1     M         0.875   0.875   0.875   1.086   1.086   1.086   0.875   0.875   0.875
2     Q         0.875   0.875   0.875   0.910   0.910   0.910   0.875   0.875   0.875
3     P         0.875   0.875   0.875   0.820   0.820   0.820   0.875   0.875   0.875
4     S        -1.109  -1.109  -1.109  -1.071  -1.071  -1.071  -1.109  -1.109  -1.109
5     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     T        -1.109  -1.109  -1.109  -1.207  -1.207  -1.207  -1.109  -1.109  -1.109
8     A        -1.109  -1.109  -1.109  -1.138  -1.138  -1.138  -1.109  -1.109  -1.109
9     A         0.875   0.875   0.875   0.635   0.635   0.635   0.875   0.875   0.875
10    P        -1.109  -1.109  -1.109  -1.138  -1.138  -1.138  -1.109  -1.109  -1.109
11    K        -1.109  -1.109  -1.109  -1.207  -1.207  -1.207  -1.109  -1.109  -1.109
12    E        -1.109  -1.109  -1.109  -1.207  -1.207  -1.207  -1.109  -1.109  -1.109
13    K        -1.109  -1.109  -1.109  -1.277  -1.277  -1.277  -1.109  -1.109  -1.109
14    T        -1.109  -1.109  -1.109  -1.005  -1.005  -1.005  -1.109  -1.109  -1.109
15    S        -1.109  -1.109  -1.109  -1.071  -1.071  -1.071  -1.109  -1.109  -1.109
16    S        -1.109  -1.109  -1.109  -0.939  -0.939  -0.939  -1.109  -1.109  -1.109
17    E         0.875   0.875   0.875   0.910   0.910   0.910   0.875   0.875   0.875
18    K         0.875   0.875   0.875   0.541   0.541   0.541   0.875   0.875   0.875
19    K        -1.109  -1.109  -1.109  -1.005  -1.005  -1.005  -1.109  -1.109  -1.109
20    D         0.875   0.875   0.875   0.820   0.820   0.820   0.875   0.875   0.875
21    N         0.875   0.875   0.875   0.998   0.998   0.998   0.875   0.875   0.875
22    Y         0.875   0.875   0.875   1.086   1.086   1.086   0.875   0.875   0.875
23    I         0.875   0.875   0.875   0.728   0.728   0.728   0.875   0.875   0.875
24    I        -1.109  -1.109  -1.109  -1.071  -1.071  -1.071  -1.109  -1.109  -1.109
25    K         0.875   0.875   0.875   0.541   0.541   0.541   0.875   0.875   0.875
26    G         0.875   0.875   0.875   1.086   1.086   1.086   0.875   0.875   0.875
27    V        -1.109  -1.109  -1.109  -0.875  -0.875  -0.875  -1.109  -1.109  -1.109
28    F         0.875   0.875   0.875   0.998   0.998   0.998   0.875   0.875   0.875
29    W         0.875   0.875   0.875   1.086   1.086   1.086   0.875   0.875   0.875
30    D        -1.109  -1.109  -1.109  -1.005  -1.005  -1.005  -1.109  -1.109  -1.109
31    P         0.875   0.875   0.875   0.820   0.820   0.820   0.875   0.875   0.875
32    A        -1.109  -1.109  -1.109  -1.207  -1.207  -1.207  -1.109  -1.109  -1.109
33    C         0.875   0.875   0.875   1.086   1.086   1.086   0.875   0.875   0.875
34    V         0.875   0.875   0.875   0.910   0.910   0.910   0.875   0.875   0.875
35    I         0.875   0.875   0.875   0.728   0.728   0.728   0.875   0.875   0.875
36    A         0.875   0.875   0.875   0.635   0.635   0.635   0.875   0.875   0.875
* 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/P34165
Output conservation file - output/P34165
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
