BEAM is a beam-search algorithm that finds unambiguous words that are statistically over-represented in your group of genes relative to their frequency of occurrence in the genome. These motifs may be 5 or more nucleotides long, though it is rare for long, non-degenerate motifs to be overrepresented. For details see our paper: Carlson* JM, Chakravarty* A, and Gross RH. "BEAM: A beam search algorithm for the identification of cis-regulatory elements in groups of genes." Journal of Computational Biology, 2006; 13(3):686-701.