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$promoters_regex[0] = qr/[NT][GCATN][NG][NC][NG][NT][NG]/;
$promoters_regex[1] = qr/[NG][NT][NG][NC][NG][GCATN][NT]/;
$promoters_regex[2] = qr/[NA][GCATN][NC][NG][NC][NA][NC]/;
$promoters_regex[3] = qr/[NC][NA][NC][NG][NC][GCATN][NA]/;
...
$permutations_total++ while $string =~ $promoters_regex[$j];

    for (@promoters_regex) {
        $total++ while $string =~ $_;
    }