1     M         0.674   0.674   0.682   1.525   1.522   1.474   0.688   0.688   0.695
2     G         0.674   0.674   0.682   1.092   1.090   1.074   0.688   0.688   0.695
3     K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
4     R         0.674   0.674   0.682   0.959   0.955   0.952   0.688   0.688   0.695
5     F         0.674   0.674   0.682   1.549   1.547   1.497   0.688   0.688   0.695
6     S         0.674   0.674   0.682   1.273   1.272   1.242   0.688   0.688   0.695
7     E         0.674   0.674   0.682   0.312   0.313   0.355   0.688   0.688   0.695
8     S         0.674   0.674   0.682   1.273   1.272   1.242   0.688   0.688   0.695
9     A         0.674   0.674   0.682   0.429   0.429   0.463   0.688   0.688   0.695
10    A         0.674   0.674   0.682   0.429   0.429   0.463   0.688   0.688   0.695
11    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
12    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
13    A         0.674   0.674   0.682   0.429   0.429   0.463   0.688   0.688   0.695
14    A        -1.130  -1.124  -1.178  -1.724  -1.709  -1.829  -1.217  -1.207  -1.275
15    G         0.674   0.674   0.682   1.092   1.090   1.074   0.688   0.688   0.695
16    L        -1.130  -1.106  -1.177  -0.652  -0.617  -0.744  -1.217  -1.182  -1.273
17    A         0.674   0.674   0.682   0.429   0.429   0.463   0.688   0.688   0.695
18    R         0.674   0.674   0.682   0.959   0.955   0.952   0.688   0.688   0.695
19    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
20    R         0.674   0.674   0.682   0.959   0.955   0.952   0.688   0.688   0.695
21    D        -1.130  -1.106  -1.177  -0.652  -0.599  -0.924  -1.217  -1.182  -1.273
22    Q         0.674   0.674   0.682   1.196   1.192   1.171   0.688   0.688   0.695
23    A         0.674   0.674   0.682   0.429   0.429   0.463   0.688   0.688   0.695
24    H        -1.130  -1.155  -1.181  -0.097  -0.134  -0.229  -1.217  -1.253  -1.279
25    A        -1.130  -1.106  -1.177  -1.093  -1.069  -1.016  -1.217  -1.182  -1.273
26    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
27    Q        -2.440  -2.437  -2.294  -2.032  -2.031  -1.810  -2.170  -2.165  -1.965
28    R        -1.130  -1.106  -1.177  -0.795  -0.764  -0.859  -1.217  -1.182  -1.273
29    A         0.674   0.674   0.682   0.429   0.429   0.463   0.688   0.688   0.695
30    Q        -1.130  -1.155  -1.181  -1.384  -1.413  -1.330  -1.217  -1.253  -1.279
31    M        -2.440  -2.437  -2.294  -1.739  -1.726  -1.540  -2.170  -2.165  -1.965
32    E        -1.130  -1.106  -1.177  -1.784  -1.736  -1.846  -1.217  -1.182  -1.273
33    Q        -2.440  -2.437  -2.294  -2.349  -2.329  -2.102  -2.170  -2.165  -1.965
34    L        -2.440  -2.437  -2.294  -1.937  -1.935  -1.722  -2.170  -2.165  -1.965
35    E         0.674   0.674   0.682   0.312   0.313   0.355   0.688   0.688   0.695
36    A         0.674   0.674   0.682   0.429   0.429   0.463   0.688   0.688   0.695
37    E         0.674   0.674   0.682   0.312   0.313   0.355   0.688   0.688   0.695
38    E         0.674   0.674   0.682   0.312   0.313   0.355   0.688   0.688   0.695
39    A         0.674   0.674   0.682   0.429   0.429   0.463   0.688   0.688   0.695
40    S        -1.130  -1.106  -1.177  -0.843  -0.792  -1.061  -1.217  -1.182  -1.273
41    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
42    W         0.674   0.674   0.682   1.549   1.547   1.497   0.688   0.688   0.695
43    E         0.674   0.674   0.682   0.312   0.313   0.355   0.688   0.688   0.695
44    Q        -1.130  -1.124  -1.178  -0.434  -0.429  -0.500  -1.217  -1.207  -1.275
45    G         0.674   0.674   0.682   1.092   1.090   1.074   0.688   0.688   0.695
46    S        -1.130  -1.124  -1.178  -0.843  -0.829  -1.066  -1.217  -1.207  -1.275
