##maf version=1
a score=2047408.0
s hg17.chr1              147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG 
s panTro1.chr1           129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG 
s baboon.ENr231_1            81874 85 +    657133 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG 
s marmoset.ENr231_1         131543 85 +    772620 ATGGCGTCGGCCTCCTCCGGGATGTCGTCGGCGGTCGGTTTTTCATCCTTTGATCCCGGCGTCCCTTCCTGTACCTCGTCCTCAG 
s galago.ENr231_1            75476 82 +    825110 ATGGCGTCGGCCTCCTCTGGGCCGCCGGCTCC---CGGATTTTCGTCCTGTGATCCCGGGGTCCCTCCCTGTGCCTCGACTTCAG 
s rn3.chr2                68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG 
s mm6.chr3                64351392 76 - 158945675 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCCGGGTTTTCATCCCTTGATGCCGGGGCCCCTGCTGGTACCGC------AG 
s rabbit.ENr231_1            70872 82 +    694075 ATGGCGTCGGCCTCTTCTGGGCCGTCGGC---GGTCGGGTGTTCAGCCTTGGATTCCGGGATCCCTTCCAGCACCTCGATCTCAG 
s cow.ENr231_1               83601 82 +   1082283 ATGGCGTCTGCCTCCTCTGGGCCGTCGGC---GGTAGGGTTTTCATCCGCGGATTCCAGCGTCCCTCCCTGCACCTCGGCCTCAG 
s canFam1.chr17           62947719 82 +  66886099 ATGGCGTCGGCCTCCTCTGGGCCGTCGGC---GGCTGGGGTTTCATCCTTTGATCCCGGGGTCCCTTCCTGTGCTTCGGCTTCAG 
s rfbat.ENr231_1             76952 82 +    561098 ATGGCGTCGGTCTCCTCTGGGCCGTCGTC---GGGCGGGTTTTCGTCGGTGGATTCCGGGGTTCCTGGCTGCACCTCGTCCTCAG 
s shrew.ENr231_8              4546 63 -      4749 ATGGCGTCGGCTCCGTTCGTAGTG----------------------CCTCCGATTCCGGGTCCTCCTCCTGCTCTATGATTATCT 
s armadillo.ENr231_1         35525 82 +    758801 ATGGCGATGGCCTCCTCTGGACCGTCGAC---GACCGCGCTTTCATCCGTGGATACCGGAGTGCCTCCCTGCACCTTATCCTCAG 
s tenrec.ENr231_3             2426 73 +      2724 ATGGCGACGGCCTCCTCTGGGCCGTCGAC---GACCGCGTATTCGCTCGCGGATTCCTG---------CAACACCTCGTCCGCAG 
s monDom1.scaffold_18720   1604680 79 -   5714867 ATGGCGTCG---TCCTCCGGGTCGTCGTC---GGCCGGGAATACCTCCTTGGAGTTGGCGAGTAGCAGCGGCTCCTCCAGCTTCG 
s tetNig1.chr21            1755128 81 +   5821691 CTAATGAAGAAATGCTCGGGGACGGCGCT---GGCCA-TCGCTCACAGCGTGGCCACACTCACCTTTCCCAGCCCTTCCCCCTGT 
s fr1.chrUn              290894076 81 + 349519338 CTAATGAAGAAATGCTCGGGGACGGCGCT---GGCTA-TCGCTCACAGTGTGGCCACACTTAGCTTTCCCAGCCCTCCCCCCGCT 

a score=2837921.0
s hg17.chr1               97444265 182 - 245522847 GTTCTCAGCTT---------CCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA 
s panTro1.chr1            99744907 182 - 229575298 GTTCTCAGCTT---------CCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA 
s baboon.ENr231_1           479199 182 -    657133 GTTCTCAGCTT---------CCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA 
s rheMac1.SCAFFOLD90935      33761 182 -     50918 GTTCTCAGCTT---------CCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA 
s marmoset.ENr231_1         544638 182 -    772620 GTTCTCAGCTT---------CCTTGCTTCCATGGTTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGCTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA 
s galago.ENr231_1           619780 182 -    825110 GTTCTCAGCTT---------CCTTGCTTCCATGGCTCCAGCACCATTCGCAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACAGAGGAGCAGCTTCAGCTACTGGTGGAGCAGATGGTAGATGGCAGCATGCGGTCCATCACCACCAAACTGTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA 
s rn3.chr2               189865459 182 + 258222147 GTTCTCAGCTT---------CCTTGCTTCCATGGCTCCAGCACCATTCGCAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGACGGCAGCATGAGGTCCATCACCACCAAACTCTACGATGGCTTCCAGTACCTCACCAATGGCATCATGTGA 
s mm6.chr3                94493590 182 + 158945675 GTTCTCAGCTT---------CCTTGCTTCCATGGCTCCAGCACCATTCGCAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGACGGCAGCATGAGGTCCATCACCACCAAACTCTACGATGGCTTCCAGTACCTCACCAATGGCATCATGTGA 
s rabbit.ENr231_1           529002 182 -    694075 GTTCTCAGCTT---------CCTTGCTTCCACGGCTCCAGCACCATTCGCAACCTCAAGGAGAGGTTCCACATGAGCA---------------------------------------------TGACGGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGACGGCAGCATGCGCTCCATCACCACCAAGCTCTACGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA 
s cow.ENr231_1              729607 182 -   1082283 GTTCTCAGCTT---------CCTTGCTTCCATGGTTTCAGCACCATCCGCAACCTCAAGGAGAGGTTCCACGTGAGCA---------------------------------------------TGACTGAGGAGCAGCTCCAGCTGCTGGTGGAGCAGATGCTGGACGGCGGCATGCGGTCTATTACCACCAAACTCTATGACAGCTTCCAGTGCCTCATCAATAGCATCATGTGA 
s canFam1.chr17            3835678 180 -  66886099 --TCTCAGCTT---------CCTTGCTTCCATGGCTCCAGCACCATCCGCAACCTCAAAGAGCGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTCCAGCTGCTGGTGGAGCAGATGGTAGATGGCAGCATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAATGGCATCATGTGA 
s rfbat.ENr231_1            414085 180 -    561098 --TCTCAGCTT---------CCTTGCTTCCACGGCTCTAGCACCATCCGCAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGACGGCAGCATGCGCTCCATCACCACCAAACTCTACGATGGCTTCCAGTACCTCACCAACGGCATCATGTGA 
s shrew.ENr231_3             15159 180 +     52788 --TCGCAGCTT---------CCTTGTTTCCACGGCTCGAGCACCATCCGAAACCTCAAGGAGCGGTTCCACATGAACA---------------------------------------------TGACAGAGGAGCAGTTGCAGCTACTGGTGGAGCAGATGGTGGACGGGAGCATGCGCTCCATCACCACCAAACTCTACGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA 
s armadillo.ENr231_1        553280 182 -    758801 GTTCTCAGCTG---------CCTTGCTTTCATGGCTCCAGCACCATCCGTAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTTCAGCTGCTGGTGGAACAGATGGTGGATGGCAGCATGCGGTCTATCACCACCAAACTCTATGATGGCTTTCAGTACCTCACCAATGGCATCATGTGA 
s tenrec.ENr231_10            2477 182 -     18834 GTTCTCAGCTT---------CCCTGCTTCCATGGCTCCAGCACCATCCGCAACCTCAAAGAGCGGTTCCACATGAGCA---------------------------------------------TGACCGAGGAGCAGCTCCAGCTGCTGGTGGAGCAGATGGTGGACGGCAGCATGCGCTCCATCACCACCAAGCTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA 
s monDom1.scaffold_18720   4029570 182 +   5714867 GTTCCCAGCTG---------CCCTGCTTCCACGGCTCCAGCACCATCCGCAACCTGAAGGAGCGCTTCCACATGAGCA---------------------------------------------TGACCGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGACGGCAGTATGCGCTCCATCACCACCAAACTCTACGATGGCTTCCAGTACCTCACCAATGGCATCATGTGA 
s galGal2.chrUn           68039628 182 - 165033910 GCTCGCAGCTC---------CCCTGCTTCCACGGCTCCAGCACCATCCGCAACCTGAAGGAGCGCTTCCACATGAACA---------------------------------------------TGACGGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGACGGCAGCATGCGCTCCATCACCACCAAACTGTACGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA 
s xenTro1.scaffold_485      499461 217 -   1001990 --ctcctgctttgaccattgccctgcttctgcctgttctctgcccttc-----------------tcctgcctNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGACGGAGGAGCAGCTGCAGGTCCTGGTGGAGCAGATGGTGGACGGCAGCATGAGGTCCATAACCACCAAACTGTACGACGGGTTCCAGTACCTGACCAACGGCATCATGTGA 
s tetNig1.chrUn_random    10240092 182 + 171761319 GGTCCCACCTG---------CCGTGCTTCCACGGTTCCAGCACCATCCGCAGCCTGAAGGAGCGCTTCCACATGTCGC---------------------------------------------TGACGGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGCTGGTGGAGGGCTCGGTGCGCTCCATCACCACCAAGCTCTACGACTCCTTCCAGTACGTCACCAACGGCATCATGTGA 
s fr1.chrUn              152584905 182 + 349519338 GGTCCCAGCTG---------CCGTGTTTCCACGGGTCGAGCACCATGCGGGGTTTGAAGGAACGTTTCCACATGAGTC---------------------------------------------TGACAGAGGAGCAGCTCCAGCTGCTGATCGATCAGCTGGTCGAGGGCTCGATGAGGTCGCTGACGACCAAACTCTACGACGGCTTCCAGTACCTGACAAATGGAATCATGTGA 
s danRer2.chr16           37377307 182 +  42763181 GTTCACAGCTC---------CCCTGCTTCCATGGCTCCAGCACTATCCGCAACCTGAAGGAGCGATTCCACATGAACC---------------------------------------------TGACGGAGGAGCAGCTGCAGGTGCTGGTGGAGCAGATGGTGGACGGCTCCATGCGCTCCATCACTACCAAACTGTACGACGGCTTCCAGTATCTGACCAACGGTATCATGTGA 

a score=409346.0
s hg17.chr1              148185136 5 + 245522847 ATGGA 
s panTro1.chr1           129935611 5 + 229575298 ATGGA 
s baboon.ENr231_1           278995 5 +    657133 ATGGA 
s rheMac1.SCAFFOLD121325     11475 5 -     22448 ATGGA 
s marmoset.ENr231_1         336864 5 +    772620 ATGGA 
s galago.ENr231_1           381115 5 +    825110 ATGGA 
s rn3.chr2                68486927 5 - 258222147 ATGGA 
s mm6.chr3                64570939 5 - 158945675 ATGGA 
s rabbit.ENr231_1           283177 5 +    694075 ATGGA 
s cow.ENr231_1              603768 5 +   1082283 ATGGA 
s canFam1.chr17           63150913 5 +  66886099 ATGGA 
s rfbat.ENr231_1            227585 5 +    561098 ATGGA 
s shrew.ENr231_13            22682 5 +     36462 ATGGA 
s elephant.ENr231_1         113827 5 +    387165 ATGGA 
s tenrec.ENr231_20              93 5 -     13226 ATGGA 
s monDom1.scaffold_18720   1804396 5 -   5714867 ATGGA 
s platypus.ENr231_1           4282 5 -     10983 gccca 

a score=625667.0
s hg17.chr1              148185141  99 + 245522847 AGCGTTTTTGGGGTCGC-----------------GGTCCGGACTTTGGGCGGGGGGTC---------CGGCCCC-AGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATCCGGC 
s panTro1.chr1           129935616  99 + 229575298 GGCGTTTTTGGGGTCGC-----------------GGTCCGGACTTTGGGCGGGGTGTC---------CGGCCCC-AGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATCCGGC 
s baboon.ENr231_1           279000  99 +    657133 AGCGTTTTTGGGGTCGC-----------------GGTCCGGACTTTGGGCGGGGGGTC---------CGGCCCC-AGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATCCAGC 
s rheMac1.SCAFFOLD121325     11480  99 -     22448 AGCGTTTTTGGGGTCGC-----------------GGTCCGGACTTTGGGCGGGGGGTC---------CGGCCCC-AGGACAGTTTTACCGCATTCCATCCACTCCCGATTCCTTCATGGATCCAGC 
s marmoset.ENr231_1         336869  99 +    772620 AGCGTTTTTGGGGTCGC-----------------GGTCCGGACTTTGGGCTGGGGGTC---------CGGCCCC-AGGACAGTTTTACCGCATTCCGTCCACTCCTGATTCCTTGATGGATCCGGC 
s galago.ENr231_1           381120  99 +    825110 ATCGTTTTTGGAGCCGT-----------------GGTCTGGACTTTGGGCCGGGGGTC---------CGGCACC-CGGACAATTTTACCGCATCCCGTGCACTCCCAGTTCCTCCATGGACCCGGC 
s rn3.chr2                68486932  99 - 258222147 AGCGTTTTGGGAGTCAC-----------------GGACTGGCCACTGGGCCGGGGGTC---------CGGCTCC-GGGGCAGTTTTACCGCGTCCCGTCCACCCCCAGCTGCCTCATGGATCCGAT 
s mm6.chr3                64570944  99 - 158945675 AGCGTTTTGGGAGTCAC-----------------GGGCTGGCCACTGGGCCGGGGGTC---------CGGCTCC-AGGGCAGTTTTACCGCATCCCGGCCACCCCCAGCGGCCTCATGGACCCGGC 
s rabbit.ENr231_1           283182  99 +    694075 AGCGTTTCTGGAGTCGC-----------------GGGCCGGGCTTTGGGCCGGGGGCC---------CAGCTCC-TGGACAGTTTTACCGCATCCCGTCCACTCCTGCTTCCTCCGTGGATCCGGC 
s cow.ENr231_1              603773  99 +   1082283 AGCACTACTGGAGTCGC-----------------GGTCCGGACTTTGGGCCGGGGGTC---------CGGCCCC-CGGGCAGTTTTACCGCATTCCGCCCACTCCCGGTTCCTCTGTGGACCCGGT 
s canFam1.chr17           63150918  99 +  66886099 AGCCTTTCTGGAGTCGC-----------------GGTCCAGAGTTTGGGCCGGTGGTC---------CCGCCCC-GGGGCAGTTTTACCACATCCCGCCTAGTTCCGTCGCCTCCGTGGAGCCGGC 
s rfbat.ENr231_1            227590  99 +    561098 ATCGTTTTGCGAGTCGC-----------------GGTCCGGACTGTGGGCTGGGGGTC---------CGGCCCC-CGGGCAGTTTTACCGCATTCCGCCCACTCCCGGTTCCTTGGTGGACCCGGC 
s elephant.ENr231_1         113832  99 +    387165 AGGGTTCTTGGAGTCAC-----------------GGTCCGGGCTTTGGGCCGGGGGTC---------CGGCTCC-GGGGCAGTTTTACCGCATCCCGCCCACTCCGAGCTCCTTCGTGGATCCGGC 
s tenrec.ENr231_20              98  76 -     13226 CGCGTTCTCGGAGCCGC-----------------GGTCTGGGCTTTgggccggcggcc---------cggcccc-ggggcAGTTTTACCGCGTCCCCTCCACT----------------------- 
s monDom1.scaffold_18720   1804401  99 -   5714867 ACCGTTGTTAGAAGTGC-----------------AGTCGGGCTTTTGGGCCGGGGGCC---------CCTCACC-GGGCCAGTTCTACCGCATCCCGCCCATCTCGGGAGCCGTTCTGGGGCCAGA 
s platypus.ENr231_1           4299 105 -     10983 gacttgcccacagttacacagctgacaagtggcagagccgggattcgaacccgcggcctctgactccccagccc-gggctctttccaccgagccgcgccgcttctc-------------------- 
s galGal2.chrUn           67951116  73 - 165033910 AGCGTGC---GCGCCGC-----------------GGCC---GTTGTGGGCCGGGGGTC---------CCTCCCCGGGGGCAG-------------CGTACAGCCCCGG-------GGGGATCGGG- 

a score=228740.0
s hg17.chr1              148185240 36 + 245522847 GTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA 
s panTro1.chr1           129935715 36 + 229575298 GTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA 
s baboon.ENr231_1           279099 36 +    657133 GTCTGCACTTTACAGAGGTCCAATCACACGGACCCA 
s rheMac1.SCAFFOLD121325     11579 36 -     22448 GTCTGCACTTTACAGAGGTCCAATCACACGGACCCA 
s marmoset.ENr231_1         336968 36 +    772620 GTCCGCGCTCCACAGAGGTCCGATCACGCGGACCCA 
s galago.ENr231_1           381219 36 +    825110 ATCGGCGCTCTCCGGGCGTCCGATTACGCGGACGCT 
s rn3.chr2                68487031 36 - 258222147 GTCTGCGCCCTGCGAGGGTCCCATCACTCGGACCCA 
s mm6.chr3                64571043 36 - 158945675 GTCGGCGCCCTGCGAGGGTCCCATCACTCGGACCCA 
s rabbit.ENr231_1           283281 36 +    694075 GTCCGCGCTCTGCGGGAGTCCGATCGCGCGGACCCA 
s cow.ENr231_1              603872 36 +   1082283 GTCCGCGCTGTACGGGAGTCCGATTACGCGCACCCA 
s canFam1.chr17           63151017 36 +  66886099 GTTTTCTCCTTACGGGGGTCCGGTTACGCGCACGCA 
s rfbat.ENr231_1            227689 36 +    561098 GTCCGCGCTCCACGGCGGCCCGATTACGCACACTCA 
s elephant.ENr231_1         113931 36 +    387165 GTCCGCACCCTACGGGGGTCCGATTACGCGGACCCA 
s tenrec.ENr231_20             174 35 -     13226 -TCCGGTCCCTGCGGGGCTCCGACTACGCGGACCCA 
s monDom1.scaffold_18720   1804500 36 -   5714867 CAGCATTGCCTGCGCAGGCCCGATTACTCGGACGCA 
s platypus.ENr231_1           3617 33 -     10983 GTCAGCGC---GGGGAGCCCCTTTCATCCGGACACA 
s galGal2.chrUn           67951189 35 - 165033910 ATTGGGGCCGGACTGCGGCCCTACAGC-CGTACCTT 

a score=555285.0
s hg17.chr10             80161942 63 - 135413628 AGT------TTGAACAATATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAAT---CTACTTCACTGTAA 
s panTro1.chr8           82159463 63 - 138322177 AAT------TTGAACAATATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAAT---CTACTTCACTGTAA 
s baboon.ENr114_1          440560 63 -    584309 AAT------TTGAACAATATTGTCGAGGAAACTGAAAAGCAATCTCACAGTCAAT---CTACTTCACTGTAA 
s rheMac1.SCAFFOLD70304     20932 63 -     66826 AAT------TTGAACAATATTGTCGAGGAAACTGAAAAGCAATCTCACAGTCAAT---CTACTTCACTGTAA 
s marmoset.ENr114_1        479983 63 -    685353 AAT------CTGAACAATATTGTCGAGGGAACTGAAAACCAATCTCACAGTCAAT---CTACTTCCCTGTAA 
s galago.ENr114_1          369087 63 -    502320 AAT------CTGAACGATATTGATGAGGGGATTGAAGGACAATCTTACAGCCAGT---CAACCTCACTGTGA 
s rn3.chr20              40770076 63 -  55296979 ACG------TTGGTTAGAGTTGTTGAAGGGATTGACGTGCAAACTCACAGTCAGT---CAACGTCCTTGTAA 
s mm6.chr10              74727059 63 + 130291745 ACG------TTGGTTAGAGTTGTTGAGGGAATTGACGTGCAACCTCACAGTCAAT---CAACATCTTTGTAA 
s rabbit.ENr114_16         116739 63 -    209963 AAT------TTGAATGATGTTGTTGAGGGAATTGAAAAACAATCTCACAGTCAAT---CTACTTCACTATAA 
s cow.ENr114_1             468464 66 -    523404 AAT------TTGCACAATATTGTTGAAGGAATTGAAAAACAGTCTCACAGTCATTCTACTACTTCACTGTAA 
s canFam1.chr26          36578478 63 +  41009621 AAT------TTGCACAGTTTTGCCGAGGAAACGGAGAACCAATCTCACAGTCAAT---CTACTTCACTGTAA 
s rfbat.ENr114_1           288291 63 -    353074 AAT------CTGCACAATATTGTCGAGGGAATTGAAAAACAATCTCACAGTCAAT---CTACTTCACTGTAA 
s shrew.ENr114_14              93 63 +      1248 AAT------TTGCAAGAAATTGTGGAAGAAAATGAAAATCAATCTCACAGTCAAT---CTACTTCACTGTAA 
s armadillo.ENr114_1       393483 63 -    434329 AAT------TTGAACAATATTGTCCAGGGATCTGAAAAACAATCTCACCATTAAC---CTACTTCACTCTTA 
s monDom1.scaffold_13316  1880926 63 +   4912536 AAC------TCTGGCTGTGCTGCTGAAGAGCTTGAGAATCAACTTTTCTTTCAAT---CTACAGCACTCTAA 
s platypus.ENr114_1         91217 69 -    121090 AATGGAACCTTGAGCAGTATTGTTGAAGAACTTGAAAAACAATTTCCATCCCAAT---CTACCGCATTATAA 
s galGal2.chr6            5980197 69 +  33893787 AACGGCAACTTGAGCTGTGTTGTGGAGGAGCTTGAGAAACGCTTTCCATCTCAGT---CGACAGCACTGTAA 
s xenTro1.scaffold_94      661136 63 +   2448135 AAC------TTGAGTTGTGTTGTCGAGGAGCTCGAAAAGCGCTTTCCTTCACAAT---CCACAGCACTGTAA 
s danRer2.chr12          32202185 63 -  35164833 AGC------ATGAACTCAGTAGTGGAGGAGCTGGAGAAACGCTTTCCATCTCAGT---CCACTGTTCTGTGA 

a score=238720.0
s hg17.chr10              80161855 87 - 135413628 TA---TCTA---CGCACAAATGTTTCAGAACTTCAAACTA-------TGTG-CC----CT-TCAGAAGTAACAAATATGGAAA-----TCACA-TCTGAA----CAAAACAAG--GGG 
s panTro1.chr8            82159376 87 - 138322177 TA---TCTA---CGCACAAATGTTTCAGAACTTCAAACTA-------TGTG-CC----CT-TCGGACGTAACAAATATGGAAA-----TCACA-TTTGCA----CAAAACAAG--GAG 
s baboon.ENr114_1           440473 87 -    584309 TA---TCTA---CGCACAAATGTTTCAGAACTTCAAACTA-------TGTG-CC----CT-TCAGAAGTAGCAAATATGGAAA-----TCACA-TCTGAA----CCAAACAAG--GAG 
s rheMac1.SCAFFOLD70304      20845 87 -     66826 TA---TCTA---CGCACAAATGTTTCAGAACTTCAAACTA-------TGTG-CC----CT-TCAGAAGTAACAAATATGGAAA-----TCACA-TCTGAA----CCAAACAAG--GAG 
s marmoset.ENr114_1         479896 87 -    685353 AA---TCTA---CGCACAAATGTTTCAGAACTTCAAACTA-------TGTG-CC----CT-TCAGAAATAACAAATATGGAAA-----TCACA-TCTCAA----CAAAACCAG--GAG 
s galago.ENr114_1           369000 87 -    502320 TA---TCCA---CTCACAAACATCTCAGAACATCAAACTA-------TTTG-CC----CT-CCAGAGATAATAAATGTGGAAA-----TCACA-CCTGAA----CAAAACCGG--GAG 
s rn3.chr20               40769989 87 -  55296979 TG---TCCA---CCCACAGAGCTCTCAAAACTCCACCCCT-------TTTG-TC----CT-GCAGAGAAAACAAACATGAAAA-----TCACA-TGTGAC----CAGAGCCAG--GAA 
s mm6.chr10               74726972 87 + 130291745 TG---CCCA---CCTGCAGATCCCTCAAAACTACACACGT-------TTTG-CC----CT-GCAGAGAAAACAGGCATGAAAA-----TCACA-CATGAC----CAGAGCCAG--GAA 
s rabbit.ENr114_16          116652 87 -    209963 TA---TCCT---CCCACAAACGTTTCAAAACTTCAAACGA-------TTTG-CC----CT-TCAGAGATAACACATATGGAAA-----ACACC-TGTGAA----CAAAACCAG--GAA 
s cow.ENr114_1              468377 87 -    523404 AA---TCCA---CCAGCACAACTCTCCAAACTTCAAATGA-------GTTG-TC----CT-TCAGAGACAACAAATACGGAAA-----TGACA-TCTGAA----TAAAACCAG--GAG 
s canFam1.chr26           36578391 87 +  41009621 TT---TCCA---GCAACACACAGCTGGAAACTAGAGACAA-------GTTG-CC----CT-CCAGAGAGAGAAAATGTGGACG-----TGACG-TCTCAA----CAACCCCAG--GGG 
s rfbat.ENr114_1            288204 87 -    353074 TA---TCCA---CTAACACACAACCCAAAATTTCAGACTA-------GTTG-CC----CT-TCAGAGATAACAAATATGGAAA-----TGACA-TCTGAA----CAAAATCAG--GAG 
s shrew.ENr114_14                5 88 +      1248 TT---CCCA---CCCAAACAGATTTCAAAACTTCCAACTA-------GTTGGCC----CT-TCTGAATTAACAAATATGGAAA-----TGAGA-TCTGAA----CAAAAACGA--GAA 
s armadillo.ENr114_1        393396 87 -    434329 AA---CCCC---CCCACACACAGTTCAAAACTTCAATTTA-------CTTG-CT----CT-CCAAAGTTAACAGATATGGAAA-----TTACA-TCTGAA----CAAACCCAG--GAG 
s monDom1.scaffold_13316   1880839 87 +   4912536 TC---ATCA---CCCACACAGAGTTCCAAGCT-CAAGCCA-------GCTG-CCA---CC-CCTCAGCCACCCACTACAGGAA-----CTGTG-ACTGAA----CAAATGCAG--CTG 
s platypus.ENr114_1          91127 90 -    121090 CA---TCCAATACCTAAGCATGTGATGAAGCCT-AAACAA-------CTCG-CT----CAACCAGCTCTTCCAAATACAGAAA-----TTGTG-GCTGAG----CAGAATCAG--CAG 
s galGal2.chr6             5980107 90 +  33893787 CACGTTCTG---CCCAAGCACATCTCTAAGCT-CAAACCA-------GTTG-CAA---CG-CCAGAGCTGCCAACTCCCGAGG-----CTGCA-GCTGAG----CACAACCAG--CAG 
s xenTro1.scaffold_94       661040 96 +   2448135 AT---TACG---TCAAAACAAATTCCAAAATCCCGATCT--------TTTA-CAACAACC-CCAGAAAATCAGATTTCAGAGA-----CTGCA-CCCGAGTATGCAAAACAAAATGGA 
s fr1.chrUn              340429676 83 - 349519338 TG---CCCA---A----------------GCTTCATCCTAAACCACAAGTG-A-----CT-GAAGAATCCGAAGACACCGAAAGTACTCAAAGCTCGGAT----CCCTGGGAT--GAG 
s danRer2.chr12           32202080 80 -  35164833 CG---CCCA---C------------TAGTGATCAACCCTAAACCGCAAGTG-T-----CT-GTCGAACCAGAGGCTGGTGTAA-----CAGAG-GCGGAG----CCTGCTCAA--GA- 

a score=938384.0
s hg17.chr10              80161742 113 - 135413628 CAGTGTGT---AAAACAGACCCT------CAG-AGAGAACCAAAAGGCATCCTCAGACACGTTAAAAACTTAGCAGA-ACTTGAAAAATCAGTAG-CTAACATGTACAGTCAAATAG---A-AAAAAAC 
s panTro1.chr8            82159262 114 - 138322177 CAGTGTGT---AAAACAGACCCT------CAG-AGAGAACCAAAAGGCATCCTCAGACATGTTAAAAACTTAGCAGA-ACTTGAAAAATCAGTAGTCTAACATGTACAGTCAAATAG---A-AAAAAAC 
s baboon.ENr114_1           440360 113 -    584309 CAGTGTGT---AAAACAGACCCT------CGG-AGAGAACCAAAAGGCATCCTCAAACATGTTAAAAACTTAGCAGA-ACTTGAAAAATCAGTAG-CTAACATGTACAGTCAAATAG---A-GAAAAAC 
s rheMac1.SCAFFOLD70304      20732 113 -     66826 CAGTGTGT---AAAACAGACCCT------CGG-AGAGAACCAAAAGGCATCCTCAAACATGTTAAAAACTTAGCAGA-ACTTGAAAAATCAGTAG-CTAACATGTACAGTCAAATAG---A-GAAAAAT 
s marmoset.ENr114_1         479785 111 -    685353 --GTGTGT---AAAACAGATCCT------CAG-AGAGAACCAAAAGGCATCCTCAAACATGTTAAAAACTTAGCAGA-ACTTGAAAAATCAGTAG-CTAACATGTACAGTCAAATAG---A-AAAAAAA 
s galago.ENr114_1           368884 116 -    502320 CAGTGGCCCCAAAGACTGACCCT------CCA-CGGGAACCAAAGGGAATCCTCAAACATATTAAAAACTTAGCAGA-ACTGGAAAAGTCAGTTG-CTAACATGTACAAGCAAATAG---A-AAAGAAC 
s rn3.chr20               40769876 113 -  55296979 CACCGTGT---GGGGCGGAACCC------CAC-AGACATCCCAAAGGGATCCTCAGGCACGTGAAAAACCTGGCAGA-GCTCGAGAAATCGGTGT-CTAACATGTACAGTCACATCG---A-GAAAAAC 
s mm6.chr10               74726859 113 + 130291745 CGCAGTGG---GGGGCAGAACCC------CAC-AGACATCCAAAAGGGATCCTCAGACATGTGAAAAACTTGGCAGA-GCTCGAGAAATCAGTGT-CTAACATGTACAGTCACATAG---A-AAAAAAC 
s rabbit.ENr114_16          116539 113 -    209963 CAGTGGGT---AATGCAGACCCT------CAG-AAAGAACCAAAAGGCATCCTCAAACATATTAAAAACTTAGCAGA-ACTTGAAAAATCAGTAG-CTAACATGTACAGTCAAATAG---A-AAAAAAC 
s cow.ENr114_1              468264 113 -    523404 CACTGTGT---AATGCAAATCCT------CAA-AGGGAACCAAAAGGCATTCTCAAACATGTAAAAAACTTAGCAGA-ACTGGAAAAGTCAGTGG-CTAACATGTACAGCCAAATAG---A-AAAAAAT 
s canFam1.chr26           36578278 113 +  41009621 CCGTGTGT---GACACAGACCCC------CAG-AAACAACCAAAGGGCATCCTCAAGCATATAAAAAACTTAGCGGA-CCTTGAAAAGTCAGTTG-CTAACATGTACAGTCAAATAG---A-AAAAAAC 
s rfbat.ENr114_1            288091 113 -    353074 CAGCATGT---CATGCAGATCCT------CAA-AGAGAGCCAAAAGGAATCCTCAAACATGTGAAAAACTTAGCAGA-ACTTGAAAAGTCAGTAG-CTAACATGTACAGTCAAATAG---A-AAAAAAC 
s armadillo.ENr114_1        393292 104 -    434329 CAGTGTGT---AGA---------------CAA-AGAGAACCAAAAGGCATCCTCAAACATATTAAAAACTTAACAGA-AATTGAAAAGTCAGTGG-CTAACATGTACAGTCAAATAG---A-GAAAAAC 
s monDom1.scaffold_13316   1880723 116 +   4912536 CAGACCCA---AGTCCTGCACCT------CGA-AGGGAACTGAAAGGCATCCTCAAAAATATCCCGAACTTAGCAGC-CATTGAGAGGTCAGTAG-CAAACATGTACAGCCACATAGGCCA-AAAACAC 
s platypus.ENr114_1          91017 110 -    121090 ---TGATA---CCCACAGGTCCT------AAG-AGGGAATTGAAAGGCATACTCAAAAATGTCCCAAATTTGGCAGA-TATTGAAAAGTCAGTGG-CTAACATGTACAACCAAATAG---A-CAAAAGG 
s galGal2.chr6             5979994 113 +  33893787 CAGTGCCA---GAGCCACCTCCC------CGT-AGGGAGCTGAAAGGTATTCTTAAAAACATTCAGAATTTAGCAGC-GATTGAAAAGTCCGTGG-CCAATATGTACAGCCAAATAG---A-CAAAAAC 
s xenTro1.scaffold_94       660924 108 +   2448135 ------CT---CAACCAGATCCTGGCCCACGC-AGAGAGCTAAAGGGAATCCTCAAACATATTCACAACTTAGCCGA-GATTGAAAAATCCGTAG-CTAACATGTACAATAAAATTG---A-CA----- 
s tetNig1.chr2             5926437 105 +  19247847 -------------CAGTACCCCT------CGA-AAGGAGCTGAAAGGGATCCTGAAGAACATCCACAACATCGCAGACCATCGAGAAGTCCGTGG-CCAACATGTTGAGCCAGATCG---ATCAGAAAC 
s fr1.chrUn              340429566 103 - 349519338 -------------CTGTGGGAGG------AAA-AAGGAGCTCAAAGGGATCCTGAAAAACATCCAGAATCTCGCTGA-CATAGAGAGGTCCATTG-CCAACATGTACAGCCAAGTAG---A-CAAAAAC 
s danRer2.chr12           32346428 105 -  35164833 -------------CAGAGCCTCC------CAAGAGGGAACTCAAGGGGATCCTTAAGAACCTCCAGAACATAGCAGA-CATCGAGAAATCTGTTG-CCAATATGTACAGTCAAATAG---ATAAAAAGC 

a score=-90144.0
s hg17.chr10              80161494 248 - 135413628 ---ccctct----------tcc---------tcttcctcctc---------ctA---------CATTTTTT----------CCACTTTC-----------------------------------CGTTTCAACGTCTGGTCCCCC--------------------------------AACACCAC-----CT------------------C---------TTCTACCTCCATTTCCAACTCCTCTTCCTCCACCACCTCCTTC---TATTC--------C--TTGCCCTCCACCTCCTT--CAGCTTCATTTCTGTCCACAGAGTGTGTCTGTATAAC---AGGTGTTA-------AATGCACGACCAACTTGATGCC-TGCCGAGAAAATTAAGTCCTCTATGACACAGCTATCAACAACGA 
s panTro1.chr8            82159037 225 - 138322177 ---------------------------------------------------------------CATTTTTT----------CCACTTTC-----------------------------------CATTTCAACGTCTGGTCCCCC--------------------------------AACACCAC-----CT------------------C---------TTCTACCTCCATTTCCAACTCCTCTTCCTCCACCACCTCCTTC---TATTC--------C--TTGCCCTCCACCTCCTT--CAGCTTCATTTCTGTCCACAGAGAGTGTCTGTATAAC---AGGTGTTG-------AATGCACGACCAACATGATGCC-TGCCGAGAAAATTAAGTCCTCTATGACACAGCTATCAACAACGA 
s baboon.ENr114_1           440115 245 -    584309 ---ccctct----------tcc---------tcttcctccGT---------CTA---------CATTTTTT----------CCACTTTC-----------------------------------CATTTCAACTTCTGGTCCCCC--------------------------------AACTCCAC-----CA------------------C---------TTCTACCTCCATTTCCAACTC---TTCCTCCACCACCTCCTTC---TATTC--------C--TTGCCCCCCACCTCCTT--CAGCTTCATTTCTGTCCACAGAGTGTGTCTGTATAAC---AGGTGTTA-------AATGCACGACCAATATGATGCC-TGCCGAGGAAATTAAGTCCTCTATGACACAGCTATCAGCAACAA 
s rheMac1.SCAFFOLD70304      20487 245 -     66826 ---ccctct----------tcc---------tcttcctcctt---------ctA---------CATTTTTT----------CCACTTTC-----------------------------------CATTTCAACTTCTGGTCCCCC--------------------------------AACTCCAC-----CA------------------C---------TTCTACCTCCATTTCCAACTC---TTCCTCCACCACCTCCTTC---TATTC--------C--TTGCCCCCCACCTCCTT--CAGCTTCATTTCTGTCCACAGAGTGTGTCTGTATAAC---AGGTGTTA-------AATGCACGACCAATATGATGCC-TGCCGAGGAAATTAAGTCCTCTATGACACAGCTATCAGCAACAA 
s marmoset.ENr114_1         479532 248 -    685353 ---ccctct----------tcc---------tcttcctcctc---------ctcc------tccACTTTTT----------CCACCATC-----------------------------------TGTTCCTTCTTCTGGTCCCCA--------------------------------AACTCCAC-----CT------------------C---------TTCTACCTCCATTTCCAACTC---TTCCTCCACCACCTCCTTC---TATTC--------C--TTGCCCACCACCTCCTT--CAGCTTCATTTCTGTCCACAGAATGTGTCTGTATAAC---AGGTATTA-------AATGCACGACCAACACAATGCC-TGCCGAGGAAATTAAGTCCTCTATGACACACCTATCAACAACAA 
s galago.ENr114_1           368657 227 -    502320 ---ccttct----------tcc---------tcctc---------------------------ccccGTTT----------CCACTTTC-----------------------------------TCTTCCTACATTGG---CAGC--------------------------------ACCTCTGC-----CC------------------C---------TTCCACCTTCACTTCCAACCC---TTCCTCCACCACCTC---------TTC--------C--TTGTCCGCTGCCTCCTT--CAGATGCATTTCTGTCCACGGAGTGTGTTTGCATGCC---AGTTGATA-------AAGGGACTATCAACAAGACACC-TGCCAGTGAAATTAAACCCTCTGTGACACAGCTTCCAGCATCAG 
s rn3.chr20               40769628 245 -  55296979 ---ccctcc----------tcg---------ccccc---------------------------aacttctt----------acattttc-----------------------------------tcttccCATTTCTACAACCCCCGCCT--------------------cttctcttcctcctc-----ct------------------c---------ctccaccatcacttcctcctc---ctcctcGACCACCAGCTCC---CCGCC--------T--TTTCCCACTGCCTCCTT--CCACTTCCGTCCCATCCACAGACAGCATCTCTACACC---AGCTGCTA-------AATGCACTGCCAGTGTCACACA-CGCCAGAGAAACTA---TGTCTACGACACAGCCACCAGCATCCA 
s mm6.chr10               74726611 245 + 130291745 ---ccctcc----------tcc---------cccac---------------------------aacttgtt----------acattttc-----------------------------------tcttcccatttctacaccccctactt--------------------cttctctacctcttc-----ct------------------c---------ctccactgtcacttcctcctc---ctcctcGGCCACCAGCTCC---CCGCC--------T--CTTCCCACAGCCTCCTT--CCACGTCCATTCCATCCACAGACAGCATCTCTGCACC---AGCTGCTA-------AATGCACTGCCAGTGCCACACA-CGCCAGAGAAACCA---CGTCTACGACACAGCCACCAGCATCCA 
s rabbit.ENr114_16          116328 208 -    209963 ----cctcc----------tct---------ccctc---------------------------cacttctc----------cccctttc-----------------------------------agttccttcatctacaccctc-----------------------------------ttctt-----ct------------------c---------ctccactaccgccgcctcttc---c-------------------------------------atgcccacctccttctG--CAGTTTCAGGACTATCCACAGAGTGTGTTTGCATACC---TCCTGATG-------AATGTACTACCAGTTTGACACC-TGCCAAGGAAAGTAAATTCTCTGTGACACAGCTACAAACACCAA 
s cow.ENr114_1              468023 232 -    523404 ----cctct----------tcc---------tccac---------------------------atct---t----------ctactttc-----------------------------------tgttccctctcctccttcctc--------------------------------tacttctc-----ct------------------c---caccttttctaccttcacttccccctc---ttcctccagcatctcctcc---tcgtc--------c--tTCGTTACTGCCTCCTT--CAATGTCAGTTCCATCCACCACGTGTGCGTTTACACC---AGCTATTG-------AACGTACTGTCAATGTGACACC-AGCCAAGGAAGTGAAATCCTCTATGATACAGTTGTCAA------ 
s canFam1.chr26           36578046 223 +  41009621 ----ccatt----------tct---------ccca-------------------------------------------------ctttc-----------------------------------caccccaccttctcctccctc--------------------------------ttcttctc-----ca------------------t---cacctcttctaccttcacttccctccc---tccccccaccatcacctcc---tcttc--------c--ttctcctcTGTCCCCTC--CGTCTTGGGCTCCATCCACTACGTGTGTCTGTGTACC---AGTTGTGA-------AGCACACTGTCAGTGTGACACC-TGCCGAGGACGTGGAGCCCTCTGTCGCACAGCTACCAG------ 
s rfbat.ENr114_1            287844 238 -    353074 ----cctct----------tcc---------ttttc---------------------------ctctgctt----------ccactttc-----------------------------------tgtgtcctcttctcctccctc--------------------------------tacttctc-----ct------------------cttccacctcttctttctTCACTTCCCTGTC---TTCCTCCAACACTCCCTCC---TCTTC--------C--TTCTCCAGCACCTCCTT--CAATTTCAGTTCCATCCACTATGTGTGTTTGTACACC---AGCTGTTA-------AACACACAGTCAGTGTGACACC-ACCCAAGGAAATGAAGTCTTCTGTGATACAGCGATCAA------ 
s shrew.ENr114_9             25340 220 +     28685 ----cttcc----------tcc---------tccac---------------------------cttttcat----------ccactttc-----------------------------------tattcc---tcctccccccac--------------------------------tacctccc-----ct------------------c---------------ctccatttcccactc---tccctccaccgcctcctcc---tcttc--------c--ttctccAGTGATTACTT--CAGCATCTTTTCCATCGCCAAAGTATGTTTGTATGC----AGATGTTA-------AGCATACTGCCAGTGTAACACCTAAACAAGGAAATGGATTCTTCTGTGATGCAACTGTCAA------ 
s armadillo.ENr114_1        393075 217 -    434329 ----tctgt----------tcc---------tcctc---------------------------cttctcct----------cctctctc-----------------------------------ttctcc-----------------------------------------------tcccccAT-----TT------------------C---------TTGCACCATCATTTCCTGCTC---TTCCTCCACCATCTCCCTT---TCTTC--------T--TTCTTCACTGCCTCCTT--CAGATTCAGTTTCATCCACAGAACGTAGTTGTAAACC---AATTGACA-------AATGCACTGTCAACTTGACACC-TGTCAAGCAAATTA---CATCTCTGTTACAGCAGTCAACATCGA 
s monDom1.scaffold_13316   1880446 274 +   4912536 AAGCCAACT----------TCT---------CCATC---------------------------TCCTTTTTGGATATCAAAACACAGTC-----------------------------------CTCAACATTATTTGTCCCCCAAGACAAGGGAGAAAATGATAGAGAATATTCCAGACCCCCCTAACAcc------------------c---------ctccacctttccctcctcctc---cccttccaccaccacc-------------------------accactgccacctc--ctgcttcactcattccctcatgctccccatccAGCCC---TGGTGTTT-------GGCATCGCTCCATGCTCTCCCC-TGCAAGAGAAAAGGACTCTTTGGCTAGGCAGCTATCCCCAGTGG 
s platypus.ENr114_1          90812 199 -    121090 ----tctcc----------aca---------tccct---------------------------cttgtctt----------ctgcctcc-----------------------------------cactcccttttctct--------------------------------------ttcttctc-----ct------------------c---------ctcccccttttcttcctcctc---ctcctACCCCACCACCACA---GTTAC--------C--TCCATCTCCACCTCCTC--CAATTCCTTTCCCAACT----------TCTGTAAATC------------------------CTATCAGCCTCTCCTC-TGTCAGACACAATAATCCCCCCAATGTGCAGCCATCAA------ 
s galGal2.chr6             5979746 233 +  33893787 AAGTTTTCT----------AGC---------TCCTCAGACCAAAGGAGAAGTTACAGAAAACATTCCAGAC----------CCACCTAA-----------------------------------AActcccccaccccctcctcc--------------------------------tctactgc-----ct------------------c---------ctccacctccatcccctcctc---ttttgccaccccatcctccaactctgc--------c--cctcgcttctgttcctt--cttcttcatctcttcctA----------------------------------------GCACCCAACACCTTTCCCC-TGCAAAGCATTCAAAATCCCCTGCCAAACAGCCAGCTG------ 
s xenTro1.scaffold_94       660688 227 +   2448135 ------TCT----------TCCAGAAGAACCCCTTG---------------------------AAATACCT----------TCACCTTC-----------------------------------TCCCACACCTCCTCCATTAGA--------------------------------TACTCCAT-----CA------------------C---------CTGCGCCACAATCTCAACCAA---CTCCTTTAGCACCTCCACC---TCCAC--------CATTTCTCCAAGACCTTCT---------CACCTCTAGC-------AGTTTACGTAATCCTTTATTTCATA-------TAGCTCCTTCCGATTTGTCTGC-TGCAAAGGACAAACTATCTCCTATCAGAACATCACCAT------ 
s tetNig1.chr2             5926174 259 +  19247847 cgcaccctcctt--cttcacct---------ccgcc---------------------------accaccCG----------CCGGGGGCTTCTCCTCACC-CTGACCAC-GGGGAAAAGACGACGCTtcctacccctccccctcg--------------------------------tcctcctc-----ct------------------c---------ctcctcctccaccaccacccc---ctcctcctTTGCCTCCCTC---A------------C--TGTCCCCCTCACTCCTGCGCCCATCCACCTTCGTCCT-----CCCGTCCCTTTCAG---AGGTGCCC-------ACGCTGCGGCCGGTGTCCCTCC-GG-----CCCACGCCGCCCCCTG---CACCCA------CCACTG 
s fr1.chrUn              340429340 225 - 349519338 T--ACCCTCC-------CATCT---------CCACA---------------------------AAC---------------CCGAGTGC------------------------------------------------CCCCTTCA--------------------------------GCCGCCTC-----CTGGATCCAGCAGCCAGGGGT---------CCCCCCCAACACCACCACCGC---TCCCCCCACCACTCTCCCC---AGCGAGCAATCAGC--TGTGCCAGCTTCTCCAG------------TTTGTTCC-----AGCATCTCTGCCGC---CGGTGTCC-------TCACTGCGTCCCGTCTCGCAGC-GA--AAACACCCCCCTCCTCCTGAGTCATCTC------AAACTG 
s danRer2.chr12           32346170 248 -  35164833 C-----CTGCAGAACTACACCA---------CTGCC---------------------------AGCTTACT----------CCAAAACT------ACACCACTGGCTTCTTGGGCCAGTCCTACACTTGACACTCCGTTCCTAGG--------------------------------AGGGGCAT-----TA-AATACAGCTGTA-----T---------CAACTCCTTCACCTTTACTCC---CTCCCTCATCATCGAACTT----------------T--TATCGTTCCATACCTTG------------TGAAGCAT-----GGGGCCGCCCTCAC---ATGCGCTCTGAGACGATGCTATGACCGCTGGTCTTGC-GG----------GCGGTGCCTTG--------C------TAACTG 

a score=-26806.0
s hg17.chr10              80161467 27 - 135413628 ttg--tcctcctccctc------------tcctccttctat 
s panTro1.chr8            82159011 26 - 138322177 ttg--tcctcctccctc------------tcctccttctA- 
s baboon.ENr114_1           440088 27 -    584309 ttg--tcctcctccctc------------tcctccttctat 
s rheMac1.SCAFFOLD70304      20460 27 -     66826 ttg--tcctcctccctc------------tcctccttctat 
s marmoset.ENr114_1         479514 18 -    685353 ttg--tcctcctcc---------------------ttctat 
s galago.ENr114_1           368630 27 -    502320 ctc--tcctccttccct------------gcctcctcatcc 
s rn3.chr20               40769604 24 -  55296979 -----tcctcttcccct------------ttcttcccctaa 
s mm6.chr10               74726587 24 + 130291745 -----tcctcttcccct------------ttctccccctaa 
s rabbit.ENr114_16          116306 22 -    209963 -----tcctcttcctcc------------ttctatccct-- 
s cow.ENr114_1              467998 25 -    523404 CAG--tcttcctccttc------------taatccacct-- 
s canFam1.chr26           36578039  7 +  41009621 --------------------------------tccacct-- 
s rfbat.ENr114_1            287819 25 -    353074 ctg--tcctcctccctg------------tcgtcctcct-- 
s shrew.ENr114_9             25303 37 +     28685 ttg--tccttctccatcaccaccttccattcctcctcct-- 
s armadillo.ENr114_1        393053 22 -    434329 -----tccacctcaacc------------tcttctactt-- 
s monDom1.scaffold_13316   1880418 24 +   4912536 -----TCCTCTTACATC------------TTCTCCACTGAC 
s platypus.ENr114_1          90796 16 -    121090 -----------tcaccc------------tcctcttcct-- 
s galGal2.chr6             5979920 24 +  33893787 tAG--CACCCAACACCT------------TTCCCCTGC--- 
s xenTro1.scaffold_94       660661 24 +   2448135 CTT--TCCAGCACCATC------------ACGTCCACC--- 
s tetNig1.chr2             5926151 23 +  19247847 --gcctccttaatcccc------------tcctcctc---- 
s fr1.chrUn              340429317 23 - 349519338 --TAGTCTGCCATCTAC------------CCCTCCTT---- 
s danRer2.chr12           32346147 23 -  35164833 --CAGTCCGCCCCCACC------------CCCTCCTC---- 

a score=-30988.0
s hg17.chr10              80161425 42 - 135413628 ---------------------t----------cctc---ttgctcctcctcctga------------------catttctc------ctttttctctttt 
s panTro1.chr8            82158969 42 - 138322177 ---------------------t----------cctc---ttgctcctcctcctga------------------catttctc------ctttttctctttt 
s baboon.ENr114_1           440046 42 -    584309 ---------------------t----------cctc---ttgctcctcctcctga------------------catttctc------ctttttctctttt 
s rheMac1.SCAFFOLD70304      20418 42 -     66826 ---------------------t----------cctc---ttgctcctcctcctga------------------catttctc------ctttttctctttt 
s marmoset.ENr114_1         479472 42 -    685353 ---------------------t----------cctc---ctgctcctcctcctga------------------cattcctc------ctttttctctttc 
s galago.ENr114_1           368588 42 -    502320 ---------------------t----------cctc---atcctcctcctcctga------------------ccttacac------ctttttctctttc 
s rn3.chr20               40769568 36 -  55296979 ---------------------G----------cctc---ttcctcaacctccta-----------------------ttgc------ctttactacttt- 
s mm6.chr10               74726551 36 + 130291745 ---------------------g----------cctc---ttcctagacctccca-----------------------ttgc------ctttaccacttt- 
s rabbit.ENr114_16          116276 30 -    209963 ---------------------t----------cctt---ttcctccac-----------------------------ttgt------ccttactcattt- 
s cow.ENr114_1              467938 60 -    523404 ---------------------t----------cctc---ctcctcttccttctcctcctcTTACGCCTCATATCCTTACTC------CTTTGGCTGTGTC 
s canFam1.chr26           36578021 18 +  41009621 ---------------------t----------cctc---ctcctcttcctcc------------------------------------------------ 
s rfbat.ENr114_1            287780 39 -    353074 ---------------------c----------cctc---ctcctcctctggt---------------------ccttactc------cttttgctctttc 
s shrew.ENr114_9             25249 54 +     28685 ---------------------t----------tctc---ctccgccacctcctcccccaccactgcc------tctttctt------cctttactcttcc 
s armadillo.ENr114_1        393014 39 -    434329 ---------------------t----------cctc---cttttcctctttc---------------------ctgtcctc------ctcttcctcctcc 
s monDom1.scaffold_13316   1880613 64 +   4912536 ---------------------ttcactcattccctc---atgctccccatccAGCCCTGGTGTTTGG------CATCGCTC------CATGCTCTCCCCT 
s platypus.ENr114_1          90757 39 -    121090 ---------------------t----------cctt---ctcctccccatcc---------------------ccattctc------ttcctcctctccc 
s galGal2.chr6             5979878 42 +  33893787 ---------------------a----------actc---tgcccctcgcttctgt------------------tccttctt------cttcatctcttcc 
s xenTro1.scaffold_94       660613 48 +   2448135 ---------------------T----------CCTA---TGCCATCCCCCTCTGATAATTT------------TATGCCTC------CACCCCCACCTTT 
s tetNig1.chr2             5926088 63 +  19247847 TCGTCGTCGTCAACCACGTCCC----------CCTT---AGTCAccacctcc---------------------cccccccccca---catctgctcctct 
s fr1.chrUn              340429257 60 - 349519338 TCCTC---------CGCCTCCC----------CCTCCAGAACGGCCACCTCC---------------------CTCCTCCCCAAAAACATCCCCTCCTTA 
s danRer2.chr12           32346107 40 -  35164833 --------------TACCTGCT----------CCAC---AACCACCACCACC---------------------GCCTCCAC------------CTCCCTC 

a score=209058.0
s hg17.chr10             80161317 108 - 135413628 -AAGAAATATTTTT--------GAAAA---TTTTGCCCATCCACCAAACATCTC---TCCTTCTGCCTGtcc------ccttccccctcctcctcctatttctcctccttctcctcctcctgctcctgc 
s panTro1.chr8           82158861 108 - 138322177 -AAGAAATATGTTT--------GAAAA---TTTTGCCCATCCACCAAACATCTC---TCCTTCTGCCTGtcc------ccttcctcctccttctcctatttctcctccttctcctcctcctgctcctgc 
s baboon.ENr114_1          439941 105 -    584309 -AAGAAATATTTTT--------GAAAA---TTTTGCCCATCCACCAAACATCTC---TCCTTCTGCCTGtcc------cc---ctcctcctcctcctatttctcctccttctcctcctcctgctcctgc 
s rheMac1.SCAFFOLD70304     20313 105 -     66826 -AAGAAATATTTTT--------GAAAA---TTTTGCCCATCCACCAAACATCTC---TCCTTCTGCCTGtcc------cc---ctcctcctcctcctatttctcctccttctcctcctcctgctcctgc 
s marmoset.ENr114_1        479376  96 -    685353 -AAGAAATATTTTT--------GAAAA---TTTTTCCCATCCACCAAACATCTCCCCTCCTTCTGCCTGTCT------CC---------------CTATTTctcctcctcctcctccatctgctcctgc 
s galago.ENr114_1          368531  57 -    502320 -AAAGAACAATTTT--------GAAAA---GTTTTCCCATC---------TCTc---tcctcctctctttcc------tc------------------------------------------ctcctcc 
s rn3.chr20              40769508  60 -  55296979 -AAGGAACTCTTTT--------GAAAT---GGTTCCCCATCCACCCAGCATCTC---------TGCTCCCCT------CC------------------------------------------CACAGCT 
s mm6.chr10              74726491  60 + 130291745 -AAGGAACTCTTTT--------GAGAT---CGCTCCCCATCCACCTAGCATCTC---------TGctcccct------cc------------------------------------------cacatcc 
s rabbit.ENr114_16         116210  66 -    209963 -AAGGCGTGATTTC--------GAAAA---TCCTTCCCACTCACCATACGTtcc---cccttgtgcccaccc------ct------------------------------------------ctcttcc 
s cow.ENr114_1             467866  72 -    523404 -AACAGACATTTTT--------GAAAA---TCTTCCCTGTCCACCAAAAACCTc---tcctccccctcctccttcttgtc------------------------------------------ctccccc 
s canFam1.chr26          36577955  66 +  41009621 -AAGGAACATTTTC--------GAAAT---CCTTCCCAAACCACCAAACATCTc---tcctccacctgcccc------tc------------------------------------------ctcctcc 
s rfbat.ENr114_1           287717  63 -    353074 -AAGGAACGTTTTC--------GAAAA---TCTCC---ATTCACCAAACATCTc---tcctcttcctcctcc------tc------------------------------------------ctcctcc 
s shrew.ENr114_9            25183  66 +     28685 -AAGTAACATTTTT--------GAAAA---TATTCCCCATCCACCAAGCATCTA---TTCCTctcctccttc------tc------------------------------------------ctccttg 
s armadillo.ENr114_1       392948  66 -    434329 -AAGGAACATTTTT--------GAAAA---TCTTCCCCATTCACCAAACATCCT---tcctcctcctcctat------tt------------------------------------------tccttac 
s monDom1.scaffold_13316  1880517  96 +   4912536 -GGAGAAAATGATA--------GAGAA---TATTCCAGACCCCCCTAACAcccc---tccacctttccctcc------tc------------ctccccttccaccaccaccaccactgccacctcctgc 
s platypus.ENr114_1         90667  90 -    121090 -AAAAAAATTGAAT--------GAAAA---TATTCCTGACCCCCCAAAAACTCC---TCCCCCAcctcctcc------tc------------------tttctctctctcctcttccttctcctcccct 
s galGal2.chr6            5979770 108 +  33893787 -AGGAGAAGTTACA--------GAAAA---CATTCCAGACCCACCTAAAActcc---cccaccccctcctcc------tctactgcctcctccacctccatcccctcctcttttgccaccccatcctcc 
s xenTro1.scaffold_94      660506 107 +   2448135 -AATGAACATGATCCGATGCTGGAAGACCCTATTCCAGATCCACCAAATATTCC---CCCTCCCCTTCCACC------AC------------TTCCCCATTCAGTATCCTGTTCACAGCTTCTTTTACC 
s danRer2.chr12          32201614  96 -  35164833 CG-AGGTCAATGTG--------GAGAT---CATTCCAGACCCTCCTGATGTACC---TGCTCCACAAccacc------ac------------caccgcctccacctccctccagtccgcccccaccccc 

a score=1123317.0
s hg17.chr10              80161020 297 - 135413628 TGAAGAGGCAAATTTGA------CAGAGAA-AG---------------------------AGGAAATAAGGCAAGGTGAA----------------------ACACTGATGATAG---------------------------AAGG---------A--------------ACAGAACAGTTGAAA------------------TC---TCT---------------------------------------------------------------------C-----TCTTCAGA-CTCTTCATT------------------TTGCT------------TTCCCAGGCCTCA---CTTCTCATTCTCCACTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATC------AGAACCTAATGTC------------ATCAGTTCTCCTGCTGAGT------GTTC------CTTGGAACTTTCTCCTT---CAAGGCCTTGTGTTTTACATTCTTCA---CTCTCTAGGAGA--GAGACACCTATTTG-------TATGTTACC-TATT----GAAACCGA 
s panTro1.chr8            82158564 297 - 138322177 TGAAGAGGCAAATTTGA------CAGAGAA-AG---------------------------AGGAAATAAGGCAAGGTGAC----------------------ACACTGATTATGA---------------------------AAGG---------A--------------AGAGAACAGTTGAAA------------------TC---TCT---------------------------------------------------------------------C-----TCTTCAGA-CTCTTCATT------------------TTGCT------------TTCCCAGGCCTCA---CTTCTCATTCTCCACTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATC------AGAACCTAATGTC------------ATCAGTTCTCCTGCTGAGT------GTTC------CTTGGAACTTTCTCCTT---CAAGGCCTTGTGTTTTAAATTCTTCA---CTCTCTAGGAGA--GCGACACCTATTTG-------TATGTTACC-TGTT----GAAACCGA 
s baboon.ENr114_1           439644 297 -    584309 TGAAGAGGCAAATTTGA------CAGAGAA-AG---------------------------AGGAAATAAGGCAAGGTGAA----------------------ACACTGATTATAA---------------------------AAGG---------A--------------ACAGAACAGTTGAAA------------------TC---TCT---------------------------------------------------------------------C-----TCTTCAGA-CTCTTCATT------------------TTGCT------------TTCCCAGGCCTCA---CTTCTCATTCTCCACTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATC------AGAACCTAATGTC------------ATCACTTCTCCTGCTGAGT------GTTC------CTTGGAACTTTCTCCTT---CAAGGCCTTGTGTTTTAAATTCTTCA---CTCTCTAGGAGA--GAGACACCTATTTG-------TATGTTAAC-TGTT----GAAACTGA 
s rheMac1.SCAFFOLD70304      20016 297 -     66826 TGAAGAGGCAAATTTGA------CAGAGAA-AG---------------------------AGGAAATAAGGCAAGGTGAA----------------------ACACTGATTATAA---------------------------AAGG---------A--------------ACAGAACAGTTGAAA------------------TC---TCT---------------------------------------------------------------------C-----TCTTCAGA-CTCTTCATT------------------TTGCT------------TTCCCAGGCCTCA---CTTCTCATTCTCCACTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATC------AGAACCTAATGTC------------ATCACTTCTCCTGCTGAGT------GTTC------CTTGGAACTTTCTCCTT---CAAGGCCTTGTGTTTTAAATTCTTCA---CTCTCTAGGAGA--GAGACACCTATTTG-------TATGTTAAC-TGTT----GAAACTGA 
s marmoset.ENr114_1         479079 297 -    685353 TGAAGAGGCAAATTTGA------CAGAGAA-AG---------------------------AGGAAATAAGGCAAGGTGAA----------------------ACACTGATTATAA---------------------------AAGG---------A--------------ACAGAACCATTGAAA------------------TC---TCT---------------------------------------------------------------------C-----GCTTCAGA-CTCTTCATT------------------TTGCT------------TTCCCAGGCCTCA---CTTCTCATTCTCCACTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATC------AGAACCTAATGTC------------ATCTCTTCTCCTGCTGAGT------GTTC------CTTGGAACTTTCTCCTT---TGAGGCCCTGTGTTTTAAATTCTTCA---CTCTCTAGGAGA--GAGACACCTATTTG-------TATGTTAGC-TGTT----GAAAATGA 
s galago.ENr114_1           368240 291 -    502320 TGATGACGGAAATTTGA------CAGAGAA-AG---------------------------AGGAAAGAGGGCAAGGCGAA----------------------ACTCTTATCCTAA---------------------------AAGG---------G--------------TCAGAACAGTTGAAA------------------TC---TCT---------------------------------------------------------------------C-----TCTTCAGA-CTCCTCATT------------------TTGCT------------CTCTCAGGCCTCC---CTTCTCAGTCTCCACTTTGCCAACTGTTTCAAGGACTGTGGAACTAGAGTC------AGAACTCAGTGTC------------ATCACCTCTCCTGCTGACT------GTAC------CTTGGAACTTTCTCCT---------CCTTGCATTTTAAATTCTTCA---CTCCCTAAGAGA--GAGACGAGTGCTTG-------TATGTTAGC-TGTT----GAAACCAA 
s rn3.chr20               40769211 297 -  55296979 CGAAGATGCCCGTGGGT------CAGAGAA-------------------------------AGAAGGGGGGCACAGAGAC----------------------ACCCTAATCGTAC---------------------------AGCA---------A--------------ACAGAGCAACTGAAA------------------TC---TCT---------------------------------------------------------------------G-----TCTTCGGG-CTCTTCTTT------------------TTCCT------------CCTCTTGGTCCCA---CTTTTCTTTCTCAACTCTACCAACAATTTCAAGAGCGGTAGAACTCGGGTC------AGAACCTGACGTT------------GTCACTTCTCCCGCTGACT------GCAC------CTTGGAACTTTCTCCTCCTCGGAGACCCCGCGTTTTAAACTCCCTA---GGCTCTAAGAGA--GAGACTCCCACTTG-------TGCCTCCGA-TACA----GAAACAAA 
s mm6.chr10               74726194 297 + 130291745 TGAAGATGCCCACGAGT------CAGAGAA-------------------------------AGAAGGGGGACACAGAGAC----------------------ACCCTAATCGTCC---------------------------AGCA---------A--------------ACAGAGCAGCTGAAA------------------TC---TCT---------------------------------------------------------------------G-----TCTTCTGG-CTCTTCTTT------------------TTCCT------------CCTCTTGGTCTCA---CTTTTCTTTCTCAACTCTGCCAACGATTTCCAGAGCGGTGGAACTCGGGTC------GGAACCTAATGTG------------GTCACTTCTCCCGCTGACT------GCAC------CTTGGAACTTTCTCCTCCTCTGAGACCCCGTATTTTAAACTCCTTA---AGCTCTAAGAGA--GAGACTCCCACATG-------TGCATCAGA-TACA----GAACCAAA 
s rabbit.ENr114_16          115912 298 -    209963 TGAATGTGCAGATCTGA------CCGAGAAGAG---------------------------AAGAAATACGGGATGGTGAG----------------------ACACTGATTCCAA---------------------------GAGA---------A--------------ACACAGCAGTTGAAA------------------TC---TCT---------------------------------------------------------------------A-----TCTTCAAC-CTCTTCATT------------------TTCCT------------CTCTTTGGCCTCA---CTTCTCATTCTCCACTTTGCCAACTGTTTCGAGAACGGTGGAACTCAAATC------AGAACCTGCTGTT------------ACCGCTTCTCCTGACGACT------GTTC------CTTGGAACTTTCTCCTC---TAAGGACTAGCACTTTAAAGGCTCCA---GTGTATGGGAAA--GAGACACCCACTTG-------TATGGTAGC-TGTT----GAAACTAA 
s cow.ENr114_1              467569 297 -    523404 CGAAGATGCAGATGTAA------CAGAAAA-AG---------------------------AGGAAACAGGGGAAAGTGAA----------------------TCACCGACTATAA---------------------------AAGG---------A--------------ACGGAGCAGTTGCAG------------------TC---TCT---------------------------------------------------------------------A-----CCTTCAGA-CTCTTCGCT------------------TTCCT------------CTCCTTGGTCTCA---CTGCTCTCTCTCCACTTTGCCAACTGTTTCGAGGACTGTGGGACTCAAATC------AGAACCTAATGTG------------GTTGTTTCTCCTGCTGACT------GTTC------CTTGGAACTTTCTCCTT---CAATGCCTTGCATTTTAAATTCTGAG---TTCCTTAGCAGA--GAGACACCTACTTG-------TTTGATGAC-GTTT----GAAACCAA 
s canFam1.chr26           36577658 297 +  41009621 TGGAGAATCCAGTGTGC------CCGAGAC-AG---------------------------GAGAAGCAAGGCCAGGCCAG----------------------CCCCTGCTCCCAC---------------------------GTGG---------A--------------GCACAGCATGTGGAA------------------TC---TCT---------------------------------------------------------------------G-----TCTTCAGA-CTCCTCATT------------------TCTCT------------CTCCTTCGTCTCA---CTCCTCCTACTCCACTTTGACAACTGTTTCGAGAACTGTGGAACTCCAGGC------AGAACCTGATGTC------------ATCATCTCTCCCGCGGACT------GTTC------TTTGGAACTTTCTCCTT---CAATGCCCTGCATTTTAAATTCCCCG---GTTTTTAGGAGA--GAGATGCCCACATG-------TCTGTTGAC-AGTT----GAAGCCGG 
s rfbat.ENr114_1            287420 297 -    353074 TAAAGGTACAAGTTTAA------GAGAGAA-AG---------------------------AGGAAATAAGGCCAGGTGAA----------------------TCACCGATTATAC---------------------------AAGG---------A--------------ATGGAACAGTTGAAA------------------TC---TCT---------------------------------------------------------------------G-----TCTTCAGA-CTCTTCATT------------------TTCCT------------CTCCTTGGTCTCA---TTCCTCACTCTCTGTTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATC------AGAACCTAATGTT------------ATCGTTTCTCCTGCTGACT------GTTC------CTTGGAACTTTCTCCTT---CAATGCCTTGCATTTTAAATTCTCCA---CTTTTAAGGAGA--GAGACACACACTTG-------TACGTTGAC-TGTT----GAAACCAA 
s shrew.ENr114_9             24889 294 +     28685 TGAAGAGATAGATTTAA------CAGAGAA-AG---------------------------AAGATA---GTCAAAATGAA----------------------TCAATGGTTATGC---------------------------CAGG---------A--------------TCAGAACAGTTGAAG------------------TC---TTT---------------------------------------------------------------------A-----TCTTCAGC-CTCTACATT------------------TTCCT------------CTTCCTGGTCTCA---TTCTTCATTTTCTACTCTGCCAACTGTTTCAAGAACTGTGGACCTCAAATC------ACAATCTAAGGTC------------GTTATTTCTCCTTCTGATT------GTTC------CTTGGGACTTTCTCCTA---CGATGCCTCGCATTTTAAATTCTCCA---CTCCTCAGGAAA--GAGGCACCAACTCA-------TATTTTAAC-TATT----GAAACGGA 
s armadillo.ENr114_1        392651 297 -    434329 TAACAATGCAAATATAA------CAGAGAA-AG---------------------------AAGAAATAAAGCAAATTGAA----------------------TCACTGATTATAC---------------------------AAGA---------A--------------ACTACACAGTCGAAA------------------TC---TCT---------------------------------------------------------------------A-----TCTTCAGA-CTCTACGTT------------------TTCTT------------CTCCTTGGCTTCA---CTCCTCATTATCTGCTTTGCCAACTGTTTCAAGAATAGTGGAACTCAAATC------AGAACCTAATATC------------ATTATTTCTCATGCTGACC------GTTC------CTTAGAACTTTCTCCTT---CAATGTCTTGCATTTATAATTCTCCA---CTTTTTAAAAGA--AAGACACCCACGCA-------TATGATGAC-TGTT----GAAACCAA 
s monDom1.scaffold_13316   1880163 354 +   4912536 TGAAGAGACAAAGTTGATAGTGGCAGAGAA-AGCCAGGCAGTTTAAAGGGCAACCTTTTCAGGAAATAAATCAAGG-GAA----------------------GCATTG-TGATGG---------------------------AAGA---------GCAACCTGGTCACCCACCCAAAAGATGCCA------------------CTAGAGCT---------------------------------------------------------------------A-----TCTACTGA-ACACTTGCT------------------TTCTT------------CTCCCTGGCACCAGTTCTCTTCTTTTCCTACTTTGCCACCTGTTTCAGGTGCTATTGAACTTGACAC------TGTGCCTCCAATC------------ATCATTTCCCATGCTGATG------CTCC------TCTTACATCTTCTCCAC---TGA---CTCAAAAGCCAACTTCTCCATCTCCTTTTTGGATATCAAAACACAGTCCTC-------AACATTATT-TGTCCCCCAAGACAAG 
s platypus.ENr114_1          90322 345 -    121090 ---AGATTCAAAGTTAA------CGGTAAA-AG---------------------------AGAAAGCACGACAATTTGAACATCATGCTTTACAGGAAATGAACAATCATGAAAACAAAAGTGCATGTTCCCCAGCACCAGGAAGG---------G--------------AGAGTACAGTAAA-------------------------ACT---------------------------------------------------------------------G-----CATCCAGA-GTACTTCCT------------------TCCTT------------CTTGTCACTGCTC---TTCTTCATTCTCCTCTTCAAGACCTTTTCCAGAGACTATGGACCTTGGCCC------ACCTCCTTCAGTA------------GTCGTCTCTCACATTGACT------GTTC------TTTAGAAGTTTCTCCTC---CACCAAATCACAAACCAACACCTCCC---CCTCTTAGGATT--CAACAATCCGATTGCCACCACTAT-TTGGC-TATT----GAATCTGA 
s galGal2.chr6             5979392 378 +  33893787 AAGTGGCCCCACGTTAA------CTGTAAA-AG---------------------------AGAAGGCAAGACAATTTGAG----------------------CAGCAGGCTTTGC---------------------------AGGA---------A--------------ATGAAGCAAGTGAAA------------------TC---TCCTGATGTCAAATCCACCCGTTCACCAACGCACAGCATCTGTTTGCAAGAAAGAGATAACACGCTAGAGCAG-----TCTCCTAA-AAGTGTGTT------------------TGCTT------------CTCCTTGCCTTCG---CTCTTCTCCTCTGTCCTCTCCAACACCTTGTGAAGTAGTTGAGCCGGAGCCCTCTGCGGTCCCCTCTGTA------------ATCATCACTCACCATGACT------ATCC------TGAAGAACTTTCTCCTC---CACCAACTCGCAAGCCAACTCCTCCG---TCTTTTAGGATA--AAGAAACCCGTTTGCCAAAG-TTTTCTAGC-TCCT----CAGACCAA 
s xenTro1.scaffold_94       660160 344 +   2448135 TAACAAATTAAGTGTAA------AAGAGCA-GGCCAGACAGTTTGAACAAAATGCCTTGCAGGAAGTAAAGCAAGTCAAA------------------------GCTGAAAATAA---------------------------AGAACTGTATTCAG--------------TGAAAGATGTTGAGT------------------TT---TAT---------------------------------------------------------------------CAGGGTTCCACAAA-GTCTACATCACAAG-------------CCAGT------------ATCTCATGCCACAGATTTCCTCCATCTTCATCTCTCCAGCGTTTGTGTGA-----GGTTCCTGCAAC------TGACCCTTCCATCTTTCCATCAATCATTATTACTCCCTCAGACC------ACTG------TGATGACATTTCTCCTC---CACCAACTCG------AAAACCAACA---CCTCCTAGTGAA--AAGAAACAT-CTAG-------CACCCGGTC-AAGT----ATATCTAA 
s fr1.chrUn              340428897 321 - 349519338 ---AGACACCAAGCTGT------CCGTCCG-TC---------------------------AGCAGGCCAAGCAGTTTGAG----------------------CAGAAGGTCATCC---------------------------AGGA---------T--------------CAAACCCTCAGGCAGAGCAGAGACTCCCCCAGTTC---TCT---------------------------------------------------------------------T-----CCATCC---ATCATTTTCAGGAACAGAAACAGTGACTCTGTAGTAGAGCTGCCCTCAGAAACCCTG---CTCTCCATCCTGGACCACAGCACG-------GCAACTGTGGGCAGGGACGC------CCCACCAGTGGTT------------GTCGTATCCCAGGGTGACGAAGCACGCCC------CCAGAGACCATCCCAGC---TTGATATCAGGAGGTTCAG--CTCCA---GT---------A--TCGGCAACTTCATG-------GCACTTCAA-CCTT----G------- 
s danRer2.chr12           32201350 264 -  35164833 ---AGAGCCCAAATTGA------CTGTAAA-AG---------------------------AGCAGGCACGACAGTTTGAG----------------------CAGCAGGCCTTGC---------------------------AGGA---------C--------------GTAAAGTTGAGGCAAGGTCAGGACTCTCGTGGGTC---ACT---------------------------------------------------------------------C-----TCTTCCGAAATTATTCTC------------------TCTGT------------TTTTGAAACCCCA---C------------ACAACAGCAGA----------------------------------CCTCCAGCGATA------------ATCATTACTCAGAGTGACTCAACACCTCCGCCCAGTCATAAGCCCACTCCGC---CAGTGCTGCGGAAGTACA-----CCA---G----------A--CTGTCTTCTTATCC-------TGACTTAGAGTCTT----A------- 

a score=46139.0
s hg17.chr10             80161003 17 - 135413628 AATCCATTGC------TT---AC----AAC 
s panTro1.chr8           82158547 17 - 138322177 AATCCATTGC------TT---AC----AAC 
s baboon.ENr114_1          439627 17 -    584309 AGTCCATTGC------TT---AC----AAC 
s rheMac1.SCAFFOLD70304     19999 17 -     66826 AATCCATTGC------TT---AC----CAC 
s marmoset.ENr114_1        479062 17 -    685353 AATCCATTGC------TT---AC----AAC 
s galago.ENr114_1          368223 17 -    502320 AATCCCTTAC------CT---GC----AAC 
s rn3.chr20              40769194 17 -  55296979 AACCTAATGG------TG---AC----AAC 
s mm6.chr10              74726177 17 + 130291745 AACGTTCTGC------TG---GC----AAC 
s rabbit.ENr114_16         115895 17 -    209963 AGTTCATCTC------TT---AC----AAC 
s cow.ENr114_1             467552 17 -    523404 AGTCCCTTGC------TT---AC----AGT 
s canFam1.chr26          36577641 17 +  41009621 AACCCCCTGC------CT---GC----AGC 
s rfbat.ENr114_1           287403 17 -    353074 GATATCTTGC------TT---AC----ATC 
s shrew.ENr114_9            24872 17 +     28685 AATCCCTTGT------TT---AC----TGC 
s armadillo.ENr114_1       392634 17 -    434329 GATCCCTTGT------TT---AC----CAC 
s monDom1.scaffold_13316  1880142 21 +   4912536 TAGCCTTTGC------CC---ATTTCAACC 
s platypus.ENr114_1         90305 17 -    121090 AGTTCTCCAT------TT---AA----TAC 
s galGal2.chr6            5979372 20 +  33893787 AGTCCACTAT------TTCAAAA----AAT 
s xenTro1.scaffold_94      660137 23 +   2448135 AGGCCATTGGAGAATGTT---AA----AAC 

a score=245908.0
s hg17.chr10              80160931 72 - 135413628 CAGTGGCAAGGCACCAGGCAGAAAGCTG-AAAATGAAAACACTGGAATCTGTACAAACAAAAGAGGTAGCAGC 
s panTro1.chr8            82158475 72 - 138322177 CAGTGGCAAGGCACCAGGCAGAAAGCTG-AAAATGAAAACACTGGAATCTGTACAAACAAAAGAGGTAGCAGC 
s baboon.ENr114_1           439555 72 -    584309 CAGTGGCAAGGCCCCAGGCAGAAAGCTG-AAAATGAAAACACTGGAATCTGTCCAAACAAAAGAGGTAGCAGC 
s rheMac1.SCAFFOLD70304      19927 72 -     66826 CAGTGGCAAGGCACCAGGCAGAAAGCTG-AAAATGAAAACACTGGAATCTGTACAAACAAAAGAGGTAGCAGC 
s marmoset.ENr114_1         478990 72 -    685353 CAGTGGCAAGGCACCAGGCAGAAAGATG-AAAATGAAAACACTGGAGTCTGTACAATCAAAAGAGGTAGCAGC 
s galago.ENr114_1           368151 72 -    502320 GCATGGCAAAGCACCAGGCAGGAAGCTG-AAAGTGGAGGTGCTGGAACCTATCCAAGCAGCAAAGGCAGCAGC 
s rn3.chr20               40769122 72 -  55296979 GAGTGGCAGATCACCAGGCAGAGAGCTG-AATGCGAAAAAACCAGATGCCACCCAAGCCAGCAAGGTAGCAGC 
s mm6.chr10               74726105 72 + 130291745 GAGTGGCAGATCACCAATCAGAGAGCTG-AATGCGAAAGCGCCAGATGCCACCCAAGCCAGAGAGGTAGCAGC 
s cow.ENr114_1              467480 72 -    523404 CAGTGGCAAAGCAACAGGCAAAAAGCTG-AAAATGAAAGCACTGGAACCAATCCAAACGAAAGAGGTAACCGT 
s canFam1.chr26           36577569 72 +  41009621 CCACGGAGGAGCCGCAGGCCGGAAGGTG-GGAAGGAAAGCCCTGGAACCCCTCCAAACCAGAGAGGTAGTAGG 
s rfbat.ENr114_1            287331 72 -    353074 CAATGGCGAAACAATAGGCAGAAAGCTG-AAAATGAAATTCCTGGAACCTATCCAAACACAAGAGGTAGCAGG 
s shrew.ENr114_9             24800 72 +     28685 CAATGGCAAAGCAATAAGCAAAACATAG-GGCATGAAAGTATGGGAACCTATTCAAACAAAGGAGGTAGCTGC 
s armadillo.ENr114_1        392562 72 -    434329 CTATGGCGAAGCGACAGGCACAAAGCTG-AAAATGAAAGTACTGGACACTATCGAAACAAAAGAGGTAGCAGT 
s monDom1.scaffold_13316   1880074 68 +   4912536 CAGTGGGAAAATGAACGCCTCCAAGCAG-AAGCTGAAATAACTGAATAC----CAGTCCAATATGGTGGCTGC 
s platypus.ENr114_1          90233 72 -    121090 CAGGGGCAAAAGGAAAAATTCAGAACTG-AATTTGAAAGGAATGGAGGCCAGCAAAGTAAGGTGGATGAGTTT 
s galGal2.chr6             5979300 72 +  33893787 CAGTGGCAACAGGAAAGACTCAAAGCAG-AGAATGAAGGAACTGAAAATCAGCATAGCAGAGTTGATATTAGC 
s xenTro1.scaffold_94       660068 69 +   2448135 CAGGGCCAACATAAAAGG-ACACAGCAGCAGAGTGAACCGAGCGAAA---ATTCACACAAAACTGATTGCCCT 
s fr1.chrUn              340428838 53 - 349519338 ----------------GCATCAGA---A-GCCAGGAAAAGGCTGCAGAGTTTCAATACACTTCAGCTAGGAGA 
s danRer2.chr12           32201276 68 -  35164833 CAGCTGCTAAAGGCCAGCCTTAAGGACA-GCAAGGAGATGATTGATGGGTTT-GATGGACTTGGG---GATGA 

a score=569593.0
s hg17.chr10              80160820 111 - 135413628 -TCTCTGAGGGGCCCAAGA---------GAAAAGATTCA----GAGGCTG----TGGAGTCAGTCAGTCAGCTTACCCAGGAGGCTGATGAGGAAAGT--TCCAAATAGACCAGAGATCATAGATCTGCAG 
s panTro1.chr8            82158364 111 - 138322177 -TTCCTGAGGGGCCCAAGA---------GAAAAGATTCA----GAGGCTG----TGCAGTCTGTCAGTCAGCTTACCCAGGAGGCTGATGAGGAAAGT--TCCAAATAGACCAGAGATCATAGATCTGCAG 
s baboon.ENr114_1           439444 111 -    584309 -TCTCTGAGGGGCCCAAGA---------GAAAAGATACA----GAGGCTG----TGGAGTCAGTCAGTCAGCTTACCCAGGAGGCTGATGAGGAAAGT--TCCAAATAGACCAGAGATCATAGATCTGCAG 
s rheMac1.SCAFFOLD70304      19816 111 -     66826 -TCTCTGAGGGGCCCAAGA---------GAAAAGATACA----GAGGCTG----TGGAGTCAGTCAGTCAGCTTACCCAGGAGGCTGATGAGGAAAGT--TCCAAATAGACCAGAGATCATAGATCTGCAG 
s marmoset.ENr114_1         478879 111 -    685353 -TCTCTGAGGGGCCCAAGA---------GAAAAGATTCA----GAGGCTC----TGGAGTCAGTCAGTCAGCTTACCCAGGAGGCTGAGGAGGAAAGT--TCCAAATAGACCAGAGATCATAAATCTTCAG 
s galago.ENr114_1           368040 111 -    502320 -TCTCTGAGGGGCCCAAGA---------GAAAAGATTCA----GAGGACG----TGGAGTCAGCCGGTCAGTTTCCCTAAGAGACTGATGAGAAAAGT--TTCAAATAGGCCAGAAATCATAGATCTGCAA 
s rn3.chr20               40769011 111 -  55296979 -TCCCTGAGGGGCCCAAGA---------GAAAAGATCCA----GAGGGTG----TGGAATCAGTCTGTGAGGTTTCCTAGGCGGCTGATGTGGAAAAC--TCCAAACAGACCAGAGACCATAGACCTAGTG 
s mm6.chr10               74725994 111 + 130291745 -TCTCTGAGGGGCCCAAGA---------GAAAAGATCCA----GAGGGTG----TGGAATCAGTCTGTGAGCTTTCCTAGGCGGCTCATGTGGAAAGC--CCCAAACAGGCCAGAGACCATAGACCTGGTG 
s rabbit.ENr114_16          115683 111 -    209963 -TCTCTGAGGGGTCCTCGA---------GAAAAAATTAA----GAGGATG----TGGAAGCAGCCAGTCAGCTTACCTAAGAGACTGATGGGGAAGGT--TCCAAAGAGACCAGAAACCATTGATCTAGTG 
s cow.ENr114_1              467369 111 -    523404 -TTTCTGAGGGGCCCAAGG---------GAAAAGATTCA----GAGGATG----TGGAATCGCCCAACCTGCTTACCTAGGAGACCAATGTGGGAACT--TCCTGATAGATCAGAAACCATAGCTCTAAAG 
s canFam1.chr26           36577458 111 +  41009621 -TCCCTGAGGGGCCCAAGG---------GAAATGTTTCA----GAGGATA----TGGCATCAGCCAGTGTGCTTCCCTCAGAGACCAGTGTGGGAACT--TCCCAGAAGGCCAGAAACCCTAGAGCTGGAG 
s rfbat.ENr114_1            287220 111 -    353074 -CCTCTGAGGGGCCCAAGA---------GAAAGCATTCA----GAAGATG----TGGAATCAGACAATCTGCTTACCTAGGAGACCAATATGGGAACT--TCCCAATAGACCAGAAACCATAGAACTGGAG 
s shrew.ENr114_9             24689 111 +     28685 -TCTCTCAGGGCCCCAAGG---------GAAAAGATACA----GAAGATG----TGGAATCATTCATTCTGTTTCTCTGGGGGATCCAGGTGGGAGTT--TCCAAGCAGATCAGATACCATAGATCTGGAA 
s armadillo.ENr114_1        392451 111 -    434329 -TCGCTGAAGAGCACCCGA---------GAAAACACACA----AAGGACA----CAGAATCAGCCAGTTTGCTTACCCATGAGACCAATGTGGGAAGT--TCCAAACAGACAAGAAATCATAAATCCGGAG 
s monDom1.scaffold_13316   1879963 111 +   4912536 -TGTCGGAAATACCCAGCA---------GAAAGCACTCA----TCGGGCA----TGGACTCTACCAACCAGCTTCACTCGGAGGCAGATGTATGAGGT--TCTGAATAGACCAGTCATTATGGATCCTATC 
s platypus.ENr114_1          90122 111 -    121090 -GCTCTAAGGTGTCCTTCA---------GAAAACATTCA----ACGGGCT----TGGACTTTGCCAAAGTGTTTTACTAGGAGACAAGTCTATGAAGT--TTTAAGCAGGCCAGTAATCCTAGATCCATTC 
s galGal2.chr6             5979201  99 +  33893787 -TCTTTGGGAGGC---------------------AGTCA----CCGTGCA----TGGACAGTACCAGCTCACGTTACTAAGAGGCACGCGCCTGGTTC--TCTGAGCAGGCCGGTTATCATGGACCCTGTT 
s xenTro1.scaffold_94       659948 120 +   2448135 -TCTCTCAAAGATTCATTGTTAAACTCCGAGGGCATTCA----TCGTGCT----TGGACTCTGCCAACGTGCTTCTCTAAAAGGCACGCTTATGATAT--CCTTAACAGTCCTGTTATAATGGACCCGATC 
s fr1.chrUn              340428753  76 - 349519338 ---ATCAGTGCCTGCTCGC---------------ATTCA----CAG--------TGGAC------TGCCGGGTTGCGAGGG-------------------GCCAAGGAGGCAAGCTCTTATGGACCCAGAC 
s danRer2.chr12           32201153 111 -  35164833 TCCATTATGGGATTCCCGA---------------ATTCAGGCTCAGGACATTCCTGGACATTACCTTCTCGGTTGCACAAGTGG-----GACGAATCTCAGCGGAGTAGGAGGGTGGTGATGGATCCAGTT 

a score=197865.0
s hg17.chr10              80160757 63 - 135413628 GACATTTCACAGAGAA---CA---GATTTTGTAGAC-CCA----------------TTTTCACCCAAAATACAAGCCAAGAGTAAG 
s baboon.ENr114_1           439381 63 -    584309 GACATTTCCCTGAGAA---CA---GATTTTGTAGAC-CCA----------------TTTTTACCCAAAATACAAGCCAAGAGTAAG 
s rheMac1.SCAFFOLD70304      19753 63 -     66826 GACATTTCCCTGAGAA---CA---GATTTTGTAGAC-CCA----------------TTTTTACCCAAAATACAAGCCAAGAGTAAG 
s marmoset.ENr114_1         478816 63 -    685353 GACATGTCATTGAGAA---CA---GATTTTGCAGAC-CCA----------------TTTTTACCCATAACACAAGCCAAGAGTAAG 
s galago.ENr114_1           367977 63 -    502320 GGCTTTTCGCTGAGAA---CA---GATTTTGCGGAC-CCA----------------TTTTTACCCAAAACACAAGCCAAGAGTGAG 
s rn3.chr20               40768948 63 -  55296979 GACCTTCAGCCTGGAA---CA---GAGTTTGGAGAG-CTA----------------TTTGTACCCAGAACACAAGTTAAGAGTCAG 
s mm6.chr10               74725931 63 + 130291745 GACCTTCAGCCACGAA---CA---GATTTTGAAGAG-CTG----------------TTGGCACCCAGAACACAAGTTAAGAGTCAG 
s rabbit.ENr114_16          115620 63 -    209963 AACTTTCCCATGAGAA---CA---GAAGTGGTAAAC-CCA----------------TTTTTACCCAGAACCCATGTCAAGAGTCAG 
s cow.ENr114_1              467306 63 -    523404 GACTTTTTACTAAGAA---CA---GATTTTGTTAAG-TCA----------------TTTTTACCCAAAACACAAGCCAAGAATGAG 
s canFam1.chr26           36577395 63 +  41009621 GACTTTTTACTAAGAA---CA---GATTTTATAGAC-TCA----------------TTTTTGCCCAAAACACAAGCCAGGAGTAAG 
s rfbat.ENr114_1            287157 63 -    353074 GACTTTTCACTGAGAA---CA---GATTCTGTAGGG-TCA----------------TTTTTACCCATCACTCAAGCCAAGAAAGAC 
s shrew.ENr114_9             24626 63 +     28685 GAGTTTTCACCAAGAA---CT---GACTTTGCAGAC-TCA----------------TTTTTATCCAAAACACAAGTAAAGAATGAT 
s armadillo.ENr114_1        392388 63 -    434329 AATTTTTCTCTAAGAA---CA---GATTTTCTATGC-CCA----------------TTTTTATCTAAAACACAAGCCAAAATTGAG 
s monDom1.scaffold_13316   1879897 66 +   4912536 GGATTTCCATGGAGAAAACCA---GGCTTACTAGAC-AAG----------------CTCTCCCCTCGAAGGCTAGCTAAGAAAGGT 
s platypus.ENr114_1          90056 66 -    121090 GGCTATTTATGGAGAAATACA---AGCTTATTAGAC-AAG----------------TTTTCACCTAGAAGACTAGCCAAGAAAGAG 
s galGal2.chr6             5979132 66 +  33893787 GGGTTACTGCGGAAAA---GAAGCGATGCCCTAGAT-ACT----------------CTTTCTCCTATGCAATTAGTCTTGAGAGAT 
s xenTro1.scaffold_94       659901 46 +   2448135 -AGCTAGCGTGGAGAAG--TA---GATTT----------G----------------CCCTTG--------GCAAACCAGGAAGAAA 
s fr1.chrUn              340428691 62 - 349519338 --------------GG---CT---TGCCTGAAAAGCGATGGACCGCCTCCCCTTCCTATTCACCCGGGTCGGGGGGGTTCAG---- 
s danRer2.chr12           32201104 49 -  35164833 --------------GA---GT---TACCTCTTAGAC-ATG----------------TATTCACCCAGTATGAGAGGTCTGAGTAAG 

