my $matched = ( $q ^ substr( $t, 0, length( $q ) ) ) =~ tr[\0]
+[\0];
        if(  $matched >= ( length( $q ) -1 ) )
[download]

Sure.

During the first iteration, the first of those lines will come down to:

my $matched = ( 'GCGAT' ^ 'GNGAT' ) =~ tr[\0][\0];
[download]

In words, the first of the query strings is exclusive-Or'd (^) with the first 5 characters of the first target string.

Where the aligned characters in those two string are the same, the result of xoring them will be zero. Where the two characters differ, the result will be non-zero:

$xord = 'GCGAT' ^ 'GNGAT';;

print unpack 'C*', $xord;;
0 13 0 0 0
[download]

In order to know how many characters matched, all we need to do is count the zeros, which is efficiently done using the transliteration operator:

$matched = ( 'GCGAT' ^ 'GNGAT' ) =~ tr[\0][\0];;

print $matched;;
4
[download]

The result of the first line is that $matched is assigned the number of characters that matched between the two strings.

As you want all characters, except one in any position, to match, the second line tests the number that matched against the length of the query string minus 1:

if(  $matched >= ( length( $q ) -1 ) ) {
    ## we have a winner
[download]

If you know all your query strings are always five characters, then you could hard code the value 4 instead of ( length( $q ) -1 ). Ditto for the usage of length in the substr, but it never hurts to be flexible if there is little cost involved in doing so.

---

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

The OP seems to want to match at the start of the target string with either

• an exact match to the query string, or
• a match to a string formed by replacing a single character anywhere in the query string with a single 'N'.

>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'
[download]

Here's a variation that avoids this (although the conditional logic is a bit obscure).

>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'
[download]

If the possibility your describe can happen, I think this is a computationally simpler solution:

#! perl -slw
use strict;

my @queries = qw[ GCGAT CACGT ];

chomp( my @targets = <DATA> );

for my $q ( @queries ) {
    for my $t ( @targets ) {
        my $matched = ( $q ^ substr( $t, 0, length( $q ) ) ) =~ tr[\0]
+[\0];
        if(
            $matched == length( $q )
        or  $matched == length( $q )-1 
        and substr( $t, 0, length( $q ) ) =~ tr[N][N] == 1
        ) {
            print "$q matched $t";
        }
    }
}

__DATA__
GNGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
GCGANBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
CNCGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
GBGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
[download]

---

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

The code of Re: string match using with an N in any position matches 'CACGT' against 'CBCGTNNN' ('B' vice 'N').

Agreed. But in the genomic encoding scheme of things, the 'N' means 'aNy'. Whereas 'B' means 'any except A'.

With my very limited understanding, 'N' therefore encompasses 'B' in as much as there is no mention in his post of excluding strings that have an 'A' in the wild-card position. Nor is there any mention in the post of the possibility of "targets"(*) ever contains 'B's in the relevant positions.

In this case, the OP seems satisfied with the solution for his particular problem. I'll leave it up to him to know his data and problem domain.

(*An unusual term in this context -- the wild-cards are usually in the query -- but whatever :)

---

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

... in ... genomic encoding ... 'N' means 'aNy' [w]hereas 'B' means 'any except A'.

I did not know that.

With my very limited understanding...

Well, your understanding is nowhere near as limited as mine and, as you say, the OPer seems happy, so...