1     M         1.576   1.608   1.734   1.724   1.778   1.980   1.744   1.790   1.999
2     V         0.296   0.346   0.423   0.055   0.109   0.197  -0.029   0.043   0.119
3     V         1.576   1.608   1.734   1.624   1.662   1.884   1.744   1.790   1.999
4     H        -0.582  -0.758  -0.819  -0.158  -0.375  -0.508  -0.500  -0.711  -0.765
5     I         0.818   0.807   0.622   0.828   0.844   0.565   0.871   0.847   0.499
6     L        -0.234  -0.248  -0.283  -0.279  -0.284  -0.314  -0.376  -0.384  -0.437
7     G         1.576   1.608   1.734   1.441   1.496   1.710   1.744   1.790   1.999
8     K         0.445   0.366   0.436   0.249   0.103   0.201   0.248   0.081   0.144
9     G        -1.560  -1.520  -1.347  -1.741  -1.651  -1.423  -1.373  -1.295  -1.076
10    F        -0.234  -0.271  -0.277  -0.111  -0.143  -0.223  -0.376  -0.413  -0.428
11    K        -0.234  -0.347  -0.322  -0.343  -0.522  -0.448  -0.376  -0.543  -0.497
12    G        -1.428  -1.504  -1.358  -1.325  -1.372  -1.136  -1.249  -1.282  -1.085
13    K        -1.428  -1.504  -1.358  -1.362  -1.414  -1.170  -1.249  -1.282  -1.085
14    E        -1.428  -1.399  -1.341  -1.252  -1.226  -1.120  -1.249  -1.197  -1.070
15    V        -1.560  -1.410  -1.328  -1.618  -1.415  -1.291  -1.373  -1.215  -1.061
16    I         0.246   0.447   0.500  -0.020   0.347   0.406  -0.126   0.233   0.269
17    K        -0.948  -0.971  -0.855  -1.204  -1.194  -0.996  -0.999  -0.980  -0.815
18    I        -0.582  -0.789  -0.850  -0.438  -0.704  -0.809  -0.500  -0.747  -0.801
19    A         0.182   0.241   0.395  -0.276  -0.177   0.069  -0.251  -0.162   0.063
20    L         1.576   1.608   1.734   1.470   1.524   1.737   1.744   1.790   1.999
21    A        -0.582  -0.789  -0.850  -0.438  -0.731  -0.864  -0.500  -0.747  -0.801
22    S        -0.234  -0.248  -0.283  -0.226  -0.193  -0.318  -0.376  -0.384  -0.437
23    K        -0.168  -0.315  -0.324  -0.249  -0.466  -0.468  -0.251  -0.469  -0.492
24    F        -0.234  -0.248  -0.283  -0.111  -0.108  -0.236  -0.376  -0.384  -0.437
25    Y         0.246   0.278   0.406   0.297   0.352   0.519  -0.126  -0.087   0.085
26    G         1.576   1.608   1.734   1.441   1.496   1.710   1.744   1.790   1.999
27    I        -0.383  -0.395  -0.297  -0.634  -0.642  -0.489  -0.625  -0.612  -0.470
28    G         1.576   1.608   1.734   1.441   1.496   1.710   1.744   1.790   1.999
29    K        -1.908  -1.844  -1.716  -1.665  -1.504  -1.371  -1.498  -1.410  -1.220
30    T        -2.256  -2.024  -1.986  -1.952  -1.599  -1.596  -1.623  -1.420  -1.295
31    T        -0.582  -0.789  -0.850  -0.365  -0.681  -0.832  -0.500  -0.747  -0.801
32    A         0.818   0.733   0.616   0.879   0.796   0.609   0.871   0.729   0.489
33    E         0.097  -0.051  -0.207   0.340   0.130  -0.180   0.123  -0.088  -0.323
34    K        -0.234  -0.120  -0.227  -0.448  -0.247  -0.413  -0.376  -0.186  -0.354
35    I         0.246   0.289   0.403  -0.147  -0.072   0.077  -0.126  -0.067   0.079
36    C         0.097  -0.014  -0.178   0.564   0.395   0.109   0.123  -0.036  -0.280
37    S         0.246   0.447   0.500  -0.006   0.366   0.407  -0.126   0.233   0.269
38    K         1.576   1.608   1.734   1.459   1.527   1.726   1.744   1.790   1.999
39    L        -0.863  -0.938  -0.879  -0.931  -1.038  -0.926  -0.875  -0.936  -0.837
40    G         0.445   0.366   0.436   0.243   0.120   0.206   0.248   0.081   0.144
41    F        -0.383  -0.393  -0.320  -0.473  -0.487  -0.413  -0.625  -0.621  -0.498
42    Y         0.445   0.366   0.436   0.636   0.504   0.563   0.248   0.081   0.144
43    P         0.818   0.736   0.603   1.132   1.022   0.816   0.871   0.734   0.465
44    W        -1.777  -1.841  -1.716  -1.422  -1.657  -1.539  -1.373  -1.402  -1.220
