>perl -wMstrict -le
"my @queries = qw[ GCGAT CACGT ];
 ;;
 my @targets = qw(GNGATNNN GCGANBBB CNCGTNNN   CBCGTNNN  );
 ;;
 for my $q (@queries) {
   for my $t (@targets) {
     my $matched = ($q ^ substr($t, 0, length $q)) =~ tr[\0][\0];
     if($matched >= (length($q) - 1)) {
       print qq{'$q' matched '$t'};
       }
     }
   }
"
'GCGAT' matched 'GNGATNNN'
'GCGAT' matched 'GCGANBBB'
'CACGT' matched 'CNCGTNNN'
'CACGT' matched 'CBCGTNNN'

##</code><code>##

>perl -wMstrict -le
"use List::MoreUtils qw(uniq);
 ;;
 my @queries = qw(GCGAT CACGTT);
 ;;
 my $n_diff =
   join '',
   uniq
   map  { sprintf '\x%02x', ord($_ ^ 'N') }
   map  { split // }
   @queries
   ;
 $n_diff = eval qq{ sub { return \$_[0] =~ tr/$n_diff/$n_diff/; } };
 ;;
 my @targets = qw(
   GNGATNNNHIT GCGANBBBHIT CNCGTTNNNHIT CACGTTNNNHIT
   CBCGTTNNNMISS CNNGTTNNNMISS NCACGTTNNNMISS
   );
 ;;
 for my $q (@queries) {
   my $len_q = length $q;
   TARGET:
   for my $t (@targets) {
     my $mask  = $q ^ substr $t, 0, $len_q;
     my $nulls = $mask =~ tr{\0}{\0};
     next TARGET if $len_q > $nulls + 1
                 or $len_q > $nulls && $n_diff->($mask) != 1
                  ;
     print qq{'$q' matched '$t'};
     }
   }
"
'GCGAT' matched 'GNGATNNNHIT'
'GCGAT' matched 'GCGANBBBHIT'
'CACGTT' matched 'CNCGTTNNNHIT'
'CACGTT' matched 'CACGTTNNNHIT'