Phyloscan

Phyloscan is a web service for DNA sequence analysis that is free and open to all users (without login requirement). For locating matches to a user-specified sequence motif for a regulatory binding site, Phyloscan provides a statistically sensitive scan of user-supplied mixed aligned and unaligned DNA sequence data. Phyloscan's strength is that it brings together
 * the Staden method for computing statistical significance,
 * the "phylogenetic motif model" scanning functionality of the MONKEY software that models evolutionary relationships among aligned sequences,
 * the use of the Bailey & Gribskov method for combining statistics across non-aligned sequence data, and
 * the Neuwald & Green technique for combining statistics across multiple binding sites found within a single gene promoter region.