1     M         1.899   1.942   2.028   2.147   2.212   2.346   2.130   2.194   2.351
2     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     V        -0.403  -0.364  -0.400  -0.411  -0.353  -0.417  -0.532  -0.495  -0.510
7     K        -1.252  -1.249  -1.213  -1.430  -1.378  -1.370  -1.001  -0.987  -0.927
8     C         1.899   1.942   2.028   2.001   2.066   2.198   2.130   2.194   2.351
9     G        -0.760  -0.794  -0.805  -0.522  -0.608  -0.618  -0.688  -0.723  -0.714
10    I         0.464   0.500   0.315   0.624   0.682   0.431   0.408   0.462   0.165
11    C         1.899   1.942   2.028   2.001   2.066   2.198   2.130   2.194   2.351
12    R        -1.252  -1.149  -1.189  -1.025  -0.853  -0.920  -1.001  -0.894  -0.907
13    G        -0.914  -0.892  -0.879  -0.917  -0.896  -0.880  -0.853  -0.825  -0.789
14    V        -1.609  -1.572  -1.524  -1.572  -1.525  -1.439  -1.158  -1.115  -1.045
15    D         0.176   0.300   0.202   0.030   0.216   0.085  -0.062   0.133  -0.022
16    G        -0.760  -0.741  -0.806  -0.597  -0.609  -0.631  -0.688  -0.668  -0.715
17    K         1.160   1.214   1.069   1.013   1.115   0.865   1.190   1.276   0.996
18    Y         1.899   1.942   2.028   2.031   2.100   2.228   2.130   2.194   2.351
19    K         0.464   0.500   0.315   0.427   0.507   0.231   0.408   0.462   0.165
20    C         1.899   1.942   2.028   2.001   2.066   2.198   2.130   2.194   2.351
21    P         1.899   1.942   2.028   2.065   2.107   2.263   2.130   2.194   2.351
22    K         1.899   1.942   2.028   1.723   1.811   1.915   2.130   2.194   2.351
23    C         1.160   1.214   1.069   1.312   1.390   1.179   1.190   1.276   0.996
24    G        -0.403  -0.340  -0.369  -0.394  -0.314  -0.329  -0.532  -0.437  -0.465
25    V        -0.403  -0.462  -0.407  -0.363  -0.424  -0.361  -0.532  -0.586  -0.516
26    R        -0.760  -0.768  -0.801  -0.469  -0.475  -0.549  -0.688  -0.695  -0.710
27    Y         1.899   1.942   2.028   2.031   2.100   2.228   2.130   2.194   2.351
28    C         1.899   1.942   2.028   2.001   2.066   2.198   2.130   2.194   2.351
29    S         1.899   1.942   2.028   1.821   1.867   2.015   2.130   2.194   2.351
30    L         1.160   1.208   1.069   1.027   1.082   0.904   1.190   1.264   0.997
31    K        -1.252  -1.215  -1.202  -1.025  -0.943  -0.944  -1.001  -0.959  -0.918
32    C         1.899   1.942   2.028   2.001   2.066   2.198   2.130   2.194   2.351
33    Y         0.464   0.347   0.276   0.793   0.654   0.569   0.408   0.220   0.105
34    K         1.899   1.942   2.028   1.723   1.811   1.915   2.130   2.194   2.351
35    D        -0.895  -0.919  -0.860  -0.932  -0.963  -0.893  -0.845  -0.855  -0.774
36    A        -0.914  -0.914  -0.867  -0.842  -0.830  -0.747  -0.853  -0.841  -0.778
37    A        -0.914  -0.892  -0.861  -1.060  -1.025  -0.982  -0.853  -0.819  -0.772
38    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    H         1.160   1.214   1.069   1.404   1.491   1.271   1.190   1.276   0.996
40    V        -1.252  -1.243  -1.197  -1.087  -1.054  -0.996  -1.001  -0.983  -0.913
41    H         0.176   0.138   0.134   0.241   0.135   0.132  -0.062  -0.135  -0.137
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    K        -0.403  -0.344  -0.394  -0.624  -0.531  -0.584  -0.532  -0.457  -0.500
56    E        -1.252  -1.249  -1.213  -1.183  -1.140  -1.099  -1.001  -0.987  -0.927
