use strict;
use Data::Dumper;
use List::MapMulti 'iterator_multi';

my @userDefined = qw(AAA AAC ACA CAA);
my $string      = 'AAAAA AAACACA CAACAAA';

my %results = map { $_ => 0; } @userDefined;

my $iter = iterator_multi [0..length($string)-1], [1..length($string)];
while (my ($start, $end) = $iter->())
{
	next unless $end > $start;
	my $substr = substr $string, $start, ($end - $start);
	$results{$substr}++ if exists $results{$substr};
}

print Dumper \%results;