715e2acf2dd9ef6106cc42ce79c724e1e52ad62e braney Thu Mar 12 09:14:28 2026 -0700 NoDots MAF alignment display for hgc mafClick, with i-row preservation and mafFrag -noDots flag hgMaf.c: add hgMafFragHelperNoDots and public wrappers (hgMafFragNoDots, hgBigMafFragNoDots, hgMafFragFromMafListNoDots) that return a list of maf blocks containing only species with actual sequence — no dot-filled rows. Blocks are broken when the species set changes; gaps between same-species blocks are filled with native sequence for the reference and dashes for others. Preserve i-row data (leftStatus/rightStatus/leftLen/rightLen) through the NoDots path so insert annotations appear in emitted blocks. hgMaf.h: declare the new NoDots public functions. mafClick.c: use NoDots path when mafClickMafFrag is enabled. Fix block numbering (aliIx was never incremented in useMafFrag path). Use full textSize for NoDots line width. Use dots instead of spaces in diff mode for both paths. Fix species label width computation to check labelHash consistently so long assembly names don't misalign sequences. Strip ref gap columns where no other species has sequence. mafFrag: add -noDots option to invoke hgMafFragNoDots from the command line, with 4 new tests (noDots, noDotsRev, noDotsOutName, noDotsLarger). refs #21477 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> diff --git src/hg/ratStuff/mafFrag/tests/expected/noDotsLarger.maf src/hg/ratStuff/mafFrag/tests/expected/noDotsLarger.maf new file mode 100644 index 00000000000..1375217953c --- /dev/null +++ src/hg/ratStuff/mafFrag/tests/expected/noDotsLarger.maf @@ -0,0 +1,254 @@ +##maf version=1 scoring=zero +a score=0.000000 +s hg38.chr1 100000 117 + 248956422 actaagcacacagagaataatgtctagaatctgagtgccatgtt--atcaaa-ttgtactgagactcttgcagtcacacaggc-tgacatg-taagcatcgccatgcctagtacagactctc +s ponAbe2.chr1 223770897 117 - 229942017 actaaacacacagagaataatgtatagaatctgagtgccatatt--atcaaa-ttatactgagactcttgcagtcacacgggc-tgatatg-taagcatcgtcatgcctagtacagactctc +i ponAbe2.chr1 C 0 C 0 +s nomLeu3.chr7b_GL397639_2_random 52831 117 + 172226 actaagcacacagagaataatgtacagaatctgagtgccatgtt--atcaaa-ttatactgagacgcttgcagtcacacaggc-tgatatg-taagcatcgtcatgcctagtacagactctc +i nomLeu3.chr7b_GL397639_2_random C 0 C 0 +s rheMac3.chr1 14400752 117 - 229590362 actaagcacacagagaataatgtatggaatctgagtgccatgtt--atcaaa-ttatactgagactcttgcagtcacacgggc-tgatatg-caaccattgtcacgcctagtacagactctc +i rheMac3.chr1 C 0 C 0 +s macFas5.chr1 221132935 117 - 227556264 actaagcacacagagaataatgtatggaatctgagtgccatgtt--atcaaa-ttatactgagactcttgcagtcacacgggc-tcatatg-taagcattgtcatgcctagtacagactctc +i macFas5.chr1 C 0 C 0 +s chlSab2.chr25 80073330 117 + 85787240 actaagcacacagagaataatgtatggaatctgagtgtcatgtt--atcaaa-ttatactgagactcttgcagtcacacgggc-tgatata-taagcattgtcatgcctagtacagactctc +i chlSab2.chr25 C 0 C 0 +s saiBol1.JH378177 6411233 117 - 11194871 actaagcacacagagaataatgtgtagaatctgggtgtcatgtt--atcaaa-atacctggagattcttatagtcacatgggc-tgatatg-taagcattgtcatgcctagtacattctctc +i saiBol1.JH378177 C 0 C 0 +s otoGar3.GL873660 