57    S        -0.895  -0.889  -0.861  -0.974  -0.966  -0.915  -0.845  -0.829  -0.775
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    E        -0.914  -0.892  -0.879  -0.964  -0.949  -0.939  -0.853  -0.825  -0.789
63    Q        -0.498  -0.430  -0.438  -0.648  -0.566  -0.555  -0.640  -0.556  -0.551
64    P         0.752   0.741   0.794   0.680   0.652   0.728   0.425   0.381   0.436
65    R        -1.609  -1.572  -1.524  -1.548  -1.542  -1.416  -1.158  -1.115  -1.045
66    A        -1.252  -1.138  -1.189  -1.197  -0.994  -1.105  -1.001  -0.882  -0.906
67    G        -0.895  -0.837  -0.850  -0.818  -0.712  -0.710  -0.845  -0.777  -0.765
68    T         0.076   0.102   0.099   0.071   0.103   0.117  -0.214  -0.189  -0.187
69    E         1.160   1.238   1.067   1.108   1.205   0.993   1.190   1.314   0.992
70    A        -0.895  -0.930  -0.860  -0.814  -0.850  -0.772  -0.845  -0.863  -0.774
71    N        -0.895  -0.812  -0.842  -0.935  -0.831  -0.850  -0.845  -0.753  -0.758
72    V        -1.252  -1.245  -1.215  -1.004  -0.967  -0.939  -1.001  -0.985  -0.928
73    E        -1.252  -1.246  -1.203  -1.263  -1.228  -1.178  -1.001  -0.985  -0.919
74    V         0.821   0.913   0.860   0.777   0.935   0.811   0.564   0.727   0.578
75    V        -0.760  -0.762  -0.802  -0.787  -0.825  -0.870  -0.688  -0.690  -0.711
76    N        -1.609  -1.572  -1.524  -1.503  -1.428  -1.370  -1.158  -1.115  -1.045
77    N        -0.760  -0.741  -0.806  -0.636  -0.600  -0.715  -0.688  -0.668  -0.715
78    D        -0.403  -0.462  -0.412  -0.336  -0.406  -0.336  -0.532  -0.591  -0.522
79    K        -0.895  -0.918  -0.865  -1.049  -1.021  -0.989  -0.845  -0.853  -0.778
80    I        -0.895  -0.896  -0.853  -0.794  -0.765  -0.721  -0.845  -0.835  -0.768
81    I        -0.002   0.047   0.076  -0.286  -0.221  -0.165  -0.325  -0.259  -0.219
82    N        -0.502  -0.368  -0.435  -0.453  -0.232  -0.360  -0.632  -0.457  -0.540
83    S         0.997   0.993   0.956   0.912   0.898   0.835   0.902   0.882   0.774
84    S        -0.502  -0.514  -0.467  -0.564  -0.603  -0.531  -0.632  -0.644  -0.579
85    L        -1.002  -0.964  -0.910  -1.129  -1.040  -0.989  -0.939  -0.890  -0.819
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    N         0.025   0.030   0.080  -0.298  -0.319  -0.238  -0.267  -0.265  -0.204
90    K        -0.600  -0.574  -0.503  -0.846  -0.785  -0.700  -0.747  -0.709  -0.621
91    T        -0.340  -0.343  -0.373  -0.411  -0.445  -0.495  -0.427  -0.434  -0.463
92    L        -0.340  -0.180  -0.350  -0.171   0.061  -0.202  -0.427  -0.213  -0.433
93    K        -0.340  -0.390  -0.392  -0.423  -0.502  -0.485  -0.427  -0.491  -0.487
94    T        -0.895  -0.909  -0.862  -1.027  -1.078  -0.970  -0.845  -0.845  -0.776
95    K        -0.760  -0.605  -0.767  -0.820  -0.575  -0.851  -0.688  -0.503  -0.673
96    A        -0.181  -0.238  -0.312  -0.274  -0.381  -0.488  -0.218  -0.301  -0.385
97    F         0.089   0.015   0.115   0.120  -0.007   0.151  -0.218  -0.298  -0.170
98    D        -0.403  -0.437  -0.403  -0.397  -0.460  -0.413  -0.532  -0.561  -0.508
99    D        -1.252  -1.232  -1.215  -1.203  -1.190  -1.115  -1.001  -0.974  -0.929
100   I         0.089   0.126   0.120  -0.192  -0.142  -0.118  -0.218  -0.168  -0.163
101   Y        -0.538  -0.569  -0.469  -0.693  -0.734  -0.590  -0.688  -0.704  -0.586
102   Q        -1.252  -1.256  -1.201  -1.179  -1.216  -1.119  -1.001  -0.994  -0.917
