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";