### Typical sequence lengths are 10-50k letters
my $sub = "CGAGCGTTGACGCNNAGCTAGT";
my @bases = 

### Count base frequencies
while ($sub =~ /([GCATN])/g) {
	if ($1 eq 'G') { $bases{g}++; }
	if ($1 eq 'C') { $bases{c}++; }
	if ($1 eq 'A') { $bases{a}++; }
	if ($1 eq 'T') { $bases{t}++; }
	if ($1 eq 'N') { $bases{n}++; }
	}

### I need to create an array of bases to pass to rand()
my @bases = (	('G') x $bases{g},		('C') x $bases{c},
		('A') x $bases{a},		('T') x $bases{t},
		('N') x $bases{n}		);

### These are sample regex's: I actually test 24 different ones
$promoters_regex[0] = '[NT][GCATN][NG][NC][NG][NT][NG]';
$promoters_regex[1] = '[NG][NT][NG][NC][NG][GCATN][NT]';
$promoters_regex[2] = '[NA][GCATN][NC][NG][NC][NA][NC]';
$promoters_regex[3] = '[NC][NA][NC][NG][NC][GCATN][NA]';

### I would like $permutations_count = 100_000
for (my $i = 0; $i < $permutations_count; $i++) {

	my $string;

	# create new string
	for (my $j = 0; $j < length($sub); $j++) {
		$string .= $bases[rand @bases];
		}

	# test string for matches
	for (my $j = 0; $j < scalar(@promoters_regex); $j++) {
		while ($string =~ /$promoters_regex[$j]/g) {
			$permutations_total++;
			}
		}
	}