##maf version=1
a score=164425.000000
s hg18.chr16               67328590 61 +  88827254 CGCGC-TGCTGATTGGCTGTGGCC--GGCAGGTGAACCCTCAG-CCAATCAGCGGTACGGGGGGC
s oryCun1.scaffold_208757     14128 62 -     67083 CGCGC-CGCTCATTGGCTGCTGCCA-GGCAGGTGCATCCTCAG-CCAATCAGAGCCGCCAGGGGC
i oryCun1.scaffold_208757 C 0 C 0
s rn4.chr19                36442585 62 +  59218465 AGTGCGGGCTCCTTGGTTGCCACC--TGCAGGTGCGTCCCCAG-CCAATCAGCGGCGCCGGGGGC
i rn4.chr19               C 0 C 0
s mm8.chr8                109492391 61 + 132085098 CCTGC-AGTTCCTTGGCTGCCACC--TGCAGGTGCGTCCCCAG-CCAATCAGCGGCGCCGGGGGC
i mm8.chr8                C 0 C 0
s canFam2.chr5              8133481 61 -  91976430 cgcgc-cgcTCATTGGCCGCCCGC--CGCAGGTGCAGCCGCAG-CCAATCAGCGGCGCGGGGGGC
i canFam2.chr5            C 0 C 0
s bosTau2.chr18            42196292 60 -  56508949 CTCGC-CGCTCATTGGTTGCGGCC--GGCAGGTGCATCCTCAG-CCAATCC-TGGTGCCGGGGGC
i bosTau2.chr18           C 0 C 0
s panTro1.chr18_random      8848462 61 -  44954803 CGCGC-TGCTGATTGGCTGTGGCC--GGCAGGTGAACCCTCAG-CCAATCAGCGGTACGGGGGGC
i panTro1.chr18_random    C 0 C 0
s rheMac2.chr20            67094546 61 +  88221753 CGCGC-TGCTGATTGGCTGTGGCC--GGCAGGTGAACCCTCAG-CCAATCAGCGGTACGGGGGGC
i rheMac2.chr20           C 0 C 0
s loxAfr1.scaffold_7780        2185 62 -     58825 CACGT-CGCCTATAGGCTGCGGCCAGGGCAGGTGCATCTTCAG--CAATCAGTGGCGCTGGGGGC
i loxAfr1.scaffold_7780   I 5 M 704
s echTel1.scaffold_111749       374 63 +       939 CTCGC-CGCTGATTGGTTGCGGCCGGGACAGGTGCGTCCTCAG-CCAATCCGCGGCTCTGGGGGC
i echTel1.scaffold_111749 I 5 C 0
s monDom4.chr1             85064393 65 - 748055161 CAGGCTCGCTCATTGGCTCCTCCCGGCGCAGGTGTGCCTGCGGGCCAATCAGAGGCGTGGGAGGG
i monDom4.chr1            C 0 C 0
e dasNov1.scaffold_28661      37868 1684 +     54757 I

a score=70546.000000
s hg18.chr16               67328651 39 +  88827254 GGTGCCTCCGGGGCTCACCTGGC-TGCAGCCA-CGCACCCC
s oryCun1.scaffold_208757     14190 39 -     67083 GGAGCCCTCGGGGCTCACCTGGC-GGCTGCGG-CGCTGCCC
i oryCun1.scaffold_208757 C 0 C 0
s rn4.chr19                36442647 39 +  59218465 GGTGCCTGC-GGGCTCACCTGGC-GGCCGCAGCCTCTGCTT
i rn4.chr19               C 0 C 0
s mm8.chr8                109492452 39 + 132085098 GGTGCCTGC-GGGCTCACCTGGC-GGCCGCAGCCTCTGCGC
i mm8.chr8                C 0 C 0
s canFam2.chr5              8133542 37 -  91976430 GGGGCC-TCGCGGCTCACCTGGCGGCCGGACG-CGGCC--C
i canFam2.chr5            C 0 C 0
s bosTau2.chr18            42196352 39 -  56508949 GGGACCGTCGAGGCTCACCTGGC-TCCCGCCG-CGCCCCGC
i bosTau2.chr18           C 0 C 0
s panTro1.chr18_random      8848523 39 -  44954803 GGTGCCTCCGGGGCTCACCTGGC-GGCAGCCG-CGCACCCT
i panTro1.chr18_random    C 0 C 0
s rheMac2.chr20            67094607 39 +  88221753 GGTCCCTCCGAGGCACACCTGGC-GGCAGCAG-CGCACCCC
i rheMac2.chr20           C 0 C 0
s loxAfr1.scaffold_108284     32660 39 +     33377 GGCACCCTCGGGACTCACCTGGT-GGCCGCAG-CGCTGCTC
i loxAfr1.scaffold_108284 I 2714 C 0
s echTel1.scaffold_111749       437 39 +       939 GGCGCCCTCGGGGCTCACCTGGC-GGCCGCTG-CGCCGCAG
i echTel1.scaffold_111749 C 0 C 0
s monDom4.chr1             85064459 32 - 748055161 GAGTCTCTCGGAGCTCACCTGGC-TGCC-----CGCTG---
i monDom4.chr1            C 0 I 275
e dasNov1.scaffold_28661      37868 1684 +     54757 I