Even though you declared this problem as solved, I have been thinking about the skip ahead technique. It could be used if
- you know a minimum length of the pattern, say at least 100,
- and you know that the number of errors is small compared to the length of the pattern, say at most 5.
You could then try finding a repeat of the first 100 chars somewhere later in the string using some tolerant matching technique, say at position 5000, and then lengthen the pattern to the first 5000 characters. This will not be as efficient as the original skip ahead but might speed up things somewhat. Not sure how it compares to the frequency analysis.
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