804885 117 - 5244756 actaaacaaacagaaaataatacatagaaccaagttgacaagtt--atcaaa-ttatactgagacttctgctgccacacatgc-taaaatg-ttagcattatcatgcgtagtacatcctctc +i otoGar3.GL873660 C 0 C 0 +s tupChi1.KB320992 2664137 111 + 10005445 ACTAAGCTTACCAAGAAAAATGTATGGAAACAGGGTGTCAAGTT--CTCAAA-TTATACAGAGACTTTTGCAATCACATGGGC-TGAAATG-TTAGTAT---CATACC---CACATTTTCTC +i tupChi1.KB320992 C 0 C 0 +s speTri2.JH393336 2752899 95 - 10378366 actaagcatacagaaaataatatatagaa--------ctagTCA---------------TGGACTGGTTGCAGTCATATGAGC-TGAAAT--TTAATACTGTTatgtctagtaaactctcc- +i speTri2.JH393336 C 0 C 0 +s octDeg1.JH651532 12389308 108 - 24977595 attaagcccacagaaaataatgtatagca--------ccaagta--agcaaa-tcatactggatcctttgcagcaccatgggt-tgaaata-tttgcattctcatgcctagtatattctct- +i octDeg1.JH651532 C 0 C 0 +s orcOrc1.KB317031 2637457 117 + 2653784 attaagcacacagaaaataatgtatagaacccagatgccaagtt--accaaa-ttatactgaaatgtttgcattgacatgggc-tgaaatg-ttagcattgtcatacctaatatatattctc +i orcOrc1.KB317031 C 0 C 0 +s panHod1.KE114623 3169388 116 - 5476734 gttaagcacac--aaaataatgtatagaaccaaggtgccaagtt--accaaa-ttatcttgcaatgtttgtagtgacatgggt-tgaaatgtttagcattgtcatgcctaatatattttctc +i panHod1.KE114623 C 0 C 0 +s bosTau8.chr16 46890323 118 - 81724687 actaagcacatggaaaataatgtatagaaccaaggtgccaagtt--accaaa-ttatgttgaaatgtttgtagtgacatgggt-tgaaatgtttagcattgtcatgcctaatatattttctc +i bosTau8.chr16 C 0 C 0 +s oviAri3.chr12 46886277 116 - 79100223 gttaagcacac--aaaataatgtatagaaccaaggtgccaagtt--accaaa-ttatgttgcaatgtttgtagtgacatgggt-tggagtgtttagcattgtcatgcctaatatattttctc +i oviAri3.chr12 C 0 C 0 +s capHir1.chr16 45899140 116 - 77678508 gttaagcacac--aaaataatgtatagaaccaaggtgccaagtt--accaaa-ttatgttgcaatgtttgtagtgacatgggt-tgaaatgtttagcattgtcatgcctaatatattttctc +i capHir1.chr16 C 0 C 0 +s equCab2.chr30 28133151 117 - 30062385 tctaagcacacagagaataatgtatagaaccaaggggccaagtc--atcaaa-ttatgctgagacttctgcattgacatggac-tgaaatt-ttagcgttgtcatgcctagtacattctctc +i equCab2.chr30 C 0 C 0 +s cerSim1.JH767803 8191412 118 + 10096343 actaagcacacagagaataatgtatagaaccatggtgccaagtt--atcaaa-ttatgctgagacttttgcagtgatatggacttgaaatg-ttagcattgtcatgcctcatacattctctc +i cerSim1.JH767803 C 0 C 0 +s felCat8.chrF1 63230081 116 - 70119229 accaagaacatagagaacattgtatagaactaagatgccaagtc--atcaaa-ttatactgacatttttgcagt-acgtggac-tgaaatg-ttagcattgtcaagcctagcatattctctc +i felCat8.chrF1 C 0 C 0 +s canFam3.chr7 34216009 116 + 80974532 actaagaacatagagaatattgtataaaactaagatgccaagtt--atcaaa-ttatactgcgattcttgcagt-acaggggc-tgaaatg-ttagcattgtcaagcctagtacattctctc +i canFam3.chr7 C 0 C 0 +s musFur1.GL896953 6821010 116 + 11679101 actaagaacatagagaatattgtatagaactaagatgccaagtt--atcaaa-ttatactgagatttttgcagt-acatgggc-tgaaatg-ttagcattgtcgagcctagtacagtctctc +i musFur1.GL896953 C 0 C 0 +s odoRosDiv1.KB228994 454553 116 + 4135311 actaagaacatagagaatattgtatagaactaagatgccaagtt--atcaaa-ttatactgagatttttgcagt-acatgggc-tgaaatg-ttagcattgtcaagcctagcacattctttc +i odoRosDiv1.KB228994 C 0 C 0 +s pteAle1.KB030717 476346 118 + 4757641 actaagcacacagagaataaagtatagaaccaaggtgccaagtt--gtcaaatttatactgagatctttgcagtgacatgagc-tgaaatg-ttagcactgtcatgcctactacattttctc +i pteAle1.KB030717 C 0 C 0 +s loxAfr3.scaffold_16 42660441 118 + 51904812 actaagctcacagataggaatgtatagaactaggttaccagggtacatcaaa--tatagtgagacttctgtagtcacatgggc-tgaaatg-tcagcattgtcatacctagcacattctctc +i loxAfr3.scaffold_16 C 0 C 0 +s triMan1.JH594645 4489022 116 + 20212048 actaagctcacagatataaatgtatggaactagggtaccagggt--atcaaa--tatagtaagacttctgtagtcacatggac-tgaaatg-tcagcattgtcatacctagcacattctacc +i triMan1.JH594645 C 0 C 0 + +a score=0.000000 +s hg38.chr1 100117 261 + 248956422 cctgca-gatgaaattatatgggatgctaaattataatgagaacaatgtttggtgagcca-aaactacaacaaggg-------aagctaattggatgaatttat-aaaaatatgcctcagccaaaatagcttaattcactctcccttatcataagg------a---taatcttgccta-aagggacagtaatattAAAGAC-ACTAGGAATAACCTCTGTACTTTGGACAGT----AGACCTGCATAGCCCa-ttaggcctcaatgaagtcttatgcaagaccagaa +s panTro4.chr10 94481038 261 - 133524379 cctgca-gatgaaattatatgggatgccaaattataatcagaacaatgtttggtgagcca-aaactacaacaaggg-------aagctaattggatgaatttat-aaaaatatgcctcagccaaaatagcttaattcagtctcccttatcataagg------a---taatcttgccta-aagggacagtaatattAAAGAC-ACTAGGAATAACCTCTGTACTTTGGACAGT----AGACCTGCATAGCCCa-ttaggcctcaatgaagtcttatgcaagaccagaa +i panTro4.chr10 I 9 C 0 +s ponAbe2.chr1 223771014 259 - 229942017 tctgca-gatgaaattatatgggttgctaaattataatcagaacaatgtttggtgagcca-aaactacaacaaggg-------aagctaattggatgaatttat-aaaaatatgcctcagccaaaatagcttaatgcagtctcccttaccataagg------a---taa--ttgccta-aagggacagtaatattaaagac-actaggaataacctctctactttggacagt----AGACCTGCATAGCCCa-ttaggcctcaatgaagtcttatgcaagaccagaa +i ponAbe2.chr1 C 0 C 0 +s nomLeu3.chr7b_GL397639_2_random 52948 261 + 172226 cctgca-gatgaaattatatgggatgctaaattataatcagaacaatgtttggtgagcca-gaactacaacaaggg-------aagctaattggatgaatttat-aaaaatatgcctcagccaaaatagcttaatgcagtctcccttatcataagg------a---taatcttgccta-aagggacagtaatattaaagac-actaggaataacctctctactttggacagt----AGACCTGCATAGCCCa-ttaggcctcaatgaagtcttatgcaagaccagaa +i nomLeu3.chr7b_GL397639_2_random C 0 C 0 +s rheMac3.chr1 14400869 256 - 229590362 cctgca-gatgaaattatatggcatgctaaattacaatcagaacaatgtttggtgagcca-aaactacaatgaggg-------aagctaattggatgaatttat-aaaaatatgcctcagccaaaatagcttaatgcagtctcccttatcaaaaga------a---taatcttgccta-aagggatagtaat-----aGAC-ACTAGGAATGACTTCTGTACTTTGGACAGT----AGACCTGCAGGGCCCa-ttaggcctcaatgaagtcttatgcaagaccagaa +i rheMac3.chr1 C 0 C 0 +s macFas5.chr1 221133052 256 - 227556264 cctgca-gatgaaattatatggcatgctaaattacaatcagaacaatgtttggtgagcca-aaactacaatgaggg-------aagctaattggatgaatttat-aaaaatatgcctcagccaaaatagcttaatgcagtctcccttatcaaaaga------a---taatcttgccta-aagggatagtaat-----aGAC-ACTAGGAATGACTTCTGTACTTTGGACAGT----AGACCTGCAGGGCCCa-ttaggcctcaatgaagtcttatgcaagaccagaa +i macFas5.chr1 C 0 C 0 +s chlSab2.chr25 80073447 248 + 85787240 cttgca-gatgaaattatatggcatgctaaattacaatcagaacaatgtttggtgagc---------caatgaggg-------aagctaattggatgaatttat-aaaaatatgcctcagccaaaatagtttaatgcagtctcccttatcaaaaga------a---taatcttgccta-aagggatagtaat-----aGAC-ACTAGGAATGACTTCTGTACTTTGGACAGT----AGACCTGCAGGGCCCa-ttaggcctcaatgaagtcttatgcaagaccagaa +i chlSab2.chr25 C 0 C 0 +s saiBol1.JH378177 6411350 261 - 11194871 