##maf version=1 scoring=autoMZ.v1 a score=3195.000000 s hg19.chr11_gl000202_random 0 26 + 40103 TGCCAGAAAAGGGTGTGTGTTGGAGG-- s panTro2.chr11 68187172 26 + 134204764 TGCCAGAAAAGGGTGTGTGTTGGGGG-- i panTro2.chr11 N 0 C 0 s ponAbe2.chr11 125981900 26 - 132107971 TGCCAGAAAAGGGTGTGTATTGGAGC-- i ponAbe2.chr11 N 0 C 0 s rheMac2.chr14 128145357 26 - 133002572 TGCCAGAAAAGGGTGTGCATGGGAGG-- i rheMac2.chr14 N 0 C 0 s tupBel1.scaffold_125018.1-1020051 169616 1 - 1020051 -------------------------G-- i tupBel1.scaffold_125018.1-1020051 N 0 I 22621 s bosTau4.chr29 48965017 18 + 51998940 TGCCAGAGAAG----------GTGGGCA i bosTau4.chr29 N 0 C 0 s canFam2.chr18 7528168 6 - 58872314 ----------------------GAGGCG i canFam2.chr18 N 0 C 0 a score=39387.000000 s hg19.chr11_gl000202_random 26 56 + 40103 GGGTGTCTTTCACAATA-TATTTTTAATTTTGACTACTTCAGAAAAGAACAAAGCAg------- s rheMac2.chr14 128145383 56 - 133002572 GGGTGTCTTCCACAACA-TATTTTTAGTTTTGACTACTTCAGAAAAGAACAAAGCAg------- i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125981926 56 - 132107971 GGATGTCTTTCACAATA-TATTTTTAATTTTGACTACTTCAGAAAAGAACAAAGCAg------- i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68187198 56 + 134204764 GGGTGTCTTTCATAGTA-TATTTTTAATTTTGACTACTTCAGAAAAGAACAAAGCAg------- i panTro2.chr11 C 0 C 0 s bosTau4.chr29 48965035 52 + 51998940 GGGAGTTTTTTA-CGTACTACTTGAAAATCTGACTTCTTCAGAAAGGAACCAA----------- i bosTau4.chr29 C 0 I 777 s canFam2.chr18 7528174 62 - 58872314 GTGAGTTTGTAA-AGTA-TATTTTTCAATGTGATTGCTTCAAAAAAGAGCCAAGTGAAAAGCAG i canFam2.chr18 C 0 I 711 e tupBel1.scaffold_125018.1-1020051 169617 22621 - 1020051 I a score=136739.000000 s hg19.chr11_gl000202_random 82 267 + 40103 gccagttgtggtggctcacgcctgtaatcccaacagcttgagaggctgaggcgggcagatcacttgaggccaggagttgaagaccagcctggccaacatagtgaaactccgtctctactaaaaataccaaaaattacctgtgtatgctggtgtgcacctgtcgtccctgctactcgggagtctgaggcacgagaatcacttgaacctgggaggcagaggttgcagtgagctgagatcatgtcactgcactccagcctgggcaacaga s rheMac2.chr14 128145439 267 - 133002572 gccagatgtggtggctcatgcctgtcatcccaacaatttgagaggctgaggcgggcagatcacttgaggacaggagttcaagaccagcctggccaacatagtgaatctcaatctctactaaagataccaaaatttagctgggtatggtggtgcacacctgtcatcccagctactcgggagtctgaggcatgagaatcacttgaacctgggaggcagaggttgcagtgagccgagatcgtgtcactgcactccagcctgggcaacaga i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125981982 267 - 132107971 gtcaggtatggtggctcacgcctgtaatcccaacaatttgagaggctgaggtgagcagatcacttgaggccaggagttcaagaccagcctggccaacacagtgaaactccgtctctactaaaaataccaaaaattagccaggtatggtggtgtgcacctgtcgtccctgctactcaggagtctgaggcacgagaatcgcttgaacctgggaggcagaggttgcagtgagctgagatcatgtcactgcactccagcctgggcaacaga i ponAbe2.chr11 C 0 I 18 s panTro2.chr11 68187254 267 + 134204764 gccaagtgtggtggctcacgcctgtaatcctaacaacttgagaggctgaggcgggcagatcacttgaggccaggagttgaagaccagcctggccaacatagtgaaactccgtctctactaaaaataccaaaaattacctgtgtatgctggtgtgcacctgtcgtccctgctactcgggagtctgaggcacgagaatcacttgaacctgggaggcagaggttgcagtgagctgagatcatgtcactgcactccagcctgggcaacaga i panTro2.chr11 C 0 C 0 e canFam2.chr18 7528236 711 - 58872314 I e bosTau4.chr29 48965087 777 + 51998940 I e tupBel1.scaffold_125018.1-1020051 169617 22621 - 1020051 I a score=14830.000000 s hg19.chr11_gl000202_random 349 30 + 40103 --gcgagtctgtcagaaagaaggaaggaaaaa s rheMac2.chr14 128145706 32 - 133002572 gcaagagtctgtcggaaagaaggaaggaaaaa i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0228258 0 30 - 5482 --GCGAGTTTGTCAgaaagaaggaaggaaaaa i gorGor1.Supercontig_0228258 N 0 C 0 s panTro2.chr11 68187521 30 + 134204764 --gcgagtccgtcagaaagaaggaaggaaaaa i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125982267 10 - 132107971 ----------------------gaaggaaaaa i ponAbe2.chr11 I 18 C 0 e canFam2.chr18 7528236 711 - 58872314 I e bosTau4.chr29 48965087 777 + 51998940 I e tupBel1.scaffold_125018.1-1020051 169617 22621 - 1020051 I a score=102531.000000 s hg19.chr11_gl000202_random 379 104 + 40103 aggaaGGGAGGGAG-GACCTCGTCTCTGGAAATGTGGTCCGGGGGTTCAGGT-------GCAAGGAAGGGAGAAT------TTCACACTTCCCGAAGCATGTGATTTTCTTCCGTCTA s ponAbe2.chr11 125982277 104 - 132107971 aggaaGGGAGGGAG-GACCTTGTCTCTGGAAATGCAGTCCAGGGGTTCCAGT-------GCGAGGAAGGGAGAAT------TTCACACTTCCCGAAGCATGTGATTATCTTCCATCTA i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68187551 104 + 134204764 aggaaGGGAGGGAG-GACCTTGTCTCTGGAAATGTGGTCCGGGGGTTCAGGT-------GCGAGGAAGGGAGAAT------TTCACACTTCCCGAAGCATGTGATTTTCTTCCGTCTA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 30 104 - 5482 aggaagggagggag-gaCCTCGTCTCTGGAAATGTGGTCCGGGGGTTCAGGT-------GCGAGGAAGGGAGAAT------TTCACACTTCCCGAAGCATGTGATTTTCTTCCGTCTA i gorGor1.Supercontig_0228258 C 0 C 0 s rheMac2.chr14 128145738 104 - 133002572 aggaaGGGAGGGAG-GGCCGTGTCTCTGGAAATGCTGTCGAGGGATTCAGGT-------GTGGGGAAGTGAGAAT------TTCACACTTCCCGAAGCATGTGATTGTCTTCTGTCTA i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48965864 109 + 51998940 -AGAAGAGGCGAACAGAACCTAACTCTCAAAGACAGGTCTCAGGTCAGGGCAT------GAGAAGAAGAGAGAATTGTTACTTTACTTTTTGTGAT-CGTTTGATGATCTTTT-CCTA i bosTau4.chr29 I 777 C 0 s equCab2.chr12 28927189 105 + 33091231 AGGAAGCAGTGGACTGAGCTTAACTCTGGAAAACGGGTCTCAGGCCTGGGGG-------GAGGGGAAATGAGGGTTTTCCTTTTACGCTTCCTGAG-----CGTTCATTTTTT-TCTA i equCab2.chr12 N 0 C 0 s canFam2.chr18 7528947 97 - 58872314 ---------------GAACTTAACTCTGGAAAGCGGGTCTCTGGGCTGAAGGTGAGAAAAAGGGAGAAGGAGAGAAATGCCT-----CTTCCTGAAGCATTTGATTATTTTCT-TCTA i canFam2.chr18 I 711 C 0 e tupBel1.scaffold_125018.1-1020051 169617 22621 - 1020051 I a score=142542.000000 s hg19.chr11_gl000202_random 483 65 + 40103 ACCACACAGGAATGGTTTGCTTTTACTTAAGGACAACTAAGCACATCTCTGAGGAATGCCGCCAG s rheMac2.chr14 128145842 65 - 133002572 ACCACAAAGGAATGGTTTGCTTTTATTTAAGGACAACTAAGCACATCTCTGAGGAATATCACCAG i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0228258 134 65 - 5482 ACCACACAGGAATGGTTTGCTTTTACTTCAGGACAACTAAGCACATCTCTGAGGAATGCCGCCAG i gorGor1.Supercontig_0228258 C 0 C 0 s panTro2.chr11 68187655 65 + 134204764 ACCACACAGGAATGGTTTGCTTTTACTTAAGGACAACTAAGCACATCTCTGAGGAATGCCGCCAG i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125982381 65 - 132107971 ACCACACAGGAATGGTTTGCTTTTATTTAAGGACAACTAAACACATCTCTGAGGAATGTCACCAG i ponAbe2.chr11 C 0 C 0 s tupBel1.scaffold_80971.1-5047 442 65 + 5047 ACCACATAGGGAAGGTTTACTTTTATTGAAGGACAGCTAAACACACCTCTGAAGTCAGTGGCCCG i tupBel1.scaffold_80971.1-5047 n 22621 C 0 s bosTau4.chr29 48965973 65 + 51998940 ACTATACAGGCATGACTTACTTTTGTTTAAGGACGATGAAATACACATCTGAAAACAGCAGCTAG i bosTau4.chr29 C 0 I 83 s equCab2.chr12 28927294 65 + 33091231 ACTGCACAGGAATGGTTTGCTTTTATTTAAGGACAAATAAACGTACCTCTGAAGACGACAGCTGG i equCab2.chr12 C 0 C 0 s canFam2.chr18 7529044 65 - 58872314 ACTACACAGAAATGGTGGACTTGTATTCAAGGACAACTAAACGCACCCCTCAAGGCAGCAGCTGG i canFam2.chr18 C 0 C 0 a score=166394.000000 s hg19.chr11_gl000202_random 548 182 + 40103 CCCCAGGGCTGGGCACGGGAGGCTGGATGGGGTGGCCTTCATGGTCTCTGGCTTCACCCTAGGAACAGAACTGGCAGCCCAGAGGCCCCTCGAGGCCCTGC--TC-ACTGCCAGGGCGG-TTGGCCATGACAATTTGAATGTGGACATGTGGAGGCCACATGCCAGCTCCAGGCTCAGTCCGGCTG- s rheMac2.chr14 128145907 181 - 133002572 CCCCAGGGCCAGGCAC-GGAGGCTGGATGGGGCGGCCTTCACGGTCTCTGGCTTCACCCTAGGAGCAGAATTGGCAGCCCAGAGGCCCCGCGAGGCCCCAC--GC-ACCGCCCGGGCGT-TTGGCCATGACAATTTGAGTGTGGACACGCGGGGGCCACATTCCAGCCCCAGGCTCGGTCCGGCTG- i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0228258 199 182 - 5482 CCCCAGGGCTGGGCACGGGAGGCTGGATGGGGTGGCCTTCATGGTCTCTGGCTTCACCCTAGGAACAGGACTGGCAGCCCAGAGGCCCCGCGAGGCCCTGC--TC-ACTGCCAGGGCGT-TTGGCCATGACAATTTGAATGTGGACATGTGGAGGCCACATGCCAGCTCCAGGCTCAGTCGGGCTG- i gorGor1.Supercontig_0228258 C 0 C 0 s panTro2.chr11 68187720 182 + 134204764 CCCCAGGGCTGGGCACGGGAGGCTGGATGGGGTGGCCTTCATGGTCTCTGGCTTCACCCTAGGAACAGAACTGGCAGCCCAGAGGCCCCACGAGGCCCTGC--TC-ACTGCCAGGGCGG-TTTGCCATGACAATTTGAACGTGGACATGTGGAGGCCACATGCCAGCTCCAGGCTCAGTCCGGCTG- i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125982446 182 - 132107971 CCCCAGGGCCAGGCATGGGAGGCTGGATGGGGCAGCCTTCACGGTCTCTGGCTTCACCCTAGGAACAGAACTGGCAGCCCAGAGGCCCCACAAGGCCCCAC--TC-GCTGCCAGGGCAT-TTGGCCATGACAATTTGAATGTGGACACGTGGGGGCCACATGCCAGCTCCAGGCTCAGTCCGGCTG- i ponAbe2.chr11 C 0 C 0 s tupBel1.scaffold_80971.1-5047 507 168 + 5047 GTCAAGGGTTGAGGACG----------TGGTGTG----CTAAGTCCTTTGGCTTCACCAAACAAATAGGGTTGACAGCCCAGAGGTCCTATAAGCACCCTC--ACAACCTCCATGGCG--TTGGCCACCCCAAGTCAAGGGTGAAAATGGGGGGACAGCTGCCTAGCTTCAAGCTCAGTCCAGTCT- i tupBel1.scaffold_80971.1-5047 C 0 C 0 s canFam2.chr18 7529109 145 - 58872314 GCCACGAGCCGGGGAGAGGAGGCCGCACGAGCTG-CTGTTGAGACCTGGGGCTTCA---------------------CCCAGGGGCTCTGCGCAGGCCCCCACTC-GGTTTCCTGGGGTCCTGGCT---------------CAGGAACGCGGGGACAGCTGCTCAACCTCGGCC----TCCAGCAGC i canFam2.chr18 C 0 C 0 s equCab2.chr12 28927359 116 + 33091231 GCTACAGGCCAAGGAGAAGGGGCTGGATGGGCTG-TTTCTAAGGGCTCCGGCTTCA---------------------CCCAGCGCCCCCGTGGGGGCCCCCA-TC-ACCTCCACCGGGT-CTGACC---------------CGGA-----------------CCATTCTCAGC-------------- i equCab2.chr12 C 0 C 0 e bosTau4.chr29 48966038 83 + 51998940 I a score=64690.000000 s hg19.chr11_gl000202_random 730 52 + 40103 CTCCAGAAA----------------GCCCAGCCTCCAGACATGCTATATCCTCAGGCCTCCTCCAG-GG s rheMac2.chr14 128146088 36 - 133002572 --------------------------------CTCCAGACATAGTGTGTCCTCAGGCCTACTCCAG-GG i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0228258 381 52 - 5482 CTCCAGAAA----------------GCCCAGCCTCCAGACATGCTATATCCTCAGGCCTCCTCCAG-GG i gorGor1.Supercontig_0228258 C 0 C 0 s panTro2.chr11 68187902 52 + 134204764 CTCCAGAAA----------------GCCCAGCCTCCAGACATGCTATATCCTCAGGTCTCCTCCAG-GG i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125982628 52 - 132107971 CTCCAGAAA----------------GCCCGGCCTCCAGACATGCTGTATCCTCAGGCCTCCTCCAG-GG i ponAbe2.chr11 C 0 C 0 s tupBel1.scaffold_80971.1-5047 675 37 + 5047 --------------------------------TTACAGTGATACTGTTCCCTCAGACGTCCTTTAGAGG i tupBel1.scaffold_80971.1-5047 C 0 C 0 s bosTau4.chr29 48966121 51 + 51998940 CTGTGGAAA----------------GCCCGGCTTCCAACAATGCTGTTCCCTCAA-CCTCCTCTAG-GG i bosTau4.chr29 I 83 I 126 s equCab2.chr12 28927475 49 + 33091231 --CCGGAGG----------------GCCTGGCCTCCAGCGGTACTGATCCCTCAG-GCTCCTCCGG-GG i equCab2.chr12 C 0 C 0 s canFam2.chr18 7529254 67 - 58872314 CTCCAGTGGCCTCCACCCGGCCTCCACCTGGCAGCCAGTGAGGCTGTTCCCTCGG-CCTCCTCCAG-AG i canFam2.chr18 C 0 C 0 a score=77370.000000 s hg19.chr11_gl000202_random 782 109 + 40103 AAGCCCAGGAGGTCAG-GCCCAGGTGA------------CCCGT-------------------GGGC-----AGCCCCCGGAAGGGGCTTCTTTTTCTCTTTTCCTCTGATGGACAAGGAAGTAGAATGTGCAAGAGTTAATGCTC s rheMac2.chr14 128146124 109 - 133002572 AAGCCCCGGAGGTCGG-GCCCAGGTGA------------CCCGT-------------------GGGC-----AGCCCCTGGAAGGGGCTTCTTTTTCTCTTTTCCTCCGATGGAcaaagaagcagaatgtacaagagttaacgctc i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0228258 433 109 - 5482 AAGCCCAGGAGGTCAG-GCCCAGGTGA------------CCCGT-------------------GGGC-----AGCCCCCNGAAGGGGCTTCTTTTTCTCTTTTCCTCTGATGGACAAGGAAGTAGAATGTGCAAGAGTTAATGCTC i gorGor1.Supercontig_0228258 C 0 C 0 s panTro2.chr11 68187954 109 + 134204764 AAGCCCAGGAGGTCAG-GCCCAGGTGA------------CCCGT-------------------GGGC-----AGCCCCCGGAAGGGGCTTCTTTTTCTCTTTTCCTCTGATGGACAAGGAAGTAGAATGTGCAAGAGTTAATGCTC i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125982680 109 - 132107971 AAGCCTGGGAGGTCAG-GCCCAGGTGA------------CCCGT-------------------GGGC-----AGCCCCTGGAAGGGGCTTCTTTTTCTCTTTTCCTCCGGTGGACAAGGAAGCAGAATGTGCAAGAGTTAACGCTC i ponAbe2.chr11 C 0 C 0 s tupBel1.scaffold_80971.1-5047 712 122 + 5047 GCGCCTTTGAGGCCA---CCCTGGCGA------------CCTCTCAGAGCTCCTGAGAGCAAGGGGCCCGATAGCCACAGGAGGTGGCATCTGTTTCTCAGTGGAGCCAATGGGCAAG--------ATGTGCGGGGGTTCATGCT- i tupBel1.scaffold_80971.1-5047 C 0 C 0 s equCab2.chr12 28927524 49 + 33091231 GAGCCC-TGAGAACTGTGCCCAGGACA------------GCCCA-------------------CGAC-----AGCCGCGAACCAGG------------------------------------------------------------ i equCab2.chr12 C 0 C 0 s canFam2.chr18 7529321 124 - 58872314 GAGCCCATGAGAACTGTGCTCAGGCCATGTCCTCGGGGGGCTCAATCAGGTCAGGAGGCC---CAGC-----AGCCCCAAGAAGGGTGTCCTTCCCCTTAGCGGAGCTGATGGGTGGGTTGGTGG---GGGCGGG----------- i canFam2.chr18 C 0 C 0 e bosTau4.chr29 48966172 126 + 51998940 I a score=34733.000000 s hg19.chr11_gl000202_random 891 89 + 40103 ggccaggcgcagaggctcacgcctgtaatcccagcactttgggaggctgaggcgggcggatcaggaggtcaggagatcgagaccatcct s panTro2.chr11 68188063 89 + 134204764 ggccaggcgcagaggctcacgcctgtaatcccagcactttgggaggctgaggcgggcggatcaggaggtcaggagatcgagaccatcct i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 542 89 - 5482 ggccaggcgcagaggctcacgcctgtaatcccagcactttgggaggctgaggcgcatggatcaggaggtcaggagatcgagaccaacct i gorGor1.Supercontig_0228258 C 0 C 0 s ponAbe2.chr11 125982789 89 - 132107971 ggccgggcgcggaggctcatgcctgtaatcccagcactttgggaggccgaggcgggcagatcaggagggcaggagatcgagaccatcct i ponAbe2.chr11 C 0 C 0 s tupBel1.scaffold_80971.1-5047 834 38 + 5047 ---------CAGAGCCCCA----------------AATTTGGAAG---------------------AGTCTGGGGA-----ACCATCCC i tupBel1.scaffold_80971.1-5047 C 0 I 57 s equCab2.chr12 28927573 25 + 33091231 ---------------------------------------TGAGGGGCTG-GGCGGCCCCAGCAAG------------------------ i equCab2.chr12 C 0 I 35 e canFam2.chr18 7529445 0 - 58872314 C e bosTau4.chr29 48966172 126 + 51998940 I e rheMac2.chr14 128146233 0 - 133002572 C a score=69612.000000 s hg19.chr11_gl000202_random 980 135 + 40103 ggctaacaccgtgaaaccccgtctctacttaaaaaatac-aaaaaaaattagctgggcatggtgatgggtgcctgtagtcccagttacatgggaggctgaggcaggagaatggcgtgaacccaggaggcggagctt s ponAbe2.chr11 125982878 136 - 132107971 ggctaacaccgtgaaaccccgtctctacttaaaaaatacaaaaaaaaattagccgggcgtggtggcggttgcctgtagtcccagttacactggaggctgaggcaggagaatggcgtgaacccaggaggtggagctt i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 631 135 - 5482 ggctaacactgtgaaaccctgtctctacttaaaaaatacaaaaaaaaattagctgggcatggtggtgggtgcctgtagtcccagttacacgggaggctgaggcaggagaatggcgtgaacccaggaggcggagct- i gorGor1.Supercontig_0228258 C 0 M 1252 s panTro2.chr11 68188152 135 + 134204764 ggctaacaccgtgaaaccccgtctctacttaaaaaatac-aaaaaaaattagctgggcatggtggtgggtgcctgtagtcccagttacacgggaagctgaggcaggagaatggcgtgaacccaggaggcggagctt i panTro2.chr11 C 0 C 0 e equCab2.chr12 28927598 35 + 33091231 I e canFam2.chr18 7529445 0 - 58872314 C e bosTau4.chr29 48966172 126 + 51998940 I e tupBel1.scaffold_80971.1-5047 872 57 + 5047 I e rheMac2.chr14 128146233 0 - 133002572 C a score=5641.000000 s hg19.chr11_gl000202_random 1115 114 + 40103 gcagtgagtggagatgcaccactgcactccagcctgggagacagagcgagacactgtctcagaaaacaacaacaacaacaaaacaacaacaacaacaacaacaaaataacaaAG s panTro2.chr11 68188287 114 + 134204764 gcagtgagtggagatgcaccactgcactccagcctgggagacagagcgagacactgtctcagaaaacaacaacaacaacaaaacaacaacaacaacaacaacaaaataacaaAG i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125983014 87 - 132107971 gcagtgagcggaga--------tacattccagcctgggagacagagcaagacac--tctcagaaaaca--------aacaaacaaacagcaaca---------aaaTAACAAAG i ponAbe2.chr11 C 0 C 0 s equCab2.chr12 28927633 21 + 33091231 GTGGGGGGTCAGGATGCACCA--------------------------------------------------------------------------------------------- i equCab2.chr12 I 35 C 0 s tupBel1.scaffold_80971.1-5047 929 42 + 5047 ------AGTGGAGATGG-----TGAGTTCCAGCCCCCAGGACGCAGGGAG-------------------------------------------------------------AAG i tupBel1.scaffold_80971.1-5047 I 57 n 57 e gorGor1.Supercontig_0228258 766 1252 - 5482 M e canFam2.chr18 7529445 0 - 58872314 C e bosTau4.chr29 48966172 126 + 51998940 I e rheMac2.chr14 128146233 0 - 133002572 C a score=157146.000000 s hg19.chr11_gl000202_random 1229 129 + 40103 AGTTAA--------------TGCTGAagcagatctctgaattccgaggagcttggggagcag-cccagctccaccctgtattaat---gaggg----------gcctggggcaagt------------ctct--agcctcaatttcctcctctgcaaaatggggacagtaa s panTro2.chr11 68188401 129 + 134204764 AGTTAA--------------TGCTGAagcagatctctgaattccgaggagcttggggagcag-cccagctccaccctgtattaat---gaggg----------gcctggggcaagt------------ctct--agcctcaatttcctcctctgcaaaatggggacagtga i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125983101 129 - 132107971 AGTTAA--------------TGCTCAagcagatctctgaattccgaggagcttggggagcag-cccagctccaccctgtattaat---gaggg----------gcctggggcaagt------------ctct--aacctcgatttcctcctctgcaaaatggggactgtga i ponAbe2.chr11 C 0 C 0 s bosTau4.chr29 48966298 145 + 51998940 AGTCAG--------------TGCCTAGGCAGGTTCCCAAAT-------GGCCTGGGGAGCAGCCCCGGGGGTTCCCTGTACCAACGGGGAGCGGGGGAGTGGTGccttgggcacgtcagg----ttgccttcgtggcctcagtttcctcc-ctgaataatgggggcagtga i bosTau4.chr29 I 126 I 2 s equCab2.chr12 28927654 135 + 33091231 AGTCAA--------------CGCCCCAGCAGGTTCCCAAATGCCGTGGGGCCAGGGGAGCGATCCCAGGGGCACACCGAACCAAC---GAgcg----------gcctcaggcaagtcctgtgttctctctcc--ggcctccatttcctcctctgccaaaggggg------- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7529445 150 - 58872314 -GTCAGGTTGCACAGGGTCTGGACCCAAGTGGCTTccaggtgctacgggacctgggaagcaatcccaagttcaccttgtactgac---cagtg----------gcct-gggcaagtcatg----cttcctct--ggcccaaatgtcctgctctgtaaaatgggggcagaga i canFam2.chr18 C 0 I 99 s rheMac2.chr14 128146233 118 - 133002572 -------------------------aagcagatcctcaaattccaaggagcttggggagcgg-ccccgctccaccctgtatgaat---gaagg----------gcctggggcaagt------------ctct--ggcctcaatttcctcctctgcaaaatggggacagtga i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0228258 2031 127 - 5482 --TTAA--------------TGCGGAAGCAGATCTCTGAATTCCGaggagcttggggagcag-cccagctccaccctgtattaat---gaggg----------gcctggggcaagt------------ctct--agcctcaatttcctcctctgcaaaatggggacagtga i gorGor1.Supercontig_0228258 M 1252 C 0 e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=54761.000000 s hg19.chr11_gl000202_random 1358 52 + 40103 ccacctcacaggACAC---AAAAAGGACCTAGGAC-------------------------TCGTCACT--------GGTGGTCATTGC s ponAbe2.chr11 125983230 52 - 132107971 ccacctcacaggACAC---AAGAAGGACCTAGGAC-------------------------TCGCCACT--------GGCGGTCATTGC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 2158 52 - 5482 ccacctcacaggACAC---AAGAAGGACCTAGGAC-------------------------TCGCCACT--------GGTGGTCATTGC i gorGor1.Supercontig_0228258 C 0 C 0 s panTro2.chr11 68188530 52 + 134204764 ccacctcacaggACAC---AAGAAGGACCTAGGAC-------------------------TCGCCACT--------GGTGGTCATTGC i panTro2.chr11 C 0 C 0 s rheMac2.chr14 128146351 55 - 133002572 tcacctcacaggACACAGGAAGAAGGACCTAGGAC-------------------------TCACCACT--------GGCGGTCATTGC i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48966445 55 + 51998940 ccgcctcccgggatgttggaagaaGGACAGAGGAC---------------------CTCCACGT------------GGCGGTGGTTAC i bosTau4.chr29 I 2 I 90 s equCab2.chr12 28927789 86 + 33091231 --CCCTCGCAGGACGTCGGAAAAAGGACAGAGGACTTGCTGCATTGCTCACCATCTCCCCTCGCCACTCGGGGCCGGGCAGCGGCTGC i equCab2.chr12 C 0 I 52 e canFam2.chr18 7529595 99 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=336702.000000 s hg19.chr11_gl000202_random 1410 338 + 40103 CAGGCTTGTC---------CTTTGGGGGACTTCACGTCCCCAATCACCTCACTCCCTCTCACCTTGTCCCCCTACCTTTGA------AAAAAAAATATAAAGACA-------AGAGCCAGGCAAAGAGTCTCACAGG----------------------GGCTGTGAGCTCAG-GACCGCACGTCATCC-CACTCATCTGAAT-------CTCTAGGGCTGGGAGCCGGCAATCTTCCT------------------------------------------------------AGGCATATTGATT-------------TGAGAAGCTTCCTCCCAGGATGTATGGTCAAACCACAAAGCGCACACGGGACATGGTGGGTGAT-AACCCACACCAGGCAGAGCCACGACCCTTGCCCCATGCTGCCTGGCAAGAACTGACCCAGC----------ACCCTCTAGAACCC s ponAbe2.chr11 125983282 379 - 132107971 CAGGCTTGCC---------CTTCGGGGGACTTCACCTCCCCAATCACCTCACTCTGTCTCACCTTGTCTCCCTCCCCTTGA------AAAAAAAA-ACAAAGACA-------AGAGCCAGGCAAAGAGTCTCACAGG----------------------GGCTGCGAGCTCAG-GACCGCATGTCATcc-cactcatctgaat-------ctctagggctgggagccggcaatcttccccttaacccccttaacaagagcccgggg----------------------ttccgaggcacattgatt-------------tgagaaGCTTCCTCCCAGGATGTGTGGTCAAACCGTGAAGCGCACACGGGACATGGTGGGTGAT-AACCCACACCAGGCAAAGCCCCGACCCTTGCCCCATGCTGCCCAGCAAGCACTGACCCAGCATcctctagaaccatctagaaccc i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 2210 348 - 5482 CAGGCTTGTC---------CTTTGGGGGACTTCACCTCCCCAATCACCTCACTCCCTCTCACCTTGTCCCCCTACCCTTGA------AAAAAAAATATAAAGACA-------AGAGCCAGGCAAAGAGTCTCACAGG----------------------GGCTGTGAGCTCAG-GACCGCACGTCATCC-CACTCCTCTGAAT-------CTCTAGGGCTGGGAGCCGGCAATCTTCCT------------------------------------------------------AGGCATATTGATT-------------TGAGAAGCTTCCTCCCAGGATGTATGGTCAAACCACAAAGCGCACACGGGACATGGTGGGTGAT-AACCCACACCAGGCAGAGCCACGACCCTTGCCCCATGCTGCCCGGCAAGAACTGACCCAGCaccctgtagaaccctctagaaccc i gorGor1.Supercontig_0228258 C 0 C 0 s panTro2.chr11 68188582 338 + 134204764 CAGGCTTGTC---------CTTTGGGGGACTTCACCTCCCCAATCACCTCACTCCCTCTCACCTTGTCCCCCTACCCTTGA------AAAAAAAATATAAAGACA-------AGAGCCAGGCAAAGAGTCTCACAGG----------------------GGCTGTGAGCTCAG-GACCGCACGTCATCC-CACTCATCTGAAT-------CTCTAGGGCTGGGAGCCGGCAATCTTCCT------------------------------------------------------AGGCATATTGATT-------------TGAGAAGCTTCCTCCCAGGATGTATGGTCAAACCACAAAGCACACACGGGACATGGTGGGTGAT-AACCCACACCAGGCAGAGCCACGACCCTTGCCCCATGCTGCCCGGCAAGAACTGACCCAGC----------ACCCTCTAGAACCC i panTro2.chr11 C 0 C 0 s rheMac2.chr14 128146406 382 - 133002572 CAAGCTTGTC---------CTTGGGGGGACTTCACCTCCCCAGTCACCTCACTCCCTCTCATCCTGTCCCCCTCCCCTTG--------AAAAAAATACAAAGACAAAGG---AGAGCCAGGCAAAGAGTCTCAGAGG----------------------GGCTGCGAGCTCAg-gaccgcacgtcatcc-cactcatctaaat-------ctctagggctgggagccggcaatctgccccttagcccccttcacgagagcccgggg----------------------tgccaaggcacattgatt-------------tgagaaccTTCCTCCCGGGATGTAGGGTCAAACCATGAAGCGCACCCGGGAAGTGGTGGGTGAT-AACCCACACCAGGCAGAGCCACGACCCTTGCCCCGTGCTGCCTGGCAAGCTCTGACCCAGCaccctctggaaccctctagaaccc i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48966590 382 + 51998940 CAGAGGCGTCCCACAAGTGGTTCCGGGGCCTTC--CTCCCCGACAG-CTCACTCTCCCTTGTCTTCTCCACCTCCCCATTTAGGAAGAAAGAAAACACAAAGA---------TGCTTAGGGCAGAAATCCTCACAGGTAATTCAAAGGCACCCCCTGGAGGCTGCTAGCATTGAGGCCTCACCACACCC-CACTTCATGGGGACCCCCCCTCCTCAGGATGGAACCC----------CAAACCTGCAGCCCAATGAGAGCCTGGGT---------------------GTTCCAAGGCACACCAGTT-------------TGAGAACCA---CCCCAGGCTCTAAA-----------------ACAAACCGTACCGCGGGTGATGAGTCCAGGTCACACAAGGCCACCACCCTTACCCAGTGCTGCCCGGCAAGCAGTGACCCACA----------AGCACCTCAAACTC i bosTau4.chr29 I 90 C 0 s equCab2.chr12 28927927 407 + 33091231 CAGACTTGTCGCACAAGGGCCAGGTGGGACTTCCTCTCCCTGATAACCTCCCTCCCTCTTACCTTGTCCACCTCTTCTTTG--GGAAAAAAAATATACAAAGAGGAAAGAATTGCCCAGGGCAGAGACCCTCACAGGGGGTTCACGGGCATCCCCTGGAGCCCACTGGCTCAGAggcctcttctcatccccacttaagtggaa------cctctagggatgggacccagaaaatctgCACATCTGCTGCTTAATGAGAGTGGGAGGTGGTGGGGAGGGCGATGGGGGGTTCCCAGGCACATGAGTT-------------TGAGAACCA--CCCCCAGGCT-----------------------------GTGCTGTGGCTGATGAATCTGGGTCCCACAGGGCCACGACCTTTGCCCAGTGCCACCTGGCCGGCCCTGACCCAAG----------ATCATCTCAAACCC i equCab2.chr12 I 52 C 0 s canFam2.chr18 7529694 358 - 58872314 CAGGCTTATCACACAAGGGCCAGGTGAGACTTCACCTCCCCGTGAACCTCACT--CTCTTATCTTGTCTACTCCCTTTTTT--------AAAACATCCAAGGAGAAAGAAAC---------------CCCCCATAGGTGGCTCCTGGGCATCCCCTCCATGCTATTAGCTCAGAggcctctcttcacctgcacttaatcctaa-------ctctggggataggacccag-gaatctgCTGACCTGCTGCTTATTGAGAGCCTGGGG-------------------------------------GTTCCAAGGCACACAGTGTGGACTG--CCCCCAGGCTGGAGG-----------------ACACGGAGTGC-ATGGGCGATGCATCCAGGGCAGACAGAGCCATAGTCCTTACCCAGTGACACTTGGCAAGCCCTG-CCCACA----------GTCA---------- i canFam2.chr18 I 99 C 0 e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=102451.000000 s hg19.chr11_gl000202_random 1748 120 + 40103 TCTAGAACCCAGGGCTTGGGGTCCCAGTGGAGCAGCAACATCAGCCCCGCTCCCCACACCAAGCTGCTCCCACAGCCTCTGGCTTCCATGGGGATCTCTCACCTTTGTAGCTTTGG-CTGG s canFam2.chr18 7530052 74 - 58872314 TCCCCAGCCCAGGGCC---------------------------------------------AGGGGCTCCCACAACCTCTGACTTCTGGGGGTGTCTCTC-CCTCC-CGGCTCCACCCTAA i canFam2.chr18 C 0 C 0 s bosTau4.chr29 48966972 71 + 51998940 ---TGGGCCAGGGTCC---------------------------------------------ACCAGCTGCTCCAGCCTCCAACTTCTGTGGG-GTCTCTG-TGTCAGTCGCTTCAGCCTGA i bosTau4.chr29 C 0 C 0 s rheMac2.chr14 128146788 120 - 133002572 tctagaacccAGGGCATGGGATCCCAGGAGAGCAGCAACATCAGCCCCGCTCCCCATGCCAAGCTGCTCCCACAGCCTCTGGCTTCCATGGGGGTCTCTCACCTTTGTAGCTTTCA-CAGG i rheMac2.chr14 C 0 C 0 s panTro2.chr11 68188920 120 + 134204764 TCTAGAACCCAGGGCTTGGGGTCCCAGTGGAGCAGCAACATCAGCCCTGCTCCCCACACCAAGCTGCTCCCACAGCCTCTGGCTTCCATGGGGATCTCTCACCTTTGTAGCTTTGG-CTGG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 2558 120 - 5482 tctagaacccAGGGCTTGGGGTCCCAGTGGAGCAGCAACATCAGCCCNGCTCCCCACGCCGAGCTGCTCCCACAGCCTCTGGCTTCCATGGGCATCTCTCACCTTTGTAGCTTTGG-CTGG i gorGor1.Supercontig_0228258 C 0 C 0 s ponAbe2.chr11 125983661 120 - 132107971 tctagaacccAGGGCTTGGGTTCTCAGGAGAGCAGCAACATCAGCCCCGCTCCCCACACCAAGCTGCTCCCACAGCCTCTGGCTTCCATGGGGATCTCTCATCTTTGTAGCTTTGG-CTGA i ponAbe2.chr11 C 0 C 0 e equCab2.chr12 28928334 0 + 33091231 C e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=68556.000000 s hg19.chr11_gl000202_random 1868 69 + 40103 AGTCTGCTC--TCAGC--ATCCAAGGGTGCTGCCCACAACCTCGTCCCAATTTTTCAT---GGAGACCACTGTCCC-- s xenTro2.scaffold_3931 8300 68 - 9845 AGCTTGTAC--CCAGCCAATATGCAGATACTGCAGCCAATCAGGACAC----TCCCAT----GTACCCACTGTGCCAA i xenTro2.scaffold_3931 N 0 C 0 s canFam2.chr18 7530126 74 - 58872314 GCTCTGCTCGATCAGC--ATCCAGAGGTGCCATCTTAACCCTATGCCCTGCTTTTCCTGTGGGGGACCACCGACCC-- i canFam2.chr18 C 0 C 0 s bosTau4.chr29 48967043 70 + 51998940 GGTCAACACACTCAGT--ATCCAGAGGGGCCGGCCCCTTCCTGTGCCCAGATTGTTCTCCAGG----CAGTCACCC-- i bosTau4.chr29 C 0 C 0 s rheMac2.chr14 128146908 69 - 133002572 CATCTGCTG--TCAGC--ATCCAAGGGTGCTGCCCACAACCTCGTCCCAGTTTTCCAT---GGAGACCACTGTCCC-- i rheMac2.chr14 C 0 C 0 s panTro2.chr11 68189040 69 + 134204764 AGTCTGCTC--TCAGC--ATCCAAGGGTGCTGCCCACAACCTCGTCCCAATTTTTCAT---GGAGACCACTGTCCC-- i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 2678 69 - 5482 AGTCTGCTC--TCAGC--ATCCAAGGGTGCTGCCCACAACCTCGTCCCAATTTTTCAT---GGAGACCACTGTCCC-- i gorGor1.Supercontig_0228258 C 0 C 0 s ponAbe2.chr11 125983781 69 - 132107971 AGTCTGCTC--TCAGC--ATCCAAGGTTGCTGCCCACAACCTCGTCCCAATTTTTCAT---GGAGACCACTGTCCC-- i ponAbe2.chr11 C 0 C 0 e equCab2.chr12 28928334 0 + 33091231 C e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=12743.000000 s hg19.chr11_gl000202_random 1937 39 + 40103 TCCCCAGGTGCTGGTGGGCAGT---ATGGGCCCC--CCCATCCA s gasAcu1.chrXIII 18893685 38 - 20083130 TCCCCAGGTCCCTGAGGAGATTTAGGGGGACTTA--CCTG---- i gasAcu1.chrXIII N 0 C 0 s xenTro2.scaffold_3931 8368 35 - 9845 CTCCCATGTACCCACGG----T---GCCAACTCC--CACATACC i xenTro2.scaffold_3931 C 0 C 0 s canFam2.chr18 7530200 34 - 58872314 CTCCC-CGACCCTGTGGGC--------TGGCCCCAGCCTATCC- i canFam2.chr18 C 0 C 0 s bosTau4.chr29 48967113 5 + 51998940 CTCCC--------------------------------------- i bosTau4.chr29 C 0 I 4 s rheMac2.chr14 128146977 39 - 133002572 TCCCCAGGTGCTGGTGAGCAGT---GTGGGCACC--CCCATCCA i rheMac2.chr14 C 0 C 0 s panTro2.chr11 68189109 39 + 134204764 TCCCCAGGTGCTGGTGGGCAGT---ATGGGCCCC--CCCATCCA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 2747 39 - 5482 TCCCCAGGTGCTGGTGGGCAGT---ATGGGCCCC--CCCATCCA i gorGor1.Supercontig_0228258 C 0 C 0 s ponAbe2.chr11 125983850 39 - 132107971 TCCCCAGGTGCTGGTGGGCAGT---GTGGGCCCC--CCCATTCA i ponAbe2.chr11 C 0 T 1 e equCab2.chr12 28928334 0 + 33091231 C e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=14980.000000 s hg19.chr11_gl000202_random 1976 45 + 40103 CACAGTG--TC----CCCAGGTTCCAGTGGA----CGGTGTGATCTCCCCAATTC s gorGor1.Supercontig_0228258 2786 45 - 5482 CACAGTG--TC----CCCAGGTTCCAGTGGA----TGGTGTGATCTCCCCAATTC i gorGor1.Supercontig_0228258 C 0 C 0 s panTro2.chr11 68189148 45 + 134204764 CACAGTG--TC----CCCAGGTGCCAGTGGA----CGGTGTGATCTCCCCAATTC i panTro2.chr11 C 0 C 0 s rheMac2.chr14 128147016 45 - 133002572 CACAGTG--TC----CTCAGGTCCCGGTGGA----TGGTGTGGCCTCCCCCGTAC i rheMac2.chr14 C 0 C 0 s echTel1.scaffold_320013 3405 40 - 41141 GACAGG-----------CAGGACCGAGTGTC----CAGTGCACTCTATCCACCTC i echTel1.scaffold_320013 N 0 I 2 s xenTro2.scaffold_3931 8403 45 - 9845 CACAGTG--CCTACTCCCATGTACC----CA----CGGTGCCAACTCCCACATAC i xenTro2.scaffold_3931 C 0 C 0 s gasAcu1.chrXIII 18893723 45 - 20083130 --CAATGGTTC----CCCAGGTCCCTGAGGAGGTTTAGGGGGACTTACCTG---- i gasAcu1.chrXIII C 0 C 0 s petMar1.Contig8322 11346 45 - 27039 CACAATG--TC----TAGGGCTCCAGGTACA----CAGTGTCTTGGGCTCCAGGT i petMar1.Contig8322 N 0 C 0 e equCab2.chr12 28928334 0 + 33091231 C e canFam2.chr18 7530234 0 - 58872314 C e bosTau4.chr29 48967118 4 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125983889 1 - 132107971 T a score=37851.000000 s hg19.chr11_gl000202_random 2021 57 + 40103 TCACAGTGTCCCCAGGTCCCA-GTGGAC----AGTGTGGC--CTCCCCCATCCCCACAGTGTCC s ponAbe2.chr11 125983888 57 - 132107971 ACACAGTGTCCCCAGGTCCCA-GTGGAC----AGTGTGGC--CTCCCCCATCCCCACAATGTCC i ponAbe2.chr11 T 1 T 70 s gorGor1.Supercontig_0228258 2831 57 - 5482 CCACAGTGTCCCCAGGTCCCG-GTGGAC----AGTGTGGC--CTCCCCCATCCCCACAGTGTCC i gorGor1.Supercontig_0228258 C 0 C 0 s panTro2.chr11 68189193 57 + 134204764 CCACAGTGTCCCCAGGTCCCA-GTGGAC----AGTGTGGC--CTCCCCCATCCCCACAGTGTCC i panTro2.chr11 C 0 C 0 s echTel1.scaffold_320013 3447 50 - 41141 CCAGAGAG---CCAGGACCCA-GTGTCC----AGTGCACC--CTATTCACCTCCCCCAGA---- i echTel1.scaffold_320013 I 2 I 3 s xenTro2.scaffold_3931 8448 57 - 9845 CCACTGTG---CCAACTCCCACGTGCCC----ACTGTGCCAACTCCCACGTGCCCACAGTGCCA i xenTro2.scaffold_3931 C 0 I 3 s gasAcu1.chrXIII 18893768 55 - 20083130 -CAATGGTTCCCCAGGTCCCT-GAGGACGTTTAGGGGGAC--TTACC-----TTCAAAGGGTTG i gasAcu1.chrXIII C 0 C 0 s petMar1.Contig8322 11391 57 - 27039 ACACAATGTCTAGGGCTCCAG-GTAGAC----AATGTCTA--GGGCTCCAGGTACACGGTGTCT i petMar1.Contig8322 C 0 C 0 e equCab2.chr12 28928334 0 + 33091231 C e canFam2.chr18 7530234 0 - 58872314 C e bosTau4.chr29 48967118 4 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e rheMac2.chr14 128147061 0 - 133002572 C a score=7254.000000 s hg19.chr11_gl000202_random 2078 127 + 40103 CCA--CTTCC-TGCTGGATGGTG--TGGCCTCCCCATTTCCAGTG--TCC--CCAA--GTCCCAGTGGATAGTGT---GGCC----TCC---------------------CCATTTCCACAGTGTCCCCAGGTCCTGGTGGACGGTGT---GGCC--TCCCCATTTCCACA s panTro2.chr11 68189250 127 + 134204764 CCA--GTTCC-TGGTGGATGGTG--TGGCCTCCCCATTTCCAGTG--TCC--CCAG--GTCCCAGTGGATAGTGT---GGCC----TCC---------------------CCATTTCCACAGTGTCCCCAGGTCCCGGTGGACGGTGT---GGCC--TCCCCATTTCCACA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 2888 127 - 5482 CCA--GTTCC-TGGCGGATGGTG--TGGCCTCCCCATTTCCAGTG--TCC--CCAA--GTCCCAGTGGATAGTGT---GGCC----TCC---------------------CCATTTCCACAGTGTCCCCAGGTCCCGGTGGATGGTGT---GGCC--TCCCCATTTCCACA i gorGor1.Supercontig_0228258 C 0 I 179 s otoGar1.scaffold_15045.1-114179 44599 130 - 114179 CCA--CTTTTGTAGAGGACAGTA--TAGGCCCCGTCCTCCCACCC--CCC--CCACTTGTTGTAGAGGACAGTGT---AGGC----CCC---------------------GTCCTCCCACCCTGCCCACCTGTTGTAGAGGACAGTGT---AGGC--CCCGTCCTCCCACC i otoGar1.scaffold_15045.1-114179 N 0 C 0 s echTel1.scaffold_320013 3500 129 - 41141 GCA--GGACC-GAGTGTCCAGTG--CACCCTATTCACCTCCCCCA--GACAGCCAG--GACCCACTGTCCAGTGT---GCCC----TAT---------------------CCACCTCCCCCAGACAGCCAGGACCCACTGTCCAGTGT---GCCC--TATCCACCTCCCCG i echTel1.scaffold_320013 I 3 C 0 s xenTro2.scaffold_3931 8508 127 - 9845 CCAATGTTCC------CACGGTG--CCAACTCCCATGTACCCGTG--TTG--CCAA--CTCCCATGTACCCATGT---TGCCAACTCCC---------------------ACATACCCACAGTG---CTAACTCCCATGTACTCATGT---TGCCAACTCCCATGTGCCCA i xenTro2.scaffold_3931 I 3 I 2 s gasAcu1.chrXIII 18893823 129 - 20083130 CAA--GGTCC-CTGAGGAGGTTT--AGGGGGACTTACCTGCAATGGTTCC--CCAG--GTCCCTGAGGAGGTTTA---GGGG----GAC---------------------TTACCTGCAATGGTTCCCCAGGTCCCTGAGGACGTTTA---GGGG--GACTTACCTTCAAA i gasAcu1.chrXIII C 0 C 0 s petMar1.Contig8322 11448 153 - 27039 ---GGGCTCC-AGGTACACGGTGTCTGGGCTCCAGGTAGACAATG--TCT--AGGG--CTCCAGGTAGACAATGTCTAGGGC----TCCAGGTAGACAATGTCTAGGGCTCCAGGTAGACAATGTCTAGGGCTCCAGGTAGACAATGTCTAGGGC--TCCAGGTAGACA-- i petMar1.Contig8322 C 0 C 0 e equCab2.chr12 28928334 0 + 33091231 C e canFam2.chr18 7530234 0 - 58872314 C e bosTau4.chr29 48967118 4 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e rheMac2.chr14 128147061 0 - 133002572 C e ponAbe2.chr11 125983945 70 - 132107971 T a score=21273.000000 s hg19.chr11_gl000202_random 2205 110 + 40103 GTGTCCCCAGGTCCCGGTGGATGGTGT---GGCC----TCC---------------------CCATTTCCACAGTGTCCCCAGGTCCCAGTGGACAGCGTGGCC---TCCCCCATCCCCACAGTGTCC----CCAGTTCCTGGTG s gorGor1.Supercontig_0228258 3194 110 - 5482 GTGTCCCCAGGTCCCAGTGGATGGTGT---GGCC----TCC---------------------CCATTTCCACAGTGTCCCCAGGTCCCAGTGGACAGTGTGGCC---TCCCCCATCCCCACAGTGTCC----CCAGTTCCTGGTG i gorGor1.Supercontig_0228258 I 179 C 0 s panTro2.chr11 68189377 110 + 134204764 GTGTCCCCAGGTCCCGGTGGATGGTGT---GGCC----TCC---------------------CCATTTCCACAGTGTCCCCAGGTCCCAGTGGACAGTGTGGCC---TCCCCCATCCCCACAGTGTCC----CCAGTTCCTGGTG i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125983875 70 - 132107971 ------------------------------GGCC----CCC---------------------CCATTCACACAGTGTCCCCAGGTCCCAGTGGACAGTGTGGCC---TCCCCCATCCCCACAATGTCC----------------- i ponAbe2.chr11 T 70 T 56 s otoGar1.scaffold_15045.1-114179 44729 87 - 114179 CTACCCACCTGTTGTAGAGGACAGTGT---GGGC----CCC---------------------GTCCTCCCACCCTGCCCACCCGTTGTAGAGGACAGTGTAGGC---CCCGTCCTCCC--------------------------- i otoGar1.scaffold_15045.1-114179 C 0 N 0 s echTel1.scaffold_320013 3629 116 - 41141 AGAGAGCCAGGACCCAGTGTCCAGTGC---ACCC----TAT---------------------CCACCTCCCCCAGACAGCCAGGACCCAGTGTCCAGTGCACCCTA-TCCACCTCCCCCAGAGAGCCAGGACCCAGTGTCCAGTG i echTel1.scaffold_320013 C 0 N 0 s xenTro2.scaffold_3931 8637 109 - 9845 ---GTGCCAACTCCCATGTACCCGTGT---TGCCAACTCCC---------------------ATGTACCCACGGTG---CCAACTCCCATGTACCCGTGTTGCCAACTCCCACGTACCCACGGTGCCA------ACTCCCACGTG i xenTro2.scaffold_3931 I 2 I 2 s gasAcu1.chrXIII 18893952 109 - 20083130 GGGTTGCAAGGTCCCTGAGGAGGTTTA---GGGG----GAC---------------------TTACCTTCAAAGGGTTGCAAGGTCCCTGAGGA-GGCTTAGGG---GGACTTACCTTCAAAGGGTTG----CAAGGTCCCTGAG i gasAcu1.chrXIII C 0 I 3 s petMar1.Contig8322 11601 134 - 27039 ATGTCTAGGGCTCCAGGTAGACAATGTCTAGGGC----TCCAGGTAGACAATGTCTAGGGCTCCAGGTAGACAATGTCTAGGGCTCCAGGTAGACAATGTCTAG---GGCTCCAAGTACACAGTGTCT----AGGGCTCCAGGTA i petMar1.Contig8322 C 0 C 0 e equCab2.chr12 28928334 0 + 33091231 C e canFam2.chr18 7530234 0 - 58872314 C e bosTau4.chr29 48967118 4 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e rheMac2.chr14 128147061 0 - 133002572 C a score=12083.000000 s hg19.chr11_gl000202_random 2315 66 + 40103 GATGATGTGGCCTCCC-CATTTCCACAGTGTTCCCAGATCCCG---GTGGA----CGGTGTGGCCTCCCCATTT s panTro2.chr11 68189487 66 + 134204764 GATGATGTGGCCTCCC-CATTTCCACAGTGTCCCCAGATCCCG---GTGGA----TGGTGTGGCCTCCCCATTT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 3304 66 - 5482 GATGATGTGGCCTCCC-CATTTCCACAGTGTCCCCAGATCCCG---GTGGA----CGGTGTGGCCTCCCCATTT i gorGor1.Supercontig_0228258 C 0 C 0 s xenTro2.scaffold_3931 8748 65 - 9845 CACTGTGCCAACTCCCACGTGCCCACTGTG---CCAACTCCCATGTGCCCA----CAGTGCCAACT-CCCATG- i xenTro2.scaffold_3931 I 2 C 0 s gasAcu1.chrXIII 18894064 63 - 20083130 GCTTAGGGGGACTTAC-C---TTCAAAGGGTTGCAAGGTCCCT---GAGGAGGCTTAGGGGGACTTACCT---- i gasAcu1.chrXIII I 3 C 0 s petMar1.Contig8322 11735 66 - 27039 CACGGTGTGTGGGCTC-CAGGTACACAATGTCTAGGGCTCCAG---GTACA----CGGTGTGTGGGCTCCAGGT i petMar1.Contig8322 C 0 C 0 e equCab2.chr12 28928334 0 + 33091231 C e canFam2.chr18 7530234 0 - 58872314 C e bosTau4.chr29 48967118 4 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e rheMac2.chr14 128147061 0 - 133002572 C e ponAbe2.chr11 125983945 56 - 132107971 T a score=-2730.000000 s hg19.chr11_gl000202_random 2381 12 + 40103 CCACAGT---------------------------------------------GTCCC s gorGor1.Supercontig_0228258 3370 57 - 5482 CCACAGTGTCCCCAAGTCCCAGTGGACGGTGTGGCCTCCCCATTTCCACAGTGTCCC i gorGor1.Supercontig_0228258 C 0 C 0 s panTro2.chr11 68189553 10 + 134204764 CCACAGT-----------------------------------------------CCC i panTro2.chr11 C 0 C 0 s rheMac2.chr14 128147061 12 - 133002572 CCACAGG---------------------------------------------GTCCC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125983889 11 - 132107971 -CACAGT---------------------------------------------GTCCC i ponAbe2.chr11 T 56 C 0 s xenTro2.scaffold_3931 8813 12 - 9845 TACCCGT---------------------------------------------GTTGC i xenTro2.scaffold_3931 C 0 C 0 s gasAcu1.chrXIII 18894127 12 - 20083130 TCAAAGG---------------------------------------------GTTGC i gasAcu1.chrXIII C 0 C 0 s petMar1.Contig8322 11801 12 - 27039 ACACAAT---------------------------------------------GTCTA i petMar1.Contig8322 C 0 C 0 e equCab2.chr12 28928334 0 + 33091231 C e canFam2.chr18 7530234 0 - 58872314 C e bosTau4.chr29 48967118 4 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=34676.000000 s hg19.chr11_gl000202_random 2393 39 + 40103 CAGGTCCCAGTGGA----TGGTGTGGC---CTCCCCC---ATCCC--------CACA s ponAbe2.chr11 125983900 39 - 132107971 CAGGTCCCAGTGGA----CAGTGTGGC---CTCCCCC---ATCCC--------CACA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128147073 39 - 133002572 CAGTTCCCAGTGGA----TGGTGTGGC---CTCCCCC---ATCCT--------CACA i rheMac2.chr14 C 0 C 0 s panTro2.chr11 68189563 39 + 134204764 CAGGTCCCAGTGGA----TGGTGTGGC---CTCCCCC---ATCCC--------CACA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 3427 39 - 5482 CAGGTCCCAGTGGA----TGGTGTGGC---TTCCCCC---ATCCC--------CACA i gorGor1.Supercontig_0228258 C 0 C 0 s bosTau4.chr29 48967122 51 + 51998940 CAGGTCCCCGGGAACACCTAGGGTGGC---CCCACCT---GTCCTGCCCCTGGCTCA i bosTau4.chr29 I 4 I 5 s xenTro2.scaffold_3931 8825 42 - 9845 CAACTCCCATGTAC----CCATGTTGCCAACTCCCAC---ATACC--------CACA i xenTro2.scaffold_3931 C 0 N 0 s gasAcu1.chrXIII 18894139 46 - 20083130 AAGGTCCCTGAGGAGGCTTAGGGGGAC---TTACCTTCAAAGGTT--------TGCA i gasAcu1.chrXIII C 0 C 0 s petMar1.Contig8322 11813 38 - 27039 GGGCTCCAGGTACA----CGGTGT-GT---GGGCTCC---AGGTA--------CACA i petMar1.Contig8322 C 0 C 0 e equCab2.chr12 28928334 0 + 33091231 C e canFam2.chr18 7530234 0 - 58872314 C e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=35057.000000 s hg19.chr11_gl000202_random 2432 47 + 40103 GTGTC-----CTCTGGGCAGGC--CTGGGTCAGGCTGCATTC--CTGACCCTGAGG s bosTau4.chr29 48967178 47 + 51998940 ACGTG-----CCCCAGGTGTGT--CTTGGGTAGGGTGCATTC--CTGACCTTGAGG i bosTau4.chr29 I 5 C 0 s cavPor3.scaffold_42 9657293 48 + 15951348 GTGAT-----CACTGGTTAGGCCACAGGGTCGGG-TGCTTTC--CTAGCCTGGAGC i cavPor3.scaffold_42 N 0 C 0 s ponAbe2.chr11 125983939 47 - 132107971 ATGTC-----CTCTGGGCAGGC--CTGTGTCAGGCTGCATTC--CTGACCCTGAGG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128147112 47 - 133002572 GTGTC-----CTCCTGGCAGGC--CTGGGTCAGGCTGCACTC--CTGACCCTGAGG i rheMac2.chr14 C 0 C 0 s panTro2.chr11 68189602 47 + 134204764 GTGTC-----CTCTGGGCAGGC--CTGGGTCAGGCTGCATTC--CTGACCCTGAGG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 3466 47 - 5482 GTGTC-----CTCTGGGCAGGC--CTGGGTCAGGCTGCATTC--CTGACCCTGAGG i gorGor1.Supercontig_0228258 C 0 C 0 s canFam2.chr18 7530234 22 - 58872314 --------------------------------TGCTCCAGGC--CTGCTCTTGAGG i canFam2.chr18 C 0 C 0 s gasAcu1.chrXIII 18894185 48 - 20083130 -AGGT-----CCCTGAGGAGGT--TTAGGGGAACTTACCTTTAAAGGTTCCCCAGG i gasAcu1.chrXIII C 0 C 0 s petMar1.Contig8322 11851 38 - 27039 ATGTCTAGGGCCCCAGGTAGAC-AATGTGTAGGGCTCCA----------------- i petMar1.Contig8322 C 0 N 0 e equCab2.chr12 28928334 0 + 33091231 C e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=7849.000000 s hg19.chr11_gl000202_random 2479 57 + 40103 -------T--GTGGAACTCTCTCTccctga-gcttttgcagaaacgtgg--gggcaacttgctctcctt s gorGor1.Supercontig_0228258 3513 29 - 5482 -------T--GTGGAACTCTCTCTCCCTGA-GCTTTTGC------------------------------ i gorGor1.Supercontig_0228258 C 0 I 21 s panTro2.chr11 68189649 57 + 134204764 -------T--GTGGAACTCTCTCTccctga-gcttttgcagaaacgtgg--gggcaacttgctctcctt i panTro2.chr11 C 0 C 0 s rheMac2.chr14 128147159 59 - 133002572 -------TGAGCGGAGCTCTCTCTCTCCTA-GCTTTTGCAGAAATGTGG--GGGCAACATGCTCTCCTT i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125983986 57 - 132107971 -------T--GTGGAGCTCTCTCTCCCTGA-GCTTTTGCAAAAACGTGG--GGGCAACTTGCTCTCCTT i ponAbe2.chr11 C 0 C 0 s cavPor3.scaffold_42 9657341 53 + 15951348 -------TGAGCGTGGTCCCTTGTGCCCG--GCTTTGATGGTGATGGGG--GAG-----TTCTCTCCTT i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48967225 54 + 51998940 -------TCAGCGGGGCGCACTATTTCCTGC--------AGAAATGTAGAAGGGGGACCCGCTTTCCTT i bosTau4.chr29 C 0 C 0 s canFam2.chr18 7530256 41 - 58872314 -------TCAGCAGGGGGCCCTCTTTCCTG---------------------GGGACACATGCTCTTCTT i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 75165 55 + 1045236 ---------TGTGGGCACCCTCATCCCAGA-GCCTTTGT-CAAACGTGG--GGCTCAGGTCCTC-CCTT i loxAfr3.scaffold_159 N 0 C 0 s gasAcu1.chrXIII 18894233 64 - 20083130 TGGCGGTT--TTGGGAGCCTGACTTTTAAA-GGTTCACCTGGTCCATGG--AGGCGTCTAGAGGGCCTT i gasAcu1.chrXIII C 0 N 0 e equCab2.chr12 28928334 0 + 33091231 C e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=64746.000000 s hg19.chr11_gl000202_random 2536 67 + 40103 ctgcaggactcaaa--ggtgggagatgctggcctagagcagccagaggcttcctaccgggtgacgggga s panTro2.chr11 68189706 67 + 134204764 ctgcaggactcaaa--ggtgggagatgccggcctagagcagccagaggcttcctaccgggtgacgggga i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125984043 67 - 132107971 CTGCAGGACTCAAA--GGTGGGAGATGCCGGCCTAGAGCAGCCAGAGGCTTCCTACCAGGTGACAGGGA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128147218 67 - 133002572 CTACAGGACTCAAA--GGTGGGAGATGCCATCCTATAGCAGCCAGAGGCTTCCTACTGGGTGATGGGGA i rheMac2.chr14 C 0 C 0 s cavPor3.scaffold_42 9657394 66 + 15951348 CCCCAGGGCTCCCCCTGGAGAGAGATGCCTG-CTAAGGCTGCCAG-GGCTTCGTAGGGAGTATCTGGG- i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48967279 63 + 51998940 CCC-AGGACT--CA--GGCCGGAGAAGCTAGCTAGGACCTGCCGG-GGCATCATACAGGGTGACGGGGG i bosTau4.chr29 C 0 I 8 s canFam2.chr18 7530297 64 - 58872314 CCTGAGGACTCACA--GGTGAGAAATGCCTGCCTGGAGCTTCTGG-GGCTTC--ACAGGGTGACAGGGG i canFam2.chr18 C 0 I 1 s loxAfr3.scaffold_159 75220 64 + 1045236 CTGCAGGACTCAGG--GTGGGAGGGCACCGGCCTAGAGCTGC-AG-GGTTGCAGATGGGCTGATGGGG- i loxAfr3.scaffold_159 C 0 C 0 e equCab2.chr12 28928334 0 + 33091231 C e gorGor1.Supercontig_0228258 3542 21 - 5482 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=89695.000000 s hg19.chr11_gl000202_random 2603 92 + 40103 gagggtgcctgcc-ccagagtgaggccagcagagaCCAGACTCACAGAACAACAGAGACCAGCCAC-TCAC------TCAGCTG------TGAG---CCAGATGCACAT s panTro2.chr11 68189773 92 + 134204764 gaggttgcctgcc-ccagagtgaggccagcagagaCCAGACTCACAGAACAACAGAGACCAGCCAC-TCAC------TCAGCTG------TGAG---CCAGATGCACAT i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125984110 92 - 132107971 GAGGGTGCCTGCC-CCAGAGTGAGGCCAGCAGGGACCAGACTCACAGAACAACAGAGACCAGCCAC-TCAC------TCAGCTG------TGGG---CCAGATGCACAT i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128147285 92 - 133002572 GAGGGTGCCTGCC-CCAGAGTGAGGCCAGCAGAGACCAGACTCGCAGAACAACAGAGATCAGCCAC-TCAC------TCAGCTG------CGGG---CCAGATGCACAT i rheMac2.chr14 C 0 C 0 s cavPor3.scaffold_42 9657460 94 + 15951348 GAGGGCGCCTG-C-CCGGAGTGAAGACA-CAGAGACCACACGCG-AGAAGGACAGAAACCAGAGTC-ACAC------CAAGCTGCAGCTCTGCA---CCAGACGCGCA- i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48967350 94 + 51998940 CAGGGTGCCTGTCACCGTCCAGAGGGACACAGAGGCCAGACA-TGAGAACCGCAAGGGCCAGTCTC-ACGC-----TCGAGCTG------CAGGGC-CCGGG-GCCCTT i bosTau4.chr29 I 8 C 0 s equCab2.chr12 28928334 94 + 33091231 GGGGACACCTGTC-CCCAAGGGAGGCCCGCAGAGACCAGACACTGAGAAC------GAGCAGGGTC-ACACGTTGTTGGAGCTG------CAGGAC-CCAGATGCCCTT i equCab2.chr12 C 0 C 0 s canFam2.chr18 7530362 100 - 58872314 GGGAGTGCCTGCC-CTGGAGCGAGGTCAGCAGAGACCAGACACCTCGGACAACAGTGACCAGAGTC-CCACGTTATTTGAGCTG------GGGAAC-TCAGATGCCCAT i canFam2.chr18 I 1 C 0 s loxAfr3.scaffold_159 75284 80 + 1045236 ---------------CAGAGGGTGGCAAGTGGAGATCAGGGCCA---AGAGACCAAGGCCAGAGCCTTCAT-----TTGAGCTA------CGGGGCTCCCTGTGCTCAG i loxAfr3.scaffold_159 C 0 C 0 e gorGor1.Supercontig_0228258 3542 21 - 5482 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=52932.000000 s hg19.chr11_gl000202_random 2695 52 + 40103 AG---TCTGTTTGAGGTGATTTCTTCACTGGCTACCAAGAAAAAAC--------AAATAAAAA s panTro2.chr11 68189865 52 + 134204764 AG---TCTGTTTGAGGTGATTTCTTCACTGGCTACCAAGAAAAAAC--------AAATAAAAA i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125984202 52 - 132107971 AG---TCTGTTTGAGGTGGTTTCTTCACTGGCTACCAAGAAAAAAC--------AAATAAAAA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128147377 52 - 133002572 AG---TCTGTTTGAGGTGGTTTCTTCACTGGCTACCAAGAAAAAAC--------AAATAAAAA i rheMac2.chr14 C 0 C 0 s cavPor3.scaffold_42 9657554 21 + 15951348 ---------------------------------ACCAA-AACAAAC--------AAACAGCAA i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48967444 50 + 51998940 AATGCCCGCTTTGAAGGGGCTTCTTCCCCTGCAACCAAGGG-------------GTAAAAACA i bosTau4.chr29 C 0 I 11 s equCab2.chr12 28928428 36 + 33091231 AAAG-CCACTTTGCG-------------TTTTAATCGAGGA-------------AAACAAAAC i equCab2.chr12 C 0 I 4 s canFam2.chr18 7530462 62 - 58872314 AAAG-CCACTTTGAGGTGGTTTCTTCACTTGCAACAAAGAAAAAACAAAAACTGAAACAAAAT i canFam2.chr18 C 0 I 3 s loxAfr3.scaffold_159 75364 52 + 1045236 AG---CCCGTTTGAGGCGGTTTCTTCACTTGAAACCAAAAAACTCC--------GAATAAAAA i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 10833 52 - 46842 AG---CCTCTTTGAGGCGGTTTCTTTATTTGCCACCAAAAACCCCC--------AAGTGAACA i proCap1.scaffold_13667 N 0 C 0 e gorGor1.Supercontig_0228258 3542 21 - 5482 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=7593.000000 s hg19.chr11_gl000202_random 2747 21 + 40103 TACATACAAAGCCCACTGGG--C s rheMac2.chr14 128147429 21 - 133002572 TACATGCAAAGCCCACTGGA--C i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125984254 21 - 132107971 TACATACAAAGCCCACTGGG--C i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 0 21 + 2579 TACATACAAAGCCCACTGGG--C i gorGor1.Supercontig_0069572 n 21 C 0 s panTro2.chr11 68189917 21 + 134204764 TACATACAAAGCCCACTGGG--C i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9657575 13 + 15951348 --------AAGCCTCTGGCC--C i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48967505 19 + 51998940 AAGACACAAAGCTCA----GTCC i bosTau4.chr29 I 11 C 0 s equCab2.chr12 28928468 23 + 33091231 AAAACAAGAGGCCCACTGGGCCC i equCab2.chr12 I 4 C 0 s canFam2.chr18 7530527 22 - 58872314 -AGACACAAAGCCCACTAGGCCC i canFam2.chr18 I 3 C 0 s loxAfr3.scaffold_159 75416 1 + 1045236 ----T------------------ i loxAfr3.scaffold_159 C 0 I 120 s proCap1.scaffold_13667 10885 14 - 46842 -------AAAATCCCCTGGGC-- i proCap1.scaffold_13667 C 0 I 649 e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=66340.000000 s hg19.chr11_gl000202_random 2768 37 + 40103 --TGAGTC-CTCCACCTGGAGAAAGCACTGCAAATGTCAC s rheMac2.chr14 128147450 37 - 133002572 --TGAGTC-CTCCACCTGGAGAAGACCCTGCAAATGCCAC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125984275 37 - 132107971 --TGAGTC-CTCCACCTGGAGAAAGCACTGCAAATGTCAC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 21 37 + 2579 --TGAGTC-CTCCACCTGGAGAAAGCACTGCAAATGTCAC i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68189938 37 + 134204764 --TGAGTC-CTCCACCTGGAGAAAGCACTGCAAATGTCAC i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9657588 32 + 15951348 --TGAGCC------CCAGCAGGAAACTGCTACAGTGCCAC i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48967524 38 + 51998940 --AGAGCCCCTCCAACTGGAAAGGTCACCAGAAGCATCAC i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28928491 38 + 33091231 --TGAGCCCCTCCACCTGGAGAAGCTACCACAAATGTCAC i equCab2.chr12 C 0 C 0 s canFam2.chr18 7530549 38 - 58872314 --TGAGCCCCTCCACCCAGGGAAGTTACAGATCATGTCAT i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 75537 38 + 1045236 CCCAAGGG-CTCCACCTGGAGAAGA-ACTGCAAACCTAGC i loxAfr3.scaffold_159 I 120 C 0 e proCap1.scaffold_13667 10899 649 - 46842 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=79072.000000 s hg19.chr11_gl000202_random 2805 96 + 40103 CAG-TGTTCAAGGGTCCTCCTCCCCCATCCAGC--CCCCATCCCACCACCTTCTGCTGTGC-GTCCCACAACCCTGT--T----CCCTA-GGGGAGTGGTGGGCACA s rheMac2.chr14 128147487 96 - 133002572 CAG-TGTTCACAGGTCTTCCTCCCCCATCCAGC--CCCCAACCCACGGCCTTCCGCTGTGC-GTCCCACAACCCTGT--C----CCCCA-GGGAAGTGGTGGGCACA i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125984312 96 - 132107971 CAG-TGTTCAAGGGTCCTCCTCCCCCATCCAGC--CCCCATCCCACCACCTTCTGCTGTGC-GTCCCACAACCCTAT--C----CCACA-GGGGAGTGGCAGGCACG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 58 96 + 2579 CAG-TGTTCAAGGGTCCTCCTCCCCCATCCAGC--CCCCATCCCACCACCTTCTGCTGTGC-GTCCCACAACCCTGT--C----CCCTA-GGGGAGTGGTGGGCACA i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68189975 96 + 134204764 CAG-TGTTCAAGGGTCCTCCTCCCCCATCCAGC--CCCCATCCCACCACCTTCTGCTGTGC-GTCCCACAACCCTGT--T----CCCTA-GGGGAGTGGTGGGCACA i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9657620 84 + 15951348 CGTCTGCT---GGGTC--CCCCACCCGGCCAGC--CCCC--TCCAGCGCTTGCCGCTGGGT-CCCCC---CTCCTGT--C----CC----GGCCAGCGGCTGGCTCG i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48967562 92 + 51998940 CGG-GTTC--AGCGGCCCCTTCCCCAGCCA----GCCCAGCACAGAGGCCT---GCAGAGACGCCCCGCCGGCCCCT--CCCACCCC---GTCCCGGGCCCAGGCCA i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28928529 93 + 33091231 CAG-CTTTCACGTGGCCTCTTCCCCAGCCCAGCCGCAC---CCGGGGGCCTCCCGCTGTGG-GCCCCACCGTCCCCT--C----CCC---AAGGAAGGGCCGGCTCA i equCab2.chr12 C 0 C 0 s canFam2.chr18 7530587 84 - 58872314 TGG-TTTTCAGGTGGCTCCTTCCCCAGCCCCACTGCCCTGTCCAGGGGCCT---ACTGTTG-GCCCCACGGCCCCCT--C----------------GGGCTGAATCA i canFam2.chr18 C 0 C 0 s proCap1.scaffold_13667 11548 86 - 46842 GAG-CTCCCAGCAG--CTCTTGGCCTGGCCAGC--CCCCTCCCAGGCTCCT---------G-GACACCCAGGTCTGC--C----CTCGAGGGGAATGGGCTGGCCCA i proCap1.scaffold_13667 I 649 C 0 s loxAfr3.scaffold_159 75575 89 + 1045236 CAG-TTCCCAGCAG-CCTCTTCTCCCAGTCCAC--CCCCTCCCAGATGCCT---------G-GGTCCCCATTCCTCCTGC----CCCCAGGGGAAGGGGCTGGCTCA i loxAfr3.scaffold_159 C 0 C 0 e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=557742.000000 s hg19.chr11_gl000202_random 2901 273 + 40103 GAAAGCCCT-CGGGTCTG-TCCTCTTATCTT---TTGCAAGCCTAGCT-GGCCTC----TGCTCCACCCCAGGCCTGGTTCTGGAGCGCGCGTGTAGAAATGGGGCTGGCTGCTACGGCGGGCTTATCTGGGCCTGCAGGGCCGCCTTATCTCCCACAGCTTCTCATTGCCAGTCACTGGTTTATGCTTTTATGAGTG--CAG-TTTGCTCCTTCTAGGGAAGCACTGAGCGATCTCTGAAGGTGCCTGGCCA----TG----GGGGCA-CAGGGTTCCTTCCTCCTAAAGCGCT s rheMac2.chr14 128147583 274 - 133002572 GGAAGCCCT-TGGCTGTG-TCCTCTTATCTT---TTGCAAGCCCAGCT-GGCCTC----TGCTCCACCCCAGGCCTGGTTCTGGAGTGCGCGTGTAGAAATGGGGCTGGCTGCTACGGCGGGCTTATCTGGGCCTGCAGGTCCACCTTATCTCCCACAGCTTCTCATTGCCAGTCACTGGTTTATGCTTTTGTGAGTG--CAG-TTTGCTGCTTCTAGGGAATCACTGAGCAATCTCTGAAGGTGCCTGGTTG----TG----GGGGCAGCAGGGTTCCTTCCTCCTAAAGTGCT i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125984408 273 - 132107971 GGAAGCCCT-CAGCTCTG-TCCTCTTATCTT---TTGCAAGCCCAGCT-GGCCTC----TGCTCCACCCCAGGCCTGGTTCTGGAGCACGCGTGTAGAAATGGGGCTGGCTGCTACGGCGGGCTTATCTGGGCCTGCAGGGCCGCCTTATCTCCCACAGCTTCTCACTGCCAGTCACTGGTTTATGCTTTTATGAGTG--CAG-TTTGCTCCTTCTAGGGAAGCACTGAGCAATCTCTGAAGGTGCCTGGTCC----TG----GGGTCA-GAGGGTTCCTTCCTCCTAAAGCGCT i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 154 273 + 2579 GGAAGCCCT-CGGCTCTG-TCCTCTTATCTT---TTGCAAGCCCAGCT-GGCCTC----TGCTCCACCCCAGGCCTGGTTCTGGAGCGCGCGTGTAGAAATGGGGCTAGCTGCTACGGCGGGCTTATCTGGGCCTGCAGGGCCGCCTTATCTCCCACAGCTTCTCATTGCCAGTCACTGGTTTATGCTTTTATGAGTG--CAG-TTTGCTCCTTCTNGGGAAGCACTGAGCGATCTCTGAAGGTGCCTGGCCG----TG----GGGGCA-CAGGGTTCCTTCCTCCTAAAGCGCT i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68190071 273 + 134204764 GAAAGCCCT-CGGCTCTG-TCCTCTTATCTT---TTGCAAGCCCAGCT-GGCCTC----TGCTCCACCCCAGGCCTGGTTCTGGAGCGCGCGTGTAGAAATGGGGCTGGCTGCTACGGCGGGCTTATCTGGGCCTGCAGGGCTGCCTTATCTCCCACAGCTTCTCATTGCCAGTCACTGGTTTATGCTTTTATGAGTG--CAG-TTTGCTCCTTCTAGGGAAGCACTGAGCGATCTCTGAAGGTGCCTGGCCG----TG----GGGGCA-CAGGGTTCCTTCCTCCTAAAGCGCT i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9657704 247 + 15951348 GGCAATTC--CTCAGCTGCTCCTCTTATCTCCCTTTGCCA-------------------CCCCCCACCCTGGGCCTGGTGCTGG---CCACATCCA-----AGGGCCGGATGCCACTGTCATCTTATCTGGTCATAAAGGGCGGCCTTATCTCCAGCCGCTTTCCACTGCCAGTCACTGGTTTATGCTTTTACGAGGG--CAG-TTTGTTTCTCTGGAAG----GCCAAGAGCTCTCCCAAGGTTCATGG-------AG----GGGACA-GCAGATGCCTTCTCTGCACAGCTGT i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 18641 234 + 42081 GGAAGTCC--CAGCTCTG-TCCTCTTATCTTCTGTTGCCAGCTGGGGG-GGCCTCCAGGTCCCCTCCCCCAGGCCTGGCGCTGGA--CCACATGGA-----AGGGCCCGATGCTA-TCTCG-CTTATCTGGTCATAAA-GTCCGCCTTATCTCCTGCTGCTTTCCACCGCCAGTCACTGCTTTATGCTTTTACGAGGG--GGGACTCGCTGCTCCTGGGG----GGCGGGAG---------GGGGCGTGG-------GG---------A-GCTGAGGCTT--------------- i oryCun2.chrUn0985 N 0 C 0 s bosTau4.chr29 48967654 272 + 51998940 GGAAGCCCA-GCGCGCTC-TCCGCTTATCTT---CTGCAAGCCCAGCTGGGCATC----CGCTCCGCCT--GGCCTGGTGCTGCACCAAACGCACA------GGGCCGGACGCTATTGTTAGC-TATCTGGTTGTAAAGGTCTGCCTTATCTCCAGCCGCCTCTCACTGCCAGTCACTGGTTTATGCTTTTACGAGGG--CAG-TTTGCTTCTCCTGGAGAAGGAG-GTGCAGTCTCCGAAGGCGCCTGGGAGTGGGGGTGGCGGGGGC-TGCGGTTTCTTCCTTGTAAAGCAAC i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28928622 269 + 33091231 GGAAGCCCACTGGCTCTG-TCCCCTTATCTT---CTGCAAGCCCAGCTGGGCATC----CGCTCCACCCTGGGCCTGGCGCTGGACCACGTTTTCA------GGGGACAGCACTATTGTCAGCTTATCTGGTTGTAAATGGCCATCTTATCTCCAGCCGCCTCTCACTGCCAGGCACTGGTTTATGCCTTTACGAGAG--CAG-TTTGCCTTTCTCGGGAAAGCAG-GAGCAGTCTCCGGAGGTGCCTGGTGGC---GG----GGCAGC-CGGGCTTTCTTCCTTATAAAGTGGT i equCab2.chr12 C 0 C 0 s canFam2.chr18 7530671 258 - 58872314 GCAAATCCA-TGGCTCTG-CCCTCTTATCTT---CTGCAAGGCCGGCTGGGCATC----CGCGGCACTC-AGGCCTGGTGCTGGACCAAATTTAAG------GGGCCGGATGCTGTCATCAGCTTATCTGGTCATAAAGGCCTGCCTTATCTCCAGCCGCCTCTCACTGCCAGTCACTGGTTTATGCTTTTACAAGGG--CAG-TACGC--TTCTCAGGGAAGCAG-GAGCAATCCTTGAAGGCGCCTGCTGGCAGGGG----GGTAAC-CAGGACTCCTTCCTT---------- i canFam2.chr18 C 0 C 0 s proCap1.scaffold_13667 11634 221 - 46842 GGAAGCCCT-GGCCCCTG-GTCCCTTATCTC---CAGCTAGCCCTGCCCGCCATC----GGCTCTGGCC----CCTGGC-----AGTACATTTGAG------GGGCCAGCAG--GGTGTGGGCTTATCTGGTTGTAAAGGCCTATGTTAT------CTGCCTCTCACTGCCAGTCACTGCTTTATGCTTTTATGACAG--TAG-TTGACTTGCCCTCAG--------GAGT--------------------------GG----GGGTGG-CTTGGTTTCTTCCTTGTTAAGAACG i proCap1.scaffold_13667 C 0 C 0 s loxAfr3.scaffold_159 75664 212 + 1045236 GGAAGCCCT-GTCCTCTG-GTCTTTTATCTG---CTGCAAGCTCCCCTGGGCATC----CGCTCTGGCC----CACGGC-----ACCACATGTGAG------GGGTGGATAG--AGTGCAGGCTTATCTCGTCCTAAAGGTCTGTGTTATCTGTAGCTGCCTTTCACTGCCAGTCACAGCTTTATGCTTTTACGAGAGGCTGA-TTG-CTTCCTCTCGGA-------GAGT--------------------------GG----GGGGAG-A-----------------GGGGAAG i loxAfr3.scaffold_159 C 0 C 0 e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=58268.000000 s hg19.chr11_gl000202_random 3174 122 + 40103 GGTCCC-ATGCCAGCCC--TGGCTCTGCAGCTG--------CTGTG-------GGTATCTTGCATGG---GTGAGTGCCTGAGT------------------GGAGGCTGTGGTGGT-------------------------------CTCAAGGGGCTTTTGCC----------------------AGAAGTGAT-CAGAAGAGGAGCCTTCAG s rheMac2.chr14 128147857 122 - 133002572 GGTCCC-ATGCCAGCCC--TGGCTCTGCAGCTG--------CTGTG-------GGCATCTTGCATGG---GTGGGTGCCTGAGT------------------GGAGGCCGTGGTGGT-------------------------------CTT---GGGCTTTTGCC-------------------AGGAGAGGCGAT-CAGAAGAGGAGCCTTCAG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125984681 125 - 132107971 GGTCCC-ATGCCAGCCC--TGGCTCTGCAGCTG--------CTGTG-------GGTATCTTGCATGG---GTGAGTGCCTGAGT------------------GGAGGCCATGGTGGT-------------------------------CTCAAGGGGCTTTTGCC-------------------AGGAGAAGTGAT-CAGAAGAGGAGCCTTCAG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 427 122 + 2579 GGTCCC-ATGCCAGCCC--TGGCTCTGCAGCTG--------CTGTG-------GGTATCTTGCATGG---GTGGGTGCCTGAGT------------------GGAGGCTGGGGTGGT-------------------------------CTCAAGGGGCTTTTGCC----------------------AGAAGTGAT-CAGAAGAGGAGCCTTCAG i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68190344 122 + 134204764 GGTCCC-ATGCCAGCCC--TGGCTCTGCAGCTG--------CTGTG-------GGTATCTTGCATGG---GTGGGTGCCTGAGT------------------GGAGGCTGTGGTGGT-------------------------------CTCAAGGGGCTTTTGCC----------------------AGAAGTGAT-CAGAAGAGGAGCCTTCAG i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9657951 145 + 15951348 GGCTCC-GTGCCAACTC--C-GCTCTGCAGCTG--------CCAGGCACCCGTGGGAACCTGAGTGG---GTGGGCATGGGAGCAGAGGCTAGAAGCGGGCAGGAAGCAGTCGCAAT-------------------------------CCTTAGGGGCTCTGGCC----------------------AGGGAGGACACCAAGGAGGA--CTCCAG i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 18875 106 + 42081 --CTAC-CTCCCAAAGC--A-GCCCAGT-------------CCAGG-ATCGGTGGGCCCCCGCGTGG---GCGGGCGGGGTAG-------------------GGAAG-----------------------------------------CCCCAGAG----TGACC----------------------AGGGGAGGTGACGGAGCGGAGCCTCCAG i oryCun2.chrUn0985 C 0 I 105 s bosTau4.chr29 48967926 158 + 51998940 GGCCCT-GTGCCAGCCC--TGGCTCAGCAACTGTGTGGGCCCCCTG-------GGAACC---CGGGG-GGGGGGGGGCAAGGGT------------------GGATGCCCCGGAGGGTGG----------------------GGAGGACCCA--GGTCACCAGCCCCACCGCGAGAAGCAAAGCCGGGGGAGGTGA-CATAAGGGGACCCTCTGG i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28928891 162 + 33091231 GGGCCGGGTGCCAGCCC--TGGCTCAGCAGCTGCCT-GGCCCTGTG-------GGAGCCCTGCGTGG-GGGCAGGGGGCAGGGC------------------GGAGGCCACAAGGGGCAG----------------------GGACAACCCA-GGGTCACCAGCCCCACAGTGGGGAGCAGAGCCGGGGGAGTGAC-GGGAAGAGGGGCCTCCGG i equCab2.chr12 C 0 C 0 s canFam2.chr18 7530929 148 - 58872314 -------GGGCCAGCCA--TGGCTCAGCAGCTGCAT-GGCCCCACG-------AAAGCCTTACATGGCAGGTGTGGGGCCGGGG------------------GGAGGCCGAGGAGGG----------------------------CAACCT---GGTCACCAGGCCTTCAAGGGGCAGCAGAGCCTGGGAGGTGAT-GGGAAGAGGAGCCTCTGG i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 75876 149 + 1045236 AGCCCG-CTGCCAGGCC--TGGCTAGCTGGCC---------CTGTG-------GGAACCCT---------GGGGGTGAACAGGC------------------AGGGCCGACACAGGATCACCAGCCCTATAACGAGGCGCAAAGCCACCACTCAGGGCTTTTGCC-------------------CAGAGCGGTGCC-AGAAAGAGGAGCCTGTAG i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 11855 135 - 46842 GGCCAA-GTGCCAGGTC--TGGCCCAGCTGCC---------CGGTG-------GGAACCCTG--------GGGGGCGATTGGAT------------------GGGACTAGTACAGGGTTA-CAGCTCTTTATTGAGAAGCAAAGCCTCCACCTGGGGCTTTTG-C-------------------CAGGGAGGTGCC-AGG-------------AG i proCap1.scaffold_13667 C 0 C 0 s dasNov2.scaffold_107233 3388 146 - 8172 GGCTCC-AGGCCAGCCCGTTCTCCCAGCTGCC---------C-ACG-------GGAACCC-----------GGAGCGGATgggccg----------------gggggcggcggggggTGG--ACCCCCGCAGGGTGCACCGAGGACGAGGCT--GGACTTCTGCC-------------------AGGGGCGGTGGC-AGGGAGAGGCTCCTCCGG i dasNov2.scaffold_107233 N 0 C 0 e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=23268.000000 s hg19.chr11_gl000202_random 3296 46 + 40103 GAGGGAAACCCCAGGT----GGCCCC-------CACAC-----CTTCTTT-----------TGTTTGCCCATT s rheMac2.chr14 128147979 46 - 133002572 GAAGGACACCCCAGGT----GGCCCC-------CACAC-----CTTCTCT-----------TGTTTGCCCATT i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125984806 46 - 132107971 GAGGGACACCCCCGGT----GGCCCC-------CACAC-----CTTCTTT-----------TGTTTGCCCATT i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 549 46 + 2579 GAGGGACACCCCAGGT----GGCCCC-------CACAC-----CTTCTTT-----------TGTTTGCCCATT i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68190466 46 + 134204764 GAGGGACACCCCAGGT----GGCCCC-------CACAC-----CTTCTTT-----------TGTTGGCCCATT i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9658096 40 + 15951348 GAGGGAGGATTCTGA-----GGCCCT-------TGC----------TGAC-----------TGACTGACTGTT i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48968084 38 + 51998940 GAGGGATAACTCTGGG----GTGCCC--------------------TTCC-----------TGTTCCCCCTTT i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28929053 43 + 33091231 GAG----------GGG----TGTCCCAGCCCTTCACAC-----CTTTCCT-----------CGTTCCCCCTTT i equCab2.chr12 C 0 C 0 s canFam2.chr18 7531077 52 - 58872314 GAGGGAGAACCCTGGG----GGTCCCAGTCCCACCCAC-----ATGGTCT-----------CATT-CCCTTTT i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 76025 66 + 1045236 GAGGGGAACCTAAGAGTCCCAGCCCC-------CACCTCCCTGCTTTTTTGTGCCTGTGTGTGTGTGCCGCTT i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 11990 48 - 46842 GAGGAGAAGCTGGGAGAACCGGGCCC-------CACCT-----CTTTCTT-------------TGTGCCCCTT i proCap1.scaffold_13667 C 0 I 1575 s dasNov2.scaffold_107233 3534 40 - 8172 AAGGGGCATACCCAGGGCCCAGCACC-------CACCC---CGTTTCCTT----------------------- i dasNov2.scaffold_107233 C 0 C 0 e oryCun2.chrUn0985 18981 105 + 42081 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=201571.000000 s hg19.chr11_gl000202_random 3342 159 + 40103 TGAT---C----TGCCCCACACCGG----ACACACTTTGATCTCACCAGCCCAGTCTCTAAGGTCCTGCCTGAGAGGG-----------TGGGCCAAGTCCTGCA---CTGGAAGCTGGGAGGCTGGAA-TCAGATCTTCACACTG-TGCCTCCACTGTCctctgagcctcagtttcctcacctgt s rheMac2.chr14 128148025 159 - 133002572 TGCT---C----TGCCCTACGCTGG----ATACACCTCGATCTCACCAGCCCAGTCTCCAAGGTCCAGCCTTAGAGGA-----------TGGGCCAAGTCCTGCA---CTGGAAGCTGGGAGGCTGGAA-TCAGATCCTCACATTG-TGCCTCCGCTGTCctctgagcctcagtttcctcacctgt i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125984852 159 - 132107971 TGAT---C----TGCCCTACACCGG----ACACACCTTGATCTCACCAGCCCAGTCTCCAGGGTCCCGCCTGAGAGGG-----------TGGGCCAAGTCCTGCA---CTGGAAGCCGGGATGCTGGAA-TCAGATCCTCATGCTG-TGCGTCCACTGTCctctgagcctcagtttcctcacctgt i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 595 159 + 2579 TGAT---C----TGCCCCACACCGG----ACACACCTTGATCTCACCAGCCCAGTCTCTAAGGTCCTGCCTGAGAGGG-----------TGGGCCAAGTCCTGTA---CTGGAAGCTGGGAGGCTGGAA-TCAGATCCTCACACTG-TGCCTCCACTGTCctctgagcctcagtttcctcacctgt i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68190512 159 + 134204764 TGAT---C----TGCCCCACACCGG----ACACACCTTGATCTCACCAGCCCAGTCTCTAAGGTCCTGCCTGAGAGGg-----------tgggccaagtcctgca---ctggaagccaggaggctggaa-tcagatcctcacactg-tgcctccactgtcctctgagcctcagtttcctcacctgt i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9658136 154 + 15951348 GGAT---C------CCCTGCCCAGGGTCAGCACACTTTAGCCCCA-CAGCCTAGGCTCTGAGGTCCTGCTAGGTTGCA-----------TGGGCAAAGCCACAGAGGCCCGAAAATTGGAAAGATGGTG-GCAGGTCCTTCCTCTG-AGCCTTCA-------CTGAGCCTCAGTTTCCTC-CTTG- i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48968122 161 + 51998940 CCATCCTC----TGGCTCTCCT-------G-ACACTTGCATCCCACCAGCCCACCCACTGCTATCCTGCCTGTGGGGGCTGGGGGACGACGGGCCAAGCCCTGAG----------CCTGGAGGCTGGGA-TTCTGCCTTTGCTCGA-TGCCTCCATCATCCTCCCAGCCTCAGTTTTC-CCTCTCC i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28929096 142 + 33091231 CCATGTCC----TGCCTCTCAC-------GCACACCTGGATC-------------------TGTCCTGTGTGCGGGGGGCAGGGGGC--GGGGCACAGCCCTGGG----------CCTGGAGGCCAGGG-TTGGACCTGTGCTTGG-TGCCTCCTGCATCctcccagcctcagtttcctcccctgt i equCab2.chr12 C 0 C 0 s canFam2.chr18 7531129 133 - 58872314 CAATTTCC----TGCTCGTCACA------GCATGCCTGGATCCCTCCAGCCTGGGCTCCGTTGTCCTGCCTGCCAACA-----------TGGGCAAATTGCTGGG----------CCTGGAGCCT--GG-CTAGGCCGTTGtct-g-tgcctc-----------------cgctgtcctcacctgt i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 76091 144 + 1045236 ------------TGGTCT---CCTG----CCCCACACTGGGC--------TCCGTCTCTGCTGTCcagcctgagatga-----------tgggaaaagtgctgga---cttagaatcagaaagcccaag-ttagatccttgctctgttgccttggctgccctaggagcctcagtttctccatctgt i loxAfr3.scaffold_159 C 0 C 0 s dasNov2.scaffold_107233 3574 156 - 8172 -------CATCATGTCCCA-GCCAG----GCCCACCTTGGTCCCACCTG-CCCTCCTGTGCTGTCCTGCCTCAggtgg-----------cgggaaaaac-cccga---tttggagccaggaagcctgggactcgatcc-aactctgctgcc-gggctggcctcggagcctcagtttacccacctgt i dasNov2.scaffold_107233 C 0 C 0 e oryCun2.chrUn0985 18981 105 + 42081 I e proCap1.scaffold_13667 12038 1575 - 46842 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=-5798.000000 s hg19.chr11_gl000202_random 3501 25 + 40103 aacatgagcagaaagtttg-------cagcca s rheMac2.chr14 128148184 25 - 133002572 aacatgagcagaaggtatg-------gggcca i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125985011 25 - 132107971 aacatgagcagaaagtatg-------cagcca i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 754 25 + 2579 aacatgagcagaaagtttg-------cagcca i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68190671 25 + 134204764 aacatgagcagaaagtttg-------cagcca i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9658290 15 + 15951348 ----------GGTGATTTT-------GACCTC i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48968283 23 + 51998940 ACAGTGGGCGTAAGATGCT-------GGGC-- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28929238 16 + 33091231 aacatgagcataaga--------------c-- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7531262 23 - 58872314 aaaatgggcataagatgct-------gagt-- i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 76235 26 + 1045236 aaaatgAACACACCACTTTCCAGCCA------ i loxAfr3.scaffold_159 C 0 I 2186 s proCap1.scaffold_13667 13613 19 - 46842 AACATAAGCTGAGCCCCGT------------- i proCap1.scaffold_13667 I 1575 C 0 s dasNov2.scaffold_107233 3730 19 - 8172 gaaatgagcctaacaagct------------- i dasNov2.scaffold_107233 C 0 I 4 e oryCun2.chrUn0985 18981 105 + 42081 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=215998.000000 s hg19.chr11_gl000202_random 3526 108 + 40103 cctcgcct-ggcaggatggccatggggaACCACAGGAGGGGAGGGGGCAGCGTCGAGGGTCCCAT-GGCCAGCCAGCATGGGCCAACCCATGTGTCACAGTTCATAGAAG s rheMac2.chr14 128148209 102 - 133002572 cct-gcct-ggcaggatggccatggggCACCCCA-----GGAGGGGGCAGCGTCGAGGGTCCCAT-GGCCAGCCAGCATGGGCCAGCCCATGTGTCACAGTTCATAGAAG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125985036 105 - 132107971 cctcgcCT-GGCA-GATGGCCATGGGGAACCCAAGGAGGGGAGGGG-CAGCGTCAAGGGTCCCAT-GGCCAGCCATCATGGGCC-ACCCATGTGTCACAGTTCATAGAAG i ponAbe2.chr11 C 0 I 1034 s gorGor1.Supercontig_0069572 779 108 + 2579 cctcgcct-ggcaggatggccatggggaaccacacgagGGGAGGGGACAGCATCGAGGGTCCCAT-GGCCAGCCAGCATGGACCAACCCATGTGTCACAGTTCATAGAAG i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68190696 108 + 134204764 cctcgcct-ggcaggatggccatggggaACCACAGGAGGGGAGGGGGCAGCGTCGAGGGTCCCAT-GGCCAGCCAGCATGGGCCAACCCATGTGTCACAGTTCACAGAAG i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9658305 104 + 15951348 CCTGATCT-TGCCAAGCAGCCACAGGGAACTGCA-----GGAGGTGGCAGCATTGAGGGTCCTATAGGTCAACTGGCATAGTTTGACCCACGTGGTGTTGCTCACAGAAG i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48968306 105 + 51998940 CCCCCAGTGTGCAGGGTGGCCGTGGGGACCCCCA-----GAACAGAGCAGTGTTGAGAGTTCTGTCAACCAGCCCGTGAGGTCCGACTCACGCAGCATCCACCGTAGAAA i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28929254 104 + 33091231 ccttgcat-tgcagggtggctgtggggacccaca-----ggaggtGGCAGCATCCAGGGTCCTGGAAACCAGCTGGTGCCGTCAGACCCACGTGCCGTCCTTCATCAAGG i equCab2.chr12 C 0 C 0 s canFam2.chr18 7531285 103 - 58872314 cccctcct-tgcagggtgaccgtggggaACCACA-----GGAGGTGGCAGGGTCTGGGGTCCTGTTAACCAGCTGGCGTGGTCTGACCCATGGG-TGTTGTTTATAGGAG i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 78447 86 + 1045236 CCTCACCT-CATAGAGTGACTGTAGGGAACC----------------------CCAGGATCCTGTAAACCAGTAGGTGT-GTCCAACACACGTGGCATTGTTCATAGAAG i loxAfr3.scaffold_159 I 2186 C 0 s proCap1.scaffold_13667 13632 102 - 46842 CCTCACCT-CACAGAGTGGCTATAGGGAACCCAG-------GAAAGGGAACGTCCAGGGTCCAGTAAACTAGTAGGTGTAGTTCAGTACACACACCATTGTTCACAGAAG i proCap1.scaffold_13667 C 0 C 0 s dasNov2.scaffold_107233 3753 81 - 8172 ccccatct-tgcagggtggctcca-ggaaccaca-------gagaGGCGGCAGCGAGGG-CCTGTAAACCAGCAGGTGT-G------------------GGCCACGGAAG i dasNov2.scaffold_107233 I 4 C 0 e oryCun2.chrUn0985 18981 105 + 42081 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=26501.000000 s hg19.chr11_gl000202_random 3634 43 + 40103 GTCTTAGGA-GCCTGGTccctcccc-ctccccctcccccCAGGAT s rheMac2.chr14 128148311 42 - 133002572 GTCCTAGGA-GTCTGGTCCCTTCCC-CTCCCCCT-ATCCCGTGAT i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0069572 887 37 + 2579 GTCTTAGGA-GCCTGGT------CC-CTCCCCCTCCCCCCAGGAT i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68190804 43 + 134204764 GTCTTAGGA-GCCTGGTccctcccc-ctccccctcccccCAGGAT i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9658409 31 + 15951348 GCCCTGGAATGCCCAATCCCT--------------ACCTTAGGTT i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 19086 28 + 42081 GTTCTAGCA-GCCTGACCCCC--------------ACCCCAGG-- i oryCun2.chrUn0985 I 105 C 0 s bosTau4.chr29 48968411 38 + 51998940 GTTCTAGGA-GGCTGATCCTTTGGT-CGCC-----CCCGCAGGAT i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28929358 14 + 33091231 GTTCCAGAG-GCCTG------------------------------ i equCab2.chr12 C 0 C 0 s canFam2.chr18 7531388 38 - 58872314 GTTCTAGGA-GCCCAGTCTATGATC-CCTC-----CGTGCAGGAT i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 78533 39 + 1045236 GCTCTAGAA-GCCTGATTCCTGCCCGCTTC-----CTCCCAGGAT i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 13734 39 - 46842 GTTCTAGAA-GCTTGATTCCTGACCTCTTC-----CTCCCAGGAT i proCap1.scaffold_13667 C 0 I 4713 s dasNov2.scaffold_107233 3834 37 - 8172 GTTCCGGGC-ACCTGACCTCTGACC-CCGC-----TTCCCAGAC- i dasNov2.scaffold_107233 C 0 C 0 e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=79272.000000 s hg19.chr11_gl000202_random 3677 78 + 40103 GTTTGTAGGG-TGAGGCAA--CCGGCAGGTGCCTGGTTAAGCCC----TG-GGG-------------TCTGGAGAGCGGTTTCTAACTCCAGGCCCCTG s rheMac2.chr14 128148353 78 - 133002572 GTTTGTAGTT-TGAGGCAA--CAGGCAGATGCCTGGTTAAGCCC----CA-GGG-------------TCTGGAGAGCGGTTTCTAACTCCAGGCCCCTA i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0069572 924 78 + 2579 GTTTGTAGGG-TGAGGCAA--CCGGCAGGTGCCTGGTTAAGCCG----TG-GGG-------------TCTGGAGAGCGGTTTCTAACTCCAGGCCCCTG i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68190847 78 + 134204764 GTTTGTAGGG-TGAGGCAA--CCGGCAGGTGCCTGGTTAAGCCC----TG-GGG-------------TCTGGAGAGCGGTTTCTAACTCCAGGCCCCTG i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9658440 72 + 15951348 GTTCCTATTT-GCACACAG--C-AGCAGCC-CCAGGCTGAGTCCCTGTCT-GGG-------------G-----GAGAGGCTTCTTGCTC--TGC-CCTG i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 19114 50 + 42081 -----------------------AGCAG------GGCCGGGCCC----CA-GGG-------------GCCACTGGGAGGTTTCTAATGC--AGCACCTG i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48968449 92 + 51998940 GTTTGCACTCTTGAGGCCA--TCAGCATGGGTCAGGCTGAGCCC----CA-GGGATTGTGTACTCCATCAGGTGAGAAGTTTCTAACTCCAGGACCCTG i bosTau4.chr29 C 0 I 557 s equCab2.chr12 28929372 76 + 33091231 ----GAAGTG-GGAGGCAG--CTGGCAGGGGTCAGGCCGAGCCC----CA-GGC--TGCGTGTTGCATCAGGTGAGAGGTCTCTAACTCC--------- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7531426 90 - 58872314 GTCTGCACTC-TGAGGTGG--CTGGCAGGGGCCAGGCCGAGTCC----CACAGG--TGCAGGCTGTGTCAGGTGAGAGGTTCCTAACTCCAGTCGTCTG i canFam2.chr18 C 0 I 1585 s loxAfr3.scaffold_159 78572 91 + 1045236 ATTTACACTT-TAAAGTAGG-CGGGCAGGGACCAGGCTGAACCC----CA-GGG-ATGCATGTTCGGTATGGCAAGAGGTTTCTACCTCCAGTCCCCTG i loxAfr3.scaffold_159 C 0 C 0 s dasNov2.scaffold_107233 3871 87 - 8172 ATTTGCGCTT-TAAGGCAGGTCCAGCAGGGTCCAGTTTGAACC--------AGG-ATGCATG--AGGTCTGCCGAGAAGTTTCTAATTCCAGCATCTTG i dasNov2.scaffold_107233 C 0 C 0 e proCap1.scaffold_13667 13773 4713 - 46842 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=-21750.000000 s hg19.chr11_gl000202_random 3755 40 + 40103 TGAGCTGCCAA-GACCTCCACCTC----------------------------------------------------------------------------------CTCCCTAGGGCCCCCGG--------------------------------------------------------------------- s rheMac2.chr14 128148431 40 - 133002572 TGAGCTGCCAA-GGCCTCCACCTC----------------------------------------------------------------------------------CTCCCCAGGGCCCCCGA--------------------------------------------------------------------- i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0069572 1002 40 + 2579 TGAGCTGCCAA-GACCTCCACCTC----------------------------------------------------------------------------------CTCCCTAGGGCCCCCAG--------------------------------------------------------------------- i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68190925 40 + 134204764 TGAGCTGCCAA-GACCTCCACCTC----------------------------------------------------------------------------------CTCCCTAGGGCCCCCAG--------------------------------------------------------------------- i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9658512 37 + 15951348 TGTGTCACCAAGGTCCCCTGCC-C----------------------------------------------------------------------------------CTCCAGAGGCCGCT------------------------------------------------------------------------ i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 19164 35 + 42081 CAAGCCCCCAA-GCCCTCCACC-C----------------------------------------------------------------------------------CTCCCCAGGCCCC------------------------------------------------------------------------- i oryCun2.chrUn0985 C 0 C 0 s equCab2.chr12 28929448 9 + 33091231 ------------------------------------------------------------------------------------------------------------------GGTCCCCGG--------------------------------------------------------------------- i equCab2.chr12 C 0 C 0 s loxAfr3.scaffold_159 78663 191 + 1045236 TGGATAACTGA-AGCTCACACCTCCTACaaaaaacaaaaaaacccgaacctgttgccgtcgagtcgattccgactcacagtgaccctataggacagagtagaactgccccatagagtttccaaggagcacctggaggattccaactgctgacctttgattagcagtcgagcacttatccactgctccaccag i loxAfr3.scaffold_159 C 0 C 0 s dasNov2.scaffold_107233 3958 34 - 8172 TGGGTCCCTGA-AACACCCACCCCC---------------------------------------------------------------------------------CCCCACAGGG---------------------------------------------------------------------------- i dasNov2.scaffold_107233 C 0 C 0 e proCap1.scaffold_13667 13773 4713 - 46842 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48968541 557 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=54925.000000 s hg19.chr11_gl000202_random 3795 99 + 40103 ----------------------------------GGGTCTGTTTGCTCTGTCTGCTTTT----GAGAATCAGA-TTATAATGGGAGCCTGGGTCAGTTTCTGGATTTGTGGCCTCAGGACCTCCcagaaggagcagag s rheMac2.chr14 128148471 99 - 133002572 ----------------------------------GGGTCTGTTTGCTCCTTCTGCTTTT----GAGAATCAGA-TTGTAATGGGAGCCTGGGTCAGTTTCTGGATTTGTGGGCTCAGGACCTCCcaggagcagcagag i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0069572 1042 99 + 2579 ----------------------------------GGGTCTGTTTGCTCTGTCTGCTTTT----GAAAATCAGA-TTATAATGGGAGCCTGGGTCAGTTTCTGGACTTGTGGGCTCAGGACCTCCcagaaggagcagag i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68190965 99 + 134204764 ----------------------------------GGGTCTGTTTGCTCTGTCTGCTTTT----GAGAATCAGA-TTATAATGGGAGCCTGGGTCAGTTTCTGGATTTGTGGCCTCAGGACCTCCcagaaggagcagag i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9658549 96 + 15951348 ------------------------------------GTCTCTGGTTCCTTGCTGCCTCTCTGGGAGAACAAAG-CTGTGATGGGAA-CTGAGGAGGCCTTTGGGTCTGTCGA-TCAGCACCTTCCAGCAGcggga--- i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 19199 72 + 42081 -------------------------------------CCTTTTCTTCTGAGCT-CCCCTCCACCCCAGACGGG-TTACAGTGGGAG------------TTTGGCT----------AGCACCTGCCGGAGGCAG----- i oryCun2.chrUn0985 C 0 C 0 s loxAfr3.scaffold_159 78854 134 + 1045236 ggctccTCGCCGCCTCCCAGCCCCCTTCCTTCCTCTGCTTCTTTGCTCCTGTTCTCTCT----GAGAGCAAGGCCTGTAAGGGTAGCTGGGGGCCTTTTCTCAATCAGTCAACTCAGCACCTCACAGAAACAGCAGGG i loxAfr3.scaffold_159 C 0 I 174 s dasNov2.scaffold_107233 3992 104 - 8172 ---------------------CCGCCCTCTTTTCCTGCTTCTTTGCT---------TCT----CATAACAGGGCTTTCCGTGGGAGCCTTGGACGGCTTCTGGATCTGCCCTCTTAGCACCTCACggaagcagcaggg i dasNov2.scaffold_107233 C 0 C 0 e proCap1.scaffold_13667 13773 4713 - 46842 I e equCab2.chr12 28929457 0 + 33091231 C e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48968541 557 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=84779.000000 s hg19.chr11_gl000202_random 3894 139 + 40103 ctga----aggccaagagcctggctcctg-----tcctgtcctgtcacttactgccctgtgaccacaggca--------ggtcactgcacctctctgagtcacagctttctcatcttccaagcggggagAG-------TCCT--TGAAAC--AGGCTGCAACCAT-TA s rheMac2.chr14 128148570 141 - 133002572 ctga----aggccgagagcctggctcctg-----tcctgtcctgtcacttactgccctgtgaccacaggca--------tgtcactgcacctctctgagccacagctttctcatcttctgagtggggAAAG-------TCCT--TGAAACAGAGGCTGCAACCGT-TA i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0069572 1141 139 + 2579 ctga----aggccaagagcctggctcctg-----tcctgtcctgtcacttactgccctgtgaccacaggca--------ggtcactgtacctctctgagtcacagctttctcatcttccaagcggggagAG-------TCCT--TGAAAC--AGGCTGCAACCAT-TA i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68191064 139 + 134204764 ctga----aggccaagagcctggctcctg-----tcctgtcctgtcacttactgccctgtgaccacaggca--------ggtcactgcacctctctgagtcacagctttctcatcttccaagcggggagAG-------TCCT--TGAAAT--AGGCTGCAACCAT-TA i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9658645 128 + 15951348 ----------------ggtctggggacag---aggcctatcctgccactgagtgctgtgtggcgacagccgacagtcg-agtctcttcagctctctgagcctc----------acttACGATGTGGGGGAG-------CCCCTGTGATGC---TGCTGTGGGTGTCTC i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 19271 96 + 42081 ----------------AGCCTGGCTCCCGCCCAGGCC--CCCCGCTGCCCAGGG------------AGCGGCCACTTGTGGTCCCTTCGCCTCTCTGGACAGC---------TGCTTGCGAGCGGGGAGGG-------TCCT-------------------------- i oryCun2.chrUn0985 C 0 I 1342 s loxAfr3.scaffold_159 79162 134 + 1045236 CTgg----aggctgaaaagctgggttcag----ttcttgccctgcca-ttactgctgtgtgaccacagacc--------agtcactgctcctctcagagccacggtctcctcgtcttccaaatgaagaggA--------------GAGGG--ATGCTGTAATGAC-GA i loxAfr3.scaffold_159 I 174 C 0 s dasNov2.scaffold_107233 4096 152 - 8172 ctgggggtgggcagaaagcccggttgtga----gtcttgtccccccacttagcactggggggccgcagtca--------ggtgacttcacctcttagagctgcag-cttttcacctccaaaatggagagaacgatgcctcctcgtgaagg--gtggcgtaagggt-ta i dasNov2.scaffold_107233 C 0 C 0 e proCap1.scaffold_13667 13773 4713 - 46842 I e equCab2.chr12 28929457 0 + 33091231 C e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48968541 557 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=59191.000000 s hg19.chr11_gl000202_random 4033 58 + 40103 Gattcattcattcaaca--------aatatttgctgagcatctactatgtgccag-gca------tgtgtgct s rheMac2.chr14 128148711 58 - 133002572 Cattcattcattcaacc--------aatattcgctgaacgtctgctatgtgccag-gca------tgtgtgct i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0069572 1280 58 + 2579 Gattcattcattcaaca--------aatatttgctgagcatctactatgtgccag-gca------tgtgtgct i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68191203 58 + 134204764 Gattcattcattcaaca--------aatatttgctgagcatctactatgtgccag-gca------tgtgtgct i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9658773 58 + 15951348 Gattcagtctctcagca--------aggatgcgccaagcttctcctgtgggccag-gca------catgtgct i cavPor3.scaffold_42 C 0 I 2089 s equCab2.chr12 28929457 52 + 33091231 Gactcgttcattcaaca--------aatatttcttgagcgtctactctgtgcc----ca------atggt--- i equCab2.chr12 C 0 C 0 s loxAfr3.scaffold_159 79296 64 + 1045236 GATACGGtcactcagtg--------agtattcatggagcaccttctatgtgccgg-gcagaggtctaggggcc i loxAfr3.scaffold_159 C 0 C 0 s dasNov2.scaffold_107233 4248 69 - 8172 gaGCCACTCATCCAACGCCTTCCACAATATTTACCGAGCATCTTCCA----CCGGCGAGGAGCTCTAGGTACT i dasNov2.scaffold_107233 C 0 C 0 e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48968541 557 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=26066.000000 s hg19.chr11_gl000202_random 4091 50 + 40103 ggggacacaatagagatctaaacagacaacaaacaagatattacttttaa s rheMac2.chr14 128148769 50 - 133002572 gggggcacgatagagatctaaacagacaaCAAACAAGACATTACTTTTAA i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0069572 1338 45 + 2579 ggggacacaatagagatctaaacagacaacaaac-----attacttttaA i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68191261 50 + 134204764 ggggacacaatagagatctaaacagacaacaaacaagatattacttttaa i panTro2.chr11 C 0 C 0 s equCab2.chr12 28929509 37 + 33091231 ggggatacagcagagaacgagacagacagc-------------ctttaca i equCab2.chr12 C 0 C 0 s loxAfr3.scaffold_159 79360 34 + 1045236 cggggcccagcagggatcaaagcagacaaagtcc---------------- i loxAfr3.scaffold_159 C 0 C 0 s dasNov2.scaffold_107233 4317 40 - 8172 GAGATTGCCCCAGAAAGCAGAGC---CAAGACCC-------TACCTGCAG i dasNov2.scaffold_107233 C 0 I 88 e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e cavPor3.scaffold_42 9658831 2089 + 15951348 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48968541 557 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=7450.000000 s hg19.chr11_gl000202_random 4141 29 + 40103 tgacaaaactgttttgc-----cattcattttaa s rheMac2.chr14 128148819 29 - 133002572 TGACAAAACTGTTTTGC-----CATTCGTTTTCA i rheMac2.chr14 C 0 I 337 s gorGor1.Supercontig_0069572 1383 29 + 2579 TGACAAAACTGTTTTGC-----CATTCATTTTAA i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68191311 29 + 134204764 tgacaaaactgttttgc-----cattcattttaa i panTro2.chr11 C 0 C 0 s equCab2.chr12 28929546 6 + 33091231 ccccaa---------------------------- i equCab2.chr12 C 0 C 0 s loxAfr3.scaffold_159 79394 26 + 1045236 --------ctggtctgcaagagcctacactccag i loxAfr3.scaffold_159 C 0 C 0 e dasNov2.scaffold_107233 4357 88 - 8172 I e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e cavPor3.scaffold_42 9658831 2089 + 15951348 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48968541 557 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=28852.000000 s hg19.chr11_gl000202_random 4170 75 + 40103 tggcaaaaacttttaacagccattacttttaatggcagaaactgcaattattttcgcaccaacctaacacataag s panTro2.chr11 68191340 75 + 134204764 tggcaaaaacttttaacagccattacttttaatggcagaaactgcaattattttcgcaccaacctaacacataag i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 1412 75 + 2579 TGGCAAAAACTTTTAACAgccattacttttaatggcagaaactgcaattattttcgcaccaacctaaCACataag i gorGor1.Supercontig_0069572 C 0 C 0 s rheMac2.chr14 128149185 74 - 133002572 TGGCAAAAACTTTTAACAgccatta-ttttaatgggagaaaccgcaattattttcgcaccaacctaatacataag i rheMac2.chr14 I 337 C 0 s equCab2.chr12 28929552 34 + 33091231 tgggagca------aacagacaata-----------------------------------aacaggacaagtaag i equCab2.chr12 C 0 I 12 s loxAfr3.scaffold_159 79420 37 + 1045236 tggaggtg------aacagacaaga------atcgaggtaaatgggatc-------------------------- i loxAfr3.scaffold_159 C 0 C 0 e dasNov2.scaffold_107233 4357 88 - 8172 I e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e cavPor3.scaffold_42 9658831 2089 + 15951348 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48968541 557 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=18192.000000 s hg19.chr11_gl000202_random 4245 33 + 40103 taaaatgtatggtgatgaca-caaagcaggaagg s panTro2.chr11 68191415 33 + 134204764 taaaatgtatggtgatgaca-caaagcaggaagg i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 1487 33 + 2579 taaaatgtatggtgatgaca-caaagcaggaagg i gorGor1.Supercontig_0069572 C 0 C 0 s rheMac2.chr14 128149259 33 - 133002572 taaaatgtatcatgatgacg-caaagcaggaaga i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48969098 34 + 51998940 tcAGTTGTGtgctgttgagagctaaacaggaaaa i bosTau4.chr29 I 557 C 0 s equCab2.chr12 28929598 31 + 33091231 tgcgttacgtggtgatgagaccta---tggaaac i equCab2.chr12 I 12 C 0 s loxAfr3.scaffold_159 79457 28 + 1045236 ----gtgtacggtgagcgcg-cttgagaggaag- i loxAfr3.scaffold_159 C 0 C 0 e dasNov2.scaffold_107233 4357 88 - 8172 I e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e cavPor3.scaffold_42 9658831 2089 + 15951348 I e canFam2.chr18 7531516 1585 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=121927.000000 s hg19.chr11_gl000202_random 4278 145 + 40103 ttcagtagggaatggagacaggcacgtctggggtggaggtggaaactcaattttcaatcgt--gtggctaggaaaggcct-------ctccaaggcaggcgacaactgagtcaagacccaaaagagatggga--------gagtgagatgtggagattctgg s panTro2.chr11 68191448 145 + 134204764 ttcagtagggaatggagacaggcacgtctggggtggaggtggaaactcaattttcaatcgt--gtggctaggaaaggcct-------ctccaaggcaggcgacaactgagtcaagacccaaaagagatggga--------gagtgagatgtggagattctgg i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 1520 123 + 2579 ttcagtagggaatggagacaggcacatctggggtggaggtggaaactcaattttcaatcat--gtggctaggaaaggcct-------ctccaaggcaggcgacaactgagtcaagacccaaaagagatgggA------------------------------ i gorGor1.Supercontig_0069572 C 0 I 33 s rheMac2.chr14 128149292 144 - 133002572 ttcagtaggaaatggggacgggcacgtctggggtggaggtggaaactcaattttcaatcat--gtggttaggaaaggcct-------cgcc-aggcaggtggcaactgagtcaagacccaaaagagatggga--------gagtgagatgcagagattctgg i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48969132 137 + 51998940 tccagaag------atgatgggcatgcctgtggtggggatgaagcctcggttctctatagg--gtagccagggaaagcct-------cacc-aggtgtgtgacacccaagtcaaga-ccaaaggcaatgagg--------aaatgagacgtggagagactgg i bosTau4.chr29 C 0 I 7 s equCab2.chr12 28929629 144 + 33091231 ttctggagggaatagggacaggcacatctggggtggggatggagcctcagttttcaatggg--gtggtcagggaagccct-------cacc-aggcaggtgacacctgagctgagacccgaaggagttgagc--------aagggagacacggagattccca i equCab2.chr12 C 0 I 7 s loxAfr3.scaffold_159 79485 117 + 1045236 -tcagcagggagtggggggggg-gtgcccggggtg----------------------------ggggctagaggaggcct-------caga-ggacaggtgacacct------gggtcagaaacccaaggggacag-gagactggaggtctccggaaagagg i loxAfr3.scaffold_159 C 0 C 0 s dasNov2.scaffold_107233 4445 155 - 8172 CTCAGCAGGGAGTTGGCGGGG----GCCTGCAGTGGGGATGGAGCCTCAATTTTGGGTTGTGTGGGGCCAG-GAAGGCCTGAGCATGCAGG-GGACAGTTGAGATTTGA-TGAGGACAGGAAGGACATGGGGGGAGTGCGACCCCAGATCTGCAGATCTAGG i dasNov2.scaffold_107233 I 88 I 1456 e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e cavPor3.scaffold_42 9658831 2089 + 15951348 I e canFam2.chr18 7531516 1585 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=14884.000000 s hg19.chr11_gl000202_random 4423 30 + 40103 ggtccagaca-caatcacggcatgagctgag s panTro2.chr11 68191593 30 + 134204764 ggtccagaca-caatcacggcatgagctaag i panTro2.chr11 C 0 C 0 s rheMac2.chr14 128149436 30 - 133002572 ggtccagacg-caatcatgacatgagctaag i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48969276 29 + 51998940 ggtctggacagtggtca--gcttgtgcaaag i bosTau4.chr29 I 7 C 0 s equCab2.chr12 28929780 30 + 33091231 ggtccagacagtggtcac-acatgtgcaaag i equCab2.chr12 I 7 C 0 s loxAfr3.scaffold_159 79602 30 + 1045236 aggccagtgagtggtcatagc-tgtgcaaag i loxAfr3.scaffold_159 C 0 C 0 e dasNov2.scaffold_107233 4600 1456 - 8172 I e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e cavPor3.scaffold_42 9658831 2089 + 15951348 I e gorGor1.Supercontig_0069572 1643 33 + 2579 I e canFam2.chr18 7531516 1585 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=77180.000000 s hg19.chr11_gl000202_random 4453 65 + 40103 gccctgggacaggag-----ctggtgtgtgcagagaatggcaaggaggccagagggacagaaggtgaggg s gorGor1.Supercontig_0228258 3563 65 - 5482 GCCCTGGCACAGGAG-----CTGGTGTGTGCAGAGAATGGCAAGGAGGCCAGAGGGACAGAAGGTGAGGG i gorGor1.Supercontig_0228258 I 21 C 0 s panTro2.chr11 68191623 65 + 134204764 gccctgggacaggag-----ctggtgtgtgcagagaatggcaaggaggccagagggacagaaggtgaggg i panTro2.chr11 C 0 C 0 s rheMac2.chr14 128149466 65 - 133002572 gccctggggcaggag-----cgggtgtgtgcagagaatggcaaggaggccagagggacagaaggtgaggg i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48969305 57 + 51998940 gctctggggcaggag----acctgtatattcagagaatggccggagggct---------ggaggtcaggg i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28929810 57 + 33091231 gccctggggcaggag----cctggtgtgttcagagactggccagagggct---------ggaggcgaggg i equCab2.chr12 C 0 C 0 s loxAfr3.scaffold_159 79632 68 + 1045236 gccctgaggcaggagcaggcctggtgtatgcagagaatggcaggaagcc--gaggggctggaggaggggg i loxAfr3.scaffold_159 C 0 I 1407 e dasNov2.scaffold_107233 4600 1456 - 8172 I e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e cavPor3.scaffold_42 9658831 2089 + 15951348 I e canFam2.chr18 7531516 1585 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=72033.000000 s hg19.chr11_gl000202_random 4518 126 + 40103 atcagtacca-ggtccagagaggaggtggaaggggcaggtaactggtcatggtatgtct-----tt-ggctgtgaagccagtgggatggagcctgggggattctgagcccaag-aaaaacaggatgggtttatg s gorGor1.Supercontig_0228258 3628 128 - 5482 ATCAGTACCAGGGTCCAGAGAGGAGGTGGAAGGAGCAGGTAACTGGTCACGGTATGTCT-----TT-GGCTGTGAAGCCAGTGGGNTGGAGCCTGGGGGATTCTGAGCCCAAGAAAAAACAGGATGGGTTTATG i gorGor1.Supercontig_0228258 C 0 C 0 s panTro2.chr11 68191688 127 + 134204764 atcagtacca-ggtccagagaggaggtggaaggggcaggtaactggtcatggtatgtct-----tttggctgtgaagccagtgggatggaacctgggggattctgagcccaag-aaaaacaggatgtgtttatg i panTro2.chr11 C 0 C 0 s rheMac2.chr14 128149531 118 - 133002572 atcagtacca-ggtccagagaggaggtggaaggg--------caggtcatggtatgtct-----tt-ggctgtgaagccagtgggacggagcctgggggactctgagcagaag-aacaacaggatgggtttatg i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48969362 113 + 51998940 gtcaatgagaaggtcagaagaggagatcagagag----gtaaagggccagcatatagacttgcttt-gactctg-----agtgagaaggggcctggaggattttgagcccagg---agagataata-------- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28929867 112 + 33091231 atcagagagggg---aggagaggagatcaaggat----gtaaagggccagcatgtggac-----cc-ggctttg-----agggcgacggagcctgagggattaggagcccagg---agagaggatg-gtctatg i equCab2.chr12 C 0 I 1289 e dasNov2.scaffold_107233 4600 1456 - 8172 I e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9658831 2089 + 15951348 I e canFam2.chr18 7531516 1585 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=32013.000000 s hg19.chr11_gl000202_random 4644 90 + 40103 ggctaggcatcttgctttttttttttttcacacaggtgacaacattctgtcacccaagttggagtgcagtggaggaatcccagctcactg s gorGor1.Supercontig_0228258 3756 87 - 5482 GGCTTGGCATCTTGCtttttttttt---cacacaggtgacaacattctgtcacccaagttggagtgcagtggagcaatcccgcctcactg i gorGor1.Supercontig_0228258 C 0 C 0 s panTro2.chr11 68191815 87 + 134204764 ggctcagcatcttgctttttttttt---cacacaggtgacaacattctgtcacccaagttggagtgcagtggagcaatcccggcccactg i panTro2.chr11 C 0 C 0 s rheMac2.chr14 128149649 83 - 133002572 ggctcagcaccttgcttttttttga-------catgggatgtcattctttcaccaaatttggaatgcagtggagcaatcccagctcactg i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48969475 35 + 51998940 -----gtctacttgctttt--------------------------------------------------tgaaagaccccctggccactg i bosTau4.chr29 C 0 I 7 e dasNov2.scaffold_107233 4600 1456 - 8172 I e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9658831 2089 + 15951348 I e equCab2.chr12 28929979 1289 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=57591.000000 s hg19.chr11_gl000202_random 4734 108 + 40103 caacctccacctcccaggctaagccttcctcccacctcagcctcctgagtggctgagaccacaggtgcacaccaccatgcccagctaatttttttgcactttttgtaa s rheMac2.chr14 128149732 107 - 133002572 caacctccacctcccaggctaagccatcctcccacctcagcctcctgagcagctgagaccacaggtgcacaccaccatgcccagctaa-ctttttgtactttttgtaa i rheMac2.chr14 C 0 C 0 s panTro2.chr11 68191902 108 + 134204764 caacctccacctcccaggctaagccatcctcccacctcagcctcctgagtggctgagaccacaggtgcacatcaccatgcccagctaatttttttgtactttttgtaa i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 3843 108 - 5482 caacctccacctcccaggctaagccatcctcccacctcagcctcctgagtggctgagaccacaggtgcgcaccaccatgcccagctaatttttttgtactttttgtaa i gorGor1.Supercontig_0228258 C 0 C 0 e dasNov2.scaffold_107233 4600 1456 - 8172 I e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9658831 2089 + 15951348 I e equCab2.chr12 28929979 1289 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969510 7 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125985141 1034 - 132107971 I a score=129852.000000 s hg19.chr11_gl000202_random 4842 152 + 40103 agaggg-tttttgccatgttgcccaggttggtttcaaactcctgagctcagatgattcacccacctcggcctcccaaactgctgggattacaggtgtgagccaccacgccgtgcctagcatcttgcttgagagatgaattcaccgctgggtag s gorGor1.Supercontig_0228258 3951 153 - 5482 agacgggtttttgccatgttgcccaggttggtttcaaactcctgagctcagatgattcacccacctcggcctcccaaactgctgggattacaggtgtgagccaccacgccGTGCCTAGCATCTTGCTTGAGAGATGAATTCACCGCTGGGTAG i gorGor1.Supercontig_0228258 C 0 C 0 s panTro2.chr11 68192010 153 + 134204764 agaggggtttttgccatgttgcccaggttggtttcaaactcctgagctcagatgattcacccacctcggcctcccaaactgctgggattacaggtgtgagccaccacgccgtgcctagcatcttgcttgagagatgaattcaccgctgggtag i panTro2.chr11 C 0 C 0 s rheMac2.chr14 128149839 153 - 133002572 agacgggtttttgccatgttgcccaggctggtctcaaactcctgagctcagatgattcacccacctcggcctcccaaagtgctgagattacaggtgtgagccaccgtgccgtgcctagcaccttgcttgagagatgaattcactgctaggtag i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125986175 147 - 132107971 -----ggtttttaccgtgttgcccagggtggtgtcagactcgtgagctcagatgattcacccacctcggcctcccaaagtgctgggattacaggtgtgagccaccacgccGTGCCTAGCATCTTGCTTGag-gatgaattcaccgctgggtag i ponAbe2.chr11 I 1034 C 0 e dasNov2.scaffold_107233 4600 1456 - 8172 I e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9658831 2089 + 15951348 I e equCab2.chr12 28929979 1289 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969510 7 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=357114.000000 s hg19.chr11_gl000202_random 4994 365 + 40103 agtagactgaaggggcgggccagaagcagaggaagcaggcaggaggcccctgcagccactcgggccacagttgg-agctcagagactagaggcagcaaagaaggaggtggggcccagcggctgcacactgggcctccatggaggccagagc-aggttggcggatggacgtccatgctggggctgcaacccagagggga-CACAGCGtcgagcctgcatgggggaccaggcaccattctatgcatttcacatgtcctagact--cagaatcctttctaccaagaaggtactcttacca-cactttcagggtggggaaactgaggcagggagcggccacagagcttCAACTTTAGGTTGGGCCCAGCATTCAT s panTro2.chr11 68192163 365 + 134204764 agtagactgaaggggcgggccagaagtagaggaagcaggcaggaggcccttgcagccactcgggccacagttgg-agctcagagactagaggcagcaaagaaggaggtggggcccagcggctgcacactgggcctccatggaggccagagc-aggttggcggatggacgtccatgctggggctgcaacccagagggga-CACAGCATCAAGCCTGCATGGGGGAccaggcacctttctatgcatttcacatgtcctagact--cagaatcctttctaccaagaaggtactcttaccc-cactttcagggtggggaaactgaggcagggagcggccacagagcttCAACTTTAGGTTGGGCCCAGCATTCAT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 4104 365 - 5482 AGNAGACTGAAGGGGCGGGCCAGAAGCAGAGGAAGCAGGCAGGAGGCCCTTGCAGCCACTCGGGCCACAGTTGG-AGCTCAGAGACTAGAGGCAGCAAAGAAGGAGGTGGGGCCCAGCGGCTGCACACTGGGTCTCCATGGAGGCCGGAGC-AGGTTGGCGGATGGACGTCCATGCTGGGGCTGCAACCCAGAAGGGA-CACAGCATCGAGCCTGCATGGGGGAccaggcaccattctatgcatttcacatgtcctagact--cagaatcctttctaccaagaaggtactcttaccc-cactttcagggtggggaaactgaggcagggagcggCCACAGAGCTTCAACTTTAGGTTGGGCCCAGCATTCAT i gorGor1.Supercontig_0228258 C 0 C 0 s ponAbe2.chr11 125986322 365 - 132107971 agtagactgaaggggcggggcaggagcaggggaagcaggcaggaggcccttgcagccactcgggccacagttgg-agctcagagactagaggcagcaaagaaggaggtgggacccagcggctgcacactgggcctccgcggaggctggagc-aggttggcggatggaggtccatgctggggctgcgacccagagggga-CACAGCCtcgagcccgcatgggggaccaggcaccgttctacgcatttcacatgtccttgact--cagaatcctttctgccaagaaggtactcttaccc-cactttcagggtggggaaactgagtcagggagcggccacagagcttCAACTTTAGGTTGGGCTCGGCATTCCT i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128149992 366 - 133002572 agtagactgaaggggcggggcagaagcagagtgaacaggcaggaggcccttgcagcccctcgggccacagtggg-agctcagaggctagaggcagcaaagaaggaggtggtgcccagcggctgaacactgggcctccatggaggctggagc-aggttggcggatggaCGTCCACACTGGGGCTGCAACCCAG-GGGGA-CACAGCattgagcctacacggaggaccaggcaccattctacacatttcacatgtccttgactcacagaatcctttctgccaagaagctactcttaccc-cactttcagggtgggaaaactgaggcagggagaggccacagagcttcaactccaggtTGGGCCCCGCATTTCT i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48969517 324 + 51998940 agcagatgagaagggctggacagaagtagggagagcaggtaggaggctcttgca-ccatctgagcaagagcgggcggcagggagaccaatgatagcagacaggttgccggg----aggggctgcaggctgggtctttgcgggggacggagcaaggtttgccagtggatgtgcctggcgggg-tgagacaggaaggggagCACAGCCCCGAGCCCTCGCAGGG-------------------CTCATCACATACCCTTGACTCCCGAGATCCTCTCTGCCACGGAGGTGCGGTCGTCCGCACTTTCAGGATGGAGGAGCTGAGACACAGGGTACCCACAGAGTCACGACT---------------------- i bosTau4.chr29 I 7 I 1185 e dasNov2.scaffold_107233 4600 1456 - 8172 I e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9658831 2089 + 15951348 I e equCab2.chr12 28929979 1289 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=391996.000000 s hg19.chr11_gl000202_random 5359 412 + 40103 GCCCCTCAGGGCTCCTGTCCCTGACAAGGAGCTCCTG---------GGAG-GTAGTTTTCCTTTAAAACACtgctgagcacataccgtatg-tggggcactggggtgtgtctcatacagaccttttcttgtttcaccttcatccccactctgtgaTCTGCAGGGCCGCTCAGTAAGCC----CAGAGGCGG-------ACACCAAAACATG--------------AGAAGTATTAAAAAATGTTGTTTTTTAAAAAATTCATAAAACACACAAACACC--AATGTAGCCGGAACTGACATTATCATGTAACAATATTTTTATCATGAATTTTGTATGGGAGG-TATAGtgggttcaacta--------catcccccaaaagatacatccacctcttaacccctggaacctcagaagctggctttgtttggaatcaggatcttgcagatgtaatgaaggt s panTro2.chr11 68192528 412 + 134204764 GCCCCTCAGGGCTCCTGTCCCTGACAAGGAGCTCCTG---------GGAG-GTAGTTTTCCTTTAAAACACtgctgagcacataccgtatg-tggggcactggggtgtgtctcatacggaccttttctcgtttcaccttcatccccactctgtgaTCTGCAGGGCCGCTCAGTAAGCC----CAGAGGGGG-------ACACCAAAACATG--------------AGAAGTATTAAAAAATGTTGTTTTTTAAAAAATTCATAAAACACACAAACACC--AATGTAGCCGGAACTGACATTATCATGTAACAATATTTTTATCATGAATTTTGTATGGGAGG-TATAGtgggttcaacta--------catcccccaaaagatacatccacctcttaacccctggaacctcagaagctggctttgtttggaatcaggatcttgcagatgtaatgaaggt i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 4469 412 - 5482 GCCCCTCAGGGCTCCTGTCCCTGACAAGGAGCTCCTG---------GGAG-GTAGTTTTCCTTTAAAACACTGCTGAGCACATACCGTATG-TGGGGCACTGGGGTGTGTCTCATACAGACCTTTTCTCGTTTCACCTTCATCCCCACTCTGTGATCTGCAGGGCCGCTCAGTAAGCC----CAGAGGGGG-------ACACCAAAACATG--------------AGAAGTATTAAAAAATGTTGTTTTTTAAAAAATTCATAAAACACACAAACACC--AGTGTAGCCGGAACTGACATTATCATGTAACAATATTTTTATCATGAATTTTGTATGGGAGG-TATAGtgggttcaactg--------catcccccaaaagatacatccacctcttaacccctggaacctcagaagctggctttgtttggaatcaggatcttgcagatgtaatgaaggt i gorGor1.Supercontig_0228258 C 0 C 0 s ponAbe2.chr11 125986687 416 - 132107971 GCCCCTCAGGGCTCCTGCCCCTGACAAGGAGCTCCTG---------GGAG-GTAGTTTTCCTTTAAAACACtgctgagcacataccgtatgttggggcactggggtgtgtctcatacagacgttttctcgtttcatcttcatccccactctgtgaTCTGCAGGGCTGCTCAGTCGGCC----CAGAGGCGG-------ACACCAAAACATG-----------AGAAGAAGTATTAAAAAATGTTGTTTTTTAAAAAATTCATAAAACACACAAACACC--AATGTAGCCGGAACTGACATTATCATGTAACAATATTTTTATCATGACTTTTGCATGGGAGG-TATAGtgggttcaactg--------catcccccaaaagatacatccacctcttaacccctggaacctcagaagctggctttgtttggaatcaggatcttgcagatgtaatgaaggt i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128150358 413 - 133002572 GCCCCTCAGGACTCCTGTCCCTGACAAGGAGCTCCTGGCTGGGGGCGGGG-GTAGTTTTCCTTTAAAACACTTCTAAGCACATACCGTATG-TGGGGCACCGTGGTGTGTCTCATACAGACCGTTTCTCGTTTCACCTTCATCCCCACTTGGTGACCTGCAGGGCCACTCAGTAGGCC----CAGAGGGGG-------ACACCAAAACATT-----------TGAAGAAGTATTTTAAAAAGTTGCTTTTTAAAAAATGCATAAAACACACAAACACC--AATGTAGCTGGAACTGAC---GTCATGTAACAATATTTTTATCATGAATTTTGTATGTG-GG-TATAGtgggttcaactg--------tatccacc-------ccatccacctcttaacccctggaacctcagaagctggctttgtttggaatcaggatgttgcaggtgtaatgaaggt i rheMac2.chr14 C 0 C 0 s equCab2.chr12 28931268 429 + 33091231 GCCCCTCATTGCTCCAGTCCCTGACAATGACCTCCTG---------GGGGTGTTCGTCCCTTTTAAAACCTTATTGATCACTTACCGCGTGCTGGGTCCGCACGGCTTGGCTCACA---GCCTTCCCTCGGTG-----------ACAGCAAGTGTGGAGCGAGGGGGTTCAACCCGCCGTGTCTGCGAGGGAATGGACACAACGAAAAATGGAAAAATGAGAAGAGAAAGTATTGAAAAGGATT--TTTTAAAAATACACGTAACACACACAGAGACTCAAACGTTTCTGGACCTGATTTTATCCTGTAATGTTATTCTTATCCCGGATTTCGTAGGAGGGGTTATAGTGGGGtgagttgaatcctttcgtcccccacaagatgtgtccacgtcttaacctccgggat----gaatgtgac-ttatttcaacaaagggttttgcagacgtaactaaggt i equCab2.chr12 I 1289 C 0 e dasNov2.scaffold_107233 4600 1456 - 8172 I e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9658831 2089 + 15951348 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=406708.000000 s hg19.chr11_gl000202_random 5771 388 + 40103 gaggatccctagctgagattcgtctggattagggt-ggccctaaatgcaatgatgtgtgtccttataggcgaacaggagaaga-------------gacacagag------acagggcacaggagaaggcagaggctggagcatctcagccac-ggccaagaaacgtctgtagcc-ccaggagctggaagaggcaggaatgtccctccc---ctagaacccttggatggagcgtggccctgccgacaccgtgatctcagacttctggctcccaggctacaagggaat--ggatttc---tgttctaagccaccaagcacgtggtcattcgtta-------cacatcacgggaaactcatacGGGGGGTGTGCACCCAGCAATTTGAGTCTGTGAAGTCTTAAC-CCAGCTCTGGGTGAGGTGAATA s rheMac2.chr14 128150771 388 - 133002572 gaggatcctgagctgagattaatctggattagggt-ggccctaaaggcaatgaagtgtgtctttataggcggacaggagaaga-------------gacgcagag------accgggcacaggagaaggcagaggttggagcattgcagccac-agtctaggagtgcccagagcc-ccaggatctggaagaggcaggaaggtccccccc---ctagaacccttcgagggagcgtggccctgctgacaccgtgatctcagacttctggctcccgggctgcaagagaat--ggatttc---tgttctaagccaccaagcgtgtggtcattcatta-------cacaccatgggaaactcacacCGGGGGTGTGCACCCAGCAATTTGAGtcagtgaagtcttaac-ccagctctgggtgaggtgaata i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125987103 388 - 132107971 gaggatcctgagctgagatttgtctggattagggt-ggccctaaatgcaatgatgtgtgtccttataggcgaacaggagaaga-------------gacacagag------acagggcacaggagaaggcagaggctggagcatcgtagccac-agccaaggaacgtctgcagcc-ccaggagctggaagaggcaggaatgtccctccc---ctagaacccttggatggagcgtggccctgccaacaccgtgatctcagacttctggctcccaggctgcaagagaat--ggatttc---tgttctaagccaccaagcacgtggtcattcgtta-------cacatcacgggaaactcacacGGTGGGTGTGCACCCAGCAGTTTGAGTCTGTGAAGTCTTAAC-CCAGCTCTGGGTGAGGTGAATA i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 4881 388 - 5482 gaggatcccaagctgagattcgtctggattagggt-ggccctaaatgcaatgatgcgtgtccttataggcgaataggagaaga-------------gacacagag------acagggcacaggagaaggcagaggctggagcatctcagccac-agccaagaaacntctgtagcc-ccaggagctggaagaggcaggaatgtccctccc---ctagaacccttggatggagcgtggccctgccgacaccgtgatctcagacttctggctcccaggctacaagggaat--ggatttc---tgttctaagccaccaagcacgtggtcattcgtta-------cacatcacgggaaactcacacGGAGGGTGTGCACCCAGCAATTTGAGTCTGTGAAGTCTTAAC-CCAGCTCTGGGTGAGGTGAATA i gorGor1.Supercontig_0228258 C 0 C 0 s panTro2.chr11 68192940 388 + 134204764 gaggatcccgagctgagattcttctggattagggt-ggccctaaatgcaatgacgtgtgtccttataggcgaacaggagaaga-------------gacacagag------acagggcacaggagaaggcagaggctggagcatctcagccac-ggccaagaaacgtctgtagcc-ccaggagctggaagagacaggaatgtccctccc---ctagaacccttggatggagcgtggccctgccgacaccgtgatctcagacttctggctcccaggctacaagggaat--ggatttc---tgttctaagccaccaagcacgtggtcattcgtta-------cacatcacgggaaactcacacGGGGGGTGTGCACCCAGCAATTTGAGTCTGTGAAGTCTTAAC-CCAGCTCTGGGTGAGGTGAATA i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9660920 375 + 15951348 GAGGATCTTTACCCGAGTAGAACATGGATT-----------TAACCCGAATGATCCGCATCCGTTTAG--AGATGAGAAAGCA-------------GGAGCAGAG--------------TTGGAGAAGGCTGAGGTCCAAATGAAACAGTCAT-AGCC-AGGGATACCTGCCTGC-TCCCCAGCTGCAGGAGGCAGGAAGATCCACCCCTATCTTGAGCCCGCTGG-GGACCACATCCCTGCGGACAGCTTAAGTTAGGACCACTGGCCTGCAGATTGTGAGCAACTCAGCACTGT---CCTTCTGCGACA-TGAGCGTGTGGTCATG-ATTACAGCAGTCACAGGATAAGACACTCACACAAGGGCTATGGGCTTCACACTTCAGGTCCTTGAAGTCCTGAC-CTGGTTCCAGGCAGGGAAGTC- i cavPor3.scaffold_42 I 2089 C 0 s equCab2.chr12 28931697 392 + 33091231 aaggctctcgagatgagagcatcctggattcgggtgggcccgagacccagtgatgggtgtcctcatagg-agacaggaaaagagaagatgtacacggacacagaggagggggccgggcgaagatggaggcagagatgggagggacgcggccacaagcccggggacgcctggagccaccagaagctgaaagaggcaggaaggaccctccc---ctggagcctcgggaggcagcgccgccct-ttgacaccttgacttcagacttctggcctccagacc-caggagagg--ataattccaatgcttctaaccaggccgtatgtggtcactggttctggcag-cac----caggaCGCTCCCACGGGGCTCATGCGCC-----------GTC------ATCTCCACTTCGGGTCTGGAGCGGGTG---- i equCab2.chr12 C 0 C 0 e dasNov2.scaffold_107233 4600 1456 - 8172 I e oryCun2.chrUn0985 19367 1342 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=96438.000000 s hg19.chr11_gl000202_random 6159 112 + 40103 TGttt-tacaggtgcaggaaacc--gaggtctatagaaaaccagcaccttgcaagcgccaccatgctggt-----cagctctgatg------tggccaagg------ctggtgccagggtGAGGCGAGGGTG s equCab2.chr12 28932089 49 + 33091231 GGTCT-TACAGGTGAGGG--ATT--GAGGTCTGCAGAG----TGGATCTTGCA-GGGCT------------------------------------------------------------------------- i equCab2.chr12 C 0 C 0 s oryCun2.chrUn0985 20709 130 + 42081 TGCTT-TGCA-GGGGGGGGGACTCGGAGGGCAGCCGACACGCAGCTCCTGGCAGGGGCCGCGGGGCCGGTGAGCCCAGCTCTGCTGACCGGATGCGCACGAGATGTCCCGGTGCCAGGCTAATGCAGAGGCC i oryCun2.chrUn0985 I 1342 C 0 s cavPor3.scaffold_42 9661295 114 + 15951348 TGCTTCTCCA-ATGAGGGAGACT--GAGGCCTGCAAAAGGCCCGTACCTTTCA-GGGCTACCTGGTCAG------CAGCTTTGGTG-TTGCCTGGACAGAACGGACACTGGTG-------AGGGTAGAGGCC i cavPor3.scaffold_42 C 0 C 0 s panTro2.chr11 68193328 112 + 134204764 TGttt-tacaggtgcaggaaacc--gaggtctatagaaaaccagcaccttgcaagcgccaccatgctggt-----cagctctgaTG------TGGCCAAGG------CTGGTGCCAGGGTGAGGCGAGGGTG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 5269 112 - 5482 TGTTT-TACATGTGCAGGAAACC--GAGGTCTATAGAAAACCAGCACCTTGCAAGCGCCACCATGCTGGT-----CAGCTCTGATG------TGGCCAGGG------CTGATGCCAGGGTGAGGCGAGGGTG i gorGor1.Supercontig_0228258 C 0 C 0 s ponAbe2.chr11 125987491 112 - 132107971 