A-site ribosome density at each codon and its relation to codon use. (A) The A-site ribosome density of the 61 coding codons (average ± SD of three samples each from cultures treated with Cm or Tet). (B–G) The ribosome density shown in (A) was modified as average equal to one within each amino acid codon and compared with relative use at the transcript level (total use of each codon was defined = 1). (B, C) Comparison of use and ribosome density of two codon families (B) and multicodon families (C). (D–G) Relative ribosome density (D), (F) and use (E), (G) of codon pairs decoded by a single tRNA. The pair of codons shown in blue and red share one tRNA for decoding.