1     M         0.648   0.653   0.668   1.067   1.059   1.026   0.669   0.676   0.699
2     P         0.648   0.653   0.668   0.843   0.845   0.844   0.669   0.676   0.699
3     R        -0.686  -0.823  -0.817  -1.019  -1.215  -1.143  -0.795  -1.016  -1.049
4     A         0.648   0.653   0.668   0.592   0.605   0.640   0.669   0.676   0.699
5     P         0.648   0.653   0.668   0.851   0.856   0.851   0.669   0.676   0.699
6     R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
7     T        -1.371  -1.607  -1.698  -0.942  -1.264  -1.550  -1.279  -1.550  -1.654
8     Y        -0.612  -0.658  -0.801  -0.214  -0.282  -0.588  -0.687  -0.763  -1.023
9     S         0.648   0.653   0.668   0.770   0.782   0.784   0.669   0.676   0.699
10    K         0.648   0.653   0.668   0.566   0.584   0.619   0.669   0.676   0.699
11    T         0.648   0.653   0.668   0.939   0.941   0.922   0.669   0.676   0.699
12    Y        -0.612  -0.749  -0.828  -0.294  -0.521  -0.810  -0.687  -0.901  -1.068
13    S        -0.890  -0.977  -0.833  -0.948  -1.122  -0.957  -1.110  -1.263  -1.076
14    T        -1.098  -1.024  -0.834  -1.135  -1.036  -0.762  -1.449  -1.341  -1.076
15    P         0.648   0.653   0.668   0.851   0.856   0.851   0.669   0.676   0.699
16    K        -1.613  -1.665  -1.709  -1.823  -1.969  -1.833  -1.618  -1.705  -1.666
17    R        -0.171  -0.153  -0.790  -0.349  -0.320  -1.029  -0.094  -0.075  -1.005
18    P         0.648   0.653   0.668   0.851   0.856   0.851   0.669   0.676   0.699
19    Y        -1.047  -1.046  -0.837  -0.913  -0.928  -0.661  -1.364  -1.379  -1.081
20    E         0.648   0.653   0.668   0.592   0.599   0.640   0.669   0.676   0.699
21    S        -0.171  -0.402  -0.796   0.105  -0.171  -0.860  -0.094  -0.398  -1.016
22    S        -0.890  -0.703  -0.806  -1.033  -0.731  -0.915  -1.110  -0.831  -1.031
23    R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
24    L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
25    D         0.648   0.653   0.668   0.809   0.816   0.816   0.669   0.676   0.699
26    A        -0.171  -0.402  -0.796  -0.054  -0.315  -0.900  -0.094  -0.398  -1.016
27    E         0.648   0.653   0.668   0.592   0.599   0.640   0.669   0.676   0.699
28    L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
29    K         0.648   0.653   0.668   0.566   0.584   0.619   0.669   0.676   0.699
30    L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
31    A        -0.961  -1.177  -1.684  -0.691  -0.946  -1.638  -0.771  -1.033  -1.638
32    G         0.648   0.653   0.668   0.712   0.718   0.737   0.669   0.676   0.699
33    E         0.648   0.653   0.668   0.592   0.599   0.640   0.669   0.676   0.699
34    F        -1.047  -0.929  -0.829  -0.913  -0.714  -0.644  -1.364  -1.185  -1.068
35    G         0.648   0.653   0.668   0.712   0.718   0.737   0.669   0.676   0.699
36    L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
37    K        -0.890  -0.977  -0.833  -1.258  -1.458  -1.251  -1.110  -1.263  -1.076
38    N         0.648   0.653   0.668   1.002   0.999   0.973   0.669   0.676   0.699
39    K         0.648   0.653   0.668   0.566   0.584   0.619   0.669   0.676   0.699
40    K        -1.371  -1.365  -1.684  -1.497  -1.484  -1.827  -1.279  -1.294  -1.638
41    E         0.648   0.653   0.668   0.592   0.599   0.640   0.669   0.676   0.699
42    I        -0.171  -0.402  -0.796   0.151  -0.120  -0.766  -0.094  -0.398  -1.016
43    Y        -0.890  -0.977  -0.833  -0.554  -0.691  -0.537  -1.110  -1.263  -1.076
44    R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
45    I        -0.890  -0.977  -0.833  -0.847  -1.014  -0.837  -1.110  -1.263  -1.076
46    S        -2.575  -2.659  -2.337  -2.549  -2.690  -2.305  -2.296  -2.338  -1.968
47    F        -1.047  -1.047  -0.836  -1.243  -1.325  -1.003  -1.364  -1.379  -1.081
48    Q        -0.890  -0.977  -0.833  -0.652  -0.810  -0.655  -1.110  -1.263  -1.076
