1     M         1.154   1.160   1.228   1.319   1.328   1.423   1.236   1.243   1.338
2     V        -1.249  -1.293  -1.279  -1.084  -1.129  -1.089  -1.149  -1.195  -1.125
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     S        -0.684  -0.685  -0.744  -0.588  -0.605  -0.714  -0.768  -0.768  -0.826
6     T        -1.864  -1.877  -1.726  -1.391  -1.419  -1.238  -1.547  -1.551  -1.330
7     P         1.154   1.160   1.228   1.408   1.413   1.506   1.236   1.243   1.338
8     E        -0.077  -0.117  -0.036  -0.151  -0.231  -0.123  -0.354  -0.426  -0.311
9     L         1.154   1.160   1.228   0.838   0.849   0.972   1.236   1.243   1.338
10    K         0.282   0.205   0.076   0.342   0.241   0.054   0.242   0.121  -0.113
11    K         0.282   0.309   0.081   0.326   0.363   0.028   0.242   0.283  -0.105
12    Y         1.154   1.160   1.228   1.364   1.374   1.464   1.236   1.243   1.338
13    M        -0.802  -0.751  -0.754  -0.905  -0.828  -0.877  -0.950  -0.889  -0.842
14    D         1.154   1.160   1.228   1.160   1.169   1.274   1.236   1.243   1.338
15    K         0.282   0.255   0.081   0.342   0.309   0.061   0.242   0.200  -0.105
16    K        -0.524  -0.513  -0.707  -0.363  -0.350  -0.602  -0.553  -0.536  -0.778
17    I        -0.802  -0.799  -0.748  -1.237  -1.234  -1.136  -0.950  -0.935  -0.834
18    L        -1.417  -1.433  -1.308  -1.450  -1.482  -1.293  -1.348  -1.355  -1.155
19    L        -0.802  -0.780  -0.760  -1.233  -1.202  -1.150  -0.950  -0.920  -0.850
20    N         0.282   0.298   0.085   0.574   0.591   0.265   0.242   0.266  -0.098
21    I         0.282   0.298   0.085   0.026   0.046  -0.269   0.242   0.266  -0.098
22    N         1.154   1.160   1.228   1.240   1.246   1.349   1.236   1.243   1.338
23    G         1.154   1.160   1.228   1.067   1.087   1.187   1.236   1.243   1.338
24    S         0.282   0.205   0.076   0.418   0.312   0.114   0.242   0.121  -0.113
25    R         1.154   1.160   1.228   1.263   1.272   1.370   1.236   1.243   1.338
26    K         0.282   0.350   0.089   0.358   0.442   0.106   0.242   0.343  -0.090
27    V        -0.077  -0.098  -0.027  -0.358  -0.398  -0.307  -0.354  -0.392  -0.295
28    A        -0.802  -0.799  -0.748  -0.803  -0.805  -0.684  -0.950  -0.935  -0.834
29    G         1.154   1.160   1.228   1.067   1.087   1.187   1.236   1.243   1.338
30    I        -0.187  -0.178  -0.048  -0.577  -0.567  -0.352  -0.553  -0.538  -0.334
31    L         1.154   1.160   1.228   0.838   0.849   0.972   1.236   1.243   1.338
32    R         1.154   1.160   1.228   1.263   1.272   1.370   1.236   1.243   1.338
33    G         1.154   1.160   1.228   1.067   1.087   1.187   1.236   1.243   1.338
34    Y         1.154   1.160   1.228   1.364   1.374   1.464   1.236   1.243   1.338
35    D         1.154   1.160   1.228   1.160   1.169   1.274   1.236   1.243   1.338
36    I        -1.249  -1.230  -1.254  -1.313  -1.277  -1.362  -1.149  -1.126  -1.100
37    F         1.154   1.160   1.228   1.408   1.417   1.506   1.236   1.243   1.338
38    L         1.154   1.160   1.228   0.838   0.849   0.972   1.236   1.243   1.338
39    N         1.154   1.160   1.228   1.240   1.246   1.349   1.236   1.243   1.338
40    V        -0.802  -0.833  -0.755  -1.122  -1.182  -1.085  -0.950  -0.975  -0.843
