1     M         0.866   0.896   0.940   1.229   1.229   1.234   0.868   0.913   0.978
2     E         0.866   0.896   0.940   0.855   0.902   0.971   0.868   0.913   0.978
3     N         0.866   0.896   0.940   0.820   0.890   0.947   0.868   0.913   0.978
4     D        -0.237  -0.501  -0.583  -0.226  -0.569  -0.707  -0.206  -0.573  -0.730
5     K        -2.276  -2.490  -2.198  -1.924  -2.390  -2.016  -1.894  -2.090  -1.695
6     G         0.866   0.896   0.940   0.750   0.791   0.897   0.868   0.913   0.978
7     Q        -1.287  -1.354  -1.515  -0.911  -1.081  -1.384  -1.127  -1.213  -1.361
8     L        -0.237  -0.450  -0.583  -0.201  -0.468  -0.714  -0.206  -0.500  -0.730
9     V         0.866   0.896   0.940   0.785   0.838   0.922   0.868   0.913   0.978
10    E        -0.780  -0.923  -0.634  -0.894  -1.233  -0.787  -0.973  -1.221  -0.809
11    L         0.866   0.896   0.940   0.750   0.829   0.897   0.868   0.913   0.978
12    Y         0.866   0.896   0.940   0.993   1.050   1.068   0.868   0.913   0.978
13    V        -0.237   0.062  -0.558  -0.166   0.187  -0.648  -0.206   0.166  -0.691
14    P         0.866   0.896   0.940   1.184   1.191   1.203   0.868   0.913   0.978
15    R         0.866   0.896   0.940   0.703   0.767   0.864   0.868   0.913   0.978
16    K         0.866   0.896   0.940   0.901   0.952   1.004   0.868   0.913   0.978
17    C         0.866   0.896   0.940   1.206   1.195   1.219   0.868   0.913   0.978
18    S         0.866   0.896   0.940   0.715   0.793   0.872   0.868   0.913   0.978
19    A         0.866   0.896   0.940   0.643   0.725   0.822   0.868   0.913   0.978
20    T         0.866   0.896   0.940   1.106   1.104   1.148   0.868   0.913   0.978
21    N        -0.237  -0.450  -0.583  -0.136  -0.415  -0.685  -0.206  -0.500  -0.730
22    R         0.866   0.896   0.940   0.703   0.767   0.864   0.868   0.913   0.978
23    I         0.866   0.896   0.940   0.785   0.824   0.922   0.868   0.913   0.978
24    I        -0.237  -0.029  -0.560  -0.101   0.123  -0.485  -0.206   0.057  -0.694
25    K        -0.237  -0.501  -0.583  -0.023  -0.379  -0.549  -0.206  -0.573  -0.730
26    A        -0.237  -0.450  -0.583  -0.318  -0.579  -0.808  -0.206  -0.500  -0.730
27    D        -1.071  -0.724  -0.608  -1.391  -0.803  -0.698  -1.434  -0.907  -0.767
28    D         0.866   0.896   0.940   0.715   0.781   0.872   0.868   0.913   0.978
29    H         0.866   0.896   0.940   1.251   1.253   1.250   0.868   0.913   0.978
30    A        -1.986  -1.887  -1.536  -2.413  -2.211  -1.665  -2.047  -1.841  -1.386
31    S         0.866   0.896   0.940   0.715   0.793   0.872   0.868   0.913   0.978
32    V        -0.237  -0.450  -0.583  -0.104  -0.364  -0.523  -0.206  -0.500  -0.730
33    Q         0.866   0.896   0.940   0.970   0.985   1.052   0.868   0.913   0.978
34    I         0.866   0.896   0.940   0.785   0.824   0.922   0.868   0.913   0.978
35    N        -1.287  -1.201  -1.509  -1.029  -0.940  -1.390  -1.127  -1.057  -1.355
36    V        -1.071  -0.921  -0.634  -1.458  -1.261  -0.785  -1.434  -1.218  -0.809
37    A        -0.237  -0.501  -0.583  -0.245  -0.542  -0.607  -0.206  -0.573  -0.730
38    K        -2.276  -2.056  -2.176  -1.901  -1.740  -1.936  -1.894  -1.680  -1.676
39    V         0.866   0.896   0.940   0.785   0.838   0.922   0.868   0.913   0.978
40    D         0.866   0.896   0.940   0.715   0.781   0.872   0.868   0.913   0.978
41    E        -0.237  -0.501  -0.583  -0.116  -0.497  -0.705  -0.206  -0.573  -0.730
42    E        -1.769  -1.494  -1.530  -1.767  -1.479  -1.512  -1.741  -1.465  -1.380
43    G         0.866   0.896   0.940   0.750   0.791   0.897   0.868   0.913   0.978
44    R         0.866   0.896   0.940   0.703   0.767   0.864   0.868   0.913   0.978
