------------------------------------------GAATACATTTAAGTTATCTTAggctgcacctgtggctcaaaccttaaagaatctacctacaatgtggaagacctggattcagtccttaggttggaagatcccctagagaagagaatgg i bosTau4.chr1 I 286 I 113 s equCab2.chr26 13364384 127 + 41866177 TCCAAAGGAAACCATGAGTCCTTGTGCTTGGGCTCACAGAGCAAGAACATT----TTGC-TTGAATGTCACGAATGAAG---A------------------------------------------------------------------------------------------------CTTTTGTAATCATTCATAGAATTC------------------------------------------------------------------------TACTGCATTTAAGCCATCTT------------------------------------------------------------------------------------------GAGAATAG i equCab2.chr26 C 0 C 0 s canFam2.chr31 14113638 131 + 42263495 TACAAAGGAAACCGTGTGTTTTTGTGCTTGAGTTCACAGAGCAAGAACATTTAGCTTGC-TTGGATATCACTAAAGAAG---A------------------------------------------------------------------------------------------------ATTTTATAATTATTTATAGAATTC------------------------------------------------------------------------TAACTCATTTAAGCCATCTT------------------------------------------------------------------------------------------GAGAGTAG i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20613343 288 - 62548349 ---AAAGTAAAACAGATGTGCTTAGGCT--------CAGAGCATGAGTATTTAATTTGC-TCTGATGTAAATGATGAGG---AGCActggtggcacagtggttaagtgctcggccactaaccaaaagtcagtggttcgaacccatcagctgctccatgagagaaagatgtggtactctgcttctgtaaagaattacagccttggaaaccctatggtgcagttgtactctgtcttatggggttgctatgagtcaaaatcaactgggtggcagtgGGTAATTCATTTAAACCATTTT------------------------------------------------------------------------------------------GAAAGTAA i loxAfr3.scaffold_13 C 0 C 0 e ponAbe2.chr3 159741935 938 - 202140232 I a score=234083.000000 s hg19.chrUn_gl000245 16249 191 + 36651 AGCCCC---TAGGGAAAACTACAAATGGAAAATTCATTG-ATTTTTGATTTTGCTTTCCTATGGATTAAATTTAACACTTTCTTGTAAA-TCTCTCCCT--TTACAGATCATATGTGATAAATAGTTATCCAACTTTCTAGATGTCCACCCAGAGCTGCTTCCATATGAAGAGGTG-------------------GAAACGGATTCTGTGCATGATA s panTro2.chrUn 47412923 191 - 58616431 AGCCCC---TAGGGAAAACTACAAATGGAAAATTCATTG-ATTTTTGATTTTGCTTTCCTATGGATTAAATTTAACACTTTCTCGTAAA-TCTCTCCCT--TTACAGATCTTATGTGATAAATAGTTATCCAACTTTCTAGATGTCCACCCAGAGCTGCTTCCATATGAAGAGGTG-------------------GAAACGGATTCTGTGCATGATA i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189459765 191 - 189746636 AGCCCC---TAGGGAAAACTACAAATGGAAAATTCATTG-ATTTTTGATTTGACTTTCCTATGGATTAAATTTAGCACTTTCTTATAAA-TCTCTCCCT--CTGCAGATCATATGTGATCAATAGTTATCCAACTTTCTAGATGTTCATCCAGCGCTCCTTCCATAAGAAGAGGTG-------------------GAAATGGATTCTGTGCATGATA i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15813275 195 - 24440124 AGACCA---TGAGGAAAGTAACATATGTAAAGTTCA----ATTTTT--------TGTCACTTGAATTAAATTTAACACATTCTTATAGG-TTG-TCCCT--TTGCAGATCATATT--ATAAATGTCCATCTAACTTTCTAGCTGTCTATATAGAGATACTTCCATAAGTAGAGATCTCACCAGG-CCCTTTGCCCAACAGTGATATTCTGCAAGATA i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141892956 177 + 163896628 AGTCTA---CGGGGAAAAGAACATATGGAAAGTTGA----CTTTTT--------ATTTCTCTATATTAAATTTAATACTTTCTTATAAA-TCT-TCTCTAATTGCAGATCATATGTAACAAATATCTATACATCATCCTGGCTGCCCACCCAGAGCTA----------------------CAAG-CCCTACATCCTACAGGGATTCTCTGCATGATC i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138183982 194 - 161106243 GACCC----TGGGGAAAAGAACATATGGAAAGCTAATTG-TTCTTTGATTTGGCATTCCTCTGGATT-AATTTAGCACTTTCTTCTAAACTCTCTTCCT--TTGCAGGTGATGTGTAATA-----------AACTTTCTACCTGTACAAGCAGAGCTACTTCCATAGGAAGGAATG---GAAAA-CCCAGTATCAAACAGGGATAATTTGCTTGATA i bosTau4.chr1 I 113 I 43 s equCab2.chr26 13364511 210 + 41866177 CACATATTCTGGGGAAAAGAACATTTGGAAAGCTCATTG-TGTTTTGATTTGACATTCCTCTGGATTAAATTAAGCACTTTCTTTTAAACTGTTTCCCT--TTGCAGGTCATATGTGGTAAATATCAACCCAACTTTCTAGCTGCATATTCAGATCCTCTTCCATCGGCAGAGGTA---GAAAG-CCCTATACTCAAGGGGGATTCTTTACATGATA i equCab2.chr26 C 0 I 419 s canFam2.chr31 14113769 208 + 42263495 CACCCA---TGAGAAAAAGAACATATGGAAAGCTTATTGTTTTTTTGGTTGGGCATTCCTTTGGGTTAAATTTAGCACTTCCTTTTAAACTATCTCCCT--TTGTAGGTCATGTATGATTTATATACACTTAACTTTCTAGGTATACACCCAGAGTTACTTTCACAGGAAGAAGTA---GAGAG-CCTTGTACCCAACAAGGATTCTTTGTTTGATT i canFam2.chr31 C 0 I 158 s loxAfr3.scaffold_13 20613631 193 - 62548349 -AGCCA---GTGGGGAAAGAACATATGGAAAGTTTATTG--TTTCTGATTTGGCATGCCTCTGTGTTATATTTAGCAC-TCCATATAAATCCTGTCCCT--TTGTGGGATATTTGTAGCAAATATCTATTTGACTTTCTAGCTATACA------------TCCATTAGGAGAGGTA---GAGAGCCCCTAAACCCAACACAGATTCTCTAAATGACG i loxAfr3.scaffold_13 C 0 C 0 e ponAbe2.chr3 159741935 938 - 202140232 I a score=-6395.000000 s hg19.chrUn_gl000245 16440 17 + 36651 ---------------------------------------------------------------CTGGTTAGGATCGGGAA s panTro2.chrUn 47413114 17 - 58616431 ---------------------------------------------------------------CTGGTTAGGATCGGGAA i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189459956 17 - 189746636 ---------------------------------------------------------------CTAGTTAGGCTGGGGCA i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15813470 16 - 24440124 ---------------------------------------------------------------TTA-CTTGGCTAGTGTA i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141893133 17 + 163896628 ---------------------------------------------------------------CTCTCTAGGCCACAGCG i oryCun2.chr14 C 0 C 0 s loxAfr3.scaffold_13 20613824 80 - 62548349 CTAGCTCCCTAGGCCATTTTCTAAATGTGCATCACAATGCTCTTCTGAATTCAGTTAATTTTCCCACTTATGCCCTGGAA i loxAfr3.scaffold_13 C 0 I 109 e ponAbe2.chr3 159741935 938 - 202140232 I e bosTau4.chr1 138184176 43 - 161106243 I e canFam2.chr31 14113977 158 + 42263495 I e equCab2.chr26 13364721 419 + 41866177 I a score=244337.000000 s hg19.chrUn_gl000245 16457 214 + 36651 CTGTTT--------------------------------------------------------------------------------------------------------------------------------------TT---------------------------------------------------------------------------------------------------TTTT---------------------------------AAAGGAGATTTTTAAAA----TTTGTTT---TCCTTGTACACATAGCCTTAATATTGTGTTGCTAACTGCCCTCTGGGAACAAAGTCATACCAATCACAAATACATTGCCT-AAAGTGGGATGGTTATTACTCTGCTGTGAATTGCACCTCCTATTATGTTTTAAAGATGCTACAAACTTGAGACATTACTATGTAGATGACATTCCCAG s panTro2.chrUn 47413131 213 - 58616431 CTG-TT--------------------------------------------------------------------------------------------------------------------------------------TT---------------------------------------------------------------------------------------------------TTTT---------------------------------AAAGGAGATTTTTAAAA----TTTGTTT---TCCTTGTACACATAGCCTTAATATTGTGTTGCTAACTGCCCTCTGGGAATAAAGTCATACCAATCACAAATACATTGCCT-AAAGCGGGAGGCTTATTACTCTGCTGTGAATTCCATCTCCTATTATGTTTTAAAGATGCTACAAACTTGAGACATTACTACGTAGATGACATTCCCAG i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189459973 217 - 189746636 CTG-TG--------------------------------------------------------------------------------------------------------------------------------------TT---------------------------------------------------------------------------------------------------TTTC---------------------------------AAAGGAGATTAAACAAATGTGTCTGTTT---TCCTTGTACACATAGCCATAATATTGTGTTGCTAACTGCCCTCTGGGAACAAAGTCATACCAATCACAAATACATTGCCT-AAAGGGGGAGGCTTATTACTCTGCTGTGAATTCCATCTCCTATTGTGTCTTAAAGATGCTACAAACTTGAGACATTACTATGTAGATGGCATTCCCAG i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15813486 371 - 24440124 CTT-TCTAAAGATGTATCA--------------------------CAAGCAATGCT----------------------------------------------------------------------GTTTTAGGTTAAGATT-----ATTAGGTATGCCTTGAAAAATTCCATCTGTATATGTCATTTATAAAACTATACTAAG-----AATTCTCAAATCCAGCATTCACAGATTGTAGATTTTGGCAAAAAATGTTAATGAATTGGGTTAAAATC-AAAAGACATTTTAAAAT----TTGTTTT---TCCTTGTATTTACAGTCATAAAATTGTACTGCTTACTGCCTTCTGGGAGCAAATTCATGTGATTTACAAACCCAAATCCT-AAAGAGAGATGTTTATTATTGTGCTACAAAATCTATCTTCCATTATGCTTTAAA-ATGCGACATACTTGAGACATTACTATATAGATGACATAAACAA i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141893150 343 + 163896628 CTA-TC------------------------------------------ACAATGTT----------------------------------------------------------------------CTTTGGGATTCAGATTATGAAATGAAGCATGCCCAG-AAAATTCCATCAGTTTATGCCATTTGCAAAGCTACACTGAGTTCACAAGTCT-------AGCATTCACAGATTTTAGATTTT-GCAAAAAA----AATTAATTCTGTGTAA----AAAAGGGACTTT---AT----CTAATAT---TTCCTGTATACACAGTCATAACA---TGATGCTAACTGCCCTCTGGGAG-AAAGTCATACCAATCACAAATATCTGTACT-AAAGAGAGATGCTTACTACTTTGCTATGTATTCCATTTCTTAGTATGCTTTAAAGACACTACAAACTTGACACATAACTGTGTAAATGACATTCCCAG i oryCun2.chr14 C 0 I 335 s bosTau4.chr1 138184219 332 - 161106243 ------------TCTTTCAGATTTATTTATTCATCCAAGCACACCCTGAAAATCCTGTTTATAAAGCTAAACTAAGAGGTTACAAGTGTAACATTCACAGACTTCAGCATCTAACAAAAAATAATTCTACCCAGTTCAGATA---------------------------------------------------------------------------------------------------TTAT----------------------------------------TTTTTTCTTG----TCTGTTT-TATGCTTCTGCACACAGTCATAATGCTGTTTTGCTAACTGCCCTCTGGAAACAAATTCATACCAGCCACAAATAGAGACCCTAAAAGAGAGATGTTTATTACTCTGCTATGAATTCTATCTCCTATTATGCTTTAAGAATGCTACAAACTTGAGCCATTACGTTGTAGATGACATTTCTAG i bosTau4.chr1 I 43 C 0 s equCab2.chr26 13365140 204 + 41866177 --------------------------------------------------------------------------------------------------------------------------------------------TT---------------------------------------------------------------------------------------------------TTTT----------------------------------------TTTTTACTTAT---TTGTTTT-TATCCTTGTACGCATAGTCATAACGCTGTGTTGCTAAGTGCCCTCTGGGAGCAAAGTCATACCATTCACAAATACAGAGCCT-AAAGAGAGATGTTTATTACTCTGCTATGAATTCCATCTCCTATTATGTGTTAAAGATGCTACAAACTTGAGCCATTACTATGTAGATGGCATTTCCAG i equCab2.chr26 I 419 C 0 s canFam2.chr31 14114135 247 + 42263495 ------------TCTGACAAAAATAATAATTCTGTGTTGAAGTCAAAAGGAATTCT------------------------------------------------------------------------------------TT---------------------------------------------------------------------------------------------------GTTT----------------------------------------GTTTCACTTA----TTATTTT-TATCCTTGCACACACAGTCATATTTCTGTGTTGCTGACTGCCCTCTGGGAGCAGAGTCATACCAATCACAAATACATACCCC-AAAAAGAAATGTTTATTCCTCTTCTACGAAGTCCATCTCCTTTTATGCTTTAAAGATACTACAAACTTGAGCCATTACTATGTAAATGACATTTCCAG i canFam2.chr31 I 158 C 0 s loxAfr3.scaffold_13 20614013 213 - 62548349 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTTGAGGTTAAAGGGCGATTTTGCTTG----TTTGTTTTTATCCTTGTATATACAGTCATAATGTTGTGTTGC----TGTCTTCTGGGAGAAAAGCGAGACCAATCACCAATGCATACCCT-AAAGAGAGATGTTTATTACTCTACTCTGAATTCCATCTCCAATTATGCTTTAAAGATGCTACAAACTTGAGCCATTACTATGTAGATGACATTCCCAG i loxAfr3.scaffold_13 I 109 C 0 e ponAbe2.chr3 159741935 938 - 202140232 I a score=505896.000000 s hg19.chrUn_gl000245 16671 308 + 36651 CAAA-TCCCCAAACAACACTTAATGAGATTTCAAATACCAGGATCATGAAACAGTAAGAGATATAAGGAAATAAAGAAAAACACAGTATATGTGTAGA-------AGGC-ATTAAAACACAAATTTTATAATTACGAATGCATATAATAAGGAATAAGTTTTAT--------TCTAAATAGCAATTATATCAGAACT----ACGATACAGGGAATAAA--------AGTGAATATTAAGCCATTGTACCAACAATAACAGAGCCCCTTTTCTGCTGCGTGATGGAATTTAGTGTTTACTAAGGAAGAAAAAAATGCAAGATATCT---TAAATTTGGTAC s panTro2.chrUn 47413344 307 - 58616431 CAAA-TCCCCAAACAACACTTAATGAGATTTCAAATACCAGGATCATGAAACAGTAAAAGATATAAGGAAATAAAGAAAAGCACAGTATATGTGTAGA-------AGGC-ATTAAAACACAAATTTTTTAATTATGAAT-CATATAATAAGGAATAAGTTTTAT--------TCTAAATGGCAATTAAATCAGAACT----ACGATACAGGGAATAAA--------AGTGAATATTAAACCATTGTACCGACAATGACAGAGCCCTTTTTCTGCTGCGTGATGGAATTTAATGTTTACTAAGGAAGAAAAAAATGCAAGATATCT---TAAATTTGGTAC i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189460190 308 - 189746636 CAAATTCCCCAAATAACACTTAACGAGATTTCAAATACCAGGATTATGAAACAGTAAAAGATAAAAGGAAATAAACAAAAGCACAGTATATGTGTAGA-------AGGC-ATTAAGACACAAATTTTGTAATTACAAAAGCACATAATAAGGAACAGGTTTTAT--------TCTAAATAGCAATTAAATCAGAACC----ACCATACAGGGAATAAA--------AGTGAATATTAAACCATGGTACTGACAATAACAGAACCCTTTTTCTGCTGCACGATGGAATATAGCGTTTACTAAGGAAG-AAAAAATGCAAGAGATCT---TAAATTTGGTAC i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15813857 299 - 24440124 AAAG-CCTTCAAATAGCAGGT------ATTTCAGATGCCATGATTATGAAACAGTGAGAGGT----AGAAAGAGAGAAAAGCACAGTATACGTGTAGA-------AGGC-ATCGCAACACAAATTTTGAAATTAAGAAAGCATGTAATAAACAACATGCTTTAT--------TCTAAATACCAATTAAACCAGAACCAGTGACTATTAAACTATTGCACCAATAAGAGTGACTATTAAACTATTGCACCAATAACAACAAAATATTT-------TGCATGACAGAATGTAATGTTTAC-AAAGGAAAGGAACATACAAAATGCCTGAAAGAACC------ i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141893828 280 + 163896628 cagg-ccCCCAAATAACATTTTATAAGATTTCAGGTGTCATGGTTATGAAACAGTAAGA-AT----GGGAAGAAAATAAAGTATGATATATGAGTAGA-------ATAT-ATTAAAACACAAATTTTGTTATTACGAAAGCATTTAAGTAGCAA---GCTTTAT--------TCTTAACACCAATTAAATCAGAACT----ACCACACAGGGATTGGA--------AGTTAATATTAAACCATTATACCAACAGCAACAAAACCTTT---CTCCTGCATGACAAAGTA-----------AAGGAAAATGAGAATACAAGATGCCT---ATAATT------ i oryCun2.chr14 I 335 C 0 s bosTau4.chr1 138184551 306 - 161106243 CAAG-TCCCCAAATAATGTTTTATGAGATTTCAAATGTCATGATTATGAGACAGTAAAAGATTTAAGGAAATAAAGGAAAGCACAGtatgtatatatacatatatatataatttatatataca-tTTGCAGTTATAAAAACATATAATAAGTAGTAAGCTTTAT--------TTTAAACACCAATTAAATCAGAACC----ACCCCACAGGTAATAAA--------AGTGAATATTAAACCACTGTGCCAACAGTAACAAAA----CTTTCTCCTACGTGATGGAATTTAGCATTTACTAAGGAAA-GTCTAAAATTAGAT-TATCTAAGAATT------ i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13365344 303 + 41866177 CAAG-CCCCCAAATAACATTTTATGAGATTTCAAATGCCGTGATTATGAAACAGTAAAAAATTTAAGGAAATAAAGAAAAGCACAGTATATATGTGGA-------AGGT-ATTAAAACACAAA-TTTGCAATTATGAAAGCAGATAATAAGTAGGGAGCTTTAT--------TCTAAACACCAATTAAATCAGAAGT----ACCACACAGGGAATAAA--------AATGAATATTAAACCATTGTACCAACAGTAACGAAACTCTCTTCCTTCTGCATGATGGAATTTAGCATTTACTAAGGAAA-GCATAGCACAAGATCTCCATAAAAATC------ i equCab2.chr26 C 0 C 0 s canFam2.chr31 14114382 302 + 42263495 CAAG-CCCCCAAATAACATCTTACGAGATTTCAAATGCCATGATTATGAAACAGTAAAAGACTTAAGAAAATAAAGAAAAGCACAGTATATGTATAGA-------ATAT-ATTAAAACACAAA-TTCTTAATTGTGAAAACCTATAATAAATAGTGAACTTTAT--------TCTTAACACCAATTAAATCAAAACC----ACCACACAAGGAATACA--------AGGACATATTAAACCA-TATACCAGCAAAAACAAAAATCTCATTCTTCTGCATGATGAAATTTAGCATTTGCTAAGGAAA-GCATAACATAAAATGCCTATAAAAATC------ i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20614226 311 - 62548349 CAAG-CCCCCAAGTAACATTTTATGAGATTTCAAATGCCATGACTGTAATACACTAAAAGATTTGAGGAAATAAAGAAAAGCACCGTATATGTGTAGA-------AGGC-ATTGAAACACGAATTTTGCAATAATAAATGTATATCATAAGTAGCAAGTTTAACCAATTAAATTAGAACACCAATTAAATCAGAA-T----ACCACACAAGGAATAAA--------AGTGAATATTAAGCCATGGTATTAACAACAACAAAGCCTTCATTCTGTTGCATGACAGAATTTACTATTTACTAAGAAAA-ACACAATATAAAATGCCTGTAAGTATC------ i loxAfr3.scaffold_13 C 0 C 0 e ponAbe2.chr3 159741935 938 - 202140232 I a score=67340.000000 s hg19.chrUn_gl000245 16979 48 + 36651 TTTCCAACAAATTTAAGAAATGTGTACACACTTGAGG-AGA-CTTAAGAA s panTro2.chrUn 47413651 48 - 58616431 TTTCCAACAAATTTAAGAAATGTGTACACACTTGAGG-AGA-CTTAAGAA i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159742873 49 - 202140232 TTTCCAACAAATTTAAGAAATGGGTACACTCTGGAGGAAGG-CTTAAGAA i ponAbe2.chr3 I 938 C 0 s rheMac2.chr2 189460498 48 - 189746636 TTTCCAACAAATTTAAGAAATGTGTACATTCTTGAGG-AGA-CTTAAGAA i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15814156 46 - 24440124 TTTCCACCAAACTTAACACAGACGTCCATGATT--AG-AGG-CCTAAAAT i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141894108 48 + 163896628 CCTCTACCAAATATCAGAAATGAATACATTATTGCAA-AGG-CTTAAAAA i oryCun2.chr14 C 0 I 384 s bosTau4.chr1 138184857 26 - 161106243 CATCTATCAAACTTAAGAATTGCATA------------------------ i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13365647 48 + 41866177 CTTCCACCAAACCTAAGAAATGCATACATTCTTGGAG-AGA-CTTAAAAA i equCab2.chr26 C 0 C 0 s canFam2.chr31 14114684 48 + 42263495 CTTCCATC-AACTTGAGAAATGTATACACTCTTGAAA-AGATTTTAAAAA i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20614537 46 - 62548349 CTTTCACCAAATATAAGAAATATACATACAATTAAGA-AGA-CTTCAG-- i loxAfr3.scaffold_13 C 0 I 7889 a score=2146788.000000 s hg19.chrUn_gl000245 17027 1273 + 36651 GTCTCTGACTAAAACACTAGAAAAGAAAAGCA-GTGAAAA--ACCAAATAA--GTATTA-----CTCAAC-----AAT---AACAACATTTGTTACTATTATATTAATATTA---A----ACACACTATTAAGCAACAACATTTCAGTTACTCACTGAGCCCAAAGTCATTTTTCATGAACCATTCACAACACTGATAACCTATTGAAAAA-----------TGATTGAAAACAAAAAAgcttatttctttccaagtccttttaaagccttctcatgtgtcatttcatataat-ccttataacaaatctatggagtatatactgact--ttatc-tctgtacagaaaagaaaactgaatcacattcagaataagttgcaaagatccccagataatcagtgtcataggtgaaatatgatgtcacagtgtactcaagagtAATTTAGGGAAGcagtacaaatgatggttgaaagcacaggttctggggtaaatagcctgaagtcaaaatct--agttcatatcctcagtggctgtgtgatct-tgggaaatttcccttaactctctgtgtcttgattttatagtttcatccatttttgcctctcatatgatctggtgagcgttacactagtttatgcttctaggacactgaaaac----agtgcctggctcttgataaatattaacaatTTTGTTTCATTTTCTTCACCTTGAGTATTTCATGGCCAGATGGAAATCAATGTCAATATGAAAAAATGTTCAT-AATTCAGCAGGAAGAAATACAAAACCATATAAACAACTTTGTTTTATTGGCAAGTGTATTTGGAAGCTATGTTAAATTGAGAAGGGGAAGGGAAAGCCTCTAAGG--------ATATCGATTAATCAATGACTGAAAGCTGATGAGACTTGTCTGGAA-----TTTTTTTTTTGGAGACTCTGAGACTT----------AAA----ATTTTGACAAA-ATAAGGAGATGAATT--GAGTAGTGT--GGAAGAGACATTTTCTGAAGTCAGCAGA--------------GAAAGGAGAGACAAATATGGTAAGGGGAAAATGGTATGAAGTAATAATATGAATGAAGTGCTTTCTAAAGTATAACACATGTAAGTTGTGTTAAATGTAAACTA---TCAT---GATT---ATATCATTA-CTGTCTGACTGATACAACTAT--ATCCACCTCAGTTAGCCAC-ATAAGATCAATTTTCCTATATCTTAGAGAATACCAGTAACCTCCAGTTCAGAAACAGCAT-AAATA-TCTATCCACAGCTGAGCAGACACATACAGCTAGCTACCAGATGAAATGGGCTATATCTTCAAATACTATTGTTTTCCAttttttaactgtgg s panTro2.chrUn 47413699 1271 - 58616431 GTCTCTGACTTAAACACTAGAAAAGAAAAGCA-GTGAAAA--GCCAAATAA--CTATTA-----CTCAAC-----AAT---AACAACATTTGTTACTATTATATTAATATTA---A----ACACACTATTAAGCCACAACATTTCAGTTACTCACTGAGCCCAAAGTCATTTTTCATGAACCATTCACAACACTGATAACCTATTGAAAAA-----------TGATTGAAAACAAAAAAgcttattgctttccaagtccttttaaagccttctcatgtgtcatttcatataat-ccttataacgaatctatgcagtatatactgact--ttatc-tctgtacagaaaagaaaactgaatcacattcagaataagttgcaaagttccccagataatcagtgtcataggtgaaatctgaTGTCACAGTGTACTCAAGTGTAATTTAGGGAAGcagtacaaatgatggttgaaagcacaggttctggggtaaatagcctgaagtcaaaatct--agttcatatcctcagtggctatgtgatct-tgggaaatttcccttaactctctgtgtcttggttttatagtttcatccatttttgcctctcatatgagctggtgagcattacactagtttatgcttctaggacactgaaaac----agtacctggctcttgataaatattaacaatTTTGTTTCATTTTCTTCACCTTGAGTATTTCATGGCCAGATGGAAATCAATGTCAATATGAAAAAATGTTCAT-AATTCAGCAGGAAGAAATACAAAACCATATAAACAACTTTGTTTTACTGGCAAGTGTATTTGGAAGCTATGTTAAATTGAGAAGGGGAAGGGAAAGCCTCTAAGG--------ATATCGATTAATCAATGACCGAAAGCTGATGAGACTTGTCTGGAA-------TTTTTTTTGGAGACTCTGAGACTT----------AAA----ATTTTGACAAA-ATAAGGAGATGAATT--GAGTAGTGT--GGAAGAGACATTTTCTGAAGTCAGCAGA--------------GAAAGGAGAGACAAATATGATAAGGGGAAAATGGTATGAAGTAATAATATGAATGAAGTGCTTTCTAAAGTATAACACATGTAAGTTGTGTTAAATGTAAACTA---TCAT---GATT---ATATCATTA-CTGTCTGACTGATACAACTTT--ATCCACCTCAGTTAGCCAC-ATAAGATCAATTTTCCTATACCTTAGAGAATACCAGTAACCTCCAGTTCAGAAACAGCAT-AAATA-TCTATCCACAGCTGAGCAGACACATACAGCTAGCTACCAGATGAAATGGGCTATATCTTCAAATACTATTATTTTCCGttttttaactgtgg i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159742922 1255 - 202140232 GTCTCTGACT-AAACAGTGGAAAAGAAAAACAGGGGAAAA--GCAAAATAA--CTATTA-----CTCAAC-----AAT------AACATTTATTACCTTTATATTAATATTA---A----ACACACTATTAAGCATCAACATTTCAGTTACTCAGTGAGCCCAAAGTCATTTTTCATGAACCATTCACAACACTGATAACCT----------------------ATTGAAAACAAAAAAgcttattgttttccaagtccttttaaagccttctcatgtgtcatttcatataat-ccttataatgaatctatggggtatatactgact--ttatc-tctgtacagaaaagaaaactgagtcgtattcagaataagttgcaaagttcccctgatattcagtgtcataggtgaaatttgatgtcacagtctagTCAAGTATAATTTAGGGAAGcagtacaaatgatggttgaaagcgcaggctctggggtaaatagcctgaagtcaaaatct--agttcacagccttagtggctgtgtgatct-tgggaaatttcccttaactctctgtgtcttggttttatagtttcatccatttttgcctctcatatgagctggtgagcatcacactagtttatgcttctaggacacttaaaac----agtacctggctcttgataaATATTAACCATTTTGTTTCATTTTCTTCACCTTGAGTA-TTCATGGCCAGATGGAAATCAATGTCAATATGAAAAAATGTTCAT-AATTCAACAGGAAGAAATACAGAAGCATATAAACAACTTTGTTTTACCGGCAAGTGTTTTTGGAAGCTATGTTAAATTGAGAAGGGGAAGGGAAAGCCTCTAAGG--------GCATTGATTAATCAATGACTGAAAGCTGATGAGACTTGTCTGGAA-------TTTTTTTTGGAGACTCTGAGACTT----------AAA----ATTTTGACAAAGATAAGGAGATGAATT--GAGTAGTGT--GGAAGAGACATTTTCTGCAGTCAGCAGA--------------GAAAGGAGAGACAAATATGGTAAGGGGAAAATGGTATTAAGTAATAATAACTATGAAGTGCTTTCTAAAGTATAACACATGTAAATTGTGTTAAATATAAACTA---TCAT---GATT---ATATCATTA-CTGCCTGACTGATACAACTAT--ATCCACCTCAGTTAGCCAC-ATAAGATCAATTTTTCTATACCTTAGAGAATACCAGTAACCTCCAGCTCAGAGACAGCAT-AAATA-TCTATCCACAGCTGAGCAGACACATACAGCTAGCTACCAGATGAAATGGGC--TATCTTCAAATACTATTGTTTTCCAttttttaattgtgg i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189460546 1276 - 189746636 GTCTCTGACTAAAACACTGGAAAAGAAAAGCA-G-GAAAA--GCAAAATAA--CTATTA-----CTCAAC-----AAT---AACAACGTTTATTACTATTATATTAATATTA---A----GCACACTATTAAGCATCAACATTTCAGTTACTCACTGAGCCCAAAGTCATTTTTCATAATCCATTCACAACACTGATAACCTATTAAAA---------------AATGAGAACAAAAAAgcttattgctttccaagtccttttaaagccttctcatgtgtcatttcatataat-ccttataatgaatctatgaggtatataccaact--ttatc-tctgcacagaaaagaaaactgagtcatatacagaataagttgcaaagtt-tccaaataatcagtgtcataggtgaaatttgatgtcacagtctagTCAAGTATAATTTAGGGAAGcagtacaaatgatggttgaaagcacaggctctggggtaaacagcctgaagtcaaaatct--agttcatatccttagtggctgtgtgatct-tgggaaatttcccttaactctctgtgtcttggttttatagtttcatccatttttgcctctcatgtgagctggtgagcatcacacttgtttatgcttctaagacacttaaaac----tgtacctggctcttgataaATATTGACCATTTTGTATCATTTTCTTCACCTTGAGTATTTCATGGCCAGATTGAAATCAATGTCAATATGAATAAATGTTCAT-AATTCAACAGGAAGAAATACAAAATCATATAAACAACTTTGTTTTACTGGCAAGTGTATTTGGAAGCTGTGTTAAATTGAGACGGGGAAGGGAAAGCCTCTAAGG--------ACACTGATTAATCAATGACTGAAAGCTGATGACACTTGTCTGGAATTTTTTTTTTTTTTTGGAGACTCTGAGACTT----------AAA----ATTTTGACAAAGATAAGGAGATGAATT--GAGTAATGT--GGAAGAGACATTTTCTGAAGTCAGTAGA--------------GAAAGGAGAGACAAATATGGTAAGGGGGAAATGGTATTAAGTAATAATATCTATGAAGTGCTTTCTAAAGTATAACACATGTAAATTGTGTTAAATGTAAACTA---TCAT---GATTATAATATCATTA-CTGTCTGACTGATACAACTAT--ATCAACCTCACTTGGCCAC-ATAAGAACAATTTTTCTATACCTTAGAGAATAGCAATAACCTCCAGTTCAGAGAGAGCAT-AAATA-TCTATTCACAGTTGAGCAGACACATACAGCTAGCTATCATATGAAATGGGCTATATCTTCAAACATTATTGTTTTTCAtttttttattgtgg i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15814202 1209 - 24440124 TTCTCTGAGTTAGAAACTGGAAAAGCAAAACA-CTTCAAAATGCAAATTAA---TATTA--CCATTAGAC-----AAA---CTCCACATGTATTACAGTTATGCTCATAATA--TACTGGAAACACTAATAAGCATTTTCATTACTGTTTTTCTATGCATCAAAACGGGTAATTTC--AACTACATACAATGTTGATGAACTGTTAGTAAATTTATGACAGGTTATTAGGAAAAtaagagcttactatcatgcatg-------------tgtaattctgttcatac---------ctcataatccatctgtgagatatacactgatt--ttgtc-attgcactgagaagaaaactgagtgacatagagaataacgtacagtttcagtaagataatcagtggcagagctgagattttatgtcagaaact-------tttaatctagagAAGAAGTA-AAATGATGGTTG-------ATAACCTGGGTTAAGTACCCTCAATTCACAATGT--AGCTCATCTCTTTAGCAACTAAATGAACC-TGAGAATTTCCTCTTAATTTTGTGTCTTTTATATTTATATC-------ATCTGTGCTTCTCACATTGGTTGGTGAGCCTTACATGTGTTTATCCTTGTAGGAAACTT---------AGTACCCGACTCTTGTTAAA-------TATTTTGTAGCATTTTTTTCACCCTGAGTAGGTCATGGCCAGATGGAAATCAATGTCAATGTAAATAAATGCTCAT-AAGGCAACAGGAAGAAATACAAAACCATATAAACAGCTCCATTTTACTGGAAAG-GTATTTGAAAGCCGTGTTAAATTGAGATGGGGAAGGAAAAGTCCCTCGGG--------ACCTTAGTGAATCGGTGACTGGAAACTGATGAGTCTTGTCTGGAA------TATTTTCTTGGAGACTCTGAGACTT----------AAA--GAGTTTTGATAA---AAGGAAGATGATTGAAGAGCATTAT--GGGAGAAACA-TTTCTGAAGTCAGCAGA--------------GACAGGAGAGACAAATATAGCAA-CGGTAAATGGTACTCAGTAATAATGTCTATAAAGTGCTTTCTCAGGTATTACAAATGTAGAATGTTATAAAAGTAAATTA---TCATTATGATTATGATACCATTA-TCACTAGGGTGATATAACTAT--CTCCATATGAATTGGCCAC-ATGAGTTCTATTTTCCAATATTTTGGAGAATGTAATTAA-----AA-GCAGTCCC------AAATT-CCTTTACACAGCTAAACATATACA--------------TACTGACATTAACTAAACTTGCTCATGTGACT-TTTTCCATTTTTT-----CAg i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141894540 1192 + 163896628 ATCTCTCGTTGGAAATCTGGAGAAGAAAAACT-CTTAAAA--GCAAAATGAATTTATTAGGCAATTAAAT-----AA----------CTAAATTATTATTATCTGAATAATG--TA----AAAT-----TCAATGTTAACATTTCTGTTATTCATGGAGTCAAAATCACTTAATACATAGTCATAAACAACACTGATAAA----------------------TTAACAGGAAAAtaagaacttgctatcttccaggtccttctaagtcctgtacttgtgtcatttc--------tcttattatcaatctattacatatgtactgaccaatcgtt--ttttacagaaaaggagactgagtcatatagagattaagctgtaagaccacccagataatcagtggcattactgagattcgatgccaca----------------------------------------gctg-------gggctctggggtaa-----ctc-----------t--agtttatctctttagtaactggccaatct-tgagaaagctctgttacctctctgtgccttagctttacatttgcaacaatctgtacctcccttatgggataatgtgtattgcactactttatgcttatagaacacttagggcaggcagcacctggctcttgataaacattagctatcatATACCATTTCCTTCATCTTGCGTACTTCTTGGCCTGACAGAAATCAATGTCAATATGGATAAATGCTCAT-AAGGCAACAGGAAGAAATACAAAACCGTATAAACAACTCCATTTTACTGGAAAG-GTATTTGAAAGCTATGTTAAACTGGGA-AGGGAAGAGAAATTCTCTAAGG--------ACATTGTTGAATCAGTGACTGGAAACTGATGAAGCTTGTCTGAAA------TACTTTCTTGAAGACCCTGAGATTT----------AAAAGAAGTTTTGACAACGGGAAGAAGATGATTGAAGGGTGTTGT--GGAAAAGATATTTTCTGTAGTCAGCAGA--------------GACCGGAGAGACAAATGTGGTAAGAGGAAGACGATATTCAGTAATAACATCTATGGAGTGCTTTCTAAAGGGTAATGTATAAAGCATAT--TAAATGTAAGTTA---TCATTAAGATTATAGCATCAGTA-TCATCTGGCTGACACAACTAT--ATCCACACCACTTGATTAAGATGGATCAATTTTTCCCATACCTTGGAGGTTACCAATAACATCTAG-GCAGAGCTATCAAAAAATA-TCTGTCCATAGGTAAGCAGACACA--------ACAATCTGATAAAATGGTCTTTGTTTCTAAACACAATT-TTTTTCAtttttc-attgtgg i oryCun2.chr14 I 384 C 0 s bosTau4.chr1 138184883 1162 - 161106243 --GCCTGGAAAATAAGT--AAATAAAAAGAAA-TAG--------AAAATAA--GTATTA-----GTCAAC----AACT---AATTACATTTATTACCTTTATGTTAATAATATGTT-----AGCATTATTAAGCATTAACATTT----CATTCTCTGAGCCAAAACATACGTAACACCAGCCATACACAACAGTAATATACT----------------------ATTGAGAAAACAAAAGATTACCATCTTCCAGCTCCTTCTAAATCTTGTACA--TATTATTTCAGGCAATAAATTACAATAAAGCTATGAGGTATACACCGACT--TTAT-------ACAGAGT------------------------ACATTGTAATGACGTCCAGATAACCAGTGGCATAGTTGAGGCCTGAAGTC--------------------TTAGGAAAGAAATACAAATGATGGATAAAAGTGTGGGTTctgg--------------attcaaattctagaccatctccc-ttagtatctgtgtgatttgggggaaagttcccttacctctctctgtcttagctttacatacacatt-gtttgtgcctctcctgtgagctggtgggtattatactagctgatgcttacgggacactcagagc----cgtgcctggctcttgataaAGATTAACCA-CTTGTACCATTTTCTTTACCTTGAATAGTTTATGGCCTGATAGAAATCAATGTCAATATGGATAAATGCTTATAAAGGCAACAGGAGGAAATATAAAACCATATAAACAACTACATTTTACTGGAAAGGCTA-TTGAAAGCT-TGTTAAATTGAGAAGGGGAAGGGAAAGCCTCTAAGGATGAGATCACAGTTGGGAATCAGTGACTGGAAACTGACCAGGCTTGTCTGGAA------TAATCTCTTAGAGACCCTGAGACTT---------AAAA----GTTTTGACAGAGGAAAAAAGATGATT---GAACAGTGTTGGGAAAGGACA-TTTCTGAAGTCAACAGATATGACAGTTCAATAAC----AAGACAAATGCAGTAA-AGGGAAAC------AAGTAATAACATACTTGAAGTGCTTTCTAAAGGGTAACGTGTGCAAAACCTGTTACATGTAAGTTA---TTAT---GATTACAGGATC---A-TTTCCTGGCTGATACAGCTAC--AGCTATGTCACCTAGCCAC-GTGAGATCAACTG-CCTATGCCTC--AGAATACCAGTAACATCTAA-TCAGAGGTATCAG-TAATA-TCTGTCCAGGGCTGAGGAGATCCTTACAGCTA------AGGTGAAA------TCGTCTTTAAATGCCACT-TTT------------------ i bosTau4.chr1 C 0 I 235 s equCab2.chr26 13365695 1241 + 41866177 GTCTCTGGCCAAAAAGC--AAAAAGAAAAACA-CTAAAAA--GCAAAATAA--ATATTA-----GTAAACAGTTAAAT---AATTATATTTAT---TGTTACATT-ACATTATGTT----GAACACTATTAAGCATTAACATTTCAGTCATTCATTGAGCCCAAATTCACTTACCATCAACCATACACAACACTGATATACt----------------------attgagaaaat----gtttacccttttccagttctttctgaagactttacgtgtgttatttcacgcaat-ccttaaaataaatctatgaaatatatacaggct--ttatc-atttcacagagaaggaaactgagtcacatgga----aagttgtattgacacccagataatcagtggtatagctgagatttgaagtcaCCAACTAGCAACGTATAATTTAGGAGAGAagtacagttgatggttgaaaacacaggctctgg--------------attcaaatgct--atcgcattcc-ttagtagctgtgtgattc-tgggaatgttcctttacctctctgtaacttactttagaattcgcatcaatttgtgactctcttatgagctggtgagtattagactagtttaagcttattggctacttagaac----agtacctggctcatgatgaatactAGCCATCTTGTACCATTTTCTTCATCTTGAGTAGTTCATGGCCTGACAGAAATCAATGTCAATATGGATAAATGCTTATAAAGGCAACAGGAAGAAATACAAAACCGTATAAACAACTCCATTTTACTGGAAAGCATATTTGAAAGCTATGTTAAATCGAGAAAGGGAAGGGAAAGCCTCTAAGGATGAGATCACAATGGTGAATCAGTGACTGGAAACTGACAAGGCTCGTCTG-AA------TGTTTTCTTGGAGGTCCCAAGACTT------AAAAAAT----GTTTTGACAAAGGGAAGAGGATGATT---GAGTAGTGTTGGGAAGAGACATTTTCTGAAGTCAGCAGATATGATAGTTCAATAACAGGAAAGACAAATGCAGTAA-GAGGAAAGCATATAAAGTAATAACGTATTTGAAGTGCTTTCTCAAGGATA----ATGTAAAATCTGTTATATGTAAATTATCGTTAT---GATTATAATATCATTA-TTGCCTGACTGATACAACTACTTGGCCACATCACTTGGCCAT-GTGAAATCAATTT--CCGTGACTCAGAGAATACCAATAACATCCAA-TCAGAGGTATCAG-AAATCAGAGGTCCAGAGCTGAGCAGACCTCTACAGCTG----TTAGGAGAAATTGACTATGTCTTCAAA------------------------TGTGG i equCab2.chr26 C 0 C 0 s canFam2.chr31 14114732 1188 + 42263495 GTCTCTGGACAAAGACC--------AAAAACA-CTA--------AGAATGA--ATATCA-----GTCAATAGTGAAAT---AACTACATTTATTAATGTTATATTAATAATACATT----GAATACTGTTAACCATTAACATTT-ATTCATTTATTGAGCCAAAACTCACTTAACATCAACTGTATATGACATTGATATACT----------------------ATTGAGAAAAtaagagcttaccatcttctaattccttctaaagcctttacatgtgtgattttatgcaat-ccttataataaatttatgagatatatactgatt--ttata-attccacagagaagaaaattgagtcttatagatagtaagttgtaataacacttggataatcagtgacattgttgatatttgaagtcaCAGGatagtaaagtataa-ttaagagaagagcaaaatt-atggttgaaagcataggctcttg--------------attaaaatttt--acctcctccctttggcagctgtgcaattc-tgggaaatttcccttacctctctgtgccttagtttTACATATGCATCAGTTTGTCCCTCTCTTATGGGCTG----CTATTACACTA----------------TACTTACAAC----AGTAGCTGGCTTTTGACAAATATTAGTCATCTTGTACCATTTTCTTCACCTTGTATAGCTTATGGTCTGATAGAAATCAATGTCAAGATGAATAAATGGTTATAAAGGCACCAGGAAGAAATGCAAAACCATAGAAACAATTCTATTTGACTGTAAAGCACATTTGAAAGCTCTGTTAAATTGAGAAGGGG--------------AAGGATGAGATCACAACGGTGAATCAGCGACTGGAAACTCATGAGGCTTGTTAGAAA------TATTCTGTTGGAGATCCTAAGTCTTAAAAAAAAAAAAA----GTTTTGACAAAGGGAAGGAGATGATT---GAATAATGTTGGGAAAAGACATTTTCTGAAATCAGCAAGTATTCTTGTTCAATAACAAGAAAGACAAATACAGTAA-AGGAAAACAATATAAAGTAAAAATGTATTTGAAGTGCTTTCTAAAGGGTAACACATGTAAAATCGGCTGTATGtaaatta---ttac---aattataatattatta-ttCCCTGGCTAATGCA---CCCCAGCCATATCACTTGGCCAT-GTGAGATCAATTT-CCCATGCCTCAAAGAATACCAATAATATCTAA-TCAGAGGTATCAG-CAACC-TCTGTCCACAGCTGAGTAGACCCTCACAGCTA----TTGGGTGAAA---------------------------------------------- i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20622472 1216 - 62548349 GGCTCTGGCTAAAAACCTGAAAAAGAAAAATG-CCCAAAA--GTAAAATGA--ATATTA-----GCCAAC-----AATTAGAACTACCTTTATGAA----GTATCCATAATATGCT----TAACGCTATTAA-------CATTTTCGTTCTTCATTGAGTCAAAACTCATTTCATGTCAACCAAGTACAATGTCACCATACT----------------------ATTGAAAA---AAAACTttaccatattccagaccatcctaacctctttatatgtgttattttgtgcaat-ctttataaaaaatttatgagatacatactgact--ttatcatttttacagagaaggaaacttagtcatataaagagtaggtcttacggtcacccaggtaatcagaggcagagccgagatttgaagtcatagtatagtagagtATGACTTATGGAGGcaatacaaacagtggttgaaagcatgggctctgggataaacag-ctgtacttaaaatct--agctcaaccccttagtggatgtgtgagcc-tgggcaagcttcttaatgtctccatgcctt-----------tgtAAAAATTTATATCTGTCTT-------------------ACCAGTCTGTACTTGAACGGCACTTCGGAT----TTTACCTATTTCTCAATAAATATTACCTTACTCATCACATCTTCCT---CTGGGCTAGCTCCTGGCCTACTAGGAATCAATGCCAACGTTGCCACATTATCATAAAGGGAACAGGAAGAAATACAAAACCATATAAACAACTCCATTTTACTGGTCAGCACATTTGAAAGCTGTGTTAAATTGAGAAGGGGGAGGGAAGACCGCTAAGAATGAGATCACTATGGTGAATCAGTGACTGGAAACTGATGAGGCTTGTCTGGAA------TATTTTCATGGAGACCCTGAGACTT----------AAA----GTTTTGATGAG-GGAAAGAGATGATT---GAATAGTGT--GGGAGAGACGTTTTCTGAAGTCAGCAGAAAAGATAGCTCTATATCAGGAAAAACAAATATGATAAGGAGAAAATGATATAAAACAATAACGTATATGAAGTTCTTTCTAAAGAGTAACACATATAAAAT-TGTTCTTTGTAAATTA---TGATTACAATTATGACATCATTATTTACCTCGCTGATACAAATGC--ATTCATGCAACTTGGCCAT-ACAAGATCAACTGTCCAATGCCTAGGAGAATACAAATAACCCCCAG--TGTAGATACTAG-AAATT-GCTTTTCACAGCTGAGTAGACCCTTACAGCTA----TCAAATGACACTGACTATGTATTCAAATAT-------------------------- i loxAfr3.scaffold_13 I 7889 C 0 a score=144920.000000 s hg19.chrUn_gl000245 18300 209 + 36651 caaaacacactcaacaa---tttgcatcttaaccactgttaagtatacaattcagtgtcattaa-atgtattcac-aatgt-tgtgcaagcatcaccaccacccatctccataattctttttgtcttgtaaaattgaaatcctgtacccattaaaaagtgactccccattccccgccctcccagggcaactacagctttactttctgtcttgatg s panTro2.chrUn 47414970 209 - 58616431 caaaacacactcaacaa---tttgcatcttaaccactgttaagtatacaattcagtgtcattaa-atgtattcac-aatgt-tgtgcaagcatcaccaccacccatctccataattctttttgtcttgtaaaattgaaatcctgtatccattaaaaagtgactccccattccccgccctcccaggacaactacagctttactttctgtcttgatg i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159744177 209 - 202140232 caaaatacactcaacaa---tttgcatcttaaccactgttaagtatacaagtcagtgttattaa-atgtgttcac-aatgt-tgtgcaagcatcaccaccacccatctccataattctttttgtcttgtaaaattgaaatcctgtacccattaaacagtgactccccattccttgccctcccagggcaactaaagctttactttctgtctTGAAG i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189461822 207 - 189746636 caaaatacactcaacaa---tttgcatcttaaccacttttaagtctacaattcagtgttattaa-atgtattcac-aacgt-tgtgcaagcatcaccaccacccatgtccataat--tttttgttttgtaaagttgaaatcctgtacccattaaacagtgactccccattccccgccctcccagggcaactaccgctttactttctgtcttgatg