103   N         0.821   0.934   0.900   0.787   0.990   0.897   0.564   0.768   0.661
104   S        -0.181  -0.265  -0.332  -0.131  -0.277  -0.359  -0.218  -0.333  -0.410
105   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   E        -0.895  -0.926  -0.872  -0.873  -0.932  -0.814  -0.845  -0.860  -0.785
107   L         1.160   1.274   1.081   1.198   1.359   1.073   1.190   1.374   1.019
108   Q        -0.046  -0.029   0.041  -0.170  -0.159  -0.065  -0.375  -0.353  -0.264
109   E        -0.760  -0.814  -0.833  -0.839  -0.940  -0.966  -0.688  -0.743  -0.743
110   L         1.160   1.208   1.069   1.070   1.124   0.975   1.190   1.264   0.997
111   L         1.160   1.019   1.034   1.027   0.816   0.848   1.190   0.929   0.928
112   K        -0.895  -0.927  -0.853  -1.030  -1.100  -0.961  -0.845  -0.861  -0.768
113   Y        -0.760  -0.797  -0.810  -0.434  -0.521  -0.499  -0.688  -0.726  -0.719
114   N        -0.181  -0.124  -0.299  -0.025   0.060  -0.207  -0.218  -0.139  -0.367
115   T         0.089   0.017   0.105  -0.098  -0.184  -0.050  -0.218  -0.296  -0.181
116   V        -0.403  -0.474  -0.431  -0.548  -0.689  -0.620  -0.532  -0.602  -0.541
117   K         0.176   0.092   0.141  -0.064  -0.188  -0.134  -0.062  -0.171  -0.118
118   F         0.464   0.328   0.266   0.736   0.511   0.401   0.408   0.192   0.088
119   H         1.899   1.942   2.028   2.094   2.167   2.292   2.130   2.194   2.351
120   L         1.160   1.019   1.034   1.027   0.816   0.848   1.190   0.929   0.928
121   A        -1.252  -1.266  -1.220  -1.149  -1.131  -1.126  -1.001  -1.001  -0.933
122   K        -0.181  -0.124  -0.299  -0.207  -0.098  -0.369  -0.218  -0.139  -0.367
123   V         0.650   0.682   0.765   0.440   0.490   0.612   0.212   0.256   0.374
124   Y        -0.914  -0.910  -0.877  -0.778  -0.773  -0.731  -0.853  -0.837  -0.788
125   R         0.335   0.356   0.223   0.230   0.270   0.069   0.212   0.242   0.020
126   I         1.087   1.077   0.980   1.111   1.101   0.912   1.064   1.035   0.822
127   L         1.087   1.100   0.988   0.944   0.957   0.791   1.064   1.077   0.838
128   S        -0.914  -0.884  -0.857  -1.011  -0.964  -0.940  -0.853  -0.810  -0.768
129   -         0.886   0.861   0.881   0.842   0.804   0.810   0.691   0.626   0.620
130   S        -0.340  -0.307  -0.383  -0.293  -0.248  -0.344  -0.427  -0.379  -0.475
131   T         0.335   0.305   0.202   0.301   0.245   0.040   0.212   0.164  -0.012
132   V        -0.340  -0.360  -0.417  -0.251  -0.292  -0.395  -0.427  -0.446  -0.518
133   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   S         0.176   0.092   0.141  -0.004  -0.159  -0.079  -0.062  -0.171  -0.118
139   S        -1.002  -0.961  -0.910  -1.103  -1.093  -0.962  -0.939  -0.888  -0.819
140   G        -1.252  -1.246  -1.203  -0.980  -0.949  -0.909  -1.001  -0.985  -0.919
141   K        -0.538  -0.477  -0.465  -0.854  -0.762  -0.744  -0.688  -0.619  -0.582
142   M        -0.403  -0.474  -0.431  -0.321  -0.479  -0.395  -0.532  -0.602  -0.541
143   N        -0.895  -0.899  -0.851  -0.864  -0.851  -0.790  -0.845  -0.838  -0.766
144   S        -0.760  -0.814  -0.833  -0.797  -0.890  -0.936  -0.688  -0.743  -0.743
145   D         0.821   0.904   0.884   0.604   0.730   0.687   0.564   0.711   0.626
146   L        -1.609  -1.572  -1.524  -1.355  -1.328  -1.219  -1.158  -1.115  -1.045
147   Q        -0.403  -0.433  -0.406  -0.510  -0.559  -0.498  -0.532  -0.564  -0.514