a score=1184117.0
s hg17.chr10              80160588 169 - 135413628 CTTTTCTTCCAATACTATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAGAGCAACAAACTGAAGTCTGCAAGAAAATTCACATTTCTATCTGATGAGGATGACTTAAGTGCCCATAATCCCCTTTATAAGGAAAACATAAGTCAA-GTA---------------TCAACAAATTCA 
s panTro1.chr8            82158094 169 - 138322177 CTTTTCTTCCAATACTATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAGAGCAACAAACTGAAGGCTGCAAGAAAATTCACATTTCTATCTGATGAAGATGACTTAAGTGCCCATAATCCCCTTTATAAGGAAAACATAAGTCAA-GTA---------------TCAACAAATTCA 
s baboon.ENr114_1           439212 169 -    584309 CTTTTCTTCCAATACTATTGAGGCTCACAAGGCAGCTCATGTAGACGGATCACTTAAGAGCAACAAACCGAAGTCTGCAAGAACATTCACATTTCTATCTGATGAGGATGCCTTAAGTGCCCATAATCCCCTTTATCAGGAAAACATAAGTCAA-GTA---------------TCAACAAATTCA 
s rheMac1.SCAFFOLD70304      19584 169 -     66826 CTTTTCTTCCAATACTATTGAGGCTCACAAGGCAGCTCATGTAGACGGATCACTTAAGAGCAACAAACCGAAGTCTGCAAGAACATTCACATTTCTATCTGATGAGGATGCCTTAAGTGCCCATAATCCCCTTTATCGGGAAAACATAAGTCAA-GTA---------------TCAACAAATTCA 
s marmoset.ENr114_1         478647 169 -    685353 CTTTTCTTCCAATACTATTGAGGCTCACAAGTCAGCTCATGTAGATGGATCACTTAAGAGCAACAATCCGAAGTCTGCAAGAAAATTAACATTTCTATCTGATGAGGATGCCTTAAGTGCCCATAATCCCCTTTATAAAGAAAACATAAGTCAA-GTA---------------TCAACAAATCCA 
s galago.ENr114_1           367808 169 -    502320 CTTTTCTGCCAATCCTATTGAGGCTCCCAAGCCAGCTCAGATAGACGAATCACTTAAGAACAACCAACCAAAGTCTACAAGAAAATTCACATTTCCATCTGATGAGGAAATCTTACGTACCCATAATCTCCTTTATAATGAAAATGTAGACCAA-AGA---------------TCAAGAAATTCA 
s rn3.chr20               40768782 166 -  55296979 CTTTTCCTCCAGTACCACTGAGTCTCATGAGCCAGCTCATGTAGAGGGACCACTT---GACAACCAAGCTAACCCAGCAAGGACGTTCTCATTTCTTCCAGATGAGGATGACTTAAGTACCCATAACCCCCTTTATATGGAAAGTATAGGTCAA-AGG---------------TCAACAAATTCC 
s mm6.chr10               74725762 169 + 130291745 CTTTTCCTCCAGTACCACTGAGTCTCATGAGCCAGCTCATGTAGAGGGACCACTTAAGGAGAGCCAGCCTAACCCAGCAAGGACGTTCTCATTTGTTCCTGATGAGGATAACTTAAGTACCCATAATCCCCTTTACATGGAAAGTATAGGTCAA-AGG---------------TCAACAAACTCA 
s rabbit.ENr114_16          115451 169 -    209963 CATTGCTTCCAATACTATTGAGGCTCAAAGGACACCTCATATATATGGATCACTTGAGAACAGCCAGCGGGAGTCTACAAGGAAATTCTCATGTCTATCTCAAGAAGACAGCTTAAGTACCCATAATTCTCTTTATAAGGAACACATAGGTCAA-AGA---------------CCAACAAATTCC 
s cow.ENr114_1              467138 168 -    523404 -TTTTCTTCCCGCACTGTTGAGGCTCACAAGCAGACTCACGTAGATGGATCTCTTAAGAACAGCTGGCCCAGGTCTGCAAGAGATTTCACACTGATGTCTGGTGAGGATGCCTTAAATGCCCACAGTACCATTTACAAGGAATACACAGATCAA-AGA---------------TCAACAAATTCA 
s canFam1.chr26           36577226 169 +  41009621 TTTTCCTTCCAGCACTATTGAGGCTCACAAGCAGGCTCATGTAGATGGATCCCTTAGGAACAACCAGCCCAAGTCAGCAAGGAAGTTCACACTGATGTCTGAGGAGGACGCCTTCAGTCTCCACAGTACTCTTTATAAGGAAGCTGTAGATCCA-AGA---------------CCAACAAACTCC 
s rfbat.ENr114_1            286988 169 -    353074 CTTTTCTTCCAATCCTACTGAGGCTCACAAGCAGGCTTATATAGATGGATCCCTTAAGAACAACCAGCCCGAGTCTGCAAGAAAATTCACATTGGTATCTGATGAAGATGCCTTAAGTACTCATAGTGCCCTTTATAAGGAAAATATAGATCAA-AGA---------------TCAACAAAATTG 
s shrew.ENr114_9             24457 169 +     28685 CTTTTCTCCTAAAACTATGGAGACTCACAATCAGGCCCATATAGACGGAGCACTTAAGAACAGCCAGTCCAAGTCTGCAAGAAACTTCACAGTGCTCCCTGCTGAGGATGATCTCAGGAGTCAGAATAAACTTTACCAGGAAAATACAGATGTG-AGA---------------CCAATGACTTTG 
s armadillo.ENr114_1        392219 169 -    434329 TTTTCCTTCTTGTACTATTGAGGCTCACAAGCAGACTCACATAGACAAATCACTTAAGAACAACCAGCCCACGTCTCCAAGAAAATTCAAATTTCTTTCTGATGAAGACTCCTTAAGTACCCACAATCCCCTTTATATGGAAAATATAAGTCAA-GGA---------------TCAATAAATTCG 
s monDom1.scaffold_13316   1879728 169 +   4912536 CGTAGCTTCCCGGGCAATTGAGGCACACAAGCAGGCTCGGAAAACTGGATCACTCAGGAATAACCTACCCAAGTCTGCAAGTAACATCACACTTTTGTCTGATGATAACCCCTTAACTACCCACAACCCTCTATATGTGGAAGGGGGAGGTCCA-AGT---------------TCAACAATCCCG 
s platypus.ENr114_1          89887 169 -    121090 CTTTGCTTCCCGTGCTATTGAGGCTCACAAGCAGTCTCATGTCAATGGATCAGTCAAGAATAATCTACCCAAATCTGCAAGTAACATCACAATTCTGTCTGATGATAACCCATTAATTATCGAGAATCCTCTTTATGTGGAAGGTATAGGTCAA-GGG---------------TCTACAGGTGCT 
s galGal2.chr6             5978963 169 +  33893787 CTTTGCTTCCCGTGCTATTGAGGCTCACAAGCAATCTAATATCAATGGATCATTGAACAATAACCTCCCCAAATCTTCAAGTAACATTACTTTCTTATCTGACGAGAACCCACTAACTACTCAAAACCCACTGTATGTGGAAGGTGTCACTCAA-AGT---------------CCTGCTGCTGCT 
s xenTro1.scaffold_94       659731 170 +   2448135 TTTGGCATCACGTGCAATCGAAGCCCACAAGCTTTCTGGTCCCAGTGGATATCTAAACAATAAACTTCCCAAGTCGGCCAGTAACATTACCTTTCTCTCTGACACCAATCCACTCACAACTCAAAACCCATTGTACATTGAAGGCTCAGGTCAATGTA---------------ATGATAGCATTG 
s fr1.chrUn              340428522 169 - 349519338 ATTCGCCTGTCGCGCCATCACAGCCCGCAG------------CAACGGAGCGCTGCAGGTTAATTTGCCCAGGTCGGAAAGCAACGTGACGTTCCTTTCCGACTGCAACCCACTCACCACTCGCAACCCCCTCTA---TGATGACAGCAGTCCC-AGCAGTCCTGATGTCTTTGCACAGAGGCGC 
s danRer2.chr12           32200927 177 -  35164833 ATTCGCTTCCCGTGCTATCACTGCTCACAAGCTGTCCACCGCCAACGGAATCCTGCTCAACAACTTTCCCAAGTCGGAGAGCAACATTACCTTTCTTTCAGATGACAACCCACTTACTACAACCAACCCCCTGTACCGTGATGATGTCACTCTT-GGCAGCCCTGA-------GCACCAAAATCG 

a score=509847.0
s hg17.chr10              80160527 61 - 135413628 -------AACAAAG-CAGGGGAAATAACTCAGTCTCAGAAGACAGGAAACATCAACAAGTTGTGATGCC 
s panTro1.chr8            82158033 61 - 138322177 -------AACAAAG-CAGGGGAAATAACTCAGTCTCAGAAGACAGGAAACATCAACAAGTTGTGATGCC 
s baboon.ENr114_1           439154 58 -    584309 -------AACAAAG-CAGGGGAAATCACTCAGTCTCAGAAGACAGCAAACATCAA---GTTGTGATGCC 
s rheMac1.SCAFFOLD70304      19523 61 -     66826 -------AACAAAG-CAGGGGAAATCACTCAGTCTCAGAAGACAGCAAACATCAACAAGTTGTGATGCC 
s marmoset.ENr114_1         478586 61 -    685353 -------AACAAAG-CAGGGGAAATAACTCAGTCTCAGAAGACAGGAAGCATCAACAAGTTGTGATGCC 
s galago.ENr114_1           367747 61 -    502320 -------AACAAAG-CAGGGGAAATAACTCAGACTCAGAAGACAGGAAACCTCAGGAAGTTGTGCTGCC 
s rn3.chr20               40768721 61 -  55296979 -------AACAAAG-CAGGGGAAATAACCCAGTCCCGGAAGACAGGAGCAGTCATCGTGACGGGATGGC 
s mm6.chr10               74725701 61 + 130291745 -------AACAAAG-CAGGGGAAATAACTCAGTCCCAGAAGACAGGAGCAGTCATCGCGATGGGATGGC 
s rabbit.ENr114_16          115390 61 -    209963 -------AACAAAG-CAGGGGAAATAACTCAGTCTCAGAAGACAGGAGACCTCACCAAGTTGTGATGCC 
s cow.ENr114_1              467088 50 -    523404 -------AACAAAG-CAGGGAAAATAAATCAGTCTCAGAAGACAGGAAACATCAGCGC----------- 
s canFam1.chr26           36577165 61 +  41009621 -------AACAAAG-CAGGGGAGATAAGTCAGTCTCAGAAGACAGGAAAAGTCCACACAGTGTGATGCC 
s rfbat.ENr114_1            286927 61 -    353074 -------AACAAAG-CAGGGGAAATAAGTCAGTTCCAGAAGACAGGAAACATCAGCACGTTGTGATGCC 
s shrew.ENr114_9             24396 61 +     28685 -------AACAAAG-CAGGGGAAATAAGTCAGTCTCAGAAGACAGGAAACATCAACACACTATGATGCC 
s armadillo.ENr114_1        392158 61 -    434329 -------AACAAAG-CAGGGGAAATAAGTCTGTCTCAGAAGACAAGAAACATCAGCGAGTTGTGACACC 
s monDom1.scaffold_13316   1879667 61 +   4912536 -------AACAAAG-CAGGGGAAACAAATCAGTCTTAGAAGAAGGAGAACGTCAAAGAGTTATAAGCCA 
s platypus.ENr114_1          89826 61 -    121090 -------AACAAAG-CAGGGGAAAAAAGTCATTCTTAGAAGAAGGAGAACGTCAAAGAGTCATAAGCCA 
s galGal2.chr6             5978902 61 +  33893787 -------AACAAAG-CAGGGGAAAAAAGTCAGTCTTAGAAGAAGGAGATCGGCAGAGAGTTATAAGCAG 
s xenTro1.scaffold_94       659670 61 +   2448135 -------ATCAAAG-CAGGGGAAAAAAGTCAGTTTTGCAAGAAGGCGACCGGCAAAGACTGATAAGTAA 
s tetNig1.chr17            6643879 68 +  11214114 CACTTTTACTGGGG-CAGGGCTAAAAAGTCTGTCATCGAAGAGGCAGAGCGCCAAAGGCTTCTTAGCAC 
s fr1.chrUn              340428454 68 - 349519338 CTCTTTTACTGTGG-CAGGGCTAAAAAGTCTGTCATTGAAGAGGCAGAGCGCCAACGGCTCCTTAGCAC 
s danRer2.chr12           32200858 69 -  35164833 CACACTTGCTGAAATCAGGACTAAGAGGTGTGTTCTGAAGGATGGTGATCGGCAGCGTCTCATTAGCTC 

a score=706447.0
s hg17.chr10              80160504 23 - 135413628 T----------------CTTTT-CCTTCTCTACCATTTTC 
s panTro1.chr8            82158010 23 - 138322177 T----------------ATTTT-CCTTCTCTACCATTTTC 
s baboon.ENr114_1           439131 23 -    584309 T----------------CTTTT-CCTTCTCTGCCATTTTC 
s rheMac1.SCAFFOLD70304      19500 23 -     66826 T----------------CTTTT-CCTTCTCTACCATTTTC 
s marmoset.ENr114_1         478563 23 -    685353 T----------------CTTTT-CCTTCTCTACCATTTTC 
s galago.ENr114_1           367724 23 -    502320 T----------------CTTTT-CCTTCTCTACCATTTTC 
s rn3.chr20               40768698 23 -  55296979 T----------------CTTTT-CCTTCTCTACCATTTTG 
s mm6.chr10               74725678 23 + 130291745 T----------------CTTTT-CCTTCTCTACCATTTTG 
s rabbit.ENr114_16          115367 23 -    209963 T----------------CTTTT-CCTTCTCTACCATTTTC 
s cow.ENr114_1              467065 23 -    523404 T----------------CTTTT-CCTTCTCTACCATTTCC 
s canFam1.chr26           36577142 23 +  41009621 T----------------CTTTT-CCTTCTCTACCATTTCC 
s rfbat.ENr114_1            286904 23 -    353074 T----------------CTTTT-CCTTCTCTACCATTTCC 
s shrew.ENr114_9             24373 23 +     28685 T----------------CTTTT-CCTTCTCTACCATTTCC 
s armadillo.ENr114_1        392135 23 -    434329 T----------------CTTTT-TCTTCTCTACCATTTTC 
s tenrec.ENr114_9              963 24 +      8943 T----------------CTTTTCCCTTCTCTACCACTTTC 
s monDom1.scaffold_13316   1879644 23 +   4912536 T----------------CTTTT-CCTTCTGTACCATTTCC 
s platypus.ENr114_1          89803 23 -    121090 T----------------CTTTT-TCTTCTCTACCATTTCC 
s galGal2.chr6             5978879 23 +  33893787 T----------------CTTTT-TCTTCTCTACCATTTCC 
s xenTro1.scaffold_94       659647 23 +   2448135 T----------------CTTTT-TCTTCTCTATCATTTTC 
s tetNig1.chr17            6643841 38 +  11214114 GAGTTTTCCTTTTCCTTTTCTT-TCTTCTTCTTCACCTC- 
s fr1.chrUn              340428432 22 - 349519338 G----------------TTTTT-TCTTCTTCTTCACCTC- 
s danRer2.chr12           32200840 18 -  35164833 T----------------TCATC-TTTATCTCTT----TC- 

a score=1227436.0
s hg17.chr11              18327883 94 - 134452384 ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGGCAGTGGAGGAACTTGCCTACAAATGGAGTGTTGAGGATAT--GTAA 
s panTro1.chr9            18516885 94 - 136640551 ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGGCAGTGGAGGAACTTGCCTACAAATGGAGTGTTGAGGATAT--GTAA 
s baboon.ENm003_1           250730 94 -    625247 ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGGCAGTGGAGGAACTTGCCTACAAATGGAGTGTTGAGGATAT--GTAA 
s rheMac1.SCAFFOLD85336      23857 94 -     72861 ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGGCAGTGGAGGAACTTGCCTACAAATGGAGTGTTGAGGATAT--GTAA 
s marmoset.ENm003_1         430652 94 -    718711 ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAAGCAGTGGAGGAACTTGCCTACAAATGGAGTGTTGAGGATAT--GTAA 
s galago.ENm003_1           444225 94 -    721696 ATCCAATGGATTTGAACAAAAGCGCTTTGCCAGACTTGCCAGCAAGAAGGCAGTGGAGGAACTTGCCTACAAATGGAGTGTGGAAGACAT--GTAA 
s rn3.chr8                49295396 94 + 129061546 ATCCAATGGCTTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAAGCTGTGGAGGAGCTTGCCTACAAGTGGAGTGTTGAGGACAT--GTGA 
s mm6.chr9                46311748 94 + 124135709 ATCCAATGGCTTTGAACAGAAGCGCTTTGCCAGGCTCGCCAGCAAGAAGGCTGTGGAGGAGCTTGCCTACAAGTGGAGTGTGGAGGATAT--GTGA 
s rabbit.ENm003_12             344 94 -     63772 ATCCAATGGATTTGAACAGAAGCGCTTCGCCAGGCTTGCCAGCAAGAAGGCAGTGGAAGAGCTCGCCTACAAGTGGAGCGTTGAGGATAT--GTGA 
s cow.ENm003_1              430704 94 -    607368 ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGGCGGTGGAGGAACTTGCCTACAAGTGGAGTGTTGAGGATAT--GTAA 
s canFam1.chr5            19796448 94 +  92064832 ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGGCGGTGGAGGAACTTGCCTACAAGTGGAGTGTTGAGGATAT--GTAA 
s rfbat.ENm003_1            241700 94 -    387831 GTCCAATGGATTTGAACAGAAGCGCTTTTCCAGGCTTGCCAGCAAGAAGGCGGTGGAGGAACTTGCCTACAAGTGGAGTGTTGAGGATAT--GTAA 
s shrew.ENm003_8              4525 94 +      9365 ATCCAACGGGTTCGAGCAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGGCGATCGAGGAAATGGCTTATAAGTGGAGTGTGGAGGATAT--GTAA 
s elephant.ENm003_1         394462 94 -    658450 ATCTAATGGATTTGAGCAGAAGCGCTTTGCCAGACTTGCCAGCAAAAAGGCAGTGGAGGAACTTGCCTACAAGTGGAGTGTTGAGGATAT--GTAA 
s monDom1.scaffold_14981    361474 94 +   1219285 GTCCAATGGCTTTGAGGAGAAGCGTTTTTCCAGAATTGCCAGCAAGAAAGCCGTTGAAGAACTTGCCTATAAATGGAGTGTTGAGGATAT--GTAG 
s galGal2.chr24            1135433 96 -   5910111 GTCCAATGGATTTGAGCAGCAGTTCTTTGCCAGGATGGCCAACAAGAAGGCAGCTCAGGAGTTTGCATACAAGTGGAGCATTGAAGACTTTCGCAA 
s xenTro1.scaffold_18      1560255 94 +   3986068 GTCCAATGGATTTGAGAAGCAATTCTTTGCTAGGATGGCAGAAAAGACAGCTGTACAGGAGGAAGCATACAAGTGGAGTGTAGAAGATAT--GTGA 
s tetNig1.chr7             3695771 94 +  11099225 ATCAAATGGTTTTGAGAAGAAACGCTATGAGAGGATGGCAGATAAAAGAGCTGCTCAGGAGGCAGCCTACAAGTGGAGTGTAGAAGATAT--GTAA 
s fr1.chrUn              143036024 94 - 349519338 GTCAAATGGTTTTGAGAAGAAACGCTATGAGAGAATGGCAGATAAAAGAGCTGCTCAGGAGGCAGCCTATAAGTGGAGTGTAGAAGATAT--GTGA 
s danRer2.chr21           25799084 94 -  40848751 GTCCAACGGTTTTGAGCAGAAGCGATACTCCAGAATGGCCGATAACAAAGCTGTCCAAGAGATGGCGTACAAGTGGAGTGTTGAAGACAT--GTAG 

a score=1346472.0
s hg17.chr11             116206508 45 + 134452384 ATGCAGCCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTG 
s panTro1.chr9           118206938 45 + 136640551 ATGCAGCCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTG 
s rheMac1.SCAFFOLD60240      11058 45 -     98479 ATGCAGCCCCGGGTACTCCTTGTTGCTGCCCTGCTGTCACTCCTG 
s marmoset.ENm003_1         365379 45 +    718711 ATGCAGCCCCGGGTACTCCTTGTTACTGCCTTCCTGGCACTCCTG 
s galago.ENm003_1           352409 45 +    721696 ATGCAGTCCCGGGTGGTCCTCGCTGTCGCCCTGGTGGCACTACTG 
s mm6.chr9                77887743 45 - 124135709 ATGCAGCCCCGGACGCTCCTCACTGTGGCCCTCTTGGCTCTCCTG 
s cow.ENm003_1              257582 45 +    607368 ATGCAGCCCCGGCTGCTCCTTCTTGCTGCCTTCCTGGCGCTCCTG 
s canFam1.chr5            72342544 45 -  92064832 ATGCAGCCCCGGGTCCTCCTCGTCGCTGCCCTCCTGGCGCTCCTG 
s armadillo.ENm003_1        388688 45 +    560540 ATGCAGCCCCGGGTGCTCCTCGCTGCTGCCCTCCTGGCGCTCCTG 
s elephant.ENm003_1         369463 45 +    658450 ATGCAGAGCAGGGTCCTTCTCGTTGCTGCCCTCCTGGCGCTCTTG 
s monDom1.scaffold_14981    971779 45 -   1219285 ATGCAGCCCCGAGTTTTCCTTGTTGCTGTGTTCCTGACCCTACTG 

a score=106697.0
s hg17.chr11             116206553 10 + 134452384 GCCTCTGCCC 
s panTro1.chr9           118206983 10 + 136640551 GCCTCTGCCC 
s rheMac1.SCAFFOLD60240      11103 10 -     98479 GCCTCTGCCA 
s marmoset.ENm003_1         365424 10 +    718711 GCCTCTGCCC 
s galago.ENm003_1           352454 10 +    721696 GCCTCTGCCC 
s mm6.chr9                77887788 10 - 124135709 GCATCTGCCC 
s cow.ENm003_1              257627 10 +    607368 GTCTTGCCTG 
s canFam1.chr5            72342589 10 -  92064832 GCCTCCGCCC 
s armadillo.ENm003_1        388733 10 +    560540 GCCTCCGCCC 
s elephant.ENm003_1         369508 10 +    658450 GCCACTGCCC 
s monDom1.scaffold_14981    971824 10 -   1219285 GTCTATGCTA 
s galGal2.chr24            4798236 10 +   5910111 GCTCCTGCTT 

a score=62473.0
s hg17.chr11             18240604 47 - 134452384 TCCTGAGCGCTCTCGAGGAGTACACTAAGAAGCTCAACACCCAG---------TGA 
s panTro1.chr9           18428421 47 - 136640551 TCCTGAGCGCTCTCGAGGAGTACACTAAGAAGCTCAACACCCAG---------TGA 
s rheMac1.SCAFFOLD60240     82275 47 +     98479 TCCTGAGCGCTCTCGAGGAGTACACTAAGAAGCTCAGCACCCAG---------TGA 
s marmoset.ENm003_1        348304 46 -    718711 TCCTGAGCGCGCTCGAGGAGTACACCAAGA-GCTGAGCTCCCAG---------TGA 
s galago.ENm003_1          364471 47 -    721696 TCCTGAGCGCCCTGGATGAGGCCGCCAAGAAGCTGAACACCCAG---------TAA 
s mm6.chr9               46243608 47 + 124135709 TCCAGAGTGTGATCGACAAGGCCAGCGAGACTCTGACTGCCCAG---------TGA 
s cow.ENm003_1             332811 47 -    607368 TCCTGGCCGCCATAGACGAGGCCTCCAAGAAGCTGAACGCCCAG---------TGA 
s canFam1.chr5           19717841 47 +  92064832 TGCTGGCTGCCATCGACGAGGCCACCAAGAAGCTGAACGCGCAG---------TGA 
s shrew.ENm003_10            7317 47 +     26607 CCGGGGTCGCCTGGGACCAGGTCCACCAGCAGCTCGAGAGCCAG---------TGA 
s armadillo.ENm003_1       168389 47 -    560540 TCCAGAACGCCCTGGATGAGGCCTCCAAGAAGCTGAAACCCAGC---------TGA 
s elephant.ENm003_1        284268 47 -    658450 TCCTGACCGCCGTCGATGAGGCTGCCAAGAAGCTGAACGCCCAG---------TGA 
s monDom1.scaffold_14981   241876 47 +   1219285 TTCTGAACTTCCTGGAGGAAGCCCGGAAGTCCTTGAGCAGCTCA---------TAA 
s galGal2.chr24           1113679 50 -   5910111 --CTGACACCGCTGGCCGACGAGCTGAAGGAGCAGGTGGCACAG----AGCGTGGA 
s xenTro1.scaffold_18     1462633 52 +   3986068 ----AAACAACCTGGCAAAAATTTGGGAAAATCTGAGAGCCAAGCTCCAAAGACAG 
s danRer2.chr16          24190654  1 +  42763181 -------------------------------------------------------A 

a score=383490.0
s hg17.chr11             18240473 131 - 134452384 CGGCGCCAGA-CTGGCCGAGTACCACGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAG----------------------CCCGCGCTCGAGGACCTCCGCCAAGGCCTGCTGCCC-GTGCT----GGAGAGCTTCAAGGTCAGCT 
s panTro1.chr9           18428290 131 - 136640551 CGGCGCCAGA-CTGGCCGAGTACCACGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAG----------------------CCCGCGCTCGAGGACCTCCGCCAGGGCCTGCTGCCC-GTGCT----GGAGAGCTTCAAGGTCAGCT 
s rheMac1.SCAFFOLD60240     82144 131 +     98479 CGGCGCCCGC-CTGGCCGAGTACCACGCCAAGGCCAGCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAG----------------------CCCGCGCTCGAGGACCTCCGCCAGGGCCTGCTGCCC-GTGCT----GGAGAGCTTCAAGGTCAGCT 
s marmoset.ENm003_1        348173 131 -    718711 CGGCGCCAGC-CTGGCCGAGTACCACGCCAAGGCCAGCGAGCATCTGAGCACACTCGGCGAGAAGGCCAAG----------------------CCCCTGCTCGAGGACCTTCGCCAAGGCCTGCTGCCC-GTGCT----GGAGAGCTTCAAGGCCAGCT 
s galago.ENm003_1          364340 131 -    721696 CACCGCCAGC-CTAGCTGACTACCACGCCAAGGCCAGCGAGCACCTGAGCGCGCTGGGCGAGAAAGCCAAG----------------------CCCGCGCTGGAGGACCTGCGCCAGGGCCTGATGCCC-GTGCT----GGAGAGCTTCAAGGTCAGCC 
s mm6.chr9               46243477 131 + 124135709 CAACCCTACC-TTGAACGAGTACCACACCAGGGCCAAAACCCACCTGAAGACACTTGGCGAGAAAGCCAGA----------------------CCTGCGCTGGAGGACCTGCGCCATAGTCTGATGCCC-ATGCT----GGAGACGCTTAAGACCCAAG 
s cow.ENm003_1             332683 128 -    607368 CGG---CAGC-CTGGCCGAGTACCACGCCAAGGCCAGCGAGCAGCTGAAGGCGCTGGGCGAGAAGGCCAAG----------------------CCGGTGCTGGAGGACCTCCGCCAGGGCCTGCTGCCC-GTGCT----GGAGAGCCTCAAGGTCAGCA 
s canFam1.chr5           19717710 131 +  92064832 CGGCGCCAGC-CTGGCCGAGTACCACGCCAGGGCCAGCGAGCAGCTGAGCGCGCTCGGCGAGAAGGCCAGG----------------------CCCGCGCTCGAGGACCTGCGCCAGGGCCTGCTGCCC-GTGCT----GGAGAGCTTCAAGGTCAGCC 
s shrew.ENm003_10            7196 121 +     26607 -----------CTGGCGGACTACCACAGCAAGGCCAGCGAGCAGCTGAGCGCACTGCGCGACAGGACCAAG----------------------CCCGCGCTGGACGACCTCGTGCTGGGCCTCCTGCCC-GTGTG----GGAGAACATCAAGTCCAGCG 
s armadillo.ENm003_1       168258 131 -    560540 CGGCGCCAGC-CTCGCCCAGTACCAGGCCAAGGCCTCAGAGCAGCTGCGGGAGCTCGGCGAGAAGGCCAAG----------------------CCCGCTTTCGAGGACTTCCGGCAGGGCCTTCTGCCC-GTGCT----GGAGAGCCTCAAGGTCAGCT 
s elephant.ENm003_1        284146 122 -    658450 C----------TTCGCCGAGTACCGCAGCAAGGCCTTGGAGCACCTGAGCGCGCTCGGCGACAAGGCCAAG----------------------CCGGTGCTGGAGGACTTCCGCCAGAGCCTCCTGCCC-GTGTT----TGAGAACCTCAAGGTCAGTT 
s monDom1.scaffold_14981   241745 131 +   1219285 C-TTGCCCTCTCCCGCTGACTATCAAACCAAGATAACCGAGCAGCTCAAAGCCTTGAAGGAAAAATTCTCC----------------------CCCATCCTGGAGGACCTCAAAACAAG--TGCTGACC-CTATTTCCCAGAAAGC--CAAAGCCGATA 
s galGal2.chr24           1113538 141 -   5910111 CGGCG--GGCGCTGG---------AGCCCTTTGCCACCGAGCTGCGGGAGAAGCTGCAGGACAACGCCGACAGCATCCAGGCCTCTCTGGGCCCCTACGCCGAGCGGCTGCAGCAGCAGATCGACAGCA-GCGTG----GAGGGGCTGAAGGGGCAG-- 
s xenTro1.scaffold_18     1462510 123 +   3986068 AGGTCCCAGA-GCTGAGGAGTACAGAGCCCAACTGTCACAGCATATTGAGAATTTGAAGGAGAAGTATGGA----------------------CCCCTGGCCCAGAGCATCAGAGAACGCCTGGTACCCCATGCA----GAGGAG-------GCCAG-- 
s danRer2.chr16          24197809  99 +  42763181 -GACTCCC---CTGACCGAG------------------GATCTGCAGGTCCAGATTAGAGAGAGAGCCCAG----------------------ATGG------------TCCAGCAGAGTCTTACACCCTATGCT----GAAGATGTGAAGGAGAAGCT 

a score=226759.0
s hg17.chr11             18240398 75 - 134452384 CACGCATCTGGCCCCCTACAGCGAC--GAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTCTCAAGGAGAACGG 
s panTro1.chr9           18428215 75 - 136640551 CACGCATCTGGCCCCCTACAGCGAC--GAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTCTCAAGGAGAACGG 
s rheMac1.SCAFFOLD60240     82069 75 +     98479 CACGCATTTGGCGCCCTACAGCGAT--GAGCTGCGCCAGCGCCTGGCCGCGCGCCTTGAGGCGCTCAAGGAGAACGG 
s marmoset.ENm003_1        348098 75 -    718711 CACACAACTGGCACCCTACAGCGAC--AAGCTGCGCCAGCGCTTGGCCACGCGCCTCGAGGCGCTCAAGGAGAGCGG 
s galago.ENm003_1          364265 75 -    721696 CACTCAGCTGGCTCCCTACAGCGAC--GACCTGCGCCAGCGCCTGGCCACGCGCCTCGAGGCCCTCAAGGAGGGCGG 
s mm6.chr9               46243408 69 + 124135709 CACACAGCTAGCGCCCCACAGCGAA--CAGATGCGCGAGAGCCTGGCCCAGCGCCTGGCTGAGCTCAAG------AG 
s cow.ENm003_1             332608 75 -    607368 GCAGCAGCTGGCGCCCTACAGCGAC--GACCTGCGCCAGCGGCTGACCGCGCGCCTGGAGGCGCTCAAGGAGGGCGG 
s canFam1.chr5           19717635 75 +  92064832 CGCCCAGCTGGCCCCCTACAGCGAC--GACCTGCGCGAGCGCCTGGCCGCGCGGCTGCAGGCGCTCAAGGAGGGCGG 
s armadillo.ENm003_1       168183 75 -    560540 CTCGCAGCTGAGCCCCCACAGCGAG--GAGCTGCGCCAGCGGGTGATGGCCCGGCTCGAGGCGCTCAAGGAGGGCGG 
s elephant.ENm003_1        284071 75 -    658450 CTCGCAGCTGACCCCGTACAGCGAG--GAGCTGCGCCAGCGGCTGGCCAGCCGGCTCGAGGCGCTCAAGGAGGGCAG 
s monDom1.scaffold_14981   241670 75 +   1219285 GGAATTTGTGAAGCCCTACCACGAGCAGATCAAGACCAGCG--TGAGCCAGAAGATTCAGGAGCTCCGGGAGAAAGG 
s galGal2.chr24           1113474 64 -   5910111 GGCCAAGCTGAGCCCCTACGCCGAT--GAGCTGCGCTCGCAGGTGGAC--------CGCGGCACC---GGGGAGCTG 
s xenTro1.scaffold_18     1462435 75 +   3986068 CTCAAGGCTCACACCCTACAGTGAA--GAGGTCAGGGTAAAGCTGGTCGAGAAACTAGAAGAGCTTAAGGCCAATGC 
s danRer2.chr16          24197734 75 +  42763181 GGTTCAGCTGGAGCCCTACACTGCT--GAACTCAAGGAGAAAGTGGACCAGCATCTGCAGGAGTTCCAGAAGACCGT 

a score=90684.0
s hg17.chr11             18240365 33 - 134452384 ---CGACCGCGCGCGCGCCCATGTGGACGCGCTGCG 
s panTro1.chr9           18428182 33 - 136640551 ---CGACCGCGCGCGCGCCCATGTGGACGCGCTGCG 
s baboon.ENm003_1          216124 29 -    625247 ---CAGCTGCTGGGGGGC----GTGGACGAGGCGCG 
s rheMac1.SCAFFOLD10815      5283 29 +     45664 ---CAGCTGCTGGGGGGC----GTGGACGAGGCGCG 
s marmoset.ENm003_1        348065 33 -    718711 ---CGACCGCGCACGCGTCCACGTGGACACGCTGCG 
s galago.ENm003_1          364232 33 -    721696 ---CGACCGCGCGCGCGCCCACGTGGACACGCTGCG 
s mm6.chr9               46243375 33 + 124135709 ---CGACCGCATGCGCACACACGTAGACTCTCTGCG 
s cow.ENm003_1             332575 33 -    607368 ---CGACCGCGCGCGCGCCCACGTGGAGACGCTGCG 
s canFam1.chr5           19717602 33 +  92064832 ---GGACCGCGCGCGCACCCACGTGGACGCGCTGCG 
s armadillo.ENm003_1       168150 33 -    560540 ---CGACAGCGTGCGCACCTACGTGGACTTGCTGCG 
s elephant.ENm003_1        284038 33 -    658450 ---CGACCGCGCCCGCGTCCATGTGGATGCGCTGCG 
s monDom1.scaffold_14981   241637 33 +   1219285 ---GGATCGGGCCCAGGGCCACATAGAAACGGTTCA 
s galGal2.chr24           1113441 33 -   5910111 ---CCAGCAGATCGGCACCAACATCCGCGAGCTGCA 
s xenTro1.scaffold_18     1462402 33 +   3986068 ---GGACAAAGTGAGAGTGGATGTTGACTCCCTTCG 
s danRer2.chr16          24190565 33 +  42763181 AGGAAACCTGGAGCAGA---GTGTGAAGGAGCTGCA 

a score=651650.0
s hg17.chr11             18240101 264 - 134452384 CGAACAGCTCGGC-CCTGTGACC-----CAGGAGTTCTGGGATAACCTGGAAAAGGAGACA------------GAGGGCCTGAGGCA---GGAGATGAGCAAGGATCTGGAGGAGG------------TGAA-------------------------------------------GGCCAAGGTGCAGCCCTACCTGGACGACTTC---------------CAGA---AG------AAGTGGCAG------------------GAGGAGAT--GGAGCTC----------TACCGCCAGAAGGTGGAGCCGCTGCGCGCAGAGCTCCAAG-AGGGCGC---GCG--C--------------------------------CAGAAGCTGCACGAGCTGCAAGAGAAGCTGAGCCCACTGGGCGAGGA----GATGCG 
s panTro1.chr9           18427918 264 - 136640551 CGAACAGCTCGGC-CCTGTGACC-----CAGGAGTTCTGGGATAACCTGGAAAAGGAGACA------------GAGGGCCTGAGGCA---GGAGATGAGCAAGGATCTGGAGGAGG------------TGAA-------------------------------------------GGCCAAGGTGCAGCCCTACCTGGACGACTTC---------------CAGA---AG------AAGTGGCAG------------------GAGGAGAT--GGAGCTC----------TACCGCCAGAAGGTGGAGCCGCTGCGCGCCGAGCTCCAAG-AGGGCGC---GCG--C--------------------------------CAGAAGCTGCACGAGCTGCAAGAGAAGCTGAGCCCACTGGGCGAGGA----GATGCG 
s baboon.ENm003_1          215856 268 -    625247 GGAAAAGCTCAGG-CCTCTGAGTGGGAGCGAGGCTCCTCGGCTCCC-----ACAGGACCCA------------GTGGGCATGCGGCA---GCAGCTGCAGGAGGAGTTGGAGGAGG------------TGAA-------------------------------------------GGCGCGCCTCCAGCCCTACATGG-----------------------CAGA---AGCGCACGAGCTGGTGG------------------GCTGGAATTTGGAAGGC----------TTGCGGCAGCAACTGAAGCC-CTACACGATG-GATCTGAT-GGAGCAG---GTGGCC--------------------------------CTGCGCGTGCAGGAGCTGCAGGAGCAGTTGCGCGTGGTGGGAGAAGACACCAAGGCC 
s rheMac1.SCAFFOLD10815      5015 268 +     45664 GGAAAAGCTCAGG-CCTCTGAGTGGGAGCGAGGCTCCTCGGCTCCC-----ACAGGACCCG------------GTGGGCATGCGGCA---GCAGCTGCAGGAGGAGTTGGAGGAGG------------TGAA-------------------------------------------GGCGCGCCTCCAGCCCTACATGG-----------------------CAGA---AGCGCACGAGCTGGTGG------------------GCTGGAATTTGGAAGGC----------TTGCGGCAGCAACTGAAGCC-CTACACGATG-GATCTGAT-GGAGCAG---GTGGCC--------------------------------CTGCGCGTGCAGGAGCTGCAGGAGCAGTTGCGCGTGGTGGGAGAAGACACCAAGGCC 
s marmoset.ENm003_1        347801 264 -    718711 CGAACAGCTCGGC-CCGGTGACC-----CAGGAGTTCTGGGAAAACCTGGAAAAGGAGACA------------GAGGTGCTGAGGCA---GGAGATGAGCAAGGACCTGGAGGAGG------------TGAA-------------------------------------------GGCCCAGGTGCAGCCCTACCTGGACGACTTC---------------GAGA---AG------AAGTGGGAG------------------GAGGAGAT--GAAACTC----------TATTCCCAGAAGTTAGAACCGCTGCGCACGGAGCTCCAGG-AGGGCGC---GCT--C--------------------------------CAGAAGCTGCAGGATCTGCAGGAGAAGCTGAGCTCGCTGGGAGAGCA----GGTGCG 
s galago.ENm003_1          363968 264 -    721696 TGAGCAGCTGGGC-ACAGTGAGC-----CAGGAGTTTTGGGATAAGCTGGAGAAGGAGACT------------GAGGGACTGCGGCA---GGAGATGAACAAGGATCTGGAGGAGG------------TGAA-------------------------------------------GCAGAAGGTGCAGCCCTACCTGGACGAGTTC---------------CAAA---AG------AAGTGGCAG------------------GAGGAGGT--GGAACGC----------TACCGTCAGAAGGTGGAGCCGCTGGGCTCCGAGCTGCGCG-AAGGCGC---GCG--C--------------------------------CAGAAGCTGCAGGAGCTGCACGAGAAGCTGGTCCCGCTAGGCGAGGA----CTTGCG 
s mm6.chr9               46243111 264 + 124135709 GGAACGGCTGGGC-CCATTGACT-----CGGGACTTCTGGGATAACCTGGAGAAAGAAACA------------GATTGGGTGAGACA---GGAGATGAACAAGGACCTAGAGGAAG------------TGAA-------------------------------------------ACAGAAGGTGCAGCCCTACCTGGACGAATTC---------------CAGA---AG------AAATGGAAA------------------GAGGATGT--GGAGCTC----------TACCGCCAGAAGGTGGCGCCTCTGGGCGCCGAGCTGCAGG-AGAGCGC---GCG--C--------------------------------CAGAAGCTGCAGGAGCTGCAAGGGAGACTGTCCCCTGTGGCTGAGGA----ATTTCG 
s cow.ENm003_1             332311 264 -    607368 TGAACAGCTGGGC-CCAGTGACC-----CAGGAGTTCTGGGACAACCTGGAAAAGGAGACC------------GCGTCGCTGAGGCA---GGAGATGCACAAGGACCTGGAGGAGG------------TGAA-------------------------------------------GCAGAAGGTGCAGCCCTACCTGGACGAGTTC---------------CAGA---AG------AAGTGGCAC------------------GAGGAGGT--GGAGATC----------TACCGCCAGAAGGTGGCGCCGCTGGGCGAGGAGTTTCGCG-AGGGCGC---GCG--C--------------------------------CAGAAGGTGCAGGAGCTGCAGGACAAGCTGAGCCCTCTGGCCCAGGA----GCTCCG 
s canFam1.chr5           19717338 264 +  92064832 CGAACAGATCGGC-CCGGTCACG-----CAGGAGTTCTGGGATAACCTGGAGAAGGAGACG------------GAGGTGCTGCGGCA---GGAGATGAGCAAGGACCTGGAGGAGG------------TGAA-------------------------------------------GCAGAAGGTGCAGCCCTACCTGGACGACTTC---------------CAGA---AG------AAGTGGCAG------------------GAGGAGGT--GGAGCTG----------TACCGCCAGAAGGTGGCGCCGCTGGGCTCGGAGCTGCGCG-AGGGCGC---GCG--C--------------------------------CAGAAGCTGCAGGAGCTGCAGGAGAAGCTGAGCCCGCTGGGCGAGGA----GCTGCG 
s armadillo.ENm003_1       167898 252 -    560540 CGAGCAGCTCAGC-CCAGTGACC-----CAGCAGTTCTGGGATAACCTGGAAAAGGAGACC------------GCAGGGCTGAGGCA---GGAGCTCAGCCAGGACGTGCAGGAGA------------TCAA-------------------------------------------GCAGAAGATGCAGCCCTACCTGGACGACTTC---------------CAGA---AG------AAGTGGCAG------------------GAGACGGC--GGAGCGG----------TACCGCCAGAAAGTGACGCCGCTGGGC------------G-AGGACGC---GCG--C--------------------------------CACAAGCTGCAGGAGCTGCAGGGGCAGCTGGGCGAGCTGGGCCAGGA----GGTGCG 
s elephant.ENm003_1        283774 264 -    658450 GGAGCAGATAGGC-CCCGTAACC-----CAGCAGTTCTGGGATAACCTGGAAAAGGACATC------------GCCCACCTGCGGCA---GGAGATGAACAAGGACCTGGAGGAGG------------TGAG-------------------------------------------GCAGAAGGTGCAGCCCTACCTGGACGACTTC---------------CAGA---AG------AAGTGGCAG------------------GAGGAAGT--GGAGCTC----------TACCGCCATAAGGTGGGGCCGCTGGGCGACGAGTTCCGCG-ACAGCGC---GCG--C--------------------------------CAGAAGCTGCAGCAGCTGCAGGAGAAGCTGAGCCCGTTGGCCGAGGA----GCTGCG 
s monDom1.scaffold_14981   241373 264 +   1219285 TGAGGAGATTAAC-CCTACCTTC-----GAGGAAATCAAGGAAACCATCATCAAGGAAACC------------TCGGACCTCCGCCA---AGAGATGACCAAGGGCTTGGAAGCAG------------TCAA-------------------------------------------GAAGAGTATCGATCCCCACCTGGAGGAGTTT---------------CAGA---AG------AAGTGGGCC------------------GCAGATGT--AGAAAAT----------TTCCGCCAGAGGGTAGGCCCACTGACCCAGGATCTGAAGG-ACAGCAC---CAA--G--------------------------------CAGAAGTTCGATGAGCTGCACCAGAAGCTGAGCCCCATTGGCAAGGA----GATTCG 
s galGal2.chr24           1113082 359 -   5910111 CAAGCAGCTCAA-----GTGAGC-----GGAGGGACCACCGAGGCTCTGGGGTTGGGGGCA------------GGGGAG----GGCACAGGGTGCTGAGTGCTGAGCGCTGGGAGG------------TGGGTGTTGCATGCTGGGCACCCGGCGCTGCGCTCTGGGTGCTGCGTGTAAGACACGGGGCACTGACTGCCCGCTCTCCACAGCACCCTGCTGCAGA---GC------AACCTGCAGAGCGCAAACTCATACGCCGAGGAGCT--GCAGCGG----------CGCC---------TGGTGCCCTTTGCCACGGAGCTGCAGGCACAGCTG---GTG--CAGGACTCACAGCGGCTGAAGAAGCAGATCCAGCAGGAGCTGGCCGAGCTGCAGGCCAAGCTGGCTCCTTACGCCGACGA----GGTGCA 
s xenTro1.scaffold_18     1462118 284 +   3986068 -GAGAAGCTTGACACCTTTGGTA-----CCAATGCTATG----AACCTGAGAAAGCAAATAAATCCCTATGTAGAAAATATCAGGGA---ACAGGTGTCCAAAGAGCTAGAAAAGGAACTCCCAGTAATCAA-------------------------------------------GGAGAAAATCCGCCCCATCCTGGAAGCTTTC---------------CAGA---AA------CGTTGGGCT------------------GATGATGC--AAAGGCT----------TACCAGGAGAAAATCTCTCCCCTGGTAGCTGAGCTTCAAA-AGCAAAC---CAA--G--------------------------------AACAACCTGGATTCCTTGTATAAAAAGATCACTCCTATTGCTGAAGA----GATAAG 
s danRer2.chr16          24197456 278 +  42763181 -AAACAGGTGGAT-CCTCTGACT-----GAAGAGCTGATGAACAAAATCACCAAGGAGACT------------GAAGTGCTGAGGGA---GCGTCTGGGCCAGGACCTGATCAATG------------TGAG-------------------------------------------AGATAAACTCGAGCCCTATGCTGACAACATG---------------AAGAGCCAG------ATCCAGCAG------------------AGAGTGGA--GGAGCTCAGGGCGGCCATGGCTCCGTATGCTGACTCC-CTGGATTCTGAGACCCTGA-AGGCCACTCTGCT--C--------------------------------CAGAAGAGTGAGGAGCTGAGAGGAAACCTGGAGCAGAGTGTGAAGGA----GCTGCA 

a score=33826.0
s hg17.chr11             18240059 42 - 134452384 T---GACAACTGGGACA-------GCGTGACC----TCCAC--CTTCAGCAAGCTGCG 
s panTro1.chr9           18427876 42 - 136640551 T---GACAACTGGGACA-------GCGTGACC----TCCAC--CTTCAGCAAGCTGCG 
s baboon.ENm003_1          215815 41 -    625247 ----GACAGCCTTGA---------GCAAGACC----TCAACAATATGAACAAGTTCCT 
s rheMac1.SCAFFOLD10815      4974 41 +     45664 ----GACAGCCTTGA---------GCAAGACC----TCAACAATATGAACAAGTTCCT 
s marmoset.ENm003_1        347759 42 -    718711 G---GACAACTGGGACA-------GCTTGACC----TCCAC--TGTCAACAAGCTGCG 
s galago.ENm003_1          363926 42 -    721696 G---GACAACTGGGACA-------GCTTGACC----CCCAC--CTTGACCAAGCTCCG 
s mm6.chr9               46243069 42 + 124135709 G---GAAAACTGGGACA-------CTCTGGGT----TCAAC--CGTTAGTCAGCTGCA 
s cow.ENm003_1             332269 42 -    607368 G---GACAACTGGGACA-------CCCTGGCC----AGCAC--GTTGTCCAAAGTGCG 
s canFam1.chr5           19717296 42 +  92064832 G---GACAACTGGGACA-------GCCTGAGC----AGCAC--GGTGACCAAGCTGCG 
s armadillo.ENm003_1       167856 42 -    560540 G---GACAACTGGGACA-------CGTTCAGC----AGCAG--TGTCACCAAACTGCG 
s elephant.ENm003_1        283732 42 -    658450 G---GACAACTTGGACA-------CCCTGAGC----AGCAG--CTTCACCAAGCTGCA 
s monDom1.scaffold_14981   241325 48 +   1219285 ----GATAACAGAAACAATGACTTCCCTGAAA----GCAGC--CTTGGACGCTTTCTA 
s galGal2.chr24           1113031 46 -   5910111 G---GGCAGCAGTGCCA-------AGGAGACCGTGGACCAA--CTGCAGCAAGCTGAG 
s danRer2.chr16          24197416 40 +  42763181 GAGTGCTGATATGGCCA-------GTGAATAC----GCCGT--CGTCCTCAAG----- 

a score=11846.0
s hg17.chr11             18240047 12 - 134452384 ---CCTAAAGCTCCT 
s panTro1.chr9           18427864 12 - 136640551 ---CCTAAAGCTCCT 
s baboon.ENm003_1          215805 10 -    625247 GAGCCTGAAA----- 
s rheMac1.SCAFFOLD10815      4964 10 +     45664 GAGCCTGAAA----- 
s marmoset.ENm003_1        347747 12 -    718711 ---CCTGAAGCTCCT 
s galago.ENm003_1          363914 12 -    721696 ---CCTGAAACTCCT 
s mm6.chr9               46243057 12 + 124135709 ---CCTGAATCTCCT 
s cow.ENm003_1             332257 12 -    607368 ---CCTGAAACTCCT 
s canFam1.chr5           19717284 12 +  92064832 ---CCTGAAACTCCT 
s armadillo.ENm003_1       167844 12 -    560540 ---TCTGAAGCTCCT 
s elephant.ENm003_1        283720 12 -    658450 ---CCTGAAGCTCCT 
s monDom1.scaffold_14981   241319  6 +   1219285 ---CCTGAA------ 
s galGal2.chr24           1113009 12 -   5910111 ---TCTGGAGGTACT 
s xenTro1.scaffold_18     1462105 12 +   3986068 ---CCTGAAGATCAC 
s danRer2.chr16          24197401 12 +  42763181 ---TGAAAGACTGAC 

a score=242126.0
s hg17.chr11              1812377 30 + 134452384 ATGCTCCACCT--------------GCATGGCTGGCAAACCATG 
s panTro1.chr9            2001217 30 + 136640551 ATGCTCCACCT--------------GTATGGCTGGCAAACCACG 
s baboon.ENm011_1           74768 29 +    550206 ATGTTCCACCT--------------GCACGGCTGG-AAACCATA 
s rheMac1.SCAFFOLD85282     30078 29 +     69065 ATGCTCCACCT--------------GCACGGCTGG-AAACCATA 
s galago.ENm011_1           99833 30 +    434578 ACACTCCACCC--------------ATGTGGCTGGTGAACTGTG 
s rn3.chr1              202843226 25 + 268121971 CAACTAGAC-------------------TGCCTTGTAGAAGATG 
s mm6.chr7              136850702 25 + 139739827 CAACTGGAC-------------------TACCGTGTAGAAGATG 
s canFam1.chr18          56425269 44 +  66173745 AGGCTCCACCTGTGTGACTCCACCCGTGTGACCGACAAACCATG 
s tenrec.ENm011_6            1101 17 +      2615 -------------------------ATTTGGCTG--CAAACAAA 
s galGal2.chr5           44640419 38 -  56310377 ccacaccacctctttctcCTCC---ATGCAGCA---AAACCACA 

a score=405831.0
s hg17.chr13            112381694 71 + 114142980 ATGAACTCACCAGAGGCGAGGCTCTGCGT-TGCTCAATGCAGAGACTCTTACCCAGGGTGTCAGCCTCTGAA 
s panTro1.chr14          95994697 71 +  97804244 ATGAACTCACCAGAGGCGAGGCTCTGCGT-TGCTCAATGCAGAGACTCTTACCCAGGGTGTCAGCCTCTGAA 
s baboon.ENr132_1            3666 68 +    498334 ATGAACTCACCAGAGGC---GTCCTGGGT-TGCTCAACGCAGAGACTCTTACCCAGGGTGTCAGCCTCTGAA 
s rheMac1.SCAFFOLD30317     75494 68 -     86939 ATGAACTCACCAGAGGC---GTCCTGGGT-TGCTCAACGCAGAGACTCTTACCCAGGGTGTCAGCCTCTGAA 
s marmoset.ENr132_1         44583 67 +    578614 ATGAACCCTCCAGAGGC---GTTCTGGGT-TGCTCAATGCAGAGACTCTTATCCA-GGTGTCAGCCTCTGAA 
s rn3.chr16               8607378 65 -  90224819 ATCCATTTACCAGAGC----GACCTGGCC-TCCTGCCTAGGGGGGCTCATTCCCAAGG-ACCGGTCT-TGAA 
s mm6.chr8               12126968 65 + 127867632 ATTTGTTCACCAGAGT----GTCCTGGCC-TCCTGCCTATGTGGACTCATTCCCAAGG-ACCAGCCT-TGAA 
s canFam1.chr22          63116876 49 +  64236280 ATGTGCTGGTC-------------------TGCTCAGGGCAGGAGCTCTTCGCCGGAT-GTCAGTCCCG--- 
s rfbat.ENr132_1            27632 65 +    379529 ATGCGCTGGCCAGAGGT---GTGCTGGTTTTGTTCTGGGCAGTGGCCCTTAACCAGGG-ATCAGCCTTT--- 

a score=12611.0
s hg17.chr13            112381765 144 + 114142980 AGATACACGTGCCTGGGCCTCTTCCCTGAAGATGGACCCGGCAGGTCTGGAGGGAGGCCC-CCGTGATGAATCCCGTGAT-GAGCCGCC---------GATCCGAGCTCAGG-CTGCG---TCATGGGACCAGCCACAAGGTTGCCTGACCTATAAAGG 
s panTro1.chr14          95994768 144 +  97804244 AGATACACGTGCCTGGGCCTCTTCCCTGAAGATGGACCCGGCAGGTCTGGAGGGAGGCCC-CTGTGATGAATCCCGTGAT-GAGCCGCT---------GATCCGAGCTCGGG-CTGCG---TCATGGGACCAGCCACAAGGTTGCCTGACCTATAAAGG 
s baboon.ENr132_1            3734  97 +    498334 AGATACACGTGCCTGGGCCTCTTTCCTGAAGATGGACCCAGCAGGTCTGGAGGGAGGGCC-CTGTGATGCACCCTGTGAT-GAGCCGCT---------GATCCGAGCT--------------------------------------------------- 
s rheMac1.SCAFFOLD30317     75562 107 -     86939 AGATACACGTGCCTGGGCCTCTTTCCTGAAGATGGACCTAGCAGGTCTGGAGGGAGGGCC-CTGTGATGCACCCTGTGAT-GAGCCGCT---------GATCCGAGCT-------------TCGTGGAACC---------------------------- 
s marmoset.ENr132_1         44650 133 +    578614 AGAG--ACGTGCCTGGGCTTCCTCTCTGAAGATGGACCTGGCAGGTCTGGAGGGAGGCCC-CTGTGATGAACCCTGTGAT-AAGCCACT---------GATT---------G-CTGTG---TCATGGGAACAGCCACAAGGTCGACTGACCTATAAAGG 
s rn3.chr16               8607443  81 -  90224819 GGGTGTAT-TATATGG-----TTTCATGAAG-----------------GGAGGGAGGTCT-GTGTGA----CCCTGGGACACCGCTACA---------GGT------------CAGT----------------------GATTG-------TTCGGAAG 
s mm6.chr8               12127033  79 + 127867632 GGACGCAA-TGTAGGG-----CTCCATGGA------------------GGAGGGAGGTCT-GTGTGA----CACTGGGAC-TTGCCACA---------GGT------------CAGT----------------------GATTG-------TTCAGAGG 
s canFam1.chr22          63116925 101 +  64236280 AGACGCACATGCCTGGGCTTCTCCCTCA-------------CAGGACTGCAGCAAGGACCACCACGGTGGACACTGAG---GAGGCCCC---------G--------CCAGGCCGA-GGGATGGAGGAGA-GGCCA----------------------- 
s rfbat.ENr132_1            27836 112 +    379529 aGATGTACATGCCTGGGCTTCTCCCATA-------------CAGGTCCAAAGCAAGGTCCACTGTGGCAGATACTGTGAC-AAGGTCACACCTAGTTGG--------CCAGGTCTA-GTGATGATGTAAA-TGTCG----------------------- 

a score=7383.0
s hg17.chr13        112381909 44 + 114142980 TCGCAGGAGTGCCTCAGGGACACAGAAGCAGTTACAGCTGCCAG 
s panTro1.chr14      95994912 44 +  97804244 TCACAGGAGTGCCTCAGGGAGACAGAAGCAGTTACAGCTGTCAG 
s marmoset.ENr132_1     44783 32 +    578614 TCACAGGAGTGCCTCAGGGAGGCAGTAGCA------------AG 
s rn3.chr16           8607524 44 -  90224819 TCACAGGAATGCCACCCTCAGGAAGAGTTATCTATCTTTTCCAG 
s mm6.chr8           12127112 44 + 127867632 TCACAGGAGTGCCACCCTCAGGCAGAGTCATCTGTCTTTTCCAG 
s canFam1.chr22      63117026 32 +  64236280 TCGATGGAGCAGCATGGGGTCGTCATGGTG------------GG 
s rfbat.ENr132_1        27948 32 +    379529 CAGGAGGAGTGACCTAGTGCGACAGTGGCG------------GT 

a score=84131.0
s hg17.chr14              7658335 10 - 106368585 GAGGAGCTAA 
s panTro1.chr15           7746476 10 - 106954593 GAGGAGCTAA 
s baboon.ENr322_1          325090 10 -    705101 GAGGAGCTAA 
s rheMac1.SCAFFOLD65194     74587 10 +    139520 GAGGAGCTAA 
s marmoset.ENr322_1        314879 10 -    740094 GAGGAGCTAA 
s galago.ENr322_1          375410 10 -    713249 GAGGAGCTAA 
s rn3.chr6               15343184 10 - 147642806 GAGGAGCTAA 
s mm6.chr12              12401629 10 - 115788303 GAGGAGCTAA 
s rabbit.ENr322_1          324585 10 -    557677 GCGCAGCTGA 
s cow.ENr322_1             357229 10 -    609512 GAGGAGCTAA 
s canFam1.chr8            6815616 10 -  77374719 GAGGAGCTAA 
s rfbat.ENr322_1           313473 10 -    530160 GAGGAGCTAA 
s elephant.ENr322_1        239178 10 -    422862 GCGCAGCTAA 
s monDom1.scaffold_15016   401058 10 -   2367050 AAGAAGCTAA 
s platypus.ENr322_1         85131 10 -    159352 AAGAAGCTAA 
s galGal2.chr5           11716518 10 -  56310377 AAGAAGCTAA 
s xenTro1.scaffold_588     534661 10 -    833634 AAGAAGCTAA 
s danRer2.chr17          30167684  4 -  42274751 ------CTAA 

a score=7882659.0
s hg17.chr14               7657711 624 - 106368585 CGCCAA------G---CGCATCAAGGTGGAGAAGGACCTGGAGCTGCCGCCCGCCGCGCTCATCCCGTCCGAGAACGTGTACTCGCAGTGGCTGGTGGGCTACGCGGCGTCGCGGCACTTCATGAAGGACCCCTTCCTGGGCTTCACGGACGCACGACAGTCGCCCTTCGCCACGTCGTCCGAGCACTCGTCCGAGAACGGCAGCCTGCGCTTCTCCACGCCGCCCGGGGACCTGCTGGACGGCGGCCTCTCGGGCCGCAGCGGCACGGCCAGCGGAGGCAGCACCCCGCACCTgggcgg---cccgggccccgggcggcccAGCTCCAAGGAGGGCCGCCGCAGCGACACGTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACTTGACGGTGCACCGGCGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGCACCCTGGAGAAACACATGAAAAAGTGGCACGGCGAGCACTTGCTGACTAACGACGTCAAAATCGAGCAGGCCGA 
s panTro1.chr15            7745853 623 - 106954593 CGCCAA------G---CGCATCAAGGTGGAGAAGGACCTGGAGCTGCCGCCCGCCGCGCTCATCCCGTCCGAGAACGTGTACTCGCAGTGGCTGGTGGGCTACGCGGCGTCGCGGCACTTCATGAAGGACCCCTTCCTGGGCTTCACGGACGCACGACAGTCGCCCTTCGCCACGTCGTCCGAGCACTCGTCCGAGAACGGCAGCCTGCGCTTCTCCACGCCGCCCGGGGACCTGCTGGACGGCGGCCTCTCGGGCCGCAGCGGCACGGCCAGCGGGGGCAGCACCCCGCACCTgggcgg---cccgggccccgggcggcccAGCTCCAAGGAGGGCCGCCGCAGCGACACGTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACTTGACGGTGCACCGGCGGAGCCACACCGGCGAGCGGCC-TACAAGTGCGAGCTGTGCAACTACGCGTGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGCACCCTGGAGAAACACATGAAAAAGTGGCACGGCGAGCACTTGCTGACTAACGACGTCAAAATCGAGCAGGCCGA 
s baboon.ENr322_1           324466 624 -    705101 CGCCAA------G---CGCATCAAGGTGGAGAAGGACCTGGAGCTGCCGCCCGCCGCGCTCATCCCGTCGGAGAACGTATACTCGCAGTGGCTGGTGGGCTACGCGGCGTCGCGGCACTTCATGAAGGACCCCTTCCTGGGCTTCACGGACGCACGACAGTCGCCCTTCGCCACGTCGTCTGAGCACTCGTCCGAGAACGGCAGCCTGCGCTTCTCCACGCCGCCCGGGGACCTGCTGGACGGCGGCCTCTCGGGCCGCAGTGGCACGGCCAGCGGAGGCAGCACCCCGCACCTgggcgg---ccccggccccgggcggcccAGCTCCAAGGAGGGCCGCCGCAGCGACACGTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACCTGACAGTGCACAGGCGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCATGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGCACCCTGGAGAAACACATGAAAAAGTGGCACGGCGAGCACTTGCTGACTAACGACGTCAAAATCGAGCAGGCCGA 
s rheMac1.SCAFFOLD65194      73963 624 +    139520 CGCCAA------G---CGCATCAAGGTGGAGAAGGACCTGGAGCTGCCGCCCGCCGCGCTCATCCCGTCCGAGAACGTGTACTCGCAGTGGCTGGTGGGCTACGCGGCGTCGCGGCACTTCATGAAGGACCCCTTCCTGGGCTTCACGGACGCACGACAGTCGCCCTTCGCCACGTCGTCTGAGCACTCGTCCGAGAACGGCAGCCTGCGCTTCTCCACGCCGCCCGGGGACCTGCTGGACGGCGGCCTCTCGGGCCGCAGTGGCACGGCCAGCGGAGGCAGCACCCCGCACCTgggcgg---ccccggccccgggcggcccAGCTCCAAGGAGGGCCGCCGCAGCGACACGTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACCTGACGGTGCACAGGCGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCATGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGCACCCTGGAGAAACACATGAAAAAGTGGCACGGCGAGCACTTGCTGACTAACGACGTCAAAATCGAGCAGGCCGA 
s marmoset.ENr322_1         314255 624 -    740094 CGCCAA------G---CGCATCAAGGTGGAGAAGGACCTGGAGCTGCCGCCCGCCGCGCTCATCCCGTCCGAGAACGTGTACTCGCAGTGGCTGGTGGGCTACGCCGCGTCGCGGCACTTCATGAAGGACCCCTTCCTGGGCTTCACGGACGCGCGCCAGTCGCCCTTCGCCACGTCGTCCGAGCACTCGTCCGAGAACGGCAGCCTGCGCTTCTCCACGCCGCCCGGGGACCTGCTGGACGGCGGCCTCTCGGGCCGCAGCGGCACGGCCAGCGGAGGCAGCACTCCGCACCTgggcgg---gcccgggcccgggcggcccAGCTCCAAGGAGGGCCGCCGCAGCGACACGTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACCTGACGGTGCACCGGCGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGTGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGCACCCTGGAGAAACACATGAAAAAGTGGCACGGCGAGCACTTGCTGACTAACGACGTCAAAATCGAGCAGGCCGA 
s galago.ENr322_1           374786 624 -    713249 GGCCAA------G---CGCATCAAGGTGGAGAAGGACCTGGAGCTGCCGCCCGCTGCGCTCATCCCATCCGAGAACGTGTATTCACAGTGGCTCGTGGGCTACGCGGCGTCACGGCACTTCATGAAGGACCCCTTCCTGGGCTTCACGGACGCGCGCCAGTCGCCCTTCGCCACATCGTCCGAGCACTCATCCGAGAACGGCAGCCTGCGCTTCTCCACACCGCCTGGTGACCTGCTGGACGGCGGTCTGTCGGGCCGCAGCGGTACGGCCAGCGGGGGCAGCACGCCGCACCTGGGTgg---cccgggcccggggcggcccAGCTCCAAGGAGGGCCGCCGCAGCGACACGTGTGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACCTGACGGTGCACCGGCGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGCACCCTGGAGAAACACATGAAAAAGTGGCATGGCGAGCACTTGCTGACTAACGATGTCAAAATCGAGCAGGCCGA 
s rn3.chr6                15342560 624 - 147642806 GGCCAA------G---CGCATCAAGGTGGAGAAGGACCTGGAGCTGCCACCCGCCGCCCTCATCCCATCCGAGAACGTGTACTCGCAGTGGCTCGTGGGCTACGCGGCGTCGCGCCACTTCATGAAGGACCCGTTCCTGGGCTTCACGGATGCGCGCCAGTCGCCTTTCGCCACGTCGTCGGAACATTCCTCTGAGAACGGCAGCCTGCGCTTCTCCACGCCACCCGGGGACCTGCTGGACGGCGGGCTGTCGGGGCGCAGTGGCACGGCGAGCGGGGGCAGCACGCCTCACCTGGGTGG---CCCGGGTCCTGGGCGGCCGAGCTCCAAGGAGGGCCGCCGCAGCGACACGTGCGAGTACTGCGGCAAGGTCTTCAAAAACTGTAGCAACCTGACGGTGCACCGGAGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGCGCGCAGAGCAGCAAGCTTACGCGCCACATGAAGACGCACGGTCAGATCGGCAAGGAGGTGTACCGCTGCGATATCTGCCAGATGCCCTTCAGTGTCTACAGTACCCTGGAGAAACACATGAAAAAGTGGCACGGTGAACACTTGCTGACTAATGATGTCAAAATCGAGCAGGCTGA 
s mm6.chr12               12401005 624 - 115788303 GGCCAA------G---CGCATCAAGGTGGAGAAAGACCTGGAGCTGCCACCTGCCGCCCTCATCCCATCTGAGAACGTGTACTCGCAGTGGCTCGTGGGCTACGCAGCATCGCGCCACTTCATGAAGGACCCATTCCTGGGCTTCACGGATGCGCGCCAGTCGCCTTTCGCCACATCGTCGGAACATTCCTCTGAGAACGGCAGCCTGCGCTTCTCAACGCCACCCGGGGACCTGCTGGACGGCGGGCTGTCCGGGCGCAGTGGCACGGCGAGCGGGGGCAGCACACCTCACCTGGGTGG---TCCGGGTCCTGGGAGGCCGAGCTCCAAGGAGGGCCGCCGCAGCGACACATGTGAGTACTGCGGCAAGGTCTTCAAGAACTGTAGCAACCTGACGGTGCACCGGAGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGCACCCTGGAGAAACACATGAAAAAGTGGCACGGTGAACACTTGCTGACTAATGATGTCAAAATCGAGCAGGCTGA 
s rabbit.ENr322_1           323975 610 -    557677 -----------------------AGGTGGAGAAGGACCTGGAGCTGCCGCCCGCCGCGCTCATCCCCTCCGAGAACGTGTACTCGCAGTGGCTCGTGGGCTACGCCGCGTCGCGCCACTTCATGAAGGACCCCTTCCTGGGCTTCACCGACGCGCGCCAGTCGCCCTTCGCCACGTCGTCGGAGCACTCGTCCGAGAACGGCAGCCTGCGCTTCTCCACGCCGCCCGGGGACCTGCTGGACGGCGGCCTGTCCGGGCGCAGCGGCACGGCCAGCGGCGGCAGCACGCCGCACCTgggcgg---cccgggccccgggcggcccAGCTCCAAGGAGGGCCGCCGGAGCGACACGTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACCTCACCGTGCACCGCCGCAGCCACACGGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGCGCGCAGAGCAGCAAGCTGACTCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGCACCCTGGAGAAACACATGAAGAAGTGGCACGGCGAGCACTTGCTGACGAACGACGTCAAGATAGAGCAGGCCGA 
s cow.ENr322_1              356605 624 -    609512 GGCCAA------G---CGCATCAAGGTGGAGAAGGACCTAGAGCTGCCGCCTGCCGCGCTCATCCCGTCGGAGAATGTGTACTCGCAGTGGCTGGTGGGCTACGCGGCGTCGCGGCACTTCATGAAGGACCCCTTCCTGGGCTTCACGGACGCGCGCCAGTCGCCCTTCGCCACGTCGTCCGAGCACTCGTCCGAGAACGGCAGCCTGCGCTTCTCCACGCCACCCGGGGACCTGCTGGATGGCGGGTTGTCGGGCCGTAGCGGCACGGCCAGCGGGGGCAGCACGCCGCATCTgggcgg---cccgggccccgggcggccgAGCTCCAAGGAGGGGCGGCGCAGCGACACGTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACCTCACGGTGCACCGACGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAAATGCCCTTCAGCGTCTATAGCACCCTGGAGAAACACATGAAAAAGTGGCACGGCGAGCACTTGCTGACTAACGACGTCAAAATCGAGCAGGCGGA 
s canFam1.chr8             6814992 624 -  77374719 GGCCAA------G---CGCATCAAGGTGGAGAAGGACCTGGAGCTGCCGCCCGCCGCGCTCATCCCGTCCGAGAACGTGTACTCGCAGTGGCTCGTGGGCTACGCCGCGTCGCGGCACTTCATGAAGGACCCGTTCCTGGGCTTCACGGACGCGCGCCAGTCGCCCTTCGCCACGTCGTCCGAGCACTCGTCCGAGAACGGCAGCCTGCGCTTCTCCACGCCGCCCGGGGACCTGCTGGACGGCGGGCTGTCGGGCCGCAGCGGCACGGCCAGCGGGGGCAGCACGCCGCACCTgggcgg---cccgggccccgggcggccgAGCTCCAAGGAGGGCCGGCGCAGCGACACGTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACCTGACGGTGCACCGGCGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGCACCCTGGAGAAACACATGAAAAAGTGGCACGGCGAGCACTTGCTGACTAACGACGTCAAAATCGAGCAGGCCGA 
s rfbat.ENr322_1            312849 624 -    530160 GGCCAA------G---CGCATCAAGGTGGAGAAGGACCTAGAGCTGCCGCCCGCCGCGCTCATCCCGTCTGAGAACGTGTACTCGCAGTGGCTGGTGGGCTACGCGGCGTCGCGGCACTTCATGAAGGACCCCTTCCTGGGCTTCACGGACGCGCGCCAGTCCCCCTTCGCCACGTCGTCGGAGCACTCGTCCGAGAATGGCAGCCTGCGCTTCTCCACGCCGCCCGGGGACCTGCTGGACGGCGGCCTGTCGGGCCGCAGCGGTACCGCCAGCGGCGGCAGCACGCCACACCTGGGTGG---CCCCGGCCCTGGGCGGCCGAGCTCCAAGGAGGGCCGCCGCAGCGACACGTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACCTGACGGTGCACCGGCGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGTGCGCAGAGCAGCAAGCTCACACGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGCACCCTGGAGAAACACATGAAAAAGTGGCACGGCGAGCACTTGCTGACTAACGACGTCAAAATCGAGCAGGCCGA 
s elephant.ENr322_1         238554 624 -    422862 GGCCAA------G---CGCATCAAGGTGGAGAAGGACCTGGAGCTGCCGCCGGCCGCGCTCATTCCCTCGGAGAACGTGTACTCGCAGTGGCTCGTGGGCTACGCCGCGTCTCGCCACTTCATGAAGGACCCCTTCCTGGGCTTCACGGACGCGCGCCAGTCGCCCTTCGCCACGTCGTCCGAGCACTCGTCTGAGAACGGCAGCCTGCGCTTCTCCACGCCGCCCGGCGACCTGCTGGACGGCGGGCTGTCGGGGCGCAGCGGCACGGCCAGCGGGGGCAGCACGCCGCACCTgggcgg---cccgggcccggggcggcccAGCTCCAAGGAGGGCCGGCGCAGCGACACGTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACCTGACGGTGCACCGGCGGAGCCACACCGGTGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGTGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGCACCCTGGAGAAACACATGAAAAAGTGGCACGGCGAGCACTTGCTGACTAACGACGTCAAAATCGAGCAGGCCGA 
s monDom1.scaffold_15016    400434 624 -   2367050 ATCCAA------G---AGGATAAAGATAGAAAAGGACTTGGACTTGCCACCAGCAACCATCATTCCTTCAGAAAATGTTTACTCGCAGTGGCTGGTGGGATACGCGGCCTCGAGACACTTCATGAAGGATCCATTTCTCGGGTTCACAGATTCGCGACAGTCGCCCTTCGCCACTTCTTCGGAGCACTCCTCAGAGAATGGGAGCCTGCGTTTCTCCACCCCACCTGGGGACATGTTGGATGGAGGCCTCTCAGGACGCAGTGGGACAGCCAGTGGAGGCAGTACCCCCCACATAAGTGG---GCCGGGGCCTGGCCGACCGAGCTCCAAGGAAGGGCGCCGCAGCGACACGTGTGAGTACTGTGGCAAGGTTTTTAAGAACTGCAGCAACTTGACGGTCCACCGTCGGAGCCACACAGGAGAAAGGCCTTACAAATGTGAGCTCTGCAACTACGCATGCGCCCAGAGCAGTAAGCTAACCCGCCATATGAAAACCCATGGCCAGATAGGGAAAGAGGTCTACCGGTGTGATATTTGCCAGATGCCATTCAGCGTTTATAGCACCCTGGAAAAACACATGAAAAAGTGGCATGGAGAACATTTGCTGACAAACGATGTGAAAATAGAGCAGGCGGA 
s platypus.ENr322_1          84507 624 -    159352 GTCCAA------G---AGGATAAAGATAGAAAAGGATCTGGACTTGCCACCAGCAACGATCATCCCTTCCGAGAACGTCTACTCCCAGTGGCTGGTCGGGTACGCGGCCTCTCGGCACTTCATGAAGGATCCGTTCCTCGGGTTCACGGACTCCCGACAGTCCCCGTTCGCCACCTCTTCCGAGCATTCTTCGGAGAACGGCAGCCTGCGTTTCTCCACCCCGCCGGGCGACATGCTAGACGGGGGCCTCTCAGGGCGCAGCGGGACCGCCAGCGGGGGCAGCACCCCCCACATcggcgg---gcccggccccggccgACCCAGCTCCAAGGAAGGGCGGAGGAGCGACACGTGCGAGTACTGTGGCAAGGTCTTCAAGAACTGCAGCAACCTCACCGTGCACCGTCGCAGCCATACCGGCGAACGGCCTTATAAATGTGAGCTCTGCAATTATGCCTGCGCTCAGAGCAGTAAGCTCACCCGCCACATGAAAACGCACGGCCAGATAGGGAAGGAGGTGTACCGCTGTGACATCTGCCAGATGCCATTCAGCGTATACAGCACGCTGGAGAAACATATGAAAAAGTGGCACGGAGAACACTTGCTGACAAACGATGTCAAAATCGAGCAGGCGGA 
s galGal2.chr5            11715894 624 -  56310377 ATCTAA------A---CGAATAAAAGTTGAGAAAGATTTGGACTTGCCACCAGCAACAATAATACCTTCCGAAAATGTTTACTCCCAGTGGCTGGTAGGGTACGCGGCATCAAGGCACTTCATGAAGGATCCGTTTCTAGGATTCACAGACTCCCGACAATCTCCCTTCGCCACCTCTTCCGAGCATTCGTCGGAGAATGGGAGCCTGCGTTTCTCCACCCCGCCGGGGGACATGCTGGATGGGGGGCTCTCAGGGCGCAGCGGCACGGCCTCCGGAGGCAGCACCCCCCACATCAGCGG---CCCAGGCCCTGGGCGACCCAGCTCGAAGGAAGGGCGCAGGAGCGATACATGTGAGTACTGTGGCAAGGTCTTTAAGAACTGCAGCAATTTGACGGTGCACCGTCGGAGCCACACTGGAGAGCGGCCTTACAAATGCGAGCTCTGCAACTATGCATGTGCCCAGAGCAGTAAGCTGACGCGTCACATGAAAACGCATGGCCAGATAGGGAAGGAGGTCTACCGCTGCGACATTTGCCAGATGCCCTTCAGTGTTTACAGCACCCTGGAGAAACACATGAAAAAGTGGCATGGAGAACATTTGCTGACAAATGACGTCAAAATTGAGCAGGCAGA 
s xenTro1.scaffold_588      534037 624 -    833634 ATCAAA------A---AGGATAAAAATTGAGAAAGATCTAGATTTACCCCCAACACCAATAATCCCATCAGAAAACGTTTACTCACAGTGGCTAGTAGGATATGCAGCATCAAGGCACTTCATGAAGGATCCATTTCTAGGATTCACAGACTCTCGACAATCTCCTTTTGCAACTTCTTCTGAGCACTCTTCAGAAAATGGAAGTCTGCGGTTCTCTACACCACCAGGTGACATGCTGGATGGAGGTCTCTCAGGGCGAAGTGGGACAGCGAGTGGCGGCAGCACACCACATATCAGTGG---ACCAGGGCCTGGCCGGCCAAGTTCAAAAGAAGGAAGAAGAAGTGACACATGCGAATTCTGTGGCAAAGTGTTTAAGAACTGCAGCAACCTCACGGTCCACCGCAGAAGCCACACTGGGGAACGGCCTTACAAATGCGAGCTCTGCAACTATGCATGTGCCCAGAGCAGCAAGCTGACACGCCACATGAAAACGCATGGCCAGATAGGTAAGGAGGTCTACCGCTGTGACATTTGCCAGATGCCCTTCAGTGTTTACAGCACCCTGGAGAAACACATGAAAAAATGGCATGGAGAACACTTGCTGACAAATGACGTCAAAATTGAGCAGGCAGA 
s tetNig1.chrUn_random   145482037 624 - 171761319 CACAAA------TAAAAGGATAAAGACTGAGAAGGACACGGATGGTTCCCCAGCACCCCTCATTCCCTCTGAAAATGTCTACTCTCAGTGGCTGGTGGGATATGCTGCCTCTCGCCATTTTATAAAAGACCCTTTTCTTGGCTTCAGTGACTCGCGACAATCTCCCTTCGGCACGTCATCTGAGCACTCCTCTGAAAATGGCAGCCTGCGCTTTTCGACGCCCCCAGGAGACCTGATAGACGGTGGCTTGTCAGGTCGTAGCGGTACTGCGAGTGGAGGCAGTACCCCTCATCTCAGTGG------AGGTCCTGGCAGACCCAGCTCAAAGGACGGCAGGAGGTCCGACACCTGTGAGTTCTGTGGCAAAGTTTTTAAAAACTGCAGCAACCTGACCGTGCACCGGCGCAGCCATACTGGTGAGAGGCCCTACAAGTGTGAGCTGTGCAACTACGCCTGCGCTCAGAGCTCCAAGCTCACTCGCCACATGAAGACGCACGGCCAGCTCGGTAAGGAGGTCTATCGATGTGACATTTGCCAAATGCCATTCAGCGTGTACAGCACCCTTGAGAAACACATGAAAAAGTGGCATGGAGAACACTTGATGTCTAATGAGATCAAACTTGAACAAGCAGA 
s danRer2.chr17           30167045 633 -  42274751 GGCTAAGCTCTCG---AGGATCAAAATTGAAAAGGATTTGGACATACCCCCAGCCCCCCTAATCCCATCTGAAAATGTCTACTCCCAGTGGCTGGTGGGCTATGCAGCATCCCGCCACTTCATCAAAGATCCTTTCCTTGGCTTCACCGACTCCAGACAATCTCCATTCGCCACCTCCTCGGAACACTCCTCCGAGAACGGAAGCTTGCGATTCTCTACGCCGCCAGGGGACCTGCTGGACGGGGGCCTCTCCGGCCGCAGTGGTACTGCTAGCGGAGGCAGCACCCCGCACCTGGGTGGGGGGCCAGGACCAGGCCGGCCTAGCTCGAAAGAGAGCCGGAGGAGTGACACCTGTGAGTACTGTGGGAAGGTGTTCAAGAACTGTAGCAATCTGACAGTGCACAGACGCAGCCACACAGGCGAGAGGCCCTACAAGTGTGAGCTTTGTAACTACGCCTGCGCCCAGAGCAGCAAGCTCACCCGCCACATGAAGACACACGGCCAGCTCGGTAAGGAAGTGTACCGCTGTGACATTTGCCAAATGCCCTTCAGCGTCTACAGCACGCTTGAGAAACACATGAAAAAGTGGCATGGGGAACATTTGATGACGAATGAGGTCAAAATTGAACAAGCAGA 

a score=534248.0
s hg17.chr14               7657624 87 - 106368585 gggcggCTTCGCGCCAGGCACCGAGCCCTTCCCCGGGCTCTTCCCGCGCAAGCCCGCGCCGCTGCCCAGCCCCGGGCTCAACAG------------CGC 
s panTro1.chr15            7745766 87 - 106954593 gggcggCTTCGCGCCAGGCACCGAGCCCTTCCCCGGGCTCTTCCCGCGCAAGCCCGCGCCGCTGCCCAGCCCCGGGCTCAACAG------------CTC 
s baboon.ENr322_1           324379 87 -    705101 gggcggCTTCGCGCCGGGCACCGAGCCTTTCCCTGGGCTTTTCCCGCGCAAGCCCGCACCGCTGCCCAGCCCGGGGCTCAACAG------------CGC 
s rheMac1.SCAFFOLD65194      73876 87 +    139520 gggcggCTTCGCGCCGGGCACCGAGCCTTTCCCTGGGCTTTTCCCGCGCAAGCCCGCGCCGCTGCCCAGCCCGGGGCTCAACAG------------CGC 
s marmoset.ENr322_1         314168 87 -    740094 GGGCGGCTTCGCGCCGGGCGCCGAGCCCTTCCCCGGGCTCTTCCCGCGCAAGCCCGCGCCTCTGCCCAGCCCCGGGCTCAACAG------------CGC 
s galago.ENr322_1           374699 87 -    713249 CGGTGGCTTCGCGCCAGGCGCCGAGCCCTTCCCAGGTCTCTTCCCGCGCAAGCCGGCGCCGCTACCCAGCCCTGGGCTCAACAG------------CGC 
s rn3.chr6                15342461 99 - 147642806 CGGGGCCTTCGCGCCAGGCGCAGAGCCCTTCCCAGCGCTCTTCCCACGCAAGCCCGCACCGCTGCCCAGCCCGGGGCTTGGTGGTCCTGCGCTACACGC 
s mm6.chr12               12400906 99 - 115788303 CGGGGCCTTCGCGCCAGGCGCAGAGCCCTTTCCAGCTCTCTTCCCACGCAAGCCAGCACCGCTGCCCAGCCCTGGGCTCGGTGGTCCCGCGCTGCACGC 
s cow.ENr322_1              356518 87 -    609512 cggtggcTTCGCGCCGGGCACCGAGCCTTTCCCGGGCCTCTTCCCGCGCAAGCCGGCACCGCTGCCCAGCCCCGGCCTCAACAG------------CGC 
s canFam1.chr8             6814905 87 -  77374719 cggcggcTTCGCACCGGGCGCCGAGCCCTTCCCGGGGCTGTTCCCGCGCAAGCCGGCGCCGCTGCCCAGCCCCGGGCTCAACAG------------CGC 
s rfbat.ENr322_1            312762 87 -    530160 CGGTGGCTTCGCGCCAGGCACCGAGCCCTTCCCGGGCCTCTTCCCGCGCAAGCCGGCGCCGCTGCCCAGCCCCGGGCTCAACAG------------CGC 
s elephant.ENr322_1         238473 81 -    422862 ---TGGCTTC---CCGGGCGCCGAGCCCTTCCCGGGGCTCTTCCCGCGCAAGCCGGCGCCGCTGCCCAGCCCCGGGCTGCCCAG------------CGC 
s monDom1.scaffold_15016    400351 83 -   2367050 -AGAAGCTTTGGTCCTGGT---GAGCCCTTCCCGGGCCTCTTCCCCAGGAAGCCGACACCTATTACGAGTCCCAGTTTAAACAA------------TTC 
s platypus.ENr322_1          84424 83 -    159352 -AGAAACTTCGGGCCTAGC---GAGCCCTTCCCGGGACTCTTTCCCCGCAAGCCCACGCCCATCACGAGCCCCAGCCTGAACAA------------TTC 
s galGal2.chr5            11715811 83 -  56310377 -AGAAACTTTGGCCCAGGC---GAGCCCTTCCCAAACTTGTTCCCTCGGAAGCCAACACCTATCACAAGCCCCAGCTTAAATAA------------CTC 
s xenTro1.scaffold_588      533957 80 -    833634 ----AATTTTGGCCCAGGT---GAACCATTTCCAGGCTTGCTCCCACGAAAGCCAATGCCTATTTCTAGTTCTGGACTAAACAA------------CTC 
s tetNig1.chrUn_random   145481953 84 - 171761319 CCGAAACTGTAGATCAGAT---GATTCTCTTGTCAGTTTATTTCCCCATAAACCCACTTCCATCACTAGCTCTGGTCTGTCCAA------------CTC 

a score=209661.0
s hg17.chr14               7657562 62 - 106368585 ga---cgacgacgacgcgggcggctgcgggga------cgcgggcgcgggcggcgcggtcaacgggcgcgg 
s panTro1.chr15            7745704 62 - 106954593 ga---cgacgacgacgcgggcggctgcgggga------cgcgggcgcgggcggcgcggtcaacgggcgcgg 
s baboon.ENr322_1           324317 62 -    705101 ga---cgacgacgacgcgggcggctgcgggga------cacgggagcgggcggcgcggtcaacgggcgcgg 
s rheMac1.SCAFFOLD65194      73814 62 +    139520 ga---cgacgacgacgcgggcggctgcgggga------cacgggcgcgggcggcgcggtcaacgggcgcgg 
s marmoset.ENr322_1         314106 62 -    740094 GA---CGACGACGACGCGGGCGACTACGGGGA------CGCGGGCGCGGGCGGCGCGGTCAACGGTCGCGG 
s galago.ENr322_1           374637 62 -    713249 GA---CGACGACGACGCAGGAGGCTGTGGCGA------CGCAGGTACGGGTGGCGCAGTAAACGGGCGCGG 
s rn3.chr6                15342401 60 - 147642806 -----TGACACCGGAGCTGGTGGCTGCGGGGA------TGCAGGTGCACCGGGCGCAGTGAACGGGCGTGG 
s mm6.chr12               12400846 60 - 115788303 -----TGATGCCGGAGCTGTTGGCTGTGGGGA------CGCGGGTGCACCGGGTGCAGTGAACGGGCGCGG 
s cow.ENr322_1              356456 62 -    609512 ga---cgacgatgacgccgggggctgcggcga------cgcgggccccgggggcgcggtcaacgggcgcgg 
s canFam1.chr8             6814843 62 -  77374719 ga---cgacgacgacgcgggcggctgcgggga------cgcgggcaccggcggcgcggtcaacaggcgcgg 
s rfbat.ENr322_1            312700 62 -    530160 GA---CGACGATGACGCGGGTGGCTGCGGTGA------TGCGGGCCCGGGCGGTGCGGTCAACGGGCGCGG 
s elephant.ENr322_1         238411 62 -    422862 GA---CGATGAGGACGCGGGTGGCTGCGGGGA------CGCGGGCGCAGGCGGCGCGGTCAACGGGCGCGG 
s monDom1.scaffold_15016    400299 52 -   2367050 -----AGACTCCGTGGCCGGAGAGCTTGACCG------TACGGA---GGAAGGGACGGTCAACGGA----- 
s platypus.ENr322_1          84372 52 -    159352 -----AGACTCCGTGGTGGGTGAGCTGGAGCG------TCCGGA---GGAAGGGGCCGTCAACGGG----- 
s galGal2.chr5            11715759 52 -  56310377 -----AGACTCAGTGGTAGGAGAGCTGGACCG------CACCGA---GGAGGGGACAGTCAATGGA----- 
s xenTro1.scaffold_588      533900 57 -    833634 CA---TGAAGATACAGTGGAGAGAGAAATAAT------CCCCAATGATGAAGGGACAGTTAATGGA----- 
s tetNig1.chrUn_random   145481891 62 - 171761319 GATGAAGATTCGGTGCCTGAGGAGTCAGACCACCATCCACCAAA---AAGGACAATCATAAATGG------ 
s danRer2.chr17           30166628 56 -  42274751 GATGACGATTCAGTAGTGGGGGAAATGGACCA------AGTAGA---GCGGGCAACTGTGAATGG------ 

a score=225811.0
s hg17.chr14               7657471  91 - 106368585 AGGCGCACTGCCGCAGTACGGCGAGCTCCTGGCCGACAAGCAGAAGCGCGGCGCCTTCCTGAAGCG----------------------------TGCggc---------gggcgg---cg--gggacgcgggc 
s panTro1.chr15            7745613  91 - 106954593 AGGCGCACTGCCGCAGTACGGCGAGCTCCTGGCCGACAAGCAGAAGCGCGGCGCCTTCCTGAAGCG----------------------------TGCggc---------gggcgg---cg--gggacgcgggc 
s baboon.ENr322_1           324226  91 -    705101 GGGCGCACTGCCGCAGTATGGCGAGCTCTTGGCCGACAAGCAGAAGCGCGGCGCCTTCCTGAAGCg----------------------------cgcggc---------tggcgg---cg--gggacgcgggc 
s rheMac1.SCAFFOLD65194      73723  91 +    139520 GGGCGCACTGCCGCAGTATGGCGAGCTCTTGGCCGACAAGCAGAAGCGCGGCGCCTTCCTGAAGCg----------------------------cgcggc---------tggcgg---cg--gggacgcgggc 
s galago.ENr322_1           374546  91 -    713249 GGGCGCGCTGCCTCAGTATGGCGACCTGCTGGCTGACAAGCAGAAGCGCGGCGCCTTCCTGAAGCG----------------------------CGGGGC---------GGGCGG---CG--GTGATGCTGGC 
s rn3.chr6                15342338  63 - 147642806 GGGCGCACTGCCGCAGTATGGGGA------------------GAAGCGAGGCGCCTTCCTGAAGCG----------------------------TGCAG-----------------------GCGACGCGGG- 
s mm6.chr12               12400783  63 - 115788303 GGGCGCACTGCCGCAGTATGGGGA------------------GAAGCGGGGCGCCTTCCTGAAGCG----------------------------TGCAG-----------------------GCGACACGGG- 
s cow.ENr322_1              356356 100 -    609512 GGGCGCGCTGCCGCCCTATGGCGACCTGCTGGCTGACAAGCAGAAGCGCGGCGCCTTCCTGAAGCG----------------------------Cgcggccggcggtgggggcgg---cg--gggacccaggc 
s rfbat.ENr322_1            312609  91 -    530160 GGGCGCGCTGCCGCAGTACGGCGAGCTGCTGGCCGACAAGCAGAAGCGCGGGGCCTTCCTGAAGCG----------------------------CGCGGC---------GGGCGG---TG--GGGACACGGGT 
s elephant.ENr322_1         238323  88 -    422862 ------GCCGCCGCAGTATGGCGAGCTGCTGGCCGACAAGCAGAAGCGCGGCTCCTTCCTGAAGCG----------------------------CGCGGG---------CAGCGTGGCCG--GCGACCCCGGC 
s monDom1.scaffold_15016    400173 116 -   2367050 CGGTGCCATCCAGCAATACAACGACATGTTGGCTGAGAAACAGAAGAGGAGCAGCTTCATGAAAAGGAGCTCAGATCAGCGAGACCTTTGTTCTCGAGAC---------CTGTGT---CA--GAGAGACA--- 
s platypus.ENr322_1          84246 121 -    159352 GGGTGCCATCCAGCAGTACAACGACATGCTCGCTGAGAAGCAGAAGAGGAGCAGCTTCATGAAAAGGTCCGCAGACCAGCGTGACCTCTGCCCCCGAGAC---------TTGTGC---CAGCGGGATCCGGGC 
s galGal2.chr5            11715633 116 -  56310377 CGGTGCCATCCAGCAATACAATGACATGCTAGCTGAGAAACAGAAGAGGAGTAGCTTCATGAAAAGGTCTTCTGACCAAcgagacctgtgtccccgagac---------ctgtgc---cc--gagaGACA--- 
s xenTro1.scaffold_588      533797  98 -    833634 AGGAGGCATGCAGGCATATAGTGATATGCTGCATGAAAAACAAAAAAGAAGTCATTTCATGAAACG---ATCTGATCAG---------------CAAATT---------TTATGT---AG--GAGAATTC--- 
s tetNig1.chrUn_random   145481797  91 - 171761319 GACTTCTATTCAACACTATAATAATTTAATAGTTGACAATCGCAACAGGACTGAATTGTCCAAGAGGTG-------------------------CTCAGA---------CGACCA---GC--GGGACACG--- 
s danRer2.chr17           30166534  92 -  42274751 CAGCTCCATCCAGCAGTACAATAACTTAATAGTTGACAATCGGAAAAGGCTTCCATTCTCTAAAAGGAT-------------------------CTCGGA---------AGTGCA---GA--GGGAAGTGG-- 

a score=301329.0
s hg17.chr14               7657408 63 - 106368585 gg---------ccAAGGCGCTGGCTGACGAGAAG--GCGCTGG-TGCTGGGCAAGGTCATGGAGAACGTGGGCCT 
s panTro1.chr15            7745550 63 - 106954593 gg---------ccAAGGCGCTGGCTGACGAGAAG--GCGCTGG-TGCTGGGCAAGGTCATGGAGAACGTGGGCCT 
s baboon.ENr322_1           324163 63 -    705101 GG---------CCAAGGCACTGGCTGACGAGAAG--GCCCTGG-TGCTGGGCAAGGTCATGGAGAACGTGGGCCT 
s rheMac1.SCAFFOLD65194      73660 63 +    139520 gg---------ccAAGGCACTGGCTGACGAGAAG--GCCCTGG-TGCTGGGCAAGGTCATGGAGAACGTGGGCCT 
s galago.ENr322_1           374474 72 -    713249 GGGCGGTGCTGCCAAGGCTCTGGCTGATGAGAAG--GCCCTTG-TGCTGGGCAAGGTCATGGAGAACGTGGGCCT 
s rn3.chr6                15342275 63 - 147642806 AG---------CTGCGGCTCTGGCAGATGAGAAG--GCGCTGG-CATTGGGCAAGGTGATGGAGGACGCAGGGCT 
s mm6.chr12               12400720 63 - 115788303 AG---------CTGCGGCTCTGGCGGATGAGAAG--GCTCTGG-CCCTGGGCAAGGTGATGGAGGACGCAGGGCT 
s rabbit.ENr322_1           323803 53 -    557677 -g---------gcgcggggctgg-----gcgcgg--gcgcggg-cggcgggcccgg-gctgccgggcgcggg--- 
s cow.ENr322_1              356293 60 -    609512 gg---------ccAAGGCGCTGGCCGACGAGAAG--GCGCTGG-TGCTGGGCAAGGTCATGGAGAACGTGGG--- 
s rfbat.ENr322_1            312546 61 -    530160 gg---------ccAAGGCGCTGGCCGAGGAGAAG--GCGCTGG-TGCTGGGCAAGGTCATGGAGAACGTGGGC-- 
s elephant.ENr322_1         238254 60 -    422862 gg---------ccAAG---CTGGCCGACGAGAAG--GCGCTGG-TGCTGGGCAAGGTCATGGAGAACGTGGGCCT 
s monDom1.scaffold_15016    400111 62 -   2367050 -T---------CCAAGTCACTACCAGACGAAAAG--TCCCTCG-TTCTTGGAAAAGTGATCGAGAATGTCAGCCT 
s platypus.ENr322_1          84183 63 -    159352 GT---------CCAAGTCGCTCCCTGATGAGAAG--TCCCTGG-TCCTGGGGAAAGTGATTGAGAACGTGAGCCT 
s galGal2.chr5            11715571 62 -  56310377 -T---------CCAAATCACTGCCAGATGAGAAA--TCCCTTG-TCCTGGGAAAAGTGATAGAGAATGTAAGTCT 
s xenTro1.scaffold_588      533734 63 -    833634 AG---------CAAAGCCAATCCATGATGAGAAG--TCCCTTG-TTCTTGGAAAAGTTATGGAGAATGTACATTT 
s tetNig1.chrUn_random   145481733 61 - 171761319 -----------CCAAACAGCTGTCTGAGGAGAAGTCATCATTTGCTTTTAATAAAATGATGGAAACTCGTGG--- 
s danRer2.chr17           30166473 58 -  42274751 -----------CAAAGCCTCCTTCAGATGAGAAG--ACCCTTT-CGTTAGGAAAGATGGTGGAAAATGTAGG--- 

a score=30812.0
s hg17.chr14             7657375 33 - 106368585 GGTgcccggggtcccg-----ggcgcggggggcg------gcgc 
s panTro1.chr15          7745517 33 - 106954593 GGTgcccggggtcccg-----ggcgcggggggcg------gcgc 
s baboon.ENr322_1         324130 33 -    705101 GGTGGCCGGGGTCCCG-----GGCACGGGGGGCG------GCGC 
s rheMac1.SCAFFOLD65194    73627 33 +    139520 ggtggccggggtcccg-----ggcgcggggggcg------gcgc 
s galago.ENr322_1         374441 33 -    713249 GGTGCCGGGGGTGCCC-----GGAGCTGGGGGCG------GCGT 
s rn3.chr6              15342245 30 - 147642806 GCCACCAGGGGTGGCG-----GGCGCGGGGGCTG---------C 
s mm6.chr12             12400690 30 - 115788303 GCCACCGGGGGTGGCG-----GGCGCAGGGGCTG---------C 
s rabbit.ENr322_1         323775 28 -    557677 -----cggcggcggcgCgctgggcgc-ggggctg---------- 
s cow.ENr322_1            356257 36 -    609512 GGTggccggcgtgccg-----ggcgcgggcggcg---gcgccgc 
s rfbat.ENr322_1          312507 39 -    530160 ggtgcccggggtgccc-----ggcgcgggcggcgtgggcggcgc 
s elephant.ENr322_1       238222 32 -    422862 ggc-ggcgtggccgtg-----ggcgcgggcgcgg------gcgc 
s danRer2.chr17         30166472  1 -  42274751 -----------T-------------------------------- 

