1     M         0.856   0.856   0.856   1.187   1.187   1.187   0.856   0.856   0.856
2     S        -1.151  -1.151  -1.151  -1.095  -1.095  -1.095  -1.151  -1.151  -1.151
3     A        -1.151  -1.151  -1.151  -0.839  -0.839  -0.839  -1.151  -1.151  -1.151
4     E        -1.151  -1.151  -1.151  -1.331  -1.331  -1.331  -1.151  -1.151  -1.151
5     N        -1.151  -1.151  -1.151  -1.161  -1.161  -1.161  -1.151  -1.151  -1.151
6     I        -1.151  -1.151  -1.151  -0.870  -0.870  -0.870  -1.151  -1.151  -1.151
7     S        -1.151  -1.151  -1.151  -1.161  -1.161  -1.161  -1.151  -1.151  -1.151
8     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    Q        -1.151  -1.151  -1.151  -1.194  -1.194  -1.194  -1.151  -1.151  -1.151
16    P        -1.151  -1.151  -1.151  -0.839  -0.839  -0.839  -1.151  -1.151  -1.151
17    S        -1.151  -1.151  -1.151  -1.262  -1.262  -1.262  -1.151  -1.151  -1.151
18    S         0.856   0.856   0.856   0.877   0.877   0.877   0.856   0.856   0.856
19    E         0.856   0.856   0.856   0.646   0.646   0.646   0.856   0.856   0.856
20    V        -1.151  -1.151  -1.151  -0.626  -0.626  -0.626  -1.151  -1.151  -1.151
21    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    N        -1.151  -1.151  -1.151  -1.262  -1.262  -1.262  -1.151  -1.151  -1.151
32    E        -1.151  -1.151  -1.151  -1.401  -1.401  -1.401  -1.151  -1.151  -1.151
33    R        -1.151  -1.151  -1.151  -1.128  -1.128  -1.128  -1.151  -1.151  -1.151
34    M        -1.151  -1.151  -1.151  -0.933  -0.933  -0.933  -1.151  -1.151  -1.151
35    M        -1.151  -1.151  -1.151  -0.686  -0.686  -0.686  -1.151  -1.151  -1.151
36    R        -1.151  -1.151  -1.151  -0.933  -0.933  -0.933  -1.151  -1.151  -1.151
37    Q        -1.151  -1.151  -1.151  -1.331  -1.331  -1.331  -1.151  -1.151  -1.151
38    T         0.856   0.856   0.856   0.922   0.922   0.922   0.856   0.856   0.856
39    K         0.856   0.856   0.856   0.832   0.832   0.832   0.856   0.856   0.856
40    L         0.856   0.856   0.856   0.455   0.455   0.455   0.856   0.856   0.856
41    L         0.856   0.856   0.856   0.455   0.455   0.455   0.856   0.856   0.856
42    K        -1.151  -1.151  -1.151  -0.997  -0.997  -0.997  -1.151  -1.151  -1.151
43    D         0.856   0.856   0.856   1.012   1.012   1.012   0.856   0.856   0.856
44    T         0.856   0.856   0.856   0.922   0.922   0.922   0.856   0.856   0.856
45    L         0.856   0.856   0.856   0.455   0.455   0.455   0.856   0.856   0.856
46    D         0.856   0.856   0.856   1.012   1.012   1.012   0.856   0.856   0.856
47    L         0.856   0.856   0.856   0.455   0.455   0.455   0.856   0.856   0.856
48    L         0.856   0.856   0.856   0.455   0.455   0.455   0.856   0.856   0.856
49    W         0.856   0.856   0.856   1.357   1.357   1.357   0.856   0.856   0.856
50    N         0.856   0.856   0.856   0.786   0.786   0.786   0.856   0.856   0.856
51    K         0.856   0.856   0.856   0.832   0.832   0.832   0.856   0.856   0.856
52    T         0.856   0.856   0.856   0.922   0.922   0.922   0.856   0.856   0.856
53    L         0.856   0.856   0.856   0.455   0.455   0.455   0.856   0.856   0.856
54    E         0.856   0.856   0.856   0.646   0.646   0.646   0.856   0.856   0.856
55    Q         0.856   0.856   0.856   0.922   0.922   0.922   0.856   0.856   0.856
56    Q        -1.151  -1.151  -1.151  -0.933  -0.933  -0.933  -1.151  -1.151  -1.151
57    E        -1.151  -1.151  -1.151  -1.401  -1.401  -1.401  -1.151  -1.151  -1.151
58    V        -1.151  -1.151  -1.151  -1.194  -1.194  -1.194  -1.151  -1.151  -1.151
59    C         0.856   0.856   0.856   1.357   1.357   1.357   0.856   0.856   0.856
60    E        -1.151  -1.151  -1.151  -1.437  -1.437  -1.437  -1.151  -1.151  -1.151
61    Q         0.856   0.856   0.856   0.922   0.922   0.922   0.856   0.856   0.856
62    L         0.856   0.856   0.856   0.455   0.455   0.455   0.856   0.856   0.856
63    K        -1.151  -1.151  -1.151  -1.401  -1.401  -1.401  -1.151  -1.151  -1.151
64    Q         0.856   0.856   0.856   0.922   0.922   0.922   0.856   0.856   0.856
65    E         0.856   0.856   0.856   0.646   0.646   0.646   0.856   0.856   0.856
66    N         0.856   0.856   0.856   0.786   0.786   0.786   0.856   0.856   0.856
67    D        -1.151  -1.151  -1.151  -1.262  -1.262  -1.262  -1.151  -1.151  -1.151
68    Y        -1.151  -1.151  -1.151  -0.965  -0.965  -0.965  -1.151  -1.151  -1.151
69    L         0.856   0.856   0.856   0.455   0.455   0.455   0.856   0.856   0.856
70    E        -1.151  -1.151  -1.151  -1.401  -1.401  -1.401  -1.151  -1.151  -1.151
71    D         0.856   0.856   0.856   1.012   1.012   1.012   0.856   0.856   0.856
72    Y         0.856   0.856   0.856   1.272   1.272   1.272   0.856   0.856   0.856
73    I         0.856   0.856   0.856   1.272   1.272   1.272   0.856   0.856   0.856
74    G        -1.151  -1.151  -1.151  -0.997  -0.997  -0.997  -1.151  -1.151  -1.151
75    N         0.856   0.856   0.856   0.786   0.786   0.786   0.856   0.856   0.856
76    L         0.856   0.856   0.856   0.455   0.455   0.455   0.856   0.856   0.856
77    M         0.856   0.856   0.856   1.187   1.187   1.187   0.856   0.856   0.856
78    R        -1.151  -1.151  -1.151  -0.933  -0.933  -0.933  -1.151  -1.151  -1.151
79    S         0.856   0.856   0.856   0.877   0.877   0.877   0.856   0.856   0.856
80    S         0.856   0.856   0.856   0.877   0.877   0.877   0.856   0.856   0.856
81    N         0.856   0.856   0.856   0.786   0.786   0.786   0.856   0.856   0.856
82    V         0.856   0.856   0.856   1.272   1.272   1.272   0.856   0.856   0.856
83    L         0.856   0.856   0.856   0.455   0.455   0.455   0.856   0.856   0.856
84    E        -1.151  -1.151  -1.151  -1.262  -1.262  -1.262  -1.151  -1.151  -1.151
85    K         0.856   0.856   0.856   0.832   0.832   0.832   0.856   0.856   0.856
* 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/Q3E784
Output conservation file - output/Q3E784
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
