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