Table 1.
The top 10 most conserved avoided codon pairs in the organisms studied
| 12 ↓ codon pairs | % | log2(obs/exp) | A – B | type | |
| ORFeome (A) | genome (B) | ||||
| UUCGCA | 86 | -0.81 | -0.86 | 0.05 | 6A |
| GGGGGU | 83 | -1.12 | -0.43 | -0.69 | 8A |
| UUCGAA | 82 | -0.76 | -0.75 | -0.01 | 6A |
| CUUAUG | 79 | -0.92 | -0.63 | -0.29 | 1A |
| GCUAUG | 76 | -0.76 | -0.28 | -0.48 | 1A |
| ACUAUG | 73 | -0.71 | -0.21 | -0.50 | 1A |
| GUUAGC | 73 | -0.92 | -0.52 | -0.40 | 1A |
| CUUAGU | 73 | -0.94 | -0.83 | -0.11 | 1A |
| UUCGCG | 72 | -0.84 | -0.56 | -0.28 | 3A |
| GUUAUG | 72 | -0.71 | -0.30 | -0.41 | 1A |
Codon pairs 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 avoided. 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 avoided pattern types see Table 2. For the full lists of codon pairs avoided in at least 50% of the organisms studied see [additional file 1].