$ cat 938725.pl 
#!/usr/bin/perl
use strict;
use warnings;

my @search = ('GCGAT','CACGT');

# build regexes
my @newsearch;
for my $str (@search) {
    my @tmp;
    for my $char_idx (0 .. length($str)-1) {
        my $t = $str;
        substr($t,$char_idx,1,"[N".substr($t,$char_idx,1)."]");
        push @tmp, $t;
    }
    push @newsearch, "^(".join("|",@tmp).")";
}

while (<DATA>) {
    print "$.: $_";
    for my $t (@newsearch) {
        print "MATCH for /$t/\n" if /$t/;
    }
}
__DATA__
GNGATNNNNNNNNNNNNNNN
GCGANBBBBBBBBBBBBBBB
CNCGTNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNN

$ perl 938725.pl
1: GNGATNNNNNNNNNNNNNNN
MATCH for /^([NG]CGAT|G[NC]GAT|GC[NG]AT|GCG[NA]T|GCGA[NT])/
2: GCGANBBBBBBBBBBBBBBB
MATCH for /^([NG]CGAT|G[NC]GAT|GC[NG]AT|GCG[NA]T|GCGA[NT])/
3: CNCGTNNNNNNNNNNNNNNN
MATCH for /^([NC]ACGT|C[NA]CGT|CA[NC]GT|CAC[NG]T|CACG[NT])/
4: NNNNNNNNNNNNNNNNNNNN