1     M         1.309   1.322   1.350   1.515   1.528   1.578   1.367   1.383   1.421
2     F         1.309   1.322   1.350   1.425   1.431   1.492   1.367   1.383   1.421
3     G         0.003   0.032  -0.098   0.249   0.247   0.096  -0.079  -0.035  -0.241
4     L        -1.105  -1.144  -1.085  -1.066  -1.134  -0.998  -1.042  -1.077  -0.990
5     P         0.003   0.032  -0.098   0.239   0.248   0.067  -0.079  -0.035  -0.241
6     Q         0.003  -0.119  -0.136  -0.243  -0.419  -0.410  -0.079  -0.266  -0.302
7     Q        -1.105  -1.144  -1.085  -1.258  -1.289  -1.160  -1.042  -1.077  -0.990
8     E        -0.300  -0.263  -0.196  -0.770  -0.700  -0.594  -0.561  -0.499  -0.398
9     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    S         1.309   1.322   1.350   1.456   1.469   1.521   1.367   1.383   1.421
11    E         1.309   1.322   1.350   1.272   1.303   1.347   1.367   1.383   1.421
12    E         0.003  -0.119  -0.136   0.104  -0.058  -0.064  -0.079  -0.266  -0.302
13    E         0.003  -0.119  -0.136  -0.118  -0.338  -0.418  -0.079  -0.266  -0.302
14    K         1.309   1.322   1.350   1.146   1.241   1.228   1.367   1.383   1.421
15    R        -0.300  -0.245  -0.185  -0.420  -0.317  -0.265  -0.561  -0.469  -0.381
16    A         0.003   0.123  -0.079  -0.159   0.023  -0.306  -0.079   0.100  -0.211
17    H         0.003  -0.119  -0.136   0.153  -0.090  -0.180  -0.079  -0.266  -0.302
18    Q         0.003  -0.119  -0.136  -0.308  -0.479  -0.512  -0.079  -0.266  -0.302
19    E        -1.105  -1.094  -1.069  -1.493  -1.430  -1.422  -1.042  -1.023  -0.972
20    Q        -1.105  -1.144  -1.085  -1.133  -1.132  -1.012  -1.042  -1.077  -0.990
21    T        -1.105  -1.086  -1.075  -0.987  -1.023  -0.980  -1.042  -1.014  -0.978
22    E        -1.909  -1.825  -1.748  -1.858  -1.733  -1.621  -1.524  -1.424  -1.317
23    K        -1.105  -1.094  -1.069  -1.301  -1.196  -1.199  -1.042  -1.023  -0.972
24    T         1.309   1.322   1.350   1.456   1.465   1.521   1.367   1.383   1.421
25    L         1.309   1.322   1.350   1.178   1.197   1.258   1.367   1.383   1.421
26    K        -1.105  -0.993  -1.043  -1.147  -0.934  -1.037  -1.042  -0.897  -0.941
27    Q        -1.105  -1.094  -1.069  -0.948  -0.927  -0.957  -1.042  -1.023  -0.972
28    A         1.309   1.322   1.350   1.146   1.161   1.228   1.367   1.383   1.421
29    A        -1.105  -1.144  -1.085  -1.120  -1.191  -1.051  -1.042  -1.077  -0.990
30    Y        -1.105  -1.144  -1.085  -0.652  -0.757  -0.646  -1.042  -1.077  -0.990
31    V        -1.105  -1.086  -1.075  -1.013  -0.996  -0.992  -1.042  -1.014  -0.978
32    A         1.309   1.322   1.350   1.146   1.161   1.228   1.367   1.383   1.421
33    A         0.003  -0.119  -0.136  -0.087  -0.290  -0.277  -0.079  -0.266  -0.302
34    F        -1.105  -1.003  -1.051  -1.258  -1.123  -1.170  -1.042  -0.909  -0.951
35    L         1.309   1.322   1.350   1.178   1.197   1.258   1.367   1.383   1.421
36    W         1.309   1.322   1.350   1.456   1.477   1.521   1.367   1.383   1.421
37    V         0.003   0.137  -0.079   0.064   0.259  -0.099  -0.079   0.120  -0.211
38    S         0.003  -0.119  -0.136   0.114  -0.121  -0.178  -0.079  -0.266  -0.302
39    P         1.309   1.322   1.350   1.486   1.486   1.549   1.367   1.383   1.421
40    M        -1.105  -1.086  -1.075  -0.897  -0.882  -0.891  -1.042  -1.014  -0.978
41    I         0.003   0.032  -0.098   0.249   0.256   0.065  -0.079  -0.035  -0.241
42    W         0.003  -0.119  -0.136   0.201   0.002  -0.038  -0.079  -0.266  -0.302
43    H         0.003   0.032  -0.098   0.333   0.372   0.171  -0.079  -0.035  -0.241
44    L        -1.105  -1.094  -1.069  -0.935  -0.918  -0.900  -1.042  -1.023  -0.972
45    V        -0.300  -0.263  -0.196  -0.289  -0.255  -0.123  -0.561  -0.499  -0.398
46    K         1.309   1.322   1.350   1.146   1.241   1.228   1.367   1.383   1.421
47    K        -0.300  -0.245  -0.185  -0.420  -0.247  -0.199  -0.561  -0.469  -0.381
48    Q         1.309   1.322   1.350   0.985   1.023   1.075   1.367   1.383   1.421
49    W        -1.105  -1.086  -1.075  -0.987  -1.008  -0.980  -1.042  -1.014  -0.978
50    K         1.309   1.322   1.350   1.170   1.198   1.250   1.367   1.383   1.421
* 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/P80967
Output conservation file - output/P80967
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
