1     M         1.758   1.800   1.921   1.859   1.903   2.061   1.914   1.982   2.181
2     T        -0.114   0.106  -0.081  -0.406  -0.119  -0.307  -0.274   0.053  -0.224
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     I        -0.403  -0.355  -0.237  -0.660  -0.559  -0.393  -0.660  -0.605  -0.447
7     A         0.229   0.071  -0.053  -0.041  -0.265  -0.420   0.241   0.017  -0.180
8     P         1.758   1.800   1.921   1.929   1.961   2.127   1.914   1.982   2.181
9     I         0.975   0.890   0.784   0.869   0.801   0.642   1.013   0.874   0.649
10    T         0.975   0.870   0.784   1.115   0.974   0.861   1.013   0.842   0.649
11    G         1.758   1.800   1.921   1.605   1.636   1.824   1.914   1.982   2.181
12    T        -0.114  -0.270  -0.188   0.017  -0.200  -0.072  -0.274  -0.498  -0.387
13    I        -0.114  -0.088  -0.103  -0.167  -0.087  -0.155  -0.274  -0.215  -0.258
14    K         0.589   0.649   0.618   0.412   0.505   0.416   0.369   0.460   0.335
15    R         0.589   0.796   0.711   0.492   0.790   0.635   0.369   0.718   0.512
16    R        -0.114  -0.076  -0.112  -0.163  -0.101  -0.191  -0.274  -0.201  -0.270
17    V         0.229   0.220  -0.018   0.213   0.232  -0.096   0.241   0.224  -0.129
18    I        -0.474  -0.537  -0.657  -0.404  -0.459  -0.615  -0.403  -0.495  -0.613
19    M        -1.124  -1.117  -1.161  -0.872  -0.862  -0.977  -0.918  -0.915  -0.908
20    D         1.758   1.800   1.921   1.906   1.957   2.105   1.914   1.982   2.181
21    I         0.975   0.890   0.784   0.864   0.795   0.630   1.013   0.874   0.649
22    V        -0.988  -0.960  -0.785  -0.864  -0.832  -0.575  -1.046  -0.997  -0.768
23    L        -0.474  -0.616  -0.680  -0.419  -0.575  -0.672  -0.403  -0.581  -0.641
24    G         0.229   0.071  -0.053   0.213  -0.030  -0.249   0.241   0.017  -0.180
25    F        -0.114  -0.262  -0.188   0.017  -0.236  -0.126  -0.274  -0.490  -0.387
26    S        -1.348  -1.446  -1.243  -1.543  -1.668  -1.358  -1.175  -1.239  -0.988
27    L        -1.124  -0.935  -1.139  -0.899  -0.635  -0.957  -0.918  -0.714  -0.886
28    G         1.758   1.800   1.921   1.605   1.636   1.824   1.914   1.982   2.181
29    G        -0.267  -0.250  -0.162  -0.370  -0.300  -0.168  -0.532  -0.470  -0.347
30    V        -1.348  -1.356  -1.217  -1.310  -1.261  -1.112  -1.175  -1.158  -0.966
31    M        -0.764  -0.850  -0.752  -0.699  -0.860  -0.777  -0.789  -0.862  -0.728
32    A         0.975   0.870   0.784   0.622   0.475   0.365   1.013   0.842   0.649
33    S        -1.708  -1.760  -1.628  -1.180  -1.284  -1.127  -1.304  -1.339  -1.144
34    Y        -0.403  -0.393  -0.255  -0.543  -0.558  -0.373  -0.660  -0.652  -0.471
35    W         0.383   0.440   0.562   0.320   0.398   0.550  -0.017   0.068   0.224
36    W         1.758   1.800   1.921   1.883   1.923   2.083   1.914   1.982   2.181
37    W        -0.988  -0.934  -0.813  -0.841  -0.787  -0.602  -1.046  -0.989  -0.798
38    G         0.229   0.409   0.002   0.265   0.481  -0.055   0.241   0.488  -0.099
39    F        -0.492  -0.365  -0.225  -0.578  -0.388  -0.193  -0.789  -0.617  -0.430
40    H         1.758   1.800   1.921   1.987   2.026   2.181   1.914   1.982   2.181
41    M         0.589   0.599   0.601   0.452   0.475   0.446   0.369   0.369   0.300
42    D        -0.114   0.106  -0.081   0.186   0.493   0.233  -0.274   0.053  -0.224
43    K        -2.204  -2.159  -1.940  -2.242  -2.202  -1.838  -1.561  -1.508  -1.244
44    I        -0.474  -0.716  -0.722  -0.503  -0.831  -0.888  -0.403  -0.697  -0.690
45    N        -1.348  -1.257  -1.210  -1.196  -1.124  -0.996  -1.175  -1.090  -0.961
46    K        -0.764  -0.777  -0.754  -0.930  -1.010  -0.915  -0.789  -0.826  -0.736
47    R         0.975   0.870   0.784   1.055   0.895   0.761   1.013   0.842   0.649
48    E         0.383   0.387   0.541   0.268   0.280   0.487  -0.017  -0.035   0.181
49    K        -0.474  -0.576  -0.676  -0.640  -0.750  -0.860  -0.403  -0.531  -0.636
50    F        -0.267  -0.316  -0.180  -0.246  -0.299  -0.085  -0.532  -0.573  -0.381
51    Y         1.758   1.800   1.921   1.788   1.825   1.995   1.914   1.982   2.181
52    A         0.229   0.071  -0.053  -0.014  -0.219  -0.364   0.241   0.017  -0.180
53    E        -1.124  -1.016  -1.142  -0.961  -0.850  -0.987  -0.918  -0.805  -0.890
54    L         0.975   0.870   0.784   1.060   0.910   0.788   1.013   0.842   0.649
55    A        -0.764  -0.685  -0.750  -1.103  -0.992  -1.009  -0.789  -0.729  -0.731
56    E        -0.764  -0.792  -0.751  -0.831  -0.862  -0.848  -0.789  -0.820  -0.732
57    R        -0.852  -0.663  -0.736  -0.697  -0.454  -0.545  -0.918  -0.705  -0.717
58    K         0.229   0.266  -0.011   0.333   0.381   0.039   0.241   0.284  -0.119
59    K        -1.124  -1.034  -0.833  -1.398  -1.174  -0.961  -1.175  -1.070  -0.816
60    Q        -0.474  -0.470  -0.652  -0.610  -0.580  -0.781  -0.403  -0.403  -0.607
61    E         0.229   0.054  -0.056   0.466   0.254   0.088   0.241  -0.007  -0.185
62    N        -0.825  -0.877  -0.812  -0.467  -0.591  -0.495  -0.832  -0.900  -0.792
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P07255
Output conservation file - output/P07255
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