45    A        -0.237  -0.501  -0.583  -0.280  -0.601  -0.704  -0.206  -0.573  -0.730
46    I         0.866   0.896   0.940   0.785   0.824   0.922   0.868   0.913   0.978
47    P        -1.769  -1.680  -1.529  -1.472  -1.369  -1.318  -1.741  -1.582  -1.378
48    G         0.866   0.896   0.940   0.750   0.791   0.897   0.868   0.913   0.978
49    E        -0.780  -0.546  -0.606  -0.894  -0.552  -0.722  -0.973  -0.638  -0.765
50    Y        -1.986  -1.840  -1.526  -2.058  -1.793  -1.386  -2.047  -1.775  -1.374
51    I        -1.769  -1.499  -1.529  -1.709  -1.443  -1.390  -1.741  -1.473  -1.379
52    T        -0.237  -0.450  -0.583   0.155  -0.196  -0.497  -0.206  -0.500  -0.730
53    Y         0.866   0.896   0.940   0.993   1.050   1.068   0.868   0.913   0.978
54    A         0.866   0.896   0.940   0.643   0.725   0.822   0.868   0.913   0.978
55    L        -0.237  -0.501  -0.583  -0.201  -0.544  -0.714  -0.206  -0.573  -0.730
56    S        -0.237  -0.029  -0.560  -0.174   0.088  -0.536  -0.206   0.057  -0.694
57    G         0.866   0.896   0.940   0.750   0.791   0.897   0.868   0.913   0.978
58    Y        -1.769  -1.612  -1.535  -1.431  -1.288  -1.187  -1.741  -1.624  -1.385
59    V        -0.780  -0.440  -0.586  -0.939  -0.444  -0.697  -0.973  -0.485  -0.733
60    R         0.866   0.896   0.940   0.703   0.767   0.864   0.868   0.913   0.978
61    S        -2.302  -1.925  -1.546  -2.855  -2.276  -1.678  -2.354  -1.891  -1.396
62    R        -1.287  -1.697  -1.535  -1.093  -1.634  -1.366  -1.127  -1.603  -1.384
63    G        -0.237  -0.086  -0.562  -0.221  -0.040  -0.730  -0.206  -0.013  -0.697
64    E         0.866   0.896   0.940   0.855   0.902   0.971   0.868   0.913   0.978
65    S        -1.163  -0.914  -0.626  -1.800  -1.343  -0.878  -1.587  -1.207  -0.797
66    D         0.866   0.896   0.940   0.715   0.781   0.872   0.868   0.913   0.978
67    D         0.866   0.896   0.940   0.715   0.781   0.872   0.868   0.913   0.978
68    S        -0.237  -0.501  -0.583  -0.174  -0.476  -0.565  -0.206  -0.573  -0.730
69    L        -0.237  -0.501  -0.583  -0.201  -0.544  -0.714  -0.206  -0.573  -0.730
70    N         0.866   0.896   0.940   0.820   0.890   0.947   0.868   0.913   0.978
71    R         0.866   0.896   0.940   0.703   0.767   0.864   0.868   0.913   0.978
72    L         0.866   0.896   0.940   0.750   0.829   0.897   0.868   0.913   0.978
73    A        -0.780  -0.812  -0.632  -0.970  -1.022  -0.697  -0.973  -1.044  -0.805
74    Q        -0.237  -0.501  -0.583   0.065  -0.314  -0.454  -0.206  -0.573  -0.730
75    N        -1.769  -1.569  -1.516  -1.659  -1.405  -1.428  -1.741  -1.452  -1.362
76    D         0.866   0.896   0.940   0.715   0.781   0.872   0.868   0.913   0.978
77    G         0.866   0.896   0.940   0.750   0.791   0.897   0.868   0.913   0.978
78    L        -0.237  -0.086  -0.562  -0.201   0.011  -0.677  -0.206  -0.013  -0.697
79    L         0.866   0.896   0.940   0.750   0.829   0.897   0.868   0.913   0.978
80    K        -0.237  -0.501  -0.583  -0.040  -0.401  -0.594  -0.206  -0.573  -0.730
81    N        -1.287  -1.697  -1.535  -1.101  -1.742  -1.596  -1.127  -1.603  -1.384
82    V         0.866   0.896   0.940   0.785   0.838   0.922   0.868   0.913   0.978
83    W         0.866   0.896   0.940   1.251   1.253   1.250   0.868   0.913   0.978
84    S        -0.237  -0.450  -0.583  -0.231  -0.486  -0.721  -0.206  -0.500  -0.730
85    Y        -0.237  -0.450  -0.583   0.099  -0.159  -0.411  -0.206  -0.500  -0.730
86    S        -0.780  -0.923  -0.634  -0.947  -1.201  -0.722  -0.973  -1.221  -0.809
87    R         0.866   0.896   0.940   0.703   0.767   0.864   0.868   0.913   0.978
* 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/Q3E754
Output conservation file - output/Q3E754
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
