1     M         0.952   0.962   1.013   1.260   1.269   1.322   0.985   0.999   1.075
2     I         0.952   0.962   1.013   0.936   0.934   1.036   0.985   0.999   1.075
3     E         0.952   0.962   1.013   1.042   1.058   1.130   0.985   0.999   1.075
4     V        -0.324  -0.337  -0.307  -0.573  -0.604  -0.580  -0.528  -0.552  -0.536
5     V        -1.508  -1.506  -1.621  -1.547  -1.545  -1.682  -1.284  -1.279  -1.353
6     V        -1.349  -1.356  -1.120  -1.342  -1.331  -0.971  -1.435  -1.440  -1.131
7     N         0.952   0.962   1.013   1.181   1.201   1.252   0.985   0.999   1.075
8     D         0.952   0.962   1.013   0.864   0.859   0.972   0.985   0.999   1.075
9     R         0.952   0.962   1.013   1.249   1.257   1.312   0.985   0.999   1.075
10    L         0.078   0.093  -0.233  -0.100  -0.070  -0.587   0.077   0.098  -0.412
11    G         0.952   0.962   1.013   0.972   0.996   1.067   0.985   0.999   1.075
12    K         0.952   0.962   1.013   0.680   0.674   0.810   0.985   0.999   1.075
13    K         0.952   0.962   1.013   0.680   0.674   0.810   0.985   0.999   1.075
14    V        -0.504  -0.476  -0.330  -0.908  -0.873  -0.620  -0.830  -0.787  -0.575
15    R        -1.086  -0.982  -1.074  -0.975  -0.881  -1.022  -1.133  -1.022  -1.078
16    V         0.078   0.032  -0.239   0.004  -0.048  -0.548   0.077   0.013  -0.421
17    K         0.952   0.962   1.013   0.680   0.674   0.810   0.985   0.999   1.075
18    C         0.952   0.962   1.013   1.294   1.309   1.352   0.985   0.999   1.075
19    L        -0.324  -0.375  -0.320  -0.559  -0.637  -0.497  -0.528  -0.615  -0.557
20    A        -1.771  -1.645  -1.645  -1.364  -1.213  -1.233  -1.587  -1.463  -1.378
21    E        -1.349  -1.349  -1.115  -1.506  -1.561  -1.187  -1.435  -1.432  -1.126
22    D         0.952   0.962   1.013   0.864   0.859   0.972   0.985   0.999   1.075
23    S         0.078   0.123  -0.236   0.338   0.391  -0.146   0.077   0.140  -0.417
24    V        -0.504  -0.489  -0.332  -0.908  -0.899  -0.622  -0.830  -0.809  -0.577
25    G         0.952   0.962   1.013   0.972   0.996   1.067   0.985   0.999   1.075
26    D         0.952   0.962   1.013   0.864   0.859   0.972   0.985   0.999   1.075
27    F        -0.746  -0.748  -1.048  -0.376  -0.392  -1.050  -0.679  -0.681  -1.045
28    K         0.952   0.962   1.013   0.680   0.674   0.810   0.985   0.999   1.075
29    K         0.952   0.962   1.013   0.680   0.674   0.810   0.985   0.999   1.075
30    V        -1.349  -1.356  -1.120  -1.837  -1.889  -1.490  -1.435  -1.440  -1.131
31    L        -0.746  -0.841  -1.046  -0.891  -1.049  -1.380  -0.679  -0.803  -1.042
32    S        -1.086  -1.165  -1.092  -0.843  -0.949  -0.910  -1.133  -1.232  -1.100
33    L        -1.349  -1.306  -1.108  -1.671  -1.578  -1.268  -1.435  -1.385  -1.117
34    Q         0.952   0.962   1.013   1.204   1.225   1.272   0.985   0.999   1.075
35    I        -1.086  -1.110  -1.073  -1.271  -1.288  -1.253  -1.133  -1.136  -1.076
36    G         0.952   0.962   1.013   0.972   0.996   1.067   0.985   0.999   1.075
37    T         0.078   0.173  -0.229   0.355   0.458  -0.092   0.077   0.207  -0.406
