foreach $qbase ( @qbase ) {
  if ( uc($qbase) eq 'N' ) {
    ++$ncount;
  }
}
foreach $sbase ( @sbase ) {
  if ( uc($sbase) eq 'N' ) {
    ++$ncount;
  }
}

##</code><code>##

  do { $ncount++ if /n/i } foreach ( @qbase, @sbase );

##</code><code>##

foreach my $idx ( 1..$#query_sequence ) {
  if ( $query_sequence[$idx] =~ /n/i && $subj_sequence[$idx] !~ /n/i ) {
    $ncount++;
  } elsif ( $subj_sequence[$idx] =~ /n/i && $query_sequence[$idx] !~ /n/i ) {
    $ncount++;
  }
}

##</code><code>##

$ncount = grep { ($qbase[$_] =~ /n/i && $sbase[$_] !~ /n/i) || ($qbase[$_] !~ /n/i && $sbase[$_] =~ /n/i) } 1..$#qbase;