Just be pragmatic:

my $str = "GCGAT";
my @PATS = map {
    my $s = $str;
    substr $s, $_, 1, "N";
    $s;
} 0 .. length($str) - 1;
push @PATS, $str;
foreach my $str (@PATS) {
    if (index $value, $str) == 0) {
        print "Oh, joy, it's a match";
    }
}
[download]

There's no reason to be clever. But do note the above code is untested.