We use the phylogenetic trees (topology and branch lengths) given in [9] to derive the pairwise weights, and use the motif lengths provided. For each of the eight datasets, our approach identifies the optimal motif using the SP scoring measure (Table 4). The consensus sequences for the discovered motifs are listed in Table 4 along with the description of their DNA regions. (The motif reported for the c-fos promoter dataset was discovered second, after having discarded the poly-A repeat region.) All the motifs we find have been documented in the TRANSFAC database [45], and the majority of them correspond to those that have been reported by [9]. Two motifs differ from those of [9]: the first, a c-fos motif, shares its consensus sequence with a known c-fos regulatory element, the binding site of the serum response factor (SRF) protein (accession number R02246). The second, a c-myc motif, also corresponds to a known c-myc binding site in the P1 promoter (accession number R04621). The e-values of the found motifs range from 10-18 to 10-5. We note that though the notion of significance according to our method merely rejects the hypothesis that all the motif instances are unrelated, and a scheme that takes phylogeny into account such as [46] may be better suited for this problem in general, our significance evaluation attests to the presence of a highly conserved motif instance in every input sequence.