Here is my attempt at reproducing your problem

$_ = "ATGGACTGCACCTGGAGGATCCTCTTCTTGGTGGCAGCAGCTACAGgcaagagaatcctgagtt
+ccagggctgatgaggg";

print $_ . "\n";
print "The first occurance of little a is: ", index($_,"a"), "\n";
print "The first occurance of little c is: ", index($_,"c"), "\n";
print "The first occurance of little g is: ", index($_,"g"), "\n";
print "The first occurance of little t is: ", index($_,"t"), "\n";

__END__
ATGGACTGCACCTGGAGGATCCTCTTCTTGGTGGCAGCAGCTACAGgcaagagaatcctgagttccaggg
+ctgatgaggg
The first occurance of little a is: 48
The first occurance of little c is: 47
The first occurance of little g is: 46
The first occurance of little t is: 55
[download]

As you can see it works perfectly here. Is there something else you might be excluding that is influencing it?