i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15815411 188 - 24440124 caaaatgcacataacaaaatataccatcttaaccat-tttacaagttcagtccaatgttgttaatatatatacatatgtgcatataaaatgtgtatcaccatcagc---------------catc------aactgaattcctataacctttaaacagtgctatctcagtc---tcccttccccA--AACTACTATTCAGCTCTTACTTTTTATG i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141895732 200 + 163896628 aaaaaca-----gacaagacttaccaacttaactatctttaagtgtacagttcagtggtactaa-ataagtttat-tatgc-cgcacagtcatcaacaccatccac-tccataactctttgcatcctgcaaaattgaatccctgaacccattaaacaatgattcccca------tacctcccctagcaatcaccattccactttctgtctttatg i oryCun2.chr14 C 0 C 0 e bosTau4.chr1 138186045 235 - 161106243 I e loxAfr3.scaffold_13 20623688 0 - 62548349 C e canFam2.chr31 14115920 0 + 42263495 C e equCab2.chr26 13366936 0 + 41866177 C a score=-181.000000 s hg19.chrUn_gl000245 18509 22 + 36651 a--------------------------------------atCATACAATATCAAATGGAA s oryCun2.chr14 141895932 54 + 163896628 atttt------gatattttaggaattttatataagcagaaacttataatatCAAATACAA i oryCun2.chr14 C 0 I 721 s cavPor3.scaffold_34 15815599 42 - 24440124 GCTTTAGACCAAATATATTAG------------------AACCTATGTAGCCAAATGCAA i cavPor3.scaffold_34 C 0 I 977 s rheMac2.chr2 189462029 22 - 189746636 a--------------------------------------atCATACAGTATCAAATGGAA i rheMac2.chr2 C 0 C 0 s ponAbe2.chr3 159744386 22 - 202140232 A--------------------------------------GTCATACAATATCAAATGCAG i ponAbe2.chr3 C 0 C 0 s panTro2.chrUn 47415179 22 - 58616431 a--------------------------------------atCATACAATATCAAATGGAA i panTro2.chrUn C 0 C 0 s loxAfr3.scaffold_13 20623688 12 - 62548349 --------------------------------------AATTTTACAATA---------- i loxAfr3.scaffold_13 C 0 C 0 e bosTau4.chr1 138186045 235 - 161106243 I e canFam2.chr31 14115920 0 + 42263495 C e equCab2.chr26 13366936 0 + 41866177 C a score=902579.000000 s hg19.chrUn_gl000245 18531 726 + 36651 TTTTTAAGATATTTAAAATCTTTTGTCTGGAAGCGAAGTGGAAG----TTAATATCAATGGCTATGCCTTCAGTGAGTTCTCAGACCACATTGCAATGT----------AGTTAAC-TATTTATCTTTTATT---ACGTTCTAGAC--CTATTATTTCTTTCTGGCACAAAA---ATATCTTCTTTGTAGATTATGGCATTTACCTCTATCTCCACACCTTTCTGCGTCTGTCATCCACAGATCATCAGCCTCTTGCTTAGTC-TCCATTTAATGACAATTTCTATTTAGTATACAAGAGTCCTTCCCCCCGCAATGCAATTTCTTCAC--TCTGAAAAGCTCTG----ACTCTGGCTACTGGTCTCTGTTATGTACT-CATCCCTAGAGCCATGTCTTCAAATATTT--CTCAGAACTTCTTCACATCTAAAAATCTAGGATTAATGTATTGC--TCTCTGATTATATTCTTCT----GGTATTTCAAGTATCCTGTATAACTTCTTCATCTGCCCTTGCTTTTCTTCTACATCAAGATGTC-AAGTTCATGGA-CTTCC-CAATTAATCA----TTTTAAAAATTTAT--TTCAAGCCTTTATGAGTCACTACAATGTACATATGTTCTCAGGAATTATGACCCTACAATTTGTATA-TGAGAATagttcctgtgtcaggcattatggaca--taagagtaaataaattct-agcccctgcctacaaggagctaattcccagcctaagac-agattgtaagccaataatatgtagag s panTro2.chrUn 47415201 723 - 58616431 TTTTTAAGATATTTAAAATCTTTTGTCTGGAAGCAAAGTGGAAG----TTAATATCAATGGCTATGCCTTCAGTGAGTTCTGAGACCACATTACAGTGT----------AGTTAAC-TATTTATCTTTTATT---ACTTTCTAGAC--CTATTATTTCTTCCTGGCACAAAA---ATATCTTCTTTGTAGATTATGGCATTTACCTCTGTCTCCACACCATTTTGCATCTCTCATCCACAGATCATCAGCCTCTTGCTTAGTCTTCCATTTAATGACAATTTCTATTTAGTATACAACAGTCCTTCCCCCTGCAATGCAATTTCTTCAC--TCTTTAAAGCTCTG----ACTCTGGCTACTGGTCTCTGTTATGTACT-CATACCTAGAGCCATGTCTTCAAATATTT--CTCAGAACTTCTTCACATCTAAAAATCTAGGATTAATTTATTGC--TCTCTGATTATATTATTCT----GGTATTTCAAGTATCCTGTATAACTTCTTCATCTGCTCTTGCTTTTCTTCTACATCAAGATGTC-AAGTTCATGGA-CTTCC-CAATTAATCA----TTTTAAAAATTTAT--TTCAAGCCTTTATGAGTCACTACAATATACATATGTTCTCAGGAATTATGGCAATACAATTTG-----TGACAATAGTTCctgtgtcaggcattatggaca--taagagtaaataaattct-agcccctgcctacaaggagctaattcccagcctaagac-agattgcaagccaataatatgcagag i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159744408 727 - 202140232 TTTTTAAGATATTTAAAATCTTTTGTATGGAAGCAAAGTGGAAG----TTAATATCAATGGCTATGCCTTCAGTGAGTTCTCAGACCACATTACAATGT----------AGTTAAC-TATTTATCTTTTATT---ACATTCTAGAC--CTATTCTTTCTTCCTGGCATGAAA---ATATCTTCTTTGTAGATGATGGCATTTGCCTCTATCTCCACACCTTTTTGCATCTCTCATCCACAGATCATCAGCCTCTTGCTTAGTCTTCCATTTAATGACAATTTCTGTTTAGTATACAACAGCCCTTCCCCCTGCAATGCAATTTCTTCAC--TCTGAAAAGCTCTG----ACTCTGGCTACTGGTCTCTGTTATGTACT-CATTCCTAGAGCCATGTCTTCAAATATTT--CTCAGAACTTCTTCACATCTAAAAATATAGGATTAACTTATTGC--TCTCTGACTATATGCTTCT----GGTATTTCAAGTATCCTGTATAACTTCTTCGTCTCCCCTTGCTTTTCTTCTACATCGAGATGTC-AAGTTCCTGGA-CTTCC-CAACTCATCA----TTTAAAAAATTTAT--TTCAAGCCTTTATGAGTCACTACAATATACATATGTTCTCAGGAATTATGGCCCTACAATTTATATG-TGAGAATagttcctgtgtcaggcattatggaca--taagagtaaataaattct-agcccctgcctgcaaggagctaactcccagcctaagac-agattgcaagcaaataatatgcagag i ponAbe2.chr3 C 0 I 949 s rheMac2.chr2 189462051 728 - 189746636 TTTTTAAGATGTTTAAAATCTTTTGTCTGGAAGCAAAGTGGAGG----TTAATATCAATGGATATGCCTTCAGTGAGTTCTCAGACCACATTACAATGT----------AGTTACC-TATTTATCTTTTATT---ACATTCTAGAC--CTATTCTTTCTTCCTGGCACAAAA---ATATCTTCTTTGAAGATTATGTCATCTACCTCTATCTCCACACTTTTTTGCGTCTCTCATCCACAGATCATCAGCCTCTTGCTTAGTCTTCCATTTAATGACAATTTCTGTTAAGTATACAACAGCCCTTCTCCCTGCAATGCAATTTCTTCAC--TCTTAAAAGCTCTG----ACTCTGGAAACTGGTCTCTGTTATGTACT-CATTTCTAGAGTCATGTCTTTAAATATTT--CTCAGAACTTCTTCACATCTAAAAATCTAGGATTAATGTATTGC--TCTCTGACTATATTCTTCT----GGTATTGCAGGTATCCTGTATAACTTCTTCATCTGCTCTTGCTTTTCTTCTACATGGAGAGGTC-AAGGTCATGGA-CTTCCTCAATTCATCA----TATTTAAAATTTAT--TTCAAGCCTTTATGAGTCACTACAATATACATATGTTCTCAGGAATTACAGCCCTACAATTGGTATA-TGAGAATAGATCCTGTGTCAGGCATTATGGACATTTAAGAGTAAATAAATTCT-GGCCTCTGACTACAAGGAGCTAATTCCTAGCCTAAG---AGATTGCAAGCAAATAATATGCAGAG i rheMac2.chr2 C 0 C 0 s canFam2.chr31 14115920 686 + 42263495 --TTTAAGATATTAAAAACCTATTGCCAGTAAGCAAAATATAGG----TTGCCATC-ACACGTCTGCTTTTAGTG-GGTCTCAGATCACATTACAGTAC----------GATTACC-AATTTATCTTTTATC---ACATTCCAAAC--TTACTCCTTC---CTGGTGCAAAAA--ATATTTTCTTTGAAAATTGTGGAATCTAGCTATATCTCTATACC-TTTTGAGGCTGGCATCCACTGACTATCAACCTCTTAGTCTTCCATTTATCCTATGACAGCTCTTGC------------------------CCCAGTGCAGTTCCCGGACTGTATTGCTAGTACTGGTAAAATCTGGTTACTGGGCTCTCTCACCCTTTCCATTCCCTGAGCTACATCTCCAAGTATTTCTCTCCAAACCTCTTCACCACTAAGCACCTAGGATCAATTTCTTAT--TTTCTGACTATACTTCCCT----AGTGTTTCAGACAGCCAC----ATCACCTCTTCTACTCTTGTTTTTCATCTGCACAGAGATGTCAAAGTTCACAGATTCTTC-CAATTTCTCACA--TTTT---CACTTAT--TCCAAGCCTTTATTGGTCCCTACAGTGTGTGTATGTCTTCGGGAATTATGGTCCTACAATGTGTATA-TGACCATAGGCTTCACGGCAGGCAT----------------TAAATATATCC--AAACCATGCCTATAGGGAGCTAGTTTCTAGCCTAATGC-AC-TGACAAACAAGCAAATTGCAAAA i canFam2.chr31 C 0 C 0 s equCab2.chr26 13366936 685 + 41866177 TTTTTAGGATATTAAACATCTACTGTCCATGAGCAAGGTGGAGG----TTACCATCAACAACTTTGTCTTTGCTACATTCTCAGATCCTATTACAATGT----------AATT-----ATTTATCTTCTATC---ACATTCCAGAC--TTACTCCTCCTTTCCGGTGCAAAAACGCCTTCTTCCTTGAAGACGGTGGCATCTAGTCCTATCTCAACACC-TTTTGGGTCTGTCATCCCCAGGCCATCAGCCTCTTGCTTTGTCTTCTGTTTAATGCCAAATTCTGCT--------------------TCTCCTGTAACAGTGCCCTGACTGTCTTGCTAGCATTG----ACTCTGGTCACTGGGCTCTGTTACTCACTCCATTCCCAAAGCTACATCTTTG---TTTTCTCTCCAAACTTCCTCACCTCTAAGCACCTAG----------------CTGCTGACTACACTTCCC-----AGTGTTTCAACCATCCCC------TGTCACTTCTACTCTTGCTTTTCATCTACATAAAGAGGCC-AAGTTCATTAACCCCTC-CAATTTCTCAAA--TTTT---CATTTAT--TCCAAGACTTTATGGGTCTCCACAAAGTGTATATATCCTCATAAATTATGGTCCTGCAATGTGCAGA-TGACAATAGactctatgttaggcattagggaaa--taagaataaataaatcct-ggcccctgcctccagggaggtagcttccagcctaatgt-ag-caacaagcaagtaagatgtaaag i equCab2.chr26 C 0 C 0 s bosTau4.chr1 138186280 691 - 161106243 ------acatctcttaagtctcctgc--attggcaggg---gggttctttaccactagca---ccacctggaaagAGCGCTCAGATCACATTACAGTGCATAACAGTGTAACT-----ATTTATCTTCTGTC---ACGTTCCAGAC--ATTCTTTTTC---CT-GTGCAAA----ACGTCTTCTGTGAAGATCATGGC----------ATCTCTACACC-TTTTAGGTCTGTCAT-CACAGACCATCAGCCTCTTGCTTGGTCTTCTGTTTAACCCTGAATTCTGTTTGTCCTGTGTCGGTCCT--CTCCCCCAAAGCATGTTCTTGACTGTATTTCTCGTAGTG----AATGTGGTTACTTGGTTATGTTTCCCATTCCATTTCCTGAGCTATGTCTTTAAATATTTCTCTCTGAA---CTTGACCTCTAAGCCCCTAGAATCAATTTCTTGC--TTTCTGACTATACTTTCTTTCCCAGTGTTCCACATATCACCT---ATTATCTCTTTTACTCCTGCTTTTTAC--------AAATGCA-AAATTTATTGA-CCCTC-TAACTTATCACATTTTTT---TATTTAC--TCCAAGCC---ATGTGTCCCTACAATGTGTACATGTCCCCAGGAATTATGGCCCCACAATGTATTTA-TGACAATAGACCCTATATTAGGCAT-----TAT--AAAGTAAGAATAAATCCT-AGCCTCTGCCTATAAGCAGCTAGTTTCCAGTCTAAAAT-AC-TGACAAGAAATGAAAATGCAAAA i bosTau4.chr1 I 235 C 0 s oryCun2.chr14 141896707 668 + 163896628 ------------TCAAAACCAATTTTCTGTGAGCTAAGTAGAGG----CTACTATCAACACCTACACCTTCAGTGAGTTCTCAAACCATATTATAATGT----------AGTTGTC-TGTTTATTTAGTATC---ACATTCCAG-------TTTTTCTTTCCTGATTGAAAA---ATACTTTCTTTGAAAATTGTGGCATCTTGCCCTGTTTCTACACCTTTTTGGGTCTTTCATCTGTAAGTCAACAGACTCTTGCTTGGTCCTCCATTTAATCACACATTTGATTTATCATATGAGAACATT---------AATACAGCTTCTTAACTGTCTTGGAACCACTA----ATGCTGGCTACTAGCCTATTTGAGCTACTCCATTCCCTAAGCTATGACTTCAAATATTTCCCTCAGAAGTTTTAAACATCTAAGAGTCTGGAACTTTTTTTTTTCTGTCTCTGATCATACTTTTCC----ACTATTTAAGGTA-----------------------------------TTTGCATACAGATATC-AAGTTCCTTGA-CCTCC-AGAAT----G----TATTAAATATTGTTTATCCAAGCTACTATAGGTCCTTACACTACACATCTGTCCTCATGAACTATGGTTCCACAGTATGCAAA-TGACAGTAAG-CCTGGACTATGCAATAAATACA--TAAAAATAAATAAATCCT-GATTCTTGGCTATAAGGAGCTAATTCCCAACCTAATGTGAGATC---AATAAATAATATGCAAAG i oryCun2.chr14 I 721 C 0 s loxAfr3.scaffold_13 20623700 679 - 62548349 ----------ATCAAAAATCTATTGTC---------------AG----TGAACATCAACACCTTTACCTTTAGTGGCTTCTTAGATCATATTATCTTAT----------AAATATCTTAGTTATCCTTTTTTTTAATATTCCAAATTGTTATTTTTCCTTCCTGGTACAAAA---TCATC-TCTTTGAAGATTGTGGCATCAAGCCATATCTCTAGTCCTCTTTAGATCTGTCATCCACAGCCCGATAGCCTCTTGCTTACTCTTCC-TTTAAT-CCAAATTATGTTTATCATACAA-----CCTCCTTCCCCCATTCAGTTCCCTATCTGTATGAGTAGCATTG----ATCTTGGTTTACAGTCCCTGTCACCTACTTCATCCTCCAGACTTTGTCTGGAAGTATTCCTCTCAGAACTTCTTCTCATCTAAACACCTATAATCAATTTCTTGC--TTTCCAACTACACTTTCCT----AGTGTTTCAGGAATCCTATAACACTTCTTTTATTATCGTTGCTTTTCATCTATCTAGGGATGTC-AAGTTCCTTAACCTCTC-TAACTTTTCCAA--TTTT---TATGTAT--TCTCACCCTTTATGGG---------------------CTTACGATTTATGGTCCTATAATATATGTCTTGACAATAGGCCCT--GTTGGACATTATGGAGA--CAAGAATAAAGAAACCATGAGCCCTTGCTTACAAGGAGCACATTTACAGCCCAATGC-AG-----AGACAAGTAAGATACAGCG i loxAfr3.scaffold_13 C 0 C 0 e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=119298.000000 s hg19.chrUn_gl000245 19257 110 + 36651 ttgtaagtctaaggaaactgattgggatgtacct--aattcgagctgggaatatcagaagaaaaactttttgaaagtcatgagacatgagctgtgcctaaaagaAT-AAAAAT s panTro2.chrUn 47415924 111 - 58616431 atgtaagtctaaggaaactgattgggatgtacct--aattcgagctgggaatatcagaagaaaaactttttgaaagtcatgagacatgagctgtgcctaaaagaATAAAAAAT i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159746084 111 - 202140232 tggtaagtctaatgaaactgattaggatatacct--aattcaagctgggaatatcaaaagaaaaactttttgaaagtcatgagacatgagctgtgcctaaaagaataaaaaat i ponAbe2.chr3 I 949 C 0 s rheMac2.chr2 189462779 111 - 189746636 TGGTAAGTCTAAGGAAACGGATTAGGATGCACCT--AATTCAAGCTGGGAATATCAGAAGAAAAGCTTTTTGAAAGTCACGAGACATGAGCTGTGCCTAAAAGAATAAAAAAT i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141897375 103 + 163896628 TGATAAGTCTAAGGCAA-TAAAGAAAATGTA-TT--AATTCACACTGGAAATACCAGAGGAAA--CTTTTGGAAAAACATG---TCCaaattttttttaaaaatat-aaatat i oryCun2.chr14 C 0 I 16 s canFam2.chr31 14116606 105 + 42263495 GAGTAAATCTCCAGAAGTTCATCTACATATGcct--aattcagactgagaatatcagagaaaa--c--tttgaaagtagttatac-tacactatgcccagaagaatgaAAAA- i canFam2.chr31 C 0 C 0 s equCab2.chr26 13367621 104 + 41866177 tagtaagtctccggaagctgatgaggatgtacctaaaattcagattggaaagatcagggaaaa--ctttttgaaggtggtgatac-tgctctgtgcc-----ggcccaaaaa- i equCab2.chr26 C 0 C 0 s bosTau4.chr1 138186971 104 - 161106243 TGGTAAGTCTCCAGAAGCTGACGAGCATGTACCC--AGTTGAGACTGAGAATATTAAGGAAAA--ATTCTCAAAAGTGATGATAA-TGCACTGTGACCA---GAATAACAAT- i bosTau4.chr1 C 0 C 0 s loxAfr3.scaffold_13 20624379 105 - 62548349 GGAAAAGTCTAGGGAAACCATTGAGAAGACATCT--AATTCAGATTGGGAACATTTGGGTAAA---TATGTGAAAG--ATAATACTTGAGCTATTTCCATAATAATAATAAT- i loxAfr3.scaffold_13 C 0 C 0 e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=188870.000000 s hg19.chrUn_gl000245 19367 175 + 36651 AGAGTGAGAAATAAGAATAAATAAAT-----TAGGGAATGAGATGGGTATAATAGTAGAAAAAGGAAATCTCTTT-----------------AGATAAAACAGGTTATGAGAGTATATA-GGAGGCTTATTAACTCAGTGTGGTTGGAGAAAACAGGTTGAAAGGAGAAATAGGGGAGAAAGTTACAAAGGGAATCAA s panTro2.chrUn 47416035 175 - 58616431 AGAGAGAGAAATAAGAAGAAATAAAT-----TAGGGAATGAGATGGGTATAATAGTAGAAAAAGGAAATCTCTTT-----------------AGATAAAACAGGGTATGAGAGTACATA-GGAGGCTTATTAACTCAGTGTGGTTGGAGAAAACAGGTTGAAAGGAGAAATAGGGGAGAAAGTTACAAAGGGAATCAA i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159746195 193 - 202140232 atagagataaataagaagaaataaat-----taggggatgagatgagtataatcgtagaaaaaggaaatctctctaggtcaagggagcttagagatgaaacagggtatgagagtatatagggaggctcgttaactcagtgtggttggagaaaacaggttgaaaggagaaataggggagagagttacaaagggaatcaA i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189462890 193 - 189746636 ATAGAGAGAAACAAAAAGAAATAAAT-----TAGGGAATGAGATGCGTATAAGAGTAGAAAAAGGAGATCTCTTTAGGTCAAGGGCGCTGAGAGATGAAACAGGGTATGAGAGTATACAGGGAGACTCACTAACTCAGTGCGGTTGGAGAAAACGGGTTGAAAGGAGAAATAGGGGAGAAAGTTACAAAGGGAATCAA i rheMac2.chr2 C 0 C 0 s canFam2.chr31 14116711 183 + 42263495 AAAAT-AGAAATAAATAAAAGTAAAT-----TAGAGGATGATATAGTTATGATGGTAGGTAAAGGATATCTCTTCAGGCCAA-GGAACTTGGAGATGAGAGAAGCCATGAGAACA------AAGATTCATTGCCTCACTAAGGTTGGAGAAAATGGTATGAAAGGAAAGGCAGGAATAAAGGCTATGAAGGAAATT-- i canFam2.chr31 C 0 I 283 s equCab2.chr26 13367725 180 + 41866177 aaaat----------tagaaataaat-----tagaggatggcatgggtgtgatagaagggaaaggacatctctttaagccaagggagtttggagatgagaaaaggcacaagagtatacaggaaagttcattagctcgatttggttggagaaaattatatgaaaagaa---taggagaaaagactgagaaaggcattaa i equCab2.chr26 C 0 I 268 s bosTau4.chr1 138187075 187 - 161106243 AAAGA----------CAGAAGTAAATGGAAATAGAGGATTATATGGACATGAGTGTAGGGAAAGGACATCCATGTAGGCCAAAGGATCTTGGAGATGAGA-CAGGTGTGAGAGCATATAGGAAAGTTCATTAGCATAATATGGCTGGAGAAAAGCTTGTGAAAGGAAAACCACGAGAGGAGGATATACAGATAATTAA i bosTau4.chr1 C 0 I 132 s loxAfr3.scaffold_13 20624484 163 - 62548349 ------------------AAATTAGTAATGCCAGGGGGAAAGATAGCTGTAATAATAGGGAAGGAAAGTTTCTTCAGGTAAAGGGAGCATGAAGATGAGAAAATATATGA-----------AAAGTTCATTAACTCAGTTTTGTCAGAGAACAGACTATGAAAGAAG------TGTGCCACACTGCAAAGGGAGTTAA i loxAfr3.scaffold_13 C 0 I 1695 e oryCun2.chr14 141897478 16 + 163896628 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=10100.000000 s hg19.chrUn_gl000245 19542 25 + 36651 A------TGTGTTAGTAGTTGAGGGAAAAGC s panTro2.chrUn 47416210 25 - 58616431 A------CGTGTTAGTAGTTGAGGGAAAAGC i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159746388 25 - 202140232 A------CGTGTTAGTAGTTGAGGGAAAAGC i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189463083 25 - 189746636 A------CGTGTTAGGAGTTGGGGGAAAAGC i rheMac2.chr2 C 0 C 0 s equCab2.chr26 13368173 24 + 41866177 A------TGTATT-GGGGTAGAGGGAAAAAT i equCab2.chr26 I 268 C 0 s canFam2.chr31 14117177 24 + 42263495 G------TGCATT-GGGGTACTGAAAAAAAT i canFam2.chr31 I 283 C 0 s bosTau4.chr1 138187394 30 - 161106243 TGTGGAAGATGCT-GAGGAAGGAGGAAAAAC i bosTau4.chr1 I 132 I 119 s loxAfr3.scaffold_13 20626342 6 - 62548349 -------------------------AAAAGT i loxAfr3.scaffold_13 I 1695 C 0 e oryCun2.chr14 141897478 16 + 163896628 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=141695.000000 s hg19.chrUn_gl000245 19567 103 + 36651 AAATATTGAATACGACCCATAGAT---CTTGGATAACCCAGTGTTTGGTAGTAGCTTACATA-AAAGGTT---GTGACAAAATAACCAGAGATATGTGGAGAAAATAATA s panTro2.chrUn 47416235 103 - 58616431 AAATATTGAATACGACCCACAGAT---CTTGGATAACCCAGTGTTTGGTAATAGCTTACATA-AAAAGTT---GTGACAAAATAACCAGAGGTATGCGGAGAAAATAATA i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159746413 103 - 202140232 AAATATTGAATACAACCCATAGAT---CTTGGATAACTCAGTGTTTGGTAGTAGCTTACATA-AAAGGTT---GTGACAAAATAGCCAGAGATATACGGAGAAAATAATA i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189463108 104 - 189746636 AAACATTGAAGATGACCCACAGAT---CTTGGATAACCCTGTGTTTGGTAGCAGCTTTTACGTAAAGGTT---GTGACAAAACAGCCAGAGACATACGGAGAAAACAATC i rheMac2.chr2 C 0 C 0 s bosTau4.chr1 138187543 104 - 161106243 AAATGCTGAGTATGACCGATGGCTAGAAGTGGATAACCGAGTGTCTAGTAGTAACTTTCACA-AAAGATA---GAGAGGTAACAGCCAGAGAAGTAAGGAGAAAATTA-- i bosTau4.chr1 I 119 C 0 s equCab2.chr26 13368197 103 + 41866177 AAATGCTGAGTACGACCCATAGTT---CTTGGATGACCCAGTGCCTGGTGGTAGCTTTCATA-AAAGGTT---GAGAAATAATAGCCAGAGAGGTAAGGAGAAAATGATC i equCab2.chr26 C 0 C 0 s canFam2.chr31 14117201 106 + 42263495 CAATGTTGAGTATGACCCATAACT---CTTGGATGAAACAGTGCCTGCTAGTAGTTTTCACA-AAATGTTAACAAGTAATAATAGCCAAAGAGATAAAGAGATCATTATA i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20626348 103 - 62548349 TAATGCTGAATATGACTTATAGGT---CTTGGATGACCCAGTGACTGATGGTGTTGTTCCCA-AAAGACT---AAGAAATAATAGCAGGAGAGGTAAGCAGAAAAGTAGC i loxAfr3.scaffold_13 C 0 C 0 e oryCun2.chr14 141897478 16 + 163896628 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=112720.000000 s hg19.chrUn_gl000245 19670 154 + 36651 ACTGAGTGTTATATTTCC-TCTCAGTAGAAACCT-AAAAAAAAAAA-------------TGTA------------ATCACATA-CTGATCTTTTAACTGACCTCCACTTATCTTGCTGCCTGGATTGGTATATATAGTCCTCTGCCTGAAAAATTGCTCAACACTTTTGAAAGGTTGTTTct- s panTro2.chrUn 47416338 155 - 58616431 ACTGAGTGTCATATTTCC-TCTCAGTAGAAACATAAAAAAAAAAAA-------------TGTA------------ATCACACA-CTGATCTTTTAACTGACCTCCACTTATCTTCCCGCCTGGATTGGCATACATATTCCTCTGCCTGAAAAATTGCCCAACACATTTGAAAGGTTGTTTCT- i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159746516 167 - 202140232 ACTGAGTGTTATATTTCC-TCTCAGTAGAAACCT-AAAAAAAAAAACAAAAAAAAAATGTGTA------------ATCACAAC-CTGATCTTTTAACTGAACTCCACTTATCTTGCTGCCTGGATTGGCATACATATTCCTCTGCCTGAAAAACTGCTCAACACTTTTGAAAGGTCATTTct- i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189463212 141 - 189746636 ACCGAGTGTTATATTTCC-TCTCAGTAGAAACCT-AAACAGAAACG-------------TGTA------------ATCACATACCTGAACTTTTAAGTGGCCTCCACCTACCTTGCTCCCCGGATTGGCATACATACTCCTCTGCCTGAAACACTGCTCTACACTTTT--------------- i rheMac2.chr2 C 0 I 7 s bosTau4.chr1 138187647 159 - 161106243 TTGGAGTGTTATATTTCCTTTTTAGTGGAAATCT-AAGTAAAACT--------------TTTATGTTTTAAAAAGGCCAAATACTTGATCTTTTAACTGATCTTTGCTTATATAGCT-TCTGAATTAACATACAT----TTCAGTCTGAAAAA---CTTAACAATTTTGGCTAGCAAGTTTG- i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13368300 151 + 41866177 GCAGAGTGTTATTTTTCTTTCTTAGTTGAAGTCT-AAGCAAAATT--------------TATA------------ATCAAACACTTGATCTTTTAACTGACCTTTACTGATTTTACTCCCTGGATTAGCATACTT----TTCCACCTGAAAAACTgctgaacacttttgactggcaggtttc- i equCab2.chr26 C 0 I 1 s loxAfr3.scaffold_13 20626451 131 - 62548349 AGAAAGTGTTGTTTTTCCTTCCTAGAAGAAACTT-AAGCAAAAAT--------------TATA------------ATGAAGTACTTTCCTTTTTAACTGACTTCTACCTACCATGCTCCCT-------------------------TGTAGAACTGCTCAACACGTGTGGTTGTTAGATTTCT i loxAfr3.scaffold_13 C 0 C 0 e oryCun2.chr14 141897478 16 + 163896628 I e canFam2.chr31 14117307 0 + 42263495 C e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=382432.000000 s hg19.chrUn_gl000245 19824 283 + 36651 cactgttactcccaggcatttctgctaacaccagctgagttgtaaggggccctccaggaggcctaggttgttctccttatcacatatattattttcatttatcaatttacccagaacatctaatgaaatattatggacaccaataac---atgaatacaaatacagctatagtccctaaaaag--taaattgatgtctcttgaaagactGTCATGTCTTAGATGCTAAATTTGGAGTATGTGTTTCTAATAAATAAATAGCTTGCTTTAATAATTCTGATTTATGAAT s panTro2.chrUn 47416493 283 - 58616431 CACTGTTACACCCAGGCATTTCTGCTAACACCAGCTGAGTTGTAAGGGGCCCTCCAGGAGGCCTAGGTTGTTCTCCTTATCACATACATTATTTTCATTTATCAGTTTACCCAGAACATCCAATGAAATATTATGGACACCAATAAC---ATGAATACAAATATAGCTATAGACCCTAAAAAG--TAAATTGATATCTCTTGAAAGGCTGTCATGTCTTAGATGCTAAATTTGGAGTATGTGTTTCTAATAAATAAATAGCTTGCTTTAATCATTCTGATTTATGAAT i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159746683 281 - 202140232 cactgttacacccaggcatttctgctaacaccagctgagttgtaATGGGCCCTCTAGGAGGCCTAGGTTGTTCTCCTTATCATATACATTATTTTCATTTATCAATTTACCCAAAACATGTAATGAAATATTATGGACACCAATAAC-----GAATACAAATATAGCTATGGACACTAAAAAG--TAAATTGATGTCTCTTGAAAGGCTGTCATGTCTTAGATGCTAAATTTGGAGTATGTGTTTCTAATAAATAAATAGCTTGCTTTAATCATTCTGATTTATGAAT i ponAbe2.chr3 C 0 C 0 s bosTau4.chr1 138187806 277 - 161106243 --CTATTATATCCACATATTTCTGCTAATACCAGCTGAAATGTA--GGTTTGCCAAGGATGCCTAACTTGTTCTCTA--ATATATGCAGTATTTTCTCTTGTCATTGTATGTA-GAGATGTATTTAAATATTATGAACAGCAATAAC---ATGAGTATAAATTTAGTTGTAAATACTGTAAAGGTTAAATTGATATTTTTTAAATGGCTGTCACACCTTAGACACTGAGTTTTGAGTATGTGTTTCTAATAAATAGAATGATTACACAAACTA-TCTGATTTATGACT i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13368452 275 + 41866177 tgctgttatacccagtcatttctgctaaccctagatgagttata--ggtttaccaagggtgcctgggttgtttcccactatgtgtgcactatttacacttatcattatactcaaaaaatttaagtaaatatt---aacaccaataat---atgagtgcaaatttagttgtaaa---catgaagactaatttgatgccttttcaaaggctGTCACGTCTTAGATGCTGAGTTTAAAGTATGTG-TTCTAACAAAGAGA-AGTTTGATTTAATCATTTGGATTAATGAAT i equCab2.chr26 I 1 C 0 s canFam2.chr31 14117307 282 + 42263495 CCCTATTATACCCTGACACTTCTGCCAATACC-GCTGAGTTGTA--GGTTTACTAACAGCGCATACTTTATTCCTCATTGTATATAGACTATTTTCTGTTATCCCTGTACATACAAAACTTAATTAAATATTATAAACACCAATGAT---AAGAGTGCAAATATAGATGTAAATGCTATGAAGATGAAATTGGTGCCTTTTCAAAGCTTGCCACGTCTTAGATGCTGAGTTTGGAGTACATGTTTCTAGTACGTGGATAGTTTGCTTTAATCATTCTGATTAGTGACT i canFam2.chr31 C 0 I 283 s rheMac2.chr2 189463360 278 - 189746636 -----TCACACCCAGGCATTTCTGCTAACACCAGCTGAGTTGTAAGGGGCCCTCCAGGAGGCCTGGGTTGCTCTCCTTATCATATACATTATTTTCATTTATCAAGTTAGCCAGAACATCTAATGAAATATTATGGACACCAATAAC---ATGAATACAAATACAGCTATAGACACTAAAAAG--TAAATTGATGTCTCTTGAAAGGCTGTCATGTCTTAGATGCTAAATTTGGAGTATGTGTTTCTAATAAGTAAATAACTTGCTTTAATCATTTTGATTCATGAAT i rheMac2.chr2 I 7 C 0 s loxAfr3.scaffold_13 20626582 269 - 62548349 CCCTGTta----------------ctcacaccagctgaatgata--ggtttaccaagggtgcctaggttgtcctgcaacatatgtatactacttgtacttgtcattgtat-caccaaatttaattaaatagtctgaacaccaaagagccagtgagtgcaaaTTTAGTTGTAGATATTGTAAAGATTACACTGATGTCTTTTCAAAGGCTGTTGCATGGTAGATGCTGACTTTGGAATATATGTTCCTAACAAATGGGTAGTTTGATTTAATCATTCTGATTCATGAAT i loxAfr3.scaffold_13 C 0 C 0 e oryCun2.chr14 141897478 16 + 163896628 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=31312.000000 s hg19.chrUn_gl000245 20107 48 + 36651 GTAATATAGGGGAGCAGCTTTTATTTCATCCTTAATCTT-AAAaaacaa s panTro2.chrUn 47416776 48 - 58616431 GTAATATAGGGGAGCAGCTTTGATTTCACCCTTAATCCT-AAAaaacaa i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159746964 49 - 202140232 GTAATATAAGGGAGCAGCTTTGATTTTGCCCTTAACTTTAAAAaaacaa i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189463638 48 - 189746636 GTAATATAGGGGAGCAGCTTTGATTTTGCCCTTAATCTT-AAAAAGCAA i rheMac2.chr2 C 0 C 0 s bosTau4.chr1 138188083 36 - 161106243 -GTCTATAAGGGAGAG-----actcttgcctggaaaatc-------caa i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13368727 43 + 41866177 GTAATATAGGAGAGACGCTTTAATCTTGCCCTGAAACTT-AGAA----- i equCab2.chr26 C 0 I 3 s canFam2.chr31 14117872 45 + 42263495 ataaTATCTGGGAGTGGCTTTACTCTTACCCT-AAACTT-AGAAAAA-- i canFam2.chr31 I 283 I 6 s loxAfr3.scaffold_13 20626851 27 - 62548349 ---------------------CTTCCTGCCCTTAAATTT-AGAAAATAA i loxAfr3.scaffold_13 C 0 C 0 e oryCun2.chr14 141897478 16 + 163896628 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=23197.000000 s hg19.chrUn_gl000245 20155 55 + 36651 ttagccgggtgtggtggcgggcacctgtagtccc--agctactcaggaggctgaagc s panTro2.chrUn 47416824 55 - 58616431 ttagctgggtgtggtgatgggcacctgtagtccc--agctactcaggaggctgaagc i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159747013 55 - 202140232 ttagccgggcatggtggtgggcacctgtagtacc--agctacccaggaggctgaggc i ponAbe2.chr3 C 0 C 0 s rheMac2.chr2 189463686 54 - 189746636 TGAgccgggcgcggtggc-ggcgcctgtggtccc--agctcctcgggaggcggaagc i rheMac2.chr2 C 0 I 168 s bosTau4.chr1 138188119 54 - 161106243 tggacggaggagcctgatagg---ctgtagtccatggggtcgctaggagtcagacac i bosTau4.chr1 C 0 I 42 e loxAfr3.scaffold_13 20626878 0 - 62548349 C e oryCun2.chr14 141897478 16 + 163896628 I e canFam2.chr31 14117917 6 + 42263495 I e equCab2.chr26 13368770 3 + 41866177 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=13559.000000 s hg19.chrUn_gl000245 20210 94 + 36651 --agaaggatg-----------------------------------------gtgtgcacctgggaggcggagct---tgctgtaagccaaaattgt-----------gccactgcactccagcct-gagtgacagtgt------gagactctgtctc---- s panTro2.chrUn 47416879 94 - 58616431 --aggggaatg-----------------------------------------gtgtgcacctgggagacagagct---tgcagtaagccaaaattgt-----------gccactgccctccagcct-gagtgacagtgc------aagactctgtctc---- i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159747068 96 - 202140232 --aggagaatg-----------------------------------------gtgtgaacctgggaggtgaagct---tgcagtgagccaaaatcgt-----------gccactgcactccagcctggggtgacagtgt-----ggagactccgtcct---- i ponAbe2.chr3 C 0 I 363 s bosTau4.chr1 138188215 161 - 161106243 agaaggaaatgggaacccactccagtattcttgcctggagaatctcagggatgggggagcctggtaggctgacatctatggggtcacacagagtcggacacggctgaagcgacttagcagcagcag-cagcagcagcaTAGGGGAGAGACTTAATATTGCTC i bosTau4.chr1 I 42 C 0 e loxAfr3.scaffold_13 20626878 0 - 62548349 C e oryCun2.chr14 141897478 16 + 163896628 I e canFam2.chr31 14117917 6 + 42263495 I e equCab2.chr26 13368770 3 + 41866177 I e rheMac2.chr2 189463740 168 - 189746636 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=217269.000000 s hg19.chrUn_gl000245 20304 185 + 36651 --aaa---aaaaaa-aaaaGATCATACAAGGAGTAAATGATGATTTAGCATAAAACACAACTTGAGCCTAAAACACAGATCATAGGGCTCAAACTTTGTTATTTTATG-GG----ATTATAC-TAACCAG--------------------TTAATATTCAAAATTTACCATTTCAAAAGAAGAAATATTGGTCTGGGAAAATTGCCATTGCTTATAC s equCab2.chr26 13368773 174 + 41866177 ---------------AAAAGATCATAAGAGTAGTGAATGGTGATTCAGAGT-CTGTACAACTTTAGCACGACACACAGTTCACCTGAGTTAAACTTTGTTACTTTATA-GG----ATTACAC-TTATCAG--------------------TCAGTATTCAAAATTTACAATTTCAAAAGCAG-AACGTTGGTCTGGAAGAATTACCCTTGCATACAT i equCab2.chr26 I 3 C 0 s bosTau4.chr1 138188376 189 - 161106243 TGAAACTTAGGAAACAAAGGACCAGAAAATGAGTAAATGGTGATTAAGAGC-CTGTACAACCTTAGCATAAAACACAGTTCACCTAAGTCAGACATTATTGCCTTAGG-GA----TTTACAC-TCTTTAG--------------------TCAGTTCCCAAAATTTACAGTTTCAAAAATTG-GACATTGGTCTGGGAAAATTACCATTGTATATAT i bosTau4.chr1 C 0 C 0 s rheMac2.chr2 189463908 183 - 189746636 ----a---aaaaaa-gaaaaaTGATACAAGGAGTAAATGATGATTTAGCATAAAACACAACTTTAGCCAAAAACACAGTTCACAGGACTCAAACTTTCTTATTTTATG-GG----ATTATAC-TAACCAG--------------------TTAATCTTCAAAATTTACTGTTTCAAAAGAAAAAATATTGGTCTTGGAAAACTGCCATTGCTTATAC i rheMac2.chr2 I 168 I 1 s panTro2.chrUn 47416973 181 - 58616431 --aaa---aaaaaa-a----aTCATGCAAGGAGTAAATGATGATTTAGCATAAAACACAACTTTAGCCTAAAACACAGTTCATAGGGCTCAAACTTTGTTATTTTATG-GG----ATTATAC-TAACCAG--------------------TTAATATTCAAAATTTACCATTTCAAAAGAAGAAATATTGGTCTGGGAAAATTGCCATTGTTTATAC i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159747527 184 - 202140232 --AAA---AAAAAA-AAAAAATCATACAAGGAGTAAATGATGATTTAGCATAAAACACAACTTTAGCATAAAACACAGTTCACAGGACTCAAACTTTGTTATTTTATG-GG----ATTATAC-TAACCAG--------------------TTAATATTCAAAATTTA-CATTTCAAAAGAAGAAATATTGGTCTGGGAAAATTGCCATTGCTTATAC i ponAbe2.chr3 I 363 C 0 s loxAfr3.scaffold_13 20626878 191 - 62548349 -----------------AAGACCATA-GAGAAGTGAATGGTGAATCACACT-CTGTGCAACTTAAGAGTAGAACACAGTATACCTGAGTTGAACTTTGTTATTTTACATAG----ATTATACTTTATCAGTTAATCCCATGAGttaatttttaatatttaaaatttaC---TTTGAAAGCAGAAACATTGGCCTGGGCAAATTGTCATTGCTTTTAT i loxAfr3.scaffold_13 C 0 C 0 s canFam2.chr31 14117923 174 + 42263495 -------------------GACCATATGAGAAGTGGACAGTGATGCAGAGT-CTGTACAACTTTAGCATAAAACACAACTCACTTAGGTCAAACTTTGTTATTTTAAG-GGAGTAAGTAAAC-TAATCAG--------------------TCGATATTTAAATTTTACAATTTCAAAAACAG-AACATTGGACTAGGAAAGTTATTATTGTATGTAT i canFam2.chr31 I 6 C 0 e oryCun2.chr14 141897478 16 + 163896628 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=260417.000000 s hg19.chrUn_gl000245 20489 392 + 36651 ------------AGAAGAATG----------GAGGAATCTTTTTG-AGAACAACAATTCTAATGATCTTCTTCATCACTGGTT-CCAAAACCAAGCCCATGGAAGGCCTGCATAGGGATAATGTGGAGAA-CATGCAAAAGAAATACACATCACCAGCTCCTCAACTCAGAGCTCCAAGGGAATGGCCAAGGAAGCTGTATTGTCCTAAGAAATTTGAGACTGTTTTGACTTACAATAAATCCTGCTCAATCATATGTATGTATacacacacacacacacacacacacacacacacacaGACGGTGTTGTCAGTG-AAGCCTCTAACATTGCATCTTGACTGGACAG-ATTT-----GACAATTAAAATGGCTGGAAGAAAATA-GGCTTCATAAGTGTCACTT-ACTATTCACATTACACATTAA s ponAbe2.chr3 159747711 389 - 202140232 ------------AGAAGAATG----------GAGGAATCCTTTTG-AGCACAACAATTCTAATGATATTCCTCATCACTGGTT-CCAAAACCAAGCCCAAGGAAGGCCTGCATAGGGATAATGTGGAGAA-CATGCAAAAGAAATACACATCACCAGCTCCTCAACCCAGAGCTCCAAGGGAATGGCCAAGGAAGCTGTATTGTCCTGAGAAACTTGAGACTGTTTTGACTTACATTAAATCCTGCTCAATCATACGTATGTAT----acacacacacacacacacacacaaacacacaGACGGTGTTGTCAGTG-AAGCCTCTAACAATGCATCTTGACTGGGCAG-ATTT-----GATAATTAAAATGGCTAGAAGAAAATTGGGCTTCATAAGTGGCACTT-ACTATTCACATTACACATTAA i ponAbe2.chr3 C 0 C 0 s panTro2.chrUn 47417154 391 - 58616431 ------------AGAAGAATG----------GGGGAATCTTTTTG-AGCACAACAATTCTAATGATCTTCCTCATCACTGGTT-CCAAAACCAAGCCCATGGAAGGCCTGCATAGGGATAATGTGGAGAA-CATGCAAAAGAAATACACATCACCAGCTCCTCAACTCAGAGCTCCAAGGGAATGGCCAAGGAAGCTGTATTGTCCTAAGAAATTTGAGACTGTTTTGACTTACATTAAATCCAGCTCAATCATATGTATGTAT--acacacacacacacacacacacacacacacacaGACGGTGTTGTCAGTG-AAGCCTCTAACAATGCATCTTGACTGGACAG-ATTT-----GACAATTAAAATGGCTGGAAGAAAATAGGGCTTCATAAGTGGCACTT-ACTATTCACATTACACATTAA i panTro2.chrUn C 0 C 0 s bosTau4.chr1 138188565 314 - 161106243 ------------GAAAAGGTG----------TAGAAATCTTCCTG-AACATAGAAATTCTAATTATTTCCTTCATCAGTTGTTTGCAAATGTAAGCCCATGGAAAACATACATAAAGGTTATTTGGAAAG--ATGTAAAAGAAATACACATCCCCAGCTCCCCAACCCAGAAATCTAGGAGAAAGGCTAAAA-CCCTGC--------CCAATCATAGATAGAGATCT-----CTATGCTATAGTG--TTGCTAGTAA-----------------------------------------------------------AGGCCTCTAACCATGCCTCTTGGTTACACCAAATTT-----AACAATTAAAATGACTGAAAGAC-------TCTCACAAATGGTACTTAACTATCCACATGATATATCAA i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13368947 341 + 41866177 ------------GAAAGAATG----------GAGGAGTC-TGCTGCGGCATAGGAATTCTTATGATTTTTTTCATTAAAGGTTCCCAAATGCAAGCCCATGGAAAATCCACATAAGAATGTTCCAGAAGAACATGCAAAAGAAATGCATATCCCCAGCTCCCCAGACCAGAGCTCTAAGGGAAAGGCCAAAG-GCCTGT--TGTCCTAACAGTTTTGAGACTGCTGTGAATTACATTACATCGTGCTGCATCatatatatgtat----------------------------------------------------agatgtctgtatgta-tatctatctatataGCATTGGATTTGACAATTAAAATGGCTGGAAGATAA-----ACTCACACATTGCACAT-ACTATTCACATCACATATTAA i equCab2.chr26 C 0 C 0 s canFam2.chr31 14118097 328 + 42263495 ------------GGAAGAATG----------GAAGAATT-TCCTG-AGCATAGCAATTCTAATAA---TCTCCATCAGTGTTTGCCAAATGCAA--CACTGGAAAATCTGCATAAGTATAATTTGGAAGGACATGTGAAAGAAATACATAAGCCCAGCTCCCCAACCCAGAAACCTAGAAGAAAGGTCAAAATACTTAC--TAATCACAAAATATTGATAGTTATCTGTCTATATCTATATAATG--ACATCAAAGA-----------------------------------------------------------AGGCCTCTAACTGTGCTTCCTGACTACCCAGAATTA-----GGCAATTAAAATGACTGGAAGGTAGTAGACCTTTACAAATGGCATTT-ACAATTCACATCACATATTAA i canFam2.chr31 C 0 I 398 s loxAfr3.scaffold_13 20627069 369 - 62548349 GGACTCTTTTTGAGCAAATTGTCATTGCTTTTATGACTCTTTTTG-AGCATTGCAATTCTAATGATTTCCCACATCGGTGACTCCAAAATGCAAGCTCATGGAAAGTCAACATAAGGATAATCTGAAGGGACATGTAAAAGAAACACATATCTCCAGCTCTGCAACCCAGAGCTCTAGGGCAA-GGCCAAGGAAACTCTATCGTTTTAACAGATTTGGGACCACGATGAGTTAGATTACACCCTGCCCAATCACATGTATATGG----------------------------------------TCTCGTCAGTGAAGGCCTGTGACAATGCTTCTTGATTGTACCAGATTT-----GACAATTAAAATGGCTGGAAGAAAG---------ATAAATGGCACTT-ACTATTCATACCACACATTGA i loxAfr3.scaffold_13 C 0 C 0 e oryCun2.chr14 141897478 16 + 163896628 I e rheMac2.chr2 189464091 1 - 189746636 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=18165.000000 s hg19.chrUn_gl000245 20881 28 + 36651 AAGGACATCTCCT-----------AAATTAAATCTTGTC s panTro2.chrUn 47417545 28 - 58616431 GAGGACATCTCCT-----------AAATTAAATCTTATC i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159748100 28 - 202140232 AAGGACATCTCCT-----------AAATTAAATCTTGTC i ponAbe2.chr3 C 0 C 0 s oryCun2.chr14 141897494 13 + 163896628 AAGGACATCTCtt-------------------------- i oryCun2.chr14 I 16 I 1856 s bosTau4.chr1 138188879 28 - 161106243 AACAACATTCCTC-----------AAATCAAGCATTGTC i bosTau4.chr1 C 0 I 3 s equCab2.chr26 13369288 28 + 41866177 AAGAATATCTTCC-----------AAACTAAATCCTGTT i equCab2.chr26 C 0 I 3 s canFam2.chr31 14118823 27 + 42263495 AAGAACATTTCCC-----------AAACTAAAT-ATGTC i canFam2.chr31 I 398 I 3 s loxAfr3.scaffold_13 20627438 36 - 62548349 AAGAACAACTCTATGATGaaaaaaaaaaaaaaaatt--- i loxAfr3.scaffold_13 C 0 C 0 e rheMac2.chr2 189464091 1 - 189746636 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=121985.000000 s hg19.chrUn_gl000245 20909 97 + 36651 