search repeats in DNA G. Benson A method for fast database search for all k-nucleotide repeats, by Gary Benson and Michael S. Waterman, Nucleic Acids Research (1994) Vol. 22, No. 22, pp 4828-4836. motifs nucleic:motifs repeats repeats seqlab repeats perl "repeats" 0 seq Sequence File perl " $value" 1 2 alpha match bonus (input as positive) (Alpha) perl " $value" 2 beta mismatch penalty (input as positive) (Beta) perl " $value" 3 delta indel penalty (Delta) perl " $value" 4 reportmax Score to report an alignment (Reportmax) perl " $value" 5 Size Pattern size (Size) perl " $value" 6 A possible repeat is found if *lookcount* characters are repeated at a separation of *size*. lookcount Number of characters to match to trigger dynamic programming (Lookcount) perl " $value" 7 A possible repeat is found if *lookcount* characters are repeated at a separation of *size*. noshortperiods Patterns with shorter periods are excluded ? (Noshortperiods) perl ($value)? " 1 ":" 0" 0 8