1     M         1.181   1.184   1.194   1.533   1.536   1.543   1.226   1.229   1.240
2     I        -0.542  -0.538  -0.510  -0.212  -0.206  -0.166  -0.691  -0.683  -0.637
3     A         1.181   1.184   1.194   0.527   0.532   0.558   1.226   1.229   1.240
4     Q        -0.542  -0.538  -0.510  -0.138  -0.132  -0.093  -0.691  -0.683  -0.637
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    S         1.181   1.184   1.194   0.851   0.855   0.875   1.226   1.229   1.240
11    T        -0.542  -0.538  -0.510  -0.364  -0.358  -0.315  -0.691  -0.683  -0.637
12    R        -0.542  -0.538  -0.510  -0.364  -0.358  -0.315  -0.691  -0.683  -0.637
13    L        -0.542  -0.538  -0.510  -0.312  -0.306  -0.265  -0.691  -0.683  -0.637
14    A        -0.542  -0.538  -0.510  -0.953  -0.946  -0.892  -0.691  -0.683  -0.637
15    A        -0.542  -0.538  -0.510  -1.015  -1.008  -0.953  -0.691  -0.683  -0.637
16    A         1.181   1.184   1.194   0.527   0.532   0.558   1.226   1.229   1.240
17    V        -0.542  -0.538  -0.510  -0.236  -0.231  -0.190  -0.691  -0.683  -0.637
18    S        -1.550  -1.539  -1.506  -1.258  -1.215  -1.191  -1.330  -1.313  -1.263
19    S        -0.401  -0.439  -0.459  -0.396  -0.425  -0.434  -0.478  -0.532  -0.561
20    S        -1.550  -1.539  -1.506  -1.365  -1.335  -1.296  -1.330  -1.313  -1.263
21    A        -0.401  -0.439  -0.459  -0.855  -0.896  -0.912  -0.478  -0.532  -0.561
22    A        -1.550  -1.539  -1.506  -1.694  -1.640  -1.617  -1.330  -1.313  -1.263
23    S        -1.550  -1.539  -1.506  -1.383  -1.353  -1.314  -1.330  -1.313  -1.263
24    A        -0.401  -0.439  -0.459  -0.647  -0.664  -0.661  -0.478  -0.532  -0.561
25    G        -1.550  -1.539  -1.506  -1.365  -1.374  -1.296  -1.330  -1.313  -1.263
26    V        -0.401  -0.439  -0.459  -0.290  -0.370  -0.457  -0.478  -0.532  -0.561
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    S        -0.401  -0.439  -0.459  -0.824  -0.881  -0.958  -0.478  -0.532  -0.561
31    R        -0.401  -0.408  -0.470  -0.238  -0.255  -0.365  -0.478  -0.487  -0.577
32    I        -0.401  -0.408  -0.470   0.036   0.025  -0.065  -0.478  -0.487  -0.577
33    A        -0.401  -0.439  -0.459  -0.794  -0.824  -0.838  -0.478  -0.532  -0.561
34    A        -1.550  -1.539  -1.506  -1.777  -1.737  -1.700  -1.330  -1.313  -1.263
35    S        -0.542  -0.538  -0.510  -0.717  -0.710  -0.661  -0.691  -0.683  -0.637
36    A        -0.542  -0.538  -0.510  -1.015  -1.008  -0.953  -0.691  -0.683  -0.637
37    M        -0.542  -0.538  -0.510  -0.717  -0.710  -0.661  -0.691  -0.683  -0.637
38    A        -0.401  -0.335  -0.449  -0.423  -0.292  -0.555  -0.478  -0.379  -0.545
39    S        -0.401  -0.408  -0.470  -0.590  -0.595  -0.684  -0.478  -0.487  -0.577
40    T        -1.550  -1.539  -1.506  -1.932  -1.918  -1.851  -1.330  -1.313  -1.263
41    I        -0.401  -0.408  -0.470  -0.061  -0.076  -0.187  -0.478  -0.487  -0.577
42    F         1.181   1.184   1.194   1.371   1.370   1.384   1.226   1.229   1.240
43    K        -0.542  -0.538  -0.510  -0.507  -0.500  -0.455  -0.691  -0.683  -0.637
44    R        -0.542  -0.538  -0.510  -0.507  -0.500  -0.455  -0.691  -0.683  -0.637
45    S        -0.401  -0.408  -0.470  -0.492  -0.492  -0.561  -0.478  -0.487  -0.577
46    P        -0.401  -0.408  -0.470  -0.316  -0.328  -0.512  -0.478  -0.487  -0.577
