1     M         1.450   1.455   1.493   1.718   1.726   1.766   1.566   1.572   1.649
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     D        -0.954  -0.946  -0.735  -0.562  -0.557  -0.304  -1.063  -1.053  -0.793
5     S         0.464   0.418   0.241   0.834   0.774   0.456   0.471   0.400   0.089
6     A        -1.459  -1.456  -1.306  -0.895  -0.889  -0.762  -1.283  -1.275  -1.087
7     K         0.057   0.033   0.125   0.322   0.282   0.375  -0.187  -0.230  -0.113
8     I         1.450   1.455   1.493   0.965   0.970   1.083   1.566   1.572   1.649
9     I        -1.268  -1.327  -1.262  -1.575  -1.657  -1.539  -1.063  -1.124  -1.043
10    N        -1.941  -1.930  -1.759  -1.092  -1.067  -0.909  -1.493  -1.480  -1.272
11    I         0.141   0.127   0.121  -0.380  -0.402  -0.361  -0.044  -0.068  -0.120
12    I         0.553   0.496   0.245   0.200   0.134  -0.144   0.600   0.517   0.096
13    L        -1.344  -1.346  -1.269  -1.687  -1.686  -1.595  -1.171  -1.165  -1.051
14    S         0.553   0.553   0.255   0.724   0.728   0.364   0.600   0.601   0.113
15    L        -0.641  -0.604  -0.649  -1.274  -1.213  -1.253  -0.688  -0.639  -0.690
16    F         0.141   0.132   0.172   0.026   0.003  -0.009  -0.044  -0.060  -0.032
17    L         1.450   1.455   1.493   1.034   1.043   1.145   1.566   1.572   1.649
18    P         1.450   1.455   1.493   1.573   1.580   1.635   1.566   1.572   1.649
19    P         1.450   1.455   1.493   1.573   1.580   1.635   1.566   1.572   1.649
20    V        -0.044  -0.037   0.099  -0.468  -0.455  -0.246  -0.366  -0.354  -0.161
21    A        -0.044  -0.038   0.106  -0.152  -0.144   0.065  -0.366  -0.355  -0.149
22    V         1.450   1.455   1.493   1.440   1.445   1.513   1.566   1.572   1.649
23    F         1.450   1.455   1.493   1.544   1.550   1.608   1.566   1.572   1.649
24    L        -1.344  -1.374  -1.257  -1.062  -1.121  -0.995  -1.171  -1.199  -1.043
25    A        -1.344  -1.320  -1.296  -0.755  -0.742  -0.706  -1.171  -1.150  -1.077
26    R        -0.292  -0.238  -0.606   0.411   0.475  -0.047  -0.205  -0.134  -0.628
27    G         1.450   1.455   1.493   1.558   1.563   1.621   1.566   1.572   1.649
28    W        -1.344  -1.366  -1.296  -0.891  -0.911  -0.837  -1.171  -1.185  -1.077
29    G         0.141   0.173   0.121   0.328   0.370   0.275  -0.044   0.009  -0.121
30    T        -0.747  -0.715  -0.689  -0.503  -0.468  -0.377  -0.849  -0.816  -0.739
31    D        -1.074  -1.074  -1.232  -0.406  -0.400  -0.694  -0.849  -0.848  -1.013
32    C        -0.641  -0.696  -0.661  -0.840  -0.903  -0.812  -0.688  -0.756  -0.701
33    I        -1.777  -1.698  -1.710  -1.831  -1.730  -1.654  -1.332  -1.253  -1.232
34    V        -0.292  -0.346  -0.614  -0.654  -0.737  -1.152  -0.205  -0.273  -0.638
35    D        -0.292  -0.346  -0.614   0.371   0.308  -0.089  -0.205  -0.273  -0.638
36    I        -0.292  -0.240  -0.582  -0.654  -0.585  -1.099  -0.205  -0.138  -0.597
37    I        -0.911  -0.908  -0.731  -1.608  -1.623  -1.309  -1.010  -1.004  -0.788
38    L         1.450   1.455   1.493   1.034   1.043   1.145   1.566   1.572   1.649
39    T        -0.044  -0.047   0.087   0.135   0.129   0.299  -0.366  -0.371  -0.182
40    I        -0.044  -0.034   0.102  -0.484  -0.476  -0.234  -0.366  -0.348  -0.155
41    L        -0.641  -0.662  -0.667  -0.844  -0.860  -0.785  -0.688  -0.702  -0.708
42    A        -0.911  -0.908  -0.731  -1.145  -1.132  -0.942  -1.010  -1.004  -0.788
43    W        -0.044  -0.038   0.106   0.223   0.232   0.405  -0.366  -0.355  -0.149
44    F        -1.074  -1.058  -1.232  -0.879  -0.846  -1.351  -0.849  -0.829  -1.013
45    P         1.450   1.455   1.493   1.573   1.580   1.635   1.566   1.572   1.649
46    G         0.141   0.174   0.149   0.218   0.270   0.175  -0.044   0.012  -0.072
47    M         0.141   0.112   0.144  -0.258  -0.291  -0.176  -0.044  -0.093  -0.081
48    L        -0.641  -0.623  -0.668  -1.221  -1.199  -1.239  -0.688  -0.667  -0.710
49    Y         0.141   0.112   0.144   0.551   0.506   0.485  -0.044  -0.093  -0.081
50    A         1.450   1.455   1.493   1.425   1.433   1.500   1.566   1.572   1.649
51    L         1.450   1.455   1.493   1.034   1.043   1.145   1.566   1.572   1.649
52    Y         1.450   1.455   1.493   1.675   1.681   1.727   1.566   1.572   1.649
53    I        -0.044  -0.041   0.090  -0.641  -0.637  -0.380  -0.366  -0.361  -0.177
54    V        -0.044  -0.038   0.106  -0.529  -0.518  -0.280  -0.366  -0.355  -0.149
55    L         0.553   0.598   0.259   0.300   0.354  -0.039   0.600   0.665   0.119
56    Q        -0.292  -0.346  -0.614   0.358   0.296  -0.069  -0.205  -0.273  -0.638
57    D        -0.044  -0.038   0.106   0.144   0.152   0.333  -0.366  -0.355  -0.149
* 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/P87284
Output conservation file - output/P87284
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
