As a further step, associating patterns with their counts and (cached) regex objects in a hash may be worthwhile: 
>perl -wMstrict -le
"my $sequence = 'GGGGGGGAGAAAAAAAAAAAAAAAGAAGGA';

 my %patterns =
   map { $_ => { count => 0,  regex => qr{ (?= \Q$_\E) }xms } }
   qw(AAAAA GGGGG GGAGA GAAGG)
   ;

 $patterns{$_}{count} =()=
   $sequence =~ m{ $patterns{$_}{regex} }xmsg
     for keys %patterns;

 print qq{$_: $patterns{$_}{count}} for sort keys %patterns;
"
AAAAA: 11
GAAGG: 1
GGAGA: 1
GGGGG: 3

[download]
or 
>perl -wMstrict -le
"my $sequence = 'GGGGGGGAGAAAAAAAAAAAAAAAGAAGGA';

 my %patterns =
   map { $_ => { count => 0,  regex => qr{ (?= \Q$_\E) }xms } }
   qw(AAAAA GGGGG GGAGA GAAGG)
   ;

 $_->{count} =()= $sequence =~ m{ $_->{regex} }xmsg
     for values %patterns;

 print qq{$_: $patterns{$_}{count}} for sort keys %patterns;
"
AAAAA: 11
GAAGG: 1
GGAGA: 1
GGGGG: 3

[download]

In reply to Re^3: Regex KungFu help needed by AnomalousMonk
in thread Regex KungFu help needed by drblove27

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