I was wandering around SuperSearch looking for something else when I saw this and wondered "Are the xor's with 'N' different than the xor's with ACGT?". Turns out they are, and so there is no need for any of the masking in this post.

#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=766743
use warnings;

my %thexor; # check for N mismatches different from non-N mismatches
for my $x ( qw( A T G C N ) )
  {
  for my $y ( qw( A T G C N ) )
    {
    $x lt $y and $thexor{$x ^ $y} .= "$x$y ";
    }
  }
use Data::Dump 'dd', 'pp'; dd \%thexor; # yes they are

# mismatch "\2\4\6\23\25\27"
#    match "\0\t\r\17\32"

local $/ = '';
while( <DATA> )
  {
  my ($x, $y) = split;
  my $bad = ($x ^ $y) =~ tr/\2\4\6\23\25\27//; # therefore this counts
+ mismatches
  print "$x ^ $y => ", pp($x ^ $y), $bad ? ' FAIL' : ' ok', "\n";
  }

__DATA__
ATGNCNC
ATGACNN

ATGNCNC
TTGNNNC
[download]

Outputs:

{
  "\2"  => "AC ",
  "\4"  => "CG ",
  "\6"  => "AG ",
  "\t"  => "GN ",
  "\r"  => "CN ",
  "\17" => "AN ",
  "\23" => "GT ",
  "\25" => "AT ",
  "\27" => "CT ",
  "\32" => "NT ",
}
ATGNCNC ^ ATGACNN => "\0\0\0\17\0\0\r" ok
ATGNCNC ^ TTGNNNC => "\25\0\0\0\r\0\0" FAIL
[download]