1     M         1.980   2.011   2.107   2.347   2.405   2.573   2.304   2.359   2.533
2     I        -0.769  -0.754  -0.751  -0.968  -0.948  -0.977  -0.780  -0.758  -0.739
3     S        -0.197  -0.150  -0.153  -0.332  -0.261  -0.256  -0.437  -0.374  -0.366
4     S         0.591   0.621   0.684   0.393   0.443   0.538   0.248   0.296   0.377
5     C        -0.880  -0.862  -0.792  -0.852  -0.838  -0.711  -0.909  -0.880  -0.785
6     V        -0.197  -0.182  -0.157  -0.491  -0.458  -0.404  -0.437  -0.411  -0.371
7     T        -0.165  -0.186  -0.153  -0.245  -0.289  -0.257  -0.373  -0.407  -0.361
8     R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     C        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    C        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    C        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    I         0.820   0.859   0.801   0.726   0.794   0.657   0.698   0.765   0.619
71    S         0.019  -0.018  -0.052  -0.101  -0.175  -0.267  -0.095  -0.150  -0.209
72    T        -1.340  -1.319  -1.259  -1.336  -1.317  -1.209  -1.123  -1.092  -1.006
73    N        -0.769  -0.705  -0.716  -1.012  -0.912  -0.942  -0.780  -0.697  -0.698
74    S        -0.769  -0.754  -0.751  -0.548  -0.513  -0.520  -0.780  -0.758  -0.739
75    N        -1.340  -1.319  -1.259  -1.398  -1.377  -1.272  -1.123  -1.092  -1.006
76    K        -0.769  -0.765  -0.730  -0.994  -0.981  -0.927  -0.780  -0.769  -0.714
77    A        -1.340  -1.319  -1.259  -1.077  -1.049  -0.942  -1.123  -1.092  -1.006
78    A        -0.769  -0.702  -0.755  -0.639  -0.531  -0.609  -0.780  -0.693  -0.743
79    E        -1.240  -1.189  -1.226  -1.336  -1.263  -1.289  -1.028  -0.971  -0.976
80    A        -0.763  -0.710  -0.720  -0.662  -0.598  -0.575  -0.790  -0.724  -0.710
81    P        -1.240  -1.226  -1.194  -1.037  -1.033  -0.960  -1.028  -1.007  -0.945
82    I        -0.107  -0.052  -0.087  -0.406  -0.351  -0.387  -0.314  -0.257  -0.279
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    F         1.050   0.939   0.909   1.279   1.111   1.038   1.114   0.913   0.832
88    P         1.980   2.011   2.107   2.116   2.172   2.336   2.304   2.359   2.533
89    K        -0.583  -0.652  -0.664  -0.777  -0.897  -0.920  -0.552  -0.635  -0.634
90    L         1.050   1.104   0.934   1.047   1.113   0.864   1.114   1.204   0.879
91    E        -0.107  -0.052  -0.064  -0.169  -0.068  -0.075  -0.314  -0.218  -0.235
92    D        -0.763  -0.803  -0.728  -0.678  -0.745  -0.631  -0.790  -0.819  -0.716
93    V        -0.107  -0.180  -0.125  -0.411  -0.533  -0.454  -0.314  -0.405  -0.327
94    K        -0.287  -0.260  -0.190  -0.666  -0.610  -0.522  -0.552  -0.512  -0.416
95    M        -1.717  -1.683  -1.640  -1.230  -1.172  -1.100  -1.266  -1.226  -1.153
96    H        -1.717  -1.683  -1.640  -1.552  -1.536  -1.430  -1.266  -1.226  -1.153
97    E         0.190   0.075   0.022   0.410   0.237   0.151   0.162  -0.012  -0.095
98    L         0.190   0.158   0.039   0.199   0.133  -0.048   0.162   0.106  -0.068
99    I        -0.287  -0.262  -0.188  -0.606  -0.556  -0.459  -0.552  -0.516  -0.413
100   G        -0.107  -0.180  -0.125  -0.091  -0.186  -0.102  -0.314  -0.405  -0.327
101   N        -0.583  -0.587  -0.659  -0.393  -0.423  -0.484  -0.552  -0.557  -0.628
102   N        -0.583  -0.539  -0.646  -0.339  -0.268  -0.431  -0.552  -0.500  -0.611
103   N        -0.165  -0.095  -0.122  -0.344  -0.236  -0.274  -0.373  -0.266  -0.315
104   F         0.190   0.118   0.023   0.484   0.362   0.221   0.162   0.051  -0.093
105   G         0.947   0.948   0.853   1.124   1.131   0.978   0.933   0.930   0.722
