Figure 1

Changes in binding site strength in the absence of selection. a) shows time courses for the strength of a transcription factor binding site (S) in a simulation of evolution without selection. The strength of a real binding site (dotted trace) usually decreases from the strength expected for real binding sites (E[S|motif]) to that expected under background residue frequencies (E[S|bg]). An example of a binding site created from background sequence in the absence of selection (solid trace) is also shown. b) shows the probability (p) of observing a change in score of size ΔS given than a sequence is a binding site (dotted trace) or a background sequence (solid trace).