Conservation of clustering distinguishes positive and negative pCRMs. Each panel compares positive, negative and ambiguous pCRMs and random 1,000-bp non-coding regions based on (a) binding site density in D. melanogaster, (b) percent identity, (c) density of aligned sites, and (d) density of aligned plus preserved sites. The top portion of each panel contains a histogram of the values for randomly chosen 1,000-bp regions of the D. melanogaster genome. The blue line plots the cumulative distribution. The colored asterisks show the average values for each class of pCRM. The unshaded panel below the histogram shows the values for each pCRM (each dot represents one pCRM, with positives in blue, negatives in red, ambiguous in green). The shaded panel at the bottom shows the average value for 1,000-bp non-coding sequences within 20 kb of each pCRM.