I've posted code here that seems to be about 7000 times faster than BrowserUk's solution

1. The results I posted were those for finding all the LCSs for all pairings. If I only search for the single longest LCS, and make the same minimum match assumption as you:

   [ 8:05:03.68] P:\test>484593-3 -MIN=128 bioman.dat
   Best match len:1271 between string 0:82 & string 2:82
    15 trials of bioman.dat (   5.443s total), 362.894ms/trial
   [download]

   Which means your still 500+ X faster, but it allows me to save face (a little :).

2. You're making an assumption in your code that you cannot make for a general solution, that of a minimum match length of 128, and produce no output if you set it too high.

   Whilst your comments say that this can be adjusted to a lower power of 2, when I tried this, I got strangely 'almost correct' values for both length and offset. I tracked this down to ...

3. Your algorithm only produces the correct output if the input strings are an exact multiple of the minimum size specified.

   To demonstrate, I trimmed 1 character from the front of each line in biomain's data and ran your code with $subStrSize = 128 and got:

   P:\test>gf bioman2.dat
   Completed in 0.009606
   Best match: >string 1  - >string 3 . 1273 characters starting at 80 an
   +d 80.
   [download]

   Note that the length has increased by 2 when it should be the same, and both offsets have reduced by 2 when they should have reduced by 1?

   I also tried setting $subStrSize = 1, as thought that might correct the problem, but apart from running much more slowly, it still produced the same, slightly wrong output:

   [ 7:49:55.56] P:\test>gf bioman2.dat
   Completed in 76.466764
   Best match: >string 1  - >string 3 . 1273 characters starting at 80 an
   +d 80.
   [download]

All that said, your algorithm is blazingly fast and the anomolies can probably be corrected.

If so, or if bioman only needs the single LCS, and can live with specifying a minimum match and arranging for his input data to always be a multiple of that minimum size, it blow's what I have into dust.

At least, until I can adapt my code to use elements of your search technique :). Nice++