1     M         1.419   1.434   1.477   1.657   1.672   1.752   1.535   1.553   1.618
2     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     Q        -0.365  -0.431  -0.474  -0.195  -0.309  -0.415  -0.422  -0.508  -0.559
4     Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     A        -0.562  -0.567  -0.538  -0.641  -0.599  -0.558  -0.702  -0.697  -0.647
6     P         1.419   1.434   1.477   1.516   1.543   1.613   1.535   1.553   1.618
7     F         0.480   0.462   0.334   0.419   0.403   0.221   0.417   0.385   0.158
8     L         1.419   1.434   1.477   1.222   1.235   1.322   1.535   1.553   1.618
9     L         0.480   0.462   0.334   0.527   0.492   0.241   0.417   0.385   0.158
10    G         0.155   0.150   0.190  -0.037  -0.048   0.006  -0.143  -0.157  -0.101
11    K         0.155   0.147   0.188  -0.127  -0.160  -0.088  -0.143  -0.163  -0.103
12    F        -1.603  -1.575  -1.524  -1.173  -1.134  -1.049  -1.261  -1.227  -1.148
13    S        -1.082  -1.127  -1.088  -1.188  -1.226  -1.136  -0.982  -1.020  -0.956
14    D         1.419   1.434   1.477   1.677   1.701   1.771   1.535   1.553   1.618
15    P         1.419   1.434   1.477   1.516   1.543   1.613   1.535   1.553   1.618
16    L        -1.082  -1.007  -1.063  -1.162  -1.057  -1.092  -0.982  -0.894  -0.931
17    L        -1.082  -1.083  -1.066  -0.985  -0.999  -0.988  -0.982  -0.975  -0.934
18    A         0.155   0.164   0.196   0.102   0.113   0.149  -0.143  -0.132  -0.090
19    I        -0.562  -0.559  -0.538  -0.684  -0.678  -0.671  -0.702  -0.687  -0.647
20    M        -1.603  -1.575  -1.524  -1.413  -1.353  -1.287  -1.261  -1.227  -1.148
21    V        -0.562  -0.559  -0.538  -0.522  -0.486  -0.458  -0.702  -0.687  -0.647
22    G         1.419   1.434   1.477   1.455   1.477   1.552   1.535   1.553   1.618
23    C        -1.082  -1.055  -1.064  -0.805  -0.748  -0.753  -0.982  -0.947  -0.932
24    L        -1.082  -1.061  -1.062  -1.344  -1.335  -1.292  -0.982  -0.954  -0.930
25    S         0.480   0.434   0.333   0.542   0.479   0.293   0.417   0.340   0.157
26    Y         1.419   1.434   1.477   1.308   1.337   1.407   1.535   1.553   1.618
27    Y         1.419   1.434   1.477   1.308   1.337   1.407   1.535   1.553   1.618
28    V        -0.365  -0.342  -0.453  -0.562  -0.522  -0.681  -0.422  -0.389  -0.531
29    Y         1.419   1.434   1.477   1.308   1.337   1.407   1.535   1.553   1.618
30    E         1.419   1.434   1.477   1.577   1.599   1.673   1.535   1.553   1.618
31    R        -0.562  -0.567  -0.538  -0.641  -0.669  -0.619  -0.702  -0.697  -0.647
32    K        -1.082  -1.127  -1.088  -1.119  -1.187  -1.118  -0.982  -1.020  -0.956
33    M        -0.533  -0.542  -0.537  -0.308  -0.316  -0.328  -0.650  -0.658  -0.642
34    G         0.480   0.434   0.333   0.563   0.502   0.354   0.417   0.340   0.157
35    R         1.419   1.434   1.477   1.434   1.452   1.531   1.535   1.553   1.618
36    P         0.480   0.537   0.353   0.547   0.641   0.326   0.417   0.506   0.192
37    Q        -1.603  -1.575  -1.524  -1.394  -1.360  -1.268  -1.261  -1.227  -1.148
38    G         0.480   0.449   0.329   0.537   0.495   0.306   0.417   0.365   0.150
39    H        -0.365  -0.431  -0.474  -0.220  -0.341  -0.459  -0.422  -0.508  -0.559
40    H        -0.562  -0.568  -0.533  -0.585  -0.594  -0.545  -0.702  -0.700  -0.642
41    L         1.419   1.434   1.477   1.222   1.235   1.322   1.535   1.553   1.618
42    H        -0.365  -0.422  -0.488  -0.195  -0.286  -0.403  -0.422  -0.495  -0.578
43    E         0.480   0.449   0.329   0.657   0.615   0.419   0.417   0.365   0.150
44    L         1.419   1.434   1.477   1.222   1.235   1.322   1.535   1.553   1.618
45    I        -1.082  -1.127  -1.088  -1.043  -1.116  -1.076  -0.982  -1.020  -0.956
46    K        -1.603  -1.575  -1.524  -1.778  -1.765  -1.648  -1.261  -1.227  -1.148
47    K        -0.562  -0.569  -0.532  -0.780  -0.790  -0.714  -0.702  -0.702  -0.641
48    R         0.480   0.462   0.334   0.435   0.401   0.189   0.417   0.385   0.158
49    W        -0.562  -0.521  -0.536  -0.578  -0.495  -0.502  -0.702  -0.649  -0.645
50    D        -0.533  -0.524  -0.525  -0.494  -0.457  -0.499  -0.650  -0.635  -0.627
51    D        -1.184  -1.159  -1.108  -1.178  -1.131  -1.055  -1.087  -1.052  -0.975
52    -         0.224   0.185   0.209   0.379   0.298   0.331  -0.018  -0.093  -0.066
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    -         0.224   0.185   0.209   0.009  -0.077  -0.043  -0.018  -0.093  -0.066
59    -        -0.644  -0.620  -0.572  -0.648  -0.598  -0.530  -0.795  -0.759  -0.687
60    R        -1.082  -1.048  -1.065  -1.297  -1.273  -1.278  -0.982  -0.939  -0.933
61    K         0.155   0.164   0.196  -0.043  -0.032   0.029  -0.143  -0.132  -0.090
* 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/Q02820
Output conservation file - output/Q02820
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
