1     M         1.812   1.908   2.035   2.009   2.169   2.372   2.011   2.172   2.388
2     A        -0.129  -0.074  -0.177  -0.229  -0.153  -0.342  -0.251  -0.171  -0.325
3     D        -0.312  -0.257  -0.220  -0.412  -0.344  -0.288  -0.513  -0.439  -0.387
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     Q        -0.129  -0.090  -0.177  -0.017   0.043  -0.140  -0.251  -0.194  -0.325
6     V        -0.910  -0.867  -0.833  -1.075  -1.022  -0.981  -0.897  -0.837  -0.771
7     P        -0.910  -0.877  -0.864  -0.920  -0.877  -0.873  -0.897  -0.849  -0.806
8     V         0.437   0.503   0.594   0.127   0.214   0.343   0.072   0.161   0.280
9     T        -0.343  -0.300  -0.250  -0.398  -0.339  -0.281  -0.574  -0.516  -0.433
10    T        -0.910  -0.877  -0.849  -0.826  -0.781  -0.721  -0.897  -0.849  -0.789
11    Q        -0.910  -0.876  -0.831  -0.829  -0.782  -0.701  -0.897  -0.848  -0.769
12    L        -0.910  -0.877  -0.834  -1.028  -0.991  -0.942  -0.897  -0.849  -0.772
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    P        -0.312  -0.301  -0.257  -0.338  -0.329  -0.254  -0.513  -0.502  -0.440
17    P        -0.312  -0.260  -0.219  -0.359  -0.286  -0.231  -0.513  -0.443  -0.386
18    I        -0.129  -0.073  -0.156  -0.160  -0.079  -0.204  -0.251  -0.170  -0.294
19    K        -0.910  -0.867  -0.833  -1.071  -1.018  -0.976  -0.897  -0.837  -0.771
20    P        -0.910  -0.877  -0.864  -0.930  -0.888  -0.847  -0.897  -0.849  -0.806
21    E        -1.476  -1.454  -1.350  -1.331  -1.297  -1.134  -1.220  -1.182  -1.037
22    H        -0.910  -0.876  -0.831  -0.758  -0.709  -0.635  -0.897  -0.848  -0.769
23    E        -0.910  -0.877  -0.831  -1.007  -0.968  -0.883  -0.897  -0.849  -0.769
24    V        -0.129  -0.073  -0.190  -0.139  -0.059  -0.241  -0.251  -0.170  -0.345
25    P         0.437   0.498   0.592   0.311   0.395   0.533   0.072   0.151   0.277
26    L        -0.910  -0.877  -0.864  -1.090  -1.053  -1.028  -0.897  -0.849  -0.806
27    D        -0.910  -0.867  -0.831  -1.028  -0.975  -0.908  -0.897  -0.838  -0.769
28    A        -0.129  -0.074  -0.159  -0.163  -0.084  -0.220  -0.251  -0.171  -0.298
29    G        -0.910  -0.877  -0.849  -0.735  -0.686  -0.622  -0.897  -0.849  -0.789
30    G        -0.343  -0.300  -0.231  -0.549  -0.497  -0.391  -0.574  -0.516  -0.410
31    S         1.812   1.908   2.035   1.713   1.858   2.062   2.011   2.172   2.388
32    P        -1.476  -1.454  -1.350  -1.569  -1.549  -1.384  -1.220  -1.182  -1.037
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    V        -0.312  -0.218  -0.220  -0.434  -0.289  -0.318  -0.513  -0.382  -0.388
36    G        -0.312  -0.301  -0.244  -0.478  -0.484  -0.422  -0.513  -0.503  -0.422
37    N        -0.312  -0.301  -0.244  -0.277  -0.285  -0.224  -0.513  -0.503  -0.422
38    M        -1.476  -1.454  -1.350  -1.414  -1.387  -1.222  -1.220  -1.182  -1.037
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    G        -0.343  -0.299  -0.253  -0.532  -0.477  -0.421  -0.574  -0.515  -0.436