cgttt-tacaggtgcaggaaacc--gaggtctatagaaaaccagcaccttgcaagggccaccatgctggt-----cagctctgatg------tggccaggg------ctggtgccagggtGAGGCGAGGATG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128151159 112 - 133002572 cgttt-tacaggtgcaggaaacc--gaggtctatagaaaaccagcaccttgtaagggccaccatgctggt-----cagctctgatg------tggccaggg------ctggtgcccgggtGAGGCGAGGGTG i rheMac2.chr14 C 0 C 0 e dasNov2.scaffold_107233 4600 1456 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=95980.000000 s hg19.chr11_gl000202_random 6271 101 + 40103 ACCTGGACTTTGGAATCCCTCAGccc----tgggcaggtc--------------tcttcatctccccag--------------gtggccactt---aatcatctgaaaaatagggC---TAGCCC-CGGA---GACGGTGGGG s rheMac2.chr14 128151271 101 - 133002572 ACCTGAACTTTGGAATCCCTCAGccc----tgggcaggtc--------------ccttcatctccccaa--------------gtgaccactt---cttcatctgaaaaatagggt---taGCCC-CAGA---GACAGTGGGG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125987603 101 - 132107971 ACCTGGACTTTGGAATCCCTCAGccc----ttggcaggtc--------------tcttcatgtccccag--------------gtggccactt---attcatctgaaaaatagggC---TAGCCC-TAGA---GACGGTGGGG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0228258 5381 101 - 5482 ACCTGGACTTTGGAATCCCTCAGccc----tgggcaggtc--------------tcttcatctccccag--------------gtggccactt---attcatctgaaaaatagggC---TAGCCC-CGGA---GACGGTGGGG i gorGor1.Supercontig_0228258 C 0 n 0 s panTro2.chr11 68193440 101 + 134204764 ACCTGGACTTTGGAATCCCTCAGccc----tgggcaggtc--------------tcttcatctccccag--------------gtggccactt---attcatctgaaaaatagggC---TAGCCC-CGGA---GACGGTGGGG i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9661409 137 + 15951348 ACCTGGGTATC-GGGACCCCCAGCCT----CGTGGGTCCCAGGTTTGCCCCCTATCCTGGGCGACCCAGGAATTTTCCCTTAAATTGCCCCTCTAGCATCCCCCTCTTCATCCAACACACAGGAC-TGGGCTGGACGAGGAAG i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 20839 90 + 42081 ACCTGGCCTTCAGAGCCCCCCAGCCC----TGGGCGGCTC---------------CCTCAACGTCCCGG--------------AGTGCCCCTC---CGTTCCCTGGGAAACCGGAC---CAGCAC-TGGA------------- i oryCun2.chrUn0985 C 0 I 183 s dasNov2.scaffold_107233 6056 102 - 8172 ACCTGGGC---AGGGACCCCCAGCCCCTCACGGGCAGGTC---------------GCTCGTCAACCTGG--------------GCAGCCGCGC---CCTCCTCTGAAATCCACAGC---CACCCCATGGA---GGAGGCAGGA i dasNov2.scaffold_107233 I 1456 C 0 e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e equCab2.chr12 28932138 0 + 33091231 C e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=36835.000000 s hg19.chr11_gl000202_random 6372 100 + 40103 AAGTTGCAAGGAAGGAATCATGGCTGCGCCCCCGCTGGGGGCTGG---CCCAAAATTAGTGCTCCAGAGCACTCATAGTCCACCCTGaataatgatgctaact s rheMac2.chr14 128151372 100 - 133002572 AAGTTACAGGGAAGGAATCGTGGCTGCGCCCCCGCGGGAGGCTGG---CCCAAAATTAGTGCTCCAAGGTACTCATGCCCCACCCTGaataacagtactagtt i rheMac2.chr14 C 0 I 1 s ponAbe2.chr11 125987704 100 - 132107971 AAGTTGCAAGGAAGGAATCACGGCTGTGCCCCTGTCGGGGGCTTG---CCCAAAATTAGTGCTCCAGAGCACTCATGGCCCACCCTGagtaacagtgctaatt i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68193541 100 + 134204764 AAGTTGCAAAGAAGGAATCATGGCTGCGCCCCCGCTGGGGGCTGG---CCCAAAATTAGTGCTCCAGAGCACTCATAGTCCACCCTGaataatggtgctaact i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9661546 42 + 15951348 GGGCTGCAA----------ATGGC-------------------------------------------------CATGGCCACCCC--AGTGATGCTGCTAATT i cavPor3.scaffold_42 C 0 I 1 s dasNov2.scaffold_107233 6158 46 - 8172 -------------------------------------GGGTCTGGGAAGCCCCGGCTGGTGCTCAAAGGTGCTCA--------------------TGCTAATT i dasNov2.scaffold_107233 C 0 I 1 e oryCun2.chrUn0985 20929 183 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e equCab2.chr12 28932138 0 + 33091231 C e gorGor1.Supercontig_0228258 5482 0 - 5482 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=38447.000000 s hg19.chr11_gl000202_random 6472 35 + 40103 gtaagcacttac--tgtgca-----------------cggggccaagcccctga s oryCun2.chrUn0985 21112 54 + 42081 GTGAGCACCGACTGTGTGCACGGCACCACGTGCGCCCCAGGGCCAGGCTGCCGA i oryCun2.chrUn0985 I 183 I 132 s cavPor3.scaffold_42 9661589 37 + 15951348 ATAGCTGCTTACTATGTGCA-----------------CAGGGCCGAGATCTTCA i cavPor3.scaffold_42 I 1 C 0 s panTro2.chr11 68193641 35 + 134204764 gtaagcacttac--tgtgca-----------------cggggccaagcccctga i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125987804 35 - 132107971 gtaagcacttac--tgtgca-----------------cggggccaagcccctga i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128151473 35 - 133002572 gtgaggacttac--tgtgca-----------------cagggccaagcccctga i rheMac2.chr14 I 1 C 0 s equCab2.chr12 28932138 23 + 33091231 --------------TGCAca-----------------cggtgccgagcccccga i equCab2.chr12 C 0 C 0 s dasNov2.scaffold_107233 6205 37 - 8172 GGgggcacctactgcatgca-----------------cagttccaaaccctcga i dasNov2.scaffold_107233 I 1 C 0 e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e gorGor1.Supercontig_0228258 5482 0 - 5482 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=40392.000000 s hg19.chr11_gl000202_random 6507 117 + 40103 cctgcagtggcacaggtaagtgtcacaaaaaGTGGACACACGTGCTGTTGGACGCCAGCTCCTCTCTGGGTCACCATGAGAGATTCCTGAACCTCAGCTCCCTTGTCAGCGCCCTTC s rheMac2.chr14 128151508 117 - 133002572 cctgcagggacacaggtaattgttacaaaaaATGGACACGCCTGCTGTTGGACGCCAGCTCCTCTCTGGGTCACCATGAGAGGTTCCTGAGCCTCAGCTCCCTTGTCAGCGCCCTAC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125987839 117 - 132107971 cctgcagtggcacaggtaattgtcacaaaaaGTGGACACGCGTGCTGTTGGATGCCAGCTCCTCTCTGGGTCACCACGAGAGATTCCTGAACCTCAGCTCCCTTGTCAGCGCCCTTC i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68193676 117 + 134204764 cctgcagtggcacaggtaattgtcacaaaaaGTGGACACGCGTGCTGTTGGACGCCAGCTCCTCTCTGGGTCACCATGAGAGATTCCTGAACCTCAGCTCCCTTGTCAGCGCCCTTC i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9661626 33 + 15951348 CCTGTGG-GGCTTAGGTAACTGTCACAAAA---------------------------------------------------------------------------------CCCC-- i cavPor3.scaffold_42 C 0 C 0 s equCab2.chr12 28932161 34 + 33091231 cccacagtgactcaggtagttgccacaaag---------------------------------------------------------------------------------cccc-- i equCab2.chr12 C 0 C 0 s dasNov2.scaffold_107233 6242 34 - 8172 cctggagtaatgca-gtaatggc----------------------------gcggcagcccct------------------------------------------------------ i dasNov2.scaffold_107233 C 0 C 0 e oryCun2.chrUn0985 21166 132 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e gorGor1.Supercontig_0228258 5482 0 - 5482 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=61978.000000 s hg19.chr11_gl000202_random 6624 121 + 40103 CAGGAGGgagggaggtagcagcactacccccatctaacagaggaggaaactgaggcacgagagatgaagacactgcccacgt-----cacgctgctggtcagtgacagagtg-----ggaC-CGGGTGCAGT s rheMac2.chr14 128151625 109 - 133002572 CAGGAgggagggagaaggcagcgctacccccatctaacagaggaggaaactgaggcacgagaaatgaagacactgccca-----------------ggtcagtgacacagtg-----ggac-caggtgcagG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125987956 121 - 132107971 CAGGAGGgagggaggtggcagcactaccctcatctaacagaggaggaaactgaggcatgagagatgaagacactgcccactt-----cacgctgctggtcagtgacagagtg-----ggaC-CGGGTGCAGT i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68193793 121 + 134204764 CAGGAGGgagggaggtagcagcactacccccatctaacagaggaggaaactgaggcacgagagatgaagacactgcccacgt-----cacgctgctggtcggtgacagagtg-----ggaC-CGGGTGCAGT i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9661659 39 + 15951348 ----------------------------------------AAGGAGGGAGAGAGGTG--------------------------------------------GTGACAGAGCC-----AGAC-CTGGAGG--- i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 21298 96 + 42081 CAGGAGGAGGGG-------ATCGCCATCCTCATTTGACAGAGGGGGGAAGTGAGATGGGACAGA---------TGCCCG----------------TGGTCAGCGACAGAGCCCCCGGACTC-CAGGCAG--- i oryCun2.chrUn0985 I 132 C 0 s equCab2.chr12 28932195 98 + 33091231 -----gggaggcaggtactgtcactgccc-catctaac--agggggaaactgaggcacaggacaagaagac---------------------ttctggtcagggacagaggc-----ggactcaggggcagc i equCab2.chr12 C 0 C 0 s dasNov2.scaffold_107233 6276 113 - 8172 ------ggaggcaggtacagcccacaccctcatttagcggaggaggaaaccgaggcacGTGTGACGAAGGCCTGGCTCGCGTCGCCACGCGCTCACGTGCGGT--CAGGCTT-----GGGT-CCGGT----- i dasNov2.scaffold_107233 C 0 C 0 e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e gorGor1.Supercontig_0228258 5482 0 - 5482 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=483267.000000 s hg19.chr11_gl000202_random 6745 435 + 40103 TGTCCA-GCAGT-GCACCTAGATGGGGGAGAGGAGCTTGGTGAATATTAAAAGAGGTTTTGTCTGGGAACAGAGAGGCGGCT-GCTGGGTGACCCCAGCCTCC----------CA-------TCCAAAGGCGGGCTGTGGG-GTGA-CTGGCTGGACCTCCTCC--AGACCCTCCCATCACACGTGTGCTCAGCCGGCTCAGCCAGCAGCAGGCGC--CCACCCACCACGGGCCCCTT-CTCTGAGCCAGCGTGCACAGCTTCCTGGAAGGGACACGGAGCGCACAGATGTGCACAGC-AGGTGGC----CTGTTCTGCTCTCCCTCCAGCCAGACAGGGCCGGGACCCA-GGACTGGCAG--GAAGACCTGGCCAGCCATGGCTGTGAACACTGAGGAAACACTTCCCGGAGCAGCCAGGGCC---------CTGGGAGCT---------------GGAGTC-GATCCCCACATCTGGGCTCCTC----------CTGGAGCCA s rheMac2.chr14 128151734 435 - 133002572 TGTCCA-GCAGC-GCACCTAGATGGGGGAGAGGTGCTCGGTGAATATTAAAAGGGGTTTTGTCTGGGAAAATTGAGGCGGCT-GCTGCGTGACCCCAGCCTCC----------TC-------TCTGAAGGCGGGCTGTGGG-GTGA-CCGGCTGGCCCTCCTCC--AGGCCCTCCCCCCACACGTGTGCTCATCCAGCTCAGCCAGCAGCAGGCGC--CCACCCACCACGGGCCCCTT-CTCTGAGTCAGCGTGCACAGCTTCCTGGAAGGGACGTGGGGTGCACAGATGTGCACAGC-AGGTGGC----CTGTTCTGCTCTCCCTCCAGCCAGACAGGGCTGGGACCCA-GCACTGACAG--GACGGCCTGGCCAGCCATGGCTGTGACCACTGAGGAAACACTTCCCAGAGCAGGCAGGGCC---------CTGGGAGCT---------------GGAGTC-GATCCCCACATCTGGGCTCCTC----------CTGGGGCCA i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125988077 435 - 132107971 TGTCCA-GCAGT-GCACCTACATGGGGGAGAGGTGCTTGGTGAATATTAAAAGAGGTTTTGTCTGGGAACAGAGAGGCGGCT-GCGGGGTGACCCCAGCCTCC----------CC-------TCCGAAGGCGGGCTGTGGG-GTGA-CTGGCTGGACCTCCTCC--AGACCCTCCCACCACACGTGTGCTCAGCCAGCTCAGCCAGCAGCAGGCGC--CCACCCACCACGGGCCCCTT-CTCCGAGCCAGCGTGCACAGCTTCCTGGAAGGGACCCGGGGCGCACAGATGTGCACAGC-AGGTGGC----CTGTTCTGCTCTCCCTCCAGCCAGACAGGGCCGGGACCCA-GGACTGGCAG--GAGGGCCTGGCCAGCCATGGCTGTGAACACTGAGGAAATACTTCCCGGAGCAGCCAGGGCC---------CTGGGAGCT---------------GGAGTC-GATCCCCACATCTGGGCTCCTC----------CTGGGGCCA i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 1676 435 + 2579 TGTCCA-GCAGT-GCACCTAGATGGGGGAGAGGAGCTTGGTGAATATTAAAAGAGGTTTTGTCTGGGAACAGAGAGGCGGCT-GCTGGGTGACCCCAGCCTCC----------CC-------TCCAAAGGCGGGCTGTGGG-GTGA-CTGGCTGGACCTCCTCC--AGACCCTCCCACCACACGTGTGCTCAGCCGGCTCAGCCAGCAGCAGGCGC--CCACCCACCACGGGCCCCTT-CTCTGAGCCAGCGTGCACAGCTTCCTGGAAGGGACACGGGGCGCACAGATGTGCACAGC-AGGTGGC----CTGTTCTGCTCTCCCTCCAGCCAGACAGGGCCGGGACCCA-GGACTGGCAG--GAGGGCCTGGCCAGCCATGGCTGTGAACACTGAGGAAACACTTCCCGGAGCAGCCAGGGCC---------CTGGGAGCT---------------GGAGTC-GATCCCCACATCTGGGCTCCTC----------CTGGAGCTA i gorGor1.Supercontig_0069572 I 33 C 0 s panTro2.chr11 68193914 435 + 134204764 TGTCCA-GCAGT-GCACCTAGATGGGGGAGAGGAGCTTGGTGAATATTAAAAGAGGTTTTGTCTGGGAACAGAGAGGCGGCT-GCTGGGTGACCCCAGCCTCT----------CA-------TCCAAAGGCGGGCTGTGGG-GTGA-CTGGCTGGACCTCCTCC--AGACCCTCCCATCACACGTGTGCTCAGCCGGCTCAGCCAGCAGCAGGCGC--CCACCCACCATGGGCCCCTT-CTCTGAGCCAGCGTGCACAGCTTCCTGGAAGGGACACGGGGCGCACAGATGTGCACAGC-AGGTGGC----CTGTTCTGCTCTCCCTCCAGCCAGACAGGGCCGGGACCCA-GGACTGGCAG--GAGGGCCTGGCCAGCCATGGCTGTGAACACTGAGGAAACACTTCCCGGAGCAGCCAGGGCC---------CTGGGAGCT---------------GGAGTC-GATCCCCACATCTGGGCTCCTC----------CTGGAGCCA i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9661698 360 + 15951348 TGGCCATGCAGCAGAGGCTGCAC-GGGGCCAATCACTGGAC----ATGAAACGGGGTTTTGTGTGGGGGCAGA-ACCCGGCT-CTCAGGTGGCTCTGAGCCTC----------CA-------------------CTCTGGG-GTGA-CTGGATGGGCCTCCTCT----CACCCTCC--------TGAGACAGACCTA-GCAGCAGCAAGCAGGTGA--CCACACACCCATGTC-CCTC-CTCTG----GGC-CCTGGTACAGTCCCAAGTGGACAGGAGGCTCACAGATGTG-ACATC-AGGTGGC----CTGCTCTGC-CTCCCTCCA-GCAGGCGGCGCCAAGACCCA-GGGCTGGTGA-----------CCCAGGCCTGGC------CTC------AGTGCCACC-----AGGTCA--CTG---------CTAG--------------------AGGAGC-CAGCCCCACATCTGGGGTCTTC----------TTG------ i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 21394 399 + 42081 TGGCCA-GCAGC-GAGCTTGGGA-GGAGCGAGCTGTCCGGCCGGTGTCCAGCGGGGTTTTGTCTGGGAGCAGAGAGGTGGCT-GCTGGGTAAGCACGAGCCCC----------CAGGAAGGGCCCCACGGCAGGCTCTGGC-GTGA-C----AGCGGCTCCTCTGCAGCCCCTCCC--------TGCGCCCCAC--------------------GC--CCACCCACCAGGGGCGCCTT-CTCTGAGCTGGC-CGTGAAGCTGCC-----TGGCCAGGAGGACC-----TGTG-GCTTC-TGGGGGCCGCTCTGCCCCTC-CTCCCGCCAGGCAGGCGAGGCTGGGACAcgcgggcgggcgggggcggggcTCGCCTGCTGTGGC------CTCTGAGGGAATGCTCCCTGGAGCGGCCAAGCTG---------CGGGGGGCT---------------GGGGGC-GGGCCCCACATCTGGGCTCCTC----------CTGGAGCAG i oryCun2.chrUn0985 C 0 C 0 s equCab2.chr12 28932293 395 + 33091231 tgtccg-ggagc-gagcctggacagGGGAGAGACGTC--------------AGAGGGGATGCCTGGGAGCAGAGAG-------GTCGGGTGACCCCAAACCTCTTCCAGATGACC-------CCCAAAGGCAGGCTCTGGGAGTGAGCAGGGGGCCCCCCCTCC--AGGGCCTCCC--------CGTGACACCCCTG--CAGCAGGCAGCCAGCGC--CCACCCACCAGGGGCCCCTTGCTGCCGGCCAGCAGCTGCGGCTTCCAGGA-TGGGCCTGGGGCTC-------------TC-AGATGGC----CGCCTCCGCTCTGCCCCCAGCCCTGTGGGGCCTG--CCCA-------------------CCCACCTGCCGTGGATG----AAGGGAAGAAACACTTCCTGGAGCAGCCGGGGCC-------AGCTGGGAGCC---------------GGGGTCGGGGCCCCACACCTGGCCTCCTCGGGGTTAGGGTTAGGGTTA i equCab2.chr12 C 0 C 0 s dasNov2.scaffold_107233 6389 391 - 8172 TGTCCA-GGAGC-CAGCCTGGACAGGGGGGCAGGGGACCGGGGATGCGACATGGGATTCCGTCCCAGCACAGAGAGGCGGGTGGCCGGGGCACCCCGAGTTCC----------GG------------------------GA-GTGA-GTGGGTGGTCC-CCTGC--AGACCCCCGGGTGGCTCCTCTGTGCCACGTG--CAGTGAGCAGCAGGCACAGCTGTCCCCACCAAGCCCCGC-AGCTGTCCC----CACCAAGCCT-------TGGACACGACGCGGCCTGATGTGGGGGGCGAAACGGC-------TTCTGC---------AGGCAGCCGGGGGCCG---CCA-GAGGCTGCAG----------GGCCACGCTGGGCT------------------CCTCACGGGTCCATCAGGGCCGGTACGGAGCTGGGGGCTTCCGGCGAGGGCTGCAGGGTG-TGTCCCCGCCCCCGACCTTCTC----------CCGGGGACA i dasNov2.scaffold_107233 C 0 I 136 e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=17804.000000 s hg19.chr11_gl000202_random 7180 30 + 40103 A-CCAGGGCTGTCTGG-----AAGCCTGTA----------------------------------GGGAGA s rheMac2.chr14 128152169 30 - 133002572 A-CCAGGGCTGTCTGG-----AAGCCTGCA----------------------------------GGGAGA i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125988512 30 - 132107971 A-CCAGGGCTGTCTGG-----AAGCGTGTA----------------------------------GGGAGA i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 2111 30 + 2579 A-CCAGGGCTGTCTGG-----AAGCCTGTA----------------------------------GGGAGA i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68194349 30 + 134204764 A-CCAGGGCTGTCTGG-----AAGCCTGTA----------------------------------GGGAGA i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9662058 31 + 15951348 ---------CGGCTGCACACAACGCTGGGGCAAG------------------------------GTGGGG i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 21793 64 + 42081 A-TGGGGGCCGGGTGC-----AGGCCTGGGCACgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtTGGGGGG i oryCun2.chrUn0985 C 0 C 0 s equCab2.chr12 28932688 31 + 33091231 AGGCAGGGCAGTCTGC-----AAGCCAGAG----------------------------------TGGATA i equCab2.chr12 C 0 C 0 e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=66989.000000 s hg19.chr11_gl000202_random 7210 33 + 40103 TCCACCGAGGT----TTCGG----GAGAGTCAGTGCCCGCC s rheMac2.chr14 128152199 33 - 133002572 TCTAGCGAGGT----TTCGG----GAGAGTCAATACCCACC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125988542 33 - 132107971 TCCAGCGAGGT----TTCGG----GAGAGTCAGTGCCCGCC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 2141 33 + 2579 TCCAGCGAGGT----TTCGG----GAGAGTCAGTGCCCGCC i gorGor1.Supercontig_0069572 C 0 C 0 s panTro2.chr11 68194379 33 + 134204764 TCCAGCGAGGT----TTCGG----GAGAGTCAGTGCCCGCC i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9662089 33 + 15951348 GC-ACCCGGGA--AGATTAG----GGGGAGTTGGGGCTCC- i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 21857 36 + 42081 GC-AGCCAGGCCTGGGTCAG----GAGCATCAGCACCCGCC i oryCun2.chrUn0985 C 0 I 221 s turTru1.scaffold_92122 105243 29 - 105371 CCAGACAGGGT----TTAGG----GAGAGTCAGTACC---- i turTru1.scaffold_92122 N 0 C 0 s equCab2.chr12 28932719 28 + 33091231 -TGAAGGGGGT----TTCGA----GAGAGTCAGTGCC---- i equCab2.chr12 C 0 C 0 s myoLuc1.scaffold_155660 32804 29 - 124081 CCAGAAAGGGT----TTCGG----GAGACTCAGCACT---- i myoLuc1.scaffold_155660 N 0 C 0 s micMur1.scaffold_17226 10007 35 + 15119 --CAGCGAGGT----TTCCATCTCAGGAGTCGGCGCCCGGC i micMur1.scaffold_17226 N 0 C 0 s calJac1.Contig6069 77674 31 + 235769 --CAGTGAGGT----TTCGG----GAGAGTCAGTGCCCCCC i calJac1.Contig6069 N 0 C 0 s papHam1.scaffold6638 68340 31 + 109049 --TAGCGAGGT----TTCGG----GAGAGTCAATACCCACC i papHam1.scaffold6638 N 0 C 0 e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=125944.000000 s hg19.chr11_gl000202_random 7243 48 + 40103 CACATCCCCTGGCCCC--AGGATGA-----GGCCGTGGCTCCCCAC----AGTCCCTCC s panTro2.chr11 68194412 48 + 134204764 CACATCCCCTGGCCCC--AGGATGA-----GGCCCTGGCTCCCCAC----AGTCCCTCC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 2174 48 + 2579 CACATCCCCTGGCCCC--AGGATGA-----GGCCGTGGCTCCCCAC----AGTCCCTCC i gorGor1.Supercontig_0069572 C 0 C 0 s ponAbe2.chr11 125988575 48 - 132107971 CACATCCCCTGGCTTC--AGGATGA-----GGCCGTGGCTCCCCAC----AGTCCCTCC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128152232 48 - 133002572 CACATCCCCTGGCCCC--AGGATGA-----GGCCACGGCGCCCCAC----AATCCCTCC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 68371 48 + 109049 CACATCCCCTGGCCCC--AGGATGA-----GGCCGCGGCGCCTCAC----AATCCCTCC i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 77705 48 + 235769 TACATGCCCTGGCCCC--AGGATGA-----GGCCAAGGCTCCCTAC----AGTCCCTCC i calJac1.Contig6069 C 0 C 0 s micMur1.scaffold_17226 10042 46 + 15119 CTCATCCC--AGCCCT--GGGCAGA-----GGCCGCAGCGACCCAG----CGTCCCTCC i micMur1.scaffold_17226 C 0 C 0 s cavPor3.scaffold_42 9662122 57 + 15951348 CAGAACCCTGGACCTC--AGGCTGACCACCTGCCTTACTCCCCCGCTTCTGCTCCCTAC i cavPor3.scaffold_42 C 0 C 0 s turTru1.scaffold_92122 105272 48 - 105371 CTGATTGGCTGGCCCC--GGGCCAC-----TGCTGTGGCGACCCTC----TGTCCTTCC i turTru1.scaffold_92122 C 0 N 0 s equCab2.chr12 28932747 49 + 33091231 CAGATTGGC-CGCCCCCCCGGCGAT-----GGCGGTGGCCACCCAC----TGTCCCTCC i equCab2.chr12 C 0 C 0 s myoLuc1.scaffold_155660 32833 50 - 124081 CAGATCGGTGGGCCCCCGGGGCTGC-----AGCTGGGGCCACCCAC----CCTCTCTCC i myoLuc1.scaffold_155660 C 0 C 0 e dasNov2.scaffold_107233 6780 136 - 8172 I e oryCun2.chrUn0985 21893 221 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=136953.000000 s hg19.chr11_gl000202_random 7291 97 + 40103 CACAGGAGCCTCTC-GCCCTCCCACTC-ACACAGTGTGGCCAGGCATGGTGGCCCAGCCTGCCCT-------------------------------GAACTAAGAGCTTCTGCTCGGTCCCCAGGG--GC----CA s panTro2.chr11 68194460 97 + 134204764 CACAGGAGACTCTC-GCCCTCCCACTC-ACACAGTGTGGCCAGGCATGGTGGCCCAGCCTGCCCT-------------------------------GAACTAAGAGCTTCTGCTCGGTCCCCAGGG--GC----CA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 2222 97 + 2579 CACAGGAGCCTCTC-GCCCTCCCACTC-ACACAGTGTGGCCAGGCATGGTGGCCCAGCCTGCCCT-------------------------------GAACTAAGAGCTTCTGCTCGGTCCCCAGGG--GC----CA i gorGor1.Supercontig_0069572 C 0 C 0 s ponAbe2.chr11 125988623 94 - 132107971 CACAGGAGCCTCTC-GCCCTCCCAC-C-ACACAGTGTGGCCAGGCATGGTGGCCCAGCCTGCCCC-------------------------------GAACTAAGAGCTTCTGCTC-GTCCCCA-GG--GC----CA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128152280 97 - 133002572 CATGGGAGTCTCTC-GCCCTCCCACCC-ACACAGTGTGGCCAGGCATGGTGGCCCAACCTTCTCC-------------------------------GAAGCAAGAGCTTCTGCTTGGTCCCCAGGG--GC----CA i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 68419 97 + 109049 CATGGGAGCCTCTC-GCCCTCCCACCC-ACACAGTGTGGCCAGGCATGGTGGCCCAACCTTCCCC-------------------------------GAAGCAAGAGCTTCTGCTTGGTCCCCAGTG--GC----CA i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 77753 82 + 235769 CA-AGGAGGCTCT----CCCCTCACCC-ACACACTGTGGCCAGGCAGGGTGGCCCAGCC------------------------------------------AAGAGCTTCCGCTTGGTCCCCAGGG--GC----CA i calJac1.Contig6069 C 0 C 0 s micMur1.scaffold_17226 10088 100 + 15119 CACGGGAGCCGCCCTGCCCTCCTACCC-ACGAAGTGTGGACAGGCCTGGCAGCCCACACTGCCCC-------------------------------AAAGCCAGCACTGCTGCTGGGTCCCCACAGCTGC----CA i micMur1.scaffold_17226 C 0 C 0 s cavPor3.scaffold_42 9662179 74 + 15951348 CAATGGGGCT-----CCCATCTCA-----------GGGGAAGGTCCTGACAGTC--GCC----------------------------------------ACATGGGCTG-TGCCTGG-CCCCGGAT--GCTTAGCA i cavPor3.scaffold_42 C 0 C 0 s equCab2.chr12 28932796 93 + 33091231 ---------------------CTGTCC-GAGCGGTCTGGAAGGGCATGGTG----AGCCCGTCCTCATCCCCACCCCTCAATCTCG----------GAAGAAAG-GCTCACCCTCCATCCCCAGGG--GC----CA i equCab2.chr12 C 0 I 1 s myoLuc1.scaffold_155660 32883 105 - 124081 ---------------------CCGTCCAGAGCA---CGGAAGGGCCTGGTGGCCCAGCGTGTCCTCACCCACACCCTTCAATCCAGAGGGTGGGCCAAAGAAAGCGCTTTTCCTTGGT-CCCAGGG--GC----CA i myoLuc1.scaffold_155660 C 0 I 335 e dasNov2.scaffold_107233 6780 136 - 8172 I e oryCun2.chrUn0985 21893 221 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=22415.000000 s hg19.chr11_gl000202_random 7388 17 + 40103 TGGC------------------------------CCTTCTGTTAGGG s panTro2.chr11 68194557 17 + 134204764 TGGC------------------------------CCTTCTGTTAGGG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 2319 17 + 2579 TGGC------------------------------CCTTCTGTTAGGG i gorGor1.Supercontig_0069572 C 0 C 0 s ponAbe2.chr11 125988717 12 - 132107971 TGTC------------------------------CCTTCTGT----- i ponAbe2.chr11 C 0 I 556 s rheMac2.chr14 128152377 17 - 133002572 CGGC------------------------------CCTTCTGTTAGGG i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 68516 17 + 109049 CGGC------------------------------CCTTCTGTTAGGG i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 77835 17 + 235769 CAGC------------------------------CCTTCTGTTAGGG i calJac1.Contig6069 C 0 I 5 s micMur1.scaffold_17226 10188 16 + 15119 -GGC------------------------------CCTTCTGTGGGGc i micMur1.scaffold_17226 C 0 C 0 s cavPor3.scaffold_42 9662253 16 + 15951348 TGGT------------------------------GCAGCCAGCAGG- i cavPor3.scaffold_42 C 0 C 0 s equCab2.chr12 28932890 47 + 33091231 CGGCCAGGGGGTGCAGCGTCCACGACAGACAGCACCCTCTGATGGGG i equCab2.chr12 I 1 C 0 e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e oryCun2.chrUn0985 21893 221 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=37346.000000 s hg19.chr11_gl000202_random 7405 47 + 40103 GCTGCCGCCCTCCT-----------------CTTGCCCACTCCCCACACCCCG---GGGTCCCTGCA s panTro2.chr11 68194574 47 + 134204764 GCTGCCGCCCTCCT-----------------CTTGCCCACTTCCCACACCCTG---GGGTCCCTGCA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 2336 47 + 2579 GCTCCCGTCCTCCT-----------------CTTGCCCACTCCCCACACCCCG---GGGTCCCTGCA i gorGor1.Supercontig_0069572 C 0 C 0 s rheMac2.chr14 128152394 45 - 133002572 GTTCCCACCCTCCT-----------------CTTGCCCACTCCC--TACCCTG---GGGTCCCTGCT i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 68533 45 + 109049 GTTCCCGCCCTCCT-----------------CTTGCCCACTCCC--CACCCCG---GGGTCCCTGCT i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 10204 65 + 15119 tctcccaccctcctcccttctctcccttccccctctctactccc--cacccCGTGAGTGTCCCTGCG i micMur1.scaffold_17226 C 0 I 56 s cavPor3.scaffold_42 9662269 34 + 15951348 ---------ATTGT-----------------CTTTTCCTCTGTC--CGTCT-----GTCCTTCTGCA i cavPor3.scaffold_42 C 0 I 1 s equCab2.chr12 28932937 36 + 33091231 ----TCTCCTTCCC-----------------CTTTCCTATGCCC--CAC---G---GGGGTCCTG-- i equCab2.chr12 C 0 I 330 e calJac1.Contig6069 77852 5 + 235769 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e oryCun2.chrUn0985 21893 221 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125988729 556 - 132107971 I a score=30481.000000 s hg19.chr11_gl000202_random 7452 30 + 40103 ACAGGCCCCCACCCA-------------------------AAGGGCCTGAAAGTC s panTro2.chr11 68194621 30 + 134204764 ACAGGCCCCCACCCA-------------------------AAGGGCCTGAAAGTC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 2383 30 + 2579 ACAGGCCCCCACCCA-------------------------AAGGGCCTGAAAGTC i gorGor1.Supercontig_0069572 C 0 C 0 s rheMac2.chr14 128152439 30 - 133002572 GCAGGCCCCCACCCA-------------------------AAGGGCCTGAAAGTC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 68578 30 + 109049 GCAGGCCCCCACCCA-------------------------AAGGGCCTGAAAGTC i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 10325 55 + 15119 CCAGTCACTCACCAAGCTGGGCAACCCCTCCCTTCCTGCCAGGGGCTGGGGGGTC i micMur1.scaffold_17226 I 56 I 232 s otoGar1.scaffold_5322.1-37474 32351 30 - 37474 ACAGGTGCCCCCCAG-------------------------AAGGGCTTGGAAGTC i otoGar1.scaffold_5322.1-37474 N 0 C 0 s cavPor3.scaffold_42 9662304 24 + 15951348 CCTCGCCCTCTTCAA-------------------------AA--GACAGCA---- i cavPor3.scaffold_42 I 1 C 0 e calJac1.Contig6069 77852 5 + 235769 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e oryCun2.chrUn0985 21893 221 + 42081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e equCab2.chr12 28932973 330 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125988729 556 - 132107971 I a score=137478.000000 s hg19.chr11_gl000202_random 7482 163 + 40103 TCCAC--AATGACATGATGGCCAGCAG--AGGGCGCATGGCCCTGGGGACCTCGACCCCTCTCCAGGGGACACCCTCTCTGGCTTTAATTTCTATTTTAAGGTGGGCTGTGACTATCATAAGTAGGTGGGGGTGAGACCTCAGCAGCAGTC-CCAGCCGAGGGGTCCT s panTro2.chr11 68194651 163 + 134204764 TCCAC--AATGACATGATGGCCAGCAG--AGGGCGCATGGCCCTGGGGACCTCGACCCCTCTCCAGGGGACACCCTCTCTGGCTTTAATTTCTATTTTAAGGTGGGCTGTGACTATCATAAGTAGGTGGGGGTGAGACCTCAGCAGCAGTC-CCAGCTGAGGGGTCCT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0069572 2413 163 + 2579 TCCAC--AATGACATGATGGCGAGCAG--AGGGCGCATGGCCCTGGGGACCTCGACCCCTCTCCAGGAGACACCCTCTCTGGCTTTAATTTCTATTTTAAGGTGGGCTGTGACTATCATAAGTAGGTGGGGGTGAGACCTCAGCAGCAGTC-CCAGCCGAGGGGTCCT i gorGor1.Supercontig_0069572 C 0 N 0 s rheMac2.chr14 128152469 155 - 133002572 TCCAC--AGTGACGTGACAGTGAGCAG--AGAGTACATGGCCCTGGGGACCCTGACCTCTCTCCAGGGGAAACCCTGTCCGGCTTGAGTTTCTATATTAAGCGGGGCTGTGACTATC--------GTGGGGGTGAGACCTCAGCAACACTT-CCAACCGAGGGGTCCT i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 68608 155 + 109049 TCCAC--AGTGACGTGACAGTGAACAG--AGAGTACATGGCCCTGGGGACCCTGACCTCTCTCCAGGGGACACCCTGTCTGGCTTGAGTTTCTATATTAAGCGGGGCTGTGACTATC--------GTGGGGGTGAGACCTCAGCAACACTC-CCAGCCGAGGGGTCCT i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 10612 143 + 15119 TCAGT--AGTAGGGTGGCAGTGAACAGACATAGCACATGTCCCCGCAGCCCCCAGCCCCTCTGGAGGGGAAACCCTCCCCAGCTTTGGCTTCTGT-TTCAGGTGGGCCAGG--------------GCGGGAG------CCCAGCAGC-CTC-CCAGCGGAAGGGTCCT i micMur1.scaffold_17226 I 232 C 0 s otoGar1.scaffold_5322.1-37474 32381 142 - 37474 TCAGT--AGTGAGGTGACTGTGAGCAGACAGAGCACATGTCTCTGAGGACCCCAACCCCTCTGGAGGGGCACCCCTGCCCGGCTTTAGTTTCTGT-TTGAGATGGGCCAAG--------------ATGGAAG-------CCAGCAGC-CTC-CCAGATGAAGGGTCTT i otoGar1.scaffold_5322.1-37474 C 0 C 0 s cavPor3.scaffold_42 9662328 114 + 15951348 TCCTGACAGTGCCATGACCAGACACAG--ATGGTGACCATCCCTGTGG-CCCTGGCCTCTGG----------------------------------CAGGAGATGGTGATAAATAGC------------AGGATGCACATCAGCAGC--TC-CCAGCC--AGGGCCCT i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 22114 117 + 42081 TCAGG--AGCATCAGCACCCG-CGCAG--A----------CCCCGTGG-CCCTGGCCACTGTGC--------TCCTGCCTCCCCTGGGGCC-----CCGGGGCTGGTGGGGTCT------------------CTGTGCTCCCTTTGC--TCTCCAGGC--TGGGACCC i oryCun2.chrUn0985 I 221 C 0 e calJac1.Contig6069 77852 5 + 235769 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e equCab2.chr12 28932973 330 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125988729 556 - 132107971 I a score=116032.000000 s hg19.chr11_gl000202_random 7645 217 + 40103 GGGGATCCCCAAGT-GCTCCTGAGG----C-------CCGGGACAGGCCC-CT-------------CAATGTTGCCAGGAAGTCC---CACGGGCCCACGTCTTCCCC--TCCAGCTCTGT---GGAGCGGGTGCTG--TGCCCTCGTTTACT----------GACAAGG--AGGCTG--AAGCTCAGGACTC-------TTACGGTGACACAGTGAGGGCTGGGTGTCCACCAG-ACATGGGCCCACAAGACATCCTCAGTGTGGGTGCTGACG s panTro2.chr11 68194814 217 + 134204764 GGGGATCCCCAAGT-GCTCCTGAGG----C-------CCGGGACAGGCCC-CT-------------CAATGTTGCCAGGAAGTCC---CATGGGCCCACGTCTTCCCC--TCCAGCTCTGT---GGAGCGGGTGCTG--TGCCCTCGTTTACT----------GACAAGG--AGGCTG--AAGCTCAGGACTC-------TTACGGTGACACAGTGAGGGCTGGGTGTCCACCAG-ACACGGGCCCGCCAGACATCCTCAGTGTGGGTGCTGACG i panTro2.chr11 C 0 C 0 s rheMac2.chr14 128152624 233 - 133002572 GGGGATCCCCAAGG-GCTCATGAGG----C-------CCTGGACAGGCCC-CTCACAGGTGCCAACCAATGTCGCCAGGAAGTCC---CACGGGCCCACGTCTTCCCC--TCCAGCTCTGT---GGAGCGGGTGCTG--TGCCCTCGTTTACT----------GACAAGG--AGGCTG--AAGCTCTGGACTC-----TGTCACGGTGACACAGTGAGGGCTGGGTGTCCCCCAGTACACGGGCCTACCGGACATCTGCAGTGTGGGTGCTGACA i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 68763 233 + 109049 GGGGATCCCCGAGG-GCTCATGAGG----C-------CCTGGACAGGCCC-CTCACAGGTGCCAACCAATGTCGCCAGGAAGTCC---CACGGGCCCACGTCTTCCCC--TCCAGCTCTGT---GGAGCGGGTGCTG--TGCCCTCGTTTACT----------GACAAGG--AGGCTG--AAGCTCTGGACTC-----TGTCACGGTGACACAGTGAGGGCTGGGTGTCCCCCAGTACACGGGCCTACCGGACATCTGCAGTGTGGGTGCTGACA i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 10755 223 + 15119 -GGGGTGCAGGGG----TCTCACGGCTG-C-------TCTGGACAGGCCCTCA--CAGGCAGCAGCCAATGTCCCTAGAAAGTCA---CATGGGGCCATTTCTTCTCCATTTCCTCTCTGT---GGAG-GGGGGCTGCAGCCCCTCACTTGCT----------GACAAGG--GAGCTG--GGGTTCAGGGCTG-----TCTCACGGTGACAC-----------AGTGGCCGCAGGAACATGTGTCCAGGGGGCACCTGCGGTGTGGTTGCTGGCC i micMur1.scaffold_17226 C 0 C 0 s otoGar1.scaffold_5322.1-37474 32523 223 - 37474 GGGGGTACCGGGG--GATCTCATGGCTACC-------CCTGGACAGGCCC-CT--TGGGCACCAACCACTGTCCCTAGCACGTCA---CATGGGGCCATTTCTTTCCCGTTCCTACCCTGT---G--------------GCCCCTCATTTACT----------GACAAGG--GAGCTG--GAGCTCAGGACTC-----TCTCATGGTGACACTGCAAGGGGTTGGCATCTGTGGGAACACGTGTCTGCTGGGCATCCACCATGTGGTTG-TGGGA i otoGar1.scaffold_5322.1-37474 C 0 C 0 s cavPor3.scaffold_42 9662442 197 + 15951348 --TGGTGTCTGGG--AGTCCCATGGCTGCT-------CCTCCACAGGGCC-TT-----GTCCCTGGCACAGAGCACAGGTAATTC---------TCTCCCTGCCCCTA--TCCTGTACCAA--------GGGCACTG--TGACTCCCCTATCT----------GATGAGGAAGAACTGAAAGTTTGGAGAAGACCCTGTCCCCTGATGACATGGTGAGGGGC---------------CCCAGGTGTCC---------------CAGGGGCTCAGG i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 22231 235 + 42081 --TGCCCTCCAGAGCAGGCCTAATGCTGCTGGGGGCCCCGGGGCACCACC-GT-----GCCGAGGGCTGGGGGGGCAGGGCGTGCAGGGCTGAGCCTCCCGGCCCCCA---CCAGCCCCAGCTGGCTGCGTGCTCTC--GGCCTGCTCCCTCTTTTATTCACGGATGAGG--GACCCG--AGTTTCAAGATGC-----GCTCACGGCGACACGCAGGGCTGC---TGTCCCCTGCCACCCCTGTCCAC---------------TGGGTGCTGGTG i oryCun2.chrUn0985 C 0 C 0 e calJac1.Contig6069 77852 5 + 235769 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e equCab2.chr12 28932973 330 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e ponAbe2.chr11 125988729 556 - 132107971 I a score=101624.000000 s hg19.chr11_gl000202_random 7862 144 + 40103 GTC-----------ACTGAGAAGCCCTGGCCCAGTG----GAGCTTG-----------TGGTG------------GGACGGAGGGTGGGGGTCA---GT---GTCTAACCACAGG-----CCCATCCTAGCAGGACTCCAGCAAAGACACCTTCCATAGGGTTGGGTC-CT-----------------TCCCCACCCCTGGGAGTCTTGAC s panTro2.chr11 68195031 143 + 134204764 GTC-----------ACTGAGAAGCCCTGGCCCAGTG----GAGCTTG-----------TGGTG------------GGACGGAGGGTGGGGGTCA---GT---GTCTAACCATAGG-----CCCATCCTAGCANGACTCCAGCAAAGACACCTTCCATAGGGTTGGGTC-CC-----------------TCCCCACCCCTGGGAGTCTTGA- i panTro2.chr11 C 0 I 298 s ponAbe2.chr11 125989285 143 - 132107971 GTC-----------ACTGAGAAGCCTCGGCCCAGTA----AAGCTTA------------GGCA------------GGACGGAGGGTGGGAGTCA---GT---GTCTAACCACAGG-----CCCATCCTAGCAGGGCTCCTGCAAAGGCACCCACCGTAGGGTTGGGTC-CT-----------------TCCCCACCCCTGGGAGTCTTGAC i ponAbe2.chr11 I 556 C 0 s rheMac2.chr14 128152857 144 - 133002572 GTC-----------ACTGAGAAGCCCCAGCCCGGTG----GAGTTTG-----------TGGTG------------GGAGGGAGGGCGGGTGTCA---GT---GTCTAACCACAGG-----CCCATCCTAGCAGGACTCCAGCAAAGGCACCCCCCATAGGGTTGGGTC-CC-----------------TCCCCACCCCTAAGAGTCTTGAC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 68996 144 + 109049 GTC-----------ACTGAGAAGCCCCAGCCCAGTG----GAGTTTG-----------TGGTG------------GGAGGGAGGGCGGGGGTCA---GT---GTCTAACCACAGG-----CCCATCCTAGCAGGACTCCAGCAAAGGCACCCCCCATAGGGTTGGGTC-CC-----------------TCCCCACCCCTAAGAGTCTTGAC i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 10978 147 + 15119 GTC-----------ACTGCTGAGACCTGGCCA-GCGCTCAGAGCCTGCCCTGCC---CTGGGG------TGA---GGACGG-GGACGGATGGCC---GT---GTCTGACCGCAGGCTAGCCCTGTCCCTGCAGGACTCGAGCAAAGAC--------------TGGCTC-CC-----------------GTCCACCCTCAGGCAGTCTT-GC i micMur1.scaffold_17226 C 0 C 0 s otoGar1.scaffold_5322.1-37474 32746 169 - 37474 GTC-----------ACTGCTGAGACCCAGCCAGGGGCTCAGACTCTGCCCTGCCCTACTGGGGCTTATATGACCGGGACGG-GGGCAGATGGCCCATGTCTGGTCTGACTGCAGGCTGACCCTCTCCCAATGGGACTTGAGCAAACACG-------------TGGCTCGCC-----------------CTCCACCCTCTGCAAGTCTTGGC i otoGar1.scaffold_5322.1-37474 C 0 C 0 s cavPor3.scaffold_42 9662639 128 + 15951348 GCC-----------CCT-----CTGCTGGTATGACA----GAGCAGA-----------TGGCC------------AGCACCGGACCACAGCCTG---CT------------CTGT-----CCTGAATCAG------TCAAGCAAAGACA-------------TGGTTC-CCACTCCATGCAACTGGGCCACCCACTCCCAGGAGCCTTGGT i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 22466 105 + 42081 GTCACCACGCGGAGCCT-----GCCCTGACCCAGTG----GAGCTCG-----------TGGTG------------A------GGCCAGAGGCAG---GT-------------GGC-----CCCGGACCAGCTGGGCTCAAGCAAAGAAG-------------GGGCTC-TC---------------------------------CCTTGGA i oryCun2.chrUn0985 C 0 C 0 e calJac1.Contig6069 77852 5 + 235769 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e equCab2.chr12 28932973 330 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=41476.000000 s hg19.chr11_gl000202_random 8006 44 + 40103 CAGTCCCAGGAGAGGCCACTTTCTCCCGACCGGGTCCTTTACCT s papHam1.scaffold6638 69140 44 + 109049 CAGTCCCAGGAGAAGCCACTTTCTCCCGACGGGATCCTTTACCT i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128153001 44 - 133002572 CAGTCCCAGGAGAAGCCACTTTCTCCCGACGGGATcctttacct i rheMac2.chr14 C 0 I 170 s ponAbe2.chr11 125989428 44 - 132107971 CAGTCCCAGGAGAGGTCACTTTCTCCCGACTGGGTCCTTTATCT i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68195472 44 + 134204764 CAGTCCCAGGAGAGGCCACTTTCTNCCGACCGAGTCCTTTACCT i panTro2.chr11 I 298 C 0 s micMur1.scaffold_17226 11125 43 + 15119 CCGTCCTGGGAGAGTCC-CTGTCCCACGATGGGCCTCTTCAGCT i micMur1.scaffold_17226 C 0 C 0 s otoGar1.scaffold_5322.1-37474 32915 43 - 37474 CAATCCTGGGGGAGACC-CCATCCCAGGATGGGCTCCTTCACCT i otoGar1.scaffold_5322.1-37474 C 0 C 0 s cavPor3.scaffold_42 9662767 16 + 15951348 CAGCCCTGGAAGGGGC---------------------------- i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 22571 19 + 42081 CGGGCTGGGGCTGGGCC-CT------------------------ i oryCun2.chrUn0985 C 0 C 0 e calJac1.Contig6069 77852 5 + 235769 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e equCab2.chr12 28932973 330 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=22901.000000 s hg19.chr11_gl000202_random 8050 51 + 40103 CTCTGCCACTGTCTCCCTC--CTGACAGGGTCCTTTACCTCTCTGATCCCTCC s panTro2.chr11 68195516 51 + 134204764 CTCTGCCACTGTCTCCCTC--NTGACAGGGTCCTTTACCTCTCTGACCCCTCC i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125989472 51 - 132107971 CTCTGCCACTGTCTCCCTC--CTGACAGGGTCCTTTACGTCTCTGACCCCTCC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128153215 51 - 133002572 CTCTGCCGCTGTCTCCCTC--CCGACGGGGTCCTTTACCTCTCTGACCCCTCC i rheMac2.chr14 I 170 C 0 s papHam1.scaffold6638 69184 31 + 109049 CTCTGCTGCTGTCTCCCTC--CTGACGGGGTcc-------------------- i papHam1.scaffold6638 C 0 I 132 s calJac1.Contig6069 77857 51 + 235769 CCCTGCCACTGTCTCCCTC--CCGACAGGGTCCTTTACCTCTCTGGCCCCTCC i calJac1.Contig6069 I 5 T 5062 s micMur1.scaffold_17226 11168 9 + 15119 ----------CTCACCCTC---------------------------------- i micMur1.scaffold_17226 C 0 C 0 s otoGar1.scaffold_5322.1-37474 32958 11 - 37474 ----------CTCACCCCCTG-------------------------------- i otoGar1.scaffold_5322.1-37474 C 0 C 0 s cavPor3.scaffold_42 9662783 36 + 15951348 ------TTCTGCCACCCTC--ATGATGGCCTCTGTCACCTCTCA--------- i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 22590 32 + 42081 ------CCCTGTCCCCGGC--ACTGTGGCCAAT----CCTCTTA--------- i oryCun2.chrUn0985 C 0 C 0 e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e equCab2.chr12 28932973 330 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=82193.000000 s hg19.chr11_gl000202_random 8101 91 + 40103 TGGTAAGGGAAG---TAGAATCATTGTCACTGAGGCAGTCAGGAGAGCAGCTCCCCCAACCTTGGCAGAGAAAGGGACAGTCCCTCACCTGC-AA s papHam1.scaffold6638 69347 91 + 109049 TGGCAAGGGAAG---TAGAATCATTGTCACTGAGGGAGTCAGGAGAGCAGCTCCCCCAACCTCGGCAGAGAAAGGAACAGTCCCTCACCTGC-AC i papHam1.scaffold6638 I 132 C 0 s rheMac2.chr14 128153266 91 - 133002572 TGGCAAGGGAAG---TAGAATCATTGTCACTGAGGGAGTCAGGAGAGCAGCTCCCCCAACCTCGGCAGAGAAAGGAACAGTCCCTCACCTGC-AC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125989523 91 - 132107971 TGGTAAGGGAAG---TAGAATCATTGTCACCGAGGCGGTCAGGAGAGCAGCCTCCCCAACCTCGGCAGAGAAAGGGACAGTCCCTCACCTAC-AA i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68195567 91 + 134204764 TGGTAAGGGAAG---TAGAATCATTGTCACTGAGGCAGTCAGGAGAGCAGCTCCCCCAACCTCGGCAGAGAAAGGGACAGTCCCTCACCTGC-AA i panTro2.chr11 C 0 C 0 s micMur1.scaffold_17226 11177 85 + 15119 AGGTGAGGGA-----GATAGTCCTTGCCACTGAATGGATCCGGAGAGCAGC-CCTCCAACTC---CGCAGAGCGTGGCGACCCCTCACCTCT-GC i micMur1.scaffold_17226 C 0 I 2 s otoGar1.scaffold_5322.1-37474 32969 78 - 37474 TGGTTAGGGAAG---AGGAGTCACTGCCGCTGTGCAGCGTGGGAGGGCAGTGTCCCCAACTCT-GCACAGAGTATGGCAGCC------------- i otoGar1.scaffold_5322.1-37474 C 0 C 0 s cavPor3.scaffold_42 9662819 86 + 15951348 CAGTAAAGGAAGTGACAGAGCCA--GACTCTGCACAAATCAGGAGAGCA-CCCCCCCAACCTCAGT--AGAATGCGA---CCCCCACCTTGTGA- i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 22622 42 + 42081 C-------------------------------------------------CCCGCCCGGGCTCAGC--AGAGCGTGACGCCCCCCGCCCTGC-A- i oryCun2.chrUn0985 C 0 C 0 e calJac1.Contig6069 77908 5062 + 235769 T e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e equCab2.chr12 28932973 330 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=136097.000000 s hg19.chr11_gl000202_random 8192 92 + 40103 TCCTTCTGCCAGCCCTGGCTTGCGTGGTGTC-AAGGGACATGAGCTTGGGGAGGCCACTCATTCCTTCTC------C------CGGACGGAAGATTTGGGTGGGA- s panTro2.chr11 68195658 92 + 134204764 TCCTTCTGCCAGCCCTGGCTTGCGTGGTGTC-AAGGGACATGAGCTTGGGGAGGCCACTCATTCCTTCTC------C------CGGACGGAAGATTTGGGTGGGA- i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125989614 92 - 132107971 TCCTCCTACCAGCCCTGGCTTGCGTGCTGTC-AAGGGACATGAGCTTGGGGAGGCCACTCATTCCTTCTC------C------CGGACAGAAGATTTGGGTGGGA- i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128153357 92 - 133002572 TCCTCCTGCCAGCCCTGGTTTGCGTGGTATC-AAGGGACACGAGCTTGGGGAGGCCACTCATTCCTCCTC------C------CAGACAGAGGATTTGGGTGGGA- i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 69438 93 + 109049 TCCTCCTGCCAGCCCTGGTTTGCGTGGTATCAAAGGGACATGAGCTTGGGGAGGCCACTCATTCCTTCTC------C------CAGACAGAGGATTTGGGTGGGA- i papHam1.scaffold6638 C 0 M 50 s calJac1.Contig6069 72846 91 + 235769 TCCTCCTGCCAGTCCTGGCTTTCGTGGGGTC-AAAAG-CATGAGCTTGGGGATGCCACTTATTCCTTCTC------C------TGGACAGAAGGTCTGTGGGGCA- i calJac1.Contig6069 T 5062 C 0 s micMur1.scaffold_17226 11264 93 + 15119 TCCTCCCGCCATGCCTGGCGTGGGTGGTGTT--GGGGACTTGAGCTTGGGGAGGCCACTTCCCCCTTTTCCCACCTC------CGGACACAGG-TGTGGGTG---- i micMur1.scaffold_17226 I 2 C 0 s otoGar1.scaffold_5322.1-37474 33047 94 - 37474 -CTTTCCGCCATGTCTGGCATGGGTGGTATC-AGGGGACCCGAGCTCAGGGCAGCCATTTATTCCTTCTACCTCATC------CAG--AGAGG-CATGGGTGGGG- i otoGar1.scaffold_5322.1-37474 C 0 I 1 s cavPor3.scaffold_42 9662905 97 + 15951348 --CCACCCCCAGCACTGGACCAGGTGGCGTG-GGAAGCATCAGCTTTAGGGGGCACAATTCTTCCTTCTC------CCACCTGTGGATGGAAGGTGGGGATGGGGA i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 22664 58 + 42081 --CTGCCCACCGGCCCGGACTGGGTG------------------------------------CCTCCCTC------CCACCC-CGGAGGGAAGGTGTG---GGGGG i oryCun2.chrUn0985 C 0 C 0 e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e equCab2.chr12 28932973 330 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=94530.000000 s hg19.chr11_gl000202_random 8284 126 + 40103 GGCACCTCCTAAAAATGACGTTTGGGCAGCAGACA-TGATGAGGAC--------AGGGCCTTAT--GAGTCCCCTCCCCAGGACACCTCAAGACCACTCGGCCAGGAATGCTGACGTGCCATGCACATTCACTTGGG s rheMac2.chr14 128153449 128 - 133002572 GGCACCTCCTGAAAATGACGTTTGGGTAGCAGACA-TGACGAGGAC--------AGGGCCATATACGAGTCCCCTCCCCAGGACGCCTCAAGACCTCTTGGCCAGGAATGCTGATGTGCCATGCACATTCACGTGGG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125989706 128 - 132107971 GGCACCTCCTAAAAATGACGTTTGGGCAGCAGACA-TGATGAGGAC--------AGGGCCATATACGAGTCCCCTCCCCAGGACACCTCAAGACCTCTCGGCCAGGAATGCTGATGTGCCACGCACATTCACGTGGG i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68195750 126 + 134204764 GGCACCTCCTAAAAATGACGTTTGGGCAGCAGACA-TGATGAGGAC--------AGGGCCTTAT--GAGTCCCCTCCCCAGGACACCTCAAGACCACTCGGCCAGGAATGCTGACGTGCCATGCACATTCACTTGGG i panTro2.chr11 C 0 C 0 s calJac1.Contig6069 72937 128 + 235769 GGCACCTCCTGAAAATGACCTTGGGGCAGCAGATG-TGACAAGGAC--------AGGGCCATATACGAGTCCCGTCCCCAGGATGCCACAAGACCCCTCGGTCAGGAATGCTGACATGCCATGCACGTTCACATGGG i calJac1.Contig6069 C 0 C 0 s micMur1.scaffold_17226 11357 56 + 15119 --------------------------------------------------------GGCCGGGCAGGGGC----------------------ATCCCTTGGCCAGG--TGCTGAGGCTCTCCGCACAACCT-GTGGG i micMur1.scaffold_17226 C 0 C 0 s otoGar1.scaffold_5322.1-37474 33142 102 - 37474 GGCACCTCCTGCCAAGGACCTCTGGGCAGCAGACA-CAATGCAGA-----------GGACGGGCAGGGGC----------------------ATCCCTTGGCCAGG-ATGCTGTGGCCCCACACACATCCTCGTGGA i otoGar1.scaffold_5322.1-37474 I 1 C 0 s cavPor3.scaffold_42 9663002 117 + 15951348 AGCAGCTCC-ACAAGTGACATTGGGG-AGCAGATGGCAGCAAGGAGGCCTGCG-GAGGCAATGT--GAGC--TCTCCCTGG-----------GCCCCTCCGCCAGGAGTG-TGGGCCACCGTGC-TGTCCACCCAGG i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 22722 93 + 42081 AGGACCTCCTGGCAGTGACCTTTGGGCCCCAGACAGCAGCAAGGGCGGCTGGGCGGGGCCACGG--GACT----------------------GCCCCTTCTCCAGG-----------GCCCTGC-TG--------GA i oryCun2.chrUn0985 C 0 C 0 e papHam1.scaffold6638 69531 50 + 109049 M e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e equCab2.chr12 28932973 330 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=132319.000000 s hg19.chr11_gl000202_random 8410 94 + 40103 ATCCTGAACCTCCCTCCCAGGTCTGTCCTTCCCCCTGGCCAGCAGAAGCCACCAGGGGCCACTCCTTCCCTTCCCCTGAGAGGTCAGAAGCAGC s panTro2.chr11 68195876 94 + 134204764 ATCCTGAACCTCCCTCCCAGGTCTATCCTTCCCCCTGGCCAGCAGAAGCCACCAGGGGCCACTCCTTCCCTTCCCCTGAGAGGTCAGAAGCAGC i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125989834 94 - 132107971 ATCCTGAACCTCCCTCCCAGGCCTGCCCTTCCCCCTGGCCAGCAGAAGCCACCAGGGGCCACTCCTTCCCTTCCCCTGAGAGGTCAGAAGCAGC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128153577 94 - 133002572 ATCCCGAACCTCCCTCCCAGGCCTGCCCTTCCCCCTGGCCAGCAGAAGCCACCAGGGGCCACTCCTTCCCTTCCCCTGAGAGGTCAGAAGCAGC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 69581 94 + 109049 ATCCTGAACCTCCCTCCCAGGCCTGCCCTTCCCCCTGGCCAGCAGAAGCCACCAGGGGCCACTCCTTCCCTTCCCCTGAGAGTTCAGAAGCAGC i papHam1.scaffold6638 M 50 C 0 s calJac1.Contig6069 73065 92 + 235769 ACCCCGGGCCTCCCTCCCAGGCCTGCCCTTCCCTCC-ACCAGCAGAAGCCACCAGGGGCCACTCCTTCTCTTCCCCTGAGAGGTCAG-AGCAGC i calJac1.Contig6069 C 0 C 0 s micMur1.scaffold_17226 11413 73 + 15119 ACCCGTTGCTTCTGTCCTGGGCCTGCCCCTCCCCCG--------------------GCCTGCCCCTCCCCTCCAGCTG-GGGGCCAGAAGCAGC i micMur1.scaffold_17226 C 0 I 1640 s otoGar1.scaffold_5322.1-37474 33244 57 - 37474 CCACGGGGCCTCCCTCTTGGGTGTACCCCCTCCCCA------------------------GCCCCTTCTCTC---GTG-GGCGCC--------- i otoGar1.scaffold_5322.1-37474 C 0 C 0 s cavPor3.scaffold_42 9663119 84 + 15951348 --ACCCTGCCTCTCGCTCCTGGGCAGCTCCTCCCTCGGCCATCAGAGGCCG--AGAAGCTACTTCCTCCCTTGAACTGAAAGCCAAAA------ i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 22815 59 + 42081 --CCCCAGCCGCCTGCACAAG----------CCCCCGGCT-----------------GCCGCTCCTTCCTTCCAGCTGGGAGGCCAGA------ i oryCun2.chrUn0985 C 0 C 0 e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e equCab2.chr12 28932973 330 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=127202.000000 s hg19.chr11_gl000202_random 8504 139 + 40103 GTGTGCTGCGTGAGCC--GG---CCCGCAGGCTCCGGGCAGGTCCGCCTGGATCTGAGCTCGGCAGTACTGGGTGTCTGCAGCGAGGGCACACGGGGCCATGAGGGGTTTTCCCCAAATCTGAAAACAGCCCCTTCCGCAGACG s oryCun2.chrUn0985 22874 36 + 42081 --------------------------GCAGGCCC----------------------------------------------AAGGGTGCC------------GA--------GCCCA------GG----------GCCATGGCGC i oryCun2.chrUn0985 C 0 C 0 s cavPor3.scaffold_42 9663203 60 + 15951348 --------------------------GCAGCCCC-----------------------------------TGCGTGCTGGTGGGGGTGACACAC--TGTCATGA--------CCCCA---CTGAG----------CCCCCAGAGG i cavPor3.scaffold_42 C 0 C 0 s otoGar1.scaffold_5322.1-37474 33301 140 - 37474 ATGTGCTGAGAAGCCCAGGG---CTCACAGACCCTGGGAAGGTCAGCCCAGCTCTAGACTCTGCAGTGTGAGGCCCCTCTGGGTGTGGCATGTGGCACCAGGACAGATTCTCCCTGAATCCAAATGCAGCCCC-TCCCCTGACA i otoGar1.scaffold_5322.1-37474 C 0 C 0 s calJac1.Contig6069 73157 139 + 235769 ATATGCTGGGTGAACC--GGGGCCCCACAGGCTCCAGGCAGA---GCCCGGCTCTGAGCTTGGCGGCACTGAGTATCTGCATCAGGGCCACACAGGGTCGTGAGGGGTTCTCCCCAGATCTGAAAGCAGCCCCTTCCCCAGACA i calJac1.Contig6069 C 0 C 0 s papHam1.scaffold6638 69675 139 + 109049 GTGTGCTGGGTGAGCG--GG---CCCGCAGGCTCCGGGCAGGTCCGCCTGGCTCTGAGCTCGGCAGCACTGGGTGCCTGCAGGGAGGGCACGCACGGCTGTGAGGGGTTCTCCCCAAATCTGAAAACAGCCCTTTCCCCAGACA i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128153671 139 - 133002572 GTGTGCTGGGTGAGTG--GG---CCCGCAGGCTCTGGGCAGGTCCGCCTGGCTCTGAGCTCAGCAGCACTGGGTGCCTGCAGGGAGGGCACGCACGGCTGTGAGGGGTTCTCCCCAAATCTGAAAACAGCCCTTTCCCCAGACA i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125989928 139 - 132107971 GTGTGCTGGGTGAGCC--GG---CCCGCAGGCTCTGGGCAGGTCGGCCTGGCTCTGAGCTCGGCAGCACTGGGTGTCTGCAGCGAGGGCACATGGGGCCGTGAGGGGTTCTCCCCAAATCTGAAAACAGCCCCTTCCCCAGACA i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68195970 139 + 134204764 GTGTGCTGCGTGAGCC--GG---CCTGCAGGCTCTGGGCAGGTCCGCCTGGGTCTGAGCTCGGCAGTACTGGGTGTCTGCAGCGAGGGCACACGGGGCCATGAGGGGTTTTCCCCAAATCTGAAAACAGCCCCTTCCGCAGATG i panTro2.chr11 C 0 C 0 e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e equCab2.chr12 28932973 330 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=327665.000000 s hg19.chr11_gl000202_random 8643 393 + 40103 GTGCCTGGGA-------GGGGAGCCAGAGGGAGCAGGTCCAGAAGGACGGGACA--TCGCCACC-GG-----CTGGACAGCACTGAGGAGGCCGACGGGAGAGAAGGTCACACCTGA--CTGA--------AGCAGA-GCTGGCAGCCTGGAGATCCCTGATTCTCTCCT-----CCC-------AAGTGGGGG---GACAGGAGGTGGCGGAGG--------CTGCAGC-GGCCCCAG-----AG---AGCAGGGCAGAGCAGAGTGCTGGGCCCAAGCAG-----GAAGGGTGGGTTTCACTC-GGGAGCT---------GCAGGCACCGCGCCTCGCAGGACTC-ACTTTGACCACAGTGGGAGGA--------TGCATCGGC----CCCAGGGAGGCCAATGGGGAGGCCAGCGTGAGCTCCAGT-GGAGGTGCTGGCACCCGGACCTGGGGC--TGGGCGC----GGGGATGGTGGGAAGC s panTro2.chr11 68196109 392 + 134204764 GTGCCTGGGA-------GGGGAGCCAGAGGGAGCAGGTCCAGAAGGACGGGACA--TCGCCACC-GG-----CTGGACAGCACTGAGGAGGCCGACGGGAGAGAAGGTCACACCTGA--CTGA--------AGCAGA-GCTGGCAGCCTGGAGATCCCTGATTCTCTCCT-----CCC-------TAGTGGGGG----ACAGGAGGTGGCGGGGG--------CTGCAGC-GGCCCCAG-----AG---AGCAGGGCAGAGCAGAGTGCTGGGCCCAAGCAG-----GAAGGATGGGTTTCACTC-GGGAGCT---------GCAGGCACCGCACCTTGCAGGACTC-ACTTTGACCACAGTGGGAGGA--------TGCATCGGC----CCCAGGGAGGCCAATGGGGAGGCCAGCGTGAGCTCCAGC-AGAGGTGCTGGCACCCGGACCTGGGGC--TGGGCGC----GGGGATGGTGGGAAGC i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125990067 398 - 132107971 GTGCCTGGGA-------GGGGAGCCAGAGGGAGCAGGTCCAGAAGGATGGGACA--TCGCCACC-CG-----CTGGACAGCACTGAAGAGGCCGACAGGAGAGAAGGTCACATCCGA--CTGA--------AGCAGA-GCCGGCAGCCTGGAGACCCCTGATTCTCTCCT-----TCC-------GAGCGGGGG---GACAGGAGGTGGTGGGGG--------CTGCAGC-GGCCCCAGACAGCAG---GGCAGGGCAGAGCAGAGTGCTGGGCCCAAGCAG-----GAAGGGTGGGTTTCACTT-GGGAGCT---------GCAGGCACTGCGCCTCGCAGGACTC-ACTTTGACCTCAGCGGTAGGA--------CGCGTCTGC----CCCAGGGAGGCCGATGAGGAGGCCAGTGTGAGCTCCAGC-AGAGGTGCCGGCGCCCGGACCTCGGGC--TCGGCGC----GGGGATGGTGAGAAGC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128153810 403 - 133002572 GTGCCTGGGA--------GGGAGCCACAGGAAACAGGTCCAGAAAGACGGGACA--TCGCCGCC-TGCCGGACCGGACCGCACTGAGGAGGCTGACTGGAGAGAAGGGCGCACCTGA--CTAACACAGAGCCGCAGA-GCCGGCAGCCTGGAGACCCC-GATTCTCTCCT---------------GAGCGGGGGACAGACAGGAGGTGACGGGGG--------CTGCAGC-GGCTCCGG-----AG---AGCAGGGCAGAGCAGAGTGCTGGGCCCAAGCAG-----GAAGGGTGGG-TTCACTC-GGGAGCT---------GCGGGCACTGTGCCTCACAGGACTC-ACTTTGACTGCAGCAGGAGGA--------CGCGTCAGC----CCCAGGGAGGCCGATGGGGAGGCCAGGGAGAGCTCCTGC-GGAGGTGGTGGCGCCTGGACCTGGGGC--TGGGCTC----GGGGGTGGTGAGAAGT i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 69814 390 + 109049 GTGCCTGAGA--------GGGAGCCACAGGAAACAGGTCCAGAAAGATGGGACA--TCGCCACC-TG-----CTGGACCGCAATGAGGAGGCTGACCGGAGAGAAGGACGCACCTGA--CTAA--------CGCAGA-GCCGGCAGCCTGGAGATCCT-GATTCTCTCCT---------------GAGCGGGGGGCACACAGGAGGTGGCGGGGG--------CTGCAGC-GGCTCCAG-----AG---AGCAAGGCAGAGCAGAGTGCTGGGCCCAAGCAG-----GAAGGGTGGG-TTCACTC-GGGAGCT---------GCGGGCACTGTGCCTCACAGGACTC-ACTTTGACTGCAGCAGGAGGA--------CGCGTCAGC----CCCAGGGAGGCCGATGGGGAGGCCAGGGAGAGCTCCTGC-GGAGGTGGTGGCACCTGGACCTGGGGC--TGCGCGC----GGGGATGGTGAGAAGT i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 73296 395 + 235769 GTGCCTGGGA-------GAGGAGCCAGAGGAAGCAGGCCCAGAAGGAC-GGACA--TCACCACC-CA-----CTGGGCAGTGCTGAGGAGGCCAACGAG-GAGAAGGTCACACCAGA--CTCA--------GGCAGG-GCCAGTGGCCTGGAGACCCCTGACTCTCTCCT-----CCTGA-CGGGGGGCGGGGG----GCAGGAGGTGGCAGGGG--------CTGCAGC-AGCCCCAG-----AG---GGCAGGGCAGAGCGGAGTGCTGGGTCGGAGCGG-----GAAGGGTGGGCTTCACTC-GGGAGCT---------G-AGGCACTGCACCTCACAGGACTC-ACTTTGACCATAGTGGGAGGA--------CGAGTCTGC----CCCAGGGAAGCTGACGGGGAAGCCAGTGTGAGCCCCAGG-GGAGCTGCTGGCGCCTGGACCCAGGGC--TGGGAGC----AGGGATGGTGAGAAGC i calJac1.Contig6069 C 0 I 5102 s otoGar1.scaffold_5322.1-37474 33441 395 - 37474 GTGACAGGGCAGGTTGGGGGCAACTGGATGAAGCAAGTGCAGAACAGCTGGACATCTCACCACC-C------CTCTACAGCACTGAAGAGGCTGGGGAGGAACGAGGTCACGTCCAA--GTTG--------GACAGA-GCCAG-AGACCAGAGTCCCCCAAGTCTCTCCT-----CTCTATCCTTAAGCTGTGG--ACAAAGGAAGGGGTGAGAAGGTGTCTCCTCTGGT-GGCTGAGA-----GGTGAGGCAGGGGAGGGGCAGGCACAGGACC----CAG-----CGGGGGCAGGCTTGATTCTGATGGCT---------GTGGGCAACGTGGCT-GCAGGGT------------------GGGGGG--------CTTGT-GGG----CCCAGGGAGGCTGATGGCCAGGCCATTGTGAAAACCAGG-AGAGATGCTGGTGCCTGG--CCAGAGT--GGGCTGT----GGGGATTGTGGGATGT i otoGar1.scaffold_5322.1-37474 C 0 C 0 s cavPor3.scaffold_42 9663263 314 + 15951348 GTTCCTGGGA-------G----------GGAAGCAGCCCCAGGAGGTCTGGACA--TCGCCCCT--------CTTGACAGTGTCCAAGAGGCTGCAGGGAGGGGAGGTCG----GGA--GCCA--------GGCAGGCGGGGACAGCCAAGTTTTCTC----TGCCCTGT-----CCC-------AGATTGAGG--------GAGGTT-----GA--------C--------------------AG---TGGAGCACAGAACTGAGCTCGTGAGCCCAGCAG----------------------G-GAGGGCT---------GCGGC------GCCTCTCAGAAGTT--CCGGGGCCACAGTGGGGGGACACTTCAGTGCACAAGC----CCACAGGCCACCACTGGGAAGATAAT---------------GAGGTGCAGGCCTGGAAAGGGGAGGC--------C----ACCGGTAGGGGAAAGC i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 22910 248 + 42081 GTTCCCCCGA-------GT-------CCGAACACGGCTGCAAGTGGGCTGGATG--GCGCCCC----------------------------CTGCTGGCCACAGCGATGG----GGACCACCA--------GAAAG--GGGCGCACCCGAGGGCCCCT-GA-TGTCCCCT-----CCC-------------TGG--------GAGCTG-----AG--------C--------------------GG---TGCGG---------------GTGGGGCTGACAG--------------------CCG-GGGAGCT---------GTGGC-------------------------TGATAACCAAGGGAGGG----------------------CACAGGTGTTGGCTGGGGAG--------------------GGGGTGTCGCAGCGGAGCAGAGTGGCGGTGGGGGT----GCCTGCAGTGGAGCCT i oryCun2.chrUn0985 C 0 C 0 s pteVam1.scaffold_21855 9683 406 - 10445 GCGCCGGAGT-------GCGGAGCGAGAGGACGCAGGTCCCGGGAGACTGGATG--TCGCCACC-CC-----CTGGACAGCGCTGAAGAGGCCGGTGGGACAG-AGATCACATGCCG--A-GA--------AGCAGG-GG----AGCCAGGAGACCCCGGTTTCTCTCCTTTCTGTCC-------CAGCAGCGT----GACGAGGGCCCCAGGAG--------CTAAGGC-CGCTGAAT-----GA---AGGGGAAAGAGGCCAAGTGGGTGAGGAAGACAGAGGCACAGGGGTGAG-CGTGCAC-AGGGGTGCGAG-----GCGGG-GCGGGGACA-GCGGAGGGAGGCGGAGACAGCGgggggcggg--------gacagcggagggggcggggacagcggagggggcggggacagcggaggcggggccgggggagtggaggcggggccggggg---tggggccggATGACACTGGAGGCAGGG i pteVam1.scaffold_21855 N 0 I 3 s equCab2.chr12 28933303 390 + 33091231 ------GAGT-------GGGGAGCCAGACGAAGCAGGTCCAGAGGGAGCCGGGG--T--CCACCACC-----CTGGACAGCACTGCAGAGGTCGGTGGGACAGAAGGTCGCATCTCA--A-GG--------AGCAGA-TG----AGCCAGGAGGCCCTGGGGTCTCTCCTTGGGGCCC-------TCGAATTGG----GCAGGAAGACTGAGGTG--------CCCGTGTGAGCCGGGG-----AG---ATGCGGGAGGGGACAGGGGGCTGCAGGGACCAG-----CAGGAAGCAG-AGCGCAC-GGGCACTCGAGTCCCAGCGGG-AAGGCGCCC-TCGGCAGTC-GCTTTGGCTGTGGTGGGAGGA--------CGCGACGGA----GCCTGGGAGGCGGGCGGGACGGCCGCTGTGAAAACCGGG--GTGATGCTGGGCCCTGGCCCCGGGG---TGGCGGC----GAGGATGGTGAGAAGG i equCab2.chr12 I 330 C 0 e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=1053.000000 s hg19.chr11_gl000202_random 9036 67 + 40103 GAGCATTT---AGATTTAG------------------GAGGTTGAGTGC----C--CAGGGTGGGGG--TGTTGGGGG-ATGTGGCCCTGAAATGCC s papHam1.scaffold6638 70204 67 + 109049 GAGCATTT---AGATTTAG------------------GAGGTCGAGGGC----C--CAGGGCGGGGG--TGTTGGGGG-CTGTGGCCCTGGAATGCC i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128154213 54 - 133002572 GAGCATTT---A-------------------------------GAGGGC----C--CAGGGCGGGGG--TGTTGGGGG-TTGTGGCCCTGGAATGCC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125990465 67 - 132107971 GAGCATTT---AGATTTAG------------------GAGGTCGAGTGC----C--CAGGGTGGGGG--TGTTGGGGG-ATGTGGCCCTGAAATGCC i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68196501 67 + 134204764 AAGCATTT---AGATTCAG------------------GGGGTTGAGTGC----C--CAGGGTGGGGG--TGTTGGGGG-ATGTGGCCCTGAAATGCC i panTro2.chr11 C 0 C 0 s otoGar1.scaffold_5322.1-37474 33836 33 - 37474 AGACATTC---AGATTTAG------------------GAGGTCAAATAC----C--CAGG------------------------------------- i otoGar1.scaffold_5322.1-37474 C 0 C 0 s cavPor3.scaffold_42 9663577 63 + 15951348 GGACATTT---ACACTTAA------------------TAGAC--AGTGC----C--CAGGGTGGAGATTTGTGG-----AAGGGACCTTGGGGAGGC i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 23158 60 + 42081 GGGCCT-------------------------------GGGGT--AGCGCTGGAC--CAGGGCGGGTTCCTGCTGGAGACAAGGGACTTTCGGAAG-- i oryCun2.chrUn0985 C 0 C 0 s pteVam1.scaffold_21855 10092 58 - 10445 GGGGACTGCGGAGACTGGGCCAAGGCACAgcgaggacggggtcgggaac----agcggggac----------------------------------- i pteVam1.scaffold_21855 I 3 C 0 s equCab2.chr12 28933693 38 + 33091231 GGACGTTTTCAAGATTTGG------------------GAGGTCGAGTAT----G--GGGGAC----------------------------------- i equCab2.chr12 C 0 C 0 e calJac1.Contig6069 73691 5102 + 235769 I e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=7112.000000 s hg19.chr11_gl000202_random 9103 58 + 40103 AGCTGGTTTTGGCTCTGGGCCAGGCC-AGGGGCCGAG--G-GGGGTGGACCCAGGACAAGAG s panTro2.chr11 68196568 58 + 134204764 AGCTGGTTTTGGCTCTGGGCCAGGCC-AGGGGCTGAG--G-GGGATGGACCCAGGACAAGAG i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125990532 58 - 132107971 AGCTGGTTTTGGCTCTGGGCCAGGCC-AGGGGCCGAG--G-GGGGTGGACCCCGGACAAGAG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128154267 58 - 133002572 AGCTGGTTTTGGCTCTGGGCCAGGCC-AGGGGCCAAG--G-GGGGTGGACCCAGGACCAGAG i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 70271 58 + 109049 AGCTGGTTTTGGCTCTGGGCCAGGCC-AGGGGCCAAG--G-GGGGTGGACCCAGGACCAGAG i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 78793 61 + 235769 AGCTGGTTTTGGCTCTGAGCCAGGCCGGGGGGCCAAGCAG-GGGGTGCACCCAGGACAAGAG i calJac1.Contig6069 I 5102 C 0 s otoGar1.scaffold_5322.1-37474 33869 7 - 37474 ----------------------------------------------GGATCTG--------- i otoGar1.scaffold_5322.1-37474 C 0 C 0 s cavPor3.scaffold_42 9663640 38 + 15951348 -ACCACTTTCTACTCCAG---AAGCG-AGTGGCCA----GTGGGGTG--------------- i cavPor3.scaffold_42 C 0 I 392 s oryCun2.chrUn0985 23218 27 + 42081 -----------ATTTAGG---AGGTC-AGGGGCTC----G-GGGTTG--------------- i oryCun2.chrUn0985 C 0 C 0 s pteVam1.scaffold_21855 10150 31 - 10445 ----------------------------ggggccggg--g-gaggcggagacggggctgggg i pteVam1.scaffold_21855 C 0 N 0 s equCab2.chr12 28933731 3 + 33091231 ----------------------------GGG------------------------------- i equCab2.chr12 C 0 C 0 e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=83459.000000 s hg19.chr11_gl000202_random 9161 100 + 40103 TCCCATGCCCCACCTGGCATTCCTGCAGGGGGAGGCCAGGCAGAGAGGTACAGTTTTCTGGCTCCAGTGAA--GCGGGGGCCGGC--AGTGTCTTCTGCTGGGA s panTro2.chr11 68196626 100 + 134204764 TCCCATGCCCCACCTGGCTTTCCTGCAGGGGGAGTCCAGGCAGAGAGGCACAGTTTTCTGGCTCCAGTGAA--GCGGGGGCCGGC--AGTGTCTTCTGCTGGGA i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125990590 98 - 132107971 TCCCATGCCCCACCTGGGGTTCCTGCAGAGGGAGGCCAGGC--AGAGGCACGGTTTTCTGGCTCCAGTGAA--GCGGGGGCCGGC--AGTGTCTTCTGCTGGGA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128154325 92 - 133002572 CCCCATGCCCCACCTGGGGCTCCTGCAGGGGGAGGCCAGGC--------ACAGTTCTCTGGCTCCAGTGAA--GTGGGAGCTGGC--AGTGTCTTCTGCTGGGA i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 70329 98 + 109049 CCACATGCCCCTCCTGGGGTTCCTGCAGGGGGAGGCCAGGC--AGAGGCACAGTTCTCTGGCTCCAGTGAA--GTGGGAGCTGGC--AGTGTCTTCTGCTGGGA i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 78854 69 + 235769 CCCCATGGCCCACCTGGGGTTCCTGCAGGAGAAGGCCAGGC--AGAGGCACAGTTTGATGGCTCCAGTGAA--------------------------------- i calJac1.Contig6069 C 0 T 4670 s otoGar1.scaffold_5322.1-37474 33876 81 - 37474 ---------------GGGATTATTG--GGGGCAGTCCCGGC--AGAGGCATAGCTTTCTGCCTCTTGTGTGAAGGGGTGGCCAGT--GGTATCTTCCGCTAG-- i otoGar1.scaffold_5322.1-37474 C 0 C 0 s oryCun2.chrUn0985 23245 36 + 42081 ------------------------------------------GAAGGGGTTAGGTTTC---------------GCGGGGGTGG-----------TCAGCTGGGA i oryCun2.chrUn0985 C 0 C 0 s equCab2.chr12 28933734 78 + 33091231 ------------------ATTCATAGAGAAGGTGGG-------GGAGGCACAGCTTTCCAGA-CGAACGAAGAGAAGGGGTGGGCGGGGTGTCTCCTGCTGGGC i equCab2.chr12 C 0 C 0 e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9663678 392 + 15951348 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=54984.000000 s hg19.chr11_gl000202_random 9261 82 + 40103 TGCCATAGAGATGTAAACAGACAACTAACAAGATAATTAAGTAAAACGTGTGGCGATGACAACAAACAGGATATTCCATAAG s panTro2.chr11 68196726 82 + 134204764 TGCGATAGAGATGTAAACAGACAACTAACAAGATAATTAAGTAAAACGTGTGGCGATGACAACAAACAGGATATTCCATAAG i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125990688 82 - 132107971 CACAATAGAGATGTAAACAGACAACTAACAAGATAATTAAGTAAAATGTGTGGCGATGACAGCAAACAGGATGTTCCGTAAG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128154417 61 - 133002572 CACAACAGAGATGTAAACAGACAGCTAACAAGAGAATTAGGTAAAACGTGTGGCGATGACA--------------------- i rheMac2.chr14 C 0 M 1056 s papHam1.scaffold6638 70427 82 + 109049 AACAACAGAGATGTAAACACACAGCTAACAAGAGAATTAGGTAAAACGTGTGGCGATGACAGCAAACAGGATGTTGCATAAG i papHam1.scaffold6638 C 0 C 0 e calJac1.Contig6069 78923 4670 + 235769 T e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e oryCun2.chrUn0985 23281 0 + 42081 C e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9663678 392 + 15951348 I e otoGar1.scaffold_5322.1-37474 33957 0 - 37474 C e equCab2.chr12 28933812 0 + 33091231 C e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48969841 1185 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=133612.000000 s hg19.chr11_gl000202_random 9343 195 + 40103 GAATGGGGGCCTTGGGT--GAAGGTGGCCCAGAAGGCGAAG---TGGGTTTGGAGGGAGGGTGCTGG-TTCCGCTTTGGGAAGACACAGAACTCAGGTT-CCAGAG-GACACACAGGTGGGACCTCCCAGTGGGCAGTTAGACCAGCGGACCC-CAGCCGGGGGAGCGACCTTCACATCTGCTCTCCCTGCTGTGGCCCTGCTG s papHam1.scaffold6638 70509 195 + 109049 GAATGGGGGCCTTGGGT--GGAGGTGGCCCAGAAGGCGAAG---TGGGTTTGGAGGGAGGGTGCCGG-TTCCACTTTGGGCAGACACAGAACTCAGGTT-CCAGAG-GACACGCAGGCGGGACCTCCTAGTGGGCAGTTAGACCAGTGGACCC-AAGCTGGGGGAGCAACCTCCACATCTGCCCTCCCTGCTGTGGCCCTGCTG i papHam1.scaffold6638 C 0 I 11 s ponAbe2.chr11 125990770 195 - 132107971 GAATAGGGGCCTTGGGT--GAAGGTGGCCCAGAAGGCGAAG---TGGGTTTGGAGGGAGGGTGCTGG-TTCCGCTTTGGGAAGACACAGAACTCAGGTT-CCAGAG-GACACGCAGGCGGGACCTCCCAGTGAGCAGTTAGACCAGCGGACCC-AAGGCGGGGGAGCGACCTTCACATCTGCTCTCCCTGCTGTGGCCCTGCGG i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68196808 195 + 134204764 GAATGGGGGCCTTGGGT--GAAGGTGGCCCAGAAGGCGAAG---TGGGTTTGGAGGGAGGGTGCTGG-TTCCGCTTTGGGAAGACACAGAACTCAGGTT-CCAGAG-GACACACAGGCGGGACCTCCCAGTGGGCAGTTAGACCAGCGGACCC-CAGCCGGGGGAGCGACCTTCACATCTGCTCTCCCTGTTGTGGCCCTGCTG i panTro2.chr11 C 0 C 0 s bosTau4.chr29 48971026 167 + 51998940 GGACAGGGGTCTTCTGCTGGGAGGGGACCCGGAAG---AAG---TGGGTTTGGAGGCAGGTTGCTGGCTTCTGCTTTGCACGT-CCCAG---CCGGGTT-GGGGCA-GGCA-CCATGCGGAGGC-ACCAGTGGGCAGGTGGGT-AGTGGGCCC-AGAGCCAGGGAGG--CCTGAGTGTCTCCC-TC------------------ i bosTau4.chr29 I 1185 C 0 s otoGar1.scaffold_5322.1-37474 33957 158 - 37474 -------------------GAGGGCAGCCCA-------AAG---TGGCTTTGGAAGGAAGATGCTGG-GTGTGCCT--------------ACTTGGGTT-CCAGAGAGACAC-CAGGCGGAACAGGCCAGCGGGCAGTGAGATGAGCAGACCCTTAGCTGGGGAAGCGGCCTCAGTGTCTACCCTCCATGCAGTGGCCCTGCTG i otoGar1.scaffold_5322.1-37474 C 0 C 0 s oryCun2.chrUn0985 23281 111 + 42081 -----------------------GAGGCCCAGGAGATGCAGGTCTGGGT---GAGGGAGGGCCGCGG-GTCTGCTG--------------------------GGGG-GGCCCCCAGGT---------CACTGGG---------GAGCAGTCCC-TG--------------------AGCTGCCTCCCTGGCGGTGGCCTGGCCC i oryCun2.chrUn0985 C 0 C 0 s equCab2.chr12 28933812 151 + 33091231 ----------------------GGGGACCCGGAAG---AAG---CTGGTTTGGAGGAAGGGTGCCAGGTTCCACTTTGGAAGCGCCCAG---TTGGGTTCGGGGGA-GACACCCAGGCGGAGCCGGCCAGTGGGCAGTTAGATAAGTGGACCA-GAGGTGAGGGGGC--CCTGCATGTCCCCCTTC------------------ i equCab2.chr12 C 0 C 0 e calJac1.Contig6069 78923 4670 + 235769 T e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9663678 392 + 15951348 I e canFam2.chr18 7531516 1585 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e rheMac2.chr14 128154478 1056 - 133002572 M a score=-1608.000000 s hg19.chr11_gl000202_random 9538 44 + 40103 GGGCCACAGTGTGCACACTGCCATCTGCTGCCCACCTAACAGTG s ponAbe2.chr11 125990965 44 - 132107971 GGGCCACGGTGTGCACACTGCCATCTGCTGCCCACCTAACAGTG i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68197003 44 + 134204764 GGGCCACAGTGTGCACACTGCCATCTGCTGCCCACCTAACAGTG i panTro2.chr11 C 0 C 0 s otoGar1.scaffold_5322.1-37474 34115 6 - 37474 --GCCCCG------------------------------------ i otoGar1.scaffold_5322.1-37474 C 0 C 0 s oryCun2.chrUn0985 23392 19 + 42081 --GTCCCG---AGGACACCGCTAG-------------------- i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48971193 20 + 51998940 -----------------TTGCTGTCAGGCCTCCACCT------- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28933963 20 + 33091231 -----------------CTGCCATCAGGCCTCCACCT------- i equCab2.chr12 C 0 C 0 e papHam1.scaffold6638 70704 11 + 109049 I e calJac1.Contig6069 78923 4670 + 235769 T e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9663678 392 + 15951348 I e canFam2.chr18 7531516 1585 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e rheMac2.chr14 128154478 1056 - 133002572 M a score=769.000000 s hg19.chr11_gl000202_random 9582 57 + 40103 GCCACTGTTAGG---TGCCCACTCTGGCCC--TTC-CCCCTCATCCCCTACTATGTGGAGCCA s panTro2.chr11 68197047 57 + 134204764 GCCACTGTTAGG---TGCCCACTCTGGCCC--TTC-CCCCTCATCCCCTACTATGTGGAGCCA i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125991009 44 - 132107971 GCCACTGTTAGC---TGCCCACTCTGGGCCGGTTC-CCCCTCACCCCC--------------- i ponAbe2.chr11 C 0 I 546 s papHam1.scaffold6638 70715 57 + 109049 AACACTGTTAGG---GGCCCACTCTGGCCC--TTT-CCCCTCACCCCCCACTATGTGGAGCCA i papHam1.scaffold6638 I 11 C 0 s otoGar1.scaffold_5322.1-37474 34121 47 - 37474 GGTACTATTAG-----GCCACCTCTAACCC--TTC-TTCCTC--------CTGCATGAAGCCA i otoGar1.scaffold_5322.1-37474 C 0 C 0 s oryCun2.chrUn0985 23411 39 + 42081 GCCCCTGCTATGAACTTCCTGCTCCGGCAC--TT----------------------GGAGCCC i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48971213 29 + 51998940 -----------------------CTGACTC--TCC-TTTCCCGGCTCC-------TGGA-CTC i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28933983 31 + 33091231 -----------------------CCCAATC--TTCATCGCCTGGCACC-------TTGAGCCC i equCab2.chr12 C 0 C 0 e calJac1.Contig6069 78923 4670 + 235769 T e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9663678 392 + 15951348 I e canFam2.chr18 7531516 1585 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e rheMac2.chr14 128154478 1056 - 133002572 M a score=25474.000000 s hg19.chr11_gl000202_random 9639 56 + 40103 CATCGTCCCAGCCCCAGCACTGGCCCTGAGTCCCCTGGCCTTGGCCCAGCTGGCCT s equCab2.chr12 28934014 28 + 33091231 TGGCCTCTCAGCCCC-CCGCCAGC---------------------------GGCCT i equCab2.chr12 C 0 C 0 s bosTau4.chr29 48971242 29 + 51998940 TGTCCTGCCTGCCCCGCTGCCAAC---------------------------AGCCT i bosTau4.chr29 C 0 C 0 s oryCun2.chrUn0985 23450 55 + 42081 CGTCCccccagccccagctccagccc-gagcccccagcccACGGGCCAGCCTGCCT i oryCun2.chrUn0985 C 0 C 0 s otoGar1.scaffold_5322.1-37474 34168 30 - 37474 GGTCCTCCCAGTCCC--------------------------TGGGCCAGCTATCCT i otoGar1.scaffold_5322.1-37474 C 0 C 0 s panTro2.chr11 68197104 56 + 134204764 CGTCGTCCCAGCCCCAGCACTGGCCCTGAGTCCCCTGGTCTTGGCCCAGCTGGCCT i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125991599 44 - 132107971 CATCGTCCCAGCCCCAGCACTGGCCCTGAGCCCCCTGGC----------CTGGC-- i ponAbe2.chr11 I 546 C 0 s papHam1.scaffold6638 70772 56 + 109049 CATGGTCCCAGCCCCAGCACTGGCCCTGAAACCCCTGGCCGTGGCCCAGCCGGCCT i papHam1.scaffold6638 C 0 C 0 e calJac1.Contig6069 78923 4670 + 235769 T e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e dasNov2.scaffold_107233 6780 136 - 8172 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9663678 392 + 15951348 I e canFam2.chr18 7531516 1585 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e rheMac2.chr14 128154478 1056 - 133002572 M a score=34974.000000 s hg19.chr11_gl000202_random 9695 36 + 40103 GGC-TAGGACGCCATGTAGGGCAGTGTCTCCTGAGGA--- s papHam1.scaffold6638 70828 36 + 109049 GGC-TAGGACGCCATGTAGGGCAGTGgctcccgagga--- i papHam1.scaffold6638 C 0 C 0 s ponAbe2.chr11 125991643 34 - 132107971 --C-TAGGACGCCATGTAGGGCAATgtttcctgagga--- i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68197160 36 + 134204764 GGC-TAGGACGCCATGTAGGGCAGTGTCTCCTGAGGA--- i panTro2.chr11 C 0 C 0 s otoGar1.scaffold_5322.1-37474 34198 37 - 37474 GGCATGGGACCTTGTATGGGGCAGTGGCTCCTGAAAA--- i otoGar1.scaffold_5322.1-37474 C 0 I 2170 s oryCun2.chrUn0985 23505 36 + 42081 GAC-CCAGAGCCGGCGTGGGGCACGGACTCCCGAGGG--- i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48971271 27 + 51998940 TGC-TGGGACCCCATGGGGGG---------CTGACCA--- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28934042 33 + 33091231 GGC-TGGGACCCCGTGTGGGGCAGCGT---CTGAGCA--- i equCab2.chr12 C 0 C 0 s dasNov2.scaffold_107233 6916 38 - 8172 GGC-CAGGGCGTCA-GCAGGACCCTCGCCCCTCCCGGCCC i dasNov2.scaffold_107233 I 136 C 0 e calJac1.Contig6069 78923 4670 + 235769 T e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9663678 392 + 15951348 I e canFam2.chr18 7531516 1585 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e rheMac2.chr14 128154478 1056 - 133002572 M a score=128965.000000 s hg19.chr11_gl000202_random 9731 119 + 40103 CGGAACCTGC-------A-ct-tggtcaccctcagggatgcctggcacacagttggcgctcagtacatgtccgatgaatgaGAGCCGCTCCGTGGACATGCGGCAGAG---GCAGCACATACCGAGCCATC s papHam1.scaffold6638 70864 123 + 109049 cagaacctgc-------atct-tggtcaccctcagggatgcctggcacacagttggcactcagtacatgtccagtgaatgaGCGCCACTCGGTGGACGTGCAGCAGAGGCAGCAGCACGTACCAAGCCGTC i papHam1.scaffold6638 C 0 C 0 s ponAbe2.chr11 125991677 119 - 132107971 cggaacctgc-------a-ct-tggtcaccctcagagatgcctggcacacagttggtgctcagtacatgtccgatgaatgaGAGCCGCTCCGTGGACGTGCAGCAGAG---GCAGCACATACCGAGCCATC i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68197196 119 + 134204764 CGGAACCTGC-------A-CT-TGGTCACCCTCAGGGAtgcctggcacacagttggcgctcagtacatgtctgatgaatgaGAGCCGCTCCGTGGACATGCGGCAGAG---GCAGCACATACCGAGCCATC i panTro2.chr11 C 0 C 0 s oryCun2.chrUn0985 23541 105 + 42081 CAGGG-CTGC-------A-CTGTGGTTACCCCCAGGGATGGCTGGTTTACAGGTGGCGCCCAGTATGTGTCTGATGACGGAGGG---GTCTGTGGGA--------------GCAACCCCTGCCCAGGCCGC i oryCun2.chrUn0985 C 0 I 1 s bosTau4.chr29 48971298 120 + 51998940 CAGAGCCTGC-------ATCT-TGGACGCTCTCTGGGATGCTGGGCATACAACTGGTGCTCAATACGTGTCTAATGAAGGAGAGTCTAGCCACGGAGACCCAGTGGAC---ACAGCAAGCTTCTGGGCAGC i bosTau4.chr29 C 0 I 1 s equCab2.chr12 28934075 117 + 33091231 CAG-GCCTGC-------GCCT-CGGTCAATCTCCGGGTTGCCCAGCACACAGTCGGCACTCAGTACGTGCCTAATGAAGGAGAGCCTCCCCGTGGAGACCCGGTGG-----ACAGCACACTCCTGGGCCAG i equCab2.chr12 C 0 I 1 s dasNov2.scaffold_107233 6954 112 - 8172 CTGCACCCGCTGACCTGA-CT-GGGTCACGCTCAGGGA-GCTCAGCACACAGCTGGTGCTCAATAAGTGCCTGATGGAGGAGACCCG-TCCCTGGGGAGCCAGTGGGC---ACAGCCCA------------ i dasNov2.scaffold_107233 C 0 C 0 e calJac1.Contig6069 78923 4670 + 235769 T e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9663678 392 + 15951348 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I e canFam2.chr18 7531516 1585 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e rheMac2.chr14 128154478 1056 - 133002572 M a score=135116.000000 s hg19.chr11_gl000202_random 9850 103 + 40103 CCCTGGCTG--GAACAAG--GGCCCGGGTGGGGCGTGGATCA--CTTGCCCTGGTGTCCACCCGACTTGACCCCAGGCCTGGCCCAGAGCCAAAACCAGCTGGCATTCC s panTro2.chr11 68197315 103 + 134204764 CCCTGGCTG--GAACAAG--GGCCCAGGTGGGGCGTGGATCA--CTTGCCCTGGTGTCCACCCGACTTGACCCCAGGCCTGGCCCAGAGCCAAAACCAGCTGGCATTCC i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125991796 103 - 132107971 CCCTGGCTG--GAACAAG--GGCCCAGGTGGGGCCTGGAGTG--CTTGCCCTGGTGTCCACCCGACTTGACCCCTGGCCTGGCCCAGAGCCAAAACCAGCTGGCATTCC i ponAbe2.chr11 C 0 C 0 s papHam1.scaffold6638 70987 103 + 109049 CCCTGGCTG--GAACAAG--GGCCCAGGTGGGGCCTGGGGTG--CTTGCCCTGGTGTCCACCCGACTTGACCCCTGGCCTGGCCCAGAGTCAAAACCAGCTGGCATTCC i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 74253 103 + 235769 CCCTGACCG--GAATGAG--GGCCCGGGTGGGGTGTGGGGCA--CTTGCCCTGGTGTCCACATGACTTGGGCCCTGGCCTGGCCCAGAGCCAAAGCCAGCTGGCATTCC i calJac1.Contig6069 T 4670 C 0 s gorGor1.Supercontig_0015245 40612 78 + 115376 -----------------------------GGGGCGTGGATCA--CTTGCCCTGGTGTCCACCCAACTTGACCCCAGGCCTGGCCCAGAGCCAAAACCAGCTGGCATTNC i gorGor1.Supercontig_0015245 N 0 C 0 s oryCun2.chrUn0985 23647 99 + 42081 CTTTGGGCAGTGTGTGAG--AGCCTAGGTGGGGTGTGGCTCC-TCATGGCCTGGTGTCC------CTCACCCCCGGGCCTGGCCCAGAGCCAAACCCA-CTGGCCTTCC i oryCun2.chrUn0985 I 1 C 0 s bosTau4.chr29 48971419 80 + 51998940 TTCTGGCCA--GTGTAGACT---------------------------GGCCCGGTGTCCACTCCCTCACTCCTCTGGCCTGACTGAGAGCCAAGAACAGCTGCTGTTCC i bosTau4.chr29 I 1 I 187 s equCab2.chr12 28934193 107 + 33091231 TTCTGGCCA--GTCCGAGTTGGCCAGGGAGGGGCGTGTGGGGCTCTCGGCCTGGGGTCCACCCGCCCGTGCCTCTGGGCTGGCCCAGAGCCAAGAACAGCTGGTGCCCC i equCab2.chr12 I 1 I 7 s dasNov2.scaffold_107233 7066 34 - 8172 ------------------------CGGGGCAGGCATGGGGCC--GGCACGCCTGTGCCCA------------------------------------------------- i dasNov2.scaffold_107233 C 0 C 0 e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9663678 392 + 15951348 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I e canFam2.chr18 7531516 1585 - 58872314 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e rheMac2.chr14 128154478 1056 - 133002572 M a score=540223.000000 s hg19.chr11_gl000202_random 9953 397 + 40103 AGGGCCACAG-ACCCAAGACCCTAAAGTCCACCCT-GGTTGTCTCCATCAAGCATCTCCTGTTTGTCCAGAGCTGTGAG-CCCAGGGCAGGTGAAAGAGGCCGAGCCACAGCCCTGCCGTGGGCCCAGTCCGGTGCACGAGTGGGTCACGCAGCAGAGGGAGAACCGGATGTGGTCTCTAAATGGAGTTATGCGTTGAGGGACTCGGATGGCACCAAGGCACACGGGGGAGCCGGTGTGGACTCTAGAGCAGGGCGGTGCTG---TGCCGAGGAGGGTGCTGTGCTGGAGAGCAGCTCCCTGCCTCCCATGAT------------------GGAAACCGAGGCCGGGGCA-ATCCCAGAGGAGGCTGCTGCAGCATTA-G-GGGACCCGCTGTGG-----------CTCTCACCAACCCGGTGGCCCCCGGGAGG- s panTro2.chr11 68197418 397 + 134204764 AGGGCCACAG-ACCCAAGACCCTAAAGTCCACCCT-GGCTGTCTCCATCAAGCATCTCCTGTTTGTCCAGAGCTGTGAG-CCCAGGGCAGGTGAAAGAGGCCGAGCCACAGCCCTGCCGTGGGCCCAGGCTGGTGCACGAGTGGGTCACGCAGCAGAGGGAGAACCGGATGTGGTCTCTAAATGGAGTTATGCGTTGAGGGACTCGGATGGCACCAAGGCACACGGGGGAGCCGGTGTGGACTCTAGAGCAGGGCGGTGCTG---TGCCGAGGAGGGTGCTGTGCTGGAGAGCAGCTCCCTGCCTCCCATGAT------------------GGAAACCGAGGCCGGGGCA-ATCCCAGAGGAGGCTGCTGCAGCATTA-G-GGGACCCGCTGTGG-----------CTCTCACCAACCCGGTGGCCCCCGGGAGG- i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125991899 396 - 132107971 AGGGCCACAG-GCCCAAGACCCTAAAATCCACCCT-GGCCGTCTCCATCAAGCATCCCCTGTTTGTCCAGAGCTGTGAG-CCCAGGGCAGGTGAAAGAGGCCGAGCCACGGCCCTGCCCTGGGCCCAGGCCGGAGCATGAGTGGGTCGGGCAGCAGAGGGAGAACCGGATGTGGTCTCTAAATGGAGTTATGCGTTGAGGGACTCGGATGGCACCAAGGCACACAGGGGAGCCGGTGTGGACTCTAGAGCAGGGCAGTGCTA---TGCCGAGGAGGATGCTGTGCTGGAGAGCAGCTCCCTGCCTCCCATGAT------------------GGAAACCAAGTCTGGGGCA-ATCCCAGAGGAGGCTGCTGCAGCATTA-G-GGGACCCGCTGTGG-----------CTCTCCCCAACCCCGTGG-TCCGGGGAGG- i ponAbe2.chr11 C 0 C 0 s papHam1.scaffold6638 71090 395 + 109049 AGGGCCACAG-ACCCAAGACCCTGAAGTCCACCCT-GGCCGTCTCCATCAAGCATCTCCTGTTTGTCCAGAGCTGTGAG-CCCAGGGCAGGTGAAGGAGGCCAAGCCACAGCCCTGCCCTGGGCCCAGGCTGGAGCACGAGCGGGGTGGGCAGCAGAGGGAGAAACAGATGTGGTCTCTAAATGGAGTTGTGCACTGAGGAACTTGGATGGCACCAAGGTGCCC-GGGGAGCCGGTGTGGACTCTAGAACAGGGCAGTGCCA---TGCCAAGGAGGGTGCTGTGCTGAAGAGCAGCTCCCTGCCTCCCATGAG------------------GGAAACTGAGGCCGGGGCA-ATCCCAGAGGAGGTTGCTGCAGCATTA-G-GGGACCGGCTGTGA-----------CTCTTACCAACCCTGTGG-CCCAGGGAGG- i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 74356 380 + 235769 AGGGCCACAGCCCCCAAGACTCTCAAGTCCACCCT-GGCGGTCTCCATTAAGCGTGTCCTGTTTCTCCAGAGCTGTGAG-CCCAGGGCAGG-GACAGAGGTGGAG--ACAGCCCTGTCCTGGGCCCAGGCCGGAGCACAAGCTGGTTGGGCAGCTGAGGGAGGGCCTGATGTGGTGTCTAAATGGATTTGTGCGTGGAGGGACTCGG-TGGCACCAAGGCGCACGGAGGAGCCAGTGTGGACTCTGGGGCCGGGCAGTGCC---------------GCGCTGTGCTGGGGAGCAGCTCCC-GCCTCCTGTGAT------------------GGCAGCCGAGGCCGGGGCA-ATCCCAGAGGAGGCGGCTACAGCGTTA-G-GAGGCCAGATGCGG-----------CCCTTGCCAGCCCTGTGA-CCCCAAGCAC- i calJac1.Contig6069 C 0 C 0 s gorGor1.Supercontig_0015245 40690 397 + 115376 AGGGCCACAG-ACCCAAGACCCTAAAGTCCACCCT-GGCCGTCTCCATCAAGCATCTCCTGTTTGTCCAGAGCTGTGAG-CCCAGGGCAGGTGAAAGAGGCAGAGCCACAGCCCTGCCGTGAGCCCAGGCCGGTGCACGAGTGGGTCACGCAGCAGAGGGAGAACCGGATGTGGTCTCTAAATGGAGTTATGCGTTGAGGGACTTGGATGGCACCAAGGCACACAGGGGAGCCGGTGTGGACTCTAGAGCAGGGCAGTGCTG---TGCCGAGGAGGGTGCTGTGCTGGAGAGCAGCTCCCTGCCTCCCACGAT------------------GGAAACTGAGGCCGGGGCA-ATCCCAGAGGAGGCTGCTGCACCATTA-G-GGGACCCGCTGTGG-----------CTCTCACCAACCCGGTGGCCCCCGGGAGG- i gorGor1.Supercontig_0015245 C 0 C 0 s oryCun2.chrUn0985 23746 260 + 42081 AGGTCAGC-G-CCCCAGAACCCC--AGTCCA---------GCCTCTGGCGCGATGCCCCCGTGTGTCCTGTGCCAGGCG-CCTGGGGCAGGTGAGGTAGA-GGAGCCCCAGGCCCTGCCCGGGCCCAGGC--------------------------AGGGAG--------------------CGGGGCTAGGCGT---GGGGCTCCAGTGGCGCCCAGGGCCGCAGGGAGTCAGCAGCACAC------ACAGGGCA---------------------------GACAGGGGACA-------------------------------------GGGAGCCGAG-CCAGGACA-TCCT------------------------G-AGGCACTGCTGGGC-----------CTCTCGCTGACCCCATGG---CCTGGTGG- i oryCun2.chrUn0985 C 0 C 0 s equCab2.chr12 28934307 316 + 33091231 GGGGTCGCTG-CCCCGAGACCCCAAAACCCG-GCT-GGCTGCCTGCATGGAGCACCTCTTGTCTGTTGGGCGCCGTGAG-TCCAGGTCCAG-GACAGACGCTGCA-------CCTGCACGTGGC-----------------------------------------------------------------GTGTTTTGAGGGACTCAGATCACTCCAGGGC-CAT-GGGGAGCCAGTGTGGACTCTAGAGCAGGGTGGTGCCACCCTACAGAGTAGGGGACTG-GCTGGAGGGCAGCTCCATGCCTCCCGGAAC-----------------AGGACACCAAGGCCAGG-CA-GTCCCAGCGG-GGAGGCTGGGGCATTA-GAGAAATCTGGAGGGA------------------GGACTCTGCTGTGCCCGGGAGG- i equCab2.chr12 I 7 I 1 s dasNov2.scaffold_107233 7100 406 - 8172 --GGCCACCG-CCCCAAGACCCCCAAATCCCCCCCGGGCCGCCTTCAGCGCGTCTCTCCTGTTCGTCCAGTGCTACGAATTCTGGGGCAGGTGGAAGAGATGGAGCCCCTGCCCTGCCCTGGGA-------GGGGGACGCGCTTGTCAC--------GGGAGGCCCCGACGCAGCCTCTAAATGGAGCTGT-TGACCAGGGACTCAGGCGGCACCCGTGGGCACATGGGAGCCACTGCGGGCTCTCGAGCGGGGTAGTGCTA---CATCGAG------GCCTTGCCAGAGGGCAGCCCCACGATGCCTGCGACACGGGTGGGGTCTGCCCAGGAAACCGAGGCCAGGGCAGATCCCGGGGGAGGCGGCTGTGACGCCACG-GAGACCTGGAGGGAGAAGCCAGCTCGTCGTGTCCGCTCCCCGA-GCCCGGAAGGG i dasNov2.scaffold_107233 C 0 C 0 e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9663678 392 + 15951348 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48971499 187 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e rheMac2.chr14 128154478 1056 - 133002572 M a score=32757.000000 s hg19.chr11_gl000202_random 10350 47 + 40103 ACTCTGGCCTCCGGGCAGGGCT-TGTGAGGAGTGAG------AAGACGGGGTGC s panTro2.chr11 68197815 47 + 134204764 ACTCTGGCCTCCGGGCAGGGCT-TGTGAGGAGTGAG------AAGACGGGGTGC i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125992295 47 - 132107971 ACTCT-GCCTCCGGGCAGGGCTGGGTGAGGAGTGAG------AAGACGGGGTGC i ponAbe2.chr11 C 0 C 0 s papHam1.scaffold6638 71485 48 + 109049 ACTCTGGCCTCCGGGCAGGGCTGGGTAAGGAGTGAG------AAGATGGGGTGC i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 74736 46 + 235769 ACTCTGGCCTCT-GGCAGGGCTGGGTGAGGAGCGAG------GAGATGGTGTG- i calJac1.Contig6069 C 0 C 0 s gorGor1.Supercontig_0015245 41087 47 + 115376 ACTCTGGCCTCCGGGCAGGGCT-TGTGAGGAGTGAG------AAGACGGGGTGC i gorGor1.Supercontig_0015245 C 0 C 0 s oryCun2.chrUn0985 24006 21 + 42081 GCTCTGG---------AGGACT------------------------CCGTGTGC i oryCun2.chrUn0985 C 0 C 0 s equCab2.chr12 28934624 53 + 33091231 ACAGTGGCC-CCAGGCAGGGCTGGGTGGGGACTGAGCAAGACGGGCCTGAGGAA i equCab2.chr12 I 1 C 0 s felCat3.scaffold_135390 54509 18 + 302526 ------------------------------ACTGTG------GAGCCCGGGGAG i felCat3.scaffold_135390 N 0 C 0 s dasNov2.scaffold_107233 7506 47 - 8172 -----ACCCTCTGCGCGGGGCTGGGCGAGGGGGGCGCGAGACAAGCGTGAGC-- i dasNov2.scaffold_107233 C 0 C 0 e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e cavPor3.scaffold_42 9663678 392 + 15951348 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48971499 187 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e rheMac2.chr14 128154478 1056 - 133002572 M a score=18633.000000 s hg19.chr11_gl000202_random 10397 25 + 40103 ACACTGCCA----------TCTGCTGCC------CATGCAA----------------- s panTro2.chr11 68197862 25 + 134204764 ACACTGCCA----------TCTGCTGCC------CATGCAA----------------- i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125992342 25 - 132107971 ACACTGCCA----------TCTGCTGCC------CACGCAA----------------- i ponAbe2.chr11 C 0 C 0 s papHam1.scaffold6638 71533 25 + 109049 ACACTGCCA----------TCTGCTGCC------CACGCAG----------------- i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 74782 25 + 235769 ACACTGCCC----------TCTGCTGCC------CACACTA----------------- i calJac1.Contig6069 C 0 C 0 s gorGor1.Supercontig_0015245 41134 25 + 115376 ACACTGCCA----------TCTGCTGCC------CACGCAA----------------- i gorGor1.Supercontig_0015245 C 0 C 0 s cavPor3.scaffold_42 9664070 31 + 15951348 ATACTGCCAGCTGTG----CCTGCTGCC------CACACAG----------------- i cavPor3.scaffold_42 I 392 I 1 s oryCun2.chrUn0985 24027 24 + 42081 ----------CTGTGGACACTTGCTGCC------TGGA-GC----------------- i oryCun2.chrUn0985 C 0 I 1 s equCab2.chr12 28934677 25 + 33091231 AGTCTGCGA----------CCAGAGGCC------CCCAGGG----------------- i equCab2.chr12 C 0 I 1 s felCat3.scaffold_135390 54527 30 + 302526 AGTCTGTGA----------AC-GAGGTCGGATGTCCCACGG----------------- i felCat3.scaffold_135390 C 0 I 1 s dasNov2.scaffold_107233 7553 37 - 8172 -----TTCA----------TCTGCTGCC------CGCACAGGACGCTCACCCCACAGA i dasNov2.scaffold_107233 C 0 C 0 e micMur1.scaffold_17226 11486 1640 + 15119 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48971499 187 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I e rheMac2.chr14 128154478 1056 - 133002572 M a score=287265.000000 s hg19.chr11_gl000202_random 10422 107 + 40103 TGGGGCGCACACTCCCAGG--CA----CCACGT-GGTAG-----GACCT-GATTCGGATGCAGCTCCTGGGTT--CACAAAC-TTTGAATTTGGGCT------CTGGGAGGAGGTGACTGCTCC------------CTTCC s micMur1.scaffold_17226 13126 102 + 15119 ---GGCGCTCTCCCTCGCA--CC----CCACCA-GGCAG-----GGCCC-ACTTC-GCTGCAGCT-CTGGGTC--TGAGAAC-TTTGAATTTGGGCC------CAGGGAGGAGGTGGCCACCTC------------CTTCT i micMur1.scaffold_17226 I 1640 C 0 s panTro2.chr11 68197887 107 + 134204764 TGGGGCGCACACTCCCAGG--CA----CCACGT-GGTAG-----GACCT-GATTCGGATGCAGCTCCTGGGTT--CACAAAC-TTTGAATTTGGGCC------CTGGGAGGAGGTGACTGCTCC------------CTTCC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 41159 107 + 115376 TGGGGCGCACACTCCCAGG--CA----CCACGT-GGTAG-----GACCT-GATTCGGATGCAGCTCCTGGGTT--CACAAAC-TTTGAATTTGGGCC------CTGGGAGGAGGTGACTGCTCC------------CTTCC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125992367 107 - 132107971 TGGGGTGCACACTCCCAGG--CA----CCACGT-GGTAG-----GACCT-GCTTCAGACGCAGCTCCTGGCTT--CACAAAC-TTTGACTTTGGGCC------CTGGGAGGAGGTGACTGCTCC------------CTTCC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128155538 107 - 133002572 TGGGGCGTGCACTCCCAGG--CG----CCACGT-GGTAG-----GACCT-GCTTTGGATGCAGCTCCTGGGTT--CACAAAC-TTTGAATTTGGGAC------CCGGGAGGAGGTGACTGCTCC------------CTTCC i rheMac2.chr14 M 1056 C 0 s papHam1.scaffold6638 71558 107 + 109049 TGGGGCGTGCACTCCCAGG--CG----CCACGT-GGTAG-----GACCT-GCTTTGGATGCAGCTCCTGGGTT--CACAAAC-TTTGATTTTGGGAC------CCGGGAGGAGGTGACTGCTCC------------CTTCC i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 74807 107 + 235769 TGGGGCACTCACTCCCATG--TG----CCACGT-GGTAG-----GACCT-GCTTCTCTCTCAGCTCCTGAGTT--CACAGAC-CTTGAATTTAGGCC------CTGGGAGGAGGCGACTGCTCC------------CTTCC i calJac1.Contig6069 C 0 C 0 s cavPor3.scaffold_42 9664102 101 + 15951348 CTGGGAGCTCACTCCCACA--CG----CTGTGG-CCCGGGCTTGGCCCT-GCTGGGGCTAACGGA-CAG-GCT--CAT-TAG-TGCAAAT--------------AGGGGTGAAGTGATTGCCCC------------CTTCA i cavPor3.scaffold_42 I 1 C 0 s oryCun2.chrUn0985 24052 106 + 42081 CGGGGAGCTCACGCCCACACCCG----CCACCA-GCCGG----AGCCTG-GCTTGCGCTGCAGCC-CTGTGCT--CAT-GAC-CTTGGATCTGGG-C------CCGGGGGGAAGTG-CTGCCTC------------CTTCC i oryCun2.chrUn0985 I 1 C 0 s equCab2.chr12 28934703 108 + 33091231 CAGGGAGCTCACTCCCACG--CA----CGGTACACGTAG-----GACCC-CTATCTGCGGCAGCTCCTGGGTT--CGCACAC-TTTGAAGTTGGCCC------CAGGGAGGAGGCGACTGTCTC------------CCTCG i equCab2.chr12 I 1 I 16 s felCat3.scaffold_135390 54558 121 + 302526 CAGGGAGCTCACTCCCATG--CATGGCCGGTGCAGGCAG-----GACCCGGCATTGGCAGCAGTCCCTGGGTTGACTCGCAC-TTTGAAATCGGCCCTGGGGGCGGGGGGGAGCTGACCGCCTC------------CCTCA i felCat3.scaffold_135390 I 1 I 16 s dasNov2.scaffold_107233 7590 119 - 8172 CGGGGAGCTCACCCCCTcg--cc----ccgcgg-cacgc-----ctccc-gcccccgc-gcggcacccgggct--cccgcgcAGCTGCACTTGGCCC------GGGGGAGGAGGCGACTGCGCCGATTCAGCATCACTTCT i dasNov2.scaffold_107233 C 0 C 0 e myoLuc1.scaffold_155660 32988 335 - 124081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48971499 187 + 51998940 I e tupBel1.scaffold_80971.1-5047 971 57 + 5047 I a score=195504.000000 s hg19.chr11_gl000202_random 10529 79 + 40103 CTTAGTGATAACAA-CTTCCAG----------------------GG-CCCTGCTGGGTGGCCCCTTCGGCTGGTGGGCT----CAAGGGAC--TGCAGGG---AGTG----G------GTGG s calJac1.Contig6069 74914 79 + 235769 CTTAGTGATGACAA-ACACCAG----------------------GGCCCCCGCTATGTAGCCCCTTCAGCTGGTGGGTT----CAAAGGGC--TGCAGGG---AGCG----G------GT-G i calJac1.Contig6069 C 0 C 0 s papHam1.scaffold6638 71665 71 + 109049 CTCAGTGATGACAA-CCACCAG----------------------GG-CCCCGCTGGGTGGCCCCTTCGGCTGGTG------------GGAC--TGCAGGG---AATG----G------GTGG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128155645 71 - 133002572 CTCAGTGATGACAA-CCACCAG----------------------GG-CTCCGCTGGGTGGCCCCTTCGGCTGGTG------------GGAC--TGCAGGG---AATG----G------GTGG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125992474 79 - 132107971 CTTAGTGATAACAA-CCATCAG----------------------GG-CCCTGCTGGGTGGCCTCTTCGGCTGGTGGGCT----CAAAGGAC--TGCAGGG---AGCA----G------GTGG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 41266 79 + 115376 CTTAGTGATAACAA-CCTCCAG----------------------GG-CCCTGCTGGGTGGCCCCTTCGGCTGGTGGGCT----CAAGGGAC--TGCAGGG---AGCG----G------GTGG i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68197994 79 + 134204764 CTTAGTGATAACAA-CTTCCAG----------------------GG-CCCTGCTGGGTGGCCCCTTCGGCTGGTGGGCT----CAAGGGAC--TGCAGGG---AGCG----G------GTGG i panTro2.chr11 C 0 C 0 s micMur1.scaffold_17226 13228 83 + 15119 GCCAGCGATGACAG-CCGCCAG----------------------AG-CCCCGCTGGGTGGCCCCTTTGGCTGGTGGGCT----CCAGGAGC--CGTAGGA---AGTGGGCAG------GTGG i micMur1.scaffold_17226 C 0 C 0 s tupBel1.scaffold_50294.1-1651 250 74 - 1651 CTTAGGGATGACAG-CCACCAG----------------------GG-CCCAGGTGGGTAGCCTGTCTGGCTGGTG-GCT----CA--GAGC--TATGGGA---AGTG------------CTG i tupBel1.scaffold_50294.1-1651 n 57 C 0 s cavPor3.scaffold_42 9664203 65 + 15951348 ATC-------ACA--------G----------------------GG-CTCTGCTGGGTGGCCCCTCTGCCCGGGGGGCT----CGAGGAAC--CATAGGA---AGTG----G------GTGG i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 24158 62 + 42081 CTCTGCGGGGACAA-TGGCGGG----------------------GG-TCCTGCTGGGTGGTCCGCTCGCCAGGTGGG--------------------------GGCG----G------GCAG i oryCun2.chrUn0985 C 0 C 0 s equCab2.chr12 28934827 107 + 33091231 GTTAGTGAAGACAA-GCACCAGGGAGCTGAGGAGGGTCCCGCTGGG-CC-CGCTGGGTGGCCCCTGC--CTGGTGGGCC----CAAGGAGC--CGGCGGGCCCAGCG----TGATGCTGCAG i equCab2.chr12 I 16 C 0 s felCat3.scaffold_135390 54695 112 + 302526 GTTAGTGATGGTAA-CCACCAGGTGGCTGAGAAAGGTCGTGCTCGG-CCTTGCTGGGCGGCCCCTCCAGCCAGTGGGCC----CGAGGAGCTGCACTTGGCCTAACA----GAGCTTCACAG i felCat3.scaffold_135390 I 16 C 0 s dasNov2.scaffold_107233 7709 106 - 8172 GTCGGCGGGGACGGTTCCCCAGAGGAGAGGCAAGGGTCGTGCGCGG-CCCCACCGTGCGGCCCCTCGGGCTGGTGAGCTGGGGCGGGAGGC--GGCGGGA---AGGG----G------CCGG i dasNov2.scaffold_107233 C 0 I 9 e myoLuc1.scaffold_155660 32988 335 - 124081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 79700 1407 + 1045236 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48971499 187 + 51998940 I a score=425424.000000 s hg19.chr11_gl000202_random 10608 157 + 40103 GCCACCGGCCATCTTGCTGCCAGCTGGGCCCTGCTCCTGCCCTCACAGAAGCCCCAAGTCACACCTTTC---------------GGGGTGAGAT-CCCAGATCCTGCATCTCGGGGCTAGAA---------AGG----GACCCCTCTAAGAAACCCAGCAG---------G--------TCCCTGGGACTCC-----------ACCCCAACCT------------C------------ s calJac1.Contig6069 74993 161 + 235769 GCCACTGGTCATCTGGCTGCCAGCTGGGTGCTGCTCCTGCCCCCATGGAGGCCCCAAGTCACACCTTCC---------------AGGGTGAGAT-CCCAGAACCTGCGTCTCAGGGCTAGAA---------AGGGAGAGACCCCTCTAAGAAACCCAGCAT---------G--------TCTCTGGGACTCC-----------ACCCCAGCCT------------C------------ i calJac1.Contig6069 C 0 I 1656 s papHam1.scaffold6638 71736 157 + 109049 GCCACTGGCCGTCTTGCTGCCAGCTGGGCCCTGCTCCTGCCCCCATGGAAACCCCAAGTCACACCTTTC---------------AGGGTCAGAT-CCCAGATCCTGCATCTCGGGGCTAGAA---------AGG----GACCCCTCCAAGAAACCCAGCAT---------G--------TCCCTGGGACTCC-----------ACCCCAACCT------------C------------ i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128155716 157 - 133002572 GCCACTGGCCGTCTTGCTGCCAGCTGGGCCCTGCTCCTGCCCCCATGGAAACCCCAAGTCACACCTTTC---------------AGGGTCAGAT-CCCAGATCCTGCATCTCGGGGCTAGAA---------AGG----GACCCCTCCAAGAAACCCAGCAT---------G--------TCCCTGGGACTCC-----------ACCCCAACCT------------C------------ i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125992553 157 - 132107971 GCCACCGGCCATCTTGCTGCCAGCTGGGCCCTGCTCCTGCCCCCACAGAAGCCCCAAGTCACACCTTTC---------------AGGGTGAGAT-CCCAGATCCTGCATCTCGGGGCTAGAA---------AGG----GACCGCTCTAAGAAACCCAGCAG---------G--------TCCCTGGGACTCC-----------ACCCCAACTT------------C------------ i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 41345 157 + 115376 GCCACCGGCCATCTTGCTGCCAGCTGGGCCCTGCTCCTGCCCCCACAGAAGCCCCAGGTCACACCTTTC---------------GGGGTGATAT-CCCAGATCCTGCATCTCGGGGCTAGAA---------AGG----GACCCCTCTAAGAAACCCAGCAG---------G--------TCCCTGGGACTCC-----------ACCCCAACCT------------C------------ i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68198073 157 + 134204764 GCCACCGGCCATCTTGCTGCCAGCTGGGCCCTGCTCCTGCCCCCACAGAAGCTCCAAGTCACACCTTTC---------------GGGGTGAGAT-CCCAGATCCTGCATCTCGGGGCTAGAA---------AGG----GACCCCTCTAAGAAACCCAGCAG---------G--------TCCCTGGGACTCC-----------ACCCCAACCT------------C------------ i panTro2.chr11 C 0 C 0 s micMur1.scaffold_17226 13311 166 + 15119 GCTAC-----------CTGCCATCTGGACCCGGTTCCTGCCACCACC-AGGCCCCAGCTCACAGCTTTCCAAATGAG-CCTTT-GAGGTGCGAT-TCCGGGTCCAGCGTCGCAGGGTT-GAC---------AGG----GGCCTCTCTAACGCACCCAGGATGTCCCCAGCG--------TCCCTGGGACCCT-----------GCTGCAACCT------------C------------ i micMur1.scaffold_17226 C 0 C 0 s tupBel1.scaffold_50294.1-1651 324 161 - 1651 GACCCCAACCATTGGGCCCGCAGCTGTGCCCTGCTCCTGCCGTCACTGAGGCCCCAAGTCACGCCTTTT---CCAAGCCCTCT-GGGATAAGGC-CCCAGATCCAGCGTCACTGGGCTGGGAGTGAGGGGCAGG----GAC----------AGCCCACCAA---------C--------TCCCCAGG----------------GACCAGACCT------------------------- i tupBel1.scaffold_50294.1-1651 C 0 C 0 s cavPor3.scaffold_42 9664268 187 + 15951348 GCT-CTGAGCATCTGGCTGCCAGCTGGGCCCTGCT-GTGCCACCACCGAGGTCCCGAGTCACACCTTTTCAAATGAGCCTTT--TGGGAGGGAT-CCCAGATTCAGCATCGCCAGGCTAGCCA--------AGG----GGCCCCTTTAAC-TAACCAGCGT---------GCCCCAAGGTCTCTGGGACCCCTCTCCCCGACTCCCCAAACCT------------C------------ i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 24220 104 + 42081 GC-------CATCTGGCTGCCAGCTGGGC-----------------------CCCAAGTCACAC---TTTGCACGCAGCCTT--TGGGTGAGAT-CCCAG-CCCAGGGCCTCCAGGCCA--------------G----GGCCCCCTCA----GACCCGCAC---------G------------------------------------------------------C------------ i oryCun2.chrUn0985 C 0 C 0 s equCab2.chr12 28934934 173 + 33091231 CCCCCCCACCATCTGGCTCCCAGCTGGGCCCTGGTTCTGCCACCGTTGAGGCCCCAAGTCACACC-TTCCACATGAGGCTTTG-GGGGAGAA----CCAGATCCAGCTTCAC-GGGCTAGAA---------AGG----GAC-CCTCTAACTGACCCAGGAT---------G--------TCCCCAGGGCCTCTGGGACCT---CCCCCGACCT------------C------------ i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 54807 186 + 302526 GCCCCGAGCA--CTGGCTCCCAGCTGGGCCCCGCTTCCCCCACCGCTGAGGCCCCAGGTCACACCTTTCCAAGTGAGCCTTTGAGGGGACGA----CCAGATCCCGCTGCAC-TGGCCAGAA---------AGG----GACACTTCTAACTGACCTAAGAT---------C--------TCCACAGGGCCTCTGAGACAC---CCCCTGCCCCAGCCCGCCCCAAC------------ i felCat3.scaffold_135390 C 0 C 0 s loxAfr3.scaffold_159 81107 178 + 1045236 GCAAACAACCATCTGGCTCCCAGCTGGGCCCTGCTTTCACCACCCCCAAGGCT---GACCAGGCCCTTT---------------GGGGTAAGAATCCCATAGCTCAGGTCATTGGGCTTGAA---------AGA----GAC-CCTCTAACCCACCCAGGATGTCCACAGAG--------CCTCCGGGACCCCCCA--------CCCCCACCCC------------TGCTGCCAACCTC i loxAfr3.scaffold_159 I 1407 C 0 s dasNov2.scaffold_107233 7824 139 - 8172 GTCTGCGGCCATCTGGTCCCCAGATGGGCCC--CTTCCCCCACCCCGA------------------------------------GGGGGGAGAG-CCCAGACCCCGGGCC-CCGGGCTTGAG---------AGG----GGC-CCGCCGGCTGATCTGGGGCATC------G--------CCGCCGG--CCTCCAG--------ACCCCACTCC------------CAC---------C i dasNov2.scaffold_107233 I 9 C 0 e myoLuc1.scaffold_155660 32988 335 - 124081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48971499 187 + 51998940 I a score=80321.000000 s hg19.chr11_gl000202_random 10765 63 + 40103 TTGCTT-CCTGCCAGGAGGTA---AAC-CTCA--GGCTTTCCTATCCCCAATGTCTGGATA---------AGGAAACAA s papHam1.scaffold6638 71893 63 + 109049 TTGTTT-CCTGCCAGGAGGTA---AAC-ACCA--GACTTCCCTATCCCCAGTGTCCGGATA---------AGGAAACAG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128155873 63 - 133002572 TTGTTT-CCTGCCAGGAGGTA---AAC-ACCA--GACTTCCCTATCCCCAGTGTCCGGATA---------AGGAAACAG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125992710 63 - 132107971 TTGTTT-CCTGCCCGGAGGTA---AAC-CCCA--GGCTTTCCTATCCCCAATGTCTGGATA---------AGGAAACAG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 41502 63 + 115376 TTGCTT-CCTGCCAGGAGGTA---AAC-CTCA--GGCTTTCCTATCCCCAATGTCTGGATA---------AGGAAACAA i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68198230 63 + 134204764 TTGCTT-CCTGCCAGGAGGTA---AAC-CTCA--GGCTTTCCTATCCCCAATGTCTGGATA---------AGGAAACAA i panTro2.chr11 C 0 C 0 s micMur1.scaffold_17226 13477 62 + 15119 TCATGT-CCCGCCAGgaggta---gac-agagc-agctttcctgtccccgtcacacagacg---------aatgaac-- i micMur1.scaffold_17226 C 0 C 0 s tupBel1.scaffold_50294.1-1651 485 66 - 1651 GCGCTG-TGAGCAGGGGAGGG---AGT-ATGG--AGC---CCCGTCCCCAG---GCAGGTACTGCCCCCTGGAGGCCAG i tupBel1.scaffold_50294.1-1651 C 0 C 0 s cavPor3.scaffold_42 9664455 42 + 15951348 TTACGT-CCTGCCAGGAGGCC---ACAAACCA--AGCTTCCCCGTCTC------------------------------- i cavPor3.scaffold_42 C 0 I 578 s oryCun2.chrUn0985 24324 24 + 42081 TTGTGTGCCGGCTGCGGGGGG---ACG---------------------------------------------------- i oryCun2.chrUn0985 C 0 C 0 s equCab2.chr12 28935107 63 + 33091231 TTGTTT-CCTGCCCGgaggca---ggc-agaatgggccctcttggccccattgtatagatg---------aggaaac-- i equCab2.chr12 C 0 I 6 s felCat3.scaffold_135390 54993 62 + 302526 CCGTTT-CCTGCCAGgaggcc---gac-agaacagatgctc-tggccccattgtatagatg---------aggaaac-- i felCat3.scaffold_135390 C 0 I 4 s loxAfr3.scaffold_159 81285 66 + 1045236 TTGTTT-CCTGCCAGgaggtagatggg-ggca--gacttttttagccctgttgtacagatg---------gggaaacaa i loxAfr3.scaffold_159 C 0 I 37 s dasNov2.scaffold_107233 7963 55 - 8172 CAGATT-CCCGCCaga--------gag-agcc--ggcattcgactccccg-tgtacaggtg---------aggaaac-- i dasNov2.scaffold_107233 C 0 N 0 e calJac1.Contig6069 75154 1656 + 235769 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48971499 187 + 51998940 I a score=18943.000000 s hg19.chr11_gl000202_random 10828 42 + 40103 TCTCAGCTATCTT--GTTAGTTGTCTATTTACATCTCTGTTATG s papHam1.scaffold6638 71956 42 + 109049 TCTCAACTATCTT--GTTAGTTGTCTACTTACATCTCTGTTGTG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128155936 42 - 133002572 TCTCAACTATCTT--GTTAGTTGTCTACTTACATCTCTGTTGTG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125992773 42 - 132107971 TCTCAACTATCTT--GTTAGTTGTCTATTTACATCTCTGTTGTG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 41565 42 + 115376 TCTCAGCTATCTT--GTTAGTTGTCTATTTACATCTCTGTTATG i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68198293 42 + 134204764 TCTCAGCTATCTT--GTTAGTTGTCTATTTAAGTCTCTGTTATG i panTro2.chr11 C 0 C 0 s micMur1.scaffold_17226 13539 4 + 15119 ----------------------------------------cgag i micMur1.scaffold_17226 C 0 I 12 s tupBel1.scaffold_50294.1-1651 551 44 - 1651 TCCCAGAAACCACAGGGTGAGCATCCAGGTGCAGCTTGGGCAGG i tupBel1.scaffold_50294.1-1651 C 0 I 21 s oryCun2.chrUn0985 24348 14 + 42081 -----------------------------CACAGCTCGCCTGT- i oryCun2.chrUn0985 C 0 C 0 s felCat3.scaffold_135390 55059 6 + 302526 gctcag-------------------------------------- i felCat3.scaffold_135390 I 4 C 0 e calJac1.Contig6069 75154 1656 + 235769 I e myoLuc1.scaffold_155660 32988 335 - 124081 I e proCap1.scaffold_13667 13773 4713 - 46842 I e loxAfr3.scaffold_159 81351 37 + 1045236 I e cavPor3.scaffold_42 9664497 578 + 15951348 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I e equCab2.chr12 28935170 6 + 33091231 I e canFam2.chr18 7531516 1585 - 58872314 I e bosTau4.chr29 48971499 187 + 51998940 I a score=82765.000000 s hg19.chr11_gl000202_random 10870 63 + 40103 TCCCAGAGGTT-CTG-CACCTGGGGGGCACTT-------GCCAGG--AGCCAG-----GCTGGAACCCAGATC--CC-----------GGGC s calJac1.Contig6069 76810 52 + 235769 ------------CTG-CACCTGGGGGACACTT-------GCCAGG--AGCCGG-----GCTGGAACCCACATC--CC-----------AGGC i calJac1.Contig6069 I 1656 C 0 s micMur1.scaffold_17226 13555 52 + 15119 ------------ctg-ca-ctaggaagaactt-------gccagg--ggctga-----gctggaacccagacc--cct----------gggc i micMur1.scaffold_17226 I 12 C 0 s tupBel1.scaffold_50294.1-1651 616 66 - 1651 ------------GTC-CCCCTGGGGGATTCCTGGGTCCAGCTGGG--AGCC-T-----GCTGGAAT---GTTC--CTTGTGTGTGGGGGGGG i tupBel1.scaffold_50294.1-1651 I 21 C 0 s canFam2.chr18 7533101 61 - 58872314 CCCAGGCAGGCACTGCCCCCTGGAGGGCAGTC-------TCAGGA--GCCAGG-----GCGGGAGC----ATC--CC-----------TGGG i canFam2.chr18 I 1585 I 1 s equCab2.chr12 28935176 63 + 33091231 t-ccgagaggttctg-gatgtgggcgggattt-------gcccaa--ggctgg-----gctggaacccagatc--tc-----------tgaa i equCab2.chr12 I 6 I 1 s myoLuc1.scaffold_155660 33323 69 - 124081 CCCAGGCAGGCACTGCCCCCTGGAGGGCAGTC-------TCGGAACTGCTAGG-----GCAGGGCCCAGTCTCATCC-----------AGGG i myoLuc1.scaffold_155660 I 335 I 2 s felCat3.scaffold_135390 55065 59 + 302526 -----agaggttctg-gatctggatgggactt-------ggcaga--ggctgg-----ccttgaacccaggtc--tc-----------tgag i felCat3.scaffold_135390 C 0 I 1 s panTro2.chr11 68198335 63 + 134204764 TCCCAGAGGTT-CTG-CACCTGGGGGGCACTT-------GCCAGG--AACCAG-----GCTGGAACCCAGATC--CC-----------GGGC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 41607 63 + 115376 TCCCAGAGGTT-CTG-CACCTGGGGGGCACTT-------GCCAGG--AACCAG-----GCTGGAACCCACATC--CC-----------GGGC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125992815 63 - 132107971 TCCCAGAGGTT-CTG-CTCCTCGGGGGCACTT-------GCCAGG--AACCGG-----GCTGGAACCCAGATC--CG-----------GGGC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128155978 63 - 133002572 TCCCAGAGGGT-CTG-CACCTGGGGCGCACTT-------GCCAGG--GACCAG-----GCTGGAACCCAGATC--CT-----------GGGC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 71998 63 + 109049 TCCCAGAGGGT-CTG-CACCTGGGGCGCACTT-------GCCAGG--GACCAG-----GCTGGAACCCAGATC--CT-----------GGGC i papHam1.scaffold6638 C 0 C 0 s loxAfr3.scaffold_159 81388 51 + 1045236 ----------------cacatgggtggaaacc-------agcaga--ggctgg-----acttgaacccaggccttcc-----------gagc i loxAfr3.scaffold_159 I 37 C 0 s oryCun2.chrUn0985 24362 43 + 42081 ------------------CCTGGGGTGCACGT-------G-GGGA--AGCCGA-----GGTG---TCCCAGTC--TG-----------GGGC i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48971686 49 + 51998940 --------------------TAGGGGGGCCTT-------GTCCAA--GGAGGGACCCTGCTGGAATCTGTCTA--CT-----------AGG- i bosTau4.chr29 I 187 I 1 e proCap1.scaffold_13667 13773 4713 - 46842 I e cavPor3.scaffold_42 9664497 578 + 15951348 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I a score=-26942.000000 s hg19.chr11_gl000202_random 10933 15 + 40103 CCTG-----------------TTGCAGTGCCT s panTro2.chr11 68198398 15 + 134204764 CCTG-----------------TTGCAGTGCCT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 41670 15 + 115376 CCTG-----------------TTGCAGTGCCT i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125992878 15 - 132107971 CCCG-----------------TTGCAATGTCT i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128156041 15 - 133002572 CCCG-----------------TTGCAATGCCT i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 72061 15 + 109049 CCCG-----------------TTGCAATGCCT i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 76862 15 + 235769 CCCA-----------------TTGCAGTGCCT i calJac1.Contig6069 C 0 C 0 s micMur1.scaffold_17226 13607 14 + 15119 ccca-----------------ttccagggcc- i micMur1.scaffold_17226 C 0 I 359 s tupBel1.scaffold_50294.1-1651 682 15 - 1651 CCGA-----------------GGGGAGGGTGT i tupBel1.scaffold_50294.1-1651 C 0 C 0 s oryCun2.chrUn0985 24405 1 + 42081 C------------------------------- i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48971736 2 + 51998940 CC------------------------------ i bosTau4.chr29 I 1 C 0 s equCab2.chr12 28935240 14 + 33091231 ccca-----------------ttccagggcc- i equCab2.chr12 I 1 I 670 s canFam2.chr18 7533163 6 - 58872314 GCTG-----------------CT--------- i canFam2.chr18 I 1 C 0 s felCat3.scaffold_135390 55125 14 + 302526 ccca-----------------ttcctgggcc- i felCat3.scaffold_135390 I 1 I 1883 s myoLuc1.scaffold_155660 33394 29 - 124081 CCCGGGCAAGAGGGCAGCTGCCT--GGAATC- i myoLuc1.scaffold_155660 I 2 I 8 s pteVam1.scaffold_22742 664 12 - 9737 CCTG-----------------CT--GGAGCC- i pteVam1.scaffold_22742 N 0 I 2 s loxAfr3.scaffold_159 81439 15 + 1045236 cctg-----------------ttccagcccct i loxAfr3.scaffold_159 C 0 I 559 e proCap1.scaffold_13667 13773 4713 - 46842 I e cavPor3.scaffold_42 9664497 578 + 15951348 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I a score=199360.000000 s hg19.chr11_gl000202_random 10948 97 + 40103 GA-ATTGTGGG--CCAACTGCT------GCC--CGAG-----ACTC---C------CACACAGGCATCCCGAGGCCCACTCACTCACCAGGGGACCTC--ACAGGATTCCTTGGGACTCGAGGA s cavPor3.scaffold_42 9665075 93 + 15951348 ---ATTGTGGT--CAGAGCTGC------CCA--CAGG-----ACTC---C------TCAAATGGT-CCCCAAAGCCCACTCA-TCACCAGGGGCTCTC--AAAGGATTCTTTGGGTCTTATGGG i cavPor3.scaffold_42 I 578 C 0 s bosTau4.chr29 48971738 77 + 51998940 -----AGAGGGTGTCAGCGGCT------GCC--CAAGGG---GCTC---C------CAGGCGCGC-TCTGGAGGCCCACTCACCTGTCAGGGGCCCTC--AAAG-------------------G i bosTau4.chr29 C 0 C 0 s myoLuc1.scaffold_155660 33431 93 - 124081 -----TCGGGGTGTCAACCTCG------GCC--CAAGAG---ACTC---C------CAGGTGGGC-ACCCCAGG-CCACTCACCTGCCAGAGGACCTC--AAAGGGTTCCTTGGACCTCCT--G i myoLuc1.scaffold_155660 I 8 C 0 s pteVam1.scaffold_22742 678 102 - 9737 -----TGAGGGTTAGATCCTCGACCAATGCC--CAAGAG---ACTC---C------CAGCTGGGA-GCCCGAGGCCCGCTCACCTGCCAGGAGACCTC--AAAGGGTTCCTCGGGCCTCTTAGG i pteVam1.scaffold_22742 I 2 C 0 s canFam2.chr18 7533169 76 - 58872314 CAGGTCAGGGG-------TGCT------GAT--CCAGAC---ACGCTGTC------CAAGCAGG------------GG---ACCTGCTGGAATCTGT---------TTCCTAGGGCTTTGGGGG i canFam2.chr18 C 0 C 0 s equCab2.chr12 28935924 101 + 33091231 GAGGTGGGGGGTGTCAACTGCT------GCC--CAAGAT---ACTC---C------CAAGTGGGC-CCCCGAGGGCGGCCCACCTGCCGGGGGGCCTC--AAAGAATTGCTCGGGCCTCATGGG i equCab2.chr12 I 670 C 0 s tupBel1.scaffold_50294.1-1651 697 95 - 1651 TC-ATCATGGA--TCAGCCACT------GCCCACGAG-----ACTC---C------CCAAGTGGACACCTGAGGCCCATTCTGCCA----GTAACCTC--AAAGGATTTCTCGGACCTCACAGG i tupBel1.scaffold_50294.1-1651 C 0 C 0 s calJac1.Contig6069 76877 95 + 235769 GA-ATTGTGGG--TCAGTTGCT------GTC--AGTT-----GCTC---C------CACACAGGCACCCCAAGG-CCACTCACTCACT-GGGCACCTC--ACAGGATTCTTTGGGACTCCAGGG i calJac1.Contig6069 C 0 C 0 s papHam1.scaffold6638 72076 97 + 109049 GA-ATTGTGGG--CCAGCTGCT------GCC--CGAG-----ACTC---C------CACATGGGCACCCCGAGGCCCACTCGCTCACCAGGGGACCTC--ACAGGATTCCTTGGGACTCCAGGG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128156056 97 - 133002572 GA-ATTGTAGG--CCAGCTGCT------GCC--CGAG-----ACTC---C------CACATGGGCACCCCGAGGCCCACTCACTCACCAGGGGACCTC--ACAGGATTCATTGGGACTCCAAGG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125992893 97 - 132107971 GA-ATTGTGGG--CCAACTGCT------GCC--CGAG-----ACTC---C------CACACGGGCACCCCGAGGCCCACTCACTCACCAGGGGACCTC--ACAGGATTCCCTGGGACTCGAGGA i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 41685 97 + 115376 GA-ATTGTGGG--CCAACTGCT------GCC--CGAG-----ACTC---C------CACACAGGCACCCCGAGGCCCACTCACTCACCAGGGGACCTC--ACAGGATTCCTTGGGACTCGAGGA i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68198413 97 + 134204764 GA-ATTGTGGG--CCAACTGCT------GCC--CGAG-----ACTC---C------CACACAGGCACCCCGAGGCCCACTCACTCACCAGGGGACCTC--ACAGGATTCCTTGAGACTCGAGGA i panTro2.chr11 C 0 C 0 s loxAfr3.scaffold_159 82013 102 + 1045236 ------GTTGG--TCAGCCACA------GCC--TTGGAG---ACTC---CAGGACTCTGAAGGGCATTCCCTGACCCACCCACCCACTGGGGGGCTCCCTAGAGGATTCCTTGAACTTCACGGG i loxAfr3.scaffold_159 I 559 I 8 s oryCun2.chrUn0985 24406 74 + 42081 -------------CCAACCCCA------TCT--CGGGGGTCCACTC---C------CTCACCTGC-CCGGTGGGCTCCCCAG-TTACCAAGCAACCTC------------------CTGGTAGG i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 435 55 - 12933 ------------GTCAACTCCT------GCC--CAAGAG---ACTC---C------CAGGTGGG----------------CACCTGCCAGGGGGCCTC--GAAG-------------------G i turTru1.scaffold_93657 N 0 C 0 e felCat3.scaffold_135390 55139 1883 + 302526 I e micMur1.scaffold_17226 13621 359 + 15119 I e proCap1.scaffold_13667 13773 4713 - 46842 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I a score=77245.000000 s hg19.chr11_gl000202_random 11045 37 + 40103 CC-----------CCCAAGAGCCCCATCTCTGGGGCAGGGACTCCCCA s panTro2.chr11 68198510 37 + 134204764 CC-----------CCCAAGAGCCCCATCTCTGGGGCAGGAACTCCCCA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 41782 37 + 115376 CC-----------CCCAAGAGCCCCATCTCTGGGGCAGGGACTCCCCA i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125992990 37 - 132107971 CT-----------CCCAAGAGCCCCATCTCTGGGGCAGGGACTCCCCA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128156153 37 - 133002572 TC-----------CCTAAGAACCCCATTTCTGGGGCAGGGACTCCCCA i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 72173 37 + 109049 CC-----------CCTAAGAACCCCATTTCTGGGGCAGGGACTCCCCA i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 76972 36 + 235769 GC-----------CCCGAGCGCCCCATCTCTGGAGCAGG-ACTCCCCA i calJac1.Contig6069 C 0 C 0 s micMur1.scaffold_17226 13980 35 + 15119 CC-----------CCCTGGAGGTCAGTCTCGGAAACCGCGG--CCTCA i micMur1.scaffold_17226 I 359 C 0 s tupBel1.scaffold_50294.1-1651 792 37 - 1651 GC-----------CTCAAGAGCCCTTCCCTGAGTGCAGGGCCTTCCCA i tupBel1.scaffold_50294.1-1651 