$ perl -Mstrict -wle '
> my $seq  = q{GGGGGGGAGAAAAAAAAAAAAAAAGAAGGA};
> my %pats = map {
>    $_, scalar( () = $seq =~ m{(?=\Q$_\E)}g );
>    } qw{ AAAAA GGGGG GGAGA GAAGG };
> print qq{$_: $pats{ $_ }} for sort keys %pats;'
AAAAA: 11
GAAGG: 1
GGAGA: 1
GGGGG: 3
$