rf)Ern0 HPP-81-5

The maximum size of bulge loops or insertions and deletions is three bases. MINMATCH - MINMATCH is the minimum number of exact matches in a homology or symmetry that must be met before SEQ will print out the match. If set to 10 for example, only homologies that have at least 10 nucleotides matched will be reported. MINMATCH effects the number of comparisons made near the ends of sequences. If set to 10, for insiance, the first 10 nucleotides of one sequence will not be paired with the last ten of the other. PERCENTMATCH - PERCENTMATCH is the minimum ratio of matched nucleotides to total nucleotides in a homology or a symmetry in order for that match to be printed. However, it has an additional consequence due to the fact that the SEQ searching algorithm proceeds unidirectionally along a sequence. The homologies that are generated by sequence comparisons can never be less matched than PERCENTMATCH at any point in the homology. This means that the homologies that are printed will start off well paired and will then degenerate.