Given the DNA-binding specificities (motifs) of one or more transcription factors, an important bioinformatics problem is to discover significant clusters of binding sites for the transcription factors(s). Such clusters often correspond to cis-regulatory modules mediating regulation of an adjacent gene. In earlier work, we developed the Stubb program that uses a probabilistic model and a maximum likelihood approach to efficiently detect cis-regulatory modules over genomic scales. It may optionally exploit a second related genome to improve module prediction accuracy. We describe here the use of a web-based interface for the Stubb program. The interface is equipped with a special post-processing step for in-depth analysis of specific modules, in order to reveal individual binding sites predicted in the module. The web server may be accessed at the URL http://stubb.rockefeller.edu/.