##maf version=1
a score=64549.0
s hg17.chr1     147962192 9 + 245522847 TCATTTAAT 
s panTro1.chr1  129698808 9 + 229575298 TCATTTAAT 
s mm5.chr3       65458475 7 - 160575607 --ATTTGAT 
s rn3.chr2       68236843 7 - 258222147 --ATTTGAT 
s canFam1.chr17  62929731 9 +  66886099 TTATTTGAT 

a score=37247.0
s hg17.chr1     147962201 43 + 245522847 GACAATTTTCTGGCGCAAGGCTCGGGGCCCAGAGCCAGGGAGG 
s panTro1.chr1  129698817 43 + 229575298 GACAATTTTCTGGCGCAAGGCTCGGGGCCCAGAGCCAGGGAGG 
s mm5.chr3       65458482 43 - 160575607 GACAATCTTCTGACGCAAGGCTCGAGGCCCAGAGCCAGGTAGT 
s rn3.chr2       68236850 43 - 258222147 GACAATCTTCTGACGCAAGGCTCGGGGCCCAGCGCCAGGGAGT 
s canFam1.chr17  62929740 43 +  66886099 GACAATTTTCTGGCGCAAGGCTCGGGGCCCAGAACCAGGGAGG 
s danRer1.chr10  19400803 43 +  25436222 GGCGCTCTGCTTGAGCACAGCTTTGGGTCGTGCGCTCTTCAAA 

a score=1000.0
s hg17.chr1     147962244 1 + 245522847 G 
s panTro1.chr1  129698860 1 + 229575298 G 
s mm5.chr3       65458525 1 - 160575607 G 
s rn3.chr2       68236893 1 - 258222147 G 
s canFam1.chr17  62929783 1 +  66886099 G 

a score=0.0
s hg17.chr1 147962244 3 + 245522847 GGC 

a score=3000.0
s hg17.chr1     147962245 2 + 245522847 GC 
s panTro1.chr1  129698861 2 + 229575298 GC 
s mm5.chr3       65458526 2 - 160575607 GC 
s rn3.chr2       68236894 2 - 258222147 GC 
s canFam1.chr17  62929784 2 +  66886099 GC 
s fr1.chrUn     290886762 2 + 349519338 GC 

a score=18092.0
s hg17.chr1     147962247 26 + 245522847 TCAGGAGGTGGCGGGCCGGGGCC-----CAG 
s panTro1.chr1  129698863 26 + 229575298 TCAGGAGGTGGCGGGCCAGGGCC-----CAG 
s mm5.chr3       65458528 26 - 160575607 TCGGGGGGTGGGGGCCCGGGGCC-----CAG 
s rn3.chr2       68236896 26 - 258222147 TCGGGGGGTGGGGGCCCGGGGCC-----CAG 
s canFam1.chr17  62929786 26 +  66886099 TCGGGAGGTGGTGGGCCAGGGCC-----CAG 
s fr1.chrUn     290886764 26 + 349519338 TGATGAGGAATCGAGTCCTGTGG-----CAG 
s danRer1.chr10  19400846 31 +  25436222 TTAGCAGGTGAATCGCTAGCGTCGGTGTTAG 

a score=219213.0
s hg17.chr1     147962273 178 + 245522847 GGCTGAGGCAGTGGGCGGCAGTCCATGGGCAGTAATGTACTTCTTGTAAGCCTCACGAATGATCTTGAAGGCTCGAGCAGTGGCATAGGGTATGTCTGTAACAGGGTCCCGGTATAGGGCTGGACGATGGGTCACTGGACAGACCTCACGAACAGGGACTTTTGGG---GGCCGCCCTTGG 
s panTro1.chr1  129698889 178 + 229575298 GGCTGAGGCAGTGGGCGGCAGTCCATGGGCAGTAATGTACTTCTTGTAAGCCTCACGAATGATCTTGAAGGCTCGAGCAGTGGCATAGGGTATGTCTGTAACAGGGTCCCGGTATAGGGCTGGACGATGGGTCACTGGACAAACCTCACGAACAGGGACTTTTGGG---GGCCGCCCTTGG 
s mm5.chr3       65458554 178 - 160575607 CGCCGAGGCGGTGGGTGGAAGTCCGTGGGCAGTGATGTACTTCTTGTACGCCTCACGGATGATCTTGAAGGCTCTAGCAGTGGCATAGGGTATGTCTGTAACAGGGTCCCGGTACAAAGCTGGACGGTGGGTCACTGGGCAGACCTCCCGCACCGGGACCTTCGGG---GGTCGCCCCTGG 
s rn3.chr2       68236922 178 - 258222147 CGCTGAGGCAGTGGGTGGTAGTCCGTGGGCAGTGATGTACTTCTTGTACGCCTCACGGATGATCTTGAAGGCTCTAGCAGTGGCATAGGGTATGTCTGTAACAGGGTCCCGGTACAAAGCTGGACGGTGGGTCACTGGGCAGACCTCCCGAACAGGGACCTTTGGT---GGTCGCCCTTGG 
s canFam1.chr17  62929812 178 +  66886099 GGCTGAGGCAGTGGGCGGCAGTCCGTGGGCAGTGATGTACTTCTTGTAGGCCTCACGGATGATCTTGAAGGCTCGAGCAGTGGCGTAGGGGATGTCTGTGACAGGGTCCCGGTACAGGGCTGGGCGATGGGTCACGGGGCAGACCTCCCGAACAGGGACCTTTGGG---GGCCGGCCTTGG 
s fr1.chrUn     290886790 179 + 349519338 CTCCAGG--AGTGTTTGGGAAGCCGTGTGCAGCCACGTATTTACGGTAAGCTTCTCGGATGATGCGGAAGGCTCGTGCGTTAGCATAAGGTATGTCTGTGACCGGATCTCTGTACAGTGCGATCTTATGCGTGACGGGACAAATCTCCTGGACGGGCAGCTGAGGGCTCGGCTGCCCCTTG 
s danRer1.chrUn 128306408 178 - 367113659 GGATGGGCCAGTGCAGGGCAGGCCATGAGCAGCCACATACTTCTTATAGGCCTCCCGAATTATCCTGAAGGCCTGTACATTAGCGTAAGGAATGTCAGTGATGGGGTCCCGGTAGAGCGCAGGCTTATGGGTAACAGGACAGACCTCCTGGACAGGTACTCGAGGA---GCAGGCGACTGG 

a score=84843.0
s hg17.chr1     147962451 56 + 245522847 GGGAACCATTCCTCGAAAGTTGCATCATCACTAAAAGTGATGAAGGTACGTGAGCA 
s panTro1.chr1  129699067 56 + 229575298 GGGAACCATTCCTCGAAAGTTGCATCATCACTAAAAGTGATGAAGGTACGTGAGCA 
s mm5.chr3       65458732 56 - 160575607 GGGAACCACTCTTCAAACGTTGCATCATCACTGAACGTGATGAAGGTGCGAGAGCA 
s rn3.chr2       68237100 56 - 258222147 GGGAACCATTCTTCAAACGTGGCATCATCACTGAATGTGATGAAGGTACGTGAGCA 
s canFam1.chr17  62929990 56 +  66886099 GGAAACCATTCCTCAAATGTTGCATCATCACTAAAAGTGATGAAAGTACGCGAGCA 
s galGal2.chrUn  96971568 56 + 165033910 GGGGAAGAACGTTCGAAGGTTTCGTCGTCGCTGAAGGCATTGAAGGTGCGCGAGCA 
s fr1.chrUn     290886972 56 + 349519338 GAAAAGGCCACCTTAAAAGCTTCGTCGTCGCTGAACGTGATGTAAGTACGGGAGCA 
s danRer1.chrUn 128306586 56 - 367113659 GGAAAGACACGCTGGAAGGACTCATCATCACTGAATGTGATGTAGGTGCGAGAGCA 

a score=25539.0
s hg17.chr1     147962507 63 + 245522847 GCG-----AGCAGGGGGGTTGA------------CGGGT------CCAGTCCCAGCATG--AGGAGTCAATGCAGACACCGAGGGAG-C 
s panTro1.chr1  129699123 63 + 229575298 GCG-----AGCAGGGGGGTTGA------------CGGGT------CCAGTCCCAGCATG--AGGAGTCAATGCAGAAGGGGAGGGAG-C 
s mm5.chr3       65458788 75 - 160575607 GTG-----AGCAGGAGGGGTGGCAGCGGCAGCTCCAGTC------CCGGTCCCAGCATG--TGGAGCCAGTGCAGAGGCTGTAGGAG-C 
s rn3.chr2       68237156 63 - 258222147 GTG-----AGGAGGAGGGACGG------------CAGGT------CCAGTGCCAGCATG--TGCAGTCAGTGCAGAGGACGTAGGAG-C 
s canFam1.chr17  62930046 63 +  66886099 GCG-----AGGTGGAGGGACAA------------CGGGT------CCAGTGCCGGCATG--GGGAGTCAGTGCAGAAGCTGTGGGAG-T 
s galGal2.chrUn  96971633 66 + 165033910 GCA-----GGCCGGGGCTGCGG------------CCGGG------GCGGCGTCTGCCTGCTGCGGGTCCTGGTCCAACCTGCAAGAGCC 
s danRer1.chrUn 128306646 74 - 367113659 GTGTTTACAGCAGCTGTGTTTG------------TGAATGGGACACCGGGTGCTGCGGA--AAGCGTTGATTCGGACTGGGAAAGAG-C 

a score=14242.0
s hg17.chr1     147962570 10 + 245522847 AGGATCAAGT 
s panTro1.chr1  129699186 10 + 229575298 AGGATCAAGT 
s mm5.chr3       65458863 10 - 160575607 AGGATCAAGG 
s rn3.chr2       68237219 10 - 258222147 AGGATCAAGT 
s canFam1.chr17  62930109 10 +  66886099 AGGATCCAGC 
s galGal2.chrUn  96971699 10 + 165033910 GGGGTCAGCT 

a score=550634.0
s hg17.chr1     147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG 
s panTro1.chr1  129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG 
s mm5.chr3       65474800 76 - 160575607 ATGGCGTCCGCCTCCTCAGGGCCAGCG---GCGGCCGGGTTTTCATCCCTTGATGCCGGGGCCCCTGCTGGTA------CCGCAG 
s rn3.chr2       68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCG---GCGGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTA------CCGCAG 
s canFam1.chr17  62947719 82 +  66886099 ATGGCGTCGGCCTCCTCTGGGCCGTCG---GCGGCTGGGGTTTCATCCTTTGATCCCGGGGTCCCTTCCTGTGCTTCGGCTTCAG 

a score=365854.0
s hg17.chr1     148078400 182 + 245522847 TCACATGATGCCGTTGGTGAGGTACTGGAAGCCGTCATAGAGTTTGGTGGTGATAGACCGCATACTGCCATCCACCATCTGCTCCACCAGCAGCTGCAGCTGCTCCTCAGTCATGCTCAT-GTGGAACCTCTCTTTGAGGTTTCGAATGGTGCTGGAGCCATGGAAGCAAGGAAGCTGAGA-AC 
s panTro1.chr1  129830209 182 + 229575298 TCACATGATGCCGTTGGTGAGGTACTGGAAGCCGTCATAGAGTTTGGTGGTGATAGACCGCATACTGCCATCCACCATCTGCTCCACCAGCAGCTGCAGCTGCTCCTCAGTCATGCTCAT-GTGGAACCTCTCTTTGAGGTTTCGAATGGTGCTGGAGCCATGGAAGCAAGGAAGCTGAGA-AC 
s mm5.chr3       65575311 182 - 160575607 TCACATGATGCCATTGGTGAGGTACTGGAAGCCATCGTAGAGTTTGGTGGTGATGGACCTCATGCTGCCGTCCACCATCTGCTCCACCAGCAGCTGCAGCTGCTCCTCAGTCATGCTCAT-GTGGAACCTCTCTTTGAGGTTGCGAATGGTGCTGGAGCCATGGAAGCAAGGAAGCTGAGA-AC 
s rn3.chr2       68356506 182 - 258222147 TCACATGATGCCATTGGTGAGGTACTGGAAGCCATCGTAGAGTTTGGTGGTGATGGACCTCATGCTGCCGTCCACCATCTGCTCCACCAGCAGCTGCAGCTGCTCCTCAGTCATGCTCAT-GTGGAACCTCTCTTTGAGGTTGCGAATGGTGCTGGAGCCATGGAAGCAAGGAAGCTGAGA-AC 
s canFam1.chr17  63050241 182 +  66886099 TCACATGATGCCATTGGTGAGGTACTGGAAGCCGTCATAGAGTTTGGTGGTGATAGACCGCATGCTGCCATCTACCATCTGCTCCACCAGCAGCTGGAGCTGCTCCTCAGTCATGCTCAT-GTGGAACCGCTCTTTGAGGTTGCGGATGGTGCTGGAGCCATGGAAGCAAGGAAGCTGAGA-AC 
s galGal2.chrUn  96994100 182 + 165033910 TCACATGATGCCGTTGGTGAGGTACTGGAAGCCGTCGTACAGTTTGGTGGTGATGGAGCGCATGCTGCCGTCCACCATCTGCTCCACCAGCAGCTGCAGCTGCTCCTCCGTCATGTTCAT-GTGGAAGCGCTCCTTCAGGTTGCGGATGGTGCTGGAGCCGTGGAAGCAGGGGAGCTGCGA-GC 
s fr1.chrUn     196934251 182 - 349519338 TCACATGATTCCATTTGTCAGGTACTGGAAGCCGTCGTAGAGTTTGGTCGTCAGCGACCTCATCGAGCCCTCGACCAGCTGATCGATCAGCAGCTGGAGCTGCTCCTCTGTCAGACTCAT-GTGGAAACGTTCCTTCAAACCCCGCATGGTGCTCGACCCGTGGAAACACGGCAGCTGGGA-CC 
s danRer1.chrNA  19436521 184 - 390413307 TCACATGATACCGTTGGTCAGATACTGGAAGCCGTCGTACAGTTTGGTAGTGATGGAGCGCATGGAGCCGTCCACCATCTGCTCCACCAGCACCTGCAGGTGCTCCTCCGATAAGTACATGGGGGAATAACTCCTTCAGGTTGCGGATAGTGCTGGAGCCATGGAAGCGAGGGAGCTGTGACAC 

a score=172494.0
s hg17.chr1     148185136 140 + 245522847 ATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGCCCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATCCGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA 
s panTro1.chr1  129935611 140 + 229575298 ATGGAGGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGTGTCCGGCCCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATCCGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA 
s mm5.chr3       65694347 140 - 160575607 ATGGAAGCGTTTTGGGAGTCACGGGCTGGCCACTGGGCCGGGGGTCCGGCTCCAGGGCAGTTTTACCGCATCCCGGCCACCCCCAGCGGCCTCATGGACCCGGCGTCGGCGCCCTGCGAGGGTCCCATCACTCGGACCCA 
s rn3.chr2       68486927 140 - 258222147 ATGGAAGCGTTTTGGGAGTCACGGACTGGCCACTGGGCCGGGGGTCCGGCTCCGGGGCAGTTTTACCGCGTCCCGTCCACCCCCAGCTGCCTCATGGATCCGATGTCTGCGCCCTGCGAGGGTCCCATCACTCGGACCCA 
s canFam1.chr17  63150913 140 +  66886099 ATGGAAGCCTTTCTGGAGTCGCGGTCCAGAGTTTGGGCCGGTGGTCCCGCCCCGGGGCAGTTTTACCACATCCCGCCTAGTTCCGTCGCCTCCGTGGAGCCGGCGTTTTCTCCTTACGGGGGTCCGGTTACGCGCACGCA 

a score=69091.0
s hg17.chr10    55251623 116 + 135413628 TTACAGTGAAGTAGATTGACTGTGAGATTGTTTTTCAGTTCCCTCGACAATATTGTTCAAACTC--------CC------CTTGTTTTGTTCAGATGTGA----TTTCCATATTTGTTA------CTTCTGAAG-GGCACA---- 
s panTro1.chr8  56162651 116 + 138322177 TTACAGTGAAGTAGATTGACTGTGAGATTGTTTTTCAGTTCCCTCGACAATATTGTTCAAATTC--------TC------CTTGTTTTGTGCAAATGTGA----TTTCCATATTTGTTA------CGTCCGAAG-GGCACA---- 
s mm5.chr10     56176594 116 - 130633972 TTACAAAGATGTTGATTGACTGTGAGGTTGCACGTCAATTCCCTCAACAACTCTAACCAACGTT--------TC------CTGGCTCTGGTCATGTGTGA----TTTTCATGCCTGTTT------TCTCTGCAG-GGCAAA---- 
s rn3.chr20     14526840 116 +  55296979 TTACAAGGACGTTGACTGACTGTGAGTTTGCACGTCAATCCCTTCAACAACTCTAACCAACGTT--------TC------CTGGCTCTGGTCACATGTGA----TTTTCATGTTTGTTT------TCTCTGCAG-GACAAA---- 
s canFam1.chr26  4431080 116 -  41009621 TTACAGTGAAGTAGATTGACTGTGAGATTGGTTCTCCGTTTCCTCGGCAAAACTGTGCAAATTC--------CC------CTGGGGTTGTTGAGACGTCA----CGTCCACATTTTCTC------TCTCTGGAG-GGCAAC---- 
s galGal2.chr6  27913521 123 -  33893787 TTACAGTGCTGTCGACTGAGATGGAAAGCGTTTCTCAAGCTCCTCCACAACACAGCTCAAGTTG--------CCGTTCTGCTGGTTGTGCTCAGCTGCAG----CCTCGGGAGTTGGCA------GCTCTGGCGTTGCAAC---- 
s danRer1.chr12  3415306 139 +  24175710 TCACAGAACAGTGGACTGAGATGGAAAGCGTTTCTCCAGCTCCTCCACTACTGAGTTCATGCTTGGATTGGGCT------CTGATGGTGGTCCTTCTTGAGCAGGCTCCGCCTCTGTTACACCAGCCTCTGGTTCGACAGACACT 

a score=137977.0
s hg17.chr10    55251739 126 + 135413628 TAGTTTGAAGTTCTGAAACATTTGTGCGTAGA---TAGTTTTTTTCTATTTGACTGTACATGTTAG-CTACTGATTTTTCAAGTTCTGCTAAGTTTTTAACGTGTCTGAGGATGCCTTTTGGTTCTCTCT 
s panTro1.chr8  56162767 127 + 138322177 TAGTTTGAAGTTCTGAAACATTTGTGCGTAGA---TAGTTTTTTTCTATTTGACTGTACATGTTAGACTACTGATTTTTCAAGTTCTGCTAAGTTTTTAACATGTCTGAGGATGCCTTTTGGTTCTCTCT 
s mm5.chr10     56176710 126 - 130633972 ACGTGTGTAGTTTTGAGGGATCTGCAGGTGGG---CAGTTTTTTTCTATGTGACTGTACATGTTAG-ACACTGATTTCTCGAGCTCTGCCAAGTTTTTCACATGTCTGAGGATCCCTTTTGGATGTCTGT 
s rn3.chr20     14526956 126 +  55296979 AGGGGTGGAGTTTTGAGAGCTCTGTGGGTGGA---CAGTTTTTCTCGATGTGACTGTACATGTTAG-ACACCGATTTCTCGAGCTCTGCCAGGTTTTTCACGTGCCTGAGGATCCCTTTGGGATGTCTGT 
s canFam1.chr26  4431196 126 -  41009621 TTGTCTCTAGTTTCCAGCTGTGTGTTGCTGGA---AAGTTTTTTTCTATTTGACTGTACATGTTAG-CAACTGACTTTTCAAGGTCCGCTAAGTTTTTTATATGCTTGAGGATGCCCTTTGGTTGTTTCT 
s galGal2.chr6  27913644 128 -  33893787 TGGTTTG-AGCTTAGAGATGTGCTTGGGCAGAACGTGGTTTTTGTCTATTTGGCTGTACATATTGG-CCACGGACTTTTCAATCGCTGCTAAATTCTGAATGTTTTTAAGAATACCTTTCAGCTCCCTAC 
s fr1.chrUn      9089644 117 + 349519338 TAGGATGAAGCTTGGGCACCTT---------G---TAGTTTTTGTCTACTTGGCTGTACATGTTGG-CAATGGACCTCTCTATGTCAGCGAGATTCTGGATGTTTTTCAGGATCCCTTTGAGCTCCTTTT 
s danRer1.chr12  3415445 124 +  24175710 -----TGCGGTTTAGGGTTGATCACTAGTGGGCGCTGCTTTTTATCTATTTGACTGTACATATTGG-CAACAGATTTCTCGATGTCTGCTATGTTCTGGAGGTTCTTAAGGATCCCCTTGAGTTCCCTCT 

a score=13160.0
s hg17.chr10     55251865 17 + 135413628 GAGGGTCTGTTTTACAC 
s panTro1.chr8   56162894 17 + 138322177 GAGGGTCTGTTTTACAC 
s mm5.chr10      56176836 17 - 130633972 GGGGTTCTGCCCCCCAC 
s rn3.chr20      14527082 17 +  55296979 GGGGTTCCGCCCCACAC 
s canFam1.chr26   4431322 17 -  41009621 GGGGGTCTGTGTCACAC 
s galGal2.chr6   27913772 17 -  33893787 GGGGAGGTGGCTCTGGC 
s fr1.chrUn     137770001 14 + 349519338 GAGGA---GTTTCGGGC 
s danRer1.chr12   3415572 17 +  24175710 GAGGCTCTGGCTCAGAC 

a score=14118.0
s hg17.chr10     55251882 71 + 135413628 ACTG---TCGTTGTTGATAGCTGTGTCATAGAGGACTTAATTTTCTCGGCAGGCATCAAGTTGGTCGT-GCATTT 
s panTro1.chr8   56162911 71 + 138322177 ACTG---TCGTTGTTGATAGCTGTGTCATAGAGGACTTAATTTTCTCGGCAGGCATCATGTTGGTCGT-GCATTC 
s mm5.chr10      56176853 71 - 130633972 TGCGGGTTGGATGCTGGTGGCTGTGTCGTA---GACGTGGTTTCTCTGGCGTGTGTGGCACTGGCAGT-GCATTT 
s rn3.chr20      14527099 71 +  55296979 GGTGGGTTGGATGCTGGTGGCTGTGTCGTA---GACATAGTTTCTCTGGCGTGTGTGACACTGGCAGT-GCATTT 
s canFam1.chr26   4431339 74 -  41009621 ACGGTCGTGGATGCTGGTAGCTGTGCGACAGAGGGCTCCACGTCCTCGGCAGGTGTCACACTGACAGT-GTGCTT 
s galGal2.chr6   27913789 44 -  33893787 ACTGCGGCCGGTGGTGGTA------------------------------CAGCTGGCTGTTTGGCAGG-GGATTT 
s fr1.chrUn     137770015 54 + 349519338 TCTGTAGTGGGAGCAGGGG--------------------GTGGTGTTGGCCGGAGAGACACTGGCCGCAGCGTT- 

a score=9016.0
s hg17.chr10     55251953 19 + 135413628 AACACCTGTTATACAGACA 
s panTro1.chr8   56162982 19 + 138322177 AACACCTGTTATACAGACA 
s mm5.chr10      56176924 19 - 130633972 AGCAGCTGGTGCAGAGATG 
s rn3.chr20      14527170 19 +  55296979 AGCAGCTGGTGTAGAGATG 
s canFam1.chr26   4431413 19 -  41009621 CACAACTGGTACACAGACA 
s fr1.chrUn     137770069 19 + 349519338 GGTGCCTCCGAAAGGGACG 

a score=71637.0
s hg17.chr10    55251972 300 + 135413628 CACTCTGTGGACAGAAATGAAGCTgaaggaggtggagggcaaggaatagaaggaggtggt---ggaggaagaggagttggaaatggaggtagaagaggtggTGTTGGGGGACCAGACGTTGAAACGGAAAGTGGAAAAAATGTaggaggaggaagaggaagagggatagaaggaggagagggaggaggacaaaaaagagaaaaaggagaaatgtcaggaggaggagcaagaggagcaggagcaggaggaggagaaggaggagaaataggaggaggagggggaaggggaCAGGCAGAAGGAGAG 
s panTro1.chr8  56163001 276 + 138322177 CTCTCTGTGGACAGAAATGAAGCTgaaggaggtggagggcaaggaatagaaggaggtggt---ggaggaagaggagttggaaatggaggtagaagaggtggTGTTGGGGGACCAGACGTTGAAATGGAAAGTGGAAAAAATG------------------------TagaaggaggagagggaggaggacaaaaaagagaaaaaggagaaatgtcaggaggaggagcaagaggagcaggagcaggaggaggagaaggaggagaaataggagaaggaggaggaaggggaCAGGCAGAAGGAGAG 
s mm5.chr10     56176943 243 - 130633972 CTGTCTGTGGATGGAATGGACGTGGAAGGAGGCTGTGGGAAGAGGCGGGGAGCTGGTGGCCGAGGAGGAGGAGGAAGTGACAGTGGAGGAGGAAGAGGTAGAGAAGAAGTAGGGGGTGTAGAAATGGGAA---GAGAAAATGTAACAAGTTGTGGGGGAGGAGGGTTAGGGGGAGAAAGGGGAAGAGG---------------------------------------AAAAGTGGTAAAGGCAATGGGAGGTCTAGG---------AAGAGGCGGATGTGGGAGGGG---------AGCAGAG 
s rn3.chr20     14527189 243 +  55296979 CTGTCTGTGGATGGGACGGAAGTGGAAGGAGGCAGTGGGAAAAGGCGGGGAGCTGGTGGTCGAGGAGGAGGAGGAAGTGATGGTGGAGGAGGAGGAGGAAGAGAAGAGGCGGGGGTTGTAGAAATGGGAA---GAGAAAATGTAAGAAGTTGGGGGCGAGGAGGGTTAGGGGAAGAAAGGGGAAGAGG---------------------------------------AAAAGTAGTAAAGGCAATAGGAGGTTGAGG---------AAGAGGCAGCTGTGGGAGGGG---------AGCAGAG 
s canFam1.chr26  4431432 195 -  41009621 CACGTAGTGGATGGAGCCCAAGACGGAGGGGACAgaggagaaggaagaggaggtgatggt---ggggggagggag---ggaagtgaaggtagaagaggtgatg------------------------------gagaagaag---------agggaggagaaggtggggtggaaagtgggagaaatgg---------------------------aggtggaggaggaagaggaggaggaggaggaggaggggcagg---------------------------tgg---------aggagAG 

a score=139704.0
s hg17.chr10    55252272 227 + 135413628 ATGTTTGGTGGATGGGCAAAATTTTCAAAAATATTTCTTTCGGTTTCAATAGGTAACATA------CAAATAGGTGTCTCTCTCCTAGAGAGTGAAGAATGTAAAACACAAGGCCTT---GAAGGAGAAAGTTCCAAGGAACACTCAGCAGGAGAACTGATGACATTAGGTTCT------GATTTGAGTTCCACAGTTCTTGAAACAGTTGGCAAAGTGGAGAATGAGAAGTGAGGCCTGGG 
s panTro1.chr8  56163277 227 + 138322177 ATGTTTGGTGGATGGGCAAAATTTTCAAACATATTTCTTTCGGTTTCAACAGGTAACATA------CAAATAGGTGTCGCTCTCCTAGAGAGTGAAGAATTTAAAACACAAGGCCTT---GAAGGAGAAAGTTCCAAGGAACACTCAGCAGGAGAACTGATGACATTAGGTTCT------GATTTGAGTTCCACAGTTCTTGAAACAGTTGGCAAAGTGGAGAATGAGAAGTGAGGCCTGGG 
s mm5.chr10     56177186 230 - 130633972 ATGCTAGGTGGATGGGGAGCGATCTCAAAAGAGTTCCTTTTTGGTTCTGTATCTGATGCA------CATGTGGGAGTCTCTCTCTTAGAGCTTAAGGAGTTTAAAATACGGGGTCTCAGAGGAGGAGAAAGTTCCAAGGTGCAGTCAGCGGGAGAAGTGACCACATTAGGTTCC------GACCCGAGTTCCACCGCTCTGGAAATCGTTGGCAGAGTTGAGAAAGAAAAGTGAGACCAAGA 
s rn3.chr20     14527432 230 +  55296979 ATGCTGGGTGGATGGGGAACCATTTCAAAAGAGTTCCTTTTTGTTTCTGTATCGGAGGCA------CAAGTGGGAGTCTCTCTCTTAGAGCCTAGGGAGTTTAAAACGCGGGGTCTCCGAGGAGGAGAAAGTTCCAAGGTGCAGTCAGCGGGAGAAGTGACAACGTCAGGTTCT------GACCCGAGTTCTACCGCTCTTGAAATTGTTGGTAGAGTTGAGAAAGAAAAGTGGGACCAAGA 
s canFam1.chr26  4431627 227 -  41009621 ATGTTTGGTGGTTTGGGAAGGATTTCGAAAATGTTCCTTCCGGCTTCAACTGTCAACAGA------CATGTGGGCATCTCTCTCCTAAAAACCGGGGAATTTAAAATGCAGGGCATT---GAAGGAGAAAGTTCCAAAGAACAGTCCGCGGGAGAGATGATGACATCAGGTTCT------GCCTGGAGTTCCACAGTTCTCGAAACAGTTGTCAAAGTGGAGTAGGAGGAGTGAGACGAAGG 
s galGal2.chr6  27913978 239 -  33893787 gTTTTAGGTGGGTCTGGAATGTTTTCTGTAACTTCTCCTTTGGTCTGAGGAGCTAGAAAACTTTGGCAAACGGGTTTCTTTATCCTAAAAGACGGAGGAGTTGGCTTGCGAGTTGGT---GGAGGAGAAAGTTCTTCAGGATAGTCATGGTGAGTGATGATTACAGAGGGGACCGCAGAGGGCTCCGGCTCAACTACTTCACAAGGTGTTGGAGAGGACAGAGGAGAAGAGCGAAGGCAAGG 

a score=27341.0
s hg17.chr10    55252499 121 + 135413628 AAAGCAAAATG-------AAGAGTCT--G--------------------------AAGAGA------------------------------------GAGATTTCAACTGTTCTGTTCCTTCTATCATCAGTGTTTCACCTTGCCTTATTTCCTCTTTCTCTGTC-AAATTTGCCTCTTCAGTTGT--AAGCAAT 
s panTro1.chr8  56163504 121 + 138322177 AAAGCAAAATG-------AAGAGTCT--G--------------------------AAGAGA------------------------------------GAGATTTCAACTGTTCTCTTCCTTTCATAATCAGTGTGTCACCTTGCCTTATTTCCTCTTTCTCTGTC-AAATTTGCCTCTTCAGTTGT--AAGCAAT 
s mm5.chr10     56177416 118 - 130633972 GGAGGAAAAAG-------AAGAGCCA--G--------------------------AAGACA------------------------------------GAGATTTCAGCTGCTCTGTTTGCTGGACGATTAGGGTGTCTCTGTGTC---CCCCTTCTTTCTCTGAC-TCGTGGGCATCTTCAGTTGC--CAGCAGA 
s rn3.chr20     14527662 118 +  55296979 GGAGGAAAAAG-------AAGAGCCC--G--------------------------AAGACA------------------------------------GAGATTTCAGTTGCTCTGTTTGCTGTACGATTAGGGTGTCTCTGTGCC---CCCCTTCTTTCTCTGAC-CCACGGGCATCTTCGGTTGT--CACCATT 
s canFam1.chr26  4431854 121 -  41009621 AGAGAGAAATG-------AGGAGTCT--G--------------------------AAGACA------------------------------------GAGATTCCACATGCTGTGCTCCACGTGGGAGCAGGGGCTGGCCTGGCCTTGCTTCTCCTGTCTCGGGC-ACACTGGATTCTCCAGCTGC--AGGCAGG 
s galGal2.chr6  27914217 193 -  33893787 AGAAGCAAACACACTTTTAGGAGACT--GCTCTAGCGTGTTATCTCTTTCTTGCAAACAGATGCTGTGCGTTGGTGAACGGGTGGATTTGACATCAGGAGATTTCACTTGCTTCATTTCCTGCAAAGCCTGCTGCTCAAATTGTCTTGCCTTCTCTTTTACAGTTAACGTGGGGCCACTTATTTTTTGAAATAGT 
s danRer1.chr12  3416078 117 +  24175710 AAAACAGAGAG-------AATAATTTCGG--------------------------AAGAGA------------GTGACCCAC---------------GAGAGTCCTGACCTTGCCTCAACTTTAC-------GTCCTGCAAGGCC--------TGCTGCTCAAAC-TGTCGTGCCTGCTCTTTTAC--AGTCAAT 

a score=18054.0
s hg17.chr10    55252620 34 + 135413628 GGATTGCTGCTACCTCTTTTGTTTGTACAGATTC 
s panTro1.chr8  56163625 34 + 138322177 GGATTGCTGCTACCTCTTTTGTTTGTACAGATTC 
s mm5.chr10     56177534 34 - 130633972 ACGTTGCTGCTACCTCTCTGGCTTGGGTGGCATC 
s rn3.chr20     14527780 34 +  55296979 AGGTTGCTGCTACCTTGCTGGCTTGGGTGGCATC 
s canFam1.chr26  4431975 34 -  41009621 GGGTTCCTACTACCTCTCTGGTTTGGAGGGGTTC 
s galGal2.chr6  27914410 34 -  33893787 GGACTGCTAATATCAACTCTGCTATGCTGATTTT 

a score=75824.0
s hg17.chr10    55252654 151 + 135413628 CAGTGTTTTCATTTTCAGCTTTCTGCCTGGTGCCTTG------------CCACTGCTGCAGATCTATGATCTCTGGTCTATT----TGGAACT--TTCCTCATCAGCCTCCTGGGTAAGCTGACTGACTGACTCCACAGCCTCTGAATCTTTTCTCTTGGGCCCCTCAG- 
s panTro1.chr8  56163659 151 + 138322177 CAGTGTTTTCATTTTCAGCTTTCTGCCTGGTGCCTTG------------CCACTGCTGCAGATCTATGATCTCTGGTCTATT----TGGAACT--TTCCTCATCAGCCTCCTGGGTAAGCTGACTGACAGACTGCACAGCCTCTGAATCTTTTCTCTTGGGCCCCTCAG- 
s mm5.chr10     56177568 151 - 130633972 TGGCGCTTTCGCATTCAGCTCTCTGATTGGTGATCTG------------CCACTCCACCAGGTCTATGGTCTCTGGCCTGTT----TGGGGCT--TTCCACATGAGCCGCCTAGGAAAGCTCACAGACTGATTCCACACCCTCTGGATCTTTTCTCTTGGGCCCCTCAG- 
s rn3.chr20     14527814 151 +  55296979 TGGTTTTTTCGCATTCAGCTCTCTGCCTGGTGATCTG------------CCACTCCACTAGGTCTATGGTCTCTGGTCTGTT----TGGAGTT--TTCCACATCAGCCGCCTAGGAAACCTCACAGACTGATTCCACACCCTCTGGATCTTTTCTCTTGGGCCCCTCAG- 
s canFam1.chr26  4432009 151 -  41009621 CAGGGCTTTCCTTCCCACCTTCCGGCCTGCGGCTCCT------------CCGTGGCTCCAGCTCTAGGGTTTCTGGCCTTCT----GGGAAGT--TCCCACACTGGTCTCTGAGGGAAGCACACTGGCTGATGCCATATCCTCTGAAACATTTCCCTTGGGCCCCTCAG- 
s galGal2.chr6  27914444 139 -  33893787 CAGTTCCTTCATTCTCTGCTTTGAGTCTTTCCTGTTG------------CCACTGAACAGGGTCCATGATAACCGGCCTGCT----CAGAGAA--CCAGGCGCGTGCCTCTTAGTAACGTGAGCTGGTACTGTCCATGCACGGTGACT------------GCCTCCCAA- 
s danRer1.chr12  3416235 163 +  24175710 CAATCATCTCCTTGCTGTCCTTAAGGCTGGCCTTTAGCAGCTGCAGCTCCCACTGAACTGGATCCATCACCACCCTCCTACTCCGCTGAGATTCGTCCCACTTGTGCAACCGAG--AAGGTAATGTCCAG-----GAATGTCCTGAGCCTGAATTCGGGAATCCCATAAT 

a score=17919.0
s hg17.chr10    55252805 66 + 135413628 AGACTTACTCTTGGCTTGTATTTTGGGTGAAAATGGGTCTACAAAATC---TGTTCTCTGTGAAATGTC 
s mm5.chr10     56177719 66 - 130633972 AGACTGACTCTTAACTTGTGTTCTGGGTGCCAACAGCTCTTCAAAATC---TGTTCGTGGCTGAAGGTC 
s rn3.chr20     14527965 66 +  55296979 GGACTGACTCTTAACTTGTGTTCTGGGTACAAATAGCTCTCCAAACTC---TGTTCCAGGCTGAAGGTC 
s canFam1.chr26  4432160 66 -  41009621 GGACTTACTCCTGGCTTGTGTTTTGGGCAAAAATGAGTCTATAAAATC---TGTTCTTAGTAAAAAGTC 
s galGal2.chr6  27914586 69 -  33893787 GGCATCTCTCAAGACTAATTGCATAGGAGAAAGAGTATCTAGGGCATCGCTTCTTTTCCGCAGTAACCC 
s danRer1.chr12  3416398 52 +  24175710 GGACTTACTCAGACCTCTCATACTGGGTGAATACATGTCTAAGAGGTA---ACTC-------------- 

a score=243755.0
s hg17.chr10    55252871 253 + 135413628 TGAATTTGTTGAT--------ACTTGACTTATGTTTTCCTTATAAAGGGGATTATGGGCACTTAAGTCATCCTCATCAGATAGAAATGTGAATTTTCTTGCAGACTTCAGTTTGTTGCTCTTAAGTGATCCGTCTACATGAGCTGACTTGTGAGCCTCAATAGTATTGGAAGAAAAGGGCATCACAACTTGTTGATGTTTCCTGTCTTCTGAGACTGAGTTATTTCCCCTGCTT--------TGTTGAAAATGGTAGAGAAGGA--------AAAGA 
s panTro1.chr8  56163914 253 + 138322177 TGAATTTGTTGAT--------ACTTGACTTATGTTTTCCTTATAAAGGGGATTATGGGCACTTAAGTCATCTTCATCAGATAGAAATGTGAATTTTCTTGCAGCCTTCAGTTTGTTGCTCTTAAGTGATCCGTCTACATGAGCTGACTTGTGAGCCTCAATAGTATTGGAAGAAAAGGGCATCACAACTTGTTGATGTTTCCTGTCTTCTGAGACTGAGTTATTTCCCCTGCTT--------TGTTGAAAATGGTAGAGAAGGA--------AAATA 
s mm5.chr10     56177785 253 - 130633972 TGAGTTTGTTGAC--------CTTTGACCTATACTTTCCATGTAAAGGGGATTATGGGTACTTAAGTTATCCTCATCAGGAACAAATGAGAACGTCCTTGCTGGGTTAGGCTGGCTCTCCTTAAGTGGTCCCTCTACATGAGCTGGCTCATGAGACTCAGTGGTACTGGAGGAAAAGGCCATCCCATCGCGATGACTGCTCCTGTCTTCTGGGACTGAGTTATTTCCCCTGCTT--------TGTTCAAAATGGTAGAGAAGGA--------AAAGA 
s rn3.chr20     14528031 250 +  55296979 GGAATTTGTTGAC--------CTTTGACCTATACTTTCCATATAAAGGGGGTTATGGGTACTTAAGTCATCCTCATCTGGAAGAAATGAGAACGTCCTTGCTGGGTTAGCTTGGTTG---TCAAGTGGTCCCTCTACATGAGCTGGCTCATGAGACTCAGTGGTACTGGAGGAAAAGGCCATCCCGTCACGATGACTGCTCCTGTCTTCCGGGACTGGGTTATTTCCCCTGCTT--------TGTTCAAAATGGTAGAGAAGGA--------AAAGA 
s canFam1.chr26  4432226 253 -  41009621 GGAGTTTGTTGGT--------CTTGGATCTACAGCTTCCTTATAAAGAGTACTGTGGAGACTGAAGGCGTCCTCCTCAGACATCAGTGTGAACTTCCTTGCTGACTTGGGCTGGTTGTTCCTAAGGGATCCATCTACATGAGCCTGCTTGTGAGCCTCAATAGTGCTGGAAGGAAAAGGCATCACACTGTGTGGACTTTTCCTGTCTTCTGAGACTGACTTATCTCCCCTGCTT--------TGTTGGAAATGGTAGAGAAGGA--------AAAGA 
s galGal2.chr6  27914655 253 -  33893787 AGCAGCAGCAGGA--------CTTTGAGTGACACCTTCCACATACAGTGGGTTTTGAGTAGTTAGTGGGTTCTCGTCAGATAAGAAAGTAATGTTACTTGAAGATTTGGGGAGGTTATTGTTCAATGATCCATTGATATTAGATTGCTTGTGAGCCTCAATAGCACGGGAAGCAAAGCTGCTTATAACTCTCTGCCGATCTCCTTCTTCTAAGACTGACTTTTTTCCCCTGCTT--------TGTTGGAAATGGTAGAGAAGAA--------AAAGA 
s danRer1.chr12  3416450 277 +  24175710 CGATTTTGGTGCTCAGGGCTGCCAAGAGTGACATCATCACGGTACAGGGGGTTGGTTGTAGTAAGTGGGTTGTCATCTGAAAGAAAGGTAATGTTGCTCTCCGACTTGGGAAAGTTGTTGAGCAGGATTCCGTTGGCGGTGGACAGCTTGTGAGCAGTGATAGCACGGGAAGCGAATGAGCTAATGAGACGCTGCCGATCACCATCCTTCAGAACACACCTCTTAGTCCTGATTTCAGCAAGTGTGGAAAGAGATAAAGATGAACTTAACAGAGAAT 

a score=136951.0
s hg17.chr11    116124407 94 + 134452384 TTAC--ATATCCTCAACACTCCATTTGTAGGCAAGTTCCTCCACTGCCTTCTTGCTGGCAAGCCTGGCAAAGCGCTTCTGTTCAAATCCATTGGAT 
s panTro1.chr9  118123572 94 + 136640551 TTAC--ATATCCTCAACACTCCATTTGTAGGCAAGTTCCTCCACTGCCTTCTTGCTGGCAAGCCTGGCAAAGCGCTTCTGTTCAAATCCATTGGAT 
s mm5.chr9       77776147 94 - 124177049 TCAC--ATATCCTCCACACTCCACTTGTAGGCAAGCTCCTCCACAGCCTTCTTGCTGGCGAGCCTGGCAAAGCGCTTCTGTTCAAAGCCATTGGAT 
s rn3.chr8       79766056 94 - 129061546 TCAC--ATGTCCTCAACACTCCACTTGTAGGCAAGCTCCTCCACAGCTTTCTTGCTGGCAAGCCTGGCAAAGCGCTTCTGTTCAAAGCCATTGGAT 
s canFam1.chr5   72268290 94 -  92064832 TTAC--ATATCCTCAACACTCCACTTGTAGGCAAGTTCCTCCACCGCCTTCTTGCTGGCAAGCCTGGCAAAGCGCTTCTGTTCAAATCCATTGGAT 
s galGal2.chr24   4774582 96 +   5910111 TTGCGAAAGTCTTCAATGCTCCACTTGTATGCAAACTCCTGAGCTGCCTTCTTGTTGGCCATCCTGGCAAAGAACTGCTGCTCAAATCCATTGGAC 
s fr1.chrUn     206483220 94 + 349519338 TCAC--ATATCTTCTACACTCCACTTATAGGCTGCCTCCTGAGCAGCTCTTTTATCTGCCATTCTCTCATAGCGTTTCTTCTCAAAACCATTTGAC 

