This program takes as input a set of aligned DNA sequence motifs (e.g., a set of transcription factor binding sites) and finds similar motifs in a DNA sequence (e.g., a prokaryotic chromosome). The primary output is a set of coordinates in the analyzed DNA sequence of motifs similar to those in the alignment. These coordinates can be subsequently passed to other programs (r-scan statistics, pattern vicinity analysis) in order to provide additional information about the distribution of the matching motifs in the analyzed sequence and with respect to genes.
Easy to input, but results are hard to read and interprete.