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; }