T.aestivum TBP became marginally significant when this constraint was applied, while significance for tymovirus sequences was eliminated entirely. Because scores are awarded both to tri- and tetranucleotide motifs, and because tetranucleotides attract a higher score, the frequency distribution of scores attibuted to motifs within the sequence is not smooth. The frequency distribution of scores within the test and random sequences is counted. By default, the program regards a score with a significance of 0.9, corresponding to a ten times greater value of fo than fe, as significantly high. The threshold value for significance can be altered by the user based on a table of value of S presented in the .S3 file, or otherwise, to lower or raise the stringency of the search.
Documentation is also available.
Acknowledgements We thank Adrian Gibbs for suggesting the use of positional randomization and the tymovirus sequences as tests. Compensatory slippage in the evolution of ribosomal RNA genes. Nucleic Acids Res. Nucleotide sequence of the genome of an Australian isolate of turnip yellow mosaic virus. Virology 172, 536-546.