Fig. 3
Genomic context of the rTSSs. a The genomic sequence surrounding each of the 2018 detected rTSSs (from position -45 to +5, relative to the rTSS) were used to generate a logo-plot (as described in Materials and Methods), without any attempt at alignment of motifs. The -10 element is clearly visible, even without any attempt to align the promoter sequences to optimize the similarity, however, the -35 element is almost indistinguishable, both because it is less conserved than the -10 element, but also because the distance to the TSS is highly variable, causing the signal to dissipate. b Logo-plot of the rTSSs where no σA -10 element could be identified, as difined by more than 2 mismatches to the TATAAT consensus sequence. The logo-plot was generated as described for panel a. c Plot showing cumulative percentage of the distance to the nearest (annotated) downstream ORF for each rTSS