One or more integer pair can be indicated for a single sequence. However, if no integer pairs are given, the whole sequence will be used for seeding matrices. By default, the program uses the frequencies observed in your own sequence data for the prior probabilities of the letters. The normalization is based on the relative prior probabilities of the letters. Complementary letters may use the same normalization number.
Any integer permitted by the machine is a permissible symbol.
This option prevents a strong pattern found in only a subset of the sequences from overwhelming the algorithm and eliminating other potential patterns. This undesirable situation can occur when a subset of the sequences share an evolutionary relationship not common to the majority of the sequences. This option results in a significant speed up in the program, but the algorithm becomes dependent on the order of the sequence-file names. If the integer is a 1, then there is no restriction on the overlap. A negative value means print all the top matrices.