1     M         1.153   1.176   1.251   1.516   1.535   1.639   1.213   1.245   1.348
2     A        -0.915  -0.989  -1.106  -0.724  -0.814  -0.758  -0.846  -0.935  -1.034
3     R         1.153   1.176   1.251   1.048   1.078   1.219   1.213   1.245   1.348
4     G         1.153   1.176   1.251   1.441   1.454   1.571   1.213   1.245   1.348
5     N         1.153   1.176   1.251   1.486   1.515   1.612   1.213   1.245   1.348
6     Q         1.153   1.176   1.251   1.161   1.207   1.320   1.213   1.245   1.348
7     R         1.153   1.176   1.251   1.048   1.078   1.219   1.213   1.245   1.348
8     D        -0.499  -0.422  -0.252  -0.393  -0.269  -0.055  -0.846  -0.720  -0.459
9     L         0.079  -0.056  -0.203   0.631   0.503   0.297   0.069  -0.130  -0.378
10    A         0.079  -0.056  -0.203  -0.036  -0.203  -0.322   0.069  -0.130  -0.378
11    R         1.153   1.176   1.251   1.048   1.078   1.219   1.213   1.245   1.348
12    Q        -1.258  -1.220  -1.114  -1.275  -1.314  -1.093  -1.304  -1.254  -1.045
13    K         0.079  -0.056  -0.203  -0.385  -0.547  -0.740   0.069  -0.130  -0.378
14    N         1.153   1.176   1.251   1.486   1.515   1.612   1.213   1.245   1.348
15    L         0.079  -0.056  -0.169   0.590   0.446   0.247   0.069  -0.131  -0.322
16    K         1.153   1.176   1.251   0.553   0.617   0.775   1.213   1.245   1.348
17    K         1.153   1.176   1.251   0.553   0.617   0.775   1.213   1.245   1.348
18    Q         0.079  -0.056  -0.203   0.340   0.192   0.021   0.069  -0.130  -0.378
19    K         0.079   0.243  -0.160   0.141   0.377  -0.374   0.069   0.298  -0.308
20    D        -0.499  -0.416  -0.255  -0.430  -0.304  -0.096  -0.846  -0.709  -0.465
21    M        -1.325  -1.091  -1.124  -1.101  -0.871  -0.769  -1.361  -1.057  -1.055
22    A         0.079   0.230  -0.164  -0.029   0.136  -0.263   0.069   0.282  -0.314
23    K        -1.809  -1.932  -1.754  -1.855  -1.965  -1.559  -1.532  -1.640  -1.366
24    N        -2.017  -1.906  -1.747  -1.617  -1.596  -1.210  -1.761  -1.632  -1.360
25    Q        -0.915  -0.989  -1.106  -0.684  -0.847  -1.095  -0.846  -0.935  -1.034
26    K         1.153   1.176   1.251   0.553   0.617   0.775   1.213   1.245   1.348
27    K         0.079  -0.056  -0.203  -0.359  -0.505  -0.673   0.069  -0.130  -0.378
28    S        -2.683  -2.561  -2.253  -2.179  -2.094  -1.674  -2.081  -1.947  -1.559
29    G         1.153   1.176   1.251   1.441   1.454   1.571   1.213   1.245   1.348
30    D         1.153   1.176   1.251   1.410   1.419   1.544   1.213   1.245   1.348
31    P         0.079   0.294  -0.152   0.695   0.956   0.184   0.069   0.367  -0.295
32    K        -0.364  -0.381  -0.257  -0.686  -0.654  -0.329  -0.617  -0.650  -0.468
33    K         1.153   1.176   1.251   0.553   0.617   0.775   1.213   1.245   1.348
34    R         1.153   1.176   1.251   1.048   1.078   1.219   1.213   1.245   1.348
35    M        -0.915  -0.989  -1.106  -0.215  -0.332  -0.605  -0.846  -0.935  -1.034
36    E         1.153   1.176   1.251   1.224   1.291   1.377   1.213   1.245   1.348
37    S         0.079  -0.056  -0.203   0.593   0.357  -0.025   0.069  -0.130  -0.378
38    D         0.079  -0.056  -0.203   0.506   0.296   0.015   0.069  -0.130  -0.378
39    A         1.153   1.176   1.251   0.815   0.850   1.010   1.213   1.245   1.348
40    E         0.079  -0.056  -0.169   0.371   0.228   0.042   0.069  -0.131  -0.322
41    I         0.079  -0.056  -0.169   0.652   0.422   0.042   0.069  -0.131  -0.322
42    L        -0.499  -0.402  -0.237  -0.176  -0.025   0.163  -0.846  -0.685  -0.435
43    R         1.153   1.176   1.251   1.048   1.078   1.219   1.213   1.245   1.348
44    Q        -0.915  -1.142  -1.098  -0.737  -1.132  -1.186  -0.846  -1.120  -1.025
45    K         1.153   1.176   1.251   0.553   0.617   0.775   1.213   1.245   1.348
46    Q         1.153   1.176   1.251   1.161   1.207   1.320   1.213   1.245   1.348
47    A        -0.915  -0.914  -1.093  -1.004  -1.041  -1.271  -0.846  -0.848  -1.020
48    A        -0.915  -0.989  -1.076  -1.117  -1.217  -1.467  -0.846  -0.935  -0.999
49    A         0.079  -0.056  -0.169  -0.029  -0.193  -0.269   0.069  -0.131  -0.322
50    D        -1.112  -1.021  -1.090  -0.610  -0.537  -0.729  -1.093  -0.972  -1.015
51    A        -0.451  -0.322  -0.219  -0.722  -0.467  -0.380  -0.764  -0.553  -0.404
52    R        -0.040  -0.052  -0.193  -0.136  -0.165  -0.541  -0.105  -0.124  -0.361
53    R        -0.040   0.087  -0.178  -0.548  -0.359  -0.701  -0.105   0.081  -0.336
54    E        -0.451  -0.448  -0.256  -0.722  -0.794  -0.511  -0.764  -0.764  -0.466
55    A        -0.040   0.095  -0.180  -0.416  -0.225  -0.754  -0.105   0.093  -0.341
56    E         1.153   1.176   1.251   1.184   1.239   1.341   1.213   1.245   1.348
57    K        -1.362  -1.218  -1.122  -1.905  -1.708  -1.647  -1.423  -1.237  -1.054
58    L        -0.188  -0.386  -0.242   0.211  -0.064   0.092  -0.331  -0.659  -0.443
59    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    K        -1.325  -1.312  -1.135  -1.785  -1.612  -1.406  -1.361  -1.343  -1.068
63    A        -0.040  -0.195  -0.214  -0.174  -0.383  -0.318  -0.105  -0.346  -0.396
64    E        -2.023  -1.983  -1.760  -1.609  -1.580  -1.300  -1.752  -1.693  -1.371
65    K        -0.040  -0.052  -0.193  -0.624  -0.635  -0.878  -0.105  -0.124  -0.361
66    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    R        -0.499  -0.441  -0.253  -1.174  -1.108  -0.787  -0.846  -0.752  -0.461
68    R        -1.258  -1.244  -1.098  -1.602  -1.511  -1.211  -1.304  -1.250  -1.026
* 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/Q3E7B7
Output conservation file - output/Q3E7B7
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
