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

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

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

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