Codon bias shapes bacterial small RNA binding sites within protein-coding sequences

Overall conservation of positional base-pairing across all targets of RyhB. We counted for each position of the binding site the number of putatively fulfilled base-pairing interactions across all RyhB targets and across all genomes in all families (except for Enterobacteriaceae, which were analyzed separately). Presented are the fractions of genomes putatively fulfilling a positional base-pairing interaction out of all genomes in the analysis. Prime positions are shaded in blue. The reading frame corresponding to the dominant alignment of the prime positions of RyhB binding site is marked (N1, N2, N3).