Comparison of Cluster-site scores and Luciferase Activity. This graph compares the estimated relative binding affinity given by the cluster-site score to the luciferase activity from four experiments for four different p53 cluster-sites. The four cluster-sites regulate the genes DDB2 (blue), CKM (red), IGFBP3 (green), and TP53I3 (cyan). In all four experiments the luciferase activity of truncated mutants of the respective p53 cluster-site were compared to the luciferase activity of the full cluster-site. In the case of the TP53I3 cluster-site, four different mutants of varying lengths were measured for luciferase activity. All cluster-site scores and activity measurements are normalized by the full-site (two half-sites) measurement. The cluster-site scores are attained by summing the estimated binding affinity of all viable full-sites in the cluster-site that have an affinity above a lower bound and spacer-lengths below an upper bound. The full-site affinity lower bound and spacer-length upper bound were chosen to best match the experimental data. The best fit was attained by enforcing that spacer-lengths not exceed 14 bp and affinity scores exceed 27.5.