a score=0
s hg18.chr11 93103350 112 - 134452384 --AUGGGUCAUUUCAAAGAGGGCUUAUGAGGCUGUGAAACCCAGAGCUCUUAACGCUGUGACCAAAGAUGGAAGUUCUCUAUAGGAAGCCAUA-GCACUCCUAAUGUU--UGGUGCU
s dasNov1.scaffold_192792 1455 99 - 5195 --AUAGGUCAUUUCAAAGAGGGCUUGUGGGACUG--AAACCAGGAGCUCUUAACGCUGUGACCAAAGAUUAAGGUUCUCCACAGGACGACAGA--CACU------------AGUGCU
s canFam2.chr21 44003034 107 + 54024781 CAGUAGGUCAUUUCAAAGAGGGCUUGUGGGACUA--AAACCAAGAGCUCUUAACGCUGUGACCAAAUAUUGGAGUUCUCCAUAGGAUGUAAUAGUUACU--------CAAUAGUGCU
s bosTau2.chr29 546947 104 - 45822729 --GUAGGUCAUUUCAAAGAGGGCUGAUGGGACCA--AAUCCUGGAGCCCUUAACGCUGUGACCAAAGACUGAA-UUCUCCAUUGGAUAUAAUAGUCACU--------UGAUAGUGCU
s oryCun1.scaffold_215179 58588 110 - 62759 --AAAGGUCAUUUCAAAGAGGGCUUGUGGAGCCAUGAGACCAAGAGCUCUUAACGCUGUGACCAAAGACUGAUGUUCUCCACAGGAUGCCAUAAUCACU-----CAGUAGUAGUGCU
s rn4.chr8 116924828 109 + 129041809 --GAAGGUCAUUUCAAAGAGGGCUUGGUGG-CUGUAAAACCAAAAGCUCUUAACGCUGUGACCAAAGAUUGAUGUUCUUCACAGAGCAGACCAUGCACU-----UUGUGAUAGUGCU

