CrmMiner was evaluated on nine testing sets that were composed of CNEs found in 39 heart-specific gene loci. PCRMs stand for putative CRMs. Controls(+) stand for CRMs predicted among the control sequences. All mixed sets included CNEs in the region between -10 kbp and +10 kbp. Mixed sets were expanded as before. The number of CNEs in the mixed set did not always increase when the number of the closest CNEs, n, was increased because we randomly partitioned the loci into three sets every time n was increased. The Fisher's exact test was used to calculate the P-values.