C 0 C 0 s cavPor3.scaffold_42 9665168 33 + 15951348 -------------ACCTGGAGCCTC--TCTGGGAGGAGGATCACCCCA i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 24480 9 + 42081 -------------AC--------------------------CACCTGG i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48971815 31 + 51998940 AA-----------TCCAAGAGCCCCCTCTCTGGGCCAGGGTC------ i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28936025 35 + 33091231 GT-----------CCCAAGAG-CCCCGCTCAGTGGCAGGGTCCCCCA- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7533245 39 - 58872314 GTGTCAGCTGATGCCCAGGAG-GCT--CCAAGT-----GGGCACCTG- i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 33524 22 - 124081 AC-----------CCCAGAA--CCCCCCTCTGGGG------------- i myoLuc1.scaffold_155660 C 0 I 125 s pteVam1.scaffold_22742 780 36 - 9737 AC-----------CCCAAGAGTCCCCGCTCTGGGGCAGGGTCCCCCA- i pteVam1.scaffold_22742 C 0 C 0 s turTru1.scaffold_93657 490 31 - 12933 AC-----------TCCAAGAGCCCCCTCTCTGGGGCAGGGTC------ i turTru1.scaffold_93657 C 0 C 0 s loxAfr3.scaffold_159 82123 37 + 1045236 AC-----------CCCAAGAGCTCCCTCCCTGGGACAGGGTCTCCCCA i loxAfr3.scaffold_159 I 8 C 0 e felCat3.scaffold_135390 55139 1883 + 302526 I e proCap1.scaffold_13667 13773 4713 - 46842 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I a score=141860.000000 s hg19.chr11_gl000202_random 11082 77 + 40103 GGGGCCGT--GGGACAGCC---AGTAG-CATCATCGGTTCACTGGGCAGATGGTGACGGCCCACCGCCCCTGAGTGCCCAGGT s panTro2.chr11 68198547 77 + 134204764 GGGGCCGT--GGGACAGCC---AGTAG-CATCATCGGTTCACTGGGCAGATGGTGACGGCTCACCGCCCCTGAGTGCCCAGGT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 41819 77 + 115376 GGGGCCGT--GGGACAGCC---AGTAG-CATCATCGGTTCACTGGACAGATGGTGATGGCTCACCACCCCTGAGTGCCCAGGT i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125993027 77 - 132107971 GGGGCTGT--GGGACAGCC---AGCAG-CATCATCGGTTCACTGGGCAGATGGTGATGGCTCACCGGCCCTGAGTGCCCAGGT i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128156190 77 - 133002572 GGGGCCGT--GGGACAGCC---AGCAG-CATCATCGGTTCACTGGGCAGATGGTGGTGGCTCACCGGCCCCGAGTACCCAGGT i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 72210 77 + 109049 GGGGCCGT--GGGACAGCC---AGCAG-CATCATCGGTTCACTGGGCAGATGGTGGTGGCTCACCGGCCCCGAGTACCCAGGT i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 77008 77 + 235769 GAGGCTGT--GGGACAGCC---AGCAG-CAGCGTCCACGAACCAGGCAGATGGGAATGGCTCAAGGGCCCCAAGTGCCCAGGT i calJac1.Contig6069 C 0 C 0 s micMur1.scaffold_17226 14015 77 + 15119 GGTTGCAC--GTGACAGCC---ACCGG-CATCATTGATTCACAGGGCAGACTGTGTTTGCTCACCTGCCCTGGGTGCACAGGT i micMur1.scaffold_17226 C 0 M 156 s tupBel1.scaffold_50294.1-1651 829 74 - 1651 GGGGCCAC--GGACCATCC---AGCAG-CAACGTCAGCTCACAGGGCCGA--GTGTTTGTCCAGCTGTTC-GAGCGCCCAGGT i tupBel1.scaffold_50294.1-1651 C 0 C 0 s cavPor3.scaffold_42 9665201 51 + 15951348 GGGGTCAC--ATGACACCC---GATAG-CACCACTCACCCA--GAGCTGCAGGGGCCAG------------------------ i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 24489 30 + 42081 GGGATCCC--A-GTTTCCT---GCTTT-GACTCCACA---------------------------------------------- i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 521 70 - 12933 ------AC--TGGGGGCACC--GACAG-CACCCTGCATGCAC-AGGCGAACGGTGTCTGCTCAGCTGCCCCAGGTACCCAGC- i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48971846 68 + 51998940 -------T--TAGGGCGGCC--AGCAG-TGTCCTGCACGCAC--GCCAAGCAGAGGCTGCTCATCTGCTCCAGGTGCTCAGC- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28936060 66 + 33091231 GGGGTAAT--GGGGGTCACCCAG-----CATCCTTCATTCAC-GGGCGAACAGCATCTGCTCAC--------TGTGCCCAGC- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7533284 76 - 58872314 AGGCCGGC--TGGCCTTCCCCAGAAGGTCATCACTCATTCCC-AGGCAAACAGCATGTGCTCACCT---CTTTGTGCTCAGC- i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155661 4246 78 - 4599 GGGGTTAT--GGGAGGCACCGGAGCAG-CACCCCTCACTCAG-AGGCAAATAGCATCTGCCCACATGCCCTGTGTGCCCAGC- i myoLuc1.scaffold_155661 n 125 C 0 s pteVam1.scaffold_22742 816 75 - 9737 GGAGTCAC-GGGGAGGCACCCAGGCAG-CATCCTTCATCCAC-AGGC----AGTGTCTGCTCACCTGCCGTGTGTGCCCAGC- i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 82160 79 + 1045236 GGGGTCACCAGAGGCACTC---AGCAG-CATCACTCATCCACAGGGTAAACAGTGTGTGCACACCTGTCCCAGGTACCCAGGC i loxAfr3.scaffold_159 C 0 C 0 e felCat3.scaffold_135390 55139 1883 + 302526 I e proCap1.scaffold_13667 13773 4713 - 46842 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I a score=55455.000000 s hg19.chr11_gl000202_random 11159 31 + 40103 ACTGGGCTAGGC-----AGAGAAG---------GCAGGA------GCCTCC s panTro2.chr11 68198624 31 + 134204764 ACTGGGCTAGGC-----AGAGAAG---------GCAGGA------GCCTCC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 41896 30 + 115376 -CTGGACTAGGC-----AGAGAAG---------GCAGGA------GCCTCC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125993104 31 - 132107971 ACTGGGCCAGGC-----AGAGAAG---------GCAGGA------GCCTCC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128156267 31 - 133002572 ACTGGGCCAGGC-----ACAGAAG---------GCAGGA------GCCTCC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 72287 31 + 109049 ACTGGGCCAGGC-----AGAGAAG---------GCAGGA------GCCTCC i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 77085 30 + 235769 ACTGG-TCAGGC-----AGAGAAG---------GCAGGA------GCCTCC i calJac1.Contig6069 C 0 I 1884 s tupBel1.scaffold_50294.1-1651 903 36 - 1651 GCTGGGCCAGGTGGGGAGGAGGGG---------GCAGGA------GCAGCC i tupBel1.scaffold_50294.1-1651 C 0 C 0 s cavPor3.scaffold_42 9665252 22 + 15951348 -CTGGGCTGGGC----------------------CTGGA------GCCTCC i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 24519 22 + 42081 -CTGGGCCCAGT----------------------TCCCA------GCCGCC i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 591 39 - 12933 GCTGGGCCAGGC-----TGGGGGC-------GGGCAGAAGCAGCCCCCTTC i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48971914 33 + 51998940 ACTGGGCCAGCT-----ACAGGG-------------GGAGCAGCGCCCTTT i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28936126 42 + 33091231 AC-GGGCCAGGT-----GGGGGGGCGGGGGTGGCCGGGAGCA---GCCCCC i equCab2.chr12 C 0 C 0 s canFam2.chr18 7533360 25 - 58872314 GCTGGGCCAGGT-----GGAAGGG---------------------GCCCCC i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155661 4324 38 - 4599 GCTGGGTCAGGC-----CGAGGGG-------GCACAGGAGCATC-ACCACC i myoLuc1.scaffold_155661 C 0 C 0 s pteVam1.scaffold_22742 891 38 - 9737 ACCGGGCCCGGC-----TGACAGG-------GTGCAGGAGCAGC-AACCCC i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 82239 14 + 1045236 GCCAAGCCAGGC-----AG-------------------------------- i loxAfr3.scaffold_159 C 0 C 0 e felCat3.scaffold_135390 55139 1883 + 302526 I e micMur1.scaffold_17226 14092 156 + 15119 M e proCap1.scaffold_13667 13773 4713 - 46842 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I a score=-41061.000000 s hg19.chr11_gl000202_random 11190 40 + 40103 CTG-AGTCCCTCCTCCTTACGGCCCCACAGTCCTGCCCCAC s papHam1.scaffold6638 72318 39 + 109049 CTG-AGTCCCGCCTCCCTACAGCCCCACAGCCCTGCCCCA- i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128156298 39 - 133002572 CTG-AGTCCCGCCTCCCTACAGCCCCACAGCCCTGCCCCA- i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125993135 40 - 132107971 CTG-AGTCCCGCCTCCTTACAGCCCCACAGCCCTGCCCCAC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 41926 40 + 115376 CTG-AGTCCCTCCTCCTTATGGCCCCACAGTCCTGCCCCAC i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68198655 40 + 134204764 CTG-AGTCCCTCCTCCTTACGGCCCCACAGTCCTgccccac i panTro2.chr11 C 0 C 0 s tupBel1.scaffold_50294.1-1651 939 21 - 1651 -TG-CACTCTGCCT-----------------CGTGCCCCA- i tupBel1.scaffold_50294.1-1651 C 0 C 0 s cavPor3.scaffold_42 9665274 34 + 15951348 -TG-TGCCCCCTCCCT---CAGCCCCCAGGGCCCG-CCCA- i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 24541 31 + 42081 -CGATGTCCACCTGCTGTCCAGCCT----GGC----CTCT- i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 630 23 - 12933 CTG-AAGCCCCTGTCCCTACA---------GCC-------- i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48971947 12 + 51998940 CTG-AA----------CTAC----------GCC-------- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28936168 39 + 33091231 CTG-AGCCCCACCTCCCTCCAGCCCTGGCAGCCTGGCCCA- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7533385 26 - 58872314 CTC-G-------CACCCTTCAGCT------GCCCGGTTCA- i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155661 4362 35 - 4599 CTG-GACTCA--CCCCCCACAGAGCCAGCAGCC--GGCCA- i myoLuc1.scaffold_155661 C 0 n 0 s pteVam1.scaffold_22742 929 26 - 9737 CT--------------CCTTGAACCCAGCAGCCTGGGCCT- i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 82253 19 + 1045236 ---------CCCCTCCCTGCAGACCTGC------------- i loxAfr3.scaffold_159 C 0 C 0 e felCat3.scaffold_135390 55139 1883 + 302526 I e calJac1.Contig6069 77115 1884 + 235769 I e micMur1.scaffold_17226 14092 156 + 15119 M e proCap1.scaffold_13667 13773 4713 - 46842 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I a score=23823.000000 s hg19.chr11_gl000202_random 11230 69 + 40103 CCCACCCCTGCCAAATGGGACTCTTTGGGGCTGACCCCCAGGGAC---CCTAGTTTTTATGATCTCCCACCT s papHam1.scaffold6638 72357 69 + 109049 CCCACCCCTGTCAAATGGGACTCTTTGGGGCCGACACCCAGGGAT---CCCAGTTTTTATGATCTCCCACCT i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128156337 69 - 133002572 CCCACCCCTGTCAAATGGGACTCTTTGGGGCCGACACCCAGGGAT---CCCAGTTTTTATGATCTCCCACCT i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125993175 69 - 132107971 CCCACCCCTGCCAAATGGGACTCTTTGGGGCTGACCCCCAGGGAC---CCCAGTTTTTATGATCTCCCACCT i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 41966 69 + 115376 CCCACCCCTGCCAAATGGGACTCTTTGGGGCTGACCCCCAGGGAC---CCTAGTTTTTATTATCTCCCACCT i gorGor1.Supercontig_0015245 C 0 M 159 s panTro2.chr11 68198695 69 + 134204764 cccacccctgccaaatgggactctttggggctgacccccagggac---cctagtttttatgatctcccaCCT i panTro2.chr11 C 0 C 0 s tupBel1.scaffold_50294.1-1651 960 44 - 1651 ------GCTGCTGGATGGGGACCTTGGGGGCCACACCCTGGGGAC---CTTGG------------------- i tupBel1.scaffold_50294.1-1651 C 0 C 0 s cavPor3.scaffold_42 9665308 61 + 15951348 CCCACACCTGCAGATGGAGCCTC---GGGGCTGCACCC--AGGAC---CCATG--TTCATCATCTTGCCTC- i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 24572 42 + 42081 CCCACAGCTGGAGGAAGGGCC-A---GGGGCTGGGCCG--GGCAA---TCA--------------------- i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 653 42 - 12933 ----------TTGAATGCGACTCTGTGGGGCTGCTCCCGGGG-CCCCGCTCAG------------------- i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48971959 33 + 51998940 ----------CCCAACACAGC---------CTGCACTCGGGGCCC-TGCTCAG------------------- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28936207 52 + 33091231 CCTGCACGGGCTGAGTGGGAATCTG-GGGGCTGTGCCCCGGGGAACGGCTCAG------------------- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7533411 24 - 58872314 TCTGCACCTGCAAGATGGG---------------GCCCC--------------------------------- i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 33671 51 - 124081 CCCACACCGGCTGGATGGGGATCTGTGGGGCTGGTCCCTGGGGACC--CCTCG------------------- i myoLuc1.scaffold_155660 I 125 C 0 s pteVam1.scaffold_22742 955 53 - 9737 CCCACCCTTGCTGAATGGGCATCTGGGGGGCTGCGCCCCGAGGACCTGCTCAG------------------- i pteVam1.scaffold_22742 C 0 C 0 s micMur1.scaffold_17226 14250 42 + 15119 --------------------------GGGGCTGCACCCTGGGGAC---CTGGGTTCCCAGAGTCGCTCCTT- i micMur1.scaffold_17226 M 156 C 0 s loxAfr3.scaffold_159 82272 40 + 1045236 ----------TCAACTAGGATCTCTGGGATCTGTGTTTTAGAGTC---TCTCT------------------- i loxAfr3.scaffold_159 C 0 C 0 e felCat3.scaffold_135390 55139 1883 + 302526 I e calJac1.Contig6069 77115 1884 + 235769 I e proCap1.scaffold_13667 13773 4713 - 46842 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I a score=-80898.000000 s hg19.chr11_gl000202_random 11299 43 + 40103 --AAGTGGGAACATGGGCC-------------------AACAT----------GATGGGGCAGGTGTGGCTGGG- s panTro2.chr11 68198764 43 + 134204764 --AAGTGGGAACATGGGCC-------------------AACAT----------GATGGGGCAGGTGTGGCTGGG- i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125993244 43 - 132107971 --AAGTGGGAACATGGGCC-------------------AACAT----------AATGAGGCAGGTGTGGCTGGG- i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128156406 43 - 133002572 --GAGTGGGAACATGGGCC-------------------AACGT----------GATGGGGCAGGTGTGGCTGGG- i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 72426 43 + 109049 --GAGTGGGAACATGGGCC-------------------AACGT----------GATGGGGCAGGTGTGGCTGGG- i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 14292 42 + 15119 --GGGTGGGAACATGAGCT-------------------GGCAC----------T-CAGGCCAAGTGTGGCTTGG- i micMur1.scaffold_17226 C 0 C 0 s tupBel1.scaffold_50294.1-1651 1004 15 - 1651 --------------GGGCC--------------------ACAC----------CCTGGG---------------- i tupBel1.scaffold_50294.1-1651 C 0 C 0 s cavPor3.scaffold_42 9665369 30 + 15951348 -----TGGGAGTGGGG----------------------GGCAG----------TCTGGTGCTTG-------AGG- i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 24614 13 + 42081 --------------------------------------GACGG----------GACGGTGC-------------- i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 695 54 - 12933 --ATGTGGGAATGGGGGCTAGAC-----TCCGT--GGGAACA-----------GGTGGCGCAGCTGTGGCTCAG- i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48971992 59 + 51998940 --GTGTGGGAACGTGGGCTAAACCCACACCTGT--GCCGGCA-----------GGTGAAGCAGGCGTGGCTCCG- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28936259 64 + 33091231 --GTGTGGGAACGTGGGCTGGACTCGCCCCTCC--GCTGGCACCGTCGGGGCAGGTGG------GGCGGCTCAG- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7533435 60 - 58872314 ----------ACAGGGGCCGGACTCACACCTGA--GCTCGCATCCTCAGGGCTGGGGGAG--GCGGTGGCTAGG- i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 33722 45 - 124081 --GTGTGGGGACGTGAGCTGGGCTCGCACCTGG--GCTGGCAT-------------------------ATTTGG- i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 1008 32 - 9737 --GTGTGGGGCTGCGGGCAGGACTCACGCTTGG--A--------------------------------------- i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 82312 62 + 1045236 GAGTGTGGGGCCATGGGGTGGGCTTGTGCCACGTAGCCAGCAT----------GGTTGG---GGCGGAACCTGGA i loxAfr3.scaffold_159 C 0 I 5 e felCat3.scaffold_135390 55139 1883 + 302526 I e calJac1.Contig6069 77115 1884 + 235769 I e proCap1.scaffold_13667 13773 4713 - 46842 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I e gorGor1.Supercontig_0015245 42035 159 + 115376 M a score=-129414.000000 s hg19.chr11_gl000202_random 11342 120 + 40103 ACCCAGGCCTGGGC-TCCCCC----AGGCT---CCTCCTTGGATCTGAAGCCAGA------------TCC-ACCGAT-GGGAAATAAGCCCTT------TGG--AGCATGACGTTGCCGGGGAGGGGGTTGTGGGGA-----------CAGGAGATGATAA s panTro2.chr11 68198807 120 + 134204764 ACCCAGGCCTGGGC-TCCCCC----AGGCT---CCTCCTTGGATCTGAAGCCAGA------------TCC-ACCGAT-GGGAAATAAGCCCTT------TGG--AGCATGATGTTGCCGGGGAGGGGGTTGTGGGGA-----------CAGGAGATGATAA i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125993287 120 - 132107971 ATCCAGGCCTGGGC-TCCCCC----AGGCT---CCTCCTTGGATCTGAAGCCAGA------------TCC-ACCGAT-GGGAAATAAGCCCTT------TGG--AGCATGATGTTGGCGGGGAGGGGGTCATGGGGA-----------CAGGAGATGATAA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128156449 91 - 133002572 ACACAGATTCG---------------------------------CTGAAGCCACA------------TCC-ACTGAT-GCGAAATAAGCCCTT------TGG--AGCAGGATGG----AGGGGGTGGGTCATGGGGA-----------CAGGAGATGGTAA i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 72469 90 + 109049 ACACAGATTCG---------------------------------CTGAAGCCAGA------------TCC-ACTGAT-GCGAAATAAGCCCTT------TGG--AGCAGGATG-----GAGGGGTGGGTCGTGGGGA-----------CAGGAGACGGTAA i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 14334 108 + 15119 GC-CAGGCCTG-GC-TCCCCC----AGGCC---CCTTCCCAGATTTGGAGCCAGG------------TCTGGCAGAC-AGGAAATAAGCCCTT------CAG--AGC-----------TCGGGGGGTGTCCTAGGGA-----------CAGAAGGGGAGGA i micMur1.scaffold_17226 C 0 I 3 s tupBel1.scaffold_50294.1-1651 1019 109 - 1651 -----GACCTGGGG-ACCTCC------------CCTCCTCAGAGCCAGGACCAGA-GC--CTAAGTCCCC-ACTGAC-AGGAAACCAGTCCTT-------GG--TGCAT---------CAGGGAGTTGTAATGGGGA-----------CAGCAGATGGCAA i tupBel1.scaffold_50294.1-1651 C 0 C 0 s cavPor3.scaffold_42 9665399 110 + 15951348 ACCCAGGTCTGGGC-TCCCCG-----------------TTAGGTCTGAGACGAGGAGA--GAAAGGCCAA-GTTGAT-GGGAAAGAGGCCTT-------CAG--AGCAC---------CAGCGAGCTGTGGTGGTGA-----------GTGAAGAAGGCGA i cavPor3.scaffold_42 C 0 I 4 s oryCun2.chrUn0985 24627 70 + 42081 AGCCAGGGTGGGGC-------------------------------------------------------------AC-TGGAAGGAAGCCCCTCACTCACAG--AGCAG---------CCCCCGGCC----TGG-GA-----------GTGGGGA--GAGG i oryCun2.chrUn0985 C 0 I 4 s turTru1.scaffold_93657 749 114 - 12933 ACCCAGGCCGAGGT---CCCC----CGCTCTGCCCTTCTCCCACCTGGGCCTGGGCGCTGGGAGAGTCCA-GTCGAT---GGAGAAAGCCCTT------CCG--AGCAC----------------CTGTTGTGAGGA-----------CAG-AAGGGGTGA i turTru1.scaffold_93657 C 0 I 3 s bosTau4.chr29 48972051 115 + 51998940 GCCCAGACCGAGGA---CCCG----AG-GCTCCCCTTCTCCCATC-AGGACTGGGCGCCGGGAAGGCCCA-GCCAGTGGGGGAGAAAGCCCTT------CCG--GGCAC----------------CGGTCTCGGGGA-----------CAG-GCGAAACGA i bosTau4.chr29 C 0 I 3 s equCab2.chr12 28936323 118 + 33091231 ACCCAGGCCTGGGCTTTCCCC----CGGCTCCCCGTCCTTGCATCCAGGACCGGGCGCTGGGAAGGTCTT-GCTGGT---GGAATAAGCCCTT------CAG--AGCAT----------------CCTTTTAGGGGA-----------CAGTAGGACATGA i equCab2.chr12 C 0 I 3 s canFam2.chr18 7533495 116 - 58872314 ACCAAGTCTTGGGC-TCCCCC----AGGCTCCCCCTTCTCGCATCTGGGACGGGGTGCTGGGAAGGCCCA-GCGGAT---AGAATTAGCCCTT------CAA--AGCAT----------------CTGTTGTGGGGT-----------CAG-AGGATGTGA i canFam2.chr18 C 0 I 3 s myoLuc1.scaffold_155660 33767 80 - 124081 ACCCTGGCCTGAGC-TCC-CC----TGACTCTCCCTTCTCACACCCGGGACCAGTGGTGGGGAGGCCC-A-GCAGAT---GGAATCCCCCC---------------------------------------------------------------------- i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 1040 79 - 9737 --CCCAGCCCGAGC-TCCACC----AGGCTCCCCCTTCTTGACTCCAGGATCAGGTGCTGGGAAGGGC-A-GAGGGC---GGAACACACCC---------------------------------------------------------------------- i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 82379 127 + 1045236 ATCCAGACCTTGAC-TCCCCCAGGTAGGCTTGTCCCTCTGGGATCGGGGACCCAGTTGTGGCCGGGAAGC-CCAGAT-----GACAGGCCCTT------CAGGAAGCAC---------CCTGGGTCT-TTGTGGGAA-----------TGGAAAGGGACAC i loxAfr3.scaffold_159 I 5 I 2 s proCap1.scaffold_13667 18486 127 - 46842 ATCCAGGCCCGGAC-TCACCC----AGGCTCATCCTTCTGGGACCGGGTACTCTGGTGTGACAGGGAAAC-CCAGAT----AGACAGGCCCTT------TAGGAAGCAC---------CCTAG---------GGGAGCACCAGCTCTCCAGAAGGGGTGGC i proCap1.scaffold_13667 I 4713 I 3 e felCat3.scaffold_135390 55139 1883 + 302526 I e calJac1.Contig6069 77115 1884 + 235769 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I e gorGor1.Supercontig_0015245 42035 159 + 115376 M a score=-51251.000000 s hg19.chr11_gl000202_random 11462 39 + 40103 GGCACCCACACTC----C-----GGGGGTCCACC-CTGTAG-AAACT-CTG s panTro2.chr11 68198927 39 + 134204764 GGCACCCACACTC----C-----GGGGGTCCACC-CTGTAG-AAACT-CTG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 42194 39 + 115376 GGCACCCACACTC----C-----GGGGGTCCACC-CTGTAG-AAACT-CTG i gorGor1.Supercontig_0015245 M 159 C 0 s ponAbe2.chr11 125993407 39 - 132107971 GGCACCCACACTC----C-----GGGGGTCCACC-CTGTAG-CAACT-CTG i ponAbe2.chr11 C 0 I 318 s rheMac2.chr14 128156540 39 - 133002572 GGCACCCACACTC----C-----GGGGGTCCGCT-CTGCAG-CAACT-CTG i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 72559 39 + 109049 GGCACCCACACTC----C-----GGGGGTCCGCT-CTGCAG-CAACT-CTG i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 14445 43 + 15119 GGCACCCACCCCCAGAAA-----GGGCAGCTGCC-CTGCAG-CAACA-CTG i micMur1.scaffold_17226 I 3 C 0 s tupBel1.scaffold_50294.1-1651 1128 23 - 1651 -------------------------GCTGTCACC-CTTCAG-AAAGG-GTG i tupBel1.scaffold_50294.1-1651 C 0 C 0 s cavPor3.scaffold_42 9665513 44 + 15951348 GCCACCTGCACTC----CAGACAGGGCAGCTATG-CCATAG-CAACC-CCG i cavPor3.scaffold_42 I 4 C 0 s oryCun2.chrUn0985 24701 24 + 42081 GCCACCCTGAGGC----C--ACAGGCCAGC--------------------- i oryCun2.chrUn0985 I 4 C 0 s turTru1.scaffold_93657 866 42 - 12933 ACCACCCACACT-----CTGAGAGGGAGGCAGC--CGGACA-GCAGC-CCG i turTru1.scaffold_93657 I 3 C 0 s bosTau4.chr29 48972169 40 + 51998940 GCCACC--CACC-----TTGAGAGGGCGGCAGC--CTGCCC-GCAGC-CTG i bosTau4.chr29 I 3 C 0 s equCab2.chr12 28936444 46 + 33091231 GACACCCACACTG----CAGAGAGGGTGGCAGCC-CCCACAGCAAGACCAA i equCab2.chr12 I 3 C 0 s canFam2.chr18 7533614 45 - 58872314 GCTACCCACACTC----CAGAGAGGATGGCAGCT-CCGACAGCAAGA-CGG i canFam2.chr18 I 3 C 0 s myoLuc1.scaffold_155660 33847 41 - 124081 ---TGACACACTG----AAGAGAGGGTGGGGGCC-TTGACA-CAAGA-CTG i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 1119 41 - 9737 ---ACCCACACTG----CAGAGAGGGTGGGTGCC-CCGACA-CAAGA-CTG i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 82508 35 + 1045236 GCCACCATCACCC----A-----GAAAGGTCACCAAGGTCA-CCA------ i loxAfr3.scaffold_159 I 2 C 0 s proCap1.scaffold_13667 18616 35 - 46842 GACAACACTGGAC----A-----CTGATGTGGCCTCAGTCA-CTA------ i proCap1.scaffold_13667 I 3 C 0 e felCat3.scaffold_135390 55139 1883 + 302526 I e calJac1.Contig6069 77115 1884 + 235769 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I a score=-199388.000000 s hg19.chr11_gl000202_random 11501 59 + 40103 AGACCCA-C------CTCTCTGTG---ACC----AT----CAGGCTCTC-CCTGG--------------CCAGAAGCAGG---GAGCAG---------------CGTCCA s gorGor1.Supercontig_0015245 42233 59 + 115376 AGACCCA-C------CTCTCTGTG---ACC----AT----CAGGCTCTC-CCTGG--------------CCAGAAGCAGG---GAGCAG---------------CGTCCA i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68198966 59 + 134204764 AGACCCA-C------CTCTCTGTG---ACC----AT----CAGGCTCTC-CCTGG--------------CCAGAAGCAGG---GAGCAG---------------CGTCCA i panTro2.chr11 C 0 C 0 s rheMac2.chr14 128156579 59 - 133002572 AGACCCA-C------CTGCCTGTG---ACC----AT----CAGCCTTTC-CCTGG--------------CCAGAAGCAGG---GAGCAG---------------CGTCTA i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 72598 59 + 109049 AGACCCA-C------CTCCCTGTG---ACC----AT----CAGCCTTTC-CCTGG--------------CCAGAAGCAGG---GAGCAG---------------CGTCTA i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 14488 36 + 15119 GGACCTG-C--------------------------------------TG-GCTGA--------------CCAGAGG-AGG---GGTCGG---------------CGCCA- i micMur1.scaffold_17226 C 0 C 0 s tupBel1.scaffold_50294.1-1651 1151 43 - 1651 GCTGCCA-C------CTCACTGTG---ACC----AT----CAGCCACAG-CCTGG--------------CCCTAAG---------------------------------- i tupBel1.scaffold_50294.1-1651 C 0 C 0 s cavPor3.scaffold_42 9665557 66 + 15951348 AAAACCC-TCCATTGCGGCCCCGGCTCGGC----CC----CAGCCTGGCTTCTGG------------------AAGCTGGA--GAGCAG---------------CATCCG i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 24725 44 + 42081 ---------------CTGCCCCTG---GGC----GT----CAGCC-----TCTGG--------------------GCTGGGCTGGCCAA---------------CATCAG i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 908 79 - 12933 -AGCCCA-C------GGCACTGTG---GCC----AC----CAGCCCCAG-CCTCCAGCTC----GGC-TGCAGAAGTGCAT--CGAGGGGTGGAGCCTGCTGTGCA---- i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48972209 56 + 51998940 -AGCCCC-A------GTCTCCGGG---ACC----CT----CAGCCTC-G-CCTCCTGCCC----AGC-TCCAGAAGGGGA------------------------CA---- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28936490 72 + 33091231 -AGCCCA-T------GTCAGTGTG---GTCATCAGCACCCCAGCCCCGC-CCTCC----C----GGCTTCCAGAAGCA-GA--CGGCAG---------------CATCCG i equCab2.chr12 C 0 C 0 s canFam2.chr18 7533659 63 - 58872314 -AGCCAC-C------GTCACCATG---ATTCCCAGCA---GGGCCTCCG-TCTAC-----------TTTCCAGAAGCAGGA--CGGCGG---------------TA---- i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 33888 58 - 124081 -AACCCCAC------ATCTCTGTT---ACC----AT----CAGCCTCAA-CCTCCCGCCC----AGCCCCCAGCAGCAGGA----------------------------- i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 1160 73 - 9737 -AACCCC-C------ATCTCTGTG---ATCATCGAT----CGGCCCCAA-CCTCCTGCCC----GGCTTTCTGAGACGGGA--TGGTGG---------------CATCCA i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 82543 49 + 1045236 ------------------------------------------GCTCCCA-GCTCCTTTTCCAGAAGCTTCTGGAAGCAGG---ACAGAG---------------CACCCA i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 18651 49 - 46842 ------------------------------------------GCCTCTA-GCTCCTTTTCCAGAAACTTCTGGAAGCAGG---AGAAAA---------------CACCCA i proCap1.scaffold_13667 C 0 C 0 e felCat3.scaffold_135390 55139 1883 + 302526 I e calJac1.Contig6069 77115 1884 + 235769 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I e ponAbe2.chr11 125993446 318 - 132107971 I a score=-47788.000000 s hg19.chr11_gl000202_random 11560 28 + 40103 GG--CTGGGCCCAGCCC-----TGC-AGCCCCAAGG s panTro2.chr11 68199025 28 + 134204764 GG--CTGGGCCCAGCCC-----TGC-AGCCCCAAGG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 42292 28 + 115376 GG--CTGGGCCCAGCCC-----TGC-AGCCCCAGGG i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125993764 28 - 132107971 GG--CTGGGTCCAGCCT-----TGC-AGCCCCAGGG i ponAbe2.chr11 I 318 C 0 s rheMac2.chr14 128156638 28 - 133002572 GG--CTGGGCCCAGCCC-----TGC-AGCCCTAGGG i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 72657 28 + 109049 GG--CTGGGCCCAGCCC-----TGC-AGCCCTAGGG i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 14524 18 + 15119 GG--CCAGGCCCAGCTT-----TGC----------- i micMur1.scaffold_17226 C 0 C 0 s tupBel1.scaffold_50294.1-1651 1194 3 - 1651 ---------------------------------AAG i tupBel1.scaffold_50294.1-1651 C 0 C 0 s cavPor3.scaffold_42 9665623 30 + 15951348 GG--CTGGGCCGCTTATGC---CAC-TGCCCCAGGA i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 24769 35 + 42081 AGAACTGCGTCCCCCTGGCGGGCAC-TGCCCCCTGG i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 987 13 - 12933 -G--CCGGGCCCCACG-------------------- i turTru1.scaffold_93657 C 0 I 4 s bosTau4.chr29 48972265 13 + 51998940 -G--CAGTGTCCAGAG-------------------- i bosTau4.chr29 C 0 I 4 s equCab2.chr12 28936562 25 + 33091231 GG--CCAGGCCCAGCTC-----TGC-AGCCTGG--- i equCab2.chr12 C 0 I 11 s canFam2.chr18 7533722 21 - 58872314 -G--CCAGGCCCTGCGAG----TGC-AGG------- i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 33946 15 - 124081 -----------CAGCTT-----TACGAGCCT----- i myoLuc1.scaffold_155660 C 0 I 8 s pteVam1.scaffold_22742 1233 25 - 9737 GG--CCGGGCCCGGTTC-----TGC-AGCCTGG--- i pteVam1.scaffold_22742 C 0 I 11 s loxAfr3.scaffold_159 82592 23 + 1045236 ----AGATGGCCAGCTT-----TGC-GGCCTGG--- i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 18700 23 - 46842 ----ATGCAGCCAGCTT-----TGC-AGCATGG--- i proCap1.scaffold_13667 C 0 C 0 e felCat3.scaffold_135390 55139 1883 + 302526 I e calJac1.Contig6069 77115 1884 + 235769 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I a score=-6335.000000 s hg19.chr11_gl000202_random 11588 71 + 40103 -----------CTCTCA---CTGGGAACAC-AGGGTCT-CAGGCTAA-AATAGGTGGAGCCCCTCAGCCGAGCTCAGGAGCCCTT--GGG s panTro2.chr11 68199053 71 + 134204764 -----------CTCTCA---CTGGGAACAC-AGGGTCT-CAGGCTAA-AATAGGTGGAGCCCCTCAGCCGAGCTCAGGAGCCCTT--GGG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 42320 71 + 115376 -----------CTCTCA---CTGGGAACAC-AGGGTCT-CAGGCTAA-AATAGCTGGAGCCCCTCAGCCGAGCTCAGGTGCCCTT--GGG i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125993792 71 - 132107971 -----------CTCTCA---CTGGGAACAC-AGGGTCT-CAGGCTAA-AATAGCTGGAGCCCTTCAGCCGAGCTCAGGAGCCCTC--GGG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128156666 70 - 133002572 -----------C-CTCA---CTGGGAACAC-AAGGTCT-CGGGCTAA-ACTAGCTGGAGCCCCTCGGCCAAGCTCAGGAACCCTC--GGG i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 72685 70 + 109049 -----------C-CTCA---CTGGGAACAC-AAGGTCT-CGGGCTAA-ACTAGCTGGAGCCCCTCGGCCAAGCTCAGGAACCCTC--GGG i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 14542 71 + 15119 -----------CCCTCG---ATGGGGACAG-GTTGTCT-CCAGCAGA-GAATGGCAGAGCCCACCAGCCGAGCTCGGGGGCACTC--CGG i micMur1.scaffold_17226 C 0 C 0 s tupBel1.scaffold_50294.1-1651 1197 73 - 1651 -----------CCCTCG---CTGGGAACAA-ACCGTCT-CAAACCCACCATGGCCAGAGCCCAT-AGCTGAGCTCAGGAGCCCTCCGGGG i tupBel1.scaffold_50294.1-1651 C 0 C 0 s cavPor3.scaffold_42 9665653 29 + 15951348 -----------GACCCTGG-CTGGTAATGC----------------------------------------------GCTGTCC-C--AGG i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 24804 65 + 42081 -----------AGCTCAGTCCTGGTACTGC-AGCGT---------GA-ACCTGCTGCTCAGATCCGGGTGGGGGCAGCTATCC-C--AGG i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 1004 56 - 12933 -----------CCCTCA---CGGGGAGCAGAGTGGTCC-CAGACCGA-GAACAGCCGGGCGCATCAGCGGAG------------------ i turTru1.scaffold_93657 I 4 C 0 s bosTau4.chr29 48972282 52 + 51998940 -----------CCTTCC---CAGGGAACA----AGTCT-CTAACTGC-GGACAGCTGAGCCCACCGGTGCCG------------------ i bosTau4.chr29 I 4 C 0 s equCab2.chr12 28936598 73 + 33091231 -----------CCCTCC---CTGGGAACAGAAGGGTCT-CGAACTGA-GAATGGCTGGGCCTGCCACCTGAGGCCCGGACCCCCT-GGGC i equCab2.chr12 I 11 C 0 s felCat3.scaffold_135390 57022 74 + 302526 -----------CCCTCG---CCGGGAACAGAACGGTCTCCCCCCCGA-GGACAGCCGGG-CCACCTGCTGCGCTCCGGAGCCCCTGGGGG i felCat3.scaffold_135390 I 1883 C 0 s canFam2.chr18 7533743 57 - 58872314 -------------------------------AGGGTCT-CCCCCTGA-GGACAGCTGGGCCCACCTGCTGAGCCCTGGAGCCTCTCGGGG i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 33969 71 - 124081 -----------CCCTCA---CTGAGGACGA-ATGGTCT-CAAA-CAA-GGGTGGCTGGGCCCATCTGCCAAGCTTAGGAGCC-CTGGGGG i myoLuc1.scaffold_155660 I 8 C 0 s pteVam1.scaffold_22742 1269 63 - 9737 -----------CCTTCA---CTG-GGGCAG-ATGGTCT-CAAACCGA-GGGGGGCTGGGCTCATCAGCTGAGCTCA---------GGGGG i pteVam1.scaffold_22742 I 11 C 0 s loxAfr3.scaffold_159 82615 83 + 1045236 CCTTACAAGTCCCCTCA---TTGGGAATAGCATTGAAC-AAACCAAG-AAAGGCCCAGGCCGACAACCTGAGCTCAGGGGCCCTT--TGC i loxAfr3.scaffold_159 C 0 I 3 s proCap1.scaffold_13667 18723 61 - 46842 C--------------TG---TGAGCAGCAGCACTGAAC-AAATC----AAAGGTGGGAACCGACG----GAGCTCA-GGGCCCTT--TAG i proCap1.scaffold_13667 C 0 I 290 e calJac1.Contig6069 77115 1884 + 235769 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I a score=-69734.000000 s hg19.chr11_gl000202_random 11659 67 + 40103 CAGCA-CTGGGAG-CTGCTGGAGCCAGCGCCTTGT-----CTTCCCTCT--ACCTGTCTAGGCCCCAGAAGGCTGC s panTro2.chr11 68199124 67 + 134204764 CAGCA-CTGGGAG-CTGCTGGAGCCAGCGCCTTGT-----CTTCCCTCT--ACCTGTCTAGGCCCCAGAAGGCTGC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 42391 67 + 115376 CAGCA-CTGGGAG-CTGCTGGAGCCAGCGCCTTGT-----CTTCCCTCT--ACCTGTCTAGGCCCCAGAAGGCTGC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125993863 67 - 132107971 CGGCA-CCGGGAG-CTGCTGGAGCCAGTGCCTTGT-----CTTCCCTCT--ACCTGTCTAGGCCCCAGAAGGCTGC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128156736 67 - 133002572 CAGCA-CCGGGAG-CTGCTGGAGGCAGCGCCTCAT-----CTTCCTTCC--ACCTGTCTAGGCCCCAGAAGGCTGC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 72755 67 + 109049 CAACA-CCTGGAG-CCGCTGGAGGCAGTGCCTCAT-----CTTCCCTCC--ACCTGTCTAGGCCCCAGAAGGCTGC i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 14613 35 + 15119 -------------------------GGCGGCTCAC-----CTGCCCTCTGCACCTGCC-----------GGGCAGC i micMur1.scaffold_17226 C 0 C 0 s tupBel1.scaffold_50294.1-1651 1270 65 - 1651 CAGCC-CCAAGGT-GGCCCAGAGTCAGCGTGTCAT-----CTCCCATCT--GC--ATCCTCGCCCCAGCAGGTGGC i tupBel1.scaffold_50294.1-1651 C 0 C 0 s cavPor3.scaffold_42 9665682 13 + 15951348 CTGA----------------GAGTCCTGG----------------------------------------------- i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 24869 31 + 42081 CAGGA-CCTG----CTTCTTGGGGCCGGGGATATG-----C----------------------------------- i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 1060 53 - 12933 -----CCCAGGAGTCCCCCTGAGTCAGCACATCC------TCTCCCGCC--GCTGGCCTGAGTCCG---------- i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48972334 61 + 51998940 ------CCAGGAG-CCCCCTGCCTCAGCACATGG------ACTCCCTCT--GTTGGCCCAAGTGCAGGCAGTGGGC i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28936671 68 + 33091231 CGGCACCCAGGAGTCGCCCTGAGCCATCGAGGCA------TCTCCCGCC--GCTGGTCTAAGTCCGGGCAGCTGGC i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 57096 51 + 302526 CAGCACCCA-----CGCGCTCA------------------TCTCCCTCT--GCTGGTCTAAGACGGGGCGGTCGGC i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7533800 72 - 58872314 CGGCCCCCAGGACTCGCCCTGAGCCA--GAGCCTTACCTCCCTCCCTGT--GCTGGCCCACGTCCAGGCAGTTGGC i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 34040 26 - 124081 GAAGCACCAGGAGTCCCCCGGAGCCA-------------------------------------------------- i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 1332 61 - 9737 CAGCCCCCAGGAGTCCCCCAGAGCCAGGGAGACA------CCCCACTCT--GCTAGTCCAGGTCC-------CAGG i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 82701 55 + 1045236 -------------TAACCCTGAGTTGGCA-GTCAC-----CTCCCCATG--GCACGCCCAGGTGCCGGTGTCCAGC i loxAfr3.scaffold_159 I 3 C 0 e calJac1.Contig6069 77115 1884 + 235769 I e proCap1.scaffold_13667 18784 290 - 46842 I e otoGar1.scaffold_5322.1-37474 34235 2170 - 37474 I a score=757353.000000 s hg19.chr11_gl000202_random 11726 361 + 40103 AGCCAGGGAGGGGGCTGGGCATCTTAAGGAGGGCCGGCTCTCTCTAGCA---GAGT-------------C--CT--GGGAGAAGAGGCC-A--GGGCCTTCACCGACAGCGCagcacctc-cagtttccgcggcacct-ccacggccc-tctcgcctaagcctctcca--cccctg-----tgtggg--gg---------gcttgctgtggttctgctttacagggggagaaactg----------agggcccag--------aaggtcaggCTGCGGC---------------------TGAAGGT--------GCAAGGA--------------------------CTCA--------------------AAGGCTG----------------------------ACTCCG----------GGGTGGGGACGGGTTTGGAATTTCCTGTTCCTCCTCACCTTTGAGAGGTG-TCC-T-GG------CTGGGCTGTGCC-AGGCTGGGAAGTGTCTCCGGAGGCTCCACACCCACCCACACCTGG s panTro2.chr11 68199191 361 + 134204764 AGCCAGGGAGGGGGCTGGGCATCTTAAGGAGGGCTGGCTCTCTCTAGCA---GAGT-------------C--CT--GGGAGAAGAGGCC-A--GGGCCTTCACCGACAACGCAGCACCTC-CAGTTTCCGTGGCACCT-CCACGGCCC-tcccgcctaagcctctcca--cccctg-----tgtggg--gg---------gcttgctgtggttctgctttacagggggagaaactg----------agggcccag--------aaggtcaggCTGCGGC---------------------TGAAGGT--------GCAAGGA--------------------------CTCA--------------------AAGGCTG----------------------------ACTCCG----------GGGTGGGGACGGGTTTGGAATTTCCTGTTCCTCCTCACCTTTGAGAGGTG-TCC-T-GG------CTGGGCTGTGCC-AGGCTGGGAAGTGTCTCCGGAGGCTCCACACCCACCCGCACCTGG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 42458 361 + 115376 AGCCAGGGAGGGGGCTGGGCATCTTAAGGAGGGCCGGCTCTCTCTAGCA---GAGT-------------C--CT--GGGAGAAGAGGCC-A--GGGCCTTCACCGACAGAGCagcacctc-cagtttccgcggcacct-ccacgaccc-tcccgcctaagcctctcca--cccctg-----tgtggg--ga---------gcttgctgtggttctgctttacagggggagaaactg----------agggcccag--------aaggtcaggCTGCGGC---------------------TGAAGGT--------GCAAGGA--------------------------CTCA--------------------AAGGCTG----------------------------ACTCCG----------GGGTGGGGACGGGTTTGGAATTTCCTGTTCCTCCTCACCTTTGAGAGGTG-TCC-T-GG------CTGGGCTGTGCC-AGGCTGGGAAGTGTCTCCGGAGGCTCCACACCCACCCGCACCTGG i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125993930 357 - 132107971 AGCCAGGGAGGGGGCTGAGCATCTCAAGGAGGGCCGGCTCTCTCTAGCA---GAGT-------------C--CT--GGGAGAAGAGGCC-A---GGCCTTCACCGACAGCGCAGCA-CTC-CAGTTT-TGCGGCACCT-CCACGGCCC-TCCCGCCTGAGCCTCTCCG--CCCCTC-----TGTGGG--G----------GCTTGCTGTGGTTCTGCTTTACAGGGGGAGAAACTG----------AGGGCCCAG--------GAGGTCAGGCTGCGGC---------------------TGAAGCT--------GCAGGGA--------------------------CTCA--------------------AAGGCTG----------------------------ACCCTG----------GGGTGGGGACGGGTTTGGAATTTCCTGTTCCTCCTCACCTTTGAGAGGTG-TCC-T-GG------CTGAGCTGTGCC-AGGCTGGGAAGTGTCTCCGGAGGCTCCACACCCACCCGCACCTGG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128156803 364 - 133002572 AGCCGGGGAGGGGGCTGGGCATCTCAAGGGGGACCGGCTCTGTCGAGCA---GAGT-------------C--CT--GGGACAGGAGGCC-A--GAGCTTTCACTGAGAGCACAACACCCC-CAGCTTTCACGACACCTCCCACAGCCT-TCCGGCCtgagcctctcagactccctg-----tgtagg--gg---------gcttattatggttctgctttacaggggaagaaactg----------agggcccag--------gaggtcaCGCTGTGGC---------------------TGAAGCT--------GCAGGGA--------------------------CTCT--------------------AAGGCTG----------------------------ACCCCG----------GGGTGGGGACGGGTTTGGAATTTCCTGTTCCTCCTCACCTTTGAGAGGTG-TCC-T-GG------CTGGGCTGTGCC-AGGCTGGGAAGTGTCTCCGGAGGCGCCACACCCACCCGCACCTGG i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 72822 364 + 109049 AGCCGGGGAGGGGGCTGGGCATCTCAAGGGGGACCGGCTCTGTCGAGCA---GAGT-------------C--CT--GGGAGAGGAGGCC-A--GGGCTTTCACTGAGAGCACAACACCCC-CAACTTTCACGACACCTCCCACAGCCT-tcccgcctgagcctctcagactccctg-----tgtagg--gg---------gcttattatggttctgctttacaggggaagaaactg----------agggcccag--------gaagTCACGCTGTGGC---------------------TGAAGCT--------GCAGGGA--------------------------CTCT--------------------AAGGCTG----------------------------ACCCCG----------GGGTGGGGATGGGTTTGGAATTTCCTGTTCCTCCTCACCTTTGAGAGGTG-TCC-T-GG------CTGGGCTGTGCC-AGGCTGGGAAGTGTCTCCGGAGGCGCCACACCCACCCGCACCTGG i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 14648 297 + 15119 -------------------CGCCGGAGAAGGGGCTAG---------GCA---GAGT-------------C-TCA--GGGCGAGCCAG-------GGCCTTCAGCAGGAGTGCAGTCCCAA-GCGCCT----GG------CGCGGGCCC-TCCCACCTGCG-CTCACGC--CCACCG-----TGCGGG-------------ACTCGCTGTGGCTCCATTTCACAGATGAAGACACCG----------AGGCCCCAG--------CAGGCCAGGCCGCTGT------------------------------------AAGGAGG--------------------------GACT--------------------GAGGCCG-------------------CCT----CTCCTACT----------GGGCGGGGACGG--CTGGAATT--------------TCCTTTGCGTGGCG-GCC-C-GG------CCAGCTCGTGCC-AGGCTGGGAAGTCTCTCTGGA--TTCCACACCCA-CTGCACCTGG i micMur1.scaffold_17226 C 0 C 0 s otoGar1.scaffold_5322.1-37474 36405 365 - 37474 AACTTGGCAGGCAGCTGTGCCCTGGCAGAGGGGCTGA---------GCA---AAGT-------------CATCA--GAGAGAGCAGGCC-C---AGGCTTTAGCAAGGGCAGAGCTGCCA-TGGTTT------------TCAAGGTAC-GCCCCCCTGGGCCTCTCGC--CCACCT----CTgtagg-------------gcttgctgtggctccactttacagatgaggaaacca----------aggtgccag--------ga-gccaggcagctgc---------------------tcaaggGGG------GAGGGGG--------------------------GCTG--------------------GAGGCCGCTCACTGGCCTCTAAGCCTCCT----CCTCCTCC----------GGGTGGGGAGGGGTTTGGAATTTCCTGTTGCTCCTATCCTTTGTGTGGTG-TCC-CAGG------CCAGGCGGTGCC-AGGCTGTGAAGTGTCTCTCAA-GTCCCACACCCA-CCGCACCTGG i otoGar1.scaffold_5322.1-37474 I 2170 C 0 s tupBel1.scaffold_50294.1-1651 1335 316 - 1651 -----------------AGCA-------------------------GCA---GGAC-------------T--CA--GAGGAGCCAAGCC-A--GGGCCTTTAACAGCAgcacagcccttc-ccagtttacaggcaccc-ccgtgg-gc-tcccacctgagcctcacac--ccactg-gtgccacggg-------------gcttgttgtggctccattttacagatggagaagccg----------aggcccagg--------gaggtcaggCC-CATC---------------------TGCTGGC-----------------------------------------CTCC--------------------AAGGCAC--------------------CC----CTCCCATT----------GAGGGAAGACACACTAGGAATTT-CTGTGGCTCCTCGCCTCTGAGCGGTGTTCC-C-AG------CTGGACGGTGCCAAGGCTGGGAGGTCACTCC-GAGGTTCCACACCCACCTGCACCTGG i tupBel1.scaffold_50294.1-1651 C 0 n 0 s cavPor3.scaffold_42 9665695 318 + 15951348 ----------------------------------------------GCA-GGAAGC-------------C--CTAGGAGAGAGCAGGCC-G--GGGC---CACTGAGACCCCAGCA-----CAGTCT-------------------CC-TCCCCCCTGAGCTGCCCTC--CCACCT-----GGGCAG--GG---------GG-------TGCTCTGCAGCACAGAGGATGACACC-----------AAGGCCAGG--------GAGGCCAGGCAGCAGC---------------------TGTTTGG--------GTAGGGGGACCTGAAGGCCAACCGGATTCAGGCCTCT--------------------GAGGTTG-------------------CCT----CTCCCACT----------GGGTGGGGACGGGTTTGGAATTTCCTGTCCCTCCCCACCTTGGAGAGGTG-TCTTC-AG------CCAGGCCGTGCC-AGGCTGGGAAATCTCTCCGCAGCCTCCACACCCATCTGTACCTGG i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 24900 327 + 42081 -----GGGGAGGGGTTCAGCA-------------TGGCTCTGTCT-GCACGGAGGA-------------C--CTCAGGGAGAGCAGGCA-G--GGCA---CCCACAGTTCCCAG--------------------------------GC-ACCCGGCGGGGCCCCTCTC--CCAccc-----ggggcg--gg---------gc-------ggggtggcggggccgTGCGTGGctccatttcacaggtaaggacact--------gaggccag-----agc---------------------tgtggaA--------GCAGTGGGCGCTGACCGTC--CCGGCCCCTGGCCTCC--------------------AAGGCCG-------------------CTT----CTCCCGCT----------GGGTGGGG-TAGGCTTGGCATTTCCTGCGGCTGCTCCCC-------GG-------C-GG------CCACGCGGTGCC-AGGCCGGGAAGTCTCGCCCGAGGC-CCACGCCCACTCGCACCTGG i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 1113 274 - 12933 -----------------------------------------------------------------------------------------------------------------------------------------TTCCAAAGCTC-TGTCGTCCCCACCT----------------GGGGCGGG--GGC--------TCTGGTTGTGGCTCCGTTTTTCAGATGCGGAAACCG----------AGACGCGGG--------GAGACCGGGCAGCTGTTAGGTGGGGGCCGGGGTGGGGTGGGGGAGT-----TGGGGGGC--------------------------CTCC--------------------GAGGCCG-------------------CCT----CTCCTGCA------CGTGGGGTGGGGTCAGGTTTGGAACTTCCTGTTGCTCTTCACCTTTGAGTGGTG-TCGGC-GG------CCAGGCGGTGCC-AGGCTGGGAAGTCTCTCTGGAAGCTCCACACCCAGC-ACACCTGG i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48972395 409 + 51998940 ATCC-TGGATAGGC----------------CGAGCCACTCAGG---GAG-GCTGCTGTGAGCAGGGGGTC--CTCAGAGAGAGCAAGCCTG--GGGCCTGCAGCGGGCACTCCgcaccctacagtttatgaggcacctcccagggtccatgtcctccaagcctcgcac--ccaccggaggaggcggg--ggtaggggtgagcttgttgcggctccatttttcagatgtggaaactg----------aggcccagg--------gcagccaggcagctGT---GTAAGAACTGGGTGGGGAGGAAGGCGT-----CGGCGGG------------------------------G--------------------GAGGGCG-------------------GGTCAGGCACGTGCAGGCCCCTGCGGGGTGGGGCCAGGCTTGGAATTTCC---TGCTCCTCACCCTGGAGTGGTG-TCCGA-GG------CCAGGCGGTGCC-AGGCTGGGAAGTCTCTCAGAAACCTCCACGCCCGCC-ACACCTGG i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28936739 375 + 33091231 AGCCGTGGAGGGGT----------------TGAGCGGCTCTGA---GCA-GAGGGT-------------C--CTCGGAGGGAAGGGG-------GGCCCGTAGCAGGA--GCagcaccgcccggtttacagggcccctcccgtgggc--tctcctcccagcctcgcac--ccaccttgggtgggggg--aa---------gcttgttgtggctccatttttcagatgaggaaaccg----------aggcccagg--------aaggccaggccactgt---------------------tccaggccc-----cagccggc--------------------------gtctgcaggctggtggcagggctCAAGGTCA-------------------CCT----TTCCTGCC----------AGGTGGGGCCGGGTTTGGAATTTCCTGTCACTCCTCGCCTTTGGGTGATG-TCCCC-GG------CCGGGCGGTGCC-AGGCTGGGCGGTCTCTGCAGAGGTTTCACATGCACCCACACCTGG i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 57147 332 + 302526 GGCCGTG-----------------------GGGGCTGCCCCGA---GCC-GAGGGT-------------C--CTCAGAGAGAGCAAGCC-G--GGGCCCGTGGCGGGG-CACAGCCCTCCACAGCGGACGAGGCAGGTCCCACAGACCGTCTCCTCTGAGCCCCACAC--CCACCC----GGGCGGG--GG---------GCTCGCTGTGGCTCCATTTTCCGGGCGAGGAAGCCG----------AGGTCCGGG--------CCGGCT----------------------------------------------GGGTGGC--------------------------CGTCG-------------------AAGGCCG-------------------CCT----CTCCTGCT----------GGGTGGGGCCAGGTTCAGAATTTCCGGTCGCTCCCCGCCTTCGAGCGGTG-TCCCC-AG------CCGGGCGGTGCC-AGGCTGGGAAGTCGCTCTGGAGACTCCACACCCACCCGCACCTGG i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7533872 262 - 58872314 AGCCGTGGGATGAGGTGGGCGGCC---CCAGGGGCTGCTCTGA---GCA-GAGGGT-------------C--CTCA-AGAGAGCAAGCC-------------------------------------------------------------------------------------------------A--GA---------GCTTGTTGGGGCTCCGTTTTCCAGGCGAGGACCCCG----------AGGCCCAGG--------CTGGCC-----------------------------------------------ACTGGC--------------------------CTCCG--------------------AGGCCG-------------------CCT----CTCCCACT----------GGGTGGGGACAGGTTTGGAATGTCCTGCTGCTGCTCACCTTTGAGTGGTG-TCCCT-GG------CCGGGCGGTGCC-AGGCTGAGAAGTTTCTCCGGAGGTTCCACACCCACCCGCACCTGG i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 34066 258 - 124081 -----------------------------------------------------------------------------------------------GCCTGCAGCGGGAGCACCGCACCCCACACTTTACAAGGC-ACCTCCAT-GGCACTCTCCTCTG-GCCTCACAC--CCAC----------------------------------------------------GAG------------------GGCCCAGG--------GAGGCCAGGCCGCTGT---------------------TTGAGGCCA-----CA--GGGC--------------------------CTCC--------------------AGGGCCG-------------------CCT----CTCCTGCT----------GGGTGGGGCCGGGTTTGGAATTTCCTGTTGCTCCTCACCTTTGCATGGTG-TCCCC-GGCCAGGCCCAGGCCGTGCC-AGGCTGGGAAGGCTCCCCAGAGGTTCCACACCCACCCGCACCTGG i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 1393 379 - 9737 AGCCACGGAGAGGGGTGACCAGCT--GAGGGACGCTGCTCTGT---GCA--AGAGT-------------C--CTTGGAGAGAGCAA-CC-T--AGGCCCACAGCAGGAGCGCagcaccccacagtttgcaaggcaaactccatgggctctctcctctgagcctcgcac--ccacct----ggggtgg--ga---------gcttgctgtggctccatttttcagatgaggaaaccg----------aggtctggg--------gaagccaggcagctgc---------------------ctaaggcca-----caGCGGGT--------------------------CTTCGCAGGTGG------------GCGGCAG-------------------CCT----CTCCCGCG----------GGGCGAGGCCAGGTTTGGAATTTCCCGTCATCCCTCACCTTTGCGTGGTG-TCCCC-GG------TCAGGTGGTGCC-GGGCCGGGAAGGCTCGCCAGAGGCTCCACACCCACCTGCACCTGG i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 82756 310 + 1045236 -----------------------------------------------------AGC-------------C--AT--GCAGGGGTGGGGT-GGTGAGACCTCGGAGAAAgcatagcactccacagcctacaagggccct-caggagctc-tctcacctgagcctcacac--ccacct-----gggaggtagg---------gcttgttgggactccattttacaggtggggaaactg----------aggtccggggctcaagagaggagaagcagcacc---------------------tgaagaccacaTCCCTGCTGAC--------------------------ATCC--------------------AAGGCTG-------------------CTT----GTCCTGCT----------GGGTGGGGACAGGTGTGGAATTTCCTGT-GTCCCTCACCTTCCAGAGGTG-TCC-C-CT-----------------C-AGG---------------AGCAGTTGCACACCCACCCACACCTGG i loxAfr3.scaffold_159 C 0 C 0 e calJac1.Contig6069 77115 1884 + 235769 I e proCap1.scaffold_13667 18784 290 - 46842 I a score=299911.000000 s hg19.chr11_gl000202_random 12087 43 + 40103 TATTTTTGTTCCCAG--------GTGGGTCTGATGCCAGGAGGA--TGTGG-TT s panTro2.chr11 68199552 43 + 134204764 TATTTTTGTTCCCAG--------GTGGGTCTGATGCCAGGAGGA--TGTGG-TT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 42819 43 + 115376 TATTTTTGTTCCCAG--------GTGGGTCTGATGCCAGGAGGA--TGTGG-TT i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125994287 43 - 132107971 TATTTTTGTTCCCAG--------GTGGGTCTGATGCCAGGAGGA--TGTGG-TT i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128157167 43 - 133002572 TATTTTTATTCCCAG--------GTGGGTCTGATGCCAGGAGGA--TGTGG-TT i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 73186 43 + 109049 TATTTTTATTCCCAG--------GTGGGTCTGATGCCAGGAGGA--TGTGG-TT i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 14945 43 + 15119 TATTTTTATTCCCAG--------GTGAGTCTGATGCCAGGAGAA--TGTGG-TT i micMur1.scaffold_17226 C 0 I 1 s otoGar1.scaffold_5322.1-37474 36770 43 - 37474 TATTTTGATGCCCAG--------ATGCGTCTGATGCCAGGGGAA--TGTGG-TT i otoGar1.scaffold_5322.1-37474 C 0 I 1 s cavPor3.scaffold_42 9666013 41 + 15951348 TATTTTTAT--TCCT--------GAGAGTTCGATGCCAGGGGAA--CATGA-TC i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 25227 44 + 42081 TATTTTTGTCGCCGT--------GTGAGGCTGATGCCAGGCGAA--CGCGGCCC i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 1387 43 - 12933 TATTTTTATTCCTGT--------GTAAGTCTGATGCCAGGAGAA--TGTGG-TT i turTru1.scaffold_93657 C 0 I 1 s bosTau4.chr29 48972804 43 + 51998940 TATTTTTATTCCCAT--------GTAAGTCTGATGCCAGGAGAA--CGTGG-TT i bosTau4.chr29 C 0 I 1 s equCab2.chr12 28937114 25 + 33091231 TATTTTT-------------------------ATGCCA---GGAGCCGTGG-TT i equCab2.chr12 C 0 I 1 s felCat3.scaffold_135390 57479 40 + 302526 TATTTTTATTCCCGT--------GTGAGTCTGATGCCA---GAA--GGTGG-TT i felCat3.scaffold_135390 C 0 I 1 s canFam2.chr18 7534134 40 - 58872314 TATTTTTATTCCCGT--------GCAAGACTGATGCCA---GAA--CGTGG-TT i canFam2.chr18 C 0 I 1 s myoLuc1.scaffold_155660 34324 42 - 124081 TA-TTTTATTCCCAA--------GTGCGTCTGCTGCCAGCGGAA--GGCGG-TT i myoLuc1.scaffold_155660 C 0 I 1 s pteVam1.scaffold_22742 1772 40 - 9737 AA-GTTTATGCCCAT--------GTGGGTCCGATGCCAGGAGAA----TCG-TT i pteVam1.scaffold_22742 C 0 I 1 s loxAfr3.scaffold_159 83066 51 + 1045236 TATTTTTATTCCCATGAGAGAGAGAGAGGCTGATGCTGGGAGAG--CCCAG-CA i loxAfr3.scaffold_159 C 0 I 6 e calJac1.Contig6069 77115 1884 + 235769 I e proCap1.scaffold_13667 18784 290 - 46842 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=1070515.000000 s hg19.chr11_gl000202_random 12130 127 + 40103 AAGCTCGAGGCCCTGCT-------GTCTCCTTCCATGCC---CGGGGTCAATGGATCC-TTATCTGGCAAGATCTTATCTGTGTGTCCTTGAC-A--------------GACTC-TG-GAGCAGGCTCCTGGAGGTACCGGGAGGCCCA-GGTGGG s panTro2.chr11 68199595 127 + 134204764 AAGCTCGAGGCCCTGCT-------GTCTCCTTCCATGCC---CGGGGTCAATGGATCC-TTATCTGGCAAGATCTTATCTGTGTGTCCTTGAC-A--------------GACTC-TG-GAGCAGGCTCCTGGAGGTACCGGGAGGCCCA-GGTGGG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 42862 127 + 115376 AAGCTCGAGGCCCTGCT-------GTCTCCTTCCATGCC---CGGGGTCAATGGATCC-TTATCTGGCAAGATCTTATCTGTGTGTCCTTGAC-A--------------GACTC-TG-GAGCAGGCTCCTGGAGGTACCGGGAGGCCCA-GGTGGG i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125994330 128 - 132107971 AAGCTCGAGGCCCTGCT-------GTCTCCTTCCATGCC---CGGGGTCAATGGATCC-TTATCTGGCAAGATCTTATCTGTGTGTCCTTGACAA--------------GACTC-TG-GAGCAGGCTCCTGGAGGTACTGGGAGGCCCA-GGTGGG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128157210 127 - 133002572 AAGCTCGAGGCCCTGCT-------GTCTCCTTCCATGCC---CGGGGTCAATGGATCC-TTATCTGGCAAGATCTTATCTGTGTGTCCTTGAG-A--------------GACTC-TG-GAGCTGGCTCCTGGAGGTACCGGGAGGCCCA-GGTGGG i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 73229 127 + 109049 AAGCTCGAGGCCCTGCT-------GTCTCCTTCCATGCC---CGGGGTCAATGGATCC-TTATCTGGCAAGATCTTATCTGTGTGTCCTTGAG-A--------------GACTC-TG-GAGCTGGCTCCTGGAGGTACCGGGAGGCCCA-GGTGGG i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_17226 14989 129 + 15119 AAGCTCGAGGCCCTGCC-------GTTTCCTGCCATGTC---TGGGATCAATGGGTCCCTTATCTGGCGAGATCTTATCTGCGTGTCCTTGAC-C--------------GGTTC-TGAGAGCTGGCTCCCCGAGGTACAGAGAGGCCCA-GGTGGG i micMur1.scaffold_17226 I 1 N 0 s otoGar1.scaffold_5322.1-37474 36814 127 - 37474 AAGCTC-AGGCCCTGCT-------GTCTCCTTCCATGTC---TGGTATCAATGGGGCCTTTATCAGGTGAGATCTTATCTAAGTGTCCTTGAC-C--------------AGTTC-TG-GAGCTGGCTCCTCAAGGTACAGAGAGGCCCA-GGTGGG i otoGar1.scaffold_5322.1-37474 I 1 C 0 s cavPor3.scaffold_42 9666054 122 + 15951348 ACACTCGAGGATCTGCT-------CCTT---CCTAGGTCGGTC-------ATGGGTCCCTTATCTGGAGAAATCTTATCTGCGTGTCCTTGAA-G--------------GATTCCTG-GAGCTGGCTCCTGGAGGTACAGGGAGGCCCA-GGTGGA i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 25271 128 + 42081 GGGCCCCGGGCTCTGCC-------TCCTTCCCCCACACCAGCCGGGGTCAATGGATCCCTTATCTGCA-AGATCTTATC-GCTCGGCCTTGGC-C--------------GACTC--G-GAGCTGGCTCCCCAAGGTACAGGGAGGCCCA-GGTGGG i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 1431 120 - 12933 AAGC-------CCTGCT-------GTCTCCTTCCATGCC---CAAGGTCAAGGGATCCCTTATCTGGCGAGATCTTATCTGCATGTCCTTGCT-G--------------GATTC-TG-GAGCTGGCTCCTGGAGGTAC-AGGAAGCCCC-AGCGGG i turTru1.scaffold_93657 I 1 C 0 s bosTau4.chr29 48972848 124 + 51998940 AGGC-------CCTGCCTTCCATGGTTGCCTTCCATGCC---C-AGGTCAAGGGA-CCCTTATCTGGAGAGATTTTATCTGCATGTCCT--CC-G--------------GGTCC-TG-GAGCTGGCTCCTGGAGGTAC-AGGAGGCCCCGGGCGGG i bosTau4.chr29 I 1 C 0 s equCab2.chr12 28937140 123 + 33091231 AAGCTCGTGGCCCTGCC-------GTCTCCTTCCAGGGC---CGGGGTCAAGGGATCCTTTATCTGGCGTGATCTTATCTGCGCGTCCTTGAC-G------------------C-CG-GAGCTGGCTCCTGGAGGTAC-CGGAGGCCCA-GGTGGG i equCab2.chr12 I 1 C 0 s felCat3.scaffold_135390 57520 126 + 302526 AAGCTCACGG-CCCGCT-------GTTTCCGTCCACGGC---CGGGGTCAATGGATCACTTATCTGGCGAGATCTTATCTGCCCGTCCTTGCT-G--------------GATTC-TG-GAGCTGGCTCCTGGAGGTAC-AGGAGGCCCC-GGTGGG i felCat3.scaffold_135390 I 1 C 0 s canFam2.chr18 7534175 127 - 58872314 AAGCTCACGGCCCCGAG-------GTTTCCTTCCATGTC---CGGGGTCAATGGATCACTTATCTGGCGAGATCTTATCTGCATGTCCTTGCT-G--------------GATTC-TG-GAGCCGGCTCCCAGAGGTAC-AGGAGGCCCA-GGTGGG i canFam2.chr18 I 1 C 0 s myoLuc1.scaffold_155660 34367 113 - 124081 AAGCTCAGAC-----------------TCCTT-CATGTC---CGGGGTCAAT-GATC-CTTATCTGGTGAGATCTTATCAGCGTGTCCTTTCG-G--------------GATCT-CG-GAG-CGGCTCCTGGAGGCCC-GGGAGGCCCA-GGTGGG i myoLuc1.scaffold_155660 I 1 C 0 s pteVam1.scaffold_22742 1813 124 - 9737 TGGCTGAGGC-CCTGTT-------ATTTCCTT-CATGCC---CAGGGTCAATGGGTC-CTTATCTGCTAAGATCTTATCTGTGTGTCCTTGTG-G--------------GATCC-TG-GAGCCGGCTCTTGGAGGTAC-GGGAGGCCCA-GGTGGG i pteVam1.scaffold_22742 I 1 C 0 s loxAfr3.scaffold_159 83123 138 + 1045236 AAGGTCAAGGCCCTGCT-------GTTTTCTTCCAT------CAAGGTCAATGGGCCC-TTATCTGGTGAGGTCTTATCTGCATGTCTTTGCC-CCTGTCCCTGCCCCGTCCTC-TG-GAGCTGGCTCCTAGAGGTACAGGGAGGCCCA-GGTAGT i loxAfr3.scaffold_159 I 6 C 0 s proCap1.scaffold_13667 19074 124 - 46842 AAACTCCAGGCCCTTCT-------CTTTCCTTCCAT------CAAGGCCAATGGGCCC-TTATCTAGTGAGATCTTATCTGCATGTCCTTGCC-TC-------------TTCTC-AG-GAGCTGTCCCCTGGAGGTACAGGGAGGCCC--GGCTGA i proCap1.scaffold_13667 I 290 C 0 e calJac1.Contig6069 77115 1884 + 235769 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=202492.000000 s hg19.chr11_gl000202_random 12257 106 + 40103 TAATCACGGGTGCCAAGAAGTGGCCTG-T-GGGGGGGGG---------CCCTCCAT-CTTGGGACCCAACCCGGGACCCCCCTGC---------CCCCG-AGACTGCTTCTCAACCATGCCTTCCCCT- s panTro2.chr11 68199722 107 + 134204764 TAATCACGGGTGCCAAGAAGTGGCCTG-TGGGGGGGGGG---------CCCTCCAT-CTTGGGACCCCACCCGGGACCCCCCTGC---------CCCCG-AGACTGCTTCTCAACCATGCCTTCCCCT- i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 42989 107 + 115376 TAATCACGGGTGCCAAGAAGTGGCCTG-TGGGGGGGGGG---------CCCTCCAT-CTTGGGACCCCACCCGGGAGCCCCCTGC---------CCCCG-AGACTGCTTCTCAACCGTGCCTTCCCCT- i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125994458 92 - 132107971 TAATCACAGGTGCCAAGAACTGTCCTA-T-GGGAGGAGG---------GCCTCCAT-CTTGGGACCCCACCCGGGAGCCCCCTGC---------CCCTG-AGACTGCTTCTCAA--------------- i ponAbe2.chr11 C 0 I 244 s rheMac2.chr14 128157337 106 - 133002572 TAATCACGGGTGCCAAGAACTGGCCTG-T-GGGAGGGGG---------GCCTCCAC-CTTGGGACCCCACCCGAGAGTCCCCTGT---------CCCCA-GGACTACTTCTCAACCATGCCTTCCCCT- i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 73356 106 + 109049 TAATCACGGGTGCCAAGAACTGGCCTG-T-GGGAGGGGG---------GCCTCCAC-CTTGGGACCCCACCCGAGAGTCCCCTGT---------CCCCA-GGACTACTTCTCAACCATGCCTTCCCCT- i papHam1.scaffold6638 C 0 C 0 s otoGar1.scaffold_5322.1-37474 36941 70 - 37474 CAATCA--AGTGCCAGGGATTGGCCCA-G-GGGAGGGGG-----------------------------------AACCCCTTTGC---------CC----------TTCCCCAACAGTGCCTTCCCTG- i otoGar1.scaffold_5322.1-37474 C 0 C 0 s cavPor3.scaffold_42 9666176 97 + 15951348 CAATCAG-GCTGCCAAAGACCAGCCCACAGGGCAGAGGG---------GCCCTCGTGCCAGGGACCCCGCCTGCCCCTCC--------------CC-------CTACTCCTCAGCAGTACCTCACCCT- i cavPor3.scaffold_42 C 0 I 1501 s oryCun2.chrUn0985 25399 80 + 42081 CAATCAC-GCT-CGGGGGATTGGCCTG-GGGGGGGCGGG---------GCCTCCAGCCTCGGGAGCCCGCCTCCGACCGCGTCAT---------CC-------CTGCT--------------------- i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 1551 92 - 12933 CAATCCAGGGCACCAAGGATCGGCCCT-G-AGGGGTGGG---------GCCTC-------------CCGCCTCTG--TCCCCTCC---------CCCCA-GCACCGCTTCCCTCTGAGGCCTCTCCCT- i turTru1.scaffold_93657 C 0 I 2 s bosTau4.chr29 48972972 82 + 51998940 CGAT-CAAGGTGCCAAGGATTG--TCT-G-CAGGGTAGG-----------------------------GCCTCTG--TCCCTGTC---------CCCGT-ACACCGCCTCCCCAGGAGGCCTTTCCGC- i bosTau4.chr29 C 0 I 2 s equCab2.chr12 28937263 104 + 33091231 CAATCAAGGGTGTCAGGGATTGGCCCG-G-AGGGGTGGG---------GCCTCCCG-TCTCCGGACCTACCTCCG--TCCCTTTC---------CCCCA-GCACTGCTTCCCTCTGACGCCTGTCCCT- i equCab2.chr12 C 0 I 2 s felCat3.scaffold_135390 57646 103 + 302526 CAATCAC-GGCGCCAGGCCTTGACCC--G-AGGGGTGGG---------GCCTCCCG-CCTTGGGACCCGCCTCTG--CCCCCTTC---------CCCCAAGCGCTGCCTCCCTACGGCTCCTTTCCCT- i felCat3.scaffold_135390 C 0 I 2 s canFam2.chr18 7534302 98 - 58872314 CAATCACGGGTGCCAGGGACTGACCCA-G-AGGGGTGGG---------GCCTCACA-CCTTGGGACCCGCCTCTG--TCCCCTTC---------CCCCATGGGCTG-CTCTCTACAGAGGCT------- i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 34480 90 - 124081 CAATCGTGGGTGCTGAGGATCAGCC------GGAGAGGG---------GCCTCAGT-CC-------CTGTCCCTG--TCCCTGTC---------CC-CA-GCACTGCTTCCCTAGATG-CCT-TTCCT- i myoLuc1.scaffold_155660 C 0 I 2 s pteVam1.scaffold_22742 1937 101 - 9737 CAATCAAGGGTGCGGCGGACGGTCC---A-GGGGGCGGG---------GCCTCCCG-CCTGGGGAGCCGCCCCTG--TCCCCTTC---------CCTCC-GCATTGCTTCCCTCCATATCCT-TCCCT- i pteVam1.scaffold_22742 C 0 I 2 s loxAfr3.scaffold_159 83261 116 + 1045236 CCATCTAGGGTGCCA-GGACTGGCCCA-T-GGGAGGCGGCAGGGTGGGGCCACCTGCCTTGGGACCCTGCCTTTGTCCTCCCCTC---------CCCCA-GGACTGCTTCTCAACGATACCTTCCCTCT i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 19198 125 - 46842 CCATGAAGGGTGCCA-GGATTGGCCCA-G-GAGAGGGGGCAGGGTGAGGCTGCCTGCCTTGGGTCCCTGTCTTTGTCCACTTCTCCCCCTTCCACCCCA-GAATTGCTTCTCAAAGACACCTTTCCCCC i proCap1.scaffold_13667 C 0 C 0 e calJac1.Contig6069 77115 1884 + 235769 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=499119.000000 s hg19.chr11_gl000202_random 12363 191 + 40103 TGCCCTGCTCCTTGCTGCCTG------CTGGGAG--------------------------------GCACAGGCA-GTG--------------TACTA--GGAAGCCCAAA--------AGAG--AAGCCCAAAGC----AGAACAG--G----------GCA---------------------TCCTCCAGGGCCCAAG---------GGGAGAGGCTTTGGACCTCACTTACAcaa-actgggtgggagcttcctagcagccaaagcaaagaggaaaGAAGCTGAAGGAAGGTGGAGGTGG s panTro2.chr11 68199829 191 + 134204764 TGCCCTGCTCCTTGCTCCCTG------CTGGGAG--------------------------------GCACAGGCA-GTG--------------TACTA--GGAAGCCCAAA--------AGAG--AAGCCCAAAGC----AGAACAG--G----------GCA---------------------TCCTCCAGGGCCCAAG---------GGGAGAGGCTTTGGACCTCACTTACAcaa-actgggtgggagcttcctagcagccaaagcaaagaggaaaGAAGTTGAAGGAAGGTGGAGGTGG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 43096 191 + 115376 TGCCCTGCTCCTTGCTCCCTG------CTGGGAG--------------------------------GCACAGGCA-GTG--------------TACTA--GGAAGCCCAAA--------AGAG--AAGCCCAAAGC----AGAACAG--G----------GCA---------------------TCCTGCAGGGCCCAAG---------GGGAGAGGTTTTGGACCTCACTTACACAA-ACTGGGTGGGAGCTTCCTAGCAGCCAAGGCAAAGAGGAAAGAAGTTGAAGGAATGTGGAGGTGG i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125994794 191 - 132107971 TGCCCTGCTCCTTGCTCCCTC------CTGGGAG--------------------------------GCACAGGCA-GTG--------------TACTA--GGAAGCTCAAA--------AGAG--AAGCCCAAAGC----AGAACAG--G----------GCA---------------------TCCTCCAGGGCCCAAG---------GGCAGAGGCTTTGGACCTCACTTACACAA-ACTGGGTGGGAGCTTCCCAGCAGCCAAAGCAAAGAGGAAAGAAGTTGAAGGAAGGTGGAGGTGG i ponAbe2.chr11 I 244 C 0 s rheMac2.chr14 128157443 187 - 133002572 TGCCCTGCTCCTTGCTCCCTG------CTGGGAG--------------------------------GCACAGGCA-GCG--------------TGCTA--GGAAGCTCGAA--------AGAG--AAGGCCAAAGC----AGAGCAG--G----------GCA---------------------TCCTCCAGGGTCCAAG---------GGGAGAGGCTTCAGACCTC----ACAcaa-actgggtgggagcttcctagcagccaaggcaaagaggaaaGAAGTTGAAGGAAGGTGGAAGTGG i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 73462 185 + 109049 TGCCCTGCTCCTTGCCCCCTG------CTGGGAG--------------------------------GCACAGGCA-GCG--------------TGCTA--GGAAGCTCGAA--------AGAG--ATGGCCAAAGC----AGAGCAG--G----------GCA---------------------TCCTCCAGGGTCCAAG---------GGGAGAGGCTTCAGAcctc------acaa-actgggtgggagcttcctagcagccaaggcaaagaggaaaGAAGTTGAAGGAAGGTGGAGGTGG i papHam1.scaffold6638 C 0 C 0 s otoGar1.scaffold_5322.1-37474 37011 180 - 37474 TCACCCCACCTCGGCTCC------------AGCA--------------------------------GCATTGGTG-GTGGCC-----------GGCGA--GGATACCCTGA--------GAAC--AGGAGCAGGGC----AGGGAGG--G----------G-----------------------------AGGGCCCAAG---------GTAGGAGATTTCAGCCCTTGGCTACACAG-ACGGTGTGGGAACTTCCTAGTAGCCAAGGCAACGGGGAAAGCAGCTGGAGGAAGGTGGAGGTGG i otoGar1.scaffold_5322.1-37474 C 0 C 0 s oryCun2.chrUn0985 25479 226 + 42081 TGCTCTGTTTGTCGCTGTCTGGGGGATCCGGGCGAATGCTTTCAGTCCCCCCCCCCCCCCCCGCACGCACACCCA-GAG--------------TGAGACCGGAAGTCAGAG--------GGGG--AGGAGCCAGGC----AGGGAGGGAG----------GGA---------------------GCTCTCGGGGCCCACGGAAGACACCGGAAGACACGGCGGCCCCTGGTTGCACGACGCTGCGGGG------------AGCCAAGGCAAAGGGGAGGA-----GGAGGAAGGTGGGGGTGG i oryCun2.chrUn0985 C 0 I 1568 s turTru1.scaffold_93657 1645 230 - 12933 TGC-----------TCACCTGCCCACCCTCCACA--------------------------------GCACTGGAG-GTGTCAGGCAA------TAAAA--GGGAGATAGAAAGCAAGTCAGAA--CAAGCAGGAGC----TGAGCAG--A-GAGGGGACGGGG-TGGGGAAGAGGAGGGGTAGGCTTTCCAGGGCCCCAG---------GG-AGCTGTTTCAGCCCTGGGTTACAcaa-actggctctgagcttcctagcagccagggcaaaagggaaaGAAGTTGAAGGAAGGTGGAGTCAG i turTru1.scaffold_93657 I 2 C 0 s bosTau4.chr29 48973056 202 + 51998940 GGCT-------GTGTCATCTGCCTGCACCCCACG--------------------------------GCACTGGAG-GTGTCAGGCCA------TAAAA--AGGACTTAGGAAG---------------------------------G--A-GAGGGGA--GGC-TGGAG--GAGGAAAGCAAGGTTTTCCAGGGCTCCAG---------GG-ATCTGCTTCCGTCCCAGGTCCCACaa-gctggctctgagcttcctggcagccaaggcaaatgggaaaacCATCGAAGGAAGGTGGAGG-AG i bosTau4.chr29 I 2 C 0 s equCab2.chr12 28937369 180 + 33091231 CGCCCTGT---TCGCCACCTGCCTATTCTCCGCA--------------------------------GCCCTAG----------------------------AGAGTTAG----------AGAG--AGAGCAGGAGC----AGAGCGG--G-------------------------------GGTGCCCCAGGGCCCCAGG---------GG-AGACAGTTCAGCCCTTGGTTACACaa-gctggcttcaagcttcctagcagccaaggcaaaagggaaaGAAGTTGAAGGAAGGTGGAGGTGG i equCab2.chr12 I 2 C 0 s felCat3.scaffold_135390 57751 217 + 302526 TG---------CTGTCACCTGCCCGATCTCTGCA--------------------------------GCACTGGGATGCGACAGGCAA------TGAAA--AGGAGTC------------GGAA--ACAGCAGAAGC----AGAGCAG--G-GAGGGGA--CAG-AAGGG--ACGACAGGAGGGAGGTCTTCGGGCCTCAG---------GG-AGATATTTCGACCCCTGGCTACACAA-GCTGGCTCCGAGCTTCCTAGCGGCCGAGGGAAAAGGGAAAGACGTCGAGGGAAGGGAGAGGTGG i felCat3.scaffold_135390 I 2 C 0 s canFam2.chr18 7534400 216 - 58872314 -----------CTGTCACCTGCCCACTCCAAGCT--------------------------------GCGCTGGGACGTATCAGGCCG------TGACA--CGGGGTCA-----------GAAA--AAAGCAGAAGC----AGAGCAG--G-GAGGGGA--GAG-AAGGG--ATAACAGGCAGGAGTTCTTTGGGCCCAAG---------GG-AGATATTTCAGCCCCTGGTTACACAA-GCCggctcagagcttcctagcagccaaggtaaaagggaaaGAGGTTGGGGGAAGGGAGAGGCAG i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 34572 231 - 124081 TGTCCTGC---TGGCCACCTGCCTACTCTCTGCA--------------------------------GCATCGGGG-GTGGCAGGTGA------TGAAA--GGCAGTTAGAAAGGAAATCAGAA--AGAGCAGGAGC----AGAGCAG--G--AGGCAG--GGG-AGGGC--AGAGGACGGTGGCTTCTCCAGGGCCTAAG---------GG-AGATAGGACAGCTGTGGTTCACA--A-GCCGGCTCAGAGCCTTCTAGCAGCCAAGGCCAAAGGGAAGGAAGTTGGATGAAGGTGCAGGTGG i myoLuc1.scaffold_155660 I 2 C 0 s pteVam1.scaffold_22742 2040 214 - 9737 TG-------------------------CCCCGCA--------------------------------GCATAGGGG-GCGGCAGGTAA------CGGAA--AGGAGTTAG-ACGAAAATCGGAAAGAGAGCAGGGGC----AGAGCAG--GCAAGGCAG--GGGCAGAGG--AGAGGAGGGCAAGCACTCCAGGGCCCGAG---------GG-AGAGACTTCAGTTCTTGGTTACGC-A-GCTGGCCCAGAGCTTCCTAGCCGCCAAGGCAAAAGGGAAAGAAGTTGAAGAGAAGTGGAGGTGG i pteVam1.scaffold_22742 I 2 C 0 s loxAfr3.scaffold_159 83377 216 + 1045236 -------TGTTCCGTCACCTGTCTACTCTCCACA--------------------------------GCAATGAAA-ACAGACAGCTAGGGGTTAAACA--GGAAGTCAGAA--------AGAG--AGAGCAGGAGT---GGGGGT----G----------GGG--------GGCAGGGGAAGGACTCTCTAGGGCATGAG---------GGGGACTATTTCAGCCCTGGGTTATAcaa-actgattctgagcttcctagcagccaaggtgaaagggaaagaagatGGAGGAAGATGGAGGTGG i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 19323 207 - 46842 -------TTCTCAGT----TGTCCACTCTCCACA--------------------------------GCAATGAAA-ACAGACAGCTAGCAGTTAAATA--GGAAGTCAGAA--------AGAG--AAAGCAGGAGTTGGGAGGGTTG--G----------GTG--------GACAGGGGAAGCACTCTCCAGGGCATGAG---------GGGGCATACTTCAGCCTGGGGTTGTATAT-ACGCCTtctgagctccctagcagccaaagtgaaagggAGA----------GAAGACAGAAATGG i proCap1.scaffold_13667 C 0 C 0 e calJac1.Contig6069 77115 1884 + 235769 I e cavPor3.scaffold_42 9666273 1501 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=172316.000000 s hg19.chr11_gl000202_random 12554 46 + 40103 TGTAAGAGGTTGGTCTGAGGCATGGACCCCAGGATG-CTCCCCAGAA s otoGar1.scaffold_5322.1-37474 37191 45 - 37474 GGCAAGAGGCCAGTCCCATAGA-GGAGCCCAGGATG-TTCCCCAGAA i otoGar1.scaffold_5322.1-37474 C 0 C 0 s papHam1.scaffold6638 73647 46 + 109049 TGTGAGAGACATGTCTGACGGATGGACCCCAGGATG-CTCCCTGGAA i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128157630 46 - 133002572 TGTAAGAGACATGTCTGACAGATGGACCCCAGGATG-CTTCCTGGAA i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125994985 46 - 132107971 TGTAAGAGGTTGGTCTGATGCATGGACCCCAGGATG-CTCCCCAGAA i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 43287 46 + 115376 TGTAAGAGGTTGGTCTGATGCATGGACCCCAGGATG-CTCCCCAGAA i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68200020 46 + 134204764 TGTAAGAGGTTGGTCTGATGCATGGACCCCAGGATG-CTCCCCAGAA i panTro2.chr11 C 0 C 0 s turTru1.scaffold_93657 1875 46 - 12933 AATAGGAGACTGGTGTCATGCACAGAGCCTAGACCA-TTCCCTAGAT i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48973258 46 + 51998940 AATAGGAGATGAGTCTGATGGACAGAGCCTGGAACG-TTCCCCAGAT i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28937549 46 + 33091231 CGTAGGAAACTGGTCTGACGGATGCAGCCTACAACC-TTCCCCAGAA i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 57968 47 + 302526 CGTAGGAGACTGGTCTCATGGACAGAGCCCGGAACAGTCCCCCAGAA i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7534616 44 - 58872314 TGGAGGAG--TGGTCTGATGGACGGAGCCCAGAACA-TTCCCCGGAA i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 34803 38 - 124081 -------CACCTCAGTGGT-ACTGGCACCTGGAACA-CCCCCCAGAA i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 2254 46 - 9737 GACAGGAGACTGCTGTGATGGATGGCGCCCAGAATG-TTCCCCAGAG i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 83593 42 + 1045236 ---GGTAGACT-GTCTGACGGACATTGCCTAGAACA-TTCTCAGGAA i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 19530 40 - 46842 ---AATAGAA--AACCGATAGGGGTAG-CTAGACTA-TTCCCCAAAA i proCap1.scaffold_13667 C 0 C 0 e calJac1.Contig6069 77115 1884 + 235769 I e oryCun2.chrUn0985 25705 1568 + 42081 I e cavPor3.scaffold_42 9666273 1501 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=14371.000000 s hg19.chr11_gl000202_random 12600 19 + 40103 GTTGTCTGAGTCATCCT---TT s panTro2.chr11 68200066 19 + 134204764 GTTGTCTGAGTCATCCT---TT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 43333 19 + 115376 GTTGTCTGAGTCATCCT---TT i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125995031 19 - 132107971 GTTGTCTGAGTCATCCT---TG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128157676 19 - 133002572 GTTGTCTGAGCCATCCT---TG i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 73693 19 + 109049 GTTGTCTGGGCCATCCT---CG i papHam1.scaffold6638 C 0 C 0 s otoGar1.scaffold_5322.1-37474 37236 19 - 37474 GTTACACGAGTGATCCT---TG i otoGar1.scaffold_5322.1-37474 C 0 C 0 s cavPor3.scaffold_42 9667774 19 + 15951348 GTTCTCTGGGCCCTACC---CA i cavPor3.scaffold_42 I 1501 C 0 s turTru1.scaffold_93657 1921 19 - 12933 GTTGTTTCACTAATCCT-TT-- i turTru1.scaffold_93657 C 0 I 1612 s bosTau4.chr29 48973304 7 + 51998940 GGTGTCT--------------- i bosTau4.chr29 C 0 I 2554 s equCab2.chr12 28937595 17 + 33091231 TTTGTTTGATGAATCCT----- i equCab2.chr12 C 0 I 1613 s felCat3.scaffold_135390 58015 17 + 302526 TTAGTTTCGCCCATCCT----- i felCat3.scaffold_135390 C 0 I 678 s canFam2.chr18 7534660 17 - 58872314 TTTGTTCCACTAAGCCT----- i canFam2.chr18 C 0 I 1370 s myoLuc1.scaffold_155660 34841 18 - 124081 GTTGTTTCATGGATCCTT---- i myoLuc1.scaffold_155660 C 0 I 2279 s pteVam1.scaffold_22742 2300 18 - 9737 GTTACTTCACTGACCCTT---- i pteVam1.scaffold_22742 C 0 I 1223 s loxAfr3.scaffold_159 83635 18 + 1045236 GTGATCTGGGTAATCCT---T- i loxAfr3.scaffold_159 C 0 I 2355 s proCap1.scaffold_13667 19570 18 - 46842 GTTATCTGGCTCATTCT---T- i proCap1.scaffold_13667 C 0 I 1217 e calJac1.Contig6069 77115 1884 + 235769 I e oryCun2.chrUn0985 25705 1568 + 42081 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=63997.000000 s hg19.chr11_gl000202_random 12619 27 + 40103 GG----ACATA-GCAGGACTC-AGTACAT-----------TCAT s myoLuc1.scaffold_155660 37138 29 - 124081 GC----ACATA-GTAGGACTC-GATAGAT---------CGTCAT i myoLuc1.scaffold_155660 I 2279 C 0 s cavPor3.scaffold_42 9667793 28 + 15951348 GC----ACAAG-GTGGAATTCAAGCTAAT-----------TCAT i cavPor3.scaffold_42 C 0 C 0 s otoGar1.scaffold_5322.1-37474 37255 34 - 37474 GGGCCAGCACAGGCAGGACTC-AGTACAT---------GCTCAC i otoGar1.scaffold_5322.1-37474 C 0 C 0 s papHam1.scaffold6638 73712 27 + 109049 GG----ACATA-GCAGGACTC-AGTACAT-----------TCAT i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128157695 27 - 133002572 GG----ACATA-GCAGGACTC-AGTACAT-----------TCAT i rheMac2.chr14 C 0 M 605 s ponAbe2.chr11 125995050 27 - 132107971 GG----ACATA-GCAGGACTC-AGTACAT-----------TCAT i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 43352 27 + 115376 GG----ACATA-GCAGGAGTC-AGTACAT-----------TCAT i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68200085 27 + 134204764 GG----ACATA-GTAGGACTC-AGTACAT-----------TCAT i panTro2.chr11 C 0 C 0 s proCap1.scaffold_13667 20805 24 - 46842 ------ACATG-GTGGGA-TC-ACTGTAT-----------TCTT i proCap1.scaffold_13667 I 1217 C 0 s turTru1.scaffold_93657 3552 36 - 12933 ------ACATA-AGAGGACTC-AATGCCTACTCGAGTCTTGCAT i turTru1.scaffold_93657 I 1612 C 0 s bosTau4.chr29 48975865 26 + 51998940 ------ACAGA-GTAGGATTT--GTGCAT---------TTTCAT i bosTau4.chr29 I 2554 C 0 s pteVam1.scaffold_22742 3541 27 - 9737 ------ACATC-GTAGGGTTC-AATACCT---------TTTAAC i pteVam1.scaffold_22742 I 1223 C 0 s equCab2.chr12 28939225 9 + 33091231 --------------------------TAT---------TTTCAT i equCab2.chr12 I 1613 C 0 s felCat3.scaffold_135390 58710 27 + 302526 ------acata-gtaagactc-aatacgt---------tttctt i felCat3.scaffold_135390 I 678 C 0 s canFam2.chr18 7536047 27 - 58872314 ------ACCTG-GTAAGACTC-AGTACAT---------TTTCTT i canFam2.chr18 I 1370 C 0 e calJac1.Contig6069 77115 1884 + 235769 I e oryCun2.chrUn0985 25705 1568 + 42081 I e loxAfr3.scaffold_159 83653 2355 + 1045236 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=254824.000000 s hg19.chr11_gl000202_random 12646 98 + 40103 ----TGAACAAACAAGGCACTAGACACT-CATT--GCTA---TATTTTTAAGGCCCCTCGTTGAAGTG-AATCACAGCCTCGTTCCCAGTCTCCTGGGCTTTCACCC---TG---------- s papHam1.scaffold6638 73739 88 + 109049 ----TGAACAAACAAGG-------CACT-CATT--GCTA---TGTTTTTAAGGCGCCTACTTGAAGTGAAATCACAACCTGGTTCCCAGTCTCCTGGG----AACCC---CG---------- i papHam1.scaffold6638 C 0 C 0 s panTro2.chr11 68200112 98 + 134204764 ----TGAACAAACAAGGCACTAGACACT-CATT--GCTA---TATTTTTAAGGCCCCTGGTTGAAGTG-AATCACAGCCTCGTTCCCAGTCTCCTGGGCTTTCACCC---TG---------- i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 43379 98 + 115376 ----TGAACAAACAAGGCACTAGACACT-CATT--GCTA---TATTTTTAAGGCCCCTCGTTGAAGTG-AATCACAGCCTCGTTCCCAGTCTCCTGGGCTTTCACCC---TG---------- i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125995077 98 - 132107971 ----TGAACAAACAAGGCACTAAACACT-CATT--GCTA---TATTTTTAAGGCCCCTTGTTGAAGTG-AATCACAGCCTCGTTCCCAGTCTCCAGGGCTTTCACCC---TG---------- i ponAbe2.chr11 C 0 C 0 s otoGar1.scaffold_5322.1-37474 37289 90 - 37474 ----TGAACAAGTAAA----CAAGCACT-CATT--GTTA---GATTTTTAAGGCCCCCAATTGAAATG-AATCA-ATGCGCGTTCCCAGTCTCCTTGGCTCACATG---------------- i otoGar1.scaffold_5322.1-37474 C 0 I 2 s cavPor3.scaffold_42 9667821 87 + 15951348 ----GGAGCAAATAAG---CAAATCCCT-CATT--GGCA---CTTTTTTTAAAC-------TGCAATA-AATGGCAGCCT-GATGCCAGTCTCCTGGGCTTTCACCA---TG---------- i cavPor3.scaffold_42 C 0 I 15 s myoLuc1.scaffold_155660 37167 95 - 124081 ----TAAGCG---AAGACACAAGGCATC-CACT--GTTA---CATTTTTAAGGCCCCATTTGGAAATC-AATTGCTGCCCAGTTCCCAGACTCCTGAGCTCTCCCTC---TG---------- i myoLuc1.scaffold_155660 C 0 I 15 s canFam2.chr18 7536074 91 - 58872314 ----TGAACA---AAGACACAAAGCACT-TATT--GTTA---TGTTTTTAAGGCCTCAAAAGGAAATG-CATTGCAGC--AGTTGCCCAACTGCTGGCCTTTTACCT--------------- i canFam2.chr18 C 0 I 5 s felCat3.scaffold_135390 58737 76 + 302526 ----cgaaca---AAGGTATGAGGCACT-CGTT--GTTA---CATTTTCAAGGCCCCCAAAGGAAATA-AAC-----------------GCAGCCGGATCCCTGACT--------------- i felCat3.scaffold_135390 C 0 I 5 s equCab2.chr12 28939234 92 + 33091231 ----TGAACA---AAGACACAAGGCACT-C-----GTTA---TATTTTTATGGCCTCAAATGAAAACA-GATTGCAGCCTGCTTCCCAAACTCCTAGACTTTCATCC---TG---------- i equCab2.chr12 C 0 I 15 s pteVam1.scaffold_22742 3568 87 - 9737 ----CAGGCA---AAGACACAAAAAAGCGCGTT--GTTA----AGATCGAAGGCCCCAGATGGAAATA-AGTCGCGGCTC--------GATTCCTGGGCGCTCACTC---TG---------- i pteVam1.scaffold_22742 C 0 I 14 s bosTau4.chr29 48975891 93 + 51998940 ----AGAACA---AAGACACAGAACACT-CATT--GTTA---CACTTTTAAGGCCCCAAATGGAACTA-AACTGCAGCCCAGCTCCTCGATTCCTGGGCTTTC--CC---TG---------- i bosTau4.chr29 C 0 I 15 s turTru1.scaffold_93657 3588 94 - 12933 ----TGAGCA---AAGACACGAAACACA-CATT--GTTT---TACTTTTAAGGCCGCAAATGGAAATC-AATTGCAACCCGGTTCCTAGACTCCTGGGCTTTC--TC--ATG---------- i turTru1.scaffold_93657 C 0 I 15 s proCap1.scaffold_13667 20829 117 - 46842 TGTTTGGACA---AATACAGGAAGTACC-CTCTTAGTTAGAGTGTGTTTAAGGTTCCAAGTTGAAACA-AATTGCAACTTTGTTCCCATAGTCCTGGGTTTTCACCTGCATGGGTCCCACTT i proCap1.scaffold_13667 C 0 C 0 e calJac1.Contig6069 77115 1884 + 235769 I e oryCun2.chrUn0985 25705 1568 + 42081 I e loxAfr3.scaffold_159 83653 2355 + 1045236 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e rheMac2.chr14 128157722 605 - 133002572 M a score=165253.000000 s hg19.chr11_gl000202_random 12744 75 + 40103 -CCCCACGG--ACAG----GAT-GCTGGCTCTTCCCTGTCGCCCCGCATTGTGACTGGCTGTGTTCCACATGGTGCAAACT-TA s ponAbe2.chr11 125995175 75 - 132107971 -CCCCACGG--ACGG----GGT-GCTGGCTCTTCCCTGTCGCCCCGCATTGTGACTGGCTGTGTTCCACATGGTGCAAACT-TA i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 43477 75 + 115376 -CCCCACGG--ACGG----GAT-GCTGGCTCTTCCCTGTCGCCCCGCATTGTGACTGGCTGTGTTCCACATGGTGCAAACT-TA i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68200210 75 + 134204764 -CCCCACGG--ACGG----GAT-GCTGGCTCTTCCCTGTCGCCCCGCATTGTGACTGGCTGTGTTCCACATGGTGCAAACT-TA i panTro2.chr11 C 0 C 0 s papHam1.scaffold6638 73827 74 + 109049 -CCCCACGG--ACGG----GGT-GCTGGCTGTTCCCTGTCG-CCTGCATTGTTACCGGCTGTGTTCCACATGGTGCAAACT-TA i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 78999 75 + 235769 -CCCCACGG--ACGG----CGT-GCTGGCTCTTCCCTGTCACCCCACATTGTGACCGGCTGTGCTCCACATGGCACAAACT-TA i calJac1.Contig6069 I 1884 C 0 s otoGar1.scaffold_5322.1-37474 37381 70 - 37474 -TCCCATGG----TG----GGT-GCTGGC---CCCCAGTCACCCTGCATTGTAACTGGCTATGCTCCAAGCAACACAACCT-GA i otoGar1.scaffold_5322.1-37474 I 2 C 0 s cavPor3.scaffold_42 9667923 71 + 15951348 -CCCCACTC--ACGG----C-T-GCCAGC---TCCCAGTGCCCCAAAGTTCTCATTGGCTCAGTAATGAGGGGTGCACACG-GC i cavPor3.scaffold_42 I 15 C 0 s myoLuc1.scaffold_155660 37277 68 - 124081 -CCCCAC----AGAG----GGT-GCCAGC---ACCCAGTCACCCCACATTGTGACCGGCTGTGTTCC-AGCAACACCCAC--TA i myoLuc1.scaffold_155660 I 15 C 0 s canFam2.chr18 7536170 73 - 58872314 -CCCCACGT--AGGG----AGT-GCCAGG---CCCCCTTCTCCCCACGCTGTGACCTGCtgggctctgagcgacaggaactgta i canFam2.chr18 I 5 C 0 s felCat3.scaffold_135390 58818 64 + 302526 -CCCCACGT--AGGG----GAT-ACCCGC---TCCTAGCCTCTCCGCACTGGGACCGGCTGGGTTCTGAGTGACA--------- i felCat3.scaffold_135390 I 5 C 0 s equCab2.chr12 28939341 73 + 33091231 -CCCCATGG--AGCG----GGT-GCCATC---TCCCAGTCGCCCCCCATTGAGACCAGCTGAACTCCAAGTGACACAAACCCTA i equCab2.chr12 I 15 C 0 s pteVam1.scaffold_22742 3669 75 - 9737 -TCCCATGTCGGGGG----GGTGGCCAGC---TCCCTGTCACCCCGCAGTGGGACAGGAGGCACGCA-AGCAGCACAAACCGTG i pteVam1.scaffold_22742 I 14 C 0 s bosTau4.chr29 48975999 59 + 51998940 -CCCAACAT--GGTG----GA-----ACC---TCCTGGTCACCCCATATTGTG----------CTCCAAGCAACGCAAACCACA i bosTau4.chr29 I 15 C 0 s turTru1.scaffold_93657 3697 63 - 12933 -CCCGACGC--AGGG----GAT-GCCAGC---TCCCAGCCAGCCTACGCTGTG----------CTCCGAGCAGCACAAACCGTA i turTru1.scaffold_93657 I 15 C 0 s proCap1.scaffold_13667 20946 57 - 46842 CCTCCAGGG--TTGGTAACAGT-GCCTATTTTTCCCCACATCTCAGCAACAGGGACATCT------------------------ i proCap1.scaffold_13667 C 0 C 0 e oryCun2.chrUn0985 25705 1568 + 42081 I e loxAfr3.scaffold_159 83653 2355 + 1045236 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e rheMac2.chr14 128157722 605 - 133002572 M a score=43750.000000 s hg19.chr11_gl000202_random 12819 22 + 40103 TTCCC-AATTGACCCGTGGGGTC s ponAbe2.chr11 125995250 22 - 132107971 TTCCC-AATTGACCCGTGGGGTC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 43552 22 + 115376 TTCCC-AATTGACCCGTGGGGTC i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68200285 22 + 134204764 TTCCC-AATTGACCCGTGGGGTC i panTro2.chr11 C 0 C 0 s papHam1.scaffold6638 73901 23 + 109049 TTCCCTAATTGACCCATGGGGTA i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 79074 23 + 235769 TTCCCTAATTGACCCATGGGGTC i calJac1.Contig6069 C 0 C 0 s otoGar1.scaffold_5322.1-37474 37451 23 - 37474 TTCCCCAGTTACTCCATGGAGTC i otoGar1.scaffold_5322.1-37474 C 0 N 0 s cavPor3.scaffold_42 9667994 21 + 15951348 TTCCCTGACGGAGCC--TGGGTC i cavPor3.scaffold_42 C 0 C 0 s myoLuc1.scaffold_155660 37345 22 - 124081 TTCCCTGCGTAACCCATCCTGT- i myoLuc1.scaffold_155660 C 0 C 0 s canFam2.chr18 7536243 22 - 58872314 ttccctgat-gagtctgcatgtc i canFam2.chr18 C 0 C 0 s felCat3.scaffold_135390 58882 10 + 302526 -------------CTCACGTGTC i felCat3.scaffold_135390 C 0 C 0 s equCab2.chr12 28939414 23 + 33091231 TTCCCTGATGGAGCCACCGTGTC i equCab2.chr12 C 0 C 0 s pteVam1.scaffold_22742 3744 23 - 9737 TTCCCTGATGACTCGGTCGTGTG i pteVam1.scaffold_22742 C 0 C 0 s bosTau4.chr29 48976058 17 + 51998940 TTTCCCGATTGAGCCCT------ i bosTau4.chr29 C 0 C 0 s turTru1.scaffold_93657 3760 17 - 12933 TTCCCTGATTGACTCCT------ i turTru1.scaffold_93657 C 0 C 0 s loxAfr3.scaffold_159 86008 22 + 1045236 -TCCCTGATTAATTCATCGAGTC i loxAfr3.scaffold_159 I 2355 C 0 s proCap1.scaffold_13667 21003 22 - 46842 -TGCCCAATTCACTGATGGAGTC i proCap1.scaffold_13667 C 0 C 0 e oryCun2.chrUn0985 25705 1568 + 42081 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e rheMac2.chr14 128157722 605 - 133002572 M a score=228850.000000 s hg19.chr11_gl000202_random 12841 118 + 40103 TGCTGGAGCCCTAGGGCTGACCACAGGGG---------------------------------------------------CTGCA------------------------------------GGGCAT---------------------------GGTTGCCCTG-----------GGAGCCCTG--------------------CAGCTC--AGGTCCACTTAGCACTTTCTGGAAAAGCAA--CCGCCTCTAGggggcagcacagt s ponAbe2.chr11 125995272 118 - 132107971 TGCTGGAGCTCTAGGGCTGACCACAGGGG---------------------------------------------------CTGCA------------------------------------GGGGTT---------------------------GGCTGTCCTG-----------GGAGCCCTG--------------------CAGCTC--AGGTCCGCTTAGCACTTTCTGGAAAAGCAA--CCGCCTCTAGggggcagcacagt i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 43574 118 + 115376 TGCTGGAGCCCTAGGGCTGGCCACAGGGG---------------------------------------------------CTGCA------------------------------------GGGCAT---------------------------GGTTGCCCTG-----------GGAGCCCTG--------------------CAGCTC--AGGTCCACTTAGCACTTTCTGGAAAAGCAA--CCGCCTCTAGggggcagcacagt i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68200307 118 + 134204764 TGCTGGAGCCCTAGGGCTGACCACAGGGG---------------------------------------------------CTGCA------------------------------------GGGCAT---------------------------GGTTGCCCTG-----------GGAGCCCTG--------------------CAGCTC--AGGTCCACTTAGCACTTTCTGGAAAAGCAA--CCGCCTCTAGggggcagcacagt i panTro2.chr11 C 0 C 0 s papHam1.scaffold6638 73924 118 + 109049 TGCTGGAGCTCTAGGGCTGACTACAGGGT---------------------------------------------------CTGCA------------------------------------GGGGAT---------------------------GGTTGTCCTG-----------GGAGCCCCG--------------------CAGCTC--AGGTCAGCTTGGCACTTTCTGGAAAAGCAG--TCGCCTCTggggggcagcacagt i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 79097 145 + 235769 AGCTGGAGCTGTAGGGCTGCCCACAGGGG---------------------------------------------------CTGCA------------------------------------GGGAATGATGGCCGTCCCAGGACCCCTAGGGAGGGTCGTCCCG-----------GGACCCCTG--------------------CGGCTC--AGGTCCACCCAGCACTTTCTGAAAGAGCAG--TCGCCTCTGGGGGGCAGCACAGT i calJac1.Contig6069 C 0 C 0 s cavPor3.scaffold_42 9668015 86 + 15951348 ATCTTGAGCTCTCTACCTGACCGCAGAG----------------------------------------------------CTGC----------------------------------------------------------------------AGCTACTCAG-----------GG----------------------------------------------TCACTTTCCGGAAATCAAA--CCACCTCTGGGGGGCAGCATGGT i cavPor3.scaffold_42 C 0 C 0 s myoLuc1.scaffold_155660 37367 105 - 124081 GTGT-CAGCTCTGGATCTGACGGTGGGAG---------------------------------------------------CTGGG------------------------------------GAGG-----------------------------GACGCTCCTA-----------GAAGCCTCT--------------------CGGCT--------------CCACTCCCTGGAAAACCAGACTCACCTCTAGggggcagcatggt i myoLuc1.scaffold_155660 C 0 C 0 s canFam2.chr18 7536265 118 - 58872314 gcctccagctcagcctctggcTGTGGGAG---------------------------------------------------CTGGG------------------------------------GAGA-----------------------------GACACCCCCA-----------GGAGCAGCT----------------------ACTCCGGGGTCAGTTTAGCCCTTTCTGGAAAATCAGACTGACCTCTggggggcagcatggc i canFam2.chr18 C 0 C 0 s felCat3.scaffold_135390 58892 114 + 302526 ACCTCCAGCCCTGGGTCTAACCGTGGG-G---------------------------------------------------CCCGG------------------------------------GAGG-----------------------------GACACCCCCA-----------GGCGCTGTC----------------------GCTTCTGGGTCAGTTT---CCTTTCTGGAAAATCAGACTCACCTCTggggggcagcatggt i felCat3.scaffold_135390 C 0 C 0 s equCab2.chr12 28939437 97 + 33091231 ACCTCCAGCTCTGAGTCTGACGGTGGGAG---------------------------------------------------CCG-------------------------------------------------------------------------------------------------CGCT----------------------GCTCCACCGTCAGCTTAGAACTCTCTGGAAAACCACACTCGCCTCTggggggcagcatgat i equCab2.chr12 C 0 C 0 s pteVam1.scaffold_22742 3767 120 - 9737 GTGTCCAGCCCGGGGTCTGACCGT-GGCG---------------------------------------------------CTGAG------------------------------------GCGG-----------------------------GATGCGCCCA---------CGGGAGCCACT--------------------GGGCTGC-GTGTCCCCTTAGCACTCACTGCAAAACCGGGCCCGCCTCTggggggcagcatggt i pteVam1.scaffold_22742 C 0 C 0 s bosTau4.chr29 48976075 238 + 51998940 GTCTCCAGCTCTGGATCTGACTGAGGGAGCCCCAGCCAGTTTGtgtgtgcgtgctcagtcactcagtcgtgtccaactctctgtgacaccgtggaccacagcctgccaggctcctctgtccatgg-----------------------------gattctccaggcaagaatactggagtgggttccatgccctcctccaggggagtcttcccagccAGCTTAGCACTCTTAAGAAAACCAGACCTACCACTggggggcggcatggt i bosTau4.chr29 C 0 C 0 s turTru1.scaffold_93657 3777 87 - 12933 GTCTCCAGGTCTGGATCTGACCCTGGGGG---------------------------------------------------CTGTG---------------------------------------------------------------------------------------------------------------------------------GCTAGCTCTGCACTCTCCGAAAAACTAGACCCGCCGCTggggggcagcatggt i turTru1.scaffold_93657 C 0 C 0 s loxAfr3.scaffold_159 86030 124 + 1045236 ATCTCCAGCTCAGGATAAGACC-CAAGAG---------------------------------------------------CTGGA------------------------------------GGAGGGA--------------------------GGCCTGCCCA---------GGCGAGCCCTG--------------------GCGTTCACAGGTCAGCACGGCACTTTCCGGAAAGCCAAACTCACTCCTGGGGAGCAGCATAGT i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 21025 123 - 46842 CTCTCCAGCTTGGGATAAGACC-CAAGTG---------------------------------------------------CTGGA------------------------------------CGAAG----------------------------GGCCCACCCA--------CCAAAAGCTCTG--------------------GGGTTCACATGTCAGCACAGTACTTTCCAGAAAACCAGACTGACCCCTGGAGAGCAGCACGGT i proCap1.scaffold_13667 C 0 I 5848 e oryCun2.chrUn0985 25705 1568 + 42081 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e rheMac2.chr14 128157722 605 - 133002572 M a score=178018.000000 s hg19.chr11_gl000202_random 12959 71 + 40103 gtcaccgggaaaag-ccgga-cgtggcttcggg-gacctgggcttggatccaggatccagcccc--tgcc-gcttca s ponAbe2.chr11 125995390 71 - 132107971 gtcaccaggaaaag-cggga-cgtggcttcggg-gacctgggcttggatccaggatccagcccc--tgcc-gcttca i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 43692 71 + 115376 gtcaccgggaaaag-ccgga-cgtggcttcggg-gacctgggcttggatccaggatccagcccc--tgcc-gcttca i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68200425 71 + 134204764 gtcaccgggaaaag-ccgga-cgtggcttcggg-gacctgggcttggatccaggatccagcccc--tgcc-gcttca i panTro2.chr11 C 0 C 0 s papHam1.scaffold6638 74042 71 + 109049 gacactgggaaaag-ccgga-catgacttcggg-gacctgggcttggatccaggatccagcccc--tgcc-gcttca i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 79242 71 + 235769 GTCACCAGGAAAAG-CCGGA-CATGGCTTCCGG-GCCCTGGGCTTGTATCCAGGAGCCAGCCCC--TGCC-GCGCCA i calJac1.Contig6069 C 0 C 0 s cavPor3.scaffold_42 9668101 48 + 15951348 GTCACAGGAGGACA-TGCAT-GGTGTCTCCAGGTGGCCCAGGCTTGGACA--------------------------- i cavPor3.scaffold_42 C 0 C 0 s myoLuc1.scaffold_155660 37472 68 - 124081 gtcatgggaaaaag-ccagatgctggcttcagagcacctgggtctgggtc-------tggatccagtgctggctgc- i myoLuc1.scaffold_155660 C 0 C 0 s canFam2.chr18 7536383 63 - 58872314 gtcatgggaaaaag-ccg---actggcttcaggtgacctgggtctggatc-------caggccc--tgct-gcttca i canFam2.chr18 C 0 C 0 s felCat3.scaffold_135390 59006 64 + 302526 gtcgtaggaaaaagccca---actggcttcccgtgacctgggtctggatc-------cgagccc--tgct-gcctca i felCat3.scaffold_135390 C 0 C 0 s equCab2.chr12 28939534 67 + 33091231 gtcgtgggaaaaaggctggatgctggcttccggtgacctgagcctggaac-------cgactcc--tgcc-ggttca i equCab2.chr12 C 0 C 0 s pteVam1.scaffold_22742 3887 66 - 9737 gtcacggggagaag-ctcttcgctggc-tcagaggatctgggccgggatc-------cggttcc--tgccagcttca i pteVam1.scaffold_22742 C 0 C 0 s bosTau4.chr29 48976313 62 + 51998940 gtcatgggaaaaag-ccgga----agctttgggtgacctgggtttagatc-------tagcccc--tgcc-cctcca i bosTau4.chr29 C 0 C 0 s turTru1.scaffold_93657 3864 62 - 12933 gtcgtgggaaaaag-ccgga----agcttcaggggacctgggtctggatg-------aggcccc--tgcc-ccttcg i turTru1.scaffold_93657 C 0 C 0 s loxAfr3.scaffold_159 86154 41 + 1045236 -------------------------GTCAcaggtggcccggg-ttggacc-------cagccct--ggca-gctggg i loxAfr3.scaffold_159 C 0 C 0 e oryCun2.chrUn0985 25705 1568 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e rheMac2.chr14 128157722 605 - 133002572 M a score=805008.000000 s hg19.chr11_gl000202_random 13030 426 + 40103 gcagtg-gagtgatgggggccaagtcacttccacccca-agcctcagtgtctccCTGCACCCCTCCACCCCCTATAGAGTGGGACTAA---GAGT--GTTCTGAGCCAGGC---------------TTCCAGTG----AGGTGGGGGTGGGGAGG------GCAG-------GACAGACG----GGTCAG-T------------------------------------GTCCTCGC----T---CCTGGCCCCTTTTCACCTCTGATGTTGAAGTTAAACATTCAACAAATTATGAGAAAAT----AAAGCAACAGTTT--AAAAATAGGAGAAAACGTATCCCAA-AAGAATGTT-CTATGATTTCCGGCTGGGTCACTCTTGGCA-GGCTCCAGCAGGGA----GGAGCAGGGCAGGGC-----C--GGGGC-------------ATGGCTCAGGGAATG-GGGGAGCGCTCT-CCCTAAGACCCCAGC-------CCCAGCCTCCGCCTTGTCCTCAGGCAGCCAGGA--------------GCAGGC-ACAGCTGCCTCGCTTCCC s calJac1.Contig6069 79313 385 + 235769 GCGGGG-GAGTGACG-GGGCCAAGTCACTTCCGCCCCA-AGCCTCACTGTC--------CCCCTCCACCCCC-ATCAAGTGGGTCTAA---GAGT--GTTCCGAGCCAGGC---------------TCCCGGTG----AGGTGGGGGTGGGGACG------GCGG-------GACAGACG----GGG-AG-C------------------------------------GTCCT-GC----T---CCTGGCCCCTTTTCACCTCTGATGCTGAAGTTAAACATTCGACAGGCTATGACAAAAT----GAAGCAACCGTTT--AAAAATAGGAG----------------AGAATGTT-CTGTGATTTCCGGCTGGGTCACTCTTGGCG-GGCTGTGGCAGGGA----GGGGCAGGGCAGGGC-----T---GAGC-------------GTGGCTC-GGGAAGC-GGGGAGCTCTCT-CCCTAAGCACCCA-------------------GCCCAGCCCTCAGGACTCCAGGA--------------GCAGGC-ACAGCCGCCTCCCTTCCC i calJac1.Contig6069 C 0 C 0 s papHam1.scaffold6638 74113 425 + 109049 gcagtg-gagtgatgcggaccacgtcacttccgcccca-agcctcagtgtctccCTGCACCCCTACACCCCCTATAAAGTGGGACTAA---GAGT--GTTCTGAGCCAGGC---------------TCCCGGTG----AGGTGGGGGTGGGGAGG------GCAG-------GACAAACG----GGACAG-C------------------------------------ATCCTTGC----T---CCTGTCCCCTTTTCACCTCTGACGCTGAAGTTAAACATTCAACAAATTATGAGAAAAT----AAAGCAACAGTTT--AAAAATAGGAGAAAACGTATCCCAA-AAGAATGTT-CTATGATTTCCGGCTGGGTCATTTTTGGCA-GGCTCCGGCAGGGA----GGAGCAGGGCAGGGC-----C--AGGGC-------------ATGGCTCGGGGAAGG-GGGAAGCTCTCT-CCCTAACCCCCCA-C-------CCCAGCCTCTGCCCTGTCCTCAGGCAGCCAGAA--------------GCAGGC-ACAGCTGCCTCACTTCCC i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128158327 426 - 133002572 GCAGTG-GAGTGATGGGGGCCACGTCACTTCCGCCCCA-AGCCTCAGTGTCTCCCTGCACCCCTCCACCCCCTATAAAGTGGGACTGA---GAGT--GTTCTGAGCCAGGC---------------TCCCGGTG----AGGCGGGGGTGGGGAGG------GCAG-------GACAAACG----GGACAG-C------------------------------------ATCCTTGC----T---CCTGGCCCCTTTTCACCTCTGACGCTGAAGTTAAACATTCAACAAATTATGAGAAAAT----AAAGCAACAGTTT--AAAAATAGGAGAAAACGTATCCCAA-AAGAATGTT-CTATGATTTCCAGCTGGGTCACTTTTGGCA-GACTCTGGCAGGGA----GGAGCAGGGCAGGGC-----C--AGGGC-------------ATGGCTCGGGGAAGG-GGGAAGCTCTCT-CCCTAAGCCCCCCAC-------CCCAGCCTCTGCCCTGTCCTCAGGCAGCCAGGA--------------GCAGGC-ACAGCTGCCTCGCTTTCC i rheMac2.chr14 M 605 C 0 s ponAbe2.chr11 125995461 426 - 132107971 gcagtg-gagtgatgggggccaagtcacttccgcccca-ggcctcagtgtctccctgcacccctccaccccctataaagtgggactaa---gagt--gtTCTGAGCGAGGC---------------TTCCAGTG----AGGTGGGGGTGGGGAGG------GCAG-------GACAGACG----GGTCAG-T------------------------------------GTCCTCGC----T---CCTGGCCCCTTTTCACCTCCGATGTTGAAGTTAAACATTCAACAAATTATGAGAAAAT----AAAGCAACAGTTT--AAAAATAGGAGAAAACGTATCCCAA-AAGAATGTT-CTATGATTTCCGGCTGGGTCACTCTTGGCA-GGCTCCGGTAGGGA----GGAGCAGGGCAGGGC-----C--GGGGC-------------ATGGCTCAGGGAATG-GGGGAGCTCTCT-CCCTAAGACCCCAGC-------CCCAGCCTCCGCCCTGTCCTCAGGCAGCCAGGA--------------GCAGGC-ACAGCTGCCTCGCTTCCC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 43763 426 + 115376 gcagtg-gagtgatgggggccaagtcacttccgcccca-agcctcagtgtctccCCGCACCCCTCCACCCCCTATAGAGTGGGACTAA---GAGT--GTTCTGAGCCAGGC---------------TTCCAGTG----AGGTGGGGGTGGGGAGG------GCAG-------GACAGACA----GGTCAG-C------------------------------------GTCCTCGC----T---CCTGGCCCCTTTTCACCTCTGATGTTGAAGTTAAACATTCAACAAATTATGAGAAAAT----AAAGCAACAGTTT--AAAAATAGGAGAAAACGTATCCCAA-AAGAATGTT-CTATGATTTCCGGCTGGGTCACTCTTGGCA-GGCTCCAGCAGGGA----GGAGCAGGGCAGGGC-----C--GGGGC-------------ATGGCTCAGGGAATG-GGGGAGCGCTCT-CCCTAAGACCCCAGC-------CCCAGCCTCCGCCTTGTCCTCAGGCAGCCAGGA--------------GCAGGC-ACAGCTGTCTCGCTTCCC i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68200496 426 + 134204764 gcagcg-gagtgatgggggccaagtcacttccgcccca-agcctcagtgtctccCTGCACCCCTCCACCCCCTATACAGTGGGACTAA---GAGT--GTTCTGAGCCAGGC---------------TTCCAGTG----AGGTGGGGGTGGGGAGG------GCAG-------GACAGACG----GGTCAG-T------------------------------------GTCCTCGC----T---CCTGGCCCCTTTTCACCTCTGATGTTGAAGTTAAACATTCAACAAATTATGAGAAAAT----AAAGCAACAGTTT--AAAAATAGGAGAAAACGTATCCCAA-AAGAATGTT-CTATGATTTCCGGCTGGGTCACTCTTGGCA-GGCTCCAGCAGGGA----GGAGCAGGGCAGGGC-----C--GGGGC-------------ATGGCTCAGGGAATG-GGGGAGAGCTCT-CCCTAAGACCCCAGC-------CCCAGCCTCCGCCTTGTCCTCAGGCAGCCAGGA--------------GCAGGC-ACAGCTGCCTCGCTTCCC i panTro2.chr11 C 0 C 0 s oryCun2.chrUn0985 27273 340 + 42081 -CAAGG-CAGTGAGGCTGGCCAAGTCCCTTCTGC-------------TGTGCCACAGTTTCCCCCCTCCACCAGCCCCGGGCGCTGAGGCTCAGT--GTTGCAAGCC----------------------------------TGGGGGCCTGGCTG------GCAGAGGCGGTGGCGGGAT----GGACAT-G------------------------------------GTCCTGGTCCCAT---CCCGGCCCCT-TCCCACCTCGGTGCTG-----------TCCCAGTGTTCTGGGAAAAG----AAAGCGAC-ATTT--AAAAATAGGAGGCCGCATCTCCGGA-AAGAACGTTCCCGCG-GGTCCCACCGGGACGCTCTTGGCA-GGCAGTGGCGGGGACGGTCGGGGGCGGCACGGC-----C-CGGGG----------------CGCTC------CT-GGGAGGCTGCCT----------------------------------CCCGGGCCTGGGACAGC-------------------------------------------- i oryCun2.chrUn0985 I 1568 C 0 s cavPor3.scaffold_42 9668149 337 + 15951348 --AGCT-GAGCGACACTGGCCAAGCCCTGTCCA---------------------------CCCCTGAGCCCTTGCATAGGGTGGTGAG---TAGC--AATGCGGG-------------------------------------GGGGGGGTGTCTGTGTACCGCCACCACATCAAGTGGAC----GGCCAC--------------------------------------ATCCTTGT----T---TCTGGCCTCTGTCCAACTCCGACGCTGAAGTTAAACACTTACAAAGCGATGGGAAAAT----AAAG-----GTTT--AAAAATAGGAGGAAATATGTCCAAA-ATGAACACT-CTATA-TTTCCTGCTGGGTCACTCTTGGCA-GACTCTGGTGGGGG----TGAGGAGGGCAGGGC-----TGTGGGG----------------GGCCC------TT-GAGGAGCTTTCT----GGGGGCTCCTAC-------CCCAA-----GTTCAGGCCTCAG------------------------------------------------- i cavPor3.scaffold_42 C 0 C 0 s myoLuc1.scaffold_155660 37540 410 - 124081 ----------------tgaccgcttcccctcctg-----agcctcagtgttg---------------ccctctgtaaagtggg--------------acttagaatCGGACG---------TGCCAGGCAGCCC----CGAGGGGAGGCGGTGGG------CGTG-------GAGGGCAGGCTGTGCCAC-C-------TGA----GATGATGTCAGACAGACCGGGGAGCACGGC----T---CCCGGCCCCTTC-------------------TGAACATCCAAAAAGCTGT--GGGAAA----CAGGCAATGGTTT--AAAAATAGGAGGAAACGTG-TCCAA-AAGAACGTT-CTATTATTTCCCGCGGGGTCGCTCTCGGCA-GGCTCTGG--GGGA----GGAGCCGGGCAGGGCCGTGCC--GAGGCTG--TTGCTAATGAGAGCTC------TT-CGGGGGCTCTGAGCGCTAAACCACGGG--------CCCAGCCTCCGGCC-CTCCTCGGGCAGCCAGGC------AGACGAGAGTGGGA-ACAGCTGCCT-GCTTCCC i myoLuc1.scaffold_155660 C 0 C 0 s canFam2.chr18 7536446 402 - 58872314 ggagcc-a-gtgaccctggctgagtcacttgggctcccgagcctcagggtc----------------ccctccgtaaag----------------------tgcggCGGCTGCG-TGTGCT-----GCCCGGGG----AGGTGGTGGCGCGTGGT------GCCA-------GGACTCTG----CGCCCC-C--------GA----GATGCTTTCAGACAGGCTGGGGAGCCTCGC----------TGGCCCCTTTACTCCCCGGATGCCGAAGTTCAACATCCAAACAGTTAT-GGGAAAA----AAAGCAACAGTTT--AAAAATAGGAGGAAACATGTCCAAG-AAGAACGTT-CTATTATTTCTCTCT-GGTCGCTTTTGGCA-GGCTCTGGC-GGGA----GGAGCAGGACAGGG------C--AGGACCGTCTCAGTAGCTAGAGCTC------TC-AGGGGCCTCCCGGCCCTCGGCCGCCAGC------CCCCA-CCTCTGCCC-CTCCTTGGGCAACCAGGC--------------------------------------- i canFam2.chr18 C 0 I 10 s felCat3.scaffold_135390 59070 441 + 302526 ggagcc-g-gcgacactggctgagtcacttctgctcccgagccccagcgtccGA------------ACCTTCCAT-----------------------------GCCGGGTGGA-TGTGCTCAGTGGCGGGGGG----AGGTGAGGGCATAGACT------GCGG-------GGACCCTG----TGCCCC-C--------GA----GACACCTTCAGACAGACTAGCGGACGTTGC----T---GGTGGCCGTTTTTCTCCCCGGATGCTGAAGTCAAACGTGCTAACAGTTCTGGGGGAAA----AAAGCAACAGTTT--AAAAATAGGAGGAAACATGTCCAAACAGGAACATT-CTATTATTTCTCTCT-GGTCGCGCTTGGCA-AGCCCTGGC-GGGA----GGAGCAGGAGAAGG------C--AGGGCCGTCTCACTAGCCAGAGCTC------CT-GGGGGGCTCCCAGCCCCGAGCCCCCCGC------CCCCAGCCTCGGCCC-CTCCTTGGGCAGCCGGGA------CACTGAGGGCCGTC-ACAGCTACCT-GCTTCCT i felCat3.scaffold_135390 C 0 I 3 s equCab2.chr12 28939601 439 + 33091231 caggcc-gagaggtgttagtcacgtcgcctcagctccc-agcctcagtgtc----------------ccctccagaaaggggggCCGT---CAT---CTTTCGGGCCGGGCAGC-TGCACTCGCCGGCCGGAGA----AGCAGTGGGCACGCAGG------GCCA-------CGACTCTG----CGCCACGC--------CA----GGTAGAGTCAGACAGACCGGAGCGTCGATC----------CGGCCCCTGTGCACCTCGGATGCTGGAGGTGCGTCCCCCAAAAGCTAC--GGGGAA----AACGCAACAGTTA--AAATGTAGGAGGAAACATG---------------T-CTGTTACTTCCCGCTGGGTGGCTCTTGGCAGGGCTCGGCC-AGGA----GGAGCCGGGCAGGG------T--GGTGCGG------------GAGCTC------CCTGGGGGGCCCTGAGCCCTCAGCCCCCGGC------CCCCAGCCGCCACCCTCTCCTCGGGCAGCCAGGCCTCGGAGAAGGAGAGCAGAC-ACCGCCACCT-GCTCCCC i equCab2.chr12 C 0 C 0 s pteVam1.scaffold_22742 3953 433 - 9737 tcggtc-gagtgacaacgcctgagtcacctccaggccc-ggcctcggtgtcc---------------gcctcagtaaagtggggctgc---caagacacctcgTGCTGGGCGGC-TGCACTCGCTGGCGAGGGT----GGCAGGGAGTGTGCAGG------GCCG-------GGCCTCCGGGCCCCCCAC-C--------GA----GATCACGCCGGACTGACCGGGGAGCTTCGC----T---CCTGGCCCCTTT-------------------CCAACGTTCAAAAAGTTAT--AAGGGG-----AAGCAATGGCTTTAAAAAATAGGAGGAAAGAT--CCAAG-AAGAACATT-CGATTACTTCCCGCTGGGTGGCTGTCACCA--ACTCTGGCTGGGA----GGAG-CGGGAGGGACCGTGGC--AAGGCCGACCGGCTGGCGAGAGATC------TT-TGGGGGCTCTGAGCTCTCA----------------CCTGGCCCCCGG-----CCTCAGGCAGACAGGC------TGACGAGAGCAGGACACAGCCACCT-GC----- i pteVam1.scaffold_22742 C 0 C 0 s bosTau4.chr29 48976375 371 + 51998940 tgagcc-g-gggagactggcccagtcacttctgctcccaagcctcagtgttc---------------ccctccataaagtggg--------------CTCACCTGCCGGG-AGA------------------------GGGAATGAGCATAAAGG------GGCA-------GGACCCTG----TGCCCC-C-------CGA----GATAATTTCAGACGGACTGGGGACCATTGC----T---CCCAGCTCCTTT-------------------TCAATATCCGAAGAGTTATGGGGGGGAGAGGGAAGCAACAGTTT--AAAAATAGGAGGACACATG-TCCAG-AAGGACATT-CTATCATTTCCCACTTGGTCGCTCTTGGCA-GGCTCCAGCTGGGA----GGAGCGGGGAAGGGCTGTGCT--GAGGCCATCGTGCTGTCTGGGTCTC------TT-TGGGGGTTCTG---------------------------AGCCTAAGCCCCCTCCTTGGGCAGCCA------------------------------------------ i bosTau4.chr29 C 0 C 0 s turTru1.scaffold_93657 3926 415 - 12933 tgagcctg-gtgacgctggcccagccacgtctgctcccgagcct-ggagttt---------------ccctccacaaagtggggctaG---GACT--CTTCCGTGCCAGGCAGA-TGCGCTTGCTGACC--GTG----GAGACAGGGCGTGAAAG------GCCA-------GGACCCTG----TGCCAC-C-------CGA----GATAATTTCAGACAGACTGGGGACCAAGGC----T---CCCAGGCCTTTT-------------------CCAACATGCAAAACGTTACAGGGGGAA----AAAGCAACAGTTT--AAAAATAGGAGGACACATG-TCCAA-AAGAACGTT-CTATCATTTCCCACTGGGTCTCTCTTGGCA-GGCTCTGGCTGGGA----GGAGCAGGGACAGGCCACGGC--GAGGCCATCTCGCTATCAAGAGCTC------TC-TGGGGGCTCTGGGTCCTAAGCCCCTGGC------CCCCAGCCTTTGCCCCCTCCTTGGACAGCCA------------------------------------------ i turTru1.scaffold_93657 C 0 C 0 s loxAfr3.scaffold_159 86195 454 + 1045236 tgagct-gagtgacgctgaccaagtcatatccactcct-gggcctgatgt-----------------tctcctgtaaggtagggtggA---GAAT---CTGGGTGCCAGGGAGGCCGTGCT-----GCTCGGGGGCAAAGTCTTGTGGGTGAAAG------GCCA-------GGACGCAC----GGCCAT-GAGCTGAGCGAAACTGGTGACCATAGATGGACAGGA-AGCATCGC----CCTGCCCAACCCCTTTTCACCTC-AACACCCAGGCTAAACGCTCAAGAAGTGATGGGAAAAT----GAAGC--CTGGTT--TAAAATAGGACGAAGCATG-TCCAG-AAGAAGGTG-CCATTATTTCCAGCGGGGCTGCTCTTGGCA-AGCTCTGGCAGGGA----GGAACAGGGCAGGGCTGCGGT--GTGGC------CTGAGTGGGAGCTC-------A-TGAGGACTCTGAGCCCTGAGCCCCTGGAGCTGAGGCCCAGCCTCCACCT-CTGCCCGGGCAACCAGGC----------------------------CCCTGCTTCT- i loxAfr3.scaffold_159 C 0 C 0 e proCap1.scaffold_13667 21148 5848 - 46842 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=8318.000000 s hg19.chr11_gl000202_random 13456 101 + 40103 CTGGGAGAACGCT--GGCTCCT--TCAACTTCCCCCCGAAAGGCATCCAGAGGCCTCCAGCTGGCC--CCCTCCCCTCTTTCCCCCAGCTTTGGGGTCTGGGCAGA-G s calJac1.Contig6069 79698 97 + 235769 CTGGGAG---GCG--GCCTCCT--TCAGCTTCCCCACCAAGGGCACCCAGAGGCCTCCAGCCAGC---CCCTCCCCTCCTAGCCCCAGCTTTGGGGTCTGGGCAGA-G i calJac1.Contig6069 C 0 I 1952 s papHam1.scaffold6638 74538 101 + 109049 CTGGGAGAACACA--GGCTCCT--TCAACTTCCCCACCAAAGGCATCCAGAGGCCTCCAGCTGGCC--CCCTCCCCTCATTCCCCCAGCTTTGGGGTCTGGGCAGA-G i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128158753 101 - 133002572 CTGGGAGAACACA--GGCTCCT--TCAACTTCCCCACCAAAGGCATCCAGAGGCCTCCAGCTGGCC--CCCTCCCCTCATTCCCCCAGCTTTGGGGTCTGGGCAAA-G i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125995887 101 - 132107971 CCGGGAGAACGCT--GGCTCCT--TCAACTTCCCCGCGAAAGGCATCCAGAGGCCTCCAGCTGGCC--CCCTCCCCTCCTTCCCCCAGCTTTGGGGTCTGGGCAGA-G i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 44189 101 + 115376 CTGGGAGAACGCT--GGCTCCT--TCAACTTCCCCCCAAAAGGCATCCAGAGGCCTCCAGCTGGCC--CCCTCCCCTCTTTCCCCCAGCTTTGGGGTCTGGGCAGA-G i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68200922 101 + 134204764 CTGGGAGAACGCT--GGCTCCT--TCAACTTCCCCCCGAAAGGCATCCAGAGGCCTCCAGCTGGCT--CCCTCCCCTCTTTCCCCCAGCTTTGGGGTCTGGGCAGA-G i panTro2.chr11 C 0 C 0 s oryCun2.chrUn0985 27613 36 + 42081 ---------------------------------------------------GGCCCCCAGCCGGC---CCCTCCCTTCCTTTCCC-------GG---CTG-------- i oryCun2.chrUn0985 C 0 C 0 s cavPor3.scaffold_42 9668486 39 + 15951348 ---------------------------------------------------GGTCTTCAGCCAAC---CCCTCCTTGCCCACCTT-------GAGGTCTA-------- i cavPor3.scaffold_42 C 0 C 0 s turTru1.scaffold_93657 4341 67 - 12933 --GGGAGAACTGA--GGCTGCT--TCAGTGTCCCCACAAGA------------------------C--TGCCTCG-------GGCTGGCTTTGGGGTCTGGGCAGA-- i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48976746 68 + 51998940 --GGGAGAACTGA--GTCTGCT--TCTGTATCCCCACAAGG---------------------------TCCTTCC-------GGCCAGCTCTGGGGTCTGGGCAGATT i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28940040 82 + 33091231 CGGGGTGGGGGGA--GGGAAC---------------CGAGG-CGACTCCCGCCCGCCCGCACGGCC--ACCACCTC-----AAGCCGGCTTTGGGGTCTGGACGGA-G i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 59514 85 + 302526 --GGGGGCGGAGGCTGCCTGCC--TCAGCTTCCCTGCAAGG-CCACCTGGCCCCCCCTGGTCGGCC--CCCTCCC--------CTCCTCGCTCTGCTCTG-------- i felCat3.scaffold_135390 I 3 C 0 s canFam2.chr18 7536858 90 - 58872314 --GGGAGAGGAGA--GGCTGCC--TCAGTTTCCCCACAAGG-CCATC-AGCCGCCTCTGGCCTGCC--CCCCCCC-------ACTCCCCTTTGGGCTCCAGGCATT-G i canFam2.chr18 I 10 C 0 s myoLuc1.scaffold_155660 37950 37 - 124081 ---------------------------------------------------------CGGGAAACT--GAGGCTG-------CTTCAGCTCT----CCCCTCCCCC-G i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 4386 25 - 9737 ----------------------------------------------------------------------------------CCCCAGCTTTGGGGCCCGGGCAGA-G i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 86649 81 + 1045236 --------------------CTGGCCATCCTCCCCACCAAAGGCACGTAA------CCAGCTGGACATCCCTTCTCCCCTCGCCCCAGCTTTGGCGACTAGGCAGA-G i loxAfr3.scaffold_159 C 0 C 0 e proCap1.scaffold_13667 21148 5848 - 46842 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=134156.000000 s hg19.chr11_gl000202_random 13557 127 + 40103 TGAGGCTGGAGT-CCAC---CTTCCGGGCA-----TTGGGA----GTACA-----------GGAAACAGTCCCAAGGGACCTCT----TTCACTGAGAAGGCACA-GAATCCCTTCCTAGAACGGGATAtgtgtttgtttccaacggctgctgcaa s panTro2.chr11 68201023 127 + 134204764 TGAGGCTGGAGT-CCAC---CTTCCGGGCA-----TTGGGA----GTACA-----------GGAAACAGTCCCAAGGGACCTCT----TTCACTGAGAAGGCACA-GAATCCCTTCCTAGAACGGGATAtgtgtttgtttccaacggctgctgcaa i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 44290 60 + 115376 TGAGGCTGGAGT-CCAC---CTTCCGGGCA-----TTGGGA----GTACA-----------GGAAACAGTCCCAAGGGACCTCT------------------------------------------------------------------------ i gorGor1.Supercontig_0015245 C 0 M 1611 s ponAbe2.chr11 125995988 127 - 132107971 TGAGGCTGGAGT-CCAA---CTTCCTCGCA-----TTGGGA----GGACA-----------GGAAACAGTCCCAAGGGACCTCT----TTCACTGAGAAGGCACA-GAATCCCTTCCTAGAACGGGATAtgtgtttgtttccaacggctgctgcaa i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128158854 128 - 133002572 TGGGGCTGGAGT-CCAC---CTTCCGGCCA-----CTGGGA----GGACA-----------GGAGACTGTCCCAAGGGACCTCT----TTCACTTAGAAGGCGCAGGAATCCCTTCCTAGAACGGGACCtgtgtttgtttccaacggcggctgcaa i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 74639 128 + 109049 TGGGGCTGGAGT-CCAC---CTTCCGGCCA-----CTGGGA----GGACA-----------GGAGACTGTCCCAAGGGACCTCT----TTCACTTAGAAGACGCAGGAATCCCTTCCTAGAACGGGACCtgtgtttgtttccaacggctgctgcaa i papHam1.scaffold6638 C 0 C 0 s cavPor3.scaffold_42 9668525 121 + 15951348 TATGATTGGGTT-GCACCCGCCCATGGGCG-----CAGAGT----G---------------GGGGGCAGTCCCGAGGGACTTCTTCGGATC-----AAAAACTCA-AGATCACTTCCTAGAATGGAACCTGTGTCGTTTCCCA----CTGCTGTGA i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 27649 82 + 42081 TGGGTCTGGGGT--------CCCGCGGGCGGACATCAGGGT----GACCCT-GAGTGCCATGGAAACACCCCCGCGAGACCTTCTATTGTCACTG------------------------------------------------------------- i oryCun2.chrUn0985 C 0 I 156 s turTru1.scaffold_93657 4408 84 - 12933 --------------------------------------GGG----GGG------------------------CTCGTGACCCCC----TTCATTTAGAGGACGGT-AACCCACTTCCTAGAACGGGACCTGCCttcgtgtcccac-gctgctgtca i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48976814 99 + 51998940 TCGGGATGGAGTCCCTC---CCAACGGGCA-----CT-GGG----TGATGT-AAATGCTTTGGAAACAGACCCACGTGACCCCA----TCCATTTAGAGGACAGT-AAACCACTTCCT-------------------------------------- i bosTau4.chr29 C 0 I 663 s equCab2.chr12 28940122 131 + 33091231 CGGGGCTGGAGA-CCCT---CCGGTAGGCA-----CTGGGA----CGACGG-GAGCCT-GCAGAATCAGTCCCAGCT-----CT----CTCGTTTAGAAGACACC-GTGTCACTTTCCAGAACAGGACCtgtcctcggttcccctcgctgctccga i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 59599 136 + 302526 -GGGTCTGGAGTCCCCT---CCGGATGGCA-----CTGGGGTGACTGACAT-GAGCCC--TGGGGACAGTCCCGAGCGAC--CT----GTCATTTGCAGGACACC-G-ATGACTCCCTGGAACAGGACCTGTGTGAGTTTCCCGTCCCTGCTGTAA i felCat3.scaffold_135390 C 0 I 144 s canFam2.chr18 7536948 136 - 58872314 CGGGGCTGGAGT-CCCT---CCCGATGGCA-----CCAGGA----TGGCAT-GAGCGCTGTGGGAACAGCCCCGAGTGACCTCT----GTCGTTTAGAGGACACT-G-AAGACTCCCTGGAACGGGACCAGGGTCGCTTTGCTAGCGCTGCTGTAA i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 37987 129 - 124081 CAGGGCCA------CCT---CAGCCCAGCG-----TTGGGG----TGACGT-GGGTGCTGTGGAATCGGCCCCAAGTGCCTGC-----TTCACTGAGAGGACACT-AAACCACGTCCTAGAATGGGACCtgtgttagttccccat--ctgcggaca i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 4411 135 - 9737 TGGGGCTAGAGTCCCTC---CCGACAGACA-----AGGGGA----TGACGT-GAG-GCTGCGGACTGAGCCCCGAGTGACCGCT----TTCATTCGGAGGACACT-GAGTCACATCCCAGAATGGCACCCAtgttagtctcatca--ccgccgtca i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 86730 107 + 1045236 TAGGGCTGGAGT-CCCA---CCCACAGGAA-----TTGGGA----TGATATAGAGGGATGTATAGACAGTCTCAAGTGACCACC----TTTATTTAAAAGACA---AGATCACTTCCTAGAAAGGGA----------------------------- i loxAfr3.scaffold_159 C 0 I 524 e