1     M         0.820   0.832   0.889   1.110   1.114   1.166   0.853   0.874   0.949
2     A         0.011  -0.100  -0.325   0.217   0.042  -0.367   0.000  -0.169  -0.545
3     H         0.820   0.832   0.889   0.871   0.895   0.972   0.853   0.874   0.949
4     E         0.820   0.832   0.889   1.005   1.015   1.081   0.853   0.874   0.949
5     N        -0.387  -0.338  -0.374  -0.470  -0.418  -0.532  -0.610  -0.547  -0.630
6     V         0.011  -0.180  -0.325   0.325   0.051  -0.227   0.000  -0.292  -0.545
7     W         0.820   0.832   0.889   1.110   1.114   1.166   0.853   0.874   0.949
8     F        -0.759  -0.776  -1.087  -0.562  -0.598  -1.040  -0.732  -0.768  -1.133
9     S         0.820   0.832   0.889   0.691   0.748   0.827   0.853   0.874   0.949
10    H         0.011  -0.100  -0.325   0.091  -0.077  -0.559   0.000  -0.169  -0.545
11    P         0.820   0.832   0.889   1.110   1.114   1.166   0.853   0.874   0.949
12    R         0.820   0.832   0.889   0.359   0.421   0.558   0.853   0.874   0.949
13    R        -2.527  -2.414  -2.092  -2.755  -2.511  -1.989  -2.195  -2.042  -1.636
14    F        -0.600  -0.575  -0.392  -0.782  -0.746  -0.442  -0.975  -0.958  -0.661
15    G         0.820   0.832   0.889   0.691   0.710   0.827   0.853   0.874   0.949
16    K         0.820   0.832   0.889   0.789   0.799   0.906   0.853   0.874   0.949
17    G         0.820   0.832   0.889   0.691   0.710   0.827   0.853   0.874   0.949
18    S         0.011  -0.180  -0.325  -0.044  -0.290  -0.559   0.000  -0.292  -0.545
19    R         0.820   0.832   0.889   0.359   0.421   0.558   0.853   0.874   0.949
20    Q        -0.759  -1.026  -1.105  -0.433  -0.864  -1.090  -0.732  -1.085  -1.155
21    C         0.820   0.832   0.889   0.898   0.933   0.994   0.853   0.874   0.949
22    R         0.011  -0.009  -0.317  -0.340  -0.326  -0.679   0.000  -0.035  -0.531
23    V        -1.412  -1.340  -1.148  -1.382  -1.326  -1.056  -1.585  -1.497  -1.207
24    C        -1.112  -1.092  -1.126  -0.989  -0.996  -1.046  -1.219  -1.235  -1.182
25    S        -1.783  -1.893  -1.673  -1.885  -2.029  -1.623  -1.707  -1.790  -1.469
26    S        -1.484  -1.716  -1.662  -1.498  -1.866  -1.843  -1.341  -1.601  -1.459
27    H        -1.484  -1.716  -1.662  -1.321  -1.713  -1.745  -1.341  -1.601  -1.459
28    T        -2.387  -2.365  -2.085  -2.218  -2.217  -1.752  -2.073  -2.003  -1.631
29    G         0.011  -0.180  -0.325  -0.006  -0.267  -0.449   0.000  -0.292  -0.545
30    L         0.011  -0.180  -0.325   0.291   0.032  -0.211   0.000  -0.292  -0.545
31    V         0.011   0.187  -0.303   0.211   0.400  -0.233   0.000   0.235  -0.508
32    R         0.820   0.832   0.889   0.359   0.421   0.558   0.853   0.874   0.949
33    K         0.820   0.832   0.889   0.789   0.799   0.906   0.853   0.874   0.949
34    Y         0.820   0.832   0.889   0.965   0.973   1.049   0.853   0.874   0.949
35    D        -0.600  -0.354  -0.348  -0.859  -0.488  -0.443  -0.975  -0.574  -0.585
36    L         0.820   0.832   0.889   0.978   0.991   1.059   0.853   0.874   0.949
37    N         0.011   0.171  -0.301   0.186   0.356  -0.244   0.000   0.214  -0.504
38    I        -0.387  -0.406  -0.381  -0.353  -0.418  -0.385  -0.610  -0.661  -0.641
39    C        -0.759  -0.693  -1.084  -0.510  -0.424  -1.027  -0.732  -0.657  -1.129
40    R         0.820   0.832   0.889   0.359   0.421   0.558   0.853   0.874   0.949
41    Q         0.820   0.832   0.889   1.018   1.032   1.092   0.853   0.874   0.949
42    C        -0.600  -0.569  -0.397  -0.866  -0.838  -0.577  -0.975  -0.946  -0.669
43    F         0.820   0.832   0.889   0.830   0.866   0.939   0.853   0.874   0.949
44    R         0.820   0.832   0.889   0.359   0.421   0.558   0.853   0.874   0.949
45    E         0.820   0.832   0.889   1.005   1.015   1.081   0.853   0.874   0.949
46    K        -1.112  -0.887  -1.082  -1.324  -0.919  -1.262  -1.219  -0.905  -1.126
47    A         0.820   0.832   0.889   0.952   0.951   1.038   0.853   0.874   0.949
48    N        -1.412  -1.205  -1.123  -1.571  -1.266  -1.142  -1.585  -1.335  -1.178
49    D         0.820   0.832   0.889   1.045   1.066   1.113   0.853   0.874   0.949
50    I         0.820   0.832   0.889   0.898   0.903   0.994   0.853   0.874   0.949
51    G         0.820   0.832   0.889   0.691   0.710   0.827   0.853   0.874   0.949
52    F         0.820   0.832   0.889   0.830   0.866   0.939   0.853   0.874   0.949
53    H        -2.387  -2.167  -2.081  -2.062  -1.782  -1.623  -2.073  -1.856  -1.628
54    K         0.820   0.832   0.889   0.789   0.799   0.906   0.853   0.874   0.949
55    Y        -1.112  -1.188  -1.122  -0.999  -1.152  -1.077  -1.219  -1.313  -1.177
56    R         0.820   0.832   0.889   0.359   0.421   0.558   0.853   0.874   0.949
* 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/P41058
Output conservation file - output/P41058
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
