In that case, it seems like a fairly simple regex should do it. I'd think one regex would be faster than using index to check 16384 different substrings, but a benchmark would tell for sure. I'm also not sure why he's reading the entire huge file into a hash; it seems like that could be running him into swap, slowing things down severely. Unless I'm missing something, it seems like this would work (as long as it's not necessary to match overlapping matches): 

#!/usr/bin/env perl
use Modern::Perl;

my %c;

while(<DATA>){
    chomp;
    while(/([ACGT]{7})/g){
        $c{$1}++;
    }
}
say "$_ : $c{$_}" for sort keys %c;

__DATA__
NNNAGTACANNNNTAGCNNNNNNAGGTNNNNNAATCCGATNNNNNNTAGGGGGGTTTAAANNNNN
NNNAGTCCCACANNNNTAAAAGCNNNNNNAGGTNNNNNAATCCGATNNNNNNTAGGGGGGTTTAAANNNN
+N
NNNAGTACANNNNTAGCNNNNNNAGGTNNNNNAATCCGATNNNNNNTAGGGGGGTTTAAANNNNN

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Aaron B.
Available for small or large Perl jobs; see my home node.

In reply to Re^4: counting the number of 16384 pattern matches in a large DNA sequence by aaron_baugher
in thread counting the number of 16384 pattern matches in a large DNA sequence by anonym

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