calJac1.Contig6069 79795 1952 + 235769 I e proCap1.scaffold_13667 21148 5848 - 46842 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=60691.000000 s hg19.chr11_gl000202_random 13684 35 + 40103 tcaat-gcctgc-aaa-cttacaggctggaaatggcac s panTro2.chr11 68201150 35 + 134204764 tcaat-gcctgc-aaa-cttacaggctggaaacggcac i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125996115 35 - 132107971 tcaat-gcctgc-aaa-cttacaggctggaaatggcac i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128158982 35 - 133002572 tcaat-gcctgc-aaa-cttacaggctcgaaatggcac i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 74767 35 + 109049 tcaat-gcctgc-aaa-cttacaggctggaaatggcac i papHam1.scaffold6638 C 0 C 0 s cavPor3.scaffold_42 9668646 37 + 15951348 TCCCTGGcttgcgaaa-gctggaggtcagaagtgccac i cavPor3.scaffold_42 C 0 I 130 s turTru1.scaffold_93657 4492 35 - 12933 caaat-gaccac-agt-cttaccgacttgaaacgacgc i turTru1.scaffold_93657 C 0 C 0 s equCab2.chr12 28940253 35 + 33091231 gaagt-ggccac-aaa-ggtaccagcttgaaacagcac i equCab2.chr12 C 0 C 0 s canFam2.chr18 7537084 32 - 58872314 --CAG-GATCAC-ACA-TGGGCCAGCTCGAAAT-GCAC i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 38116 35 - 124081 caaac-gactac-aaa-tgtactgccttgaaacatcac i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 4546 36 - 9737 caaac-ggccac-agattttactggcttgaaaccacgc i pteVam1.scaffold_22742 C 0 C 0 e felCat3.scaffold_135390 59735 144 + 302526 I e calJac1.Contig6069 79795 1952 + 235769 I e oryCun2.chrUn0985 27731 156 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 86837 524 + 1045236 I e gorGor1.Supercontig_0015245 44350 1611 + 115376 M e bosTau4.chr29 48976913 663 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=45287.000000 s hg19.chr11_gl000202_random 13719 42 + 40103 aagtggatt---ctcctgacag---ttctggaagtcagaaatGCCGCT s panTro2.chr11 68201185 42 + 134204764 aagcggatt---ctcctgacag---ttctggaagtcagaaatGCCGCT i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 125996150 42 - 132107971 aggcggatt---ctcttgacag---ttctagaagtcagaaatGCCGCT i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128159017 42 - 133002572 aggcggatt---ctcctgacag---tcctggaagtcagaaatGCCACT i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 74802 42 + 109049 aggcggatt---ctcctgacag---tcctggaagtcagaaatGCCACT i papHam1.scaffold6638 C 0 C 0 s turTru1.scaffold_93657 4527 32 - 12933 ----ggatttattctcttgcgc---ttctagaaatcaga--------- i turTru1.scaffold_93657 C 0 I 161 s equCab2.chr12 28940288 41 + 33091231 ----agatttaccccccagcag---ttctggaggtcaagagtccctct i equCab2.chr12 C 0 I 193 s canFam2.chr18 7537116 39 - 58872314 ----AGATTCGTCCCTC--CAG---CCCTGGAGGGCCACGGTGTCACT i canFam2.chr18 C 0 I 1840 s myoLuc1.scaffold_155660 38151 38 - 124081 ----agatttactctctaccagactccctgggggtcgggagt------ i myoLuc1.scaffold_155660 C 0 I 322 s pteVam1.scaffold_22742 4582 32 - 9737 ----ggatttcctctccaacaa----tctggagctcagaa-------- i pteVam1.scaffold_22742 C 0 I 135 e felCat3.scaffold_135390 59735 144 + 302526 I e calJac1.Contig6069 79795 1952 + 235769 I e oryCun2.chrUn0985 27731 156 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 86837 524 + 1045236 I e cavPor3.scaffold_42 9668683 130 + 15951348 I e gorGor1.Supercontig_0015245 44350 1611 + 115376 M e bosTau4.chr29 48976913 663 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=507290.000000 s hg19.chr11_gl000202_random 13761 674 + 40103 CATCAgccgggcatggtggctcacacctgtaatccttgcactttgggaggccgaggcaggcaggtcacttgaggtcaggagctcaagaccagcctggcaaacatggcaaaacctcatctcAgccgggtgcagtggctcacgcctgtaatcccaccactttgggaggccaaggcaggtggatcacgaggtcaagagttcaagaccagcctggccaacatggtgaaa-cccgtctctactaaaaatacaaaaaattggctgggcatggtggctggcacctgtaatcccagctgctcaggaggctgaggcaggagaatcacttgaacctggtaggcagagattgcagtgagctgagattacaccacagcaccccagccctggtgacagagcaagactctgtctcaaaaaaag----------aaaaagaaaaaaaagaagaaa-------aAAGGAATGCcactagtctagaatcaaggtgtctgcagggctacatttctcctggagagtctaggagaacccaagccttgtcttttccagcttccagaggcagcttgtgctccttggcttgtggccccttcctccatcttcaaagtcagcagcactgcccctcctgggaagattttcctctctctccctctccctctctccctctct--tctctctctccctctctcccctccctctctctctctct s panTro2.chr11 68201227 674 + 134204764 CATCagccgggcatggtggctcacacctgtaatccttgcactttgggaggccgaggcaggcaggtcacttgaggtcaggagctcgagaccagcctggcaaacatggcaaaacctcatctcagccgggtgcagtggctcacgcctgtaatcccaccactttgggaggccaaggcaggtggatcacgaggtcaagagttcaagatcagcctggccaacatggtgaaa-cccgtctctactaaaaatacaaaaaattggctgggcatggtggcaggcacctgtaatcccagctgctcaggaggctgaggcaggagaatcacttgaacctggtaggcagagattgcagtgagctgagattgcaccacagcaccccagccctggtgacagagcaagactctgtctcaaaaaaag----------aaaaagaaaaaaaagaagaaa-------aAAGGAATGCcactagtctagaatcaaggtgtctgcagggctacatttctcctggagagtctaggagaacccaagccttgtcttttccggcttccagaggcagcttgtgctccttggcttgtggccccttcctccatcttcaaagtcagtagcactgcccctcctgggaagattttcctctctctccctctccctctctccctctct--tctatctctccctctctccccaaactctctctctctct i panTro2.chr11 C 0 I 623 s ponAbe2.chr11 125996192 637 - 132107971 CAGCagccgggcgcggtggctcacacctgtaatcctagcactttgggaggccgaggcgggcaggtcacttgaggtcaggagcttgagaccagcttggcaaacatggcaaaacctcgcctcagccgggcgtagtggcgcacacctgtaatcccagcactttgggaggccaaggctggtggatcacgaggtcaagagttcaagaccagcctggccaacatggtgaaaccccgtctctactaaaaatacaaaaaattggctgggcatggtggcaggcacctgtaatcccggctgctcgggaggctgaagcaggagaatcacttgaacctggtaggcagaggttgcagtgagccgagattgtaccacagcactccagccctggtgacagagcaagactctgtctcaaaaaaag----------aaaaagaaaaaaaagaaggaa-------aAAGGAATGCcactagtctagaatcgaggtgtctgcagggctacatttcaactggagactctaggagaatccaagccttgccttttccggcttccagtggcagcttgtgctccttggcttgtggccccttcttccatcttcaaagtcagcagcactgtccctccTGGGAAGATTTTcctctctctccctctctctccctctccctct---------------------------------------- i ponAbe2.chr11 C 0 I 1079 s rheMac2.chr14 128159059 652 - 133002572 CATCagctgggcgcggtggctcacacctgtaatcctagcactctggagggccaaggtgggcggatcacttgaggtcaggagttcaagaccagcctggccaacatggcaaaacctcgtctcagccggatgcaatggctcactcttgtaatcctagcactttcggaggccaaggcaggcagatcatgaggtcaagagtttgagaccagcctggccaacatggtgaaacactgtctctactaaaaatacaaaacattagctgggcgtggtggtgtgcacctgtcatcccagcagctcaggaggctgaggcaggagaattacttgaacctgggaggtggaggttgcagtgagccaagatcatgccacagcactccagcctgagtgacagagcaagactctgtctcacaaaaagaaaaattaaaaaaaagaaaagaaaGAAAGAAAAGAAATAAAGGAATGCCACTCATCT-Gaatcaagatgtctaaagggttgcatttctcctggagactctaggagaatccaagccttgccttttccggcttccaggggaggcttgtgctccttggcttgtggccccttcctccatcttcaaagtcagcagcactgtctctcctgggaagattttcctctcactccctctctctcgctctctctc----------------------------------------- i rheMac2.chr14 C 0 I 93 s papHam1.scaffold6638 74844 668 + 109049 CATCAgctgggcgctgtggctcacacctgtaatcctagcactctggaaggccgaggtgggcggatcacttgaggtcaggagttcaagaccagcctggccaacatggcaaaacctcgtctcggccggatgcagtggctcactcctgtaatcctagcactttcggaggccaaggcaggaggatcatgaggtcaagagtttgagaccagcctagccaacatggtgaaacactgtctctactaaaaatacaaaacattagctgggcgtggtggtgcgcacctgtcatcccagcagctcaggaggctgaggcaggagaattacttgaacctgggaggtggaggttgcagtgagccaagatcatgccacagcactccagcctgagtaacagagcaagactctgtctcacaaaaagaaaaattaaaaaaaagaaaagaaaGAAAGAAAagaaataaaggaatgccactcatctagaatcgagatgtctaaagggttgcatttctcctggagactctaggagaatccaagtcttgccttttccggcttccaggggaggcttgtgctccttggcttgtggccccttcctccatcttcaaagtcagcagcactgtctctccTGGGAAGATTTTCctctctctccctctctctccctctccctctctcctctctccccc-------------------------- i papHam1.scaffold6638 C 0 I 720 e felCat3.scaffold_135390 59735 144 + 302526 I e pteVam1.scaffold_22742 4614 135 - 9737 I e calJac1.Contig6069 79795 1952 + 235769 I e myoLuc1.scaffold_155660 38189 322 - 124081 I e turTru1.scaffold_93657 4559 161 - 12933 I e oryCun2.chrUn0985 27731 156 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 86837 524 + 1045236 I e cavPor3.scaffold_42 9668683 130 + 15951348 I e equCab2.chr12 28940329 193 + 33091231 I e gorGor1.Supercontig_0015245 44350 1611 + 115376 M e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48976913 663 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=0.000000 s hg19.chr11_gl000202_random 14435 477 + 40103 ctccttctctcctctccctctctctcctgagccatgccctggccctgccctgctcctccctgcctctctccctctctcttctctctctccctctctctttttctctctccctctcttctctctctctcctctccctctctcctctctctctcctctccctctctccctccctctcctctttctcctctccctctctctctccctctcttctctctctctccctctcccctccctctctctctctccctctcttctcttctcccccgcttctctctctctccccctctcccctcccctctttctctcccttctcttctctctcccactctcttctccctcctctctctccctttctcctctctatttctctctctctccctctctcctctccctctctctccctctctcctctctctctctctccctctctcctctctctctccctctctggccccctccccttctctcttctcttct e felCat3.scaffold_135390 59735 144 + 302526 I e pteVam1.scaffold_22742 4614 135 - 9737 I e papHam1.scaffold6638 75512 720 + 109049 I e calJac1.Contig6069 79795 1952 + 235769 I e myoLuc1.scaffold_155660 38189 322 - 124081 I e turTru1.scaffold_93657 4559 161 - 12933 I e oryCun2.chrUn0985 27731 156 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 86837 524 + 1045236 I e cavPor3.scaffold_42 9668683 130 + 15951348 I e equCab2.chr12 28940329 193 + 33091231 I e gorGor1.Supercontig_0015245 44350 1611 + 115376 M e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48976913 663 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e rheMac2.chr14 128159711 93 - 133002572 I e ponAbe2.chr11 125996829 1079 - 132107971 I e panTro2.chr11 68201901 623 + 134204764 I a score=10564.000000 s hg19.chr11_gl000202_random 14912 174 + 40103 ctctcccactctcttctccctctctc-ctctcc-ctctctctccctctctcctctctctctctct-ccctctctcctctctctctccctctctggccccctccccttctctcttctcttctctctcccactc--tcttctccctctctcctctctctctccgtttccctctctctctcc s rheMac2.chr14 128159804 174 - 133002572 ctctccctctctcctctccctctctctctctcctctctctctccctctctcctctctctccctctgtcctctctctcctctctctccctctct-----cctctctctctcccctctctcctctctccctctccttctcctctctctctcccccctccttctctatctctctctctcccc i rheMac2.chr14 I 93 I 38 e felCat3.scaffold_135390 59735 144 + 302526 I e pteVam1.scaffold_22742 4614 135 - 9737 I e papHam1.scaffold6638 75512 720 + 109049 I e calJac1.Contig6069 79795 1952 + 235769 I e myoLuc1.scaffold_155660 38189 322 - 124081 I e turTru1.scaffold_93657 4559 161 - 12933 I e oryCun2.chrUn0985 27731 156 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 86837 524 + 1045236 I e cavPor3.scaffold_42 9668683 130 + 15951348 I e equCab2.chr12 28940329 193 + 33091231 I e gorGor1.Supercontig_0015245 44350 1611 + 115376 M e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48976913 663 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e ponAbe2.chr11 125996829 1079 - 132107971 I e panTro2.chr11 68201901 623 + 134204764 I a score=0.000000 s hg19.chr11_gl000202_random 15086 37 + 40103 cccgtctctccctctcttctctctctccctctctcct e felCat3.scaffold_135390 59735 144 + 302526 I e pteVam1.scaffold_22742 4614 135 - 9737 I e papHam1.scaffold6638 75512 720 + 109049 I e calJac1.Contig6069 79795 1952 + 235769 I e myoLuc1.scaffold_155660 38189 322 - 124081 I e turTru1.scaffold_93657 4559 161 - 12933 I e oryCun2.chrUn0985 27731 156 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 86837 524 + 1045236 I e cavPor3.scaffold_42 9668683 130 + 15951348 I e equCab2.chr12 28940329 193 + 33091231 I e gorGor1.Supercontig_0015245 44350 1611 + 115376 M e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48976913 663 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e rheMac2.chr14 128159978 38 - 133002572 I e ponAbe2.chr11 125996829 1079 - 132107971 I e panTro2.chr11 68201901 623 + 134204764 I a score=9520.000000 s hg19.chr11_gl000202_random 15123 189 + 40103 ctccctctctccttctct-cactctctcc---ctctctctcctctcttctctctctccctctctctcttctctgcctctcttctctatctccctctctccgttttctctttctccctctctcctct----ttctctctctccctctc-tctctccctctctcctctctctctccctctctctcttcccc-ctctcttct s rheMac2.chr14 128160016 193 - 133002572 ctctctctccccttctcttctctctctcctctctctctcccccctcttctctctctctccccatctcttctctccctctctcccctcttctcctctatcc-----ctctctctccccctctcctctatccctctttctccccctctcctctctctttctctcctctatccctctctcccccccttctcctctatcc-ct i rheMac2.chr14 I 38 C 0 e felCat3.scaffold_135390 59735 144 + 302526 I e pteVam1.scaffold_22742 4614 135 - 9737 I e papHam1.scaffold6638 75512 720 + 109049 I e calJac1.Contig6069 79795 1952 + 235769 I e myoLuc1.scaffold_155660 38189 322 - 124081 I e turTru1.scaffold_93657 4559 161 - 12933 I e oryCun2.chrUn0985 27731 156 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 86837 524 + 1045236 I e cavPor3.scaffold_42 9668683 130 + 15951348 I e equCab2.chr12 28940329 193 + 33091231 I e gorGor1.Supercontig_0015245 44350 1611 + 115376 M e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48976913 663 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e ponAbe2.chr11 125996829 1079 - 132107971 I e panTro2.chr11 68201901 623 + 134204764 I a score=19593.000000 s hg19.chr11_gl000202_random 15312 101 + 40103 ctctctccctctctcctctatccctctctctccctctctcctctatccctctctc----------------tccctctctcct-ctatccctctctctccctctctcccccttctctt s rheMac2.chr14 128160209 106 - 133002572 ctctctccccctctcctctatccctctttctccccctctcctctctctttctctc-----------ctctatccctctctcccacccttctcctctatccctctcttccccctc-ctt i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 76232 117 + 109049 ctctctctttctctcctctatccctctctctccccttctactctatccctctctctctcccttctcctctatccctctctcccacccttctcctctatcgctctcttccccctc-ctt i papHam1.scaffold6638 I 720 C 0 e felCat3.scaffold_135390 59735 144 + 302526 I e pteVam1.scaffold_22742 4614 135 - 9737 I e calJac1.Contig6069 79795 1952 + 235769 I e myoLuc1.scaffold_155660 38189 322 - 124081 I e turTru1.scaffold_93657 4559 161 - 12933 I e oryCun2.chrUn0985 27731 156 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 86837 524 + 1045236 I e cavPor3.scaffold_42 9668683 130 + 15951348 I e equCab2.chr12 28940329 193 + 33091231 I e gorGor1.Supercontig_0015245 44350 1611 + 115376 M e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48976913 663 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e ponAbe2.chr11 125996829 1079 - 132107971 I e panTro2.chr11 68201901 623 + 134204764 I a score=7539.000000 s hg19.chr11_gl000202_random 15413 32 + 40103 ctctctctctccctctctcc-------------tctatccctctc s ponAbe2.chr11 125997908 31 - 132107971 ctctccctctctctctctcc--------------ctctccctctc i ponAbe2.chr11 I 1079 C 0 s rheMac2.chr14 128160315 45 - 133002572 ctctctctctccccctctcctctctcctctctctctctctctctc i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 76349 31 + 109049 ctctctctctccccctctcc-------------tctctc-ctctc i papHam1.scaffold6638 C 0 C 0 s loxAfr3.scaffold_159 87361 13 + 1045236 --------------------------------ctccgtccgtgcc i loxAfr3.scaffold_159 I 524 C 0 e felCat3.scaffold_135390 59735 144 + 302526 I e pteVam1.scaffold_22742 4614 135 - 9737 I e calJac1.Contig6069 79795 1952 + 235769 I e myoLuc1.scaffold_155660 38189 322 - 124081 I e turTru1.scaffold_93657 4559 161 - 12933 I e oryCun2.chrUn0985 27731 156 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9668683 130 + 15951348 I e equCab2.chr12 28940329 193 + 33091231 I e gorGor1.Supercontig_0015245 44350 1611 + 115376 M e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48976913 663 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e panTro2.chr11 68201901 623 + 134204764 I a score=98873.000000 s hg19.chr11_gl000202_random 15445 84 + 40103 tttctcCCCCCCCcccccgcttcttctt-----gtcacatct-tttctgtgactc----cctcctgcctccctcttac-aggaagctggaggtt--a--------- s ponAbe2.chr11 125997939 84 - 132107971 tctctctccctctcctctgcttcttctt-----gtcacatct-tttctgtgactc----cctcctgcctccctcttac-aggaacctggaggtt--a--------- i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128160360 84 - 133002572 tctctctctctcccctctgcttcttctt-----gtcacatct-tttctgtgactc----cctcctgcctccctcttac-aggaacctcaaggtt--a--------- i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 76380 84 + 109049 tctctctctctcccctctgcttcttctt-----gtcacatct-tttctgtgactc----cctcctgcctccctcttac-aggaacctcaaggtt--a--------- i papHam1.scaffold6638 C 0 C 0 s bosTau4.chr29 48977576 88 + 51998940 --tctcaccctctctccgacctct-ctt-cagcatcgcatct-tttctctga--ctgtccctcctgcctccctgttgtaaggaccctcgcgatg--g--------- i bosTau4.chr29 I 663 I 7 s turTru1.scaffold_93657 4720 93 - 12933 tctctctccctccctccagcctctgctt-cagcgtcacatct-tttctctgactctgaccctcctgcctccctcttgtaaggaccctcgtgatg--a--------- i turTru1.scaffold_93657 I 161 I 7 s pteVam1.scaffold_22742 4749 78 - 9737 -----------ccctc---cctctgcct-ctgcttcacgtca-cccctccgactc-ggccctgctgccttcctcccataaggaccctcgtgacg--a--------- i pteVam1.scaffold_22742 I 135 I 8 s equCab2.chr12 28940522 54 + 33091231 ----------------------------------------ct-gttctctgactctgaccctcctgcttccctctgataaagacccttgtggtg--a--------- i equCab2.chr12 I 193 I 7 s cavPor3.scaffold_42 9668813 49 + 15951348 -------------------------------------------tctctctgacac----cctcctgctcccctctgac-agatctctaaagactgca--------- i cavPor3.scaffold_42 I 130 C 0 s oryCun2.chrUn0985 27887 39 + 42081 ------------------------------------------------------C----CCTCCTGCCTCCCTCCCACAAGGACTCCTGAGATTGAA--------- i oryCun2.chrUn0985 I 156 C 0 s gorGor1.Supercontig_0015245 45984 66 + 115376 ------------------gcttcttctt-----gtcacatct-tttctgtgactc----cctcctgcctccctcttac-aggaagctggaggtt--a--------- i gorGor1.Supercontig_0015245 M 1611 C 0 s loxAfr3.scaffold_159 87374 94 + 1045236 ----------tcactccagtggctgcttccatcctcacgtctccttccctgagcctcatcctcccacctcccttttacaaggacccctctggtt--gcactggccg i loxAfr3.scaffold_159 C 0 C 0 e felCat3.scaffold_135390 59735 144 + 302526 I e calJac1.Contig6069 79795 1952 + 235769 I e myoLuc1.scaffold_155660 38189 322 - 124081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e panTro2.chr11 68201901 623 + 134204764 I a score=17478.000000 s hg19.chr11_gl000202_random 15529 50 + 40103 ccca--------cgac--------cgtctgggat---catctc-cacctc-agaatccttgctccgtgaca s gorGor1.Supercontig_0015245 46050 49 + 115376 ccca--------cgac--------catctgggat---catctc-cacctc-agaatccttGCTC-GTGACA i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125998023 50 - 132107971 ccca--------cgac--------cgtctgggat---catctc-cacctc-agaatccttgctccgtgaca i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128160444 50 - 133002572 ctca--------ggac--------tgtctgggat---catctc-cacctc-agaatccttgcttcgtgaca i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 76464 50 + 109049 ctca--------ggac--------cgtccgggat---catctc-cacctc-agaatccttgcttcgtgaca i papHam1.scaffold6638 C 0 C 0 s oryCun2.chrUn0985 27926 51 + 42081 CTTA--------GGGT--------AGCCCAGGGG---GACGCC-CACCCCTGGGACCCCACCCTGGCCACA i oryCun2.chrUn0985 C 0 C 0 s cavPor3.scaffold_42 9668862 62 + 15951348 ttta--------gggcccagccagagcccccaggaccagctcc-tacatccagatactccacttggttgcc i cavPor3.scaffold_42 C 0 C 0 s turTru1.scaffold_93657 4820 54 - 12933 ccca-----cctgggg--------gacccaagaa---aagctcgcctctc-cactcttcaagttcatcaca i turTru1.scaffold_93657 I 7 C 0 s bosTau4.chr29 48977671 54 + 51998940 ccca-----cccagat--------aatccaagaa---aatctcccccgtt-ggcccctcaagctcaccgca i bosTau4.chr29 I 7 C 0 s equCab2.chr12 28940583 55 + 33091231 cccg-----cctggat--------aatcggagga---aatctcccttctcgggatcctcagcttcatccca i equCab2.chr12 I 7 C 0 s felCat3.scaffold_135390 59879 50 + 302526 cccg--------ggag--------aatccagcgt---cacctgacatctc--aacccttgacccggtcgca i felCat3.scaffold_135390 I 144 C 0 s pteVam1.scaffold_22742 4835 50 - 9737 ccct-----cccagat--------aacccaggat---cctctcctatcccaggatcct-----ttgtcaca i pteVam1.scaffold_22742 I 8 C 0 s loxAfr3.scaffold_159 87468 55 + 1045236 cccaccccccccggag--------aatccaggct---ggtcccccatatc-aggagcc----tccatcaca i loxAfr3.scaffold_159 C 0 C 0 e calJac1.Contig6069 79795 1952 + 235769 I e myoLuc1.scaffold_155660 38189 322 - 124081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e panTro2.chr11 68201901 623 + 134204764 I a score=168309.000000 s hg19.chr11_gl000202_random 15579 267 + 40103 tcggtagaatg------tctttggccacggaagggaacatgttc---atagg-tcctgggcactaagatgtgggggat-tccattactggt---g-gggggtt--------ccattat--ttggttgaccacCGACCTGGTACACAGTGGGTGCCCCTGGGATTTG-----------------------TTGTAGCAGGGAGCACT-GGCTGCA-GCA-GGAGCCTGACCCTC------GCGGGAGCGTCTAGCC-------AGCCT-----TGGTG-CC---------AGGTAGGCCGTGGCATTT-AGCTCTCT----GGCC----CAgag--cctcagcaaggccacggcgctc s gorGor1.Supercontig_0015245 46099 268 + 115376 TCGGTAGGATG------TCTTTGGCCACGGAAGGGAACACGTTC---ATAGG-TCCTGGGCACTAAGATGTGGGGGAT-TCCATTATTGGT---G-GGGGGTT--------CCATTAT--TTGGTTGACCACCGACCTGGTACACAGTGGGTGCCCCTGGGATTTG-----------------------TTGTAGTAGGGAGCACT-GGCTGCA-GCA-GGAGCCTGACCCTC------GCGGGAGCGTCTAGCC-------AGCCT-----TGGTG-CC---------AGGTAGGCCGTGGCATTT-AGCTCTCC----gggc---acagag--gctcagcaaggccacggcgctc i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125998073 261 - 132107971 tgggtagagtg------tctttggccacggaagggaacatgttc---atagt-tcctgggcactaagatgtggacgcc-t------ttggt---g-gggggtt--------ccattat--ttggttgaccacCGACCTGGTACACAGTGGGTGCCCCTGGGATTTG-----------------------TTGTAGTAGGGGGCACT-GGCTGCA-GCA-GGAGCCTGACCCT-------GCGGGAGCGTCTAGCC-------AGCTT-----TGGTG-CC---------AGGTAGGCCTTGGCATTT-AGCTCTCC----CGGC---acagag--gctcagcaaggccacggcgctc i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128160494 258 - 133002572 tcggcagagtg------tctttggccacggaagggaacatgttc---atagg-tcctgggcactcagatgtggacgcc-t------ttggt---g-gggggtt--------ccattat--ttggttgaccacCGACCTGGTACACAGTCGGTGCCCCTGGGATTTG-----------------------TTATAGTAGGGAGCACT-GGCTGCA-GCA-GGAGCCTGACCCTC------GCGGGAGTGTCTAGCC-------AGCCT-----TGGTG-CC---------AGTTTCAC-----AATTT-GGCTCTCT---GGGGC---ACAGAG--GCTCGGCAAGGCCACAGCGCTT i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 76514 272 + 109049 tcggcagagtg------tctttggccacggaagggaacatgttc---atagg-tcctgggcactcagatgtggacgcc-t------ttggt---g-gggggtt--------ccattat--ttggttgaccacCGACCTGGTACATAGTCGGTGCCCCTGGGATTTG-----------------------TTATAGTAGGGAGCACT-GGCTGCA-GCA-GGAGCCTGACCCTC------GCGGGAGTGTCTAGCC-------AGCCT-----TGGTG-CCAGTTTCACAAGGTAGGCTGTGGCATTT-GGCTCTCT---Ggggc---acagag--gctcagcaaggccacagcgctt i papHam1.scaffold6638 C 0 C 0 s oryCun2.chrUn0985 27977 250 + 42081 CCTGCAGAGCCTCTGCCTCCAAGGCCCCCGTG-----------C---ACAGG--CGTTGGGCCCAGGACG-GGACACC-C--------GGC---G-GGCG-----------CCCCAGCCTGGGGTCTGCCCCAGGCCCAGGCCACAGCAGGTGGCACAGGGACTC------------------------TCCAAACGACGAACATC-ACCCGCACGTG-GGGGTCTCACCTTCCCCTC--CCAGGACCCCTGACCTTG----ACC-------------CC---------AGGTTGTA---GGATTTC-CGCTCCCCAG-GGGAA---ACCGAG--CCACAGCAAGGC--AGGCTCTC i oryCun2.chrUn0985 C 0 C 0 s cavPor3.scaffold_42 9668924 275 + 15951348 cctgaagagcc-------ctgaggtcacagag----------tt---acagt--cctatgcattgaaact-gagcacc-t---------tt---g-gggg-----------ccattgc--agggtcta-cACAGATGCAGGACACAG--GCAGCCCCAGGGGCTTGTTAGGACTCAGAAGCCCCTGTGACCTCAGCCAGGCACAGCTGTCCACATGCC-TGGCCTTTACCTTGCCCTTTGTAAAGGTGCCTGACCTGGCATCACCTT-----TGACAGTC---------AGGTCTTC---AAAATTC-GGTTTCTTAGAGGGAA---ACAGAG--GCATGGCAAAGTCAAGG----- i cavPor3.scaffold_42 C 0 C 0 s turTru1.scaffold_93657 4874 239 - 12933 cccaaaaagtc------tcttttgccacataaggtcacatatgtgacctggg-ttctgggcattaagatgtggatatc-c------ttgggggtg----------------tcctttt--tcagcctaccacaGACCCTGTGCACCGCTGGTGCCCAAGGGACTTA-----------------------TTATAAT-ATAGGCACC-AACTGCATGCCGTGGGTGTGCCT---------CTGAGGATTTCTATTCTGACACCGGTTTT----TTGAA-GC---------AGGTAGT----ATTATTCCAGATCCCA----GGGC-----------ACT------------------- i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48977725 213 + 51998940 tctgaaaagtc------cctttcaccccataagttcacataCGT------------------TTTAGCTTCTCACATCGC------TTAGG---T----------------CCATTTT--CCAGTCTGTCACAGGCCTTGCACACCATTGGTGCCTGGGGTACTTA-----------------------TTACAATAATAAGCACC----------CTGGGGGTCTCTCCCTG------CTGAGGA--CATATTTCGACACCAGTTTC----TCGGG-GC---------AGGTGGT----GTTATTTTTGGTCCCA----GGGC-----------ACT------------------- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28940638 262 + 33091231 tctgcaaagcc-------ctttgtccgcgtaggaccacgtcttc---gccag-ttctgggcattgagatgtgcacgtc-g------tgggg---g-gggt-----------ccatttt--ttggcctgccacaGACCCTGCACACAGTTGGTGCTCAAGAGACTTC-----------------------TTATAATACTGAGCACC-GACTGCATGCT-GGAGCCTTACCCTC------CTGGGGATTTTGAGCCTGACTCCAGTTT-----GGGGG-GC---------GGGTGT-----GGAATTCCTGGTCCCC----AGGGAA-ACAGAG--GCTCGG-GAGGCCGAGGTGAC- i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 59929 238 + 302526 cctgcaaagtc------acgctccccacgcaaggtcacggcttc---acggg-ttctggacatcaacatgtgcacgtc-c------tgggg---gcgggg-----------ccgtgtt--t----cagccGCAGCCCCTGCACACAGCTGGTGCTCAAGGGGC-----------------------------TGGCCGTGACCACG-AGCTGCACGCCGGGGGCCTCGCCGGC------CTGGGGA--------CACACACCAGTCTGGGGAGGGGG-GC---------GGGTCTC----GGGGCTCCTGATTCTC----GGGGGACACTGAG--GCTC------------------ i felCat3.scaffold_135390 C 0 C 0 s myoLuc1.scaffold_155660 38511 241 - 124081 tcggcaaagcc-------cctgtgccacgtaagaccacgtaccc---acagg-tcctgagtgctaagttgcggacatc-c------tcggg---g-g--------------cccccgt--ttggcctgtcaGAGACCCTGCACACAGCTGGTGCTCAAGGGAC--------------------------TTATGGTAATGAGCACC-GGCTGTGTGCC-CGGCCGTCCCCGC------------------------GACACCAGCTGG----GGAAG-GC---------GGGCGGT----GGCATCC-TGATCCCA----GGGG---ACAGAGAAGCTCCGTGAGACCGCGCCGCCT i myoLuc1.scaffold_155660 I 322 C 0 s pteVam1.scaffold_22742 4885 263 - 9737 tcggcaaagca-------tttccgtcctgtaagacctcgtg-tc---acagg-ttctggacactaagatgtgaacgtc-c------tgggc---g-ggGAGTAGGGAGAGTCCATTTC--TCAGTCTGTGACTGACCCTGCACACAGCCAGGGCTCAGGGGAC--------------------------TTAGAGCGATGAATGCC-CACTGCGTGCG-GGGGCCTTACCCCC------C-GAGGACTTCCATCTGGACACCAGCGTG----GGGAC-AC---------AGGTCGT----GGAATTTGTGACCCCA----GAGG---AAAGAG--GCTTGGCAAAGCCAA------- i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 87523 270 + 1045236 ccggcaaagcc------ccttttcttaggtaaggtctcagttgc---acagtttccgggggattaggacatggacatc-t------ttgtg---g-gggga----------gcattac--cctgtctaccgcaGATGTTGTATACAGGCGGTGCTCAAAGGATGCA-----------------------CTATAATAATTAGAGCC-GATTGCATGCAGGGGGCTTCACCCAC------CTGAGGACTTCTAACCTGCCCCCGGCTCT----GCAAG-GC---------CGGCTGT----GGCGTTCCTGTCTCCC--AGGGAG---ACAGAG--GCTCAGCCAGGCCCAGGCTCTT i loxAfr3.scaffold_159 C 0 C 0 e calJac1.Contig6069 79795 1952 + 235769 I e proCap1.scaffold_13667 21148 5848 - 46842 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e panTro2.chr11 68201901 623 + 134204764 I a score=-45336.000000 s hg19.chr11_gl000202_random 15846 89 + 40103 ggccagaggaacacag-ccacccagcgg-----------------agagccaagactcagcccagacgtcccagacgccaggcccTTTC------CTGGGTG----------CC-CTC---AGCACG s gorGor1.Supercontig_0015245 46367 89 + 115376 ggccagaggaacacag-ccacccagcgg-----------------agagccaagactcagcccagacgtcacagacgccaggcccTTTC------CTGGGTG----------CC-CTC---AGCACG i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125998334 89 - 132107971 agccagaggaacacag-tcacccagcgg-----------------agagccaagactcagcccagacgtcccagacgccaagcccTTTC------CTCGGTG----------CC-CTC---AGCACG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128160752 89 - 133002572 GGCCAGAGGAACACAG-TCACCCAGCGG-----------------AGAGCCAAGACTCAGCCCAGACACCCCGGACCCCAGGGCCTTTC------CTGGGTG----------CC-CTC---AGCACC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 76786 88 + 109049 -gccagaggaacacag-tcacccagcgg-----------------agagccaagactcagcccagacatcccggacgccagggccTTTC------CTGGGTG----------CC-CTC---AGCACC i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 81747 88 + 235769 GGCCAGAGGAACACAG-TCACCCAGCAG-----------------AGAGCCAGGACTCAGCCCAGATGCCCCGGACGCCAGGCTCTCTC------CTGGGTG----------CC-CTC---AGCAC- i calJac1.Contig6069 I 1952 C 0 s cavPor3.scaffold_42 9669199 69 + 15951348 ---------GACACA---GACTCTG--G-----------------GGGGCGAGCA-------AGGATCCGCCACAAGCCCATCTCTTTC------CTGGATG----------CC-TGC---AGCACA i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 28227 53 + 42081 --------CTCCACA---CACTCAGCCG-----------------ACAGCCAGGA-------CAGACCCCCTGCTGG-------------------GGGGCG----------CC-TGC--------- i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 5113 71 - 12933 GGCCACCAGAACACAA-ACACTCAGC--------------------TAGCCAGGACTTTCTCCAGGCT------------------TTC------CTGGGGG----------CC-CGCTGCAGCATG i turTru1.scaffold_93657 C 0 I 1 s bosTau4.chr29 48977938 70 + 51998940 GGCCCCTGGAACACAG-ATGCTCAGT--------------------GAGCCATG-CCCTCCCCGGGCT------------------TTG------CTGGGGG----------CC-CATTGCTGCACA i bosTau4.chr29 C 0 I 1 s equCab2.chr12 28940900 93 + 33091231 GGCCACAGGCGCACAA-GTACTCGGT--------------------GGGCCGGGGCTTGTCCCAGGCTTTCTG------GGAGCAGCTT------CAGGGAATGCCCCCGGCCC-CCGTGCAGCGTG i equCab2.chr12 C 0 I 1 s felCat3.scaffold_135390 60167 72 + 302526 ----------------------------------------------AAGCCAGGACTTGTCCCACGTTTCC--------GTTTCCCCTTTTCTTCCAGGTAATGACCTCGGCCT-TCACGCAGGGTG i felCat3.scaffold_135390 C 0 I 1 s myoLuc1.scaffold_155660 38752 77 - 124081 GGCCCCAGGAACACGGCGT---------------------------GAGCTAGG-ACCCACTCCGGCT--------------TCTGCTG------TCGGGAATGTTCCCGCCCC-CCGGG-AGCATG i myoLuc1.scaffold_155660 C 0 I 1 s pteVam1.scaffold_22742 5148 75 - 9737 GGCCACA-GAACACAA------------------------------ACGCTCAG-CTCGCCACAGGCT-------------GGCTGCTG------CGGGGGATGCTCTTGACCCGCTATG-AGCTGG i pteVam1.scaffold_22742 C 0 I 1 s loxAfr3.scaffold_159 87793 98 + 1045236 GGGCAGAGGAATGTGG-ACACTCAGAGGGGACCGACCAGGCCTGTGGGGCTCTAGCCCTTCCCGAACCTGCTGCCGGTGAGCGATCTCT------TTGG-------------CC-TAC---A----- i loxAfr3.scaffold_159 C 0 C 0 e proCap1.scaffold_13667 21148 5848 - 46842 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e panTro2.chr11 68201901 623 + 134204764 I a score=524225.000000 s hg19.chr11_gl000202_random 15935 229 + 40103 CCCCACCCCCA------------------------------------CCCCGTGAGGACGTCTGCCCGGGCTCCGGATG-CCCCAGGGCCTTGGACCA-----CCAGGGACTGTGCCTTAGGGGCA-------GGGTGACCCTGCGGTGCTGGGCGTTTGACACGGCCTTTCC----CCCTGGAAGCCTCTGTCGCCCT--Cga--t-------aca--atgtgaagagttgg--gctgtagggtcaggcgga-----gagattggggttcacatctggattctggcatccacgggcagagc s panTro2.chr11 68202524 229 + 134204764 CCCCACCCCCA------------------------------------CCCCGGGAGGACGTCTGCCCGGGCTCCGGATG-CCCCAAGGCCTTGGATCA-----CCAGGGACTGTGCCTTAGGGGCA-------GGGTGACCCTGCGGTGCTGGGCGTTTGACACGGCCTTTCC----CCCTGGAAGCCTCACTCGCCCT--Cga--t-------aca--atgtgaagagttgg--gctgtagggtcaggcgga-----gagactggggttcacatctggattctggcatccacgggcagagc i panTro2.chr11 I 623 C 0 s gorGor1.Supercontig_0015245 46456 229 + 115376 CCCCACCCCCA------------------------------------CCCCGTGAGGACGTCTGCCCGGGCTCCGGATG-CCCCAGGGCCTTGGACCA-----CCAGGGACTGTGCCTTAGGGGCA-------GGGTGACCCTGCGGTGCTGGGCGTTTGACACGGCCTTTCC----CCCTGGAAGCCTCTGTCGCCCT--Cga--t-------aca--acgtgaagagttgg--gctgtagggtcaggcgga-----gagattggggttcacatctggattctggcatccacgggcagagc i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125998423 229 - 132107971 CCCCACCCCCA------------------------------------CCCCGTGAGGAGGTCTGCCCGGGCTCTGGATG-CCCCAGGGCCTTGGACCA-----CCAGGGATTGTGCCTTAGGGGCA-------GGGTGACCCTGCGGTGCTGGGCGTTTGAGACGGCCTTTCC----CCCTGGAAGCCTCAGTCGCCCT--Cga--t-------aca--atgtgaagagttgg--gctgtagggtcaggcgga-----gagattggggttcaaatctggattctggcacccacgggcagagc i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128160841 227 - 133002572 --CCCCCCCCA------------------------------------CCCTGTGAGGATGTCTGCCCAGGCTCCGGATGCCCCCAGGGCCTTGGACCA-----CCAGGGATTGTGCCTCAGGGACA-------GGGTGACCCTGCAGTGCTGGACGTTTGAGATGGCCTTTCC----CCC-AGAAGCCTCAGTCGCTCT--Cga--t-------aca--gtgtgaagagctgg--gctgtggggtcaggcgga-----gagaccggggttaaaatctggattctggcacccacgggcagagc i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 76874 228 + 109049 CCCCACTCCCA------------------------------------CCCTGTGAGGATGTCTGCCCAGGCTCCGGATGCCCCCAGGGCCTTGGACCA-----CCAGGGATTGTGCCTC-GGGGCA-------GGGTGACCCTGCAGTGCTGGACGTTTGAGATGGCCTTTCC----CCC-AGAAGCCTCAGTCCCTCT--tga--t-------aca--gtgtgaagagctgg--gctgtggggtcaggcgga-----gagaccggggttaaaatctggattctggcacccatgggcagagc i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 81835 230 + 235769 CCCTGCCCCCA------------------------------------CCACACAAGGACCTCTGCCCAGGCTCCAGATG-CCCCAGGGCCCT-GACCA-----CCAGGGAGAGTGCTTT-AGGGCA-------GGACAGCCCTG-GGCACTGGGCATTGGAGATGGCCGTTCC----CCG-GGAGGCCTCCATCGCCCT--CCA--T-------ACA--ATGTGAAGAGTTGG--GCTGTGGGGTCAGGCCAACTCTTGAGATCGGGGTTCAAATCTGGATTCTGGTGCCCACGGACAGAGC i calJac1.Contig6069 C 0 C 0 s cavPor3.scaffold_42 9669268 210 + 15951348 ---CACGTCCA------------------------------------CCCCACGAAGGCTTCTGTGCAGG-TTCAGACA-CCCCAGGACCTTAAACCA-----GTGGGGTGAGTGACTTAGTGACA-------GAGTGACCCTCTGATGCT--------------GCCACTCC----ACCCTAGAGCCT--GTTTCCCCGTCTA--G-------ACG--GTGTGAAGAG-GGG--GCTGTGGGGTCAGGTGCA-----AGGGTTAGGATTCAGATCGAAACTCCATCCCCTGTTGGCAGTAC i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 28280 175 + 42081 -----------------------------------------------CCCCTCCTGGGCATCCCTGGAGG---AATGCT-GCCCAGGGCCTGGGACCC-----CTGGGGCGAGCGGCTTAGGGGCAACAAGGTGTGGGACTCGGGGGTG---------------------------------AGAGCCTCAGCTCCCCC-----------------------CGCAG----------CGTGGGGCCAGGCGGA-----GGGGTCAGGGCTCAGATCTGCGCTCCGTCACCCGTGGGCGGAGG i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 5185 217 - 12933 CCTTCACCCCACAAGAC-TT---------------------------CCCCACGAGG-CATCTGCTT-----------------AGGGCCCCGGACCA-----TTGGGGTGAAA-TCTTCGGGGAA-------GGGTGACCCTCCGACGCA-GGTGTCtgggatggtcattcc---accccctgagcctcagtttcccc--gtt--t-------gtaa-atgggaagggtggg--gctg-gGGGTCA--CGTG-----GGGGACTGGGGTTAAGTCTGGATTCTGTCAGCTGCAGGCAGAGC i turTru1.scaffold_93657 I 1 I 2 s bosTau4.chr29 48978009 215 + 51998940 CC-ACACCCCACGAGACACC---------------------------CCCCAGGAGA-CGTCTGCTTAGTCTCGGGTC--CCCCAGGGCCCTGGACCA-----TTGAGGTGAAC-TCTTAGAAGGA-------CAGAGACACCCCAA-----------------GGCTTCTCC---ACCGCATGAACCTCACTTTGCCC--ATT--T-------GTAA-ATGTGAAGAGTGGG--GCTA-GGGGGC---CGGG-----TGGGAGGTGGGTCAGGTCTGGAGTCTGTTAACTATTGGCCCTGC i bosTau4.chr29 I 1 I 11 s equCab2.chr12 28940994 258 + 33091231 CCCCCACCCCACGAGACGTCCCCCACAAGACGTCCCCCATGAGATGTCCCCACGAGA-CGTCCACCCAGTGTCTGGAT--CCCCAGGGCCCTGCACCC-----CTGGAGTGAACAGCTTAGGGGCA-------GGGCAGCCCTCTGAAGCC-GGCGTTTGGGACGGCCA--------CCCCGTGAGCTTCAGTTTCTCC--CC---T-------GCGACATGTGAGGAGTC-A--GCTGTGGGGTCAGGCGGA-----GAGGGTGCGGCTCCAGTCTGGATTCTGCGAGCGATTGGCAGAGC i equCab2.chr12 I 1 C 0 s felCat3.scaffold_135390 60240 212 + 302526 CTCCTCCCTCTAGAGATGTCC--------------------------CCCCACGAGG-C------------CCGGGAT--CCCCAGGGTCCTGGACCA-----CTGAGGCCGACAGCTTA-GGGCA-------GGGCGGCCCTCTGATGCT-GGTG-TTGGGACAG-----------TCCCAGGGACCTCAGCCCCGCC--CCCAGC-------ATAAAATGTGAACAGTAGA--GCTGT-GGGTCCAGCGGA-----GAGGTCGGGGTTCGAGTCTGGATTCTATGG------GACAGGCC i felCat3.scaffold_135390 I 1 C 0 s myoLuc1.scaffold_155660 38830 236 - 124081 CCCCCCACGCACGGGATGTC---------------------------CAGCGCGTGG-CATCTGCTCAGTCTCCAGCT--TCCCAGGGTCCCG-ACCA-----CCGGGGTTAACGGCGTAGGGGCA-------GGGCAACATCCC-GTGCT-GGTGATCCCGGCGGCCGGTcc---tcccggtgagcct--gtttcccc--ggc--t-------gtaacatgtgaggagtggactaCTGTGGGGTCAGGTGAA-----GAGATTGGGGCTCAGGTCTGGATTCCGTTAGCTATCAGCTGAGC i myoLuc1.scaffold_155660 I 1 C 0 s pteVam1.scaffold_22742 5224 172 - 9737 CCCTCCA--------------------------------------------------------GCCCAGACCCC---------------------------------------CAGCTCAGGGGCA-------GGGTGACCCCCCAGTGCT-Ggagtttgggacggccattct---accccatgagcctcagtttcccc--tgc--t-------ataaaacgTGACGAGCAGG--GCTG-GGGGTCAAGTGGA-----GAGATTGGGGTTCAAATCTGGATTCCATGGGCTGT-AGCT---- i pteVam1.scaffold_22742 I 1 C 0 s loxAfr3.scaffold_159 87891 232 + 1045236 CCCCGCCTCCA------------------------------------C------AGGATGTCTTCAGAGCACCCGGTTC-CCCTGCAAACTCGGGCCAGGCCGTCGGGGTGAGCGGCTCA-GGCCT-------GGGGACCCCTCTGATGCTGGGTGTTTGGTACAGCCACGTCCGCCACCTGTGAGCCTCAGTTTCCCC--CTG--CCAGCTCAGCAG-GTGTGAGCAGT-----GCTGAGGGGCCAGGTGGG-----GCGCCCGGGCCTGGAATGTGA---TTGTTTCCTCTTGGCGGGT- i loxAfr3.scaffold_159 C 0 C 0 e proCap1.scaffold_13667 21148 5848 - 46842 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=58362.000000 s hg19.chr11_gl000202_random 16164 80 + 40103 gaccaggaccagtcTGAGAAA-----CGGGGTCCTC--------ACTCTAAACGTCCGGACGGCCCCTGCCTTAGAGGGAGTGGGGGA-TGAAA s panTro2.chr11 68202753 80 + 134204764 gaccaggaccagtcTGAGAAA-----CGGGGTCCTC--------ACTCTAAACGTCCGGACGGCCCCTGCCTTAGAGGGAGTGGGGGA-TGAAA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 46685 80 + 115376 gaccAGGACCAGGCTGAGAAA-----CGGGGTCCTC--------ACTCTAAACGTCCGGACGGCCCCTGCCTTAGAGGGAGTGGGGGA-TGATA i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125998652 80 - 132107971 gaccAGGACCAGGCTGAGAAA-----CCGGGTCCTC--------ACTCTAAATGGCCGGACGGCCCCTGCCTTAGAGGGAGTGGGGGA-TGAAA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128161068 80 - 133002572 gacGAGGACCAGGCCGAGAAA-----CGGCTTCCTC--------ACTCTACACGCCCCGACGGCCCCTGCCTTAGAGGGAGTGGGGGA-TGAAA i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 77102 80 + 109049 gacGAGGACCAGGCCGAGAAA-----CAGCTTCCTC--------ACTCTACACGCCCCGACGGCCCCTGCCTTAGAGGGAGTGGGGGA-TGAAA i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 82065 79 + 235769 AAGCAGGACCAGGCTGGGAAA-----CCGA-CCCTC--------ACTCTAAACGCCCTGACGGCCCCTGCCTTAGAGGGAGCTGGGGA-TGAAA i calJac1.Contig6069 C 0 C 0 s cavPor3.scaffold_42 9669478 69 + 15951348 GCCCAGGG-CAGGCTGGGAGA-CT--CAGTGTCCTC---TGAGAACCGGTGGAGGTG----------TTCCTCAGAAGGGGTGGAG-------- i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 28455 64 + 42081 GCCCAGGG-CAGG-GGGGAAG-CTGGCAGAGTCCTCCAGTGCAAACCCTCGGGGCCTGGACGTCGCC--------------------------- i oryCun2.chrUn0985 C 0 I 407 s turTru1.scaffold_93657 5404 60 - 12933 CCAGGCCA-GGCGTCTGTAAA-----CAGG----CC----------------------AGCAG-CCCTGCCTTCGAGGGCGTTGGAGG-ATGAC i turTru1.scaffold_93657 I 2 I 1 s equCab2.chr12 28941252 56 + 33091231 CACCAGGA-CGGGCTGGTGGG-----AAGG----CC----------------------GACAGCCCCTGCCTTAGGGGCCGTTGGGGA------ i equCab2.chr12 C 0 I 1 s felCat3.scaffold_135390 60452 49 + 302526 CG--------GTGTCTGTAAA-----CGGG----CC----------------------AGCAGCCCCTGCCTCAGAGGAGGGGGTGGA------ i felCat3.scaffold_135390 C 0 I 1 s myoLuc1.scaffold_155660 39066 62 - 124081 CATGGGGA-CACCCTAGTAAA-----CAGT----CC----------------------CATAGCCCCTGCTTTAGAGGGTGAGTGGGGAATAAA i myoLuc1.scaffold_155660 C 0 I 1 s pteVam1.scaffold_22742 5396 57 - 9737 ----AGGA-CAGGCTGGTAAA-----CGAG----TC----------------------CACAGGCCCTGCCTGGGACAGTGTCTGGGG-CTAAA i pteVam1.scaffold_22742 C 0 I 1 s loxAfr3.scaffold_159 88123 77 + 1045236 GGTCAGGG-CAGGCTGGTGAGGCT--CAGC-TTCTG--------TTTGTAGACGGCA-GGCAGCCCCCACTTAATGGGGGCCAGGTGA-AA--- i loxAfr3.scaffold_159 C 0 C 0 e proCap1.scaffold_13667 21148 5848 - 46842 I e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48978224 11 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=32256.000000 s hg19.chr11_gl000202_random 16244 48 + 40103 TGTAGCAATGT-----CCCCTGCACATGGAGAAGC-------------CTCCTCAGGCGAGGC-CGG-- s panTro2.chr11 68202833 48 + 134204764 TGTAGCAATGT-----CCCCAGCACATGGAGAAGC-------------CTCCTCAGGCGAGGC-CGG-- i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 46765 48 + 115376 TGTAGCAATGT-----CCCCTGCACATGGAGAAGC-------------CTCCTCAGGCGAGGC-CGG-- i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125998732 48 - 132107971 TGTAGCAATGT-----CCCCTGCACATGGAGAAGC-------------CTCCTCAGGCGAGGC-CGG-- i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128161148 47 - 133002572 TGTAGCAATGT-----CCCCGGTACGTGGAGAAGC-------------CTCCTCAGGC-AGGC-CAG-- i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 77182 47 + 109049 TGTAGCAACGT-----CCCCGGTAGGTGGAGAAGC-------------CTCCTCAGGC-AGGC-CAG-- i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 82144 48 + 235769 GGTCGCAGTGT-----CCCCGGCACGTGGAGGAAC-------------CTCCTTAGATGGGGC-CAG-- i calJac1.Contig6069 C 0 I 104 s cavPor3.scaffold_42 9669547 47 + 15951348 ---CGCGCTGA-----TGGCAGCACCTTGTGAAGC------------TCCCCTTGCGGGATGCACAG-- i cavPor3.scaffold_42 C 0 C 0 s turTru1.scaffold_93657 5465 37 - 12933 TGTAATAATGT-----CCCC-----------CCGC-------------CCCCCAACACAAGGC-CGC-- i turTru1.scaffold_93657 I 1 C 0 s bosTau4.chr29 48978235 46 + 51998940 TGTAATAATGT-----CCCCCCCACCC--CGCCGA-------------CCCCGAACACAAGGA-CAC-- i bosTau4.chr29 I 11 C 0 s equCab2.chr12 28941309 29 + 33091231 ----GAAATGTGCCCGTCCC-----------CTG--------------TCCTGTGTAC----------- i equCab2.chr12 I 1 C 0 s felCat3.scaffold_135390 60502 36 + 302526 AGTAGAAATGT-----CCCC-----------CTG--------------CCCCCAGCACGAGGC-TGC-- i felCat3.scaffold_135390 I 1 C 0 s myoLuc1.scaffold_155660 39129 40 - 124081 AGCAGTGATGT--CAGCTCT-----------CCGC-------------CCCCCAGCGCCAGGC-CAC-- i myoLuc1.scaffold_155660 I 1 C 0 s pteVam1.scaffold_22742 5454 40 - 9737 AGTAGTGATAT--CTGTCCC-----------CTGC-------------CCCCCAACTCGGGGC-CAC-- i pteVam1.scaffold_22742 I 1 C 0 s loxAfr3.scaffold_159 88200 61 + 1045236 ---TGCCATAT----GTCCCTGCACTGGGCAATGCACACCCCTGCCCACCCCGAACACGAGGC-TCCAG i loxAfr3.scaffold_159 C 0 C 0 e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=88452.000000 s hg19.chr11_gl000202_random 16292 75 + 40103 -GGGATCAGGC-AGCTCGCGCCCGGAAGGCT--TCGCATATAATGCAC-----CGTCTATTTCAGCTCGCCGGGGTCTTGCTGC s panTro2.chr11 68202881 75 + 134204764 -GGGATCAGGC-AGCTCGCGCCCGGAAGGCT--TCGCATATAATGCAC-----CGTCTATTTCAGCACGCCGGGGTCTTGCTGC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 46813 75 + 115376 -GGGATCGGGC-AGCTCGCGCCCGGAAGGCT--TCGCATATAATGCAC-----CGTCTATTTCAGCACGCGGGGGTCTTGCTGC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125998780 73 - 132107971 -GGGGTCAGGC-AGCT--CGCCCGGAAGGCT--TCGCATATAATGCAC-----CTTCTGTTTCAGTCCCCGGGGGTCTTGCAGC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128161195 73 - 133002572 -CGGATCACGC-AGCT--CGCCAGGAAGGTT--TCGCATATAATGCAC-----CTTCTATTTTAGTGCCCCGGGGTCTTGCTGC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 77229 73 + 109049 -CGGATCACGC-AGCT--CGCCAGGAAGGTT--TCGCATATAATGCAC-----CTTCTATTTTAGTGCCCCGGGGTCTTGCTGC i papHam1.scaffold6638 C 0 C 0 s cavPor3.scaffold_42 9669594 62 + 15951348 ----------A-GTCT--CAGCAGAAAGACC--TTGCCTGGAGTGCGC-----CTCATATTTCAACCCGCC--AGTCCGGCTGC i cavPor3.scaffold_42 C 0 C 0 s turTru1.scaffold_93657 5502 73 - 12933 -TGGGTCACTCAGCCT--CACTCGGGAGGTC--TTGTGTG-AACACGC-----TTTCTTCCTCAGCCTCCGAGGGCCTTGAGGC i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48978281 73 + 51998940 -TGGGGCACTCAGCCT--CACTCAGGAGGTC--TCATGTA-AACCCAT-----CTTCTTTCTCAGCCTCCAAGGGCCCTGATGC i bosTau4.chr29 C 0 I 333 s equCab2.chr12 28941338 36 + 33091231 ------------ATCT--CACCTC-----TC----------------------------TCTCGGGCCCCAAGGG-TTTGCAGC i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 60538 52 + 302526 -CGGACCACGGGGCCT--CACTCTGAAGGTC----------------------------CCCCGGCCTCGGAGGG-TTTGCCGC i felCat3.scaffold_135390 C 0 C 0 s myoLuc1.scaffold_155660 39169 77 - 124081 -TGGGTCATCC-GCCT--CACTCGGAAGGTCTGGTGTGT--AACGCATCGCACCTTCTATCAAAGCCTCCTCGGC-TTTGCTGC i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 5494 73 - 9737 -TGGGTCACCCAGGCT--CACACAGAAAGTCTGTCATAT--AACGCAT-----CTTCTGTCTCAGCCCCCGAGGG-TCCACGAC i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 88261 69 + 1045236 AGGAGT------AGCT-GTACCCAGAGGGCC--CTGTGTATAGCACAC-----CCTCTGTCTTAGCCTCCTGGAT-CTTTCTGT i loxAfr3.scaffold_159 C 0 C 0 e calJac1.Contig6069 82192 104 + 235769 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=-8914.000000 s hg19.chr11_gl000202_random 16367 51 + 40103 AAAGTTGCGCAACAGAA-------AATGTGAGAG--ACGCGGCAGTCACTCCACTAAGCG s panTro2.chr11 68202956 51 + 134204764 AAAGTTGCGCAACAGAA-------AATGTGAGAG--ACGCGGCAGTCACTCCACTAAGCG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 46888 51 + 115376 AAAGTTGTGCAACAGAA-------AATGTGAGAG--ACGCGGCAGTCACTCCACTAAGCG i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125998853 49 - 132107971 AAAGTTGTGCAACAGAA-------AATGTGAGGG--AAGCCACAGTCGCTCCACTGA--G i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128161268 51 - 133002572 AAAGTTGTGCAACAGGA-------AATGCGAGGG--ACGCGACACTCACTCCACTAAGCG i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 77302 30 + 109049 AAAGTTGTGCAACAGGA-------AATGCGAGGG--ACG--------------------- i papHam1.scaffold6638 C 0 M 50 s cavPor3.scaffold_42 9669656 40 + 15951348 GAAGTTTTG-----------------TGGTGAAG--ACCCTAC-TCCATGCTACACAGTG i cavPor3.scaffold_42 C 0 I 5 s turTru1.scaffold_93657 5575 38 - 12933 GAAGTTGTGCGATGGAA--AATTTAATGTTACAG--GCCGAT------------------ i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48978687 35 + 51998940 AAAGTTGTGCGATGGAA-------AATGTCTCAGTAGACCAA------------------ i bosTau4.chr29 I 333 C 0 s equCab2.chr12 28941374 40 + 33091231 AAAGTTGTGCGACGGGAACAGTTTTAAATTCTGG--ACCGCG------------------ i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 60590 38 + 302526 AAAGTTGCCCCGCGCCA--AGGTTTGAACTGGGG--AGCACA------------------ i felCat3.scaffold_135390 C 0 C 0 s myoLuc1.scaffold_155660 39246 35 - 124081 CAAGTGGTGCCATGGAA--ATTT---AATTACGG--ACCGCA------------------ i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 5567 36 - 9737 --AGCTGTGCAATGGAA--AATTCTAAATTACAG--AGCACG------------------ i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 88330 30 + 1045236 AAAGCCGCCTCATGGGA-------GACATGACAA--GCA--------------------- i loxAfr3.scaffold_159 C 0 C 0 e calJac1.Contig6069 82192 104 + 235769 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=161876.000000 s hg19.chr11_gl000202_random 16418 94 + 40103 GGACA-GG-G----CC------------AGGCCCGCCGCCAGGGGGCAGCATCGCCTCTCCCGGCCGAGCCTTCCTG-GGAGTCCCGCGGGGGCTGCTC----------CCCAAAGGACAGAG s rheMac2.chr14 128161319 94 - 133002572 GGACA-GG-G----CC------------CGGCCCACCGCCAGGGGGCAGCATCGCCTCTCCCGGCGGAGCCTTCCCG-GGAGCCCCGCGGGGGCCGCTC----------CCCAGAGGACAGAG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125998902 94 - 132107971 GGACA-GG-G----CC------------CGGCCCACCGCCAGGGGGCAGCATCGCCTCTCCCGGCCGAGCCTTCCTG-GGAGCCCCGCGGGGGCCGCTC----------CCCAAAGCACAGAG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 46939 95 + 115376 GGACAGGG-G----CC------------CGGCCCACCGCCAGGGGGCAGCATCGCCTCTCCCGGCCGAGCCTTCCTG-GGAGCCCCGCGGGGGCTGCTC----------CACGAAGGACAGAG i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68203007 94 + 134204764 GGACA-GG-G----CC------------CGGCCCGCCGCCAGGGGGCAGCATCGCCTCTCCCGGCCGAGCCTTCCTG-GGAGCCCCGCGGGGGCTGCTC----------CCCAAAGGACAGAG i panTro2.chr11 C 0 C 0 s calJac1.Contig6069 82296 91 + 235769 GGGTT-GG-G----CC------------CGGCCCGCCGCCAGGGGGCAGCATCGCCCCTCATGGCCCAGCCCTCCTG-GGAGCC---CAGGGGCAGCTC----------CTCAAAGGACAGAG i calJac1.Contig6069 I 104 C 0 s cavPor3.scaffold_42 9669701 83 + 15951348 GGACA-GG-GAGCTCG------------CTCTCCACCACCAGGGGGCAGCGCCAGGGCTCCC-ACTAACTCTTTCCT-GGAGGGTTGGGGGGCTGGCTC------------------------ i cavPor3.scaffold_42 I 5 I 1978 s turTru1.scaffold_93657 5613 101 - 12933 TGACA-GAGG----TT------------CTCTCCACCACCAGGGGGCAGCATTGCCCCTCACTGCTGAGCCTTCCTTGGGGGACCC-----AGCTGCACCCACCCCACCCGCCAAGGGCAGAG i turTru1.scaffold_93657 C 0 I 2 s bosTau4.chr29 48978722 96 + 51998940 CGATG-GA-G----TT------------CTCTCCACCACCAGGGGGCAGCATTGGCCCTCACCGCTGAGCCTTCCTT-GGAGACCC-----AGCTACAC---CCCCAACCCCCAAGGTCAGAG i bosTau4.chr29 C 0 I 2 s equCab2.chr12 28941414 94 + 33091231 GGGCG-GA-G----G--------------CCACCCCCACCAGGGGGCAGTGTCCGCTCTCACAGCTGAGTCTCCCCC-AGAGGCC-----GGGCCGC---CTGCCCACCAGGGAACGGCAGAG i equCab2.chr12 C 0 I 2 s felCat3.scaffold_135390 60628 64 + 302526 GGACG-GG-C----A--------------CATCCACCACCAGGGGGCAGCCTCAGCTCTCACCTCTGAGTC-CCTCC-AGGGGTCT------------------------------------- i felCat3.scaffold_135390 C 0 I 548 s myoLuc1.scaffold_155660 39281 96 - 124081 GGACG-GA-G----GC------------TCACCCACCACCAGGGGGCGGCATCAGTTCTCACCTCCGAGTCTA--GC-AGGG----GCCCTGGCCGCG--TCTGACTCTGGGCAAGGGCAGAG i myoLuc1.scaffold_155660 C 0 M 276 s pteVam1.scaffold_22742 5603 89 - 9737 GGATG-GA-G----GC------------ACCCCCACCACT-GGGGGCGGCATCGGTCCTCTCCTCAGAGTTT--------------GCCTTGGCCGCAC-CCCCACTCCCCGGAAGGGCAGCG i pteVam1.scaffold_22742 C 0 I 1 s loxAfr3.scaffold_159 88360 107 + 1045236 GGACA-AG-A----CCACGACCGAGCCTCCCTCCACCACCAGGGGGCAGCAGCGGACCTCATCCTGCAACTG---TG-GGGGTACCTCGCCGCCTCCCC------CAACCCCACAGGATCGAG i loxAfr3.scaffold_159 C 0 I 2 e papHam1.scaffold6638 77332 50 + 109049 M e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=127377.000000 s hg19.chr11_gl000202_random 16512 63 + 40103 CTCCGGGTTCATGGGGAACGGGGTGCCGAGAAAGCCTGCCTG------GCCCT-CCCAGGCCCCACTTCC s rheMac2.chr14 128161413 62 - 133002572 CTCCGGGTTCATCGGGGACGGGGCACCGAGAAAGCCTGCCTG------GCCCT-TCCAGA-CGCACGTCC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125998996 63 - 132107971 CTCCGGGTTCATGGGGGACGGGGCGCCGAGAAAGCCTGCCTG------GCCCT-CCCAGACCCCACTTCC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 47034 63 + 115376 CTCCGGGTTCATGGGGAACGGGGCGCCGAGAAAGCCTGCCTG------GCCCT-CCCAGGCCCCACTTCC i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68203101 63 + 134204764 CTCCGGGTTCATGGGGAACGGGGTGCCGAGAAAGCCTGCCTG------GCCCT-CCCAGGCCCCACTTCC i panTro2.chr11 C 0 C 0 s calJac1.Contig6069 82387 50 + 235769 CTGGGGGTTCAAGGGGGACTGGG-------------TGCCTG------GCTTT-CCCAGACCCCACTTCC i calJac1.Contig6069 C 0 C 0 s turTru1.scaffold_93657 5716 61 - 12933 CTCTGGGTTCGCGGGA---TGTGGGCTCTGAAAGCCTGCCTG------GCCCTTTCCAGACACTACGTCC i turTru1.scaffold_93657 I 2 C 0 s bosTau4.chr29 48978820 66 + 51998940 CTCTGGGTTCATGGCC---TAGGGGC-CTGAAAGCCTGACTGAGCCCCGCCCCACCCAGACCTCACCTCC i bosTau4.chr29 I 2 C 0 s equCab2.chr12 28941510 58 + 33091231 CTCTTGGCTCACCAGG---AGGGGACAGTGTCAGCCTGCCCG------GCCCTTCCCGCAGC---CTCCC i equCab2.chr12 I 2 C 0 s pteVam1.scaffold_22742 5693 61 - 9737 CCCTAGGTTCATGGCG---TGGGGGCGGTGAAAGCCTGCCCG------GCTCTTCTCAGACCCCACCCCC i pteVam1.scaffold_22742 I 1 C 0 s loxAfr3.scaffold_159 88469 51 + 1045236 CTTTGGGGTCATGGGG---TGGGCG--GTGAAAGCCTGCCTG------GCCCCTCCTAGACC-------- i loxAfr3.scaffold_159 I 2 C 0 e felCat3.scaffold_135390 60692 548 + 302526 I e papHam1.scaffold6638 77332 50 + 109049 M e myoLuc1.scaffold_155660 39377 276 - 124081 M e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=172130.000000 s hg19.chr11_gl000202_random 16575 86 + 40103 TTGTTCTTACAAACCTAAGGAAGAGTGGGCTCC-TGGGATTAACTCGGCGTCACGAAACCCTGG-CCCTGAGGGACGGACCTCTCAGC s panTro2.chr11 68203164 86 + 134204764 TTGTTCTTACAAACCTAAGGAAGAGTGGGCTCC-TGGGATTAACTCGGCGTCATGAAACCCTGG-CCCTGAGGGACGGACCTCTCAGC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 47097 86 + 115376 TTGTTCTTACAAACCTAAGGAAGAGTGGGCTTC-TGGGATTAACTCGGCGTCATGAAACCCTGG-CCCTGAGGGACGGACCTCCCAGC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125999059 86 - 132107971 TTGTTCTTACAAACCTAAGGAAGAGTTGGCTCC-CGGGATTAACTCAGCGTCATGAAACCCTGG-CCCTGAGGGACGGACCTCCCAGC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128161475 86 - 133002572 TTGTTCTTACAAACCTAAGGAAGAGTGGACTCC-CGGGATTAACTCAGCGCCATGAAACCCTGG-CCCTGAGGGGCGGACCTCCCAGC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 77384 87 + 109049 TTGTTCTTACAAACCTAAAGAAGAGTGGACTCC-CGGGATTAACTCAGCACCATGAAACCCTGGCCCCTGAAGGGCGGACCTCCCAGC i papHam1.scaffold6638 M 50 C 0 s calJac1.Contig6069 82437 86 + 235769 TTGTTCTTACAAACCCAAGGGAGAGTGGGCTCC-CAGGATTAACTCAGCGCCATGAAACCCCAG-CCCTGAGGGACGGCCCGCCCTGC i calJac1.Contig6069 C 0 C 0 s turTru1.scaffold_93657 5777 73 - 12933 CTGTTCCC----ACCTAAGGAG----TGGCTCC-CAAGATTGACTA-GAAGCTTGAAA----GG-CCCTGGTGGACCGTCCTCCTGGC i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48978886 72 + 51998940 TTGTTCCC----TCCGAAGCAG----TGGCCAC-CAAGACTGATCA--AACCTTGAAA----GG-CCGCAACAGGAGGGCCTCCCGGC i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28941568 73 + 33091231 CGGTCCCTACAAACCTAAGGAG----CGGCTGCCCAAGATTAGCCT-----CGCGAAA----GG-CC-CAGTGGATGGTCCTTCCAGC i equCab2.chr12 C 0 C 0 s pteVam1.scaffold_22742 5754 61 - 9737 CCATCCCCACAAACCCAGATA-------------TAACA----CCC-----CGTGAAA----GG-CCGTGGTGGACCATCCTCCCCAC i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 88520 77 + 1045236 -TGTTATTACAAACCTA--GAAGTAGGGACCCTGCAAGGTGAGCTT-GCCTGATGA-----TGG-CAAGAGTGGACAGTCC-CCCAGC i loxAfr3.scaffold_159 C 0 C 0 e felCat3.scaffold_135390 60692 548 + 302526 I e myoLuc1.scaffold_155660 39377 276 - 124081 M e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=36676.000000 s hg19.chr11_gl000202_random 16661 74 + 40103 CTGGGTCAGGCCAAGGACATCTGAG---TGGCCCCACCG---CGAACTCCTGTGAGCCCCTGGAGCGAGC----AGTGGCCTCG s loxAfr3.scaffold_159 88597 75 + 1045236 CTGGGTCACGCCAAGGGCATCCGGCATTAAACCCCA---------ACACTCATGGGCCATTACACTCGACCGCAGGCAGCCTCA i loxAfr3.scaffold_159 C 0 C 0 s pteVam1.scaffold_22742 5815 65 - 9737 T-GGGTCTCTCTGG---GCCCCCGC---CAACACCCC------TGGGCCCTGTGACCCCC--GAGCCCAC----AGCAACCTTC i pteVam1.scaffold_22742 C 0 C 0 s equCab2.chr12 28941641 65 + 33091231 C-TGGTCCCTGCGGCGAGGTCCTGC---AGGGGCTAT--------GGCCCTCTGCCCCCT--GA-CCCAC----AGCAGCCCCG i equCab2.chr12 C 0 C 0 s bosTau4.chr29 48978958 69 + 51998940 CGGGGTTCCTGCGGTGAAATCCCGC---CAATGCTCC-----TTGGCCCTTATGCTCCCT--GA-CGCCT----GGCAACCTCC i bosTau4.chr29 C 0 C 0 s turTru1.scaffold_93657 5850 47 - 12933 CTGGGTTCCTGCTGTGA------------AATGCTCC--------GCCTTTATGCTCCC-----------------CAACCCCC i turTru1.scaffold_93657 C 0 C 0 s calJac1.Contig6069 82523 74 + 235769 CTGGGTCAGGCCAAGGACATCTGAG---CGACCCCACAG---CCAGCCCCTGGGGGCCCCTGGAGCCCAC----AGTGGCCTTG i calJac1.Contig6069 C 0 C 0 s papHam1.scaffold6638 77471 74 + 109049 CTGGGTCAGGCCAAGGACATCTGAG---CGGCCCCACCG---CGAACCCCTGTGAGCCCCGGGAGCCAGC----AGTGGCCTCG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128161561 74 - 133002572 CTGGGTCAGGCCAAGGACATCTGAG---CGGCCCCACCG---CGAACCCCTGTGAGCCCCGGGAGCCAGC----AGTGGCCTCG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125999145 74 - 132107971 CTGGGTCAGGCCAAAGACATCTGAG---TGGCCCCACCG---CGAACCCTTGTGAGCCCCTGGAGCGAGC----AGTGGCCTCG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 47183 74 + 115376 CTGGGTCAGGCCAAGGACATCTGAG---TGGCCCCACCG---CGAACTCCTGTGAGCGCCTGGAGCGAGC----AGTGGCCTCG i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68203250 74 + 134204764 CTGGGTCAGGCCAAGGACATCTGAG---TGGCCCCACCG---CGAACTCCGGTGAGCCCCTGGAGCGAGC----AGTGGCCTCG i panTro2.chr11 C 0 C 0 s xenTro2.scaffold_753 73367 68 - 469580 CTGAGTCCTACCTCTGCCCGCTGAG---TCCTCCCTCTG--------CCCGCTGAGTTCCCTCTGCCCAC----TGAGTCCTC- i xenTro2.scaffold_753 N 0 C 0 s ornAna1.Contig4144 14494 54 + 64285 ------------------AGCCGAG---GGGCCCCCACGGGCCGGGGCCTCGC---CACAGTGAGCGGAG----AGGAGCCG-- i ornAna1.Contig4144 N 0 I 122 e felCat3.scaffold_135390 60692 548 + 302526 I e myoLuc1.scaffold_155660 39377 276 - 124081 M e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=77816.000000 s hg19.chr11_gl000202_random 16735 86 + 40103 AGTCTGTGCCCACCTCCTTTC--ACGCCCCTCTTCCCTGGCTGGCCATCTT--------GGCATCCCTCCTCCCCT--GCCACTCTATCTTGGCCTCC s loxAfr3.scaffold_159 88672 83 + 1045236 ---CCGAGCCTGCCTCTTTCTGGAAACTTCTCTCCCCTGGAA--CCACCCT--------GGCCTCCTTCCTCTGACCAGGCACGTC--CTCGACCCCC i loxAfr3.scaffold_159 C 0 C 0 s pteVam1.scaffold_22742 5880 57 - 9737 AGTCTGTGGCCTCCTCCT---------------CCCCTGACC------CCT--------GGGGTCCCCCCTCTCCTAGGCCACTGT------------ i pteVam1.scaffold_22742 C 0 C 0 s equCab2.chr12 28941706 73 + 33091231 CGGCCCTGGCTTCCTCCCTCT--GGAGCCC-CATCCCTGACC--ACGTCCC--------TGTTTCTCCTCCCGCCCCGGCCGATCC------------ i equCab2.chr12 C 0 C 0 s bosTau4.chr29 48979027 55 + 51998940 TTCCGGAG----CCCCCT---------------TCCCTGACC--CAG-CCT--------GGATT-CCCCCTCCCCCAGGCTGCTGT------------ i bosTau4.chr29 C 0 C 0 s turTru1.scaffold_93657 5897 58 - 12933 TTCCTGAG---CCCCCCT---------------TCCTTGACC--CCGTCCT--------GGCTTCCCCCCTCCCCCAGGCTGCTGT------------ i turTru1.scaffold_93657 C 0 C 0 s calJac1.Contig6069 82597 64 + 235769 AGTCCACACTTGCCTCCTTCC--CGTGCTCTCTTCCCTGGCCGGCCATCCT--------GGCTTCCCTCCTCCC------------------------ i calJac1.Contig6069 C 0 I 13 s papHam1.scaffold6638 77545 87 + 109049 AGTCTGTGCCCACCTCTTTTC-GGGGCCCCTCTTCCCTGGCTGGCCGTCCT--------GGAGCCCCTCCTCCCCT--GCCTCTCCATCTTGGCCTCC i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128161635 87 - 133002572 AGTCTGTGCCCACCTCCTTTC-GGGGTCCCTCTTCCCTGGCTGGCCGTCCT--------GGAGCCCCTCCTCCCCT--GCCTCTCCATCTTGGCCTCC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125999219 86 - 132107971 AGTCTGTGCCCACCTCCTTTC--ACGGCCCTCTTCCCTGGCTGGCCATCCT--------GGCGTCCCTCCTCCCCT--GCCACTCTATCTTGGCCTCC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 47257 86 + 115376 AGTCTGTGCCCACCTCCTTTC--ACGCCCCTCTTCCCTCGCTGGCCATCTT--------GACGTCCCTCCTCCCCT--GCCACTCTATCTTGGCCTCC i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68203324 86 + 134204764 AGTCTGTGCCCACCTCCTTTC--ACGCCCCTCTTCCCTGGCTGGCCATCTT--------GGCGTCCCTCCTCCCCT--GCCACTCTATCTTGGCCTCC i panTro2.chr11 C 0 C 0 s xenTro2.scaffold_753 73435 69 - 469580 --CCTCTGCCCGCTGAGTTCC------CTCTGCCCGCTGAAT--CCTCCCTCTGCCCACTGATTCCTACCTCTG------------------CCCGC- i xenTro2.scaffold_753 C 0 N 0 e ornAna1.Contig4144 14548 122 + 64285 I e felCat3.scaffold_135390 60692 548 + 302526 I e myoLuc1.scaffold_155660 39377 276 - 124081 M e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=134803.000000 s hg19.chr11_gl000202_random 16821 164 + 40103 TGGGCCGGCT-------CCCAC---CCCCC---GGTTCCCATGCTTCCTCCCCGCAGAGAGGGACCCAGAGGTGCCAC-CA---------------CCTT--GGGGTGACC--AAGTCCCAGTGCTATGTTCGGCCCCAGGGCTCCTTCACTTCACTCACGGGCGCCTTTCTCTGCAGCTCACACAGGCACAAAGTA s panTro2.chr11 68203410 164 + 134204764 TGGGCCGGCT-------CCCAC---CCCCC---GGTTCCCATGCTTCCTCCCCTCAGAGAGGGACCCAGAGGTGCCAC-CA---------------CCTT--GGGGTGACC--AAGTCCCAGTGCTATGTTCGGCCCCAGGGCTCCTTCACTTCACTCACAGGCACCTTTCCCTGCAGCTCATACAGGCACAAAGTA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 47343 164 + 115376 TGGGCCGGCT-------CCCAC---CCCCC---GGTTCCCATGCTTCCTCCCCCCAGAGAGGGACCCAGAGGTGCCAC-CA---------------CCTT--GGGGTGACC--AAGTCCCAGTGCTATGTTCAGCCCCAGGGCTCCTTCACTTCACTCACAGGCGCCTTTCCCTGCAGCTCACACAGGCACACAGTA i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125999305 169 - 132107971 TGGGCCGGCT-------CCCAC---TCCCCCCGGGTTCCCATGCTTCCTCTCCCCAGAGAGGAACCCAGAGGTGCCAC-CA---------------CCTT--GGGGTGACCAAAAGTCCCAGTGCCATGTTCAGACCCAGGGCTCCTTCACTTCACTCACAGGCACCTTTCCCTGCAGCTcacacagatacgcagca i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128161722 175 - 133002572 TGGGCCGGCT-------CCCAC---CCCCT---GGTTCCCATGCTTCCTCCCC-CGGAGAGAGACCCAGAGGCGCCAC-CACCGGGCGGGTTGAG-CCTT--GGGGTGACC--AAGTCCCAGTGCCACGTTTAGCCCCAGGGCTCCTTCACTTCACCCACAGGCGCCTTTCCCTGCAGTTCACGGAG--ACAGGGTG i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 77632 177 + 109049 TGGGCTGGCT-------CCCAC---CCCCT---GGTTCCCATGCTTCCTCCCC-CAGAGAGAGACCCAGAGGCGCCAC-CACCGGGTGGGTTGAG-CCTT--GGGGTGACC--AAGTCCCAGTGCCACGTTTAGCCCCAGGGCTCCTTCACTTCACCCACAGGCGCCTTTCCCTGCAGTTCACGGAGGCACAGGGTG i papHam1.scaffold6638 C 0 C 0 s loxAfr3.scaffold_159 88755 133 + 1045236 TTGGCCGGCCTCTTGTGCCCACCTGCCCCA---GGCTCACTCCTTTCCTCC---CAGGGAA------------------TG--------GTGGGG-CTTCGAAGGGTGGCC--ACTACCCAGGGTAACATTCAGGGTTACAGCTCCTTCTCCCCA-------------------GGTGCTcacactc---------- i loxAfr3.scaffold_159 C 0 C 0 s ornAna1.Contig4144 14670 111 + 64285 T-----GGCTCAGCCTCTCAGC---ACCCC---ATTTCCGGGACCCCCTCCCA-CTGCCGG-CACCCAGGGAC------CG------------GG-------AGGGTTATC--CCCACCCCCGTCCACTTCCCACGCCCCGATTCCACAGC---------------------------------------------- i ornAna1.Contig4144 I 122 C 0 s pteVam1.scaffold_22742 5937 158 - 9737 ---------------------C---GCCCC-----TTTACACCTGCCCTCACC-CAGAGAG-CACTGGGAGGCCTCAC-CGCCCTGATGGGGGGGACCTTGGAGGTCGATG--GCACCCCTGTGCCACATGTGGCCTCACAGCTCCTCCGCCCCACACA--GGCGTGGCTCCCTAGTGCTCCcacagacacgca--- i pteVam1.scaffold_22742 C 0 I 3 s equCab2.chr12 28941779 95 + 33091231 ---------------------C---CCGCT--GGGTGCTCGTCTGCCTTTGCC-CAGAGAG-GACTGGGAGACCCCAG-TGCCCGG-----------------------------------GTGCCACA---------------------CCCCATTCA--CACGT---------GTACACACGCAGA---GCA--- i equCab2.chr12 C 0 I 5 s bosTau4.chr29 48979082 144 + 51998940 --------------------------CCCT---GGTTCACTCCTGCCCTGGCC-CAGAGAG-CCCTGGGAGACCCCTC-TGCTAGGATGGTGGAG-CCTCCAAGGCTGATG--GCCCTCCTGAGCCACT-TGGGGCTCACAGCCCCTTCACTCCCGCCA---GTGTGGCTCCCTGGCGCTCTC-------------- i bosTau4.chr29 C 0 C 0 s turTru1.scaffold_93657 5955 146 - 12933 ---------------------C---CCCCT---GGTTCACACCAGGCCTCGCC-CAGAGCG-GACTGGGGGGCCCCTAGCGCCCGGATGGTGGAG-CCTCCAAGGGTGATG--GACCTCCTGGGCTATG-CTCCGCTCACAG-CCCTTCACTCCAGCTG---GCCCGGCTCCCTGGTGCTCCc-------------- i turTru1.scaffold_93657 C 0 C 0 s calJac1.Contig6069 82674 173 + 235769 -GAGCCGGAC-------CCCAC---CCCCC---AGTTCCCATGATTCCTCCC--CAGAGAAGTACCCAGAGATGCCAA-CACCAGGTGGGTTGAG-CCTT--GGGGTGACC--GAGCCCCAGTGACACTTTTAGCCCCAGGGCTCCTTCACTTCAGCCACAGACACCTTTCCCTGCAGCTCACATGCGCACAGA--A i calJac1.Contig6069 I 13 C 0 e felCat3.scaffold_135390 60692 548 + 302526 I e myoLuc1.scaffold_155660 39377 276 - 124081 M e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=5501.000000 s hg19.chr11_gl000202_random 16985 55 + 40103 -----ACAC------ACGTGCCCGCACACTCGTGTATACACGCACA----------------------------------CAGGCACACA------CT-------------ACTGCTCA s panTro2.chr11 68203574 55 + 134204764 -----ACAC------ACGTGCCCGCACACTCGTGTATACACGCACA----------------------------------CAGGCACACA------CT-------------ACTGCTCA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 47507 55 + 115376 -----ACAC------ACGTGCCCGCACACTCGTGTATACATGCACA----------------------------------CAGGCACACA------CT-------------ACTGCTCA i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125999474 54 - 132107971 -----acac------acgtgcccgcacactcgtgcatacacgcaca----------------------------------caggcataca------ct-------------actgctc- i ponAbe2.chr11 C 0 I 235 s rheMac2.chr14 128161897 54 - 133002572 -----ACAC------ACGTGCCCGCACACTCGTGTATACACGCACG----------------------------------CAGGCACA-A------CT-------------GCTGCTCA i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 77809 54 + 109049 -----ACAC------ACGTGCCCGCATACTCGTGTATACACGCACG----------------------------------CAGGCACA-A------CT-------------ACTTCTCA i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 82847 37 + 235769 -----ACAC------ATGCGCCTGCACACTTGTGTATACACGCACA----------------------------------CA------------------------------------- i calJac1.Contig6069 C 0 I 72 s turTru1.scaffold_93657 6101 46 - 12933 ---------------acacacgtgcacacacacacgtgcacacatg----------------------------------ccgagacaca------cg-------------gc-----a i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48979226 42 + 51998940 ---------------AGacacacgaacacacgtgcattcacacatg----------------------------------c----acaca------ca-------------gc-----a i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28941879 103 + 33091231 -----ACACACGTGTGTGCACGCACGCATGCGGGTGCACACAGGTCACACATGGTACAAACTCATGTGTTcacacatatgcccggacaca------cacaggaactcaaatac-----a i equCab2.chr12 I 5 C 0 s myoLuc1.scaffold_155660 39657 65 - 124081 -----acacaagtgcacacacactaacacacgcgcactcacaaatc------------gactca----------------cttttacaca------tat----------gtgc-----a i myoLuc1.scaffold_155660 M 276 C 0 s pteVam1.scaffold_22742 6098 48 - 9737 -----------------acacgcagacacgtgtgcacacgcagac--------------acgca----------------cccagacaca------ca-------------gc-----a i pteVam1.scaffold_22742 I 3 C 0 s loxAfr3.scaffold_159 88888 53 + 1045236 -----aagc------acacacacacacacgcagatgtacacaaaca----------------------------------cattcacacaTGTGTTC---------------------A i loxAfr3.scaffold_159 C 0 C 0 s ornAna1.Contig4144 14781 50 + 64285 AGGGCACGC------ATATACGTGTATACATGTACACACGCACACG----------------------------------CTTGTGCAG-----------------------------A i ornAna1.Contig4144 C 0 N 0 e felCat3.scaffold_135390 60692 548 + 302526 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=-16973.000000 s hg19.chr11_gl000202_random 17040 64 + 40103 CAT-----------------GCACATAAGTGCA---ATGTGTCCTCACATG-AACATGAGTGCA-----------------------------------------------ATGGGAacactctt------------------------aca-------cacc s papHam1.scaffold6638 77863 64 + 109049 CAT-----------------GCACGTAAGTGCA---ATGTGTACTCACACG-AACATGAAGGCA-----------------------------------------------ATGGGAACACGCTT------------------------CCA-------CACC i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128161951 64 - 133002572 CAT-----------------GCACATAAGTGCA---ATATGTACTCACACG-AACATGAATGCA-----------------------------------------------ATGGGAACACGCTT------------------------CCA-------CTCC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125999763 65 - 132107971 CAT-----------------GCACATAAGTGCA---ATATGTACTCACAAG-AA------TGCA-----------------------------------------------ATGGGAACACTCTT------------------------CTATTGTGGGTTCC i ponAbe2.chr11 I 235 C 0 s gorGor1.Supercontig_0015245 47562 64 + 115376 CAT-----------------GCACATAAGTGCA---ATGTGTACTCACATG-AACATGAATGCA-----------------------------------------------ATGGGAACACTCTT------------------------CCA-------CACC i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68203629 62 + 134204764 CAT-----------------GCACATAAGTGCA---ATGTGTCCTCACATG-AACATGAGTGCA-----------------------------------------------ATGGGAACACT--T------------------------CCA-------CACC i panTro2.chr11 C 0 C 0 s turTru1.scaffold_93657 6147 54 - 12933 cac-----------------acacac--------------gtgcacacaca-cacacgtgcaca----------------------------------------------------catgcccag------------------gcacactca-------caca i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48979268 55 + 51998940 ctc-----------------acacat--------------gcgcacacacg-cactcactccca---------------------------------------------------gcacactcat------------------acatgtgca-------caca i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28941982 151 + 33091231 catacagatccactgacgtgccacacaagt-cc---atgagtacacacattacacccatgcaca-cgctcccacacagatcacccgcacacgctcacctgtatacacatgctcttgtacactcacacccattcacgctaactcacacgcaca-------caca i equCab2.chr12 C 0 C 0 s myoLuc1.scaffold_155660 39722 57 - 124081 cac-----------------cgacata-------------gtgtatccact-cacacatgcacatagctctc-------------------------------------------gagcactcac-------------------------ga-------taca i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 6146 51 - 9737 cat-----------------ccacacacGT----------GTGTGCACATT-CACACATGTACA-------------------------------------------------------ACTCAT----------------------Tcaga-------caca i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 88941 46 + 1045236 TGT-----------------GTACACACGAGCATTcacacatccacacaca-gacatacacaca--------------------------------------------------------------------------------------------------- i loxAfr3.scaffold_159 C 0 C 0 e felCat3.scaffold_135390 60692 548 + 302526 I e calJac1.Contig6069 82884 72 + 235769 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=55981.000000 s hg19.chr11_gl000202_random 17104 23 + 40103 agttca--cagaca----cccacatgcac s calJac1.Contig6069 82956 27 + 235769 AGCTca--cagacacacgcacacatacac i calJac1.Contig6069 I 72 C 0 s papHam1.scaffold6638 77927 23 + 109049 AGCTca--cagaca----cccacatgcac i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128162015 23 - 133002572 AGCTca--cagaca----cccacatgcac i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125999828 23 - 132107971 AGTTCA--CAGACA----CCCACATACAC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 47626 23 + 115376 AGTTca--cagaca----cccacatgcac i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68203691 23 + 134204764 AGTTca--cagaca----cccacatgcac i panTro2.chr11 C 0 C 0 s turTru1.scaffold_93657 6201 22 - 12933 cgttt---cacaca----cacacgtgcac i turTru1.scaffold_93657 C 0 I 2 s bosTau4.chr29 48979323 25 + 51998940 cCCATGGACAAGCA----CATACATGCAC i bosTau4.chr29 C 0 I 64 s equCab2.chr12 28942133 23 + 33091231 tgcacg--cacgct----cactcatgctc i equCab2.chr12 C 0 I 6 s myoLuc1.scaffold_155660 39779 23 - 124081 ttcatg--tacaca----cacagagacgt i myoLuc1.scaffold_155660 C 0 I 2 s pteVam1.scaffold_22742 6197 23 - 9737 tgcctg--cacact----cacacaagtcc i pteVam1.scaffold_22742 C 0 I 2 s loxAfr3.scaffold_159 88987 23 + 1045236 ggcaca--cagaaa----tacacacgcag i loxAfr3.scaffold_159 C 0 C 0 e felCat3.scaffold_135390 60692 548 + 302526 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7537155 1840 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=86294.000000 s hg19.chr11_gl000202_random 17127 40 + 40103 acactccac--------------cacacatgcataca------cacagacaggtacacac s calJac1.Contig6069 82983 54 + 235769 acactccatcgtgcatacacacacacacacacacaca------cacacagaagcacacac i calJac1.Contig6069 C 0 C 0 s papHam1.scaffold6638 77950 40 + 109049 acactccac--------------cacacgtgcataca------cacatacaggtacacac i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128162038 40 - 133002572 acactccac--------------cacacgtgcataca------cacatacaggtacacac i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125999851 40 - 132107971 ACACTCCAC--------------CAGACATGCATACA------GACGTACAGGTACACAC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 47649 40 + 115376 acactccac--------------cacacatgcataca------cacatacaggtacacac i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68203714 40 + 134204764 acactccac--------------cacacatgcataca------cacagacaggtacacac i panTro2.chr11 C 0 C 0 s turTru1.scaffold_93657 6225 36 - 12933 gtgcccaga--------------cacacg-gcacact------cacacacgg---cacac i turTru1.scaffold_93657 I 2 I 887 s equCab2.chr12 28942162 46 + 33091231 atacataca--------------tatacacacccacTCGCTTGCACACATGAGTGCACAC i equCab2.chr12 I 6 I 45 s myoLuc1.scaffold_155660 39804 40 - 124081 ctacacata--------------cgtgcacacCTGCT------TACGTGTGGACACATAC i myoLuc1.scaffold_155660 I 2 I 8 s pteVam1.scaffold_22742 6222 40 - 9737 gtgcacaca--------------aacacacactaacc------cacacactggtacacgc i pteVam1.scaffold_22742 I 2 I 210 s loxAfr3.scaffold_159 89010 39 + 1045236 acacatcta--------------tacacatgcacaca------cacagccacacacaca- i loxAfr3.scaffold_159 C 0 I 467 e felCat3.scaffold_135390 60692 548 + 302526 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48979348 64 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=104304.000000 s hg19.chr11_gl000202_random 17167 58 + 40103 TCCTCCAGGG-CTCTTG-----GGAA--------TAGTCCTCTGTT--TTGTCACCA-AGCTCCCAG------GAAAGCTG s myoLuc1.scaffold_155660 39852 66 - 124081 ACACACAGCACTCCCAG-----AGCATTCCTCTCAGGTCCTCTCTG--TTGCCACC--AGCTGCCCT------AGGAGTCA i myoLuc1.scaffold_155660 I 8 C 0 s equCab2.chr12 28942253 59 + 33091231 TCCTCCAACG-TTCTGG-----GGCA--------GGGTCCTGTCTGCATCATCACC--AGCCGCCCT------GGGAGTCG i equCab2.chr12 I 45 C 0 s panTro2.chr11 68203754 58 + 134204764 TCCTCCAGGG-CTCTTG-----GGAA--------TAGTCCTCTGTT--TTGTCACCA-AGCTCCCAG------GAAAGCTG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 47689 58 + 115376 TCCTCCAGGG-CTCTTG-----GGAA--------TAGTCCTCTGTT--TTGTCACCA-AGCTCCCAG------GAAAGCTG i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 125999891 58 - 132107971 TCCTCCAGGG-CTCTTG-----GGAA--------AGGTCCTCTGTT--TTGTCACCA-AGCTCCCAG------GAGAGCTG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128162078 58 - 133002572 TCCTCCAGGG-CTCTTG-----GGAA--------AGGTTCTCTGTT--TTGTTACCA-AGCTCCCAG------GAGAGCTG i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 77990 58 + 109049 TCCTCCAGGG-CTCTTG-----GGAA--------AGGTCCTCTGTT--TTGTTACCA-AGCTCCCAG------GAGAGCTG i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 83037 58 + 235769 TCCTCCTGGG-CACTTG-----GGAA--------AGGTCCTCAGTT--TTGTCACCA-AGCTGCTGG------GAGAGCTG i calJac1.Contig6069 C 0 C 0 s petMar1.Contig15836 20417 67 - 25532 --cttGAGAG-CTCTCTCTAGCGTGA--------GAGCTCCCTCTT--ATAGCGTGAGAGCTCCCAATAGCGTGAGAGCT- i petMar1.Contig15836 N 0 C 0 e felCat3.scaffold_135390 60692 548 + 302526 I e pteVam1.scaffold_22742 6262 210 - 9737 I e turTru1.scaffold_93657 6261 887 - 12933 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89049 467 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48979348 64 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=52490.000000 s hg19.chr11_gl000202_random 17225 47 + 40103 CCCCTCCCTGCTGGCTCCAG-------------GGC-----CTGTC---ACCAGCCATCCAGCTCTTG s xenTro2.scaffold_1256 42226 38 - 115066 CACCCTCCGGCTGCCCGCTG-------------AGT-----CCTCC---CTCTGCCCGC--------- i xenTro2.scaffold_1256 N 0 C 0 s calJac1.Contig6069 83095 47 + 235769 CCCCTCCCTGCTGGGTCCAG-------------GGC-----CTGTC---ACCAGCCAACCAGTTCTCA i calJac1.Contig6069 C 0 C 0 s papHam1.scaffold6638 78048 47 + 109049 CGCCTCCCTGCTAGCTCCAG-------------GGC-----CTGTC---ACCAGCCATCCAGCTCTTG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128162136 47 - 133002572 CCCCTCCCTGCTAGCTCCAG-------------GGC-----CTGTC---ACCAGCCATCCAGCTCTTG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125999949 47 - 132107971 CTCCTCCCTGCTGGCTCCAG-------------GGC-----CTGTC---ACCAGCCATCCAGCTCTTG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 47747 47 + 115376 CCCCTCCCTGCTGGCTCCAG-------------GGC-----CTGTC---ACCAGCCATCCAGCTCTTG i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68203812 47 + 134204764 CCCCTCCCTGCTGGCTCCAG-------------GGC-----CTGTC---ACCAGCCATCCAGCTCTTG i panTro2.chr11 C 0 C 0 s equCab2.chr12 28942312 38 + 33091231 CCCCTTCCCGTTGACACCTG-------------GAGACCCCCTGTC---CTGAG-------------- i equCab2.chr12 C 0 C 0 s myoLuc1.scaffold_155660 39918 23 - 124081 CCCCTCCCCATGGACACCTG-------------GAG-------------------------------- i myoLuc1.scaffold_155660 C 0 C 0 s gasAcu1.chrUn 23677902 36 - 62550211 ---CTCCCTGCTGAG---------------GGTGGG-----ATTTC---CCCTGCTACCCTG------ i gasAcu1.chrUn N 0 C 0 s fr2.chrUn 362411393 56 + 400509343 -CTCTCTGAGCTGgttccagaaccttcagcagcaga-----atctctggctccgcccccatg------ i fr2.chrUn N 0 C 0 s petMar1.Contig15836 20484 43 - 25532 ---CCCTCTTCTAGcttcag-------------ag------ctccc---tctagcttGATAACTCCCT i petMar1.Contig15836 C 0 C 0 e felCat3.scaffold_135390 60692 548 + 302526 I e pteVam1.scaffold_22742 6262 210 - 9737 I e turTru1.scaffold_93657 6261 887 - 12933 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89049 467 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48979348 64 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=13125.000000 s hg19.chr11_gl000202_random 17272 35 + 40103 CCTGGAG--------------------TGAGTCCTCCCTCCTCAG--------GGT--GAGTCCT s calJac1.Contig6069 83142 35 + 235769 CCTGTAG--------------------TGAGTCCTCCCTCTTTCG--------GGT--GAATCCT i calJac1.Contig6069 C 0 C 0 s papHam1.scaffold6638 78095 55 + 109049 CCTGGAGTGAGCCTTCCCTCCTCAGCGTGAGTCCTCCCTCCTCAG--------GGT--GAGACCT i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128162183 35 - 133002572 cctggag--------------------tgagtcctccctcctcag--------cgt--gagtcct i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 125999996 55 - 132107971 CCTGGAGTGAGTCCTCCCACCTCAGGATGAGTCCTCCCTCCTCAG--------GGT--AAGTCCT i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 47794 35 + 115376 CCTGGAG--------------------TGAGTCCTCCCTCCTCAG--------GGT--GAGTCCT i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68203859 35 + 134204764 CCTGGAG--------------------TGAGTCCTCCCTCCTCAG--------GGT--GAGTCCT i panTro2.chr11 C 0 C 0 s dasNov2.scaffold_51901 3557 34 + 12839 CCCAGA--------------------GGGAATATCTCTTCCCGAG--------GGA--GGTCTC- i dasNov2.scaffold_51901 N 0 C 0 s micMur1.scaffold_2067 214 22 + 264097 --------------------------------CCTCCCTCCACAG--------AG---AAAACCT i micMur1.scaffold_2067 N 0 C 0 s turTru1.scaffold_93657 7148 35 - 12933 ----------------------------GGGTTCTTCCTCCCCAGCGACACCCGGA--GGCTCCC i turTru1.scaffold_93657 I 887 I 1 s otoGar1.scaffold_15940.1-60550 44839 29 + 60550 ------G--------------------TGAATCCTGCCTCCTAAG--------GGT--GGATCCT i otoGar1.scaffold_15940.1-60550 N 0 C 0 s xenTro2.scaffold_1256 42264 28 - 115066 ---------------------------TGGGTCCTCCCTCTGCCC--------GCT--GGGTCCT i xenTro2.scaffold_1256 C 0 C 0 s fr2.chrUn 362411449 31 + 400509343 ---------------------tgagcctgg-----tcctggtcct--------ggtcctggtcct i fr2.chrUn C 0 I 9 s gasAcu1.chrUn 23677938 36 - 62550211 --------------------CTAAGGTTGGGATCTCTCTGCTAAG--------GGTCGGGATCT- i gasAcu1.chrUn C 0 I 9 s petMar1.Contig15836 20527 35 - 25532 ------------------CTTCTAGCGTGAGAGCTCCCGATAGCG--------TGA--GAGCT-- i petMar1.Contig15836 C 0 C 0 e felCat3.scaffold_135390 60692 548 + 302526 I e pteVam1.scaffold_22742 6262 210 - 9737 I e myoLuc1.scaffold_155660 39941 0 - 124081 C e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89049 467 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942350 0 + 33091231 C e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48979348 64 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=-43381.000000 s hg19.chr11_gl000202_random 17307 57 + 40103 TCCTCCT-TGGGGTGAG--------------------TT----------CCCCTCCT-G----------------------GGGTGAGTCCTCCTTCC-TGAGGTAAGTCCT s panTro2.chr11 68203894 57 + 134204764 TCCTCCT-TGGGGTGAG--------------------TT----------CCCCTCCT-G----------------------GGGTGAGTCCTCCTTCC-TGAGGTAAGTCCT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 47829 57 + 115376 TCCTCCT-TGGGGTGAG--------------------TT----------CCCCTCCT-G----------------------AGGTGAGTCCTCCTTCC-TGAGGTAAGTCCT i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126000051 57 - 132107971 TCCTCCT-CAGGGTGAG--------------------TT----------CCCTCCCT-A----------------------GGGTGAGTCCTCCCTCC-TGAGGTAAGTCCT i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128162218 16 - 133002572 ccctgct-cagggtgag----------------------------------------------------------------------------------------------- i rheMac2.chr14 C 0 I 248 s papHam1.scaffold6638 78150 61 + 109049 TCCTCCT-CAGGGTAAATCCTTCCTCCTAGGGGTGAGTT----------CCTCTCCT-G----------------------GGGTGAGTCCTCCT----------------- i papHam1.scaffold6638 C 0 I 132 s calJac1.Contig6069 83177 56 + 235769 CCCTCCT-TGGGGTGAG--------------------TT----------CCCCTCCT-G----------------------GGATGAGTTTCCC-TCC-TGGGGTAAGTCCT i calJac1.Contig6069 C 0 I 37 s otoGar1.scaffold_15940.1-60550 44868 58 + 60550 GCCTCCT-AAGGAATAT--------------------AC----------TGTTTCCTAA----------------------GGGTGAATCCTGCCTCC-TAAGGTATATACT i otoGar1.scaffold_15940.1-60550 C 0 C 0 s micMur1.scaffold_2067 236 57 + 264097 CCCTCTA-CAGAGAGGA--------------------CC----------TCCCTCCACA----------------------GAGAGGA-CCTCCCTCC-ACAGAGAGGACCT i micMur1.scaffold_2067 C 0 C 0 s dipOrd1.scaffold_39490 9275 58 + 16834 CCCTCCTGCAGTCAGTG--------------------TC----------CCCCTCCT-G----------------------CGGTCAGCACCCCCTCC-TGTGGTCAGCGTC i dipOrd1.scaffold_39490 N 0 I 1 s turTru1.scaffold_93657 7184 29 - 12933 GTGTCCT-------GAG--------------------------------CTCCTCCT-G----------------------GGGTGAGGCC--------------------- i turTru1.scaffold_93657 I 1 C 0 s dasNov2.scaffold_51901 3591 57 + 12839 TCTCCCC-GGAGATGAT--------------------CT----------CTCTCCCT-G----------------------AGGGGGATCTCTCTCCC-CGAGAGGTGGTAT i dasNov2.scaffold_51901 C 0 C 0 s xenTro2.scaffold_1256 42292 80 - 115066 CCCTCTG-TCTGCTGGG--------------------TC----------CTCCCTCT-GCCCACTGATTCCTCCCTCTGCCCGTTGGGTCCTCCCTCTGCCCTCTGGGTCCT i xenTro2.scaffold_1256 C 0 C 0 s fr2.chrUn 362411489 50 + 400509343 cctggtc-ctggtcctg--------------------gt---cctggt-ccctgTTG-G----------------------AGGCCGTTTCCCC--------------ACCG i fr2.chrUn I 9 I 9 s gasAcu1.chrUn 23677983 67 - 62550211 CCTGGCT-AAGGGTGGG--------------------ATCTACCTGCTACCCTGCTA-A----------------------GGGTGGGATCTCCCTGC-TAAGGTGGGATCT i gasAcu1.chrUn I 9 I 9 s petMar1.Contig15836 20562 57 - 25532 CCCTCTTCTAGCgtgag--------------------ag----------ctccctct-a----------------------gcgtgAGAGCGCCCTC--TAGCttgagagct i petMar1.Contig15836 C 0 C 0 e felCat3.scaffold_135390 60692 548 + 302526 I e pteVam1.scaffold_22742 6262 210 - 9737 I e myoLuc1.scaffold_155660 39941 0 - 124081 C e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89049 467 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942350 0 + 33091231 C e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48979348 64 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=40342.000000 s hg19.chr11_gl000202_random 17364 151 + 40103 CCCTTCTCAGGGTTAGTCCTCTCT-CCTCAGGGTGAG-TTTCCCT-CCTG--GGGTTAGT---CCTCCTG-CCTCT-GAGTGAGTTCCCCCTCCTCAGGGTGAGTCCTC------------------C---TCAGGGTGAGT--TCCCCCTCC-TTGGGTGAATGCTCCCTTCTCA------CGGTGAGT-T- s dipOrd1.scaffold_39490 9334 152 + 16834 CCCTCCTGTGGTCAGCGTCCCCCT-CCTGCAGACAGC-GCCCCCT-CCTG--CGGTCAGCATCCCTCCTG-------CAGTCAGTGTCCCCCTCCTGCGGTCAGCACCCCCTC--------------C---TGTGGTCAGCG--TCCCCCTCC-TGTGATCAACACTCCCTCCT-G------TGATCAAC-A- i dipOrd1.scaffold_39490 I 1 C 0 s micMur1.scaffold_2067 293 163 + 264097 CCCTCCACAGAGAAGA-CCTTCCT-CTACAGAGAGGA-CCTCCCT-CCAG--AGAGGGGA-----------CCTCTACAGAGAGGACCTCCCTCCACAGAGAGGACCTCCCTctacagagaggacctc---tacagagagga--cctccctct-acagagaggacctccctccaca------gagaagacct- i micMur1.scaffold_2067 C 0 C 0 s otoGar1.scaffold_15940.1-60550 44926 156 + 60550 GTCTCCTAAGGGTAGATTCTGCCT-CCTAAGGGTTAT-ACTGTCT-CCTA--AGGGTGAA-----TCCTGCCTCCTAGGGTGAATCCTGTCTCCTAAGGGTAGATCCTGCCTC--------------C---TAAGGGTAGAT--CCTGCCTCC-TAAGGGTTATACTGTCTCCTAA------GGGTGAATCC- i otoGar1.scaffold_15940.1-60550 C 0 C 0 s papHam1.scaffold6638 78343 151 + 109049 CCCTTCTCAGGGTGAGTCCTCTCT-CTTCAGGGTGAG-TATCTCT-CCCG--GGGTTAGT---CCTCCTG-CCTCT-GAGTGACTTCCCCCTCCTCAGGATGAGTCCTC------------------C---TCAGGGTAAGT--TCCCCCTCC-TAGGGTCAATGCTCCCTTCTCG------GGGTGAGT-T- i papHam1.scaffold6638 I 132 C 0 s panTro2.chr11 68203951 151 + 134204764 CCCTTCTCAGGGTGAGTCCTCTCT-CCTCAGGGTGAG-TTTCCCT-CCTG--GGGCTAGT---CCTCCTG-CCTCT-GAGTGAGTTCCCCCTCCTCAGGGTGAGTCCTC------------------C---TCAGGGTGAGT--TCCCCCTCC-TTGGGTGAATGCTCCCTTCTCA------GGGTGAGT-T- i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 47886 151 + 115376 CCCTTCTCAGGGTGAGTCCTCTCT-CCTCAGGGTGAG-TTTCCCT-CCTG--GGGTTAGT---CCTCCTG-CCTCT-GAGTGAGTTCCCCCTCCTCAGGGTGAGTCCTC------------------C---TCAGGGTGAGT--TCCCCCTCC-TTGGGTGAATGCTCCCTTCTCA------GGGTGAGT-T- i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126000108 135 - 132107971 CCCTTCTCAGGGTGAGTCCTCTCT-CCTTAGGGTGAG-TTTCCCT-CCTG--GGGTTAGT---CCTCCTG-CCTCT-GAGTGAGTTCCTCCTCCTCAGGATGAGTC---------------------------------------CCCCCTCC-TTGGGTGAATGCTCCCTTCTCG------GGGTGAGT-T- i ponAbe2.chr11 C 0 C 0 s dasNov2.scaffold_51901 3648 151 + 12839 --CTCTCCCGGGAGGCGTCTCTCTACCCGGGGGCTCG-TCTCTCTCCCTG--GGACTGGT---CTCTCTT-CCT---AGGGCTGGTCTCTCTCCCCGGGGCTCGTCTCT------------------C---TCCCGGGAGCTCGTCTCTCTCC-CTGAGACGCATCTCTCTCCCAG------GGGCTCGT-C- i dasNov2.scaffold_51901 C 0 C 0 s xenTro2.scaffold_1256 42372 158 - 115066 CCCTTTGCCTGCTGAGTCCTCCCT-CTGCCCGTTGGG-TCCTCCC-TCTGCCCGCTGAGT---CCTCCCT-CTGCC-CGCTGGGTCCTCCCTCTGCCCGCTGGGTCCTCCTTC--------------T---GTCTGCTGGGT--CCTCCCTCTGCCCACTGATTCCTCCCTCTGCC------CGTTGGGT-C- i xenTro2.scaffold_1256 C 0 C 0 s fr2.chrUn 362411548 97 + 400509343 TTC---------TGGGCTCAGCGT-CT---GTACGAG-TCT---T-TACA-------------ACCTCTG-------ACCTGA----TCCC------AGGTGAGTTTCA------------------C-------------------ACCTAC---AGGTGAGTTTTCACACCTAC------AGGTGATT-T- i fr2.chrUn I 9 C 0 s gasAcu1.chrUn 23678059 146 - 62550211 CCCTGCTAAAGGTGGGATCTACTG-CTAAGGTGGGGA-TCTACCT-GCTA-------------ACTGCTA-------AGGTGGGATCTCCCTGCT-AAGGTGGGATCTA------------------CCTGCTAAGGTGGGA--TCTACCTGC-TAAGGTGGAATCTACCTGCTACCTGCTAAGGTGGGA-T- i gasAcu1.chrUn I 9 I 1 s petMar1.Contig15836 20619 151 - 25532 --ccctctagcgtgAGAACTCCCT-CTAGCGTGAGAGCTCCCTCT-TCTA--GCgtgaga---gctccct-cta---gcgtgAGAGCGCCCTCTAGCttgagagctccc------------------t---ctagcgtgAGAACTCCCTCTTC-TAGtttcagagctccctctagc------ttGAGAAC-TC i petMar1.Contig15836 C 0 C 0 e felCat3.scaffold_135390 60692 548 + 302526 I e pteVam1.scaffold_22742 6262 210 - 9737 I e calJac1.Contig6069 83233 37 + 235769 I e myoLuc1.scaffold_155660 39941 0 - 124081 C e turTru1.scaffold_93657 7213 0 - 12933 C e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89049 467 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942350 0 + 33091231 C e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48979348 64 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e rheMac2.chr14 128162234 248 - 133002572 I a score=53563.000000 s hg19.chr11_gl000202_random 17515 70 + 40103 CCCCTCCTAGA--GTGA------------------GTCCTGCCTCCTC-------TGG-------------------GTGAG-TCCCCCTCCTG--GGAT-GCGTCCTCCCTCCTGAGAT s dipOrd1.scaffold_39490 9486 70 + 16834 CCCCTCCTGTG--GTCA------------------GCGCCCCCTCCTG-------CGG-------------------TCAGC-ACCCCCTCCTG--TGGT-CAGTGCCCCCTCCTGCGGT i dipOrd1.scaffold_39490 C 0 C 0 s micMur1.scaffold_2067 456 69 + 264097 ccctctacaga--gagg------------------a-cctccctctac-------aga-------------------gagga-cctccctccac--agag-aggacctccctccacagag i micMur1.scaffold_2067 C 0 C 0 s otoGar1.scaffold_15940.1-60550 45082 72 + 60550 TGCCTCCTAGG--GTGA------------------ATCCTGTCTCCTA-------AGG-------------------GTGGATCCTGCCTCCTA--AGAGTAGATCCTGCCTCCTAAGGG i otoGar1.scaffold_15940.1-60550 C 0 C 0 s papHam1.scaffold6638 78494 88 + 109049 CCCATCCTAGA--GTGAGTCCCCATCCTAGAGCGGGTCCTCCCTCCTC-------TGG-------------------CAGAG-TCCCCCTCGTG--GGAT-GAGTCCTCCCTCCTGAGAT i papHam1.scaffold6638 C 0 C 0 s panTro2.chr11 68204102 70 + 134204764 CCCCTCCTAGA--GTGA------------------GTCCTGCCTCCTC-------TGG-------------------GTGAG-TCCCCCTCCTG--GGAT-GCGTCCTCCCTCCTGAGGT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48037 70 + 115376 CCCCTCCTAGA--GTGA------------------GTCCTGCCTCCTC-------TGG-------------------GTGAG-TCCCCCTCCTG--GGAT-GAGTTCTCCCTCCTGAGGT i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126000243 70 - 132107971 CCCCTCCTAGA--GTGA------------------GTCCTCCCTCCTC-------TGG-------------------GTGAG-TCCCCCTCCTG--GGAT-GAGTCCTCCCTCCTGAGGG i ponAbe2.chr11 C 0 C 0 s dasNov2.scaffold_51901 3799 56 + 12839 TCTCTCCCTGA--GGCG------------------CGTCTCTCTCCGT-------GGG-------------------GCGCG-TCTCTCTCCCG--GGGC-GCGTC-------------- i dasNov2.scaffold_51901 C 0 C 0 s xenTro2.scaffold_1256 42530 74 - 115066 CTCCCTCTGCCCTCTGG------------------GTCCTCCCTTTGC-------CTG-------------------CTGAG-TCCTCCCTCTGCCCGTT-GGGTCCTCCCTCTGCCCGC i xenTro2.scaffold_1256 C 0 I 1 s fr2.chrUn 98767932 58 - 400509343 CTTCAGCTCGT--CCAG------------------ATCCGACCAGTTATCGATCTGGT-------------------TATCG-TTCATCTGCCG--GGAC-------------------- i fr2.chrUn n 0 C 0 s gasAcu1.chrUn 23678206 51 - 62550211 TCCCTGCTAAG--GTGG------------------GATCTCCCTGCTA-------AGG-------------------TGGGA-TCTCCCTGCTA--AGGT-------------------- i gasAcu1.chrUn I 1 C 0 s petMar1.Contig15836 20770 88 - 25532 CCTCTTCTAGC--TTGA------------------GAGCTCCCTCTTC-------TAGCgtgagagctccctctagcttgag-agctccctcta--gcgt-gagagctccctctagcgt- i petMar1.Contig15836 C 0 C 0 e felCat3.scaffold_135390 60692 548 + 302526 I e pteVam1.scaffold_22742 6262 210 - 9737 I e calJac1.Contig6069 83233 37 + 235769 I e myoLuc1.scaffold_155660 39941 0 - 124081 C e turTru1.scaffold_93657 7213 0 - 12933 C e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89049 467 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942350 0 + 33091231 C e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48979348 64 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e rheMac2.chr14 128162234 248 - 133002572 I a score=-36820.000000 s hg19.chr11_gl000202_random 17585 65 + 40103 A-AGTCCATCCTTCT---CAGGGTGAGTC-CTCCT----CAGGGTGA---GTTCCCCCT---C-------CTAGGGTGACCCCTCCT s dipOrd1.scaffold_39490 9556 48 + 16834 C-AGCGC--------------------CC-CTCCT----GCAGTCAG---TGTCCCCCT---C-------CTGTGATCAACACTCCC i dipOrd1.scaffold_39490 C 0 C 0 s micMur1.scaffold_2067 525 48 + 264097 a-agacc--------------------tt-cctct----acagagag---gacctcccT---C-------CACAGAGAGGACCTCCC i micMur1.scaffold_2067 C 0 C 0 s otoGar1.scaffold_15940.1-60550 45154 49 + 60550 ATATACT--------------------GC-CTCCT----AAGGGTAG---ATTCTGCCT---C-------CTAAGGGTTATACTGCT i otoGar1.scaffold_15940.1-60550 C 0 C 0 s papHam1.scaffold6638 78582 65 + 109049 A-AGTCCTCCCTTCT---CAGGGTGAGTC-CTCCT----CAGGGTGA---GTTCCCCCT---C-------CTAGGGCAAATCCTCCT i papHam1.scaffold6638 C 0 C 0 s panTro2.chr11 68204172 65 + 134204764 A-AGTCCATCCTTCT---CAGGGTGAGTC-CTCCT----CAGGGTGA---GTTCCCCCT---C-------CTAGGGTGACTCCTCCT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48107 65 + 115376 A-AGTCCTCCCTTCT---CAGGGTGAGTC-CTCCT----CAGGGTGA---GTTCCCCCT---C-------CTAGGGTGACCCCTCCT i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126000313 65 - 132107971 A-AGTCCTCCCTTCT---AAGGGTGAGTC-CTCCT----AAGGGTTA---GTTCCACCT---C-------CTAGGGTGAACCCTTCT i ponAbe2.chr11 C 0 C 0 s echTel1.scaffold_300476 9789 65 - 48103 ----AAAACCATTCTGGTCATGGTGACTC-CTCCT----CAGGGCGA---CTCCTCCTA---C-------CCAGGGCGACTCCTCCT i echTel1.scaffold_300476 N 0 N 0 s dasNov2.scaffold_51901 3855 55 + 12839 -------TCTCTCCCGG--AGTGCGTCTCTCTCCC----TGGAGCTC---GTCTCTCTC---C-------CTGGGG------CTCGT i dasNov2.scaffold_51901 C 0 C 0 s felCat3.scaffold_135390 61240 51 + 302526 ------------------CAGGGCAGGCC-CTCCC----TGTGCTGT---TGCCCCGCT---G-------CCTGGGGGTCGCCCCCC i felCat3.scaffold_135390 I 548 C 0 s xenTro2.scaffold_1256 42605 72 - 115066 -GAGTCCTCCCTCTG---CCCGCTGGGTC-CTCCCTTTGCCCGCTGA---GTCCTCCCTCTGC-------CCCGGGTCCTCCCTCTG i xenTro2.scaffold_1256 I 1 I 13 s fr2.chrUn 98767990 53 - 400509343 -------------------AGAAAGGAAC-GTTTT----CAGGGTGGGCAGATCTACCC---TCC-----CTGAGCT--GATCTACC i fr2.chrUn C 0 I 2 s gasAcu1.chrUn 23678257 55 - 62550211 -------------------GGGATCTACC---TGC----TAAGGTGG---GATCTACCT---GCTACCTGCTAAGGTGGGATCTACC i gasAcu1.chrUn C 0 C 0 s petMar1.Contig15836 20858 70 - 25532 -gAGAGCTCCCTCTTCTAGCTTGATAGCT-CCCTT----TAGCGTGA---GAGCTCCCT---CTT-----CTAGCGTGAGAACTCCC i petMar1.Contig15836 C 0 C 0 e pteVam1.scaffold_22742 6262 210 - 9737 I e calJac1.Contig6069 83233 37 + 235769 I e myoLuc1.scaffold_155660 39941 0 - 124081 C e turTru1.scaffold_93657 7213 0 - 12933 C e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89049 467 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942350 0 + 33091231 C e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48979348 64 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e rheMac2.chr14 128162234 248 - 133002572 I a score=-88295.000000 s hg19.chr11_gl000202_random 17650 35 + 40103 TCCTCAACCCGGAGTTC----CCCTCCTG--------G---GG-------------------------------------------------------------------------------------------------TGA-GTCC s ponAbe2.chr11 126000378 132 - 132107971 TCCTCAACCCTGAGTTC----CGCTCCTG--------G---GGTGAGTGTTCCCACCTCCAGGTGAGTTCTCCCTCCTCAGGGTGAGCTTCCCTCCTGGATGAGTCCCCCCTCCTCTGGGTGAGTCCCCCCTCCTCTGGATGA-GTCC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48172 35 + 115376 TCCTCAACCCTGAGTTC----CCCTCCTG--------G---GG-------------------------------------------------------------------------------------------------TGA-GTCC i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68204237 35 + 134204764 TCCTCAACCCTGATTTC----CCCTCCTG--------G---GG-------------------------------------------------------------------------------------------------TGA-GTCC i panTro2.chr11 C 0 C 0 s papHam1.scaffold6638 78647 35 + 109049 TCCTCAACCCTGAGTTC----CCCTCCTG--------G---GG-------------------------------------------------------------------------------------------------TGA-GTCC i papHam1.scaffold6638 C 0 C 0 s otoGar1.scaffold_15940.1-60550 45203 35 + 60550 TCCTAAGGGTGGATCCT----GCCTCCTA--------A---GG--------------------------------------------------------------------------------------------------GATATAG i otoGar1.scaffold_15940.1-60550 C 0 C 0 s micMur1.scaffold_2067 573 33 + 264097 TCCACAGAGAGGA-CCT----CCCTCCAC--------A---GA--------------------------------------------------------------------------------------------------GA-AGAC i micMur1.scaffold_2067 C 0 C 0 s dipOrd1.scaffold_39490 9604 45 + 16834 TCCTCTGGTC--AGCGC----CCCTCCTG--------T---GGTCAGCGTCCCCC-------------------------------------------------------------------------------------TCA-ACAC i dipOrd1.scaffold_39490 C 0 C 0 s felCat3.scaffold_135390 61291 30 + 302526 ACTGACACCCGGAGGCT----CCCC----------------GG-------------------------------------------------------------------------------------------------CGA-AACC i felCat3.scaffold_135390 C 0 C 0 s dasNov2.scaffold_51901 3910 38 + 12839 CTCTCTCCCTGGGGCTCGTCTCTCTCCCT--------G---GG-------------------------------------------------------------------------------------------------CGT-GTG- i dasNov2.scaffold_51901 C 0 C 0 s xenTro2.scaffold_1256 42690 38 - 115066 CCCTCTGCCCCAGGGTC----CTCCCTTT--------GCCCGC-------------------------------------------------------------------------------------------------TGA-GTCC i xenTro2.scaffold_1256 I 13 C 0 s fr2.chrUn 98768045 32 - 400509343 -TCCTGAGCAGATCTAC----CCTTCCTGAGCTGATC--------------------------------------------------------------------------------------------------------------- i fr2.chrUn I 2 n 2 s gasAcu1.chrUn 23678312 24 - 62550211 -TGCTAAGGTGGGATCT----CCCTGCTA----------------------------------------------------------------------------------------------------------------------- i gasAcu1.chrUn C 0 C 0 s petMar1.Contig15836 20928 35 - 25532 TCTTCTAGCTTGAGAAC----TCCCTCTA--------G---TG-------------------------------------------------------------------------------------------------TGA-GCTC i petMar1.Contig15836 C 0 C 0 e pteVam1.scaffold_22742 6262 210 - 9737 I e calJac1.Contig6069 83233 37 + 235769 I e myoLuc1.scaffold_155660 39941 0 - 124081 C e turTru1.scaffold_93657 7213 0 - 12933 C e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89049 467 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942350 0 + 33091231 C e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48979348 64 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e rheMac2.chr14 128162234 248 - 133002572 I a score=72200.000000 s hg19.chr11_gl000202_random 17685 78 + 40103 TCTCACCTCT--GGGTGAGTTCCCCCTCCTCAGGG-TGAGTTCCCCTCCTG--AGGTGAGTCCTCCCTTCT-------CTGG---GTGAGTTC s ponAbe2.chr11 126000510 78 - 132107971 CCCCTCCTCT--GGGTGAGTCCCCCCTCCTTAGGG-TGAGTTCCCCTCCTG--AGGTGAGTCCTGCCTTCT-------CAGG---GTGAGTTC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48207 78 + 115376 TCTCACCTCT--GGGTGAGTTCCCCCTCCTCAGGG-TGAGTTCCCCTCCTG--AGGTGAGTCCTCCCTTCT-------CTGG---GTGAGTTC i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68204272 78 + 134204764 TCTCACCTCT--GGGTGAGTTCCCCCTCCTCAGGG-TGAGTTCCCCTCCTG--AGGTGAGTCCTCCCTTCT-------CTGG---GTGAGTTC i panTro2.chr11 C 0 C 0 s papHam1.scaffold6638 78682 75 + 109049 TCCCGCCTGT--GGGTGAGTTTCCCTTCCT-GGGG-TGAATTTCCCTCCTG--GGCTAAGTCCTCCCCCTT-------CTGG---GTGAGT-- i papHam1.scaffold6638 C 0 I 139 s otoGar1.scaffold_15940.1-60550 45238 79 + 60550 TGCCTCCTAA--AGGTAGATTTTGCCTCCTAAGGGTTATACTGCCTCCTAA--GGGTAGATCCTGCCTCCT-------AAGT---GTAGATCC i otoGar1.scaffold_15940.1-60550 C 0 I 1 s micMur1.scaffold_2067 606 77 + 264097 CTTCCTCTAC--AGAGAGGACCTCCCTCCACAGAG-AGGACCTCCCTCTAC--AGAGAGGACCTCCCTCCA-------CAGA---G-AGGACC i micMur1.scaffold_2067 C 0 I 1 s dipOrd1.scaffold_39490 9649 75 + 16834 TCCCTCCTGT--GATCAA--CACCCCTCCTCTGGT-CAGCGCCCCCTCCTG--TGGTCAGCACCCCCTCCT-------GCG----GTCAGCAC i dipOrd1.scaffold_39490 C 0 C 0 s felCat3.scaffold_135390 61321 69 + 302526 ---------------GGAGCTGCCCCTC---AGGG-TGAGGCCCCTGACTC--AGGTGAGGACACCCCTCTGGGGGCCCGGG---GTGAGCCG i felCat3.scaffold_135390 C 0 I 4 s dasNov2.scaffold_51901 3948 76 + 12839 TCTCTCCCTG--GGGCATGTCTCTCTCCCTGGGGC-TCGTCTCTCTCCCTG--GGGCGCGTCTCTCTCCCT---------GG---GCGCGTCT i dasNov2.scaffold_51901 C 0 C 0 s xenTro2.scaffold_1256 42728 80 - 115066 TCCCTCTGCC--CGCTGGGTCCTCCCTTTGCCCGC-TGAGTCCTCCCTCTGCCCGCTGGGTCCTCCCTTTG-------CCTG---CTGAGTCC i xenTro2.scaffold_1256 C 0 C 0 s fr2.chrUn 362411645 79 + 400509343 TCACACCTCC--AGGTGAGTTTTCACACCTCCAGG-TGAGTTTCACACCTA-CAGGTGAGTTTTCACACCT-------CCAG---GTGAGTTT i fr2.chrUn C 0 I 1 s gasAcu1.chrUn 23678336 74 - 62550211 -----CCTGCTAAGGTGGGATCTCCCTGCTAAGGT-GGGATCTCCCTGCTA--AGGTGGGATCTCCCTGCT--------AAG---GTGGGATC i gasAcu1.chrUn C 0 I 1 s petMar1.Contig15836 20963 55 - 25532 ------------------------CCTCT--AGCT-TGAAAACTCCCTCTA--GCTTGAGAACTCCCTCTT-------CTAGCttgagagc-- i petMar1.Contig15836 C 0 C 0 e pteVam1.scaffold_22742 6262 210 - 9737 I e calJac1.Contig6069 83233 37 + 235769 I e myoLuc1.scaffold_155660 39941 0 - 124081 C e turTru1.scaffold_93657 7213 0 - 12933 C e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89049 467 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942350 0 + 33091231 C e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48979348 64 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e rheMac2.chr14 128162234 248 - 133002572 I a score=54068.000000 s hg19.chr11_gl000202_random 17763 48 + 40103 CCCTCCTGA--GGTG-AGTCCTGCCTCCTCAGG-GTGAGTT----CCCCTCCTGGG- s ponAbe2.chr11 126000588 48 - 132107971 CCCTCCTGA--GGTG-AGTCCTGCCTCCTCAGA-GTGAGTT----CTCCTCCTGGA- i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48285 48 + 115376 CCCTCCTGA--GGTG-AGTCCTGCCTCCTCAGG-GTGAGTT----CCCCTCCTGGG- i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68204350 48 + 134204764 CCCTCCTGA--GGTG-AGTCCTGCCTCCTCAGG-GTGAGTT----CCCCTCCTGGG- i panTro2.chr11 C 0 C 0 s papHam1.scaffold6638 78896 50 + 109049 CCCTCCTGA--GGTG-AGTCCCCCCTCCTCTGG-GTGAGTTTC--CCCCTCCTGGG- i papHam1.scaffold6638 I 139 I 59 s calJac1.Contig6069 83270 47 + 235769 CCCTCCTGA---GTG-AGTCCTCCCTCCTCACG-GTGAGTT----CCCCCTCTGGG- i calJac1.Contig6069 I 37 I 24 s otoGar1.scaffold_15940.1-60550 45318 49 + 60550 GCCTCCTAA--GTGATATACTGTCTCCTAAGGG-TAGATCC----TGCCTCCTAAG- i otoGar1.scaffold_15940.1-60550 I 1 I 2 s micMur1.scaffold_2067 684 48 + 264097 CCCTCCACA--GAGA-AGACCTTCCTCTACAGA-GAGGACC----TCCCTCCACAG- i micMur1.scaffold_2067 I 1 I 2 s dipOrd1.scaffold_39490 9724 48 + 16834 CCCTCCTGC--AGAC-AGTGTCCCCCTCCTCTG-GTCAGCG----CCCCTCCTGTG- i dipOrd1.scaffold_39490 C 0 I 1 s felCat3.scaffold_135390 61394 45 + 302526 CCCCTCTGC--GGCG-A---CTCCCCTCTCGGG-GTCCTTC----ATCTCCCCGGC- i felCat3.scaffold_135390 I 4 C 0 s dasNov2.scaffold_51901 4024 47 + 12839 CTCTCCCTG--GGCG-CGTCTCTCTCCCTGGGG-CTCGTCT----CTCTCCCTGG-- i dasNov2.scaffold_51901 C 0 C 0 s xenTro2.scaffold_1256 42808 50 - 115066 TCCCTCTGCCCGTTG-GGTCCTCCCTTTGCCCG-CTGAGTC----CTCCCTCTGCC- i xenTro2.scaffold_1256 C 0 I 3 s fr2.chrUn 362411725 50 + 400509343 ACACCTACA--GGTG-AGTTTTCACACCTCCAG-GTGAGTTTCACACCTAC--AGG- i fr2.chrUn I 1 C 0 s gasAcu1.chrUn 23678411 37 - 62550211 ACCTGCTAA--GGTG-GGATCTCCCTGCT----------------ACCTGCTAAGG- i gasAcu1.chrUn I 1 C 0 s petMar1.Contig15836 21018 50 - 25532 tccctctag--cttA-AGAActccctcttctagcgagagat----ctccctctagct i petMar1.Contig15836 C 0 C 0 e pteVam1.scaffold_22742 6262 210 - 9737 I e myoLuc1.scaffold_155660 39941 0 - 124081 C e turTru1.scaffold_93657 7213 0 - 12933 C e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89049 467 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942350 0 + 33091231 C e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48979348 64 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e rheMac2.chr14 128162234 248 - 133002572 I a score=2058.000000 s hg19.chr11_gl000202_random 17811 34 + 40103 TGAGTGCCCCCC--CCTCTAGATGAGTTCCCC------------------CTCC s ponAbe2.chr11 126000636 52 - 132107971 TGAGTCCTCCCT--CCTCTGGGTGAGTTCCCCTCCTGAGGTGAGTCCTCTCTCC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48333 34 + 115376 TAAGTGCCCCCT--CCTCTAGATGAGTTCCCC------------------CTCC i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68204398 34 + 134204764 TGAGTGCCCCCT--CCTCTAGATGAGTTCCCC------------------CTCC i panTro2.chr11 C 0 C 0 s otoGar1.scaffold_15940.1-60550 45369 33 + 60550 TAGATCCTACCT--CCTA-AGGGTTATACTGC------------------CTCC i otoGar1.scaffold_15940.1-60550 I 2 C 0 s micMur1.scaffold_2067 734 32 + 264097 GGGA-CCTCCCT--CCAC-AGAGGGGACCTCC------------------CTCC i micMur1.scaffold_2067 I 2 C 0 s dipOrd1.scaffold_39490 9773 34 + 16834 TCAGCGTCCCCC--TCCTGTGATCAATGCTCC------------------CTCC i dipOrd1.scaffold_39490 I 1 C 0 s felCat3.scaffold_135390 61439 36 + 302526 CGGCTTCCACCCTGCCTCTCTCTGGACTGTCT------------------CTTC i felCat3.scaffold_135390 C 0 I 121 s dasNov2.scaffold_51901 4071 34 + 12839 GGCTCGTCTCTC--TCCCTGGGTGCGTCTCTC------------------TGCC i dasNov2.scaffold_51901 C 0 C 0 s xenTro2.scaffold_1256 42861 34 - 115066 TGGGTCCTCCCT--CTGCCCACTGAGTCCTCC------------------CTCT i xenTro2.scaffold_1256 I 3 I 4 s fr2.chrUn 362411775 34 + 400509343 TGAGTTTTCACA--CCTACAGGTGAGTTTTCA------------------CACC i fr2.chrUn C 0 C 0 s gasAcu1.chrUn 23678448 27 - 62550211 TGGGATCTCCCT--GCTA-AGGTGGGATCT------------------------ i gasAcu1.chrUn C 0 C 0 s petMar1.Contig15836 21068 32 - 25532 tgagagctctct--ctagcgtgagagctctct------------------cG-- i petMar1.Contig15836 C 0 C 0 e pteVam1.scaffold_22742 6262 210 - 9737 I e papHam1.scaffold6638 78946 59 + 109049 I e calJac1.Contig6069 83317 24 + 235769 I e myoLuc1.scaffold_155660 39941 0 - 124081 C e turTru1.scaffold_93657 7213 0 - 12933 C e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89049 467 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942350 0 + 33091231 C e canFam2.chr18 7537155 1840 - 58872314 I e bosTau4.chr29 48979348 64 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I e rheMac2.chr14 128162234 248 - 133002572 I a score=-65115.000000 s hg19.chr11_gl000202_random 17845 44 + 40103 TCTGG-GTGAG-------TCC----------------CCCTCCTTAGGGT---GAGTT-CCCCT-------CCTGAGGT s ponAbe2.chr11 126000688 44 - 132107971 TCTGG-GTGAG-------TTC----------------CCCTCCTGA-GGT---GAGTTCCCCCT-------CCTGGGGT i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48367 44 + 115376 TCTGG-GTGAG-------TCC----------------CCCTCCTTAGGGT---GAGTT-CCCCT-------CCTGAGGT i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68204432 44 + 134204764 TCTGG-GTGAG-------TCC----------------CCCTCCTTAGGGT---GAGTT-CCCCT-------CCTGAGGT i panTro2.chr11 C 0 C 0 s otoGar1.scaffold_15940.1-60550 45402 33 + 60550 TAAGG-GTGGAT------CCT----------------GCCTCCTAAGGGT---AGATC-C------------------- i otoGar1.scaffold_15940.1-60550 C 0 C 0 s micMur1.scaffold_2067 766 34 + 264097 ACAGA-GAGGA-------CCT----------------CCCTCCACAGAGA---GGACC-A-----------------GA i micMur1.scaffold_2067 C 0 C 0 s dipOrd1.scaffold_39490 9807 45 + 16834 TGTGGTCAGCG-------CCC----------------CCCTCCTGTGATC---AATGT-TCCCT-------CCTGTGGT i dipOrd1.scaffold_39490 C 0 C 0 s canFam2.chr18 7538995 54 - 58872314 CTTGG-GTCAC-------CCC----------------TCCCCATTAACACCTGGAGGC-TCCCTGGTGAGCCCTGAGGT i canFam2.chr18 I 1840 C 0 s papHam1.scaffold6638 79005 41 + 109049 ------GTGAG-------TCCT---------------CCCTCCTCTGGGT---GAGTTTCCCTT-------CCTGGGGT i papHam1.scaffold6638 I 59 C 0 s rheMac2.chr14 128162482 39 - 133002572 ------gtgag-------ttc----------------ccctcctgg-ggt---gagtcctccct-------cctgaggt i rheMac2.chr14 I 248 C 0 s dasNov2.scaffold_51901 4105 44 + 12839 -TGGG-GCTCG-------TCT----------------CTCTGCCTGGGGC---GCGTC-TCTCTG------CCTGGGGC i dasNov2.scaffold_51901 C 0 C 0 s xenTro2.scaffold_1256 42899 42 - 115066 GCTGG-GT----------CCT----------------CCCTTTGCCTGCT---GAGTCCTCCCT-------CTGCCCGT i xenTro2.scaffold_1256 I 4 I 1 s fr2.chrUn 362411809 45 + 400509343 ---------------------TCCAGGGGAGTTTCACACCTAC---AGGT---GAGTTTCACAC-------CTACAGGG i fr2.chrUn C 0 I 1 s gasAcu1.chrUn 23678475 31 - 62550211 -------------------------------------ACCTGCT-AAGGT---GGGATCTACCT-------GCTAAGAT i gasAcu1.chrUn C 0 I 1 s petMar1.Contig15836 21100 37 - 25532 -----------Ttagagctcc----------------cactcgttagaga---g-----ctcct-------cctagaga i petMar1.Contig15836 C 0 C 0 e felCat3.scaffold_135390 61475 