1     M         0.929   0.946   1.003   1.323   1.353   1.387   0.941   0.973   1.055
2     A        -0.092   0.111  -0.416  -0.238   0.014  -0.553  -0.065   0.192  -0.561
3     K         0.929   0.946   1.003   0.120   0.265   0.424   0.941   0.973   1.055
4     S         0.929   0.946   1.003   1.112   1.137   1.218   0.941   0.973   1.055
5     K         0.929   0.946   1.003   0.120   0.265   0.424   0.941   0.973   1.055
6     N         0.929   0.946   1.003   0.958   0.980   1.094   0.941   0.973   1.055
7     H        -0.092  -0.178  -0.430   0.183   0.082  -0.274  -0.065  -0.186  -0.584
8     T        -0.092  -0.178  -0.430   0.350   0.243  -0.158  -0.065  -0.186  -0.584
9     A        -1.512  -1.576  -1.366  -1.471  -1.602  -1.195  -1.501  -1.573  -1.265
10    H         0.929   0.946   1.003   0.905   0.976   1.052   0.941   0.973   1.055
11    N         0.929   0.946   1.003   0.958   0.980   1.094   0.941   0.973   1.055
12    Q         0.929   0.946   1.003   1.274   1.276   1.348   0.941   0.973   1.055
13    T        -1.981  -2.161  -1.995  -1.030  -1.438  -1.272  -1.645  -1.820  -1.565
14    R        -0.950  -0.750  -0.494  -1.674  -1.480  -1.035  -1.357  -1.060  -0.686
15    K         0.929   0.946   1.003   0.120   0.265   0.424   0.941   0.973   1.055
16    A         0.929   0.946   1.003   0.484   0.601   0.715   0.941   0.973   1.055
17    H         0.929   0.946   1.003   0.905   0.976   1.052   0.941   0.973   1.055
18    R         0.929   0.946   1.003   0.813   0.839   0.978   0.941   0.973   1.055
19    N         0.929   0.946   1.003   0.958   0.980   1.094   0.941   0.973   1.055
20    G         0.929   0.946   1.003   1.124   1.171   1.228   0.941   0.973   1.055
21    I         0.929   0.946   1.003   1.299   1.320   1.367   0.941   0.973   1.055
22    K         0.929   0.946   1.003   0.120   0.265   0.424   0.941   0.973   1.055
23    K        -0.595  -0.661  -0.502  -1.272  -1.378  -1.025  -0.783  -0.913  -0.697
24    P        -0.092  -0.033  -0.425   0.529   0.570   0.040  -0.065   0.009  -0.575
25    K        -1.065  -1.124  -1.334  -1.338  -1.385  -1.493  -0.926  -1.031  -1.229
26    T        -1.065  -1.124  -1.334  -0.509  -0.793  -1.227  -0.926  -1.031  -1.229
27    Y        -1.712  -1.581  -1.352  -1.182  -1.172  -0.916  -1.788  -1.580  -1.250
28    K        -0.595  -0.704  -0.503  -1.272  -1.436  -1.012  -0.783  -0.984  -0.699
29    Y         0.929   0.946   1.003   1.225   1.268   1.308   0.941   0.973   1.055
30    P        -1.065  -1.246  -1.347  -0.224  -0.535  -0.815  -0.926  -1.161  -1.243
31    S         0.929   0.946   1.003   1.112   1.137   1.218   0.941   0.973   1.055
32    L         0.929   0.946   1.003   1.149   1.208   1.248   0.941   0.973   1.055
33    K         0.929   0.946   1.003   0.120   0.265   0.424   0.941   0.973   1.055
34    G        -0.092  -0.358  -0.444   0.416   0.086  -0.096  -0.065  -0.444  -0.606
35    V        -1.065  -1.365  -1.350  -0.166  -0.702  -0.856  -0.926  -1.293  -1.246
36    D         0.929   0.946   1.003   1.311   1.333   1.377   0.941   0.973   1.055
37    P        -0.864  -0.665  -0.484  -1.058  -0.824  -0.555  -1.214  -0.920  -0.669
38    K         0.929   0.946   1.003   0.120   0.265   0.424   0.941   0.973   1.055
39    F         0.929   0.946   1.003   1.287   1.309   1.358   0.941   0.973   1.055
40    R        -0.092   0.199  -0.410  -0.047   0.251  -0.708  -0.065   0.299  -0.552
41    R         0.929   0.946   1.003   0.813   0.839   0.978   0.941   0.973   1.055
42    N         0.929   0.946   1.003   0.958   0.980   1.094   0.941   0.973   1.055
43    H        -0.092  -0.358  -0.444   0.207  -0.099  -0.221  -0.065  -0.444  -0.606
44    K        -0.595  -0.583  -0.498  -0.797  -0.948  -0.973  -0.783  -0.789  -0.692
45    H        -2.005  -1.757  -1.381  -1.452  -1.276  -0.844  -2.076  -1.758  -1.282
46    A         0.929   0.946   1.003   0.484   0.601   0.715   0.941   0.973   1.055
47    L        -0.092  -0.358  -0.444   0.404   0.043  -0.192  -0.065  -0.444  -0.606
48    H        -1.512  -1.440  -1.357  -1.278  -1.364  -1.372  -1.501  -1.424  -1.257
49    G         0.929   0.946   1.003   1.124   1.171   1.228   0.941   0.973   1.055
50    T        -0.092  -0.033  -0.425   0.328   0.381  -0.211  -0.065   0.009  -0.575
51    A        -0.092  -0.358  -0.444  -0.204  -0.437  -0.481  -0.065  -0.444  -0.606
52    K        -0.092  -0.358  -0.444  -0.569  -0.770  -0.728  -0.065  -0.444  -0.606
53    A        -0.092   0.144  -0.410  -0.244   0.046  -0.563  -0.065   0.232  -0.552
54    L        -0.092  -0.358  -0.444   0.452   0.135  -0.048  -0.065  -0.444  -0.606
55    A        -1.065  -1.365  -1.350  -1.172  -1.678  -1.838  -0.926  -1.293  -1.246
56    A        -2.652  -2.434  -1.997  -2.638  -2.215  -1.746  -2.363  -2.076  -1.567
57    A        -1.981  -1.727  -1.965  -1.847  -1.571  -2.033  -1.645  -1.387  -1.539
58    K        -0.950  -0.729  -0.494  -1.674  -1.464  -1.035  -1.357  -1.024  -0.685
59    -        -0.292  -0.331  -0.441  -0.415  -0.419  -0.501  -0.336  -0.405  -0.600
60    -        -0.428  -0.558  -0.482   0.190  -0.097  -0.099  -0.530  -0.749  -0.667
61    -         0.929   0.946   1.003   0.117   0.240   0.421   0.941   0.973   1.055
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    K        -0.864  -0.505  -0.452  -1.701  -1.033  -1.079  -1.214  -0.667  -0.618
* 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/P05747
Output conservation file - output/P05747
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