48    T         0.437   0.498   0.592   0.170   0.248   0.383   0.072   0.151   0.277
49    N        -0.910  -0.877  -0.831  -0.758  -0.706  -0.654  -0.897  -0.849  -0.769
50    S        -0.129  -0.074  -0.177  -0.181  -0.103  -0.310  -0.251  -0.171  -0.325
51    N        -0.312  -0.301  -0.244  -0.306  -0.315  -0.262  -0.513  -0.503  -0.422
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    N        -1.476  -1.454  -1.350  -1.376  -1.348  -1.182  -1.220  -1.182  -1.037
61    N        -0.910  -0.877  -0.864  -0.723  -0.673  -0.658  -0.897  -0.849  -0.806
62    N        -1.476  -1.454  -1.350  -1.514  -1.492  -1.327  -1.220  -1.182  -1.037
63    E        -0.910  -0.877  -0.849  -0.906  -0.864  -0.782  -0.897  -0.849  -0.789
64    L        -0.910  -0.877  -0.864  -0.979  -0.939  -0.919  -0.897  -0.849  -0.806
65    G        -1.377  -1.382  -1.336  -1.314  -1.346  -1.272  -1.130  -1.120  -1.025
66    D         0.040   0.168  -0.140  -0.017   0.171  -0.304  -0.009   0.180  -0.270
67    V        -0.254  -0.287  -0.218  -0.476  -0.536  -0.447  -0.457  -0.485  -0.388
68    F         0.892   0.783   0.771   1.103   0.956   0.935   0.889   0.689   0.629
69    D        -0.140  -0.070  -0.170  -0.290  -0.180  -0.315  -0.297  -0.186  -0.322
70    R         0.185   0.261  -0.077   0.207   0.303  -0.186   0.198   0.312  -0.177
71    I         0.974   0.821   0.749   1.020   0.826   0.694   1.022   0.757   0.588
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    K         1.812   1.908   2.035   1.676   1.811   2.022   2.011   2.172   2.388
75    T         1.812   1.908   2.035   1.809   1.965   2.162   2.011   2.172   2.388
76    H         0.185   0.022  -0.065   0.603   0.362   0.235   0.198  -0.040  -0.160
77    F         0.974   0.821   0.749   1.185   0.975   0.851   1.022   0.757   0.588
78    P         1.812   1.908   2.035   1.894   2.059   2.251   2.011   2.172   2.388
79    P        -0.797  -0.862  -0.817  -0.765  -0.859  -0.805  -0.792  -0.841  -0.756
80    A         0.974   0.821   0.749   0.965   0.756   0.617   1.022   0.757   0.588
81    K         0.417   0.510   0.593   0.190   0.332   0.446   0.033   0.175   0.278
82    V         0.417   0.462   0.577   0.105   0.151   0.327   0.033   0.080   0.247
83    K         1.812   1.908   2.035   1.676   1.811   2.022   2.011   2.172   2.388
84    K         0.974   0.821   0.749   0.956   0.750   0.657   1.022   0.757   0.588
85    I         0.974   1.026   0.780   1.016   1.106   0.736   1.022   1.105   0.646
86    M         0.974   0.821   0.749   1.263   1.065   0.921   1.022   0.757   0.588
87    Q         0.974   0.821   0.749   1.149   0.929   0.787   1.022   0.757   0.588
88    T        -0.140  -0.223  -0.196  -0.213  -0.307  -0.279  -0.297  -0.391  -0.359
89    D         1.812   1.908   2.035   1.789   1.932   2.141   2.011   2.172   2.388
90    E         0.974   1.026   0.780   0.909   0.995   0.630   1.022   1.105   0.646
91    D         0.974   1.125   0.820   1.027   1.238   0.790   1.022   1.261   0.722
