I would split the strings into character arrays and then count the matches returned by the each_array function of the module List::MoreUtils.
Eeek! No... don't do that. And, for that matter, don't use the approach I gave above either. I just wanted to show how, yes, it could easily be done just by automating the way you might do it by hand.
If you want efficiency, resort to bit twiddling!
my ($a, $b, $c) = qw (AAATGCCTT AAAAGCGTC AAAGGCGTC);
my $bits = ($a ^ $b) | ($b ^ $c);
my $c = $bits =~ tr/\0/\0/;
print "Similar: $c\n";
"My two cents aren't worth a dime.";
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