Identification of expected motifs in the muscle specific data set (group a). Sequences in the muscle-specific gene set were examined with MEME for de novo prediction of common motifs. The top 15 motifs were then compared to expected muscle TFBSs described in . The motifs are displayed along with the number of sequences containing each motif and the number of sites observed in all sequences in column 1. Sequence logos for the predicted motif and the expected TFBS are displayed, as are the calculated dissimilarity scores (S) and p-values (P) for each comparison. Orientation of the predicted motifs may be reverse to the reference motif, as we consider both strands when predicting the motifs. Motifs marked with (†) have no similar hits in the random sets.