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. 2014 Mar 4;9(3):e90905. doi: 10.1371/journal.pone.0090905

Table 1. Nucleotide composition analysis of CHIKV genomes (%).

No A U G C A3 U3 G3 C3 AU GC GC1 GC2 AU3 GC3 GC12 ENC
1 29.0 19.9 25.7 25.4 27.1 16.7 26.8 29.3 48.9 51.1 53.7 43.5 43.8 56.2 48.6 55.13
2 28.9 20.0 25.7 25.4 27.0 16.7 26.9 29.3 48.9 51.1 53.7 43.3 43.7 56.3 48.5 55.11
3 28.9 20.3 25.9 24.9 26.7 17.7 27.4 28.2 49.2 50.8 53.5 43.3 44.4 55.6 48.4 55.66
4 28.9 19.9 25.8 25.4 26.7 16.9 27.2 29.2 48.8 51.2 53.8 43.4 43.6 56.4 48.6 55.09
5 28.9 20.1 25.7 25.3 27.0 17.2 27.0 28.9 49.0 51.0 53.7 43.4 44.2 55.9 48.6 55.54
6 29.0 20.1 25.7 25.3 27.2 16.9 26.7 29.2 49.1 51.0 53.7 43.4 44.1 55.9 48.6 55.33
7 28.8 20.4 25.9 24.9 26.6 17.9 27.4 28.1 49.2 50.8 53.5 43.3 44.5 55.5 48.4 55.95
8 28.8 20.4 25.9 24.9 26.6 17.9 27.4 28.1 49.2 50.8 53.5 43.3 44.5 55.5 48.4 55.94
9 28.8 20.4 25.9 24.9 26.6 17.9 27.3 28.1 49.2 50.8 53.5 43.4 44.5 55.5 48.5 55.91
10 28.7 20.1 25.9 25.2 26.0 17.2 27.8 28.9 48.8 51.2 53.4 43.4 43.2 56.7 48.4 54.93
11 28.7 20.1 25.9 25.3 26.2 17.0 27.7 29.1 48.8 51.2 53.4 43.4 43.2 56.8 48.4 54.81
12 28.7 20.2 25.9 25.2 26.2 17.3 27.7 28.8 48.9 51.1 53.4 43.4 43.5 56.5 48.4 54.97
13 28.9 20.4 25.8 24.9 26.8 18.0 27.3 28.0 49.3 50.7 53.5 43.3 44.8 55.2 48.4 55.88
14 28.9 20.4 25.8 24.9 26.8 18.0 27.2 28.0 49.3 50.7 53.5 43.3 44.8 55.2 48.4 55.84
15 28.8 20.5 25.9 24.8 26.6 18.2 27.5 27.7 49.3 50.6 53.5 43.2 44.8 55.3 48.4 56.09
16 29.0 20.0 25.7 25.4 27.1 16.9 26.8 29.1 49.0 51.0 53.7 43.4 44.0 55.9 48.6 55.24
17 28.8 20.5 25.9 24.8 26.6 18.1 27.6 27.7 49.3 50.7 53.5 43.3 44.7 55.3 48.4 56.04
18 29.0 20.2 25.7 25.1 27.0 17.5 26.9 28.6 49.2 50.8 53.6 43.4 44.5 55.5 48.5 55.52
19 28.7 20.1 25.9 25.3 26.2 17.1 27.7 29.1 48.8 51.2 53.4 43.4 43.3 56.7 48.4 54.92
20 28.7 20.0 26.0 25.3 26.1 17.0 27.8 29.2 48.7 51.3 53.4 43.5 43.1 56.9 48.5 54.66
21 28.9 20.2 25.7 25.2 26.2 17.1 27.6 29.1 49.1 51.2 53.4 43.5 43.3 56.7 48.5 54.85
22 29.0 20.1 25.7 25.3 27.0 17.3 27.0 28.8 49.1 50.9 53.6 43.5 44.3 55.8 48.6 55.53
