1     M         1.434   1.463   1.552   1.659   1.702   1.826   1.555   1.594   1.739
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    T        -1.229  -1.314  -1.224  -1.252  -1.338  -1.239  -1.068  -1.143  -1.016
14    L        -1.364  -1.368  -1.222  -1.470  -1.454  -1.231  -1.213  -1.201  -1.016
15    V        -0.325  -0.274  -0.294  -0.520  -0.490  -0.492  -0.565  -0.517  -0.494
16    G         0.754   0.645   0.546   0.775   0.612   0.449   0.774   0.598   0.390
17    K         0.240   0.306   0.379   0.089   0.231   0.290  -0.118  -0.001   0.072
18    L        -0.504  -0.415  -0.682  -0.576  -0.444  -0.865  -0.453  -0.335  -0.659
19    V        -0.756  -0.797  -0.793  -0.820  -0.916  -0.888  -0.788  -0.839  -0.795
20    H         1.434   1.463   1.552   1.693   1.733   1.859   1.555   1.594   1.739
21    I        -0.950  -0.957  -0.837  -1.041  -1.043  -0.873  -1.011  -1.008  -0.841
22    S        -0.191  -0.277  -0.271  -0.344  -0.489  -0.472  -0.341  -0.443  -0.454
23    I        -0.950  -0.924  -0.825  -1.003  -0.993  -0.825  -1.011  -0.974  -0.829
24    D         1.434   1.463   1.552   1.495   1.532   1.669   1.555   1.594   1.739
25    L         0.419   0.447   0.401   0.163   0.201   0.114   0.216   0.259   0.116
26    V         0.754   0.645   0.546   0.771   0.627   0.478   0.774   0.598   0.390
27    L         1.434   1.463   1.552   1.242   1.282   1.427   1.555   1.594   1.739
28    V        -0.443  -0.407  -0.337  -0.712  -0.661  -0.575  -0.676  -0.622  -0.540
29    S         1.434   1.463   1.552   1.306   1.329   1.489   1.555   1.594   1.739
30    T        -0.191  -0.164  -0.261  -0.326  -0.278  -0.441  -0.341  -0.308  -0.440
31    C        -0.325  -0.317  -0.293  -0.187  -0.183  -0.136  -0.565  -0.548  -0.490
32    L         0.754   0.645   0.546   0.628   0.480   0.325   0.774   0.598   0.390
33    A         1.434   1.463   1.552   1.468   1.500   1.644   1.555   1.594   1.739
34    G         0.754   0.797   0.553   0.798   0.847   0.513   0.774   0.838   0.402
35    I        -0.325  -0.343  -0.290  -0.419  -0.432  -0.312  -0.565  -0.577  -0.488
36    K         0.754   0.645   0.546   0.858   0.739   0.566   0.774   0.598   0.390
37    R         1.434   1.463   1.552   1.512   1.570   1.686   1.555   1.594   1.739
38    N        -0.325  -0.306  -0.296  -0.446  -0.464  -0.432  -0.565  -0.549  -0.496
39    T         0.754   0.645   0.546   0.702   0.569   0.381   0.774   0.598   0.390
40    G         1.434   1.463   1.552   1.397   1.429   1.576   1.555   1.594   1.739
41    L         0.419   0.380   0.394   0.191   0.126   0.145   0.216   0.137   0.103
42    T         0.106   0.021  -0.172   0.091  -0.020  -0.359   0.105  -0.016  -0.304
43    P        -0.191  -0.258  -0.283   0.082  -0.055  -0.108  -0.341  -0.448  -0.472
44    K        -0.756  -0.807  -0.772  -0.626  -0.671  -0.629  -0.788  -0.832  -0.768
45    L        -0.832  -0.857  -0.791  -1.136  -1.155  -1.026  -0.899  -0.912  -0.795
46    E        -0.325  -0.324  -0.290  -0.311  -0.318  -0.225  -0.565  -0.559  -0.487
47    T        -1.694  -1.626  -1.549  -1.736  -1.616  -1.510  -1.345  -1.279  -1.143
48    L        -1.068  -1.031  -1.146  -0.848  -0.787  -1.042  -0.899  -0.849  -0.941
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    D        -1.576  -1.546  -1.517  -1.209  -1.154  -1.155  -1.234  -1.197  -1.116
