1     M         0.699   0.702   0.732   1.013   0.987   0.983   0.711   0.717   0.758
2     V         0.699   0.702   0.732   0.554   0.559   0.642   0.711   0.717   0.758
3     L         0.699   0.702   0.732   0.473   0.502   0.582   0.711   0.717   0.758
4     V        -1.522  -1.565  -1.577  -1.618  -1.747  -1.765  -1.484  -1.583  -1.522
5     Q        -1.522  -1.729  -1.577  -1.383  -1.790  -1.628  -1.484  -1.748  -1.522
6     D         0.699   0.702   0.732   0.975   0.965   0.955   0.711   0.717   0.758
7     L         0.699   0.702   0.732   0.473   0.502   0.582   0.711   0.717   0.758
8     L         0.699   0.702   0.732   0.473   0.502   0.582   0.711   0.717   0.758
9     H        -1.099  -1.025  -0.734  -1.026  -0.952  -0.548  -1.484  -1.390  -0.964
10    P         0.699   0.702   0.732   0.792   0.789   0.819   0.711   0.717   0.758
11    T        -0.967  -0.735  -0.699  -1.432  -1.006  -1.006  -1.265  -0.918  -0.907
12    A        -1.753  -1.707  -1.566  -1.712  -1.598  -1.410  -1.814  -1.708  -1.509
13    A        -1.090  -1.211  -1.552  -0.743  -0.907  -1.381  -0.936  -1.099  -1.493
14    S        -0.687  -0.686  -0.714  -0.911  -0.919  -1.038  -0.826  -0.842  -0.931
15    E         0.699   0.702   0.732   0.956   0.945   0.941   0.711   0.717   0.758
16    A        -1.090  -1.397  -1.559  -0.733  -1.132  -1.364  -0.936  -1.314  -1.501
17    R        -1.522  -1.373  -1.568  -1.289  -1.148  -1.485  -1.484  -1.340  -1.512
18    K        -1.090  -1.091  -1.552  -0.937  -0.974  -1.607  -0.936  -0.961  -1.493
19    H         0.699   0.702   0.732   0.937   0.930   0.927   0.711   0.717   0.758
20    K         0.699   0.702   0.732   0.584   0.598   0.664   0.711   0.717   0.758
21    L         0.699   0.702   0.732   0.473   0.502   0.582   0.711   0.717   0.758
22    K         0.699   0.702   0.732   0.584   0.598   0.664   0.711   0.717   0.758
23    T        -0.214  -0.409  -0.686  -0.337  -0.538  -0.906  -0.167  -0.436  -0.886
24    L         0.699   0.702   0.732   0.473   0.502   0.582   0.711   0.717   0.758
25    V         0.699   0.702   0.732   0.554   0.559   0.642   0.711   0.717   0.758
26    Q        -0.687  -0.674  -0.710  -0.562  -0.573  -0.700  -0.826  -0.824  -0.924
27    G        -3.286  -3.137  -2.662  -3.037  -2.877  -2.245  -2.692  -2.547  -1.991
28    P         0.699   0.702   0.732   0.792   0.789   0.819   0.711   0.717   0.758
29    R         0.699   0.702   0.732   0.831   0.823   0.848   0.711   0.717   0.758
30    S         0.699   0.702   0.732   0.574   0.592   0.657   0.711   0.717   0.758
31    Y        -1.753  -1.531  -1.572  -1.445  -1.220  -1.213  -1.814  -1.577  -1.517
32    F         0.699   0.702   0.732   0.850   0.838   0.863   0.711   0.717   0.758
33    L        -0.967  -0.735  -0.699  -0.992  -0.608  -0.693  -1.265  -0.918  -0.907
34    D         0.699   0.702   0.732   0.975   0.965   0.955   0.711   0.717   0.758
35    V         0.699   0.702   0.732   0.554   0.559   0.642   0.711   0.717   0.758
36    K         0.699   0.702   0.732   0.584   0.598   0.664   0.711   0.717   0.758
37    C         0.699   0.702   0.732   0.684   0.684   0.739   0.711   0.717   0.758
38    P        -0.967  -0.883  -0.724  -1.041  -0.940  -0.729  -1.265  -1.153  -0.947
39    G         0.699   0.702   0.732   0.782   0.774   0.812   0.711   0.717   0.758
40    C         0.699   0.702   0.732   0.684   0.684   0.739   0.711   0.717   0.758
41    L        -1.522  -1.565  -1.577  -1.547  -1.652  -1.490  -1.484  -1.583  -1.522
42    N        -0.214  -0.275  -0.680   0.253   0.144  -0.647  -0.167  -0.254  -0.877
