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Table 3 Forty three sequence positions in the EF data show the highest differences between covarion site likelihood and RAS site likelihood.

From: PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis

  Position* Lambda** Covarion site*** Bivar P-value****
1 34 7.280 c <0.001
2 36 6.503 c <0.001
3 325 6.246 c <0.001
4 305 5.652 c <0.001
5 138 5.458 c <0.001
6 336 4.873 c <0.001
7 329 4.790 c <0.001
8 153 4.702 c <0.001
9 327 4.632 c 0.014
10 35 4.595 c 0.022
11 123 4.438 c 0.004
12 311 4.199 c 0.003
13 189 4.034 c 0.007
14 103 3.906 c 0.001
15 69 3.726 c 0.004
16 131 3.430 c 0.002
17 256 3.256 c2 0.122
18 351 3.202 c 0.027
19 38 3.120 c1 0.043
20 51 3.073 c1 0.013
21 42 3.057 c1 0.029
22 106 2.896 c1 0.064
23 67 2.866 c 0.120
24 271 2.793 c1 0.064
25 133 2.789 c 0.045
26 144 2.700 c1 0.002
27 163 2.604 c 0.006
28 263 2.588 c 0.033
29 31 2.557 c1 0.012
30 39 2.442 c1 0.065
31 160 2.274 c 0.073
32 64 2.23 c1 0.038
33 32 2.143 c 0.147
34 82 2.116 c1 0.029
35 96 2.092 c1 0.080
36 326 2.060 c 0.021
37 178 2.047 c1 0.341
38 37 1.935 c1 0.081
39 40 1.921 c1 0.023
40 350 1.875 c1 0.071
41 355 1.818 c1 0.039
42 288 1.755656 c1 0.043
43 356 1.694422 c1 0.111
  1. * Sequence position is based on the EF alignment [24]. **Λ = ln(lcov) - ln(lras). ***c: sites were found to be covarion sites of functional or structural significance in [24]; c1: sites having typical covarion site pattern but missed in [24]; c2: site showing non-typical covarion site pattern. ****P-values from a Bivar analysis of the EF data.