a score=0
s 2R_DroMel_CAF1 17667494 115 + 20766785 GUCACUGCAGCAGAAGCAACAGCAGCAGC----ACACUUGCUGCGCCGCUGCUGCGACAUGGGGAUAAUCACAUUGAUAUGCCUAAUUAGCUGCAACAGCGACCACUGCCUAACUGGCC
s DroSec_CAF1 20892 119 + 1 GUCACUGCAGCAGAAGCAACAUCAGCAGCAGCAACACUUGCUGCGCCGCUUCUGCGACAUGGGGAUAAUCACAUUGAUAUGCCUAAUUAGCUGCAACAGCGACCACUGCCUAACUGGCC
s DroEre_CAF1 21343 107 + 1 GUCACAGCAGCAGA---AGCAGCA---------ACACUUGCUGCACCGCUGCUGCGACAUGGGGAUAAUCACAUUGAUAUGCCUAAUUAGCUGCAACAGCGACUACUGCCUAACUGGCU