1     M         0.681   0.681   0.681   0.935   0.935   0.935   0.681   0.681   0.681
2     Q         0.681   0.681   0.681   0.559   0.559   0.559   0.681   0.681   0.681
3     P         0.681   0.681   0.681   0.750   0.750   0.750   0.681   0.681   0.681
4     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     S        -1.425  -1.425  -1.425  -1.458  -1.458  -1.458  -1.425  -1.425  -1.425
9     T        -1.425  -1.425  -1.425  -1.678  -1.678  -1.678  -1.425  -1.425  -1.425
10    Q        -1.425  -1.425  -1.425  -1.318  -1.318  -1.318  -1.425  -1.425  -1.425
11    A         0.681   0.681   0.681   0.559   0.559   0.559   0.681   0.681   0.681
12    T         0.681   0.681   0.681   0.461   0.461   0.461   0.681   0.681   0.681
13    Q         0.681   0.681   0.681   0.559   0.559   0.559   0.681   0.681   0.681
14    K         0.681   0.681   0.681   0.362   0.362   0.362   0.681   0.681   0.681
15    D         0.681   0.681   0.681   0.559   0.559   0.559   0.681   0.681   0.681
16    K        -1.425  -1.425  -1.425  -1.458  -1.458  -1.458  -1.425  -1.425  -1.425
17    S        -1.425  -1.425  -1.425  -1.458  -1.458  -1.458  -1.425  -1.425  -1.425
18    S        -1.425  -1.425  -1.425  -1.388  -1.388  -1.388  -1.425  -1.425  -1.425
19    E         0.681   0.681   0.681   0.843   0.843   0.843   0.681   0.681   0.681
20    K         0.681   0.681   0.681   0.362   0.362   0.362   0.681   0.681   0.681
21    K        -1.425  -1.425  -1.425  -1.318  -1.318  -1.318  -1.425  -1.425  -1.425
22    D         0.681   0.681   0.681   0.559   0.559   0.559   0.681   0.681   0.681
23    N         0.681   0.681   0.681   0.843   0.843   0.843   0.681   0.681   0.681
24    Y         0.681   0.681   0.681   0.935   0.935   0.935   0.681   0.681   0.681
25    I         0.681   0.681   0.681   0.461   0.461   0.461   0.681   0.681   0.681
26    I        -1.425  -1.425  -1.425  -1.388  -1.388  -1.388  -1.425  -1.425  -1.425
27    K         0.681   0.681   0.681   0.362   0.362   0.362   0.681   0.681   0.681
28    G         0.681   0.681   0.681   0.935   0.935   0.935   0.681   0.681   0.681
29    L        -1.425  -1.425  -1.425  -0.986  -0.986  -0.986  -1.425  -1.425  -1.425
30    F         0.681   0.681   0.681   0.843   0.843   0.843   0.681   0.681   0.681
31    W         0.681   0.681   0.681   0.935   0.935   0.935   0.681   0.681   0.681
32    D        -1.425  -1.425  -1.425  -1.388  -1.388  -1.388  -1.425  -1.425  -1.425
33    P         0.681   0.681   0.681   0.750   0.750   0.750   0.681   0.681   0.681
34    A        -1.425  -1.425  -1.425  -1.530  -1.530  -1.530  -1.425  -1.425  -1.425
35    C         0.681   0.681   0.681   0.935   0.935   0.935   0.681   0.681   0.681
36    V         0.681   0.681   0.681   0.843   0.843   0.843   0.681   0.681   0.681
37    I         0.681   0.681   0.681   0.461   0.461   0.461   0.681   0.681   0.681
38    A         0.681   0.681   0.681   0.559   0.559   0.559   0.681   0.681   0.681
* 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/P34166
Output conservation file - output/P34166
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