a score=311622.0
s hg17.chr11   116206508 55 + 134452384 ATGCAGCCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTCTGCCC 
s panTro1.chr9 118206938 55 + 136640551 ATGCAGCCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTCTGCCC 
s mm5.chr9      77840023 55 - 124177049 ATGCAGCCCCGGACGCTCCTCACTGTGGCCCTCTTGGCTCTCCTGGCATCTGCCC 
s canFam1.chr5  72342544 55 -  92064832 ATGCAGCCCCGGGTCCTCCTCGTCGCTGCCCTCCTGGCGCTCCTGGCCTCCGCCC 

a score=21699.0
s hg17.chr11   116211733 24 + 134452384 TCACTGGGTGTTGAGCTTCTTAGT 
s panTro1.chr9 118212083 24 + 136640551 TCACTGGGTGTTGAGCTTCTTAGT 
s mm5.chr9      77844334 24 - 124177049 TCACTGGGCAGTCAGAGTCTCGCT 
s canFam1.chr5  72346944 24 -  92064832 TCACTGCGCGTTCAGCTTCTTGGT 

a score=166504.0
s hg17.chr11    116211757 354 + 134452384 GTACTCCTCGAGAGCGCTCAGG---------AAGCTGACCTTGAAGCTCTCCAGCACGGGCAGC-AGGCCTTGGCGGAGGTCCTCGAGCGCGGGCTTGGCCTTCTCGCTGAGCGTGCTCAGATGCTCGGTGGCCTTGGCGTGGTACTCGGCCAGTCTGGCGCCGCCGTTCTCCTTGAGAGCCTCAAGGCGCGCGGCCAAGCGCTGGCGCAGCTCGTCGCTGTAGGGGGCCAGATGCGTGCGCAGCGCGTCCACATGGGCGCGCGCGCGGTCGCGCATCTCCTCGCCCAGTGGGCTCAGCTTCTCTTGCAGCTCGTGCAGCTTCTGGCGCGCGCCCTCTTGGAGCTCTGCGCGCAGCGGCTCCAC 
s panTro1.chr9  118212107 354 + 136640551 GTACTCCTCGAGAGCGCTCAGG---------AAGCTGACCTTGAAGCTCTCCAGCACGGGCAGC-AGGCCCTGGCGGAGGTCCTCGAGCGCGGGCTTGGCCTTCTCGCTGAGCGTGCTCAGATGCTCGGTGGCCTTGGCGTGGTACTCGGCCAGTCTGGCGCCGCCGTTCTCCTTGAGAGCCTCAAGGCGCGCGGCCAAGCGCTGGCGCAGCTCGTCGCTGTAGGGGGCCAGATGCGTGCGCAGCGCGTCCACATGGGCGCGCGCGCGGTCGCGCATCTCCTCGCCCAGTGGGCTCAGCTTCTCTTGCAGCTCGTGCAGCTTCTGGCGCGCGCCCTCTTGGAGCTCGGCGCGCAGCGGCTCCAC 
s mm5.chr9       77844358 348 - 124177049 GGCCTTGTCGATCACACTCTGG---------ACTTGGGTCTTAAGCGTCTCCAGCATGGGCATC-AGACTATGGCGCAGGTCCTCCAGCGCAGGTCTGGCTTTCTCGCCAAGTGTCTTCAGGTGGGTTTTGGCCCTGGTGTGGTACTCGTTCAAGGTAGGGTTGC------TCTTGAGCTCAGCCAGGCGCTGGGCCAGGCTCTCGCGCATCTGTTCGCTGTGGGGCGCTAGCTGTGTGCGCAGAGAGTCTACGTGTGTGCGCATGCGGTCGCGAAATTCCTCAGCCACAGGGGACAGTCTCCCTTGCAGCTCCTGCAGCTTCTGGCGCGCGCTCTCCTGCAGCTCGGCGCCCAGAGGCGCCAC 
s canFam1.chr5   72346968 354 -  92064832 GGCCTCGTCGATGGCAGCCAGC---------AGGCTGACCTTGAAGCTCTCCAGCACGGGCAGC-AGGCCCTGGCGCAGGTCCTCGAGCGCGGGCCTGGCCTTCTCGCCGAGCGCGCTCAGCTGCTCGCTGGCCCTGGCGTGGTACTCGGCCAGGCTGGCGCCGCCGCCCTCCTTGAGCGCCTGCAGCCGCGCGGCCAGGCGCTCGCGCAGGTCGTCGCTGTAGGGGGCCAGCTGGGCGCGCAGCGCGTCCACGTGGGTGCGCGCGCGGTCCCGCAGCTCCTCGCCCAGCGGGCTCAGCTTCTCCTGCAGCTCCTGCAGCTTCTGGCGCGCGCCCTCGCGCAGCTCCGAGCCCAGCGGCGCCAC 
s galGal2.chr24   4799439 363 +   5910111 GGACTTCTGGAGTTCGTCCAGGAAGGAGATCAAGCGGTTCTTGAGGTTCT-CAGCATAGGGGGTGAGGCGCTCCCTGAATTCCTGCACCAGAGGCGTCATCTTCTCACGCAGGTTGCTGAGCTGCTCCATCACCTTGGCCTGGTACTCGGAAGCCTGGGGGATGCCCTTCTCGCGGATCTCCTCCAGCTTCTGGCTCAGCTTCTGCCGCAGCTCATCGCTGTATGGCGCCAGGTTCTTGCGCAGCTCCTCCACGTGCCCACGCAGACGATCCCGCGCCTCCTCAGCCACCGGGGTCAGCTTGGCCTGCATCAGCTCCACCTTCTGCTTGGTGAGCTCCTTCAGCTCCTGAGCCACGGGCGTCAG 

a score=84013.0
s hg17.chr11    116212111 105 + 134452384 CTTCTGGCGGTAGAGCTCCATCTCCTCCTGCCACTTCTTCTGGAAGTCGTCCAGGTAGGGCTGCACCTTGGCCTTCACCTCCTCCAGATCCTTGCTCATCTCCTG 
s panTro1.chr9  118212461 105 + 136640551 CTTCTGGCGGTAGAGCTCCATCTCCTCCTGCCACTTCTTCTGGAAGTCGTCCAGGTAGGGCTGCACCTTGGCCTTCACCTCCTCCAGATCCTTGCTCATCTCCTG 
s mm5.chr9       77844706 105 - 124177049 CTTCTGGCGGTAGAGCTCCACATCCTCTTTCCATTTCTTCTGGAATTCGTCCAGGTAGGGCTGCACCTTCTGTTTCACTTCCTCTAGGTCCTTGTTCATCTCCTG 
s rn3.chr2      192507462 102 + 258222147 CTCCTCTCGGAAATGCACGATCTCATCCTGC---TTCTCCTGCAAGTCTTCCAGAAGCTGCCGCCGCTCAGCCTTCTGCTGCTCCAGCTCCTTCTCCAGCTCCTG 
s canFam1.chr5   72347322 105 -  92064832 CTTCTGGCGGTACAGCTCCACCTCCTCCTGCCACTTCTTCTGGAAGTCGTCCAGGTAGGGCTGCACCTTCTGCTTCACCTCCTCCAGGTCCTTGCTCATCTCCTG 
s galGal2.chr24   4799802 105 +   5910111 GCGCTGGCGGTACTGCTCCAGCTCCTCCGTCCACTTGGCGGAGAACTGGTCCAGGAAGGGCCGGATCTTCTCCTTCACCTCCTCCAGGTCCTTGGTCAGCTCAGC 

a score=57194.0
s hg17.chr11    116212216 121 + 134452384 CCTCAGGCCCTCTGTCTCCTTTTCCAGGTTATCCCAGAACTCCTGGGTCACAGGGCCGAGCTGTTCGCGCAGCTTGCTGAAGGTGGAGGTCACGCTGTCCCAGTTGTCAAGGAGCTTTAGG 
s panTro1.chr9  118212566 121 + 136640551 CCTCAGGCCCTCTGTCTCCTTTTCCAGGTTATCCCAGAACTCCTGGGTCACAGGGCCGAGCTGTTCGCGCAGCTTGCTGAAGGTGGAGGTCACGCTGTCCCAGTTGTCAAGGAGCTTTAGG 
s mm5.chr9       77844811 121 - 124177049 TCTCACCCAATCTGTTTCTTTCTCCAGGTTATCCCAGAAGTCCCGAGTCAATGGGCCCAGCCGTTCCTGCAGCTGACTAACGGTTGAACCCAGAGTGTCCCAGTTTTCCAGGAGATTCAGG 
s canFam1.chr5   72347427 121 -  92064832 CCGCAGCACCTCCGTCTCCTTCTCCAGGTTATCCCAGAACTCCTGCGTGACCGGGCCGATCTGTTCGCGCAGCTTGGTCACCGTGCTGCTCAGGCTGTCCCAGTTGTCCAGGAGTTTCAGG 
s galGal2.chr24   4799907 121 +   5910111 ACGCAGAGCCTCGGTGTCCTTCAGCCACATCTCGCGCACCTCCTTGTAGTAGGGAGCCATGTCCTCACGCAGCTTGGCAGCCGCGGCACTCAGCGTGTCCAGGTTGTCAGCCAGCTTCAGG 

a score=4872.0
s hg17.chr11      1812377 30 + 134452384 ATGCTCCACCTGCATGGCTG--------------GCAAACCATG 
s panTro1.chr9    2001217 30 + 136640551 ATGCTCCACCTGTATGGCTG--------------GCAAACCACG 
s mm5.chr7      130142453 26 + 133051633 -----CCAACTGGACTACCGT-------------GTAGAAGATG 
s rn3.chr1      202843225 26 + 268121971 -----CCAACTAGACTGCCTT-------------GTAGAAGATG 
s canFam1.chr18  56425269 44 +  66173745 AGGCTCCACCTGTGTGACTCCACCCGTGTGACCGACAAACCATG 
s danRer1.chrNA 165962846 24 - 390413307 -----AGTTCAGGAAGTCCA--------------GGAAGAGA-G 

a score=333744.0
s hg17.chr12     38440094 227 + 132449811 TTATTCCACATCAGAAGCATCATTGTCAGAAAGATGATAGTTACTTCCCTTTACCCGAATATATTCAATATATCTCCCTTCATCAGAATCTG---AAGTGCCACATGTACATAGCCTGTTGTCAAAGAGTGATTCAATTTCCTCTAATTTTTTGCCTTTGGTCTCAGGAAGACAGCCATAGATGAAAAGGAGTCCCACAGCAGCAAATCCAGCATAGAGGAAGAAAGCTC 
s panTro1.chr10  39016533 227 + 135301796 TTATTCCACATCAGAAGCATCATTGTCAGAAAGATGATAGTTACTTCCCTTTACCCGAATATATTCAATATATCTCCCTTCATCAGAATCTG---AAGTGCCACATGTACATAGCCTGTTGTCAAAGAGTGATTCAATTTCCTCTAATTTTTTGCCTTTGGTCTCAGGAAGACAGCCGTAGACGAAAAGGAGTCCCACAGCAGCAAATCCAGCATAGAGGAAGAAAGCTC 
s mm5.chr15      91666098 227 + 104138553 TTACTCCACGTCAGAAGCGTCGTTGTCGGAGAGATGATAGTTGCTTCCCTTCACGCGGATGTACTCAATGTACCTCCCTTCATCCGAGTCGG---CAGCGCCACATGAACATAGCCGGTGGTCAAAGAGCGATTCGATTTCCTCCAATTTTTTCCCCTTGGTTTCAGGGAGGCAGCCATAGACAAAAAGCAGTCCCACAGCGGCGAATCCGGCGTAGAGGAAGAATGCTC 
s rn3.chr7      129719269 227 + 143082968 TCACTCCACGTCCGAGGCGTCGTTGTCGGAGAGATGGTAGTTACTTCCCTTCACGCGGATGTACTCGATGTACCTGCCCTCGTCCGAGTCCG---CGGTGCCGCAGGTGCACAGCCGGTGGTCGAAGAGCGATTCGATTTCCTCTAGTTTTTTCCCTTTGGTTTCAGGAAGACAGCCATAGACGAAAAGCAGTCCCACAGCGGCGAATCCGGCGTAGAGGAAGAACGCTC 
s canFam1.chr27  32235556 227 -  49087461 TTATTCCACATCAGAAGCATCGTTGTCAGAAAGATGATAGTTACTTCCCTTCACCCGAATATATTCAATATATCGCCCTTCATCAGAATCTG---AAGCACCACATGTACATAACCTGTTGTCAAAGAGTGATTCAATTTCCTCTAATTTTTTCCCTTTGGTCTCAGGAAGACAGCCATAGATGAAAAGGAGTCCCACACCAGCGAATCCAGCATACAGGAAGAAGGCTC 
s galGal2.chr1  179729132 227 - 188239860 TTATTCCACATCAGAAGCATCATTGTCAGAAAGATGGTAATTACTTCCCTTCACCCGAATATATTCAATATACCTCCCTTCATCAGAATCTG---ACATACCACATGTACATAGCCTGCTTTCAAACAAAGATTCAATTTCCTCTAGTTTTTTCCCTTTAGTCTCAGGAAGGCAGCCATAGATGAAAAGGAGTCCCAGGCCAGCAAACCCTGCGTACAGAAAGAAGGCTC 
s fr1.chrUn     213944794 227 + 349519338 CTAGTCCACATCAGAGGCGTCGCTCTCAGACAGGCGGTAGTTGCTGCCCTTTACCCGGATGTACTGCACGTTCCGGCGGTCGTTGCGGGAGG---AGGCTCCGCAGGAGCAGAGCGGACCGGAGAACAGGCTCTCGATGTCCTCCAGCTGCAGGCCCTGGGTCTCCGGGAGGCAGCCCAGGATGAAGAAGAGGCCCAGCACCACCAGGCCAGCGTACATGAAGAACGCCC 
s danRer1.chrUn  27538197 206 + 367113659 TCACTCCTCCTCATCCTCGTCTTCATCAGAG---CGGGAGTTTCCTCCGTTTACCCGCATGTACT---------------------GATCTGTGTGGGCTCCGCAGCTGCAGAGTCGCCTGCTGAACAGAGACTCGATCTCCTCCAAGCGCAAACCCTTGGTCTCCGGCAGACACCCCGACACGAACACGAAGCCCAGCAGAGCCAGAGCAGCGTACAGGAAAAACGCTC 

a score=115495.0
s hg17.chr13    112381694 259 + 114142980 ATGAACTCACCAGAGGCGAGGCTCTGCGTTGCTCAATGCAGAGACTCTTACCCAGGGTGTCAGCCTCTGAAAGATACACGTGCCTGGGCCTCTTCCCTGAAGATGGACCCGGCAGGTCTGGAGGGAGG-CCCCCGTGATGAATCCCG-TGATGAGCCGCCGATCCGAGCTCAGGCTGCGTCATGGGACCAGCCACAAGGTTGCCTGACC-TATAAAGGTCGCAGGAGTGCCTCAGGGACACAGAAGCAGTTACAGCTGCCAG 
s panTro1.chr14  95994697 259 +  97804244 ATGAACTCACCAGAGGCGAGGCTCTGCGTTGCTCAATGCAGAGACTCTTACCCAGGGTGTCAGCCTCTGAAAGATACACGTGCCTGGGCCTCTTCCCTGAAGATGGACCCGGCAGGTCTGGAGGGAGG-CCCCTGTGATGAATCCCG-TGATGAGCCGCTGATCCGAGCTCGGGCTGCGTCATGGGACCAGCCACAAGGTTGCCTGACC-TATAAAGGTCACAGGAGTGCCTCAGGGAGACAGAAGCAGTTACAGCTGTCAG 
s mm5.chr8       12764663 188 + 128688707 ATTTGTTCACCAGAG----TGTCCTGGCCTCCTGCCTATGTGGACTCATTCCCAAGG-ACCAGCCT-TGAAGGACGCA---ATGTAGGGCTCC---------ATGGA------------GGAGGGAGG-TCTGTGTGACA-----------------------------------------CTGGGACTTGCCACAGGTCAG--TGATTGTTCAGAGGTCACAGGAGTGCCACCCTCAGGCAGAGTCATCTGTCTTTTCCAG 
s rn3.chr16       8607378 190 -  90224819 ATCCATTTACCAGAG----CGACCTGGCCTCCTGCCTAGGGGGGCTCATTCCCAAGG-ACCGGTCT-TGAAGGGTGTA---TTATATGGTTTC---------ATGAA-----------GGGAGGGAGG-TCTGTGTGACC----------CTGGGACACCGCT------------------------------ACAGGTCAG--TGATTGTTCGGAAGTCACAGGAATGCCACCCTCAGGAAGAGTTATCTATCTTTTCCAG 
s canFam1.chr22  63116876 177 +  64236280 A------------------TGTGCTGGTCTGCTCAGGGCAGGAGCTCTTCGCCGGAT-GTCAGTCC-CGA--GACGCACATGCCTGGGCTTCT-------------CCCTCACAGGACTGCAGCAAGGACCACCACGGTGGACACTGAGGAGGCCCCGCCAGGCCGA----------------GGGATGGAGGAGAGGCCAT--CGATG------GAGCAGCATGGGGTCGTCAT--------------------------G 

a score=694393.0
s hg17.chr14     98710240 325 + 106368585 TTAGCTCCTCTCGGCCTGCTCGATTTTGACGTCGTTAGTCAGCAAGTGCTCGCCGTGCCACTTTTTCATGTGTTTCTCCAGGGTGCTGTAGACGCTGAAGGGCATCTGGCAGATGTCGCAGCGGTACACCTCCTTGCCGATCTGCCCGTGCGTCTTCATGTGGCGCGTGAGCTTGCTGCTCTGCGCGCACGCGTAGTTGCACAGCTCGCACTTGTAAGGCCGCTCGCCGGTGTGGCTCCGCCGGTGCACCGTCAAGTTGCTGCAGTTCTTGAACACCTTGCCGCAGTACTCGCACGTGTCGCTGCGGCGGCCCTCCTTGGAGCTg 
s panTro1.chr15  99208107 324 + 106954593 TTAGCTCCTCTCGGCCTGCTCGATTTTGACGTCGTTAGTCAGCAAGTGCTCGCCGTGCCACTTTTTCATGTGTTTCTCCAGGGTGCTGTAGACGCTGAAGGGCATCTGGCAGATGTCGCAGCGGTACACCTCCTTGCCGATCTGCCCGTGCGTCTTCATGTGGCGCGTGAGCTTGCTGCTCTGCGCGCACGCGTAGTTGCACAGCTCGCACTTGTA-GGCCGCTCGCCGGTGTGGCTCCGCCGGTGCACCGTCAAGTTGCTGCAGTTCTTGAACACCTTGCCGCAGTACTCGCACGTGTCGCTGCGGCGGCCCTCCTTGGAGCTg 
s mm5.chr12     102664235 325 + 115071072 TTAGCTCCTCTCAGCCTGCTCGATTTTGACATCATTAGTCAGCAAGTGTTCACCGTGCCACTTTTTCATGTGTTTCTCCAGGGTGCTGTAGACGCTGAAGGGCATCTGGCAGATGTCGCAGCGGTACACCTCCTTGCCGATCTGCCCGTGCGTCTTCATGTGGCGCGTGAGCTTGCTGCTCTGCGCGCACGCGTAGTTGCACAGCTCGCACTTGTAAGGCCGCTCGCCGGTGTGGCTCCTCCGGTGCACCGTCAGGTTGCTACAGTTCTTGAAGACCTTGCCGCAGTACTCACATGTGTCGCTGCGGCGGCCCTCCTTGGAGCTC 
s rn3.chr6      132299612 325 + 147642806 TTAGCTCCTCTCAGCCTGCTCGATTTTGACATCATTAGTCAGCAAGTGTTCACCGTGCCACTTTTTCATGTGTTTCTCCAGGGTACTGTAGACACTGAAGGGCATCTGGCAGATATCGCAGCGGTACACCTCCTTGCCGATCTGACCGTGCGTCTTCATGTGGCGCGTAAGCTTGCTGCTCTGCGCGCACGCGTAGTTGCACAGCTCGCACTTGTAAGGCCGCTCGCCGGTGTGGCTCCTCCGGTGCACCGTCAGGTTGCTACAGTTTTTGAAGACCTTGCCGCAGTACTCGCACGTGTCGCTGCGGCGGCCCTCCTTGGAGCTC 
s canFam1.chr8   70559093 325 +  77374719 TTAGCTCCTCTCGGCCTGCTCGATTTTGACGTCGTTAGTCAGCAAGTGCTCGCCGTGCCACTTTTTCATGTGTTTCTCCAGGGTGCTGTAGACGCTGAAGGGCATCTGGCAGATGTCGCAGCGGTACACCTCCTTGCCGATCTGCCCGTGCGTCTTCATGTGGCGCGTGAGCTTGCTGCTCTGCGCGCACGCGTAGTTGCACAGCTCGCACTTGTAAGGCCGCTCGCCGGTGTGGCTCCGCCGGTGCACCGTCAGGTTGCTGCAGTTCTTGAACACCTTGCCGCAGTACTCGCACGTGTCGCTGCGCCGGCCCTCCTTGGAGCTc 
s galGal2.chr5   44593849 325 +  56310377 TTAGCTTCTTTCTGCCTGCTCAATTTTGACGTCATTTGTCAGCAAATGTTCTCCATGCCACTTTTTCATGTGTTTCTCCAGGGTGCTGTAAACACTGAAGGGCATCTGGCAAATGTCGCAGCGGTAGACCTCCTTCCCTATCTGGCCATGCGTTTTCATGTGACGCGTCAGCTTACTGCTCTGGGCACATGCATAGTTGCAGAGCTCGCATTTGTAAGGCCGCTCTCCAGTGTGGCTCCGACGGTGCACCGTCAAATTGCTGCAGTTCTTAAAGACCTTGCCACAGTACTCACATGTATCGCTCCTGCGCCCTTCCTTCGAGCTG 
s fr1.chrUn     275909939 325 + 349519338 TTACACCGTCTCTGCTTGTTCCAGTTTGATGTCATTGGTCATCAAATGTTCTCCATGCCACTTTTTCATGTGTTTCTCCAGAGTGCTGTACACACTGAAAGGCATTTGGCAAATGTCACAACGAAAGACCTCCTTACCAAGCTGGCCATGCGTCTTCATGTGGCGCGTTAGCTTTGAGCTCTGGGCACACGCGTAGTTGCACAGCTCACACTTGTAGGGCCTCTCACCCGTGTGACTGCGTCGGTGCACTGTCAGGTTGCTGCAGTTTTTAAAAACTTTGCCACAGAACTCACAGGTGTCAGACCGCCGGCTGTCCTTTGAGCTG 
s danRer1.chrUn 103629515 325 + 367113659 TTAGCTTCTCTCTGCTTGTTCAATTTTGACCTCATTCGTCATCAAATGTTCCCCATGCCACTTTTTCATGTGTTTCTCAAGCGTGCTGTAGACGCTGAAGGGCATTTGGCAAATGTCACAGCGGTACACTTCCTTACCGAGCTGGCCGTGTGTCTTCATGTGGCGGGTGAGCTTGCTGCTCTGGGCGCAGGCGTAGTTACAAAGCTCACACTTGTAGGGCCTCTCGCCTGTGTGGCTGCGTCTGTGCACTGTCAGATTGCTACAGTTCTTGAACACCTTCCCACAGTACTCACAGGTGTCACTCCTCCGGCTCTCTTTCGAGCTA 

a score=20235.0
s hg17.chr14     98710565 24 + 106368585 ggccgcccggggcccgggccgccc 
s panTro1.chr15  99208431 24 + 106954593 ggccgcccggggcccgggccgccc 
s mm5.chr12     102664560 24 + 115071072 GGCCTCCCAGGACCCGGACCACCC 
s rn3.chr6      132299937 24 + 147642806 GGCCGCCCAGGACCCGGGCCACCC 
s canFam1.chr8   70559418 24 +  77374719 ggccgcccggggcccgggccgccc 

a score=4011.0
s hg17.chr14     98710589 2 + 106368585 AG 
s panTro1.chr15  99208455 2 + 106954593 AG 
s mm5.chr12     102664584 2 + 115071072 AG 
s rn3.chr6      132299961 2 + 147642806 AG 
s canFam1.chr8   70559442 2 +  77374719 AG 
s fr1.chrUn     275910285 2 + 349519338 AG 
s danRer1.chrUn 103629867 2 + 367113659 AG 

a score=517186.0
s hg17.chr14     98710591 277 + 106368585 GTGCGGGGTGCTGCCTCCGCTGGCCGTGCCGCTGCGGCCCGAGAGGCCGCCGTCCAGCAGGTCCCCGGGCGGCGTGGAGAAGCGCAGGCTGCCGTTCTCGGACGAGTGCTCGGACGACGTGGCGAAGGGCGACTGTCGTGCGTCCGTGAAGCCCAGGAAGGGGTCCTTCATGAAGTGCCGCGACGCCGCGTAGCCCACCAGCCACTGCGAGTACACGTTCTCGGACGGGATGAGCGCGGCGGGCGGCAGCTCCAGGTCCTTCTCCACCTTGATGCGC 
s panTro1.chr15  99208457 277 + 106954593 GTGCGGGGTGCTGCCCCCGCTGGCCGTGCCGCTGCGGCCCGAGAGGCCGCCGTCCAGCAGGTCCCCGGGCGGCGTGGAGAAGCGCAGGCTGCCGTTCTCGGACGAGTGCTCGGACGACGTGGCGAAGGGCGACTGTCGTGCGTCCGTGAAGCCCAGGAAGGGGTCCTTCATGAAGTGCCGCGACGCCGCGTAGCCCACCAGCCACTGCGAGTACACGTTCTCGGACGGGATGAGCGCGGCGGGCGGCAGCTCCAGGTCCTTCTCCACCTTGATGCGC 
s mm5.chr12     102664586 277 + 115071072 GTGAGGTGTGCTGCCCCCGCTCGCCGTGCCACTGCGCCCGGACAGCCCGCCGTCCAGCAGGTCCCCGGGTGGCGTTGAGAAGCGCAGGCTGCCGTTCTCAGAGGAATGTTCCGACGATGTGGCGAAAGGCGACTGGCGCGCATCCGTGAAGCCCAGGAATGGGTCCTTCATGAAGTGGCGCGATGCTGCGTAGCCCACGAGCCACTGCGAGTACACGTTCTCAGATGGGATGAGGGCGGCAGGTGGCAGCTCCAGGTCTTTCTCCACCTTGATGCGC 
s rn3.chr6      132299963 277 + 147642806 GTGAGGCGTGCTGCCCCCGCTCGCCGTGCCACTGCGCCCCGACAGCCCGCCGTCCAGCAGGTCCCCGGGTGGCGTGGAGAAGCGCAGGCTGCCGTTCTCAGAGGAATGTTCCGACGACGTGGCGAAAGGCGACTGGCGCGCATCCGTGAAGCCCAGGAACGGGTCCTTCATGAAGTGGCGCGACGCCGCGTAGCCCACGAGCCACTGCGAGTACACGTTCTCGGATGGGATGAGGGCGGCGGGTGGCAGCTCCAGGTCCTTCTCCACCTTGATGCGC 
s canFam1.chr8   70559444 277 +  77374719 GTGCGGCGTGCTGCCCCCGCTGGCCGTGCCGCTGCGGCCCGACAGCCCGCCGTCCAGCAGGTCCCCGGGCGGCGTGGAGAAGCGCAGGCTGCCGTTCTCGGACGAGTGCTCGGACGACGTGGCGAAGGGCGACTGGCGCGCGTCCGTGAAGCCCAGGAACGGGTCCTTCATGAAGTGCCGCGACGCGGCGTAGCCCACGAGCCACTGCGAGTACACGTTCTCGGACGGGATGAGCGCGGCGGGCGGCAGCTCCAGGTCCTTCTCCACCTTGATGCGC 
s galGal2.chr5   44594200 277 +  56310377 GTGGGGGGTGCTGCCTCCGGAGGCCGTGCCGCTGCGCCCTGAGAGCCCCCCATCCAGCATGTCCCCCGGCGGGGTGGAGAAACGCAGGCTCCCATTCTCCGACGAATGCTCGGAAGAGGTGGCGAAGGGAGATTGTCGGGAGTCTGTGAATCCTAGAAACGGATCCTTCATGAAGTGCCTTGATGCCGCGTACCCTACCAGCCACTGGGAGTAAACATTTTCGGAAGGTATTATTGTTGCTGGTGGCAAGTCCAAATCTTTCTCAACTTTTATTCGT 
s fr1.chrUn     275910287 277 + 349519338 GTGAGGCGTGCTGCCTCCACTTGCGGTCCCACTACGGCCCGACAAGCCACCGTCCATCAGGTCTCCTGGGGGCGTGGAGAAGCGCAGGCTTCCATTTTCAGAGGAGTGCTCCGATGAAGTGCCGAAGGGAGATTGTCTCGAGTCACTGAAGCCTAGAAAAGGGTCTTTTATGAAATGGCGAGAGGCAGCATAGCCCACTAACCACTGGGAGTAGACATTTTCAGAGGGTATGAGGGGTGCCGGGGAACCATCCCCGTCCTTCTCTGTCTTTATCCTC 
s danRer1.chrUn 103629869 277 + 367113659 GTGCGGGGTGCTGCCTCCGCTAGCAGTACCACTGCGGCCGGAGAGGCCCCCGTCCAGCAGGTCCCCTGGCGGCGTAGAGAATCGCAAGCTTCCGTTCTCGGAGGAGTGTTCCGAGGAGGTGGCGAATGGAGATTGTCTGGAGTCGGTGAAGCCAAGGAAAGGATCTTTGATGAAGTGGCGGGATGCTGCATAGCCCACCAGCCACTGGGAGTAGACATTTTCAGATGGGATTAGGGGGGCTGGGGGTATGTCCAAATCCTTTTCAATTTTGATCCTC 

a score=56079.0
s hg17.chr14     98710868  71 + 106368585 TTG------------GCGGCG---CTGTTGAGCCCGGGGCTGGGCAGCGGCGCGGGCTTGCGCGGGAAGAGCCCGGGGAAGGG---------------------------------------CTC 
s panTro1.chr15  99208734  71 + 106954593 TTG------------GCGGAG---CTGTTGAGCCCGGGGCTGGGCAGCGGCGCGGGCTTGCGCGGGAAGAGCCCGGGGAAGGG---------------------------------------CTC 
s mm5.chr12     102664863  83 + 115071072 TTGGCCGCGTGCAGCGCGGGA---CCACCGAGCCCAGGGCTGGGCAGCGGTGCTGGCTTGCGTGGGAAGAGAGCTGGAAAGGG---------------------------------------CTC 
s rn3.chr6      132300240  83 + 147642806 TTGGCCGCGTGTAGCGCAGGA---CCACCAAGCCCCGGGCTGGGCAGCGGTGCGGGCTTGCGTGGGAAGAGCGCTGGGAAGGG---------------------------------------CTC 
s canFam1.chr8   70559721  71 +  77374719 TTG------------GCCGCG---CTGTTGAGCCCGGGGCTGGGCAGCGGCGCCGGCTTGCGCGGGAACAGCCCCGGGAAGGG---------------------------------------CTC 
s galGal2.chr5   44594477 110 +  56310377 TTA------------GATGAG---TTATTTAAGCTGGGGCTTGTGATAGGTGTTGGCTTCCGAGGGAACAAGTTTGGGAAGGGCTCGCCTGGGCCAAAGTTTCTTCCATTGACTGTCCCCTCCTC 
s fr1.chrUn     275910564  85 + 349519338 TTACTC---------ATGGAG---TTAGCCAGGCCAGAACCAGCGACGGAAGCGGGTTTGTAGGGAAATAAGCTTGGAAGAGA----------------------------ATCATCCGATCCGC 
s danRer1.chr5    4282954  74 +  40038624 TTG------------GCGGAAGATCCAGAGAGGCTGGAGCTGGAAATGGGCATTGGCTTACGATGGAACATCGCAGAGATGGA---------------------------------------ATC 

a score=4995.0
s hg17.chr14     98710939 5 + 106368585 GGTGC 
s panTro1.chr15  99208805 5 + 106954593 GGTGC 
s mm5.chr12     102664946 5 + 115071072 TGCGC 
s rn3.chr6      132300323 5 + 147642806 TGCGC 
s canFam1.chr8   70559792 5 +  77374719 GGCGC 
s galGal2.chr5   44594587 5 +  56310377 GGTGC 
s fr1.chrUn     275910649 5 + 349519338 TGTTC 

a score=9825.0
s hg17.chr14     98710944 10 + 106368585 CTGGCGCGAA 
s panTro1.chr15  99208810 10 + 106954593 CTGGCGCGAA 
s mm5.chr12     102664951 10 + 115071072 CTGGCGCGAA 
s rn3.chr6      132300328 10 + 147642806 CTGGCGCGAA 
s canFam1.chr8   70559797 10 +  77374719 CCGGTGCGAA 
s fr1.chrUn     275910654 10 + 349519338 CTGCCATTAA 

a score=42070.0
s hg17.chr14     98710954 72 + 106368585 Gccgcccccgcgcccgttgaccgcgccgcccgcgcccgcgtccccgcagccgcccgcgtcgtcgtcgtcgcc 
s panTro1.chr15  99208820 72 + 106954593 Gccgcccccgcgcccgttgaccgcgccgcccgcgcccgcgtccccgcagccgcccgcgtcgtcgtcgtcgcc 
s mm5.chr12     102664961 69 + 115071072 GGCCCCGCCGCGCCCGTTCACTGCACCCGGTGCACCCGCGTCCCCACAGCCAACAG---CTCCGGCATCACC 
s rn3.chr6      132300338 69 + 147642806 GGCCCCGCCACGCCCGTTCACTGCGCCCGGTGCACCTGCATCCCCGCAGCCACCAG---CTCCGGTGTCACC 
s canFam1.chr8   70559807 72 +  77374719 gccgccgccgcgcctgttgaccgcgccgccggtgcccgcgtccccgcagccgcccgcgtcgtcgtcgtcgcc 

a score=1846.0
s hg17.chr14     98711026 19 + 106368585 cgcgtccccgccgcccgcc 
s panTro1.chr15  99208892 19 + 106954593 cgcgtccccgccgcccgcc 
s mm5.chr12     102665030 10 + 115071072 CGTGTCGC---------CT 
s rn3.chr6      132300407 10 + 147642806 CGCGTCGC---------CT 
s canFam1.chr10  63975552 18 +  72717409 AGTGTCCCTGTGGGCC-TC 

a score=1381.0
s hg17.chr14     98711045 5 + 106368585 GCACG 
s panTro1.chr15  99208911 5 + 106954593 GCACG 
s mm5.chr12     102665040 5 + 115071072 GCACG 
s rn3.chr6      132300417 5 + 147642806 GCACG 
s canFam1.chr10  63975570 2 +  72717409 G---G 
s fr1.chrUn      86333360 5 + 349519338 GGATA 

a score=13475.0
s hg17.chr14     98711050 19 + 106368585 CTTCAGGAAGGC-GCCGCGC 
s panTro1.chr15  99208916 19 + 106954593 CTTCAGGAAGGC-GCCGCGC 
s mm5.chr12     102665045 19 + 115071072 CTTCAGGAAGGC-GCCCCGC 
s rn3.chr6      132300422 19 + 147642806 CTTCAGGAAGGC-GCCTCGC 
s canFam1.chr10  63975572 20 +  72717409 CCTCGGCCAGGTGGCCGCGC 
s galGal2.chr5   44594680 19 +  56310377 TTTCATGAAGCT-ACTCCTC 
s fr1.chrUn      86333368 19 + 349519338 CCCGGTGAAGTC-GTGCTGC 

a score=43602.0
s hg17.chr14     98711069 105 + 106368585 TTCTGCTTGTCGGCCAGGA---------------------GCTCGCCGTAC-TGCGGCAGTGCGCCTAGGCCCACGTTCTCCATGACCTTGCCCAGCACCAGCGCCTTCTCGTCAGCCAGCGCCTTg- 
s panTro1.chr15  99208935 105 + 106954593 TTCTGCTTGTCGGCCAGGA---------------------GCTCGCCGTAC-TGCGGCAGTGCGCCTAGGCCCACGTTCTCCATGACCTTGCCCAGCACCAGCGCCTTCTCGTCAGCCAGCGCCTTg- 
s mm5.chr12     102665064  87 + 115071072 TT---------------------------------------CTCCCCATAC-TGCGGCAGTGCGCCCAGCCCTGCGTCCTCCATCACCTTGCCCAGGGCCAGAGCCTTCTCATCCGCCAGAGCCGCA- 
s rn3.chr6      132300441  87 + 147642806 TT---------------------------------------CTCCCCATAC-TGCGGCAGTGCGCCCAGCCCTGCGTCCTCCATCACCTTGCCCAATGCCAGCGCCTTCTCATCTGCCAGAGCCGCA- 
s canFam1.chr10  63975592  92 +  72717409 TTATGCTTCTCGCCCAGGA---------CCTGGTGGAAGGCCTCGCTGAAG-TGCTGCATGGAGCTGAGCACCATGCCCTGCATGACCTCGGGCAGCG-------------------------CGCG- 
s galGal2.chr5   44594699 105 +  56310377 TTCTGTTTCTCAGCTAGCA---------------------TGTCATTGTAT-TGCTGGATGGCACCGAGACTTACATTCTCTATCACTTTTCCCAGGACAAGGGATTTCTCATCTGGCAGTGATTTG- 
s fr1.chrUn      86333387 120 + 349519338 TTCTCGTAGTGCTCCCGCAGACGTCTCAGCAGCGTGAAGGTCTTGTCGCACATGGTGCACTGCA--TGGGCCGGTG-----CATGAGCTTGTGCCGCTCGAACGCCGGCTCGTTGGCGAGGATCTTC- 
s danRer1.chrUn 103630787 106 + 367113659 TTCCGATTGTCAACTATTA---------------------AGTTATTGTAC-TGCTGGATGGAGCTGAGCCCTACATTTTCCACCATCTTTCCTAACGAAAGGGTCTTCTCATCTGAAGGAGGCTTTG 

a score=10567.0
s hg17.chr14     98711174 32 + 106368585 gccgcgccgccccccgcgcccgggaccccggg 
s panTro1.chr15  99209040 32 + 106954593 gccgcgccgccccccgcgcccgggaccccggg 
s mm5.chr12     102665151 29 + 115071072 GCTG---CAGCCCCTGCGCCCGCCACCCCCGG 
s rn3.chr6      132300528 29 + 147642806 GCTG---CAGCCCCCGCGCCCGCCACCCCTGG 
s canFam1.chr10  63975684 26 +  72717409 GCCC--TCGTCGCCCACGCCCACCACCG---- 

a score=4398.0
s hg17.chr14     98711206 12 + 106368585 cACCCCAC---CACC 
s panTro1.chr15  99209072 12 + 106954593 cACCCCAC---CACC 
s mm5.chr12     102665180 12 + 115071072 TGGCACGC---CACC 
s rn3.chr6      132300557 12 + 147642806 TGGCACAC---CACC 
s canFam1.chr8   70560183 15 +  77374719 CACCCCGCCCACGCC 

a score=-114.0
s hg17.chr14  98711217 1 + 106368585 C 
s fr1.chrUn  275910877 1 + 349519338 A 

a score=135397.0
s hg17.chr14     98711218 72 + 106368585 GCCGTTCTCGCGGTTGCGGCTCAGCTCCGAGTCCATGCTGAAGCTCGACTCGGGCCGGCTCTCGTTCTCCAG 
s panTro1.chr15  99209084 72 + 106954593 GCCGTTCTCGCGGTTGCGGCTCAGCTCCGAGTCCATGCTGAAGCTCGACTCGGGCCGGCTCTCGTTCTCCAG 
s mm5.chr12     102665192 72 + 115071072 TCCGTTCTCGCGGCCACGGCCCAGCTCCGAGTCCATGCTGAAGCTCGACTCAGGCCGGCTCTCGTTCTCCAG 
s rn3.chr6      132300569 72 + 147642806 CCCATTCTCGCGGCCACGGCCCAGCTCCGAGTCCATGCTGAAGCTCGACTCAGGTCGGCTTTCATTCTCCAG 
s canFam1.chr8   70560198 72 +  77374719 GCCGTTCTCGCGGTTGCGGCTCAGCTCCGAGTCCATGCTGAAGCTCGACTCGGGCCGGCTCTCGTTCTCCAG 
s galGal2.chr5   44594806 72 +  56310377 GCCGTTTTCTCGGTTACGACTCAGCTCTGAGTCCATACTAAAGCTTGACTCTGGCCTGCTCTCATTTTCCAA 
s fr1.chrUn     275910878 72 + 349519338 GCCGTTCTCCCTGTTCCGGTATAATTCGGACTCCATGCTAAAGTTTGATTCTGGTCGACTCTCACTCTCTAG 
s danRer1.chrUn 103630894 72 + 367113659 GCCATTTTCCCTATTCCGACAGAACTCAGAGTCCATGCTGAAGTTTGACTCAGGCCTGCTTTCATTTTCCAA 

a score=501.0
s hg17.chr14     98711290 1 + 106368585 T 
s panTro1.chr15  99209156 1 + 106954593 T 
s mm5.chr12     102665264 1 + 115071072 C 
s rn3.chr6      132300641 1 + 147642806 C 
s canFam1.chr8   70560270 1 +  77374719 C 
s galGal2.chr5   44594878 1 +  56310377 C 
s fr1.chrUn     275910950 1 + 349519338 t 

a score=295.0
s hg17.chr14     98711291 1 + 106368585 A 
s panTro1.chr15  99209157 1 + 106954593 A 
s mm5.chr12     102665265 1 + 115071072 A 
s rn3.chr6      132300642 1 + 147642806 A 
s canFam1.chr8   70560271 1 +  77374719 A 
s galGal2.chr5   44594879 1 +  56310377 t 

a score=33922.0
s hg17.chr14     98711292 47 + 106368585 GCAGctcctcctcctcctcctcctcctcctcgtcctcctcctccGGC 
s panTro1.chr15  99209158 47 + 106954593 GCAGctcctcctcctcctcctcctcctcctcgtcctcctcctccGGC 
s mm5.chr12     102665266 44 + 115071072 GCAGCTCCTCTTCTTCCTCCTCCTCGTCCTCG---TCGTCCTCAGGC 
s rn3.chr6      132300643 44 + 147642806 GCAGCTCTTCTTCTTCCTCCTCCTCGTCCTCG---TCGTCCTCAGGC 
s canFam1.chr8   70560272 47 +  77374719 GCAGctcctcctcctcctcctcctcctcctcgtcgtcctcctcGGGC 

