Smoothed distributions of percent identity values for the three groups of cis-regulatory element sequences, excluding sequences with no aligned bases. The KS test can be viewed as answering the question “are these curves different?” All three curves are significantly different (see Table 2). The true CREs show a distinctive peak in the 80%–90% identity range, presumably a consequence of stabilizing selection. The rise on the left is due to unaligned or mostly deleted sequences.