1     M         1.317   1.327   1.393   1.584   1.585   1.660   1.432   1.441   1.540
2     A         1.317   1.327   1.393   1.347   1.359   1.435   1.432   1.441   1.540
3     V        -1.142  -1.127  -1.075  -1.099  -1.074  -1.047  -1.109  -1.083  -0.991
4     Q         1.317   1.327   1.393   1.374   1.369   1.461   1.432   1.441   1.540
5     T         1.317   1.327   1.393   1.506   1.519   1.586   1.432   1.441   1.540
6     P         1.317   1.327   1.393   1.467   1.471   1.549   1.432   1.441   1.540
7     R        -0.550  -0.612  -0.531  -0.839  -0.911  -0.753  -0.724  -0.789  -0.670
8     Q         1.317   1.327   1.393   1.374   1.369   1.461   1.432   1.441   1.540
9     R         1.317   1.327   1.393   1.467   1.460   1.549   1.432   1.441   1.540
10    L        -0.550  -0.609  -0.533  -0.822  -0.874  -0.743  -0.724  -0.783  -0.670
11    A         1.317   1.327   1.393   1.347   1.359   1.435   1.432   1.441   1.540
12    N         1.317   1.327   1.393   1.480   1.495   1.562   1.432   1.441   1.540
13    A        -0.550  -0.605  -0.531  -0.625  -0.730  -0.639  -0.724  -0.779  -0.669
14    K         0.485   0.546   0.323   0.219   0.310   0.017   0.452   0.543   0.158
15    F         0.142   0.182   0.188   0.194   0.239   0.246  -0.136  -0.069  -0.088
16    N        -1.138  -1.147  -1.064  -0.976  -0.996  -0.871  -1.116  -1.115  -0.982
17    K         1.317   1.327   1.393   0.951   0.980   1.060   1.432   1.441   1.540
18    N        -1.138  -1.157  -1.062  -1.162  -1.137  -1.018  -1.116  -1.123  -0.979
19    N        -0.285  -0.347  -0.463   0.004  -0.104  -0.297  -0.332  -0.427  -0.572
20    E         0.142   0.189   0.209   0.200   0.274   0.277  -0.136  -0.055  -0.049
21    K        -0.285  -0.353  -0.460  -0.501  -0.586  -0.709  -0.332  -0.435  -0.568
22    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    K        -0.285  -0.353  -0.460  -0.497  -0.580  -0.703  -0.332  -0.435  -0.568
25    Y        -1.991  -1.941  -1.819  -1.601  -1.540  -1.362  -1.509  -1.455  -1.292
26    G         1.317   1.327   1.393   1.374   1.379   1.461   1.432   1.441   1.540
27    K         0.485   0.522   0.321   0.199   0.262  -0.024   0.452   0.506   0.154
28    K        -0.550  -0.606  -0.534  -0.660  -0.715  -0.639  -0.724  -0.780  -0.672
29    K        -0.285  -0.373  -0.463  -0.482  -0.589  -0.682  -0.332  -0.460  -0.572
30    E        -1.564  -1.546  -1.480  -1.542  -1.467  -1.323  -1.313  -1.286  -1.169
31    G        -1.564  -1.546  -1.480  -1.364  -1.356  -1.268  -1.313  -1.286  -1.169
32    K        -1.564  -1.550  -1.478  -1.645  -1.583  -1.436  -1.313  -1.290  -1.166
33    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    E        -0.977  -0.865  -1.000  -1.115  -0.956  -1.087  -0.920  -0.785  -0.912
35    K         0.485   0.529   0.319   0.258   0.325   0.080   0.452   0.516   0.149
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    T        -0.550  -0.613  -0.532  -0.351  -0.437  -0.334  -0.724  -0.789  -0.671
42    A        -0.550  -0.539  -0.530  -0.732  -0.758  -0.743  -0.724  -0.716  -0.669
43    P        -1.564  -1.466  -1.459  -1.265  -1.122  -1.130  -1.313  -1.209  -1.151
44    V         0.485   0.524   0.316   0.718   0.760   0.445   0.452   0.509   0.145
45    I         0.142   0.189   0.209   0.140   0.214   0.214  -0.136  -0.055  -0.049
46    S         1.317   1.327   1.393   1.467   1.466   1.549   1.432   1.441   1.540
47    K        -0.285  -0.373  -0.463  -0.438  -0.530  -0.611  -0.332  -0.460  -0.572
48    T        -1.138  -1.154  -1.055  -0.863  -0.902  -0.748  -1.116  -1.121  -0.973
49    W         1.317   1.327   1.393   1.571   1.578   1.648   1.432   1.441   1.540
50    L        -0.285  -0.193  -0.431  -0.431  -0.300  -0.615  -0.332  -0.207  -0.529
51    G        -1.991  -1.941  -1.819  -1.707  -1.649  -1.463  -1.509  -1.455  -1.292
52    I        -0.977  -0.878  -1.013  -0.747  -0.619  -0.824  -0.920  -0.799  -0.926
53    L         0.485   0.554   0.319   0.281   0.381   0.055   0.452   0.554   0.149
54    L        -0.285  -0.368  -0.471  -0.438  -0.548  -0.679  -0.332  -0.453  -0.583
55    F         1.317   1.327   1.393   1.387   1.383   1.473   1.432   1.441   1.540
56    L         0.485   0.350   0.286   0.278   0.100   0.001   0.452   0.226   0.091
57    L         0.038   0.059   0.152  -0.338  -0.287  -0.149  -0.332  -0.296  -0.156
58    V        -1.138  -1.156  -1.069  -0.817  -0.860  -0.743  -1.116  -1.123  -0.986
59    G         1.317   1.327   1.393   1.374   1.379   1.461   1.432   1.441   1.540
60    G         1.317   1.327   1.393   1.374   1.379   1.461   1.432   1.441   1.540
61    G        -0.550  -0.606  -0.534  -0.656  -0.764  -0.680  -0.724  -0.780  -0.672
62    V         0.038   0.059   0.152  -0.056  -0.033   0.107  -0.332  -0.298  -0.155
63    L         0.485   0.350   0.286   0.275   0.097  -0.004   0.452   0.226   0.091
64    Q         0.485   0.524   0.316   0.674   0.720   0.400   0.452   0.509   0.145
65    L         0.485   0.350   0.286   0.278   0.100   0.001   0.452   0.226   0.091
66    I        -0.977  -0.995  -1.030  -0.834  -0.916  -0.977  -0.920  -0.942  -0.944
67    S         0.142   0.189   0.209   0.218   0.277   0.290  -0.136  -0.055  -0.049
68    Y        -0.977  -1.018  -1.020  -0.915  -0.962  -0.881  -0.920  -0.967  -0.933
69    I        -0.550  -0.493  -0.516  -0.805  -0.721  -0.717  -0.724  -0.643  -0.650
70    L         0.142   0.182   0.189  -0.053   0.015  -0.044  -0.136  -0.068  -0.087
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -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/P38374
Output conservation file - output/P38374
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