49    L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
50    S         0.648   0.653   0.668   0.770   0.782   0.784   0.669   0.676   0.699
51    K         0.648   0.653   0.668   0.566   0.584   0.619   0.669   0.676   0.699
52    I         0.648   0.653   0.668   0.798   0.808   0.807   0.669   0.676   0.699
53    R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
54    R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
55    A         0.648   0.653   0.668   0.592   0.605   0.640   0.669   0.676   0.699
56    A         0.648   0.653   0.668   0.592   0.605   0.640   0.669   0.676   0.699
57    R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
58    D        -1.613  -1.790  -1.708  -1.466  -1.690  -1.579  -1.618  -1.798  -1.665
59    L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
60    L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
61    T         0.648   0.653   0.668   0.939   0.941   0.922   0.669   0.676   0.699
62    R        -0.890  -0.977  -0.833  -1.504  -1.683  -1.391  -1.110  -1.263  -1.076
63    D         0.648   0.653   0.668   0.809   0.816   0.816   0.669   0.676   0.699
64    E         0.648   0.653   0.668   0.592   0.599   0.640   0.669   0.676   0.699
65    K         0.648   0.653   0.668   0.566   0.584   0.619   0.669   0.676   0.699
66    D         0.648   0.653   0.668   0.809   0.816   0.816   0.669   0.676   0.699
67    P         0.648   0.653   0.668   0.851   0.856   0.851   0.669   0.676   0.699
68    K         0.648   0.653   0.668   0.566   0.584   0.619   0.669   0.676   0.699
69    R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
70    L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
71    F         0.648   0.653   0.668   0.915   0.914   0.902   0.669   0.676   0.699
72    E         0.648   0.653   0.668   0.592   0.599   0.640   0.669   0.676   0.699
73    G         0.648   0.653   0.668   0.712   0.718   0.737   0.669   0.676   0.699
74    N         0.648   0.653   0.668   1.002   0.999   0.973   0.669   0.676   0.699
75    A         0.648   0.653   0.668   0.592   0.605   0.640   0.669   0.676   0.699
76    L        -0.612  -0.658  -0.801  -0.817  -0.877  -1.044  -0.687  -0.763  -1.023
77    I         0.648   0.653   0.668   0.798   0.808   0.807   0.669   0.676   0.699
78    R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
79    R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
80    L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
81    V         0.648   0.653   0.668   0.752   0.745   0.770   0.669   0.676   0.699
82    R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
83    V        -2.575  -2.559  -2.335  -2.549  -2.567  -2.144  -2.296  -2.273  -1.967
84    G         0.648   0.653   0.668   0.712   0.718   0.737   0.669   0.676   0.699
85    V        -0.612  -0.658  -0.801  -0.442  -0.519  -0.784  -0.687  -0.763  -1.023
86    L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
87    S        -1.613  -1.665  -1.709  -1.416  -1.506  -1.524  -1.618  -1.705  -1.666
88    E         0.648   0.653   0.668   0.592   0.599   0.640   0.669   0.676   0.699
89    D        -1.371  -1.547  -1.703  -0.991  -1.245  -1.479  -1.279  -1.513  -1.660
90    K        -1.047  -1.047  -0.836  -1.608  -1.651  -1.274  -1.364  -1.379  -1.081
91    K        -1.047  -0.897  -0.816  -1.005  -0.704  -0.712  -1.364  -1.133  -1.047
92    K         0.648   0.653   0.668   0.566   0.584   0.619   0.669   0.676   0.699
93    L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
94    D         0.648   0.653   0.668   0.809   0.816   0.816   0.669   0.676   0.699
95    Y         0.648   0.653   0.668   0.953   0.956   0.933   0.669   0.676   0.699
96    V         0.648   0.653   0.668   0.752   0.745   0.770   0.669   0.676   0.699
97    L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
98    A         0.648   0.653   0.668   0.592   0.605   0.640   0.669   0.676   0.699
99    L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
