Table 1 Model parameters (except binding intensities) used to obtain results in Tables 2-3

Core-enzyme position on DNA

[-15, +20] nt

Holoenzyme position on DNA

[-44, +20] nt

Phage-type RNA polymerase position on DNA

[-15, +4] nt

PEP elongation rate

9.2 nt/s at 21°C

12.1 nt/s at 23°C

15.0 nt/s at 25°C

36.8 nt/s at 40°C

NEP elongation rate

45 nt/s at 23°C

Average duration of the abortive process

0.4 s

Average length of abortive RNA

4 nt

Modeled real time (Loci 1, 3)

24 hr

Duration of the heat shock (Locus 2)

1.5 hr

Aftershock time (Locus 2)

0.25 hr