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CJFIELDS / BioPerl-1.6.923 / t / data / testaln.xmfa 
>1:1-598 + chrY 
TCCAAGTCGGCTTTATGTTTGCTTCTGCCAGGCATTCTAGATGCCCCATGTCTAGGATCT
CTTTAGGCAGGAGAGAGGGTGATGGTGTAGGAGGACCCATTTCTTGGCTTGCAGATTCCA
ATAATAAAAAAGTCACAGATTTAAACCCCAAACTTTGATGAAATGCAGGTCTAGGGTTTT
AAAATATAATGAGAGTTAAATACTTTTGTATTTTCTTCATCCAGAGATGGGGCAAGCTTC
CTCATCTGCTCGTTCATGGGTGATTTATATTTTCCCCACTCCATCCTTTTCCTAAGGTAT
TTTTTTTTTAGGGACAATGGCTTTTTGCAGAGTACTCAGTTCCAGCTCCGGGGGCACCGG
TTGAGCCCTTACCGTCCTGCCCCTAAACATCCAGACCTCAAGTTAGAGAGGGGAGTAACA
TTTGGGGGGTGCCCACACCTAGGAGGACCAATCCTTCTGGTTTCCTTAGGGATGCAGGAA
TTTGGGGGGGGGGGGCTCAGTGCTAAAACCAGTAGAGTCCTGGGCAAACGAGTATGACTG
AAGATGCTTTGAACACCCTAGCGTTATGTCGATCGCATGCATCGTAGTGTCGCTGATG
>2:5000-5534 - chr17 
TGCAGATTGGCCTT-TGTTTCGTTTTTC-AAGCGTT-TAAA--CGCCTTGCCTAAGAATC
TTTT--GCAGGGAAGGGGATAGTGAACTGGGAAAACCTGGCTCTTCCTTTCGAGATTCCA
GTAACAAACATGTCATAACTATAAACGCCAAACTTGG--AGAGCGCAGGAATGGAAGGTC
AAACACCAATGAGAGTTAGATGGTTTTGGGTTT----------------------GCT--
CTAGTCTGCACG-------GTGCTCCCCGTCCCCTCACGTCCGTGCTTTTCCTCAGGATG
ATGCCTTGCCAGAACACCGGTGTGCTGCAAGGTGCTCAGCTCCAAATCGGGCTGCACCGC
TTCAGCTTTCCCCATCCAGCCA--ACGCAGGAAGGCCTGGAGCTACAGAGTTTAGAGCCA
TCTCTCCGCTGCTCAT--------TAACCAACCATTCCAGCT-------GTCTGTAGTGG
GTTTTTTTCTT----CTCTACACTAAAATGAGGACAGTCCAGGCCCTTTG--TTAGACTG
AAGATGCTTTGAACACCCTAGCGTTATGTCGATCGCATGCATCGTAGTGTCGCTGATG
>3:19000-19537 - chr7 
TCCAGACTGTCTTT-TGCTCCCTTTTTCCGAGCATT-TAAAAATACCATGCCTAAGAATC
TTTT--GCAGGGAAGGGGATAGCGAGCTGGGAAGGCCTATTTCTTCATTTCGAGATTCTG
GTAATAAACATGTCATAAATATAAATGCCAAACTCCG--GAAATGCAGGTGTAGAGCGTC
AGATTCTATTTGGACTTAAATGATGTGGTGTTTT---------------------GCT--
CTAATTTCTACC-------GTGCTCTCCGTTCC-TCAAGTCCATGCATTTCCTTAGGGTG
CTGCCTTTCCAGAGTACTGGTATGCTGCAGGGTGCTCAGTTCCACATCTGTCTGCACTAT
TTCAAAGTTTCCC-TCCAGCCC--ACACAACTATGCCTAGAGCTA--GAGGTTAGAACCG
TCTGTCCA-TGCTCTT--------TAACCAACCACTCCAGAT-------AGGTGTGGTGG
TTTTTTTTTTTTTTTCTCTGTACTAAAATTAGGACAGTCCAGGCCTGTTG--TTAGACCA
AAGATGCTTTGAACACCCTAGCGTTATGTCGATCGCATGCATCGTAGTGTCGCTGATG
= score = 111
>1:1000-1059 + chrY 
CACTCTAATAGTAAAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCAT
>2:6000-6055 + chr17 
CACTCTAATACTAAACTTTCTTTTCCTCTCCACA----CTTTACTTTAATTACATCCCAT
>3:20000-20055 - chr12 
CACTCTAATAGTAAAGTTTCTT----TGTGCAGAAGCTCTTAGTTTTAATTAGATCCCAT
= score = 11