100   K        -2.094  -2.107  -2.320  -1.987  -2.024  -2.255  -1.788  -1.812  -1.953
101   V        -2.575  -2.597  -2.333  -2.341  -2.353  -2.054  -2.296  -2.283  -1.965
102   E         0.648   0.653   0.668   0.592   0.599   0.640   0.669   0.676   0.699
103   D         0.648   0.653   0.668   0.809   0.816   0.816   0.669   0.676   0.699
104   F         0.648   0.653   0.668   0.915   0.914   0.902   0.669   0.676   0.699
105   L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
106   E         0.648   0.653   0.668   0.592   0.599   0.640   0.669   0.676   0.699
107   R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
108   R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
109   L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
110   Q         0.648   0.653   0.668   0.929   0.925   0.913   0.669   0.676   0.699
111   T         0.648   0.653   0.668   0.939   0.941   0.922   0.669   0.676   0.699
112   Q        -0.171  -0.402  -0.796   0.323   0.063  -0.504  -0.094  -0.398  -1.016
113   V         0.648   0.653   0.668   0.752   0.745   0.770   0.669   0.676   0.699
114   Y        -1.098  -1.046  -0.837  -1.011  -0.930  -0.661  -1.449  -1.378  -1.082
115   K         0.648   0.653   0.668   0.566   0.584   0.619   0.669   0.676   0.699
116   L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
117   G         0.648   0.653   0.668   0.712   0.718   0.737   0.669   0.676   0.699
118   L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
119   A         0.648   0.653   0.668   0.592   0.605   0.640   0.669   0.676   0.699
120   K        -0.612  -0.539  -0.808  -0.753  -0.630  -1.180  -0.687  -0.589  -1.034
121   S         0.648   0.653   0.668   0.770   0.782   0.784   0.669   0.676   0.699
122   V        -1.047  -0.897  -0.816  -1.133  -0.866  -0.802  -1.364  -1.133  -1.047
123   H         0.648   0.653   0.668   0.991   0.986   0.964   0.669   0.676   0.699
124   H         0.648   0.653   0.668   0.991   0.986   0.964   0.669   0.676   0.699
125   A         0.648   0.653   0.668   0.592   0.605   0.640   0.669   0.676   0.699
126   R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
127   V         0.648   0.653   0.668   0.752   0.745   0.770   0.669   0.676   0.699
128   L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
129   I         0.648   0.653   0.668   0.798   0.808   0.807   0.669   0.676   0.699
130   T        -2.426  -2.542  -2.334  -1.997  -2.199  -2.077  -2.126  -2.220  -1.966
131   Q         0.648   0.653   0.668   0.929   0.925   0.913   0.669   0.676   0.699
132   R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
133   H         0.648   0.653   0.668   0.991   0.986   0.964   0.669   0.676   0.699
134   I         0.648   0.653   0.668   0.798   0.808   0.807   0.669   0.676   0.699
135   A        -1.047  -1.047  -0.836  -1.584  -1.634  -1.257  -1.364  -1.379  -1.081
136   V         0.648   0.653   0.668   0.752   0.745   0.770   0.669   0.676   0.699
137   G         0.648   0.653   0.668   0.712   0.718   0.737   0.669   0.676   0.699
138   K         0.648   0.653   0.668   0.566   0.584   0.619   0.669   0.676   0.699
139   Q         0.648   0.653   0.668   0.929   0.925   0.913   0.669   0.676   0.699
140   I         0.648   0.653   0.668   0.798   0.808   0.807   0.669   0.676   0.699
141   V         0.648   0.653   0.668   0.752   0.745   0.770   0.669   0.676   0.699
142   N         0.648   0.653   0.668   1.002   0.999   0.973   0.669   0.676   0.699
143   I        -1.098  -1.012  -0.830  -1.237  -1.097  -0.834  -1.449  -1.321  -1.070
144   P         0.648   0.653   0.668   0.851   0.856   0.851   0.669   0.676   0.699
145   S         0.648   0.653   0.668   0.770   0.782   0.784   0.669   0.676   0.699
146   F         0.648   0.653   0.668   0.915   0.914   0.902   0.669   0.676   0.699
147   M        -1.613  -1.599  -1.704  -1.162  -1.241  -1.350  -1.618  -1.649  -1.661
