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Background  Small RNAs (sRNAs) are key regulators of gene expression in bacteria. In addition to modulating translation initiation, sRNAs can interact with mRNA coding regions to regulate mRNA stability and translation efficiency, enhancing or impeding progression of the ribosome along the mRNA. Since most amino acids are decoded by more than one codon (synonymous) we asked as to whether there is a codon bias in the interaction of sRNAs with coding regions of mRNAs. Therefore, we explored whether there are differences in codon usage or tRNA availability according to whether an mRNA is regulated by sRNAs or not. We also explored these parameters in the coding interaction regions in mRNAs. We focused our analysis on sRNAs that regulate multiple mRNAs.    Results  We found differences in codon adaptation index and tRNA adaptation index between sRNA-regulated and non-sRNA-regulated mRNAs. Interestingly, the sRNA-mRNA interacting regions tended to be enriched in unpreferred codons decoded by scarce tRNAs. We also found that sRNAs with multiple targets often contained modular segments capable of recognizing conserved motifs among these mRNAs.    Conclusions  Our results show that sRNAs in  E. coli  tend to recognize mRNA coding regions in which the ribosome is predicted to advance at low speeds. Identified motifs in interacting regions are conserved among mRNAs that are recognized by the same sRNA.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5038-6) contains supplementary material, which is available to authorized users.

Codon usage and modular interactions between messenger RNA coding regions and small RNAs in Escherichia coli