How about having a hash of proper pairs let it have the name %pairs? And than comparing a concatenation of the letters from the first and second string like this 
for my $i (0 .. $#dna){
    if(! exists $pairs{$dna[$i].$comp[$i]}){
        print "mismatch: ....";
    }
}

[download]
Disclaimer: I don't anderstand your code - but from your description I think it is what you wanted.

In reply to Re: need help comparing DNA compliments by zby
in thread need help comparing DNA compliments by Anonymous Monk

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