a score=441852.0
s hg17.chr14               7657325 50 - 106368585 TTCAGCATGGACTCGGAGCTGAGCCGCAACCGCGAGAACGGCGGTGGTGG 
s panTro1.chr15            7745467 50 - 106954593 TTCAGCATGGACTCGGAGCTGAGCCGCAACCGCGAGAACGGCGGTGGTGG 
s baboon.ENr322_1           324080 50 -    705101 TTCAGCATGGACTCGGAGCTGAGCCGCAACCGCGAGAACGGCGGTGGTGG 
s rheMac1.SCAFFOLD65194      73577 50 +    139520 TTCAGCATGGACTCGGAGCTGAGCCGCAACCGCGAGAACGGCGGTggcgg 
s galago.ENr322_1           374391 50 -    713249 TTTAGCATGGACTCGGAGCTGAGCCGCAACCGCGAGAACGGTGGCGGCGG 
s rn3.chr6                15342195 50 - 147642806 TTCAGCATGGACTCGGAGCTGGGCCGTGGCCGCGAGAATGGGGGTGGTGT 
s mm6.chr12               12400640 50 - 115788303 TTCAGCATGGACTCGGAGCTGGGCCGTGGCCGCGAGAACGGAGGTGGCGT 
s rabbit.ENr322_1           323725 50 -    557677 TTCAGCATGGACTCGGAGCTGAGCCGCAACCGGGAGAAcggcggcggcgg 
s cow.ENr322_1              356192 50 -    609512 TTCAGCATGGACTCGGAGCTGAGCCGCAACCGGGAGAAcggtggtggcgg 
s canFam1.chr8             6814479 50 -  77374719 TTCAGCATGGACTCGGAGCTGAGCCGCAACCGCGAGAACGGCGGCGTGGG 
s rfbat.ENr322_1            312457 46 -    530160 TTCAGCATGGACTCGGAGCTGAGCCGCAACCGGGAGAAcggcggcg---- 
s elephant.ENr322_1         238171 50 -    422862 TTCAGCATGGACTCGGAGCTGAGCCGCAGCCGCGAGAAcggcggcggcgt 
s monDom1.scaffold_15016    400069 42 -   2367050 TTCAGCATGGATTCGGAGCTAAGCCGCAACCGAGAGAATGGT-------- 
s platypus.ENr322_1          84142 41 -    159352 TTCAGCATGGACTCGGAGTTGAGCCGGAACCGAGAGAACGG--------- 
s galGal2.chr5            11715529 42 -  56310377 TTTAGTATGGACTCAGAGCTGAGTCGTAACCGAGAAAACGGC-------- 
s xenTro1.scaffold_588      533693 41 -    833634 TTCAGTATGGACTCTGAAATGAGCCGCAATCGTGAAAATGG--------- 
s tetNig1.chrUn_random   145481690 43 - 171761319 TTTAGTATGGAGTCTGAGTTGTACCGTAACAGGGACAATGACT------- 
s danRer2.chr17           30166430 43 -  42274751 TTCAGCATGGACTCTGAGTTCTGTCGGAATAGGGAAAATGGCT------- 

a score=7979638.0
s hg17.chr14               7656629 696 - 106368585 CACCTGGACCCGCAC---------CGCCTCAGTGCCGAGGAGATGGGGCTCGTCGCCCAGCACCCCAGTGCCTTCGACCGAGTCATGCGCCTGAACCCCATGGCCATCGACTCGCCCGCCATGGACTTCTCGCGGCGGCTCCGCGAGCTGGCGGGCAA---CAGCTCCACGCCGCCGCCCGTGTCCCCGGGCCGCGGCAACCCTATGCACCGGCT------CCTGAACCCCTTCCAGCCCAGCCCCAAGTCCCCGTTCCTGAGCACGCCGCCGCTGCCGCCCATGCCCCCTGGCGGCACGCCGCCCCCGCAGCCGCCAGCCAAGAGCAAGTCGTGCGAGTTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCGCAGTCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCGTGCTCGCAGGCCAGCAAGCTCAAGCGCCACATGAAGACGCACATGCACAAGGCCGGCTCGCTGGCCGGCCGCTCCGACGACGGGCTCTCGGCCGCCAGCTCCCCCGAGCCCGGCACCAGCGAGCTGGCGGGCGAGGGCCTCAAGGCGGCCGACGGTGACTTCCGCCACCACGAGAGCGACCCGTCGCTGGGCCACGAGCCggaggaggaggacgaggaggaggaggaggaggaggaggagCTGCTACTGGAGAACGAGAGCCGGCCCGAGTCGAGC 
s panTro1.chr15            7744771 696 - 106954593 CACCTGGACCCGCAC---------CGCCTCAGTGCCGAGGAGATGGGGCTCGTCGCCCAGCACCCCAGTGCCTTCGACCGAGTCATGCGCCTGAACCCCATGGCCATCGACTCGCCCGCCATGGACTTCTCGCGGCGGCTCCGCGAGCTGGCGGGCAA---CAGCTCCACGCCGCCGCCCGTGTCCCCGGGCCGCGGCAACCCTATGCACCGGCT------CCTGAACCCCTTCCAGCCCAGCCCCAAGTCCCCGTTCCTGAGCACGCCGCCGCTGCCGCCCATGCCCCCTGGCGGCACGCCGCCCCCGCAGCCGCCGGCCAAGAGCAAGTCGTGCGAGTTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCGCAGTCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCGTGCTCGCAGGCCAGCAAGCTCAAGCGCCACATGAAGACGCACATGCACAAGGCCGGCTCGCTGGCCGGCCGCTCCGACGACGGGCTCTCGGCCGCCAGCTCCCCCGAGCCCGGCACCAGCGAGCTGGCGGGCGAGGGCCTCAAGGCGGCCGACGGCGACTTCCGCCACCACGAGAGCGACCCGTCGCTGGGCCACGAGCCggaggaggaggacgaggaggaggaggaggaggaggaggagCTGCTACTGGAGAACGAGAGCCGGCCCGAGTCGAGC 
s baboon.ENr322_1           323384 696 -    705101 CACCTGGACCCGCAC---------CGCCTCAGTGCCGAGGAGATGGGGCTTGTTGCCCAGCACCCCAGTGCCTTCGACCGAGTCATGCGCCTGAACCCCATGGCCATCGACTCGCCCGCCATGGACTTCTCGCGGCGGCTCCGTGAGCTGGCGGGCAA---CAGCTCCACGCCGCCGCCCGTGTCCCCGGGCCGCGGAAACCCTATGCACCGGCT------CCTGAACCCCTTCCAGCCCAGCCCCAAGTCCCCGTTCCTGAGCACGCCGCCGCTGCCGCCCATGCCCCCTGGCGGCACGCCGCCCCCGCAGCCGCCGGCCAAGAGCAAGTCGTGCGAGTTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACAGGCGCAGTCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCATGCTCGCAGGCCAGCAAGCTCAAGCGCCACATGAAGACGCACATGCACAAGGCCGGCTCGCTGGCTGGCCGCTCCGACGACGGGCTCTCGGCCGCCAGCTCCCCCGAGCCCGGCACAAGCGAGCTGGCGGGCGAGGGCCTCAAGGCGGCCGATGGCGACTTCCGCCACCATGAGAGCGACCCGTCGCTGGGCCACGAGCCggaggaggaggacgaagaggaggaggaggaggaggaggagTTGCTGCTGGAGAACGAGAGCCGGCCCGAGTCGAGC 
s rheMac1.SCAFFOLD65194      72881 696 +    139520 CACCTGGACCCGCAC---------CGCCTCAGTGCCGAGGAGATGGGGCTCGTTGCCCAGCACCCCAGTGCCTTCGACCGAGTCATGCGCCTGAACCCCATGGCCATCGACTCGCCCGCCATGGACTTCTCGCGGCGGCTCCGCGAGCTGGCGGGCAA---CAGCTCCACACCGCCGCCCGTGTCCCCGGGCCGCGGAAACCCTATGCACCGGCT------CCTGAACCCCTTCCAGCCCAGCCCCAAGTCCCCGTTCCTGAGCACGCCGCCGCTGCCGCCCATGCCCCCTGGCGGCACGCCGCCCCCGCAGCCGCCGGCCAAGAGCAAGTCGTGCGAGTTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTCATTGTGCACAGGCGCAGTCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCATGCTCGCAGGCCAGCAAGCTCAAGCGCCACATGAAGACGCACATGCACAAGGCCGGCTCGCTGGCTGGCCGCTCCGACGACGGGCTCTCGGCCGCCAGCTCCCCCGAGCCCGGCACAAGCGAGCTGGCGGGCGAGGGCCTCAAGGCGGCCGATGGCGACTTCCGCCACCATGAGAGCGACCCGTCGCTGGGCCACGAGCCggaggaggaggacgaggaggaggaggaggaagaggaggagTTGCTGCTGGAGAACGAGAGCCGGCCCGAGTCGAGC 
s marmoset.ENr322_1         313311 695 -    740094 CACCTGGACCCGCAC---------CGCCTCAGTGCCGAGGAGATGGGGCTCGTCGCCCAGCACCCCAGTGCCTTCGACCGAGTCATGCGCCTGAACCCCATGGCCATCGACTCGCCTGCCATGGACTTCTCGCGGCGGCTCCGCGAGCTGGCGGGCAA---CAGCTCCACGCCGCCGCCCGTGTCCCCGGGCCGCGGCAACCCTATGCACCGGCT------CCTGAACCCCTTCCAGCCCAGCCCCAAGTCCCCGTTCCTGAGCACGCCGCCGCTGCCGCCCATgccccccggcggcacgccgcccccgcagccgccggccAAGAGCAAGTCGTGCGAGTTCTGCGGGAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCGCAGCCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCGTGCTCGCAGGCCAGCAAGCTCAAGCGCCACATGAAGACGCACATGCACAAGGCCGGTTCGCTGGCCGGCCGCTCCGACGACGGGCTCTCGGCCGCCAGCTCCCCCGAGCCCGGCACCAGCGAGCTGGCGGGCGAGGGCCTCAAGGCCGCCGACGGCGACTTCCGCCACCACGAGAGCGACCCGTCGCTGGGCCACGAGCCggaggaggaggacgaggaggaagat-aggaggaggaggagCTGCTGCTGGAGAACGAGAGCCGGCCCGAGTCGAGC 
s galago.ENr322_1           373695 696 -    713249 CACCTGGACCCGCAC---------CGCCTCAGTGCGGAGGAGATGGGGCTCGTCGCCCAGCACCCCAGTGCCTTTGACCGAGTCATGCGCCTGAATCCCATGGCCATCGACTCTCCCGCCATGGACTTCTCGCGGCGGCTCCGCGAGCTGGCGGGCAA---TAGCTCCACACCGCCGCCCGTGTCGCCGGGCCGCGGCAACCCTATGCACCGGCT------CCTGAACCCCTTCCAGCCCAGCCCCAAGTCCCCGTTCCTGAGCACGCCACCGCTGCCGCCCATGCCTCCCGGTGGCACGCCACCACCGCAGCCGCCGGCCAAGAGCAAGTCGTGTGAGTTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCGCAGCCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCATGCGTGCTCGCAGGCGAGCAAGCTCAAGCGCCACATGAAGACACACATGCACAAGGCCGGCTCCCTGGCCGGCCGCTCTGATGACGGGCTCTCGGCTGCCAGCTCCCCGGAGCCTGGCACCAGCGAGCTGACCGGCGAGGGCCTCAAGGCAGCTGACGGCGACTTCCGCCACCACGAGAGCGACCCGTCGCTGGGCCACGAGCCCgaggaggaggacgaggaggaggaggaggaggaggaggagCTGCTACTTGAGAATGAGAGCCGACCCGAGTCGAGC 
s rn3.chr6                15341508 687 - 147642806 CACTTGGACCCACAC---------CGCCTCAGTGCAGAGGAGATGGGGCTCGTGGCCCAGCACCCCAGTGCCTTCGACCGAGTCATGCGCCTGAACCCCATGGCCATAGACTCTCCCGCCATGGACTTCTCTCGGCGGCTGCGAGAACTGGCCGGTAA---CAGCTCCACACCGCCGCCCGTGTCCCCAGGCCGTGGCAACCCTATGCACCGGCT------GCTGAACCCTTTTCAGCCCAGCCCCAAGTCCCCGTTCCTCAGCACGCCACCGCTGCCACCCATGCCCACGGGC---ACGCCGCCACCGCAGCCGCCTGCCAAGAGCAAGTCCTGTGAGTTCTGCGGCAAGACCTTCAAATTCCAGAGCAATCTCATCGTGCACCGGCGCAGCCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCGTGCTCGCAGGCGAGCAAGCTCAAGCGCCACATGAAGACGCACATGCACAAGGCGGGCTCGCTGGCTGGCCGCTCAGACGATGGGCTCTCGGCCGCCAGCTCCCCAGAGCCCGGCACCAGCGAGCTGCCAGGTGAC---CTCAAAGCGGCCGATGGCGACTTCCGCCACCATGAGAGCGACCCATCTCTGGGACCCGAGCCTgaggacga---cgaggacgaggaggaggaagaagaagagCTGCTGCTGGAGAATGAAAGCCGACCTGAGTCGAGC 
s mm6.chr12               12399953 687 - 115788303 CACTTGGACCCACAC---------CGCCTCAGTGCAGAGGAGATGGGGCTCGTGGCCCAGCACCCCAGTGCCTTCGACCGAGTCATGCGCCTGAACCCCATGGCCATAGACTCTCCTGCCATGGACTTCTCCCGGCGGCTGCGAGAACTGGCCGGCAA---CAGCTCCACGCCGCCGCCCGTGTCCCCAGGCCGTGGCAACCCTATGCACCGGCT------GCTGAACCCTTTCCAGCCCAGTCCCAAGTCCCCGTTCCTCAGCACGCCACCGCTGCCACCCATGCCTGCGGGC---ACACCGCCACCGCAGCCGCCTGCCAAGAGCAAGTCCTGTGAGTTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCGCAGCCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCATGCGTGCTCGCAGGCGAGCAAGCTCAAGCGCCACATGAAGACGCACATGCACAAGGCGGGCTCTCTGGCTGGCCGCTCAGACGACGGGCTCTCAGCTGCCAGCTCCCCTGAGCCGGGCACCAGCGAGCTGCCAGGTGAC---CTGAAAGCGGCCGATGGCGACTTCCGCCACCATGAGAGCGACCCATCTCTGGGCCCCGAGCCTgaggacga---cgaggacgaggaggaggaagaagaggagCTGCTGCTGGAGAACGAGAGCCGGCCTGAGTCGAGC 
s rabbit.ENr322_1           323029 696 -    557677 CACCTGGACGCGCAC---------CGCCTGAGCGCCGAGGAGATGGGGCTCGTGGCCCAGCACCCCAGTGCCTTCGACCGAGTCATGCGCCTGAACCCCATGGCCATGGACTCGCCCGCCATGGACTTCTCGCGGCGGCTGCGCGAGCTGGCGGGCAA---CAGCTCCACGCCGCCACCCGTGTCGCCAGGCCGCGGCAACCCTATGCACCGGCT------CCTGAACCCCTTCCAGCCCGGCCCCAAGTCCCCGTTCCTCGGCACGCCGCCGCTGCCGCCCATgccccccggcggcacgcccccgccgcagccgccggccAAGAGCAAGTCGTGCGAGTTCTGCGGCAAGACGTTCAAGTTCCAGAGCAATCTGATCGTGCACCGCCGCAGCCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCGTGCTCGCAGGCCAGCAAGCTCAAGCGCCACATGAAGACGCACATGCACAAGGCGGGCTCGCTGGCCGGGCGCTCGGACGACGGGCTGTCGGCCGCCAGCTCGCCCGAGCCCGGCACCAGCGAGCTGGCGGGCGACGCGCTCAAGGCGGCCGACGGCGACTTCCGCCACCACGAGAGCGACCCGTCGCTGGGCCCCGAGCCCgaggaggaggacgaggaggaggaggaggaggaggaggagCTGTTGCTGGAGAACGAGAGCCGGCCCGAGTCGAGC 
s cow.ENr322_1              355496 696 -    609512 CACCTGGACCCGCAC---------CGCCTCAGCGCCGAGGAGATGGGGCTCGTCGCCCAGCACCCCAGTGCCTTCGACCGAGTCATGCGCCTGAACCCCATGGCCATCGACTCGCCCGCCATGGACTTCTCGCGGCGGCTCCGCGAGCTGGCGGGCAA---CAGCTCCACGCCGCCGCCCGTGTCCCCGGGCCGTGGCAACCCTATGCACCGGCT------CCTGAACCCCTTCCAGCCCAGCCCCAAGTCCCCGTTCCTGAGCAcgccgccgctgccgcccatgccccccggtggcacgccgccgccgcagccgccgGCCAAGAGCAAGTCGTGCGAGTTCTGCGGCAAGACGTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCGCAGCCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCGTGCTCGCAGGCGAGCAAGCTCAAGCGCCACATGAAGACGCACATGCACAAGGCCGGCTCGCTGGCCGGCCGCTCCGACGACGGGCTCTCGGCTGCCAGCTCCCCCGAGCCCGGCACCAGCGAGCTGACCGGCGAGGGCCTCAAGGCGGCCGACGGTGACTTCCGCCACCACGAGAGCGACCCTTCCCTGGGCCATGAGCCCgaggaggaggacgaagaggaggaggaggaggaggaggagCTGCTGCTGGAGAACGAGAGCCGGCCCGAGTCGAGC 
s canFam1.chr8             6813783 696 -  77374719 CACCTGGACCCGCAC---------CGCCTCAGTGCCGAGGAGATGGGGCTCGTCGCCCAGCACCCCAGTGCCTTCGACCGAGTCATGCGCCTCAACCCCATGGCCATCGACTCGCCCGCCATGGACTTCTCGCGGCGGCTCCGCGAGCTGGCGGGCAA---CAGCTCCACGCCGCCGCCCGTGTCTCCGGGCCGCGGCAACCCTATGCACCGGCT------CCTGAACCCCTTCCAGCCCAGCCCCAAGTCCCCGTTCCTGAGCACGCCGCCGCTGCCGCCCATgccccccgggggcacgccgccgccgcagccgcccgccAAGAGCAAGTCGTGCGAGTTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCGCAGCCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCGTGCTCGCAGGCGAGCAAGCTCAAGCGCCACATGAAGACGCACATGCACAAGGCCGGCTCGCTGGCCGGCCGCTCCGACGACGGGCTCTCGGCCGCCAGCTCCCCCGAGCCCGGCACCAGCGAGCTGGCCGGCGAGGGCCTCAAGGCGGCCGACGGCGACTTCCGCCACCACGAGAGCGACCCGTCGCTGGGCCACGAGCCCgaggaggacgacgaggaggaggaggaggaggaggaggagCTGCTGCTGGAGAACGAGAGCCGGCCCGAGTCGAGC 
s rfbat.ENr322_1            311761 696 -    530160 CACCTGGACCCGCAC---------CGCCTCAGTGCCGAGGAGATGGGGCTTGTCGCCCAGCACCCCAGTGCCTTTGACCGAGTCATGCGCCTGAACCCCATGGCCATTGACTCACCCGCCATGGACTTCTCGCGGCGGCTCCGCGAGCTGGCGGGCAA---CAGCTCCACGCCGCCGCCTGTGTCACCGGGCCGCGGCAACCCTATGCACCGGCT------CCTCAACCCCTTCCAGCCCAGCCCCAAGTCCCCGTTCCTGAGCACGCCGCCGCTGCCACCCATGCCCCCCGGTGGCACGCCACCGCCGCAGCCGCCTGCCAAGAGCAAGTCCTGTGAGTTCTGTGGCAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCGCAGCCACACAGGCGAGAAGCCCTATAAGTGCCAGCTGTGCGACCACGCGTGCTCGCAGGCGAGCAAGCTCAAGCGCCACATGAAGACGCACATGCACAAGGCTGGCTCGCTGGCCGGCCGCTCCGACGACGGCCTCTCGGCTGCCAGCTCCCCGGAGCCCGGCACCAGCGAGCTGGCCGGCGAGGGCCTCAAGGCGGCCGATGGCGACTTCCGCCACCACGAGAGCGACCCGTCGCTGGGCCACGAGCCCgaggaggaggaagaggaggaagacgaggaggaggaagagCTGCTGCTGGAGAACGAGAGCCGGCCCGAGTCGAGC 
s elephant.ENr322_1         237478 693 -    422862 CACCTGGACCCGCAC---------CGCCTCAGTGCCGAGGAGATGGGACTCGTCGCCCAGCACCCCAGTGCCTTTGACCGAGTCATGCGCCTGAACCCCATGGCCATCGACTCGCCCGCCATGGACTTCTCGCGGAGGCTGCGCGAGCTGGCGGGCAA---CAGCGCCACGCCGCCGCCCGTGTCGCCGGGCCGCGGCAACCCTATGCACCGGCT------CCTGAACCCCTTCCAGCCCAGCCCCAAGTCCCCGTTCCTGAGCAcgccgccgctgccgcccatgccgcccggtggcacgccgccgccgcagcccccgACCAAGAGCAAGTCCTGCGAGTTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTGATCGTGCACCGGCGCAGCCACACAGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCGTGCTCGCAGGCCAGCAAGCTCAAGCGGCACATGAAGACGCACATGCACAAGGCCGGCTCGCTGGCCGGCCGCTCCGACGACGGGCTCTCGGCTGCCAGCTCCCCGGAGCCGGGCACCAGCGAGCTGGCCGCCGAGGGCCTCAAGGCGGCCGACGGCGACTTCCGCCAC---GAGAGCGACCCGTCGCTCGGCCACGAGCCCgaggaggaggacgaagaggaggaggaggaggaggaggagCTGCTACTGGAGAACGAGAGCCGGCCCGAGTCGAGC 
s monDom1.scaffold_15016    399385 684 -   2367050 CATCTGGACCCACAT---------CGCCTTAGTGCCGAAGAAATGGGGTTAGTTGCCCAGCATCCCAGTGCCTTTGACAGAGTCATGCGTTTGAACCCCATGGCAATCGATTCGCCAGCGATGGATTTCTCCAGGAGGCTCCGAGAGCTGGCGGGAAA---CAACTCGACCCCTCCTCCAGTCTCACCAAACCGCAGCAACCCTATGCATCGCTT------ATTGAACCCCTTTCAGCCAAGCCCTAAATCACCTTTTTTGAGTACCCCGCCACTGCCCCCCATGCCTCCTAGCAGTACTACCCCTCCCCAACCTCAGGCGAAGAGTAAATCCTGTGAATTCTGTGGGAAAACGTTCAAGTTTCAGAGTAATCTCATTGTCCATCGCCGTAGTCACACGGGAGAGAAGCCCTACAAGTGTCAGCTCTGCGACCACGCTTGCTCCCAGGCCAGTAAACTGAAGCGTCATATGAAAACACATATGCACAAAGCCGGCTCCATGACAGGCAGGTCAGATGACGGACTCTCTACCACCAGTTCTCCAGAGCCAGGCACCAGTGAGCTTACTGGGGAGGGGCTGAAATCCAGCGAGGCTGACTTCAGGAAT---GAGAGCGATCCCTCCCTAGGCCACGACAATgaagaagaggaagaggaggaggaggaggaagagga---------ATTGGAGAATGAGAGCCGGCCGGAGTCAAGT 
s platypus.ENr322_1          83458 684 -    159352 CACCTGGACCCGCAC---------CGCCTTAGTGCCGAAGAAATGGGGTTAGTCGCCCAACACCCCAGTGCCTTTGACAGAGTTATGCGTTTGAACCCCATGGCAATTGAATCGCCCGCGATGGATTTCTCCCGGAGGCTCCGAGAACTGGCGGGGAA---TAACTCCACCCCTCCCCCAGTCTCACCCAATCGCAGCAACCCTATGCATCGCTT------ACTGAACCCCTTCCAGCCGAGTCCCAAGTCACCTTTTTTAAGCACCCCACCACTGCCCCCCATGCCTCCCAGCAGCACGACCCCTCCCCAACCTCAGGCGAAGAGCAAATCCTGTGAATTCTGTGGGAAAACATTCAAGTTCCAGAGCAATCTCATAGTGCATCGGCGAAGTCACACCGGCGAGAAGCCCTACAAGTGTCAGCTCTGCGACCACGCCTGCTCCCAAGCCAGCAAGCTCAAGCGTCATATGAAAACCCACATGCATAAAGCGGGCTCCATGACGGGCCGGTCGGACGACGGGCTGTCCGCTACCAGCTCCCCTGAGCCGGGCACGAGCGAGCTGACGGGGGAAGGCCTGAAACCTGGGGAGACGGACTTCAGGAAC---GAGAGCGACCCCTCCCTGGGCCATGACAACgaagaggaggaggaggaggaggaggaagaggagga---------gCTGGAGAACGAGAGCAGGCCCGAGTCGAGC 
s galGal2.chr5            11714845 684 -  56310377 CATCTGGATCCACAT---------CGCCTTAGTGCCGAAGAAATGGGGTTAGTTGCCCAGCATCCCAGTGCCTTTGACAGAGTTATGCGTTTAAACCCCATGGCAATTGAGTCCCCAGCGATGGATTTCTCCAGAAGGCTTCGAGAGCTGGCAGGAAA---CAGTTCCACCCCTCCGCCAGTCTCGCCCAGTCGCACCAACCCTATGCATCGCCT------GTTGAATCCTTTCCAGCCGAGTCCTAAATCACCTTTTTTGAGCACCCCACCACTGCCCCCCATGCCCCCAAGCAGCACTACGCCTCCCCAGCCTCAGGCCAAGAGTAAGTCCTGCGAATTCTGTGGGAAAACCTTCAAGTTCCAGAGCAACCTTATCGTCCACCGGCGTAGTCACACAGGAGAAAAGCCCTACAAATGTCAGCTATGTGACCATGCTTGCTCCCAGGCCAGCAAGCTAAAGCGTCACATGAAAACGCATATGCATAAAGCTGGCTCCATGACAGGCAGGTCAGACGATGGACTGTCCACCACGAGTTCTCCTGAGCCAGGCACGAGCGAGCTCACTGGAGAGGGACTGAAATCCAGTGAGACAGACTTCAGGAAT---GAGAGCGATCCCTCCCTGGGCCATGACAATgaagaagaggaagaggaggaggaggaagaagaaga---------GTTGGAAAATGAGAGCAGGCCAGAGTCAAGC 
s xenTro1.scaffold_588      533003 690 -    833634 CATCTGGACCCGCAT---------CGCCTTAGTGCCGAAGAAATGGGGTTAGTTGCCCAGCATCCTAGTGCCTTTGACAGAGTTATGCGCTTAAACCCCATGACAATTGAATCTCCAGCAATGGATTTTTCCCGAAGGCTAAGAGAACTAGCAGGGAA---CAACTCCACTCCACCACCAGTGTCACCGAACCGCGGCAATCCTATGCATCGCCT------GTTAAACCCTTTTCAGCCAAGCCCTAAGTCACCTTTTATTAGTACACCACCATTGCCACCCATGCCCCCCAGCAGTACTACTCCACCACAGACCCAGGCAAAGAGCAAATCCTGTGAATTCTGTGGGAAAACCTTCAAGTTCCAGAGTAATTTAATAGTCCACCGTCGCAGTCACACGGGAGAAAAACCTTATAAGTGTCAGCTGTGTGATCATGCATGTTCCCAAGCAAGCAAGTTAAAACGTCACATGAAAACACATATGCACAAAGCTGGTTCAATGACTGGAAGGTCTGATGATGGACTGTCTGCTACTAGCTCACCAGAGCCAGGCACAAGTGATTTAACAGGAGAGGGTGTAAAATCCAGTGAGACAGATTTTAGAAAT---GAAAGTGATCCATCTTTAGGCCATGAAAATgaagaagaagaggaagaagaagaagaggaggaggaggagga---aATAGAGAATGAAAGTAGGCCAGAGTCAAGC 
s tetNig1.chrUn_random   145481030 660 - 171761319 CATCTTGACTCCCACAGGCTAGAATGCCTTAGCACAGAAGAAATGGGTCTGATCTCGCAGCACCCCAGTGCCTTTGAAAAGGTGATGCGTCTTACACCCATGTCTATGGAGTCCCACTCAATGGACTTCTCCAGGAGGCTACGTGAATTGGCTGGCAATACCAACAGTACAACACCACCGCTGTCACCAAGCCGGGCGAACCATATGCACCGACTTATTAACCCCAACCCCTTTCAAATGGGGAGAAAGTCACCCTTTCTGTGCACCCCTCCCCTGCCGCTAGTTCCCACAAACAGCACCAGCCCTCCGCAGACACAGAACAAAATCAAATCCTGTGAGTTCTGTGGAAAAACCTTCAAGTTTCAAAGCAACTTGGTGGTGCATCGACGTAGCCACACTGGAGAAAAACCATACAAGTGCCAGCTGTGTGACCATGCATGTGCTCAGGCAAGCAAACTGAAACGCCACATGAAGACCCACATGCACAAACCTGGTTCTTTGGCTGGGCGCTCTGAGGATGGACTATCTACTACAAGCTCCCCAGAGCCAGGCACAAGCGA------------GTGCATAAAAAACCACAATGGTGACTTCCTagta---gaagg---------------------------aaacgaagaggaagaagaggaggaggagga------------aCTTGAGAATGAGAGTCGACCAGAATCAAAT 
s danRer2.chr17           30165743 687 -  42274751 CATTTAGATCCCCATCGCCTGGAACGCCTTAGCGCAGAGGAAATGGGTTTAATCTCCCAGCATCCCAGTGCCTTCGAAAGAGTGATGCGCATGACACCCATGGCCATGGAGTCCCAGTCCATGGATTTCTCCCGCCGATTGAGAGAGCTTGCTGGAAA---CAACAATTCCACTCCACCATTGTCACCGAGCCGTGCTAACCCTATGCATCGCCTTCTCAATCCCAACCCCTTTCAGCCCAGCCCGAAATCACCCTTTCTGAGCACCCCTCCACTGCCTCCCATGCCCCCTAACAGCACCACCCCGCCACAGACACAGGGCAAGTCGAAATCTTGCGAGTTCTGTGGCAAGACCTTCAAGTTTCAGAGTAATCTGGTTGTTCATCGGCGAAGCCACACAGGCGAGAAACCTTACAAGTGCCAATTGTGTGACCACGCTTGTTCTCAAGCGAGCAAATTAAAACGCCACATGAAGACCCACATGCACAAATCTGGTTCCATGACAGGGCGCTCTGACGATGGCCTGTCCACCACCAGCTCACCTGAGCCAGGCACTAGTGACGTCACTGGGGAGGGTATAAAAAATCGGGATGGTGATTTCAAAGGC---GAGGGCA---------TGCTCCAAGACAATgaagaggaggaggaagaggaagaggaggagga------------gTTGGAAAATGAAAGCAGGCCTGAGTCAAAC 

a score=616570.0
s hg17.chr14               7656579 50 - 106368585 AGGGCCGCCTGCCGGGCACGCCGCCTCTCTTCAGTCCCCCGCCGCGCCAC 
s panTro1.chr15            7744721 50 - 106954593 AGGGCCGCCTGCCGGGCACGCCGCCTCTCTTCAGTCCCCCGCCGCGCCAC 
s baboon.ENr322_1           323334 50 -    705101 AGGGCCGCCTGCCGGGAACGCCGCCTCTCTTCAGCCCCCCGCCGCGCCAC 
s rheMac1.SCAFFOLD65194      72831 50 +    139520 AGGGCCGCCTGCCGGGCACGCCGCCTCTCTTCAGCCCCCCGCCGCGCCAC 
s marmoset.ENr322_1         313261 50 -    740094 AGGGCCGCCTGCCGGGAACGCCGCCGCTCTTCAGCCCCCCGCCGCGCCAC 
s galago.ENr322_1           373645 50 -    713249 AGGGCCGCCTGCCTGGTACGCCGCCACTCTTCAGCCCACCGCCACGCCAC 
s rn3.chr6                15341458 50 - 147642806 AGGGCCGCCTGCCCGGTACGCCACCGCTCTTCAGCCCACCGCCACGCCAT 
s mm6.chr12               12399903 50 - 115788303 AGGGCCGCTTGCCAGGTACGCCACCGCTCTTCAGCCCACCGCCACGCCAT 
s rabbit.ENr322_1           322979 50 -    557677 AGGGCCGCCTGCCCGGCACGCCGCCGCTCTTCAGCCCGCCGCCGCGCCAC 
s cow.ENr322_1              355446 50 -    609512 AGGGCCGCCTGCCTGGCACGCCGCCGCTCTTCAGCCCGCCGCCGCGCCAC 
s canFam1.chr8             6813733 50 -  77374719 AGGGCCGCCTGCCCGGCACGCCGCCGCTCTTCAGCCCGCCGCCGCGCCAC 
s rfbat.ENr322_1            311711 50 -    530160 AGGGCCGCCTGCCCGGCACGCCGCCGCTCTTCAGCCCGCCGCCGCGCCAC 
s shrew.ENr322_5              1242 49 -     18853 AGGGCCGC-TGCCCGGCACGCCGCCCCTCTTCAGCCCGCCGCCGCGCCAC 
s elephant.ENr322_1         237428 50 -    422862 AGGGCCGCCTGCCTGGCACGCCGCCGCTCTTCAGCCCGCCGCCGCGCCAC 
s monDom1.scaffold_15016    399335 50 -   2367050 AGGGCCGGCTCCCCAACACTCCCCCACTTTTCAGCCCACCGCCCCGTCAC 
s platypus.ENr322_1          83408 50 -    159352 AGGGTAGGATCCCCAACACCCCTCCACTCTTCAGCCCTCCGCCTCGTCAT 
s galGal2.chr5            11714795 50 -  56310377 AGGGTCGGCTCCCAAACACGCCTCCACTATTCAGCCCACCACCTCGTCAT 
s xenTro1.scaffold_588      532953 50 -    833634 AGGCTCGGCTCCCAAACACACCCCCACTTTTCAGCCCACCCCCACGCCAC 
s tetNig1.chrUn_random   145480980 50 - 171761319 AGAACCGACTCCCCAACATGCCTCCGTTTGTTAGCCCTCCTCCCCGCCAC 
s danRer2.chr17           30165693 50 -  42274751 AAAACCGTATCCCCAATACGCCTCCCTTTGTCAGCCCCCCTCCACGCCAT 

a score=3481803.0
s hg17.chr14               7656300 279 - 106368585 GT---AAA-GATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCGTGGTTCCTGCTGCAGCA----------CGCGCAGAACACGCACGGCTTCCGCATCTACCTGGAGCCCGGGCCGGCCAGCAGCTCGCT--CACGCCGCGGCTCACCATCCCGCCGCCG-------CTCGGGCCGGAGGCCGTGGCGCAGTCCCCGCTCATGAATTTCCTGGGCGACAGCAACCC-----CTTC---AACCTG-CTGCGCATGAC-------------GGGCCCCATCCTGCGGGA--CCACCCGGG--CTTCGGCG 
s panTro1.chr15            7744442 279 - 106954593 GT---AAA-GATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCGTGGTTCCTGCTGCAGCA----------CGCGCAGAACACGCACGGCTTCCGCATCTACCTGGAGCCCGGGCCGGCCAGCAGCTCGCT--CACGCCGCGGCTCACCATCCCGCCGCCG-------CTCGGGCCGGAGGCCGTGGCGCAGTCCCCGCTCATGAATTTCCTGGGCGACAGCAACCC-----CTTC---AACCTG-CTGCGCATGAC-------------GGGCCCCATCCTGCGGGA--CCACCCGGG--CTTCGGCG 
s baboon.ENr322_1           323055 279 -    705101 GT---AAA-GATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCGTGGTTCCTGCTGCAGCA----------CGCGCAGAACACGCACGGCTTCCGCATCTACCTGGAGCCCGGGCCGGCCAGCAGCTCGCT--CACGCCACGGCTCACCATCCCGCCGCCG-------CTCGGGCCGGAGGCCGTGGCGCAGTCCCCGCTCATGAATTTCCTGGGCGACAGCAACCC-----CTTC---AACCTG-CTGCGCATGAC-------------GGGCCCCATCCTGCGGGA--CCACCCGGG--CTTCGGCG 
s rheMac1.SCAFFOLD65194      72552 279 +    139520 GT---AAA-GATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCGTGGTTCCTGCTGCAGCA----------CGCGCAGAACACGCACGGCTTCCGCATCTACCTGGAGCCCGGGCCGGCCAGCAGCTCGCT--CACGCCACGGCTCACCATCCCGCCGCCG-------CTCGGGCCGGAGGCCGTGGCGCAGTCCCCGCTCATGAATTTCCTGGGCGACAGCAACCC-----CTTC---AACCTG-CTGCGCATGAC-------------GGGCCCCATCCTGCGGGA--CCACCCGGG--CTTCGGCG 
s marmoset.ENr322_1         312982 279 -    740094 GT---AAA-GATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCGTGGTTCCTGCTGCAGCA----------CGCGCAGAACACGCACGGCTTCCGCATCTACCTGGAGCCCGGGCCGGCCAGCAGCTCGCT--CACGCCGCGGCTCACCATCCCGCCGCCG-------CTCGGGCCAGAGGCCGTGGCGCAGTCCCCGCTCATGAATTTCCTGGGCGACAGCAACCC-----CTTC---AACCTG-CTGCGCATGAC-------------GGGCCCCATCCTGCGGGA--CCACCCGGG--CTTCGGCG 
s galago.ENr322_1           373366 279 -    713249 GT---AAA-GATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCGTGGTTCCTGCTGCAGCA----------CGCGCAGAACACGCATGGCTTCCGCATCTACCTGGAGCCCGGGCCGGCCAGCAGCTCGCT--CACACCGCGGCTCACCATCCCGCCGCCA-------CTCGGGCCTGAGGCCGTGGCGCAGTCCCCGCTCATGAATTTCCTGGGCGACAGCAACCC-----CTTC---AACCTG-CTGCGCATGAC-------------AGGCCCCATCCTACGCGA--CCACCCGGG--CTTCGGCG 
s rn3.chr6                15341179 279 - 147642806 GT---AAA-GATGAGCCTTCCAGCTACATTTGCACAACATGTAAGCAGCCCTTCAACAGCGCCTGGTTCCTGCTGCAACA----------TGCGCAGAACACGCATGGCTTCCGCATCTACCTGGAGCCCGGGCCCGCCAGCACCTCGCT--CACGCCCAGGCTCACCATCCCGCCGCCG-------CTCGGGCCGGAGGCCGTGGCGCAGTCCCCACTCATGAATTTCCTCGGGGACAGCAATCC-----TTTC---AACCTG-CTGCGCATGAC-------------GGGCCCCATCCTGCGGGA--CCACCCCGG--CTTCGGAG 
s mm6.chr12               12399624 279 - 115788303 GT---AAA-GATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCCTGGTTCCTGCTGCAGCA----------CGCACAGAACACACATGGCTTCCGAATCTACCTGGAGCCTGGGCCGGCCAGCACCTCGCT--CACGCCCAGGCTCACCATCCCGCCACCG-------CTCGGGCCGGAGACCGTGGCGCAGTCCCCACTCATGAATTTCCTGGGGGACAGCAATCC-----TTTC---AACCTG-CTGCGCATGAC-------------GGGCCCCATCCTGCGGGA--CCACCCTGG--CTTCGGTG 
s rabbit.ENr322_1           322700 279 -    557677 GT---AAA-GATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCACCAGCGCGTGGTTCCTGCTGCAGCA----------CGCGCAGAACACGCACGGCTTCCGCATCTACCTGGAGCCCGGGCCGGCCAGCAGCTCGCT--CACGCCGCGGCTCACCATCCCGCCGCCG-------CTGGGGCCCGAGGCCGTGGCGCAGTCGCCCCTCATGAACTTCCTGGGCGACAGCAACCC-----CTTC---AACCTG-CTGCGCATGAC-------------GGGCCCCATCCTGCGCGA--GCACCCGGG--CTTCGGCG 
s cow.ENr322_1              355167 279 -    609512 GT---AAA-GATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCGTGGTTCCTGCTGCAACA----------CGCGCAGAACACGCACGGCTTCCGCATCTACCTGGAGCCCGGGCCGGCCAGCAGCTCGCT--CACGCCGCGGCTTACCATCCCGCCGCCG-------CTGGGACCCGAGGCCGTGGCCCAGTCCCCACTCATGAATTTCCTGGGCGACAGCAACCC-----CTTC---AACCTG-CTGCGCATGAC-------------GGGCCCCATCCTGCGGGA--CCACCCAGG--CTTCGGTG 
s canFam1.chr8             6813454 279 -  77374719 GT---AAA-GATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCGTGGTTCCTGCTGCAGCA----------CGCGCAGAACACGCACGGCTTCCGCATCTACCTGGAGCCCGGGCCGGCCAGCAGCTCGCT--CACGCCGCGGCTCACCATCCCGCCGCCG-------CTGGGACCCGAGGCCGTGGCCCAGTCCCCGCTCATGAATTTCCTGGGCGACAGCAACCC-----CTTC---AACCTG-CTGCGCATGAC-------------GGGCCCCATCCTGCGGGA--CCACCCGGG--CTTCGGCG 
s rfbat.ENr322_1            311432 279 -    530160 GT---AAA-GATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCGTGGTTCCTGCTGCAGCA----------CGCGCAGAACACGCATGGCTTCCGCATCTACCTGGAGCCAGGGCCGGCCAGCAGCTCACT--CACGCCACGGCTCACCATCCCGCCGCCG-------CTCGGGCCGGAGGCCGTGGCCCAGTCCCCACTCATGAATTTCCTGGGCGACAGCAACCC-----ATTC---AATCTG-CTGCGCATGAC-------------GGGCCCCATCCTGCGGGA--CCACCCAGG--CTTCGGCG 
s shrew.ENr322_5               960 282 -     18853 GT---AAAAGACGAGCCTTCCAGCTACATTTGCACGACATGCA-GCAGCCCTTCACCAGCGCGTGGTTCCTGCTGCAGCA----------CGCGCAGAACACGCACGGTTTCCGCATCTACCTGGAGCCGGGCCCGGCCAGCAGCTCGCT--CACGCCGCGGCTGACCATCCCGCCGCCG-------CTGGGGCCCGAGGCCGTGGCGCAGTCCCCGCTCATGAATTTCCTGGGCGACAGCAACCC-----CTTC---AAGCTGGCTGCGCATGAC-------------GGGGCCGCTGCTGCGGGA--CCACCCGGGGCTTTCGGCG 
s elephant.ENr322_1         237149 279 -    422862 GT---AAA-GACGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCACCAGCGCCTGGTTCCTGCTGCAGCA----------CGCGCAGAACACGCACGGCTTCCGCATCTACCTGGAGCCGGGCCCGGCCAGCAGCTCGCT--CACGCCGCGCCTCACCATCCCGCCGCCG-------CTCGGGCCCGAGGCGGTGGCCCAGTCGCCGCTCATGAATTTCCTGGGTGACAGCAACCC-----CTTC---AACCTG-CTGCGCATGAC-------------GGGCCCCCTCCTGCGCGA--GCACCCGGG--CTTCGGAG 
s monDom1.scaffold_15016    399056 279 -   2367050 GT---AAA-GATGAGCCTTCAAGCTATATTTGCACAACATGCAAGCAACCTTTTAACAGCGCCTGGTTCTTGCTTCAACA----------TGCCCAAAACACACATGGATTCCGCATCTATTTGGAAACAAGCCCTTCAAACAGTTCCCT--TACTCCACGGATCACCATCCCTCCTCCT-------CTGGGACCAGAGGCTGTTGCACAGTCCCCGCTGATGAACTTCCTCGGAGATAACAACCC-----TTTT---AGTCTC-TTACGAATGAC-------------AGGCCCCATCCTGCGTGA--CCACCCCGG--CTTTGGCG 
s platypus.ENr322_1          83129 279 -    159352 GT---AAA-GATGAGCCTTCAAGCTATATTTGCACAACATGCAAGCAGCCTTTTAATAGCGCTTGGTTCCTGCTCCAGCA----------TGCCCAGAATACCCATGGATTCCGCATCTACCTGGAAACCAGTCCGTCCAACAGTTCCCT--TACTCCTCGCATCACCATCCCTCCTCCT-------CTGGGACCGGAGGCTGTTGCACAGTCCCCGCTGATGAATTTCCTGGGAGATAACAACCC-----CTTC---AGTCTC-CTGCGGATGAC-------------GGGCCCCATCCTGCGTGA--TCATCCCGG--CTTCGGTG 
s galGal2.chr5            11714516 279 -  56310377 GT---AAA-GATGAGCCTTCAAGCTATATTTGCACAACATGCAAGCAGCCTTTTAATAGCGCTTGGTTCTTGCTTCAGCA----------TGCCCAGAACACACATGGATTCCGCATCTACCTGGAAACAAGCCCTTCCAACAGTTCCCT--TACTCCACGCATCACCATCCCTCCTCCT-------CTGGGACCAGAGACTGTTGCACAGTCCCCGCTGATGAATTTCCTTGGAGACAACAACCC-----TTTT---AATCTT-CTGCGGATGAC-------------AGGACCCATTTTGCGTGA--ACATCCTGG--CTTTGGTG 
s xenTro1.scaffold_588      532674 279 -    833634 GT---AAA-GATGAGCCTTCAAGCTATATTTGCACAACATGCAAGCAGCCTTTTAACAGCGCATGGTTCCTGCTTCAGCA----------TGCTCAAAATACACATGGATTTCGTATCTACCTGGAAACAAGCCCATCTAGTAACTCTCT--TACTCCACGTATCACTATCCCTCCACCT-------CTGGGACCGGAGACTGTTGCACCATCCCCTCTGATGAATTTCCTTGGGGACACTAATCC-----CTTC---AACCTT-TTAAGAATGAC-------------AGGACCTATTCTACGTGA--TCACCCAGG--CTTTGGTG 
s tetNig1.chrUn_random   145480695 284 - 171761319 GTCGTAAA-GATGAGCCTTCAAGCTATATATGTACGACATGTAAGCAGCAGTTTTCCAACGCCTGGTTCCTGCTACAGCA----------CGCTCAGAACACCCATGGCATTCGCATTTACCTGGAGTCAGATCCTTCTAACACTGCCCT--AACGCCACGCATTACTATGCCTCCACAA-------ATTGGTAATGACTGCATCCCTCATTCCCCCTTGATCAACTTTCTTGGGGAAAACAACCC-----CTTC---CAGCTC-CTGCGAATGAC-------------AGGCCCAGTAAGTCGAGAGCCTGCCCCAG--CTTTTATT 
s danRer2.chr17           30165607 279 -  42274751 GT---AGA-GATGAACCCTCAAGTTACATATGCACAACGTGCAAACAACCCTTTTACAACGCCTGGTTCCTTCTGCAGCANNNNNNNNNN-----AAAAC-----CGTATCCCCAATACGCCT----------CCCTTTGTCAGCCCCCCTCCACGCCATCATTTAGATCCCCATCGCCTGGAACGCCTTAGCGCAGAGGAAATGG-------------GTTTAATCTCC-------CAGCATCCCAGTGCCTTCGAAAGAGTG-ATGCGCATGACACCCATGGCCATGGAGTCCCAGTCCATGGAT--TTCTCCCGC--CGATTGAG 

a score=1849402.0
s hg17.chr15              41673708 149 + 100338915 ATGGCTGGTCCCTTCTCCCGT---CTGCTGTCCGCCCG----CC------------CGGGACTCAGGCTCCTGGCTTTG--GCCGGAGCGGGGTCTCTA-GCCGCTGGGTTTCTGCTCCGACCGGAACCTGTACGAGCTGCCA---GTGAACGAC------GGAGGCTGTATCCCCCGAG 
s panTro1.chr16_random    12462177 149 +  32210112 ATGGGTGGTCCCTTCTCCCGT---CTGCTGTCCGCCCG----CC------------CGGGACTCATGCTCCTGGCTTTG--GCCGGAGCGGGGTCTCTA-GCCGCTGGGTTTCTGCTCCGACCGGAACCTGTACGAGCGGCCA---GTGAACGAC------GGAGGCTGTATCCCCCGAG 
s baboon.ENr233_1           275767 149 +    766046 ATGGCTAGTCCCTTCTCCCGT---CTGCTGTCCGCCCG----CC------------CGGGAATCAGGCTCCTGGCTTTG--GCCGGAGCGGGGTCTCTA-GCCGCTGGGTTTCTGCTGCGACCGGAACCTGTACGAGCGGCCA---GTGAACGAC------GGAGGCTGTATCCCCCGAG 
s rheMac1.SCAFFOLD51386      39935 149 -     50003 ATGGCTGGTCCTTTCTCCCGT---CTGCTGTCCGCCCG----CC------------CGGGAATCAGGCTCCTGGCTTTG--GCCGGAGCGGGGTCTCTA-GCCGCTGGGTTTCTGCTGCGACCGGAACCTGTACGAGCGGCCA---GTGAACGAC------GGAGGCTGTATCCCCCGAG 
s marmoset.ENr233_1         268074 149 +    638869 ATGGCTGGTCCCTTCTCCCGT---CTGCTGTCTGCCCG----CC------------CGGGACTCAGGCTCCTGACTTTG--GCCGGAGCGGGGTCTCTA-GCCGCTGGCTTTCTGCTCCGACCGGAACCTGTACGAGCGGCCA---GTGAACGAC------GGAGGCTGTATCCCCCGAG 
s galago.ENr233_1           224810 146 +    677616 ATGGCTGGTCCCTTCTCCCGT------CTGTCTGCACG----CC------------CAGGACTCAGGCTCCTGGCTTTG--GCCGGAGCTGGGTCTCTA-GCCGCTGGTTTTCTGCTCCGCCCGGAACCTGTACGAGCCGCTA---GTGAACGAC------GGAGGCTGTATCCCCCGAG 
s rn3.chr3               108059196 152 + 170969371 ATGGCTGGTCCCTTCTCCCGT---CTGCTGTCTGCCCG----CC------------CCGGACTCAAGCTCCTGGCTTTG--GCTGGAGCTGGGTCTCTC-GCCGCCGGGATTCTGCTCCGTCCGGAATCTGTACGAGCGGCCACCGGTGAACGGA------GGAGACTGTATCCCCCGAG 
s mm6.chr2               120872699 152 + 181764313 ATGGCTGGTCCCTTCTCCCGT---CTGCTGTCTGCCCG----CC------------CTGGACTCAGGCTCCTGGCTTTG--GCTGGAGCTGGGTCTCTC-ACCGCCGGGATTCTGCTCCGCCCGGAATCTGTAGGAGCTGCCGCTGCTGAACGGA------GGAGACTGTATCCCCCGAG 
s rabbit.ENr233_1           252387 149 +    590291 ATGGCTGGTCCCTTCTCCCGT---CTGCTGTCTGCCCG----CC------------CGCGGCTCGGGCTCCTGGCTTTG--GCCGGAGCTGGGTCTCTA-GCCGCTGGGTTTCTGCTCCGCCCGGAACCTGTTCGAGCAGCCA---GCGAACGAA------GGAGGCTGTATCCCCCAAG 
s cow.ENr233_1              287506 149 +    683299 ATGGCTGGTCCCTTCTCTCGT---CTGCTGTCTGCCCG----CC------------CCGGGCTCAGGCTCCTGGCTTTG--GCTGGAGCTGGTTCTCTC-GCCGCTGGGTTTCTACTCCGATCGGAACCTGTTCGAGCCGCCA---GTGAACGGC------GGAGGCTGTATCCCCCGAG 
s canFam1.chr30           13349240 149 +  43165425 ATGGCTGGTCCCTTCTCTCGT---CTGCTGTCCGCGCG----CC------------CGGGGCTCAGGCTCCTAGCTTTG--GCTGGAGCTGGGTCTCTA-GCCGCTGGGTTTCTGCTCCGCCCGGAACCTGTAAGAGCCGCCA---GTGAACGAC------GGAGGCTGTATCCCCCAAG 
s rfbat.ENr233_1            232312 149 +    554556 ATGGCCGGTCCTTTCTCTCGT---CTACTGTCCGCCCG----CC------------CGGGGCTCAGGCTCCTGGCTTTG--GCTGGAGCTGGGTCTCTA-GCTGCTGGGTTTCTGCTCCGCCCGGAACCTGTACGAGCCGCCA---GTGAACGAC------GGAGGCTGTATCCCCCGAG 
s shrew.ENr233_9             13897 149 +     18972 ATGGCAGGTCCCTTTTCTCGT---CTGCTATCTGCCCG----CC------------CGAGGCTCGGGCTCTTAGCTCTG--GCCGGAGCTGGGTCTCTA-GCCGCTGGGTTTCTGCTCCGCCCGGAACCTTTACGAGCTGCCA---GTGAACGAC------GGAGGCTCTATCCCCCGAG 
s armadillo.ENr233_1        235169 149 +    483679 ATGGCTGGTCCCTTCTCCCGC---CTGCTGTCCACCCG----CC------------CGGGGCTCAGGCTCCTGGCTTTG--GCTGGAGCTGGATCTCTA-GCCGCTGGGTTTCTGCTCCGCCCGGAACCTGTGCGAGCCGCCA---GTGAACGAC------GGAGGCTGTATCCCCCGAG 
s tenrec.ENr233_19            1520 149 -      5596 ATGGCTGGTCCCTTCTCCCGC---CTGCTGTCTGCCCG----CC------------CAGGGCTCAAGTTTGTGGCTTTG--GCCGGAGCTGGATCTCTA-GCCGCCGGGTTTCTGCTTCGCCCGGAACCTGTGCGAGCCGCTG---TTGAACGAC------GGAGGCTCTATCCTCCGAG 
s monDom1.scaffold_15056   2404279 149 -   4736853 ATGGCTAGTTCCTTCTCCCGA---TTACTCTCTGCTCG----CC------------CGGGACTCGGGCTTCTTGCTGTG--GCTGGCGCAGGGTCTCTG-GCTGCTGGGTTCCTGCTCCGCCCTGACCCACTACGAGCCGCTG---GCGAGCGAA------GAAGGCTGTACCCACCCAG 
s galGal2.chr10             215477 162 -  20909726 GGGGCTGCTCTCTGCTCCCATGCAATGCCAGCAGCTCT----CTTTGTGGGGACAGCATGGCTCTCCCTGCCCACCCT---GCTGCGG--GGGTCTCCATAGGGCAGGGGCACCACT------GGGGCCTGGAGTGGATGACA---GTTGATGGCCGCTCAGCAGCACTCACTGCCCTCA 
s tetNig1.chrUn_random    25826102 143 + 171761319 ATGGCGAGCAGCTTCTCCAGA---CTTCTGACCTCCAGAAACCT------------CCGGA----------TGGCGTCGCTGCTGGGG--GGCTCGCTC-ACGGCCGGGGTCCTGCTGCAGCGGCACCATGTCGGCGCCGACG---GCCCCACAC------GGAGGCGGTACCCCGCCAG 

a score=1872217.0
s hg17.chr15             58659665 89 - 100338915 GTCGAAGTACAGCCTGGGGCCTCCAGGACTGGTCACGACCTTCCTGGTCCCTGGTATTGACTATCAGCTTCCTTGGCCACCTGCTATGA 
s panTro1.chr16          59853104 89 - 101535987 GTCGAAGTACAGCCTGGGGCCTCCAGGACTGGTCACGACCTTCCTGGTCCCTGGTATTGACTATCAGCTTCCTTGGCCACCTGCTATGA 
s baboon.ENr233_1          484755 89 -    766046 GTCGAAGTACAGCCTGGGGCCTCCAGGACTGGTCACGACCTTCCTGGTCCCTGGTATTGACTATCAGCTTCCTTGGCCACCTGCTCTGA 
s rheMac1.SCAFFOLD51386      4555 89 +     50003 GTCGAAGTACAGCCTGGGGCCTCCAGGACTGGTCACGACCTTCCTGGTCCCTGGTATTGACTATCAGCTTCCTTGGCCACCTGCTCTGA 
s marmoset.ENr233_1        365317 89 -    638869 GTCGAAGTACAGCCTGGGGCCTCTGGGACTGGTCACAACCTTCCTGGTCCCTGGTATTGACAATCAGCTTCCTTGACCACCTGCTCTGA 
s galago.ENr233_1          447153 89 -    677616 GTCGAAGCACAGCTTCGGGTCTCCAGGACTTGTCACAACCTTCCTGGGATCTGGCACTGACCATTAGCTTCCTTGTCCACCTGCTATCA 
s rn3.chr3               62905043 89 - 170969371 GTCGAAGCTCAGCCTGGGGTCTCTGTGACTGGTTCCATGCTTCCTGGGCTCTGACACTAACCATCAGCTTTTTTGGCCACCTATTATAA 
s mm6.chr2               60886399 89 - 181764313 GTCGAAACTCAGCCTGGGGTCTCTACGACTGGTTCCAAGCCTCCTGGGCCCTGGCATTGCCCGTCAGCATTTTTGGCCACCTATTATGA 
s rabbit.ENr233_1          332689 89 -    590291 GTCGAAACACAGCCAGGGGCCTCCAGGACTGGTTACAAGCCTCCTGGGCCCTGTCATTGACCATCAGCTTCCTTGGCCACCTTCTCTGA 
s cow.ENr233_1             390540 89 -    683299 GTCGAAGCACAGCCTGGGGTCTCCAGGACTGGTCACAACCCTCCTGGGCCCTGGCATTGACCATCTGCTTCCTTGGCAATCTGCTATGA 
s canFam1.chr30          29810975 89 -  43165425 GTCGAAGCACAGCCTGGGGCCTTCAGGACTGGTCACAACCCTCCTGGGCCATGGCATTGACCATCTGCTTCCTTGGCAACCTGATATGA 
s rfbat.ENr233_1           316923 89 -    554556 ATCGAAGCACAGCCTGGGGCCTCCAGAACTGGTCACGACCTTCCTGGGCCCTGGTATTAACCATCTGCTTCCTTGGCAACCTGCTATGA 
s shrew.ENr233_15           34275 86 +     34619 GTCGAAGCACAGCCTGGGGCCTCCAA---TGGCCACGACCCTTCTGGGCCCTTGCATTGACCATCTGCTTCCTCAGCAACCTGCTATGA 
s armadillo.ENr233_1       242733 89 -    483679 GTCGAAGCACAGCCTGGGCCCTCCAGGACTGGTCTCAGCCTTCCTGGGCTCTGGCACTGACCATCTGCTTCCTTGTCCACTTGCTCTGA 
s tenrec.ENr233_15          12487 89 -     12988 GTCGAAGTACAGCCTCCGGCCTCCAGGACTGGCCACAGCTCTCCTGGGCCTTAGCATCGACCATATACCTCCGTGGCCAACTCTTCTGA 
s monDom1.scaffold_15056  2326803 89 +   4736853 GGCGTAACACAGCTTGGGGCCTCCAGGAACAGACAGTTTCCTTCTGGACCCCAACATTGATTATCTTCCTACTTAGCAGCTTACCCTGA 
s platypus.ENr233_14          548 88 -      1028 GTCGAAGTGCAGCCAGTATGCCTCCCGCGTGGTCGCCGTCCCCGTGGGTCCTCGCCCTGACCATCGGTCTGCTTGGTT-TCGGGGCCGA 

a score=221644.0
s hg17.chr15             41826029 40 + 100338915 ATGCGCCTCCGCCGCCTAGCGCTGTTCCCG--------GGTGTGGCGC------ 
s panTro1.chr16          41735415 40 + 101535987 ATGCGCCTCCGCCGCCTAGCGCTGTTCCCG--------GGTGTGGCGC------ 
s baboon.ENr233_1          405108 40 +    766046 ATGCGCCTTCGCCGCCTTGCGCTATTCCCG--------GGCGTGGCGC------ 
s rheMac1.SCAFFOLD76070     11415 40 +     30364 ATGCGCCTTCGCCGCCTTGCGCTATTCCCG--------GGCGTGGCGC------ 
s marmoset.ENr233_1        324800 40 +    638869 ATGCGCCTCTGCCGCCTAACGCTGTTCCCG--------GGTGTGGCGC------ 
s galago.ENr233_1          293301 40 +    677616 ATGCGCCTCCGCCGCCTAACCCTGGTCCGG--------GGCGTGGCGC------ 
s rn3.chr3              108117268 40 + 170969371 ATGCGCTTCAGCTGCCTTGCGCTGCTCCCG--------GGCGTGGCGT------ 
s mm6.chr2              120927888 40 + 181764313 ATGCGCTTCAGCTGCCTAGCTCTGCTCCCG--------GGCGTGGCGC------ 
s rabbit.ENr233_1          318514 31 +    590291 ATGC---------GCCTAGCGATGTTTCCC--------GGCGTGGCGT------ 
s cow.ENr233_1             334343 40 +    683299 ATGCGCCTCCGCCGCCTAGCGCTGTTCCCA--------GGCCTGGCGC------ 
s canFam1.chr30          13397631 40 +  43165425 ATGCGCCCCCGCTGCCGAGCGCTGCTCCCG--------GGCGTGGCGC------ 
s rfbat.ENr233_1           274419 40 +    554556 ATGCACCTCCGCCGCCTAGCGCTGTTCTTC--------GGTGTGGAGC------ 
s shrew.ENr233_15           21613 39 -     34619 atgcgcctccgc-gcctagcgctgttcccc--------ggcgtggccc------ 
s armadillo.ENr233_1       313470 40 +    483679 ATGCGCCTCCCTTGCCTAGCGCTGTTCCCG--------GTCGTGGCGC------ 
s galGal2.chr10            220607 42 -  20909726 gggcggc------gcggAGCAACGGGTCCGGGAGTAACGGAGTGACGG------ 
s xenTro1.scaffold_358     516555 17 -   1257219 TTCTTCC------------------TCCTG--------GCTGT----------- 
s tetNig1.chrUn_random   25833237 42 + 171761319 --GGACCAGCAGAGCTCACC--CGCTGCGG--------GCTACGATGCTAGCGC 
s fr1.chrUn              97210623 31 - 349519338 TAGTACCGAAAAAG---------------A--------GCTACGATGCTCAAGC 

a score=1052677.0
s hg17.chr15             41826069 127 + 100338915 TGCTTCTTGCCG---CG---GCCC---GCCTCGCCGCTGCC---------------TCCGACGTGCTAGAACTCACGGACGACAACTTCGAGAGTCGCATCTCCGACACGGGCTCTGC--G-GGCCTCATGCTCGTCGAGTTCTTCGCCCCCTG 
s panTro1.chr16          41735455 127 + 101535987 TGCTTCTTGCCG---CG---GCCC---GCCTCGCCGCTGCC---------------TCCGACGTGCTAGAACTCACGGACGACAACTTCGAGAGTCGCATCTCCGACACGGGCTCTGC--G-GGCCTCATGCTCGTCGAGTTCTTCGCCCCCTG 
s baboon.ENr233_1          405148 127 +    766046 TGCTTCTCGCCG---CG---GCCC---GCCTCGCCGCTGCC---------------TCCGACGTGCTAGAACTCACGGACGACAACTTCGAGAGTCGCGTCTCCGACACGGGCTCTGC--G-GGCCTCATGCTCGTGGAGTTCTTCGCCCCCTG 
s rheMac1.SCAFFOLD76070     11455 127 +     30364 TGCTTCTCGCCG---CG---GCCC---GCCTCGCCGCTGCC---------------TCCGATGTGTTAGAACTCACGGACGACAACTTCGAGAGTCGCGTCTCCGACACGGGCTCTGC--G-GGCCTCATGCTCGTGGAGTTCTTCGCCCCCTG 
s marmoset.ENr233_1        324840 127 +    638869 TGCTTCTTGCCG---CG---GCCC---GCTTAGCCGCTGCC---------------TCCGACGTGCTGGAACTCACGGACGACAACTTCGAGAGTCGCGTCTCTGACACGGGATCTGC--G-GGCCTCATGCTTGTCGAGTTCTTCGCCCCCTG 
s galago.ENr233_1          293341 130 +    677616 TGTTTCTCACGGGTCTC---GCCG---GTCTCGCTGCTGCC---------------TCCGATGTGCTGGAACTCACGGACGACAACTTCGAGAGTCGCGTCTCCGATACCGGGTCCGC--G-GGCCTCATGCTGGTCGAGTTCTTTGCCCCCTG 
s rn3.chr3              108117308 142 + 170969371 TGCTGctcgcct---cg---gccc---tcctcgcctccgccctcctcgcctccgccTCAGACGTGTTGGAACTGACGGACGAAAACTTCGAGAGTCGCGTCTCCGACACGGGCTCAGC--T-GGGCTCATGCTAGTCGAGTTCTTCGCCCCATG 
s mm6.chr2              120927928 127 + 181764313 TGCTGCTCGCCT---CG---GCCC---GTCTCGCCGCCGCC---------------TCCGATGTGTTGGAACTGACGGACGAAAACTTCGAGAGTCGCGTCTCCGACACGGGCTCGGC--G-GGGCTCATGCTAGTCGAGTTCTTCGCCCCCTG 
s rabbit.ENr233_1          318545 127 +    590291 TGCTTCTCGCCG---CA---GCCC---GCCTCGCCGCTGCC---------------TCCGACGTCCTGGAACTCACAGACGACAACTTCGAGAGTCGCATCACCGACACGGGCTCTGC--T-GGCCTCATGCTCGTCGAGTTCTTCGCCCCTTG 
s cow.ENr233_1             334383 127 +    683299 TGCTCCTCGCCG---CG---GCCC---GCCTCGCTGCTGCC---------------TCCGATGTGCTGGAACTCACGGACGACAACTTCGAGAGTCGCATCACCGACACGGGCTCTTC--T-GGCCTCATGCTTGTCGAGTTCTTCGCCCCCTG 
s canFam1.chr30          13397671 127 +  43165425 TGCTTTTCGCCG---CG---GCCG---GTCTCGCCTCTGCC---------------TCCGACGTGCTGGAACTCACTGACGACAACTTCGAGAGTCGCATCTCCGACACGGGCTCTGC--G-GGCCTCATGCTCGTCGAGTTCTTCGCTCCCTG 
s rfbat.ENr233_1           274459 127 +    554556 TCCTTCTCATCA---CG---GCCT---GCCTTGCAGCTGCA---------------TCCGACGTGCTGGAACTCACGGACGACAACTTCGAGAGTCGCATCTCCGACACGGGCTCTGC--G-GGCCTCATGCTTGTTGAGTTCTTCGCCCCCTG 
s shrew.ENr233_15           21652 127 -     34619 tgcttttcgccg---cg---gccc---gcctcgTTGCTGCT---------------TCCGACGTGCTGGAACTCACGGACGACAACTTCGAGAGTCGCGTCTCGGACACGGGCTCCGC--G-GGCCTCATGCTGGTCGAGTTTTTCGCCCCCTG 
s armadillo.ENr233_1       313510 127 +    483679 TGCTTCTCGCCG---CG---GACC---GCCTCGCCGCTGCC---------------TCCGATGTGCTGGAACTCACGGATGACGACTTCGAGGATCGCATCGGCGACACGGGCTCTGC--G-GGCCTCATGCTCGTCGAGTTCTTCGCCCCCTG 
s galGal2.chr10            220649 114 -  20909726 CGGAGCGAGCCG---CG---GCCC---G-------GCAGCC---------------TCGGTTAT-CTGAAGGCGGCGGGTGG-------GAGGAAGGCGTCCTCCTTTTGAGCAGAGCCTG-GTGCTGCTGCTCGGACAGAGCAGCGCCCTTCG 
s xenTro1.scaffold_358     516572 111 -   1257219 -------CACCG---CC---GGCA---CTCAGGCCGCAGGT---------------TCAGACGTCCTGGATCTCACTGACGATAACTTTGAAAGCACCGT----------GTCTCAGC--ACAGCATCCTGCTAGTGGAATTCTTCGCTCCCTG 
s tetNig1.chrUn_random   25833282 121 + 171761319 TGCTTTTGGCGG---CGCTCGCCG---GCTTCACGCAGGCC---------------AGCGATGTGCTGGAGTTCACGGATAACGATTTCGAAAGTAAAATC---------GGAGACCA--C-GAAATCATTCTTGTGGAGTTTTTCGCACCTTG 
s fr1.chrUn              97210657 124 - 349519338 TGCTTTTAGCAG---CGCTCACCG---GCTTCACGCAGGCC------------GCCAGTGATGTGCTGGAGTTCACGGATAACGATTTCGAAAGTAAAATC---------GGAGACCA--T-GAAATTATTCTTGTGGAGTTTTTCGCACCCTG 
s danRer2.chr16          26031109 124 +  42763181 TGATCTGTGCTG---TGCTGACTGTGTGGCTCGTGGAGGGC---------------AGCGATGTGCTGGAGCTCGGAGATTCTGACTTTGACCGGAGCGCA---------GGCATGCA--T-GACACTCTGCTAGTGGAGTTCTTCGCACCTTG 

a score=813756.0
s hg17.chr16               142908 95 +  88827254 A---TGTCTCTGACCAAGACTGAGAGGACCATCATTGTGTCCATGTGGGCCAA----GATCTCCACGCAGGCCGACACCATCGGCACCGAGACTCTGG-AGAG 
s panTro1.chr18            150233 95 +  83875239 A---TGTCTCTGACCAAGACTGAGGGGACCATCATTGTGTCCATGTGGGCCAA----GATCTCCACGCAGGCCGACACCATCGGCACCGAGACTCTGG-AGAG 
s baboon.ENm008_1          126530 95 +    646721 A---TGTCTCTGACCAAGACTGAGAGGACCCTCATTGTGTCCATGTGGGCCAA----GATCTCCACCCAGGCCGACACCATTGGCACCGAGACTCTGG-AGAG 
s rheMac1.SCAFFOLD56242      8130 95 +     11012 A---TGTCTCTGACCAAGACTGATAGGACCCTCATTGTGTCCATGTGGGCCAA----GATCTCCACTCAGGCCGACACCATCGGCACCGAGACTCTGG-AGAG 
s marmoset.ENm008_1        263219 87 +    609522 G---TCTCCC--------GCCGACAAGAGCAACGTCAAGGCCGCCTGGGGTAA----GGTCGGCAGCCACGCTGGCGACTATGGTGCCGAGGCCCTGG-AGAG 
s galago.ENm008_1          316366 95 +    764343 A---TGTCTCTGACCAAGACTGAGAGGGCCATCATTGTGTCCATGTGGGGCAA----GATCTCCACACAGGCCGACACCATTGGCACTGAGACCCTGG-AGAG 
s rn3.chr10              95139962 95 - 110733352 A---TGTCTCTGATGAAGAATGAGAGAGCTATCATCATGTCCATGTGGGACAA----AATGGCGCCTCATGCAGAGCCCATTGGCACTGAGACTCTGG-AGAG 
s mm6.chr11              32171455 98 + 121803636 ACCATGTCTCTGATGAAGAATGAGAGAGCTATCATCATGTCCATGTGGGAGAA----GATGGCTGCTCAGGCCGAGCCCATTGGCACTGAGACTCTAG-AGAG 
s rabbit.ENm008_1          189022 95 +    203479 A---TGTCTCTGACCAAGAGCCAGAGGACCATCATCATGTCCCTCTGGGACAA----GGTCTCCTCCCAGTCTGAGGACATTGGCGCAGAGGCCCTGG-AGAG 
s cow.ENm008_1             252523 95 +    491063 A---TGTCTCTGACCAGAGCTGAGAGGACCATCATCGTGTCCATGTGGAGCAA----GATCTCCACACAGGCGGACCTCATTGGCACCGAGACCCTGG-AGAG 
s canFam1.chr6           37152261 96 -  79106041 A---TGTCTCTGACCAAGGCCGAGAGGACCATCATCCTGTCCATGTGGGGCAA----GATCTCCACCCAGGCGGATGCTATTGGCACCGAGGCCCTGGAAGAG 
s rfbat.ENm008_1           159281 95 +    557006 A---TGTCTCTGACCAAGGCTGAGAGGACCATCATCACATCCATGTGGAACAA----GATCTCCACACAGGCGGACGCCATCGGCACCGAGGCCCTGG-AGAG 
s shrew.ENm008_3            19118 75 -     44886 A---TGTCGCTGACCAAGGCCGAGAGGACCATCATCCTGTCCATGTGGGGCAA----GATCTCCACACAGGCGGATGTCATC--------------------- 
s armadillo.ENm008_1       215339 95 +    489446 A---TGTCGCTGACCAAGGCCGAGAGGACCATCATCGTGTCCATGTGGGGCAA----GATCGCCTCGCAGGCCGACGCCATCGGCACCGAGGCCCTGG-AGCG 
s elephant.ENm008_1         44698 95 +    364520 A---TGTCTCTGACCAAGGTGGAGAGGACCATCATCACGTCCATGTGGGGCAA----GGTCTCCACACAGGCTGACAGCATCGGCACCGAGGCCCTGG-AGAG 
s monDom1.scaffold_13198   999078 95 +   1560775 A---TGTCTCTGACCAAGACCGACAAGGCTATCATCCTCACCATCTGGAACAA----GATCGCCACTCAGGCTGACTCTGTTGGTACTGAGGCCTTGG-AACG 
s platypus.ENm008_14        23821 95 -     31480 A---TGTCTCTGACCAAGGCCGACAAGACCGCAGTCATCTCCCTCTGGGGAAA----GGCGGCCACCCAGGCTGACGCCATCGGGGCCGAGTCTCTGG-AGAG 
s galGal2.chr14          13958597 95 +  20603938 A---TGGCACTGACCCAAGCTGAGAAGGCTGCCGTGACCACCATCTGGGCAAA----GGTGGCTACCCAGATTGAGTCCATTGGGCTGGAATCACTGG-AGAG 
s tetNig1.chr3           11754597 95 +  14679700 A---TGTCTCTTAACGCTAATGACAAGAAAGTGATCACCACCTTCTGGGGCAA----AGCCTCGGCACAGGCTGACGCCATCGGATCGGATGCTCTGG-GAAG 
s danRer2.chrUn          33997195 93 + 173451396 G---AGTCTCTC--TGATACGGACAAGGCTGTTGTTAAGGCCATCTGGGCTAAGATCAGCCCCA----AGGCCGATGAAATTGGTGCTGAAGCCCTCG-CCAG 

a score=835584.0
s hg17.chr16             88647254 37 -  88827254 TCGGGCTTCCCGGGACCGAAGTGCGAAATACAAGTAA 
s panTro1.chr18          83679420 37 -  83875239 TCGGGCTTCCCGGGACCGGAGTGCGAAATACAAGTAA 
s baboon.ENm008_1          483258 37 -    646721 TCGGGCTTCCCGGGACCGGAGTGCGAAATACAAGTAA 
s rheMac1.SCAFFOLD35869     32826 37 +     37522 TCGGGCTTCCCGGGACCGGAGTGCGAAATACAAGTAA 
s marmoset.ENm008_1        335205 37 -    609522 TCGGGCTTCCCGGGACCGGAGTGCGAAATACAAGTAA 
s galago.ENm008_1          398924 37 -    764343 CCGGGCTTCCCGGGACCGGAGTGCGAAATACAAGTAA 
s rn3.chr10              15549542 37 + 110733352 ACGGGCTTCCAGGGACCGGAGTACAAAATACAAGTAA 
s mm6.chr17              24073266 37 +  92867660 CCGGGCTTCCAGGGACCGGAGTACAAAATACAAGTAA 
s rabbit.ENm008_1            6761 37 -    203479 CCGGGTTTCCCGGGACGGGAGTGCGAAATACAAGTAA 
s cow.ENm008_1             204953 37 -    491063 ACGGGCATCCAGGGACCGGAGCTCGAAATACAAGTAA 
s canFam1.chr6           41920007 37 +  79106041 CCGGGCTTCCAGGGACCGGAGTGCGAAATACAAGTAA 
s rfbat.ENm008_1           369494 37 -    557006 CTGGGCTTCCAGGGACCAGAGTGCGAAATACAAGTAA 
s shrew.ENm008_3            11072 37 +     44886 CCGGGCCTCCAGGGACCGGAGTTCGAAATACAAGTAA 
s armadillo.ENm008_1       252273 37 -    489446 CCGGGCTTCCAGAGACCGGAGTTCGAAATACAAGTAA 
s elephant.ENm008_1        300962 37 -    364520 CCGGGCCTCCAGGGATCGGAGCTCGAAATACAAGTAA 
s tenrec.ENm008_6           29249 37 -     30140 CCGGGCCTCCAGAGACCGCAGCTCGAGACACAAGTAA 
s monDom1.scaffold_13198   478522 37 -   1560775 CCGAGGTTCCAGAGACAGAAGTTCGAAACACAAGTAA 
s platypus.ENm008_21         9488 37 -     16755 CCGGGGCTCCAGAGACCGCAGTTCCAAACACAAGTAA 

a score=1575168.0
s hg17.chr16             88647119 135 -  88827254 GTCACGCTCCCGGGATCGGCGTCGGAGGCGGTCAAGATCTACCTCCCGAGAGCG------ACGGAAATTGTCCCGGTCCCGGTCCCGAGATAGACATCGGCGCCACCGCAGCCGTTCCCGGAGCCACAGCCGGGGACATCG 
s panTro1.chr18          83679285 135 -  83875239 GTCACGCTCCCGGGATCGGCGTCGGAGGCGGTCAAGATCTACCTCCCGAGAGCG------ACGGAAATTGTCCCGGTCCCGGTCCCGAGATAGACATCGGCGCCACCGCAGCCGTTCCCGGAGCCACAGCCGGGGACATCG 
s baboon.ENm008_1          483123 135 -    646721 GTCACGCTCCCGGGATCGGCGTCGGAGGCGGTCAAGATCTACCTCCCGAGAGCG------ACGGAAGTTGTCCCGGTCCCGGTCGCGAGATAGACATCGGCGCCACCGCAGCCGTTCCCGGAGCCACAGCCGGGGACATCG 
s rheMac1.SCAFFOLD35869     32691 135 +     37522 GTCACGCTCCCGGGATCGGCGTCGGAGGCGGTCAAGATCTACCTCCCGAGAGCG------ACGAAAGTTGTCCCGGTCCCGGTCCCGAGATAGACATCGGCGCCACCGCAGCCGTTCCCGGAGCCACAGCCGGGGACATCG 
s marmoset.ENm008_1        335070 135 -    609522 GTCACGCTCCCGGGATCGGCGTCGGAGGCGGTCAAGATCTACCTCCCGAGAGCG------ACGGAAGTTGTCCCGGTCCCGGTCCCGAGATAGACATAGGCGCCACCGCAGCCGTTCCCGGAGCCACAGCCGGGGACATCG 
s galago.ENm008_1          398783 141 -    764343 GTCACGCTCCCGGGACCGGCGTCGGAGGCGGTCAAGGTCTACATCCCGGGAGCGGGAGCGACGGAAGTCTTCCCGGTCCCGGTCCCGAGACAGACACCGGCGCCACCGTAGCCGTTCCCGGAGTCACAGCCGGGGACACCG 
s rn3.chr10              15549407 135 + 110733352 GTCACGTTCCCGGGATCGTCGAAGGAGGCGGTCTAGGTCTACCTCCCGAGAGCG------GCGGAAGTTTTCCCGTTCCAGGTCCCGAGATAGATACCGGCGACATCGCAGCCGTTCCCGGAGCCACAGCCGGGGTCACCG 
s mm6.chr17              24073131 135 +  92867660 GTCACGCTCCCGGGATCGTCGACGGAGGCGGTCTAGGTCTACCTCCAGAGAGCG------GCGGAAGTTTTCCCGTTCCAGATCCCGAGATAGATACAGGCGCCATCGCAGCCGTTCCCGGAGCCACAGCCGGGGTCACCG 
s rabbit.ENm008_1            6626 135 -    203479 GTCACGTTCCCGGGAGCGGCGTCGAAGGCGGTCAAGGTCTGCCTCCCGAGAGCG------GAGGAAGTCTTCCCGGTCCCGGTCCCGAGACAGACACCGACGCCACCGCAGCCGTTCGCGGAGCCACAGCCGGGGTCACCG 
s cow.ENm008_1             204818 135 -    491063 GTCGCGCTCCCGGGACCGACGTCGCAGGCGATCGAGGTCAACTTCCAGAGAGCG------GCGGAAGTCGTCCCGCTCCCGGTCCCGAGACAGACACCGGCGCCACCGAAGCCGCTCCCGGAGCCACAGCCGTGGCCATCG 
s canFam1.chr6           41919872 135 +  79106041 GTCACGCTCCCGGGACCGGCGTCGGAGGAGGTCCAGATCTACCTCCAGGGAGCG------ACGAAAGTCATCCCGGTCCCGGTCCCGAGACAGACACCGGCGCCACCGCAGCCGTTCCCGGAGCCACAGCCGGGGCCACCG 
s rfbat.ENm008_1           369359 135 -    557006 GTCGCGTTCCCGGGACCGGCGTCGGCGGCGGTCAAGATCTACCTCCAGAGAAAG------ACGAAAATCATCCAGGTCCCGCTCCCAAGACAGACACCGGCGCCACCGCAGTCGTTCCCGGAGCCACAGCCGGGGCCACCG 
s shrew.ENm008_3            10937 135 +     44886 GTCACGTTCCAGGGAGAGACGTCGGAGACGGTCCAGATCTGCCTCCAGAGAGCG------ACGGAAGTCTTCCCGGTCTCGGTCTCGAGACAGACACCGGCGCCACCGAAGCCGTTCCCGTAGCCACAGCAGGGGCCACCG 
s armadillo.ENm008_1       252138 135 -    489446 GTCCCGTTCTCGAGACCGGCGCCGTAGGCGGTCCAGGTCCACCTCCCGGGAGCG------GCGGAAGTCTTCCCGGTCCCGGTCCCGAGACAGACACCGGCGCCACCGGAGCCGCTCCCGGAGCCACAGCCGGGGCCACCG 
s elephant.ENm008_1        300827 135 -    364520 GTCGCGCTCTCGGGACCGGCGTCGGAGGCGGTCAAGATCTACCTCCCGTGAGCG------ACGCAAGTCTTCCCGGTCCTGGTCCCGAGACAGACACCGGCGCCACCGGAGCCGTTCCCGGAGCCACAGTCGGGGCCACCG 
s tenrec.ENm008_6           29114 135 -     30140 GTCTCGCTCTCGGGACCGGCGAAGGAGGCGGTCAAGGTCAGCCTCCAGAGAGCG------GCGGAAATCCTCGAGATCTAGGTCCCGAGACAGACACCGGCGACACCGCAGCCGGTCCAGAAGCCACAGCCGGGGCCACCG 
s monDom1.scaffold_13198   478390 132 -   1560775 GTCACGATCTCGGGACAGACGACGAAGGCGGTCAAGGTCAGGCTCTCGTGAGAG------GCGAAAGT---CCCGTTCCCGATCTCGGGACAGACATAGGCGCCACCGCAGCCGCTCACGTAGCCATAGCAGGGGCCATCG 
s platypus.ENm008_21         9356 132 -     16755 GTCACGATCTCGGGACAGGCGGCGGAGGCGGTCGAGGTCGGCCTCCCGCGAGCG------GCGGAAGT---CCCGCTCCCGCTCCCGCGAGCGCCACAGGCGCCATCGGACCCGCTCGCGCAGCCCCAGCCGGGGCCACCG 
s galGal2.chr1           45874840 129 + 188239860 ATCTAGGTCCCGAGATCGTCGCAGACATCGCTCTCGCTCAGCCTCCAGGGAACG------GAAAAGAAGAACTCGCTCTAAATCCCGTGAGAAACGCCATCGCCACAGGTCTCGCTCCAACAGCCGCAGCCGGAG------ 
s tetNig1.chr2            4561145 132 +  19247847 GTCTCGCTCTCGCGACCGCAGGAGGAGACGCTCGCGCTCCACATCACGAGACAG------GCGCCGCT---CGCGCTCGCGTTCCAGGGAGAGGAGGAGGAGGCATCGCAGCAGATCAGGCTCGCGCACCAGGGGACACCG 

a score=66271.0
s hg17.chr16                244413 3 +  88827254 ATG 
s panTro1.chr18             262355 3 +  83875239 ATG 
s baboon.ENm008_1           236575 3 +    646721 ATG 
s marmoset.ENm008_1         325096 3 +    609522 ATG 
s galago.ENm008_1           444137 3 +    764343 ATG 
s rn3.chr10               95244723 3 - 110733352 ATG 
s mm6.chr17               68853941 3 -  92867660 ATG 
s cow.ENm008_1              211703 3 +    491063 ATG 
s canFam1.chr6            37249961 3 -  79106041 ACG 
s rfbat.ENm008_1            229422 3 +    557006 ATG 
s shrew.ENm008_10            12439 3 -     17082 ATG 
s elephant.ENm008_1         148321 3 +    364520 ATG 
s tenrec.ENm008_7            18660 3 +     30195 ATG 
s monDom1.scaffold_13198   1237364 3 +   1560775 ATG 
s galGal2.chr14            6505196 1 -  20603938 A-- 
s tetNig1.chr2            14692253 0 -  19247847 --- 
s fr1.chrUn              145488188 0 + 349519338 --- 

a score=446949.0
s hg17.chr16                244416 121 +  88827254 TTGGACCACAAGGACTTAGAGGCCGAAATCCACCCCTTGAAAAATGAAGAAAGAAAATCGCAGGAAAATCTGGGAAATCCAT------CAAAAAATGAGGATAACGTGAAAAGCGCGCCTCCACAG------T--- 
s panTro1.chr18             262358 121 +  83875239 TTGGACCACAAGGACTTAGAAGCCGAAATCCACCCCTTGAAAAATGAAGAAAGAAAATCGCAGGAAAATCTGGGAAATCCAT------CAAAAAATGAGGATAACGTGAAAAGCGCGCCTCCACAG------T--- 
s baboon.ENm008_1           236578 121 +    646721 TTGGACCACCAGGACTTAGAAGCTGAAGTCCACCCCTTGAAAAATGAAGAAAGAAAATCGCAGGAAAATCTGGGAAACCCAT------CGAAAAATGAGGATAACTTGAAAAGCACACCTCCACAG------T--- 
s marmoset.ENm008_1         325099 121 +    609522 TTGGACAACAAGGACTTAGAAGCCGAAATCTACCCCTTGAAAAATGAAGAAAGAAAATCGCAGGAAAATCTGGGAAACCCAT------CGAAAAATGAAGATAACTTGAAAAGCACGCCTCCACAA------G--- 
s galago.ENm008_1           444140 121 +    764343 ATGGACAGCAGGGATCAAGAAGCTGAAATCCACCCCTTGAAAAATGAAGACAGAAAATCACAGGAAAACCTGGGAAACCAAC------TAAAAAATGAAGATAACTTGAAAAGTATGCCTCTGCAG------T--- 
s rn3.chr10               95244726 121 - 110733352 ATGGATGACAAGGATCTAGAAGCTGAAATACATCCCTTGAAGAATGAGGACAAAAAGTCACAGGAAAACCTAGGAAACCTAC------CAAAGACCGAGGACAACTTGAAGAACAAGCCTGTGCCT------T--- 
s mm6.chr17               68853944 121 -  92867660 ATGGACAACAAGGACTTAGAAGCTGAAATACACCCCTTGAAGAATGAGGACAAGAAATCACAGGAAAACCCAGGAAACCTAC------CAAGAAACGAAGATAACTTGAAGAGCAAGCCTGTGCCT------T--- 
s cow.ENm008_1              211706 118 +    491063 ACGGACGGCAAGGACTTGGAGGCCGAGATCCACCCGCTCAAAAGCGAGAACAGGAAGGTACCGGAGAACGCGGGGGCCCTGG------CAGGAAAGGAGCCCCG--CGGGACGCCGGCCCCG-CAG------A--- 
s canFam1.chr6            37249964 121 -  79106041 ATGGACAGCAAGGACCTAGAAGCCGAAATCCACCCCCTGAGGAACGAAGACAAGAGGCTGCCCGAGACCCCGGGAAACCCGGGCCACGCAGACGAGAAGCT------GAAAAGCTCGCCCCGGCAG------C--- 
s rfbat.ENm008_1            229425 121 +    557006 ATGGACAGCAAGGACCTAGAAGCGGAAATCCACCCCTTGAAGAACGAAGATGGGAAATTGCAGGAGAATCTGGAAAACCCAG------CGAAAAAGGAAGAGCACTCGAAAAGCACCCCCGTGCGG------T--- 
s shrew.ENm008_10            12442 121 -     17082 ATGGAGCACAAGGACTTGGAAGCTGAGATCCGCCCCTTGAAAAATGAAGACAGGAAATTGCAGGGGACTCTGGGAACGCAGG------CGGGCAAGGAGGACCCCCTGAAGGGGACCCCACAGCTG------T--- 
s elephant.ENm008_1         148324 121 +    364520 ATGGACAACAAGGATTTAGAAGCTGAAATCCACCCCTTGAAGAATGAGGACCGGACATCGCAGGAGAACCTGGGGAACCGCA------CTGAAAAGGAAGACCCCTGTAAGAGCCTGCCTCCACAG------T--- 
s tenrec.ENm008_7            18663 127 +     30195 GTGGACAACAAAGACCTGGACGCGGAAATCCACCCCTTGAAGAGCGAAGACGGGAGACCGGCCGAGAGCGGGCGAAGCCCCT------CTGAGAAGGAGGAGCCCGGCCTGAGCAGCCCCGCACGGCGGCACT--- 
s monDom1.scaffold_13198   1237367 115 +   1560775 ------GACAAAGAATTAGAAGCTGAAATCCACCCCTTGAAACATGATGACAAAGTACCTCAGAGCAATTTGAAAAACCAAA------CTGAAAAAGATGGTTCTTTTAAGAAAGCATCTCGGCAT------T--- 
s galGal2.chr14            6505217 121 -  20603938 ATGGATAACAAAGACTCAGAAGCTGAGATCCACCCCCTGAAGACAGAGGACGTGAAAGCTCAAGAGAACCATGAGAACTCTG------TTGAGAGGAGAATCATCATCAAGCAGTCGTCGCAGCTG------T--- 
s tetNig1.chr2            14692253 106 -  19247847 -TGGAGAATACAGCCAGCGCTGCAGAGGCTGACCCTCTAAAGAGAGCAGACGA-------TGGGGG----CGAGATGCCTTC------------ATCAACAGAGCTGAGGAAGAAGAGCTGCAAAG------AAGT 
s fr1.chrUn              145488188 106 + 349519338 -TGGAGAATACAGTCATTGCTGCAGAGGTGGACCCTCTAAAGAGAGCAGAGGA-------TGGGGG----TGAGGTGCCTTC------------ATCAGCAGAGCTGAAGAAGAAGACCTGCAATG------GAGT 

a score=925944.0
s hg17.chr16                244537 144 +  88827254 CCCGGCTCTCCCGGTGCCGAGCGGCGGCGTTTTTTCTTTCATTGTTTCTCTGCCTTTTTGTGGTGTTCGTCGTCTCATTCGTCATCCCGTGTCCAGACCGGCC--GGCGTCACAGCGAATGTGGAGGATAGACTACAGTGCCGCTG 
s panTro1.chr18             262479 144 +  83875239 CCCGGCTCTCCCGGTGCCGAGCGGCGGCGTTTTTTCTTTCATTGTTTCTCTGCCTTTTTGTGGTGTTCGTCGCCTCATTCGTCATCCCGTGTCCAGACCGGCC--GGCGTCACAGCAAATGTGGAGGATAGACTACAGTGCCGCTG 
s baboon.ENm008_1           236699 144 +    646721 CCCGGCTCTCCCGTTGCCGAACGGTGGCGTTTTTTCTTTCATTGTTTCTCTGCCTTTTTGTGGTGTTTGTCGTCTCATTCGTCATCCCGTGTCCAGACCGGCC--AGCGTCACAGCGAATGTGGAGGATCGACTACAATGCCGCTG 
s marmoset.ENm008_1         325220 144 +    609522 CCCAGCTCTCCCGATGCCGTTCCGTGGCGTTTTTTATTTCGTTGTTTCTCTGCCTTTTTGTGGTGTTTGTCGTCTCATTCGTCATCCCGTGTCCAGACCGGCC--AGCGTCACAGCGAATGTGGAGGATGGACTACAATGCCGCTG 
s galago.ENm008_1           444261 144 +    764343 CCCGGTTGTCCCGATGCCGAGCAGTGGCTTTTTTCCTTTCATTGTTTATCTGCCTTTTTGTGGTGTTTGTCATCTCATTCATCATCCCATGCCCTGACCGACC--TGCGTCACAGCGCATGTGGAGGGTCGATTATAGTGCAGCAG 
s rn3.chr10               95244847 144 - 110733352 CTCGCTTGTCCCGGTGTCGCACGGTGGCATTTTTCCTTTCCCTGTTCATCTGTCTCTTTGTGGTGTTTGTCCTCTCTTTCATCATCCCATGCCCAGACCGACC--GTCCTCTGAGGACAAGTGGAGGCTGGACTACGACTATGCAG 
s mm6.chr17               68854065 144 -  92867660 CCCGCTTGTCCCGGTGCCGCACAGTGGCATTTTTCCTTTCCCTGTTCACCTGCCTCTTCGTGGTGTTTGTCCTGTCTTTCATCATCCCATGTCCAGACCGTCC--CTCCTCACAGGGCACGTGGAAGCTTGACTACAACAATGCAG 
s cow.ENm008_1              211824 144 +    491063 CTCGCCTCTCGCACTGCCGGACCGCGGCCTTCTTCCTCTCCCTGTTTGCCTGCCTCCTCGTGGTGTTCGTGGTCTCCTTCATCATCCCGTGTCCGGACCGGCC--GGCGTTGCAGGGGGTGTGGAGGATCGATTACAATGCGGCAG 
s canFam1.chr6            37250085 144 -  79106041 CCCGCCTCTCCCGGTGCCGCACCGTTGTGTTTTTTCTTTCACTGTTTGTCTGCCTGTTCGTAGTGTTCGTGGTTTCGTTCATCATCCCGTGCCCGGAACGGCC--CGTGTCGCAGGGGATGTGGCGGATAGACTACAGCGCGGCAG 
s rfbat.ENm008_1            229546 141 +    557006 CCCGTCTCTCCGGATGCCGGACGGCCGTGTTTTTCCTCTCGCTGTTTATCTGCCTTTTGGTGGTGTTTGTGATTTCCTTCATCATCCCGTGTCCAGATCGACC--AGCGTCACA---GACGTGGAGAATCGATTACAACACGGCAG 
s shrew.ENm008_10            12563 144 -     17082 CCCGCCTCTCCCGCTGCCGCACAGTGGTCTTCTTCCTCTCTCTCTTCATCTGCCTCTTCACAGTCTTCGTGGTCTCCTTCATCGTCCCCTGCCCAGAGAGGTC--TGCGTCCCAGGGGACGTGGAGGATCAACTTCAGCCAAGCAG 
s elephant.ENm008_1         148445 144 +    364520 CCCAGCTATCCCGGTGCCGGACAGTGGCATTTTTTCTCTCCCTGTTTATCTGCCTTTTTGTGGTGTTTGTCGTCTCATTCATCATCCCGTGTCCAGACCGGCC--TGTATCACAGCAAATGTGGAGAATCAATTACGACACAGCAG 
s tenrec.ENm008_7            18790 144 +     30195 CCCGGCTGTCGCGGTGCCGGGCGGTGGCCTTCTTCCTTTCCCTCTTCCTCTGCCTGCTCGTAGCCTTCATCGTGTCCTTCATCATCCCCTGTCCCGAGCGGCC--CGAGTCTCAGCGGGAGTGGAGGATTGATTACAACAGAGCAG 
s monDom1.scaffold_13198   1237482 144 +   1560775 CCCGGTTTGCCCAGTGCCGCACAATGTTTTTTTTCTTTTCATTATTTACCTGCCTCTTTGTGGTATTTATCATCTCATTCATCATCCCATGTCCAGATCGACC--AGTATCACAAAAAACATGGAAAATAAATTATGACAAAGCAG 
s galGal2.chr14            6505338 144 -  20603938 CTCGGCTGTCCCGCTGGCGCACCGCCGCCTTCTTCATCTCATTATTTCTGTGTCTCATCATCGTGTTTGCCTTCTCCTTTATCATTCCTTGCCCTGAGAGGCC--TGTCTCAGAGAGAACGTGGCTCCGAAACTATGACAATGCAG 
s tetNig1.chr2            14692370 144 -  19247847 CCAAACTGACCCACTGGCGAACGGCGGTGTTCTTCCTCTCCCTGTTCCTTTGCCTCACCATCGTGTTTGCCTTCTCCTTCATCATTCCATGTCCCGTCAGACCACAGTATCTCATTT--CCTGGAACAGAACTTTCCTCGATGCAG 
s fr1.chrUn              145488305 144 + 349519338 CCAAACTGACCCACTGGCGAACAGCGGTTTTCTTCCTCTCCATATTCCTTTGCCTCGCCATAGTGTTTGCCTTCTCCTTCATCATTCCATGTCCTGTCCGACCACAGTATCTCATTT--CCTGGAACAGAACTTTCCCCGAAGCAG 

