Figure 4

Spontaneous thermal opening probability simulated at 303 K by the average stacking PBD model [26]of a promoter sequence. (A) The pattern I (orange dot line) of the R40 promoter is compared to the four patterns, A, B, C and D (cyan line, black line, magenta line, and green line, respectively) simulated from 16 R40 -derived promoters (from L01 to L16). The grouping is shown (Table 1). (B) The pattern E (black dot line) and F (green dot line) of L21 and L22 promoters, respectively, are compared to the pattern B (black line) and the pattern I (orange dot line). (C) The patter G (black dash-dot line) and H (gray line) of P_trc1O and L31 promoters, respectively, are compared to pattern A (cyan line) and C (magenta line). Position +1 is the TSS of a given promoter. The opening probability at a position is read as the probability of a base pair to open at that position and its consecutive downstream 5 base pairs with the amplitude larger than 2.8 Å.