45    M        -0.582  -0.758  -0.819  -0.245  -0.528  -0.639  -0.500  -0.711  -0.765
46    R         0.818   0.733   0.616   0.734   0.602   0.435   0.871   0.729   0.489
47    M         0.818   0.736   0.603   1.053   0.945   0.739   0.871   0.734   0.465
48    H        -1.080  -1.074  -0.916  -1.178  -1.250  -1.016  -1.124  -1.089  -0.877
49    Q        -0.234  -0.360  -0.321  -0.081  -0.283  -0.248  -0.376  -0.555  -0.498
50    L         1.576   1.608   1.734   1.470   1.524   1.737   1.744   1.790   1.999
51    S        -0.234  -0.145  -0.218  -0.154   0.031  -0.105  -0.376  -0.222  -0.342
52    E        -0.582  -0.789  -0.850  -0.209  -0.505  -0.606  -0.500  -0.747  -0.801
53    P        -0.582  -0.789  -0.850  -0.247  -0.611  -0.789  -0.500  -0.747  -0.801
54    Q         0.097  -0.051  -0.207   0.411   0.213  -0.047   0.123  -0.088  -0.323
55    I        -0.234  -0.272  -0.284  -0.364  -0.414  -0.468  -0.376  -0.415  -0.445
56    M        -0.234  -0.181  -0.289  -0.144  -0.127  -0.288  -0.376  -0.356  -0.451
57    S        -1.211  -1.068  -1.237  -0.980  -0.794  -1.012  -0.999  -0.847  -0.969
58    I         0.246   0.245   0.395  -0.147  -0.170   0.057  -0.126  -0.152   0.063
59    A        -1.428  -1.376  -1.324  -1.328  -1.265  -1.190  -1.249  -1.179  -1.056
60    S        -0.948  -0.978  -0.888  -1.062  -1.063  -0.947  -0.999  -0.985  -0.847
61    E         0.818   0.736   0.603   1.020   0.920   0.678   0.871   0.734   0.465
62    L         0.818   0.807   0.622   0.781   0.775   0.496   0.871   0.847   0.499
63    S         0.818   1.021   0.642   0.975   1.282   0.719   0.871   1.165   0.536
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    T        -1.428  -1.402  -1.316  -1.275  -1.288  -1.109  -1.249  -1.198  -1.050
66    M        -0.234  -0.248  -0.283  -0.178  -0.209  -0.298  -0.376  -0.384  -0.437
67    T         0.818   0.807   0.622   0.948   0.950   0.646   0.871   0.847   0.499
68    I         0.818   0.807   0.622   0.828   0.844   0.565   0.871   0.847   0.499
69    E         1.576   1.608   1.734   1.713   1.778   1.969   1.744   1.790   1.999
70    G         0.097  -0.051  -0.207   0.119  -0.078  -0.307   0.123  -0.088  -0.323
71    D         0.445   0.500   0.499   0.656   0.737   0.702   0.248   0.329   0.268
72    A         0.182   0.256   0.409  -0.254  -0.134   0.114  -0.251  -0.131   0.091
73    R        -0.234  -0.248  -0.283  -0.482  -0.520  -0.579  -0.376  -0.384  -0.437
74    A        -1.428  -1.399  -1.341  -1.495  -1.504  -1.355  -1.249  -1.197  -1.070
75    I        -0.948  -0.978  -0.888  -1.199  -1.198  -1.065  -0.999  -0.985  -0.847
76    V        -0.383  -0.409  -0.328  -0.616  -0.679  -0.551  -0.625  -0.637  -0.508
77    K        -1.080  -0.850  -0.869  -1.351  -0.995  -1.040  -1.124  -0.862  -0.829
78    D        -1.080  -0.995  -0.885  -0.979  -0.893  -0.719  -1.124  -1.011  -0.847
79    N         0.182   0.256   0.409   0.089   0.205   0.461  -0.251  -0.131   0.091
80    I         1.576   1.608   1.734   1.499   1.579   1.765   1.744   1.790   1.999
81    A        -0.948  -0.960  -0.877  -1.122  -1.079  -0.953  -0.999  -0.967  -0.834
82    L        -0.383  -0.359  -0.310  -0.727  -0.717  -0.565  -0.625  -0.579  -0.483
83    K         0.445   0.366   0.436   0.198   0.040   0.115   0.248   0.081   0.144
84    R         0.097   0.145  -0.173   0.069   0.105  -0.342   0.123   0.174  -0.273
85    K        -1.428  -1.453  -1.319  -1.387  -1.380  -1.181  -1.249  -1.232  -1.052
86    I         0.097  -0.051  -0.207   0.187   0.013  -0.235   0.123  -0.088  -0.323
87    G         0.818   0.736   0.603   0.742   0.627   0.412   0.871   0.734   0.465
88    S         0.097  -0.076  -0.214   0.375   0.196  -0.045   0.123  -0.123  -0.334