a score=-53981.0
s hg17.chr16              88567979 7 -  88827254 GGCCTAG 
s baboon.ENm008_1           394295 7 -    646721 GGCCTAG 
s rheMac1.SCAFFOLD20467      36591 7 +     46047 GGCCTAG 
s marmoset.ENm008_1         271497 7 -    609522 GGCCTAG 
s galago.ENm008_1           301757 7 -    764343 GGTCTAG 
s rn3.chr10               15478449 7 + 110733352 GGACTAA 
s mm6.chr17               24003897 7 +  92867660 GTAGTAG 
s cow.ENm008_1              269608 7 -    491063 GACCTAG 
s canFam1.chr6            41844530 5 +  79106041 GAC--AG 
s rfbat.ENm008_1            317901 7 -    557006 GGCCTAG 
s tenrec.ENm008_7             2982 7 -     30195 GGCCTAG 
s monDom1.scaffold_13198    292597 7 -   1560775 GGAAGAA 
s platypus.ENm008_4          12792 7 +     36466 GAAGTGG 
s xenTro1.scaffold_142     1991987 7 -   2099714 AGAACAG 
s tetNig1.chr15            2732532 5 +   7231322 --CATCT 
s fr1.chrUn              317248718 5 - 349519338 --CAACG 
s danRer2.chr1            55770458 5 -  62208023 --CAATT 

a score=-36308.0
s hg17.chr16              88567970  9 -  88827254 AG------ATGG----------G---------------------GT 
s baboon.ENm008_1           394286  9 -    646721 AG------ATGG----------G---------------------GT 
s rheMac1.SCAFFOLD20467      36582  9 +     46047 AG------ATGG----------G---------------------GT 
s marmoset.ENm008_1         271488  9 -    609522 AG------ATGG----------G---------------------GT 
s galago.ENm008_1           301750  7 -    764343 --------ATGG----------G---------------------GA 
s rn3.chr10               15478440  9 + 110733352 CA------ATGA----------G---------------------GA 
s mm6.chr17               24003888  9 +  92867660 CG------ATGG----------G---------------------GA 
s cow.ENm008_1              269602  6 -    491063 ---------TGG----------G---------------------GA 
s canFam1.chr6            41844524  6 +  79106041 ---------TGC----------G---------------------GG 
s rfbat.ENm008_1            317892  9 -    557006 TC------CTGG----------G---------------------GA 
s tenrec.ENm008_7             2973  9 -     30195 GG------ATGG----------G---------------------GA 
s monDom1.scaffold_13198    292578 19 -   1560775 AA------CTGAAGAATGGCCAG---------------------GA 
s platypus.ENm008_4          12756 36 +     36466 AGTCTGGCATAG----------GCCAGCCCCTCTCCCGGGCACAGT 
s xenTro1.scaffold_142     1991979  8 -   2099714 -------AAGAG----------G---------------------GA 
s fr1.chrUn              317248678  7 - 349519338 --------AGCA----------G---------------------GA 

a score=-69441.0
s hg17.chr16              88567942 28 -  88827254 CCACA---GC--GGCTTGTGG------C-----CCTGGGGGTGG 
s baboon.ENm008_1           394258 28 -    646721 CCACA---GC--GGCTGGTGG------C-----CCTGGGGGAGG 
s rheMac1.SCAFFOLD20467      36554 28 +     46047 CCACA---GC--GGCTGGTGG------C-----CCTGGGGGAGG 
s marmoset.ENm008_1         271460 28 -    609522 CCACA---GC--GGCCAGTGG------C-----CCTGCGGGAGG 
s galago.ENm008_1           301723 27 -    764343 CCATG---GT--GGTTGGCAG------C-----CCTCGGGGTG- 
s rn3.chr10               15478412 28 + 110733352 CTGCA---GC--TACCAGCTC------C-----CCTGCAGGTGG 
s mm6.chr17               24003860 28 +  92867660 CTGCA---GC--AACCAGTTC------C-----CCTGAAGGTGC 
s cow.ENm008_1              269583 19 -    491063 CCGTGGGTGG--AGATGGTGA----------------------- 
s canFam1.chr6            41844498 26 +  79106041 CTGTGACTGC--TGCAAGTGA------C-----CCTGCG----- 
s rfbat.ENm008_1            317861 31 -    557006 GTGCGGCTGC--TCCTGGGGG------T-----CCTGGGGGTGG 
s tenrec.ENm008_7             2948 25 -     30195 CCAGA---GG--AGC---TGC------C-----CCTGAGGGTGG 
s monDom1.scaffold_13198    292545 33 -   1560775 CCGCT---GT--GAGGAGAGC------CAAGGACCTGGGGGCAA 
s platypus.ENm008_4          12728 28 +     36466 CAGGC---AC--TGCTGAGGG------T-----CCTGACGCTAC 
s galGal2.chr14           14084168 13 +  20603938 CCGAG---GC-----CAAGGG----------------------- 
s tetNig1.chr15            2732498 34 +   7231322 --ATG---GAGCGGCCAGGAGAGCCGGC-----CAGGGAAGCAG 
s fr1.chrUn              317248684 34 - 349519338 --ACG---GACAGGCCAAGAGAGCCGGG-----CAGGGAAGCGG 
s danRer2.chr1            55770424 34 -  62208023 --ATG---GGAAGGCAAAAAACTCAAAC-----TCTGTCAAAAG 

a score=19813.0
s hg17.chr16              88567928 14 -  88827254 CACCCCTGTGGA----GC 
s baboon.ENm008_1           394244 14 -    646721 CGCCCCTGTGGA----GC 
s rheMac1.SCAFFOLD20467      36540 14 +     46047 CACCCCTGTGGA----GC 
s marmoset.ENm008_1         271446 14 -    609522 CACCCCTGTGGA----GC 
s galago.ENm008_1           301709 14 -    764343 CACCTCTGGGGA----GC 
s rn3.chr10               15478398 14 + 110733352 GACCTCTGGGGA----GC 
s mm6.chr17               24003846 14 +  92867660 TACCCCCAGGGA----GC 
s cow.ENm008_1              269569 14 -    491063 GGCCTCTGGGGA----GC 
s canFam1.chr6            41844484 14 +  79106041 CACATCTGCAGA----GC 
s rfbat.ENm008_1            317847 14 -    557006 AACCTCTGGGGA----TT 
s tenrec.ENm008_7             2934 14 -     30195 TGCTTCTGGGGA----GC 
s monDom1.scaffold_13198    292528 17 -   1560775 -CCTTCTGTGGAATGGGT 
s platypus.ENm008_4          12714 14 +     36466 TGCGGCTCCGGG----GC 
s galGal2.chr14           14084154 14 +  20603938 GCCCGCCGGTGA----CA 
s xenTro1.scaffold_142     1991965 14 -   2099714 GCCCCAGGGGGA----GC 
s tetNig1.chr15            2732478 14 +   7231322 CGCCCCGATGGA----GG 
s fr1.chrUn              317248664 14 - 349519338 GGCCCGGATGGC----GG 
s danRer2.chr1            55770405 13 -  62208023 -ACCCATACCAC----AG 

a score=324439.0
s hg17.chr16              88567871 57 -  88827254 CGTGTTCCC---GTTTACGTGGAGGCCAC-GGCACTCG--------------AGCCCCAGCCCTGCAC--TCCTTCC 
s panTro1.chr18           83596110 57 -  83875239 CGTGTTCCC---AATTACGTGGAGGCCAC-GGCACTCG--------------AGCCCCAGCCCTGCAC--TCCTCCC 
s baboon.ENm008_1           394187 57 -    646721 CGTGTTCCC---GTTCTCGCGGAGGCCAC-GGCACTCA--------------GGCCCCAGCCCTGCAC--TCCTTCC 
s rheMac1.SCAFFOLD20467      36483 57 +     46047 CGTGTTCCC---GTTCTCGCGGAGGCCAC-GGCACTCA--------------AGCCCCAGCCCTGCAC--TCCTTCC 
s marmoset.ENm008_1         271392 54 -    609522 CATGTTCCT---GTTCACACGGAGGCCGC-G---CTTG--------------AGCCCCAGCCCTGCAC--TCCTTCC 
s galago.ENm008_1           301652 57 -    764343 GGTGTTCCC---ATTCACATGGCAGCCAC-GGCACTCA--------------AGCCCCAGCCCTGCTC--TTCTTCC 
s rn3.chr10               15478341 57 + 110733352 GCCATTCCC---ATTCTTGCGGAAGCCTC-TGCACTCA--------------AGTCCCAGCCCTGCTC--TCCAGTC 
s mm6.chr17               24003789 57 +  92867660 GCCATTTCC---ATTCTTGCGGAAGCCTC-TGCACTCA--------------AGCCCCAGCCCTGCTC--TCCAGTC 
s cow.ENm008_1              269506 57 -    491063 GGTGTTCCC---GTTCACGCGGAAGCCCC-GGCACTCC--------------AGCCCCAGCCCTGCTC--TCCTTCC 
s canFam1.chr6            41844421 57 +  79106041 GGCCTTTCC---GTTCCTGCGGAAGCCGC-CACACCCG--------------AGCCCCAGCCCCACGC--TCCTTCC 
s rfbat.ENm008_1            317784 57 -    557006 GGTGTTCCC---GTTCATGTGGAAGCCAC-GGCGTTCG--------------AGCCCCAGCCCTGCTC--TCCTTCC 
s tenrec.ENm008_7             2883 51 -     30195 TGTGTTCCC---ATTCATGAGGAAGCCTC-GCT--------------------GCTCCAGCCCCACCC--TCCTGCC 
s monDom1.scaffold_13198    292460 68 -   1560775 TCACCACTC---CATTATGTGAGAGAGTT-GGAATTGGGAATTACCATGATCAGCCTCA---CTGTAT--CCCCTTC 
s platypus.ENm008_4          12643 61 +     36466 TGGCTGGCCTGGGCTGGCAGGGGGTTCACAGGCATTTG--------------GAGTCACCCGCTGCTC--TCCTCGC 
s galGal2.chr14           14084097 57 +  20603938 GGTGTTCCC---CTTCATGCGCAAGCAGC-GACACTCC--------------AGCCCCAGCCCGGCCC--TGCTCCT 
s xenTro1.scaffold_142     1991908 57 -   2099714 AGTTTTCCC---ATTCATGAGAAGGCAGC-GACACTCC--------------AGCCCCAGTCCAGCGT--TCTTACT 
s tetNig1.chr15            2732421 57 +   7231322 CGTCTTCCC---CTTCATGAGACGCCAGC-GGCACTCC--------------AGCCCCTCCCCGGCCCAGGCGTC-- 
s fr1.chrUn              317248607 57 - 349519338 CGTCTTCCC---CTTCATGAGACGCCAGC-GGCACGCC--------------AGCCCCTCCCCCGCGCAGGCATC-- 
s danRer2.chr1            55770350 55 -  62208023 TGTGTTCCC---GTTCATGCGTCGGCAGC-GCCACTCC--------------AGCCCCTCGCCTGCTC--TCGTC-- 

a score=7501055.0
s hg17.chr18              52330965 74 -  76117153 ACTATGATTACCTGAACGACTGGGGGCCACGGTTCAAGAAACTTGCTGACATGTATGGTGGAGGTGATGACTGA 
s panTro1.chr17           53626596 74 -  73346066 ACTATGATTACCTGAACGACTGGGGGCCACGGTTCAAGAAACTTGCTGACATGTATGGTGGAGGTGATGACTGA 
s baboon.ENr213_1           488501 74 -    647425 ACTATGATTACCTGAACGACTGGGGGCCACGGTTCAAGAAACTTGCTGACATGTATGGTGGAGGTGATGACTGA 
s rheMac1.SCAFFOLD126155     38397 74 +     41707 ACTATGATTACCTGAACGACTGGGGGCCACGGTTCAAGAAACTTGCTGACATGTATGGTGGAGGTGATGACTGA 
s marmoset.ENr213_1         535348 74 -    758875 ACTATGATTACCTGAACGACTGGGGGCCACGGTTCAAGAAACTTGCTGACATGTATGGTGGAGGTGATGACTGA 
s galago.ENr213_1           487089 74 -    702536 ACTATGATTACCTGAACGACTGGGGGCCACGGTTCAAGAAACTCGCTGAAATGTATGGTGGAGGTGATGACTGA 
s rn3.chr18               79288257 74 -  87338544 ACTATGACTACCTGAATGACTGGGGACCCCGCTTCAAGAAGCTGGCCGACATGTATGGTGGTGGTGATGACTGA 
s mm6.chr18               73523476 74 -  90308396 ACTATGACTACCTGAATGACTGGGGACCCCGCTTCAAGAAACTGGCGGACATGTACGGCGGTGGTGACGACTGA 
s rabbit.ENr213_1           419472 74 -    525974 ACTATGATTACCTGAACGACTGGGGACCACGCTTCAAGAAACTCGCTGACATGTACGGTGGAGGTGATGACTGA 
s cow.ENr213_1              128271 74 -    283180 ACTATGACTATCTGAACGACTGGGGGCCCCGCTTCAAGAAACTCGCTGACATGTACGGTGGAGGTGATGACTGA 
s canFam1.chr7            63605739 74 +  83037113 ACTATGACTACCTGAACGACTGGGGGCCACGGTTCAAGAAACTTGCTGACATGTATGGTGGAGGTGATGACTGA 
s shrew.ENr213_2             53493 74 +     70744 ACTATGACTACCTGAACGACTGGGGGCCGCGCTTCAAGAAACTCGCTGACATGTATGGTGGAGGTGATGACTGA 
s armadillo.ENr213_1        348613 74 -    467874 ACTATGACTACCTGAACGACTGGGGGCCGCGGTTCAAGAAGCTCGCTGACATGTACGGTGGAGGGGACGACTGA 
s elephant.ENr213_1         366442 74 -    402523 ACTATGATTACCTGAACGACTGGGGGCCCCGGTTCAAGAAACTGGCTGACATGTACGGCGGAGGTGATGACTGA 
s monDom1.scaffold_13637   1060635 74 -   3280295 ACTATGATTACCTAAATGACTGGGGCCCACGCTTCAAGAAACTTGCCGATATGTACGGCGGAGGTGATGACTGA 
s platypus.ENr213_1         287463 74 -    296930 ACTATGATTACCTAAATGACTGGGGACCGCGTTTCAAGAAACTCGCCGACATGTACGGCGGGGGCGACGACTGA 
s galGal2.chr2            43614053 74 - 147590765 ACTATGACTACCTAAATGACTGGGGCCCACGTTTCAAGAAACTTGCTGACATGTACGGTGGAGGTGATGACTGA 
s tetNig1.chr15             437763 74 -   7231322 ACTACGATTACCTCAACGACTGGGGCCCTCGCTTTAGAAAACTGGCGGACATGTACGGCGGGTGCGACGACTAG 
s danRer2.chrNA          279348809 74 + 318297480 ACTATGACTACCTCAACGATTGGGGCCCTCGCTTCCGCAAACTCGCCGACATGTACGGAGGTAACGACGACTAG 

a score=1838655.0
s hg17.chr18              52330832 133 -  76117153 GGCCTTAAAGCGGCTGACAATGACCCCACAGCTCCACCATATGACTCCCTGTTAGTGTTTGACTATGAAGGCAGTGGCTCCACTGCTGGGTCC-TTGAGCTCCCT--TAATTCCTCAAGTAGTGG-TGGTGAGCAGG 
s panTro1.chr17           53626463 133 -  73346066 GGCCTTAAAGCGGCTGACAATGACCCGACAGCTCCACCATATGACTCCCTGTTAGTGTTTGACTATGAAGGCAGTGGCTCCACTGCTGGGTCC-TTGAGCTCCCT--TAATTCCTCAAGTAGTGG-TGGTGAGCAGG 
s baboon.ENr213_1           488368 133 -    647425 GGCCTTAAAGCGGCTGACAATGACCCCACAGCTCCACCATATGACTCCCTGTTAGTGTTTGACTATGAAGGCAGTGGCTCCACTGCTGGGTCC-TTGAGCTCCCT--TAATTCCTCAAGTAGTGG-TGGTGAGCAGG 
s rheMac1.SCAFFOLD126155     38264 133 +     41707 GGCCTTAAAGCGGCTGACAATGACCCCACAGCTCCACCATATGACTCCCTGTTAGTGTTTGACTATGAAGGCAGTGGCTCCACTGCTGGGTCC-TTGAGCTCCCT--TAATTCCTCAAGTAGTGG-TGGTGAGCAGG 
s marmoset.ENr213_1         535215 133 -    758875 GGCCTTAAAGCTGCTGACAATGACCCCACAGCTCCACCATATGACTCCCTGTTAGTGTTTGACTATGAAGGCAGTGGCTCCACTGCTGGGTCC-TTGAGCTCCCT--TAATTCCTCAAGTAGTGG-TGGTGAGCAGG 
s galago.ENr213_1           486956 133 -    702536 GGCCTTAAAGCTGCTGACAATGATCCCACAGCTCCACCATATGACTCCCTCTTAGTCTTTGACTACGAAGGCAGTGGCTCTACGGCGGGGTCC-TTGAGCTCCCT--AAATTCCTCAAGTAGTGG-CGGTGAGCAGG 
s rn3.chr18               79288124 133 -  87338544 GGCCTTAAAGCTGCTGACAATGACCCCACGGCGCCACCATATGACTCCCTTTTAGTCTTCGACTATGAGGGCAGCGGCTCCACGGCTGGCTCC-TTGAGCTCTCT--CAACTCCTCCAGCAGCGG-CGGGGACCAGG 
s mm6.chr18               73523343 133 -  90308396 GGCCTTAAAGCTGCTGACAACGACCCCACGGCGCCACCGTATGACTCCCTCTTAGTCTTTGACTACGAGGGCAGCGGCTCCACGGCTGGCTCC-TTGAGCTCCCT--CAACTCCTCCAGTAGCGG-TGGGGACCAGG 
s rabbit.ENr213_1           419339 133 -    525974 GGCCTTAAAGCTGCTGACAATGATCCCACAGCCCCACCCTACGACTCTCTCTTAGTTTTTGACTATGAAGGCAGTGGCTCCACCGCTGGGTCT-TTGAGCTCCCT--TAATTCCTCAAGTAGTGG-TGGTGAGCAGG 
s cow.ENr213_1              128138 133 -    283180 GGCCTTAAAGCTGCTGACAACGATCCCACCGCTCCGCCCTACGACTCCCTCTTAGTCTTTGACTATGAAGGCAGTGGCTCCACGGCCGGGTCC-TTGAGCTCCCT--TAATTCCTCCAGTAGTGG-AGGTGAGCAGG 
s canFam1.chr7            63605606 133 +  83037113 GGCCTTAAAGCTGCTGACAATGATCCCACAGCTCCACCATATGACTCCCTCTTAGTCTTTGACTACGAAGGCAGTGGCTCTACCGCTGGGTCT-TTGAGCTCCCT--TAATTCTTCAAGTAGTGG-TGGCGAGCAGG 
s shrew.ENr213_2             53360 133 +     70744 GGCCTTAAAGCTGCTGACAATGACCCTACAGCCCCGCCATATGACTCCCTCTTAGTCTTTGACTATGAAGGCAGTGGCTCCACTGCCGGGTCC-TTGAGCTCCCT--GAATTCCTCGAGTAGCGG-TGGCGAACAGG 
s armadillo.ENr213_1        348480 133 -    467874 GGCCTTAAAGCTGCCGACAATGATCCCACTGCTCCGCCATATGACTCGCTCTTAGTCTTTGACTATGAAGGCAGTGGCTCCACGGCTGGGTCC-TTGAGCTCCCT--TAATTCCTCAAGTAGTGG-TGGCGAGCAGG 
s elephant.ENr213_1         366309 133 -    402523 GGCCTTAAAGCTGCTGACAATGACCCCACAGCTCCGCCCTATGACTCCCTCTTAGTCTTTGATTACGAAGGCAGTGGTTCCACCGCCGGGTCC-TTGAGCTCCCT--AAATTCCTCAAGTAGTGG-TGGCGAGCAGG 
s tenrec.ENr213_11            7864 137 -     14033 GGCCTGAAAGCTGCTGACAACGATCCCACTGCTCCACCATATGACTCCCTCTTAGTCTTTGACTATGAAGGCAGTGGCTCCACTGCTGGGTCCTTTGAGCTCCCTTCAACTCCTTCAAGTAGTGGTTGGTGAACAGG 
s monDom1.scaffold_13637   1060502 133 -   3280295 GGACTCAAAGCTGCTGACAATGACCCCACAGCTCCACCGTATGACTCCCTTCTAGTGTTTGATTATGAAGGCAGTGGTTCCACCGCTGGTTCT-TTGAGCTCCCT--GAACTCCTCCAGTAGTGG-TGGTGAACAGG 
s platypus.ENr213_1         287330 133 -    296930 GGACTGAAAGCTGCGGACAACGATCCCACAGCACCGCCCTACGACTCTCTCCTAGTCTTCGACTACGAAGGCAGCGGCTCCACCGCGGGGTCT-TTGAGTTCCCT--GAATTCCTCAAGTAGCGG-CGGTGAGCAAG 
s galGal2.chr2            43613920 133 - 147590765 GGACTTAAAGCAGCCGACAACGACCCTACAGCCCCGCCATACGATTCCCTCTTAGTCTTTGACTATGAAGGAAGCGGCTCCACTGCTGGATCC-TTGAGCTCTCT--TAATTCCTCAAGTAGCGG-TGGTGAGCAAG 
s tetNig1.chr15             437630 133 -   7231322 GGACTGAAGGCAGCGGACAACGACCCCACCGCGCCCCCGTACGACTCGCTCTTGGTGTTCGACTACGAGGGCAGCGGCTCCACAGCCGGCTCC-CTCAGCTCCCT--CAACTCCTCCAGCAGCGG-GGGCGACCAGG 
s danRer2.chrNA          279348676 133 + 318297480 GGCCTCAAGGCAGCCGACACCGATCCCACGGCCCCTCCGTATGACTCCCTGCTGGTGTTTGACTACGAGGGCAGCGGCTCCACGGCCGGCTCA-CTAAGCTCCCT--TCACTCGTCCAGCAGCGG-AGGAGACCAGG 

a score=572221.0
s hg17.chr18              16661081 140 -  76117153 CTGCCACCGC---TGT-----AGTAGTAGTCGAATTATCATCTCCTTCAACTAATGAA---------GAGTTCTGTTGTAATCACCCTTTCCTATTCTTCATAAGGCAAAATAAGACCAACAGCATCCTCTTCTATGGCAGATTCTCATCCCCAT--AG 
s panTro1.chr17           17047191 140 -  73346066 CTGCCACCGC---TGT-----AGTAGTAGTCGAATTATCATCTCCTTCAACTAATGAA---------GAGTTCCATTGTAATCACCCTTTCCTATTCTTCATAAGGCAAAATAAGACCAACAGCATCCTCTTCTATGGCAGATTCTCATCCCTGT--AG 
s baboon.ENr122_1           511458 140 -    593854 CTGCCACCGC---TGT-----AGTAACAGGGTTTACATCACCTCTTTTAACTAATGAA---------GAGTTCCATTGTAATCACCCTTTCCTATTCTTCATCAGGCAAAATAAGACCAACAGCATCCTCTTCTTTGGCAGATTCTCATCCCCTT--AG 
s rheMac1.SCAFFOLD81184      16099 140 +     35702 CTACCACCGC---TCT-----AGTAACAGAGCTTTCATCACCTCTTTTAACTAATGAA---------GAGTTCCATTGTAATCACCCTTTCCTATTCTTCATCAGGCAAAATAAGACCAACAGCATCCTCTTCTTTGGCAGATTCTCATCCCCTT--AG 
s marmoset.ENr122_1         609017 140 -    677515 CTGCCACCGG---GGT-----GACAACAGGAATCACATCACCTCCTCCAACTAATGAA---------GAGTTCCATTGTAATCACCCTTTCCTATTCTTCATCAGGCAAAATAAGACCAACAGCATCCTCTTCTTTGGCAGATTCTCATCCCCTT--AG 
s galago.ENr122_1           170022 137 +    408645 CTGGCACAGG---GAG-----TGAGGTGGG------------TTTTCGAATTAAATACCCCTCCATTGAATTCAACGTAGATCACCCATTCCTCTTCTTCATCAGGCACAACAAAACCAATAGCATCCTCTTTTATGGAAGATTCTGCTCCCCGT--AA 
s rn3.chr13               98009375 137 - 111348958 CTGCCACAGG---GGT-----GGAAACCCGCATACTATC---TGCACCAAGGACCACA---------GAATTTACTTGTAATCGCCCTTTCATAGTCTTCATAAAGCCAAACAACACCAACAGCATCCTCTTCTTTGGAAGAGTATCTTCCCCTT--AA 
s mm6.chr1                88146111 128 - 195109612 CTACCACGGG---GAT-----AAAATCCCATAATTTATC---TTTACAGATTACAGAA---------GATTTCTATTGTGATCATCCAT---TGGTC------AAGCACAGTAAGACCAACAGCATCCTCTTCTTTGGCACAATCTCTTCCCCTT--AA 
s rabbit.ENr122_1           129367 133 +    384214 CGGCCACAGG---AAA-----CAACATTGTAGAAAAGCAACTTCCTGAATCTAC---A---------GTGTTCAGAGCTGATCACCCATTCCTATTTGTCATCAGGAAAGATGA------CATCATCTTGTTTAGTGGCAAAGTCTCTTGCCCTTGAAA 
s cow.ENr122_1              688596 140 -    707333 CTGCTACCGG---TGT-----GGGTGTTGCTGTCATCACATCATTGCCGATTCGTGAG---------AGTTTCCGCTGCGATCACCCTTTCCTGTTCCTCATCAAGCACATCAAGACCAACAGCATCCTCTTCGGTGGCCGAGTCTCTTCCCCTT--AG 
s canFam1.chr1            16357850 134 + 124897793 CCTCCACAGA---CGT-----AGAAGTTATTGCCAAATC---AGCACCAATCTAT------------CCTTTTCATTGCGATCACCCTTTCCTGTTCTTCATCAAGCACAATAAGACCAACAGCATCCTCTTCTTGGGCAGAGTCTCTTCCCCTT--AG 
s rfbat.ENr122_1            373480 137 -    374400 CTGCTACTGG---CAT-----AGTAATTGGTCGAACATC---AGTACAGATGTATGAA---------CACTTCCATTGCGATCACCCTTTCCTTTTCTTCATCAAGCACAATGAGACCAACAGCATCCTCTTTTTTGGCAGAATCTCTACCCCTG--AC 
s shrew.ENr122_3             27244 137 +     45941 CTGGCACCGG---AGT-----GGGCTTTGCCGTCA---CGCCAGCGCCAGGCTGCGAG---------GATTTCCTCTGCAATCACCCCTTCCTGTTCTTCATCAGGCACAGCGACTCCGACAGCGTCCTCTTCTTCGGCCGGTTTTCTTCTCCTT--AG 
s armadillo.ENr122_1        308349 137 -    310133 CTGCCACCGG---TGT-----AGAAGCGGTTGCATTGTC---ATCACCAGTTTATGAA---------GAGTTGCGTGTTGATCACTCTTTCCTGTTCTTCATTAGGAAGAGATTAACCGACAGCATCCTCTTCCTTGGCAGAGTCTGTTCTCCTT--AG 
s elephant.ENr122_1         308540 137 +    383286 CAGCCACCGC---GGTGGTC-AGGAACAGCCGGAGCCTC---AGCATAGAGCCA-------------AGGTTTTGTGCAGACCACCCTTTCCTCATGTTCATCAGACACCACAAGACCAACAGCATTCTATTCTGCGGCAGGTTCTCATCTCCGT--GA 
s tenrec.ENr122_17            4442 137 +      6830 CGGCCACGGC---CGTGGTT-AGGAACTCGCGCAGCGCC---CGCACCGACCCG-------------CGCTTCTGTGCCGACCACCCATTCTTGCTGGTCATCTGCCACCGCGCCACCCACAGCCTGGTGTTCTGTGGCCGGGTCTGCTCGCCTT--GA 
s monDom1.scaffold_15171   1812559 137 -   2219062 CTGGCACAGG---GGG-----TGTCATGACAGGGCGAAC---TGGTCATATTGGACTG---------CAAGTTGTGGCAGATCATCCTTTCCTTTTCTTTATCATACATAAGAAAACCAATACTATCCTTTTCTTTGGCAGATTCTGCTCCCCCT--AA 
s platypus.ENr122_1          31388 137 -     72535 CTGGCATTGGGAGTGT-----CTTGACAGTACAAATGACATATCCTTTGATT---------------ACTTTTAATGCAGATCACCTGTTCCTCTTTTTCATCAGACATAACCACACTAATAACATTCTCTTCCTTGGCAGGTTCTGTTCCCCTT--AG 
s galGal2.chr2            80207329 131 - 147590765 CTACTGCTGG---CAT-----TGCAATGCTTTGCATGGT---------TATAGAAGAG---------GATTTCAATGCTGACCATCCTTTCCTTTTCTTTCTTCGCCACAACCCAACGAAAAGCATAGTTTTCTTTGGCAGATATGCTTCTCCAT--GA 
s tetNig1.chrUn_random   126447808 134 - 171761319 CAGCCAC------AGT-----GGCCATGGTTACATTCTG---TATGTTGAGGGAGGAA---------CACTTCACGGCAGACCATCCCTTCCTCTTCTTCATTAGACACAATAAGACCAAGTCCATCCTCTTCCTGGGGAGATACTCGTCTCCTC--AG 
s danRer2.chr19             174375 125 +  52023587 CGGCCACTGC---TGCCATCGCGAAGTTTCTGTGCTATA---TTCCCCCAGTG--------------TCTTTTAATGCAGATCATCCGTTCCTTTTCTTCATCCGACACAATCCCACCAAGAGCATTCTGTTTTATGGACGCTTC-------------- 

a score=1602009.0
s hg17.chr18              16660816 265 -  76117153 CTTGAAGAGAAACTCACTGCTGAGAAATTGATGGAATGGACAAGTTTGCAGAATATGAGAGAGAC---ATGTG---TCGATTTACACTTACCTCGGTTCAAAATGGAAGAGAGCTATGACCTCAAGGACACGTTGAGAACCATGGGAATGGTGAATATCTTCAAT---GGGGATGCAGACCTCTCAGGCATGACCTGGAGCCACGGTCTCTCAGTATCTAAAGTCCTACACAAGGCCTTTGTGGAGGTCACTGAGGAGGGAGTGGAAGCTGCAG 
s panTro1.chr17           17046926 265 -  73346066 CTTGAAGAGAAACTCACTGCTGAGAAATTGATGGAATGGACAAGTTTGCAGAATATGAGACAGAC---ACATG---TCGATTTACACTTACCTCGGTTCAAAATGGAAGAGAGCTATGACCTCAAGGACACGTTGAGAACCATGGGAATGGTGAATATCTTCAAT---GGGGATGCAGACCTCTCAGGCATGACTGGGAGCCGCGGTCTCTCGGTATCTAAAGTCCTACACAAGGCCTTTGTGGAGGTCACTGAGGAGGGAGCGGAAGCTGCAG 
s baboon.ENr122_1           511193 265 -    593854 CTTGAAGAGAAACTCACTGCTGAGAAATTGTTGGAATGGACAAGTTTGCAGAATATGAGAGAGGC---ACATG---TGGATTTACACTTGCCTCGGTTCAAAGTGGAAGAGAGCTATGACCTCAAGGACACGTTGAGAAACATGGGAATGGTGGATCTCTTCAAT---GGGGATGCAGACCTCTCAGGCATGACTGGGAGCCACGGTCTCACGGTATCTAAAGTCCTACACAAGGCCTTTGTGGAGGTCACTGAGGAGGGAGCGGAGGCTGCAG 
s rheMac1.SCAFFOLD81184      15834 265 +     35702 CTTGAAGAGAAACTCACTGCTGAGAAATTGTTGGAATGGACAAGTTTGCAGAATATGAGAGAGGC---ACATG---TGGATTTACACTTGCCTCGGTTCAAAGTGGAAGAGAGCTATGACCTCAAGGACACGTTGAGAAACATGGGAATGGTGGATCTCTTCAAT---GGGGATGCAGACCTCTCAGGCATGACCGGGAGCCGCGGTCTCACGGTATCTAAAGTCCTACACAAGGCCTTTGTGGAGGTCACTGAGGAGGGAGCGGAGGCTGCAG 
s marmoset.ENr122_1         608755 262 -    677515 CTTGAAGAGAAACTCACTGCTGAAAAATTGATGAAATGGACAAGTTTGCAGAATATGAGAAAGGT---GGATG---TGAATTTACGCTTACCTCGGTTCAAAGTGGAAGAGGCCTATGATCTCAAGGACACATTGAGAACCATGGGAATGGTGGATGTCTTCAGT---G---ATGCAGACCTCTCAGGCATGGCTGGGAGCCGGAATCTCGTGATATCTAAAGTTCTACACAAGGCCTTTGTGGAGGTCACTGAGGAGGGAGCGGAGGCTACAG 
s galago.ENr122_1           169754 268 +    408645 CTAGAAAAGGCCATCACCTATGAGAAGCTGAATGAGTGGACCAGT--GCAGA-CATGATGGAGTT---GTATGACGTGCAGCTGTCTCTGCCCAAGTTCAAGCTGGAAGAGAGTTATGACCTCAAGTCCACCCTGAGCAGTATGGGGATGAGCGATGCCTTCAACCCGAGCAAAGCTGATTTCTCAGGAATGTCTTTAGAGAGAAACCTATATCTGTCCAATATTTTCCACAAGGTTTTTGTGGAAATAAATGAAGAAGGTACTGAGGCTGCAG 
s rn3.chr13               98009107 268 - 111348958 CTTGAAGAAAAACTAAGTGCTGACACGTTGCTAGCGTGGACAAGCCCAAAGAACATGCGGATGAC---GCAGT---TGAATTTATCTTTGCCTCGGTTCAAAGTGCAAGAGAAGTATGACCTCCCAGGTCCATTGGAGCACATGGGGATGGTCGATGCTTTCAATCCACAGAAGGCTGATTTCTCTGGCATGAGCAGCACTAAAGGTCTAGTGGTGTCTAAAGTTTTACACAAATCCTTTTTGGAGGTAAATGAAGAGGGAGCTGAAGCTGCTG 
s mm6.chr1                88145843 268 - 195109612 CTTGAAGAACAACTCTCTACTGAAAAGTTACTAGAATGGACAAGAGCAGAAAATATGCATATGAC---CGAGT---TGTATTTATCTTTGCCTCGGTTCAAAGTGGAAGAGAAGTATGACCTCTCAGTTCCATTGAAACACATGGGGATGGTTGGCGCCTTTGATCCACAGAAGGCTGACTTCTCTGGCATGAACAGCACTCAAGGTCTTGTGGTGTCTAAAGTTTTACACAAGTCCTTTGTGGAGGTAAATGAAGAGGGAACAGAAGCTGCTG 
s rabbit.ENr122_1           129099 268 +    384214 GTTGAAAACAAACTGACCTTTCGGAATCTAATGGACTGGACCAGTCCAAGAAGAATGAAATCTCA---GTATG---TTGAGGTGTTTCTTCCTCGGTTCAAGATAGAGAAGAATTATGAAATCAAAGAACACCTGCGAGCCCTGGGGCTGAGTGATATCTTTGATGAATCAAGAGCTGATCTCTCTGGCATCGCCTCGGGAGGTCGCCTCTACATATCGAAACTGATGCACAAATCATTCATAGAGGTTTCTGAGGAGGGAACCGAGGCAACAG 
s cow.ENr122_1              688328 268 -    707333 CTTGAAGACCAGCTCACTGCTGAGAAGTTAATAGCGTGGACGAGCCCACAGAATATGGGGAAGAG---AGAAG---TGGACTTATACCTGCCTCGGTTTAAAGTGGAAGAGAGCTACGACCTCGTGCCCACACTGAAAGCCCTGGGGATGGTGGATGCCTTCAATGACAAGGTTGCCAACTTCTCGGGCATGACCGGGAGACGTGATCTGGTGGTATCAAAGGTCTTCCACAAGTCCTTTGTGGAGGTGACCGAGGAGGGCACGGAGGCCGCAG 
s canFam1.chr1            16357582 268 + 124897793 CTTGAAGATCAACTCACTGCTGAGAACCTAATAGAGTGGACGAGCTCACAGAATATGAGCAATGG---GCAGG---TGGATTTATACTTACCCCGGTTCAAAGTAGAAGAGAGTTATGAGCTCAAGGCCACGCTGAAAGCCCTGGGAATGGTGGATGCCTTCAACACAAAGAGGGCCAACTTCTCAGGCATGACAGGGAGGCAGGATCTTGTGGTGTCTAAAGTCAGGCACAAGTCCTTTGTGGAGGTCACCGAAGAGGGCACGGAGGCTGCAG 
s rfbat.ENr122_1            373212 268 -    374400 CTTGAAGATCAACTCACCGCTGAGAAATTAATAGAGTGGACAAGCTCACAGAATATGAGCAAGAG---AAAGG---TGGAGTTGCGCTTGCCTCGGTTCAAAGTGGAAGAGAGCTATGCCCTCGGGGACACAATGAGAGCGCTGGGGATGGGGAATGCCTTCACTCCAGGGGACGCCGACTTCTCAGGCATGACAGGGAGCCGGGGTTTCGTGCTGTCTCAAATAGTACACAAGTCCTTTGTGGAGGTGACCGAGGAGGGCACAGAGGCCGCAG 
s shrew.ENr122_6              9914 268 -     63987 TTGGAAAGTGAAATAACTTTCGACAAATTCAACAAGTGGACGAGCAAAAGCACAATGACTGAAGA---TGACG---TTGAGGTGTTCATCCCTAAGTTCCGACTGGAAGAGAGTTATGAACTCAAACCCATACTGAGAAGCCTGGGGATGAAGGACGCCTTCGCCAAAGGCCAGGCCAATTTCTCAGGGATGTCAGAAGGGAATGAGCTATTTCTGTCCGAAGTGTTCCACAAAGCCATCGTGGATGTCAATGAGGAGGGCACTGAGGCAGCTG 
s armadillo.ENr122_1        308087 262 -    310133 CTTGAAGATAAGCTGACCGCTGAGAAATTAAAAGAGTGGGTGAGCTCACCAGTTATGCGCGAGAG---GCACG---TGCATCTGCAGTTACCTCGGTTCCGCCTGGAGGAGAGCTACGACCTCCCACCGCCGCTGCAGCACTTGGGGATGGTGCACGCCTTT------CAGGACGCCGACTTCTCTGGCATGACCGGGGGCCGGGATCTCAGAATATCTAAAATCCTGCACAAGTCCAGTGTGGAGGTGACGGAAGAGGGCACGGAGGCGGAGG 
s elephant.ENr122_1         308272 268 +    383286 GTGGAAAAGGAACTTACATATGAGAAGTTCAAAGCCTGGACAAATCCAGAAAAGATGACTCCAAG---TAAAG---TTCAAGTTTTCCTTCCCCGGTTAAAGTTGGAGGAGAGTTATGACTTGGAGTCTTTTCTTCGGCGTTTAGGAATGACTGATGCTTTTGAGGAAGTCAAGGCTGACTTTTCTGGGTTGTCAACCGAGAAGAATGTGCCCGTGTCCAGGGTTGCACACAAGTGCTTCGTGGAGGTAAATGAGGAGGGCACAGAGGCAGCTG 
s tenrec.ENr122_17            4174 268 +      6830 TTAGAAGAGGAACTGACCTACGAGAAGCTGCGAGCGTGGACAGACCCCGAGACGCTGACGCCCAG---GAAAG---CGGACGTGCTTCTCCCGCGACTGAGGCTGGCGGAGAGCTACGACCTGGAGCCCATCCTTCGGGGCCTGGGCATGACCGATGCCTTTGAAGAAGTTAAGGCCGACTTCTCCGGCATGTCTACCAAAAAGAACGTGCCCGTGTCCAAGGTGGCACACAAGTGCTTCATCGAGGTCAACGAGGAGGGCACCGAGGCGGCCG 
s monDom1.scaffold_15171   1812291 268 -   2219062 CTAGAAAGAGAAATAACCTATGAAAAACTTACTGCATGGATCAAAAAAGCCACAATGGAGAGTAA---TGATG---TTCATGTGTTCCTGCCCAAATTCAAGATGGAAAAGAATTATGAATTCAAGTCCATCCTGCAGAGCATGGGGATGAATGATGCCTTTAGCAAAATTCAAGCCAATTTTTCAGGAATGTCAGAGAGTAATGATCTCTTTCTGTCTGAAGTGTTCCATCAAGCTTCAGTAGATGTCAATGAAGAGGGCACTGAGGCAGCTG 
s platypus.ENr122_1          31120 268 -     72535 CTGGAAAATGAAATTACATATGAGAAGTTAAATGACTGGACTTGTGCTGACATGATGGATACAGG---TGAAG---TGCAAGTATATCTACCCAGATTCAAGATGGAAGAGAGTTATGACCTCAAATCCACACTGATCAGCATGGGAATGAGAGATCCCTTCAGTCAGGGCAGAGCTGATTTCTCTGGAATATCGGAGAGAAGAGATCTGTTCCTTTCGCATGTTTTTCATAAGGCTTTTGTGGAAGTCAATGAGGAAGGCACAGAAGCAGCAG 
s galGal2.chr2            80207058 268 - 147590765 CTGGAGCAGCAGCTCACCTTAGAGAAGCTCCAGGAGTGGACACGTCCAGAGCATCTATATTCCAC---TGATG---TCCATGTGCATTTGCCAAAATTTAAGCTAGAAGAAAGCTATGACCTTAAATCAGATTTATCAGCTATGGGCTTGTTGGACATATTTGACAGTGCCAAGGCTGACTTGTCAGGAATGTCAGGGGCACACGACCTTTTCCTCTCTAAAATTGTCCACAAGGCTTTTGTAGAAGTGAACGAGGAAGGCACAGAAGCTGCAG 
s tetNig1.chrUn_random   126447537 271 - 171761319 CTGGAAAATGAGCTGACTCGGGAGAAGCTTGACGAATGGACCAACAGAGAAAACATGGACGTCAGCTCTGAAG---TCCTCGTCCACCTGCCCAAATTTAAGCTGGAGGAAAACTACGAGATGAAGGAAGCTCTGGCCAAACTTGGCATGACCGACGTGTTCTGCGCAGGGAAGGCCGACCTGTCTGGTATGAACTCTGATGGAGGACTGTTCTTGTCCACGGTGGCCCATAAGGCCTTTGTGGAGGTGAACGAGGAGGGGACGGAGGCTGCTG 
s danRer2.chr19             174107 268 +  52023587 CTTGAGAAGGCACTGACCTACGAGAAGCTCATGGAGTGGACCAAACCTAGCATGATGTGTCAACA---GGAAG---TACAAGTCTCTCTGCCCAAATTCAAGACGGAGCAAACCTACGACATGAAGAGTCTTCTGGTCAGCATGGGGATGGAGGATGTGTTTGACCCACAGAAGGTTAATCTAACAGGCATGTCCTCCAGCAATGACCTGGTGCTGTCCAAGGTCATTCATAAAGCCTTTGTTGAAGTCAATGAAGAAGGAACCGAAGCGGCTG 

a score=1509913.0
s hg17.chr18              59600586 137 +  76117153 ATGGCCTCCCTTGCTGCAGCAAATGCAGAGTTTTGCTTCAACCTGTTCAGAGAGATGGATGACAATCAA--GGA------AATGGAAATGTGTTCTTTTCCTCTCTGAGCCTCTTCGCTGCCCTGGCCCTGGTCCGCTTGGGCGC 
s panTro1.chr17           56457248 137 +  73346066 ATGGCCTCCCTTGCTGCAGCAAATGCAGAGTTTTGCTTCAACCTGTTCAGAGAGATGGATGACAATCAA--GGA------AATGGAAATGTGTTCTTTTCCTCTCTGAGCCTCTTCGCTGCCCTGGCCCTGGTCCGCTTGGGCGC 
s baboon.ENr122_1           210387 137 +    593854 ATGGCCTCCCTTGCTGCAGCAAATGCAGAGTTTTGCTTCAACCTGTTCAGAGAGATGGATGATAATCAA--GGA------AATGGAAATGTGTTCTTTTCCTCTCTGAGCCTCTTCGCTGCCCTGGCCCTGGTCCGCTTGGGTGC 
s rheMac1.SCAFFOLD75029      42469 137 +    234848 ATGGCCTCCCTTGCTGCAGCAAATGCAGAGTTTTGCTTCAACCTATTCAGAGAGATGGATGATAATCAA--GGA------AATGGAAATGTGTTCTTTTCTTCTCTGAGCCTCTTCGCTGCCCTGGCCCTGGTCCGCTTGGGTGC 
s marmoset.ENr122_1         176627 137 +    677515 ATGGCCTCCCTTGCTGCAGCAAATGCCGAGTTTTGCTTCAACCTGTTCAGAGAGATAGATAACAATCAA--GGA------AATGGAAATGTGTTCTTTTCCTCTCTGAGCCTCTTCACTGCCCTGGCCCTGGTCCGCTTGGGCGC 
s galago.ENr122_1            63962 137 +    408645 ATGGCCTCCCTTGCTGCAGCAAATGCAGAATTTTGCTTCAACTTGTTCCGAGAGATGGATAACAATCAA--GGA------AATGGAAATATGTTCTTCTCCTCTCTGAGCCTCTTCACTGCGCTGGCCCTGATCCGTCTGGGGGC 
s rn3.chr13               13464817 137 + 111348958 ATGGCCTCCCTTGCTGCAGCAAATGCAGAATTTGGCTTCGACTTATTCAGAGAGATGGATAGTAGTCAA--GGA------AACGGAAATGTATTCTTCTCTTCCCTGAGCATCTTCACTGCCCTGAGCCTAATCCGTTTGGGTGC 
s mm6.chr1               107417121 137 + 195109612 ATGGCCTCCCTTGCTGCAGCAAATGCAGAATTTGGCTTCGACTTATTCAGAGAGATGGATAGTAGCCAA--GGA------AATGGAAATGTATTCTTCTCTTCCCTGAGCATCTTCACTGCCCTGACCCTAATCCGTCTGGGTGC 
s rabbit.ENr122_1            97853 137 +    384214 ATGGCCTCCCTTGCTGCAGCAAATGCAGAATTTTGCTTCAATCTCTTCAGAGAGATGGATAACAATCAC--GGC------AATGGAAATGTGTTCTTTTCCTCTTTGAGCCTCTTCACTGCCCTGGCCCTGGTCCGTTTGGGTGC 
s cow.ENr122_1              153037 137 +    707333 ATGGCCTCCCTCGCTGCAGCAGACGCGGACTTTTGCTTCAACCTGTTCAGAGAGATGGACAGCAGTCAA--GGG------GGTGAAAACGTGTTCTTTTCCTCTCTGAGCCTCTTCACTGCCCTGGCCCTGGTTCGTTTGGGTGC 
s canFam1.chr1           108653495 137 - 124897793 ATGGCCTCCCTTGCTGCAGCAAATGCAGAGTTTTGCTTCAATCTGTTCAGAGAGATGGATAACAATCAA--GGA------AGTGAAAATGTGTTCTTTTCTTCCCTGAGCATCTTCACTGCCTTGGCCCTGGTCCGTTTGGGCGC 
s rfbat.ENr122_1             91022 137 +    374400 ATGGCCTCCCTTGCGGCAGCGAATGCAGAATTTTCCATCAACTTGTTCCAAGAGATGGATAACAATCAA--GCA------AGTGGAAATGTGTTCTTTTCCTCTCTGAGCATCTTCACTGCCCTGGCCATGATCCGTTTGGGCGC 
s shrew.ENr122_4             15409 137 +     35451 ATGGCCTCCCTTGCTGCAGCAAATGCAGAATTTTGCTTCAACCTGTTCCGAGAGATGGACAATAACCAA--GGC------ACTGGAAACGTCTTCTTCTCTTCTCTGAGCATCTTCACGGCCCTGGCCCTGGTCCGGCTGGGCGC 
s armadillo.ENr122_1         58066 137 +    310133 ATGGGTTCCCTCAGCACAGCGAGTGTTGAATTTTGCTTTGATGTGTTCAAAGAGCTGAACAGTAACAAT--GGA------GGAGATAACATCTTCTTTTCTCCACTGAGTCTGCTTTATGCCCTAAGTATGGTCTTCCTTGGTGC 
s elephant.ENr122_1         104200 137 +    383286 ATGGCCTCCCTTGCTGCAGCCAATGCAGACTTTTGCTTCAACCTGTTCAGAGAGTTGGACAACAATCAA--GGG------AATGGAAATGTGTTCTTCTCCTCTCTGAGCCTCTTCACTGCCCTGGCCCTGGTCCGTCTGGGGGC 
s tenrec.ENr122_6             9033 137 -     12907 ATGGCCTCCCTTAGTGCAGCCAATGCAGAGTTTTGCTTCAACTTATTCCGCGAGATGGACAACAACCAG--GGG------AGTGGCAATGTCTTCTTCTCCTCTCTCAGCATCTTCACAGCGCTGGCGCTGATCCGCCTGGGGGC 
s monDom1.scaffold_15171   1669190 143 -   2219062 ATGGTCTCCCTTGCTGCAGCAAATGCAGAATTTTGCTTTGATCTTTTCAAAGAGATGAACACCAGTCAA--GGAAATAGCAATGGCAACGTCTTCTTTTCTCCCCTGAGTATCTTCATTGCTCTGTCCCTGGTGCGAATGGGTTC 
s platypus.ENr122_1          20523 137 -     72535 ATGGACACCCTATCGGCTTCAAACAATCAGTTTGCTCTTGATCTTAGCAAAAGGCTGGCTG--AATCAGCTGCA------GGAAAAAACATCTTCTTTTCCCCCTGGAGCATCTCTACCTCCCTGGCTATGGTCTATTTGGGTAC 
s galGal2.chr2            80110486 137 - 147590765 ATGGGCTCCATCAGTGCAGCAAATGCAGAATTTTGTTTTGATGTATTCAATGAGCTGAAAGTCCAGCAC--ACA------AATGAGAACATCTTGTATTCCCCCTTGAGCATCATTGTAGCCTTGGCCATGGTCTATATGGGAGC 
s tetNig1.chrUn_random   126454462 137 - 171761319 ATGGCAGCCATCAGCAGTTCAAACACAGCTTTTGCCTTGGACCTGCTCCGCATTCTGAGCCAAGGAAAT--CCC------AGTGGGAACATCTTCATGTCCCCGCTGAGCATCAGCTCGGCCCTGGCTATAGTTTATCTGGGAGC 
s danRer2.chr20           28300259 137 -  59369745 ATGGAGGGAGTCTCTCGTGCTAACAGTCTCTTCGCTCTGGATCTCTATCGGGCTCTGAGCGCCAGCAGT--GCT------GAGGGAAACATCTTCTTTTCTCCATTGAGCATCAGTGCAGCGCTCAGCATGGTCTACTTGGGGGC 

a score=273348.0
s hg17.chr18              59600723 31 +  76117153 TCAAGATGACTCCCTCTCTCAGATTGATAAG 
s panTro1.chr17           56457385 31 +  73346066 TCAAGATGACTCTCTCTCTCAGATTGATAAG 
s baboon.ENr122_1           210524 31 +    593854 TCGAGGTGACTGTGTCTCTCAGATTGATAAG 
s rheMac1.SCAFFOLD75029      42606 31 +    234848 TCGAGGTGACTGTGTCTCTCAGATTGATAAG 
s marmoset.ENr122_1         176764 31 +    677515 TCGAGGCGACTGTGTCTCTCAGATTGACAAG 
s galago.ENr122_1            64099 31 +    408645 TCGAGGTGACTGTGCTTCTCAGATTGATAAG 
s rn3.chr13               13464954 31 + 111348958 TCGAGGTGACTGTGCACGTCAGATTGACAAG 
s mm6.chr1               107417258 31 + 195109612 TCGAGGTGACTGTGCACGTCAGATTGACAAG 
s rabbit.ENr122_1            97990 31 +    384214 CAGAGGTGACTGTGCAGCTCAGATTGATAAG 
s cow.ENr122_1              153174 31 +    707333 GAGGGGTGACTGTGCTTCTCAGATTGATAAG 
s canFam1.chr1           108653632 31 - 124897793 ACGGGGTGATTGTGTTTCCCAGATTGATAAG 
s rfbat.ENr122_1             91159 31 +    374400 GCGAGGTGACTGTGCTTCTCAGATTGATAAG 
s shrew.ENr122_4             15546 31 +     35451 GCGGGGTGATTGTGCTGCCCAGATTGATAAG 
s armadillo.ENr122_1        256069 31 +    310133 AAGAGGAAACACAGCTGCCCAGATGTCTGAG 
s elephant.ENr122_1         104337 31 +    383286 CCGAGGGGACTGTGCAGCTCAGATTGATAAG 
s tenrec.ENr122_6             9170 31 -     12907 TCGAGGGGACTGTGCATCTCAGCTGGATCAG 
s monDom1.scaffold_15171   1669333 31 -   2219062 CAGAGGTGACTGCGCAAAGCAAATTGATAAG 
s platypus.ENr122_1          20660 31 -     72535 AAAAGGTAATACTGCTGCTCAGATAGTGGAG 
s galGal2.chr2            80110623 31 - 147590765 AAGAGGCAACACTGAGTACCAGATGGAGAAG 
s tetNig1.chrUn_random   126454599 31 - 171761319 TAAAGGAGACACGGCAGCACAGATGGCTCAG 
s danRer2.chr20           28300396 31 -  59369745 CCGAGGAGACACTGCTGGAGAAATGGAGAAG 

a score=2569019.0
s hg17.chr19              59068595 572 +  63811651 ATGCCAGTGACGGTAACCCGCACCACCATCACAACCACCACGACGTCATCTTCGGGCCTGGGGTCCCCC-ATGATCGTGGGGTCCCCTCGGGCCCTGACACAGCCCCTGGGTCTCCTTCGCCTGCTGCAGCTGGTGTCTACCTGCGTGGCCTTCTCGCTGGTGGCTAGCGTGGGCGCCTGGACGGGGTCCATGGGCAACTGGTCCATGTTCACCTGGTGCTTCTGCTTCTCCGTGACCCTGATCATCCTCATCGTGGAGCTGTGCGGGCTCCAGGCCCGCTTCCCCCTGTCTTGGCGCAACTTCCCCATCACCTTCGCCTGCTATGCGGCCCTCTTCTGCCTCTCGGCCTCCATCATCTACCCCACCACCTATGTCCAGTTCCTGTCCCACGGCCGTTCGCGGGACCACGCCATCGCCGCCACCTTCTTCTCCTGCATCGCGTGTGTGGCTTACGCCACCGAAGTGGCCTGGACCCGGGCCCGGCCCGGCGAGATCACTGGCTATATGGCCACCGTACCCGGGCTGCTGAAGGTGCTGGAGACCTTCGTTGCCTGCATCATCTTCGCGTTCAT 
s panTro1.chr20           56482145 572 +  61571712 ATGCCAGTGACGGTAACCCGCACCACCATCACAACCACCACGACGTCATCTTCGGGCCTGGGGTCCCCC-ACGATCGTGGGGTCCCCTCGGGCCCTGACACAGCCCCTGGGTCTCCTTCGCCTGCTGCAGCTGGTGTCTACCTGCGTGGCCTTCTCGCTGGTGGCTAGCGTGGACGCCTGGACGGGGTCCATGGGCAACTGGTCCATGTTCACCTGGTGCTTCTGCTTCTCCGTGACCCTGATCATCCTCATCGTGGAGCTGTGCGGGCTCCAGGCCCGCTTCCCCCTGTCTTGGCGCAACTTCCCCATCACCTTCGCCTGCTACGCGGCCCTCTTCTGCCTCTCGGCCTCCATCATCTACCCCACCACCTATGTCCAGTTCCTGCCCCACGGTCGTTCGCGGGACCACGCCATCGCCGCCACCTTCTTCTCCTGCATCGCGTGTGTGGCTTACGCCACCGAAGTGGCCTGGACCCGGGCCCGGCCCGGCGAGATCACTGGCTATATGGCCACCGTACCCGGGCTGCTGAAGGTGCTGGAGACCTTCGTGGCCTGCATCATCTTCGCGTTCAT 
s rheMac1.SCAFFOLD6742       16271 573 -     16848 ATGCCAGTGACGGTCACCCGCACCACCATCACGACCACCACGACGTCGTCCTCGGGCCTGGGGTCCCCCCACGATCGTGGGGTCCCCTCGGGCCCTGACACAGCCCCTGGGTCTCCTTCGCCTGCTGCAGCTGGTGTCTACCTGCGTGGCCTTCTCACTGGTGGCTAGCGTTGGCGCCTGGACGGGGTCCATGGGCAACTGGTCTATGTTCACCTGGTGCTTCTGCTTCTCCGTGACCCTGATCATCCTCATCGTGGAGCTGTGCGGGCTCCAGGCCCGCTTCCCCCTGTCTTGGCGCAACTTCCCCATCACCTTCGCCTGCTATGCGGCCCTCTTCTGCCTCTCCGCCTCCATCATCTACCCCACCACCTACGTCCAGTTCCTGTCCCACGGCCGTTCCCGGGACCACGCCATCGCCGCCACCTTCTTCTCCTGCATCGCTTGTGTGGCTTATGCCACCGAAGTGGCCTGGACCCGGGCCCGGCCCGGCGAGATCACTGGCTACATGGCCACCGTGCCCGGGCTGCTGAAGGTGCTGGAGACCTTCGTGGCCTGCATCATCTTCGCGTTCAT 
s marmoset.ENm007_1          83810 572 +    816697 ATGCCAGTGACGGTTACCCGCACAACTGTCACGACTACCATGACGACGTCCTCGGGCCTGGGGTCCCCC-ACCATCGTGGGGTCCCCTCGTGCCCTGACCCAGCCCCTGGGTCTCCTTCGCCTGCTGCAGCTGGTGTCCACCTGCGTGGCCTTCTCTCTGGTGGCCAGCGTGGGTGCCTGGACGGGGTTCATGGGTAACTGGTCCATGTTCACCTGGTGCTTCTGCTTCTCCGTGACTCTGATCATCCTCATCGTGGAGCTGTGCGGGCTCCAGGCCCGCTTCCCCCTGTCTTGGCGCAACTTCCCCATCACGTTCGCCTGCTATGCGGCCCTCTTCTGCCTCTCAGCCTCCATCATCTACCCCACCACCTATGTCCAGTTCATGTCCCACGGCCGTTCCCGGGACCACGCCATCGCCGCCACCTTCTTCTCCTGCGTTGCCTGCGTGGCTTATGCCACCGAAGTGTCCTGGACCCGGGCACGGCCGGGCGAGATCACAGGCTACATGGCCACCGTGCCGGGGCTGCTGAAGGTGCTGGAGACCTTCGTGGCCTGCATCATCTTTGTCTTCAT 
s galago.ENm007_1             4643 572 +   1097823 ATGCCGGTGACAGTGACCCGCACAACCATCACGACCACCACGTCGTCCTCCTCCGGCCTGGGGTCCCCA-GCCATCGTGGGGTCTCCTCGGGCCCTGGCACATCCCTTGGGCCTCCTCCGCTTGCTGCAGCTGCTGTCCACCTGCATAGCCTTCTCACTGGTGGCCAGCGTGGATGCCTGGACAGGGCCCATGGGTAACTGGTCCATGTTCACCTGGTGCTTCTGCTTTGCCGTGACCCTGGTCATCCTCATCATCGAGTTATGTGGGCTCCAGGCCCGCTTCCCCCTGTCTTGGCGCAACTTCCCCATCACCTTTGCCTGCTACGCAGCCCTCTTCTGCCTCTCAGCCTCCATCATCTACCCAACTACCTACGTCCAGTTCATGTCTCACGGCCGATCTCGGGACCACGCCATTGCCGCCACCTTTTTCTCCTGCATCGCTTGCGTGGCTTACGCCACTGAAGTGGCCTGGACCCGGGCACGGCCCGGTGAGATCACTGGCTACATGGCCACTGTGCCAGGGTTGCTCAAGGTGCTGGAGACCTTCGTGGCCTGCATCATCTTCGCGTTCAT 
s rn3.chr1               203863650 554 - 268121971 ATGCCGGTCACAGTCACCCGTACAACCATCACAACTACATCATCA------------------TCCTCC-ACCACTGTGGGGTCCGCCCGGGCGCTGACCCAGCCCCTGGGCCTCCTCCGCCTCCTGCAGCTAGTATCCACCTGTGTGGCTTTCTCACTGGTGGCCAGTGTGGGTGCTTGGACAGGGCCCATGGGTAACTGGGCCATGTTCACCTGGTGTTTCTGCTTTGCTGTTACCCTCATCATCCTGATTGTGGAGTTAGGTGGATTCCAGGCCCGCTTCCCCCTGTCATGGCGAAACTTCCCTATCACCTTCGCCTGTTACGCGGCCCTCTTCTGCCTGTCGTCTTCCATCATCTATCCCACCACCTACGTGCAGTTCCTACCTCACGGACGTTCCCGGGACCACGCCATCGCTGCCACCACCTTCTCCTGCGTTGCCTGTTTGGCGTATGCTACTGAAGTGGCCTGGACTCGTGCAAGGCCTGGTGAGATCACTGGCTACATGGCTACCGTGCCAGGGCTGCTCAAAGTGTTCGAGACCTTCGTAGCCTGCATCATCTTTGCCTTCAT 
s mm6.chrUn_random        15658799 554 -  81221341 ATGCCGGTAACAGTAACTCGTACAACCATCACGACTACAACGTCA------------------TCCTCC-ACCACTGTGGGGTCCGCTCGGGCGCTGACCCAGCCGCTGGGCCTCCTCCGCCTCCTGCAGCTAATATCCACCTGTGTGGCTTTCTCGCTGGTGGCCAGTGTGGGTGCCTGGACAGGGCCCATGGGTAACTGGGCCATGTTCACCTGGTGTTTCTGCTTTGCTGTTACCCTCATCATCCTGATTGTGGAGTTAGGTGGACTCCAGGCCCACTTCCCCCTGTCATGGCGAAACTTCCCCATCACCTTTGCCTGCTACGCGGCCCTCTTCTGCCTGTCGTCTTCCATCATCTATCCCACCACCTATGTGCAGTTCCTAGCTCATGGACGTACCCGGGACCATGCCATCGCTGCCACCACTTTCTCCTGCGTTGCCTGTTTGGCGTATGCCACTGAAGTGGCCTGGACCCGTGCAAGGCCCGGTGAGATCACTGGCTATATGGCTACCGTGCCAGGGCTGCTCAAAGTTTTTGAGACCTTCGTAGCCTGTATCATCTTTGCCTTCAT 
s canFam1.chr1            18886888 572 - 124897793 ATGCCTGTGACGGTGACCCGCACGACCATCACAACCACCACGTCGTCATCCTCAGGCCTGGGCTCCCCA-ACCATCGTGGGGTCCCCTCGGGCGCTGACCCAGCCCCTGGGCCTCCTCCGTCTGCTGCAGCTGCTGTCCACCTGTGTGGCCTTCTCCCTGGTGGCCAGTGTGGGTGCTTGGACCGGGGCCATGGGCAACTGGTCCATGTTCACATGGTGCTTCTGCTTCGCTGTGACCCTCATCATCCTAATAGTCGAGTTAGGTGGCCTCCAGTCCCGCTTCCCCCTGTCCTGGAGAAACTTCCCCATCACCTACGCCTGCTACGCTGCCCTCTTCTGCCTGTCGGCCTCCATCATCTACCCCACCACCTACGTTCAGTTCCTGTCTCATGGCCGCTCCCGGGACCATGCCATCGCCGCCACTGCCTTCTCCTGCATCGCTTGTGTGGCTTATGCCACCGAAGTGGCCTGGACCCGGGCCCGTCCCGGAGAGATCACCGGCTACATGGCCACTGTGCCGGGCCTGCTCAAGGTGCTGGAGACCTTTGTGGCCTGCATCATCTTCGCCTTCAT 
s elephant.ENm007_39         32502 572 -     37667 ATGCCGGTGACGGTGACCCGCACGACCATCACGACCACGACATCGTCGTCCTCGGGCCTGGGCTCCCAC-ACCATTGTTGGGTCCCCTCGGGCATTGACCCAGCCCCTGGGCCTCCTCCGTCTGTTGCAGCTGCTGTCCACCTGTGTCGCCTTCTCTCTGGTGGCCAGTGTGAACGCCTGGACAGGGCCCATGGGTGACTGGTCCATGTTCACCTGGTGCTTCTGCTTTGCCGTGACCCTGATCATTCTCATCGTCGAGGTCGGCGGCCTCCAGCCCCGATTCCCCCTGTCCTGGCGCAACTTCCCCATCACGTACGCCTGCTACGCTGCCCTCTTCTGCCTCTCCACCTCCATCATCTACCCCACCACCTACGTCCAGTTCCAGCCCCACGGCCGTGTTCGGGACCACGCTATCGCCGCCACTGTCTTCTCCTGCATAGCTTTCGTGGCTTATGCCACCGAAGTGGCCTGGACCCGGGCCCGGCCTGGTGAGATCACAGGATACATGGCTACTGTACCAGGGCTGCTCAAGGTGCTGGAGACCTTTGTGGCCTGTGTCATCTTCGCCTTTCT 
s tenrec.ENm007_2             1557 572 -      7471 ATGCCGGTGACGGTGACCCGCACAACCATTACGACCACCACATCGCCGGCCGCGGGCCTGGGCTCCCCC-ACCATCGTGGGGTCCCCGAGGGCGCTGACCCAGCCCCTGGGCCTTCTGCGTCTGCTGCAGCTGCTGTCTACCTGCATCGCCTTCTCCCTGGTGGCCAGTGTGGGCGCCTGGACGGGGTCCATGGGCAACTGGTCCATGTTCACCTGGTGCTTCTGCTTTTCCGTGACCCTGATCATCCTCATCGTGGAGGTGTTCGGCTTCCAGCAGCGATTCCCGCTCTCCTGGCGCAACTTCCCCATCACCTTCGCCTGCTACGCAGCCCTCTTTTGCCTCTCCACTTCCATCATCTACCCCACCACCTACGTCCAGTTCCTGCCCCACGGCCGCGTGCGGGACCACGCCATCGCAGCCACCACCTTCTCCTGCGTGGCCTTCCTGGCTTACGCCCTCGAGGTGACCTGGACCCGCGCCCGCCCGGGCGAGATCACGGGCTACATGGCCACCGTGCCGGGGCTGCTGAAGGTGCTGGAGACCTTCGTGGCCTGCATCATCTTCGCCTTCAT 
s monDom1.scaffold_12105      6407 572 +     38894 ATGGCGGTGACTGTGACCCGCACCACGGTGACCACCACCACCACCACCTCCTCCAGCCTGGGCTCCCCC-TACGTGGTGGGCTCTCCTCGGGCGCTGACGTCCAAGCTGGGCCTCCTGCGCCTGCTGCAGCTCGTGTCCACGTGCGTGGCCTTCTCCCTGGTGGCGCACGTGGGGGCCTGGGACGGGGTCATGGGCCACTGGGCCATGTTCGCCTGGTGTTTCTGCTTCGCCATGACGCTGGTGATCCTGGTGGTGGAGGTGGGCGGCCTGCAGCCGCGATTCCCGCTCTCGTGGCGCAACTTCCCCATCGCCTACGCCTGCTACGCCACGCTGCTGTGCCTGTCGGCCTCCATCATCTACCCCACCACGTACGTGCAGTTCATGGGCGAGGGCCAGAGGCGGGACCACGCCATCGCCGCCACCTTCTTCTCGTGCGTGGCCTCCGTGGCCTACGCCGTGGAGGTGGCCTGGACCCGAGCCCGGCCGGGGGAGGTCACGGGCTACATGGCCACCGTCCCCGGCCTGCTCAAGGTCTTCGAGACCTTCGTGGCCTGCATCATCTTCGCCTTCGC 
s platypus.ENm007_2           6254 569 -     22795 ATGCCAATCACGGTCACCCGCACGACCATCACCACCACCAATATGTCGTCCAGCGGC---GGCAATCAC-ACTATCGTGGGTTCCCCCCGGGCTCTGACGACTCCGCTGGGCATCGTCCGCCTGCTCCAGCTACTCTTCACCTGCATCGCCTTCTCCCTGGTGGCCCACATTGGTGGGTGGTTTGGCCCCATGGGAGACTGGTGCATGTTCTCCTGGTGCTTTTGCTTCGCCATGACGCTCGTCATCCTCCTGGTGGAGATGGGAGGGCTCCAGCCACGGGTCCCCGTGTCCTGGCGCAACTTTCCCATCACCTTTGCCTGCTATGCGGCCCTCTTCTGCCTCTCCGCCTCCATCATCTACCCGGTCACCTTCATCAAACACCACGATAAAAGCGAGGAGAAGGACTGTAGGATTGCCGCCACGGTCTTCTCCATCCTCGCCTTCCTGGCCTACACCACTGAGGTTTGCTGGACCCGAGCCCGCCCAGGTGAGGTGACGGGCTACATGGCGACCGTGCCGGGCCTCCTGAAGGTGGTGGAGACCTTCGTGGCTTGCATCATCTTCGTCTTCAT 

a score=1177830.0
s hg17.chr19              59069167 392 +  63811651 CAGCGACCCCAACCTGTACCAGCACCAGCCGGCCCTGGAGTGGTGCGTGGCGGTGTACGCCATCTGCTTCATCCTAGCGGCCATCGCCATCCTGCTGAACCTGGGGGAGTGCACCAACGTGCTACCCATCCCCTTCCCCAGCTTCCTGTCGGGGCTGGCCTTGCTGTCTGTCCTCCTCTATGCCACCGCCCTTGTTCTCTGGCCCCTCTACCAGTTCGATGAGAAGTATGGCGGCCAGCCTCGGCGCTCGAGAGATGTAAGCTGCAGCCG------CAGCCATG------CCTACTACGTGTGTGCCTGGGACCGCCGACTGGCTGTGGCCATCCTGACGGCCATCAACCTACTGGCGTATGTGGCTGACCTGGTGCACTCTGCCCACCTGGTTTTTGTCAAGG 
s panTro1.chr20           56482717 392 +  61571712 CAGCGACCCCAACCTGTACCAGCACCAGCCGGCCCTGGAGTGGTGCGTGGCGGTGTACGCCATCTGCTTCATCCTAGCGGCCATCGCCATCCTGCTGAACCTGGGGGAGTGCACCAACGTGCTACCCATCCCCTTCCCCAGCTTCCTGTCGGGGCTGGCCTTGCTGTCTGTCCTCCTCTATGCCACTGCCCTTGTTCTCTGGCCCCTCTACCAGTTCGATGAGAAGTATGGCGGCCAGCCTCGGCGCTCGAGAGATGTAAGCTGCAGCCG------CAGCCATG------CCTACTACGTGTGTGCCTGGGACCGCCGACTGGCTGTGGCCATCCTGACGGCCATCAACCTACTGGCGTATGTGGCTGACCTGGTGCACTCTGCCCACCTGGTTTTTGTCAAGG 
s marmoset.ENm007_1          84382 392 +    816697 CAGCAGCGCCCACCTGTACCAGCACCAACCCGCCCTGGAGTGGTGCGTGGCAGTCTACGCCATCTGCTTCATCCTTGCGGCCGTCGCCATCCTGCTGAACCTGGGAGAGTGCACCAACGTGCTGCCCATCCCCTTCCCCAGCTTCCTGTCGGGGCTGGCCTTGCTGTCTGTCCTCCTCTACGCCACTGCCCTCGTCCTCTGGCCACTCTACCAGTTCGACGAGAAGTATGGCGGCCAGCCCCGGCGCGCGCGAGATGTGGGCTGCGGCAG------CCGGCACA------ACTACTACGTGTGTGACTGGGACCGCCGGCTGGCTGTGGCCATCCTGACGGCCATCAACCTACTGGCGTATGTGGCCGACCTGGTGTACTCTGCCCACCTGGTTTTTGTCAAGG 
s galago.ENm007_1             5215 392 +   1097823 CAGCAGCCCCTACCTGTACCAGCACAAACCTGCCCTGGAGTGGTGTGTGGCAGTGTACGCCATCTGCTTCATACTGGCAGCTGTTGCCATCCTGTTGAACCTGGGGGACTGCACCAACATGTTGCCCATCCCCTTCCCTAGTTTCCTTTCAGGACTGGCCTTGTTGTCTGTCCTCTTCTATGCCACTGCCCTTGTCCTCTGGCCCCTCTACCAGTTTGATGAAAGGTATGGTGGCTATCCTCGGAGGTCAAGAGATGTGGGTTGCAGTAA------CAGGCACT------CCTACTACGTGTGTGACTGGGACCGCCGACTGGCTGTGGCTATTTTGACAGCCATCAACCTGTTGGCATATGTGGCTGACTTGGTGTACTCTGCCCGCCTGGTTTTTGTTAAAG 
s rn3.chr1               203864204 398 - 268121971 CAGTGAGCCGAGCCTGTACCAGCAAAGGCCGGCCCTGGAATGGTGTGTGGCAGTCTATGCCATCTGCTTCATCCTAGCAGCAGTGACCGTCCTACTCAACCTGGGGGATTGTACCAACATGCTGCCCATCCCTTTCCCTACCTTCCTGTCAGGCCTGGCCTTACTGTCTGTGCTCCTTTACGCCACTGCCATCGTCCTCTGGCCCCTCTACCAATTTGATCAGAGGTATAACAGCCAACCCCGCCGTTCAATGGATCCAAGCTGCTCTCG------TAGTTATGTACAACCCAATGAAGTGTGTAACTGGGACCGACGGCTGGCGGTGTCCATCCTGACAGGTATCAACCTGCTGGCATATGTGTCTGATCTGGTGTATTCCACCCGTCTGGTGTTCGTCAAGG 
s mm6.chrUn_random        15659353 404 -  81221341 CAGTGAGCCGCTCCTGTATAATCAGAAGCCAGCCCTGGAGTGGTGTGTGGCAGTCTATGCCATCTGCTTCATACTAGCAGGGGTGACCATCCTGCTCAACCTGGGGGATTGTACCAACGTGTTGCCCATCCCTTTCCCCACCTTCCTCTCAGGCTTGGCCTTACTCTCTGTTCTCTTTTACGCCACTGCCATCGTCCTCTGGCCCCTCTACCAATTTGATCAGAGATATCAGGGCCAACCCCGCCGTTCAATGGATCCAAGCTGCACTCGTAGTATTAGTTATATACAACCCAACACGGTGTGTTTCTGGGACCGACGACTGGCGGTGTCCATCCTGACAGGTATCAACCTGCTGGCATATGTGTCTGATCTGGTGTACTCCACTCGTCTGGTGTTCGTCAAGG 
s canFam1.chr1            18887460 392 - 124897793 CAGCAACCCCTCCCTGTACCAGCACCAGCCGGCCCTGGAGTGGTGTGTGGCCGTCTACTCCATCTGTTTCATCCTGGCGGCTGTGGCCATCCTACTGAACCTGGGGGACTGCACCAACATGCTGCCCATCTCCTTCCCCAGTTTCCTGTCGGGCCTGGCCCTGCTCTCCGTCCTGCTGTATGCCACGGCTCTGGTTCTCTGGCCGCTCTACCAGTTCAACGAGAAGTATGGTGGCCAGCCCCGTCGGTCGAGGGATGTTAGCTGCGCCGA------CAGGCACA------CCTACTACGTGTGTACCTGGGACCGCCGCCTGGCTGTGGCCATCCTGACAGCCATCAACCTGCTGGCTTACGTGGCTGACCTGGTGTACTCGGCCCGCCTGGTTTTTGTTAGGG 
s elephant.ENm007_39         33074 392 -     37667 CAGTGACCCCGGTCTGTACCAGCACCACCGGGCGCTGGAGTGGTGCGTGGCTGTGTACGCCATCTGCTTCATCTTGGCAGCCGTGGCCATCCTACTGAACCTGGGCGACTGCACCAATGCGCTGCCCATCTCCTTCCCCAGCTTTCTTTCAGGGCTGGCCTTGCTCTCCGTCCTCCTCTATGCCACCGCCCTTGTCCTCTGGCCCCTCTACCAATTCGATGAGCGCTATGGTGGCCAGCCCCAGCGGCGCAAGGATAGGTCCTGTGGCAG------CTCACACA------ACTACTATATCTGTGGCTGGGACCGCCGGCTGGCCATTGCCATCTTGACAGCCGTCAACCTGCTGGCCTATGTGGCTGACCTGGTGTACTCTGCCCGCCTGGTTTTTGTCAGGG 
s tenrec.ENm007_2             2129 392 -      7471 CAGCGACCCCTACCTGTACCAGTCCCAGGCGGCGCTGGAGTGGTGCGTGGCCGTCTATGCCATCTGCTTCATCCTGGCGGCGGTGGCCATCTTGCTGAACTTAGGCGACTGCACCAATGCGCTGCCCATCTCCTTCCCCACCTTCCTCTCGGTGCTGGCCTTCCTCTCCGTCATCCTCTACGCCACCGCCCTCGTCATCTGGCCCCTCTACCAGTTCAACGAGCGCTACGGCGGCCAGCCCCGGAGAGGCAGGGATGTGTCCTGCAGCAG------ATCACACG------CCTACTACGTCTGCACCTGGGACCGCAAGCTGACGGTCGCCATCTTGACCGGCATCAACCTGCTGGCCTACTTGGTCGACCTGGCCTACTCCAGCCGCCTGGTCTTCGTCAAGG 
s monDom1.scaffold_12105      6979 392 +     38894 CAGCGACCCGCCTATCTACCGGCGCCACTCGGCGCTCGAGTGGTGCCTGGCCGTCTACTGCATCTGCTTCATCCTGTCGGCCGTGGCCATCCTCCTGAGCCTGGGCGACTGCACGGGCCAGCTGCCCGTCTCCTTCCCCAGCTTCCTCACGGGCCTGGCCGTCCTGGCCGTGGCCCTCTACGCCTCGGCCCTGGTGCTCTGGCCTCTCTACCAGTTTGACGACCGCAAGGGCGGCCGGCCGCGCAGGCGGGACGACTCGGGCTGCCCCCG------GCACCACG------CCTTCGCCGTGTGCGACTGGGATCGCCGGCTGACCGTGGCCATCCTCACGGCCGTCAACTTCCTGGCCTACGTGGCCGACCTGGTGTACTCGGCCCGGCTGGTCTTCATCCGGG 
s platypus.ENm007_2           6823 380 -     22795 CAGCGACACCAATTCCTACGAGCGCCACGGAGCCCTCAAGTGGTGCCTGGCCGTCTACTGCATCTTCTTCATCCTTTCTCTGGCGGCCATTCTGCTCTGTGTGGGCGAATGCACCAGCTGGCTCCCCTGCTCTTTCCACACTTTCCTCAGTGGCTACACGCTCCTGGCCGTCCTGGCCTATGCCACCGCCACGGTCCTCTGGCCACTGTACCAGTTCAGCCATCGGTATGGGGGCCAGAGCCGGC------------CAAATCACTGCCT------TCGGGAAT------ACGGTACCTTATGCTTCTGGGACAAGCTGTTGGTGGTGGCTGTGCTGACCGCCGTCAACTTGCTGGCCTACTTGGCTGACCTGATTCACTCTGCCCGGCTCATCTTCGTCCACG 

a score=-160357.0
s hg17.chr19          59069559 5 +  63811651 TCTAA 
s panTro1.chr20       56483109 5 +  61571712 TCTAA 
s marmoset.ENm007_1      84774 5 +    816697 TCTAA 
s galago.ENm007_1         5607 5 +   1097823 TCTAA 
s rn3.chr1           203864602 5 - 268121971 TCTAA 
s mm6.chrUn_random    15659757 5 -  81221341 TCTGA 
s canFam1.chr1        18887852 5 - 124897793 TTTGA 
s elephant.ENm007_39     33466 5 -     37667 TCTGA 
s tenrec.ENm007_2         2521 5 -      7471 TCTGA 
s platypus.ENm007_2       7203 5 -     22795 TGTGA 

a score=79744.0
s hg17.chr19              4575595 30 -  63811651 TCTCATGAATATGCGGCACTGAAAGTGTAG 
s panTro1.chr20           4891556 30 -  61571712 TCTCGTGAATATGCGGCACTGAAAGTGTAG 
s baboon.ENm007_1          752663 30 -    895810 TCTCATGAATATGCGGCAGTGAAAGTGTAG 
s rheMac1.SCAFFOLD86224      9271 30 +     11837 TCTCATGAATATGCGGCAGTGAAAGTGTAG 
s marmoset.ENm007_1        582445 30 -    816697 TCTCACGAATATGTGGCACTGAAAGTGTAG 
s galago.ENm007_1          965809 13 -   1097823 -----------------ACTGAAAGTATAG 
s rabbit.ENm007_9           18130 30 -     43722 GCCTCTGAGCATGCGGCAGTGACCGTGTAG 
s canFam1.chr1          105902916 30 + 124897793 TCTTGTGAATGTGCAGTGCGGCAGGTGAAG 
s armadillo.ENm007_1       132025 30 -    133630 GACTCTGAGTATTCGGCAGTGAAGGCATAG 
s elephant.ENm007_36            2 29 +      1066 -CTTGTGAATGTGCAGCCCTGAAGGTGTAG 
s tenrec.ENm007_21           2731 20 +     10095 CCCGACGA----------CCGACGGAGTGG 

a score=154755.0
s hg17.chr19              4575505 90 -  63811651 ACGGCAGACC---CCCAAGGAGTGACCTAT-GCTGAGCTAAGCACCAGCGCCCTGTCTGAGG---CAGCTTCAG-ACACCACCCAGGAGCCCCCAGGA 
s panTro1.chr20           4891466 90 -  61571712 ACGGCAGACC---CCCAAGGAGTGACCTAT-GCTGAGCTAAGCACCAGCGCCCTGTCTGAGG---CAGCTTCAG-ACACCACCCAGGAGCCCCCAGGA 
s baboon.ENm007_1          752573 90 -    895810 ACGGCGGACC---CCCAAGGAGTGACGTAT-GCTGAGCTAAACATCAATGCCCTGTCTGAGG---CAGCTTCTG-ACACCACCCAGGAGCCCCCAGGA 
s rheMac1.SCAFFOLD86224      9181 90 +     11837 ACGGCAGACC---CCCAAGGAGTGACGTAT-GCTGAGCTAAACATCAATGCCCTGTCTGAGG---CAGCTTCTG-ACACCACCCAGGAGCCCCCAGGA 
s marmoset.ENm007_1        582355 90 -    816697 ACCGCAGACC---CCCAAGGAGTGACCTCT-GCTGAGCTAAGCACCCACGCCCTGTCTGAGG---CAGCTGCTG-ACACTACCCTGGAGCCCCCAGGA 
s galago.ENm007_1          965723 86 -   1097823 GCTGAAGACCTGGCCCAAGGAGTGACCTTT-GCTGAGTTAAATGCCAATGCGCCAACCGAGG---CAGTTTCTG-TCCCCACTGAGGAGTC------- 
s rabbit.ENm007_9           18048 82 -     43722 --------CC---TCCAGGGAGTGACCTGT-GCTGAACTAAACCCTACTGCAC---CTGAGGACACGGCTTCTG-TGCCCACTGAGGAGCCCCCAGGC 
s canFam1.chr1          105902833 83 + 124897793 --------CC---CCCAGGGAGTGAGCCAT-GCTGATCTAAACCCCAAGGCACCACCTAAGG---CAGCTTCTGTGCCCCACCGAGGAGTCCCCAGGA 
s armadillo.ENm007_1       131935 90 -    133630 GCTGCAGAAC---CGGATGGGGTCGACTAT-GTTGAGCTGGACCCTGGAGCCCTAAGCCAGG---GCCCTCCAG-GCTTTAAGGAGCAGCCTCTTGAG 
s tenrec.ENm007_21           2643 88 +     10095 TCTGCAGA-----CCTGGGAAGTGACCTAGAGCCAAGGTGAACTCAAGGATGCTGTGCGAGC---CAGCGTGGC-TCTTCAC-AGGGAGCCCGTACAC 

a score=135801.0
s hg17.chr19              59297998 10 +  63811651 ATGGCTGCGA 
s baboon.ENm007_1           200279 10 +    895810 ATGGCTGCGA 
s marmoset.ENm007_1         275329 10 +    816697 ATGGCCGCGA 
s galago.ENm007_1           197685 10 +   1097823 ATGGCTGCTA 
s rn3.chr1               204132123 10 - 268121971 ATGGCTGCTA 
s mm6.chr7_random          9786029 10 +  31620006 ATGGCCGGGA 
s rabbit.ENm007_18             885 10 +      4309 ATGGCTGGGA 
s canFam1.chr1            19108689 10 - 124897793 ATGGCCGGGA 
s shrew.ENm007_17            37425 10 +     37525 ATGGCCGGGA 
s armadillo.ENm007_1         50684 10 +    133630 ATGGCTGCGA 
s elephant.ENm007_47          7981 10 +     14112 ATGGCGGCTA 
s tenrec.ENm007_16            7619 10 +      8364 ATGGCGACGA 
s monDom1.scaffold_14939     33568 10 -    261239 ATGGCAGGCA 
s platypus.ENm007_3          12247 10 -     65209 ATGGCGGCGA 

a score=627044.0
s hg17.chr19               4509373 110 -  63811651 AGGAAGACTTTGGCTTTGA-------AGCAGA--------TGAGGCCCT-GGATTCCAGTTGGGTTTCTCGGGGTCCAGACAAACTGCTGCCCTACCCGACCCTGGCCAGCCCAGCCTCTGAC-TGA 
s panTro1.chr20            4827682 110 -  61571712 AGGAAGACTTTGGCTTTGA-------AGCAGA--------TGAGGCCCT-GGATTCCAGTTGGGTTTCTCGGGGTCCAGACAAACTGCTGCCCTACCCGACCCTGGCCAGCCCAGCCTCTGAC-TGA 
s baboon.ENm007_1           692428 110 -    895810 AGGAAGACTTTGGCTTTGA-------AGCAGA--------TGAGGCCCT-GGATTCCAGCTGGGTTTCTCGGGGTCCAGATAAACTGCTGCCCTACCCAACTCTGGCCAGCCCAGCCTCTGAC-TGA 
s rheMac1.SCAFFOLD11117      19131 110 -     19659 AGGAAGACTTTGGCTTTGA-------AGCAGA--------TGAGGCCCT-GGATTCCAGCTGGGTTTCTCGGGGTCCAGATAAACTGCTGCCCTACCCAACTCTGGCCAGCCCAGCCTCTGAC-TGA 
s marmoset.ENm007_1         537662 110 -    816697 AGGAAGACTTTGGCTTTGA-------AGCAGA--------CGAGGCCCT-GGATTCCAGTTGGGTGTCTCGGGGTCCAGACAAACTGCTGCCCTACCCGACCCTAGCCAGCCCACCCTCTGAT-TGA 
s galago.ENm007_1           897271 110 -   1097823 AGGAAGACTTTGCCTTTGA-------AGCAGA--------TGAGGCTCT-GGATTCCAGTTGGGTTTCTCGGGGGCCAGATAAACTGCTGCCCTACCCTACCCTAGCCAGCCCACCCTTTGAT-TGA 
s rn3.chr1                63986932 110 + 268121971 AGGAAGACTTTGGCTTTGA-------AGCAGA--------TGAGGCCTT-GGATTCAAGTTGGGTTTCCCGAGGGCCAGACAAATTGCTACCCTACCCTACCCTAGCTAGCCCACCCTTTGAC-TAA 
s mm6.chr7_random         21830910 110 -  31620006 AGGAAGACTTTGGCTTTGA-------AGCAGA--------TGAGGCCTT-GGATTCAAGTTGGGTTTCCCGAGAGCCAGACAAATTGCTACCCTACCCTACCCTGGCCAGCCCACCCTTTGAC-TAA 
s rabbit.ENm007_36            3663 126 -     45741 AGGCAGCCTGTGGCTTGGAGCTGGCCAGCAGCGGTTGGGTTGGGGCCCTCGGACCCCAGCTGCTTCCCCCAGCCGCCCACCCACCTCCCACCATAGCTGACTGTGGCAGCTTCAGCCCCAGGC-CAC 
s canFam1.chr1           105786677 110 + 124897793 AGGAAGACTTTGGCTTCGA-------AGCAGA--------TGAGGCCCT-GGACTCCAGTTGGGTTTCTCGGGGGCCAGACAAACTGCTGCCCTACCCCACCCTAGCCAGTCCCCCATTTGAC-TGA 
s armadillo.ENm007_1         80469 110 -    133630 AGGAAGACTTTGGCTTTGA-------AGCAGA--------CGAGGCTCT-GGATTCAAGCTGGGTTTCTCGGGGGCCAGACAAACTCCTACCATACCCCACCCTAGCCAGCCCCCCCTTTGAC-TGA 
s elephant.ENm007_47          2665 110 -     14112 AGGAAGACTTTGGCTTCGA-------AGCGGA--------TGAGGCCCT-GGATTCAAGCTGGGTGTCTCGGGGGCCAGACAAACTGCTGCCCTACCCCACCTTGGCCAGCTCCCCCTTCGAC-TAA 
s monDom1.scaffold_14939    226434 111 +    261239 AGGATGACTTCAGCTTCGA-------GCCAGA--------TGAGGCCCT-CACCACAGGCTGGGCAGCCCGAGGCCCTGACAAACTGCTCTCCTACCCCACTCTGGCCAGCCCTCCCTTTGACATTA 
s platypus.ENm007_4           8717 110 -      9157 AAGACGATTTTGGCTTTGA-------ACCCGA--------AGAAACGCT-GGGCTCGAGCTGGGCCTCCCGGGGCTCTGACAAGCTGCTCCAGTATCCCGGCCTGGTCAGTCCTCCCTTTGAC-TGA 

a score=127897.0
s hg17.chr19               4509363 10 -  63811651 ATTAAGGTTG 
s panTro1.chr20            4827672 10 -  61571712 ATTAAGGTTG 
s baboon.ENm007_1           692418 10 -    895810 ATTAAGGTCG 
s rheMac1.SCAFFOLD11117      19121 10 -     19659 ATTAAGGTCG 
s marmoset.ENm007_1         537652 10 -    816697 ATTAAGGTCG 
s galago.ENm007_1           897261 10 -   1097823 ATTAAGGTTG 
s rn3.chr1                63986922 10 + 268121971 ATTAAGGTCG 
s mm6.chr7_random         21830900 10 -  31620006 ATTAAGGTTG 
s canFam1.chr1           105786667 10 + 124897793 ATTAAGGTCG 
s armadillo.ENm007_1         80459 10 -    133630 ATTAAGGTCG 
s elephant.ENm007_47          2655 10 -     14112 ATCAAGGTCG 
s monDom1.scaffold_14939    226424 10 +    261239 ATCAAAGTTG 
s platypus.ENm007_4           8707 10 -      9157 ATCAAAACCG 

