1     M         1.659   1.664   1.681   1.822   1.825   1.856   1.768   1.775   1.796
2     F         1.659   1.664   1.681   1.679   1.687   1.714   1.768   1.775   1.796
3     F         0.038   0.016  -0.016   0.004  -0.042  -0.106  -0.074  -0.108  -0.159
4     S         0.038   0.030  -0.006  -0.106  -0.135  -0.192  -0.074  -0.086  -0.143
5     Q        -1.138  -1.133  -1.117  -0.799  -0.749  -0.763  -0.995  -0.985  -0.956
6     V        -1.138  -1.133  -1.117  -1.176  -1.160  -1.139  -0.995  -0.985  -0.956
7     L         0.038   0.016  -0.016   0.071   0.029  -0.019  -0.074  -0.108  -0.159
8     R         0.038   0.016  -0.016   0.017  -0.016  -0.038  -0.074  -0.108  -0.159
9     S         0.038   0.016  -0.016  -0.106  -0.153  -0.211  -0.074  -0.108  -0.159
10    S        -1.138  -1.133  -1.117  -1.082  -1.086  -1.046  -0.995  -0.985  -0.956
11    A         0.038   0.016  -0.016  -0.191  -0.211  -0.292  -0.074  -0.108  -0.159
12    R        -1.138  -1.133  -1.117  -1.100  -1.094  -1.064  -0.995  -0.985  -0.956
13    A        -1.138  -1.133  -1.117  -1.119  -1.091  -1.083  -0.995  -0.985  -0.956
14    A         0.038   0.016  -0.016  -0.010  -0.020  -0.076  -0.074  -0.108  -0.159
15    -        -0.106  -0.102  -0.084   0.042   0.097   0.078  -0.304  -0.298  -0.268
16    -        -0.106  -0.102  -0.084  -0.013  -0.022   0.022  -0.304  -0.298  -0.268
17    -        -0.106  -0.102  -0.084   0.042   0.067   0.078  -0.304  -0.298  -0.268
18    -        -0.106  -0.102  -0.084  -0.214  -0.176  -0.179  -0.304  -0.298  -0.268
19    -         1.659   1.664   1.681   1.291   1.254   1.326   1.768   1.775   1.796
20    -        -0.106  -0.102  -0.084  -0.098  -0.083  -0.063  -0.304  -0.298  -0.268
21    -        -0.106  -0.102  -0.084  -0.458  -0.503  -0.422  -0.304  -0.298  -0.268
22    -        -0.106  -0.102  -0.084  -0.426  -0.469  -0.391  -0.304  -0.298  -0.268
23    -        -0.106  -0.102  -0.084  -0.458  -0.503  -0.422  -0.304  -0.298  -0.268
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    P        -1.138  -1.133  -1.117  -0.973  -0.954  -0.937  -0.995  -0.985  -0.956
26    I        -1.138  -1.133  -1.117  -1.253  -1.252  -1.217  -0.995  -0.985  -0.956
27    K        -1.138  -1.133  -1.117  -1.176  -1.135  -1.139  -0.995  -0.985  -0.956
28    R        -1.138  -1.133  -1.117  -1.273  -1.281  -1.236  -0.995  -0.985  -0.956
29    Y        -1.138  -1.133  -1.117  -0.833  -0.815  -0.797  -0.995  -0.985  -0.956
30    T        -1.138  -1.133  -1.117  -1.312  -1.299  -1.276  -0.995  -0.985  -0.956
31    G         0.038   0.016  -0.016   0.098   0.080   0.032  -0.074  -0.108  -0.159
32    G         0.038   0.030  -0.006  -0.106  -0.130  -0.192  -0.074  -0.086  -0.143
33    R         1.659   1.664   1.681   1.443   1.444   1.478   1.768   1.775   1.796
34    I         0.038   0.030  -0.006   0.071   0.054  -0.002  -0.074  -0.086  -0.143
35    G         1.659   1.664   1.681   1.562   1.567   1.597   1.768   1.775   1.796
36    E         0.038   0.016  -0.016   0.343   0.311   0.254  -0.074  -0.108  -0.159
37    S         0.038   0.030  -0.006  -0.092  -0.098  -0.175  -0.074  -0.086  -0.143
38    W         1.659   1.664   1.681   1.793   1.801   1.828   1.768   1.775   1.796
39    V        -1.138  -1.133  -1.117  -1.253  -1.252  -1.217  -0.995  -0.985  -0.956
