1     M         1.517   1.522   1.541   1.616   1.613   1.656   1.605   1.610   1.634
2     L        -1.222  -1.216  -1.190  -1.467  -1.462  -1.414  -1.077  -1.067  -1.023
3     -         1.517   1.522   1.541   1.472   1.472   1.513   1.605   1.610   1.634
4     -        -0.211  -0.208  -0.182  -0.385  -0.386  -0.336  -0.406  -0.400  -0.359
5     G        -1.222  -1.216  -1.190  -1.190  -1.170  -1.138  -1.077  -1.067  -1.023
6     M        -0.070  -0.073  -0.112   0.011   0.021  -0.063  -0.183  -0.187  -0.247
7     I        -0.070  -0.073  -0.112  -0.069  -0.066  -0.137  -0.183  -0.187  -0.247
8     R        -0.070  -0.097  -0.122  -0.128  -0.176  -0.181  -0.183  -0.225  -0.263
9     W        -0.070  -0.097  -0.122   0.101   0.049  -0.003  -0.183  -0.225  -0.263
10    V        -1.222  -1.216  -1.190  -1.285  -1.272  -1.233  -1.077  -1.067  -1.023
11    V        -0.070  -0.097  -0.122  -0.069  -0.105  -0.154  -0.183  -0.225  -0.263
12    E        -0.070  -0.073  -0.112   0.056   0.096  -0.020  -0.183  -0.187  -0.247
13    G        -0.070  -0.073  -0.112  -0.432  -0.430  -0.503  -0.183  -0.187  -0.247
14    T        -0.070  -0.097  -0.122   0.145   0.097   0.056  -0.183  -0.225  -0.263
15    L         1.517   1.522   1.541   1.254   1.269   1.296   1.605   1.610   1.634
16    V        -0.070  -0.097  -0.122  -0.247  -0.301  -0.369  -0.183  -0.225  -0.263
17    A        -0.070  -0.097  -0.122   0.067   0.010  -0.032  -0.183  -0.225  -0.263
18    M        -0.070  -0.024  -0.092  -0.000   0.074  -0.038  -0.183  -0.112  -0.216
19    L        -0.070  -0.073  -0.112  -0.247  -0.252  -0.346  -0.183  -0.187  -0.247
20    L         1.517   1.522   1.541   1.254   1.269   1.296   1.605   1.610   1.634
21    S        -0.070  -0.073  -0.112   0.067   0.053  -0.012  -0.183  -0.187  -0.247
22    A        -1.222  -1.216  -1.190  -1.175  -1.177  -1.122  -1.077  -1.067  -1.023
23    I        -0.070  -0.073  -0.112  -0.332  -0.318  -0.386  -0.183  -0.187  -0.247
24    R         1.517   1.522   1.541   1.360   1.351   1.402   1.605   1.610   1.634
25    R         1.517   1.522   1.541   1.360   1.351   1.402   1.605   1.610   1.634
26    E        -0.070  -0.073  -0.112  -0.035  -0.010  -0.107  -0.183  -0.187  -0.247
27    T        -0.070  -0.097  -0.122   0.167   0.120   0.083  -0.183  -0.225  -0.263
28    G        -0.070  -0.097  -0.122  -0.104  -0.149  -0.172  -0.183  -0.225  -0.263
29    M        -1.222  -1.216  -1.190  -1.367  -1.351  -1.314  -1.077  -1.067  -1.023
30    I        -0.070  -0.073  -0.112  -0.069  -0.066  -0.137  -0.183  -0.187  -0.247
31    F        -1.222  -1.216  -1.190  -1.367  -1.344  -1.314  -1.077  -1.067  -1.023
32    F        -1.222  -1.216  -1.190  -1.190  -1.184  -1.138  -1.077  -1.067  -1.023
33    Y         1.517   1.522   1.541   1.565   1.562   1.606   1.605   1.610   1.634
34    N        -0.070  -0.073  -0.112   0.056   0.109  -0.005  -0.183  -0.187  -0.247
35    Q        -1.222  -1.216  -1.190  -0.921  -0.919  -0.869  -1.077  -1.067  -1.023
36    Y        -1.222  -1.216  -1.190  -1.159  -1.163  -1.107  -1.077  -1.067  -1.023
37    Q        -1.222  -1.216  -1.190  -1.053  -1.023  -1.001  -1.077  -1.067  -1.023
38    L        -0.070  -0.024  -0.092  -0.332  -0.259  -0.358  -0.183  -0.112  -0.216
39    G        -1.222  -1.216  -1.190  -1.269  -1.271  -1.217  -1.077  -1.067  -1.023
40    G        -0.070  -0.097  -0.122  -0.104  -0.149  -0.172  -0.183  -0.225  -0.263
41    W        -0.070  -0.097  -0.122   0.101   0.049  -0.003  -0.183  -0.225  -0.263
42    I         1.517   1.522   1.541   1.641   1.669   1.681   1.605   1.610   1.634
43    H        -0.070  -0.097  -0.122   0.189   0.131   0.080  -0.183  -0.225  -0.263
44    R        -0.070  -0.024  -0.092  -0.332  -0.269  -0.373  -0.183  -0.112  -0.216
45    Y         1.517   1.522   1.541   1.565   1.562   1.606   1.605   1.610   1.634
46    L         1.517   1.522   1.541   1.254   1.269   1.296   1.605   1.610   1.634
47    S        -1.222  -1.216  -1.190  -0.964  -0.952  -0.913  -1.077  -1.067  -1.023
48    W         1.517   1.522   1.541   1.764   1.773   1.804   1.605   1.610   1.634
49    G         1.517   1.522   1.541   1.438   1.443   1.479   1.605   1.610   1.634