a score=715836.0
s hg17.chr2              118288583  85 + 243018229 ATGTCACACCTGCCGATGAAACTCCTGCGTAAGAAGATCGAGAAGCGGAACCTCAAATTGCGGCAGC---------------------GGAACC------TAAAGTTTCAGG 
s panTro1.chr13            4310009  85 + 134309081 ATGTCTCACCTGCCGATGAAACTCCTGCGTAAGAAGATCGAGAAGCGGAACCTCAAATTGCGGCAGC---------------------GGAACC------TAAAGTTGCAGG 
s baboon.ENr121_1           351346  85 +    685430 ATGTCTCACCTGCCGATGAAACTCCTGCGTAAGAAGATCGAGAAGCGGAATCTCAAATTGCGGCAGC---------------------GGAACC------TAAAGTTGCAGG 
s rheMac1.SCAFFOLD80271      32809  85 +     65232 ATGTCTCACCTGCCGATGAAACTCCTGCGTAAGAAGATCGAGAAGCGCAACCTCAAATTGCGGCAGC---------------------GGAACC------TAAAGTTGCAGG 
s marmoset.ENr121_1         367855 106 +    725777 ATGTCTCACCTGCCGATGAAACTCCTGCGCAGGAAGATCGAGAagcggaacctcaaattgcggcagcggaacctaaagttgcagcagtggaacc------taaagttgcagG 
s galago.ENr121_1           343029  85 +    644928 ATGTCTAACCTGCCCATGAAACTCCTGCGCAAGAAGATCGAGAAGCGGAACCTCAAGTTGCGGCGGC---------------------GAAACC------TAAAGCTGCAGG 
s rn3.chr13               77744300  85 - 111348958 ATGTCGCAGTTACAGATGAAACTCCTGCGCAAGAAGATCGAAAAGCGGAACGCCAAGCTGCGGCAAC---------------------GGAACC------TGAAGCTGCAAG 
s mm6.chr1                73778529  85 - 195109612 ATGTCGCAGTTACAGATGAAACTCCTGCGCAGGAAGATCGAGAAGCGGAATGCCAAGCTGCGGCAGC---------------------GAAACC------TGAAGCTGCAAG 
s cow.ENr121_1              270963  85 +    402711 ATGTCTCATTTACCGATGAAACTTCTACGCAAGAAGATCGAGAAGCGGAACCTCAAATTGCGACAAC---------------------GAAACC------TAAAGCTCCAGG 
s canFam1.chr19           21837737  84 -  56914383 ATGTCCCATCTACCCATGAAACTCCTGCGCAAGAAGATAGAGAAACGGAATCTCAAGTTGCGCCAGC---------------------GAAACC------TGAAGCTCCGG- 
s rfbat.ENr121_1            261821  85 +    531148 ATGTCTCATCTACCGATGAAACTCCTGCGCAAGAAGATCGAGAAGCGCAACCTCAAACTGCGACAGC---------------------GGAACC------TAAAGCTACAGG 
s armadillo.ENr121_1        268362  85 +    538776 ATGTCTCACCTACAGATGAAACTCCTGCGCAAAAAGATCGAGAAGCGGAATTTAAAATTGCGGCAGC---------------------GAAATC------TAAAGCTACTGG 
s elephant.ENr121_1         174761  85 +    500612 ATGTCTCACCTACCGATGAAGCTCCTGCGCAAGAAGATCGAGAAGCGGAACCTGAAGTTGCGGCAGC---------------------GAAACC------TAAAGCTCCAGG 
s tenrec.ENr121_24           16184  85 -     20207 ATGTCTCACCTGCCGATGAAACTCCTGCGCAAGAAGATCGAGAAGCGGAATCAGAAATTGCGGCAAC---------------------GAAACC------TGAAGCTACAGG 
s monDom1.scaffold_15141    668904  91 -   2865334 ATGTCGCACTTACCGATGAAGTTGCTGCGCAAGAAGATCGAGAAGCGCAATGAGAAGCTGCGTCAGA---------------------GGAACCAGCGGTTGAAGATGAAAG 
s galGal2.chr7             7730657  78 -  37338262 -------ACCTGCCCATGCGGCTGCTCCGCAAGAAGATCCACAAGAGGAACCTGAAGCTGCGGCAGC---------------------GCAACC------TGAAGCTGCGGG 
s tetNig1.chr2            18793916  84 +  19247847 ATGGCGGACTTGCAGATGAAGCTTCTTCGGAAGAAAATCCAGAAACGAAATGAAAATAGGAAAAAGC---------------------GCAAGT------TG-CTCAGTAAA 
s fr1.chrUn              153487626  84 + 349519338 ATGGCGGACCTGCAGATGAAGCTTCTTCGGAAGAAAATTCAGAAAAGAAATGAAAATAAGAAAAAGC---------------------GCAAGT------TG-CCCAGTAAA 
s danRer2.chr11           36964133  82 +  37613378 ATGGCGGACATGCAGATGAAGATTCTTCGCAAGAAAATTCAAAAGATAAGCGAAAAAAATAAACAAC---------------------GCAAAC------TG-CT--GCAAT 

a score=692917.0
s hg17.chr2              124624027 54 - 243018229 GAGGGCCGCAAGAACGAGATGCTGCTGTCCAAGGTGAAAGCGAAGG---CCTCCTGA 
s panTro1.chr13          129893165 54 - 134309081 GAGGGCCGCAAGAATGAGATGCTGCTGTCCAAGGTGAAAGCGAAGG---CCTCCTGA 
s baboon.ENr121_1           244064 54 -    685430 GAGGGCCGCAAGAATGAGATGCTGCTGTCCAAGGTGAAAGCGAAGG---CCTCCTGA 
s rheMac1.SCAFFOLD106162     12703 54 -     29563 GAGGGCCGCAAGAATGAGATGCTGCTGTCCAAGGTGAAAGCGAAGG---CCTCCTGA 
s marmoset.ENr121_1         273698 54 -    725777 GAGGGCCGCAAGAATGAGATGCTGCTGTCCAAGGTGAAAGCCAAGG---CCTCCTGA 
s galago.ENr121_1           222533 54 -    644928 GAGGGCCGTAAGAACGAGGTCCTGTTGTCCAAGATGAAAGCCAAGG---CCTCCTGA 
s rn3.chr13               33537059 54 + 111348958 GAGGGCCGAAAGAATGAGCTATTACTGTCTAAGATCAAAGCCAAGG---CCTCCTGA 
s mm6.chr1               121264397 54 + 195109612 GAGGGCCGAAAGAATGAGCTATTACTATCTAAGATCAAAGCCAAGG---CCTCCTGA 
s rabbit.ENr121_1           166427 54 -    468456 GAGGGCCGAAAGAATGAGGTGTTGCTGTCCAAGGTGAAAGGCAAGG---CCTCCTGA 
s canFam1.chr19           35014939 54 +  56914383 GAGGGCCGCAAGAATGAGGTGCTGCTGTCCAAGGTGAAAGCCAAGG---CCTCCTGA 
s rfbat.ENr121_1            205277 54 -    531148 GAGGGCCGCAAGAACGAGGTGCTGCTGTCCAAGGTGAAAGCCAAGG---CCTCCTGA 
s shrew.ENr121_2             92412 54 +    117850 GAGGGCCGCAAGAACGAGGTCCTGCTCGCCAAGGTGAAAGCCATGG---CCTCCTGA 
s armadillo.ENr121_1        134595 51 -    538776 GAGGGCCGCAAGAATGAGGTGCTGTTGTCCAAGGTGAAAGCCAAAG---CCT---GA 
s elephant.ENr121_1         230537 54 -    500612 GAGGGCCGCAAGAACGAGGTGCTGCTGTCCAAGGTCAAAGCCAAGG---CTTCCTGA 
s tenrec.ENr121_27            6328 54 +      6946 GAGGGTCGCAGGAACGAGCTGCTGCTGTCCAGGATGGGAGCCAAGA---CTTCCTGA 
s monDom1.scaffold_15141   2100651 54 +   2865334 GAATGCCGCAAGAATGAAATCCTGCTGTCCAAGGTGAAATCCCATG---TTTCCTGA 
s galGal2.chr7            29585249 54 +  37338262 GAATGTCGTAAGAACGAAATGCTGCTGTCCAAGCTGAAAGCTAGTT---CTTCCTGA 
s fr1.chrUn               30172281 57 - 349519338 GAATGTCGGAAAAACGAGATGCTGCTGTCCAAGCTGAGAGCTAAAGGAGCGTCGTAG 
s danRer2.chr11             611238 57 -  37613378 GAGTGCCGTAAGAATGAGATGCTGTTGTCTAAACTGAGGGCTAAAGGAGCTTCATAA 

a score=218849.0
s hg17.chr2              220190202 26 + 243018229 ATGCTCAAAGCGGTGATCCTGATT---------GG 
s panTro1.chr13          110354917 26 + 134309081 ATGCTCAAAGCGGTGATCCTGATT---------GG 
s baboon.ENr331_1           231517 26 +    760113 ATGCTCAAAGCGGTGATCCTGATT---------GG 
s rheMac1.SCAFFOLD5684       22101 26 -     31497 ATGCTCAAAGCGGTGATCCTGATT---------GG 
s marmoset.ENr331_1         239524 26 +    701030 ATGCTCAAAGCGGTGATCCTGATT---------GG 
s galago.ENr331_1            97776 26 +    573868 ATGCTCAAAGCTGTGATCCTGATT---------GG 
s rn3.chr9                74861356 26 + 113649943 ATGCTCAAAGCTGTGATCCTCATT---------GG 
s mm6.chr1                75727522 26 + 195109612 ATGCTCAAAGCTGTGATTCTCATT---------GG 
s rabbit.ENr331_1            89387 26 +    462957 ATGCTCAAGGCCGTGATCCTGATT---------GG 
s cow.ENr331_1              240811 26 +    534390 ATGCTCAAAGCTGTGATCCTGATT---------GG 
s canFam1.chr37           28991402 26 +  33897405 ATGCTCAAAGCTGTGATCCTGATT---------GG 
s armadillo.ENr331_1         83891 26 +    582518 ATGCTCAAAGCTGTGATCCTGATT---------GG 
s monDom1.scaffold_13176   1153603 35 +   2254034 CTGCCCCCTCCCTCAATCCCCCTTCCCCCTCAGTG 
s xenTro1.scaffold_31       647117 26 -   3348553 ATGCTGAAAGCCGTCATCCTGATT---------GG 
s tetNig1.chr2             4669484 26 -  19247847 ATGTTAAAGGCAGTAATTTTAATC---------GG 
s danRer2.chr9             6164853 26 +  44268068 ATGCTGAAGGCTGTCATTCTTATC---------GG 

a score=140861.0
s hg17.chr2              220190228 14 + 243018229 AGGCCCTCAAA--AGG 
s panTro1.chr13          110354943 14 + 134309081 AGGCCCTCAAA--AGG 
s baboon.ENr331_1           231543 14 +    760113 AGGCCCTCAAA--AGG 
s rheMac1.SCAFFOLD5684       22127 14 -     31497 AGGCCCTCAAA--AGG 
s marmoset.ENr331_1         239550 14 +    701030 AGGCCCTCAAA--AGG 
s galago.ENr331_1            97802 14 +    573868 AGGCCCTCAGA--AGG 
s rn3.chr9                74861382 14 + 113649943 AGGACCCCAGA--AGG 
s mm6.chr1                75727548 14 + 195109612 AGGCCCCCAGA--AGG 
s rabbit.ENr331_1            89413 14 +    462957 AGGCCCTCAAA--AGG 
s cow.ENr331_1              240837 14 +    534390 AGGCCCTCAAA--AGG 
s canFam1.chr37           28991428 14 +  33897405 AGGCCCTCAAA--AGG 
s armadillo.ENr331_1         83917 14 +    582518 AGGCCCCCAAA--AGG 
s monDom1.scaffold_13176   1153638 16 +   2254034 ATACACTCATGCTAAG 
s galGal2.chr7            14389393 14 -  37338262 AGGCACTGAAA--AGG 
s xenTro1.scaffold_31       647143 14 -   3348553 TGGCCCCCAGA--AGG 
s tetNig1.chr2             4669510 14 -  19247847 AGGCCCACAGA--AGG 
s danRer2.chr9             6164879 14 +  44268068 AGGCCCCCAAA--AAG 

a score=6113830.0
s hg17.chr2               22787833 787 - 243018229 AGCTGCGGCTGAGCGTGACCTGGCCCCTGGCTTCTTGGAGGCCTTTGCCACTGCAGCACTGGAGCCTGGTGATGCTGCGGCAGCCCTGACCCTGCTGCTACTGTATGAGCCGCGCCAGGCCCAGCGCGTGGCCCATGCAGATGTCTTCGCACCTGTCAAGGCCCACGTGGCAGAGCTGGAGCGGCGTTTCCCCGGTGCCCGGGTGCCATGGCTCAGTGTGCAGACAGCCGCACCCTCACCACTGCGCCTCATGGATCTACTCTCCAAGAAGCACCCGCTGGACACACTGTTCCTGCTGGCCGGGCCAGACACGGTGCTCACGCCTGACTTCCTGAACCGCTGCCGCATGCATGCCATCTCCGGCTGGCAGGCCTTCTTTCCCATGCATTTCCAAGCCTTCCACCCAGCTGTGGCC---------CCACCACAAGGG----CCTGGGCCCCCAGAGCTGGGCC------GTGACACTGGCCGCTTTGATCGCCAGGCAGCCAGCGAGGCCTGCTTCTACAACTCCGACTATGTGGCAGCCCGTGGGCGC-CTGGCGGCAGCCTCAGAACAAGAAGAGGAG---CTGCTGGAGAGCCTGGATGTGTACGAGCTGTTCCTCCACTTCTCCAGTCTGCATGTGCTGCGGGCGGTGGAGCCGGCGCTGCTGCAGCGCTACCGGGCCCAGACGTGCAGCGCGAGGCTCAGTGAGGACCTGTACCACCGCTGCCTCCAGAGCGTGCTTGAGGGCCTCGGCTCCCGAACCCAGCTGGCCATGCTACTCTTTGAACAGGAGCAGGGCAACAGCACCTGA 
s panTro1.chr13           23913590 787 - 134309081 AGCTGCGGCTGAGCGTGACCTGGCCCCTGGCTTCTTGGAGGCCTTTGCCACTGCAGCACTGGAGCCTGGTGATGCTGCGGCAGCCCTGACCCTGCTGCTACTGTATGAGCCGCGCCAGGCCCAGCGCGCGGCCCACGCAGATGTCTTCGCACCTGTCAAGGCCCACGTGGCAGAGCTGGAGCGGCGTTTCCCCGGTGCCCGGGTGCCATGGCTCAGTGTGCAGACAGCCGCACCCTCACCACTGCGCCTCATGGATCTACTCTCCAAGAAGCACCCGCTGGACACACTGTTCCTGCTGGCCGGGCCAGACACGGTGCTCACGCCTGACTTCCTGAACCGCTGCCGCATGCATGCCATCTCCGGCTGGCAGGCCTTCTTTCCCATGCATTTCCAAGCCTTCCACCCAGCTGTGGCC---------CCACCACAAGGG----CCTGGGCCCCCAGAGCTGGGCC------GTGACACTGGCCGCTTTGATCGCCAGGCAGCCAGCGAGGCCTGCTTCTACAACTCCGACTACGTGGCAGCCCGTGGGCGC-CTGGCGGCAGCCTCAGAACAAGAAGAGGAG---CTGCTGGAGAGCCTGGATGTGTACGAGCTGTTCCTCCACTTCTCCAGTCTGCATGTGCTGCGGGCGGTGGAGCCGGCGCTGCTGCAGCGCTACCGGGCCCAGACGTGCAGCGCGAGGCTCAGTGAGGACCTGTACCACCGCTGCCGCCAGAGCGTGCTTGAGGGCCTCGGCTCCCGAACCCAGCTGGCCATGCTACTCTTTGAACAGGAGCAGGGCAACAGCACCTGA 
s baboon.ENr331_1           488314 787 -    760113 AGCTGCGGCTGAGCGTGACCTGGCCCCTGGCTTCCTGGAGGCCTTTGCCACTGCAGCACTGGAGCCTGGTGATGCTGCGGCAGCCCTGACCCTGCTGCTACTGTATGAGCCACGCCAGGCCCAGCGCGCAGCCCACGCAGATGTCTTCGCACCTGTCAAGGCCCACGTGGCAGAGCTGGAGCGGCGTTTCCCCGGCGCCCGGGTGCCATGGCTCAGTGTTCAGACAGCCGCACCCTCACCACTGCGCCTCATGGATCTACTCTCCAAGAAGCACCCACTGGACACACTGTTCCTGCTGGCCGGGCCAGACACGGTGCTCACGCCTGACTTCCTGAACCGCTGCCGCATGCATGCCATCTCCGGCTGGCAGGCCTTCTTTCCCATGCACTTCCAAGCCTTCCACCCAGCTGTGGCC---------CCACCACAAGGG----CCTGGGCCCCCAGAGCTGGGCC------GTGACACTGGCCGCTTTGATCGCCAGGCAGCCAGCGAGGCCTGCTTCTACAACTCCGACTACGTGGCAGCCCGTGGTCGC-CTGGCGGCAGCCTCAGAACAAGAAGAGGAG---CTGCTGGAGAGCCTGGACGTGTACGAGCTGTTCCTCCACTTCTCCAGTCTGCATGTGCTGCGGGCAGTGGAGCCGGCGCTGCTGCAGCGCTACCGGGCCCAGACATGCAGCGCGAGGCTCAGTGAGGACCTATACCACCGCTGCCGCCAGAGTGTGCTTGAGGGCCTCGGATCCCGAACCCAGCTGGCCATGCTACTCTTTGAGCAGGAGCAGGGCAACAGCACCTGA 
s rheMac1.SCAFFOLD120758     11603 787 +     41722 AGCTGCGGCTGAGCGTGACCTGGCCCCTGGCTTCCTGGAGGCCTTTGCCACTGCAGCACTGGAGCCTGGTGATGCTGCGGCAGCCCTGACCCTGCTGCTACTGTATGAGCCGCGCCAGGCCCAGCGCGCAGCGCACGCAGATGTCTTCGCACCTGTCAAGGCCCACGTGGCAGAGCTGGAGCGGCGTTTCCCCGGCGCCCGGGTGCCATGGCTCAGTGTTCAGACAGCCGCACCCTCACCACTGCGCCTCATGGATCTACTCTCCAAGAAGCACCCACTGGACACACTGTTCCTGCTGGCCGGGCCAGACACGGTGCTCACGCCTGACTTCCTGAACCGCTGCCGCATGCATGCCATCTCCGGCTGGCAGGCCTTCTTTCCCATGCACTTCCAAGCCTTCCACCCAGCTGTGGCC---------CCACCACAAGGG----CCTGGGCCCCCAGAGCTGGGCC------GTGACACTGGCCGCTTTGATCGCCAGGCAGCCAGCGAGGCCTGCTTCTACAACTCCGACTACGTGGCAGCCCGTGGTCGC-CTGGCGGCAGCCTCAGAACAAGAAGAGGAG---CTGCTGGAGAGCCTGGACGTGTACGAGCTGTTCCTCCACTTCTCCAGTCTGCATGTGCTGCGGGCAGTGGAGCCGGCGCTGCTGCAGCGCTACCGGGCCCAGACATGCAGCGCGAGGCTCAGTGAGGACCTATACCACCGCTGCCGCCAGAGTGTGCTTGAGGGCCTCGGATCCCGAACCCAGCTGGCCATGCTACTCTTTGAGCAGGAGCAGGGCAACAGCACCTGA 
s galago.ENr331_1           439435 787 -    573868 GGCTGCAGCTGAGCGTGACCTGGCCCCTGGCTTCCTGGAGGCCTTTGCCACTGCAGCATTAGAGCCTGGTGATGCTGCAGCAGCCCTGACCCTGTTGCTACTGTATGAGCCACGCCAGGCCCAGCGGGCAGCCCATGCAGATGTCTTTGCACCTGTCAAGGCCCACGTGGCAGAGCTGGAACGGCGTTTCCCCGGTGCCCGGGTGCCATGGCTCAGTGTGCAGACATCTGTACCCTCACCACTGCGCCTCATGGATCTGCTCTCCAAGAAGCACCCACTGGACACCTTGTTCCTGCTGGCCGGGCCAGACACGGTGCTCACACCTGACTTCCTGAACCGCTGCCGCATGCATGCCATCTCTGGTTGGCAGGCCTTCTTCCCCATGCACTTCCAAGCCTTCCACCCAGCTGTGGCC---------CCACCACAAGGC----CCTGGGCCACCAGAGCTGGGCC------GCGACACAGGCCGCTTTGATCGCCAGGTGGCCAGCGAGGCCTGCTTCTACAACTCTGACTACGTGGCAGCCCGTGGGCGA-CTGGCAGCGGCCTTAGAGCAGGAGGAGGAG---CTGCTGGAGAGCCTGGATGTATACGAGCTGTTCCTGCGTTTCTCGGGACTGCATGTGCTGCGGGCAGTGGAGCCAGCACTACTACAGCGCTACCGGGCCCAGACATGCAGTGCCCGGCTCAGTGAAGATCTGTACCACCGCTGCCGCCAGAGCATGCTTGAAGGCCTTGGCTCCCGAACCCAGCTGGCCATGCTGCTCTTTGAGCAGGAGCAGGGCAACAGCACCTGA 
s rn3.chr9                38751749 784 - 113649943 GGCTGCAGCAGAGTGTGACCTGGCATCTGGCTTCCTAGAAGCCTTTGCCACTGCAGCACTGGAACCTGGCGATGCCGC---AGCCTTGACCCTGCTGCTGCTGTATGAGCCACGCCAGGCCCAGCGGGCAGCCCACGCAGATGTCTTCGCACCCGTCAAAGCCCACGTGGCCGAGCTAGAGCGGCGTTTCCCTGGTGCCCGAGTGCCCTGGCTCAGTGTACAGACATCCGCGCCCTCTCCGCTGCGCCTCATGGATCTACTCTCCAAGAAGCACCCGCTGGACACTCTGTTCCTGCTGGCCGGGCCAGACACAGTGCTCACACCCGACTTCCTGAACCGCTGCCGCATGCACGCCATCTCGGGCTGGCAAGCCTTCTTTCCCATGCACTTCCAGGCCTTCCACCCTGCTGTGGCT---------CCACCTCAGGGC----CCTGGGCCACCAGAACTGGGCC------GTGACACCGGCCACTTTGATCGTCAGGCTGCCAGCGAGGCATGCTTCTACAACTCCGACTATGTGGCGGCCCGTGGACGG-CTGGTGGCAGTCTCCGAGCAGGAGGAGGAG---CTGCTGGAGAGCCTGGATGTGTATGAGTTGTTTCTACGCTTCTCTAGCTTGCATGTGCTGAGGGCAGTGGAACCAGCCTTGCTGCAGCGCTACCGGGCCCAGCCATGCAGCGCTCGGCTCAGCGAGGACCTTTATCACCGCTGTCGCCAGAGCGTGCTTGAGGGCCTTGGCTCCCGCACCCAGCTTGCCATGCTGCTCTTTGAACAGGAACAGGGTAACAGCACCTAA 
s mm6.chr1               119343135 784 - 195109612 GGCTGCAGCGGAACGAGACCTGGCTTCTGGCTTCTTAGAAGCCTTTGCCACTGCAGCCCTGGAACCTGGTGATGCAGC---AGCCTTGACCCTGCTGCTGCTGTATGAGCCACGCCAGGCCCAGCGGGCAGCCCACTCAGACGTCTTCGCACCTGTCAAGGCCCACGTGGCAGAGCTAGAGCGGCGTTTCCCTGGTGCCCGGGTGCCCTGGCTCAGTGTGCAGACAGCAGCGCCCTCTCCACTGCGTCTCATGGATCTGCTGTCCAAGAAGCACCCACTAGACACTCTGTTCCTGCTGGCCGGGCCAGACACGGTACTCACACCTGATTTCCTGAACCGCTGCCGCATGCATGCCATCTCTGGCTGGCAGGCCTTCTTCCCCATGCACTTCCAGGCCTTCCACCCTGCTGTGGCT---------CCACCTCAGGGC----CCTGGGCCACCAGAGCTGGGCC------GTGACACCGGTCACTTTGATCGCCAGGCTGCCAGTGAGGCATGCTTCTACAACTCCGACTATGTGGCGGCCCGTGGCCGG-CTGGTGGCGGCCTCGGAGCAGGAGGAGGAG---CTGCTGGAGAGCCTGGATGTGTACGAGTTGTTTCTGCGCTTCTCCAACTTGCACGTGCTGAGAGCAGTAGAGCCAGCCTTGCTGCAGCGCTACCGGGCCCAGCCGTGCAGTGCACGGCTCAGTGAAGACCTTTACCACCGCTGTCGCCAGAGCGTACTTGAGGGCCTTGGCTCCCGCACCCAGCTTGCCATGCTGCTCTTTGAGCAGGAACAGGGGAACAGCACCTAA 
s rabbit.ENr331_1           342005 787 -    462957 GGCCGCGGCGGAGCGTGACCTGGCCGCCGGCTTCCTGGAGGCCTTCGCCACGGCGGCCCTGGAGCCCGGGGACGCCGC---AGCCCTGACCCTGCTGCTGCTGTACGAGCCCCGCCAGGCTCAGCGTGCCGCGCACTCGGACGTCTTCGCACCCGTCAAGGCCCAGGTGGCTGAGCTGGAGCGGCGATTCCCCGGCGCGCGGGTGCCCTGGCTCAGCGTGCAGACGGCCGTGCCTGCCCCCCTGCGCCTCATGGATCTCCTCTCCAAGAAGCACCCGCTGGACACACTGTTCCTGCTGGCCGGGCCGGACACGGTGCTCACCCCCGACTTCCTGAACCGCTGTCGCATGCACGCCATCTCTGGCTGGCAGGCCTTCTTCCCCATGCACTTCCAGGCCTTCCACCCGGCCGTAGCC---------CCGCCTCAGGGG----CCGGGGCCGCCCGAGCTGGGCC------GGGACACAGGTCACTTCGACCGCCAAGCGGCCAGCGAGGCCTGCTTCTACAACTCTGACTACGTGGCGGCCCGTGGGCGG-CTGGCAGCCGCCGCGGAGCAGGAGGAGGAGGAGCTACTGGAGAGCCTGGACGTGTACGAGCTGTTCCTGCGCTACTCCAGCCTGCACGTGCTGCGGGCCGTGGAGCCGGCACTGCTGCAGCACTACCGCGCCCAGACGTGCAGCGCGCGGCTCAGCGAGGACCTGTACCACCGCTGCCGCCAGAGCGTGCTGGAGGGCCTGGGCTCGCGCACCCAGCTGGCCATGCTACTCTTCGAACAAGAGCAGGGCCACAGCACCTGA 
s cow.ENr331_1              437563 787 -    534390 AGCCGCAGCCGAGCGTGACCTGGCCCCTGCCTTCCTGGAGGCCTTCGCCACGGCGGCGCTGGAGCCTGGCGATGCTGCCGCAGCCCTGACCCTACTGCTACTGTATGAGCCCCGACAGGCCCAGCGGGCGGCCCACGCCGATGTCTTTGCCCCCGTCAAGGCCCATGTGGCAGAGCTGGAGCGGCGTTTCCCCGGTGCCCGGGTGCCCTGGCTCAGCGTGCAGACAGCCGCACCCTCACCACTGCGCCTCATGGATCTCCTCTCCAAGAAGCACCCGCTGGACACGCTGTTCCTGCTGGCCGGGCCAGACACGGTGCTCACGCCTGACTTCCTGAACCGCTGCCGCATGCATGCCATCTCTGGCTGGCAGGCCTTCTTTCCCATGCACTTCCAGGCCTTCCACCCGGCCGTGGCC---------CCACCCCAGGGC----CCGGGACCCCCCGAACTGGGCC------GCGACACAGGCCGTTTCGATCGCCAGGCGGCCACCGAGACCTGCTTCTACAACTCTGACTACGTGGCGGCCCGAGCACGG-CTGGCAGCGTCCTCGGACCAGGAGGAGGAG---CTGATGGAGAGCCTGGATGTGTACGAGCTGTTCCTGCGTTTCTCCAGCCTGCATGTGCTGCGGGCGGTGGAGCCGGCGTTGCTGCAGCGCTATCGGGCACAGACGTGCAGTGCGCGGCTCAGCGAAGACCTATACCACCGCTGCCGCCAGAGCGCGCTCGAGAGCCTCGGCTCCCGCACGCAGCTGGCCATGCTGCTCTTTGAGCAGGAGCAGGGCAACAGCACCTGA 
s canFam1.chr37            4867817 787 -  33897405 GGCTGCGGCCGAGCGGGACCTGGCCCCTGGCTTCCTGGAGGCCTTCGCCACCGCGGCGCTGGAGCCGGGTGACGCGGCTGCAGCCCTGACCCTGCTGCTCCTGTACGAGCCACGACAGGCCCAGCGGGCGGCCCACGCAGATGTCTTTGCGCCTGTCAAGGCCCACGTGGCGGAACTCGAGCGGCGTTTCCCGGGTGCCCGGGTGCCCTGGCTCAGCGTGCAGACAGCTGCACCCTCGCCGCTGCGCCTCATGGACCTGCTCTCCAAGAAGCACCCGCTGGACACGCTGTTCCTGCTGGCCGGGCCCGACACGGTGCTCACGCCCGACTTCCTGAACCGCTGCCGCATGCACGCCATCTCTGGCTGGCAGGCCTTCTTCCCCATGCACTTCCAGGCCTTCCAcccggccgtggcg---------cccccccagggc----cccgggcccccggAGCTGGGCC------GAGACACGGGCCGCTTCGACCGCCAGGCGGCCAGCGAGGCCTGCTTCTACAACTCCGACTACGTGGCAGCCCGCGGACGG-CTGGCAGCGGCCTCGGAGCAGGAAGAGGAG---CTGCTGGAGAGCACGGACGTGTACGAGCTGTTCCTGCGCTTCTCGGGCCTACACGTGCTGCGCGCCGTGGAACCAGCGCTGCTGCAGCGCTACCGGGCGCAGGCGTGCAGCGCGCGGCTCAGCGAGGACCTGTACCACCGCTGCCGCCAGAGCGAGCTGGAGGGCCTGGGCTCCCGCACCCAGCTGGCCATGCTGCTCTTTGAGCAGGAGCAGGGCAACAGCACCTGA 
s rfbat.ENr331_1            395725 787 -    579985 GGCTGCGACTGAGCGTGACCTGGCCCCTGGCTTCCTGGACGCCTTTGCCTCAGCAGCACTGGAGCCTGGTGATACTGCAGCAGCCCTGACCCTGCTGCTACTGTATGAGCCACGACAGGCCCAGCGGGCAGCCCATGCAGATGTCTTTGCACCTGTCAAGGCCCACGTGGCAGAGCTGGAGCAGCGTTTCCCTGGTGCCCGGGTGCCCTGGCTCAGTGTGCAGACAGCTGCCCCCTCACCACTGCGCCTCATGGATCTGCTCTCCAAGAAGCACCCGCTGGACACACTGTTCCTGCTGGCTGGGCCAGACACAGTGCTCACGCCGGACTTCCTGAACCGCTGCCGCATGCATGCCATCTCTGGCTGGCAGGCCTTCTTTCCCATGCACTTCCAGGCTTTCCACCCAGCCGTGGCC---------CCACCACAGGGC----CCGGGGCCCCCGGAGCTGGGCC------GAGACACGGGCCACTTTGATCGCCAGGCAGCCAGTGAGGCCTGCTTCTACAACTCCGACTATGTGGCAGCCCGTGGGCGG-CTGGCTGCTGCCTTGGAGCAGGAGGAGGAG---CTCCTGGAGAGCATGGATGTGTATGAGCTGTTCCTGCGCTTCTCTGGCCTGCATGTGCTGCGGGCAGTGGAGCCAGCGCTGCTGCAGCGCTACCGGGCCCAGACATGCAGCGCGCGGCTCAGCGAGGACTTGTACCATCGCTGTCGCCAGAGCACGCTCGAGGGCCTGGGCTCCCGCACCCAGCTCGCCATGCTGCTCTTTGAGCAGGAGCAAGGCAACAGCACCTAA 
s armadillo.ENr331_1        461362 787 -    582518 GGCCGCGGCCGAGTGTGACCTGGCCCCTGGCTTCCTGGAGGCCTTCGCGGCTGCAGCCCTGGAGCCTGGTGACACCGCAGCCGCCCTGACCCTGCTGCTACTGTATGAGCCTCGCCAGGCCCAGCGCGCAGCCCACGCTGACATTTTCGCACCCGTCAAAGCCCACGTGGCAGAGCTGGAGCGGCGTTTCCCTGGCGCCCGGGTGCCCTGGCTCAGTGTGCAGACGGCTGCACCCTCAACCCTGCGCCTCATGGACCTGCTCTCCAAGAAGCACCCCCTGGACACGCTGTTCCTGCTGGCCGGGCCGGACACAGTGCTCACGCCTGACTTCCTGAACCGCTGCCGCATGCATGCCATCTCCGGCTGGCAGGCCTTCTTTCCCATGCACTTCCAGGCCTTCCACCCGGCGGTGGCC---------CCCCCACAGGGC----CCCGGGCCACCGGAGCTGGGCC------GCGACACGGGCCGCTTCGACCGCCAGGCGGCCAGCGAGGCCTGCTTCTACAATTCCGACTACGTGGCGGCCCGCGGGCGA-CTGGCAGCGGCCTTGGAGCAGGAGGAGGAG---CTGCTGGAGAGCCTGGACGTGTATGAGCTGTTCCTGCGCTTCTCGGAGCTGCACGTGCTGCGGGCCGTGGAGCCCTCGCTGCTGCAGAGATACCGGGCCCCGATGTGCAGCGCGCAGCTCAGCGAGGACCTGTACCACCGCTGCCGCCAGAGCGCACTGGAGGGCCTCGGCTTGCGCACCCAGCTCGCCATGCTGCTCTTCGAGCAGGAGCAGGGCAATAGCACCTGA 
s monDom1.scaffold_13176   1058656 787 -   2254034 GGCGGCCAGCGATCTCGATATGGCGCCCCGCTTCCTGGAGGCCTTTGCCGCTGCTGCTCTTGAGCCGGGGGACACTGCGGTGGCTCTGACCCTGCTGCTGCTCTACGAGCCCCGTCAAGCCCAGCATGTGACCCATGCTGACATCTTCGCTTCAGTGAAGAGCCGTGTGGCAGAGCTGGAGCGACGCTACCCTGGCTCCCAAGTCCCCTGGCTCAGCGTGCAGACAGCTGTCCCAACGCCCCTTCGTCTGCTGGACCTGCTCTCCAAGAAACACCCCCTGGACACGCTCTTCCTGCTGGCGGGGCCAGCCACGGTCCTCACTTCTGATTTCCTGAACCGATGTCGGATGCACGCCATCGCGGGATGGCAGGCTTTCTTCCCCATGCACTTCCAGGCCTACCATCCTGCCGTGGCG---------CCCCCACAGGCC----CCAGGGACCCCTGAGCTGGGCC------GGGATACGGGACACTTTGACCGCCACGTAGCCAGCGAAGCCTGCTTCTACAACTCGGACTACGTGGCAGCCCGAGGCCAG-CTGGCAAAAGCCTGGGAGCAGGAAGAGGAG---ATGCTGGAGGGCCTGGATCTATATGAATTCTTCCTGAAGTTCTCCAGCCTGCATGTGCTTCGAGCTGTGGAGCCGGCCCTGCGGCAGCCCTACCGACACCAGCCCTGCAGTGCCCAGCTCAGTGAGAGCCTGTATCACCACTGCCGCCAGAGCGTCTTCGAGGGTCTGGGCTCCCGCTCCCAGCTAGCCATGCTGCTCTTCGAGCAAGAGCAGGGAAACAGCACCTGA 
s galGal2.chr7            22907113 790 +  37338262 CACTGCCCACGAACGGGACCATGCCGCACGCTTCCTGGAGGCCTATGCGGCAGCTGCCTTTGAGAGCAGCGAGAACGC---GGTGCTCACCTTCCTGTTCATCTACGATCCATTCGAGGCCCAGCAGGTGACCCAGAACGACATCTTTGCCCCTGTGAAGGCCCAGATCACAGAGTATGAGCGCAAGTATGCCGAGGTGAAGATCCCGTGGATCAGCGTGAAGACAGATGCCCCCTCCCAAATCAAGGTCATGGACATCATCTCCAAGAAGCATCCCGTGGACACGCTGTTCTTTGTGGCCGGTGTGGGCACAGAGGTCACCGTCGACTTCCTGAACCGCTGCCGGATGAACACCATCAACAACTGGCAGGTCTTCTTCCCCATCCACTTCCAGGGCTACAACCCCGCCGTCGCCTA-------CCACAACCAGGC----ACCG--CCTGCCACACTGGACCTCCTGCGGGATGCAGGGCGCTTTGACCGCGATGTCTTCCATGAGGCCTGCTTCTACAATGCTGACTACATGGCAGCACGCACCCGC-ATGGCGGGTGACGTGCAGGAGAATGAGGAC---ATCCTGGAGACCCTGGACATCTACGATATGTTCATCAAGTACTCCAACCTTCACGTCTTCCGGGCCGTGGAGCCCGCCCTGCTGCAGCACTACCGGCACCAGGCCTGCAACCCGCGGCTCAGTGAGGAGATCTACCACCGCTGCGTGCAGAGCAGCCTGGAGGGCGTTGGGTCCCGCTCCCAGTTGGCCATGGTGCTCTTTGAGCAGGAGCAGGGGAACAGCACCTGA 
s xenTro1.scaffold_1262     138034 787 +    226782 GACGGCGCAGGATCGGGAACACGCCGCTCGGTTCCTCCAGGCCTTCACGG--ACATCCAAGGCAACGAGAACTCCCTC-------CTCACCTTGCTTTTTATCTACGACCCGTTCCAAGCCCAGCAGGTCAGCCAGAACGACATATTTGGCCAAGTCAAAAGTATCATCGCAGAATACGAGCGCAAATACCGTGACCTTAAAATCCCTTGGATCAGCGTGAAGACCGACGCTCCCTCCCAGATCCGTTTAATGGACATCATCTCCAAAAAGCACCCGGTAGACACGCTCTTCTTCCTCGCCGGCGTGGGCAGCCACTTGAACACCGAGTTCCTCAACCGCTGTCGTATGAACACCATCAACAACTGGCAGGTCTTCTTCCCCATCCACTTCCAAGGCTACAACCCCGAGGTGTCGGAGCACGGGCAGCAGCCGCAT----TCTGCCACGCTGGAGCTGTTGC------GGGACGCCGGGCGCTTCGACAGGGACGTGTTCGAGGAGTCCTGCTTCTACAATGCCGACTACATGTCCGCCCGCTCCAAA-ATGAGCGCCGACGCTCAAGAAAACGAAGAG---ATTCTGGAGATGTTGGACATTTACGAGATGTTCATCCGCTACTCCGGGCTCCACGTCTTCCGGGCCGTGGAACCGGCGCTGCTTCAGCAATACAGGTCGAGGGCCTGTAACCCGCGGCTCAGCGAGGAGATCTATCACCGGTGCGTGCAGAGCAATCTGGAGGGTCTGGGCTCTCGGTCTCAGCTTGCCATGCTGCTGTTTGAGCAAGAGCAGGGGAATAGCACTTGA 
s tetNig1.chr2            14458621 791 +  19247847 CACCCTGCAGGAGCGCGGTTTCGCCAGCCGTTTCCTGGAAGTGTTTGCCTCCAAAGCTTTGGAGACCAGCGAAAACGC---TATCCTGACATTTCTGTTCATCTACGACCCCGTGGAGGCGCAGCAGGTTAACCAGAACGACATCTTCGCCGGCGTGAAGAGCCAGATCAGCGCGTACGAACACAAGCACCCCGCTGCCAAGATTCCCTGGATCAGCGTCAAGACGGAAACGCCGTCCCAGATTAAGTTCATGGACATCATCTCCAAGAAGCACCCCGTGGACACGCTCTTCTTCCTGGCTAACGCTAACACGGAAATCAACTCGGAGTTCCTCAACCGCTGCCGCATGAATTCCATCAACAACTGGCAGGTGTTCTTCCCAGTCCACTTCCAGGACTACAAGCCGGAAGTGGCCTA-------TCACAAGCAGCCGCCGCCCGTCGCCACCCACCTGGTCA------AGGAGGCGGGGCATTTCGACCGCCTGTCTTTCGGAGAGGCCTGTTTTTACAACTCGGACTACATGGCGACGCGCACGCGGAATGGTGGCAGACGTGCAGGAGAACGAGGAG---ATCCTGGAGACGCTGGACATCTACGACATGTTCGTGAAGTACTCGGACCTGCACGTGTTCAGGGCGGTGGAGCCGGCGCTGCACCAGAAGTACGCGTACCAGGTGTGCAACCCACGGCTGAGCGAGGACACCTACCACCGGTGCATCCAGAGCAACCTGGAGGGCCTGGGCTCCCGCTCGCAGCTCGCCATGCTGCTCTTTGAGCAGGAACAAGGGAACAGTACCTGA 
s danRer2.chr9            37579402 790 -  44268068 TACTCTTCAAGATCGAGATTACGTTCATCAGTTTTTAGAAGTGTATGCCACAAATGCATTCGAAACCAGCGAGAATGC---GATCTTGACGTTCCTCTTCATCTACGATCCAATAGAGGCCCAACAAGTCAACCAGAATGACATCTTCTCCAGCATCAAAGCACAAATCAGTACGTACGAACATCGATATCCTGCAGTCAAAATCCCCTGGATTAGTGTTAAAAGCGAAAGTCCGTCTCAAATCAAATTCATGGACATCATCTCCAAGAAGCACCCGGTTGACACGTTGTTCTTCATTGCGACGGTAAAAACAAGCATCAGTTCAGAGTTCCTCAATCGCTGTCGGATGAACTCCATCAACAACTGGCAGGTGTTCTTTCCAATCCACTTCCAGTACTACAATCCTGACATCGCTTA-------TCACAACCAGCCTCTTCCCAGTGCGTTGGATTTGGTCA------AAGAGGCTGGTCTTTTCGATCGCAGCTCCTTCACCGAAGCTTGCTTCTACAACTCGGACTACATGGCGACCCGTACCCGG-ATGTCATCGGATGTGCTGGAGAATGAGGAG---ATCCTGGAGAACCTTGATATCTATGACATGTTCGTCAAATACTCTGGCCTCCATGTTTTCCGAGCAGTGGAGCCGGCCCTGCATCAGAAATACAGCTACCAAACGTGTAATCCTCGCCTTAGTGAAGAAATCTACCAGAGGTGTGTACAAAGCACCCTGGATAGCCTTGGATCACGCTCTCAGCTCGCCATGCTGCTGTTTGAACAGGAACAGGGCAACAGTACTTAA 

a score=4269263.0
s hg17.chr2               22787360 473 - 243018229 TGGGAGATCCAGAATACCAGCCATCTGGCCGTTGATGGGGACCAGGCAGCTGCTTGGCCCGTGGGTATTCCAGCACCATCCCGCCCGGCCTCCCGCTTTGAGGTGCTGCGCTGGGACTACTTCACGGAGCAGCACGCTTTCTCCTGCGCCGATGGCTCACCCCGCTGCCCACTGCGTGGGGCTGACCGGGCTGATGTGGCCGATGTTCTGGGGACAGCTCTAGAGGAGCTGAACCGCCGCTACCACCCGGCCTTGCGGCTCCAGAAGCAGCAGCTGGTGAATGGCTACCGACGCTTTGATCCGGCCCGGGGTATGGAATACACGCTGGACTTGCAGCTGGAGGCACTGACCCCCCAGGGAGGCCGCCGGCCCCTCACTCGCCGAGTGCAGCTGCTCCGG-CCGCTGAGCCGCGTGGAGATCTTGCCTGTGCCCTATGTCACTGAGGCCTCACGTCTCACTGTGCTGCTGCCTCT 
s panTro1.chr13           23913117 473 - 134309081 TGGGAGATCCAGAATACCAGCCGTCTGGCCGTTGATGGGGACCGGGCAGCTGCTTGGCCCGTGGGCATTCCAGCACCATCCCGCCCGGCCTCCCGCTTTGAGGTGCTGCGCTGGGACTACTTCACGGAGCAGCACGCTTTCTCTTGCGCCGATGGCTCACCCCGCTGCCCACTGCGTGGGGCTGACCGGGCTGATGTGGCCGATGTTCTGGGGACAGCTCTAGAGGAGCTCAACCGCCGCTACCACCCGGCCTTGCGGCTCCAGAAGCAGCAGCTGGTGAATGGCTACCGACGCTTTGATCCGGCCCGGGGTATGGAATACATGCTAGACTTGCAGCTGGAGGCACTGACCCCCCAGGGAGGCCGCCGGCCCCTCACTCGCCGAGTGCAGCTGCTCCGG-CCACTGAGCCGCGTGGAGATCTTGCCTGTGCCCTATGTCACTGAGGCCTCACGTCTCACTGTGCTGCTGCCTCT 
s baboon.ENr331_1           487841 473 -    760113 TGGGAGATCCAGAATACCAGCCGTCTGGCCATTGATGGTGACCGGGCAGCTGCCTGGCCTGTGGGCATTCCAGCACCATCCCGCCCGGCCTCCCGCTTTGAGGTGCTGCGCTGGGACTATTTCACAGAGCAGCACGCTTTCTCCTGCGCCGATGGCTCACCCCGCTGCCCACTGCGTGGGGCTGATCGGGCTGATGTGGCTGATGTTCTGGGAACAGCTCTAGAGGAGCTCAACCGCCGCTACCACCCGGCCTTGCGGCTCCAGAAGCAGCAACTGGTGAATGGCTACCGACGCTTTGATCCAGCCCGGGGTATGGAATACACACTGGACTTACAACTGGAGGCACTGACCCCCCAGGGAGGCCGCCGGCCCCTCACTCGCCGAGTACAGCTGCTCCGG-CCACTGAGCCGCGTGGAGATCTTGCCTGTGCCCTATGTCACTGAGGCCTCACGTCTCACTGTGCTCCTGCCTCT 
s rheMac1.SCAFFOLD120758     11130 473 +     41722 TGGGAGATCCAGAATACCAGCCGTCTGGCCGTTGATGGTGACCGGGCAGCTGCCTGGCCTGTGGGCATTCCAGCACCATCCCGCCCGGCCTCCCGCTTTGAGGTGCTGCGCTGGGACTATTTCACGGAGCAGCACGCTTTCTCCTGCGCCGATGGCTCACCCCGCTGCCCACTGCGTGGGGCTGATCGGGCTGATGTGGCTGATGTTCTGGGGACAGCTCTAGAGGAGCTCAACCGCCGCTACCACCCGGCCTTGCGGCTCCAGAAGCAGCAACTGGTGAATGGCTACCGACGCTTTGATCCAGCCCGGGGTATGGAATACACACTGGACTTGCAACTGGAGGCACTGACCCCCCAGGGAGGCCGCCGGCCCCTCACTCGCCGAGTACAGCTGCTCCGG-CCGCTGAGCCGGGTGGAGATCTTGCCTGTGCCCTATGTCACTGAGGCCTCACGTCTCACTGTGCTCCTGCCTCT 
s galago.ENr331_1           438962 473 -    573868 TGGGAAATCCAGAACACCAGCCATCTGGCAGTTGATGGGGAGCGGGCAGCTGCCTGGCCTGTGGGCATCCCAGCACCATCCCGCCCAGCCTCTCGCTTTGAGGTGCTGCGCTGGGACTACTTCACGGAGCAGCATGCTTTCTCCTGCGCTGATGGCTCACCCCGCTGCCCATTGCGTGGGGCTGATCGGGCTGATGTGGCTGATGTCCTGGGAGCAGCCCTGGAGGAACTCAATCGCCGCTACCACCCGGCCCTGCGGCTCCAGAAGCAGCAGCTGGTTAATGGTTACCGCCGTTTTGATCCAGCCCGGGGTATGGAGTACATGCTGGACTTGCAGCTGGAGGCCCTGACCCCTCAGGGTGGCCGGTGGCCCCTCACTCACCGGGTGCAGCTGCTCCGG-CCTCTGAGCCGTGTGGAGATCTTACCTGTGCCCTATGTCACTGAGGCCTCCCGTCTCACTGTGCTGCTGCCTCT 
s rn3.chr9                38751276 473 - 113649943 TGGGAGATCCAGAATACCAGCAGACTGGCTGCTGATGGGGAGAGGGCTTCTACCTGGCCAGTGGGCATTCCAGCGCCGTCTCGCCCTGCCTCGCGCTTTGAGGTTCTGCGCTGGGACTACTTCACGGAACAGCACACTTTCTCCTGTGCTGACGGCTCACCCCGCTGCCTGCTGCGTGGGGCCGACCAGGCCGATGTGGCTGATGTCCTAGGAACAGCCTTAGAGGAGCTCAACCGCCGTTACCAGCCAGCACTGCGGCTCCAGAAGCAACAGCTGGTGAATGGCTACCGGCGTTTTGATCCAGCCCGAGGTATGGAGTACACACTAGACTTGCAGCTGGAAGCGCTGACGCCCCAGGGTGGCCGCTGGCCCCTCACCCACAGGGTACAGCTCCTTCGG-CCCTTGAGCCGAGTGGAGATCTTGCCTGTGCCCTATGTCACCGAGGCTTCTCGGGTCACTGTGCTGCTGCCTCT 
s mm6.chr1               119342662 473 - 195109612 TGGGAGATCCAGAATACCAGCCGACTGGCTGCTGATGGGGAGAGAGCCTCTGCCTGGCCAGTGGGCATCCCAGCACCGTCTCGCCCTGCCTCACGCTTTGAGGTTCTGCGCTGGGACTACTTCACAGAACAATACGCGTTCTCCTGCGCCGATGGCTCTCCCCGCTGCCCGTTGCGTGGGGCCGACCAGGCTGATGTGGCTGACGTCCTGGGGACAGCCTTAGAGGAGCTCAACCGCCGTTACCAGCCAGCGCTGCAGCTCCAGAAGCAACAGCTGGTGAACGGCTACCGGCGTTTTGATCCAGCCCGAGGCATGGAGTACACACTAGACCTGCAGCTGGAAGCGCTGACACCCCAGGGTGGCCGCTGGCCCCTCACCCGCAGGGTGCAGCTCCTTCGG-CCCTTGAGCCGAGTGGAGATCTTGCCTGTACCCTATGTCACCGAGGCTTCTCGGCTCACTGTGCTACTGCCGCT 
s rabbit.ENr331_1           341532 473 -    462957 TGGGAGATCCAGAACACCAGCCGCCTGGCCGCTGACCGGGAGCGGGCCACCGCCTGGCCCGTGGGGATCCCGGCGCCCTCGCGGCCGGCGTCCCGCTTCGAGGTGCTGCGCTGGGACTACTTCACGGAGCAGCACGCCTTCTCCTGTGCCGACGGCTCGCCCCGCTGCCCGCTGCGTGGGGCCGATCGGGCGGATGTGGCCGACGTACTGGGAGCCGCCCTGGAGGAGCTCAATCGCCGCTACCACCCGGCCCTGCGGCTCCAGAAGCAGCAGCTGGTGAACGGCTACCGGCGCTTTGACCCGGCGCGGGGTATGGAGTACACGCTGGACTTGCAGCTGGAGGCGCTCACCCCGCAGGGCGGCCGCCGGCCCCTCACCCGCCGGGTGCAGCTGCTCCGG-CCCCTGAGCCGTGTGGAGATCTTGCCCGTGCCCTACGTCACCGAGGCCTCACGCCTCACCGTGCTGCTGCCTCT 
s cow.ENr331_1              437090 473 -    534390 TGGGAGATCCAGAACACCAGCCGCCTGGCAGCGGATGGGGAGCGGGCAGCTGCCTGGCCAGTGGGCATTCCAGCACCGTCTCGCCCCGCCTCCCGCTTTGAGGTGCTGCGCTGGGACTATTTCACAGAGCAACATGCTTTCTCCTGCGCTGATGGCTCCCCACGCTGCCCGCTGCGTGGGGCTGACCGGGCTGATGTGGCGGACGTTCTGGGGGCAGCCCTAGAGGAGCTCAACCGCCGATACCACCCAGCCCTGCGGCTCCAGAAACAGCAACTGGTTAATGGCTACCGACGCTTCGATCCTGCCCGGGGGATGGAGTACACGCTGGACTTGCAGCTGGAGGCACTGACCCCCCAGGGGGGCCGCAGGCCCCTCACCCGCCGGGTGCAGCTGCTACGG-CCACTGAGTCGCGTGGAGATCTTGCCCGTGCCCTACGTCACCGAGGCCTCGCGTCTCACTGTGTTACTCCCACT 
s canFam1.chr37            4867344 473 -  33897405 TGGGAGATCCAGAACACCAGCCACCTGGCAGCTGACGGCGAGCGGGCGGCCGCCTGGCCCGTGGGCATTCCCGCACCATCCCGCCCGGCCTCTCGCTTCGAGGTGCTGCGCTGGGACTATTTCACAGAGCAGCACGCCTTCTCCTGCGCCGACGGCTCGCCCCGCTGCCCGCTGCGAGGGGCCGACCGGGCCGACGTGGCCGACGTGCTGGGTGCCGCCCTGGAAGAGCTCAACCGCCGCTACCACCCGGCCCTGCGGCTCGAGAAGCAGCAGCTGGTCAACGGCTACCGGCGCTTCGATCCTGCCCGCGGCATGGAGTACACGCTGGACCTGCAGCTGGAGGTGCTGACCCCGCAGGGCGGCCGCCGGCCCCTCACCCGCCGGGTGCAGCTGCTGCGG-CCCCTGAGCCGCGTGGAGATCCTGCCTGTGCCCTACGTCACCGAGGCGTCGCGTCTCACCGTGTTGCTGCCTCT 
s rfbat.ENr331_1            395252 473 -    579985 TGGGAGATCCAGAACACTAGCCGCCTGGCAGCTGATGGGGAGCGTGCAGCCTCCTGGCCCATAGGCATTCCAGCACCATCTCGTCCAGCTTCCCGCTTTGAGGTGCTACGTTGGGACTATTTCACTGAGCAGCATGCTTTCTCCTGTGCTGATGGCTCGCCCCGCTGCCCTCTGCGTGGGGCTGACCGGGCTGACGTGGCTGACATTCTGGGGGCAGCCTTGGAAGAGCTCAACCGCCGCTACCACCCAGCCCTGCGGCTCCAGAAGCAGCAGCTGGTTAATGGCTACCGACGCTTTGATCCTGCCCGGGGTATGGAGTACACACTGGACTTGCAGCTGGAGGCACTGACCCCCCAGGGCGGCCGCTGGCCCCTCACCCGCCGGGTGCAGCTGCTACGG-CCACTGAGCCGTGTGGAGATCTTGCCTGTGCCCTATGTCACCGAGGCCTCACGTCTCACCGTGTTACTTCCTCT 
s shrew.ENr331_31              384 473 +      4063 TGGGAGATCCAGAACACCAGCCGTCTGGCCGCTGATGGGGATCGGGCAGCCGCCTGGCCCGTGGGCATCCCCGCCCCCTCGCGCCCCGCCTCCCGCTTCGAGGTGCTGCGCTGGGACTATTTCACGGAGCAGCACGCGTTCTCCTGCGCGGACGGCTCGCCCCGCTGCCCGCTCCGAGGGGCCGACCGCGCCGACGTGGCGGACGTCCTGGGGGCTGCTCTGGAAGAGCTCAACCGCCGCTACCACCCAGCTCTGCGGCTCCAGAAGCAGCAGCTGGTGAACGGCTACCGCCGCTTTGACCCGGCGCGAGGCATGGAGTACACGCTGGACTTGCAGCTGGAGGCGCTGACTCT-CAGGGCGGGCGGCAGCCGCTCACCCGCCGGGTGCAGCTGCTCCGGGCTGCTGAGCCGCGTGGAAATCTTGCCGGTACCATATGTCACCGAAGCGTCGCGTCTCACCGTGTTGCTGCCTCT 
s armadillo.ENr331_1        460889 473 -    582518 TGGGAGATCCAGAACACCAGCAGCCTGGCAGCCGACGGGGACCAGGCAGCTGCGTGGCCTGTGGGCATTCCAGCCCCATCCCGCCCGGCTTCCCGCTTTGAGGTGCTGCGCTGGGACTACTTCACGGAGCAGCACGTGTTCTCCTGCGCCGATGGTTCACCCCGCTGTCCGCTGCGGGGAGCTGACCGGGCTGACGTGGCCGACATTCTGGGGACAGCGCTGGAGGAGCTCAACCGCCGCTACCATCCAGCCCTGCGGCTCCAGAAGCAGCGACTGGTTAACGGCTACCGCCGCTTCGATCCTGCCCGGGGCATGGAGTACACGCTGGACTTGCAGCTGGAGGCGCTGACCCCCGAGGGCGGCCGCCAGCCCCTCACCCGCCGGGTGCAGCTGCTACGG-CCGCTGAGTCGCGTGGAAATCCTGCCCGTGCCCTACGTCACCGAGGCCTCACGCCTCACGGTGCTGCTGCCACT 
s monDom1.scaffold_13176   1058183 473 -   2254034 TGGGAGATCCAGAACACAAGCCGGCTCTCTGTGGACGGGGAACAGGAGGCATCCTGGCCGCTAGGCATCCCAGCCCCATTCCGTCCCTCTTCTCGATTCGAGGTGTTGAGCTGGGACTACTTCACGGAGCAGCACGTTTTCTCATGCGCGGATGGCTCCCCTCGTTGCCCCTTGCGGGGAGCCGACCGGGATGATGTAGCAGATGTCCTGGGGGCGGCCTTGGAAGAGCTGAATCGCCGCTACCACCCGGCTCTTCAGCTTCGCAAACAACAGCTGCTCAACGGCTACCGCCGCTTTGACCCAACGAGAGGCATGGAGTACACGCTGGACTTGGAGTTGGAGGCGCTGACCCCAGAGGGGGCCCGCCAGCACCTCACCCGTCGAGTGCAGCTCCTGAGG-CCCCTGAGCCGGGTGGAAATCCTGCCGGTGCCCTACGTTACTGAGGCGTCCCGCCTTACGGTGCTGCTGCCGCT 
s galGal2.chr7            22906640 473 +  37338262 CTTGAGATCCAGAATGCCAGCAGCCTGTCTGCAGATGGGGACCACAGTGCCGCGTGGCCTGTCGGCATCCCTCCTCCATTCCAGCCCAAAACTCGCTTCGAGGTGCTGCGCTGGGACTACTTCACAGAGGATCAGGTCTATGCCTGCGTGGATGGCTCCCCCAAATGCGAGCTGCAGGGCGCAGACCTAGCTGATGTGGCTGACGTGGTGGCCACAGCCATGGAGGAGCTGAACCGCAAGTACCAGCCGGTGCTGCATGTCCGCAAGCAGCAGCTGGTGAATGGCTACCGGCGCTTTGACCCTACGCGCGGCATGGAGTACACGCTGGACCTGCAGGTGGAGGTGGTCACGCAGAAGGGTCACAGCCGCTCTGTCACCAAGCGCGTGCACCTGGTGCGG-CCCCTCAGCGAGGTGGAGATCATCCCTATGCCCTATGTGACGGAGGCCAGCCGCATCAACGTCATCTTGCCGCT 
s xenTro1.scaffold_1262     137561 473 +    226782 AGGGAGATACAGAACACCAGCAGCCTGTCGGTAGAGGGGGAACATTCTGCTACCTGGCCCCTAGGGATCAATTCTCCCTTCCAGCCACGGACGCGGTTTGAAGTTCTACGCTGGGACTACTTCACCGAGGACCAAACCTTCTCCTGCACCGATGGCTCCCCAAAGTGCGAGCTGATTGGGGCAGACCTTGCCGATGTCACAGACGTCATAAGCACGGCAGTGGATGAGTTGAACCGCAAGTACCAGCCGGTGCTACACGTGCGCAAACAGCAGCTGCTGAACGGCTACCGGCGCTTTGACCCAACGCGGGGCATGGAGTACACCTTGGATCTGCAGCTGGAGTTGGTGACCCAGAGGGGACACAGTCGCTCTATCACCAAACGTGTGCACCTTGTGCGG-CCGCTCAGCGAGGTGGAGATCATCCCGATGCCGTATGTGACCGAAGCCAGCCGGATCAATATCATCCTCCCTCT 
s tetNig1.chr2            14458148 473 +  19247847 GCAGAAATCATGAACGTGAGCGCCGACGCCTTCGAGGGCAGCTGGAGCTCCCAGTGGCCAGTGGGAGTGAACCCGCCTTTTCAGCCGCAGTCTCGATTCGAAGTCCTAAAATGGGAGTATTTTACAGAGGAGGAGATTTATTCCTGCGTGGACGGCTCTCCCAAGTGCGAGCTGAGGGGCATCGATCGTCTGGACGTGGCTAACGTGATCGACGCAGCGATGGGGGAGCTGAACAGGAAGTACAAGCCCGTCCTGCACCTCAAAAAGCAGCAGCTCATTAATGGTTACAGGCGCTTCGACCCCACGCGGGGCATGGAGTACACCCTGGACCTCCAGGTGGAGGCCGTCAACCAGAAAGGCCACAGCCGCTCCATCACCAAGCGGGTTCACCTGGTGCGA-CCGCTGAGCAAGACTGAGATCATTCCCATGCCCTACGTCACCGAGGCAACGCGGGTTCACGTCATTCTGCCGCT 
s danRer2.chr9            37578929 473 -  44268068 GCGGAAATTAGAAATGTCAGTGTAGTGGCTTTTGAGGGCAACCGCAGTGCTTTGTGGCCAGTTGGAATCAATCCACCCTTTGAGCCCAAAACACGATTCGAGGTCCTGCGGTGGGATTACTTCACTGAGGATCAGGTTTACTCTTGCATCGATGGCTCTCCGAAATGCGAGCTTCGTGGAGTTGACAAGCTAGACGTAGCCGATGTCATTGAGACAGCAATGGGTGAACTGAATAAAAAGTACAAGCCTGTGTTGTACCTAAAGAAGCAACAGCTAATCAATGGATACAGACGTTTTGACCCCACCAGAGGTATGGAGTACACCCTGGACCTACAATTGGAGGTAGTTAACCAAAAAGGACACAGTCGCTCTATTACCAAGAGGGTCCACTTAGTAAGA-CCTCTCAGTCGCATCGAGATCATCCCTATGCCTTACGTTACAGAAGCAACTAGAGTTCATATCATCTTACCCGT 

a score=1338359.0
s hg17.chr20            29105541 10 -  62435964 ---------CCTCACCTGA 
s panTro1.chr21         30130007 10 -  65473740 ---------CCTCACCTGA 
s baboon.ENr333_1         576800 10 -    736337 ---------CCTCACCTGA 
s rheMac1.SCAFFOLD75573    25486 10 +     63072 ---------CCTCACCTGA 
s marmoset.ENr333_1       640773 10 -    790936 ---------CCTCACCTGA 
s galago.ENr333_1         503915 10 -    573009 ---------CCTCACCTGA 
s mm6.chr2              26487264 10 - 181764313 ---------CCTCACATGA 
s rabbit.ENr333_1         401904 10 -    443838 ---------CCTTACCTGA 
s cow.ENr333_1            506404 10 -    562778 ---------CCTCACCTGA 
s canFam1.chr24         23543357 10 -  50732077 ---------CCTCACCTGA 
s rfbat.ENr333_1          334089 10 -    446645 ---------CCTTACCTGA 
s shrew.ENr333_14           3779 10 +     19671 ---------CCTCACCTGA 
s armadillo.ENr333_1      571206 10 -    702150 ---------CCTCACCTGA 
s elephant.ENr333_1       504940 10 -    535973 ---------CCTTACCTAA 
s platypus.ENr333_3         5031 19 -     23526 GCCGCTGTACCCGGACTGA 

a score=847132.0
s hg17.chr20              33513606 95 +  62435964 ATGGAGACAAGAAGCCCTGGGTTGAACAACATGAAGCCCCAGTCACTGCAGCTGGTACTGGAAGAGCAGGTGCTGGCACTACAGCAGCAGATGGC 
s panTro1.chr21           35533536 95 +  65473740 ATGGAGACAAGAAGCCCTGGGTTGAACAACATGAAGCCCCAGTCACTGCAGCTGGTACTGGAAGAGCAGGTGCTGGCACTACAGCAGCAGATGGC 
s baboon.ENr333_1           340416 95 +    736337 ATGGAGACAAGAAACCCTGGGTTGAACAACATGAAGCCCCAGTCACTGCAGCTGGTGCTGGAAGAGCAGGTACTGGCACTACAGCAGCAGATGGC 
s rheMac1.SCAFFOLD80437      46216 95 -     61260 ATGGAGACAAGAAACCCTGGGTTGAACAACATGAAGCCCCAGTCACTGCAGCTGGTGCTGGAAGAGCAGGTGCTGGCACTACAGCAGCAGATGGC 
s marmoset.ENr333_1         341462 95 +    790936 ATGGAGACAAGAAGCTCTGGGTTGAATAACATGAAGCCCCCGTCACTGCGGCTGATGCTGGAAGAGCAGGTGCTGGCACTACAGCAGCAGATGGC 
s galago.ENr333_1           263831 95 +    573009 ATGGAAGCAGGAAGCCCTGGGTTGAACAACATGAAGTCCCAGTCACTGCAGCTAGTGCTGGAGGAGCAAGTGCTAGCACTACAGCAGCAGATGGC 
s mm6.chr2               155418909 92 + 181764313 ATGGAGACAGGGAGCCCCGGGTTG---AACATGAAGCCCCAGTCCTTGCAGCTGGTGCTGGAGGGGCAGGTGCTGGCGCTGCAGCAGCAGATGGC 
s cow.ENr333_1              457166 95 +    562778 ATGGAGACAGGGGGCCCTGGGTTGAACAATATGAAGCCCCGGTCCCTGCAGCTGGTGCTGGAAGAGCAAGTGCTGGCACTGCAGCAGCAGATGGC 
s canFam1.chr24           27350813 95 +  50732077 ATGGAGACGCGAGGCCCTGGGTTGAACAATATGAAGCCCCAGTCACTGCAGTTGGTGCTGGAGGAGCAAGTACTAGCACTACAGCAGCAGATGGC 
s shrew.ENr333_5              1658 95 +      2244 ATGGAGCCGGGCAGCGCCGAGCACGGCACCATGAGGTCCCCGCCCCTGCAGCTGGTCCTGGAGGAGCAAGTGCTGGCCCTCCAGCAGCAAATGGC 
s armadillo.ENr333_1        317729 95 +    702150 ATGGAGACAAGAGGTGCTGGGTTGAACACCATGAAGCCCCAGTCACTGCAGCTGGTGCTGGAAGGGCAAGTGCTAGCTCTACAGCAACAGATGGC 
s monDom1.scaffold_15037    457774 92 -   4718213 ATGGAGGCAAGAGACCAAGGGC---ACAACATGAAGCCCCAGCCTCTGAATATGGTGCTGGAGAAGCAGATCCTGGCACTGCAGCAGCAAATGGC 

a score=583786.0
s hg17.chr20              33513701 91 +  62435964 AGAGAAT--CAGGCAGCCTCCTGGCGGAAGCTGA----AGAACTCCCAGGAGGCCCAGCAGAGACAAGCAACCCTTGTGAGGAAGCTGCA---------GGCCAAG 
s panTro1.chr21           35533631 91 +  65473740 AGAGAAT--CAGGCAGCCTCCTGGCGGAAGCTGA----AGAACTCCCAGGAGGCCCAGCAGAGACAAGCAACCCTTGTGAGGAAGCTGCA---------GGCCAAG 
s baboon.ENr333_1           340511 91 +    736337 AGAGAAT--CAGGCAGCCTCCTGGCGGAAGCTGA----AGAACTCCCAGGAGGCCCAGCAGAGACAAGCAACCCTTGTGAGGAAGCTGCA---------GGCCAAG 
s rheMac1.SCAFFOLD80437      46311 91 -     61260 GGAGAAT--CAGGCAGCCTCCTGGCGGAAGCTGA----AGAACTCCCAGGAGGCCCAGCAGAGACAAGCAACCCTTGTGAGGAAGCTGCA---------GGCCAAG 
s marmoset.ENr333_1         341557 91 +    790936 TGAGAAT--CAGGCAGCCTCTTGGCGGAAGCTGA----AGAACTCCCAGGAGGCCCAGCAGAGACAAGCAACCCTTGTGAGGAAGCTGCA---------GGCCAAG 
s galago.ENr333_1           263926 91 +    573009 AGAGAAT--CAGGCAGCCTCCTGGCGGAAGCTGA----AGAACTCCCAAGAGGCCCAGCAGAAGCAAGCAACCCTTGTGAGGAAGCTACA---------GGCCAAG 
s mm6.chr2               155419001 91 + 181764313 CGAGAAT--CAGGCTGCCTCCTGGCGGAAACTGA----AGAACTCCCAAGAGGCCCAGAAGAGACAAGCAACCCTCGTGAGGAAGCTGCA---------GGCCAAG 
s cow.ENr333_1              457261 91 +    562778 CGAGAAC--CAGGCAGCCTCATGGAGGAAGCTGA----AGAGCTCCCAGGAGGCCCAGCAGAGGCAAGCAGCTCTCGTGAGGAAGCTGCA---------GGCCAAG 
s canFam1.chr24           27350908 91 +  50732077 AGAGAAC--CAAGCAGCCTCCTGGCGGAAGCTGA----AGAACTCCCAGGAGGCCCAGCAGAGGCAAGCAACCCTCGTGAGGAAGCTGCA---------GGCCAAG 
s shrew.ENr333_5              1753 91 +      2244 CGAGAAC--CAGGCTGTGTCCTGGAGGAAGCTGA----AGAGCTCCCAGGAGGCGCAGCAAAGGCAGGCAAGCCTAGTGAGGAAGCTGCA---------GGCCAAG 
s armadillo.ENr333_1        317824 91 +    702150 CGAGAAC--CAGGCAACCTCCTGGCGGAAGCTGA----AGAACTCCCAAGAGGCCCAGCAGAGGCAAGCAACCCTCGTGAGGAAGCTGCA---------GGCTAAG 
s monDom1.scaffold_15037    457866 91 -   4718213 CGAGAAC--CAGGCTGCTTCCTGGCACAAGCTGA----AGATCTCCCAGGAGGCCCAACAGAGACAAGCAGTACTTGTGAGAAAGTTGCA---------AGCCAAG 
s galGal2.chr20           12376081 96 -  13506680 AAAGAATGACAGGAGGCCTTGTGCAAGGAGTTCACCTGAAACATCACAGGAGG---AAAGAAGATGGACCA-------GTGGGAATTGCATCCCACAGGAGCCTAG 

a score=110145.0
s hg17.chr20             28856437 27 -  62435964 ATT--TTGGAAGATGGTCTGGTTCCCTAG 
s panTro1.chr21          29873839 27 -  65473740 ATT--TTGGAAGATGGTCTGGTTCCCTAG 
s baboon.ENr333_1          324965 27 -    736337 ATT--TTGGAAGACGGTCTGGTTCCCTAG 
s rheMac1.SCAFFOLD100460     7855 27 +     69370 ATT--TTGGAAGATGGTCTGGTTCCCTAG 
s marmoset.ENr333_1        374702 27 -    790936 ATT--TTGGAAGATGGTCCAGTTCCCTAG 
s galago.ENr333_1          319433 24 +    573009 ATT--TC---AGATGGTCCAGTACCCTGG 
s rn3.chr3               24652290 26 - 170969371 ATT--TTGGAAGACG-TCTGATTCCCTAG 
s mm6.chr2               26304889 27 - 181764313 ATT--TTGGAAGATGGTCTGATTCCCTAG 
s rabbit.ENr333_1          155457 27 -    443838 ATT--TTGGAAGATGGTCTGGCTCCCTAG 
s cow.ENr333_1             195343 27 -    562778 ATT--TCTGAAGGTGGTCCAGTTCCCTAG 
s canFam1.chr24          23320253 27 -  50732077 ATT--TTGGAGGGTGGTCCAGTGCCCTCG 
s shrew.ENr333_11           24243 26 -     31768 ATT--TT-GAAAAAGATTCATCCCTCCAG 
s armadillo.ENr333_1       300111 24 -    702150 ATT--TC---AGTTATTTCAGTTCCCTGC 
s tenrec.ENr333_25           6648 24 +     10962 ATT--TC---AGATAGTCCGGTTCCGTAA 
s monDom1.scaffold_15037  4213878 24 +   4718213 ACCCATTGGAAGGT--TCCCACTC---AG 
s galGal2.chr20           1064381 16 +  13506680 -----------GCTG--CCAGCTCCTCTC 

a score=1374686.0
s hg17.chr20              33593260 88 +  62435964 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCCAAGACTTTGGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACCG 
s panTro1.chr21           35611606 88 +  65473740 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCCAAGACTTTGGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACCG 
s baboon.ENr333_1           425615 88 +    736337 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCCAAGACTTTGGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACGG 
s rheMac1.SCAFFOLD100460      4061 88 -     69370 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCCAAGACTTTGGAGGACTTCCGGGTCAAGACCTGCGGGGGTGCCACGG 
s marmoset.ENr333_1         454589 88 +    790936 ATGGAGGCGTTGGGGAAGCTGAAGCAGTTCGATGCCTACCCCAAGACTCTGGAGGACTTCCGGGTCAAGACCTGTGGGGGCGCCACGG 
s galago.ENr333_1           345539 88 +    573009 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCCAAGACTCTGGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACCG 
s rn3.chr3               146322266 88 + 170969371 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCTAAGACTCTGGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACGG 
s mm6.chr2               155465078 88 + 181764313 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCTAAGACTCTGGAGGACTTCCGGGTCAAGACCTGCGGGGGTGCCACGG 
s rabbit.ENr333_1           293571 88 +    443838 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTATCCCAAGACTCTGGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACGG 
s cow.ENr333_1              377662 88 +    562778 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTATCCCAAGACTCTGGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACGG 
s canFam1.chr24           27422888 88 +  50732077 ATGGAGGCGCTGGGGAAGCTCAAGCAGTTCGATGCCTACCCCAAGACTCTGGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACGG 
s shrew.ENr333_11            10613 88 +     31768 ATGGAGGCGCTGGGGAAGCTCAAGCAGTTCGATGCCTACCCCAAGACTCTGGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACAG 
s armadillo.ENr333_1        420266 88 +    702150 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCCAAGACTCTGGAAGACTTCCGGGTCAAGACCTGCGGGGGCGCCACGG 
s elephant.ENr333_1         205306 88 +    535973 ATGGAGGCTCTGGGGAAACTGAAGCAGTTCGATGCCTACCCCAAGACTCTGGAAGACTTCCGGATCAAGACCTGCGGGGGCGCCACGG 
s tenrec.ENr333_27            2450 88 -      7185 ATGGAGGCGCTGGGGAAATTGAAGCAGTTCGATGCCTACCCCAAGACTTTGGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACGG 
s monDom1.scaffold_15037    539882 88 -   4718213 ATGGAGGCGCTGGGGAAATTGAAGCAGTTCGATGCCTACCCAAAGACCCTGGAGGACTTCCGGGTCAAGACATGCGGCGGGGCCACAG 
s tetNig1.chrUn_random   159954985 88 - 171761319 ATGGATACTTTTAGCAAACTGAAACAGTTTGACGCTTACCCGAAAACTCTCGAGGATTTTAGAGTGAAGACTTGGGGCGGAGCGACCG 
s danRer2.chr20           12624529 88 -  59369745 ATGGATGCGTTAAATAAACTCAAACAATTTGACGCGTATCCGAAAACTCTAGAGGACTTCAGGATCAAAACATGTGGAGGAGCCACGG 

a score=1153346.0
s hg17.chr21             32707032 79 +  46944323 ATGCTTCTGCCGGGAC----GCGCACGCCAACCGCCGACGCCCCAGCC--------------CGTGCAGCATCCCGGCCTCCGCCGGCAGGTAGAGC 
s panTro1.chr22          32678009 79 +  47338174 ATGCTTCTGCCGGGAC----CCGCACGCCAACCGCCGACGCCCCAGCC--------------CGTGCAGCATCCCGGCCTCCGCCGGCAGGTAGAGC 
s baboon.ENm005_1           38130 79 +   1530599 ATGCTCCTGCCGGGAC----CTGCACGCCAGCCGCCGGCGCCCCAGCC--------------CGCGCAGCATCCCGGCCTCCGCCGGCAGGTAGAGC 
s rheMac1.SCAFFOLD20175    129125 79 +    143704 ATGCTCCTGCCCGGAC----CTGCACGCCAGCCGCCGGCGCCCCAGCC--------------CGCGCAGCATCCCGGCCTCCGCCGGCAGGTAGAGC 
s marmoset.ENm005_1        156820 79 +   1506416 ATGCTTCTGCCGGGAc----ccgcgcgcccgccgccggcgccccAGCC--------------CGCTCAGCATCCCGGCCTCCGCAGGCAGGTAGAGC 
s galago.ENm005_1          164352 79 +   1691059 ATGCTCCTGCCGGGAC----Acgcgcgcccgccgcccgcgccccagcc--------------cgcgcAGCATCCTGGCCTCCGTCGGCAGGTAGAGC 
s rn3.chr11              30818860 79 +  87800381 ATGGTCTTGCCCGGAC----ACCCGCGTCTGCCGCCCGGGCCACAGCC--------------ACCGCAGAATCCCGGCCTCCGCAGGCAGGTAGAGC 
s mm6.chr16              89988309 79 +  97408558 ATGCTCCTGCCAGGAC----ACCCGCGTCCACCACCCGCGCCCCAATC--------------GGCGCAGAATCAGGGCCTCCGCAGGCAGGTAGAGC 
s rabbit.ENm005_90            447 79 +      1899 ATGCTCCTGCTGGGAC----Acgcgcgcccgccgcccgcgccccagcc--------------cgcccAGCATCCCGGCCTCCGCAGGCAGGTAGAGC 
s cow.ENm005_1             153686 79 +   2199270 ATGCTGCTGCCGGGCC----ACGCGCGCCCACCGTCCGCCCCGCAACC--------------CGCGCAGCATCCCGGCCTCCGCAGGCAGGTAGAGC 
s canFam1.chr31          30192155 79 +  41215879 ATGCTTCTGCCTGGAC----Acgcgcgcccgccgcccgcgccgcagcc--------------cgcgcAGCATCCCGGACTCCGCCGGCAGGTAGAGC 
s rfbat.ENm005_1           170396 79 +   1483291 ATGCTCCTGCCCGGAC----CCGCGCGCCCGCCGCCCGCACCCCAGCC--------------CGCGCAGCATCCTGGCCTCCGCAGGCAGGTAGAGC 
s armadillo.ENm005_1        58509 79 +   1490896 ATGCTCCAGCCGGGAC----CCGAgcgcccgccgcccgcgccccagcc--------------ggcgcAGCATCCCGGCCCCCGCCGGCAGGTAGAAC 
s elephant.ENm005_1         82159 79 +   1396438 ATGCTCCCGCGGGGAC----GCGAGCGCCAGTCTCTCGCGCCCCAGCC--------------GGCTCAGCATCCTGGCCTCCGCAGGCAGGTAGAGC 
s tenrec.ENm005_3             448 79 +      3605 ATGCTTCTGCGGGGAC----TCGAGCGCCGGTCTCCGGGGCCCCTGCC--------------CGCTCAGCATCCCAGCCTCCGCAGGCAGGTAGAGC 
s monDom1.scaffold_13487  1286340 70 +   4289508 ATGTTTCAGCGGGATC----G---GTGGCAGCTCACGTCGCCCCAG--------------------CAGCATCCCAGCCTCCGGAGACAGGTAGATC 
s galGal2.chr1           98706217 97 + 188239860 CGGCACCGGGCAGGGCTGCTCCGCCCCCCCGCTGCCCTCTCCCGCACCATGAGGGGAGGGGACGCGGGGCAGCACCCACGCCGGCGGCAGGTAGAGC 
s xenTro1.scaffold_390     770127 60 +   1157250 ATGTGAGTGCCAGGTC-------CGCATC--------ATGACCCAGCG--------------AGATGGGCACCAAG------GGAGACAGGTGA--T 

a score=936869.0
s hg17.chr21             32707111 81 +  46944323 CGCCGGGGCAGCTCCTGCGCCTCTTCTACTGCACTGTCCTGGTCTGCT---CCAAAGAGATCTCAGCGCTCACCGACTTCTCTG 
s panTro1.chr22          32678088 81 +  47338174 CGCCGGGGCAGCTCCTGCGCCTCTTCTACTGCACTGTCCTGGTCTGCT---CCAAAGAGATCTCAGCGCTCACCGACTTCTCTG 
s baboon.ENm005_1           38209 81 +   1530599 CGCCGGGGCAGCTCCTGCGCCTCTTCTACTGCACTGTCCTCGTCTGCT---CCAAAGAGATCTCAGCGCTCAGCGACTTCTCTG 
s rheMac1.SCAFFOLD20175    129204 81 +    143704 CGCCGGGGCAGCTCCTGCGCCTCTTCTACTGCACTGTCCTCGTCTGCT---CCAAAGAGATCTCAGCGCTCAGCGACTTCTCTG 
s marmoset.ENm005_1        156899 81 +   1506416 CGCCGGGGCAGCTCCTGCGCCTCTTCTACTGCACTGTGCTGGTCTGCT---CCAAAGAGATCTCAGCGCTCACCGACTTCTCTG 
s galago.ENm005_1          164431 81 +   1691059 AGCCGGGGCAGCTCCTCCGCCTCTTCTACTGCACTGTCCTGGTCTGCT---CCAAAGAGATCGCAGCGCTCTCGGACTTCTCCG 
s rn3.chr11              30818939 81 +  87800381 CTCCAGGGCAGCTTCTGCGCCTCTTCTACTGCACGGTCCTAGTGTGCT---CCAAAGAGACCTCCGCGCTCACCGATTTTTCCG 
s mm6.chr16              89988388 81 +  97408558 CTCCGGGGCAGCTTCTGCGCCTGTTCTACTGCACGGTCCTAGTGTGCT---CCAAAGAGACCTCCGCGCTCACCGATTTCTCTG 
s rabbit.ENm005_90            526 81 +      1899 CGCCGGGGCAGTTCCTGCGCCTCTTCTACTGCACCGTCCTGGTGTGCT---CCAAAGAGATCGCAGCGCTCACGGACTTCTCCG 
s cow.ENm005_1             153765 81 +   2199270 CTCCGGGGCAGCTCCTGCGTCTGTTCTACTGCACCGTCCTGGTTTGCT---CCAGAGAGATCGCGGCGCTCACGGACTTCTCCG 
s canFam1.chr31          30192234 81 +  41215879 CTCCCGGGCAGCTCCTGCGCCTCTTCTACTGCACCGTCCTGGTCTGTT---CCAAGGAGATCGCGGCGCTCACGGACTTCTCCG 
s rfbat.ENm005_1           170475 81 +   1483291 CGCCGGGGCAGCTCCTGCGCCTCTTCTACTGCACTGTCCTGGTCTGCT---CCAAAGAGATCGCAGCGCTCACGGACTTCTCCG 
s hedgehog.ENm005_1         33512 78 +    709315 CCCCGGGGGGG---CTGCGCCTCTTCTACTGCGCGGTGCTGGTCTGCT---CCCGGGAGATCGCGGCGCTCACCGACTTCTCCG 
s armadillo.ENm005_1        58588 81 +   1490896 CTCCCGCGCAGCTCCTGCGTCTCTTCTACTGCACTGTCCTGGTCTGTT---CCAAAGAGATCGCAGCGCTCACGGACTTCTCCG 
s elephant.ENm005_1         82238 81 +   1396438 CGCCGGGGCAGTTCCTGCGCCTCTTCTACTGTACCGTCCTGGTCTGCT---CCAAAGAGATCGCGGCGCTCACGGACTTCTCTG 
s tenrec.ENm005_3             527 81 +      3605 CTCCGGGGCAGCTCCTGCGCCTTTTCTACTGCACTGTCCTGGTCTGCT---CCAGAGAGATCGCCGCGCTCACGGACTTTTCTG 
s monDom1.scaffold_13487  1286410 78 +   4289508 ---CTGTGCTACTATTTCGCCTCTTCTATTGTACCTTCTTGGTGTGCA---CCAAAGAGATCGCAGCCCTCACTGACTTCTCCG 
s galGal2.chr1           98706314 78 + 188239860 ---GCGGGAGGCTGCTGCCTCTCCTCTCCTGCGCCATCCTCGCGTGCT---GCGCCGAGGTGGCGGCGCTCCGGGACTTCTCAG 
s xenTro1.scaffold_390     770187 74 +   1157250 ---TGGCACAA-------GCCTTCTGTACTGCATCCTCCTCCTCCTCTGGGCTAAAGAGCTCTCTGCCCTGGCTGACTTCTCAG 

a score=378843.0
s hg17.chr21            14074301 381 - 46944323 ATGGAGCGCCCTCTCATCTGGCACCTTCCTGGCCTCTTTCCCAGGCCCCAGTTCTGTCCATGCAGCTGTGGGTGCTTCCTGCATTGCGGGTCTCACGGGGAGGAGACGAGAGTGCCCCTGGTTGAGTCAGGAAAGAATTCTATCTTCACGTCGCTGCCAGCAAATGACCACAGCAGCTTCACGACCTCTGCAGGAACCTATCTTGGTAAAGAAACGGGGCCTATGTGgtggccgagcctcaggtgtggccgagcttcaggtgtggccCTTATGCACAGCACAGCCCAAGCCTGTGGGCACCACTCGCCCTGGGCTGCCTGGCACCTGGACTCCTTCCCATCCTTGGCCGAGGTCTGCGTGGCCCTTCAGGGCCGAATCTGA 
s panTro1.chr22         14495269 381 - 47338174 ATGGAGCGCCCTCTCATCTGGCACCTGCCTGGCCTCTTTCCCAAGCCCCAGTTCTGTCCATGCAGCTGTGGGTGCTTCCTGCATTGCGGGTCTCACGGGGAGGAGCCAAGAGTGCCCCTGGTTGAGTCAGGAAAGAATTCTATCTTCACGTCGCTGCCAGCAAATGACCACAGCAGCTTCACGACCTCTGCAGGAACCTATCTCGGTAAAGAAACAGAGCCTATCTGgtggctgagcctcaggtgtggccgagcttcaggtgtggccCTTATGCACAGCACAGCCCAAGCCTGTGGGCACCACTCGCCCTGGGCTGCCTGGCACCTGGACTCCTTCCCATCCTTGGCCGAGGTCTGCGTAGCCCTTCAGGGCCGAATCTGA 
s baboon.ENm005_1        1332018 381 -  1530599 ATGGAGTGCCCTCTCGTGTGGCACCTGCCTGGCCCCTTTCCCACGCCCCAGTTCTGTCCATGCAGCTGTGGGTGCTTCCTGCATTGGGGGTCCTGCCGGGAGGAGCCAAGAGTGCCCCTAGGGGAGTCAGGAAAGAATTCCCTCTTCACCTCGCTGCCAGAAAATGACCATAGCAGCTTCACAACCCCTGCAGGAACCTATCTCGGTAAAGAAATAGAGCCTATGTGgtggccgagcctcaggtgtggccaagcttcaggtgtggccCTTATGCACAGCACAGCCCAAGCCTGCGGATACCATTCGCTCTGGGCTGCCTGGCACCTGGACTCCTTCCCATCCTTGGCCAAGGCCTGTGTGGCCCTTCAGGGCTGAACCCGA 
s rheMac1.SCAFFOLD20377    39438 294 -   119232 ATGGAGTGCCCTCTCGTGTGGCACCTGCCTGGCCCCTTTCCCAAGCCCCAGTTCTGTCCATGCAGCTGTGGGTGCTTCCTGCATTGGGGGTCCCGCCGGGAAGAGCCAAGAGTGCCCCTGGGGGAGTCAGGAAAGAATTCCCTCTTCACCTCGCTGCCAGAAAATGACCATAGCAGCTTCGCCACCCCTGCAGGAACCTATCTCGGTAAAGAAATGGAGCCTATGTGGTGGCCGAGCCTCAGGTGTGGCTAAGCTTCGGGTGTGACCCTTATGCACAGCACAGCC-------------------------------------------AC--------------------------------------------AACCCGA 

a score=776439.0
s hg17.chr21             33321040 80 + 46944323 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCAGAGCCCGATGACCTTTTTCTGCCGGCCCGGAGTAA 
s panTro1.chr22          33286911 80 + 47338174 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCAGAGCCCGATGACCTTTTTCTGCCGGCCCGGAGTAA 
s baboon.ENm005_1          604977 80 +  1530599 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCAGAGCCCGATGACCTTTTTCTGCCGGCCCGGAGTAA 
s rheMac1.SCAFFOLD95266     35303 80 +    85465 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCAGAGCCCGATGACCTTTTTCTGCCAGCCCGGAGTAA 
s marmoset.ENm005_1        665850 80 +  1506416 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCAGAGCCCGATGACCTTTTTCTGCCGGCCCGGAGTAA 
s galago.ENm005_1          699777 80 +  1691059 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCGGAACCCGATGACCTTTTTCTACCTGCTCGGAGCAA 
s rn3.chr11              31244293 80 + 87800381 ATGGACTCGGACGCCAGCCTGGTGTCTAGTCGCCCGTCGTCGCCAGAACCCGATGATCTTTTTCTGCCGGCCCGGAGCAA 
s mm6.chr16              90383436 80 + 97408558 ATGGACTCGGACGCCAGCCTGGTGTCTAGTCGCCCATCGTCCCCAGAACCCGATGATCTTTTTCTGCCCGCCCGGAGCAA 
s rabbit.ENm005_59           9006 80 +    43844 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCGGAACCCGATGACCTTTTCCTGCCGGCCCGGAGCAA 
s cow.ENm005_1            1041619 80 +  2199270 ATGGACTCGGACGCCAGCCTGGTGTCTAGCCGGCCGTCGTCGCCGGAGCCCGATGACCTTTTCCTGCCGGCCCGGAGCAA 
s canFam1.chr31          30690225 80 + 41215879 ATGGACTCGGACGCCAGCCTGGTGTCCAGTCGCCCGTCGTCACCAGAGCCCGATGACCTGTTTCTGCCGGCCCGGAGCAA 
s rfbat.ENm005_1           573600 80 +  1483291 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCAGAGCCCGATGACCTTTTCCTGCCGGCCCGGAGCAA 
s armadillo.ENm005_1       570431 80 +  1490896 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCCGAGCCCGATGACCTTTTCCTGCCGGCGCGGAGCAA 
s elephant.ENm005_1        587237 80 +  1396438 ATGGACTCTGACGCCAGCTTGGTGTCTAGCCGCCCGTCGTCGCCAGAGCCCGATGACCTTTTCCTGCCGGCTCGGAGCAA 
s monDom1.scaffold_13487  2075962 80 +  4289508 ATGGACTCCGATGCCAGTCTGGTGTCCAGCCGCCCGTCCTCACCGGAGACGGATGACATCTTCCTTACCACCCGGAGCAA 
s xenTro1.scaffold_390    1097815 78 +  1157250 ATGGACTCAGACGCCAGCCTGGGCTCTAGCCGAGCCTCCTCCCCGGAGACAGATGACCTGTTCCTACACTCACGGAAA-- 

a score=1032384.0
s hg17.chr21             33321120 153 + 46944323 GGGCAGCA---------GCGGCAGCGCCTTCACTGGGGGCACCGTGTCCTCGTCCACCCCGAGTGACTGCCCGCCGGAGCTGAGCGCCGAGCTGCGCGGCGCTATGGGCTCTGCGGGCGCGCATCCTGGGGACAAGCTA---GGA---------GGCAGTGGCTTCAAGTCATC 
s panTro1.chr22          33286991 153 + 47338174 GGGCAGCA---------GCGGCAGCGCCTTCACTGGGGGCACCGTGTCCTCGTCCACCCCGAGCGACTGCCCGCCGGAGCTGAGCGCCGAGCTGCGCGGCGCTATGGGCTCTGCGGGCGCGCATCCTGGGGACAAGCTA---GGA---------GGCAGTGGCTTCAAGTCATC 
s baboon.ENm005_1          605057 153 +  1530599 GGGCAGTA---------GCGGCAGCGCCTTCACTGGGGGCACAGTGTCCTCGTCCACCCCGAGCGACTGCCCGCCGGAGCTGAGCGCTGAGCTGCGCAGCGCTATGGGCTCTGCGGGCGCGCATCCTGGTGACAAGCTA---GGA---------GGCAGCGGCTTCAAGTCATC 
s rheMac1.SCAFFOLD95266     35383 153 +    85465 GGGCAGTA---------GCGGCAGCGCCTTCACTGGGGGCACAGTGTCCTCGTCCACCCCGAGCGACTGCCCGCCGGAGCTGAGCGCTGAGCTGCGCAGCGCTATGGGCTCTGCGGGCGCGCATCCTGGTGACAAGCTA---GGA---------GGCAGCGGCTTCAAGTCATC 
s marmoset.ENm005_1        665930 153 +  1506416 GGGCAGCA---------GCGGCAGCGCCTTCACTGGGGGCACCGTGTCCTCGTCCACGCCGAGCGACTGCCCGCCGGAGCTGAGCGCTGAGCTGCGCGGCGCTATGGGCTCCGCAGGCGTGCATCCTGGGGACAAGCTA---GGA---------GGCAGTGGCTTCAAGTCATC 
s galago.ENm005_1          699857 153 +  1691059 GAGCAGCA---------GCGGCGGCGGCTTTACCGGGGCCACAGTGTCCTCGTCCACGCCAAGCGACTGCCCGCCGGAGCTAAGCGCGGAGCTGCGCGGCGCCATGGGCTCAGCGGGAGCGCACTCTGGGGACAAGCTG---GGA---------AGCGGAGGCTTCAAGTCATC 
s rn3.chr11              31244373 153 + 87800381 GGGGGGAA---------GCAGCAGCGGCTTCACAGGAGGAACCGTGTCCTCATCCACGCCGAGCGACTGCCCGCCAGAGCTGAGCTCCGAGCTGCGAGGAGCCATGGGCACGGCGGGCGCGCATCCCGGGGACAAACTG---GGC---------GGCGGTGGCTTCAAGTCATC 
s mm6.chr16              90383516 153 + 97408558 GGGGGGAA---------GCAGCAGCGGCTTCACAGGAGGGACTGTGTCCTCGTCCACGCCGAGCGACTGCCCGCCAGAGCTGAGCTCCGAGCTACGAGGGGCCATGGGCGCGTCAGGCGCGCATCCCGGGGACAAACTG---GGC---------GGCGGTGGCTTCAAGTCATC 
s rabbit.ENm005_59           9086 156 +    43844 GGGCAGCA---------GCGGCGGCGGCTTCACGGGGGGCACTGTGTCCTCGTCCACGCCGAGCGACTGCCCGCCGGAGCTGAGCGCCGAGCTGCGCGGAGCCATGGGCGCGGCGGGTGCGCACCCCGGGGACAAGCTGGGCGGC---------GGCGGCGGCTTCAAGTCCTC 
s cow.ENm005_1            1041699 162 +  2199270 GGGCAGCG---------GGGGCGGCGGCTTCACGGGAGGCACCGTGTCGTCGTCCACGCCGAGCGACTGCCCGCCGGATCTGAGCGCCGAGCTGCGCGGTGCCATGGGCGCGGCGGGCGCGCACCCGGGGGACAAGCTG---GGCGGCGGCGTTGGCGGCGGCTTCAAGTTATC 
s rfbat.ENm005_1           573680 153 +  1483291 GGGCAGCG---------GCGGCAGCGGCTTCACAGGGGGCACGGTGTCTTCGTCCACGCCGAGCGACTGCCCGCCAGAGCTGAGCGCCGAGCTGCGCGGCGCCATGGGCGCTGCGGGCGTGCACCCCGGGGACAAGCTG---GGC---------GGCGGCGGCTTCAAGTCGTC 
s armadillo.ENm005_1       570511 150 +  1490896 ------AG---------GCAGCGGCGGCTTCTCCGGAGGCACGGTGTCGTCGTCCACCCCGAGCGACTGCCCGCCAGAGCTGAGCACCGAACTGCGCGGCGCCATGGGCGCGGCGGGCGCGCACCCCGGGGACAAGCTGGGCGGC---------GGCGGCGGCTTCAAGTCCTC 
s elephant.ENm005_1        587317 153 +  1396438 GGGCAGCG---------GCGGCAGCGGCTTCTCGGGGGGCACCGTGTCCTCCTCTACACCAAGCGACTGTCCGCCTGAGCTGAGCACCGAGCTGCGCGGCGCCATGGGCGCGGCGGGTGCGCACGCCGGGGACAAGCTG---GGC---------GGCGGTGGCTTCAAGTCCTC 
s monDom1.scaffold_13487  2076042 162 +  4289508 GGGTAGCAGCAGCGGGGGCGGCGGCGGATTCTCCGGTGGCACGGTCTCCTCCTCTACACCAAACGACTGCCAGCCGGAGCTGAGCGCGGAGCTTCGAAACGCCATGGGCGCGGCGGGCGTGCACCCAGGGGACAAGCTG---GGC---------GGCGGCTGCTTTAAGtcctc 
s xenTro1.scaffold_390    1097893 124 +  1157250 -------------------------GGCTTCTCTGG---CGCAGTGTCTTCCTCCACTATGAGCGACTCCCCCGCGGAGCTGAGTGCGGAGCTCCGTAACGCCATGG---CTATGGCTGCGGCAGCGGGCGACAAGTTG---GGC---------G-----CGTTTAAAGCTG-- 

