1     M         0.751   0.753   0.761   0.814   0.818   0.826   0.770   0.772   0.780
2     S         0.751   0.753   0.761   0.631   0.636   0.652   0.770   0.772   0.780
3     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     F        -2.055  -2.034  -1.962  -1.750  -1.742  -1.605  -1.849  -1.819  -1.711
5     Y         0.751   0.753   0.761   1.035   1.041   1.035   0.770   0.772   0.780
6     T        -0.875  -0.828  -0.933  -0.896  -0.793  -1.015  -0.976  -0.905  -1.052
7     V         0.751   0.753   0.761   0.578   0.560   0.603   0.770   0.772   0.780
8     V        -0.875  -0.828  -0.929  -1.069  -1.018  -1.131  -0.976  -0.905  -1.046
9     G        -2.055  -2.034  -1.962  -1.948  -1.889  -1.793  -1.849  -1.819  -1.711
10    V        -0.875  -0.828  -0.929  -1.188  -1.130  -1.283  -0.976  -0.905  -1.046
11    F         0.751   0.753   0.761   0.856   0.843   0.866   0.770   0.772   0.780
12    I         0.751   0.753   0.761   0.796   0.796   0.809   0.770   0.772   0.780
13    V        -0.875  -0.828  -0.929  -1.069  -1.018  -1.131  -0.976  -0.905  -1.046
14    V        -0.875  -0.828  -0.929  -1.054  -1.005  -1.113  -0.976  -0.905  -1.046
15    S        -2.055  -2.034  -1.962  -2.385  -2.313  -2.207  -1.849  -1.819  -1.711
16    A         0.751   0.753   0.761   0.547   0.542   0.573   0.770   0.772   0.780
17    M        -0.875  -0.931  -0.944  -1.173  -1.232  -1.215  -0.976  -1.057  -1.069
18    S         0.751   0.753   0.761   0.673   0.738   0.692   0.770   0.772   0.780
19    V        -2.055  -2.034  -1.962  -1.929  -1.944  -1.775  -1.849  -1.819  -1.711
20    L         0.751   0.753   0.761   0.418   0.414   0.451   0.770   0.772   0.780
21    F        -0.875  -0.931  -0.944  -1.069  -1.170  -1.137  -0.976  -1.057  -1.069
22    W         0.751   0.753   0.761   0.976   0.974   0.979   0.770   0.772   0.780
23    I        -0.875  -0.828  -0.933  -0.967  -0.895  -1.095  -0.976  -0.905  -1.052
24    M        -0.875  -0.931  -0.944  -0.771  -0.856  -0.885  -0.976  -1.057  -1.069
25    A         0.751   0.753   0.761   0.547   0.542   0.573   0.770   0.772   0.780
26    P         0.751   0.753   0.761   0.826   0.825   0.838   0.770   0.772   0.780
27    K         0.751   0.753   0.761   1.064   1.068   1.063   0.770   0.772   0.780
28    N        -0.875  -0.931  -0.944  -0.570  -0.657  -0.672  -0.976  -1.057  -1.069
29    N         0.751   0.753   0.761   1.093   1.091   1.091   0.770   0.772   0.780
30    Q        -0.875  -0.931  -0.944  -0.703  -0.788  -0.781  -0.976  -1.057  -1.069
31    A        -0.875  -0.931  -0.944  -0.953  -1.077  -1.117  -0.976  -1.057  -1.069
32    V         0.751   0.753   0.761   0.578   0.560   0.603   0.770   0.772   0.780
33    W        -0.875  -0.828  -0.933  -0.676  -0.612  -0.792  -0.976  -0.905  -1.052
34    R         0.751   0.753   0.761   0.826   0.825   0.838   0.770   0.772   0.780
35    S         0.751   0.753   0.761   0.673   0.738   0.692   0.770   0.772   0.780
36    T        -0.875  -0.931  -0.944  -0.967  -1.006  -1.061  -0.976  -1.057  -1.069
37    V         0.751   0.753   0.761   0.578   0.560   0.603   0.770   0.772   0.780
38    I         0.751   0.753   0.761   0.796   0.796   0.809   0.770   0.772   0.780
