Oh, now your question is clearer. The easiest thing is to use a hash to track the frequencies, eg.

my $str = "aaaabdbbdaccdacdaaabdcd"; 
my $n = 3; 
my %freq; 
for my $p (0 .. length($str) - $n) { 
    $freq{substr($str, $p, $n)}++; 
} 
for my $ng (sort keys %freq) { 
    printf "%3d %s\n", $freq{$ng}, $ng; 
}
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