a score=386002.0
s hg17.chr21             33321273 57 +  46944323 CTCGTCCAGCAC------CTCGTCGTCTACGTCGTCG------GCGGCTGC--GTCGTCCACCAAGAAGGA 
s panTro1.chr22          33287144 57 +  47338174 CTCGTCCAGCAC------CTCGTCGTCTACGTCGTCG------GCGGCTGC--GTCGTCCACCAAGAAGGA 
s baboon.ENm005_1          605210 57 +   1530599 CTCGTCCAGCAC------CTCGTCGTCCACGTCGTCG------GCGGCCGC--GTCGTCCACCAAGAAGGA 
s rheMac1.SCAFFOLD95266     35536 57 +     85465 CTCGTCCAGCAC------CTCGTCGTCCACGTCGTCG------GCGGCCGC--GTCGTCCACCAAGAAGGA 
s marmoset.ENm005_1        666083 57 +   1506416 CTCGTCCAGCAC------CTCGTCGTCCACCTCGTCG------GCGGCCGC--ATCGTCCACCAAGAAGGA 
s galago.ENm005_1          700010 57 +   1691059 GTCATCCAGCAC------CTCATCGTCCACGTCGTCG------GCGGCCGC--ATCGTCCACCAAGAAGGA 
s rn3.chr11              31244526 57 +  87800381 TTCCTCCAGCAC------CTCCTCGTCCACGTCGTCG------GCGGCCAC--GTCTTCCACCAAGAAAGA 
s mm6.chr16              90383669 57 +  97408558 TTCCTCCAGCAC------CTCCTCGTCCACGTCCTCG------GCGGCCAC--GTCTTCCACCAAGAAAGA 
s rabbit.ENm005_59           9242 57 +     43844 CTCGTCCAGCAC------CTCGTCATCCACGTCGGCG------GCGGCCGC--GTCGTCCACCAAGAAAGA 
s cow.ENm005_1            1041861 57 +   2199270 CTCGTCCAGCAC------CTCTTCGTCCACGTCGTCG------GCGGCCGC--GTCGTCCACCAAGAAGGA 
s canFam1.chr31          30734310 47 +  41215879 ------------------cccggcgcgcacgcgggcg------gcggctcccgggcggACCCCAAAGAGGA 
s rfbat.ENm005_1           573833 57 +   1483291 CTCGTCCAGCAC------GTCGTCGTCCACGTCGTCG------GCGGCTGC--GTCGTCCACCAAGAAGGA 
s armadillo.ENm005_1       570661 57 +   1490896 CTCGTCCAGCAC------CTCTTCGTCCACGTCGTCG------GCGGCGGC--GTCGTCCACCAAGAAGGA 
s elephant.ENm005_1        587470 57 +   1396438 CTCGTCCAGCAC------CTCCTCGTCCACATCGTCG------GCCGCCGC--ATCGTCCACCAAGAAGGA 
s monDom1.scaffold_13487  2076204 69 +   4289508 gtcctccaccacttcgtcttcctcttccacctcatcgtcttcctcGGTCGC--ATCTTCTACCAAGAAGGA 
s galGal2.chr1           98916206 43 + 188239860 ---GGCGTGGAC-----------TTTCCAAGTTGGCA------G-----AC--GTTGT-CACCATGCAAAA 
s xenTro1.scaffold_390    1098017 37 +   1157250 --------------------------CTGCAGCGGCC------GCAGCGGC--TGTCGCGGCCAAGAAGGA 

a score=1280125.0
s hg17.chr21             33321330 139 + 46944323 CAAGAAGCAAATGACAGAGCCGGAGCTGCAGCAGCTGCGTCTCAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGATGGCCTCCGCGAGGTCA---TGCCGTAC------GCACACGGCC------CTTCGGTG 
s panTro1.chr22          33287201 139 + 47338174 CAAGAAGCAAATGACAGAGCCGGAGCTGCAGCAGCTGCGTCTCAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGATGGCCTGCGCGAGGTCA---TGCCGTAC------GCACACGGCC------CTTCGGTG 
s baboon.ENm005_1          605267 139 +  1530599 CAAGAAGCAAATGACAGAGCCAGAGCTGCAGCAGCTGCGTCTCAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGACGGCCTGCGCGAGGTCA---TGCCGTAC------GCGCACGGCC------CTTCGGTG 
s rheMac1.SCAFFOLD95266     35593 139 +    85465 CAAGAAGCAAATGACAGAGCCAGAGCTGCAGCAGCTGCGTCTCAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGACGGCCTGCGCGAGGTCA---TGCCGTAC------GCGCACGGCC------CTTCGGTG 
s marmoset.ENm005_1        666140 139 +  1506416 CAAGAAGCAAATGACGGAGCCGGAGCTGCAGCAGCTTCGTCTCAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGACGGCCTGCGCGAGGTCA---TGCCTTAC------GCGCACGGCC------CTTCGGTG 
s galago.ENm005_1          700067 139 +  1691059 CAAGAAGCAGATGACTGAGCCGGAGCTGCAGCAGCTGCGCCTCAAAATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATAGCCATGGACGGCCTGCGCGAGGTCA---TGCCATAC------GCGCACGGCC------CGTCGGTG 
s rn3.chr11              31244583 139 + 87800381 TAAGAAGCAGATGACTGAGCCCGAGCTGCAGCAGCTGCGCCTGAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGACGGCCTGAGGGAGGTCA---TGCCGTAC------GCGCACGGCC------CGTCGGTG 
s mm6.chr16              90383726 139 + 97408558 CAAGAAGCAGATGACTGAGCCCGAGCTGCAGCAGCTGCGCCTGAAGATCAACAGCCGCGAACGCAAGCGCATGCACGACCTCAACATCGCCATGGACGGCCTGCGGGAGGTCA---TGCCTTAC------GCGCACGGGC------CGTCGGTG 
s rabbit.ENm005_59           9299 139 +    43844 CAAGAAACAGATGACCGAGCCGGAGCTGCAGCAGCTGCGGCTGAAAATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGACGGGCTGCGCGAGGTCA---TGCCGTAC------GCGCACGGCC------CGTCGGTG 
s cow.ENm005_1            1041918 139 +  2199270 TAAGAAACAGATGACGGAGCCCGAGCTGCAGCAGCTGCGCCTCAAGATCAACAGCCGCGAGCGCAAGCGGATGCACGACCTCAACATCGCCATGGACGGGCTGCGCGAGGTCA---TGCCGTAC------GCGCACGGCC------CGTCGGTG 
s canFam1.chr31          30734357 133 + 41215879 ---------------------GCAGCAACAGCAGCTGCGGCGCAAGATCAACAGCCGCGAGCGGAAGCGCATGCAGGACCTGAACCTGGCCATGGACGCGCTGCGCGAGGTCATCCTGCCCTACTCGGCGGCGCACTGCCAGGGCGCGCCCGGC 
s rfbat.ENm005_1           573890 139 +  1483291 CAAGAAGCAGATGACGGAGCCGGAGCTGCAGCAGCTCCGCCTGAAGATCAACAGCCGCGAGCGCAAGCGCATGCATGACCTCAACATCGCCATGGACGGGCTGCGCGAGGTCA---TGCCGTAC------GCTCACGGCC------CGTCGGTG 
s armadillo.ENm005_1       570718 139 +  1490896 CAAGAAGCAGATGACGGAGCCCGAGCTGCAGCAGCTGCGCCTGAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGACGGGCTGCGCGAGGTCA---TGCCCTAC------GCGCACGGCC------CTTCGGTG 
s elephant.ENm005_1        587527 139 +  1396438 CAAGAAGCAGATGACGGAACCCGAGCTGCAGCAGCTGCGCCTCAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGACGGGCTGCGCGAGGTCA---TGCCCTAC------GCGCACGGCC------CGTCGGTG 
s monDom1.scaffold_13487  2076273 139 +  4289508 CAAGAAGCAGATGACTGAGCCAGAGCTCCAGCAGCTTCGGCTCAAGATCAACAGCCGGGAGCGCAAGCGGATGCACGACCTCAACATCGCCATGGACGGCCTTCGTGAAGTCA---TGCCGTAC------GCGCACGGAC------CCTCGGTG 
s xenTro1.scaffold_390    1098054 139 +  1157250 CAAGAAGCAGATGAACGAGTGCGAGTTGCAGCAGCTGAGGCTGAAGATTAACAGCCGGGAGCGCAAGCGAATGCACGATCTGAATATCGCCATGGACGGGCTGCGGGAGGTGA---TGCCCTAC------GCACACGGGC------CCTCGGTG 

a score=968430.0
s hg17.chr21             33321469 93 + 46944323 CGCAAGCTTTCCAAGATCGCCACGCTGCTGCTGGCGCGCAACTACATCCTCATGCTCACCAACTCGCTGG-AGGAGATGAAGCGACTGGTGAGC 
s panTro1.chr22          33287340 93 + 47338174 CGCAAGCTTTCCAAGATCGCCACGCTGCTGCTGGCGCGCAACTACATCCTCATGCTCACCAACTCGCTGG-AGGAGATGAAGCGACTGGTGAGC 
s baboon.ENm005_1          605406 93 +  1530599 CGCAAGCTTTCCAAGATCGCCACGCTGCTCCTGGCGCGCAACTACATCCTCATGCTCACCAACTCGCTGG-AGGAGATGAAGCGACTGGTGAGC 
s rheMac1.SCAFFOLD95266     35732 93 +    85465 CGCAAGCTTTCCAAGATCGCCACGCTGCTCCTGGCGCGCAACTACATCCTCATGCTCACCAACTCGCTGG-AGGAGATGAAGCGACTGGTGAGC 
s marmoset.ENm005_1        666279 93 +  1506416 CGCAAGCTCTCCAAGATCGCCACGCTGCTGCTGGCGCGCAACTACATCCTCATGCTCACCAACTCGCTGG-AGGAGATGAAGCGACTGGTGAGC 
s galago.ENm005_1          700206 93 +  1691059 CGCAAGCTCTCCAAGATCGCCACGCTACTACTGGCGCGCAACTACATCCTCATGCTCACCAACTCACTGG-AGGAGATGAAACGACTGGTGAGC 
s rn3.chr11              31244722 93 + 87800381 CGCAAGCTCTCCAAGATCGCCACGCTGCTGCTGGCGCGAAACTACATCCTGATGCTCACCAACTCGCTGG-AGGAGATGAAGAGACTGGTGAGC 
s mm6.chr16              90383865 93 + 97408558 CGCAAGCTCTCCAAGATCGCCACGCTGCTGCTGGCGCGAAACTACATCCTCATGCTCACCAACTCGCTGG-AGGAGATGAAGCGACTGGTGAGC 
s rabbit.ENm005_59           9438 94 +    43844 CGCAAGCTCTCCAAAATCGCCACGCTGCTGCTGGCGCGTAACTACATCCTCATGCTCACCAACTCGCTGGAAGGAGATGAAGCGCCTGGTGAGC 
s cow.ENm005_1            1042057 93 +  2199270 CGCAAGCTCTCCAAGATCGCCACATTGCTGCTGGCGCGCAACTACATCCTCATGCTCACCAACTCGCTGG-AGGAGATGAAGCGACTGGTGAGC 
s canFam1.chr31          30734490 93 + 41215879 CGCAAGCTCTCCAAGATCGCCACGCTGCTGCTCGCCCGCAACTACATCCTGCTGCTGGGCAGCTCGCTGC-AGGAGCTGCGCCGCGCGCTGGGC 
s rfbat.ENm005_1           574029 93 +  1483291 CGCAAGCTCTCCAAGATCGCCACGCTGTTGCTGGCGCGCAACTACATTCTCATGCTCACCAACTCCCTGG-AGGAGATGAAGCGACTGGTGAGC 
s armadillo.ENm005_1       570857 93 +  1490896 CGCAAGCTCTCCAAGATCGCCACGCTGCTGCTGGCGCGCAACTACATCCTCATGCTCACCAACTCTCTGG-AGGAGATGAAGCGACTGGTGAGC 
s elephant.ENm005_1        587666 93 +  1396438 CGCAAGCTCTCCAAGATCGCCACCCTGCTGCTGGCACGCAATTACATCCTCATGCTCACCAACTCGCTGG-AGGAGATGAAGCGGCTGGTGAGC 
s tenrec.ENm005_54           1327 93 -    10647 CGGAAGCTCTCCAAGATCGCCACGCTGCTGCTCGCCCGTAACTACATCCTGCTGCTGGGCAGCTCGCTGC-AGGAGCTGCGCCGCGCCCTGGGA 
s monDom1.scaffold_13487  2076412 93 +  4289508 CGCAAGCTCTCCAAGATAGCTACTCTTCTTCTAGCCCGCAACTACATCCTCATGCTCACCAACTCCTTAG-AGGAAATGAAGCGGCTGGTCAGC 
s xenTro1.scaffold_390    1098193 93 +  1157250 CGCAAACTATCAAAGATCGCAACGCTGCTACTAGCGCGCAATTACATCCTGATGCTAAACAACTCGCTGG-AGGAGATGAAGCGCCTGGTCAGT 

a score=792867.0
s hg17.chr21             33321562 133 + 46944323 GAGATCTACGGGGGCCACCAC------------------------------GC--TGGCTTCCACCCGTCGGCCTG---CGGCGGCCTGGCG-CACTCCGCGCCCCTGC-CCGCCGCCACCGCGCACCCGGCAGCAGCAGCGCACGCCGCACATCACC---------------------------CCGCGGTGCACC 
s panTro1.chr22          33287433 133 + 47338174 GAGATCTACGGGGGCCACCAC------------------------------GC--TGGCTTCCACCCGTCGGCCTG---CGGCGGCCTGGCG-CACTCTGCGCCCCTGC-CCGCCGCCACCGCGCACCCGGCAGCAGCAGCGCACGCCGCACATCACC---------------------------CCGCGGTGCACC 
s baboon.ENm005_1          605499 133 +  1530599 GAGATCTACGGGGGCCACCAC------------------------------GC--TGGCTTCCACCCGTCGGCCTG---TGGGGGCCTGGCG-CACTCCGCGCCCCTGC-CCGCAGCCACCGCGCACCCGGCAGCAGCAGCGCACGCAGCACATCACC---------------------------CCGCGGTGCACC 
s rheMac1.SCAFFOLD95266     35825 133 +    85465 GAGATCTACGGGGGCCACCAC------------------------------GC--TGGCTTCCACCCGTCGGCCTG---TGGGGGCCTGGCG-CACTCCGCGCCCCTGC-CCGCAGCCACCGCGCACCCGGCAGCAGCAGCGCACGCAGCACATCACC---------------------------CCGCGGTGCACC 
s marmoset.ENm005_1        666372 133 +  1506416 GAGATCTACGGGGGCCATCAC------------------------------GC--TGGCTTCCACCCGTCGGCCTG---CGGCGGCCTGGCG-CACTCCGCTCCCCTGC-CCGCTGCCACCGCGCACCCGGCAGCCGCAGCGCATGCCGCACATCACC---------------------------CCGCGGTGCACC 
s galago.ENm005_1          700299 130 +  1691059 GAGATCTATGGCGGCCACCAT------------------------------GC--TGGCTTCCACCCGTCGGCCTG---TGGCGGCCTGGCT-CACTCCGCGCCGCTGC-CCGCCACCACCGCGCACCCCGCGGCC---GCGCACGCCGCGCACCACC---------------------------CGGCAGTGCACC 
s rn3.chr11              31244815 133 + 87800381 GAGATTTACGGGGGTCACCAC------------------------------GC--CGGCTTCCACCCGTCGGCCTG---TGGCGGGCTGGCA-CACTCGACGCCTCTAC-CCACCGCCACGGCGCACCCTGCAGCCGCCGCGCACGCCGCGCACCACC---------------------------CGGCGGTGCATC 
s mm6.chr16              90383958 133 + 97408558 GAGATCTACGGGGGTCACCAC------------------------------GC--CGGCTTCCACCCATCGGCCTG---TGGCGGGCTGGCA-CACTCGGCGCCTCTAC-CCACCGCCACGGCGCACCCCGCGGCCGCCGCGCACGCCGCGCACCACC---------------------------CGGCCGTGCACC 
s rabbit.ENm005_68            490 130 +     8945 gagggc-gccgggcccgccgc------------------------------gccACGCCTGCTGCTGGCCGGCCTGCCCTTGCTGGCCGCCG-CGCCCGG---CTCTGTGCTGCTGGCGCCGGGCGCCGTGGGACCGCCGGACGCACTGCG-----CC---------------------------CCGCCAAGTACC 
s cow.ENm005_1            1042150 133 +  2199270 GAGATCTACGGAGGCCACCAC------------------------------GC--CGGCTTCCACCCATCGGCCTG---CGGCGGCCTGGCG-CACTCTGCGCCCCTGC-CTGCCGCCACGGCTCATCCGGCGGCCGCGGCGCACGCGGCGCACCACC---------------------------CGGCGGTGCACC 
s canFam1.chr31          30734583 103 + 41215879 GAGGgc-gccgggcccgccgc------------------------------gccgcgcctgctgctggccggcctg--------------------------cccctgc-tggccgcc-----gcgcccggc----tccgtgctgctggcgcctggcg---------------------------ccgtggggcccc 
s rfbat.ENm005_1           574122 133 +  1483291 GAGATCTACGGCGGCCACCAC------------------------------GC--GGGCTTCCACCCGTCAGCCTG---CGGCGGCCTGGCG-CACTCAGCGCCCCTGC-CCGCCGCCACTGCGCACCCCGCGGCCGCCGCCCACGCGGCGCACCACC---------------------------CCGCGGTGCACC 
s armadillo.ENm005_1       570950 133 +  1490896 GAGATCTACGGCGGTCACCAC------------------------------GC--CGGCTTCCACCCCTCGGCCTG---CGGCGGCTTGGCG-CACTcggcgcccctgc-ccgccgccaccgcgcaccccgcggccgccgcgcacgccgcgcACCACC---------------------------CGGCCGTGCACC 
s elephant.ENm005_1        587759 130 +  1396438 GAGATCTACGGCGGCCACCAC------------------------------TC--CGGCTTCCACCCGTCGGCCTG---CGGGGGCCTGGCG-CACTCTgcgcccctgc-cggccgccacggcgcacccggcggcc---gcgcacgccgcgcACCACC---------------------------CAGCGGTGCACC 
s tenrec.ENm005_54           1420 162 -    10647 GAGGGC-GCCGGGCCCGCCGC------------------------------TCCGCGCCTGCTGCTGGCCGGCCTG---CCGCTGCTCGCCGCCGCGCCGGGCTCGGTG-CTGCTGGCGCCCGGCGCCGTGGGGCCCCCGGATGCGCTGCGCCCCGCCAAGTACCTGTCCCTGGCGCTGGACGAGTCGCCCTGCGGC 
s monDom1.scaffold_13487  2076505 130 +  4289508 GAGATCTATGGCGGCCACCAC------------------------------GC--TGGTTTCCACCCCTCAGCCTG---CGGAAGTTTGGCA-CATTCGGCGCCTCTGC-AGGCAGCCGCTGCGCACCCAGCAGCA---GCGCACGCCTCCCACCATC---------------------------CCGCAGTCCATC 
s xenTro1.scaffold_390    1098286 124 +  1157250 GAGATCTACGGGGGGCACCACCACCATGCGGCCGCCGCAGCCGCAGCAGCAGC--CGCCTACCATCCCTCGGCCTG---CGGGGGGATGAGC-CATGGGGCCCCCTTGC----------CCGGACACCCAGTGGCC------------------CACC--------------------------------------- 

a score=176126.0
s hg17.chr21             33321695 42 + 46944323 A-CCCCATCctgccgcccgccgccgcagcggctg-ctgccgccg 
s panTro1.chr22          33287566 43 + 47338174 AACCCCATCctgccgcctgccgccgcagcggctg-ctgccgccg 
s baboon.ENm005_1          605632 42 +  1530599 A-CCCCATCctgccgcccgccgccgcagcggctg-ctgcagccg 
s rheMac1.SCAFFOLD95266     35958 42 +    85465 A-CCCCATCctgccgcccgccgccgcagcggctg-ctgcagccg 
s marmoset.ENm005_1        666505 42 +  1506416 A-CCCCATCctgccgcccgccgccgccgcggctg-ctgcggccg 
s galago.ENm005_1          700429 42 +  1691059 A-CCCCATCCTGCCGCCCGCAgctgctgccgccg-ctgctgccg 
s rn3.chr11              31244948 42 + 87800381 A-CCCCATCCTCCCTCCAgcagccgcggccgcag-ccgccgcag 
s mm6.chr16              90384091 42 + 97408558 A-CCCCATCCTCCCTCccgcagccgccgccgccg-ccgcagccg 
s cow.ENm005_1            1042283 33 +  2199270 A-TCCCATCCTGCCTCCGGCCGCCGCCGCCGCCG---------- 
s canFam1.chr31          30734686 38 + 41215879 ----ccgacgcgctgcgccccgccA-AGTACCTG-TCGCGGGCG 
s rfbat.ENm005_1           574255 42 +  1483291 A-TCCCATCCTGCCTCccgcagccgcggccgccg-ccgctgcag 
s armadillo.ENm005_1       571083 42 +  1490896 A-CCCCATCCTgccgcccgccgccgcggccgccg-cggccgccg 
s elephant.ENm005_1        587889 39 +  1396438 A-CCCCATCCTGCCACCGGCAGCCGCCGCTG----CAGCCGCCG 
s tenrec.ENm005_54           1583 30 -    10647 A-GTTCGCACTCCCAGGCGGCGGCGCTGGGG------------- 
s monDom1.scaffold_13487  2076635 42 +  4289508 A-CCCAATATTGCCGCCCgctgcggcagcagcag-ctgcagctg 
s xenTro1.scaffold_390    1098410 43 +  1157250 A-CCCTCTCCTGCCCACCCCAGCCTCCCTGGCAGCTTCCAGCCT 

a score=170439.0
s hg17.chr21             33321737 48 + 46944323 ct------gcagccgcggctgTGTCCAG----CGCCTCTCTGCCCGGATCCGGGCTGC 
s panTro1.chr22          33287609 48 + 47338174 ct------gcagccgcggctgTGTCCAG----CGCCTCTCTGCCCGGATCCGGGCTGC 
s baboon.ENm005_1          605674 48 +  1530599 ct------gccgctgcggcGGTGTCCAG----CGCCTCTCTGCCCGGTTCGGGGCTGC 
s rheMac1.SCAFFOLD95266     36000 48 +    85465 ct------gccgctgcggcGGTGTCCAG----CGCCTCTCTGCCCGGTTCGGGGCTGC 
s marmoset.ENm005_1        666547 48 +  1506416 ct------gccgcagcggcAGTGTCCAG----CGCCTCTCTGCCCGGCTCCGGGCTGT 
s galago.ENm005_1          700471 48 +  1691059 ct------gcggccgctgcGGTGTCCAG----CGCCTCTTTGCCTGGCTCCGGGCTGT 
s rn3.chr11              31244990 48 + 87800381 cc------gctgccgcagcGGTGTCCAG----CGCTTCTCTGCCGGGCTCCGGGCTGT 
s mm6.chr16              90384133 48 + 97408558 cc------gccgccgcAGCGGTGTCCAG----CGCCTCTCTACCGGGCTCCGGGCTGT 
s canFam1.chr31          30734724 54 + 41215879 CTCGACGAGCCGCCCT----GCGGCCAGTTCGCGCTccccggcggcggcgcgggcggc 
s rfbat.ENm005_1           608451 54 +  1483291 CTCGAGGAGCCTCCGT----GCGGCCAGTTCTCGCTccccggcggcggcgcgggcggc 
s armadillo.ENm005_1       571125 48 +  1490896 cc------gccgccgccgccgTCTCCAG----CGCCTCCCTGCCGGGCTCCGGGCTGT 
s elephant.ENm005_1        587928 48 +  1396438 CC------GCAGCTGCGGCGGTGTCCAG----CGCCTCCCTGCCCGGCTCGGGGCTGT 
s tenrec.ENm005_54           1635 46 -    10647 CT------GCACCTGC-GCTGTCTGCAA-----GTTCCCTCACCTGGTTCCCGCCGGC 
s monDom1.scaffold_13487  2076677 48 +  4289508 ca------gcagccgccgcggTTTCCAG----CGCCTCTCTTCCAGGCTCGGGCCTTT 
s xenTro1.scaffold_390    1098455 42 +  1157250 CT------GGGGTGAGGGCAGCACCCCC----ACCGCCTCCACCCCCTCCTG------ 

a score=327365.0
s hg17.chr21             33321785 88 + 46944323 CGT-CGGTCGGCTCCATCC--GTCCACCGCACGGCCTACTCAAGTCTCCGTCTGCTgccgcggccgccccgctggggggcgggggcggcgg 
s panTro1.chr22          33287657 88 + 47338174 CGT-CGGTCGGCTCCATCC--GTCCACCGCACGGCCTACTCAAGTCTCCGTCTGCTGCCGCAgccgccccgctggggggcgggggcggcgg 
s baboon.ENm005_1          605722 88 +  1530599 CGT-CGGTCGGCTCCATCC--GTCCACCGCACGGCCTACTCAAGTCTCCGTCTGCTgccgcggccgccccgctggggggcgggggTGGCGG 
s rheMac1.SCAFFOLD95266     36048 88 +    85465 CGT-CGGTCGGCTCCATCC--GTCCACCGCACGGCCTACTCAAGTCTCCGTCTGCTgccgcggccgccccgctggggggcgggggTGGCGG 
s marmoset.ENm005_1        666595 88 +  1506416 CGT-CTGTCGGCTCCATAC--GTCCACCGCACGGCCTGCTCAAGTCTCCGTCTgccgccgccgccgcccctctgggaggcgggggcggcgg 
s galago.ENm005_1          700519 88 +  1691059 CGT-CGGTCGGATCCATTC--GGCCTCCGCACAGCCTGCTAAAGTCTCCGTCTGCAGCCGCGGCCGCCCCGCTcgggggcgggggcggtgg 
s rn3.chr11              31245038 88 + 87800381 CCT-CGGTCGGATCCATCC--GGCCTCCTCACGGCCTGCTCAAGTCTCCATCGGCAGCCGCGGCCGCCCCTCTCGGAGGCGGGGGTGGAGG 
s mm6.chr16              90384181 88 + 97408558 CCT-CGGTCGGATCCATCC--GGCCTCCGCACGGCCTGCTCAAGTCACCGTCGGCAGCCGCAGCCGCCCCTCTCGGAGGCGGGGGTGGAGG 
s canFam1.chr31          30734778 76 + 41215879 ggcgcgggcggcccgggccTGTGCACCTGCGCGGTCTGC--AAGTTCCCGCACCTGGTCCCCGCCGGCCT------GGGCCTGG------- 
s rfbat.ENm005_1           608505 76 +  1483291 ggcccgggcggccccggccTCTGCACCTGCGCTGTCTGT--AAGTTCCCGCACCTGGTCCCGGCCGGCCT------GGGCCTGG------- 
s armadillo.ENm005_1       571173 88 +  1490896 CGT-CGGTCGGCTCGATCC--GGCCTCCGCACGGCCTTCTCAAGTCTCcgtcggcggccgcggcggcgccgctcggggcggggggcggcgg 
s elephant.ENm005_1        587976 88 +  1396438 CAT-CGGTTGGCTCCATCC--GTCCCCCTCATGGCCTGCTCAAGTCTCcgtcggcggccgcggcggcccctctgggggccgggggcggcgg 
s monDom1.scaffold_13487  2076725 88 +  4289508 CCG-CGGTCAGCTCCATAC--GACCCCCGCATGGCTTGCTCAAGTCGCCCTCGGCGTCCGTGGCCACCCCGTTGGGCAGTGGAGGGGGAGG 
s xenTro1.scaffold_390    1098497 63 +  1157250 CCC-CACCTGCCTCCCATC--CATCTTCCCACGGTTTGCTGAAGTCTCC-----CAGTC--------------------CGGGGGCGCTGG 

a score=403510.0
s hg17.chr21             33321873 69 + 46944323 cAGTGGGGCGAGCGGGGGCTTCCAGCACTGGGGCGGCATGCCCTGCCCC----TGCAGCATGTGCCAGGTGCC 
s panTro1.chr22          33287745 69 + 47338174 cAGTGGGGCGAGCGGGGGCTTCCAGCACTGGGGCGGCATGCCCTGCCCC----TGCAGCATGTGCCAGGTGCC 
s baboon.ENm005_1          605810 69 +  1530599 CAGTGGGGGCAGCGGGGGTTTCCAGCACTGGGGCGGCATGCCCTGCCCC----TGCAGCATGTGCCAGGTGCC 
s rheMac1.SCAFFOLD95266     36136 69 +    85465 CAGTGGGGGCAGCGGGGGTTTCCAGCACTGGGGCGGCATGCCCTGCCCC----TGCAGCATGTGCCAGGTGCC 
s marmoset.ENm005_1        666683 69 +  1506416 cagcgggggcagcgggggcTTCCAGCACTGGGGCGGCATGCCTTGTCCT----TGCAGCATGTGCCAGGTGCC 
s galago.ENm005_1          700607 69 +  1691059 cagcgggggtagcgggggcTTCCAGCACTGGGGAGGTATGCCCTGTCCC----TGCAGCATGTGCCAGGTGCC 
s rn3.chr11              31245126 69 + 87800381 CAGCGGTGGCAGCGGTGGCTTCCAGCACTGGGGTGGCATGCCGTGCCCC----TGCAGCATGTGCCAGGTGCC 
s mm6.chr16              90384269 69 + 97408558 CAGCGGTGGCAGCGGTGGCTTCCAGCACTGGGGCGGCATGCCGTGCCCC----TGCAGCATGTGCCAGGTGCC 
s canFam1.chr31          30734854 71 + 41215879 CCGCGGTGCAGGCGCAGTTTTCCA--AGTGAggggccccgcgcgggcccggggcgcgACCTAGGCCCGGCCTC 
s rfbat.ENm005_1           574433 69 +  1483291 cagcgggggcagcggcggcTTCCAGCACTGGGGCGGCATGCCCTGCCCC----TGTAGCATGTGCCAGGTGCC 
s armadillo.ENm005_1       571261 69 +  1490896 cagcgcgggcagcggcggTTTCCAGCACTGGGGTGGCATGCCCTGCCCC----TGCAGCATGTGCCAGGTGCC 
s elephant.ENm005_1        588064 69 +  1396438 cagcgggggcagcagcagcTTCCAGCACTGGGGCGGCATGCCCTGCCCC----TGCAGCATGTGCCAGGTGCC 
s monDom1.scaffold_13487  2076813 60 +  4289508 ---------CGGTGGTAGTTTCCAGCACTGGGGTGGGATGCCCTGCCCG----TGTAGCATGTGCCAGGTGCC 
s xenTro1.scaffold_390    1098560 57 +  1157250 -----------GTGGGGGGTTCCCCCATTGGAGCGGAATGCCCTGTCCG----TGCAGTATGTGCCAAGTGC- 

a score=184225.0
s hg17.chr21             33321942 33 + 46944323 GCCGCCG-----CACCACCACGTGTCGGCTATGGGCG-C 
s panTro1.chr22          33287814 33 + 47338174 GCCGCCG-----CACCACCACGTGTCGGCCATGGGCG-C 
s baboon.ENm005_1          605879 33 +  1530599 GCCGCCG-----CACCACCACGTGTCGGCCATGGGCG-C 
s rheMac1.SCAFFOLD95266     36205 33 +    85465 GCCGCCG-----CACCACCACGTGTCGGCCATGGGCG-C 
s marmoset.ENm005_1        666752 33 +  1506416 ACCTCCG-----CACCACCATGTGTCGGCCATGGGCG-C 
s galago.ENm005_1          700676 33 +  1691059 ACCGCCA-----CACCACCACGTGTCGGCCATGGGCG-C 
s rn3.chr11              31245195 33 + 87800381 GCCGCCA-----CACCACCACGTGTCGGCTATGGGCG-C 
s mm6.chr16              90384338 33 + 97408558 GCCGCCG-----CACCACCACGTGTCGGCTATGGGCG-C 
s canFam1.chr31          30691121 31 + 41215879 GCCGCCG-----CACCCCCACGTGCCGGCCATGGGC--- 
s rfbat.ENm005_1           574502 33 +  1483291 ACCGCCG-----CACCACCACGTGTCGGCCATGGGCG-C 
s armadillo.ENm005_1       571330 33 +  1490896 ACCGCCG-----CACCACCACGTGTCGGCCATGGGCG-C 
s elephant.ENm005_1        588133 32 +  1396438 ACCGCCG-----CACCATCACGTGTCGGCCATGGGCG-- 
s monDom1.scaffold_13487  2076873 33 +  4289508 TCCACCC-----CACCACCATGTTTCTGGTATGAGCA-C 
s xenTro1.scaffold_390    1098617 28 +  1157250 -CCGCCAGTGCCCATCACCA---------TCTGAGCAG- 

a score=559815.0
s hg17.chr21             33321975 37 + 46944323 C-GGCAGCCTGCCGCGCCTCACCTCCGACGCCAAGTGA--------- 
s panTro1.chr22          33287847 37 + 47338174 C-GGCAGCCTGCCGCGCCTCACCTCCGACGCCAAGTGA--------- 
s baboon.ENm005_1          605912 37 +  1530599 C-GGCAGCCTGCCGCGCCTCACCTCCGACGCCAAGTGA--------- 
s rheMac1.SCAFFOLD95266     36238 37 +    85465 C-GGCAGCCTGCCGCGCCTCACCTCCGACGCCAAGTGA--------- 
s marmoset.ENm005_1        666785 37 +  1506416 C-GGCAGCCTGCCGCGCCTCACCTCCGATGCCAAGTGA--------- 
s galago.ENm005_1          700709 37 +  1691059 G-GGCAGCCTGCCCCGCCTCACTTCCGACGCCAAGTGA--------- 
s rn3.chr11              31245228 37 + 87800381 C-GGCACCTTGCCGCGCCTCACCTCCGACGCCAAGTGA--------- 
s mm6.chr16              90384371 37 + 97408558 C-GGCACCTTGCCGCGCCTCACCTCCGACGCCAAGTGA--------- 
s cow.ENm005_1             853320 37 +  2199270 C-GGCAGCCTGCCGCGCCTCACCTCGGACGCCAAGTGA--------- 
s canFam1.chr31          30691155 36 + 41215879 --GGCAGCCTGCCGCGCCTTGCCTCCGACGCCAAGTGA--------- 
s rfbat.ENm005_1           574535 37 +  1483291 C-GGGAGCTTGCCGCGCCTCACCTCTGACGCCAAGTGA--------- 
s armadillo.ENm005_1       571363 37 +  1490896 C-GGCAGCCTGCCGCGCCTCACCTCCGACGCCAAGTGA--------- 
s elephant.ENm005_1        588165 38 +  1396438 CGGGCAGCCTGCCGCGCCTCACCTCCGACGCCAAGTGA--------- 
s monDom1.scaffold_13487  2076907 36 +  4289508 --ACCAGCCTCCCCAGACTCACTTCTGACGCCAAATGA--------- 
s xenTro1.scaffold_390    1098645 46 +  1157250 C-GCCACCCTGTCCCGGCTCAGCGCAGATACCAAGTGACTGCCCCAT 

a score=1681795.0
s hg17.chr21             13199283 46 -  46944323 CACTCTGATCTACAAATTTGGAAGAACCGAAGAGCTATGGACCTGA 
s panTro1.chr22          13617237 46 -  47338174 CACTCTGATCTACAAATTTGGAAGAACCGAAGAGCTATGGACCTGA 
s baboon.ENm005_1          495696 46 -   1530599 CACTCTGATCTACAAATTTGGAAGAACTGAAGAGCTATGGACCTGA 
s rheMac1.SCAFFOLD88249      2926 46 +     20534 CACTCTGATCTACAAATTTGGAAGAACTGAAGAGCTATGGACCTGA 
s marmoset.ENm005_1        559337 46 -   1506416 CACTCTGATCTACAAATTTGGAAGAACCGAAGAGTTATGGACCTGA 
s galago.ENm005_1          549204 46 -   1691059 CACTCTGATCTATAAATTTGGAAGAACTGAAGAGCTATGGACCTGA 
s rn3.chr11              56225824 46 -  87800381 CACTCTGATCTACAAATTCGGAAGAACTGAAGAGCTCTGGGCCTGA 
s mm6.chr16               6675235 46 -  97408558 CACTCTGATCTACAAATTTGGAAGAACTGAAGAGCTCTGGGCCTGA 
s rabbit.ENm005_60           8264 46 +     52615 CACTCTGATCTACAAGTTTGGAAGAACTGAAGAGCTATGGACCTGA 
s cow.ENm005_1             585999 46 -   2199270 CACTCTGATCTACAAATTTGGAAGAACTGAAGAGCTGTGGACCTGA 
s canFam1.chr31          10137555 46 -  41215879 CACTCTGATCTACAAATTTGGAAGAACTGAAGAGCTTTGGACCTGA 
s rfbat.ENm005_1           527825 46 -   1483291 CACTCTGATCTACAAATTTGGAAGAACTGAAGAACTATGGACCTGA 
s shrew.ENm005_8             7331 46 +      9131 CACTCTGATCTACAAATTCGGAAGGACGGAGGAGCTGTGGAGCTGA 
s armadillo.ENm005_1       463744 46 -   1490896 CACTCTGATCTACAAATTTGGAAGAACTGAGGAGCTGTGGACCTGA 
s elephant.ENm005_1        338758 46 -   1396438 CACTCTGATCTACAAGTTTGGAAGAACTGAGGAGCTATGGACCTGA 
s monDom1.scaffold_13487  1613530 46 -   4289508 CACCCTCATCTACAAATTTGGACGAACAGAAGAATTATGGGGATAA 
s platypus.ENm005_22        11594 46 -     23874 TACTCTAATCTACAAGTTTGGAAGACTAGAAGAATTATGAGCGGGA 
s galGal2.chr1           89195096 46 - 188239860 TACTCTGATCTACAAGTTTGGAAGAACAGAGGAGTTATGGGGATGA 

a score=967135.0
s hg17.chr22             19394206 85 -  49554710 GTTTGGCTCAGATGTGCTACAGCAACCCCTGCCCTCCATGCCCGCC---AAAGTTATCAGTGTAGATGAATTGGAATACCGACAGTGA 
s panTro1.chr23_random    9155376 85 +  16744317 GTTTGGCTCAGATGTGCTACAGCAACCCCTGCCCTCCATGCCCGCC---AAAGTTATCAGTGTAGATGAATTGGAATACCGACAGTGA 
s baboon.ENm004_1         1700418 85 -   1847427 GTTTGGCTCAGATGTGCTACAGCAACCCCTGCCTTCGATGCCTGCC---AAAGTTATCAGTGTAGATGAATTGGAATACCGACAGTGA 
s rheMac1.SCAFFOLD66396      1762 85 -     18526 GTTTGGCTCAGATGTGCTACAGCAACCCCTGCCTTCGATGCCTGCC---AAAGTTATCAGTGTAGATGAATTGGAATACCGACAGTGA 
s marmoset.ENm004_1       1550138 85 -   1756918 GTTTGGCTCAGATGTGCTACAGCAACCCCTGCCCTCCATGCCCACC---AAAGTTATCAGTGTAGATGAATTGGAATACCGACAGTGA 
s rn3.chr14              83860507 85 + 112220682 GTTTGGCTCAGATGTGCTACAGCAGCCTCTGCCCTCCATGCCCACC---AAAGTCATCAGTGTAGATGAACTGGAATATAGACAGTGA 
s mm6.chr11               3138792 85 + 121803636 GTTTGGCTCAGATGTGCTACAGCAGCCTCTGCCCTCCATGCCCACC---AAAGTCATCAGTGTAGATGAACTGGAATATAGACAGTGA 
s cow.ENm004_1            1803695 85 -   1995970 GTTTGGCTCAGATGTGCTACAGCAGCCCCTGCCCTCCATGCCCACC---AAAGTCATCAGTGTAGATGAACTGGAGTACCGACAGTGA 
s canFam1.chr26          13515973 85 -  41009621 GTTTGGCTCAGATGTGCTACAGCAACCCCTGCCCTCCATGCCTGCC---AAAGTCATCAGTGTAGATGAATTGGAGTACCGTCAATGA 
s shrew.ENm004_1            34232 85 -     45715 GTTTGGCTCGGATGTGTTACAGCAGCCTCTGCCCTCCATGCCCGCC---AAAGTCATCAGTGTAGATGAATTGGAATACCGACAGTGA 
s armadillo.ENm004_1      1505334 85 -   1528255 GTTTGGTTCAGACGTGCTGCAGCAGCCCCTGCCCTCTATGCCCGCC---AAAGTCATCAGTGTAGATGAACTGGAATACCGACAGTGA 
s elephant.ENm004_1       1756517 85 -   1794427 GTTTGGCTCAGATGTGCTGCAGCAGCCCCTCCCCTCTATGCCCGCC---AAAGTCATCAGCGTAGATGAGTTGGAATACCGACAGTGA 
s tenrec.ENm004_1           28922 84 +     32497 GTTTAGCTCAGATGTGCTGCAGCA-CCCTTGCCTTCTATGCCTGCC---AAAGTCATCAGTGTAGACGAGCTGGAGTACCGACCGTGA 
s monDom1.scaffold_14874   438522 85 -    760883 GTTCGGCTCAGACGTGCTGCAGCAGCCCCTGCCCTCGATGCCCTCC---AAAGTCATCAGCGTGGATGAGCTGGAGTATAGGCAGTGA 
s platypus.ENm004_5         47617 85 +     51213 GTTTGGCTCGGATGTCTTGCAACAACCTCTCCCTTCTATGCCCTCC---AAAGTTATCAGCGTAGATGAACTGGAATATCGTCAGTGA 
s galGal2.chr15           8931619 85 +  12438626 GTTTGGTTCAGATGTCTTGCAGCAGCCTCTCCCTTCCATGCCATCC---AAAGTCATCAGTGTAGATGAACTGGAATATCGGCAGTGA 
s xenTro1.scaffold_169    1819560 85 -   1919217 GTTTGGTTCTGATGTTTTGCAACAACCTCTACCTTCTATGCCAGCA---AAAGTCATAAGTGTGGATGAACTGGAGTACCGACAATAA 
s danRer2.chr6           24380872 88 +  33212616 GTTTGGTTCAGACATGCTGCAGCAGCCTCTCCCTTCCATGCCTTCCACTAAAGTGATCAGTGTTGATGAGCTCGAGTTCCGCCAGTGA 

a score=1156177.0
s hg17.chr22             19394049 157 -  49554710 TTCTGCATCCTCCAGGCTCTGGTTCCCATGCAGCAGCTGTCAGCGTTCAGACAAC-CCCTCAGAACGTGCCCAGCCGGTCAGG-CCTGCCCCACATGCACTCCCAGCTGGAGCATCGCCCCAGCCAGAGGAG------CAGCTCCCCTGTGGGCCTTGCCAAATG 
s panTro1.chr23_random    9155219 157 +  16744317 TTCTGCATCCTCCAGGCTCTGGTTCCCATGCAGCAGCTGTCAGCGTTCAGACAAC-CCCTCAGAACGTGCCCAGCCGGTCAGG-CCTGCCCCACATGCACTCCCAGCTGGAGCATCGCCCCAGCCAGAGGAG------CAGCTCCCCTGTGGGCCTTGCCAAATG 
s baboon.ENm004_1         1700261 157 -   1847427 TTCTGCATCCTCCAGGCTCTGGTTCCCAGGCAGCAGCTGTCAGCGTTCAGACAAC-TCCTCAGAACATGCCCAGCCGGTCGGG-CCTGCCCCACATGCACTCCCAGCTGGAGCATCGCCCCAGCCAGAGGAG------CAGCTCCCCTGTGGGCCTTGCCAAATG 
s rheMac1.SCAFFOLD66396      1605 157 -     18526 TTCTGCATCCTCCAGGCTCTGGTTCCCAGGCAGCAGCTGTCAGCGTTCAGACAAC-TCCTCAGAACATGCCCAGCCGGTCGGG-CCTGCCCCACATGCACTCCCAGCTGGAGCATCGCCCCAGCCAGAGGAG------CAGCTCCCCTGTGGGCCTTGCCAAATG 
s marmoset.ENm004_1       1549981 157 -   1756918 TTTTGCATCCTCCAGGCTCTGGTTCCCAGGCAGCAGCTGTCAGTGTTCAAACAGC-CCCTCAGAATGTGCCCAGCCGGTCAGG-CCTGCCCCACATGCACTCCCAGCTGGAGCATCGCCCCAGCCAGAGGAG------CAGCTCCCCCGTGGGACTCGCCAAATG 
s rn3.chr14              83860353 154 + 112220682 TTCTGCATCCTCCAGGCTCTAGTTCCCAGGCAGCAGCTATCAACGTTCAGA---C-TCCTCCGAATGTACCCAGCCGGTCAGG-CCTGCCCCATATGCACTCCCAGCTGGAGCATCGCACCAGCCAAAGGAG------CAGCTCCCCCGTGGGTCTTGCCAAGTG 
s mm6.chr11               3138638 154 + 121803636 TTCTGCATCCTCCAGGCTCTAGTTCCCAGGCAGCAGCTATCAGCGTTCAGA---C-TCCTCAGAATGTACCCAGCCGGTCGGG-CATGCCCCACATGCACTCCCAGCTGGAGCATCGTACCAGCCAAAGGAG------CAGCTCCCCTGTGGGCCTTGCCAAATG 
s cow.ENm004_1            1803538 157 -   1995970 TTCTTCATCCTCCAGGCTCTGGTTCCCAGGCAGCTGCTGTCAGCGTTCAGACGAC-TCCTCAGAATGTGCCCAGCCGGTCAGG-CCTGCCGCATGTGCACTCCCAGCTCGAGCACCGCCCCAGCCAGAGGAG------CAGCTCCCCTGTGGGCCTCGCCAAATG 
s canFam1.chr26          13515816 157 -  41009621 TTCTTCATCCTCCAGGCTCTGGTTCCCCGGCAGCAGCTGTCAGCGTTCAGACAAC-CCCTCAGAATGTGCCCACCAGGTCAGG-CCTGCCCCACGTGCACTCCCAGCTGGAACATCGCCCCAGCCAGAGGAG------CAGCTCCCCAGTAGGCCTCGCTAAGTG 
s shrew.ENm004_1            34074 158 -     45715 TTCTTCATCCTCCAGGCTCTGGTTCCCAGGCAGCAGCTGTCAGCATTCAGACAAC-CCCTCAGAATGTGCCCAGTCGGTCAGGGCCTGCCCCACATGCACTCCCAGCTGGAGCACCGCCCCAGCCAGAGGAG------CAGCTCCCCAGTGGGCCTCGCCAAATG 
s armadillo.ENm004_1      1505177 157 -   1528255 TTCTGCATCCTCCAGGTTCTGGTTCCCAGGCAGCAGCCGTTGGCGTTCAGACAAC-CCCCCAGAATGTGCCCAGCCGGTCAGG-CCTGCCCCACATGCACTCTCAGCTGGAGCACCGCACCAGCCAGAGGAG------CAGCTCCCCTGTGGGCCTCGCCAAGTG 
s elephant.ENm004_1       1756360 157 -   1794427 TTCTGCATCCTCCAGGCTCCGGTTCCCAGGCAGCAGCTGTCAGCATTCCGACAAC-TCCCCAAAATGTGCCCAGCCGGTCAGG-CCTGCCCCACGTGCACTCCCAGCTGGAGCACCGCTCCAACCAGAGGAG------CACCTCCCCGGTGGGCCTTGCCAAATG 
s monDom1.scaffold_14874   438365 157 -    760883 TCCTCCATCCCCCGGGCTCTGGCTCACAGGGAACAGCCATTGGTGTCCAGACGCC-CCCCCAGAACCTGTCGGGCCGGCCGGG-CCTGCCCCACATTCCCCCACAGCTGGAGCACCGCCCCAGCCAGAGGAG------CACCTCCCCTGTGGGCTTGGCCAAGTG 
s platypus.ENm004_5         47460 157 +     51213 TCTTACATTCTCCAAGCTCCAGCTCCCAGGGAATGACTGGTGGTGGACAAACCAC-CTCCCAGAACACGCCTGGTCGTTCTGG-ACTGCCTCATGTACACTCGCAGCTCGACCATCGCTCCAGCCAGCGAAG------TGGTTCTCCTGTTGGCCTTGCAAAATG 
s galGal2.chr15           8931462 157 +  12438626 CTTTACATTCCACAGGCACTGGAGCACAGGGATCACCTGCTGGTGTGCAAACAAC-ACCTCAGAATGTGCCGTCTCGGACTGG-ATTATCTCATGGGCACGCGCAGCTCGACCATCGTCCCAGCCAGAGAAG------TGGCTCTCCCATTGGCCTTGCAAAGTG 
s xenTro1.scaffold_169    1819440 120 -   1919217 CTATGT-TTTTTTAGGTTCGGGTCTACATGC-----------------------T-CCTCCGCAAGGTAT-------GACAAA-CCGCCCCAACATGCAC------ATTGAGCAGCGTCCTTCTCAGAGAAG------TACTTCTCCTGTAGGCCTGGCCAAGTG 
s danRer2.chr6           24380745 127 +  33212616 TTTTAACGCCTATTTTCTCTTCAG------------------ATCTTCATGTGGCTCCCTCAGGAGGCCCCCAGTC--------CCAGAGCCACGGTCCC------------CATCGGACAAACCAGCGGAGAGGTGCAAGTCCCCCTCTGGGCCTGGCCAAGTG 

a score=467760.0
s hg17.chr22             30665273  2 +  49554710 AT------------------ 
s panTro1.chr23          30832251  2 +  50034486 AT------------------ 
s baboon.ENm004_1          683101  2 +   1847427 AT------------------ 
s marmoset.ENm004_1        768746  2 +   1756918 AT------------------ 
s galago.ENm004_1          253015  2 +   1606733 AT------------------ 
s rn3.chr14              28756724  2 - 112220682 AT------------------ 
s mm6.chr5               31507522  2 + 150339831 AT------------------ 
s rabbit.ENm004_46          12119  2 +     60438 AT------------------ 
s rfbat.ENm004_1           374904  2 +   1039260 AT------------------ 
s armadillo.ENm004_1       547125  2 +   1528255 AT------------------ 
s elephant.ENm004_1        583363  2 +   1794427 AT------------------ 
s tenrec.ENm004_40            545  2 +     21576 AT------------------ 
s monDom1.scaffold_14498    25170  2 -    165350 AT------------------ 
s galGal2.chr15           3672628  2 -  12438626 AT------------------ 
s xenTro1.scaffold_169     238168  0 +   1919217 -------------------- 
s danRer2.chr10           8473064 20 +  36600514 AGCGTTTGACCAGAGAGCAT 

a score=1023332.0
s hg17.chr22             30665275 85 +  49554710 GGGG--GACCGGGAGCAGCTGCTGCAGCGGGCGCGGCTGGCCGAGCAGGCGGAGCGCTACGACGACATGGCCTCCGCTATGAAGGCG 
s panTro1.chr23          30832253 85 +  50034486 GGGG--GACCGGGAGCAGCTGCTGCAGCGGGCGCGGCTGGCCGAGCAAGCGGAGCGCTACGACGACATGGCCTCCGCCATGAAGGCG 
s baboon.ENm004_1          683103 85 +   1847427 GGGG--GACCGGGAGCAGCTGCTGCAGCGGGCGCGGCTGGCCGAGCAGGCGGAGCGCTACGACGACATGGCCTCCGCCATGAAGGCG 
s marmoset.ENm004_1        768748 85 +   1756918 GGGG--GACCGGGAGCAGCTGCTGCAGCGGGCGCGGCTGGCCGAGCAGGCGGAGCGCTACGACGACATGGCCTCCGCCATGAAGGCG 
s galago.ENm004_1          253017 85 +   1606733 GGGG--GACCGGGAGCAGCTGCTGCAGCGGGCGCGGCTGGCCGAGCAGGCGGAGCGCTACGACGACATGGCCTCCGCCATGAAGGCG 
s rn3.chr14              28756726 85 - 112220682 GGGG--GACCGAGAGCAGCTGCTGCAGCGGGCGCGACTGGCGGAGCAGGCGGAGCGCTACGACGACATGGCCTCCGCCATGAAGGCG 
s mm6.chr5               31507524 85 + 150339831 GGGG--GATCGAGAGCAGCTGCTGCAGCGGGCGCGACTGGCGGAGCAGGCGGAGCGCTACGACGATATGGCCTCCGCCATGAAGGCG 
s rabbit.ENm004_46          12121 85 +     60438 GGGG--GACCGTGAGCAGCTGCTGCAGCGGGCGCGGCTGGCCGAGCAGGCGGAGCGCTACGACGATATGGCCTCCGCCATGAAGGCG 
s canFam1.chr26          27923330 81 +  41009621 ------GACCGAGAGCAGCTGCTGCAGCGGGCGCGGCTGGCCGAGCAGGCGGAGCGCTACGACGACATGGCCTCCGCCATGAAGGCG 
s rfbat.ENm004_1           374906 85 +   1039260 GGGG--GACCGGGAGCAGCTGCTGCAGCGGGCGCGGCTGGCCGAGCAGGCGGAGCGCTACGACGACATGGCCTCCGCCATGAAGGCG 
s armadillo.ENm004_1       547127 85 +   1528255 GGGG--GACCGGGAGCAGCTTTTGCAGCGGGCGCGGCTGGCCGAACAGGCGGAGCGCTACGACGACATGGCCTCCGCCATGAAGGCG 
s elephant.ENm004_1        583365 85 +   1794427 GGGG--GACCGGGAGCAGCTGCTGCAGCGGGCGCGGCTGGCCGAGCAGGCGGAGCGCTACGACGACATGGCCTCCGCCATGAAGGCG 
s tenrec.ENm004_40            547 85 +     21576 GGGG--GACCGGGAGCAGCTCCTTCAGCGGGCCCGGCTGGCCGAGCAGGCGGAGCGCTACGATGACATGGCGTCGGCCATGAAAGCG 
s monDom1.scaffold_14498    25172 85 -    165350 GGGG--GACCGGGAGCAGCTGCTGCAGCGCGCGCGGCTGGCCGAGCAGGCGGAGCGCTACGACGATATGGCCTCCGCCATGAAGGCG 
s galGal2.chr15           3672630 85 -  12438626 GGGG--GACCGAGAGCAGCTGCTGCAGCGAGCCCGCCTGGCCGAGCAGGCGGAGAGATACGACGACATGGCCTCGGCCATGAAGTCG 
s xenTro1.scaffold_169     238168 81 +   1919217 ------GATCGGGAGCAGCTGCTGCAGAGAGCCCGCTTAGCGGAGCAGGCGGAAAGATATGAGGACATGGCGGCAGCAATGAAATCG 
s tetNig1.chr16           4004616 85 +   8976435 --GGTCGACCGCGAGCAGCTGGTGCAGAAAGCCAGGCTGGCTGAACAGGCTGAGAGGTATGATGATATGGCCGCTGCAATGAAATCG 
s danRer2.chr10           8473084 85 +  36600514 --GGCTGACCGGGAACAACTGATCCAAAGAGCCCGTCTGGCGGAGCAGGCGGAGCGCTATGATGATATGGCCTCCGCGATGAAGCTG 

a score=1983894.0
s hg17.chr22             18615464 192 -  49554710 GGATGCCTCAAGAAAGCTTATGACTTG-TTCTGCGGTTTG------CAGAAG---GGACCCAAGCTAACCAAGGAGGAGGAGGAAGCCTTGAGCAAGAAGCTCACAGACACGTCTGAGAGGCCCTCGTGGAGGACAATAGTGAACATCAACGCCATCCTCCTCCTGGCTGTGGTGGTCTTTATTCACGGCTACTATGCCTGA 
s panTro1.chr23          18939900 192 -  50034486 GGATGCCTCAAGAAAGCTTATGACTTG-TTCTGCGGTTTG------CAGAAG---GGACCCAAGCTAACCAAGGAGGAGGAGGAAGCCTTGAGCAAGAAGCTCACAGACACGTCTGAGAGGCCCTTGTGGAGGACAATAGTGAACATCAACGCCATCCTCCTCCTGGCTGTGACGGTCTTTATTCACGGCTACTATGCCTGA 
s baboon.ENm004_1          909091 192 -   1847427 GGATGCCTCAAGAAAGCTTATGACTTG-TTCTGCGGTTTG------CAGAAG---GGACCCAAGCTAACCAAGGAGGAAGAGGAAGCCTTGAGAAAGAAGCTCACAGACACATCTGAGAGGCCCTTGTGGAGGGCAATAGTGAACATCAACGCCATCCTCCTCCTGGCTGTGGTGGTCTTTATTTATGGCTACTATGCCTGA 
s rheMac1.SCAFFOLD115250    60460 192 +     79719 GGATGCCTCAAGAAAGCTTATGACTTG-TTCTGCGGTTTG------CAGAAG---GGACCCAAGCTAACCAAGGAGGAAGAGGAAGCCTTGAGAAAGAAGCTCACAGACACATCTGAGAGGCCCTTGTGGAGGACAATAGTGAACATCAACGCCATCCTCCTCCTGGCTGTGGTGGTCTTTATTTATGGCTACTATGCCTGA 
s marmoset.ENm004_1       1061547 192 +   1756918 GGATGCCTCAAGAAGACTTATGACTTG-TTCTGTGGTTTG------CAGAAG---GGACCCAAGCTAACCAAGGAGGAGGAGGAAGCCCTGAGCAAGAAGCTCACAGACACATCTGAGAGGCCCTTGTGGAGGACAGTAGTAAACATCAACGCCATCCTCCTTCTAGCTGTGGTGGTCTTTATTCATGGCTACTACGCCTGA 
s galago.ENm004_1         1116678 195 -   1606733 GGATGTCTCAGGAAGACTTGGGACTTA-TTCTGCGGTTTG------CAGGAGACGGGACCCAAGCTGACCAAGGAGGAGGAAGAGGCCCTTAGGAAGAAGCTGACCGACACGTCTGAGAGGCCCTTCTGGAGGACTGTGGTAAACATCAACGCCATCCTCCTCCTGGCTGTGGTTGTCTTTGTTTACGCCTATTTTGCCTGA 
s rn3.chr20              42420521 195 -  55296979 GGATGTCTCAAGAAGACTTATGACCTA-TGCTGTGGTTTG------CAAAGAGCGGAACCCAAGCTGACTAAAGAGGAGGAAGAAGCCCTGAAGAAGAAGCTGACAGACACATCCGAGAAGCCCTTCTGGCGGACGGTCGTGAACGTCAATGTCATTGTCCTCTTGGCCGTGGCGGCTTTTTTCTATGGCTATTTTGCCTGA 
s mm6.chr10              76290819 183 + 130291745 GGATGTCTCAAGAAGACGTGTGACCTA-TTCTGTGGTTTG------CAAAGAGCTGAATTCAAGTTGACTAAAGTAGAGGAGGAAGCT------------CTGACAGACACAACAGAGAAGCCCTTCTGGCGGACGGTCATGAACGTCAATGTCATCCTCCTCTTGGCTGTAGCAGCGTTTTTCTATGGCTATTTTGCCTGA 
s rabbit.ENm004_9            6617 195 +     12454 GGCTGTCTCAAGAAGGCATATGACCTG-TTCTGCGGCTTG------CAGAAGATGGGACACAAGCTGACCCCAGAGGAGAAGAAAGCCCTGGGGCAGAAGCTGACAGACACATCGGAGAAGCCCTTGTGGAGGATGGTAGTGAACATTAACGCCATCATCCTCCTGGCCGTGACCGTCTTTATGCATGCCTATTTTGCCTGA 
s cow.ENm004_1            1306372 195 -   1995970 GGATGTCTCAGGAAGGCTTACGACTTG-TTCTGCGGTTTG------CAGAGGAAAGGCCCCAAACTGAGCGAAGAGGAGGAAGAAGCCCGGAAGAAGAAGCTGACAGACACGTCTGAGAAGCCCTTATGGAGGACAGTAGTGAACATCAACGCCATCATCCTCCTGGCAGTGGCAGTCTTTGTCCATGGCTACTTTGCCTGA 
s canFam1.chr26          12905889 195 -  41009621 GGATGCCTCAGGAAGGCTTATGACATA-TTTTGTGGTTTG------CAGAAGACAGGTCCCAAACTGAGCAAAGAAGAGGAAGAAGCCCAGAAAAAGAAGCTGACAGACACATCTGAGAAGCCTTTATGGAGGACTATAGTGAATGTCAATGCCATTCTACTCCTAGCAGTGGCTGTCTTTGCCCATGGCTATTTTGCCTGA 
s rfbat.ENm004_1           526255 195 -   1039260 GGATGTCTCAGGAAGACTTATGACTTA-TTCTGCGGTTTG------CAGAAGAAAGGCCCCAAGCTGAGCAAAGAGGAGGAAGAAGCCCTGAAGAAGAAGCTAACAGACACATCTGAAAAGCCTTTATGGAGGACGATAGTGAACCTCAATGCCATACTCCTCCTGACAGTGGCAGTTTTTGTCCATGCCTATTTTGCCTGA 
s shrew.ENm004_6            32727 195 +     33761 GGCTGTTGCAGGCAGGCTTGTGACTTA-TTCTGTGGTCTG------CCAAAAAAAGGTCCCAAGCTGACCGAAGAGGAAAAAGAAGCTCAGATGAAGAAGTTGACAGACACATCAGAGAAGCCCTTTTGGAAGAGAGTAGTGAACGTTAATGCCATCCTCCTCCTAGCGGTGGCAGTCTTTTTCCATGGATATTATGCATAA 
s elephant.ENm004_1        928200 195 -   1794427 GGGTGTTTCAAGAAGGCTTATGACTTA-TTCTGCGGTTTG------CAGAAGAAAGGCCCCAAGTTGACCAAAGAGGAGAAAGAAGCCCTGGAGAAGAGGCTGAAGGACACATCTGAGAAGCCCTTGTGGAGGACTGTCGTAAACATCAACGGCATCCTCCTCCTGGCAGTGACGGTCTTTGTCCATGGCTACTATGCCTGA 
s tenrec.ENm004_55           2735 198 -      6654 GGATGCTGCAGGAAGTTCTATGACCTG-TTCTGTGGGCTGGACCAACAGAAG---GGCCCTAAAATGACCAAGGAAGAAGAGGCAGCAATGAAGGAGAAAATGATGGACACGTCTGAGAAGCCTTTGTGGCGGACAATCGTGAATATCAATGGTGTCATCCTCCTGACTGTTGCCGTCTTCTGCCATGCCTATTTTGCCTGA 
s monDom1.scaffold_12762   409827 198 -    595644 GGGTGTTTCAAGAGGACCTGGGATTTA-TTGTGTGGGCTGGAG---CCAAAGAAAGGCCCCAAGCTGACCAAGGAGGAGGAAGCTGCCCTGAAGAAGAAGTTGACAGACACGTCCGAAAAGCCCTTCTGGAGGAACGTGGTCAACGTCAGCGTCATCCTGCTCTTGACTGTGTATGTCTTCTACCACGGTTATTTTGCCTGA 
s platypus.ENm004_21        38364 198 -     61797 GGATACTTTAAGCGTGCCTATGACTTC-TTCTGTGGTTTGGAAGTGCAGAAA---ACCCATAAAATGACTGAAGAGGAGGAGAAAGCTCTGAGAATAAGGCTTACTGACATTTCAGAGAAGCCCTTCTGGAAAAACATAGTGAATATCAACGCCATCATTCTCCTGGCTGTGGCTGTTTTCTTTCATGCTTATTTTGCATAA 
s galGal2.chr15           3732727 198 -  12438626 GGATGCCTAAAGAAAGCTTACAACTGG-TTCTGTGGCTTAGACCAACAAAAA---GGACCCAAACTGAGCAAGGAGGAAGAGGAAGCGCTGAAGAAGAAACTGACTGACACATCAGAAGTGCCACTTTGGAGGAATGTTGTGAATATCAACGGCATCATCCTACTGACTGTGGCTGTATTTTGCCATGCCTTTTTTGCATAG 
s xenTro1.scaffold_169     280442 187 +   1919217 AGTTGCTGGAGGAAATCTTACAACTGG-TTCTGTGGATTTGATGATAAGAAG---CCCCCCAAACTGAGTGAGGAAGAGAAGAAGGCCCTGGAGCAAAAGATGACGGACACTTCAGAGAAGCCCCTGTGGAGGAACGTGGTCAACATCAACGGCATCATCCTGCTGGCTGTAGCTGTGTTCTGCCATGCAT----------- 
s tetNig1.chr4            4958064 195 -   6212533 ---TTGTGCAAGA-GGCTGGTAATGGGCTTCTGTGGGCTGGAA---CAGAACCAGGCGGTCAAACTGACCAAAGAAGAAGAAGCCGAGTTGCAGCGGAAGCTCACGGACACCACGGAGAAGCCGCTGTGGAGGAACGTGGTCAACGTCAACGCCCTCATCCTCCTGGCTGTTGCTTTCTTCTGTCATGGCTTTTTCGCATAA 
s danRer2.chr10           8504904 198 +  36600514 GGCTGTTGTAAGAAGGCCTACAACTGG-TTCTGCGGCTTCGAT---CAAGGCAATGCTCCCAAACTGACTAAAGAACAGGAGGCTGAGCTGAAGATGAAGCTCACCGACACCACTGAGAAACCTCTATGGAGAAATGTGGTCAACGCTAACGCCGTTATCCTCCTCACCGTCTGCGTCTTTTTCCACGGTTTCTTCGGTTAA 

a score=149114.0
s hg17.chr22             18615444 20 -  49554710 ATTATCCTGAGAA--ATCACGT 
s panTro1.chr23          18939880 20 -  50034486 ATTATCCTGAGAA--ATCACGT 
s baboon.ENm004_1          909071 20 -   1847427 ATTATCCTGAGCA--ATCACGT 
s rheMac1.SCAFFOLD115250    60440 20 +     79719 ATTATCCTGAGCA--ATCACGT 
s marmoset.ENm004_1       1061527 20 +   1756918 ATTATCCTGAGCA--ATCACGT 
s galago.ENm004_1         1116658 20 -   1606733 ATTATTCTGAACA--ATCTCGT 
s rn3.chr20              42420501 20 -  55296979 ACCAAACGGAGAA--ACCTCGT 
s mm6.chr10              76290799 20 + 130291745 ACCAAACTGAGAA--ACCTCGT 
s rabbit.ENm004_9            6597 20 +     12454 ATTCTCCCAAGAA--ATCTCGT 
s cow.ENm004_1            1306352 20 -   1995970 ATAATCCTGAGGA--AACTCGT 
s canFam1.chr26          12905869 20 -  41009621 ATAATCCTGAGAA--ACCCCGT 
s rfbat.ENm004_1           526235 20 -   1039260 ATAATCCTGAGGA--AACTCGT 
s shrew.ENm004_6            32707 20 +     33761 ATAATTCTGAGGA--AACTCGT 
s elephant.ENm004_1        928180 20 -   1794427 ATAATTCTGAAGA--AACTCGT 
s monDom1.scaffold_12762   409807 20 -    595644 CTGACCCTGAGGA--ATCACCA 
s platypus.ENm004_21        38344 20 -     61797 ATGTTCCTGAGAC--AACTAAG 
s galGal2.chr15           3732710 17 -  12438626 AGGAAAGTGAAGA--CCCA--- 
s xenTro1.scaffold_169     280422 20 +   1919217 GTCATGCAGAGAA--AAAGCTG 
s tetNig1.chr4            4958042 22 -   6212533 AGAACCCTCAGAACCACCAGGT 
s danRer2.chr10           8504887 20 +  36600514 AGATGCGTGAGGA--GCCAGGC 

a score=1595854.0
s hg17.chr5           131424298 162 + 180857866 ATGAGCCGCCTGCCCGTC------CTGCTCCTGCTCCAACTCCTGGTCCGCCCCGGACTCCAAGCTCCCATGACCCAGACAACGCC-------CTT------GAAGACAAGCTGGGT----T---AACTGCTCTAACATGATCGATGAAATTATAACACACTTA---AAGCA---GCCACCTTTGCCTTTGCTG 
s panTro1.chr4        137757118 162 + 188378868 ATGAGCCGCCTGCCCGTC------CTGCTCCTGCTCCAACTCCTGGTCCGCCCCGGACTCCAAGCTCCCATGACCCAGACAACGTC-------CTT------GAAGACAAGCTGGGT----T---AACTGCTCTAACATGATCGATGAAATTATAACACACTTA---AAGCA---GCCACCTTTGCCTTTGCTG 
s baboon.ENm002_1        186587 162 +   1082345 ATGAGCTGCCTGCCCGTC------CTGCTCCTGCTCCATCTCCTGGTCAGCCCCGGACTCCAAGCTCCCATGACCCAGACAACGTC-------CTT------GAAGACAAGCTGGGC----T---AACTGCTCTAACATGATCGATGAAATTATAACACACTTA---AACCA---GCCACCTTTGCCTTCGCCG 
s rheMac1.SCAFFOLD172     91842 162 -    130365 ATGAGCCGCCTGCCCGTC------CTGCTCCTGCTCCATCTCCTGGTCAGCCCCGGACTCCAAGCTCCCATGACCCAGACAACGTC-------CTT------GAAGACAAGCTGGGC----T---AAGTGCTCTAACATGATCGATGAAATTATAACACACTTA---AACCA---GCCACCTTTGCCTTCACCG 
s marmoset.ENm002_1      131755 159 +   1056904 ATGAGCCACCTGCCCATC------CTGCTC---CTCCTACTCCTGGTCAGCCCTGGACTTCAAGCTGCCCCAACCCAGACAATGCC-------CTT------GAAGACAACTCAGGT----T---AACTGCTCTAACTTGAGGGAGGAAATTGTAACACTCCTA---AACCA---GCCACCTTTGGCTTCATCA 
s galago.ENm002_1        312632 168 +   1185430 CTGAGCAGCCTCCGTATCCTGCATCTGCACCTGCTCCTGCTGCTGCTCAGCCTTGGAGATCAAGCTTCCCAGGCTCAGGAGACATT-------CTC------AACAATACCATGGGA----T---AATTGCCACTCCATGCTCAGAGAAATTAGGGAATACCTA---AACAA---GCCACCTTTGCCTTCGCAG 
s rn3.chr10            71032732 139 - 110733352 ACCAGCATCCTCTGCATG------CTGCTTCCGCTCCTGATGCTCTTCCACCAGGGACTCCAGTTT--------TCAGGCAGTG---------CCC------ACCGTTTACTCAGGACGTTG---GATTGCAGGACTATTGCCTTGGAGATTTTGGTGAAGCTC-----------------------CCAGTGA 
s mm6.chr11            67783565 148 - 121803636 ACCAGCATCCACACCATG------CTGCTCCTGCTCCTGATGCTCTTCCACCTGGGACTCCAAGCT--------TCAATCAGTGGCCGGGATACCC------ACCGTTTAACCAGAACGTTG---AATTGCAGCTCTATTGTCAAGGAGATTATAGGGAAGCTC-----------------------CCAGTGA 
s rabbit.ENm002_27       155026 141 -    159147 ACAAGCAGCCTCCTTGTC------CTGCACCTGCTCCTGCTCCTGTTCAGCCTTGGGCTCCAAGCT---------------------------CCC------ATAG----CCCAGGA----G---TACTGTGATACGACCATCGATGAAATTGCACATGATCTCAGCATGCT---TTCACCCTTGTTCTTGAAA 
s cow.ENm002_1            88336 156 +   1026482 ATGAGCAGTCTCTCCATC------TTGCACCTCCTTCTGCTCCTG------CTTGCACTCCATGCTCCTCAGGCAAAGGGGTTGCC-------TGT------CGTGACATCGAGGAC----T---CCATATTCTATGTTGATGAAGGAAATTATGGATGACCTA---AAGAA---AATAACTCCGAGTCCAGAA 
s canFam1.chr11        21697475 159 +  75769841 ATGAGCAGCTTCCCCATC------CTGCACCTTCTCTTGCTCCTG------CTTGGATGCCAAGTCCCACAGGCACAGGGGAGGCC-------TTT------TTCGACAGACCTGCC----TAAGCAATACTTCACAATGATCAATGAAATTATGGAGATGTTA---AACAA---GTCACCCTCGCCTTCAGAA 
s rfbat.ENm002_1         196855 165 +   1031937 ATGAGCAGCCGCCCCATC------CTGCACGTGTTTCTGCTCCTG------CTCACACTCCACGCCCCTCGGGCACAGGCGCAGCC-------CATAAGGCAATCGAGGCAATTGAC----TAAGGACTATGCCAACATGATGGCAGAACTTGAGACCATCCTC---AACAA---TCCTACTGTGCCTCCGCCA 
s shrew.ENm002_4          12091 141 +     27863 ATGAGCTGCCTTCCCA------------GACTTCTCTTGCTCGTT------CTCGGACTCCATGTGACTCAGGTCCAGGGG---------------------ACCGACAGCTTAAAA----T----CCTGCTTCCAGAGGACCACTGAAATTAGGACCATCCTA---AAGAA---CTCAACTTCACCTTCACCA 
s armadillo.ENm002_1     188393 162 +   1193614 ATGGGGACACTCCCTGCC------CTGCCCCTGCTCCTGCTCCTGCTAGGCCTCGGGCTCCGAGCCCCTCAGGCCCAGGGGCTGCC-------GGT------GAACATCACTTTTAA----G---AAGTGCCAGATCATGGTCAAAGAAATTCAACAATTGCTA---AACAT---GATAACTTTGCGTCCAGGG 
s elephant.ENm002_1      163836 162 +    635078 ATGAGCAGCCTCCCCACC------CTACACCTTCTCCTGCTCCTGCTCAGCCTTGAACTTCAAGCCCCCAAGGCCCAGGGGATGCC-------TGT------GACAGCACCCCAGCA----T------TACAGTGTGATGATCAATGAAATCAAGGAGATCTTA---CAGAAGTCTCCACCTTTGAATTCAGCA 
s tenrec.ENm002_17         5979 168 -     11374 TCAAGCAGCCTCCGCAGC------CTGCACTTTCTTCTGCTCGCGCTTGTCCTTGGGCTTCAAGTCCCTCAGAGCCAGGAGATGCC-------TCT------GACAACACTCTCGCC----TAATGAATACTGTGACATGATCACCGAAATCCTGCATATCCTA---AATTCCTGGCCACCTGCACATCCATGG 

a score=1226763.0
s hg17.chr5              49301194 71 - 180857866 TCTCCAATAAGTGGTTCCATGAACGAGGACAGGAGTTCTTGAGACCTTGTGGATCAACAGAAGTTGACTGA 
s panTro1.chr4           50489570 71 - 188378868 TCTCCAATAAGTGGTTCCATGAACGAGGACAGGAGTTCTTGAGACCTTGTGGATCAACAGAAGTTGACTGA 
s baboon.ENm002_1          769100 71 -   1082345 TCTCCAATAAGTGGTTCCATGAACGAGGACAGGAGTTCTTGAGACCTTGTGGATCAACAGAAGTTGACTGA 
s rheMac1.SCAFFOLD125981    56370 71 -     83070 TCTCCAATAAGTGGTTCCATGAACGAGGACAGGAGTTCTTGAGACCTTGTGGATCAACAGAAGTTGACTGA 
s marmoset.ENm002_1        801321 71 -   1056904 TCTCCAATAAGTGGTTCCATGAACGAGGACAGGAGTTCTTGAGGCCTTGTGGATCAACAGAAGTTGACTGA 
s galago.ENm002_1          714714 71 -   1185430 TCTCCAATAAGTGGTTCCATGAACGAGGACAAGAGTTCTTGAGGCCTTGTGGATCAACAGAAGTTGACTGA 
s rn3.chr10              39564174 71 + 110733352 TCTCCAATAAGTGGTTCCATGAGCGAGGACAGGAGTTCTTGAGGCCTTGTGGGACAACGGAAGTCGATTGA 
s mm6.chr11              53884031 71 + 121803636 TCTCCAACAAGTGGTTCCATGAGCGAGGACAGGAGTTCTTAAGACCTTGTGGAACAACGGAAGTTGATTGA 
s rabbit.ENm002_15         124175 71 -    131241 TTTCCAACAAGTGGTTTCATGAACGAGGACAGGAGTTCCTGAGACCTTGTGGATCAACAGAAGTTGACTGA 
s cow.ENm002_1             739358 71 -   1026482 TCTCCAATAAGTGGTTCCATGAACGAGGACAGGAATTCTTGAGGCCGTGTGGATCGACAGAAGTTGACTGA 
s canFam1.chr11          53887430 71 -  75769841 TCTCCAATAAGTGGTTCCATGAACGAGGACAGGAATTCTTGAGGCCATGTGGATCAACAGAAGTTGACTGA 
s rfbat.ENm002_1           709196 71 -   1031937 TCTCCAATAAGTGGTTCCATGAACGAGGCCAGGAGTTCTTGAGGCCGTGTGGATCAACAGAAGTCGACTGA 
s shrew.ENm002_26           17278 71 -     36978 TCTCCAATAAATGGTTCCATGAGCGAGGACAGGAGTTCTTGAGGCCATGTGGATCAACAGAAGTTGACTGA 
s armadillo.ENm002_1       766196 71 -   1193614 TCTCCAATAAATGGTTCCATGAACGAGGACAGGAATTCTTGCGGCCTTGTGGATCCACAGAAGTTGACTGA 
s elephant.ENm002_1        374697 67 -    635078 TTTCCAATAGGTGGTTCTGTGAGTGAGGACAAGAGTTCTTAAGAC----TGGATCAACAGAAGTTGACTGA 
s tenrec.ENm002_37           2073 71 +      3017 TTTCCAATAAGTGGTTCCACGAGCGAGGACAGGAGTTCTTGAGGCCGTGTGGATCAACAGAGGTCGACTGA 
s monDom1.scaffold_13206  2440934 71 -   4254530 TTTCCAATAAATGGTTCCATGAGCGGGGGCAGGAGTTCTTGAGACGATGTGGATCAACAGAAGTCGACTGA 
s platypus.ENm002_17         4555 71 -     11151 TTTCAAATAAATGGTTCCATGAACGAGGACAGGAATTCTTGCGGCCTTGCGGATCCACAGAAGTTGATTGA 
s galGal2.chr13           1525722 71 -  17279963 TTTCAAACAAATGGTTTCATGAAAGAGGAAACGAATTCTTAAGACCCTGTGGGAGAACAGAGGTTGACTGA 
s tetNig1.chrUn_random    9715025 71 + 171761319 TATCCAACAAATGGATCCACGAACGAGGACAAGAGTGGCGACGACCTTGTGGCCTAGCTGAGGCTGAATGA 
s danRer2.chr17          16610097 71 +  42274751 TATCGAACAAATGGATACATGAACGAGGTCAAGAATTCAGACGGCCCTGTGCATTATCTGAGGTGGAATGA 

a score=1189329.0
s hg17.chr5              131621326 93 + 180857866 ATGCCCCATTCCGTGACCCTGCGCGGGCCTTCGCCCTGGGGCTTCCGCCT-GGTGGGCGGCC-GGGACTTCAGCGCGCCCCTCACCATCTCACGG 
s panTro1.chr4           137954377 93 + 188378868 ATGCCCCATTCCGGGACCCTGCGCGGGCCTTCGCCCTGGGGCTTCCGCCC-GGAGGGCGGCC-GGGACTTCAGCGCGCCCCTCACCATCTCACGG 
s baboon.ENm002_1           378441 93 +   1082345 ATGCCCCATTCCGTGACCCTGCGCGGGCCTTCGCCCTGGGGCTTCCGCCT-GGTGGGCGGCC-GGGACTTCAGCGCGCCCCTCACCATCTCGCGG 
s rheMac1.SCAFFOLD35277       8673 93 +     87441 ATGCCCCATTCCGTGACCCTGCGCGGGCCTTCGCCCTGGGGCTTCCGCCT-GGTGGGCGGCC-GGGACTTCAGCGCGCCCCTCACCATCTCGCGG 
s marmoset.ENm002_1         318554 93 +   1056904 ATGCCCCATTCCGTGACCCTGCGCGGGCCTTCGCCCTGGGGCTTCCGCCT-GGTGGGCGGCC-GGGACTTCAGCGCGCCCCTCACCATCTCGCGG 
s galago.ENm002_1           532402 93 +   1185430 ATGCCCCACTCCGTGACCCTGCGCGGGCCTTCGCCCTGGGGCTTCCGCCT-GGTGGGCGGCC-GGGACTTCAGCGCACCCCTCACCATCTCGCGG 
s rn3.chr10               71238657 93 - 110733352 ATGACCCACTCGGTGACCCTGCGCGGCCCTTCACCCTGGGGCTTCCGCCT-GGTGGGCGGCC-GTGACTTCAGTGCCCCCCTCACCATCTCGCGG 
s mm6.chr11               67981862 93 - 121803636 ATGACCCACTCGGTGACCCTGCGCGGCCCTTCACCCTGGGGCTTCCGCCT-GGTGGGCGGCC-GGGACTTCAGTGCTCCCCTCACCATCTCGCGG 
s rabbit.ENm002_15           73204 95 +    131241 ATGCCCCACTCCGTGACCCTGCGCGGCCCTTCGCCCTGGGGCTTCCGCCTTGGTGGGGAGCCCGGGACTTCAGCGCGCCCCTCACCATCTCGCGG 
s cow.ENm002_1              342255 93 +   1026482 ATGCCCCACTCGGTGACCCTGCGCGGCCCTTCACCCTGGGGCTTCCGCCT-GGTGGGCGGCC-GGGACTTCAGCGTACCCCTCACCATCTCGCGG 
s canFam1.chr11           21937834 93 +  75769841 ATGCCGCACTCCGTGACCCTACGCGGCCCGTCGCCCTGGGGCTTCCGCCT-GGTAGGCGGCC-GGGACTTCAGCGCACCCCTCACCATCTCGCGG 
s rfbat.ENm002_1            375487 93 +   1031937 ATGCCCCACTCCGTGACTCTGCGCGGCCCTTCGCCCTGGGGCTTCCGCCT-GGTGGGCGGCC-GGGACTTCAGCGCACCCCTCACCATCTCGCGG 
s shrew.ENm002_2             15566 93 +    110226 ATGTCCCTCTCCGTGACCCTGCGCGGCCCTTCGCCCTGGGGCTTCCGCCT-GGTGGGCGGCC-GGGACTTCAGCGCGCCCCTCACCATCTCGCGG 
s armadillo.ENm002_1        504657 93 +   1193614 ATGCCCCACTCCGTGACCCTGCGCGGGCCTTCGCCCTGGGGCTTCCGCCT-GGTGGGCGGCC-GAGACTTCAGCGCGCCCCTCACCATCTCGCGG 
s monDom1.scaffold_13206   2142138 92 +   4254530 ATGCCCCACACAGTCACTCTCCAGGGTCCCTCACCCTGGGGCTTCCG-CT-GGTGGGCGGCA-AGGACTTTAGTACCGCTCTCACCATCTCCCGG 
s galGal2.chr13           15804608 93 +  17279963 ATGCCGCACTCGGTGGCCCTGCGCGGCCCCTCGCCGTGGGGTTTCCGCCT-GGTGGGCGGTA-AGGACTTCAGCACGCCGCTGACCATCTCCAGG 
s tetNig1.chr7             2651983 93 -  11099225 ATGACTCAGACCGTGACACTGAAAGGACCCTCTCCTTGGGGGTTCCGGCT-GGTGGGAGGAC-GTGATTTCAGCACCCCTTTAACCATCTCCAGG 
s fr1.chrUn              144492794 93 + 349519338 ATGTCGCAGACCGTTACACTAAAGGGACCCTCTCCTTGGGGGTTCCGGCT-GGTGGGAGGAC-GCGATTTCAGCACCCCGTTAACCATCTCCAGG 
s danRer2.chr13           21369717 93 -  37658979 ATGCCTCAGCGGGTTGTTTTACAAGGTCCCGGGCCATGGGGATTCCGTCT-GGTCGGGGGTA-AAGATTTCGAGCAGCCTCTGACTATCTCGAGG 

a score=125058.0
s hg17.chr5              49010314 11 - 180857866 GTGCACCGTAG 
s panTro1.chr4           50198344 11 - 188378868 GTGCACCGTAG 
s rheMac1.SCAFFOLD40231     28602 11 +     82136 GTGCACCATAG 
s marmoset.ENm002_1        515263 11 -   1056904 GTGCACCGTAG 
s galago.ENm002_1          406123 11 -   1185430 GTGCACCGTAG 
s rn3.chr10              39235970 11 + 110733352 GTGCACCATAA 
s mm6.chr11              53529277 11 + 121803636 GTGCACCATAG 
s rabbit.ENm002_24          70135 11 -    167141 GTGCACCGTAG 
s cow.ENm002_1             468636 11 -   1026482 GCGCACCATAG 
s canFam1.chr11          53628245 11 -  75769841 GTGCACCATAG 
s rfbat.ENm002_1           457276 11 -   1031937 GTGCCCCGTAG 
s shrew.ENm002_10           11167 11 -     19628 GCGCACCCTAG 
s armadillo.ENm002_1       468151 11 -   1193614 GTGCACCGTAG 
s monDom1.scaffold_13206  2624204 11 +   4254530 GTGGGCAGTAA 
s platypus.ENm002_9         15235  4 -     39966 -------GCAG 
s galGal2.chr13           1369938  4 -  17279963 -------GCAG 

a score=879196.0
s hg17.chr5              49010200 114 - 180857866 GGGATATTGGGCTGAGTCTACAGCGTGTCTTCACAGATCTGAAGAACA---TGGATGCCACC---TGGCTGGACAGCCTGCTGACCCCA---GTCCG---GTTGCCCTCC---ATCCAGGCCATTCCCT 
s panTro1.chr4           50198230 114 - 188378868 GGGATATTGGGCTGAGTCTACAGCGTGTCTTCACAGATCTGAAGAACA---TGGATGCCACC---TGGCTGGACAGCCTGCTGACCCCA---GTCCG---GTTGCCCTCC---ATCCAGGCCATTCCCT 
s baboon.ENm002_1          481253 114 -   1082345 GTGATATTGGGCTGAGTCTACAGCGCGTCTTCACAGATCTGAAGAACA---TGGATGCCACC---TGGCTGGACAGCCTGCTGACCCCA---GTCCG---GTTGCCCTCC---ATCCAGGCCATTCCCT 
s rheMac1.SCAFFOLD40231     28488 114 +     82136 GTGATATTGGGCTGAGTCTACAGCGCGTCTTCACAGATCTGAAGAACA---TGGATGCCACC---TGGCTGGACAGCCTGCTGACCCCA---GTCCG---GTTGCCCTCC---ATCCAGGCCATTCCCT 
s marmoset.ENm002_1        515149 114 -   1056904 GTGATATTGGGCTGAGTCTACAGCGTGTCTTCACAGATCTGAAGAACA---TGGATACCACC---TGGCTGGACAGCCTGTTTACTCCA---GTCCG---GTTGCCCTCC---ATTCAGGCTATTCCCT 
s galago.ENm002_1          406006 117 -   1185430 GGGATACTGGGCTGAACCTACAACGCGTCTTCACAGATCTGAAGAACA---TGGACACCAGC---TGGCTGGACAGCCTGCTGACCCCA---GTCAG---GCTGCCCTCCTCTATCCAGGCCATTCCTT 
s rn3.chr10              39235850 120 + 110733352 GGGACATCGAGATAGGCATACAGCGTGTCTTCACAGAGATGAAGAATA---TGGACCCCGTCATGTGGATGGACACCCTGCTGGGCAACTCTACCAG---GCCGCCCTCC---ATTCAGGCTATTCCTT 
s mm6.chr11              53529154 123 + 121803636 GGGACATTGGGATAGGCATACAACATGTCTTCACGGAGATGAAGAATA---TGGACTCCATCATGTGGATGGACAGCCTGCTGGGCAACTCTGTGAGGCTGCCGCCCTCT---ATTCAGGCCATTCCTT 
s rabbit.ENm002_24          70021 114 -    167141 GGGACATTGGTCTGAGCCTACACCGCGTCTTCACAGATCTCAAGAACA---TGGACAGCAGC---TGGTTGGACAGCCTGCTGCCCCAA---GTCAG---GCTGCCTTCT---ATCCAGGCCATTCCTT 
s cow.ENm002_1             468534 102 -   1026482 GTTATATTGGCCTGA------------TATCTTCAGATATGAAGAACA---TGGATCCCAGC---TGGTTGGACAGCCTGCTCACCCCA---GTCAG---GCTGCCCTCC---ATCCAGGCCATTCCTT 
s canFam1.chr11          53628143 102 -  75769841 GGTATGTTGGGCTGA------------TCTCTTCAGATCTGAAGAACA---TGGACACCAGC---TGGCTGGACAGCCTGTTGACTCCA---GTCAG---ACTGCCCTCC---ATCCAGGCCATTCCTT 
s rfbat.ENm002_1           457162 114 -   1031937 GGGATATCGGGCTGAGCCTACACCGTGTCTTCACAGATCTGAAGAACA---TGGACACCAGC---TGGCTGGACAGTCTGCTGACCCCA---GTCAG---GCTGCCCTCC---ATCCAAGCCATTCCTT 
s shrew.ENm002_10           11053 114 -     19628 GGGACCCGGGGATGAGCGTACACCCTGTCTTCACAGACCTGAAGAACA---TGGACTCCATC---TGGCTGGATAACATGCTCACCCCA---GTCAG---GCTGACTTCC---GTCCAGCCCATTCCCT 
s armadillo.ENm002_1       468037 114 -   1193614 GAGATATTGGGCTGAGTCTCCAACGCGTTTTCACAGATCTGAAGAATA---TGGATGCCAGC---TGGCTGGAGAACCTGCTGACCCCC---GTCAG---GCTGTCTTCC---ATCCAGGCCATTCCTT 
s monDom1.scaffold_13206  2624090 114 +   4254530 AAGTTATTGAATTGAATTTACATCAAGCCTTCACAGAGCTGAGAACCT---TGGATGCAAGT---TGGATGGACACCTTGTTGATGCCT---GTCCG---ACAAACTAGT---ATCCAAGCTATTTCCT 
s platypus.ENm002_9         15133 102 -     39966 GGGACATCGAGCTGAAT------------TTCACTGACCTGAAAAGCT---TGGACCCCACC---TGGATGGACTCCATGCTGACCCTC---GTCCG---GCCCCCCAAC---ATCCAAGCCATCTCCT 
s galGal2.chr13           1369845  93 -  17279963 GTGCAGCAGAGTTGGAGTTCCG------CATGATGGACCAGAAGAGCAGCCTGGACTTCTCC---TGGCTGGACACC---------------GTCAG---AC------CC---ATGCAGGCCATCTCCT 

a score=590628.0
s hg17.chr6              108594662 25 + 170975699 ATGAGCAAGCCAGCCGGATCAACAA 
s panTro1.chr5           110895281 25 + 175429504 ATGAGCAAGCCAGCCGGATCAACAA 
s baboon.ENr323_2           350996 25 +    781787 ATGAGCAAGCCGGCCGGATCAACAA 
s rheMac1.SCAFFOLD106250      5074 25 +     19134 ATGAGCAAGCCGGCCGGATCAACAA 
s marmoset.ENr323_1         410083 25 +    749449 ATGAGCAAGCCGGCCGGATCAACAA 
s galago.ENr323_1           271254 25 +    716639 ATGAGCAAGCCCGCAGGATCAACAA 
s rn3.chr20                8761429 25 -  55296979 ATGAGCAAGCCCGCCGGATCAACAA 
s mm6.chr10               87602147 25 - 130291745 ATGAGCAAGCCCGCCGGATCAACAA 
s rabbit.ENr323_1           252898 25 +    552800 ATGAGCAAGCCGGCTGGATCAACAA 
s cow.ENr323_1              266114 25 +    670861 ATGAGCAAGCCGGCCGGATCAACAA 
s canFam1.chr12           68179741 25 +  75455811 ATGAGCAAGCCGGCCGGATCAACAA 
s rfbat.ENr323_1            259972 25 +    601958 ATGAGCAAGCCCGCCGGATCAACAA 
s shrew.ENr323_13            12916 25 +     40410 ATGAGCAAGCTCGCCGGATCAACAA 
s tenrec.ENr323_22            7701 25 -     11388 ATGAGCAAGCCGGCCGGATCAACAA 
s monDom1.scaffold_18722   1528134 25 -  10654489 ATGAGCAAGCCGACGGGATCAACAA 
s platypus.ENr323_6           1768 25 +      6185 ATGAACAAGCCGGCCGGATCAACAA 
s galGal2.chr3            42740700 25 - 108638738 ATGAGCAAGCCGGCGGGATCAACAA 
s xenTro1.scaffold_975      180618 25 -    405956 ATGAGCAAACCGACAGGATCAACAA 
s tetNig1.chr14            6199319 25 -   9655887 ATGAGTAAAGCGGCCGGCTCAACAA 
s fr1.chrUn              210130082 25 + 349519338 ATGAGCAAAGCCGCCGGCTCAACAA 
s danRer2.chr16            5047159 25 +  42763181 ATGAGCAAGCCTGCTGGTTCAACAA 

