I've posted code here that seems to be about 7000 times faster than BrowserUk's solution result posted here and therefore about 3 million times faster than OP's original code.
The six strings provided in bioMan's scratchpad were used as the test set with the same match result as BrowserUk's in about 0.01 seconds. Note that the claimed match position given in BrowserUk's result is wrong (checked by a manual examination of the data), but the match length is right.
Perl is Huffman encoded by design.
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