Only positive charge is systematically capable of explaining ribosomal slowing, including the severest slowing.

Quantiles of the difference in average ribosomal density between the most highly occupied and most lowly occupied windows identified within a transcript are shown, with q1 representing the smallest differences and q4 the largest. A score of 1 indicates the putative retarding feature is more present within the more occluded intra-transcript window; −1, less present; 0, present in both windows in equal amounts. Related yet alternative ways of calculating both the rare pair and PARS scores are given in italics (see Methods, “The Relative Contributions of Charge, Folding, and Codon Usage to Extremes of Slowing Within Transcripts” for details). A low codon optimality, if anything, tends to pair more with the less dense (faster translated) window. Similarly, not only do rare pairs and rare 6 -mers tend to be found more often in the faster translated window, but their presence decreases as the difference in degree of ribosomal slowing grows. Additionally, a greater likelihood of transcript secondary structure at or just before the identified window is associated not with the more occluded windows, but with the less dense (faster translated) ones, and the presence of secondary structure in fact decreases as the difference in ribosomal slowing between the windows increases. Positive charge, however, is consistently associated with the higher density (more slowly translated) window, and increasingly so as the difference in densities between the two windows becomes larger. Window pairs that have the same number of charges each (charge score, 0) do not show such a trend between quantiles.