a score=21186.0
s hg17.chr14     98711339 20 + 106368585 TCGTGGCCCAGCGACGGGTC 
s panTro1.chr15  99209205 20 + 106954593 TCGTGGCCCAGCGACGGGTC 
s mm5.chr12     102665310 20 + 115071072 TCGGGGCCCAGAGATGGGTC 
s rn3.chr6      132300687 20 + 147642806 TCGGGTCCCAGAGATGGGTC 
s canFam1.chr8   70560319 20 +  77374719 TCGTGGCCCAGCGACGGGTC 
s galGal2.chr5   44594918 20 +  56310377 TCATGGCCCAGGGAGGGATC 

a score=13223.0
s hg17.chr14     98711359 13 + 106368585 GCTCTCGTGGTGG 
s panTro1.chr15  99209225 13 + 106954593 GCTCTCGTGGTGG 
s mm5.chr12     102665330 13 + 115071072 GCTCTCATGGTGG 
s rn3.chr6      132300707 13 + 147642806 GCTCTCATGGTGG 
s canFam1.chr8   70560339 13 +  77374719 GCTCTCGTGGTGG 
s galGal2.chr5   44594938 10 +  56310377 GCTCTCA---TTC 
s danRer1.chrUn 103631014 13 + 367113659 GCCCTCGCCTTTG 

a score=0.0
s hg17.chr14 98711372 3 + 106368585 CGG 

a score=4230.0
s hg17.chr14     98711372 3 + 106368585 CGG 
s panTro1.chr15  99209238 3 + 106954593 CGG 
s mm5.chr12     102665343 3 + 115071072 CGG 
s rn3.chr6      132300720 3 + 147642806 CGG 
s canFam1.chr8   70560352 3 +  77374719 CGG 
s galGal2.chr5   44594948 3 +  56310377 CTG 
s fr1.chrUn     275910990 3 + 349519338 TGG 

a score=1089095.0
s hg17.chr14     98711375 631 + 106368585 AAGTCACCGTCGGCCGCCTTGAGGCCCTCGCCCGCCAGCTCGCTGGTGCCGGGCTCGGGGGAGCTGGCGGCCGAGAGCCCGTCGTCGGAGCGGCCGGCCAGCGAGCCGGCCTTGTGCATGTGCGTCTTCATGTGGCGCTTGAGCTTGCTGGCCTGCGAGCACGCGTGGTCGCACAGCTGGCACTTGTAGGGCTTCTCGCCCGTGTGACTGCGCCGGTGCACGATGAGATTGCTCTGGAACTTGAAGGTCTTGCCGCAGAACTCGCACGACTTGCTCTTGGCTGGCGGCTGCGGGGGCGGCGTGCCGCCAGGGGGCATGGGCGGCAGCGGCGGCGTGCTCAGGAACGGGGACTTGGGGCTGGGCTGGAA------GGGGTTCAGGAGCCGGTGCATAGGGTTGCCGCGGCCCGGGGACACGGGCGGCGGCG---TGGAGCTGTTGCCCGCCAGCTCGCGGAGCCGCCGCGAGAAGTCCATGGCGGGCGAGTCGATGGCCATGGGGTTCAGGCGCATGACTCGGTCGAAGGCACTGGGGTGCTGGGCGACGAGCCCCATCTCCTCGGCACTGAGGCG---------GTGCGGGTCCAGGTGGTGGCGCGGCGGGGGACTGAAGAGAGGCGGCGTGCCCGGCAGGCGGCCCT 
s panTro1.chr15  99209241 631 + 106954593 AAGTCGCCGTCGGCCGCCTTGAGGCCCTCGCCCGCCAGCTCGCTGGTGCCGGGCTCGGGGGAGCTGGCGGCCGAGAGCCCGTCGTCGGAGCGGCCGGCCAGCGAGCCGGCCTTGTGCATGTGCGTCTTCATGTGGCGCTTGAGCTTGCTGGCCTGCGAGCACGCGTGGTCGCACAGCTGGCACTTGTAGGGCTTCTCGCCCGTGTGACTGCGCCGGTGCACGATGAGATTGCTCTGGAACTTGAAGGTCTTGCCGCAGAACTCGCACGACTTGCTCTTGGCCGGCGGCTGCGGGGGCGGCGTGCCGCCAGGGGGCATGGGCGGCAGCGGCGGCGTGCTCAGGAACGGGGACTTGGGGCTGGGCTGGAA------GGGGTTCAGGAGCCGGTGCATAGGGTTGCCGCGGCCCGGGGACACGGGCGGCGGCG---TGGAGCTGTTGCCCGCCAGCTCGCGGAGCCGCCGCGAGAAGTCCATGGCGGGCGAGTCGATGGCCATGGGGTTCAGGCGCATGACTCGGTCGAAGGCACTGGGGTGCTGGGCGACGAGCCCCATCTCCTCGGCACTGAGGCG---------GTGCGGGTCCAGGTGGTGGCGCGGCGGGGGACTGAAGAGAGGCGGCGTGCCCGGCAGGCGGCCCT 
s mm5.chr12     102665346 625 + 115071072 AAGTCGCCATCGGCCGCTTTCAGG---TCACCTGGCAGCTCGCTGGTGCCCGGCTCAGGGGAGCTGGCAGCTGAGAGCCCGTCGTCTGAGCGGCCAGCCAGAGAGCCCGCCTTGTGCATGTGCGTCTTCATGTGGCGCTTGAGCTTGCTCGCCTGCGAGCACGCATGGTCGCACAGCTGGCACTTGTAGGGCTTCTCGCCCGTGTGGCTGCGCCGGTGCACGATGAGATTGCTCTGGAACTTGAAGGTCTTGCCGCAGAACTCACAGGACTTGCTCTTGGCAGGCGGCTGCGGTGGCGGTGTGCCCGCA---GGCATGGGTGGCAGCGGTGGCGTGCTGAGGAACGGGGACTTGGGACTGGGCTGGAA------AGGGTTCAGCAGCCGGTGCATAGGGTTGCCACGGCCTGGGGACACGGGCGGCGGCG---TGGAGCTGTTGCCGGCCAGTTCTCGCAGCCGCCGGGAGAAGTCCATGGCAGGAGAGTCTATGGCCATGGGGTTCAGGCGCATGACTCGGTCGAAGGCACTGGGGTGCTGGGCCACGAGCCCCATCTCCTCTGCACTGAGGCG---------GTGTGGGTCCAAGTGATGGCGTGGCGGTGGGCTGAAGAGCGGTGGCGTACCTGGCAAGCGGCCCT 
s rn3.chr6      132300723 625 + 147642806 AAGTCGCCATCGGCCGCTTTGAGG---TCACCTGGCAGCTCGCTGGTGCCGGGCTCTGGGGAGCTGGCGGCCGAGAGCCCATCGTCTGAGCGGCCAGCCAGCGAGCCCGCCTTGTGCATGTGCGTCTTCATGTGGCGCTTGAGCTTGCTCGCCTGCGAGCACGCGTGGTCGCACAGCTGGCACTTGTAGGGCTTCTCGCCCGTGTGGCTGCGCCGGTGCACGATGAGATTGCTCTGGAATTTGAAGGTCTTGCCGCAGAACTCACAGGACTTGCTCTTGGCAGGCGGCTGCGGTGGCGGCGTGCCCGTG---GGCATGGGTGGCAGCGGTGGCGTGCTGAGGAACGGGGACTTGGGGCTGGGCTGAAA------AGGGTTCAGCAGCCGGTGCATAGGGTTGCCACGGCCTGGGGACACGGGCGGCGGTG---TGGAGCTGTTACCGGCCAGTTCTCGCAGCCGCCGAGAGAAGTCCATGGCGGGAGAGTCTATGGCCATGGGGTTCAGGCGCATGACTCGGTCGAAGGCACTGGGGTGCTGGGCCACGAGCCCCATCTCCTCTGCACTGAGGCG---------GTGTGGGTCCAAGTGATGGCGTGGCGGTGGGCTGAAGAGCGGTGGCGTACCGGGCAGGCGGCCCT 
s canFam1.chr8   70560355 631 +  77374719 AAGTCGCCGTCGGCCGCCTTGAGGCCCTCGCCGGCCAGCTCGCTGGTGCCGGGCTCGGGGGAGCTGGCGGCCGAGAGCCCGTCGTCGGAGCGGCCGGCCAGCGAGCCGGCCTTGTGCATGTGCGTCTTCATGTGGCGCTTGAGCTTGCTCGCCTGCGAGCACGCGTGGTCGCACAGCTGGCACTTGTAGGGCTTCTCGCCCGTGTGGCTGCGCCGGTGCACGATGAGATTGCTCTGGAACTTGAAGGTCTTGCCGCAGAACTCGCACGACTTGCTCTTggcgggcggctgcggcggcggcgtgcccccggggggcATGGGCGGCAGCGGCGGCGTGCTCAGGAACGGGGACTTGGGGCTGGGCTGGAA------GGGGTTCAGGAGCCGGTGCATAGGGTTGCCGCGGCCCGGAGACACGGGCGGCGGCG---TGGAGCTGTTGCCCGCCAGCTCGCGGAGCCGCCGCGAGAAGTCCATGGCGGGCGAGTCGATGGCCATGGGGTTGAGGCGCATGACTCGGTCGAAGGCACTGGGGTGCTGGGCGACGAGCCCCATCTCCTCGGCACTGAGGCG---------GTGCGGGTCCAGGTGGTGGCGCGGCGGCGGGCTGAAGAGCGGCGGCGTGCCGGGCAGGCGGCCCT 
s galGal2.chr5   44594951 631 +  56310377 AAGTCTGTCTCACTGGATTTCAGTCCCTCTCCAGTGAGCTCGCTCGTGCCTGGCTCAGGAGAACTCGTGGTGGACAGTCCATCGTCTGACCTGCCTGTCATGGAGCCAGCTTTATGCATATGCGTTTTCATGTGACGCTTTAGCTTGCTGGCCTGGGAGCAAGCATGGTCACATAGCTGACATTTGTAGGGCTTTTCTCCTGTGTGACTACGCCGGTGGACGATAAGGTTGCTCTGGAACTTGAAGGTTTTCCCACAGAATTCGCAGGACTTACTCTTGGCCTGAGGCTGGGGAGGCGTAGTGCTGCTTGGGGGCATGGGGGGCAGTGGTGGGGTGCTCAAAAAAGGTGATTTAGGACTCGGCTGGAA------AGGATTCAACAGGCGATGCATAGGGTTGGTGCGACTGGGCGAGACTGGCGGAGGGG---TGGAACTGTTTCCTGCCAGCTCTCGAAGCCTTCTGGAGAAATCCATCGCTGGGGACTCAATTGCCATGGGGTTTAAACGCATAACTCTGTCAAAGGCACTGGGATGCTGGGCAACTAACCCCATTTCTTCGGCACTAAGGCG---------ATGTGGATCCAGATGATGACGAGGTGGTGGGCTGAATAGTGGAGGCGTGTTTGGGAGCCGACCCT 
s fr1.chrUn     275910993 637 + 349519338 AAGTCACCACCGTGGTTCTTCATGC------------GCTCACTTGTGCCTGGCTCCGGGGAACTTGTAGTTGATAGTCCATCATCCGAACGCCCAGTCAGTGAACCAGGCTTGTGCATGTGGGTCTTCATGTGGCGTTTCAGCTTACTCGCCTGAGAACATGCATGGTCACACAGCTGGCACTTGTAGGGTTTCTCTCCGGTGTGGCTTCGGCGATGCACAACCAAGTTGCTTTGGAACTTAAATGTCTTACCACAGAACTCACAGGATTTGACTTTGTTCTGCATCTGTGGAGGGCTAGTGCTGTTTGCGGGAGCCGGTGGTAAGGGAGGAGTGCACACAAAGGGTGACTTTGGCCCAATTTGAAAGGTGTTGGGGTTGAGTAATCGGTGAATATGGTTGGCCCTGCCTGGCGACAGCGGCGGTGTTGTACTGTTGCTATTACCCGCCAATTCACGTAACCTCCTGGAGAAGTCCATGGAGTGGGACTCCATGGACACGGGCGCGAGACGCATCACCTTTTCAAAGGCACTTGGGTGCTGTGAGATGAGACCCATTTCTTCTGTGCTAAGGCATTCTAGCCTATGGGAGTCCAGGTGGTGGCGGGCAGGGGGGCTAACAAATGCAGGCATGTTGGGCAGTCGGTTCT 
s danRer1.chrUn 103631027 646 + 367113659 AAATCACCATCCCGATTTTTTATACCCTCCCCAGTGACGTCACTAGTGCCTGGCTCAGGTGAGCTGGTGGTGGACAGGCCATCGTCAGAGCGCCCTGTCATGGAACCAGATTTGTGCATGTGGGTCTTCATGTGGCGTTTTAATTTGCTCGCTTGAGAACAAGCGTGGTCACACAATTGGCACTTGTAAGGTTTCTCGCCTGTGTGGCTTCGCCGATGAACAACCAGATTACTCTGAAACTTGAAGGTCTTGCCACAGAACTCGCAAGATTTCGACTTGCCCTGTGTCTGTGGCGGGGTGGTGCTGTTAGGGGGCATGGGAGGCAGTGGAGGGGTGCTCAGAAAGGGTGATTTCGGGCTGGGCTGAAAGGGGTTGGGATTGAGAAGGCGATGCATAGGGTTAGCACGGCTCGGTGACAATGGTGGAGTGG---AATTGTTGTTTCCAGCAAGCTCTCTCAATCGGCGGGAGAAATCCATGGACTGGGACTCCATGGCCATGGGTGTCATGCGCATCACTCTTTCGAAGGCACTGGGATGCTGGGAGATTAAACCCATTTCCTCTGCGCTAAGGCGTTCCAGGCGATGGGGATCTAAATGATGGCGTGGAGGGGGGCTGACAAAGGGAGGCGTATTGGGGATACGGTTTT 

a score=309091.0
s hg17.chr14     98712006 203 + 106368585 CGCCGAAGCCC---G-GGTGGTCCCGCAGG--ATGGGGCCCGTCATGCGCAGCAGGTTGAAGGGGTTGCTG---TCGCCCAGGAAATTCATGAGCGGGGACTGCGCCACGGCCTCCGGCCCGAGCGGCGGCGGGATGGTGAGCCGCGGCGTGAGCGAGCTGCTGGCCGGCCCGGGCTCCAGGTAGATGCGGAAGCCGTGCGTGTTCTGCGCG 
s panTro1.chr15  99209872 203 + 106954593 CGCCGAAGCCC---G-GGTGGTCCCGCAGG--ATGGGGCCCGTCATGCGCAGCAGGTTGAAGGGGTTGCTG---TCGCCCAGGAAATTCATGAGCGGGGACTGCGCCACGGCCTCCGGCCCGAGCGGCGGCGGGATGGTGAGCCGCGGCGTGAGCGAGCTGCTGGCCGGCCCGGGCTCCAGGTAGATGCGGAAGCCGTGCGTGTTCTGCGCG 
s mm5.chr12     102665971 203 + 115071072 CACCGAAGCCA---G-GGTGGTCCCGCAGG--ATGGGGCCCGTCATGCGCAGCAGGTTGAAAGGATTGCTG---TCCCCCAGGAAATTCATGAGTGGGGACTGCGCCACGGTCTCCGGCCCGAGCGGTGGCGGGATGGTGAGCCTGGGCGTGAGCGAGGTGCTGGCCGGCCCAGGCTCCAGGTAGATTCGGAAGCCATGTGTGTTCTGTGCG 
s rn3.chr6      132301348 203 + 147642806 CTCCGAAGCCG---G-GGTGGTCCCGCAGG--ATGGGGCCCGTCATGCGCAGCAGGTTGAAAGGATTGCTG---TCCCCGAGGAAATTCATGAGTGGGGACTGCGCCACGGCCTCCGGCCCGAGCGGCGGCGGGATGGTGAGCCTGGGCGTGAGCGAGGTGCTGGCGGGCCCGGGCTCCAGGTAGATGCGGAAGCCATGCGTGTTCTGCGCA 
s canFam1.chr8   70560986 203 +  77374719 CGCCGAAGCCC---G-GGTGGTCCCGCAGG--ATGGGGCCCGTCATGCGCAGCAGGTTGAAGGGGTTGCTG---TCGCCCAGGAAATTCATGAGCGGGGACTGGGCCACGGCCTCGGGTCCCAGCGGCGGCGGGATGGTGAGCCGCGGCGTGAGCGAGCTGCTGGCCGGCCCGGGCTCCAGGTAGATGCGGAAGCCGTGCGTGTTCTGCGCG 
s galGal2.chr5   44595582 203 +  56310377 CACCAAAGCCA---G-GATGTTCACGCAAA--ATGGGTCCTGTCATCCGCAGAAGATTAAAAGGGTTGTTG---TCTCCAAGGAAATTCATCAGCGGGGACTGTGCAACAGTCTCTGGTCCCAGAGGAGGAGGGATGGTGATGCGTGGAGTAAGGGAACTGTTGGAAGGGCTTGTTTCCAGGTAGATGCGGAATCCATGTGTGTTCTGGGCA 
s fr1.chrUn     275911630 206 + 349519338 CGATAAAAGCA---GAGGCGGGCTCTCGAGTCACTGGGCCTGTCATTCTTAAGAGCTGGAAAGGGTTGTTT---TCCCCCAGAAAGTTGATGAGGGGGGGATGAGGGATGCAGTCATTGCCCATGGGTGGAGGCATGGTGATGCGTGGAGTTAGGGCTGCGCTCGAGGGATCTGACTCCAGGTATATGCGAATGCCATGCGTGTTTTGAGCA 
s danRer1.chr5    4283993 209 +  40038624 CGATGTAGCCATGCG-GCGGTTCTCGTAGC--AGTGGGGCACCCATACGCAACAGCTGGAAAGGGTTGCTGCCATCACCCAGAAAGCTGGCAAGTGGGGAACGAGGCAAGGCATCAGCCCCCAGTGGTGGAGGAAGAGCCATGCGAGGGGTAAGAGAGCAGCTAGTAGGGTGGGTGTCCAGGTAGATGCGTATCCCATGGGTGTTCTGTGCA 

a score=170742.0
s hg17.chr14     98712209 76 + 106368585 TGCTGCAGCAGGAACCACGCGCTGTTGAAGGGCTGCTTGCATGTTGTGCAAATGTAGCTGGAAGGCTCATCTTT---AC 
s panTro1.chr15  99210075 76 + 106954593 TGCTGCAGCAGGAACCACGCGCTGTTGAAGGGCTGCTTGCATGTTGTGCAAATGTAGCTGGAAGGCTCATCTTT---AC 
s mm5.chr12     102666174 76 + 115071072 TGCTGCAGCAGGAACCAGGCGCTGTTGAAGGGCTGCTTGCATGTTGTGCAAATGTAGCTGGAAGGCTCATCTTT---AC 
s rn3.chr6      132301551 76 + 147642806 TGTTGCAGCAGGAACCAGGCGCTGTTGAAGGGCTGCTTACATGTTGTGCAAATGTAGCTGGAAGGCTCATCTTT---AC 
s canFam1.chr8   70561189 76 +  77374719 TGCTGCAGCAGGAACCACGCGCTGTTGAAGGGCTGCTTGCATGTTGTGCAAATGTAGCTGGAAGGCTCATCTTT---AC 
s galGal2.chr5   44595785 76 +  56310377 TGCTGAAGCAAGAACCAAGCGCTATTAAAAGGCTGCTTGCATGTTGTGCAAATATAGCTTGAAGGCTCATCTTT---AC 
s fr1.chrUn     275911836 79 + 349519338 TGCTGTAGCAGGAACCAGGCATTGGAAAACATCTGCTTACACGTGGTGCAGATATAACTGGAGGGCTCATCCCTCTGAC 
s danRer1.chrUn 103631683 76 + 367113659 TGCTGCAGAAGGAACCAGGCGTTGTAAAAGGGTTGTTTGCACGTTGTGCATATGTAACTTGAGGGTTCATCTCT---AC 

a score=412979.0
s hg17.chr15     41486872 188 + 100338915 TTAGTGAGAAACATAATCGTGTTTATATTTTGGATGCTGCTTGAATCCAATTCTCTCCCCAACAATGAGGCACTGGATCACCCACTCTTGTGACACCACAGGCAGCTGCAATGCTTCAGCACACTTCAGCACCGAGGCTGGGCATGAGGGGTCCGTCACCACCACATCAAATACCCCTAAAGCAATAT 
s panTro1.chr16  41478602 188 + 101535987 TTAGTGAGAAACATAATCGTGTTTATATTTTGGATGCTGCTTGAATCCAATTCTCTCCCCAACAATGAGGCACTGGATCACCCACTCTTGTGACACCACAGGCAGCTGCAATGCTTCAGCACACTTCAGCACCGAGGCTGGGCATGAGGGGTCCGTCACCACCACATCAAATACCCCCAAAGCAATAT 
s mm5.chr2      120979995 188 + 181686250 TTAGTGAGAAACATAATCATGTTTATATTTTGGATGCTGCTTGAATCCAATTCTCTCCCCAACAATGAGGCACTGGATCACCCATTCTTGTGATACCACAGGCAGTTGCAAGGCTTCAGCACACTTGAGCACCGAGGCTGGGCATGAGGGGTCTGTCACCACCACATCAAATACCCCTAAAGCAATGT 
s rn3.chr3      107897216 188 + 170969371 TTAGTGAGAAACATAATCATGTTTGTATTTTGGATGCTGCTGGAATCCAATTCTCTCCCCAACAATGAGGCACTGGATCACCCATTCTTGTGATACCACAGGCAGCTGCAAGGCTTCAGCACACTTGAGCACCGAGGCTGGGCATGAGGGGTCTGTCACCACCACATCAAATACCCCTAAAGCAATGT 
s canFam1.chr30  13173383 188 +  43165425 TTAGTGAGAAACATAATCATGTTTGTATTTTGGATGCTGCTTGAATCCAATTCTCTCCCCAACAATGAGGCACTGGATCACCCACTCTTGTGACACCACAGGCAGCTGCAATGCTTCAGCACACTTCAGCACCGAGGCTGGGCATGAGGGATCCGTCACCACCACGTCAAATACCCCTAAAGCAATAT 
s galGal2.chr10     80159 188 -  20909726 TTAACGAGGGACATAGTCATGTTTGTATTTTGGATGCTTGTTGTAGCCTACTCTCTCTCCAGCAATAAGGCTCTGGATCACCCACTCTTGTGAGACAACAGGCAACCTTAATGCTTCTGCGCACTTCAAGACAACAGCTGGGCAGGAAAGATCAGTCACCACCACATCATAAACACCCAATGCAATAT 
s fr1.chrUn     325491827 188 - 349519338 GGATTATGACGCGTAGTTGTGGCGATACCGAGGCAGGCTATGGAAACCCAGGCACTCCCCACAGATCACACTCTGGATGAGCCACTCGGGAGACACCAGCGGCACTTCCTGTGATGCCATGTTCTTCTCCACTAGTGGGGAGCAGGTGTGGTCCGTCACCACAACGTCAAACTTGCCGGCAGGAATGT 
s danRer1.chrUn 117181337 182 - 367113659 TTACGTAGATGT---GTTGTGGCAGAATTCAGAATTGCTGTCGAAGTTGAGGCACTTTCCACAGATCAAGCTCTGAATCAGCCACTCCAGAGAGACAACAGGCATGTTTGAGGCC---ACACGCTTCACTTCCTTTGATGTACATGCTGATGATGTCACTGCCACATCAAACTTCACATCTGGAATGT 

a score=145507.0
s hg17.chr15            41673708 149 + 100338915 ATGGCTGGTCCCTTCTCCCGTCTGCTGTCCGCCCGCCCGGGACTCAGGCTCCTGGCTTTGGCCGGAGCGGGGTCTCTAGCCGCTGGGTTTCTGCTCCGACCGGAACCTGTACGAGCTGCC---AGTGAACGACGGAGGCTGTATCCCCCGAG 
s panTro1.chr16_random  12462177 149 +  32210112 ATGGGTGGTCCCTTCTCCCGTCTGCTGTCCGCCCGCCCGGGACTCATGCTCCTGGCTTTGGCCGGAGCGGGGTCTCTAGCCGCTGGGTTTCTGCTCCGACCGGAACCTGTACGAGCGGCC---AGTGAACGACGGAGGCTGTATCCCCCGAG 
s mm5.chr2             121140425 152 + 181686250 ATGGCTGGTCCCTTCTCCCGTCTGCTGTCTGCCCGCCCTGGACTCAGGCTCCTGGCTTTGGCTGGAGCTGGGTCTCTCACCGCCGGGATTCTGCTCCGCCCGGAATCTGTAGGAGCTGCCGCTGCTGAACGGAGGAGACTGTATCCCCCGAG 
s rn3.chr3             108059196 152 + 170969371 ATGGCTGGTCCCTTCTCCCGTCTGCTGTCTGCCCGCCCCGGACTCAAGCTCCTGGCTTTGGCTGGAGCTGGGTCTCTCGCCGCCGGGATTCTGCTCCGTCCGGAATCTGTACGAGCGGCCACCGGTGAACGGAGGAGACTGTATCCCCCGAG 
s canFam1.chr30         13349240 149 +  43165425 ATGGCTGGTCCCTTCTCTCGTCTGCTGTCCGCGCGCCCGGGGCTCAGGCTCCTAGCTTTGGCTGGAGCTGGGTCTCTAGCCGCTGGGTTTCTGCTCCGCCCGGAACCTGTAAGAGCCGCC---AGTGAACGACGGAGGCTGTATCCCCCAAG 
s galGal2.chrZ          28834466 152 +  33651169 ATGGCTGGCACCTTTGGTCGTCTCCTGGCTGGCCGTGTGACTGCTGCACTTTTTGCAGCAGCAGGCACAGGGGTACTCACCACTGGGTACCTCCTCAACCAGCAAAATGTGAAAGCTACTGTGCATGAGAAGCGGAAGCTCTTCCCTCCCAG 
s fr1.chrUn             97204237 143 - 349519338 ATGGCGAGTAGCTTCTCCAGGGTTCTGATCTCCAG---AAACATCCGGATCCTGTCGCTGTTGGG---GGGTTCGGTCACAGCCGGGATCCTGCTGCAGCGGCACCATGTCGGCGCCGAC---GGCCCCACACGGAGGAGGTACCCCGCCAG 
s danRer1.chr4            497203 149 -  30025136 ATGGCTGGTTCAATTGGCAAGATGATGTCGAGCCGCACCACTGGCCTGCTCATGGCAAGCCTCGGAGCTGGTGCTTTGGCGACCGGATATATGATGAGTGACAGTGCTGCAATCTCTGCG---GACGAGAAGAGGAAACTCTACCCTCCCAG 

a score=250959.0
s hg17.chr15     41679161 89 + 100338915 TCATAGCAGGTGGCCAAGGAAGCTGATAGTCAATACCAGGGACCAGGAAGGTCGTGACCAGTCCTGGAGGCCCCAGGCTGTACTTCGAC 
s panTro1.chr16  41682794 89 + 101535987 TCATAGCAGGTGGCCAAGGAAGCTGATAGTCAATACCAGGGACCAGGAAGGTCGTGACCAGTCCTGGAGGCCCCAGGCTGTACTTCGAC 
s mm5.chr2      121145551 89 + 181686250 TCATAATAGGTGGCCAAAAATGCTGACGGGCAATGCCAGGGCCCAGGAGGCTTGGAACCAGTCGTAGAGACCCCAGGCTGAGTTTCGAC 
s rn3.chr3      108064239 89 + 170969371 TTATAATAGGTGGCCAAAAAAGCTGATGGTTAGTGTCAGAGCCCAGGAAGCATGGAACCAGTCACAGAGACCCCAGGCTGAGCTTCGAC 
s canFam1.chr30  13354361 89 +  43165425 TCATATCAGGTTGCCAAGGAAGCAGATGGTCAATGCCATGGCCCAGGAGGGTTGTGACCAGTCCTGAAGGCCCCAGGCTGTGCTTCGAC 

a score=50892.0
s hg17.chr15     41826029 40 + 100338915 ATGCGCCTCCGCCGCCTAGCGCTGTTCCCGGGTGTGGCGC 
s panTro1.chr16  41735415 40 + 101535987 ATGCGCCTCCGCCGCCTAGCGCTGTTCCCGGGTGTGGCGC 
s mm5.chr2      121195614 40 + 181686250 ATGCGCTTCAGCTGCCTAGCTCTGCTCCCGGGCGTGGCGC 
s rn3.chr3      108117268 40 + 170969371 ATGCGCTTCAGCTGCCTTGCGCTGCTCCCGGGCGTGGCGT 
s canFam1.chr30  13397631 40 +  43165425 ATGCGCCCCCGCTGCCGAGCGCTGCTCCCGGGCGTGGCGC 

a score=11434.0
s hg17.chr15     41826069 20 + 100338915 TGCTTCTTGCCGCG---------------GCCCGC 
s panTro1.chr16  41735455 20 + 101535987 TGCTTCTTGCCGCG---------------GCCCGC 
s mm5.chr2      121195654 20 + 181686250 TGCTGCTCGCCTCG---------------GCCCGT 
s rn3.chr3      108117308 35 + 170969371 TGCTGCTCGCCTCGGCCCTCCTCGCCTCCGCCCTC 
s canFam1.chr30  13397671 20 +  43165425 TGCTTTTCGCCGCG---------------GCCGGT 
s fr1.chrUn      97210657 23 - 349519338 TGCTTTTAGCAGCG------------CTCACCGGC 

a score=118454.0
s hg17.chr15     41826089 107 + 100338915 CTCGC---CGCTGCCTCCGACGTGCTAGAACTCACGGACGACAACTTCGAGAGTCGCATCTCCGACACGGGCTCTGCGGGCCTCATGCTCGTCGAGTTCTTCGCCCCCTG 
s panTro1.chr16  41735475 107 + 101535987 CTCGC---CGCTGCCTCCGACGTGCTAGAACTCACGGACGACAACTTCGAGAGTCGCATCTCCGACACGGGCTCTGCGGGCCTCATGCTCGTCGAGTTCTTCGCCCCCTG 
s mm5.chr2      121195674 107 + 181686250 CTCGC---CGCCGCCTCCGATGTGTTGGAACTGACGGACGAAAACTTCGAGAGTCGCGTCTCCGACACGGGCTCGGCGGGGCTCATGCTAGTCGAGTTCTTCGCCCCCTG 
s rn3.chr3      108117343 107 + 170969371 CTCGC---CTCCGCCTCAGACGTGTTGGAACTGACGGACGAAAACTTCGAGAGTCGCGTCTCCGACACGGGCTCAGCTGGGCTCATGCTAGTCGAGTTCTTCGCCCCATG 
s canFam1.chr30  13397691 107 +  43165425 CTCGC---CTCTGCCTCCGACGTGCTGGAACTCACTGACGACAACTTCGAGAGTCGCATCTCCGACACGGGCTCTGCGGGCCTCATGCTCGTCGAGTTCTTCGCTCCCTG 
s fr1.chrUn      97210680 101 - 349519338 TTCACGCAGGCCGCCAGTGATGTGCTGGAGTTCACGGATAACGATTTCGAAAGTAAAATCGGAGACC---------ATGAAATTATTCTTGTGGAGTTTTTCGCACCCTG 
s danRer1.chr17  15314657  98 +  35757233 CTCGT---GGAGGGCAGCGATGTGCTGGAGCTCGGAGATTCTGACTTTGA---------CCGGAGCGCAGGCATGCATGACACTCTGCTAGTGGAGTTCTTCGCACCTTG 

a score=88002.0
s hg17.chr16             142908 95 +  88827254 ATG----TCTCTGACCAAGACTGAGAGGACCATCATTGTGTCCATGTGGGCCAAGATCTCCACGCAGGCCGACACCATCGGCACCGAGACTCTGG-AGAG 
s panTro1.chr18          150233 95 +  83875239 ATG----TCTCTGACCAAGACTGAGGGGACCATCATTGTGTCCATGTGGGCCAAGATCTCCACGCAGGCCGACACCATCGGCACCGAGACTCTGG-AGAG 
s mm5.chr11            32172234 95 + 121648857 ATG----TCTCTGATGAAGAATGAGAGAGCTATCATCATGTCCATGTGGGAGAAGATGGCTGCTCAGGCCGAGCCCATTGGCACTGAGACTCTAG-AGAG 
s rn3.chr10            95139962 95 - 110733352 ATG----TCTCTGATGAAGAATGAGAGAGCTATCATCATGTCCATGTGGGACAAAATGGCGCCTCATGCAGAGCCCATTGGCACTGAGACTCTGG-AGAG 
s canFam1.chr6         37152261 96 -  79106041 ATG----TCTCTGACCAAGGCCGAGAGGACCATCATCCTGTCCATGTGGGGCAAGATCTCCACCCAGGCGGATGCTATTGGCACCGAGGCCCTGGAAGAG 
s galGal2.chr14        13958597 95 +  20603938 ATG----GCACTGACCCAAGCTGAGAAGGCTGCCGTGACCACCATCTGGGCAAAGGTGGCTACCCAGATTGAGTCCATTGGGCTGGAATCACTGG-AGAG 
s fr1.chrUn           269729641 95 + 349519338 ATG----AGTCTGAGCAGGACTGACAAGGAGGCCGTGAAGGCCATTTGGGCCAAAATGTCCAAGAGCATTGATGTCATCGGGGCCGAGGCGTTTG-GCAG 
s danRer1.chrFinished  33475840 95 -  40167097 ATGAGTCTCTCTGCCAAAGAC----AAAGCTGCCGTCAAAACCCTGTGGGCCAAGATCGCTGGAAAGGCTGACGACATCGGACACGATGCTCTCT-CCAG 

a score=39370.0
s hg17.chr16       179963 35 +  88827254 TTACTTGTATTTCGCACTTCGGTCCCGGGAAGCCC- 
s panTro1.chr18    195782 35 +  83875239 TTACTTGTATTTCGCACTCCGGTCCCGGGAAGCCC- 
s mm5.chr17      68693958 35 -  93559791 TTACTTGTATTTTGTACTCCGGTCCCTGGAAGCCC- 
s rn3.chr10      95183773 35 - 110733352 TTACTTGTATTTTGTACTCCGGTCCCTGGAAGCCC- 
s canFam1.chr6   37185997 35 -  79106041 TTACTTGTATTTCGCACTCCGGTCCCTGGAAGCCC- 
s fr1.chrUn     145482403 32 + 349519338 TTACTTGTGTCTGGAGCCGTGCTC----GTGGCTGT 

a score=142911.0
s hg17.chr16       179998 137 +  88827254 GACGATGTCCCCGGCTGTGGCTCCGGGAACGGCTGCGGTGGCGCCGATGTCTATCTCGGGACCGGGACCGGGACAATTTCCGTCGC---TCTCGGGAGGTAGATCTTGACCGCCTCCGACGCCGATCCCGGGAGCGTGAC 
s panTro1.chr18    195817 137 +  83875239 GACGATGTCCCCGGCTGTGGCTCCGGGAACGGCTGCGGTGGCGCCGATGTCTATCTCGGGACCGGGACCGGGACAATTTCCGTCGC---TCTCGGGAGGTAGATCTTGACCGCCTCCGACGCCGATCCCGGGAGCGTGAC 
s mm5.chr17      68693993 137 -  93559791 GGCGGTGACCCCGGCTGTGGCTCCGGGAACGGCTGCGATGGCGCCTGTATCTATCTCGGGATCTGGAACGGGAAAACTTCCGCCGC---TCTCTGGAGGTAGACCTAGACCGCCTCCGTCGACGATCCCGGGAGCGTGAC 
s rn3.chr10      95183808 137 - 110733352 GTCGGTGACCCCGGCTGTGGCTCCGGGAACGGCTGCGATGTCGCCGGTATCTATCTCGGGACCTGGAACGGGAAAACTTCCGCCGC---TCTCGGGAGGTAGACCTAGACCGCCTCCTTCGACGATCCCGGGAACGTGAC 
s canFam1.chr6   37186032 137 -  79106041 GGCGGTGGCCCCGGCTGTGGCTCCGGGAACGGCTGCGGTGGCGCCGGTGTCTGTCTCGGGACCGGGACCGGGATGACTTTCGTCGC---TCCCTGGAGGTAGATCTGGACCTCCTCCGACGCCGGTCCCGGGAGCGTGAC 
s galGal2.chr1  142364883 137 - 188239860 GGCTGCGACTCCGGCTGCGGCTGTTGGAGCGAGACCTGTGGCGATGGCGTTTCTCACGGGATTTAGAGCGAGTTCTTCTTTTCCGT---TCCCTGGAGGCTGAGCGAGAGCGATGTCTGCGACGATCTCGGGACCTAGAT 
s fr1.chrUn     145482435 134 + 349519338 GACGGTGTCCTCGGTTGCGGGAGCCCGATCTGCTGCGATGCCTCCTCCTCCTGTCCCTGGAGCGCGAACGGGAA------CGGCGCTTGTCTCGAGACGTCGAACGCGAGCGTCTCCTCCTGCGGTCACGAGAGCGGGAC 

a score=23245.0
s hg17.chr16      244413 4 +  88827254 ATGT 
s panTro1.chr18   262355 4 +  83875239 ATGT 
s mm5.chr17     68753542 4 -  93559791 ATGA 
s rn3.chr10     95244723 4 - 110733352 ATGA 
s canFam1.chr6  37249961 4 -  79106041 ACGA 

a score=198450.0
s hg17.chr16      244417 264 +  88827254 TGGACCACAAGGACTTAGAGGCCGAAATCCACCCCTTGAAAAATGAAGAAAGAAAATCGCAGGAAAATC-TGGGAAATCCATCAAAAAATGAGGATAA----CGTGAAAAGCGCGCCTCCACAGTCCCGGCTCTCCCGGTGCCGAGCGGCGGCGTTTTTTCTTTCATTGTTTCTCTGCCTTTTTGTGGTGTTCGTCGTCTCATTCGTCATCCCGTGTCCAGACCGGCCGGCGTCACAGCGAATGTGGAGGATAGACTACAGTGCCGCTG 
s panTro1.chr18   262359 264 +  83875239 TGGACCACAAGGACTTAGAAGCCGAAATCCACCCCTTGAAAAATGAAGAAAGAAAATCGCAGGAAAATC-TGGGAAATCCATCAAAAAATGAGGATAA----CGTGAAAAGCGCGCCTCCACAGTCCCGGCTCTCCCGGTGCCGAGCGGCGGCGTTTTTTCTTTCATTGTTTCTCTGCCTTTTTGTGGTGTTCGTCGCCTCATTCGTCATCCCGTGTCCAGACCGGCCGGCGTCACAGCAAATGTGGAGGATAGACTACAGTGCCGCTG 
s mm5.chr17     68753546 264 -  93559791 TGGACAACAAGGACTTAGAAGCTGAAATACACCCCTTGAAGAATGAGGACAAGAAATCACAGGAAAACC-CAGGAAACCTACCAAGAAACGAAGATAA----CTTGAAGAGCAAGCCTGTGCCTTCCCGCTTGTCCCGGTGCCGCACAGTGGCATTTTTCCTTTCCCTGTTCACCTGCCTCTTCGTGGTGTTTGTCCTGTCTTTCATCATCCCATGTCCAGACCGTCCCTCCTCACAGGGCACGTGGAAGCTTGACTACAACAATGCAG 
s rn3.chr10     95244727 264 - 110733352 TGGATGACAAGGATCTAGAAGCTGAAATACATCCCTTGAAGAATGAGGACAAAAAGTCACAGGAAAACC-TAGGAAACCTACCAAAGACCGAGGACAA----CTTGAAGAACAAGCCTGTGCCTTCTCGCTTGTCCCGGTGTCGCACGGTGGCATTTTTCCTTTCCCTGTTCATCTGTCTCTTTGTGGTGTTTGTCCTCTCTTTCATCATCCCATGCCCAGACCGACCGTCCTCTGAGGACAAGTGGAGGCTGGACTACGACTATGCAG 
s canFam1.chr6  37249965 264 -  79106041 TGGACAGCAAGGACCTAGAAGCCGAAATCCACCCCCTGAGGAACGAAGACAAGAGGCTGCCCGAGACCC-CGGGAAACCCGGGCCACGCAGACGAGAA----GCTGAAAAGCTCGCCCCGGCAGCCCCGCCTCTCCCGGTGCCGCACCGTTGTGTTTTTTCTTTCACTGTTTGTCTGCCTGTTCGTAGTGTTCGTGGTTTCGTTCATCATCCCGTGCCCGGAACGGCCCGTGTCGCAGGGGATGTGGCGGATAGACTACAGCGCGGCAG 
s galGal2.chr14  6505218 264 -  20603938 TGGATAACAAAGACTCAGAAGCTGAGATCCACCCCCTGAAGACAGAGGACGTGAAAGCTCAAGAGAACCATGAGAACTCTGTTGA-----GAGGAGAATCATCATCAAGCAGTCGTCGCAGCTGTCTCGGCTGTCCCGCTGGCGCACCGCCGCCTTCTTCATCTCATTATTTCTGTGTCTCATCATCGTGTTTGCCTTCTCCTTTATCATTCCTTGCCCTGAGAGGCCTGTCTCAGAGAGAACGTGGCTCCGAAACTATGACAATGCAG 

a score=3883.0
s hg17.chr16       259268 28 +  88827254 C-TAGGCCACCCCAT----CTCCACCCCCAGGG 
s mm5.chr17      68763356 29 -  93559791 CCTACTACTCCCCAT----CGGCACCTTCAGGG 
s rn3.chr10      95254895 29 - 110733352 CTTAGTCCTCCTCAT----TGCCACCTGCAGGG 
s canFam1.chr6   37261496 28 -  79106041 -CTAGGTGCCCCTGT----CCCCGCACGCAGGG 
s fr1.chrUn      32270640 32 + 349519338 -CTTGGCCTGTCCGTCCTGCTCCGCCATCCGGG 
s danRer1.chrNA 221970878 28 + 390413307 CCCTGGGGCCTCTAT-----TGCAAGTCCAGGG 

a score=-1898.0
s hg17.chr16     259296 9 +  88827254 CCACAAGCC 
s mm5.chr17    68763385 9 -  93559791 GAACTGGTT 
s rn3.chr10    95254924 9 - 110733352 GAGCTGGTA 
s canFam1.chr6 37261524 9 -  79106041 TCACTTGCA 
s fr1.chrUn    32270672 9 + 349519338 CCGATGCCT 
s danRer1.chr1  5581271 9 +  40858791 CCATCATCC 

