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.