Here we give extensions to address the issue of multiple motifs existing in a set of sequences. Discovery of distinct multiple motifs, such as sets of binding sites for two different transcription factors, can be done iteratively by first locating a single optimal motif, masking it out from the problem instance, and then looking for the next one. We mask the previous motif by deleting its solution vertices from the original graph, and then reapplying the LP/DEE techniques to locate the next optimal solution and its corresponding motif.