root/galaxy-central/test-data/6_mask_cpg.maf

##maf version=1
a score=356676.0
s hg18.chr1      2817 1438 + 247249719 GTCATCCCCTTCACTCCCAGCTCAGAGCCCAGGCCAGGGGCCCCCAAGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAAGCCTGGCTGCCTCCAGCTGGGT#GACAGACAGG#GCTGGAGAAGGGGAGAAGAGGAAAGTGAGGTTGCCTGCCCTGTCTCCTACCTGAGGCTGAGGAAGGAGAAGGGGATGCACTGTTGGGGAGGCAGCTGTAACTCAAAGCCTTAGCCTCTGTTCCCA##AAGGCAGGGCCATCAGGCACCAAAGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACA#GCTGTTGGCCTGGATCTGAGCCCT#GTGGAGGTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCACTCCTGCCTTTTCCTTTCCC#AGAGCCTCCACCACCCC#AGATC#CATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGG##CTG#GCCCTTCCTTTGCTCTGCCC#CTGGAGA#GGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGTGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCC#TTGGAGAAAACAGGGGAATCCC#AAGAAATGGTGGGTCCTGGCCATCC#TGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCAATCTGTCTTCCATCCTG##TGGCCGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATT--TGTCCTGCCCACCTTCTTAGAAG##AGA#GGAGCAGACCCATCTGCTACTGCCCTTTCTATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTAGTCTCAATTTAAGAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCATTCCTGCAGCCTTGCTCCCTAACCTGCCCCACAGCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGT##ATGGCACCTCCCTCCCTCTCAACCACTTGAGCAAACTCCAAGACATCTTCTACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCC#TGTCTGTCACTGAAACCTTTTT#GTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGGACCAACAGGGGCAGGAGGCAGTCACTGACCCC#AGA##TTTGCATCCTGCACAGCTAGAGATCCTTTATTAAAAG 
s panTro2.chr15 16051 1440 - 100063422 GTCATCCCCTTCACTCCCAGCTCTGAGCCCAGGCCAGGGGCCCCCAAGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAAGCCTGGCTGCCTCCAGCTGGGT#GACAGACAGG#GCTGGAGAAGGGGAGAAGAGGAAAGGGGGGCTGCCTGCCCTGTCTCCCACCTGAGGCTGAGGAAGGAGAGGGGGATGCACTGTTGGGGAGGCAGCTGTAACTCAAAGCCCTAGCCTCTGTTCCCA##AAGGCAGGGCCATCAGGCACCAAAGGGATTCTGCCAGCATAATGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACA#GCTGTTGGCCTGGATCTGAGCCCT#GTGGAGCTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCAGTCCTGCCTTTTCCTTTCCC#AGAGGCTCCACCACCCC#AGATC#CACTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGG##CTG#GCCCTTCCTTTGCTCTGCCC#CTGGAGA#GGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGTGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCC#TTGGAGAAAACAGGGGAATCCC#AAGAAATGGTGAGTCCTGGCCATCC#TGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCAATCTGTCTTCCATCCTG##TGGCAGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATTTCTGTCCTGCCCACCTTCTAAGAAG##AGA#GGAGGACACCCATCTGCTTCTGCCCTTTCCATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTAGTCTCTATTTAAAAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCACTTCTGCAGCCTTGCTCCCTAACCTGCCCCACAGCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGT##ATGGCACCTCCCTCCCTCTCAACTACTTGAGCAAACTTGAAGACATCTTCAACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCC#TGTCTGTCACTGAAACCTTTTT#GTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGCACCAACAGGGGCAGGAGGCAGTCACTGACCCC#AGA##TTTGCATCCTGCACAGCTAGAGGTCCTTAATTAAAAG 

a score=33380.0
s hg18.chr1      4393 135 + 247249719 GTGTGGCCTCAAGCCAGCCTTCC#CTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCC#TCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCC#TGTCAGAGCAA#GGCCCAAGTCTG 
s panTro2.chr15 17634 135 - 100063422 GTGTGGCCTCAAGCCAGCCTTCC#CTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCC#TCACCCCCTCCCAGGGAAGCAGGTCTCAGCAGCTTGTCCTGGCTGTGTCC#TGTCAGAGCAA#GGCCCAAGTCTG 

a score=364526.0
s hg18.chr1      4528 1436 + 247249719 GGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTA#GATTCCCAGT##TCCTC#TCCTCCTCTGCCTGTGGCTGCTG#GGTGG#GGCAGAGGAGGGATGGAGTCTGACA###GGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTTGGTGGGAAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAGGCAGGACAGAATTACAAGGTGCTGGCCCAGGG#GGGCAG#GGCCCTGCCTCCTACCCTTG##CCTCATGACCAGCTTGTTGAAGAGATCC#ACATCAAGTGCCCACCTTGGCT##TGGCTCTCACTGCAA#GGGAAAGCCACAGACTGGGGTGAAGAGTTCAGTCACATG#GACCGGTGACTCCCTGTCCCCACCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTCAGAGCCTCAGT##ATCCCTGACCCAGCACCGGGC#CTGATGAGACAG#GGCTGTTTGAGGAGCCACCTCCCAGCCACCT#GGGGCCAGGGCCAGGGTGTGCAGCAccactgtacaatggggaaactggcccagagaggtgaggcagcttgcctggggtcacagagcaaggcaaaagcag##ctgggtacaagctcaAAACCATAGTGCCCAGGGCACTGCC#CTGCAGG##CAGGCAT##CATCACA-----CCAGTGTCTG##TTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCATTGCCTTGGACC#CTCTTGGCAGT##AAGAAGATTCTCCTGTCA--GTTTGAGCTGGGTGAGCTTAGAGAGGAAAGCTCCACTATGGCTCCCAAACCAGGAAGGAGCCATAGCCCAGGCAGGAGGGCTGAGGACCTCTGGTGG#GGCCCAGGGCTTCCAGCATGTGCCCTAGGGGAAGCAGGGGCCAGCTGGCAAGAGCAGGGGGTGGGCAGAAAGCACCCGGTGGACTCAGGGCTGGAGGGGAGGAGG##ATCTTGCCCAAGGCCCTCC#ACTGCAAGCTCCAGGGCCC#CTCACCTTGCTCCTGCTCCTTCTGCTGCTGCTTCTCCAGCTTT##CTCCTTCA#GCTG##CAGCTTGGCCTTGCC#ATGCCCCCAGCTTGG#GGATGGACTCTAGCAGAGTGGCC-AGCCACCGGAGGGGTC#ACCACTTCCCTGGGAGCTCCCTGGACTGGAGCCGGGAGGTGGGGAACAGGGCAAGGAGGAAAGGCTGCTCAGGCAGGGCTGGGGAAGCTTACTGTGTCCAAGAGCCTGCTGGGAGGGAAGTCACCTCCCCTCAAA##AGGAGCCCTG##CTGGGGAGGCCGGACCTTTGGAGACTGTGT 