23 28.8 20.5 25.9 24.8 26.7 18.1 27.5 27.8 49.3 50.7 53.4 43.3 44.8 55.3 48.4 56.08
24 28.7 20.1 25.9 25.4 26.0 17.1 27.7 29.2 48.8 51.3 53.5 43.4 43.1 56.9 48.5 54.80
25 29.1 20.0 25.6 25.3 27.2 17.2 26.7 28.9 49.1 50.9 53.6 43.5 44.4 55.6 48.6 55.48
26 28.8 20.5 25.9 24.8 26.6 18.2 27.4 27.7 49.3 50.6 53.5 43.3 44.8 55.1 48.4 56.11
27 28.8 20.5 25.9 24.8 26.6 18.1 27.5 27.8 49.3 50.7 53.5 43.2 44.7 55.3 48.4 56.02
28 28.9 20.5 25.9 24.8 26.7 18.1 27.5 27.8 49.4 50.7 53.5 43.2 44.8 55.3 48.4 56.02
29 29.1 20.0 25.6 25.3 27.4 16.9 26.7 29.1 49.1 50.9 53.7 43.4 44.3 55.8 48.6 55.08
30 28.9 20.0 25.7 25.3 27.0 16.9 26.9 29.2 48.9 51.0 53.5 43.4 43.9 56.2 48.5 55.32
31 28.8 20.5 25.9 24.8 26.5 18.2 27.6 27.7 49.3 50.7 53.4 43.4 44.7 55.3 48.4 56.15
32 28.7 20.0 26.0 25.4 25.9 16.9 27.9 29.3 48.7 51.3 53.4 43.4 42.8 57.2 48.4 54.57
33 28.6 20.0 26.0 25.3 26.0 17.0 27.8 29.2 48.6 51.3 53.6 43.4 43.0 57.0 48.5 54.56
34 28.8 20.6 25.9 24.7 26.6 18.4 27.5 27.5 49.4 50.6 53.5 43.3 45.0 55.0 48.4 56.26
35 28.8 20.6 25.9 24.7 26.6 18.3 27.6 27.5 49.4 50.6 53.4 43.3 44.9 55.1 48.4 56.22
36 28.8 20.6 25.9 24.7 26.6 18.3 27.5 27.6 49.4 50.6 53.4 43.3 44.9 55.1 48.4 56.28
37 29.0 20.1 25.7 25.3 26.9 17.3 27.0 28.8 49.1 50.9 53.6 43.4 44.2 55.7 48.5 55.55
38 28.7 20.1 25.9 25.2 26.1 17.2 27.7 29.0 48.8 51.1 53.4 43.3 43.3 56.7 48.4 54.55
39 29.0 20.0 25.7 25.3 26.9 17.1 27.0 29.1 49.0 51.0 53.6 43.3 44.0 56.0 48.5 55.45
40 29.0 20.0 25.7 25.3 26.9 17.1 27.0 29.1 49.0 51.0 53.6 43.3 44.0 56.0 48.5 55.45
41 28.9 20.1 25.7 25.3 26.4 16.8 27.1 29.7 49.0 51.4 53.8 43.7 43.2 56.8 48.8 55.44
42 28.8 19.7 25.9 25.6 26.7 18.4 27.4 27.5 48.5 50.5 53.4 43.3 45.1 54.9 48.4 56.25
43 28.8 20.7 25.9 24.6 26.9 17.2 26.9 29.0 49.5 50.9 53.6 43.3 44.1 55.9 48.5 55.51
44 29.0 20.1 25.7 25.3 26.7 18.4 27.3 27.5 49.1 50.5 53.4 43.3 45.1 54.9 48.4 56.28
45 28.8 20.7 25.9 24.6 26.7 18.4 27.4 27.5 49.5 50.6 53.5 43.3 45.1 54.9 48.4 56.23
46 28.8 20.7 25.9 24.6 26.8 17.2 27.0 29.0 49.5 51.0 53.6 43.3 44.0 56.0 48.5 55.49
