my $first_counter = 0;
my $second_counter = 0;

my $sequence = "GGGGGGGAGAAAAAAAAAAAAAAAGAAGGA";

# This is what I initially did, but did not get the right answer

$first_counter++ while $sequence =~/AAAAA/g; #Here I get 3

# Because I want to count the overlapping AAAAA in the sequence I hunted around and found this solution

$sequence =~ /AAAAA(?{$second_counter++})(?!)/; # This gives the right answer of 11

print "First counter: $first_counter\n";
print "Second counter: $second_counter\n";

##</code><code>##

my @real_count = (0,0,0,0);
my $sequence = "GGGGGGGAGAAAAAAAAAAAAAAAGAAGGA";
my @pattern;
$pattern[0] = "AAAAA";
$pattern[1] = "GGGGG";
$pattern[2] = "GGAGA";
$pattern[3] = "GAAGG";

for (my $i=0; $i <= 3; $i++) {
    $sequence =~ /$pattern[$i](?{$real_count[$i]++})(?!)/;
}

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