1     M         1.297   1.323   1.407   1.454   1.496   1.606   1.374   1.411   1.534
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     V         1.297   1.323   1.407   1.093   1.147   1.270   1.374   1.411   1.534
4     T        -1.221  -1.145  -0.974  -1.363  -1.205  -0.984  -1.257  -1.164  -0.944
5     Q        -0.653  -0.745  -0.869  -0.394  -0.532  -0.844  -0.599  -0.711  -0.831
6     F        -0.906  -0.760  -0.876  -0.907  -0.741  -0.895  -0.928  -0.779  -0.847
7     K        -0.653  -0.678  -0.846  -0.453  -0.547  -0.836  -0.599  -0.643  -0.806
8     T        -0.906  -0.936  -0.899  -0.738  -0.793  -0.748  -0.928  -0.952  -0.870
9     A        -0.906  -0.816  -0.872  -1.203  -1.003  -1.139  -0.928  -0.801  -0.839
10    S        -0.653  -0.745  -0.869  -0.389  -0.559  -0.768  -0.599  -0.711  -0.831
11    E         0.613   0.598   0.402   0.710   0.698   0.418   0.607   0.579   0.226
12    F         1.297   1.323   1.407   1.268   1.299   1.433   1.374   1.411   1.534
13    D        -1.536  -1.408  -1.324  -1.443  -1.282  -1.139  -1.366  -1.234  -1.084
14    S        -1.732  -1.757  -1.640  -1.405  -1.465  -1.329  -1.366  -1.371  -1.198
15    A        -0.039  -0.081  -0.306  -0.217  -0.264  -0.555  -0.051  -0.109  -0.430
16    I        -0.473  -0.463  -0.417  -0.578  -0.568  -0.510  -0.709  -0.681  -0.593
17    A        -1.417  -1.370  -1.310  -1.572  -1.497  -1.316  -1.257  -1.200  -1.073
18    Q        -2.166  -2.077  -1.918  -1.787  -1.682  -1.486  -1.585  -1.501  -1.289
19    D        -0.039  -0.174  -0.328   0.220   0.060  -0.146  -0.051  -0.240  -0.460
20    K        -0.653  -0.745  -0.869  -0.492  -0.613  -0.759  -0.599  -0.711  -0.831
21    L         0.613   0.483   0.386   0.721   0.552   0.400   0.607   0.399   0.197
22    V         0.613   0.598   0.402   0.515   0.516   0.251   0.607   0.579   0.226
23    V         0.613   0.615   0.405   0.510   0.533   0.243   0.607   0.606   0.231
24    V        -0.039  -0.189  -0.331  -0.066  -0.254  -0.463  -0.051  -0.260  -0.465
25    D         1.297   1.323   1.407   1.323   1.363   1.484   1.374   1.411   1.534
26    F         0.613   0.483   0.386   0.633   0.436   0.240   0.607   0.399   0.197
27    Y         0.276   0.354   0.286   0.279   0.382   0.289   0.059   0.183   0.014
28    A         1.297   1.323   1.407   0.944   0.989   1.132   1.374   1.411   1.534
29    T         1.297   1.323   1.407   1.353   1.379   1.512   1.374   1.411   1.534
30    W         1.297   1.323   1.407   1.554   1.585   1.698   1.374   1.411   1.534
31    C         1.297   1.323   1.407   1.501   1.534   1.649   1.374   1.411   1.534
32    G         1.297   1.323   1.407   1.413   1.447   1.567   1.374   1.411   1.534
33    P         1.297   1.323   1.407   1.389   1.421   1.545   1.374   1.411   1.534
34    C         1.297   1.323   1.407   1.501   1.534   1.649   1.374   1.411   1.534
35    K         1.297   1.323   1.407   1.175   1.221   1.347   1.374   1.411   1.534
36    M         0.276   0.197   0.250   0.281   0.097   0.091   0.059  -0.096  -0.053