43    I         0.699   0.702   0.732   1.051   1.032   1.011   0.711   0.717   0.758
44    T         0.699   0.702   0.732   0.411   0.464   0.536   0.711   0.717   0.758
45    T         0.699   0.702   0.732   0.411   0.464   0.536   0.711   0.717   0.758
46    V         0.699   0.702   0.732   0.554   0.559   0.642   0.711   0.717   0.758
47    F         0.699   0.702   0.732   0.850   0.838   0.863   0.711   0.717   0.758
48    S         0.699   0.702   0.732   0.574   0.592   0.657   0.711   0.717   0.758
49    H         0.699   0.702   0.732   0.937   0.930   0.927   0.711   0.717   0.758
50    A         0.699   0.702   0.732   0.724   0.737   0.768   0.711   0.717   0.758
51    Q         0.699   0.702   0.732   0.821   0.823   0.841   0.711   0.717   0.758
52    T         0.699   0.702   0.732   0.411   0.464   0.536   0.711   0.717   0.758
53    A        -0.967  -0.980  -0.733  -1.226  -1.312  -0.922  -1.265  -1.313  -0.962
54    V         0.699   0.702   0.732   0.554   0.559   0.642   0.711   0.717   0.758
55    T        -1.522  -1.729  -1.577  -1.618  -1.880  -1.617  -1.484  -1.748  -1.522
56    C         0.699   0.702   0.732   0.684   0.684   0.739   0.711   0.717   0.758
57    E        -2.731  -2.637  -2.196  -2.408  -2.345  -1.767  -2.472  -2.355  -1.822
58    S        -1.090  -1.278  -1.553  -0.883  -1.119  -1.443  -0.936  -1.171  -1.495
59    C         0.699   0.702   0.732   0.684   0.684   0.739   0.711   0.717   0.758
60    S        -1.090  -1.321  -1.559  -0.985  -1.302  -1.730  -0.936  -1.224  -1.501
61    T        -0.214  -0.409  -0.686  -0.370  -0.585  -1.015  -0.167  -0.436  -0.886
62    I        -0.214  -0.073  -0.674  -0.164  -0.022  -0.702  -0.167   0.002  -0.868
63    L         0.699   0.702   0.732   0.473   0.502   0.582   0.711   0.717   0.758
64    C         0.699   0.702   0.732   0.684   0.684   0.739   0.711   0.717   0.758
65    T        -1.753  -1.823  -1.582  -2.033  -2.074  -1.660  -1.814  -1.882  -1.528
66    P         0.699   0.702   0.732   0.792   0.789   0.819   0.711   0.717   0.758
67    T        -0.214  -0.037  -0.674  -0.370  -0.124  -0.996  -0.167   0.045  -0.868
68    G         0.699   0.702   0.732   0.782   0.774   0.812   0.711   0.717   0.758
69    G         0.699   0.702   0.732   0.782   0.774   0.812   0.711   0.717   0.758
70    K         0.699   0.702   0.732   0.584   0.598   0.664   0.711   0.717   0.758
71    A         0.699   0.702   0.732   0.724   0.737   0.768   0.711   0.717   0.758
72    K        -0.967  -0.980  -0.733  -1.226  -1.278  -0.855  -1.265  -1.313  -0.962
73    L         0.699   0.702   0.732   0.473   0.502   0.582   0.711   0.717   0.758
74    S        -1.753  -1.707  -1.566  -2.117  -1.943  -1.647  -1.814  -1.708  -1.509
75    E         0.699   0.702   0.732   0.956   0.945   0.941   0.711   0.717   0.758
76    G         0.699   0.702   0.732   0.782   0.774   0.812   0.711   0.717   0.758
77    T        -0.967  -0.735  -0.699  -1.328  -0.915  -0.933  -1.265  -0.918  -0.907
78    S         0.699   0.702   0.732   0.574   0.592   0.657   0.711   0.717   0.758
79    F         0.699   0.702   0.732   0.850   0.838   0.863   0.711   0.717   0.758
80    R         0.699   0.702   0.732   0.831   0.823   0.848   0.711   0.717   0.758
81    R        -0.214  -0.361  -0.687   0.054  -0.159  -0.739  -0.167  -0.370  -0.888
82    K         0.699   0.702   0.732   0.584   0.598   0.664   0.711   0.717   0.758
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P35997
Output conservation file - output/P35997
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
