1     M         0.930   0.930   0.930   1.244   1.244   1.244   0.930   0.930   0.930
2     S         0.930   0.930   0.930   0.667   0.667   0.667   0.930   0.930   0.930
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    A         0.930   0.930   0.930   0.302   0.302   0.302   0.930   0.930   0.930
11    W         0.930   0.930   0.930   1.289   1.289   1.289   0.930   0.930   0.930
12    R         0.930   0.930   0.930   1.058   1.058   1.058   0.930   0.930   0.930
13    K         0.930   0.930   0.930   0.866   0.866   0.866   0.930   0.930   0.930
14    A         0.930   0.930   0.930   0.302   0.302   0.302   0.930   0.930   0.930
15    G         0.930   0.930   0.930   1.105   1.105   1.105   0.930   0.930   0.930
16    I        -1.058  -1.058  -1.058  -0.765  -0.765  -0.765  -1.058  -1.058  -1.058
17    S         0.930   0.930   0.930   0.667   0.667   0.667   0.930   0.930   0.930
18    Y         0.930   0.930   0.930   1.058   1.058   1.058   0.930   0.930   0.930
19    A        -1.058  -1.058  -1.058  -1.633  -1.633  -1.633  -1.058  -1.058  -1.058
20    A        -1.058  -1.058  -1.058  -1.633  -1.633  -1.633  -1.058  -1.058  -1.058
21    Y        -1.058  -1.058  -1.058  -0.599  -0.599  -0.599  -1.058  -1.058  -1.058
22    L         0.930   0.930   0.930   0.962   0.962   0.962   0.930   0.930   0.930
23    N        -1.058  -1.058  -1.058  -1.193  -1.193  -1.193  -1.058  -1.058  -1.058
24    V        -1.058  -1.058  -1.058  -0.632  -0.632  -0.632  -1.058  -1.058  -1.058
25    A         0.930   0.930   0.930   0.302   0.302   0.302   0.930   0.930   0.930
26    A         0.930   0.930   0.930   0.302   0.302   0.302   0.930   0.930   0.930
27    Q        -1.058  -1.058  -1.058  -0.731  -0.731  -0.731  -1.058  -1.058  -1.058
28    A        -1.058  -1.058  -1.058  -1.508  -1.508  -1.508  -1.058  -1.058  -1.058
29    I        -1.058  -1.058  -1.058  -0.632  -0.632  -0.632  -1.058  -1.058  -1.058
30    R         0.930   0.930   0.930   1.058   1.058   1.058   0.930   0.930   0.930
31    S        -1.058  -1.058  -1.058  -1.009  -1.009  -1.009  -1.058  -1.058  -1.058
32    S         0.930   0.930   0.930   0.667   0.667   0.667   0.930   0.930   0.930
33    L         0.930   0.930   0.930   0.962   0.962   0.962   0.930   0.930   0.930
34    K         0.930   0.930   0.930   0.866   0.866   0.866   0.930   0.930   0.930
35    T        -1.058  -1.058  -1.058  -1.082  -1.082  -1.082  -1.058  -1.058  -1.058
36    E         0.930   0.930   0.930   1.105   1.105   1.105   0.930   0.930   0.930
37    L         0.930   0.930   0.930   0.962   0.962   0.962   0.930   0.930   0.930
38    Q         0.930   0.930   0.930   1.105   1.105   1.105   0.930   0.930   0.930
39    T         0.930   0.930   0.930   0.817   0.817   0.817   0.930   0.930   0.930
40    A        -1.058  -1.058  -1.058  -1.269  -1.269  -1.269  -1.058  -1.058  -1.058
41    S        -1.058  -1.058  -1.058  -1.633  -1.633  -1.633  -1.058  -1.058  -1.058
42    V         0.930   0.930   0.930   1.151   1.151   1.151   0.930   0.930   0.930
43    L        -1.058  -1.058  -1.058  -0.698  -0.698  -0.698  -1.058  -1.058  -1.058
44    N        -1.058  -1.058  -1.058  -0.632  -0.632  -0.632  -1.058  -1.058  -1.058
45    R         0.930   0.930   0.930   1.058   1.058   1.058   0.930   0.930   0.930
46    S        -1.058  -1.058  -1.058  -1.009  -1.009  -1.009  -1.058  -1.058  -1.058
47    Q        -1.058  -1.058  -1.058  -0.868  -0.868  -0.868  -1.058  -1.058  -1.058
48    T         0.930   0.930   0.930   0.817   0.817   0.817   0.930   0.930   0.930
49    D         0.930   0.930   0.930   1.244   1.244   1.244   0.930   0.930   0.930
50    A         0.930   0.930   0.930   0.302   0.302   0.302   0.930   0.930   0.930
51    F        -1.058  -1.058  -1.058  -1.118  -1.118  -1.118  -1.058  -1.058  -1.058
52    Y         0.930   0.930   0.930   1.058   1.058   1.058   0.930   0.930   0.930
53    T         0.930   0.930   0.930   0.817   0.817   0.817   0.930   0.930   0.930
54    Q        -1.058  -1.058  -1.058  -0.868  -0.868  -0.868  -1.058  -1.058  -1.058
55    Y         0.930   0.930   0.930   1.058   1.058   1.058   0.930   0.930   0.930
56    K        -1.058  -1.058  -1.058  -0.868  -0.868  -0.868  -1.058  -1.058  -1.058
57    N        -1.058  -1.058  -1.058  -0.799  -0.799  -0.799  -1.058  -1.058  -1.058
58    G         0.930   0.930   0.930   1.105   1.105   1.105   0.930   0.930   0.930
59    T        -1.058  -1.058  -1.058  -1.231  -1.231  -1.231  -1.058  -1.058  -1.058
60    A        -1.058  -1.058  -1.058  -1.269  -1.269  -1.269  -1.058  -1.058  -1.058
61    A        -1.058  -1.058  -1.058  -1.467  -1.467  -1.467  -1.058  -1.058  -1.058
62    S         0.930   0.930   0.930   0.667   0.667   0.667   0.930   0.930   0.930
63    E        -1.058  -1.058  -1.058  -0.599  -0.599  -0.599  -1.058  -1.058  -1.058
64    P         0.930   0.930   0.930   1.105   1.105   1.105   0.930   0.930   0.930
65    T        -1.058  -1.058  -1.058  -0.868  -0.868  -0.868  -1.058  -1.058  -1.058
66    P         0.930   0.930   0.930   1.105   1.105   1.105   0.930   0.930   0.930
67    I        -1.058  -1.058  -1.058  -0.765  -0.765  -0.765  -1.058  -1.058  -1.058
68    T        -1.058  -1.058  -1.058  -0.903  -0.903  -0.903  -1.058  -1.058  -1.058
69    K        -1.058  -1.058  -1.058  -0.868  -0.868  -0.868  -1.058  -1.058  -1.058
* 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/P21306
Output conservation file - output/P21306
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
