1     M         1.642   1.682   1.750   1.895   1.899   2.060   1.759   1.812   1.917
2     V        -0.055   0.069  -0.273   0.088   0.236  -0.236  -0.020   0.141  -0.317
3     K         1.642   1.682   1.750   1.074   1.124   1.278   1.759   1.812   1.917
4     V        -0.499  -0.541  -0.431  -0.820  -0.937  -0.777  -0.666  -0.683  -0.538
5     K        -0.395  -0.495  -0.423  -0.862  -0.886  -0.792  -0.505  -0.616  -0.527
6     S        -1.239  -1.206  -1.047  -1.361  -1.403  -1.129  -1.151  -1.079  -0.896
7     K        -0.817  -0.893  -0.986  -1.029  -1.141  -1.171  -0.666  -0.751  -0.829
8     N        -1.080  -1.090  -1.018  -0.699  -0.725  -0.656  -0.990  -0.968  -0.867
9     S        -0.055  -0.109  -0.293   0.179   0.058  -0.169  -0.020  -0.110  -0.344
10    V        -0.395  -0.479  -0.423  -0.351  -0.486  -0.375  -0.505  -0.593  -0.523
11    I         0.186   0.237   0.336   0.057   0.102   0.251  -0.181  -0.115   0.025
12    K         1.642   1.682   1.750   1.106   1.179   1.309   1.759   1.812   1.917
13    L         1.642   1.682   1.750   1.625   1.655   1.803   1.759   1.812   1.917
14    L        -1.080  -0.980  -1.003  -0.986  -0.885  -0.844  -0.990  -0.881  -0.854
15    S         1.642   1.682   1.750   1.732   1.775   1.905   1.759   1.812   1.917
16    T        -0.055  -0.074  -0.308   0.169   0.124  -0.211  -0.020  -0.045  -0.365
17    A         1.642   1.682   1.750   1.576   1.612   1.757   1.759   1.812   1.917
18    A        -1.661  -1.529  -1.472  -1.701  -1.552  -1.415  -1.313  -1.171  -1.066
19    S         0.768   0.907   0.563   0.914   1.065   0.648   0.789   0.984   0.430
20    G         1.642   1.682   1.750   1.906   1.947   2.071   1.759   1.812   1.917
21    Y        -0.395  -0.464  -0.418  -0.151  -0.258  -0.238  -0.505  -0.572  -0.520
22    S        -1.080  -1.143  -1.053  -0.680  -0.734  -0.610  -0.990  -1.022  -0.899
23    R        -0.395  -0.479  -0.423  -0.680  -0.715  -0.722  -0.505  -0.593  -0.523
24    Y        -2.083  -1.917  -1.892  -1.293  -1.183  -1.108  -1.475  -1.315  -1.230
25    I        -1.239  -1.202  -1.053  -1.117  -1.073  -0.903  -1.151  -1.076  -0.900
26    S        -1.502  -1.365  -1.466  -1.033  -0.843  -1.019  -1.151  -1.000  -1.056
27    I        -0.395  -0.297  -0.415  -0.302  -0.222  -0.419  -0.505  -0.429  -0.517
28    K        -0.395  -0.100  -0.335  -0.434   0.094  -0.301  -0.505  -0.111  -0.403
29    K         0.186   0.247   0.349  -0.467  -0.314  -0.212  -0.181  -0.095   0.049
30    G        -1.661  -1.570  -1.491  -1.263  -1.189  -1.071  -1.313  -1.193  -1.079
31    A        -0.055   0.016  -0.315   0.112   0.185  -0.257  -0.020   0.073  -0.373
32    P        -0.055  -0.074  -0.308   0.295   0.330  -0.070  -0.020  -0.045  -0.365
33    L        -0.499  -0.432  -0.425  -0.937  -0.855  -0.806  -0.666  -0.552  -0.526
34    V        -0.499  -0.432  -0.425  -0.610  -0.485  -0.439  -0.666  -0.552  -0.526
35    T        -0.395  -0.479  -0.423  -0.237  -0.384  -0.286  -0.505  -0.593  -0.523
36    Q        -0.395  -0.479  -0.423  -0.039  -0.171  -0.120  -0.505  -0.593  -0.523