41    V         0.282   0.309   0.081   0.293   0.342   0.042   0.242   0.283  -0.105
42    L         1.154   1.160   1.228   0.838   0.849   0.972   1.236   1.243   1.338
43    D        -0.524  -0.528  -0.693  -0.321  -0.332  -0.561  -0.553  -0.557  -0.760
44    D         0.282   0.205   0.076   0.395   0.288   0.094   0.242   0.121  -0.113
45    A        -0.524  -0.616  -0.699  -0.169  -0.294  -0.439  -0.553  -0.674  -0.768
46    M        -1.249  -1.194  -1.251  -1.309  -1.235  -1.351  -1.149  -1.082  -1.096
47    E         0.282   0.205   0.076   0.438   0.338   0.156   0.242   0.121  -0.113
48    I        -1.417  -1.372  -1.300  -1.615  -1.552  -1.481  -1.348  -1.300  -1.147
49    N        -1.864  -1.850  -1.722  -1.729  -1.691  -1.534  -1.547  -1.528  -1.327
50    G        -2.311  -2.294  -2.072  -2.200  -2.174  -1.870  -1.745  -1.724  -1.449
51    E        -1.417  -1.382  -1.294  -1.404  -1.356  -1.242  -1.348  -1.308  -1.142
52    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    A         0.282   0.298   0.085   0.316   0.346   0.056   0.242   0.266  -0.098
55    N         0.282   0.298   0.085   0.418   0.437   0.129   0.242   0.266  -0.098
56    N        -0.524  -0.581  -0.697  -0.445  -0.534  -0.728  -0.553  -0.628  -0.765
57    H        -1.417  -1.396  -1.301  -1.160  -1.134  -0.956  -1.348  -1.322  -1.148
58    Q        -0.684  -0.695  -0.733  -0.584  -0.606  -0.634  -0.768  -0.780  -0.812
59    L        -0.802  -0.853  -0.756  -1.144  -1.212  -1.008  -0.950  -1.004  -0.846
60    G         1.154   1.160   1.228   1.067   1.087   1.187   1.236   1.243   1.338
61    L        -1.864  -1.860  -1.712  -1.573  -1.569  -1.372  -1.547  -1.537  -1.319
62    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    T        -0.077  -0.069  -0.023  -0.042  -0.015  -0.025  -0.354  -0.340  -0.288
64    V        -0.524  -0.513  -0.707  -0.414  -0.387  -0.627  -0.553  -0.536  -0.778
65    I        -0.077  -0.084  -0.024  -0.364  -0.385  -0.304  -0.354  -0.366  -0.290
66    R         1.154   1.160   1.228   1.263   1.272   1.370   1.236   1.243   1.338
67    G         1.154   1.160   1.228   1.067   1.087   1.187   1.236   1.243   1.338
68    N         0.282   0.350   0.089   0.463   0.544   0.163   0.242   0.343  -0.090
69    S         1.154   1.160   1.228   1.183   1.194   1.295   1.236   1.243   1.338
70    I        -0.077  -0.069  -0.023  -0.364  -0.358  -0.302  -0.354  -0.340  -0.288
71    I        -0.802  -0.759  -0.749  -1.118  -1.051  -1.071  -0.950  -0.900  -0.838
72    S        -0.077  -0.069  -0.023  -0.078  -0.070  -0.008  -0.354  -0.340  -0.288
73    L        -0.802  -0.748  -0.742  -1.089  -1.013  -0.950  -0.950  -0.877  -0.826
74    E         1.154   1.160   1.228   1.183   1.194   1.295   1.236   1.243   1.338
75    A        -0.524  -0.616  -0.699  -0.127  -0.244  -0.369  -0.553  -0.674  -0.768
76    L         1.154   1.160   1.228   0.838   0.849   0.972   1.236   1.243   1.338
77    D        -0.077  -0.044  -0.019  -0.162  -0.112  -0.096  -0.354  -0.296  -0.281
78    A        -1.864  -1.821  -1.717  -1.516  -1.470  -1.316  -1.547  -1.501  -1.323
79    I        -0.524  -0.616  -0.699  -0.554  -0.715  -0.845  -0.553  -0.674  -0.768
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P40204
Output conservation file - output/P40204
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
