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Main step of the information-retrieval method for detecting identical sequences across multiple genomes. Identical sequences are detected between each pair of chromosomes (Chr), Ai and Bj, of two genomes, A and B. To find all LIMEs between a pair of chromosomes, the method first detects the matches of small (8 bp) search words using hash maps of substring locations, followed by extension of the matched regions to be at least 100 bp long.
