Finding Repeats with Fixed Gap

Authors:
R. Kolpakov;G. Kucherov
Affiliations:
-;-
Venue:
SPIRE '00 Proceedings of the Seventh International Symposium on String Processing Information Retrieval (SPIRE'00)
Year:
2000

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Abstract

We propose an algorithm for finding, within a word, all pairs of occurrences of the same subword within a given distance r. The obtained complexity is O(n log r + S), where S is the size of the output. We also show how the algorithm can be modified in order to find all such pairs of occurrences separated by a given word. The solution uses an algorithm for finding all quasi-squares in two strings, a problem that generalizes the well-known problem of searching for squares.