a score=2916.0
s hg17.chr16      259305 2 +  88827254 GC 
s mm5.chr17     68763394 2 -  93559791 GC 
s rn3.chr10     95254933 2 - 110733352 GC 
s canFam1.chr6  37261533 2 -  79106041 GC 
s galGal2.chr14  6519763 2 -  20603938 GC 
s fr1.chrUn     32270681 2 + 349519338 GC 
s danRer1.chr1   5581280 2 +  40858791 TC 

a score=1053.0
s hg17.chr16      259307 19 +  88827254 TG---TGGGCTCCACAGGGGTG 
s mm5.chr17     68763396 19 -  93559791 TG---CAGGCTCCCTGGGGGTA 
s rn3.chr10     95254935 19 - 110733352 TG---CAGGCTCCCCAGAGGTC 
s canFam1.chr6  37261535 22 -  79106041 AGTCACAGGCTCTGCAGATGTG 
s galGal2.chr14  6519765 19 -  20603938 CT---CGGTGTCACCGGCGGGC 
s danRer1.chr1   5581282 13 +  40858791 TG---TGG------TATGGGTG 

a score=-178.0
s hg17.chr16    259307 28 + 88827254 TGTGGGCTCCACAGGGGTGGGAAGGAGT 
s danRer1.chr1 5581282 19 + 40858791 TGTGG------TATGGGTGACGAGA--- 

a score=499.0
s hg17.chr16      259326 3 +  88827254 GGA 
s panTro1.chr18   279072 3 +  83875239 GGG 
s mm5.chr17     68763415 3 -  93559791 GAC 
s rn3.chr10     95254954 3 - 110733352 GAC 
s canFam1.chr6  37261563 3 -  79106041 GGA 
s galGal2.chr14  6519784 3 -  20603938 AGG 

a score=4058.0
s hg17.chr16      259329 6 +  88827254 AGGAGT 
s panTro1.chr18   279075 6 +  83875239 AGGAGT 
s mm5.chr17     68763418 6 -  93559791 TGGAGA 
s rn3.chr10     95254957 6 - 110733352 TGGAGA 
s canFam1.chr6  37261566 6 -  79106041 AGGAGC 
s galGal2.chr14  6519787 6 -  20603938 AGCAGG 
s danRer1.chr1   5581295 6 +  40858791 ACGAGA 

a score=70372.0
s hg17.chr16      259335 48 +  88827254 GCAGGGCTGGGGCTCGAGTGCCGTGGCCTCCACGTAAACGGGAACACG 
s panTro1.chr18   279081 48 +  83875239 GCAGGGCTGGGGCTCGAGTGCCGTGGCCTCCACGTAATTGGGAACACG 
s mm5.chr17     68763424 48 -  93559791 GCAGGGCTGGGGCTTGAGTGCAGAGGCTTCCGCAAGAATGGAAATGGC 
s rn3.chr10     95254963 48 - 110733352 GCAGGGCTGGGACTTGAGTGCAGAGGCTTCCGCAAGAATGGGAATGGC 
s canFam1.chr6  37261572 48 -  79106041 GTGGGGCTGGGGCTCGGGTGTGGCGGCTTCCGCAGGAACGGAAAGGCC 
s galGal2.chr14  6519793 48 -  20603938 GCCGGGCTGGGGCTGGAGTGTCGCTGCTTGCGCATGAAGGGGAACACC 
s fr1.chrUn     32270683 48 + 349519338 GCGGGGGAGGGGCTGGCGTGCCGCTGGCGTCTCATGAAGGGGAAGACG 
s danRer1.chr1   5581301 48 +  40858791 GCAGGCGAGGGGCTGGAGTGGCGCTGCCGACGCATGAACGGGAACACA 

a score=5348.0
s hg17.chr18     23786114 2 +  76117153 TC 
s panTro1.chr17  19719396 2 +  73346066 TC 
s mm5.chr18      16960413 2 +  91083707 TC 
s rn3.chr18       8050213 2 +  87338544 TC 
s canFam1.chr7   19431300 2 -  83037113 TC 
s galGal2.chr2  103976638 2 + 147590765 TC 
s fr1.chrUn     291830820 2 - 349519338 TC 
s danRer1.chrNA 203940100 2 - 390413307 TC 

a score=389078.0
s hg17.chr18     23786116 205 +  76117153 AGTCATCA---CCTCCACCATACATGTCAGCAAGTTTCTTGAACCGTGGCCCCCAGTCGTTCAGGTAATCATAGTCCTGCTCACCACCACTACTTGAGGAATTAAGGGAGCTCAAGGACCCAGCAGTGGAGCCACTGCCTTCATAGTCAAACACTAACAGGGAGTCATATGGTGGAGCTGTGGGGTCATTGTCAGCCGCTTTAAGGCC 
s panTro1.chr17  19719398 205 +  73346066 AGTCATCA---CCTCCACCATACATGTCAGCAAGTTTCTTGAACCGTGGCCCCCAGTCGTTCAGGTAATCATAGTCCTGCTCACCACCACTACTTGAGGAATTAAGGGAGCTCAAGGACCCAGCAGTGGAGCCACTGCCTTCATAGTCAAACACTAACAGGGAGTCATATGGTGGAGCTGTCGGGTCATTGTCAGCCGCTTTAAGGCC 
s mm5.chr18      16960415 205 +  91083707 AGTCGTCA---CCACCGCCGTACATGTCCGCCAGTTTCTTGAAGCGGGGTCCCCAGTCATTCAGGTAGTCATAGTCCTGGTCCCCACCGCTACTGGAGGAGTTGAGGGAGCTCAAGGAGCCAGCCGTGGAGCCGCTGCCCTCGTAGTCAAAGACTAAGAGGGAGTCATACGGTGGCGCCGTGGGGTCGTTGTCAGCAGCTTTAAGGCC 
s rn3.chr18       8050215 205 +  87338544 AGTCATCA---CCACCACCATACATGTCGGCCAGCTTCTTGAAGCGGGGTCCCCAGTCATTCAGGTAGTCATAGTCCTGGTCCCCGCCGCTGCTGGAGGAGTTGAGAGAGCTCAAGGAGCCAGCCGTGGAGCCGCTGCCCTCATAGTCGAAGACTAAAAGGGAGTCATATGGTGGCGCCGTGGGGTCATTGTCAGCAGCTTTAAGGCC 
s canFam1.chr7   19431302 205 -  83037113 AGTCATCA---CCTCCACCATACATGTCAGCAAGTTTCTTGAACCGTGGCCCCCAGTCGTTCAGGTAGTCATAGTCCTGCTCGCCACCACTACTTGAAGAATTAAGGGAGCTCAAAGACCCAGCGGTAGAGCCACTGCCTTCGTAGTCAAAGACTAAGAGGGAGTCATATGGTGGAGCTGTGGGATCATTGTCAGCAGCTTTAAGGCC 
s galGal2.chr2  103976640 205 + 147590765 AGTCATCA---CCTCCACCGTACATGTCAGCAAGTTTCTTGAAACGTGGGCCCCAGTCATTTAGGTAGTCATAGTCTTGCTCACCACCGCTACTTGAGGAATTAAGAGAGCTCAAGGATCCAGCAGTGGAGCCGCTTCCTTCATAGTCAAAGACTAAGAGGGAATCGTATGGCGGGGCTGTAGGGTCGTTGTCGGCTGCTTTAAGTCC 
s fr1.chrUn     291830822 205 - 349519338 AGTCATCGTCCCCTCCACCGTACAGGTCGGCCAGCTTCTTGAAGCGGGGGCCCCAGTCGTTGAGGTAGTCGTAGTCCTGGTCGCCCGAGCTGAT---GGAGTTGAGCGAGCTGACGGAGCCGGCTGTCGAGCCGGTGCCCTCGTAGTCGAACACCAGCAGGGAGTCGTAGGGAGGGGCCGTGGGGTCGTTATCCGCTGCTCTCAGACC 
s danRer1.chrUn 257546281 205 - 367113659 AGTCGTCG---TTACCTCCGTACATGTCGGCGAGTTTGCGGAAGCGAGGGCCCCAATCGTTGAGGTAGTCATAGTCCTGGTCTCCTCCGCTGCTGGACGAGTGAAGGGAGCTTAGTGAGCCGGCCGTGGAGCCGCTGCCCTCGTAGTCAAACACCAGCAGGGAGTCATACGGAGGGGCCGTGGGATCGGTGTCGGCTGCCTTGAGGCC 

a score=581809.0
s hg17.chr18     59406881 165 +  76117153 ATGGATTCACTTGGCGCCGTCAGCACTCGACTTGGGTTTGATCTTTTCAAAGAGCTGAAGAAAACAAATGATGGCAACATCTTCTTTTCCCCTGTGGGCATCTTGACTGCAATTGGCATGGTCCTCCTGGGGACCCGAGGAGCCACCGCTTCCCAGTTGGAGGAG 
s panTro1.chr17  56243482 165 +  73346066 ATGGATTCACTTGGCGCCGTCAGCACTCGACTTGGGTTTGATCTTTTCAAAGAGCTGAAGAAAACAAATGATGGCAACATCTTCTTTTCCCCTGTGGGCATCTTGACTGCAATTGGCATGCTCCTCCTGGGGACCCGAGGAGCCACCGCTTCCCAGTTGGAGGAG 
s mm5.chr1      106957557 165 + 195203927 ATGGACTCACTAGGCACAGCAGCCACACAGTTCCTGTTTGATCTTTTCAAAGAACTGAATAAAACAAATGATGGCAACGTCTTCTTTTCCCCTGTGGGCATCTCAACAGCCATTGGCATGATCATCCTGGGGACCCGAGGAGCCACTGCTTCTGAGTTACAGAAG 
s rn3.chr13      13176896 165 + 111348958 ATGGACTCACTAAGCACAGCAACCACACATTTCCTGTTTGATCTTTTCAAAGAACTGAATAAAACAAGTGACGGCAATGTCTTCTTTTCTCCTTTGGGCATCTCAACAGCCATTGGCATGATCCTCTTGGGGACCCAAGGAGCCACTGCCTCTGAGTTACAGAAG 
s canFam1.chr1  108508362 165 - 124897793 ATGGATTCACTTGGTGCAGCATACACTCACTTTGGGTTTAATCTCTTCCAAAAGCTGAATAAAATAAATGATGGCAACATCTTCTTTTCCCCTGTGGGCATTTCTGCTGCCATTGGCATGCTCATCCCAGGGGCCCGAGAAGCTACCGCCATGCAGTTGCAGAGG 

a score=1700.0
s hg17.chr18     59455932 2 +  76117153 CT 
s panTro1.chr17  56296086 2 +  73346066 CT 
s mm5.chr1      106995539 2 + 195203927 TT 
s rn3.chr13      13306377 2 + 111348958 TT 
s canFam1.chr1  108539809 2 - 124897793 CT 
s galGal2.chr2   67392007 2 + 147590765 TA 
s fr1.chrUn      39424675 2 - 349519338 CT 
s danRer1.chr20  11152772 2 +  31913010 TT 

a score=2707.0
s hg17.chr18     59455934 3 +  76117153 ATG 
s panTro1.chr17  56296088 3 +  73346066 ACG 
s mm5.chr1      106995541 3 + 195203927 AAG 
s rn3.chr13      13306379 3 + 111348958 AAG 
s canFam1.chr1  108539811 3 - 124897793 AAG 
s galGal2.chr2   67392009 3 + 147590765 ATG 
s fr1.chrUn      39424677 3 - 349519338 CAG 
s danRer1.chr20  11135889 3 +  31913010 ATG 

a score=316154.0
s hg17.chr18     59455937 400 +  76117153 GGGATGAGAATCTGCCATAGAAGAGGATGCT-GTTGGTCTTATTTTGCCTTATGAAGAATAGGAAAGGGTGATTACAACAGAACTCTT--CATTAGTTGAAGGAGAT-GAT---------AATTCGACT-------ACTACTACAGCGGTGGCAGCTGCAGCTTCCACTCCCTCCTCAGTGACCTCCACAAAGGCCTTGTGTAGGACTTTAGATACTGAGAGACCGTGGCTCCAGGTCATGCCT-------------------------------------------------------------------------------------GAGAGGTCTGCATCCC---CATTGAAGATATTCACCATTCCCATGGTTCTCAACGTGTCCTTGAGGTCATAGCTCTC---TTCCATTTTGAACCGAGGTAAGTGTAAATCGACACATGTCT---CTCTCATATTCTGCAAACTTGTCCATTCCATCAATTTCTCAGCAGTGAGTTTCTCTTCAAG 
s panTro1.chr17  56298740 400 +  73346066 GGGATGAGAATCTGCCATAGAAGAGGATGCT-GTTGGTCTTATTTTGCCTTATGAAGAATAGGAAAGGGTGATTACAATGGAACTCTT--CATTAGTTGAAGGAGAT-GAT---------AATTCGACT-------ACTACTACAGCGGTGGCAGCTGCAGCTTCCGCTCCCTCCTCAGTGACCTCCACAAAGGCCTTGTGTAGGACTTTAGATACCGAGAGACCGCGGCTCCCAGTCATGCCT-------------------------------------------------------------------------------------GAGAGGTCTGCATCCC---CATTGAAGATATTCACCATTCCCATGGTTCTCAACGTGTCCTTGAGGTCATAGCTCTC---TTCCATTTTGAACCGAGGTAAGTGTAAATCGACATGTGTCT---GTCTCATATTCTGCAAACTTGTCCATTCCATCAATTTCTCAGCAGTGAGTTTCTCTTCAAG 
s mm5.chr1      106995544 391 + 195203927 GGGAAGAGATTGTGCCAAAGAAGAGGATGCT-GTTGGTCTTACTGTGCTTGACCAAT---------GGATGATCACAATAGAAATCTT--CTGTAATCTGTAAAGATAAAT---------TATGGGATT-----------TTATCCCCGTGGTAGCAGCAGCTTCTGTTCCCTCTTCATTTACCTCCACAAAGGACTTGTGTAAAACTTTAGACACCACAAGACCTTGAGTGCTGTTCATGCCA-------------------------------------------------------------------------------------GAGAAGTCAGCCTTCTGTGGATCAAAGGCGCCAACCATCCCCATGTGTTTCAATGGAACTGAGAGGTCATACTTCTC---TTCCACTTTGAACCGAGGCAAAGATAAATACAACTCGGTCA---TATGCATATTTTCTGCTCTTGTCCATTCTAGTAACTTTTCAGTAGAGAGTTGTTCTTCAAG 
s rn3.chr13      13306382 400 + 111348958 GAGAAGACATTCTGCCAAAGAAGAGGATGCT-GTTGGTAGCATTGTGCTTGATGAGGAATAAGAAAGGGTGATCACAATTGAAGTCTT--CGGTTATCTGTGCTGAT-GTT---------AAACTGACT----------TCTACCCCCGTGGCAGCAGCAGCTTCTGTCCCCTCTTCATTTACCTCCACAAAGGACTTGTGTAAAACTTTAGACACCATTAGACCTTGAGTGCTGCTCATGCCT-------------------------------------------------------------------------------------GAGAAGTCAGCCTTCTTTGAGTCAAAGGCGTCCACCATCCCCATGTGCTGCAACGGACCTGGGAGGTCATACTTCTC---TTCCACTTTGAACCGTGGCAAAGACAAATACAAGTCGATCA---TGTTCATGTTCTCTGCTCTTGTCCACTCTAGTAACTTGTCAGCAGTGAGCTGTTCTTCAAG 
s canFam1.chr1  108539814 397 - 124897793 GGGAAGAGACTCTGCCCAAGAAGAGGATGCT-GTTGGTCTTATTGTGCTTGATGAAGAACAGGAAAGGGTGATCGCAATGAAA-----------AGGATAGATTGGT-GCT---------GATTTGGCA----ATAACTTCTACGTCTGTGGAGGCTGCAGCCTCCGTGCCCTCTTCGGTGACCTCCACAAAGGACTTGTGCCTGACTTTAGACACCACAAGATCCTGCCTCCCTGTCATGCCT-------------------------------------------------------------------------------------GAGAAGTTGGCCCTCTTTGTGTTGAAGGCATCCACCATTCCCAGGGCTTTCAGCGTGGCCTTGAGCTCATAACTCTC---TTCTACTTTGAACCGGGGTAAGTATAAATCCACCTGCCCAT---TGCTCATATTCTGTGAGCTCGTCCACTCTATTAGGTTCTCAGCAGTGAGTTGATCTTCAAG 
s galGal2.chr2   67392038 400 + 147590765 GAGAGCAATATCTGCCACAGAACAAAATACT-GGAAGTTTTGTTGTGCCGGATGAAGAAGAGGAAGGGATGATCGGCAGTGAA------------GTCGGGAACGAT-CAT---------AGCACAACGGAGCACCATCACTCCTGCTGTGGCAGCTGCTGCTTCAGTGCCTTCTTCGTTGACCTCCACGAAGGACTTGTGAACCACTTCAGAGAGCACAAGCTCGTTACCAGAGGAGATTCCT-------------------------------------------------------------------------------------GAGAAGTTCGCCATCCGTAAGTCAAACGCATCACGCATTCCCATGTTGCTCAGGATGGGTTTCAGATCATAATTTTC---TTCCAGTTTAAATCTGGGTAAAGACAGCCTCACTTCTGTAC---TGTCCATCATTTCAGGATTGATCCAATCCATCAGCTTCTCGTATGTAAGTTCTCTTTCCAG 
s fr1.chrUn      39424680 486 - 349519338 GAGAGCAATATCTACCAGCAAACAGAATGTTCCTTGGAGGGGTTGTGTCTGATGAAGAAGAGGAAAGGATGGTCTGCATAGAA-----------ATTCTGAGGGAAT-ACTGCACAGTGCAAAGTGAAG----------ACAACACCAGTGGCAGCAGCAGCCTCAGTTCCCTCCTCATTGACTTCCACAAAAGCTTTGTGAATCACTTCTGACAGGACCAGGTCATTGGCTGGAGACATGCCTGTCAGTCAGAGGGAAAGAGAATATTTCCCATTAATATGATGGCTTGTCTCTTCTGAAAAGGCTCTTTGGAGAAAGTCTCCTACCAGAGAAGTCGCTCGCGGCTACATCAAAGGCATCCACCATGCCCATGCTGACCAGGATGTTCTTCATGTTACATTTCTC---CTCCATCTTGAACCGTGGCAGACCCACCTGGACTTCGACTA---CATTCATCATGTCTGGACGAGTCCACTCCATGAAGTTGTCATAGGTCAGCAGCTTCTCCAG 
s danRer1.chr20  11135892 406 +  31913010 GGGCTCTGAATCTGCCCAGAAAAAGGATGCT-GTTAGTGGGGTTGTGTCTGATGAAGAACATGAAGGGATGATCGGCTATGAAATCATGAAATGCACCTTGACAAGC-ACT---------GATTGGTAA---------TAACAATGCAGTTGCTGCTGCTGCTTCAGTTCCTTCCTCATTGACCTCAACAAAAGCCTTGTGAATCACTGCTGAAAGAAAGAGACCACCATTACTGCTCATGCCT-------------------------------------------------------------------------------------GTCAGATCAGCCTTGGTTTCCTGGAACACAGAGCTCATGCCCATCTTTTCCAGTGTTTCTGATAG---ACAGCTCTCAATCTCCAACTTGAACTTTGGCAGACGGACAATGATCTTTCTCCATGTGTCCATTTTGCCTCTACTGGTCCAGTCAAGCAGCTTTTGGAGGTTCAACTCGCTCTCCAG 

a score=170132.0
s hg17.chr18     59600586 168 +  76117153 ATGGCCTCCCTTGCTGCAGCAAATGCAGAGTTTTGCTTCAACCTGTTCAGAGAGATGGATGACAATCAAGGAAAT------GGAAATGTGTTCTTTTCCTCTCTGAGCCTCTTCGCTGCCCTGGCCCTGGTCCGCTTGGGCGCTCAAGATGACTCCCTCTCTCAGATTGATAAG 
s panTro1.chr17  56457248 168 +  73346066 ATGGCCTCCCTTGCTGCAGCAAATGCAGAGTTTTGCTTCAACCTGTTCAGAGAGATGGATGACAATCAAGGAAAT------GGAAATGTGTTCTTTTCCTCTCTGAGCCTCTTCGCTGCCCTGGCCCTGGTCCGCTTGGGCGCTCAAGATGACTCTCTCTCTCAGATTGATAAG 
s mm5.chr1      107433492 168 + 195203927 ATGGCCTCCCTTGCTGCAGCAAATGCAGAATTTGGCTTCGACTTATTCAGAGAGATGGATAGTAGCCAAGGAAAT------GGAAATGTATTCTTCTCTTCCCTGAGCATCTTCACTGCCCTGACCCTAATCCGTCTGGGTGCTCGAGGTGACTGTGCACGTCAGATTGACAAG 
s rn3.chr13      13464817 168 + 111348958 ATGGCCTCCCTTGCTGCAGCAAATGCAGAATTTGGCTTCGACTTATTCAGAGAGATGGATAGTAGTCAAGGAAAC------GGAAATGTATTCTTCTCTTCCCTGAGCATCTTCACTGCCCTGAGCCTAATCCGTTTGGGTGCTCGAGGTGACTGTGCACGTCAGATTGACAAG 
s canFam1.chr1  108653495 168 - 124897793 ATGGCCTCCCTTGCTGCAGCAAATGCAGAGTTTTGCTTCAATCTGTTCAGAGAGATGGATAACAATCAAGGAAGT------GAAAATGTGTTCTTTTCTTCCCTGAGCATCTTCACTGCCTTGGCCCTGGTCCGTTTGGGCGCACGGGGTGATTGTGTTTCCCAGATTGATAAG 
s danRer1.chrNA  84211897 168 + 390413307 ATGGAGTCTCTGTCTGCAGCAAACACACAGTTTTCCCTCAACCTGTTCAAGAAGAT------CAGCGGAGGAAACGCATCAGGAAATGTGTTTTATTCTCCTGTCAGCATCTCCTCGGCTCTGGCCATGGTGTCGCTCGGTGCCAAAGGAAACACCGCAGATCAGATGTTTAAG 

a score=40916.0
s hg17.chr19        59068595 56 +  63811651 ATGCCAGTGACGGTAACCCGCACCAC----------CATCACAACCACCACGACGTCATCTTCGGG 
s panTro1.chr20     56482145 56 +  61571712 ATGCCAGTGACGGTAACCCGCACCAC----------CATCACAACCACCACGACGTCATCTTCGGG 
s mm5.chrUn_random  23451477 45 - 102265694 ATGCCGGTAACAGTAACTCGTACAAC----------CATCACG---ACTACAACGTCA-------- 
s rn3.chr1         203863650 45 - 268121971 ATGCCGGTCACAGTCACCCGTACAAC----------CATCACA---ACTACATCATCA-------- 
s canFam1.chr1      18886888 56 - 124897793 ATGCCTGTGACGGTGACCCGCACGAC----------CATCACAACCACCACGTCGTCATCCTCAGG 
s danRer1.chr2       9429255 61 -  32943701 ACGTCAAACCAAAGTACTCCCATTACTCCTGTCTGACATCACAGTCCCTGTAAC-TCTCCTC---- 

a score=19097.0
s hg17.chr19        59068651 29 +  63811651 CCTGGGGTCCC-CCATGATCGTGGGGTCCC 
s panTro1.chr20     56482201 29 +  61571712 CCTGGGGTCCC-CCACGATCGTGGGGTCCC 
s mm5.chrUn_random  23451522 22 - 102265694 -------TCCT-CCACCACTGTGGGGTCCG 
s rn3.chr1         203863695 22 - 268121971 -------TCCT-CCACCACTGTGGGGTCCG 
s canFam1.chr1      18886944 29 - 124897793 CCTGGGCTCCC-CAACCATCGTGGGGTCCC 
s fr1.chrUn        129654883 29 + 349519338 CCTGCGATTTC-CCGCCATGCCGGTGTTCA 
s danRer1.chr2       9429316 30 -  32943701 TCTGTGATCCCATCATGGCAGTGGTGTTGC 

a score=0.0
s hg17.chr19 59068680 4 + 63811651 CTCG 

a score=2300.0
s hg17.chr19        59068680 4 +  63811651 C--TCG 
s panTro1.chr20     56482230 4 +  61571712 C--TCG 
s mm5.chrUn_random  23451544 4 - 102265694 C--TCG 
s rn3.chr1         203863717 4 - 268121971 C--CCG 
s canFam1.chr1      18886973 4 - 124897793 C--TCG 
s fr1.chrUn        129654912 6 + 349519338 CGGTCA 

a score=66381.0
s hg17.chr19        59068684 64 +  63811651 GGCCCTGACACAGCCCCTGGGTCTCCTTCGCCTGCTGCAGC--TGGTGTCTACCTGCGTGGCCTTC 
s panTro1.chr20     56482234 64 +  61571712 GGCCCTGACACAGCCCCTGGGTCTCCTTCGCCTGCTGCAGC--TGGTGTCTACCTGCGTGGCCTTC 
s mm5.chrUn_random  23451548 64 - 102265694 GGCGCTGACCCAGCCGCTGGGCCTCCTCCGCCTCCTGCAGC--TAATATCCACCTGTGTGGCTTTC 
s rn3.chr1         203863721 64 - 268121971 GGCGCTGACCCAGCCCCTGGGCCTCCTCCGCCTCCTGCAGC--TAGTATCCACCTGTGTGGCTTTC 
s canFam1.chr1      18886977 64 - 124897793 GGCGCTGACCCAGCCCCTGGGCCTCCTCCGTCTGCTGCAGC--TGCTGTCCACCTGTGTGGCCTTC 
s galGal2.chr18      4859021 64 +   8919268 GGCTGTGACATCTCCAGTGGGAATAGTTCGTTTGCTGCAGA--TGATGTTTGGATGCACCACGTTC 
s fr1.chrUn        129654918 59 + 349519338 TGCTCTCCCAGGTCTTCTGGGT-------GCGTTTAGCAGCTTTGTTGTTCACCTGTGTGGCCTTC 
s danRer1.chr2       9429346 59 -  32943701 GTTCCTCACCTCTCCTGTGGACCCGAGTGGCTGCCA-------TGGTTTTCGCCTGCGTGGCCTTC 

a score=20765.0
s hg17.chr19        59068748 35 +  63811651 TCGCTGGTGG-C---TAGCGTGGGCGCCTGGACGGGGTC 
s panTro1.chr20     56482298 35 +  61571712 TCGCTGGTGG-C---TAGCGTGGACGCCTGGACGGGGTC 
s mm5.chrUn_random  23451612 35 - 102265694 TCGCTGGTGG-C---CAGTGTGGGTGCCTGGACAGGGCC 
s rn3.chr1         203863785 35 - 268121971 TCACTGGTGG-C---CAGTGTGGGTGCTTGGACAGGGCC 
s canFam1.chr1      18887041 35 - 124897793 TCCCTGGTGG-C---CAGTGTGGGTGCTTGGACCGGGGC 
s galGal2.chr18      4859085 36 +   8919268 AGCCTGGTGGCC---CACCAGGGGGGATTCAGCGCAGCA 
s fr1.chrUn        129654977 35 + 349519338 AGCTTGGCAG-CGCACGGCGCCAACGTCC--ACGGGGG- 

a score=827754.0
s hg17.chr19        59068783 773 +  63811651 CATGGGCAACTGGTCCATGTTCACCTGGTGCTTCTGCTTCTCCGTGACCCTGATCATCCTCATCGTGGAGCTGTGCGGGCTCCAGGCCCGCTTCCCCCTGTCTTGGCGCAACTTCCCCATCACCTTCGCC-TGCTATGCGGCCCTCTTCTGCCTCTCGGCCTCCATCATCTACCCCACCACCTATGTCCAGTTC-----C--------TGTCCCACGGCCGTTCGCGG------GACCACGCCATCGCCGCCACCTTCTTCTCCTGCATCGCGTGTGTGGCTTACGCCACCGAAGTGGCCTGGACCCGGGCCCGGCCCGGCGAGATCACTGGCTATATGGCCACCGTACCCGGGCTGCTGAAGGTGCTGGAGACCTTCGTTGCCTGCATCATCTTC---GCGTTCATCAGCGACCCCAACCTGTACCAGCACCAGCCGGCCCTGGAGTGGTGCGTGGCGGTGTACGCCATCTGCTTCATCCTAGCGGCCATCGCCATCCTGCTGAACCTGGGGGAGTGCACCAACGTGCTACCCATCCCCTTCCCCAGCTTCCTGTCGGGGCTGGCCTTGCTGTCTGTCCTCCTCTATGCCACCGCCCTTGTTCTCTGGCCCCTCTACCAGTTCGATGAGAAGTATGGCGGCCAGCCTCGGCGCTCGAGAGATGTAAGCTGCAGCCGCAGC------------CATGCCTACTACGTGTGTGCCTGGGACCGCCGACTGGCTGTGGCCATCCTGACGGCCATCAACCTACTGGCGTATGTGGCTGACCTGGTGCACTCT--GCCCACCTGGTTTTTGT-CA 
s panTro1.chr20     56482333 773 +  61571712 CATGGGCAACTGGTCCATGTTCACCTGGTGCTTCTGCTTCTCCGTGACCCTGATCATCCTCATCGTGGAGCTGTGCGGGCTCCAGGCCCGCTTCCCCCTGTCTTGGCGCAACTTCCCCATCACCTTCGCC-TGCTACGCGGCCCTCTTCTGCCTCTCGGCCTCCATCATCTACCCCACCACCTATGTCCAGTTC-----C--------TGCCCCACGGTCGTTCGCGG------GACCACGCCATCGCCGCCACCTTCTTCTCCTGCATCGCGTGTGTGGCTTACGCCACCGAAGTGGCCTGGACCCGGGCCCGGCCCGGCGAGATCACTGGCTATATGGCCACCGTACCCGGGCTGCTGAAGGTGCTGGAGACCTTCGTGGCCTGCATCATCTTC---GCGTTCATCAGCGACCCCAACCTGTACCAGCACCAGCCGGCCCTGGAGTGGTGCGTGGCGGTGTACGCCATCTGCTTCATCCTAGCGGCCATCGCCATCCTGCTGAACCTGGGGGAGTGCACCAACGTGCTACCCATCCCCTTCCCCAGCTTCCTGTCGGGGCTGGCCTTGCTGTCTGTCCTCCTCTATGCCACTGCCCTTGTTCTCTGGCCCCTCTACCAGTTCGATGAGAAGTATGGCGGCCAGCCTCGGCGCTCGAGAGATGTAAGCTGCAGCCGCAGC------------CATGCCTACTACGTGTGTGCCTGGGACCGCCGACTGGCTGTGGCCATCCTGACGGCCATCAACCTACTGGCGTATGTGGCTGACCTGGTGCACTCT--GCCCACCTGGTTTTTGT-CA 
s mm5.chrUn_random  23451647 785 - 102265694 CATGGGTAACTGGGCCATGTTCACCTGGTGTTTCTGCTTTGCTGTTACCCTCATCATCCTGATTGTGGAGTTAGGTGGACTCCAGGCCCACTTCCCCCTGTCATGGCGAAACTTCCCCATCACCTTTGCC-TGCTACGCGGCCCTCTTCTGCCTGTCGTCTTCCATCATCTATCCCACCACCTATGTGCAGTTC-----C--------TAGCTCATGGACGTACCCGG------GACCATGCCATCGCTGCCACCACTTTCTCCTGCGTTGCCTGTTTGGCGTATGCCACTGAAGTGGCCTGGACCCGTGCAAGGCCCGGTGAGATCACTGGCTATATGGCTACCGTGCCAGGGCTGCTCAAAGTTTTTGAGACCTTCGTAGCCTGTATCATCTTT---GCCTTCATCAGTGAGCCGCTCCTGTATAATCAGAAGCCAGCCCTGGAGTGGTGTGTGGCAGTCTATGCCATCTGCTTCATACTAGCAGGGGTGACCATCCTGCTCAACCTGGGGGATTGTACCAACGTGTTGCCCATCCCTTTCCCCACCTTCCTCTCAGGCTTGGCCTTACTCTCTGTTCTCTTTTACGCCACTGCCATCGTCCTCTGGCCCCTCTACCAATTTGATCAGAGATATCAGGGCCAACCCCGCCGTTCAATGGATCCAAGCTGCACTCGTAGTATTAGTTATATACAACCCAACACGGTGTGTTTCTGGGACCGACGACTGGCGGTGTCCATCCTGACAGGTATCAACCTGCTGGCATATGTGTCTGATCTGGTGTACTCC--ACTCGTCTGGTGTTCGT-CA 
s rn3.chr1         203863820 779 - 268121971 CATGGGTAACTGGGCCATGTTCACCTGGTGTTTCTGCTTTGCTGTTACCCTCATCATCCTGATTGTGGAGTTAGGTGGATTCCAGGCCCGCTTCCCCCTGTCATGGCGAAACTTCCCTATCACCTTCGCC-TGTTACGCGGCCCTCTTCTGCCTGTCGTCTTCCATCATCTATCCCACCACCTACGTGCAGTTC-----C--------TACCTCACGGACGTTCCCGG------GACCACGCCATCGCTGCCACCACCTTCTCCTGCGTTGCCTGTTTGGCGTATGCTACTGAAGTGGCCTGGACTCGTGCAAGGCCTGGTGAGATCACTGGCTACATGGCTACCGTGCCAGGGCTGCTCAAAGTGTTCGAGACCTTCGTAGCCTGCATCATCTTT---GCCTTCATCAGTGAGCCGAGCCTGTACCAGCAAAGGCCGGCCCTGGAATGGTGTGTGGCAGTCTATGCCATCTGCTTCATCCTAGCAGCAGTGACCGTCCTACTCAACCTGGGGGATTGTACCAACATGCTGCCCATCCCTTTCCCTACCTTCCTGTCAGGCCTGGCCTTACTGTCTGTGCTCCTTTACGCCACTGCCATCGTCCTCTGGCCCCTCTACCAATTTGATCAGAGGTATAACAGCCAACCCCGCCGTTCAATGGATCCAAGCTGCTCTCGTAGT------TATGTACAACCCAATGAAGTGTGTAACTGGGACCGACGGCTGGCGGTGTCCATCCTGACAGGTATCAACCTGCTGGCATATGTGTCTGATCTGGTGTATTCC--ACCCGTCTGGTGTTCGT-CA 
s canFam1.chr1      18887076 773 - 124897793 CATGGGCAACTGGTCCATGTTCACATGGTGCTTCTGCTTCGCTGTGACCCTCATCATCCTAATAGTCGAGTTAGGTGGCCTCCAGTCCCGCTTCCCCCTGTCCTGGAGAAACTTCCCCATCACCTACGCC-TGCTACGCTGCCCTCTTCTGCCTGTCGGCCTCCATCATCTACCCCACCACCTACGTTCAGTTC-----C--------TGTCTCATGGCCGCTCCCGG------GACCATGCCATCGCCGCCACTGCCTTCTCCTGCATCGCTTGTGTGGCTTATGCCACCGAAGTGGCCTGGACCCGGGCCCGTCCCGGAGAGATCACCGGCTACATGGCCACTGTGCCGGGCCTGCTCAAGGTGCTGGAGACCTTTGTGGCCTGCATCATCTTC---GCCTTCATCAGCAACCCCTCCCTGTACCAGCACCAGCCGGCCCTGGAGTGGTGTGTGGCCGTCTACTCCATCTGTTTCATCCTGGCGGCTGTGGCCATCCTACTGAACCTGGGGGACTGCACCAACATGCTGCCCATCTCCTTCCCCAGTTTCCTGTCGGGCCTGGCCCTGCTCTCCGTCCTGCTGTATGCCACGGCTCTGGTTCTCTGGCCGCTCTACCAGTTCAACGAGAAGTATGGTGGCCAGCCCCGTCGGTCGAGGGATGTTAGCTGCGCCGACAGG------------CACACCTACTACGTGTGTACCTGGGACCGCCGCCTGGCTGTGGCCATCCTGACAGCCATCAACCTGCTGGCTTACGTGGCTGACCTGGTGTACTCG--GCCCGCCTGGTTTTTGT-TA 
s galGal2.chr18      4859121 763 +   8919268 TAC-GGCACTTTCTGCATGTTCGTCTGGACCTTCTGCTTTGCTGTCACTGTCTTTATCATTACCTGCGAGTTCACGCACCTGCACAGCTGTCTGAGCATCTCCTGGGGAAACTTCACAGCTGCGTTCGCCATGCT-CGCCACGCTCATGTCGGTCACAGCGGCGGTGATCTACCCGCTCTACTTCGTGCAGCTCGGCTGC--------TACCCCATCACC-TGCGAGG-TGAGAGACTTCCGCATAGCGGCCAGCGTCTTTGCCGGCCTCGTGTTCGTTGTGTATGGCGCGGAGGTGTTCTTGACCAGAGCCAAACCAGGACAGGTCACCAGCTACATGGCCACTGTCTCTGGGCTCCTGAAGATCGTACAGGCCTTTGTGGCTTGCATCATCTTTGGGGCGCTGGTGAACGA---CAGCCAGTATAGCAAATACGTGGCCACACAGTGGTGCGTGGCCGTCTACAGCTTCTGCTTTATGGTCACGGTGGTGGTGGTCGCCTTCAGTGTCACTGGTAAGACCGCCCAGCTGTGCTTCCCCTTCGAGCGCTCTGTGGTCGTCTACACTTTCGGGGCCGTCCTGCTGTACGTGAGCGCGGCCGTCATCTGGCCGGTGTTCTGCTTTGACAGCAAGTACGGCTCCCCGCAGCGCC---------------------CCAGCGCC------------TGTGCCAAGGGCAGGTGCCCCTGGGACAGCCAGCTGGTGGTGGCCATCTTCACCTACGTCAACCTGCTGCTCTACGTGGTAGACCTGGCGTACTCCCAGCGCATCCGCTTCGTATCCC 
s fr1.chrUn        129655012 728 + 349519338 CATGGCTGACTGGTGCATCTTCTGCTGGGTGTTCAGCTTCACCTGCACTCTGCTGGTCCTGCTGGTGGAGCAGTTTGGCCTTCAGGCCCGCATCCCAGTCTCCTGGTCCAACTTCCCCATCACCGTGGCC-TGCTACGCCGCCCTCCTCTGCCTGTCTGCTTCCGTCATCTTTCCCCTGTTCTTCCTGAAGGAG-----CAGGGGTGGTGGTACGCCGACGAACGCAG--------CTTCCGCATCACCTCCACGATCTTCTCCTGCCTGGCGGCGGTGGCCTACATCTGCGAGGTGAGCCTGACCAAGGCGAAACCCGGACAGGTGGCGGGATACATGGCCACGGTCCCGGGCCTCCTGAAGGTGTGCCAGACCGTTGTGGCCTGCATCATCTTC---ATCCTGATCAGCAACCCCGTCTCCTACAGCCACCACGCGGCGCTGGAGTGGTGCATGGCCGTTTACTGCATCTGCTTCATCGTCTCCATGGTGGTGGTGATCCTGTGCGTGGGCGAATGCACCGGGTTTCTCCCGGTCCCCTTCTCCCAGTTCCTGTCAGCGTACGGCCTCCTGGCCTTCCTCATGTACTTGTCAGCTGTCATCGTCTGGCCCATTTTCACGTTTGACAAAAAGTA------------CCGGCGTGGAGGCGATAT--------GTCAAAGC-----------------------------------AGATCGGCG--TGGCAGTG------CTCACCGCCATCAACATGCTGCTGTACCTCGCTGACCTGGTCTACACC--GCTCACCTGGTGTTCAT-CA 
s danRer1.chr2       9429440 764 -  32943701 CACCGGCGACTGGTGCGTGTTCTGCTGGAGCTTCAGTTTCGTGGGAACTCTTCTAATCATCCTAGTGGAGATGTTTGGCCTGCAGACGCGTGCCCCAGTCTCGTGGAAGAACTTTCCCATCACGTTCGCC-TGCTACGCCTCTCTCCTCTGCCTCTCTGCGTCCATCATATTCCCCTTGTACTTCCTGAAGGGC-----T--------T---TGCTGGGCGCACTGAGATGATTAACTGCCGCATCGTGTCCACTGTATTTTCTTGCCTTGCTACTATCGCCTATTTAAGCGAGGTGAGTCTCAGTAAGGCCCGTCCAGGAGAAGTGTCCGGCTACATGGCTACCGCACCAGGGCTGCTAAAAGTGTGCGAAACCTTCATCGCCTGCATCATCTTC---GTCTTCATCAGCGAGCCCGAGTCGTACAAACAGAATGCGGCGACCCAGTGGTGTTTGGCTGTGTACTGCATCTGCTTCATTTTATCGGCAGGCATCATTGTGATGTGTGTTGGCGAATGCACAGGTTGCTTGCCTTTCTCCTTCGCCCGCTTCCTATCCACGTATGCCCTGCTGGCTGTGAGCATGTATCTGTCGGCCACCATCATCTGGCCCATTTATAAGTTCGACAATAAGCACGGAGGCCAGAGCCACCGACCAA------------ACATCTGCGGG------------TCCAGCATTGGACTTTGCCCGTGGGACAAACTGGTCGCCATTACTGTGCTCAGCTCGCTTAACTTCATTCTTTATCTGGCTGATCTCATTTACTCC--GCAAGGCTAGTGTTTGT-TA 

a score=10623.0
s hg17.chr19        59069556 8 +  63811651 AGGTCTAA 
s panTro1.chr20     56483106 8 +  61571712 AGGTCTAA 
s mm5.chrUn_random  23452432 8 - 102265694 AGGTCTGA 
s rn3.chr1         203864599 8 - 268121971 AGGTCTAA 
s canFam1.chr1      18887849 8 - 124897793 GGGTTTGA 
s galGal2.chr18      4859884 8 +   8919268 ACATCTGA 
s danRer1.chr2       9430204 8 -  32943701 ATGCTTAA 

a score=64200.0
s hg17.chr19    59236026 120 +  63811651 CTACACTTTCAGTGCCGCATATTCATGAGATCCTGGGGGCTCCTGGGTGGTGT-CTGAAGCTGCCTCAGACAGGGCGCTGGTGCTTAGCTCAGCATAGGTCACTCCTTGGGGG--TCTGCCGT 
s panTro1.chr20 56680126 120 +  61571712 CTACACTTTCAGTGCCGCATATTCACGAGATCCTGGGGGCTCCTGGGTGGTGT-CTGAAGCTGCCTCAGACAGGGCGCTGGTGCTTAGCTCAGCATAGGTCACTCCTTGGGGG--TCTGCCGT 
s canFam1.chr1  18994847 123 - 124897793 CTTCACCTGCCGCACTGCACATTCACAAGATCCTGGGGACTCCTCGGTGGGGCACAGAAGCTGCCTTAGGTGGTGCCTTGGGGTTTAGATCAGCATGGCTCACTCCCTGGGGGGTCTTTCAGT 

a score=41374.0
s hg17.chr19       59297998 10 +  63811651 ATGGCTGCGA 
s mm5.chr7_random  31672903 10 +  46185828 ATGGCCGGGA 
s rn3.chr1        204132123 10 - 268121971 ATGGCTGCTA 
s canFam1.chr1     19108689 10 - 124897793 ATGGCCGGGA 

