1     M         0.863   0.894   0.939   1.218   1.225   1.234   0.864   0.912   0.978
2     E         0.863   0.894   0.939   0.850   0.901   0.971   0.864   0.912   0.978
3     N         0.863   0.894   0.939   0.816   0.888   0.947   0.864   0.912   0.978
4     D        -0.230  -0.494  -0.583  -0.216  -0.561  -0.707  -0.199  -0.566  -0.729
5     K        -2.251  -2.474  -2.198  -1.890  -2.372  -2.015  -1.869  -2.077  -1.694
6     G         0.863   0.894   0.939   0.747   0.790   0.897   0.864   0.912   0.978
7     Q        -1.271  -1.345  -1.514  -0.893  -1.074  -1.388  -1.110  -1.207  -1.361
8     L        -0.230  -0.445  -0.583  -0.189  -0.460  -0.709  -0.199  -0.495  -0.729
9     V         0.863   0.894   0.939   0.770   0.830   0.914   0.864   0.912   0.978
10    E        -0.768  -0.914  -0.634  -0.875  -1.220  -0.787  -0.958  -1.211  -0.809
11    L         0.863   0.894   0.939   0.747   0.827   0.897   0.864   0.912   0.978
12    Y         0.863   0.894   0.939   0.986   1.048   1.068   0.864   0.912   0.978
13    V        -0.230   0.063  -0.558  -0.166   0.182  -0.651  -0.199   0.166  -0.690
14    P         0.863   0.894   0.939   1.175   1.187   1.203   0.864   0.912   0.978
15    R         0.863   0.894   0.939   0.700   0.766   0.864   0.864   0.912   0.978
16    K         0.863   0.894   0.939   0.896   0.950   1.004   0.864   0.912   0.978
17    C         0.863   0.894   0.939   1.197   1.191   1.218   0.864   0.912   0.978
18    S         0.863   0.894   0.939   0.712   0.792   0.872   0.864   0.912   0.978
19    A         0.863   0.894   0.939   0.642   0.724   0.822   0.864   0.912   0.978
20    T         0.863   0.894   0.939   1.098   1.101   1.148   0.864   0.912   0.978
21    N        -0.230  -0.445  -0.583  -0.127  -0.410  -0.685  -0.199  -0.495  -0.729
22    R         0.863   0.894   0.939   0.700   0.766   0.864   0.864   0.912   0.978
23    I         0.863   0.894   0.939   0.793   0.829   0.930   0.864   0.912   0.978
24    I        -0.230  -0.025  -0.560  -0.081   0.134  -0.478  -0.199   0.060  -0.694
25    K        -0.230  -0.494  -0.583  -0.016  -0.371  -0.549  -0.199  -0.566  -0.729
26    A        -0.230  -0.445  -0.583  -0.307  -0.572  -0.808  -0.199  -0.495  -0.729
27    D        -1.056  -0.723  -0.609  -1.365  -0.806  -0.701  -1.414  -0.909  -0.770
28    D         0.863   0.894   0.939   0.712   0.780   0.872   0.864   0.912   0.978
29    H         0.863   0.894   0.939   1.240   1.249   1.249   0.864   0.912   0.978
30    A        -1.963  -1.870  -1.535  -2.372  -2.185  -1.664  -2.021  -1.823  -1.384
31    S         0.863   0.894   0.939   0.712   0.792   0.872   0.864   0.912   0.978
32    V        -0.230  -0.445  -0.583  -0.107  -0.365  -0.530  -0.199  -0.495  -0.729
33    Q         0.863   0.894   0.939   0.964   0.984   1.052   0.864   0.912   0.978
34    I         0.863   0.894   0.939   0.793   0.829   0.930   0.864   0.912   0.978
35    N        -1.271  -1.193  -1.509  -1.008  -0.933  -1.389  -1.110  -1.052  -1.355
36    V        -1.056  -0.914  -0.634  -1.426  -1.251  -0.785  -1.414  -1.212  -0.809
37    A        -0.230  -0.494  -0.583  -0.234  -0.533  -0.607  -0.199  -0.566  -0.729
38    K        -2.251  -2.021  -2.174  -1.868  -1.702  -1.933  -1.869  -1.651  -1.675
39    V         0.863   0.894   0.939   0.770   0.830   0.914   0.864   0.912   0.978
40    D         0.863   0.894   0.939   0.712   0.780   0.872   0.864   0.912   0.978
41    E        -0.230  -0.494  -0.583  -0.107  -0.489  -0.705  -0.199  -0.566  -0.729
42    E        -1.748  -1.485  -1.530  -1.735  -1.469  -1.512  -1.717  -1.456  -1.380
43    G         0.863   0.894   0.939   0.747   0.790   0.897   0.864   0.912   0.978
44    R         0.863   0.894   0.939   0.700   0.766   0.864   0.864   0.912   0.978
