1     M         0.603   0.604   0.608   1.122   1.105   1.074   0.611   0.611   0.615
2     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     L         0.603   0.604   0.608   0.323   0.332   0.365   0.611   0.611   0.615
4     P         0.603   0.604   0.608   1.058   1.037   1.018   0.611   0.611   0.615
5     G         0.603   0.604   0.608   0.667   0.662   0.670   0.611   0.611   0.615
6     G         0.603   0.604   0.608   0.667   0.662   0.670   0.611   0.611   0.615
7     V        -1.402  -1.449  -1.439  -1.300  -1.322  -1.247  -1.460  -1.523  -1.502
8     I         0.603   0.604   0.608   0.109   0.110   0.174   0.611   0.611   0.615
9     L        -1.402  -1.449  -1.439  -1.749  -1.785  -1.724  -1.460  -1.523  -1.502
10    V         0.603   0.604   0.608   0.531   0.547   0.550   0.611   0.611   0.615
11    F        -1.402  -1.449  -1.439  -1.208  -1.295  -1.362  -1.460  -1.523  -1.502
12    I         0.603   0.604   0.608   0.109   0.110   0.174   0.611   0.611   0.615
13    L         0.603   0.604   0.608   0.323   0.332   0.365   0.611   0.611   0.615
14    V         0.603   0.604   0.608   0.531   0.547   0.550   0.611   0.611   0.615
15    G         0.603   0.604   0.608   0.667   0.662   0.670   0.611   0.611   0.615
16    L         0.603   0.604   0.608   0.323   0.332   0.365   0.611   0.611   0.615
17    A         0.603   0.604   0.608   0.463   0.459   0.489   0.611   0.611   0.615
18    C        -1.402  -1.408  -1.436  -1.330  -1.313  -1.254  -1.460  -1.465  -1.499
19    I        -1.402  -1.408  -1.436  -1.178  -1.198  -1.378  -1.460  -1.465  -1.499
20    A        -1.402  -1.449  -1.439  -1.816  -1.906  -1.889  -1.460  -1.523  -1.502
21    I         0.603   0.604   0.608   0.109   0.110   0.174   0.611   0.611   0.615
22    I        -1.402  -1.408  -1.436  -1.749  -1.733  -1.828  -1.460  -1.465  -1.499
23    A         0.603   0.604   0.608   0.463   0.459   0.489   0.611   0.611   0.615
24    T        -1.402  -1.242  -1.427  -0.943  -0.660  -1.070  -1.460  -1.233  -1.485
25    I         0.603   0.604   0.608   0.109   0.110   0.174   0.611   0.611   0.615
26    I         0.603   0.604   0.608   0.109   0.110   0.174   0.611   0.611   0.615
27    Y         0.603   0.604   0.608   1.122   1.105   1.074   0.611   0.611   0.615
28    R         0.603   0.604   0.608   0.531   0.533   0.550   0.611   0.611   0.615
29    K         0.603   0.604   0.608   1.122   1.105   1.074   0.611   0.611   0.615
30    W         0.603   0.604   0.608   1.122   1.105   1.074   0.611   0.611   0.615
31    Q         0.603   0.604   0.608   0.800   0.800   0.788   0.611   0.611   0.615
32    A        -1.402  -1.408  -1.436  -0.972  -0.985  -1.137  -1.460  -1.465  -1.499
33    R         0.603   0.604   0.608   0.531   0.533   0.550   0.611   0.611   0.615
34    Q         0.603   0.604   0.608   0.800   0.800   0.788   0.611   0.611   0.615
35    R         0.603   0.604   0.608   0.531   0.533   0.550   0.611   0.611   0.615
36    G        -2.858  -2.794  -2.649  -2.514  -2.456  -2.155  -2.496  -2.416  -2.223
37    L         0.603   0.604   0.608   0.323   0.332   0.365   0.611   0.611   0.615
38    Q        -1.402  -1.449  -1.439  -1.330  -1.403  -1.422  -1.460  -1.523  -1.502
39    R         0.603   0.604   0.608   0.531   0.533   0.550   0.611   0.611   0.615
40    F         0.603   0.604   0.608   0.995   0.989   0.961   0.611   0.611   0.615
* 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/P32903
Output conservation file - output/P32903
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
