1     M         0.686   0.690   0.714   1.003   0.976   0.968   0.698   0.707   0.739
2     V         0.686   0.690   0.714   0.535   0.543   0.619   0.698   0.707   0.739
3     L         0.686   0.690   0.714   0.464   0.497   0.566   0.698   0.707   0.739
4     V        -1.529  -1.579  -1.594  -1.633  -1.776  -1.788  -1.491  -1.601  -1.544
5     Q        -1.529  -1.744  -1.594  -1.392  -1.824  -1.651  -1.491  -1.767  -1.544
6     D         0.686   0.690   0.714   0.966   0.956   0.940   0.698   0.707   0.739
7     L         0.686   0.690   0.714   0.464   0.497   0.566   0.698   0.707   0.739
8     L         0.686   0.690   0.714   0.464   0.497   0.566   0.698   0.707   0.739
9     H        -1.107  -1.027  -0.751  -1.032  -0.952  -0.563  -1.491  -1.389  -0.984
10    P         0.686   0.690   0.714   0.783   0.780   0.804   0.698   0.707   0.739
11    T        -0.975  -0.706  -0.713  -1.438  -0.948  -1.017  -1.272  -0.870  -0.924
12    A        -1.759  -1.691  -1.581  -1.717  -1.567  -1.424  -1.819  -1.684  -1.529
13    A        -1.098  -1.231  -1.569  -0.750  -0.931  -1.399  -0.944  -1.123  -1.516
14    S        -0.696  -0.700  -0.731  -0.918  -0.937  -1.057  -0.834  -0.861  -0.953
15    E         0.686   0.690   0.714   0.947   0.937   0.926   0.698   0.707   0.739
16    A        -1.098  -1.420  -1.576  -0.740  -1.161  -1.382  -0.944  -1.341  -1.524
17    R        -1.529  -1.387  -1.585  -1.295  -1.170  -1.503  -1.491  -1.358  -1.534
18    K        -1.098  -1.109  -1.569  -0.944  -0.996  -1.626  -0.944  -0.983  -1.516
19    H         0.686   0.690   0.714   0.928   0.922   0.912   0.698   0.707   0.739
20    K         0.686   0.690   0.714   0.575   0.591   0.649   0.698   0.707   0.739
21    L         0.686   0.690   0.714   0.464   0.497   0.566   0.698   0.707   0.739
22    K         0.686   0.690   0.714   0.575   0.591   0.649   0.698   0.707   0.739
23    T        -0.224  -0.427  -0.704  -0.345  -0.555  -0.925  -0.178  -0.459  -0.909
24    L         0.686   0.690   0.714   0.464   0.497   0.566   0.698   0.707   0.739
25    V         0.686   0.690   0.714   0.535   0.543   0.619   0.698   0.707   0.739
26    Q        -0.696  -0.688  -0.727  -0.569  -0.594  -0.718  -0.834  -0.843  -0.947
27    G        -3.288  -3.132  -2.678  -3.040  -2.874  -2.262  -2.695  -2.543  -2.013
28    P         0.686   0.690   0.714   0.783   0.780   0.804   0.698   0.707   0.739
29    R         0.686   0.690   0.714   0.822   0.814   0.833   0.698   0.707   0.739
30    S         0.686   0.690   0.714   0.565   0.585   0.642   0.698   0.707   0.739
31    Y        -1.759  -1.519  -1.588  -1.450  -1.202  -1.229  -1.819  -1.556  -1.538
32    F         0.686   0.690   0.714   0.841   0.829   0.847   0.698   0.707   0.739
33    L        -0.975  -0.706  -0.713  -0.999  -0.553  -0.703  -1.272  -0.870  -0.924
34    D         0.686   0.690   0.714   0.966   0.956   0.940   0.698   0.707   0.739
35    V         0.686   0.690   0.714   0.535   0.543   0.619   0.698   0.707   0.739
36    K         0.686   0.690   0.714   0.575   0.591   0.649   0.698   0.707   0.739
37    C         0.686   0.690   0.714   0.675   0.675   0.723   0.698   0.707   0.739
38    P        -0.975  -0.893  -0.741  -1.047  -0.956  -0.746  -1.272  -1.166  -0.969
39    G         0.686   0.690   0.714   0.773   0.766   0.797   0.698   0.707   0.739
40    C         0.686   0.690   0.714   0.675   0.675   0.723   0.698   0.707   0.739
41    L        -1.529  -1.579  -1.594  -1.551  -1.669  -1.503  -1.491  -1.601  -1.544
42    N        -0.224  -0.291  -0.698   0.245   0.124  -0.667  -0.178  -0.273  -0.900
