a score=0
s hg18.chr11 93103792 112 - 134452384 CCAAGGCUUUUAGAAUGCAGUUUCUCAUUUGCUGUGGACAUGACCAUAAAAA-AAUUUC--CCAGUAGGUUUU-C-UAUCUGCUACUUUGCUAGCAAUCAGCUUAUUGGGAACAGUU
s rn4.chr8 116925096 113 + 129041809 CCAAGGCUUUUAGAAUGCAGUUUCUCAUUUGCUGUGGACAUGACCAUAAAGAAAAAUUC--CCAUUAGGUUUU-C-CAUAUGCUACUUGAGUAGCACUUAACCUGUUGGGAACAUUU
s bosTau2.chr29 547350 114 - 45822729 CCAAGGCUUUUAGAACGCAGUUUCUAAUUUGCUGUGGACAUGACCGUAAAACAAAAUCC--CAACUAGGUUUUUC-UUCCUGCUACUUUGUUAGCAUACAGCCUGUUGGGAACAUUU
s dasNov1.scaffold_2894 17074 112 - 85457 CCAAGGCUUUUAGAAUGCAGUUUCUGAUUUGCUGUGGAGUUGACCAUAAAAAAAACUCU--CCACUGGGCUUU-C-U-UUUGCUACCUUGCUAGCCUUCAGCCUGUUGGGAACAUUC
s echTel1.scaffold_316886 80434 112 + 105239 CCAAGGCUUUUAGAAUGUGGUUUCUGAUUUGCUGUGGACAUGACCAUAG--ACAAUUUC--CCAGGAGGUUUU-UGUUUUUGCUACCUUGCUAGCAUAUAACCGAUUGGGGACAUUG
s monDom4.chr4 174693365 113 + 430141050 CCAAGGCUUUUAGAAUGCAGUUUCUGAUU-GCUGUGGACAUGACCAUAAAAAAAAUUAUAUCCAACAGGUUU--A-UAUUUGCUAUCUUACUAGCAUCUAACCUGUUGGGAACAGUU

