1     M         1.581   1.600   1.649   1.744   1.772   1.846   1.695   1.720   1.793
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     S         1.581   1.600   1.649   1.504   1.538   1.615   1.695   1.720   1.793
6     N         1.581   1.600   1.649   1.612   1.643   1.719   1.695   1.720   1.793
7     I         1.581   1.600   1.649   1.612   1.639   1.719   1.695   1.720   1.793
8     L         0.694   0.766   0.540   0.642   0.733   0.443   0.667   0.776   0.392
9     A        -0.127  -0.168  -0.293  -0.107  -0.169  -0.370  -0.154  -0.217  -0.382
10    V         0.694   0.766   0.540   0.790   0.895   0.543   0.667   0.776   0.392
11    F         1.581   1.600   1.649   1.577   1.610   1.685   1.695   1.720   1.793
12    N         1.581   1.600   1.649   1.612   1.643   1.719   1.695   1.720   1.793
13    P         1.581   1.600   1.649   1.522   1.531   1.633   1.695   1.720   1.793
14    P         1.581   1.600   1.649   1.522   1.531   1.633   1.695   1.720   1.793
15    P        -0.127  -0.192  -0.307  -0.065  -0.178  -0.339  -0.154  -0.248  -0.401
16    Q         0.328   0.411   0.405   0.189   0.320   0.309   0.051   0.195   0.153
17    R         1.581   1.600   1.649   1.630   1.658   1.737   1.695   1.720   1.793
18    E        -0.411  -0.355  -0.359  -0.310  -0.193  -0.235  -0.565  -0.473  -0.476
19    L        -0.127  -0.127  -0.300  -0.116  -0.114  -0.347  -0.154  -0.151  -0.392
20    E        -1.038  -0.931  -0.962  -0.925  -0.796  -0.788  -0.976  -0.864  -0.856
21    K        -1.038  -0.923  -0.948  -0.949  -0.802  -0.823  -0.976  -0.854  -0.843
22    E        -0.127  -0.256  -0.319  -0.001  -0.173  -0.315  -0.154  -0.329  -0.417
23    E         0.328   0.338   0.374   0.193   0.216   0.244   0.051   0.065   0.096
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    T         0.474   0.328   0.380   0.580   0.336   0.418   0.308   0.046   0.108
28    M        -0.467  -0.477  -0.427  -0.475  -0.547  -0.430  -0.616  -0.636  -0.563
29    D         0.474   0.328   0.380   0.636   0.374   0.421   0.308   0.046   0.108
30    C         1.581   1.600   1.649   1.787   1.813   1.888   1.695   1.720   1.793
31    V        -1.038  -1.039  -0.981  -1.056  -1.056  -0.947  -0.976  -0.963  -0.874
32    P         0.694   0.560   0.497   0.769   0.582   0.527   0.667   0.449   0.318
33    C         1.581   1.600   1.649   1.787   1.813   1.888   1.695   1.720   1.793
34    Q         0.328   0.338   0.374   0.362   0.362   0.415   0.051   0.065   0.096
35    V        -0.582  -0.544  -0.448  -0.696  -0.641  -0.491  -0.771  -0.716  -0.590
36    M        -0.411  -0.487  -0.416  -0.365  -0.506  -0.412  -0.565  -0.647  -0.551
37    S        -0.411  -0.296  -0.372  -0.414  -0.224  -0.350  -0.565  -0.403  -0.493
38    T         0.328   0.338   0.374   0.258   0.269   0.302   0.051   0.065   0.096
39    M        -1.493  -1.414  -1.381  -1.309  -1.197  -1.158  -1.181  -1.095  -1.034
40    F        -0.411  -0.417  -0.407  -0.409  -0.416  -0.379  -0.565  -0.575  -0.543
