SPACER finds motifs separated by 0 to 15 non-critial characters, such as GAL4 (CCGnnnnnnnnnnnCGG). The ends may be of aribtrary length (at least 3 bases), making it ideal for bacterial sequences. By sending the bipartite motifs through PRISM, SPACER also finds long degenerate motifs found in your group of genes relative to their frequency of occurrence in the genome as a whole. For detail see our paper: Carlson* JM, Chakravarty* A, Khetani RS, DeZiel CE, and Gross RH. "Robust identification of cis-regulatory elements with non-contiguous critical residues." submitted.