1     M         1.310   1.310   1.310   1.473   1.472   1.473   1.310   1.310   1.310
2     L        -0.753  -0.753  -0.753  -1.170  -1.176  -1.170  -0.753  -0.753  -0.753
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     S         1.310   1.310   1.310   1.383   1.381   1.383   1.310   1.310   1.310
6     K        -0.753  -0.753  -0.753  -0.495  -0.496  -0.495  -0.753  -0.753  -0.753
7     E        -0.753  -0.753  -0.753  -0.888  -0.892  -0.888  -0.753  -0.753  -0.753
8     A        -0.753  -0.753  -0.753  -0.495  -0.496  -0.495  -0.753  -0.753  -0.753
9     L        -0.753  -0.753  -0.753  -0.992  -0.996  -0.992  -0.753  -0.753  -0.753
10    I         1.310   1.310   1.310   1.338   1.336   1.338   1.310   1.310   1.310
11    K        -0.753  -0.753  -0.753  -0.558  -0.560  -0.558  -0.753  -0.753  -0.753
12    I        -0.753  -0.753  -0.753  -0.655  -0.657  -0.655  -0.753  -0.753  -0.753
13    L        -0.753  -0.753  -0.753  -1.207  -1.213  -1.207  -0.753  -0.753  -0.753
14    S        -0.753  -0.753  -0.753  -1.170  -1.176  -1.170  -0.753  -0.753  -0.753
15    Q         1.310   1.310   1.310   1.518   1.561   1.518   1.310   1.310   1.310
16    N        -0.753  -0.753  -0.753  -0.464  -0.465  -0.464  -0.753  -0.753  -0.753
17    E         1.310   1.310   1.310   1.200   1.197   1.200   1.310   1.310   1.310
18    G         1.310   1.310   1.310   1.518   1.516   1.518   1.310   1.310   1.310
19    G        -0.753  -0.753  -0.753  -0.495  -0.496  -0.495  -0.753  -0.753  -0.753
20    N        -0.753  -0.753  -0.753  -0.527  -0.496  -0.527  -0.753  -0.753  -0.753
21    D         1.310   1.310   1.310   1.246   1.243   1.246   1.310   1.310   1.310
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    M        -0.753  -0.753  -0.753  -0.527  -0.528  -0.527  -0.753  -0.753  -0.753
25    K        -0.753  -0.753  -0.753  -0.527  -0.528  -0.527  -0.753  -0.753  -0.753
26    I         1.310   1.310   1.310   1.338   1.336   1.338   1.310   1.310   1.310
27    A        -0.753  -0.753  -0.753  -0.495  -0.496  -0.495  -0.753  -0.753  -0.753
28    D        -0.753  -0.753  -0.753  -0.992  -0.996  -0.992  -0.753  -0.753  -0.753
29    E         1.310   1.310   1.310   1.200   1.197   1.200   1.310   1.310   1.310
30    V        -0.753  -0.753  -0.753  -0.371  -0.372  -0.371  -0.753  -0.753  -0.753
31    V        -0.753  -0.753  -0.753  -0.622  -0.624  -0.622  -0.753  -0.753  -0.753
32    P        -0.753  -0.753  -0.753  -0.402  -0.372  -0.402  -0.753  -0.753  -0.753
33    M        -0.753  -0.753  -0.753  -1.098  -1.103  -1.098  -0.753  -0.753  -0.753
34    I        -0.753  -0.753  -0.753  -1.207  -1.213  -1.207  -0.753  -0.753  -0.753
35    Q        -0.753  -0.753  -0.753  -0.787  -0.756  -0.787  -0.753  -0.753  -0.753
36    K        -0.753  -0.753  -0.753  -0.402  -0.403  -0.402  -0.753  -0.753  -0.753
37    Y         1.310   1.310   1.310   1.778   1.779   1.778   1.310   1.310   1.310
38    L        -0.753  -0.753  -0.753  -1.207  -1.213  -1.207  -0.753  -0.753  -0.753
39    D        -0.753  -0.753  -0.753  -0.992  -0.996  -0.992  -0.753  -0.753  -0.753
40    I        -0.753  -0.753  -0.753  -1.207  -1.213  -1.207  -0.753  -0.753  -0.753
41    F         1.310   1.310   1.310   1.606   1.605   1.606   1.310   1.310   1.310
42    I        -0.753  -0.753  -0.753  -0.720  -0.723  -0.720  -0.753  -0.753  -0.753
