PromMute

ev

PPE

Length of motifs

5-20 bp

6 bp

5-9 bp

Motifs available from these species

all kinds

hypothetical

7 different species

Mutation model

random

random

stochastic

Mutation, selection, replication cycle per generation

yes

yes

no

Number of occurrence of motifs

1

16

one to a few

Positioning of motif

unrestricted

restricted

unrestricted

Promoter length

1 Kbp

250 bp

200 bp; 2 Kbp

Real promoter sequence

no

no

yes

Real TFBS’s used

yes

no

yes

Selection applied to parts of motifs

no

yes

yes

TFBS matching and scoring

PWM

two’s complement

PWM

Table 4: List of similarities and differences between PromMute, ev, and PPE.