50    E         1.517   1.522   1.541   1.616   1.691   1.656   1.605   1.610   1.634
51    M        -0.070  -0.097  -0.122  -0.035  -0.096  -0.131  -0.183  -0.225  -0.263
52    C        -0.070  -0.097  -0.122   0.101   0.045  -0.039  -0.183  -0.225  -0.263
53    Y        -0.070  -0.073  -0.112  -0.012  -0.027  -0.090  -0.183  -0.187  -0.247
54    T        -1.222  -1.216  -1.190  -1.098  -1.068  -1.046  -1.077  -1.067  -1.023
55    R        -1.222  -1.216  -1.190  -1.334  -1.348  -1.281  -1.077  -1.067  -1.023
56    T        -0.070  -0.073  -0.112  -0.283  -0.278  -0.329  -0.183  -0.187  -0.247
57    L        -1.222  -1.216  -1.190  -1.301  -1.296  -1.249  -1.077  -1.067  -1.023
58    K        -1.222  -1.216  -1.190  -1.068  -1.067  -1.016  -1.077  -1.067  -1.023
59    M        -0.070  -0.024  -0.092  -0.035   0.030  -0.076  -0.183  -0.112  -0.216
60    V        -0.070  -0.097  -0.122  -0.035  -0.083  -0.113  -0.183  -0.225  -0.263
61    K        -0.070  -0.097  -0.122  -0.058  -0.079  -0.146  -0.183  -0.225  -0.263
62    R         1.517   1.522   1.541   1.360   1.351   1.402   1.605   1.610   1.634
63    S         1.517   1.522   1.541   1.590   1.595   1.631   1.605   1.610   1.634
64    K        -1.222  -1.216  -1.190  -0.935  -0.944  -0.884  -1.077  -1.067  -1.023
65    F        -1.222  -1.216  -1.190  -1.038  -1.043  -0.986  -1.077  -1.067  -1.023
66    F         1.517   1.522   1.541   1.641   1.642   1.681   1.605   1.610   1.634
67    R         1.517   1.522   1.541   1.360   1.351   1.402   1.605   1.610   1.634
68    K        -0.070  -0.024  -0.092   0.056   0.112   0.032  -0.183  -0.112  -0.216
69    Q         1.517   1.522   1.541   1.813   1.819   1.853   1.605   1.610   1.634
70    L        -1.222  -1.216  -1.190  -1.301  -1.281  -1.249  -1.077  -1.067  -1.023
71    N        -1.222  -1.216  -1.190  -0.807  -0.797  -0.757  -1.077  -1.067  -1.023
72    E        -1.222  -1.216  -1.190  -1.129  -1.082  -1.076  -1.077  -1.067  -1.023
73    D         1.517   1.522   1.541   1.690   1.711   1.731   1.605   1.610   1.634
74    G        -0.070  -0.097  -0.122  -0.199  -0.251  -0.285  -0.183  -0.225  -0.263
75    F         1.517   1.522   1.541   1.641   1.642   1.681   1.605   1.610   1.634
76    G        -1.222  -1.216  -1.190  -1.485  -1.489  -1.431  -1.077  -1.067  -1.023
77    R        -1.222  -1.216  -1.190  -1.253  -1.246  -1.201  -1.077  -1.067  -1.023
78    I        -0.070  -0.097  -0.122   0.123   0.103   0.053  -0.183  -0.225  -0.263
79    N        -1.222  -1.216  -1.190  -1.023  -0.986  -0.971  -1.077  -1.067  -1.023
80    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    P        -0.211  -0.208  -0.182  -0.029  -0.013   0.018  -0.406  -0.400  -0.359
84    K        -0.211  -0.208  -0.182  -0.531  -0.555  -0.482  -0.406  -0.400  -0.359
85    R        -0.211  -0.208  -0.182  -0.531  -0.555  -0.482  -0.406  -0.400  -0.359
86    R         1.517   1.522   1.541   1.306   1.303   1.348   1.605   1.610   1.634
87    G        -0.211  -0.208  -0.182  -0.273  -0.302  -0.224  -0.406  -0.400  -0.359
88    R        -0.211  -0.208  -0.182  -0.751  -0.763  -0.701  -0.406  -0.400  -0.359
89    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    E         1.517   1.522   1.541   1.622   1.630   1.663   1.605   1.610   1.634
100   L        -0.211  -0.208  -0.182  -0.431  -0.423  -0.382  -0.406  -0.400  -0.359
101   D        -0.211  -0.208  -0.182  -0.150  -0.142  -0.102  -0.406  -0.400  -0.359
* gap fraction no less than  0.50; conservation set to M-S
  M: mean;  S: standard deviation

al2co - The parameters are:

Input alignment file - ../mafft-mac/clustal/Q3E7A7
Output conservation file - output/Q3E7A7
All 9 methods are used - true 
   1. unweighted entropy measure; 2. Henikoff entropy measure;
   3. independent count entropy measure;
   4. unweighted variance measure; 5. Henikoff variance measure;
   6. independent count variance measure;
   7. unweighted matrix-based sum-of-pairs measure;
   8. Henikoff matrix-based sum-of-pairs measure;
   9. independent count matrix-based sum-of-pairs measure;
Window size - 1
Conservation normalized to zero mean and unity variance
Gap fraction to suppress calculation -  0.50