s panTro2.chr15 18013 1444 - 100063422 GGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTA#GATTCCCAGT##TCCTC#TCCTCCTCTGCCTGTGGCTGCTG#GGTGG#GGCAGAGGAGGGATGGAGTCTGACA###GGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTTGGTGGGAAACCCTGCTTCCCCCAGCCCCCAGAGACTTAAATACAGGAAGAAAAAGGCAGGACACAATTACAATGTGCCGGCCCAGGG#GGGCAG#GGCCCTGCCTCCTACCCTTG##CCTCATGACCAGCTTGTTGAAGAGATCC#ACATCAAGTCCCCACCTTGGCT##TGGCTCTCACTGCAA#GGGAAAGCCACAGACTGGGGTGAAGAGTTCAGTCACATG#GACCGGTGGCTCCCTGTCCCCAGCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTCAGAGCCTCAGT##ATCCCTGACCCAGCACCGGGC#CTGATGAGAAAG#GGCTGTTTGAGGAGCCACCTCCCAGCCACCT#GGGGACAGGGCCAGGGTGTGCAGCACcactgtacaatggggaaactggcccagagaggtgaggcagcttgcctggggtcacagagcaaggcaaaagcag##ctgTGTACAAGCTCAAAACCATAGTGCCCAGGGCATTGCC#CTGCAGG##CAGGCAT##CATCACATCACACCAGTGTCTG##TTCACAGCAGGCATCATCAGTAGCCTCAAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCATTGCCTTGGACC#CTCTTGGCAGT##AAGAAGATTCTCCTGTCACAGTTTGAGCTGGGTGAGCTTAGAGAGGAAAGCTCCACTATGGCTCCCAAACCAGGAAGGAGCCATAGCCCAGGCAGGAGGGCTGAGGACCTCTGGTGG#GGCCCAGGGATTCCAGCATGTGCCCTAGGAGAAGCAGGGGCCAGCTGCCAAGAGCAGGGGGTGGGCAGAAAGCACCCAGTGGACTCAGGGCTGGAGGGAAGGAGG##ATCTTGCCCAAGGCCCTCC#ACCGCAGGCTCCAGGGCCC#Ctcaccttgctcctgctccttctgcttcttcttctccagcttt##ctccttcA#GCTG##CAGCTTGGCCTTGCC#ATGCCCCCAGCTTGG#GGATGGATTCTAGCAGAGTGGCCCGGCCACCGGAGGGGTC#ACCACTTCCCTGGGAGCTCCCTGGACTGGAGCCGGGAGGTGGGGAACAGGGCAAGGAGGAAAGGCTGCTCAGGCAGGGCTGGGGAAGCTTATTGTATCCAAGAGCCTGCTGGGAGGGAAGTCACCTCCCCTCAAA##AGGAGCCCCG##CTGGGGAGGCCGGACCTTTGGAGACTGTGT 

a score=521291.0
s hg18.chr1      5995 1988 + 247249719 CCTGAG#GCGGGCATCCTGTGTGCAGATACTCCCTGCTTCCTCTCTAGCCCCCACCCTGCAGAGCTGGACCCCTGAGCTAGCCATGCTCTGACAGTCTCAGTTGCACACA#GAGCCAGCAGAGGGGTTTTGTGCCACTTCTGGATGCTAGGGTTACACTGGGAGACACAGCAGTGAAGCTGAAATGAAAAATGTGTTGCTGTAGTTT-----GTTATTAGACCCCTTCTTTCCATTGGTTTAATTAGGAATGGGGAACCCAGAGCCTCACTTGTTCAGGCTCCCTCTGCCCTAGAAGTGAGAAGTCCAGAGCTCTACAGTTTGAAAACCACTATTTTATGAACCAAGTAGAACAAGATATTTGAAATGGAAACTATTCAAAAAATTGAGAATTTCTGACCACTTAACAAACCCACAGAAAATCCACCC#AGTGCACTGAGCA##CCAGAAATCAGGTGGCCTCAAAGAGCTGCTCCCACCTGAAGGAGA####CTGCTGCTGCTGT##TCCTGCCTGG##CCTTGGCCTACAGGGGCC##GGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCtgggggtggtggtggggg#ggtgggggtggtg---------ttagtACCCCATCTTGTAGGTCTGAAACACAAAGTGTGGGGTGTCTAGGGAAGAAGGTGTGTGACCAGGGAGGTCCCCGGCCCAGCTCCCATCCCAGAACCCAGCTCACCTACCTTGAGAGGCT#GGCTACCTCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGT#GGCAATGTACATGAGGT##TTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCAGGGACATGTGAGAGGTGACAGGGACCTGCAGGGGCAGCCAACAAGACCTTGTGTGCACCTCCCATGGGTGGAATAAGGGGCCCAACAGCCTTGACTGGAGAGGAGCTCTGGCAAGGCCCTGGGCCACTGCACCTGTCTCCACCTCTGTCCC#CCCCTCCCACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACCTACAGAGG##ACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAG#GTGCACTGTGGGGTCCCAGGCCTCCC#AGCC#AGCCACCC#TCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAGGCCGGGCCTCCC#CCCACACCCCT#GGCCCTGCCCTCTGGCCATACAGGTTCT#GGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCAT##TCCT#GGGCTCCGGCTTGGTGCTCA##CACACAGGAAAGTCCTTCAGCTTCTCCTGAGAGGGCCAGGATGGCCAAGGGATGGTGAATATTTGGTGCTGGGCCTAATCAGCTGCCATCCCATCCCAGTCAGCCTCCTCTGGGGGACAGAACCCTATGGTGGCCCCGGCTCCTCCCCAGTATCCAGTCCTCCTGGTGTGTGACAGGC-----TATATG###GGCCAGCAGACCTGCAGGGCCC#CTC#TCCAGGGGG#GGTGCTTGCTCTGGATCCTGTGG#GGGGG##TCTCTGCAGGCCAGGGTCCTGGG##CCC#TGAAGATGGAGCCATATTCCTGCAGG##CCCTGGAGCAGGGTACTTGGCACTGGAGAACACCTGTGGACACAGGGACAAGTCTGAGGGGGCCCCAAGAGGCTCAGAGGGCTAGGATTGCT 
s panTro2.chr15 19485 2006 - 100063422 CCTGAG#GCAGGCATCCTGTGTGCAGATACTCCCTGCTTCCTCTCTAGCCCCCACCCTGCAGAGCTGGACCCCTGAGCTAGCCATGCTCTGACAGTCTCAGTGGCACACA#GAGCCAGCAGAGGGGTTTTGTGCCACTTCTGGATGCTAGGGTTAGACTGGGAGATACAACAGTGAAGCTGAGAAGAAAAATGTGTTGCTGTAGTTTAGTTGGTTATTAGACCCCTTCTTTCCATTGGTTTAATTAGGAATGGGGAACCCAGAGCCTCACTTGTTCAGGCTCCCTCTGCCCTAGAAGTGAGAAGTCCAGAGCTCTACAGTTTGAAAACCACTATTTTATGAACCAAGTAGAACAAGATATTTGAAATGGGAACTATTCAAAAAATTGAGAATTTCTGACCACTTAACAAACCCACAGAAAATACACCC#AGTGCACTGAGCA##CCAGAAATGAGGTGGCCTCAAAGAGCTGCTCCCACCTGAAGGAGA####CTGCTGCTGCTGT##TCCTGCCTGG##CCTTGGCCTACAGGGGCC##GGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCtgggggaggtggtggggg#ggtgggggtggtgggggtgctgttagtACCCCATCTTGTAGGTCTGAAACACAAAGTGTGGGGTGTCTAGGGAAGAAGGTGTGTGAGCAGGGAGGTCCCCAGCCCAGCTCCCATCCCAGAGCCCAGCTCACCTGCCTTGAGAGGCT#GGCTACCTCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGT#GGCACTGTACATGAGGT##TTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCAGGGACATGTGAGAGGTGACAGGGACCTGCAGGGGCAGCCAACAAGACCTTGTGTGCACCTCCCATGGGTGGAATAAGGGGCTCAACAGCCTGGACTGGAGAGGAGCTCTGGCAAGGCCCTGGGCCACTGCACCTGTCTCCACCTCTGTCCC#CCCCTCCCACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTGTACCTACAGGGG##ACATGGGGGTCAGGCAAGCTGACACCTGCTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAG#GTGCACCGTGGGGTCCCAGGCCTCCC#AGCC#AGCCACCC#TCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAGGCCGGGCCTCCC#CCCACACCCCT#GGCCCTGCCTTCTGGCCATACAGGTTCT#GGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCAT##TCCT#GGGCCCCGGCTTGGTGCTCA##CACACAGGAAAGTACTTCAGCTTCTCCTGGGAGGGCCAGAATGGCCAAGGGATGGTGAATATTTAGTGCCGGGCCTAATCAGCTGCCACCCCATCCCGGTCAGCCTCCTCTGGGGGACAGAACCCT-TGGTGGCCCCGGCTCCTCCCCAGTATCCAGTCCTCCTGGTGTGTGACAGGCTAAGTTATGTG###GGCCAGCAGACCTGCAGGGCCC#CTC#TCCAGGGGG#GGTGCTTGCTCTGGATCCTGTGG#GGGGG##TCTCTGCAGGCCAGGGTCCTGGG##CCC#TGAAGATGGAGCCATATTCCTGCAGG##CTCTGGAGCAGGGTACTTGGCACTGGAGAACACCTGTGGACACAGGGACAAGTCTGAGGGGGCCCCAAGAGGCTCAGAGGGCTAGGATTGCT 

