1     M         0.986   0.986   0.986   0.940   0.940   0.940   0.986   0.986   0.986
2     I         0.986   0.986   0.986   0.768   0.768   0.768   0.986   0.986   0.986
3     S         0.986   0.986   0.986   0.768   0.768   0.768   0.986   0.986   0.986
4     D         0.986   0.986   0.986   1.189   1.189   1.189   0.986   0.986   0.986
5     E        -0.986  -0.986  -0.986  -0.596  -0.596  -0.596  -0.986  -0.986  -0.986
6     Q         0.986   0.986   0.986   1.107   1.107   1.107   0.986   0.986   0.986
7     L         0.986   0.986   0.986   0.768   0.768   0.768   0.986   0.986   0.986
8     N         0.986   0.986   0.986   1.107   1.107   1.107   0.986   0.986   0.986
9     S        -0.986  -0.986  -0.986  -1.019  -1.019  -1.019  -0.986  -0.986  -0.986
10    L         0.986   0.986   0.986   0.768   0.768   0.768   0.986   0.986   0.986
11    A        -0.986  -0.986  -0.986  -1.084  -1.084  -1.084  -0.986  -0.986  -0.986
12    I        -0.986  -0.986  -0.986  -1.216  -1.216  -1.216  -0.986  -0.986  -0.986
13    T        -0.986  -0.986  -0.986  -1.019  -1.019  -1.019  -0.986  -0.986  -0.986
14    F         0.986   0.986   0.986   1.270   1.270   1.270   0.986   0.986   0.986
15    G         0.986   0.986   0.986   1.189   1.189   1.189   0.986   0.986   0.986
16    I        -0.986  -0.986  -0.986  -1.283  -1.283  -1.283  -0.986  -0.986  -0.986
17    V         0.986   0.986   0.986   0.680   0.680   0.680   0.986   0.986   0.986
18    M         0.986   0.986   0.986   0.940   0.940   0.940   0.986   0.986   0.986
19    M        -0.986  -0.986  -0.986  -1.149  -1.149  -1.149  -0.986  -0.986  -0.986
20    T        -0.986  -0.986  -0.986  -0.832  -0.832  -0.832  -0.986  -0.986  -0.986
21    L         0.986   0.986   0.986   0.768   0.768   0.768   0.986   0.986   0.986
22    I         0.986   0.986   0.986   0.768   0.768   0.768   0.986   0.986   0.986
23    V        -0.986  -0.986  -0.986  -1.084  -1.084  -1.084  -0.986  -0.986  -0.986
24    I        -0.986  -0.986  -0.986  -1.216  -1.216  -1.216  -0.986  -0.986  -0.986
25    Y         0.986   0.986   0.986   1.270   1.270   1.270   0.986   0.986   0.986
26    H         0.986   0.986   0.986   1.189   1.189   1.189   0.986   0.986   0.986
27    A        -0.986  -0.986  -0.986  -0.713  -0.713  -0.713  -0.986  -0.986  -0.986
28    V        -0.986  -0.986  -0.986  -1.283  -1.283  -1.283  -0.986  -0.986  -0.986
29    D        -0.986  -0.986  -0.986  -0.654  -0.654  -0.654  -0.986  -0.986  -0.986
30    S         0.986   0.986   0.986   0.768   0.768   0.768   0.986   0.986   0.986
31    T         0.986   0.986   0.986   1.024   1.024   1.024   0.986   0.986   0.986
32    M        -0.986  -0.986  -0.986  -1.149  -1.149  -1.149  -0.986  -0.986  -0.986
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    S        -0.986  -0.986  -0.986  -0.894  -0.894  -0.894  -0.986  -0.986  -0.986
37    P        -0.986  -0.986  -0.986  -0.482  -0.482  -0.482  -0.986  -0.986  -0.986
38    K        -0.986  -0.986  -0.986  -0.654  -0.654  -0.654  -0.986  -0.986  -0.986
39    N        -0.986  -0.986  -0.986  -0.956  -0.956  -0.956  -0.986  -0.986  -0.986
* 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/Q99380
Output conservation file - output/Q99380
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
