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Table 1 The top 10 most conserved avoided 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)

  

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

  1. 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].