1     M         1.749   1.761   1.839   2.000   2.020   2.142   1.929   1.946   2.067
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    K         0.047   0.044   0.001  -0.043  -0.056  -0.180  -0.125  -0.130  -0.205
38    K         0.853   0.860   0.779   0.543   0.561   0.441   0.755   0.763   0.581
39    A        -0.637  -0.618  -0.588  -0.570  -0.544  -0.509  -0.713  -0.688  -0.641
40    H         0.047   0.044   0.001  -0.277  -0.273  -0.331  -0.125  -0.130  -0.205
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    G        -0.632  -0.614  -0.586  -0.890  -0.867  -0.798  -0.721  -0.698  -0.643
43    G        -0.062  -0.026  -0.041  -0.119  -0.061  -0.087  -0.313  -0.264  -0.279
44    K         1.749   1.761   1.839   1.415   1.442   1.556   1.929   1.946   2.067
45    M        -0.632  -0.640  -0.588  -0.851  -0.835  -0.753  -0.721  -0.723  -0.645
46    K         0.942   0.984   0.832   0.654   0.720   0.503   0.910   0.976   0.682
47    P        -0.476  -0.474  -0.534  -0.350  -0.348  -0.454  -0.517  -0.512  -0.577
48    E        -0.632  -0.637  -0.592  -0.897  -0.859  -0.788  -0.721  -0.719  -0.649
49    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    P         0.047   0.081  -0.002   0.013   0.057  -0.123  -0.125  -0.077  -0.211
59    P        -0.637  -0.637  -0.600  -0.996  -0.990  -0.910  -0.713  -0.710  -0.654
60    P         0.853   0.916   0.779   0.970   1.062   0.842   0.755   0.861   0.581
61    R         0.853   0.796   0.763   0.501   0.423   0.363   0.755   0.649   0.550
62    T        -1.046  -1.015  -0.994  -0.988  -0.949  -0.904  -0.925  -0.890  -0.842
63    I        -0.538  -0.571  -0.545  -0.469  -0.510  -0.470  -0.617  -0.640  -0.596
64    A        -0.538  -0.588  -0.556  -0.552  -0.645  -0.616  -0.617  -0.668  -0.612
65    N        -0.538  -0.583  -0.547  -0.457  -0.521  -0.468  -0.617  -0.657  -0.601
66    Q        -0.538  -0.523  -0.537  -0.733  -0.732  -0.747  -0.617  -0.602  -0.592
67    D         0.678   0.674   0.665   0.779   0.773   0.736   0.432   0.420   0.357
68    H         0.038   0.040   0.015   0.176   0.203   0.142  -0.167  -0.147  -0.194
69    F         0.038  -0.030  -0.016   0.245   0.151   0.177  -0.167  -0.262  -0.243
70    H         0.038   0.019  -0.016   0.105   0.076   0.032  -0.167  -0.194  -0.245
71    R         1.749   1.761   1.839   1.819   1.830   1.960   1.929   1.946   2.067
72    L        -0.183  -0.195  -0.117  -0.354  -0.374  -0.259  -0.467  -0.483  -0.380
73    N         0.526   0.529   0.603   0.261   0.261   0.376   0.132   0.132   0.231
74    Y         1.749   1.761   1.839   1.939   1.961   2.080   1.929   1.946   2.067
75    L         1.749   1.761   1.839   1.702   1.721   1.843   1.929   1.946   2.067
76    Y         0.038   0.052  -0.006   0.132   0.149   0.046  -0.167  -0.153  -0.231
77    Q         1.749   1.761   1.839   1.899   1.915   2.040   1.929   1.946   2.067
78    I        -0.538  -0.536  -0.546  -0.574  -0.571  -0.605  -0.617  -0.608  -0.601
79    S         1.749   1.761   1.839   1.731   1.741   1.873   1.929   1.946   2.067