TATGATAAAAAGGCAGAAAATCATGACCCAAGGCTCATTTATA---ACTG--CAGAAATGTTCAAGATAGACCAATGCTTGCTATGTTTAGGAAGTGACAAG s panTro2.chrUn 47417573 97 - 58616431 TATGATAAAATGGCAGAAAATCATGACCCAAGGCTAGTTTATC---ACTG--TAGAAATGTTCAAGATAGACCAATGCTTGCTATGTTTAGGAACGGACAAG i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159748128 97 - 202140232 TACGATAAAAAGGCAGAAAATCATGATCCAAGGCTAGTTTATA---ACTG--CAGAAATGTTCAAGGCAGACCAATGCTTGCTATGTTCAGGAACTGAGAAG i ponAbe2.chr3 C 0 C 0 s oryCun2.chr14 141899363 99 + 163896628 TGTGATACATTAGTAGAAAATCATAACTCAAGGTTAGTTCATA---ATAACCCAGAAATGTTTAAGACATGCCAATACTAGCAGCACTGAGAGAGAAACATG i oryCun2.chr14 I 1856 C 0 s bosTau4.chr1 138188910 100 - 161106243 CATGATAAATAGCCACAAAGTCATGACCCAAGCTTAGTCCATAATGACTG--CCAAAACACTCAAGAGAGATCAATGCCTCCTCTGTTTAGAGATTAAAAAG i bosTau4.chr1 I 3 C 0 s equCab2.chr26 13369319 89 + 41866177 TCAGATAAAGAGGCAGAAAAATATGAC-----------CCATATTAACTG--CAGAAGCATTCAAAACAGACCAATGCCTGCTCTATTTAGGGATTAACAAG i equCab2.chr26 I 3 C 0 s canFam2.chr31 14118853 100 + 42263495 TACGATAAGTAGGCAGAAAATAATGACCCAAGTTTAGTCCATAATAACTG--CAGAAATATTCAAGACAAACTAATGCCTGCTCTATTTAGGGGTTAACAAG i canFam2.chr31 I 3 I 120 s loxAfr3.scaffold_13 20627474 100 - 62548349 tatGGTAAATAGGGAGAAAATCATCACCCAAGGTCAGTCCGTAACAACTA--CAGAAAGCTTCGAGACACACTAAAGCCTTTTCTGTTTAGACAGAAACAAG i loxAfr3.scaffold_13 C 0 C 0 e rheMac2.chr2 189464091 1 - 189746636 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=118582.000000 s hg19.chrUn_gl000245 21006 101 + 36651 AAAGTACAGGTCTTTATAATCTACCATTTTGCCCCTTTTGATACCAGGTGCCCTTCATAATGCAGGCTATAGAGAATTACAAGATTTGTCAGAGATTTCAG s panTro2.chrUn 47417670 101 - 58616431 AAAATACGGGTCGTTATAATCTACCATTTTGCCTCATTTGATACCAGGTGACCTTCATAATGCAGGCAATAGAGAATTGCAAGATTTGTCAGAGATTTCAG i panTro2.chrUn C 0 C 0 s ponAbe2.chr3 159748225 101 - 202140232 AAAGTACAGGTCTTCCTAATCTACCATTTTGCCTGATTTGGTACCAGGTGACCTTCATAATGCAGGCAATAGAGAATTGCAAGATTTGTCAGAGATTTCAG i ponAbe2.chr3 C 0 N 0 s oryCun2.chr14 141899462 99 + 163896628 ATTGTGTGTGTCCTCATAGTCTAATATTCTGCAGCATTTGGTACTACATAATTTTTGTGAGGCAGAAAACAGAAAATTGCTAGATCTTTC--AGACTTCAG i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138189010 95 - 161106243 AAAGTGCACACTCTTAAAATGCAAAATTTTATCTTATTTGACAACAGGTAACC---ATTAGGCAG-CAATAGAGAATTCTAGAATGTGT--GAGATTCCAG i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13369408 100 + 41866177 AAAGTACATCTCCTTATAACCTAATATTTTGCCTCCTTTGATACCAGGTGACCTTTATTATGTAG-CAGTAGGGAATTCTAGGATTTATCAGAGATTCCAG i equCab2.chr26 C 0 C 0 s canFam2.chr31 14119073 100 + 42263495 AAAGTACCTGTTTTTGTAACATAAAAATTTGCCTCATTTGACACCAGGTGATCCTCATTTTTCAG-TACTAGAGAATACCAAGATATATCAGACATTCTAC i canFam2.chr31 I 120 C 0 s loxAfr3.scaffold_13 20627574 97 - 62548349 ----TACATATTCTTATCATCTATTTTTTTGCCTCATTTGATACCAAGTAATCTTCATTGTGCAAGCAATAGAAAATCCCGAGGCTTATCAGAGATTCCAG i loxAfr3.scaffold_13 C 0 C 0 e rheMac2.chr2 189464091 1 - 189746636 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=121162.000000 s hg19.chrUn_gl000245 21107 154 + 36651 GTCTTTGGAAAGCTATGCTCT-TTCACAAGAACAGCCATGGAAACAGGAAG--AAAGTCAATTCCCACTTAAGGTAATCAGAATTTACAAATA--TTCCTTT-------CTTCATT---GAAATCTCAA-TAGGCACTTCGATATTATATTTAATTAATTCTTTTGTTAc--- s ponAbe2.chr21_random 850915 157 - 4212913 GTCTTTGG-AAGCTGTGCTCTCTTCACAGGAACAGCCATGGAAACAGGACGTTAAAAACAATTCCCACTTAAGGTAATCAGAATATACAAATA--T--CTTCAATAAAACTTCATT---GAAATCTTAA-TAGGCACTTCAATATTATCC----TTAATTCTTTTGTTAc--- i ponAbe2.chr21_random N 0 C 0 s panTro2.chrUn 47417771 154 - 58616431 GTCTTTGGAAAGCTATGCTCT-TTCACAAGAACAGCCATGGAAACAGGAAG--AAAGTCAATTCCCACTTAAGATAATCAGAATTTACAAATA--TTCCTTT-------CTTCATT---GAAATCTCAA-TAGGCACTTCAATATTATCTTTAATTAATTCTTTTGTTAc--- i panTro2.chrUn C 0 C 0 s oryCun2.chr14 141899561 150 + 163896628 GTCCTTGGGAAACGGTAGTAT-CCAAAGGGAGCAGTTATGAGAGCAGGAAC--GAAGTCAATCACCATTTCAGAGAATCAGAATTCAAGAAAA--CACCTCC-------TTGCAATGGGGACATCTCAACTAGACACTTCACTAATATTC-TGATTATTTCCT---------- i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138189105 144 - 161106243 TTTCTCAGGAAGCTG--ACAT-TTCAAGAG-GTAGCCATGAAGGAAGAAAG--AAAGTCAACTCTCATTTCAGGTAATCAGAACTTAGCAAGC--ACCCTTC-------CTTTGTT---GAATTTGCAA-TGGGCACTTCAGTGCTATCATTAATTATTTCAT---------- i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13369508 134 + 41866177 GTGCTCAGGAAGCTGCAGCAT-TTCAAGAGAACAACCATGAGAGCAGGAAG--AAAGTCAATTCCCATTTCAGGTG-------------------ATTTTTT-------TGTTGTT---GAAATCACAA-TGGGCCCTTCAACACTATAGTTAATTAATTCCT---TCAT--- i equCab2.chr26 C 0 C 0 s canFam2.chr31 14119173 145 + 42263495 ATTCCTGGGCAGCTGCAGCAT-TTC---AGAACAGTTATGTGAGAAGGAAG--G-----AATTCCCTCTTCAGGTGATCAGAATTTAACAAACACATCTTTC-------ATTTGTT---GAAATCCCGG-TGGGCACTTCAGTACTATTATTTATTAATTCCT---T---CAT i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20627671 147 - 62548349 GTTCTCACAAAGCTGCAGCAT-TTCAAAAGAAAAACCATG--AGCAAGAAG--GAAGTCAGCTCCTATTTCACATGATCCAAATTCAGCAAACACATCTTGA-------CTTTGTT---GAGACCTCAG-TGGGCACTTCAATATTACCATTAATTAATCCTT---------- i loxAfr3.scaffold_13 C 0 C 0 e rheMac2.chr2 189464091 1 - 189746636 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=99005.000000 s hg19.chrUn_gl000245 21261 374 + 36651 aatcatgcatcacataacaacattttggtcaaggatagtgcacttgtatgacagtggtgcaataaaatcataacactgtatttgtactgtacctcttgtatgtttagacatgtatagatacacttactgtatagatataagtaagtatagatatacttaactgttgtgttacaattgcctacagtattcagtacagtaatatgctgcacagttttgtagcctaggaggaataggctataccacctaacctaggtatgtaatcagctatagcatctaggtttgtgtaagtaaactctgtgatgttcatacaataataaaattgtccagcaatgcatttctcagacacacccctgtcattaagtgacacatgactg s panTro2.chrUn 47417925 374 - 58616431 aatcatgcatcacataacaacattttggtcaaggatagtgcacatgtatgacagtggtgcaataaaatcataacactgtatttttactgtacctcttgtatgtttagacatgtatagatacacttactgtatagatataagtaagtatagatatacttaactgttgtgttacaattgcctacagtattcagtacagtaacatgctgcacaggtttgtagcctaggaggaataggctataccacctaacctaggtatataatcagctaaagcatctaggtttgtgtaagtaaactctgtgatgttcatacaataataaaattgtccagcaatgcatttctcagacacacccctgtcattaagtgacacatgactg i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 851072 374 - 4212913 agtcatgcatcacataacaacattttggtcaaggatggtgcacatatatgacagttgagcaataaaatcataacattgtatttttactgtacttcttctatgtttagacatgtatagatacacttactgtatagatataagtaagtatagatatacttaactgttgtgttacaattgcctacagtattcagtacagtaacatgctgcacaggtttgtagcctaggaggaataggctataccacataacctaggtatgtaatcagctataacatctaggtttgtgtaagtaaactctgtgacgttcatacaacaataaaattgtccaggaatgcatttctcagacatacccctgtcattaagtgacacatgactg i ponAbe2.chr21_random C 0 C 0 e bosTau4.chr1 138189249 0 - 161106243 C e loxAfr3.scaffold_13 20627818 0 - 62548349 C e oryCun2.chr14 141899711 0 + 163896628 C e canFam2.chr31 14119318 0 + 42263495 C e equCab2.chr26 13369642 0 + 41866177 C e rheMac2.chr2 189464091 1 - 189746636 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=89236.000000 s hg19.chrUn_gl000245 21635 66 + 36651 TATTAGTTAACACTATGGGAACTTCATGGGAAATGGACACTCTAGCTCCACCATAAATAGAAACTG--- s ponAbe2.chr21_random 851446 66 - 4212913 TATTAGTTAACACTGTGGGAACTTCATGGGAAATGGACTCTGCCGCTCCATCATAAATAGAAACTG--- i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47418299 66 - 58616431 TACTAGTTAACACTATGGGAACTTCATGGGAAATGGACACTGCAGCTCCACCATAAATAGAAACTG--- i panTro2.chrUn C 0 C 0 s oryCun2.chr14 141899711 61 + 163896628 TATCAGCTAATACTGTGTAAACTTCATGGGAAATGGGCACCAGAGCTCCATCATAAATAAA-------- i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138189249 66 - 161106243 TATAAGATAATATTATGGGAACTTTATGGGAAATGGTCACTAGAGGTCCATCACAAATAGAAACAA--- i bosTau4.chr1 C 0 I 7 s equCab2.chr26 13369642 65 + 41866177 TATTGGACAATACTAT-GGAACTTCATGGGAAATGGACACCATAGCACCACCACAAATAGAAATAA--- i equCab2.chr26 C 0 I 3 s canFam2.chr31 14119318 55 + 42263495 TATGAGATATTACT-----------ATAGGAAATGGACACTATATCTCCATCACAATCAGAAAAAA--- i canFam2.chr31 C 0 I 8 s loxAfr3.scaffold_13 20627818 69 - 62548349 TATTAGGTAAAGCTATGGGAATTTCATGGGAAGTGGGTACTATAGCGCCATCACAGATATAAATAATTT i loxAfr3.scaffold_13 C 0 C 0 e rheMac2.chr2 189464091 1 - 189746636 I e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=83354.000000 s hg19.chrUn_gl000245 21701 61 + 36651 TTTATGTCAAAAA-ACACATAAAAGCATAGTTGCAAGATTACAATTCCTTCCAGATATTTCA s panTro2.chrUn 47418365 61 - 58616431 TTTATGTCAAAAA-ACACATAAAAGCGTAGTTGCAAGATTACAATTCCTTCCAGATATTTCA i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 851512 61 - 4212913 TTTATGTCAAAAA-ACACATAAAAGCATAGCTGCAAGATTACAATTCCTTCCAGATATTTCA i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189464092 61 - 189746636 TTTATGTCAAAAA-ACACATACAAGCATAGTTGCAAGATTACAGTCTCTTCTAGATATTTCA i rheMac2.chr2 I 1 C 0 s oryCun2.chr14 141899772 44 + 163896628 ------TCATAAA-TCACATTTGAG-----------GATCACATCTATCAGCAGATACTGGA i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138189322 59 - 161106243 TTTATGAGAAGAATCCCCATAAAAGCACAGTTGTAAGATCATA---TCTCCCAGATATTTCA i bosTau4.chr1 I 7 C 0 s equCab2.chr26 13369710 61 + 41866177 TTTATGACAATAA-CCACGTAAATGCACAGTTGAAAGATCATAACCACCTCTGGATATTTAA i equCab2.chr26 I 3 C 0 s canFam2.chr31 14119381 57 + 42263495 TTTATAGCAATGA-CCACTTTAAGG-AAAGTTGCAAGGTCACA---ACTTCCAGATATTACA i canFam2.chr31 I 8 C 0 s loxAfr3.scaffold_13 20627887 61 - 62548349 TTCATGACAAGAA-TGACATAAAAGCACTTTTGCAAAAATAAAACCACTTTCAAATATTTCA i loxAfr3.scaffold_13 C 0 C 0 e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=294334.000000 s hg19.chrUn_gl000245 21762 268 + 36651 TTTAGTATCTCCACAGATCACTAACTTCCTGAATAGCATTCTTCTGTCTCCACTGCCTCACATTTGATTTCAGGTCATTCCATCAATTGTCAAAGACGCATCCAACATTAACTTTCCAACTACTGGTTTGGATTGTGTCAACATTGTCATTCTGGGCCACAACAACACAAAAGGCTAACTCAGTGAGGTAACATAGACACTGATCAGTGAGATTTTGCTGATGGGTGGTACCATTTTTTACCAAGATCAAGGGTATTCATACCTTCAG s ponAbe2.chr21_random 851573 268 - 4212913 TTTAGTATCTCCACAGATCACTAACTGCCCAAATAGCATTCTTGAGTCTCCACTGCCTCACATTTGATTTTAGGTCATTCCATCAATTGTCAAAGATGCATCCAACACTAACTTTCCAACTACTGGTTTGGATTGTGTCAACATTGTCATCCTGGGCCACAACAACACAAAAGGCTAACTCAGTGAGGTAACATAGACACTGATCGGTGAGATTTTGCTGACGGGTGGTACCATTTTTTACCAAGATCAAGGGTATTCATACCTTCAG i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189464153 268 - 189746636 CGTAGTGTCTCCACAGATCACTAACTGCCTGAATAGCATTCTTGAGTCTCCACTGCCTCACATTTGATTTCAGGTCATTCCATCAACTGTCACAGAAGCATCCAACATTAACTTTCCAACTACTGGTTTGGATTATGTCAACATTGTCATTCGGGGCCACAACAACACAAAAGGCTAACTCAGTGAGGTGACATAGACACCAATCGGTGACATTTTGCTGAGGGGTGGCACCATTTTTTACCAAGATCAAGGGTATTCATACCTTCAG i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141899816 254 + 163896628 GTTAGTATCTCCACTGGTCACTAACTGT----ACAGACTTCTTGAATTTTCATGTGTTCACACTTGGTTCCAGGTCATTCCATCAATTGTCAGGGAAGCA--AAGCAGTGGATACCCAACCGCTGCT---GTTTATGTCACCATTGTCATGCTGAGCATC-----CAGTAAAGGTTCACTCAGTCAGGTAATACACATGCTGGTCAGTGAAGTCTTGTCAACACATATTATCTTTTTCCTCCAGCACCAAGAGCAATCAGATTAACAA i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138189381 262 - 161106243 CTTATTACCTCTACTGATAATGAATTGTCTGATCAGCTTTCCTGTATATTCACCTGTTCACATTTAATTCCA--TCATTCTGTGAGTTGTTATATAAGCTTCTTACATTAGTGTCCTAACTACTGATTCATGTAATGTCACCA-TGCCATCTTGAGCAACAAAAA---ATGGGTCTCACTCATTGATGTGATGCAGGCGCTGGCCAGTGAACTCTTGCTTATATATGACACCATATTCTACCAACGCCAAAGGCAGCCATACCTACAA i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13369771 249 + 41866177 CTTAGTATCTCTACAGATCACAAACTGTCTGAACAGC--TCTCGAGTCTTCACTTGTTTACATTTTATCCCAAGTCATTCCATCAGTTACTATAGAAGCATGTTACATTAACTTCCCAACGACTGCTTTCAATTATGTCACCATTGTCATCTTGAGCAACAAAAA---ATGGGGGTCACTCAGTGAGGTGATATAGACACTGGCCAGTGA--------------ATGGTACCATTTTCCACCAACACCAAAGGCAGCCATACCTGCAT i equCab2.chr26 C 0 C 0 s canFam2.chr31 14119438 260 + 42263495 CTTAATATTTCCACAGGTCACGAATGTTCTGAACAGCTTTCTTGCATCTCTGCTTG-TTACATTTGATTTTA--TCATTCACTCTATTGTTCCAGAAGCATCTTACATTAATTTCCCAACTACCACTTTTTGTTATGTTACTATTGC--TCCTGAACAACAAAAA---ATAGAACTCACTCAGTGAGGTGGTATACACACTGGTCAGTTAAGTCTTGTGTTTATATGACACCATTTTACACCCGCACCAAGAGCAGCCATATCTACAG i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20627948 253 - 62548349 CTTATTT------CAGAT-ATTGGCTGTCTGAACAGCTTTCTCAAATCATCACGTGTTCCCATTTGATTTCAGATCATTCTGTCAGTCATCACAGCA-CATCT-ACATTAACTTCCTACCTACTGCTTTGTATCACGTCACCACTGCCATCTCGA-CAGCAAAAA----AGGGGTTCACCCAATGTGATGATGTAAAGGATGGCCAGTGAAATCTTGCTTATCTATGGCACCATTTCCTACCAAAACCAA-GGCAGTCATACCTATAG i loxAfr3.scaffold_13 C 0 C 0 e panTro2.chrUn 47418426 0 - 58616431 C e cavPor3.scaffold_34 15815641 977 - 24440124 I a score=105164.000000 s hg19.chrUn_gl000245 22030 61 + 36651 GCATCTAGATAACAT--TGAAAAGGGCAGGTTCATAGATAAAAAGGGAAAGAGGAAGGGTTTT s panTro2.chrUn 47418426 61 - 58616431 GCATCTAGATAACAT--TGAAAAGGGCAGGTTCATAGATAAAAAGGGAAAGAGGAAGGGTTTT i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 851841 61 - 4212913 GCATCTAGATAACAT--TGAAAAGGGCAGGTTCGTGGATAAAAAGGCAATGAGGAAGGGTTAT i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189464421 61 - 189746636 ACATCTAGATAACAC--TGAAAAGGGTGAGTTTGTAGATAAAAAGGCAATGAGGAAGGGTTAT i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141900070 62 + 163896628 CCATCAAGATAACACGGGAAAAGGGGTGAGTTCATAGATAAAAA-GCAAGGAGGCTGGTTTGT i oryCun2.chr14 C 0 C 0 s cavPor3.scaffold_34 15816618 45 - 24440124 -----------------TAAAATAGATAAATTCATAGACTAAAA-ATAACAACAAAGAGTTGT i cavPor3.scaffold_34 I 977 C 0 s bosTau4.chr1 138189643 59 - 161106243 CCACCTAGAGAACAC--TGAAATGGGAGAGTCCATAGATAAAAACGCAATAATAAAGGGTT-- i bosTau4.chr1 C 0 I 618 s equCab2.chr26 13370020 60 + 41866177 CAATCTAGAGAGTAC--TGAAAAGGGAGAGTCGATAGACAAAAA-ACAATGATGAAGGGTTGG i equCab2.chr26 C 0 C 0 s canFam2.chr31 14119698 61 + 42263495 CCATGTAGAGAACAT--TGAAAAGAGAGAATCCATAGATAAAAAGGCAATGATGAAATGTTGG i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20628201 60 - 62548349 CCATCTAGAGAAAAT--TGAAAAGTGAGAGTCCACAGGTGAAAAGACAATGACTGAGGAATT- i loxAfr3.scaffold_13 C 0 C 0 a score=265756.000000 s hg19.chrUn_gl000245 22091 161 + 36651 TGCAGTATATATGAGCTACCATGTCTCCTGTTTAACCTGAGTCT--GAAGAGATTC---AAAGTGC---AGGTGCCATGAATGCCTCTTTAATAGCTCCATGTCGATTGA-T-TTTCTGGGCTACACTTCACAGCATTCAAATTGCTAAATGCATATAAACTACTAGTG-GA s panTro2.chrUn 47418487 161 - 58616431 TGCAGTATACATGAGCTACTGTGTCTCCTGTTTAACCTGAGTCT--GAAGAGATTC---AAAGTGC---AGGTGCCATGAATGCCTCTTTAATAGTTCAATGTCGATTGA-T-TTTCTGGGCTATACTTCCCAGCATTCAAATTGCTAAATGCATATAAACTACTACTG-AA i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 851902 161 - 4212913 TGCAGTATACATGAGCTACCGTGTCTCCTG-TTAACCTGAGTCT--GAAGAGATTC---AAAGTGC---AGGTGCCATGCATGCCTCTTTAATAGTTCCATGTCGATTGATT-TTTCTGGGCTACACTTCCCAGCATTCAAATTGCTAAATGCATATAAACTACTACTG-AA i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189464482 161 - 189746636 TGCGGTATACATGAGACACCGTGTCTCCTGTTTAACCTGAGTTT--GAAGAGATTC---AAAGTGC---AGGTGCCATGCACGCCTCTTTAATAGTTCCATGTCTGTTGA-T-TTTCTGGGCTACACTTCCCAGCACTCAAATTGCTAAATGCATATAAAATACTACTG-AA i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141900132 162 + 163896628 TAAGGGATACAAGGACTACCTTGTCTGTTGCTGAATGTTAGTGT--GAACAGCTTC---AAAGTAC---AATTGCCATGTGTGCATCTTAAACAATTCCATATCTCTTGG-TGTTTCTGGGCTTCAATTTCCAAGTCTTAGACTGTTAAATGTACAGAAAATACTACTG-AA i oryCun2.chr14 C 0 C 0 s cavPor3.scaffold_34 15816663 151 - 24440124 ---AGGAAACATAAGCCACCTTGTCT-TTGCTGA--TTCGGTCT--GA----TTAC---AGAGTAC---AAGTATTATGTACACATCTTCAATAGTTACACATCAATTAA-T-TTTCTGAGCTTTGATTTCACTGT-TGAGGCTACTCAGTAAATAAAAAGAACCACCGAAA i cavPor3.scaffold_34 C 0 C 0 s bosTau4.chr1 138190320 154 - 161106243 TGCAGGATAAATAGGCTACCTGGCCTTCTGCTTAATCCAAAGCT--AAATAGATGC---AAAGTGC---TATTGTTATTTATGCCTCGTCAACAGTTCCAGATATA---------TCTGGGCTAAACTTTCCGCTGCTAAAGTTACTAAGTGTAGAGAAAATACTACTG-AA i bosTau4.chr1 I 618 C 0 s equCab2.chr26 13370080 163 + 41866177 TGTGGGATAAATGGGCTACCTAGCCTCCTGCTTAACCTCAGTCT--GAA-AGATTC---AAAGAACAGGTAGTACCATTCACACCTCTTGAACACTTCCATATTTATTAG-T-ATTCTGGGCTGCACCTTCCGCTGCTAAGGCTGCTACAGTTATAGCAAATACCACTG-AA i equCab2.chr26 C 0 C 0 s canFam2.chr31 14119759 161 + 42263495 TGCAGGATAAATGGACTATCCAACATCCTGCTTAACCTGAGTCT--GAACACATCC---AATGTGC---TATTGCTATTCATGCCTCTTCAACAATCCCAAATTTAATGA-T-TTTCTGGGCTGTACCTTCCACAGCTAGGACCGCTAAATGTATAGGAAATACCACTG-AA i canFam2.chr31 C 0 I 343 s loxAfr3.scaffold_13 20628261 140 - 62548349 --------------------------CCATCTTAACCTGAATCTACAAATAGACTCAAAAAAGTGC---AGGTACCATTTGTGCTTCTTGAACAGTTCCATACTTATTGA-T-CTTCTAGGCTGCAGCTTCCACTCTTCAAGCTATTAAATGAATTGAAACTACCATTG-AA i loxAfr3.scaffold_13 C 0 C 0 a score=545974.000000 s hg19.chrUn_gl000245 22252 393 + 36651 TATTTATTACCTGG------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTTGTGCTTCTGAGTGACCTTAT-CTATAGTTATGTGCTT-----CAGTGATCCAACTTGGGGTGCACTCCAAACTTT---------GATAA--------ATTAAAGACCC-------TGCATA-TTCCTTGAGTAATGCTACACTGACAACTGATTTAGTGA------------ATGCCACTGTGAAAATAATAAACCTCTTGGTGAATATATTTAGA-------CATGTCTTGGAACCTGTACACATCTTAACCAGGGATGTTACTTGGTCTTTTTATGTTC-AGGAGTGTCTGGAGATAGAAAAACATACAGGA-----TTGTAATTGTTGCC------------TGTGAGACTAACAG------------------------AAAATTCAAGCTAGTGAAGTATGCTTATGCATGGCACACT-TCTCACCAGCAATTTTAGGAAGTTCTACCCAC----------------------------------------------AACCCATATGTC s panTro2.chrUn 47418648 393 - 58616431 TATTTATAACCTGG------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTTGTGCTTTTCAGTGACCTTAT-CTATAGTTATGTGCTT-----CAGTGATCCAACTTGGGGTGGACTCCAAACTTT---------GATAA--------ATTAAAGACCC-------TGCTTA-TTCCTTGAGTGTTGCTACACTAACAACTGATTTAGTGA------------ATGCCACTGTGAAAATAATAAACCTCTTGGTGAATATATTTAGA-------CATATCTTGTAACCTGTACACATCTTAACCAGGGATGTTACTTGGTCTTTCTATGCTC-AGGAGTGTGTGGAGATAGAAAATCATACAGGA-----TTGTAATTGTTGCC------------TGTGAGACTAACAG------------------------AAAATTCAACCTAGTGAAGTATGTTTATGCATGGCACACT-TCTCACCAGCAATTTTAGGAAGTTCTACCCAC----------------------------------------------AACCCATATGTC i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 852063 393 - 4212913 TATTTATAACCTGG------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTTGTGCTTTTGAGTGACCTTAT-CTATAGTTATGTGTTT-----CAGTGATCTAACTTGGGGTGGACTCCAAACTTT---------GATAA--------AGTAAAGACCC-------TGCTTA-TTCCTTGAGTATTGCTACACTGACAACCAATTTAGTGA------------ATGCCACTGTGAAAATAATAAACCTCTTGGTGAATATGTTTAGA-------CATGCCTTGTAATCTGTACACATTTTAACCAGGGATGTTACTTGGTCTTTCTATGTAC-AGGAGTGTGTAGAGATAGAACAACATACAGGA-----TTGCAACTGTTGCC------------TGTGAGACTAATAG------------------------AAAATTCAAGCTAGTGGAGTATGTTTATGCATGGCACACT-TCTCACCAGCAATTTTAGGAGGTTCTACCCAC----------------------------------------------AACCCATATGTC i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189464643 394 - 189746636 TATTTATAACCTAG------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTTGTGCTTTTGAGTGACCTTAT-CTATAGTTATGTGCTT-----CAGTGATCTAAATTGGGATTGACTCCAAACTTT---------GATAAAG------AGTTTATTCCC-------TGCTTA-TTCCTTGATTATTGTTACATCGATAACTGATGTAGTGA------------ATGCCACTGTGAAAATAATAAACCTCTTGGTGAACATATTTAGA-------CATATCTTGTGACCTGCACACATCTTACCCAGGTATGGTACTTGGTCTTTCTATGAAC-AGGAGTGTGTGGCGATAGAACAACATACAGGA-----TTGCAATTGTTGCC------------TGTGAGACCAACAG-------------------------AAATGCAAGCTAGTAAAGTATGTTTATGTGCGGCACGTT-TTCCACCAGCAATTTTAGGAAGTTCTACCCAC----------------------------------------------AACCCATATGTC i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141900294 331 + 163896628 TATGTGCAACCTAG------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTGTGCCTTTGAGAGAGATCCTCCTATGCTTGTGTGCAC-----CAGTGATCTCACCTGAGATTAATCCCATACTTT---------GATAT--------ATTTGAGT----------TAGTTA-----TTAAATATTGCTACATTTATAACTGGTAAAATGA------------AAGCCATAGTAAGAAGAAT--GCACCTTCATGAAAATATTTAGAGTGCTTGTGTATCTTA------------------ACTAGTTATTTTCCTTGATCTTCTTATGTAC-AAGAGGGTGAAGAGATAAAGTG-TTTGCAGGATAGGTTTGCAAATGTTGCC------------CACTAAATTAACAG------------------------GAAATTCAGACCAGTAAAGT----------------------------------------------TGCT--A----------------------------------------------AGCCTATAGATT i oryCun2.chr14 C 0 C 0 s cavPor3.scaffold_34 15816814 428 - 24440124 TACTTATAACTTGG------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTCCA-CTTTGAGTGATGTAAT-CTAGAGTTCTACTTTA-----TAATGATGTAACTTGATGTTGGTCCCAAACTTT---------GATAA--------AGTAGAGTTGCTAGTAGGTAGCTAATTCCTGAATTATTAATACACTGAGATCTGAATTATTGA------------ATGCCACAGT--GAATAAG--AGCTCTTGGTGAAGACATTTAGA-------CATATCTTATAACCTGGGCACAGTTTTACCAGGTTTGCTACTTGGTCTTGCTATGAAC-AAGAGTATGTAGAGATTCAGTGACCTGCAGGA-----TTGCAGTTATTCCCTGGGAGACTAATCAGAAAATTATCAGAGAAAGTGAAAAAATCAGAGAAGTGAAAATCAGAGAAGTGAAAT-TTTCAATGCATGGCTCATT-TCCC-TTAGCAATTTTAGAAAGCTCTGCT--A----------------------------------------------CAGCCATTTATC i cavPor3.scaffold_34 C 0 C 0 s bosTau4.chr1 138190474 401 - 161106243 TTTTGATAACCTCA------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTGTACTTTTGACTGCCC-TAT-CTATAGTTGTGTGTTC-----CAATTATCTAATTTAGGTTTAAACCCTAACTTTACTTGCCTTGATAAGGAACACTTGTTAAGATTC-------TGCTTA-TTTATTGATTCTTGTTAGATCAATACTTGATTTACTGA------------ATTCAATAGTGAGAATAGTACATTTCTTTTGTAACAAA--TAAA-------TGCGTCTTGTAAGCTGGGCACATCTTAACCAGGCATATTCCTTGGTCTTGCTTTGTAC-AGAAGTGTGCAGAGATAG-ATAGCCTGCATTG-----TTGTATTTGTTGCC------------TATGAGATC-----------------------------GAAATGCTGGCTACAGAGGTTTGCTTATGCAAGGCACATT-TCCCACCAGCAATTTGGAGAGGTTTTACCCAC----------------------------------------------AGTGCATATATC i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13370243 406 + 41866177 TATTTATAACCTGG------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTAGTGCTTTTGAGTTCCCTTAT-CTATACTTGTATATTC-----CAATGATGTAATTTGGGGTTGACCCCGAATTTT-CTTGCCTTGATAAGGTAGAGTTGTTAAGAGTC-------TGCTTA-TCTCTTGATTATTGCTACACCAATAATTGATTTACTGA------------ATTCCACAGTAAGAATAATAAATATCTTGC-TAATAAA--TAAA-------TCTGTCTTGTCCCCTGGACACATCTTAACCAGGTGTGTTCCTTGGTCTTGCTATGTAC-CAGAGTGTGTGGAGATAGAATGACCTGTCTCA-----TCACAATTGTTCTC------------CCTGAGACTGACAG------------------------GAAATGCAGGCTACTGAGGTTTGCTCATGCATGGCACATT-CCCCTTCAGCAATTTTGAGAAGCTCTACCCAC----------------------------------------------AGCCCAAATATC i equCab2.chr26 C 0 C 0 s canFam2.chr31 14120263 386 + 42263495 TATTTATAAATTGG------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTTGTGCCTTGAAGTGCTCTTAT-TTATTGCTATATGTTC-----CAGTGAACTAACTTGTGGTTTACCC-------------------TAAGGTGGAGTTGTTAAGACTT-------TGCTTA-TTTCTTGATTATTGTTATACCAGTAA-TGATTTACTGA------------ATTTCACAGTAAGAATAATTAACTTCCTG--TAATAAA--TAAA-------CATATCTTGTAAACTAGACACATCTTAGCCAACTGTGTTCCTTAGTCTTGCTATGTAT-AAGAGTGGGTAGAAACAGAATGAACTGCACAG-----TTATAGTTTTTGCC------------CAAGAAGTTCATGG------------------------GAGATGCAGGCTACTGAGGTGTGCTTATGCATGAAACACT-TCCCACCAGCAATTTTGGGAAGCTCTGACCAC----------------------------------------------ACCTCATTTATC i canFam2.chr31 I 343 C 0 s loxAfr3.scaffold_13 20628401 627 - 62548349 TATTTATAAACtaggagtcctggtggcacagaggttaagagcttggctgctaaccagaagatcggcagttcaaatccaccagctgcttcctggaaactatatggggcagtactactctgtcctatagggatgctatgacttggaattgacttgatggcaatgggtttATAAATTGATTTTGTGCCTTTAAATGCTCTTAT-TTATAGGTGTGTGCTTTGCTGTAGGGATCTAACTTCGGCTTGACCCCAGCTTTTTATTACCATGATAATGTAAAGCTGTTAAGGTCA-------TGCTTA-TTGCTTATGTATTGTTGCACTAGCAACTTATTTACTAAATTGCTACCTTGATGCCACAGTGAGGGTAACAGACTTCCTGCTG---------ATA-------CGTATCTCTTAACCTGGACATATGGTAACCATGTATGTTCC-CGGTCTTTCTATGTACAAGGAGTATGAGGAGATATTATGTCCTGTAGTA-----CTGAAATTGTTACC------------TGTGCTGCAGATGG------------------------CTGATGAAGGCAAGAGATGTTTTCTTATGTCTGGCACATTGTTCTCTCAGCATATTTGAGAAGCTCTATTTACAGACAtggaaaccctggtggcatagtggctaagtgctatggctgctaaccaaaaggtc i loxAfr3.scaffold_13 C 0 I 125 a score=413064.000000 s hg19.chrUn_gl000245 22645 232 + 36651 TTTTGATATGTGGGTTACCTTGGAGAGAGAAAAAGAAACTCTGAACACAAGCATGAAATACTTTCGAATTTTATCTAGAGTTGGACTTGTCCAAAAGCTTTTGTAT-AAACTTGCTTGATGAGGAACTGTTGTCCACTGGTAC--CTTCACCGTACAATCCACACACAACCAAACTTCACAACTGGACACCT------------AAATTTGCACTT--TGTTTGGTAAAGTTGAA--TGAAAAATGT--T----------------------GTC s panTro2.chrUn 47419041 232 - 58616431 TTTTGATATGTGGGTTACCTTGGAGAGAGAAAAAGAAACTCTGAACACAAGCATGAAATACTTTTGAATTTTATCTAGAGTTGGACTTGTCCGAAAGCTTTTGTAT-AAACTTGCTAGATGAGCAACTGTTGTCCACTGGTAC--CTTCACTGTACAATCCACACACAACCAAACTTCACAACTGGACACCT------------AAATTTGCACTT--TGTTTGGTAAAGTTGAA--TGAAAAATGT--T----------------------GTC i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 852456 231 - 4212913 TTTTGATATGTGGGTTACCTTGGAGAGAGAAAAA-AAACTCTGAACACAAGCATGAAATACTTTAGAATTTTATCTAGAGTTAGACTTGTCCCAAAGCTTTTGTAT-AAACTTGCTTGATGAGCAACTGTTGTCCACTGGTAC--CTTCACTGTACAATCCACAAACAACCAAACTTCACAACTGGAGACCT------------AAATTTGCACTT--TGTTTGGTAGAGTTGAA--TGAAAAATGT--T----------------------GTC i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189465037 232 - 189746636 TTTTGAGATGTGGGTTATCTTGGAGAGAGAAAAAGAAACTCTGAACACAAGCATGAAATACTTTACCATTTTATCTAGAGTTGGACTTGTCCCAAAGCTTTTGTAT-AAACTTACTTGATGAGCAACTATCGTCCATTGGTAC--CTTCACTGTACAATCCACACACAACCAAATTTCACAAATGCAGACCT------------AAATTTGCACTT--TGTTTGGTAAAGTTGAA--TGAAAAATGT--T----------------------GTC i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141900625 237 + 163896628 TTTGAAAATGTAGGTTACCTCTGAGGGACAGAAACAGATCTTCAC--ATAGCATCAAATACTTCACAATTTTGCCTGGAGCCTGAACTCTCCCAAAGGTTTTGCATAAAACTTATTTGATAAGCAACTGTTGTCTATTAGCACAGATTCACTATATAATCTATATACGATCAAACTTTAAAATTTGGGATTT------------AAATTTGTATTTCATGttttataaaattaaa--tttaaaatGTTAT----------------------TTC i oryCun2.chr14 C 0 C 0 s cavPor3.scaffold_34 15817242 245 - 24440124 TTTTGATATGTGGGTTGCTACTGAGGGAGAGAAAGAAACTCTGATTAGAAACATCCAATATTTCATAACTCCACCTAGACCGGGGCCTTTCCCAAAGCTTTGGCAC-AAACTTGTTTTATAAGCAACTATTGTCCTTTGGCAC--ATTCACTGCACACTTTACACACTATTACACTTTGCAACTGGGAGTTTACATTTACTGTAAAGTTTGTATTTAGTATTTTGTAAAACTGAA---TTAAAATGC--C----------------------TTC i cavPor3.scaffold_34 C 0 C 0 s bosTau4.chr1 138190875 222 - 161106243 TTTTGATATGTGAATTACTTCTAAGGA----AGAAAAACTCTGAACACAAGAT------------CAACTTTACATAGAGCTGGACCTGTCCCAAAGCTTTTGCAT-AAGTTTGCTTATTAAACAACTGTTGTACATGGGCAC--ATTC--------------ACACCATCAGACTTCAAAACAAGAGACCA------------AAATGTATATTTTGTGTTTTATAAAATTTGG---TAAAAATAT--TTTTAAGCTTTGTGGTTGTTgtt--- i bosTau4.chr1 C 0 I 101 s equCab2.chr26 13370649 208 + 41866177 TTTTGATATGTAGATCTC-TCTGAAAC------------------CACAAGCTTCAAGTACTTTACAACTTTATCTAGAGCTAGACCTGTCCCAAAGCTTTTTTAT-AAACTTA-TTAATAAGCAACTGATATCCACTGGCGC--ATTCACTGTACAAT--ACAGACCATGAGACTTTAAAACAAGAGCCCG------------AAATATGTATTTTTTATTTTGTAAAGTGTAA---TAAAAATGT--T------------------------- i equCab2.chr26 C 0 C 0 s canFam2.chr31 14120649 226 + 42263495 TGTTGATATGTGGGTTACGTCTGAAACAGAGAAAGAAACTCTGAATGCAAGCATCAAATATTTTACAACGTTACCTAGAGCTGGACCTGTCCCAAAGCTTTTGCAT-AAACTTGCTTAATAAGCAATGGTTGTCCATTGGCAC--ATTCACTGTACAAT--A-ACACTATCAAACTTCAAAACAGGAGACCA------------Gaatttatattttatacttcataaaatttaa---taaaaaca---t------------------------- i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20629153 224 - 62548349 TATTAATACTTGGGTTACCTCTGAAGAACAAAAA-GAACTTTGAACGCAAGCTCCAAATACTTGACAGCTTCACCTACAGCCAGACTTGCCCCAAAGCTTTTACGT-AAATTAGCTTAATGAACAGTTGTTGTCCACATGCCT--GTACACAACACAACCCACACAC--------TTTGAAACAGGAGACCC------------CAATTTACCTTTCATGTTTTGTAAAATTTAAAATAAAAAGGGT--T------------------------- i loxAfr3.scaffold_13 I 125 C 0 a score=262538.000000 s hg19.chrUn_gl000245 22877 161 + 36651 TTTTAAGCTTATGTTCTCTTATGAAA----------GCTGTTATTAGATTAA--TTTTA---------CTCCAAGATATGCCAGTTAGGAAAT-----AACTTCCCATTTAATTTCACCAGCTCCCTGTGGGTGGACTAATTACTCATACATCACACTTA---CTCTGGTGGTGAAATGCCTCAAAAGAA s panTro2.chrUn 47419273 157 - 58616431 TTTTAAACA---GCTGTCTTATGAAA----------GCTGTTATTAGATGAA--TTT-A---------ATCCAAGATATGCCAGTTAGGAAAT-----AACTTCCAATTTAATTTCACCAGCTCCCTGTGGGTGGACTAATTAGTCATACATCACACTTA---CTCTGGTGGTGAAATGCCTCAAAAGAA i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 852687 161 - 4212913 TTTTAAGCTTATGCTCTCTTATGAAA----------GCTGTTATTAGATTAA--TTTTA---------CTCCAAGATATGCCAGTTAGGAAAC-----AACTTCCAATTTAATTTCACCAGCCCCCTGTGGGTAGATTAATTAGTCATACATCACACTTA---CTCTGGTGGTGAAATGCCTCAAAAGAA i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189465269 161 - 189746636 TTTTAAGCTTATGCTCGCTTATGAAA----------GCTGTTATTAGATTAA--TTTTA---------CTCCAAGATATGCCAGTAAGGAAAT-----AACTGCCAATTTAATTTCACCAGCCCCCCGTGGGTGGACTAATTAATCATACATCACACTTA---TTCTGGTGGAGAAATGCCTCAAAAGAA i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141900862 165 + 163896628 CTTCTAACTTTTATACTCTTACAAAA----------GCTATTATTAGAATTT--TTTTA--------GTTTCAAGATATCCCAATTGGGAAAT-----TACTTTCAATTTAATTTAACCAGCTCCCTGTGGGTAGACTAATTAGTTACATGCCACACTTATACTTGTGGCCGTGGAAGGTCTCCAGAGCA i oryCun2.chr14 C 0 I 305 s cavPor3.scaffold_34 15817487 161 - 24440124 TTTAAAACTTACACTCTCTTTCAAAA----------ACTTTTATTACTTTAT--TTTTA---------TTTCAGGATAAGCCAATTAGGAAATTGTGGTAATTACAATTTGATTCAGCCAGCCCTCTGTGTATAGGGTAATGATTTGTACATCAC-CGTA---TTAAGGTAGTCAAAAGTCTCTAA---- i cavPor3.scaffold_34 C 0 C 0 s bosTau4.chr1 138191198 159 - 161106243 TTTTAAGTTTATAC--TCTTACAAAT----------GCTGTTATTAGATTTTTATGGCA---------TATTAGGATATGTCAATTGGGAGAT-----TACTTTCAATTTAATTTAACCAGT-CCCTGGAGGTGGGCTAGTTAG-TATACATCACAGTTA---TATTGCTGGCCATGGGTCTCACAAAAA i bosTau4.chr1 I 101 C 0 s equCab2.chr26 13370857 160 + 41866177 TTTTAAGCTTATACTTTCTTACAAAT----------GC---TATTAGATTTTTTTTTCA---------TTCCAGGATATACCAATGGGGAAAT-----TACTTCCAATATAATTTAACCAGCCCCTTGAAAGTGAGCTAATTAGTTATACACTGCAGTTA---TACTGGTGGCCATGGGTCTCACAAGAA i equCab2.chr26 C 0 C 0 s canFam2.chr31 14120875 133 + 42263495 ttttaaGC-TATACCTCTCTTAAAAT----------GC----------------TTTTA---------TTCCAGGATAT------------TT-----TACTTCCAGTTAAATTTAACCAACGCCCTGTAGGTGGGCTAATTAGTTATAAATTGCAGTTA---TATTGGTGGCTAT-GGTCTCACAAGAA i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20629377 165 - 62548349 TTTTAAGCTTATATGCTCCTCCATGATTTTGGAGCTGTTGTTGTTAGGAGCT--TTTTAAAATTGCTATTCCAGGATATACCAATTAGGTAAT--------------------TTAATCAGTCTCCTGTGGGCAGAGTAATCACTTATAAATGACAGTTC---TATTGGTGGCCATGGGTTTCAAAAGAA i loxAfr3.scaffold_13 C 0 C 0 a score=94271.000000 s hg19.chrUn_gl000245 23038 64 + 36651 GGTCTCCAGAGTGTTGCTTTACC--TAGAAGGACAAGAATGAA---GAGAC--ATAAAAATCATTCATTAA s panTro2.chrUn 47419430 64 - 58616431 GGTCTCCAGAGTGTTGCCCTACC--TAGAAGGACAAGAATGAA---GAGAC--ATAAAAATCATTCATTAA i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 852848 64 - 4212913 GGTCTCCAGAGTATTGCTCTACC--TAGAAGGACATGAATGAA---GAGAC--ATAAAAATCATTCATTAA i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189465430 64 - 189746636 GGTCTCCAGAGTGTTGCCCTACC--TAGAAGGACATGAATGAA---GAGAC--ATAAAAATCATTCATTAA i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15817648 56 - 24440124 GTTCTACAGAGTGCTGCTCCTCCTATATATGGACATAAATATA---GAATC--ATAAAAAT---------- i cavPor3.scaffold_34 C 0 C 0 s bosTau4.chr1 138191357 66 - 161106243 GGTCTCATAAATGTTGCTCCACC--TACAAGACCATGAATGAA---TAGACTTAGGAAAATTAATAATTAC i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13371017 69 + 41866177 GGTCTCAAGAGTGTTGCTCCACC--TACAAGGACATGAATGAAGAGGAGACTTACAGAAATTAATCATTCA i equCab2.chr26 C 0 C 0 s canFam2.chr31 14121008 66 + 42263495 ATTCTTGAGAGTGTTGCTGCCCT--TATAAGGACATGAATAAA---AATATTTCTACAAATCAATTATTAA i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20629542 61 - 62548349 GGTCT-GAGAGTGTCACTCCACCTGCACGAAGATATGAATGAA---GAGAT--ATAAAATTCACGAA---- i loxAfr3.scaffold_13 C 0 C 0 e oryCun2.chr14 141901027 305 + 163896628 I a score=111890.000000 s hg19.chrUn_gl000245 23102 86 + 36651 GAAGGAAGAAGATTTTCCTTG--------------------------------------------------------------------------CCTAGATTTTCACTTGTAGGATGCAATTAATTTTATCACTTAATATTTTGTCATGGTGGGCATTC s panTro2.chrUn 47419494 86 - 58616431 GAAGGAAGAAGATTTTCCTTG--------------------------------------------------------------------------CCTAGATTTTCACTTGCAGGATCCAATTAATTTTATCACTTAATATTTTGTCCTGGTGGACATTC i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 852912 86 - 4212913 GAAGGAAGAAGATTTTCCTTG--------------------------------------------------------------------------CCTAGATTTTCACTTGTAGGATCCAATTAATTTTATCACTTAATATTTTGTCCTGCTGGGCATTC i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189465494 86 - 189746636 GAAGGAAGAAGATTTTTCTTG--------------------------------------------------------------------------CCTAGATTTTCACTTGTAGGATCCAATTAATTTTATCACTTAATATTTTGTCCTAGTGGGCATTC i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15817704 6 - 24440124 ---------GCATTC------------------------------------------------------------------------------------------------------------------------------------------------- i cavPor3.scaffold_34 C 0 I 107 s