a score=0
s hg18.chr11 93103387 103 - 134452384 GUAUGUAUGCAUUAGAAAAGACAUUUGU--AUGGGUCAUUUCAAAGAGGGCUUAUGAGGCUGUGAAACCCAGAGCUCUUAACGCUGUGACCAAAGAUGGAAGUUC
s dasNov1.scaffold_192792 1481 94 - 5195 ------AGACAAUGGGAAAGACAUUU-U--AUAGGUCAUUUCAAAGAGGGCUUGUGGGACUG--AAACCAGGAGCUCUUAACGCUGUGACCAAAGAUUAAGGUUC
s canFam2.chr21 44003066 103 + 54024781 GUAUGUGCACAUUUGAAAAAAUACCUUGCAGUAGGUCAUUUCAAAGAGGGCUUGUGGGACUA--AAACCAAGAGCUCUUAACGCUGUGACCAAAUAUUGGAGUUC
s bosTau2.chr29 546979 100 - 45822729 GUAUGUACACAUUAGAGAAAUAGUUUUU--GUAGGUCAUUUCAAAGAGGGCUGAUGGGACCA--AAUCCUGGAGCCCUUAACGCUGUGACCAAAGACUGAA-UUC
s oryCun1.scaffold_215179 58623 101 - 62759 GUACGUACACA--UGAGAAAAAAAUAAU--AAAGGUCAUUUCAAAGAGGGCUUGUGGAGCCAUGAGACCAAGAGCUCUUAACGCUGUGACCAAAGACUGAUGUUC
s rn4.chr8 116924863 98 + 129041809 GUAUGUGUA----UGGGAAGCGGGUAGC--GAAGGUCAUUUCAAAGAGGGCUUGGUGG-CUGUAAAACCAAAAGCUCUUAACGCUGUGACCAAAGAUUGAUGUUC

