Worm CNEs are enriched for transcription factor binding sites. Sequence logo representation of the motif significantly overrepresented in wCNEs associated with pharyngeal genes, according to the Weeder motif discovery algorithm . The first six bases of this motif (with consensus TGTTTGGCAACT) agree with the first six bases of the consensus binding site of the PHA-4 transcription factor (TRTTKRY, where R = A/G, K = T/G, and Y = T/C) [33, 34]. Note that the seventh position of the predicted motif has low information content, indicating that sites with differences in this position are still likely to represent variants of the same transcription factor binding site.
Vavouri et al. Genome Biology 2007 8:R15 doi:10.1186/gb-2007-8-2-r15