I'd keep them separate in case ($#qbase != $#sbase), and since you're not doing anything else with the index, just loop through them all... 
foreach $qbase ( @qbase ) {
  if ( uc($qbase) eq 'N' ) {
    ++$ncount;
  }
}
foreach $sbase ( @sbase ) {
  if ( uc($sbase) eq 'N' ) {
    ++$ncount;
  }
}

[download]
or more concisely... 
  do { $ncount++ if /n/i } foreach ( @qbase, @sbase );

[download]
 Update: disregard, read the OP wrong

Update: re-read, and the answer doesn't take into account if subj_sequence is n and query is not... 
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++;
  }
}

[download]
(Note that it is assumed that $#query_sequence = $#subj_sequence)

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

[download]

In reply to Re^3: Why does this happen? by Transient
in thread Why does this happen? by dusk

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