1     M         0.654   0.682   0.715   0.892   0.940   0.942   0.674   0.708   0.753
2     H         0.654   0.682   0.715   0.909   0.939   0.956   0.674   0.708   0.753
3     L         0.654   0.682   0.715   0.454   0.504   0.590   0.674   0.708   0.753
4     M         0.654   0.682   0.715   0.892   0.940   0.942   0.674   0.708   0.753
5     Y         0.654   0.682   0.715   0.731   0.752   0.813   0.674   0.708   0.753
6     T        -0.369  -0.721  -0.743  -0.490  -1.008  -1.038  -0.392  -0.904  -0.959
7     L        -0.369  -0.198  -0.720  -0.553  -0.310  -1.132  -0.392  -0.152  -0.921
8     G        -1.849  -1.948  -1.640  -1.942  -2.016  -1.535  -1.990  -2.007  -1.592
9     P        -3.209  -3.070  -2.742  -3.029  -2.888  -2.367  -2.700  -2.494  -2.068
10    D        -1.849  -1.706  -1.630  -1.904  -1.640  -1.515  -1.990  -1.762  -1.581
11    G         0.654   0.682   0.715   0.821   0.886   0.885   0.674   0.708   0.753
12    K         0.654   0.682   0.715   0.301   0.358   0.468   0.674   0.708   0.753
13    R         0.654   0.682   0.715   0.529   0.567   0.651   0.674   0.708   0.753
14    I        -1.048  -0.908  -0.768  -1.077  -0.864  -0.662  -1.457  -1.205  -1.000
15    Y         0.654   0.682   0.715   0.731   0.752   0.813   0.674   0.708   0.753
16    T         0.654   0.682   0.715   0.472   0.558   0.606   0.674   0.708   0.753
17    L         0.654   0.682   0.715   0.454   0.504   0.590   0.674   0.708   0.753
18    K        -0.369  -0.216  -0.720  -0.607  -0.405  -0.977  -0.392  -0.176  -0.921
19    K         0.654   0.682   0.715   0.301   0.358   0.468   0.674   0.708   0.753
20    V        -2.715  -2.455  -2.256  -2.785  -2.397  -2.043  -2.523  -2.207  -1.885
21    T        -0.837  -0.914  -0.772  -1.239  -1.381  -1.111  -1.102  -1.217  -1.007
22    E        -1.331  -1.521  -1.621  -1.001  -1.341  -1.578  -1.280  -1.519  -1.569
23    S        -1.728  -1.469  -1.618  -1.818  -1.428  -1.624  -1.813  -1.446  -1.567
24    G        -0.369  -0.286  -0.722  -0.092   0.035  -0.630  -0.392  -0.269  -0.926
25    E        -0.369  -0.721  -0.743  -0.087  -0.669  -0.836  -0.392  -0.904  -0.959
26    I        -0.369  -0.721  -0.743   0.061  -0.465  -0.603  -0.392  -0.904  -0.959
27    T         0.654   0.682   0.715   0.472   0.558   0.606   0.674   0.708   0.753
28    K         0.654   0.682   0.715   0.301   0.358   0.468   0.674   0.708   0.753
29    S         0.654   0.682   0.715   0.676   0.711   0.769   0.674   0.708   0.753
30    A        -0.369  -0.721  -0.743  -0.063  -0.623  -0.768  -0.392  -0.904  -0.959
31    H         0.654   0.682   0.715   0.909   0.939   0.956   0.674   0.708   0.753
32    P         0.654   0.682   0.715   0.767   0.820   0.842   0.674   0.708   0.753
33    A         0.654   0.682   0.715   0.909   0.974   0.956   0.674   0.708   0.753
34    R         0.654   0.682   0.715   0.529   0.567   0.651   0.674   0.708   0.753
35    F         0.654   0.682   0.715   0.962   1.002   0.998   0.674   0.708   0.753
36    S         0.654   0.682   0.715   0.676   0.711   0.769   0.674   0.708   0.753
37    P         0.654   0.682   0.715   0.767   0.820   0.842   0.674   0.708   0.753
38    D         0.654   0.682   0.715   0.731   0.772   0.813   0.674   0.708   0.753
39    D         0.654   0.682   0.715   0.731   0.772   0.813   0.674   0.708   0.753
40    K         0.654   0.682   0.715   0.301   0.358   0.468   0.674   0.708   0.753
41    Y         0.654   0.682   0.715   0.731   0.752   0.813   0.674   0.708   0.753
42    S         0.654   0.682   0.715   0.676   0.711   0.769   0.674   0.708   0.753
43    R         0.654   0.682   0.715   0.529   0.567   0.651   0.674   0.708   0.753
44    Q         0.654   0.682   0.715   0.927   1.059   0.970   0.674   0.708   0.753
45    R         0.654   0.682   0.715   0.529   0.567   0.651   0.674   0.708   0.753
46    V        -0.369  -0.721  -0.743  -0.054  -0.659  -0.743  -0.392  -0.904  -0.959
47    T         0.654   0.682   0.715   0.472   0.558   0.606   0.674   0.708   0.753
48    L         0.654   0.682   0.715   0.454   0.504   0.590   0.674   0.708   0.753
49    K         0.654   0.682   0.715   0.301   0.358   0.468   0.674   0.708   0.753
50    K         0.654   0.682   0.715   0.301   0.358   0.468   0.674   0.708   0.753
51    R         0.654   0.682   0.715   0.529   0.567   0.651   0.674   0.708   0.753
52    F        -0.837  -0.704  -0.754  -0.753  -0.549  -0.734  -1.102  -0.876  -0.977
53    G        -1.849  -1.947  -1.637  -1.760  -1.882  -1.431  -1.990  -2.005  -1.589
54    L        -0.369  -0.721  -0.743  -0.477  -0.998  -0.962  -0.392  -0.904  -0.959
55    V        -0.369  -0.226  -0.720  -0.477  -0.294  -0.930  -0.392  -0.189  -0.921
56    P        -0.369  -0.721  -0.743  -0.241  -0.841  -0.969  -0.392  -0.904  -0.959
57    G        -2.222  -1.949  -2.237  -2.180  -1.767  -2.076  -1.990  -1.645  -1.869
58    Q         0.654   0.682   0.715   0.909   0.975   0.956   0.674   0.708   0.753
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -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/Q6Q547
Output conservation file - output/Q6Q547
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