37    V         0.186   0.232   0.335  -0.000   0.081   0.243  -0.181  -0.123   0.023
38    R        -0.658  -0.603  -0.485  -1.170  -1.129  -0.987  -0.828  -0.752  -0.600
39    Y         1.642   1.682   1.750   1.883   1.908   2.049   1.759   1.812   1.917
40    D         1.642   1.682   1.750   1.872   1.962   2.038   1.759   1.812   1.917
41    P         1.642   1.682   1.750   1.744   1.843   1.917   1.759   1.812   1.917
42    V        -1.080  -1.084  -1.009  -1.172  -1.240  -1.133  -0.990  -0.967  -0.859
43    V        -0.395  -0.479  -0.418  -0.437  -0.552  -0.475  -0.505  -0.593  -0.520
44    K         0.768   0.601   0.534   0.405   0.241   0.184   0.789   0.518   0.379
45    R         0.367   0.374   0.386  -0.024   0.019  -0.101   0.142   0.133   0.117
46    H        -0.055  -0.243  -0.354   0.451   0.175  -0.028  -0.020  -0.275  -0.426
47    V         0.367   0.430   0.406   0.356   0.444   0.439   0.142   0.231   0.153
48    L         1.642   1.682   1.750   1.625   1.655   1.803   1.759   1.812   1.917
49    F         1.642   1.682   1.750   1.826   1.859   1.994   1.759   1.812   1.917
50    K        -0.395  -0.422  -0.429  -0.677  -0.596  -0.550  -0.505  -0.553  -0.534
51    E         1.642   1.682   1.750   1.837   1.926   2.005   1.759   1.812   1.917
52    A        -1.239  -1.158  -1.054  -1.061  -0.916  -0.807  -1.151  -1.038  -0.900
53    K         0.768   0.848   0.560   0.326   0.464   0.055   0.789   0.899   0.425
54    K        -0.055  -0.243  -0.354  -0.326  -0.542  -0.643  -0.020  -0.275  -0.426
55    R         0.768   0.601   0.534   0.665   0.463   0.243   0.789   0.518   0.379
56    K         0.285   0.255   0.337  -0.388  -0.423  -0.292  -0.002  -0.081   0.026
57    V        -0.207  -0.317  -0.387  -0.080  -0.205  -0.285  -0.222  -0.377  -0.470
58    A         0.285   0.370   0.364   0.181   0.322   0.286  -0.002   0.126   0.076
59    E         0.682   0.531   0.467   0.948   0.698   0.565   0.659   0.403   0.262
60    R        -1.006  -1.087  -1.054  -0.881  -0.983  -0.899  -0.882  -0.960  -0.899
61    K        -0.514  -0.504  -0.448  -0.867  -0.750  -0.615  -0.662  -0.643  -0.555
62    P        -0.207  -0.317  -0.387  -0.110  -0.334  -0.559  -0.222  -0.377  -0.470
63    L        -0.514  -0.569  -0.470  -0.738  -0.787  -0.670  -0.662  -0.713  -0.582
64    D         0.682   0.531   0.467   0.896   0.623   0.436   0.659   0.403   0.262
65    F        -0.207  -0.356  -0.397   0.254   0.035  -0.028  -0.222  -0.426  -0.484
66    L        -1.006  -1.087  -1.054  -0.655  -0.753  -0.701  -0.882  -0.960  -0.899
67    R         0.682   0.531   0.467   0.500   0.236   0.071   0.659   0.403   0.262
68    T        -0.514  -0.569  -0.470  -0.650  -0.785  -0.683  -0.662  -0.713  -0.582
69    A        -0.700  -0.596  -0.482  -0.635  -0.450  -0.329  -0.882  -0.744  -0.595
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    K        -1.192  -1.187  -1.050  -1.573  -1.450  -1.269  -1.102  -1.063  -0.896
* 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/P36533
Output conservation file - output/P36533
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