a score=139739.0
s hg17.chr19       59302168 120 +  63811651 TCAGTCAGAGGCTGGGCTGGCCAGGGTCGGGTAGGGCAGCAGTTTGTCTGGACCCCGAGAAACCCAACTGGAATCCAGGGCCTCATCTGCTTCAAAGCCAAAGTCTTCCTCAACCTTAAT 
s panTro1.chr20    56743920 120 +  61571712 TCAGTCAGAGGCTGGGCTGGCCAGGGTCGGGTAGGGCAGCAGTTTGTCTGGACCCCGAGAAACCCAACTGGAATCCAGGGCCTCATCTGCTTCAAAGCCAAAGTCTTCCTCAACCTTAAT 
s mm5.chr7_random  31675860 120 +  46185828 TTAGTCAAAGGGTGGGCTGGCCAGGGTAGGGTAGGGTAGCAATTTGTCTGGCTCTCGGGAAACCCAACTTGAATCCAAGGCCTCATCTGCTTCAAAGCCAAAGTCTTCCTCAACCTTAAT 
s rn3.chr1        204134929 120 - 268121971 TTAGTCAAAGGGTGGGCTAGCTAGGGTAGGGTAGGGTAGCAATTTGTCTGGCCCTCGGGAAACCCAACTTGAATCCAAGGCCTCATCTGCTTCAAAGCCAAAGTCTTCCTCGACCTTAAT 
s canFam1.chr1     19111006 120 - 124897793 TCAGTCAAATGGGGGACTGGCTAGGGTGGGGTAGGGCAGCAGTTTGTCTGGCCCCCGAGAAACCCAACTGGAGTCCAGGGCCTCATCTGCTTCGAAGCCAAAGTCTTCCTCGACCTTAAT 

a score=46787.0
s hg17.chr2     118288583 7 + 243018229 ATGTCAC 
s panTro1.chr13   4310009 7 + 134309081 ATGTCTC 
s mm5.chr1       73854532 7 - 195203927 ATGTCGC 
s rn3.chr13      77744300 7 - 111348958 ATGTCGC 
s canFam1.chr19  21837737 7 -  56914383 ATGTCCC 

a score=62416.0
s hg17.chr2     118288590 78 + 243018229 ACCTGCCGATGAAACTCCTGCGTAAGAAGATCGAGAAGCGGAACCTCAAATTGCGGCAGCGGAACCTAAAGTTTCAGG 
s panTro1.chr13   4310016 78 + 134309081 ACCTGCCGATGAAACTCCTGCGTAAGAAGATCGAGAAGCGGAACCTCAAATTGCGGCAGCGGAACCTAAAGTTGCAGG 
s mm5.chr1       73854539 78 - 195203927 AGTTACAGATGAAACTCCTGCGCAGGAAGATCGAGAAGCGGAATGCCAAGCTGCGGCAGCGAAACCTGAAGCTGCAAG 
s rn3.chr13      77744307 78 - 111348958 AGTTACAGATGAAACTCCTGCGCAAGAAGATCGAAAAGCGGAACGCCAAGCTGCGGCAACGGAACCTGAAGCTGCAAG 
s canFam1.chr19  21837744 78 -  56914383 ATCTACCCATGAAACTCCTGCGCAAGAAGATAGAGAAACGGAATCTCAAGTTGCGCCAGCGAAACCTGAAGCTCCGGG 
s galGal2.chr7    7730657 78 -  37338262 ACCTGCCCATGCGGCTGCTCCGCAAGAAGATCCACAAGAGGAACCTGAAGCTGCGGCAGCGCAACCTGAAGCTGCGGG 

a score=141298.0
s hg17.chr2     118394148 8 + 243018229 TCAGGAGG 
s panTro1.chr13   4415862 8 + 134309081 TCAGGAGG 
s mm5.chr1       73920237 8 - 195203927 TCAGGAGG 
s rn3.chr13      77811845 8 - 111348958 TCAGGAGG 
s canFam1.chr19  21899390 8 -  56914383 TCAGGAGG 
s galGal2.chr7    7752959 8 -  37338262 TCAGGAAG 

a score=65234.0
s hg17.chr2     118394156 46 + 243018229 CCTTCGCTTTCACCTTGGACAGCAGCATCTCGTTCTTGCGGCCCTC 
s panTro1.chr13   4415870 46 + 134309081 CCTTCGCTTTCACCTTGGACAGCAGCATCTCATTCTTGCGGCCCTC 
s mm5.chr1       73920245 46 - 195203927 CCTTGGCTTTGATCTTAGATAGTAATAGCTCATTCTTTCGGCCCTC 
s rn3.chr13      77811853 46 - 111348958 CCTTGGCTTTGATCTTAGACAGTAATAGCTCATTCTTTCGGCCCTC 
s canFam1.chr19  21899398 46 -  56914383 CCTTGGCTTTCACCTTGGACAGCAGCACCTCATTCTTGCGGCCCTC 
s galGal2.chr7    7752967 46 -  37338262 AACTAGCTTTCAGCTTGGACAGCAGCATTTCGTTCTTACGACATTC 
s danRer1.chr9    4164500 46 -  28422069 CTTTAGCCCTCAGTTTAGACAACAGCATCTCATTCTTACGGCACTC 

a score=68843.0
s hg17.chr2     220190202 40 + 243018229 ATGCTCAAAGCGGTGATCCTGATTGGAGGCCCTCAAAAGG 
s panTro1.chr13 110354917 40 + 134309081 ATGCTCAAAGCGGTGATCCTGATTGGAGGCCCTCAAAAGG 
s mm5.chr1       75883503 40 + 195203927 ATGCTCAAAGCTGTGATTCTCATTGGAGGCCCCCAGAAGG 
s rn3.chr9       74861356 40 + 113649943 ATGCTCAAAGCTGTGATCCTCATTGGAGGACCCCAGAAGG 
s canFam1.chr37  28991402 40 +  33897405 ATGCTCAAAGCTGTGATCCTGATTGGAGGCCCTCAAAAGG 
s fr1.chrUn     298594715 40 - 349519338 ATGTTGAAGGCAGTTATTTTAATCGGAGGCCCACAGAAGG 
s danRer1.chrUn 200789632 40 + 367113659 ATGCTGAAGGCTGTCATTCTTATCGGAGGCCCCCAAAAAG 

a score=2052.0
s hg17.chr2     220229609 2 + 243018229 TC 
s panTro1.chr13 110394704 2 + 134309081 TC 
s mm5.chr1       75920524 2 + 195203927 TT 
s rn3.chr9       74897410 2 + 113649943 TT 
s canFam1.chr37  29028801 2 +  33897405 TC 
s galGal2.chr7   14430359 2 -  37338262 TC 
s fr1.chrUn     298724631 2 - 349519338 TC 
s danRer1.chrUn 144716830 2 + 367113659 TT 

a score=1675466.0
s hg17.chr2     220229611 1258 + 243018229 AGGTGCTGTTGCCCTGCTCCTGTTCAAAGAGTAGCATGGCCAGCTGGGTTCGGGAGCCGAGGCCCTCAAGCACGCTCTGGAGGCAGCGGTGGTACAGGTCCTCACTGAGCCTCGCGCTGCACGTCTGGGCCCGGTAGCGCTGCAGCAGCGCCGGCTCCACCGCCCGCAGCACATGCAGACTGGAGAAGTGGAGGAACAGCTCGTACACATCCAGGCTCTCCAGCAGCTCCTCTTCTTGTTCTGAGGCTGCCGCCAGGCGCCCACGGGCTGCCACATAGTCGGAGTTGTAGAAGCAGGCCTCGCTGGCTGCCTGGCGATCAAAGCGGCCAGTGTCACGGCCCAGCTCTGGGGGCCCAGG----CCCTTGTGGTGG----------------------GGCCACAGCTGGGTGGAAGGCTTGGAAATGCATGGGAAAGAAGGCCTGCCAGCCGGAGATGGCATGCATGCGGCAGCGGTTCAGGAAGTCAGGCGTGAGCACCGTGTCTGGCCCGGCCAGCAGGAACAGTGTGTCCAGCGGGTGCTTCTTGGAGAGTAGATCCATGAGGCGCAGTGGTGAGGGTGCGGCTGTCTGCACACTGAGCCATGGCACCCGGGCACCGGGGAAACGCCGCTCCAGCTCTGCCACGTGGGCCTTGACAGGTGCGAAGACATCTGCATGGGCCACGCGCTGGGCCTGGCGCGGCTCATACAGTAGCAGCAGGGTCAGGGCTGCCGCAGCATCACCAGGCTCCAGTGCTGCAGTGGCAAAGGCCTCCAAGAAGCCAGGGGCCAGGTCACGCTCAGCCGCAGCTAGAGGCAGCAGCACAGTGAGACGTGAGGCCTCAGTGACATAGGGCACAGGCAAGATCTCCACGCGGCTCAGCGGCCGGAGCAGCTGCACTCGGCGAGTGAGGGGCCGGCGGCCTCCCTGGGGGGTCAGTGCCTCCAGCTGCAAGTCCAGCGTGTATTCCATACCCCGGGCCGGATCAAAGCGTCGGTAGCCATTCACCAGCTGCTGCTTCTGGAGCCGCAAGGCCGGGTGGTAGCGGCGGTTCAGCTCCTCTAGAGCTGTCCCCAGAACATCGGCCACATCAGCCCGGTCAGCCCCACGCAGTGGGCAGCGGGGTGAGCCATCGGCGCAGGAGAAAGCGTGCTGCTCCGTGAAGTAGTCCCAGCGCAGCACCTCAAAGCGGGAGGCCGGGCGGGATGGTGCTGGAATACCCACGGGCCAAGCAGCTGCCTGGTCCCCATCAACGGCCAGATGGCTGGTATTCTGGATCTCCCA 
s panTro1.chr13 110394706 1258 + 134309081 AGGTGCTGTTGCCCTGCTCCTGTTCAAAGAGTAGCATGGCCAGCTGGGTTCGGGAGCCGAGGCCCTCAAGCACGCTCTGGCGGCAGCGGTGGTACAGGTCCTCACTGAGCCTCGCGCTGCACGTCTGGGCCCGGTAGCGCTGCAGCAGCGCCGGCTCCACCGCCCGCAGCACATGCAGACTGGAGAAGTGGAGGAACAGCTCGTACACATCCAGGCTCTCCAGCAGCTCCTCTTCTTGTTCTGAGGCTGCCGCCAGGCGCCCACGGGCTGCCACGTAGTCGGAGTTGTAGAAGCAGGCCTCGCTGGCTGCCTGGCGATCAAAGCGGCCAGTGTCACGGCCCAGCTCTGGGGGCCCAGG----CCCTTGTGGTGG----------------------GGCCACAGCTGGGTGGAAGGCTTGGAAATGCATGGGAAAGAAGGCCTGCCAGCCGGAGATGGCATGCATGCGGCAGCGGTTCAGGAAGTCAGGCGTGAGCACCGTGTCTGGCCCGGCCAGCAGGAACAGTGTGTCCAGCGGGTGCTTCTTGGAGAGTAGATCCATGAGGCGCAGTGGTGAGGGTGCGGCTGTCTGCACACTGAGCCATGGCACCCGGGCACCGGGGAAACGCCGCTCCAGCTCTGCCACGTGGGCCTTGACAGGTGCGAAGACATCTGCGTGGGCCGCGCGCTGGGCCTGGCGCGGCTCATACAGTAGCAGCAGGGTCAGGGCTGCCGCAGCATCACCAGGCTCCAGTGCTGCAGTGGCAAAGGCCTCCAAGAAGCCAGGGGCCAGGTCACGCTCAGCCGCAGCTAGAGGCAGCAGCACAGTGAGACGTGAGGCCTCAGTGACATAGGGCACAGGCAAGATCTCCACGCGGCTCAGTGGCCGGAGCAGCTGCACTCGGCGAGTGAGGGGCCGGCGGCCTCCCTGGGGGGTCAGTGCCTCCAGCTGCAAGTCTAGCATGTATTCCATACCCCGGGCCGGATCAAAGCGTCGGTAGCCATTCACCAGCTGCTGCTTCTGGAGCCGCAAGGCCGGGTGGTAGCGGCGGTTGAGCTCCTCTAGAGCTGTCCCCAGAACATCGGCCACATCAGCCCGGTCAGCCCCACGCAGTGGGCAGCGGGGTGAGCCATCGGCGCAAGAGAAAGCGTGCTGCTCCGTGAAGTAGTCCCAGCGCAGCACCTCAAAGCGGGAGGCCGGGCGGGATGGTGCTGGAATGCCCACGGGCCAAGCAGCTGCCCGGTCCCCATCAACGGCCAGACGGCTGGTATTCTGGATCTCCCA 
s mm5.chr1       75920526 1255 + 195203927 AGGTGCTGTTCCCCTGTTCCTGCTCAAAGAGCAGCATGGCAAGCTGGGTGCGGGAGCCAAGGCCCTCAAGTACGCTCTGGCGACAGCGGTGGTAAAGGTCTTCACTGAGCCGTGCACTGCACGGCTGGGCCCGGTAGCGCTGCAGCAAGGCTGGCTCTACTGCTCTCAGCACGTGCAAGTTGGAGAAGCGCAGAAACAACTCGTACACATCCAGGCTCTCCAGCAGCTCCTCCTCCTGCTCCGAGGCCGCCACCAGCCGGCCACGGGCCGCCACATAGTCGGAGTTGTAGAAGCATGCCTCACTGGCAGCCTGGCGATCAAAGTGACCGGTGTCACGGCCCAGCTCTGGTGGCCCAGG----GCCCTGAGGTGG----------------------AGCCACAGCAGGGTGGAAGGCCTGGAAGTGCATGGGGAAGAAGGCCTGCCAGCCAGAGATGGCATGCATGCGGCAGCGGTTCAGGAAATCAGGTGTGAGTACCGTGTCTGGCCCGGCCAGCAGGAACAGAGTGTCTAGTGGGTGCTTCTTGGACAGCAGATCCATGAGACGCAGTGGAGAGGGCGCTGCTGTCTGCACACTGAGCCAGGGCACCCGGGCACCAGGGAAACGCCGCTCTAGCTCTGCCACGTGGGCCTTGACAGGTGCGAAGACGTCTGAGTGGGCTGCCCGCTGGGCCTGGCGTGGCTCATACAGCAGCAGCAGGGTCAAGGCTGCT---GCATCACCAGGTTCCAGGGCTGCAGTGGCAAAGGCTTCTAAGAAGCCAGAAGCCAGGTCTCGTTCCGCTGCAGCCAGCGGCAGTAGCACAGTGAGCCGAGAAGCCTCGGTGACATAGGGTACAGGCAAGATCTCCACTCGGCTCAAGGGCCGAAGGAGCTGCACCCTGCGGGTGAGGGGCCAGCGGCCACCCTGGGGTGTCAGCGCTTCCAGCTGCAGGTCTAGTGTGTACTCCATGCCTCGGGCTGGATCAAAACGCCGGTAGCCGTTCACCAGCTGTTGCTTCTGGAGCTGCAGCGCTGGCTGGTAACGGCGGTTGAGCTCCTCTAAGGCTGTCCCCAGGACGTCAGCCACATCAGCCTGGTCGGCCCCACGCAACGGGCAGCGGGGAGAGCCATCGGCGCAGGAGAACGCGTATTGTTCTGTGAAGTAGTCCCAGCGCAGAACCTCAAAGCGTGAGGCAGGGCGAGACGGTGCTGGGATGCCCACTGGCCAGGCAGAGGCTCTCTCCCCATCAGCAGCCAGTCGGCTGGTATTCTGGATCTCCCA 
s rn3.chr9       74897412 1255 + 113649943 AGGTGCTGTTACCCTGTTCCTGTTCAAAGAGCAGCATGGCAAGCTGGGTGCGGGAGCCAAGGCCCTCAAGCACGCTCTGGCGACAGCGGTGATAAAGGTCCTCGCTGAGCCGAGCGCTGCATGGCTGGGCCCGGTAGCGCTGCAGCAAGGCTGGTTCCACTGCCCTCAGCACATGCAAGCTAGAGAAGCGTAGAAACAACTCATACACATCCAGGCTCTCCAGCAGCTCCTCCTCCTGCTCGGAGACTGCCACCAGCCGTCCACGGGCCGCCACATAGTCGGAGTTGTAGAAGCATGCCTCGCTGGCAGCCTGACGATCAAAGTGGCCGGTGTCACGGCCCAGTTCTGGTGGCCCAGG----GCCCTGAGGTGG----------------------AGCCACAGCAGGGTGGAAGGCCTGGAAGTGCATGGGAAAGAAGGCTTGCCAGCCCGAGATGGCGTGCATGCGGCAGCGGTTCAGGAAGTCGGGTGTGAGCACTGTGTCTGGCCCGGCCAGCAGGAACAGAGTGTCCAGCGGGTGCTTCTTGGAGAGTAGATCCATGAGGCGCAGCGGAGAGGGCGCGGATGTCTGTACACTGAGCCAGGGCACTCGGGCACCAGGGAAACGCCGCTCTAGCTCGGCCACGTGGGCTTTGACGGGTGCGAAGACATCTGCGTGGGCTGCCCGCTGGGCCTGGCGTGGCTCATACAGCAGCAGCAGGGTCAAGGCTGCG---GCATCGCCAGGTTCCAGTGCTGCAGTGGCAAAGGCTTCTAGGAAGCCAGATGCCAGGTCACACTCTGCTGCAGCCAGAGGCAGCAGCACAGTGACCCGAGAAGCCTCGGTGACATAGGGCACAGGCAAGATCTCCACTCGGCTCAAGGGCCGAAGGAGCTGTACCCTGTGGGTGAGGGGCCAGCGGCCACCCTGGGGCGTCAGCGCTTCCAGCTGCAAGTCTAGTGTGTACTCCATACCTCGGGCTGGATCAAAACGCCGGTAGCCATTCACCAGCTGTTGCTTCTGGAGCCGCAGTGCTGGCTGGTAACGGCGGTTGAGCTCCTCTAAGGCTGTTCCTAGGACATCAGCCACATCGGCCTGGTCGGCCCCACGCAGCAGGCAGCGGGGTGAGCCGTCAGCACAGGAGAAAGTGTGCTGTTCCGTGAAGTAGTCCCAGCGCAGAACCTCAAAGCGCGAGGCAGGGCGAGACGGCGCTGGAATGCCCACTGGCCAGGTAGAAGCCCTCTCCCCATCAGCAGCCAGTCTGCTGGTATTCTGGATCTCCCA 
s canFam1.chr37  29028803 1258 +  33897405 AGGTGCTGTTGCCCTGCTCCTGCTCAAAGAGCAGCATGGCCAGCTGGGTGCGGGAGCCCAGGCCCTCCAGCTCGCTCTGGCGGCAGCGGTGGTACAGGTCCTCGCTGAGCCGCGCGCTGCACGCCTGCGCCCGGTAGCGCTGCAGCAGCGCTGGTTCCACGGCGCGCAGCACGTGTAGGCCCGAGAAGCGCAGGAACAGCTCGTACACGTCCGTGCTCTCCAGCAGCTCCTCTTCCTGCTCCGAGGCCGCTGCCAGCCGTCCGCGGGCTGCCACGTAGTCGGAGTTGTAGAAGCAGGCCTCGCTGGCCGCCTGGCGGTCGAAGCGGCCCGTGTCTCGGCCCAGCTccgggggcccggg----gccctggggggg----------------------cgccacggccgggTGGAAGGCCTGGAAGTGCATGGGGAAGAAGGCCTGCCAGCCAGAGATGGCGTGCATGCGGCAGCGGTTCAGGAAGTCGGGCGTGAGCACCGTGTCGGGCCCGGCCAGCAGGAACAGCGTGTCCAGCGGGTGCTTCTTGGAGAGCAGGTCCATGAGGCGCAGCGGCGAGGGTGCAGCTGTCTGCACGCTGAGCCAGGGCACCCGGGCACCCGGGAAACGCCGCTCGAGTTCCGCCACGTGGGCCTTGACAGGCGCAAAGACATCTGCGTGGGCCGCCCGCTGGGCCTGTCGTGGCTCGTACAGGAGCAGCAGGGTCAGGGCTGCAGCCGCGTCACCCGGCTCCAGCGCCGCGGTGGCGAAGGCCTCCAGGAAGCCAGGGGCCAGGTCCCGCTCGGCCGCAGCCAGAGGCAGCAACACGGTGAGACGCGACGCCTCGGTGACGTAGGGCACAGGCAGGATCTCCACGCGGCTCAGGGGCCGCAGCAGCTGCACCCGGCGGGTGAGGGGCCGGCGGCCGCCCTGCGGGGTCAGCACCTCCAGCTGCAGGTCCAGCGTGTACTCCATGCCGCGGGCAGGATCGAAGCGCCGGTAGCCGTTGACCAGCTGCTGCTTCTCGAGCCGCAGGGCCGGGTGGTAGCGGCGGTTGAGCTCTTCCAGGGCGGCACCCAGCACGTCGGCCACGTCGGCCCGGTCGGCCCCTCGCAGCGGGCAGCGGGGCGAGCCGTCGGCGCAGGAGAAGGCGTGCTGCTCTGTGAAATAGTCCCAGCGCAGCACCTCGAAGCGAGAGGCCGGGCGGGATGGTGCGGGAATGCCCACGGGCCAGGCGGCCGCCCGCTCGCCGTCAGCTGCCAGGTGGCTGGTGTTCTGGATCTCCCA 
s galGal2.chr7   14430361 1258 -  37338262 AGGTGCTGTTCCCCTGCTCCTGCTCAAAGAGCACCATGGCCAACTGGGAGCGGGACCCAACGCCCTCCAGGCTGCTCTGCACGCAGCGGTGGTAGATCTCCTCACTGAGCCGCGGGTTGCAGGCCTGGTGCCGGTAGTGCTGCAGCAGGGCGGGCTCCACGGCCCGGAAGACGTGAAGGTTGGAGTACTTGATGAACATATCGTAGATGTCCAGGGTCTCCAGGATGTCCTCATTCTCCTGCACGTCACCCGCCATGCGGGTGCGTGCTGCCATGTAGTCAGCATTGTAGAAGCAGGCCTCATGGAAGACATCGCGGTCAAAGCGCCCTGCATCCCGCAGGAGGTCCAGTGTGGCAGGCGGTGCCTGGTTGTGG--------------------TAGGCGACGGCGGGGTTGTAGCCCTGGAAGTGGATGGGGAAGAAGACCTGCCAGTTGTTGATGGTGTTCATCCGGCAGCGGTTCAGGAAGTCGACGGTGACCTCTGTGCCCACACCGGCCACAAAGAACAGCGTGTCCACGGGATGCTTCTTGGAGATGATGTCCATGACCTTGATTTGGGAGGGGGCATCTGTCTTCACGCTGATCCACGGGATCTTCACCTCGGCATACTTGCGCTCATACTCTGTGATCTGGGCCTTCACAGGGGCAAAGATGTCGTTCTGGGTCACCTGCTGGGCCTCGAATGGATCGTAGATGAACAGGAAGGTGAGCACCGCG---TTCTCGCTGCTCTCAAAGGCAGCTGCCGCATAGGCCTCCAGGAAGCGTGCGGCATGGTCCCGTTCGTGGGCAGTGAGCGGCAAGATGACGTTGATGCGGCTGGCCTCCGTCACATAGGGCATAGGGATGATCTCCACCTCGCTGAGGGGCCGCACCAGGTGCACGCGCTTGGTGACAGAGCGGCTGTGACCCTTCTGCGTGACCACCTCCACCTGCAGGTCCAGCGTGTACTCCATGCCGCGCGTAGGGTCAAAGCGCCGGTAGCCATTCACCAGCTGCTGCTTGCGGACATGCAGCACCGGCTGGTACTTGCGGTTCAGCTCCTCCATGGCTGTGGCCACCACGTCAGCCACATCAGCTAGGTCTGCGCCCTGCAGCTCGCATTTGGGGGAGCCATCCACGCAGGCATAGACCTGATCCTCTGTGAAGTAGTCCCAGCGCAGCACCTCGAAGCGAGTTTTGGGCTGGAATGGAGGAGGGATGCCGACAGGCCACGCGGCACTGTGGTCCCCATCTGCAGACAGGCTGCTGGCATTCTGGATCTC--- 
s fr1.chrUn       3409912 1273 + 349519338 AAGTGCTGTTGGCCTGCTCCTGCTCAAAGAGCGCCATGGCCAGGTGGGAGCGCGAGCCCAGCCCCTGTAGGTTACTGAGGACGCAGCGGTGGTAGACGTCCTCGCTGAAGCGGGGGTTGCAGGTCCGTCTCACGTACTTCTGGATCAGAGCCGGCTCCACGGCCCTGAAGACGTGCAGCCCCGAGTACCGCACAAATATGTCGTACACGTCCATGCTCTCCAGGAGCTCCTCGTTGTCCAAGAGGTCGGCCGCCATCTTGGTCCTCGCCGTCATGTAGTCGGCGTTGTAGAAGCAGGCCTCGTCAAACACGTGGCGGTCGAAGCGGCC---GTCCCGCAGCGACTC-GGAGGCGAAGG----CGGACGAGGCGGCCGAGGGCTGCTGGTCCCGGTACATGACGGCGGGGCTGAACTCCTGGAAGTGGATGGGGAAGAACACCTGCCAGTTGCTGATGGTGTTCATCCTGCAGCGGTTCAGGAAGTCGGCGTTGACCTCCGTCCACACGCTCGCCAGGAAGAAAAGCGTGTCCACCGGGTGCTTCTTGGAGATGATGTCCATCAGCTTGACCTGCGAGGGCACCTCCGTCTTCACGCTGATCCAGGGGATCTTCACGTCCCCGTAGCGCTTCTCCACCTCTCCGATCATGGCCTTGATGCCCGCGAACACGTCGGCCTGACTGACGCGCTGCGCGTCGAACGGGTCGTAGATGAACAGGAACGTGAGCAGGACG---TTGTCGCGGGCGTCCAAGGTGTTCATCACGTACATATCCAGGAAGTTGCCGACAAAGTCCTGGTCCTGGGCGGTGACGGGGAGGATGACCTGCACCCGGGTGGCCTCCGTCACGTACGGCATGGGGATGATCTCCACGGCGCTCAGAGGGCGCAGCAGGTTCACGCGCTTGGCGATGACTTGGCTGTGGTCCTTCTGGGTGTACGCCTCCAGCGCCAGGTCCAGCACGTACTCCATGCCGCGGGTGGGGTCGAAGCGCCTGTAACCGTTGAGCAGACGCCGCTTGGTGAAGCGGAGCTGCGGCTGGTAGCGCTCGTTCAGGCGCTCCACCGCGATCTCCAACACGGCGTCGACGTCCGCGCGGTCGGCGCCTCTCATCTCGCACTTGGGCGAGCCGTCGACGCAGGAGTAGATGTGCTCTTCCGTGAAGTATTCCCAGTTTATCACCTCGAAGCGAGTTCTCGGCTTAAACGGGGAGTTGATGCCGACGGGCCACGTGACTCCGGCTTTGCCCTCGGGCGTCAGCTCGCTCAGGTTGTTGATCTGCGT 
s danRer1.chrUn 144716832 1261 + 367113659 AAGTACTGTTGCCCTGTTCCTGTTCAAACAGCAGCATGGCGAGCTGAGAGCGTGATCCAAGGCTATCCAGGGTGCTTTGTACACACCTCTGGTAGATTTCTTCACTAAGGCGAGGATTACACGTTTGGTAGCTGTATTTCTGATGCAGGGCCGGCTCCACTGCTCGGAAAACATGGAGGCCAGAGTATTTGACGAACATGTCATAGATATCAAGGTTCTCCAGGATCTCCTCATTCTCCAGCACATCCGATGACATCCGGGTACGGGTCGCCATGTAGTCCGAGTTGTAGAAGCAAGCTTCGGTGAAGGAGCTGCGATCGAAAAGACCAGCCTCTTTGACCAAATCCAACGCACTGGGAAGAGGCTGGTTGTGA--------------------TAAGCGATGTCAGGATTGTAGTACTGGAAGTGGATTGGAAAGAACACCTGCCAGTTGTTGATGGAGTTCATCCGACAGCGATTGAGGAACTCTGAACTGATGCTTGTTTTTACCGTCGCAATGAAGAACAACGTGTCAACCGGGTGCTTCTTGGAGATGATGTCCATGAATTTGATTTGAGACGGACTTTCGCTTTTAACACTAATCCAGGGGATTTTGACTGCAGGATATCGATGTTCGTACGTACTGATTTGTGCTTTGATGCTGGAGAAGATGTCATTCTGGTTGACTTGTTGGGCCTCTATTGGATCGTAGATGAAGAGGAACGTCAAGATCGCA---TTCTCGCTGGTTTCGAATGCATTTGTGGCATACACTTCTAAAAACTGATGAACGTAATCTCGATCTTGAAGAGTAACGGGTAAGATGATATGAACTCTAGTTGCTTCTGTAACGTAAGGCATAGGGATGATCTCGATGCGACTGAGAGGTCTTACTAAGTGGACCCTCTTGGTAATAGAGCGACTGTGTCCTTTTTGGTTAACTACCTCCAATTGTAGGTCCAGGGTGTACTCCATACCTCTGGTGGGGTCAAAACGTCTGTATCCATTGATTAGCTGTTGCTTCTTTAGGTACAACACAGGCTTGTACTTTTTATTCAGTTCACCCATTGCTGTCTCAATGACATCGGCTACGTCTAGCTTGTCAACTCCACGAAGCTCGCATTTCGGAGAGCCATCGATGCAAGAGTAAACCTGATCCTCAGTGAAGTAATCCCACCGCAGGACCTCGAATCGTGTTTTGGGCTCAAAGGGTGGATTGATTCCAACTGGCCACAAAGCACTGCGGTTGCCCTCAAAAGCCACTACACTGACATTTCTAATTTCCGC 

a score=133281.0
s hg17.chr20     33330413 10 +  62435964 TCAGGTGAGG 
s panTro1.chr21  35343723 10 +  65473740 TCAGGTGAGG 
s mm5.chr2      155883450 10 + 181686250 TCATGTGAGG 
s rn3.chr14      87484150 10 + 112220682 TCATGTGAGT 
s canFam1.chr24  27188710 10 +  50732077 TCAGGTGAGG 

a score=135043.0
s hg17.chr20     33513606 186 +  62435964 ATGGAGACAAGAAGCCCTG---GGTTGAACAACATGAAGCCCCAGTCACTGCAGCT---GGTACTGGAAGAGCAGGTGCTGGCACTACAGCAGCAGATGGCAGAGAATCAGGCAGCCTCCTGGCGGAAGCTGAAGAACTCCCAGGAGGCCCAGCAGAGACAAGCAACCCTTGTGAGGAAGCTGCAGGCCAAG 
s panTro1.chr21  35533536 186 +  65473740 ATGGAGACAAGAAGCCCTG---GGTTGAACAACATGAAGCCCCAGTCACTGCAGCT---GGTACTGGAAGAGCAGGTGCTGGCACTACAGCAGCAGATGGCAGAGAATCAGGCAGCCTCCTGGCGGAAGCTGAAGAACTCCCAGGAGGCCCAGCAGAGACAAGCAACCCTTGTGAGGAAGCTGCAGGCCAAG 
s mm5.chr2      156025320 183 + 181686250 ATGGAGACAGGGAGCCCCG---GGTTG---AACATGAAGCCCCAGTCCTTGCAGCT---GGTGCTGGAGGGGCAGGTGCTGGCGCTGCAGCAGCAGATGGCCGAGAATCAGGCTGCCTCCTGGCGGAAACTGAAGAACTCCCAAGAGGCCCAGAAGAGACAAGCAACCCTCGTGAGGAAGCTGCAGGCCAAG 
s rn3.chr5       13191474 192 - 173106704 CTGCAGCTGGAGCAGGCTGTGCGGCTGGAGACTGGGGAGCTGGAGGCACAGGAGCCCCGGGGTCTGGTGCGGCAGAGCGTGGAGCTGAGGAGGCAGCTGCAGGAGGAGCAGGCCTCCTACCGGCGCAAGCTACAGGCCTACCAGGAGGGCCAGCAGCGGCAGGCCCAGCTAGTGCAGCGGCTGCAGGCCAAG 
s canFam1.chr24  27350813 186 +  50732077 ATGGAGACGCGAGGCCCTG---GGTTGAACAATATGAAGCCCCAGTCACTGCAGTT---GGTGCTGGAGGAGCAAGTACTAGCACTACAGCAGCAGATGGCAGAGAACCAAGCAGCCTCCTGGCGGAAGCTGAAGAACTCCCAGGAGGCCCAGCAGAGGCAAGCAACCCTCGTGAGGAAGCTGCAGGCCAAG 

a score=79158.0
s hg17.chr20     33579500 27 +  62435964 CTAGGGAACCAGACCATCTTCCAAAAT 
s panTro1.chr21  35599874 27 +  65473740 CTAGGGAACCAGACCATCTTCCAAAAT 
s mm5.chr2      156065808 27 + 181686250 CTAGGGAATCAGACCATCTTCCAAAAT 
s rn3.chr3      146317055 26 + 170969371 CTAGGGAATCAGA-CGTCTTCCAAAAT 
s canFam1.chr24  27411797 27 +  50732077 CGAGGGCACTGGACCACCCTCCAAAAT 

a score=183752.0
s hg17.chr20     33593260 88 +  62435964 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCCAAGACTTTGGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACCG 
s panTro1.chr21  35611606 88 +  65473740 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCCAAGACTTTGGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACCG 
s mm5.chr2      156071489 88 + 181686250 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCTAAGACTCTGGAGGACTTCCGGGTCAAGACCTGCGGGGGTGCCACGG 
s rn3.chr3      146322266 88 + 170969371 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCTAAGACTCTGGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACGG 
s canFam1.chr24  27422888 88 +  50732077 ATGGAGGCGCTGGGGAAGCTCAAGCAGTTCGATGCCTACCCCAAGACTCTGGAGGACTTCCGGGTCAAGACCTGCGGGGGCGCCACGG 
s fr1.chrUn      60145707 88 - 349519338 ATGGATACTTTTAGCAAACTGAAACAGTTTGACGCTTATCCCAAAACTCTGGAGGATTTTAGGGTGAAGACATGGGGCGGTGCGACCG 
s danRer1.chr20  18851405 88 +  31913010 ATGGATGCGTTAAATAAACTCAAACAATTTGACGCGTATCCGAAAACTCTAGAGGACTTCAGGATCAAAACATGTGGAGGAGCCACGG 

a score=802859.0
s hg17.chr21    32707032 160 + 46944323 ATGCTTCTGCCGGGACGCGCACGCCAACCGCCGACGCCCCAGCCCGTGCAGCATCCCGGCCTCCGCCGGCAGGTAGAGCCGCCGGGGCAGCTCCTGCGCCTCTTCTACTGCACTGTCCTGGTCTGCTCCAAAGAGATCTCAGCGCTCACCGACTTCTCTG 
s panTro1.chr22 32678009 160 + 47338174 ATGCTTCTGCCGGGACCCGCACGCCAACCGCCGACGCCCCAGCCCGTGCAGCATCCCGGCCTCCGCCGGCAGGTAGAGCCGCCGGGGCAGCTCCTGCGCCTCTTCTACTGCACTGTCCTGGTCTGCTCCAAAGAGATCTCAGCGCTCACCGACTTCTCTG 
s mm5.chr16     91265497 160 + 98801893 ATGCTCCTGCCAGGACACCCGCGTCCACCACCCGCGCCCCAATCGGCGCAGAATCAGGGCCTCCGCAGGCAGGTAGAGCCTCCGGGGCAGCTTCTGCGCCTGTTCTACTGCACGGTCCTAGTGTGCTCCAAAGAGACCTCCGCGCTCACCGATTTCTCTG 
s rn3.chr11     30818860 160 + 87800381 ATGGTCTTGCCCGGACACCCGCGTCTGCCGCCCGGGCCACAGCCACCGCAGAATCCCGGCCTCCGCAGGCAGGTAGAGCCTCCAGGGCAGCTTCTGCGCCTCTTCTACTGCACGGTCCTAGTGTGCTCCAAAGAGACCTCCGCGCTCACCGATTTTTCCG 
s canFam1.chr31 30192155 160 + 41215879 ATGCTTCTGCCTGGACAcgcgcgcccgccgcccgcgccgcagcccgcgcAGCATCCCGGACTCCGCCGGCAGGTAGAGCCTCCCGGGCAGCTCCTGCGCCTCTTCTACTGCACCGTCCTGGTCTGTTCCAAGGAGATCGCGGCGCTCACGGACTTCTCCG 

a score=93692.0
s hg17.chr21    32869641 381 + 46944323 TCAGATTCGGCCCTGAAGGGCCACGCAGACCTCGGCCAAGGATGGGAAGGAGTCCAGGTGCCAGGCAGCCCAGGGCGAGTGGTGCCCACAGGCTTGGGCTGTGCTGTGCATAAGGGCCACACCTGAAGCTCGGCCACACCTGAGGCTCGGCCACCACATAGGCCCCGTTTCTTTACCAAGATAGGTTCCTGCAGAGGTCGTGAAGCTGCTGTGGTCATTTGCTGGCAGCGACGTGAAGATAGAATTCTTTCCTGACTCAACCAGGGGCACTCTCGTCTCCTCCCCGTGAGACCCGCAATGCAGGAAGCACCCACAGCTGCATGGACAGAACTGGGGCCTGGGAAAGAGGCCAGGAAGGTGCCAGATGAGAGGGCGCTCCAT 
s panTro1.chr22 32842524 381 + 47338174 TCAGATTCGGCCCTGAAGGGCTACGCAGACCTCGGCCAAGGATGGGAAGGAGTCCAGGTGCCAGGCAGCCCAGGGCGAGTGGTGCCCACAGGCTTGGGCTGTGCTGTGCATAAGGGCCACACCTGAAGCTCGGCCACACCTGAGGCTCAGCCACCAGATAGGCTCTGTTTCTTTACCGAGATAGGTTCCTGCAGAGGTCGTGAAGCTGCTGTGGTCATTTGCTGGCAGCGACGTGAAGATAGAATTCTTTCCTGACTCAACCAGGGGCACTCTTGGCTCCTCCCCGTGAGACCCGCAATGCAGGAAGCACCCACAGCTGCATGGACAGAACTGGGGCTTGGGAAAGAGGCCAGGCAGGTGCCAGATGAGAGGGCGCTCCAT 

a score=62310.0
s hg17.chr21     33321040 51 +  46944323 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCAGAGCCC 
s panTro1.chr22  33286911 51 +  47338174 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCAGAGCCC 
s mm5.chr16      91660624 51 +  98801893 ATGGACTCGGACGCCAGCCTGGTGTCTAGTCGCCCATCGTCCCCAGAACCC 
s rn3.chr11      31244293 51 +  87800381 ATGGACTCGGACGCCAGCCTGGTGTCTAGTCGCCCGTCGTCGCCAGAACCC 
s canFam1.chr31  30690225 51 +  41215879 ATGGACTCGGACGCCAGCCTGGTGTCCAGTCGCCCGTCGTCACCAGAGCCC 
s galGal2.chr3   53622667 51 + 108638738 ATGAATTCTGACTCCAGCTCCGTCTCCAGCAGAGCCTCCTCGCCGGACATG 
s fr1.chrUn     314816718 51 - 349519338 ATGGACTCAGATACGAGCCGCATGTCGAGCAGACCCTCCTCCCCCGAGGTG 

a score=19085.0
s hg17.chr21     33321091 26 +  46944323 GATGACCTTTTTCTGCCGG----------------------------CCCGGAG 
s panTro1.chr22  33286962 26 +  47338174 GATGACCTTTTTCTGCCGG----------------------------CCCGGAG 
s mm5.chr16      91660675 26 +  98801893 GATGATCTTTTTCTGCCCG----------------------------CCCGGAG 
s rn3.chr11      31244344 26 +  87800381 GATGATCTTTTTCTGCCGG----------------------------CCCGGAG 
s canFam1.chr31  30690276 26 +  41215879 GATGACCTGTTTCTGCCGG----------------------------CCCGGAG 
s galGal2.chr3   53622718 54 + 108638738 GACGAGATGTACCTGCGGGAGcaccgccaccaccaccaccaccaccaccCGGAG 
s fr1.chrUn     314816769 22 - 349519338 GACGACATCTTCATGTCCA----------------------------GCC---- 
s danRer1.chr24  18057443 31 +  23152154 CATCAGCTGTTTCGAGCAA-----------------------AACGACCCGGAC 

a score=-194.0
s hg17.chr21     33321117 3 +  46944323 TAA 
s panTro1.chr22  33286988 3 +  47338174 TAA 
s mm5.chr16      91660701 3 +  98801893 CAA 
s rn3.chr11      31244370 3 +  87800381 CAA 
s canFam1.chr31  30690302 3 +  41215879 CAA 
s fr1.chrUn     314816791 3 - 349519338 TGA 
s danRer1.chr24  18057475 2 +  23152154 CG- 

a score=36.0
s hg17.chr21     33321117 7 +  46944323 TAAGGGC 
s fr1.chrUn     314816791 7 - 349519338 TGAAGAC 
s danRer1.chr24  18057474 7 +  23152154 CCGGTGC 

a score=260.0
s hg17.chr21     33321120 4 +  46944323 GGGC 
s panTro1.chr22  33286991 4 +  47338174 GGGC 
s mm5.chr16      91660704 4 +  98801893 GGGG 
s rn3.chr11      31244373 4 +  87800381 GGGG 
s canFam1.chr1   91988693 4 - 124897793 catc 
s fr1.chrUn     314816794 4 - 349519338 AGAC 
s danRer1.chr24  18057477 4 +  23152154 GTGC 

