a score=0
s hg18.chr11 93105204 116 - 134452384 UCAUAAUUGCACUGCAUGGUAUCUGCACUCAGCAGUUU-ACACCUGCUAGGGUGUUCAAAGGUCAGUGCUAUAGAAAUUCAGUAUCUGGCAUCGUUGGUUUU---CUUGGCUUUGUGCUU
s rn4.chr8 116926073 107 + 129041809 -------UGCACUGCAUGGUAUCUGCACUCAGCAGUUC-UUUCCUGUUGGG-UGUUCAAAAGACAGUGCGAUAGAAAUUCAUUAUCUGGCAUCGUUGGUUU----CUUGGCUUUGUGCAU
s mm8.chr9 108935325 111 + 124000669 AUUU---UGCACUGCAUGGUAUCUGCACUCAGCAGUUC-UUUCCUGUUGGG-UGUUCAAAAGACAGUGCUAUAGAAACUCACUAUCUGGCAUCGUUGGUUU----CUUGGCUUUGUGCAU
s canFam2.chr21 44004670 116 + 54024781 UCAGGAUUGCACUGCAUGGUAUCUGCACUUAGCAGCUCAGGUCCUGCUGGG-UGUUCAAAAGACAGUGCAAUAGAAAUUCAGUAUCUGGCAUCGUUGGUUUU---CUUGGCUUCGUGCAU
s loxAfr1.scaffold_28145 17317 113 + 37299 UCGC---UGCACUGCAUGGUAUCUGCAUUCAGCAGUUC-ACUCCUGCUGGGAUGUUCCAAGGACAGUGCGACAGAAAUUCAGUAGCUGGCAUCGUUGGUUUU---CUUGGCUUUGUGCAU
s monDom4.chr4 174695190 114 + 430141050 UCAAGACUGCACUGUAUGGUAUCUGCAUCCAGCAAU---AUUAUUGUUGGGGUGUUCAAAAGACAGUGCUAUAGAAAUUCAGUAUCUGGCAUCGUUGGUUUCAUGCUUG---UCAUGCAU

