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Table 4 Codon pairs with minimum and maximum codon context bias values

From: Codon usage and codon context bias in Xanthophyllomyces dendrorhous

Groups of ORFs with different expression level
R** 1-30** 31-70** 71-100** 101-990** ≥1,000**
Avoided codon pairs
TCG-CGA; −46 CTT-AAG; −34 CCT-AAG; −34 CCT-AAG; −35 TCT-AAG; −37 GCT-AAC; −37
GAT-AAG; −53 GAG-TCC; −34 TCT-AAG; −33 TCT-AAG; −31 GAT-AAG; −32 GCT-AAG; -37
GAG-CGA; −44 ACT-AAG; −33 CTT-AAG; −33 CCT-GAG; −31 CTT-AAG; −32 CTT-AAG; -36
AAC-CGA; −43 GCT-AAA; −33 GCT-AAG; −31 GAG-TCC; −31 CCT-AAG; −32 GGA-CTC; -35
CCT-AAG; −45 TCT-GAG; −32 GAG-TCT; −31 CTT-AAG; −30 GGT-AAG; −31 TCG-CGA; -34
Preferred codon pairs
CCG-ATA; 211 CGT-CAA; 74 TCA-TCC; 57 AAG-AAG; 61 GAA-GAA; 59 CCG-ATA; 58
CGT-CGT; 175 GTT-CCC; 59 AAG-AAG; 50 TCA-TCC; 50 AAG-AAG; 56 AGA-AGA; 57
AAT-TTA; 159 GTG-TTC; 56 GAA-GAA; 49 GAA-GAA; 49 TCA-TCC; 45 TGT-GGA; 53
TTA-ACA; 153 AGG-AAA; 56 TCT-TCT; 45 TCG-ACC; 47 CTT-CGA; 43 CGC-TTA; 52
ATA-TCA; 145 ACT-CCT; 55 GAA-GAG; 45 GCG-CTC; 47 TCT-TCC; 41 GTA-AGC; 50
  1. Codon pairs shared by two groups are in italics, and those shared by three or more groups are in bold. The residual value is given after the semicolon; positive values indicate good context, and negative values indicate bad context. *Ribosomal ORFs; **: RPKM value ranges according to HV grouping.