Effects of histidine codons translation rates (Model 3). This effect was analysed under circumstances where scanning rate was decreased by 3-fold (A and B), and 5'-initiation rate was increased to 3-fold (C and D). To ensure a constant GCN4 reinitiation rate, Ternary complex binding rate was set to maintain its derepressing ratio with the scanning rate under each condition (10 and 30 nt/s, respectively). Other parameters were the same as in Figure 6. The two histidine codon rates were changed to the same degree, from 0.0001-to 1-fold relative to its repressing value (i.e. relative codon rate). Simulations results were obtained and averaged in the same way as Figure 8. 5'-and 3'-polysome sizes (A, C) and uORF1 to GCN4 translation rate ratio (B, D) were plotted against relative codon rate.