43    D        -0.753  -0.753  -0.753  -0.720  -0.723  -0.720  -0.753  -0.753  -0.753
44    E         1.310   1.310   1.310   1.200   1.197   1.200   1.310   1.310   1.310
45    A        -0.753  -0.753  -0.753  -0.558  -0.560  -0.558  -0.753  -0.753  -0.753
46    V         1.310   1.310   1.310   1.473   1.472   1.473   1.310   1.310   1.310
47    L         1.310   1.310   1.310   0.817   0.811   0.817   1.310   1.310   1.310
48    R         1.310   1.310   1.310   1.562   1.561   1.562   1.310   1.310   1.310
49    S         1.310   1.310   1.310   1.383   1.381   1.383   1.310   1.310   1.310
50    L         1.310   1.310   1.310   0.817   0.811   0.817   1.310   1.310   1.310
51    Q        -0.753  -0.753  -0.753  -0.787  -0.756  -0.787  -0.753  -0.753  -0.753
52    S        -0.753  -0.753  -0.753  -0.622  -0.624  -0.622  -0.753  -0.753  -0.753
53    H        -0.753  -0.753  -0.753  -0.371  -0.372  -0.371  -0.753  -0.753  -0.753
54    K        -0.753  -0.753  -0.753  -0.558  -0.560  -0.558  -0.753  -0.753  -0.753
55    D         1.310   1.310   1.310   1.246   1.243   1.246   1.310   1.310   1.310
56    I        -0.753  -0.753  -0.753  -0.720  -0.723  -0.720  -0.753  -0.753  -0.753
57    N        -0.753  -0.753  -0.753  -1.027  -1.031  -1.027  -0.753  -0.753  -0.753
58    G        -0.753  -0.753  -0.753  -0.558  -0.560  -0.558  -0.753  -0.753  -0.753
59    E        -0.753  -0.753  -0.753  -0.992  -0.996  -0.992  -0.753  -0.753  -0.753
60    R        -0.753  -0.753  -0.753  -0.527  -0.528  -0.527  -0.753  -0.753  -0.753
61    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    E        -0.753  -0.753  -0.753  -0.720  -0.723  -0.720  -0.753  -0.753  -0.753
68    L        -0.753  -0.753  -0.753  -1.098  -1.103  -1.098  -0.753  -0.753  -0.753
69    S        -0.753  -0.753  -0.753  -0.854  -0.857  -0.854  -0.753  -0.753  -0.753
70    H        -0.753  -0.753  -0.753  -0.311  -0.310  -0.311  -0.753  -0.753  -0.753
71    Q        -0.753  -0.753  -0.753  -0.590  -0.560  -0.590  -0.753  -0.753  -0.753
72    D         1.310   1.310   1.310   1.246   1.243   1.246   1.310   1.310   1.310
73    L         1.310   1.310   1.310   0.817   0.811   0.817   1.310   1.310   1.310
74    E         1.310   1.310   1.310   1.200   1.197   1.200   1.310   1.310   1.310
75    R        -0.753  -0.753  -0.753  -0.527  -0.528  -0.527  -0.753  -0.753  -0.753
76    I        -0.753  -0.753  -0.753  -0.720  -0.723  -0.720  -0.753  -0.753  -0.753
77    V        -0.753  -0.753  -0.753  -0.590  -0.592  -0.590  -0.753  -0.753  -0.753
78    G         1.310   1.310   1.310   1.518   1.516   1.518   1.310   1.310   1.310
79    L         1.310   1.310   1.310   0.817   0.811   0.817   1.310   1.310   1.310
80    L         1.310   1.310   1.310   0.817   0.811   0.817   1.310   1.310   1.310
81    L         1.310   1.310   1.310   0.817   0.811   0.817   1.310   1.310   1.310
82    M         1.310   1.310   1.310   1.473   1.472   1.473   1.310   1.310   1.310
83    D         1.310   1.310   1.310   1.246   1.243   1.246   1.310   1.310   1.310
84    M        -0.753  -0.753  -0.753  -0.527  -0.528  -0.527  -0.753  -0.753  -0.753
85    -        -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/Q3E829
Output conservation file - output/Q3E829
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