a score=311095.0
s hg18.chr1      7983 1272 + 247249719 TGGCAGGAGAGGGTGGAGTTGGAAGCCTGGG##AGAAGAAAGCTCAAGGTACAGGTGGGCAGCAGGGCAGAGACTGGGCAGCCTCAGAGGCA#GGGGAAATGGAGGGACTGCCCAGTAGCCTCAGGACACAGGGGTATGGGGACTACCTTGATGGCCTTCTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGCCTGCACCTGGCTCCGGCTCTGCTCTACCTGCTGGGAGATCCTGCCATGGAGAAGATCACAGAGGCTGGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGCCGATCTTGGTGCCATCCAGGGGGCCTCTACAAGGATAATCTGACCTGCAGGGT##AGGAGTTGA#GGTGCTGAGTTCCCTGCACTCTCAGTAGGGACAGGCCCTATGCTGCCACCTGTACATGCTATCTGAAGGACAGCCTCCAGGGCACACAGAGGATGGTATTTACACATGCACACATGGCTACTGATGGGGCAAGCACTTCACAACCCCTCATGATCA##TGCAGCAGACAATGTGGCCTCTGCAGAGGGGGAA#GGAGACCGGAGGCTGAGACTGGCAAGGCTGGACCTGAGTGTC#TCACCTAAATTCAGA#GGGGAACTGCCCCTGCACATACTGAA#GGCTCACTGAGCAAACCCCGAGTCCC#ACCACC#CCTCAGTGTGGTCTAGCTcctcacctgcttccatcctccctggtg#ggggtgggcccagtgatatcagctgcctgctgttccccagatgtgccaagtgcattcttgtgtgcttgcatctcatggaac#ccatttccccagacatccctgtggctggctcctGATGCCC#AGGCCCAAGTGTCTGATGCTTTAAGGCACATCACCCCACTCATGCTTTTCCATGTTCTTTGGCC#CAGCAAGGCC#CTCTCACTGCAAAGTTAACTCTGATG##TGTGTAACACAACATCCTCCTCCCAGT##CCCCTGTAGCTCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCCACACTCCA##TGCAGAGCAGCCTCAGCACTCACCGGGCA##AG##AGCCTGTGTGGTG##CAGGGATGAGAAGGCAGAGG####ACTGGGGTTC#TGAGGAAGGGCAGGAGGAGGGTGTGGGATGGTGGAGGGGTTTGAGAAGGCAGAGG##C 
s panTro2.chr15 21491 1270 - 100063422 TGGCAGGAGAGGGTGGAGTTGGGAGCCTGGG##AGAAGAAAGCCCAAGGTAGAGGTGGGCAGCAGGGCAGAGACTGGGCAGCCTCAGAGGCA#GGGGAAATGGAGGGACTGCCCAGTAGCCTCAGGACACAGGGGCATGGGGACTACCTTGATGGCCTTCTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGCCTGCACCTGGCTCCGGCTCTGCTCTACCCGCTGGGAGATCCTGCCATGGAGAAGATCACAGAGGCTGGGCTGCTCCCCACCCCCTGCACACCTCCTGCTCCTAACAGCAGAGCTGCCAGGCCAGGCCCTCAGGCAAGGGCTCTTAAGTCAGGGTCACCTGCTTGCCAGGGCTGATCTTGGTGCCATCCAGGGGGCCTCTACAAGGATAATCTGACCTGCAGGGT##AGGAGTTGA#GGTACTGAGTTCCCTGCACTCTCAGTAGGGACAGGCCCTATGCTGCCACCTGTACATGCTATCTGAAGGACAGCCTCCAGGGCACACAGAGGATGGTATTTACACATGCACACATGGCTATTGATGGGGCAAGCATTTCACAACCCCTCATGATCA##TGCAGCAGACAAAGTAGCCTCTGCAGAGGGGGAA#GGAGACCGGAGGCTGAGACTGGCAAGGCTGGACCTGAGTGTC#TCACCTAAATTCAGA#GGGGAACTGCCCCCGCACATAGTGAA#GGCTCACTGAGCAAACCCTGAGTCCC#ACCACC#CCTCAGTGTGGTCTAGCTcctcacctgcttccatcctccctggtg#ggggtgggcccagtgatatcagctgcctgctgttccccagatgtgccaagtgcattcttatgtgcttgcatctcatggaac#ccatttccccagacatgcctgtggctggctcctGGTGCCC#AGGCCCAAGTGTCTGATGCTTTAAGGCACATCACCCCACTCATGCTTTTCCATGTTCTTTGGCC#CAGCAAGGCC#CTCTCACTGCAAAGTTAACTCTGATG##TGTGTA--ACAACATCCTCCTCCCAGT##CCCCTGTAGCTCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCCACACTCCA##TGCAGAGCAGCCTCAGCACTCACCGGGCA##AG##AGCCTGTGTGGTG##CAGGGATGAGAAGGCAGAGG####ACTGGGGTTC#TGAGGAAAGGCAGGAGGAGGGTGTGGGATGGTGGAGGGGTTTGAGAAGGCAGAGG##C 

a score=268744.0
s hg18.chr1      9255 1055 + 247249719 GACTGGGGTTCATGAGGAAAGGGAGGGGGAGGATGTGGGATGGTGGAGGGGCTGCAGACTCTGGGCTAGGGAAAGCTGGGATGTCTCTAAAGGTTGGAATGAATGGCCTAGAATCCGACCCAATAAGCCAAAGCCACTTCCACCAA##TTAGAAGGCCTTGGCCCCCAGAGAGCCAATTTCACAATCCAGAAGTCCCC#TGCCCTAAAGGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCATGGCAGGGCTGGGAGTACCAGCAGGCACTCAAG#GGCTTAAGTGTTCCATGACAGACTGGTATGAAGGTGGCCACAATTCAGAAAGAAAAAAGAAGAGCACCATCTCCTTCCAGTGAGGAAG#GGGACCACCACCCAG##TGTGCTCCATCTTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGGTCCTCCAGCACAAGCTGTCTTAATTGACCCTAGTTCCCAGGGCAGCCTC#TTCTGCCTTGGGTGCTGACA##ACCTT#GGTAGGTGCATAAGCTCTGCATT##AGGTCcacaggggcagtgggagggaactgagactggggagggacaaaggctgctctgtcctggtgctcccacaaagg--agaagggctgatcactcaaagttg##aacaccaagctcaacaatgagccctggaaaatttctggaatggattattaaacagagagtctgtaagcacttagaaaaggcc##ggtgagtcccaggggccagcactgct##aaatgtacagcatttctctttgtaacaggattattagcctgctgtgcccggggaaaacatgcagcacag#gcatct##agtcagcaggattt#ga#ggcttctaacaaaatcttgtagacaagatggagctatgggggttggaggagagaacatataggaaaaatcagagccaaatgaaccacagccccaaagggcacagttgaacaatggactgattccagccttgca#ggagggatctggcagagtccatccagttcattcaacacctggttagaaaactggggccag 
s panTro2.chr15 22901 1056 - 100063422 GACTGGGGTTCATGAGGAAAGGCAGGAGGAGGGTGTGGGATGGTGGAGGGGCTGCAGACTCTGGGCTTGGGAAAGCTGGGGTGTCTCTAAAGGTTGGAATGAATGGCCTAGAATCGGACCCAATAAGCCAAAGCCACTTCCACCAA##TTAGAAGGCCTTGGCCCCCAGAGAGCCAATTTCACAATCCAGGAGTCCCC#TGCCCTAATGGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCATGGCAGGGCTGGGAGTACCAGCAGGCACTCAAG#GGCTTAAGTGTTCCATGACAGACTGGTATGAAGGTGGCCACAATTCAGAAAGAAAAAAGAAGAGCACCATCTCCTTCCAGTGAGGAAG#GGGGCCACCACCCAG##TGTGCTCCATCTTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGGTCCTCCAGCACAAGCTGTTTTAATTTACCCTAGTTCCCAAGGCAGCCTC#TTCTGCCTTGGGTGCTGACA##ACCTT#GGTAGGTGCATAAGCTCTGCATT##AGGTCcacaggggcagtgggagggaactgagactggggagggacaaaggctgctctgtcctggtgctcccacaaaggacagaagggctgatcactcaaagttg##aacaccaagctcaacaatgagccctggaaaatttctggaatggattattacacagagagtctgtaagcacttagaaaaggcc##ggtgagtcccaggggccagcactgct##aagtgtacagcatttctctttgtaacaggattagtagcttgctgtgcccggggagaacatgcagcacag#gcatct##agtcagcaggattt#ga#ggcttctaacaaaatcctgtagacaagatggagctatgggggttggaggagagaacatatagg-aaaatcagagccaaatgaaccacagccccaaagggcacagttgaacaatggactgattccagccttgca#ggagggatctggcagagtccatccggttcATTCAACACCTGGTTAGAAAACTGGGGCCAG 