106   K        -0.197  -0.182  -0.157  -0.667  -0.630  -0.606  -0.437  -0.411  -0.371
107   K         0.591   0.595   0.670   0.148   0.151   0.266   0.248   0.242   0.348
108   T        -0.763  -0.780  -0.751  -0.804  -0.831  -0.784  -0.790  -0.796  -0.742
109   Y         1.050   0.939   0.909   1.365   1.220   1.181   1.114   0.913   0.832
110   Y        -0.763  -0.806  -0.733  -0.521  -0.563  -0.457  -0.790  -0.823  -0.723
111   V         0.550   0.575   0.658   0.128   0.173   0.295   0.162   0.200   0.322
112   E        -1.240  -1.256  -1.221  -0.912  -0.944  -0.862  -1.028  -1.035  -0.971
113   R         0.667   0.677   0.715   0.474   0.481   0.507   0.400   0.410   0.442
114   S         0.550   0.587   0.666   0.295   0.367   0.494   0.162   0.226   0.340
115   R        -0.763  -0.762  -0.746  -0.970  -0.964  -0.935  -0.790  -0.780  -0.736
116   T        -1.717  -1.683  -1.640  -1.547  -1.502  -1.426  -1.266  -1.226  -1.153
117   G         0.190   0.090   0.030   0.331   0.160   0.038   0.162   0.010  -0.083
118   N         0.667   0.677   0.715   0.651   0.668   0.738   0.400   0.410   0.442
119   L         0.667   0.677   0.715   0.610   0.615   0.703   0.400   0.410   0.442
120   P         1.980   2.011   2.107   2.116   2.172   2.336   2.304   2.359   2.533
121   V         1.980   2.011   2.107   1.917   1.971   2.132   2.304   2.359   2.533
122   Y         1.980   2.011   2.107   2.221   2.279   2.444   2.304   2.359   2.533
123   S        -1.240  -1.256  -1.221  -1.413  -1.478  -1.413  -1.028  -1.035  -0.971
124   A        -0.107  -0.027  -0.098  -0.141  -0.033  -0.110  -0.314  -0.213  -0.287
125   Y         0.190   0.183   0.012   0.416   0.412   0.090   0.162   0.154  -0.110
126   K        -0.107  -0.076  -0.104  -0.289  -0.237  -0.261  -0.314  -0.273  -0.296
127   N         0.190   0.118   0.023   0.351   0.255   0.121   0.162   0.051  -0.093
128   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   G         0.820   0.881   0.793   0.829   0.941   0.746   0.698   0.806   0.602
130   N         0.550   0.587   0.666   0.331   0.402   0.528   0.162   0.226   0.340
131   K         1.980   2.011   2.107   1.806   1.864   2.018   2.304   2.359   2.533
132   I         0.667   0.691   0.700   0.376   0.424   0.390   0.400   0.438   0.410
133   I        -0.763  -0.752  -0.747  -0.943  -0.931  -0.932  -0.790  -0.772  -0.738
134   T         1.980   2.011   2.107   2.108   2.161   2.328   2.304   2.359   2.533
135   E         1.050   0.939   0.909   1.228   1.070   1.008   1.114   0.913   0.832
136   I         1.980   2.011   2.107   1.943   2.005   2.158   2.304   2.359   2.533
137   R         0.667   0.677   0.715   0.474   0.481   0.507   0.400   0.410   0.442
138   K         0.550   0.574   0.658   0.165   0.205   0.341   0.162   0.199   0.323
139   I         1.050   1.070   0.928   1.030   1.074   0.837   1.114   1.146   0.868
140   E        -0.763  -0.764  -0.716  -0.568  -0.548  -0.466  -0.790  -0.783  -0.705
141   G         1.980   2.011   2.107   2.141   2.201   2.361   2.304   2.359   2.533
142   D         1.050   1.104   0.934   1.329   1.414   1.161   1.114   1.204   0.879
143   V        -1.717  -1.683  -1.640  -1.706  -1.669  -1.589  -1.266  -1.226  -1.153
144   I        -1.240  -1.246  -1.223  -1.358  -1.364  -1.337  -1.028  -1.027  -0.973
145   Q         0.190   0.090   0.030   0.477   0.336   0.208   0.162   0.010  -0.083
146   L         1.050   1.050   0.929   1.107   1.100   0.956   1.114   1.112   0.870
147   R         0.667   0.691   0.700   0.474   0.512   0.468   0.400   0.438   0.410
148   N        -0.583  -0.640  -0.661  -0.564  -0.674  -0.714  -0.552  -0.621  -0.630
149   D         1.050   0.939   0.909   1.343   1.186   1.143   1.114   0.913   0.832
