$ perl -e'$_="ATGGACTGCACCTGGAGGATCCTCTTCTTGGTGGCAGCAGCTACAGgcaagagaatcctgagttccagggctgatgaggg"; print "a", index($_,"a"), $/, "c", index($_,"c"), $/, "g", index($_,"g"), $/, "t", index($_,"t"), $/'
a48
c47
g46
t55