a score=24176.0
s hg17.chr21     33321124 110 +  46944323 AGCAGCGGCAGCGCCTTCACTGGGGGCACCGTGTC--------CTCGTCCACCCCGAGTGACTGCCCGCCGGAGCT----GAGCGCCGAGCTGCGCG-GCGCTATGGGCTCTGCGGGCGCGCA 
s panTro1.chr22  33286995 110 +  47338174 AGCAGCGGCAGCGCCTTCACTGGGGGCACCGTGTC--------CTCGTCCACCCCGAGCGACTGCCCGCCGGAGCT----GAGCGCCGAGCTGCGCG-GCGCTATGGGCTCTGCGGGCGCGCA 
s mm5.chr16      91660708 110 +  98801893 GGAAGCAGCAGCGGCTTCACAGGAGGGACTGTGTC--------CTCGTCCACGCCGAGCGACTGCCCGCCAGAGCT----GAGCTCCGAGCTACGAG-GGGCCATGGGCGCGTCAGGCGCGCA 
s rn3.chr11      31244377 110 +  87800381 GGAAGCAGCAGCGGCTTCACAGGAGGAACCGTGTC--------CTCATCCACGCCGAGCGACTGCCCGCCAGAGCT----GAGCTCCGAGCTGCGAG-GAGCCATGGGCACGGCGGGCGCGCA 
s canFam1.chr1   91988697  97 - 124897793 accaccgccaccaccaccaccaGGAGAGCCGTCTCAACTCGGTCTCCTCCACTCAGGGCGACATGGTGCAGAAGAT----GCCCGGGGAG---------------AGTCTCT-------CGCG 
s galGal2.chr3   53622772  75 + 108638738 ---------AGCCGCCTCA--------ACCCCGT---------CTCTTCCACGCAGGGCGACCTGGTGCAGAAGAT----GGCCGGGGAG---------------GGCCTGGCCCGGGGC--- 
s fr1.chrUn     314816798  83 - 349519338 --ATCCGTGCACGGCTTCTCCGGA---ACCGTGTC--------C---TCCACGCAGAGCGACTCCCCGCCGGACAT-------CGGGAGCCTGCGC---------GGCCTCTCCG-------- 
s danRer1.chr24  18057481  91 +  23152154 AGCCCGGGGGGCG-----AGCGGGCACGCTGGGTC---------------------------TGCCGACCGGATCTTTGTGTGTGAAATACGGCGAGAGCGCCAACAGGACTTCAGGCGCGGA 

a score=6480.0
s hg17.chr21     33321234 22 +  46944323 TCCTGGGGACAAGCTAGGAGGC 
s panTro1.chr22  33287105 22 +  47338174 TCCTGGGGACAAGCTAGGAGGC 
s mm5.chr16      91660818 22 +  98801893 TCCCGGGGACAAACTGGGCGGC 
s rn3.chr11      31244487 22 +  87800381 TCCCGGGGACAAACTGGGCGGC 
s canFam1.chr1   91988794 22 - 124897793 GGCCGGCGCCAAGGCCACGGGC 
s galGal2.chr3   53622847 18 + 108638738 ----GGCCCCAAGGCGCAGGGG 
s fr1.chrUn     314816881 12 - 349519338 --CCACTGACGAGG-------- 

a score=215890.0
s hg17.chr21     33321256 192 +  46944323 AGTGGCTTCAAGTCATCCTCGTCCAGCACCTCGTCGTCTACGTCG-TCGGCGGCTGCGTCGTCCACCAAGAAGGACAAGAAGCAAATGACAGAGCCGGAGCTGCAGCAGCTGCGTCTCAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGATGGCCTCCGCGAGGTCATGCCG 
s panTro1.chr22  33287127 192 +  47338174 AGTGGCTTCAAGTCATCCTCGTCCAGCACCTCGTCGTCTACGTCG-TCGGCGGCTGCGTCGTCCACCAAGAAGGACAAGAAGCAAATGACAGAGCCGGAGCTGCAGCAGCTGCGTCTCAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGATGGCCTGCGCGAGGTCATGCCG 
s mm5.chr16      91660840 192 +  98801893 GGTGGCTTCAAGTCATCTTCCTCCAGCACCTCCTCGTCCACGTCC-TCGGCGGCCACGTCTTCCACCAAGAAAGACAAGAAGCAGATGACTGAGCCCGAGCTGCAGCAGCTGCGCCTGAAGATCAACAGCCGCGAACGCAAGCGCATGCACGACCTCAACATCGCCATGGACGGCCTGCGGGAGGTCATGCCT 
s rn3.chr11      31244509 192 +  87800381 GGTGGCTTCAAGTCATCTTCCTCCAGCACCTCCTCGTCCACGTCG-TCGGCGGCCACGTCTTCCACCAAGAAAGATAAGAAGCAGATGACTGAGCCCGAGCTGCAGCAGCTGCGCCTGAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGACGGCCTGAGGGAGGTCATGCCG 
s canFam1.chr1   91988816 138 - 124897793 GAGAGTAGCAAGT-------------------------------------------------------ACAAAATCAAGAAGCAGCTGTCGGAGCAGGACCTACAGCAATTACGGCTGAAGATCAACGGCCGCGAGCGCAAGCGGATGCACGACCTCAACCTAGCCATGGACGGGCTGCGCGAGGTCATGCCC 
s galGal2.chr3   53622865 138 + 108638738 GAGGGCGGCAAGT-------------------------------------------------------ACAAGATCAAGAAGCAGCTCTCGGAGCAGGACCTGCAGCAGCTGCGGCTCAAGATCAACGGGCGGGAGCGCAAGCGGATGCACGACCTCAACCTGGCCATGGACGGGCTGCGGGAGGTGATGCCC 
s fr1.chrUn     314816893 149 - 349519338 ------------------------AGTCCCTCGCCATCCG--------------------GCTCGCAAAGAAAGATCGGAAAGTGCTTTCGGACAACGAACTGCAGACGATCCGCCTCAAAATCAACAGCCGCGAGAGGAAAAGGATGCACGACCTCAACGTGGCCATGGACGGACTCCGGGAAGTCATGCCC 
s danRer1.chr25  10119771 182 -  17189730 AGCTGCTGCAGAAGATGGCCAGCGAGCACCTC----TCCAAGACGCCCAGCGGCAGCAAGT-------ACAAGCTGAAGAAGCAGGTGACCGAGCATGAGATCCAGCAGCTGCGGCTCAAGATCAACGGGAGGGAGCGCAAGCGCATGCACGACCTGAATTTGGCGATGGACGGGCTCCGAGAGGTCATGCCG 

a score=323301.0
s hg17.chr21     33321448 176 +  46944323 TACGCACACGGCCCTTCGGTGCGCAAGCTTTCCAAGATCGCCACGCTGCTGCTGGCGCGCAACTACATCCTCATGCTCACCAACTCGCTGGAGGAGATGAAGCGACTGGTGAGCGAGATCTACGGGGG------------C------CACCACGCTGGCTTCCACCCGTCGGCCTGCGGCGGCCTGGCGCACTC 
s panTro1.chr22  33287319 176 +  47338174 TACGCACACGGCCCTTCGGTGCGCAAGCTTTCCAAGATCGCCACGCTGCTGCTGGCGCGCAACTACATCCTCATGCTCACCAACTCGCTGGAGGAGATGAAGCGACTGGTGAGCGAGATCTACGGGGG------------C------CACCACGCTGGCTTCCACCCGTCGGCCTGCGGCGGCCTGGCGCACTC 
s mm5.chr16      91661032 176 +  98801893 TACGCGCACGGGCCGTCGGTGCGCAAGCTCTCCAAGATCGCCACGCTGCTGCTGGCGCGAAACTACATCCTCATGCTCACCAACTCGCTGGAGGAGATGAAGCGACTGGTGAGCGAGATCTACGGGGG------------T------CACCACGCCGGCTTCCACCCATCGGCCTGTGGCGGGCTGGCACACTC 
s rn3.chr11      31244701 176 +  87800381 TACGCGCACGGCCCGTCGGTGCGCAAGCTCTCCAAGATCGCCACGCTGCTGCTGGCGCGAAACTACATCCTGATGCTCACCAACTCGCTGGAGGAGATGAAGAGACTGGTGAGCGAGATTTACGGGGG------------T------CACCACGCCGGCTTCCACCCGTCGGCCTGTGGCGGGCTGGCACACTC 
s canFam1.chr1   91988954 167 - 124897793 TACGCGCACGGGCCCTCGGTGCGCAAGCTCTCCAAGATCGCCACTCTCCTGCTGGCCAGAAACTACATCCTCATGCTCACCAGCTCCCTGGAGGAGATGAAGAGGTTGGTTGGCGAGATCTACGGGGG------------C------CACCACTCTGCCTTCCA---------CTGCGGGACCGTGGGCCACTC 
s galGal2.chr3   53623003 167 + 108638738 TACGCGCACGGCCCCTCCGTCCGGAAACTCTCCAAAATCGCCACCCTGCTGCTGGCCAGAAACTACATCCTGATGCTCACCAGCTCCCTGGAGGAGATGAAGCGCCTGGTGGGGGAGATCTACGGTGG------------C------CACCACTCGGCCTTCCA---------CTGCGGCACCGTGGGCCACTc 
s fr1.chrUn     314817042 182 - 349519338 TACGCGCACGGACCGTCGGTGCGCAAACTCTCCAAAATCGCCACGCTGCTCCTGGCGAGAAATTACATCCTGATGCTGAGCAACTCGCTGGAAGAGATGAAGCGGCTGGTGAGCGAGATCTACGGCAG------------CGGCGCACACCACGGTGGCTTCCACCCGACAGCTTGTGGGACAATGACACACGC 
s danRer1.chrNA 310476113 188 - 390413307 TACGCTCACGGGCCGTCTGTGCGCAAGCTCTCTAAAATAGCCACTCTGCTGCTCGCGCGCAACTACATCCTTATGCTGAGCAACTCGCTGGAGGAGATGAAGCGGCTCGTGAGCGAGATCTACGGCGGAGGGAGCGGGGCC------CATCACGCCGGTTTCCATCCGTCCAGTTGTGGCACTCTTACGCACGC 

a score=23510.0
s hg17.chr21     33321624 71 +  46944323 CGCGCCCCTGCCC-GCCGC-----------CACCGCGCACCCGGCAGCAGCAG-CGCACGCCGCACATCACCCCGCGGTGCACC 
s panTro1.chr22  33287495 71 +  47338174 TGCGCCCCTGCCC-GCCGC-----------CACCGCGCACCCGGCAGCAGCAG-CGCACGCCGCACATCACCCCGCGGTGCACC 
s mm5.chr16      91661208 71 +  98801893 GGCGCCTCTACCC-ACCGC-----------CACGGCGCACCCCGCGGCCGCCG-CGCACGCCGCGCACCACCCGGCCGTGCACC 
s rn3.chr11      31244877 71 +  87800381 GACGCCTCTACCC-ACCGC-----------CACGGCGCACCCTGCAGCCGCCG-CGCACGCCGCGCACCACCCGGCGGTGCATC 
s canFam1.chr1   91989121 45 - 124897793 CGC-----------------------------CGGC-CACCCAGCACACGCCG-CCAACGCCGTGCACC------CGGTGCA-- 
s galGal2.chr20   5296387 84 -  13506680 CACGGCCTTGCCCGGCTGCCCCGAGAAATGCACTGCCTTCACAGGAGCCGCCTCCGCGCTCTGCAAACACTGCAGCGACAAGCC 
s fr1.chrUn     314817224 56 - 349519338 GGGGCCCGTGCCGGGACAC-----------CCGAGCACAT--------------CTCACAGCTCACACC---CGGCGGTGCACC 
s danRer1.chrNA 310476301 62 - 390413307 GGCGGCGGCTCC--GTTAC-------------CGGGTCACCCCGCTGCTGTCT-CGCATTCCTCTCACC------CGGTGCACC 

a score=9256.0
s hg17.chr21     33321695  9 +  46944323 A-CCCCATCc 
s panTro1.chr22  33287566 10 +  47338174 AACCCCATCc 
s mm5.chr16      91661279  9 +  98801893 A-CCCCATCC 
s rn3.chr11      31244948  9 +  87800381 A-CCCCATCC 
s canFam1.chr1   91989166  8 - 124897793 --CCCCATCC 
s fr1.chrUn     314817280  9 - 349519338 A-CCCGCTCC 
s danRer1.chrNA 310476363  9 - 390413307 A-TCCTCTGC 

a score=14345.0
s hg17.chr21    33321704 48 +  46944323 tgccgcccgccgccgcagcggctgctgccgccgctgcagccgcggctg 
s panTro1.chr22 33287576 48 +  47338174 tgccgcctgccgccgcagcggctgctgccgccgctgcagccgcggctg 
s mm5.chr16     91661288 48 +  98801893 TCCCTCCCGCAGCCGCCGCCGCCGCCGCAGCCGCCGCCGCCGCAGCGG 
s rn3.chr11     31244957 48 +  87800381 TCCCTCCAGCAGCCGCGGCCGCAGCCGCCGCAGCCGCTGCCGCAGCGG 
s canFam1.chr1  91989174 39 - 124897793 TG------GGCGGCGCGCTCTCGTCCGGCAACGCCTC-GTCGCCGC-- 

a score=4230.0
s hg17.chr21     33321752 3 +  46944323 TGT 
s panTro1.chr22  33287624 3 +  47338174 TGT 
s mm5.chr16      91661336 3 +  98801893 TGT 
s rn3.chr11      31245005 3 +  87800381 TGT 
s canFam1.chr1   91989213 3 - 124897793 TGT 
s fr1.chrUn     314817304 3 - 349519338 TGT 

a score=2889.0
s hg17.chr21     33321755 6 +  46944323 CCAGCG--- 
s panTro1.chr22  33287627 6 +  47338174 CCAGCG--- 
s mm5.chr16      91661339 6 +  98801893 CCAGCG--- 
s rn3.chr11      31245008 6 +  87800381 CCAGCG--- 
s canFam1.chr1   91989216 6 - 124897793 CCGCCG--- 
s fr1.chrUn     314817307 6 - 349519338 CCACGG--- 
s danRer1.chrNA 310476387 9 - 390413307 CCACCGCAG 

a score=65057.0
s hg17.chr21     33321761 77 +  46944323 CCTCTCTGCCCGGATCCGGGCTGCCGTCGGTCGGCTCCATCCGTCCACCGCACGGCCTACTCAAGTCTCCGTCTGCT 
s panTro1.chr22  33287633 77 +  47338174 CCTCTCTGCCCGGATCCGGGCTGCCGTCGGTCGGCTCCATCCGTCCACCGCACGGCCTACTCAAGTCTCCGTCTGCT 
s mm5.chr16      91661345 77 +  98801893 CCTCTCTACCGGGCTCCGGGCTGTCCTCGGTCGGATCCATCCGGCCTCCGCACGGCCTGCTCAAGTCACCGTCGGCA 
s rn3.chr11      31245014 77 +  87800381 CTTCTCTGCCGGGCTCCGGGCTGTCCTCGGTCGGATCCATCCGGCCTCCTCACGGCCTGCTCAAGTCTCCATCGGCA 
s canFam1.chr1   91989222 60 - 124897793 CCTCGCTGCCGG---------------CCATCGGCACCATTCGACCTCCCCACTCTCTGCTCAAGGCGCCCTCCA-- 
s galGal2.chr3   53623259 74 + 108638738 CGTCGCTGCCAG---CCTCGCTGCCGGCCCTGGGCACCATCCGGCCGCCCCACTCCCTGCTGAAGACCCCCTCCACT 
s fr1.chrUn     314817313 77 - 349519338 CGTCTCTGTCGGCACCTGGCATCGCCGCCGTCACATCTGTCAGACCTCATCATGGACTCCTCAAAGCTCCCGGTACC 
s danRer1.chrNA 310476396 68 - 390413307 CATCTCTTTCCGGGACGGGGCTTTCAGCCGTCA---------GGCCGCATCACGGACTCCTCAAAGCCCCGTCAGCC 

a score=100.0
s hg17.chr21     33321838 1 +  46944323 g 
s danRer1.chrNA 310476464 1 - 390413307 G 

a score=16973.0
s hg17.chr21    33321838 36 +  46944323 gccgcggccgccccgctggggggcgggggcggcggc 
s panTro1.chr22 33287710 36 +  47338174 GCCGCAgccgccccgctggggggcgggggcggcggc 
s mm5.chr16     91661422 36 +  98801893 GCCGCAGCCGCCCCTCTCGGAGGCGGGGGTGGAGGC 
s rn3.chr11     31245091 36 +  87800381 GCCGCGGCCGCCCCTCTCGGAGGCGGGGGTGGAGGC 
s canFam1.chr1  91989282 15 - 124897793 --CGCCGCCGGCCCT-------------------GC 

a score=-1380.0
s hg17.chr21  33321838 36 +  46944323 gccgcggccgccccgctggggggcgggggcggcggc 
s fr1.chrUn  314817391  1 - 349519338 G----------------------------------- 

a score=627.0
s hg17.chr21     33321874 1 +  46944323 A 
s panTro1.chr22  33287746 1 +  47338174 A 
s mm5.chr16      91661458 1 +  98801893 A 
s rn3.chr11      31245127 1 +  87800381 A 
s canFam1.chr1   91989297 1 - 124897793 A 
s galGal2.chr3   53623346 1 + 108638738 A 
s fr1.chrUn     314817392 1 - 349519338 T 

a score=101521.0
s hg17.chr21     33321875 67 +  46944323 GTGGGGC----GAGCGGGGGCTTCCAGCACTGGGG---------C---GGCATGCCCTGCCCCTGCAGCATGTGCCAGGTGCC 
s panTro1.chr22  33287747 67 +  47338174 GTGGGGC----GAGCGGGGGCTTCCAGCACTGGGG---------C---GGCATGCCCTGCCCCTGCAGCATGTGCCAGGTGCC 
s mm5.chr16      91661459 67 +  98801893 GCGGTGG----CAGCGGTGGCTTCCAGCACTGGGG---------C---GGCATGCCGTGCCCCTGCAGCATGTGCCAGGTGCC 
s rn3.chr11      31245128 67 +  87800381 GCGGTGG----CAGCGGTGGCTTCCAGCACTGGGG---------T---GGCATGCCGTGCCCCTGCAGCATGTGCCAGGTGCC 
s canFam1.chr1   91989298 63 - 124897793 GCTGG--------GCAGCGGCTTCCAGCACTGGGC---------C---GGGCTGCCCTGCCCCTGCACCATCTGCCAGATGCC 
s galGal2.chr3   53623347 63 + 108638738 GCTCG--------GCGGAGGCTTCCAGCACTGGGC---------C---GGCTTGCCGTGCCCCTGCACCATCTGCCAGGTGCC 
s fr1.chrUn     314817393 80 - 349519338 GCGGGGCCCCTGGGAAGCAGTTTCCAGCACTGGGGTGTGGGCACC---GGGATGCCTTGTCCGTGCAGCATGTGCCAAGTTCC 
s danRer1.chrNA 310476467 74 - 390413307 GCTGGGCCTCTGGGCGCGGGTTTCCAGCACTGGGG---------TGCGGGGATCCCTTGTCCGTGTAGCATGTGCCAGGTGCC 

a score=77095.0
s hg17.chr21     33321942 70 +  46944323 GCCGCCGCACCACCACGTGTCGGCTATGGGCGCCGGCAGCCTGCCGCGCCTCACCTCCGACGC------------CAAG-TGA 
s panTro1.chr22  33287814 70 +  47338174 GCCGCCGCACCACCACGTGTCGGCCATGGGCGCCGGCAGCCTGCCGCGCCTCACCTCCGACGC------------CAAG-TGA 
s mm5.chr16      91661526 70 +  98801893 GCCGCCGCACCACCACGTGTCGGCTATGGGCGCCGGCACCTTGCCGCGCCTCACCTCCGACGC------------CAAG-TGA 
s rn3.chr11      31245195 70 +  87800381 GCCGCCACACCACCACGTGTCGGCTATGGGCGCCGGCACCTTGCCGCGCCTCACCTCCGACGC------------CAAG-TGA 
s canFam1.chr31  30691121 70 +  41215879 GCCGCCGCACCCCCACGTGCCGGCCATGGGCGGGGGCAGCCTGCCGCGCCTTGCCTCCGACGC------------CAAG-TGA 
s galGal2.chr3   53623413 76 + 108638738 CCCGCCGCACCTC------TCTGCCCTCTCCGCCTCCGGCATGGGCCGGATCTCGGCGGACACCAAGGACCTGCTCAAG-TGA 
s fr1.chrUn     314817473 65 - 349519338 CCCTCCACACGTC------CCGGCCATCAGTACCGTTACCATGTCAAGGCTGTCCAGCGACTC------------CAAGTTGA 
s danRer1.chrNA 310476541 64 - 390413307 TCCGTCTCACGTT------CCCGGTATGAGCGCCGTCAGCATGCCACGGCTGACCAGTGACTC------------AAAA-TAA 

a score=113636.0
s hg17.chr21    33744994 2 + 46944323 TC 
s panTro1.chr22 33720891 2 + 47338174 TC 
s mm5.chr16     92040468 2 + 98801893 TC 
s rn3.chr11     31574511 2 + 87800381 TC 
s canFam1.chr31 31078278 2 + 41215879 TC 

a score=61167.0
s hg17.chr21     33744996 44 +  46944323 AGGTCCATAGCTCTTCGGTTCTTCCAAATTTGTAGATCAGAGTG 
s panTro1.chr22  33720893 44 +  47338174 AGGTCCATAGCTCTTCGGTTCTTCCAAATTTGTAGATCAGAGTG 
s mm5.chr16      92040470 44 +  98801893 AGGCCCAGAGCTCTTCAGTTCTTCCAAATTTGTAGATCAGAGTG 
s rn3.chr11      31574513 44 +  87800381 AGGCCCAGAGCTCTTCAGTTCTTCCGAATTTGTAGATCAGAGTG 
s canFam1.chr31  31078280 44 +  41215879 AGGTCCAAAGCTCTTCAGTTCTTCCAAATTTGTAGATCAGAGTG 
s fr1.chrUn     305707709 44 + 349519338 AGCCCCATAAATCTTCAGTGCGTCCGAACTTGTAGATCAGGGTG 

a score=71764.0
s hg17.chr22     30120223 42 +  49554710 ATGAGCAGCACCTTAGCTAAGATCGCGGAGATAGAAGCAGAG 
s panTro1.chr23  30222612 42 +  50034486 ATGAGCAGCACCTTAGCTAAGATCGCGGAGATAGAAGCAGAG 
s mm5.chr11     118487759 42 - 121648857 ATGAGCGGGACCTTAGCGAAGATCGCGGAGATCGAAGCCGAG 
s rn3.chr14      28338530 42 - 112220682 ATGAGTGGGACCTTAGCGAAGATCGCGGAGATCGAAGCCGAG 
s canFam1.chr26  27465575 42 +  41009621 ATGAGCAGCACCTTAGCGAAGATCGCGGAGATCGAAGCCGAG 
s galGal2.chr15   3499721 42 -  12438626 ATGAGTGGGACTCTGGCGAAGATCGCGGAGATCGAGGCTGAG 
s fr1.chrUn     242087985 39 - 349519338 ATGAGT---ATTCTTGCTAAAATAGCAGAGATTGAAAATGAG 

a score=249684.0
s hg17.chr22            30160419 187 +  49554710 TCACTGTCGGTATTCCAATTCATCTACACTGATAACTTTGGCG---GGCATGGAGGGCAGGGGTTGCTGTAGCACATCTGAGCCAAACCATTTGGCAAGGCCCACAGGGGAGCT------GCTCCTCTGGCTGGGGCGATGCTCCAGCTGGGA--GTGCATGTGGGGCAGGCCTGACCGGCTGGGCACGTTCTGAGGG 
s panTro1.chr23_random   7588856 187 -  16744317 TCACTGTCGGTATTCCAATTCATCTACACTGATAACTTTGGCG---GGCATGGAGGGCAGGGGTTGCTGTAGCACATCTGAGCCAAACCATTTGGCAAGGCCCACAGGGGAGCT------GCTCCTCTGGCTGGGGCGATGCTCCAGCTGGGA--GTGCATGTGGGGCAGGCCTGACCGGCTGGGCACGTTCTGAGGG 
s mm5.chr11            118509980 187 - 121648857 TCACTGTCTATATTCCAGTTCATCTACACTGATGACTTTGGTG---GGCATGGAGGGCAGAGGCTGCTGTAGCACATCTGAGCCAAACCATTTGGCAAGGCCCACAGGGGAGCT------GCTCCTTTGGCTGGTACGATGCTCCAGCTGGGA--GTGCATGTGGGGCATGCCCGACCGGCTGGGTACATTCTGAGGA 
s rn3.chr14             28360090 187 - 112220682 TCACTGTCTATATTCCAGTTCATCTACACTGATGACTTTGGTG---GGCATGGAGGGCAGAGGCTGCTGTAGCACATCTGAGCCAAACCACTTGGCAAGACCCACGGGGGAGCT------GCTCCTTTGGCTGGTGCGATGCTCCAGCTGGGA--GTGCATATGGGGCAGGCCTGACCGGCTGGGTACATTCGGAGGA 
s canFam1.chr26         27493563 187 +  41009621 TCATTGACGGTACTCCAATTCATCTACACTGATGACTTTGGCA---GGCATGGAGGGCAGGGGTTGCTGTAGCACATCTGAGCCAAACCACTTAGCGAGGCCTACTGGGGAGCT------GCTCCTCTGGCTGGGGCGATGTTCCAGCTGGGA--GTGCACGTGGGGCAGGCCTGACCTGGTGGGCACATTCTGAGGG 
s galGal2.chr15          3506922 187 -  12438626 TCACTGCCGATATTCCAGTTCATCTACACTGATGACTTTGGAT---GGCATGGAAGGGAGAGGCTGCTGCAAGACATCTGAACCAAACCACTTTGCAAGGCCAATGGGAGAGCC------ACTTCTCTGGCTGGGACGATGGTCGAGCTGCGC--GTGCCCATGAGATAATCCAGTCCGAGACGGCACATTCTGAGGT 
s danRer1.chrNA        320160139 177 + 390413307 TCACTGGCGGAACTCGAGCTCATCAACACTGATCACTTTAGTGGAAGGCATGGAAGGGAGAGGCTGCTGCAGCATGTCTGAACCAAACCACTTGGCCAGGCCCAGAGGGGGACTTGCACCTCTCCGCTGGTTTGTCCGATG--------GGGACCGTGGCTCTGGGAC-------------TGGGGGCCTCCTGAGGG 

a score=49183.0
s hg17.chr22            30160606 55 +  49554710 GTTGTCTGAACGCTGACAGCTGCTGCATGGGAACCAGAGCCTGGAGGATGCAGAA 
s panTro1.chr23_random   7589043 55 -  16744317 GTTGTCTGAACGCTGACAGCTGCTGCATGGGAACCAGAGCCTGGAGGATGCAGAA 
s mm5.chr11            118510167 52 - 121648857 ---GTCTGAACGCTGATAGCTGCTGCCTGGGAACTAGAGCCTGGAGGATGCAGAA 
s rn3.chr14             28360277 52 - 112220682 ---GTCTGAACGTTGATAGCTGCTGCCTGGGAACTAGAGCCTGGAGGATGCAGAA 
s canFam1.chr26         27493750 55 +  41009621 GTTGTCTGAACGCTGACAGCTGCTGCCGGGGAACCAGAGCCTGGAGGATGAAGAA 
s galGal2.chr15          3507109 55 -  12438626 GTTGTTTGCACACCAGCAGGTGATCCCTGTGCTCCAGTGCCTGTGGAATGTAAAG 

a score=2821.0
s hg17.chr22     30665273 6 +  49554710 ATGGGG 
s panTro1.chr23  30832251 6 +  50034486 ATGGGG 
s mm5.chr5       31452558 6 + 149219885 ATGGGG 
s rn3.chr14      28756724 6 - 112220682 ATGGGG 
s galGal2.chr15   3672628 6 -  12438626 ATGGGG 
s fr1.chrUn     333993217 6 - 349519338 ATGGTC 
s danRer1.chr10   6576471 6 -  25436222 ATGGCT 

a score=177812.0
s hg17.chr22     30665279 81 +  49554710 GACCGGGAGCAGCTGCTGCAGCGGGCGCGGCTGGCCGAGCAGGCGGAGCGCTACGACGACATGGCCTCCGCTATGAAGGCG 
s panTro1.chr23  30832257 81 +  50034486 GACCGGGAGCAGCTGCTGCAGCGGGCGCGGCTGGCCGAGCAAGCGGAGCGCTACGACGACATGGCCTCCGCCATGAAGGCG 
s mm5.chr5       31452564 81 + 149219885 GATCGAGAGCAGCTGCTGCAGCGGGCGCGACTGGCGGAGCAGGCGGAGCGCTACGACGATATGGCCTCCGCCATGAAGGCG 
s rn3.chr14      28756730 81 - 112220682 GACCGAGAGCAGCTGCTGCAGCGGGCGCGACTGGCGGAGCAGGCGGAGCGCTACGACGACATGGCCTCCGCCATGAAGGCG 
s canFam1.chr26  27923330 81 +  41009621 GACCGAGAGCAGCTGCTGCAGCGGGCGCGGCTGGCCGAGCAGGCGGAGCGCTACGACGACATGGCCTCCGCCATGAAGGCG 
s galGal2.chr15   3672634 81 -  12438626 GACCGAGAGCAGCTGCTGCAGCGAGCCCGCCTGGCCGAGCAGGCGGAGAGATACGACGACATGGCCTCGGCCATGAAGTCG 
s fr1.chrUn     333993223 81 - 349519338 GACCGCGAGCAGCTGGTGCAGAAAGCCAGGCTGGCTGAACAGGCTGAGAGATATGATGATATGGCCGCTGCAATGAAATCG 
s danRer1.chr10   6576477 81 -  25436222 GACCGGGAACAACTGATCCAAAGAGCCCGTCTGGCGGAGCAGGCGGAGCGCTATGATGATATGGCCTCCGCGATGAAGCTG 

a score=239048.0
s hg17.chr22     30939054 212 +  49554710 TC-AGGCATAGTAGCCGTGAATAAAGACCACCACAGCCAGGAGGAGGATGGCGTTGATGTTCACTATTGTCCTCCACGAGGGCCTCTCAGACGTGTCTGTGAGCTTCTTGCTCAAGGCTTCCTCCTCCTCCTTGGTTAGCTTGGGTC---CCTTCTG---------CAAACCGCAGAA-CAAGTCATAAGCTTTCTTGAGGCATCCACGTGATTTCTCAGGATAAT 
s panTro1.chr23  31094394 212 +  50034486 TC-AGGCATAGTAGCCGTGAATAAAGACCGTCACAGCCAGGAGGAGGATGGCGTTGATGTTCACTATTGTCCTCCACAAGGGCCTCTCAGACGTGTCTGTGAGCTTCTTGCTCAAGGCTTCCTCCTCCTCCTTGGTTAGCTTGGGTC---CCTTCTG---------CAAACCGCAGAA-CAAGTCATAAGCTTTCTTGAGGCATCCACGTGATTTCTCAGGATAAT 
s mm5.chr10      54573933 203 - 130633972 TC-AGGCAAAATAGCCATAGAAAAACGCTGCTACAGCCAAGAGGAGGATGACATTGACGTTCATGACCGTCCGCCAGAAGGGCTTCTCTGTTGTGTCTG------------TCAGAGCTTCCTCCTCTACTTTAGTCAACTTGAATTCAGCTCTTTG---------CAAACCACAGAA-TAGGTCACACGTCTTCTTGAGACATCCACGAGGTTTCTCAGTTTGGT 
s rn3.chr20      12876263 215 +  55296979 TC-AGGCAAAATAGCCATAGAAAAAAGCCGCCACGGCCAAGAGGACAATGACATTGACGTTCACGACCGTCCGCCAGAAGGGCTTCTCGGATGTGTCTGTCAGCTTCTTCTTCAGGGCTTCTTCCTCCTCTTTAGTCAGCTTGGGTTCCGCTCTTTG---------CAAACCACAGCA-TAGGTCATAAGTCTTCTTGAGACATCCACGAGGTTTCTCCGTTTGGT 
s canFam1.chr26  28103537 215 +  41009621 TC-AGGCAAAATAGCCATGGGCAAAGACAGCCACTGCTAGGAGTAGAATGGCATTGACATTCACTATAGTCCTCCATAAAGGCTTCTCAGATGTGTCTGTCAGCTTCTTTTTCTGGGCTTCTTCCTCTTCTTTGCTCAGTTTGGGACCTGTCTTCTG---------CAAACCACAAAA-TATGTCATAAGCCTTCCTGAGGCATCCACGGGGTTTCTCAGGATTAT 
s galGal2.chr15   8705700 216 +  12438626 CCTATGCAAAAAAGGCATGGCAAAATACAGCCACAGTCAGTAGGATGATGCCGTTGATATTCACAACATTCCTCCAAAGTGGCACTTCTGATGTGTCAGTCAGTTTCTTCTTCAGCGCTTCCTCTTCCTCCTTGCTCAGTTTGGGTC---CTTTTTG---TTGGTCTAAGCCACAGAA-CCAGTTGTAAGCTTTCTTTAGGCATCC---TGGGTCTTCACTTTCCT 
s fr1.chrUn     241992320 217 - 349519338 TT-ACGCGAAAAAGCCGTGGCAGAAGAAAGCGACAGCCAGGAGGATGAGGGCGTTGACGTTGACCACGTTCCTCCACAGCGGCTTCTCCGAGGTGTCCGTGAGCTTCCGCTTCATCTCGGCTTCTTCTTCCGGGGTCAGTTTGA------CCGTTTGGTTCTGTTCCAGCCCGCAGAAGCACATCAC-CGCCTTCTTGC-ACAGACCCGGTTGTTCTTGGGGTTCT 
s danRer1.chrUn  30145435 215 + 367113659 TT-AACCGAAGAAACCGTGGAAAAAGACGCAGACGGTGAGGAGGATAACGGCGTTAGCGTTGACCACATTTCTCCATAGAGGTTTCTCAGTGGTGTCGGTGAGCTTCATCTTCAGCTCAGCCTCCTGTTCTTTAGTCAGTTTGGGAGCATTGCCTTG------ATCGAAGCCGCAGAA-CCAGTTGTAGGCCTTCTTACAACAGCC---TGGCTCCTCACGCATCT 

a score=593066.0
s hg17.chr5     131424298 81 + 180857866 ATGAGCCGCCTGCCCGTCCTGCTCCTGCTCCAACTCCTGGTCCGCCCCGGACTCCAAGCTCCCA----TGACCCAGACAACGCCC 
s panTro1.chr4  137757118 81 + 188378868 ATGAGCCGCCTGCCCGTCCTGCTCCTGCTCCAACTCCTGGTCCGCCCCGGACTCCAAGCTCCCA----TGACCCAGACAACGTCC 
s mm5.chr11      67741889 85 - 121648857 ACCAGCATCCACACCATGCTGCTCCTGCTCCTGATGCTCTTCCACCTGGGACTCCAAGCTTCAATCAGTGGCCGGGATACCCACC 
s rn3.chr10      71032732 73 - 110733352 ACCAGCATCCTCTGCATGCTGCTTCCGCTCCTGATGCTCTTCCACCAGGGACTCC-AGTTTTCA-----------GGCAGTGCCC 
s canFam1.chr11  21697475 75 +  75769841 ATGAGCAGCTTCCCCATCCTGCACCTTCTCTTGCTCCTG------CTTGGATGCCAAGTCCCAC----AGGCACAGGGGAGGCCT 

a score=7416.0
s hg17.chr5     131424379 81 + 180857866 TTGAAGACAAGCTGGGTTA---ACTGCTCTAACATGATCGATGAAATTATAACACACTTAAAGCAGCCACCTTTGCCTTTGCTG 
s panTro1.chr4  137757199 81 + 188378868 TTGAAGACAAGCTGGGTTA---ACTGCTCTAACATGATCGATGAAATTATAACACACTTAAAGCAGCCACCTTTGCCTTTGCTG 
s mm5.chr11      67741976 57 - 121648857 TTAACCAGAACGTTGAATT---GCAGCTCT---ATTGTCAAGGAGATTATAG------GGAAGCTCCCA--------------- 
s canFam1.chr11  21697550 84 +  75769841 TTTTCGACAGACCTGCCTAAGCAATACTTCACAATGATCAATGAAATTATGGAGATGTTAAACAAGTCACCCTCGCCTTCAGAA 

a score=137534.0
s hg17.chr5     131556601 71 + 180857866 TCAGTCAACTTCTGTTGATCCACAAGGTCTCAAGAACTCCTGTCCTCGTTCATGGAACCACTTATTGGAGA 
s panTro1.chr4  137889227 71 + 188378868 TCAGTCAACTTCTGTTGATCCACAAGGTCTCAAGAACTCCTGTCCTCGTTCATGGAACCACTTATTGGAGA 
s mm5.chr11      67877858 71 - 121648857 TCAATCAACTTCCGTTGTTCCACAAGGTCTTAAGAACTCCTGTCCTCGCTCATGGAACCACTTGTTGGAGA 
s rn3.chr10      71169107 71 - 110733352 TCAATCGACTTCCGTTGTCCCACAAGGCCTCAAGAACTCCTGTCCTCGCTCATGGAACCACTTATTGGAGA 
s canFam1.chr11  21882340 71 +  75769841 TCAGTCAACTTCTGTTGATCCACATGGCCTCAAGAATTCCTGTCCTCGTTCATGGAACCACTTATTGGAGA 
s galGal2.chr13  15754170 71 +  17279963 TCAGTCAACCTCTGTTCTCCCACAGGGTCTTAAGAATTCGTTTCCTCTTTCATGAAACCATTTGTTTGAAA 
s fr1.chrUn     144469271 71 + 349519338 TCAATCCACTTCTGTCAAACCGCAGGGTCTCCTGAATTCTTGACCTCGCTCATGAATCCACTTGTTCGACA 
s danRer1.chr17  23182922 71 -  35757233 TCATTCCACCTCAGATAATGCACAGGGCCGTCTGAATTCTTGACCTCGTTCATGTATCCATTTGTTCGATA 

a score=153108.0
s hg17.chr5     131621326 93 + 180857866 ATGCCCCATTCCGTGACCCTGCGCGGGCCTTCGCCCTGGGGCTTCCGCCTGGTGGGCGGCCGGGACTTCAGCGCGCCCCTCACCATCTCACGG 
s panTro1.chr4  137954377 93 + 188378868 ATGCCCCATTCCGGGACCCTGCGCGGGCCTTCGCCCTGGGGCTTCCGCCCGGAGGGCGGCCGGGACTTCAGCGCGCCCCTCACCATCTCACGG 
s mm5.chr11      67940186 93 - 121648857 ATGACCCACTCGGTGACCCTGCGCGGCCCTTCACCCTGGGGCTTCCGCCTGGTGGGCGGCCGGGACTTCAGTGCTCCCCTCACCATCTCGCGG 
s rn3.chr10      71238657 93 - 110733352 ATGACCCACTCGGTGACCCTGCGCGGCCCTTCACCCTGGGGCTTCCGCCTGGTGGGCGGCCGTGACTTCAGTGCCCCCCTCACCATCTCGCGG 
s canFam1.chr11  21937834 93 +  75769841 ATGCCGCACTCCGTGACCCTACGCGGCCCGTCGCCCTGGGGCTTCCGCCTGGTAGGCGGCCGGGACTTCAGCGCACCCCTCACCATCTCGCGG 
s fr1.chrUn     144492794 93 + 349519338 ATGTCGCAGACCGTTACACTAAAGGGACCCTCTCCTTGGGGGTTCCGGCTGGTGGGAGGACGCGATTTCAGCACCCCGTTAACCATCTCCAGG 
s danRer1.chrUn 204956892 93 + 367113659 ATGTCTCACACTGTGACTCTCAGCGGTCCCTCGCCCTGGGGTTTTCGGCTGGTGGGTGGACGAGACTTCAGCACACCGCTCACCATTTCCAGA 

a score=705535.0
s hg17.chr5     131847541 125 + 180857866 CTACGGTGCACAGGGAATGGCCTGGATGGAG---GGCAACCGGACTGGGGT---CAGCAGGCTGTCCAGCCA---GGTGGCATCCATGTTCTTCAGATCTGTGAAGACACGCTGTAGACTCAGCCCAATATCCC 
s panTro1.chr4  138180513 125 + 188378868 CTACGGTGCACAGGGAATGGCCTGGATGGAG---GGCAACCGGACTGGGGT---CAGCAGGCTGTCCAGCCA---GGTGGCATCCATGTTCTTCAGATCTGTGAAGACACGCTGTAGACTCAGCCCAATATCCC 
s mm5.chr11      68232672 134 - 121648857 CTATGGTGCACAAGGAATGGCCTGAATAGAGGGCGGCAGCCTCACAGAGTTGCCCAGCAGGCTGTCCATCCACATGATGGAGTCCATATTCTTCATCTCCGTGAAGACATGTTGTATGCCTATCCCAATGTCCC 
s rn3.chr10      71497371 131 - 110733352 TTATGGTGCACAAGGAATAGCCTGAATGGAG---GGCGGCCTGGTAGAGTTGCCCAGCAGGGTGTCCATCCACATGACGGGGTCCATATTCTTCATCTCTGTGAAGACACGCTGTATGCCTATCTCGATGTCCC 
s canFam1.chr11  22141585 113 +  75769841 CTATGGTGCACAAGGAATGGCCTGGATGGAG---GGCAGTCTGACTGGAGT---CAACAGGCTGTCCAGCCA---GCTGGTGTCCATGTTCTTCAGATCTGAAGAGA------------TCAGCCCAACATACC 

a score=0.0
s hg17.chr6 108299600 2 + 170975699 TT 

a score=2325.0
s hg17.chr6     108299600 2 + 170975699 TT 
s panTro1.chr5  110600637 2 + 175429504 TT 
s mm5.chr10      87897895 2 - 130633972 TT 
s rn3.chr20       8534936 2 -  55296979 TT 
s canFam1.chr12  67925618 2 +  75455811 TT 
s galGal2.chr3   42632727 2 - 108638738 TT 
s fr1.chrUn     159061419 2 + 349519338 TC 

a score=237362.0
s hg17.chr6     108299602 142 + 170975699 AGTCATCATCTTCTTCTTCCTCCTCTTCTTCCTCAAAGCTATCTTCAAAGCCCTCACTGTCCTCCTGGTCTTCATCCCCCTCTATTGC------TGTATCCCACTGTGGGTGATTTTCTGGCACAGGCTTAGCCTCATGAACTTCCAA 
s panTro1.chr5  110600639 142 + 175429504 AGTCATCATCATCTTCTTCCTCCTCTTCTTCCTCAAAGCTATCTTCAAAGCCCTCACTGTCCTCCTGGTCTTCATCCCCCTCTATTGC------TGTATCCCACTGTGGGTGATTTTCTGGCACAGGCTTAGCCTCATGAACTTCCAA 
s mm5.chr10      87897897 142 - 130633972 AGTCTCCACCTTCCTCTTCCTCCTCCTCTTCCTCAAAGCTGTCTTCAAATCCTTCACTGTCTTCCTGGTCTTCGTCACCTTCTATCGC------TGTGTCCCACTGTGGGTGGTTTTCTGGCACAGGCTTGGCCTCATGAACTTCCAA 
s rn3.chr20       8534938 142 -  55296979 AGTCACCACCCTCCTCTTCCTCCTCCTCTTCCTCAAAGCTGTCTTCAAATCCTTCACTGTCTTCCTGGTCTTCGTCACCTTCTATTGC------TGTGTCCCACTGTGGGTGGTTTTCTGGCACGGGCTTGGCCTCATGAACTTCCAA 
s canFam1.chr12  67925620 142 +  75455811 AGTCATCATCTTCCTCCTCTTCTTCCTCCTCCTCAAAGCTATCTTCAAAGCCTTCGCTGTCCTCCTGGTCTTCATCCCCCTCTATTGC------TGTATCCCACTGTGGGTGATTTTCTGGTACAGGCTTAGCCTCATGAACTTCCAA 
s galGal2.chr3   42632729 142 - 108638738 AATCATCATCTTCCTCCTCTTCCTCTTCTTCCTCAAAACTGTCTTCAAAGCCCTCGCTGTCTTCCTGGTCCTCATCACCTTCTATTGC------TGTATCCCACTGAGGATGATTTTCTGGCACTGGTTTTGCTTCATGAACTTCCAG 
s fr1.chrUn     159061421 136 + 349519338 AGTCATTGTCCTCGTCGTCGTCTTC------------ACTCTCCTCGATGCCGTCGCTGTCCTCCTGCTCCTCGTCCTCCTCCTCCGTGTCGGGGATGTCCCACTGAGGGTGATTGTCCAGCATAGCCTTGGCTTCGTGGACCTCCAG 
s danRer1.chr8   26343964 145 -  36410523 AATGATTTTAGTCGTTGTCTTCTTCGTCTTCCTCAGA---CTCCTCAATGCCGTCACTGTCCTCCTGGTCATCCTCCTCTTCCTCAGTTTCTGGGATGTCCCACTGCGGGTGGTTATCCATCATGGCCTTCGCCTCATGAACCTCCAG 