a score=95099.0
s hg18.chr1             10310 371 + 247249719 cacacaggggaagggtaagctggtttcatgat##aatcaaggctcagacaatttttaaaggccagagggtagactgcaatcaccaagatgaaatttacaaggaacaaatgtgaagcccaacatttaggttttaaaaatcaag##tataaatacagaaggtggagggaacttgctttagacacagttcaggtgaagaaagacctggaaacttctgttaactataagctcagtaggggctaaaagcatgttaat#ggcataaaaaggcaatgagatcttaggGCACACAGCTCCCC#CCCCTCTTCTGCCCTTCATCCTTCTTTCAATCAGCAGGGACCGTGCACTCTCTTGGAGCCACCACAGAAAACAGAG 
s panTro2.chr9_random 4675776 371 +   7733331 cacacaggggaagggtaagttggtttcatgat##aatcaaggctcagacaattttcaaaggccagagggtagactgcaatcacccagatgaaatttacaaggaacaaatgtgaagcccaacatttaggttttaaaaatcaag##tataaatatagaaggtggagggaacttgttttagacacagttcaggtgaagaaagacctggaaacttctgttaactataagctcagtaggggctaaaagcatgttaat#ggcataaaaaggcaatgagatcttaggGCACACAGCTCCCC#CCCCTCTTCTGCCCTTCATCCTTCTTTCAATCAGCAGGGACGGTGCACTCTCTTGGAGCCACCACAGAAAACAGAG 

a score=33853.0
s hg18.chr1        10770 227 + 247249719 CAGAGCAGGAGGAGAGAGCACAGCCTGCAATGCTAATTTGCCAGGAGCTCACCTGCCTG##TCACTGGGCACAGA#GCCAGTGAGGCCAGAGGCCGGGCTGTGCTGGGGCCTGAG-CCGGGTGGTGGGGAG-------AGAGTCTCTCCCCTGCCC--CTGTCTCTTCCGTGCAGGAGG---------------AGCATGTTTAAGGGGACGGGTTCAAAGCTGGTCACATCCCCACCGAAAAAGCCCATGG 
s panTro2.chr12 77693524 219 - 135371336 CAGAGCAGGAGGAGAGAGCATGGCCAGGAATGCTAATTTGCCAGGAGCTCACCTGCCTG##TCACAAGGCACAGG#GCCAATGAGGCCAGGGTCCAGTCTG-----GGGCATGAGATGGGGTGGTGGGGAGGAGAGAGACAGTCTCTCCTCTACCCACCTGTCTCTTCTGTGCAGGTGGTTTCCGAGCAGGTGAAGCACATTTAAAGGGGGAGGTTCTAAACTG---------------------------- 

a score=83473.0
s hg18.chr1             10997 329 + 247249719 ACAA##AAAAGCCCACTAGCTTGTCCAGTGCCACAGGAGGGGCAAGTGGAGGAGGAGAGGTGG#GGTGCTCCCCACTCCACTGCCAGTC#TCACTGGCTCTCCCTTCCCTTCATCCT##TTCCCTATCTGTCACCATTTCCTGT##T##TTTCCTCTGAATGTCTCACCCTGCCCTCCCTGCTTGCAAGTCCCCTGTCTGTAGCCTCACCCCTGTC#TATCCTGACTACAATAACAGCTTCTGGGTGTCCCTGGCATCCACTCTCTCTCCCTTCTTGTCCCTTCC#TGA#GGATGCCTGAGGAACCTTCCCCAAACTCTTCTGTCCCAT 
s panTro2.chr9_random 4677170 329 +   7733331 ACAA##AAAAGCCCACTTGCTTGTCCAGTGCCACAGGAGGGGCAAGTGGAGGAGGAGAGGTGG#GGTGCTCCCCACTCCACTGCCAGTC#TCACTGGCTCTCCCTTCCCTTCATCCT##TTCCCTATCTGTCACCATTTCCTGT##T##TTTCCTCTGAATGTCTCACCCTGCCCTCCCTGCTTGCAAGTCCCCTGTCTGTAGCCTCACCCCTGTC#CATCCTGACTACAATAACAGCTTCTGGGTGTCCCCAGCATCCACTCTCTCTCCCTTCTTGTCCCTTCC#TGA#GGATGCTTGAGGAACCTTCCCCAAACTCTTCCGTCCCAT 

a score=1716519.0
s hg18.chr1     11326 6774 + 247249719 CCCTGCCCTGCTCAAAATCCAATCACAGCTCCCTAACAC#CCTGAATCAACTTGAAGTCCTGTCTTGAGTAATCC#TGGGCCCTAACTCACTCATCCCAACTCTTCACTCACTGCCCTGCCCCACACCCTGCCAGGGAGCCTCCC#TGGCACC#TGGGGACACAAAGGAACCAGGGCAAAGCTCCCTCAGCCCCATTCAAAGAGGCCTGGCCCACAGGCTCA#GGAAAGTCAGCCTCTCATGCCCC#AGAGCTGAGTGCAAGGGAGAGGCAG##CTGTCTGTGCTTCCCATGCAGAAGCACCCCCCTCCCACCCCTGTGCAGGCCGGCCTTC##GGCAGACCACCATACACCA##TTCCAAGCCACACTGAGGCCTCCCTCCAAGCCTGCAGCCCCCATTTCCAGACCCTGCCAGGGCAACCTGCATATCCACCTCCCTACCCTGCCCCCCTCTTCCAGGAGTCTGCCCTATGTGGAGTAAGCA##tggttttcctcttcagcaactatttcctttttactcaagcaatggccccatttcccttggggaatccatctctct##caggcttagtcccagagcttcaggtggggctgcccacagagctcctcagtctaagccaagtggtgtgtcatagtcccctggccccattaatggattctgggatagacatgaggaccaagccaggTGGGATGAGTGAGTGTGGCTTCTGGAGGAAGTGGGGACACAGGACAGCATTCTTTCCTGCTGGACCTGACCCTGTGTCATGTCACCTTGCTACCA##AGAGCATGGCCTGTCTGGGAATGCAGCCAGACCCAAAGAAGCAAACTGACATGGAAGGAAAGCAAAACCAGGCCCTGAGGACATCATTTTAGCCCTTACTCC#AAGGCTGCTCTACTGATTGGTTAATTTTTGCTTAGCTTGGTCTGGGGAGTTCTGACAGG##TGCCACCAATTCTTACC#ATTTCTCTCCACTCTAGACCCTGAGAAGCCCA###GGTTCATGCTAGCAATTAACAATCAATCT##CCCTATGTGTTCCCATTCCAGCCTCTAGGACACAGTGGCAGCCACATAATTGGTATCTCTTAAGGTCCAGCA##AGGTGGAGCACATGGTGGAGAGACAGATGCAGTGACCTGGAACCCAGGAGTGAGGGAGCCAGGACTCAGGCCCAAGGCTCCTGAGAGGCATCTGGCCCTCCCTG#GCTGTGCCAGCAGCTTGGAGAACCCACACTCAATGAA##CAGCACTCCACTACCCAGGAAATGCCTTCCTGCCCTCTCCTCATCCCATCCCTGGGCAGGGGACATGCAACTGTCTACAAGGTGCCAAGTACCAGGACAGGAAAGGAAAGA#GCCAAAAATCCAG#GCTGCCCTCAGAGAAGGGCAACCA#GCAGTCCCCATCTTGGCAAGGAAACACAATTTCC#AGGGAATGGTTTTGGCCTCCATTCTAAGTGCTGGACATGGGGTGGCCATAATCTGGAGCTGATGGCTCTTAAAGACCTGC#TCCTCTTCCCTAGG#GTCCCT#GGGCACATTTAGCACAA#GATAAGCACAAAAGGTGCATCCAGCACTTT--GTTACTATTGGTGGCAGGTTTATGAATGGCAACCAAAGGCAGTGTA#GGGTCAAGATTATCAACAGGGAAGAGATagcatttcctgaaggcttcctaggtgccaggcactgttccattcctttgcatgttttgattaatttaatatttaaaataattctaccaggaag--------------ctaccattattaccacaacttcacaaatgagaacaccgaggcttagaggggttgggttgcccaaggttacagaggaagaaaacaggggagctggatctgagccaaggcatcaactccaaggtAACCCCTCAGTCACTTCACTG#GTGTCCCCTGGTTACTGGGACATTCTTGACAAACT#GGGGCAAGCCGGTGAGTCAGTGGGGGAGGACTTTCAGGAAGAGGTGGGTTCCCAGTTGGTGACAGAAGAGGAGGCTGCAAAGTGAAGGAGCAGGGGCTCCAGGTCTGG##ACAACCAGGGAAGGGACAGGGCAGGGATGGCTTGGACCA##AGAGGCACCTGAGTCAGGCAGTCACATACTTCCC#CTGGGGTCTACCATGTGAGGCATGGTGTGGGATCCTGGGAAGGAGACCAAGCCTCATTTCAGTTTGCTTATGGCCAAAGACAGGACCTGTGTACCC#ACAACCCCTGGGACCTTTACCAAAAAAAGAGCAAACACCATTCACTCACTCATGTTAGATAAACACTGAGTGAAGTCACTGGAGCCCAAGGACTGTG##AGGTCAGC#CTGCCAATACAAGAAGCTGCAGCCCTCCAGCT##Cctccctcaatggccactccgtgctccagccatgctggcttccttttaggtcctccacctccaggctgtagttcatgtgcttctttctggaatgttcttcccaacctacccactcaaccctcagactttaccataaatgtcatttcctcac#tctgccttccctgacctgagaccaagccaggCTTCCCATGA##AGCCTCACAGTACCCCATCTCC#CTGAACAGATGCAGTAATAACCTACATAACccggggccatgatctatggctttgaatcctggctctgtcactaggccaggtctctcagcccttctgtgcctcagtttcctcatctataaaatgagatga#ggcagtgcctgctcatgaagtgtgagttaatgcactcaaatcaatggttgtgca#ggtttatatgaatattagtgattaCAAAATATTATCAatagaccttgtcacaactgttattgaagaactaatcatctattgcttatttaggtctttctctcctgccagaatgtg##ctccaggtggagaggtatgttgccttatcc#tggctggatatatagagattcccacactgccttgcacac#agcactgctgggtaaatatttgttggctgcaggaaAA##TGAAGGAATAGGCCCTCCAATGGGAGGAAAAGCA#GAGTTGTGAGAGCAGAGCCACCACAGGAAACCAGGAGGCTAAGTGGGGTGGAAGGGAGTGAGCTCT#GGACTCCCAGGAGTAAAAGCTTCCAAGTTGGGCTCTCACTTCAGCCCCTCCCACACAGGGAAGCCAGATGGGTTCCCCAGGACCGGGATTCCCCAAGGGGGCTGCTCCCAGAGGGTGTGTTGCTGGGATTGCCCAGGACAGGGATGGCCCTCTCATCAGGTGGGGGTGAGTGGCAGCACCCACCTGCTGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCC#CCATCTGCTGGA#GGCCTCCTCT##CC#CAGGTCTGGCTGGATGAAGGGCA#GGCATAGGTCTGACCTGCCAGGGAGTGCTGCATCCTCACAGGAGTCATGGTGCCTGTGGGT#GGAGCCGGAGC#TCAGAGCCACCCA##ACCACCGGCAC#CCCCCACCACAGGGCAG##TGGTGTTGAGACAACACAGCCCTCATCCCAACTATGCACATAGCTTCAGCCTGCACAGATAGGGGAGTAGGGGACAGAGCATTTGCTGAGAGGCCAGGAG##CATAGATGGGACTCTGCTGATGCCTGCTGAGTGAATGAGGGAAAGGGCAGGGCCCGGGACTGGGGAATCTGTAGGGTCAATGGAGGAGTTCAGAGAAGGTGCAACATTTCTGACCCCCTACAAGGTGCTTGCTACCTGCCAGGCACCCTTTCCATACCTTGTCTCAGTTCAGCTCCCCACCTTGGATAAACAAGAAACCTTGGTTGCAGAGGAAAAAAGAGGCTGGAAACAAAGGGGTAGAAATGGGGTAGCAGGGGAGATTGCCTGATCAACTGCCAAATGGTACACAGTTCTGGAAAAGCACAAAAAATGTGCACACA#GGGTTCTTCCCACTTTAACCCCTGAGGAATCTGAGGCCTGCTCCTGAAACAGACTGGGCAGTGGCTAGTGACTCTAGGTATAGGAGTATCCAGCCCTGCTCACCCAGGCTAGAGCTTAGGGGGACAAGAGGAAAGAGGTGCCTGTGGGGGTGGAGGACAGGAAGGAAAAACACTCCTGGAATTGCAAAGTGAGGGCAGAGTCTATTTATATTGGGTTTAATTAACTCCTCTCCCTGGTGCCACTAAAGCAGCAATCACACTGCAGACAGCACTGATTTGATTGGCAAGAGATGCACCAGGCAGAATATTAAGGGACCAGGCCCCTATAAATAGGCCTAATCACAGCCCCTC#CTGGAAAATGGTAAGGAAGACATTAATCAGGCCTGGCACTGTGCCCTAGACCTGCTCCCCTAGGCACTACAGTGGGGCCCTTGGTTGCAACACAAGTAGGTAGGGATGGATGAGTGTGGCATGAAGGGCCTAGGAGATTTCACTTGGGTTTAAAATGCTGTGACCTTGAGTAAGTTGCCGTCTCTGAATCTGATCCTTTC#ATTTCCCATTCTCCAAACTGAGAACTAGCACTGCTGAGA##TGGTTATTTCCAATAATAATTTGTATATTTTACATAA##CACCACACCAACATCTTCACCCAGTTGGAGCCTACTCCTTTGCTCCC#CTGCTGGCTTCCCCAGCCCTCCCTTCTGCCCTCCTCAGGCCAGCACTTTTCAGTGAGTTCCTCCTTTGCATACAGGCTTTCCAGATCTGTACTTGCCTTGAATACTCATCAGAGCCCAGGAGTTACTCCTCACCTCCCACTTATTTTTCCTCCCATCAAATAACTAAAGCATGGCCAGCTGATGCCCAGCCAACTGAGAAACCCAACCCTCTGAGACCAGCACACCCCTTTCAAGCATGTTCCTCCCTCCCCTTCTTTGTATTTATACTGA#GCAAGTTTGCTGGCTGTcctaacttatttctgtgcctcagttctcccatatgtaagatcacaaagggggtaaagaTGCAAGATATTTCCTGTGCACATCTTCAGATGAATTTCTTGTTAGTGTGTGTGTGTTTGCTCACACATATG##TGAAAGAAGAGTACATACACAGATCTCCTCAAAAAGGAGGCAGCAAGCCC#TTCAAGAATGGGACTGAATACACCTGATGAGTGGTTTACTTTCTGTCTGCAAACATCTACTGATCATCTGTTAGGTGCAGGCCATGATCACAACAAAGA##AATAAGACACTACACTAGCCAGGGAGAGTCTCAAAAACAACTAAACTCAAATTAAATTCATTCTACTCCAGTCATGGGTACAAAGCTAAGGAGTGACAAATCCCTCTTGGAGTTAGGGGAGTCAGGAAAAAGCTCTTAGCAGAATGTGTGCCTCT#ggccgggc#cag#ggctca##cctgtaatcccagcactttgggagg##aaggcaggcagatcacctgaggtcgggagtt##agaccagtctgaccaacatggtgaaactccatctctactaaaaatacaaaattagccagg##tggtggtgcatgcctgtaatccccgctact#gggaggctgaggaaggagaatcacttgaaccaggaaggt#gaggttgcagtgtgcc#agat####ccatggcactccagcctaggcaac#agggtgaaCCAGGTCCAGGAAGAAGGTGCAAAGACAGCATTCCAGGTAAAAGAAACAGCTTGAACAAAAAGTGTGTAGGGGAACCGCAAG#GGTCTTGAGTGCTGAGGGTACAATCATCCTTGGGGAAGTACTAGAAGAAAGAATGATAAACAGAGGCCAGTTTGTTAAAAACACTCAAAATTAAAGCTAGGAGTTTGGACTTGTGGCAGGAATgaaatccttagacctgtgctgtccaatatggtagccaccaggcacatgcagccactgagcacttgaaatgtggatagtctgaattgagatgtgccataagtgtaaaatatgcaccaaatttcaaaggctagaaaaaaagaatgtaaaatatcttattattttatattgattac#tgctaaaataaccatatttgggatatactggattttaaaaatatatcactaatttcatctgtttctttttacttttAGAAATCACATATGTGACTTAAATATTTCTTTTCTTTTTCTTTCCTCTCACTCAG##TCCTGTGATTCCAAAGAAATGAGTCTCTGCTGTTTTTGGGCAGCAGATATCCTAGAATGGACTCTGACCTAAGCATCAAAATTAATCATCATAA##TTATCATTTTATGGCCCCTTCTTCCTATATCTGGTAGCTTTTAAATGATGACCATGTAGATAATCTTTATTGTCCCTCTTTCAGCAGA#GGTATTTTCTTATGCTACAGTATGACTGCTAATAATACCTACACA#GTTAGAACCATTCTGACTCCTCAAGAatctcatttaactcttattatcagtgaatttatcatcatcccctattttacataaggaaatggggttagaaagaccaaataacattttttcaacatcaaaacactagcttgagatcaagcccagacttggatctgt#gtctgaattccaagctttttgttatttattgatatgttttgttgtTTTCATGCAATAATGCAAATCTTAGCCCAAACATTTTGTTAGTAGTACCAACTGTAAGTCACCTTATCTTCATACTTTGTCTTTATGTAAACCTAAATTAGATCTGTTTTTGATACTGAGGGAAAAACAAGGGAATctaacactaaccagccc#tagtgtgtggtcaacacttt##ttactttagtatacatcaccccaattgtttgtcttcaccacacactt 