41    S        -0.866  -0.900  -0.915  -0.928  -1.003  -1.049  -0.771  -0.808  -0.803
42    V        -1.493  -1.463  -1.389  -1.340  -1.290  -1.202  -1.181  -1.144  -1.040
43    G         0.694   0.715   0.535   0.564   0.591   0.346   0.667   0.699   0.384
44    F         0.216   0.256   0.333  -0.166  -0.114   0.015  -0.154  -0.087   0.020
45    G         1.581   1.600   1.649   1.375   1.399   1.491   1.695   1.720   1.793
46    S        -1.038  -1.039  -0.981  -1.271  -1.270  -1.185  -0.976  -0.963  -0.874
47    Y         1.581   1.600   1.649   1.718   1.752   1.821   1.695   1.720   1.793
48    L         0.694   0.560   0.497   0.620   0.430   0.336   0.667   0.449   0.318
49    A        -0.866  -0.799  -0.898  -0.745  -0.655  -0.812  -0.771  -0.688  -0.786
50    S         0.694   0.715   0.535   0.664   0.701   0.417   0.667   0.699   0.384
51    G        -0.411  -0.432  -0.405  -0.653  -0.678  -0.609  -0.565  -0.590  -0.540
52    K        -1.493  -1.492  -1.413  -1.358  -1.312  -1.231  -1.181  -1.168  -1.061
53    P        -0.866  -0.799  -0.898  -0.804  -0.730  -0.866  -0.771  -0.688  -0.786
54    F         1.581   1.600   1.649   1.577   1.610   1.685   1.695   1.720   1.793
55    K        -0.127  -0.192  -0.307  -0.043  -0.117  -0.292  -0.154  -0.248  -0.401
56    Y        -0.411  -0.487  -0.416  -0.239  -0.340  -0.248  -0.565  -0.647  -0.551
57    G        -1.042  -1.061  -0.983  -1.219  -1.218  -1.110  -0.968  -0.982  -0.875
58    K        -0.467  -0.478  -0.427  -0.649  -0.652  -0.608  -0.616  -0.638  -0.563
59    K        -0.467  -0.478  -0.427  -0.702  -0.785  -0.685  -0.616  -0.638  -0.563
60    E         0.474   0.324   0.380   0.432   0.217   0.286   0.308   0.039   0.108
61    A        -1.493  -1.493  -1.412  -1.427  -1.405  -1.307  -1.181  -1.169  -1.059
62    K        -0.127  -0.256  -0.319  -0.098  -0.277  -0.399  -0.154  -0.329  -0.417
63    R        -1.038  -1.028  -0.978  -1.237  -1.226  -1.121  -0.976  -0.954  -0.871
64    G        -0.411  -0.487  -0.416  -0.718  -0.818  -0.707  -0.565  -0.647  -0.551
65    I        -0.127  -0.192  -0.307   0.029  -0.079  -0.252  -0.154  -0.248  -0.401
66    S        -1.493  -1.505  -1.417  -1.291  -1.306  -1.159  -1.181  -1.178  -1.063
67    L        -0.411  -0.442  -0.378  -0.492  -0.500  -0.420  -0.565  -0.582  -0.501
68    T        -1.038  -1.064  -0.957  -0.815  -0.832  -0.672  -0.976  -0.985  -0.852
69    E        -1.038  -1.039  -0.981  -1.028  -1.011  -0.923  -0.976  -0.963  -0.874
70    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    N         1.581   1.600   1.649   1.617   1.649   1.724   1.695   1.720   1.793
75    P         1.581   1.600   1.649   1.553   1.569   1.663   1.695   1.720   1.793
76    Q        -1.589  -1.548  -1.432  -1.476  -1.449  -1.252  -1.264  -1.213  -1.076
77    W         1.581   1.600   1.649   1.710   1.751   1.814   1.695   1.720   1.793
78    W         1.581   1.600   1.649   1.718   1.759   1.821   1.695   1.720   1.793