a score=78207.0
s hg17.chr6     108594662 25 + 170975699 ATGAGCAAGCCAGCCGGATCAACAA 
s panTro1.chr5  110895281 25 + 175429504 ATGAGCAAGCCAGCCGGATCAACAA 
s mm5.chr10      88143690 25 - 130633972 ATGAGCAAGCCCGCCGGATCAACAA 
s rn3.chr20       8761429 25 -  55296979 ATGAGCAAGCCCGCCGGATCAACAA 
s canFam1.chr12  68179741 25 +  75455811 ATGAGCAAGCCGGCCGGATCAACAA 
s fr1.chrUn     210130082 25 + 349519338 ATGAGCAAAGCCGCCGGCTCAACAA 
s danRer1.chr20  17232749 25 +  31913010 ATGAGCAAGCCTGCTGGTTCAACAA 

a score=89508.0
s hg17.chr6     108640045 50 + 170975699 TCAGGCATGTCTTATTTTAGATGGAGTATAGCTTTTATCTATTATTTCAT 
s panTro1.chr5  110940096 50 + 175429504 TCAGGCATGTCTTATTTTAGATGGAGTATAGCTTTTATCTATTATTTCAT 
s mm5.chr10      88191839 50 - 130633972 TCAGGCATGTCTTATTTTAGATGGAGTATAGCTTTTATCTATAATTTCAT 
s rn3.chr20      52647276 50 -  55296979 TCAGGCATGTCTTAGTTTAGATGGAGTATAGCTTTTATCTATGATTTCAT 
s canFam1.chr12  68222804 50 +  75455811 TCAGGCATGTCTTATTTTAGATGGTGTATAGCTTTTATCTATAATTTCGT 
s galGal2.chr3   42753356 50 - 108638738 TCAAGTATGTCTTATTTTGGATGGTGTGTAGTTTTTGTCTATTACTTCAT 
s fr1.chrUn     210136674 50 + 349519338 TCAGGCTTGTCTGATCTTAGAGGGGGTGTAGTTCTTGTCCAAGACCTTGT 
s danRer1.chr20  17245947 50 +  31913010 TTAGGCTTGTCTAATTTTGGAAGGGGTGTAGTTTTTATCCACAGACTCAT 

a score=92653.0
s hg17.chr6     108640095 56 + 170975699 CTTGTAAAAACATGTGAAGACAACG-TTCGTTCTGTGCCAGAGGATGACCAGCGACC 
s panTro1.chr5  110940146 56 + 175429504 CTTGTAAAAACATGTGAAGACAACG-TTCGTTCTGTGCCAGAGGATGACCAGCGACC 
s mm5.chr10      88191889 56 - 130633972 CCTGTAAAAACATGTGAAGACAACG-TTCATTCTGGGCCAGAGGATGACCAGCGACC 
s canFam1.chr12  68222854 57 +  75455811 CCTGTAAAAACATGTGAAGACAACGTTTCATTCTGTGCCAGAGGATGACCAGCAACC 
s galGal2.chr3   42753406 56 - 108638738 CTTGTAAGAACATATGAAGACAGCG-CTCATTCTGTGCCAGTGGGTGGCCTGCAACC 
s fr1.chrUn     210136724 56 + 349519338 CCTGTAGAAACATGTGCAGGCATCG-CTCGTTCTGGGCGAGAGGATGACCGGCCACT 
s danRer1.chr20  17245997 56 +  31913010 CCTGTAGGAACATGTGCAGGCAGCG-CTCATTTTGGGCCAATGGATGACCAGCAACT 

a score=53058.0
s hg17.chr6    108722976 139 + 170975699 ATGGCGGCCTCCTGGTCGCTCTTGGTTACCCTGCGCCCCTTAGCACAGAGCCCGCTGAGAGGGAGATGTGTTGGGTGCGGGGCCTGGGCCGCCGCTCTCGCTCCTCTGGCCACCGCCCCTGGGAAGCCCTTTTGGAAAG 
s panTro1.chr5 111023287 139 + 175429504 ATGGCGGCCTCCTGGTCGCTCTTGGTTACCCTGCGCCCCTTAGCACAGAGCCCGCTGAGAGGGAGATGTGTTGGGTGCGGGGCCTGGGCCGCCGCTCTCGCTCCTCTGGCCACCGCCCCTGGGAAGCCCTTTTGGAAAG 
s mm5.chr10     88248538 139 - 130633972 ATGGCGGCCTCCTGGTCGCCCTTGGTTACTCTGCGCTCCGCCGCGCGCAGCCGGCTGACTGGGAGAGGTGTTGGGTGCGGGGCGCGGGTCGTCGCAATCCCTCCTCCGGCCCCTGGCCCTGGGAAACCCCTGTGGAAAG 
s galGal2.chr3  42777490 100 - 108638738 ATGGCGGCGCCCGTGTCGCCCTTGGTTACT------------GCGTGGTGCCTGCTGCGGGCA--------TCGGCGCGGCGTGTTGTCCGTC--------------TGCTGCCGGCACGGG-----CCCTGCCGAGAG 

a score=607969.0
s hg17.chr7     113660517 168 + 158628139 ATGATGCAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTA---AGCAGCCAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACCAGCTCTGAAGTAAGCACAGTAGAACTGCTGCATCTGCAACAACAGCAG 
s panTro1.chr6  115716623 168 + 161576975 ATGATGCAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTA---AGCAGCCAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACCAGCTCTGAAGTAAGCACAGTAGAACTGCTGCATCTGCAACAACAGCAG 
s mm5.chr6       14955268 168 + 149721531 ATGATGCAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTTTA---AGCAGCCAATTAGATGCTGGCAGCAGGGATGGGAGATCAAG---TGGTGACACCAGCTCTGAAGTAAGCACAGTGGAGCTGCTGCATCTGCAACAACAGCAG 
s rn3.chr4       40844510 168 + 187371129 ATGATGCAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTA---AGCAGCCAATTAGATGCTGGCAGCAGGGATGGGAGATCAAG---TGGTGACACTAGCTCAGAAGTAAGCACAGTGGAGCTGCTGCATCTGCAACAACAGCAG 
s canFam1.chr14  56181068 168 +  63549963 ATGATGCAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTA---AGCAGCCAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACCAGCTCGGAAGTAAGCACAGTAGAACTGCTGCATCTGCAACAACAGCAG 
s galGal2.chr1  165171657 168 - 188239860 ATGATGCAGGAATCTGCGACAGAGACAATAAGCAACAGTTCAATGAATCAAAATGGAATGAGCACTCTA---AGCAGCCAATTAGATGCTGGCAGCAGAGATGGAAGATCAAG---TGGTGACACGAGCACTGAAGTAAGCACAGTGGAACTCCTGCATCTGCAACAACAGCAG 
s fr1.chrUn     206218864 174 + 349519338 ATGATGCAGGAGTCGGCCACAGAGACAATAAGCAACAGTTCAATGAGTCAAAATGGAATGAGCACCCTAAGCAGCAGCCAATTAGAGGCTGGCAGTAGAGATGGGAGATCAAGCGCTGGTGACACGAGCAGCGAAGTAAGCACAGTCGAGCTGCTGCATCTGCAACAACAGCAG 
s danRer1.chrUn 132907084 167 + 367113659 ATGATGCAGGAGTCGGCCAATGAGACAATAAGCAACAGTTCAATGAGTCAAAATGGAATGAGCAGCCTA---AGCAGCCAATTAGATGCTGGCAGTAGAGATGGAAGATCAAG---TGGGGAGACGAGCAGTGAAGTAAGCGCAGTCGAGCTGCTGCATCTGC-ACAACAGCAG 

a score=398171.0
s hg17.chr7     116512159 230 + 158628139 TCATGTAGCGGTTGTCCAGTCAGCGTTCTTGGGGGCCTTGCATGTGTGCACATCCAGAGCTTCCAGGCAGTCCTGACAGCGCACGGCGCAGCACCAGTGGAACTTACACCCACACTTGGTCATCCGGGTGACATGGGAGGTGTCGTAGCCTCTCCCACAGCACATGACTTCACAGCTGTCCATGCCCCGGGAAGTCAGGTTGCACACACGGCCTGCTGTACCCAGGGAGC 
s panTro1.chr6  118798885 230 + 161576975 TCATGTAGGGGTTGTCCAGTCAGCGTTCTTGGGGGCCTTGCATGTGTGCACATCCAGAGCTTCCAGGCAGTCCTGACAGCGCACGGCGCAGCACCAGTGGAACTTACACCCACACTTGGTCATCCGGGTGACATGGGAGGTGTCGTAGCCTCTCCCACAGCACATGACTTCACAGCTGTCCATGCCCCGGGAAGTCAGGTTGCACACACGGCCTGCTGTACCCAGGGAGC 
s mm5.chr6       17732295 230 + 149721531 TCATGTAGGCGTCGCCCAGTCGGCACTCTTGGGGGCCTTGCATGTGTGCACGTCCAGGGCCTCCAGGCAGTCCTGACAGCGCACGGCACAGCACCAGTGGAATTTACACTCACACTTGGTCATCCGGGTGACGTGGGATGTGTCATAGCCTCTCCCACAACACATAACTTCGCAGCTGTCCATGCCTCGGGAAGTCAAGTTGCACACACGGCCCGCTGTACCCAGGGAGC 
s rn3.chr4       43819674 230 + 187371129 TCATGTAGGAGTTGTCCAGTCGGCACTCTTGGGGGCCTTGCATGTGTGCACGTCCAGGGCTTCCAGGCAGTCCTGACAGCGCACGGCACAGCACCAGTGGAATTTACACTCACACTTGGTCATCCGGGTGACATGGGATGTGTCATAGCCTCTCCCACAACACATAACTTCGCAGCTGTCCATGCCTCGGGAAGTCAAGTTGCACACACGGCCTGCTGTACCCAGGGAGC 
s canFam1.chr14  58698446 230 +  63549963 TCATGTGGGAGCCGCCCAGTCGGCGCTCGTGGGGGCCTTGCACGTGTGCACGTCTAGGGCCTCCAGGCAGTCCTGACAGCGCACGGCGCAGCACCAGTGGAACTTACACTCGCACTTGGTCATCCGCGTGACGCGGGACGTGTCGTAGCCTCTCCCGCAGCACATGACCTCGCAGCTGTCCATGCCGCGGGAAGTCAGGTTGCACACGCGGCCCGCCGTCCCCGGGGAGC 
s galGal2.chr1  166556534 230 - 188239860 TCATGTCCGGGAGGCCCAGCCCGCAGCCTTGGGCGCCTTGCACGTGTGGATGTCCACCTCCTCCAGGCAGTCCTGGCAGCGCACCGCGCAGCACCAGTGGAACTTGCACTCGCATTTGGTCATCCTGCTGACGCGCAACGTGTCGTAGCCACGGCCGCAGCACATCACCTCACAGCTGTCCATGCCGCGGGACGTCTGGTTGCACACCCGGCCGGCCGTCCCCGGAGAGC 
s fr1.chrUn     117668262 224 - 349519338 --CCGCGGGGGGGGGCCAGGTCACGTC----AGGCCCTTGCAGGTGTGCACGTCCACCTGCTGGTGGCAGTCTCGGCAGAGCACGGCGCAGCACCAGTGGAACTTGCACTCGCACTTGGTGGTGCGGCCGACCCGGGACGTGTCGTAGCCCCGGCCGCAGCACATCACCTCGCAGCCGTCGGTGCCGGGGGACGTCCTGTTGCAGAGGCGCCCGCCGGTCCCCAGCGACC 
s danRer1.chrUn 193800262 230 - 367113659 TCAAGTCAAATCGAGCCAGTCGGGTTTCTTGTGTAGTTTACAAGTGTGGACGTCCACCGTTTCCTCGCAGTCTCTGCACTCCACAGCGCAGCACCATTTAAACTTGCACTCGCATTTGGTCATGCGGTTTACACGGGTGGTGTCGTACCCGCGGCCGCAGCACATGATCTCACAGCCGTCCATGCCTCTGGAGGACTTGTTGCACACCCGTCCTGACGTACCCAGAGAAC 

a score=266204.0
s hg17.chr7     116714099 53 + 158628139 ATGCAGAGGTCGCCTCTGGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTTCAG 
s panTro1.chr6  119004369 53 + 161576975 ATGCAGAGGTCGCCTCTGGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTTCAG 
s mm5.chr6       17978854 53 + 149721531 ATGCAGAAGTCGCCTTTGGAGAAAGCCAGCTTTATCTCCAAACTCTTCTTCAG 
s rn3.chr4       44072448 53 + 187371129 ATGCAGAAGTCGCCTCTGGAGAAAGCCAGCTTTATCTCCAAACTCTTCTTCAG 
s canFam1.chr14  58860070 53 +  63549963 ATGCAGAGGTCGCCCCTGGAAAAGGCCAGCGTCCTCTCCAAACTTTTCTTCAG 

a score=435383.0
s hg17.chr7     116945541 246 + 158628139 CTATTTGTTAGGTTTTTCTAGGTGTTCATTTTT---GTGTAAGTTCCAATTCAC---TTCTTTTGAGTTGTTGTTGATTTCTATTTGCCTTGTATTA---CTGCTGCTGCTGCTTCTTTTGGTGTTCTGGGAACACTGGGTGACTTTACTTCTAGGAACAGGAAGAAAAGATTTAACTCTTGAAACACCCAACTCAGTCTTTGATTTACTGTTGCTGCATTCAGTAGTTTGATGGCTGCTGAGAGGACTGACC---TC 
s panTro1.chr6  119229725 246 + 161576975 CTATTTGTTAGGTTTTTCTAGGTGTTCATTTTT---GTGTAAGTTCCAATTCTC---TTCTTTTGAGTTGTTGTTGATTTCTATTTGCCTTGTATTA---CTGCTGCTGCTGCTTCTTTTGGTGTTCTGGGAACACTGGGTGACTTTACTTCTAGGAACAGGAAGAAAAGATTTAACTCTTGAAACACCCAACTCAGTCTTTGATTTACTGTTGCTGCATTCAGTAGTTTGATGGCTGCTGAGAGGACTGACC---TC 
s mm5.chr6       18175809 246 + 149721531 CTATTTGTTTGGTTTTTCTACTTGTTCGTGTTT---GTCTAAGGTCCAATTCTC---TTCTTTGGAGTTGTTGTTGATTTCTAGTTGCCTTGTATTG---CTGCTGCTGCTGTTTCTTTTGGTGTTCTGGGAACACTGAGCGACTTTGCTTCTAGGAACAGGAAGAAAAGATTTAACGCTTGAGACACCCATCTCAGTCTTTGATTTACTGTTGCTGCATTCGGCAGTTTGACGGCTGCTGGGAGGACTGGCT---TC 
s rn3.chr4       44334350 249 + 187371129 CTATTTGTTACGTTTTTCTACGTGTTCGTGTTT---GTCTACGTTCCAATTCTC---TTCTTTGGAGTTGTTATTGATTTCTAGTTGCCTTGTATTACTGCTGCTGCTGCTGCTTCTTTTGGTGTTCTGGGAACACTGGGCGACTTTACTTCTAGGAACAGGAAGAAAAGATTTAACTCTTGAGACACCCAACTCAGTCTTGGATTTACTGTTGCTGCATTCGGTAGTTTGATGGCTGCTGAGAGGACTGGCT---TC 
s canFam1.chr14  59084680 249 +  63549963 CTGTTGGTTTGGTTTTGCGACTTGTTCGTTTTTTTGGTGGAAGTTTCAAATCTC---TTCTTTTGAGTTGTTGTTGATTTCGGTTTGCCTTGTATTA---CTGCTGCTGCTGCTTCTTTTGGTGTTCGGGGAACACTGGGTGGCTTTACTTCTAGGAACAGGAAGAAAAGATTTAACTCTCGAAACACCCAACTCCGTCTTGGATTGCCTGTTGCTGCATTCGGCCGCTTGGTGGCTGCTGAGAGGACTGGGC---TC 
s galGal2.chr1  166718518 245 - 188239860 TTATT-GTAAAATTTTTCTGTTTGTTCTTTTTTTT-GTGCAAATTCCAAATCTCTCTTTTTTTTGTGTCGTTATCTGCCTCTATTTGCCTTGTATTA---CTGCTGCTGCT--TTTTTTTAGTACTCTGAGAAGGCTGGGTGACTTTACTTCTCGGTACAGGAAGAAAAGATTTAACTCTTGAACCACCCAGCTCTGTCTTTGAT------TTGCTGCTTTCTACAGTTCGACTGCTGCTGAGAGGACGGATTCCATC 

a score=404599.0
s hg17.chr8     118881131 186 + 146274826 TC---------AAAGTCGCTCAATGTCTCGGTATTTCTTCCTCAAAATAGAGACCTGGTCTTTAAAGAGGACGGGGTCGAGCCTCATCTGAGAGTGGATCAGCGGCATGTAGCCAAACCAGCTGGCAAACGTATTCATGCAGCTCTGTCGCTGGGCAAAGTGGTCAGGGTCAGCCCAACGGGAAGCCCGAGAAGT 
s panTro1.chr7  121606752 186 + 149542033 TC---------AAAGTCGCTCAATGTCTCGGTATTTCTTCCTCAAAATAGAGACCTGGTCTTTAAAGAGGACGGGGTCGAGCCTCATCTGAGAGTGGATCAGCGGCATGTAGCCAAACCAGCTGGCAAACGTATTCATGCAGCTCTGTCGCTGGGCAAAGTGGTCAGGGTCAGCCCAACGGGAAGCCCGAGAAGT 
s mm5.chr15      53109074 186 + 104138553 TC---------AAAGTCGTTCAATGTCTCTGTATTTCTTCCTCAGAATTGAGACTTGGTCTTTAAAGAGGACCGGGTCCAGCCTCATCTGAGAATGGATCAGCGGCATGTAGCCAAACCAGCTGGCAAATGTATTCATGCAGCTCTGTCGCTGGGCAAAGTGGTCAGGGTCGGCCCAGCGGGATGCTCGGGAAGT 
s rn3.chr7       89414686 186 + 143082968 TC---------AAAGTCGTTCAATGTCTCTGTATTTCTTCCTCAGGATTGAGACTTGGTCTTTAAAGAGGACCGGGTCGAGCCTCATCTGAGAGTGGATCAGCGGCATGTAGCCAAACCAGCTGGCAAACGTATTCATGCAGCTCTGTCGCTGGGCAAAGTGGTCAGGGTCAGCCCAGCGAGATGCTCGGGAAGT 
s canFam1.chr13  20213465 186 +  66159989 TC---------AAAGTCGCTCAATGTCTCGGTATTTCTTCCTCAGAATAGAGACCTGGTCTTTAAAGAGGACAGGGTCGAGCCTCATCTGCGAGTGGATCAGCGGCATGTAGCCAAACCAGCTGGCAAACGTATTCATGCAGCTCTGTCGCTGGGCAAAGTGGTCAGGGTCAGCCCAGCGGGAAGCCCGAGAAGT 
s galGal2.chr2   14208956 186 - 147590765 TC---------AGAGTCGTTCAATGTCTCGGTATTTCTTCCTCAGGATGGAGACCTGGTCTTTAAAGAGGACAGGGTCGAGCCTCATCTGAGAGTGGATCAGCGGCATATAGCCAAACCAGCTGGCAAAAGTGTTCATGCAGCTCTGCCGTTGGGCGAAGTGGTCGGGGTCGGCCCAGCGTGAGGCCCGGGATGT 
s fr1.chrUn     293823575 195 - 349519338 TCTGGATGGTTATAGCCTCTCTATGTCCCTGTACTTCTTCCTCAGTATGGACACCTGGTCTTTGAAAAGGACCGGGTCCAGCCTCATCTGTGAGTGGACCAGGGGCATGCTGCCAAACCAGCTGGCAAACTTGTTCATGCAGGTCTGACGCTGGGCAAAGTGGTCCGGGTCGGCCCAGCGAGACGCTCGGGAGCT 
s danRer1.chrNA  25951001 186 + 390413307 TC---------AGAGTCGCTCGATGTCTCTGTACTTCTTGCGCAGTATTGATACCTGGTCCCTGAACAGAACAGGATCCAGTCTCATTTGCGAATGGACCAGGGGCATTGTGCCAAACCAGCTGGCAAATTTGTTCATGCACGTCTGCCTCTGGGCAAAATGGTCAGGGTCGGCCCAACGTGATGCACGGGACGT 

a score=116382.0
s hg17.chr9     128764156 33 + 138429268 ATGGCCTGCCTGAGCCCCTCGCAGCTCCAGAAG 
s panTro1.chr11 113605485 33 + 123086034 ATGGCCTGCCTGAGCCCCTCGCAGCTCCAGAAG 
s mm5.chr2       30226931 33 + 181686250 ATGGCCTGCCTGAGTCCCTCACAACTCAAGAAG 
s rn3.chr3        9310853 33 + 170969371 ATGGCCTGCCTGAGTCCCTCACAACTCAAGAAG 
s canFam1.chr9    6350671 33 -  53642819 ATGGCCTGCCTGAGCCCCTCGCAGCTCCAGAAG 

a score=-3882.0
s hg17.chr9    128787519 1 + 138429268 C 
s mm5.chr2      30244450 0 + 181686250 - 
s rn3.chr3       9330108 0 + 170969371 - 
s canFam1.chr9   6365310 0 -  53642819 - 
s fr1.chrUn    290357729 0 - 349519338 - 

a score=2555.0
s hg17.chr9     128787520 5 + 138429268 TAGGC 
s mm5.chr2       30244450 5 + 181686250 TAGGC 
s rn3.chr3        9330108 5 + 170969371 TAGGC 
s canFam1.chr9    6365310 5 -  53642819 TATGC 
s galGal2.chr17   5207254 5 -  10632206 TAAAC 
s fr1.chrUn     290357729 5 - 349519338 CAAAG 

a score=71382.0
s hg17.chr9     128787525 62 + 138429268 CATCAGCAATATCAGGAGGTAGAGAGGCAGAAGGAGATTGTCTATCTGTGTAGTGTATGCTT 
s mm5.chr2       30244455 62 + 181686250 CATCAGCAATATCAGTAGGTAGAGAGGCAACAGGAGATTGTCTATCTGAGTAGTGTACGCTT 
s rn3.chr3        9330113 62 + 170969371 CATCAGCAAAATCAGTAGGTAGAGGGGCAACAGGAGATTGTCTATCTGAGTTGTGTATGCTT 
s canFam1.chr9    6365315 62 -  53642819 CATCAGCAATATCAGGAGGTAGAGAGGCAACAGGAGATTGTCTATCTGTGTCGTGTATGCTT 
s galGal2.chr17   5207259 62 -  10632206 CATAAACATGATCTGGAGGTAGAGAGGTAACAGCAAATTATCAATTTGGGTTGTGTAAGCTT 
s fr1.chrUn     290357734 62 - 349519338 CAACAGCAGGATAAAGAGGTAAAGTGGGAGGAGGAGGTTGTCTATTTGGAAGGTGTAAGCTT 
s danRer1.chr21  12648417 62 -  13488766 CAGCAGGAGGATGTAGAGATACAGAGGAAGCAGAAGGTTGTCAATCTGCGACGTATAGGCCT 

a score=2211540.0
s hg17.chr9            128787587 1515 + 138429268 CCAGGAGGGACA---CAGTGCTGATGGACCCCAAA--ATCCAAGCATAACTGTAGTTTAGGTCCACTCCACTGTCAAAGATTAAGATCAGAGCTACAGAAATGATCTGCGCAAATATAGATGTCATGGTCCCCTCAAAAGTCTTTTTGGTTCCAGGCCAGCGGATCTCCCCCATGGTGCTACCGAAGATGGAGGCCACAGTATCACCCACACCCACAGCCAGGACACCGGCATAGGGGACGAGGGCCCTGGCTCCTCCCAGGCTACCCTTCTGTGTGCAGGGTCTGGGGATCAGCCAGATGGGAAGAGACATGCCCAGGAGCAGGTAGATGTGTGTCAGAATGAGTGGTCCACTGTCTCGTTCATCCAGAAAAAGGGACAGGAAGCTCCGTAGAGTGTGACCCAAAGGCTTGATGCGGAAGTAGCGCACATACTCCAGGAAGATGAAGACCGCCAGGCATACAGTGGCGGCTACATAGAGCAGTGGCCGGTCAAAGATGATACCTGGGATGTAGGTGGCTACCACAATGAGGTGGAAATACTTTCGGGCGATGGTGGGGGCCTGGTGCTTCTTGGACTCGGAAGATGACCGCTTGGCATTCTGGTACAGCACCACCAGGCAGGCCAAGGTGGCCAGCAGAGACCAATAGGCTAGGAGGTAGATGCGGGTGTCTGTCTGGAAGAGAAACTGAAGAAGCCAGAGCAGGGGATTCCTGCGGATGAGCCGGTGCAGCCAGGGTAGGACCACACCAAGGCTCAGCACACAGGTCATGAGGTGGAAGAAGATGGAGGAGGCCCAGGTGCCTGAGTCCATGAAGACAAACAGAGTGCTGAAGAAAATGCCCATGAGTACCATCCCTACTACCACCACCAGCAGGAAGAAGTCCACTGGGTC---CCCCTGACTTTCCACCAGTGTCAGAGAGCGCTTGATGAGCTGGTTGAGGACAAAGCTAATGCCACCCAATACCAGCAGTGCCTCACCAGGGGTGAAGCAGCGGGGCAGCAGGTACAGCAGGATCATGTTGAGATAAACGAAGATCAGAAGGACTTCCAGGACTTCGATCACCTCCCCCACGCTCAACGAGTGCTTCATGATATAAATGATAACACCTCCAGCCAAGCCCAAGATGACACAAGTGTTGGTTGGCACTGGGCGAGTGATGCCGAGCGCCAACACTGATGAGAAGAGGGCCACTGCCATGCCAGTGGCTGCCACCACAATGCCAAAACGCTCAAAGAACGGGTTCCCAGCAGTCTGGCACCGCTCCTTCATGACTAGTCCAAGCAAAGGCATGACCATGGAGGCGGGCAATAGGCCACTGTTTGCGGACATTCGGAACTGGAAGACGGCGCTTCCCTGCTGTAGCAGCCGGTCCCACTTGTATTGGACGTAGAAGGCCTGCACTGCGAGGGCCACGGCGCACCACGAGTATCGGTCCCATACGGTTGCGTGGATGCTCAGCACCACTGCAAACACTACTGCCGCCTCTGCCAGCACCGATCCACTCAGCGGAGCCCCAG 
s panTro1.chr11_random  46298820 1517 -  53199993 CCAGGAGGGGCATGCC--TGCAGATGGACTCTAGAGGATCCAAGCATAACTGTAGTTTAGGTCCACTCCACTGTCAAAGATTAAGATCAGAGCTACAGAAATGATCTGCGCAAATATAGATGTCATGGTCCCCTCAAAAGTCTTTTTGGTTCCAGGCCAGCGGATCTCCCCCATGGTGCTACCGAAGATGGAGGCCACAGTATCACCCACACCCACAGCCAGGACACCGGCATAGGGGACGAGGGCCCTGGCTCCTCCCAGGCTACCCTTCTGTGTGCAGGGTCTGGGGATCAGCCAGATGGGAAGAGACATGCCCAGGAGCAGGTAGATGTGTGTCAGAATGAGTGGTCCACTGTCTCGTTCATCCAGAAAAAGGGACAGGAAGCTCCGTAGAGTGTGACCCAAGGGCTTGATGCGGAAGTAGCGCACATACTCCAGGAAGATGAAGACCGCCAGGCATACAGTGGCGGCTACATAGAGCAGTGGCCGGTCAAAGATGATACCTGGGATGTAGGTGGCTACCACAATGAGGTGGAAATACTTTCGGGCGATGGTGGGGGCCTGGTGCTTCTTGGACTCGGAAGATGACCGCTTGGCATTCTGGTACAGCACCACCAGGCAGGCCAAGGTGGCCAGCAGAGACCAATAGGCTAGGAGGTAGATGCGGGTGTCTGTCTGGAAGAGAAACTGAAGAAGCCAGAGCAGGGGATTCCTGCGGATGAGCCGGTGCAGCCAGGGTAGGACCACACCAAGGCTCAGCACACAGGTCATGAGGTGGAAGAAGATGGAGGAGGCCCAGGTGCCTGAGTCCATGAAGACGAACAGAGTGCTGAAGAAGATGCCCATGAGTACCATCCCTACTACCACCACCAGCAGGAAGAAGTCCACTGGGTC---CCCCTGACTTTCCACCAGTGTCAGAGAGCGCTTGATGAGCTGGTTGAGGACAAAGCTAATGCCACCCAATACCAGCAGTGCCTCGCCAGGGGTGAAGCAACGGGGCAGCAGGTACAGCAGGATCATGTTGAGATAAACGAAGATCAGAATGCCTTCCAGGACTTCGATCACCTCCCCCACGCTC-CCTAGAGCTTCATGATATAAATGATAACACCTCCAGCCAAGCCCAAGATGACACAAGTGTTGGTTGGCACTGGGCGAGTGATGCCGAGCGCCAACACTGATGAGAAGAGGGCCACTGCCATGCCAGTGGCTGCCACCACAATGCCAAAACGCTCAAAGAACGGGTTCCCAGCAGTCTGGCACCGCTCCTTCATGACTAGTCCAAGCAAAGGCATGACCATGGAGGCGGGCAATAGGCCACTGTTTGCGGACATTCGGAACTGGAAGACGGCGCTTCCCTGCTGTAGCAGCCGGTCCCACTTGTATTGGACGTAGAAGGCCTGCACTGCGAGGGCCACGGCGCACCACGAGTATCGGTCCCATACGGTTGCGTGGATGCTCAGCACCACTGCAAACACTACTGCCGCCTCTGCCAGCACCGATCCACTCAGCGGAGCCCCAG 
s mm5.chr2              30244517 1509 + 181686250 CCAGAAGGGATA---CAGTGCTGATGGACCCCAAA--ATCCAGGCATAACTGTAGTTCAGGTCTACTCCACTGTCAAAGATTAAGATTAGAGCTACAGAGATGATTTGTGCAAATATAGATGTCATAGTCCCCTCGAAGGTTTTCTTAGTTCCAGGCCAGCGGATCTCTCCCATGGTGCTGCCAAATATGGAGGCCACAGTATCACCCACACCCACAGCCAAGACCCCAGCATAGGGGACCAGGGCTCTTGCTCCTTCCAGGCTGTCCTTCTGTGTACAGGGTCTGGGGATCAGCCAAATAGGAAGAGACATGCCCAGAAGCAGGTAGATGTGTGTTAGGATAAGGGGTCCACTGTCTCGTTCATCCAGGAAGAGGGACAGAAGGCTTCGCAGAGTGTGACCCAAGGGCTTTATTCGGAAATAGCGCACATACTCCAGGAAGATGAAGACTGCCAGGCACACAGTGGCGGCCACATACAGCAGTGGCCGGTCAAAGATGATGCCCGGGATATAAGTGGCTACCACAATGAAGTGGAAATACTTTCTTGTAATGGTAGGCGCCCTGTGCTTCTTGGACTCAGAAGACGACCGCTTAGCATTCTGGTACAGCACCACCAGGCAGGCCACAGAGGCCAGCAAAGACCAATAGGCAAGGAGGTAGATGCGAGTTTCAGTGTAGAAGAGGAACTGAAGAAGCCAAAGCAGGGGGTTCCTACGAATGAGCCAGTGCAGCCAGGGCAGAACCACACCAAGGCCCAGCACACAGGTCATGAGGTGGAAGAAGATGGAAGAGGCCCAGGTGCCTGAATCCATGAAGACAAAGAGGGTGCTGAAAAAGACACCCATGAGCACCATCCCTACCACCACCACCAACAGGAAGAAGTCCACTGGGTC---CCCCTGGCTTTCA------GTCAGAGAGCGCTTGATGAGTTGGTTAAGGACGAAGCTAATGCCACCCAATACCAGCAGTGCCTCCCCAGGAGTGAAGCATCGGGGCAGCAGGTACAGCAGGATCATGTTGAGATAAACAAATATTAGCAGGACTTCCAGGACCTCGATCACCTCGCCTACACTGAGCGAGTGCCTCATAATATAAATGATAACGCCTCCAGCCAAACCAGAGATGGCACAAGTATTGGTGGGCACCGGGCGAGTAATGCCCAGTGCCAACACGGAGGAGAAGAGGGCCACTGCCATGCCAGTAGCTGCAACCACAATGCCGAAGCGCTCGAAGTATGGGTTCCCTGCAGTCTGGCAGCGCTCCTTCATGACTAGCCCAAGCAAAGGCATGACCATGGAGGCCGGCAGTAAGCCGCTGTTCGCGGACATCCGGAACTGGAAAACGGCATTGCCCTGCTGGAGCAGCCGGTCCCACTTGTACTGGACGTAGAAGGCCTGCACCGCGAGGGCCACCGCGCACCAGGAGTATCGGTCCCACACTGCAGCGTGGATGCTCAACACCACGGCGAACACCACTGCAGCCTCCGCCAGCACCGACCCGCTCAGCGCAGCCCCAG 
s rn3.chr3               9330175 1509 + 170969371 CCAGAAGCGACA---CAGTGCTGATGGACCCCAAA--ATCCAAGCATAGCTGTAGTTCAGGTCTACTCCACTGTCAAAGATTAGGATCAGAGCCACAGAGATGATTTGTGCAAATATAGATGTCATAGTTCCCTCGAATGTTTTCTTAGTTCCAGGCCAGCGGATCTCCCCCATGGTGCTGCCAAATATGGAGGCCACAGTATCGCCCACACCCACAGCCAGGACCCCAGCATAGGGGACCAGGGCTCTTGCTCCTCCGAGGCTGCCCTTCTGTGCACAGGGTCTGGGGATCAGCCAAATGGGAAGAGACATGCCCAGAAGCAGGTAGATGTGCGTCAGGATGAGGGGCCCGCTGTCCCGTTCATCCAGGAAGAGGGACAGAAGGCTGCGCAGAGTGTGACCCAGGGGCTTGATTCTGAAATAGCGCACATACTCCAGGAAGATGAAGACGGCCAGACACACGGTGGCGGCCACATACAGCAGTGGCCGGTCAAAGATGATACCGGGGATGTAAGTGGCCACCACAATGAAGTGGAAATACTTTCTGGTAATGGTAGGAGCCTTGTGCTTCTTGGACTCAGAAGATGACCGCTTGGCATTCTGGTACAGCACCACCAGGCAGGCCATGGTGGCCAGCAAGGACCAATAGGCTAGGAGGTAGATGCGAGTTTCTGTGTAGAAGAGGAACTGAAGAAGCCAGAGCAGGGGGTTCCTACGAATGAGCCAGTGCAGCCAGGGCAGAACCACACCAAGGCCCAGCACACAGGTCATGAGGTGGAAGAAGATAGAAGAGGCCCAGGTGCCCGAATCCATGAAGACAAAGAGGGTGCTGAAAAAGACACCCATGAGCACCATCCCCACCACCACCACCAACAGGAAGAAGTCCACTGGGTC---CCCCTGGCTTTCA------GTCAGAGAGCGCTTGATGAGCTGGTTGAGGACGAAGCTAATGCCACCCAATACCAGCAGTGCCTCCCCAGGAGTGAAGCAGCGGGGCAGCAGGTACAGCAGGATCATGTTGAGATAAACGAATATTAGCAGGACTTCCAGGACCTCGATCACCTCGCCCACACTGAGCGAGTGCTTCATAATATAAATGATAATACCTCCGGCCAAACCCGAGATGGCACAAGTATTGGTGGGCACCGGGCGAGTAATGCCCAGTGCCAACACCGAGGAGAAGAGGGCCACTGCCATGCCAGTGGCTGCAACCACAATGCCGAAGCGCTCGAAGTATGGGTTCCCTGCAGTCAGGCAGCGCTCCTTCATGACCAGCCCAAGCAAAGGCATGACCATGGAGGCCGGTAGTAAGCCACTGTTCGCGGACATTCGGAACTGGAAAACAGCATTCCCCTGCTGGAGCAGCCGGTCCCACTTGTACTGGACGTAGAAGGCCTGCACTGCTAAGGCCACGGCGCACCAGGAGTATCGGTCCCACACTGCAGCGTGGATGCTCAGCACCACTGCGAACACCACTGCAGCCTCCGCCAGCACTGACCCGCTCAGCGCAAACCCAG 
s canFam1.chr9           6365377 1515 -  53642819 CTAGGAGGGACA---CGATGCTGATAGAGCCCAAA--ATCCAAACATAACTGTAGTTTAGGTCCACTCCACTATCAAAGATTAAGATCAGAGCTACAGAAATGATCTGGGCAAATATAGAGGTCATGGTCCCCTCAAAGGTCTTTTTGGTTCCAGGCCAGTGGATTTCCCCCATTGTGCTGCCAAAAATGGAGGCCACAGTGTCCCCCACACCCACAGACAGGACTCCTGCATAAGGGACTAGGGCTCTTGCTCCCCCCAAGTTGCCCTTCTGTGTGCAGGGCCTGGGAACCAGCCAAATTGGAAGAGACATGCCCAAGAGCAGGTAGATATGTGTCAGGATGAGTGGTCCACTGTCTCGTTCATCTAAGAAAAGGGACAGGAGGCTCCTCAGAGTGTGGCCCAGGGGCTTGATGCGGAAATAGCGCACATATTCTAGGAAGATAAAGACTGTTAGGCATATGGTGGCAGCTACATAGAGCAGTGTCCGGTCAAGGATGATACCGGGGATGTAGGTGGCCACCACAATGAAGTGGAAATACTTTCGGGCAATGGTGGGGGCCTGGTGCTTCTTAGACTCAGAAGATGACCGCTTGGCATTCTGGTAAAGCACCACCAGGCAGGCTAAGGTGGCCAGCAGAGACCAGTAGACCAGGAGGTAGATGCGGGTCTCTTTCTGGAAGAGGAATTGAAGAAGCCAGAGCAGGGGGTTCTTGCGGATAAGCCGGTGCAGCCAGGGAAGGACCACGCCAAGGCCCAGCACACAAGTCATAAGGTGGAAGAAGATGGAGGAAGCCCAGGTACCTGAGTCCATGAAGACAAAGAGTGTGCTGAAGAAGACGCCCATAAGCACCATCCCTACTACCACCACCAGCAGGAAGAAATCCACTGGGTC---GCCCTGGCTCTCCACCACAGTCAGAGAACGCTTGATGAGCTGGTTGAGCATGAAGCTGATGCCACCTAATACAAGCAGTGCCTCCCCAGGGGTAAAGCAGCGGGGCAGCAGGTACAGCAGGATCATGTTGAGGTAGACGAAGATCAGCAGGACCTCCAGGACCTCGATCACCTCGCCCACACTCAGTGAGTGCTTCATGATATAAATGATGACACCTCCAGCCAAGCCTGAGATGACACAAGTGTTGGTGGGCACTGGGCGAGTGATGCCCAGTGCCAGTACCGACGAGAAGAGGGCCACTGCCATCCCAGTGGCTGCCACCACAATTCCAAAGCGCTCAAAATATGGGTTCCCCATGGACTGGCAGCGCTCCTTCATGACCAGTCCGAACAAAGGCATGACCATTGATGCGGGCAGCAGGCCACTGTTTGCGGACATGCGGAACTGGAAGACAGCGCTTCCCTGCTGCAGCAGCCGGTCCCACTTGTACTGGACGTAGAAGGCCTGCACTGCGAGAGCCACGGCGCACCACGAGTATCGGTCCCACACGGCTGCGTGGATGCTCAGCACCACTGCGAACACTACTGCTGCCTCCGCCAGCACTGACCCACTCAGCGGAGCCCCGG 
s galGal2.chr17          5207321 1512 -  10632206 CCAAAAGAGAAA---CTAAGCTCACAGACACCAGA--ATCCAGGCATAGCTGGAGTTCAGGTTCACGCTGCTGTCAAAGATCAGAATAAGAGCCACAGCAATGATCTGAGCAAAAATTGCTGTCATTGTCCCTTCAAAGGTCTTCTTTGTGCCCGGCCATTTGATTTCCCCCATGGTACTGCCAAAAACAGAGGCCATGGTGTCTCCTACCCCTACTGCAAGCACCCCAGCATAGGGCACCAGTGCTCCTGCCCCAGACAAGGCACCTTTAGGGGCACAGGATCTGGGGAACAACCACACTGGGAGGGACATGCCAAGAAGAAGATAAATGTGAGTCAAGATTAGAGGCCCACTGTCTCTTTCATCCAAGAAGAGAGACAGCAAATAGCGAAGAGTTTGGCCAAACGGTTTGATCCTGAAGTACCGAATGTACTCTAAGAATATGAACACTGCCAGACACAGGACTGCAGCAACATGGAGAAGCTGGCGGTCATAAATTAGTCCAGGAACATAAGTTGCTACAACAATGAAATGGAAATACTTCCTGGTTATGGTTGAGGCCTGGTGTTTTTTAGATTCG---GACGATCTCTTGGCATTCTGGTAGAAAACTATGCCACACGCTGAAGCAGCCAATAAAGTCCAATATATGAGAAGGTAAACCCTCGTCTGTGTCTGAAACAGAAACTGGAGCAGCCAAAACAAAGGGTTCCTCCGGATCAGTCGGTAAAGCCAAGGCATGATGACCCCTAAGCCTAGCACTGCTGTCATCATGTGGAAAAACATGGAGGAGATCCACGTACCCGAATCCATGAAAATGAAGAGAACAGTGAAAAAAAGCCCAAGGATAACAACTCCAATAACTGCCACCAGAAGGAAGAAGTCTATGGGTTC---ACCTCTGCCCTCGATTACATTCAGTGAGCGTTTAATGAGCTGATTGAGAACAAAACTTATACCTCCGAGAACTAGCAATGCTTCTCCAGGAGTAAAACACCGAGGCAGCAGGTAGAGCAAGATCATACTGAGGTAGACAAAAATTAGCAGCACTTCTAGGACCTCTATCACTTCTGAAACAGTCAAAGAGTGCTTCATGGTATAGATAATTATACTGCCAGCAACACCACTGAGTATGCAGGTGTTGGTGGGCACAGGTTTTGTGATGCCAACAGCAATTACAGACAAAAATAGAGCAACCAACATGCCAGTGGAAGCTACAACTATGCCAAAGCGTTCAAAGTACACGATACCAGCAGCCTTGCACCTCTCCTTCATTGCTATCCCCAGCAAGGGGATGACCATGCTGGCAGGCAGGAGCCCACTGTTCGCTGTGGTGCGGAACTGGAACACAGCCCCCCCCTGCTGCAGCAGGCGGTCCCATTTAAACTGGACATAGAAAGCCTGGATGGCAAGAGCTACAGCACACCAGGAGTAGCGGTCCCACACCACTGCATGCACGCACAGAACGATGCTGAAGACGATCAGGGATTCCACCAGCACTGGTTTGTTTAACATGGTTCCAG 
s fr1.chrUn            290357796 1512 - 349519338 CTAGCATTGCCA---CCAGAGTGATAGAACCAACA--ATCCAGGAGTAGCTGGAGTTCAGATTGATGCCAGTATCAAAGATTAGAAAGATGGCCACAGCAATAATCTGTGCAAACACAGATGTTGCAGTCCCCTCAATGGTTTTCTTAGTACCGGGCCAACGAATCTCTCCCATGGTGCTGCCAAACACAGATGCCACAGTATCTCCTACCCCGACAGCCAGGACACCTGCATATGGTATCAGCCCACCGGCACCAGGAAGTATTCCTTTTGGGGCACATGGTCCAGGGAACAGCCATATGGGAAGAGACATGCCCAAAAGGAGGTAAATGTGGGTCAGGATAAGAGGCCCAGAGTCCCGCTCATCCAGGAACAATGTAAGAACCTGTCTGAGCACCTGACCCAGTGGCCTGATCCGAAAGTAGCGCACGTACTCCAGGAACAAAAAGACTGCCAAGCAGCCAACAGAGGCCACATGGAGCAGGTGCCGGTCGTATATGAGACCTGGAACATAGGTGGCCACCACAATTAGATGGAAGTACTTCCGGACTACAGTCGAGGCTTGGTGTTTCTTGGACCCA---GACTGACGTTGATAGTTCTGGTGTAACACAACACAGGTGGCCAGGACCACCAGAAACACCCAGTATGCCAGCAGAGAGAGCCTTCTGTCAGTGAATGTGACAAAGTCCAGTAGCCACATGATGGGATGCCTGCCGATGAACAGGGATAGCCATGGCAACAGAATTCCCAGACTGAGAACGGCTGTCATGATGTGGAAAAAAACAGATGACACCCAGGTCTCTGATTCCATGAAGCAAAACAGCAGAGCAAAGAACACGCCCAGCAACAACGAGCCTACTACCACGACCGGCAGGAAATAATTTATTGGATC---GCCTTTGACCTCTGTCAAGTTCAGTGAGCGCTTGATAAGCTGGTTGACAATGAAACTGATTCCACCGATGATGAGAAGGGCTTCTCCGGGTGTGAAGCAGCGAGGCAGCAGGAAAAGCACGATCAGGCTGAGATAGACGAAGATCAACAACACCTCTAAGACTTCGATGACCTCAGACACCGTTAACGTCTGTTTCGTCATGTACAGAATTGCACTGGCGGCCATGCCTGCAATCACACAAGTGTTGGTGGGTACAGGTCTTGTAATGCCTAAGGCGATCAGGGAGAGGAACAGTGCCAGCATCATGCCGGTGATGGTGATGACCATGGAGAAGCGCTCGAGGTAAACGTTCCCTGATTCAGAGCACCTTAGTCTCAGCACCAAGCCCAGCAAAGGCATCACCATGGAGGCTGGGACGATGCCACTGTTTGCTGCTGGACGGAACTGGAACACGGCACCCCCCGACTTGAGCAAACGATCCCATTTGTGCTGAACGTAGAAAGCCTGGATGAAGAGTGCAATGCTGCACCAGGAATGCTGGTTCCACAGCACCATGTGGACCCACCCCACAATGGCAAAAACTATAGCGGACTCTACAAAGACTGGATTAATCTCCATTGCCACTG 
s danRer1.chr21         12648479 1515 -  13488766 CCAACATGGCCA---CCATAGAGATGGATCCCACC--ACCCACGAGTAGCTGGCGTTCAGGTTAATACTGCTGTCGGCGATGAGGAAAACCACCACAGCGATAATCTGAGCGAACACAGAGGACGCCGTGCCCTCAAATGTCTTCTTAGTCCCAGGCCAGCGGATTTCACCCACGTTGCTGCCGAAAACGGATGCCACTGTGTCCCCGACCCCTACAGCAAGGACTCCAGCATAGGGTACTAGCCCACTAGCGCCCCCTAGGCCTCCTTTTGGGGTGCACATCCCAGGTGTCAACCACAGTGGAAGAGAAACGCCAAGAAGAAGATAAATATGAGTGAGAATAAGTGGTCCTGAATCTCTCTCATCAAGGAATAAGGTGAGAAGACGTCGAAGCGGAGCCCCGAATGGTCGAATGCGAAAATAGCGGACATATTCGAGAAACAAAAATGCAGAGAGGCAAACAACCGCAGACAAATGCAGCAAAGGACGATCCAGAGCGAGTCCGGGAGCGAAGGTTAAAACGGTGAGCAGGTGGAAATACTTCCGCACTGTCGTTGATGCTTGATGCTTCTTGCTGCCTGCAGAT---CGATGACTATTTTGATGCATCACAACGGCAACTGCTAGAAGCGCCAAAGCGGCCCAAAACCCAATGAGCCAAAGTCGAGTGTTTGATTCAGTGATGAAATGCATCAACCAAGTGATTGGATGGTGCTGCGTGAGTAGAGATAGCCAAGGAACCAATAACCCCAATCCCAAAACCGCAGTCATGGTATGGAAGAAGAGCGACGCTGACCAGGTTTCAGATTCCATGAATATAAAAAGCACGGCGAAGAATATTCCCAACAGCACTAACCCTAAAACAGCTACCGGGAGGAAATACGGAAGCGGGTCTGAGTTTGCATTTCCAGACGAAGCCAGAGAGCGCTTAATTAGCTGGTTGATGATAAAACTAATCCCGCCAAGGATCAGAAGGGCTTCGCCGGGGGTGAAGCAACGTGGAAGGAGGTACAGCAGGATTAAACTTAGATACACAAAAATCAGAAGCACCTCCAAGACTTCGATGACCTCAGACACTGTTAGTGTTTGCTTCACGGTGTACAGAATAGCACTACTAGCAATTCCGGCGATAACACAAGTGTTTGTTGGCACCGGCCGCGTGATTCCCAATGCGATGAGCGAGAGGAATAGAGCCAACATCATTCCGATTACTGTGATGACCATTGCGAATCGCTCCATGTAGACGTTTCCCACAGCGAGGCAGCGGCCTCGTAGGGTGAGTCCCAGTAGTGGCAGCACCATACTGGCTGGCAGGACGCCGCTGTTGGCTGAAGGACGAAACTGGAAGACGGCGGCACCAGAGCGAATCAGACGATCCCATTTGTGCTGCACATAAAAAGCCTGGACGGCCAATGCCATGCAGCACCAGGACAGCTGATTCCACACGGCCATGTGTACGGAAACCACCATGGCGAACACCACCGCAGATTCAACCAGCACTGGATCCATCTGCATGACTGCAG 