s panTro2.chr15 23957 6770 - 100063422 CCCTGCCCTGCTTAAAATCCAATCACAGCTCCCTAACAC#CCTGAATCAACTTGAAGTCCTGTCTTGAGTAATCC#TGGGCCCTAACTCACTCACCCCAACTCTTCACTCACTGCCTTGCCCCACACCCTGCCAGGGAGCCTCCC#TGGCACC#TGGGGACACAAAGGAACCAGGGCAAAGCTCCCTCAGCCCCATTCAAAGAGGCCTGGCCCACAGGCTCA#GGAAAGTCAGCCTCTCATGCCCC#AGAGATGAGTGCAAGGGAGAGGCAG##CTGTCTGTGCTTCCCATGCAGAAGCACCCTCCTCCCACCCCTGTGCAGGCCGGCCTTC##GGCAGACCACCATACACCA##TTCCAAGCCACACTGAGGCCTCTCTCCAAGCCCGCGGCCCCCATTTCCAGACCCCACCAGGGCAACCTGCATATCCACCTCCCTACCCTGCCCCCCTCTTCCAGGAGTCTGCCCTATGTGGAGTAAGCA##tggttttcctcttcagcaactatttcctttttactcaagcaatggccccatttcccttggggaatccatctctct##caggcttagtcccagagcttcaggtggggctgcccacagagttcctcagtctaagccaagtggtgtgtcatagtcccctggccccagtaatggattctgggatagacatgaggaccaagccaggtgggatgggtaagtgtggcttctggaggaagtggggacacaggagagcattctttcctgctggACCTGACCCTGTGTCATGTCACCTTGCTACCA##ACAGCATGGCCTGTCTGGGAATGCAGCCAGACCCAAAGAAGCAAACTGACATGGAAGGAAAGCAAAACCAGGCCCTGAGGACATCATTTTAGCCCTTACTCC#AAGGCTGCTCTACTGATTGTTTAATTTTTGCTTAGCTTGGTTTGGGGAGTTCTGACAGG##TGCCACCAATTCTTACC#ATTTCTCTCCACTCTAGACCCTGAGAAGCCCA###GGTTCATGCTAGCAATTAACAATCAATCT##CCCTATGTGTTCCCATTCCAGCCTCTAGGACACAGTGTCAGCCACATAATTGGTATCTCTTAAGGTCCAGCA##AGGTGGAGCACATGGTGGAGAGACAGATGCAGTGACCTGGAACCCAGGAGTGAGGGAGCCAGGACTCAGGCCCAAGGCTCCTGAGAGGCATCCGGCCCTCCCTG#GCTGTGCCAGCAGCTTGGAGAACCCACACTCAATGAA##CAGCACTCCACTACCCAGGAAATGCCTTCCTGCCCTCTCCTCATCCCATCCCTGGGCAGGGGACATGCAACTGTCTACAAGGTGCCAAGTACCAGGACAGGAAAGGAAAGA#GCCAAAAATCCAG#GCTGCCCTCAGAGAAGGGCAACCA#GCAGTCCCCATCTTGGCAAGGAAACACAATTTCC#AGGGAATGGTTTTGGCCTCCATTCTAAGTGCTGGACATGGGGTGGCCACAATCTGGAGCTGATGGCTCTTAAAGACCTGC#TCCTCTTCCCTAGG#GTCCCT#GGGCACATCTAGCACAA#GATAAGCACAAAAGGTGCATCCAGCACTTTCTGTTACTATTGGTGGCAGGTTCATGAATGGCAACCAAAGGCAGTGTA#GGGTCAAGATCATCAACGGGGAAGAGATagcatttcctgaaggcttcctaggtgccaggcactgttccattcctttgcatgttttgattaatttaatatttacaataattctaccaggaagaattattaccattattaccattattaccacaacttcacaaatgagaacactgaggcttagaggggttgggttgtccaaggttacagaggaagaaaacaggggagctggatctgagccaaggcatcaactccaaggtAACCCCTCAGTCACTTCAGTG#GTGTGCCCTGGTTACTGGGACATTCTTGACAAGCT#GGGGCAAGCCGGTGAGTCAGTGGGGGAGGACTTTCAGGAAGAGGTGGGTTCCCAGTTGGTGACAGAAGAGGAGGCTGCAAAGTGAAGGAGCAGGGGCTCCAGGTCTGG##ACAACCAGGGAAGGGACAGGGCAGGGATGGCTTGGACCA##AGAGGCACCCGAGTCAGGCAGTCACATACTTCCC#CTGGGGTCTACCATGTGAGGCATGGTGTGGGATCCTGGGAAGGAGACCAAGCCTCATTTCAGTTTGCTTATGGCCAAAGACAGGACCTGTGTACCC#ACAACCCCTGGGACCTTTGCCAAAAAAACAGCAAACACCATTCACTCACTCATGTTAGATAAACACTGAGTGAAGACACTGGAGCCCAAGGACTGTG##AGGTCAGC#CTGCCAATACAAGAAGCTGCACCCCTCCAGCT##Cctccctcaatggccactctgtgctccagccatgctggcttccttttaggtcctccacctccaggctgtagttcatgtgcttctttctggaatgttcttcccaacctacccactcaaccctcagactttaccataaatgtcatttcctcac#tctgccttccctgacctgagaccaagccaggcttcccatga##agcctcacagtacccCATCTCC#CTGAACAGATGCAGTAATAACCTACATAACccggggccatgatctatggctttgaatcctggctctgtcacttggccaggtctctcagcctttctgtgcctcagtttcctcatctataaaatgagatga#ggcagtgcctgctcatgaagtgtgagTTAATGCACTCAAATCAATGGTGGTGCA#GGTTTATATGAATATTAGTGATTACAAAATATTATCAATAGACCTTGTCACAACTGTTATTGAAGAATTAATCATGTAttggttatttaggtctctctctcctgccagaatgtg##ctcca--tggagaggtatgttgccttatcc#tggctggatatatagagattcccacactgccttgcacac#agcactgctgggtaaatatttgctggctgcaggaaAA##TGAAGGAATAGGCCCTCCAGTGGGAGGAAAAGCA#GAGTTGTGAGAGCAGAGCCACCACAGGAAACCAGGAGGCTAAGTGGGGTGGAAGGGACTGAGCTCT#GGACTCCCAGGAGTAAAAGCTTCCAAGTTGGGCTCTCACTTCAGCCCCTCCCACACAGGGAAGCCAGATGGGTTCCCCAGGACCAGGATTCCCCAAGGGGGCTGCTCCCAGAGGGTGTGTTGCTGGGATATCCCAGGACAGGGATGGCCCTCTCATCAGGTGGGGGTGGGTGGCAGCACCCACCTGCCGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCC#CCATCTGCTGGA#GGCCTCCTCT##CC#CAGGTCTGGCTGGATGAGGGGCA#GGCATAGGTCTGACCTGCCAGGGAGTGCTGCATCCTCACAGGAGTCATGGTGCCTGTGGGT#GGAGCCGGAGC#TCAGAGCCACCCA##ACCACCTGCAC#CACCCACCACAGGGCAG##TGGTGTTGAGACAACACAGCCCTCATCCCAACTATGCACATAGCTTCAGCCTGCACAGATAGGGGAGTAGGGGACAGAGCATTTGGTGAGAGGCCAGGAG##CATAGATGGGACTCTGCTGATGCCTGCTGAGTGAATGAGGTAAAGGGCAGGACCAGGGACTGGGGAATCTGTAGGGTCAATGGAGGAGTTCAGAGAAGGTGCAACATTTCTGACCCCCTACAAGTTGCTTGCTACCTGCCAGGTACCCTTTCCATACATTGTCTCAGTTCAGCTCCCTACCTTGGATAAACAAGAAACCTTGGTTGCGGAGGAAAAAAGAGGCTGGAAACAAAGGGGTAGAAATGGGGTAGTGGGGGAGATTGCCTGATCAACTGCCAAATGGTACCCAGTTCTGGAAAAGCACAAAAAATGTGCACACA#GGGTTCTTCCCACTTTAACCCCTGAGGAATTTGAGGCCTGCTCCTGAAACAGACTGGGCAGTGGCTAGTGACTCTAGGTATAGGAGTATCCAGCCCTGCTCACCCAGGCTAGAGCTTAGGGGGCCAAGAGGAAAGAGGTGCCTGTGGGGGTGGAGGACAGGAAGGAAAAACACTCCTGGAATTGCAAAGTGAGGGCAGAGTCTATTTATATTGGGTTTAATTAACTCCTCTCCCTGGTGCCACTAAAGCAGCAATCACACTGCAGACAGCACTGATTTGATTGGCAAGAGATGCACCAGGCAGAATATTAAGGGACCAGGCCCCTATAAATAGGCCTAATCACAGCCCCTC#CTGGAAAATGCTAAGGAAGACATTAATCAGGCCTGGCACTGTGCCCTAGACCTGCTCCCCTAGGCACTACAGTGGGGCCCTTGGTTGCAACACAAGTAGGTAAGGATGGATGAGTCTGGTATGAAGGGCCTAGGAGATTTCATTTGGGTTTAAAATGCTGTGACCCTGAGTAAGTTGCTGTCTCTGAATCTGATCCTTTC#ATTTCCCATTCTCCAAACTGAGAACTAGCACTGCTGAGA##TGGTTATTCCCAATAATAATTTGTATATTTTACATAA##TACCACACCAACATCTTCACCCAGCTGGAGCCTACTCCTTTGCTCCC#CTGCTGGCTTCCCCAGCCCTCCCTTCTGCCCTCCTCAGGCCAGCACTTTTCAGTGAGTTCCTCCTTTGCATACAGGCTTTCCAGATCTGTACTTGCCTTGAATACTCATCAGAGCCCAGGAGTTACTCCTCACCTCCCACTTATTTTTCCTCCCATCAAATAACTAAAGCATGGCCAGCTGATGCCCAGCCAACTGAGAAACCTAACCCTCTGAGACCACCACACCCCTTTCAAGCATGTTCCTCCCTCCCCTTCTTTGTATTTATACTGA#GCAAGTTTGCTGGCTGTcctaacttatttctgtgcctcagttctcccatatgtaagatcacaaagggggtaaagatgcaagATATTTCCTGTGCACATCTTCAGATGAATTTCT------TGTGTGTGTGTTTGCTCACACATATG##TGAAAGAAGAGTACATACACAAAT---CTCAAAAAGGAGGCAGCAAGCCC#TTCAAGAATGGGACTGAATACACCTGATGAGTGGTTTACTTTCTGTCTGCAAACATCTACTGATCATCTGTTAGGTGCAGGCCATGATCACAACAAAGA##AATAAGACACTACACTAGCCAGGGAGAGTCTCAAAAACAACTAAACTCAAATTAAATTCATTCTAATCCAGTCATGAGTACAAAGCTAAGGAGTGACAAATCCCTTTTGGAGTTAGGGGAGTCAGGAAAAAGCTCTTAGCAGAATGTGTGCCTCT#ggctgggc#cag#ggctca##cctgtaatcccagcactttgggagg##aaggcaggcagatcacctgaggtcaggagtt##agaccagtctgaccaacatggtgaaactccatctctactaaaaatacaaaattagccagg##tggtggtgcatgcctgtaatcccagctact#gggaggctgaggaaggagaatcacttgaaccggggaggt#gaggttgcagtgtgcc#agat####ccattgcactccagcctgggcaac#aaagtgaaCCAGGTCCAGGAAGAAGGTGCAAAGACAGCATTCCAGGTAAAAGAAACAGCTTGAACAAAAAGTGTGTAGGGGAACAGCAAG#GGTCTTGAGTGCTGAGGGTACAATCATCCTTGGGGAAGTACTAGAAGAAAGAATGATAAACAGAGGCCAGTTTGTTAAAAACACTCAAAATTAAAGCTAGGAGTTTGGACTTGTGGCAGGAATgaaatccttagacctgtgctgtccaatatggtagccaccaggcacatgcagccactgagcacttgatatgtggatagtctgaattgagatgtgccataagtgtaaactatgcaccaaatttcaaagactagaaaaaaagaatgtaaaatata-----attttatattgattac#tgctaaaataaccatatttgggatatactggattttaaaaatatattgctaatttcatctgtttctttttacttttAGAAATCACATATGTGACTTAAATATTTCTTTTCTTTTTCTTTCCTCTCACTCAG##TCCTGTGATTCCAAAGAAATGAGTCTCTGCTCTTTTTGGGCAGGAGATATCCTAGAATGGACTCTGACCTAAGAATCAAAATTAATAATCATAA##TTATCATTTTATGGCCCCTTCTTCCTATATCTGGTAGCTTTTAAATGATGACCATGTAGATAATCTTTATTATCCCTCTTTCAGCAGA#GGTATTTTCTTATGCTACAGTATGACTGCTAATAATACCTACATA#GTTAGAACCATTCTGACTCCTCAAGAatctcatttaactcttattatcagtgaatttatcatcatccccaattttagataaggaaatggggttagaaagaccaaataacattttttcaacatcaaaacactagcttgagatcaagcccaaacttggatctgt#gtctgaattccaagctttttg----ttattgatatgttttgttgtTTTCATGCAATAATGCAAATCTTAGCCCAAACATTTTGTTAGTAGTACCAACTGTAAGTCACCTTATCTTGATACTTTGTCTTTATGTAAACCTAAATTAGATCTGTTTTTGATACTGAGGGAAAAACAAGGGAATCTAACACTAACCagccc#tagtgtgtggtcaacacttt##ttactttagtatacatcaccccaattgtttgtcttcaccacacactt 

a score=407272.0
s hg18.chr1     18260 1630 + 247249719 GATTTTGTTGG#GGAAAAAAAAATTTATCAAAAGT##TCTTCTATCAGGGAGTTTTATGAGAAACCCTAGCTCCTCAGTTCCACAGTGGGTAACTGTAATTCATTCTAGGTCTG##ATATTTCCTGCCTATCCATTT#GTTAACTCTTCAATGCATTCCACAAATACCTAAGTATTCTTTAATAATGGTGGTTTTTTTTTTTTTTTGCATCTATGAAGTTTTTTCAAATTCTTTTTAAGTGACAAAACTTGTACATGTGTAT##CTCAATATTTCTAGT##ACAGCACTGCTTT##AGAATGTAAACC#TGCACTCCCAGGAAAATGCAGACACAGC###CCTCTTTGGGACC##GGTTTATACTTT#GAAGTGCT#GGAGCCCTTCCTCCAGACC#TTCTCCCACACCCC#CTCCAGGGTCTCTCCCGGAGTTACAAGCCT##CTGTAGGCCCCGGGAACCCAA###GGTGTCAGAGAAGTGGGGTCCCCTA##AGGGACCAGGAGCTCCGGG#GGGCAGCAGCTG#GGAAGAGCC#####AGGCTTCCCAGAACCCGGCAGGGG#GGGAAGA##CAGGAGTGGGGAGG#GGAACCGGGACCCC#CAGAGCCCGGGTCCCTG##CCCCACAAGCCTTGGCTTCCCTGCTAGGGCCGGGCAAGGCCGGGTGCAGGG###GGCTCCAGGGAGGAAGCTCCGGGG##AGCCCAAGA##CCTCCCGGG#GGT#GGGGCCCAG#GG#GG##TT##CAGTGGAGCCGGGCACCGGGCAG#GGCC##GGAACACCAGCTTGG##CAGGCTTCT#GGTCAGGAA#GGTCCCGGGCCTCCC#CCC#CCTCCCTCCAGCCCCTCCGGGTCCCCTACTT##CCCC#CCAGGCCCCCA##ACCCTACTTCCC##GGCCCCGGA##CCTCCTCACCTG##AGCC#CCCTCCCGGAAGCTCCC#CC#CC#CTTCC#CTCTGCCGGAGCC#CTGGGTCCTAGCCCC#CC#CCCCCAGTCC#CCC###CCTCCGGGTCCTAA##CC#CC#CTC#CCCTCC#CTG##CCCTCCCC#AG###GGCTCCAGGACCCC#T##ACCCGGAG##CTGTCCTGT#GGGCC#AGT###GGGCCTGGGCA#GGAACTCA##CTCACTCC#AGCTCCC#A##TGCACA#GGCTCCCATGC#TTGTCTTCC#AG##TCAGGCC#CCCCTACCC#TGCTTTCTGCTCTGCAGACCCTCTTCCTAGACCTCC#TCCTTTGTCCCAT##CTGCCTTCCCCTCAAGCTCAGGGCCAAGCTGTCC#CCAACCT#GGCTCCTCCGGGCAGCCCT##CCCGGGGTG##CCCCGGGGCAGGACCCCCAGCCCA#GCCCAGGGCCC#CCCCTGCCCTCCAGCCCTAC#CCTTGACCC#CTTTCCTGC#TCTCTCAGCCTACCTGACCTTGTCTTTACCTCTGTGGGCAGCTCCCTTGTGATCTGCTTAGTTCCCACCCCCCTTTAAGAATTCAATAGAGaagccaga##caaaactacagatat##tatgagtccagttttgtgaagtgcctagaatagtcaaaattcacagagacagaagcagtggt##ccaggaatggggaagcaagg#ggagttgggcagct 
s panTro2.chr15 30886 1625 - 100063422 GATTTTGTTGG#GGAAAAAAAAATTTATCAAAAGT##TCTTCTATC--GGAGTTTTATGAGAAACCCTAGCTCCTCAGTTCCACAGTGGGTAACTGCAATTCATTCTAGGTCTG##ATATTTCCAGCCTATCCATTT#GTTAACTCTTCAATGCATTCCATAAATGCCTAAGTATTCTTTAATAATGGTGG--TTTTTTTTTTTTTGCATCTATGAAGTTTTTTCAAATTCTTTTTAAGTGACAAAACTTGTACATGTGTAT##CACAATATTTCTAGT##ACAGCACTGCTTT##AGAATGTAAACC#TGCACTCCCAGGAACATGCAGACACAGC###CCTCTTTGGGACC##GGTTCATAATTT#GGAGTGCT#GGAGCCCTTCCTCCAGACC#TTCTCCCACACCCC#CTCCAGGGTCTCTCCCGGAGTTACAGGCCT##CTGTAGGTCCCGGGAACCCAA###GGTGTCAGAGAAGTGGGGTCCCCTA##AGGGACCAGGAGCTCCGGG#GGGCAGCAGCTG#GGAAGAGCC#####AGGCTTCCCAGAACCCGGCCGGGG#GGGAAGA##CAGGAGTGGGGAGG#GGAACCGGGACCCC#CAGAGCCCGGGTCCCTG##CCCCACAAGCCTTGGCTTCCCTGCTAGGGCCGGGCAAGGCCGGGTGCAGGG###GGCTCCAGGGAGGAAGCTCCGGGG##AGCCCAAGA##CCTCCCGGG#GAT#GGGGCCCAG#GG#GG##TT##CAGTGGAGCCGGGCACCGGGCAG#GGCC##GGAACACCAGCTTGG##CAGGCTTCT#GGTCAGGAA#GGTCCCGGGCCTCCC#CCC#CCTCCCTCCAGCCCCTCCGGGTCCCCTACTT##CCCC#CCAGGCCCCCA##ACCCTACTTCCC##GGCCCCGGA##CCTCCTCACCTG##AGCC#CCCTCCCGGAAGCTCCC#CC#CC#CTTCC#CTCTGCCGGAGCC#CTGGGTCCTAGCCCC#CC#CTCACAGTCC#CCC###CCTCCGGGTCCTAA##CC#CC#TTC#CCCTCC#CTG##CCCTCCCC#AG###GGCTCCAGGACCCC#T##ACCCGGAG##CTGTCCTGG#GGGCC#AGT###GGGCCTGGGCA#GGAACTCA##CTCACTCC#AGCTCCC#A##TGCACA#GGCTCCCATCC#TTGTCTTCC#AG##CAGGGCC#CCCCTACCC#TGCTTTCTGCTCTGCAGACCCTCTTCCCAGACCTCC#TCCTTTGTCCCAT##CTGCCTTCCCCTCAAGCTCAGGGCCAAGCTGTCC#CCAGCCT#GGCTCCTCCGGGCAGTCCT##CCCTGGGTG##CCCCGGGGCAGGACCCCCAGCCCA#GCCCAGGGCCC#CCCCTGCCCTCCAGCCCTAC#CCTTGACCC#CTTTCCTGC#TCTCTCAGCCTACCTGACCTTGTCTTTACCTCTGTGGGCAGCTCCCTTGTGATCTGCTTAGTTCCCA-CACCCTTTAAGAATTAAATAGAGaagccaga##caaaactacagatat##tatgagtccacttttgtgaagtgcctagaatagtcaaaattcacagagacagaagcagtggt##ccaggaatggggaagcaagg#ggagatgggcagct 

a score=458960.0