79    K        -0.866  -0.683  -0.895  -0.618  -0.348  -0.694  -0.771  -0.552  -0.782
80    V        -1.493  -1.463  -1.389  -1.405  -1.396  -1.274  -1.181  -1.144  -1.040
81    T        -0.127  -0.168  -0.293  -0.112  -0.200  -0.377  -0.154  -0.217  -0.382
82    L        -0.411  -0.296  -0.372  -0.522  -0.316  -0.451  -0.565  -0.403  -0.493
83    R         0.328   0.387   0.369   0.209   0.327   0.248   0.051   0.152   0.087
84    S        -0.411  -0.327  -0.361  -0.746  -0.615  -0.662  -0.565  -0.451  -0.484
85    F        -0.411  -0.366  -0.352  -0.611  -0.537  -0.503  -0.565  -0.491  -0.467
86    G         1.581   1.600   1.649   1.375   1.399   1.491   1.695   1.720   1.793
87    G        -1.038  -1.026  -0.979  -1.184  -1.147  -1.085  -0.976  -0.953  -0.872
88    L        -0.582  -0.550  -0.454  -0.818  -0.769  -0.619  -0.771  -0.722  -0.598
89    L        -0.127  -0.165  -0.295  -0.118  -0.169  -0.343  -0.154  -0.213  -0.385
90    I        -0.127  -0.256  -0.319  -0.019  -0.231  -0.350  -0.154  -0.329  -0.417
91    A        -0.411  -0.334  -0.377  -0.590  -0.497  -0.522  -0.565  -0.472  -0.501
92    F        -0.411  -0.334  -0.377  -0.520  -0.420  -0.440  -0.565  -0.472  -0.501
93    G         1.581   1.600   1.649   1.375   1.399   1.491   1.695   1.720   1.793
94    F        -1.038  -0.931  -0.962  -1.068  -0.916  -0.961  -0.976  -0.864  -0.856
95    V        -0.127   0.042  -0.256   0.131   0.374  -0.079  -0.154   0.076  -0.332
96    R         1.581   1.600   1.649   1.627   1.654   1.734   1.695   1.720   1.793
97    G         0.256   0.250   0.328  -0.080  -0.091   0.048  -0.080  -0.099   0.012
98    T         0.256   0.250   0.328   0.056   0.013   0.133  -0.080  -0.099   0.012
99    E         0.694   0.560   0.497   0.799   0.633   0.507   0.667   0.449   0.318
100   G        -0.411  -0.432  -0.405  -0.642  -0.670  -0.589  -0.565  -0.590  -0.540
101   W        -0.127  -0.127  -0.300   0.085   0.099  -0.225  -0.154  -0.151  -0.392
102   L        -0.127  -0.256  -0.319  -0.092  -0.268  -0.335  -0.154  -0.329  -0.417
103   W        -0.866  -0.953  -0.953  -0.560  -0.694  -0.719  -0.771  -0.862  -0.844
104   H        -1.493  -1.493  -1.412  -1.271  -1.297  -1.159  -1.181  -1.169  -1.059
105   K        -0.866  -0.953  -0.953  -0.751  -0.855  -0.865  -0.771  -0.862  -0.844
106   N        -1.038  -1.074  -0.962  -1.000  -1.051  -0.887  -0.976  -0.995  -0.856
107   K         0.694   0.715   0.535   0.704   0.766   0.485   0.667   0.699   0.384
108   E        -1.038  -1.073  -0.963  -1.056  -1.073  -0.937  -0.976  -0.993  -0.856
109   Y        -0.866  -0.953  -0.953  -0.621  -0.778  -0.804  -0.771  -0.862  -0.844
110   K        -0.866  -0.953  -0.953  -0.778  -0.863  -0.904  -0.771  -0.862  -0.844
111   N        -1.149  -1.069  -1.005  -1.197  -1.089  -0.984  -1.079  -0.984  -0.896
112   Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   N        -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/Q12082
Output conservation file - output/Q12082
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