150   L         1.980   2.011   2.107   1.959   1.995   2.175   2.304   2.359   2.533
151   Q        -0.107  -0.180  -0.125  -0.128  -0.271  -0.188  -0.314  -0.405  -0.327
152   E        -1.240  -1.274  -1.230  -1.012  -1.073  -0.992  -1.028  -1.051  -0.979
153   Q        -1.717  -1.683  -1.640  -1.383  -1.329  -1.256  -1.266  -1.226  -1.153
154   L         0.190   0.183   0.012   0.285   0.265   0.041   0.162   0.154  -0.110
155   P         1.050   0.939   0.909   1.183   1.010   0.940   1.114   0.913   0.832
156   F        -1.240  -1.274  -1.230  -0.815  -0.844  -0.778  -1.028  -1.051  -0.979
157   I        -0.583  -0.674  -0.700  -0.596  -0.750  -0.788  -0.552  -0.660  -0.678
158   P         0.667   0.677   0.715   0.489   0.501   0.522   0.400   0.410   0.442
159   K        -0.165  -0.186  -0.153  -0.399  -0.443  -0.370  -0.373  -0.407  -0.361
160   K         0.947   0.857   0.844   0.820   0.689   0.668   0.933   0.760   0.704
161   S        -0.769  -0.695  -0.730  -0.617  -0.504  -0.566  -0.780  -0.692  -0.714
162   W        -0.107  -0.121  -0.116  -0.024  -0.101  -0.109  -0.314  -0.339  -0.320
163   S        -1.717  -1.683  -1.640  -1.496  -1.399  -1.373  -1.266  -1.226  -1.153
164   V         1.050   1.070   0.928   1.010   1.047   0.820   1.114   1.146   0.868
165   V        -0.107   0.014  -0.080  -0.328  -0.115  -0.292  -0.314  -0.141  -0.262
166   M        -0.763  -0.660  -0.706  -0.967  -0.855  -0.868  -0.790  -0.674  -0.695
167   Q        -0.583  -0.674  -0.700  -0.373  -0.553  -0.616  -0.552  -0.660  -0.678
168   S        -0.107  -0.180  -0.125  -0.146  -0.240  -0.150  -0.314  -0.405  -0.327
169   K        -0.107  -0.027  -0.098  -0.244  -0.115  -0.248  -0.314  -0.213  -0.287
170   K        -0.583  -0.674  -0.700  -0.644  -0.749  -0.788  -0.552  -0.660  -0.678
171   I         0.667   0.627   0.682   0.376   0.292   0.351   0.400   0.309   0.373
172   I        -0.763  -0.780  -0.751  -0.931  -0.950  -0.907  -0.790  -0.796  -0.742
173   I         0.190   0.075   0.022   0.144  -0.043  -0.153   0.162  -0.012  -0.095
174   K         1.050   1.151   0.937   0.938   1.088   0.789   1.114   1.285   0.886
175   G         1.980   2.011   2.107   2.141   2.201   2.361   2.304   2.359   2.533
176   N         0.550   0.575   0.658   0.414   0.452   0.591   0.162   0.200   0.322
177   A        -0.763  -0.780  -0.751  -0.621  -0.630  -0.556  -0.790  -0.796  -0.742
178   V        -0.107  -0.062  -0.101  -0.367  -0.314  -0.353  -0.314  -0.265  -0.295
179   E        -0.583  -0.587  -0.659  -0.559  -0.567  -0.744  -0.552  -0.557  -0.628
180   A        -1.240  -1.212  -1.193  -0.853  -0.824  -0.759  -1.028  -0.995  -0.944
181   V        -0.107  -0.076  -0.104  -0.411  -0.367  -0.415  -0.314  -0.273  -0.296
182   K         1.050   0.939   0.909   0.931   0.781   0.733   1.114   0.913   0.832
183   R        -0.763  -0.803  -0.728  -0.742  -0.788  -0.667  -0.790  -0.819  -0.716
184   V        -1.240  -1.256  -1.221  -1.056  -1.039  -0.986  -1.028  -1.035  -0.971
185   L         1.050   1.050   0.929   1.107   1.100   0.956   1.114   1.112   0.870
186   T        -1.240  -1.236  -1.198  -0.957  -0.941  -0.879  -1.028  -1.016  -0.949
187   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   K        -1.240  -1.236  -1.198  -1.280  -1.245  -1.198  -1.028  -1.016  -0.949
191   K        -0.583  -0.594  -0.636  -0.512  -0.523  -0.627  -0.552  -0.567  -0.599
192   F         0.190   0.183   0.012   0.447   0.445   0.144   0.162   0.154  -0.110
* 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/P25642
Output conservation file - output/P25642
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