s hg18.chr1        19890 1848 + 247249719 cgtgttcaatgggtagagtttcaggctggggtgatggaagggtgctggaaatgagtggtag#gatgg#ggc#caacagtgtgaatctacttaatcccactgaactgtatgctgaaaaatggtttaga#ggtgaattttaggttatgtatgttttaccacaatttttaaaaaGCTAGTGAAAAGCTGGTAAAAAGAAAGAAAAGAGGCTTTTTTAAAAAGTTAAATATATAAAAAGAGCATCATCAGTCCAAAGTCCAGCAGTTGTCCCTCCTGGAATCC#TTGGCTTGCCTCCGGCATTTTTGGCCCTTGCCTTTtagggttgccagattaaaagacaggatgcccagctagtttgaattttagataaacaa##aataattt##tagcataaatatgtcccaagcttagtttgggacatacttatgctaaaaaacattattggttgtttatctgagattcagaattaagcattttatattttatttgctgcctctggccaccctaCTCTCTTCCTAACACTCTCTCCCTCTCCCAGTTTTGTCC#CCTTCCCTGCCTCCTCTTCTGGGGGAGTTAGAT##AGTTGTAACAAGAACATGCCACTGTCTC#CTGGCTGCAG##TGTGGTCCCCTTACCAGAGGTAAAGAAGAGATGGATCTCCACTCAtgttgtagacagaatgtttatgtcctctccaaatgcttatgttgaaaccctaacccctaatgtgatggtatgtggagatgggcctttggtaggtaatta#ggttagatgaggtcatggggtggggccctcattatagatctggtaagaaaagagaGCATTGtctctgtgtctccctctctctctctctctctctctctcatttctctctatctcatttctctctctctcgctatctcatttttctctctctctctttctctcctctgtcttttcccaccaagtgaggatg##aagagaaggtggctgtctgcaaaccaggaagagagccctcaccgggaaccc#tccagctgccaccttgaacttggacttccaagcctccagaactgtgagggataaatgtatgattttaaagt##cccagtgtgtggtattttgttttgactaatacaaCCTGAAAACATTTTCCCCTCACTCCACCTGAGCAATATCTGAGTGGCTTAAGGTACTCAGGACACAACAAAGGAGAAATGTCCCATGCACAAGGTGCACCCATGCCTGGGTAAAGCAGCCTGGCACAGAGGGAAGCACACAGGCTCAGggatctgctattcattctttgtgtgaccctgggcaagccatgaatggagcttcagtcaccccatttgtaatgggatttaattgtgcttgccctgcctccttttgagggctgtagagaaaagatgtcaaagtattttgtaATCTggctggg##tggtggctcatgcctgtaatcctagcactttggtaggctga####agaggactgcttgagcccaagagtttgagatcagcctgggcaatattgtgagattccatctctacaaaaataaaataaaatagccagtcatggtgtcacacacctgtagtcccagctacatgggaggctgagg#gggaggatcacttgagcttgggagat##aggctgcagtgagctatgattgtaccactgcactccaggctggg##acagagagagaccctgtctcagaaaaaaaaaaaaaaGTACTTTGTAATCTGTAAGGTTTATTTCAACACACACAAAAAAAGTGTATATGCTCCA##ATGCCTGTGAATATACACACACACCACATCATATACCAAGCCTGGCTGTGTCTTCTCACAAATGC#CTGCTAGGCACCACCC 
s panTro2.chrUn 57103829 1814 -  58616431 tgtgttcaatgggtagagtttcaggctggggtgatggaagggtgctggaaatgagtggtag#gatgg#ggc#caacagtgtgaatctacttaatcccactgaactgtatgcttaaaaatggtttaga#ggtgaattttaggttatgtatgttttaccacaatttttaaaaaGCTAGTGAAAAGCTGGTAAAAAGAAAGAAAAGAGGCTTTTTTAAAAAGTTAAATATATAAAAAGAGCATCATCAGTCCAAAGTCCAGCAGTTGTCCCTCCTGGAATCC#TTGGCTTGCCTCCGGCATTTTTGGCCCTTGCCTTTtagggttgccagattaaaatacaggatgcccagttagtttgaattttagataaacaa##aataattt##tagcataaatatgtcccaagcttagtttgggacatacttatgctaaaaaacattattggttgtttatctgagattcaaaattaagcattttatattttatttgctgcctctggccaccctaCTCTCTTCCTGACACTCTCTCCCTCTCCCAGTTTTGTCC#CCTTCCTTGCCTCCTCTTCTGGGGGAGTTAGAT##AGTTGTAACAAGAACATGCCACTGTCTC#CTGGCTGCAG##TGTGGTCCCCTTACCAGAGGTAAGGAAGAGATGGATCTCCACTCAtgttgtagacagaatgtttatgtcctctccaaattcttatgttgaaaccctaacccctaatgtgatggtatgtggagatgggcctttggtaggtaatta#ggttagatgaggtcatggggtggggccctcattatagatctggtaagaaaagagagcattgtctctctgtctccctctc-----------------------tctctctatgtcatttctctctct----ctatctca--tttctctctctctctctctctcctctgtcttttcccaccaagtgaggatg##aagagaaggtggctgtctgcaaaccaggaagagagccctcaccaggaaccc#tccagctgccaccttgaacttggacttccaagcctccagaactgtgagggataaatgtatgattttaaagt##cccagtgtgtggtattttgttttgactaatacaaCCTGAAAACATTTTCCCCTCACTCCACCTGAGGAATATCTGAGTGGCTTAATGTACTCAGGACACAACAA---AGAAATGTCCCATGCACAAGGTGCACCCATGCCtgggtaaagcagcctggcacagagggaagcacacaggctcagggctctgctattcattctttgtgtgaccctgggcaagccatgaatggagcttcagtcaccccatttgtaatgggatttaattgagcttgccctgcctccttctgagggctgtagagaaaagatgtcaaagtattttgtaatctggctggg##tggtggctcatgcctgtaatcccagcactttggtaggctga####agaggactgcttgagcccaagagtttgagatcagcctgggcaatattgtgagattccatctctacaaaaataaaataaaatagccagtcatggtgtcacacacctgtagtcccagctacatgggaggctgagg#gggaggatcacttgagcttgggagat##aggctgcagtgagctatgattgtaccactgcactccaggctggg##acagagagagaccctgtctcag--aaaaaagaaaaagtactttgtaatctgtaaggtttatttcaacacACACAAAAAAAGTGTATATGCTCCA##ATGCCTGTGAATATACACACACACCACATCATATACCAAGCCTGGCTGTGTCTTCTCACAAATGC#CTGCTGGGCACCACCC 

a score=97796.0
s hg18.chr1        21738 409 + 247249719 CCAGTTCTAGAATCACACCAGCCAGTTCACCCTCCAGA#GGTTCACCCTCAACTTCATAAAAGTTCCCTACCTAATCTACT---GACAGGCTCATCCCCGACCTAATTTTAAAGATTTCCTAGGA----------------------------------GCTGCAGTGGGAATCCTGGACCTCAGC#TGGACAAAGAACAGCTGCAGGTCATTCTCATGTGTGGACACAGAAGCTCTGCCTGCCTTTGCTGGCCAGCTGGGCTGAG#GGGCCTGGGAA-TTAAGGCTGCAGGGTTGGTCCCAGGCAGTCTTGCTGAAGCTTGCCACATCCCCCAGCCTCCTGGATTTGCCAGGATCCAAGAGCATGGACTTTAGGAATTCCTGGTGGAGGAGTGAAGAAAATGTGACAGGGTGTCCTAAGCCCC#ATCTACAGGAAGAAAACTGGAA 
s panTro2.chrUn 57107006 446 -  58616431 CCAGTTCTAGAACCAGACCAGACAGTTCACCCTCCAGA#GGTTCACCCTCAACTGTATAAAAGTTCTCTACCTAATCTACTACTGACAGACTCATCTCAGACCTAATTTTAAAGATTTCCTAGGAACTGAATTGCAAAAACTTTTACCCTCACCCTAGAGCTGCAATGGGAATCCTG-ACCTCAGC#TAGACAAAGAAAAGCTGCAGGTCATTCTCATGTGTGGACACGGAAGCCCTGCCTGCCTTTGCTGGCCAGCTGGGCTGAG#GGGCCTGGGAAATTAAGGCTGCAGGGTTGGTCCCAGGCAGTCTTGCTGAAGCTTGCCACATCCCCCAGCCTCCTGGATTTGCCAGGATCCAAGAGCATGGACTTTAGGAATTCCTGGTGGAGGAGTGAAGAAAATGTGACAGGGTGTCCTAGGCCCC#ATCTACAGGAAGAAAACTGGAA 

a score=7233.0
s hg18.chr1        22147 35 + 247249719 ATAAGACTGAGGACTTAGTTTAAGATGTTCCTACT 
s panTro2.chrUn 57107452 35 -  58616431 ATAAGACTGAGGACTTAGTTTAAGATGTTCCTACT