Regular expression are not the best tool to do what you want actually. Not because your problem is impossible or even difficult to solve with regular expressions, but because there is a much better option. The bitwise xor operator "^" will yield a 0 anywhere the two strings are equal, but 1 for every bit that is different between the two.
my $first = "Fool";
my $second = "Foot";
my $diff = ($first ^ $second);
print unpack "B*", $diff; # Print the binary representation of the dif
my @diff_char = split //, $diff; # get a char by char difference.
With that, and maybe the use of ord
(you don't actually need it but it may help make things clearer) you should be able to do what you want.