148   K        -0.760  -0.810  -0.812  -0.712  -0.738  -0.751  -0.688  -0.739  -0.721
149   E        -0.181  -0.205  -0.313  -0.186  -0.263  -0.381  -0.218  -0.260  -0.385
150   L         0.089   0.017   0.105  -0.203  -0.289  -0.149  -0.218  -0.296  -0.181
151   A         1.160   1.019   1.034   1.366   1.186   1.207   1.190   0.929   0.928
152   V        -0.760  -0.741  -0.806  -0.682  -0.705  -0.780  -0.688  -0.668  -0.715
153   N        -0.403  -0.415  -0.410  -0.631  -0.673  -0.643  -0.532  -0.538  -0.517
154   Y        -0.403  -0.474  -0.431  -0.399  -0.484  -0.437  -0.532  -0.602  -0.541
155   L         1.899   1.942   2.028   1.703   1.751   1.894   2.130   2.194   2.351
156   N        -0.181  -0.286  -0.333  -0.075  -0.239  -0.339  -0.218  -0.359  -0.412
157   T        -0.760  -0.814  -0.833  -0.638  -0.706  -0.761  -0.688  -0.743  -0.743
158   L         1.160   1.019   1.034   1.027   0.816   0.848   1.190   0.929   0.928
159   R         1.160   1.019   1.034   1.429   1.242   1.262   1.190   0.929   0.928
160   Y        -1.252  -1.266  -1.220  -1.027  -1.037  -0.987  -1.001  -1.001  -0.933
161   G         1.160   1.019   1.034   1.410   1.231   1.243   1.190   0.929   0.928
162   G         1.160   1.019   1.034   1.423   1.249   1.267   1.190   0.929   0.928
163   I         0.176   0.136   0.132  -0.023  -0.147  -0.158  -0.062  -0.137  -0.139
164   H         0.176   0.215   0.165   0.217   0.293   0.186  -0.062   0.002  -0.081
165   Y        -0.498  -0.500  -0.465  -0.452  -0.460  -0.409  -0.640  -0.631  -0.580
166   N         1.899   1.942   2.028   1.932   1.995   2.128   2.130   2.194   2.351
167   E         1.160   1.019   1.034   1.117   0.918   0.961   1.190   0.929   0.928
168   A         0.176   0.092   0.141   0.093  -0.046  -0.002  -0.062  -0.171  -0.118
169   I        -0.403  -0.428  -0.406  -0.412  -0.422  -0.411  -0.532  -0.555  -0.512
170   E         1.899   1.942   2.028   1.765   1.818   1.957   2.130   2.194   2.351
171   E         0.464   0.347   0.276   0.405   0.212   0.108   0.408   0.220   0.105
172   F         1.160   1.019   1.034   1.405   1.189   1.197   1.190   0.929   0.928
173   C         0.176   0.092   0.141   0.242   0.134   0.194  -0.062  -0.171  -0.118
174   Q         0.464   0.347   0.276   0.629   0.442   0.310   0.408   0.220   0.105
175   I        -0.403  -0.418  -0.410  -0.288  -0.278  -0.299  -0.532  -0.541  -0.517
176   L        -1.609  -1.572  -1.524  -1.364  -1.295  -1.228  -1.158  -1.115  -1.045
177   L         1.160   1.265   1.074   1.038   1.165   0.929   1.190   1.360   1.005
178   D        -0.403  -0.312  -0.370  -0.440  -0.317  -0.364  -0.532  -0.415  -0.472
179   K         0.668   0.690   0.769   0.131   0.158   0.267   0.251   0.274   0.384
180   L         0.176   0.083   0.136   0.060  -0.065   0.041  -0.062  -0.185  -0.128
181   N        -0.760  -0.794  -0.805  -0.536  -0.596  -0.590  -0.688  -0.723  -0.714
182   A        -0.002   0.031   0.077  -0.238  -0.182  -0.113  -0.325  -0.279  -0.217
183   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
184   K        -0.600  -0.574  -0.503  -0.619  -0.563  -0.470  -0.747  -0.709  -0.621
185   K         0.076   0.097   0.113  -0.176  -0.132  -0.104  -0.214  -0.183  -0.165
* 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/P46973
Output conservation file - output/P46973
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