52    N         0.754   0.837   0.556   1.003   1.115   0.713   0.774   0.897   0.408
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    Q        -1.263  -1.189  -1.191  -1.082  -0.985  -0.959  -1.122  -1.052  -0.990
55    T        -0.325  -0.312  -0.285  -0.470  -0.412  -0.364  -0.565  -0.526  -0.477
56    M        -0.504  -0.416  -0.707  -0.386  -0.268  -0.686  -0.453  -0.337  -0.689
57    R        -0.756  -0.793  -0.790  -0.630  -0.687  -0.680  -0.788  -0.832  -0.792
58    N        -2.007  -2.006  -1.838  -1.795  -1.818  -1.573  -1.457  -1.443  -1.240
59    Y         0.106  -0.035  -0.189   0.357   0.175  -0.046   0.105  -0.090  -0.328
60    M        -1.694  -1.626  -1.549  -1.592  -1.523  -1.369  -1.345  -1.279  -1.143
61    K        -1.263  -1.204  -1.187  -1.185  -1.070  -1.088  -1.122  -1.049  -0.985
62    R         0.419   0.479   0.411   0.381   0.494   0.332   0.216   0.316   0.135
63    Y         1.434   1.463   1.552   1.503   1.552   1.678   1.555   1.594   1.739
64    L         1.434   1.463   1.552   1.242   1.282   1.427   1.555   1.594   1.739
65    N        -0.756  -0.761  -0.775  -0.591  -0.599  -0.655  -0.788  -0.782  -0.774
66    L        -0.443  -0.484  -0.357  -0.793  -0.872  -0.653  -0.676  -0.730  -0.568
67    G         1.434   1.463   1.552   1.397   1.429   1.576   1.555   1.594   1.739
68    E         1.434   1.463   1.552   1.582   1.612   1.752   1.555   1.594   1.739
69    S        -0.325  -0.319  -0.298  -0.387  -0.368  -0.289  -0.565  -0.562  -0.497
70    V        -0.504  -0.573  -0.711  -0.409  -0.507  -0.734  -0.453  -0.535  -0.693
71    Y        -0.325  -0.312  -0.285  -0.346  -0.317  -0.239  -0.565  -0.526  -0.477
72    D         1.434   1.463   1.552   1.495   1.532   1.669   1.555   1.594   1.739
73    Y        -0.756  -0.783  -0.794  -0.559  -0.586  -0.609  -0.788  -0.827  -0.796
74    S         0.240   0.291   0.367  -0.163  -0.079   0.025  -0.118  -0.030   0.050
75    V        -0.191  -0.206  -0.264  -0.331  -0.396  -0.474  -0.341  -0.378  -0.446
76    A         0.754   0.790   0.561   0.849   0.893   0.548   0.774   0.826   0.417
77    T        -0.832  -0.833  -0.794  -0.911  -0.887  -0.797  -0.899  -0.884  -0.796
78    C        -1.263  -1.257  -1.188  -1.161  -1.166  -1.022  -1.122  -1.096  -0.985
79    G         0.754   0.769   0.548   0.775   0.787   0.453   0.774   0.794   0.394
80    S        -0.191  -0.144  -0.248  -0.359  -0.303  -0.439  -0.341  -0.276  -0.422
81    S         1.434   1.463   1.552   1.306   1.329   1.489   1.555   1.594   1.739
82    T        -1.263  -1.269  -1.196  -1.339  -1.366  -1.201  -1.122  -1.118  -0.994
83    Y         0.419   0.346   0.388   0.501   0.392   0.444   0.216   0.074   0.090
84    F         1.434   1.463   1.552   1.495   1.516   1.669   1.555   1.594   1.739
85    A        -1.576  -1.501  -1.506  -1.307  -1.185  -1.212  -1.234  -1.152  -1.108
86    R         0.754   0.645   0.546   0.911   0.787   0.603   0.774   0.598   0.390
87    K        -0.871  -0.944  -0.823  -0.937  -1.052  -0.886  -0.922  -0.986  -0.826
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -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/Q2V2P4
Output conservation file - output/Q2V2P4
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
