my $dna1 = 'CACTATGAGTGATCGC';
my $dna2 = 'ACTGACTAATGCGTTG';

print "$dna1\n$dna2\n";

for (0 .. length($dna1)-1) {
    if (substr($dna1,$_,1) eq substr($dna2,$_,1)) {
        print ' ';
    } else {
        print '*';
    }
}
print "\n";

__END__
# prints this:

CACTATGAGTGATCGC
ACTGACTAATGCGTTG
**** ** *  *****