This is what came to my mind:

    my $line1= "CACTATGAGTGATCGC";
    my $line2= "ACTGACTAATGCGTTG";
    my $diff= $line1 ^ $line2;     # Do a bit-wise xor
    $diff =~ tr/\0-\xff/ */;       # Change zero bytes to " ", others 
+to "*"
    print "$line1\n$diff\n$line2\n";
[download]

which prints

    CACTATGAGTGATCGCG
    *   ************
    GACTGACTAATGCGTTG
[download]

I'm not certain it would be a good fit for you, though.

        - tye (/me shifts his cart into "overgolf")