89    Y         0.818   0.930   0.634   1.128   1.286   0.839   0.871   1.034   0.521
90    S        -1.560  -1.406  -1.348  -1.647  -1.495  -1.335  -1.373  -1.208  -1.077
91    G         1.576   1.608   1.734   1.441   1.496   1.710   1.744   1.790   1.999
92    M        -0.514  -0.507  -0.369  -0.630  -0.675  -0.489  -0.750  -0.743  -0.558
93    R         1.576   1.608   1.734   1.430   1.465   1.698   1.744   1.790   1.999
94    H         1.576   1.608   1.734   1.757   1.845   2.011   1.744   1.790   1.999
95    T        -0.234  -0.148  -0.292  -0.288  -0.224  -0.387  -0.376  -0.313  -0.458
96    L        -0.863  -0.887  -0.874  -0.913  -0.965  -0.904  -0.875  -0.907  -0.836
97    H         0.818   1.008   0.639   0.790   1.026   0.584   0.871   1.147   0.531
98    L         0.097   0.014  -0.193   0.183   0.082  -0.185   0.123   0.005  -0.302
99    P         1.576   1.608   1.734   1.801   1.851   2.053   1.744   1.790   1.999
100   V         1.576   1.608   1.734   1.624   1.662   1.884   1.744   1.790   1.999
101   R         0.097  -0.049  -0.221   0.073  -0.159  -0.416   0.123  -0.084  -0.343
102   G         1.576   1.608   1.734   1.441   1.496   1.710   1.744   1.790   1.999
103   Q         1.576   1.608   1.734   1.730   1.792   1.985   1.744   1.790   1.999
104   H        -1.211  -1.265  -1.303  -1.138  -1.275  -1.260  -0.999  -1.054  -1.034
105   T         1.576   1.608   1.734   1.641   1.708   1.900   1.744   1.790   1.999
106   R         0.818   0.807   0.622   0.734   0.706   0.445   0.871   0.847   0.499
107   N         0.246   0.248   0.395   0.075   0.044   0.281  -0.126  -0.146   0.063
108   N         0.818   0.733   0.616   0.990   0.874   0.725   0.871   0.729   0.489
109   A        -0.863  -0.874  -0.875  -0.985  -1.039  -1.042  -0.875  -0.888  -0.835
110   K        -0.582  -0.610  -0.797  -0.505  -0.540  -0.817  -0.500  -0.536  -0.740
111   T        -0.234  -0.139  -0.282  -0.192  -0.123  -0.290  -0.376  -0.304  -0.444
112   A         1.576   1.608   1.734   1.545   1.613   1.808   1.744   1.790   1.999
113   R         0.097   0.098  -0.176   0.073   0.037  -0.340   0.123   0.114  -0.278
114   K        -0.383  -0.338  -0.302  -0.736  -0.654  -0.562  -0.625  -0.545  -0.476
115   L         0.097   0.172  -0.171   0.145   0.253  -0.231   0.123   0.214  -0.271
116   N         1.576   1.608   1.734   1.647   1.685   1.905   1.744   1.790   1.999
117   K         0.182   0.240   0.395  -0.350  -0.269  -0.001  -0.251  -0.162   0.063
118   I        -0.948  -0.860  -0.846  -1.098  -0.966  -0.920  -0.999  -0.886  -0.806
119   D        -1.080  -0.883  -0.889  -0.935  -0.679  -0.678  -1.124  -0.909  -0.851
120   R         0.818   0.981   0.638   0.759   0.944   0.527   0.871   1.109   0.528
121   R         0.670   0.593   0.542   0.591   0.453   0.424   0.636   0.494   0.351
122   G        -0.168  -0.115  -0.263  -0.232  -0.159  -0.385  -0.251  -0.195  -0.404
123   I        -0.545  -0.405  -0.350  -0.531  -0.319  -0.257  -0.810  -0.633  -0.534
124   H        -0.335  -0.475  -0.370  -0.238  -0.519  -0.402  -0.490  -0.695  -0.558
125   T         0.570   0.465   0.480   0.615   0.435   0.425   0.467   0.266   0.231
126   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   C        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   F        -1.102  -1.017  -0.903  -1.056  -0.943  -0.796  -1.129  -1.023  -0.861
157   G        -2.336  -2.174  -2.026  -2.269  -2.035  -1.834  -1.676  -1.523  -1.320
158   K        -1.938  -1.818  -1.697  -1.765  -1.566  -1.410  -1.513  -1.389  -1.206
* 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/P53937
Output conservation file - output/P53937
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
