Trust me, that's not fast. Using that script on 100 strings takes 76 seconds and 90MB:

c:\test>junk90 junk90.dat
Loaded. Generating combos...
000001 and 000002: 127 chars
... starting at 37 and 872, respectively.
000008 and 000089: 10 chars
... starting at 550 and 355, respectively.
000040 and 000081: 11 chars
... starting at 219 and 623, respectively.
000046 and 000056: 12 chars
... starting at 808 and 845, respectively.
000058 and 000069: 11 chars
... starting at 837 and 276, respectively.
Best overall match: 127 chars
000002:872 and 000001:37
Completed in 76.985
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Using String::LCSS_XS it takes 15 seconds and 5MB:

c:\test>LCSS10 junk90.dat
000001(37) and 000002(872): 127 '5808821137152553645216516684787076304
+368738347768274782252043367265484547586755564151615422250715355234473
+558428710868782135070'
000008(550) and 000089(355): 10 '3252367176'
000040(219) and 000081(623): 11 '61341721171'
000046(808) and 000056(845): 12 '876526361506'
000058(837) and 000069(276): 11 '00666788082'
Took: 14.594 seconds
[download]