oryCun2.chr14 141901332 156 + 163896628 gagggaagagctttctctctgtctctctctctctcactgtctaactctatctgtcaaataaattaaaaaaaaaaaaaaaGAATGAAATAGAGTGACCTAACTTGCTACTTGTAGGATCCaatttattttattatttaatatttt----tggtaaatattt i oryCun2.chr14 I 305 C 0 s bosTau4.chr1 138191423 84 - 161106243 AAAGGAAGA--ATTTTTGTAA--------------------------------------------------------------------------CCTAGCTTTTCACTTGTAAGATCCAATTAAATTTGCCCCTTAATATTTTATTCTGGTAGGCATTC i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13371086 84 + 41866177 GAAGGAAGA--ACTACGGTGG--------------------------------------------------------------------------CCCAGCTTTTTCCTTGTAGGATCCAATTAATTTTATCACTTAATATTTTATACTGGTAGGCATTC i equCab2.chr26 C 0 C 0 s canFam2.chr31 14121074 84 + 42263495 GAAAGAAGA--ACTGAAGTGG--------------------------------------------------------------------------CGTAGCTTTTCACTTGTAGGAACCAATTTATTTTACCATTTAATATTTTATCCTGATTGGTATTC i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20629603 80 - 62548349 AAGGGAGGA--ACTCCAGTGA--------------------------------------------------------------------------CCTAACTTATCACATGCAGGACA----TACTTTTACCACTTAATATTTTATCCTGGCAGGCAATC i loxAfr3.scaffold_13 C 0 C 0 a score=219113.000000 s hg19.chrUn_gl000245 23188 143 + 36651 ACTTTACAAATTTGTAAGGTCAGTAGAAAT---GGAAACTT-TTGGAAATCAAACTGTAAATGTTCTGTAGACGT-TGACAGAA---ATAGCTATTTGGAGCTGCGCTTTTGCCAACTAGACACTCTGAGAAAA-TCTGTGACAGGATATTT s panTro2.chrUn 47419580 144 - 58616431 ATTTTACAAATTTGTAAGGTCAGGAGAAAT---GGAAACTT-TTGGAAATCAAACTGTAAATGTTCTGTAGACGT-TGACAGAA---ATAGCTATTTGGAGCTGTGCTTTTGCCAACTAGACACTCTGAGAAAAATCTGCGAGAGAATATTT i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 852998 143 - 4212913 ATTTTACAAATTTGTAAGGTCAGTAGAAAT---GGAAACTT-TCGGAAATCGAACTGTAAATGTTCTGTAGACAT-TGACAGAA---ATAGCTATTTGGAGCTGTGCTTTTGCCAACTAGACACTCTGAGAAAA-TCTGTGAGAGGATATTT i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189465580 141 - 189746636 ATTTTACAAATTTGTAAGGTCAGTAGAAAT---GGAAACTT-TCAGAAGTGGAACTGTAAATGTTCTGTAGGCGT-TGATAGAA---ATCGCTATTTGGAGCTGTGCTTTTGCCAACTAGACA--CTGAGAAAA-TCTGTGAGAGGATATTT i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15817817 115 - 24440124 ATTTTGTAGACT--TAAGTTTTGGGGAAGT------AACTC-CTTGGAA-------TTAAACATTCCAAGAAAGTCTTTTGGAA---GTAGCTCCTTGGAATTAT---------------AAACCTCAAGAAAA-TC-AATAAGTGAT-TTT i cavPor3.scaffold_34 I 107 C 0 s oryCun2.chr14 141901488 115 + 163896628 atcttataaatttGTAAGGATAGTGTAA--------AACT----------------GTAAATGTTCCATAGATGT-TATTAGAA---CTAGCTATTTGTAGTTGTGCTTTTGC-------ATACTCCAAGGAAT-TT-GTGGAAGGATATTT i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138191507 143 - 161106243 CTCTTAAAAACCTGTAAGAATAGTAGAACT---TGAAACTTGCTGAAAATCCAACTATAAGTGTGATATACACTT-TGACAGAG---GTAGCTGTTTCGAGTTGAGCTTTTGCAAATTAGATATCCCTCGAAAA-TCTGTTGG-GGATATTT i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13371170 144 + 41866177 ATCTTATAAATTTGTAAGGATAGTAGAACT---TGAAGCTTGCTGAAAATCAAACTGCAAATGTTCTATAGACTT-TGACAGAG---GTAGCTGTTCGGAGCTGAGCTTTTGCCAACTGGACAACACCAGAAAA-TCTGTTGGGGGATATTT i equCab2.chr26 C 0 C 0 s canFam2.chr31 14121158 146 + 42263495 ATCTTATAAATTTGTAAGGAAGGC--AACTTGCTGAAATGTGCTGAAAATGAAACTGTAAATGTCCT-TACACTT-TGATGAAGGTAGTAGCTATTTGGGGCTGAGCTTTTGCCAGTGAGACACTCCTAGAAAA-TCCATTGGAAGATA-GT i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20629683 145 - 62548349 ATGTTATAAACTTGTAAGGACAGTAAAACT---TGAAACTTTCAGATAATCAAACTGTAAATAATCTGTACACCTTTGAAGGTG---GCGGCTGTTTGGAGCTGTGGTTTTGCCCACTAGACACTTCTAGAAAA-TGTCTTCAGggatattc i loxAfr3.scaffold_13 C 0 I 268 a score=404348.000000 s hg19.chrUn_gl000245 23331 238 + 36651 TCAGGAAGTCATTGAACCCCCT-AAAAATCAAGTTTATTGC--TTTTACCataaatataaat-------------------------------------aatttatttaCTATCAACCACTTTCAATATTCGAATAAGTAAC-TTTATTGTTTATTTCATTGACATGATCTACATAGAC----------------------ATGCAATTTATCTTCTTTTGCGATACATTCAGAAAATTTGCTGCCTGAAAAAGCCATGTTTTGAAATTACCACCTGTTTGATGAttttttttttatactt s panTro2.chrUn 47419724 239 - 58616431 TCAGGAAGTCATTGAACCCCCT-AAAAATCAAGTTTATTGC--TTTCACCataaatataaat-------------------------------------aatttatttattatCAACCACTTTCAATATTCCAATAAGTAACCTTTATTGTTTATTTCATTGACATGATCTACATAGAC----------------------ACACAATTTATCTTCTTTTGTGATACATTCAGAAAATTTGCTGCCTGGAAAAGCCATGTTTTAAAATTACCACCTGTTTGATGAtttttttttcatactt i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 853141 239 - 4212913 TCAGGAAGTCACTGAACCCCCT-AAAAATCAAGTTTATTGC--TTTTATCataaatataaat-------------------------------------aatttatttattatCAACCACTTTCAATATTCCAATAAGTAACCTTTATTGTTTATTTCATTGGCATGATCTACATAGAC----------------------ACACGATTTATCTTCTTTTGCGATACATTCAGAAAATTTGCTGCCTGGAGAAGCCATGTTTTGAAATTACCACCTGTTTGATGAttttttttttatactt i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189465721 227 - 189746636 TCAGGAAGTCGTTGAACTCCCT-AAAAATCAAGTTTATGGC--TTTTATCataaatataaat-------------------------------------aatttatttattatCAACCACTTTCAATATTCCAATAAGTAACCTTTATTGTTTATTTCATTGTCATGATCTACATAGAC----------------------ACATGATTTATCTTCTTTTGTGATACATTCAGAAAATTTGCTGCCTGGAAAAGCCATGTTTTAAAATTACCACCTGTCTGATGATTTT------------ i rheMac2.chr2 C 0 I 10 s cavPor3.scaffold_34 15817932 223 - 24440124 TTAGAAAGCCAATGTA-ATGTT-AAAAACCAAATTTAGTAA--TTCTAACA-GAATACAAAG-------------------------------------AATCTGTTCACACTAGAACACGTTCAGTGCTTCAACAAATA-ACTTGTTA---TTTTTTATTGGTATGATTTACAAAAGC----------------------AC-------ATCGTCATTTGTGGCACATACAATAAA--AGATATCTGGAAAAGTAGCGTTTTTAAATTACCACACT-TCGTCGATTATCTTATAAAACTT i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141901603 229 + 163896628 TCAGGAAGTCATCACACCCCCT-AAAAATCAAGCTTATTCC--TTTTAATATAAATAAAAAC-------------------------------------AATGTATCCATCATCAATTGCTTTTAGTGGTACAACAAATAGGCTTTTCAGCTTTTGTCATTGCCATACTCTACAGAAACATCTGTGACTACATCTATGTCTAC-------ATTCACAGCTGTGAAGCATTCAGAAAA--TATTTCTTAGTAAAGTCATGTTTTGAAATGACTGCCTGT----------------------- i oryCun2.chr14 C 0 I 22 s bosTau4.chr1 138191650 258 - 161106243 TCAGGAGGTCATCACACCACCT-ATAAATCAAGGTTACTGa--ttttaacataaatataaatataacctaaatatatatttaacataaatataaaCATAACTTCATTCACTATCAACCACTTTGAAGAGTCCAATAAACAGTGCTTATTGCTTGTTGCACTGGCATGATCTACATGAAA----------------------A----ACGAGCCATCTTCTGTGGTATATTCAGAAAG--CCCTACCTGGTAAAGT--CATTTTGAAGTTACCTTTCCTCTGATAATTTTTT---------- i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13371314 226 + 41866177 TCAGGAAACCATCACACGCCCT-AAAAATTAAGGGTATTAT--TTTTAACATAAATACTAAT-------------------------------------AATTCATCCACTATCAACCACTTTCAAGATTCCAATAAATATCTCCTATTGCTTATTGCACTGGCGTTATCTACATGAAC----------------------AGGTGATCCGTCATCTTCTGTGGTACATTCAGAAAA--TGCTACCTGGTTACAT--CGTTTTGAAATTACCTCCCATATGATGATTTTCTT--------- i equCab2.chr26 C 0 C 0 s canFam2.chr31 14121304 222 + 42263495 TCAAGAGGTCATTACACTCCTT-AAAAATCAAGATTATTGC--TTTTAACATAAGTATAAAT-------------------------------------AATTCATCCACTATCAACCATTTGTAAGACTATAATACATAGCCTTCATGGCTTATTTCCATGGCATAACTTACATAAAC----------------------AGGTGATCAATCAGCTCATGTGATACATTTAGAAAA--CGCTACCTGATAAAGTCACGTTTTGAAATGACCTCCCACATGACCAT--------------- i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20630096 222 - 62548349 TCAGGAAGTCATTGCCCTCCTTAAAAAATCAAAGTTATTGCTTTTTTAACGTAAATATAAAT-------------------------------------AATTTATCCACT---------TTTCAGTACTCCAATAAATAGCATTTGTTGCACACTACATTGGCATAGTCTACATAAAC----------------------CTGTGCTCCATCAGCTTCTATGATACATTCAGAAAA--TACTACCTGGAAAAGTCACATTTTAAAATAATCTCCCATCTAATCATTTTCTT--------- i loxAfr3.scaffold_13 I 268 C 0 a score=33399.000000 s hg19.chrUn_gl000245 23569 141 + 36651 taagttttagggcacatgtgcacaacgtgcagtttagttacatatgtatacatgtgccatgttggtgtgctgcacccattaactcgtcatttagcattaggtatatctcctaatgctatccctaccccctccccccacccc s ponAbe2.chr21_random 853380 141 - 4212913 taagttttagggtacatgtgcacaaggtgcaggttagttacatatgtatacatgtgccatgttggtgtgctgcacccattaactcgacatttagcattaggtatatctcctaatgctatgtctcgctgctccccccacccc i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47419963 140 - 58616431 taagttttagggcacatgtgcacaacgtacagtttagttatatatgtatacatgcaccatgttggtgtgctgcacccattaactcatcatttatcattaggtatatctcctaacgctatccctcccccctccccc-acccc i panTro2.chrUn C 0 C 0 e bosTau4.chr1 138191908 0 - 161106243 C e loxAfr3.scaffold_13 20630318 0 - 62548349 C e oryCun2.chr14 141901832 22 + 163896628 I e canFam2.chr31 14121526 0 + 42263495 C e equCab2.chr26 13371540 0 + 41866177 C e rheMac2.chr2 189465948 10 - 189746636 I e cavPor3.scaffold_34 15818155 0 - 24440124 C a score=12218.000000 s hg19.chrUn_gl000245 23710 72 + 36651 gcaacaggccctggtgtgtgatgttcccctccctgtgtgcatgggttctcattgttcaattcccacctatga s panTro2.chrUn 47420103 72 - 58616431 acaacaggccctcgtgtgtgatatttcccttcctgtgtccatgtgttctcattgttcaattcccacctatga i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 853521 72 - 4212913 acaacaggccccggtgtgtgatgttccccttcctgtgtccatgtgttctcgttgttcaattcccacctatga i ponAbe2.chr21_random C 0 C 0 s loxAfr3.scaffold_13 20630318 7 - 62548349 ACAACAA----------------------------------------------------------------- i loxAfr3.scaffold_13 C 0 C 0 e bosTau4.chr1 138191908 0 - 161106243 C e oryCun2.chr14 141901832 22 + 163896628 I e canFam2.chr31 14121526 0 + 42263495 C e equCab2.chr26 13371540 0 + 41866177 C e rheMac2.chr2 189465948 10 - 189746636 I e cavPor3.scaffold_34 15818155 0 - 24440124 C a score=286143.000000 s hg19.chrUn_gl000245 23782 249 + 36651 gtgagaacatgcagtgtttcatttCCACTTAAGTAT-----CTATCTCTATTTGTCCTTTATTTTCACTTCCATCCTAGCTCTATCCCTTGTCTCCTTCG----TGTGTCTCAGGATAAGTGCCCTATAACATTTTATACTTCTGGAAACCCTTCAATATAATGTTATTACATGTAAAAATAAAAAGTCTGTT-TTAGCGAACT---CTTTCTTCACAAATTATCTTTTCCTAGTTCCCTATTAGA-CAA-TTTTTGTAGGCTC s ponAbe2.chr21_random 853593 246 - 4212913 gtgagaacatgtggtgtttcatttCCACTTAAGTAT-----CTATCTCTATTTGTCCTTTATTTTCACTTCCATCCTAGCTGTATCCCTTGTCTCCTTCG----TGTGTCTTGGGATAAGCACCCTATAACATTATATATTTCTGGAAACCCTTCAATATAAAGTTATTACATGTAAA---AAAAAGTATGTT-TCAGCAAACT---TTTTGTTCACAGATTATCTTTGCCTACTTGCCTATTAGA-CAA-TTTTTGTAGGCTC i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47420175 249 - 58616431 gtgagaacatgcagggtttcatttCCACTTAAGTAT-----CTATCTCTATTTGTCCTTTATTTTCACTTCCATCCTAGCTCTATCCCTTGTCTCCTTCG----TGTGTCTCAGGATAAGTGCCCTATAACATTTTATATTTCTGGAAACCCTTCAATATAAAGTTATTACATGTAAAAATAAAAAGTCTGTT-TTAGTGAACT---TTTTCTTCACAAATTACCTTTTCCTACTTCCCTATTAGA-CAA-TTTTTGTAGGCTC i panTro2.chrUn C 0 C 0 s bosTau4.chr1 138191908 228 - 161106243 ATAAGAA------------CATATCCACTTGGAGGC-----CTATTTCTGTTT-TTCCTCATTTTCACCTCCACCA------CATCTTTTGCCTCCTGCC----TTTACCTCATAATCTGTGCCTTACAGCCTTAAATA-TTCTGCAAACCCTTCAACATAAACATATTAGATATAGG---GAAAAAAGCACT-TTATTAAACTCTGTTTTATTCATGGA-TGTCTGGACATGCTCACCTA-TAGA-TAACTATTTAGAGATTC i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13371540 234 + 41866177 ATAAAAA------------CATTCCCACTTAAGAGC-----CTATTTTCATGTGTTCCTCGTTTTCATCTCCACTC------TATCCTTTGTCTCCTGCCTGTATGTACCTCATGATCAGTGGCCAGCAGTATGACATATTTCTGGAAACGCTTCATCATAAAGATATTACAT-ATGG---AAAAAATGTATCTCTATCAAACTTTGTTTTACTCACAGA-TGTCTTTGTCTACTCACATA-TAGA-CAACTCTTTATAGGTTC i equCab2.chr26 C 0 C 0 s canFam2.chr31 14121526 200 + 42263495 ----------------------TTTCTTATAAAAACAACTTCACTTTCTATTTGTTCCTCATTTTCATCTCTATTC------CATCCTTTGCCTCTTGCC----TGTTCCTCATGATCAGTGACCTACAGCATGACGTACTTCTGGAAACCCTCCAACATAAAGATACTACATAAAGA---AAAAAAAGCATC----TCAAAC--------ATTCCCAGA-TGTCTTTGTCTATACACCTG-TAGA-CAA-------------- i canFam2.chr31 C 0 I 380 s oryCun2.chr14 141901854 202 + 163896628 --------------------ATTACTTCTTAAGTGA-----CTATTTCTAATCGTTCCTTATTTTCACCTCCATCC------CTTCCCTTATCTCCTGTA----CATCCTTGA-TATAAGTGTCCTGCGGCTTTACAAATTTCTGGAAACCCTTAAACATCAAGAT-------AT------GACAAGTTTCT--------GAGTATGTTTCACTCAGAGA-AATCTTTGTCTACTCA-GTATTAGG-AAA-CTC-TACCCATTT i oryCun2.chr14 I 22 C 0 s cavPor3.scaffold_34 15818155 205 - 24440124 ----------------------TTTAACTTAAGAGC-----CTATTTCTGTTTGTTC----TTCTGTCCTGCA-----------TATCTTATCTCCTGTG----TGTACCTCA----GGATCTCCTACGGCACTACGCATTTCAGGAAATCCTTCAATATAAAGATATTGTGCAT------AAAAAATTCTTT-ATAGTGAAATTTGTTTTGCTCATAGA-TATCTTCATCTATTCACCTGTTAGACAAA-CTCTTGTATGTCT i cavPor3.scaffold_34 C 0 C 0 s rheMac2.chr2 189465958 226 - 189746636 -------------------CATTTCCACTTAAGTAT-----CTATCTCTATTTGTCCTTTATTTTCACTTCCATCCTAGCTCTATCCCTTGTCTCCTTCA----TGTGTCTCAGGATAAGTGCCCTATAACATTATATATTTCTGGAAATCCTTCAACATAAAGTTATTACATGTAA----AAAAAGTATGTT-TTAGCAAACT---TTTTGTTCACAGATTATCTTTGCCTGCTTACCTATTAGA-CAA-TTTTTGTAGGCGC i rheMac2.chr2 I 10 C 0 s loxAfr3.scaffold_13 20630325 210 - 62548349 -------------------CATTTCAACCTGAGAGT-----CTGTTTCTATTGTTTCCTCATTTCCACCTCT-------------------TCTCCCCCA----CATATGTCATGATCAGTGCCCCGAAGCATTACATATTCCTGGAAACTCTTCGACATAAAGATATTACACACACC---AAAAAATGCATCTCTATCGAACTC--TTTTATTGACAGC-TGTCTTTGTTTGTTCATCTATTAAA-TAATTCTTTAAATGTTC i loxAfr3.scaffold_13 C 0 C 0 a score=96674.000000 s hg19.chrUn_gl000245 24031 89 + 36651 CATATGCTATTAATTTATATTCACTTTTAGAAGAATTTTCATCAAAAGCAAA-AGTCTTATGTAA------------------ATTGTTT--------ATATG---CTATTTGTA-----------------CTTC--------------------------------------------------------------------------------------- s rheMac2.chr2 189466184 99 - 189746636 CATATGTTATTAATTTATATTTACTTTTAGAAGAATTTTCATCAAAAGCAAA-AGTCTTATGTAA------------------ATTGATT--------ATGTG---CTATTTGTACTGCATAGTG-------CTTC--------------------------------------------------------------------------------------- i rheMac2.chr2 C 0 C 0 s ponAbe2.chr21_random 853839 89 - 4212913 CGTATGCTACTAATTTATATTCACTTTTAGAAGAATTTTCATCAAAAGCAAA-AGCCTTATGTAA------------------ATTGATT--------ATATG---CTATTTGTA-----------------CTTC--------------------------------------------------------------------------------------- i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47420424 89 - 58616431 CATATGCTATTAATTTATATTCACTTTTAGAAGAATTTTAATCAAAAGCAAA-ATTCTTATGTAA------------------ATTGATT--------ATATG---CTATTTGTA-----------------CTTC--------------------------------------------------------------------------------------- i panTro2.chrUn C 0 C 0 s cavPor3.scaffold_34 15818360 99 - 24440124 AATGTGTTATTGTTGTATACA---GTTTTTAAGAATGTTCTCCAAAGTAAAA-ATATTTTTATAA----------------TCATTGCCTTTCCTCCCATATGTTTCCATTTGTA-----------------TTTC--------------------------------------------------------------------------------------- i cavPor3.scaffold_34 C 0 I 1547 s oryCun2.chr14 141902056 134 + 163896628 CCTATGCTATTAATTTATATGTACGTTTAGAAGAATTTCTTCAAAAATGATA-GTTTTTGAATAACAATTTTGTTAAGATTTTATGGTATTTCCATTCATATTTCACAATTTATA-AACAGAAAGAGTTAACTTCC--------------------------------------------------------------------------------------- i oryCun2.chr14 C 0 I 50 s bosTau4.chr1 138192136 95 - 161106243 CATATGCT----ATTTATATGCA-TTTTGAAAAAATTTCCTTTAACATCAAA-AGTTTTACAAAA------------------TTTAAATT-------GCCTG---CTGTTGTTACTATACAGTG-------CTTC--------------------------------------------------------------------------------------- i bosTau4.chr1 C 0 I 56 s equCab2.chr26 13371774 100 + 41866177 CATATGCTATTAATTTATATGCACTTTTAGAAGACTTTTCTTCAGAAGCAAA-AGTTTTGCACAA------------------CTTAACTT-------ATATG---CTGTTGTTACTCTACAGTG-------CTTC--------------------------------------------------------------------------------------- i equCab2.chr26 C 0 I 91 s canFam2.chr31 14122106 99 + 42263495 TATATGCTCTTAATTTATATATACTTTTAGAGGAATTTTCTGCC-AAATGAA-AGCCTTGTAGGA------------------TTTAAATT-------ATATG---CTATTGTAACTATATAGTG-------CTTT--------------------------------------------------------------------------------------- i canFam2.chr31 I 380 I 55 s loxAfr3.scaffold_13 20630535 187 - 62548349 CTTATGCTATTAATTTATATGAAATTTTAAGAGCATTTTTTTCAAAAGTAAGCATTTTTTCATAG------------------TTTAATT--------ATATG---CTATTTTTACTATATGGTG-------TTTCACTAGCATTTCACAACTTAAAAATTGAAGAAATCAATTTCAGTTGCATAGAATTACAAAATAAGGCCCAAAGGTTGCTACTGAAAGC i loxAfr3.scaffold_13 C 0 C 0 a score=-3487.000000 s hg19.chrUn_gl000245 24120 35 + 36651 TGTGT-ATATATAC------------------ACGCA--------------------------TAGCCACA------TA----CATATAT s panTro2.chrUn 47420513 35 - 58616431 TATGT-ATATATAC------------------ACACA--------------------------TAGCCACA------TA----CATATAT i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 853928 35 - 4212913 TATGT-ATATATAT------------------ACACA--------------------------TAGCCACA------TG----CATATAT i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189466283 35 - 189746636 TATGT-ATATATAC------------------ACACA--------------------------TAGCCACA------TA----CATATAT i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141902240 50 + 163896628 TATGT-CTTTATAT------------------TTGTATCT-----------------AATTTCTATTCATAAGATATTA----TATGTAC i oryCun2.chr14 I 50 I 2 s bosTau4.chr1 138192287 82 - 161106243 TATA--ATATAGGCACAAAGGTTGCTACAGAAAGCCATCTTCCATATACATGTGCCTAATGACTGTTTACA------TAATTTCATATAT i bosTau4.chr1 I 56 I 4 s equCab2.chr26 13371965 47 + 41866177 TCTG--CTTTATAT------------------ATGCGTCT-----------------AATAACTGATGATA------TGATTTTGTATAT i equCab2.chr26 I 91 I 4 s canFam2.chr31 14122260 79 + 42263495 TATG--CTATAAGTCCAAAGGCTGTTACAGAAAGGCATCTGCTTTAT---TTTGTCAAATTACTCTTTATA------TAATTTCATATAT i canFam2.chr31 I 55 I 3 s loxAfr3.scaffold_13 20630722 49 - 62548349 TGTGTAATTTATAC------------------ATGTGTCA-----------------AATCACCGTTTGTA------TGATCTCATATAT i loxAfr3.scaffold_13 C 0 I 4 e cavPor3.scaffold_34 15818459 1547 - 24440124 I a score=116004.000000 s hg19.chrUn_gl000245 24155 79 + 36651 GTAACTCC-AGAGGCCTGCCTGGACTGTTAAATA---ACTGTATTGAACAAGAGCAAGAAA-----------------------AAGCTTTTCAAATTTCAAACAA s panTro2.chrUn 47420548 79 - 58616431 GTAACTCC-GGAGGCCTGCCTAGACTCTTTAATA---ACTGTATTGAACAAGAGCAAGAAA-----------------------AAGCTGTTCAAATTTCAAACAA i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 853963 78 - 4212913 GTAACTCTGGGAGGCCTGCCTGGACTGTTTAATA---ACTGTATTGAAC-AGAGCAAGAAA-----------------------AAGCTGTTC-AATTTCAAACAA i ponAbe2.chr21_random C 0 I 225 s rheMac2.chr2 189466318 78 - 189746636 GTAACTCT-GGAGGCCTGCCTGGACTGTTTAATA---AATGTACTGAACAAGAGCAAG-AA-----------------------AAGCTGCTCAAATTTAAAACAA i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15820006 70 - 24440124 GTAACTCT-GGAGTCCTG----GATTGTTCAGAA---ATTATATTAAACAAAAAGAAGAAA-------------------------GTTGTTCAAATTTCA---AA i cavPor3.scaffold_34 I 1547 C 0 s oryCun2.chr14 141902292 101 + 163896628 ATAACTCT-GGAGACCTG----AACCATTAAGAGAGCATTAAaaaaaaaaaaaaaaagaaagaaagaaagaaagaaagaaagaaagGCTACTCAAATTTTAACCAA i oryCun2.chr14 I 2 C 0 s bosTau4.chr1 138192373 73 - 161106243 GTAACTCT-GGAAGCCTG----GACTAGTCAATA---ATTATATTAAACAAAAGAAAG-AA-----------------------AGATTGCTCAAATTTCAACGA- i bosTau4.chr1 I 4 C 0 s equCab2.chr26 13372016 73 + 41866177 GTAACTCT-GGAGGCCTG----GACTGGTCAGTA---AGTCTGTTAAATAAAAGAAAG-AC-----------------------AGGTTGTTCAAATTTCAGCAA- i equCab2.chr26 I 4 C 0 s canFam2.chr31 14122342 69 + 42263495 GCAAAGTT-GGAGGCTTG----GACTGGTCAGTA---ACTATATTAAAAAGAAGAA----------------------------AAGTTGCTCAAATTTCAACAA- i canFam2.chr31 I 3 C 0 s loxAfr3.scaffold_13 20630775 74 - 62548349 GTAATTCT-AGAGGTCTG----AACTGGTCAGTA---ACCATATTAAACAAAAAGAAG-AA-----------------------AGGCAAATCGACTTCCAACCAA i loxAfr3.scaffold_13 I 4 C 0 a score=133985.000000 s hg19.chrUn_gl000245 24234 109 + 36651 CAAGTTGAACTGAAGAGCTCACATCTTTGAATGAAATAGACACTAG-TAGCCTTTAAAAATTAAACATTTCTACTGTTTTA-AAAAATTATA--GGCATCATAGTATGAGGAA s panTro2.chrUn 47420627 109 - 58616431 AAAGTTGAACTGAAGAGCTCACATCTTTGAACTAAATAGACACTAG-TAGCCTTTAAAAATTAAACATTTCTACTGTTTTA-AAAAATTATA--GCCATCATAGTATGAGGAA i panTro2.chrUn C 0 C 0 s rheMac2.chr2 189466396 109 - 189746636 CAAGTTGAACTGAAGAGTTCACAACTTTGAATAAAATAGACACTAG-CAGCTTTTAAAAATTAAACATTTCTACTGTTTTA-AAAAATTATA--GCCATCATATTATGAGGAA i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15820076 78 - 24440124 TGAGCTA--------------------------------ACACTAG-CAGTCTTTAAAAAATATACA-TTTCAGTATTGTA-AAAAATCATAGAGCTATGAATGTGTGAGAAA i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141902393 110 + 163896628 TAAACTAAATTGGGGAGTTCACCTACTTGAATAAAATAGACATTAA-CAGCCTTT-AAAATTAAACATTTTCAATGTTTTT-AAAAATCATATGGTCATCACGGTGAGAAAGG i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138192446 108 - 161106243 CCAGCCAAACTGAAAAGCTTATCCCTTTGACTAAAA---ATGCTAGACAGCCttt-aaaattaaatattttaactatttta-aGAAACTATATAACCATCAGAGGATGAGGGG i bosTau4.chr1 C 0 I 2 s equCab2.chr26 13372089 109 + 41866177 TCAGCTAAACTGAGGAGCTCACCGCTTGGAATAAAACAGATACTAGACAGCCTTTAAAAATTAAACATTTTCACTGTTTAAAAAAAATCGTATAACCACCAGAGTATGA---- i equCab2.chr26 C 0 I 2 s canFam2.chr31 14122411 92 + 42263495 CCAGCTTAATGAAGGAGCTGACCCCTTTGAATAAAACAGACACAAGATGGCCTTTAAAAATTAAACATGTTCACTGTTTCAGAAAAAGT-----------------TGA---- i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20630849 111 - 62548349 CTTGCAAAATTGAGGAGCTCACCCTTTGGAATAAAACAGACATTAG-CAGCCTTTTAAAAATGAACATTTTCACTGTTTTT-CAAAACCATATAGCCCTCCTAGTTTGAGGGG i loxAfr3.scaffold_13 C 0 I 1 e ponAbe2.chr21_random 854041 225 - 4212913 I a score=2123726.000000 s hg19.chrUn_gl000245 24343 908 + 36651 AAAATGTAATAATCCTT-TTTAATTCTTGCCATTTTATTAACCACGGACTCCTTATGCCCTGACTTCATTGGTA-CCCCTTTGAGATTAAACAGAACAA-T--TAATTTAAAATTCTGATAAATAAATAAATTACACCATTTACTTGAGGTACTCTTTCACCTTTCAAGAAATATTTTGAGAATTCATTAGCTAAATATTGCTATAATGCAGGCTAGTAATAAATAGAAATAATGAT-TTCATTGTAAAGTTTAAACTAATGATGGTATGATCTGGAATTTTTGTTAACCTAGAAGACATAATTAGCTCTACAGGTGAAATGAAAGAC-AAAATCACTTCAC-ATATTAG---TAAAAAACAAATA-------------ATATAACTTTATAAGCTACTGCTGTTCTTTTGCTGTTAAGAACCAATGACATCTGTAATTAGGGAAGATTATG--------------------GAAAGGTTAAAGGTGAGAATACATGCAGTCTATATACAGGAAACCCAAACTGTTTAGGTTAAGGAAATGTCTGCAAAAGTCATATTAATTAGCAGGTTCACAGGAAACTAACATTTATTGTATAAATTCCATGGTCAAATGTATTAGGGCTCCACGCACACAACTGTGC-GCCATCTATGTTACCACACAGTGCTTACTTCTTTCAGTCTT-TATTCATTTCTCTCCTAATGGTCTGTATGGTAT----TATTA---CATAGTTCTAAAAACCTTCCATGAGGCAGAAATTTCATTTAATGATACAGCTTCAAAAATAATGAAAACCAGTA---------------------------GAAACT--TTCTATTTT--TTTATGAAGCAGAATTATTGAATTTTC--AGTTTCATTTATTTAATG-T----TACAAGAGGACAAACATATTTCTTTAAT----TTCTTC----TTGTTATTTTTGTCTAACATCAACCAAAGCCATTTCTTTCATTTGAAGGTGAAAACT--GCCCAT s panTro2.chrUn 47420736 908 - 58616431 AAAATGTAATAATCCTT-TTTAATTCTTGCCATTTTATTAACCACGGAGTCCTTATGCCCTAACGTCATTGGTA-CCCCTTTGAGATTAAACAGAACAC-T--TAATTTAAAATTCTGATAAATAAATTAATTACACCATTTACTTGAGGTACTCTTTCACCTTTCAAGAAATATTTTGAGAATTCATTAGCTAAATATTGCTATAATGCAGGCTACTAATAAATGGTAATAATGAG-TTCATTGTAAAGTTTAAACTAATGATGGCATGATCTGGAATTTTTGTTAACCTAGAAGACATAATTAGCTCTAGAGGTGAAATGAAAGAC-AAAATCACTTCAC-ATATTAG---TAAAAAACAAATA-------------ATATAACTTTATAAGCTACTGCTGTTCTTTTGCTAGTAAGAACCAATGACACCTGTAATTATGGAAGATTATG--------------------GAAAGGTTAAAGGTGAAAATACATGCAGTCTATCTACAGGAAACCTAAACTGTTTAGGTTAAGGAAAGGTCTGTGAAAGTCATATTAATTAGCAGGTTCACAGGAAACTAACATTTATTGTATAAATTCCATGGTAAAATGTATTAGGGCTCCATGCACACAACTGTGC-ACCATCTATGTTACCACACAGTGCTTACTTCTTTCAGTCTT-TATTCATTTCTCTCCTAATGGTCTGTATGGTAT----TATTA---CATAGTTCTAAAAACCTTCTATGAGGCAGAAATTTCATTTAATGATATAGCTTCGAAAATAATGAAAAACAGTA---------------------------GAAACT--TTCCATTTT--TTTATGAAGCAGAATTGTTGAATTTTC--AGTTTCATTTATTTAATG-T----TACAAGATGACAAACATATTTCTTTAAT----TCCTTC----TTGTTATTTTTGTCTAACATCAACCAAAGCCATTTCTTTCATGTGAAGGTGAAAACT--GCTCAT i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 854266 906 - 4212913 AAAATGTAATAATCCTT-TTTAATTCTTGCCGTTTTATTAACCATGGAGTCTTTATGCCCTAACTTCATTGGTA-CCCCTTTGAGATTAAACAGAAC---T--TAATTTAAAATTCTGATAAATAAATTAATTACACCATTTACTTGAGGTACTCTTTCACCTTTCAAGAAATATTTTGAGAATTCATTAGCTAAATATTGCTATAATGCAGGCTAGTAATAAATGGAAATAATGAG-TTCATTGTAAAGTTTAAACTAATGATGGTATAATCTGGAA--TTTGTTAACCTAGAATACATAATTAGCTCTAGAGGTGAAATGAAAGAC-AAAATCACTTCAC-ATATTAG---TAAAAAAAAAATA-------------ATATAACTTTATAAGCTACTGCTGTTCTTTTGCTATTAAGAACCAATGACATCTGTAATTAGGGAACATTATG--------------------GAAAGGTTAAAGATGAGAATACATGCAGTCTATCTACAGGAAACCTAAACTGTTTAGGTTAATGAAATATCTGCGAAAGTCATATTAATTAGCAGGTTCACAGGAAACTAACATTTATTGTGTAAATTCCATGGTAAAATGTATTAGGGCTCCATGCTCACAACTCTGC-GTCATCTACATTACCACACAGTGCTTACTTCTTTCAGTCTT-TATTCATTTCTTTCCTAATGGTCTGTATGTTAT----TATTA---CATAGTTCTAAAAATCTTCCATGAGGCAGAAATTTCATTTAATGATATAGCTTTGAAAATAATGAAAAACAGTA---------------------------GAAACT--TTCTATTTT--TTTATGAAGCAGAATTGTTGAATTTTCAAAGTTTCATTTATGTAATG-T----TACAAGATGACAAACATATTTCTTTAAT----TCCCTC----TTGTTATTTTTTTCTAACATCAACCAAAGCCATTTCTTTCATTTGAAGGTGAAAACT--GCTCAT i ponAbe2.chr21_random I 225 C 0 s rheMac2.chr2 189466505 834 - 189746636 -AAATATAATAATCCTT-TTTAATTCTTGCCATTTTATTAACCAGGGAGTCCTTACACCCTAACTTCACTGGTA-TCCCTTTGAGATTAAAAAGAACAC-T--TAATTTAAAATTCTGATAAATAAATTAATTACACCATTTACTTGAAGTACTCTTTCACCTTTCAAGAAATATTTTGAGAATCCATTAGCTAAATATTGCTATAATGCAGGCTAGTAATAAATGGGAATAATGAG-TTCATTGTAAAGTTTAAACTAATGATGGTGTGATCTGGAATTTTTGTAAACCTAG-ATACATAATTAGCTCTAGAGGTGAAATGAAAGAC-AAAATCACT------------------------------------------------------------------------------------------------------------------NNNNNNNNNNNNNNNNNNNNGAAAGGTTAAAGATGAGAATACATGCAGTCTATCTACTGGAAACCTAAACTGTTTAGGTTAATGAAATGTCTGTGAAAGTCATATTAATTAGCAGGTTCACAGGAAACTAACATTTATTGTATAAATTCCATGGTAAAATGTATTAGAGCTCCATGCACACAACTGTGC-ACCATCTACATTACCACACAGTGCTTACTTCTTTCAGTCTT-TATTCATTTCTCTCCTAATGATCTGTATGTTAT----TATTA---CATAGTTCTAAAAATCTTCCATGAGGCAGAAATTTCACTTAATGATATAGCTTTGAAAATAATGAAAAACAGTA---------------------------GAAACT--TTCTATTTT--GTTATAAAACAGAATTGTTGAATTTTCAAAGTTTTATTTATGTAATG-T----TACAAGATGACAAACTTATTTCTTTAATAGC-CTCTTG----TTGTTATTTTGCTCTAACATCAACCAAAGCCATTTCTTTCATTTGAAGGTGAAAACT--GCTCAT i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15820154 903 - 24440124 AAAATACAATAATCCATCTTTTACTTTTGCAGTTTAATTAACCAA--ACTCCTCACTTCCTAACTTCATTAGTT-TCCTTTTGACATTAGAAAGAAATCTT--TTATAGCAAATACAGATAAATAAATGAATCTGGACATTTATTTGAGGTAGTCTTTAACCTCTCAAGAAACACTTTGAGAATTCATCAGCTACGCAATGCTATAATTCA-GCGAGTAATGAATGATAATAATGAG-TTCATTGTAAAGTTGAAACCAGTGATAGCATGATTAGGAATTTTCGTTAACCTAGAATAAATAATGAGCTCCAAAGGGGAAATAAAAGAC-AAAATCACCTCAT-ATAATAG---GGAAAAATAATTA-----------GTATATAACTTTATAAAGTA-----------TTGCTATT---AATCAGCAGAATTTATAATTAGAGAACATTGTA--------------------GAAAGGTTAAGCATGAGAATACACACAATCTATCTACAAGAAACCTCAACCATTTAGGTTAATGAAATGTCTGTGGAAGTCATAGTAATTAGCAAGTTCACAGGAATCCAACTTTTCTTTTATACATGCCCTGGTA-ATTGTGTTAGGCTTTCATGAACACAGATGTGT-CCCATCTACATCAGCATACAGTGCCTACTTCATTTAGTCTTTTGTCCATTGTTTCCATATTGATCAGTTTGCTATTAAGTATTT---GATATTTAGGGAAAGTATTTCTAAGGCAGAAATTTCATTTAATGATGCAGCTTTGAAGTTATTGAGAAACAGT----------------------------AAAATT--TTTCAAATT--TTTAGAAATGCGA---GTTGAATTTTCAAAGCTTCATTAACATAATG-TTTGCTATAAGA-GCACAAGTCATATTTTTAATTCCTTTCATG----TTATTATTTCTGTTTAATATCAAGCTAAACCACTTCTATCATTCAAAAGTGAGAATC---GTGTT i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141902503 951 + 163896628 AAAATGCATTAGTCTAT-TTGAACTTTTGCAATCTCATTAACCAAAGAGTTTTCACAGCTTAACTTAAGTCGTTATCCTTAGGAGGTTAAAAGGAAAAC----TTACTGAAAAATCAGATAAATAAATTAATTTTGGCATTTACTTGAGGTACTCTTTAACCTCCCAAGAAATATTTTGAAGATTCATTAACTACATATTGCCATAATGAA-GCTAGTAATAAACGGAAATAATGAG-TTCATTGTAAAGTTTAAAGCAATGATAGCATGATTAGAAAATTTTGTTAACCTAGAATACATCATTAGCTCTAGAGGTGAAATGAAAGAC-GCTATCACTTCAC-ATATTAG--TAAAAAAAAAAAAA-----------AAACATTGTTTTATAAACTACAAATGTTCTCTTGCTATTAAGAATCAATGAAATCTGTACTTAGGGAACATTATA--------------------GAAAGGTTAAAGATGAGAATACATGCAGTCTATCTACTGGAAGCCTAAAGTGTTGAGGTTAATGAAATGTCTATGGAAGTCACATTAATTAGC-AGTTCACAGGAATCTCACTGCTATTTCGTAAACGTTTTGGTAGAAAGTAATAGAGTTCCATGCACACAACTGTGT-GTCATCTAGATTTCTGCACAGGGCTTATCTCTTTCAGTCTTACATCCATTTTCCCTCTGGTAACCTCTGTGTTATTATGTATTG---CATGTTTCTATAAATCCTTTATGATACAGAAAGTTCCTTTAATAAAATAGTTTTGACAATAGTGAGAAACAGTATTTTATAACAGTATTTATAAACAATAGAAAATTGCTTATAAATTTGTTTATAAATGAGGACTGTTGATTTTTCAGTGTTGTATCAACATAATG-T----TACAAGATGAAAAACCTAAGTCTTTATTTTTTTCCTTG----TTGTCATTTCTATCTAATATTAACCAAAATCAATTTTTT--TTCAAAATTTGGTTTTCAGCTGTT i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138192556 886 - 161106243 AAAATGAAGTAATCTAC-TTTAACTTTTTAAATTTCATTAACCAGAGAGTGCTTATAACCTAACTACATTAGTG-TCC-TTTAGAGTTAAAAATAAAAC-TTGTTTTTGAAAATTCACACAAATAAATTAATGTTGGCATTCATTTGAGG-ACTGTTTAACCTCTCAGACATCATTTTGAGAACTCATTAGCCAAATACCACCATAATGCAAGCAAGTAATACATGGAAATAATGAT-TTCATTGTAAAGTTTAAATCAATGCTAGTATGATCAGGAAATTTCATTAACCCAGAATTCTTAATTAGCTCTAGAGGTGAAAAGAAAGATAAAAATCACTTCAC-ATATTAG--TAAAAAAACAAATT----------AGAATATAACTTTATAAACTACTGCTGTTCCTTTGCTATTAAGAATCAATGAAATCTATAATTAGGGACCATTATG--------------------AAAAGGTTAAAGATGAGAATACATGCAGTCTATCTACAGGAAATCTAAACTATTTAGGTTAATGAAATGTCTGTAAAAGTCATACTAATTAGCAAGTTCATGGGAACCTAACTTTAATTTTACAAATGCCATGATGGGAAGTATTATGGCTCCATGCACACC--TGTGT-CCCAACTAGATTACTGCACAGTGC-TACCTCTTTCAAATTTCTCTTCATTTCCCCCTCAGTGATCTGGATGCTACTAAGTATAACACCACATTTCTGAAAATTCTCCATG-------------ATTTAATGATATAGATTTTAAGATGATGAGAAAC---A---------------------------GAAACT--TTCTATTTT---TTAGATAAGAGGATTGTTGAATTTTCAATGTGGCACTAACA------T----AATAAGATGACAT----ATTTCCTTATT----TTCTT-----TTATTATTTCT-----ATGTCAACCAAAACCATTTTT----TTCAAAAGTGAAAAGTTTGCCCAT i bosTau4.chr1 I 2 C 0 s equCab2.chr26 13372200 914 + 41866177 AAAAT--AATAATCCAT-TTTAACTTTTGCAATGTTATTAACCAGAGAGTGCGTGCATCCTAACTTCATCAGTG-TCC-TTTGAGGTTAAAAAGAAAAC-T--TTTTTGAAAATTCATAACAGTAAATTAACGTTGGCATTTACTTCAGGTACTCTTTCACCCCTCAAAAAACATTTCGAGAACTCATCAGCCATGTATTGCCTTAATGCAGGCTAGTAATAAATGGAAATAATGAG-TTCATTGTAAAGTTTAAACCAAGGATAGCATGATCAGGAATTTTTGTCAACCTAGAATGCGTAATTAGCCATAGAGGTGAAATGAAAGAC-AAAATCACTTCAT-ATATTAG---AAAAAAACAAATG----------AGAACATAACTTTATAATCCACTACTGTTCCCTTGCTATTAAGAATCGATGGAATCTGTAATTAGGGAACATTATG--------------------AAAAGGTTAAAGATGAGAACACATGCAGTCTGTCTACAGGAAACCTAAACGCCTTAGGTTAATGAAATGTCTATGGAAGTCATATTAATTAGCAGATTCACAGGAACCTAACTTTTATTTCATAAATGCCATGATGGAAAGTATTAAGTC-TCATGCACACAACTGTGT-CCCATCTAGATTACCACACAGTGCTTACCTCTTTCAATCTTCTATCCATTTTCCTCCTAATCATCTGGATGCTATTAAGTATTG---CATATCTCTGGAAATCCCTCATGAAGTAGAAGTTTCATTTAATGACATGGCTTTGAAGATAATGAGAAACTGTA---------------------------GAAACT--TTCTATTTT---TTAGAAAAGAGGATTGTTGAATTTTCAATGTTTCATTAATATAATG-T----TATAAGATGACAAAC--ATTTTCTTATT----TTTCCCT---TTGTTAGTTCTTTCTAATATCAATCAAAGCCATTCCTTACATTCAAAAGTGAGAATTTTGCCCAT i equCab2.chr26 I 2 I 264 s canFam2.chr31 14122503 915 + 42263495 -------AATAGTCCAT-TTTAACTTTTGCAGTTTTATTAACCAGAGAGAACTCATATCCTAACTTCATTAGTA-TCC-TTTGAGGGTAAAAAAGAAAA-C--TTTTTAAAAATTCAGA----TAAATTAATGTTGACATTTATTTGAAGTATCCTTTAACCTCTCAAAAAACATTTTGACAACTCATTAGCCACATATCACTGTAATGCAGTCTAGTAATAAATGGAAATAATGAGTTTCATTATAAAGTTTAAGCCAATGGTAGCATGATCAGGAATTTTTGTTAACCTAGAATGCATAATTAGCTCTAGAGGGGAAATGAAAGGC-AAAATTGCTTTAC-TCATTAGTGTAAAAAAAAAAGTGTAAAAAAATTAGAACATAACTTTATAAACCACTATTGTCCCATTGCTATTAAGAATCAATGAAACCTGTAATTAGGAAACATTATG--------------------GAAAGGTTAAAGATGAGGATACATGTGGTCTATCTACAGGAAACCTAAACTGCTTAGGTTAATGAAATGCCTATGACAGTCATATTAATTAGCAGGTTCACAGGAACCTAACTATTATTTTATAAATGCCATGATAAAAAGTATTAAGGCTTCGTGCACACAG-TGTGT-TCCATCTAGATTACCGCACAGTGCTTACCTCTTTCAATCTTCTATCTATTTCCCCCCTAATGATCTGGATGCTATTAAGT-TTG---CATATTTCTGGAAATCCTTCATGAGGCAGAAATTATATTTAATGATATTGTTTTGAAGATAATGAGAAAC---A---------------------------GAAACT--TTCTACTTT---TTAG--AAGAGGATTGTTGAATTTTAAATGTTTCATCAATATAATGAT----AATAAGATGACAG----ATCTCCTTATT----TTCCTCTTTGTTGTTATTTCTGTCTAAGGTCAACCGAAACCCTTTCTTTCATTCAAAAGTAAGAGTGTTGTCCAT i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20630961 907 - 62548349 AAAATGCAATAGCCCAT-TTGAACTTTTGCAACTTCATTAACCAGAAAGTCCTTATATCCTAACTTCATTAGTG-CCACTTTAAAGTTAAAAAGAAAACTT--TTATTGAAAACTCAGATAAATAAATAAATTTTGGCAGTTACTTGAAGCACTCTTTAACCTCTCAAGAAATATTTTGAG-ATTCATTAGCAACATATCACCATAATGTACTTTAGTAATAAATGGAAATAATGAG-TTCATTGTCAAGTTTAAACCAATGATAGCGTGATCATGAATTTTTGTTAACCTAGAATGCATAATTAGCTCTAGAGGTGAAAAAGGAGGC-AAAACCACTTCACAATATTAG---TAAAAAACAAATT----------AGAACATAACTTTATCGACTACTGCTGTTCTTTTGCTATTAAGAATCAATGAAATCTGTAATTAGGGAACATTATG--------------------GAAAGGTTAAAGATGAGAATACATGCAGTTTATCTACAGGAAACCTAAAACGTTTAGGTTAATGAAATGTCTATGAAAGTCATATTAATTAGCAGGTTCGCAGGAGTCTAACTTTTATTTTATAAATGCCGTGGTAGAAAGCATTAGGGCTTCCTGCACACAACTGTGTCCCCATCTAGATTATCACACAGGGA------------------TACCCATTTTCCCCCTCGTGATCTGTATGCTATTAAGGATTG---CATACTTCTGGAAATCCTTAGTGATGCAGAAATTACACTTAATGATATGGCTTTGAAGATAATGAGAAACAGCA---------------------------GAAACT--TTCCATTTT---TTAGAAAAGAATGTTATTGAATTTTCAATGTTTCATTAATTTAATA-T----TACAAGATGGCAAACATCTATCCTTGTT----TTCTTCTATGTTGTTATTTCTGTCTACTGTCAACAATAATCATGCCTTTCTTTTAAAACTGAGAATTTTGCCCAT