It works for me,

$ perl -e'$_="ATGGACTGCACCTGGAGGATCCTCTTCTTGGTGGCAGCAGCTACAGgcaagagaat
+cctgagttccagggctgatgaggg"; print "a", index($_,"a"), $/, "c", index($
+_,"c"), $/, "g", index($_,"g"), $/, "t", index($_,"t"), $/'
a48
c47
g46
t55
[download]

Are you doing something more besides in the real code?