Figure 2. Frequency Matrices for the −10 and −35 Motifs of σ⁷⁰ Promoters in E. coli .

This matrix pair (Matrix_18_15_13_2_1.5) was selected for searching across bacterial genomes from a collection of optimized matrices defined for E. coli in [1]. Note that in order to compare these matrices with the canonical patterns (TTGACA and TATAAT), the spacers of 13 bp to 19 bp between the two boxes correspond to the 15 bp to 21 bp reported in the literature, as the TGT triplet is considered as part of the −10 box. Before searching for promoter-like signals, these matrices were calibrated using the noncoding base composition of each target genome.