1     M         0.667   0.676   0.715   0.971   0.973   0.982   0.664   0.682   0.739
2     A        -1.002  -0.812  -0.952  -0.902  -0.681  -0.951  -1.105  -0.859  -1.100
3     K         0.667   0.676   0.715  -0.152  -0.106   0.144   0.664   0.682   0.739
4     V        -0.432  -0.762  -0.950  -0.240  -0.608  -0.920  -0.347  -0.791  -1.097
5     H         0.667   0.676   0.715   1.147   1.139   1.113   0.664   0.682   0.739
6     G         0.667   0.676   0.715   0.592   0.610   0.699   0.664   0.682   0.739
7     S         0.667   0.676   0.715   0.791   0.821   0.848   0.664   0.682   0.739
8     L        -0.432  -0.762  -0.950   0.086  -0.272  -0.595  -0.347  -0.791  -1.097
9     A         0.667   0.676   0.715   0.805   0.801   0.858   0.664   0.682   0.739
10    R         0.667   0.676   0.715   0.461   0.497   0.601   0.664   0.682   0.739
11    A         0.667   0.676   0.715   0.805   0.801   0.858   0.664   0.682   0.739
12    G         0.667   0.676   0.715   0.592   0.610   0.699   0.664   0.682   0.739
13    K         0.667   0.676   0.715  -0.152  -0.106   0.144   0.664   0.682   0.739
14    V         0.667   0.676   0.715   0.563   0.596   0.678   0.664   0.682   0.739
15    K         0.667   0.676   0.715  -0.152  -0.106   0.144   0.664   0.682   0.739
16    S         0.667   0.676   0.715   0.791   0.821   0.848   0.664   0.682   0.739
17    Q         0.667   0.676   0.715   0.902   0.905   0.931   0.664   0.682   0.739
18    T         0.667   0.676   0.715   0.819   0.821   0.869   0.664   0.682   0.739
19    P         0.667   0.676   0.715   0.721   0.753   0.795   0.664   0.682   0.739
20    K         0.667   0.676   0.715  -0.152  -0.106   0.144   0.664   0.682   0.739
21    V         0.667   0.676   0.715   0.563   0.596   0.678   0.664   0.682   0.739
22    E        -0.432  -0.355  -0.938   0.278   0.327  -0.462  -0.347  -0.262  -1.079
23    K        -0.432  -0.355  -0.938  -0.973  -0.873  -1.402  -0.347  -0.262  -1.079
24    T        -1.488  -1.221  -1.934  -0.720  -0.474  -1.541  -1.231  -0.954  -1.729
25    E         0.667   0.676   0.715   1.039   1.036   1.033   0.664   0.682   0.739
26    K         0.667   0.676   0.715  -0.152  -0.106   0.144   0.664   0.682   0.739
27    P        -0.432  -0.553  -0.943  -0.209  -0.368  -1.283  -0.347  -0.510  -1.086
28    K         0.667   0.676   0.715  -0.152  -0.106   0.144   0.664   0.682   0.739
29    K        -3.162  -3.229  -2.662  -3.261  -3.357  -2.482  -2.748  -2.754  -2.071
30    P         0.667   0.676   0.715   0.721   0.753   0.795   0.664   0.682   0.739
31    K        -1.488  -1.686  -1.946  -1.807  -2.077  -2.193  -1.231  -1.500  -1.741
32    G         0.667   0.676   0.715   0.592   0.610   0.699   0.664   0.682   0.739
33    R         0.667   0.676   0.715   0.461   0.497   0.601   0.664   0.682   0.739
34    A         0.667   0.676   0.715   0.805   0.801   0.858   0.664   0.682   0.739
35    Y        -1.002  -1.219  -0.976  -0.698  -1.228  -1.216  -1.105  -1.463  -1.137
36    K        -0.432  -0.314  -0.938  -0.949  -0.808  -1.317  -0.347  -0.214  -1.079
37    R         0.667   0.676   0.715   0.461   0.497   0.601   0.664   0.682   0.739
38    L         0.667   0.676   0.715   0.847   0.867   0.889   0.664   0.682   0.739
39    L        -0.432  -0.553  -0.943   0.033  -0.107  -0.774  -0.347  -0.510  -1.086
40    Y         0.667   0.676   0.715   1.053   1.062   1.043   0.664   0.682   0.739
41    T        -1.002  -0.766  -0.931  -0.747  -0.460  -0.880  -1.105  -0.795  -1.068
42    R         0.667   0.676   0.715   0.461   0.497   0.601   0.664   0.682   0.739
43    R         0.667   0.676   0.715   0.461   0.497   0.601   0.664   0.682   0.739
44    F         0.667   0.676   0.715   1.147   1.139   1.113   0.664   0.682   0.739
45    V        -0.432  -0.762  -0.950  -0.195  -0.535  -0.760  -0.347  -0.791  -1.097
46    N         0.667   0.676   0.715   0.916   0.907   0.941   0.664   0.682   0.739
47    V         0.667   0.676   0.715   0.563   0.596   0.678   0.664   0.682   0.739
48    T         0.667   0.676   0.715   0.819   0.821   0.869   0.664   0.682   0.739
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    L        -1.339  -1.221  -0.967  -1.084  -0.952  -0.742  -1.610  -1.465  -1.123
51    V        -1.498  -1.392  -0.977  -1.609  -1.508  -0.985  -1.863  -1.738  -1.138
52    N        -1.339  -1.221  -0.967  -1.191  -1.077  -0.885  -1.610  -1.465  -1.123
53    G         0.667   0.676   0.715   0.592   0.610   0.699   0.664   0.682   0.739
54    K         0.667   0.676   0.715  -0.152  -0.106   0.144   0.664   0.682   0.739
55    R         0.667   0.676   0.715   0.461   0.497   0.601   0.664   0.682   0.739
56    R        -1.498  -1.316  -0.969  -2.494  -2.239  -1.608  -1.863  -1.616  -1.126
57    M         0.667   0.676   0.715   0.971   0.973   0.982   0.664   0.682   0.739
58    N         0.667   0.676   0.715   0.916   0.907   0.941   0.664   0.682   0.739
59    P        -0.432  -0.762  -0.950  -0.083  -0.453  -0.825  -0.347  -0.791  -1.097
60    G        -2.733  -2.530  -1.962  -2.506  -2.258  -1.674  -2.678  -2.469  -1.758
61    P         0.667   0.676   0.715   0.681   0.716   0.765   0.664   0.682   0.739
62    S        -1.454  -1.350  -0.976  -1.446  -1.333  -0.902  -1.792  -1.671  -1.136
63    V        -1.488  -1.508  -1.939  -0.894  -0.943  -1.791  -1.231  -1.279  -1.734
64    Q        -2.286  -2.404  -1.959  -1.822  -1.999  -1.590  -2.242  -2.339  -1.756
* 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/P0CX34
Output conservation file - output/P0CX34
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
