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Table 3 The top 10 most conserved preferred codon pairs in the organisms studied

From: Preferred and avoided codon pairs in three domains of life

12 ↑ codon pairs % log2(obs/exp) A – B type
   ORFeome (A) genome (B)   
GGGCUU 76 0.99 0.44 0.55 1P
GAGCAG 70 0.51 0.64 -0.13 1P
GGGCAU 69 0.83 0.39 0.44 1P
UUUGAA 66 0.31 0.12 0.19  
GACAGC 64 0.70 0.21 0.49 2P
UUUGCC 64 0.51 0.07 0.44 4P
GGAACA 64 0.82 0.52 0.30  
UACAAC 64 0.58 0.36 0.22 2P
AUCAUC 64 0.42 0.53 -0.11 2P
CUUUCU 61 0.91 0.29 0.61 3P
  1. Codon pair containing out-frame UAA or UAG triplets on the sense and/or antisense strand are marked in bold. The observed/expected ratios in logarithmic scale for each codon pair in the ORFeome and genome are shown. % – the percentage of organisms in which the codon pair is significantly preferred. A – B – difference between log2 (obs/exp) ratios in the ORFeome and the genome. A – B > 0 represents a stronger effect on the ORFeome level. For the preferred pattern types see Table 4. For the full lists of codon pairs preferred in at least 50% of the organisms studied see [additional file 2].