47 29.0 20.1 25.7 25.3 26.9 17.2 26.9 28.9 49.1 50.9 53.6 43.3 44.1 55.9 48.5 55.53
48 29.0 20.1 25.7 25.3 27.0 17.1 26.9 29.0 49.1 51.0 53.7 43.3 44.1 55.9 48.5 55.42
49 29.0 20.0 25.7 25.3 26.8 17.2 27.0 29.0 49.0 50.9 53.6 43.3 44.0 55.9 48.5 55.46
50 29.0 20.0 25.7 25.3 26.9 17.1 27.0 29.1 49.0 51.0 53.6 43.3 44.0 56.0 48.5 55.46
51 28.9 20.1 25.7 25.3 26.8 17.2 27.0 29.0 49.0 51.0 53.6 43.3 44.0 56.0 48.5 55.46
52 29.0 20.1 25.7 25.3 26.8 17.2 27.0 29.0 49.1 50.9 53.6 43.3 44.0 55.9 48.5 55.51
53 29.0 20.1 25.7 25.3 26.9 17.1 27.0 29.0 49.1 51.0 53.6 43.4 44.0 56.0 48.5 55.44
54 29.0 20.1 25.7 25.3 26.8 17.2 27.0 29.0 49.1 51.0 53.6 43.3 44.0 56.0 48.5 55.47
55 28.9 20.1 25.7 25.3 26.9 17.2 26.9 29.0 49.0 50.9 53.5 43.3 44.1 55.9 48.4 55.46
56 29.0 20.1 25.7 25.3 26.8 17.2 27.0 28.9 49.1 51.0 53.6 43.4 44.0 55.9 48.5 55.53
57 28.9 20.1 25.7 25.3 26.9 17.2 27.0 28.9 49.0 50.9 53.6 43.3 44.1 55.9 48.5 55.52
58 29.0 20.1 25.7 25.3 26.9 17.2 26.9 29.0 49.1 51.0 53.6 43.3 44.1 55.9 48.5 55.43
59 29.0 20.1 25.7 25.3 26.9 17.3 27.0 28.9 49.1 50.9 53.6 43.3 44.2 55.9 48.5 55.53
60 29.0 20.1 25.7 25.3 26.9 17.3 27.0 28.9 49.1 50.9 53.7 43.2 44.2 55.8 48.5 55.54
61 29.0 20.1 25.7 25.3 26.9 17.3 26.9 28.9 49.1 50.9 53.6 43.2 44.2 55.8 48.4 55.49
62 29.0 20.1 25.7 25.3 26.8 17.1 27.0 29.0 49.1 51.0 53.6 43.3 43.9 56.0 48.5 55.44
63 29.0 20.0 25.7 25.3 26.9 17.0 27.0 29.1 49.0 51.0 53.6 43.3 43.9 56.1 48.5 55.45
64 29.0 20.1 25.7 25.3 26.8 17.2 27.0 29.0 49.1 50.9 53.6 43.3 44.0 56.0 48.5 55.50
65 29.0 20.1 25.7 25.3 26.9 17.2 26.9 29.0 49.1 51.0 53.6 43.3 44.1 55.9 48.5 55.50
66 29.0 20.1 25.7 25.3 26.9 17.2 27.0 29.0 49.1 50.9 53.6 43.3 44.1 55.9 48.5 55.49
67 28.7 20.1 25.9 25.3 26.9 17.1 26.9 29.1 48.8 51.0 53.6 43.4 44.0 56.0 48.5 55.49
68 29.0 20.1 25.7 25.3 26.8 17.2 27.0 29.0 49.1 51.0 53.6 43.3 44.0 56.0 48.5 55.50
69 29.0 20.1 25.7 25.3 26.9 17.2 26.9 29.0 49.1 50.9 53.5 43.3 44.1 55.9 48.4 55.52
70 29.1 20.0 25.9 25.0 27.1 16.9 27.1 28.9 49.1 50.9 53.7 43.2 44.0 56.0 48.5 55.11
71 28.7 20.6 26.0 24.7 26.9 17.2 27.0 28.9 49.3 50.9 53.6 43.3 44.1 55.9 48.5 55.42
