XMFA multiple alignment format
From BioPerl
A modification of the FASTA multiple alignment format that allows for multiple alignments in a file. More information is on the MAUVE site
The defline contains the following in its header: >seqname:start-stop strand comments
>1:1-598 + chrY TCCAAGTCGGCTTTATGTTTGCTTCTGCCAGGCATTCTAGATGCCCCATGTCTAGGATCT CTTTAGGCAGGAGAGAGGGTGATGGTGTAGGAGGACCCATTTCTTGGCTTGCAGATTCCA ATAATAAAAAAGTCACAGATTTAAACCCCAAACTTTGATGAAATGCAGGTCTAGGGTTTT AAAATATAATGAGAGTTAAATACTTTTGTATTTTCTTCATCCAGAGATGGGGCAAGCTTC CTCATCTGCTCGTTCATGGGTGATTTATATTTTCCCCACTCCATCCTTTTCCTAAGGTAT TTTTTTTTTAGGGACAATGGCTTTTTGCAGAGTACTCAGTTCCAGCTCCGGGGGCACCGG TTGAGCCCTTACCGTCCTGCCCCTAAACATCCAGACCTCAAGTTAGAGAGGGGAGTAACA TTTGGGGGGTGCCCACACCTAGGAGGACCAATCCTTCTGGTTTCCTTAGGGATGCAGGAA TTTGGGGGGGGGGGGCTCAGTGCTAAAACCAGTAGAGTCCTGGGCAAACGAGTATGACTG AAGATGCTTTGAACACCCTAGCGTTATGTCGATCGCATGCATCGTAGTGTCGCTGATG >2:5000-5598 - chr17 TGCAGATTGGCCTT-TGTTTCGTTTTTC-AAGCGTT-TAAA--CGCCTTGCCTAAGAATC TTTT--GCAGGGAAGGGGATAGTGAACTGGGAAAACCTGGCTCTTCCTTTCGAGATTCCA GTAACAAACATGTCATAACTATAAACGCCAAACTTGG--AGAGCGCAGGAATGGAAGGTC AAACACCAATGAGAGTTAGATGGTTTTGGGTTT----------------------GCT-- CTAGTCTGCACG-------GTGCTCCCCGTCCCCTCACGTCCGTGCTTTTCCTCAGGATG ATGCCTTGCCAGAACACCGGTGTGCTGCAAGGTGCTCAGCTCCAAATCGGGCTGCACCGC TTCAGCTTTCCCCATCCAGCCA--ACGCAGGAAGGCCTGGAGCTACAGAGTTTAGAGCCA TCTCTCCGCTGCTCAT--------TAACCAACCATTCCAGCT-------GTCTGTAGTGG GTTTTTTTCTT----CTCTACACTAAAATGAGGACAGTCCAGGCCCTTTG--TTAGACTG AAGATGCTTTGAACACCCTAGCGTTATGTCGATCGCATGCATCGTAGTGTCGCTGATG >3:19000-19598 - 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 >1:1000-1060 + chrY CACTCTAATAGTAAAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCAT >2:6000-6060 + chr17 CACTCTAATACTAAACTTTCTTTTCCTCTCCACA----CTTTACTTTAATTACATCCCAT >3:20000-20060 - chr12 CACTCTAATAGTAAAGTTTCTT----TGTGCAGAAGCTCTTAGTTTTAATTAGATCCCAT = score = 11