a score=491.0
s hg17.chr9            128789102 2 + 138429268 GC 
s panTro1.chr11_random  46300337 2 -  53199993 GC 
s mm5.chr2              30246026 2 + 181686250 AC 
s rn3.chr3               9331684 2 + 170969371 AC 
s canFam1.chr9           6366892 2 -  53642819 GG 
s galGal2.chr17          5208833 2 -  10632206 TC 
s fr1.chrUn            290359308 2 - 349519338 GC 

a score=-383.0
s hg17.chr9            128789104 1 + 138429268 C 
s panTro1.chr11_random  46300339 1 -  53199993 C 
s mm5.chr2              30246028 1 + 181686250 T 
s rn3.chr3               9331686 1 + 170969371 T 
s canFam1.chr9           6366894 1 -  53642819 A 
s galGal2.chr17          5208835 1 -  10632206 C 

a score=46199.0
s hg17.chr9            128789105 31 + 138429268 CCGGGGCCGGAGATGGGCACTCTCGGGTCAT 
s panTro1.chr11_random  46300340 31 -  53199993 CCGGGGCCGGAGATGGGCACTCTCGGGTCAT 
s mm5.chr2              30246029 25 + 181686250 CCTGG------GGAGGGCACTGTCGGGTCAT 
s rn3.chr3               9331687 31 + 170969371 CCGGGGCTTGGGGAGGGCACTGTCGGGTCAT 
s canFam1.chr9           6366895 25 -  53642819 CCGGG------GGAGCGTGCTCTCGGGTCAT 

a score=145262.0
s hg17.chr9            128882427 96 + 138429268 ATGGCGTTCCGGAGGGCCGAGGGCACGTCTATGATCCAGGCCCTGGCCATGACGGTGGCCGAGATCCCCGTGTTCCTGTACACGACGTTTGGGCAG 
s panTro1.chr11_random  46393737 96 -  53199993 ATGGCGTTCCGGAGGGCTGAGGGCACGTCTATGATCCAGGCCCTGGCCATGACGGTGGCCGAGATCCCCGTGTTCCTGTACACGACGTTTGGGCAG 
s mm5.chr2              30327714 96 + 181686250 ATGGCATTCCGGAGGACTGAGGGTATGTCCATGATCCAGGCTCTGGCCATGACTGTGGCTGAGATTCCAGTGTTCCTGTACACAACTTTTGGTCAG 
s rn3.chr3               9412966 96 + 170969371 ATGGCATTCCGTAGGACTGAGGGTATGTCCATGATCCAGGCTCTGGCCATGACTGTGGCTGAGATACCAGTGTTCCTGTACACGACTTTTGGTCAG 
s canFam1.chr9           6452102 96 -  53642819 ATGGCATTCCGGAGGACTGAGGGCATGTCCATGATCCAGGCACTGGCCATGACGGTGGCCGAGATCCCTGTGTTCCTGTATACAACGTTTGGGCAG 
s fr1.chrUn            120365676 96 + 349519338 ATGTCACTCAGACAAGCGGAAGGGATGTCCATTGCCCAGGCTTTGGCAATGACGGTAGCAGAGATCCCAGTGTTCCTTTATTCCACGTTTGGACAG 
s danRer1.chrNA         88880074 96 + 390413307 ATGTCATTCAGAAGTGCAGAGGGCGTGTCCATCATGCAGGCCTTGGCCATGACTGTGGCTGAGATACCTGTGTTTCTCTATTCCACCTTTGGGCAG 

a score=359580.0
s hg17.chr9     128937229 216 + 138429268 TCAGAGCTTGGCCCGG---GGGTGGCTCTGCAGCAGGGCACGCATGTCCAGGAGCGCCTTCTCCAGGTAATGCGCCAGGCGGGCGGCGTTGGTCTCCGCGCAGCTGTTGTAGGCCGACAGGGAGAAGTTGATGTGGGCCTCCATGGGGTTATAGCAGACACCGTAGCCGTCGGGGACCACGGGCCCGAAGAACATGACACAGTCTGTCTTGGCAGGGAC 
s panTro1.chr11 113780157 216 + 123086034 TCAGAGCTTGGCCCGG---GGGTGGCTCTGCAGCAGGGCACGCATGTCCAGGAGCGCCTTCTCCAGGTAATGCGCCAGGCGGGCGGCGTTGGTCTCTGCGCAGCTGTTGTAGGCCGACAGGGAGAAGTTGATGTGGGCCTCCATGGGGTTATAGCAGACACCGTAGCCGTCGGGGACCACGGGCCCGAAGAACATGACACAGTCTGTCTTGGCAGGGAC 
s mm5.chr2       30362600 216 + 181686250 TCAGAGCTTGGCCCTG---GGGTGGTTCTGGAGTAGGGTGCGCATGTCCAGCAGAGCTTTCTCCAAGTAGTGAGCCATGCGGGCAGCGTTGGTCTCAGCACAGCTGTTGTAGGCTGACACGGAGAAGTTGATATGGGCCTCCATGGGGTTGTAGCAGATGCCATAACCATCTGGGACCACAGGTCCGAAGAACATGACACAGTCTGTCTTGGCAGGGAC 
s rn3.chr3        9448511 216 + 170969371 TCAGAGCTTGGCCCTG---GGGTGGTTCTGGAGTAAGGTGCGCATGTCCAGCAGAGCTTTCTCCAAGTAGTGAGCCATGCGGGCAGCGTTGGTCTCAGCACAGCTGTTGTAGGCTGACACGGAAAAGTTGATATGGGCCTCCATGGGATTGTAGCAGATGCCGTAACCGTCTGGGACCACAGGTCCGAAGGACATGACACAGTCTGTCTTGGCAGGGAC 
s canFam1.chr9    6500360 216 -  53642819 TCACAGCTTGGCCCGA---GGGTGACTCTGCAGCAGAGCGCGCATGTCCAGGAGTGCCTTCTCCAGGTAGTGCGCCAGGCGGGCTGCATTGGTCTCGGCACAGCTGTTGTAGGCTGACACAGAGAAGTTGATGTGCGTCTCCATGGGGTTGTAGCACACGCCATAGCCGTCTGGGACCACGGGCCCAAAGAACATGACGCAATCTGTCTTGGCAGGGAC 
s galGal2.chr17   5301443 216 -  10632206 TTACAGTTTGGATTTG---GGGGTAGATTGGAGCAAGCTTCTCATGTCTAGCAGTGCTTTCTCAAGATAATGTGCCATGCGAGCTGCATTTGTGTCAGCACAGCTGTTGAATGCTGAAATGGCAAAGTTGATGTGTTCATCCATAGGGTTGTAACAGATTCCATAGCCATCTGGAACCACGGGACCAAAACACATCACACAGTCTGTCTTTGCTGGGAC 
s fr1.chrUn      47430687 219 + 349519338 TCACTGCTGGGCCGTGGCTGCGGCATCTTCCAGGAGAGCTCTCATGTCCAACAGGGCGCCCTCTACAGCCTGGGCGAAGCGAGCGGCGTTGGTCTCCTCACAGCTGTTGAAGGCCGTGATGGCCACGTTGATGTGCTCCTCCATGGGATTGTAACACACGCCGTAACCGTCTGGCACCATCGGACCAAAGCACATCACGCAGTCTGTCTTCGAGCCGAC 
s danRer1.chr8    1065541 216 -  36410523 TTAAAGCTTGGCTCTG---GGTGTCTGCTCCAGCAGGGTCCTCATGTCCAGCAGAGCGTCCTCCAGACCCTGAGCCAGACGGACAGCATTTGTGTCCTGGCAGCTGTTGAACGCAGATACTGCAAAGTTAATGTGGGTATCCATGGGATTGTAGCATACGCCATAACCATCAGGCACCACCGGCCCAAAGCACATCACACAGTCAGTTTTAGCTGGCAC 

a score=134850.0
s hg17.chrX     122745047 138 + 154824264 ATGACTTTTAACAGTTTTGAAGGATCTAAAAC----TTGTGTACCTGCAGACATCAATAAGGAAGAAGAATTTGTAGAAGAGTTTAATAGATTAAAAACTTTTGCTAATTTTCCAAGTGGTAGTCCTGTTTCAGCATCAACA- 
s panTro1.chrX  126858618 138 + 160174553 ATGACTTTTAACAGTTTTGAAGGATCTAAAAC----TTGTGTACCTGCAGACATCAATAAGGAAGAAGAATTTGTAGAAGAGTTTAATAGATTAAAAACTTTTGCTAATTTTCCAAGTGGTAGTCCTGTTTCAGCATCAACA- 
s mm5.chrX       34442683 138 + 160634946 ATGACTTTTAACAGTTTTGAAGGAACTAGAAC----TTTTGTACTTGCAGACACCAATAAGGATGAAGAATTTGTAGAAGAGTTTAATAGATTAAAAACATTTGCTAACTTCCCAAGTAGTAGTCCTGTTTCAGCATCAACA- 
s rn3.chrX      157748736 138 - 160775580 ATGACTTTTAACAGTTTTGAAGGATCTAGAAC----TGTTGTACCTGCAGACACCAATAAGGATGAAGAATTTGTAGAAGAGTTTAATAGATTAAAAACATTTGCTAACTTCCCAAGCAGCAGTCCTGTTTCAGCATCAACA- 
s canFam1.chrX   98422419 138 + 126913094 ATGACTTTTAACAGTTTTGAAGGAGCTAAAAC----TTGTGTACCTGCAGGCATCAATAAGGATGAAGAATTTGTAGAAGAGTTTAATAGATTAAAAACTTTTGCTAATTTTCCAAGTAGCAGTCCTGTTTCAGCATCAACG- 
s galGal2.chr4   75226910 138 -  90634903 ATGACGTGTAATGGCCCAGATAGCTCTGAATC----TGGTGCCACTCCAGCCACTGACGGTGACCAGGAGTGGACACAGGAACACTACCGACTAGGAACCTTTGTGGAGTTTCCCCATGATTGTCCAGTTTCAGCATCAGCG- 
s danRer1.chr14  14605069 142 -  34612130 TTTAGTTACTACAAATATGGCACACTCAACTCATAATGGCGAATTGGAATCTGACAATGTGGCAGCTGATTGGTCAGTCATGAAGAATCGGGTGAACTCTTTTCAACGTTTTCCATATTCTGAAGACATTTCAGCA-CAGCGG 

a score=158991.0
s hg17.chrX     122745185 115 + 154824264 CTGGCACGAGCAGGGTTTCTTTATACTGGTGAAGGAGATACCGTGCGGTGCTTTAGTTGTCATGCAGCTGTAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACAGGA 
s panTro1.chrX  126858756 115 + 160174553 CTGGCACGAGCAGGGTTTCTTTATACTGGTGAAGGAGATACCGTGCGGTGCTTTAGTTGTCATGCAGCTGTAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACAGGA 
s mm5.chrX       34442821 115 + 160634946 TTGGCGCGAGCTGGGTTTCTTTATACCGGTGAAGGAGACACCGTGCAATGTTTCAGTTGTCATGCGGCAATAGATAGATGGCAGTATGGAGACTCAGCTGTTGGAAGACACAGGA 
s rn3.chrX      157748874 115 - 160775580 TTGGCGCGAGCGGGGTTTCTCTACACTGGTGAAGGAGACACCGTGCAGTGTTTCAGTTGTCACGCGGCAGTAGATAGATGGCAGTATGGAGACTCAGCTGTTGGAAGACACAGGA 
s canFam1.chrX   98422557 115 + 126913094 TTAGCACGAGCTGGTTTTCTGTATACTGGTGAAGGAGATACTGTGCGGTGCTTTAGTTGTCATGCATCAATAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACAGGA 
s galGal2.chr4   75227048 115 -  90634903 CTAGCTCGAGCTGGCTTTGTTTATACTGGAGAAGGTGATAAAGTCAAGTGCTTCAGTTGCCATGTAACTGTTGAAGGATGGGAGCCTGGGGATTCTGCAATTGACAGACACAAAA 
s fr1.chrUn     143073633 115 - 349519338 CTGGCCCGGGCCGGCTGGTTCTACACGGGGGTGGGCGACCGCGTGCAGTGTTTCAAGTGCAACGTGACAGCCGAGGGCTGGCAGGCTGGAGACTGTCCCACCGAAAAACACAGGC 
s danRer1.chr14  14605211 115 -  34612130 CTGGCCCGAGCGGGCTTTTACTTCACAGGCGAGGGGGACAGGGTGCAATGTTTCAGCTGCAGTGCCACTGTGCAGAACTGGAACAGAGGTGACACCCCATTGGAGAGACATCAAC 

a score=509291.0
s hg17.chrX     122745300 448 + 154824264 AAGTATCCCCAAATTGCAGATTTATCAACGGCT---TTTATCTTGAAAATAGTGCCACGCAGTCTACAAATTCTGGTATCCAGAATGGTCAGTACAAAGTTGAAAACTATCTGGGAAGCAGAGAT---------CATTTTGCCTTAGACAGGCCATCTGAGACACATGCAGACTATCTTTTGAGAACTGGGCAGGTTGTAGATATATCAGACACCATATACCCGAGGAACCCTGCCATGTATAGTGAAGAAGCTAGATTAAAGTCCTTTCAGAACTGGCCAGACTATGCTCACCTAACCCCAAGAGAGTTAGCAAGTGCTGGACTCTACTACACAGGTATTGGTGACCAAGTGCAGTGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCTTGTGATCGTGCCTGGTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTTTGGGCCGGAA 
s panTro1.chrX  126858871 448 + 160174553 AAGTATCCCCAAATTGCAGATTTATCAACGGCT---TTTATCTAGAAAATAGTGCCACGCAGTCTACAAATTCTGGTATCCAGAATGGTCAGTACAAAGTTGAAAACTATCTGGGAAGCAGAAAT---------CATTTTGCCTTAGACAGGCCATCTGAGACACATGCAGACTATCTTTTGAGAACTGGGCAGGTTGTAGATATATCAGACACCATATACCCGAGGAACCCTGCCATGTATAGTGAAGAAGCTAGATTAAAGTCCTTTCAGAACTGGCCAGACTATGCTCACCTAACCCCAAGAGAGTTAGCAAGTGCTGGACTCTACTACACAGGTATTGGTGACCAAGTGCAGTGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCTTGTGATCGTGCCTGGTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTTTGGGCCGGAA 
s mm5.chrX       34442936 448 + 160634946 GAATATCCCCAAATTGCAGATTTATCAATGGTT---TTTATTTTGAAAATGGTGCTGCACAGTCTACAAATCCTGGTATCCAAAATGGCCAGTACAAATCTGAAAACTGTGTGGGAAATAGAAAT---------CCTTTTGCCCCTGACAGGCCACCTGAGACTCATGCTGATTATCTCTTGAGAACTGGACAGGTTGTAGATATTTCAGACACCATATACCCGAGGAACCCTGCCATGTGTAGTGAAGAAGCCAGATTGAAGTCATTTCAGAACTGGCCGGACTATGCTCATTTAACCCCCAGAGAGTTAGCTAGTGCTGGCCTCTACTACACAGGGGCTGATGATCAAGTGCAATGCTTTTGTTGTGGGGGAAAACTGAAAAATTGGGAACCCTGTGATCGTGCCTGGTCAGAACACAGGAGACACTTTCCCAATTGCTTTTTTGTTTTGGGCCGGAA 
s rn3.chrX      157748989 448 - 160775580 GAATATCCCCAAATTGCAGATTTATCAATGGTT---TTTATTTTGAAAACGGTGCCACACAGTCTACATCTCCTGGCATCCAAAATGGCCAGTACAAATCTGAAAACTGTGTGGGAAACAGAAAT---------CATTTTGCTCTTGACAGGCCGTCGGAGACTCATGCAGATTATCTCCTGAGAACTGGACAGGTTGTAGATATTTCAGATACCATATACCCGAGGAACCCGGCCATGTGTAGTGAAGAAGCCAGACTGAAGACGTTTCAGAACTGGCCAGACTATGCCCATTTAAGCCCCAGAGAGTTAGCTAGTGCTGGACTCTACTACACGGGGATTGATGATCAAGTGCAATGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCCTGTGACCGTGCCTGGTCAGAGCACAGGAGACACTTTCCCAACTGCTTCTTCGTTTTGGGCCGGAA 
s canFam1.chrX   98422672 448 + 126913094 AAGTATCCCCAAATTGCAGATTTATCAATGGCT---TTTATTTTGAAAACACTGCTGCACAACCTACAAATCCAGGTATCCAAAATGGTCAATATAATGCAGAAAACTATCTGAGAAACAGAGAT---------CATTTTGTTTTAGACAGACCATCTGAGACTCATGCAGATTATCTTTTGAGAACTGGACAGGTCGTAGATATATCAGACACCACATACCCGGAGAACCCTGCCATGTATAGTGAAGAAGCTAGATTAAACTCATTTCAGAACTGGCCAGACTATGTCCACTTGACCCCAAGAGAGTTAGCTAGTGCTGGATTCTACTACACAGGTATTGACGATCAAGTGCAGTGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCGTGTGATAATGCATGGTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTCTGGGCCGGAA 
s galGal2.chr4   75227163 442 -  90634903 ACCTTTCCCCAGATTGCAGATTTATTACTGGGTCTGCTTTTTTGGAAAATAACG------------TACATCCTCTTGTGCAGAGCCACCAGCATAGAACTGAAAAT------GGCTCCAGCAATTTGGCCCTCCCCTCTGCTCTGGAGGACTTGTCTGATGTGGAGGCAGATTACCTGTTGAGAACCAGGCAGGTTGTGGACATGTCCGATACTTTGTATCCTAAAAACCCTGCTATGTGCAGTGAAGAAGCCAGGCTGAAGTCCTTTCACAATTGGCCCCCCTATGGCCTATTGACGCCAAAGGAATTAGCTAGTGCAGGACTCTACTATACAGGTGTTGGTGATCAAGTTGCATGTTTCTGTTGCGGTGGAAAACTGAAAAACTGGGAACCTGGTGATCGAGCTTGGTCTGAGCACAAGAGGCATTTTCCCAAATGCTTTTTTGTCCTGGGTCGGGA 
s fr1.chrUn      74286897 397 + 349519338 AGGTTTCTCCATTTTGCAAATTTCTCAGTTGTA---TTTATC---GAACCAGTTCCAATC------CGATTCCTGGCA-CCTCACTGACGA--ACGGCTCTGCCTACAATG-AAGAAGCAGAAGA---------TAT--------------------------------GGAATATCGTCTGAGAACAGGACAGGTGGTCGAT------GAGTCCATTTATCCAGTGGTCCCTCATATGAGGAGTGAAGAAAGCCGGCTTCACACCTTTTCTACGTGGCCCTTGACTGCACCAGTGAGCCCGTGCGATCTGGCCCAAGCTGGCCTTTACTACTTAGGGCAGTGTGACCAGGTTCAGTGTTTCTGCTGTGGTGGCACACTGGCTGACTGGGAAATCGGGGATTCCGCCTGGGCAGAACACAGCAAACATTTCCCTTTCTGCTTTTTCATCCTGGGGCACGA 
s danRer1.chr14  14605326 382 -  34612130 TGGCATCTCCGGACTGCAGGTTCCTCAGCTGTG---CTCATGGTATGAGAAACT------------CTAATTCG---ATCCAGAGTCCTGATTACGATG-------------AAGAGGCCGAGAA---------TAG--------------------------------AGAGTTCCTCCTCCGCACGGGAGAGGTGGTGGAC------GAGTCCATGTATCCTGTTGTACCGCACATGAAGAGTGAAGAAGCGCGACTGAGTACTTTCAACAACTGGCCAGCAGACTCTCCAGTTCGGCCTGAAGACCTGGCAGAAGCAGGGATGTATTACATTGGGATAGACGACAATGTGCAGTGCTTCTGTTGCGGAGGGGGTCTGAGTGGATGGGAGCAAGGCGACGATCCTTGGAGTGAACATGCGAAGTACTACTCAAACTGCTTCTTCTTCTTGGGCCACAA 

a score=18792.0
s hg17.chrX    122745748 22 + 154824264 TCTT---AATATTCGAAGTGAATCT 
s panTro1.chrX 126859319 22 + 160174553 TCTT---AATATTCGAAGTGAATCT 
s mm5.chrX      34443384 22 + 160634946 CGTT---AATGTTCGAAGTGAATCT 
s rn3.chrX     157749437 22 - 160775580 TGTT---AATGTTCGAAGTGAGTCT 
s canFam1.chrX  98423120 22 + 126913094 TGTT---AATATTCGAAGTGAATCT 
s galGal2.chr4  75227605 25 -  90634903 CGTTGGAAATGTTTCAACTGATTCT 
s fr1.chrUn     74287294 16 + 349519338 TGTTGGCAATAT---------ACCT 

a score=0.0
s hg17.chrX 122745748 27 + 154824264 TCTTAATATTCGAAGTGAATCTGATGC 

a score=-3673.0
s hg17.chrX    122745770 5 + 154824264 GATGC 
s panTro1.chrX 126859341 5 + 160174553 GATGC 
s mm5.chrX      34443406 2 + 160634946 GG--- 
s rn3.chrX     157749459 2 - 160775580 GG--- 
s canFam1.chrX  98423142 5 + 126913094 GATGT 
s galGal2.chr4  75227630 5 -  90634903 ATCTG 

a score=43762.0
s hg17.chrX     122745775 54 + 154824264 TGTGAGTTCTGATAGGAATTTCCCAAATTCAACAAAT--CTTCCAAGAA-----ATCCATC 
s panTro1.chrX  126859346 54 + 160174553 TGTGAGTTCTGATAGGAATTTCCCAAATTCAACAAAT--CTTCCAAGAA-----ATCCATC 
s mm5.chrX       34443408 54 + 160634946 TGTGAGTTCTGATAGGAATTTCCCAAATTCAACAAAC--TCTCCAAGAA-----ATCCAGC 
s rn3.chrX      157749461 54 - 160775580 TGTGAGTTCAGATAGGAATTTCCCAAATTCAACAAAT--TCTCCAAGAA-----ATCCAGC 
s canFam1.chrX   98423147 54 + 126913094 TGCGAGTACTGATAGGAACGTCCCAAATTCAACAAGT--ATTCCAGAAA-----ATCCAGC 
s galGal2.chr4   75227635 54 -  90634903 TGCTGAGCTTGGGAGAAGCTGTCTAAA--CAACGAACAGCATCCAAGGA-----ATCCATC 
s danRer1.chr14  14605708 50 -  34612130 TGTGGGC---------AACGTCCCCCTGACAACACCT--AGGCCAAGGGCTAATGTCCACC 

a score=105732.0
s hg17.chrX     122745829 95 + 154824264 CATGGCAGATTATGAAGCACGGATCTTTACTTTTG-GGACATGGATATACTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG 
s panTro1.chrX  126859400 95 + 160174553 CATGGCAGATTATGAAGCACGGATCTTTACTTTTG-GGACATGGATATACTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG 
s mm5.chrX       34443462 95 + 160634946 CATGGCAGAATATGAAGCACGGATCGTTACTTTTG-GAACATGGACATCCTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG 
s rn3.chrX      157749515 95 - 160775580 CATGGCAGAATATGACGCACGGATCGTTACTTTTG-GAACATGGCTATACTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG 
s canFam1.chrX   98423201 95 + 126913094 CATGGCAGATTATGAAGCACGGATCGTTACTTTTC-GGATGTGGATGTGTTCAATTAACAAGGAGCAACTTGCAAGAGCTGGATTTTATTCTTTAG 
s galGal2.chr4   75227689 95 -  90634903 CATGGCAGAATATGAGAGGCGGATACAAACATTTT-TAGCTTGGATATACCCTGTTAACAAGGAACATCTTGCTGAAGCAGGGTTCTACAGCACAG 
s fr1.chrUn      74287369 95 + 349519338 CATGGGGACATTTGAGGAAAGGCTGAGGAGTTTTGCTGGTGTCAAC-CACCCTCTAAACATAGAGAGGCTTGCGAGAGCTGGCTTCTACAGCAATG 
s danRer1.chr14  14605759 95 -  34612130 TACAGACACTTTTGAGGGGCGTCTTGATAGCTTCA-AAGGCAGACAGCATCCCATTGACCCTGAGAGATTGGCCAGAGCTGGTTTCTACAGCACAG 

a score=-8579.0
s hg17.chrX     152648964 14 + 154824264 CTATTCTAGGGCCA 
s panTro1.chrX  157964696 14 + 160174553 CTATTCTAGGGCCA 
s mm5.chrX       65413418 14 + 160634946 CTATTCTAGGGCTA 
s rn3.chrX      159861438 14 + 160775580 CTATTCTAGGGCTA 
s canFam1.chrX  124765428 14 + 126913094 CTACTCTAGGGCCC 
s galGal2.chr26   3679526 14 -   4255270 CTACGCTAATGAGT 
s fr1.chrUn     230132755 14 - 349519338 TTAGACGAATGAGT 
s danRer1.chr10  12185566 12 +  25436222 -TGGGCGGAGGCA- 

a score=283274.0
s hg17.chrX     152648978 218 + 154824264 CGGCAGGGTTGATGGGGGAAGTGGCCCCTGAGCTGT-CATTGCCCCCTGCCGCCTCCTTCTCCTTCTTGCCACTGTACTGGCCAATGAACGAACCATCCTCGTTGAACTGAACATCCA---CGCTGCCCCCATAATCGGCCAGGCTGTCGTCACTGCCCAGGGGCTTGATGTCCCCGTTGAGCGATGGCTGGCT-GCTGCCAAAGGCCTTCTCCTCGTTGTCA 
s panTro1.chrX  157964710 218 + 160174553 CGGCAGGGTTGATGGGGGAGGTGGCCCCTGAGCTGT-CATTGCCCCCTGCCGCCTCCTTCTCCTTCTTGCCACTGTACTGGCCAATGAACGAACCATCCTCGTTGAACTGAACATCCA---CGCTGCCCCCATAATCGGCCAGGCTGTCGTCACTGCCCAGGGGCTTGATGTCCCCGTTGAGCGATGGCTGGCT-GCTGCCAAAGGCCTTCTCCTCGTTGTCA 
s mm5.chrX       65413432 218 + 160634946 CTGCAGGATTGATAGGAGAGGTAGCCCCTGAACTGT-CATTGCCTCCTGCTGCCTCCTTCTCTTTCTTGCCACTGTACTGGCCGATGAAAGAGCCATCCTCATTGAACTGGACGTCCA---CACTGCCCCCATAATCAGCCAGGCTGTCATCACTGCCTAGGGGTTTGATGTCTCCGTTGAGAGATGGCTGGCT-GCTGCCAAAGGCCTTCTCTTCATTGTCA 
s rn3.chrX      159861452 218 + 160775580 CTGCAGGATTGATAGGAGAGGTAGCCCCTGAGCTGT-CATTGCCTCCCGCTGCCTCCTTCTCTTTTTTGCCACTGTATTGGCCGATGAAAGAGCCATCCTCATTGAACTGGACATCCA---CACTGCCCCCATAATCAGCCAGACTGTCATCACTGCCTAGGGGTTTGATGTCTCCATTGAGAGATGGCTGGCT-GCTGCCGAAGGCCTTCTCTTCATTGTCA 
s canFam1.chrX  124765442 218 + 126913094 CGGCAGGGTTGATGGGGGAGGCGGCCCCTGAGCTGT-CGTTGCCGCCTGCTGCCTCCTTCTCCTTCTTGCCGCTGTACTGGCCGATGAAGGAGCCGTCCTCGTTGAACTGCACGTCCA---CGCTGCCCCCGTAGTCGGCCAGGCTGTCGTCACTGCCCAGGGGCTTGATGTCCCCATTGAGGGACGGCTGGCT-GCTGCCAAAGGCCTTCTCCTCGTTGTCA 
s galGal2.chr26   3679540 218 -   4255270 AGATAGCATTGACTGGGGACGTGGCTTCTGAGCTCT-CGTTGCCTTCCGTTTCCTCCTTGTCCTTTTTCACTGTGTACTGGCCAATGAAGGAGCCGTCCTCGTTGAACTGCCCTTCCC---CACCCTCTCCGTAGTCCACCAAGCTGTCGTCACTCTCCTGTTGCTTTATCGTGCCATCCAGGGAGGTCTGACT-GTTGGGCAGTGGTTTGTTGTCTTCATCG 
s fr1.chrUn     329627114 209 - 349519338 CGGCAGGGTTGAGGGGGGAGTTGTCCGGTACGCCGTGGAACGGCTCCGGCC-------CCTCGCTGTGGCGGCTGAACTGGCTGGCCAGGGACTCGTCCATGTTGAGCTCCGTGGTTACGGCGCTGCTGCCGTTGAAGTCCAGGTTGTCCTCGCTGCACA---GCTTGCTGTCCTCGCCCAGCGAAGGCTGGCTGGCTGT----GCGCTTCTCTTCGAGGTCA 
s danRer1.chr10  12185578 200 +  25436222 TGTTGGGGTTGACCGGCGACACGGCGCCAGAGCTGT-CGTGCCCGCGTG---------GATCCCTTCGACCGCTGTACTGCCCGATGAAGGAGCCGTCCTCATTGAACTGGATGTCCA---CGCTGTCCCCGTAATCCGCCAGACTGTCGTTGCTGCT---GCGCTTGCTCTCGCACCC---CGACGGCTGGCT-GATGG---AGCACTTCTCCATATCACTG 

a score=102002.0
s hg17.chrX    152691446 25 + 154824264 ATGCTCATGGCGTCCACCACTTCCG 
s mm5.chrX      65450627 25 + 160634946 ATGATCCTGGTGTCTACCACGTCTG 
s rn3.chrX     159897295 25 + 160775580 ATGCTCCTGGTGTCTACCGTGTCCG 
s canFam1.chrX 124808548 25 + 126913094 ATGCTCCTGGCATCCACCACCTCGG 

a score=45779.0
s hg17.chrX     152694029 80 + 154824264 TCAGTGTG---GCTTGGGGGTCGTGTCTAGGCCCTGGGGGTGGGAAGCTGAGGGTGAGGCTGGGGCCCCAGGGCCCCGGGAGA 
s panTro1.chrX  158011192 80 + 160174553 TCAGTGTG---GCTTGGGGGTCGTGTCTAGGCCCTGGGGGTGGGAAGCTGAGGGTGAGGCTGGGGCCCCAGGGCCCCGGGAGA 
s mm5.chrX       65453119 80 + 160634946 TCAGACTG---GCTTGCGAGTTGAATCTGGACCCTGGGGATGGGAGGTTGAGGGGGAAATTGGAGCCCCAGGTCCCCGGGAGA 
s rn3.chrX      159899770 80 + 160775580 TCAGACTG---GCTTGCGAGTTGAATCTGGACCCTGGGGATGGGAAACTGAGGGGGAAACTGGAGCCCCAGGTCCCCGGGAGA 
s canFam1.chrX  124811065 77 + 126913094 TCAGT------GCTTAAGTGGAGAGTCCAGGCCCTGGGGATGGGACGCCGAGGGGGACGCCGGGGCCCCGGAGCCGCGGGAGA 
s galGal2.chr26   3294210 66 -   4255270 TCAGGGCG---GCT--------------GCGCCATGGAACTGAAATGCACACCGTGCCCTGGCACCCCCATCACCCCTGGGGA 
s danRer1.chrNA 128898465 70 + 390413307 CCAGACTGCAAGCACAGGGAGAGTGTCTGGCCCCCAGGGC-----AGCT--------CGCTGGGGCCAGAGAGCCTCTGGTGA 

a score=18883.0
s hg17.chrX     152694109 35 + 154824264 AGCCTTTGTTCCTGCCCAGGCGGCTGCTGGGCGGG 
s panTro1.chrX  158011272 35 + 160174553 AGCCTTTGTTCCTGCCCAGGCGGCTGCTGGGCGGG 
s mm5.chrX       65453199 35 + 160634946 AGACTTTGTTTTTGCTGATGCTGCTGCAGGCCAGG 
s rn3.chrX      159899850 35 + 160775580 AGACTTTGTTTTTGCTGAAGCTGCTGCAGGCCAGG 
s canFam1.chrX  124811142 35 + 126913094 AGCCTTTGCTCCTACCCAGGCGGCCGGAGGCCGGA 
s galGal2.chr26   3294276 30 -   4255270 CATC----CCCCTGTCAGCACTGCT-CGGGGCGGG 

a score=7409.0
s hg17.chrX     152694144 26 + 154824264 GCCTTTGGGCTTCGGGGCCCAGGACT 
s panTro1.chrX  158011307 26 + 160174553 GCCTTTGGGCTTCGGGGCCCAGGACT 
s mm5.chrX       65453234 20 + 160634946 GGCGTCAGAGTT------CCTAGACT 
s rn3.chrX      159899885 26 + 160775580 GGCTTCAGGTTTCGAGTTCCTAGACT 
s canFam1.chrX  124811177 26 + 126913094 GGCTTCAGGCTGCAgggcccggggcc 
s galGal2.chrUn  50576950 22 + 165033910 -GTTCTGAG---CGAGGAACAGCACC 

a score=24632.0
s hg17.chrX     152694170 31 + 154824264 GGGAGAGGTGGTAGATGCTGGCCCAAGGCCC 
s panTro1.chrX  158011333 31 + 160174553 GGGAGAGGTGGTAGATGCTGGCCCAAGGCCC 
s mm5.chrX       65453254 31 + 160634946 CGGGGAGGCTGTAGATGCTAACCCATGGCCC 
s rn3.chrX      159899911 31 + 160775580 GGGGGAGGCTGTAGATGCTAGCCCATGGCCC 
s canFam1.chrX  124811203 31 + 126913094 gggggagccggtggacgcgggccccgcgccc 
s galGal2.chrUn  50576972 31 + 165033910 GGGAGAGGCGGCAGCGGCTGCCCCCGAGCTC 
s fr1.chrUn     329777075 24 - 349519338 GGACGAGGAGGTGGAGGAAGGATC------- 

a score=47489.0
s hg17.chrX    152694201 49 + 154824264 TGGCGGACAGAGGTCTTTCCCAAGAGCTCCTTAAACACAGAGTCCATGT 
s panTro1.chrX 158011364 49 + 160174553 TGGCGGACAGAGGTCTTTCCCAAGAGCTCCTTAAACACAGAGTCCATGT 
s mm5.chrX      65453285 49 + 160634946 TGGCGGACAGCAGTCTTTCCCAAGAGCTCCTTAAACACAGAATTCATGT 
s rn3.chrX     159899942 49 + 160775580 TGGCGGACAGCAGCCTTTCCCAAGAGCTCCTTAAACACAGAATCCATGT 
s canFam1.chrX 124811234 49 + 126913094 tggcgggcggAGGTCTTTCCCAGGAGCTCCTTAAACACGGAATCCATGG 
s fr1.chrUn    329777109 37 - 349519338 TGGCGTGTG------------AGGAGCTCCTTAAAAACAGAGTCCATGT 

a score=175616.0
s hg17.chrX    152694250 13 + 154824264 TCTGTGCCACAGC 
s panTro1.chrX 158011413 13 + 160174553 TCTGTGCCACAGC 
s mm5.chrX      65453334 13 + 160634946 TCTGTGCCACAGC 
s rn3.chrX     159899991 13 + 160775580 TCTGCGCCACAGC 
s canFam1.chrX 124811283 13 + 126913094 TCTGTGCCACAGC