45    A        -0.230  -0.494  -0.583  -0.270  -0.592  -0.704  -0.199  -0.566  -0.729
46    I         0.863   0.894   0.939   0.793   0.829   0.930   0.864   0.912   0.978
47    P        -1.748  -1.669  -1.529  -1.445  -1.360  -1.318  -1.717  -1.574  -1.377
48    G         0.863   0.894   0.939   0.747   0.790   0.897   0.864   0.912   0.978
49    E        -0.768  -0.540  -0.606  -0.875  -0.546  -0.721  -0.958  -0.633  -0.765
50    Y        -1.963  -1.823  -1.526  -2.023  -1.773  -1.386  -2.021  -1.760  -1.374
51    V        -2.153  -1.791  -1.540  -2.273  -1.795  -1.409  -2.173  -1.746  -1.390
52    T        -0.230  -0.445  -0.583   0.161  -0.191  -0.492  -0.199  -0.495  -0.729
53    Y         0.863   0.894   0.939   0.986   1.048   1.068   0.864   0.912   0.978
54    A         0.863   0.894   0.939   0.642   0.724   0.822   0.864   0.912   0.978
55    L        -0.230  -0.494  -0.583  -0.189  -0.533  -0.709  -0.199  -0.566  -0.729
56    S        -0.230  -0.025  -0.560  -0.165   0.092  -0.536  -0.199   0.060  -0.694
57    G         0.863   0.894   0.939   0.747   0.790   0.897   0.864   0.912   0.978
58    Y        -1.748  -1.601  -1.535  -1.404  -1.276  -1.186  -1.717  -1.613  -1.385
59    V        -0.768  -0.419  -0.584  -0.927  -0.421  -0.696  -0.958  -0.459  -0.731
60    R         0.863   0.894   0.939   0.700   0.766   0.864   0.864   0.912   0.978
61    S        -2.276  -1.910  -1.545  -2.808  -2.255  -1.677  -2.325  -1.877  -1.395
62    R        -1.271  -1.685  -1.535  -1.071  -1.620  -1.366  -1.110  -1.592  -1.383
63    G        -0.230  -0.083  -0.562  -0.211  -0.038  -0.730  -0.199  -0.012  -0.697
64    E         0.863   0.894   0.939   0.850   0.901   0.971   0.864   0.912   0.978
65    S        -1.148  -0.902  -0.625  -1.768  -1.322  -0.876  -1.565  -1.192  -0.795
66    D         0.863   0.894   0.939   0.712   0.780   0.872   0.864   0.912   0.978
67    D         0.863   0.894   0.939   0.712   0.780   0.872   0.864   0.912   0.978
68    S        -0.230  -0.494  -0.583  -0.165  -0.468  -0.565  -0.199  -0.566  -0.729
69    L        -0.230  -0.494  -0.583  -0.189  -0.533  -0.709  -0.199  -0.566  -0.729
70    N         0.863   0.894   0.939   0.816   0.888   0.947   0.864   0.912   0.978
71    R         0.863   0.894   0.939   0.700   0.766   0.864   0.864   0.912   0.978
72    L         0.863   0.894   0.939   0.747   0.827   0.897   0.864   0.912   0.978
73    A        -0.768  -0.805  -0.632  -0.949  -1.011  -0.697  -0.958  -1.036  -0.805
74    Q        -0.230  -0.494  -0.583   0.071  -0.307  -0.454  -0.199  -0.566  -0.729
75    N        -1.748  -1.566  -1.517  -1.629  -1.406  -1.429  -1.717  -1.452  -1.363
76    D         0.863   0.894   0.939   0.712   0.780   0.872   0.864   0.912   0.978
77    G         0.863   0.894   0.939   0.747   0.790   0.897   0.864   0.912   0.978
78    L        -0.230  -0.083  -0.562  -0.189   0.015  -0.672  -0.199  -0.012  -0.697
79    L         0.863   0.894   0.939   0.747   0.827   0.897   0.864   0.912   0.978
80    K        -0.230  -0.494  -0.583  -0.032  -0.394  -0.594  -0.199  -0.566  -0.729
81    N        -1.271  -1.685  -1.535  -1.079  -1.727  -1.596  -1.110  -1.592  -1.383
82    V         0.863   0.894   0.939   0.770   0.830   0.914   0.864   0.912   0.978
83    W         0.863   0.894   0.939   1.240   1.249   1.249   0.864   0.912   0.978
84    S        -0.230  -0.445  -0.583  -0.221  -0.481  -0.721  -0.199  -0.495  -0.729
85    Y        -0.230  -0.445  -0.583   0.104  -0.155  -0.410  -0.199  -0.495  -0.729
86    S        -0.768  -0.914  -0.634  -0.927  -1.188  -0.722  -0.958  -1.211  -0.809
87    R         0.863   0.894   0.939   0.700   0.766   0.864   0.864   0.912   0.978
* 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/P0C0V8
Output conservation file - output/P0C0V8
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