tctgca-gatgaaattatacgggatgctaaattataatcagaacaatgtatggtgagcaagaaagtacaacaaggg-------aagctaattggatgaatttat-aaaaatatgcctcagccaaaatagcctaatgcaatctccctcatcataagg------g---taatcttgccta-aagggacagtaatgttgaagac-actaggaaaaacttctctactttggacaAC----AGACCTGCATAGCCTA-TTAAGCCTCAATTCAGTCTTATGT-ATATCAGAA +i saiBol1.JH378177 C 0 C 0 +s otoGar3.GL873660 805002 241 - 5244756 cctaca-ggtggaactatata-------acatcataatcagaataatgtctgatgatcaaggaaccaaaacaatgg-------aaattaattggataaatct-t-agaaatatacctcagccacaatagcttaaggcagtcttcctcatcagaagg------g---taatcttgcccc-atgagacagtaatattgaagAC-ATTAGGAATAACTTCTCTACTTTAGATAGT-----------------CCA-TTAGCCTTTAATTAAGTCCTATACAAGACCAAAA +i otoGar3.GL873660 C 0 C 0 +s tupChi1.KB320992 2664248 256 + 10005445 CCTGCA-GATGGAATTATATGAGATGCTGAATTATAATAAGAATCATGTTTCATGAGCACGGATACACAAC------------AAGTTATTTGAATAAATTTGT-AGACATATGCTTCAGCCAAAATAGCATAAGGCAGTGTCCCTTGT---AAGG------A---TAATCTTGCCCA-ATGGGACAGTAATACTGaagac-acaagaaaaaaatcctcaattTTGGACAGTTC--TGACTTGCATAGTCCAGTTAGCCTTCAGTTCAGTCTTATACAAAACC-TAA +i tupChi1.KB320992 C 0 C 0 +s speTri2.JH393336 2752994 246 - 10378366 tctgca-gatggaatcatatgggattatg-attataataaga--------ttgtgggtaagtaaccacaactttgg-------aaataaagtagataaatttgt-agaagtatgcccctgtctaaatagcatacggcagtctccctcatcataaggataagga---taatcttgctca-atgggacagtaatattgagca--------agctactcctctgctttagacagttc------ttgcctggCTCA-TTGAGCT--CATAAAGTTTCATAGAAAATCAA-- +i speTri2.JH393336 C 0 C 0 +s octDeg1.JH651532 12389416 264 - 24977595 cctgcgtgatgaaattacatgaggtgttgaattataaccaaa-taatgcctggtgagcgaggaa--aaaacaatag-------aagttaactggacaatttttt-agaaatataccacagccaaaacaacataaagcagcccctctcctcataggga-----a---t-atcttaacca-atggagcagtaatattAAAGAC-AAAAAGAATAACTCATTTACTTCGGACAGTTCCTGGATTTGTGTGGTCCA-TTAACCTGCAATTAAGTCATGTGCAAAACCAAAA +i octDeg1.JH651532 C 0 I 132 +s orcOrc1.KB317031 2637574 273 + 2653784 tctaca-gctagaattatatgggatgttgaattataatcagaataatgtttggtgagcaagaaaccacaacaggggaagttaaaagttaattggatgcattttt-agaaacatacctcagccaaaacagcttaggacagtctcccttacaatagga------a---taatcttgccca-atgaggtagtaagattgaagac-actaggagtgacttccctactttgaacagtttctggatttgcacagtcca-gcagccttctgtgaAGTCTTACGCAAGACCAGAA +i orcOrc1.KB317031 C 0 C 0 +s panHod1.KE114623 3169504 266 - 5476734 cctgca-gatggaattttatgggatgttgaatcataatcagaataatgtttggtgagcaagaaaccacaacaaagg-------aagttaattggatgcattttt-agaaacatgcctcagccaaaatagtgtgaggcagtctccctcacgaaggga------a---taatctagccCA-GTGAAGTGGTAAGATTGAATAC-ACTAGGAATGGCATCCCTACTTTGAATGGCTTCTGAATTTGCACAGTCCA-TTAGCCTTCTCTTAGGTTTCATGGAAGACTACAT +i panHod1.KE114623 C 0 C 0 +s bosTau8.chr16 46890441 266 - 81724687 cctgca-gatggaattttatgggatgttgaatcataatcagaataatgtttggtgagcaagaaaccacaacaaagg-------aagttaattggatgcattttt-agaagcatgcctcagccaaaatagcttgaggcagactccctcacgatggaa------a---taatctagccca-atgagGTGGTAAGATTGAATAC-ACTAGGAATGACATCCCTACTTCGAATGGTTTCTGAATTTGCACAGTCCA-TTAGCCTTCTCTTAGGTTTCATGGAAGACTAGAA +i bosTau8.chr16 C 0 C 0 +s oviAri3.chr12 46886393 266 - 79100223 cctgca-gatggaattttatgggatgttgaatcataatcagaataatgtttggtgagcaagaaaccacaacaaagg-------aagttaattggatgcattttt-agaaacatgcctcagccaaaatagcttgaggcagtctccctcacgatggga------a---taatctagccCA-GTGAAGTGGTAAGATTGAATAC-ACTAGGAATGGCGACCCTACTTTGAATGGTTTCTGAATTTGCACAGTCCA-TTAGCCTTCTCTTAGGTTTCATGGAAGACTAGAA +i oviAri3.chr12 C 0 C 0 +s capHir1.chr16 45899256 266 - 77678508 cctgca-gatggaattttatgggatgttgaatcataatcagaataatgtttggtgagcaagaaaccacaacaaagg-------aagttaattggatgcattttt-agaaacatgcctcagccaaaatagcttgaggcagtctccctcacgatggaa------a---taatctagccCA-GTGAAGTGGTAAGATTGAATAC-ACTAGGAATGGCGTCCCTACTTTGAATGGTTTCTGAATTTGCACAGTCCA-TTAGCCTTCTCTTAGGTTTCATGGAAGACTAGAA +i capHir1.chr16 C 0 C 0 +s equCab2.chr30 28133268 249 - 30062385 cctgca-gatggaattatatgggatgctgaactgaaatcagaataatgtttggtgagcaaggaagcataacaagag-------aagttaattggataattTTTT-AGAAACATATCTCAGACAGAACAGCTTAAGTCAGTCTCTCTCACAACACAG------G---TAATCTTGCCCA------------------AAGAT-GCTAAGAATGACCTTTCTACTTTGGACAGTTTCTGGACTTGCACAGTCCA-TTAGCCTTCTGTTAAGTCTTATACAAGACCAGAA +i equCab2.chr30 C 0 C 0 +s cerSim1.JH767803 8191530 250 + 10096343 cctgca-gatggaattaaacgggatgctgaactggaatcagaatgatgtttgatgagcaaggaaccacatcgaggg-------aagctaactggataaattttt-agaaacatgtctcagccaaaacagcttaaggtagtctccctcacaacagag------a---cagtcttgccCA------------------ACAACGGCCAAGGATGACCTCCCTACTTCGGAAAGTTTCTCGACTTGCACAGTCCA-TTAGTCTTCTATTAAGTCTTATACAAGACCAGAA +i cerSim1.JH767803 C 0 C 0 +s felCat8.chrF1 63230197 267 - 70119229 cctcta-gatggaattatatgaaatgctgaattataatcagaatagtgttttgtgagcaaagaatcacaacaaggg-------aagttaattggataaattttt-agaaacatgcctcagccaaaacagcttaagacagtcaccctcagagtaggg------a---taatcttgctcaagggggatagtaatattgaagAT-ACTAGAAATGACTCCTCAACTTTGGATAGTTTCTGGGCTTGAACAGTCTA-TTGGCCTTCTTATAAGTCTTAGGGAAGATCAGAA +i felCat8.chrF1 C 0 C 0 +s canFam3.chr7 34216125 260 + 80974532 cctgta-catggagttatatgagttgctgaattataatcagaatagtgtttggtgagcaaagaatcacaacaaggg-------aagtt-attggataaATTTT--AGAAATGTGCCTTGGTCAAAATAGCTTAAGGCGGTCC------CAGGGGGT------ATATTAATCTTGCCCAGGGGGTATATTAA--TTGAAGAT-ACTAGGAATGGCCCTTCGACTTTGGACAGTTTCTGGGCTGGAACAGTCTA-TTGGCGGTTTTATAAGTCTTATGCAAGACCAGAA +i canFam3.chr7 C 0 C 0 +s musFur1.GL896953 6821126 264 + 11679101 cc-ata-gctggaat--tatgagatgctgaattataatcagaatcgtgtttggtgagcaaagaatcacaacaaggg-------aagtcaattggataaattttt-agaaacgtgcctcagccaaaacagcttaagacaatccgcctcacagtaggg------a---taatcttgccCAGAGGGGATAGCAAGGTTGAAGAT-ACTAGGAATGTCCCCCGGACTTTGGACAGTTTCTGGGCTTGAACAGTCTG-ATGGCCTTTTACAAAGTCTTATGCAAGACCAGAA +i musFur1.GL896953 C 0 C 0 +s odoRosDiv1.KB228994 454669 264 + 4135311 cctgta-gatggaattatatgaaatgctgaattataatcagaatagtgtttggtgagcaaagaatc---acaaggg-------aagttaattggataaatgtttaagaaacgtgcctcagccaaaacagctcaatacagtacccctcacaataggg------a---caatcttgcccaggggGGATATTAATGTTGAAGAT-ACTGAGAATGG-CCCTGGACTTTGGACAGTTTCTGGGCTTGAACAGTCTA-TTGGCCTTCTTATAAATCTTTTGCAAGACCAGAA +i odoRosDiv1.KB228994 C 0 C 0 +s pteAle1.KB030717 476464 261 + 4757641 cctgca-gatggaattatatgggacgctgaattataattagaataatg-ttggtgaacaaggaaccac-acaatgg-------aagttaattggataaaatttt-agaaacacatttcagcccaaacagagtaagacagcctcacttacaataggg------a---caatcttgctta-ccgggacAGACAGATTGA--AC-ACTAGGAATGACCGCTCTACATTGGACAGTTTCT-GACTTGCACAGTCCA-TTAGGCCTTTATTAAGTCTTATACAAGACCAGGA +i pteAle1.KB030717 C 0 C 0 +s loxAfr3.scaffold_16 42660559 264 + 