37    I         1.297   1.323   1.407   1.317   1.348   1.478   1.374   1.411   1.534
38    A         1.297   1.323   1.407   0.944   0.989   1.132   1.374   1.411   1.534
39    P         1.297   1.323   1.407   1.389   1.421   1.545   1.374   1.411   1.534
40    M        -1.102  -1.095  -0.955  -1.009  -1.032  -0.841  -1.147  -1.122  -0.927
41    I        -1.102  -1.070  -0.939  -1.182  -1.163  -0.971  -1.147  -1.091  -0.911
42    E        -0.338  -0.437  -0.402  -0.370  -0.544  -0.540  -0.489  -0.611  -0.570
43    K         0.613   0.587   0.405   0.608   0.591   0.353   0.607   0.563   0.231
44    F         0.613   0.483   0.386   0.720   0.563   0.451   0.607   0.399   0.197
45    S        -0.338  -0.210  -0.346  -0.350  -0.105  -0.374  -0.489  -0.293  -0.488
46    E        -1.102  -0.991  -0.932  -1.302  -1.091  -1.050  -1.147  -1.019  -0.905
47    Q        -0.338  -0.235  -0.379  -0.269  -0.171  -0.323  -0.489  -0.386  -0.538
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    Y         0.276   0.202   0.251   0.435   0.282   0.302   0.059  -0.088  -0.052
51    P        -1.732  -1.671  -1.617  -1.386  -1.351  -1.269  -1.366  -1.304  -1.181
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    Q        -1.536  -1.460  -1.330  -1.365  -1.271  -1.089  -1.366  -1.278  -1.090
54    A        -0.039  -0.174  -0.328  -0.256  -0.446  -0.670  -0.051  -0.240  -0.460
55    D        -1.536  -1.514  -1.335  -1.398  -1.336  -1.079  -1.366  -1.317  -1.092
56    F         1.297   1.323   1.407   1.268   1.299   1.433   1.374   1.411   1.534
57    Y        -1.102  -1.129  -0.951  -1.036  -1.141  -0.895  -1.147  -1.151  -0.924
58    K         0.613   0.598   0.402   0.632   0.630   0.404   0.607   0.579   0.226
59    L        -1.417  -1.406  -1.301  -1.407  -1.377  -1.198  -1.257  -1.215  -1.062
60    D         1.297   1.323   1.407   1.323   1.363   1.484   1.374   1.411   1.534
61    V         1.297   1.323   1.407   1.093   1.147   1.270   1.374   1.411   1.534
62    D         1.297   1.323   1.407   1.323   1.363   1.484   1.374   1.411   1.534
63    E        -0.338  -0.459  -0.410  -0.330  -0.536  -0.495  -0.489  -0.646  -0.581
64    L        -0.039  -0.026  -0.303   0.079   0.086  -0.377  -0.051  -0.035  -0.425
65    G        -0.669  -0.636  -0.475  -0.660  -0.623  -0.390  -0.928  -0.880  -0.663
66    D        -0.984  -0.972  -0.903  -1.026  -1.008  -0.925  -1.037  -1.003  -0.877
67    V        -0.592  -0.611  -0.476  -0.855  -0.879  -0.661  -0.818  -0.847  -0.664
68    A         1.297   1.323   1.407   0.944   0.989   1.132   1.374   1.411   1.534
69    Q        -0.039  -0.013  -0.298   0.185   0.214  -0.292  -0.051  -0.020  -0.418
70    K        -0.338  -0.091  -0.325  -0.344   0.041  -0.314  -0.489  -0.131  -0.457
71    N        -1.417  -1.486  -1.334  -1.252  -1.386  -1.230  -1.257  -1.295  -1.092
72    E        -0.984  -0.888  -0.908  -0.869  -0.708  -0.732  -1.037  -0.912  -0.880
73    V         0.613   0.483   0.386   0.510   0.360   0.213   0.607   0.399   0.197