148   V         0.648   0.653   0.668   0.752   0.745   0.770   0.669   0.676   0.699
149   R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
150   L         0.648   0.653   0.668   0.371   0.378   0.460   0.669   0.676   0.699
151   D        -0.612  -0.536  -0.820  -0.436  -0.324  -0.883  -0.687  -0.585  -1.053
152   S        -0.961  -1.042  -1.681  -0.516  -0.598  -1.535  -0.771  -0.867  -1.634
153   E        -1.047  -0.897  -0.816  -1.110  -0.822  -0.793  -1.364  -1.133  -1.047
154   K         0.648   0.653   0.668   0.566   0.584   0.619   0.669   0.676   0.699
155   H         0.648   0.653   0.668   0.991   0.986   0.964   0.669   0.676   0.699
156   I         0.648   0.653   0.668   0.798   0.808   0.807   0.669   0.676   0.699
157   D         0.648   0.653   0.668   0.809   0.816   0.816   0.669   0.676   0.699
158   F         0.648   0.653   0.668   0.915   0.914   0.902   0.669   0.676   0.699
159   A         0.648   0.653   0.668   0.592   0.605   0.640   0.669   0.676   0.699
160   P        -2.575  -2.338  -2.330  -2.634  -2.333  -2.294  -2.296  -2.057  -1.962
161   T        -1.945  -1.919  -1.706  -1.626  -1.590  -1.371  -1.957  -1.924  -1.663
162   S         0.648   0.653   0.668   0.770   0.782   0.784   0.669   0.676   0.699
163   P         0.648   0.653   0.668   0.851   0.856   0.851   0.669   0.676   0.699
164   F        -1.098  -1.046  -0.837  -1.011  -0.927  -0.660  -1.449  -1.378  -1.082
165   G         0.648   0.653   0.668   0.712   0.718   0.737   0.669   0.676   0.699
166   G         0.648   0.653   0.668   0.712   0.718   0.737   0.669   0.676   0.699
167   A        -1.047  -0.897  -0.816  -1.298  -1.012  -0.940  -1.364  -1.133  -1.047
168   R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
169   P        -0.612  -0.539  -0.808  -0.394  -0.288  -0.827  -0.687  -0.589  -1.034
170   G         0.648   0.653   0.668   0.712   0.718   0.737   0.669   0.676   0.699
171   R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
172   V        -0.612  -0.658  -0.801  -0.358  -0.429  -0.626  -0.687  -0.763  -1.023
173   A        -1.728  -1.786  -1.700  -2.020  -2.047  -1.989  -1.788  -1.792  -1.656
174   R         0.648   0.653   0.668   0.279   0.291   0.386   0.669   0.676   0.699
175   R        -0.612  -0.563  -0.821  -0.753  -0.668  -1.214  -0.687  -0.624  -1.055
176   N        -1.613  -1.767  -1.703  -1.477  -1.711  -1.774  -1.618  -1.765  -1.660
177   A        -2.707  -2.523  -2.324  -2.742  -2.499  -2.203  -2.380  -2.203  -1.957
178   A        -3.623  -3.619  -3.221  -3.436  -3.472  -2.799  -2.719  -2.685  -2.269
179   R        -2.426  -2.446  -2.330  -2.459  -2.500  -2.418  -2.126  -2.160  -1.962
180   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   A        -2.119  -2.017  -1.707  -2.165  -2.020  -1.601  -2.155  -2.038  -1.663
182   E         0.648   0.653   0.668   0.597   0.606   0.644   0.669   0.676   0.699
183   A        -1.371  -1.256  -1.684  -1.157  -0.986  -1.651  -1.279  -1.138  -1.637
184   S        -0.961  -0.911  -1.676  -0.595  -0.534  -1.635  -0.771  -0.718  -1.628
185   G        -2.426  -2.246  -2.322  -2.284  -2.014  -2.116  -2.126  -1.930  -1.956
186   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   A        -2.024  -1.942  -1.715  -2.245  -2.113  -1.791  -2.050  -1.958  -1.673
192   D        -1.613  -1.438  -1.693  -1.599  -1.351  -1.661  -1.618  -1.411  -1.648
193   E        -0.612  -0.539  -0.808  -0.651  -0.543  -1.006  -0.687  -0.589  -1.034
194   A        -1.047  -1.035  -0.837  -1.403  -1.387  -1.064  -1.364  -1.359  -1.082
195   D        -1.047  -1.013  -0.836  -1.214  -1.162  -0.924  -1.364  -1.323  -1.080
196   E         0.648   0.653   0.668   0.592   0.599   0.640   0.669   0.676   0.699
197   E         0.648   0.653   0.668   0.592   0.599   0.640   0.669   0.676   0.699
* 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/O13516
Output conservation file - output/O13516
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
