Table 1. Parameters and range of empirical estimates for our population-genetic model of binding site evolution.

Parameter	Meaning	Value range
μ	Per-nucleotide per-generation mutation rate	10−7−10−9 per generation (Drake et al. 1998; Lynch 2010)
K	Number of true targets: genomic positions at which selection favors a functional binding site	100−103 binding sites (Lee et al. 2002; Münch et al. 2003; Harbison et al. 2004; Teixeira et al. 2006; Gama-Castro et al. 2011)
L	Number of false targets: genomic positions at which selection disfavors a functional binding site	105−107 binding sites (for a genome with 103−105 genes) (Lynch and Conery 2003)
n	Binding-site length	5−40 nt (Münch et al. 2003; Harbison et al. 2004; Bryne et al. 2008; Gama-Castro et al. 2011)
r	Binding degeneracy: the average number of different bases at each nucleotide that produce functional binding	1.0−4.0 bases (empirical mean = 1.6 bases) (Münch et al. 2003; Harbison et al. 2004; Bryne et al. 2008; Gama-Castro et al. 2011)
I	Average information content per nucleotide in a binding site, $I={\text{log}}_2\left[4/r\right]$	0.25−2 bits (empirical mean = 1.3 bits) (Münch et al. 2003; Harbison et al. 2004; Bryne et al. 2008; Gama-Castro et al. 2011)
N	Effective population size	104−107 individuals (Lynch 2010)
Ns+	Strength of selection on true targets	∼10 (Mustonen et al. 2008; He et al. 2011)
Ns−	Strength of selection on false targets	≲1 (Hahn et al. 2003)
P	Number of TF proteins in a cell	100−103 (Thattai and Van Oudenaarden 2001; Gerland et al. 2002)
ε	Mismatched nucleotide binding energy contribution	1−3 (units of kBT) (Gerland et al. 2002; Lässig 2007)