39    L         0.751   0.753   0.761   0.418   0.414   0.451   0.770   0.772   0.780
40    T        -2.055  -2.034  -1.962  -1.929  -1.907  -1.775  -1.849  -1.819  -1.711
41    L         0.751   0.753   0.761   0.418   0.414   0.451   0.770   0.772   0.780
42    A        -0.875  -0.931  -0.944  -1.098  -1.157  -1.238  -0.976  -1.057  -1.069
43    M         0.751   0.753   0.761   0.886   0.934   0.895   0.770   0.772   0.780
44    M        -0.875  -0.931  -0.944  -0.557  -0.637  -0.709  -0.976  -1.057  -1.069
45    F        -0.875  -0.931  -0.944  -0.623  -0.731  -0.770  -0.976  -1.057  -1.069
46    L         0.751   0.753   0.761   0.418   0.414   0.451   0.770   0.772   0.780
47    M         0.751   0.753   0.761   0.886   0.934   0.895   0.770   0.772   0.780
48    W         0.751   0.753   0.761   0.976   0.974   0.979   0.770   0.772   0.780
49    A         0.751   0.753   0.761   0.547   0.542   0.573   0.770   0.772   0.780
50    I         0.751   0.753   0.761   0.796   0.796   0.809   0.770   0.772   0.780
51    T         0.751   0.753   0.761   0.826   0.825   0.838   0.770   0.772   0.780
52    F        -0.875  -0.828  -0.933  -0.703  -0.649  -0.780  -0.976  -0.905  -1.052
53    L         0.751   0.753   0.761   0.418   0.414   0.451   0.770   0.772   0.780
54    C        -2.055  -2.034  -1.962  -2.042  -1.942  -1.882  -1.849  -1.819  -1.711
55    Q         0.751   0.753   0.761   1.093   1.091   1.091   0.770   0.772   0.780
56    L         0.751   0.753   0.761   0.418   0.414   0.451   0.770   0.772   0.780
57    H         0.751   0.753   0.761   1.122   1.124   1.118   0.770   0.772   0.780
58    P         0.751   0.753   0.761   0.826   0.825   0.838   0.770   0.772   0.780
59    L         0.751   0.753   0.761   0.418   0.414   0.451   0.770   0.772   0.780
60    V        -0.875  -0.931  -0.944  -0.799  -0.929  -0.980  -0.976  -1.057  -1.069
61    A         0.751   0.753   0.761   0.547   0.542   0.573   0.770   0.772   0.780
62    P         0.751   0.753   0.761   0.826   0.825   0.838   0.770   0.772   0.780
63    R         0.751   0.753   0.761   0.826   0.825   0.838   0.770   0.772   0.780
64    R         0.751   0.753   0.761   0.826   0.825   0.838   0.770   0.772   0.780
65    S         0.751   0.753   0.761   0.673   0.738   0.692   0.770   0.772   0.780
66    D         0.751   0.753   0.761   1.093   1.096   1.091   0.770   0.772   0.780
67    L         0.751   0.753   0.761   0.418   0.414   0.451   0.770   0.772   0.780
68    R         0.751   0.753   0.761   0.826   0.825   0.838   0.770   0.772   0.780
69    P         0.751   0.753   0.761   0.826   0.825   0.838   0.770   0.772   0.780
70    E         0.751   0.753   0.761   0.976   0.979   0.979   0.770   0.772   0.780
71    F        -1.019  -1.012  -0.957  -1.079  -1.078  -0.969  -1.195  -1.179  -1.089
72    A        -1.019  -1.012  -0.957  -1.079  -1.078  -0.969  -1.195  -1.179  -1.089
73    E        -2.055  -2.034  -1.962  -1.562  -1.539  -1.427  -1.849  -1.819  -1.711
* 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/Q3E7B6
Output conservation file - output/Q3E7B6
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
