in reply to counting the number of 16384 pattern matches in a large DNA sequence

You could try to match for the 16384 patterns in one go by building one big regex with Regexp::Assemble.

CountZero

A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James

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