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sub gen;
sub gen{
...
}

print "$_ ::= $counts{ $_ }" for @patterns;

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[ 0:15:31.00] C:\test\humanGenome>..\junk999 chr21.fa
16384 patterns.
...
Using custom indexing found 35106546 matches; took 34.536852 seconds
Using custom index2 found 35106546 matches; took 31.354438 seconds
Simple search found 35106546 matches; took 2970.517883 seconds