Skip to main content
. 2014 Dec 9;3:e04531. doi: 10.7554/eLife.04531

Table 2.

Composition and codon usage of E7 wt and mutant insert sequences

DOI: http://dx.doi.org/10.7554/eLife.04531.010

Region Sequence (Symbol) G+C content CpG Total* O/E ratio†,‡ UpA Total* O/E ratio†,‡ Codon Usage
CAI ENc CP Bias
1 Native (WT) 47.6% 51 (−) 0.730 62 (−) 0.742 0.685 56.5 −0.043
Permuted (P) 47.6% 51 (0) 0.730 2 (0) 0.742 0.694 55.8 −0.025
CpG/UpAL (cu) 47.5% 0 (−51) 0 19 (−43) 0.227 0.686 43.5 0.087
Max-U 50.1% 47 (−4) 0.610 43 (−19) 0.573 0.708 49.6 0.328
Min_E 47.5% 51 (0) 0.736 62 (0) 0.735 0.748 54.3 −0.131
Min_U 47.5% 69 (+18) 0.992 76 (+14) 0.939 0.709 58.3 −0.134
Min_H 49.8% 106 (+55) 1.400 79 (+17) 0.981 0.696 49.2 −0.130
2 Native (WT) 47.1% 18 (−) 0.320 48 (−) 0.695 0.743 53.2 0.015
Permuted (P) 47.6% 18 (0) 0.320 48 (0) 0.695 0.739 49.0 0.013
CpG/UpAL (cu) 48.5% 0 (−18) 0 48 (0) 0.214 0.739 47.2 0.118
Max-U 46.3% 24 (+6) 0.440 43 (−3) 0.601 0.750 46.1 0.311
Min-E 45.7% 18 (0) 0.343 48 (0) 0.657 0.785 53.3 −0.091
Min-U 47.4% 37 (+19) 0.649 50 (+2) 0.738 0.767 57.6 −0.083
Min-H 47.8% 68 (+50) 1.172 65 (+15) 0.970 0.715 49.7 −0.085
*

Total number of CpG and UpA dinucleotides in sequence. Changes in numbers between mutated and original WT sequence are indicated in parentheses.

†

Ratio of observed dinucleotide frequency (O) to that expected based on mononucleotide composition (E) that is, f(CpG)/f(C) × f(G).

‡

Values deliberately changed are shown in red (maximised) and blue (minimised).