40    I         0.038   0.030  -0.006   0.071   0.054  -0.002  -0.074  -0.086  -0.143
41    T         0.038   0.016  -0.016  -0.205  -0.252  -0.302  -0.074  -0.108  -0.159
42    E         1.659   1.664   1.681   1.878   1.891   1.912   1.768   1.775   1.796
43    G        -1.138  -1.133  -1.117  -1.176  -1.154  -1.139  -0.995  -0.985  -0.956
44    R         0.038   0.016  -0.016  -0.065  -0.074  -0.135  -0.074  -0.108  -0.159
45    R         1.659   1.664   1.681   1.443   1.444   1.478   1.768   1.775   1.796
46    L         1.659   1.664   1.681   1.650   1.653   1.685   1.768   1.775   1.796
47    I        -1.138  -1.133  -1.117  -1.195  -1.213  -1.159  -0.995  -0.985  -0.956
48    P         1.659   1.664   1.681   1.793   1.801   1.828   1.768   1.775   1.796
49    E         0.038   0.085   0.020  -0.010   0.033  -0.025  -0.074  -0.001  -0.101
50    I         0.038   0.016  -0.016   0.071   0.029  -0.019  -0.074  -0.108  -0.159
51    F        -1.138  -1.133  -1.117  -0.991  -0.989  -0.955  -0.995  -0.985  -0.956
52    Q        -1.138  -1.133  -1.117  -0.816  -0.806  -0.780  -0.995  -0.985  -0.956
53    W         0.038   0.030  -0.006   0.317   0.306   0.257  -0.074  -0.086  -0.143
54    S        -1.138  -1.133  -1.117  -1.233  -1.215  -1.197  -0.995  -0.985  -0.956
55    A        -1.138  -1.133  -1.117  -1.312  -1.302  -1.276  -0.995  -0.985  -0.956
56    V         0.038   0.085   0.020   0.098   0.171   0.068  -0.074  -0.001  -0.101
57    L         0.038   0.030  -0.006   0.071   0.051  -0.002  -0.074  -0.086  -0.143
58    S        -1.138  -1.133  -1.117  -1.195  -1.205  -1.159  -0.995  -0.985  -0.956
59    V         0.038   0.030  -0.006   0.031   0.014  -0.049  -0.074  -0.086  -0.143
60    C        -1.138  -1.133  -1.117  -0.902  -0.926  -0.866  -0.995  -0.985  -0.956
61    L         1.659   1.664   1.681   1.650   1.653   1.685   1.768   1.775   1.796
62    G         1.659   1.664   1.681   1.562   1.567   1.597   1.768   1.775   1.796
63    W         1.659   1.664   1.681   1.793   1.801   1.828   1.768   1.775   1.796
64    P         1.659   1.664   1.681   1.793   1.801   1.828   1.768   1.775   1.796
65    G        -0.106  -0.102  -0.084  -0.249  -0.250  -0.213  -0.304  -0.298  -0.268
66    A        -0.106  -0.102  -0.084  -0.315  -0.283  -0.279  -0.304  -0.298  -0.268
67    V        -0.106  -0.102  -0.084  -0.184  -0.184  -0.148  -0.304  -0.298  -0.268
68    Y         0.038   0.030  -0.006   0.317   0.304   0.237  -0.074  -0.086  -0.143
69    F         0.038   0.030  -0.006   0.098   0.081   0.024  -0.074  -0.086  -0.143
70    F        -1.138  -1.133  -1.117  -0.902  -0.893  -0.866  -0.995  -0.985  -0.956
71    S        -1.138  -1.133  -1.117  -1.119  -1.074  -1.083  -0.995  -0.985  -0.956
72    K         1.659   1.664   1.681   1.765   1.828   1.800   1.768   1.775   1.796
73    A         0.038   0.016  -0.016  -0.024  -0.032  -0.092  -0.074  -0.108  -0.159
74    R        -1.138  -1.133  -1.117  -0.732  -0.708  -0.696  -0.995  -0.985  -0.956
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    K         1.659   1.664   1.681   1.762   1.772   1.797   1.768   1.775   1.796
84    A        -0.106  -0.102  -0.084  -0.189  -0.182  -0.154  -0.304  -0.298  -0.268
* 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/Q2V2P9
Output conservation file - output/Q2V2P9
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