51904812 cctgaa-gatgaaattatatggggtgctgaattataataagaatagtatttggtaagtaaggaaccacaacaagga-------acgttaattggataatttttt-agaaaaatgtcttagtcaaaatagcttaaggctttctccttcaccataagg------a---taatcttgcc-a-acgaaacagtaatattgaagAT-GCTAGGAATGATCCCTCTAC-TAGGACTAGTCCTGGGCTTGCACAGCCCA-GAAGCCTTCAGTTAAGCCTTATACAAGACCAGAA +i loxAfr3.scaffold_16 C 0 C 0 +s triMan1.JH594645 4489138 260 + 20212048 cctaaa-gatg-aattatatggaatgttgaattataatcagaataatgtttgataagtaaggaacgacaacaaggg-------a-gtcaattggataaattttt-agaaacataccttagtcaaaatagcttaaggcagtctccttcaccataagg------a---taatcttgcc-a-gtggaacagtaatattgtagac-actaggaatgacccctctac-ttggacaattcctggGCTTG--GAGTCCA-TTAGCCTTCAGTTAAGCCTTATACAAGATCAGAA +i triMan1.JH594645 C 0 C 0 + +a score=0.000000 +s hg38.chr1 100378 16 + 248956422 gccaatttgccattt-a +s panTro4.chr10 94481299 17 - 133524379 gccaatttgccgtttta +i panTro4.chr10 C 0 C 0 +s ponAbe2.chr1 223771273 17 - 229942017 gccaatttaccatttta +i ponAbe2.chr1 C 0 C 0 +s nomLeu3.chr7b_GL397639_2_random 53209 17 + 172226 gccaatttaccatttta +i nomLeu3.chr7b_GL397639_2_random C 0 C 0 +s rheMac3.chr1 14401125 17 - 229590362 gccaatttaccatttta +i rheMac3.chr1 C 0 C 0 +s macFas5.chr1 221133308 17 - 227556264 gccaatttaccatttta +i macFas5.chr1 C 0 C 0 +s chlSab2.chr25 80073695 17 + 85787240 gccaatgtaccatttta +i chlSab2.chr25 C 0 C 0 +s saiBol1.JH378177 6411611 17 - 11194871 GCCAATTTACCATTTGA +i saiBol1.JH378177 C 0 C 0 +s otoGar3.GL873660 805243 16 - 5244756 GCCggctcggcgccta- +i otoGar3.GL873660 C 0 I 660 +s tupChi1.KB320992 2664504 17 + 10005445 GCCAGTTTACCATTTGA +i tupChi1.KB320992 C 0 C 0 +s speTri2.JH393336 2753240 17 - 10378366 ATTAATTCATCATTTTA +i speTri2.JH393336 C 0 C 0 +s orcOrc1.KB317031 2637847 17 + 2653784 ATCAGCTTATCATTTTA +i orcOrc1.KB317031 C 0 C 0 +s panHod1.KE114623 3169770 17 - 5476734 ATCAACTTATCATTTTA +i panHod1.KE114623 C 0 C 0 +s bosTau8.chr16 46890707 17 - 81724687 ATCAACTTATCATTTTA +i bosTau8.chr16 C 0 C 0 +s oviAri3.chr12 46886659 17 - 79100223 ATCAACTTATCATTTTA +i oviAri3.chr12 C 0 C 0 +s capHir1.chr16 45899522 17 - 77678508 ATCAACTTATCATTTTA +i capHir1.chr16 C 0 C 0 +s equCab2.chr30 28133517 17 - 30062385 ATCAATTTCTCATTTTA +i equCab2.chr30 C 0 C 0 +s cerSim1.JH767803 8191780 17 + 10096343 ACTGATAAATCATTTTA +i cerSim1.JH767803 C 0 C 0 +s felCat8.chrF1 63230464 17 - 70119229 ATCAGCTTGTCATCTTA +i felCat8.chrF1 C 0 C 0 +s canFam3.chr7 34216385 17 + 80974532 ATCAATGTGTCATCCTA +i canFam3.chr7 C 0 C 0 +s musFur1.GL896953 6821390 17 + 11679101 ATCAATTTGTCATCCTA +i musFur1.GL896953 C 0 C 0 +s odoRosDiv1.KB228994 454933 17 + 4135311 ATCAATTTGTCATCCTA +i odoRosDiv1.KB228994 C 0 C 0 +s pteAle1.KB030717 476725 17 + 4757641 ATCAACTTCTCATTTTA +i pteAle1.KB030717 C 0 C 0 +s loxAfr3.scaffold_16 42660823 17 + 51904812 GTCAGTTTACCATCTTA +i loxAfr3.scaffold_16 C 0 C 0 +s triMan1.JH594645 4489398 17 + 20212048 GTCAGTTTATTATCTTA +i triMan1.JH594645 C 0 C 0 + +a score=0.000000 +s hg38.chr1 100394 53 + 248956422 aggtgattctcca-tgtttctgctcta-aCTGTGCTTCACAA-TACTCAAAACACT +s panTro4.chr10 94481316 53 - 133524379 