92    I         0.974   0.821   0.749   1.009   0.804   0.665   1.022   0.757   0.588
93    G         0.974   0.821   0.749   1.205   1.047   0.941   1.022   0.757   0.588
94    K         0.974   0.821   0.749   0.992   0.811   0.747   1.022   0.757   0.588
95    V         0.974   0.821   0.749   1.062   0.888   0.820   1.022   0.757   0.588
96    S         0.417   0.508   0.595   0.060   0.204   0.319   0.033   0.171   0.284
97    Q         0.974   0.821   0.749   1.202   1.023   0.924   1.022   0.757   0.588
98    A         1.812   1.908   2.035   1.716   1.866   2.065   2.011   2.172   2.388
99    T         0.974   0.821   0.749   1.058   0.855   0.710   1.022   0.757   0.588
100   P         0.974   0.821   0.749   1.142   0.945   0.791   1.022   0.757   0.588
101   V         0.185   0.022  -0.065   0.280   0.030  -0.089   0.198  -0.040  -0.160
102   I         0.185   0.022  -0.065   0.275   0.034  -0.112   0.198  -0.040  -0.160
103   A        -0.797  -0.838  -0.830  -0.857  -0.927  -0.916  -0.792  -0.821  -0.772
104   G         0.185   0.022  -0.065   0.407   0.173   0.005   0.198  -0.040  -0.160
105   R         0.185   0.022  -0.065   0.410   0.146   0.003   0.198  -0.040  -0.160
106   S         0.417   0.510   0.593   0.058   0.206   0.312   0.033   0.175   0.278
107   L         0.974   0.821   0.749   1.046   0.827   0.720   1.022   0.757   0.588
108   E         1.812   1.908   2.035   1.649   1.796   1.994   2.011   2.172   2.388
109   F        -0.392  -0.346  -0.257  -0.494  -0.456  -0.313  -0.627  -0.571  -0.442
110   F         1.812   1.908   2.035   1.926   2.077   2.285   2.011   2.172   2.388
111   I        -0.140  -0.223  -0.196  -0.013  -0.131  -0.139  -0.297  -0.391  -0.359
112   A         0.185   0.022  -0.065   0.216  -0.038  -0.189   0.198  -0.040  -0.160
113   L        -0.797  -0.862  -0.817  -0.732  -0.873  -0.779  -0.792  -0.841  -0.756
114   L         1.812   1.908   2.035   1.783   1.911   2.134   2.011   2.172   2.388
115   V         0.185   0.022  -0.065   0.257   0.002  -0.136   0.198  -0.040  -0.160
116   K        -0.797  -0.835  -0.830  -0.980  -1.040  -1.020  -0.792  -0.819  -0.772
117   K        -0.797  -0.700  -0.798  -1.015  -0.925  -1.040  -0.792  -0.696  -0.740
118   S         0.185   0.022  -0.065   0.247   0.005  -0.134   0.198  -0.040  -0.160
119   G        -1.759  -1.735  -1.709  -1.301  -1.204  -1.196  -1.286  -1.250  -1.162
120   E        -2.164  -2.114  -2.058  -1.940  -1.825  -1.774  -1.451  -1.394  -1.282
121   M        -1.354  -1.381  -1.320  -1.218  -1.265  -1.143  -1.121  -1.126  -1.013
122   A         1.812   1.908   2.035   1.716   1.866   2.065   2.011   2.172   2.388
123   R         0.417   0.467   0.578   0.190   0.224   0.399   0.033   0.090   0.248
124   G        -1.759  -1.760  -1.721  -1.512  -1.528  -1.401  -1.286  -1.269  -1.171
125   Q        -0.140  -0.008  -0.165  -0.044   0.143  -0.092  -0.297  -0.121  -0.319
126   G         0.185   0.022  -0.065   0.454   0.221   0.097   0.198  -0.040  -0.160
127   T        -1.354  -1.357  -1.310  -1.252  -1.247  -1.135  -1.121  -1.106  -1.004