80    A        -1.026  -0.989  -0.993  -0.947  -0.895  -0.903  -0.916  -0.879  -0.844
81    Y        -1.026  -0.992  -0.984  -0.826  -0.789  -0.736  -0.916  -0.881  -0.837
82    Q        -1.026  -1.034  -0.986  -0.815  -0.841  -0.750  -0.916  -0.915  -0.837
83    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    A         0.195   0.182   0.084   0.353   0.341   0.174   0.095   0.071  -0.081
90    R        -0.632  -0.621  -0.594  -0.612  -0.601  -0.545  -0.721  -0.703  -0.651
91    T        -1.381  -1.375  -1.327  -1.122  -1.124  -1.037  -1.066  -1.056  -0.977
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    D        -0.538  -0.571  -0.545  -0.382  -0.418  -0.385  -0.617  -0.640  -0.596
95    A        -1.381  -1.391  -1.330  -1.400  -1.395  -1.279  -1.066  -1.069  -0.979
96    H        -1.026  -1.042  -0.991  -0.741  -0.750  -0.676  -0.916  -0.923  -0.842
97    T        -1.381  -1.379  -1.326  -1.042  -1.044  -0.965  -1.066  -1.059  -0.976
98    P        -1.381  -1.397  -1.333  -1.216  -1.250  -1.150  -1.066  -1.073  -0.981
99    L         1.749   1.761   1.839   1.702   1.721   1.843   1.929   1.946   2.067
100   A         0.323   0.270   0.119   0.400   0.316   0.096   0.282   0.203  -0.029
101   R         1.015   0.978   0.864   1.155   1.101   0.948   1.031   0.967   0.741
102   N        -1.381  -1.364  -1.334  -1.166  -1.139  -1.094  -1.066  -1.047  -0.982
103   Y         1.015   1.075   0.887   1.290   1.372   1.128   1.031   1.126   0.784
104   I        -0.538  -0.484  -0.540  -0.521  -0.438  -0.520  -0.617  -0.554  -0.593
105   K        -0.183  -0.186  -0.111  -0.594  -0.615  -0.511  -0.467  -0.470  -0.371
106   S         0.038   0.009  -0.004   0.005  -0.042  -0.075  -0.167  -0.211  -0.224
107   M        -0.538  -0.537  -0.543  -0.423  -0.424  -0.437  -0.617  -0.613  -0.597
108   D        -0.892  -0.913  -0.937  -0.730  -0.783  -0.846  -0.767  -0.786  -0.786
109   L        -0.892  -0.930  -0.943  -0.822  -0.874  -0.892  -0.767  -0.803  -0.792
110   I         0.526   0.523   0.601   0.388   0.379   0.500   0.132   0.120   0.227
111   S         0.038   0.097   0.025  -0.058   0.030  -0.074  -0.167  -0.076  -0.182
112   K         0.323   0.229   0.122   0.139   0.023  -0.117   0.282   0.145  -0.025
113   K         1.749   1.761   1.839   1.428   1.454   1.569   1.929   1.946   2.067
114   T         0.038   0.054   0.011  -0.011   0.003  -0.064  -0.167  -0.149  -0.204
115   K         0.038   0.038  -0.016  -0.063  -0.094  -0.201  -0.167  -0.177  -0.245
116   T        -0.538  -0.522  -0.532  -0.537  -0.503  -0.517  -0.617  -0.594  -0.585
117   S        -0.538  -0.499  -0.532  -0.778  -0.683  -0.758  -0.617  -0.561  -0.581
118   L         1.015   0.956   0.869   1.025   0.949   0.820   1.031   0.930   0.751
119   L         0.323   0.250   0.126   0.401   0.292   0.109   0.282   0.175  -0.018
120   P         1.749   1.761   1.839   1.888   1.908   2.029   1.929   1.946   2.067
121   T        -0.892  -0.936  -0.942  -0.591  -0.673  -0.693  -0.767  -0.810  -0.791
122   I        -0.049  -0.026  -0.026  -0.196  -0.163  -0.131  -0.317  -0.288  -0.267
123   K         1.749   1.761   1.839   1.428   1.454   1.569   1.929   1.946   2.067
