Rather than using such advanced approaches, you can allow overlapping regular expressions using Look Around Assertions. Specifically, match on the first letter, and require it be followed by the others of interest. You can then use standard techniques for counting matches. 

#!/usr/bin/perl
use strict;
use warnings;

my @real_count = (0,0,0,0);
my $sequence = "GGGGGGGAGAAAAAAAAAAAAAAAGAAGGA";
my @pattern;
$pattern[0] = "A(?=AAAA)";
$pattern[1] = "G(?=GGGG)";
$pattern[2] = "G(?=GAGA)";
$pattern[3] = "G(?=AAGG)";

foreach my $i (0..$#pattern) {
    $real_count[$i]++ while ($sequence =~ /$pattern[$i]/g);
}

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

[download]

Note I also swapped your error prone for loop for a foreach loop with the range operator.

In reply to Re: Regex KungFu help needed by kennethk
in thread Regex KungFu help needed by drblove27

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