1     M         0.642   0.643   0.647   1.147   1.132   1.102   0.650   0.651   0.654
2     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     S        -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     L         0.642   0.643   0.647   0.357   0.366   0.398   0.650   0.651   0.654
7     P         0.642   0.643   0.647   1.084   1.066   1.046   0.650   0.651   0.654
8     G         0.642   0.643   0.647   0.696   0.690   0.700   0.650   0.651   0.654
9     G         0.642   0.643   0.647   0.696   0.690   0.700   0.650   0.651   0.654
10    V        -1.325  -1.352  -1.357  -1.249  -1.249  -1.203  -1.378  -1.412  -1.414
11    I         0.642   0.643   0.647   0.144   0.142   0.209   0.650   0.651   0.654
12    L        -1.325  -1.352  -1.357  -1.694  -1.704  -1.673  -1.378  -1.412  -1.414
13    V         0.642   0.643   0.647   0.562   0.582   0.581   0.650   0.651   0.654
14    F        -1.325  -1.352  -1.357  -1.159  -1.212  -1.308  -1.378  -1.412  -1.414
15    I         0.642   0.643   0.647   0.144   0.142   0.209   0.650   0.651   0.654
16    L         0.642   0.643   0.647   0.357   0.366   0.398   0.650   0.651   0.654
17    V         0.642   0.643   0.647   0.562   0.582   0.581   0.650   0.651   0.654
18    G         0.642   0.643   0.647   0.696   0.690   0.700   0.650   0.651   0.654
19    L         0.642   0.643   0.647   0.357   0.366   0.398   0.650   0.651   0.654
20    A         0.642   0.643   0.647   0.562   0.565   0.581   0.650   0.651   0.654
21    C        -1.325  -1.352  -1.357  -1.219  -1.229  -1.164  -1.378  -1.412  -1.414
22    I        -1.325  -1.352  -1.357  -1.129  -1.207  -1.333  -1.378  -1.412  -1.414
23    A        -1.325  -1.352  -1.357  -1.694  -1.746  -1.780  -1.378  -1.412  -1.414
24    I         0.642   0.643   0.647   0.144   0.142   0.209   0.650   0.651   0.654
25    I        -1.325  -1.352  -1.357  -1.694  -1.730  -1.780  -1.378  -1.412  -1.414
26    S        -1.325  -1.352  -1.357  -1.189  -1.194  -1.126  -1.378  -1.412  -1.414
27    T        -1.325  -1.159  -1.344  -0.897  -0.605  -1.018  -1.378  -1.143  -1.395
28    I         0.642   0.643   0.647   0.144   0.142   0.209   0.650   0.651   0.654
29    I         0.642   0.643   0.647   0.144   0.142   0.209   0.650   0.651   0.654
30    Y         0.642   0.643   0.647   1.147   1.132   1.102   0.650   0.651   0.654
31    R         0.642   0.643   0.647   0.562   0.565   0.581   0.650   0.651   0.654
32    K         0.642   0.643   0.647   1.147   1.132   1.102   0.650   0.651   0.654
33    W         0.642   0.643   0.647   1.147   1.132   1.102   0.650   0.651   0.654
34    Q         0.642   0.643   0.647   0.828   0.828   0.818   0.650   0.651   0.654
35    A        -1.325  -1.352  -1.357  -0.897  -0.952  -1.056  -1.378  -1.412  -1.414
36    R         0.642   0.643   0.647   0.562   0.565   0.581   0.650   0.651   0.654
37    Q         0.642   0.643   0.647   0.828   0.828   0.818   0.650   0.651   0.654
38    R         0.642   0.643   0.647   0.562   0.565   0.581   0.650   0.651   0.654
39    G        -2.752  -2.686  -2.546  -2.453  -2.387  -2.105  -2.391  -2.309  -2.123
40    L         0.642   0.643   0.647   0.357   0.366   0.398   0.650   0.651   0.654
41    Q        -1.325  -1.352  -1.357  -1.249  -1.286  -1.330  -1.378  -1.412  -1.414
42    R         0.642   0.643   0.647   0.562   0.565   0.581   0.650   0.651   0.654
43    F         0.642   0.643   0.647   1.021   1.015   0.989   0.650   0.651   0.654
* 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/P40975
Output conservation file - output/P40975
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