124   R         1.749   1.761   1.839   1.819   1.830   1.960   1.929   1.946   2.067
125   T         0.323   0.310   0.127   0.494   0.468   0.193   0.282   0.261  -0.016
126   I        -0.538  -0.508  -0.537  -0.469  -0.417  -0.460  -0.617  -0.579  -0.590
127   C         1.749   1.761   1.839   1.922   1.937   2.063   1.929   1.946   2.067
128   K         1.749   1.761   1.839   1.428   1.454   1.569   1.929   1.946   2.067
129   K         0.038   0.002  -0.001  -0.305  -0.342  -0.333  -0.167  -0.215  -0.221
130   C         1.749   1.761   1.839   1.922   1.937   2.063   1.929   1.946   2.067
131   H        -1.026  -1.037  -0.984  -1.033  -1.059  -0.987  -0.916  -0.919  -0.837
132   R        -0.538  -0.571  -0.545  -0.553  -0.607  -0.566  -0.617  -0.640  -0.596
133   L        -0.317  -0.282  -0.443  -0.317  -0.266  -0.531  -0.317  -0.273  -0.466
134   L         1.015   0.978   0.864   1.038   0.993   0.834   1.031   0.967   0.741
135   W        -0.538  -0.539  -0.544  -0.404  -0.404  -0.387  -0.617  -0.616  -0.598
136   T         0.323   0.331   0.139   0.554   0.567   0.275   0.282   0.293   0.002
137   P         0.195   0.174   0.068   0.353   0.325   0.150   0.095   0.062  -0.106
138   K        -1.381  -1.327  -1.326  -1.581  -1.513  -1.473  -1.066  -1.014  -0.976
139   K        -0.538  -0.581  -0.546  -0.657  -0.730  -0.708  -0.617  -0.658  -0.600
140   L        -1.026  -0.989  -0.993  -0.885  -0.845  -0.810  -0.916  -0.879  -0.844
141   E        -1.381  -1.365  -1.325  -1.335  -1.334  -1.251  -1.066  -1.047  -0.975
142   I         0.038   0.045   0.003   0.119   0.139   0.080  -0.167  -0.144  -0.214
143   T        -1.381  -1.389  -1.331  -1.275  -1.306  -1.230  -1.066  -1.068  -0.980
144   -        -0.476  -0.535  -0.540  -0.347  -0.432  -0.454  -0.517  -0.589  -0.585
145   -         0.942   0.952   0.833   1.215   1.232   1.065   0.910   0.923   0.684
146   -         0.195   0.096   0.052   0.227   0.069  -0.047   0.095  -0.054  -0.129
147   -        -0.637  -0.655  -0.600  -0.885  -0.885  -0.849  -0.713  -0.733  -0.654
148   -         1.749   1.761   1.839   1.723   1.729   1.865   1.929   1.946   2.067
149   -         0.544   0.533   0.612   0.007  -0.003   0.123   0.168   0.140   0.250
150   -        -0.637  -0.554  -0.580  -0.995  -0.894  -0.892  -0.713  -0.610  -0.632
151   -         0.047  -0.002  -0.017  -0.339  -0.412  -0.424  -0.125  -0.202  -0.233
152   -        -0.637  -0.655  -0.600  -0.674  -0.703  -0.612  -0.713  -0.733  -0.654
153   -        -0.637  -0.577  -0.600  -0.867  -0.796  -0.832  -0.713  -0.639  -0.654
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   S        -0.538  -0.576  -0.551  -0.639  -0.693  -0.700  -0.617  -0.651  -0.606
158   D        -1.026  -1.014  -0.992  -0.924  -0.893  -0.873  -0.916  -0.898  -0.843
159   G        -0.538  -0.572  -0.555  -0.417  -0.475  -0.450  -0.617  -0.654  -0.610
160   A        -0.317  -0.324  -0.456  -0.075  -0.087  -0.308  -0.317  -0.326  -0.482
161   L         1.015   1.090   0.887   1.060   1.155   0.907   1.031   1.149   0.784