aggtgattctcca-tgtttctgctcta-aCTGTGCTTCACAA-TACTCAAGACACT +i panTro4.chr10 C 0 C 0 +s ponAbe2.chr1 223771290 53 - 229942017 aggtgattctcca-tgtttctgctcta-aCTGTGATTCACAA-TACTCAAGACACC +i ponAbe2.chr1 C 0 C 0 +s nomLeu3.chr7b_GL397639_2_random 53226 53 + 172226 aggtgattctcca-tgtttctgctcta-aCTGTGCTTCACAA-TACTTAAAACACT +i nomLeu3.chr7b_GL397639_2_random C 0 C 0 +s rheMac3.chr1 14401142 53 - 229590362 aggtgattctcca-tgtttctgctcta-aCTGTGCTTTACAA-TACTCAAAACACT +i rheMac3.chr1 C 0 C 0 +s macFas5.chr1 221133325 53 - 227556264 aggtgattctcca-tgtttctgctcta-aCTGTGCTTTACAA-TACTCAAAACACT +i macFas5.chr1 C 0 C 0 +s chlSab2.chr25 80073712 53 + 85787240 aggtgattctcca-tgtttctgctcta-aCTGTGCTTCACAA-TACTCAAAACACT +i chlSab2.chr25 C 0 C 0 +s saiBol1.JH378177 6411628 51 - 11194871 AGGTGATTCTCCA-TGTTTCTGCTCTA-AGTGTGCTTCACAG-TACTCGAAACA-- +i saiBol1.JH378177 C 0 C 0 +s tupChi1.KB320992 2664521 51 + 10005445 ATGTGTTTTTCCA-GATCTGTGCTCTA-A--GTAACTCACAG-GGCTGGAGACCCT +i tupChi1.KB320992 C 0 C 0 +s speTri2.JH393336 2753257 54 - 10378366 AGGTGTTTCACTATTATCTCTGTTTTA-ACTCTGGTTCAAAT-GACTCAAGACATC +i speTri2.JH393336 C 0 C 0 +s orcOrc1.KB317031 2637864 229 + 2653784 AGGTGACTCTCCG-TATCTCTTATCTA-ACTCTgcccCACAA-TGTTTAAGATGCT +i orcOrc1.KB317031 C 0 C 0 +s panHod1.KE114623 3169787 56 - 5476734 AGGTGACTTTCTG-TATCTCTTCTCTA-ACTCTGACTTATAAAGGTTTAAGACCCT +i panHod1.KE114623 C 0 C 0 +s bosTau8.chr16 46890724 56 - 81724687 GGGTGACTCTCCG-TATCTCTTCTCTA-ACTCTGACTCACAAAGGTTTAAGACCCT +i bosTau8.chr16 C 0 C 0 +s oviAri3.chr12 46886676 56 - 79100223 AGGTGACTTTCTG-TATCTCTTCTCTA-ACTCTGACTCACAAGGGTTTAAGACCCT +i oviAri3.chr12 C 0 C 0 +s capHir1.chr16 45899539 56 - 77678508 AGGTGACTTTCTG-TATCTCTTCTCTA-ACTCTGACTCACAAAGGTTTAAGACCCT +i capHir1.chr16 C 0 C 0 +s equCab2.chr30 28133534 49 - 30062385 AAACGACTCTC------CCATTTTCTA-ACTCTAATTCACAA-T-TTCAAGACGCT +i equCab2.chr30 C 0 C 0 +s cerSim1.JH767803 8191797 55 + 10096343 AGATGACTCTCCA-TGTCTCCTCTCTA-ACTCTGATTCGCAA-TGTTCAGGACACT +i cerSim1.JH767803 C 0 C 0 +s felCat8.chrF1 63230481 53 - 70119229 AGGGGA--TGACA-TATCTGTTCTCCA-ACTCTGATTCACAC-TGTTCAAGACATT +i felCat8.chrF1 C 0 C 0 +s canFam3.chr7 34216402 52 + 80974532 AGGGGACTCTCCA-TATCTGTTCTTTA-ACTCTGATT--CAG-TGTTCAAGACAT- +i canFam3.chr7 C 0 I 10 +s musFur1.GL896953 6821407 54 + 11679101 AGAGGACCCTCCA-TATCTGTTCTCTA-ACTCTGGTTCACAG-GGTTCAACATTC- +i musFur1.GL896953 C 0 I 22 +s odoRosDiv1.KB228994 454950 54 + 4135311 AGGGAACTCTTCA-TATCTATTTTCTA-ATTCTGATTCACAG-TGTTCAAGATTC- +i odoRosDiv1.KB228994 C 0 I 26 +s pteAle1.KB030717 476742 54 + 4757641 AGGAGACTCTCCA-TATCTCTTCTCTA-ACTCTACTTAACCA-TGTTCAAGATACT +i pteAle1.KB030717 C 0 C 0 +s loxAfr3.scaffold_16 42660840 50 + 51904812 AATTCACTCTCTA-TATCTCTGTTCTA----CTATTGCACAG-TGCTCAAAACACT +i loxAfr3.scaffold_16 C 0 C 0 +s triMan1.JH594645 4489415 54 + 20212048 AGTTGACTCTCCA-TATCTCTCTTCTAGTCTGTGTTTCACAA-TACTCAAAACACT +i triMan1.JH594645 C 0 C 0 + +a score=0.000000 +s hg38.chr1 100447 53 + 248956422 A----------AATCAGGATGTTTCCTGGAGTTCAGGGAGCTGTCCGTGTTACTGAGCAGTTC +s panTro4.chr10 94481369 53 - 133524379 