For each diagonal, Repeat slides a window along the pair of sequences. The match values for each pair of symbols within the window are summed to determine a score at each position. When the score under the window is greater than or equal to the set stringency, then the match criterion has been met and the repeat is recorded. Before the repeats are presented, they are nibbled from both ends so that the symbol pair on each end has a scoring matrix value at least as great as the average positive non-identical comparison value in the matrix. Thus, repeats less than the minimum repeat length may be shown.
Repeat chooses a default minimum stringency that is appropriate for the scoring matrix it reads.
All parameters for this program may be added to the command line. Use -CHE ck to view the summary below and to specify parameters before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. The files described below supply auxiliary data to this program. For more information see Chapter 4, Using Data Files in the User's Guide.