72 29.0 20.1 25.6 25.2 26.6 18.3 27.5 27.7 49.1 50.6 53.4 43.4 44.9 55.1 48.4 56.28
73 29.0 20.1 25.7 25.3 26.9 17.2 27.0 28.9 49.1 50.9 53.6 43.3 44.1 55.9 48.5 55.57
74 29.0 20.1 25.7 25.2 26.9 17.2 27.0 28.9 49.1 51.0 53.6 43.3 44.1 55.9 48.5 55.55
75 29.0 20.1 25.7 25.3 26.9 17.3 27.0 28.9 49.1 50.9 53.6 43.3 44.2 55.8 48.5 55.55
76 29.0 20.1 25.7 25.3 26.9 17.2 26.9 28.9 49.1 50.9 53.6 43.2 44.1 55.9 48.4 55.49
77 29.0 20.1 25.7 25.2 26.8 17.3 27.0 28.9 49.1 51.0 53.7 43.4 44.1 55.9 48.6 55.61
78 28.9 20.1 25.7 25.3 26.9 17.2 27.0 29.0 49.0 51.0 53.7 43.4 44.1 56.0 48.6 55.58
79 29.0 20.1 25.7 25.2 26.9 17.3 27.0 28.9 49.1 50.9 53.6 43.3 44.2 55.9 48.5 55.58
80 28.9 20.1 25.7 25.2 26.9 17.3 27.0 28.9 49.0 50.9 53.5 43.4 44.2 55.9 48.5 55.55
81 28.9 20.1 25.7 25.3 26.8 17.2 27.0 29.0 49.0 51.0 53.6 43.3 44.0 56.0 48.5 55.55
82 28.9 20.1 25.7 25.3 26.8 17.2 27.0 29.0 49.0 50.9 53.6 43.3 44.0 56.0 48.5 55.51
83 29.0 20.1 25.6 25.2 27.0 17.3 26.8 28.9 49.1 50.8 53.5 43.3 44.3 55.7 48.4 55.63
84 29.0 20.1 25.7 25.2 26.8 17.3 27.0 28.8 49.1 50.9 53.6 43.3 44.1 55.9 48.5 55.60
85 28.9 20.1 25.7 25.3 26.9 17.3 27.0 28.9 49.0 50.9 53.6 43.3 44.2 55.8 48.5 55.48
86 28.9 20.1 25.7 25.3 26.8 17.3 27.0 28.8 49.0 50.9 53.6 43.3 44.1 55.8 48.5 55.61
87 29.0 20.1 25.7 25.3 26.8 17.2 27.0 29.0 49.1 50.9 53.6 43.3 44.0 56.0 48.5 55.51
88 28.9 20.1 25.7 25.2 27.0 17.2 26.8 29.0 49.0 50.9 53.6 43.3 44.2 55.8 48.5 55.53
89 29.0 20.1 25.6 25.3 26.8 17.3 27.0 28.9 49.1 50.9 53.6 43.3 44.1 56.0 48.5 55.58
90 29.0 20.1 25.6 25.3 26.9 17.2 27.0 29.0 49.1 50.9 53.6 43.2 44.1 55.9 48.4 55.38
91 29.0 20.1 25.6 25.3 27.0 17.3 26.8 28.9 49.1 50.9 53.6 43.3 44.3 55.8 48.5 55.54
92 29.0 20.1 25.7 25.3 27.0 17.2 26.9 29.0 49.1 50.9 53.6 43.3 44.2 55.8 48.5 55.53
93 29.0 20.1 25.7 25.3 26.9 17.2 27.0 29.0 49.1 50.9 53.6 43.2 44.1 56.0 48.4 55.44
94 29.0 20.1 25.7 25.3 26.9 17.2 27.0 28.9 49.1 50.9 53.6 43.2 44.1 55.9 48.4 55.42
95 28.9 20.1 25.7 25.2 26.8 17.3 27.0 28.9 49.0 50.9 53.6 43.3 44.1 55.9 48.5 55.59