a score=1513845.0
s hg17.chr6               62335548 106 - 170975699 GGTCGCTGGTCATCCTCTGGCACAGAACGAA-CGTTGTCTTCACATGTTTTTACAAGATGAAATAATAGATAAAAGCTATACTCCATCTAAAAT-AAGACATGCCTGA 
s panTro1.chr5            64489302 106 - 175429504 GGTCGCTGGTCATCCTCTGGCACAGAACGAA-CGTTGTCTTCACATGTTTTTACAAGATGAAATAATAGATAAAAGCTATACTCCATCTAAAAT-AAGACATGCCTGA 
s baboon.ENr323_2           384851 106 -    781787 GGTCGCTGGTCATCCTCTGGCACAGAATGAA-CGTTGTCTTCACATGTTTTTACAAGATGAAATAATAGATAAAAGCTATACTCCATCTAAAAT-AAGACATGCCTGA 
s rheMac1.SCAFFOLD121188     42427 106 -     60196 GGTCGCTGGTCATCCTCTGGCACAGAATGAA-CGTTGTCTTCACATGTTTTTACAAGATGAAATAATAGATAAAAGCTATACTCCATCTAAAAT-AAGACATGCCTGA 
s galago.ENr323_1           401453 106 -    716639 GGTCGCTGGTCATCCTCTGGCACAGAATGAA-CGTTGTCTCCACATGTTTTTACAGGATGAAATAATAGATAAAAGCTATACTCCATCTAAAAT-AAGACATGCCTGA 
s mm6.chr10               42641343 105 + 130291745 GGTCGCTGGTCATCCTCTGGCCCAGAATGAA-CGTTGTCTTCACATGTTTTTACAGGATGAAATTATAGATAAAAGCTATACTCCATCTAAAAT-AAGACATGCCTG- 
s rabbit.ENr323_1           261258 106 -    552800 GGTCGCTGGTCATCCTCTGGCACAGAATGAA-CGTTGTCTTCACATGTTTTTACAGGATGAAATCATAGATAAAAGCTATACTCCCTCTAAAAT-AAGGCATGCCTGA 
s cow.ENr323_1              492746 106 -    670861 GGTCGCTGGTCACCCTCTGGCACAGAATGAA-CGTTGTCTTCACATGTTTTTACAGGATGAAATTATAGATAAAAGCTATACTCCATCTAAAAT-AAGACATGCCTGA 
s canFam1.chr12            7232900 107 -  75455811 GGTTGCTGGTCATCCTCTGGCACAGAATGAAACGTTGTCTTCACATGTTTTTACAGGACGAAATTATAGATAAAAGCTATACACCATCTAAAAT-AAGACATGCCTGA 
s rfbat.ENr323_1            301856 106 -    601958 GGTCGCTGGTCATCCTCTTGCACAGAATGAA-CGTTGTCTTCACATGTTTTTACAGGATGAAATAATAGATAAAAGCTATACTCCATCTAAAAT-AAGACATGCCTGA 
s shrew.ENr323_14             3002 107 -     16130 GGTCGCTGGTCATCCTCTGGCACAAAATGAA-CGATGTCTTCACATGTTTTTACAAGATGAAATAATAGATAAAAGCTATACTCCATCTAAAATTGAGACATGCCTGA 
s armadillo.ENr323_1        357954 106 -    592733 GGTCGCTGGTCATCCTCTGGCACAGAATGAA-CGTTGTCTTCACATGTTTTTACAGGACGAAATAATCGATAAAAGCTACACTCCATCCAAAAT-AAGACATGCCTGA 
s tenrec.ENr323_29           11724 106 +     27677 GGTCGCTGGGCATCCTCTGGCACAGAATGAG-CGTTGTCTTCACATGTTTTTACAGGACGAAATCATAGATAAAAGCTATACTCCATCCAAAAT-AAGACATGCCTGA 
s monDom1.scaffold_18722   9049824 106 +  10654489 GGTTGCCGGCCACCCCTTGGCACAGAACGAA-CGCTGTCTTCACATGTTTTTACAAGATGAAATAATAGATAAAAGTTATACTCCATCCAAAAT-CAGACATGCCTGA 
s platypus.ENr323_2         103834 106 +    109570 GGTCGCTGGCCATCCTCTGGCGCAGAATGAG-CGTTGCCTGCATATGTTTCTACAAGACGAGATCATAGATAAGAGCTACACGCCATCCAAAAT-CCGGCATGCTTGA 
s galGal2.chr3            65885276 106 + 108638738 GGTTGCAGGCCACCCACTGGCACAGAATGAG-CGCTGTCTTCATATGTTCTTACAAGATGAAGTAATAGACAAAAACTACACACCATCCAAAAT-AAGACATACTTGA 
s xenTro1.scaffold_975      199631 106 +    405956 AGTTGCGGGACATCCATTGGCGCAGAATGAA-CGGTGCCTTCATATGTTTTTACAAGATGAAATTTTAGACAAGAACTACACCCCATCCAAAAT-AAGACATGCCTAA 
s tetNig1.chr14            3449270 106 +   9655887 AGTGGCCGGTCATCCTCTAGCGCAGAACGAG-CGATGTCTGCACATGTTTCTACAGGACAAAGTCTTGGACAAGAACTACACCCCGTCCAAGAT-CAGACAAGCCTGA 
s fr1.chrUn              139382558 106 - 349519338 AGTGGCCGGTCATCCTCTCGCCCAGAACGAG-CGATGCCTGCACATGTTTCTACAGGACAAGGTCTTGGACAAGAACTACACCCCCTCTAAGAT-CAGACAAGCCTGA 
s danRer2.chr16           37703340 106 -  42763181 AGTTGCTGGTCATCCATTGGCCCAAAATGAG-CGCTGCCTGCACATGTTCCTACAGGATGAGTCTGTGGATAAAAACTACACCCCTTCCAAAAT-TAGACAAGCCTAA 

a score=556773.0
s hg17.chr6              108722976 68 + 170975699 ATGGCGGCCTCCTGGTCGCTCTTGGTTACCCTGCGCCCCTTAGCACAGAGCCCGCTGAGAGGGAGATG 
s panTro1.chr5           111023287 68 + 175429504 ATGGCGGCCTCCTGGTCGCTCTTGGTTACCCTGCGCCCCTTAGCACAGAGCCCGCTGAGAGGGAGATG 
s baboon.ENr323_2           480166 68 +    781787 ATGGCGGCCTCCTGGTCGCTCTTGGTTACCTTGCGCCCCTTAGCACAGAGCCCGCTGAGAGGGAGATG 
s rheMac1.SCAFFOLD90296      34859 68 -    128257 ATGGCGGCCTCCTGGTCGCTCTTGGTTACCTTGCGCCCCTTAACACAGAGCCCGCTGAGAGGGAGATG 
s galago.ENr323_1           392338 68 +    716639 ATGGCGGCCTCCTGGCCGCTCGTGGTTACCCTGAGCTCGTTAGCTCGGGGCCAACTGAGAGGGAGATG 
s mm6.chr10               87706663 68 - 130291745 ATGGCGGCCTCCTGGTCGCCCTTGGTTACTCTGCGCTCCGCCGCGCGCAGCCGGCTGACTGGGAGAGG 
s rabbit.ENr323_1           370933 68 +    552800 ATGGCGGCCTCCTGGTCGCCCTTGGTTACCCTGCGCTCCTTAACGCAATGCCGGCTGAGAGGGAAATG 
s cow.ENr323_1              449447 65 +    670861 ATGGCGGCCTCATGGTCGCCCTTGGTTACCCTGTGC---TTAACGCAGAGCCGGCTGAGAGGGAGATG 
s rfbat.ENr323_1            353445 65 +    601958 ATGGCGGCCTCCCTGTCGCCCTTGGTTACTCTGCGA---TTAGTGCAGAGCCGGCTGAGAGGGAGATG 
s shrew.ENr323_20             5644 48 +     47540 CTGGTGATCTCCTGGATGCTTGTGGTTACCCTGCTT---TT-------AGCCAGCAAA---------- 
s armadillo.ENr323_1        326123 68 +    592733 ATGGCGGTCTCCTGGTCGCCCTTGGTTGCTCTACGTTCCTTAGTGCCGAGCCGGCTGAGAGGGAGATG 
s elephant.ENr323_1         501362 68 +    591253 ATGGCGACCTCCCGGTCTCCCTGGCTTGCTCTGCGCTCTTTAGTGCAGAGGCGGCTGAGAAGGAGATG 
s tenrec.ENr323_36           10006 68 -     17812 ATGGCGACCTCCTGTGCTCCCTTGCTGACTGTGCGCTCGCTCGTGCAGAGGCGGTTGAGGGGGAGATT 
s monDom1.scaffold_18722   1735980 68 -  10654489 ATGGCGGCTTCCTTGTCGCCCTGGGTTACTGTGCGGCCCCTGGTGCAGACCTGGGTGCGGGGCAGATG 
s platypus.ENr323_2          40319 59 -    109570 GAGCCGGACGCTT-----CCCCTG----CCCTGCGCTCCACGATGCGCTCCAGCCCGAGGGGGAGAGG 
s galGal2.chr3            42786700 30 - 108638738 AGGCTAGCATTCTCATCTTTTCTGGTTAAC-------------------------------------- 
s xenTro1.scaffold_975      244927 53 -    405956 ATGGCGGGTGCCGGTTCGCCCTTGGTTTCTATTCGTT---TGCTATGGAG----------GGTACC-- 

a score=389664.0
s hg17.chr6              108723044 71 + 170975699 TGTTGGGTGCGGGGCCTGG------------GCCGCCGCTCTCGCTCCTCTGGCCACCGCCCCTGG-GAAGCCCTTTTGGA-----AAG 
s panTro1.chr5           111023355 71 + 175429504 TGTTGGGTGCGGGGCCTGG------------GCCGCCGCTCTCGCTCCTCTGGCCACCGCCCCTGG-GAAGCCCTTTTGGA-----AAG 
s baboon.ENr323_2           480234 71 +    781787 TGTTGGGTGCGGGGCCCGG------------GCCGCCGCTCTCGCTCCTCTGGCCACCGCCCCTGG-GAAGCCCCTTTGGA-----AAG 
s rheMac1.SCAFFOLD90296      34927 71 -    128257 TGTTGGGTGCGGGGCCCGG------------GCCGCCGCTCTCGCTCCTCTGGCCACCGCCCCTGG-GAAGCCCCTTTGGA-----AAG 
s galago.ENr323_1           392406 71 +    716639 TGTTGGGTGTGGGGCTCGG------------GCCGCCGCTCTCGCTCCTCTGGCCACCGCCCCTGG-AAAGCCCCTATGGA-----AAG 
s mm6.chr10               87706731 71 - 130291745 TGTTGGGTGCGGGGCGCGG------------GTCGTCGCAATCCCTCCTCCGGCCCCTGGCCCTGG-GAAACCCCTGTGGA-----AAG 
s rabbit.ENr323_1           371001 71 +    552800 TGTGGGGTTCGGGGCCTGG------------GTCGCTGCCCCTGCTCCTCCCGCCACCGCCCCTGG-GAAGCCCCTTTGGA-----AAG 
s cow.ENr323_1              449512 71 +    670861 TGTTGGGTGCAGGGCTTGG------------GCCGCTGCTCTCACCCCTTCGGCCATCGCCCCTGG-AAACCCTCTTTGTA-----AAG 
s rfbat.ENr323_1            353510 71 +    601958 TTTTGGGTGCAGAGCCTGG------------TCCGCTGCTCTCGCCCCTCCGGCCACCGCCCCTGG-GAACCCCTTTTGGA-----AAG 
s shrew.ENr323_20             5692 62 +     47540 ---------------CCGG------------CCTGTTCCTCTAGTTTCTCTGGCCTTCATCCCTGGAAAAATCCTTTTAGATCTTCACA 
s armadillo.ENr323_1        326191 71 +    592733 TATTGGGTGCGGGGCCTGG------------GCCGCCGCTCTCGGCCCTCAGGTCGCCGATCCTAG-GAAGCCCCTTTCGA-----AAG 
s elephant.ENr323_1         501430 71 +    591253 TGTTGGGTTCGGGGACTGG------------GCCGCTGCTCTCGCCCCTCCGGCCGCCGCCCCTGG-GAAGCCCTTTTGGA-----AAG 
s tenrec.ENr323_36           10074 50 -     17812 GGTTAGGTGCGGGGACTG---------------------------------GGCCGCCGCCCCTGG-GAAGCCCCTTTGGA-----AAG 
s monDom1.scaffold_18722   1736048 83 -  10654489 CACCTGGTGGGGGGCTCGGGCAGCAGCCGCAGCCGCCGTTGGCTCTGCCCCTGCGACCGTCCCCGG-GAGGCCCCCTCGGA-----AAG 
s galGal2.chr3            42777543 47 - 108638738 -----GGCGCGGCGTGTTG------------TCCGTC--------------TGCTGCCGGCACGGG------CCCTGCCGA-----GAG 

a score=5085599.0
s hg17.chr7              113660517 168 + 158628139 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACCAGCTCTGAAGTAAGCACAGTAGAACTGCTGCATCTGCAACAACAGCAG 
s panTro1.chr6           115716623 168 + 161576975 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACCAGCTCTGAAGTAAGCACAGTAGAACTGCTGCATCTGCAACAACAGCAG 
s baboon.ENm012_1           268738 168 +   1163540 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACCAGCTCTGAAGTAAGCACAGTAGAACTGCTGCATCTGCAACAACAGCAG 
s rheMac1.SCAFFOLD40450      60344 168 +     79367 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACCAGCTCTGAAGTAAGCACAGTAGAACTGCTGCATCTGCAACAACAGCAG 
s marmoset.ENm012_1         156071 168 +   1183722 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACCAGCTCTGAAGTAAGCACAGTAGAACTGCTGCATCTGCAACAACAGCAG 
s galago.ENm012_1           214008 168 +   1130250 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACCAGCTCTGAAGTCAGCACAGTGGAACTGCTGCATCTGCAACAACAGCAG 
s rn3.chr4                40844510 168 + 187371129 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGGGATGGGAGATCAAG---TGGTGACACTAGCTCAGAAGTAAGCACAGTGGAGCTGCTGCATCTGCAACAACAGCAG 
s mm6.chr6                15184557 168 + 150245815 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTTTAAGCAGC---CAATTAGATGCTGGCAGCAGGGATGGGAGATCAAG---TGGTGACACCAGCTCTGAAGTAAGCACAGTGGAGCTGCTGCATCTGCAACAACAGCAG 
s rabbit.ENm012_30           37009 168 +    133243 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACCAGCTCTGAAGTAAGCACAGTAGAACTGCTGCATCTGCAACAACAGCAG 
s canFam1.chr14           56181068 168 +  63549963 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACCAGCTCGGAAGTAAGCACAGTAGAACTGCTGCATCTGCAACAACAGCAG 
s rfbat.ENm012_1            138663 168 +   1126473 ATGATG---CAGGAGTCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACCCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACGAGCTCTGAAGTAAGCACAGTGGAGCTGCTGCACCTGCAACAACAGCAG 
s shrew.ENm012_22             7166 168 -     11301 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACCAGCTCTGAAGTAAGCACAGTAGAACTGCTGCATCTTCAACAACAGCAG 
s armadillo.ENm012_1        176742 168 +   1087501 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACCAGCTCTGAAGTAAGCACAGTAGAACTGCTGCATCTGCAACAACAGCAG 
s elephant.ENm012_1         156619 168 +   1140293 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACCAGCTCTGAAGTAAGCACAGTGGAACTGCTGCACCTGCAACAACAGCAG 
s monDom1.scaffold_12363   4741898 168 -   6632154 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACGAGCACTGAAGTAAGCCCAGTAGAACTGCTGCATCTGCAACAACAGCAG 
s platypus.ENm012_1         161955 168 +    981645 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCACAATGGAATGAACACTCTGAACAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGACCAGG---CAGTGATACGAGCAGTGAAGTAAGCACAGTAGAACTGCTGCATCTGCAACAACAGCAG 
s galGal2.chr1           165171657 168 - 188239860 ATGATG---CAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACGAGCACTGAAGTAAGCACAGTGGAACTCCTGCATCTGCAACAACAGCAG 
s xenTro1.scaffold_17      1043536 168 +   3981052 ATGATG---CAGGAATCTGCAACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTAAGCAGC---CAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TAGTGACACGAGCAGTGAAGTAAGCACAGTAGAACTGCTGCATCTGCAACAACAGCAG 
s tetNig1.chr19             770904 177 -   5206847 ATGATGATGCAGGAGTCGGCCACAGAGACAATAAGCAACAGTTCAATGAGTCAAAATGGAATGAGCACCCTAAGCAGCAGCCAATTAGAGGCTGGCAGTAGAGATGGGAGATCAAGCGCTGGTGACACGAGCAGCGAAGTAAGCACAGTCGAGCTGCTGCATCTGCAACAACAGCAG 
s fr1.chrUn              206218861 177 + 349519338 ATGATGATGCAGGAGTCGGCCACAGAGACAATAAGCAACAGTTCAATGAGTCAAAATGGAATGAGCACCCTAAGCAGCAGCCAATTAGAGGCTGGCAGTAGAGATGGGAGATCAAGCGCTGGTGACACGAGCAGCGAAGTAAGCACAGTCGAGCTGCTGCATCTGCAACAACAGCAG 
s danRer2.chrUn           63954790 167 - 173451396 ATGATG---CAGGAGTCGGCCAATGAGACAATAAGCAACAGTTCAATGAGTCAAAATGGAATGAGCAGCCTAAGCAGC---CAATTAGATGCTGGCAGTAGAGATGGAAGATCAAG---TGGGGAGACGAGCAGTGAAGTAAGCGCAGTCGAGCTGCTGCATCTGCA-CAACAGCAG 

a score=5769709.0
s hg17.chr7                42115750 230 - 158628139 GCTCCCTGGGTACAGCAGGCCGTGTGTGCAACCTGACTTCCCGGGGCATGGACAGCTGTGAAGTCATGTGCTGTGGGAGAGGCTACGACACCTCCCATGTCACCCGGATGACCAAGTGTGGGTGTAAGTTCCACTGGTGCTGCGCCGTGCGCTGTCAGGACTGCCTGGAAGCTCTGGATGTGCACACATGCAAGGCCCCCAAGAACGCTGACTGGAC----------------------A-ACCGCTACAT-GA 
s panTro1.chr6             42777860 230 - 161576975 GCTCCCTGGGTACAGCAGGCCGTGTGTGCAACCTGACTTCCCGGGGCATGGACAGCTGTGAAGTCATGTGCTGTGGGAGAGGCTACGACACCTCCCATGTCACCCGGATGACCAAGTGTGGGTGTAAGTTCCACTGGTGCTGCGCCGTGCGCTGTCAGGACTGCCTGGAAGCTCTGGATGTGCACACATGCAAGGCCCCCAAGAACGCTGACTGGAC----------------------A-ACCCCTACAT-GA 
s colobus_monkey.ENm001_1    890225 230 -   1990688 GCTCCCTGGGTACAGCAGGCCGAGTGTGCAACCTGACTTCCCGGGGCATGGACAGCTGCGAAGTCATGTGCTGTGGGAGAGGCTACGACACCTCCCATGTCACCCGGATGACCAAGTGTGGATGTAAGTTCCACTGGTGCTGTGCCGTGCGCTGTCAGGACTGCCTGGAGGCCCTGGACGTGCACACATGCAAGGCCCCCAAGAACGCTGACTGGAC----------------------A-ACCCCCACAT-GA 
s baboon.ENm001_1            666649 230 -   1730495 GCTCCCTGGGTACAGCAGGCCGTGTGTGCAACCTGACTTCCCGGGGCATGGACAGCTGCGAAGTCATGTGCTGTGGGAGAGGCTACGACACCTCCCATGTCACCCGGATGACCAAGTGTGGGTGTAAGTTCCACTGGTGCTGCGCCGTGCGCTGTCAGGACTGCCTGGAGGCCCTGGATGTGCACACATGCAAGGCCCCCAAGAACGCTGACTGGAC----------------------A-ACCCCCACAT-GA 
s rheMac1.SCAFFOLD105306       3693 230 +    127482 GCTCCCTGGGTACAGCAGGCCGTGTGTGCAACCTGACTTCCCGGGGCATGGACAGCTGCGAAGTCATGTGCTGTGGGAGAGGCTACGACACCTCCCATGTCACCCGGATGACCAAGTGTGGGTGTAAGTTCCACTGGTGCTGCGCCGTGCGCTGTCAGGACTGCCTGGAGGCCCTGGATGTGCACACATGCAAGGCCCCCAAGAACGCTGACTGGAC----------------------A-ACCCCCACAT-GA 
s dusky_titi.ENm001_1        898051 230 -   2096432 GCTCCCTGGGTACAGCAGGCCGTGTGTGCAACCTGACTTCCCGGGGCATGGACAGCTGTGAAGTCATGTGCTGTGGAAGAGGCTATGACACCTCCCATGTCACCCGGATGATCAAGTGTGGGTGTAAGTTCCACTGGTGCTGTGCTGTGCGCTGTCAGGACTGCCTGGAAGCCCTGGACGTGCACACGTGCAAGGCACCCAAGAACGCTGACTGGAC----------------------A-ACCCCCACAT-GA 
s owl_monkey.ENm001_1        840611 230 -   2053814 GCTCCCTGGGTACAGCAGGTCGTGTGTGCAACCTGACTTCCCGGGGCATGGACAGCTGTGAAGTCATGTGCTGTGGAAGAGGCTACGACACCTCCCATGTCACCAGGATGATCAAGTGTGGGTGTAAGTTCCACTGGTGCTGTGCCGTGCGTTGTCAGGACTGCCTGGAAGCCCTGGACGTGCACACGTGCAAAGCACCCAAGAACGCTGACTGGAC----------------------A-AGCCCCACAT-GA 
s marmoset.ENm001_1          737214 230 -   1952403 GCTCCCTGGGTACAGCAGGCCGTGTGTGCAACCTGACTTCCCGGGGCATGGACAGCTGTGAAGTCATGTGCTGTGGAAGAGGCTACGACACCTCCCATGTCACCCGGATGATCAAGTGTGGGTGTAAGTTCCACTGGTGCTGTGCCGTGCGCTGTCAGGACTGCCTGGAAGCCCTGGACGTGCACACATGCAAGGCACCCAAGAACGCTGACTGGAA----------------------A-AGCCCCACAT-GA 
s mouse_lemur.ENm001_1       616267 230 -   1575427 GCTCCCTGGGTACAGCAGGCCGTGTGTGCAACCTGACTTCCCGGGGCATGGACAGCTGCGAAGTCATGTGCTGCGGGAGAGGCTATGACACCTCCCGTGTCACCCGGATGACCAAGTGCGAGTGTAAGTTCCACTGGTGCTGCGCTGTGCGCTGTCAGGACTGCCTGGAGGCCCTGGACGTGCACACGTGTAAGGCCCCCAAGAACGCTGACTGGGC----------------------G-ACCCCCACAT-GA 
s galago.ENm001_1            668888 230 -   1783853 GCTCCCTGGGTACAGCAGGCCGTGTGTGCAACCTGACGTCCCGGGGCATGGACAGCTGTGAAGTCATGTGCTGCGGGAGAGGCTATGACACCTCCCGTGTCACCCGGATGACCAAGTGCGAGTGTAAGTTCCACTGGTGCTGCGCCGTCCGCTGTCAGGACTGCCTGGAGGCCTTGGATGTGCACACATGCAAGGCCCCCAAGAACGCCGACTGGAC----------------------A-ACCCCCACAT-GA 
s rn3.chr4                143551225 230 - 187371129 GCTCCCTGGGTACAGCAGGCCGTGTGTGCAACTTGACTTCCCGAGGCATGGACAGCTGCGAAGTTATGTGTTGTGGGAGAGGCTATGACACATCCCATGTCACCCGGATGACCAAGTGTGAGTGTAAATTCCACTGGTGCTGTGCCGTGCGCTGTCAGGACTGCCTGGAAGCCCTGGACGTGCACACATGCAAGGCCCCCAAGAGTGCCGACTGGAC----------------------A-ACTCCTACAT-GA 
s mm6.chr6                132272329 230 - 150245815 GCTCCCTGGGTACAGCGGGCCGTGTGTGCAACTTGACTTCCCGAGGCATGGACAGCTGCGAAGTTATGTGTTGTGGGAGAGGCTATGACACATCCCACGTCACCCGGATGACCAAGTGTGAGTGTAAATTCCACTGGTGCTGTGCCGTGCGCTGTCAGGACTGCCTGGAGGCCCTGGACGTGCACACATGCAAGGCCCCCAAGAGTGCCGACTGGGC----------------------G-ACGCCTACAT-GA 
s rabbit.ENm001_1            669436 230 -   1889755 GCTCCCCGGGTACAGCAGGTCGTGTGTGCAACCTGACGTCCAGAGGCATGGACAGCTGTGAAGTCATGTGCTGCGGGAGAGGCTACGACACCTCCCGCGTCACCCGGATGACCAAGTGCGAGTGTAAGTTCCACTGGTGCTGTGCCGTGCGTTGCCAGGACTGCCTGGAGGCCCTGGACGTGCACACATGCAAGGCTCCCAAGAGTGCTGACTGGAC----------------------A-ACCCCAACAT-GA 
s cow.ENm001_1               942111 230 -   2061479 GCTCCCTGGGTACAGCGGGCCGTGTGTGCAACCTGACTTCCCGGGGCATGGACAGCTGCGAAGTCATGTGCTGTGGCAGAGGCTACGACACCTCCCACATTACCCGGAAGACCAAGTGTGAGTGTAAGTTCCACTGGTGCTGTGCCGTGCGCTGCCAGGACTGCGTGGAGGCCCTGGACGTGCACACGTGCAAGGCCCCGAAGAGCCCCGACTGGGC----------------------T-GCTCCGACAT-GA 
s canFam1.chr14             4851287 230 -  63549963 GCTCCCCGGGGACGGCGGGCCGCGTGTGCAACCTGACTTCCCGCGGCATGGACAGCTGCGAGGTCATGTGCTGCGGGAGAGGCTACGACACGTCCCGCGTCACGCGGATGACCAAGTGCGAGTGTAAGTTCCACTGGTGCTGCGCCGTGCGCTGTCAGGACTGCCTGGAGGCCCTAGACGTGCACACGTGCAAGGCCCCCACGAGCGCCGACTGGGC----------------------G-GCTCCCACAT-GA 
s rfbat.ENm001_1             669070 230 -   1737318 GCTCCCTGGGTACAGCAGGACGTGTGTGCAACCTGACCTCCCGAGGCATGGACAGCTGTGAAGTCATGTGCTGCGGGAGAGGCTACGACACGTCCCGCGTCACGAGGATGACCAAGTGTGAGTGTAAGTTCCACTGGTGCTGTGCTGTGCGTTGTCAGGACTGCCTGGAGGCCCTGGACGTACACACATGCAAGGCTCCGAAGAGTGCCGACTGGGC----------------------A-GCTCCCACAT-GA 
s shrew.ENm001_34              1814 230 -     60085 GCTCCTTGGGTACAGCAGGCCGTGTGTGCAACCTGACTTCCCGAGGCATGGACAGCTGTGAAGTCATGTGCTGCGGGAGAGGCTATGACACCTCCCGAGTCACCCGGATGACCAAATGCGAGTGTAAGTTCCACTGGTGCTGCGCCGTGCGCTGTCAGGACTGCCTGGAGGCCCTCGATGTGCACACGTGCAAGGCCCCCAAGAGCGCTGATTGGGC----------------------A-GCTCCCACTT-GA 
s armadillo.ENm001_1         733040 230 -   1656816 GCTCTCTGGGTACAGCAGGCCGTGTGTGCAACCTGACTTCCCGAGGCATGGACAGCTGCGAAGTCATGTGCTGCGGGAGAGGCTACGACACCTCCCATGTCACCCGGATGACCAAATGTGAGTGTAAATTCCACTGGTGCTGTGCTGTGCGCTGTCAGGACTGCCTGGAGGCTCTGGACGTGCACACATGCAAGGCCCCCAAGAGTGCTGACTGGGC----------------------A-GTTCCCACAT-GA 
s elephant.ENm001_1          505343 230 -   1533827 GCTCCCCGGGTACAGCAGGTCGAGTGTGCAACCTGACTTCCCGAGGCATGGACAGCTGCGAAGTCATGTGCTGCGGGAGAGGCTACGACACCTCTCGCATCACCCGGATGACCAAGTGCGAGTGTAAGTTCCACTGGTGCTGCGCCGTGCGCTGTCAGGACTGCCTGGAGGCTCTGGATGTGCACACGTGCAAGGCCCCCAAGAGCGCCGACTGGGC----------------------A-GCTCCTACAT-GA 
s tenrec.ENm001_104           44299 230 -     64374 GCTCCCCAGGTACAGCAGGCCGAGTCTGCAACCTGACCTCCCGAGGCATGGACAGCTGCGAAGTCATGTGCTGCGGGAGAGGCTACGACACCTCCCGCGTCACCCGCATGACCAAGTGTGAGTGTAAGTTCCACTGGTGCTGTGCCGTGCGCTGTCAGGACTGCCTGGAGGCTCTGGACGTGCACACCTGCAAAGCCCCCAAGAGCGCCGACTGGGC----------------------G-GTGCCCACAT-GA 
s monDom1.scaffold_13572    3944555 230 +   5827465 GTTCCCTGGGTACTGCAGGTCGGGTGTGCAACCTGACCTCCCGTGGCATGGACAGCTGTGAAGTCATGTGCTGCGGAAGGGGCTATGACACTTCCCGGGTCACCCGAATGACCAAATGCGAGTGTAAGTTCCATTGGTGCTGTGCTGTGCGCTGTCAGGACTGTTTGGAAGTAGTGGACGTGCACACGTGCAAAGCCCCCAAGAGTCCTGATTGGGT----------------------G-GCACCCACAT-GA 
s platypus.ENm001_1          574264 230 -   1321799 GCTCCCTAGGGACGGCGGGCCGGGTGTGCAACCTGACGTCCCGCGGCATGGACAGCTGCGAGGTCATGTGCTGCGGGAGGGGCTACGACACGGCCCGCGTCACCAGGATGACCAAGTGCGAGTGCAAGTTCCACTGGTGCTGCGCCGTCCGCTGCCAGGACTGCCTGGAAGCCCTCGACGTGCACACGTGCAAAGCCCCCAGCAGCGCCAGCGAGGG----------------------C-GCCCCCACAT-GA 
s galGal2.chr1             21683096 230 + 188239860 GCTCTCCGGGGACGGCCGGCCGGGTGTGCAACCAGACGTCCCGCGGCATGGACAGCTGTGAGGTGATGTGCTGCGGCCGTGGCTACGACACGTTGCGCGTCAGCAGGATGACCAAATGCGAGTGCAAGTTCCACTGGTGCTGCGCGGTGCGCTGCCAGGACTGCCTGGAGGAGGTGGACATCCACACGTGCAAGGCGCCCAAGGCTGCGGGCTGGGC----------------------C-TCCCGGACAT-GA 
s xenTro1.scaffold_17       1744814 231 -   3981052 GTTCCCTTGGAACAGCTGGAAGAATCTGCAACCAGACCTCCCGTGGCATGGACAGCTGTGAGGTCATGTGCTGTGGTAGAGGGTATGACACTGCTCGCATCACCAAGATGTCAAAATGTGAGTGCAAGTTCCACTGGTGCTGCTCAGTACGGTGCAAGGACTGCATAGAAACTGTGGATATTCACACATGCAAAGCACCCAAAGGTGTCATCTGGAA----------------------GGAAAATTACAT-GA 
s tetNig1.chr13             1695957 226 -  12408495 GCTCGATGGGCACCGGGGGGCGTGTCTGCAACAGGACGTCCCGTGGCGTGGATGGCTGCGAGGTGATGTGCTGCGGCCGCGGTTACGACACGTCCCGGGTCAGCCGCACCACCAAGTGCGAGTGCAAGTTCCACTGGTGCTGCGCCGTGCTGTGCCGGGACTGCCAGCAGCAGGTGGACGTGCACACCTGCAAGGGCCAGACG-----TGACCGGGA----------------------C-GCTCCGGTCCTCG 
s fr1.chrUn               231850852 248 + 349519338 GGTCGCTGGGGACCGGCGGGCGCCTCTGCAACAGGACGTCCCCCGGCACCGACGGCTGCGAGGTGATGTGCTGCGGCCGGGGCTACGACACGTCCCGGGTCGGCCGCACCACCAAGTGCGAGTGCAAGTTCCACTGGTGCTGCGCCGTGCTCTGCCGAGACTGCCACCAGCAGGTGGACGTGCACACCTGCAAGGGCCTGACG-----TGACCTGGCCCCCCCCCGCGGAACCAGCAGTC-GTCCCGGCCCGCG 
s danRer2.chr6               760809 224 -  33212616 GTTCTCTGGGTACGTCAGGACGGGTGTGCAACAAGTCCTCCAGAGGCATGGACGGCTGTGAGATCATGTGCTGCGGCCGCGGGTACGACACCACCCGTGTAAACCGCATGACCAAATGCGAGTGCAAGTTTAAATGGTGCTGCGCTGTGGAGTGCAGAGACTGCGAGGAAACGGTGGACGTCCACACTTGTAAACTACACAAG-----AAACCCGAC----------------------T-GGCTCGAT--TTG 

a score=1087008.0
s hg17.chr7              116714099 15 + 158628139 ATGCAGAGGTCGCCT 
s panTro1.chr6           119004369 15 + 161576975 ATGCAGAGGTCGCCT 
s baboon.ENm001_1          1260793 15 +   1730495 ATGCAGAGGTCGCCT 
s rheMac1.SCAFFOLD76133      25410 15 -     43354 ATGCAGAGGTCGCCT 
s dusky_titi.ENm001_1      1381123 15 +   2096432 ATGCAGAGGTCGCCT 
s marmoset.ENm001_1        1408109 15 +   1952403 ATGCAGAGGTCGCCT 
s mouse_lemur.ENm001_1     1100561 15 +   1575427 ATGCAGAGGTCGCCT 
s galago.ENm001_1          1272967 15 +   1783853 ATGCAGAGGTCGCCT 
s rn3.chr4                44072448 15 + 187371129 ATGCAGAAGTCGCCT 
s mm6.chr6                18219815 15 + 150245815 ATGCAGAAGTCGCCT 
s rabbit.ENm001_1          1422589 15 +   1889755 ATGCAGAAGTCGCCT 
s cow.ENm001_1             1310721 15 +   2061479 ATGCAGAGGTCGCCT 
s canFam1.chr14           58860070 15 +  63549963 ATGCAGAGGTCGCCC 
s rfbat.ENm001_1           1231531 15 +   1737318 ATGCAGAGGTCGCCT 
s hedgehog.ENm001_1        1597441 15 +   2136267 ATGCAGAGGTCGCCT 
s shrew.ENm001_58            26619 15 -     61370 ATGCAGAGGTCGCCC 
s armadillo.ENm001_1       1169562 15 +   1656816 ATGCAGAGGTCGCCT 
s elephant.ENm001_1        1165372 15 +   1533827 ATGCAGAAGTCGCCT 
s monDom1.scaffold_13572   2152204 15 -   5827465 ATGCAGAGATCACCC 
s platypus.ENm001_1         911324 15 +   1321799 ATGCAGAGATCACCG 
s galGal2.chr1           166629624 15 - 188239860 ATGCAAAGGTCCCCC 
s xenTro1.scaffold_17      2343562 15 +   3981052 ATGCAGAGATCCCCT 
s tetNig1.chr13           10730568 15 +  12408495 ATGCAGAAGTCACCA 
s fr1.chrUn              117688050 15 - 349519338 ATGCAGAAGTCACCA 

a score=935599.0
s hg17.chr7               116714114 38 + 158628139 CTGGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTTCAG 
s panTro1.chr6            119004384 38 + 161576975 CTGGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTTCAG 
s colobus_monkey.ENm001_1   1280159 38 +   1990688 CTGGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTTCAG 
s baboon.ENm001_1           1260808 38 +   1730495 CTGGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTTCAG 
s rheMac1.SCAFFOLD76133       25425 38 -     43354 CTGGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTTCAG 
s dusky_titi.ENm001_1       1381138 38 +   2096432 CTGGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTTCAG 
s marmoset.ENm001_1         1408124 38 +   1952403 CTGGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTTCAG 
s mouse_lemur.ENm001_1      1100576 38 +   1575427 CTGGAAAAGGCCAGCGTCCTCTCCAAACTTTTTTTCAG 
s galago.ENm001_1           1272982 38 +   1783853 CTGGAAAAGGCCAGCGTCTTCTCCAAACTTTTTTTCAG 
s rn3.chr4                 44072463 38 + 187371129 CTGGAGAAAGCCAGCTTTATCTCCAAACTCTTCTTCAG 
s mm6.chr6                 18219830 38 + 150245815 TTGGAGAAAGCCAGCTTTATCTCCAAACTCTTCTTCAG 
s rabbit.ENm001_1           1422604 38 +   1889755 CTGGAGAAGGCCGGCGTCCTCTCCAAACTTTTTTTCAG 
s cow.ENm001_1              1310736 38 +   2061479 CTGGAAAAGGCCAGCGTCGTCTCCAAACTTTTTTTCAG 
s canFam1.chr14            58860085 38 +  63549963 CTGGAAAAGGCCAGCGTCCTCTCCAAACTTTTCTTCAG 
s rfbat.ENm001_1            1231546 38 +   1737318 CTGGAAAAGGCCAGCGTCATCTCCAAACTTTTTTTCAG 
s hedgehog.ENm001_1         1597456 38 +   2136267 CTGGAAAAGGCCAGCGTCATCTCCAAACTTTTTTTCAG 
s shrew.ENm001_58             26634 38 -     61370 CTGGAAAAGGCCGGCGTCATCTCCAAACTTTTTTTCAG 
s armadillo.ENm001_1        1169577 38 +   1656816 CTGGAAAAAGCCAGCGTCATCTCCAAACTTTTCTTCAG 
s elephant.ENm001_1         1165387 38 +   1533827 TTGGAAAGGGCCAGCGTCATCTCCAAACTTTTCTTCAG 
s monDom1.scaffold_13572    2152219 38 -   5827465 CTGGAAAAGGCAAATCTCCTCTCGAAACTTTTCTTCAG 
s platypus.ENm001_1          911339 38 +   1321799 CTGGAGCGAGCCAACCTCTTCTCCAAACTTTTCTTCAG 
s galGal2.chr1            166629639 38 - 188239860 CTGGAGAAGGCGAACATCTTCTCCAAACTTTTCTTCAG 
s xenTro1.scaffold_17       2343577 38 +   3981052 CTGGAGAAAGCCAGCATCTTTTCACAGATTTTCTTTAG 
s tetNig1.chr13            10730583 38 +  12408495 GTGGAAGATGCCAACTTCTTATCCAAATTTTTCTTCTG 
s fr1.chrUn               117688065 38 - 349519338 GTGGAAGATGCCAACTTCTTATCCAAATTTTTCTTCTG 

a score=3642203.0
s hg17.chr7                41682427 171 - 158628139 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGTCACCCAGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATCAACAA-CAACTCAAAAGAA---GTGAATTGGAACTTACAC---AAAAATGAACACC----TAGAAAAACCTAACAA---------AT----AG 
s panTro1.chr6             42347079 171 - 161576975 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGTCACCCAGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATCAACAA-CAACTCAAAAGAA---GAGAATTGGAACTTACAC---AAAAATGAACACC----TAGAAAAACCTAACAA---------AT----AG 
s colobus_monkey.ENm001_1    475144 171 -   1990688 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGTCACCCTGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATCAACAA-CAACTCAAAAAAA---GAGAATTGGAACTTACAC---AAAAATGAACACC----TAGACAAACCTAACAA---------AT----AG 
s baboon.ENm001_1            246747 171 -   1730495 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGTCACCCTGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATCAACAA-CAACTCAAAAGAA---GAGAATTGGAACTTACAC---AAAAATGAACACC----TAGACAAACATAACAA---------AT----AG 
s rheMac1.SCAFFOLD5248        90481 171 +     99469 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGTCACCCTGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATCAACAA-CAACTCAAAAGAA---GAGAATTGGAACTTACAC---AAAAATGAACACC----TAGACAAACCTAACAA---------AT----AG 
s dusky_titi.ENm001_1        484922 171 -   2096432 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGTCACCCAGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGCA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATCAACAA-CAACTCAAAAGAA---GAGAATTGGAACTTACAC---AAAAATGAACACC----TAGAAAAAGCTAACAA---------AT----AG 
s owl_monkey.ENm001_1        431969 171 -   2053814 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGTCACCCAGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATCAACAA-CAACTCAAAAGAA---GAGAATTAGAACTTACAC---AAAAATGAACACC----TAGAAAAACCTAACAA---------AT----AG 
s marmoset.ENm001_1          318377 171 -   1952403 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGTCACCCAGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATCAACAA-CAACTCAAAAGAA---GAGAATTGGAACTTACAC---AAAAATGAACACC----TAGAAAAACCTAACAA---------AT----AG 
s mouse_lemur.ENm001_1       263688 171 -   1575427 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGTCACCCAGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATCAACAA-CAACTCAAAAGAA---GAGAATTGGAACTTACAC---AAAAATGAACAAACACATAGAAAAACTTAA-------------T----AG 
s galago.ENm001_1            291093 171 -   1783853 AGAGCTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGCCACCCAGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATAAACAA-CAACTCAAAAGAA---GAGAATTGGAACTTACAC---AAAAACGAACAAA----TAGAAAAACCTAACAA---------AT----AG 
s rn3.chr4                143036605 174 - 187371129 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGTCGCCCAGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGCAGTAATACAAGGCA----------ACTAG--------------------------AAATCAATAA-CAACTCCAAAGAA---GAGAATTGGAACGTAGAC---AAACACGAACACG----TAGAAAAACGTAACAA---------AT----AG 
s mm6.chr6                131828874 171 - 150245815 AGCGTTAAATCTTTTCTTCCTGTTCCTAGAAGCAAAGTCGCTCAGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------ACAGCAGCAGCAGCA---ATACAAGGCA----------ACTAG--------------------------AAATCAACAA-CAACTCCAAAGAA---GAGAATTGGACCTTAGAC---AAACACGAACAAG----TAGAAAAACCAAACAA---------AT----AG 
s rabbit.ENm001_1            186398 171 -   1889755 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAATCGCCCAGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------ACCAG--------------------------AAATCAACAA-CAACTCCAAAGAA---GAGAATTGGAACCTACAC---AAACATGAACAAG----TAGAAAAACCTAACAC---------AT----AG 
s cow.ENm001_1               443929 166 -   2061479 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGTCACCCAGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATAAACAA-CAACTC-----AA---GAGATTTGGAACCTACGC---AAAAATGAACAAG----TAGAAAAATCTAGCAA---------AT----AG 
s canFam1.chr14             4465109 174 -  63549963 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGCCACCCAGTG---------------------------------------T-TC----CCCGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AACCG--------------------------AAATCAACAA-CAACTCAAAAGAA---GAGATTTGAAACTTCCACCAAAAAAACGAACAAG----TCGCAAAACCAAACCA---------AC----AG 
s rfbat.ENm001_1             305098 171 -   1737318 AGAGTTAAATCTTTTCTTCCTGTTCCTCAAAGTAAAGCCACCCTGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATAAACAA-CAACTCAAAAGAA---GAGATTTGGAACTTACAC---AAAAATGAACAAG----TAGAAAAACCTAACAA---------AT----AG 
s hedgehog.ENm001_1          244322 168 -   2136267 AGAGTTAGATCTTTTCTTCCTGTTCCTAGAAGTAAAGTCACCCAGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATAAACAA-CAACTCAAAAGAA---GAGATTTGGAACTTACGC--AAAAAATGAA---A----TAGAAAACCCTAAC-A---------AT----AG 
s shrew.ENm001_27             13134 168 -     34682 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGTCACCCAGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATCAACAA-CAACACAAAAGAA---GATATTTGGAATTTACGC---AAAAACGAA---G----TAGAAAAACCTAACAA---------AT----AG 
s armadillo.ENm001_1         188459 171 -   1656816 AGAGTTAAATCTTTTCTTCCTGTTCCTAGAAGTAAAGTCTCCCAGTG---------------------------------------T-TC----CCAGA------------ACACCAAAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AACAG--------------------------AACTAAATAA-CAACTCAAAAGAA---GAGATTTGGAACTTATGC---AAAAATGAACAAG----TACAAAAACCTAACAA---------AT----AG 
s elephant.ENm001_1          103256 171 -   1533827 AGAGTGAAATCTTTCCTTCCTGTTCCTAGAAGTAAAGTCGCCCAGTG---------------------------------------T-TC----CCAGA------------ACACCAGAAGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATAAATAA-CAACTCAAAAGAC---GAGATTTGGAACTTACGC---AAAAATGAACAAG----TAGAAAAACCTAACAA---------AT----AG 
s tenrec.ENm001_138            5076 171 -      6927 AGAGTTAAATCTTTTCTCCCTGTTCCTAGAAGTAAAATCACCCAGTG---------------------------------------C-TC----CCAGA------------ACACCAAACGAA------GCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AAATCAATAA-CAACTCAAAAGAC---GAGATTTGGAACTTACGC---AACAATGAACAAA----TAGAAAAACCTAACCA---------AT----AG 
s monDom1.scaffold_13572    3408903 171 +   5827465 AGAGTAAAATCTTTTCTCCCTGTACCTAGAAATAAAGTCACCCAGTG---------------------------------------T-TC----TCCGA------------ACACCAAAAGAA---ACAGCAGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AA---GGAAA-TAACTCAAAAGAA---GAGATTTGGAACTCACGC---CAAAATGTGCAAA----TAGAAAAAACACACAA---------AT----AG 
s platypus.ENm001_1          208147 176 -   1321799 AGAGTGAAATCTTTCCTCCCTGTGCCCAGGAATAAAGTCGCACAGTG---------------------------------------T-TC----TCCGA------------ACCCCAAAAGAAGTAACAGCAGCAGCAGCAGTA---ATACAAGGCA----------AAGAG--------------------------AAATTAACAA-CAACTTAAAAGAA---GAGTTTTGGGTCTTACGC---AAAAACATACAA-----TAGGTATACCTAACCA---------AT----AG 
s galGal2.chr1             21521169 173 + 188239860 AGAGTTAAATCTTTTCTTCCTGTACCGAGAAGTAAAGTCACCCAGCC---------------------------------------T-TC----TCAGA------------GTACTAAAAAAA--------AGCAGCAGCAGTA---ATACAAGGCA----------AATAG--------------------------AGGCAGATAA-CGACACAAAAAAAAGAGAGATTTGGAATTTGCAC-AAAAAAAAGAACAAA----CAGAAAAATTTTAC-A---------AT----AA 
s xenTro1.scaffold_17       1540977 169 -   3981052 AAAGCCAAGTCCTCGCTCCCTGTACCTCGAAACAAAGTTACCGCATG---------------------------------------TGTT----CCAG----------------CCAACAGAA------GGAGCAGCAGCA------ATACAAGGCA----------AAAAG--------------------------AGATCAATCA-TGACTCACACAAC---GAGATTTGGAACTTGCAC---AAAAATATTGAGA----TTAATAATGCAAACAA---------ATGATCAG 
s tetNig1.chr13             1658180 232 -  12408495 -GGGCCAGATCGCAGCTCCCCGTCCCGAGCAGCAGGGGCCACCAGCC-ACGAGGCTCCGCCGCTTCCACCAGCAACGGCAGCCCCGT-CCGAAACCAGACGC---------CCCCCACCCGGG------GCAGAATCAGCAGCA---GAAGCAAGCCGATGCCCCCCAGCAG-------------CCcagcagcagcagcagcagcag-cCAAACACAAGAA---GACATCTGGATCCTCAAC---AGAGACG----------TGCATGACAGCAACAA---------AT----CG 
s fr1.chrUn               192215464 240 - 349519338 -GCGCCAGATCGCAGCTCCCCATCCCGAGCAGCAGGGGGCAGCAGAC-ACGA------GCCGCTTCCACCGCCAACGGCAGCCCCGT-CCGCAACCAGACGC---------CCCCCACCCGGG------GCAGAATCAGCAGCA---GAACGAAGCCGATGCCCCCCAGCAGCAGCAACAACAACCTCTACCGTAACAACATCAACAACCCAAACACAAGAA---GACATCTGGATCTTCAAC---AGAGACG----------TGCATGACAACAACAA---------AT----AG 
s danRer2.chr18            26884723 210 +  47708464 AGGCCCAGGTCCCATCTACCTGTCCCGAGCAGCAGAGGATCTCAGCAGATGA-------------------TCAGCAGCAGCTCTTC-CCT---TCAGACTCACAGCAGAGCCTCCACCAG---------------CAGCAGCA---GAACAAGGCAGCCCCCGTCCAACAA------------------------CAACACAAACAA-CCTCTCACAAGAC---CACATCTGGTTCCTGGAC---CCCAACT----------CTAATGAAAACTACAGTACCCACGGAT----AG 

a score=1575037.0
s hg17.chr7                41682352 75 - 158628139 GA---GG---TCAGTCCTCTCAGCAGCCATCAAAC------TACTGAATGCAGCAACAG---TAAATCAAAGACTGAGTTGGGTGTTTCA 
s panTro1.chr6             42347004 75 - 161576975 GA---GG---TCAGTCCTCTCAGCAGCCATCAAAC------TACTGAATGCAGCAACAG---TAAATCAAAGACTGAGTTGGGTGTTTCA 
s colobus_monkey.ENm001_1    475069 75 -   1990688 GA---GG---TCAGTCCTCTCAGCAGCCATCAAAC------TACTGAATGCAGCAACAG---TAAATCAAAGACTGAGTTGGGTGTTTCA 
s baboon.ENm001_1            246672 75 -   1730495 GA---GG---TCAGTCCTCTCAGCAGCCATCAAAC------TACTGAATGCAGCAACAG---TAAATCAAAGACTGAGTTGGGTGTTTCA 
s rheMac1.SCAFFOLD5248        90406 75 +     99469 GA---GG---TCAGTCCTCTCAGCAGCCATCAAAC------TACTGAATGCAGCAACAG---TAAATCAAAGACTGAGTTGGGTGTTTCA 
s dusky_titi.ENm001_1        484847 75 -   2096432 GA---GG---TCTGTCCTCTCAGCAGCCATCAAAC------TACTGAATGCAGCAACAG---TAAATCAAAGACTGAGTTGGGTGTTTCA 
s owl_monkey.ENm001_1        431894 75 -   2053814 GA---GG---TCTGTCCTCTCAGCAGCCATCAAAC------TACTGAATGCAGCAACAG---TAAATCAAAGACTGAGTTGGGTGTTTCA 
s marmoset.ENm001_1          318302 75 -   1952403 GA---GG---TCTGTCCTCTCAGCAGCCATCACAC------TACTGAATGCAGCAACAG---TAAATCAAAGACTGAGTTGGGTGTTTCA 
s mouse_lemur.ENm001_1       263613 75 -   1575427 GA---GG---TCAGTCCCCTCAGCAGCCACCAAAC------TACCGAATGCAGCAACAA---TAAATCAAAGACTGAGCCGGGTGTTTCA 
s galago.ENm001_1            291015 78 -   1783853 GA---GG---TTAGTCCTCTCAGCAGCCACCAAAC------TACCGAATGCAGCAACAACAGTAAATCCAAGCCTGAGTCGGGTGTTTCA 
s rn3.chr4                143036530 75 - 187371129 GA---AG---CCAGTCCTCTCAGCAGCCATCAAAC------TACCGAATGCAGCAACAG---TAAATCCAAGACTGAGTTGGGTGTCTCA 
s mm6.chr6                131828799 75 - 150245815 GA---AG---CCAGTCCTCCCAGCAGCCGTCAAAC------TGCCGAATGCAGCAACAG---TAAATCAAAGACTGAGATGGGTGTCTCA 
s rabbit.ENm001_1            186323 75 -   1889755 GA---GG---TCAGTCCTCTCAGCAGCCATCAAGC------TACCGAATGCAGCACCAG---TAAATCAAAGACTGAGTTGGGTGTTTCA 
s cow.ENm001_1               443854 75 -   2061479 GA---GG---TCAGTCCTCTCAGCAGCCATCAAAC------AACCGAATGCAGCAACAG---TAAATCAAAGACTGAGTTGGGTGTTTCA 
s canFam1.chr14             4465034 75 -  63549963 GA---GC---CCAGTCCTCTCAGCAGCCACCAAGC------GGCCGAATGCAGCAACAG---GCAATCCAAGACGGAGTTGGGTGTTTCG 
s rfbat.ENm001_1             305023 75 -   1737318 GA---GG---TCAGTCCTCTCAGCAGCCATCAAAC------TACCGAATGCAACGACAG---TAAATCCAAGACTGAGTCGGGTGTTTCA 
s hedgehog.ENm001_1          244247 75 -   2136267 GA---GG---TCAGTCCTCTCAGCAGCCATCAAAC------TACCGAGTGCAGCAACAA---TAAATCTAAGACCGAGTTGGGTGTTTCA 
s shrew.ENm001_27             13053 81 -     34682 GA---GG---TCAGTCCTCTCAGCAGCCATCAAACCACCACTACCGAGTGCAGCAACAA---TAAATCAAAGACTGAGTTGGGTGTATCA 
s armadillo.ENm001_1         188384 75 -   1656816 GA---GG---TCAGTCCTGTCAGCAGCCATCAAAC------TACAAAACGCAGCACCAG---TACGTCAAAGACTGAGTTGAGTGTTTCA 
s elephant.ENm001_1          103181 75 -   1533827 GA---GG---TCAGTCCTCTCAGCAGCCATCAAAC------TACAGAATGCAGCAATAG---TAAATTAAAGACCGAGTTGGGTGTTTCA 
s tenrec.ENm001_138            5001 75 -      6927 GA---GG---TCAGTCCTCTCAGCAGCCATCAAAC------TATGGAACGCAGCAACAG---GACGCTAAAGACCGAGTTGGGCGTTTCA 
s monDom1.scaffold_13572    3408828 75 +   5827465 GA---TG---TCTGTCCTCTCAGCAGCAGTCCAAC------TGTAGAATGCAGTATCAG---CAAACCAAAAATTGAGTTGGGCGTTTCA 
s platypus.ENm001_1          208072 75 -   1321799 GA---GG---TCTGTCCTCTTAGCAGCAATCCAAC------TCTTGAATGCAGCAACAA---CACACCGAAACCCGAGTCGGGGGTTTCG 
s galGal2.chr1             21521097 72 + 188239860 GA---TGGAATCCGTCCTCTCAGCAGCAGTCGAAC------TGTAGAA------AGCAG---CAAATCAAAGACAGAGCTGGGTGGTTCA 
s xenTro1.scaffold_17       1540905 72 -   3981052 GACATGG---CCTGTCCTCTAAGCAGCAGAAAGAA------TTTAGAATCCAGCATTCA---GAAACCAAAAGCGGAACCTGG------G 
s tetNig1.chr13             1658653 71 -  12408495 TA---TT---CCAGTGC----ATCAACTTGCAAAC------TACAGTATTCAGCCAGAG---TATGCTCATGAAGTATTTGACTGCCTCA 

a score=-12248.0
s hg17.chr9                9641745 4 - 138429268 CTAG 
s baboon.ENr232_1           577390 4 -    695787 CTAG 
s marmoset.ENr232_1         520982 4 -    681407 CTAG 
s galago.ENr232_1           341981 4 -    445664 TTAG 
s rn3.chr3               161639260 4 - 170969371 CTAG 
s mm6.chr2               151547720 4 - 181764313 CTAG 
s rabbit.ENr232_18            5089 4 -      6581 CTAG 
s cow.ENr232_1              436915 4 -    749201 CTAG 
s canFam1.chr9            47277506 4 +  53642819 ATAG 
s rfbat.ENr232_1            411482 4 -    445008 CTAG 
s armadillo.ENr232_1        409108 4 -    420596 TTAG 
s monDom1.scaffold_12698    353949 4 +   3488899 TTAG 
s galGal2.chr17            5424949 4 +  10632206 TTAA 
s tetNig1.chr4             4165038 4 +   6212533 CCAG 

a score=242807.0
s hg17.chr9                9641707 38 - 138429268 CTCCTTCTGCCTCTCTACCTCCTGATATTGCTGATGGC 
s baboon.ENr232_1           577352 38 -    695787 CTCCTTCTGCCTCTCTACCTCCTGATACTGCTGATGGC 
s marmoset.ENr232_1         520944 38 -    681407 CTCCTTCTGCCTCTCTACCTCCTGATATTGCTGATGGC 
s galago.ENr232_1           341943 38 -    445664 CTCCTTTTGCCTCTCTACCTCCTGATATTGCTGATGGC 
s rn3.chr3               161639222 38 - 170969371 CTCCTGTTGCCCCTCTACCTACTGATTTTGCTGATGGC 
s mm6.chr2               151547682 38 - 181764313 CTCCTGTTGCCTCTCTACCTACTGATATTGCTGATGGC 
s rabbit.ENr232_18            5051 38 -      6581 CTCCTGCTGCCTCTCTACCTCCTGATACTGCTGATGGC 
s cow.ENr232_1              436877 38 -    749201 CTCCTTTTGCCTCTGTACCTCTTGATATTGCTGATGGC 
s canFam1.chr9            47277468 38 +  53642819 CTCCTGTTGCCTCTCTACCTCCTGATATTGCTGATGGC 
s rfbat.ENr232_1            411444 38 -    445008 CTCCTTTTGCCTCTCTATCTCCTGATATTGCTGATGGC 
s armadillo.ENr232_1        409070 38 -    420596 CTCCTTTTGCCTCTCTACCTCCTGATATTGCTGATGGC 
s monDom1.scaffold_12698    353911 38 +   3488899 CTTATGTTACCACTCTATCTCCAGATTCTGCTGATGGC 
s galGal2.chr17            5424911 38 +  10632206 TTGCTGTTACCTCTCTACCTCCAGATCATGTTTATGGT 
s tetNig1.chr4             4164996 37 +   6212533 CTACTGCTCCCGCTTTACCTCTTTATCCTGCTCTTG-C 
s danRer2.chr21            1735685 37 +  40848751 CTTCTGCTTCCTCTGTATCTCTACATCCTCCTGCTG-C 

a score=462361.0
s hg17.chr9                9641644 63 - 138429268 TGGATTTTGGGGTCCATCAGCACTGTGTCCCTCCTGGAAGCATACACTACACAGATAGACAAT 
s panTro1.chr11_random     6903869 63 +  53199993 tagatTTGGGAGTCGATCTGCACTGTGTCCCTCCCAGAATTGTACACTACACAGATAGTGAAT 
s baboon.ENr232_1           577289 63 -    695787 TGGATTTTGGGGTCCATCAGCACTGTGTCCCTCCTGGAAGCATACACTACACAGATAGACAAT 
s marmoset.ENr232_1         520881 63 -    681407 TGGATTTTGGGATCCATCAGCACTGTGTCCCTCCTGGAAGCATACACCACACAAATAGACAAT 
s galago.ENr232_1           341880 63 -    445664 TGGATTTTGGGGTCCATCAGCACTGTGTCCCTCCTAGAAGCATATACTACACAGATAGACAAT 
s rn3.chr3               161639159 63 - 170969371 TGGATTTTGGGGTCCATCAGCACTGTGTCGCTTCTGGAAGCATACACAACTCAGATAGACAAT 
s mm6.chr2               151547619 63 - 181764313 TGGATTTTGGGGTCCATCAGCACTGTATCCCTTCTGGAAGCGTACACTACTCAGATAGACAAT 
s rabbit.ENr232_18            4988 63 -      6581 TGGATCCTGGGCTCCATCAGCACCGTGTCCCTGCTCGAAGCGTACACCACGCAGATAGACAAT 
s cow.ENr232_1              436814 63 -    749201 TGGATTTTGGGATCCATCAGCACCGTATCCCTCCTGGAAGCCTACACTACGCAGATAGACAAT 
s canFam1.chr9            47277405 63 +  53642819 TGGATTTTGGGCTCTATCAGCATCGTGTCCCTCCTAGAAGCATACACGACACAGATAGACAAT 
s rfbat.ENr232_1            411381 63 -    445008 TGGATTTTGGGGTCCATCAGCACGGTGTCCCTCCTAGAAGCATACACTACGCAGATAGACAAT 
s armadillo.ENr232_1        409007 63 -    420596 TGGATTTTGGGGTCCATAAGCACTGTGTCCCTTCTAGAAGCATACACTACACAGATAGACAAT 
s monDom1.scaffold_12698    353848 63 +   3488899 TGGATTCTAGGGTCTATCACTATAATCTCCCTACTGGAAGCTTACACCACCCAAATAGACAAT 
s galGal2.chr17            5424848 63 +  10632206 TGGATTCTGGTGTCTGTGAGCTTAGTTTCTCTTTTGGAAGCTTACACAACCCAAATTGATAAT 
s tetNig1.chr4             4164933 63 +   6212533 TGGATTGTTGGTTCCATCGCTCTGGTGGCCATGCTCGAAGCTTACACTGTTCAAATAGACAAC 
s danRer2.chr21            1735622 63 +  40848751 TGGGTGGTGGGATCCATCTCTATGGTGGCCATGTTGGAGGCCTATACGTCGCAGATTGACAAC 

a score=8255688.0
s hg17.chr9                9640546 1098 - 138429268 AACACTTGTGTCATCTTGGGCTTGGCTGGAGGTGTTATCATTTATATCATGAAGCACTCGTTGAGCGTGGGGGAGGTGATCGAAGTCCTGGAAGTCCTTCTGATCTTCGTTTATCTCAACATGATCCTGCTGTACCTGCTGCCCCGCTGCTTCACCCCTGGTGAGGCACTGCTGGTATTGGGTGGCATTAGCTTTGTCCTCAACCAGCTCATCAAGCGCTCTCTGACACTGGT---GGAAAGTCAGGGGGACCCAGTGGACTTCTTCCTGCTGGTGGTGGTAGTAGGGATGGTACTCATGGGCATTTTCTTCAGCACTCTGTTTGTCTTCATGGACTCAGGCACCTGGGCCTCCTCCATCTTCTTCCACCTCATGACCTGTGTGCTGAGCCTTGGTGTGGTCCTACCCTGGCTGCACCGGCTCAT-CCGCAGGAATCCCCTGCTCTGGCTTCTTCAGTTTCTCTTCCAGACAGACACCCGCATCTACCTCCTAGCCTATTGGTCTCTGCTGGCCACCTTGGCCTGCCTGGTGGTGCTGTACCAGAATGCCAAGCGGTCATCTTCCGAGTCCAAGAAGCACCAGGCCCCCACCATCGCCCGAAAGTATTTCCACCTCATTGTGGTAGCCACCTACATCCCAGGTATCATCTTTGACCGGCCACTGCTCTATGTAGCCGCCACTGTATGCCTGGCGGTCTTCATCTTCCTGGAGTATGTGCGCTACTTCCGCATCAAGCCTTTGGGTCACACTCTACGGAGCTTCCTGTCCCTTTTTCTGGATGAACGAGACAGTGGACCACTCATTCTGACACACATCTACCTGCTCCTGGGCATGTCTCTTCCCATCTGGCTGATCCCCAGACCCTGCACACAGAAGGGTAGCCTGGGAGGAGCCAGGGCCCTCGTCCCCTATGCCGGTGTCCTGGCTGTGGGTGTGGGTGATACTGTGGCCTCCATCTTCGGTAGCACCATGGGGGAGATCCGCTGGCCTGGAACCAAAAAGACTTTTGAGGGGACCATGACATCTATATTTGCGCAGATCATTTCTGTAGCTCTGATCTTAATCTTTGACAGTGGAGTGGACCTAAACTACAGTTATGCT 
s panTro1.chr11_random     6900036 1097 +  53199993 AACACTTGTGTCATCTTGGGCTTGGCTGGAGGTGTTATCATTTATATCATGAAGCTCTAGG-GAGCGTGGGGGAGGTGATCGAAGTCCTGGAAGGCATTCTGATCTTCGTTTATCTCAACATGATCCTGCTGTACCTGCTGCCCCGTTGCTTCACCCCTGGCGAGGCACTGCTGGTATTGGGTGGCATTAGCTTTGTCCTCAACCAGCTCATCAAGCGCTCTCTGACACTGGT---GGAAAGTCAGGGGGACCCAGTGGACTTCTTCCTGCTGGTGGTGGTAGTAGGGATGGTACTCATGGGCATCTTCTTCAGCACTCTGTTCGTCTTCATGGACTCAGGCACCTGGGCCTCCTCCATCTTCTTCCACCTCATGACCTGTGTGCTGAGCCTTGGTGTGGTCCTACCCTGGCTGCACCGGCTCAT-CCGCAGGAATCCCCTGCTCTGGCTTCTTCAGTTTCTCTTCCAGACAGACACCCGCATCTACCTCCTAGCCTATTGGTCTCTGCTGGCCACCTTGGCCTGCCTGGTGGTGCTGTACCAGAATGCCAAGCGGTCATCTTCCGAGTCCAAGAAGCACCAGGCCCCCACCATCGCCCGAAAGTATTTCCACCTCATTGTGGTAGCCACCTACATCCCAGGTATCATCTTTGACCGGCCACTGCTCTATGTAGCCGCCACTGTATGCCTGGCGGTCTTCATCTTCCTGGAGTATGTGCGCTACTTCCGCATCAAGCCCTTGGGTCACACTCTACGGAGCTTCCTGTCCCTTTTTCTGGATGAACGAGACAGTGGACCACTCATTCTGACACACATCTACCTGCTCCTGGGCATGTCTCTTCCCATCTGGCTGATCCCCAGACCCTGCACACAGAAGGGTAGCCTGGGAGGAGCCAGGGCCCTCGTCCCCTATGCCGGTGTCCTGGCTGTGGGTGTGGGTGATACTGTGGCCTCCATCTTCGGTAGCACCATGGGGGAGATCCGCTGGCCTGGAACCAAAAAGACTTTTGAGGGGACCATGACATCTATATTTGCGCAGATCATTTCTGTAGCTCTGATCTTAATCTTTGACAGTGGAGTGGACCTAAACTACAGTTATGCT 
s baboon.ENr232_1           576191 1098 -    695787 AACACTTGTGTCATCTTGGGCTTGGCTGGAGGTGTTATCATTTATATCATGAAGCACTCGCTGAGCGTGGGGGAGGTGATCGAAGTCCTGGAAGTCCTGCTGATCTTCGTTTATCTCAACATGATCCTGCTGTACCTGCTGCCCCGCTGCTTCACCCCTGGTGAGGCACTGCTGGTATTGGGTGGCATTAGCTTTGTCCTCAACCAGCTCATCAAGCGCTCTCTGACACTGGT---AGAAAGTCAGGGGGACCCAGTGGACTTCTTCCTGCTGGTGGTGGTAGTAGGGATGGTACTCATGGGCATCTTTTTCAGCACTCTCTTTGTCTTCATGGACTCAGGCACCTGGGCCTCCTCCATCTTCTTCCACCTCATGACCTGTGTGCTGAGCCTTGGTGTGGTCCTTCCCTGGCTGCACCGGCTCAT-CCGCAGGAACCCCCTGCTCTGGCTTCTGCAGTTCCTTTTCCAGACAGACACCCGTATCTACCTCCTAGCCTATTGGTCTCTGCTGGCCACCTTGGCCTGCCTGGTGGTGCTGTACCAGAATGCCAAGCGGTCATCTTCCGAGTCCAAGAAGCACCAGGCCCCCACCATCGCCCGAAAGTATTTCCACCTCATTGTGGTAGCCACCTACATCCCAGGTATCATCTTTGACCGGCCACTGCTCTATGTAGCTGCCACTGTATGTCTGGCGGTCTTCATCTTCCTGGAGTATGTGCGCTACTTCCGCATCAAGCCCTTGGGTCACACTCTACGGAGCCTCCTGTCCCTTTTTCTGGATGAACGAGACAGTGGACCACTCATTCTGACACACATCTACCTGCTCCTGGGCATGTCTCTTCCCATCTGGCTGATCCCCAGACCCTGCACACAGAAGGGTAGCCTGGGGGGAGCCAGGGCCCTCGTCCCCTATGCTGGTGTCCTGGCTGTGGGTGTGGGTGATACTGTGGCCTCCATCTTTGGTAGCACCATGGGGGAGATCCGCTGGCCTGGAACCAAAAAGACTTTTGAGGGGACCATGACATCTATATTTGCGCAGATCATTTCCGTAGCTCTGATCTTAATCTTTGACAGTGGAGTGGACCTAAACTACAGTTACGCT 
s marmoset.ENr232_1         519783 1098 -    681407 AACACTTGTGTCATCTTGGGCTTGGCTGGAGGTGTTATCATTTATATCATGAAGCACTCGCTGAGCGTCGGGGAGGTGATCGAAGTCCTGGAAGTCCTGCTGATCTTCGTTTATCTCAACATGATCCTGCTGTACCTGCTGCCCCGCTGCTTCACCCCTGGCGAAGCACTGCTGGTATTGGGTGGCATTAGCTTTGTCCTCAACCAGCTCATCAAGCGCTCTCTGACACTGGT---GGAAAGCCAGGGGGATCCAGTGGACTTCTTCCTGCTGGTGGTGGTAGTAGGGATGGTACTTATGGGCATCTTCTTCAGCACTCTCTTTGTTTTCATGGACTCAGGCACCTGGGCCTCCTCTATCTTCTTCCACCTCATGACTTGTGTGCTGGGCCTTGGTGTGGTCCTGCCCTGGCTGCACCGGCTCAT-CCGCAGGAACCCCCTGCTCTGGCTGCTTCAGTTCCTCTTCCAAACAGATACCCGGATCTACCTCCTAGCCTATTGGTCTCTGCTGGCCACCTTGGCCTGCCTGGTAGTGCTATATCAGAATGCCAAGCGGTCATCATCTGAGTCCAAGAAGCACCAGGCCCCCACCATTGCCCGAAAGTATTTCCACCTCATTGTGGTAGCCACCTACATCCCAGGTATCATCTTTGACCGGCCACTGCTCTACGTAGCCGCCACTGTATGTCTGGCAGTCTTCATCTTCCTCGAGTATGTGCGCTACTTCCGCATCAAGCCCCTGGGTCACACTCTGCGAAGCCTCCTGTCCCTTTTTCTGGATGAACGAGACAGTGGACCACTCATTCTGACACACATCTACCTGCTGCTGGGCATGTCTCTTCCCATCTGGCTGATCCCCAGACCCTGCACACAGAAGGGTAGCCTGGGGGGAGCCAGGGCCCTCGTCCCCTATGCTGGTGTCCTGGCCGTGGGTGTGGGTGATACTGTGGCCTCCATCTTCGGTAGCACCATGGGGGAGATCCGCTGGCCTGGAACCAAAAAGACTTTTGAGGGGACCATGACATCTATATTTGCACAGATCATTTCTGTAGCTCTGATCTTAATCTTTGACAGTGGAGTGGACCTTAACTACAGTTACGCT 
s galago.ENr232_1           340785 1095 -    445664 AACACTTGTGTTATCTCGGGTTTGGCCGGAGGTGTTATCATTTATATCATGAAACACTCCTTGAGTGTGGGTGAAGTGATTGAGGTCCTAGAAGTCCTGCTAATCTTTGTTTATCTCAACATGATCCTGTTGTACCTGCTGCCTCGCTGCTTCACCCCTGGAGAGGCGCTGCTAGTATTGGGTGGCATTAGTTTTGTCCTCAACCAGCTCATTAAGCGCTCTCTGACAGTGGT---GGAAAGCCAGGGAGACCCAGTGGATTTCTTCCTGCTGGTGGTGGTGGTAGGGATGGTGCTTATGGGCGTCTTCTTCAGCACTCTCTTTGTCTTCATGGACTCAGGGACCTGGGCCTCCTCCATCTTCTTCCACCTCATGACCTGTGTGCTGGGCCTTGGTGTGGTCTTACCCTGGCTGCACCGGCTCAT-CCGCAGGAACCCCCTGCTTTGGCTTCTACAGTTCCTCTTCCAGACAGACACTCGCATCTACCTCCTAGCCTATTGGTCTCTACTGGCCACCTTGGCCTGCCTGGTGGTGCTCTACCAGAATGCCAAGCGGTCATCT---GAGTCCAAGAAACACCAGGCCCCCACCATAGCCCGAAAGTATTTCCACTTCATTGTTGTAGCCACCTACATCCCAGGTATCATCTTTGACCGGCCACTGCTGTATGTGGCTGCCACTGTATGTCTAGCAGTCTTCATCTTCCTGGAGTATGTGCGCTACTTCCGCATCAAGCCTCTGGGTCACACTCTGAGGAACCTCCTGTCCCTCTTCCTGGATGAACGAGACAGCGGACCACTCATTCTGACACACATCTACCTGCTCCTGGGCATGTCTCTTCCTGTTTGGCTGGTCCCTAGACCCTGCACACAGAAGGGTAGCTTCGGGGGAGCCAGGGCCCTAGTCCCCTATGCCGGTGTCCTGGCTGTAGGTGTGGGTGATACTGTGGCCTCCATCTTTGGCAGCACCATGGGGGAGATTCGCTGGCCTGGAACCAAAAAGACTTTTGAGGGGACTATGACTTCTATATTTGCACAGATCATTTCTGTAGCTTTAATCCTAATCTTTGACAGTGGAGTAGACCTAAACTACAGTTACACT 
s rn3.chr3               161638067 1092 - 170969371 AATACTTGTGCCATCTCGGGTTTGGCCGGAGGTATTATCATTTATATTATGAAGCACTCGCTCAGTGTGGGCGAGGTGATCGAGGTCCTGGAAGTCCTGCTAATATTCGTTTATCTCAACATGATCCTGCTGTACCTGCTGCCCCGCTGCTTCACTCCTGGGGAGGCACTGCTGGTATTGGGTGGCATTAGCTTCGTCCTCAACCAGCTCATCAAGCGCTCTCTGACTG---------AAAGCCAGGGGGACCCAGTGGACTTCTTCCTGTTGGTGGTGGTGGTGGGGATGGTGCTCATGGGTGTCTTTTTCAGCACCCTCTTTGTCTTCATGGATTCGGGCACCTGGGCCTCTTCTATCTTCTTCCACCTCATGACCTGTGTGCTGGGCCTTGGTGTGGTTCTGCCCTGGCTGCACTGGCTCAT-TCGTAGGAACCCCCTGCTCTGGCTTCTTCAGTTCCTCTTCTACACAGAAACTCGCATCTACCTCCTAGCCTATTGGTCCTTGCTGGCCACCATGGCCTGCCTGGTGGTGCTGTACCAGAATGCCAAGCGGTCATCTTCTGAGTCCAAGAAGCACAAGGCTCCTACCATTACCAGAAAGTATTTCCACTTCATTGTGGTGGCCACTTACATCCCCGGTATCATCTTTGACCGGCCACTGCTGTATGTGGCCGCCACCGTGTGTCTGGCCGTCTTCATCTTCCTGGAGTATGTGCGCTATTTCAGAATCAAGCCCCTGGGTCACACTCTGCGCAGCCTTCTGTCCCTCTTCCTGGATGAACGGGACAGCGGGCCCCTCATCCTGACGCACATCTACCTGCTTCTGGGCATGTCTCTTCCCATTTGGCTGATCCCCAGACCCTGTGCACAGAAGGGCAGCCTCGGAGGAGCAAGAGCCCTGGTCCCCTATGCTGGGGTCCTGGCTGTGGGTGTGGGCGATACTGTGGCCTCCATATTTGGCAGCACCATGGGGGAGATCCGCTGGCCTGGAACTAAGAAAACATTCGAGGGAACTATGACATCTATATTTGCACAAATCATCTCTGTGGCTCTGATCCTAATCTTTGACAGTGGAGTAGACCTGAACTACAGCTATGCT 
s mm6.chr2               151546527 1092 - 181764313 AATACTTGTGCCATCTCTGGTTTGGCTGGAGGCGTTATCATTTATATTATGAGGCACTCGCTCAGTGTAGGCGAGGTGATCGAGGTCCTGGAAGTCCTGCTAATATTTGTTTATCTCAACATGATCCTGCTGTACCTGCTGCCCCGATGCTTCACTCCTGGGGAGGCACTGCTGGTATTGGGTGGCATTAGCTTCGTCCTTAACCAACTCATCAAGCGCTCTCTGACTG---------AAAGCCAGGGGGACCCAGTGGACTTCTTCCTGTTGGTGGTGGTGGTAGGGATGGTGCTCATGGGTGTCTTTTTCAGCACCCTCTTTGTCTTCATGGATTCAGGCACCTGGGCCTCTTCCATCTTCTTCCACCTCATGACCTGTGTGCTGGGCCTTGGTGTGGTTCTGCCCTGGCTGCACTGGCTCAT-TCGTAGGAACCCCCTGCTTTGGCTTCTTCAGTTCCTCTTCTACACTGAAACTCGCATCTACCTCCTTGCCTATTGGTCTTTGCTGGCCTCTGTGGCCTGCCTGGTGGTGCTGTACCAGAATGCTAAGCGGTCGTCTTCTGAGTCCAAGAAGCACAGGGCGCCTACCATTACAAGAAAGTATTTCCACTTCATTGTGGTAGCCACTTATATCCCGGGCATCATCTTTGACCGGCCACTGCTGTATGTGGCCGCCACTGTGTGCCTGGCAGTCTTCATCTTCCTGGAGTATGTGCGCTATTTCCGAATAAAGCCCTTGGGTCACACTCTGCGAAGCCTTCTGTCCCTCTTCCTGGATGAACGAGACAGTGGACCCCTTATCCTAACACACATCTACCTGCTTCTGGGCATGTCTCTTCCTATTTGGCTGATCCCCAGACCCTGTACACAGAAGGACAGCCTGGAAGGAGCAAGAGCCCTGGTCCCCTATGCTGGGGTCTTGGCTGTGGGTGTGGGTGATACTGTGGCCTCCATATTTGGCAGCACCATGGGAGAGATCCGCTGGCCTGGAACTAAGAAAACCTTCGAGGGGACTATGACATCTATATTTGCACAAATCATCTCTGTAGCTCTAATCTTAATCTTTGACAGTGGAGTAGACCTGAACTACAGTTATGCC 
s rabbit.ENr232_18            3890 1098 -      6581 AACACGTGCGCCATCTCGGGCCTGGCGGGCAGCGTCATCCTGTACGTCATGCGGCACTCGCTGAGCGTGGGCGAGGTGATCGAGGTTCTGGAAGTCCTGCTCATCTTCGTGTACCTGAACATGATCCTGCTGTACCTGCTGCCCCGCTGCTTCACCCCCGGGGAGGCGCTGCTGGTGCTGGGGGGCTTCAGCTTCCTGCTCAACCAGCTCATCAAGCGCTCGCTGACCGTGGT---GGAGACGCAGGGGGACCCGGTGGACTGCTTCCTGCTCGTGGTGGTGGTGGGCATGGTGCTGCTGGGGGTCTTCTTCAGCACCCTCTTCGTCTTCATGGACTCGGGCACCTGGGCCTCGTCCATCTTCTTCCACCTCATGACCTGCGTGCTGGGCCTCGGCGTGGTCCTGCCCTGGCTGCACTGGCTCAC-CCGCAGGAACCCCCTGCTCTGGCTCCTGCAGTTCCTCTTCCAAACCGACACCCGCGTCTACCTCCTTGCCTACTGGTCGCTGCTGGCTGCCTTGGCCTGCCTGGTGGTGCTGTACCAGAACGCCAAGCGGGCCGCTTCCGAGTGCAAGAAGCACCAGGCCCCCACCATCGCGCGGAAGTATTTCCACTTCCTCGTGGTGGCCACCTACATCCCCGGCATCATCTTCGACCGGCCGCTGCTCTACGTGGCCGCCACCGTGTGCCTGGCGGTCTTCATCTTCCTGGAGTACGTGCGCTACTTCCGCATCAAGCCCCTGGGCCACCCGCTGCGCAGCCTGCTGGCGCTCTTCCTGGACGAGCGGGACAGCGGCCCGCTCATCCTCACGCACATCTACCTGCTCCTGGGCATGTCCCTTCCCATTTGGCTGGTCCCCAGGCCCTGCGCCCAGAAGGGCAGCCTGGGAGGAGCCAGGGCCTTGGTCCCCTATGCCGGCGTCCTGGCTGTGGGCGTGGGCGACACCGTGGCCTCCATCTTCGGCAGCACCATGGGCGAGATCCGCTGGCCTGGAACCAAGAAGACGTTCGAGGGCACCATGACGTCCATCTTCGCACAGATCATCTCTGTGGCGCTCATCTTGGTCTTCGACAGCGGGGTCGACCTGAACTGCGGCTACGCC 
s cow.ENr232_1              435716 1098 -    749201 AACACCTGTGTCATCTCGGGCTTGGCTGGAGGCGTCATCATTTACATCATGAAGCACTCGCTGAGTGTCGGCGAGGTGATCGAGGTCCTGGAGGCCCTGCTGATCTTCGTGTACCTCAACATGATCCTGCTGTACCTGCTGCCTCGCTGCTTCACCCCCGGAGAGGCGCTGCTGGTCCTGGGTGGCATCAGCTTCATGCTCAACCAGCTCATCAAGCGCTCTCTCACTGTGGT---GGAAAGCCAGGGGGACCCCTTGGACTTCTTCCTGCTCGTGGTGGTGGTAGGCATGGTGCTCATGGGCATCTTCTTCAGCACCCTCTTTGTATTCATGGACTCGGGCACCTGGGCCTCTTCCATCTTCTTCCACCTCATGACCTGCGTCCTGGGCCTTGGCGTCGTCCTGCCCTGGCTGCACCGCCTCAT-CCGCAGGAACCCCCTGCTGTGGCTTTTTCAATTCCTCTTCCAGACAGAGACCCGAGTCTACCTCCTAGCTTATTGGTGTCTGCTGGCCACCGTGGCCTGCCTGGTGGTTCTGTACCAGAATGCCAAGCGGTCATCTTCTGAGTCCAAGAAGCACCAGGCCCCCACCATCACTCGAAAGTATTTCCACTTCATTGTGGTAGCCACCTACATCCCAGGTATCATTTTGGACCGGCCCCTGCTCTACGTGGCCGCCACCGTATGTCTGGCTGTCTTCATCTTCCTGGAGTATGTGCGCTACTTCCGCATTAAGCCCCTGGGCCATACCCTGCGAAGCCTTCTGTCCCTCTTCCTGGATGAACGAGACAGTGGGCCGCTCATCCTGACCCACATCTACCTGCTCCTAGGCATGTCTCTTCCCATCTGGTTAGTCCCCAGGCCCTGCACACAGAAGGGTAGCTTAGGAGGAGCCAGGGCCCTAGTGCCCTATGCAGGCGTCCTGGCCGTCGGTGTGGGTGACACTGTGGCCTCCATATTCGGCAGCACCATGGGGGAGATTCGCTGGCCTGGAACCAAAAAGACTTTTGAGGGAACCATGACATCTATATTTGCTCAGATCATTTCTGTAGCTCTGATCTTAATCTTTGACAGTGGAGTGGACCTGAACTACAGTTATGCT 
s canFam1.chr9            47276307 1098 +  53642819 AACACTTGTGTCATCTCAGGCTTGGCTGGAGGTGTCATCATTTATATCATGAAGCACTCACTGAGTGTGGGCGAGGTGATCGAGGTCCTGGAGGTCCTGCTGATCTTCGTCTACCTCAACATGATCCTGCTGTACCTGCTGCCCCGCTGCTTTACCCCTGGGGAGGCACTGCTTGTATTAGGTGGCATCAGCTTCATGCTCAACCAGCTCATCAAGCGTTCTCTGACTGTGGT---GGAGAGCCAGGGCGACCCAGTGGATTTCTTCCTGCTGGTGGTGGTAGTAGGGATGGTGCTTATGGGCGTCTTCTTCAGCACACTCTTTGTCTTCATGGACTCAGGTACCTGGGCTTCCTCCATCTTCTTCCACCTTATGACTTGTGTGCTGGGCCTTGGCGTGGTCCTTCCCTGGCTGCACCGGCTTAT-CCGCAAGAACCCCCTGCTCTGGCTTCTTCAATTCCTCTTCCAGAAAGAGACCCGCATCTACCTCCTGGTCTACTGGTCTCTGCTGGCCACCTTAGCCTGCCTGGTGGTGCTTTACCAGAATGCCAAGCGGTCATCTTCTGAGTCTAAGAAGCACCAGGCCCCCACCATTGCCCGAAAGTATTTCCACTTCATTGTGGTGGCCACCTACATCCCCGGTATCATCCTTGACCGGACACTGCTCTATGTAGCTGCCACCATATGCCTAACAGTCTTTATCTTCCTAGAATATGTGCGCTATTTCCGCATCAAGCCCCTGGGCCACACTCTGAGGAGCCTCCTGTCCCTTTTCTTAGATGAACGAGACAGTGGACCACTCATCCTGACACATATCTACCTGCTCTTGGGCATGTCTCTTCCAATTTGGCTGGTTCCCAGGCCCTGCACACAGAAGGGCAACTTGGGGGGAGCAAGAGCCCTAGTCCCTTATGCAGGAGTCCTGTCTGTGGGTGTGGGGGACACTGTGGCCTCCATTTTTGGCAGCACAATGGGGGAAATCCACTGGCCTGGAACCAAAAAGACCTTTGAGGGGACCATGACCTCTATATTTGCCCAGATCATTTCTGTAGCTCTGATCTTAATCTTTGATAGTGGAGTGGACCTAAACTACAGTTATGTT 
s rfbat.ENr232_1            410283 1098 -    445008 AACACTTGTGTCATCTTGAGCTTGGCGGGAGGTGTCATCATTTATATCATGAAGCACTCACTGAGCGTGGGTGAGGTGATCGAGGTCCTGGAGGTCCTGCTGATCTTTGTCTACCTCAACATGATCCTGCTGTACCTGCTGCCCCGCTGCTTCACCCCTGGGGAGGCACTGCTGGTGTTGAGCGGCATCAGCTTCATGCTCAACCAGCTCATCAAGCGCTCTCTGACAGTGGT---GGAAAGCCAGGGGGACCCCGTGGACTTCTTCCTGCTGGTGGTGGTGGTCGGCATGGTGCTCATGGGCATCTTCTTCAGCATCCTCTTTGTCTTCATGGACTCAGGTACCTGGGCCTCCTCCATCTTCTTCCACCTGATGACCTGTGTGCTGGGCCTTGGCGTGGTCGTGCCCTGGCTGCAGCGGCTCAT-CCACAGGAACCCCCTGCTCTGGCTTCTTCAATTCCTCTTCCAGACGGAAACCCGCCTCTACCTCCTAGCCTACTGGTCCCTACTGGCCGCTTTTGCCTGCCTGGTAGTGCTGTACCAGAATGCCAAGCGATCATCTTCCGAGTCCAAGAAGCACCAGGCCCCCATCATTGCCCGGAAGTATTTCCACTTCATTGTGGTAGCCACCTACATACCAGGTATCATCTTTGACCGGCCTCTGCTCTACGTGGCTGCCACTGTATGTCTGGCAGTCTTCGTCTTCCTGGAGTATGTGCGCTATTTCCGCATTAAGCCTCTGGGCCACACTCTGCGGAGCCTCCTGTGCCTCTTCCTTGATGAACGAGACAGCGGACCACTCATCCTGACACACATCTACCTGCTCCTGGGCATGTCTCTTCCCATTTGGCTAGTCCCCAGACCCTGCACGCAGAAGGATAGCCTGGGTGGGGCGAGGGCCCTAGTCCCCTATGCCGGTGTCCTGGCTGTGGGTGTGGGCGACACGGTGGCCTCCATCTTTGGCAGCACCATGGGGGAGATCCGCTGGCCTGGAACCAAAAAGACTTTCGAGGGGACCATGACATCTATATTTGCCCAGATCATTTCTGTAGCTCTGATCTTAATCTTTGACAGTGGAGTGGACCTAAACCACAGTTACGCT 
s armadillo.ENr232_1        407912 1095 -    420596 AACACTTGTGTCATCTCAGGCTTGGCTGGAGGCATCATCATTTACATCATGAAGCACTCACTTAGCGTCGGCGAGGTGATTGAGGTCCTGGAGGTCCTACTGATCTTTGTCTACCTCAACATGATCCTGCTGTACCTGCTACCCCGCTGCTTCACCCCTGGGGAGGCACTGCTGGTATTGGGTGGCATCAGCTTTGTGCTCAACCAGCTCATCAAGCGTTCTCTCACTGTGGT---AGAGAGCCAGGGGGATCCCGTGGACTTCTTCCTGCTGGTGGTGGTGGTAGGGATGGTGCTGATGGGCATCTTCTTCAGCACTCTCTTTGTCTTCATGGACTCAGGCACCTGGGCCTCTTCCATCTTCTTTCACCTAATGACTTGCGTCCTGGGCCTCGGGGTGGTCCTGCCTTGGCTGCACCGGCTCAT-CCGCAGGAACCCCCTGCACTGGCTCCTTCAATTCATCTTCCAGACAGACACCCGCATCTATCTCTTGGTCTACTGGTCTCTGCTGGCCACCTTGGCCTGCCTGGTGGTGCTGTACCAGAATGCCAAGCGGTCATCT---GAGTCCAAGAAGCACCAGGCTCCCACCATCACACGGAAGTATTTCCACTTCATTGTGGTTGCCACCTATATCCCAGGTATCATCTTTGACCGGCCACTGCTCTACGTGGCTGCCACCGTATGCCTGGCAGTCTTCGTTTTCCTGGAGTATGTGCGCTACTTCCGCATCAAACCTCTGGGCCACACTCTGCGGAGCCTCCTTTCTCTCTTCCTAGATGAACGAGACAGTGGACCGCTCATCCTGACACACATCTACCTGCTCCTGGGCATGTCTCTTCCCATTTGGCTGGTCCCCAGACCTTGTACCCAGAAGGGTAGCCTGGGGGGAGCACGGGCCCTAGTCCCCTATGCTGGTGTCTTGGCTGTGGGTGTGGGCGACACTGTGGCCTCTGTCTTTGGCAGCACAATGGGAGAAATCCGCTGGCCCGGAACCAAAAAGACTTTCGAGGGAACCATGACTTCTATATTTGCCCAGATCATTTCTGTAGCTCTCATCTTAATCTTTGACAGTGGAGTGGACCTAAACTATAGTTATGCT 
s monDom1.scaffold_12698    352750 1098 +   3488899 AACACTTGTGTCATTTCTGGCATGGCTGGAAGTGTCATCATCTATATCATGAAACATTCCTTGAGTGTGGCAGAGGTCATAGAGGTCCTGGAGGTCCTGCTGATCTTTGTCTATCTCAACATGATCCTACTGTACCTGCTACCCAGATGCTTTACCCCAGGGGAGGCATTGCTTATTCTAGGGGGCATCAGTTTTGCCCTCAACCAGCTCATCAAACGATCCCTGAATGTTAT---CCAAGGTCGAGGAGACCCAGTGGATTTCTTTCTCCTGGTGGTAGTAGTAGGGATGGTTATCATGGGCATCTTCTTCAGCATGTTTTTTGCCTTCATGGACTCTGGAACCTGGACATCTTCTCTTTTCTTTCACTTAATGACAGGTGTGCTGGGCCTTGGTGTCATCATGCCCTGGTTGTATCACCTAAT-CCGGGAGAATCCCTTGCTCTGGCTTTTCCAATTCCTGTTCCAGACAGACACTCGTATCTACCTCCTTATCTATTGGTCACTGCTTGCTGCTTCAGCTTGCATAGTTGTGATGTACCAAAATGCTAAGAGGTTGTCTTCTGAATCAAAGAAACATCAGGCCTCTACAGTTACCCGGAAGTATTTCCACTTCATCATAGTGGCTACCTATGTACCAGGACTCATATATGACCGACTATTACTATATGTTGCAGCTGTGGTCTGCCTAGCTGTCTTTATCATCCTTGAGTATATTCGCCTCTTCCGAATTAAGCCCCTAGGCCAGACCCTAAGGAACTTGCTATCTCTCTTTCTGGATGAAAGGGACAGTGGCCCCCTCATCCTGACTCACATTTACCTGCTGCTGGGCATGTCTCTCCCTCTCTGGCTATTCCCAAGACCTTGTGCTCCAAAGGGTAGCCTGGGAAGTGTTGGGGCTCTGGTCCCTTATGCAGGAGTGCTGGCTGTGGGAGTAGGTGACACTATTGCTTCCATTTTTGGCAGTACAGTGGGAGAGATTCATTGGCCAGGGACTGTAAAAACTTTTGAGGGGACAATGTCTTCCATATTTGCTCAAATCATTTCTGTAGCTTTAATCTTAATCTTTGACAGTAAGGTAGACCTTAACTCCAGCTATGCT 
s galGal2.chr17            5423753 1095 +  10632206 AACACCTGCATACTCAGTGGTGTTGCTGGCAGTATAATTATCTATACCATGAAGCACTCTTTGACTGTTTCAGAAGTGATAGAGGTCCTAGAAGTGCTGCTAATTTTTGTCTACCTCAGTATGATCTTGCTCTACCTGCTGCCTCGGTGTTTTACTCCTGGAGAAGCATTGCTAGTTCTCGGAGGTATAAGTTTTGTTCTCAATCAGCTCATTAAACGCTCACTGAATGTAAT---CGAGGGCAGAGGTGAACCCATAGACTTCTTCCTTCTGGTGGCAGTTATTGGAGTTGTTATCCTTGGGCTTTTTTTCACTGTTCTCTTCATTTTCATGGATTCGGGTACGTGGATCTCCTCCATGTTTTTCCACATGATGACAGCAGTGCTAGGCTTAGGGGTCATCATGCCTTGGCTTTACCGACTGAT-CCGGAGGAACCCTTTGTTTTGGCTGCTCCAGTTTCTGTTTCAGACACAGACGAGGGTTTACCTTCTCATATATTGGACTTTATTGGCTGCTTCAGCGTGTGGCATAGTTTTCTACCAGAATGCCAAGAGATCGTCC---GAATCTAAAAAACACCAGGCCTCAACCATAACCAGGAAGTATTTCCATTTCATTGTTGTAGCAACTTATGTTCCTGGACTAATTTATGACCGCCAGCTTCTCCATGTTGCTGCAGTCCTGTGTCTGGCAGTGTTCATATTCTTAGAGTACATTCGGTACTTCAGGATCAAACCGTTTGGCCAAACTCTTCGCTATTTGCTGTCTCTCTTCTTGGATGAAAGAGACAGTGGGCCTCTAATCTTGACTCACATTTATCTTCTTCTTGGCATGTCCCTCCCAGTGTGGTTGTTCCCCAGATCCTGTGCCCCTAAAGGTGCCTTGTCTGGGGCAGGAGCACTGGTGCCCTATGCTGGGGTGCTTGCAGTAGGGGTAGGAGACACCATGGCCTCTGTTTTTGGCAGTACCATGGGGGAAATCAAATGGCCGGGCACAAAGAAGACCTTTGAAGGGACAATGACAGCAATTTTTGCTCAGATCATTGCTGTGGCTCTTATTCTGATCTTTGACAGCAGCGTGAACCTGAACTCCAGCTATGCC 
s tetNig1.chr4             4163838 1095 +   6212533 AACACTTGCGTTATTGCAGGCATGGCCGCCAGTGCGATTCTCTACACGACAAAACAAACGTTAACCGTGTCTGAGGTCATCGAAGTTTTGGAGGTGTTGTTGATCTTCGTTTATCTCAGCCTGATTGTGCTCTACCTGCTGCCTCGCTGCTTCACACCCGGAGAAGCACTTCTTATCATTGGTGGAATCAGTTTCATTGTCAACCAGCTCATCAAGCGCTCACTGAACTTGAC---AGAGGTCAAAGGTGATCCGGTCAATTACTTCCTGCCGGTGGTGGTGGTGGGCTCCTTGTTACTGGGCGTTTTCTTCACTCTGCTTTTTTGCTTCATGGAATCAGAGACCTGGGTGTCGTCGGTTTTTTTCCATATGATGACAGCTGTTCTCAGTCTGGGAATTCTGCTGCCGTGGCTCTCCCTGTTCAT-CGGCAGACACCCCATCATGTGGCTACTGGACTTTGTCACGTTCACTGACATAAGACTCTCTCTGCTGGCGTACTGGGTCTTCCTTGCTGTCCTGGCCACCTGTGTTGTGTTGCATCAGAACTACCAACGCCAGTCT---GGGTCCAAGAAGCACCAGGCCTCCACTGTTGTCAGGAAGTACTTCCATGTCATTGTTGTGGCCACGTACGTTCCAGGTCTAATAAACGACCGGCACCTGCTCCACGTGGCATCTGTTGGCTGCCTGGCAGCCTTCTTGTTCCTGGAGTATGTGCGGTACTTTCGGATCAGACCGCTGGGCCAGGTGCTCAGGCAGGTTCTTACATTGTTCCTGGACGAGCGGGACTCTGGGCCTCTTATCCTGACCCACATCTACCTTCTGTTGGGGATGTCTCTTCCCATATGGCTGTTCCCCGGACCATGTGCCCCCAAAGGAGTACTTCCTGGTGCCGGTGGCCTGGTGCCATATGCTGGTGTCCTGGCTGTTGGGGTAGGAGACACTGTGGCATCTGTGTTCGGCAGCACCATGGGAGAGATTCGTTGGCCTGGTACTAAGAAAACGGTGGAGGGGACTGCAACGTCTGTGTTTGCCCAGATCATCGCTGTGGCCGTCTTTCTAATCTTTGATAGTGGCATCAATTTGAACTCAACCTACTCC 
s danRer2.chr21            1734524 1098 +  40848751 AACACTTGTGTTATCGCCGGAATTGCTAGTAGTGCTATTCTGTACACCGTGAAGCAAACACTAACAGTGTCTGAGGTCATCGAAGTCTTGGAGGTGCTTCTGATTTTTGTGTATCTAAGTTTAATCCTGCTGTACCTCCTTCCACGTTGCTTCACCCCCGGCGAAGCCCTTCTGATCCTTGGCGGGATTAGTTTTATCATCAACCAGCTAATTAAGCGCTCTCTGGCTTCGTCTGGAAATGCAAACTCAGACCCGCTTCCGTATTTCCTCCCGGTAGCTGTTTTAGGGTTAGTGCTGTTGGGAATATTCTTCGCCGTGCTTTTTATATTCATGGAATCTGAAACCTGGTCAGCGTCGCTCTTCTTCCATACCATGACTGCGGTTTTGGGATTGGGGTTATTGGTTCCTTGGCTATCTCTACTCACGCAGCA-CCATCCAATCACTTGGTTGATGCATTTCATCACTGAATCAAACACTCGACTTTGGCTCATTGGGTTTTGGGCCGCTTTGGCGCTTCTAGCAGTTGCCGTTGTGATGCATCAAAATAGTCATCGATCTGCA---GGCAGCAAGAAGCATCAAGCATCAACGACAGTGCGGAAGTATTTCCACCTGCTCACCGTTTTAACCTTCGCTCCCGGACTCGCTCTGGATCGTCCTTTGCTGCATTTGTCTGCGGTTGTTTGCCTCTCTGCATTTTTGTTTCTCGAATATGTCCGCTATTTTCGCATTCGACCATTCGGGGCTCCGCTTCGACGTCTTCTCACCTTATTCCTTGATGAGAGAGATTCAGGACCACTTATTCTCACTCATATTTATCTTCTTCTTGGCGTTTCTCTTCCACTGTGGTTGACACCTGGGATGTGCACCCCAAAAGGAGGCCTAGGGGGCGCTAGTGGGCTAGTACCCTATGCTGGAGTCCTTGCTGTAGGGGTCGGGGACACAGTGGCATCCGTTTTCGGCAGCAACGTGGGTGAAATCCGCTGGCCTGGGACTAAGAAGACATTTGAGGGCACGGCGTCCTCTGTGTTCGCTCAGATTATCGCTGTGGTGGTTTTCCTCATCGCCGACAGCAGTATTAACCTGAACGCCAGCTACTCG 