47    G         1.181   1.184   1.194   1.453   1.455   1.464   1.226   1.229   1.240
48    N         1.181   1.184   1.194   1.316   1.310   1.330   1.226   1.229   1.240
49    S         1.181   1.184   1.194   0.913   0.930   0.936   1.226   1.229   1.240
50    F         1.181   1.184   1.194   1.371   1.370   1.384   1.226   1.229   1.240
51    N        -1.550  -1.539  -1.506  -1.632  -1.656  -1.558  -1.330  -1.313  -1.263
52    S        -0.401  -0.439  -0.459  -0.590  -0.642  -0.669  -0.478  -0.532  -0.561
53    F         1.181   1.184   1.194   1.371   1.370   1.384   1.226   1.229   1.240
54    K         1.181   1.184   1.194   1.118   1.107   1.137   1.226   1.229   1.240
55    E         1.181   1.184   1.194   1.480   1.479   1.491   1.226   1.229   1.240
56    Y         1.181   1.184   1.194   1.453   1.452   1.464   1.226   1.229   1.240
57    R         1.181   1.184   1.194   1.288   1.293   1.303   1.226   1.229   1.240
58    E         1.181   1.184   1.194   1.480   1.479   1.491   1.226   1.229   1.240
59    N        -1.550  -1.539  -1.506  -1.122  -1.127  -1.057  -1.330  -1.313  -1.263
60    A         1.181   1.184   1.194   0.637   0.658   0.665   1.226   1.229   1.240
61    K        -0.401  -0.408  -0.470  -0.396  -0.429  -0.509  -0.478  -0.487  -0.577
62    T        -0.401  -0.408  -0.470  -0.396  -0.430  -0.509  -0.478  -0.487  -0.577
63    Y         1.181   1.184   1.194   1.453   1.452   1.464   1.226   1.229   1.240
64    G         1.181   1.184   1.194   1.453   1.455   1.464   1.226   1.229   1.240
65    P         1.181   1.184   1.194   1.426   1.427   1.438   1.226   1.229   1.240
66    L         1.181   1.184   1.194   1.232   1.231   1.248   1.226   1.229   1.240
67    S         1.181   1.184   1.194   0.913   0.930   0.936   1.226   1.229   1.240
68    A         1.181   1.184   1.194   0.637   0.658   0.665   1.226   1.229   1.240
69    S        -0.401  -0.408  -0.470  -0.590  -0.595  -0.684  -0.478  -0.487  -0.577
70    L         1.181   1.184   1.194   1.232   1.231   1.248   1.226   1.229   1.240
71    A         1.181   1.184   1.194   0.637   0.658   0.665   1.226   1.229   1.240
72    T        -0.401  -0.408  -0.470  -0.251  -0.274  -0.327  -0.478  -0.487  -0.577
73    R        -0.401  -0.335  -0.449  -0.316  -0.236  -0.379  -0.478  -0.379  -0.545
74    R         1.181   1.184   1.194   1.288   1.293   1.303   1.226   1.229   1.240
75    H        -1.550  -1.539  -1.506  -0.819  -0.823  -0.761  -1.330  -1.313  -1.263
76    L         1.181   1.184   1.194   1.232   1.231   1.248   1.226   1.229   1.240
77    A        -0.401  -0.439  -0.459  -0.855  -0.897  -0.912  -0.478  -0.532  -0.561
78    H        -1.550  -1.539  -1.506  -0.850  -0.853  -0.791  -1.330  -1.313  -1.263
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    A         1.181   1.184   1.194   0.527   0.532   0.558   1.226   1.229   1.240
83    P         1.181   1.184   1.194   1.372   1.375   1.385   1.226   1.229   1.240
84    K        -0.542  -0.538  -0.510  -0.262  -0.256  -0.215  -0.691  -0.683  -0.637
85    L        -0.401  -0.439  -0.459  -0.290  -0.364  -0.393  -0.478  -0.532  -0.561
* 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/Q3E7A3
Output conservation file - output/Q3E7A3
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