i loxAfr3.scaffold_13 I 1 C 0 a score=43230.000000 s hg19.chrUn_gl000245 25251 61 + 36651 CAAAATCC--AGTTTAAGCTGAGAAACA----A------AGAACTAAATTTTGC----ATGAGACATTATACA----CTGC s panTro2.chrUn 47421644 61 - 58616431 CAAAATCC--AGTTTAAGCTGAGAAACA----A------AGAACTAAATTTTGC----ATGAGAGATTATACA----CTGC i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 855172 61 - 4212913 CAAAATCC--AGTTTAAGCTGAGAAACA----A------AGAACTAAATTTTGT----ATGAGAGATTATACA----CTGC i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189467339 65 - 189746636 CAAAAGCC--AGTTTAAGCTGAGAAACAAAGGA------AGAACTAAATTTTAC----ATGAGAGGTTATACA----CTGC i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15821057 31 - 24440124 CATAAATCCTAACTTAACCTAGATAACA----A------AG---------------------------------------- i cavPor3.scaffold_34 C 0 I 170 s oryCun2.chr14 141903454 43 + 163896628 CAAAATTC--AACTTAAGCTGG-------------------AAGCAAATTTTGT----ATATGAGATT------------- i oryCun2.chr14 C 0 I 3328 s bosTau4.chr1 138193442 67 - 161106243 AAATATCT--AGTGTAAACTGGGAAACA----AAAAGCTAGAATCGAATCATATGTGAGGGATTGATTATATA-------- i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13373378 63 + 41866177 CAAAATCC--AGTTTAATCTGGGAAAC-----AAAAGCCAGTATCAAAGTATAT-------GGAGATTATATACCAT---- i equCab2.chr26 I 264 I 44 s canFam2.chr31 14123418 63 + 42263495 AAAAATCC--AATTTATGCCAGGAAACA----AAAAGCCAGAATCAAATTGTAT----AGGAGAGATTATACA-------- i canFam2.chr31 C 0 I 4 s loxAfr3.scaffold_13 20631868 67 - 62548349 GAAAATCC--AGTTTAACCTGAGATACA----AAAAACCCTAACCAAATTGTTT----GTAGGAGAGTACATG----ATGT i loxAfr3.scaffold_13 C 0 C 0 a score=202149.000000 s hg19.chrUn_gl000245 25312 192 + 36651 ATAAATATAAAACAGGACCAGAAACAATGGTAGATTAGCAATTTTTAAAAAGACAAAAG------CAGGTTATCA------------------------TCA-AATCAATTG---------------------------------------------------------------------------------------------------------TTACCAACACCCCA--------------------ATTCCACCTCTAGGCCAGAAAATTAGCCACTTACCCACGGGAAAACAATGATTGAAGACAAAGTTCACCAGTGAAAGTTGGTTA---TTTTTTTCCATCC s panTro2.chrUn 47421705 192 - 58616431 ATAAGTATAAAACAGGACCAGAAACAATGGTGGATTAGCAATTTTTAAAAAGACAAAAG------CAGGTTATCA------------------------TCA-AATCAATTG---------------------------------------------------------------------------------------------------------TTACCAACACACCA--------------------ATTCCACCTCTAGGCCAGAAAATTAGCCACTTACCCACGGGAAAACAATGATTGAAGACAAAGTTCACCAGTGAAAGTTGGTTA---TTTTTTTCCATCC i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 855233 193 - 4212913 ATAAGTATAAAACAGGAACAGAAACAATGGTGGATTAGCAATTTTTAAAAAGACCGAAG------CAGGTTATCA------------------------TCA-AATCAATTG---------------------------------------------------------------------------------------------------------TTACCAACACACCA--------------------ATTCCACCTCTAGGCCAGAAAATTAGCCACTTACCCACAGGAAAACAATGATTGAAGACAAAGTTCACCAGTGAAAGTTGGTTA--TTTTTTTTCCACCT i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189467404 192 - 189746636 ATAAGTATAAAACAGGACCAGAAACAATGGTGGATTAGCAATTTTTAAAAAGACAAAAG------CACGTTATCA------------------------TCA-AATCAATTG---------------------------------------------------------------------------------------------------------TTACCAACACACCA--------------------ATTCCACCTCTACGCCAGAAAATTAGCCACTTATCTACAGGAAAACA---ACTGAAGATAAAGTTCACCAGTGAAAGCTGGTTATTTTTTTTTTCCATCC i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141906825 187 + 163896628 ATAAATGT----CATGACTGGGAACAAAGGAGAATTCGAATTTACAAAAAAGAAAAAGT------CAGAATATCA------------------------TCAGAAACAATTA---------------------------------------------------------------------------------------------------------TTACTGTTGTGTC----------------------TTATATTTCCAAACTATAAAACTAACTTTTTACCCACTGAAAACCA-TCACTGAAGAGAA--TTCACCAGTGAAATGTGGTTGTTATTTTTTTACCTCC i oryCun2.chr14 I 3328 C 0 s bosTau4.chr1 138193509 157 - 161106243 ATAAGTAG----CAGGG----------------------A--TACAAAAAAGAAAAAAA------CAGAATGTTA------------------------CCAAAATCAATCA---------------------------------------------------------------------------------------------------------TTACCACAAAAACA--------------------ATTTCAATTCTGTACCATGAAGTTAACCTCTTGTTCACAG--------TCACTGAAGACAGAATTCTTGGGTGAAAGTTGGTTA---TTGTTGTCATTCC i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13373485 189 + 41866177 ATAGGTAG----CAGGACAAGAAACAAAGGTGAGTTAGCA--TAAAAAAAAAAAGACAA--AACCCAGAATACTT------------------------ATC-AATCAATCA---------------------------------------------------------------------------------------------------------TTACCACCACACCA--------------------ATTCCATTTTTATACCACGAAGTTCACCACTTATCCGCAGGAAAACAATCACTGAAGACAGCATTCT-TAGAGAAAGTCACTTA---TTGCTATTCTTCT i equCab2.chr26 I 44 C 0 s canFam2.chr31 14123485 190 + 42263495 AGAGGTTG----CAGGACGTAA---AAAGGGGAATCAACA--TAAAAAAAAAAAAAAAGACAAACTAGAATATTA------------------------ACAGAATCATGCC---------------------------------------------------------------------------------------------------------TTACCACCACACCA--------------------ATTCTCTTTCTATACCATGAGGTTAACCACTTACCCACAGGAAAACAACCACTGAGGACACAATTATCTGGTAAAAATTGGTTA---TTGTTATTCTTGC i canFam2.chr31 I 4 C 0 s loxAfr3.scaffold_13 20631935 338 - 62548349 ATAGGTAG----CAGAACCAGAGACACAGGTGAGTTAGCATTAGTAAAAAAGACAAAAC------TAGGCTATCATACACCCACCACCACATGCtgttgtca-agttgattccaactcatagcaaccctacaggacagagtagaactgccccacagggtttccaaggagcagctggtggattcaaactgccgaccttctcattagcagctgagctcttaaccactgtaccaccagggctccATCAGAATCCATCCCATTTCTACCCCATAAAAGTAACAACTAACCCACAGGAAAATCATCATTGCAGACAGAATCCACAAGTAAAAGTTGGTTA--TTTTTTGTGCTTAC i loxAfr3.scaffold_13 C 0 C 0 e cavPor3.scaffold_34 15821088 170 - 24440124 I a score=314069.000000 s hg19.chrUn_gl000245 25504 218 + 36651 TTGCATCAACTAAAATGATATCTA----CACTTCCTCTT----AACACTTTTCTTACTTTC-AAATATGTGGGTATGCTTCATTAGCTGAGGCCATGTTCCATATGTACATCTGGCTA--CAAGGGAAACTGGGAATGTGAGCCCTGATC----CTAATGTTTGTAGAG-TATTTAGAAGTTTGAGAATTCCCTCCA-AATAA-AGAG-TTTTCTAAAACATTGTTAGACAAAAAGT s panTro2.chrUn 47421897 218 - 58616431 TTGCATCAACTAAAATGATATCTA----CAGTTCCTCTT----AACACTTTTCTTACTTTC-AAATATGTGGGTATGCTTCATTAGCTGAGGCCATGTTCCATATGTACATCTGGCTA--CAAGGGAAACTGGGAATGTGAGCCCTGATC----CTAAAGTTTGTAGAG-TATTTAGAAATTTGACAATTCCCTCCA-AATAA-AGAG-TTTTTAAAAACATTGTTAGACAAAAAGT i panTro2.chrUn C 0 I 21 s ponAbe2.chr21_random 855426 218 - 4212913 TTGCATCAACTAAAATGATATCTA----CAGTTCCTCTT----AACACTTTTCTTACTTTC-AAATATgtgggtatgcttaattagctgaggccatgtttcatatgcccatctggcta--caagggaaactgggaatgtgagCCCTGATC----CTAATGTTTGTAGAG-TATTTAGAAATTTGAGAATTCCCTCTA-AATAA-AGAG-TTTTTTAAAACATTGTTAGACAAAAAGT i ponAbe2.chr21_random C 0 I 21 s rheMac2.chr2 189467596 215 - 189746636 TCACATCCACTAAAATGATCTCTA----CGGTGCATCTT----AACACTTTTCTTACTTTC-AAATATGTCGGTATGCTTAATTAGCTGAGGCCATGTTTCATATGCACATCCGGTTA--CAAGGAAACCTGGGAATTTGAGCCCTGATC----CTAATGTTCGCAGAG-TATTTAGAAATTTGAGAATTCCCTCCA-AATAA-AGAGTTTTTTTTAAACATTGTTAGACAAA---- i rheMac2.chr2 C 0 I 24 s cavPor3.scaffold_34 15821258 214 - 24440124 TTGCATCAACTAAAATGAGAACAAAATATAATACTTTTT----ATCATTATATTTGTATTC-AAATATGTGCATATGACTCATTATCTGTGGACAGAC------TGTACACTTTTCTAGTTATGAGAAACTAGAGATTTGATCTTAA-TT----CTAGAGTTT-CAGAGGAAATAAAAACTTGGGAAATTCTCTAAC-TATAGAAAAG-ATTTTCAAAAGT-TGATATAC---ATTT i cavPor3.scaffold_34 I 170 I 19 s oryCun2.chr14 141907012 209 + 163896628 TTGTATCAGCTAAGATACACACAA---GCAGCACTTTTTTAAAGTCACT-TTTCTATTTTC-AAGTGTATAGATTAGAC-AATGGTCTAATGA------------GCACAGTTGTCTA--TAAGAGAAATAAGGAATATGAACCCTG-TT----CTAATGTTTGCAGAGAGATTCTGAATTTTGAAAGGTCCATGTA-TATAG-GAAG-ATTTTTAAAATTGTACTAGACAAAAGTT i oryCun2.chr14 C 0 I 23 s bosTau4.chr1 138193666 215 - 161106243 AGGTATCAAGTAAAACATTGTCTATGAACAATATCTTTT----ATCACTTTTCTTACTTTC-AAACGTATGGGCATATCTGATTAGCTGAGCCTAAGTTTCATGTGCACATCTGCCTC--CAAGGGATGTTGGTAATTCAAACCTTG-------ATTATATTTACAGAAGGATTGACAACTTGGAAACTTTTTTAAATTTTAG-AAAA-ATTGTTCAAAAT------GTTCAAATGT i bosTau4.chr1 C 0 I 22 s equCab2.chr26 13373674 228 + 41866177 CTGCATCGACTAAAATGATATCTACAGATAGTGcctttt----atcacttttctcactttcaaaatgtgtgggtatatctgattagctgagcctaagtttcatatacacatctgcctc--caagggaaattgggaatttgagccctgatttttactcctgtttacagaggcatttacaacttggaaaagtcctcaaa-tctag-agag-gtttttcaaaAGAAAATAGACAAATAGT i equCab2.chr26 C 0 I 22 s canFam2.chr31 14123675 220 + 42263495 CTGCATCAATTAAAATGATATCTATAAAGAGTGCCTCTT----ATCACTTTTCATACTTTC-AAATgcatgagtatgtctgattagctgaacctaagattcaagtgcacatctgccta--caaaggaaatagaggatttgagccttg-------cttcattttacagaggaattcacagcttgggaaatttcttaaa-tagag-agag-gtttttcaaaagatgagagacagaaagT i canFam2.chr31 C 0 I 22 s loxAfr3.scaffold_13 20632273 215 - 62548349 CTGGAGCACCTAATCTGATATCTACAAACAGTGCCTATT--GTATCATGTTTCATATTTCT-AAGTATgtgagtatgtctgattatctgagcctagattatctatgtgtatctagcta--caagtgaaattggg--------ctctgatt----ctagtgtttgaagagggattcggaactttgaaatttccccaaa-tat---agag-gtttttcaaaaggtgaatgacAcagagt i loxAfr3.scaffold_13 C 0 I 22 a score=65902.000000 s hg19.chrUn_gl000245 25722 44 + 36651 TAGCTCAGGT----CT----AAACCAAATGCAGGG-AAAAAACTATTAACTCT s panTro2.chrUn 47422136 45 - 58616431 TAGCTCAGGT----CT----AACTCAAATGCTGGGAAAAAAACTATTAACTCT i panTro2.chrUn I 21 I 1 s ponAbe2.chr21_random 855665 45 - 4212913 tagctcatgt----ct----aactcaaatgcaggaaaaaaaactataaactct i ponAbe2.chr21_random I 21 I 1 s rheMac2.chr2 189467835 45 - 189746636 TAGCTCATGT----CT----AACTCAAATGCAGAGGAAAAAAACATAAACTCt i rheMac2.chr2 I 24 I 1 s cavPor3.scaffold_34 15821491 48 - 24440124 TAGCTTATAT----CTAATAAACCTGAATTCAAGTGAAAAAATTACAAACT-T i cavPor3.scaffold_34 I 19 I 1 s oryCun2.chr14 141907244 47 + 163896628 AAGGTAACAT----TTACCTAATCCAAAAGTAATTG-AAAAATGATAAGCT-A i oryCun2.chr14 I 23 I 1 s bosTau4.chr1 138193903 48 - 161106243 TAGCTCATATCTGACT----AACTCAAATGCAGATA-AAAAATGATAAACTCT i bosTau4.chr1 I 22 I 4 s equCab2.chr26 13373924 44 + 41866177 TAACTTGTAT----CT----AACTCAGATGCAGATG-AAAAGTTATAAACGCT i equCab2.chr26 I 22 I 4 s canFam2.chr31 14123917 48 + 42263495 CAGCTCACATCTGACT----AACCCAAATGCAGAGG-AAAAATTATAAACTCT i canFam2.chr31 I 22 I 225 s loxAfr3.scaffold_13 20632510 47 - 62548349 tagttcatat----ctgagtaacccgtatgtaaaa--aaaaattataaactct i loxAfr3.scaffold_13 I 22 C 0 a score=60493.000000 s hg19.chrUn_gl000245 25766 54 + 36651 ----AAAAAA--ATTAAATA----CACATTTGATGGTAATG--AGAAACAGAAAACAGGCAG---AAAT s panTro2.chrUn 47422182 54 - 58616431 ----AAAAAA--ATTAAATA----CACATTTGATGGTAATG--AGAAACAGAAAACAGGCAG---AAAT i panTro2.chrUn I 1 C 0 s ponAbe2.chr21_random 855711 54 - 4212913 ----aaaaaa--attaaata----cacatttgatggtgatg--agaaacagaaaacaggcag---aaat i ponAbe2.chr21_random I 1 C 0 s rheMac2.chr2 189467881 52 - 189746636 ----aaaata----tatata----tatatttGATGGTAATG--AGAAACAGAAAATAGGAAG---AAAT i rheMac2.chr2 I 1 C 0 s cavPor3.scaffold_34 15821540 54 - 24440124 ----AACTTT--TTTAAAAA----TGCATTTCATGGTAGTA--GAGAACAGAAAATAGGCAT---AAAA i cavPor3.scaffold_34 I 1 C 0 s oryCun2.chr14 141907292 58 + 163896628 ----AAAATTGCTTTAGAAA----TACATTTGATGGTACT---GAAAACAGAAAATGACCACCAAAAAA i oryCun2.chr14 I 1 C 0 s bosTau4.chr1 138193955 57 - 161106243 ----AAACCA--TTTAAAAA---ACACATTTGATGCAACAGAATGAAAAAGAAAATAGGTAG---AGAT i bosTau4.chr1 I 4 I 2154 s equCab2.chr26 13373972 50 + 41866177 ----AAAACA--TTAAAAAAATCCCACATTTGATGACAAAG----------AAAACAGTCAG---AAAT i equCab2.chr26 I 4 C 0 s canFam2.chr31 14124190 50 + 42263495 ----aaaa-----taaaatacacacatatttgatgttatgg------gggaaaaataggcag---aaa- i canFam2.chr31 I 225 C 0 s loxAfr3.scaffold_13 20632557 58 - 62548349 acatgatata--ttaaataa----cacatttgaagatactg--aacaacagaaaacaggcag---aagt i loxAfr3.scaffold_13 C 0 C 0 a score=80469.000000 s hg19.chrUn_gl000245 25820 61 + 36651 AGTAGAATACTCCACTAATGATGAAGTATTTGACCATTGAATAAAGAAAATTGCAATGATT s panTro2.chrUn 47422236 61 - 58616431 AGTAGAATATTCAACCACTGATGAAGTATTTGACCATTGAATAAAGAAAATTGCAATGATT i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 855765 60 - 4212913 actagaatattcaac-actgatgaagtatttgaccattgaataaagaaaattgcaatgatt i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189467933 61 - 189746636 AGTAGAATATTCAACCACTGATGAAGTATTTGACCATTGAATAAAGAAAATTGCAATGATT i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15821594 61 - 24440124 GTTAGGATATTTGATCACTGACAGACTATCTGATCATTGAAAGAAAATGATTACAGTGGTT i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141907350 57 + 163896628 AATAGACTATTTGGTCAATGAGAGAGCAT-TAACCACTGAAAGATGAAGTTCC---TGGTT i oryCun2.chr14 C 0 C 0 s canFam2.chr31 14124240 60 + 42263495 atcagaatattcatccaatgactgaatacttgaccatcaaaggaagataactgctctga-t i canFam2.chr31 C 0 C 0 s equCab2.chr26 13374022 61 + 41866177 ATCAAAGTATTTGACCATTGACAGAGTATTCGACCATCGAAAGAAGATAACTGCATTGGTT i equCab2.chr26 C 0 C 0 s loxAfr3.scaffold_13 20632615 41 - 62548349 -------------------gtcagggtatttgacaactgaaagaagaaaactacactggt- i loxAfr3.scaffold_13 C 0 C 0 e bosTau4.chr1 138194012 2154 - 161106243 I a score=51752.000000 s hg19.chrUn_gl000245 25881 30 + 36651 TAAATTTGCATCAAGGCAACTTCA-CACCTG s panTro2.chrUn 47422297 30 - 58616431 TACATTTGCATCAATGCAACTTCA-CACCTG i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 855825 30 - 4212913 taaatttgcatcaatgcaacttca-cacctg i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189467994 30 - 189746636 TAAATTTGCATTAATGCAACTTTA-CACCTG i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15821655 30 - 24440124 TAAGGTCACGCTGATGCAATTTCA-TACCAG i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141907407 28 + 163896628 TAAG--TATGCTTTAGAAGTTTTC-TATCTG i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138196166 31 - 161106243 TAAGTTTGCATTAATTCAGTTTTATCATCTA i bosTau4.chr1 I 2154 C 0 s equCab2.chr26 13374083 30 + 41866177 TAAGCTTGCGTTCATACAGCTTTA-CACCTG i equCab2.chr26 C 0 I 210 s canFam2.chr31 14124300 30 + 42263495 taagtgtgctttactgcagctttc-tacctg i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20632656 30 - 62548349 taggtttgccttgacatagcttta-cacctt i loxAfr3.scaffold_13 C 0 C 0 a score=519625.000000 s hg19.chrUn_gl000245 25911 461 + 36651 ATGACGCTTCCCAGTCTGTGCAAAATTAGATGTCTACGAGTAAAGCGGTGA-GTTTTACTAGCTTGAGGAATAAGAGCACAGAGTTCCAGGCTGACAGAAAAGA-----GGAACTG----GGAAATTTGAATGACATGGGAGGACATCTCAC----ACAACTGAAAGTCACAGAGGAGAATATCAC--AGAGTAAAAATCTAAAATCAGCACTTCAACTTCATTCAAATATAT-G-ATGGCTGCTACATTTCACATTCATAAAAGGAGACTCCA-TAGAATCCAGCAGAAAACAACAGCTAAATTGCTAGTACAGAGCAGAGATTTC------------------------------------------------------------------------AA---------------------CCATTGCATATAGCTCAGGAGTGAAAGTTTGGTGTTTGACTACGGAAAGAAGACTAATGTTAGAAAAGAGTcattcttcaaaggaaaataaacaaaccta-------tctctacaa--------------------------------------------------aatatcatacacataatctaacatataatt-taatctgcctag s panTro2.chrUn 47422327 461 - 58616431 CTGACACTTCCCAGTCTGTGCAAAATTAGATGTCTATGAGTAAAGCGGTGA-GTTTTACTAGCTTGAGGAATAACAGCACAGAGTTCCAGGCTGACAGAAAAGA-----AGAACTG----GGAAATTTGAATGACATGGGAGGAAATCTCAC----ACAACTGAAAGTCACAGAGGAGAATGTCAC--AGAGTAAAAATCTAAAATCAGCACTTAAACTTCATTCAGATATAT-G-ATGGCTGCTACATTTCACATTCATAAAAAGAGACTCCA-TAGAATCCAGCAGAAAACAACAGCTAAATTGCTAGTACAGAGCAGAGATTTC------------------------------------------------------------------------AA---------------------CCATTGCATATAGCTCAGGAGTGAAAGTTTGGTGTTTGAATACAGAAAGAAGACTAATGTTAGAAAAGAGTcactcttcaaaggaaaataaaagaaccta-------tctctacaa--------------------------------------------------aatatcatacacataatctaacatataatt-taacctgcctag i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 855855 458 - 4212913 atgacactccctggtctgtgcaaaattagatgtctacaagtaaagtggtga-gttttactagcttgaggaataagagcacagagttccaggcTGACAGAAAAGA-----AGAACTG----GGAAATTTGTATGACATGGGAGGAAATCTCAC----ACAACTGAAAGTCACAGAGGAGAATGTCAC--AGAGTAAAAATCTAAAATCAGCACTTAAACTTCATTCAGATATAC-G-ATGGCTGCTACATTTCACATTCATAAAAAGAGACTCCA-TAGAATCCAGAAGAAAACAACAGCTAAATTGCTAGTACAGAGCAGAGATTTC------------------------------------------------------------------------AA---------------------CCATTGCATATAGCTCAGGAGTGAAAGTTTGGTGTTTGACTACAGA---AAGACTAATGTTAGAAAAGAGTcactcttcaaaggaaaataaaataaccta-------tctctacaa--------------------------------------------------aatatcatccacataatctaacatataatt-taacctgcctaa i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189468024 461 - 189746636 ATGACACTCCCCGGGCTGTGCAAAATTGGATGTCTACAAGTAAAGCGGTGA-GTTTTACTGGTTTGAGGAATAAGAGTACAGACTTCCAAGCTGACACAAAAGA-----AGAACTG----GGAAATTTGAGTGACATGGGAGGAAATTTCAC----ACAAGGGAAAGTCACAGAGGAGACTGTCAC--TGAGTAAAAATCTAAAATCAGCACTTAAACTTCATTCAGATATAT-G-ATGGCTGCTACATTGCACATTCATAAAAAGAGACTCCA-TAGAATCCAGCGGAAAACAACAGCTAAATTGCTAGTACAGAGCAGAGATTTC------------------------------------------------------------------------AA---------------------CCACTGCATGTAGCTCAGGAGTGGAAATTTGGTGTTTGACTACAGAAAGAAGACTAATGTTAGAACAGAGTcactcttcaaaggaaaataaaagaaccta-------tctctacaa--------------------------------------------------aatatcatccacataatctaacatataatt-taacatgcctag i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15821685 444 - 24440124 ATGAAACTT---------CGCATAATTGCAC-TGTGCAACTAAATCAGCAA-ATTCTACTTGCTTGAAGAGTCATAGTACAAAGTTGTAGACAGACAACTTGGAAATTGAGAGATGTAGAAGAGACTCCAACA----CAAAAAAT---------------------ATCACAAAGGAGAGTATCATAAAGATTAAAGATCT-AATGCTGCATATAAACTCCTTGGATATGTATGG-GTAGTCTCTAAATTACTTATGAATATAA-GAGACTTGA-GATGCTCCTACAGAAAGCAATGACAGGAGAACTAGAAAAGGGTAGAAATTTC------------------------------------------------------------------------AG---------------------CTTCTGCACACCACAGAGGTGTGATAATTTGGTGTTTGTATACAAAAATATAAATAATGTTACagaaaagtcact--tcaaagaaaaataacaagacccagtcagtgtctctacaa--------------------------------------------------attattctccac-tagttcagcaaattata-tgcaatggctag i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141907435 431 + 163896628 TTGATACTC---AGTCTATGTACAATTGGATGTTGGTGAATAAAGCTGTAA-Attttactagcttgaagaataagagtacaaaaatctgggcagatagaataga-----agagttg-----gaaacttgagtg----ggaagga----------------------atctcataggtgaaagtcaccgagagtc---actg-aaacctgtatgtaaaccccagtgagatg-gtgg-acggttgctaaactgcacaggtactgaa-gagactccatgggtctccagcagaaaacaaaG-CTGGAAGACTA-AAACGAACAGATATTTC------------------------------------------------------------------------AT---------------------TGACAGCACACCACAAAGAAGTGAAAGTTTGATATTTCAGTACAAAAAGATGAATAACGTCAGAAAAGAGTCACTCGTCAAAGGAAAATAACA------ACTCAGAGTTTCTATAA--------------------------------------------------GACATCATCATG-TAATTTTGTAGACAATT-TAAGATGGCTAG i oryCun2.chr14 C 0 I 8974 s bosTau4.chr1 138196197 441 - 161106243 ATGATGCTCTGCAATCTGTGGAGAACTGAATGACTATA--TGAAGCAGCAATGTTTTTCCAGTTTGAGGA--ATAAGCACATAGTTCCAGATTAA-AAAACAGA-----AGAGCTG----GGAAA-TTGAATGGGGTGGGAGAGGATACCAT----GCAAATGAAAGTCACAAAGGAGAA------------TGAAGATTTGAACTATGTATCTAAGCACCATTCAAAT-TAT-GAGTAACTTATAAATTGCACACCCATAGAG-GAAATGCCATTAGACCCCAGCAGAAACCAATAGCTCAGAAAT-----TAGAGCAGAGACTCC------------------------------------------------------------------------AATATTAC---------------CCACTACA--------GAGGAACGAAATCTGATGTTTGAGTACAGATAGATGGATAATACTAGAAAAGGATcactcttc-aaggaaaataacagaaccca----gagtctctacaa--------------------------------------------------tatataagccacaaaatctagtatattact-taaaataaccaa i bosTau4.chr1 C 0 C 0 s canFam2.chr31 14124330 556 + 42263495 atga--cactgcagtct-tgaagaactggatggctacaactggagcagcaattttattccagtgtgaggagtatgagcacagagttccaagctaacaaaacaga-----agaactg----ggaaa-ttgagtggagtgggagagaatcccatacaagtaagtgaaagtcatagaagaaaatgtcacagatggtgaagatctgaaatattcatataaactccatccagat-tac-g-gtgactattaagttgcacatgcattgag-gatactcca-tagatcccagcagaaagcaatatctgaGGGACAGGCATAGAGCATAGATTTCATCCACCATTCAGCACTGTTACTACAATGAGTTACTATGATTTTTATAATCAGGatttaaaataattttttaaatCTCACTAATTCAAACAAATTCCATTCCATCTCACATGAAGTGAGAagtttggtgtttgagtacagatagatgagtaatactagaaaaag-tcactcctcaaagaaaaataacaggactca----gagtctctacaa--------------------------------------------------tatatcagcc-ccaaatccagtatataatt-aaaaacagctat i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20632686 490 - 62548349 agagcacttctcagtctgcgcagagtggaatggctatgactgaaacagcaa-attttaccagcttgaaggatgtgagtacagagttccaggctgaca-----ga-----agagctg----gaaaa-ttgaggggggcaggagggaattacat----aaaagtgaaagtcacagaggggaAAGTCAC--AGAGTAGAGCCCAACAATTGGC---------------AAACATTT-G-GTGACTCCTGAATTGCACAGGTATAGAA-GTAACGCCC-TGGTGTCTAGCAGAAAGCAACAGCTTGAGGACTAGAATAGAGC--AAGTTTC------------------------------------------------------------------------AA---------------------CTACTGCACACAACAGTGAAGTAAAAGGTTAGTGTTTGAGTATAAAAAAAGGAAC-CTGCTAGAAAAGAATCACTTAAAAAAAAAAAACAAAACAATCTA----GAGTGTCTACAATGTCccaagcctaaggccatcgagtagattctgactcatagcaaccctagagTATAatgcacaaaacccagtgtacaattaaaaaattattag i loxAfr3.scaffold_13 C 0 C 0 e equCab2.chr26 13374113 210 + 41866177 I a score=102109.000000 s hg19.chrUn_gl000245 26372 92 + 36651 acat-------agaaccaggaaaatatgacaca----taacaaaaaaagtaaacaatggattaagacattgaaatggcccacacgctggaattagaatataag s panTro2.chrUn 47422788 92 - 58616431 acat-------agaaccaggaaaatatgacaca----taacataaaaagtaaacaatggattaagacattgaaatggcccacatgctggaattagaagataag i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 856313 91 - 4212913 acat-------agaaccagg-aaatatgacgca----taagaaaaaaagtaaacaatggattaagacattgaaatggccctcatgctgggattagaagataag i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189468485 91 - 189746636 acat-------agaaccaggaaaatataattta----taaga-aaaaagtaaacaatggattaagacattgaaatagcccacatgctgggattagaagataag i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15822129 84 - 24440124 acat-------aaaa-aatgaaaacatgacaca----gaaaaacaaaagcacata------tagaatcttgagat-gtccatgtgttggaattagaagccaaa i cavPor3.scaffold_34 C 0 C 0 s bosTau4.chr1 138196638 90 - 161106243 atgt----aaaagaaattggaaaatatatttta--------a-caaaagcagacagtagaaagagacattgagatggtgtacatgttggaatttgaacacaag i bosTau4.chr1 C 0 C 0 s canFam2.chr31 14124886 97 + 42263495 gcattaaaaaaaaatacaggaaaatataacaca----tagga-aaaaagtagacaatggaaagacacgttgaggtggccta-atttgggaattagaaggcaag i canFam2.chr31 C 0 I 209 s loxAfr3.scaffold_13 20633176 100 - 62548349 acat--aaaaaagaaacaagaaaatatgacccacagtcaaga-aaaaagtaggcaatagaaacagacatcgagatggcctagatgtttgaattaggagacaag i loxAfr3.scaffold_13 C 0 C 0 e oryCun2.chr14 141907866 8974 + 163896628 I e equCab2.chr26 13374113 210 + 41866177 I a score=305335.000000 s hg19.chrUn_gl000245 26464 274 + 36651 aaatttaaaataagctattataagcatattcaaggatttaagga--atagatggtcataagagggaatatatggagaatctcaacag-agaagtaaaaat-------gataaagagataataggac--------aaattttagaactgagagacagagtatcttatataaaaatgtcattttatgtacataccagtaaattaaagatggcacaaaaaattatcagtgcacttaaaaacagatcaagaaca--atttcccaatacagtt---aatacaaacgaagaaaaat-aataaaa s panTro2.chrUn 47422880 270 - 58616431 aaatttaaaatcagctattataagcatattcaaggatttaagga--atagatggtcataagagggaatatatgaagaatctcaacag-agaagtaaaaat-------gataaagagataataggac--------aaattttagaactgagagacagaatatcttatataaaagtgtgattttatgcacattccagtaaattaaagatggcagaaaaaactatcagtgcacttaaaaatagatcaagaaca--atttcccaatacagtt---aatacaaa-ggagaaa----aataaaa i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 856404 277 - 4212913 aaatttaaaataagctattataagcatattcaaggatttaagga--atagatggtcataagagggaacatatggagaatctcaacag-ggaagtaaaaat-------gataaagaaataataggac--------aaattttagaactgaaggacagaatatcttatagaaaaatgtcattgtatgcacataccagtaaattaaagatggcagaaaaaactatcagtgcacttaaaaacagatcaaggaca--atttcccaatacagttaagaatacagaggaagaaaaat-aataaaa i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189468576 277 - 189746636 aaatttaaaataagctattataagcatcttcaaggatttaagaa--atagatggtcataagagtgaatatatggagaatcttgacaa-agaagcaaaaac-------tataaagaaataatggaac--------aaaatttagaactgagggacagaatatcttatataaaaatgccattgtatgcacataccagtaaattaaagatggcagaaaaaactatcagtacacttaaaaacagatcaagaaca--atttcccaatacagttaagaatacagaggaagaaaaat-aataaat i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15822213 263 - 24440124 gagtgtaagtcag--tattataaatatgatcaaggattaaagga--gtagatggtcaagaggatgaaaatatggggaatctcagaagcagaaataaaaat-------tctaa----ataatgaaac--------taaaactaaaactgaggaactcagtatctgatatgaaagtgtcactaacttggcttagcaataaatcagagatgacaggacaaaataata-tacaattgaagccatatcaagcata--atatcgcattataa-----aggatagagaaggaaa----aaTGAAG i cavPor3.scaffold_34 C 0 C 0 s bosTau4.chr1 138196728 266 - 161106243 aactttaaattaa-ctattataagtatgttcaa-aattaaagga--atgtgttgtcatacatatacatatatggggaatttcaggca-agaaataaaaac-------tgtggagaaataaggaaata------taagttctaaaactgaggaatacaatatctgatatgaaaattttacttaatgggcttaccag--------agatatcagaagaaaatatcagtaaacttgaagacaagtcaagagca---atttccaatatgaag---aatacagaggaaaaaaTACTAATTAAA i bosTau4.chr1 C 0 I 2796 s canFam2.chr31 14125192 257 + 42263495 gattgtatgttag-ctagtataagtaaactcaagaattaaagaa--atagatggtcatacatgtgaatatatggggaatttcaacaa-gggaataaaaac-------aac-aagaaaaaaggaaata------gaaatgctagcactgatgaatataatatttaatatgaaaaatttactagataggcttaccag--------atgtgatagaaaaaagtatcaataaatctgaagata----aagaacattttttttcaaaatgaag---aatacagaggaaaaaatat-------- i canFam2.chr31 I 209 I 1887 s loxAfr3.scaffold_13 20633276 290 - 62548349 aactttaaatcag-ctattataaatatgttcaaggattaaaagaacatagataggcataaatatgaacatataggaaatctcagcag-aaaaaggaacacctatatatataaataaaaaaaaagaccaaaaatgaaattctagaatgaaataatgtaatacctgatatgaaaagtttacttgactggcttaacagtagcttagagatgacagaagaaaatgtcagtaaacttgaagacagagcaatagaa--atgatccaatatgaaa---aatacagaggggaaaaaat-aataaaa i loxAfr3.scaffold_13 C 0 C 0 e oryCun2.chr14 141907866 8974 + 163896628 I e equCab2.chr26 13374113 210 + 41866177 I a score=28887.000000 s hg19.chrUn_gl000245 26738 56 + 36651 atagggc---------------------------cagtctagcactaatataattggagtcct--agaaagagtagag---aagtaaa s panTro2.chrUn 47423150 56 - 58616431 atagggc---------------------------cagtctagcactaatataattggactcct--agaaagagtagag---aagaaaa i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 856681 59 - 4212913 atagggc---------------------------cagtctagaactaatataattggagtcct--agaaagagtagagaacaagaaaa i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189468853 59 - 189746636 ataggac---------------------------cagtatagaactaacataattggagtact--agaaagagtagagaaggagaaaa i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15822476 40 - 24440124 TTAGTGT---------------------------AATCCt---------gtaaatggagaccc--agaaag----------gggaaag i cavPor3.scaffold_34 C 0 C 0 s loxAfr3.scaffold_13 20633566 85 - 62548349 atagggccacggtgactatggaaacaataacaagcagtctagcagtaatgttattggactctcaAaaaaagagtaaaa---cagtaaa i loxAfr3.scaffold_13 C 0 I 2080 e bosTau4.chr1 138196994 2796 - 161106243 I e oryCun2.chr14 141907866 8974 + 163896628 I e canFam2.chr31 14125449 1887 + 42263495 I e equCab2.chr26 13374113 210 + 41866177 I a score=143556.000000 s hg19.chrUn_gl000245 26794 245 + 36651 tgagacagaaaaagctatttgaaaaagtaaagaccaaaagttttcctaattgtc--agcatatatcaacttacaggtttaagaaactcaaaga--------------------------acagaataaaaataaagagaaccaaatgtagacataccatagtcaaaccactgggcaaaaaaaagagtaaatcttgaaagta--gctaaagggagggagaaaataatttacatccgtggaaacaaatagacagatgacctatcatcagaaatgaca-------------------------- s panTro2.chrUn 47423206 244 - 58616431 tgagacagaaaaagctgtttgaaaaagtaaagaccaaaagttttcctaattgtc--agcatatatcaacttacaggtttaagaaactcaaaga--------------------------acagaataaaaataaagacaaccaaatgtagacatgccatagtcaaaccactaggc-aaaaaaagagtaaatcttgaaagta--gctaaagggagggagaaaataatttacatacgtggaaacaaatagacagatgacctgtcatcagaaatgaca-------------------------- i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 856740 242 - 4212913 tgagacagaaaaagctatttgaaaaagtaaagaccaaaagttttcctaattgtc--agcatatatcaacttacaggtttaagaaactcaaaga--------------------------acagaataaaa--aaagagaacgaaatgtagacataccatagtcaaaccactgggc-aaaaaaacagtaaatcttgaaagta--gctaaagggagggagaaaataatttacatacatggaaacaaatagacagatgacctgtcatcagaaatgaca-------------------------- i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189468912 244 - 189746636 tgagacagaaaaagctatttgaaaaagtaaagaccaacagttttcctaattgtc--agcatatatcaacttacagattcaagaaactcgaaga--------------------------acagaataaaaataaagagaaccaaatgtagacataccatagtcaaaccactgggc-aaaaaaagagtaaatcttgaaagta--gctaaagggatagagaaaataatttacatacatggaaacaaatagagagatgacctgtcatcagaaaTGACA-------------------------- i rheMac2.chr2 C 0 I 499 s cavPor3.scaffold_34 15822516 292 - 24440124 tgagatggaaaaa---aattgagaatgtataatccaaaa--tttcccaaatggcagagaaaatattaatttatagattcaagaaaataagtgaaaaagtagaaaacacatcaactctatataggacaaaaatgaagaaaac-aaatgtagccatatcagagtcaaagcacaag---tgagacggattgaatgtagaaagcattgttgatcgaaaagtgaaaacaaattatataaataggaacaaaagtaaaaatgacagttgatttcagttgacttccgtataaaatcaatagagcaaata i cavPor3.scaffold_34 C 0 C 0 e bosTau4.chr1 138196994 2796 - 161106243 I e loxAfr3.scaffold_13 20633651 2080 - 62548349 I e oryCun2.chr14 141907866 8974 + 163896628 I e canFam2.chr31 14125449 1887 + 42263495 I e equCab2.chr26 13374113 210 + 41866177 I a score=30511.000000 s hg19.chrUn_gl000245 27039 106 + 36651 ctttaaaaagcaatgaaactacatcttc------aaaagaaaa--ctgtcaactccaaattctataactagataaagtaattcttgagaaaagaaagatttattcagataaaag s ponAbe2.chr21_random 856982 114 - 4212913 gtttaaaaagcaatgaaactacatcttcaaaataaaaaaaaaaacctgtcaactccaaattctataactagaaaaagtcattgttgagaaaataaagatttaatcagataaaag i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47423450 112 - 58616431 ctttaaaaagcaatgaaactacatcttcaaaataaaaaaaaaa--ctgtcaactccaaattctataactagaaaaagtaattcttgagaaaataaagatttattcagataaaag i panTro2.chrUn C 0 C 0 s cavPor3.scaffold_34 15822808 79 - 24440124 ctttaaaattcaaagaaagaatgccttt--------------------ccaactctaaattctata-------------tTTCTTTCCAAaat--agatttattcatataaaag i cavPor3.scaffold_34 C 0 I 8902 e bosTau4.chr1 138196994 2796 - 161106243 I e loxAfr3.scaffold_13 20633651 2080 - 62548349 I e oryCun2.chr14 141907866 8974 + 163896628 I e canFam2.chr31 14125449 1887 + 42263495 I e equCab2.chr26 13374113 210 + 41866177 I e rheMac2.chr2 189469156 499 - 189746636 I a score=201377.000000 s hg19.chrUn_gl000245 27145 817 + 36651 aaagcttcaaacaattgtcattagcagaccaagatacaagaaatgcaaacggaaattttttaggctaaagaaagataacaacagacggaaattctgacctacaggaagcaaggagaagctctaggaatggcatgtgcataaacgtgaaaaactaaggctttttt-ttttagttttataacaaacaactgatgctttgaataaaaaattaagtgtactattgataatgtgt-----gtaaaatattctaaattaatagctctgacaggagactaaacgcaacaattttgccgcaacttttccttatgttacatgaaaacgctgactattaacactaagtggactgcgataagcccaggatgtttattataatccctagagaaccaccacattatatgaagatattcttctaaaatgccaataaaggaattaaaatggaacgctgaatattgttcagttaatataaaaaggcatgaaagaa-----agaggagcaaaaaatgatggagcaaatagaacataagagcaaaataggctgggcgcagtggctca-gcctgtaatcccagcactttgggaggccgaggcgggtggatcacgaggtcaggagatcgagaccatcctggctaacacggtgaaacgccgtctctactaaaaatac-aaaaattagccgggcatggcggcgggcacctgtagtaccagctactccggatgctgaggcaggaaaatggcgtgaacccaggaggcagagcttgcagtgagccgagatcccgccactgcactccagcctgggtgacagggccagactccgtctcaaaaaaaaaaaaaaaaaa---------------------a s ponAbe2.chr21_random 857096 826 - 4212913 aaagcttcgaatatttgtcattagcagacctaaatacaagaaatgcaaacggaaatgttttaggctaaagaaagat---aacagatggaaattcggacctacaggaagcaaggagaagctctaggaatgccaagtgcataaacatgaaaaattaaggcttttttcttttagttttataacaaacaactgatggtttaaataaaaaattaagtgtactattgataatgtatgtagagtaaaatattctaagttaatagctctgacaggagactaaacgcaacaatcttgctgcaacatttcttcatgttacatgaaaacattgactattaacactaattgcactgcgataag-ccaggatgcttattataatccctagagaaccaccagattatatgaagatattcttctaaaatgccaataaaggaattaaaatggaacgctgaatattgttcagttggtataaaaaggcatgaaagaaagaacagaggagcaaaaaatgatggaacaaatagaacataagagcaaaataggccgggtgcagtggctcacgcctgtcatcccagcactttgggaggccgaggcgggtggatcacgaggtcaggagatcgagaccatcctggctaacacggtgaaaccctgtctctactaaaaatacaaaaaattacccgggtgtggtggc-ggcgcctgtagtcccagctactcgggaggctgaggcaggagaatggcgtgaacccgggaggcagagcttgcagtgagctgggatcgcaccactgcactccagcctgggtgacagagcgagactccatctcaaaaaaaaaaaaaagaaag--------------------c i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47423562 849 - 58616431 