G----------AATCAGGATGTTTCCTGGAGTGCAGGGAGCTGTCCGTGTTACTGAGCAGTTC +i panTro4.chr10 C 0 C 0 +s ponAbe2.chr1 223771343 53 - 229942017 A----------AATCAGGATGTTCCCTGGAGTGCAGGGAGCTGTCCGTGGTCCTGAGCAGCTC +i ponAbe2.chr1 C 0 C 0 +s nomLeu3.chr7b_GL397639_2_random 53279 53 + 172226 G----------AATCAGGATGTTCCCTGGAGTTCAGGGAGCTGTCCGTGGTCTTGAGCAGCTC +i nomLeu3.chr7b_GL397639_2_random C 0 C 0 +s rheMac3.chr1 14401195 53 - 229590362 G----------AATCAGGATGTTCCCTGGAGGTCAGGGAGCTGTCCGTGGTCCTGAGCAGCTC +i rheMac3.chr1 C 0 C 0 +s macFas5.chr1 221133378 53 - 227556264 G----------AATCAGGATGTTCCCTGGAGATCAGGGAGCTGTCCGTGGTCCTGAGCAGCTC +i macFas5.chr1 C 0 C 0 +s chlSab2.chr25 80073765 53 + 85787240 G----------AATCAGGATGTTCCCTGGAGGTCAGGGAGCTGTCCATGGTCCTGAGCAGCTC +i chlSab2.chr25 C 0 C 0 +s saiBol1.JH378177 6411679 53 - 11194871 G----------AATCACGATGTTCCCTGGAGTTCAGGGAGCTGTCCGTGGTCCTGAGCAGCTC +i saiBol1.JH378177 C 0 C 0 +s tupChi1.KB320992 2664572 60 + 10005445 GA-AGTAGGGTAACCAAGATCTTCCCTAGAGTG-ACAGAGCTGTCCGTGGTGCTGAACCAA-A +i tupChi1.KB320992 C 0 C 0 +s speTri2.JH393336 2753311 38 - 10378366 A----------AAATAG---------TGG------GGGAGTTGTCCATGGTCCTGAACCATTA +i speTri2.JH393336 C 0 C 0 +s orcOrc1.KB317031 2638097 50 + 2653784 ----------TGAGGAAGACGGTTCCTAGAG---GGATAGCTGTCCGTGGTCCTGAACCACTA +i orcOrc1.KB317031 I 4 C 0 +s panHod1.KE114623 3169847 50 - 5476734 ----------TGAGGAAGATGGGTCCTAGAG---GGATAGCTGTCCGTGGTTCTGAACCACTA +i panHod1.KE114623 I 4 C 0 +s bosTau8.chr16 46890784 50 - 81724687 ----------TGAGGAGGATGGTTCCTAGAG---GGATAGCTGTCCATGGTTCTGAACCACTA +i bosTau8.chr16 I 4 C 0 +s oviAri3.chr12 46886736 50 - 79100223 ----------TGAGGAAGATGGTTCCTAGAG---GGATAGCTGTCCGTGGTTCTGAACCACTA +i oviAri3.chr12 I 4 C 0 +s capHir1.chr16 45899599 50 - 77678508 ----------TGAGGAAGATGGTTCCTAGAG---GGATAGCTGTCCATGGTTCTGAACCACTA +i capHir1.chr16 I 4 C 0 +s equCab2.chr30 28133592 49 - 30062385 ----------CAACTCAGACGGTGCCTGCTG----GGGAGTTGTCCATGGTCCTGAACCACTA +i equCab2.chr30 I 9 C 0 +s cerSim1.JH767803 8191861 49 + 10096343 ----------CAACTAAGATACTGCCTAGGG----GGGAGCTGTCCGCAGTCCTGAACCACTG +i cerSim1.JH767803 I 9 C 0 +s felCat8.chrF1 63230543 50 - 70119229 ----------TAACCAAGAC-TTTTCTGGAGT--GGGGAACTGTCCGTGGTTCTGAACAACTA +i felCat8.chrF1 I 9 C 0 +s canFam3.chr7 34216464 51 + 80974532 ----------TAACCAAAATGTTTCCTGGAGC--AGGGAGCTGTCCCTGGTTCTGAACAACTA +i canFam3.chr7 I 10 C 0 +s musFur1.GL896953 6821483 50 + 11679101 ----------AAGCAAGAGC-TGTCCTGGAGT--AGGGAGCTGTCCCTGGTTCTGAACAACCA +i musFur1.GL896953 I 22 C 0 +s odoRosDiv1.KB228994 455030 46 + 4135311 ----------AAACTGG-----TTCCTGGAGC--AGGGAGCTGTCCCTGGTTCTGAACAACTA +i odoRosDiv1.KB228994 I 26 C 0 +s pteAle1.KB030717 476805 49 + 4757641 ----------TGACCAAGATAGTTCCTGCAG---GGAGCACTCTCCA-GGTCCTGGACCACTA +i pteAle1.KB030717 I 9 C 0 +s loxAfr3.scaffold_16 42660890 61 + 51904812 -GAAGCAGAATAACCACGATGTTTCCTGGACCA-TGTGTGCTGTCCATGGTGCTGAACCACTG +i loxAfr3.scaffold_16 C 0 C 0 +s triMan1.JH594645 4489469 61 + 20212048 -GAAACAGCATAACCAAGATGTTTCCTGGAGCA-TGGGTGCTGTCCGTGGTTCTGAACCACTA +i triMan1.JH594645 C 0 C 0 +