96 29.0 20.1 25.7 25.2 26.9 17.2 27.0 29.0 49.1 50.9 53.6 43.3 44.1 55.9 48.5 55.43
97 29.0 20.1 25.7 25.3 26.8 17.3 27.0 28.9 49.1 50.9 53.5 43.3 44.1 55.9 48.4 55.57
98 28.9 20.2 25.7 25.2 26.9 17.2 27.0 29.0 49.1 50.9 53.6 43.2 44.1 56.0 48.4 55.42
99 29.0 20.1 25.7 25.3 26.8 17.3 27.0 28.9 49.1 50.9 53.6 43.3 44.1 55.9 48.5 55.59
100 28.9 20.2 25.7 25.2 27.0 17.2 26.9 29.0 49.1 50.9 53.6 43.3 44.2 55.9 48.5 55.41
101 29.0 20.1 25.7 25.3 26.7 17.3 27.1 28.9 49.1 50.9 53.6 43.3 44.0 56.0 48.5 55.56
102 29.0 20.1 25.7 25.3 26.8 17.3 27.0 28.9 49.1 50.9 53.5 43.2 44.1 56.0 48.4 55.59
103 29.0 20.1 25.7 25.3 26.8 17.3 27.0 28.9 49.1 50.9 53.6 43.3 44.1 55.9 48.5 55.63
104 28.9 20.1 25.7 25.2 26.8 17.3 27.0 28.9 49.0 51.0 53.6 43.3 44.1 55.9 48.5 55.58
105 28.9 20.1 25.7 25.3 26.8 17.2 27.0 29.0 49.0 51.0 53.7 43.4 44.0 56.0 48.6 55.56
106 28.9 20.1 25.7 25.2 26.8 17.3 27.0 28.8 49.0 50.9 53.6 43.3 44.1 55.8 48.5 55.60
107 28.9 20.1 25.7 25.2 26.8 17.3 27.0 28.9 49.0 50.9 53.6 43.3 44.1 55.9 48.5 55.63
108 28.9 20.1 25.7 25.3 26.8 17.3 27.0 28.9 49.0 50.9 53.6 43.3 44.1 55.9 48.5 55.65
109 28.9 20.1 25.7 25.2 26.8 17.3 27.0 28.9 49.0 50.9 53.6 43.3 44.1 55.9 48.5 55.65
110 28.9 20.1 25.7 25.2 26.8 17.3 27.0 28.9 49.0 50.9 53.6 43.3 44.1 55.9 48.5 55.63
111 28.9 20.1 25.7 25.2 26.8 17.3 27.0 28.9 49.0 50.9 53.6 43.3 44.1 55.9 48.5 55.66
112 28.9 20.1 25.7 25.2 26.8 17.3 27.0 28.8 49.0 50.9 53.6 43.3 44.1 55.8 48.5 55.67
113 28.9 20.1 25.7 25.2 26.8 17.3 27.0 28.9 49.0 50.9 53.6 43.3 44.1 55.8 48.5 55.63
114 28.9 20.1 25.7 25.2 26.8 17.2 27.0 28.9 49.0 50.9 53.6 43.3 44.0 56.0 48.5 55.58
115 29.0 20.2 25.6 25.2 26.9 17.4 26.9 28.8 49.2 50.8 53.5 43.3 44.3 55.7 48.4 55.62
116 29.0 20.1 25.6 25.2 27.0 17.3 26.8 28.9 49.1 50.9 53.6 43.3 44.3 55.7 48.5 55.59
117 28.9 20.1 25.7 25.2 26.3 17.0 27.2 29.5 49.0 51.4 53.8 43.7 43.3 56.7 48.8 55.49
118 28.8 19.8 25.9 25.5 26.8 17.4 27.0 28.8 48.6 50.9 53.6 43.3 44.2 55.8 48.5 55.63
119 28.9 20.1 25.7 25.3 26.8 17.3 27.0 28.9 49.0 50.9 53.6 43.3 44.1 55.9 48.5 55.59