aaagcttcgaacaattgtcattagcagacctagatacaagaaatgcaaacggaaattttttagactaaagaaagataacaacagatggaaattctgacctacaggaagcaaggagaatctctaggaatggcatgtgcataaacatgaaaaactaaggcttttttcttttagttttataacaaacaactgatggtttaaataaaaaattaagagtactattgataatatatgtagagtaaaatattctaaattaatagctctgacaggagactaaacgcaacaattttgccgcaacttttctttatgttacatgaaaacgttgactattaacagtaagtggactgcgataagcccaggatgtttattataatccctagagaaccaccacattatatgaagatattcttctaaaatgccaataaaggaattaaaatggaaagctgaatattgttcagttaatataaaaaggcatgaaagaaagaacagaggagcaaaaaatgatggaacaaatagaacataagagcaaaataggctgggcgcggtggctca-gcctgtaatcccagcactttgggaggccgaggcgggtggatcacgaggtcaggagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaatac-aaaaattagccgggcatagtggcgggcgcttgtagtcccagctactccggatgctgaggcaggaaaatggcgtgaacccgggaggcggagcttgcagtgagccgagatcccgccactgcactccagcctgggtgacagggccagactccgtctcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagca i panTro2.chrUn C 0 C 0 e bosTau4.chr1 138196994 2796 - 161106243 I e loxAfr3.scaffold_13 20633651 2080 - 62548349 I e oryCun2.chr14 141907866 8974 + 163896628 I e canFam2.chr31 14125449 1887 + 42263495 I e equCab2.chr26 13374113 210 + 41866177 I e rheMac2.chr2 189469156 499 - 189746636 I e cavPor3.scaffold_34 15822887 8902 - 24440124 I a score=942710.000000 s hg19.chrUn_gl000245 27962 1960 + 36651 aaaatagtaggcttaaatccaaccttttcagtaattatttcaaatgtaatttaaatactccaaataaaacacagattgtcaaactggataataaaagtacctataagagatgcatgccaaatattatggtatagataagttgagagtaaaataatttccaagtataccaaggaaacaacaaggacaagaaatcttatgtggctatattaatataagaaaaagtagacctccaaacgagcaatattacaacagacagctatttcataatgacaaaatgtcaagtaattatgaagacataatgctgtattg----ctgacagaataactaaagaaaattaagataaaataattttgacaacagcttgacctaatcgatattgaccaagacaatagaatatatgttctattatgctacacatgaaacatttatcaataggctatagaccacaaaatatctctcaagaagtttcaaaacactgtaatcatggaaagtatgctttctgaccataatgaaaatgagttgaaatgggtaaaaacaagctacccaggaaagtctacactattggaagatttaaatacaccttaaaatgccctttagctcaatgaagaaatcataagaaacacctttaaatacattgaactgaatacaaataaaaatatactatatcaaaaggtatgggataaagttaagcagacccagagtaaattttttgtataaatgcttattctagaaaagagaagttcaaaacaagtgaactaa-tttctaccttaaaaagaaaatctaaaacaagagagcaaattaagtccaaaacaagtagaggaaaggaaataaaacagaaattagaaatcaatgagacagaaaacagaaacaggagaaaatcaacatggccaaaagttagttctgtgagaaagaaagaaaacgcaaattatacatatcagggattaatgagattgtacagttgtagacacaagagactttaacaagataatggaatattgtgaaacattatatacaaattttcattacttggatgaaagggtgacttccttg--aaaaaaacttataaaaaatttcacaagatttaatggaacataggaagtaattgacatttattaaagtaattaaattaattgtaaaatacctgcacataaaaacataaaattaaat-aaataaaaaaataagcaaaccccagatctaaagaatttcactggtgaattctttcaaacgttttaaa--aaaataaaatttttaaattatttcagaaataaagaagggggaaattccaaacttgttttatgagtcagaatcctgataccaaaaT--TACAAAACCTAGGAATGCAAAATTGACTTCAACTTAAAGAgctatcaccattctaatctgtgattctaatgaatttggctatcttagatactttatacaagtggaatcatacagtttgtccttctgtgactgatttactttacttagcattaatgtcctctaggttcatccatgttgcatattgatgggctttctt-gttttaaagctgaataatattccgttgtatgaatataccacattttctttatcttttcatctgccaatagacattaaccttattcccacattttaattagtgtaaataatgctgcaatgagcctgagaatcatcccaatctccattctttcagataaataacctgaagtgagactactagatcatatgctagttctactttcttaatttatttgaggaaccaccgtactgttttccatagaggatgcacagttttactttcccagaaacactgtagaagtgttccaatttctcc---ccattgttaacactcgttatctttttcttttaataagaccattctaaagggcttgaggcaa-tatctctttgtggttttgatttgcatttccc---tgattagtgatgctgagcatttttttcatgtatctgttggtcatgtggatattttctttggaga s rheMac2.chr2 189469655 1958 - 189746636 aaaatagtaagcttaaatccaaccttatcaataattatttcaaatgtaatttaaacactccaaataaaacacagattgtccagctggataataaaagtacctataagagttgcatggcaaatattatggtacagataagttgagagtaa---aatttccaaatataccatagaaacaacaatcacaagaaatcttatgtggccatattaatataagaaaacatagatctccaaacaagcaatattacgccagaaggctatttcataatgataaaatgtcaagtagttatgaagacataaTGCTATATTGCtaactgatagaataactaaagaaagttaagatgaaataattttgacaacagcttgaccgaatcaatattgaccaagactgtagaatatatgttctattatactacacgtgaaacatttatcagtagactatagaccacaaaatatctctcaagaagtttcaaaacact----ttatagaaagtatgctttctgaccataatgaaaatgagttgaaatgggt-aaaacaagctgtccagaaaagtctacactattgaaagatttaaatacaccttaaaatgccctttagctcaaggaagaaatcataagaaacaccttaaaatacattgaactgaatacaaataaaaatatactatatcaaaatgtgtgggataaagttaagcaaacctagaataaattttttgtataaatacttgttctaaaaaagagaagttcaaaacaaatgaactaattttctaccttaaaaagaaaatctaaaacaagagagcaaattaagcccaaaacaagtagaagaaaggaaataaaacagaaattagaaatcaatgagacagaaaacagacattggggaaaattaacatggccaaaa-ttagttctgtgag--aaaaagaaaatgcaaattacaaatatcagggactaatgagattgtgcagctgtagacacaagagacactaacaagataatggaatattgtgaaacattttatagcaattctcattacttggatgaaagggtcaattccttgaaaaaaaaacttacaaaaaacctcacaagactaaatggaatattggaagtaactg----ttattaaagtaattaaattaattgtcaaatacctgcacataaaaacataaaactaaagaaaatttaaaaataaggaaactccacatccaaagagttttgctggcaaattctttcaaacattaaaaaataaaataaaatttctaaattatttcagaaataaagaagggggaaatgccaaacttgttttatgagtcagaatcctgaaaccaaaactttacaaaACCCAGGAAGGCAAAATCGATTTCCACTTAAAGAgctatcaccattctaatctgtgattctaatgaatttggctatcttagatacttcatacaagtggaatcatacagtttgtccttctgggactgatttactctacttagcattaatgtcctccaggttcatccatgctgcatattgcagggctttcttctttttaaagctgaataatattccattgtatgaatatactaca-----tttatctattcatctgccaatagacattaaccttatttccacattttgaatagtgtaaataatgctgcaatgagcctgagaatcatcccaatttcaattatttcagataaataacctgaagtgagattgctagatcatacagtagttctactttgtt-atttttttgaggaaccaccatactgttttccatagaggctgcacagttttacattcccagaaacactgtacaagtgttccaatttctccccaccattgttaacactcattatctttttcttttaataagaccagtctaacaggtttgaggcaattatctcttcgtggttttgatttgcatttccctgatgattagtgatgttgagcattg-tttcatgtacctgttggtcatttggatattttctttggaga i rheMac2.chr2 I 499 C 0 s ponAbe2.chr21_random 857922 1957 - 4212913 aaaatagtaggcttaaatccaaccttatcaataattatttcaaatgtaatttaaatactccaaataaaacacagattgtccaactggataataaaagtacctataagagatgcatgccaaatataatggtatagataagttgagagtaaaataatttccaagtttaccatggaaacaacaagcacaagaaatattatgtggctatattaatctaagaagaagtagacctccaaacaagcaatattacaacagaaagctatttcataatgataaaatgtcaagtaattatgaagacataatgctatattgctaactgatagaataattaaagaaagttaagataaaataattttgacaacaacttgacctaatcgatattgaccaagacgatagaatatatcttctattatgcgacacatgacacatttatcaatagactatagaccacaaaatatctctcaagaagtttcaaaacactgtaatcatagtaagtatgctttctgaccataatgaaaatgagttgaaatgggtaaaaacaagctatccaggaaagtccacagtattggaagatttaaatacaccttaaaatgccctttagctcaaggaagaaatcataagaaacaccttaaaatacattgaactgaatacaaataaaaatatactataccaaaatgtgtaggataaagttaagcagacccagagtaaattttttgtataaatgcttattctaaaa---------tctcgacaagtgaactaattttctaccttaaaaagaaaatctaaaacaagagagcaaattaagtccaaaacaagtagaagaaaggaaataaaacagaaattagaaatcaatgaggcagaaaacagacacaggagaaagttaacatggccaaaagttagttctgtgagaaagaaagaaaactcaaattataaatatcagggattaatgagattgtacagttgtagacacaagagacattaacaagataatggaatattgtgaaacattttataccaattttcattacttggatgaaagggtgaattccttgaaaaaaaaacttataaaaaaattcacaagattaaatggaacatttgtagtaattgacatttcttaaagtaattaaattaattgtcaaatacctgtacataaaaacataaaactaaagaaaatttaaaaataagcaaactccagatccaaagagttttgctggtgaattctttcaaatgtttaaaa--aaaatagaaattttaaattatttcagaaataaagaagggggaaattccaaacttgttttatgagtcagaatcctgataccaaaac--tacaaaacacaggaatgcaaaattGATTTCAACTTAAAGAgctatcaccattctaatctgtgattctaatgaatttgg----cttagatactttatacaagtggaatcatatggtttgtccttctgtgactgatttactttacttagcattaatgtcctctaggttctcccatgttgcatattgccgggctttctt-gttttaaagctgaataatattccg-tgtatgaatataccacattatctttatctattcatctgccaatagacattaaccttatttccacattttgattagtgtaattaatgctgcaatgagcctgagaatcatctcaatttcaattctttcagataaataacctgaagtgagattgctagaccatattgtagttctactttcttaatttttttgaggaatcaccgtactcttttccatagaggctgcacagttttaaattcccagaaacactgtacaagtgttccaatttctcc---ccattgttaactctcgttatctttttctttcaataagaccattctaacaggtttgaggcaa-tatctctttgtggttttgatttgcatttccctgatgattagtgatgttaaacatttctttcatgtacctgttggttatttggatattttctttggaga i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47424411 1955 - 58616431 aaaatagtaggcttaactccaaccttatcaataattatttcaaatgtaatttaaatactccaaataaaacacagattgtccaactatataataaaagtacctataagagatgcatgccaaatattatggtatagataagttgagagtaaaataatttccaagtataccaaggaaacaacaagcacaagaaatcttatgtggctatattaatataagaaaaagcagacctccaaacaggcaatattacaacagaaagctatttcataatgataaaatgtcaagtaattatgaagacataaTGCTGTATTG----CTGATAGAATAACTAAagaaagttaagacaaaataattttgacaacagcttgacctaatcgatactgaccaagacaatagaatatatgttctattatgctacacatgaaacatttatcaataggctatagaccacaaaatatctctcaaaaagtttcaaaacactgtaatcatagaaagtatgctttctgaccataatgaaaatgagttgaaatgggtgaaaacaagctacccaggaaagtctacactattggaagatttaaatacaccttaaaatgtcctttagctcaaggaagaaagcataagaaacaccataaaatacattgaactgaatacaaataaaaatatactatatcaaaatatgtgggataaagttaagcagacccagagtaaattttttgtataaatgcttattctaaaaaagagaagttcaaaacaagtgaactaattttctaccttaaaaagaaaatctaaaacaagagagcaaattaagtccaaaacaagtagaagaaagaaaataaaacagaaattagaaatcaatgagacagaaaacagacacaggagaaaattaacatggccaaaagttagttctgtg----agaaagaaaacacaaattataaatatcagggattaatgagattgtacagttgtagacacaagagacattaacaagataatggaatattgtgaaacattttatactaattttcattaattggatgaaagggtgaattccttg--aaaaaaaacattaaaaaaattcacaagattaaatggaatatatgaagtaattgacatttattaaagtaattaaattaattgtcaaatacctgcacataaaaacataaaactaaag-aaataaaaaattaagcaaactccacatccaaagagttttgctggtgaattctttcaaacgttttaaa--aaaataaattttttaaattatttcag-----aagaagggggaaattccaaacttgttttatgagtcagaatcctgatagcaaaac--tacaaaacccaggaatgcaaaattGATTTCAACTTAAAGggctatcaccattttaatctgtgattctaatgaatttggctatcttagacactttatagaagtggaatcatacagtttgtccttctgtgactgatttactttacttagcattaatgtcctctaggttcatccatgttgcatattgccggattttctt-gttttaaagctgaataatattccgttgtatgaatataccacattttctttatctattcatctgccaatagacattaaccttatttccacattttgattagtgtaaataatgctgcaatgagcctgagaatcatcccaatctcaattctttcagataaataacctgaagtgagactgctagatcatatggtagttctactttcttaatttttttgaggaaccaccgtactgttttccatagaggctgcacagttttactttccaagaaacactgtacaagtgttccaatttctcc---ccattgttaacactcgttatctttttcttttaataagaccattctaacaggcttgaggcaa-tatctctttgtggttttgatttgcatttccctgatgattagtgatgctgagcatttttttcatgtacctgttggtcatttggatattttctttggaga i panTro2.chrUn C 0 C 0 e bosTau4.chr1 138196994 2796 - 161106243 I e loxAfr3.scaffold_13 20633651 2080 - 62548349 I e oryCun2.chr14 141907866 8974 + 163896628 I e canFam2.chr31 14125449 1887 + 42263495 I e equCab2.chr26 13374113 210 + 41866177 I e cavPor3.scaffold_34 15822887 8902 - 24440124 I a score=186639.000000 s hg19.chrUn_gl000245 29922 341 + 36651 aatatctattGCTGATTTAAAAAA------------------------------------------Aaaaaactctcagcaagctagataaagaaattttct------------------------cgaagtgatggaaagcatccacaacaaaacatataaacaatactatatttaatggtgaaagcgtaaatgtttaaaccacatagattaggacaagaaagggatgtgtgtgttcatcacctctattcaacattgtactggtgatcctagATTTTGAGTATAAATATTTAGGGGACAACTATTGTCACTGAAGCCCAAATCTTGGTCATCCTCAG----------AAAAAAAAAAAAGTTGATTAGGTTGTATATAATCTAATTTTACTTGC--------------------------------------------------------------------------TAATTTAATTTCT-----------CTAAAATTG s panTro2.chrUn 47426366 337 - 58616431 aatatctatCGCTGATTT--AAAA------------------------------------------Aaaaaactctcagcaagctagaaaaagaaattttct------------------------cgaagtgatggaaactatccacaacaaaacatataaacaatattatatttaatggtgaaagcataaatgtttaaaccacatagattaggacaagaaagggatgtgtgtgttcatcacctctattcaacattgtactggtgatcctagATTTTGAGTATAAATATTTAGGGGACAACTATTGTCACTGAAGCCCAAATCTTGGTCACCCTCAG------------AAAAAAAAAAGTTGATTAGGTTGTATATAATCTAATTCCACCTGC--------------------------------------------------------------------------TAATTTAATTTGT-----------CTAAAATTA i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 859879 424 - 4212913 aatatctaCTGCTGATTA-AAAAA------------------------------------------Aaaaaatgctcagcaagctagaaaaagaaattttct------------------------ccaagtgatggaaagcatccacaacaaaacatataaacaatattatatttaatggtgaaagcgtaaatgtttaaaccacagaaattaggacaagaaaaggatgtgtgtattcgtcacctctattcaacattgtactggtgatcctagATTTTGAGTATAAATATTTAGGGGACAACTACTGTCAGTGAAGCCCAAATCTTGGTCATCCTCAGGaaaaaaaaaaaaaaaaaaaaaGTTGATTAGGTTGCATATAATCTAATTCTACTTGCTTTGGGCTTAATTTTAGAGAAATTAAATTAAGTTGCTTACTTTAAAAAAGTTGCTTAAATTAAATTAAGCAACTTAATTTAATTTCT-----------CTAAAATTA i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189471613 438 - 189746636 aatatctattGCTGATTTaaaaaaaaaaaaaaagaaaaagaaaaagaaacaaacaaacaaaCTAACAaaaaactctcagtaagctagaaagagaaattttct------------------------caaagtgatggaaagcatccacaacaaaacacataaacaatactatatttaatggtgaaatcctaaatgtttaaaccacatagattaggacaagaaaaggatgtgtgtgttcttcacctctattcaacattgtaccggtgatcctagATTTTGAGTATGAATGTTTAGGGGACAACTATTGTCACTGAAGCCCAAATATTGGTCATTCTCAG---GAAAAAAAAAAAAAAAAAAGTTGATTAGGTTGTATACAATCTAATTCTACTTGTTTTGGGCTTAATTTTAGAGAAATtaaatt------------------aagttgct-------------------taatttaatttctaaattaaattgctaaaATTA i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15831789 279 - 24440124 aacatctactgctgatta---------------------------------------------------aagctgtcagcaaat-----gaagaaacctccc------------------------caaaatgatatacaacatccata-------aCACAAACAATACTGTATT-----------ATATGTGAGTTTAAATATAATAGTTTAATATAAGCAAAGGATATCTACCTTCATTCATACCATTCATCATGAAATT------------------ATATGATTATTTATAGGATAAGTATTATCATGAAGGAAAACATCTTGGTTTTTCTCA---------------GGAAAAAATTTGATTCAATTCTATGTGTTCTAAATATT-------------------------------------------------------------------------------AAACTTAATTTAT-----------CAAAAAT-- i cavPor3.scaffold_34 I 8902 I 2055 s oryCun2.chr14 141916840 293 + 163896628 aatagccattgctgatca------------------------------------------------------ctctcagcaaactaaagaaagaaactcctccgagtcgttgatcgcatcactaggcaaggtggtaaataatat-------------tacaaataatggtg-gct-----------gtctagatgtttgattcctatagaataggacaagaaaaggatgcctccatgtgtgatttctgttcaacattgtactggaggtcctcaaacttgagcaTGAGTATTTAGAAAACAACTATTGTCATTAAGTCCCAAATCTTTGTTATCCTCAG-------------GGGGAACATCCTGATTAGACTATATACTTTCTAA--------------------------------------------------------------------------------------------------------------------- i oryCun2.chr14 I 8974 I 3197 e bosTau4.chr1 138196994 2796 - 161106243 I e loxAfr3.scaffold_13 20633651 2080 - 62548349 I e canFam2.chr31 14125449 1887 + 42263495 I e equCab2.chr26 13374113 210 + 41866177 I a score=101124.000000 s hg19.chrUn_gl000245 30263 158 + 36651 --CAGCTTGTATCAACTCTAGAATTTATTGGGCACCTCCTAGGACATAAACAC-----TGGAATTTGGTGAGAGACGT------------------------CAAATAGGAAAGAACCTGGCTCTG-ACATAAATTCAACACACGGAGGGGGACACATGTTATGAGACTGACCTGGCCTCTTCATCTCAT s panTro2.chrUn 47426703 158 - 58616431 --CAGCTTGTATCAACTCTAGAATTTATTGGGCACCTCCTAGGACATAAACAC-----TGGAATTTGGTGAGAGACAT------------------------CAAATAGGAAAGAACCTGGCTCTG-ACATAAATTCAACACACGGAGGGGGACACATGTTATGAGACTGACCTGGCCTCTTCATCTCAT i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 860303 154 - 4212913 --CAGCTTGTATCAATTCTAGAATTTATTGGGCACCTCCTAGGACATAAACAC-----TAGAATTTGGTGAGAGACAT------------------------CAAATAGGAAAGAGCCTGGCTCTG-ACATAAA-TCAACACATGGAGGGGGACACATGTT---AGACTGACCTGCTTTCTTCATGTCAT i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189472051 158 - 189746636 --CAGCTTGTATCAACTCTAGAATTTACTGGGCACCTCCTAGGACATAAACAC-----TGGAATTTGGTGGGAGAAAT------------------------CGAATTGGAAAGAGCCTAGCTCTG-ACATAAATTCAACACATGGAGGGGGACACGTGCTATGAGACTAACCTGCCTTCTCCATCTCAT i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141920330 163 + 163896628 --CAGCTTACAGCAATCCTGCAATTGATTGGGCTGCTTCTGAGATACACGCAA-----AGGAATTTGGTG-GATAAATC------------AACGAGCAGGGCAAGTAGGAAATTGCTGGGCTCTGCACGTGGA-----CACGCGGCACCAGACACGTGCTAGGAAACTG--TTGGGCTTTCAAGGTCTG i oryCun2.chr14 I 3197 C 0 s bosTau4.chr1 138199790 176 - 161106243 --CAGTTTGTATTAACCCCAGGAACTAT---GCAGACTCATGAGCAT-TATTT-----TGGAATTTTGTAGGACAGATCTAGTTACTGGGAGACAAGCTAGATAAGGAGGGAAAGGCCTTGCTCTC-ACGTAAAGTCCACACAAGGAGTAGGTTACATGCTATTACATAGACACGCCCCCCCCCCCCC-- i bosTau4.chr1 I 2796 I 264 s loxAfr3.scaffold_13 20635731 173 - 62548349 CATAGCTTCTGTCAACCCTAGGAATTGC---------TCTGGCACATGAGCATTGCCGTGGAACTTGGAG---CAGGTCTAATTACTGAGAACAGAGCCGGGCAAAGTTGGAAGAACCTGGCTCTG-CCTTAAAGTCCACAAGTGGTA----AAACATTCTGGGGAACGTCCCTACCTTCAAGATCTAAT i loxAfr3.scaffold_13 I 2080 C 0 e canFam2.chr31 14125449 1887 + 42263495 I e equCab2.chr26 13374113 210 + 41866177 I e cavPor3.scaffold_34 15832068 2055 - 24440124 I a score=132694.000000 s hg19.chrUn_gl000245 30421 146 + 36651 AAAAGGGGTTCTTGTTGCTTGTAA----CACAGATTAAAACTATTTCAATTACATTCAAGA-TAAAAAGATTAGCAATGGTATGTAAGATG-AAAAAATCAC----CCCGCTGGAAGACGAAAGTCTCACAAAAGGATATTTAAGCTAGCCAACAC s panTro2.chrUn 47426861 146 - 58616431 AAAAAGGGTTCTTGTTGCTGGTAA----CACAGATTAAAACTATTTCAATTACATTCAAGA-TAAAAAGATTAGCAATGGTATGTAAGATG-AAAAAATCAC----CCCGCAGGAAGACAAAAGTCTCACAAAAGGATATTTAAACTAGCCAACAC i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 860457 147 - 4212913 AAAAGGGGTTCGTGTTGCTGGTAA----CACAGATTAAAACTATTTCAATTACATTCAAAA-TAAAAGGATTAGCAGTGGTATGTAAGATGAAAAAAATCAC----CCCGCAGGAAGACAAAAGTCTCACAAAAGGATATTTAAACTAGCCAACAC i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189472209 146 - 189746636 AAAAGGGATTCTTGGTGTTGGTAA----CACAGATTAAAACTACTTCAATTACATTCAAGA-TAAAAGGAATAACAATGGTATCTAAGATG-AAAAAATCAC----CCCACAAGAAGACAAAAGTCCCACAAAAGGATATTTAAACTAGCCAACAC i rheMac2.chr2 C 0 C 0 s oryCun2.chr14 141920493 153 + 163896628 AGGGACTATCCTTGCTGTTGGCAAGTACTAGGGATTAAATCTATTTCAAACACATTCAAGA-CAAAAGGGTTGCAAATGACATGCAAGATG-CAAAAATTCTATCACACACAGGAAGTCACCA-TCCCCCAAGAGAGCATGTCAAATAGTCAATAC i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138200230 132 - 161106243 AAAGAAGGTCCTCTCTACTGGAAAATGATACAGAGTAAACTAA--TGAATTACATCCAAGA-AAAGTGGATTAGCAACAGTGTCTCAGATG-AAAAAGTCTA----TC----------------TCCCACAAAAGGACATTTAAAGTGACTAATAC i bosTau4.chr1 I 264 C 0 s loxAfr3.scaffold_13 20635904 139 - 62548349 AAAGACAG----------CAGTGA----TATAGATTAGAATTATTTCAATTCCATTCAAGATTTAAAAAATTGGCAGTGGTGTCTAAGATG-AAAAAGTATG-TCACCCATAGGAAGTCGAAA-CTCTACAAAAAGAAATTTAGAATAGTCAATAC i loxAfr3.scaffold_13 C 0 C 0 e canFam2.chr31 14125449 1887 + 42263495 I e equCab2.chr26 13374113 210 + 41866177 I e cavPor3.scaffold_34 15832068 2055 - 24440124 I a score=71306.000000 s hg19.chrUn_gl000245 30567 124 + 36651 TTTGAAATTCAGGCAGAGATCGTG-ATTTCTGGGT---------------------------------------------GAACTAAAGTAGCAAGAACAAAGTAGAGGCTCCAATTCTA--------------------GGAAAAAT------GGGTCCTAATAAGGTTTACAATCCAGAAACTC--AAGA--TATCCA s panTro2.chrUn 47427007 124 - 58616431 TTTGAAATTCAGGCAGAGATCGTG-CTTTCTGGGT---------------------------------------------GAACTAAAGTAGCAAGAACAAAGTAGAGGCTCCAATTCTA--------------------GGAAAAAT------GGGCCCTAATATGGTTTACAATCCAGAAACTC--AAGA--AATCCA i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 860604 124 - 4212913 TTTGAAATTCAGGCAGAGTTCGTG-CTTTGTGGGT---------------------------------------------GAACTAAAGTAGCAAGAACAAAGTAGAGGCTCCAATTTTA--------------------GGAAAAAT------GGGCCCTAATAAGGTTTACGAGCCAGAAACTC--AAGA--AATCCA i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189472355 127 - 189746636 TTTGAAATTCAGGCAGAGATCATGCCTTTCTGGGT---------------------------------------------GAACTAAAGTAGCAAGAACAAAGGAGA-GCTCCAATTCTA--------------------GGAAAAATA-----AGGCCCTAATAAGGTTTACGATCCAGAAACTCAGAAGA--AATCCA i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15834123 127 - 24440124 TTAGAATTTGAAGCAGGGATTAT--TTTTCTAGGTA--------------------------------------------GAGGAAAACTAGCAAACAGAAAGTAGA-GTTCTAATCTTT--------GTTG-------TGGAGGAAT------GCATCTTAACA-AGTTTATGATTCAAAT-TTC--AGGAT-AGTCGT i cavPor3.scaffold_34 I 2055 C 0 s oryCun2.chr14 141920646 111 + 163896628 ------TTTGAAACTCAGA------------GAGTG--------------------------------------------GAAGAAAACAAGCAAGAAGAAAAGAGA-GAGGCAATCTTA--------G-----------GAAGAAACAGG---GTATTATGAC--GGTTTATAATTCAAAGATTC--AGGAGAAGCCAA i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138200362 150 - 161106243 -TTGAAATTCAGAAAGAGTTTAGA-CCTTTAGGTT---------------------------------------------GAGTGAAACATGCAGGAAAAAAGCAGA-GATCCAGCTTTATAATAAAAGCtaataaaattaaaaaaataaaattaGACCCTACGAAGATGTATAATTCAAAAATTT--AGAAGCAGCCAA i bosTau4.chr1 C 0 C 0 s loxAfr3.scaffold_13 20636043 172 - 62548349 TTTCAAATTCAGGCAGAGATTGG--TCATCTAGGTGGCCAGTCAGTACTTGAGTCTGAGGCACTAAGTTTTACTTTCTCTGAGTAAAATTAGTAAGAACAAAGCAGA-CATTCAGTTCTA--------GGGG--------GGGAAAATG-----GGACAATAAGAAAGTTTCTACTCCTAGAGAAG--AAGG--AGCCAA i loxAfr3.scaffold_13 C 0 C 0 e canFam2.chr31 14125449 1887 + 42263495 I e equCab2.chr26 13374113 210 + 41866177 I a score=82557.000000 s hg19.chrUn_gl000245 30691 68 + 36651 GACAGAAGGATGCAGTCT-CCGCTTTCAAGGCAGCAGCAGTACCTGGATTACTAAGCCAATCCCCAACA s panTro2.chrUn 47427131 68 - 58616431 GACAGAAGGATGCAGTCT-CTGCTTTCAAGGCAGTAGCAGTACCTGGATTACTAAGCCAATCCCCAACA i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 860728 68 - 4212913 GACAGAAGGAGGCAGTCT-CTGCATTCAAGGCAGTAGCAATACCTGGATTACTAAGCCAATCCCCAAAG i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189472482 68 - 189746636 GACAGAAGGATGCAGTCT-GAGAATTCAAGGCAGTAGCAATACCTTGATTACTAGGCCAATCCCCAAAG i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15834250 47 - 24440124 AACAGAAAGATGCACCAG-GGACACTCACAGACGTGAGAAT-----------TTGGC----------AA i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141920757 68 + 163896628 AGCTAAAAGACTTATTCT-GAGCATTCAAGGTAGTAAGAATAACAGGACTACTGAGCTAATTACCAAAA i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138200512 67 - 161106243 GGCAGAAGGCT-TTCTGT-TGGGCTTCCAGGCAGTGAGAATGACTGGAATACCAAGCCAATTACCAAAA i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13374323 68 + 41866177 GACAGAAGGCTGTGCTCT-GGGACTTCAAGGCAATAAGGATAACTGGACTGCTAAACCAATTACCAAAA i equCab2.chr26 I 210 I 1 s loxAfr3.scaffold_13 20636215 68 - 62548349 GGCAGAAAAATGCATTCCGGGGCATTCAAGACAGCAAGAATAATTGGGCT-CTAAGCCAATTACCAGTG i loxAfr3.scaffold_13 C 0 I 204 e canFam2.chr31 14125449 1887 + 42263495 I a score=12857.000000 s hg19.chrUn_gl000245 30759 24 + 36651 ------------CAA----TCATAAACACAAATTTGATTG s panTro2.chrUn 47427199 24 - 58616431 ------------CAA----TCATAAACACAAATTTGATTG i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 860796 28 - 4212913 ------------CAGGAACTCATAAATGCAAATTGGATTG i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189472550 28 - 189746636 ------------CAGGAACTCATAAACACAAATTTGATTG i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15834297 26 - 24440124 ------------TGCACGTTGAAAAACAGGGATTTAGT-- i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141920825 23 + 163896628 ------------TGCAAACTCAGAAACATAGATTT----- i oryCun2.chr14 C 0 I 6 s bosTau4.chr1 138200579 28 - 161106243 ------------CAGGAGTGCAGAAATATAGATTCTTTGG i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13374392 28 + 41866177 ------------CAGGACCTCAGGAATATAGATTTTTAGG i equCab2.chr26 I 1 C 0 s loxAfr3.scaffold_13 20636487 40 - 62548349 CAATTACAAAAACGGGAACTTGGAAGGATGGATTTAATTT i loxAfr3.scaffold_13 I 204 C 0 e canFam2.chr31 14125449 1887 + 42263495 I a score=129183.000000 s hg19.chrUn_gl000245 30783 91 + 36651 AGGAAGAAGC---TTGCCCACCAGAAGATTTAG------GTTATTACAAGGTAGAATGTGATAGAGAAAATGAGCATGGGACTGGAAAGAAAAGGAGGTA s panTro2.chrUn 47427223 91 - 58616431 AGGAAGAAGC---TTGCCCACCAGAAGATTTAG------GTTATTACAAGGTAGAATGTGATAGAGAAAAAGAGCATGGGACTGGAAACAAAAGGAGGTA i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 860824 91 - 4212913 AGGAAGAAGC---TTGCCCACCAGAAGATTTAG------GTTATTACAAGGTAGAATGTGATAGAGAAAACGAGCATGGGACTGGAAACAAAAGGAGGTA i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189472578 90 - 189746636 AGGAAGAAGC---TTGCCCACCTGAATATTTA-------GTTATTACAAGGTAGAATATGATAGAGAAAAAGAGCATAGGACTGAAAACAAAAGGAGGTA i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15834323 92 - 24440124 AGGAAACATCTGGTTATGCACCAGATGGCTGAG------GTGGCCATACAGTAGAAAAGGGTTGAGAAAACAA-CACAGGAATGGAAAC-AACGTGGCTA i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141920854 89 + 163896628 AGAAGACACT---TTACTCACCAGGAGATTGAG------GGAATTTCAAGGTAGAGAGTAGTGGAGGAAAGAAGCATGGGGCTGGAATC-AAGGTGTGT- i oryCun2.chr14 I 6 C 0 s bosTau4.chr1 138200607 96 - 161106243 AGACAGAAAC---TTACTTGCCAAATTATTCAGATAATTATAATTATAAGGTATAAAGTGCTAGAGAGGAAGAGAAGAAGACTGGAAAT-AAATGGGGCA i bosTau4.chr1 C 0 C 0 s equCab2.chr26 13374420 90 + 41866177 GGGCAGAAAC---TTACTTACCAGATTACTGAG------GTAATTACAAAGTAGAAAGTGGTAGAGAGGAAGGGCGTGGAACTGGGAGC-AAATGGGATA i equCab2.chr26 C 0 C 0 s loxAfr3.scaffold_13 20636527 91 - 62548349 GTACAAAAGT---TTACTTACCAGAATATTGAG------GTGATGATGAGGTAGAGAGTTGGAGAGAGAGTAGGCATGGGGCTAGAAATAAATGGGGGTA i loxAfr3.scaffold_13 C 0 C 0 e canFam2.chr31 14125449 1887 + 42263495 I a score=86609.000000 s hg19.chrUn_gl000245 30874 53 + 36651 GCCCCATGATTACAACTGGAA------TATATGTGTCAGCGATGGTGCGGAAATAAGAC s panTro2.chrUn 47427314 53 - 58616431 GCCCCATGATTACAACTGGAA------TATATCTGTCAGAGATGGTGCGGAAATAAGAC i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 860915 53 - 4212913 GCCCCATGATTACAACTAGAA------TACATCTGTCAGAGATTGTGTGGCAATAAGAC i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189472668 53 - 189746636 GCCCCATGATTACAACTAGAA------CACATCTGTCAGAGATGGTGCAGAAATAAGAC i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15834415 50 - 24440124 GCCCCACAATTACACTT-GAA------TAAATCCATCAGAGATGACGTAGCAAT--GTC i cavPor3.scaffold_34 C 0 I 16 s oryCun2.chr14 141920943 53 + 163896628 GTCCCATGATTACATTTAGAA------TAAAGCCATCTGCTTTGAATCAAAAATAAGTC i oryCun2.chr14 C 0 I 286 s bosTau4.chr1 138200703 56 - 161106243 -GCCTAAGAACATCACTGGAA-AACTCCATAACTGTCAGAAGTGATGCAGAAATAAAA- i bosTau4.chr1 C 0 I 493 s equCab2.chr26 13374510 57 + 41866177 -GCCCATGCTCATAACTGGAA-TACTCCATAACTGTCAGAAATGATGCAGAAATAAAAC i equCab2.chr26 C 0 I 2 s canFam2.chr31 14127336 58 + 42263495 GTCTCATAATTATTACAGGAA-TACTCTACAACTATCAGAGGTGATGCATGAATACAAC i canFam2.chr31 I 1887 I 2 s loxAfr3.scaffold_13 20636618 58 - 62548349 -ACCCACAGTCACAACCTGCAATACCCTATGACTGTCAGAGGTGGTGCAGAAATAAATC i loxAfr3.scaffold_13 C 0 C 0 a score=81203.000000 s hg19.chrUn_gl000245 30927 110 + 36651 -TGAAGAGAGAGATCCTT--------------------------------------AAACCCCACGTGCCTTACATCAGGACTAATCCTGGACACAGGCTGGAAAGCATAGCCTACAGGTG-----------GTGAGGCAGGAG------------GAG-------------------------TGGGCTC--AGCTGT s panTro2.chrUn 47427367 110 - 58616431 -TGAAGAGAGAGATCCTT--------------------------------------AAACCCCACGTGCCTTACATCAGGACTAATCCTGGACACAGGCTGGAAAGCATAGCCTACAGGTG-----------GTGAGGGAGGAG------------GAG-------------------------TGGGCTC--AGCTGT i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 860968 110 - 4212913 -TGAAGAGAGAGCGCCTT--------------------------------------AAACCCCACGTGCCTTACGTCAGGACTAATCCTGGACACAGGCTGGAAAGCATAGCCTACAGGTG-----------GTGAGGGAGGAG------------GAG-------------------------TGGGCTC--AGCTGT i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189472721 110 - 189746636 -TGAAGAGAGAGCTCCTT--------------------------------------AAACCCCACGTGCCTTACGTCAGGAATAATCCTGGACACAGACAGCAAAGCATAGCCCACAGGTG-----------GTGAGGGAGGAG------------GAG-------------------------TAGGCTC--AGCTGT i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15834481 88 - 24440124 -CAAGTAACTGGGGTCTT--------------------------------------------------ACTCAGGTCAGGACCAATCATGGACATGAAGAGGAAAGAACTGCCTAAAATTG-----------------------------------GAT-------------------------TCAGCCTTAAACTGG i cavPor3.scaffold_34 I 16 C 0 s oryCun2.chr14 141921282 142 + 163896628 -caaataaataaaatctttttaaaaataaataagtcttccatgcaagctctgcgaAGTCCTCCTCCTGCCTTAGGTCAGGGCTCACCTTGGACACTGGGAAGAGAATGTAACACACAGATG-----------G------GAGAA------------GAG-------------------------TGTGCCT--AGCTGT i oryCun2.chr14 I 286 C 0 s canFam2.chr31 14127396 131 + 42263495 -CAAAAAATGAGGTCTTT--------------------------------------CAATCCCTTCTGCCATAGGTCAGGATTAGCCCTAGACACAT-------AGTGTAGCCTATGGATATT--------GGTGTGTTAGGAG------------CAGGAAAGGGAGAGGGGAGGGCTGGTAAAGGGCCA--GGCTGT i canFam2.chr31 I 2 I 1 s equCab2.chr26 13374569 116 + 41866177 -C-AAATGTGACCTCATT--------------------------------------CATTCCCTTCTACCATAGATCAGGATAGGTCCTAGAGACAGA--GGCAAGTATAGCCTACAGATATG--------TGTGTGTTAGGGG------------CAG-------------------CGCAAAAGGACCA--GGCTGT i equCab2.chr26 I 2 I 1 s loxAfr3.scaffold_13 20636676 134 - 62548349 TTCCAATGGGAGCATCTT--------------------------------------AAATCTCTTCTACCATAGGTCAAGATTGGTCTTAAAGATAGGGAGGAAAGTATAGCCTATAGGTACGTCTGGGAAGGTGTGAGACGGGCCACCCCAAGTTGGG-------------------------TAGACTC--AGCTGT i loxAfr3.scaffold_13 C 0 C 0 e bosTau4.chr1 138200759 493 - 161106243 I a score=97741.000000 s hg19.chrUn_gl000245 31037 97 + 36651 GAGAAGGAGAAGGAAATATGGCTGA-----AAACTAGATAGGGGTCTTGAAATCACAC-CGAGGATTTGGGCCTTTGCTGCTGTCTGCCAGCAGCTGCcagta s panTro2.chrUn 47427477 97 - 58616431 GAGAAGGAGAAGGCAATATGGCTGA-----AAACCAGATACGGGTCTTGAAATTACAC-AGAGAATTTGGGACTTTGCTGCTGTCTGCCACCAGCTGCcagta i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 861078 82 - 4212913 GAGGAGGAGAAGGCA--------------------AGATACGGGTCTTGAAATCACAC-AGAGGATTTGGGCCTTTGTTGCTCTCTGCCAGCAGCTGCcagta i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189472831 97 - 189746636 GAGAAGGAGAAGGCAACATGGCTGA-----AAAGCAGATACGGGTCTTGAAATCACAC-AGAGGATTGGGGCCTCTGTTGCTCTCTGATAGCAGCTGCcagta i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15834569 87 - 24440124 AGATAGCAATAG-------AGCTGA-----AAATCAGACACAGGGCTTTAAACTAGGT-CAGGGACTTTGG-TTTTGTTGCT--CTGACAGCAGCTGCTagta i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141921424 91 + 163896628 GGAGAGGAGGAGCTAGT-CGGCTAA-----AATACAGGC-----TCTGTAAACCACAC-AAGGGAGTTGAACCTTTGTTGGTTGCTGCCAGCAACTGTTAGTA i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138201252 95 - 161106243 GATAGGAGAAAAGTATTAAGGCTAA-----AAACTCA--TGCAGTCTTTAAACCCCATGGGGCTATATGGT-CTTTGTTGCTGTCTGCCAGCAGCTTCcagta i bosTau4.chr1 I 493 C 0 s equCab2.chr26 13374686 103 + 41866177 GATAGGAGAGAGGTATTAAGGTTAAGGCTGAAAACGAGTTGCAGTTTTTAAACCACACAAGGTGATTTGGCCCTTCATTGTTCTCTGTCAGTAGCTGCCAGTA i equCab2.chr26 I 1 I 927 s canFam2.chr31 14127528 90 + 42263495 AAT----GAGAGGTGTTAAGGCTGA-----AAAACTAGATGCAGTCTCTAAACCATAT-GGGAGATTTCATCCTTTGTTGCTCTCTGC---TAGTTGCTAATA i canFam2.chr31 I 1 C 0 s loxAfr3.scaffold_13 20636810 84 - 62548349 GAATTGGAACAGGGCAAAAAGCTGA-----ACCCCAGAT---AGTCTTCAAACCACAT-GGGGGATTTGGAGCTTTGTTCCTCTCAAGCCATA---------- i loxAfr3.scaffold_13 C 0 C 0 a score=63435.000000 s hg19.chrUn_gl000245 31134 103 + 36651 gttctcacactttggctggcaac---aaaatcacctggggCAGTGGTGCGGAAGCGGGGGGAGTGTT-GTAAAACCACAAGTGACCAGGCAAAAAACACCTGTATGT s panTro2.chrUn 47427574 103 - 58616431 gttctcacactttggctggcatc---aaaatcacctggggCAGTGGTGGGGAAGCGGAAGGAGTGTT-GTAAAACCACAAGTGACCAGGCAAAAAACATCTGTATGT i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 861160 103 - 4212913 gttctcacactttggctagcatc---aaaatcacctggggCAGTGGTGGGGAAGCGGGGGGAGTGTT-GTAAAACCACAAGTGACCAGGTAAAAAACACCTGTATGT i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189472928 101 - 189746636 gttctcacactttggctggcatc---aaaatcacctggggCAGTGGTGGGGCG--AGGGGTAGTGTT-GTAAAACCACAAGTGACCAGGCAAAAAACACCTGTGTGT i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15834656 77 - 24440124 gctctcacaacttaccttgcatt---gaaagcac----------------------ggaggcaggtt-gtgaaaccacagacaaccaggc----accaactgtgcag i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141921515 88 + 163896628 ATTCATAAGGATAAGATGGCATTTTAAAAAGCACCTG---------------AGTTGTGGGTGGGTTAGTACAATCACAGAGAGCCAGGC----GCCACCTGAGCAG i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138201347 54 - 161106243 gttctca-------------atc---agagttacctcgag----------------------ggctt-gtgaaaccacagttggctgggagag-------------- i bosTau4.chr1 C 0 C 0 s canFam2.chr31 14127618 54 + 42263495 GTCCTCA-------------att---agaatcacctgaag----------------------ggcct-gtgaagccacaactggctgggagag-------------- i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20636894 76 - 62548349 GAtctcacattttagcttgcatc---agaatcacctggag----------------------ggatt-gtaaaaccacgggtagctgggc--ctaacttcagag--- i loxAfr3.scaffold_13 C 0 C 0 e equCab2.chr26 13374789 927 + 41866177 I a score=1117356.000000 s hg19.chrUn_gl000245 31237 733 + 36651 TTTCCAATTCAGTAAGTACAGAAATATTAATTGGAAAAAGGTGGAGGT---------CAGACATTGATAGTGCTGTGGA--CTGCTCCAGGGACGTAAGCATGATCTTTA-GAGAGGTGAC---TCTAATCAA----------------------TTGAGGG----------------CAACCACTGGACAGAA--------------------------------------------------AGAGGTCCAGACCAA-CCATACACA--GAGACATCATACAAC-TACACTTTAGCAACCTCTCCAAATAA---CATGTCTCTTAGTGAAACTTGGGAGGTTGCAAGTTAAAAACATAAAATCCA-------------------GTGGCATT----TATGTATCCTAGG--------CACTTACATTTGTCTGA-TTCTTCCAACTTGCCTTTGCTTGGTTAGAGTTTTGGGTAGATAAGAGGTGGA-TTTACATGTGCTAGTGTGAGAACTTTGATACACTC-ATTTAGAC--ATTGAC---CTACTATCT---TGTTTGAAAG-CTAAAACCCAAAGAAATTTGTCTTCTTACATAAAACAAATTCAGCCCTTGCCTTCCTTGTAGATT----ACATCTTCCACTAGCAGTAATAAAAAAGTAACAATATGCATAAGTCAAAGTATCTTCTTAGATCCTCTGTAGTGTTTTATT---ATTTAGTTGTGTTAATTAAAGTAACTGTCTCAAAATTTCAAGGAATGCC-------TGAGAAGAAATTCATGTTCAAAGGCTGCCCTCTTGTGACAATGTGTTGTATGCTTTACT-GTAAAAG-TAACCTTATTTTACCTTATAACCTCTACAATCCAATTC---------ATAACAGCATAAAAAGGAA