128   K         0.974   1.141   0.814   0.956   1.171   0.761   1.022   1.286   0.711
129   R         0.974   0.821   0.749   1.185   0.987   0.880   1.022   0.757   0.588
130   I         0.974   1.026   0.780   1.009   1.101   0.720   1.022   1.105   0.646
131   T        -0.797  -0.826  -0.788  -0.754  -0.791  -0.714  -0.792  -0.816  -0.728
132   A         0.185   0.022  -0.065   0.338   0.152   0.050   0.198  -0.040  -0.160
133   E        -0.797  -0.838  -0.830  -0.861  -0.910  -0.905  -0.792  -0.821  -0.772
134   I        -0.797  -0.836  -0.832  -0.602  -0.666  -0.690  -0.792  -0.820  -0.773
135   L        -0.797  -0.706  -0.790  -0.776  -0.698  -0.746  -0.792  -0.698  -0.731
136   K        -0.140  -0.205  -0.185  -0.270  -0.395  -0.345  -0.297  -0.365  -0.347
137   K        -0.950  -0.904  -0.841  -1.111  -1.039  -0.919  -0.956  -0.892  -0.784
138   T        -0.240  -0.316  -0.217  -0.429  -0.535  -0.382  -0.462  -0.535  -0.391
139   I         0.417   0.461   0.578   0.105   0.148   0.328   0.033   0.078   0.249
140   L        -0.140  -0.196  -0.196  -0.231  -0.299  -0.317  -0.297  -0.350  -0.357
141   N        -0.797  -0.848  -0.801  -0.719  -0.835  -0.764  -0.792  -0.837  -0.742
142   D         0.417   0.508   0.595   0.174   0.312   0.439   0.033   0.171   0.284
143   E         0.974   0.821   0.749   0.909   0.704   0.578   1.022   0.757   0.588
144   K        -0.140  -0.010  -0.158  -0.104   0.095  -0.130  -0.297  -0.110  -0.304
145   F         1.812   1.908   2.035   1.926   2.077   2.285   2.011   2.172   2.388
146   D         0.974   0.821   0.749   1.027   0.802   0.659   1.022   0.757   0.588
147   F         1.812   1.908   2.035   1.926   2.077   2.285   2.011   2.172   2.388
148   L         1.812   1.908   2.035   1.783   1.911   2.134   2.011   2.172   2.388
149   R        -0.797  -0.862  -0.817  -0.710  -0.823  -0.733  -0.792  -0.841  -0.756
150   E         0.417   0.461   0.578   0.044   0.096   0.278   0.033   0.078   0.249
151   G        -2.164  -2.114  -2.058  -2.011  -1.934  -1.848  -1.451  -1.394  -1.282
152   L        -0.797  -0.838  -0.830  -0.819  -0.869  -0.843  -0.792  -0.821  -0.772
153   C        -1.377  -1.343  -1.322  -1.104  -1.075  -1.072  -1.130  -1.086  -1.013
154   V        -0.129  -0.089  -0.216  -0.283  -0.241  -0.477  -0.251  -0.193  -0.382
155   E        -0.910  -0.938  -0.864  -0.612  -0.660  -0.578  -0.897  -0.920  -0.806
156   E        -0.129  -0.089  -0.216  -0.036   0.021  -0.186  -0.251  -0.193  -0.382
157   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   E        -0.254  -0.148  -0.211  -0.402  -0.240  -0.364  -0.457  -0.316  -0.381
177   E        -0.904  -0.822  -0.844  -1.063  -0.964  -0.948  -0.906  -0.808  -0.786
178   S        -0.950  -0.904  -0.839  -1.202  -1.125  -1.024  -0.956  -0.891  -0.784
179   A        -1.354  -1.357  -1.307  -1.241  -1.267  -1.185  -1.121  -1.106  -1.001
* 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/P40096
Output conservation file - output/P40096
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