120 28.9 20.1 25.7 25.2 26.8 17.3 27.0 28.8 49.0 50.9 53.6 43.4 44.1 55.8 48.5 55.63
121 28.9 20.2 25.7 25.2 26.8 17.4 27.0 28.8 49.1 50.9 53.5 43.3 44.2 55.8 48.4 55.66
122 28.9 20.2 25.7 25.2 26.8 17.5 27.0 28.7 49.1 50.9 53.6 43.3 44.3 55.7 48.5 55.79
123 28.9 20.1 25.7 25.2 26.8 17.4 27.1 28.8 49.0 50.9 53.6 43.4 44.2 55.9 48.5 55.55
124 28.9 20.2 25.7 25.2 26.7 17.5 27.1 28.8 49.1 50.9 53.6 43.3 44.2 55.9 48.5 55.84
125 28.9 20.1 25.7 25.2 26.8 17.3 27.1 28.8 49.0 51.0 53.6 43.3 44.1 56.0 48.5 55.55
126 28.9 20.1 25.7 25.2 26.8 17.4 27.0 28.8 49.0 50.9 53.6 43.3 44.2 55.8 48.5 55.77
127 28.9 20.1 25.7 25.2 26.8 17.3 27.0 28.9 49.0 50.9 53.7 43.3 44.1 55.9 48.5 55.68
128 28.9 20.2 25.7 25.2 26.8 17.4 27.0 28.8 49.1 50.9 53.6 43.4 44.2 55.8 48.5 55.54
129 29.0 20.1 25.7 25.3 27.1 16.9 26.9 29.1 49.1 50.9 53.4 43.3 44.0 56.0 48.4 55.28
130 28.7 20.6 26 24.7 26.5 18.3 27.6 27.6 49.3 50.7 53.5 43.3 44.8 55.2 48.4 56.19
131 28.9 20.1 25.7 25.2 26.9 17.4 27.0 28.8 49.0 50.9 53.7 43.3 44.3 55.7 48.5 55.60
132 28.9 20.1 25.7 25.2 26.9 17.3 27.0 28.8 49.0 50.9 53.7 43.3 44.2 55.8 48.5 55.60
133 28.9 20.1 25.7 25.2 26.9 17.3 27.0 28.8 49.0 50.9 53.7 43.3 44.2 55.8 48.5 55.60
134 28.9 20.1 25.7 25.3 26.9 17.3 27.0 28.8 49.0 50.9 53.7 43.3 44.2 55.8 48.5 55.59
135 28.9 20.1 25.7 25.3 26.9 17.3 27.0 28.8 49.0 50.9 53.7 43.3 44.2 55.8 48.5 55.59
136 28.9 20.1 25.7 25.2 26.9 17.3 27.0 28.8 49.0 50.9 53.7 43.3 44.2 55.8 48.5 55.61
137 28.9 20.1 25.7 25.2 26.9 17.3 27.0 28.8 49.0 50.9 53.7 43.3 44.2 55.8 48.5 55.61
138 28.8 20.6 26.0 24.7 26.6 18.2 27.5 27.7 49.4 50.6 53.3 43.2 44.8 55.3 48.3 56.41
139 28.8 20.6 26.0 24.7 26.5 18.2 27.6 27.7 49.4 50.6 50.6 50.6 44.7 55.3 48.3 56.41
140 29.0 20.1 25.9 25.3 27.0 17.1 26.8 29.1 49.1 51.0 53.6 43.4 44.1 55.9 48.5 55.39
141 28.9 20.0 25.7 25.3 27.3 17.0 26.7 29.0 48.9 50.9 53.7 43.3 44.3 55.7 48.5 55.25
Mean 28.91 20.16 25.75 25.19 26.78 17.36 27.10 28.76 49.07 50.91 53.56 43.38 44.14 55.86 48.45 55.56
SD 0.10 0.18 0.10 0.20 0.25 0.39 0.27 0.47 0.16 0.16 0.27 0.62 0.41 0.40 0.07 0.34

SD: Standard deviation.