Two examples of predicted CRMs. (A) upstream 5 k to translational start site for gene ALDOA. (B) same for gene CNGB3. Upper panels are the "potential energy" based on TF interactions. Middle panels show the density of all known TFBSs (total 306 TFBSs) in a sliding window along the region. Bottom panels depict the conservation scores of the regions. The dashed lines are the thresholds used in our prediction. The positions with lower energy than the threshold are predicted as CRMs (indicated by vertical bars). The red dots in (A) indicate the positions of known regulatory sites.