a score=1671578.0
s hg17.chr9                9640287 259 - 138429268 GGCCTTCTACGTCCAATACAAGTGGGACCGGCTGCTACAGCAGGGAAGCGCCGTCTTCCAGTTCCGAATGTCCGCAAACAGTGGCCTATTGCCCGCCTCCATGGTCATGCCTTTGCTTGGACTAGTCATGAAGGAGCGGTGCCAGACTGCTGGGAACCCGTTCTTTGAGCGTTTTGGCATTGTGGTGGCAGCCACTGGCATGGCAGTGGCCCTCTTCTCATCAGTGTTGGCGCTCGGCATCACTCGCCCAGTGCCAACC 
s panTro1.chr11_random     6899777 259 +  53199993 GGCCTTCTACGTCCAATACAAGTGGGACCGGCTGCTACAGCAGGGAAGCGCCGTCTTCCAGTTCCGAATGTCCGCAAACAGTGGCCTATTGCCCGCCTCCATGGTCATGCCTTTGCTTGGACTAGTCATGAAGGAGCGGTGCCAGACTGCTGGGAACCCGTTCTTTGAGCGTTTTGGCATTGTGGTGGCAGCCACTGGCATGGCAGTGGCCCTCTTCTCATCAGTGTTGGCGCTCGGCATCACTCGCCCAGTGCCAACC 
s baboon.ENr232_1           575932 259 -    695787 GGCCTTCTACGTCCAATACAAGTGGGACCGGCTGCTACAGCAGGGAAGCGCCGTCTTCCAGTTCCGAATGTCCGCAAACAGTGGCCTACTGCCCGCCTCCATGGTCATGCCTTTACTTGGACTAGTCATGAAGGAACGGTGCCAGGCTGCTGGGAACCCGTTCTTTGAGCGTTTTGGCATTGTGGTGGCAGCCACTGGCATGGCAGTGGCCCTCTTCTCATCAGTGTTGGCGCTCGGTATCACTCGCCCAGTGCCAACC 
s marmoset.ENr232_1         519524 259 -    681407 GGCCTTCTACGTCCAATACAAGTGGGACCGGCTGCTGCAGCAGGGGAACGCCGTCTTTCAGTTCCGAATGTCCGCAAACAGTGGCCTACTCCCCGCCTCCATGGTCATGCCTTTGTTTGGACTAGTCATGAAAGAGCGGTGCCAGGCTGCAGGAAACCCGTTCTTCGAGCGTTTTGGCATTGTGGTCGCAGCCACTGGCATGGCAGTGGCCCTGTTCTCATCAGTGTTGGCGCTGGGCATCACTCGCCCGGTGCCAACC 
s galago.ENr232_1           340526 259 -    445664 GGCCTTCTATGTCCAATACAAGTGGGACCGGCTGCTACAGCAGGGAAGCGCCGTCTTCCAGTTCAGAATGTCCGCAAATAGTGGTCTACTGCCCGCCTCCATGGTCATGCCTCTGCTTGGACTAGTTATGAAGGAGCGCTGCCAAGCTGCAGGAAATCAGTTTTTCGAGCGTTTTGGCATTGTGGTGGCAGCCACTGGGATGGCAGTGGCCCTCTTTTCATCAGTTTTGGCGCTGGGCATAACTCGTCCTGTGCCAACT 
s rn3.chr3               161637808 259 - 170969371 GGCCTTCTACGTCCAGTACAAGTGGGACCGGCTGCTCCAGCAGGGGAATGCTGTTTTCCAGTTCCGAATGTCCGCGAACAGTGGCTTACTACCGGCCTCCATGGTCATGCCTTTGCTTGGGCTGGTCATGAAGGAGCGCTGCCTGACTGCAGGGAACCCATACTTCGAGCGCTTCGGCATTGTGGTTGCAGCCACTGGCATGGCAGTGGCCCTCTTCTCCTCGGTGTTGGCACTGGGCATTACTCGCCCGGTGCCCACC 
s mm6.chr2               151546268 259 - 181764313 GGCCTTCTACGTCCAGTACAAGTGGGACCGGCTGCTCCAGCAGGGCAATGCCGTTTTCCAGTTCCGGATGTCCGCGAACAGCGGCTTACTGCCGGCCTCCATGGTCATGCCTTTGCTTGGGCTAGTCATGAAGGAGCGCTGCCAGACTGCAGGGAACCCATACTTCGAGCGCTTCGGCATTGTGGTTGCAGCTACTGGCATGGCAGTGGCCCTCTTCTCCTCCGTGTTGGCACTGGGCATTACTCGCCCGGTGCCCACC 
s cow.ENr232_1              435457 259 -    749201 GGCCTTCTACGTTCAGTACAAATGGGACCGGCTCCTACAGCAGGGAAGCGCGGTCTTCCAGTTCCGAATGTCCGCGAACAGCGGCCTACTGCCCGCTTCGGTGGTCATGCCTTTGCTAGGACTTGTTATGAAGGAGCGCTGCCAGGCTGCGGGGAACCCATATTTCGAGCGGTTTGGAATTGTGGTGGCGGCCACGGGCATGGCAGTGGCCCTCTTCTCCTCAGTATTGGCCCTGGGCATCACTCGCCCGGTGCCCACC 
s canFam1.chr9            47276048 259 +  53642819 GGCCTTCTACGTCCAGTACAAGTGGGACCGGCTGCTGCAGCAGGGAAGCGCTGTCTTCCAGTTCCGCATGTCCGCAAACAGTGGCCTGCTGCCCGCATCAATGGTCATGCCTTTGTTCGGACTGGTCATGAAGGAGCGCTGCCAGTCCATGGGGAACCCATATTTTGAGCGCTTTGGAATTGTGGTGGCAGCCACTGGGATGGCAGTGGCCCTCTTCTCGTCGGTACTGGCACTGGGCATCACTCGCCCAGTGCCCACC 
s rfbat.ENr232_1            410024 259 -    445008 GGCCTTCTACGTCCAGTACAAATGGGACCGGCTACTACAGCAGGGAAGCGCTGTCTTCCAGTTCCGAATGTCCGCAAACAGTGGCCTCCTGCCCTCCTCGATGGTCATGCCTTTGCTCGGACTGGTCATGAAGGAGCGCTGCCAGGCTGCGGAGCACCCGTACTTCGAGCGCTTTGGAATTGTGGTAGCAGCCACTGGCATGGCAGTGGCCCTGTTCTCATCAGTGTTGGCACTGGGCATCACTCGCCCGGTGCCCACC 
s armadillo.ENr232_1        407653 259 -    420596 GGCCTTCTACGTCCAATACAAGTGGGACCGGCTGCTACAGCAGGGAAGCGCTGTCTTTCAGTTTCGAATGTCTGCCAACAGCGGCCTACTGCCCGCCTCCATGGTCATGCCTTTGCTTGGACTGGTCATGAAGGAGCGCTGCCAGGCTGCCGGGAATCCCTACTTCGAGCGCTTTGGCATTGTGGTGGCAACCACTGGCATGGCCGTGGCCCTCTTCTCATCGGTGTTGGCGCTGGGCATTACTCGCCCTGTGCCCACC 
s monDom1.scaffold_12698    352491 259 +   3488899 GGCCTTCTATGTCCAGTACAAGTGGGACAGACTGCTCCAGCAGGGGGCTGCAGTCTTTCAGTTCAGGACCACGGCTAACAGTGGCCTCCTGCCTGCCTCCATGGTCATCCCTCTGTTGGGGGTGGTGATGAAGAAGTGCTGTGAAAGTGCAGAAAACGTCTACTTTGAGCGCTTTGGCATTGTGGTGGCAGCTACAGGTATGGCATTGGCCCTATTCCTGTCCATATTGGCACTGGGCATCACCAGGCCAGTACCCACG 
s galGal2.chr17            5423494 259 +  10632206 GGCTTTCTATGTCCAGTTTAAATGGGACCGCCTGCTGCAGCAGGGGGGGGCTGTGTTCCAGTTCCGCACCACAGCGAACAGTGGGCTCCTGCCTGCCAGCATGGTCATCCCCTTGCTGGGGATAGCAATGAAGGAGAGGTGCAAGGCTGCTGGTATCGTGTACTTTGAACGCTTTGGCATAGTTGTAGCTTCCACTGGCATGTTGGTTGCTCTATTTTTGTCTGTAATTGCTGTTGGCATCACAAAACCTGTGCCCACC 
s tetNig1.chr4             4163579 259 +   6212533 GGCTTTCTACGTTCAGCACAAATGGGATCGTTTGCTCAAGTCAGGGGGTGCTGTGTTCCAGTTTCGCCCCGCAGCAAACAGTGGCATCGTCCCGGCCTCCATGGTGATGCCTTTGCTGGGCTTGGTGCTCAGACAGAGGTGCTCTGCATCAGGGAATGTTTACTTTGAGCGCTTCTCCATGGTCGTCACCATCACTGGCATGATGCTGGCACTGTTTCTCTCCCTGATAGCCTTAGGCATTACAAGACCCGTACCCACC 
s danRer2.chr21            1734265 259 +  40848751 GGCTTTTTATGTGCAGCACAAATGGGATCGTCTGATTCGCTCTGGTGCCGCCGTCTTCCAGTTTCGTCCTTCAGCCAACAGCGGCGTCCTGCCAGCCAGTATGGTGCTGCCACTACTGGGACTCACCCTACGAGGCCGCTGCCTCGCTGTGGGAAACGTCTACATGGAGCGATTCGCAATGGTCATCACAGTAATCGGAATGATGTTGGCTCTATTCCTCTCGCTCATCGCATTGGGAATCACGCGGCCGGTGCCAACA 

a score=721779.0
s hg17.chr9                9640158 129 - 138429268 CCCGG-G---------------------GCCTGGGGCTCCGCTGAGTGGAT-CGGTGCTGGCAGAGGCGGCAGTAGTGTTTGCAGTGGTGCTGAGCATCCACGCAACCGTATGGGACCGATACTCGTGGTGCGCCGTGGCCCTCGCAGTGCA 
s panTro1.chr11_random     6899648 129 +  53199993 CCCGG-G---------------------GCCTGGGGCTCCGCTGAGTGGAT-CGGTGCTGGCAGAGGCGGCAGTAGTGTTTGCAGTGGTGCTGAGCATCCACGCAACCGTATGGGACCGATACTCGTGGTGCGCCGTGGCCCTCGCAGTGCA 
s baboon.ENr232_1           575803 129 -    695787 CCCGG-G---------------------GCCTGGGGCTCCGCTGAGTGGAT-CGGTGCTGGCAGAGGCGGCAGTAGTGTTTGCAGTGGTGCTGAGCATCCATGCAACTGTATGGGACCGATACTCGTGGTGCGCCGTGGCCCTCGCAGTGCA 
s marmoset.ENr232_1         519395 129 -    681407 CCCGA-G---------------------GTCTGGGGCTCCGCTGAGTGGAT-CGGTGCTGGCAGAGACGGCAGTAGTATTTGCAGTGGTGCTGAGCATCCACGCAGCCGTATGGGACCGATACTCGTGGTGCGCCGTGGCCCTCGCAGTGCA 
s galago.ENr232_1           340394 132 -    445664 TCCCA-CCC------------------CGACCGCGACTCCGTTGAGTGGGT-CGGTGCTGGCGGAGGCGGCAGTGGTGTTTGCAATGGTGCTGAGCATCCACGCAGCTGTGTGGGACCGATACTCGTGGTGTGCCGTGGCCCTCGCGGTACA 
s rn3.chr3               161637679 129 - 170969371 CCCGG-A---------------------GTCTGGGTTTGCGCTGAGCGGGT-CAGTGCTGGCGGAGGCTGCAGTGGTGTTCGCAGTGGTGCTGAGCATCCACGCTGCAGTGTGGGACCGATACTCCTGGTGCGCCGTGGCCTTAGCAGTGCA 
s mm6.chr2               151546142 126 - 181764313 ---GG-A---------------------GTCTGGGGCTGCGCTGAGCGGGT-CGGTGCTGGCGGAGGCTGCAGTGGTGTTCGCCGTGGTGTTGAGCATCCACGCTGCAGTGTGGGACCGATACTCCTGGTGCGCGGTGGCCCTCGCGGTGCA 
s cow.ENr232_1              435328 129 -    749201 CCCTG-G---------------------GTCCGGGGCTCCGCTGAGTGGGT-CCGTGCTGGCAGAGGCGGCGGTGGTGTTCGTAGTGGTGCTGAGCATCCACGCAGCCGTGTGGGATCGATACTCGTGGTGCGCCGTGGCCCTCGCGGTGCA 
s canFam1.chr9            47275925 123 +  53642819 CCC----------------------------CGGGGCTCCGCTGAGTGGGT-CAGTGCTGGCGGAGGCAGCAGTAGTGTTCGCAGTGGTGCTGAGCATCCACGCAGCCGTGTGGGACCGATACTCGTGGTGCGCCGTGGCTCTCGCAGTGCA 
s rfbat.ENr232_1            409895 129 -    445008 CCCGG-G---------------------GATCGGAGCGCCGCTGAGCGGGT-CGGTGCTGGCAGAGGCGGCCGTGGTGTTCGCCGTGGTGCTGAGCATCCACGCGACCGTGTTGGATCGATATTCGTGGTGCGCTGTGGCCCTCGCGGTGCA 
s armadillo.ENr232_1        407524 129 -    420596 cccgg-c---------------------gcccggggcTCCGCTGAGCGGGT-CGGTGCTGGCAGAGGCGGTGGTGGTGTTCGTCATGGTGCTGAGCATCCACGCGGCCGTGTGGGATCGCTACTCGTGGTGCGCCGTGGCCCTCGCAGTGCA 
s elephant.ENr232_30         30394 129 -     30525 CCCGG-G---------------------GGCGGGAGCTCCGCTGAGCGGTT-CGGTCCTGGCAGAGGCGGCAGTGATGGTCGCCATGGTGCTGAGCATTCACGTAACCGTGTGGGTACGGTACTCGTGGTGCGCTGTGGCCCTCGCAGTGCA 
s monDom1.scaffold_12698    352341 150 +   3488899 GCTGG-CACAAACTGAGGGTAGTCGAATGGCTTCAGCCATGCCGAACAAAG-CTATGCTGGGAGAAGCCACCATCGTGTTTATGGTAGTGCTAAGCATCCATGCCTCAGTATGGGACCGTTATTCCTGGTGTACTGTAGCCCTGGCTGTTCA 
s galGal2.chr17            5423364 130 +  10632206 CACGCTG---------------------GACTGGAACCATGTTAAACAAAC-CAGTGCTGGTGGAATCCCTGATCGTCTTCAGCATCGTTCTGTGCGTGCATGCAGTGGTGTGGGACCGCTACTCCTGGTGTGCTGTAGCTCTTGCCATCCA 
s tetNig1.chr4             4163453 126 +   6212533 -CCAGCAA------------------------GTAGCAATGGAGA-TGAATCCAGTCTTTGTCGAGTCCTCCATTGTTTTTGCCATTGTGGGGTGTGTCCACATGGTGCTGTGGAACCAGCATTCCTGGTGCAGTATTGCACTCTTCATCCA 
s danRer2.chr21            1734133 132 +  40848751 -TCACACACAC------------------TCTGCAGTCATGCAGA-TGGATCCAGTGCTGGTTGAATCTGCGGTGGTGTTCGCCATGGTGGTTTCCGTACACATGGCCGTGTGGAATCAGCTGTCCTGGTGCTGCATGGCATTGGCCGTCCA 

a score=11576.0
s hg17.chr9                9640151  7 - 138429268 CTCCG-------------------------------------GC 
s panTro1.chr11_random     6899641  7 +  53199993 CTCCG-------------------------------------GC 
s baboon.ENr232_1           575796  7 -    695787 CGCCG-------------------------------------GC 
s marmoset.ENr232_1         519388  7 -    681407 CTCCG-------------------------------------AC 
s galago.ENr232_1           340387  7 -    445664 CCCCA-------------------------------------GC 
s rn3.chr3               161637672  7 - 170969371 CCCAA-------------------------------------GC 
s cow.ENr232_1              435321  7 -    749201 CCCCG-------------------------------------AC 
s canFam1.chr9            47275918  7 +  53642819 CCCCG-------------------------------------GT 
s rfbat.ENr232_1            409888  7 -    445008 CCCCG-------------------------------------GC 
s armadillo.ENr232_1        407517  7 -    420596 ccccg-------------------------------------gc 
s elephant.ENr232_30         30387  7 -     30525 CTCCG-------------------------------------AC 
s monDom1.scaffold_12698    352297 44 +   3488899 CTCCATGATCCAAATCCCTACCTCTTTGGGAGGGAAACAACCGC 
s galGal2.chr17            5423357  7 +  10632206 CCAAA-------------------------------------GC 

a score=263333.0
s hg17.chr9                9640132 19 - 138429268 --------ATGACCCGAGAGTGCCCAT 
s panTro1.chr11_random     6899622 19 +  53199993 --------ATGACCCGAGAGTGCCCAT 
s baboon.ENr232_1           575777 19 -    695787 --------ATGACCCGAGAGTGCCCAT 
s marmoset.ENr232_1         519369 19 -    681407 --------ATGACCCGAGAGTGCCCAT 
s galago.ENr232_1           340368 19 -    445664 --------ATGACTCGAGAATGCCCAC 
s rn3.chr3               161637653 19 - 170969371 --------ATGACCCGACAGTGCCCTC 
s mm6.chr2               151546119 19 - 181764313 --------ATGACCCGACAGTGCCCTC 
s cow.ENr232_1              435302 19 -    749201 --------ATGACCCGAGAGTGCGCTC 
s canFam1.chr9            47275899 19 +  53642819 --------ATGACCCGAGAGCACGCTC 
s rfbat.ENr232_1            409869 19 -    445008 --------ATGACCCGAGAGTGTGCTC 
s armadillo.ENr232_1        407498 19 -    420596 --------ATGACCCGAGATTGCGCTc 
s elephant.ENr232_30         30368 19 -     30525 --------ATGACCCGAGATAGCGCTC 
s monDom1.scaffold_12698    352278 19 +   3488899 --------TTGAAGAGAGAGCCTTTTC 
s galGal2.chr17            5422766 27 +  10632206 gttagccaatggcccagcagtgcactc 

a score=965726.0
s hg17.chr9              128882427  96 + 138429268 ATGGCG-TTCCGGAGGGCCGAGGGCACGTCTATGATCCAGGCCC-TGGCCATGACGGTGG-CCGAGATCCCCGTGTT--CCTGTACACGACGTTTGGGCAG 
s panTro1.chr11_random    46393737  96 -  53199993 ATGGCG-TTCCGGAGGGCTGAGGGCACGTCTATGATCCAGGCCC-TGGCCATGACGGTGG-CCGAGATCCCCGTGTT--CCTGTACACGACGTTTGGGCAG 
s baboon.ENr232_1           210498  96 +    695787 ATGGCG-TTCCGGAGGGCTGAGGGCACGTCCATGATCCAGGCCC-TGGCCATGACGGTGG-CTGAGATCCCCGTGTT--CCTGTACACGACATTTGGGCAG 
s rheMac1.SCAFFOLD46502      12946  96 -     13331 ATGGCG-TTCCGGAGGGCTGAGGGCACGTCCATGATCCAGGCCC-TGGCCATGACGGTGG-CTGAGATCCCCGTGTT--CCTGTACACGACGTTTGGGCAG 
s galago.ENr232_1           201534  96 +    445664 ATGGCG-TTCCGGAGGACTGAGGGCATGTCCATGATCCAGGCCC-TGGCCATGACAGTGG-CTGAGATCCCTGTGTT--CCTGTATACAACGTTTGGGCAG 
s rn3.chr3                 9412966  96 + 170969371 ATGGCA-TTCCGTAGGACTGAGGGTATGTCCATGATCCAGGCTC-TGGCCATGACTGTGG-CTGAGATACCAGTGTT--CCTGTACACGACTTTTGGTCAG 
s mm6.chr2                30299854  96 + 181764313 ATGGCA-TTCCGGAGGACTGAGGGTATGTCCATGATCCAGGCTC-TGGCCATGACTGTGG-CTGAGATTCCAGTGTT--CCTGTACACAACTTTTGGTCAG 
s rabbit.ENr232_1             3312  96 +      7820 ATGGAG-TTCCGGCGGACAGAGGGCATGTCCATGATCCAGGCCC-TGGCCATGACGGTGG-CCGAGATCCCTGTGTT--TCTGTACACGACATTTGGGCAG 
s cow.ENr232_1               52030  96 +    749201 ATGGCG-TTCCGGCGGACCGAGGGCATGTCCATGATACAGGCCC-TGGCCATGACAGTGG-CTGAGATCCCTGTGTT--CCTTTACACGACGTTCGGGCAG 
s canFam1.chr9             6452102  96 -  53642819 ATGGCA-TTCCGGAGGACTGAGGGCATGTCCATGATCCAGGCAC-TGGCCATGACGGTGG-CCGAGATCCCTGTGTT--CCTGTATACAACGTTTGGGCAG 
s rfbat.ENr232_1            101758  96 +    445008 ATGGCG-TTCCGGAGGACGGAGGGCATGTCCATGATCCAAGCCC-TGGCCATGACGGTGG-CCGAGATCCCTGTGTT--CCTGTACACGACGTTTGGGCAG 
s shrew.ENr232_3               619  92 -      4162 ATGGCG-TTCCGGAAGACCGAAGGTGTGTCCATGATCCAGGC-C-TGGGCATGAC-GTGG-ACGAGATCCCCGTGTT---CTCTACACCACGTTTGGGCA- 
s armadillo.ENr232_1        112823  96 +    420596 ATGGCG-TTCCGGAGGGCCGAGGGCATGTCTATGATCCAGGCCC-TGGCCATGACGGTGG-CTGAGATCCCTGTGTT--CCTGTACACAACGTTTGGGCAG 
s tenrec.ENr232_10             803 100 +      7252 ATGGCGTTTCCAGAGGACCGAGGGCATGTCCATGATCCAGGCCCTTGGCCATGACGGTGGCCTGAGATCCTTGTGTTTCCTTGTACACGACGTTTGG-CAG 
s monDom1.scaffold_12698   3285504  96 -   3488899 ATGGCT-TTCCGAAGAACCGAAGGCATGTCCGTGATCCAAGCTT-TGGCCATGACGGTAG-CAGAGATACCTGTGTT--TCTCTACACAACCTTTGGACAG 
s platypus.ENr232_1          48158  96 +    341161 ATGGCT-TTCCGAAGAACCGAGGGAATGTCCATGATCCAAGCTC-TGGCCATGACGGTGG-CGGAGATCCCCGTGTT--CCTCTACACGACCTTCGGACAG 
s xenTro1.scaffold_1229     139899  96 +    221164 ATGGCA-TTTCAGAGAGCAGAGGGGATGTCAATCATTCAGGCCC-TTGCCATGACGGTAG-CAGAGATACCAGTGTT--TTTGTACACGACCTTTGGACAG 
s tetNig1.chr4             3086864  96 +   6212533 ATGTCG-CTCAGACAAGCAGAAGGAATGTCCATTGCCCAGGCTC-TGGCTATGACAGTAG-CAGAGATCCCAGTGTT--CCTTTATTCCACATTTGGACAG 
s fr1.chrUn              120365676  96 + 349519338 ATGTCA-CTCAGACAAGCGGAAGGGATGTCCATTGCCCAGGCTT-TGGCAATGACGGTAG-CAGAGATCCCAGTGTT--CCTTTATTCCACGTTTGGACAG 

a score=276081.0
s hg17.chr9                9491998 41 - 138429268 TGCGTGCCCTGCTGCAGAGCCACCCCCGGGCCAAGCTCTGA 
s panTro1.chr11            9305836 41 - 123086034 TGCGTGCCCTGCTGCAGAGCCACCCCCGGGCCAAGCTCTGA 
s baboon.ENr232_1           424948 41 -    695787 TGCGTGCCCTGCTGCAGAGCCACCCCCGGGCCAAGCTCTGA 
s rheMac1.SCAFFOLD110533     13828 41 +     55344 TGCGTGCCCTGCTGCAGAGCCACCCCCGGGCCAAGCTCTGA 
s galago.ENr232_1           203214 41 -    445664 TGCGTGCCCTGTTGCACAGCCACCCTCGGGCCAAACTCTGA 
s rn3.chr3               161520819 41 - 170969371 TGCGCACCTTACTCCAGAACCACCCCAGGGCCAAGCTCTGA 
s mm6.chr2               151429532 41 - 181764313 TGCGCACCCTACTCCAGAACCACCCCAGGGCCAAGCTCTGA 
s cow.ENr232_1              652798 41 -    749201 TGCGGGCTCTGCTCCAGAGCCACCCCCGGGCCAAGCTCTGA 
s canFam1.chr9            47142418 41 +  53642819 TGCGCGCTCTGCTGCAGAGTCACCCTCGGGCCAAGCTGTGA 
s rfbat.ENr232_1            305932 41 -    445008 TGCGTGCTCTGCTGCAGAGCCACCCCCGGGCCAAGCTCTGA 
s elephant.ENr232_7          67625 41 -     70443 TGCGTGCACTGATGCAGAGCCACCCCCGGGCCAAGCTCTGA 
s monDom1.scaffold_12698    128981 41 +   3488899 TACGTACCCTGCTGCAGGAACACCCACGGGCCAAGCTATGA 
s platypus.ENr232_1         253747 41 -    341161 TGCGGACCCTGCTGCTGGCCCACCCCAAGTCTAAGCTGTGA 
s galGal2.chr17            5330722 41 +  10632206 TGAGAAGCTTGCTCCAATCTACCCCCAAATCCAAACTGTAA 
s tetNig1.chrUn_random   152446534 41 - 171761319 TGAGGACGCTCTTGGAACAAACCCCGAGAGCCAAACTGTGA 
s fr1.chrUn               31403856 41 - 349519338 TGAGGACACTGCTAGAACAAAGCCCAAGAGCTAAACTGTGA 

a score=1544970.0
s hg17.chr9                9491823 175 - 138429268 GTCCCTGCCAAGACAGACTGTGTCATGTTCTTCGGGCCCGTGGTCCCCGACGGCTACGGTGTCTGCTATAACCCCATGGAGGCCCACATCAACTTCTCCCTGTCGGCCTACAACAGCTGCGCGGAGACCAACGCCGCCCGCCTGGCGCATTACCTGGAGAAGGCGCTCCTGGACA 
s panTro1.chr11            9305661 175 - 123086034 GTCCCTGCCAAGACAGACTGTGTCATGTTCTTCGGGCCCGTGGTCCCCGACGGCTACGGTGTCTGCTATAACCCCATGGAGGCCCACATCAACTTCTCCCTGTCGGCCTACAACAGCTGCGCAGAGACCAACGCCGCCCGCCTGGCGCATTACCTGGAGAAGGCGCTCCTGGACA 
s baboon.ENr232_1           424773 175 -    695787 GTCCCTTCCAAGACAGACTGCGTCATGTTTTTTGGGCCCGTGGTCCCCGACGGCTACGGTGTCTGCTATAACCCCATGGAGGCCCACATCAACTTCTCCCTGTCGGCCTACAACAGCTGCGCAGAGACCAACGCCGCCCGCCTGGCACATTACCTGGAGAAGGCGCTCCTGGACA 
s rheMac1.SCAFFOLD110533     13653 175 +     55344 GTCCCTTCCAAGACAGACTGCGTCATGTTCTTTGGGCCCGTGGTCCCCGATGGCTACGGTGTCTGCTATAACCCCATGGAGGCCCACATCAACTTCTCCCTGTCGGCCTACAACAGCTGCGCAGAGACCAACGCCGCCCGCCTGGCACATTACCTAGAGAAGGCGCTCCTGGACA 
s galago.ENr232_1           203039 175 -    445664 GTACCTGCCAAGACAGACTGTGTCATGTTCTTTGGGCCTGTGGTCCCTGATGGCTACGGCGTCTGCTATAACCCCATGGAGGCCCACATCAACTTCTCCCTCTCCGCCTACAACAGCTGTGCAGAGACCAATGCTGCCCGCCTGGCACACTACCTGGAGAAGGCGCTGCTGGACA 
s rn3.chr3               161520644 175 - 170969371 GTCCCTGCCAAGACAGACTGTGTCATGTCCTTCGGACCTGTGGTCCCAGACGGTTACGGCATCTGCTACAATCCCATGGAGGCCCATATCAACTTTTCCGTGTCAGCCTACAACAGCTGTGCTGAGACCAACGCTGCCCGCATGGCTCACTACTTGGAGAAAGCTCTGCTGGACA 
s mm6.chr2               151429357 175 - 181764313 GTCCCTGCCAAGACAGACTGTGTCATGTTCTTCGGACCTGTGGTCCCAGATGGTTATGGCATCTGCTACAACCCCATGGAGGCCCATATCAACTTCTCCGTGTCAGCCTACAACAGCTGTGCTGAGACCAACGCTGCCCGCATGGCTCACTACTTGGAGAAAGCTCTGCTGGACA 
s cow.ENr232_1              652623 175 -    749201 GTCCCCGCCAAGACAGACTGTGTCATGTTCTTTGGGCCCGTGGTGCCAGACGGCTATGGCGTCTGCTATAACCCCATGGAGACACACATCAACTTCTCCGTGTCAGCCTACAACAGCTGTGCCGAGACCAACGCGGTCCACCTGGCGCACTATCTAGAGAAGGCACTCCTGGACA 
s canFam1.chr9            47142243 175 +  53642819 GTCCCTGCCAAGACAGATTGCGTCATGTTCTTTGGGCCCGTGGTCCCAGACGGCTATGGCGTGTGCTACAACCCCATGGAGACGCACATCAACTTCTCTGTGTCAGCCTACAACAGCTGTGCCGAGACCAATGCAGCCCGCCTGGCGCACTACCTGGAGAAGGCACTCCTGGACA 
s rfbat.ENr232_1            305757 175 -    445008 GTCCCTGCCAAGACAGACTGCGTCATGTCCTTTGGGCCCGTGGTCCCCGACGGCTACGGTGTGTGCTACAACCCCATGGAGAGCCACATCAACTTCTCTGTGTCGGCCTACAACAGCTGTGCTGAGACCAACGCGGCCCGCCTGGGGCACTACCTGGAGAAGGCGCTCCTGGACA 
s elephant.ENr232_7          67450 175 -     70443 GTCCCTGCCAAGACAGACTGTGTCATGCTCTTTGGGCCTGTGGTCCCAGACGGATATGGTGTCTGCTATAACCCCATGGAGGGGCACATCAACTTCTCTGTGTCAGCCTACAACAGCTGTGCTGAGACCAACGCTGCTCGCCTGGCACACTACCTGGAGAAGGCCCTCCTGGACA 
s monDom1.scaffold_12698    128806 175 +   3488899 GTCCCTGCCAAAACTGACTGTGTCATGTGCTTTGGACCAGTGGTCCCTGATGGTTATGGTGTCTGCTACAACCCCATGGCTGAACACATCAACTTTGTAATCTCTGCCTTCAACAGCTGTGCTGAGACCAATGCTGCCCGTCTCGCACATTACTTGGAGAAGGCCCTGCTGGACC 
s platypus.ENr232_1         253572 175 -    341161 GTCCCGGCCAAGACGGACTGCGTGATGTGCTTCGGACCGGTGGTGCCAGACGGTTACGGCGTCTGCTACAACCCCATGGCGGATCACGTCAACTTCGCCGTGTCGGCCTTCAACAGCTGCGCGGAGACCAATGCCGCGCGTATGGCCCACTACCTGGAAAAGGCCCTGCTGGACT 
s galGal2.chr17            5330547 175 +  10632206 GTCCCAGCAAAGACAGACTGTGTGATGTGTTTTGGTCCCGTGGTTCCAGATGGCTATGGAATCTGTTACAACCCTATGGATGAACACATCAACTTTGCCATTTCAGCATTCAACAGCTGTGCTGACACAAATGCAGCTCGCATGGCACATTATCTTGAGAAAGCACTGCTAGACA 
s tetNig1.chrUn_random   152446359 175 - 171761319 GTGCCATCCAAGACAGACTGCGTCATGTGTTTTGGCGCCGTCGTGGCCGACGGATACGGCGTGTGCTACAATCCCATGGACGATCACATCAACTTTGCGGTGTCCTCCTATAACGCCTGTGGAAAAACCAAGTCGGCACATTTGGCCCAAGCCATCGAGGAGGCCCTGCTTGACA 
s fr1.chrUn               31403681 175 - 349519338 GTTCCATCCAAGACAGACTGTGTCATGTGTTTTGGTCCTGTTGTGTCTGATGGCTATGGCGTGTGCTACAATCCTATGAATGATCACATCAACTTTGCAGTGTCATCCTTTAACACCTGTGAAGAGACCAACGTGATGCATCTGGCCCAGGCTATAATGGATGGCCTGCTGGACA 
s danRer2.chr8             3772853 175 -  37493003 GTTGGATCAAAGACTGACTGCGTAATGTGTTTTGGACCCATGGTTCCTGATGGTTATGGTGTCTGTTACAATCCTATGGATGATCATATCAACTTTGCTGTGACTGCTTTCAATAGCTGTGAAGAAACCAATGCCACTAAATTGTCCACGTTTCTAACGGATGCACTTCTGGACA 

a score=414635.0
s hg17.chrX              122745047 58 + 154824264 ATGACTTTTAACAGTTT-TGAAGGATCTAAAACTTGTGTACCTGCAGACATCAATAAGG 
s panTro1.chrX           126858618 58 + 160174553 ATGACTTTTAACAGTTT-TGAAGGATCTAAAACTTGTGTACCTGCAGACATCAATAAGG 
s rheMac1.SCAFFOLD61023      23303 58 -     26046 ATGACTTTTAACAGTTT-TGAAGGATCTAAAACTTGTGTACCTGCAGACATCAATAAGG 
s marmoset.ENr324_1         334825 58 +    613215 ATGACTTTTAACAGTTT-TGAAGGATCTAAAACTTGTGTACCTGCAGACATCAATAAGG 
s galago.ENr324_1            47480 58 +    139508 ATGACTTTTAACAGTTT-TGAAGGATCTAAAACTTGTATACCTGCAGACATCAATAAGG 
s rn3.chrX               157748736 58 - 160775580 ATGACTTTTAACAGTTT-TGAAGGATCTAGAACTGTTGTACCTGCAGACACCAATAAGG 
s mm6.chrX                36615195 58 + 163688980 ATGACTTTTAACAGTTT-TGAAGGAACTAGAACTTTTGTACTTGCAGACACCAATAAGG 
s rabbit.ENr324_1           208331 58 +    535234 ATGACTTTTAACAGTTT-TGAAGGATCTAAAACTTGTGTACCTGCAGACATCAATAAAG 
s canFam1.chrX            98422419 58 + 126913094 ATGACTTTTAACAGTTT-TGAAGGAGCTAAAACTTGTGTACCTGCAGGCATCAATAAGG 
s elephant.ENr324_1         305262 58 +    630467 ATGACTTTTAACAGTCT-CGAAAGATCTAGAACTTTTCCACCTGCAGACATCAGTAAAG 
s monDom1.scaffold_18542   2098955 58 +   4454299 ATGACTTTTAAGAGTTT-TGAAGATTCTAAAACTTGTGTGCCTCCAGACATCAATAAAG 
s platypus.ENr324_9          31530 58 -     41000 ATGACCTGTAACAGTCC-GGAAGAACTCAGAACTTCAAATCCTTCAGAGGTAAATAAAG 
s galGal2.chr4            75226910 58 -  90634903 ATGACGTGTAATGGCCC-AGATAGCTCTGAATCTGGTGCCACTCCAGCCACTGACGGTG 
s xenTro1.scaffold_69      2110789 52 -   2695077 ATGACATGC--CAGTGT-CCGAAGATGTCAGAC---GGTGCTTAT-GATATGGATGTGG 
s tetNig1.chr1             3637960 47 +  16827091 TTTAGTCGGCACA----ATGGAGGACCAAAGAC--------ACGACAACAGCAATCTGG 
s danRer2.chr14           27993014 47 -  59999824 TTTAGTTACTACAA-ATATGGCACACTCAACTC-----------ATAATGGCGAATTGG 

a score=5324991.0
s hg17.chrX              122745105 819 + 154824264 AAGAAG---AATTTGTAGAAGAGTTT------------AATAGATTAAAAACTTTTGCTAATTTTCCAAGTGGTAGTC-CTGTTTCAGCATCAACACTGGCACGAGCAGGGTTTCTTTATACTGGTGAAGGAGATACCGTGCGGTGCTTTAGTTGTCATGCAGCTGTAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACAGGAAAGT------------------ATCCCCAAATTGCAGATTTATCAACGGCTTTTAT---CTT---GAAAATAGTGCCACGCAGTC---------------TACAAATTCTGGTATCCAGAATGG---TCAG-------TACA---AAGTTGAAAAC-TATCTGGGAAGCAG------------AGAT---------CATTTTGCCTTAGACAGGCCATCTGAGACACATGCAGACTATCTTTTGAGAACTGGGCAGGTTGTAGATATATCAGACACCATATACCCGAGGAACCCTGCCATGTATAGTGAAGAAGCTAGATTAAAGTCCTTTCAGAACTGGCCAGACTATGCTCACCTAACCCCAAGAGAGTTAGCAAGTGCTGGACTCTACTACACAGGTATTGGTGACCAAGTGCAGTGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCTTGTGATCGTGCCTGGTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTTTGGGCCGGAATCT---T---AATATTCGAAGTGAATCTG-ATGCTGTGAGTTCTGATA----GGAAT-----------TTCCC--AAATTCAACAAAT--CTTCCAAGAAATCCATCC-ATGGCAGATTATGAAGCACGGATCTTTACTTTTGGGACATGGATATACTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG 
s panTro1.chrX           126858676 819 + 160174553 AAGAAG---AATTTGTAGAAGAGTTT------------AATAGATTAAAAACTTTTGCTAATTTTCCAAGTGGTAGTC-CTGTTTCAGCATCAACACTGGCACGAGCAGGGTTTCTTTATACTGGTGAAGGAGATACCGTGCGGTGCTTTAGTTGTCATGCAGCTGTAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACAGGAAAGT------------------ATCCCCAAATTGCAGATTTATCAACGGCTTTTAT---CTA---GAAAATAGTGCCACGCAGTC---------------TACAAATTCTGGTATCCAGAATGG---TCAG-------TACA---AAGTTGAAAAC-TATCTGGGAAGCAG------------AAAT---------CATTTTGCCTTAGACAGGCCATCTGAGACACATGCAGACTATCTTTTGAGAACTGGGCAGGTTGTAGATATATCAGACACCATATACCCGAGGAACCCTGCCATGTATAGTGAAGAAGCTAGATTAAAGTCCTTTCAGAACTGGCCAGACTATGCTCACCTAACCCCAAGAGAGTTAGCAAGTGCTGGACTCTACTACACAGGTATTGGTGACCAAGTGCAGTGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCTTGTGATCGTGCCTGGTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTTTGGGCCGGAATCT---T---AATATTCGAAGTGAATCTG-ATGCTGTGAGTTCTGATA----GGAAT-----------TTCCC--AAATTCAACAAAT--CTTCCAAGAAATCCATCC-ATGGCAGATTATGAAGCACGGATCTTTACTTTTGGGACATGGATATACTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG 
s rheMac1.SCAFFOLD61023      23361 819 -     26046 AAGAAG---AATTTGTAGAAGAGTTT------------AATAGATTAAAAACTTTTGCAGATTTTCCAAGTAGTAGTC-CTGTTTCAGCATCAACACTGGCACGAGCAGGGTTTCTTTATACTGGTGAAGGAGATACCGTGCGGTGCTTTAGTTGTCATGCAGCTGTAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACAGGAAAGT------------------ATCTCCAAATTGCAGATTTATCAATGGCTTTTAT---TTT---GAAAATAGTGCCACGCAGTC---------------TACAAATTCTGGTATCCAGAATGG---TCAG-------TACA---AAGTCGAAAAC-TATCTGGGAAGCAG------------AAAT---------CATTTTGCCTTAGACAGGCCATCTGAGACACATGCAGACTATCTTTTGAGAACTGGGCAGGTTGTAGATATATCAGACACCATATACCCGAGGAACCCTGCCATGTATAGTGAAGAAGCTAGATTAAAGTCCTTTCAGAACTGGCCAGACTATGCTCACCTAACCCCAAGAGAGTTAGCAAGTGCTGGACTCTACTACACAGGTATTGGTGACCAAGTGCAGTGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCTTGTGATCGTGCCTGGTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTTTGGGCCGGAATCT---T---AATATTCGAAGTGAATCTG-ATGCTGTGAGTTCTGATA----GGAAT-----------TTCCC--AAATTCAACAAAT--CTTCCAAGAAATCCATCC-ATGGCAGATTATGAAGCACGGATCATTACTTTTGGGACATGGATATACTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG 
s marmoset.ENr324_1         334883 819 +    613215 ATGAAG---AATTTGTAGAAGAGTTT------------AATAGATTAAACACTTTTGCTAATTTTCCAAGTAGTAGTC-TTGTTTCAGCATCAACACTGGCAAGAGCAGGGTTTCTTTATACTGGTGAAGGAGATACCGTGCGGTGCTTTAGTTGTCATGCAGCCGTAGATAGATGGCAATATGGAGACTCAGCAATTGGAAGACACAGGAAAGT------------------ATCCCCAAATTGCAGATTTATCAACGGCTTTTAT---TTT---GAAAATAGTGCCACGCAACC---------------TACAAATCCTGGTATCCAGAATGG---TCAG-------TACA---AAGTTGAAAAC-TATCTGGGAAGCAG------------AAAT---------CATTTTGCTTTAGACAGGCCATCTGAGACACATGCAGACTATCTTTTGAGAACTGGGCAGGTTGTAGATATATCAGACACCATATACCCGAGGAACCCTGCCATGTATAGTGAAGAAGCTAGACTGAAGTCCTTTCAGAACTGGCCAGACTATGCCCACCTAACCCCAAGAGAGTTAGCGAGTGCTGGACTCTACTACACAGGTATTGATGACCAAGTGCAGTGCTTTTGTTGTGGAGGAAAACTGAAAAATTGGGAACCTTGTGATCGTGCCTGGTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTTTGGGCCGCAATCT---T---AACATCCGAAGTGAATCTG-ATCCTGTGAGTTCTGATA----GGAAT-----------TACCC--AAATTCAACAAAT--CTTCCAAGAAATCCATCC-ATGGCAGATTATGAAGCACGGATCATTACTTTTGGGACGTGGATATACTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG 
s galago.ENr324_1            47538 819 +    139508 ATGAAG---AATTTGTAGAAGAGTTT------------AATAGATTAAAAACTTTTGCTAATTTTCCAAGTACTAGTC-CTGTTTCAGCATCAACACTGGCACGAGCAGGTTTTCTTTATACTGGTGAAGGAGATACCGTGCGGTGCTTTAGTTGTCATGCAGCAGTAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACAGGAAAGT------------------ATCCCCAAATTGCAGATTTATCAGCGGCTTTTAT---TTT---GAAAATAGTGCCATGCAGCC---------------TACAAATCCTGGTGTCCAGAATGG---TCAG-------TACA---AAGTTGAAAAC-TATCTGGGAAACAG------------AAAT---------CATTTTGGTTTAGACAGGCCATCTGAGACTCACGCAGACTATCTTCTGAGAACTGGACAGGTTGTAGATATATCAGACACCATTTACCCAAGGAATCCTGCCATGTGTAGTGAAGAAGCTAGATTAAAGTCATTCCAGAATTGGCCAGACTATGCCCACTTAACCCCAAGAGAGTTAGCTAGTGCTGGACTCTACTACACAGGTATTGATGATCAAGTGCAGTGCTTTTGTTGTGGTGGAAAATTGAAAAATTGGGAACCTTGCGATCGCGCCTGGTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTTTGGGCCGGAACAT---T---AATACTAGAAGTGAATCTG-ATGTTGTGAGTTCTGATA----GGAAT-----------TGCCC--AAATTCAACAAAT--CTTCCAAGAAATCCATCC-ATGGCAGATTATGAAGCACGGATCATTACTTTTGGGACGTGGATATACTCAATTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG 
s rn3.chrX               157748794 816 - 160775580 ATGAAG---AATTTGTAGAAGAGTTT------------AATAGATTAAAAACATTTGCTAACTTCCCAAGCAGCAGTC-CTGTTTCAGCATCAACATTGGCGCGAGCGGGGTTTCTCTACACTGGTGAAGGAGACACCGTGCAGTGTTTCAGTTGTCACGCGGCAGTAGATAGATGGCAGTATGGAGACTCAGCTGTTGGAAGACACAGGAGAAT------------------ATCCCCAAATTGCAGATTTATCAATGGTTTTTAT---TTT---GAAAACGGTGCCACACAGTC---------------TACATCTCCTGGCATCCAAAATGG---CCAG-------TACA---AATCTGAAAAC-TGTGTGGGAAACAG------------AAAT---------CATTTTGCTCTTGACAGGCCGTCGGAGACTCATGCAGATTATCTCCTGAGAACTGGACAGGTTGTAGATATTTCAGATACCATATACCCGAGGAACCCGGCCATGTGTAGTGAAGAAGCCAGACTGAAGACGTTTCAGAACTGGCCAGACTATGCCCATTTAAGCCCCAGAGAGTTAGCTAGTGCTGGACTCTACTACACGGGGATTGATGATCAAGTGCAATGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCCTGTGACCGTGCCTGGTCAGAGCACAGGAGACACTTTCCCAACTGCTTCTTCGTTTTGGGCCGGAATGT---T---AATGTTCGAAGTGAGTCTG-GTGT---GAGTTCAGATA----GGAAT-----------TTCCC--AAATTCAACAAAT--TCTCCAAGAAATCCAGCC-ATGGCAGAATATGACGCACGGATCGTTACTTTTGGAACATGGCTATACTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG 
s mm6.chrX                36615253 816 + 163688980 ATGAAG---AATTTGTAGAAGAGTTT------------AATAGATTAAAAACATTTGCTAACTTCCCAAGTAGTAGTC-CTGTTTCAGCATCAACATTGGCGCGAGCTGGGTTTCTTTATACCGGTGAAGGAGACACCGTGCAATGTTTCAGTTGTCATGCGGCAATAGATAGATGGCAGTATGGAGACTCAGCTGTTGGAAGACACAGGAGAAT------------------ATCCCCAAATTGCAGATTTATCAATGGTTTTTAT---TTT---GAAAATGGTGCTGCACAGTC---------------TACAAATCCTGGTATCCAAAATGG---CCAG-------TACA---AATCTGAAAAC-TGTGTGGGAAATAG------------AAAT---------CCTTTTGCCCCTGACAGGCCACCTGAGACTCATGCTGATTATCTCTTGAGAACTGGACAGGTTGTAGATATTTCAGACACCATATACCCGAGGAACCCTGCCATGTGTAGTGAAGAAGCCAGATTGAAGTCATTTCAGAACTGGCCGGACTATGCTCATTTAACCCCCAGAGAGTTAGCTAGTGCTGGCCTCTACTACACAGGGGCTGATGATCAAGTGCAATGCTTTTGTTGTGGGGGAAAACTGAAAAATTGGGAACCCTGTGATCGTGCCTGGTCAGAACACAGGAGACACTTTCCCAATTGCTTTTTTGTTTTGGGCCGGAACGT---T---AATGTTCGAAGTGAATCTG-GTGT---GAGTTCTGATA----GGAAT-----------TTCCC--AAATTCAACAAAC--TCTCCAAGAAATCCAGCC-ATGGCAGAATATGAAGCACGGATCGTTACTTTTGGAACATGGACATCCTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG 
s rabbit.ENr324_1           208389 819 +    535234 ATGAAG---AATTTGTAGAAGAGTTT------------AATAGATTAAAAACTTTTGCTAATTTTCCAAGTAGTAGTC-CTGTTTCAGCGTCAACACTGGCACGAGCAGGTTTTCTTTATACTGGTGAAGGAGACACTGTGCGATGCTTTAGTTGTCATGCAGCAGTAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACAGGAAAGT------------------ATCCCCAAATTGCAGATTTATCAACGGCTTTTAT---TTT---GAAAATAGTGCTGCACAATC---------------TACAAATCCTGGTGTCCAGAATGG---TCAA-------TACA---AAGGTGAAAAC-TACCTGGGAAACAG------------AAAT---------CATTTTGCTTTAGACAGACCATCTGAGACTCACGCAGACTATCTTTTGAGAACTGGACAGGTTGTAGATATATCAGACACCATATACCCAAGGAACCCTGCCATGTGTAGTGAAGAAGCTAGATTAAAGTCATTTCAGAACTGGCCAGACTATGCCCACCTAACCCCCAGAGAGTTAGCTAGTGCTGGGCTCTACTACACAGGTATTGATGATCAAGTGCAATGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCTTGTGATCGTGCCTGGTCGGAACATAGGCGACACTTTCCTAATTGCTTCTTTGTTTTGGGCCGGAACGT---T---AATATTCGAAGTGAATCTG-ATGTTGTGAGTTCTGATA----GGAAT-----------TTTCC--AAATTCAACAAAT--CCTCCAAGAAATCCAGCC-ATGGCAGATTATGAAGCACGGATCATTTCTTTTGGGACGTGGATATACTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG 
s canFam1.chrX            98422477 819 + 126913094 ATGAAG---AATTTGTAGAAGAGTTT------------AATAGATTAAAAACTTTTGCTAATTTTCCAAGTAGCAGTC-CTGTTTCAGCATCAACGTTAGCACGAGCTGGTTTTCTGTATACTGGTGAAGGAGATACTGTGCGGTGCTTTAGTTGTCATGCATCAATAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACAGGAAAGT------------------ATCCCCAAATTGCAGATTTATCAATGGCTTTTAT---TTT---GAAAACACTGCTGCACAACC---------------TACAAATCCAGGTATCCAAAATGG---TCAA-------TATA---ATGCAGAAAAC-TATCTGAGAAACAG------------AGAT---------CATTTTGTTTTAGACAGACCATCTGAGACTCATGCAGATTATCTTTTGAGAACTGGACAGGTCGTAGATATATCAGACACCACATACCCGGAGAACCCTGCCATGTATAGTGAAGAAGCTAGATTAAACTCATTTCAGAACTGGCCAGACTATGTCCACTTGACCCCAAGAGAGTTAGCTAGTGCTGGATTCTACTACACAGGTATTGACGATCAAGTGCAGTGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCGTGTGATAATGCATGGTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTCTGGGCCGGAATGT---T---AATATTCGAAGTGAATCTG-ATGTTGCGAGTACTGATA----GGAAC-----------GTCCC--AAATTCAACAAGT--ATTCCAGAAAATCCAGCC-ATGGCAGATTATGAAGCACGGATCGTTACTTTTCGGATGTGGATGTGTTCAATTAACAAGGAGCAACTTGCAAGAGCTGGATTTTATTCTTTAG 
s elephant.ENr324_1         305320 819 +    630467 ATGAAG---AATTTGTAGAAGAGTTC------------AGTAGATTAAAAACTTTTGCTAATTTTCCAAGTAGCAGTC-CTGTTTCAGCATCAACGCTGGCACGAGCTGGTTTTCTGTATACTGGTGAAGGAGACACCGTGCGGTGCTTTAGTTGTCATGCAGCAGTAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACAGGAAAGC------------------ATCCCCAAATTGCAGATTTATCAATGGCTTTTAT---TTT---GAAAATAATACTGCTCAACC---------------TACAAATCCTGGTGTCCAAAATGG---TCAG-------TACA---AAGTGGAAAAC-TATCCAGGAAACAG------------AAAT---------CATTTTGTTTTAGACAGGCCATCTGAGACTCATGCAGACTATCTTTTGAGAACTGGGCAAGTTGTAGATATATCGGACACCATATACCCACGGAACCCTGAGATGTGTAGTGAAGAAGCTAGATTGAAGACATTTCACAACTGGCCAGAGTATGCCCACTTAACCCCAAGAGAGTTAGCGAGTGCTGGACTCTACTACACAGGTATTGATGACCAAGTGCAGTGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCTTGTGATCACGCGTGGTCAGAACACAGGCGACACTTCCCTAACTGCTTCTTTGTTTTGGGCCGGAATAT---T---AATACTCGAAGTGAATCCG-ATGTCTTGAGTTCTGATA----GGAAT-----------TTCCC--AAATTCAACAAAT--TCTCCAAGAAACCCAGCC-ATGGCAGATTATGAAGCACGGATCATGACTTTTGGGACGTGGATGTACTCTGTGAACAAGGAGCAGCTTGCAAGAGCTGGATTTTACTCTCTAG 
s tenrec.ENr324_16            1245 818 -      3110 ATGAAG---AATGTGTAGAAGAGTTC------------AATAGAT-GAAAACCTTTGCCAAATTTACAAGCAGTAGTC-CTGTTTCCGCCTCAACGCTGGCACGAGCTGGCTTTCTCTATTCTGGTGAAAGAGACACCGTGCGGTGCTTTAGTTGTCATGCAGCAGTAGATAGATGGCAATATGGTGACTCCGCCATTGGAAGACACAGGAAAGC------------------ATCCCCTAATTGCAGATTTATCAGTGGCTTTCAT---TTT---GAAAATAAGGCTGCGCAACC---------------TACAAATTCTGGTGTCCAAAATGG---ACTG-------TACA---ACAGTGAACAC-TATGCACGAAACAA------------AAAT---------CACTTGGTTTTAGACAGGCCTTCTGAGACCCATGCAGACTATCTCTTGAGAACTGGACAAGTTGTAGATATGTCTGACACCATATACCCGAGGAACCCTGAGATGTGTAGCGAAGAAGCTAGGTTAAATTCATTTCAGAATTGGCCAGAGTATGCCCACCTAACCCCAAGAGAGCTAGCCAGTGCTGGGCTCTACTACACAGGGATCGATGATCAAGTGCAGTGCTTTTGTTGTGGCGGGAAACTGAAAAATTGGGAACCTTGTGATCGGGCCTGGTCAGAACACAAGCGACATTTTCCACATTGCTTTTTTGTGCTGGGCCGGAGTGT---T---AATGCACAAAGTGAATCTG-GTGTCTTGAGTTCTGATA----GGAAT-----------TTCCC--CAATTCAACAAAT--CCTCCAAGAAATCCAGCC-ATGGTGGATTATGAAGTACGGATCCTGACTTTTGGGACATGGATATACTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG 
s monDom1.scaffold_18542   2099013 820 +   4454299 ATGAAG---ATTTTGTAGAGGAATTT------------AATAGATTAAAGACATTTGCTAATTTCCCAAGTAGTAGCC-CTATTTCCGCATCAACATTGGCGCGAGCAGGTTTCCTCTATACTGGTGAGGGAGATACTGTCAAGTGCTTTAGCTGTCATGCAGCTGTAGATAGATGGCAGTATGGAGACTCAGCAGTTGGAAGACATAGAAAAGTG-----------------ATGCCCAAACTGCAGATTTATTAATGGTTTTTAT---TTT---GAAAAAAATGCTACACGGTT---------------TCCAAATCCCATTATCCAAAACTG---TCAG-------TACA---GAGTTGAAAAT-TGTTCAAGGAATAG------------AAAT---------CACTTTGCTTTGGAGAGACCCTCTGAAACTCATGGGGAATATCTTTTGAGAACAGGCCAGGTCATTGATATGTCAGATACCATATACCCACGGAATCCTTCCATGTGTAGTGAAGAAGCTCGACTGAGATCTTTTCAGAATTGGCCAGACTATGCTCACCTTACCCCACAGGAGTTAGCAAGTGCTGGACTCTATTACATGGGCTTTGAGGATCAAGTGCAGTGCTTTTGTTGTGGGGGCAAATTAAAGAATTGGGAACCGTGTGATCGGGCAATGTCCGAACACAAGAGGCATTTCCCTAAGTGTTTTTTTGTCTTGGGACGGGATGTTGGT---AATACACGAATTGAAACTG-ATGTT---AGCTGTGATA----GGAGT-----------TGCCC--AAACCCTACCCAT--CTCCCAAGGAATCCAGCC-ATGGCGGATTATGAAGCACGACTCATTACCTTTGCAACATGGATATACTCGGTTAACAAGGAGCAGCTTGCAAAAGCTGGATTTTATGCTTTAG 
s platypus.ENr324_9          31588 825 -     41000 ATGAAG---AATTTGCAGAAGAGCAT------------AACAGATTAAGAACTTTTGCTAATTTTCCAAGTACTAGCC-CTGTTTCTTCATCAACTCTGGCCCGAGCTGGTTTCCTTTATACGGGCGAAGAAGATGTCGTGCGATGCTTCAGTTGCCATGTAGCTGTAGATCGTTGGCAGTATGGTGACTCAGCAATTGGCAGGCACCGAAAAAT------------------TTCCCCCAACTGCAGATTTGTCAATGGATGTCAT---TTT---AAGAACTGTGCTCTGCCTTT---------------AGCAAATGCAAGTCTCCAAAACGG---TGAA-------CTCGGTCAAGTTGAAGAA-TGCCCAGGAAATCC------------AAGT---------CACCACGCTTTGGAAAGATCATCCGAAACTCATTCGGACTACCTTTTGAGAACGAGGCAGGTTGTCGACCTATCGGATACGGTATTCCCGAAGAACCCTGCCATGTGCAGCGAAGAAGCCAGACTAGAAACATTTCAGAATTGGCCCGAATATACCCTGTTATCCCCAGGGCAATTAGCTAGAGCTGGACTGTACTACTCAGGTATTGATGATCAAGTAGAATGCTTTTGTTGTGGTGGAAAGTTGAAAAACTGGGAGCCGTGCGATCGTCCGTGGTCAGAGCACAAACGGCATTTCCCAAAGTGCCTTTTTGTCTTGGGCCGGGATGT---TGGAAACATTGAAATTGAATCTG-ATAGCATCGCTTCCCAGA----GGAGT-----------TATTC--AAATTCAACTCAT--TTCCCGAGGAATCCGGCC-ATGGCAGAGTTTGAAGCCCGGATCCACACTTTTGAGACATGGACATACTCCATTGACAAGGAGCTGCTTGCAAGAGCAGGATTTTATACTCTAG 
s galGal2.chr4            75226968 816 -  90634903 ACCAGG---AGTGGACACAGGAACAC------------TACCGACTAGGAACCTTTGTGGAGTTTCCCCATGATTGTC-CAGTTTCAGCATCAGCGCTAGCTCGAGCTGGCTTTGTTTATACTGGAGAAGGTGATAAAGTCAAGTGCTTCAGTTGCCATGTAACTGTTGAAGGATGGGAGCCTGGGGATTCTGCAATTGACAGACACAAAAACCT------------------TTCCCCAGATTGCAGATTTATTACTGGGTCTGCT---TTTTTGGAAAATAACG---------------------------TACATCCTCTTGTGCAGAGCCA---CCAG-------CATA---GAACTGAAAAT-GGCTC------CAG------------CAATTTGGCCCTCCCCTCTGCTCTGGAGGACTTGTCTGATGTGGAGGCAGATTACCTGTTGAGAACCAGGCAGGTTGTGGACATGTCCGATACTTTGTATCCTAAAAACCCTGCTATGTGCAGTGAAGAAGCCAGGCTGAAGTCCTTTCACAATTGGCCCCCCTATGGCCTATTGACGCCAAAGGAATTAGCTAGTGCAGGACTCTACTATACAGGTGTTGGTGATCAAGTTGCATGTTTCTGTTGCGGTGGAAAACTGAAAAACTGGGAACCTGGTGATCGAGCTTGGTCTGAGCACAAGAGGCATTTTCCCAAATGCTTTTTTGTCCTGGGTCGGGACGT---TGGAAATGTTTCAACTGATTCTATCTGTGCTGAGCT-TGGGA----GAAGC-----------TGTCT--AAA--CAACGAACAGCATCCAAGGAATCCATCC-ATGGCAGAATATGAGAGGCGGATACAAACATTTTTAGCTTGGATATACCCTGTTAACAAGGAACATCTTGCTGAAGCAGGGTTCTACAGCACAG 
s xenTro1.scaffold_69      2110841 795 -   2695077 ACCAGA---ATTATTTTGAAGAGGAA------------GTCAGACTGGCGTCCTTTGCTAACTTCCCAAGTAGCTACC-CGGTCTCTGCTCCAGCACTAGCGCGGGCCGGCTTCTATTACACTGGAGATGGAGATCGAGTCAAGTGTTTTAGCTGCCTGGCTATGGTTGAAGGCTGGCAGCATGGAGACACGGCAATTGGCAAGCACCGGAAAAT------------------ATCCCCAAACTGTAAATTTATTAATGGCTTTAATAACTTA---CGAAGTGATTGTATCCTAAC---------------TCAAGTGCCTGTCATGCAGAATGGTTTTCAG-------AATT---CCGCTGAAGACTTGGCTGAGAGATCT------------AGTT-------------------------------CTGAGATTATGGCAGACTACTTGCTAAGGACTGGAAGAGTTGTCGATATGTCAACACCAAAATATCCCAGGCATATGGAAATGTGTAGTGAGGAAGCCCGACTGCAAACGTTTCAAAACTGGCCAGCCTATTCACCCTTAACACCAAAAGAGCTAGCCAATGCAGGTCTTTTTTATACAGGCATCAACGACCAAGTCAAATGCTTTTGCTGTGGTGGAAAACTAATGAACTGGGAACCTAGTGACAAAGCGTGGACAGAACACAAAAAACATTTTCCTGAATGCTACTTTGTTTTGGGCCGTGATGT---TGGCAATGTGGCTACCGAAGCCA-ATACACATGGTGGTAGGA----GAAGA-----------GGTTC--TGAGTTGGCCTGC--------------CCAGCC-ATGAACGACTACAATGCTCGTCTTGAGACCTTTTCATCATGGTCATTTCCAATTGACAAGGAAACACTCGCTAAAGCTGGATTTTATAGTATAG 
s tetNig1.chr1             3638007 833 +  16827091 AGACGG---ATTCCGCCGAAGATTTTTCACTGATCAAGAGTCGTCTGGAATCGTTCC-GTGGCTCCAGCCTGGTGCAGCGGGTGCCGGCTGAAAGATTAGCTCGGGCTGGCTTCTACCTTGTCGGCCCATCCGATCGCGTTCGCTGTTTTAGCTGCCAGAAAACTGTGGAAAACTGGAGCCGAGAGGACAGACCTGTTGAGAGGCATAAGGAGGTGAGTCTGCTGAGTGTGGAATCTC---AATGTCAATTTAGCGTTGTATTCTTC---CTG---GAA----TTACTTTCTAACTTTCCTCATTGTTGTAGGTTTCTCCTGTT-TGCCAATTTC---TCAGCTGCATTTACG---GAACCAGACCC-CACCAGTTAATAGACGCCTCACTGGCTAAC---------AACTCTGCCTACAATGAAGAAGC------------------------------------AGTGGTGGAT------GAGTCCATTTATCCGGTGGCCCCTCATATGAAGAGTGAGAAAAGCCGGCTTCAGACCTTCTCCTCTTGGCCCTCGGCAGTGCCCGTGAGGCCTCAAGATCTGGCCCAAGCTGGCCTCTACTACCTGGGGCAGAACGACCAGGTGCAGTGTTTCTGCTGCGGGGGCATACTGGCCAACTGGGACGCCGGGGACTCAGCCTGGGGAGAACACAACAAACATTTCCCCTCCTGCTTTTTCATCCTGGGGCACGATGT---TGGCAACATA----------CCT-TTGCAG-GGGTCCGGAGAGGAGGAGAAGAGAGTTGTCCCACCTGCAGGTGCAGGTGCT---------GGTGTCCAC---ATGGGGACATTTGAGGAACGCCTGAGGAGCTTCGCTAACGTCCAGCACCCTGTAAACACGGAGAGGCTTGCGAGAGCCGGCTTCTACAGTAAAG 
s danRer2.chr14           27993061 738 -  59999824 AATCTGACAATGTGGCAGCTGATTGGTCAGTCATGAAGAATCGGGTGAACTCTTTTCAACGTTTTCCATATTCTGAAG-ACATTTCAGCACAGCGGCTGGCCCGAGCGGGCTTTTACTTCACAGGCGAGGGGGACAGGGTGCAATGTTTCAGCTGCAGTGCCACTGTGCAGAACTGGAACAGAGGTGACACCCCATTGGAGAGACAT------------------------------------------------------------------------------------CAACT---------------GGCATCTCCGGAC-TGCAGGTTCC---TCAGCTGTGCTCATG---GTATGAGAAAC-TCTAATTCGAT---------------CCAG---------AGTCCTGATTACGATGAAGAGGCCGAGA---ATAGAGAGTTCCTCCTCCGCACGGGAGAGGTGGTGGAC------GAGTCCATGTATCCTGTTGTACCGCACATGAAGAGTGAAGAAGCGCGACTGAGTACTTTCAACAACTGGCCAGCAGACTCTCCAGTTCGGCCTGAAGACCTGGCAGAAGCAGGGATGTATTACATTGGGATAGACGACAATGTGCAGTGCTTCTGTTGCGGAGGGGGTCTGAGTGGATGGGAGCAAGGCGACGATCCTTGGAGTGAACATGCGAAGTACTACTCAAACTGCTTCTTCTTCTTGGGCCACAATGT---GGGCAACGTC----------CCC-CT--------------------GACAA-----------CACCT--AGGC-CAAGGGCT---------AATGTCCACCCTACAGACACTTTTGAGGGGCGTCTTGATAGCTTCAAAGGCAGACAGCATCCCATTGACCCTGAGAGATTGGCCAGAGCTGGTTTCTACAGCACAG 

a score=28417.0
s hg17.chrX              2175291  9 - 154824264 C---------TAGAATAG 
s panTro1.chrX           2209848  9 - 160174553 C---------TAGAATAG 
s baboon.ENm006_1         784129  9 -    802484 C---------TAGAATAG 
s rheMac1.SCAFFOLD30444    14232  9 -     57263 C---------TAGAATAG 
s marmoset.ENm006_1       671327  9 -    677071 C---------TAGAATAG 
s galago.ENm006_1         940013  9 -    952237 C---------TAGAATAG 
s rn3.chrX                914133  9 - 160775580 C---------TAGAATAG 
s mm6.chrX              95173281  9 - 163688980 C---------TAGAATAG 
s canFam1.chrX           2147657  9 - 126913094 C---------TAGAGTAG 
s rfbat.ENm006_1         1004170  9 -   1015308 C---------TGGAGTAG 
s shrew.ENm006_31          22401  9 -     74035 C---------TGGAGTAG 
s tenrec.ENm006_4          11684  9 +     15794 C---------TGGAATAG 
s monDom1.scaffold_3472    66704  9 +     94349 C---------TGGAGTAG 
s xenTro1.scaffold_317    111095  9 +   1352153 G---------TTGAATAG 
s tetNig1.chr19          1088504  9 -   5206847 T---------TCGTCTAG 
s fr1.chrUn             19892233 17 + 349519338 CGGCCACCAATGGGGCG- 
s danRer2.chr23         42356636  9 -  42830282 T---------CCGCCCAG 

a score=1791044.0
s hg17.chrX              2175068 223 - 154824264 TGACAACGAGGAGAAGGCCTTTGGCA-GC--------AGCCAGCCATCGCTCAACGGGGACATCAAGCCCCTGGGCAGTGACGACAGCCTGGCCGATTATGGGGGCAG---CGTGGATGTTCAGTTCAACGAGGATGGTTCGTTCATTGGCCAGTACAGTGGCAAGAAGGAGAAGGAGGCGGCAGGGGGCA-ATGACAGCTCAGGGGCCACTTCCCCCATCAACCCTGCC---G-TGGCC 
s panTro1.chrX           2209625 223 - 160174553 TGACAACGAGGAGAAGGCCTTTGGCA-GC--------AGCCAGCCATCGCTCAACGGGGACATCAAGCCCCTGGGCAGTGACGACAGCCTGGCCGATTATGGGGGCAG---CGTGGATGTTCAGTTCAACGAGGATGGTTCGTTCATTGGCCAGTACAGTGGCAAGAAGGAGAAGGAGGCGGCAGGGGGCA-ATGACAGCTCAGGGGCCACCTCCCCCATCAACCCTGCC---G-TGGCC 
s baboon.ENm006_1         783906 223 -    802484 TGACAACGAGGAGAAGGCCTTCGGCA-GC--------AGCCAACCATCGCTCAATGGGGACATTAAGCCCCTGGGCAGTGACGACAGCCTGGCCGATTATGGGGGAAG---CGTGGATGTTCAGTTCAACGAGGATGGCTCCTTCATTGGCCAGTATAGTGGCAAGAAGGAGAAGGAAGCGGCAGGGGGCA-ACGACAGCTCAGGGGCCACTTCCCCCATCAACCCTGCC---G-TGGCC 
s rheMac1.SCAFFOLD30444    14009 223 -     57263 TGACAACGAGGAGAAGGCCTTCGGCA-GC--------AGCCAACCATCGCTCAATGGGGACATTAAGCCCCTGGGCAGTGACGACAGCCTGGCCGATTATGGGGGAAG---CGTGGATGTTCAGTTCAACGAGGATGGCTCCTTCATTGGCCAGTATAGTGGCAAGAAGGAGAAGGAGGCGGCAGGGGGCA-ACGACAGCTCAGGGGCCACTTCTCCCATCAACCCTGCC---G-TGGCC 
s marmoset.ENm006_1       671104 223 -    677071 TGACAATGAGGAGAAGGCTTTCGGCA-GC--------AGCCAGCCCTCGCTCAATGGAGACATCAAGCCCCTGGGCAGTGATGACAGCCTGGCCGATTATGGGGGCAG---TGTGGATGTTCAGTTCAATGAGGATGGCTCCTTCATCGGCCAGTACAGTGGCAAGAAGGAGAAGGAGGTGGCAGGGGGCA-ACGACAGCTCAGGGGCTACCTCCCCCATCAACCCTGCT---G-TGGCC 
s galago.ENm006_1         939790 223 -    952237 TGACAACGAGGAGAAGGCCTTTGGCA-GT--------AGCCAGCCATCTCTCAATGGAGACATCAAACCCCTGGGTAGTGATGACAGCCTGGCTGATTACGGGGGAAG---CGTGGACGTGCAGTTCAACGAGGATGGCTCCTTCATCGGCCAATACAGTGGCAAGAAGGAGAAGGAGGCAGCAGGGGGCA-ATGACAGCTCAGGGGCCACCTCTCCCATCAACCCTGCC---G-TGGCC 
s rn3.chrX                913910 223 - 160775580 TGACAATGAAGAGAAGGCCTTCGGCA-GC--------AGCCAGCCATCTCTCAATGGAGACATCAAACCCCTAGGCAGTGATGACAGTCTGGCTGATTATGGGGGCAG---TGTGGATGTCCAGTTCAATGAGGATGGCTCTTTCATCGGCCAATACAGTGGCAAAAAAGAGAAGGAGGCAGCGGGAGGCA-ATGACAGCTCAGGGGCTACCTCTCCTATCAATCCTGCA---G-TAGCC 
s mm6.chrX              95173058 223 - 163688980 TGACAATGAAGAGAAGGCCTTTGGCA-GC--------AGCCAGCCATCTCTCAACGGAGACATCAAACCCCTAGGCAGTGATGACAGCCTGGCTGATTATGGGGGCAG---TGTGGACGTCCAGTTCAATGAGGATGGCTCTTTCATCGGCCAGTACAGTGGCAAGAAAGAGAAGGAGGCAGCAGGAGGCA-ATGACAGTTCAGGGGCTACCTCTCCTATCAATCCTGCA---G-TAGCC 
s canFam1.chrX           2147434 223 - 126913094 TGACAACGAGGAGAAGGCCTTTGGCA-GC--------AGCCAGCCGTCCCTCAATGGGGACATCAAGCCCCTGGGCAGTGACGACAGCCTGGCCGACTACGGGGGCAG---CGTGGACGTGCAGTTCAACGAGGACGGCTCCTTCATCGGCCAGTACAGCGGCAAGAAGGAGAAGGAGGCAGCAGGCGGCA-ACGACAGCTCAGGGGCCGCCTCCCCCATCAACCCTGCC---G-GGGCC 
s rfbat.ENm006_1         1003947 223 -   1015308 TGACAACGAGGAAAAGGCCTTCGGCA-GC--------AGCCAGCCATCTCTCAATGGAGACATCAAGCCCCTGGGCAGTGATGATAGCCTGGCTGACTATGGGGGCAG---CGTGGATGTCCAGTTCAATGAGGACGGCTCTTTCATTGGCCAGTACAGTGGCAAGAAGGAGAAGGAGGCAGCAGGAGGCA-ACGACAGCTCAGGAGCTGCCTCCCCCATCAACCCTGCA---G-GGACC 
s shrew.ENm006_31          22178 223 -     74035 TGACAACGAGGAGAAAGGCTTTGGCA-GC--------AGCCAGCCGTCGCTCAATGGGGACATCAAGCCGCTGGGCAGTGATGACAGCCTGGCCGACTATGGCGGCAG---CGTGGACGTGCAGTTCAACGAGGATGGCTCGTTCATCGGCCAGTACAGCGGCAAGAAGGAGAAGGAGGCAGCAGGGGGCC-ATGACAGCTCGGGGGCCGCCTCCCCCGTCAACCCCTCG---G-GGGCT 
s tenrec.ENm006_4          11461 223 +     15794 TGACAACGAGGAGAAGGCCTTTGGCA-GC--------AGCCAGCCATCCCTCAATGGGGACATTAAACCCCTGGGGAGTGATGACAGCCTGGCCGATTATGGGGGCAG---CGTGGACGTCCAGTTCAACGAGGATGGCTCCTTCATCGGCCAGTACAGTGGCAAGAAAGAGAAGGAAGCTGCAGGTGGCA-ATGACAGCTCAGGGGCCACCTCCCCCATCAACCCTGCC---G-TGACC 
s monDom1.scaffold_3472    66478 226 +     94349 TGACAACGAAGAAAAAGGCTTCGGGA-GC--------AGCCAGCCCTCCTTGAATGGGGACATCAAGCCCCTTGGCAGTGATGACAGCCTGGCCGACTATGGCGGTAG---CGTGGACGTCCAGTTCAATGAGGATGGCTCCTTCATCGGCCAGTACAGTGGCAAGAAGGAGAAAGAGGCCACTGGGGGCA-ATGACAGCTCCGGAACCACTTCCCCCATCAACCCTACCCACG-TGACC 
s xenTro1.scaffold_317    110872 223 +   1352153 TGACAATGACGAGAAGCCTTTTACTA-GC--------AGTCAGCCCTCCCTCAATGGGGAGATCAAGCAACTAGGCAGTGACGACAGCCTGGCCGACTATGGTGGTAG---CGTGGATGTCCAGTTCAATGAAGATGGCTCGTTCATTGGCCAGTACAGTGGCAAAAAGGAGAAGGAGCCAACAGGGGGCA-ATGAGAGCTCTGGAGCAACCTCTCCGGTCAACCCCAAC---G-TTGCA 
s tetNig1.chr19          1088278 226 -   5206847 TGACATGGAGGA-----CCACAAGCC-GCTAAAGGGGAGTCGGACACCGTCCAACGGGACGGTTCGCCGAGACGAGAGCTACGACAGCCTGGTGGACTACGGGGAGGG---CGGGGACGGTCAGTTCAACGAAGACGGCTCCTTCATCGGCCAGTACAGCGGCAAGAAAGAGAGGGACACGCACGAAGGCA-ACGAAAGTTCGGAGGCGCCGTCGCCCGTCAATGCCATG---A-ACTCC 
s fr1.chrUn             19892015 215 + 349519338 TGACCTCGAAGAGAAGCGC----ACA-GCC-------AGCCAGCCTTCGCTGGGCGAGGACAGCAAGC---TGTGCAGCGAGGACAACCTGGACTTCAACGGCAGCAGCGCCGTAACCACGGAGCTCAACATGGACGAGTCCCTGGCCAGCCAGTTCAGCCGCCACAGCGAGGGG-------CCGGAGCCGTTCCACGGCGTACCGGACAACTCCCCCCTCAACCCTGCC---GCCAACC 
s danRer2.chr23         42356435 201 -  42830282 TGATATGGAGAAGTGCTCCATCAGCCAGCCGTCGGGGTGCGAGA---------------------GCAAGCGCAGCAGCAACGACAGTCTGGCGGATTACGGGGACAG---CGTGGACATCCAGTTCAATGAGGACGGCTCCTTCATCGGGCAGTACAGCGGTCGAAGGGA--------TCCACGCGGGCA--CGACAGCTCTGGCGCCGTGTCGCCGGTCAACCCCA-A---C-ATGCC 

a score=86525.0
s hg17.chrX             152691446 25 + 154824264 ATGCTCATGGCGTCCACC--------ACTTCCG 
s baboon.ENm006_1           61915 25 +    802484 ATGCTCATGACGTTCACC--------ACTTCCG 
s rheMac1.SCAFFOLD28471      4143 25 -      6625 ATGCTCAGGACGTTCACC--------ACTTCCG 
s marmoset.ENm006_1         44635 25 +    677071 ATGCTCATGGCATCCACC--------ACCTCTG 
s rn3.chrX              159897295 25 + 160775580 ATGCTCCTGGTGTCTACC--------GTGTCCG 
s mm6.chrX               68552899 25 + 163688980 ATGATCCTGGTGTCTACC--------ACGTCTG 
s rabbit.ENm006_12           6345 23 -      8566 GTGCTCATGGCGTCCACC--------GCTTC-- 
s canFam1.chrX          124808548 25 + 126913094 ATGCTCCTGGCATCCACC--------ACCTCGG 
s rfbat.ENm006_1            59186 23 +   1015308 --GCTCATGGCTTCTTCC--------ACCTCCG 
s armadillo.ENm006_1        11265 25 +    637865 ATGCGCATGGCGCCCACC--------CCCTCAG 
s platypus.ENm006_33        10745 33 -     24358 ctgtccctcgcccccaccccctaccaactcccc 

a score=1335.0
s hg17.chrX              2130203 32 - 154824264 AGGGCCTAGACACGACC-CCCAAGCC-----------ACACTGA 
s panTro1.chrX           2163329 32 - 160174553 AGGGCCTAGACACGACC-CCCAAGCC-----------ACACTGA 
s baboon.ENm006_1         737961 32 -    802484 AGGGCCTGGACACAACC-CCCAAGCC-----------ACACTGA 
s marmoset.ENm006_1       629917 32 -    677071 AGGGTCTGGACTCAACC-CCCAAGCC-----------ACACTGA 
s rn3.chrX                875778 32 - 160775580 AGGGTCCAGATTCAACT-CGCAAGCC-----------AGTCTGA 
s mm6.chrX              95133557 32 - 163688980 AGGGTCCAGATTCAACT-CGCAAGCC-----------AGTCTGA 
s rabbit.ENm006_53         67761 32 +     95848 AGGGCCCGGACTCCATC-TTCAAGCC-----------GCACTGA 
s canFam1.chrX           2102000 29 - 126913094 AGGGCCTGGACTCTCCA-CTTAAG--------------CACTGA 
s rfbat.ENm006_1          953411 32 -   1015308 AAGGCCTGGACTCTCCC-TTCAAGTC-----------ACACTGA 
s shrew.ENm006_28          13170 32 -     17919 AAGGCCTGGACCCCACA-CTGAAGCC-----------ACACTGA 
s armadillo.ENm006_1      624165 26 -    637865 CGGGGCCAGAC-------CTCAAGCC-----------GCACTGA 
s monDom1.scaffold_4966     7781 31 -     16700 -TGCCCCTGCTATTTCT-TCACAGGT-----------GTATGGG 
s platypus.ENm006_33        2105 44 +     24358 GAACCCTAGCCACCCCAGCCCAGGCCCTCCCAACTCAATTCTGG 

a score=185517.0
s hg17.chrX              2130122 81 - 154824264 C--------GCCCAGCAGCCGCCTGGGC---AGGAACAAAGGCTTCT---------CCCGGGGCCCTG------GGGCCCCAGCCTCACCCTCAGCTTCCCACCCCC 
s panTro1.chrX           2163248 81 - 160174553 C--------GCCCAGCAGCCGCCTGGGC---AGGAACAAAGGCTTCT---------CCCGGGGCCCTG------GGGCCCCAGCCTCACCCTCAGCTTCCCACCCCC 
s baboon.ENm006_1         737880 81 -    802484 C--------GGCCGGCAGCCGCCTGGGC---AAGAACAAAGGCTTCT---------CCCGGGGCCCTG------GGGCCCCAGCCTCACCCTCAGCATCCCACCCCC 
s marmoset.ENm006_1       629836 81 -    677071 C--------GGTCAGCAGCCGCCTGGGA---AGGAACAAAGGCTTCT---------CCCAGGACCCTG------GGGCCCCAGCCTCACTCTCAGTGTCCCACCCCC 
s rn3.chrX                875697 81 - 160775580 T--------GGCCTGCAGCAGCTTCAGC---AAAAACAAAGTCTTCT---------CCCGGGGACCTG------GGGCTCCAGTTTCCCCCTCAGTTTCCCATCCCC 
s mm6.chrX              95133476 81 - 163688980 T--------GGCCTGCAGCAGCATCAGC---AAAAACAAAGTCTTCT---------CCCGGGGACCTG------GGGCTCCAATTTCCCCCTCAACCTCCCATCCCC 
s rabbit.ENm006_53         67683 78 +     95848 ---------GGACAGCAGCCGCCTAGGC---AGGAGCAAAG-CTTAT---------CCCGTG-CCCCG------GGGCTGCGACGGCCTCCTCAGAGTCCCATCCCC 
s canFam1.chrX           2101919 81 - 126913094 C--------GGCCTCCGGCCGCCTGGGT---AGGAGCAAAGGCTTCT---------CCCGCGGCTCCG------GGGCCCCGGCGTCCCCCTCGGCGTCCCATCCCC 
s rfbat.ENm006_1          953330 81 -   1015308 C--------AGGTTGCAGTCGCCTCGGC---AAGAACAAAGGCTTCT---------CCCGAGGCCCTG------GGGCCCCGGCCTCACCCTCAGCATCGCACCCCC 
s shrew.ENm006_28          13110 60 -     17919 C--------GGTGTGTACCCGACAGATG---AAGACCACAGGCTTTT---------CTCGGGGTGTGG------AG---------------------TTGCACCCCC 
s armadillo.ENm006_1      624084 81 -    637865 T--------GGCCCCCGGCCGCCACGGC---CGGCACAAAGGCTTCT---------TCCGAAGTCCCG------GGAGCCCGGCCTCCCCCTCAGCTGCCCGACCCC 
s monDom1.scaffold_4966     7699 82 -     16700 CCCCT----GGGACCCTCCCGAACTGGG---AAGAACAAGGTTTTCT---------CTAGAGGCGCTG------GGGGTCATGACCAATTCTGAGCTCCTCTCC--- 
s platypus.ENm006_33        2012 92 +     24358 T--------TCCCAGGAGCAGCTTCGGCGTGAGGACCAAGGGCCTCTTCAAAGCCACTGGGGGCAACG------GGGCCCAGGACTGACCCTGCGGGGCACTCA-CC 
s xenTro1.scaffold_101    953994 94 +   2407444 CTCCGATCAATCGCGTGGAAGCCCAGCA---GGGAAAAAAGGAGCTG---------CAGGAAGAACTGTGTTTGGGACCCGGAGATGAACTTCAGCTACTGATT-TC 

a score=27424.0
s hg17.chrX              2130105 17 - 154824264 CCGAAGCCCAAA-----GGCCC 
s panTro1.chrX           2163231 17 - 160174553 CCGAAGCCCAAA-----GGCCC 
s baboon.ENm006_1         737863 17 -    802484 CCGAAGCCCAAA-----GGCAC 
s marmoset.ENm006_1       629819 17 -    677071 CCGAAGCCCAAA-----GGCCC 
s rn3.chrX                875680 17 - 160775580 TCGAAACCTGAA-----GCCCC 
s mm6.chrX              95133465 11 - 163688980 TC------TGAC-----GCCCC 
s rabbit.ENm006_53         67667 16 +     95848 -CGCAGCCAAAA-----GCAGA 
s canFam1.chrX           2101902 17 - 126913094 cTGCAGCCTGAA-----GCCTC 
s rfbat.ENm006_1          953313 17 -   1015308 CCGCAGCCCAAA-----GCCTC 
s shrew.ENm006_28          13093 17 -     17919 CCGCAGCCCAAA-----GCTTC 
s armadillo.ENm006_1      624067 17 -    637865 CCGCAGCCCACA-----GCCTC 
s monDom1.scaffold_4966     7679 17 -     16700 CTGCCGCCCACA-----GCTGG 
s platypus.ENm006_33        1989 17 +     24358 CCCAGGCAAAAA-----GGGTT 
s xenTro1.scaffold_101    953965 22 +   2407444 CGGGAACTTAAACAAGTGACAC 

a score=49886.0
s hg17.chrX              2130082 23 - 154824264 ACCACCTCTCCCA--GTCCTGGGCC 
s panTro1.chrX           2163208 23 - 160174553 ACCACCTCTCCCA--GTCCTGGGCC 
s baboon.ENm006_1         737840 23 -    802484 GCCACCTCTCCCA--GCCCTGGGCC 
s marmoset.ENm006_1       629796 23 -    677071 GTCACCTCTCCCA--GCCCTGGGTC 
s galago.ENm006_1         899441 23 -    952237 GCCACCTCCCCCA--GCCCAGGGTC 
s rn3.chrX                875657 23 - 160775580 ACAGCCTCCCCCA--GTCTAGGAAC 
s mm6.chrX              95133442 23 - 163688980 ACAGCCTCCCCGA--GTCTAGGAAC 
s rabbit.ENm006_53         67644 23 +     95848 GCCCCCCTTGTCG--GCCCTTGGGC 
s canFam1.chrX           2101879 23 - 126913094 accggctcccccg--gccccgggcc 
s rfbat.ENm006_1          953290 23 -   1015308 CCCGGCTCCCCCA--GCCCTGGGTC 
s shrew.ENm006_28          13070 23 -     17919 AGCGATGCTCCTG--GCACCGGGCC 
s armadillo.ENm006_1      624044 23 -    637865 CCCAGCTCCCCCA--GCCCCGGGCC 
s monDom1.scaffold_4966     7656 23 -     16700 --GAGCTCCCCTGAGGCCTCCTGCT 
s platypus.ENm006_33        1966 23 +     24358 CCAGAGTCACCCC--AACCTGGAGC 
s xenTro1.scaffold_101    953938 23 +   2407444 GTGGACCCTGGTA--AAGCAGGAAA 

a score=406800.0
s hg17.chrX              2130001 81 - 154824264 GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGACCTCTGTCCGCCA--------GGGCCTTGGGC-----------CAGCATCT 
s panTro1.chrX           2163127 81 - 160174553 GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGACCTCTGTCCGCCA--------GGGCCTTGGGC-----------CAGCATCT 
s baboon.ENm006_1         737759 81 -    802484 GCCGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGACCTCTGTCCGCCA--------GGGCCTCGGGC-----------CAGCATCT 
s marmoset.ENm006_1       629715 81 -    677071 GCTGTGGCGCAGAACATGGGCTCTGTGTTTAAGGAGCTCTTGGGAAAGGCCTCCGCCCGCCA--------GGGCCTTGGGC-----------CAGCACCT 
s galago.ENm006_1         899360 81 -    952237 GCTGTGGCGCAGAACATGGACTCCGTGTTTCAGGAGCTCTTGGGAAAGACGGCTATTCGCCA--------GGGCCTCAGGC-----------CAGTGTCT 
s rn3.chrX                875576 81 - 160775580 GCTGTGGCGCAGAACATGGATTCTGTGTTTAAGGAGCTCTTGGGAAAGGCTGCTGTCCGCCA--------GGGCCATGGGC-----------TAGCATCT 
s mm6.chrX              95133361 81 - 163688980 GCTGTGGCACAGAACATGAATTCTGTGTTTAAGGAGCTCTTGGGAAAGACTGCTGTCCGCCA--------GGGCCATGGGT-----------TAGCATCT 
s canFam1.chrX           2101798 81 - 126913094 GCTGTGGCACAGACCATGGATTCCGTGTTTAAGGAGCTCCTGGGAAAGACCTccgcccgcca--------gggcgcggggc-----------ccgcgtcc 
s rfbat.ENm006_1          953209 81 -   1015308 GCTGTGGCACAGACTATGGATTCGGTCTTTAAGGAGCTCTTGGGAAAGACCGCTGTCCGCCA--------GGGCCTCGGGC-----------CAGCGTCC 
s shrew.ENm006_28          12998 72 -     17919 GCCGTGGCCCAGACCATGGGCTCCGTGTTCAAGGAGCTCTTGGGGAAGACC---GCCCGCCA--------GGGTCTTGGGC-----------CC------ 
s armadillo.ENm006_1      623963 81 -    637865 GCCGTGGCGCAGACCATGGACTCCGTGTTTAAGGAGCTCTTGGGGAAGACGGCTGGCCGCCA--------GGGCCTGGGGC-----------CAGCGTCC 
s monDom1.scaffold_4966     7567 89 -     16700 AGCGTGGCCCAGAAGATGGAATCTGTCTTTAAGGAGCTCTTGGGGAAGGCCCATACCAGGCACCTGCCGAAGACCTCAGAG-----------ATACTTTT 
s platypus.ENm006_33        1876 90 +     24358 GACATCACCAAGACCATGAACTACGTGTTTAAGGAGCTTATGGAGAAGACCA--GCCTGCGG--------CAAACTGGGGCGGATGATCCCCCGGCCTCT 
s xenTro1.scaffold_101    953857 81 +   2407444 AATGTGACAAAGAACATGGACAGCGTGTTCAAAGAGCTGCTTGGAAAAACTGCTCTAAAGCA--------GGTGCATTTGG-----------AAGATCCT