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

### 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},
);

##</code><code>##

my $sub = "CGAGCGTTGACGCNNAGCTAGT";
my @bases = split //, $sub;

##</code><code>##

   my $sub = 'CGAGCGTTGACGCNNAGCTAGT';
   my @bases = split //, $sub;

   my $count = 100;
   my $len = length $sub;

   @promoters_regex = (
      qr'[NT][GCATN][NG][NC][NG][NT][NG]',
      qr'[NG][NT][NG][NC][NG][GCATN][NT]',
      qr'[NA][GCATN][NC][NG][NC][NA][NC]',
      qr'[NC][NA][NC][NG][NC][GCATN][NA]',
   );

   my $permutations_total = 0;
   while ($count--)
   {
      my $ilen = $len;
      my $string;
      $string .= $bases[rand @bases] while $ilen--;

      foreach my $regex (@promoters_regex)
      {
         $permutations_totals += scalar($string =~ m/$regex/g);
      }
   }

##</code><code>##

With count == 100:
Benchmark: running mine, yours, each for at least 10 CPU seconds...
      mine: 11 wallclock secs (10.88 usr +  0.00 sys = 10.88 CPU) @ 172.52/s (n=1877)
     yours: 19 wallclock secs (18.49 usr +  0.01 sys = 18.50 CPU) @ 38.76/s (n=717)
        Rate yours  mine
yours 38.8/s    --  -78%
mine   173/s  345%    --

With count == 1000:
Benchmark: running mine, yours, each for at least 30 CPU seconds...
      mine: 33 wallclock secs (31.83 usr +  0.00 sys = 31.83 CPU) @ 17.78/s (n=566)
     yours: 33 wallclock secs (32.43 usr +  0.00 sys = 32.43 CPU) @  7.68/s (n=249)
        Rate yours  mine
yours 7.68/s    --  -57%
mine  17.8/s  132%    --

##</code><code>##

With count == 100:
Benchmark: running mine, yours, each for at least 10 CPU seconds...
      mine: 11 wallclock secs (10.43 usr +  0.00 sys = 10.43 CPU) @ 174.98/s (n=1825)
     yours: 11 wallclock secs (10.26 usr +  0.00 sys = 10.26 CPU) @ 74.37/s (n=763)
        Rate yours  mine
yours 74.4/s    --  -57%
mine   175/s  135%    --

With count == 1000:
Benchmark: running mine, yours, each for at least 30 CPU seconds...
      mine: 33 wallclock secs (31.58 usr +  0.00 sys = 31.58 CPU) @ 17.42/s (n=550)
     yours: 32 wallclock secs (31.24 usr +  0.00 sys = 31.24 CPU) @  7.55/s (n=236)
        Rate yours  mine
yours 7.55/s    --  -57%
mine  17.4/s  131%    --