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    Q        -2.353  -2.392  -2.100  -1.898  -1.985  -1.593  -1.889  -1.903  -1.565
40    P        -1.508  -1.410  -1.623  -0.894  -0.755  -1.151  -1.284  -1.179  -1.355
41    N        -1.771  -1.772  -1.658  -1.513  -1.501  -1.338  -1.587  -1.569  -1.389
42    K         0.078  -0.074  -0.250  -0.064  -0.284  -0.456   0.077  -0.141  -0.440
43    I         0.952   0.962   1.013   0.936   0.934   1.036   0.985   0.999   1.075
44    V         0.078   0.032  -0.239   0.041  -0.012  -0.453   0.077   0.013  -0.421
45    L         0.952   0.962   1.013   0.717   0.745   0.843   0.985   0.999   1.075
46    Q        -0.504  -0.436  -0.317  -0.865  -0.809  -0.555  -0.830  -0.719  -0.552
47    K         0.952   0.962   1.013   0.680   0.674   0.810   0.985   0.999   1.075
48    G         0.078  -0.074  -0.250   0.249   0.068  -0.169   0.077  -0.141  -0.440
49    G        -1.189  -1.255  -1.101  -1.197  -1.160  -1.015  -1.284  -1.334  -1.110
50    S        -0.504  -0.489  -0.332  -0.481  -0.434  -0.245  -0.830  -0.809  -0.577
51    V         0.078   0.093  -0.233   0.069   0.100  -0.372   0.077   0.098  -0.412
52    L        -1.349  -1.356  -1.120  -1.539  -1.446  -1.138  -1.435  -1.440  -1.131
53    K         0.952   0.962   1.013   0.680   0.674   0.810   0.985   0.999   1.075
54    D         0.952   0.962   1.013   0.864   0.859   0.972   0.985   0.999   1.075
55    H         0.078  -0.074  -0.250   0.477   0.272  -0.052   0.077  -0.141  -0.440
56    I         0.952   0.962   1.013   0.936   0.934   1.036   0.985   0.999   1.075
57    S         0.078   0.123  -0.236   0.338   0.391  -0.146   0.077   0.140  -0.417
58    L         0.952   0.962   1.013   0.717   0.745   0.843   0.985   0.999   1.075
59    E        -1.771  -1.755  -1.658  -1.732  -1.697  -1.509  -1.587  -1.559  -1.389
60    D         0.952   0.962   1.013   0.864   0.859   0.972   0.985   0.999   1.075
61    Y         0.952   0.962   1.013   1.100   1.256   1.181   0.985   0.999   1.075
62    E         0.952   0.962   1.013   1.042   1.058   1.130   0.985   0.999   1.075
63    V        -0.504  -0.506  -0.334  -0.908  -0.930  -0.623  -0.830  -0.839  -0.581
64    H         0.952   0.962   1.013   1.238   1.255   1.302   0.985   0.999   1.075
65    D        -0.324  -0.287  -0.301  -0.453  -0.428  -0.418  -0.528  -0.472  -0.525
66    Q        -0.746  -0.625  -1.031  -0.512  -0.361  -0.909  -0.679  -0.530  -1.024
67    T        -1.771  -1.840  -1.669  -1.411  -1.509  -1.269  -1.587  -1.642  -1.399
68    N         0.078  -0.074  -0.250   0.417   0.224  -0.106   0.077  -0.141  -0.440
69    L        -0.324  -0.320  -0.300  -0.554  -0.550  -0.475  -0.528  -0.524  -0.523
70    E         0.952   0.962   1.013   1.042   1.058   1.130   0.985   0.999   1.075
71    L         0.078  -0.074  -0.250  -0.025  -0.211  -0.421   0.077  -0.141  -0.440
72    Y         0.952   0.962   1.013   1.082   1.099   1.165   0.985   0.999   1.075
73    Y         0.952   0.962   1.013   1.082   1.099   1.165   0.985   0.999   1.075
74    L        -1.697  -1.604  -1.633  -1.625  -1.463  -1.689  -1.486  -1.388  -1.365
* 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/Q6Q546
Output conservation file - output/Q6Q546
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
