use warnings;
use strict;

my @real_count = (0,0,0,0,);
my $sequence = "GGGGGGGAGAAAAAAAAAAAAAAAGAAGGA";
my @patterns = qw/AAAAA GGGGG GGAGA GAAGG/;

for my $i ( 0 .. $#patterns ) {
    while ( $sequence =~ m/$patterns[$i]/g ){
    	$real_count[$i]++;
        ## reset start position for next global match search
    	pos($sequence) -= (length$patterns[$i]) -1; 
    }
}

foreach (@real_count) {
    print "$_\n";

  ## prints
  ## 11
  ## 3
  ## 1
  ## 1
}