121 + 302526 I e pteVam1.scaffold_22742 6262 210 - 9737 I e calJac1.Contig6069 83317 24 + 235769 I e myoLuc1.scaffold_155660 39941 0 - 124081 C e turTru1.scaffold_93657 7213 0 - 12933 C e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89049 467 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942350 0 + 33091231 C e bosTau4.chr29 48979348 64 + 51998940 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=-10413.000000 s hg19.chr11_gl000202_random 17889 41 + 40103 GAGT-TTCCCT-CCTG--GGGTAAGCCCTCCCGCTTCTGGGTGAG s papHam1.scaffold6638 79046 41 + 109049 GAAT-TTCCCT-CCTG--GGCTGAGTCCTCCCCCTTCTGGGTGAG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128162521 42 - 133002572 gagtcctccct-cctg--aggtaagtcctcccttctcagggtgag i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126000732 40 - 132107971 GAGT-TTCCCT-CCTG--GGGTAAGCCCTCCC-CCTCTGGGGGAG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48411 41 + 115376 GAGT-TTCCCT-CCTG--GGGTAAGCCCTCCCGCTTCTGGGCGAG i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68204476 41 + 134204764 GAGT-TTCCCT-CCTG--GGGTAAGCCCTCCCGCTTCTGGGTGAG i panTro2.chr11 C 0 C 0 s otoGar1.scaffold_15940.1-60550 45435 40 + 60550 -TGC-CTCCTC-CTAA--GGGTAGATCCTGCCTCCTAAGGATGAA i otoGar1.scaffold_15940.1-60550 C 0 C 0 s micMur1.scaffold_2067 800 41 + 264097 GGAC-CTCCCT-CCAC--AGAGAGGACCTCCCTCCACAGAGAGGA i micMur1.scaffold_2067 C 0 C 0 s dipOrd1.scaffold_39490 9852 40 + 16834 CAAC-ACCCCT-CCTG--TGGTCAG-CGTCCCCCTCCTGCATACA i dipOrd1.scaffold_39490 C 0 I 19 s bosTau4.chr29 48979412 33 + 51998940 -GAG-GCTCCC-TCTG--TCCTGAGCTCCCCT-------GAGGGG i bosTau4.chr29 I 64 C 0 s canFam2.chr18 7539049 27 - 58872314 --------CCC-CCTG-----AGAATACCC----TTCTGGGGGCA i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 39941 13 - 124081 --------------------------------GCTCCCTGCGGAG i myoLuc1.scaffold_155660 C 0 C 0 s dasNov2.scaffold_51901 4149 41 + 12839 GCGT-CTCTCTGCCTG--GGGCGCGTCTCTCTGCCTGGGGCTCG- i dasNov2.scaffold_51901 C 0 C 0 s xenTro2.scaffold_1256 42942 43 - 115066 GGGT-CCTCCC-TCTGCCCGCTGAGTCCTCCCTCTGCCCGCTGGG i xenTro2.scaffold_1256 I 1 C 0 s fr2.chrUn 362411855 41 + 400509343 AGTT-TTCACA-CCTC--CAGGGGAGTTTCACACCTCCAGGTGAG i fr2.chrUn I 1 C 0 s gasAcu1.chrUn 23678507 40 - 62550211 GGAT-CTCCCT-GCTA--AGGTGGGATCTCCCTGCT-AAGGTGGG i gasAcu1.chrUn I 1 C 0 s petMar1.Contig15836 21137 38 - 25532 gagc-tcccct-taga--gagcgctccctctcgagtcgaggg--- i petMar1.Contig15836 C 0 C 0 e felCat3.scaffold_135390 61475 121 + 302526 I e pteVam1.scaffold_22742 6262 210 - 9737 I e calJac1.Contig6069 83317 24 + 235769 I e turTru1.scaffold_93657 7213 0 - 12933 C e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89049 467 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942350 0 + 33091231 C e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=1834.000000 s hg19.chr11_gl000202_random 17930 22 + 40103 TCCT--CCCT--TT----TCAGGCTGAGTC s panTro2.chr11 68204517 22 + 134204764 TCCT--CCCT--TT----TCAGGCTGAGTC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48452 22 + 115376 TCCT--CCCT--TT----TCAGGCTGAGTC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126000772 22 - 132107971 TCCT--CCCT--TT----TCAGGCTGAGTC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128162563 22 - 133002572 tcct--ccct--ct----tcaggctgagtc i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 79087 22 + 109049 TCCT--CCCT--CT----TCAGGCTGAGTC i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 83341 22 + 235769 TCCT--CCCC--CT----TCTGGGTGAGTC i calJac1.Contig6069 I 24 C 0 s otoGar1.scaffold_15940.1-60550 45475 18 + 60550 TCCT--GCCT--CC----TAAGTGtg---- i otoGar1.scaffold_15940.1-60550 C 0 N 0 s micMur1.scaffold_2067 841 13 + 264097 -CCT--CCCT--CC----ACAG-------- i micMur1.scaffold_2067 C 0 N 0 s dipOrd1.scaffold_39490 9911 22 + 16834 GCAC--CCCC--TC----CTGTGGTCAGCA i dipOrd1.scaffold_39490 I 19 C 0 s bosTau4.chr29 48979445 20 + 51998940 AGCC--CCCT--TC----TGGGAGTG--AG i bosTau4.chr29 C 0 C 0 s canFam2.chr18 7539076 22 - 58872314 CACTCCCTCT--CC----CCAGGGTG--AG i canFam2.chr18 C 0 C 0 s equCab2.chr12 28942350 21 + 33091231 -----CTCCT--CCTGGGCTGGGGTG--TC i equCab2.chr12 C 0 C 0 s myoLuc1.scaffold_155660 39954 18 - 124081 TCCT--CCTG--CC----TCAGGGGG---- i myoLuc1.scaffold_155660 C 0 C 0 s loxAfr3.scaffold_159 89516 20 + 1045236 TCCT--CACTGACC----CCAGGCTG---- i loxAfr3.scaffold_159 I 467 I 7 s dasNov2.scaffold_51901 4190 21 + 12839 -TCT--CTCTG-CC----TGGGGCT-CGTC i dasNov2.scaffold_51901 C 0 C 0 s xenTro2.scaffold_1256 42985 22 - 115066 TCCT--CCCT--TT----GCCCGCTGAGTC i xenTro2.scaffold_1256 C 0 C 0 s fr2.chrUn 362411896 22 + 400509343 TTTC--ACAC--CT----TCATGCTGGATC i fr2.chrUn C 0 I 51 s gasAcu1.chrUn 23678547 22 - 62550211 ATCT--CCCT--GC----TAAGGTGGGATC i gasAcu1.chrUn C 0 I 6 s petMar1.Contig15836 21175 22 - 25532 agct--cccT--CG----ACAGGGAGAGAG i petMar1.Contig15836 C 0 C 0 e felCat3.scaffold_135390 61475 121 + 302526 I e pteVam1.scaffold_22742 6262 210 - 9737 I e turTru1.scaffold_93657 7213 0 - 12933 C e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=115516.000000 s hg19.chr11_gl000202_random 17952 25 + 40103 CT--CCCTCCTGGGGTGAGTCCTCC--CT s panTro2.chr11 68204539 25 + 134204764 CT--CCCTCCTGGGGTGAGTCCTCC--CT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48474 25 + 115376 CT--CCCTCCTGGGGTGAGTCCTCC--CT i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126000794 25 - 132107971 CT--CCCTCCTGGGGTGAGTCCTCC--CT i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128162585 25 - 133002572 ct--ccctcctggggtgagtcctcc--ct i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 79109 25 + 109049 CT--CCCTCCTGGGGTGAGTCCTCC--CT i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 83363 25 + 235769 CT--CCCTCCTAGGGTGAGTCCTCC--CT i calJac1.Contig6069 C 0 C 0 s dipOrd1.scaffold_39490 9933 25 + 16834 CC--CCCTCCTGTGGTCAGCACCCC--CT i dipOrd1.scaffold_39490 C 0 C 0 s bosTau4.chr29 48979465 11 + 51998940 CCCT----------------CCTCC--CT i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28942371 25 + 33091231 CC--CCGTCCTGTGGTGGGTCCTCC--CT i equCab2.chr12 C 0 C 0 s canFam2.chr18 7539098 25 - 58872314 TC--CCCTCCTGTAGTGGCTCCTCC--CT i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 39972 25 - 124081 AC--TCCTCCTGCCTGGGGTCCTTC--TC i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 6472 25 - 9737 AG--TCCTCCTGCCTGGGGCCCTTC--TC i pteVam1.scaffold_22742 I 210 C 0 s turTru1.scaffold_93657 7213 23 - 12933 ----CCCTTCTGGGGTGAGTCCTCC--CT i turTru1.scaffold_93657 C 0 C 0 s loxAfr3.scaffold_159 89543 25 + 1045236 CC--CATCTGTGGGGCAAGCCTCCT--CC i loxAfr3.scaffold_159 I 7 C 0 s dasNov2.scaffold_51901 4211 27 + 12839 TC--TCTGCCTGGGGCGCGTCTCTCTGCC i dasNov2.scaffold_51901 C 0 C 0 s xenTro2.scaffold_1256 43007 24 - 115066 CT--CCCT-CTGCCCCGGGTCCTCC--CT i xenTro2.scaffold_1256 C 0 C 0 s gasAcu1.chrUn 23678575 25 - 62550211 CT--ACCTGCTAAGGTGGGATCTCC--CT i gasAcu1.chrUn I 6 N 0 s petMar1.Contig15836 21197 22 - 25532 CT--TCCTCTtaagagcaggggtc----- i petMar1.Contig15836 C 0 C 0 e fr2.chrUn 362411918 51 + 400509343 I e felCat3.scaffold_135390 61475 121 + 302526 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=-79247.000000 s hg19.chr11_gl000202_random 17977 18 + 40103 CA---G------GTCCACC-----------T--CC-TCTCC s panTro2.chr11 68204564 18 + 134204764 TA---G------GTCCACC-----------T--CC-TCTCC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48499 18 + 115376 CA---G------GTCCACC-----------T--CC-TCTCC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126000819 18 - 132107971 CA---G------GTCCACC-----------T--CC-TCTCC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128162610 18 - 133002572 cA---G------GTCCACC-----------T--CC-TCTCC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 79134 18 + 109049 CA---G------GTCCACC-----------T--CC-TCTCC i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 83388 18 + 235769 CA---G------GTCCACC-----------T--CC-TCTCC i calJac1.Contig6069 C 0 C 0 s dipOrd1.scaffold_39490 9958 21 + 16834 CCTGTG------GTCAGCA-----------C--CC-CCTCC i dipOrd1.scaffold_39490 C 0 N 0 s bosTau4.chr29 48979476 12 + 51998940 GG---G------GGTCCTC-----------C--C------- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28942396 17 + 33091231 CA---G------GGTCCTC--TCCTT----C--C------- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7539123 23 - 58872314 CA---A------GGTTCTCCATCCCTAGCCC--C------- i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 39997 20 - 124081 CA---GTCACCTGCCCCCC-----------CCAC------- i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 6497 12 - 9737 TA---A------GCCCCTC-----------C--C------- i pteVam1.scaffold_22742 C 0 C 0 s turTru1.scaffold_93657 7236 12 - 12933 CG---G------GGTCCCC-----------C--T------- i turTru1.scaffold_93657 C 0 C 0 s loxAfr3.scaffold_159 89568 18 + 1045236 AG---A------GCCCAGC-----------T--CC-TCCCC i loxAfr3.scaffold_159 C 0 I 5 s dasNov2.scaffold_51901 4238 18 + 12839 TG---G------GTGCGTC-----------T--CT-CTCCC i dasNov2.scaffold_51901 C 0 I 5 s xenTro2.scaffold_1256 43031 1 - 115066 C---------------------------------------- i xenTro2.scaffold_1256 C 0 C 0 s petMar1.Contig15836 21219 17 - 25532 -----g------gcaaacc-----------t--ctggctcc i petMar1.Contig15836 C 0 C 0 e fr2.chrUn 362411918 51 + 400509343 I e felCat3.scaffold_135390 61475 121 + 302526 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=71465.000000 s hg19.chr11_gl000202_random 17995 53 + 40103 CCAGCCGGCTTCCATGGGGCTTCTTCAGTGGTTCCA----GC-TGGCGTGTGCCAGTC s panTro2.chr11 68204582 53 + 134204764 CCAGCCGGCTTCCATGGGGCTTCTTCAGTGGTTCCA----GC-TGGCGTGTGCCAGTC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48517 53 + 115376 CCAGCCGGCTTCCATGGGGCTTCTTCAGTGGTTCCA----TC-TGGCGTGTGCCAGCC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126000837 53 - 132107971 CCAGCCGGCTTCCATGGGGCTTCTTCAGTGGTTCCA----GC-TGGTGTGTGCCAGCC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128162628 53 - 133002572 CCAGCTGGCTTCCATGGGGCCTCTTCAGTGGTTCCA----GC-TGGCGTGTGCCAGCC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 79152 53 + 109049 CCAGCCGGCTTCCATGGGGCCTCTTCAGTGGTTCCA----GC-TGGCGTGTGCCGGCC i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 83406 52 + 235769 ACAGCCAGCTTCC-TTGGGCCTCTTCAGTAGTTCCA----GC-TGGCGTATGCCAGCC i calJac1.Contig6069 C 0 C 0 s bosTau4.chr29 48979488 56 + 51998940 CTACTCGGCCTCCATGGAGCCTCTCCAGAGCTCTCAGTAAGC-CCGCGTGT-CCGGGC i bosTau4.chr29 C 0 I 1 s equCab2.chr12 28942413 35 + 33091231 CCAGCT-GCTTCCATGGAGCCTTGTCAGTGCTTCCA---------------------- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7539146 49 - 58872314 CCAGCCGGCTTCCACAGAGCCTCTTCA-TGCTTTCA-------CTCCGAGTGGCAGC- i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 40017 36 - 124081 CCAGCCAGCTTCCGTGGAGCCTCCTCAAGGCTCCCA---------------------- i myoLuc1.scaffold_155660 C 0 I 17 s pteVam1.scaffold_22742 6509 56 - 9737 CCAGCCAGTGTCCATGGTGCCTCCTCGGGGCTCCAAG-GAGC-GCCCACGTGCCAGCC i pteVam1.scaffold_22742 C 0 I 4 s turTru1.scaffold_93657 7248 57 - 12933 CCCCCCTCCAGCCTTGGAGCCTCTCCAGAGCTCCCAGCAAGC-CGGTGTGTGCCGGGC i turTru1.scaffold_93657 C 0 I 1 s loxAfr3.scaffold_159 89591 45 + 1045236 CTCCCCTGGAGCCTCTGGGCG---------CTCCCA----GCAAGCTGCGTGCCCGGC i loxAfr3.scaffold_159 I 5 C 0 s dasNov2.scaffold_51901 4261 48 + 12839 CTCGTCTCTCTCCCTGGGGCGCGT------CTCTCT----GCCTGGGGCGCGTCTCTC i dasNov2.scaffold_51901 I 5 N 0 s xenTro2.scaffold_1256 43032 22 - 115066 --------TGCCCGCTGGGTCTTCCCTCTG---------------------------- i xenTro2.scaffold_1256 C 0 C 0 s petMar1.Contig15836 21236 23 - 25532 ggagccg-----catgcggctctttgag------------------------------ i petMar1.Contig15836 C 0 N 0 e fr2.chrUn 362411918 51 + 400509343 I e felCat3.scaffold_135390 61475 121 + 302526 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=20231.000000 s hg19.chr11_gl000202_random 18048 25 + 40103 CCCCAGGAGGTCCAG------------------G----------TCCT--------TTCTT s xenTro2.scaffold_1256 43054 17 - 115066 CCCCAGG--------------------------G----------TCCT--------CCCTT i xenTro2.scaffold_1256 C 0 I 4 s loxAfr3.scaffold_159 89636 24 + 1045236 CCCCT-CGTGGCCAG------------------G----------TTTG--------CCTTC i loxAfr3.scaffold_159 C 0 C 0 s canFam2.chr18 7539195 51 - 58872314 CCCCTGGAGGGCCAACTTTGACTCCCCTTCTCCG----------CCCTCTACCCTATCGTG i canFam2.chr18 C 0 C 0 s bosTau4.chr29 48979545 38 + 51998940 CCACAGCAGGGCCCGCTTGG-------------A----------CCCTTCACTTCCTCTTG i bosTau4.chr29 I 1 C 0 s turTru1.scaffold_93657 7306 38 - 12933 CCCCAGGAGGACCAGCTTGG-------------G----------CCCTTTTCCTTCTTTTC i turTru1.scaffold_93657 I 1 C 0 s calJac1.Contig6069 83458 35 + 235769 CCCCAGGAGGGCCAG------------------GTTTGACCCTTTCCT--------TTCTC i calJac1.Contig6069 C 0 C 0 s papHam1.scaffold6638 79205 25 + 109049 CCCCGGGAGGGCCAG------------------G----------CTCT--------TTCCC i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128162681 25 - 133002572 CCCCGGGAGGGCCAG------------------G----------CTCT--------TTCTC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126000890 25 - 132107971 CCCCAGGAGGCCCAG------------------G----------TCCT--------TTCTC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48570 25 + 115376 CCCCAGGAGGTCCAG------------------G----------TCCT--------TTCTC i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68204635 25 + 134204764 CCCCAGGAGGTCCAG------------------G----------TCCT--------TTCTC i panTro2.chr11 C 0 C 0 s fr2.chrUn 362411969 8 + 400509343 ----------TCCAG------------------A----------AC--------------- i fr2.chrUn I 51 C 0 e felCat3.scaffold_135390 61475 121 + 302526 I e pteVam1.scaffold_22742 6565 4 - 9737 I e myoLuc1.scaffold_155660 40053 17 - 124081 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942448 0 + 33091231 C e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=39004.000000 s hg19.chr11_gl000202_random 18073 26 + 40103 GACATT-----------TTCCTCAGCTGCT--GGGGCTG s loxAfr3.scaffold_159 89660 36 + 1045236 TCCCTTGAAGCCAACTGCACTTCAGCCGCT---CTCCAG i loxAfr3.scaffold_159 C 0 C 0 s canFam2.chr18 7539246 25 - 58872314 CACGGT-----------CTCCTGAGCAGCC---CAGATG i canFam2.chr18 C 0 C 0 s bosTau4.chr29 48979583 22 + 51998940 GACTGT-----------CTGCTTAGCGGCC------TTG i bosTau4.chr29 C 0 C 0 s turTru1.scaffold_93657 7344 28 - 12933 GTCTGT-----------TTCCTCAGCCgcagcaggggtg i turTru1.scaffold_93657 C 0 C 0 s calJac1.Contig6069 83493 25 + 235769 GAC-TT-----------TTCCTCAGCTGCC--AGGGCTG i calJac1.Contig6069 C 0 C 0 s papHam1.scaffold6638 79230 26 + 109049 AACCTT-----------TTCCTCAGCTGCT--GGGGCTG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128162706 26 - 133002572 AACCTT-----------TTCCTCAGCTGCC--GGGGCTG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126000915 26 - 132107971 GACCTT-----------TTCCTCAGCTGCC--GGGGCTG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48595 26 + 115376 GACATT-----------TTCCTCAGCTGCT--AGGGCTG i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68204660 26 + 134204764 GACATT-----------TTCCTCAGCTGCT--GGGGCTG i panTro2.chr11 C 0 C 0 s fr2.chrUn 362411977 26 + 400509343 GTCAAC-----------ACCTCTGGCtaca--gctgttg i fr2.chrUn C 0 C 0 e felCat3.scaffold_135390 61475 121 + 302526 I e pteVam1.scaffold_22742 6565 4 - 9737 I e myoLuc1.scaffold_155660 40053 17 - 124081 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e xenTro2.scaffold_1256 43071 4 - 115066 I e equCab2.chr12 28942448 0 + 33091231 C e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=148911.000000 s hg19.chr11_gl000202_random 18099 135 + 40103 C--AGGGGATGCAC-CAGCTGCATGGACGGGGT-----------------GGCATTGCCTGATCCCACCTCCCACAAACGTCTGTGCACCTGCCCCTG-CCCCTGCCCCA--GTGCTGCAGCCTCAGTGT----------AGATGTGGCCA---CACAGGGCCTGCAACCA---- s panTro2.chr11 68204686 129 + 134204764 C--AGGGGATGCAC-CAGCTGCATGGACGGGGT-----------------GGCATTGCCCGATCCCACCTCCCACAAACGTCTGTGCA------CCTG-CCCCTGCCCCA--GCGCTGCAGCCTCAGTGT----------AGATGTGGCCA---CACAGGGCCTGCAACCA---- i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48621 129 + 115376 C--AGGGGATGCAC-CAGCTGCATGGATGGGGT-----------------GGCATTGCCCGATCCCACCTCCCACAAACGTCTATGCA------CCTG-CCCCTGCCCCA--GCGCTGCAGCCTCAGTGT----------AGACGTGGCCA---CACAGGGCCTGCAACCA---- i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126000941 129 - 132107971 C--AGGGGATGCAC-CAGCTGCATGGACGGGGT-----------------GGCATTGCCCAATCCCACCTCCCACAAATGTCTGTGCA------CCTG-CCCCTGCCCCA--GCACTGCAGCCTCAGTGT----------AGATGTGGCCA---CACAGGGCCTGCAACCA---- i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128162732 130 - 133002572 C--GGGGGATGCAC-CAGCTGCACAGACGGGGT-----------------GGCATTGCCCAATCCCACCCCCCAGAAACGTCTGTGCA------CCCG-CCCCTGCCCCA--GCGCTGCAGCCTCAGTGT----------AGGTGTGGCCA--GCACAGGGCCTGCAAGCA---- i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 79256 130 + 109049 C--GGGGGATGCAC-CAGCTGCACAGACGGGGT-----------------GGCATTGCCCAATCCCACCGCCCAGAAACGTCTGTGCA------CCCG-CCCCTGCCCCA--GCGCTGCAGCCTCAGTGT----------AGGTGTGGCCA--GCACAGGGCCTGCAAGCA---- i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 83518 129 + 235769 C--AGGGGATGCAT-CAGCAGCATGGATGGAAT-----------------GGCATTGCCATACCCCACCTCCCAGAAACGTCTGTGCA------CCC--TCCCTGTCCCA--CTGCTGCAACCTCAATGT----------AGGTGTGGCCA--GTGAAGGACCTGCAGCCA---- i calJac1.Contig6069 C 0 C 0 s turTru1.scaffold_93657 7372 110 - 12933 cagcaggggtgcag-caggggCGCGG--GGAGG-----------------AGCGGTGCCC-CCTCCACCTCCCGGAAAC--TTGATGC------GCGC-ATCCTGCCCCA------------CAAAGTGT-----------------GTCT--GCAAAGAGCTTGCAGCCC---- i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48979605 107 + 51998940 GAGCATGGGTGCAG-CGGG---GCAG--GGGAG-----------------GGGGTTGCCC-TCTCCAACCCCCAGAAAT--GTGACGC------TTGA-ATCCTGCCCCA------------CGAAGTGC-----------------ATCT--GCAAAGAGCCAGCAACCA---- i bosTau4.chr29 C 0 C 0 s canFam2.chr18 7539271 99 - 58872314 C--CAGGGCGGCAG-CGAC---TTGG--GGAGG-----------------GACAGTGTCC-ACTCCACCTCCCAGGACA--CCGCTCA------CAGA-GCTCTGGCCCA------------CGCAGCGT----------------GGTCT--GCAAAGAGCT-------C---- i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 89696 128 + 1045236 C--AGGGGGCACAA-TAGCTGCACAG--GGAGG-----------------GCTGTTATCTGACTCCGGGTCCCAGAAACGTCCACGCA------CCGACCCCCTGCCCCA--GCACT-CATCACCCATGC----------CAGCGTGGTCT--GCAAAGAGCCCCTACACG---- i loxAfr3.scaffold_159 C 0 C 0 s xenTro2.scaffold_1256 43075 156 - 115066 C--AATGAGTACTC-CCTCTGCCTGC--TGAGTCCTTCCTCTGCCCACTGGGTCCTACCT-TTTCCAGCTCCCCTCAGTCCGTTCTCC------CTCG-CAGCTTCCCCGTCCCGCTGAGTCCTCTCTCTCCGCTGCCAGAGGTGAGGACGCAGTGGAGGGCCGGGTA--A---- i xenTro2.scaffold_1256 I 4 C 0 s fr2.chrUn 362412003 126 + 400509343 c--catggagacatgCAAATGCAACCTCGGGGA-----------------GGAGTCTCCG-GACTCACCTAGC--------TGGTCGG------CCAG-GTGCTTCCCTT--TCTCCGGAGGAACGACTC----------TCTCCTCGTCC--ATGTCGCACTTGTTGCCCACCA i fr2.chrUn C 0 C 0 e felCat3.scaffold_135390 61475 121 + 302526 I e pteVam1.scaffold_22742 6565 4 - 9737 I e myoLuc1.scaffold_155660 40053 17 - 124081 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942448 0 + 33091231 C e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=-53272.000000 s hg19.chr11_gl000202_random 18234 35 + 40103 ----------------CTGAGCT-CCGAAGCCCCAACCTGCA-------GCCATGGGGC s panTro2.chr11 68204815 35 + 134204764 ----------------CTGAGCT-CCGAAGCCCCAACCTGCA-------GCCATGGGGC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48750 35 + 115376 ----------------CTGAGGT-CCGAAGCCCCAACCTGCA-------GCCATGGGGT i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126001070 35 - 132107971 ----------------CTGAGCT-CCAGAGCCCCAACCTGCA-------GCCATGGGGC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128162862 42 - 133002572 ----------------CTGAGCT-CTGAAGCCCCAACCTGCAGCAAAGTGCCATGGGGC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 79386 42 + 109049 ----------------CTGAGCT-CTGAAGCCCCGACCTGCAGCAAAGTGCCATGGGGC i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 83647 27 + 235769 ----------------CTGAGCT-CCCAAGCCCCAACCTGCA-------GC-------- i calJac1.Contig6069 C 0 I 23 s turTru1.scaffold_93657 7482 17 - 12933 ----------------GTGAGCCTCCCAAGCCC-------------------------- i turTru1.scaffold_93657 C 0 I 378 s bosTau4.chr29 48979712 32 + 51998940 ----------------GTGAGCTTCCCA-----GGACCTGCG-----CGTCAGTGGGA- i bosTau4.chr29 C 0 C 0 s canFam2.chr18 7539370 19 - 58872314 ----------------CTGAGCC--------------TTTCT-----AGCCCAT----- i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 89824 28 + 1045236 ----------------CTTGAAT-CTAAGGGAAGACAC-----------GCCAGGG--- i loxAfr3.scaffold_159 C 0 C 0 s xenTro2.scaffold_1256 43231 25 - 115066 ----------------GTTACCC-TGGggggccggatctggc----------------- i xenTro2.scaffold_1256 C 0 C 0 s fr2.chrUn 362412129 13 + 400509343 ---TGATCA------CCTGAGC------------------------------------- i fr2.chrUn C 0 C 0 s danRer6.Zv8_scaffold3075 121751 22 - 281906 CTGGGGTCAAAGGCCCCTAGGT------------------------------------- i danRer6.Zv8_scaffold3075 N 0 C 0 e felCat3.scaffold_135390 61475 121 + 302526 I e pteVam1.scaffold_22742 6565 4 - 9737 I e myoLuc1.scaffold_155660 40053 17 - 124081 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942448 0 + 33091231 C e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=-18225.000000 s hg19.chr11_gl000202_random 18269 82 + 40103 GGGGGGACATGA----ATTCGAAGCCCTGTGGCATCAA-----TAGGGAAATGTGGCGG--G----TA-CC--AGGTGGGGTCC---TCCT---GCT--GCCCCAGGA- s panTro2.chr11 68204850 82 + 134204764 GGGGGTACATGA----ATCCGAAGCCCTGTGGCATCAA-----TAGGGAAATGTGGCGG--G----TA-CC--AGGTGGGGTCC---TCCT---GCT--GCCCCAGGA- i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48785 83 + 115376 GGGGGGACATGA----ATTCGAAGCCCTGTGGCATCAG-----TAGGGAAATGTGGTGG--G----TACCC--AGGCGGGGTCC---TCCT---GCT--GCCCCAGGA- i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126001105 83 - 132107971 GGGGGGACATGA----ATTTGAAGCCCTGTGGCATCAG-----TAGGGAAATGTTGCGA--G----TACCC--AGGCGGGGTCC---TCCT---GCT--GCCCCAGGA- i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128162904 81 - 133002572 GGGGG-ACATGA----ATTTGAAGCCCTGTGGCATCAG-----TAGGGAAATGTTGGGG--G----TACAC--AGGTGGGGTCC---TCCT---GCT--GCCCT-GGA- i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 79428 82 + 109049 GGGGGGACATGA----ATTTGAAGCCCTGTGGCATCAG-----TAGGGAAATGTTGGGG--G----TACAC--AGGTGGGGTCC---TCCT---GCT--GCCCC-GGA- i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 83697 55 + 235769 GGGGGGACATGA----ATTTGAATTCCTGTGGCATCAG-----TAGGGAAATGTTGGGG--G----TACC--------------------------------------- i calJac1.Contig6069 I 23 I 1256 s bosTau4.chr29 48979744 69 + 51998940 --------------------GAAGGCAGGGGGCTGTCC-----AGGAGGGGTCCGGGGGGTG----TGTCC--AGGGAGCGTCC---TCAG---GCT--GTCTCAGAT- i bosTau4.chr29 C 0 C 0 s canFam2.chr18 7539389 59 - 58872314 ------------------------------GGCACCCC-----TAGGGAGATGCTGGGG--G----TGCCC--AAGGATGGCCT---TCCC---GCCCGCTCGCGGAA- i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 89852 83 + 1045236 AGGGGCGCATCA----AGCCCAGGCCTTG--------------CAGGGCAGTTTTGGGA--GAGGATGCTCCCAGAGGGGCCCC---TCCTCTGTCT--GTCACAGGA- i loxAfr3.scaffold_159 C 0 I 5993 s xenTro2.scaffold_1256 43256 36 - 115066 ccgcgggctgta----gtttgaggacccctgGCTTAAA-----TA---------------------------------------------------------------- i xenTro2.scaffold_1256 C 0 N 0 s fr2.chrUn 362412142 76 + 400509343 GTTGTCCCACGAGTACGTCTTGATCTGCGTTGCCCTGGCAACACAAGGGAACACTGGTC--G----GACCC--GAGTGGAGCTC------------------------- i fr2.chrUn C 0 N 0 s danRer6.Zv8_scaffold3075 121773 92 - 281906 GGAGGGCCAGGAGGCAACCTGGGGCCTC----TACTGCAAGTCTAAGGAAAAA---GGT--G----GACCC--TTGGGTAGCTTGCTGGGGTCAGAA--GCCCCTAGAA i danRer6.Zv8_scaffold3075 C 0 C 0 e felCat3.scaffold_135390 61475 121 + 302526 I e pteVam1.scaffold_22742 6565 4 - 9737 I e myoLuc1.scaffold_155660 40053 17 - 124081 I e turTru1.scaffold_93657 7499 378 - 12933 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942448 0 + 33091231 C e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=244926.000000 s hg19.chr11_gl000202_random 18351 243 + 40103 --------GCGGGGCCCACCGCGG--CCTGCAGCAGCCACAG-GTGCAGGAGGGTGG------GGGAGGCTGTCAGAGGCTATCAGTGCCCAAGCTGCCTTCTGCTTGGGGACAGCCCTCAGATGAGTCCCTGGGAGCCCGGTGCTCCTCAGCGAGGGCCTGGGCTGGGGTTTGG---GGCTGCTCCCTGG--------------CTCTGCCCATCAGCAGCATGACACAGGCAGGCCGGGC--CACTCAGGGCTCCAGACTTC----TCAAGGTGCAGTGTG s papHam1.scaffold6638 79510 243 + 109049 --------GCGGGGCCCACCGTGG--CCTGCAGCAGCCACAG-GTGCAGGGGGGTGA------GGGAGGCTGTCAGAGGCTATCAGTGCCCAAGCTGCCTTCTGCTTGGGGACGGCCCTCAGACGAGTCCCTAGGAGCTCGGTGCTGCTCAGTGAGGGCCTGGGCCGGGGTTCAG---GGCTGCTCCTTGG--------------CTCTGCCCATCAGCAGCGTGACACAGGCAGGCAGGGC--CGCTCAGGGCTCCAGACTTT----TCAAGGTGCAGTGTG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128162985 242 - 133002572 --------GCAGGGCCCACCGTGG--CCTGCAGCAGCCACAG-GTGCAGG-GGGTGA------GGGAGGCTGTCAGAGGCTATCAGTGCCCAAGCTGCCTTCTGCTTGGGGACAGCCCTCAGACGAGTCCCTAGGAGCTCGGTGCTGCTCAGTGAGGGCCTGGGCCGGGGTTCAG---GGCTGCTCCTTGG--------------CTCTGCCCATCAGCAGCGTGACACAGGCAGGCAGGGC--CCCTCAGGGCTCCAGACTTT----TCAAGGTGCAGTGTG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126001188 243 - 132107971 --------GCGGGGCTCACTGCGG--CCTGCAGCAGCAACAG-GTGCAGGAGGGTGG------GGGAGGCTGTCAGAGGCTATCAGTGCCCAAGCTGCCTTCTGCTTGCAGACAGACCTCAGATAAGTCCCTGGGAGCCCGGTGCTGCTCAGTGAGGGCCTGGGCTGGGGTTTGG---GGCTGCTCCCTGG--------------CTCTGACCATCAGCAGCATGACACAGGCAGGCCGGGC--CGCTCAGGGCTCCAGACTTC----TCAAGGTGCAGTGTG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 48868 243 + 115376 --------GCGGGGCCCACCGCGG--CCTGCAGCAGCCACAG-GTGCAGGAGGGTGG------GGGAGGCTGTCAGAGGCTATCAGTGCCCAAGCTGCCTTCTGCTTGGGGACAGCCCTCAGATGAGTCCCTGGGAGCCCGGTGCTCCTCAGTGAGGGCCTGGGCTGGGGTTTGG---GGCTGCTCCCTGG--------------CTCTGCCCATCAGCAGCATGACACAGGCAGGCCGGGC--CGCTCAGGGCTCCAGACTTC----TCAAGGTGCAGTGTG i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68204932 243 + 134204764 --------GCGGGGCCCACCGCGG--CCTGCAGCAGCCACAG-GTGCAGGAGGGTGG------GGGAGGCTGTCAGAGGCTATCAGTGCCCAAGCTGCCTTCTGCTTGGGGACAGCCCTCAGATGAGTCCCTGGGAGCCCGGTGCTCCTCAGTGAGGGCCTGGGCTGGGGTTTGG---GGCTGCTCCCTGG--------------CTCTGCCCATCAGCAGCATGACACAGGCAGGCCGGGC--CGCTCAGGGCTCCAGACTTC----CCAAGGTGCAGTGTG i panTro2.chr11 C 0 C 0 s bosTau4.chr29 48979813 190 + 51998940 --------GGACCGTCTCCTTG-----CTGTACCCGCAGCACGCTGC-----GGTGG------GGAGGTCAG---GAGGGGCTCAG-------------------CCAGGTCCAGGGCCCAG-------CCTGGG--------------------GGGCCCATGCTGGCCTTGAACTTGGCCTCCTCCCGGGAGAGGGGCAGAGCTCCTTCC--------GCAGGGCCCCGAGGAGGCCGGC-----TCAGGGCT---GACCTC----CCATTAGGAAATGTA i bosTau4.chr29 C 0 I 2 s canFam2.chr18 7539448 118 - 58872314 --------GGGCTGCCCCCT-------CTGT----GTTGCAC-CTGC------------------------------CGAGATCAG-------------------CCTGGGGCAGGGC--------------------------------------GGACAGGGAGAGGCTCCGGCCAGGCTGCCACTTGG--------------TCCTG----------GCAGCACCCAGGCTACTCCAGC------------------CTTC----GCA------------ i canFam2.chr18 C 0 C 0 s danRer6.Zv8_scaffold3075 121865 230 - 281906 GGAGGGCCAAGGGGCTTCCTGGGGGCTCTACTGCAAGCACAG---GGAGAGAGGTGGACCCCCAGGTAGCTTGCTGAGG---TCAGAG---------------GCCCGTAGGTGGAGGGCCAATGAGCACCTTGGGGCCT-TTACTGCAAGTCCAGGGAGAGTGATGGAGCCCTG---GGTAGCTTGCTGG---------------------GGTCAGAAGCCAGTAGTCGGTGGGCCAGGGGGCATCCTGGGGCCTATACTGCAAGGCCAGGGAG------- i danRer6.Zv8_scaffold3075 C 0 C 0 e felCat3.scaffold_135390 61475 121 + 302526 I e pteVam1.scaffold_22742 6565 4 - 9737 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40053 17 - 124081 I e turTru1.scaffold_93657 7499 378 - 12933 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942448 0 + 33091231 C e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=373456.000000 s hg19.chr11_gl000202_random 18594 437 + 40103 GCAGGACAGCCT--CCCTGA--GGGTGTTCTGAGGACTCGGA--GCTGC---------------------CTCTGAAGTTCCTACTCACTGTTCA-CTCCAATACATGAGGTTAGGGTCAGGTCGGGT-AATCAGTGAGACACCAACCCCCTGCCACCCCTAGGAAGGTGGGGAGGGC-----CAAGTCCT--GGCTGCTCATGGCATC--CTGGCTTTTCAGGAGC-------------------------CC-TTCGGTCAAAAATAAAATGATCTGCTTGCCCTACAAGAAATAAAGCTGGGGTGACCCAGAGAGGCTGGGCT-CAG--CCTGGGAAAGGGGGTGTCCCAAGAGAAGGAGGAGGG--TAAAGGGCTGTGGCCTCTCCGGAGGGGGCCACCGGGAGTCACCGAGAGGCA------GCAGGACCAAG-GGGGAGG-----CTCTGGGCATCCTGCCGAGAGCA----CCAC---AGGTTAAAAAACC------CTACCCAAGGCCTTTGA----TCCCCTGCTG s papHam1.scaffold6638 79753 455 + 109049 GCAGGATAGCCT--CCCTG---GGGCGTTCTGAGGACTCGGAA-GCTGC---------------------CTCTGAAGCTCCTACTCACCGTTCA-CTCCAGTACATGAGGTTAGGGTCAGGTTGGGT-AATCAGTGAGACACCAACCCCCTACCACCCCTAGGAAGGTGGGGAGGGG-----CAAGTCCT--GGCTTCTTACAGCATC--CTGGCTTTTCAGGACTCCCAGGGGC-ACTAC-------CCACC-TTCTGTCAAAAACAAAATGATCTACTTGTCCTACAAGAAATAAAGCTGGGGTGACCCAGAGAGGCTGGGCT-CAG--CCTGGAAGAGGGGGTGTCCCAAGAGAAGGAGAAGGG--TAAAGGGCTGAGGCCTCTGGGGAGGGGGTCACCGGGAGTCACCGAGAGGCA------GCAGGACCAAGAGGGGAGG-----CTCTGGGCATCCTGCCTAGAGCA----CCAC---AGGTTGAAAAACC------CTACCTAAGGCCTTTGA----TCCCCCGCCG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128163227 445 - 133002572 GCAGGACAGCCT--CCCTG---GGGCGTTCTGAGGACTCGGAG-GCTGC---------------------CTCTGAAGCTCCTACTCACCGTTCA-CTCCAGTACATGAGGTTAGGGTCAGGTTGGGT-AATCAGTGAGACACCAACCCCCTACCACCCCTAGGAAGGTGGGGAGGGG-----CAAGTCCT--GGCTTCCTACAGCATC--CTGGCTTTTCAGGACCCCCAGGGGC-ACTAC-------CCACC-TTCTGTCAAAAACAAAATGATCTACTTGCCCTACAAGAAATAAAGCTGGGGTGACCCAGAGAGGCTGGGCT-CAG--CCTGGGAGAGGGGGTGTCCCAAGAGAAGGAGGAGGG--TAAAGGGCTGAGGCCTCTGGGGAGGGG----------GTCACCGAGAGGCA------GCAGGACCAAGAGGGGAGG-----CTCTGGGCATCCTGCCGAGAGCA----CCAC---AGGTTGAAAAACC------CTACCCAAGGCCTTTGA----TCCCCCGCCG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126001431 439 - 132107971 GCAGGACAGCCT--CCCTGA--GGGCGTTCTGAGGACTCGGAG-GCTAC---------------------CTCTGAAGTTCCTACTCACCGTTCA-CTCCAATACATGAGGTTAGGGTCAGGTCGGGT-AATCAGTGAGACACCAACCCCCTGCCACCGCTAGGAAGGTGGGGAGGGC-----CAAGTCCT--GGCTGCTCACGGCATC--CTGGCTTTTCAGGAGC-------------------------CC-TTCGGTCAAAAATAAAATGATCTACTTGCCTTACAAGAAATAAAGCTGGGGTGACCCAGAGAGGCTGCGCT-CAG--CTTGGGAGAGGGGCTGTCCCAAGAGAAGGAGGAGGG--TAAAGGGCTGTGGCCTCTCAGGAGGGGGCCACCGGGAGTCACCGAGAGGCA------GCAGGACCAAGAGGGGAGG-----CTCTGGGCATCCTGCTGAGAGCA----CCAC---AGGTTAAAAAACC------CTACCCAAGGCCTTTGA----TCCCCCGCCG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 49111 438 + 115376 GCAGGACAGCCT--CCCTGA--GGGCGTTCTGAGGACTCGGA--GCTGC---------------------CTCTGAAGTTCCTACTCACTGTTCA-CTACAATACATGACGTTAGGGTCAGGTCGGGT-AATCAGTGAGACACCAACCCCCTGCCACCCCTAGGAAGGCGGGAAGGGC-----CAAGTCCT--GGCTGCTCACGGCATC--CTGGCTTTTCAGGAGC-------------------------CC-TTCGGTCAAAAATAAAATGATCTGCTTGCCCTACAAGAAGTAAAGCTGGGGTGACCCAGAGAGGCTGGGCT-CAG--CCTGGGAAAGGGGGTGTCCCAAGAGAAGGAGGAGGG--TAAAGGGCTGTGGCCTCTCGGGAGGGGGCCACCGGGAGTCACCGAGAGACA------GCATGACCAAGAGGGGAGG-----CTCTGGGCATCCTGCCGAGAGCA----CCAC---AGGTTAAAAAACC------CTACCCAAGGCCTTTGA----TCCCCCGCTG i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68205175 438 + 134204764 GCAGGACAGCCT--CCCTGA--GGGTGTTCTGAGGACTCGGA--GCTGC---------------------CTCTGAAGTTCCTACTCACTGTTCA-CTCCAATACATGAGGTTAGAGTCAGGTCGGGT-AATCAGTGAGACACCAACCCCCTGCCACCCCTAGGAAGGTGGGGAGGGC-----CAAGTCCT--GGCTGCTCATGGCATC--CTGGCTTTTCAGGAGC-------------------------CC-TTCGGTCAAAAATAAAATGATCTGCTTGCCCTACAAGAAATAAAGCTGGGGTGACCCAGAGAGGCTGGGCT-CAG--CCTGGGAAAGGGGGTGTCCCAAGAGAAGGAGGAGGG--TAAAGGGCTGTGGCCTCTCGGGAGGGGGCCACTGGGAGTCACCGAGAGGCA------GCAGGACCAAGAGGGGAGG-----CTCTGGGCATCCTGCCGAGAGCA----CCAC---AGGTTAAAAAACC------CTACCCAAGGCCTTTGA----TCCCCTGCTA i panTro2.chr11 C 0 C 0 s turTru1.scaffold_93657 7877 376 - 12933 GCAGAGCTGCCTCCCCAGGAGC-------CCGAGAGTCCCGGG---CAG---------------------CTCTGAGA-TCTAGCTCACAGCTCACCTCCAGT-CATGAGATGCT-GTCCTGTGAGATCCGCTACTGAGACGTTGACCCCCTCCCCAATTCCGACAGGTGGAGAAAGAGGCACTGAGTTCGTGGGTCACTCACAGCTTC--CTGGTTTCTCAGGACC-CCAGACTC-ACCA--------CCACCATTTGTCAGAAGATAA----ACGTATTTCCCTT-CAACAGATATAGCCGGTGA----------------------------------------CCCCGACAGGAAGGGGAAGGA--GGCCAGGCTTAGACT----GGGAGGGGGAG---------TGGCCAGG------------------GGGGCAGAGGG-----CACGCTGAGA--------GCGGG----CTGC---AGGCTGGGG------------ACTCTCGGCCTGCGGG---GCCCCGTCTG i turTru1.scaffold_93657 I 378 I 53 s bosTau4.chr29 48980005 258 + 51998940 --------------TCAGGA-------------------------------------------------------------------------------------------------------GGGATCCACCCCCGAGATCCCGA-CCCCTCCCCACTTCCTG-------------------TGGGTTTCTGGGTCACCCACAGCCTC--CTGGCTTCTCTGAACC-TCAGAGTC-ACAA--------CAGCC-TTTGTCTGAAGATAA----ACATCTTTCCC-G-CAAGAAATAAAGGGGGTGA-------------------------------------------TGAGGGGCAAGGGGAGGG--AGGCAGGCTCAGACC----AGGAGGCAG------------GCTCAGGC----------------CGGGGCGGGGGG-----CCGGAGCAGT--------GAGCG----CCCC---AGG------------------------GGCCTGCGGGCCTGGCCCTCCTG i bosTau4.chr29 I 2 I 11 s canFam2.chr18 7539566 353 - 58872314 --------------CCATGA--TGGTGTC-CAAGAATTCGGGGGGCCGC---------------------TTCTAAGCTTCCTGCTCACAGTCCATCTCCAATATATGAGATGGGAATGCTGTGGGATGGGCTACTGAGACAT-AACCCCCTTCCCACTTTGGATAGGTGGGGAAGGGGTGC-TGGGTCCCTGAGCAGCTCACAGCCTC--CTGGCTCCTCAGGACC-CCAGACTT-ACCAT-------CCACC-TTTGTCGGAAGGTAA----ATGTATTTGTCCT-CAAGAAAAAAAGCCTTGGT----------------------------------AGGGGTCCCCGAGGGGAAGGAGAGGGAGTGGCCAGGTT----------AGCGGTGAGCC---------CCCTGAGAG----------------CA--GCAGAAGG-----CTGGCGGGCT--------GGGGA----CTCT---TGG------------------------GGGTGGTGG----TGCC------ i canFam2.chr18 C 0 I 5 s felCat3.scaffold_135390 61596 355 + 302526 -----------------------------CCGAGGATTCAGGGGGCTGG---------------------TTCCAAGGCTCCCACTCACAGCTCATTTCGAGTGTCTGAGATGGGGGTTACAGGGGGTCAGCTGCCGAGCCGTGAGCCCCCTCCCCACTGGGGACAGGTGGGGAAGGAGAGT-TGGGTGCCTGGGCGGCTCACAGCCTC--CTGACTCCTCAGGACC-CCAGCCTTCCCCGC-------CCACC-TTGGCCAGAAGATAC----ATTTGTTTGTCCT-CAAGGAAAAAAGCCGGGGTG---------------------------------GGGGGTCCCTGAAAGAAAGGAGAGGGAGCGGCCAGGTT----------AGCGGGGAGCA---------TCCCGAGAG----------------CAGGGAGAAGGG-----CCGGTGGGCT--------GGGGA----CCCCCGGTGG------------------------GGCTGGCGG----TCCCGTCCCG i felCat3.scaffold_135390 I 121 I 28 s danRer6.Zv8_scaffold3075 122095 455 - 281906 -AGAGGTGGACC--CCTGGG--TAGCTTGCTGGGG--TCAGAG-GCCCCTAGGTGGAGGGCCAAGAGGCACCCTGGGGCCTGTACTGCAAGACCA----------GGGAGAGTTGTGGACCCCTGGGTAGCTTGCTGGGGTCTTAGGCCCCT-------------AGGTGG--AGGGC-----CAGGG-----GGCACCCTGGGGCCTCTACTGCAAGTCCAGGGAG-AGAGGTGG-ACCCCTGGGTAGCTTGC-TGGGGTCAGAGGCCC------------------CTAGGTGGAGGGCCAGGGGGCACCCTGGGGCCTCTACTGCAAGTCCAGGGAGAGAGGTGGACCCCTGGGTAGCTTGCTGG------GGTCAGAGGCCCCTAGGTGGAGGGCCAGCGGG---CACCCTGGGGCCTCTACTGCAAGTCCAGGGAGAGAGGTGGACCCCTGGGTAGCTTGCTGGGGTCAGAGGCAAC---TAGGTGGAGGGCCAGGGGGCACCCTGGGGCCTAAAC----TGCGAGTCCA i danRer6.Zv8_scaffold3075 C 0 C 0 e pteVam1.scaffold_22742 6565 4 - 9737 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40053 17 - 124081 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942448 0 + 33091231 C e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=41895.000000 s hg19.chr11_gl000202_random 19031 97 + 40103 GGGAGAGA------------------TTGGATGTCCCTTGAACCCCA----GGAGGAACCAGA-----CCTCGGGCTGGATTTTATTCTGTGGAGACAAGTGAAGCTTCATGACATCCACGGCG s papHam1.scaffold6638 80208 97 + 109049 GGGAGAGA------------------TTGGATATCCCTTGAACCCCA----GGAGGAACCAGG-----CCTGGGGCTGGATTTTATTCTATGGAGACAAGCGAAGCATTGTGACATCCACAGAG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128163672 97 - 133002572 GGGAGAGA------------------TTGGATATCCCTTGAACCCCA----GGAGGAACCAGG-----CCTGGGGCTGGATTTTATTCTGTGGAGACAAGCGAAGCATTGTGACATCCACAGAG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126001870 97 - 132107971 GGGAGAGA------------------TTGGATGTGCCTTGAACCCCA----GGAGGAACCAGG-----CCTCGGGCTGGATTTTATTCCATGGAGACAAGCGAAGCATCGTGACATCCACGGCA i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 49549 97 + 115376 GGGAGAGA------------------TTGGATGTCCCTCGAACCCCA----GGAGGAACCAGG-----CCTCGGGCTGGATTTTATTGTATGGAGACAAGTGAAGCTTCATGACGTCCATGGCG i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68205613 97 + 134204764 GGGAGAGA------------------TTGGATGTCCCTTGAACCCCA----GGAGGAACCAGA-----CCTCGGGCTGGATTTTATTCTGTGGATATAAGTGAAGCTTCGTGACATCCATGGCG i panTro2.chr11 C 0 C 0 s bosTau4.chr29 48980274 49 + 51998940 ----------------------------GTGTTAGTCCTGCTGCCCA---------------------CCCAGGGCAGG---CCTCCCCAC--------------CTCCAGGACC--------- i bosTau4.chr29 I 11 I 3 s felCat3.scaffold_135390 61979 56 + 302526 GGCAGCGA------------------ACAAGTAAGTCCCCGTCCCCA---------------------CGCAGGGC------CTCCCCTGT--------------CTCCACGACC--------- i felCat3.scaffold_135390 I 28 I 1 s canFam2.chr18 7539924 33 - 58872314 GGTGG----------------------CCTGTGGGGCCTGGT------------------------------GGTC------CCATCCTGT--------------------------------- i canFam2.chr18 I 5 C 0 s danRer6.Zv8_scaffold3075 122550 84 - 281906 GGGAGAGAGGTGGACCCCTGTGTAGTTTGCTGGGGTCTTAGGCCCCTAGGTGGAGGGCCAAGGGGCACCATGGGGC------CTATACTG---------------------------------- i danRer6.Zv8_scaffold3075 C 0 C 0 e pteVam1.scaffold_22742 6565 4 - 9737 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40053 17 - 124081 I e turTru1.scaffold_93657 8253 53 - 12933 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942448 0 + 33091231 C e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=9444.000000 s hg19.chr11_gl000202_random 19128 91 + 40103 TGAGTCCTGGG-GAGT-------------GGAGCTGTCCAG--CCTGTGGCTC-TGGGCCTG-----CGTCACGCCACTTGTGGGTGGGCCTGTGTCACGCA-----------GCTCATGGGAC s papHam1.scaffold6638 80305 92 + 109049 TGAGTCCTGGG-GAGT-------------GGAGCTGTCCAG--CCTGGGGCTCGTGGGCCTG-----CATCACGCCACTTGTGGGTGGGTCTGTGTCACGCA-----------GCTCATGGGAC i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128163769 92 - 133002572 TGAGTCCTAGG-GAGT-------------GGAGCTGTCCAG--TCTGGGGCTCGTGGGCCTG-----CATCACGCCACTTGTGGGTGGGTCTGTGTCACACA-----------GCTCATGGGAC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126001967 91 - 132107971 TGAGTCCCGGA-GAGT-------------GGAGCTGTCCAG--CCTGTGGCTC-TGGGCCTG-----CATCACGCCGCTTGTGGGTGGGCCCGTGTCACGCA-----------ACTCATGGGAC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 49646 91 + 115376 TGAGTCCTGGG-GAGT-------------GGAGCTGTCCAG--CCTGTGGCTC-TGGGCCTG-----CGTCACGCCACTTATGGGTGGGCCTGTGTCATGCA-----------GCTCACGGGAC i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68205710 89 + 134204764 TGAGTCCTGGG-GAGT-------------GGAGCTGTCCAG--CCTGTGGCTC-TGGGCCT-------GTCATGCCACTTGTGGGTGGGCCTGTGTCACGCA-----------GCTCACGGGAC i panTro2.chr11 C 0 C 0 s turTru1.scaffold_93657 8306 45 - 12933 ----------------------------------------------TGAGCCC-TTGACCAG-------------CGCTCTCGG------CTGTGTGCCGCC-----------AGCCAGGGA-- i turTru1.scaffold_93657 I 53 C 0 s bosTau4.chr29 48980326 57 + 51998940 ----------------------------------------------GGAGCCC-TTGACCGGGCCTTTGA-ACACCTCTCTCGG------CTGTGGGCCCCC-----------ACCCAGGGG-- i bosTau4.chr29 I 3 C 0 s felCat3.scaffold_135390 62036 77 + 302526 ---------------C-------------AGGGGTCGCCGG--GCTGAGGCCA-TCAACCTG-----TGA-----GGATCTGGA------CTCTGCCCCACCCCCAGCACTCGGGGCTGGGGGC i felCat3.scaffold_135390 I 1 I 33 s canFam2.chr18 7539957 35 - 58872314 ------------------------------GGTCTTGCAGG-----GAGGCCT-TCCGTC-----------------------------------------------------AGGCAGGGGAC i canFam2.chr18 C 0 C 0 s danRer6.Zv8_scaffold3075 122634 105 - 281906 CAAGTCCAGGGAGAGTTGTGGACCCTTGGGTAGCTTGCTGGGGTCAGAGGCCC-CTGGGTGG-AGGGCAAGGGGGCACCCAGGG------GCCTATACTGCA-----------AGTCCAGGAAG i danRer6.Zv8_scaffold3075 C 0 C 0 e pteVam1.scaffold_22742 6565 4 - 9737 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40053 17 - 124081 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942448 0 + 33091231 C e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=106953.000000 s hg19.chr11_gl000202_random 19219 117 + 40103 AGAGCCAGGACACCCCGAGGAAGGCTGGGGCAGGACAGCC-----------------AGGC-CCCCATGCTCTCGCTGGCTTCACAGTCC-----AACTGG-GAGACA----AGAAA-AATGAAAATCAAGGT------------TCAGGGCTGGCGG s papHam1.scaffold6638 80397 117 + 109049 ACAGCCAGGACACCCCGAGGAAGGCTGAGGCTGGACAGCC-----------------AGGC-CCCCGTGCCCTCGCTGGCTTCACAGTCC-----AACTGG-GAGATG----AGAAA-AATGAAAATCAAGGG------------CCAGGGCTGGTGG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128163861 117 - 133002572 ACAGCCAGGACACCCCGAGGAAGGCTGAGGCTGGATAGCC-----------------AGGA-CCCTGTGCCCTCGCTGGCTTCACAGTCC-----AACTGG-GAGATG----AGAAA-AATGAAAATCAAGGG------------CCAGGGCTGGTGG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126002058 117 - 132107971 AGAGCCAGGACACCCCGAGGAAGGCTGGGGCGGGACAGCC-----------------AGGC-CCTCGTGCTCTCGCTAGCTTCACAGTTC-----AACTGG-GAGACA----AGAAA-AATGAAAATCAAGGT------------TCAGGGCTGGCGG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 49737 117 + 115376 AGAGCCAGGACACCCCGAGGAAGGCTGGGGCAGGACAGCC-----------------AGGC-CCCCGTGCTCTCGCTGGCTTCTCAGTCC-----AACTGG-GAGACA----AGAAA-AATGAAAATCAAGGT------------TCAGGGCTGGCGG i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68205799 117 + 134204764 AGAGCCAGGACACCCCGAGGAAGGCTGGGGCAGGACAGCC-----------------AGGC-CCCTGTGCTCTCACTGGCTTCACAGTCC-----AACTGG-GAGACA----AGAAA-AATGAAAATCAAGGT------------TCAGGGCTGGCGG i panTro2.chr11 C 0 C 0 s turTru1.scaffold_93657 8351 58 - 12933 ------------CCCTGGGGGAGGCGGGGCTGGGAGAGCC-----------------AGGC-CCCTG-GCCCGC---------------------GG---------TG----AGATGTGACTG----------------------------------- i turTru1.scaffold_93657 C 0 I 2 s bosTau4.chr29 48980383 62 + 51998940 --------------TGGGGGGAGGCCAGGGAAGTA-AGCC-----------------AGGC-CCCTG-GCCCTC---------------------AGCTGG-GGAATG----AGATG-GATGA----------------------------------- i bosTau4.chr29 C 0 I 2 s felCat3.scaffold_135390 62146 102 + 302526 GTGACCAGGTGTCCCGAGCGGCGGGTGGGCCAGGGGAGCC-----------------AGGC-CCACT-GCCCTC-CCGGCTTCACGGTCCAGACTGGCTGACAGAGTGCCCCAGGCA-GGTGG----------------------------------- i felCat3.scaffold_135390 I 33 I 1 s danRer6.Zv8_scaffold3075 122739 135 - 281906 AGAGGTGGACCCTTGTGTAACTTGCGGGGGCAAGAGGCCCTTAAGTGGAGGGTAAGGAGGCACCCTGGGGCCTCTTCTGC----AAGTCC-----AG--GG-----------AGAGA-GGTGGACCCCTGGGTAGCTTGCTGGGGTCAGCGCCACTAG i danRer6.Zv8_scaffold3075 C 0 C 0 e pteVam1.scaffold_22742 6565 4 - 9737 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40053 17 - 124081 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e equCab2.chr12 28942448 0 + 33091231 C e canFam2.chr18 7539992 0 - 58872314 C e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=219192.000000 s hg19.chr11_gl000202_random 19336 94 + 40103 CA------CGAGGACCCTGG----GGCTCCCTGGTGGCTGGATTTCAGCTATG-----GG--AGGA--AGAGACAGTGCGTTTCTGGGTAG--TGAGGGGCCCAGCACAGACAAG s papHam1.scaffold6638 80514 94 + 109049 CA------CGAGGACCCCAG----GGCTTCCTGGCGGCTGGATTTCAGCTATG-----GG--AGGA--GGGAACAGTGCGTTTCTGGGTAG--TGAGGGGCACAGCACAGACAAG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128163978 94 - 133002572 CA------CGAGGACCCCAG----GGCTTCCTGGCAGCTGGATTTCAGCCATG-----GG--AGGA--GGGAACAGTGCGTTTCTGGGTAG--TGAGGGGCACAGTACAGACAAG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126002175 94 - 132107971 CA------CGAGGCCCCTCG----GGCTTCCTCGTGGCTGGATTTCAGCTATG-----GG--AGGA--GGAGACAGTGCGTTTCTGGGTAG--TGAGGGGCCCAGCACAGACAAG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 49854 94 + 115376 CA------CGAGGACCCTGG----GGCTCCCTGGTGGCTGGATTTCAGCTATG-----GG--AGGA--AGAGACAGTGTGTTTCTGGGTAG--TGAGGGGCCCAGCACAGACAAG i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68205916 94 + 134204764 CA------CGAGGACCCTGG----GGCTCCCTGGTGGCTGGATTTCAGCTATG-----GG--AGGA--AGAGACAGTGCGTTTCTGGGTAG--TGAGGGGCCCAGCACAGACAAG i panTro2.chr11 C 0 C 0 s turTru1.scaffold_93657 8411 94 - 12933 CA------AGAGGG---TGGGCGTGGCTTCCTGATGGGTGGA-TTCAGCTGCC-----GGAAGGGG--TGGCACGGCACACGCCCAGGGAG--TGCAGGGCACC--GCGGACCAA i turTru1.scaffold_93657 I 2 I 1 s bosTau4.chr29 48980447 108 + 51998940 CAGTCAGCAGAGGGCCCCGGGCAGGGCTTCCTCATAGGTGGA---CAGGTGGCTTCAAACACGGGC--CGGGACAGCACACCCCGGGGGAG--GGCAGGGCACCGTGTGGGCCAG i bosTau4.chr29 I 2 I 1 s felCat3.scaffold_135390 62249 94 + 302526 CA------CAGGGGCCCCGG----GGCTTCCTGACGGCGGGAGTGCAGCCACG-----GG--AGGG--CGGGACAGCGCACTCCCGGGGAG--TGTGGGCCCAGGCGTGCACAAA i felCat3.scaffold_135390 I 1 I 1 s canFam2.chr18 7539992 79 - 58872314 CA------CGGAGGTCCCAG----GGCTTCCTGATAGCTGGAGTTCAGCACCA-----GGC-AGGG--CAGGACAGCATGTCCCCAGGGTG--TGCGGG---------------- i canFam2.chr18 C 0 I 1 s pteVam1.scaffold_22742 6569 91 - 9737 -----------GGGGCCTGG----GGCTCCGTGATGGCTGGAGCTCAGCCACA-----GG--TGGGGAAGGGCCAGCACACTCCTGGGCAG--TGTGGGGCACAGCACAGACCAA i pteVam1.scaffold_22742 I 4 I 1 s myoLuc1.scaffold_155660 40070 91 - 124081 ---------GGGGCCACAGG----GGCTCCCTGAGGGGTGGAGCTCAGCCACG-----GC--CGGG--CTGGACTGTACATTCCTGGGGAG--GGCAGGGCACGGCGTGGACAAA i myoLuc1.scaffold_155660 I 17 I 1 s equCab2.chr12 28942448 61 + 33091231 ------------------------------CTGGGGCCTGGAGTCCAGCAGCG-----GGCAGGGG--CGGGACAGCA------CAGGGCA--CCCGAG---------AGACAAA i equCab2.chr12 C 0 I 1 s danRer6.Zv8_scaffold3075 122874 84 - 281906 CA------AGAGGGCCAGGG----GGCTCCCTGGGGCCTATACTTCAAGTCCA-----GG--GAGA--AAG----GTGGACCCCTGGGTAGATTGCTGGGGTCAGAG-------- i danRer6.Zv8_scaffold3075 C 0 C 0 e calJac1.Contig6069 83752 1256 + 235769 I e oryCun2.chrUn0985 28519 407 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=218720.000000 s hg19.chr11_gl000202_random 19430 73 + 40103 GCCTGGAGGCTGGAAAGTTCGGGGTGTGCCCCGGGACTG-------GGGAGCAGGCAGGGATGGTGTGAAGTGGGTGTTG-- s panTro2.chr11 68206010 73 + 134204764 GCCTGGAGGCTGGAAAGTTCGGGGTGTGCCCCGGGACTG-------GGGAGCAGGCAGGGGTGGTGTGAAGTGGGTGTTG-- i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 49948 73 + 115376 GCCTGGAGGCTGGAAAGTTCGGGGTGTGCCCCGGGACTG-------GTGAGCAGGCAGGGGTGGTGCAAAGTGGGTGTTG-- i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126002269 73 - 132107971 GCCTGGAGGCTGGAAAGTTCGGAGTGTGCCCCGGGACTG-------GGGAGCAGGCAGGGGTGGTGCGAAGTGGATATTG-- i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128164072 73 - 133002572 GTCTGGAGGCTGGAAAGTTCGGGGTGTGCCCCGGGACTG-------GGGAGCAGGCAGGGGTGGTGCAAAGTGGGTATTG-- i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 80608 73 + 109049 GTCTGGAGGCTGGAAAGTTCGGGGTGTGCCCCGGGACTG-------GGGAGCAGGCAGGGGTGGTGCAAAGTGGGTATTG-- i papHam1.scaffold6638 C 0 C 0 s oryCun2.chrUn0985 28926 71 + 42081 GTCTGGGGGCTGGGAGGGTCCGGGTGTG--CCGAGGCTG-------GGGAGCAGGTGGGTGCGACAGGAAGCGGGTGCCG-- i oryCun2.chrUn0985 I 407 I 220 s turTru1.scaffold_93657 8506 71 - 12933 GCCCAGAGGCTGGAAAGTCCCCGGTGTGCCCAGGGGTTA-------AGGAACAGGGA--CGGGGCCAGAAGCAGGTGTCT-- i turTru1.scaffold_93657 I 1 C 0 s bosTau4.chr29 48980556 71 + 51998940 GCCCAGGGGC-AATAAGTCTCGGGTGTGCCCAGGGAGCA-------GGGAGCAGGGAG-TGGGGCCAGAAGCAGGTGTCT-- i bosTau4.chr29 I 1 C 0 s felCat3.scaffold_135390 62344 70 + 302526 GCCCAGAGGC---TGCATTCCGGGTGTGCCCAGGGCTTG-------GGGCGCGGGTGGGTGTGGCAGGAACTAGCTGCGG-- i felCat3.scaffold_135390 I 1 C 0 s canFam2.chr18 7540072 69 - 58872314 TTGCGGAGGT---CACG-ACAGACAGTGCCCAGCAATTG-------GGGCACAGGTGGGTGTGGCAGGAAGTAGGTGTGG-- i canFam2.chr18 I 1 C 0 s pteVam1.scaffold_22742 6661 62 - 9737 GCTGGAAAGT--------TCCAGATGTGTCCAGGGATTG-------GGGAGCAGACGGGCGAGGCAGGAAGTAGATG----- i pteVam1.scaffold_22742 I 1 C 0 s myoLuc1.scaffold_155660 40162 63 - 124081 GCTGGAAAGC--------TCTGGGCGGGCCCA-GGATTG-------GGGAGCGGGTGGCTGAGGCAGGAAGTAGGTGT-C-- i myoLuc1.scaffold_155660 I 1 C 0 s equCab2.chr12 28942510 63 + 33091231 GCTGGGAGT---------TCGGGGTGTGCCCAGGGATTA-------GGGAGCAGGAGGGTGTGGCAGGAAGTGCGTGT-C-- i equCab2.chr12 I 1 C 0 s danRer6.Zv8_scaffold3075 122958 80 - 281906 GCTCCTAGGT--GGAGGGTAAGGGGGCACCCTGGGGCCTCTACTGCAAGTCCAGGGAGAGACGTGGACCCCTGGGTGGCTTG i danRer6.Zv8_scaffold3075 C 0 C 0 e calJac1.Contig6069 83752 1256 + 235769 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=52048.000000 s hg19.chr11_gl000202_random 19503 42 + 40103 --GCATCTCTACACCCGCCCA-GGGCAGGACTCGG-------CTTGAGCCAC s papHam1.scaffold6638 80681 42 + 109049 --GCACCTCCACACCCACCCA-AGGCAGGACTCAG-------CTCGAGCTGC i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128164145 42 - 133002572 --GCACCCCCACACCCACCCA-AGGCAGGACTCGG-------CTCGAGCCGC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126002342 42 - 132107971 --GCATCTTTACACCCGCCCA-GGGCAGGACTCGG-------CTTGAGCCAT i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50021 42 + 115376 --GCATCTCTACACCCGCCCA-GGGCAGGACTCGG-------CTTGAGCCAC i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68206083 42 + 134204764 --GCATCTCTACACCCGCCCA-GGGCAGGACTCGG-------CTTAAGCCAC i panTro2.chr11 C 0 C 0 s turTru1.scaffold_93657 8577 44 - 12933 --GCATCGCTGTGCCCGCCTGAGAGCCGGACTAGGG------TTTGAGCAAT i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48980627 41 + 51998940 --GCGTTGCCCTGCCCGTCTGAGCG-TGGGCCAGG--------CTGAGTAGT i bosTau4.chr29 C 0 C 0 s felCat3.scaffold_135390 62414 44 + 302526 --GTGTCCCCACCTTGGCCTGAGAGCCAGACTCAGA------CTTGAGCAAT i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7540141 44 - 58872314 --GCGTCCCCACCCTGGCCTGAGAGCAAGACTCAGA------CTTGAGCAAT i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_22742 6723 25 - 9737 ---TGTCCCCACGCCTGCCCG------------------------GAGCAGC i pteVam1.scaffold_22742 C 0 C 0 s myoLuc1.scaffold_155660 40225 24 - 124081 --CTGTCCCCACGCC--CCTG------------------------GAGCAAT i myoLuc1.scaffold_155660 C 0 C 0 s equCab2.chr12 28942573 43 + 33091231 --GCGTCCCCACGCCCACCTGACATCAGGAC-CGGG------CTTGAGCAAT i equCab2.chr12 C 0 C 0 s danRer6.Zv8_scaffold3075 123038 47 - 281906 CTGGGGTCAGAGGCC--CCTAGGTGGAGGGCCAGGGGGTACCCTAGGGC--- i danRer6.Zv8_scaffold3075 C 0 C 0 e calJac1.Contig6069 83752 1256 + 235769 I e oryCun2.chrUn0985 28997 220 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=161582.000000 s hg19.chr11_gl000202_random 19545 83 + 40103 GCCTTCTGGATCAT-GGGGTGCGGAAAGTGGGGCCCTGCTGTCTGCGGGGTCGGCGTGGGGTATGTGCCTTTAGGAGAAGAT-GG s panTro2.chr11 68206125 83 + 134204764 GCCTTCTGGATCAT-GGGGTGCGGAAAGTGGGGCCCTGCTGTCTGCGGGGTCGGCGTGGGGTGTGTGCCTTTAGGAGAAGAT-GG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50063 83 + 115376 ACCTTCTGGATCAT-GGGGTGCGGAAAGTGGGGCCCTGCTGTCTGCGGGGTCGGCGTGGGGTATGTGCCTTTAGGAGAAGAT-GG i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126002384 84 - 132107971 GCCTTCTGGATCATGGGGGTGCGGAAAGCGGGGCCCTGCTCTCTGCGGGGTCAGCGTGGGATCTGTGCCTTTAGGAGAAAAT-GG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128164187 79 - 133002572 GCCTTCTGGATCATGGGGGTGCGGAAAGCGGGGCTGTGCTGTGCGCGGGGTGGGCGTGGGATCTGTGCCTTTAGGAGAA------ i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 80723 80 + 109049 GCCTTCTGGATCATGGGGGTGCAGAAAGCGGGGCCGTGCTGTGCGCGGGGTCGGTGTGGGATCTGTGCCTTTAGAAGA-----GG i papHam1.scaffold6638 C 0 C 0 s oryCun2.chrUn0985 29217 76 + 42081 GCCTCCTTGGGGGT-GGGGTGGGGGTTGGAGGACTCTACAGGGTGCCCAGGAGGTCTGGGACATGT-------TGAGGCCAT-GG i oryCun2.chrUn0985 I 220 C 0 s turTru1.scaffold_93657 8621 82 - 12933 CCTCTCCAGATGACGGGTGTGTGGAAAGCCGGCTCCTTATTTCCGCAGCCTCGGTTTGGGCACGGTGCCCTCCAGGGAGACT--- i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48980668 81 + 51998940 CCTTTCCGGATACTGGGTGTGTGCAATGCCGG-GCTTAATTTCCATGGGCTCGGTTTGGGCTCAGTGCATACTGGGGAGACT--- i bosTau4.chr29 C 0 C 0 s felCat3.scaffold_135390 62458 82 + 302526 TCTTTCCAGATAATGGGTGTGTAGAAAGCCGGGGCTTCATTCCCAAGGGCTCCGTTTGGGCTCCCAGCCCATCGGGAAGGAT--- i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7540185 82 - 58872314 TCTTTCCAGATAATGGGTGTGTGGAAAGCTGAATCTTTAATCCCAAGGGCTCAGTTTGGGCTCCCAGCCCATCAGGAAGATT--- i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_22742 6748 82 - 9737 TCTTTCCTGATAATGGACGTGTGGAAAGCTGGGCCTTCG-TTCCGAGGGCTTGGTTTGGGCTCGATGCCCATCGGGGAGGGTG-- i pteVam1.scaffold_22742 C 0 C 0 s myoLuc1.scaffold_155660 40249 79 - 124081 TCTTTCCAGAGAGTGGG-GTGTGGAAAGCTGGGTCTTCA-TCCCAAGGGCTTGGCGTGGGCTCGATGCCCATGGGGGAAG--G-- i myoLuc1.scaffold_155660 C 0 C 0 s equCab2.chr12 28942616 82 + 33091231 TCTTTCCAGGGAATGGGTGTGTGGAGAGCAGGGTCTTTCTTTCCAAGGGCTCGGTTT-GGCTTGACGCCCATGGGGGAAGATT-- i equCab2.chr12 C 0 C 0 s danRer6.Zv8_scaffold3075 123085 73 - 281906 GCCTACTGCAAGTCCAG---GTAGAGAGTTGGTCCC------CTGGGTAGCTTGCTGGGGTCAGAGGCAACTAGGTGGAGGG--- i danRer6.Zv8_scaffold3075 C 0 C 0 e calJac1.Contig6069 83752 1256 + 235769 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=-56877.000000 s hg19.chr11_gl000202_random 19628 46 + 40103 GAAAGTGACTCAT-GATGGGTGGCTCCGC-AGCTGC--------------CCCTT----CCAGGGA s equCab2.chr12 28942698 41 + 33091231 GAGGGTGACTCAC-GAAGGGCGGCACTGTCACCTGC--------------CCCCA----------A i equCab2.chr12 C 0 C 0 s myoLuc1.scaffold_155660 40328 41 - 124081 GAAGGCAATTCAT-GGTGAGTGGCACTGCCAGCTGC--------------CCTTG----------C i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 6830 26 - 9737 GGAGGTGGTTCGT-GGTGAGTGGCCCT--------------------------------------- i pteVam1.scaffold_22742 C 0 C 0 s canFam2.chr18 7540267 17 - 58872314 -AAAGTGATTCAC-GTG----------------TG------------------------------- i canFam2.chr18 C 0 C 0 s felCat3.scaffold_135390 62540 24 + 302526 -AAAGTGATTCAC-GTG----------------TGT--------------CCCCC----------A i felCat3.scaffold_135390 C 0 C 0 s bosTau4.chr29 48980749 38 + 51998940 GAAAGCAAAGCTC-CAG---CCACACCTCTAACTAT--------------CCCCT----------G i bosTau4.chr29 C 0 C 0 s turTru1.scaffold_93657 8703 38 - 12933 GACGGTAATACTC-CAG---CAGCACCTCTAACTGT--------------CCCCT----------G i turTru1.scaffold_93657 C 0 C 0 s oryCun2.chrUn0985 29293 44 + 42081 -----------------GGACAGCCAAGC-AGTAGCAAGTGGTGTCTAAACCTGT----CCCAGGC i oryCun2.chrUn0985 C 0 C 0 s otoGar1.scaffold_29804.1-1284 3 42 - 1284 GAAAGTGGCTCACAAGAGGGCATCTTCG------GC--------------CCCTG----GTCAGGA i otoGar1.scaffold_29804.1-1284 N 0 C 0 s panTro2.chr11 68206208 46 + 134204764 GAAAGTGACTCAT-GATGGGTGGCTCCGC-AGCTGC--------------CCCTT----CCAGGGA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50146 46 + 115376 GAAAGTGACTCAT-GATGGGTGGCTCCGC-AGCTGC--------------CCCTT----CCAGGGA i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126002468 46 - 132107971 GAAAGTGACTCGT-GATGGGTGGCTCCGC-AGCTGC--------------CCCTT----CCAGGGA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128164266 33 - 133002572 --------------GTTGGTTGGCTCCGC-AGCTGC--------------CCCTT----CCAGGGA i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 80803 39 + 109049 GAAAGT--------GATGGTTGGCTCCGT-GGCTGC--------------CCCTT----CCAGGGA i papHam1.scaffold6638 C 0 C 0 s danRer6.Zv8_scaffold3075 123158 39 - 281906 ------------C-CAGGGGGCACCCTGGGGCCTAT--------------CCTGCAAGTCCAGGGA i danRer6.Zv8_scaffold3075 C 0 I 23 e calJac1.Contig6069 83752 1256 + 235769 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=-54007.000000 s hg19.chr11_gl000202_random 19674 43 + 40103 CTC-------AGGCACCTCCCG---------------CTGTCACCATACCCC--TCCCTAC--T----TTCTC s papHam1.scaffold6638 80842 42 + 109049 CTC-------AGGCACCTCTCG----------------TGTCACCATCCTCC--TGCCCAC--T----TTCTC i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128164299 42 - 133002572 CTC-------AGGCACCTCTCA----------------TGTCGCCATCCTCC--TCCCCAC--T----TTCTC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126002514 43 - 132107971 CTC-------AGGCACCTCCCG---------------CTGTCACCATCCCTC--TCCCCAC--T----TTCTC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50192 43 + 115376 CTC-------AGGCACCTCCCG---------------CTGTCACCATACCCC--TCCCCAC--T----TTCTC i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68206254 43 + 134204764 CTC-------AGGCATCTCCCG---------------CTGTCACCATACCCC--TCCCCAC--T----TTCTC i panTro2.chr11 C 0 C 0 s otoGar1.scaffold_29804.1-1284 45 48 - 1284 CTC-------AG---CCTCCCACATG-----------CTGTCATCCACCCCCAGTCCCTACAGT----TCCTT i otoGar1.scaffold_29804.1-1284 C 0 C 0 s oryCun2.chrUn0985 29337 39 + 42081 CGT-------AGCCGCCAGCCG---------------CGACCTCCATTCTAT------GAC--C----GTGTC i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 8741 38 - 12933 CCC-------CGATGTCTCCTCCGCGTGGCCTCAT----------------------CAGC--T----GTCAC i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48980787 53 + 51998940 CCC-------CAGCG--TCCCCCTCGTGGTCTCATTGCGATCACCAC-------CCCCAAC--TCC--TTCTC i bosTau4.chr29 C 0 C 0 s felCat3.scaffold_135390 62564 22 + 302526 CCC-----------------------------------------------TA--CCCCCAC--CCGGCTTCTC i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7540284 17 - 58872314 ------------------------------------------------------CCCCCAC--CCTGCCTTTC i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_22742 6856 47 - 9737 ------------GTGTCTCCTGTGTGTGGCTCCCT---------CAT-CCCC--CCCAGAC--TCCATTTCTC i pteVam1.scaffold_22742 C 0 C 0 s myoLuc1.scaffold_155660 40369 57 - 124081 CCC-------AGGTGTCTCC--TGTGTGGTTTCCT--CAGCTGGCAT-CCTC--CCCTCAT--TCCATTTCTC i myoLuc1.scaffold_155660 C 0 C 0 s equCab2.chr12 28942739 64 + 33091231 CCCCCAGCCCCGGCCTCCCCTCCGTGTGGTCTCAA--TGGCTGTCAG---CA--GCCCCAC--TCCATTTCTC i equCab2.chr12 C 0 C 0 e danRer6.Zv8_scaffold3075 123197 23 - 281906 I e calJac1.Contig6069 83752 1256 + 235769 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=120524.000000 s hg19.chr11_gl000202_random 19717 162 + 40103 TACGTGGCTAAGGAGT--GGGG---------ATCT------CAGGCCAGCGGGGGGAGCCCAGGGC-------ACAG---CTCCAGCAGGG---CTG---GCCCCTCAG--A-----------------GCTTCCAG-GCTG--------------------------CAG------CAGGCAGGG--------------------------GTTGG-----AAGAGGTGAGAAGGAGCAGGGCAGTGAGTGTCCCAGGAAGCCCATTCCCGG--AACAG------ s equCab2.chr12 28942803 172 + 33091231 TGAGCAGCTGAG------G-GG---------GTCT------TAGGCCAGC--TGGTGGCTCAGGGA--------CAG---CTCC-----------GG---ACCCCTCAG--A-----------------GCTCCCAGAGCTG--------------------------CACAGCCCCCGGGAAGGGGAGCACCTGGCCCGGAGAAGCAGCA-AGTGG-----GGGACCTGGGAACTGGCTGAGA------TGTCTCAGGAAGCTGGCTCCAGG--AACAG------ i equCab2.chr12 C 0 C 0 s myoLuc1.scaffold_155660 40426 173 - 124081 TGAGTGGCCGAG------GGGG---------GTCT------CAGGCCAGC--TGGTGGCTCAGGGC-------ACAG---TTCT-----------TG---ACCCCTCAG--A-----------------GATCCTAAAG-CC--------------------------CATGGCCCCCAGGTAGGGGTGC-ACCGGCCCTGAG-CGCAGCAGGTGGA-----GGACCCTGAGGACCAGCAGAAT-----CCGGCCCAGG--AACAGACCTGGGAACCCGG------ i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 6903 169 - 9737 CAAGTGGCCAGA------GGGG---------ATCT-----------CAGC--TGCTGGCTCAGAAC-------ACAG---CTCC-----------TG---ACCCCTCGG--A-----------------GCTCTCAAAGTCC--------------------------CACGGCCTCCCAGCGGGTACCC-CCCAGCCCAGAGCCCCAGCAGCGGGG-----AGAACCTGAGGTCAGGCAGACC-----GTGGCCCAGGC-AACACTCCCAGT--CTCAG------ i pteVam1.scaffold_22742 C 0 C 0 s canFam2.chr18 7540301 154 - 58872314 TTGGTGACCAAG------GTGG---------GTTT------TAGGCCAGC--TGGTGGCTCAGGGC--------TTA---CTCC-----------TG---ACTTGTCGG--G-----------------GCTCCCAGAGCTG--------------------------TGAGGCCCCCAGGCAGGGGT-----TGG----------------GGGGC-----AGGACCTGAGCACCAGCACAGT-----GTGGTCCAGGAGACCTGCTCCAGG--AATAG------ i canFam2.chr18 C 0 C 0 s felCat3.scaffold_135390 62586 128 + 302526 TTGCTGGTCGAG------GTGG---------CTCT------TCGGCCAGC--CAGCGGCTCAGGAC--------TTA---CTCC-----------TG---GCCCCTCGG--G-----------------GCTCCCAGAGCGC--------------------------TGTGGCCCCCAGGCAGGGGTT--GCTGG----------------GGGTG-----GGGACCCGAAGACCGGCACAGT------------------------------------------ i felCat3.scaffold_135390 C 0 C 0 s bosTau4.chr29 48980840 151 + 51998940 CAAGAGCCCGA--------GGG---------GTCT------CAGGGCAGC--GGCTGGCTCCGGGC-------ACAG---CTCC-----------TG---GCCTC-CAG--G-----------------GCACCCAGAGCCG--------------------------CACGGGCTCCAGGCAGGGG-------AG----------------GTGGA--CCTGAGACACAAGAGCAGGCAGAGC-----GCGCCCTGAAAC--CCACTCCAGC--CACAG------ i bosTau4.chr29 C 0 C 0 s turTru1.scaffold_93657 8779 150 - 12933 CGAG---------------GTG---------GCCT------CAAGCCAGC--TGCTGGCTCTGGGC-------ACAG---CTCC-----------TG---GACTCTCAG--G-----------------GCGCCCAGAGCTG--------------------------CACGGCCTCCAGGTAGAAG------CAG----------------GTGGAGGCCTGGGACCTGAGAACAGACAGAGC-----GTGTCCCCAAACATCTGCTCTAGG--AACAG------ i turTru1.scaffold_93657 C 0 C 0 s oryCun2.chrUn0985 29376 156 + 42081 CAAGGGGCT-----GC--AGGC---------------------AGCCAGT------GGCTCA-GGC-------ATGG---CACCTGC--------TG---ACCCCTGGG--A-----------------GCCTCTGG-GTAGAGGGCGGCGCGCCCTTCCCCCACCCCCAG------C-GGCAGCA--------------------------GGTGG-----AGGGCGGGAGAGCAGGCAGGAAGG--------CCAGGAAGCCCATTCCGGG--AACCG------ i oryCun2.chrUn0985 C 0 C 0 s otoGar1.scaffold_29804.1-1284 93 164 - 1284 TAAGTAGCTGA-------GAGG---------GTCT------CCGGCCAGC--TGGTGGCTCAGGGC-------ACAGCACCTCCATGTGGG---CTTCTCACCCCACAG--AGGATCTGAAGTTGAGTGGCCTCCAG-GCAG--------------------------CAT------CGAGCAGGG--------------------------GC------------AGCGAGAATGGGCAG-------AGAGACCCAGAAAGCCAGTTTCCAG--AACAG------ i otoGar1.scaffold_29804.1-1284 C 0 C 0 s panTro2.chr11 68206297 162 + 134204764 TACGTGGCTAAGGAGT--GGGG---------ATCT------CAGGCCAGCGGGGGGAACCCAGGGC-------ACAG---CTCCAGCAGGG---CTG---GCCCCTCAG--A-----------------GCTTCCAG-GCTG--------------------------CAG------CAGGCAGGG--------------------------GTTGG-----AAGAGGTGAGAAGGAGCAGGGCAGTGAGTGTCCCAGGAAGCCCATTCCCGG--AACAG------ i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50235 161 + 115376 TACGTGGCTAAGGAGT--GGGG---------GTCT------CAGGCCAGT-GGGGGAGCCCAGGGC-------ACAG---CTCCAGCAGGG---CTG---CCCCCTCAG--A-----------------GCTTCCAG-GCTG--------------------------CAG------CAGGCAGGG--------------------------GTTGG-----AGGAGGTGAGAAGGAGCAGGGCAGTGAGTGTCCCAGGAAGCCCATTCCCGG--AACAG------ i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126002557 162 - 132107971 TAAGTGGCTAAGGAGCGGGGGG---------GTCT------CAGGCCAGC--GGGGATCCCAGGGC-------ACAG---CTCCAGCAGGG---CTG---GCCCCTCAG--A-----------------GCTTCCAG-GCTG--------------------------CAG------CAGGCGGGG--------------------------GCTGG-----AGGAGGTGAGAAGGAGCAGGGCAGTAAATGTCCCAGGAAGCCCATTCCCGG--AACAG------ i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128164341 170 - 133002572 TAAGTGGCTAAAGAGC--AGGGGTGGGGAGTGTCT------CAGGCCAGT-GTGGGGGCCCAGGGC-------ACAG---CTCCAGCGGGA---ATG---GACCCTCAG--A-----------------GCCTCCAG-GCTG--------------------------CAG------CAGGCAAGG--------------------------CTTGG-----AGGAGGTGAGAAGGAGCAGGGTAACGAACGTCCCAGCAAGCCCACTCCCGG--AACAG------ i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 80884 170 + 109049 TAAGTGGCTAAAGAGC--AGGGGTGGGGAGTGTCT------CAGGCCAGT-GTGGGGGCCCAGGGC-------ACAG---CTCCAGCGGGA---ATG---GACCCTCAG--A-----------------GCCTCCAG-GCTG--------------------------CAG------CAGGCAAGA--------------------------CTTGG-----AGGAGGTGAGAAGGAGCAGGGTAACGAACGTCCCAGGAAGCCCATTCCCGG--AACAG------ i papHam1.scaffold6638 C 0 C 0 s danRer6.Zv8_scaffold3075 123220 164 - 281906 TGCTTGGCTGAG------AGTG---------GCCTAGGTGGAGGGCCAAT--GGGCACCCTAGGGCCTCTACTGCAA---GTCCAGGGAGAGTTGTG---GACCCTTGGGTA-----------------ACTTGCGG-GGGT--------------------------CAGAGGCCCCTG--------------------------------GGTGG-----AGGGCAAGGGG----------------GAACCCTGGGGACTCTACTGCAAG--TCCAGGGGGAG i danRer6.Zv8_scaffold3075 I 23 C 0 e calJac1.Contig6069 83752 1256 + 235769 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=318269.000000 s hg19.chr11_gl000202_random 19879 116 + 40103 -----CGTCCTTGGGTTGGTT-CTGGGAACTGGG---GACA-CCAGGAAG---GCCCAGGGGAG---TGGG-GCTGCT--------------GGGAATGG-----CCTGGGGGAGGCCACGAGGT-------GGGTCA---GGGGTGG--AGCTG--------------------------GG-----TGTT-CTG s papHam1.scaffold6638 81054 116 + 109049 -----CGTCCTTGGGTTGGTT-CTGGGAACTGGG---GACA-CCAGGAAG---GCCCAGGGGAG---TGAG-GCTGCT--------------GGGAATGG-----CCTGGGGGAGGCCGCGAGGT-------GGGTCA---GGGGTGG--AACTG--------------------------GG-----TGTT-CTG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128164511 115 - 133002572 -----CGTCCTTGGGCTGGTT-CTGGGAACTGGG---GACA-CCAGGAA----GCCCAGGGGAG---TGAG-GCTGCT--------------GGGAATGG-----CCTGGGGGAGGCCGCGAGGT-------GGGTCA---GGGGTGG--AACTG--------------------------GG-----TGTT-CTC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126002719 116 - 132107971 -----CGTCCTTGGGTTGGTT-CTGGGAACTGGG---GACA-CCAGGAAG---GCCCAGGGGAG---CGGG-GCTGCT--------------GGGAATGG-----CCTGGGGGAGGCCACGAGGT-------GGGTCA---GGGGTGG--AGCTG--------------------------GG-----TGTT-CTG i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50396 116 + 115376 -----CGTCCTTGGGTTGGTT-CTGGGAACTGGG---GACA-CCAGGAAG---GCCCAGGGGAG---TGGG-GCTGCT--------------GGGAATGG-----CCTAGGGGAGGCCACGAGGT-------GGGTCA---GGGGTGG--AGCTG--------------------------GG-----TGTT-CTG i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68206459 116 + 134204764 -----CGTCCTTGGGTTGGTT-CTGGGAACTGGG---GACA-CCAGGAAG---GCCCAGGGGAG---TGGG-GCTGCT--------------GGGAATGG-----CCTGGGGGAGGCCATGAGGT-------GGGTCA---GGGGTGG--AGCTG--------------------------GG-----TGTT-CTG i panTro2.chr11 C 0 C 0 s otoGar1.scaffold_29804.1-1284 257 106 - 1284 -----CATCCTTGGACCGGTT-CTGGGGA-TCAG---GACA-CCAGGAA----GCCCAGGGGAA---TGAG-GTTGCT--------------GGGAATGG-----CCTA-GGGTGGCCA---------------GTGG---AAGGCAG--AGCTG--------------------------GG-----TGCTACTG i otoGar1.scaffold_29804.1-1284 C 0 C 0 s oryCun2.chrUn0985 29532 122 + 42081 -----CCTCCTTGGGTGACTT-CTGGGAACCTGG---GACC-CCAGGAAG---GCCCCGAGGGA---TGGACGCTTCC--------------AAGAACGG-----CCCAGGGGTGAAAGCGGGGG-------TGGCGG---AGCGGGG--AGCGG--------------------------GGGCCCCAGTC-CCA i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 8929 104 - 12933 -----CATTCTCGGGTTGGTT-CTGGGAACTTAC---CACT-CCAGAA-----GGCCCAGGGGA-CCCAAG-GCTGCT--------------GGGCATGG-----CCTGGGGGAGGTAGAAGGTG-------GAGCTG-------------------------------------------GG-----TGCC-CTG i turTru1.scaffold_93657 C 0 I 24 s bosTau4.chr29 48980991 104 + 51998940 -----CGTTCTTGGGCTGGTG-CTGGGACCTCGG---GACC-CCAGAA-----GGTCCAGGGGA-CCCGAG-GCTGCT--------------GGGAATGG-----CCTGGGGGAGGCGCAGGGTG-------GCGCTG-------------------------------------------GG-----CGAC-CTC i bosTau4.chr29 C 0 I 24 s felCat3.scaffold_135390 62714 103 + 302526 ------ATCCTGGGGTTGGTT-CGGGGAACTCGG---GGTG-CCCAAA-----GACCAGGGGGA-CCTGAG-GCTCCT--------------AGGGATGG-----CCCGGGGGTGGCAGAGGGCA-------GAGTAG-------------------------------------------GG-----AGTC-CTA i felCat3.scaffold_135390 C 0 I 17 s canFam2.chr18 7540455 110 - 58872314 -----CATCCTTGGGTTGGTT-CTGGGAACTC-G---GCCA-CCCAAA-----GCCCA-GGGCA-CCTGAG-GACACT--------------GAGAATGG-----CCTGGGGGAGGCCGAGAGTG-------GGGAAGTG---GGCAG--------------------------------CAG-----AGGC-CCA i canFam2.chr18 C 0 I 37 s pteVam1.scaffold_22742 7072 126 - 9737 -----CTCCCTTGGGCTGGTT-CTGGGAACTGGG---GACA-CAGAAG-----GCCCAGGGGAA-CCCAAG-GCCCCT--------------GGGGGTGG-----CCTGTGGGGAGCAGAGAGTGGAGAGGAGGGCGGTGGAAGGTGG--AGCTG--------------------------GG-----CGCC-CCG i pteVam1.scaffold_22742 C 0 C 0 s myoLuc1.scaffold_155660 40599 119 - 124081 -----CATTCTTGGGTTGGTT-CTGGAAAC-GTG---GACACCAGAAG-----GCCCAGGAGGA-CCCAAG-GCTGCT--------------GGGAATGA-----CGTGTGGGAGTCAGAGAGCT-------GGGCAGTGGAAGGCAG--AGCTG--------------------------GG-----TGCT-CTG i myoLuc1.scaffold_155660 C 0 I 343 s equCab2.chr12 28942975 132 + 33091231 -----CATCTTTGAGCT--------GAAACTTGG---GACA-CCAGGA-----G-----GGGGA-CCCGAG-GCTGCT--------------GGAAATGG-----CCTGGGGAAGGCTGGAAGTG-------GGGAGCTGG-TGGCAG--AGGGTGGCTCCGGCCCAGCACCTTCTCTGCCAG-----AGGC-CCC i equCab2.chr12 C 0 I 30 s ornAna1.Contig19813 12914 117 - 18815 -----CTTTCCTGCCCTGGTT-CCTTCAGCCTGGCCTAACT-CACGCAGG---GGCTGGGGAAC---CTGG-GTGCCC--------------CGGGGCGG-----CCTGGCGGGGGTCGCGGAAG-------GGGTCT--GGATGTCT--AGCTG--------------------------GG-----AGGA---- i ornAna1.Contig19813 N 0 C 0 s tarSyr1.scaffold_429723 0 93 - 1268 -------------------TT-CTGGGAACTTGT---GACT-CCAGGATG---GCCCAGGAGC----TGGC-GCTGCT--------------GGGAATGG-----CCCAGGGGTGG---GGGGAT-------GGGACT---GGGGCGG--GG--G--------------------------GG-----AGTT---- i tarSyr1.scaffold_429723 N 0 C 0 s danRer6.Zv8_scaffold3075 123384 146 - 281906 ATGTGGACCCCTGGGTAGCTTGCTGGGGTCAGAG---GCCC-CTAGGTGGAGAGCCAGGGGGCACCCTGGG-ACCTCTACTGCAAGTCCAGAGAGAGTGGTGGTCCCCTGGGCAGCTTGCTG----------GGGTCA---GAAGCAACTAGGTG--------------------------GA-----AGGC-CAG i danRer6.Zv8_scaffold3075 C 0 C 0 e calJac1.Contig6069 83752 1256 + 235769 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=-27673.000000 s hg19.chr11_gl000202_random 19995 13 + 40103 GGC----GGGCCTTTGA s panTro2.chr11 68206575 13 + 134204764 GGC----GGGCCTTTGA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50512 13 + 115376 GGC----GGGCCTTTGA i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126002835 13 - 132107971 GGC----TGGCCCCTGA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128164626 13 - 133002572 AGA----GGGCCCCTGA i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 81170 13 + 109049 GGA----GGGCCACTGA i papHam1.scaffold6638 C 0 C 0 s tarSyr1.scaffold_429723 93 9 - 1268 --------GGGGTCTGA i tarSyr1.scaffold_429723 C 0 C 0 s otoGar1.scaffold_29804.1-1284 363 17 - 1284 TGTTCTGGGTCCCCTGG i otoGar1.scaffold_29804.1-1284 C 0 C 0 s oryCun2.chrUn0985 29654 11 + 42081 GCC----TGCCCGTT-- i oryCun2.chrUn0985 C 0 I 14 s turTru1.scaffold_93657 9057 13 - 12933 ----AAGAGGCCTCTGG i turTru1.scaffold_93657 I 24 I 8 s bosTau4.chr29 48981119 13 + 51998940 ----GAGAAGCCTCTGG i bosTau4.chr29 I 24 I 8 s canFam2.chr18 7540602 6 - 58872314 ----CACAGG------- i canFam2.chr18 I 37 I 7 s felCat3.scaffold_135390 62834 13 + 302526 ----CATAGGGCTCTGG i felCat3.scaffold_135390 I 17 I 8 s equCab2.chr12 28943137 13 + 33091231 ----CACAGGGCTCTGG i equCab2.chr12 I 30 I 7 s ornAna1.Contig19813 13031 9 - 18815 -----TGCGGTCTT--- i ornAna1.Contig19813 C 0 C 0 s danRer6.Zv8_scaffold3075 123530 12 - 281906 -----GGGGCACCCTGG i danRer6.Zv8_scaffold3075 C 0 C 0 e pteVam1.scaffold_22742 7198 0 - 9737 C e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=-55670.000000 s hg19.chr11_gl000202_random 20008 38 + 40103 AGCCCACTGGC---------CTTCAATGCCGGGC---------------AAGCGGGAA--------GGAA- s panTro2.chr11 68206588 38 + 134204764 AGCCCACTGGC---------CTTCAATACCGGGC---------------AAGTGGGAA--------GGAA- i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50525 38 + 115376 AGCCCACTGGC---------CTTCAGTGCCGGGC---------------AAGCGGGAA--------GGAA- i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126002848 38 - 132107971 AGCCCACTGGC---------CTTCAGTGCTGGAC---------------AAGCGGGAA--------GGAA- i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128164639 38 - 133002572 AGCCCACTGGC---------CTTCAGTGCCGGGC---------------AAGCAGGAA--------GGAA- i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 81183 38 + 109049 AGCCCACTGGC---------CTTCAGTGCCGGGC---------------AAGCAGGAA--------GGAA- i papHam1.scaffold6638 C 0 C 0 s tarSyr1.scaffold_429723 102 38 - 1268 AGCCCCCCCAC---------AGGGAGCACGGAGA---------------CGGCAGGGA--------GGAA- i tarSyr1.scaffold_429723 C 0 C 0 s otoGar1.scaffold_29804.1-1284 380 27 - 1284 GTCCCACTGGC---------CCTGAG------------------------AGCAGGCA--------G--A- i otoGar1.scaffold_29804.1-1284 C 0 C 0 s oryCun2.chrUn0985 29679 47 + 42081 GACTGCCCAGCGGTCTGGTTCCCCACGCCAGCGT---------------CAGCGAGAG--------CTGG- i oryCun2.chrUn0985 I 14 C 0 s ochPri2.scaffold_12461 23502 35 - 40248 AGCCAACCAG----------CCCCAGATCAGTG-----------------GGTGGGAG--------AGGA- i ochPri2.scaffold_12461 N 0 C 0 s turTru1.scaffold_93657 9078 61 - 12933 GGGCACCTGGA---------CTGAGGTCCCACAGGGATGTGAACGccctgaccctgaccttgaccctgac- i turTru1.scaffold_93657 I 8 C 0 s bosTau4.chr29 48981140 44 + 51998940 GGGCACCTGGA---------CTGAGGTCCCACAGGG-------------GATCCGGGC----ACCTGGAC- i bosTau4.chr29 I 8 C 0 s canFam2.chr18 7540615 35 - 58872314 AGCCCTGCTGG---------TCTATGTGCTGGAAGA-------------CA-----GA--------TAAA- i canFam2.chr18 I 7 C 0 s felCat3.scaffold_135390 62855 35 + 302526 AGCCCTGCTGA---------CCTGTGTTCTGGAAGA-------------CA-----GG--------AAAA- i felCat3.scaffold_135390 I 8 C 0 s equCab2.chr12 28943157 40 + 33091231 AGGCCCCCTGG---------CCTTGAGCACTGAAGA-------------CAGCAGGGG--------GGAA- i equCab2.chr12 I 7 C 0 s pteVam1.scaffold_22742 7198 39 - 9737 -ACCCCGTGGT---------TTTGAGCGCTGAGAGG-------------CAGCCGGGA--------GGAA- i pteVam1.scaffold_22742 C 0 C 0 s ornAna1.Contig19813 13040 35 - 18815 ---CCCTTCCC---------CGGCAGTGCTAGGA---------------GTGTGGGTA--------GAAA- i ornAna1.Contig19813 C 0 N 0 s danRer6.Zv8_scaffold3075 123542 31 - 281906 --------GGC---------CTCTGATGCAAGTC---------------CAGGGAGAG--------AGGTG i danRer6.Zv8_scaffold3075 C 0 C 0 e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=-45766.000000 s hg19.chr11_gl000202_random 20046 16 + 40103 A-CCCACAGGA------GCT--------------AGG s panTro2.chr11 68206626 16 + 134204764 A-CCCACAGGA------GCT--------------AGG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50563 16 + 115376 A-CCCACAGGA------GCT--------------AGG i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126002886 16 - 132107971 A-CCCACAGGA------GCT--------------GGG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128164677 16 - 133002572 A-CCCACAGTA------ACC--------------ACC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 81221 17 + 109049 ACCCCGCAGGA------ACC--------------ACC i papHam1.scaffold6638 C 0 C 0 s tarSyr1.scaffold_429723 140 15 - 1268 G-CCCA-AGAG------GCT--------------GGG i tarSyr1.scaffold_429723 C 0 I 19 s otoGar1.scaffold_29804.1-1284 407 9 - 1284 T-GCCACTAG--------------------------- i otoGar1.scaffold_29804.1-1284 C 0 C 0 s oryCun2.chrUn0985 29726 10 + 42081 G-CCGTCAGAG-------------------------- i oryCun2.chrUn0985 C 0 C 0 s ochPri2.scaffold_12461 23537 16 - 40248 A-CCTTCAGGA------GCT--------------AGA i ochPri2.scaffold_12461 C 0 C 0 s turTru1.scaffold_93657 9139 24 - 12933 c-ctgaccctg------aGC------GGGGTTGTGTA i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48981184 30 + 51998940 C-CCGACCTTG------AACCTGAGCGGGGTTGTGTG i bosTau4.chr29 C 0 C 0 s canFam2.chr18 7540650 16 - 58872314 A-CCCACAAAG------ACC--------------ATG i canFam2.chr18 C 0 C 0 s felCat3.scaffold_135390 62890 16 + 302526 A-CCCACAAAT------ACC--------------ATG i felCat3.scaffold_135390 C 0 C 0 s equCab2.chr12 28943197 15 + 33091231 A-GCCACAAAG------G-C--------------GTG i equCab2.chr12 C 0 C 0 s pteVam1.scaffold_22742 7237 16 - 9737 C-CCCGCCAAT------GCC--------------GTG i pteVam1.scaffold_22742 C 0 C 0 s danRer6.Zv8_scaffold3075 123573 22 - 281906 G-ACCACTGGGTAGCTTGCT--------------GGG i danRer6.Zv8_scaffold3075 C 0 C 0 e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=-15354.000000 s hg19.chr11_gl000202_random 20062 32 + 40103 -------GTTCCT----------CCAGCTGGGACCCAGCTCCCC----TTGCC s panTro2.chr11 68206642 32 + 134204764 -------GTTCCT----------CCAGCTGGGACCCAGCTCCCC----TTGCC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50579 32 + 115376 -------GTTCCT----------CCAGCTGGGACCCGGCTCCCC----TTGCC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126002902 32 - 132107971 -------GTTACT----------CCAGCTGGGACCCGGCTCCCC----TTGCC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128164693 32 - 133002572 -------GTTCCT----------CCAGCTGGGACCCGGCTCCCC----TTGCC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 81238 32 + 109049 -------ACTCCT----------CCAGCTGGGACCCGGCTCCCC----TTGCC i papHam1.scaffold6638 C 0 C 0 s otoGar1.scaffold_29804.1-1284 416 16 - 1284 -------GCTCCC----------CCAGCTGAGA-------------------- i otoGar1.scaffold_29804.1-1284 C 0 C 0 s oryCun2.chrUn0985 29736 19 + 42081 --------------------------GCCGGTACTCAGCAGCCG----T---- i oryCun2.chrUn0985 C 0 C 0 s ochPri2.scaffold_12461 23553 32 - 40248 -------GCCCCT----------CCTGCTGGCACCCCACGCCCC----CCCCC i ochPri2.scaffold_12461 C 0 I 7384 s turTru1.scaffold_93657 9163 27 - 12933 -------GTTCCT---------GGTGGCCAGA-ACCTGCTCCTC--------- i turTru1.scaffold_93657 C 0 I 7 s bosTau4.chr29 48981214 19 + 51998940 -------GCTCCT---------GGTGCCCA---------TCCCC--------- i bosTau4.chr29 C 0 I 7 s canFam2.chr18 7540666 37 - 58872314 -------GTTCCT---------GACCACTAGAAACCAGCTCCCCTGCACTGCC i canFam2.chr18 C 0 I 10 s felCat3.scaffold_135390 62906 31 + 302526 -------GTTCCC---------GGCCATTAGGAACCAGCTCCTC------ACC i felCat3.scaffold_135390 C 0 I 6 s equCab2.chr12 28943212 27 + 33091231 -------GTGCCT---------GGTGGCCAGG-CCCAGCTCCCC--------- i equCab2.chr12 C 0 I 10 s pteVam1.scaffold_22742 7253 22 - 9737 -------GTTCCC---------GG------GGACCCTAGTGCGA--------- i pteVam1.scaffold_22742 C 0 I 6 s danRer6.Zv8_scaffold3075 123595 42 - 281906 GTAAGAAGGCCCTAGGTGGAGAGCCAGGGGGCACCCTGGGGA----------- i danRer6.Zv8_scaffold3075 C 0 C 0 e tarSyr1.scaffold_429723 155 19 - 1268 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=93848.000000 s hg19.chr11_gl000202_random 20094 94 + 40103 CCACACTAGCAAGTG-CTGAGGAGGACGGAGGTCCTGGGG------------------GT-----GCT-CTGTGGGAATTTAGG-----------------CTGGGCAGGtgttacagg--ctgaatttcacccaccc s panTro2.chr11 68206674 94 + 134204764 CCACACTAGCAAGTG-CTGAGGAGGACGGAGGTCCTGGGG------------------GT-----GCT-CTGTGGGAATTTAGG-----------------CTGGGCAGGtgttacagg--ctgaatttcacccaccc i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50611 94 + 115376 CCACACTAGCAAGTG-CTGAGGAGGACGGAGGTCCTAGGG------------------GT-----GCT-CTGTGGGAATTTAGG-----------------CTGGGCAGGtgttacagg--ctgaatttcacccaccc i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126002934 94 - 132107971 CCACACTAGCAAGTG-CTGGGGAGGATGGAGGTCCTGGGG------------------AT-----GCT-CTGTGGGATTTTAGC-----------------CTGGGCAGGtgttacagg--ctgaatttcacccaccc i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128164725 94 - 133002572 CCGCGTGAGCAAGTG-CTGGGGAGAACGGAGGTCCCAGGG------------------GT-----GCT-CTGTGGGATTTTAGC-----------------CTGGGCAGGtgttacggg--ctgaatttcacccaccc i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 81270 94 + 109049 CCGCGTGAGCAAGTG-CTGGGGAGAACGGAGGTCCCAGGG------------------GT-----GCT-CTGTGGGATTTTAGC-----------------CTGGGCAGGtgttacagg--ctgaatttcacccaccc i papHam1.scaffold6638 C 0 C 0 s otoGar1.scaffold_29804.1-1284 432 44 - 1284 -------------------------------------------------------------------------GGGACTTTAGC-----------------CCCAGCAGGtgtcatggg--ctgaattgtgtc--ccc i otoGar1.scaffold_29804.1-1284 C 0 C 0 s oryCun2.chrUn0985 29755 109 + 42081 --------GTGGGCG-CTGAG--GGACCTGGCCCCCGGGT------------------GTCACGGGCTGCTGAGCACACACAGGGCCGGATCGGCACCTCTCTGAGTAGGGGCTCCAAGGCCCGAGTTCTGCACCCCC i oryCun2.chrUn0985 C 0 I 170 s turTru1.scaffold_93657 9197 110 - 12933 CCGTGTGAGGGGGCGTCGGAGGGCAACAGAGGGTCAGGGTTCCCAGCGGCCCCTTTCCAC-----GCT-AAGAGGGATTTTAGC-----------------GTCTGCAGAtgtt-atgg--ttgaaatgtg-tcccc- i turTru1.scaffold_93657 I 7 C 0 s bosTau4.chr29 48981240 111 + 51998940 CTGTGTGAGGGGACGTCAGAGGGCAACAGAGGGTCAGGGTTCTCAGAGGCCGCTTTCCAC-----ACC-AAGAGGGATTGTAGC-----------------TTCTCCAGGTGAC-ACgg--ctgaattgtgttcccc- i bosTau4.chr29 I 7 C 0 s canFam2.chr18 7540713 89 - 58872314 TCAGGGTAAGCAGAGTCAGGAGACTGCA----GTCTG------------------GTCAC-----GCT-AAGAGGGATTTTAGC-----------------CTCAGCAGGCATT-Agag--ttgaactgcatccccc- i canFam2.chr18 I 10 C 0 s felCat3.scaffold_135390 62943 98 + 302526 TCTGGGTAAGCAGAGTCAGGGAACCCCAAAGGGTCTGTCC-------------TTTTCAG-----GCT-TAGAGGGATTTCAGC-----------------CTCAGCAGGtgtt-agag--ttgaattgtgtccccc- i felCat3.scaffold_135390 I 6 C 0 s equCab2.chr12 28943249 96 + 33091231 CCATGTGAGCCAGCGTCAGGGAAGCACAGAGGGTCGGGGC---------------TTCGT-----GCT-AAGAGGCATTTTAGC-----------------CTCCGTAGAtgttccggg--ctgaactgtgttctc-- i equCab2.chr12 I 10 C 0 s pteVam1.scaffold_22742 7281 94 - 9737 TCAGGGTAACAGAGGATGGGGTTCCCCAGGGCCTCCG------------------CTCAT-----GCT-AGAAGGAATTCGAGC-----------------CTCAGCAAACgttaggag--ttgaattgtgtccccc- i pteVam1.scaffold_22742 I 6 C 0 s danRer6.Zv8_scaffold3075 123637 86 - 281906 -CTCTACTGCAAGTC-CAGGGAAAGACGTAGACCCTGGGT-------------------A-----GCT-TGCTGGGGTCTTAGG-----------------CCCC-TAGGTGG--AGGG--CCAAGTTGCACCCT--- i danRer6.Zv8_scaffold3075 C 0 C 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=234709.000000 s hg19.chr11_gl000202_random 20188 98 + 40103 gagccccatgttcatatgctg-aagtccta-acgcca-----g-gactcagaacgtgaccctgttgggacacaggagcgttgcggatgtgattagtgaagatga-------gg s otoGar1.scaffold_29804.1-1284 476 100 - 1284 atcccc----ttggtgtgctg-tgggcctacactgca-----gtgcctcagaacgtggccctgtttgga---agggtcattgcagatgtgcttagttatgatgagggcaatgg i otoGar1.scaffold_29804.1-1284 C 0 C 0 s papHam1.scaffold6638 81364 98 + 109049 acgccccatgttcatatgctg-aagtcgta-acccca-----g-gactcagaacgtgaccctgtttggaaataggagcgttgcagatgtgattagtgaagatga-------gg i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128164819 98 - 133002572 acgccccatgttcatatgctg-aagtcata-acccca-----g-gactcagaacgtgaccctgtttggaaataggagcgttgcagatgtgattagtgaagatga-------gg i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126003028 98 - 132107971 aagccccgtgttcatatgctg-aagtccta-acccca-----g-gactcagaatgtgaccctgtttggacacaggagcgttgcggatgtgattagtgaagatga-------gg i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50705 98 + 115376 gagccccatgttcatgtgctg-aagtccta-acgcca-----g-gactcagaacgtgaccctgttgggacacaggagcgttgcggatgtgattagtgaagatga-------gg i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68206768 98 + 134204764 gagccccatgttcatatgctg-aagtccta-acgcca-----g-gactcagaacgtgaccctgttgggacacaggagcgttgcggatgtgattagtgaagatga-------gg i panTro2.chr11 C 0 C 0 s turTru1.scaffold_93657 9307 89 - 12933 acaacccacaaccccac------------a-acccccat---t-acctcagaatatgaccttatttggaaatagggtcattgcagatgtaattagctaagatga-------gg i turTru1.scaffold_93657 C 0 I 8 s bosTau4.chr29 48981351 95 + 51998940 tcaccccagattcatactcta-aagtcctg-agccccat---c-acctcacaacacaggcttatttagaaactgggtcattacagacgtgattagtta-----c-------gg i bosTau4.chr29 C 0 I 8 s canFam2.chr18 7540802 99 - 58872314 acaccttagatattt-tgttt-aagtccta-gcacccag---g-accccagaatgtgaccttatttggaaataggctgattacagatgtgattggttaagaaga-------gg i canFam2.chr18 C 0 I 1118 s felCat3.scaffold_135390 63041 99 + 302526 aaacgttggattcgt-tgtca-aagtccta-gcactcta---g-accccagaatggggacatatttgggaacagggaggctggagacgtgattggttaaggaga-------gg i felCat3.scaffold_135390 C 0 I 8 s equCab2.chr12 28943345 96 + 33091231 ------tcaattcgtatgctg-aattcctg-acactcaga-aa-acctcagaacgctaccttatttggagacggggtctctgcccatgcgattagttaagacga-------gg i equCab2.chr12 C 0 I 8 s pteVam1.scaffold_22742 7375 91 - 9737 aaaccccaaattcctacgttg-aagtcct-------------g-ttctctgaatatagccttatttggaggcagggtcactgcaggtacgattagttaagatga-------cg i pteVam1.scaffold_22742 C 0 I 8 s danRer6.Zv8_scaffold3075 123723 76 - 281906 --------GGGGCCTATGCTTCAAGTCCAG-GGAGAGAGGTGG-ACCCCTGGGT---AGCTTGCTGGGG------------TCAGAGGCAACTAGGTGGAG------------ i danRer6.Zv8_scaffold3075 C 0 C 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e oryCun2.chrUn0985 29864 170 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=87422.000000 s hg19.chr11_gl000202_random 20286 40 + 40103 gagcagggtggcccc------tgatccgatc-tgtctggggttcttc s otoGar1.scaffold_29804.1-1284 576 37 - 1284 gagcaaggtgggcct------ccctccaacc-tgacaggga---tcc i otoGar1.scaffold_29804.1-1284 C 0 C 0 s papHam1.scaffold6638 81462 40 + 109049 gaacagggtggcccc------tcatctgatc-tgcctggggttcttc i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128164917 40 - 133002572 gaacagggtggcccc------tcatctgatc-tgcctggggttcttc i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126003126 36 - 132107971 gagcagggtggcccc-------gatcctatc-tgtctgggg---ttc i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50803 39 + 115376 gagcagggtggcccc-------gatccgatc-tgtctggggttcttc i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68206866 40 + 134204764 gagcagggtggcccc------tgatccgatc-tgtctggggttcttc i panTro2.chr11 C 0 C 0 s turTru1.scaffold_93657 9404 40 - 12933 gggcatggtggcccc------taagccaata-tgagtggtgtcctta i turTru1.scaffold_93657 I 8 C 0 s bosTau4.chr29 48981454 40 + 51998940 gggtagggtggcccc------caatccactg-tgactggcatcctgg i bosTau4.chr29 I 8 C 0 s equCab2.chr12 28943449 40 + 33091231 gagtggggtgggccg------tggtccaaca-tgactggtgtcctta i equCab2.chr12 I 8 C 0 s felCat3.scaffold_135390 63148 39 + 302526 gagtaaggtgggcc-------taatccaatg-tgacctgtgtcctcg i felCat3.scaffold_135390 I 8 C 0 s pteVam1.scaffold_22742 7474 40 - 9737 tagtagggagccctt------taatccaata-tggctggtgtccgtc i pteVam1.scaffold_22742 I 8 C 0 s oryCun2.chrUn0985 30034 31 + 42081 ----------GCCCG------TGGCCCGACCTTGCCTGGGGCCCCCC i oryCun2.chrUn0985 I 170 I 327 s danRer6.Zv8_scaffold3075 123799 27 - 281906 GGCCAAGGGGCACCCTTTGGATTATCC-------------------- i danRer6.Zv8_scaffold3075 C 0 C 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7540901 1118 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=39068.000000 s hg19.chr11_gl000202_random 20326 41 + 40103 ttctaga-agggggaa---ctgcaggcatgtacac-aggcgaacat s panTro2.chr11 68206906 41 + 134204764 ttctaga-agggggaa---ctgcaggcatgtacac-aggcgaacat i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50842 41 + 115376 ttctaga-agggggaa---ctgcaggcatgtacac-aggcgaacat i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126003162 41 - 132107971 ttctaga-agggggaa---ctgcaggcatgtacac-aggcgaacat i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128164957 41 - 133002572 ttctaga-atggggaa---ccgcaggcatgtacat-aggtgaacat i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 81502 41 + 109049 ttctaga-agggggaa---ccacaggcatgtacat-aggtgaacat i papHam1.scaffold6638 C 0 C 0 s otoGar1.scaffold_29804.1-1284 613 37 - 1284 ttataga-aggggaga------cagaaacacaca--gggaggatgc i otoGar1.scaffold_29804.1-1284 C 0 C 0 s turTru1.scaffold_93657 9444 42 - 12933 ---taacgaggggaaacggagacagacgctcacacagggagagcg- i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48981494 41 + 51998940 ---taac-aagggaagtggagacagtcacgcacacggggagaacc- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28943489 40 + 33091231 ---taac-aaagggaa-acagatgggcgcgcacccagggagaagg- i equCab2.chr12 C 0 I 1 s felCat3.scaffold_135390 63187 37 + 302526 ---taac-aagggggg-acagacagacacgcac---aggagaacg- i felCat3.scaffold_135390 C 0 I 398 s pteVam1.scaffold_22742 7514 37 - 9737 ---taac-gggagaaacagagacagatgcacacccggggaa----- i pteVam1.scaffold_22742 C 0 I 4 s danRer6.Zv8_scaffold3075 123826 37 - 281906 TGCAAGT-CCAGGGAG-------AGAGGTGGACCCCTGGGTAGCT- i danRer6.Zv8_scaffold3075 C 0 C 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e oryCun2.chrUn0985 30065 327 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7540901 1118 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=82872.000000 s hg19.chr11_gl000202_random 20367 51 + 40103 ggcagggagactagggttctactgcggcaggccaaggagcctgcagaagcc s panTro2.chr11 68206947 51 + 134204764 ggcagggagactagggttctactgcggcaggccaaggagcctgcagaagcc i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50883 51 + 115376 ggcagggagactagggttctactgcggcaggccaaggagcctgcagaggcc i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126003203 51 - 132107971 ggcagggagactagggttctactgcggcaggccaaggagcctgcagaagcc i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128164998 49 - 133002572 ggcagggagac--gggttctactgccgcaggccaaggagcctgcagaagcc i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 81543 49 + 109049 ggcagggagac--gggttctactgccgcaggccaaggagcctgcagaagcc i papHam1.scaffold6638 C 0 C 0 s otoGar1.scaffold_29804.1-1284 650 50 - 1284 cccgtgaagCCTGGGGCTCTGCTACTGCAAGGCCAGGAACC-ACAGGAGCC i otoGar1.scaffold_29804.1-1284 C 0 C 0 s turTru1.scaffold_93657 9486 50 - 12933 catgtgaagactggcatgacacagccacgaggacaggagcca-gaggaccc i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48981535 49 + 51998940 cacgtgaagaCTGGCGTG--ACGGCCCCAAgccaaacagccaccaggagcc i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28943530 33 + 33091231 cgtccgaagattggagtgatgctgccac------------------aagcc i equCab2.chr12 I 1 C 0 s pteVam1.scaffold_22742 7555 50 - 9737 cctgcgaaggtcggagtgatgccttcacg-gccacggaaccaccgggagtc i pteVam1.scaffold_22742 I 4 C 0 s danRer6.Zv8_scaffold3075 123863 50 - 281906 -TGCTGGGGTCAGAGGCCCCTGGGTGGAGGGCCAAGGGGCACCCTGGGGTC i danRer6.Zv8_scaffold3075 C 0 N 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e oryCun2.chrUn0985 30065 327 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7540901 1118 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=87776.000000 s hg19.chr11_gl000202_random 20418 86 + 40103 cgcagagctg-ctggacactgacc-------------------------------ctgcct-----ccacccgaatcctgggccctcagcttcc-agcgctgagtgtgcgtgtgttt-ctgtggt s panTro2.chr11 68206998 86 + 134204764 cacagagctg-ctggacactgacc-------------------------------ctgcct-----ccacccgaatcctgggccctcagcttcc-agcgctgagtatgcgtgtgttt-ctgtggt i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 50934 86 + 115376 cgcagagctg-ctggacactgacc-------------------------------ctgcct-----ccacccgaatcctgggctgtcagcttcc-agcgctgagtgtgcgtgtgttt-ctgtggt i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126003254 86 - 132107971 ctcagagctg-ctggacactgacc-------------------------------ctgcct-----ccgcccgagtcctgggccctcagcttcc-agcactgagtgtgcgtgtgttt-ctgtggt i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128165047 86 - 133002572 agcagagctg-ctgggcactgacc-------------------------------ctcccg-----ccgccctaatcctgggccctcagcttcc-agctctgagcgtgcatgtgttt-ctgtggt i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 81592 86 + 109049 agcagagctg-ctgggcactgacc-------------------------------ctcctg-----ccgccctaatcctgggccctcagcttcc-agctctgagcgtgcatgtgttt-ctgtggt i papHam1.scaffold6638 C 0 C 0 s otoGar1.scaffold_29804.1-1284 700 63 - 1284 AGGATAGAGG-CCTGGGACAGACT-------------------------------GTCTCTGAGGGCTTCCAAGGGAGTGGGCCCT--GCTCAC-AGC--------------------------- i otoGar1.scaffold_29804.1-1284 C 0 N 0 s turTru1.scaffold_93657 9536 114 - 12933 aggagagagg-cctgg-atgggccacccc-gagcagcttaggggaagcaccagc-ctgccc-----acacctggacctcaggcttcaagcctcc-agaaccatgaaagaagaaattt-ctgttgt i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48981584 114 + 51998940 aggacggcgg-cctgg-acaggccacccc--cgtgtcttaggggaagcccgagcgctgccc-----acacctcaacctcagccttccagcccct-aggactgcaggataagatgttt-ctgtggg i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28943563 115 + 33091231 aagagggagg-caggg-acagacccctcccacgcaactgcgggggg-cgtggcc-ctgtca-----acaccttggtttcagacttgcaggctcctagaaccatgagaggagaaacct-ctgtgac i equCab2.chr12 C 0 C 0 s pteVam1.scaffold_22742 7605 116 - 9737 agcagggaggcccggg-acagacccttcccgagcgccttcaggggaccgtggcc-ctgctg-----acaccttgacctcaggcttccagcctcc--agaccatgagagaagaaatttcctgttat i pteVam1.scaffold_22742 C 0 C 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e oryCun2.chrUn0985 30065 327 + 42081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7540901 1118 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=85021.000000 s hg19.chr11_gl000202_random 20504 47 + 40103 ttgcgcccctc-tatggatggg---acttagttgcaggagtcctagAATgc s panTro2.chr11 68207084 47 + 134204764 ttgcgcccctc-tatggatggg---acttagttgcaggagtcctagAATgc i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 51020 47 + 115376 ttacgcccctc-tatggatggg---acttagttgcaggagtcccagAATgc i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126003340 47 - 132107971 ttacgaccctc-tatggatggg---acttagttgcaggagtcctagAATgc i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128165133 47 - 133002572 ttacgcccctc-cgtggatggc---acttagttgcagcggtcctagAATGC i rheMac2.chr14 C 0 I 890 s papHam1.scaffold6638 81678 46 + 109049 ttacgcccctc-cgtggatggc---acttagttgcagcagtcctagAATG- i papHam1.scaffold6638 C 0 I 892 s oryCun2.chrUn0985 30392 47 + 42081 ttgtgcccattgtgcagacgagaacactgaggcacagCCACCCAATA---- i oryCun2.chrUn0985 I 327 I 9 s turTru1.scaffold_93657 9650 47 - 12933 ttaagccactc-cattcgtggt---actttgtttcgagagtcccaggacag i turTru1.scaffold_93657 C 0 I 6 s bosTau4.chr29 48981698 47 + 51998940 ttaagcccttc-catctgtggt---tcttcgttccaggaatcccaggacac i bosTau4.chr29 C 0 I 310 s equCab2.chr12 28943678 36 + 33091231 ttaagcccctc-tacatgtggt---actctgttccagcag----------- i equCab2.chr12 C 0 I 1778 s pteVam1.scaffold_22742 7721 44 - 9737 ttaagccactc-tgtttgtgga---actttgttcctggacaccaatGC--- i pteVam1.scaffold_22742 C 0 I 117 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e cavPor3.scaffold_42 9669784 1978 + 15951348 I e canFam2.chr18 7540901 1118 - 58872314 I e tupBel1.scaffold_50294.1-1651 1651 0 - 1651 I a score=85904.000000 s hg19.chr11_gl000202_random 20551 32 + 40103 agtct-------ggctccagagtttgcacccttcactct s panTro2.chr11 68207131 32 + 134204764 agtct-------ggctccagagtttgcacccttcactct i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 51067 32 + 115376 agtct-------ggctccagagtttgcacccttcactct i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126003387 32 - 132107971 agtct-------ggctccagagtttgcacccttcactct i ponAbe2.chr11 C 0 C 0 s equCab2.chr12 28945492 31 + 33091231 agcct-------ggctccagagt-tgcacccttaacact i equCab2.chr12 I 1778 C 0 s canFam2.chr18 7542019 31 - 58872314 aatct-------agctccaggct-tacaccctcaacact i canFam2.chr18 I 1118 C 0 s turTru1.scaffold_93657 9703 30 - 12933 -aGCA-------GATACGGAGAA-CCCGCCGTTAACTCT i turTru1.scaffold_93657 I 6 I 1965 s oryCun2.chrUn0985 30448 38 + 42081 -ATCTATGTTCAAACCCCAGGGTCTGCACTCCTCACGCT i oryCun2.chrUn0985 I 9 C 0 s cavPor3.scaffold_42 9671762 30 + 15951348 -atct-------agctccagagcatgcac-ctgtacact i cavPor3.scaffold_42 I 1978 C 0 s tupBel1.scaffold_125018.1-1020051 192238 29 - 1020051 ---ct-------ggctccagagtctgcagtctgggcatt i tupBel1.scaffold_125018.1-1020051 I 22621 C 0 s rheMac2.chr14 128166070 31 - 133002572 -gtct-------ggctccagagtttgcacccttcacact i rheMac2.chr14 I 890 C 0 s papHam1.scaffold6638 82616 31 + 109049 -gtct-------ggctccagagtttgcacccttcacact i papHam1.scaffold6638 I 892 C 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e pteVam1.scaffold_22742 7765 117 - 9737 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e bosTau4.chr29 48981745 310 + 51998940 I a score=311632.000000 s hg19.chr11_gl000202_random 20583 187 + 40103 ttgc---tatactgCCTGAGAACCAGATGGATCAACAC------AAAGGGGCCAtgaaggatgcagtggagtgtgccaggg------------gaagaatgcagggaagaacattgtgcacagtgggaacagcatagggttgtgaggcagagcgtgacctgctccagTCACT--GG----TG-GGTGGTGGGTCTGGAAATGCATGTTTGAGTCA s papHam1.scaffold6638 82647 186 + 109049 ttgc---tatactgCCTGAGAACCAGAGGGATCAACAC------AAAGgggccgtgaaggatgcagaggagtgtgtcaggg------------gaagaatgcagggaagaacattgtgcaccatgggaacagcatCGGGT--TGAGGCAGAGCGTGACCTGCTCCAGTTGCG--GG----GGCGGTGGTGGGTCTGGAAATGCATGTTTGAGTCA i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128166101 186 - 133002572 ttgc---tatactgCCTGAGAACCAGAGGAATCAACAC------AAAGGGGCCGTGAAGGATGCAGAGGAGTGTGTCAGGG------------GAAGAATGCAAGGAAGAACATTGTGCACCATGGGAACAGCATCGGGT--TGAGGCAGAGCGTGACCTGCTCCAGTTGCG--GG----GGCGGTGGTGGGTCTGGAAATGCATGTTTGAGTCA i rheMac2.chr14 C 0 M 20 s ponAbe2.chr11 126003419 187 - 132107971 ttgc---tatactgCCTGAGAACCAGAGGGATCAACAC------AAAGGGGCTGtgatggatgcagaggagtgtgccaggg------------gaagaatgcagggaagaacattgtgcacagtgggaacagcatagggttgtgaggcagagcatgacctgctccaggcact--gg----ca-ggtggtgggtctggAAATGCATGTTTGAGTCA i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 51099 187 + 115376 ttgc---tatactgCCTGAGAACCAGAGGGATCAACAC------AAAGgggccgtgaaggatgcagaggagtgtgccaggg------------gaagaacgcagggaagaacattgtgcacagtggaaacagcatagggttgtgaggcagACCGTGACCTGCTCCAGTCACT--GG----CG-GGTGGTGGGTCTGGAAATGCATGTTTGAGTCA i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68207163 187 + 134204764 ttgc---tatactgCCTGAGAAGCAGAGGGATCAACAC------AAAGgggccgtgaaggatgcagaggagtgtgccaggg------------gaagaacgcagggaagaacattgtgcacagtgggaacagcatagggttatgaggcagagcgtgacctgctccagTCACT--GG----CG-GGTGGTGGGTCTGGAAATGCATGGTTGAGTCA i panTro2.chr11 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 192267 174 - 1020051 ttgc---tctactgCCTGGGAACCCGACGGATCCACAC------CGTGGGGACA-GAAGGGT-----GAGGGGTGTCAGGG------------G-AGCCTCCTGGGAAGGACACTGTGCA-GGTGGGACCAGCAC-GGGTTGTGGAGCAGGGCTTGGCCTGCTCCCGTCCCC--AT----AG-GG----GGCACTAGTGAAGCCTGCTCAAGTTA i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9671792 148 + 15951348 ttcc---tacactg----AGAGTCAGGGGGACTGACAA------AGAAGGGTGTTGAAGGATATAAAAGAGTGTTCTGGGG------------TG-----GCCAGGAAATCCACTGTGCCTGCTGGGAGTGGTGTAGAGTCATAAAGCAGAA-ATGACTTGTTCTCGGCATG--AG----GG-GCT----------------------------- i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 30486 90 + 42081 TCAC---TATGCTG---------CCTGGGAAC---CGT------GGAGGGGTCTCGGTGGACGCAGGGAAGGGCACGGGG-------------------------------------GCCTGC--------------AGCC------CAG-------------CACGGCCTGCAGG----GG-GCG----------------------------- i oryCun2.chrUn0985 C 0 C 0 s equCab2.chr12 28945523 169 + 33091231 ttgc---tacacCATCTGAGAGCCAGAGGGATCAACAT------GGAGGGGTCTTGAAGGATACTTAGGAGTGTGCCAGGA---------------GCATGCAGGGAAAGACAACATGCATGGTGGGAACAGGCTGGGCTTGTGAAGCAGAGCATGGCCTGGTTGAGTCACT--GG----GG-GGTGGGGGCTCTGGGGA--------------- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7542050 192 - 58872314 ttactGGTGCACCATA-GAGAACCAGAGGGATCAACATGGGATCGGGGTGGTCTTGAAAGATGCATAGGAGTGTGCAGGAAAGGGGTTGGGGGGAGGAATGCACTGA---ACATTGTACATGGTAGGAACATCATAGGGTTGCAAAGCAGAGCGTGGCCTGGCTGAGTCAGG--GGTCATGG-TGGGGGGGTTCTGGAG---------------- i canFam2.chr18 C 0 C 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e pteVam1.scaffold_22742 7765 117 - 9737 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e bosTau4.chr29 48981745 310 + 51998940 I a score=84435.000000 s hg19.chr11_gl000202_random 20770 101 + 40103 CTGGGAG-GGCTC-TGCGTGG--------CT---GGATGGAACC-C--GTGAGGGAGGAGGCAGGGACATTAAATGACTGAAGGGATCACCAGCAGCCCAGCTGCGAAGGTCCCCAA s ponAbe2.chr11 126003606 101 - 132107971 CTGGGAG-GGCTC-TGCGTGG--------CT---GGATGGAACC-C--GTGAGAGAGGAGGCAGGGACATTAAATGACTGAAGGGATCACCAGCAGCCCAGCTGCAAAGGTCCCCAA i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 51286 101 + 115376 CTGGGAG-GGCTC-TGAGTGG--------CT---GGATGGAACC-C--GTGAGGGAGGAGGCAAGGACATTAAATGAGTGAAGGGATCACCAGCAGCCCAGCTGCAAAGGTCCCCAA i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68207350 101 + 134204764 CTGGCAG-GGCTC-TGCGTGG--------CT---GGATGGAACC-C--GTGAGGGAGGAGGCAGGGACATTAAATGACTGAAGGGATCACCAGCAGCCCAGCTGCAAAGGTCCCCAA i panTro2.chr11 C 0 C 0 s papHam1.scaffold6638 82833 101 + 109049 CTGGAAG-GGCTC-TGCATGG--------CT---GGATGGAACC-T--GTGAGGGAGGAGGCAGGGACATTAAATGACTGAAGGGGTCACCAGCAGCCCAGCTGCAAAGGTTCCCCA i papHam1.scaffold6638 C 0 I 11 s tupBel1.scaffold_125018.1-1020051 192441 105 - 1020051 -TGTGAGAGGCTC-GACCTGG--------CTCCCACGTGGAACCAT--GTGGCAAGGGAGGCAGGTTCACCAGGTGACCAGAGAGCCTGGCGACGGCCTCTCTGTGAAGGACCCAAA i tupBel1.scaffold_125018.1-1020051 C 0 I 5 s cavPor3.scaffold_42 9671940 90 + 15951348 CTGGCAG-G-----GATGTTGGAGTTTCTAC---AAGTGGTTCT-G----GGGAAACAGCGTGACCCAGGGAGACAAGCACA------GGAGGTGACCCA-------AGGGGTCAGC i cavPor3.scaffold_42 C 0 I 3 s oryCun2.chrUn0985 30576 111 + 42081 CTGTGAG-GACTCAGGTGGGGGACATGAGAT---GGATGGAGCT-GTGGCGGGCAGGGGTGCGGCGATGCGGGATGAGCAAAGGCCTGGGAGGCTGCCCAGCTCCG-AGGACCCCAC i oryCun2.chrUn0985 C 0 I 6 s equCab2.chr12 28945692 66 + 33091231 ---------------------------CACT---GGATGGA---------------------AAGGGCACGGGACGGCTGAAGGGGTCAGTGGCAGCCTAGCTGTGAAGGACCCCAA i equCab2.chr12 C 0 C 0 s canFam2.chr18 7542242 84 - 58872314 ---------------------------TGCC---AGATGGAACTGT--GTGACAGATGAAGGAGGGGTATGGAATAACTGAAGGGGTCA-TGGCAACCCAGCTGTAAAGGGCCCCAA i canFam2.chr18 C 0 C 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e pteVam1.scaffold_22742 7765 117 - 9737 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e bosTau4.chr29 48981745 310 + 51998940 I e rheMac2.chr14 128166287 20 - 133002572 M a score=66796.000000 s hg19.chr11_gl000202_random 20871 40 + 40103 -------AGGCAGAGTTTTGACTTATTCCTGGGATGATGCGGCCCCA s canFam2.chr18 7542326 38 - 58872314 ACACCAGGGGAAGAGTTTGGGCTTATCCTTGGGCCC---------GA i canFam2.chr18 C 0 C 0 s equCab2.chr12 28945758 47 + 33091231 ATGCCAGGTGAAGACTTTGGACTTACTCCCGGGGCCACAGGGTCAGA i equCab2.chr12 C 0 C 0 s oryCun2.chrUn0985 30693 28 + 42081 -------GGTGGGGAGTTGGACTCATGCCTG------------CAGG i oryCun2.chrUn0985 I 6 C 0 s cavPor3.scaffold_42 9672033 37 + 15951348 -------GAAGGGAATTTGGATTC-TTCCTGGGATGA--AAGACCGG i cavPor3.scaffold_42 I 3 C 0 s tupBel1.scaffold_125018.1-1020051 192551 40 - 1020051 -------GCAAAGACTCTGCATTTATTCCTGGGACGGCAAGGACTCA i tupBel1.scaffold_125018.1-1020051 I 5 C 0 s panTro2.chr11 68207451 40 + 134204764 -------AGGCAGAGTTTTGACTTATTCCTGGGATGATGCGGCCCCA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 51387 40 + 115376 -------AGGCAGAGTTTTGACTTATTCCTGGGACAACGTGGCCCCA i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126003707 40 - 132107971 -------AGGCAGAGTTTTGACTTATTCCTGGGATGACACGGCCCCA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128166307 40 - 133002572 -------AGGCAGAGTTTTGACTTATTTCTGGGACAACGCGGCCCCA i rheMac2.chr14 M 20 C 0 s papHam1.scaffold6638 82945 40 + 109049 -------AGGCAGAGTTTCGACTTATTTCTGGGACAACGCAGCCCCA i papHam1.scaffold6638 I 11 C 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e pteVam1.scaffold_22742 7765 117 - 9737 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e bosTau4.chr29 48981745 310 + 51998940 I a score=307365.000000 s hg19.chr11_gl000202_random 20911 151 + 40103 GCA-GAGGAATATGCCAGATCTGGGTTCATGA-AATGCAGCTGGAGCTAGGACAGGGAGGA----------AAGATTTGAGTTCAGAATACAGGTTCCGTGGAGACGCTGAACTGACCAGGCTCATGCTCCAG--------CAGGATGGGTCTGGATTCAGGAAACCCACA s papHam1.scaffold6638 82985 151 + 109049 GCA-GAGGACCATAACAGATCTGGGTTCATGA-AATGCAGCTGGAGCCAGAACAGGGAGGA----------AAGATTTGAGTTCAGAATACAGGTTCCGTGGAGACGCTGAACTGACCAGGCTCATGCCTCAG--------TAGGATGGGTCTGGATTCGGGAAACCCACA i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128166347 151 - 133002572 GCA-GAGGACCATAACAGATCTGGGTTCATGA-AATGCAGCTGGAGCCAGAACAGGGAGGA----------AAGATTTGAGTTCGGAATACAGGTTCCGTGGAGACGCTGAACTGACCAGGCTTATCCCTCAG--------CAGGATGGGTCTGGATTCGGGAAACCCACA i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126003747 136 - 132107971 GCA-GAGGAATATGCCAGATCTGGGTTCATGA-AACG---------------CAGGGAGGA----------AAGATTTGAGTTCAGAATACAGGTTCCGTGGAGACGCTGAACTGACCAGGCTCATGCCCCAG--------CAGGATGGGTCTGGATTCGGGAAACCTACA i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 51427 151 + 115376 GCA-GAGGAATATGCCAGATCTGGCTTCATGA-AATGCAGCTGGAGCTAGGACAGGGAGGA----------AAGATTTGAGTTCAGAATACAGGTTCCGTGGAGACGCTGAACTGACCAGGCTCATGCTCCAG--------CAGGATGGGTCTGGAGTCGGGAAACCCACA i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68207491 151 + 134204764 GCA-GAGGAATATGCCAGATCTGGGTTCATGA-AATGCAGCTGGAGCTAGGACAGGGAGGA----------AAGATTTGAGTTCAGAATACAGGTTCCGTGGAGACGCTGAACTGACCAGGCTCATGCTCCAG--------CAGGATGGGTCTGGATTCGGGAAACCCACA i panTro2.chr11 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 192591 134 - 1020051 GCA-AAGCATCTTGCCAGGTCTGGGTTCACGA-GAGG--GCTGGAGCC---------AAGA----------AGAATGTG-----TGAATTCAGGTTCTGGGATGAGGCCAAACAGATGAGGTTCAAACCTCAA--------CCAGGTAGGTGTGGACCTGGG-GGCTCACC i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9672070 138 + 15951348 GCA-CAGCACCCTACCAGTTCTACGTCCAAGAGTAGG--TCCGGAGCCATGAGAGAGAAGA----------AGGACTTGAACTCAGAATGC---CTCTCAGCAGAAGCTGGTCTGAGG--------CCCACAG--------CTGGAGGGGCCTGGGTTC-AGGATCCCACA i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 30721 103 + 42081 GCG-CGGC------CCGGGTCCTGGTCCCCGA-CAGG--GCTGGAGCCCGGTGCAGG---------------------------------------CTCTGCAGGCGTGGCTCAGACC--------CCAACAG--------C---GCCGGCCTGGGCTCGGGGAGCCCACA i oryCun2.chrUn0985 C 0 C 0 s equCab2.chr12 28945805 160 + 33091231 GCA-AAGCACTGTGGCAGCTCTGGGCTCTGGG-------GTCGGAGCT--GAGAGAGGAGGACAGCCCAGCAGGGGCTGAGTTCAGGGCACAGGTTCCATGGAGACTCTCA-CTGACAAGGTGCAGACCCCTGATCAGATCCAGGAGGGGCCTGGATTCAGGGACCCCACA i equCab2.chr12 C 0 C 0 s canFam2.chr18 7542364 