Human codon occurrences and trinucleotide-motif preferences.

<p>On the top left are the total occurrences of the 61 non-stop codons in 33,860 human coding regions (CDSs; vertical axis) plotted against the average across-codon over-/under-representation of (“preference for”) the corresponding 61 trinucleotide motifs in the same CDSs (horizontal axis). The average preference for a motif is the average over all CDSs of the Z value for the motif's 23∥1+3∥12 “off-frame” count in each CDS, where the set of 61 Z values of each CDS is estimated using 10,000 randomizations of the locations of its synonymous codons (SCs; see M&Ms). Grey dots are for “null” motifs preferences obtained by randomizing each CDS' SC locations before estimating each CDS' motif preferences and averaging over CDSs. The other plots highlight motif groups defined by the genetic code's degeneracy. In the 2-folds plot (top middle) the “minus outlayers” R² and slope are for the “<i>3f -3aas</i>” group created by excluding the codons of three outlayer 2fold families (solid circles; see text).