47    R        -1.130  -1.124  -1.178  -1.263  -1.249  -1.475  -1.217  -1.207  -1.275
48    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
49    E        -1.130  -1.124  -1.178  -1.183  -1.176  -1.079  -1.217  -1.207  -1.275
50    N        -1.130  -1.124  -1.178  -0.214  -0.205  -0.376  -1.217  -1.207  -1.275
51    A        -2.440  -2.437  -2.294  -1.890  -1.912  -1.679  -2.170  -2.165  -1.965
52    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
53    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
54    L         0.674   0.674   0.682   1.118   1.117   1.099   0.688   0.688   0.695
55    E        -1.130  -1.155  -1.181  -1.042  -1.100  -1.267  -1.217  -1.253  -1.279
56    E         0.674   0.674   0.682   0.312   0.313   0.355   0.688   0.688   0.695
57    E         0.674   0.674   0.682   0.312   0.313   0.355   0.688   0.688   0.695
58    Q         0.674   0.674   0.682   1.196   1.192   1.171   0.688   0.688   0.695
59    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
60    R        -1.130  -1.155  -1.181  -1.651  -1.684  -1.604  -1.217  -1.253  -1.279
61    Q        -1.130  -1.124  -1.178  -0.967  -0.954  -1.193  -1.217  -1.207  -1.275
62    E         0.674   0.674   0.682   0.312   0.313   0.355   0.688   0.688   0.695
63    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
64    A        -1.130  -1.155  -1.181  -0.992  -1.048  -1.199  -1.217  -1.253  -1.279
65    R         0.674   0.674   0.682   0.959   0.955   0.952   0.688   0.688   0.695
66    A         0.674   0.674   0.682   0.429   0.429   0.463   0.688   0.688   0.695
67    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
68    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
69    E         0.674   0.674   0.682   0.312   0.313   0.355   0.688   0.688   0.695
70    R         0.674   0.674   0.682   0.959   0.955   0.952   0.688   0.688   0.695
71    D        -1.130  -1.155  -1.181  -1.210  -1.230  -1.109  -1.217  -1.253  -1.279
72    A         0.674   0.674   0.682   0.429   0.429   0.463   0.688   0.688   0.695
73    L         0.674   0.674   0.682   1.118   1.117   1.099   0.688   0.688   0.695
74    L         0.674   0.674   0.682   1.118   1.117   1.099   0.688   0.688   0.695
75    T        -1.130  -1.155  -1.181  -1.080  -1.102  -0.996  -1.217  -1.253  -1.279
76    A        -1.130  -1.155  -1.181  -1.784  -1.832  -1.854  -1.217  -1.253  -1.279
77    E         0.674   0.674   0.682   0.312   0.313   0.355   0.688   0.688   0.695
78    E         0.674   0.674   0.682   0.312   0.313   0.355   0.688   0.688   0.695
79    E        -1.130  -1.155  -1.181  -1.724  -1.777  -1.835  -1.217  -1.253  -1.279
80    Q        -1.130  -1.155  -1.181  -0.514  -0.556  -0.639  -1.217  -1.253  -1.279
81    L         0.674   0.674   0.682   1.118   1.117   1.099   0.688   0.688   0.695
82    G         0.674   0.674   0.682   1.092   1.090   1.074   0.688   0.688   0.695
83    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
84    G         0.674   0.674   0.682   1.092   1.090   1.074   0.688   0.688   0.695
85    G         0.674   0.674   0.682   1.092   1.090   1.074   0.688   0.688   0.695
86    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
87    G         0.674   0.674   0.682   1.092   1.090   1.074   0.688   0.688   0.695
88    K         0.674   0.674   0.682   0.162   0.164   0.216   0.688   0.688   0.695
89    R        -1.130  -1.106  -1.177  -1.263  -1.209  -1.470  -1.217  -1.182  -1.273
90    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    K        -1.130  -1.124  -1.178  -1.651  -1.641  -1.604  -1.217  -1.207  -1.275
* 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/Q3E772
Output conservation file - output/Q3E772
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