162 - 58872314 GCAGAGGTGCTGTCCTGAATCTGGGTTCTGGG-------GATGGAACTGAGAGAGAGAAGGACAACTCAGCAGGATTCGAAAGTAGGACACAGGTCCCAAGGAGAGTCTGA-CTGATGGAATACAGGCCCCTGATC-GATACGGGATGGGcctggattcggggaccccaca i canFam2.chr18 C 0 C 0 s choHof1.scaffold_1437 37058 160 + 46236 GCA-AAGTACCAAGCCAGATCTGGATTCAAGA-CATGGGGCT-GAGCCAAGAGAGGGAAGGATAAATCGGTAGGATTTGAATTCAGGGTGCAGATTATGTGGAGAGGCTGAACTAATGAGACTCGGACCCAGA--------TTGAATGGGCCTGGATTTGAGGATCCCACA i choHof1.scaffold_1437 N 0 N 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e pteVam1.scaffold_22742 7765 117 - 9737 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e bosTau4.chr29 48981745 310 + 51998940 I a score=112439.000000 s hg19.chr11_gl000202_random 21062 60 + 40103 Ccctcctgatctccct--------------------------------ttctctccaactgctccgggcctcagatttccctcctccaacag---- s papHam1.scaffold6638 83136 60 + 109049 Ccctcctgatctcccg--------------------------------ttctctccaactgctccgggcctcagatttctctcctgcaacag---- i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128166498 60 - 133002572 Ccctcctgatctccct--------------------------------ttctctccaactgctccgggcctcagatttctctcctgcaacag---- i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126003883 60 - 132107971 Acctcctgatcgccct--------------------------------ttctctccaactgctccgggcctcagatttccctcctccaatag---- i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 51578 60 + 115376 Ccctcctgatctccct--------------------------------ttctctccaactgctccgggcctcagatttccctcctccaacag---- i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68207642 60 + 134204764 CCCTCCTGATCTCCCT--------------------------------TTCTCTCCAACTGCTCCGGGCCTCAGATTTCCCTCCTCCAACAG---- i panTro2.chr11 C 0 M 1376 s tupBel1.scaffold_125018.1-1020051 192725 57 - 1020051 CTCGCCTGATCCCCCT--------------------------------TTCTCTTTGACAGTCCCAGGCCTCAGGCTT--TTCCTCCAAAC----- i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9672208 60 + 15951348 CTGCCCTGGTTCCCGT--------------------------------TTTTCTGCCGCTGGCCCTGGCCTCAGATCTCTTCTCTTTTGCAA---- i cavPor3.scaffold_42 C 0 I 3 s oryCun2.chrUn0985 30824 59 + 42081 CCCTCCTGGGTCCC-C--------------------------------TGCCCTGCAGCCGGCCCAGGCCTCAGAGTGCAACTCCTCCCCAG---- i oryCun2.chrUn0985 C 0 I 3 s equCab2.chr12 28945965 85 + 33091231 CGCTCctggttccctccacct---------cccctgctccgacccc--ttctctccagtgggcccaggcctcagatggttcctctgctccagcaca i equCab2.chr12 C 0 C 0 s canFam2.chr18 7542526 95 - 58872314 gtctcctggtgcccttcccttcttgctgaccccctgcccagaccccctttttccccaaggcgccca-gctgcagacctctcctcctctctaacaca i canFam2.chr18 C 0 C 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e pteVam1.scaffold_22742 7765 117 - 9737 I e calJac1.Contig6069 83752 1256 + 235769 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e bosTau4.chr29 48981745 310 + 51998940 I a score=126807.000000 s hg19.chr11_gl000202_random 21122 136 + 40103 gccctctctaggtggactcatgggtcc--tgtg-gcttgaacacgtctagaccttcatggtctccaaactcataactctac--cctctcccctgatca-ccggcccagcc-tc--cagt-gtctactccacagctccgtatggatg s gorGor1.Supercontig_0015245 51638 136 + 115376 gccctctctaggtggactcatgggtcc--tgtg-gcttgaacacgtctagaccttcatggtccccaagctcataactctac--cctctcccctgatca-ccggcccagcc-tc--cagt-gtctactccacagctctgtctggatg i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126003943 136 - 132107971 accatttctaggtggactcatgggtcc--tgtg-gcttgaacacatctagaccttcatggtccccaaactcatatctccac--cctctcccctgatca-ctggcccagcc-tc--cagt-gtctactccacagctctgtgtggatg i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128166558 131 - 133002572 gtgctctctaggtggactcatgggtcc--tgtg-gcttgaacacttctagacattcatggttcccaaattcatatctccac--cctctcccctgatc------cccagcc-tc--cagt-gtctgctccacagctctgtctgggtg i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 83196 136 + 109049 gtgctctctagatggactcatgggtcc--tgtg-gcttgaacacgtctagacattcatggtccccaaattcatatctccac--cctctcccctgatca-ccggcccagcc-tc--cagt-gtctgctccgcagctctgtctgggtg i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 85008 135 + 235769 gccctctgtagggggacccatgggtcctgtgtg-gcttgaagatgtgtagacattcatggtccccaaactggtgtctccac--cctctcccttgatca-ctg-ccca-ct-tc--cagtggtctgctctgcagctctg--tggacg i calJac1.Contig6069 I 1256 C 0 s tupBel1.scaffold_125018.1-1020051 192782 88 - 1020051 TCCCTCTTTACACCAGCTCACAGGCCT---------------------------------CTCCCAAA-------CCCCAC--TCCCTCT-------------CCCAGCTATC--TAGC-TCCTGCTCTTCAGCTCCACCTAGTTG i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9672271 87 + 15951348 ACCCTACTCAGTGGGACCCCAGACTGA--TGTC-CCTGAGTT---------------------------------TTCCAC--C----------------GGGCCCAGGT-AC--CAGT-GTCTACTCAGCAGCCCAGC-TGGGGA i cavPor3.scaffold_42 I 3 C 0 s oryCun2.chrUn0985 30886 84 + 42081 GGCCTCTCTGGGTGGGCTCACGGCCTA--GGTG-GCTGGGAC---------------------------------TCACAC----------------------TCCACGG-CC--TCTC-CCCTGCCCCACAGCTCCCCATGGAGG i oryCun2.chrUn0985 I 3 C 0 s equCab2.chr12 28946050 138 + 33091231 gcccgtcggaggc-atctcacacttcc--tgtg-ctttatacacatctgcacgatcacggtcccccag-ggacgtctccacggccactgccctgaaccacaggcccggct-ct--caacgacctgctcagcagctccacccagatg i equCab2.chr12 C 0 C 0 s canFam2.chr18 7542621 132 - 58872314 cttccttccaggtggcctctaggttct--cgtgactttaaacacatctgcacatccatgaaccccgaa-tgacatctccactgcctttcccc-------ctgCCCCTGCC-CTTCCTGCCACCCCCTCACTGACTGCGTGTGG--- i canFam2.chr18 C 0 I 85 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e pteVam1.scaffold_22742 7765 117 - 9737 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e bosTau4.chr29 48981745 310 + 51998940 I e panTro2.chr11 68207702 1376 + 134204764 M a score=410082.000000 s hg19.chr11_gl000202_random 21258 410 + 40103 c----ctcagaggcctctccagtccagc-cccctgatacggagccctgaggtccctgccagagctgcccctgactgtc--tcccttcctgaggactgaagcttgggccat----------------------cagtggctgcaaccgagaatctgcggttcaccattgccctctttttctcacgccc----------tcagtgaatc----------caagcagatccAGGAGA--GGCCCCTTCTTATGCCCCTGTGCCATGCCCCAGGTTGGTGT--GGACAGCAG--GC-AGCTGGA-GGATGAGGCC-ACACTGGCTCCAGCCACCTTGGGTTG----------GAGGTTTCCACAGGGCAG--------------CCAAGCAGGCCTGTCCGGCAGCAACAGAAGAGATTGTCTGGGGCTCGGCAGCGGGCA-ACTGGCTTGGGGAGAGGAAAGTGAG----------AGGCAAGCACCATCCCTCCTCATGGCTCCC s calJac1.Contig6069 85143 427 + 235769 c----ctcagaagcctct-cactctgg---ccctgaaacagagccccgaagtccctgtcagagctgctcctgaccgtc-ttcccttcctgaggactgaagctcaggccatccaggactgaagtttgggcatccagtgggttcaaccaagaatctggggttcacccttgccctctctttctcacgccc----------tcagtgaatc----------caagcagatccAGGACA--GGCCCCTTCTCATGCCCCTGTGCCATGCCCCAGGTTGGTGT--GGGCAGCAG--ACAAGCTGGA-GGACGAGGCC-ACGCTGGCTCCAGCCACCTCGGATTG----------GAGGTTTCCCTGGGGCAG--------------CCAAGCAG----GTGAGGCAGCAACGAAAGAGACGGTCTGGGGCTCCGCATCGGGGAGACTGGCCTGGGGAGAGGGAGGTGAG----------AGGTAAGCACCATCC-TCCTCAGGGCTCCC i calJac1.Contig6069 C 0 C 0 s papHam1.scaffold6638 83332 410 + 109049 c----ctcagaggcctctccagtccatc-cccctgatacggagccctgaggtccttgccagagctgctcctgaccacc--tcccttcccgaggactgaagctcgagccat----------------------caatggctgcaaccaagaatctggggttcacccttgccctctttttctcacgctc----------tcagtgaatc----------caagcagatccAGGACA--GGCCCTTTCTCATGCTCCTGTGCCATGCCCCAGGTTGGTGT--GGGCAGCAG--GC-AGCTGGA-GGACGAGGCC-ACACTGGCTCCAGCCACCTTGGATTG----------GAGGTGTCCAAAGGGCAG--------------CCAAGCAGGCCGGTCCAGCAACAACAGAAGAGACGGTCTGGGGCTTGGCAGTGGGCA-AATGACTTGGGGAGAGGAAAGTGAG----------AGGAAAGCACCATCCTTCCTCATGGCTCCC i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128166689 410 - 133002572 c----ctcagaggcctctccagtccatc-cccctgatacggagccctgaggtccctgccagagctgctcctgaccatc--tcccttcctgaggactgaagctcgggccat----------------------caatggctgcaaccaagaatctggggttcacccttgccctctttttctcacgctc----------tcagtgaatc----------caagcagatcAACGACA--GGCCCCTTCTCATGCTCCTGTGCCATGCCCCAGGTTGGTGT--GGGCAGCAG--GC-AGCTGGA-GGACGAGGCC-ACACTGGCTCCAGCCACCTTGGATTG----------GAGGTCTCCACAGGGCAG--------------CCAAGCAGGCCAGTCCAGCAACAACAGAAGAGACGGTCTGGGGCTTGGCAGCGGGCG-ACTGGCTTGGGGAGAGGAAAGTGAG----------AGGCAAGCGCCATCCTTCCTCATGGCTCCC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126004079 410 - 132107971 c----ctcagaggcctctccagtccagc-cccctgatacggagccctgaggtccctgccagagctgcccctgactgtc--tcccttcctgaggactgaagctcgggccat----------------------cagtggctgcagccaagaatctggggttcaccactgccctctttttctcacgccc----------tcagtgaatc----------caagcagatccAGGACA--GGTCCCTTCTTATGCCCCTGTGCCATGCCCCAGGTTGGTGT--GGACAGCAG--GC-AGCTGGA-GGACGAGGCC-ACACTGGCTCCAGCCACCTTGGGTTA----------GAAGTTTCCACAGGGCAG--------------CCAAGTAGGCCTGTCTGGCAGCAACAGAAGAGACAGTCTGGGGCTCGGCAGTGGGCA-ACTGGCTTGGGGAAAGGAAAGTGAG----------AGGCAAGCACCATCCCTCCTCATGGCTCCC i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 51774 328 + 115376 c----ctcagaggcctttcCAGTCCAGC-CCCCTGATATGGAGCCCTG----------------------------------------------------------------------------------------------------------GNNNNNNNNNNNNNNNNNNNTTTTGTCACGCCC----------TCAGTGAATC----------CAAGCAGATCCAGGAGA--GGCCCCTTCTTATGCCCCTGTGCCATGCCCCAGGTTGGTGT--GGACAGCAG--GC-AGCTGGA-GGACGAGGCC-ACACTGGCTCCAGCCACCTTGGGTTG----------GAGGTTTCCACAGGGCAG--------------CCAAGCAGGCCTGTCCGGCAGCAACAGAAGAGATGGTCTGGAGCTCGGCAGCAGGCA-ACTGGCTTGGGGAGAGGAAAGTGAG----------AGGCAAGCACCATCCCTCCTCATGGCTNCC i gorGor1.Supercontig_0015245 C 0 C 0 s cavPor3.scaffold_42 9672358 345 + 15951348 C----TGTGGTGGCCTCT------------CCCTGCA------------------------------TCCTGACTGACAGCCCCTGCC---AGACTAAAACTCTGCCTTC----------------------CTGTGAGTCCAACCAAAATTCCAACGCAGACCCTCCCCCTTTCTCTCTACTGCTCCA--------TCAGTAAGCCAGGTGGGCTGCAGGTTCAGCTGGGTCCAGGACC----------CACTCATTCCACACCTCGGGGCTGCTT--------CCT--GC-CTCTGGA-TCTCAGGACCAGTGTAGGTAGCAGGAAGCTTGGAGGGGTGAGGCTGTGGGGTTTCCATGGGGGAGACGAAGCCAGCACACCCAGCAGG-------------------AGAGA----CTGGAGC------ACAGTCA-CCT-----------------GTGAA----------AGGTAAGCACCAAGTGTCCTCCGGTGCTCA i cavPor3.scaffold_42 C 0 I 21 s oryCun2.chrUn0985 30970 252 + 42081 CATCTGGAGGTAGCCGCT------------CCCC--------------------------------------ACTGCCGGCTCCGGC---------------------------------------------------------------------------CCCACACCCTTGTCCTTCCCTCCTTCA--------TC------------------CAAGCACACCTGGGCCC--GACCACATCCCA-GCTCCCCGTCCCCTCCCCCGGGCTCTGC--------CCT--GG-TCCCGGA-TCACAGTCCC----TGGGCTCCGGCCGCCCCGGAAG-----------GCGGCTTCTGCAGGGCAG--------------CCAGGCAGGCTC----------------GGAGA----GGAGTGT------GCAGGCG-CCT-----------------GCGAG----------AGGTGAGCCCC--GTCTCCCCCTGTCCCCC i oryCun2.chrUn0985 C 0 I 18 s equCab2.chr12 28946188 423 + 33091231 -----ttaagaggcatctcgaacccacctcaccccaaatggagtcccgctgctccctccagaactgcccctcaccatc--cccgctccagagaaccagagctgcagcctt---------------------ccaggggttccaaccgaaaacctgggttcacccttcctcctctctttctctcgctccatcctgtcggctgtagctt----------caagtagatccaggaca--gacaccctctcatgcccctgag---ggcaccacgctggtctcagGGTCACAGCACC-AGCTGGAGGGACAAGGCT-GGGCCGGCTCTGGCCACCT-GAGTTG----------GAGGTCTCCATGGGGCAG--------------CCAAGCAGGCATGT----CAGTGGCGGGAGAGATGGCCGGGGACTCGGCG--AGGCA-GCC---TCTGAGAGGAGGCGGGGAGCCGCCTGTGCGGGCGAGCGTCGTCCCTCCTCATGGCTCTC i equCab2.chr12 C 0 C 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e pteVam1.scaffold_22742 7765 117 - 9737 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e canFam2.chr18 7542753 85 - 58872314 I e bosTau4.chr29 48981745 310 + 51998940 I e tupBel1.scaffold_125018.1-1020051 192870 0 - 1020051 C e panTro2.chr11 68207702 1376 + 134204764 M a score=-4535.000000 s hg19.chr11_gl000202_random 21668 61 + 40103 ---CCTGGGACCACGTTTC-----ATCACCCAGCCCCTCACCG---------ACACC-----TGCAGCCACAAGGCCAGCTCC s gorGor1.Supercontig_0015245 52102 61 + 115376 ---CCTGGGACCACGTTTC-----ATCACCCAGCCCCTCACCG---------ACACC-----TGCAGCCACAAGGCCAGCTCC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126004489 61 - 132107971 ---CCTGGGACCACGCTTC-----ATCCCCCAGCCCCTCACCA---------ACACC-----AGCAGCCACAAGGCCAGCTCC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128167099 35 - 133002572 ---CCTGGGGCCACACTTC-----ATCCCCCAGCCCCTCACTG---------------------------------------- i rheMac2.chr14 C 0 I 37 s papHam1.scaffold6638 83742 69 + 109049 ---CCTGGGGCCACACTTC-----ATCCCCCAGCCCCTCACTGACCGAAGCCACACC-----CGCAGCCCCGGGTCAACCCC- i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 85570 65 + 235769 ---CGTGAGGCTGAACATC---------CCCCGCCCCTCACCGACTGCAACCACACC-----CTCAGGC-CTGGGCCAGCCCC i calJac1.Contig6069 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 192870 73 - 1020051 ---CCTGGGGCTGCTCTTCCCTTTGCCCCCCACCCCCTCACTGACTTCAGGCACA-T-----AGCAGCCGCAGGCCCTCTCC- i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9672724 24 + 15951348 ---CCTGTGTC-ACCTCTG---------TAGTG-----CTTC----------------------------------------- i cavPor3.scaffold_42 I 21 C 0 s oryCun2.chrUn0985 31240 30 + 42081 ---GCTGGGCCGACCTTCC---------CCGTGCCTCTCTTC----------------------------------------- i oryCun2.chrUn0985 I 18 C 0 s equCab2.chr12 28946611 66 + 33091231 ATGCGCTGCCCTTCCCTTC-----AT--CCCAGGCCCTCACCG---------ACGGCGTGTGGGCAGCCCGGGCCCTGGCCC- i equCab2.chr12 C 0 C 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e pteVam1.scaffold_22742 7765 117 - 9737 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e canFam2.chr18 7542753 85 - 58872314 I e bosTau4.chr29 48981745 310 + 51998940 I e panTro2.chr11 68207702 1376 + 134204764 M a score=163215.000000 s hg19.chr11_gl000202_random 21729 171 + 40103 TGGCATGGGGGGTAGGCAGAGGGAAGAGGACCAAGCTGGTAGGGATGGAGATGTGTCCAGCTCCTGCCTTCAGTAGAGCCCATGAGACCCTCCATCCCAGCCTGCTGA-ACTTCCTGGCCTCCCAACACCACATGCTAAgctcagagctctgctccagtgggccagaatgcc s gorGor1.Supercontig_0015245 52163 171 + 115376 TGGCATGGGGGGTAGGCAGAGGGAAGAGGACCAAGCTGGGAGGGATGGAGATGTGTCCAGTTCCTCCCTTCAGTAGAGCCCATGAGACCCTCCATCCCAGCCTGCTGA-ATTTCCTGGCCTCCCAACACCACATGCTAAACTCAGAGCTCTGCTCCAGTGGGCCGGAATGCC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126004550 171 - 132107971 TGGCATGGGGGGTGGGCAGAGGGAAGAGGACCAAGCTGGGAGGGATGGAGATGTGTCCAGCTCCTGCCTTCAGTAGAGCCCATGAGACCCTCCACCCCAGCCTGCTGA-ACTTCCTGGCCTCCCAACACCACATGCTAAgctcagagctctgctccagtgggccggaatgcc i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128167171 171 - 133002572 TGTCACTGGGGGTGAGCAGAGGGAAGAGGATCAAGCTGGGAGGGATGGAGATGTGTCCAGCTCTTGCCTTCAGTAGAGACCATGAGACCCTCCAGCCCAGCCTGCTGA-ACTTccttgcctcccaacaccacatgctaagctcagagctctgctccagtggcccggaatgcc i rheMac2.chr14 I 37 C 0 s papHam1.scaffold6638 83811 171 + 109049 TGGCATTGGGGGTGAGCAGAGGGAAGAGGATCAAGCTGGGAGGAATGGAGATGTGTCCAGCTCTTGCCTTCAGTAGAGACCATGAGACCCTCCAGCTCAGCCTGCTGA-ACTTccttgcctcccaacaccacatgctaagctcagagctctgctccagtggcccggaatgcc i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 85635 135 + 235769 TGGCAT-GGGGGTGGGCAGAGGGAAGAGGATCAAGCTGGGAGGGTTGGAGATGTG-----------------------------------TCTACCCCCGCCTGCTAA-Acttcctggcctcccagcaacacacgctcctctcagagctctgctccagtggcccggagtcac i calJac1.Contig6069 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 192943 153 - 1020051 CGGCATGGGGGAGGAGGAGGGTAAAGAAGACCAAGCAGAGAGACGTGGAGATCTGTCCAGCTCCTGCCCTCGGTACAGCCTGCGAGACC-TTTACCTAAGCCTA--GA-----CCTGACCAgcccccaccacac--------tggagcacctctc---tgtccctcccagcc i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9672748 116 + 15951348 CTCCAGGTGAGGTAGGGAGGGGGAAAGAGGATCCACCTGGA-AGGAGTGAGTCTGCCTAGCACGTGCCTCCA--CACACCCAGGAGACTCA--GCCTCACCCCGCTGA---TTCCCAGCCTTTG------------------------------------------------ i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 31270 94 + 42081 CTGCAGGTGCCCTGGCGTGGG------------CACAGGGACAGGTGAGGATCCGTCCAG------------------CCCAGGAGCCTGATGGCCTCGCCCAACCCAGAGCTCCCCGCCCCCG------------------------------------------------ i oryCun2.chrUn0985 C 0 C 0 s equCab2.chr12 28946677 97 + 33091231 -TGCATG------------------------------GGGAGCGGTGGAGATCCGTCCAGCTCCAGCCCTCC--------------ACCCTCAGCCT---CCCGCAGG-AGTT--------------------TGTGAGTAtcagggctctgctccagccatctgg------ i equCab2.chr12 C 0 C 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e pteVam1.scaffold_22742 7765 117 - 9737 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e canFam2.chr18 7542753 85 - 58872314 I e bosTau4.chr29 48981745 310 + 51998940 I e panTro2.chr11 68207702 1376 + 134204764 M a score=413920.000000 s hg19.chr11_gl000202_random 21900 349 + 40103 cctctgctcctcccatactccagactcacagacctgcttcctt--cctctgcctgagatttcccaccccacctgttataggctttgccgacactgccccatccttcattctcagcttgcatgtcacttcctcagagagggtctc-ccaattccctgtca---catgctccctctgcttctccttcttcatgttccacacctgcaatttctcaatgctcccctcgccttctgtcagccccactgttggcagagtctgtccttcttgtcattgggtccacagcagcagacccaaaagggtctggtacccaaatgagacccaaagggtctggtacatgCTGGGC-TGCAGTAAATCTTT s gorGor1.Supercontig_0015245 52334 349 + 115376 CCTCTACTCctcccgtactccagactcacagacctgcttcctt--cctctgcctgagatttcccaccccacctgttataggctttgccgacactgccccatccttcattctcagcttgcatgtcacttcctcagagacggtctc-ccaattccctatca---catgctccctctgcttctccttcttcatgttccacacctgcaatttctcaatgctcccctcgccttctgtcagccccactgttggcagagtctgtccttcttgtcattgggtccacagcagcagacccaaaagggtctggtacccaaatgagacccaaagggtctggtacatgCTGGGC-TGCAGTAAATCTTT i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126004721 349 - 132107971 cctctattcctcccatgctccagactcaaagacctgcttcctt--cctctgcctgagattccccaccccacctgttgtaggctttgccaacactgccccatccttcactctcagcttgcatgtcaattcctcagagagggtctc-ccaattccctgtca---catgctccctctgcttctccttcttcatgttccacacctgcaatttctcaatgctcccctccccttctgtcagccccactcttggcacagactgtccttcttgtcattgggtccacagcaggagacccaaaagggtctggtacccaaatgagacccaaagggtctggtgcatgCTGGAC-TGCAGTAAATCTTT i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128167342 350 - 133002572 cctctgttcctcccaagctgcagactcacagatctgcttcctt--cctctgcctgagattccccaccccacctgttcttggctttgctgacactgccccatccttcactctcagctggcatgtcgcttcctcagagagggtctc-ccaattccttgtca---catgctccctctgcttctccttcttcatgttccacacttgcaatttctcaacactcccttccccttctgtcagccccactgttggcagagtctgtccttcttgtcactgggtccacagcagcagatccaaaaggatctggtacccaaatcagacccaaagggtctggtacgtgctaggcgtgcagtaaatcttt i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 83982 350 + 109049 cctctattcctcccatgctccagactcacagatctgcttcctt--cctctgcctgagattccccacaccacctgttcatggctttgccgacactgccccatccttcactctcagctggcatgtcgcttcctcagagagggtctc-ccaattccctgtca---catgctccctctgcttctccttcttcatgttccacacttgcaatttctcaacactcccttccccttctgtcagccccactgttggcagagtctgtccttcttgtcactgggtccacagcagcagatccaaaaggatctggtacccaAATCAGACCCAAAGGGTCTGATACATGCTAGGTGTGCAGTAAATCttt i papHam1.scaffold6638 C 0 I 774 s calJac1.Contig6069 85770 284 + 235769 cctctgctcctcccaagctccagactcacagacctgactcctt--cctctgcctgagactcccc------------------------------gccccacccttcactctcagcttgcatgtcacttcctcagagagggtctc-ccagttccctgtca---cacgctccttctgctcctccttcttcaggttccacacctgcaa-ttcccaatgctccctccc--------caaccctaatgttggcagagtctgtccttcctgtcactgagtccacagcggcaaaccca---------------------------aaagggtctggtacatgctgggtttgcaataagccttt i calJac1.Contig6069 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 193096 295 - 1020051 tccatgctcccgctcgcccccagactcacacacctgc-----t--cctgtgtcggagacccctt---ccacctgctcctggctttactgacatcg-cccatctttcactcttagcccacctgtcccttcctcagggaagatcttaaccattacctgcca---caggtgcc--ctgctttttcttcctcgtgtgccacacatacagtcactccatgcccgctcccatttctg--------------ggcaaggtctgtccttgtcacaactgagtccacagcatt-------------------------------ctcactgggcctagcatacgctagatgtgcaatcaatccct i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9672864 183 + 15951348 ------------------------------------------------CTGCCTG-----------------------------------------CCTA--CTTG------------------CTTTGCTCGGGGAGGAGCCC-CTCA----CTGTCA---CATGCTCCTTCTGCTTCTCCT---TCAAGGACAACACTTGC-------CAATACTCATATCC--TTCTGTGAGCACCTCTGTAGGCAAGGTCT-----------------GTCCATAGGGTC--------------CTCGCA--------AGGCCTGGA-----TGGCATGCATGAGACGTGCAATGAATCCCT i cavPor3.scaffold_42 C 0 I 7 s oryCun2.chrUn0985 31364 146 + 42081 ---------------------------------------CCTG--GCCCTGACTG-----------------------------------------CC----CTTGACTCTCAGCCCATGTGGCCCCTCCCCAGGGAGGCTCTC-CCCA----CACTCAGCCAACGCCCCCTCTGCT-----------GAGGGCAG------------------------------------GGGCTCCCCTGTTGCCA------------------------TCCCCAGCACC--------------CTGGC----------------------------------AGATGCACCACACACCACT i oryCun2.chrUn0985 C 0 I 7 s equCab2.chr12 28946774 218 + 33091231 cctccgttcctcccaggctccatgctc----------tctctc--tctcctccaga----------------------------------------cccat----------------------------------aggctctcc-ccagtggtctgtca---caggctccctctgcttctctttcttcatgtaccacacctgcaattacccagagccccctcct-gttctgttagcctcagagcagacagggtctgtccttgttgtcactgggagcacagcatc------------------------------tgtcacagggcctggcacacactag----------------- i equCab2.chr12 C 0 I 17 s canFam2.chr18 7542838 266 - 58872314 CCTCTGTTCCTCTCAGACTCTGAGATC----------TCTCTCAGTAACATCCAGATATGCTTC---CCAGCTCTGAGGCCCCAGGATGGGGCTGTCCCATCATTC------AGTTCATAAGCC-TTTCCTCACAATGCCTCTC-CCAGTTTCCTGTCA---CATGGTCCCTCTGCTTCTCCTTCTTCATGTACCACACCTGCAATTGTTCAGAGCTGCCTCCC-ATTCTGTTAACCCCATGTTAG------------------GTTAAGAGGTCTACATCATG------------------------------CATCacagggcctggcacatactag----------------- i canFam2.chr18 I 85 I 17 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e pteVam1.scaffold_22742 7765 117 - 9737 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e bosTau4.chr29 48981745 310 + 51998940 I e panTro2.chr11 68207702 1376 + 134204764 M a score=110384.000000 s hg19.chr11_gl000202_random 22249 73 + 40103 AATGAATTgatgga-------tggatgagtggatggttgtatgaatgaatgggtggatagatgggtagatgaatggatgg s gorGor1.Supercontig_0015245 52683 73 + 115376 AATGAATTgatgga-------tggatgagtggatggttgtatgaatgaatgggtggatagatgggtagatgaatggatgg i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126005070 70 - 132107971 Aatgaattgatgga-------tggatgagtggatggttgtatgaatgaatgggtggatagatgggtagatggatgga--- i ponAbe2.chr11 C 0 I 732 s rheMac2.chr14 128167692 73 - 133002572 aatgaattgatgga-------tggatgaatggatggttgtatgaatggatgggtggatagatgggtagatgaatggatgg i rheMac2.chr14 C 0 C 0 s calJac1.Contig6069 86054 73 + 235769 aataaattgatgga-------tggatgagtggatggttggatgaatggataggtggatagatgggtagatgaatgggtgg i calJac1.Contig6069 C 0 M 2151 s tupBel1.scaffold_125018.1-1020051 193391 45 - 1020051 ggtaaattagtgga-------tGAAGggatggatggtgggaaggatggaagg---------------------------- i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9673054 69 + 15951348 AGCGAGCCGCAgga-------tagatggatggacgggcgcgtgagtgagagggtggatggctggat----gaatggatgg i cavPor3.scaffold_42 I 7 C 0 s oryCun2.chrUn0985 31517 49 + 42081 TGtgggtgcacggg-------tggatggatggacag------------aggggtggag------------gggtggatgg i oryCun2.chrUn0985 I 7 C 0 s bosTau4.chr29 48982055 74 + 51998940 gatggatggatggatatttggtagatggatggacggatgtttga-cagatggatgga-----tggtagatgaacggatgg i bosTau4.chr29 I 310 C 0 s canFam2.chr18 7543121 64 - 58872314 gatgaataaatgga-------tggatggataggtggatggatga-tgaatggaaaga--------tgtgtggatggttgg i canFam2.chr18 I 17 C 0 s equCab2.chr12 28947009 57 + 33091231 gatgaataaatgca-------tGCatgcatgtatgcatgggtga--------ataga--------tggatggatggttga i equCab2.chr12 I 17 C 0 e ochPri2.scaffold_12461 23585 7384 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e pteVam1.scaffold_22742 7765 117 - 9737 I e papHam1.scaffold6638 84332 774 + 109049 I e myoLuc1.scaffold_155660 40718 343 - 124081 I e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e panTro2.chr11 68207702 1376 + 134204764 M a score=34733.000000 s hg19.chr11_gl000202_random 22322 27 + 40103 at-----aggtggatg---gatgg-atggatgga-----tg s gorGor1.Supercontig_0015245 52756 27 + 115376 at-----ggatggatg---gatgg-atggatgga-----tg i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126005872 27 - 132107971 at-----ggatggatg---ggtgg-gtggatgga-----tg i ponAbe2.chr11 I 732 C 0 s rheMac2.chr14 128167765 26 - 133002572 at-----gg-tggatg---gatgg-atggatgga-----tg i rheMac2.chr14 C 0 I 1068 s tupBel1.scaffold_125018.1-1020051 193436 27 - 1020051 at-----ggatgggtg---aatga-gagggttga-----tg i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9673123 25 + 15951348 gt-----agat-gata---aatgg-atgaat-gA-----CA i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 31566 27 + 42081 ac-----agatgggcg---gatgg-atggatgga-----CA i oryCun2.chrUn0985 C 0 I 7 s ochPri2.scaffold_12461 30969 33 - 40248 GTTGCTGgggtgggtg---gatggaatggatggg-----tg i ochPri2.scaffold_12461 I 7384 C 0 s bosTau4.chr29 48982129 25 + 51998940 ---------atagatgtttgatgg-atggatgga-----t- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28947066 22 + 33091231 ---------gtggatg---gatgg-atggatgga-----t- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7543185 21 - 58872314 ---------atggat----gatgg-atggataga-----t- i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_22742 7882 27 - 9737 ---------atggatg---gaggg-agggagggagggagg- i pteVam1.scaffold_22742 I 117 C 0 e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e papHam1.scaffold6638 84332 774 + 109049 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 40718 343 - 124081 I e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e panTro2.chr11 68207702 1376 + 134204764 M a score=53257.000000 s hg19.chr11_gl000202_random 22349 93 + 40103 gat------------ag----atgggtg-------ggtgaatggataaatgggtgggttggtgagtggatggatgggtagatagatgaataggtgg---atagatgg----------atggtt-ggatgg s ponAbe2.chr11 126005899 93 - 132107971 gat------------ag----atgggtg-------ggtgaatggataaatgggtgggttggtgggtggatagatggatgggtagatggatggatgg---atggatag----------atggat-ggatgg i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 52783 105 + 115376 gatggatggatggatag----atgggtg-------ggtgaatggataaatgggtgggttggtgagtggatggatgggtagatagatgaataggtgg---atagatgg----------atggtt-ggatgg i gorGor1.Supercontig_0015245 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 193463 76 - 1020051 ggt------------gg----atggatg-------agtagaaagataaatgggtggatgtgagggtgggtgga-gggtaggtagatgaatgggtgg---atgg--------------------------- i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9673148 69 + 15951348 GGT------------AG----GCAGAAG-------GATGAGAGGGAggg------------tggatggatggatggatggatggatggatgggtgg---gtggatgg----------------------- i cavPor3.scaffold_42 C 0 I 4 s oryCun2.chrUn0985 31600 68 + 42081 AAT------------AG----ACGGGTG-------GGTGTGGTGGGAGG-------------GAGTTTACGTATGTGAGGGTGGACAGAAGGGCAG---GCAGGTGG----------------------- i oryCun2.chrUn0985 I 7 C 0 s ochPri2.scaffold_12461 31002 87 - 40248 aat------------gg----atgggtg-------ggtggaatgaagggtgcgtgggt---tgggtgggtggatggatgagtgcgtggatgggtgg---gcagatgg-------------atg-ggatag i ochPri2.scaffold_12461 C 0 C 0 s bosTau4.chr29 48982154 98 + 51998940 ----------------gcttcatgtatggattcgtggtgggtggatggatggatggatggatgaatgt---------ttggtagatgaatgggtatttggtggatggatg------catagat-ggatgg i bosTau4.chr29 C 0 I 15 s equCab2.chr12 28947088 87 + 33091231 ----------------g----atggatg-------gatgagtgggtggatagatggatggagggatg-----------gGGTGGAT---TGGGTGG--AACAGAACAATGCCATATGGTTGATGGGATGG i equCab2.chr12 C 0 I 1131 s canFam2.chr18 7543206 87 - 58872314 ----------------g----atgaatg-------ggtgagtgtataggtgggtggatggatggatga---------tggacaaatagatgagtgg---gtagatggatg---gacagtagat-ggatgg i canFam2.chr18 C 0 I 3 s pteVam1.scaffold_22742 7909 96 - 9737 ----------------g----atggatg-------ggtgggtgggtgaatggctggctggctggctggctggctggctggctggctggctgggtggataattgatggacg------ggtggat-ggatgg i pteVam1.scaffold_22742 C 0 C 0 e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e papHam1.scaffold6638 84332 774 + 109049 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 40718 343 - 124081 I e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e rheMac2.chr14 128167791 1068 - 133002572 I e panTro2.chr11 68207702 1376 + 134204764 M a score=11440.000000 s hg19.chr11_gl000202_random 22442 89 + 40103 aagaatatatgggcaggtaggtggata---taagag------------tgggtggatggatggatgaa-------t-gggaggatggtag---gatgggagggtggatgta----tggt s ponAbe2.chr11 126005992 100 - 132107971 aagaatgtat-ggcaggtaggtggata---tatgggtaggtgaatggatggatggatgggtggatgaa-------t-gggaggatggtag---gatgggagggtggatgta----tggt i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 52888 89 + 115376 aagaatatatgggcaggtaggtggata---taaggg------------tgggtggatggatggatgaa-------t-gggaggatggtag---gatgggagggtggatgtg----tggt i gorGor1.Supercontig_0015245 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 193539 71 - 1020051 -tggatctataaacag--------------------------------tagatgggtgcatgggtgga-------t-gtgagggtgggtg---gaggggtaggtagatgaa----tggt i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9673221 33 + 15951348 -------------------------------------------------------atgggtagat-----------------gataaatg---gatgaat-----gacagg----ta-- i cavPor3.scaffold_42 I 4 C 0 s ochPri2.scaffold_12461 31089 88 - 40248 atgggtgaat---tgagtgagtggatg---agcgggtgga--------tggatgggtgggtggatgga-------t-gagtggatgggtg---gatggatgggtagatggg----tg-- i ochPri2.scaffold_12461 C 0 C 0 s bosTau4.chr29 48982267 78 + 51998940 ----------------aaggatggatgcttggtgaa------------tgggtggata-tttggtaga-------t-ggacggatggatgtttgttagtaggatagaccgatgtt---- i bosTau4.chr29 I 15 C 0 s canFam2.chr18 7543296 69 - 58872314 ----------------atggatgagtg---agtgag------------tgggtggatg-atggatgga-------tggggtggctagatg---gataggtggctagatgat-------- i canFam2.chr18 I 3 I 6 s pteVam1.scaffold_22742 8005 77 - 9737 ----------------atggagggatg---ggcggg------------tggatggatgcatggatggagggagggtgggagggatggatg---aatgggtgggtggatgga-------- i pteVam1.scaffold_22742 C 0 I 4 e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e papHam1.scaffold6638 84332 774 + 109049 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 40718 343 - 124081 I e turTru1.scaffold_93657 9733 1965 - 12933 I e oryCun2.chrUn0985 31668 0 + 42081 C e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e equCab2.chr12 28947175 1131 + 33091231 I e rheMac2.chr14 128167791 1068 - 133002572 I e panTro2.chr11 68207702 1376 + 134204764 M a score=127538.000000 s hg19.chr11_gl000202_random 22531 98 + 40103 tgagtaggtggatggatg-----------ggtgggtgggtgggtggatggatgggtag------------atagatggatgaatg---gatggatg-aatggatg--------------gatggatg-gataagtggatg s ponAbe2.chr11 126006092 94 - 132107971 tgagtaggtggatggatg-----------ggtgggtggatggatggatggatggatgg------------atgggtggatggatg---gatggatg-gacgggtg--------------gatggatg-ga----tgggtg i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 52977 98 + 115376 tgagtaggtggatggatg-----------ggtgggtgggtgggtggatggatgggtag------------atggatggatgaatg---gacggatg-aatggatg--------------gatggatg-gataggtggatg i gorGor1.Supercontig_0015245 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 193610 79 - 1020051 ggag--ggtggat----------------ggtggatgta-aggtgagtggacgggtag-----------------tagatgaatggt-gatggaggtagtagatg------------ctgatggaag-g----------- i tupBel1.scaffold_125018.1-1020051 C 0 I 2448 s bosTau4.chr29 48982345 97 + 51998940 -tggtagatggatggatg-----------aatgTGTAG-TGGTTAAatggatgaatggatgcttg-----atggatggatccatggcagatggatg-gatgtata-----------tttggtagatg------------- i bosTau4.chr29 C 0 C 0 s canFam2.chr18 7543371 107 - 58872314 tgggtagatggatggatgatggacaaatagatgagtgggtggatggatgcacaggtagatggatggacg-atggatgagtgagtg---agtgggtg-gatggat---------------gatggatg------------- i canFam2.chr18 I 6 C 0 s myoLuc1.scaffold_155660 41061 98 - 124081 tggatggatggatggatg-----------gatggatggatggacagttggacaagtagacaggtgggcatatggatggatgaatg---ggtggtta-gatggaca--------------agttgatg------------- i myoLuc1.scaffold_155660 I 343 C 0 s pteVam1.scaffold_22742 8086 85 - 9737 tggctggctggctggctg-----------gctggctggctggctggctggataattg-------------atggataggtggatg---gatggatg-gagggatg--------------gatggatg------------- i pteVam1.scaffold_22742 I 4 C 0 s speTri1.scaffold_25523 500 80 + 2129 --------tggatggacg-----------agtgggtgggtgggcagacgggt-ggtag------------gtgggtgggtgggta---aatggaca-gatggagg-----------ccgagtgggtg------------- i speTri1.scaffold_25523 N 0 C 0 s ochPri2.scaffold_12461 31177 102 - 40248 ------gg----tgaatg-----------agtgggtggatgagtggatgggtggatgg------------gtgcgtgggtgggtg---gatggatg-gatgAAGGGGCCAGCACTCTGGCATAGCTGG-TTAAGCTGCTG i ochPri2.scaffold_12461 C 0 I 241 s cavPor3.scaffold_42 9673254 76 + 15951348 ------ggcagaaggatg-----------agagggagggtggatggatggatgggtgg------------atggatggatgggtg---gatggatg-gataga------------------tggatg------------- i cavPor3.scaffold_42 C 0 C 0 s papHam1.scaffold6638 85106 92 + 109049 ------ggtggatggatg-----------ggtagatggatggatgaatgcatgggtgg------------gtaggtggatatatg---agtgggtg-gatggatg--------------gatggatg-gatgaatgtatg i papHam1.scaffold6638 I 774 C 0 e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e calJac1.Contig6069 86127 2151 + 235769 M e turTru1.scaffold_93657 9733 1965 - 12933 I e oryCun2.chrUn0985 31668 0 + 42081 C e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e equCab2.chr12 28947175 1131 + 33091231 I e rheMac2.chr14 128167791 1068 - 133002572 I e panTro2.chr11 68207702 1376 + 134204764 M a score=35480.000000 s hg19.chr11_gl000202_random 22629 41 + 40103 ga-tggatggatggatg---aatgg----atggatggatg-----------gatggatgg s papHam1.scaffold6638 85198 41 + 109049 gg-tgggtaggtggata---tatgg----gtggatggatg-----------gatggatgg i papHam1.scaffold6638 C 0 C 0 s ponAbe2.chr11 126006186 16 - 132107971 ga-tggatggatggatg------------------------------------------- i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 53075 16 + 115376 ga-tggatggatggatg------------------------------------------- i gorGor1.Supercontig_0015245 C 0 C 0 s speTri1.scaffold_25523 580 45 + 2129 ga-cagatggacagacg---ggtggccgagtgggtggaca-----------gatggacag i speTri1.scaffold_25523 C 0 C 0 s cavPor3.scaffold_42 9673330 41 + 15951348 ga-tggatggatAGGTA---GGTGG----GTGAGGAGACG-----------GATGAATGT i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48982442 55 + 51998940 ga-aggatggatggatgtttgatgg----ctgggtggatgtttggtggtaagataggttg i bosTau4.chr29 C 0 I 11 s canFam2.chr18 7543478 41 - 58872314 gatggggtggctagatg---gatgg----gtggctagat------------gatggatag i canFam2.chr18 C 0 I 3 s myoLuc1.scaffold_155660 41159 41 - 124081 ga-tggatggatggatg---gatgg----atggatggatg-----------gatggatag i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 8171 41 - 9737 ga-gggatgggtggatg---gaggg----atggagggatg-----------ggtgggtgg i pteVam1.scaffold_22742 C 0 C 0 e ochPri2.scaffold_12461 31279 241 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e felCat3.scaffold_135390 63224 398 + 302526 I e calJac1.Contig6069 86127 2151 + 235769 M e turTru1.scaffold_93657 9733 1965 - 12933 I e oryCun2.chrUn0985 31668 0 + 42081 C e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e equCab2.chr12 28947175 1131 + 33091231 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e rheMac2.chr14 128167791 1068 - 133002572 I e panTro2.chr11 68207702 1376 + 134204764 M a score=24717.000000 s hg19.chr11_gl000202_random 22670 44 + 40103 atggatggatgg-------atggatggatg---gaCGATTTAAGTGGGTGGATG s papHam1.scaffold6638 85239 37 + 109049 atggatggatgg-------atggatggatg---gatgATTTCAGTGG------- i papHam1.scaffold6638 C 0 C 0 s speTri1.scaffold_25523 625 29 + 2129 ac----gggtgg-------gtggacagagg---gatgg----GGTGG------- i speTri1.scaffold_25523 C 0 C 0 s cavPor3.scaffold_42 9673371 26 + 15951348 AC----CGATGG-------GAATATGGGAG---GATAG-------GA------- i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48982508 38 + 51998940 at----gaatgg-------gtggatgaatgttcggtg-----gatggatggatg i bosTau4.chr29 I 11 C 0 s canFam2.chr18 7543522 31 - 58872314 gt----ggatgg-------atggatgactg---gatg---------gaCAGATG i canFam2.chr18 I 3 C 0 s felCat3.scaffold_135390 63622 41 + 302526 AT----GGATGGGGCCTCCatagatggatg---gatg-----gat-gatgaatg i felCat3.scaffold_135390 I 398 C 0 s myoLuc1.scaffold_155660 41200 35 - 124081 at----gaatgg-------atagatggatg---gatg-----agtggatagatg i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_22742 8212 34 - 9737 at----gggtgg-------atggagggatg---ggtg-----ggtgga-gggtg i pteVam1.scaffold_22742 C 0 C 0 s micMur1.scaffold_10910 51426 33 + 52708 ------ggatgg-------atgaactgatg---gatg-----ggtggatggatg i micMur1.scaffold_10910 N 0 C 0 s ponAbe2.chr11 126006202 41 - 132107971 ---gatggatgg-------atggatggatg---gacgatttaagtgggtggatg i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 53091 25 + 115376 --------------------------gatg---gatgATTTAAGTGGGTGGATG i gorGor1.Supercontig_0015245 C 0 C 0 e ochPri2.scaffold_12461 31279 241 - 40248 I e tarSyr1.scaffold_429723 155 19 - 1268 I e calJac1.Contig6069 86127 2151 + 235769 M e turTru1.scaffold_93657 9733 1965 - 12933 I e oryCun2.chrUn0985 31668 0 + 42081 C e proCap1.scaffold_13667 21148 5848 - 46842 I e loxAfr3.scaffold_159 89935 5993 + 1045236 I e equCab2.chr12 28947175 1131 + 33091231 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e rheMac2.chr14 128167791 1068 - 133002572 I e panTro2.chr11 68207702 1376 + 134204764 M a score=-54304.000000 s hg19.chr11_gl000202_random 22714 53 + 40103 TGTGGATG----------------CATGGAGGGTAAT-----TCCCC---CTCTGGTCTCA-CTCC--TGATCACCTCAT s pteVam1.scaffold_22742 8246 57 - 9737 ggtgggtggaggggtggagggatagagggagggatgA-----TCG---------------T-CCCT--GTGTCCCTTTGC i pteVam1.scaffold_22742 C 0 C 0 s myoLuc1.scaffold_155660 41235 69 - 124081 gatggatgagtggatggagggatggatggGAGGCTGC-----TTGAC---CTATGGTCTCA-CCCC--TCATCACGTTGC i myoLuc1.scaffold_155660 C 0 C 0 s felCat3.scaffold_135390 63663 54 + 302526 tgtgggtg----------------gagggGAAGGCGC-----GGGGC---CTATGCTCTCA-CCTC-CGGGTCACCTCAC i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7543553 55 - 58872314 CATGGGCG----------------GAGGGGAAGCTGC-----ATGGC---CTATGCTCCCA-CCCCGAGGGTCATCTCAC i canFam2.chr18 C 0 C 0 s bosTau4.chr29 48982546 57 + 51998940 gatgggtg-------------tttggatggGAGACGC-----TAGCC---TTACGGGCTCA-CTCC-TGCATCGCTTCCC i bosTau4.chr29 C 0 C 0 s oryCun2.chrUn0985 31668 51 + 42081 --TGGGTG----------------GACGGGATGCAGTTCACCTCAGG--------GCCCCA-CCGC--CGGTCCCCGCAC i oryCun2.chrUn0985 C 0 C 0 s ochPri2.scaffold_12461 31520 39 - 40248 TAAGGCTG----------------AGTGGGGCG---------TCACT--------ACCCTG-CTGA--TGTCACT----- i ochPri2.scaffold_12461 I 241 C 0 s speTri1.scaffold_25523 654 41 + 2129 ---GGATG----------------G-----------------TCATTTAGCACATACTCTC-TTCC--TGGTCGCTCCTC i speTri1.scaffold_25523 C 0 C 0 s cavPor3.scaffold_42 9673397 37 + 15951348 ---GACTG----------------T-----------------TCACT-----CCAGCTCTCATTCC--TGGCCACCTCAC i cavPor3.scaffold_42 C 0 C 0 s micMur1.scaffold_10910 51459 50 + 52708 agtggatg----------------gat-gagGGTCAT-----TCACC---CTAT-GTCTCA-CCCC--AG-TCACCTCAT i micMur1.scaffold_10910 C 0 C 0 s papHam1.scaffold6638 85276 52 + 109049 -GTGGATG----------------CATGGAGGGTAAT-----TCACC---CCCTGGTCTCA-CTCC--TTATCACCTCAT i papHam1.scaffold6638 C 0 C 0 s ponAbe2.chr11 126006243 51 - 132107971 tgtggatg----------------aatggaGGATAAT-----TCACC-----CTGGTCTCA-CTCC--TGATCACCTCAT i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 53116 53 + 115376 TGTGGATG----------------CATGGAGGGTAAT-----TCCCC---CTCTAGTCTCA-CTCC--TGATCACCTCAT i gorGor1.Supercontig_0015245 C 0 C 0 s loxAfr3.scaffold_159 95928 40 + 1045236 ----------------------------GGAGGGCGC-----ACACT---CCCACGGTCTC-GCCA--GGGTCACCTCA- i loxAfr3.scaffold_159 I 5993 C 0 e tarSyr1.scaffold_429723 155 19 - 1268 I e calJac1.Contig6069 86127 2151 + 235769 M e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e equCab2.chr12 28947175 1131 + 33091231 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e rheMac2.chr14 128167791 1068 - 133002572 I e panTro2.chr11 68207702 1376 + 134204764 M a score=238066.000000 s hg19.chr11_gl000202_random 22767 122 + 40103 CTGGA-AGATGCTGGAGGTACAATTGCCATGATTACTAATTCAGGAGATACTCTCATCTGAATGACCCTT-TTGGCCAGAAGTATCCAGACTGGCACTGGCTGCTGCGTTTGTTCAGTCATACT s papHam1.scaffold6638 85328 122 + 109049 CTGGG-AGAGGCTGGAGGTACTATTGCCATGGTTATTAATTCAGGAGATACTCTCATCTGAATCACCCTT-TTGGCCAGAAGTATCCAGACTGGCACAGACTGCTGCATTTGTTCAATCATACT i papHam1.scaffold6638 C 0 C 0 s panTro2.chr11 68209102 122 + 134204764 CTGGA-AGATGCTGGAGGTACAATTGCCATGATTACTAATTCAGGAGATACTCTCATCTGAATGACGCTT-TTGGCCAGAAGTATCCAGACTGGCACTGGCTGCTGCGTTTGTTCAGTCATACT i panTro2.chr11 M 1376 C 0 s gorGor1.Supercontig_0015245 53169 122 + 115376 CTGGA-AGATACTGGAGGTACAATTGCCATGATTACTAATTCAGGAGATACTCTCATCTGAATGACCCTT-TTGGCCAGAAGTATCCAGACTGGCACTGGCTGCTGCATTTGTTCAGTCATACT i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126006294 121 - 132107971 CTGGA-AGATGTTGGAGGTACAATTGCCA-GATTACTAATTCAGGAGATACTGTCATCTGAATGACCCTT-TTGGCCAGAAGTATCCAGACTGGCACTGGCTGCTGCGTTTGTTCAACCATACT i ponAbe2.chr11 C 0 C 0 s micMur1.scaffold_10910 51509 120 + 52708 CTGAA-GGAGCCTGGAGATGCAATTCCCATGACTGCTAATT-AGGAGGTGCTCGTAGCCGAATGATCCTC-CTGGCC-GGAGTGTCTGGCCTGGCACAGGCTGCTGGTTTTGCGCAATCACACT i micMur1.scaffold_10910 C 0 C 0 s cavPor3.scaffold_42 9673434 106 + 15951348 CTGGT-AGAGGCTGGAGCTAC-AATGCCATGTTTGCTAATTTGGAAG------GCAGCTGAGTAATC---------CAGAAATACCCAGATCGATGCAGACG-CTAGCTGTGCATAATCACACT i cavPor3.scaffold_42 C 0 C 0 s speTri1.scaffold_25523 695 103 + 2129 CT-------TGCTGGA-CTAC-AGTGCTGTGGCCGTTCCCTCAGGGGCACG-CCTAGCTGGGTCACC-----------GAAAGGACCCGGCTGATGCGGGTGACCAGATCAGGGTGATGAGGAC i speTri1.scaffold_25523 C 0 C 0 s ochPri2.scaffold_12461 31559 92 - 40248 --------GTCCTGGACGGACCAACAGCGAAGTTGTACACCTGAAAAGTTC---TGGCCGAACAGCCCTG-TTGGCCAGAAGGCTCCGGACTGGCACGGGTT-CT------------------- i ochPri2.scaffold_12461 C 0 C 0 s oryCun2.chrUn0985 31719 120 + 42081 CC-GG-AGGCCCTGCGGACACAAATGGCACAGCTGACAACGTGGGAGGGTCCCTTAGCCGAGGGATCCCG-TGGGCCGGCCGTCTCCACGCTGGCCCAGGTG-CTGGGTTTGTGCGATCACCTT i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48982603 82 + 51998940 CTGGG------------ATGCAAACACTG------------TGGGAGGCCCTCTTAGCCCAACAACACCA-CTGGCCGTGAGCATGCAGACTGGCACCGCCTGCC-----------------CT i bosTau4.chr29 C 0 C 0 s canFam2.chr18 7543608 109 - 58872314 CTGGG-GGACACTGGAGGTGCAAATGCTGTGGCTGTTAATTCAAGAGGCACTCTTAGCCAAG--------------CAGAGGTATCCAGACTGGCACAGGCTGCTGGGTTTGTGCAATTGCACT i canFam2.chr18 C 0 C 0 s felCat3.scaffold_135390 63717 122 + 302526 CCGGG-GGACCCTGGAGGTGCAAATGCTAAGGTTGTTAATTCGGGAGGCACTTTTAGCCGAACGGTCCCG-TTGGCCAGAAGTATCCAGACCGGCACAGGCCGCTGGGTTTGCACCACTGCACT i felCat3.scaffold_135390 C 0 C 0 s myoLuc1.scaffold_155660 41304 121 - 124081 CACGG-GGAGACTGGAGGTGCAAACGCCATAGCTCTTCGTTTGGAAGGCGCTCTTAGCTGAGTGACCCCG-TTGGCCAGCAGTATGCAGCCTGGTGCAGGCCGCT-GGGTTGCACAGTCGCACT i myoLuc1.scaffold_155660 C 0 M 865 s pteVam1.scaffold_22742 8303 110 - 9737 CTTGGAGGTGACTGGAGGGGCAAAGGCCACGATGGTTCACCTGGAAGGTGCTCTCAG-TGAATGGTCCTGTTTGGCTAGAAACGCCCCGTCTGGT-------------TTTGTGCAATCGCACT i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 95968 80 + 1045236 --------------------CACACGCTGTGGCTGTTAACTCAGGA--------------------CCAA-CTCTCCAGAAGCAAGCGA--TGGCACCGGCTGCTGGG-CCATGCGGACACACT i loxAfr3.scaffold_159 C 0 C 0 e tarSyr1.scaffold_429723 155 19 - 1268 I e calJac1.Contig6069 86127 2151 + 235769 M e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e equCab2.chr12 28947175 1131 + 33091231 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e rheMac2.chr14 128167791 1068 - 133002572 I a score=88237.000000 s hg19.chr11_gl000202_random 22889 41 + 40103 CCAGCAATTTCCCTGCCAGCTGCACAGTGTGGGA-TTTTTTT s papHam1.scaffold6638 85450 40 + 109049 CCAGCAATTTCCCTGCCAACTGCGCAGTGTGGGA--TTTTTG i papHam1.scaffold6638 C 0 C 0 s panTro2.chr11 68209224 41 + 134204764 CCAGCAATTTCCCTGCCAGTTGCACAGTGTGGGA-TTTTTTT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 53291 42 + 115376 CCAGCAATTTCCCTGCCAGTTGCACAGTGTGGGATTTTTTTT i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126006415 41 - 132107971 CCAGCAATTTCCCTGCCGGTTGCACTGTGTGGGA-TTTTTTT i ponAbe2.chr11 C 0 C 0 s micMur1.scaffold_10910 51629 35 + 52708 CCAGC-ATTCCCATGCCGGTTGGACA--ACAGGA----TTTT i micMur1.scaffold_10910 C 0 C 0 s cavPor3.scaffold_42 9673540 37 + 15951348 CCATCAG-TTCCGTGCCAATTGCACACTATGGGA----TTTT i cavPor3.scaffold_42 C 0 C 0 s speTri1.scaffold_25523 798 35 + 2129 CCATCAA-GCCTACGCGGTTTG--CACCGTGGGG----TTTG i speTri1.scaffold_25523 C 0 C 0 s ochPri2.scaffold_12461 31651 30 - 40248 --------CTGGATGTCACTTGCATATGATGAAG----TTTG i ochPri2.scaffold_12461 C 0 C 0 s oryCun2.chrUn0985 31839 38 + 42081 CCAGCACCTTCCATGCCAGCTGCACAAGGGAAGG----GTTG i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48982685 37 + 51998940 CCAGCAATTTCCATGCCAGTTGCCAGGTGAGGTT-TTT---- i bosTau4.chr29 C 0 C 0 s canFam2.chr18 7543717 41 - 58872314 CCAGTAATTTCCATGCCAGCTGCCAGGTAAGATG-TTTTTTC i canFam2.chr18 C 0 C 0 s felCat3.scaffold_135390 63839 41 + 302526 CCAGCAATTTCCATGCCGGTTGCCAGGTGAGATT-TTTTTTT i felCat3.scaffold_135390 C 0 C 0 s pteVam1.scaffold_22742 8413 41 - 9737 CCAGCAATTTCCATGCCGGTTGCCAGGGGAGATT-GTTTTTT i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 96048 38 + 1045236 -TTACAATCCCCATGCCAGGTGCCCACTGTGTGA-TCGCT-- i loxAfr3.scaffold_159 C 0 C 0 e tarSyr1.scaffold_429723 155 19 - 1268 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 21148 5848 - 46842 I e equCab2.chr12 28947175 1131 + 33091231 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e rheMac2.chr14 128167791 1068 - 133002572 I a score=93401.000000 s hg19.chr11_gl000202_random 22930 110 + 40103 T-CACTACTTG----TCCCCTGACTTAGATATCCTGAAAAGC-AATGGAGTCATCCCCGACCG------TGCAAGACAGCGGC--CTCCCAGACCACAGCAGGCATCCCAGACA-----GCATCGT--CAT s papHam1.scaffold6638 85490 110 + 109049 T-CACTACTTG----TCCCCTGACTTAGAAATCCTGAAAAGC-AATGGAGTCATCCCCGACCC------TGCAGGACAGGGAC--CTCCCAGACCACAGTAGGCATCCCAGATG-----GCACTGT--CAT i papHam1.scaffold6638 C 0 C 0 s panTro2.chr11 68209265 110 + 134204764 T-CACTACTTG----TCCCCTGACTTAGATATCCTGAAAAGC-AATGGAGTCATCCCCGACCC------TGCAAGACAGCGGC--CTCCCAGACCACAGCAGGCATCCCAGACA-----GCATCGT--CAT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 53333 110 + 115376 T-CACTACTTG----TCCCCTGACTTAGATATCCTGAAAAGC-AATGGAGTCATCCCCGACCC------TGCAAGACAGCGGC--CTCCCAGACCACAGCAGGAATCCCAGACA-----GCATCAT--TAT i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126006456 110 - 132107971 T-CACTACTTG----TCCCCTGACTTAGATATCCTGAAAAGC-AATGGAGTCATCCCCGACCC------TGCAAGACAGAGGC--CTCCCAGAACACAGCAGACATCCCAGATG-----GCATCAC--CAT i ponAbe2.chr11 C 0 C 0 s micMur1.scaffold_10910 51664 107 + 52708 T-CACTACTTT----TTC---GACTTGGAAATCTTGAAAAAC-AAGGGGGTCATCCCCAAACC------TGCAGGAGAGCAGC--CTCCCAGACCCCGGCAGGTGTCACAGACA-----GCGCCCC--CAT i micMur1.scaffold_10910 C 0 C 0 s cavPor3.scaffold_42 9673577 81 + 15951348 T-CATCACTTG----TTTCC-AACTTAGAAATCTTGAAA--C-CAGACAGCAGCCTC-----C------TAGACCTTAACAGG--CTTT------GCAGGCAACACCC----C------------------ i cavPor3.scaffold_42 C 0 C 0 s speTri1.scaffold_25523 833 42 + 2129 T-CACTATTTG----TTCCC-TGACTGAAAGC-----------------GGGGCCCC-----C---------------------------------------GCACCC----C------------------ i speTri1.scaffold_25523 C 0 C 0 s ochPri2.scaffold_12461 31681 79 - 40248 T-CACTGCCTG----CCCCC-AACTCAGAATT-------------AGGAGTGGCCTCTGAACC------TGCAGGTCGACAGC--CTCC-------TGACCGATGACCATGAC------------------ i ochPri2.scaffold_12461 C 0 C 0 s oryCun2.chrUn0985 31877 95 + 42081 T-CACCGCGCG----TTCTCGGACTCTGACTTTGAAAAA--C-AACGGAGCAGCCTC-AAACC------TGCAGGTCAGCAGC--CCCC-AGCCCACGGCCCGCGGCCTTGGT------------------ i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48982722 102 + 51998940 --CACTGCTTA----TTCCCTGGCTTGGAAACATGGAGAAACAAACCTCAGCTTCCCCGAGGC------TGCA-------AGC--CTCTCCTCGCACAGCAGGCGCCCCGGCCG-----GCACCCCAC--- i bosTau4.chr29 C 0 C 0 s canFam2.chr18 7543758 103 - 58872314 T-----ACTTA----TTCCCTGGCTTGGAAATCTGGAAAAACAAACCACATCATCCCTGAGCCACGGTGTAAAGGACTGCGGC--CTCCTGCACCACAGCAGTCACCC------------TGCTCA----- i canFam2.chr18 C 0 C 0 s felCat3.scaffold_135390 63880 102 + 302526 TTTACAACTTA----TTTCCTGGCTTGGAAATCTGGAAAAACAAACCGCGTGGTCCCCAAGCC------TGCAGGACCGCAGC--CTCCTGCCCCACAGCAGGCACCC------------CGCTCA----- i felCat3.scaffold_135390 C 0 C 0 s pteVam1.scaffold_22742 8454 109 - 9737 T-TACTACTTA----CTCCCTGGCTTGAAAATCCGGGAAAAC-AACAGTGCTGTCGTCAAGCC------TGAAGGACAGCAGCG-CCCCCAGACCACAGCAGGCATCCCAGCTG-----GCACCCA-T--- i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 96086 111 + 1045236 --CACTGATTGTTCCTTCCCTGGCAAGGAAATCTGGAAAAAC-ACCCGAGTG---TCCAAGCC------CGGAGGACAGCAGCTTCCTCCGGACCACAGAGAGCACCCCAGCCGCACCCACAC-------- i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 26996 105 - 46842 T-CACTGATTG----TCCCCCGGTGGGGGGCCCTGGACAAAC-CCCTGAGTG---TCCGAGTC------AGGGGGACAGCAG---CCCTGGGACCACAGCAGGCTTCCCCTCCACACTCACAC-------- i proCap1.scaffold_13667 I 5848 C 0 e tarSyr1.scaffold_429723 155 19 - 1268 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 9733 1965 - 12933 I e equCab2.chr12 28947175 1131 + 33091231 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e rheMac2.chr14 128167791 1068 - 133002572 I a score=158400.000000 s hg19.chr11_gl000202_random 23040 83 + 40103 GTGCCCCCAGGTGTCCTGGGGA--------GCCCACTCCAGATGTGCCAGCCTGAGAAGGGAGCTTTGCCTCACCGG-CCCATGGCTCTGGG s ponAbe2.chr11 126006566 83 - 132107971 GTGCCCCCAGGTGTCCTGGGCA--------GCCcactccagatgtgccagcctgagaagggagccttggctcgccgg-cctatggctctggg i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 53443 83 + 115376 GTGCCCCCAGGTGTCCTGGGGA--------GCCCACTCCAGATGTGCCAGCCTGAGAAGGGAGCTTTGCCTCACCGG-CCCATGGCTCTGGG i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68209375 83 + 134204764 GTGCCCCCAGGTGTCCTGGGGA--------GCCCACTCCAGATGTGCCAGCCTGAGAAGGGAGCTTTGCCTCACCGG-CCCATGGCTCTGGG i panTro2.chr11 C 0 C 0 s papHam1.scaffold6638 85600 83 + 109049 GTGCCCCCAGGTGTCCTGGGCA--------GCCcactccagatgtgccagcctgagaagggagccttgccttgccgg-cccatggctctggg i papHam1.scaffold6638 C 0 C 0 s tarSyr1.scaffold_429723 174 75 - 1268 GTGCCCCCA---GCCCGTGGCA--------GTGCCCGTCAG----GGCCGCCTGCGGAGAGAGCCCAGCCTCGACGG-CC-ATGTTTCTGCG i tarSyr1.scaffold_429723 I 19 C 0 s micMur1.scaffold_10910 51771 80 + 52708 ---GCCCCGAGCGACCTGGGAG--------CCCCGCTCTGGATGCGCCCGCCTGGGGAAAGAGCCTTGGCTGGCCGG-CCCGAGGTTCTGGG i micMur1.scaffold_10910 C 0 C 0 s cavPor3.scaffold_42 9673658 82 + 15951348 TAGTGTTCCAGGGTCCTGGGCA--------GCCCACTGTTGACGCACCAGTCTGAGGAAACTGCCTTGTCCTGCTGG-TCCATGTTGCTGG- i cavPor3.scaffold_42 C 0 C 0 s speTri1.scaffold_25523 875 82 + 2129 GAGTGCCCCGGCACGCTGGGC---------GCCCACTCTGAGCGTGCGGGTCTGGGAACACCGCCTGGCCTCGCCGG-ACGCTGTCTCTGGC i speTri1.scaffold_25523 C 0 C 0 s ochPri2.scaffold_12461 31760 71 - 40248 CGGCGGCCA---GCGACGGGCG--------GGCCTCAGTGTCCTCAGCAG------GAGACCCAC----CCTGCCAGTCCCGCGTGGCCAGG i ochPri2.scaffold_12461 C 0 C 0 s oryCun2.chrUn0985 31972 85 + 42081 CAGCCCCCACGGGCGCCGGGTGTGCTGGGCGGCCGCCCCGGACACAACCG--AGGAGAGACCCTC----CACGCTGG-CCCACGGGGCTGGG i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48982824 81 + 51998940 ACTCCACCAGGTGTCCCGGCTC--------GGATGCTCTGGAA--GGCGGCCCACGGAGAGAACCCCTCCATGCCGG-CCCGTGTTCCTGGG i bosTau4.chr29 C 0 C 0 s canFam2.chr18 7543861 75 - 58872314 ----AGCCAGGTGCCCTGGGCG--------GTCTGCTCTGGAC--ACCGCCCC--AAAGACAGCCTTGCCTTGCTGG-CCCACGTTGCTGGG i canFam2.chr18 C 0 C 0 s felCat3.scaffold_135390 63982 77 + 302526 ----CCGCAGGTGTCCTGGCCA--------GTCTGCTCTGGAC--ACCGGCCCGGAGAGGGAGACTTGCCCTGCCGG-CCCGTGTTCCTGGG i felCat3.scaffold_135390 C 0 C 0 s pteVam1.scaffold_22742 8563 78 - 9737 GGGCCCCCAGGTGTCCTGGGCC--------GTCCCCCGTGGCC--ACCGTCC---GAGGAGAGCCTTGCTTTGCCAG-CCCATGTTGTTGGG i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 96197 66 + 1045236 --ATGCCTGCATGTCCCTAGCT--------GTCTGCTCTGGATGCACCGGCCACAGAAGAGAGCCTCGTTTTG-GGG--------------- i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 27101 56 - 46842 --ATGCCCACGTGTTCCCAG----------------TCTGGAT-CACAGGCCGCAGGCGAAAGCCTCATTTT--GGG--------------- i proCap1.scaffold_13667 C 0 C 0 e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 9733 1965 - 12933 I e equCab2.chr12 28947175 1131 + 33091231 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e rheMac2.chr14 128167791 1068 - 133002572 I a score=1951218.000000 s hg19.chr11_gl000202_random 23123 319 + 40103 ACAGATTT----CTAGACTCGGCTCTGAGAAAAAATAAACTTATGACAGAGTTTATCTGAAGGAGGAAGCAGCAATAAAGCGTGACACCCAGGGAGCAATG-AACAGAGAGCTCCGAGACAGACACAAAACAGGTAC-CGACAAATGTGGAACGCGTTATTTAAAATTCCCCGGGCTGACAGATCGG------ACAG-CA---TAG---CGGGCCAGACGCCG-GTTCG-AGGAGATGAAAAGAGTTCA-----TTTCCTTCCTCCAGATAAACACACTAGCAGCCAGATCTCTCTGT--GATGATAAATGGCTTCCTCCTGCCATCAGTGGGG-------------TTGTGGGGGGGCA s panTro2.chr11 68209458 319 + 134204764 ACAGATTT----CTAGACTCGGCTCTGAGAAAAAATAAACTTATGACAGAGTTTATCTGAAGGAGGAAGCAGCAATAAAGCGTGACACCCAGGGAGCAATG-AACAGAGAGCTCCGAGACAGACACAAAACAGGTAC-CGACAAATGTGGAACGCGTTATTTAAAATTCCCCGGGCTGACAGATCGG------ACAG-CA---TAG---CGGGCCAGACGCCG-GTTCG-AGGAGATGAAAAGAGTTCA-----TTTCCTTCCTCCAGATAAACACACTAGCAGCCAGATCTCTCTGT--GATGATAAATGGCTTCCTCCTGCCATCAGTGGGG-------------TTGTGGGGGGGCA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 53526 319 + 115376 ACAGATTT----CTAGACTCGGCTCTGAGAAAAAATAAACTTATGACAGAGTTTATCTGAAGGAGGAAGCAGCAATAAAGCGTGACACCCAGGGAGCAATG-AACAGAGAGCTCTGAGACAGACACAAAACAGGTAC-CGACAAATGTGGAACGCGTTATTTAAAATTCCCTGGGCTGACAGATCGG------ACGG-CA---TAG---CGGGCCAGACGCCG-GTTCG-AGGAGATGAAAAGAGTTCA-----TTTCCTTCCTCCAGATAAACACACTAGCAGCCAGATCTCTCTGT--GATGATAAATGGCTTCCTCCTGCCATCAGTGGGG-------------TTGTGGGGGGGCA i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126006649 319 - 132107971 actgattt----ctaaactcggctctgagaaaaaataaacttatgacagagtttatctgaaggaGGAAGCAGCAATAAAGCGTGACACCCAGAGAGCAATG-AACAGAGAGCTCCGAGACAGACACAAAACAGGTAC-CGACAAATGTGGAACGCGTTATTTAAAATTCCCCGGGCTGACAGATCGG------ACAG-CA---TAG---CGGGCCAGACGCCG-GTTCG-AGGAGATGAAAAGAGTTCA-----TTTCCTTCCTCCAGATAAACACACTAGCAGCCAGATCTCTCTGT--GATGATAAATGGCTTCCTCCTGCCATCAGTGGGT-------------TTGTGGGGGGGCG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128168859 318 - 133002572 ACAGATTT----CTAAACTCGGCTCTGAGAAAAAATAAACTTATGACAGAGTTTATCTGAAGGAGGAAGCAGCAATAAAGCGTGACACCCAGAGAGCAATG-AACAGAGAGCTCCAAGACAGACACGAAACAGGTAC-CGACAAATGTGGAACGCATTATTTAAAATTCCCCGAGCCGACAGATCGG------ACAG-CA---TAG---CGGGCCAGACGCCG-GTTCG-AGGAGATGAAAAGAGTTCA-----TTTCCTTCCTCCAGATAAACACGCTAGCAGCCAGATCTCTCTGT--GATGATAAATGGCTTCCTCCTGCCATCAGTGGGG-------------TTGC-GGGGAGTG i rheMac2.chr14 I 1068 C 0 s papHam1.scaffold6638 85683 318 + 109049 acagattt----ctaaactcggctctgagaaaaaataaacttatgacagagtttatctgaaggaGGAAGCAGCAATAAAGCGTGACACCCAGACAGCAATG-AACAGAGAGCTCCAAGACAGACACGAAACAGGTAC-CGACAAATGTGGAACGCATTATTTAAAATTCCCCGAGCCGACAGATTGG------ACAG-CA---TAG---CGGGCCAGACGCCG-GTTCG-AGGAGATGAAAAGAGTTCA-----TTTCCTTCCTCCAGATAAACACGCTAGCAGCCAGATCTCTCTGT--GATGATAAATGGCTTCCTCCTGCCATCAGTGGGG-------------TTGC-GGGGGGTG i papHam1.scaffold6638 C 0 C 0 s tarSyr1.scaffold_429723 249 275 - 1268 ACGGATCC----CTAAACGC-ACTCCAACAAGAAATAAACGTAGGACAGAGTTTATCTGGAGGAGGAAGTGGCAATAAAGTGTGACACCCAG-GAGCGACA-AACCCAGGGCTTC-CGAGAGGCACAAAACAGGGGC-TGACAAGGATGGAACCCTTGACTTGACATTCCCCCAGCGGACTGATGGG------A-------------------CCAGACGCCC-GTC-----GAGATGAAAAGCGTTCG-----TTTCCTTCTTCCAGATAAACACGCCGGCAGCCAGATCTCTCTGC--GATGATAAATGACTTCCTCCTG-------------------------------------- i tarSyr1.scaffold_429723 C 0 C 0 s micMur1.scaffold_10910 51851 295 + 52708 ACAGACTT----CTAAACTCGGCTCCGACAAGAAATAAACTTACGACAGAGTTTATCTAAAGGGGGAAGTGGCAATAAAGCGTGACACCCGG-GAGTGATG-AACCTCGAGCTCCGAGACAGACACAAAACAGGTAC-CG-CAGATGTGGGACCCATTATTTAAAATCCCCCGGGCTGACAAGTGGG------ACGG-CC---GAG---CGGGCCAGACGCCG-CTTGGAAAGAGATGAAAAGAGTTCA-----TTTCCTTCCTCCAGATAAACACGCCCGCGGCCAGAGCTGCTCGC--GATGATGAATGGCTTCCTCCTGCC------------------------------------ i micMur1.scaffold_10910 C 0 C 0 s cavPor3.scaffold_42 9673740 300 + 15951348 ACAGATTT----GTGAACTCAGCCCGGACAAGAAATAAATTTATGACAAAATTTATCTAAAGGAGGAAGCAGCCATAAAGCATGACACCCAGGGAGCAATG-AACCAGGATCTCCA--GGAGACACAAAGCAGGTAC-TGACAAGTGTGTGACACATTATTTAAAATTCTCCCGGC-TACAGATTGG------ACAGCCA---CGG----AGGCCAGACGCCG-CTGCA-AGGAGATGAAAAGAGTCCA-----TTTCCTTCCTCCAGATAAACACGCCAGCAGCCAGATCGCTCTGT--GATGATAAATGTCTTCCTCCTGCCG----TGGGG-------------T------------ i cavPor3.scaffold_42 C 0 C 0 s speTri1.scaffold_25523 957 282 + 2129 ACACTTTT----CTAAACTCAGCTCTGACAAAAAGCACATTTACGAC-AGATTTATCTAGAGGAGGAAGCGGCAGTGGAG-GTGACA-CCGGCGAGCCGCG-AGCGGAGAGCCC-----GAGACACAAAGCAGGTAC-TGCCAGGAGTGGGACACGTGGTCAGA-----CCCCCGT-GACAGATGGG------TCGG-CA---GGG----CGGCC-GACGCGC-CTG-G-AGGAGATGAAAAGCGTCCA-----TTTCCTTCCTGCAGATAAACACGCCAGCAGCCAGATCCCTC-GG--GATGACAAATGGCTCCTCTCCACGG----TGG---------------------------- i speTri1.scaffold_25523 C 0 C 0 s ochPri2.scaffold_12461 31831 302 - 40248 CCGCG-TT----CCAGGATG-GCCAGGACAAGAAATGAATTTATGACCACGTTTATCTGCAGGAGGAAATGGCCGTTAAACACGACGCCGGGGGAGCGATG-GACCGAGGTGTCCA---GAGACACAACGCAGGTCT-CCGGGAACGCGGGAGGCGTCACTTAGAACTCCCCCGGCCGGCGGGTCGGGATTGCTCGG-TG---GAA----GGGGTGGACGCCG--GACA-GGGGGATGAAAAGGGCTTG-----CTTCCTTCCT-CCCATAAACACGCCGCCGGCCAGATCCCCCCGC--TGTGATAAATGACTTCCT-CCGTGATC--TCCGG-------------G------------ i ochPri2.scaffold_12461 C 0 C 0 s oryCun2.chrUn0985 32057 299 + 42081 ACCCATTT----CCAAGCTC-GTGCCGCCAAGAAATAAATTTACAGCCGCGTTTATCTAAAGGCGGAAACGGCAGTAAAAGGCGACACC--GGGAGCGAGGAGCCCAAGGCTCCGG---GAGACACAAAACAGGTAC-AGAGTAACGCGGGCTTCGCTGTTTAAAA-TCCCCCGGCTGGCGGACCGA-------CGG-CG---GAC----GGGCCAGACGCCGCCTGCA-GGACG-TGGAAAGGGTTCA-----TTTCCTTCCTGCGCATAAACACGCCGGCAGCCAGATCACTCCGG--CGTGATAAATGGTTTCCTCCCGTCGTCCGTGGGG-------------G------------ i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48982905 305 + 51998940 CCAGATTT----CTAAACTCGGCTCTGACAAGCACTAAATTTATGACCGAGTTTATTTAAAGGAGGAAGCGACAGTCAAGTACGACACCCAGGAAGTGATG-AGCTGAGAGCTCCGAGGCGGACACGAAGCAGGTAC-TGACACCCGCAGGACGCGTTGTTTACAAGTCCCCCAGCTGACGGATCGG------ATGG-C----CAG---CGGGCCAGACACCG-CTCAG-AAGGGATGAAAAGAGCTTA-----TTTCCTTCCTCCCAATAAACACGCCAGCAGCCAGATCCTTCCGG--GATGATAAACAGTTTCTTCCTGCCATCAGTGCGG-------------------------- i bosTau4.chr29 C 0 I 2 s canFam2.chr18 7543936 300 - 58872314 ACAGATTT----CTAAGCTCAGCTCCAACAAGAATTAAATTTATGGCAGAGTTTATTTAAAGAAGGAAGCAGCAATAAAGTGCGACACCCAGGGAGTGATG-AGC-GAGAGCCCGGCGGGAGACACAAACCAGGTAC-TGACAA--AAGGGACTCGTTATTTAAAATTCCCCCA-CGGACGCAGCGG------ACGG-CG---GGG---CAGGCCAGACGCCC-CTTGG-AGGAGATG--AAGAGTTCA-----TTTCCTTCCTCTAGATAAACACGCCAGCAGCCAGATCCTTCCGT--GATGATAAATGGCTTCCTCCTGCCATCAGTGTGG-------------------------- i canFam2.chr18 C 0 C 0 s felCat3.scaffold_135390 64059 302 + 302526 ACAGATGTCTAACTAAGCTCGGCTCCGAC-AGCACTGAATTTATGGCAGAGTTTATTTAAAGGAGGAAGCAGCAATAAAGCGTGACACCCAGGCAGTGATG-AGC-GAGAGCCCCGCGGGAGACACAAAACAGGTAC-TGACGA--ATGGGGCTCGTTATTTAAAATTCCACCA-CGGACGTCGCGG------ACGG-C----GGG---CAGGCCAGACGCCG-CTTGG-AGGAGGTG--GAGAGTTCG-----TTTCCTTCCTCTAGATAAACAGGCCAGCAGCCAGATCCTTCCGT--GGTGATAAATGGCTTCCTCCTGCCACCGGCGTGG-------------------------- i felCat3.scaffold_135390 C 0 C 0 s pteVam1.scaffold_22742 8641 306 - 9737 ACAGACTT----TTACACTCGGCTCCAACGCGAATTAAATTTATGACGGGGTTTATTTAAAGGAGGAAGAAGCAATAAAGCG---CACCCGGGGAGTGATG-AGCGGAGGGCCCCGCGAGAGACACAAAGCAGGTAC-CGACGACGGCGAGACGCGCTGTTTAAGATTCCC----CGGGC-TGACGG------ATGG-AGTTCACG---CGGCCCAGACGCC-------------ATG--AAGAGCTCACTTCCTTTCCTTCCTCTAGATAAACACGCCAGCAGCCAGATCCCTCCGA--GATGACAAATGGCTTCCTCCTGCCGCCAgtgtgtgtgtgtgtgtgtg------------- i pteVam1.scaffold_22742 C 0 I 37 s loxAfr3.scaffold_159 96263 310 + 1045236 ACAGATTC----CTAAACCGGGCTTTGAGAAGAAATAAATCGATGGCAGAGTTTATCTAAAGGCGGAAGCTGCCATAAAGTGCAAC--CCAGGGAGCAATA-CACCCAGAACATTGCAGGAGACACAAAGCAGGTCCCCGGCAGAGGCGCGACACCTTATTTAAAATT-CTCCAGCCCAGAGCTCAG------GCGC------GGG---CGAGCCAGACGCCG-CCTGG-AAAAGATGAAAAGAGTTCA-----CATCCTTCCTCCAGATAAACA-CCCAGCAGCCAGATCCCTCCATGAGATGACAAACGGCTTCCTCCCAGCA-CGGCGGGG-------------GTGTCGG----T- i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 27157 278 - 46842 ACAGATTC----CTGAGCTGGGCTTTGAGGA-AAATAAATTGATGGTAGGGTTTATTGAAAGGAGGAAGCAGCCACAAAGGGCGAC--CTGGAGAGCAATG-AGCCCAT-ACCCTGCAGGAGACACAAAGCAGGTCC----------------------------------CCAGCCCAGAGCTCAG------CTGC------AGGGCACGGGCCAGACGCAG-CCTGG-AAAAGATGAAATGAGTTCA-----CTTCCTTCCTCCAGATAAACACCCCAGCGGCCAGATCCCTTCGTGAGATGACAAATGGCTTCCTCCCAGAA-CCGTGGGG-------------GTGTCGG------ i proCap1.scaffold_13667 C 0 I 1942 e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 9733 1965 - 12933 I e equCab2.chr12 28947175 1131 + 33091231 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I a score=146459.000000 s hg19.chr11_gl000202_random 23442 63 + 40103 GGTCACACCTCATGG--CT--GGTTGGAGCCTGT-GGCC--ATCAAAGGCA-----GGAGAAAGGCAGCCGTGGG s panTro2.chr11 68209777 63 + 134204764 GGTCACACCTCATGG--CT--GGTTGGAGCCTGT-GGCC--ATCAAAGGCA-----GGAGAAAGGCAGCCGTGGG i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 53845 63 + 115376 GGACACACCTCATGG--CT--GGTTGGAACCTGT-GGCC--ATCAAAGGCA-----GGAGAAAGGCAGCCGTGGG i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126006968 63 - 132107971 GGTCACACCTCATGG--CT--GGTTGGAACCTGT-GGCC--GTCAAAGGCA-----GGAGAAAGGCAGCCGTGGG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128169177 63 - 133002572 GGTCACACCTCATGG--CT--GACTGGAACCTGT-GGCC--ATCAAAGGCA-----GGAGAAAGGCAGCCGTGGG i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 86001 63 + 109049 GGTCACACCTCATGG--CT--GGCTGGAACCTGT-GGCC--ATCAAAGGCA-----GGAGAAAGGCAGCCGTGGG i papHam1.scaffold6638 C 0 C 0 s tarSyr1.scaffold_429723 524 65 - 1268 GGTCACGCCTCGCGG--CT--GGCCGGAACCTGG-GACCTGTCCAGGGCCC-----CGGGCGAGGCAGCCACGCG i tarSyr1.scaffold_429723 C 0 C 0 s micMur1.scaffold_10910 52146 58 + 52708 -----CCCCTCAGAGGTCG--AGCCGGAACCTGC-GGCCCCATCAAAGGCC-----GG-GAAGGGCAGC---GGC i micMur1.scaffold_10910 C 0 C 0 s cavPor3.scaffold_42 9674040 64 + 15951348 GGGAGAGCCTCAGGA--CA--GGCCAGAACCTACGGCCC--ATCACAGGCC-----CCGGAAGGGCAGTCTCGGG i cavPor3.scaffold_42 C 0 C 0 s speTri1.scaffold_25523 1239 59 + 2129 GGGTGCACCTCGGAG--CA--G--CCGGGCCCGC-GCCC--GGCAGAGGCC-----CCGCCAGGGC--CCCCAGG i speTri1.scaffold_25523 C 0 C 0 s ochPri2.scaffold_12461 32133 61 - 40248 CATTGCACATTGCCT--CT--GCTCCGAA-CGTCTGGGC--ATCTGAAGTC-----AGGGCAGGGA--CGGTGGT i ochPri2.scaffold_12461 C 0 I 2417 s oryCun2.chrUn0985 32356 49 + 42081 CGTCGCGCCTCCCAA--CT--GGCCGGAACCGGCGGCCC--ATCGGAGGCC-----CGGG--------------- i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48983212 65 + 51998940 GGTCACGCCTCTCGA--CT--GGCCAGAACCTGTGGTCC--GGCAGAGGCCC----CGGAAAGGGCAGCGGCAGG i bosTau4.chr29 I 2 C 0 s equCab2.chr12 28948306 67 + 33091231 GGTCCCGCCTTACG---ATTGGGAAGAGACTTGTTGCCC--ATCAGACGCCCAGAGAGG---GAGCAGTGGCGGG i equCab2.chr12 I 1131 C 0 s felCat3.scaffold_135390 64361 67 + 302526 GGTCGCGCCTCACG---CT--GGCCGGAACC-GTGGCCC--GTCCAATGCTCCGGGCGGGCAGGGCGGCCGCGGG i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7544236 63 - 58872314 GGTCACGCCTCGCG---CT--GGCCGGAACCTGCGGCCC--GTCCAAAGCCC----AGGGCAGGGCAG-CGCTGG i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_22742 8984 65 - 9737 TGTCACGCCCCACGA--CT--GGCCGGAACCTGTGGCTC--ATCTGAGGCCC----GGAGAAGAACAGGGGTGGG i pteVam1.scaffold_22742 I 37 C 0 s loxAfr3.scaffold_159 96573 21 + 1045236 -------CTTCACGG--CT----TTGGAACCGGG----------------------------------------- i loxAfr3.scaffold_159 C 0 C 0 e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 27435 1942 - 46842 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I a score=134461.000000 s hg19.chr11_gl000202_random 23505 61 + 40103 GAGATGCGCCCACGTTGGAATTCCC-ACAATCCCGG-CCTGTCCTCCAGCACCAGAATGCT----GC s panTro2.chr11 68209840 61 + 134204764 GAGATGCGCCCACGTTGGAATTCCC-ACAATCCCGG-CCTGTCCTCCAGCACCAGAATGCC----GC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 53908 61 + 115376 GAGATGCGCCCGCGTTGGAATTCCC-ACAATCCCGG-CCTGTCCTCCAGCACCAGAATGCT----GC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126007031 61 - 132107971 GAGATGCTCCCGCATTGGAATTCCC-ACAATCCTGG-CCTGTCCTCCAGCACCAGAATGCT----GC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128169240 61 - 133002572 GAGATGCTCCCATGTTGGAATTCCC-ACAATCCCGG-CCTGTCCTCCGGGGGCAGAATGCT----GC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 86064 61 + 109049 GAGATGCTCCTGCGTTGGAATTCCC-ACAATCCCGG-CCTGTCCTCTGGGGGCAGAATGCT----GC i papHam1.scaffold6638 C 0 C 0 s tarSyr1.scaffold_429723 589 59 - 1268 GAGGCACTCCTGCATCAGAA-TCCC-ACCGTCCCGG-CCTGTGC-CCGGCCCCAGGATGCT----AG i tarSyr1.scaffold_429723 C 0 C 0 s micMur1.scaffold_10910 52204 63 + 52708 AGGACGCGCCTGCGTCATAATTCCCGACCGTCCCGGACCTGTCCCCCGCACCCAGGATGCC----AC i micMur1.scaffold_10910 C 0 C 0 s cavPor3.scaffold_42 9674104 57 + 15951348 GAGATGACCCTGTAT-GAAATTCTC-ACAATCCCAG-CCTGTCCCCAGATACCAG---GAT----GC i cavPor3.scaffold_42 C 0 I 1 s speTri1.scaffold_25523 1298 50 + 2129 GAGACACTGCTGCCC--AGAGCCCC-ACAGCCCCGG-CCCACCCCAGGACGCCA------------- i speTri1.scaffold_25523 C 0 C 0 s oryCun2.chrUn0985 32405 58 + 42081 GAGATGGCG-TGTGC-CACATTTGC-CAAAATCCTG-CAGGTCCCCAGGCCCGGGG-TGAT----GC i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48983277 54 + 51998940 AAGACGCTCCTGCATCAGAATTCCC-AGAAGCCCGG-CCTGTCTC-------CAGGATGCC----AC i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28948373 46 + 33091231 AAGATGGGCCTGC------------------GTCAG-AAATTCCCGGGGGACCAGGATGCT--TGCT i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 64428 53 + 302526 AAGGTGC-----CAAAAGTGCCCTA----ATCCCAG-CATGTCCCCAGGCCCCAGGATTCC----AG i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7544299 63 - 58872314 AAGGTGCGCCTGCACCCACGTCCTG---CAAGCCAG-CCTGTATCCAGGCACCAGGACGCTGCTGGT i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_22742 9049 60 - 9737 AAGATGCTCCTGCCTGAGAACTCCC---CAGCCCCG-CCTGTCTCCAGGCAGCAGGGAGCC---CCC i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 96594 61 + 1045236 GACATGCTCACACGCCAGCATTCCC-CCCATCCTGC-CCTGTCTCCAGGCACCAACGAGct----gc i loxAfr3.scaffold_159 C 0 I 985 e ochPri2.scaffold_12461 32194 2417 - 40248 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 27435 1942 - 46842 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I a score=312400.000000 s hg19.chr11_gl000202_random 23566 116 + 40103 TTATCTCATCCCAGGGCCCCCACAACTATC-AAAATACATGAA----------GACACAGAATGAACTGGGGGA--------TGT---AGCTATGGCCTCCTGCTCT--TC--CCAGGGCTGTG-GGATTTAAGGAC--CTCCCA s panTro2.chr11 68209901 116 + 134204764 TTATCTCATCCCAGGGCCCCCACAACTATC-AAAATACATGAA----------GACACAGAATGAACTGGGGGA--------TGT---AGCTATGGCCTCCTCCTCT--TC--CCAGGGCTGTG-GGATTTAAGGAC--CTCCCA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 53969 116 + 115376 TTATCTCATCCCAGGGCCCCCACAACTATC-AAAATACAGGAA----------GACACAGAATGAACTGGGGGA--------TGT---AGCTATGGCCTCCTGCTCT--TC--CCAGGGCTGTG-GGATTTAAGGAC--CTCCCA i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126007092 116 - 132107971 TTATCTCATCCCAGGGCCCCCACAACTATC-AAAATACAGGAA----------GATACAGAATGAACTGGGGGA--------TGT---AGCTATGGCCTCCTGCTCT--TC--CCAGGGCTGTG-GGATTTAAGTAC--CTCCCA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128169301 116 - 133002572 TTATCTCATCCCAGGGCCCCCACAACTATC-AAAATACAGGAA----------GACACAGAATGAACTGAGGGA--------TGT---AGCTATGGCCTCCTGCTCT--TC--CCAGGGCTGTG-GGATTTAAGGGC--CTCCCA i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 86125 116 + 109049 TTATCTCATCCCAGGGCCCCCACAACTATC-AAAATACAGGAA----------GACACAGAATGAACTGAGGGA--------TGT---AGCTATGGTCTCCTGCTCT--TC--CCAGGGCTGTG-GGATTTAAGGGC--CTCCCA i papHam1.scaffold6638 C 0 C 0 s tarSyr1.scaffold_429723 648 117 - 1268 CC-TCTCATCCCAGGTCCCCCATGCCTCCC-CAAACACAGGAA----------GACGCAGAGCGCCTTGGGGGA--------CAC---AGCTGTGGCATCCAGCCCG--GC--TTGGGACTGTG-GGGTTTAAGGCCAACTCCCT i tarSyr1.scaffold_429723 C 0 C 0 s micMur1.scaffold_10910 52267 89 + 52708 TTATCTCGTCCCAGGCCCCCCACGACTCTCAAAAACACAGGAA----------GACTCAGAGGGGACGGAGGGA--------CAC---AGCGATGACATC---------------------------------GCCC--GGCCCA i micMur1.scaffold_10910 C 0 C 0 s cavPor3.scaffold_42 9674162 115 + 15951348 TCATGTTATTCCAGG-CCCCCACAACTCAC-AAAATATAGAAA----------ACAATGGAGCAAATTGGGGAA--------CAG---AATTATGACATCCTGCCCA--GC--CCAGGGCAGGG-GAGTTTAAGGAC--ATCTCA i cavPor3.scaffold_42 I 1 C 0 s speTri1.scaffold_25523 1348 93 + 2129 CCCTCTCATGCCAGC-CCCGCATGCC------------AGGGG----------A-ATTGGAGTGAACTGGGG-A--------CCG---TGTGGGGACA-CGCGCCTG--GC--CCCGGAGTGAG------TGAAGGC--CTC--- i speTri1.scaffold_25523 C 0 C 0 s oryCun2.chrUn0985 32463 86 + 42081 TCGGCTCTCTCCAGG-CCCCC-CACC----------------------------------------CCGGGA-G--------CCC---AGGGGGGCCGTCTTGCCCA--GCTGCTGCGGCTCTG-GGGTTGAATGGG--CTCCCA i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48983331 135 + 51998940 CTTGCTCTGTCCAGAGCCCCCACAATTCTC-AAAACACCGGAAAATGCAGGGGGATGGCGGGGGGCAGGGGGGAGGTGAGGTTGC---AGCTCTGACATCCTGCCCAGGGC--C-AGGACTGTG-GGATCGAAGGGG--CTCCCA i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28948419 115 + 33091231 CAACCTCCCTCCAGACCCCCCACGATTCTC-AAAATACAGGAA-----------AGACCCAGAGGGATGGGGGA--------TGC---AGCCATGACATCCTGCCCG--GC--CCAGGGCTGTGAGATTT-CAGGGC--CTCCCA i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 64481 93 + 302526 GCATCCCTCTCCAGA-CCCCCAGGGTTCTG-GAAATACA-----------------------------GAGGGA--------GGC---CGCCATGACTTCCTGCTCA--GC--T--CGGCTGCA-GAGGT-AAGGAC--CTCCCG i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7544362 97 - 58872314 GCCGCCCGCTCCAGA-CCTCCGGGGTTCTC-AAAATACA-----------------------------GGGGGA--------CGCAGAAGCTGGGACATCTCGCTCA--GC--C-GGGGCCTTG-GAAGT-GAAGAC--CTCCCG i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_22742 9109 114 - 9737 TCCTCTCACCGCAGC-CCCCCACGATGCTC-GCAGTACAGGAA----------GATGCAGGGGGGGACAGGGGA--------TGC---AGCTATGACATCCTGCCGA--CC--C-TGGCCTGTG-GAATTCCAGGGC--CTCCCG i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 97640 114 + 1045236 TTATTCTGGTTCAGACCCCAAACAGTTCTC-AAAGTACTTGGG----------GACATGGACGAAATCAGGG----------TGC---AGCTGTGACATCCTATCCA--GC--CCAGGGTTGTG-GGATTCAAGAGC--CTCCCA i loxAfr3.scaffold_159 I 985 I 2624 e ochPri2.scaffold_12461 32194 2417 - 40248 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 27435 1942 - 46842 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I a score=81850.000000 s hg19.chr11_gl000202_random 23682 59 + 40103 CC-------ACAAGCTGGTT--TCTAGGAGG-GAAGGAGCCAAAGGCAGGAGA-GGGGGCGGCCTGTTCA s pteVam1.scaffold_22742 9223 52 - 9737 GG-------ACAGGCAGAAT---CCAGAAGG-CAGGG-------GCTGGGGCGGGAGGATGGCATGGCTC i pteVam1.scaffold_22742 C 0 C 0 s canFam2.chr18 7544459 47 - 58872314 GG-------ACAGGCTGGGT--CCCAGGAGG-AAGGGA------GCTGGGGCGGGAGGGCGGT------- i canFam2.chr18 C 0 C 0 s felCat3.scaffold_135390 64574 47 + 302526 GG-------ACAGGCTGGGC--CCTCGGAGG-AAGGGA------GCCGGGGCAGGAGGGTGGT------- i felCat3.scaffold_135390 C 0 C 0 s equCab2.chr12 28948534 54 + 33091231 GG-------ACAGGCTGGAT--TTCAGAAGG-AAAGAT------GTGGGGGCAGGGAGGCGGTTTCTCCA i equCab2.chr12 C 0 C 0 s bosTau4.chr29 48983466 52 + 51998940 GC-------ACAAG----AT--TCTAGAAGG-AAGGCACC----GGGGGGGCAGGAAGGACACCTCCCTC i bosTau4.chr29 C 0 C 0 s oryCun2.chrUn0985 32549 56 + 42081 GG-------ACAAGCTGGGT--TCCAGCAGG-GGAGGAG--ACGGGGCGGGGAGGGAGGC--CCTGGCCG i oryCun2.chrUn0985 C 0 C 0 s speTri1.scaffold_25523 1441 44 + 2129 --------------CGGGACAATCCTGGGAG-----------TGGGCAGGAGGCGGAGGTGACTC-GCTG i speTri1.scaffold_25523 C 0 C 0 s cavPor3.scaffold_42 9674277 59 + 15951348 CA-------ACACATGGGGC--TCTTGAAAGAAAAGGTG--AAGGGCAGGAAAGGGAGGCAACTTGGCCA i cavPor3.scaffold_42 C 0 C 0 s micMur1.scaffold_10910 52356 43 + 52708 CA-------GCACGCTGGGC--TCCGGGAGG-GA----------GGCAGGAGAAGGAGGCAGC------- i micMur1.scaffold_10910 C 0 C 0 s tarSyr1.scaffold_429723 765 56 - 1268 CCCCCGGCAACAAGCCGGAT--TCTAGGAGG-GAAGGACCTTGGGGGAGGAG---GGAGCGG-------- i tarSyr1.scaffold_429723 C 0 C 0 s papHam1.scaffold6638 86241 59 + 109049 CC-------ACAAGCTGGAT--TCTAGAAGG-GAAGGAGCCAAAGGCAGGAGA-GGAGTCGGCCTGTTCA i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128169417 59 - 133002572 CC-------ACAAGCTGGAT--TCTAGAAGG-GAAGGAGCCAAAGGCAGGAGA-GGAGTCGGCCTGTTCA i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126007208 58 - 132107971 CT-------ACAAGCTGGAT--TCTAGGAGG-GAAGGAGCCAAAGGCAGGAGA--GGGGTGGCCTGTTCA i ponAbe2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 54085 59 + 115376 CC-------ACAATCTGGTT--TCTAGGAGG-GAAGGAGCCAAAGGCAGGAGA-GGGGGCGGCCTGTTCA i gorGor1.Supercontig_0015245 C 0 C 0 s panTro2.chr11 68210017 59 + 134204764 CC-------ACAAGCTGGTT--TCTAGGAGG-GAAGGAGCCAAAGGCAGGAGA-GGGGGCGGCCTGTTCA i panTro2.chr11 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 27435 1942 - 46842 I e loxAfr3.scaffold_159 97754 2624 + 1045236 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I a score=208279.000000 s hg19.chr11_gl000202_random 23741 156 + 40103 CTCCCATGGGGTGC--------------------------AAAGATATGG---TGCCAGCCCCTTTTTCTGGAAGTCAAGACCTAGCCCCATCTTTAGCCTTCCTGCTCCCCAGGAACATGGACAGGCTTTGGCTGAAATCTGCATCCTCTGGCTGGT-GGG-------------AAGATGGTCACCCC-------------ACATAAGA-CA s panTro2.chr11 68210076 156 + 134204764 CTCCCATGGGGTGC--------------------------AAAGATATGG---TGCCAGCCCCTTTTTCTGGAAGTCAGGACCTAGCCCCATCTTTAGCCTTCCTGCTCCCCAGGAACATGGACAGGCTTTGGTTGAAATCTGCATCCTCTGGCTGAT-GGG-------------AAGATGGTCACCCC-------------ACATAAGA-CA i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 54144 156 + 115376 CTCCCATGGGGTGC--------------------------AAAGATATGG---TGCCAGCCCCTTTTTCTGGAAGTCAGGACCTAGCCCCATCTTTAGCCTTCCTGCTCCCCAGGAACATGGACAGGCTTTGGTTGAAATCTGCATCCTCTGGCTGGT-GGG-------------AAGATGGTCACCCC-------------ACATAAGA-CA i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126007266 156 - 132107971 CTCCCATGGGGCGC--------------------------AAAGATATGG---TGCCAGCCCCTTTTTCTGGAAGTCAGGACCCACCCCCGTCTTTAGCCTTCCTGCTCCCCAGGAACATGGACGGGCTTTGGTTGAAATCTGCATCCCCTGGCTGGT-GGG-------------AAGATGGTCACCCC-------------ACATAAGA-CA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128169476 154 - 133002572 CTCCCATGGGGCGC--------------------------AAGG--ATGG---TGCCAGCCCCTTCTTCTGGAAGTCAGGACCTAGCCCCATCTTTAGCCTTCCTGCTCCCCAGGAACGTGGACGGGTTTTGGTTGAAATCTGCATCTCCTGGCTGGT-GGG-------------AAGATGGTCACCCC-------------ATATAAGA-CA i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 86300 154 + 109049 CTCCCATGGGGTAC--------------------------AAGG--ATGG---TGCCAGCCCCTTCTTCTGGAAGTCAGGACCTAGCCCCATCTTTAGCCTTCCTGCTCCCCAGGAACGTGGACGGGTTTTGGTTGAAATCTGCATCCCCTGGCTGGT-GGG-------------AAGATGGTCACCCC-------------ACATAAGA-CA i papHam1.scaffold6638 C 0 C 0 s tarSyr1.scaffold_429723 821 135 - 1268 -----ACGGG-------------------------------AGG--ATGG---TGTCCACCCCTGCTTCTGGACGCCAGGACCCAGTCCTGCAACTCAGCCTCCAGCTTCCAGAGCACATG----GGCTTGGGTTGAAGTCCGGGTCCCCTGTCTGGT-GGG-------------AAGACGGTCACCCC-------------GCACA------ i tarSyr1.scaffold_429723 C 0 C 0 s micMur1.scaffold_10910 52399 91 + 52708 -------GGGG------------------------------AGG--ATGG---CGCCAGCTCC---TTCTGGAAGCCGCGGTCCAGCCTTGTCCTGAGGC----------------------ACGGGC---------------------------GTT-GGG-------------AAGATGGTCACCCC-------------ACCAGAGA-CA i micMur1.scaffold_10910 C 0 C 0 s cavPor3.scaffold_42 9674336 151 + 15951348 CTCCCAGGGGACCG--------------------------GAGG--ATGC---TGTTGGTCCCTTTATTTGGAAGCCAG--------CCTGCTTTCTGGCTTTTAGGTCCCCAAGAACGCTGGC-----ATTGTTAAAGTCTGGTCCCC-TGGCTGGT-GGG-------------AAGATGGTCACCCCTCCCCCCTCCAATATGCATGG--- i cavPor3.scaffold_42 C 0 C 0 s speTri1.scaffold_25523 1485 147 + 2129 CTCCCTGGGGACAG--------------------------GAAG---TG----TGCTGGCCCCACCTGTAGGAATCGAGGGTCCACCCCTGTCCCTGGGCTTCTGGCTCCCCAGGAAAGTGGACGGACAGTGGCTGAAGTCCAGGTCCT---GCCTTC-AGG-------------AAGGCAGCCACCCC-------------ACACGAGA--- i speTri1.scaffold_25523 C 0 C 0 s oryCun2.chrUn0985 32605 135 + 42081 CTGCCTGGACAGCG--------------------------GGCG--GTGCG--TGTCTGCCCCTCAGCCAGGAAGGTGGAG------CCGGGCCTTGG-------------CGGGAGCGTGGGCTGGCACTGGGGGGAGTCCAGGTCC----GCTGTC-GGGGC-----------AAACTGCTCACCCC-------------ACGCGAGGCCA i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48983518 151 + 51998940 GCTCCATGGATA----------------------------GGGG--GGCG---CTCTGGGCCGTCCTTTGGGAAGCGAGAAGCCAGCTGTG--------------ACTCCCCAGGGCCAGGGACCTGCTTTGGCTGAAGTCTGAGTGCCCTGTCTGAG-GGGTCGGGAAGCAGATGAGGCCGTCACCCT-------------ACGGCAGA-CG i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28948588 134 + 33091231 TC-CTACGGGGACAGGAGGACGGCGTGAGTCCCTCCCTTCGGGA--GTGGGGATCCAG------------------------------------------------CTCACCAGGAATACGGACTGGCTTTGGATGAAGTCCGAGGACCCCGTCTGGT-GGG-------------GAGACAGTCACCGC-------------TCTTCAGA-CA i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 64621 92 + 302526 ----------------------------------------GGGG--GCCG---TCCTG------------------------------------------------CACCCCAGGAACACCGGCTGGTGTCGGTTGACGTCTG-AGCGCCCGTCTGGCGGGG-------------GAGGTGGTCACTCC-------------ACATCGGA-TG i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7544506 92 - 58872314 ----------------------------------------GCGG--GTGG---TCCCA------------------------------------------------AGCCCCAGGATCACGGGCTGGCCCTGGATTAAGTCTGCGGACCCCGTCTGGC-GGG-------------AAGATGGTCCCCCC-------------ACGTCAGA-CA i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_22742 9275 92 - 9737 TC-CTTTGGG------------------------------AGGG--CTCG---TCCCTGGGCTTCC--------------AGCC----------------------CCCCCCGGGGACAT-GGCTGGCTTTGGTTGAAGTCTG-TGTGTCTGTCATGC----------------------------------------------ATCACA-CG i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 100378 141 + 1045236 CCCCCATGGGG-----------------------------AGGG--GCGG---TGCAAGCCCCTCGCTTTGGAAGCCAG-------CTGTGCCTTGAGGCCCCCA-CTCCCCAGGAGCATGGATCAGTTTT-GTGGAAGTTCAAGCTCCCTGCCT-CT-GGG-------------ACGACCATCACGCC-------------ACATAAGA-CA i loxAfr3.scaffold_159 I 2624 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 9733 1965 - 12933 I e proCap1.scaffold_13667 27435 1942 - 46842 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I a score=395846.000000 s hg19.chr11_gl000202_random 23897 72 + 40103 AGCATCACTGCCCAGCCCC--AGGGCTGTTTCAGGAGGAAATTGGTCTTAAGGAT-AACCGGAGCCTGGAGCAGT s panTro2.chr11 68210232 72 + 134204764 AGCATCACTGCCCAGCCCC--AGGGCTGTTTCAGGAGGAAATTGGTCTTAAGGAT-AACCGGAGCCTGGAGCAGT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 54300 72 + 115376 AGCATCACTGCCCAGCCCC--AGGGCTGTTTCAGGAGGAAATTGGTCTTAAGGAT-AACCGGAGCCTGGAGCAGT i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126007422 72 - 132107971 AGCATCGCTGCCCAGCCCC--AGGGCTGTTTCAGGAGGAAATTGGTCTTAAGGAT-AACCGGAGCCTGGAGCAGT i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128169630 72 - 133002572 AGCATCACTGCCCAGCCCC--AGGGCTGTTTCAGGAGGAAATTGGTCTTAAGGAT-AACAGGAGCCTGGAGCAGT i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 86454 72 + 109049 AGCATCACTGCCCAGCCCC--AGGGCTGTTTCAGGAGGAAATTGGTCTTAAGGAT-AACAGGAGCCTGGAGCAGT i papHam1.scaffold6638 C 0 C 0 s tarSyr1.scaffold_429723 956 66 - 1268 ------GCAGCCCAGCCCC--AGGGCCGTTTCAGGAGGAAACTGATCTGAAGGAT-AACCAGAGCCCGGAGCCGT i tarSyr1.scaffold_429723 C 0 C 0 s micMur1.scaffold_10910 52490 71 + 52708 CATGGCGCTG-CCGGCCCC--TGGGCCGTTTCAGGAGGAGATTGGTCTGAAGGGC-GACCGGAGCCCGGAGCAGC i micMur1.scaffold_10910 C 0 C 0 s cavPor3.scaffold_42 9674487 63 + 15951348 --------TGCCCA-CCCC--AGGCCTCTGTCAGGAGGAAATTGGTCTGAAGGAC-AACAGGAGCCCAGGGCGGT i cavPor3.scaffold_42 C 0 C 0 s speTri1.scaffold_25523 1632 53 + 2129 --------GGAGCA-TCGC--AGCTC-----CGGAAGCACA-----CCGAAGGGC-AAGAGGAGCCCAGGGCAGC i speTri1.scaffold_25523 C 0 C 0 s oryCun2.chrUn0985 32740 58 + 42081 AGCATC-CTGCCGG-CCCC--GGGCT-GTCTCGGGAGGAAG-----CTGATGTACGGATAATAACC-------GT i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48983669 70 + 51998940 GGCGTCACGGCCCC-CGCT--GGGGCTGTTTCAGGAGGAAACTGGCTGGAAGGCT-TAGCAGAA-CTGGAACAAC i bosTau4.chr29 C 0 I 32 s equCab2.chr12 28948722 70 + 33091231 AGCATGGCTGGCCA-GCCC---GGGCGGTTTCGGGAGGAAATTGTTCTGAAGGCT-AAGCAGAGCCTGGAGCAAT i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 64713 70 + 302526 AGCATCTCTGCCCA-GCCC--GGGGCTGTTTCAGGAGGAAATTGGT-TGACAGAT-AAGTGGGACCTGGAACCAT i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7544598 71 - 58872314 AGCATCTCTGCCCA-GCCC--GGGGCTGTGTCAGGAGGAAATGGTTCTGACGGAT-GAGTGGAACCCGGAGCAAT i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_22742 9367 71 - 9737 GGCATGGCCGCCCA-GCCC--CGGGAGGTTTCAGGAGGAAATAAATCTGAAAGAT-AAGTGGGGCCTAGAGCAAT i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 100519 72 + 1045236 -ACATCACTGCCTAGCCCTTGAGGGCGGATTCAGGAGGAAATTGGTGTAAAGGAC-AACTGGAGCC-AGGGCAGT i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 29377 72 - 46842 AACATCGCTGCCCCACCCCC-AGGGCCGACCAGAGAGGAAATTGGTGCTGAGGAT-AACTCGGGCC-AGGGCCGG i proCap1.scaffold_13667 I 1942 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 9733 1965 - 12933 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I a score=608917.000000 s hg19.chr11_gl000202_random 23969 127 + 40103 CCACCCCG------GCAGTACT-CTCAAAC--AAAGTCCAAACAAAGCTATTTATAAAAAGCCAAA-TTGCTGGCATCTGCACT---GACTCCTGGGGCTGGAGGGGAGGAAGGAGATGGAGC-CCCAGCTTGCGGCTTGC s panTro2.chr11 68210304 127 + 134204764 CCACCCCG------GCAGTACT-CTCAAAC--AAAGTCCAAACAAAGCTATTTATAAAAAGCCAAA-TTGCTGGCATCTGCACT---GACTCCTGGGGCTGGAGGGGAGGAAGGAGATGGAGC-CCCAGCTTGCGGCTTGC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 54372 126 + 115376 CCACCCCG------GCAGTACT-CTCAAAC---AAGTCCAAACAAAGCTATTTATAAAAAGCCAAA-TTGCTGGCATCTGCACT---GACTCCTGGGGCTGGAGGGGAGGAAGGAGGTGGAGC-CCCAGCTTGCGGCTTGC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126007494 127 - 132107971 CCACCCCG------GCAGTGCT-CTCAAAC--AAAGTCCAAACAAAGCTATTTATAAAAGGCCAAA-TTGCTGGCATCTGCACT---GACTCCTGGGGCTGGAGGGGAGGAAGGAGATGGAGC-CCCAGCTTGCGGCTTGC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128169702 127 - 133002572 CCACCCCG------GCAGTGCT-CTCAAAC--AAAGTCCAAACAAAGCTATTTATAAATGGCCAAA-TTGCTGGCATCTGCACT---GACTCCTGGGGCTGGAGGGGAGGAAGGAGATGGAGC-CCCAGCTTGCGGCTTGC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 86526 127 + 109049 CCACCCCG------GCAGTGCT-CTCAAAC--AAAGTCCAAACAAAGCTATTTATAAATGGCCAAA-TTGCTGGCATCTGCACT---GACTCCTGGGGCTGGAGGGGAGGAAGGAGATGGAGC-CCCAGCTTGCGGCTTGC i papHam1.scaffold6638 C 0 C 0 s tarSyr1.scaffold_429723 1022 119 - 1268 CCACCTGG------CCAGCGCT-TTCAAA----------ATCCAGAGTTATTTATAAGAAGACAAG-TAATAGGCATAGGTGCC---GTCCCCCGGGGCTGGAGGGGCGGACAGAACCGGAGA-AGCAGCTGTGGCTTTAT i tarSyr1.scaffold_429723 C 0 C 0 s micMur1.scaffold_10910 52561 126 + 52708 CCACCCCG------GCAGAGCT-TGCAAA---AAGGTCCAAGCACAGTTATTTACAAA-GGCCACG-TTGCTGGCGTGTGCAGC---ACCTCCCCGGGCAGGACGGGAGGAAGGAGATGGAGCGCCCAGCTTGCGGCTTGC i micMur1.scaffold_10910 C 0 N 0 s cavPor3.scaffold_42 9674550 116 + 15951348 CCACTCCG------GCAGTGCT-TGCAAACAAAGTGAAAAAACAAAGTTATTTTTAACAGGCCAAA-TTGCTGGCAGATGAGC------CTCCCGGGT--GGCTGGGAGGA-GGCCGTGGAGC-CC-------CAGCCTGC i cavPor3.scaffold_42 C 0 C 0 s speTri1.scaffold_25523 1685 119 + 2129 CCACT--G------ACAGCGCTATTTAAAC---GGGTCCAGGTGGAGTGATTTATTCAGATCCAAA-TCAGGGGCATATGCAC----GGCCCCCGGGC---TCCGGGTAGA-GGCGGCAGGGC-CCC-TCTCACGGCTCAC i speTri1.scaffold_25523 C 0 C 0 s oryCun2.chrUn0985 32798 53 + 42081 CCACA--C------ACAGCTGTTTATAAAA------------------------------GCCGAA-TCACCGGCAGATGCAC------CGCC---------------------------GGC-CC--------------- i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 11698 129 - 12933 CCCCCCCA--ACAAATGGTGCT-TTCAAAC--AAAATCC-AGTCAGGTTATTTATAAAAGGCCAAA-TTGCTGACAGATGCACC---ACCTCCCGGGGCTGGAGGAAAGGAAGGAGTCAGA-T-CCCAGCTCGAGGCTTGC i turTru1.scaffold_93657 I 1965 C 0 s bosTau4.chr29 48983771 112 + 51998940 CCTCCCCACCCCACATGGTGCT-TTCAAAC-AAAAATCC-AACAAGGTTATTTATAAAAGGCCAAA-TTGCTGGCAGATGGACC---GCCTCCTGGGGCTGGAGAAGAAGAAAGGGGCG---------------------- i bosTau4.chr29 I 32 C 0 s equCab2.chr12 28948792 127 + 33091231 CCACCGCA------ACAGGGCT-TTCAAAC--AAAGTCCCAACGAGGTTATTTATAACATGCCAAA-TTGCCGGCGTGTG---CACTGCCTCCCGGGGCTGGAGGACAGGAAGGAGGCGGGGC-CCCAGCTCGAGGCTCAC i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 64783 119 + 302526 CCGCCC-A------ACAGCACT-TTCAAAC----AGTCCAAACGAGGTTATTTGCAAAA--GCGAA-TTGCTGCCATATG---C---GTCTCCTGGGGCTGGAGGAGAGGAAGGAGGTGAGGC-CCCAGCCTGTGGCCTGC i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7544669 123 - 58872314 CCACCCTA------ACAACGTT-TTCAAAC--AAAGTCCAAACGAGGTTATTTATAAAA-GGCCAG-TTGCTGGCGGACG---C---ACCTCCTGGGGCTGGAGGGGAGGCGGGAGGCGGAAC-CCCAGCTTGTGGCCGGC i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_22742 9438 121 - 9737 CCACCC-A------ACAGTGCT-TTCAAAC--AAAGTCCAAAC--AGTTATTTATAAAAGGCCAAA-TTGCGGGCAGATG-ACC---ACCTCCC--GCCTAGAGGAGAGGAAGGGGACGGAGC-CCCGGCCTGTGGCCTGC i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 100591 113 + 1045236 CCACCCCG------GCAGCGCT-TTTGAAC--AAAGTCCAAGC-AGGTTATTTATAAAAGGCCCAAATTGCTGGGAAGTG---------------GGGCTGGAGGA--GGGGGGAGACGAAGC-CCCAGCCTGTGGCTTGC i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 29449 108 - 46842 CCACCCCA------CCAGTGCT-TTCCAAC--CAAGTCCAGGC-AGGTTATTTATAAAAGACCGGA--TTCTGGCAAGTG---------------GGGCTGGAGGA---GGTGGAGACCGAGC-CTC--TCCGTGGCCTGC i proCap1.scaffold_13667 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I a score=316797.000000 s hg19.chr11_gl000202_random 24096 57 + 40103 AGT---GATCCATTTGCTGCCTCTGTCCGTCCTCAACATCCGAGATACATTTGTGGTTTC s panTro2.chr11 68210431 57 + 134204764 AGT---GATCCATTTGCTGCGTCTGTCCGTCCTCAACATCCAAGATACATTTGTGGTTTC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 54498 57 + 115376 AGT---GGTCCATTTGCTGCCTCTGTCCGTCCTCAACATCCGAGATACATTTGTGGTTTC i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126007621 55 - 132107971 AGT---GATCCATTTGCTGCCTCTGTCCGTCCT-AACAT-CGAGATGCATTTGTGGTTTC i ponAbe2.chr11 C 0 M 1116 s rheMac2.chr14 128169829 57 - 133002572 AGT---GATCCATTTGCTGCCTCTGTCCGTCCTTAACATCCAAGATGCATTTGTGGTTTC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 86653 57 + 109049 AGT---GATCCATTTGCTGCCTCTGTCCGTCCTTAACATCCAAGATGCATTTGTGGTTTC i papHam1.scaffold6638 C 0 C 0 s tarSyr1.scaffold_429723 1141 57 - 1268 AGC---AGTGCATTTGCTGCCTCTGACCGTCCTCGACCGCCGAGATGCATTTGTGGTTTC i tarSyr1.scaffold_429723 C 0 C 0 s micMur1.scaffold_46107 0 57 + 5307 AGC---GACCCGTTTGCCGCCTCAGTTCGTCCTCAACATCCAAGATGCATTTGTGGTTTC i micMur1.scaffold_46107 N 0 C 0 s cavPor3.scaffold_42 9674666 57 + 15951348 AGC---GATGGGTTTGCTGCCTCCATCCGTCCTCAACATCCGAGCTGCACTTGTGGTTTC i cavPor3.scaffold_42 C 0 C 0 s speTri1.scaffold_25523 1804 49 + 2129 AGC-----TCCGTTTGCT-----CATGTG-CCTCGACATCTGAGATGCATTTGTGGGTTC i speTri1.scaffold_25523 C 0 C 0 s oryCun2.chrUn0985 32851 38 + 42081 ----------------CT-----CCCCCG-GCCCCACATCTGCGATGCGTTTGTGGTTTC i oryCun2.chrUn0985 C 0 C 0 s turTru1.scaffold_93657 11827 54 - 12933 AGT---GATCCATTCGCTGCCCCATGCCCTCTA---CATCAGAGATGCATCTGTGCTTTC i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48983883 36 + 51998940 -------------TCG--GCCTCCTGGGCACCA---------AGAAGCCTCTGTGCTTTC i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28948919 57 + 33091231 AGC---GAGGCATCTGCGGCCTCCATCTGTCCTCGACATCCGAGATGCATTTGTGGTTTC i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 64902 48 + 302526 GGG---GATCCGTCTCCTG---------CTTCGGAAGGTCACAGACACATTCGTGGTTTC i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7544792 56 - 58872314 AGG---GATCCATCTGCCGCTGCCAGC-CTCCTGACCATCTGAGATGCATTTGTGGTTTC i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_22742 9559 60 - 9737 AGCACTGAGCTGCCTCCATCCATCCGGACATCCAGACATCTGAGATGCATTCGATGTTTG i pteVam1.scaffold_22742 C 0 C 0 s loxAfr3.scaffold_159 100704 57 + 1045236 AGC---TGGCCGTTTGCTGTCTGCATCCGCCCTCCGCATCTGAGGTACATTTGTGGTTTC i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 29557 57 - 46842 AGC---GGGTCATTTGCTGTCTCCATCCGCCCTCTACATCTGAGGTGCATTTGTGGTTTC i proCap1.scaffold_13667 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I a score=251747.000000 s hg19.chr11_gl000202_random 24153 51 + 40103 CTGTGCCCAATACTCACCTGGGG-GCGGGCAGGAGGACG---CAGGAGAGTAGCC s panTro2.chr11 68210488 51 + 134204764 CTGTGCCCAATACTCACCTGGGG-GCGGGCAGGAGGACG---CAGGAGAGTAGCC i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 54555 51 + 115376 CTGTGCCCAATACTCACCTGGGG-GCGGGCAGGAGGACG---CAGGAGAGTAGCC i gorGor1.Supercontig_0015245 C 0 C 0 s rheMac2.chr14 128169886 51 - 133002572 CTGTGCCCAACACTCTCCTGGGG-GCGGGCAGGAGGACG---CAGGAGAGTAGCT i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 86710 51 + 109049 CTGTGCCCAACACTCTCCTGGGG-GCGGGCAGGAGGACG---CAGGAGAGTAGCT i papHam1.scaffold6638 C 0 C 0 s tarSyr1.scaffold_429723 1198 48 - 1268 CTGTCCGCGGCACTCACCCGGGA-GAGGAC---AGGATG---CCGGGGAGAAACC i tarSyr1.scaffold_429723 C 0 C 0 s micMur1.scaffold_46107 57 47 + 5307 CTGTCCCCGGCGCTCACCTGGGG-GTGGCC----GGACG---CAGGGGAGAAGCC i micMur1.scaffold_46107 C 0 C 0 s cavPor3.scaffold_42 9674723 46 + 15951348 CTGTCCCGGATGCTACCT-GGGG-GTGGGC---AGGATG---CAGGAGAGGAGC- i cavPor3.scaffold_42 C 0 C 0 s speTri1.scaffold_25523 1853 45 + 2129 CTGCCCCGGATGCTCACC--GGG-GTGGGC---AGGATG---CAGGAGAGAAGC- i speTri1.scaffold_25523 C 0 N 0 s oryCun2.chrUn0985 32889 38 + 42081 CTGCGCCTGACGCTCACC-TGGG-GCCGGC---AGGATG---CAGG--------- i oryCun2.chrUn0985 C 0 I 1017 s turTru1.scaffold_93657 11881 51 - 12933 CTGTTCCCTGGGTTCACCTGGGG-GTGGGC---AGAAGAAGCCAGGACAGAGGCC i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48983919 48 + 51998940 CGGTTCCCTGGGCTCACCTGGGG-GTGGGC---AGGAGG---CAGGACGGACCCC i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28948976 47 + 33091231 CTG-TCCTCATGCTCACCTGGGG-GTGGGC---GGAAGG---CAGGAGAGAGGCC i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 64950 48 + 302526 CTGCCTCAGAGGCTCACCTGGGG-GTGGCC---AGAAAG---CGGGACAAAAGCC i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7544848 48 - 58872314 CTGCTCCAGAGGCTTACCTGGGG-GTGTAC---AGAAAA---CAGGACAAAGGCC i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_22742 9619 43 - 9737 CTG-TCCCCACGCTCACTTGGGGTGGGGGC---AGTGGG---CAAGAAAG----- i pteVam1.scaffold_22742 C 0 N 0 s loxAfr3.scaffold_159 100761 47 + 1045236 CTGTCCCTGA-GCTCACCTGGGG-GTCAGC---GGGAGG---CAGGAGAGCAGTC i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 29614 47 - 46842 CTGTCCTTGA-GCTCACCTGGAG-GTTAGC---CGGCAG---CAGGAGAGCAGCC i proCap1.scaffold_13667 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M a score=1993.000000 s hg19.chr11_gl000202_random 24204 59 + 40103 GCAGGACCGCAGAAGAGAAGTCCTAAGG--AAAGCTGAGG---TCC-----CTTCCCGGGGGCCAGCAT s panTro2.chr11 68210539 59 + 134204764 GCAGGACCGCAGAAGAGAAGTCCTAAGG--AAAGCCGAGG---TCC-----CTTCCCGGGGGCCAGCAT i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 54606 59 + 115376 GCAGGACCGCAGAAGAGAAGTCCTAAGG--AAAGCCGAGG---TCC-----CTTCCCGGGGGCCAGCAT i gorGor1.Supercontig_0015245 C 0 C 0 s rheMac2.chr14 128169937 59 - 133002572 GCAGGACCGCAGAAGAGAAGTCCTAAGG--AAAGCCGAGG---TCC-----CTTCCCAGGGGCCAGCAT i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 86761 58 + 109049 GCAGGACTGCAGAAGAGAAGTCCT-AGG--AAAGCTGAGG---TCT-----CTTCCCGGGGGCCAGCAT i papHam1.scaffold6638 C 0 C 0 s tarSyr1.scaffold_429723 1246 21 - 1268 ----------------GAGGTCTTCAGG--AAGGCAGAG------------------------------ i tarSyr1.scaffold_429723 C 0 N 0 s micMur1.scaffold_46107 104 40 + 5307 ----------------GAGGCCCCGAGG--AGAGCAGAG----CCC-----CCTCCCTGGG--CAGCGT i micMur1.scaffold_46107 C 0 C 0 s cavPor3.scaffold_42 9674769 43 + 15951348 ----------------GGAGTCTTGGAG--AAAGCAGAGC---TTG-----CTGTCCAGAGCCAGGCAT i cavPor3.scaffold_42 C 0 I 740 s turTru1.scaffold_93657 11932 44 - 12933 ----------------TGGGCCTAAAGA--AAACGC-------CCTCCCCGCCCCCCGGGGGGCAGCAT i turTru1.scaffold_93657 C 0 C 0 s bosTau4.chr29 48983967 38 + 51998940 ----------------TGGGTCTTAAGG--ACATTC-------CCT------TCCCCCGGGGACGGTGC i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28949023 40 + 33091231 ----------------CGGGTCTTAAGGA-AAGCTC-------CCT-----TCCTCCTGAGGCAGGAGT i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 64998 37 + 302526 ----------------TGGGACTTAAGG--GAGCCC-------CCT-----TCCCCC--GGCCCAGAGT i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7544896 39 - 58872314 ----------------TGGGACTTAAGG--CAGCCC-------CCC-----TCCCCTGGGGGCCAGAGT i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 100808 44 + 1045236 ----------------GGGGTGC--AGG--GAAGCAGCGCCCCCTC-----CTCCCCTGGGGCCAGGGT i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 29661 34 - 46842 ----------------GGGGTGC--AGGCTGGGATAGGGCGGAGAGCACAGG----------------- i proCap1.scaffold_13667 C 0 I 632 e ochPri2.scaffold_12461 32194 2417 - 40248 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e oryCun2.chrUn0985 32927 1017 + 42081 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M a score=164421.000000 s hg19.chr11_gl000202_random 24263 214 + 40103 TCAGGCTGCAG-------AGTCTTCACTCCCCACTAAGAGGTG----------------TCC---------TCTCA-----GTGTGGCTTCCCGCTCTGTAGAG-------------AGTG-----------TATGT-GGGAAActacgaaaaggaatgaagccctgatag-ctgctgtacgatggatg-cccctggaactagtgtgca----gaaaggagccagacac-aaaa-cgccacatattgcatgcttTcatttgtatgaaatgtacaaaaaattagc s panTro2.chr11 68210598 214 + 134204764 TCAGGCTGCAG-------AGTCTTCACTCCCCACTAAGAGGTG----------------TCC---------TCTCA-----GTGTGGCTTCCCGCTCTGTAGAG-------------AGTG-----------TATGT-GGGAAACCGCGaaaaggaatgaagccctgatag-ctgctgtacgatggatg-cccccggaactagtgtgca----gaaaggagccagacac-aaaa-cgccacatattgcatgcttTcatttgtatgaaatatacaaaaaattagc i panTro2.chr11 C 0 C 0 s gorGor1.Supercontig_0015245 54665 214 + 115376 TCAGACTGCAG-------AGTCTTCACTCCCCACTAAGAGGTG----------------TCC---------CCTCA-----GTGTGACTTCCTGCTCTGTAGAG-------------AGGG-----------TATGT-GGGAAAccacaaaaaggaatgaagccctgatag-ctgctgtacgatggatg-cccctggaactagtgtgcg----gaaaggagccagacac-aaaa-cgccacatattgcatgctttcatttgtatgaaatatacaaaaAATTAGC i gorGor1.Supercontig_0015245 C 0 M 105 s rheMac2.chr14 128169996 222 - 133002572 TCAGTCTGCAGGGTCCTCGGTCCTCACTCCCCGCTAAGAGGTA----------------TCC---------CCTCA-----GTGTGGCTTCCCGCTCTGTGTAG-------------AGTA-----------TATGTGGGGAAAccacagaaaggaatgaagccctgatag-ctgctgtacgatggatg-cccctggaactagtgtgca----gaaaggagccagacaa-aaac-cgccacatattgcatgattTcatttgtatgaaatatccaaaaatttagc i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 86819 222 + 109049 TCAGTCTGCAGGGTCCTCGGTCCTCACTCCCCACTAAGAGGTA----------------TCC---------CCTCA-----GTGTGGCTTGCCGCTCTGTATAG-------------GGTG-----------TATGTGGGGAAAccacataaaggaatgaagccctggtag-ctgctgtacgatggatg-cccctggaactagtgtgca----gaaaggagccagacaa-aaac-tgccacatattgcatgattTcatttgtatgaaatatccaaaaatttagc i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_46107 144 211 + 5307 CCGGCCGGCCTGCT----GGCCCCTGCGGCCTGCTAAGGGCTG----------------TCCCCCACCCCACCCTC-----TCCTGGCTCCCTGCTCTGCGGTG-------------AGGGGGACAGGGGTCTGTGT-GGGAagccacgaaaagggacgaggcactaata---------------gaca-cccctcgaaaatgcctgccgcgtgcaagaagccagacacgaagg-cggcgc---ttgcagcgtcccatgtgcgagagacg-------------- i micMur1.scaffold_46107 C 0 C 0 s turTru1.scaffold_93657 11976 193 - 12933 CCCGCCTGCCC-------AGCCGT-----------------------------------CTT---------CCCCA-----GGGCAGCTCCTTGCTCTCCAGGG-GTAGGAAGCAAGAGTG-----------CGcat-gggaag----------gaatgaaacatcggca--ccgttacggcagggatgaccctggaaaccgttctgctcagtgaaagtagccagactc-aaaa-ggctacacgtcgcacaatcccatttatatgaaacattcaga-------- i turTru1.scaffold_93657 C 0 I 3 s bosTau4.chr29 48984005 191 + 51998940 CCTGCCTGCCG-------AGCCCT-----------------------------------GAC---------TCCCA-----GGACAGCTTCTTGCTCTGCAGTG-GGAGGAGGCAGGGGTG-----------TGTAT-GGGaag----------ggatgaaacactgacc--tggcgacagcgtggatgaccctgaacactgttccgctcagtgca---agctggcctc-ccag-ggcctcacaccgctcaatcccgtttatatgaaatttccagaa------- i bosTau4.chr29 C 0 I 1082 s equCab2.chr12 28949063 227 + 33091231 CCAGCCTGCTG-------GGCCCTCACTGCTCGCTGGGAGCCG----------------ACT---------CTCCAACATGGTCCAGCTCCCTG-TCGGCTGTGAGGAGGGGGCGAGAGTG-----------TCTGT-GGG-agcct-gaggagggatgaatccctgatag-atgctacgtcacggatgaccctcaaaaacctcacgctgggtgaaagtaaccaggctc-gaag-gatcagagctcgcacgatgccgtttataggaaatatccagaa------- i equCab2.chr12 C 0 I 165 s felCat3.scaffold_135390 65035 203 + 302526 --------GGG-------GGCCCTCCCGTCCTCCAGGGGGCTGCCTCCTCCCCTCCCGTGCT---------CCCCA-----GGGCAGCTCCCTGCTCCGCAGCGAGGAGGCGGCAGGAGTG-----------TGTGT-GGGAagcca-gcaggaggaaggagccccgag---acgagacaagatgg-tgaaccccgaaaccatcctgct-cgtggaagtagccggatcc-aaaagggccacccagcgcgtg--------------------------------- i felCat3.scaffold_135390 C 0 I 986 s canFam2.chr18 7544935 197 - 58872314 CCTGCCC-ATG-------GACCGTCACCTCCCCCCGGGAGCCGTGTCCCCCTCTCCC--ACT---------CCCCA-----GGGCCGC-CCCTGCTCTGCGGCAAGGAGTGGGCAGGAGTG-----------TGTGT-GGGAAGCCT-CAGGGAGGCAGGAGGTGTGCACGCACGCTACCACATGA-CG-----------------GCC-Cgtggaagcggccggaccc-agaa-ggccacatagcacacgatcct---------------------------- i canFam2.chr18 C 0 I 13 s loxAfr3.scaffold_159 100852 172 + 1045236 ----------------------------------CCGGCAGTG----------------AGG---------ACCGA-----GGA------CCGGGCAAGAGATG-------------GCTG-----------TGCGT-GGGAagccacaaagggacacgaagcactgatcc-ctgctatgacgtgaagg-aacctggaa--aatacgctgagtgaaagaagcccgacac-aaaa-ggacgcgtagtgtttgattccaGACACAGGTAGCCCAC----------- i loxAfr3.scaffold_159 C 0 I 535 e ochPri2.scaffold_12461 32194 2417 - 40248 I e calJac1.Contig6069 86127 2151 + 235769 M e myoLuc1.scaffold_155660 41425 865 - 124081 M e oryCun2.chrUn0985 32927 1017 + 42081 I e proCap1.scaffold_13667 29695 632 - 46842 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M a score=70104.000000 s hg19.chr11_gl000202_random 24477 148 + 40103 cgggcatggtggcacttgcctgtaatcccagctactcaggaggctgaggcaggagaatcacttgaacctgggatgtggaggttgcagtaaaccgagatcatgccactgcactccagcctgggtgacagagcgagactccatctcaaaa s panTro2.chr11 68210812 148 + 134204764 cgggcatggtggcacgtgcctgtaatcccagctactcangaggctganngcagagaatcacttgaacctgggatgtggaggttgcagntaaccgagatcatgccactgcactccagcctgggtgacagagtgagactccatctcaaaa i panTro2.chr11 C 0 M 1208 s rheMac2.chr14 128170218 148 - 133002572 cagacgtggtggcacatgcctgtaatcccagctactcgggaggctgaggcaggagaaacgcttgaacctgggaggtggaggttgcagtaagctgagatctcaccactgcactccagcctgggtgacagagtgagactccatctcaaaa i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 87041 148 + 109049 cagacgtggtggcacgtgcctgtcatcccagctactcgggaggctgaggcaggagaaacgcttgaacccgggaggtggaggttgtagtgagctgagatcgcgccactgcactccagcctgggtgacagagtgagactccatctccaaa i papHam1.scaffold6638 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 65238 986 + 302526 I e calJac1.Contig6069 86127 2151 + 235769 M e micMur1.scaffold_46107 355 0 + 5307 C e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 12169 3 - 12933 I e oryCun2.chrUn0985 32927 1017 + 42081 I e proCap1.scaffold_13667 29695 632 - 46842 I e loxAfr3.scaffold_159 101024 535 + 1045236 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28949290 165 + 33091231 I e gorGor1.Supercontig_0015245 54879 105 + 115376 M e canFam2.chr18 7545132 13 - 58872314 I e bosTau4.chr29 48984196 1082 + 51998940 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M a score=27228.000000 s hg19.chr11_gl000202_random 24625 140 + 40103 aaagaaaaaaaaagaggccgggcgaggtggctcacgcctgtaatctcagcattttgggaggcccagacgggtggatcacgaggtcaggagtttgagaccagcctgaccaacatggtgaaaccccgtctctact----aaaaaaa s rheMac2.chr14 128170366 142 - 133002572 aaag--aaaaaaagaggccgggtgcggtggctcacgactgtaatctccgcactttgggaggccgaggtgggcggatcacgaggtcaggagttcgagaccaacctggccaacatggtgaaaccccgtctctactaaaaaaaaaaa i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 87189 126 + 109049 aaag--aaaaaaagaggccgggtgcggtggctcacgcctgtaatctcagcatttcgggaggccgaggagggctgatcatgaggtcaggagttcaagactgatctgaccaacatggtgaaact---------------aaaaaa- i papHam1.scaffold6638 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 65238 986 + 302526 I e calJac1.Contig6069 86127 2151 + 235769 M e micMur1.scaffold_46107 355 0 + 5307 C e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 12169 3 - 12933 I e oryCun2.chrUn0985 32927 1017 + 42081 I e proCap1.scaffold_13667 29695 632 - 46842 I e loxAfr3.scaffold_159 101024 535 + 1045236 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28949290 165 + 33091231 I e gorGor1.Supercontig_0015245 54879 105 + 115376 M e canFam2.chr18 7545132 13 - 58872314 I e bosTau4.chr29 48984196 1082 + 51998940 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=13657.000000 s hg19.chr11_gl000202_random 24765 31 + 40103 atacaaaaattagccaggcatggtggcacat s gorGor1.Supercontig_0015245 54986 31 + 115376 atacaaaaattaaccaggcatggtggcacat i gorGor1.Supercontig_0015245 M 105 C 0 s rheMac2.chr14 128170508 31 - 133002572 atacaaaaattagctgggtgtggtggcacat i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 87315 30 + 109049 atacaaaaattagct-ggcgtggtggcacac i papHam1.scaffold6638 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 65238 986 + 302526 I e calJac1.Contig6069 86127 2151 + 235769 M e micMur1.scaffold_46107 355 0 + 5307 C e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 12169 3 - 12933 I e oryCun2.chrUn0985 32927 1017 + 42081 I e proCap1.scaffold_13667 29695 632 - 46842 I e loxAfr3.scaffold_159 101024 535 + 1045236 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28949290 165 + 33091231 I e canFam2.chr18 7545132 13 - 58872314 I e bosTau4.chr29 48984196 1082 + 51998940 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=47913.000000 s hg19.chr11_gl000202_random 24796 89 + 40103 gcctgtattcccagctacttgggaggctgaggcaggagaattg---cttgaac-tcaggaggtggaggttgcaatgaggcaagattgcgtcat s papHam1.scaffold6638 87345 89 + 109049 gcctgtagtcccagctagttgggaggctgaggcaggagaattg---tttgaac-ctgggaggtggaggttgcagtgaggcaagattgcatcat i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128170539 89 - 133002572 gcctatagtcccagctagttgggaggctgaggcaggagaattg---tttgaac-ctgggaggtggaggttgcagtgaggcaaggttgcatcat i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0015245 55017 89 + 115376 gcctgtagtcccagctacttgggaggctgaggcaggagaattg---cttgaac-ccaggaggtggaggttgcaatgaggcaagattgcatcat i gorGor1.Supercontig_0015245 C 0 C 0 s proCap1.scaffold_13667 30327 89 - 46842 GCTTGGGTGTTTGGTTTCtagagacaaaaagg-agaagagttgttccttcagcactgggagtttaagg--ggaatgaggggcgactgc-tcat i proCap1.scaffold_13667 I 632 I 143 e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 65238 986 + 302526 I e calJac1.Contig6069 86127 2151 + 235769 M e micMur1.scaffold_46107 355 0 + 5307 C e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 12169 3 - 12933 I e oryCun2.chrUn0985 32927 1017 + 42081 I e loxAfr3.scaffold_159 101024 535 + 1045236 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28949290 165 + 33091231 I e canFam2.chr18 7545132 13 - 58872314 I e bosTau4.chr29 48984196 1082 + 51998940 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=25056.000000 s hg19.chr11_gl000202_random 24885 64 + 40103 tgcactccagactgggtgacagagtgagactccatctcagaaacagaaaaaaagaaaaaaaaaa--------------- s papHam1.scaffold6638 87434 70 + 109049 tgcactccagcctgggcgacagagagagactccatctcaaaaaaaaaagaaaaagaaaaagaaaaaaaat--------- i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128170628 79 - 133002572 tgcactccagcttgggtgacagagcaatactccatctcaaaaaaaaaaaaaaaagaaaaaagaaaaaagaaaaaaaaat i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0015245 55106 66 + 115376 tgcacaccagcctgggtgacagagtgagactccatctcagaaacagaaaaaaagaaaaaaaaaaaa------------- i gorGor1.Supercontig_0015245 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 65238 986 + 302526 I e calJac1.Contig6069 86127 2151 + 235769 M e micMur1.scaffold_46107 355 0 + 5307 C e myoLuc1.scaffold_155660 41425 865 - 124081 M e turTru1.scaffold_93657 12169 3 - 12933 I e oryCun2.chrUn0985 32927 1017 + 42081 I e proCap1.scaffold_13667 30416 143 - 46842 I e loxAfr3.scaffold_159 101024 535 + 1045236 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28949290 165 + 33091231 I e canFam2.chr18 7545132 13 - 58872314 I e bosTau4.chr29 48984196 1082 + 51998940 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=51806.000000 s hg19.chr11_gl000202_random 24949 63 + 40103 Gtccaga----acaggcaaatccacagagacaggac--------------------------tcacagtgttg---gttgtcagtgtgtggggtta s micMur1.scaffold_46107 355 58 + 5307 -tccggcgtgggcaggc-------cccagacaggac--------------------------gcggactggcg---cttgccggagcgtggg-ctg i micMur1.scaffold_46107 C 0 C 0 s calJac1.Contig6069 88339 54 + 235769 -----------acaggcaaatc--cagagaaaggac--------------------------gcacagtgttg---gttgtcggagtgtggggtct i calJac1.Contig6069 M 2151 C 0 s pteVam1.scaffold_74370 224 83 - 1134 -----GG----ACAGGCAGACACATGGAGACAGACCCCCAGGGACAGGCAGGCCAGGTTGGACcaggtcagtg---gctgccagaactcggagtt- i pteVam1.scaffold_74370 N 0 C 0 s turTru1.scaffold_93657 12172 54 - 12933 --------------ggcaaatccacagggacagac---------------------------gcagattgagggctgctgccagagcttggggtt- i turTru1.scaffold_93657 I 3 C 0 s canFam2.chr18 7545145 63 - 58872314 gcccaga----gtagagaaattcgtagagacagact--------------------------atagattgatg---gttgccagagttgagggtgg i canFam2.chr18 I 13 C 0 s papHam1.scaffold6638 87504 63 + 109049 gtccaga----acaggccaatctacagagacaggac--------------------------tcacagtgttg---actgtcagtgtgtgggactg i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128170707 63 - 133002572 gtccaga----acaggccaattcacagagacaggac--------------------------tcacagtgttg---actgtcagtgtgtgggactg i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0015245 55172 63 + 115376 gtccaga----acaggcaaatccacagagacaggac--------------------------tcacagtgttg---gttgtcagtgtgtggggtta i gorGor1.Supercontig_0015245 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 65238 986 + 302526 I e myoLuc1.scaffold_155660 41425 865 - 124081 M e oryCun2.chrUn0985 32927 1017 + 42081 I e proCap1.scaffold_13667 30416 143 - 46842 I e loxAfr3.scaffold_159 101024 535 + 1045236 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28949290 165 + 33091231 I e bosTau4.chr29 48984196 1082 + 51998940 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=224916.000000 s hg19.chr11_gl000202_random 25012 172 + 40103 agg--ggtgggatgggaagt---gattacttgatcgggaa-ggggttt-c-------cttt-agggtggtgaagatgttttggaacttagatagaggtgatgtttgcacagcactgtggatgtgctgagtgccgtggaactgtgcactgtaaactgattaattt--tgtcacgtgaattccacttcca-t s gorGor1.Supercontig_0015245 55235 172 + 115376 agg--ggtgggatggggagt---gattacttgatcgggaa-ggggttt-c-------cttt-agggtggtgaagatgttttggaacttagatagaggtggtgtttgcacagcactgtggatgtgctgagtgccgtggaactgtgcactgtaaactgattaattt--tgtcacgtgaattccacttcca-t i gorGor1.Supercontig_0015245 C 0 C 0 s rheMac2.chr14 128170770 169 - 133002572 tgg-cggtgggatggggagt---gactacttgaccggg-a-ggggctt-c-------cttt-ggggtggtgaagatgttttggaacttagatagagg---tgtttgcacaacattgtggtcgcgctgagtgccgtggaactgtgcactgtaaaatgattaattt--tgtcatgtgaatttcacttcca-t i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 87567 153 + 109049 tggggggtgggatggggagt---gattatttgaccgggaa-ggggctt-c-------cttt-ggggtggtgaagatgttttggaacttagatagagg---tgtttgcacagcattgtggtcgcgctgagtgccgtggaactgtgcactgtaaaattattaattt--tgtCA------------------- i papHam1.scaffold6638 C 0 I 594 s canFam2.chr18 7545208 173 - 58872314 gca--ggaggaatggggagt---aattgcttaataggcac-agagttt-c-------tttttggggtcatgagaaaggttgagaat-tggacagagttagtgggtgtgcagcagtgggaatgtgccggatgcacctgaattgttcaccttaaaatggttcattttatgccatgtgaatttcacatcaa-- i canFam2.chr18 C 0 I 220 s turTru1.scaffold_93657 12226 158 - 12933 --a--gggaaaacggggagt---gattacgtaacaggtgtgggggttt-c-------ctttgggggtaatgaaaatgtttt-gaac-ctgatagagatggtggtcataccacacaaa-------------gccgctgcactgttgacctgaaaatgattaattttatgttatgtgaatttgacctcaa-- i turTru1.scaffold_93657 C 0 I 1 s pteVam1.scaffold_74370 307 147 - 1134 -----gggggaatggggagc---agtggccacacggggac-aggcttt-c-------cttttggggt---------------gaac-ttggcagaggcggtggtcacacgacgctgagaatg--------acaccc-aatcgttcgccttgaaacggttagttttacgtcatgtggatttcgcttcgat- i pteVam1.scaffold_74370 C 0 C 0 s calJac1.Contig6069 88393 167 + 235769 cgg---gtgggatggg-agt---gctcacttgatcggtaa-ggagttt-c-------cttt-gggatggtgaagctgatttgtgatttagttagaggtggtgtttacacaacattgtggatgcactgagtgccgt-gaattgtg--ctgtaaaatgattcattt--tgtcatgtgcattccacttcca-c i calJac1.Contig6069 C 0 C 0 s micMur1.scaffold_46107 413 174 + 5307 ggg--agagaggcggggggt---ggttatttaacaggcag-agagcttcc-------cttc-ggagtcaggaaaatgttctggaac-caggtagaggtggtggccgcacaacatggcgaatgcaccaaatgccactcagctgtgcacttgcaaatggttaactttatgttatgcgaattttatctcCC-T i micMur1.scaffold_46107 C 0 C 0 s loxAfr3.scaffold_159 101559 173 + 1045236 -----agggtcgctatgagtcagaatcgactcgacgacac-tgggttt-t-------tttg-ggggggatgaaaacattctggaac-tagagggaggtgggggctgagcaacaccgtcagtgcactgagcgtccccaaactgttcactttctaatagccggttttatgttgtgtgaatttcacctcta-t i loxAfr3.scaffold_159 I 535 C 0 s proCap1.scaffold_13667 30559 158 - 46842 -----------------------aattaactcaacagcaa-tgggttt-ctttttgatttg-agggtgatgaaattgtcgtggaag-cagatagaggcaacggctgcacagctctgtgaacgcactgattgtcactgaactgctcac-ttcaaacagttgattttgtgtta-gcga--ctcacttcta-t i proCap1.scaffold_13667 I 143 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 65238 986 + 302526 I e myoLuc1.scaffold_155660 41425 865 - 124081 M e oryCun2.chrUn0985 32927 1017 + 42081 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28949290 165 + 33091231 I e bosTau4.chr29 48984196 1082 + 51998940 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=122298.000000 s hg19.chr11_gl000202_random 25184 87 + 40103 gtttta-----gaaaACTGCATCTGG-GAT-CAGCAGGGCCTCTCAGG---------AGGACCTGTGT--GGGG-CATCTGGCTCCTCGGCTCGGGCAGGTAACCT s gorGor1.Supercontig_0015245 55407 87 + 115376 gtttta-----gaaaACTGCATCTGG-GAT-CAGCAGGGCCTCTCAGG---------AGGACCTGTGT--GGGG-CATCTGGCTCCTCGGCTGGGGCAGGTAGCCT i gorGor1.Supercontig_0015245 C 0 C 0 s rheMac2.chr14 128170939 87 - 133002572 GTTCTA-----GAAAACTGCATCTGG-GAT-CAGCAGGGTCTCTCAGG---------AGGACCTGCGT--GGGG-CGTCCGGCTCCTCGGCTCGGGCAGGTAGCCC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 88314 87 + 109049 GTTCTA-----GAAAACTGCATCTGG-GAT-CAGCAGGGTCTCTCAGG---------AGGACCTGTGT--GGGG-CGTCTGGCTCCTCGGCTCGGGCAGGTAGCCC i papHam1.scaffold6638 I 594 C 0 s calJac1.Contig6069 88560 84 + 235769 ttttta-----acaaAGTCCATGTGG-GAT-CAGCAGGGCCTC---AG---------GAGACCCTCGT--GGGG-CACCTGGCTCCTCCGCTCAGGCAGGTAGCCT i calJac1.Contig6069 C 0 I 270 s micMur1.scaffold_46107 587 98 + 5307 TTATTT-----AAAAAGTGCACGTGGAGAT-CGGCCAGGCCTCTGGGGGGGGGGGGAGGGACCTGCGT--GGGGACACCTGGCTTCCCGACTCGGACAGGCAGCCC i micMur1.scaffold_46107 C 0 C 0 s turTru1.scaffold_93657 12385 87 - 12933 attttt-----taaaaaTGCAGGTGGGGAT-CCGTGTGGCCTCT-GGA---------GGGACCTGCGC--GGCGCCGGCTGGCTCCTCGGCTCAGACAGATGGCC- i turTru1.scaffold_93657 I 1 C 0 s canFam2.chr18 7545601 88 - 58872314 TTTTTT-----TAAAAGTGCACCTGGGGATGCAGCAGGGCCTCCTGGA---------GGGACCTTTAT--GGGGACATCTGGCTCCTCGGTCCCGGCAGGTA-GC- i canFam2.chr18 I 220 C 0 s pteVam1.scaffold_74370 454 78 - 1134 --ttTT-----TTAGAGTGT-----------CTGTGGGGCCTCTGGGA---------GGGAGCCGCGTGGGGGGACCCCTGGCTGATGTACTGGGGCAGGCGCCC- i pteVam1.scaffold_74370 C 0 C 0 s loxAfr3.scaffold_159 101732 79 + 1045236 -ttttcaaaaaGAAGAGTGTATGGGGGAAT-CGGCAGGGCCTC---CA---------GGGACCTACAC--AGGGACACTTGGTTCCTTGGCCCGG----------- i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 30717 68 - 46842 -ttTTC-AAAAGAAGAATGTGTGTAGGAAT-CAG------------CA---------GAGACCGACCC--GGAACCACCTGGCTCCTC-ACCTGG----------- i proCap1.scaffold_13667 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 65238 986 + 302526 I e myoLuc1.scaffold_155660 41425 865 - 124081 M e oryCun2.chrUn0985 32927 1017 + 42081 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28949290 165 + 33091231 I e bosTau4.chr29 48984196 1082 + 51998940 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=-6351.000000 s hg19.chr11_gl000202_random 25271 54 + 40103 ACGCGTACAGGTATGTTAGGAGAGAGGCACGGACGGC--CAAG-----CCTTCGACGTCAG s papHam1.scaffold6638 88401 54 + 109049 ACACGTACAGGCCTGTCAGGAGTGAGGCACGGACAGC--CAAG-----CCTTCGACATCAG i papHam1.scaffold6638 C 0 C 0 s rheMac2.chr14 128171026 54 - 133002572 ACATGTACAGGCCTGTCAGGAGTGAGGCACGGACGGC--CAAG-----CCTTCGACATCAG i rheMac2.chr14 C 0 C 0 s gorGor1.Supercontig_0015245 55494 54 + 115376 ATGCATACAGGCCTGTTAGGAGAGAGACACGGACGGC--CAAG-----CCTTCGACGTCAG i gorGor1.Supercontig_0015245 C 0 C 0 s micMur1.scaffold_46107 685 30 + 5307 ACATGCGCAGG------------------------GC--GCAG-----CCTCCCGGGTCAG i micMur1.scaffold_46107 C 0 I 9 s turTru1.scaffold_93657 12472 53 - 12933 ACGCGTGCAGCCCCCG-AGGAGAGAGGCACACACACCACCA-------CCTTCAATGGTAG i turTru1.scaffold_93657 C 0 C 0 s canFam2.chr18 7545689 42 - 58872314 CGGTTTGCAGGTCCAGCAGGAGA----------------CAGGTGCTCCCTCCAGCAG--- i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_74370 532 60 - 1134 CCATGTGCAGGCCCAG-GGGAGAGACGCATGCAGGTCAGCAGGTCACGCCTCGGGCAGCAG i pteVam1.scaffold_74370 C 0 C 0 s loxAfr3.scaffold_159 101811 20 + 1045236 --------------------AGATTGCCACCAGCAGT--CAG------------------- i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 30785 20 - 46842 --------------------AGATTGCCACCAGAAGT--CAG------------------- i proCap1.scaffold_13667 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 65238 986 + 302526 I e calJac1.Contig6069 88644 270 + 235769 I e myoLuc1.scaffold_155660 41425 865 - 124081 M e oryCun2.chrUn0985 32927 1017 + 42081 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28949290 165 + 33091231 I e bosTau4.chr29 48984196 1082 + 51998940 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=9711.000000 s hg19.chr11_gl000202_random 25325 34 + 40103 CCCCTCCTTCGGCAAATCCTAGCATcagtatcct s gorGor1.Supercontig_0015245 55548 34 + 115376 CCCCTCCTTCGGCAAATCCTAGCATcagtatcct i gorGor1.Supercontig_0015245 C 0 C 0 s rheMac2.chr14 128171080 34 - 133002572 CCCCTCCTTCAGCAAATCCTAGCGTCAGCATCCT i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 88455 34 + 109049 CCCCTCCTTCGGCAAATCCTAGCGTCAGCATCCT i papHam1.scaffold6638 C 0 C 0 s turTru1.scaffold_93657 12525 29 - 12933 TTGCTCA--TGCC---TCGGACAGTCTGAGTTCT i turTru1.scaffold_93657 C 0 C 0 s canFam2.chr18 7545731 21 - 58872314 ---------TGCC---CCTGACCGTCCAAGCTG- i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_74370 592 34 - 1134 CCCCTCCTTTGCCACACCCTACCGTCCATGTCGT i pteVam1.scaffold_74370 C 0 I 5 s loxAfr3.scaffold_159 101831 28 + 1045236 TGCCTCACTGGACACCTCCTGCCA-----GTCC- i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 30805 28 - 46842 CGCCTCCTTGGACAGTTCCCGGCG-----GTCC- i proCap1.scaffold_13667 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 65238 986 + 302526 I e calJac1.Contig6069 88644 270 + 235769 I e micMur1.scaffold_46107 715 9 + 5307 I e myoLuc1.scaffold_155660 41425 865 - 124081 M e oryCun2.chrUn0985 32927 1017 + 42081 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28949290 165 + 33091231 I e bosTau4.chr29 48984196 1082 + 51998940 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=178314.000000 s hg19.chr11_gl000202_random 25359 144 + 40103 aagctcaggac-----acgggacctccagggacttctggactcacactca-------------gctccaccgc-tgtgggttactgggttgaatgactaaacttcaggag-cctcagtctccccatctgtaaaacggAAGCCACAGA--TGC-AACGTCTGGAAAGC s micMur1.scaffold_46107 724 114 + 5307 AGACCCAGGAC-----ATGGG-CCTGCAGGTACTTCGGGACCCAAACCCA-------------GCTCAACTGG-GAAGGGCAGCTGGG-------------CTGCAGgag-cctcagtctccacatctgtaaagtggACCCCAAAGA-------------------C i micMur1.scaffold_46107 I 9 C 0 s gorGor1.Supercontig_0015245 55582 144 + 115376 aagctcaggac-----acgggatctccagggacttctggactcaaactca-------------gctccaccgc-tgtgggtaactgggtcgaatgactaaacttgaggag-cctcagtctccccatctgtaaaatggAAGCCACAGA--TGC-AACGTCTGGAAAGC i gorGor1.Supercontig_0015245 C 0 C 0 s rheMac2.chr14 128171114 144 - 133002572 Aagctcaggtc-----atgggacctccagggacttctggactcaaactca-------------gctccaccgc-tgtgggtaactgggtcgaatgactaaacttcaggag-cctcagtctccccatctataaaatggAAGCCACAGA--TGC-AATGTCTGGAAAGC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 88489 144 + 109049 AAGCTCAGGTC-----ATGGGACCTCcagggacttctggactcaaactca-------------gctccaccgc-tgtgggtaactgggtcgaatgactaaacttcaggag-cctcagtctccccatctataaaatggAAGCCACAGA--TGC-AATGTCTGGAAAGC i papHam1.scaffold6638 C 0 C 0 s turTru1.scaffold_93657 12554 138 - 12933 AGGCCCAAGAG-----ATGGT-------GGTATCTGGGGACTCGAGCCCC-------------GCTCCACTGCTTATGGGTGACTGGACCGGGTGACTGGCCTTCAAGAA-TCCT-GTCTTCACATCTGTAAAATGGAATCCACAAAGACAC-AACACC-AGAACGC i turTru1.scaffold_93657 C 0 C 0 s canFam2.chr18 7545752 138 - 58872314 AGGGCCAGGAG------TGGA-------GACACTTCTGGACTCAAGCCCA-------------ACTCCACCGCTTAGAAGTAACCAGGCCAAATATCTGGACCTCCAGAG-TCCTCAGTCTCCCGTCCCTAAGATGGAATCCACAAAGATAC-AATAAC-AGAAAGC i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_74370 631 143 - 1134 AGGTCCTGGAG------CAGA-------GGCACTTCATCACTCAAACCCATGACTCAAACACGGCTCCACGGCCTATGGGCTCCCGGGCCAGGCGGCCGGACTTCAGAAGCTCCCCCGCCCCGCCTCCCC--------TTCTGTAAAG-CAG-AACCAC-AGGAAGC i pteVam1.scaffold_74370 I 5 C 0 s loxAfr3.scaffold_159 101859 130 + 1045236 ACACCTAGGCC---------------------CTTCTAGATGCAGACCCA-------------GGTCCACCAC-TGTGGGCAGCTGGGCCACAGGACTGGACTTCAGGAGCCCTCAGTTTCCCCACCTGTAGAATGGAAGCCACAAGA-CAC-AGTGCCCAGAAAGC i loxAfr3.scaffold_159 C 0 I 2171 s proCap1.scaffold_13667 30833 151 - 46842 ATGTCTAGGACACTCTGCGTCATTTCCAGGTGCTTCTGGATGCAGACTGA-------------GCTCCGTCAC-TGTGGGTGGCTGGG-CACATGGCCAGACTTCAGGGACCCTCAGTTTGCCCATCTGAAGAATAGAAACCCCAGGG-CCCTGGTGCCCACAAAGC i proCap1.scaffold_13667 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 65238 986 + 302526 I e calJac1.Contig6069 88644 270 + 235769 I e myoLuc1.scaffold_155660 41425 865 - 124081 M e oryCun2.chrUn0985 32927 1017 + 42081 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28949290 165 + 33091231 I e bosTau4.chr29 48984196 1082 + 51998940 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=-7946.000000 s hg19.chr11_gl000202_random 25503 41 + 40103 ACGTAG--CCCAGCCCCAGCACCACACCATGGTAGAGGCACA-G s micMur1.scaffold_46107 838 16 + 5307 ACGGTG--CCCAG-------------------------CGCG-G i micMur1.scaffold_46107 C 0 C 0 s gorGor1.Supercontig_0015245 55726 41 + 115376 AGGTAG--CCCAGCCCCAGCACCACACCATGGTGGAGGCACA-G i gorGor1.Supercontig_0015245 C 0 C 0 s rheMac2.chr14 128171258 41 - 133002572 ACGTAG--CCCAGCCCCAGCACCAAGCCATGGTGGAGACACA-G i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 88633 41 + 109049 ACGTAG--CCCAGCCCCAGCACCAAGCCATGGTGGAGACACA-G i papHam1.scaffold6638 C 0 C 0 s turTru1.scaffold_93657 12692 41 - 12933 ACAGGG-CCCCGGATGCAGCTGGAAGCCGGGTTCTGCTCACG-- i turTru1.scaffold_93657 C 0 C 0 s canFam2.chr18 7545890 39 - 58872314 GCGTGG---CCAGACGCAG-TGCAGAGAGTATGTCATGCACCT- i canFam2.chr18 C 0 I 2 s pteVam1.scaffold_74370 774 12 - 1134 ACATGG-TCCCAG------------------------------- i pteVam1.scaffold_74370 C 0 C 0 s proCap1.scaffold_13667 30984 42 - 46842 ACATGGTCTCCAGGCTGACCGTTA-GCCATACTATGCACTCA-G i proCap1.scaffold_13667 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 65238 986 + 302526 I e calJac1.Contig6069 88644 270 + 235769 I e myoLuc1.scaffold_155660 41425 865 - 124081 M e oryCun2.chrUn0985 32927 1017 + 42081 I e loxAfr3.scaffold_159 101989 2171 + 1045236 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28949290 165 + 33091231 I e bosTau4.chr29 48984196 1082 + 51998940 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=-15381.000000 s hg19.chr11_gl000202_random 25544 27 + 40103 GG------C----CATTT-TTATCGCCTTGTTCCAAGC s micMur1.scaffold_46107 854 26 + 5307 GG------C----CGTCACCCACAGCTTTGTTCTGA-- i micMur1.scaffold_46107 C 0 C 0 s gorGor1.Supercontig_0015245 55767 27 + 115376 GG------C----CATTA-CTATCGCCTTGTTCCAGGC i gorGor1.Supercontig_0015245 C 0 C 0 s rheMac2.chr14 128171299 29 - 133002572 GG------T--GGAGACA-CCATCGCCTTGTTCCTGGC i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 88674 31 + 109049 GG------CCATAAGTTA-CCATCGCCTTGTTCCTGGC i papHam1.scaffold6638 C 0 C 0 s turTru1.scaffold_93657 12733 28 - 12933 GG------C----CATTGCCCGTAGCCGTGCTCCCACG i turTru1.scaffold_93657 C 0 N 0 s equCab2.chr12 28949455 34 + 33091231 ggttaattt----tatgccatgacattttatgtcaGGC i equCab2.chr12 I 165 C 0 s canFam2.chr18 7545931 28 - 58872314 GG------T----GGTGACCAGCAGCCTTGTTCCTGGG i canFam2.chr18 I 2 I 1 s pteVam1.scaffold_74370 786 29 - 1134 -----GGCC----AGCTCCTCCCGGCCTTGTTCCCTGC i pteVam1.scaffold_74370 C 0 I 2 s proCap1.scaffold_13667 31026 12 - 46842 ------------------------CATTTGTTCCTC-- i proCap1.scaffold_13667 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 65238 986 + 302526 I e calJac1.Contig6069 88644 270 + 235769 I e myoLuc1.scaffold_155660 41425 865 - 124081 M e oryCun2.chrUn0985 32927 1017 + 42081 I e loxAfr3.scaffold_159 101989 2171 + 1045236 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e bosTau4.chr29 48984196 1082 + 51998940 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=27772.000000 s hg19.chr11_gl000202_random 25571 37 + 40103 GATGGTTC------TGATTTGGGTCCATCTTTCTCACATCCTT s gorGor1.Supercontig_0015245 55794 37 + 115376 GATGCTTC------TGATTTGGGTCCATCTTTCTCACATCCTT i gorGor1.Supercontig_0015245 C 0 C 0 s rheMac2.chr14 128171328 37 - 133002572 GATGCTTC------TGATTTGGGTCCATCCCTCTCCCGTCCTG i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 88705 36 + 109049 GAT-CTTC------TGATTTGGGTCCATCCCTCTCCCATCCTG i papHam1.scaffold6638 C 0 C 0 s equCab2.chr12 28949489 37 + 33091231 GACGTTTC------TGCTGTGGGTCCAAGTCTTACCCTCCCTG i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 66224 37 + 302526 GAGGTTTC------TGGTCAGGGTCCACGTCTTACCCTCTCTG i felCat3.scaffold_135390 I 986 C 0 s canFam2.chr18 7545960 37 - 58872314 CATGTCTT------TGATTGGGGTCTGTGTGTTACCCTCCCTG i canFam2.chr18 I 1 C 0 s pteVam1.scaffold_74370 817 37 - 1134 GAGGCTCC------GGACCGGGGTCCATGTCTCCCCTTCCCAG i pteVam1.scaffold_74370 I 2 C 0 s bosTau4.chr29 48985278 17 + 51998940 --------------------------CTGTCTTACCTTCCTTG i bosTau4.chr29 I 1082 C 0 s oryCun2.chrUn0985 33944 32 + 42081 -----TTC------TGATCTGGGTCCATGTTCCACGCTTCCTG i oryCun2.chrUn0985 I 1017 C 0 s micMur1.scaffold_46107 880 24 + 5307 ------------------CTGGGTCCGTGTCTCTCCC-TCCTG i micMur1.scaffold_46107 C 0 C 0 s proCap1.scaffold_13667 31038 26 - 46842 ------AG------TGATTTCTGATTTG-----TGCCCACATG i proCap1.scaffold_13667 C 0 C 0 s loxAfr3.scaffold_159 104160 31 + 1045236 ------ag------tgggtttcgttttggttcttACCCTCCTG i loxAfr3.scaffold_159 I 2171 C 0 s choHof1.scaffold_165855 68 35 + 4825 --------TGGTGGTGATTTGTGTCCCTGTCTCATCTTCCCTG i choHof1.scaffold_165855 N 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e calJac1.Contig6069 88644 270 + 235769 I e myoLuc1.scaffold_155660 41425 865 - 124081 M e cavPor3.scaffold_42 9674812 740 + 15951348 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=93403.000000 s hg19.chr11_gl000202_random 25608 36 + 40103 TC-ACACTGCCAGTTTCTCAGAGACAGAGATGTGCCT s gorGor1.Supercontig_0015245 55831 36 + 115376 TC-ACACTGCCAGTTTCTCAGGGACAGAGATGTGCCT i gorGor1.Supercontig_0015245 C 0 C 0 s rheMac2.chr14 128171365 36 - 133002572 TC-ACACTGCCAGCTTCCCAGAGACAGAGGTGTGCCT i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 88741 36 + 109049 TC-ACACTGCCAGCTTCCCAGAGACAGAGGTGTGCCT i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 88914 36 + 235769 TC-ACACTGCCAGCTTCCCAGAGACAGAGGAGTGCCT i calJac1.Contig6069 I 270 C 0 s micMur1.scaffold_46107 904 24 + 5307 CC-GCACTGCCAGCTTCCCAGAGAC------------ i micMur1.scaffold_46107 C 0 C 0 s oryCun2.chrUn0985 33976 31 + 42081 ------CCACCGGCCTCCCAAGGACAGGGCCCAGTCT i oryCun2.chrUn0985 C 0 C 0 s equCab2.chr12 28949526 36 + 33091231 CT-AGACAGCCAGCTTCCCGGAGACAGGGGTGCATCT i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 66261 36 + 302526 CC-AGGTGGCCAGCTTCCCAGAGACGGGGGTGTGTCT i felCat3.scaffold_135390 C 0 I 7 s canFam2.chr18 7545997 36 - 58872314 CCAAAATGGCCAGTGTCCTAGAGCC-AGGGTGTGTCT i canFam2.chr18 C 0 C 0 s pteVam1.scaffold_74370 854 28 - 1134 CC---------ACCTTCCCAGAGACAGGGGCCTGTCT i pteVam1.scaffold_74370 C 0 C 0 s bosTau4.chr29 48985295 32 + 51998940 CC-AGACAGCCAGTCCC----AGACGGGGCAGTGTCT i bosTau4.chr29 C 0 C 0 s proCap1.scaffold_13667 31064 36 - 46842 TT-GCCCTCCTACGTCCCTGGGTGGCACGAGCAGTTT i proCap1.scaffold_13667 C 0 I 1105 s loxAfr3.scaffold_159 104191 35 + 1045236 CC-AGACTGCCAGCTTCCCAAG-GACAGGACACGTCT i loxAfr3.scaffold_159 C 0 C 0 s choHof1.scaffold_165855 103 36 + 4825 CC-CGACTGCCAGCTTCCCAGCAACCAGGGTGACTCT i choHof1.scaffold_165855 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e myoLuc1.scaffold_155660 41425 865 - 124081 M e cavPor3.scaffold_42 9674812 740 + 15951348 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=164018.000000 s hg19.chr11_gl000202_random 25644 63 + 40103 GTCCTGCTTTGCTGACCCCTGCAGCCAGGATTCCCAAAT-GCCAGGCA--GGAC----AGGCTGt-----cagc----------a s gorGor1.Supercontig_0015245 55867 78 + 115376 GTCCTGCTTTGCTGACCCCTGCAGCCAGGATTCCCAAAT-GCCAGGCA--GGAC----AGGCTGTGCTGATagcctgtgctgaca i gorGor1.Supercontig_0015245 C 0 C 0 s rheMac2.chr14 128171401 63 - 133002572 GTCCTGCTTTGCTGACCCCTGCAGCCAGGCTTCCCAGAT-GCCAGGCA--GGAC----AGGTTGt-----cagc----------g i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 88777 63 + 109049 GTCCTGTTTTGCTGACCCCTGCAGCCAGGCTTCCCAGAT-GCCAGGCA--GGAC----AGGTTGt-----cagc----------a i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 88950 65 + 235769 GTCTCGCTTTGCCGAGCCCTGCAGCCGGGCTTTCCCCAT-GCCAGGCA--ggac----aggctgtgc---caac----------a i calJac1.Contig6069 C 0 C 0 s oryCun2.chrUn0985 34007 67 + 42081 GCCTCTCCTCACTGACCCTCGCACCCGCGCTGCCCCAGG-GCCGGGCCACGGCC----GCATCGTGT---CAGC----------A i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48985327 70 + 51998940 GTTTCATCTCACTGTCCCC-ACAGCCTGGCTTCCCAAAT-TCCAGGCTATGGGCAAGCAGACTATGT---CAGC----------G i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28949562 64 + 33091231 GTCTCAACTCATTGTCCTCTGCAGCCGGG---GACAGAT-CCCAGGccccagac----ggaccacgt---cagc----------c i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 66304 64 + 302526 GGCTCATTCCACTGTCCCCTGCAGCCAGGCTCCCCAAAC-TCCAGGCCGAGGAC-------AGATGG---CAGG----------G i felCat3.scaffold_135390 I 7 C 0 s canFam2.chr18 7546033 64 - 58872314 GGCTCACCCGACTGTCCCCTGCAGCCAGGCTAcccaaat-tctaggccgtgcac-------ctgtgc---cagc----------c i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 42290 67 - 124081 GTCAGGCCTCACTGTCCCCTGCAGCCTGGCTTCCCCAAC-GCCAGGCCGCGGAC----AGACTGCGC---CAGC----------A i myoLuc1.scaffold_155660 M 865 C 0 s pteVam1.scaffold_74370 882 67 - 1134 GTCTCGCCTCACTGTCCCCTGCGCCCAGGCTTCCCAAAT-GCCAGGCCATGGAC----GGAGAGCGT---CAGC----------A i pteVam1.scaffold_74370 C 0 C 0 s loxAfr3.scaffold_159 104226 56 + 1045236 GCCTCAC-----TGCCCCCTGCAGCCAGGCTCCCCCAAATGCCAGGCCATGGAC----AGCCTGT-------------------- i loxAfr3.scaffold_159 C 0 I 1960 s choHof1.scaffold_165855 139 51 + 4825 GCCCTGCCTCGCCGTCCCCTGCA-----------------GCCAGGcctcaggc----aagctgtgc---cagc----------a i choHof1.scaffold_165855 C 0 C 0 s proCap1.scaffold_13667 32205 39 - 46842 ------------TGTTCCTTGCA-----------------GCCAGGTCACAGAC----ATCCTGTGT---CACT----------G i proCap1.scaffold_13667 I 1105 C 0 s micMur1.scaffold_46107 928 50 + 5307 ---------------CCCAGGCAGCCAGGCTTCCCAAAC-CTGGGCCA-CAGAT----AGG-TGTGC---CAGC----------A i micMur1.scaffold_46107 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=190707.000000 s hg19.chr11_gl000202_random 25707 72 + 40103 tctcctgggagccccttctgcaaagtcagatccctcggctctcccgccagacattcagcctcagtgcacctg s gorGor1.Supercontig_0015245 55945 72 + 115376 tctcctgggagccccttctgcaaagtcagattcctcggctctcccgccagacattcagcctcagtgcacctg i gorGor1.Supercontig_0015245 C 0 C 0 s rheMac2.chr14 128171464 72 - 133002572 tctcctgggagccccttctgcaaagtcggattcctcggctctccggccagacattcagcatcagtgcacctg i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 88840 72 + 109049 tctcctgggagccccttctgcagagtcagattcctcggctgtcctgccagacattcagcatcagcgcacctg i papHam1.scaffold6638 C 0 C 0 s calJac1.Contig6069 89015 71 + 235769 tctcctgcg-gcccctgctgcaaaattccattccttggctctcccgccagacattcagcatcgatgcacctg i calJac1.Contig6069 C 0 N 0 s micMur1.scaffold_46107 978 70 + 5307 TCTCCTGGG-CCCCTGGCTACAGATTCTG-TTCCTTGGCTCTCCTGCCAGACACTCAGCAGCGGTGCAACCA i micMur1.scaffold_46107 C 0 I 1 s oryCun2.chrUn0985 34074 61 + 42081 CCTCCCGGG-GCACCTGCTGACCCGCAGG--CTCTCAGCCCTTCTGCTGAACATTCGGCACCTG-------- i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48985397 42 + 51998940 TTTCCC--GGACTCCTGCTGAAAGTTCAGATTCCAC----------------------------CCCCACTG i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28949626 72 + 33091231 tctcccggggacgcctgctgaaaatacagattcctcagctctcttgcctgagattcagcatcggtgccactg i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 66368 43 + 302526 CCCCCTGAGGGCACATGCTAAGatttca---------------------gaccttcagca--------acta i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7546097 72 - 58872314 cctcctcagagcctttgctaaaaattcagattcctcagcgctcctgcctgacattcagcatcggggcgacta i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 42357 70 - 124081 GCCCCAG-GGGCACCTGCT-GGGCCTCAGGTGTCTCGGCTCCCCCGCCTGACCTTCCCCATCAGTGCAGCTA i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_74370 949 71 - 1134 TCCCCCC-GGGCACCTGCTAAAAATTCCGGCTCCTCAGCGGCCCTGCCTGACTGTAAGCATCAGTGCCACTG i pteVam1.scaffold_74370 C 0 C 0 s loxAfr3.scaffold_159 106242 70 + 1045236 tctcctggg-gcacctggtaaaaattcagatttcttggctctcctgccagagattcagagtcagaacaacc- i loxAfr3.scaffold_159 I 1960 C 0 s proCap1.scaffold_13667 32244 70 - 46842 TTTCccagg-gcacctgttaagcgttcagattgctcggctttcctgccagagatccagagtcagagcaccc- i proCap1.scaffold_13667 C 0 C 0 s choHof1.scaffold_165855 190 68 + 4825 tctcccatg-gcatccgccaaaaacctcgattcctgggctctcctggccaag--tcagagtcgggggacca- i choHof1.scaffold_165855 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e ponAbe2.chr11 126007676 1116 - 132107971 M e panTro2.chr11 68210960 1208 + 134204764 M a score=59947.000000 s hg19.chr11_gl000202_random 25779 26 + 40103 tgcgtgggtgtg--ggggctggagatcg s gorGor1.Supercontig_0015245 56017 26 + 115376 tgcgtgggtgtg--ggggctggagatcg i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126008811 28 - 132107971 TGCGTGGGtgtggcggtgctggagatca i ponAbe2.chr11 M 1116 C 0 s rheMac2.chr14 128171536 26 - 133002572 ggtgcaggtgtg--ggggctggagatct i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 88912 26 + 109049 ggtgcgggtgtt--gggggtggagatct i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_46107 1049 15 + 5307 -------------TGGGGCCGGAGGTGT i micMur1.scaffold_46107 I 1 C 0 s oryCun2.chrUn0985 34135 21 + 42081 -----CGCAGTG--GGGGCTGAAGACCA i oryCun2.chrUn0985 C 0 I 224 s bosTau4.chr29 48985439 18 + 51998940 -------GGGTG--GGGCCT-GCGATCT i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28949698 19 + 33091231 -------agagg--gggcctggagctct i equCab2.chr12 C 0 C 0 s felCat3.scaffold_135390 66411 19 + 302526 -------agaag--gggcctggagacct i felCat3.scaffold_135390 C 0 C 0 s canFam2.chr18 7546169 19 - 58872314 -------agatg--gggcctggagatct i canFam2.chr18 C 0 C 0 s myoLuc1.scaffold_155660 42427 19 - 124081 -------AGGGG--GGGCCTGGAGAGGT i myoLuc1.scaffold_155660 C 0 C 0 s pteVam1.scaffold_74370 1020 19 - 1134 -------AGGTG--GGGCCTGGGGACGT i pteVam1.scaffold_74370 C 0 C 0 s loxAfr3.scaffold_159 106312 19 + 1045236 -------aggtg--aggcctggaggttg i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 32314 18 - 46842 -------agatg---ggcctggagatct i proCap1.scaffold_13667 C 0 C 0 s choHof1.scaffold_165855 258 20 + 4825 ------ggggtg--gggcctggagatct i choHof1.scaffold_165855 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e panTro2.chr11 68210960 1208 + 134204764 M a score=85527.000000 s hg19.chr11_gl000202_random 25805 96 + 40103 gcattttaacaagtgcctctagtgacgtgaatgcagagcccggttcaggaaccTGCTCCCCTCCC-TCCTGTAGTG------AGGTGGG----AAGGAGGGGGAA-----GG--------- s gorGor1.Supercontig_0015245 56043 96 + 115376 gcattttaacaagtgcctctagtgacgtgaatgcagagcccggttcaggaaccTGCTCCCCTCCC-TCCTGTAGTG------AGGTGGG----AAGGAGGGGGAA-----GG--------- i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126008839 96 - 132107971 gcattttaacaagtgcctctagtgacgtgaatgcagagcctggttcaggaaccTGCTCCCCTCCC-TCCTGTAGTG------AGGTGGG----AAGGAGGGGGAA-----GG--------- i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128171562 86 - 133002572 gcattttaacaagtgcctctagtgacgtgaatgcagagcccggttcaggaaccTTCTCCCTTCCC-TCCTGTAGTG------ATGT--------------GGGAA-----GG--------- i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 88938 86 + 109049 gcattttaacaagtgcctctagtgacatgaatgcagagcccggttcaggagccTTCTCCCTTCCC-TCCTGTAGTG------ATGT--------------GGGAA-----GG--------- i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_46107 1064 101 + 5307 GCATTTCAAC-AGTTCCTCTAGTGGCCTGAATGCACAGCCAGGCTCAGGAACCTTCCTCCCTCCAGCCCTGCAGTG------GGGCGAG----CGGGAGGGCGAGCTGGCGG--------- i micMur1.scaffold_46107 C 0 C 0 s oryCun2.chrUn0985 34380 78 + 42081 GCGTGGTAAC-AGCGCCTCCAGGGCTGTGGATGCAC--CCGGGTCCCAGAACCTCCCCCCCGCGC-CCCCCCGGAG------GAGT------------------------GG--------- i oryCun2.chrUn0985 I 224 C 0 s bosTau4.chr29 48985457 70 + 51998940 ACAGGTGAGCGAGTGTCTC------------TGCACAACCAGGTTCAGGAAGCTTCTGC---------------GA------TTGGGTG----GGAAGGGGGACT-----AG--------- i bosTau4.chr29 C 0 I 2 s equCab2.chr12 28949717 96 + 33091231 gcattttagcaagtgcctctagtgactgggatccagggccctgttcggggacct-ctgCCCTCCACCCCTGCAGTG------GGCGTTG----GGAAAGGGGTCT-----GG--------- i equCab2.chr12 C 0 I 2 s felCat3.scaffold_135390 66430 97 + 302526 gcattttcgcaagtgcgtccagtgagttggatacacagccaggttcaagaacTTTCTGCCGTCTGACCTTGCAGCA------GAGGGTT----GGCAAGGCCACT-----GG--------- i felCat3.scaffold_135390 C 0 I 2 s canFam2.chr18 7546188 84 - 58872314 gcatttttgcaagtacctctcttgagttgcctgcacagccagatgcaagaacGTCCTGCCTTCTGACCCTGCAGTA------GGAG-----------------CT-----GG--------- i canFam2.chr18 C 0 I 2 s myoLuc1.scaffold_155660 42446 55 - 124081 ---------------CCCC-------------------------------ACCTTCTGCCCCGT--CCCCACACCAGCGGCCGGGCGTC----GGGGAAGGCATC-----AG--------- i myoLuc1.scaffold_155660 C 0 I 2 s pteVam1.scaffold_74370 1039 88 - 1134 GCATTCTGG------CCTCTAAGGATGTGAATGCACAGCCCGTTTCGGGAATCTTCTGCCCTCTG-CCCCACATTG------GGGCGCA----GGAAGGGGCA-------AG--------- i pteVam1.scaffold_74370 C 0 N 0 s loxAfr3.scaffold_159 106331 99 + 1045236 gtattttcacaagGGCC---------AGAGGTGCTCAGCCAGATTCCAGAACCTTCCACCCTGAACTCCTGAAGTA------AGCCTGGCCTACGGTGGGGACCT-----GGG--GGGCAC i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 32332 99 - 46842 gcaccttaacaagcact---------cca-gCGCTCCCTTGGCATCCAGAAACTTCTGCCCTGAACTCCCCAAGTA------GGCCCCATCCAGGGTGGGGATCC-----AGG-TGGGTGC i proCap1.scaffold_13667 C 0 C 0 s choHof1.scaffold_165855 278 108 + 4825 gtattttaacaagtgcctgt--caatccaggtgcacaaccaggttctggaaAGTTCCGTCCTGCCCTCCCTCAGCA------GGCCCAGCCCTTGGGAGGGGGCT-----GAGGGGGGCGC i choHof1.scaffold_165855 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e panTro2.chr11 68210960 1208 + 134204764 M a score=529.000000 s hg19.chr11_gl000202_random 25901 52 + 40103 AGGGCAAGACCGTTGGCTTGGTTGGGTTTTGGTCATG----------CAGAGAGCT-CACACC- s gorGor1.Supercontig_0015245 56139 52 + 115376 AGGGCAAGACCGTTGGCTTGGTTGCGTTTTGGTCATG----------CAGAGAGCT-CACACC- i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126008935 52 - 132107971 AGGGCAAGACCGTCGGCTTGGTTGGATTTTGGTCATG----------CAGAGAGCT-CACACC- i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128171648 51 - 133002572 AGGGCAAGA-CGTTGGCTTGGTTGGGCTTTGGGCATG----------CAGAGAGCT-CACACC- i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 89024 51 + 109049 AAGGCAAGA-TGTTGGCTTGGTTGGGCTTTGGGCATG----------CAGAGAGCT-CACACC- i papHam1.scaffold6638 C 0 C 0 s micMur1.scaffold_46107 1165 23 + 5307 GGGGCACAC-CGT-GCCTGGGCTGG--------------------------------------- i micMur1.scaffold_46107 C 0 M 1162 s oryCun2.chrUn0985 34458 35 + 42081 ----------CGCCGACTCGCCCGGGCTCTGGTCGTG----------TGGGCAGC--------- i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48985529 41 + 51998940 GGTGCACGG-CGTCCCCG----AGGACTTCAGCTCTG----------CGGACAG-------CT- i bosTau4.chr29 I 2 I 1 s equCab2.chr12 28949815 47 + 33091231 GGGGCGAGG-CGTCTGCT----TGGACTTTGGTTGAG----------CAGACGGGC-TGTGCC- i equCab2.chr12 I 2 I 1 s felCat3.scaffold_135390 66529 47 + 302526 AGGACAGAG-CGTTTGCT----TGGGCCCTGGTGGTG----------CAAACAGCC-TGTCCT- i felCat3.scaffold_135390 I 2 I 1 s canFam2.chr18 7546274 47 - 58872314 GGGAAGAGG-CATTGGCT----TGGGCTTTGGTTGAG----------CCAACAGCC-CACCCT- i canFam2.chr18 I 2 I 1 s myoLuc1.scaffold_155660 42503 37 - 124081 -----AAGG-CGT---CT----TGGGCTTTAGTC--A----------CAGGCGGTC-TGCGCG- i myoLuc1.scaffold_155660 I 2 I 1 s loxAfr3.scaffold_159 106430 44 + 1045236 -----AGGG-CATGGTCA----TGGGCTGTTGTTGTG----------CAGACAGCTATGCTATC i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 32431 43 - 46842 -----AGGG-CTTCACCA----T-GACTTCGGTTGTG----------CAGACAGCTATGCGCTC i proCap1.scaffold_13667 C 0 C 0 s choHof1.scaffold_165855 386 53 + 4825 -----AGGG-AAGCTTCT----CGGGCTGCGGATGTGGGCTGTGAATCAGGCCACT-TGTGCTC i choHof1.scaffold_165855 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e tupBel1.scaffold_125018.1-1020051 193689 2448 - 1020051 I e panTro2.chr11 68210960 1208 + 134204764 M a score=45506.000000 s hg19.chr11_gl000202_random 25953 51 + 40103 TGTCATCA----GGGGTGGCTGCAA------CAGGC----------------------ACCAGGCCCC-AGGAGACA-TTGTTTG------- s gorGor1.Supercontig_0015245 56191 51 + 115376 TGTCACCA----GGGGTGGCTGCAA------CAGGC----------------------ACCAGGCCCC-AGGAGACA-TTGTTTG------- i gorGor1.Supercontig_0015245 C 0 C 0 s ponAbe2.chr11 126008987 51 - 132107971 TGTCACCA----GGGGTGGCTGCAG------CAGGC----------------------ACCAGGCCCC-AGGAGACA-TTGTTTG------- i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128171699 52 - 133002572 TGTCACCA----GGGGTGGCTGCAG------CAGGC----------------------ACCAGGCCCC-AGGAGACATTTTTTTG------- i rheMac2.chr14 C 0 C 0 s papHam1.scaffold6638 89075 52 + 109049 TGTCACCA----GGGGTGGCTGCAG------CAGGC----------------------ACCAGGCCCC-AGGAGACATTTTTTTG------- i papHam1.scaffold6638 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 196137 51 - 1020051 TGTCAGCC----AGGTTGTCTGCAG------CACAT----------------------GCCAGGCCTCGAGCAGAC--CCGTTTC------- i tupBel1.scaffold_125018.1-1020051 I 2448 C 0 s oryCun2.chrUn0985 34493 34 + 42081 ---------------GTGA-------------GGAC----------------------ACCAGGCCCCGAGGAGCCC-CCGGCCG------- i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48985571 59 + 51998940 TGTCCCCCGCGGGGGCCGGCGGCAAGTGGGCCGGAA------------------------GAGGCCTCCACGA-ACC-CTGTTTG------- i bosTau4.chr29 I 1 I 7 s equCab2.chr12 28949863 45 + 33091231 TGTCACCT----GGGCTGGCTGCATGGGGGACG-----------------------------------AAGGAGACT-TCGTTTC------- i equCab2.chr12 I 1 I 7 s felCat3.scaffold_135390 66577 80 + 302526 TGCCGCCT----GGGGTGGTGACAGGGGGACCAGACCCTGTGCAGGCAGGGTGCAGGGTCCAGGCCTCAAGGAGACG-CTATTTG------- i felCat3.scaffold_135390 I 1 I 158 s canFam2.chr18 7546322 58 - 58872314 TGCCACCT----GGGCTGGCTGCAGGTGGACCAGAT----------------------GCCAGGCCTCAGGGAGACC-TTGTCTG------- i canFam2.chr18 I 1 I 7 s myoLuc1.scaffold_155660 42541 31 - 124081 TGTCACC-----------------------CCA------------------------------GCCTCGGGGAGACC-CCGTTGG------- i myoLuc1.scaffold_155660 I 1 I 6 s loxAfr3.scaffold_159 106474 64 + 1045236 TGTCTTCT----GGGCTGGCTGCAAGTCGACCAGAT----------------------GCCAGGACTC-AGGGGACC-CTGTCTAAGGATTG i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 32474 63 - 46842 CATCTCCC----AGGCTGGCTGCAGGTCCACAGGAT-----------------------CCAGGGCTC-AGGGCACC-CTGTGTGGGCATTG i proCap1.scaffold_13667 C 0 C 0 s choHof1.scaffold_165855 439 61 + 4825 TGCCAGCC----GGGCCGGCTGCGGCTCAGCCAGAA----------------------GCCAGAACTC-AGGGA----TGATCTGAGGGTTG i choHof1.scaffold_165855 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e cavPor3.scaffold_42 9674812 740 + 15951348 I e panTro2.chr11 68210960 1208 + 134204764 M a score=-62272.000000 s hg19.chr11_gl000202_random 26004 117 + 40103 C-------CTTCACTTCC--TCAACACGCAGCAGGATCCTGCCCTTCGTCCCAACAGGGAATGAT-C-TGTTGGAAACTCAGAGGTAT-------AAAAAGAAGCCTGTTAGGCTACTGAAGAAACTTGTCAGCC s gorGor1.Supercontig_0015245 56242 25 + 115376 C-------CTTCACTTCC--TCAACACGCAGCAG----------------------------------------------------------------------------------------------------- i gorGor1.Supercontig_0015245 C 0 N 0 s ponAbe2.chr11 126009038 109 - 132107971 C-------TTTCACTTCC--TCAACACCCGGCAGGATCCTGCCCTTCGTCCCAACAGGGAATGAT-C-TGTTGGAAATTCAGAGGTAT-------AAAAAGAAG--------GCTATTGAAGAAACTTGTCAGCC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128171751 117 - 133002572 C-------CTTCACTTCC--TCAACACCCAGCAGGATCCTGCCCTTCGTTCCAACAGGGAATGAT-C-TGTAGGAAATTCAGAGGTAT-------AAAAAGAAGGCTGTTAGGCTATTAAAGAAACTTGTCAGtc i rheMac2.chr14 C 0 I 300 s papHam1.scaffold6638 89127 25 + 109049 C-------CTTCACTTCC--TTGACACCCAGCAG----------------------------------------------------------------------------------------------------- i papHam1.scaffold6638 C 0 N 0 s tupBel1.scaffold_125018.1-1020051 196188 26 - 1020051 CAACTG--CTTCTCTTCC--CTGACAGCTG--------------------------------------------------------------------------------------------------------- i tupBel1.scaffold_125018.1-1020051 C 0 I 6007 s oryCun2.chrUn0985 34527 52 + 42081 CCAGCGGCCTCCACTGCC--TT--CGCTCAGCGAGAGCCTGCCCTTCGTCCCAACA------------------------------------------------------------------------------- i oryCun2.chrUn0985 C 0 I 424 s bosTau4.chr29 48985637 118 + 51998940 -------CAGTCACTCGC--TTGACCCTCAGCAGGACCCCATCCTTGGCCCCAACAGGAAACGATCC-TCCCGGAGACTGAGGGTTAAAAAAAAGAAGAAGAAGAAT-----TCTGTTTAAGAAACCTGTCAG-- i bosTau4.chr29 I 7 I 4 s equCab2.chr12 28949915 101 + 33091231 -------GCTTCGCTTCC--TTGACACCCAGCGGGA-CCCATCCTT--CCCCAACAGGAAATGATCC-CAGTGGGAACCCAAGG-----------GCAAAAATGAGC-----GCTGTTTAAGAAACTTGT----- i equCab2.chr12 I 7 I 5 s canFam2.chr18 7546387 72 - 58872314 -------CTTTCACTTTT--TCAGCACCCAGCAGGACCCCATCCTT--CTCCAGCAGGGAATGACCC-TCCCGGAGATCCAGGG--------------------------------------------------- i canFam2.chr18 I 7 I 51 s myoLuc1.scaffold_155660 42578 25 - 124081 -------GTTTCACGTCC--TCGACACCTAGAAG----------------------------------------------------------------------------------------------------- i myoLuc1.scaffold_155660 I 6 N 0 s loxAfr3.scaffold_159 106538 88 + 1045236 -------CTCCAAGTTCC--TTAACACTCAGCTGAATCCTGTTCTTTGTCCCACCAGGGAACAATCC-CCCTGGACATTCAGAAGTA------------------------------------AACGTGTCAGT- i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 32537 93 - 46842 -------TGCCTGCCTCC--TTAACCCTCGGCTGAATCCTGTCCTCCGTGCCAACAGGGAGCAATCC-TGCTGGACATTCAGGAGTGG-------GAGAAGAATGCTGTT------------------------- i proCap1.scaffold_13667 C 0 I 95 s choHof1.scaffold_165855 500 109 + 4825 -------CTTTAACTGCCCGTCCACGCAGGGCAGCATCTTGTTCTCCCCCCCGACAGGGAATAAACCAAACGGGAAATTCAAGGGTGA-------AAAAAGAAAGCTGTT--------GAGGAAACGGGTC---- i choHof1.scaffold_165855 C 0 I 9 e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 66657 158 + 302526 I e micMur1.scaffold_46107 1188 1162 + 5307 M e cavPor3.scaffold_42 9674812 740 + 15951348 I e panTro2.chr11 68210960 1208 + 134204764 M a score=18531.000000 s hg19.chr11_gl000202_random 26121 55 + 40103 tttttttttt-----aaatgagactgggtctcattctgtcacctgagctggagtgcagta s panTro2.chr11 68212178 57 + 134204764 tttttttttttt---aaatgagactgggtctcattctgtcacctgagctggagtgcagta i panTro2.chr11 M 1208 C 0 s ponAbe2.chr11 126009147 60 - 132107971 tttttttttttttaaaattgagactgggtctcattctgtcccccaggctggagtgcagta i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128172168 55 - 133002572 tttttttttt-----aattgagactgggtctcactctgtcacccaggctggagtgcaatg i rheMac2.chr14 I 300 C 0 s loxAfr3.scaffold_159 106626 7 + 1045236 ------------------------------TCATTCT----------------------- i loxAfr3.scaffold_159 C 0 C 0 e choHof1.scaffold_165855 609 9 + 4825 I e ochPri2.scaffold_12461 32194 2417 - 40248 I e felCat3.scaffold_135390 66657 158 + 302526 I e micMur1.scaffold_46107 1188 1162 + 5307 M e oryCun2.chrUn0985 34579 424 + 42081 I e proCap1.scaffold_13667 32630 95 - 46842 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28950016 5 + 33091231 I e canFam2.chr18 7546459 51 - 58872314 I e bosTau4.chr29 48985755 4 + 51998940 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=62713.000000 s hg19.chr11_gl000202_random 26176 124 + 40103 gtgacatcatggctcactgcagcctcaacctcctgggctcaggtgatcttcctgcctcagcctcccaagtagctgggac-cacagg-cgcatgccactacatccagctaatttttgtagtttttgt s rheMac2.chr14 128172223 124 - 133002572 gtgacatcatggctcactgtagcctcaacctcctgggctcaggtgagcttcctgcctcagcctcccaagtagctgggac-cacagg-cacatgccactacacccagctaatttttgtagtttttgt i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126009207 125 - 132107971 gtgacatcacgactcactgcagcctcaacctcctgggctcaggtgatcttcctgcctcagcctcccaagtagctgggac-cacaggccgcatgccactacatccagctaacttttgtagtttttgt i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68212235 124 + 134204764 gtgacatcatggctcactgcagcctcaacctcctgggctcaggtgatcttcctgcctcagcctcccaagtagctgggac-cacaga-cgcatgccactacatccagctaatttttgtagtttttgt i panTro2.chr11 C 0 C 0 s felCat3.scaffold_135390 66815 74 + 302526 ttgaactcatgg---accgcgagatcaaagacctgagccgaag-------------tcagccacttaacccactgagccacccagg-cgcc----------------------------------- i felCat3.scaffold_135390 I 158 N 0 e choHof1.scaffold_165855 609 9 + 4825 I e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e oryCun2.chrUn0985 34579 424 + 42081 I e proCap1.scaffold_13667 32630 95 - 46842 I e loxAfr3.scaffold_159 106633 0 + 1045236 C e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28950016 5 + 33091231 I e canFam2.chr18 7546459 51 - 58872314 I e bosTau4.chr29 48985755 4 + 51998940 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=27326.000000 s hg19.chr11_gl000202_random 26300 57 + 40103 agagatgggctttcgccatgctggccaggctgatcttgaactcctggactcaagcaa s panTro2.chr11 68212359 57 + 134204764 agagatgggctttcgccatgctggccaggctgatcttgaactcctggactcaagcaa i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126009332 57 - 132107971 agagatgggctttcgccatgttggccaggctggtcttgaactcctggactcaagcga i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128172347 57 - 133002572 agagactgggtttcgccatgttggccagactggtctttaacttctgggctccagcaa i rheMac2.chr14 C 0 C 0 e choHof1.scaffold_165855 609 9 + 4825 I e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e oryCun2.chrUn0985 34579 424 + 42081 I e proCap1.scaffold_13667 32630 95 - 46842 I e loxAfr3.scaffold_159 106633 0 + 1045236 C e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28950016 5 + 33091231 I e canFam2.chr18 7546459 51 - 58872314 I e bosTau4.chr29 48985755 4 + 51998940 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=23977.000000 s hg19.chr11_gl000202_random 26357 56 + 40103 tcctcccgccttagcctgccaaagtgctgggtttacaggcatgagctaccataccc s rheMac2.chr14 128172404 56 - 133002572 tcctcccgccttagcctgcaaaagtgctgggtttacaggcgtgagtcacaataccc i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126009389 56 - 132107971 tcctccctccttagcctgccaaagtgctgggtttacaggcatgagctaccataccc i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68212416 56 + 134204764 tcctcccgccttagcctgccaaagtgctgggtttacaggcatgagctaccataccc i panTro2.chr11 C 0 C 0 s loxAfr3.scaffold_159 106633 7 + 1045236 TCTTCCC------------------------------------------------- i loxAfr3.scaffold_159 C 0 C 0 e choHof1.scaffold_165855 609 9 + 4825 I e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e oryCun2.chrUn0985 34579 424 + 42081 I e proCap1.scaffold_13667 32630 95 - 46842 I e cavPor3.scaffold_42 9674812 740 + 15951348 I e equCab2.chr12 28950016 5 + 33091231 I e canFam2.chr18 7546459 51 - 58872314 I e bosTau4.chr29 48985755 4 + 51998940 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=704936.000000 s hg19.chr11_gl000202_random 26413 720 + 40103 agccTAGCtttttttt--ttttt----taatatgaaaa-aaaaatGTTTGGAGCCTTCCCACTAAGGAACA-ATAAGATTAAGGGATTTAAAAGAATTGATTAGTGACATGCACATTGCTGCCCCAGGAGAAAATTCTGCTATTACTC-------ATGAGAAGAGCCAGCATGAAGAG-CTCTGTGAGGTCTGAGGTCACCCTTGTAACTGCGCTCGGGGATGTCAAAGTCAGCATTGACACAACTGTGACCATAAC---------TCA-CCTGTTCCAG-----G--------------------------------------CTCTCCTGTGTACTGCACACCCATCCTCCTTCTCAGTGTTCCCAGCAGCTGTA--GGAGCTAAGAAGAGTGAAAGTAGCTATGAA-------AGACACCATCTG-TAGTTTGTTtgttccacaaactccggcctctttc--ctcttgggcacac-actaacctgcgtgtcccag--cccctggcagttagtgtggctgtagcatgtggg-tggaaatga-----------ttcag---gtatggcccacaggaagc-cccctgtcattct-ccacgtctgcctcttccctcatctacaga----------------ggactc--agggaggactcagcc-acctaagagagccagaagctggaagggagctggatccctgaatgactgtgtggagcagagtc----ccctccttaccacct--------gcctccattggattgtgacatgagagacaaagaatcttt------------ctgtgtgaaagccattgccattttagagttattgatcacagt------aggcatctcac-tccatga s canFam2.chr18 7546510 677 - 58872314 ---------TTTTTTT--TTTTT----AAATATGAAAA---GAATGTTTGGAGCTTCCCCACAAAGGAATA-ATAAGATTAAGGGATTTAGAAGAGGCGGCTGGTGACATACACAT-ACTGCCCGGAAAGAAAAATCTCTTAAT--CT-------GGGAGAGCCAAAAACGTGGGGAG-CCCTGTGAGGCCTGAGCTTACCCTGGCAGCTTCATTTGGGGATTTCAAAGTCGGCTCTGATGTGACGGTGATGACAGCTACCACGGCTCA-CCCAGGCCAG-----G--------------------------------------CCATCCCAGGCCTTCCACACCC-----CTTCCTCAGTGTCCCTAGCAGCGGCA--AGATA----TAGACCAGTGACAGGTAAGACT-----gagt----------ctggatggttgtccaaccagctctggcctctgtctcctcctgga--cacagtcggtctgcacatctcagcctcccttgcacttagtgtgaccaGGGCAGGTGGG-AGGAAATGG-----------CCCAA---GCCTGGCCCATTGGCATC------------------------------------TCtgcagg----------------ggattccggaggaagactctgaagccccaagaggaccacaagctgggaggagcctggatctccttatgaccgggtggcacaca--c----tctaccctccggccccatggccaacctgcgttgaattgcaacataagtgagaaataaaccttta----------ctgtatgaag-ccacagacgttt--gggTTATGAATGGCAGT------GGTCATCTCCCTGCTGTGA i canFam2.chr18 I 51 C 0 s equCab2.chr12 28950021 682 + 33091231 --------TTTTTTTT--TTTTT----TAATATGAAAA---GAATGATGGCAGCCTTTCCACGAAGGAGTA-ATAAGATTAAGGGATTTACAAGGGACGGCTGGTGATGTGTACAC-ACTGCCCAAGAAGAGAAATCTCTCACC--CCTGAGAGGAGGAGAGGAGCCGACGTGGGGAG--CCTGCGAGGCC-AAGCTCGCCCTGG-AGCCTCGCTCGGGGATTTCGAAGTCGACTTTGGTGTGTCGGT-ACCATAACTACCAGGCCTCA-CCCACGCCAG-----G--------------------------------------CC-TCGCGGGCCCTTCGCACCCACCGTCCAGCTTGGTGCTCCT-GCAGCTCTG--GG--------GGACGAGAGG-AGCTAAGACC-----GAGG----------CTGGCTGGTTGG-GGATGAGCCCTGGCCT-------CTCCTGGACGCACAGCCAGTCTTCACATCCCAGCTCCCCTTGGGGTTAGTGGGGTTCGGGCATATGGG-TGGAAACGG-----------CCCAG---GCTTGGCCCATAGGAACctcctttgcca-------------------tcccctgtctgccga----------------ggatcctggaggaagactctgaagccctaagaggaccacaagctggaaggagcctggatccccgaatgactttgtggagcagc--a----tcctcctccccaccc--------acctgcactgga-tgcgatgtgcgtgagaaggcaaccttta----------ttgggccagg-ccgctggcattt-ggggtcattgatcacagc------ggttatctcacccCTGGGC i equCab2.chr12 I 5 C 0 s panTro2.chr11 68212472 719 + 134204764 agccTAGCtttttttt--ttttt----taatatgaaaa-aaaaatGTTTGGAGCCTTCCCACTAAGGAACA-ATAAGATTAAGGGATTTAAAAGAATTGGTTAGTGACATGCACAT-GCTGCCCAAGGAGAAAATTCTGCTATTACTC-------ATGAGAAGAGCCAGCATGAGGAG-CTCTGTGAGGTCTGAGGTCACCCTTGTAACTGCACTCGGGGACTTCAAAGTCAGCATTGACACAACTGTGACCATAAC---------TCA-CCTGTTCCAG-----G--------------------------------------CTCTCCTGTGTACTGCACACCCATCCTCCTTCTCAGTGTTCCCAGCAGCTGTA--GGAGCTAAGAAGAGTGAAAGTAGCTATGAA-------AGACACCATCTG-TAGTTTGTTtgttccacaaactccggcctctttt--ctcttgggcacac-actaacctgcgtgtcccag--cccctggcagttagtgtggcTGTAGCATGTGGG-TGGAAATGA-----------TTCAG---GTATGACCCACAGGAAGC-CCCCTGTCATTCT-CCACGTCTGCCTCTTCCCTCATCtacaga----------------ggactc--agggaggactcagcc-acctaagagagccagaagctggaagggagctggatccctgaatgactgtgtggagcagagtc----ccctccttaccacct--------gcctccattggattgtgacatgagagacaaagaatcttt------------ctgtgtgaaagccattgccattttagagttattgatcacagt------agGCATCTCAC-TCCATGA i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126009445 705 - 132107971 agccTAGC-TTTTTTT--TTTTT----AAATATGAAAAGAAAAATGTCTGGAGCCTTCCCACTAAGGAACA-ATAAGATTAAGGGATTTAAAAGAATTGGTTAGTGACATGCACAT-TCTGCCCGAGGAGAAAATTCTGCTACTGCTC-------ATGAGAAGAGCCAGCATGAGGAG-CTCTGTGAGGTCTGAGGTCACCCTTGTAACTGCACTCGGGGACTTCAAAGTCAGCACTGACACAACTGTGACCATAAC---------TCA-CCTGTTTCAG-----G--------------------------------------CCCTCCTGTGTACTGCACACCCATCCTCCTTCTCAGTGTTCCCAGCAGCTGTA--GGAGATAAGAAGAGTGAAAATAGCTATGAC-------AGAGACCATCTGTTTGTTTGTTtgttccacaaactccggcctctttc--ctcttgggcacac-actaacctgcgtgtcccag--cccctggcagttagtgtggcTGTAGCATGCAGG-TGGAAATGA-----------ttcag---gtatgacccacgggaagc-ccccagtcattct-ccatgtctgccttttccctcatctacaga----------------ggactc--agggaggactcagcc-ccctaagagagccagaagctggaagggagctggatccctgagtgactgtgtggagcagagtc----ccctccttaccacct--------gcctccattggattgtgacatgagagacaaagaatcttt------------ctgtgtgaaagccattgccattttagagttatcgatcaca-t------aggc--------------- i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128172460 728 - 133002572 agccTAGT-------T--TTTTT----TAATATGAAAAAAGAAATGTTTGGAGCCTTCCCACTAAAGAACA-ATAAGATTAAGGGGTTTAAAAGAAATGGTTAGTGACATCCACAT-ACTGCCCGAGGAGAAAATTCTGCTATTACTC-------ATGAGAAGAGCCAACATGAGGAG-CTCTGTGAGGTCTGAGGTCACCCTTGTAACTGCACTCGGGGACTTCAAAGTCAGCGTTGACACAACTGTGACCATAAA---------TCA-CCTGTTCCAG-----GTCCTTctgtgcactgcacaccctcctgtgcaccgcacaccctcctgtgtactgcacacccatcctCCTTCTCAACGTTCCTAGCAGCTGTA--GGAGAGAAGAAGAGTGAAAGTAGCTAAGAC-------AGA------------GTCTGTTtgttccacaaactctggcctctttc--ctcttggacacac-actaacctgcgtgtcccag--cccctggcagttagtgtggcTGTAGCATGTGGG-TGGAAATGG-----------TTCAG---GTATGACCCATGGGAAGC-CCCCTGTCATCCT-CCACGTCTGCCTCTTCCCTCGTCtacaga----------------ggactc--agggaggactcggcc-ctctaaaagagccagaagctggaagagatctggatccctgaatgactttgtggagcagagtc----ccctccttaccacct--------gcctccattggattgtgacatgagagacagagaatcttc------------ttgtgtgaaa-ccattgccattttcgagttattgatcacagt------agGCATC------------ i rheMac2.chr14 C 0 C 0 s cavPor3.scaffold_42 9675552 560 + 15951348 AACTTGTCTACTTTTT--AATTT----TATCATGAGAAGAG-------TGGAGTCTTTTCACTGTAGTACACAAAAGATTAAGGGGCTTAAGAGA--TGGTTAGTGAGCTACACAC-GCTGCCTGAGGA-AAAATCTTTTCCTTGGTC-------ACGAGGGAGACCAACATGAGGCA-TGCTCTGACCCCTGAGCCTACGC-TGTACCT-CCTTCGGGGATTTCCATGTTGGCGTGGACCGACCCGTGACCATGAC---------TC--CCTGCTCTCT-----G--------------------------------------CC----------------------CCACCCCCTCAGTGCCCC-----------------------AGGATG--AGCAGC------------------------------------------------CTGGCTTCTGTC--C-CTGGGATGCA--GCCAGCCTTTGTGTCGCTGTCTCCCTGACCATGCGTGTGACCCT-GCACAAGGGACAGAGACGG-----------TCCAA---CTCTGACCCCCAAG--------------TCCT-CCACGCTCGTCTCCTCTCCCCTCCGCAAA----------------GGA-----------GACT---------TGAGAGAGCCGGA-----------------ATCCTTGGGTGACTTCGTGGAGCAGA-TC----CACCCCATGCTGCCT--------GCCTGCTCTGGATGGGGAC----GGGATGGAGAAGCCA------------------------TCATTGACACTTTGGGGATATTGGTCACGGT------GCTGGCCTACCGTCTACAA i cavPor3.scaffold_42 I 740 C 0 s proCap1.scaffold_13667 32725 667 - 46842 ------------------tgtgt----gtgtgtgtAAA---GAATGTTTGGTGCCTTCT------GGAGTA-ATAAGATGAAG----------GAGTTGGTTGGTGACACAGGCCC-CCTGCCTGAGAAGAGATGCCTTCCCTTAGTT-------ACAAGAGCAGCCAACGTGTGGAGTTCCTGTGAGGGCGA-GGTCACCGGGG------TGACTGGGGACTC-----ACAGTCTGGATGTGACTGCAGTGACAGCTGGCTTGGCTCAGCCTGTGCCTGCCGAGG---------------------------------------CCACCTGGGCCCT-CAC-TCCGTGGTCTTCCTTGCTGTGCCCCACAACTGCA--GCAGA-----AGGGTAAC-ATGGTGACCACTAATGAGAGT----------CGAGCTGACTGCACAGCCCACTCTGTCCCCTTTC--CT-----------------CCTGCACATCCCAATCTGCCTTGCGGTTCCCGTGGCTGTGGTGCAT-gg-tgggaacga-cgtagccccatccag---acctggcccataggaatt-cctcttgtggtcc----------------tccttgtctgctggctgcagcagagaatctggcttc-agaggagtatctggagg-cctcagagagccacaagctagaaggagcctggatcccggaatgactccgtggagcaggatcctc-ccctccgcaccaact--------acctacattggattgtaatgcatgtgggagatgaacctttgtttgtctcctacgtgttaag-ccactgaaggtttgaagctgtttatCA----------------------------- i proCap1.scaffold_13667 I 95 N 0 s choHof1.scaffold_165855 618 649 + 4825 --------------TTGCTTTTT----TAACACGAAAA---GAATGTTTGGATCCTTCCCACTAAGGAATA-ATGAGATTAAGGGATTTGGAAGAGGTGTTTGGTGACATGGACAC-ACTGCCCGAGAAGAAAACGCCTCTCCTACTC-------GCCAGA-CGGACGACCCGTGGTG-CTCTGTGAGGTCCCTGGAGACCAGGG------CGTTTGGGGATCTCACAGTCAGTTTTGAAGTGACCGTGACGATAAC----------------------------G---------------------------------------------------------TCCATCATCTTGC--ACTTCTCCCAGAGACCGTG--GGCCG-----TGACTGACAATCTCAGTAACCGAGCAGGGT----------CCAGCTGCCTTCCAGG--AGCCCGGCCACCCTCC--CT-----GGGCACGCCGAGCCCCTGTGTCCCGGCCTCCCTCACAGTCAGAATGGCTTGAG------GG-TGGCAGTGAGTGTGGCTGCCCGTAGGACACCCGGCC---------C-CCACCCCCAGCCC-TCAAGCCCGTCCCTTCCCTCCTCtgcaa-----------------ggaccc-tgggtagggctctgaggaccccagggagccacgagcaggacggagcctgggttccagaaggactgtgggctgccgggcc----ccctccccactgcct--------gcctgcagtgggct-taccgtgagtgagaagcaaacc----------tctcccgtgtcagg-ccgctggaatctggctgttacgtatccccgc------agttaccgcaccta----- i choHof1.scaffold_165855 I 9 C 0 s loxAfr3.scaffold_159 106640 735 + 1045236 ------------TTTT--TTTTT----TAATATGAAAA---GAATGTTTGGCTCCTACCCACTAAGAAATA-ACAAGATTAAGGGATTTAAAAGAGGTGGCTGGTGACATAGACAC-CCCGCCTGAGAAGAGAGGTCTTCTCTTATTC-------ACAACAGCAGCCAATGTGTGCAG-CCCCATGAGGGCAA-GGTTACC----------------AGGACGT-----TCGGTTTTGATGTAACCACAATGACGATTGGCATGGCTCACCCTGTGCCTGCCTAGG--------------------------------------TCTTTCCAGGCCCT-CAC-TCCATCGTCTTTCTTCTTGCTCCCAGAAACTGCAAGAGAGA-----ATAGTAACAACACTGATAAGTAAAcagagg----------tgggctgattggccaacaaaccctgtcccctttc--cttccggacacacggctggcctgcacgtctcagcctcccttgcagttactgtggccatggcatgt-gg-tggatggaa-tgtagccccatccag----cctggcctatagaaacc-cctcttgcaatcctccatgtccagctctttccttgtctgccagctacagccgagaatc-ggattc-agaggaggaccctgaggtccgaagggagccacaagctggaaggagcctgaatccctgaatgactccgtggagcagagtcctctccctccgcaccacct--------acctacactggatttcagtgtgagtgggaagttaacctttatttatttcccttgtgttaaa-ccagtgaaattttggagctgtttatcacaga------agctgagtcagcccctga- i loxAfr3.scaffold_159 C 0 I 1050 s bosTau4.chr29 48985759 664 + 51998940 ---------------T--TTTTTAAAAAAATACAAAAG---GAATGTTCAGAGCCTTCCCGCCAAGGAATA-ATAAGATTAAGGGATTT--AAGAGGTGGCTGGTGACACATCCAC-ACTCCTC----------------------CT-------GGGAGGAGC-----CGCCGGGGGCCCCAGGGAGGGCCCAGCTCCCCCTTGCAGCCTCGCTCAGGGGTGGCAAAGCCGGCTGAGGTGTAACCAGAAGGACGATTAGCATGG-TCG-TCT--GCCGG-----G--------------------------------------TCCTTGCAGGCCCTTCGTAGCCCTCACCTTTCTCAGCGCTCCA-ACTGTTGCA--GGAGGAGGTAAGAGCAGTAACAGCCAAGAC-------AGA----------CTGAGCTCCTTCCTCCTGGACACAGAGCTCCTTC--CTCCTGGACACAGAGCCAGTCTCCGTGTCCCGGCCTCCC-TGTGGTTAGCGTGGCCTCTGCCTGTGGG-TACAGACGG-----------CCCAG---GCCCGGCCCAGAGGGACC-TCCCAGGGG-------------------TCCCCCATCCgcaga----------------cgatcctagaggaagactctgaagccccaagaggaccacaagctggcaggaacctggatccctgagtgacttcctggaacagg--c----ccctgccctccccct--------tcctgtactggatggtgacttgagggagagagaaagcgtca----------ttgtatgaag-ccCTCCACTTCT--GGGCTTGGAATGTCAGCGGCACTGGCTCTCTCACC-CTGTGA i bosTau4.chr29 I 4 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e oryCun2.chrUn0985 34579 424 + 42081 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=53736.000000 s hg19.chr11_gl000202_random 27133 61 + 40103 actaatGATCTTagctacaatcaactgcactcttaccatgagc-cagacacagccctgagca s cavPor3.scaffold_42 9676112 61 + 15951348 ACT-GTGACCGTAGGTGCAATCAGCTGAATTCTTCTCATACGTGCTAACATGGCTCTCAGCA i cavPor3.scaffold_42 C 0 C 0 s rheMac2.chr14 128173188 53 - 133002572 --------TCTtagctacaatcaactgcactcttaccatgagt-cagacacagccctgagca i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126010150 61 - 132107971 actaatgatcttagctaCAatcaactgcactcttaccatgagc-cagacacagccctgagca i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68213191 61 + 134204764 ACtaatgatcttagctacaatcaactgcactcttaccatgagc-cagacacagccctgagca i panTro2.chr11 C 0 C 0 s bosTau4.chr29 48986423 57 + 51998940 ACTGGTGCGCACAGCTACGAGCGGTCAAGCTCTTAGCA----C-CAAGCACAGTCCCGAGCA i bosTau4.chr29 C 0 I 574 s equCab2.chr12 28950703 48 + 33091231 ACTAATGATCGCAGAGACGATGAATCGGg-------------c-cacacatggtgctgagca i equCab2.chr12 C 0 C 0 s canFam2.chr18 7547187 31 - 58872314 ACTGATGGTCACGGCCACAAT-------------------------------CCGCTAAGCT i canFam2.chr18 C 0 C 0 s choHof1.scaffold_165855 1267 60 + 4825 actgatGACAACagctataattaattgagcacttgatgtgagc-ca-atgcggctccaagca i choHof1.scaffold_165855 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e oryCun2.chrUn0985 34579 424 + 42081 I e loxAfr3.scaffold_159 107375 1050 + 1045236 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=11248.000000 s hg19.chr11_gl000202_random 27194 66 + 40103 ttttttgtgtattgacgcacttaatgctcacaggaggggaggggacaatgcaacccc-tgctttctc------ s panTro2.chr11 68213252 66 + 134204764 ttttttgtgtattgacgcacttaatgctcacaggaggggaggggacaatgcaacccc-tgctttctc------ i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126010211 66 - 132107971 ttttttgtgtattgatgcacttaatgctcacaGAAGGGGAGGGGACAATGCAACCCC-TGCTTTCTc------ i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128173241 66 - 133002572 ctttttgagtattgacgcacttaatgctcacaGGAGGGGAGAGGACAATGCAACCCC-CACTTCCTT------ i rheMac2.chr14 C 0 C 0 s cavPor3.scaffold_42 9676173 35 + 15951348 TTTTGTGTGCGTCAAACCAC-TGATGGGCACAAGAG------------------------------------- i cavPor3.scaffold_42 C 0 I 583 s bosTau4.chr29 48987054 57 + 51998940 cttttggtatattgatGCATTCAATACCCACCCAAGCAAACA---------AAGCCC-CGGAGGTTG------ i bosTau4.chr29 I 574 I 24 s equCab2.chr12 28950751 51 + 33091231 ctttccgtgcgttcacacatttaatgcgcacCCGAGAAAACA---------CAGCCC-------GTG------ i equCab2.chr12 C 0 I 28 s canFam2.chr18 7547218 30 - 58872314 CT---------------CATT------------GGGGAAACA---------AAGTCC-TGCATTGTG------ i canFam2.chr18 C 0 I 18 s choHof1.scaffold_165855 1327 63 + 4825 cctttcataattgaactcatctagcagtc-catgagcaaatg---------aagcacgtgggggctgggtaag i choHof1.scaffold_165855 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e oryCun2.chrUn0985 34579 424 + 42081 I e loxAfr3.scaffold_159 107375 1050 + 1045236 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=38019.000000 s hg19.chr11_gl000202_random 27260 33 + 40103 tgatccaaggtcacccagccagga------agggac--------agt s choHof1.scaffold_165855 1390 33 + 4825 tggcccagggttgcacagctagga------aggagc--------agt i choHof1.scaffold_165855 C 0 C 0 s canFam2.chr18 7547266 36 - 58872314 TGG--TTGGAAGTCACCGCCAGGACCAAG-GAGGCT--------AGG i canFam2.chr18 I 18 C 0 s equCab2.chr12 28950830 39 + 33091231 TGACCCCGGGCCACACGGCCAGGACCCGGCAAGGCT--------AGT i equCab2.chr12 I 28 C 0 s bosTau4.chr29 48987135 39 + 51998940 TGACCCAAAGCCACAAAGCTGGGAGCCAGGGAGGCT--------AGC i bosTau4.chr29 I 24 C 0 s oryCun2.chrUn0985 35003 41 + 42081 TGGCCCAGGCTCATCCTGCCGGGA------GGGGGCGCCTCCAGAAT i oryCun2.chrUn0985 I 424 C 0 s rheMac2.chr14 128173307 33 - 133002572 TGATccaaggtcacccagccaggc------agggac--------agt i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126010277 33 - 132107971 tgatccaaggtcacccagccagga------agggac--------agt i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68213318 33 + 134204764 tgatccaaggtcacccagccagga------agggac--------agt i panTro2.chr11 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e loxAfr3.scaffold_159 107375 1050 + 1045236 I e cavPor3.scaffold_42 9676208 583 + 15951348 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=136556.000000 s hg19.chr11_gl000202_random 27293 325 + 40103 cctgagg---ttggac-ctaggtagcctatccctagag----------------------cccccttttgcagagga---gacaaatgagactcagaatggtcaaaggcata---------ttcccagggtaccagctggtagttctgg------gggtgcagg-atttgaacccctggctccagtgcctccaaagctcatgctccgtg--accactttgctgttctgcGAAGGAGGGAGCCAGGAGGAGCAGCG-TGA-ACCTGCACAGAGGCCCCAGTGTGCCCACTGAGGGGAGTCTCAGAG-TGGAGGCAGCCCCTTCC---C-----ACCCTCC-T-CTGGGCCAGCCTGGGTTCTCA----------TTGGGGACAATCGTACTCCAAG s panTro2.chr11 68213351 325 + 134204764 cctgagg---ttggac-ctaggtagcctatccctagag----------------------cccccttttgcagagga---gacaaatgagactcagaatggtcaaaggcata---------ttcccagggtaccagctggtagttctgg------gggtgcagg-atttgaacccctggctccggtgcctccaaagctcatgctccgtg--accactttgctgttctgcTAAGGAGGGAGCCAGGAGGAGCAGCG-TGA-ACCTGCACAGAGGCCCCAGTGCGCCCACTGGGGGAAGTCTCAGTG-TGGAGGCAGCCCCTTCC---C-----ACCCTCC-T-CTGGGCCAGCCTGGGTTCTCA----------TTGGGGACAATCGTACTCCAAG i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126010310 325 - 132107971 cctgagg---ttagac-ctaggtagcctatccctagag----------------------ccccctattgcagagga---gacaaatgagattcagaatgatcaaaagcata---------ttcccagggtaccagctggtagttctgg------gggtgcagg-atttgaacccctggctccagggcctccaaatctcatcctccatg--accacattgctgttctgCTAAGGAGGGAGCCAGGAGGAGCAGTG-GGA-ACCTGCACAGAGGCCCCAGTGTGCCCACTGCGGGGAGTCTCAGAG-TGGAGGCAGCCTCTTCC---C-----ACCCTCC-T-CTGGGCCAGCCTGGGTTCTCA----------TTGGGGACAATCGTACTCCAAG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128173340 306 - 133002572 cctgagg---ttgtac-ctaggtagcctatccctagag----------------------cccCCTGTTGcagagga---gacaaatgagactc---------------------------ttcccagggtaccagctggtagttctgg------gggtgcagg-atttgaacccctggctccagtgcctccagagttcatgctccatg--accactttgctattctgCAAAGGAGGGAGCCAGCAGGAGCAGTG-TGA-ACCTGCACAGAGCCCCCAGTGCACCTGTCGTGGGG-GTCTCAGAG-TGGAGGCAGCCCCTTCC---C-----ACCCTCC-T-CTGGGCCAGCCTGGGTTCTCA----------ATGGGGAAAATCATACTCCAAG i rheMac2.chr14 C 0 C 0 s oryCun2.chrUn0985 35044 241 + 42081 CCTGGGG---CTGCAC-C-------CCCAACGCCCG-------------------------CCACTCTCGTGGAGTG---GGCAAACCTCACGC-----------------------------CCTGGGTTCCCAGCATGCAATTCTGG------GGAGGCGGG-GTTTGAAGCCCTCGCTC-----TCTGTGGAGCCCATGTCCCATG--AGC-CCTTGCTGCTCTGC--------AGGCAGGGAGGGGCAGTG-TGAGGGGTTTACAGG---CCCAGTGCAGCC-CCGTGG---GTCTCAGCG-TGG-GGCAGGAGCTCCC---C-----ACCCCCC-CGGGGGGCCAG-------------------------------------------- i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48987174 283 + 51998940 CTGTGAG---CTCCAC-C-------TTTGAcccctcat----------------------cttcc-ccagtagagga---gaaaagcaagattcagcaggatcgaaggagctc--------gccccaggttgccagctggtcattcttg------gggagcaggggg------------------------cagagcccatggccctg---acCAC-TTACTGTACTGCT---GAGGGAGATGGGAGCTGCAGCC-TGA-GCATCCCCAC----TGCCGTGCAACCTGGGGAGGG-GTCTCAGAGCCGG-AGGCACCAGCCCC---C-----ACCTTGC-C-AC-GGTCAGCTAAGGGTCTC-----------TTTGGGGATGATCGACTCCCAG i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28950869 303 + 33091231 CCCAAAG---CCCCCGAC-------CCTGACCCCCCAG----------------------TTCcc-ccattagagga---gaaaagtgagattcagaaaggtcaaaggaacac--------agccaaggtccccagctggtgattctgg------gggagcgggcacttgaaccactgtgtc---tgcctccagagcctgcgctcccc---accaatttgctgttctgAT---GAGGGGGATAGGGGGAGAGGCTATGG-GGGCC-CCAG----CCCTGGGTGCCCTGTG--GGG-GTCTCAGAG-TGG-GGCAGCCGGCCTC---C-----CTCCTTC-C-ATGGGCCAACCTGGGGTCT------------CTGGGGGCCATCCCACTTCCAG i equCab2.chr12 C 0 C 0 s canFam2.chr18 7547302 260 - 58872314 CCCGGAG---CCCCTCAC-------TCCGACCCCTCAG----------------------CACCCTCTAGTGGAAGA---GAAATG-GAGACTCCAAAAGACGGGAGGA------------AGCCCAGGTTGCCAGCTGGTAATTCTGG------AGGAGCAGGGACT-----------------------CCAAGCCCACGTCCCATG--ACCACTTTGCTATTCT--------GGGAAATTGGAGGAGCAGCTGTGA-ACACCTCCAG----CCTCGTGCACCCC-------------------TGG-G--AGCCCATCCC---C-----GCCCTGC-C-CTGGGCCGGCCTGAGTTCTC-----------CTGGGGACGGCCCCACTCCATG i canFam2.chr18 C 0 C 0 s choHof1.scaffold_165855 1423 263 + 4825 cccgggg---cttgaa-ccgggtactctagtcccagagACGTGGACCTTCACCCCTCAGCTTCCCCTTCACAGGGGA---GAACTGTGAG-CTCAGAAGGTTCAGTCGGACC---------TGCC-------CCAGCTGGAAATTCTGGTGCAGTTGGGGCGGGGATTTGAACCACTCTCTC---TGTGTCCACAGCCCACCTCCCG----ACCCCT----------------------------------AGTG-GGA---------------CACTGG----------------GTGTCAGGA-TGGAGGGAGCCGGCCTCCCAC-----ATCCTCC-T-GTGGG-CAGCCTGGGGTCTC-----------TTGGGGG--------------- i choHof1.scaffold_165855 C 0 I 47 s danRer6.chr21 28119884 325 + 47572505 CCTAAGGGCCTCTGAC-CCCAGCAAGCTACCCAGGGGT----------------------CCACCTCTCTCCCTGGACTTGCAGTATAGGACCCAGGGTGCCCCCTGGCCCTCCACCTAGGGGCCTAAGATCCCAGCAAGCTACCCAGG------GG-------------ACCACCTCTCTCCCTTGACT-TGAAGAATAGGCAACAGGGTGCCCACTGGCCCTCCATCT-----AGGGGCCTAGGACCCCAGCA-----AGCTACCCAGGGG-TCCAGAACTCTCCCTG------GACTTGAAG-TATAGGCCACATGTTGC---CCACTGGCCCTCCAC-CTAGG--GGCCTAAGACCCCAACAAACTACCCAGGGGTCCACAACTCTCC--- i danRer6.chr21 N 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e loxAfr3.scaffold_159 107375 1050 + 1045236 I e cavPor3.scaffold_42 9676208 583 + 15951348 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=29208.000000 s hg19.chr11_gl000202_random 27618 148 + 40103 CTGGGATGGGGGTGGGGGTTCCAGAGAG------------------------CCCTCTCCAGTGACA------GCCCCATCAGCAG-------TGGCCTCACCTT-------ACCTGCAGCACACACAGCCCTTCGCCCAAG---GCCAGCAGGCCCTTC------CCTTCAGGCACTCTG----GCAGGCAACCAGCCAGCACA s panTro2.chr11 68213676 148 + 134204764 CTGGGATGGGGGTGGGGGTTCCAGAGAG------------------------CCCTCTCCAGTGACA------GCCTCATCAGCAG-------TGGCCTCACCCT-------ACCTGCAGCACACACAGCCCTTCGCCCAAG---GCCAGCAGGCCCTTC------CCTCCAGGCACTCTG----GCAGGCAACCAGCCAGCACA i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126010635 148 - 132107971 CTGGGATGGGGGTGGGGGTTCCAGAGAG------------------------CCCTCTCCAGTGACA------GCCCCATCAGCAG-------TGGACTCATCCT-------ACCTGCAGCACACACAGCCCGTTGCCCAAG---GCCAGCAGGCCCTTC------CCTCCAGGCACTCTG----GCAGGCAACCAGCCAGCACA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128173646 154 - 133002572 CTGGGACGGAGGTGGGGGTCCCAGAGAGCC------------------AGGCCCCTCTCCAGTGACA------GCCCCATCAGCAG-------CAGCCTCACCCT-------ACCGGCAGCACACACAGCCCGTTGCCCAAG---GCCAGCAGGCCCTTC------CCTCCAGGCGCTCTG----GCAGGCGACCAGCCAGCACA i rheMac2.chr14 C 0 C 0 s oryCun2.chrUn0985 35285 106 + 42081 ---------------------CACAGAGCC------------------AGGCCCCTGCCCACCGCCA------GCCCCGGC--------------------------------TCGGTAGC-------------TGCCATGG---GCCCCGCCGCCCTGC------CCCCCTGGGGCTCTGCACACCGAGCATTCTGCCAGGGCC i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48987457 87 + 51998940 -------TGGGGACGGGGTCCTAGAGAGCC------------------AGGCCCCTTCCCACAG-CAGCTTTGGCTCCA--------------TGGGTGCCCCCC-------ACCCTGTG----------------------------------------------CCCACAGAGCC-------------------------ACA i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28951172 150 + 33091231 -CAGGGCTGGGGGCAGGGGTCCCAAGAACC------------------AGGCCCCTCTCCACCGCCAGTGTGGGTTCCACCTGCAGCCGGGTCTGGGGACCCCTC-------ACTCCGGGTGCTC-CAGCTCTGGCCCCCAG---CTCAGCAGGATGCCCCCATGTCCCACAGA-------------------------ACCACA i equCab2.chr12 C 0 C 0 s danRer6.chr21 28120209 163 + 47572505 CTGGACTTGCAGTAGAGGCCCCAGGGTCCCCCCTGGCCCTCCACCTAGGGGCCTCTGACCCCAGCAA------GCTACATAGG----------GGTCCACATCTTTCCTTGGACTTGCAGTATA----------GGCCCGAGGGTGCCCCCTGGCCCTCC------ACCTAAGGGCCTCTG----AC-----CCCAGCTAGCTA- i danRer6.chr21 C 0 C 0 e choHof1.scaffold_165855 1686 47 + 4825 I e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e loxAfr3.scaffold_159 107375 1050 + 1045236 I e cavPor3.scaffold_42 9676208 583 + 15951348 I e canFam2.chr18 7547562 0 - 58872314 C e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=46664.000000 s hg19.chr11_gl000202_random 27766 34 + 40103 GGCCGAGTCCCAGGCCAGTGTCTTCCTGAGTCCA s panTro2.chr11 68213824 34 + 134204764 GGCCGAGTCCCAGGCCAGTGTCTTCCTGAGTCCA i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126010783 34 - 132107971 GGCCACGTCCCAGGCCAGTGTCTTCCTGAGTCCA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128173800 34 - 133002572 GGCCGAGTCCCAGGCCAGTGTCTTCCTGAGTCCA i rheMac2.chr14 C 0 C 0 s oryCun2.chrUn0985 35391 33 + 42081 GGCTGCACCCCTGGCCA-CGTCGCCCTGTGTCCA i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48987544 34 + 51998940 CGCTGAGGGCACAGCCAGCTTCTTCTTGAGTCCA i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28951322 34 + 33091231 TGCTGCACACTCAGCCGGCTTCCTCCAGGGTCCA i equCab2.chr12 C 0 C 0 s canFam2.chr18 7547562 23 - 58872314 -----------CAGCCGGCTCACTCCGCAGTCCA i canFam2.chr18 C 0 C 0 s choHof1.scaffold_165855 1733 34 + 4825 GGCTGAGTCTCGGGCCAGCTGCTTCCCGAGTCCA i choHof1.scaffold_165855 I 47 N 0 s danRer6.chr21 28120372 22 + 47572505 --------TCCAGGC----GTCCACCTCTCTCCC i danRer6.chr21 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e loxAfr3.scaffold_159 107375 1050 + 1045236 I e cavPor3.scaffold_42 9676208 583 + 15951348 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=208192.000000 s hg19.chr11_gl000202_random 27800 745 + 40103 TGGG-CTGGC--CAGAAGAGATGAGGACTTAC--CTGG----CCATCTTGGCCAC-CAAACTCCCAGGGA-----CCCCGGCCCCTC----------ATCCCCATCAACATTCTCCTTATTGCCCTTCTCAGACACCAGCTGCGACCAGCTTAAACAACAACGGCATTTTTCAGATGCCAACTTG---GCAGCCTG-----------------TGGGCCTCTCAGGAGCCTAGATCCAGGTCCCCCGG-----CAGGAGTCTCCCTGACCTC-CAGTC-TCGGCTTCTCTCTGTAGGCCACC-------ACCGCCTCCACGGTGGCAGCTGCACACACA------------------------CCTGCCTCGGGCTCATGGCA-----CTGCGGTCT-----CCTCTTCCCTGACATC----------CCCCAGACCCCTGCAGG----CCTCGGCTCCAGCGCCAGCTCTG----------AAAAG-CCCCTGG-----------------GATACAGCCCCTTCCCC------CAGGAGC----CCCCTGGTCCTCCTGCAT-------AGC--CCCATCCTATTATCCATCTATTTG---CTGCT-----GTCT---------------------CC-CCCAACCT---TGCCCCTGCCACATGGGAGCCTTCCAAGGGCAGAGA-----CCCTG----TG-CATCAGAGGCCCTGATGC--CCACAGCGCCTCGTCCC-AGCACCGAGGGGCAGGGGATT---------------GGCGTGCACTGCATGGTCTGGA---AGA---------G------CAAACCCGCCATGACTTTATGACCCT-TGTTATCACCTCCTTCTGTGGTCCAAAGCCCT-GGAGCAGGGATCTGCGCACACT----ACAGACAG-----------AGCCAGG---CCTCAC----CTGCCCAGTGG--TTAGGGTGGGGTGGGGAGGTGGGGCCGCAGGAGGGAACACTCT s panTro2.chr11 68213858 744 + 134204764 TGGG-CTGGC--CAGAAGAGATGAGGACTTAC--CTGG----CCATCTTGGCCAC-CAAATTCCCAGGGA-----CCCCAGCACCTC----------ATCCCCATCAACATTCTCCTTATTGCCCTTCTCAGACACCAGCTGCAACCAGCTTAAACAACAACGGCATTTTTCAGATGCCAACTTG---GCGGCCTG-----------------TAGGCCTCTCAGGAGCCTAGATTCAGGTCCCCCAG-----CAGGAGTCTCCCTGACCTC-CAGTC-TCGGCTTCTCTCTGTAGGCCACC-------ACTGCCTCCACGGTGGCAGCTGCACACACA------------------------CTTGCCTCGGGCTCATGGCA-----CTGCGGTCT-----CCTCTTCCCTGACATC----------CCCCAGACCCCTCCAGG----CCTCGGCTCCAGTGCCAGCTCTG----------AAAAG-CCCCTGG-----------------GATACAGCCCCTT-CCC------CAGGAGC----CCCCTGGTCCTCCTGCAT-------AGC--CCCATCCTATTATCCATCTATTTG---CTGCT-----GTCT---------------------CC-CCCAACCT---TGCCCCTGCCACATGGGAGCCTTCCAAGGGCAGAGA-----CCCTG----TG-CATCAGAGGCCCTGATGC--CCACAGCGCCTCATCCC-AGCACCGAGGGGCAGGGGATT---------------GGCGTGCACTGCATGGTCTGGA---AGA---------G------CAAACCCGCCATGACTTTATGACCCT-TGTTATCACCTCCTTCTGTGGTCCAAAGCCCT-GGAGCAGGGATCTGCGCACACC----ACAGACAG-----------AGCCAGA---CCTCAC----CTGCCCAGTGG--TTAGGGTGGGGTGGGGAGGTGGGGTCGGAGGAAGGAACACTCT i panTro2.chr11 C 0 I 708 s ponAbe2.chr11 126010817 719 - 132107971 TGGG-CTGGC--CAGATGAGATGAGGACTCAC--CTGG----CCATTTTGGCCAC-CAAACTCCCAGGGA-----CCCCGGCCCCTC----------ATCGCCATCAACATTCTCCTTATTGCCCTTCTCAGACACCAACTGCAACCAGCTTAAACAACAACGGCATTTTTCGGATGCCAGCTTG---GCAGCCTG-----------------TGGGCCTCTCAAGAGCTGAGATCCAGGTCCTCCGG-----CAGCAGTCTCCCTGACCTC-CAGTC-TCGGCTTCTCTCTGTAGGCCGCC-------ACTGCCTCCACGGTGGCAGCTGTACACACA------------------------CCTGCCTCGGGCTCATGGCA-----CTGTGGTCT-----CCTCTTCCCTGACATC----------CCCCAGACCCCTCCAGG----CCTCGGCTCCAGCGCTGGCTCTG----------AAAAG-CCCCTGG-----------------GATACAGCCCCTT-CCC------CAGGAGC----CACCTGGTCCTCCTTCAT-------AGC--CCCATCCTATTATCCATCTATTTG---CTGCT-----GTCT---------------------CC-CCCAACCT---TGCCCCTGCCACATGGGAGCCTCGCAAGGGCAGAGA-----CCCTG----TG-CATCAGAGGCCCTGATGC--CCACAGAGCCTCGTCCC-AGCACCGAGGGGCAGGGGATT---------------GCCGTGCACTGCATGGTCTGGA---AGA---------G------CAAACCTGCCATGACTTTATGATCCT-TGTTAATACCTCCTTCTGTGGTCCAAAGCCCT-GGAGCAGGGATCTGAGCACGCCAGAGACAGACAG-----------AGCCAGG---CCTCAC----CTGCCCAGTGG--TTAGGGTGGGGTGG----------------------------- i ponAbe2.chr11 C 0 M 251 s rheMac2.chr14 128173834 748 - 133002572 TGGC-CTGGC--CAGATGAGATGAGGACTCAC--CTGG----ACATCTTGACCAC-CAAACTCCCAGGGA-----CCACGGCCCCTC----------ATCCCTGTCAACATTCCCTTTATTGCCCTTCTCAGACACCACCTGGAACTGGCTTAAACAGCAACAGCATTTTTCGGATGCCAATTCA---GCAGCCTG-----------------TGGGTCTCTCAGGAGCCTGGAACCAGGTCCCCCGG-----CAGGAGTCTCCCTGACCTC-CAGTC-CTGGCTTCTCTCTGTAGGCCGCC-------ACCGCCTCCACAGTGGCAGCTGCACACACA------------------------CCTGCCTTGGGCTCGTGGCA-----CTGTGGTCT-----GCTCTTCCCCGACATC----------CCCCAGACCCCTCCAGG----CCTCAGGTCCAGCACCAGCTCTG----------AAAAG-CCCCTGG-----------------GATACAGCCCCTT-CCC------CAAGAGC----CACCTGGTCCTCCTTCAC-------AGC--CCCATCTTATTATCCCTCTATTTG---CTGCT-----GTCT---------------------CC-CTCAACCT---TGCCTCTGCCACATGGGAGCCTTGCAAGGGCAGAGA-----CCCTG----TG-TATCAGAGGCCCTGATGC--CCACAGCACTTCGTCCC-AGCACTGAGGGGCAGGGGATT---------------GGCATGCACTGCATGGTCTAGA---AGA---------G------CAAACCCACCATGACTTTATGACCCT-GATTACCACCTCCTTCTGTGGTGCAGGGCCTG-GGAGCAGGGCTCTGAGCATGCCAGAGACAGACAG-----------AGCCACG---CCTCAG----CTGCCCAGTGG--TTAGGGTGGGGTGGGGAGGTGGGGCCGCAGAAGGGAACACTCT i rheMac2.chr14 C 0 C 0 s oryCun2.chrUn0985 35424 553 + 42081 CGGGCCTGGC--CAGGTCAGGTGG----CCAG--GTCA----CCGCCTGGGCCCC-CA----CCCTGGAA-----CCCTGACCCCT-----------ATCGCAGTCAACGTTTTCTCTGCTACATCTCACAGACACCAACCGCGGCCGGCGGGAG-GGCTGGGGCATTGCT-GGGTGGAAACTGG---GCACCCCA-----------------GGGGTGGCT-----------------------------------------CCTGGGGGC-CAGCC-CCTGCCTCGCTCCACCTGCTGCA-------GCCGGAGCC--------------CCACACC------------------------TCTGCCCCAGGGCCGCGTCC-----CGGAGG-----------CCCCTGTGGCCTA----------CCCCTGACCCGC---GG----CCT-------------GGCTCTG----------------------------------------------GCCCCTC-CTC----------------------GCCCTTCCACCAC-------AGG--CTCAT-------------TACCTG---CTTCTGTGTCGTCT---------------------CC-CCTCATC----TGCCCCTGGCCCA---GCCCCCACCACAGG---------------------G-CATCGGAGGCACCGGTGCAGCCGCTACGCCT-GGCCC-AGCACGGAGGAACCGGTGCCT---------------GGCGGCACCCACA---TCCAAA---GAA---------GTCACTTTAGACC--CCAGGGGTCTCAGTCCCC-T-----CACCGCCTCCTGCAGTGCAAGGGCC--------------------------------ACAC-----------AGGCGCC---CCCCCC----CTGCAGAGTTGCCCCCGGGAGGGGT---------------------------CTCT i oryCun2.chrUn0985 C 0 I 2 s bosTau4.chr29 48987578 699 + 51998940 CGGC-CTGGC--CAGGGGAA---GGGACTCGCCACTGA----CCCATTTGGACCCCCAAACTCTCGGGTA-----GCGCCGCCCCTCCCCTCCCCCTGCCGCAGTCTGGCTCATCTCCGC--------TCAGACAGCAG-CGGAGCCACCTTAAGGAAAAGGGACTTTTGCTGGGTGGAGGCTCA---GCCTCCTC---------------------TCTCTCAGGGGCC---------ACTCTC----------------------------------TCCGCTTCCC-CTGCGTGCCGCCCACCTCGCCTCCCTCCAC-GTGGTGGCCACTCACAT-------------------------CCCACCCCAACCTCACAGCA-----TCCCTGTCTGAAA-----TTCTGACGGCCC----------CCCCAGATGCCA-CAGA----CCCCCACTCG---GTCACCTGCG----------AGAGGCCTCCTGAC--CCCCGTGC------AG--CAATCTGTC-ACC------CAGCTCTCTCACCCCAGGCCTGCTCTCT-------------CCCAGTGGGTTCTCTGGTCATTTG--TCTACT-----GTCC---------------------CC-CT--------------------TACATGAGCCCCTCAATGCCAGGAA-----CTTCG----TG-TGTCTCTCGCTGTGATGTGGCCACAGGACCCGATCCCCGGAACAAAGAAGCATGTGCCA---------------AGCATCTCCCG-----TCTAAG---AAA------CTGT------TAAAATCGCTATGGTTTTTGTTACCC-TGTTAACGTCGCCCTCTGCGGTGCCAGGACCCAGGACCAGGGCTCTGGACACACC----TCATACTTGGTGGGCTCC-AGCTGTG---CCTGGCAGGTTTGCCCAGTGG--TTAGGGGTCAGAGG--------------AATAGGGAGCACCCT i bosTau4.chr29 C 0 I 4 s equCab2.chr12 28951356 775 + 33091231 CAGC-C-GGC--CAGTCAGG-TAAAGACTCAC--CTGT----CCGTCTTGGCACC--AGACCACTAGGGA-----GCACAGCCCCTC----------ACCCCAGCGCTGCTCATCTCAGCCGCACCCCTCAGACGCCAGCCGCAGCCCACTTCAGCAAAAGGGGCATTGGCAGGATGGAAACCCC---GGGGCCTCCAGACCCCCGGGCCAGCGGGACCTCTCAGGGGCCCAGGACCAGGCCCCCCTA-----CAGGATTCCCTCTGCACCT-CAAGTTCCCGCTTCTC-CTGCCTGCCACCTGCCTCGCCTCTCTCCAC-GTC-TGGGGGCAcacag-------------------------cccgtgccaagttcctgacg-----cctctgcctggaacgctcttcctgag--------------ccccagatgccctcagg----cctctgctca---gccacctcca----------agaaa-ctcccggcctccccatgcactgcgggcccctcccctc-accggactccatcact----ccctcactgccccccaa-------------cct-gcacattatctgtttattcg--tctggt-----gtcc---------------------cc-ctgcccc-------------catacatgagcccttcaaggccaggca-----cctgg----tg-catgcgacgcttcgatgtggccacactacttggcccctgggacagaaaagcaggtgccc---------------ggcatccattg-----tctgaa---agaacaaaACCAT------TAACATCGCCACAATTCTCATCACCCTTCTTACTGTCTCCCTCCACGGCACAAGGGCCTGGGAG--GGGCTCCGGGCGCACG----GCACACAC--AGGGTTCCGGGCCACG---CCTGGCAGGATGGCCGGGTGG--TTAGGGGCAGCAGG--------------AGGAGGGGGTACTCT i equCab2.chr12 C 0 I 4 s canFam2.chr18 7547585 672 - 58872314 TGCC-T-GGC--CGGGCAGT---AGGGCTTAC-------------GGTTGGGGCC--------CCCGGGG-----CCCCAGCCCCT------------GCCCCGTCCAGTGCATCGCGGGTGCA----TCAGACACCAGCCACAGTCAGCTTAATAGAAGGGGGCATTTGTTGGATGGAGA---------------------------------------CTTGGGAGCCCAGGGTCAGGC--------------------------------------CCTGCGTCTC-CTGCGTGCCGCCCGCCTGGCCTATCTCCAT-ATAGCGGCTCCACACAC-------------------------CCCATCCCAACCTCACAGCA-----CCTCTGCCCAGAACTTTCTTCTCAAG-TTC----------CTCCAAATGCCAACCTG----CCTCTACTCA---GTCACCTTCA----------AGAGGCCTCCTGACACTCCCTTGT------GATCCAGCCCCTC-ACC-CACTTCAGCCCTGCCACCCCCACTGCCCTGCCT-------------CCTGGCCCATCACCCACttatttg--tctgtc-----gtcc---------------------cctctcccca-------------catacatgagcccttcaaagccaggaa-----ctttg----tgccattggacactttgctgtggccacaacacctggtccctgatgcagaggagcaggtgctc---------------agcaTCCTCCG-----TCTGAG---AGA--CGAACCAT------TAAAACCACCGCAGTTCTCTTTACCC-TCATCCTTTCTC---CTGTGGTGCCAGGGCCTGGGAGCAGGGCTCTGGGCATGCG----GCGCACACAGAGGGGTCTGGGCCACGCCACCGTCCAGGACTGCC------------------------------------ACGGACGGGAACACT i canFam2.chr18 C 0 I 4 s danRer6.chr21 28120394 769 + 47572505 TGGA-CTTGCAGTAGAGGAGCTAGGGTACCCC--CTGGCCCTCCACCTTGGGGCT-TTATTCCCCAGCAAGCTACCCAGGGATCCAC----------CTCTCTTCCTGGACTTGCAGTAT----------AGGCCCCAGC----------------------------------GTGCCACCTTGCCCTCCACCCA-----------------TGGGCCTCT---GACCCCAG---CAAGCTACCCAGGGGTCCACAACTCTCCTTGGACTTGCAGTA-GAGGCCC----CAGGGTGCCCCC-------AGGCCCTCCAC-CTAGGGGCGGCTGACACAAGATAGCTCCCCAGGGGTCCACCTCTCTCCCTGGACTTGCAGTAGAGGCCCTCGG--------GTACCTCCTGGCCCTCCATATAGAGGCCTCTGACCCCAGCAAGTTACCCAGGGGTCCACAACTCTCCCTGGACTTGCAGTAGAGG-CCCCAGG-----------------G---TACCCCCTT-GCC------C----TC----CACCTAGTGGCCTCTGACCCTAGAAAGCTACCCAGGGTTCCACCTCTCTCCCTGGACTTGCA-----GTATAGGCTGCAGGGGGCAACCTGGCC-TTCCACCTAGGGGTCACTGACCCCAGGAAGCTACCCAGGGGTCCACCTCTCTCCCTGGACTTG-CAGAATAGGCCCCAGGGT-------GCCCCCTGGCCC-ACCACCTATGGACTTCTGACCCCAGCAAGCTACCCAGGCGTCCACATCTCTCCCTAGACTTGCA---------G------TAGAGGCCCCAGGG-----TGCCCCC-T--------TGCCCTCCAC---CCAGGGGCCT-------TTGACCCCCGCAAGTT----ACCCAAGG-----------GTCCACAAC-TCTCCC----TGGACTTGCAG--TCGAGGCC--------------------CCAGGGTGCCACTT- i danRer6.chr21 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e loxAfr3.scaffold_159 107375 1050 + 1045236 I e cavPor3.scaffold_42 9676208 583 + 15951348 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=-9622.000000 s hg19.chr11_gl000202_random 28545 40 + 40103 GGGTTCCCTCCTCCTCCTCCCTGGGT---GTGGCCTACC--CCCA s rheMac2.chr14 128174582 40 - 133002572 GGGCTCCCTCCTCCTCCTCCCTGGGT---GTGGCCTACC--CCCA i rheMac2.chr14 C 0 C 0 s oryCun2.chrUn0985 35979 32 + 42081 GAGGTCTCT----------CCTGGGTT-AGTCTCCAACC--CCCA i oryCun2.chrUn0985 I 2 C 0 s bosTau4.chr29 48988281 31 + 51998940 AGGCTCCAGGTTC-----CCCCAGGT---GTGGCCTGCA------ i bosTau4.chr29 I 4 C 0 s equCab2.chr12 28952135 32 + 33091231 GGGCTCCTGGCT------CCCTGGGT---GTGGTCTGCCGT---- i equCab2.chr12 I 4 C 0 s canFam2.chr18 7548261 31 - 58872314 AGGCTCCAGGCT------CCCGGGAC---ACAGCCTCGTG----- i canFam2.chr18 I 4 C 0 s danRer6.chr21 28121163 37 + 47572505 GGCCCTCCACCTAGGCCACTCTCAGCCAAGCAAACTA-------- i danRer6.chr21 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e loxAfr3.scaffold_159 107375 1050 + 1045236 I e cavPor3.scaffold_42 9676208 583 + 15951348 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I e ponAbe2.chr11 126011536 251 - 132107971 M e panTro2.chr11 68214602 708 + 134204764 I a score=-2182.000000 s hg19.chr11_gl000202_random 28585 59 + 40103 CCCCCC----------------AACCCTGGCCCCTGCACGGGGCT----------ATCTTGGGCCACCCAGTGCAGGTGGCTGAG------------- s panTro2.chr11 68215310 59 + 134204764 CCCCCC----------------AACCCTGGCCCCTGCACGGGGCT----------ATCTTGGGCCACCCAGTGCAGGCGGCTGAG------------- i panTro2.chr11 I 708 C 0 s rheMac2.chr14 128174622 58 - 133002572 -CCCCT----------------AACCCTGGCCCCTGCACAGGGCT----------CTCTTGGGCCATTCAGTGCAGGCGGCTGAG------------- i rheMac2.chr14 C 0 C 0 s oryCun2.chrUn0985 36011 47 + 42081 --CCCTGCTCTCAGAGTTCGGAACCCTTCGCCCTGACGCAGGGGT----------CTCT--------------------------------------- i oryCun2.chrUn0985 C 0 I 655 s bosTau4.chr29 48988312 57 + 51998940 --ATCC----------------AGCAGATGCCC--CCACGAGACTGC--------GTCTTGAGCCACACGGAGCAGGCAGCCGTG------------- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28952167 47 + 33091231 CCATCC----------------AGCAGAGGCC----CCCAGGGCTGG--------GCCTTGA----------GCAGGCGGCTGAG------------- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7548292 55 - 58872314 --GTCC----------------AGCAGAGGCCC--GCGCAAGGCTGC--------GTCTGGAGC--CACGATGCAGGTGGCCGTG------------- i canFam2.chr18 C 0 C 0 s danRer6.chr21 28121200 58 + 47572505 ------------------------------------CCCAGGGGTCCAACTATCTACCTGGAATTGCA----GTAGGGGCCCTAGGGTACCTCCTGGC i danRer6.chr21 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e loxAfr3.scaffold_159 107375 1050 + 1045236 I e cavPor3.scaffold_42 9676208 583 + 15951348 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I e ponAbe2.chr11 126011536 251 - 132107971 M a score=323637.000000 s hg19.chr11_gl000202_random 28644 672 + 40103 CCTCTGGCGATGGCTTGTGACTGGCCTGGGG--CTCATCAAATGCCCGTTGCATGAAGCCTGCCTGGC---------------------------------------------------TTCATGCATTGTTTTATGTGCATCTCAGGAC-TGGGGCAGCTGCCTGGGACAGAGATGCCTGCCAGGTCCCAGCCGCTGGGAATGGGG--CTGTCTGACTCTCCTGCAGTC--CCTGCTTCCTCTGGTCCTGGCATTCAGCAGGAAGGAGGCTCAGGGATCAGTGCCCAGGCAGAGCAGGGTCTCCAGGG---TCCCAAGGACATGGGCCAACTAAGGTAGCCCAGGACATGGTCCCTGGAGTCGCCCTT---------CCTTGTGGCCCAGTATCCCCGGT-CACTGCCATGTCCTC--TGGGAG----CCCATCTG-ACAGCCCTAGCC-GCAGCC-TTCCTGTCCTGCTCCCTGTCCCT--GGATGAAGGACT-TGACCCCAGTTAGTCA------AGTCC----TTCATCC----TTGACTTCCA------GACCAGTTGTGCTCTCAGCTGGCACACC--TGGCCTGAGCC---GTGGGGCCCTCTGC-CCACAATGCCCCCCA----CCCATCTGCACAGGGTGGGA-TCCTA---------------GGGATCAAG-GTCACCTGGTGGAGATGCCCCCTCCCCATCCACCT--CTTG---------------------------GCTTCTCACGTCACAA----CTCCATGTGTGTTTAGGGCCTCACTCACTTGTGG-AAAGGACCCTG---------------------ATGAGGCTGTGG----TGG----CCAG--------- s panTro2.chr11 68215369 672 + 134204764 CCTCTGACGATGGCTTGTGACTGGCCTGGGG--CTCATCAAATGCCCGTTGCATGAAGCCTGCCTGGC---------------------------------------------------TTCATGCATTGTTTTATGTGCCTCTCAGGGC-TGGGGCAGCTGCCTGGGACAGAGATGCCTGCCAGGTCCCAGCTGCTGGGAATGGAG--CTGTCTGACTGTCCTGCAGTC--CCTGCTTCCTCTGGTCCTGGCATTCAGCAGGAAGGAGGCTCAGGGATCAGTGCCCAGGCAGAGCAGGGTCTCCAGGG---TCCCAAGGACATGGGCCGACTAAGGTAGCCCAGGACATGGTCCCTGGAGTCGCCCTT---------CCTTGTGGCCCAGTATCCCCGGT-CACTGCCATGTCCTC--TGGGAG----CCCCTCTG-ACAGCCCTAGCC-GCAGCC-TTCCTGTCCTGCTCCCTGTCCCT--GGATGAAGGACT-TGACCCCAGTTAGTCA------AGTCC----TTCATCC----TTGACTTCCA------GACCAGCTGTGCTCTCAGCTGGCACACC--TGGCCTGAGCC---GTGGGGCCCTCTGC-CCACAATGCCCCCCA----CCCATCTGCACAGGGTGGGA-TCCTA---------------GGGATCAAG-GTCACCTGGTGGAGATGCCCCCTCCCCATCCACCT--CTTG---------------------------GCTTCTCACGTCACAA----CTCCATGTGTGTTTAGGGCCTCACTCACTTGTGG-AAAGGACCCTG---------------------ATGAGGCTGTGG----TGG----CCAG--------- i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126011787 672 - 132107971 CCTCTGAGGATGGCTTGTGACTGGCCTGGGG--CTCATCAAATGCCCATTTCATGAAGCCTGCCTGGC---------------------------------------------------TTCATGCATTGTTTTATGTGCCTCTCAGGGC-TGGGGCAGCTGCCTGGGACAGAGATGGCTGCAGGATCTCAGCCACTGGGAATGGGG--CTGTCTGACTCTCCTGCAGTC--CCTGCTTCCTCAGGTCGTGGCATTCAGCAGGAAGGAGGCTCAGGGATCAGTGCCCAGGCGGAGCAGGGTCTCCAGGG---TCCCAAGGACAAGGGCCGACTAAGGTAGCCCAGGACATGGTCCCTGGAGTTGCCCTT---------CCTTGTGTCCCAGTATCTCCGGT-CACTGCCATACCCTC--TGGGAG----CCCCTCTG-ACAGCCCTAGTC-GCAGGC-TTCCTGTCCTGGTCCCTGTCCCT--GGATGAAGGACT-TGACCCCAGTTAGTCA------AGTCC----TTCATCC----TTGACTTCCA------GACCAGCTGTGATCTCGGCTGGCACACC--TGGCCTGGGTT---GTGGGGCCCTCTGC-CCACAATGCCCCCCA----CCCATCTGCACAGGGTGGGA-TCCTC---------------GGGATCAAG-GTCACCAGGTGGAGATGCCCCCTCCCCATCCACCT--CTTG---------------------------GCTTCTCACGCCACAA----CTCCGTGTGTGCTTAGGGCCTCACTCACTTGTGG-AAAGGACCCTG---------------------ATGAGGCTGTGG----TGG----CCAG--------- i ponAbe2.chr11 M 251 C 0 s rheMac2.chr14 128174680 691 - 133002572 CCTCTGAGGATGGCTCGTGACTGCCCTGGGG--CTCATCAA---------------------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTCATGCATTGTTTTATGTGCCTCTCAGGGT-TGGGGCAGCTGCCCGGGACAGAGATGCCACCAGGGTCCCAGCCACTGGGAATGGGG--CCGTCTGATTCTCCTGCAGCC--CCTGCTTACTCTGGTCCTGGCATTCAGCAGGAAGGAGGCTCAGGGATCAGTGCCCAGGTGGAGCATGGTCTCCAGGG---TCCCAAGAACATGGGGCGACTAAGGTAGCCCAGGACATGGTCCTTGGAGTTGCCCTT---------CCTTGTGGACCAGCATCCCCGGT-CACTGCCACGTCCTC--TGGGAG----CCTCTCTG-ACAGCCCTAGCC-ATAGCC-TTCCTGTCCTGCTCTCTGTGCTT--GGATGAAGGACT-TGACCCCAGTTAGTCA------AGTCC----TTCATCC----TTGACTCCCA------GACCAGCAGTGCTCTCGGCTGGCACACC--TGGCCTGAGCT---GTGGGGCCCTCTGC-TCACAATGCCCCCCA----CCCATCTGCACAGGGTGGGC-TCCTC---------------GGGGTCAAG-GTCACCTGGTGGAGATGCCCCCTCCCCATCCACCT--CTT----------------------------GCTTCTCATGCCACAA----CTCCACAT----TTAGGGCCTCACTCACTTGTGG-AAAGGACCCTG---------------------ATGAGGCTGTGG----TGG----CCAG--------- i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48988369 637 + 51998940 CCTCTGATGATGGTTTCTGA-TGCCTTAAAAGCTTCATCAAACACC-----CCATAAAGCTGCCTGGC---------------------------------------------------TTCATGTATTGCTTTATGTAACTCTCATCA----------------------------------GAGTTCCAGGCAGCTGGAGGGGGGCCCTGCCTGGGCCTCCCAGGACA--CCTGACTCCCCTGGTCCCCACATCTAGCCAGGACAAGGCTCAGTGATCAGA-CCTAGGCAGGGGGGCGTATTCAGGG---TCAC-AGGCCACAGGCTGACCACCGCAGCACAGGATTTCATCCCCGGAAACGCCCCT---------CCTGGCCTCCCAGTG--CCTGATGACCTGCCGCTTTCTCTGTAGGAG-------GTCTGAACTGGCCAGGCC-ACAGCCTTCCCCGCCGTCCACACCCTGCCC--G--------------------------CT------TCTGC----TCCACCCACCTCCACCCTCCA------GGCTCGCCGGGCCCTCAGCTCTCAGACC------------------AGGGCCCTCTGC---------TTCCTCG---TCTCATCTCCACAGGGTGGGC-CCTTCTCAGCCGTCCAGTCCGGGCTTAAATGTCACCCT-CGCGGGTGTCACCCCAACATCCTCTC--CCTCTGAACCCCCTTGTCCTCCTCCCTCCCTGCCTCTCACATCTCATCTCACCCGCTGGGCACTTGGCTCCTCGTTCACGTGCAG-AAAGGGCTCTGA--------------------ATATGACtgtag----ggg----------------- i bosTau4.chr29 C 0 I 1903 s equCab2.chr12 28952214 640 + 33091231 CCTCTAATGATGATT-TTGA-AGGCCTGAGG-CTTTGTCAGCTGC------CGATAAAGCTGCCTGGC---------------------------------------------------TTCGTATGTGGCTTCATGCAGCTCTCACA-----------------------------------GGGGTCCAAGCAG--TGAAGGGGGCCCTGCCTGACTCTTCCAAGGGC--CCCGAGCCTCCTGGTCCTCACATCCGGTAGGGACAAGGCCCAGTGGCCAGC-ACCAGGCAAGGCTGGGTCCCCAGGG---TCCCGAGGAGGCCGGCAGACCATCCCAGCACAGGACCTCGTCCCCAGAAACACCCTT---------CCTCGTCACCCAGGA--CCTGGTGTACTGCCGCTTCTT---TGGGGG-------------ACCGTCC---CAGACAGGCTTTCCCATCCTCCTCTCCCTGCC--------------------------------------TCCCC----TTCATCTG---CCACCCTCCA------GACTCG-CGGGCCCTCTGCGCTCGCACCCTAGGCCTGCACCCGCGGGCTTCCCTCTGC-ACACAGTGCTCCCTG---CCCCACCCTCACAGGGTGGCCCACCTCTCAGCCTTCCAGTCTGGCCTTAAATGTCACCCCGAGGAGACGCCGTCCCGACCCCCTCTC--CCCGGGCACCTCCCTGTCCCTCTCTATCTCTGCCTCTCACACCACAC----CTCGCTGCAGGCTTCGCACCTCGTTTTCTTGCGG-ACAGGGTTGTGG--------------------ATGGGGCTGTGG----TG-CTGG------------- i equCab2.chr12 C 0 I 1902 s canFam2.chr18 7548347 573 - 58872314 CCTCTGAGGATGGTCGTTGA-TGGCCTAAAGTCTTCATCACATGCG-----TAAAGAATCTGCATGGC---------------------------------------------------TTCGTACATTCTTTTATGCCACCCTCGGAAC-GATGGCAG--------------GAT-----TGGGGTCCCAGGCAGA-CAAAGGAGGCCCTGCCTGAC-CCCCCATGGCC--CCTGCCTCATCTGGTCCTCGCATCGAGCAGAAACAAGGCCTGGCAATCAGC-ATTCAGCA----------TCCACGG---TCTCCCGGAGGCAGGTGGACTTCTTCTGCTCAGGATTTTGTCCCTGGAA--GCCCTT---------CCCTGTCACCCGGCA--CCTGGTGAACTGTTGCTTCTTC--TGGGAG-------------ACTGTCT---CC-ACGGGC---------------------------------------------------------------------------------CAGCCCTGCA------GGCACG-CTGGCACCCCACTCTCACACC---AGCCTGCACCCATGAGGTCCCTTCTGC-CCACA-----------------------------------CCTTCCCATCCATCCA-TCTGGGCTGAAGTGTCACCCCACGGAGACGCCTCCCCCAACACCTCCCCTCCTGGACACGTCGCTGCTCTTCCCTGCCTCCACCCCTCACATCACAC----CCAACTGCACACTTGCTTCCTTGTTCACTTGTAG-AAAGGATTCCAA--------------------ATGGGGTCgtca----tgg----------------- i canFam2.chr18 C 0 I 2406 s danRer6.chr21 28121258 684 + 47572505 CCTCCA------------------CCTAGGG---------AACTCTGATAACAGTAAG-CTACTTAGG-------------------------------------------------------------GGTCCACCTTTCTCCCCGGACTTGCAGTAGAGGCCCCAG-----GGTGCACCCAGGCCCTCCACCTAGGGGCCTCTGACCCCAGCTAGCTACCCAGGGGTCCACCTCTCTCCCTGGATCTGCAGGATAGGCCCCAGGGTGCCCCGTGTACCTCCACCTAGG--GGCCTCTGACCTCAGGAAGCTACCCAGGAGTCCACCTCTCTCCCTGGACTTGCAGTTTAGGCCCCAGGGTGCCCCCTGGCCCTCCACCTAGGGGCCTCTGACCCCTGAA-AGCTACC----------CAGGAGTCCACCTCTCTT-CTTGGTTTTGCA-GTAGAG-GCCCCAGTGTGCCCCCTGGCCTTCCACATTTTGGCCTCTGACCCCAGAAAGCTACCAATGTATCCACAACTCTCCC----TGGACTTGCAGTAGAGGGCCCAGGGTGCCTCCTGGCCCTCCACC----------------TTGGGGCCTTTGACCCCAGCAAGCTACCCAGGGGTCCACCTC-------------TCTTCTTGGACTTGCAGTAGAGGCCCCAG--------------GATGCCCCCTGGCCCTCCACCT--TTTG---------------------------GCCTCTGACGCCAGCAAGCTTCCAATGGATCCACAACTCTCCCTGGACTTGCAGTAGAGGGCCCAGGGTGCCTCCTGGCCCTCCACCTTGGGGCCTTTGACCCTAG----CAAGCTACCCAGG i danRer6.chr21 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e oryCun2.chrUn0985 36058 655 + 42081 I e loxAfr3.scaffold_159 107375 1050 + 1045236 I e cavPor3.scaffold_42 9676208 583 + 15951348 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=54187.000000 s hg19.chr11_gl000202_random 29316 75 + 40103 GTCCCTCCTCTCCCAAGTGGCTTGAAGTCCAAGTGACTGGGGTGCCCACT----GGGG-TCCCCCCCATTTCCATCTGAT--- s panTro2.chr11 68216041 75 + 134204764 GTCCCTCCTCTCCCAAGTGGCTTGAAGTCCAAGTGACTGGGGTGCCCACT----GGGG-CCCCCCCAATTTCCATCTGAT--- i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126012459 76 - 132107971 GTCCCTCCTCTGCCACGTGGCTTGAAGTTCAAGTGACTGGGGTGCCCACT----GGGGTCCCCCCCCATTTCCATCCGAT--- i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128175371 75 - 133002572 GTCCCTCCTCTGCCAAGTGGTTTGAAATCCAAGTGACTGGGGTGCCCACT----GGGG-TTCCCTCCATTTCCATCTGAT--- i rheMac2.chr14 C 0 C 0 s equCab2.chr12 28954756 75 + 33091231 GTCCTTCCCCTGCTGAGCGGCTTAAAGGCCAAGTGACTAAGAT-ATCTCTGGGCGAGG-TCCCTTCT-----CCCCAGAGC-T i equCab2.chr12 I 1902 C 0 s canFam2.chr18 7551326 71 - 58872314 --CCCATCTCTGCTGAACAGTCTGAAGGCCACGTTACTGGGATGATGTCT----GAAG-TCGCCTCT-----CACCAGAACAT i canFam2.chr18 I 2406 C 0 s cavPor3.scaffold_42 9676791 74 + 15951348 -TCTCTTTTCTGCCAAGCAGCTTGAAGAACAGGGGACAGAAACAATCTCT----GGCG-TCTCCTCTGTTTCCATCCTGT--- i cavPor3.scaffold_42 I 583 C 0 s danRer6.chr21 28121942 73 + 47572505 GGTCCACCTCTCTTCTTGGTCTTGCAGTAGAGGCC-CCAGGGTGCCCCCT----GGCC-CTCCACCTATGGGCTTCTGA---- i danRer6.chr21 C 0 N 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e oryCun2.chrUn0985 36058 655 + 42081 I e loxAfr3.scaffold_159 107375 1050 + 1045236 I e bosTau4.chr29 48989006 1903 + 51998940 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=67975.000000 s hg19.chr11_gl000202_random 29391 78 + 40103 TCTATTT-CCTAGAAGAAACAATGTGCACGACAG---CCAAAGA---AGACAAACAACCACAAAA----TCAGAAATGTGTT-GTTTCTG s canFam2.chr18 7551397 84 - 58872314 TCTATTT-CCTAAAAGAGACCACATACAGGATGG---CCAAAAAACTAGGCAAACAG-CACAAAACCCATCTGAAAAGTATT-GGTTTTA i canFam2.chr18 C 0 C 0 s equCab2.chr12 28954831 85 + 33091231 TCTATTT-CCTGAAAGGGACAGTGTACTGGGTGG---CCAAAAGACTAGACGAATGA-CACAAGACCCTCCTGAAAAATATTCATTTTTG i equCab2.chr12 C 0 C 0 s bosTau4.chr29 48990909 86 + 51998940 TCTATTT-CCTAAAAGAGGAAATGTGTAATGTGGGCCCCAGAGAA--AGACCAGCAG-CACAAACCCCACCTGAAAAGTGTCCAGGTTTG i bosTau4.chr29 I 1903 C 0 s cavPor3.scaffold_42 9676865 64 + 15951348 TGCATTTCCCCCGAGGAGACACTGCA---GGCAG---CTCAAGC-----ACAGGAGGCCACAGGG----TTCTAGA-----------CCG i cavPor3.scaffold_42 C 0 C 0 s panTro2.chr11 68216116 78 + 134204764 TCTATTT-CCTAGAAGAAACAATGTGCACGACAG---CCAAAGA---AGACAAACCACCACAAAA----TCAGAAATGTGTT-GTTTCTG i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126012535 78 - 132107971 TCTATTT-CCTAGAAGAAACAGTGTGCACGACAG---CCAAAGA---AGACAAACGACCACAAAA----TCAGAAATGCGTT-GTTTCTG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128175446 78 - 133002572 TCTATTT-CCTAGAAGAAACAATGTGCATGACAG---CCAAAGA---AGACAAATGACCACAAAA----TCAGAAATGTGTT-GTTTCTG i rheMac2.chr14 C 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e oryCun2.chrUn0985 36058 655 + 42081 I e loxAfr3.scaffold_159 107375 1050 + 1045236 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=168998.000000 s hg19.chr11_gl000202_random 29469 105 + 40103 CTGGATTTTTTCTTCTCTTAGAATTTTAGGGGAAGGAGGGCTACCGGCCACCGGTCTC-CCCAGGTGAGCACCCTGGGTCCAGGCACCTTGTCCAG------GCCATATCAG s rheMac2.chr14 128175524 105 - 133002572 CTGGGTTTTTTCTTCTCTTAGAATTTCAGGGGAAGGAGGGCTACTGGTCACCAGTCTT-CCCAGGTCAGCACCCTGGGTCCAGGCACCTTGTCCAG------GCCACATCAG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126012613 105 - 132107971 CTGGACTTTTTCTTCTCTTAGAATTTTAGGGGAAGGAAGGCTACTGGCCACCAGTCTC-CCCAGGTCAGCATCCTGGGTCCAGGCACCTTGTCCAG------GCCACATCAG i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68216194 105 + 134204764 CTGGATTTTTTCTTCTCTTAGAATTTTAGGGGAAGGAGGGCTACCGGCCACCGGTCTC-CCCAGGTCAGCACCCTGGGTCCAGGCACCTTGTCCAG------GCCATATCAG i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9676929 80 + 15951348 CAGTGAGTTTTC--CTCTTAGCATTTTGGA--------GGAGGTGGGCTGCC----------------GCA--CACAGCCC----GCCCTGCTCAGCACCCAGTCACATGGG i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48990995 95 + 51998940 CTTGACTTTTCCTTCTTTTAGCATCTGGGGGGAAGGTGGGCTGCTGACCACCAGCCCT-CCCTGGT-GGCCTCCTGGGCAGGG---------CCAG------ACCTTATCAG i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28954916 105 + 33091231 CTGGATTTTTCCTTCTTTTAGCATTTGGGGGCAAAGTGGGCCGCTGGCCACCAGCCCT-CGCAGGTCAGCATGCTGGGTCCAGACGCCTCATCCAG------GCCTCACCTG i equCab2.chr12 C 0 C 0 s canFam2.chr18 7551481 105 - 58872314 TTGTATTTTTCCTTCTCTTAGCATTTGGGGGAAGAA-GGGCTGCTGGCCACCAGCCCTGCCAAGGTCAGCACCCTGGGACCGGGCCCCTCATCCAG------GCCTCCCCAG i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 936887 105 - 1045236 CTGAAGGTTACCTCTTGGTAACATTTTGAGGGAAGGTGGGCTGCTGGCCAACAACCCA-CCCAGAACAGCCCCCTGGGTCCGGGCACCTTGTCCCC------ACCACACTGG i loxAfr3.scaffold_159 n 1050 C 0 s proCap1.scaffold_13667 12430 105 + 46842 CTGAACTTGACCCGCTGGTAACCCTTTGAGGCCAGGTGGGCTGCTGGCCAACAGTACA-CCCGGGACACGAACCTGGGTCCGGGCGTCTTGTCCAG------GGCACTCTGG i proCap1.scaffold_13667 N 0 C 0 s dipOrd1.scaffold_204994 157 63 + 859 ------------------------------GGGGGAGGGGCAGTGGGCTGCT-----------GGTCAGCA--CTGGGCACCGGGGCCCTGTCCAG------GCCACACTGG i dipOrd1.scaffold_204994 N 0 C 0 e ochPri2.scaffold_12461 32194 2417 - 40248 I e micMur1.scaffold_46107 1188 1162 + 5307 M e oryCun2.chrUn0985 36058 655 + 42081 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=21926.000000 s hg19.chr11_gl000202_random 29574 60 + 40103 AGCCAGCCAGACC-----CTCCAGTGGCTTTCCCAG-------CAGCAGACTGCTGC------TCCCTAGCCTCTGCC s rheMac2.chr14 128175629 60 - 133002572 AGCCGGCCAGACC-----CTCCAGTGGCTTTCCCAG-------CAGCAGACCGCTGC------CCCCTAGCCTCTGCC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126012718 60 - 132107971 AGCCAGCCAGACC-----CTCCAGTGGTTTTCCCAG-------CAGCAGACCGCTGC------CCCCTAGCCTCTGCC i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68216299 60 + 134204764 AGCCAGCCAGACC-----CTCCAGTGGCTTTCCCAG-------CAGCAGACTGCTGC------CACCTAGCCTCTGCC i panTro2.chr11 C 0 C 0 s dipOrd1.scaffold_204994 220 35 + 859 AGCTGGCCCGGCT------------GGCCTTCTCAG-------------------------------CCGCCTGGGCG i dipOrd1.scaffold_204994 C 0 C 0 s cavPor3.scaffold_42 9677009 48 + 15951348 AGCTGGCCAGGCT--------------CTCTCCCAG--------ATC--AACTTTGT------ACCCCAGCCTTTGAG i cavPor3.scaffold_42 C 0 C 0 s ochPri2.scaffold_12461 34611 67 - 40248 AGTGAGCCAAGCTCC---CGTGGCAACTCCCCTGAG--------AGCTGACCATTGCCTGGCAGCCCCAGCCTTGACA i ochPri2.scaffold_12461 I 2417 C 0 s bosTau4.chr29 48991090 65 + 51998940 AGCTGGCCAGA-C-----CTCGTGCTGCGTCCACAGCCAAGGACAGTTGCCCCCGCC-------CCCCAGCCTCTGCG i bosTau4.chr29 C 0 I 12 s equCab2.chr12 28955021 58 + 33091231 AGCTGGCCAGACC-----CTCCCGCGGCATCCACAG-------CAGGCACCCCGCTA-------CCCCAGCCTCTGT- i equCab2.chr12 C 0 I 11 s canFam2.chr18 7551586 59 - 58872314 AGCTGACCAACCC-----CTCCAGTGGCATCCACGG-------CAGGCAACCATTGC-------CCCCAGCCTCTGCA i canFam2.chr18 C 0 I 12 s loxAfr3.scaffold_159 936992 45 - 1045236 TGCTGGCTGGACCCTCCTCTCCTGTGGCGTTCACAG-------AGGCTGGGT-------------------------- i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 12535 45 + 46842 TGCTGGTGGGACCCTCAGTTCCTGCAGCGGCCACAG-------AGGCCAGGT-------------------------- i proCap1.scaffold_13667 C 0 C 0 e micMur1.scaffold_46107 1188 1162 + 5307 M e oryCun2.chrUn0985 36058 655 + 42081 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=154791.000000 s hg19.chr11_gl000202_random 29634 113 + 40103 AGCAGGGCCAGC-------GG-----------GGGTCCTGGCCCTTCGAG-----GCTCTTTCAG-TAACATTTGCCTGCAGCTCTTAGAGCCCCATT----CCTTTCTCTCTCATGTAAGATCTTGTTGAGGTCTGATCT s micMur1.scaffold_46107 2357 109 + 5307 AGCAGGG-CAGC-------TG-----------GGCT-CTGGCCCCTGCGG-----GCTGTTCCAG-AAACATTCTCTTGCCGC-CTCTGCAGCCCGTT----TCTTCCTTTCTCATGCAAGATCTTGTTGAGATCTGG-CA i micMur1.scaffold_46107 M 1162 C 0 s rheMac2.chr14 128175689 112 - 133002572 AGCACGTCCAGA-------GG-----------GGGTCCTGGCCCTTCCAG-----GCTCTTTCAG-TAATATTTGCCTGCAGCTCTTAGCACTCCATT----CCTTTCTCTCTCATGCAAGATCTTGTTGAGGTCTGA-CC i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126012778 112 - 132107971 AGAAGGGCCAGC-------GG-----------GGGTCCTGGCCCTTCCAG-----GCTCTTTCAG-TAACAATTGCCTGCAGCTCTTAGAGCCCCATT----CCTTTCTCTCTCATGTAAGATCTTGTTGAGATCTGA-CC i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68216359 113 + 134204764 AGCAGGGCCAGC-------GG-----------GGGTCCTGGCCCTTCGAG-----GCTCTTTCAG-TAACATTTGCCTGCAGCTCTTAGAACCCCATT----CCTTTCTCTCTCATGTAAGATCTTGTTGAGGTCTGATCT i panTro2.chr11 C 0 C 0 s dipOrd1.scaffold_204994 255 100 + 859 CGCGGACCGGGC-------GGGGGACAGGCGGGGGGG--GGCCCTTCCTG-----ACTGC----------------------CCTTTGAAGTCCTGTC----TCTTCCCTTCTTGTGCAAGATGCTGCGGAGATCTGA-TG i dipOrd1.scaffold_204994 C 0 C 0 s cavPor3.scaffold_42 9677057 127 + 15951348 AGCAGGGCTGGC-------AGTGGGGAGCAGAGTGGTTCAGCCCTTCCAG-----ACTGCACCGG-TGACACTTTCTTGCTGCCTCTGGGGCCCTTTCTCCTTCTTTCTTTCTCAGGCAAGATTTTGTTGAGATTTGA-TG i cavPor3.scaffold_42 C 0 C 0 s ochPri2.scaffold_12461 34678 111 - 40248 AGCAGGGCCAGC-------AG-----------GGGTTCCGGCTCCTCCCG-----GCTGTTCCGT-CCCTGCACATTGGGCACCTGCAGGGACCCTGT----GCCCTCCTGCTCTGGTGGGATCACGTGGCG-TCCCA-CA i ochPri2.scaffold_12461 C 0 C 0 s bosTau4.chr29 48991167 108 + 51998940 AGCAGGGGCAGC-------TG-----------GGGTCCCGGCCCCTCCAG-----GCCCT-TCAG-TAACCGTTGCTTGTCCCCTTTAGGACCATGTC----TCTTTCTTTCTCATGCAAGATC---TTGAGATCCAG-TG i bosTau4.chr29 I 12 C 0 s equCab2.chr12 28955090 118 + 33091231 AGCGGGGCCAGCCGGGCGGGG-----------GTGGTCTGACCCTTCTAG-----GCTGT-TTAA-TAACATTGGCTTGTTGCCTTTATGGCCAGCTC----TCTCTCTTTCTCATGCAAGACTTTGTTGAGATCTGA-CA i equCab2.chr12 I 11 C 0 s canFam2.chr18 7551657 63 - 58872314 AGCAGGGTCAAT-------GG-----------GAGGT------------------GCCAT-CCAA---------------------------------------TCTCTTTCTC-TGCAAGATCTGATGGAGATCTCA-CA i canFam2.chr18 I 12 C 0 s loxAfr3.scaffold_159 937037 114 - 1045236 -GCAGGGCCAGCTG-----GG-----------GAGTTCCGGCCCCTCCTG----GGCTGTTTCAG-TGACAGTCATGTCTTGCCGTCAGAGCCGTGGC----TCTTCTTTTCTGGTGGAAGATCTCGTGAATCTCTGA-AG i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 12580 116 + 46842 -GCAGGGTTC-CTG-----GG-----------GGGTTCT-GCCCCGCCTGCCCCAGCTGTTTCAGTTAACACTCATGTCTTGCCATTAGAAATGTGG-----TCCTCTTTTCTGGGGGAAGACTTTGTGACACTCTGG-TG i proCap1.scaffold_13667 C 0 C 0 e oryCun2.chrUn0985 36058 655 + 42081 I e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=70011.000000 s hg19.chr11_gl000202_random 29747 28 + 40103 GGGGTT-----TTAGGGCAG-------------------------AGTTGAGAGAC--TG s micMur1.scaffold_46107 2466 30 + 5307 GGGTTT-----TTAAGGCAG-------------------------AGTTGAAAGATTGTG i micMur1.scaffold_46107 C 0 C 0 s rheMac2.chr14 128175801 30 - 133002572 GGGGTT-----TTTGAGCAG-------------------------AGTTGAGAGACTGTG i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126012890 30 - 132107971 AGGGTT-----TTAGGGCAG-------------------------AGTTGAGAGACTGCG i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68216472 30 + 134204764 GGGGTT-----TTAGGGCAG-------------------------AGTTGAGAGACTGTG i panTro2.chr11 C 0 C 0 s dipOrd1.scaffold_204994 355 26 + 859 GGA--T-----GGAAGACAG-------------------------AGCTGGAAGGTTG-- i dipOrd1.scaffold_204994 C 0 I 2 s cavPor3.scaffold_42 9677184 28 + 15951348 GGGGTT-----TTAAGGCAG-------------------------AGTTGAAAGATTG-- i cavPor3.scaffold_42 C 0 I 2 s oryCun2.chrUn0985 36713 28 + 42081 GGGAGT-----TAGAGGCAG-------------------------CGCTGAGAGACTG-- i oryCun2.chrUn0985 I 655 C 0 s ochPri2.scaffold_12461 34789 28 - 40248 GAGGTT-----TGAAGCTGG-------------------------CCCTGACAGAGTG-- i ochPri2.scaffold_12461 C 0 N 0 s bosTau4.chr29 48991275 35 + 51998940 AGGGGTGGGGGTTAAGACCA-------------------------AGTTGAGAGATTGTG i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28955208 30 + 33091231 GGGGTT-----TTAAGGCAA-------------------------AGTTGAGAGATTGTG i equCab2.chr12 C 0 C 0 s canFam2.chr18 7551720 26 - 58872314 GGG--T-----TGGAGGCAA-------------------------AGCTGGAAGAC--TG i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 937151 30 - 1045236 GGAGAT-----TTAAGGCAG-------------------------GGTGGAGAGACTATG i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 12696 55 + 46842 GGAGAC-----TgaaggtggcaggggaggggggaggggaaggggaagtggaaggATTGCG i proCap1.scaffold_13667 C 0 C 0 e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=342382.000000 s hg19.chr11_gl000202_random 29775 281 + 40103 AATCAACATTTCAAC-CTGTCTTCAGTTTTGTAACTTCACCTGATCCCTGTGATCCTGGGAAGGGGTGTTTAAGGCAATAAATGGCAAA-ATGCAAGCCATGCAATTTGATCCCAAAGCCCTGCTGACTCTAAGCAGCTCTTCA----------ACTCA-TTCCTCCACGGTACACC-CCTCCCAGCCCCA---------------------GCTTCTCTACCTCCCAGGCCGCTG---CAGCCAGGCCGG-----------------------TGCCCG-CCACCTGCATTCCCAC------------CCCTTCCAGTCCATTCTCC-ACC-TG-CAGCTGG--AAGCAT---TAGGGCCT-C s micMur1.scaffold_46107 2496 246 + 5307 AATAAACATTTCAGCTCTGTCTTCAGTTTTGTAGCTTCGCCTGAGCCC--TGACTCTGGGAAGGAATGTTTAAGGCAATAAACGGAAAA-ATGAAAGCCGTGCAATTTGATCCCCAAACCCTGCTGATCCTAAGCAGCTCTCAG----------ACCCA-TTCCT----GCTCCGCT-CCTCCCTCCACCG---------------------CCTCCCCTGCCT----------------------GCAGG-----------------------TGCTCC-CCTCCT-CCCTCCCAC------------CCCT----GCCCACTCCTC-ACC------GCTGG--GC-CGC---TGGGGCCT-- i micMur1.scaffold_46107 C 0 C 0 s rheMac2.chr14 128175831 282 - 133002572 AATCAACATTTCAACTCTGTCTTCAGTTTTGTAACTTCGCCTGATTCCTATGATCCTGGGAAGGGATGTTGAAGGCAATAAATGGCAAA-ATGCAAGCCATGCAATTTGATCCCAAAGCCCTGCTGACTCTAAGCCGCTCTTCA----------ACCCA-TTCCTCCATGACACGCC-CCTCCCAGCCCCA---------------------GCTTCTCTACCTCCGAGGCCACTG---CAGCCAGGCTGG-----------------------TGCCCT-TCACCTGCATTCCCAC------------CCCTTCCAGTCCATTCTCC-ACC-TG-CAGCTGG--AAGCGT---TAGGGCCT-C i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126012920 282 - 132107971 AATCAACATTTCAACTCTGTCTTCAGTTTTGTAACTTCGCCTGATCCCTGTGATCCTGGGAAGGGGTGTTTAAGGCAATAAATGGCAAA-ATGCAAGCCGTGCAATTTGATCCCAAAACCCTGCTGCCTCTAAGCAGCTCTTCA----------ACTCA-TTCCTCCATGGCATGCA-CCTCCCAGCCCCA---------------------GCTTCTCTACCTCCCAGGCCGCTG---CAGCCAGGCCAG-----------------------TGCCCT-CTACCTGCATTCCCAC------------CCCTTACAGTCCATTCTCC-ACC-TG-CAGCTGG--AAGCGT---TAGGGCCT-C i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68216502 282 + 134204764 AATCAACATTTCAACTCTGTCTTCAGTTTTGTAACTTCACCTGATCCCTGTGATCCTGGGAAGGGGTGTTTAAGGCAATAAATGGCAAA-ATACAAGCCATGCAATTTGATCCCAAAGCCCTGCTGACTCTAAGCAGCTCTTCA----------ACTCA-TTCCTCCATGGTACACC-CCTCCCAGCCCCA---------------------GCTTCTCTACCTCCCAGGCCGCTG---CAGCCAGGCCGG-----------------------TGCCCC-CCACCTGCATTCCCAA------------CCCTTCCAGTCCATTCTCC-ACC-TG-CAGCTGG--AAGCAT---TAGGGCCT-C i panTro2.chr11 C 0 C 0 s dipOrd1.scaffold_204994 383 246 + 859 AATAAACATCTCCACTCCGCCTTC-GTCTTGGCCCTTCGCCTGAT-CATGTAGTTCTGGGGAGGAATGTTTAGGGCAATTTATTACAAA-ACGCAAGTCACACAATTTGCCCCCAAAGTCACGCTGACCCCAA--AGCTCAAAG----------ATCC-----------CCCATTCC-CCTACCCACACTG---------------------CCAGCTGCTTCC------------------------CAG-----------------------AAATGG-CCAGCTGCGGTCCC--------------CCCTCCTGCTTCAGCTCCC-ACAATG-CACCCCG--AGTTGT---CAGGGCTTC- i dipOrd1.scaffold_204994 I 2 N 0 s cavPor3.scaffold_42 9677214 272 + 15951348 AATAAACATTTCAACGCTGTCTTTAGTTTTGGAGTTTTGCCTGATCCCTGTGATTCTGGGAAGGAATGTTTAAGGCAATACATGGTAAA-ATGAAAGCCCTGTGATTAGAACCCCAA---------ATCCAAA--AGCTTTAGGTCCATTTCTCACCG-----------CACATGCC-CCGCCTGTCACCC---------------------CCACCCCCTTCC---------------CAGCCAGG-CAG-----------------------ACATCT-CCACAACCAGCCCCACCTGCCTTTGTAGCCTTCCTGGCCCAGCACCC-AGAAAG-CAGTCAGGAAATGTT---CAGGGCTA-- i cavPor3.scaffold_42 I 2 C 0 s oryCun2.chrUn0985 36741 222 + 42081 