s panTro2.chrUn 47427677 736 - 58616431 ATTCCAATTCAGTAAGTACAGAAATATTAATTGGAAAAAGGTGGAGGT---------CAGACATTGATAGTGTTGTGGA--CTGCTCCAGGGACATAAGCATGATCTTTA-GAGAGATGAC---TCTAATCAG----------------------TTGAGGG----------------CAACCACTGGACAGAA--------------------------------------------------AGTGGTCCAGACCAA-CCGTACACA--AAGACATCATACAAC-TACACTTTAGCAACCTCTCCAAATAA---CATGTCTCTTAGTGAAACTTGGGACGTTGAAAGTTAAAAACATAAAATCCA-------------------GTGACATT----TATGTATCCTAGG--------CACTTACATTTGTCTGA-TTCTTCCAACTTGCCTTTGCTTGGTTAGAGTTTTGGGTAGATAAGAGGTGGA-TTTACATGTGCTAGTGTGAGAACTTTGATACACTC-ATTTAGAC--TTTGAC---CTACTATCTTGATGTTTGAAAG-CTAAAACCCAAAGAAATTTGTCTTTTTACATAAAACAAATTCAGCCCTTACCTTCCTTATCAATT----ACATCTTCCACTAGCAGTAATAAAAAAGTAACAATATGCATAAGTCAAAGTATCTTCTTAGATCCTCTGTAGTGTTTTATT---ATTTAGTTGTGTTAATTAAAGTAACTGTCTCAAAATTTCAAGGAATGCC-------TGAGAAGCAGTTCATGTTAAAAGGCTGCCCTCTTGTGACAATGTGTTGTATGTTTTACT-GTGAAAG-TAATCTTATTTTACCTTATAACCTCTACAATCCAATTC---------ATAACAGCATAAAGAGGAA i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 861263 731 - 4212913 TTTCCAATTCAGTAAGTACAGAAATCTTAATTGGAACAAGGTGGAGGT---------CAGACATTGATAGTGCTGTGGA--CTGCTCCAGGGACATAAGCATGATCTTTA-GAGAGGTGGC---TCTAATCAG----------------------TTGAGGG----------------CAACCACTGGACAGAG--------------------------------------------------AGAGGTCCAGACCAA-CCGTACACA--GAGACATCATACAAT-TACACTTTAGCAACCTCTCCAAATAA---CATGTCTCTTAGTGAAACTTGGGAGGTTGAAAATTAAAAACATAAAATCCA-------------------GTGGCATT----TATGTATCCTAGG--------CACTTACATTTGTCTGG-TTCTTCCAACTTGCCTTTGCTTGGTTAGAATTTTGGGTAGATAAGAGGTGGA-TTTACATGTGCTAGTGTGAGAACTTTGATACACTC-ATTTAGAC--ATTGAC---CTACTATCTTGATGTTTGAAAG-CTACAACCCAAAGAAATTTGTCTTTTTACATAAAACAAATTCAGCCCTTGCCTTCCTTATAGATT----ACATCTTCCATTAGCAGGAATAAAAAAGTAACAATATGCGTAAGTCAAAGTATCTTCTTAGATCCTC-----TGTTTTATT---ATTTAGTTGTGTGAATTAAAGTAACTGTCTCAAAATGTCAAGGAATGCC-------TGAGAAGCAATTCATGTTCAAAGGCTGCCCTCTTGTGACAATGTGTTGTATGTTTTACC-GTAAAAG-TAATTTTATTTTACCTTATAACCTCTACAATCCAATTC---------ATAACAGCATAAAAAGGAA i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189473029 736 - 189746636 TTTCCAATTCAGTAAGTCTAGAAATCTCAGTTGGAGCAAGGTGGAGGT-------------CATTTATAATGCTGTGGA--CTGCTCCATGGACATAAGCATGATCTTTA-GAGAGGTGGC---TCTAATCAG----------------------TTGAGGG----------------CAACCACTGGACAGAG--------------------------------------------------AGGGGTCCAGACCAA-CCGTACGTC--GAGACATCATACAAT-TACACTTTACCAACGTCTCCAAATAA---TATGTCTCTTCGTGAAACTTGGGAGGTTGAAAATTAAAAACATAAAATCCA-------------------GTGGCATTTACGTATGTATCCTAGG--------CTCTTACATTTGTCTGG-TTCTTCCAAGTTGCCTTTGCTTGGTTAGAATTCTGGGTAGATAAGAGGTGGA-TTTACATGTGCTAGTGTGAGAACTTTGATACACTC-ATTTAGAC--ATTGAC---CTACTATCTTGATGTTTGAAAG-CTACAACCCAAAGAAATTTATCTTTTTACCTAAAACAAATTCAGCCCTTGCCTTCCTTATAGATT----ATGTTTTCCATTAGCAGTAATAAAAAAGTAACAAGATGCATAAGTCAAACTAGCTGCTTAGATCCTCAGTAGTGTTTTATT---ATTTAATTGTGTGAATTAAAGTAACTGTCTCAAAATTTCAAGGAATGCC-------TGCGAAGCAATTCATGTTCAAAGGCTGCCCTCTTGTGACAATGTGTTGTATATTTTACT-GTAAAAG-TAATCTTATTTTACCTTATAACCTCTACAATCCAATTC---------ATAACAGTATAAAAAGGAA i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15834733 776 - 24440124 tatgcaatccagtaATTATATAAATGCAAGTTGAGG-CAGGTGAGGAT---------CAGAAATTCATAGCACTGTGAATCCTAATTCTGGAACTTGGGCACGACCTTCT---------CC---TCTGCTCAG----------------------CAGAGAG-----------------AGTCACTGGTCAGAGAGAGACACTGATGCCGCTGATGTGACAACATCCTCTGGAAGA-----CTTAGAGATGGAGACCAG-CCAAACACC----TGCCACGTTCAAAATGCTTTTCACAAACATCTC----------CATGTATTT--GTGAAATTAGAGGGGTTGAAAATTAGAAATTTGAAAGGTTAAAAATTAGAAACAAGCAAGTAGCATT----TGTTAACCCTCGGGTCACACACACACACATGATTCTTA-TTATTCTATATTGCCTTTATTTGGTTAGAATTTCAGTTAGATCAGAGATGGA--TTCC---------TTTGAGAAATCTGTTAAATTCAAGCCAGAT--TTCAAC---TTTCTTCCTTGATATTTGAAAG-CTAAAACATAAGGAGCATTATCTTTCATCATGAAAC-AACCCAGTCCTTGAATTTCTTATACATT---AAAACATTCAATTAGCAGTAAT-AAAAAGAAACAGCATTCAT-----AAAATGTTTTCTTCAATGCCCTGCATTGTTTTATTATCATGTAGTTGTGTAGATTAAAACAACTGACTT-AAAATTCAAGAAATGCTGCAAA-TTGAGAAACAATTTATGTTAAAAGGCTGCCCTCTTGTGACAATTTGTTGAATATTTTACTGGTAAAAATTGTTCTTACCATACGTT---------TGAATCCAATTC---------ATAATACAATAAAAAAAGA i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141921603 792 + 163896628 TTTCCAATTCAATAAGCCCAGAAATCCCAGTTGGGTCCATGTGGAGAT---------CATGCAGTTAGAGTATtgtgag--ctgaccctgg-acaagagcattatcttttgaacaggtgcc---tctattcag----------------------ttgaggg---------------gcaatcacttcccagagagggttgCTGGAGCCTTTGGCCTGAGAGTGCCCTGTGTATAAGTTATGTTAGAGATCAAGAGCAGCCCACACACCAAAACGCATCGTGCAACTTATTCTTTCCCAAAATCTCCAAATAGC-TCATGCCTCT--GTGGCATTTGGGAGGTTGAGAATTTGAAACATAGAATCTT-------------------GCGACGTT----AATTTGCCCTAAG-------------------TTCTTG-TATATTGGGCTTGCCTTTGCTTGACTAGAATTTGGGCCAGATCAGATGTGAC--TCACACATGGTTATGTCAGAATTTTGGCACACTCAACTCAGACAGTGAAAT---TTAAAACCCTGAAATTCAAAAG-CTATCAACTAAGTAAATCCATCTTTCTAAATGGA---TGCTCAGGCA-CATTCTTCTTATGGATT---AATACTTTCGATTAGCAATAAT-AAACAGAAATAATATGCATAGAACAAAATACCTGCTTAAATGCTTTTT-TTGTTTTATTCTTATTTAATTATGTGGATGAAAATAACTGCCTTGAAAAACCAAGAAATGTCTGCTG-TTTAAAAGCAATTCATGTTAAAACAGTGCCCTCTTGTGACAATATGTTGTATGTCTTACTCGTAAAAGTTGATCTTATTTTACCTTATG-----CTCTATAGAATTCTACCTTATGACAATAGCATGAAAAAGAA i oryCun2.chr14 C 0 C 0 s bosTau4.chr1 138201401 771 - 161106243 tttccagttctgt-----aagAAGCCCAAATTGGAGCAAGTTGGGGCAAGA------TGGACATTTATAGCACTGTGGG--CTGCTCTTGGAAAGAACAC-TGACTTTGA-GAGAAGTAACTGGTCAGCCTCG----GACAGGGTCAGACAGCCTGGGAGAG--ATG---------TGACACTGCTGATCTGAG--------------------------GGTGCCCTCTCTGTGTCTC-----ACAGA-CAAGACCAG-CCAT-TACC--AAGA-------AAATGTACTTGTTATCAATATGTCCAAATAGCCCTGTGTCTTT---ACGCAGTTTCTGAGTTAAAAATTAGAAACAT-ACATCCA-------------------CTGACATT----CATTTGCTTGTGG--------GTAATATATCAGTCTGGATCCTTCCAGCTTGCCCTTTCTTGGTTAGAATTTTGGGTAGCTCAGAGGAGAATTTCACATTTGATCATATGA-GATTTTGGTGCATTCAACCCAGCC--ACTGAC---CTTCAG--TTGATATTTAAAAG-ATACAACCTATATAAACCCTTATTTCTACATGAAAC-CATTCAGTTCTTATTTTCCTTGTCGGttttaaatattttt-attagtaataat-acaaaaaaaaaaCATGCAGAATGCAAAATATCTGCTTGAATATTTTGTATTGTTTTATCATTATTTGGTTACGTGGATTAAAGTAACTGTCTTAAGTTACCAAGGAATGGCTTCAGGTTGAGGAACAATCCATGTTAAAAGGCTGCCCTCTTGTGACAATGTGTTTTATGTTTTATTGGTAAAAC-TGACCT----------TATACCCTTTAGAAATCAACTC---------ATAATAGTATTAAAAAGaa i bosTau4.chr1 C 0 N 0 s equCab2.chr26 13375716 790 + 41866177 tttccatttcagtgagtAAAGAAAccaaaattgaagcaaggtgaggc----------caggcatttagagcactgtggg--ctgctcccgggaaggacacgtgactttgg-gagaggcaac---tctattctgaggACACAGGAAGGGAGTGCA-GGGAGAG--ATG--------CTGATGCTGCTGAACTGAG--------------------------AGCGTCCTCTGCATGTCCA-----ACGGATCAAGACCAG-CCATACACC--AAGGCATCTTGCAATTTACTCTTTGTCAATATATGCAAATAGCATTGTGTCTTT---AGACACTTGAGAGGTTAAAATTTAGAAACAT-AAATCCA-------------------ACGACATT----CATTTGCCCTTGG--------CTGATATATCAGTCTGGATGCTTCCAGCTTGCCTTTGCCAGGTTAGAATTTTGAGTAGATCAGAGGAGAA-TTCACATTTGGTCACGTGA-AACTTTGGTATACTCAATTCAGCC--ATTGAT---CTACTGTCTTGATGTTTAAAAAGGCAGAATCTATGTAAACCCATCTTTTTATGTGAGAC-AATTCAGCCCTTGTTTTCCTTATGGACTTTAAATATTTTTAGTTAGCAGTAAT-GAAAAAAAAACAACCACACGATGCAAAGCATCTGCTTGAATGTTTTGTATTGTTTTATCATTATTTAGTTGTGTGGATTAAAGTAACTGCCTCAAAATTTCAAGGAATGTCTACAGATTGAGGAACCATTCATGTTGAAAGGCTGCCCTCTTGTGACAATGTGTTGTGTGTTTTACTGGTAAAA--TGACCTTAT-----CTTATACCCTCCAAAATCCAAGTC---------ATAATAACATAAGAAAGAC i equCab2.chr26 I 927 C 0 s canFam2.chr31 14127672 706 + 42263495 tttccagttcagtaagAAGAGAAACCCAACTTGGAGCAAGGTGGGGCAAAGTGGGGTCAGGTAGTAATAACACCATGTG--CTACTCCTGGAAACATCTCATGACTTTGG-TAGAAGTGAC---TCTATCCCG---------------------------------------------------------------------------------------------------CTGTGTT-----ACAGACCAAGCTCAG-CCATACACC--AAGACATTTTGCAACTAACTCTTTATCAATATAT-CCAACAGCATTGTGTCTCT---AGACA-TTAAAAGTTTAAAAATTAGAACAAG-CAATTCA-------------------ATTATGTT----AATTTG-CCTTGG--------CTAAAATATCAGTCTGGATGCCTCCAGCTTGCCTTTGGTTGGTTAGA--------------------------CACATTTAGTCATACAA-AACTTTGGTGCACTCAACTCAGCC--ATTGACCTACTACTGACTTGATGTTTAAAAA-GTATAATACATGTAAACCCATCTTTCTACATAAGAC-AATTCAGCCCTTGTTTTCTTTATAGATTTAAAATATTTTT-GTTAGAAGTAAT-GAAGAAAACCAACATGAATAAATTAAAATATCTGCTTGAATATTTTGTATTGTTTTATC---ATTTAGTAAAAGACATT-GAGTAACTGTCTTAAAATTTCAAGTAATGCCTACAGGTTGAAGAACAATTCATGTTAAAAGGCTGCCCTCTTGTGACAATGTGTTGTATGTTTTACTAGTAAAACTTGACCTTA--------TACCCCCACTAAAATCCAATTC---------ACGATAGGATTAAAAAGAT i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20636970 729 - 62548349 ttttcaataaaatgagtatagaaactcaaattggagc--------------------caggcattaatagcactttagg--ctgctccagggaaggggtcatgaccttgg-gagaagtgat---tctattttg----------------------ctgagggcaatGGGGAGTTTCCCATACTGCTGACCTGAG--------------------------AGTACCCTCTGTAGATCTT-----AGAGACCAATGCCAG-CCATACCAC--AAGAGTTCTTGCAATTTACTTTTTATCATCATATCCACATAACATTGTGTCT---------------GGGGCTGAAACTTTGAAACAT-ATATCCA-------------------ATTGCATC----CATTTGCCCTTGA--------CTAATACATCAGTCTGGATTCGTCCAGTTCCCCTCTGCTTAGTTCAAATTTTAGGCAGATCAGAGATAGA-TTCACGTTTGGTCACGTGAGAATTTTGGTACACTC-----AGAC--CTTGAC---GTAG----GTGATGTTTATAAA-ATATACCCTAAGGAAAACCATCTTTCTATGTGAGGC-AATTCAGCCATTGCTTTCCTTACACATTTTTAATATTTTCAATTGGCAGTAGT-AAAAAAAATTAAC----------CAACTTATCTGCTTAAATGTTTTATATTGTTTTATC---AT-TAGTTGTGTGGATTAAAGTAAC-------AGCTTTCAAGAAATTTCTACAGGTTGAGGAAAAATTTATGCTAAAAGGCTGCCCTCTTGTGACAATATGTTGTATGTTTTATTGGTAAAACCTAACTTCAT-----CTTAGACCTTTTAGAATTCAACTC---------ATAACGGCATAAAAAAGAA i loxAfr3.scaffold_13 C 0 C 0 a score=196150.000000 s hg19.chrUn_gl000245 31970 177 + 36651 -ACAAA--ACCTT-ACATAATTTTGAA-----TTTTAAAAA---GTACCTTGTTTATATGGCTCCTTTAGCTAATGAATAGTCAATTT--GGTAAATATTCAAGTGAGTTGAAGGTTTGAAT--AT-CTC---ACTTAACTAG------CTTGATGAATGTATTTCTAAACCTATACAA-CCCACTCCTCT-GCTTTTAAAAA---------------------------------AT s panTro2.chrUn 47428413 179 - 58616431 -ATAAA--ACGTT-ACATAATTTTGAA-----TTTTAAAAA---GTACCTTGTTTATATGGCTTCTTTAGCTAATGAATAGTCAATTT--GGTAAATATTCCAGTGAGTTGAAGGTTTGAATCCAT-CTC---ACTTAACTAG------CTTGATGGATGTATTTCTAAACCTATACAA-CCCACTCCTCT-GCTTTTAAAAA---------------------------------AA i panTro2.chrUn C 0 I 330 s ponAbe2.chr21_random 861994 179 - 4212913 -ATAAA--ACCTT-ACATAATTTTGAA-----TTTTAAAAA---GTACCTTGTTCATATGGCTCCTTTAGATAATGAATAGTCAATTT--GGTAAATATTCCAGTGAGTTGAAGGTTTGAATCTAT-CTC---ACTTAACTAG------CTTAATGGATGTATTTCTAAACCTATACAA-CCCACTCCTCT-GCTTTTAAAAA---------------------------------AT i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189473765 179 - 189746636 -ATAAA--ACCTT-ACATAGTTTTGAA-----TTTTAAAAA---GTACCTCGTTGGTATGGCTCCTTTAGATAATGAATAGTCAGTTT--GTTAAATATTCCAATGAGGTGAAGGTTTGAATTTAC-CTC---ACTTAATGAG------CTTAATGGATGTATTTCTAAACCTATACAA-CCCACTCCTCT-GCTTTTAAAAA---------------------------------AT i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15835509 185 - 24440124 -AGAAAACACTTTAATATGGTTTTGGA-----TTT--AAAA---ATACCTTCTTTATATGTTACTTTTGA--CAATAAAGGTTCAGTTCAGGTAGTTATTTTAGGGAGTGGAATGATTTAATCCGT-CTCATTATTTGATTAGCATAAGCATAATAAA--TATTTCTAAACATATTCAA-CTCACTTCTCT-GCTT--AAAAA---------------------------------TT i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141922395 150 + 163896628 -ATAAA--ACTTTAATGCG-------------------------------TTTGTATATGCTACCTTTGGATAAATAATGCTTTGCTTTAGGCAGATAGTTCAGGGAACTGAAAGGTTTGGTCTAT-CTCATTATTTAACCAG-------------------TTTCTAAACATATACAACCCCACTTGCTT-GCTTTAAAAAA---------------------------------AA i oryCun2.chr14 C 0 C 0 s equCab2.chr26 13376506 216 + 41866177 -ATAAA--ACCTTAATGTAACTTGGGA------TTTAAAAATATATGTATTGCTTATATTGCACCATTGGATAACGAATAGTTCTGATTAGGTAGATGTTCCTGGGAGCTGAAAGTTTAAAGCCAT-CTCATTATT----TAA------CTTAATGGATATATTTTT-AACATATACAA-CCCACTTCTCTCGCTTTTAAAAAGCTAAATTCTgggggccagcccagtggccatgtgg i equCab2.chr26 C 0 I 1 s canFam2.chr31 14128378 188 + 42263495 -ATAAA--ACCTCAATGTCATTTGTGATTTCTTTTTAAAAA---AAATCTTGCTTATATGGCAATTTTAGATAATGAATTGTTCTGATTAGATAGGTGTTCCAGGGAGCTGGAA-TGTAAACCCAT-CTCACTATTTAACTAA------CTTAATATATAAATTTCC-AATATATACAA-CCCACTTCTCT-GCTTTTAAAAA---------------------------------AG i canFam2.chr31 C 0 I 1 s loxAfr3.scaffold_13 20637699 169 - 62548349 AAGAAAGCACCTTCATGTAGCTCTGGA-----TTTTTTAAA----TACCTTGTCTATGTGCCATTTTTGAGTAATGAATATTTCTGATTAGGTATGT----------------GGTTTAAATCCATCCTCATTATTTAACTAT------TTTACTGAACATATTTCT-AATGTATACAA-CCCATT--TCT-GTTTCTAAAAA---------------------------------AA i loxAfr3.scaffold_13 C 0 C 0 a score=6191.000000 s hg19.chrUn_gl000245 32147 37 + 36651 TAA-------AGTT--------------------------------------------------------------------------------------------AGC-TGTAGATTGA--------GATGTCAG-TGACACAGT s panTro2.chrUn 47428922 37 - 58616431 taa-------aGTC--------------------------------------------------------------------------------------------AGC-TGTAGATTGA--------GGTGTCAG-TGACACAGT i panTro2.chrUn I 330 C 0 s ponAbe2.chr21_random 862173 37 - 4212913 TAA-------AGTT--------------------------------------------------------------------------------------------AGC-TGTAGATTGA--------GATGTCAG-TGACACAGT i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189473944 37 - 189746636 TAA-------AGTT--------------------------------------------------------------------------------------------AGC-TGTAGATTGA--------GATGTCAG-TGACACAGT i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15835694 31 - 24440124 TAA-------AGTT--------------------------------------------------------------------------------------------AGC-TGCAGAT--G--------TCTGTGA-----AACATT i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141922545 37 + 163896628 TAA-------AGTT--------------------------------------------------------------------------------------------AGC-TATAGATTGA--------GATGTGAC-AGGCACACT i oryCun2.chr14 C 0 C 0 s equCab2.chr26 13376723 139 + 41866177 taa-------gtttgtgcattcctcttcagcggcccagggttcatgggtttggatcctaggcacagacctacacaggtctcatcaggccatgctgtggcagtgtcccacatacaaaatgaaaaagattggcagatgctagctcaga i equCab2.chr26 I 1 I 118 s canFam2.chr31 14128567 37 + 42263495 TAA-------GTTT--------------------------------------------------------------------------------------------CAC-TACAAATTGA--------GGTATATG-TGGTGCACA i canFam2.chr31 I 1 C 0 s loxAfr3.scaffold_13 20637868 43 - 62548349 -AAAAAAATTAGTT--------------------------------------------------------------------------------------------AGC-TGTAGTTTGA--------GATGGTAC-TGACATAGC i loxAfr3.scaffold_13 C 0 C 0 a score=109343.000000 s hg19.chrUn_gl000245 32184 74 + 36651 TCATAGAAC---ATAACTTAGATTGTCATCTACATTACT--GTAACTACAAATACCA-CCCTCAGATGGAAGAATAAGTT s panTro2.chrUn 47428959 74 - 58616431 TTATAGAAC---ATAACTTAGATTGTCGTCTACATTACT--GTAACTACAAATACCA-CCCTCAGATGGAAGAATCAGTT i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 862210 74 - 4212913 TTATAGAAC---ATAAGTTAGATTGTCATCTACATTACT--GTAACTACAAATGCCA-CCCTCAGATTGAAGAATCAGTT i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189473981 74 - 189746636 TTATAGAAC---ATAACTTAGATTGTCATCTACATTACT--GTAACTACAAATGCCA-CCCTCAGATTGAAGAATCAGTT i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15835725 76 - 24440124 TCATAAAAT-TGTTGATCTAAATTTATATCCATATTACT--ACAACTATAATCATCATCTCCCAAGTTAAAGAATCGGT- i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141922582 77 + 163896628 TCAAAGAATGTGACACTTTAGGTCTTCACCTATATTTCTTAATGACTGCGA--GTCA-CTCTCAGAGTGAAAAATCAGTT i oryCun2.chr14 C 0 I 1514 s equCab2.chr26 13376980 67 + 41866177 TCATACAACTTAATAACTTAAATTGTCATCTTTGTTACT--CTAAC--TGAATGTCA-CTCTCAGATTGAAG-------- i equCab2.chr26 I 118 C 0 s canFam2.chr31 14128604 68 + 42263495 TCATAGAACTTAATAAT--------TCATCTATACTACT--GGAACTGTGAATGTCA-CTCCCAGATTGAAGAGTCAGT- i canFam2.chr31 C 0 C 0 s loxAfr3.scaffold_13 20637911 76 - 62548349 TCATAGAATTTAATAACTTATGTTGTCACCTATATTACC--GTAACTATGAATATCA-CTACCAGATTGAAGAAGCAGT- i loxAfr3.scaffold_13 C 0 C 0 a score=146529.000000 s hg19.chrUn_gl000245 32258 117 + 36651 TTATCAGTGAACATCTCTAATTGAACTATAAATGGTGTATGTC-TTCTGGTTTTTACAAGCTCTTGGTCTAACACAGGGGATATATGATGT----AAA-----AATTACAAAGCAAGGTCACTcacg s panTro2.chrUn 47429033 117 - 58616431 TTATCAGTGAACATCTCTAATTGAACTATAAATGGTGTATGTC-TTCTGGCTTTTACAAGCTCTTGGTCTAACACAGGGGATATATGATGT----AAA-----AATTACAAAGCAAggccacgcacg i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 862284 117 - 4212913 TTATCAGTAAACATCTGTAATTGAACTATAAATGGTGTATGTC-TTCCGGCTTTTACATGCTCTTGGTCTAACACAGGGGATATGTGATGT----AAA-----AATTACAAAGCAAggccgcacgca i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189474055 117 - 189746636 TTATCAGTAAACATCTCTAATTGAACTATACATAGTGTGTGTC-TTCTGGCTTTTACAAGCTCTTGGTCTAACACAGGGGATATATGATGT----AAA-----AATTACAAAGCAAggccaagcgcg i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15835801 110 - 24440124 CCATCAGCAAACACCTCTAATGGGATGGAAAATAGTGCATACCACTGTAGCTTTAAAGACCTGCAGGCACAA------------ATGATGCTACAAAC-----AATTACAAAGCAAAAATTCAAATG i cavPor3.scaffold_34 C 0 I 290 s equCab2.chr26 13377047 121 + 41866177 -GATCAGTAAACATCTTTAataaaaagatgaatagtgcatgta-ttctggctttgaggagctcttggtgtaatgcaggagacagatgatat----aaacaagcaattacaaagaaaaattgcaaatg i equCab2.chr26 C 0 C 0 s canFam2.chr31 14128672 112 + 42263495 TAATCAGTAAACATCACTAATGGAAAGATGAATAGTTTATAAC-TTCTGACTTCGAAGGGCTCTTGGTCTAATACAGGAGATAGGTGATGT----GAA----CAATTGCAAAGAAAAATCA------ i canFam2.chr31 C 0 I 846 s loxAfr3.scaffold_13 20637987 118 - 62548349 TCACCAGTAAACATTCCTAATGGaaagataaagaggacatacc-ttctagcttttaagagctctaaatctaaagcaggagacagatgatgt----aaacaaacaatcacaaagcgaaattgct---- i loxAfr3.scaffold_13 C 0 I 576 e oryCun2.chr14 141922659 1514 + 163896628 I a score=19861.000000 s hg19.chrUn_gl000245 32375 41 + 36651 --gtggctcatgcctg-----taatcccagcactttgggaggccaagg s rheMac2.chr2 189474172 41 - 189746636 --gtggctcaggcctg-----taatcccagcactttgggaggccaagg i rheMac2.chr2 C 0 C 0 s ponAbe2.chr21_random 862401 41 - 4212913 --gcggcttacgactg-----taatcccagcacttcaggaggccgagg i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47429150 41 - 58616431 --gtggctcatgcctg-----taatctcagcactttgggaggccaagg i panTro2.chrUn C 0 C 0 s equCab2.chr26 13377168 48 + 41866177 ctgtagtacaggtgtacatgctatacccggaaacatggaagagaaagg i equCab2.chr26 C 0 I 286 e loxAfr3.scaffold_13 20638105 576 - 62548349 I e oryCun2.chr14 141922659 1514 + 163896628 I e canFam2.chr31 14128784 846 + 42263495 I e cavPor3.scaffold_34 15835911 290 - 24440124 I a score=125104.000000 s hg19.chrUn_gl000245 32416 253 + 36651 cgggcggatcacaaggtcaggagatcgagatcatcctggctaatatggtgaaaccccatctctactaaaaatacaaaaattagctgggtgtggtgacacacgcctgtagtcccagctactcagtaggctgaagcaggagaatcgcttgaacccaggacgcggaggttgcagtgagccgagatcgcaccactgcactccagcctggtggcagaacaagactccatct-aaaaataaataaataaataaat-aaata s rheMac2.chr2 189474213 254 - 189746636 tgggcggatcacgaggtcaggagatcaagaccatcctggctgacatggtaaaaccccatctctactaaaaatacaaaaattagctgagtgtggtggcacatgcctgtagtcccagctactcaggaggctgaggcaggagaattgcttgaacccaggacgcggaggttgcagtgagccgagatcccaccactgcactccagcctggcgtcagaacaagactccatttcataaataaataaataaataaat-aaata i rheMac2.chr2 C 0 C 0 s ponAbe2.chr21_random 862442 255 - 4212913 cgggcggatcacaaggtcagtagatagagatcatcctggctaacacggtgaaaccccatctctactaaaaatacaaaaattagctgggtgtggtggcatacgcctgtactcccagctactcagaagactgaagcaggagaatcacttgaagccaagatgcggaggttacagtgagctgagatcccaccactgcactccagcctggtggcagaacaagactccatctcaaaaataaataaataaaaaaataaaaaa i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47429191 254 - 58616431 cgggcggatcacaaggtcaggagatcgagatcatcctggctaacacggtgaaaccccatctctactaaaaatacaaaaattagctgggtgtggtggcacacacctgtagtcccagctactcagtaggctgagagaggagaatcgcttgaacccaggacgcggaggttgcagtgagccgagatcacaccactgcactccagcctggtggcagaacaagactccatctcaaaaataaataaataaataaat-aaata i panTro2.chrUn C 0 C 0 e loxAfr3.scaffold_13 20638105 576 - 62548349 I e oryCun2.chr14 141922659 1514 + 163896628 I e canFam2.chr31 14128784 846 + 42263495 I e equCab2.chr26 13377216 286 + 41866177 I e cavPor3.scaffold_34 15835911 290 - 24440124 I a score=283631.000000 s hg19.chrUn_gl000245 32669 282 + 36651 aa-taaataataaaAT--AGCAgtgactataatg-ttttgtgatgttaaactttgagagctttttttttt------ctttcttttccc-aagt-gcctttcc-cagttccaggagcagagttattctaagcccactgatgtaaaggaatagaaagaaaa-ggtttgttggaaaacctaataacctg-----ctttctgtc--ttttgttttttaaaagcttgagcatttgggagaatttggaaagattgtggagtaagtgcaaagaa---ggaa--------tttgttaa---caaaaatcat--atagg-gtaaaatga s cavPor3.scaffold_34 15836201 269 - 24440124 ---TCAATACTACAAA--TACAGTAACCACAGTAATTTCATAATCTTAG--TTTAAAAAA--TGTGTT--------CAGTATTTTCTCAAGGTTTTTTTTCC-TAGTTACTGAAGCAAAGTTATACTATACTCACTGATTTCAAGCATACAAAGGGAAA-GCTCAAT-TAAAGTTATagtaacctgaaattctttctggc--tttatttttctaaaattgtgaatctttgggagaa-ttagaaggattggggaacagatggaaagga--------------------------taaaatctat--ataaatatgacagga i cavPor3.scaffold_34 I 290 C 0 s equCab2.chr26 13377502 285 + 41866177 -ACTCTCTAGTACAAA--TACAgtgaccataatgtttttgtgatattaa-tttttagggt--cccttttt---------ttccttcct-gggtcttcttccc-cacttctaagagcaaagttattctgggctcactgatgtagaggaataaaaaggaagcaattcatggaaaggaatagtaacttgcaattctttctgac--tgttgtcttctataagcttaagcctttggaataatttagaaggtttatagaactggtggagagaa---atat--------tttgctta---atgagagact--ataaatgtgaaagga i equCab2.chr26 I 286 I 5 s panTro2.chrUn 47429445 286 - 58616431 aa-taaataataaaAT--AGCAGTGATTATAATG-TTTTGTGATGTTAAACTTTGAGAGC-TTTTTTTTT------CTTTCTTTTTCC-AAGT-CCCTTTCC-CAGTTCCAGGAGTAGAGTTATTCTAAGCTCACTGATGTAAAGGAATAGAAAGAAAA-GGTTTGGTGGAAAAACCAATAACCTGTTATCCTTTCTGTC--TTTTGTTTTTTAAAAGCTTGAGCATTTGGGAGAATTTGGAAAGATTGTAGAGTAAGTGCAAAGAA---GGAA--------TTTGCTAA---CAAAAATTAT--ATAGG-GTAAAATGA i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 862697 282 - 4212913 aa-aaaataataaaat--aGCAgtgactataatg-ttttgtgatgttaaactttgagagc--tttttttt------ctttcttttccc-aagt-ccctttcc-cagttccaggagcagagttattctaagctcattgatgtaaaggaatagaaagaaaa-ggtttggtggaaaaaaaaaaaaataa-----cttgctatcatttctgtcttttaaaagcatgagcatttgggagaatttggaaagattgtggagtaagtgcaaagaa---ggaa--------tttgctaa---caaaaattat--atagg-gtaaaatga i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189474467 287 - 189746636 aa-taaataaataaataaaACAGTGACTGTAATG-TTTTGTGATGTTAAACTTTGAGAGT--TTTTTTTT------CTTTCTTTTCCC-AAGT-CCCTTTCC-CAATTCCAGGAGCAGAGTTATTCTAAGCTCATTGATGTAAAGGAATAGAAAGAAAA-GATTTAGTGGAAAAAATAACAACCTGCTATTATTTCTGTC--TTTTGTTTTTTAAAAGCTTGAGCATTTGGGAGAATTTGGAAAGATTGTGGAATAAGTGCAAAGAA---GGAA--------TTTGCTAA---GAAAAATTAT--ACAGG-GTAAAATGA i rheMac2.chr2 C 0 C 0 s loxAfr3.scaffold_13 20638681 296 - 62548349 ---------ACAGTAC--TACAgtgactgtagtatttttgtaatgttaa-tttttaggtt--ttttttttttcttccagtgtttttcc-aaat-cctttcctgcagtggtaggagcaaagctgttctgggctcactgatgtagagagatagaaaggaga-gttggacagaaaggaacaatagc-tgtgattctttctggc--ttttgttgcctaaaagc-tgagcctttgggaaaacttagaaggacagtggagtgggtggaaagaa---ggtaaaggtgttctttctaagtgtgaaggttgttgctacatgtgaaagga i loxAfr3.scaffold_13 I 576 C 0 s oryCun2.chr14 141924173 288 + 163896628 ---------ACAAAAA--AGAAACAACCataatgtttttgcaatgttaa--ttttaaagt--tttttttt-tcttccattatttcccc-atgtactctttcc-cagttccagaagcaaagttgttctgggctcattgatttaaaagaatagacaggagg-gtttaatggagaagaataataacctccaattctttctggc--ttttgttttctaaaagttgaagccttcaggaaaatttaaaaagctcataacataggtggaaaacagaaggca--------ttagctta-ttgaaaaaatat--gtaaatgtagaagga i oryCun2.chr14 I 1514 C 0 e canFam2.chr31 14128784 846 + 42263495 I a score=612379.000000 s hg19.chrUn_gl000245 32951 520 + 36651 g-----ttttttccagg--ttagaaaatatccactccctaccctcctacattcctttcccatggttaagaagaggaaaaaacaa-a--ggcttcttggtgagcagtggtgactt---a--ggc--ag------tttcttag-aaatattctagaaggcatagtcatctttt---aaaaaaaaaatagctacaaggatatgtctaagcagaagggtccatgggccaa--attacgtgtagatttttgcattccaaatatggtaaagaagaagcaggaagctggggctccttaacaggtcacacagaaatggacaaggaagaggccagcagcagcttgtggggacaagatgtcaagccccaaatgttaaaccc----------accaaccatcctccaaattctggctctgtttaaCAAGgctgtggtctgaca-ctacatgccgcctcagtgact----aaagcataattt-cccg-tctcctgggagtgttgacagctgactcctggcaacaatactcacagcacagtaaagttccttcatc------------------------------caag---ttcatgt-cccttctcaaggc s panTro2.chrUn 47429731 516 - 58616431 G-----TTTTTTCCAGG--TTAGAAAATATCCACTCCCTACACTCCTACATTGCTTTCCCATGGTTAAGAAGAGGAAAAAACAA-A--GGCCTTTTGATGAGCAGTGGTGACTT---A--GGC--AG------TTTCTTAG-AAATATTCTAGAAGGCATAGTCATCTTTT------AAAAAAATAGCTACAAGGATATGTCTAAGCAGAAGGGACCATGGGCCAA--ATTACGTGTAGATTTTTGCATTCCAAATATGGTGAAGAAGAAGCAGGAAGCTGGGGGGCCTAAACAGGCCACACAGAAATGGGCAAAGAAGAGGCCAGCAGCAGATTGTGGGGACAAGATGTCGAGCCCCAAATGTAAAACCC----------ACCAACCATCCTCCAAATTCTGGCTCTGTTTAACAAGGCTGTGGTCTGACA-CTACATGCCGCCTCAGTGGCT----AAAGCATAATTC-CCCT-TCTCCTGGGAGTGTTGACAGCTGAGTCCTGGCAACAATACTCACAGCACAGTAAAGTTCCTTCATC------------------------------CAAG---TTCATGT--CCTTCTCAAGGC i panTro2.chrUn C 0 I 17 s ponAbe2.chr21_random 862979 515 - 4212913 g-----tttttttcagg--ttagaaaatatccactccctacactcgtacattcctttcccatggttaagaagaggaaaaagcaa-a--ggcctcttggtgagcagtggtgactt---a--ggc--ag------tttcttag-aaatattctagaaggcatagtcatctttt-----aaaaaaaatagcaacaaggatatgtctaagcagaagggaccacgggccaa--attacgagtagatttttgcattccaaatatggta---aagaagcaggaagccggtcggcctaaacaggccacacagaaatgcacaaggaagaggccagtagcagcttgtggggacaagatgtcaagccccaaatgttaaaccc----------accatccatcctccaaattctggctctgtttaaCAAGgctgtggtctggca-ctagatgccgcctcagtgact----aaagcataattc-cccg-tctcctgggagtgttgacagctgactcctggcaacaatactcacagcacagtaaagttccttcatc------------------------------caca---ttcatgt-cccttctcaaggc i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189474754 504 - 189746636 G-----ATTTTTCCAGG--TTAGAAAATATCTACTCCCTACACTCCTACGTTCCTTT-CCACGGTTAAGAAG---------CAA-A--GGCCTCTTGGTGAGCAGTGGTGACTT---A--GGC--AG------T---TTAG-AAATATTCTAGAAGGAATCGTCATCTTTA----------AAATAGCTACAAGGATATGTCTAAGCAGAAGGGACCATGGGAGAA--ATTACTAGTATATTTTTGCATTCCAAATACAGGAAAGAAGCAGCAGGAAGCTCGTGGGCCTAAACAGGCCTCACAGAAGTGGACAAGGAAGAGGCCAGCAGCAGCTTGTGAGGACAAGAAGTCAAGCCCCAAATGTTAAACCC----------ACCGTCCATCCTCCAAATTCTGGCTCTTTTTAACAAGGCTGTGATCTGGCA-CTAGATGCCTCCTCAGTGACTAAAGAAAgcatcattc-gccc-tctcctgggagtgctgacagctgactcctggcaataatactcacagcacagtaaagttccttcatc------------------------------caag---ttcatgt-cccttctcagggc i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15836470 516 - 24440124 gaaaagtttttcccagagttgaagaagaccccactcccttcacccttgtattcctttcccgtggttaaga----gaaaacagaa-a--ggcctcttggtga--------gaatt---ataaac--agcacaatttccctagcaagtctcccagaaggaatgaagatttcag------aaaaaaaaagctaaaagagtatgtacaggcagaaggaacgatgggtaga--ttcatgagaa---ttttgtattccctatacaggaaa-aagcatcagtgagctggtgggcctatacatgctatgcagaaatagacaaaggtaagactgatagtagctgatgtggataagtggtcaaatacc-aatggccatatccaccatatccaccattcattctctgtgctctgactctgtttaaCAGG---CTGATCTGCCA-CTAGATGCATCCTTAGTAACT----GAAGCATCATTT-TCCA--CTCCTGGGACTGTTGATA-------ACTGACAGTAAAGCATATTTCTCAGTAAAATTCcttcatc------------------------------caagatatttacc---ttttcccatgag i cavPor3.scaffold_34 C 0 I 1 s oryCun2.chr14 141924461 459 + 163896628 gaaaatatttttcctgtactagaaaaacatccactcctacta-ccttacatacatttgtcctggttaaga----gaaag-agaa-a------------------------actt---atccat--ag------tttcctag-aaatatactagaaggcacaaagatcccag------aaacaaataggtgtcagtgtgtgtctagacagaaggggccatgggcaga--gtcatgagaaaatttttgcatattgaatatggtaaacaggcatcagtga-----------------------CCAGAAATAAGCAGAAG-------------AGTGTGTGTGTACTGGTGGTCAAGCACTAAATGACCGTCTC-----------CTGTCCTTCTTCCACATCCTGGCTTTGTTTAACAAGGCTGTGGTCGGCTA-CTAGGTGCCCCCTAAGTGAGC----AAATCATCAGTC-TCCA-GCTCTTGGGAGTGCTAATAGATGACTGCTGGCAATAATATCCATTCCTTAGTAAGGTCCCCTCATC------------------------------CCAG---TGCACA---CCTACTCAGGGA i oryCun2.chr14 C 0 I 1 s equCab2.chr26 13377792 520 + 41866177 ------attatccccgtttt---taaaaatccactctccccacctctacattctctccccatggttgagaggaggggaaaacag-g--ggccccttgataagcagtggatacct-ggg--agc--ag------ttccctgg-aaatatcccaggacatgtaaaggccccag-----aaataagagagctacaggtg--tgtctaggtggaagggtcaatggaaagactctcatgagaggatttttttactccaaatatggtaaagaagcagcagtgagcttgtgggcctaaacgagccatgcagaaatggacaaaggagaggccagtagcagcttgtgtgggcagatggtcaggcactaaacgcctaacc-----------atcatccatcacccatgttctggctctgCTTACAAacactgtactctgccacccagatgccttcgtcaggacc----gaagcatcattctccca-gctcctgggagtattgatagttgatgtgttgtaataatgctcacagctgaataaaatcatctcatc------------------------------caaa---ctcatagccccttctcaggga i equCab2.chr26 I 5 I 1 s canFam2.chr31 14129630 522 + 42263495 ------ATTTTCCCCAGATTAGGAAAAAATCTACTCTCCACACCTCTACATTCCATCTCTGTGGTTGAGAGGAGGGGAAAACAGAA--GGTTCCTTGATCAGCAGTGGAGACCTAGAA--AGC--AA------TTTCCTAG-AAATATCCCATGAGATCTAAATGTCCCAGAAAAAAAATAAAAAAACTACAATGG--TGTTTAGGCAGAAGCGGCCATCAGGAGA--CTCATGAGAGGATTTTTATGCTCCCAATATGAGAAAGAACCAACAGTGGGCTTGTGGGCCTCATTGAGCCATGTGGGAATGGACAAAGGAGAGACCAACAATGGCTTGTGTGGACAGGTGGTCAG---CTAAGGACCTAACT-----------ACCATCCATCTCCCACACTCTGGCTCTGCTTACCAAGGCTGTGCTCTACCACCCAGAGGCCTTCATCAGGACT----AAAGCAGCATTCTCCCA-GCTTCTAGGGCTGCTGACAGCTGACTCCTTGCAGTAATG-TCACAGCTGAATATGAATATCTCATC------------------------------CAAG---TTCATAA--ACTTCTAAGAGA i canFam2.chr31 I 846 C 0 s loxAfr3.scaffold_13 20638977 515 - 62548349 -gaaagaatttccccagattagagaaaaatc------cctcactccaacatccccttcccatggttgaaaggaggggaaaacag-agtggcctctcggttggcagtggggatct---a--ggcctag------ttttctac-aaatatccccagaggtgttaagatttcag-------aagaagtgtctgt-ggggtctgtctaggcagaaggggctgtgagcgtg--ctcttgacaagattcttgcattccaaagactgtaaa-gagcagcagtgcgctcctgggcctaaatgggccatgcat-aatggacaaaggagaggcaagcagcagactgtgtgaacagatggccatgcgtcaaatg------------------cctactcacccccaatacccttggt----------agactacgatctgccacccagatgcctccttcagggct----gaagcatgattc-cccaagcttctgggTGGACCA--GGGTGAGTCTTGAAAATAATGCTTACAGCTGAATAAAGTCACTTAATTGTGCAAATAGTTAACACGCTAAGTAGCTAACAGG---TTGATG--------------- i loxAfr3.scaffold_13 C 0 I 131 a score=44526.000000 s hg19.chrUn_gl000245 33471 112 + 36651 at-c---ccacatccgagaactgcttggtacagaaatataatggcctggttttcttgctccaattcgaggtcattaggtaaactcaccaagat-cttgtagagtggactgcggccat s ponAbe2.chr21_random 863494 113 - 4212913 at-c---ccacatccgagaactgcttggtacggaaatataatggcctggctcgcttgctccaatttgaggtcattaggtaaactcaccaagatccctgtagcgtgggctgtggccat i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189475258 113 - 189746636 at-c---ccacatccgaggactgcttggtacagaaatataatggcttggcttccttgctccaatttgaggtcattaggtaaactcatcagggtccctgaagagcgggctgtggccat i rheMac2.chr2 C 0 C 0 s cavPor3.scaffold_34 15836987 112 - 24440124 at-g---ttacagtcaaggactggccaatatagaaatataatggcttggtcactggctccc-ataggagaaagctttacaggaccatcacaatccctgtgggatgagctgaggtcat i cavPor3.scaffold_34 I 1 C 0 s oryCun2.chr14 141924921 82 + 163896628 ATCC---TTACA--CAGGGGCTGGCCAGTGTAGAGATGCAA-GGTGTAGCCACCTTctcccaacatgaggtagtttt-----------------------------gttggtgccat i oryCun2.chr14 I 1 C 0 s equCab2.chr26 13378313 89 + 41866177 ----gggccatatccaaagactggtcagtgagggcctataaaggcctggctctttcaccccaatgcaggacagttttatagacccatcAGAGT------------------------ i equCab2.chr26 I 1 C 0 s canFam2.chr31 14130152 62 + 42263495 -------CCATATCCAAAGGCTGGACAATGTAGTTACATAAAGTTCTGGCTCCTTTACACCAATTTAGG------------------------------------------------ i canFam2.chr31 C 0 I 14 s loxAfr3.scaffold_13 20639623 112 - 62548349 ----agcccacctccaaagactggtcaaaacgggg-tataaaatcttggctcccttgcaccaacttggggcagttctgtagactcatggtgacccccatagcatcagctgaggccat i loxAfr3.scaffold_13 I 131 C 0 e panTro2.chrUn 47430247 17 - 58616431 I a score=371739.000000 s hg19.chrUn_gl000245 33583 477 + 36651 gatagtgattgcattccag-ccgacttcctgctccacccaatc--ctattgctttcact-cttccacaggtgtt--------gggaatat-----------------------------------------------------------------catttcaacctccttgcatgcaaatctccaactcggagtcgg--cttcctaggacacctgactggtgataTCTCTATCACTATCACAGTACTTAGAggggag---catcttaaaatgat--tgaaggctaactgccctaacagcacaggcagatgatggcttaaaatagaatttaagtgga-tttaaaaaaacatgaaaaaagttgacattgcacgctcatatgagcttatggaTCAAACCATGTGTATGATTTCTAAGATCCCTCGTGCAGTATATATTTGCACTGTTTATAAA-TGACATCCCCTTGAATTGAATTCAGTGCAATTCAAAAC---AGTAATT----TGTGGGAAAAATTAGATATGCAGATAACCTGGACTCTAGAGAAGCACACATCATTTGGAGAATAATA s rheMac2.chr2 189475371 482 - 189746636 