74    S        -0.653  -0.818  -0.885  -0.244  -0.447  -0.523  -0.599  -0.794  -0.850
75    A         0.276   0.306   0.282  -0.084  -0.035  -0.056   0.059   0.099   0.007
76    M         1.297   1.323   1.407   1.454   1.496   1.606   1.374   1.411   1.534
77    P         1.297   1.323   1.407   1.389   1.421   1.545   1.374   1.411   1.534
78    T         0.613   0.587   0.405   0.777   0.739   0.490   0.607   0.563   0.231
79    L        -0.473  -0.427  -0.420  -0.611  -0.568  -0.550  -0.709  -0.655  -0.598
80    L        -1.417  -1.345  -1.307  -1.570  -1.489  -1.425  -1.257  -1.178  -1.069
81    L        -0.473  -0.532  -0.415  -0.565  -0.648  -0.463  -0.709  -0.759  -0.592
82    F         0.276   0.255   0.269   0.279   0.239   0.264   0.059   0.008  -0.018
83    K         1.297   1.323   1.407   1.175   1.221   1.347   1.374   1.411   1.534
84    N        -0.039   0.059  -0.295   0.249   0.371  -0.110  -0.051   0.079  -0.414
85    G         1.297   1.323   1.407   1.413   1.447   1.567   1.374   1.411   1.534
86    K        -0.473  -0.468  -0.401  -0.632  -0.558  -0.481  -0.709  -0.658  -0.567
87    E        -0.473  -0.427  -0.420  -0.680  -0.634  -0.623  -0.709  -0.655  -0.598
88    V        -0.473  -0.538  -0.423  -0.789  -0.884  -0.714  -0.709  -0.767  -0.601
89    A        -1.851  -1.829  -1.657  -1.805  -1.701  -1.470  -1.476  -1.429  -1.212
90    K        -1.102  -1.089  -0.952  -1.062  -1.029  -0.810  -1.147  -1.117  -0.925
91    V        -0.039  -0.198  -0.331  -0.073  -0.278  -0.477  -0.051  -0.273  -0.465
92    V        -0.906  -0.863  -0.901  -0.967  -0.896  -0.907  -0.928  -0.873  -0.871
93    G         1.297   1.323   1.407   1.413   1.447   1.567   1.374   1.411   1.534
94    A         1.297   1.323   1.407   0.944   0.989   1.132   1.374   1.411   1.534
95    N         1.297   1.323   1.407   1.383   1.421   1.540   1.374   1.411   1.534
96    P         0.613   0.689   0.409   0.804   0.895   0.509   0.607   0.716   0.238
97    A        -0.653  -0.759  -0.862  -0.726  -0.858  -0.936  -0.599  -0.727  -0.824
98    A         0.613   0.587   0.405   0.338   0.316   0.058   0.607   0.563   0.231
99    I         0.038   0.104   0.230  -0.174  -0.074   0.122  -0.380  -0.272  -0.093
100   K        -0.653  -0.818  -0.885  -0.534  -0.762  -0.860  -0.599  -0.794  -0.850
101   Q         0.095   0.086   0.216  -0.147  -0.244  -0.062  -0.270  -0.307  -0.119
102   A        -0.906  -0.923  -0.904  -1.163  -1.173  -1.105  -0.928  -0.946  -0.877
103   I         0.613   0.615   0.405   0.732   0.732   0.438   0.607   0.606   0.231
104   A        -0.906  -0.979  -0.922  -1.188  -1.281  -1.131  -0.928  -1.003  -0.894
105   A        -1.221  -1.205  -1.269  -1.281  -1.290  -1.291  -1.037  -1.029  -1.032
106   N        -0.039  -0.174  -0.328   0.241   0.065  -0.178  -0.051  -0.240  -0.460
107   A        -0.669  -0.646  -0.479  -1.222  -1.150  -0.891  -0.928  -0.893  -0.668
* 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/P22217
Output conservation file - output/P22217
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
