1     M         1.487   1.506   1.600   1.733   1.730   1.884   1.615   1.641   1.786
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     A        -1.020  -0.986  -0.866  -1.296  -1.167  -1.017  -1.108  -1.031  -0.857
5     N        -0.771  -0.690  -0.812  -0.563  -0.474  -0.652  -0.768  -0.665  -0.788
6     K        -1.020  -0.983  -0.861  -1.155  -1.059  -0.867  -1.108  -1.027  -0.851
7     V        -0.112  -0.062   0.026  -0.398  -0.309  -0.176  -0.427  -0.347  -0.220
8     I         1.487   1.506   1.600   1.392   1.433   1.566   1.615   1.641   1.786
9     Q        -1.679  -1.614  -1.545  -1.247  -1.231  -1.097  -1.448  -1.355  -1.224
10    L         0.298   0.173   0.131   0.131  -0.019  -0.091   0.254   0.051  -0.037
11    Q         1.487   1.506   1.600   1.629   1.632   1.787   1.615   1.641   1.786
12    K         1.487   1.506   1.600   1.348   1.379   1.525   1.615   1.641   1.786
13    I        -0.771  -0.677  -0.802  -0.905  -0.722  -0.914  -0.768  -0.650  -0.775
14    F         0.298   0.206   0.138   0.386   0.222   0.114   0.254   0.103  -0.026
15    Q         1.487   1.506   1.600   1.629   1.632   1.787   1.615   1.641   1.786
16    S        -0.771  -0.690  -0.812  -0.589  -0.512  -0.632  -0.768  -0.665  -0.788
17    S         0.298   0.173   0.131   0.396   0.200   0.141   0.254   0.051  -0.037
18    T        -1.679  -1.621  -1.546  -1.434  -1.405  -1.285  -1.448  -1.361  -1.225
19    K         0.298   0.173   0.131   0.241   0.066   0.003   0.254   0.051  -0.037
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    P        -0.771  -0.915  -0.872  -0.869  -1.102  -1.105  -0.768  -0.940  -0.862
22    L         0.298   0.474   0.196   0.075   0.358  -0.082   0.254   0.517   0.072
23    W         1.487   1.506   1.600   1.692   1.698   1.846   1.615   1.641   1.786
24    W        -1.679  -1.621  -1.546  -1.633  -1.640  -1.516  -1.448  -1.361  -1.225
25    R         1.487   1.506   1.600   1.565   1.572   1.727   1.615   1.641   1.786
26    H         0.298   0.206   0.138   0.658   0.501   0.391   0.254   0.103  -0.026
27    P         0.298   0.206   0.138   0.263   0.139  -0.028   0.254   0.103  -0.026
28    R         0.298   0.206   0.138   0.490   0.347   0.262   0.254   0.103  -0.026
29    S         1.487   1.506   1.600   1.501   1.513   1.667   1.615   1.641   1.786
30    A        -0.112  -0.088   0.029  -0.558  -0.493  -0.331  -0.427  -0.394  -0.215
31    L         0.298   0.508   0.193   0.322   0.608   0.107   0.254   0.566   0.067
32    Y        -0.771  -0.915  -0.872  -0.778  -1.046  -1.011  -0.768  -0.940  -0.862
33    L         0.298   0.206   0.138   0.109  -0.000  -0.121   0.254   0.103  -0.026
34    Y         0.298   0.206   0.138   0.370   0.224   0.105   0.254   0.103  -0.026
35    P         1.487   1.506   1.600   1.436   1.485   1.607   1.615   1.641   1.786
36    F         0.298   0.474   0.196   0.386   0.606   0.214   0.254   0.517   0.072
37    Y         0.298   0.492   0.189   0.412   0.665   0.260   0.254   0.542   0.061
38    A        -0.112   0.053   0.088  -0.354  -0.074  -0.039  -0.427  -0.149  -0.112
39    I        -0.771  -0.702  -0.813  -0.862  -0.704  -0.869  -0.768  -0.685  -0.789
40    F         0.298   0.474   0.196   0.322   0.561   0.113   0.254   0.517   0.072
41    A        -0.112  -0.055   0.027  -0.342  -0.224  -0.098  -0.427  -0.335  -0.219
42    V         1.487   1.506   1.600   1.522   1.529   1.687   1.615   1.641   1.786
43    A        -0.112  -0.088   0.029  -0.467  -0.389  -0.215  -0.427  -0.394  -0.215
44    V        -1.679  -1.621  -1.546  -1.528  -1.410  -1.327  -1.448  -1.361  -1.225
45    V        -0.771  -0.915  -0.872  -0.656  -0.898  -0.832  -0.768  -0.940  -0.862
46    T        -1.679  -1.614  -1.545  -1.660  -1.569  -1.410  -1.448  -1.355  -1.224
47    P         0.298   0.173   0.131   0.301   0.131   0.029   0.254   0.051  -0.037
48    L         0.298   0.173   0.131   0.109  -0.050  -0.132   0.254   0.051  -0.037
49    L        -0.771  -0.915  -0.872  -0.890  -1.053  -0.975  -0.768  -0.940  -0.862
50    Y         1.487   1.506   1.600   1.501   1.524   1.667   1.615   1.641   1.786
51    I        -0.771  -0.915  -0.872  -0.792  -0.989  -0.944  -0.768  -0.940  -0.862
52    P        -0.112  -0.088   0.029  -0.262  -0.189  -0.005  -0.427  -0.394  -0.215
53    N        -0.112  -0.088   0.029  -0.189  -0.189   0.008  -0.427  -0.394  -0.215
54    A         0.298   0.173   0.131   0.247   0.112   0.034   0.254   0.051  -0.037
55    I         0.298   0.474   0.196   0.263   0.519   0.109   0.254   0.517   0.072
56    R        -1.679  -1.621  -1.546  -1.651  -1.648  -1.489  -1.448  -1.361  -1.225
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    G         0.298   0.173   0.131   0.552   0.328   0.245   0.254   0.051  -0.037
60    I         1.487   1.506   1.600   1.392   1.433   1.566   1.615   1.641   1.786
61    K         0.298   0.173   0.131   0.301   0.141   0.111   0.254   0.051  -0.037
62    A         0.151  -0.005   0.053   0.018  -0.170  -0.090   0.020  -0.248  -0.173
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    K        -0.771  -0.915  -0.872  -0.676  -0.846  -0.729  -0.768  -0.940  -0.862
65    K        -1.679  -1.628  -1.542  -1.545  -1.439  -1.285  -1.448  -1.367  -1.221
66    A        -1.679  -1.614  -1.545  -1.393  -1.269  -1.197  -1.448  -1.355  -1.224
* 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/P10174
Output conservation file - output/P10174
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
