Table 5.

Simulation parameters used by PSPE for generating benchmark promoter sequences

Evolution distance per step	0.05 substitution per site
Length of root sequences	3,000 bp
Background sequence model	Markov order of third
Base frequencies	A = 0.258, C = 0.242, G = 0.242, T = 0.258
Substitution model	HKY85
Transition:transversion ratio	20:1
Rate heterogeneity	Gamma (1.0) + Iota (0.1)
Range of GC content	(0.45, 0.55)
Gap model	Negative binomial distribution (1, 0.5)