43    I         0.686   0.690   0.714   1.050   1.030   1.003   0.698   0.707   0.739
44    T         0.686   0.690   0.714   0.402   0.460   0.520   0.698   0.707   0.739
45    T         0.686   0.690   0.714   0.402   0.460   0.520   0.698   0.707   0.739
46    V         0.686   0.690   0.714   0.535   0.543   0.619   0.698   0.707   0.739
47    F         0.686   0.690   0.714   0.841   0.829   0.847   0.698   0.707   0.739
48    S         0.686   0.690   0.714   0.565   0.585   0.642   0.698   0.707   0.739
49    H         0.686   0.690   0.714   0.928   0.922   0.912   0.698   0.707   0.739
50    A         0.686   0.690   0.714   0.714   0.731   0.753   0.698   0.707   0.739
51    Q         0.686   0.690   0.714   0.812   0.813   0.826   0.698   0.707   0.739
52    T         0.686   0.690   0.714   0.402   0.460   0.520   0.698   0.707   0.739
53    A        -0.975  -0.988  -0.750  -1.236  -1.330  -0.945  -1.272  -1.323  -0.983
54    V         0.686   0.690   0.714   0.535   0.543   0.619   0.698   0.707   0.739
55    T        -1.529  -1.744  -1.594  -1.620  -1.894  -1.629  -1.491  -1.767  -1.544
56    C         0.686   0.690   0.714   0.675   0.675   0.723   0.698   0.707   0.739
57    E        -2.735  -2.629  -2.211  -2.412  -2.339  -1.783  -2.476  -2.347  -1.843
58    S        -1.098  -1.300  -1.571  -0.889  -1.145  -1.461  -0.944  -1.196  -1.518
59    C         0.686   0.690   0.714   0.675   0.675   0.723   0.698   0.707   0.739
60    S        -1.098  -1.343  -1.576  -0.991  -1.331  -1.749  -0.944  -1.250  -1.524
61    T        -0.224  -0.427  -0.704  -0.377  -0.603  -1.035  -0.178  -0.459  -0.909
62    V         0.686   0.690   0.714   0.535   0.543   0.619   0.698   0.707   0.739
63    L         0.686   0.690   0.714   0.464   0.497   0.566   0.698   0.707   0.739
64    C         0.686   0.690   0.714   0.675   0.675   0.723   0.698   0.707   0.739
65    T        -1.759  -1.830  -1.598  -2.038  -2.075  -1.676  -1.819  -1.887  -1.549
66    P         0.686   0.690   0.714   0.783   0.780   0.804   0.698   0.707   0.739
67    T        -0.224  -0.049  -0.693  -0.377  -0.131  -1.015  -0.178   0.033  -0.891
68    G         0.686   0.690   0.714   0.773   0.766   0.797   0.698   0.707   0.739
69    G         0.686   0.690   0.714   0.773   0.766   0.797   0.698   0.707   0.739
70    K         0.686   0.690   0.714   0.575   0.591   0.649   0.698   0.707   0.739
71    A         0.686   0.690   0.714   0.714   0.731   0.753   0.698   0.707   0.739
72    K        -0.975  -0.988  -0.750  -1.232  -1.287  -0.871  -1.272  -1.323  -0.983
73    L         0.686   0.690   0.714   0.464   0.497   0.566   0.698   0.707   0.739
74    S        -1.759  -1.691  -1.581  -2.121  -1.907  -1.661  -1.819  -1.684  -1.529
75    E         0.686   0.690   0.714   0.947   0.937   0.926   0.698   0.707   0.739
76    G         0.686   0.690   0.714   0.773   0.766   0.797   0.698   0.707   0.739
77    T        -0.975  -0.706  -0.713  -1.334  -0.859  -0.944  -1.272  -0.870  -0.924
78    S         0.686   0.690   0.714   0.565   0.585   0.642   0.698   0.707   0.739
79    F         0.686   0.690   0.714   0.841   0.829   0.847   0.698   0.707   0.739
80    R         0.686   0.690   0.714   0.822   0.814   0.833   0.698   0.707   0.739
81    R        -0.224  -0.379  -0.706   0.046  -0.180  -0.759  -0.178  -0.392  -0.912
82    K         0.686   0.690   0.714   0.575   0.591   0.649   0.698   0.707   0.739
83    -        -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/P38711
Output conservation file - output/P38711
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
