a score=0
s hg18.chr11 93104298 91 - 134452384 ACGAUGUUAUGAUGAUGGGCGAAAUGUUCAACUGCUCUGAAGGGGCUGAAUGAAAAUGGCCUUUCUGAACAUCCAUUU--------ACAUUAAAUAU--------UG
s oryCun1.scaffold_215179 59410 93 - 62759 GUGAUGUCAUGAUGAUGGGCCAAAUGUUCAACUGCUCUGAAUGGGCUGAAUGAAAAUAGCCUUUCUGAACAUCC------------ACAUUGAAUGUAUGC--UAUG
s canFam2.chr21 44003873 97 + 54024781 GUGAUGUUAUGAUGACAGGCAAAAUGUUCAACUGCUCUGAAUGGGCUGAAUGAAAGUAGCCUUUCUGAACAUCCAUCUAAAUGUAAAAGUUAACCAU----------
s dasNov1.scaffold_2894 17567 95 - 85457 AUGAUGUUAUGAUGAUGGGCAAAAUGUUCAACUGCUCUGAAUGGGCUGAAUGAAAGCAGCCUUUCUGAACAUCCAUCC--------ACAUUAAAUUAGGCUGU----
s rn4.chr8 116925422 78 + 129041809 AUGAUGUUGUGAUGAUGGGCAAAAUGUUCAACUGCUCUGAAUGGGCUGAAUGAAAGUAGCCUUUCUGAACAUCUGUGU-----------------------------
s echTel1.scaffold_316886 81342 91 + 105239 GGGAUGUUAUGAUGACAGGCAAAUUGUUCAACUGCUCUGAAUAGGAUGAGUGAAAAUGGCCUUUCUGAACAUCCAUGU--------ACAUUAAAGAUUG--------

