1     M         1.161   1.165   1.214   1.417   1.425   1.485   1.241   1.247   1.315
2     R         0.197   0.163   0.027   0.474   0.427   0.225   0.129   0.076  -0.159
3     P         0.197   0.169   0.027   0.330   0.287   0.009   0.129   0.085  -0.159
4     A        -0.135  -0.107  -0.067  -0.359  -0.295  -0.261  -0.427  -0.376  -0.323
5     Q        -0.135  -0.151  -0.080   0.032  -0.002   0.092  -0.427  -0.455  -0.346
6     L        -1.405  -1.441  -1.372  -1.535  -1.565  -1.391  -1.262  -1.296  -1.179
7     L         0.197   0.191   0.027  -0.121  -0.130  -0.357   0.129   0.119  -0.159
8     L         0.197   0.258   0.038  -0.069   0.011  -0.252   0.129   0.223  -0.140
9     N         1.161   1.165   1.214   1.303   1.303   1.376   1.241   1.247   1.315
10    T        -1.405  -1.426  -1.366  -1.425  -1.447  -1.333  -1.262  -1.281  -1.173
11    A         1.161   1.165   1.214   1.036   1.041   1.120   1.241   1.247   1.315
12    K         1.161   1.165   1.214   1.036   1.044   1.120   1.241   1.247   1.315
13    K         0.197   0.163   0.027   0.132   0.084  -0.113   0.129   0.076  -0.159
14    T        -1.405  -1.415  -1.358  -1.387  -1.404  -1.331  -1.262  -1.270  -1.166
15    S         0.197   0.163   0.027   0.258   0.208  -0.057   0.129   0.076  -0.159
16    G        -0.955  -0.950  -0.849  -0.765  -0.762  -0.608  -1.076  -1.068  -0.916
17    G        -0.670  -0.721  -0.786  -0.585  -0.675  -0.859  -0.705  -0.771  -0.838
18    Y        -1.939  -1.936  -1.808  -1.983  -2.006  -1.777  -1.540  -1.535  -1.362
19    K        -1.405  -1.441  -1.372  -1.438  -1.483  -1.353  -1.262  -1.296  -1.179
20    I        -1.405  -1.426  -1.366  -1.308  -1.353  -1.254  -1.262  -1.281  -1.173
21    P         1.161   1.165   1.214   1.303   1.311   1.376   1.241   1.247   1.315
22    V        -0.135  -0.126  -0.076  -0.118  -0.108  -0.021  -0.427  -0.411  -0.337
23    E         1.161   1.165   1.214   1.274   1.277   1.348   1.241   1.247   1.315
24    L         0.197   0.169   0.027  -0.069  -0.103  -0.267   0.129   0.085  -0.159
25    T        -0.670  -0.646  -0.761  -0.567  -0.521  -0.726  -0.705  -0.675  -0.806
26    P         1.161   1.165   1.214   1.303   1.311   1.376   1.241   1.247   1.315
27    L         1.161   1.165   1.214   0.802   0.810   0.895   1.241   1.247   1.315
28    F         1.161   1.165   1.214   1.288   1.292   1.362   1.241   1.247   1.315
29    L        -0.135  -0.129  -0.075  -0.672  -0.659  -0.587  -0.427  -0.416  -0.335
30    A         1.161   1.165   1.214   1.036   1.041   1.120   1.241   1.247   1.315
31    V        -0.871  -0.839  -0.817  -0.701  -0.666  -0.602  -0.983  -0.949  -0.880
32    G         1.161   1.165   1.214   1.332   1.343   1.404   1.241   1.247   1.315
33    V         1.161   1.165   1.214   1.230   1.232   1.306   1.241   1.247   1.315
34    A         1.161   1.165   1.214   1.036   1.041   1.120   1.241   1.247   1.315
35    L         0.197   0.169   0.027  -0.121  -0.161  -0.357   0.129   0.085  -0.159
36    C        -0.871  -0.885  -0.822  -0.839  -0.879  -0.778  -0.983  -0.996  -0.885
37    S         1.161   1.165   1.214   1.230   1.240   1.306   1.241   1.247   1.315
38    G         0.197   0.163   0.027   0.359   0.309   0.035   0.129   0.076  -0.159