GGTGAACACTTCATCGAG-------GCTTCGGCGCTCTGCCTGCTCCCTGTGGCTCTGGGAAGCCAAGTTCAAGGCAAGACCCGGCACA-GTGCACGCTTTACCAAGTCCCACCGAC---------CCCCGAC--AGCTCTTGG----------Acc----------------tacc-cctccctgcacac---------------------cctccaccccca----------------------------------------------------------------ccgcccctcctcgc-------ccctcctcgcccagcctcC-ACGCTG-CGGCCGGGAAGGGTTAGGTAAGGCTT-- i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48991310 308 + 51998940 AATAAACATTTCAACTCTGCCTTCAGATTTGTAGCTTTGTCTGATTCTTATGGGCCTGGGAAGGAATGTTGAAAGCAATAAATGGTGAA-ATGTTAGCTATGCAGTTATATGCCCAAGTCCCGTTGATCCCAAACAGCTCGTAG----------ACCCA-TCCCTTACTGTACACCC-CCTCCCGCTCCCCACTTTCTGAGATGAGACCAGGGTCCCGTCTGCTCCCAGACCACTGCAGCAGGCAGGCAGA-----------------------TGGGCT-GTACCTCCCTTCCCAC------------CCCTTCTAGGGCATTCTCC-ACACGG-CAGCCAGGGAATGCC---TGGGGCTT-- i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28955238 306 + 33091231 AATAAACAGTTCAGCTCTGTCTTCAGCTCTGTAGCTTTGCCTGATTCTTATGACCCTGGGAAGGAATGTTTAAAGCAATAAATGGTAAG-ATGTAAGCTGTGCGGTTTGATCCCTGAGTCCTGTTGATCCTA---AGCCCTGAG----------ACCCA-TCCCCCACTGCCCACTC-CCTCCCACCCCCGACGTTCTGGGACCGGGCCAC-GTGCCCCCAGCTCCCAGACCACCGCAACAGCCGGGCAGA-----------------------CGGCCT-GCACCTCCGTTCTCGC------------CCCTTCTAGTCCACTCTAGCCCACCAGCAGCCAGGAAATGAC---TGGGGCGT-- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7551746 304 - 58872314 AATAAACATCCCAACTCTGTCCTCAGTTTTGCAGTTTTGCCTGAGTTCTTTGACACCGGGAAGG-ATGCTGAAAGCAATACATTGCAAA-ATGTGAGCTGTGCAGTCTGATCCCAG-GTCCT--------------------AG----------ACCCA--CCCCCACTGCATAGCC-CCTTGTA-CCCAAATTTTCTGGGTTGGGGCTGC--TCCCTCCCACTCCCAGACCCCAGCAACCGCC-AGTAGACCACTCCCCCAAACCCCCACCCCCACCCC-ACATCTCCATCCTTGC------------CTCTTCTAGTCAGTTCCTG-ACACCA-CAGCCAAGAAGTGAT---TGGGGCTT-- i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 937181 269 - 1045236 GATAAACATTTCAGCTCTGCCTTCACTTTTGCAGTGTTGCCTAATCCTGAGGAGCCCGGGAAGGAATGTTAAAAGCACTAAGTTGTAAA----------ATGCAATTTGATCCTAAAGTCCTGGTGATCCTAAACAGCTCTTGG----------ACCCATTTCCTCCATTGCATACCTCCTCCCTGATGAT-----CTGAGGTC---------GGGCCACACCT-CAAGACC-CTGCAATAGCTAGA---------------------------TGGTCTCCCACCTCCGTCCTTTC------------TGCTTCTTATCGAGCCTCC-GCACTG-CATCCAGGAA------------------ i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 12751 276 + 46842 GCTAAGTGGTT-AGCTCAGTCCTCACATCTTCAGGGTCGCCTCGCCCCAGCTGGCCTGGCAAGGAACGTT-AGAGTGCAAAGCGGTAAAAACACAGACCATGCTGTTGGATCCCCAATTCCCAGAGACTCTAAACAGATCCTGG----------ACCCATTTATTCTACTGCACACC-CTTCCCTGACCAT-----CTGAGAGAG-------GGGGCTGCACCC-CCAGACCACTGCCACCACCAGA---------------------------TGGACT-CCACCTCCCTC--TGC------------CCCTTCTCAGCCCCCCTCC-ACACTG-CACCCAGGAG------------------ i proCap1.scaffold_13667 C 0 C 0 e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=90807.000000 s hg19.chr11_gl000202_random 30056 71 + 40103 GCCTGGGCCTGC-----CAAGGGCTGGATGCAAA--GACAGGCTCTG--------------------------ACAGAGAAGAGG-ATT---------TTGggggagga---agcag s micMur1.scaffold_46107 2742 68 + 5307 GCCTGGGTCTGC-----TGGGAGCCGGA-ATGAA--GACAGGATTTG--------------------------gcatgg--gagg-gat---------tccggggagga---aggag i micMur1.scaffold_46107 C 0 C 0 s rheMac2.chr14 128176113 71 - 133002572 GTTTGGGCCTGC-----CAAGGGCCGGATGCAAA--GACAGGCTCTG--------------------------ACAGTGAGGAGG-TTT---------TTCAgggaaga---aacag i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126013202 71 - 132107971 GCCTGGGCCTGC-----CAAGGGCCGGATGCAAA--GACAGGCTCTG--------------------------ACAGAGAAGAGG-TTT---------TTGggggagga---agcag i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68216784 71 + 134204764 GCCTGGGCCTGC-----CAAGGGCTGGATGCAAA--GACAGGCTCTG--------------------------ACAGAGAAGAGG-TTT---------TTGggggagga---agcag i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9677486 70 + 15951348 GTTTGAGTCCAC-----CAAGAGCCAGGTACAAA--GAGCA--TCTG--------------------------ACAGCAGAGAGG-TTT--------ACTGAggcagga---agcag i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 36963 78 + 42081 GCTTGGGTCTCCAGTTGCCAGCGCCAACGACAGG--GCTCG--TGCG--------------------------ACGCCCAAGAGA-CTT--------CTTGAGGGAGGAGCTAGCAG i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48991618 72 + 51998940 gtttgggtctgc-----tgacagccagatgcaaa--gatgcagcttg--------------------------acacagaagagg-ttt--------attgatggcgcc---atggg i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28955544 72 + 33091231 gtttgggtctgc-----caagagccagaagcaaa--gacgggatttg--------------------------acaaagaagaga-tgt--------attgagggagag---agcaa i equCab2.chr12 C 0 C 0 s canFam2.chr18 7552050 103 - 58872314 GTTTGGGT---------CAAGAGCCAGATGCAAA--GACAAGGTTGACCCTTGCTGCTGGAAGGACAGCAGATGCAAAGACAAGGTTGTCTTCCCTGATGGAAGGACAC---AGCAG i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 937450 56 - 1045236 --------------------GAGCCAGGTGCAAG--GGCAGGATTAG--------------------------ATAT-TACAAGA-TTT--------ATTAGGATtgag---agcag i loxAfr3.scaffold_159 C 0 C 0 s proCap1.scaffold_13667 13027 59 + 46842 --------------------GAGCCAGGTGCAGGGAGGGAGGATTAG--------------------------GCACATACAGGA-TTT--------ACTAGGAGAGGG---AGCAG i proCap1.scaffold_13667 C 0 C 0 e tupBel1.scaffold_125018.1-1020051 196214 6007 - 1020051 I a score=48696.000000 s hg19.chr11_gl000202_random 30127 40 + 40103 gagaacatg-aaagaggcttcaggccacaatg-aagagg-----------------------cga s panTro2.chr11 68216855 40 + 134204764 gagaacatg-aaagaggcttcaggccacaatg-aagagg-----------------------caa i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126013273 40 - 132107971 gagagcgtg-gaagaggcttcaggccacaatg-cagagg-----------------------cga i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128176184 40 - 133002572 gagagcgtg-gaagaggcttcaggccacaaca-cagagg-----------------------tga i rheMac2.chr14 C 0 C 0 s micMur1.scaffold_46107 2810 40 + 5307 gaggaagtg-gaggagccttcggactgccatg-agggcc-----------------------tga i micMur1.scaffold_46107 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 202221 40 - 1020051 GAGAAAGTg-gaagaaacttcagaccacagtg-taggtc-----------------------tga i tupBel1.scaffold_125018.1-1020051 I 6007 C 0 s cavPor3.scaffold_42 9677556 40 + 15951348 gaagaggtg-ggggagtcttcagaccacagtg-tgggtc-----------------------tga i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 37041 37 + 42081 AAAGC-----CGAGAACCTTCCGGCCACAGTACCTGGTC-----------------------TGA i oryCun2.chrUn0985 C 0 C 0 s bosTau4.chr29 48991690 41 + 51998940 gagacagagcaaagagctttcagaacacaatg-caggac-----------------------ccc i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28955616 41 + 33091231 gagaaagtgcaaagaggcatcaggccacgatg-cggggc-----------------------tga i equCab2.chr12 C 0 C 0 s canFam2.chr18 7552153 41 - 58872314 GAGGAGGTGCAAAGAGCCTTCGGACCACAGTG-CCTGGC-----------------------TGA i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 937506 55 - 1045236 cagaaagta-ggagg-----aggactgggaag-gagggtctcatgctaccatgcagtgccaa--- i loxAfr3.scaffold_159 C 0 n 0 s proCap1.scaffold_13667 13086 33 + 46842 GAGAAAGTGCACGGG-----CAGGCTGGGAGG-GAGGGG-------------------------- i proCap1.scaffold_13667 C 0 N 0 a score=120908.000000 s hg19.chr11_gl000202_random 30167 142 + 40103 cccgcatggaaggagagaaggaaggaaacagaa-----gtggacaggaggag-------------------------tctcaaactgcagtgctgt-tccactaaggttcagccctgctgaCTCT---TTCAAGGGGG-AAAAAAAAGCAGCTAAACTGGCTGAAGTAA-TCAAGAGG s panTro2.chr11 68216895 143 + 134204764 cccgcatggaaggagagaaggaaggaaacagaa-----gtggacaggaggag-------------------------tctcaaactgcagtgctgt-tccactaaggttcagccctgctgaCTCT---TTCAAGGGGGAAAAAAAAAGCAGCTAAACTGGCTGAAGTAA-TCAAGAGG i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126013313 142 - 132107971 cccgtgtggaaagagagaaggaaagaaacagaa-----gtggacaggaagag-------------------------tctcaaactgcagtgctgt-tcctctaagaGTCAGCCCTGCTGACTCT---TTCAAGGGGG-AAAAAAAAGCAGCTAAACTGGCTGAAGTAA-TCAAGAGG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128176224 141 - 133002572 cccatgtggaaggagagaaggaaggaaacagaa-----gtggacaggaggag-------------------------tctcaacctgcagtgctgt-tccaCTCAGGTTCAGCCCTGCAgactct---ttcaaggga--aaaacaaagcagctaaactggctaaagtaa-tcaagagg i rheMac2.chr14 C 0 C 0 s micMur1.scaffold_46107 2850 137 + 5307 ttc--atggagggacagagggcaggagagagga-----ctgcacaagaagaa-------------------------tcacaaatcgcagtgcagt-tccacagagcttcagccagcctgaCTCT---TCGGAGGGG----AAAAAAGtaattagactagctaaaatgg-tcaagaaa i micMur1.scaffold_46107 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 202261 137 - 1020051 -cagtgtgaaaggagagagagaagaacagagaa-----ttagacaggaaaag-------------------------tctgaaattgcaagaaaatgtcaagaaagttccaactaagctgaCTCT---TTCAAG-----TGAAAAGAGTAGCTAAACTAGC-AAAATAA-TCAAGAAA i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9677596 123 + 15951348 cattcgtggatggagaaggggaaggaaaaaaga-----tccaacaggaagag-------------------------t--------acag----gt-ccgtaaaagattcagtccggctaaCTCT---CTAGAAGGG-----AAAATGTTGTGAAACTAGCCAAAATAACTCAG---- i cavPor3.scaffold_42 C 0 C 0 s oryCun2.chrUn0985 37078 135 + 42081 CAGT-GTGGAGGGGGTGAGGGAGAGAAGGGGGAGGGGCTCGGGCAGGAAGAG-------------------------CTGCACCTGACAG--CACC-CCACGAAGGCTTCAG--CGGCTGCGTCT------GGAGGG-----GAGAAGTGGCTCTGCGGGCTGACGTTA-TCAGAGAG i oryCun2.chrUn0985 C 0 N 0 s bosTau4.chr29 48991731 126 + 51998940 tgtctctggaaggagag-aggAGCACCAGGGCC-----ACG--CAGGGTGGG-------------------------TCCCCCCCTGCAG-------CCAAGAAAGGGGCAACCAagctgacttt---ttggaggga-----aaaaggcaattaaaaccagcaaaatta----ggaaa i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28955657 156 + 33091231 cacctatggaaggagagaaggaagacagggggc-----g-----ggggtgggggggtgggggaccaggcagaaggaatctcaaacggcagcgccct-ccgagaaaggctgagcgaggctgacgCT-----GGAAGGA-----AAAAGGCAGTTGAACTCGCTaaaattg-atcaagaa i equCab2.chr12 C 0 C 0 s canFam2.chr18 7552194 128 - 58872314 -ACCTACGGAAGTGGGGCAGGAGGACCCACCGG-----G-----AGGATGGG-------------------------CCCCGTGTGG-------CT-CCAAGAACGATCCAGCCAGGAGGACTCTGGGGCGGAGGTG-----GGGAGGCAGTTAACACagctatatgaa-cccagaaa i canFam2.chr18 C 0 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I a score=14324.000000 s hg19.chr11_gl000202_random 30309 25 + 40103 AAAAGGGGATAAATGCATACACA------GG s panTro2.chr11 68217038 25 + 134204764 AAAAGGGGATAAACGCATACACA------GG i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126013455 25 - 132107971 AAAAGGGGATGAATGCATACGCG------AG i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128176365 25 - 133002572 aaaaggggatgaatgcatacgca------gg i rheMac2.chr14 C 0 C 0 s micMur1.scaffold_46107 2987 8 + 5307 caaaggga----------------------- i micMur1.scaffold_46107 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 202398 22 - 1020051 AACGGAGG---GATACATATACA------TA i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9677719 25 + 15951348 AAAAGAGGGCAAATATTTATGCA------TA i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48991857 29 + 51998940 aagagagaatatatacatacatatacaga-- i bosTau4.chr29 C 0 I 225 s equCab2.chr12 28955813 23 + 33091231 aaaagggagaataaacatgcaca-------- i equCab2.chr12 C 0 C 0 s canFam2.chr18 7552322 23 - 58872314 aaaggggagaatgcacatgcaca-------- i canFam2.chr18 C 0 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I a score=734421.000000 s hg19.chr11_gl000202_random 30334 431 + 40103 CATACACAGAGTAAGAg--------------------------------------------aatacaaatagagagatagcaacagacacagagagataagagcatcacaagagaatgctttgatc----ggctctatgcaaataagtttgtaaactcagatgaaaccag----ttcttcctggaaaaaaaaagaagtaagtcataaaa------cttaactctagaagagacagaaaaaaga--acaact----ccat-----------------c------accatt--aa-----aaaaaaa-----------------aaaaagttctta--------atccccctatcccaggccgaaacatcaccaggcca-gtaatttcacatgggagttccattgtcatttgagagaacaggagattttaataccatgtaagctgtttcaaggcatggaa--aaagtagaagagtttcaaaagtctttagaa------aaagctagtgtaacactgataccaaattcaataaagagaggacaaaaagttttaaaaggacca s panTro2.chr11 68217063 433 + 134204764 CATACACAGAGTAAGAg--------------------------------------------aatacaaatagagagatagcaacagacacagagagataagagcatcacaagagaatgctttgatc----ggctctatgcaaataagtttgtaaactcagatgaaaccag----ttcttcctggaaaaaaaaagaagtaagtcataaaa------cttaactctagaagagacagaaaaaaga--acaact----ccat-----------------c------accattaaaa-----aaaaaaa-----------------aaaaagttctta--------atccccctatcccaggccgaaacatcaccaggcca-gtaatttcacgtgggagttccatcgtcatttgagagaacaggagattttaataccatgtaagctgtttcaaggcatggaa--aaagtagaagagtttcaaaagtctttagaa------aaagctagtgtaacactgataccaaattcaataaagagaggacaaaaagttttaaaaggacca i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126013480 422 - 132107971 CATACACAGAGTAAGAg--------------------------------------------aatacaaatagagagatagcaacagac----agagataagactatcatgggagaatgctttgatc----ggctctatgcaaataagtttgtaaactcagatggaaccag----ttcttcctggaaaaaaaaag----aagtcataaaa------cttaactctagaagagacagaaaaaaga--actgct----ccat-----------------c------accatt---a-----aaaaaaa-----------------aaaaagttctta--------atccccctatcccaggccgaaacatcaccaggcca-gtagtttcacatgggagttccattgtcatttgagagaacaggagattttaataccacgtaagctgtttcaaggcatggaa--aaagtagaagagtttcaaaagtctttagaa------aaagctagtgtaacactgataccaaattcaataaagggaggacaaaaagtttaaaaaggacgg i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128176390 450 - 133002572 catacacagaataagag--------------------------------------------aatacaaat----agatagcaacagacacagagagataagagaatcacaagagaatgctttgatt----ggctctatgcaaataagtttataaactcagatgaaaccaa----ttcttccaggaaaaaaaaagaagtcaatcataaaa------cttaactctagaagagacagaaaaaaga--acaact----ccat-----------------c------accatt---a-----aaaaaaataaataaatacataaataaaaaattcttaatccc-ccatccccctatcccaggccgaaacatcaccaggcta-gtaatttcacatgggaattccatcgtcattggagggagcagaagattttaataccatgtaagctgtttcaaggcatggaa--aaagtagaagaatttcaaaagtctttagaa------aaggctagtgtaacattgataccaaattcaataaaaagagtacaaaaagtttaaaaaggaccg i rheMac2.chr14 C 0 C 0 s micMur1.scaffold_46107 2995 430 + 5307 -atacacagaataagaa--------------------------------------------aatgcaaatagagaaacatgaacagag----aaaattaaaagaatcatgagagaatgacttgatcagctagctctatgcaaccaaatttataaactgggataaaatggg----ttcttcct------aagaaaatgtaaattat-aaa------cttagccccagaagaaacagaaaaaaga--acaacc----caat-----------------t------accattttaa-----aaaaata-----------------gttaagttcttaaatca---atccacctgtcctgggcccaaacagcacgcggcca-gtgagttcacatggaaatcctaccataatttgagggaacagataattctaatagcatttaagttgtttctgggcacggaa--acagtagaagagcttcaaaagtgtttagaa------aaatatagtgcaacactagtaccaaattcaataaagatagtacagaaactttacaaactactg i micMur1.scaffold_46107 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 202420 485 - 1020051 CATATACAGAACAAAAAAATATTGGGTTGTCAAAAATGTGTCACGATTTTTCCAAAAACATaatataaatagagaaataacaacagaa----aaatgtga-agacccacaagaggatgcttcggtc----agctctatgcaaatatactcgtaaactttgatgaaatgaa----ttctttct------aagaaaatgcaaattataaaatattttctgaactccagaagagacagaaaataga--atgacc----catt-----------------ctattttaccatt--aa-----ggaaaca-----------------atgcagttcttgagtagaacttgcccttatcctgtgcccaaacagcaccaagcca-gtgagttcacataggaattctatcacagtttgag-gaacagatcattctagtatcatttaagctgttccagtgcatgaaaacaaaatagaagagtttcaaatgtctgtagga------aaagctagcacagcactgataccagattcaataaagactgtacaataaattttaaaaccacag i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9677744 411 + 15951348 CA-----------------------------------------------------------AATCAAAAT--AGAAATCATAACTTGG----AAAAGGGaaggaattacaa-aggatgtcttggtc----agctctgtgaaaatatatttgcaaatctggatgaaactca----ctct----------aagaatatttaaagtataaaa------c--aaccccagaaaagacaaacaaacca--acaacttaccccat-----------------t------gccact--at-----gcaagga-----------------aggaagttcatcaatag---atcccctcg-cttgtgctccaccagcaccaggaca-gagattttacatggaaattctatcacaaattcaggaaacagatacatctaatataattgaagctgtttcaggacatggga--aaagtagaagagcctcaaaagttcttgggaaaaaagaaaactaatgtaacactggaacaaaattcaataaagataggatgagcaattttaaaactacct i cavPor3.scaffold_42 C 0 I 1 s bosTau4.chr29 48992111 416 + 51998940 catggacagaataagac--------------------------------------------aatacaaatggagaaacatgaacagag----aaaatgggaagaaccac-gaagaatggtgtgatc----aactttatgccaatgaatctgtagacttggatgaaacaga----ttct----------aagaaactgcgaattagaaga------cttcaccccagaagagacagagaagagaaaatgacc----cagc-----------------t------accatg---a--------aaaa-----------------atgaccttctcaatcag---acagttctaggtcgtgccaaaactgcaccaggctgtgcggtttct---gggaattctaacagaattttaggggacagattattccaataccatttaaatggttccagggcatggaag-aagtagaaaagtctcaaaaaacctttagaa------aaagctagtgtaacactagtaccaaattcaataaagatagaagaa-aattttgaaaaccgtt- i bosTau4.chr29 I 225 I 40 s equCab2.chr12 28955836 423 + 33091231 catacacaagataagaa--------------------------------------------aatacaaagagagaaatatcgac--ag----caaatgaccagaaccataggaacacgctttgagc----aactctgtgcaaagaaatctatgaacttgggtgaaacggcttctttct----------aagaaaatgtaaattatagaa------cttaaccccagaagagacagaaaaaagaagatgacc----caat-----------------t------aacgtt---a-----aaaaata-----------------atgaagttcttaactag---atgcctctacgctgtgcaaaaactgtagcg-gccatgcggttccacgtgggaattctaacacggttttagggaaaatgtcgttccaataccatttaaactgttgcagactgtggaa--agacaagtaagctttcaaaaattgttagaa------cagactggtgcgacactgatacagaattcaataaagacaggacaa-aattttgaaaaccaca- i equCab2.chr12 C 0 I 1 s canFam2.chr18 7552345 436 - 58872314 cctattcagaatcagaa--------------------------------------------aatacaaatagaaaaatatcaacagag----aaaatgaatagacccacaagagtatgctttgatc----aactccatgcaaataaatgtgtaaacctggatgaaatgga----ttct----------aagaaaatgtaaattataaat------cttaactccagaagagacagaaaaaagaaaatgacc----caatcactctaataatgataat------aacaat---aataataataaca-----------------atgaggttcttaaatag---atagct-tattccatgccaaaacagcaccatgccatgcaacttcaca-agaaactctaatacaatgttagggaataagtcattccaatgccattttaactgttcc--attatgga-----acagttaaagattcaaaaatctttaaaa------aag-ctagtgtgacattgatactgaatttaataaagatagaacaa-aatttcaaaaacaaca- i canFam2.chr18 C 0 I 186 e loxAfr3.scaffold_159 937561 0 - 1045236 I a score=24238.000000 s hg19.chr11_gl000202_random 30765 45 + 40103 accaat-ctc--ttaagaaaat---t-----a-caaatttcta----aa--------------ataa---------------------------------------------------------------------------------------aatattac s panTro2.chr11 68217496 45 + 134204764 accaat-ctc--ttaagaaaat---t-----a-caaatttcta----aa--------------ataa---------------------------------------------------------------------------------------aatattac i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126013902 45 - 132107971 accaat-ctc--ttaagaaaat---g-----a-caagtttcta----aa--------------ataa---------------------------------------------------------------------------------------aatattac i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128176840 45 - 133002572 accaat-ctc--ttaagaaaat---g-----a-caaattccta----aa--------------ataa---------------------------------------------------------------------------------------aatattaC i rheMac2.chr14 C 0 C 0 s micMur1.scaffold_46107 3425 48 + 5307 accaac-ctc--ttaagactattaat-----a-taaaaatcta----aa--------------ataa---------------------------------------------------------------------------------------aatattaC i micMur1.scaffold_46107 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 202905 49 - 1020051 atcaat-ctc----atgaatattaat-----g-taaa-atctagaacaa--------------aaAA---------------------------------------------------------------------------------------AATATGAT i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9678156 48 + 15951348 accagc-ctc--ctgagaatgttaat-----t-caaaaatGtg----ga--------------ataa---------------------------------------------------------------------------------------aatattgc i cavPor3.scaffold_42 I 1 C 0 s bosTau4.chr29 48992567 157 + 51998940 acaaatcctaatttaaggacaaaaaccctcag-caaaatactg----aatcgaattgagaaacatagaaaatgattatacagtatgaccacatggcatttatcccaggaatgcagggttggtttgacatatgaaaatcgatcaacagaacatataatattgt i bosTau4.chr29 I 40 I 12 s equCab2.chr12 28956260 50 + 33091231 accgat-ctctcttaagaatatcaac-----g-caagaacctg----aa--------------atag---------------------------------------------------------------------------------------aatcttac i equCab2.chr12 I 1 C 0 s canFam2.chr18 7552967 59 - 58872314 accaat-ctctcttaagaatattagt-----gaaaaaaacctg----aa--------------ataga-----------------------------------ctaagca--------------------------------------------aacactat i canFam2.chr18 I 186 I 174 e loxAfr3.scaffold_159 937561 0 - 1045236 I a score=46892.000000 s hg19.chr11_gl000202_random 30810 33 + 40103 taaatactacagagtgatcga-----tagatgtaggaa s panTro2.chr11 68217541 33 + 134204764 taaatactacagagcgattga-----tagatgtaggaa i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126013947 33 - 132107971 taaatactacagagtgattga-----tagatgtagaaa i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128176885 32 - 133002572 TTAATACTACAGAGTGATTGa-----tagatatag-aa i rheMac2.chr14 C 0 C 0 s micMur1.scaffold_46107 3473 33 + 5307 TGAACACTGCAgatcacttga-----taaatgcagaaa i micMur1.scaffold_46107 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 202954 33 - 1020051 CGAACACTACAGATCACTTAA-----TACATGCAGGAA i tupBel1.scaffold_125018.1-1020051 C 0 C 0 s cavPor3.scaffold_42 9678204 33 + 15951348 taaacaccataggccattcca-----tagatgcagaaa i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48992736 34 + 51998940 taaa-accacaaattcaccccga---tagatgtgggga i bosTau4.chr29 I 12 C 0 s equCab2.chr12 28956310 37 + 33091231 caaacactacaaatcc-ttgtgagtatagatgcaaaaa i equCab2.chr12 C 0 I 3616 s canFam2.chr18 7553200 38 - 58872314 taaataccacaagttcatcacaagggtaggtgtggaag i canFam2.chr18 I 174 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I a score=34772.000000 s hg19.chr11_gl000202_random 30843 47 + 40103 aagcattgaacataatctaacatgctttcatgataagata---------------------------------------------------------------------------ttcagaa s panTro2.chr11 68217574 47 + 134204764 aagcattgaacaaaatctaacatgctttcatgataagata---------------------------------------------------------------------------ttcagaa i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126013980 47 - 132107971 aagcattggacataatctaacatgctttcttgatgaaata---------------------------------------------------------------------------ctcagaa i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128176917 47 - 133002572 aagcattgaacataatccaacatgctttcatgataaaaca---------------------------------------------------------------------------ctcagaa i rheMac2.chr14 C 0 C 0 s micMur1.scaffold_46107 3506 43 + 5307 aaggatttaacataatctgacatgttttcatgataaaaaa---------------------------------------------------------------------------c----ac i micMur1.scaffold_46107 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 202987 122 - 1020051 AAGCAGTGAACACAATCTAACATGCTTCCATAATAAAAAAAAATCAGTAAGGGGCCATCGGGTGGTGTGGAGGTTAAGGCGCTGGATCCCACATGGCCAGTTGCATGGTTCGAATCCCAGAC i tupBel1.scaffold_125018.1-1020051 C 0 I 168 s cavPor3.scaffold_42 9678237 42 + 15951348 aagcatttagc--aatct---attcttttgtattaataca---------------------------------------------------------------------------aacaaac i cavPor3.scaffold_42 C 0 I 5 s bosTau4.chr29 48992770 35 + 51998940 gaacatttaacaaaacat-------tttcaaaatgaaatc---------------------------------------------------------------------------ac----- i bosTau4.chr29 C 0 C 0 s canFam2.chr18 7553238 42 - 58872314 aagcatttaacaaaacataacactctttcatgatgaaaac---------------------------------------------------------------------------ac----- i canFam2.chr18 C 0 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e equCab2.chr12 28956347 3616 + 33091231 I a score=276170.000000 s hg19.chr11_gl000202_random 30890 226 + 40103 tcaataaaccaggagcagaagagaacttcctcaacctgataagagccatctatgaaa-------------------------------------ttcgtatctaacatcgtacttaatgaaaaaagaacaaacgccttcctcctaaaatcaagaacaagacaaggatgtctgctctcacc-cttccattcaacattgtactggaagttctagccagggcgattaggcaagacaatgaaataaaagacatcc---agatt-ggaaagga s panTro2.chr11 68217621 226 + 134204764 tcaataaaccaggagcagaagagaacttccttaacctgataagagccatctatgaaa-------------------------------------ttcgtatctaacatcgtacttaatgaaaaaagaacaaacgccttcctcctaaaatcaagaacaagacaaggatgtctgctctcacc-cttccattcaacattgtactggaagttctagccagggcgattaggcaagacaatgaaataaaagacatcc---agatt-ggaaagga i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126014027 226 - 132107971 tcaataaaccaggagcagaagagaacttcctcaacctgataagagccatctatgaaa-------------------------------------ttcatatctaacatcgtacttaatggaaaaagaacaaatgccttcctcctaaaatcaagaacaagacaaggatgtctgctctcacc-cttccattcaacattatactggaagttctagccagggcgattaggcaagacaatgaaataaaagacatcc---agatt-ggaaagga i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128176964 225 - 133002572 tcaataaaccaggagtagaagagaacttcctcaacctgataagggccatcta-gaaa-------------------------------------ttcatatctaacatcgtacttaatggaaaaagaacaagtgccttcctcctaagatcaggaaccagacaagggtatctgctctcacc-cttccattcaacattgtactggaagttctagccacggtgattaggcaggacaatgaaataaaaggcatgc---agatt-ggaaagga i rheMac2.chr14 C 0 C 0 s micMur1.scaffold_46107 3549 199 + 5307 tcactaaactag-----gaataaaacttcctata---aataaggg-cgtctatgaaa-----------------------------------agcccacctctgacaccacgtttagtggagagagactggctgccttcctccc-gggtcaggaacaaggca--ggtgtttgctctcac----------caa---------ggaagttctagccagggtgattaggcatggaaaagaaagaaaaggcatcc---ggtttaggaaaaaa i micMur1.scaffold_46107 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 203277 263 - 1020051 tcaaaaaaactagaatagaagagaacttccttga-cttataaaggacatctataaaagctcatagcctactggttaagggcatctataaaaaagctcacatttaacaacagacttaatggagaaagactgaatgtctggcccctaaggtcaagaacaaaatggggatgtcctctctcaccacttctgttcagcattgtactggagatgttagccagagcagttacacaaagaaaagaaaccagaggcatcc---aggct-ttaacaga i tupBel1.scaffold_125018.1-1020051 I 168 C 0 s cavPor3.scaffold_42 9678284 171 + 15951348 tcagcaaactaggaatggaagagaa------tggtctggtgaaaggtatttatgaaa-------------------------------------aacttacc---------------cggaaagaaaccaaataaatt-cacctaaactcagaaacaaaacaggattgtctgctcactctgcttct-------------------gttctcagcagggcaattaggcaaggacaagaaataaaag---------------ggaa---- i cavPor3.scaffold_42 I 5 C 0 s bosTau4.chr29 48992805 187 + 51998940 tcaacaaactaggagt-----ggaacttcttcaacatgttaagag-catctatgaaa-----------------------------------aactcacatctaacttca-acttaat-----------------------ctcgagatcagaaaaaagacaaag---------------actctggctcagcattgtattggaggttttagccagaacaataaagcgagaaaaagaaataaaatggtttcaggtaaac-atagaaag i bosTau4.chr29 C 0 I 1102 s canFam2.chr18 7553280 224 - 58872314 tcaacaaactagggatagaagggaacttcctcaaccttataagag-caactatgaaa-----------------------------------aattcaaatttaacatca-acttgat---aaaagaccggatggtttccccttaccattaggaacaagacaaagatatctgctctcggcactttgattcaacattttactggaggtcctagccagagcaattaggcaagggaaagaaataaaaggcatcc---taatt-ataagaga i canFam2.chr18 C 0 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e equCab2.chr12 28956347 3616 + 33091231 I a score=172190.000000 s hg19.chr11_gl000202_random 31116 144 + 40103 --agtaaaaac--tgtctgtatttgcagatgacatgatcttttatgcagaaaatcctaagaaacccactg------------------aaaaaactcttcaaactaataaatgagtccatcaatgtagctggaagcaagatcaatgtacaaaaattaattgtattt s panTro2.chr11 68217847 144 + 134204764 --agtaaaaac--tgtctgtatttgcagatgacatgatcttttatgcagaaaatcctaagaaacccactg------------------aaaaaactcttcaaactaataaatgagtccatcaatgtagctggaagcaagatcaatgtacaaaaattaattgtattt i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126014253 144 - 132107971 --agtaaaaac--tgtctgtatttgcagatgacatgatcttttatgtagaaaatcctaagaaacccacag------------------aaaaaactcttcaaactaataaacgagtccatcaatgtagctagaagcaagatcaatgtacgaaaattaattgtgttt i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128177189 143 - 133002572 --agtaaaaac--tgtctgtatttgcagatgacgtgatcttttatgcagaaaatcctaagaaacccactg------------------aaaaaactcttcaaactaataaacgagtccgtcgatgtaactggaagcaagatcaatgtac-aagattaattgtattt i rheMac2.chr14 C 0 C 0 s micMur1.scaffold_46107 3748 139 + 5307 --agtaaaa-------ctacatttacaaatagcatgatcttatatacagaaaatcctaaggaatctcatt------------------gaaaaaccattccaactaataaatgggttcatcaatgttgctggaaacaagatcaatgtataaaatttaattgaattt i micMur1.scaffold_46107 C 0 C 0 s tupBel1.scaffold_125018.1-1020051 203540 138 - 1020051 --aggaaagtcagtatttccattcacagacggcatgatctcatatataaa-----ctaaagattccactc-------------------agaactgattcagacta--agacagcctcaccaatatagctggaaacaagaccagcatatgaacattcattgtattt i tupBel1.scaffold_125018.1-1020051 C 0 N 0 s cavPor3.scaffold_42 9678455 121 + 15951348 --------------------------aaatgaaattattttatatatagaaaatcctaaagaatccacct-------------------aaaaactatttgaattaataaactagttaatcaacatagctagaaacaagattaatatacaaagactaattgcatgt i cavPor3.scaffold_42 C 0 C 0 s canFam2.chr18 7553504 147 - 58872314 ggaaatgaaac--tatctctgttcacagatgttatgttcttgtatacagaaaatagaaaggaatccacacatacaaaaacaaaacaaaacaaaacaatttgaactaataatttagttcatcaatgtggcaggagacaag-----------------cattgtattt i canFam2.chr18 C 0 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e equCab2.chr12 28956347 3616 + 33091231 I e bosTau4.chr29 48992992 1102 + 51998940 I a score=341926.000000 s hg19.chr11_gl000202_random 31260 437 + 40103 ctacacactggcagtgaactatctatctaaaaataaca-ttaa---aaaaatcccagcatgtgaggcaaggtataggcaaattagcttgatttagccattccacaatgtatccatatttcaaaacatcttgttgtgtaccataaatatacaca--attttgtttgtcaactta--ca-caataataaaaaaa-----tccaat--ggaaaaaaagaaaaagaaaacaaccccatttgtaatagcagcaaaaagaataaaacactcaagaataaactt----aaacaaatacagtacttgtacattaaaaactgcaaaacattattgaaatgaaagaaa--t---aaaagattacaatgaatgaaaagatattgcttgttcctgc-tcataaaa--tatcattgctgagaaggcgatactcctcaaattgatcttcaaattcaaagcaatctctatcaaaatccaa s panTro2.chr11 68217991 436 + 134204764 ctacacactggcagtgaactatctatctaaaaataaca-ttaa---aaaaatcccagcatgtgaggcaaggtataggcaaattagcttgatttagccattccacagtgtatccatatttcaaaacatcttgttgtgtaccataaatatacaca--attttgtttgtcaactta--ca-taataat-aaaaaa-----tccaat--ggaaaaaaagaaaaagaaaacaaccccatttgtaatagcagcaaaaagaataaaacactcaagaataaactt----aaacaaatacagtacttgtacattaaaaactgcaaaacattattgaaatgaaagaaa--t---aaaagattacaatgaatgaaaagatattgcttgttcctgc-tcataaaa--tatcattgctgagaaggcgatactcctcaaattgatcttcagattcaaagcaatctctatcaaaatccaa i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126014397 441 - 132107971 ctacacactggcaaaaaactatctatctaaaaataaca-ttaa---aaaaatcccagcatgtgaggtaaggcataggcaaattagcttgatttagccattccacaatgtatccatatttcaaaacaacatgttgtataccataaatatacaca--attttatttgtcaattta--ca-caataataaaaaaa-----tccaat--ggaaaaaaagaaaaagaaaacaaccccatttgtaatagcagcaaaaagaataaaacactcaagaataaacttaac-aaagaaatacagtacttgtacattaaaaactgcaaaacattattgaaatgaaagaaa--t---cgaagattacaatgaatgaaaaggtattccttgttcctgcatcagaaaa--tagcattgctgagaaggtaatactcctcaaattgatcttcagattcaaagcaatctctatcaaaatccaa i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128177332 429 - 133002572 ctacacactagcaatgaactatctatctaaaaataacatttaa---aaaaattccagcatgtgaggcaagacataggcgaattagcttgatttagccattccacaatgtatccatatttcaaaacatcatgttgtgtaccataaatatacaca--at----tttgtcaattta--ta-caataataaaaaaa-----tccagt--gtaaaaaa--aaaaagaaaataaccccattt---------gcaaaaagaataaaacactcaagaataaacttaac-aaagaaatacagtagttgtacattaaaaactgcaaaacagaaatgaaatgaaagaaatgt---caaagattacaatgaatgaaaatatattccttgttcctgcatcagaaaa--tagcattgttgaaaaggcaatgctccttaaattgatcttcagattcatagcaatctctatcaaaatccaa i rheMac2.chr14 C 0 C 0 s micMur1.scaffold_46107 3887 429 + 5307 ctatacactagccatgaa----caatctaaaaataaca-ttaagagaacaaccctagtatgcaaggtaatacatatgtgaattagcttgatttagccattccacaacgtctacatatctcgaaacatcgttttgtataccataaatatatgca--atcttgtttgtcaattaaagaa-taacgataagaaaagtgttcccgtt--gtataa----aaaagaaaaacaacctcatctgtcatagcagcaaaaggaataaaa---------------ttaac-aaagaaatgcaatactggcatgttaaacactgcaaggcatcgttgaaatgagagaaa--t---tagaagtctcagtaagtggcaagctattccttgtt-atgcatcagaacactcagcgttgctaagatggcaacactgctcaaactgagctgctgactcagagcaatctccatcaaaatcgga i micMur1.scaffold_46107 C 0 C 0 s cavPor3.scaffold_42 9678576 427 + 15951348 ctacacaacagaaatgaacaatct-----aaaataata---ag---aaaaaacctagtatgtgagataacatatattt--attaacccaatttagctgttctacattgtgtacatatttcaagaca---tgttatatattatagatgtatatagcacttcagttttcaattga--aagaaaTGATTTAAAAA-----TTCTATTCTTAAaaaaagaaaacaaaaacaatgttctttataaaagcagcaagaagaataaagtactt---aataaattt----aacaaagtgtaagacctgtatatgaaaagcctctaaaccttgctgaagtgaaataaa--t---aaaagatctcaac-aggggacagatattttttgttcatgcatgaaaaca--cagagctattaaaatgggactatttcccaaattgatctagggatCTATCATGGTTTTAGTCAGTGGCCCC i cavPor3.scaffold_42 C 0 I 227 s canFam2.chr18 7553651 274 - 58872314 ------------------------------------------------------ctatataccaggaatga-----------------------------------------------------------------------aaatctataaa------------tcaagtta--ca----tattacaaata-----tgtaat-----------------------------------------agcaagagaaagaaaatatttaagaagaaatttaacaaaaggagtttaagacttgtacactgaatgccgtaaaacattgtggaaatgtaagaaa--ttgaagaagacttaaataaatggtaaaatattctatgttcgtgcatcagatgatttaacattattaagatggagatagtcccctgcatgatttacagattcaatgtgatccttatcaaaatccaa i canFam2.chr18 C 0 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e equCab2.chr12 28956347 3616 + 33091231 I e bosTau4.chr29 48992992 1102 + 51998940 I a score=24639.000000 s hg19.chr11_gl000202_random 31697 56 + 40103 gttgagttttttgttgttgcagaaattgccaaggtgatcttttctttctttctttc s panTro2.chr11 68218427 55 + 134204764 gttgag-tttttgttgttgcagaaattgccaaggtgatcttttctttctttctttc i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126014838 36 - 132107971 gttgagttttttgttgttgcagaaattgccaaggtg-------------------- i ponAbe2.chr11 C 0 I 10 s rheMac2.chr14 128177761 37 - 133002572 gctgagttttttgttgttgcagaaattgccaagatga------------------- i rheMac2.chr14 C 0 C 0 s micMur1.scaffold_46107 4316 48 + 5307 gctgggcgttttgctgttgcagaaactgccgagctgactctgacattc-------- i micMur1.scaffold_46107 C 0 C 0 s canFam2.chr18 7553925 39 - 58872314 gtttgtttgtttgtt-ttgcagaaaataacaagctgatcg---------------- i canFam2.chr18 C 0 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e cavPor3.scaffold_42 9679003 227 + 15951348 I e equCab2.chr12 28956347 3616 + 33091231 I e bosTau4.chr29 48992992 1102 + 51998940 I a score=35704.000000 s hg19.chr11_gl000202_random 31753 91 + 40103 tttc----tttctttttttttttttttttgagacagagtttcactctgtcacccaggctgaattacagtggcatg--atctcagctcactgcaacct s micMur1.scaffold_46107 4364 52 + 5307 ------------------------atgtggacgcagaat---------------------aaccacaaTGACAGGCCATTTCAAGCCAGTGACACCT i micMur1.scaffold_46107 C 0 I 241 s rheMac2.chr14 128177798 76 - 133002572 -------------------tttattttttgagatagaacttcactctgtcacccagactggagtgcagtggtatg--atcttagctcactgcaacct i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126014884 91 - 132107971 tttc----tttcttttttttttttttttggagacagagtttcactctgtcacccaggctgaagtacagtggcatg--atctcagctcactgcaacct i ponAbe2.chr11 I 10 C 0 s panTro2.chr11 68218482 95 + 134204764 tttctttttttttttttttttttttttttgagacagagtttcactctgtcacccaggctgaagtacagtggcatg--atctcagctcactgcaacct i panTro2.chr11 C 0 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e cavPor3.scaffold_42 9679003 227 + 15951348 I e equCab2.chr12 28956347 3616 + 33091231 I e canFam2.chr18 7553964 0 - 58872314 C e bosTau4.chr29 48992992 1102 + 51998940 I a score=28666.000000 s hg19.chr11_gl000202_random 31844 67 + 40103 -------------------------ccaccacccgggtt--caagcgattatcctgcttcagcctcccgagtagctgggattacag-gtacctgc s panTro2.chr11 68218577 67 + 134204764 -------------------------ccacctcccgggtt--caagcgattatcctgcttcagcctcccgagtagctgggattacag-gtacctgc i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126014975 67 - 132107971 -------------------------ccaccttccgggtt--caagtgattatcctgcgtcagcctcccgagtagctgggattacag-gtgcctgc i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128177874 67 - 133002572 -------------------------ccacctcctggatt--caagtgattctcctgcctcagcctcccgagtagctgggattacag-gtgcctgc i rheMac2.chr14 C 0 C 0 s cavPor3.scaffold_42 9679230 86 + 15951348 ccaaaactgtaagaaataaaccttttcttctttcatgttgggaatcaggtattttgtcttaac---------aacaatgaataaagagtaactaa i cavPor3.scaffold_42 I 227 C 0 e micMur1.scaffold_46107 4416 241 + 5307 I e loxAfr3.scaffold_159 937561 0 - 1045236 I e equCab2.chr12 28956347 3616 + 33091231 I e canFam2.chr18 7553964 0 - 58872314 C e bosTau4.chr29 48992992 1102 + 51998940 I a score=24993.000000 s hg19.chr11_gl000202_random 31911 84 + 40103 caccacacccagctaatttttgtatttttagtagagatggagtttcaccatgttggccaggctggtctcgaactcctgacctca s ponAbe2.chr11 126015042 84 - 132107971 caccacgcccagctaatttttgtatttttagtagagatggggtttcaccatgttggccaggctggtctcaaactcctgacctca i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68218644 84 + 134204764 caccacacccagctaatttttgtatttttagtagagatggagtttcaccatgttggccaggctggtctcgaactcctgacctca i panTro2.chr11 C 0 C 0 s cavPor3.scaffold_42 9679316 65 + 15951348 gacaGGATCTAACCAATCTC--TCTTTTTAAAAAATtt----ttttacca-------------ggaatcaaactcatggcctcg i cavPor3.scaffold_42 C 0 I 193 e micMur1.scaffold_46107 4416 241 + 5307 I e loxAfr3.scaffold_159 937561 0 - 1045236 I e equCab2.chr12 28956347 3616 + 33091231 I e canFam2.chr18 7553964 0 - 58872314 C e bosTau4.chr29 48992992 1102 + 51998940 I e rheMac2.chr14 128177941 0 - 133002572 C a score=18190.000000 s hg19.chr11_gl000202_random 31995 72 + 40103 tgtgatccatccacctcggcctcccaaagtgctgggattacaggcgtgagccactgcacccggccatgattc s panTro2.chr11 68218728 72 + 134204764 tgtgatccatccacctcggcctcccaaagtgctgggattacaggagtgagccactgcgcccggccatgattc i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126015126 72 - 132107971 tgtgatccatccgcctcggtctcccaaagtgctgggattacaggcgtgagtcattgtgcctggccatgcttc i ponAbe2.chr11 C 0 C 0 e micMur1.scaffold_46107 4416 241 + 5307 I e loxAfr3.scaffold_159 937561 0 - 1045236 I e cavPor3.scaffold_42 9679381 193 + 15951348 I e equCab2.chr12 28956347 3616 + 33091231 I e canFam2.chr18 7553964 0 - 58872314 C e bosTau4.chr29 48992992 1102 + 51998940 I e rheMac2.chr14 128177941 0 - 133002572 C a score=21961.000000 s hg19.chr11_gl000202_random 32067 71 + 40103 taatagtcatatggacccagagtaaccaaagtgatcttgaaaaagaaaat---gtt-ggggggc-cacacttccaa s ponAbe2.chr11 126015198 72 - 132107971 taatagtcatatggacccagagtaaccaaagtgatcttgaaaaagaaagt---gttgggggggc-cacacttccAA i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68218800 71 + 134204764 taatagtcatatggacccagagtaaccaaagtgatcttgaaaaagaaaat---gtt-ggggggc-cacactttcAA i panTro2.chr11 C 0 C 0 s canFam2.chr18 7553964 73 - 58872314 tactgttcatacagacgcagaacagcccaa-caatcttaaaaagaaaaacacaatt-ggaagactcacaacttcc- i canFam2.chr18 C 0 C 0 e micMur1.scaffold_46107 4416 241 + 5307 I e loxAfr3.scaffold_159 937561 0 - 1045236 I e cavPor3.scaffold_42 9679381 193 + 15951348 I e equCab2.chr12 28956347 3616 + 33091231 I e bosTau4.chr29 48992992 1102 + 51998940 I e rheMac2.chr14 128177941 0 - 133002572 C a score=58766.000000 s hg19.chr11_gl000202_random 32138 142 + 40103 cggttccctctccacaggggacagatatagcagtggggttggccaggtgctggatgatgcccacagtta-acaggacaaaggaggacgcattgattctggaatgggga-atctattcccacacaaggcagcaagcccagggctg s panTro2.chr11 68218871 142 + 134204764 CGGTTCCCTCTCCACAGGGGACAGATATAGCAGTGGGGTTGGCCAGGTGCTGGATGATGCCCACAGTTA-ACAGGACAAAGGAGGACGCATTGATTCTGGAATGGGGA-ATCTATTCCCACACAAGGCAGCAAGCCCAGGGCTG i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126015270 142 - 132107971 CGATTCCCTCTCCACAGGGGACAGATATAGCAGTGGGGTTGGCCAGGTGCCAGATGACGCCCACAGTTA-ACAGGACAAAGGAGGACACATTGATTCTGGAATGGGGA-ATCTATTCCCACACAAGGCAGCAAGCCCAGGGCTG i ponAbe2.chr11 C 0 C 0 s micMur1.scaffold_46107 4657 132 + 5307 CTGGCCCCTCCCCACAGGGGACAGAGATAGCAGTGGGGTTGGCCAGGAGCCAGA-----CACACACTTAGGCAGAACAAAGGAGGACAGATTAATTCTGAGACGAGGAGAGACAATCCCACACAAGGTGACAAGCCC------- i micMur1.scaffold_46107 I 241 N 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e cavPor3.scaffold_42 9679381 193 + 15951348 I e equCab2.chr12 28956347 3616 + 33091231 I e canFam2.chr18 7554037 0 - 58872314 C e bosTau4.chr29 48992992 1102 + 51998940 I e rheMac2.chr14 128177941 0 - 133002572 C a score=67151.000000 s hg19.chr11_gl000202_random 32280 156 + 40103 actgtgaggacttgactagaacattgaacttgct--aca-agctgcagtaaccaagactg--gcaccggcatgaagatggacatagaggaatagaacaaaatagagtcagaaataaaccctcagattgacagccagttga-tttctgacaagggcaccaagg s cavPor3.scaffold_42 9679574 152 + 15951348 actggcagctcctgact------ttgaatttgtttacca-ggctgtaatcatcaaggatgcacccccagcacagcactgaacacagatcact--gccacagcacagtcagaaataaacccctagacttaaagccagttgg-tttttagcaagggtgctaaag i cavPor3.scaffold_42 I 193 C 0 s ponAbe2.chr11 126015412 156 - 132107971 ACTGTgaggacttgactagaacattgaacttgct--aca-agctgcaataaccaagactg--gcaccggcatgaagatggacatagaggaatagaacaaaatagagtcagaaataaaccctcagattgacagccagttga-tttctgacaagggcaccaagg i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68219013 156 + 134204764 ACTGTgaggacttgactagaacattgaacttgct--aca-agctgcaataaccaagactg--gcaccggcatgaagatggacatagaggaatagaacaaaatagagtcagaaataaaccctcagattgacagccagttga-tttctgacaagggcaccaagg i panTro2.chr11 C 0 C 0 s canFam2.chr18 7554037 131 - 58872314 ------------tgatt------tcaaacttgct--acacagctactgtaat-aagagtgcagccctggcatga-gacagac-taggggaatc-aacggaacag-------aataaagcctcacatttgcagcctcctgattttttgacaaggataccaaag i canFam2.chr18 C 0 I 1 e loxAfr3.scaffold_159 937561 0 - 1045236 I e equCab2.chr12 28956347 3616 + 33091231 I e bosTau4.chr29 48992992 1102 + 51998940 I e rheMac2.chr14 128177941 0 - 133002572 C a score=118934.000000 s hg19.chr11_gl000202_random 32436 362 + 40103 ccgttcgtcaagcaggtgggagctgttgttcgtcaccaggtgcagaggtcggagcgctgctgctggctgcatcttggtatcagagtcaccaagaaaatcacaaggcagtcaggcactggagggaa-aacatttcactcacatggaaaagggatggaacaagaccggtcagtggtaggcattggcccctcgtggcccagtgggtccctctcagcagccaatgcagggcagtcggcctgcaggcacctttcttgtgctggggtagaaggacctggttccctct-ccaca-ggggacaga------------aggggttggccaggtgccagatgattcacacagttagcaggacaaaggaggacgcattgattctggaa s panTro2.chr11 68219169 362 + 134204764 ccgttcGTCAAGCAGGTGGGAGCTGTTGTTCGTCACCAGGTGCAGAGGTTGGAGCGCTGCTGCTGGCTGCATCTTGGTATCAGAGTCACCAAGAAAATCACAAGGCAGTCAGGCACTGGAGGGAA-AACATTTCACTCACATGGAAAAGGGATGGAACAAGACCGGTCAGTGGTAGGCATTGGCCCCTCGTGGCCCAGTGGGTCCCTCTCAGCAGCCAATGCAGGGCAGTCGGCCTGCAGGCACCTTTCTTGTGCTGGGGTAGAAGGACCTGGTTCCCTCTCCCACA--GGGACAGA------------AGGNNGTGGCCCAGTGCCAGATGATGCACACAGTTAGCAGGACAAAAGGAGATGCATTGATTCTGGAA i panTro2.chr11 C 0 I 770 s ponAbe2.chr11 126015568 362 - 132107971 cctttGGTCAAGCAGGTGGGAGCTGTTGTTCGTCACCAGGCGCAGAGGTCGGAGCGCTGCTGCCGGCTGCATCTTGGTATCACAGTCACCAAGAAAATCACAAGGCAGTCAGGCACTGGAGGGAA-AACATTTCACTCACATGGAAAAGGGATGAAGCAAGACCGGTCAGTGGTAGGCATTGGCCCCTTGTGGCCCAGTGGGTCCCTCTCGGCAGCCCATGCAGGGCAGTTGGCCTGCAGGCACCTTTCCTGTGCTGGAGTAGAAGGACCCGGTTCCCTCT-CCACA-GGGGATAGA------------TGGGGTTGGCCAGGTGCTGGATGATGCACACAGTTAACAGGACAAAAGAGGATGCATTGATTCTGGAA i ponAbe2.chr11 C 0 C 0 s cavPor3.scaffold_42 9679726 348 + 15951348 tcatCTGTCCAGCAAGTGACCCTGGACACCTGTCA-CAGGAGCA-----CCGATCACTTCTGCCAGCTGTGTCTCGGCATCAGAGTCATTAAGGAAAATACA--GCAGCCAATCAAGGGAGGGGACAGTGTGTCACTCACATAGACA-------GAGTAAGATGACTTAGTGGTGGGCATCAGGTCCTGAGGTCACA--AAGTCCCTTCCAGAAGCCAGAGCAGGAGCGCTGCCTT----GCACCCTGCTGGTGCTGCAGGGGAAGGACCTGGTCCCTTCC-TCATATGGGGACAGAGATACACAGCAGTGGGGTCAGCCAGGTGCAAGGTGACACACACA-TAGGCAGAACAAAGGG----GCATTTGCTCAGA-- i cavPor3.scaffold_42 C 0 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e equCab2.chr12 28956347 3616 + 33091231 I e canFam2.chr18 7554168 1 - 58872314 I e bosTau4.chr29 48992992 1102 + 51998940 I e rheMac2.chr14 128177941 0 - 133002572 C a score=7282.000000 s hg19.chr11_gl000202_random 32798 144 + 40103 tgaggaatctattcccacacaagcggcaaggccagcgctgactgtgaggactcgactacttgatgagaaagtgtgccaggcccacagccctttctt-------agg---------------------tggc----------tgggcctggtcagactgcatgcagagactgccttcctg----aca s cavPor3.scaffold_42 9680074 100 + 15951348 --------------------AAATGACACATCCAGCACAAAATGTGGAGGCTCTGC------GTGAG----------GGACATCCAGTCC-------------ATG-----------------------------------TGGGTCAAA--AGACAGCACCACAGGACTGCCCTCTCATACCACT i cavPor3.scaffold_42 C 0 C 0 s ponAbe2.chr11 126015930 182 - 132107971 TGGGGAATCTATTCCCACACAAGCGGCAAGCCCAGTGCTGACTGTGAGGACTCGACTACTTGATGAGAAAGTGTTCCGGGCCCACAGCCCTTTCTGTCAGAAAAGGTTGTGGTCAGACAGCCTTTTCTGGCCGTCTCTGCATGGGCCTGGTCAGACTGAATGCAGGGACTGCCTTCCTG----ACA i ponAbe2.chr11 C 0 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e equCab2.chr12 28956347 3616 + 33091231 I e canFam2.chr18 7554168 1 - 58872314 I e bosTau4.chr29 48992992 1102 + 51998940 I e rheMac2.chr14 128177941 0 - 133002572 C e panTro2.chr11 68219531 770 + 134204764 I a score=19045.000000 s hg19.chr11_gl000202_random 32942 143 + 40103 cgatgtaatgagg--gagggac-ggctctccaacaaatgatgctcaacaatcggacatccacgtgcaaaagaaggaagctggaccccttccttagat----cacaga----------------------------cctaaata-taaaggttgaaattacaaaactcctataagaaaat s ponAbe2.chr11 126016112 141 - 132107971 TGAGGTaatgagg--gagggat-gtctctccaacaaatgatgctcaacaatcggacatccatgtgcaaaagaaggacgctggactccttccttagat------caga----------------------------cctaaatg-taagggttgaaattacaaaactcctataagaaaat i ponAbe2.chr11 C 0 C 0 s cavPor3.scaffold_42 9680174 173 + 15951348 CGGCATGAGGAGGCCCATGGAC-ACCTGTGCTGACCCAGAGCCTGAAGAGTtggacacccaaggtctaaagaatgaagctggatccctctcttgtgtcacccacaaaaatccactc-----ggttcctactgtagcctaaatgttaagagctgaagctataaaactcctagcagaaaat i cavPor3.scaffold_42 C 0 I 2267 s canFam2.chr18 7554169 159 - 58872314 ccacgcaggaggg--aaagaataaactttttaacaaacagtgccagaacgactggtatccacatgcaaaagattccagttggattccttccttgcatcatatagaaaaactcgctaaacagggatcctaga----cctagatg-tcagagctaacattgtaaaact------------- i canFam2.chr18 I 1 I 140 e loxAfr3.scaffold_159 937561 0 - 1045236 I e equCab2.chr12 28956347 3616 + 33091231 I e bosTau4.chr29 48992992 1102 + 51998940 I e rheMac2.chr14 128177941 0 - 133002572 C e panTro2.chr11 68219531 770 + 134204764 I a score=28144.000000 s hg19.chr11_gl000202_random 33085 325 + 40103 ctaagagtaggctaggcggggtggccacgcctgtaatcccagcactttgggaggatcacttgaggtcaggagttcgagaccagcctgggcaacatggtgaaaccctgtctctactaaaaatacaaaaattagccaggcgtggtggcgcatacctgtaatcccagctactctggaggctgaggcacaagaattgcttgaattcgggaggtggagtttgcagtgagctgagatcatgccactgcattccagcctgggtgacagagcaagactctgtgtcaaaaaagaaagagaaagaaagaaagtaagaaagaaagaaagaaggaag s ponAbe2.chr11 126016253 324 - 132107971 ctaagagtaggctaggcagggtggccatgcctgtaattccagcactttgggaggatcacttgaggtcaggagttcgagaccagcctgggcaacatggtgaaaccctgtctctactaaaaatacaaaaattagccaggcgtggtggcacatacctgtaatcccagctactccagaggctgaggcacaagaattgcttgaattcaggaggtggagtttgcagtgagctgagatcatgccactgcattccagcctgggtgacagagcaagaccctgtctcaaaaaaagaag-gaaggaaggaaagaaggaaagaaagaaagaaagaaa i ponAbe2.chr11 C 0 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e cavPor3.scaffold_42 9680347 2267 + 15951348 I e equCab2.chr12 28956347 3616 + 33091231 I e canFam2.chr18 7554328 140 - 58872314 I e bosTau4.chr29 48992992 1102 + 51998940 I e rheMac2.chr14 128177941 0 - 133002572 C e panTro2.chr11 68219531 770 + 134204764 I a score=29341.000000 s hg19.chr11_gl000202_random 33410 191 + 40103 gaaggaaggaaggaaggaaggaaggaaggaaggaagcaaggaaggaaggaaagaaagaaagaaaaagaaagaaagaaagaaagaaagaaagaaaagaaagaaagaaagaaaga--gggagggagaaagaaagagagaagaaagaaagagaaagaaagaaagagagaaagaaaagaaagaaaggaggaaggaag s ponAbe2.chr11 126016577 149 - 132107971 gaaagaaagaaagaaggaaggaaggaagaaggaaggaaaagaaggaaggaaggaaggaga-agaaataaagaaagaaaggaagaaagaaggaag-gaaggaaggaaagaaaga---------------------------------------gaaaaaaagaaatgaaagaaagaaag---gaaggaaggaag i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68220301 175 + 134204764 gaaagaaagaaagaaggaaggaaggaaggaagcaagcaaggaaggaaggaaagaaagaaagagaaagaaagaaagaaagaaagaaagaaagaaa-gaaagaaagaaagaaagaaagggagggagggag-------gaagaaagaa-------gaaagaaagagagaaaggaaagaaag---gaaggaaggaag i panTro2.chr11 I 770 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e cavPor3.scaffold_42 9680347 2267 + 15951348 I e equCab2.chr12 28956347 3616 + 33091231 I e canFam2.chr18 7554328 140 - 58872314 I e bosTau4.chr29 48992992 1102 + 51998940 I e rheMac2.chr14 128177941 0 - 133002572 C a score=204606.000000 s hg19.chr11_gl000202_random 33601 569 + 40103 aaagagaaagaaaagaaagaaaaaaagagaaagaaag--------ggaaaatctaagagtaaatc---------ttgatctagg-aaagccttcttagatacaacagcaaaagcacaagtaggaaaacacaaacagataaattggacttcatcaaaattaaaaacttttgtgctgcaaacaatatcatcaagaaagtgaaaacacaccctacagagtgggagaacaaaatgt-taagtcatatatctgataagggagtcatttctagaatatacaaagatctcttacacctcaacaataaaaagataaatcatccaacctagaaatgggcaattgaagagacattatatttgaatagacatttctcctaagaagatatacaaaat-gccagtaagcacatt-atagatgtctaac-atcatgagtttttacagaaatgcaagtcaaaaccgcaatgagatgataccacttcacacccactaggatggcttaaattaaaaagacagacaatagcaagtgttggcaaagatgtagagatattag-aacccccattcattgctggtgggaatggaaaatgatgcagccacttttt s panTro2.chr11 68220476 577 + 134204764 aaaaagaaagaaaagaaagaaaaaaagagaaagaaagaaggaaagGgaaaatctaagagtaaatc---------ttgatctagg-aaagccttcttagatacaacagcaaaagcacaagtaggaaaacacaaacagataaattggacttcatcaaaattaaaaacttttgtgctgcaaacaataccatcaaggaagtgaaaacacaccctacagagtgggagagcaaaatgt-taagtcatatatctgataaggaagtcatttctagaatatacaaagatctcttacacctcaacaataaaaagataaatcatccaacctagaaatgggcaattgaagagacattatatttgaatagacatttctcctaagaagatatacaaaat-gccagtaagcacatt-atagatgtctaac-atcatgagtttttagagaaatgcaagtcaaaaccacaatgagatgataccacttcacacccactaggatggcttaaattaaaaagacagacaatagcaagtgttgacaaagatgtagagatattag-aaccctcattcattgctggtgggaatggaaaatgatgcagccacttttt i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126016726 547 - 132107971 gaag-------aaagaaagaa------------------------agaaaatctaagagtaaatc---------ttggtttaggcaaaggcttcttagatacaacagcaaaagcacaagtaggaaaacgcaaacagataaattggacttcatcaaaattaaaaacttttgtgctgcaaacagtaccatcaagaaagtgaaaacacaccctacagagtgggagaacaaaatgt-taagtcatatatctgataagggagtcatttctagaatatacaaagatctcttacacctcaacaataaaaagataaatcatccaacctagaaatgggcaattgaagagacattatatttgaatagacatttctcctaagaagatatacaaaac-accagtaaacacatt-atagatgcctaac-atcatgagtttttagagaaatgcaagacaaaaccacaatgagatgataccacttcacacccactaggacggcttaaattaaaaagacagacaataacaagtgttggcaaagatgtagagatattag-aacccccatccattgctggtgggaatggaaaatgatgcagccacttttt i ponAbe2.chr11 C 0 I 2320 s canFam2.chr18 7554468 548 - 58872314 aaataaaattaaattaaattaaattaaaaactccaga--------agaaaatataagactaaatcctcaggatattgggttagg-caaaacttcttggatacaacaccaaaagcaagaa-aagaaaagaaaaataggtaaaccagacttcatcaa----aagactatttgtgttgcaaacactg-catcaaggaaatggaaatacaatctaaggaatgggaaaaagagatttctgaaacatatacctgataaggaatttgtttccagaatatataaagaactcctacaactcaacaat-cacagacaaaac-tccaatttagaaatgggcaa------------ggtgtttgggcagacgtttctccagaggagatgtaccaaatggtcagtaagcagatgaaaagacgcttgataatcatgggcccttagtgaaatgctaatcaaaaccaca---------------tacacactcactagagtggctcaaatgacaagaatggacaataacaagcaaaggtgagaaagcagagatgctggaaatcctcatccactgttggtgggaatgcaaaatggtgcagctgctttgg i canFam2.chr18 I 140 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e cavPor3.scaffold_42 9680347 2267 + 15951348 I e equCab2.chr12 28956347 3616 + 33091231 I e bosTau4.chr29 48992992 1102 + 51998940 I e rheMac2.chr14 128177941 0 - 133002572 C a score=366499.000000 s hg19.chr11_gl000202_random 34170 1007 + 40103 aaaacagtttggcaattcctcaaaatggtaaatgtagagttactatatgatccaataattttgatacccaagagaaatgaaaacatatgactacacaaaaacctttacatgaatatgcataacagcattattcataatactccaaaagcagaaacaacccagatgtctgtcaactaataaagtggaatattattcagccatgaaaaaagctggagtactgatgacacgttgcaacacggatgaagctcaaaatcactggctaagcaaaaagaagccagttactgaagagcacaaatggtgtaattccctttattgcagaat--------ag--gcaaatctgtagaggcagaaaatagattgcataaatgattgcctaggggtagagaaaggggaag-atgg-------------------------------ggagtgacta----taagggctatggggtgtgtttttggggtgatgaa-attgcctaaaattagactttggtcactttctacaactctgtgaatgtgtact-ttaaatgggttaattttataatatttaagttatcactcaataaagcCAT-------AGAAAGAAAAGGAAAAAAA-------------------------------------GGGTCAATTTTTCatatatatatatatatatataAAATCCATGACACAAAAATGG------ATAAATTTGACTATACAAAAATTGTCATATATTAATGGCAAGGGATTCTGCAATGTCAAAAGAAAATAACTATATAAAATACAAGCCACTCGTAGCATAGATTGAGGGCTAATTTCTCTAATGAAT-AAGAGCTTTTATGAATTGATGAAACCAAGCGCCAGTGAATCtggggtaggttatgcagcactcacaaaacagcccgcaaattgcagtggcttagaactgcaagggttt-tttctggcttggggtacgtgtctgtctagggtttgtggacattctctgctcgtc--aggtactcagggacccCATCAAACGTTGCCAGTCCACCACACCAGGTAGAAAAGAAAGAGCTCCAAGGGCCTCCAACCGTCCATTAAATGTTCAACCTGGTAGTGAAAC s ponAbe2.chr11 126019593 1001 - 132107971 aaaacaatttggcaattcctcaaaatggtaaacatagagttactatatgatccaataattttgatacccaagagaaatgaaaacatatgactacacaaaaacctatacatgaatatgcataacagcattattcataatactccaaaagcagaaacaactcagatgtctgtcaactgataaagtggaatattattcagccatgaaaaaagctggagtactgatgacacattgcaacacggatgaagctcaaaatcattggctaagcaaaaaggagccagttaccaaagagcacaaatggtgtaattccctttattccagaat--------ag--acaaatctgtagaggcagaaaatagattgcataaataattgcctaggggtagagaaaggggagg-atgg-------------------------------ggagtgactg----taagggctacggggtgtctttttggggtcatgaa-attgcctaaaattagactgtgttcactttgtacaactctgtgaatgtgtact-ttaaatgggttaattttataatatttcagttattgctcaataaagcCAC-------AGAAAGAAAAGGAAAAAAA-------------------------------------GGGTCAATTTTTCCTATATGTATAAAAA------AAATCCATGACACAAAAATGG------ATAAATTTGACTATACAAAAATTGTCATATGTTAATGGCAAGAGATTCTGCAATGTCAAAAGAAAATAACTATATAAAATATAAGCCACTCATAGCATAGATCGAGGGCTAATTTCTCTAATGAAT-AAGAGCTTTTATGAATTGATAAAACCAAgcaccagtgaatctggggtaggttatgcagcactcacaaaacagcccacaaattgcagtggcttagaactgcaagggttt-cttctggcttggggtacgtgtctgtctagggtTTGTGGACATTCTCTGCTTGTC--AGGTACTCAGGGACCCCATCAAACGTTGCCAGTCCACCATGCCAGGTAGAAAAGAAAGAGCTCCAAGGGCCTCCAACTGTCCATCAAATGTTCAACCTGGTAGTGAAAC i ponAbe2.chr11 I 2320 C 0 s panTro2.chr11 68221053 1034 + 134204764 aaaacagtttggcaattcctcaaaatggtaaatgtagagttactatatgatccaataattttgatacccaagagaaatgaaaacatatgactacacaaaaacctgtacatgaatatgcataacagcattattcataatactccaaaagcagaaacaacccagatgtctgtcaactaataaagtggaatattattcagccatgaaaaaagctggagtactgatgacacgttgcaacacggatgaagctcaaaatcactggctaagcaaaaagaagccagttactgaagagcacaaatggtgtaattccctttattgcagaat--------ag--gcaaatctgtagaggcagaaaatagattgcataaatgattgcctaggggtagagaaaggggaag-atggattgcctaggggtagagaaaggggaagatggggagtgacta----taagggctatggggtgtctttttggggtgatgaa-attgtctaaaattagactttggtcactttctacaactctgtgaatgtgtact-ttaaatgggttaattttataatatttaagttatcactcaataaagcCAT-------AGAAAGAAAAGGAAAAAAA-------------------------------------GGGTCAATTTTTCATATATATATGTATATA----AAATCCATGACACAAAAATGG------ATAAATTTGACTATACAAAAATTGTCATATATTAATGGCAAGGGATTCTGCAATGTCAAAAGAAAATAACTATATAAAATACAAGCCACTCGTAGCATAGATTGAGGGCTAATTTCTCTAATGAAT-AAGAGCTTTTATGAATTGATGAAACCAAGCGCCAGTGAATCtggggtaggttatgcagcactcacaaaacagcccgcaaattgcagtggcttagaactgcaagggttt-tttctggcttggggtacgtgtctgtctagggtttgtggacattctctgctcgtc--aggtactcagggacccCATCAAACGTTGCCAGTCCACCACACCAGGTAGAAAAGAAAGAGCTCCAAGGGCCTCCAACCGTCCATTAAATGTTCAACCTGGTAGTGAAAC i panTro2.chr11 C 0 C 0 s canFam2.chr18 7555016 1032 - 58872314 aacacagtctggcagttcctccaagcactaaacatagagttaccatatgacccagcacttccaatacccaagagaaacgaaatcatgt--ctgtgcaaaaactcatgcgtgcatggtcctaacagcattgtttgtaatagccccaaaccagaaacaacccaaatgttcatcaactggtaaaatggggcattgtccagccattcaaaggaatggagtactgat-ctgtgttatagtacagatggaactcaggagaattatgccaactgagagatgccagtagcaaaagaccacaaatggtacaattccatttgatccagaatttctatagagtcacaaatctattgagctagagagtagatt-----agtgggtgtctgaggttgggggtagggtaggaatag-------------------------------ggaatcactactatttggggccat---gtttccctttggggtgatgaagatattctaaaattagattgtggttactttgtgcaacgctgtgaatacacactattaaatgggtgaactttgtggtattttaattgtctctttaaaaagccatgaaaaaaAAAAAGGAAAGGagaaaaaaaatagagaagatctaaaaaaaaaaatgttttggagtaggcaaggccttcttacatatggaaaaa-a----aaatccatgagaaaaagcaagctgactataaagtcgactctataaaaattataatcttttaatggcaa---atgtcacaacatcaaaagaaaataac----taaactatttgtcgttcagttaatagatgaggagctactttccttaagtaatgaatagcatttacaaatcgataaaaaCACgtactaatcgatctaggatcggttttgcagta---acaacacaacgcccaaatcgtcgaggctccaaactacaatggtttacttctagctcataatgcatgtccatctaggtgctgcgggcatcctgcactcatcatagtcactcggggaccATCTCAAATGTTGCCAGTCTGCGGTGCCAGGCAGAAAA--------------------TGGTAGGTAATTCGATGCTCAACCTGGTAGTGACAC i canFam2.chr18 C 0 I 432 e loxAfr3.scaffold_159 937561 0 - 1045236 I e cavPor3.scaffold_42 9680347 2267 + 15951348 I e equCab2.chr12 28956347 3616 + 33091231 I e bosTau4.chr29 48992992 1102 + 51998940 I e rheMac2.chr14 128177941 0 - 133002572 C a score=66024.000000 s hg19.chr11_gl000202_random 35177 246 + 40103 Atttgtagttaccccatgtatatctgtatccctaggcagcaaagttaattgcaaacttttgaattgtatatacatggaaatataccatgtgctttcttcttattttatttcttttgagacaaagtcttgccctgttgcccaggctggagtgcagtggcacc--ctcagcacactggagtctccgcctcccaggttcaagcgattctcctgcctcagcctcctgagtagctgggactacaggtgcatgt s ponAbe2.chr11 126020594 248 - 132107971 AtttgtagttaccccatgtatatctgtatccctaggaagtaaagttaattgcaaacttttgaattgtatatacatggaaatataccatgtgCtttcttcttattttatttcttttgagacaaagtcttgctctgttgcccaggctggagtgcagtggcaccatctcggcacactggagcctccgcctcctgagttcaagcagttctcctgcctcagcctcctgagtagctgggactacaggtgcgtgt i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68222087 246 + 134204764 ATTTGTAGTTACCCCATGTATATCTGTATCCCTAGGCAGCAAAGTTAATTGCAAACTTTTGAATTGTATATACATGGAAATATACCATGTGCtttcttcttattttatttcttttgagacaaagtcttgctctgttgcccaggctggagtgcagtggcacc--ctcagcacactggagtctctgcctcccaggttcaagcaattctcctgcctcagcctcctgagtagctgggactacaggtgcatgt i panTro2.chr11 C 0 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e cavPor3.scaffold_42 9680347 2267 + 15951348 I e equCab2.chr12 28956347 3616 + 33091231 I e canFam2.chr18 7556048 432 - 58872314 I e bosTau4.chr29 48992992 1102 + 51998940 I e rheMac2.chr14 128177941 0 - 133002572 C a score=519970.000000 s hg19.chr11_gl000202_random 35423 1036 + 40103 caccacacctggctaatttttgtatttttagtagagatggggtttcaccatgttggccaggctggtctcgaactcctgacttcaggtgatccaccggccttggcctcccaaagtgctgggattacaggcatgaaccaccatgcccggcctaccaagtgtttttttctgttgtttagttt----tttgttttgctttgtttaacctaaccccctgttaccgacattcattccagttgtggctgcaccagtaattcactcatcgtcctggctgcatagtacccccaacggcatgaccacggctgtgtatccagccttctcccacttggttaatcccaagattttgctgttacaagca--------gagaacagccttgccatgacagcgtgctccggggactcactgggtcgcagcccacgtggctacttacagcccagtggtacctatttgtcttccaaagtgtgattccaatggacccagatccctccaccccgctctgcaggtaggatctccaggtgcttcccagcactattgtcaggcattgataaaggcagactcgtgacctttcagccgtctttttggtccgtctttttggtacaaaatggaatgcctttgtcgtgtgaattcgcctcccctaattactaatgagcatttcacctgctgaccggccacccaggcgtacccttctcagagatccctggtcaccttcttctgttccccttttctattaaattgCttttctttttttttttttttt---ctgagacagagtctcgctctgtcgcccagcctggagtgcagtggcatgatctcggctcactgcaacctctgcctcccaggttgaaatgattctcctgcctcagcctcccaagcagctgggattacaggcaagcgccatcacacctggctaatttttgtatttttagtagagacggggtttcaccatgttggtcaggctggtctcaaactcctgacctcgtgatccgcccgcttcggcctcccaaagtgctgggattacaggcgtgagccaccgcgcccggccTTAAATTGC s rheMac2.chr14 128177941 1034 - 133002572 caccacgcctagctaatttttgtatttttagtagagatggggtttcgccatgttggccaggctggtctcgaactcctgacctcaggcgatccacccgccttgggcccccaaagtgctgggatcataagcgtgagccaccgtgcctggccTACCATGTGTTTTTTTCCATTGTTCAGttttttgtttgttttgctttgtttaacctaaccccctgttaccgacatgcatgcaagtcgtggctgtgccagtcattcactcatgatcctggctgcatagcgcccccgacagcatgaccacaactgtgtatccagccttctcccgcttggttgatcccaagattttgctattacaagcagagccacggagaacagccttgccacgacacggtgctccggggaatcactgggtcgcaggccacgtggctacttacagcccagtggtacctatttgtcttctgaagtatgattccaatggaccctgatccctccaccccactccgcagataggagctccaggtgcttcccagcactatggtcaggcattgataagggcagactcgtgaccttttag-------------ccatc-ttttggcacaaaatgaaatgcccttgttgtgtgaattggcctcacctaattactaatgaggacttcacctgctggccagccacgcaggtgtacccttctcagagatccctgatcacctttttctgttccccttttctattaaattgcttttttttttttcttcttttt---ctgagacggagtctcactctgttgcccaggctggagtgcagtggcatgaactcagctcatggcaaccttcgcctcacaggttcaagtgattctcctgcctcagcctcccgagtagctgggattacaggcacatgccaccacgcccggctaatttttgtatttttagtagagacagggtttcaccatgttggtcaagctggtctcaaactcctgacctcgtgatctgcccaccttagcctcccaaagtgctgggattacaggcgtgagccaccgcgcccggccttaaattgc i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126020842 1020 - 132107971 caccacacctggctaatttttgtatttttaatagagatggcgtttcaccatgttggccaggctggtctcgaactcctgacttcaggtgatccaccagccttggcctcccaaagtgctgggattacaggcgtgaaccaccatgcccggccTACCAAGTGTTTTTTTCTGTTGTTTAGttt----tttgttttgctttgtttaacctaaccccccgttaccgacattcattcaagttgtggctgcaccagtaattcactcatcgtcctggctgcatagtaccccCAACGGCATGACCACGGCTGTGTATCCAGCCTTCTCCCACTTGGTTGATCCCAAGATTTTGCTGTTACAAGCA--------GAGAACAGCCTTGCCATGACAGCATGCTCCGAggactcactgggttgcaggccacgtggctacttatagcccagtggtacctatttgtcttccaaagtgtgattccaatggacccagatccctccactccactctgcagataggagctccaggtgcttcccagcactattgtcaggcactgataagggcagactcgtgacctttcag-------------ccatctttttggtacaaaatggaatgcccttgtcgtgtgaattggcctcccctaattactaatgagcatttcacctgctgaccggccacccaggtgtacccttctcacagatccctggtcaccttcttctgttccccttttctattaaattgctttttttttttttttttt------ctgagacagagtctcgctctgtcgcccagcctggagtgcagtggcatgatcttggctcactgcaacctccacctcccaggttgaaatgattctcctgcctcagcctcccaagtagctgggattacaggtaagcgccatcactcctggctaatttttgtattttcagcagagacggggtttcaccatattggtcaggctggtctcaaactcctgacctcgtgattcgcctgcttcggcctcccaaagtgctgggattacaggcgtgagccaccgcgcccagccttaaattgc i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68222333 1039 + 134204764 caccacacctggctaatttttgtgtttttagtagagatggggtttcaccatgttggccaggctggtcttgaactcctgacttcaggtgatccaccggccttggcctcccaaagtgctgggattacaggcgtgaaccaccatgcccggccTACCAAGTGTTTTTTTctgttgtttagttt----tttgttttgctttgtttaacctaaccccctgttaccgacattcattccagttgtggctgcaccagtaattcactcatcgtcctggctgcatagtaccccCAACAGCATGACCACGGCTGTGTATCCAGCCTTCTCCCACTTGGTTAATCCCAAGATTTTGCTGTTACAAGCA--------GAGAACAGCCTTGCCATGACAGCGTGCTCCGGGGACTCACTGGGTTGCAGCCCACGTGGCTACTTACAGCCGAGTGGTACCTATTTGTCTTCCAAAGTGTGATTCCAATGGACCCAGATCCCTCCACCCCGCTCTGCAGATAGGAGCTCCAGGTGCTTCCCAGCACTATTGTCAGGCATTGATAAAGGCAGACTCGTGACCTTTCAGCCGTCTTTTTGGTCCGTCTTTTTGGTACAAAATGGAATGCCCTTGTCGTGTGAATTGGCCTCCCCTAATTACTAATGAGCACTTCACCTGCTGACCGGCCACCCAGGCGTACCCTTCTCAGAGATCCCTGGTCACCTTCTTCTGTTCCCCTTTTCTATTAAATTGCttttctttttttttttttttttttctgagacagagtctcgctctgttgcccagcctggagtgcagtggcatgatctcggctcactgcaacctctacctcccaggttgaaatgattctcctgcctcagcctcccaagcagctgggattacaggcaagcgccatcacacctggctaatttttgtatttttagtagagacggggtttcaccatgttggtcaggctggtctcaaactcctgacctcgtgatccgcccgcttcggcctcccaaagtgctgggattacaggcgtgagccaccgcgcccggccTTAAATTGC i panTro2.chr11 C 0 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e cavPor3.scaffold_42 9680347 2267 + 15951348 I e equCab2.chr12 28956347 3616 + 33091231 I e canFam2.chr18 7556048 432 - 58872314 I e bosTau4.chr29 48992992 1102 + 51998940 I a score=78178.000000 s hg19.chr11_gl000202_random 36459 159 + 40103 TCTTTTATATCTTTT-----GAATTTCAAGCATGGGCACTACCTATTCAAAAACAAATGTAAAACACTGAATATATTATGGAGCTAATTGGACG-TTAGAGTCCCCCATGGGGTGGG----GTGGGTGA-----------TGTCATCATGCTGTGG------------CGTTCCCTAGGGACCTGGTCTCCA s panTro2.chr11 68223372 156 + 134204764 TCTTTTATATCTTTT-----GAATTTCAAGCATGGGCACTACCTATTCAAAAACAAATGTAAAACACTGAATGTATTATGGAGCTAATTGGACG-TTAGAGTCCCCCGTGGGGTGGG----GTGGGTG--------------TCATCATGCTGTGG------------CGTTCCCTGGGGACCTGGTCTCCA i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126021862 159 - 132107971 ttttttatacctttt-----gaatttcaagcatGGGAACTACCTGTTCAAAAACAAATGTAAAACACTGAATGTATTATGGAGCTAATTGGACG-TTAGAGTCCCCTGTGGAGTGGG----GTGGGTGA-----------TGTCATCATGCTGTGG------------CATTCCCCGGGGACCTGGTCTCCA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128178975 155 - 133002572 ttttttatatctttt-----gaatttcaagcatGGGCACCACCTATTCAAAAACAAATGTAAAACACTG----TATTATGGAGCTAATTGGACGTTTAGAGTCCCCCGTGGGGTGGG----GTGGGTGA-----------TGTCATCATGCCGTGG------------CGCTCCCCGGGGACCTAGTCTCC- i rheMac2.chr14 C 0 C 0 s cavPor3.scaffold_42 9682614 181 + 15951348 TCGTTCACATCTTTTTTGGGGGGGGTTAAGCAC-AGCATCGTGGACCCGGAAACAAACATCAAACACAGAGAGTCCTGCGGAGTGGAGGGGACT-CCAGAGTGGCTCGTGAGGTGGGCAGTGTGGGAGGGATGGGGGGCTGGTGAGTGTGTAATGGAGAGGGGCCAGTCGTGCCAGGAGGAGC--------- i cavPor3.scaffold_42 I 2267 C 0 e loxAfr3.scaffold_159 937561 0 - 1045236 I e equCab2.chr12 28956347 3616 + 33091231 I e canFam2.chr18 7556048 432 - 58872314 I e bosTau4.chr29 48992992 1102 + 51998940 I a score=55277.000000 s hg19.chr11_gl000202_random 36618 78 + 40103 CCCGGCCTCTGTCCTATCTCTGCTTTATTTTAACTTTCAAGGATGGATGTGACTTTCAGATGACTGATGGTTTCAG-AT s cavPor3.scaffold_42 9682795 59 + 15951348 CCTGACTTTTATCCCACTTC--------CTTAGCTTTCAGGCTCGAGTGTGTCTTGCTGATGACTTA------------ i cavPor3.scaffold_42 C 0 C 0 s rheMac2.chr14 128179130 78 - 133002572 CCCGACCTCTGTCCTATCTCTGTTTTATTTTAACTTTCAAGGACGGATGTGACTTTCAGATGACTGATGGTTTCAG-At i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126022021 76 - 132107971 CCCAGCCTCTGTCCTATCTCTG--TTATTTTAACTTTCAAGGGTAGATGTGACTTTCAGATGACTGATGGTTTCAG-At i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68223528 78 + 134204764 CCCGGCCTCTGTCCTATCTCTGCTTTATTTTAACTTTCAAGGATGGATGTGACTTTCAGATGACTGATGGTTTCAG-At i panTro2.chr11 C 0 C 0 s loxAfr3.scaffold_159 108425 76 + 1045236 CCTGGCCCTTGTCCTGGCTCC---TTTTTTCAACTTTCAAGCGTGGATTTGACTTCGAGGTGATTAGCGCCTTCAGCAT i loxAfr3.scaffold_159 I 1050 C 0 e equCab2.chr12 28956347 3616 + 33091231 I e canFam2.chr18 7556048 432 - 58872314 I e bosTau4.chr29 48992992 1102 + 51998940 I a score=106078.000000 s hg19.chr11_gl000202_random 36696 103 + 40103 -TTTTTTGCTCCTTTTTTTTTTTTTTT---------GACATTATCCCCGGATCTTTTC-AAAATAGTAATGACAGTAAAACAACAGAAAAGAACCATG------TCAGAATTCTGATCAC s panTro2.chr11 68223606 112 + 134204764 -ttttttgctccttttttttttttttttttttttttGGCATTATCCCCGGATCTTTTC-AAAATAGTAATGACAGTAAAACAACAGAAAAGAACCATG------TCAGAATTCTGATCAC i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126022097 110 - 132107971 -ttttttgctccttttttttttttttt--tttttttGGCATTATCCCCGGATCTTTTC-AAAATAGTAATGACAGTAAAACAACAGAAAAGAACCATG------TCAGAATCCTGATCAC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128179208 110 - 133002572 -tcttttgctccttttttttttttttt--cttttttGGCGTTATCCCCGGATCTTTTC-AAAATAGTAATGACAGTAAAACAACAGAAAAGAGCCGTG------TCAGAATCCTGATCAC i rheMac2.chr14 C 0 C 0 s cavPor3.scaffold_42 9682854 86 + 15951348 -------------TTATTATTATCTTT---------GGCATTGTCTCTGGATGTCTTC--AAATAGCAATGGCCCCAAAGCAGC----AACAACCACG------TCATAATCATGATTCT i cavPor3.scaffold_42 C 0 C 0 s equCab2.chr12 28959963 95 + 33091231 -TTTTTCGCtttttttttttttttttt------ttttGCCTTACCCCTGGATCTCTGC-CAAACAGTCATAACAGTAAAAGGTC-----ACAACCATG------------TCCTCACCGT i equCab2.chr12 I 3616 C 0 s canFam2.chr18 7556480 94 - 58872314 ------------ttctttctttttttc------tttTGCATTATCCCTGGATCTCTTT-GAAACCGTAATAACAGTACAAGA-------ACAATCATGGCAATCCCATAATTGTCATCAT i canFam2.chr18 I 432 I 173 s loxAfr3.scaffold_159 108501 113 + 1045236 TTCTACTGCCTCTTCTTCTTCTTTTCTTTTTTTGTTGGCATTAAGCCTGGATTTCTTTAAAAAGAGTAATAACAGTAAAGTAAC-AATAATAACAATG------CCGTAACCGTAGTTGT i loxAfr3.scaffold_159 C 0 C 0 e bosTau4.chr29 48992992 1102 + 51998940 I a score=42850.000000 s hg19.chr11_gl000202_random 36799 53 + 40103 CATCATTATTAA-ACACACAC---ATTC--CTTttcctt-caaccaatacggagcacctc s panTro2.chr11 68223718 53 + 134204764 CACCATTATTAA-ACATACAC---ATTC--CTTttcctt-caaccaatacggagcacctc i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126022207 53 - 132107971 CATCATTATTAA-ACGCACAG---ATTC--CTTttcctt-caaccaatacggagcacctc i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128179318 52 - 133002572 CCTCACTATTAA-ACGCACAT---attc--ctttccctt-caaccaataggga-cgcctc i rheMac2.chr14 C 0 C 0 s cavPor3.scaffold_42 9682940 55 + 15951348 CATCTTGGTTAATGGACACTG---attt--atttctcttccaacacacattgagcaccta i cavPor3.scaffold_42 C 0 C 0 s canFam2.chr18 7556747 57 - 58872314 CACCAGTATCAA-AAGTATGTGTAATTCG-TTTTTCCTC-CAACACATGTTGAGCGCCTC i canFam2.chr18 I 173 C 0 s equCab2.chr12 28960058 56 + 33091231 CCCTGTTATCAA-AAGTTCGCTT-ACTCG-CTTTTCCTC-CAATGACTGTCAGGCACCTA i equCab2.chr12 C 0 C 0 s loxAfr3.scaffold_159 108614 56 + 1045236 TACTATTATTAA-AGGTACATGT-GTTTATTTTTTCCTT-CAACAAACATTAAGCAACT- i loxAfr3.scaffold_159 C 0 I 578 e bosTau4.chr29 48992992 1102 + 51998940 I a score=184497.000000 s hg19.chr11_gl000202_random 36852 317 + 40103 ctatgtgccaggccccgatttaaaga----ctgcacataAGGATATTCCTGAGCTTTTGCTTCTTTT----TCTGAGCT-ACCTTAAGCATCCCTC-------------AAC-----A--CACACAT--TTCCCAGGGAGGCAGTGGC-AGCTCAGAGCTCAAAGCCGTAGAGGTTCTCAGGGCCTAGAGCCCGCGGAGGCGGAACCTCAA----AGCCG--TGTTCATGGACTCAGGGAATTTTC--------------AGGCTCTGCAGAGACAGT-CA--------GACTC-CCCGGCCC----------AAGCACCCA-GGG---TGTGCTGAAAGTTTAGATGTCACGTCCCTAAAACGTCAGCCTGTCTGTTTCCAGCCCAC----GCCGC s panTro2.chr11 68223771 317 + 134204764 ctatgtgccaggccccgatttaaaga----ctgcacataAGGATATTCCTGAGCTTTTGCTTCTTTT----TCTGAGCT-ACCTTAAGCATCCCTC-------------AAC-----A--CACACAT--TTCCCAGGGAGGCAGCGGC-AGCTCAGAGCTCAAAGCCGTAGAGGTTCTCAGGGCCTAGAGCCCGCGGAGGCGGAACCTCAA----AGCCG--TGTTCATGGACTCAGGGAATTTTC--------------AGGCTCTGCAGAGACAGT-CA--------GACTC-CCCGGCCC----------AAGCACCCA-GGG---TGTGCTGAAAGTTTAGATGTCACGTCCCTAAAACGTCAGCCTGTCTGTTTCCAGCCCAC----GCCGC i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126022260 317 - 132107971 ctatgtgccaggccccaatttagaga----ctgCACTTAAGGATATTCCTGGGCTTTTGCTTCTTTT----TCTGAACT-ACCCTAAGCATCCCTC-------------AAC-----A--CACACAT--TTCCCAGGGAGGCAGCAGC-GGCTCAGAGCTCAAAGCCGTAGAGGTGCCCAGGGCCTGGAGCCCGCGGAGGCAGAACCTCAA----AGCCG--TGTTCATAGACTCAGGGAATTTTC--------------AGGCTCTGCAGAGACAGT-CA--------GACTC-CCCGGCCC----------AAGCACCCA-GGG---TGTGCTGAAAGTTTAGATGTCACGTCCCTAAAACGTCAGCCTGTCTGTTTCCAGCCCAC----GCCGC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128179370 282 - 133002572 ctatgtgccaggccccgatttagagg----ctgCACTTAAAGATATTCTTGAGCTTTTGCTTCTTTT----TCTGAGCT-ACCTTAAGCATCCCTC-------------AAC-----A--CACACTT--TTCCCAGGGAGGCAGCAGC-GGCTCACAGCTCAAAGCCACAGAGGTGCCCAGGGCCTGGAGCTGGGGGAGGCGGAACCTTGG----AGCCG--TG-------------------TTC--------------AGGCTCCGCAGAGACAGT-CA--------GACTC-CCAGGCCC----------AAGCACCCA-GGG---TGTGCTGAAAGTTTAGAT----------------GTCAGCCTGTCTGTTTCCAGGCCCT----GCCGC i rheMac2.chr14 C 0 C 0 s cavPor3.scaffold_42 9682995 273 + 15951348 ctgcatgccaagccTCACTTGAGAGG----TCACAATGGAGG----------GTTTTCACGTATTTT----CCTGACAG-GACTCTTGC--CCCCC-------------AGC-----A--AGTACGTGGTTCCCAGCAAGG-ATTAGC-----CTGGGCCCAATGGAAGGGAGGC---------------CACGTGGAGGCCTCATCTACGGGTCAGCCT--CAGTCACGGCCT---------TCC--------------GGATACAGCAGAGAAACT-CAGTGTGCTGGTCTG-GCCGTCCCG---------GAACACCCACGGG---CAGGCTACAAGCTCAGAT------------------CTGTGTTCCTGACACCGGGCCTC-----TGGG i cavPor3.scaffold_42 C 0 C 0 s equCab2.chr12 28960114 312 + 33091231 CAACG--------------------ACGCGCTACACTTAAAG-TTTTCGGAATCTTTCGCCTCCTTT----TCTGACCTGACCCCAGGCACGTCCC-------------CAAGACACA--CACGCCT--TTCCCAGCGAGGGAGCAGCCCGTCACAAGCCTGGCG------------------CCCACAG-GGCAGGGGGCAGAGCGGGCA----GGGCAT-GGGCCGTGGCCT---------CTCCCGGGAAGGAGAAGCGG-CTTATAGAGAAAATGCA--------GATGC-TCCAGCCCAGCGGCCTCCGAACGCCCGGGGGGTTTGTGTTGAAAGTTCAGAGTTCACGTCCCTGAAAGGTCAGCCCATCTGTTTTCAGGCCCCGCTTGCTGC i equCab2.chr12 C 0 C 0 s loxAfr3.scaffold_159 109248 319 + 1045236 CTGTGTTCCAGGCATCGCTTTAGATG----TTGCACTCAGAG-ATTTCGGAATCCCTCACTTCTCTTCAGCTTTACCCTCACCCCTCACCACCACC-------------ATC-CACCC--CCCACCT--CCCCCAGTGAGGCA------GGCCTGGGGACAGAGG---------------AGAGTGACAACAGGGCTGGGCAGAGCT---G----GCTCG--CAGCCGTGGCTC--GGGAACTCGC----ACAGGAGATGTGCCTCCAT-GACATGGA-CA--------TAACC-CCCACCCT-GTAGCCTCCGGACACCCAGGGC---TGTAATGAAAGTTTAGAGCTCGTGTACCTGAAAGGTCAGCCCATCTGTTTTTAGACCCC----ACTGC i loxAfr3.scaffold_159 I 578 I 656 s canFam2.chr18 7556804 265 - 58872314 ------------------------------CTATGCTTAAAG-TTTTTGGCATCTTTCACTTCTTTG----TCC--CCTTGTCCCCTGCCCACCCC-------------CAC-CCCCA--CTCCCAT--TTCCTAGGGAGGGAGCAGC--------------------------------------------GGGGGAGGCAGAGCAGTGG----GGGTGG-GGGCCCTGGCCT---------TTC----AGTGGACACGTGGTCCTACAGAGAAGATGCA--------GATTCGCCCAGCCCAGCGGCCTCCCAATGCCCAGGGG---TGTGTTGGAAGTTTAGAGTTCGCGTTCCTGAAAAGTCAGTCCATCTGTTTTTAGGCCCC----TCTGC i canFam2.chr18 C 0 C 0 s vicPac1.scaffold_267604 73 307 - 845 ------------------------------CTCCACTTGAGG-TTTTCAGAACCTGTGGCTTCTCTT----TCTGATCCAGTCCCAGGCATCCTCCCAGCCCCATGGCCCAC-CCCCATCCTCACAG--TTCCCCACGAGTCGCCAGC-AGCC-CGAGCCCGACC------------------CCTCCAGCACCAGGAGGCAGCGCCGGCG----GCGCGCGCACCCGCAGCCT---------CTC----GCGGGAGATGTGCCTTTACAGAGAGGACGCA--------GACTCCTCCAGCCAGGCGGCCTCCGAACGCCCGGGGG---TGATTGGAAGTTTTAGAGTTCACGTTCCTGAAAAGTCAGTTCATCTGTTTTTAGGCCCC----GCCGC i vicPac1.scaffold_267604 N 0 C 0 s bosTau4.chr29 48994094 303 + 51998940 ------------CCTCAATTTAAAAA-------GAGACAAAT-TTTTCGGAATCTTTGGCTTCTTTT----CCCGACATAACCCCAGGCGTGCCCC--GCTCCCTGACGCGC-ACACA--CACACAT--TTCCCAGCAATACCCCAGC-AGCCATCAGCCTGACA------------------CCTACAGCTCAGGGAGGAGGAGCTGGTG----GC-----CTCCCCCAGCT--------------------GGAGATGAGGCTCCACAGACAAGACGCA--------GATTGCCCCTGCCCAGCAGCCTCCAAACTCCCATGGG---TGAGTGGAGAGTTTAGAGTTCACGTTCCTGAAAAGTCAGCCCATGCGTTTTCAGGCCCC----GCTGC i bosTau4.chr29 I 1102 C 0 a score=269348.000000 s hg19.chr11_gl000202_random 37169 306 + 40103 CCCAGGCTGGACTTTGGGAAGTTCTGAACAGC------CCCAGCT------TCGCTGCATTCCCC--AACTCCCTGCAACCCAGCGTAAACAACTCTGCA--------CTCAG--CCG---------CTTGGA------GAGGTTGCTAGGATATTATCGCT--TTGGGAAATGCAGGAACCAAGTTTGGAG----------------AGGCTGCACAGCAGAGGGAGGGGACACAGCTGCAAAGCGC-------CCATCC-TCCAGCCAGGCCCTCTGGGGGTTCGCCGGACCCTTGGG----TGCCCAGGGTCCGAGGCAGC---------------GCG---TGGCTCCCCAC------------------------------------------C--T-----------------------CCCCTGGC-ACCACCCACACCCCCTGG--CCTGTGTGC s panTro2.chr11 68224088 304 + 134204764 CCCAGGCTGGACTTTGGGAAGTTCTGAACAGC------CCCAGCT------TCGCTGCATTCCCC--AACTCCCTGCAACCCAGCGTAAACAACTCTTCA--------CTCAG--CCG---------CTTGGA------GAGGTTGCTAGGATATTATCGCT--TTGGGAAATGCAGGAACCAAGTTTGGAG----------------AGGCTGCACAGCAGAGCGAGGGGACACAGCTGCAAAGCGC-------CCATCC-TCCAGCCAGGCCCTCTGGGGGTTCGCCGGACCCTTGGG----TGCCCAGGGTCCGAGGCAGC---------------GCG---TGGCTCCCCAC------------------------------------------C--T-----------------------CCCCTGGC-ACCACCCAC--CCCCTGG--CCTGTGTGC i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126022577 304 - 132107971 CCCAGGCTGGACTTTGGGAAGTTCAGAACAGC------CCCAGCT------TTGCTGCATTCCCC--AACTCCCTGCAACCCAGCGTAAACAACTCTGCA--------CTCAG--CCG---------CTTGGA------GAGGTTGCTAGGATATTATCGCT--TTGGGAAATGCAGGAACCAAGTGTGGAG----------------AGGCTGCACAGCAGAGCGAGGGGACACAGCTGCAAAGCGT-------CCATCC-TCCAGCCAGGCCCTCCGGGGGCTCGCCGGACCCTTGGG----TGCCCAGGGTCCGAGGCAGC---------------GCG---TGGCTCCCCAT------------------------------------------C--T-----------------------CTCCTGGC-ACCACCCAC--TCCCTGG--CCTGTGTGC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128179652 302 - 133002572 CCCAGGCTGGACTTTGGGAAGTTCTGAACAAC------TCCAGCT------TCGCTGCATTCCCC--AACGCCCTGCGACCCAGCGTAAACAACTCTGCA--------CTCAG--CCA---------CTTGGA------GAGGTTGCTAGGATATTATCGCT--TTGGGAAATGCAGGCGCT-GGTGT-GAG----------------AGGCTGCACAGCAGAGCGAGGGGACACAGCTGCAAAGCGC-------CCGTCC-TCCAGCCAGGCCCTCCGTGGACTCGCTGGACCCTTGGG----TGCCCAGGGGCCGAGGCAGG---------------GCG---TGGCTCCCCAC------------------------------------------C--T-----------------------CCCCTGGC-ACCACCCAC--TCCCCGG--CCTGTGTGC i rheMac2.chr14 C 0 C 0 s cavPor3.scaffold_42 9683268 298 + 15951348 CTCAGGCTGTG-TCCAGGAAGTCCA--------------CCAG--------TAGATCTGGTCCTC--AG-ACCACACTGCTCAATGTAAACAACTCAGCAACT-TATCCACGG--CGC---------CTCGGGTCCCTCAGGGTCGCTGGGACACTGTCCCTG-CCGGGAGGAGGATCTGCCAAGTTGGGGGCCTGACCCGTGGCCTCAGGCCTCA---GAGAGTGATAGTTCATGGC-GCAGAG-GG-------CTGTCC-TCT-------CCGCCTGGGGTCTCAGGCCAGCTGCAGG----T-CCTAGAGGAGGAG-------------------------------CCCTAA------------------------------------------CTGT-----------------------GCCCTTGC-ACTGTCTCC--TCCCAGC--TTTGTGTGT i cavPor3.scaffold_42 C 0 C 0 s bosTau4.chr29 48994397 409 + 51998940 CCCAGGATCAACTTTTGGAAGCTCTGAACAACCATCTTCCCAGCTTTGAAATCGCCAAGTTCCCTCAAATGCCATAAAACTCAATGTAAACAGCTTTGCAACTCTAACCACGAGTGTGTCCCAGTCACCCCGA------GAGGTTGCTAGGATATTATCTCGGGCGGGGAAGTCTCTCCGCCAAGTCTGAAG----ACCAACAGCG--TGGTTTCACAGCACAGAAAGTGGACGGATCCGCACGGAACAAATGTCCTGTCC-TCCAGCCAGCCCT-CCCGGGGCATCTGGCCCTTCTGGG----TGCCCACAGGATGACGCAGC---------------AGAACTCGGCTTCCC-G-------------AATTCCAGGGTGGGCTTGGCTGTGGGTCCC--TGGGGGAAAGGCCCCCAAGCTGTATCCCTTGC-ACTGCCCCC--TCCAGCC--CCTCCACCC i bosTau4.chr29 C 0 I 4 s vicPac1.scaffold_267604 380 405 - 845 CCCAGGATCAACTTTTAGAAGTTCAGATCAACCATCCTCCCAGCTTTGAAATTGCCAAGTTCTCTTAAATGCCATAAAACCCAATGTAAACAACTTTGCAACTCTGGCCACGG--GTGTCCCCGTCACCCCGA------GAGGTTGCTGGGACATTATCTT-GGCTGGGAAGTCTATCCGCCAAGTTCGAAG----ACCAACGGCG--AGGTTTCACAGCAGAGAAAGTGGACGTGTCTGCAAAACACGAATGCCCCGTGC-CCCAGCCAGCGCT-CCCAGGGTGTCTGGCCCTTTTGGG----TGCC--CAAGAGGACGCAGC---------------GGGGCACGGCTTCCCTG-------------TCTACCAGGGTGGGCTTGGCTGTGGGCTCC--T-GGGGAATCGCCCCCAAGCTG--TCCCCTGCTGCTGCCCCC--CCACCCCGTCCTGCATTC i vicPac1.scaffold_267604 C 0 N 0 s equCab2.chr12 28960426 400 + 33091231 CCCAGGAGCGACTTCTGGACCTTCTGAGCAGCCATCCCCCCAGCCTGGCAAGAGCCAAGTTCTCTCAAATGCCATAAAACTCAATGTAAACAACTCAGCGGCCCAAACCGCGG--GTGTCCCTGGT-CCCCCC------GACGTTGCTAGGATATTATCTCCGCC-GGGAAGTCTCCCCGCCAAGTTTGAAG----ACCCACGGCG--T-GTTCCGCAGCAGAGAAAGTGGACGTGTCTGCAAAGAATGAACGCGCCGTGCTCCCAGCCGGCCCTCCCCGGGGTGTCCGGCCCTTCTGGG----TGCA-GTAGGACGTGGCAGG---------------GC----TGGCTTCCCTGACTTCTGGGGTCGGCC-------------CAGCTGTGGGATCC--T-GGGGGAAGGACCCCAAGCTGT-CCCCTTGC-ACTGCCTAC--TCCCTAC--CCTGTGTGC i equCab2.chr12 C 0 C 0 s canFam2.chr18 7557069 365 - 58872314 CCCAGGAGCGACTTTTGGAAATTCTGAACAACCATCCTCCCAGCTTCAAAATAGCCAAGTTCTCTCAAATGCCATAAAACTCAATGTAAACAGCTTTGCAACTCTAGCCACGG--GTGTCCGGGTT-ACCCGA------GAGGTTGCTAGGATATTATCTCTGCCGGGGAAGTTTATCCGCCAAGTTTAAAG----ACCAACAGAG--TGGTTTTGCAGC----AAAGTGGACGTATTTGCAAAGAACGAGTG---------------------------------CCAGCCCTTCTGGGTGCCTGCA-GAAGGATGTGGCAGGCGTGGCCGCCCTCACCG----TGGCCTGCCCG-------------------------------GCTGCAGGAT-C--T-GGGGGGAGCAGCTGCAGCTGT-CCCCTTGG-GCTGCCCCC--TCCCTGT--CCTGCTTTC i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 110223 359 + 1045236 CCCAGGGTCAACTTTTGGAAGTCGTGAACAATGATCATTCCAGCTCCTAAACAGCCTCATTCTCA--AATGCCATA-AACTCAATGCAAACAGCTTTGTGACTCTAACCGTGA--GTGTCCCCGTG-TCCCCA------GAGGTTGCTAGGATATTATCTCTG-CCCGGAAGTGGATCCGCCAAGTTTAAAG----GCCTGCAGAG--GGGTCTCGCAGCAGAGGAGCTAGACAGAGCTGCAAAGAGTGC-----CCACCCTTCCAGCCAGCCTCCCC---AGCCCAGGGTGCCCTTCTG----TGCA-------------AGC---------------A-----TCTCTTCCCAC--------------CACTCAGGCAGGGCCCAGCCCAGAACC-C--T-GGGG----------GAGATGGACCCTGGGC-ACTCCCCGG--TCCCTGC--CC------- i loxAfr3.scaffold_159 I 656 C 0 a score=351484.000000 s hg19.chr11_gl000202_random 37475 250 + 40103 ---------TGTGAGAAGGGGTCACTCAGTTCTGGGAGAGCCCGTGG-ATAGCCGAGGCCTGGGCGCTGGGCAGACTCCCAGGCTCGTTA----GCGTGGCCATCCCTGGC-GTATTTCCGGCCACAGTGCGAGAATGGGGAATGTTCTCTTTCAT--------------------GGGCAGTGA-CCCCAGGATTTGCCATTTCT--T-ATGTTTAAAGCTTGCGTTGATGGTCTGGCTGCCACCAACATTCTTCC-CCCAGAGATAATGAAGTACAAAAGCCGGATGA s panTro2.chr11 68224392 250 + 134204764 ---------TGTGAGAAGGGGTCACTCAGTTCTGGGAGAGCCCGTGG-ATAGCCGAGGCCTGGGCGCTGGGCAGACTCCCAGGCTCGTTA----GCGTGGCCATCCCTGGC-ATATTTCCGGCCACAGTGCGAGAATGGGGAATGTTCTCTTTCAT--------------------GGGCAGTGA-CCCCAGGATTTGCCATTTCT--T-ATGTTTAAAGCTTGCGTTGATGGTCTGGCTGCCACCAACATTCTTCC-CCCAGAGATAATGAAGTACAAAAGCCGGATGA i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126022881 271 - 132107971 ---------TGTGAGAAGGGGTCACTCAGTTCTGGGAGAGCCCGTGG-ATAGCTGAGGCCTGGGCGCTGGGCAGACTCCCAGGCTTGTTA----GCGTGGCCATCCCTGGC-GTATTTCCGGCCACAGTGCGGGAATGGGGAATGTTCTCTTTCATGTCTCTTCTCGGTGCCGCCAGGGCAGTGA-TCCCAGGATTTGCCGTTTCT--TAATGTTTAAAGCTTGCGTTGATGGTCTGGCTGCCACCAACATTCTTCT-CCCAGAGATAATGAAGTACAAAAGCCGGATGA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128179954 269 - 133002572 ---------TGTGAGAAGGGGTCACTCGGTTCT-GGAGAGCCCGTGG-ATAGCTGAGGCCTGGGCGCTGGGCAGACTCCCAGGCTCGTTA----GCGCGGCCATCCCGGGC-GTATTTCCGGCCACAGTGCGGGAGTGGGAAGTGTTCTCTTTCATGTCTCCTCTCGGTGCCGCCAGGGCAGTGA-CCCCAGGATTTGCCGTTTCT--T-ACGTTTAAAGCTCGCGTTGATGGTCTGGCTGCCACCAACAGTCTTCC-CCCAGAGATCGTGAAGTGCAAAGGCCGGATGA i rheMac2.chr14 C 0 C 0 s cavPor3.scaffold_42 9683566 233 + 15951348 ---------T-------GGGGCCACGACGTCCTGGGAGAGGTCTCAG---GACCCAGGCC-AGGCGCTGGGCACATGCCAAGTCTCATTA----GCACATC--TTCCCAGG-GTGTCTGCAGGCA-AACGCAGGAACTGAAAG-GCTCCCTTTCATGTCTCTTTTCCGTGTCACA-GGGTAGTGA--CCCAGGATGAGCTGTTTCT--G-ATGTTTAAAGTT----------GTTTG-----------TATCCTTTC-CTCAGAGATAATGGAGTAAAAAGGCCAGATGA i cavPor3.scaffold_42 C 0 N 0 s bosTau4.chr29 48994810 254 + 51998940 ---------AGCGAGCACAGGTCACTCAGTCCTGGGAGAGACTGCAGGGTGGCCGTGGTCAGGGCGCTGGGCAGACCCCAAAGCTTCTGA----GCGCGGCCACCTCGGGCTG--TCTCTGGCCACAGTGCGAGAACGGGGGTTGTCCTCC--------------CCGTGCCG-TGGGACAGCGA-TCCCAGGATTTGCCGTTTCT--C-ATGTTGAAAGCGCATGTTGATGATCTGAC-TCCATCAGTGTTCTTCC-CCCAGAGACAGAAGAGGAGCAGGGCAAGATGA i bosTau4.chr29 I 4 C 0 s equCab2.chr12 28960826 228 + 33091231 ---------TGTAAGAGTGGACCCCCCAGGCCTGGGAGACACCGTGGGACGACCAAGGCCAGGGTACTGGACAGACTCCAAGACTCATTATAATGCACAGCCACCCTGGGCCGTATTTCCGGCCACAGTGTGGGAATGGGGCATG---------------------------ACCGAGGCAGCGA-TCCCAGGATTTGCCATTTCT----------------CATGTTGATG--------GTTGTCAGCTTCCTTCC-CCCAGAGACAGAGAAGTAAGAAGTCCAGATGA i equCab2.chr12 C 0 C 0 s canFam2.chr18 7557434 257 - 58872314 -----------TCAGAATGGGTCACCCAGCCCTGGGAGAGCCTGCAGGACGGCCATGGCCGGGGTGCTGGGCGGACTCCAAGACTTGTTA----GCACAGCCACCCCGGGATGCATTTCTACCCACAGTACAGGAATGGGGGATGTCCTCT--------------CCTTGTCACCAGGACAACAA-GCCCAGGATTTGACATTTCTCTC-ATATTGAAAGCCCACACTGATGGCCTGACTGCCATTAGCCTTTTTCC-CCCGGAGATAGTGAAGTCAAAAGGCC-GATGA i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 110582 273 + 1045236 TACCCCCACCATGAGAATGGGTCACCCTGGGCT-GGAGAGACCACGGGGTGTCTGGGGCCAGGACGCTGGGCAGCTGCCAAGGCTCATTA----GCACAGCCATGCTACACTGTCATTCTGGCCACAGTGCTGGGAT-------GTTCTCCTTCATGTGGACattcagtgtgtccggggcagggacccccaggactta-catttct--C-GTGTTTGAAGTCTG-GGAGAAGGCCTTGTTGCCATGAGCATTCTTCCTCCTGGAGACAGGGACATAAAAAAGCCGGGTGG i loxAfr3.scaffold_159 C 0 C 0 a score=200266.000000 s hg19.chr11_gl000202_random 37725 370 + 40103 ATGTGAGCTGGGGA--CCCAGAGCACCC---AAGGA-----AGGACAAGGGAACTCAGAAGAGCGGTCACTGCCCATCCCCTCCCT--GGCTGTGCCTGGTCTGAGGGGCTCC-----------AGGGCAAATCTTTCCC----------ATTCTCCGC----------------------------AGGTGCTTCCTCGGAGCCTGCA--------------CACGCACCTGG--------------CCCTTCTCCCTGGGTTGTCT---------TCCATCCACCCCAAAGCCTGTGTCCACTGGGCAGGTGGAACTTCTGCTTAGGAACCTGCCCAAAGTGGGAGGAAGCTGCCCCCTGTCG-CCCCCATGACAGCAGGGACCACACTAGGCTGCAGCTGCCCCTGG-----TCTTGACTCTGT-CCCCCTGACATGAGCTCTTCCTGC--ACGCTTCAATTTAT-ATTCTCCTT s panTro2.chr11 68224642 370 + 134204764 ATGTGAGCTGGGGA--CCCAGAGCACCC---AAGGA-----AGGACAAGGGAACTCAGAAGAGCGGTCACTGCCCATCCCCTCCCC--GGCTGTGCCTGGTCTGAGGGGCTCC-----------AGGGCAAATCTTTCCC----------ATTCTCCGC----------------------------AGGTGCTTCCTCGGAGCCTGCA--------------CACGCACCTGG--------------CCCTTCTCCCTGGGTTGTCT---------TCCATCCACCCCAAAGCCTGTGTCCACTGGGCAGGTGGAACTTCTGCTTAGGAACCTGCCCAAAGTGGGAGGAAGCTGCCCCCTGTCG-CCCCCATGACAGCAGGGACCACACTAGGCTGCAGCTGCCCCTGG-----TCTTGACTCTGT-CCCCCTGACATGAGCTCTTCCTGC--ACGCTTCAATTTAT-ATTCTCCTT i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126023152 386 - 132107971 ATGTGAGCTGGGGA--CCCAGGGCACCC---AGGGA-----AGGACAAGGGAACTCAGAAGAGCGGTCACTGCCCACCCACTCCCACGGGCTCTGCCTGGTCTGAGGGGCTCC-----------AGGGCAAACCTTTCCC----------ATTCTCCGC----------------------------AGGTGCTTCCTAGGAGCCTGCA--------------CACGCACCGGGTGTGTGCACACGCACTCTTCTCCCTCGGTTGTCT---------TCCGTCCACCCCAAAGCCTGTGTCCACTGGGCAGGTGCAACTCCTGCTTAGGAACCTGCCCAAAGTGGGGGGAAGCTGCCCCCTGTCG-CCCCCATGACAGCAGGGACCACACTAGGCTGCAGCTGCCCCTGG-----TCTTGACTCTGT-CCCCCTGACATGAGCTCTTCCTGC--ACACCTCAATTCGT-ATTCTTCTT i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128180223 353 - 133002572 ATGTGAGCTGGGGA--CCCAGGGCACCC---AGGGA-----AGGGCAAAGAAACCTAGAAGGGCGGTCACTGCCTACCCCTTCCCC--GGCTGGGCCTGCTGCGAGGGGCTCC-----------AGGGCAAACCTGTCCC----------ACTCTCCGC----------------------------AGGCGCTT--------------------------------CATCGAG--------------CCCTTCTCCCTGGGTTGTCT---------TCCATCCCCCCCAAAGCCTGTGTCCACTGGGCAGGTGCATCTCCTGGTTAGGAGTCTGCCCAAAGTCGGGGGAAGCTGCCCCCTGTCACCCCCCACGACAGCAGGGACCACATTAGGCTGCAGCTGCCCCTGG-----TCTTGGCTCTGT-CCCACTGACATGAGTTCTTCCTGC--ACACCTCAATTCCT-ATTCTCTTT i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48995064 347 + 51998940 ACGTGTGCTGGGGA--GTAAGAGTGCCCCCGGGGGAGTAGGGGGACAATGATGCCCGGCAGGGCTGTC--------TGAGCCCGTG--GGAGGGGGCTTTTTTCCTCTTCCGT-------------------------------------CTTCTCAGCTCAGACACGTGG--GTTCACCCATCCAGTAGTGACTCCCCAGGGCCTTTG--------------CGTACTCTATG--------------CCCTC-TGCCCTGGTTGTCC----------TGGCCCACCCCAAAGCC-ACGTCCCGGGGT--GATCCAGGTC--------------------------AGGAGGCCGCCCTCTGAGA-CCCCCAGGGCAGCAGGGGCCATGTCAGGATGTCACTGGCCAGGG------CTTGGCTC----CCCAGCAACAGGAGCCTTTCCTGCCTGGGTTTCAGTTCTT-ACTCTGTTT i bosTau4.chr29 C 0 I 461 s equCab2.chr12 28961054 360 + 33091231 ACACAGGCTGGGGA--CCTGGGATGCCC---AGGGA-----GAGATAAGGGTGCCCAACAGAGAAGTC-------ACACGCTCCCA--GGCTGGGCCTGATCCCAAGGCCCCA-----------GAAGGGGCCCCTCCCTCTTCCA---GCTTCTCC-CTCGGACGGATGGGCGTTAACCcacctcggggtcactcctcagggcctttg--------------cacatgctata--------------ccatt-gggctggtctgtcc----------tggcccactccAAAGCC-GCTCCCAGGGGGCAGAGCCAGCTTCTTGTA-------------------GTAGAGGCTGCCCTCTGTGA-CCCCCGGGAGAGCAGGGACCACACTGAGCTGTGACAGCCCCCAT--------------------CTGTGA--CGAGCCATTCCCTC-GGTCTTTCAATTCTT-CCTCCTCTT i equCab2.chr12 C 0 C 0 s canFam2.chr18 7557691 371 - 58872314 ATGTGGTCTGGGGA--CTTGGG--------------------------GGATGCCCAACAG---AGTC-------ACCAGCTCCCA--AGCTGGGCCTGATTCTAAGACCCCAGGGTGGGGTGGGGGAGGGACTTTCTGCCTTCCA---GCTTCTCAGCTCAGACAGATGGACATTAACCCATTGGGGGATCACTcctcagggcctttg--------------cacatcctatg--------------ccctt-ggcctggtttgtcc---------ttgacccaCCCCAAAGCT-TCATGCACAAGACAGATCCAGCTTCTTGTT-------------------TGGGAAACTACCCTTTATTA-CACCCATGGCAGCAAGAACCACATGAAGCCATAAGTCCTCCTGTATGCATCTCTG-TC----CCCTGTGACCCGAGCCATCCCTGCTTGTGTTTCAATTCTTAACTCCCGTC i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 110855 339 + 1045236 GCGTGGACCAGGGACTCTCAGGGCATCC---AGGGA-----GGG--CAGGGTGCAGGTTAGAGCAGTC---------------ACA--CCCTGGGCCTGACCCTGGGGCCCCG-----------GGGACAAATCTGTACCTCCAAAAGTGCTTTGGCTC----------------------------AGACGATGATCATGGGCTTGAAGAGGCCATACTGGTCATGCCCCCGG--------------CCTTTGCACAGGTGGTGTCCCTCTGCCTGCTTGCCCCCCACAAAGCC-TGGCCC--------------------------------------------AGAAGTCCACCCAC------AGCCTGGGGAGGTA--GCCCACATCAGGCCACAGCTGTCGCTTT-----GCTTGGTTCTGTCCCCAGTGACACAAGACCTTCCTGCCCAAGTTTCCGTTCTT-AACCTTCTT i loxAfr3.scaffold_159 C 0 C 0 a score=37473.000000 s hg19.chr11_gl000202_random 38095 57 + 40103 AGTATTCCTAAAGCT-CAG-CCACTGCCCACCACAaattttttgtttatggatgtccag s panTro2.chr11 68225012 57 + 134204764 AGTATTCCTAAAGCT-CAG-CCACTGCCCACCACAaattttttgtttatggatgtccag i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126023538 57 - 132107971 AGTATTCCTAAAGCG-CAG-CCACTGCCCAccgcaaattttttgtttatggatgtccag i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128180576 57 - 133002572 AGTATTCCTAAAGCA-CAG-CCACTGCCCACCACACATTTTTTGTTtatggatgtccag i rheMac2.chr14 C 0 C 0 s equCab2.chr12 28961414 57 + 33091231 TATACGCCAAAAGCAGCAGCCCAGGGCCCACAGCAACTC--TTGATTAAAGATGGACAA i equCab2.chr12 C 0 C 0 s canFam2.chr18 7558062 40 - 58872314 TGTATCCCTAAAGCA-CAGCCCAGTGCACACAGCAAATCGT------------------ i canFam2.chr18 C 0 C 0 s loxAfr3.scaffold_159 111194 31 + 1045236 GGTATCCCAAAAGCC-CAGCTCAGTGCCTACC--------------------------- i loxAfr3.scaffold_159 C 0 N 0 e bosTau4.chr29 48995411 461 + 51998940 I a score=442514.000000 s hg19.chr11_gl000202_random 38152 885 + 40103 aatctattcaatcatttctcctgtttgtgaatgttgaggttgttttttgtc-actacataaaatgcttcaatATGTATTTCTCCAAAGTGGGATTTGAGATTT----TAAAACGTGCTTATTTTTATTAGGCGTGGCCAAATTAGATTCCAAGGATTATGTAGCCCAAGCAATATCGAGCAGTATCTGTTTCCCTTATACTCCCACCAGTCCTAGGTGATGCTGGTATTTTTTG------TTTTTTTAGTTTTT-ATTTCCTGGTTGTGTGATCGGTAAAAACAATACATCTTCGTATCGTTTTGTTTTGTTTTTAA--tttttttatttccataggttattggggaacaggtggtgtttgcttacatgagtaagttccttagcgatgatttgtgagtttttggtgcacccatcacccaagcagtatacactgcacccaacttgtagtcttttatccctcacccccttcccaccctttccccc-gagtccccaaagtccattgtatcattcttatgcctttgcatcctcatagcttagctcccactcatgagtgagaacacacgatgtttagttttccattcctgagttacttcacttagaataatagtctccagtctcatccaggttgctataaatgccattgcttcattccttttcatggctcagtagtattccatc-----------------------------------gtatatatatcccacagtttctttatccgctcattgattgacgggcatttgggctgcttgcacatttttgcaattgtgaattgtgctgctgtaaacatgcgtgtgcaggtatctttctcatataatgacttcttttcctctgggtagatacccagcagtgggattgctgggtcaaatggtctttctacttctagttctttaaggaatctccacactgtttt s rheMac2.chr14 128180633 927 - 133002572 aatctattcaatcacttctcctgtttgtgaatgttgaggttgttttttgtc-actacataaaatgcttcaatatgcatttctccaaagtgggatttgagattttaaaaaaaaaatgcttatttttattaggtgtggccaaattggattccaaggattatatagcccaagcaacattgagcagtatctgtttcc-ttatactcccacaggtcctgggtgatgctgatatttttag------tttttttagtttttaatttcctggttgtgtgatcggtaaaaacaatacatctttgtattgttttgttttgtttttAATTtttttttatttccataggttattgggaaacaggtggtgtttgcttacatgagtaagttccttagtgatgatttgtgagattttggtgtgcccatcagccgagcagtacacgatgtatccaacttgtagtcctttatccctcacccccttcctacccgttcctcctgagtccccaaagtccattgtgtcattcttatgcttttgcatcctcatagcttagctcccactcatgacggagaacatacgatgtttggttttccattcctgagttacttcatttagaataatagtctccagtttcatccaggttgctacaaatgccattaattcattcctttttatggctcagtagtattccatctatatctatctatctatctatctatctatctatctatctatctatgccacaatttctgtatccactcattgattgatgggcatttgggctggttgcacagttttgcgattgtgaattgtgcttctataaacatgcatgtgcaagtatctctttcgtataatgacttcttttcctctgagtagatacccagcagtggaactgctggatcaaatggtcgttctacttttagttctttaaggaatctccacactagttt i rheMac2.chr14 C 0 C 0 s ponAbe2.chr11 126023595 893 - 132107971 aatctattcaatcatttctcctgtttgtgaatgttgaggttgttttttgtctactacataaaatgcttcaatATGCATTTCTCCAAAGTGAGATTTGAGATTT----AAGAACATGCTTATTTTTATCAGGTGTGGCCAAATTAGATTCCAAGGATTATGAAGCCCAAGCAACATCGAGCAGTATCTGTTTCCCTTATACTCCCACCAGTCCTGGGTGATGCTGGTATTTTTTGTGTTTTTTTTTTTAGTTTTT-ATTTCCTGGTTGTGTGATCGGTAAAAACAATACATCTTTGTATTGTTTTGTTTTGTTTTTAA--tttttttatttccataggttattggggaacaggtggtgtttgcttacatgagtaagttccttagcgatgatttgtgagtttttggtgcacccatcacccgagcagtacacactgcatccaacttgtagtcttgtatccctcacccccttcccaccctttccccctgagtccgcagattccattgtatcattcttatgtctttgcatcctcatagcttagctcccactcatgagtgagaacatacgatgtttggttttccattcctgagttacttcacttagaataatagtctccagtctcatccagattgctccaaatgccattacgtcattccttttcatggttcagtagtattccatc-----------------------------------gtgtatatatcccacagtttctttaaccgctcgttgactgacgggcatttgggctggttgcacatttttgcaattgtgaattgtgctgctataaacatgtgtgtgcaggtatctttctcgtataatgacttcttttcctctgggtagatacccagcagtgggattgctgggtcaaatggtcgttctacttctagttctttaaggaatcgccacactgtttt i ponAbe2.chr11 C 0 C 0 s panTro2.chr11 68225069 885 + 134204764 aatctattcaatcatttctcctgtttgtgaatgttgaggttgttttttgtc-actacataaaatgcttcaatATGTATTTCTCCAAAGTGGGATTTGAGATTT----AAAAACGTGCTTATTTTTATTAGGCGTGGTCAAATTAGATTCCAAGGATTATGTAGCCCAAGCAATATCGAGCAGTATCTGTTTCCTTTATACTCCCACCAGTCCTAGGTGATGCTGGTATTTTTTG------TTTTTTTAGTTTTT-ATTTCCTGGTTGTGTGATCGGTAAAAACAATACATCTTCGTATTGTTTTGTTTTGTTTTTAA--tttttttatttccataggttattggggaacaggtggtgtttgcttacatgagtaagttccttagtgatgatttgtgagtttttggtgcacacatcacccgagcagtatacactgcacccaacttgtagtcttttatccctcacccccttcccaccctttccccc-gagtccccaaagtccattgtatcattcttatgcctttgcatcctcatagcttagctcccactcatgagtgagaacacacgatgtttagttttccattcctgagttacttcacttagaataatagtctccagtctcatccaggttgctataaatgccattgcttcattccttttcatggctcagtagtattccatc-----------------------------------gtatatatatcccacagtttctttatccgctcattgattgacgggcatttgggctggttgcacatttttgcaattgtgaattgtgctgctgtaaacatgcgtgtgcaggtatctttctcatataatgacttcttttcctctgggtagatacccagcagtgggattgctgggtcaaatggtcgttctacttctagttctttaaggaatctccacactgtttt i panTro2.chr11 C 0 C 0 e equCab2.chr12 28961471 0 + 33091231 C e canFam2.chr18 7558102 0 - 58872314 C e bosTau4.chr29 48995411 461 + 51998940 I a score=123835.000000 s hg19.chr11_gl000202_random 39037 164 + 40103 ccacagCAAATTTTTACAAAAGATGGAAAA---------------ATAGTGGACTCCTGCTCTCAGCCCCAGAGGGGCCAATGTGAGTGCAG---G-------GGAATCACAGGAATCCCAAGACCAAGCCGCC--CGAGACTGGGCTGGGC-TCCCTGGGGGTGgggcttctcacccttagcactactaac s panTro2.chr11 68225954 164 + 134204764 ccacagCAAATTTTTACAAAAGATGGAAAA---------------ATAGTGGACTCCTGCTCTCAGCCCCAGAGGGGCCAATGTGAGTGCAG---G-------GGAATCACAGGAATCCCAAGACCAAGCCCCC--CGAGACTAGGCTGGGC-TCCCTGGGGGTGgggcttctcacccttagcactactaac i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126024488 164 - 132107971 ccacagCAAATTTTTACAAAAGATGGAAAA---------------ATAGTGGACTCCTGCTCTCAGCCCCAGAGAGGCCAATGTGAGTGCAG---A-------GGAATCACAGGAACAACAAGACCAAGCCCCC--CAAGGCTGGGCTGGGC-TCCCTGGGGGTCgggcttctcacccttggcactactaac i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128181560 164 - 133002572 ccacagCAAATTTTTACAAAAGATGGAAAA---------------ATAGTGGACTCCTGCTCTCAGTCCCAGAGGGGTCAATGTGAGTGCAA---A-------GGAATCACAGGAACCCCAAGACCAAGCCCCC--CAAGGCTGGGCTGGGC-TCCCTGGGGGcggggcttctcacccttggccccactaac i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48995872 166 + 51998940 CCACAGCAAATCCTTATTAAGGACGGGAAAAAAAAAATCTCTATTAAAGACGGCCAGTGCTCTCAGCCCCAGGGGGACCAGAGTGAGTGCCAACCGGGCCACCGGGCCCCCACA----CCGTGA-------ACCAGTGAGGCTGAGCTGAGCTTCCCCCGGGGGAGGGCCCCACACC--------------- i bosTau4.chr29 I 461 I 48 s equCab2.chr12 28961471 133 + 33091231 ---------------------------------------------ATAGTGGG-CAGTGCCCTCAGCCCAGAGGGC-CCAAAGCGAGAGCCA---GAGTCACTGGGACCACAGGAGGCCCAAGACCAACCCAGCACTGAGGCCGGGCTGGGCTTCCCCCGCAGGCTGGGTTCT---------cactattggc i equCab2.chr12 C 0 C 0 s canFam2.chr18 7558102 158 - 58872314 --------------TATTAAAGATGGAAAA---------------ATAGTGGGCCGGTGCTCTCAGGCCCAAGGAG-CCAGAGTAAGTTCCT---GAGTCCCCAGGACCACAGGAATCCCAAGATCAACCCACCATGGAGGTTAGCCTGGGTTTTCCCCAGGGaaggtgtcctcac-ctgggcactattgac i canFam2.chr18 C 0 C 0 a score=226842.000000 s hg19.chr11_gl000202_random 39201 303 + 40103 acttggggctggaaccatcttagttgtagggggctgt------------------------------cccggcctctcccca-ctacatgccaatggtaccacc----ca---------agttgtgacaaccaaaagtatctccagacatagccaaag--tccccag----------ggggcaacttct----------------------tcctgatgaagaacccctgACCT-GAGCAGCCCACCCAA------TCCCTGGGAAGCTCCGCAGACCCCAGATAGCAGGAAGGAGGGAGGGAGAGAGCAAGGGTCCTGTCCGGATGTCAAGCTCTGCCTACCGAGGCCCTGGCTGGGCTGCTACCTCCCCA-CCCACTCAACACAGGA s panTro2.chr11 68226118 303 + 134204764 acttggggctggaaacatcttagttgtatggggctgt------------------------------cccggcctctcccca-ctagatgccaatggtaccacc----ca---------agttgtgacaaccaaaagtatctccagacatagccaaag--tccccag----------ggggcaacttct----------------------tcctgatgaagaacccctgCCCT-GAGCAGCCCACCCAA------TCCCTGGGAAGCTCCGCAGACCCCAGATAGCAGGAAGGAGGGAGGGAGAGAGCAAGGGTCCTGTCCGGATGTCAAGCTCTGCCTACCGAGGCCCTGGCTGGGCTGCTACCTCCCCA-CCCACTCAACACAGGA i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126024652 304 - 132107971 acctgagactggaaccatcttagttgtagggggctgt------------------------------cctggcctctcctca-ctagataccaatggtaccacc----ca---------agttgtgacaaccaaaagtatctccagacatagccaaag--tccccag----------ggggcaacttct----------------------tcctgatgaagaacccctgCCCT-GAGCAGCCCACCCAT------TCCCTGGGAGGCTCTGCAGACCCCAGATAGCAGGAAGGAGGGAGAGAGAGAGCAAGGGTCCCGTCCGGATGTCAAGCTCTACCTACCGAGGCCCTGGCTGGGCTGCTCCCTCCCCATCCCACTCAACACAGGA i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128181724 303 - 133002572 acttgggactggaaccatctcagttgtggggggctgt------------------------------cctggccactcccca-ctagat-ccaatggtaccacc----ca---------agttgtgacaaccaaaagtatctccaggcatagccgaag--tccccaa----------agggcaacttct----------------------tcctgattaagaacccctgCTCT-GACCAGCCCACCCAT------TCCCTGGGAGGCTCTGCAGACCCCAGATGGCAGGAAGGAGGGAGGGAGAGAGCAAGGGTCCCATCCTGATATCAAGCTTTGCCTCCTGAGGCCCGGGCTGGGCTGCTCCCTCCCCACCCCACTCAACACAGGA i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48996086 332 + 51998940 atctggggccggaacggcctttgttgtgg---gctgtcctgtgtcctgaagaaaggtgagcagcgcccatggccttgccccgtctagaccccaggagcac--ccactccc---------agt-----------aaaatgcctctagacatcgccaagt-gtccctgg----------gggataaaatcaccAGGCTCCCCACCCCACCCCCACCCCGCGGAGAACCTCAGCCCCAGGGTGGCTGAGCTGCCCCTGCCCCTCGGGACGCCC---------------ACAGGGAAGGGGAAGGGAGAGAACCAGAGTCC-ATCCTGAGGTCAAGCTCC-CCTCCCCACGCCCAG--CTGGCTGCGTGTTATCG--TCAACTCCGCTCAACA i bosTau4.chr29 I 48 I 1 s canFam2.chr18 7558260 338 - 58872314 atttggggtcggagcattcttcgcagtggaagcctgttgtgtgcactgcagcatatcaagcagaacccctgactcctgccca-ctagatgccaatagcaccccctcccctgcacccctgagctgtgacagccaaaactgtcacctgatgttgccaagg---ccctggcaggaggggcggggcaaaatcacTG-----------CCTCTGCAGCCCCATTGACCATCACTGCCCCCAGGCAGCCCACCTGT-----CCCCCAGGGAGGCCC---------------ACAGGAAGGCAGGAGGGAGAAGGCAAGGGTCT-GTCCTGGGGTTGAGCCCGGCATCCCCATGCATGGTTCC-CCTCC--------------ACTCAGCTCAACA i canFam2.chr18 C 0 I 136 s equCab2.chr12 28961604 311 + 33091231 atttggagccggaacattctttgtggtgg-ggcctgtcctgtgctctgtaagtccttgggtggcatccttggcctctaccca-ctagatgccagtagcactgccacttcc---------agctgtgacagccaaaaatgtctccagacatcaccgagaggcccctgg----------ggggcaaaatca--------------------gggccccattgagaagcactgCCCCAGGGCAGCCCACCCAT------CCCCAGGGAGGCCC---------------CCAGGAAGGAGGGAGGGAG-AGAAGAGGCTCC-ATCTGGATGTCAGACTCAGCCTCCCCATGCTCAGGGCTGGCTGC--------------ACTCAACCAGGAT i equCab2.chr12 C 0 I 14 a score=33198.000000 s hg19.chr11_gl000202_random 39504 92 + 40103 GCCGGAGGCTCCTTCTCAGGCCAAGTGGTTAGGGTTGAGTGGG----------AACGGCAGGGCTGAGTGC---------------ACA------------------GTGCCTGTCTGGAG-----CCGGGCAGAAAAGC s panTro2.chr11 68226421 92 + 134204764 GCCGGAGGCTCCTTCTCAGGCCAAGTGGTCAGGGTTGAGTGGG----------AACGGCAGGGCTGAGTGC---------------ACA------------------GTGCCTGTCTGGAG-----CCAGGCAGAAAAGC i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126024956 92 - 132107971 GCCGGAGGCTCCTTCTCAGGCCAAGTGGTTAGGGTTGAGTGGG----------AACGGCAGGGCTGAGTGC---------------ACA------------------GTGCCTGTCTGGAG-----CCAGGCAGAAAAGC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128182027 91 - 133002572 G-GGGAGGCTCCTTCTTGGGCCAAGTGGGCAGGATTGAGTGGG----------TATGGCAGGGCTGAGTGC---------------ACA------------------GTGCCTGTCAGGAG-----CAGGGCAGGAAAGC i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48996419 127 + 51998940 GGCAGGGCCGCC----CAG---AGGCAGGTGGGGTGGGGTGAG------GCCTGGGAGCAGGTGTGAATCCCGCCCTTGACCCCATCCACCTGTGACCTCCCTCCACGGGCCTGTGAAGGGTCGACTCAGACAGGATCAT i bosTau4.chr29 I 1 I 9 s equCab2.chr12 28961929 110 + 33091231 -GCGGGGACCC--------------------GGGCGGGGCCAGTGCACCGTCTCAGAGCAGGTGTGAATGCCGGCCGTGGCCCCACCCG-CTGTGACTT--------GGGCCTGCGAAGGGATAATTCGAACAAAATCAC i equCab2.chr12 I 14 I 10 e canFam2.chr18 7558598 136 - 58872314 I a score=51789.000000 s hg19.chr11_gl000202_random 39596 161 + 40103 AAAAGGCCTTTACGGCAAAGGGGTGCATAGGAGTCGGCCGAAGGAGGGCT-GACTCATTGGGGGAAGCCATGGCAGGGCCCCATGGCCCAGGACCACTGCCTGGGCAGCATC-GTCAGCTCAGGGT------------ACCCCCGTC-------------------------------------------------------------------------------------------------------------------CACAGGCGGTGACCTTGGAAAAATCAGC s panTro2.chr11 68226513 161 + 134204764 AAAAGGCCTTTACTGCAAAGGGGTGCATAGGAGTCGGCCGAAGGAGGGCT-GACTCATTGGGGGAAGCCATGGCAGGGCCCCATGGCCCAGGACCACTGCCTGGGCAGCATC-GTCAGCTCAGGGT------------ACCCCCGTC-------------------------------------------------------------------------------------------------------------------CACAGGCGGTGACCTCGGAAAAATCAGC i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126025048 239 - 132107971 AAAAGGCCTTTACTGCAAAGGGGTGCACAGGAGTCAGCTGAAGGAGGGCT-GACTCATCGGGGAAAGCCATGGCAGGGTCCCATGGCCCAGGACCACTGCCTGGGCAGCATC-GTCAGCTCAGGGT------------CCCCCTGTCCACAGGC-GTGACCTCGGAAAAATCAGCAGAGCAAAGGCCAGGGACAGCCGGCGAGGGGGGGCCATGG------------------------------------CAGAGCTCAGGCACAGGCGGTGACCCTGGAAAAATCAGC i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128182118 241 - 133002572 AAAAGGCCTTTACTGCAAAGGGGTGCACAGGAGTCAGCCAAAGGAGGGCTGGACTCATCGGGGGAAGCCACTGTGGGGCCTCATGGTCCAGGACCACCGCATGGGCAGCATC-ATCACCTCAGGGT------------CCCTCCGTCcacaggcggtgaccctggaaatatcagcaga------------------------------------gcaaaggccagtgacagctggcaagggggagctatggcagagctcaggcacaggcggtgaccctgaaaatatcagc i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48996555 128 + 51998940 AAGAGAGCTTTACTGCACAGAGGCTCACGGAAGCCAGCTGCAGGATGATG-GGCTTGGGAAACAAAGTCCCAGCGGGTGCCAGGCTCCCTGACCTACCCAGAGGGCAGTGCCAGTGGGCATGAGAC-AGA---------------------------------------------------------------------------------------------------------------------------------------------------------------- i bosTau4.chr29 I 9 C 0 s equCab2.chr12 28962049 132 + 33091231 AAAAAACCTCTACTGCAAAGAGCTGCAGAGGGGCCAGAGGCAG---GGCT-GGCCCAACAAACAAAACCACAGC-AGTGCCGAGCTCCCGGGACCCCCGAGTGGGCGGCCTCGGTGGGCTCGTGGT-GGAGAAGCAGC-------------------------------------------------------------------------------------------------------------------------------------------------------- i equCab2.chr12 I 10 I 13 s canFam2.chr18 7558734 91 - 58872314 AACAGATCTTTACTGCAAAGAGCTGTGAAGGAGGCAGA-TCAG---GGCT-GGCTC------------------------------CCCAGGACCACCAAGT-GGCAGCGTCAGTGGGCTTCGGGTA------------------------------------------------------------------------------------------------------------------------------------------------------------------- i canFam2.chr18 I 136 I 61 a score=18766.000000 s hg19.chr11_gl000202_random 39757 38 + 40103 AGAGCAA-----------AGGCCAGGGACAGCCAGTGAGGGGGAGCCAT s panTro2.chr11 68226674 38 + 134204764 AGAGCAA-----------AGGCCAGGGACAGCCAGTGAGGGGGAGCCAT i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126025287 38 - 132107971 AGAGCAA-----------AGGCCAGGGACAGCCAGCGAGGGGGAGCCAT i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128182359 38 - 133002572 agagcaa-----------aggccagggacagccggtgagggggagccat i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48996683 32 + 51998940 AGGACAATGATTTATCCCAGGTCC-AAATCCAT---------------- i bosTau4.chr29 C 0 C 0 s canFam2.chr18 7558886 37 - 58872314 AGGGCAA-----------AGGTCA-GAACAGCTGGGGAGTGGGAAGCTG i canFam2.chr18 I 61 I 2 e equCab2.chr12 28962181 13 + 33091231 I a score=53856.000000 s hg19.chr11_gl000202_random 39795 79 + 40103 GGCAGAGCTCAGACACAGGTGGTGACCCTGGAAAAATAAGCAGAGCAAAAGCCAGGGAAAACCGGCGAAGGGGGGCCAT s panTro2.chr11 68226712 79 + 134204764 GGCAGAGCTCAGACACAGGCGGTGACCCTGGAAAAATAAGCAGAGCAAAGGCCAGGGAAAACCGGCGAAGGGGGGCCAT i panTro2.chr11 C 0 C 0 s ponAbe2.chr11 126025325 78 - 132107971 GGCAGAGCTCAGGCACAGGCGGTGACCCTGGAAAAATCAGCAGAGCAAAGGCCAGGGACAGCCGGCG-AGGGGGGCCAT i ponAbe2.chr11 C 0 C 0 s rheMac2.chr14 128182397 79 - 133002572 ggcagagctcaggcacaggcggtgaccctggaaatatcagcagagcaaaggccagggacagccggcgagggggagccat i rheMac2.chr14 C 0 C 0 s bosTau4.chr29 48996715 65 + 51998940 --------------ACAGGCAGAGACCCAGGGGAAACCAGCAGGGCAAAGGTCAGGGCAATGAGAAGTGGGAGGCCAGC i bosTau4.chr29 C 0 C 0 s equCab2.chr12 28962194 76 + 33091231 GCTGAAACCCA--CACAGA-GGAGACCCTTGAGAAGCCAGCAGAGCACGAGTCAGGACAATTAGGGAGGGCAAAGCTGC i equCab2.chr12 I 13 I 1 e canFam2.chr18 7558923 2 - 58872314 I a score=171842.000000 s hg19.chr11_gl000202_random 39874 229 + 40103 GGCAGAGCTCAGGCCGCATTCATGCTGGAGGTCAGGACCAGA-----GCCTGCTGCCACCTGGCTCATCTCAGGA---GGGAAAGTGGCTCTGCAGAGATGGCAAATGTGTCTGCTCT-CCCCCACCTGCGCCACACTGCCCC--GCAGCATCACTTCCCG-CCCTACACCTG--------CCATGACTCCCTAGCTGCTCACCCCACCTCCATCCTG---------CCCCCTCCGATGCATGCCCCACCCCAAAAGC s panTro2.chr11 68226791 229 + 134204764 GGCAGAGCTGAGGCCGCATTCATGCTGGAGGTCAGGACCAGA-----GCCTGCTGCCACCTGGCTCATCTCAGGA---GGGAAAGTGGCTCTGCAGAGATGGCAAATGTGGCTGCTCT-CCCCCACCTGCGCCACACTGCCCC--GCAGCATCACTTCCCA-CCCTACACCTG--------CCATGACTCCCTAGCTGCTCACCCCACCTCCATCCTG---------CCCCCTCCGATGCATGCCCCACCCCAAAAGC i panTro2.chr11 C 0 N 0 s ponAbe2.chr11 126025403 229 - 132107971 GGCAGAGCTCAGGCTGCATTCATGCTGGAGGTCAGGACCAGA-----GCCTGCTGCCACCTGGCTCATCTCAGGA---GGGAAAGTGGCTCTGCAGAGATGGCAAATGTGTCTGctct-cccccatctgtaccacactgcccc--gcagcatcacttcctg-ctcgacacctg--------ccctggctccctagctgctcaccccacctccagcctg---------ccccctccgatgcatgccccaccccaaaagc i ponAbe2.chr11 C 0 N 0 s rheMac2.chr14 128182476 229 - 133002572 ggcagagctcaggcCACATTCATGCTGGAGGTCAGGACCAGA-----GCCTGCTGCCACCTGGCTCATCTCAGGA---GGGAAAGCGGCTCTGCAGAGATGGCAAATGTGTCTGCT-T-TCCCCACCTGCGCCACATTGCCCT-GGCACCGTCACTTCCCA-CCTGACACCTC--------CCCTGGCTCCCTAGCTGCCCGCCCCACCTCCATCCTG---------CCCCCTCTGATGCATGCCCCACCCCAAAAGC i rheMac2.chr14 C 0 N 0 s bosTau4.chr29 48996780 253 + 51998940 AGCCGGGCCCAGGCGGCACTTACGCTGGAGACCAGAGCTCAGGAGTGACCCGCCATGACCTGGTTTACCTTAGAA---AGGACAGC-GACCTCCAGATACCACAGGTGTGTCCTTTCC-TGCCTTCTGCTGGCACACCGCCCCGGGGGACATTACCTCTCATCTGGACAGCTGGACAGCCTCCCTGGCTTCCTACCTGCTCTCCCCACCTTCGCTGGACACGCCACCCCACCCCCAATCTTTGCTCCACCTAAAAAGC i bosTau4.chr29 C 0 N 0 s canFam2.chr18 7558925 196 - 58872314 GGCAAGGCCCGGGCTGCCTT-AGGCCAGAGACTAGAACCAGCCGGGAACCTGCCGTGACTGGTT-TATCCAAGGA---GGGCTGGT-GTTCTACCCACATTGCACACCTGTCCACGTC-CTCTCTTCACACCCACACTG---------------CTTCTCA--------------------CCCTGGCT-------TCCTCTCTTGACCCCCACTCTG---------ACCTCTCCAATCCAGGCTCCACCCAAA---- i canFam2.chr18 I 2 N 0 s equCab2.chr12 28962271 224 + 33091231 GGCACG--CCCGGCCGCCTTCACGCAGGAGCCTAGAACAAGC--GAGACCT---GTGGCCTGCT-------AGGATttggtttaat-gttctacctttgctgcgaatgcgtccgtttctccccctctgcgcccacaccgcccc--agaccatcacttctcacctggacagctg--------ccccggcttcctaactcctcccccgacccccactggg---------gcccctcctatccgtgcgccactcccaaagc i equCab2.chr12 I 1 N 0