1     M         1.287   1.333   1.371   1.421   1.474   1.542   1.348   1.414   1.471
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    T        -1.274  -1.221  -1.084  -1.108  -1.063  -0.867  -1.186  -1.112  -0.958
19    E        -0.829  -0.763  -0.702  -0.800  -0.727  -0.646  -0.940  -0.851  -0.765
20    T        -0.829  -0.765  -0.709  -0.777  -0.695  -0.614  -0.940  -0.853  -0.771
21    D        -1.179  -1.026  -1.047  -1.144  -0.952  -0.982  -1.108  -0.947  -0.927
22    K        -1.060  -0.859  -0.998  -0.919  -0.612  -0.903  -0.979  -0.750  -0.879
23    K        -1.091  -1.021  -1.018  -1.371  -1.278  -1.264  -1.027  -0.931  -0.900
24    Q        -1.746  -1.682  -1.583  -1.312  -1.230  -1.143  -1.324  -1.251  -1.122
25    E        -1.195  -1.073  -1.057  -1.506  -1.268  -1.265  -1.126  -0.991  -0.936
26    Q        -1.091  -1.119  -1.041  -1.096  -1.148  -1.074  -1.027  -1.029  -0.922
27    E        -1.366  -1.420  -1.334  -1.334  -1.378  -1.287  -1.126  -1.153  -1.038
28    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    C        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    E        -0.421  -0.375  -0.601  -0.399  -0.333  -0.643  -0.434  -0.373  -0.645
34    D        -1.091  -1.166  -1.055  -0.949  -1.106  -0.950  -1.027  -1.064  -0.934
35    K         1.287   1.333   1.371   0.923   1.011   1.067   1.348   1.414   1.471
36    P         1.287   1.333   1.371   1.314   1.354   1.439   1.348   1.414   1.471
37    K         1.287   1.333   1.371   0.923   1.011   1.067   1.348   1.414   1.471
38    P         1.287   1.333   1.371   1.314   1.354   1.439   1.348   1.414   1.471
39    C         1.287   1.333   1.371   1.147   1.208   1.280   1.348   1.414   1.471
40    C         1.287   1.333   1.371   1.147   1.208   1.280   1.348   1.414   1.471
41    V         0.687   0.547   0.478   0.950   0.752   0.642   0.655   0.421   0.268
42    C         1.287   1.333   1.371   1.147   1.208   1.280   1.348   1.414   1.471
43    K        -0.643  -0.680  -0.658  -0.826  -0.846  -0.791  -0.731  -0.743  -0.714
44    P        -0.435  -0.324  -0.279  -0.684  -0.536  -0.476  -0.731  -0.570  -0.518
45    E         0.687   0.547   0.478   0.591   0.438   0.326   0.655   0.421   0.268
46    K         0.687   0.697   0.494   0.439   0.486   0.231   0.655   0.667   0.297
47    E        -0.815  -0.858  -0.723  -1.133  -1.133  -0.959  -0.929  -0.944  -0.787
48    E        -0.264  -0.163  -0.232  -0.557  -0.445  -0.556  -0.533  -0.414  -0.465
49    R         1.287   1.333   1.371   1.491   1.548   1.609   1.348   1.414   1.471
50    D         1.287   1.333   1.371   1.323   1.394   1.448   1.348   1.414   1.471
51    T        -0.919  -0.950  -1.006  -0.820  -0.877  -0.912  -0.830  -0.861  -0.887
52    C         1.287   1.333   1.371   1.147   1.208   1.280   1.348   1.414   1.471
53    I        -0.643  -0.634  -0.691  -0.374  -0.389  -0.448  -0.731  -0.734  -0.754
54    L         1.287   1.333   1.371   1.395   1.469   1.516   1.348   1.414   1.471
55    F         0.687   0.547   0.478   0.925   0.757   0.634   0.655   0.421   0.268
56    N        -0.643  -0.639  -0.685  -0.488  -0.571  -0.665  -0.731  -0.739  -0.747
57    G         0.116  -0.096  -0.181   0.268  -0.048  -0.277   0.061  -0.238  -0.378
58    Q        -0.919  -1.065  -1.045  -0.474  -0.699  -0.674  -0.830  -0.968  -0.923
59    D        -0.264  -0.341  -0.246  -0.472  -0.521  -0.399  -0.533  -0.604  -0.481
60    S         0.116  -0.096  -0.181   0.265  -0.063  -0.179   0.061  -0.238  -0.378
61    E        -1.470  -1.463  -1.340  -1.335  -1.303  -1.155  -1.225  -1.189  -1.044
62    K        -0.146  -0.269  -0.254  -0.535  -0.700  -0.672  -0.335  -0.509  -0.490
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     *
65    C         1.287   1.333   1.371   1.147   1.208   1.280   1.348   1.414   1.471
66    K        -0.643  -0.724  -0.674  -0.847  -0.910  -0.818  -0.731  -0.791  -0.732
67    E        -1.091  -1.081  -1.051  -1.266  -1.318  -1.222  -1.027  -1.006  -0.931
68    F        -0.421  -0.418  -0.620  -0.055  -0.044  -0.342  -0.434  -0.426  -0.667
69    I         1.287   1.333   1.371   1.430   1.485   1.550   1.348   1.414   1.471
70    E        -1.091  -1.046  -1.033  -1.088  -1.022  -0.971  -1.027  -0.956  -0.915
71    K        -0.368  -0.408  -0.304  -0.687  -0.705  -0.507  -0.632  -0.685  -0.552
72    Y         0.687   0.547   0.478   0.979   0.816   0.712   0.655   0.421   0.268
73    K         0.116   0.034  -0.156  -0.045  -0.109  -0.349   0.061  -0.051  -0.342
74    E        -1.195  -1.169  -1.056  -1.328  -1.379  -1.149  -1.126  -1.077  -0.936
75    C         1.287   1.333   1.371   1.147   1.208   1.280   1.348   1.414   1.471
76    M         1.287   1.333   1.371   1.421   1.474   1.542   1.348   1.414   1.471
77    K         0.392   0.295   0.335   0.020  -0.128  -0.047   0.160  -0.039  -0.005
78    G        -0.421  -0.489  -0.615  -0.127  -0.224  -0.421  -0.434  -0.520  -0.661
79    Y         0.392   0.389   0.358   0.559   0.550   0.458   0.160   0.140   0.039
80    G         1.287   1.333   1.371   1.350   1.427   1.474   1.348   1.414   1.471
81    F         0.687   0.547   0.478   0.930   0.768   0.646   0.655   0.421   0.268
82    E        -0.919  -0.899  -0.992  -0.912  -0.894  -1.037  -0.830  -0.795  -0.874
83    V        -0.643  -0.507  -0.640  -0.342  -0.167  -0.362  -0.731  -0.553  -0.695
84    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    N        -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/Q12287
Output conservation file - output/Q12287
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