39    T         0.197   0.169   0.027   0.376   0.343   0.150   0.129   0.085  -0.159
40    Y        -0.670  -0.657  -0.773  -0.366  -0.351  -0.495  -0.705  -0.687  -0.821
41    F         1.161   1.165   1.214   1.288   1.292   1.362   1.241   1.247   1.315
42    T         0.197   0.191   0.027   0.305   0.299   0.026   0.129   0.119  -0.159
43    Y         1.161   1.165   1.214   1.403   1.410   1.472   1.241   1.247   1.315
44    K        -0.135  -0.151  -0.080  -0.346  -0.367  -0.242  -0.427  -0.455  -0.346
45    K        -0.135  -0.151  -0.080  -0.253  -0.267  -0.139  -0.427  -0.455  -0.346
46    L        -0.135  -0.107  -0.067  -0.438  -0.364  -0.348  -0.427  -0.376  -0.323
47    R        -1.405  -1.413  -1.358  -1.314  -1.334  -1.248  -1.262  -1.267  -1.166
48    T        -0.871  -0.857  -0.818  -0.607  -0.585  -0.539  -0.983  -0.967  -0.881
49    D         1.161   1.165   1.214   1.317   1.329   1.390   1.241   1.247   1.315
50    E        -0.871  -0.856  -0.826  -0.967  -0.954  -0.879  -0.983  -0.965  -0.890
51    T        -0.871  -0.856  -0.826  -0.879  -0.855  -0.803  -0.983  -0.965  -0.890
52    L         1.161   1.165   1.214   0.802   0.810   0.895   1.241   1.247   1.315
53    R         1.161   1.165   1.214   1.346   1.350   1.417   1.241   1.247   1.315
54    L         0.197   0.191   0.027  -0.121  -0.130  -0.357   0.129   0.119  -0.159
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    T        -1.405  -1.366  -1.365  -1.106  -1.027  -1.095  -1.262  -1.219  -1.172
57    G        -0.670  -0.602  -0.768  -0.713  -0.611  -0.841  -0.705  -0.615  -0.815
58    N         1.161   1.165   1.214   1.303   1.303   1.376   1.241   1.247   1.315
59    P        -0.135  -0.151  -0.080  -0.295  -0.337  -0.238  -0.427  -0.455  -0.346
60    E        -0.871  -0.885  -0.822  -0.794  -0.814  -0.711  -0.983  -0.996  -0.886
61    L        -0.670  -0.629  -0.765  -0.816  -0.764  -0.860  -0.705  -0.651  -0.811
62    S         1.161   1.165   1.214   1.230   1.240   1.306   1.241   1.247   1.315
63    S        -1.939  -1.936  -1.808  -1.771  -1.772  -1.573  -1.540  -1.535  -1.362
64    L         1.161   1.165   1.214   0.802   0.810   0.895   1.241   1.247   1.315
65    D         0.197   0.163   0.027   0.408   0.362   0.134   0.129   0.076  -0.159
66    E        -1.405  -1.378  -1.353  -1.381  -1.348  -1.273  -1.262  -1.231  -1.161
67    V         1.161   1.165   1.214   1.230   1.232   1.306   1.241   1.247   1.315
68    L         1.161   1.165   1.214   0.802   0.810   0.895   1.241   1.247   1.315
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    A        -1.405  -1.366  -1.365  -1.400  -1.327  -1.370  -1.262  -1.219  -1.172
86    K        -0.670  -0.657  -0.773  -0.499  -0.477  -0.672  -0.705  -0.687  -0.821
87    D        -1.939  -1.936  -1.808  -1.878  -1.865  -1.676  -1.540  -1.535  -1.362
88    K         0.197   0.191   0.027   0.064   0.055  -0.234   0.129   0.119  -0.159
89    D        -0.871  -0.887  -0.820  -0.884  -0.911  -0.821  -0.983  -0.999  -0.883
* 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/A5Z2X5
Output conservation file - output/A5Z2X5
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