gatagtgattgccttccag-cccacttcctgctctgcccaatc--ctattgctggcact-cttccacaggtgtt--------gggaatat----------------------------------------------------------------ccatttcaacttccttgcatgcgaatctccatctcggagctgg--cttcctaggACACATGACTGGTGACATCTCTGTCACTATCGCAATACTCAGGGGGGAG---CATCTTAAAATGAT--TTGAGGCTGACTGCCCTAACAGCACAGACAGATGGTGGCTTAAAATAGAATTTAAGTGGA-TTTAAAAAGACATGAAAAAAGTTGACATTGCATGCTCACATGAGCTTATGGATCGAACCATGTATGTGATTTCTAAGATCCCTCGTGCAGTATATATTTGCACTCTTTATAAA-TGACATCACCTTGAATTGAATTCATTGCAATTCAGAAC---AGTAATTAATCTGTGGGAAAAATTAGGTATGCAGATAGCCTGAACTCTGGAGAGGCGCACATCATTCGGAGAATAATA i rheMac2.chr2 C 0 C 0 s ponAbe2.chr21_random 863607 543 - 4212913 gatagtgattgcattccag-ccgacttcctgctctgcccaatc--ctattgctgtcact-cttccacaggtgtt--------gggaatatccatttcaacttcctgctccacccaatcctattgctggcactcttccacaggggttgggaatatccatttcaacttcctcacgtttaaatctccatctcggagttgg--cttcctaggacacctgactggtgacaTCTCTATCACTATCACAGTACTTAGAGGGGAT---CATCTTAAAATGAT--TTAAGGCTAACTGCCCTAACAGCACAGACAGATGGTGGCTTAAAATAGAATTTAAGTGGATTTTAAAAAAACATGAAAAAAGTTGACATTGCACGCTCATATGAGCTTATGGATCAAACCATGCATATGATTTCTAAGATCACTCATGCAGTATATATTTGCACTGTTTATAAA-TGACATCCCCTTGAATTGAATTCAGTGCAATTCAAAAC---AGTAATT----TGTGGGAAAAATGAGGTATGCAGATAGCCTGGACTCTAGAAAGGCACACATCATTTGGAGAATAATA i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47430264 476 - 58616431 GATAgtgatagcattccag-ccactttcntgctccacccaatc--ctattgctttcact-cttccacaggtgtt--------gggaatat-----------------------------------------------------------------catttcaacctccttgcatgcaaatctccaactcggagtcgg--cttcctaggacacttgactggtgacaTCTCTATCACTATCATAGTACTTAGAGGGAAG---CATCTTAAAATGAT--TGAAGGCTAACTGCCCTAACAGCACAGACAGATGGTGACTTAAAATAGAATTTAAGTGGA-TTTTTAAAAACATGAAAAA-GTTGACATGGCACGCTCATATGAGCTTATAGATCAAACCATGCGTATGATTTCTAAGATCCCTCTTGCAGTATATATTTGCACTGTTTATAAA-TGACATCCCCTTGAATTGAATTCAGTGCAATTCAAAAC---AGTAATT----TGTGGGAAAAATTAGATATGCAGATAGCCTGGACTCTAGAGAAGCACACATCATTTGGAGAATATTA i panTro2.chrUn I 17 C 0 s cavPor3.scaffold_34 15837099 449 - 24440124 tcttgtgatag-actgcag-tcaacttcttgttctactcagttggatgcta--tttactcccATGAGT-ATGTT--------GAAAATAT----------------------------------------------------------------CCCACTAAGCTTCCTTGAGT------CTCCAC----AAGTGTGATTTTTTGAGA-CACCTGATAGgtaaaattcctataattacaacacaacccagtagggag---cgcctaaaaacacc--ctgagactaacattcctaccacgagaggtgcagagtgtcttaaaatagaatttaaatggatttaAAAGGTGC-------------------AAAGTTCATCTGGATTTATGAATAGAGTGGTGAATGTGCTTCCTAAGAACCTTCTTGTAGTACACATTTGCATTCTGTATATA-TTATAAGCCCTTGAATCAAAGCCAGTG--GTTTAAAGC-AAAGTAATGAACCGAGGGGGAAAGTTACATACGTACACAGATTA-----TGGGGATGTGCTCATGATTTTGAAAATAATA i cavPor3.scaffold_34 C 0 C 0 s oryCun2.chr14 141925003 457 + 163896628 ccttgtgattt-actgcaa-cctgtttcttcctcttcacgatc--ctgctgcctttgct-ccaccaca-gtgct--------gggaatat----------------------------------------------------------------cctatgaagccttcttgtgtgcaaacctccattttagaatctg--cttccAAGATCAGCTCACCAGTGACGTTCCTAT-------GCACAACCCAAAAAGGAAACTTGCCAAAACAAACTAACCTAGGCTAACTTTCCT------------------TGG-TTAAAATAGAAACCAAGTGG--CTAAAGGGGACATGAACCAAATGAGCATTGAATATTGACTTGAGTTTATAGATTGAGCCATGGTTATGATTATGAAGCACCACCTTGCAATATATATTTGTATTCCATATAAATTTACAGTGCCTTGAATTACAGCCAATGCATTTTCAAAC-ACAGGAAT-AACCTATGGGAAAAGTTGTAGATGGAGGTAGACTAGACTCTGGAGAAATATCCCTGAGT---AGAATAACA i oryCun2.chr14 C 0 I 879 s loxAfr3.scaffold_13 20639735 476 - 62548349 -tttgtgactgtattgcagttcagcttcttcttctgcacaatc--ctgtttccgtcact-tctccacaggtattaatcccaaggggacac----------------------------------------------------------------cccaataaacttcct-gcatatgaatttccacctcagaatctg--ttacttgggaaacctgacctgtggcacccctataactacagcacaacccaggagccag-----ccctcaaagaat--ctgacgctaactttcctgtcagtacagtggaagggtggcttaaagtaga------------cgttagaagacatgaagaaaattgacaaggcatgctcacctgagcttac-gattgagatGTGCATATGATTCCTAAGTACCCTCGTACAATACATGTGTGCAC-GTATATAAA-TTACAACCTCTTGAATTGAAGCTAATGCATTTTGAGACAAAGACAATGAACCTATTGAAAATACGGAGTATGTAGACAGGCTAG-TTCTGGAGAGTCACTTATAATTAGAGGAATAATA i loxAfr3.scaffold_13 C 0 C 0 e canFam2.chr31 14130214 14 + 42263495 I e equCab2.chr26 13378402 0 + 41866177 C a score=58373.000000 s hg19.chrUn_gl000245 34060 79 + 36651 GTGAACCAGCTAGTCTATGAGGGAAGAAAACA--GAGTGA-----ATATAGACTATTAGTGAACAAGGATATTTTCccatgtatat s rheMac2.chr2 189475853 79 - 189746636 GTGAGCTGGCTGGTCTATGAGGGAAGAAAACT--GAGTGA-----ATATAGAATATTAGTGAACAAGGAGATTTTCccatatatat i rheMac2.chr2 C 0 C 0 s ponAbe2.chr21_random 864150 79 - 4212913 GTGAACTGGCTGGTCTATGAGGGAAAAAAATG--GAGTGA-----ATATAGACTATTAGTGAACAAGGATATTTTCccatatattt i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47430740 79 - 58616431 GTGAACTGGCTGGTCTATGAGGAAAGAAAGCA--GAGTGA-----ATATAGACTATTAGTGAACAAGGATATTTTCccatgtatat i panTro2.chrUn C 0 C 0 s cavPor3.scaffold_34 15837548 74 - 24440124 ATGGACTGGTTGCACTATGAGGAAGGCAAACA--AGGTGA-----ATATAGAATATTAGTGAATCGTGAGA-----CCATGAATAT i cavPor3.scaffold_34 C 0 N 0 s loxAfr3.scaffold_13 20640211 81 - 62548349 GTGGACTAGTTGGGCTATTGGGGAAGAAAATAACAAATAATTTCTATATTCTTCATTGGTAAATAAAGAAA-----TCATATGAtt i loxAfr3.scaffold_13 C 0 C 0 e oryCun2.chr14 141925460 879 + 163896628 I e canFam2.chr31 14130214 14 + 42263495 I e equCab2.chr26 13378402 0 + 41866177 C a score=63254.000000 s hg19.chrUn_gl000245 34139 110 + 36651 tcaaattaaggtgaacttctttagagaattgtgccttagaaagaaaaagtatttccctatatttgagtcctcacaagttttcc-tacgatgagtgcttttgtgattatttt s rheMac2.chr2 189475932 110 - 189746636 tcaaattaaggtgaatttctttacagaattataccttagaaagaaaaagtgttttcctatatttgaatcctcacaagtttttc-tatgatgagtgcttttgtgattagtat i rheMac2.chr2 C 0 C 0 s ponAbe2.chr21_random 864229 110 - 4212913 tcagattaaggtgaatttctttacagaattatgccttagaaagaaaaaatatttccctatatttgaatccttacaagttttcc-tacgatgagtgcttttgtgattatttt i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47430819 110 - 58616431 tcaaattaaggtgaacttctttacagaattgtgccttagaaacaaaaagtatttccctatatttgagtcctcacaagttttcc-tacgatgagtgcttttgtgattatttt i panTro2.chrUn C 0 C 0 s loxAfr3.scaffold_13 20640292 96 - 62548349 --------------tttttcctccaaatgtatctctcagaaagaaaaaaattccctctatatttatgtcctcacaaatctctcatattaaggATGA-TTCATGATTACCTT i loxAfr3.scaffold_13 C 0 I 2276 e oryCun2.chr14 141925460 879 + 163896628 I e canFam2.chr31 14130214 14 + 42263495 I e equCab2.chr26 13378402 0 + 41866177 C a score=41326.000000 s hg19.chrUn_gl000245 34249 82 + 36651 gaataacaaagtaatatttaaagaaactctcttgccctgaatgtactttaatttatgtcaattgatgttgcatatagagatc s rheMac2.chr2 189476042 82 - 189746636 gaataacaaactaatatttaaggaaactctcttgccctgaatatactttaatttacatcaattgatgttgcgtatagagatc i rheMac2.chr2 C 0 C 0 s ponAbe2.chr21_random 864339 82 - 4212913 gaataacaaagtaatatttaaggaaaccctcttgccctgaatgtaccttaatttatgtcaattgattttgcatatagagatc i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47430929 82 - 58616431 gaataacaaagtaatatttaaagtaactctcttgccctgaatgtactttaatttatgtcaattgatgttgcatatagagatc i panTro2.chrUn C 0 C 0 e loxAfr3.scaffold_13 20640388 2276 - 62548349 I e oryCun2.chr14 141925460 879 + 163896628 I e canFam2.chr31 14130214 14 + 42263495 I e equCab2.chr26 13378402 0 + 41866177 C a score=337246.000000 s hg19.chrUn_gl000245 34331 486 + 36651 atcagagtcaagctacaa--gaaaaagaggaacata-acttagcaaagacttagaggattagtcctaatagtgtgaaatcaaaatttcaagtgagggaataaatgcagcttttaatgattactt-aaatgaa--gtttaactctagcaggatctacaagaaattggcaac--ctttggcttcagtaacagaaactcaggatatatg-cccttcagtgagtttgcattctgcatcatattgagagacactcctttaaaca-gcaataagaaacttcctgtgacaacataa----taaattcaaaaagttctgtaactcagacaatttagatagaagtgataactttggcctataaagccctgt----tcaccct---------------------------------------------------aaagatggattaaacaatgaaaaagatattgatat---caaaagttca-atcagtaatttgattaaagcatttcattaaatgtgataatttcttagt-----------------------------atattatcttacatatgcaatattcatgtgtaacaaat s panTro2.chrUn 47431011 487 - 58616431 atcagagtcaagctacaa--gaaaaggaggaacata-acttagcaaagacttagaggattagtcctaatagtgtgaaatcaaaagttcaagtgagggaataaatgcagcttttaatgattactt-aaatgaa--gtttaactctagcaggatctacaagaaattggcaac--ctttggcttcagtaacagaaactcaggatatatg-cccttcagtgcttttggattctgcatcatattgagagagactcctttaaacaagcaataagaaacttcctgtgacaacataa----taaattcaaaaagttctgtaactcagacaatttagatagaagtgaggactttggcctagacagccctgt----tcactct---------------------------------------------------aaagatggattaaacaatgaaaaagatattgatgt---caaaaattca-atcaggaatttgattaaagcatttcattaaatgtgataatttcttagt-----------------------------atattatcttacatatgtaatattcatgtgtaacaaat i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 864421 487 - 4212913 atcagagtcaagctacaa--gaaaaggaggaacata-acttagcaaagacttagaggattagtcctaatagtgtgaaatcaaaatttcaagtgagggaataaatgcagcttttaataattactt-aaatgaa--gtttaactctagcaggatctacaagaaattgtcaac--ctttggcttcagtaacagaaactcaggatatatg-cccttcagtgcttttggattgtgcatcatattgagagagactcctttaaacaagcaataggaaacttcccgtgacaacataa----taaattcaaaaagttctgtaactcagacaatttagatagaagtgaggattttggcctagacagccctgt----tcactct---------------------------------------------------aaagatggattaaacaatgaaaaagatattgatat---caaaaattca-atcaggaatttgattaaagcatttcattaaatgtgataatttcttagt-----------------------------atattatcttacatatgtaatattcatgtgtaacaaat i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189476124 489 - 189746636 atcagagtcaagcaataa--gaaaagcagaaactta-acttagcaaagacttagaggattagtcctaatagtgtgaaatcaaaatttcaagtgAGGGAATAAATGCAGCTTTTAATGATTACTT-AAATGAA--GTTTAACTCTGGCAGGCTCTCCAAGAAATCGGCAACAGCTTTAGCTTCAGTACCAGAAACTCAGCATATATG-CCCTTCAGTGCTTTTGGATTCTGCATCATATTGAGAGAGAATCCTTTAAACAAGCAACAGGaaatttcctgtgacaacataa----taaattcaaaaagttctgtagctcaggcaatttagatagaagtgaggactttggcctagacagccctgt----tcactct---------------------------------------------------aaagatggattaaacaacgagaaaggcaccgctat---caaaaattca-gtgaggaatttgattaaagcatttcattaaacttgagaatTTCTCAGT-----------------------------GTATTATCTTACACATGCAATATTCACCTGGAACAAAT i rheMac2.chr2 C 0 C 0 s canFam2.chr31 14130228 453 + 42263495 ATCATAGTCAAGCTACAAACAAAAGGTGGGGGGGGGTGTTAATTTAGGAC---AATAATTATTTCTAATGGTGTGACATCCAAATT--------GTGATTAAACACAAC-CTTAATGATTACTT-AAATGAAAGTATTAATTCCAGTGGGA------------------------------------------------------------------------------------------------------TAAACAAAGAATAGGAAATTCCTTGTGACAACATTATATATAGATTTCAAAAGTTCTGTAACT-GAGATACTT--------------TTTATGGCCTAGAAAAGCCTGTTAGATAACGTTAGTGGCTGTATATCATGGCAATGAAATCCAAGAGATTTAAACCTTTGGTATaaaggggatttaattggta-aaaagacattgatattaaaaaaaatgcatgtgaagagtttgattaaattatttcatgaaatgtgagaatttctaagtgtaagaacttctaaaaatgtttaagaaatgtaatttcttacat----agtatgtatgattaataaat i canFam2.chr31 I 14 I 182 s equCab2.chr26 13378402 482 + 41866177 --------CAAGCTGCAA--aaaagggaggaaaataaatttatcaaagac---aacaattattcctaatgatgtgatttcaaaatt--------gcaaTTAAACATGGCATTTAATGATTACTTAAAATGAACAGTTTAACTCCAGTGGGAAAGATAAGAAATTGGTAATAGCTGTGACTCCAGGGCAGGGAACTCTGGATATATGTCCTTTTAATTCCTTTTGATTCTGCATCATGTTGAGACAGAAACCCTTAAACAAGCAATAGTCaattccctgtgacaacgttatacttagatggcaaaatttctataact-agacaacttagatagacaggaagactatggcctagaaaatcctgttagataactct----------------------------------------------------aaagggagttaactgatagaaaagacattgatat---aaagaatgcatgtgaagagtttgattaaattgtttcatgaaatatcagaatttctaagt-------------------------cagtatattaccttacat----aatacgtataattaataaat i equCab2.chr26 C 0 C 0 e loxAfr3.scaffold_13 20640388 2276 - 62548349 I e oryCun2.chr14 141925460 879 + 163896628 I a score=161913.000000 s hg19.chrUn_gl000245 34817 202 + 36651 ta-------------------------------------tatacaagtaaacatttgaccatattatctgcagcataatttacata-tcaatttacatattcagttttgctcacatgaaaacttggatcttatcaataagaaaatTTGTGAAATCTTTAATTC-CTCATCCC---------CAGGAATGTAAATAAATAAATATAAATACTGTAAGTCAGTGATTTTTTCCTAGGAAGACAGT-----------AAAAATA s panTro2.chrUn 47431498 202 - 58616431 ta-------------------------------------aatacaagtaaacatttgaccatattatctgcagcataatttacata-tcaatttacatattcagttttgctcacatgaaaacttggatcgtctcaataagaaaatTTGTGAAATCTTTAATTC-CTCATCCC---------CAGGAATGTAAATAAATAAATATAAATACTGTAAGTCAGTGATTTTTTCCTAGGAAGACAGT-----------AAAAATA i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 864908 213 - 4212913 ta-------------------------------------aatacaagtaaacatttgactatattatctgcagcataatttacata-tcaatttacatattcaattttgctcacatgaaaacttggatcttctcaataagaaaatTTGTGAAATCTTTAATTC-CTCATCCC---------CAGGAATGTAAGTAAGTCAATACAAATACTGTAAGTCAGTGATTTTTTCCTAGGAAGACAGTAAAAATTTTACAAAAATA i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189476613 213 - 189746636 TA-------------------------------------AATACAAGGAAACACTTGGCTATTTTATCTGCAGCATAATTTACATA-TCAATTTGCATATTCAGTTTTGCTCACATGAAAACTTGGATCTTGTCAATAAGAAAATTTGTGAAATATTTAATAC-CTCATCCC---------CAGGAATGTAAATAAGTCAATGTAAACAGTAAAAGTCAGTGATTTTTTCCTGGGAAGACAGTAACAATTTTACAAAAATA i rheMac2.chr2 C 0 C 0 s equCab2.chr26 13378884 200 + 41866177 ---------------------------------------attataagtagatacttga--attttacctacagcataatgta--tattcaaTGTATTTATTCAGTTTTGCTCACATGAAAACCTGGATCTTCTCAACAAGAAAATTT-CGAAATCTCTAACC--CTCTTCCCTACCCAACCCAGGGACATAAGTAGATACATATA---GTTATGGGTCAGTGA-TTTTTCCTAGGATGAAAGA-----------GAAAATA i equCab2.chr26 C 0 I 6 s canFam2.chr31 14130863 241 + 42263495 tataaataaataaataaataaataaataaataaataaatattataagtagataTTTTA--TTTTTATTCACAGCCTAACTTACCTATTCAATTTATATACTCAATTGTGCTCACATAAAAACCTGAATTTTCTTAATGAGAAAACT---GAGATTTCTAACCCACTCTCTCCTCCCCCACACAGAGATGTAAGCAGATATATATA---GTTGTGAGTCAATGA-TTTTTCCTAGGAAAAAAGA-----------GAAAATA i canFam2.chr31 I 182 I 23 e loxAfr3.scaffold_13 20640388 2276 - 62548349 I e oryCun2.chr14 141925460 879 + 163896628 I a score=88691.000000 s hg19.chrUn_gl000245 35019 201 + 36651 ---CTTTACACGCCTTCTCATtgtaaacctaaataacaaacagagaaaggctctctgaaggaaaaagacacatcttagagaggagggcactgcaatgggaatatgcatgacaaagcaaac---tatatagattcaaatggtaaaggaagacaaggactttaaaagaaaaatgatcaacctggaagtatgggggagtagaaaaaaata s panTro2.chrUn 47431700 200 - 58616431 ---CTTTACACGCATTCTCATtgtaaacctaaataacaaacagagaaaggctctctaaaggaaaaagacacatcttagggaggagggcactgcagtgggaatatgcatgacaaagcaaac---tatgtagattcaaatggtaaaggaagacaaattctttaaaagaaaaacgatcaacttggaagtatgagggagtagaaaaaa-ta i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 865121 200 - 4212913 ---CTTTAGACCCCTTCTCGTtgtaaacctaaataacaaacagagaaaggctctctaaaggaaaaagacacatcttagggaggagggcattgcaatgagaatatgcatgacaaagtaaac---tatgtagattcaaatggtaaaggaagacaaggtctttaaaagaaaaatgatcaacctggaagcatgggggagtagaaaaaa-ta i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189476826 198 - 189746636 ---CTTTAGACCCCTTCTCGTtgtaaacctaaataacaagcatagaaaggctctttaaaggaaaaagacatatcttagggaggagggcattgcaatgggaatatgcatgacagagtaaac---tatgtagattcaaataggtaaaggagacaaggtttttaaaagaaaaatgatcaacctggaagtatgggggagtaggaaaaa--- i rheMac2.chr2 C 0 C 0 s equCab2.chr26 13379090 119 + 41866177 ATATTTAAGACCCCTTATCGT----GATCTCTAT-----------------TTTTTAAA--AAAAGTACACA------------------------------------AACAAAAGAGACCCTTATCT---------TGGAAAAGGAA-----------TGGCAAAAGTATGATGAA---------ATTTGGGCCTAGAACACAATG i equCab2.chr26 I 6 I 245 e loxAfr3.scaffold_13 20640388 2276 - 62548349 I e oryCun2.chr14 141925460 879 + 163896628 I e canFam2.chr31 14131104 23 + 42263495 I a score=153704.000000 s hg19.chrUn_gl000245 35220 316 + 36651 aataagggaaaa-tgaagaggcttctataattgttttgatatagttacctttgactataaagatcaacaacaaagtcaatatcagttgaagtttgggcaggcggttgctggatagatgtcctcacagaagtgtattttgtgtaaggttgctatggcctttgtgcaaggttgtggtttttgtggtattttgtaatagttttt---atcaggcctagaagcatgagaaccctctcttcaaggccttctctgaatctatttgttcaggtttcttcttctctttttaaacattagtgacagttttgattctgataactttcata s rheMac2.chr2 189477024 314 - 189746636 aataaaggaaaaatgaagaggcttgtataattgttttgacacagttatctttgactataaagatcgacaacaaggtcgatgtcagttgtaggttgggcaggtggttgctggatagatgtccccacagaagtattttttgtgtaaggttgctacggcctttgtgcaagattgtagttttcgtggtattttgtttttgtt------atcaggccaagaagcgtaagaaccctctcttcaaggccttctctgaatttttttgtctgggttttttcttttctttttaaacattaatgacagttttgattctgataactttcaca i rheMac2.chr2 C 0 C 0 s ponAbe2.chr21_random 865321 320 - 4212913 aataaaggaaaaatgaagaggcttatataattgttctgatatagttatctttgactataaagatcaacaacaaggtcgatgtcagttgaaggttgggcaggcggttgctggatagatgtcctcacagaagtgtattttgtgtaagattgctatggcctttgtgcaaggttgtggtttttgtggtattttgtgatagtttttgccatcaggcctagaagcatgagaaccctctcttcaaggccttctctgaatctattcgtccaggttttttcttttctttttaaacattagtgacagttttgattctgataactttcata i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47431900 317 - 58616431 aataaaggaaaaatgaagaggcttatataattgtttcattatagttatctttgactataaagatcaacaacaaggtcgatgtcaattgaagtttgggcaggtggttgctggatagatgtcctcacagaagtgtattttgtgtaaggttgctatggcctttgtgcaaggttgtggttttagtggtattttgtgatagttttt---atcaggcctagaagcatgagaaccctctcttcaaggccttctctgaatctatttgtccaggttttttcttttctttttaaagattagtgacagttttgattctgataacttttata i panTro2.chrUn C 0 C 0 e loxAfr3.scaffold_13 20640388 2276 - 62548349 I e oryCun2.chr14 141925460 879 + 163896628 I e canFam2.chr31 14131104 23 + 42263495 I e equCab2.chr26 13379209 245 + 41866177 I a score=43438.000000 s hg19.chrUn_gl000245 35536 87 + 36651 TCATGATCCCTAATTTC-AAAAAAAATTA----AAC------------------------------------------------------------------------------------GTGTAACTTATTTATGAT----GTATTTGATAGGCTTGGATTTGTGAATCACCTCTACTA s panTro2.chrUn 47432217 87 - 58616431 TCATGATCCCTAATTTC-AAAAAAAATTA----AAC------------------------------------------------------------------------------------GTGTAACTTATTTATGAG----GTATTTGATAGGCTTGGATTTATGAATCACCTCTACTA i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 865641 88 - 4212913 GCATGATCCCTAATTTCAAAAAAAAATTG----AAC------------------------------------------------------------------------------------TTGTAACTTATTTATGAT----GTATTTGATAGGCTTGGATTTGTGAATCACCTCTACTA i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189477338 91 - 189746636 TCATGACCCCTAATTTC-AAAAAAAATAATAATAAC------------------------------------------------------------------------------------ATGTAACCTATTTATGGT----GTATTTGGTAGGCTTGGATTTGTGAATCACCTCTACCA i rheMac2.chr2 C 0 I 5 s canFam2.chr31 14131127 175 + 42263495 TCACAATCTCTATTTaa-aaaaaaaaaaa----aaaacaaaagcagagcaaacaaaaaaTATCCTTATTCTGGAGAACAAATGACAGAAATACAATGCAGTTCAGGCCTAGAGAGGATGGATCTAACTCATTTAGGATATGCATGTTTGGTAGGCATGGATCTGCAAACCACTTCTACTA i canFam2.chr31 I 23 I 102 e loxAfr3.scaffold_13 20640388 2276 - 62548349 I e oryCun2.chr14 141925460 879 + 163896628 I e equCab2.chr26 13379209 245 + 41866177 I a score=7342.000000 s hg19.chrUn_gl000245 35623 32 + 36651 TCTAT----------------------------------AGTGGTAGATATA----------------------------------TCTGAGCCTGCTTA s panTro2.chrUn 47432304 32 - 58616431 TCTAT----------------------------------AGTGGTAGATATA----------------------------------TCTGAGCCTACTTA i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 865729 32 - 4212913 TCTGT----------------------------------AGTGGTAGATATA----------------------------------TCTGAGCCTGCTTA i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189477434 32 - 189746636 TCTTT---------------------------------AAATAGCAGATATA----------------------------------TCTGAGCCTGCTT- i rheMac2.chr2 I 5 C 0 s canFam2.chr31 14131404 99 + 42263495 TCTATTTTGACTTTTAAAATAAAACCCATATGATTGTTAACTGGATGATACACAGTAATCCTTGTCTCTCTTTTCCCCTCACTCCTTTTGAGCCTGCCT- i canFam2.chr31 I 102 C 0 e loxAfr3.scaffold_13 20640388 2276 - 62548349 I e oryCun2.chr14 141925460 879 + 163896628 I e equCab2.chr26 13379209 245 + 41866177 I a score=117755.000000 s hg19.chrUn_gl000245 35655 139 + 36651 CACAGCACTTCCATCAGATTCT-C-TCTTCAGTGGAATTGGAAGAG-GGG---------GTTTTGGAGAAGGGAATGAAG-GAATTGTGCTGCATCAGAGGTCCCCACCTA-ACAGCACAGGGCCTTTTTCTGTGCTCTTGCCAGGCCGTTGT s panTro2.chrUn 47432336 141 - 58616431 CACAGCACTTCCATCAGATTTTTC-TCTTCAGTGGAATTGGAAGAGTGGG---------GTTTTGGAGAAGGGGATGAAG-GAATTGTGCTGCATCAGAGGTCCCCACCTA-AAAGCACAGGGACTTTTTCTGTGCTCTTGCCAGGCCGTTGT i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 865761 139 - 4212913 CACAGGACTTCCATCAGATTTT-C-TCTTCAGTGGAATTGGAAGAG-GGG---------GTTTTGGAGAAGGGGATGAAG-GAATTGTGCTGCATCAGAGGTCCCCACCTA-ACAGCACAGGGACTTTTTCTGTGCTCTTGCCAGGCCGTTGT i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189477466 138 - 189746636 -ACAGGACGTCCATCAGATTTT-C-TCTTCAGTGGAATTGGAAGAG-GGG---------GTTTTGGAGAAGGGGATGAAG-GAGTTGTGCTGCATCAGAGGCCCCCACCTA-ACAGCACAGGGACTTTTTCTGTGCTCTTGCCAGGCCATTGT i rheMac2.chr2 C 0 C 0 s equCab2.chr26 13379454 149 + 41866177 CACAGGTCTTCCACTAGGTTTT-TCCCTTTGGTGGCACTGGAAAGA-AGGTCTCAACACATTTTAGA--GAACGATGAAGAAAATTATGCCACGTTAGAAGGCCACTTCTACACAACACATGAACTTTTGTTTTCCTCTTGCCAGGCTGTTGT i equCab2.chr26 I 245 I 2445 s canFam2.chr31 14131503 149 + 42263495 -TCAGGATTTCCACTAGATTTT-G-GCTTTGATGGAGCTAGAAAGG-GGGTCTCAACATGTTTTAGAAGAAAGGATGAAAAAAATTATGCCACATTAGAAGGCCACATCTATACAACACATAAGTTTTTCTTTCACTCCTGCCAGGCTGTTGT i canFam2.chr31 C 0 I 5310 e loxAfr3.scaffold_13 20640388 2276 - 62548349 I e oryCun2.chr14 141925460 879 + 163896628 I a score=22073.000000 s hg19.chrUn_gl000245 35794 44 + 36651 ATT-ggctgatgcaaaagtaattttggttttgtcattgaaagtaa s panTro2.chrUn 47432477 45 - 58616431 Attaggctgatacaaaagtaattttggttttgtcactgaaagtaa i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 865900 45 - 4212913 Attaggctgatgcaaaagtaattttggttttgtcattgaaagtaa i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189477604 45 - 189746636 Attaggctgatgcaaaagtaattttggttttgtcaatgaaagtga i rheMac2.chr2 C 0 C 0 e loxAfr3.scaffold_13 20640388 2276 - 62548349 I e oryCun2.chr14 141925460 879 + 163896628 I e canFam2.chr31 14131652 5310 + 42263495 I e equCab2.chr26 13379603 2445 + 41866177 I a score=85001.000000 s hg19.chrUn_gl000245 35838 84 + 36651 tgAGACCATCTGACTTACAAT---GTCTGTGCCATAACCAGCTCCTAATAGCCTCCGAGGACAGCTTTGCCCTGACATATACTGTCC s rheMac2.chr2 189477649 84 - 189746636 tgAGACCATCTGACTTACAAT---GCCTGTGCCATGACCAGCTCCTAATAGCCTCCAAGGGCACCTCTGCCCTGACATATACTGTCC i rheMac2.chr2 C 0 C 0 s ponAbe2.chr21_random 865945 84 - 4212913 tgAGACCATCTGTCTTACAAT---GTCTGTGCCATGACCAGCTCCTAATAGCCTCCGAGGACAGCTTTGCCCTGACATATACTGTCC i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47432522 84 - 58616431 tgAGACCATCTGACTTACAAT---GTCTGTGCCGTAACCAGCTCCTAATAGCCTCCTAGGACAGCTTTGCCCTGACATACACTGTCC i panTro2.chrUn C 0 C 0 s oryCun2.chr14 141926339 86 + 163896628 TGAGACTATTGAACTTATAATC-AGCCTGGGCCATGACCAACTCCTAAGGAACTGAAAAGACAACCCTTCCTTGGCATGCACTGTCC i oryCun2.chr14 I 879 I 1452 s equCab2.chr26 13382048 69 + 41866177 TGAGAACATCTAGCATATAATCTAGACTA----ATGACC--------------TCAGAGTACAACATCACCCTGACGTATGCCGTCC i equCab2.chr26 I 2445 C 0 s canFam2.chr31 14136962 81 + 42263495 --AGACCATCTGACTTACAATCAAGCCAG----ATGACCAGGTTCTAATGATATCATAGCACAACCTTGCCCTGACATATAGTGTCC i canFam2.chr31 I 5310 C 0 e loxAfr3.scaffold_13 20640388 2276 - 62548349 I a score=63866.000000 s hg19.chrUn_gl000245 35922 88 + 36651 TGGGAC----CACGTCTGCTTTGTAACTCCTGAGGTAGCTGCC-------ACCA-TGACCAATGCC----TTCTCATCTTTACTCTACATGCAGGTAACAGTTA s rheMac2.chr2 189477733 85 - 189746636 TGGAAC----CACGTCTGCTTTGTAACTCCTGAGGTAGTTGCC-------ACTA-TGACCAATGCC----TTCTTCTCAT--CTTTACATGCAGGT-ACAGTTA i rheMac2.chr2 C 0 C 0 s ponAbe2.chr21_random 866029 86 - 4212913 TGGAA------ACGTCCGCTTTGTAACTCCTGAGGTAGCTGCC-------ACCA-TGACCAACACC----TTCTCATCTTTACTCTACATGCAGGTAACAGTTA i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47432606 88 - 58616431 TGGAAC----CGCGTCTGCTTTGTAACTCCTGAGGTAGCTGCC-------ACCA-TGACCAATGCC----TTCTCATCTTTACTCTACATGCAGGTAACAGTTA i panTro2.chrUn C 0 C 0 s equCab2.chr26 13382117 93 + 41866177 ----ACACAGCATGGCTGCTCTGTAACTTGTGAACTAGCTGAC-------ACCAGTGACCAATGTCTTGGTTCTTGCCTCTACCATACATAATGGTAATAGTTA i equCab2.chr26 C 0 I 28 s canFam2.chr31 14137043 100 + 42263495 ----ACACAGCATGACTGCTCTGTAACTTCTAACGTAGCTGACACCGATGACCAATGACCAATGCCTTGCTTCTCGCATTTACAATATGTAAAGGTAGTAGTCA i canFam2.chr31 C 0 I 663 e loxAfr3.scaffold_13 20640388 2276 - 62548349 I e oryCun2.chr14 141926425 1452 + 163896628 I a score=4088.000000 s hg19.chrUn_gl000245 36010 22 + 36651 TAATTAT---ATCTCTGTATATTC--A s micMur1.scaffold_3530 120776 24 + 180192 TAATTATTAGATCTCTTCATATTC--- i micMur1.scaffold_3530 N 0 N 0 s rheMac2.chr2 189477818 22 - 189746636 TAATTAT---ATCTCTGTGTATTC--A i rheMac2.chr2 C 0 C 0 s ponAbe2.chr21_random 866115 22 - 4212913 TAATTAT---ATATCTGTGTATTC--A i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47432694 22 - 58616431 TAATTAT---ATCTCTGTGTATTC--G i panTro2.chrUn C 0 C 0 s dipOrd1.scaffold_24209 5267 9 - 19403 ------------------ATAATCTGT i dipOrd1.scaffold_24209 N 0 N 0 s equCab2.chr26 13382238 21 + 41866177 ttgctat---gtctctgggtattc--- i equCab2.chr26 I 28 I 673 s canFam2.chr31 14137806 15 + 42263495 TATCTTT---GTTCCTC---------A i canFam2.chr31 I 663 I 3 e loxAfr3.scaffold_13 20640388 2276 - 62548349 I e oryCun2.chr14 141926425 1452 + 163896628 I a score=30717.000000 s hg19.chrUn_gl000245 36032 35 + 36651 CAGAACATTTAGTACATCTGGGACTTCTACAAAAT s canFam2.chr31 14137824 35 + 42263495 CATAACAGTTGGTACATCCAGCACTTCTCTAGAGT i canFam2.chr31 I 3 C 0 s equCab2.chr26 13382932 34 + 41866177 CATAATAGTTGGTCCATCCAGGACTT-TACAGAGT i equCab2.chr26 I 673 C 0 s panTro2.chrUn 47432716 35 - 58616431 CAGAACATTTAGTACATCTGGGACTTCTACAAAAT i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 866137 35 - 4212913 CAGAACGATTAGTACATCTAGGACTTCCACAAAAT i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189477840 35 - 189746636 CAGAGCAGTGAGTACATCTAGGACTTCTACAAAAT i rheMac2.chr2 C 0 C 0 e loxAfr3.scaffold_13 20640388 2276 - 62548349 I e oryCun2.chr14 141926425 1452 + 163896628 I a score=136409.000000 s hg19.chrUn_gl000245 36067 114 + 36651 TTCCCTAGCTGATTTTGGTGTTCTGGGGTACTGGCAGCTCTAGCCATGAAGGGATGATGCTTTATCAGCATTTCTGTTGAGTTTTTTGCTTTTTCTCACAAACTGATTCCACTT- s rheMac2.chr2 189477875 114 - 189746636 GTCCCTGGCTGACCCTGGTGTTCTGGTGTCCTGGCAGCTCCAGCCATGAAGGGATGATGCTTTATGAGCATTTCTGTTGAGTTTTTTGCTTTTTCTCAGAAACTGATTCCACTT- i rheMac2.chr2 C 0 C 0 s ponAbe2.chr21_random 866172 114 - 4212913 TTCCCTAGCTGATTTTGGTGTTCTGGTGTCCTGGCAGCTCTAGCCATGAAGGGATGATGCTTTATCAACATTTCTGTTGAGTTTTTTGCTTTTTCTCAGAAACTGATTCCATTT- i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47432751 114 - 58616431 TTCCCTAGCTGATTTTGGTGTTCTAGTGTCCTGGCAGCTCTAGCCATGAAGGGATGATGCTTTATCAGCATTTCTGTTGAGTTTTTTGCTTTTTCTCACAAACTGATTCCACTT- i panTro2.chrUn C 0 C 0 s equCab2.chr26 13382966 110 + 41866177 TCCTCTGGCCAATGTAAGTGTTCTGATGTCCAGGCAGTTCTTGCCATTAAGGGATGATGCTTCATGGGCATTTTTCTTCAGATC----TTTTCCCTCAGAAATCAATTTCACTT- i equCab2.chr26 C 0 C 0 s canFam2.chr31 14137859 113 + 42263495 TCGTCTACCTACTTTAGGTGTTCTGATGTTCAGGAAGTTCTTGCCATTAAGGGATGATACTTCATGGGTGTTTCTACTGAGATCTTT-TTTTTCCTCAGAAACCAATTTCACTT- i canFam2.chr31 C 0 I 178 s loxAfr3.scaffold_13 20642664 109 - 62548349 TTCCCTGGCAGATTTAGGTGATCTGATGTCCTGGCAGTTCTCACCATGAAGAAATGAGGCTTCATGGGCAATTTTGTTGAGA------TTTTTTCTCAGAATCCAATTTCTATTC i loxAfr3.scaffold_13 I 2276 C 0 e oryCun2.chr14 141926425 1452 + 163896628 I a score=52715.000000 s hg19.chrUn_gl000245 36181 66 + 36651 TTCCCACATACGTTTGACAATTCATT--TGAACTCATTTATTCTAAACCCATTATTTC--TGGTCTATTA s rheMac2.chr2 189477989 66 - 189746636 ATCCCACATACATTTGACAATTTACT--TGAGCTCATTTATTCTAAACCCATTATTTT--TTGTCTATTA i rheMac2.chr2 C 0 C 0 s ponAbe2.chr21_random 866286 66 - 4212913 TTCCCACATACTTTTGACAATTTATT--TGAACTCATTTATTCTAAACCCATTATTTT--TTGTCTATTA i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47432865 66 - 58616431 TTCCCACATATGTTTGACAATTCATT--TGAACTCATTTATTCTAAATGCATTATTTT--TTGTCTATAA i panTro2.chrUn C 0 C 0 s equCab2.chr26 13383076 67 + 41866177 -ACCCACTTATATTTGAAAACGTATCATTTAATTCATTTATTCTAATCTCTTTCTTTG--TTTTCTGTCA i equCab2.chr26 C 0 I 260 s canFam2.chr31 14138150 60 + 42263495 TTCCTGCTGACATTTGAAAATGAATC-----ATTCATTTATTCTAATCTCTT--TTTG--TAGTTTATC- i canFam2.chr31 I 178 I 206 s loxAfr3.scaffold_13 20642773 68 - 62548349 ATCTCACCTGTATTGTAAAGTTTTTCATTTAGCTC--TCATTCTAATTTCATTCTCTTCATTGTCTATTA i loxAfr3.scaffold_13 C 0 C 0 e oryCun2.chr14 141926425 1452 + 163896628 I a score=32969.000000 s hg19.chrUn_gl000245 36247 183 + 36651 TTTAATAggaagggaggcgagggataaaagattacaaatagggtgcagtgtacactgctcgggtgatgggtgcacccaaatctcacaaatctccagtaaagaacttacccatggaaccaaataccacc-gtaccccaataacctatgg--aaaaaaataaaAAATAAAGTAAAAAAGAGTCAGAAA s panTro2.chrUn 47432931 184 - 58616431 TTTAATAgggaggggggcgagggataaaagataacaaacaaggtgcagtgtacactgttcgggtgatgggtgcacccaaatctcacaaataaccagtaaagaagttattcatggaaccaaataccacc-gtaccccaataacctatgggaaaaaaaaTAAaaaataaaataaaata-agtcagaaa i panTro2.chrUn C 0 C 0 s ponAbe2.chr21_random 866352 114 - 4212913 TGTAATAGGAAGGGGG---------------------------------------------------------------------Caaatcaccactaaagaacttactcatggaaccaaataccacc-ataccccaataacctatgg--aaaaaaaTAAGAAATAAAATAAAAAAGCGTCAGAAA i ponAbe2.chr21_random C 0 C 0 s rheMac2.chr2 189478055 181 - 189746636 TTTTATAgggagaggggcaagggataaaagactacaaatagggtgcagtgtatactgcttgggtgatgggtgcaccaaaatctcacaaatcaccactaagtaaattattcatgtaaccaaataccacctgtaccccaataacctatgg--aaaaa---ataaaaTAAAATAAAAAAGAGTCCAAAA i rheMac2.chr2 C 0 C 0 s loxAfr3.scaffold_13 20642841 13 - 62548349 ----------------------------------------------------------------------------------------------AGCATAAAACTCA------------------------------------------------------------------------------- i loxAfr3.scaffold_13 C 0 C 0 e oryCun2.chr14 141926425 1452 + 163896628 I e canFam2.chr31 14138210 206 + 42263495 I e equCab2.chr26 13383143 260 + 41866177 I a score=78416.000000 s hg19.chrUn_gl000245 36430 81 + 36651 GAAAGAAAA---------TAATCACTGTACTTCCCAAGACACTTAGAAATGGTGACTAGCATTATTTGTAAGTGTCACCTAATAATATTA s rheMac2.chr2 189478236 90 - 189746636 AAAAAAAAAAAAACAAAGTAATCACTGTACTTACCATGACACTTACAAATGGTGACTAGCATTATTTATATGTGTCACCTAATAATATTA i rheMac2.chr2 C 0 C 0 s ponAbe2.chr21_random 866466 81 - 4212913 AAAAGCAAA---------TAATCACTGCACTTACCATGACACTTACAAATGGTGACTAACATTATTTGTAAGTGTCACCTAATAATATTA i ponAbe2.chr21_random C 0 C 0 s panTro2.chrUn 47433115 77 - 58616431 aaaagaaaa---------taaTCACTGTACTTACCATGACACTTAGAAATGGTGGCTAGCATTATTT----GTGTCACCTAATAATATTA i panTro2.chrUn C 0 C 0 s equCab2.chr26 13383403 81 + 41866177 AACAGGAAA---------TAAACACTACACTCACTATTACAACTAGGAATTGTGACTGGCATTATTTGTATGTGTCATCTCACAATATTA i equCab2.chr26 I 260 C 0 s canFam2.chr31 14138416 80 + 42263495 -ACAGAAAA---------TAAACACTACACACCCTACTGCAACTAGGAATGATGACTGGCATTATTTTTATATGTCATCTCACAATATTT i canFam2.chr31 I 206 C 0 s loxAfr3.scaffold_13 20642854 57 - 62548349 ---------------------------------TTATGACAACTAGTAAAGATTAGTGCCATCGTTTGTACATGTCACCTCACAATATTA i loxAfr3.scaffold_13 C 0 I 1 e oryCun2.chr14 141926425 1452 + 163896628 I a score=170986.000000 s hg19.chrUn_gl000245 36511 140 + 36651 TTATTTTTTCTTTATGCTACAA-------ACTAGCT--CTGCTATTACAATCACTACTATTTGAAGTGTTACTAAATTAAATT-----AAATCTATTGTATCCTTCTGGACTCAGAAATGGGGGTAAATGCTAAGACAATTTCAGAATATGATC s panTro2.chrUn 47433192 134 - 58616431 T--TTTTTTCTTTATGCTACAA-------ACTAGCT--CTGCTATTACAATCACTACTATTTGAAGTGTTACTAAATTAAATT-----AAATTCATTGTATCCTTCTGGACTCAGAAATGGGGGTAAATGCTAAGACAATTTCAGAATAT---- i panTro2.chrUn C 0 N 0 s ponAbe2.chr21_random 866547 135 - 4212913 TTATTTTTTCTTTATGCTACAA-------ACTAGCT--CTGCTATTACAATCACTACTATTTGAAGTGTTACTAAATTAAATT----------TATTGTATCCTTCTGGACTCAGAAGAGGGGGTAAATGCTAAGACAATTTCAGAATATGATC i ponAbe2.chr21_random C 0 N 0 s rheMac2.chr2 189478326 142 - 189746636 ---TTTTTTCTTTATGCTACAA-------ACTAGCT--CTCCTATTAGAATCACTACAATTTGAAGTGTTACtaaattaaattaaattaaattTATTGTATCCTTCTGGACTCAGAAGTGGGGGTAATTGCTAAGACAATTTCAGGATATAATC i rheMac2.chr2 C 0 N 0 s oryCun2.chr14 141927877 136 + 163896628 TTATTATTTCTTTATACTGCAAAG---TTAATGACT--CAGTTATTACAATCACTGTTATTTAAAGTAGTACCAATTAAAATC-----AAATTCATAGTATCTTTCTATGCTAGGAA-------TAATTGTTGATACCATTTCTGTATATAAT- i oryCun2.chr14 I 1452 N 0 s equCab2.chr26 13383484 144 + 41866177 -TTATTTTTCTTAATACTACAAAG---TTAATGACTGATAGTTATTATAATCATTACTATTTAAAGTAGTACTAAATAAAATT-----AAATCCATAGTATCCTTGTAGACTTAGAAATTGGACTAATTTTTAAGACCATTTCAGAATATGAT- i equCab2.chr26 C 0 N 0 s canFam2.chr31 14138496 141 + 42263495 -GGGGTTTTTTTCATAATATAAAG---ATAATAACT--TAGTTGTTTCTATCATTTGTATTTAAAGTAGCACTAAATAAAATT-----AAATTCATAGTATCCTCCTAGACTCAGAAATTAGAGTAATTCTTAATACCATTTTAGAATATGA-- i canFam2.chr31 C 0 N 0 s loxAfr3.scaffold_13 20642912 148 - 62548349 TTATTTAATCTTGCTACCATAAAGTTATTGATAACCTGTAGTTTTTATAATCACTACTGTGTAAAGTATTACTAACTAAAATT-----AAATTTATAGTATCCTTTTAGATTCAGAAATTAGAGTCATTATAAATATTATGTCAGAATACTAT- i loxAfr3.scaffold_13 I 1 N 0