162   S        -0.892  -0.956  -0.949  -0.608  -0.704  -0.702  -0.767  -0.829  -0.799
163   V        -1.026  -0.976  -0.976  -0.824  -0.760  -0.741  -0.916  -0.867  -0.829
164   M        -1.460  -1.442  -1.366  -1.393  -1.326  -1.253  -1.128  -1.108  -1.006
165   C         1.749   1.761   1.839   1.922   1.937   2.063   1.929   1.946   2.067
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   G        -1.381  -1.344  -1.334  -1.504  -1.449  -1.391  -1.066  -1.029  -0.982
168   C         1.749   1.761   1.839   1.922   1.937   2.063   1.929   1.946   2.067
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   G         0.323   0.229   0.122   0.533   0.400   0.225   0.282   0.145  -0.025
183   T        -1.026  -1.049  -0.990  -1.151  -1.147  -1.042  -0.916  -0.929  -0.841
184   V        -1.026  -0.975  -0.983  -1.142  -1.074  -1.052  -0.916  -0.867  -0.835
185   K         1.749   1.761   1.839   1.428   1.454   1.569   1.929   1.946   2.067
186   R         1.015   1.047   0.884   1.078   1.121   0.848   1.031   1.081   0.778
187   F         1.749   1.761   1.839   2.023   2.041   2.164   1.929   1.946   2.067
188   N         0.942   0.923   0.823   1.106   1.082   0.915   0.910   0.873   0.664
189   I         0.609   0.646   0.657   0.544   0.609   0.606   0.299   0.365   0.341
190   G         0.942   0.872   0.820   1.067   0.966   0.873   0.910   0.785   0.658
191   A        -0.062  -0.055  -0.052  -0.490  -0.467  -0.448  -0.313  -0.314  -0.295
192   D        -0.476  -0.507  -0.527  -0.378  -0.426  -0.511  -0.517  -0.555  -0.568
193   P        -0.140  -0.139  -0.093  -0.173  -0.171  -0.092  -0.419  -0.413  -0.348
194   N        -0.637  -0.615  -0.587  -0.638  -0.603  -0.565  -0.713  -0.684  -0.639
195   Y         1.749   1.761   1.839   1.921   1.940   2.062   1.929   1.946   2.067
196   R        -1.133  -1.118  -1.040  -1.216  -1.202  -1.077  -1.006  -0.987  -0.884
197   T         0.853   0.796   0.763   0.781   0.687   0.628   0.755   0.649   0.550
198   Y        -0.637  -0.659  -0.610  -0.283  -0.321  -0.244  -0.713  -0.737  -0.666
199   S        -0.637  -0.602  -0.591  -0.738  -0.686  -0.682  -0.713  -0.669  -0.644
200   E         0.544   0.563   0.618   0.539   0.572   0.645   0.168   0.199   0.261
201   R         0.742   0.699   0.704   0.356   0.293   0.292   0.553   0.468   0.434
202   E        -0.733  -0.721  -0.641  -0.637  -0.616  -0.497  -0.823  -0.805  -0.699
203   G        -0.113  -0.069  -0.081  -0.193  -0.119  -0.160  -0.364  -0.299  -0.327
204   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
205   N        -1.736  -1.719  -1.642  -1.718  -1.692  -1.579  -1.216  -1.197  -1.094
206   L        -1.026  -1.011  -0.985  -1.080  -1.056  -0.998  -0.916  -0.898  -0.837
207   L        -1.026  -1.013  -0.985  -1.192  -1.203  -1.146  -0.916  -0.899  -0.837
208   N        -1.381  -1.364  -1.334  -1.154  -1.136  -1.080  -1.066  -1.047  -0.982
209   S        -1.736  -1.719  -1.642  -1.381  -1.360  -1.242  -1.216  -1.197  -1.094
* 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/P40571
Output conservation file - output/P40571
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
