my $s1 = "STCATTNNNSATCGCT"; 
my $s2 = "ATCGTCGSNNNNATCG";
           ## #   0     #

# There are 4 matching positions - marked with (#) -
# and notice that matching N is not counted (0)

##</code><code>##

my $match = $s1 ^ $s2;
my $match_count = $match =~ tr/\00//;
print "$match_count\n";

# This gives 5, because N is counted.
# How can I make it to return 4 instead?

##</code><code>##


get_match_count($s1,$s2);

sub get_match_count {

    my ( $k, $l ) = @_;
    return 0 if $k eq $l;

    my $len       = length($k);
    my $num_match = 0;

    for ( my $i = 0; $i < $len; $i++ ) {
        next if ( substr( $k, $i, 1 ) eq 'N' 
                        and 
                  substr( $l, $i, 1 ) eq 'N' );
        ++$num_match if substr( $k, $i, 1 ) eq substr( $l, $i, 1 );
    }

    print "$num_match\n";
    return $num_match;
}