1     M         1.393   1.459   1.529   1.670   1.762   1.870   1.525   1.614   1.734
2     A        -1.342  -0.964  -1.341  -1.023  -0.469  -1.088  -1.118  -0.676  -1.048
3     R        -0.725  -0.558  -0.899  -0.396  -0.176  -0.702  -0.638  -0.412  -0.813
4     A         1.393   1.459   1.529   1.581   1.731   1.788   1.525   1.614   1.734
5     R        -1.555  -1.571  -1.430  -1.373  -1.442  -1.176  -1.359  -1.326  -1.133
6     K         0.088   0.119   0.240  -0.059  -0.028   0.177  -0.277  -0.239  -0.073
7     G         1.393   1.459   1.529   1.748   1.842   1.942   1.525   1.614   1.734
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     A        -0.725  -0.631  -0.908  -0.546  -0.499  -0.848  -0.638  -0.519  -0.824
10    L         0.649   0.800   0.445   0.448   0.634   0.233   0.684   0.902   0.310
11    V        -0.383  -0.321  -0.434  -0.533  -0.539  -0.717  -0.518  -0.469  -0.575
12    Q        -0.383  -0.311  -0.426  -0.332  -0.288  -0.503  -0.518  -0.452  -0.565
13    C         1.393   1.459   1.529   1.768   1.865   1.960   1.525   1.614   1.734
14    D         0.649   0.512   0.416   0.705   0.522   0.300   0.684   0.461   0.259
15    P         1.393   1.459   1.529   1.601   1.697   1.806   1.525   1.614   1.734
16    S        -0.058  -0.331  -0.384   0.264  -0.069  -0.190  -0.037  -0.401  -0.496
17    I         0.649   0.537   0.420   0.639   0.463   0.310   0.684   0.502   0.265
18    K         0.649   0.792   0.443   0.805   0.998   0.525   0.684   0.891   0.306
19    A        -0.058  -0.331  -0.384   0.285  -0.039  -0.199  -0.037  -0.401  -0.496
20    L         0.649   0.512   0.416   0.393   0.182   0.055   0.684   0.461   0.259
21    I         1.393   1.459   1.529   1.315   1.391   1.542   1.525   1.614   1.734
22    L        -0.529  -0.431  -0.441  -1.031  -0.920  -0.826  -0.758  -0.630  -0.590
23    Q        -1.555  -1.521  -1.426  -1.265  -1.223  -1.081  -1.359  -1.290  -1.130
24    I        -0.383  -0.527  -0.447  -0.512  -0.784  -0.630  -0.518  -0.687  -0.592
25    D         1.393   1.459   1.529   1.419   1.524   1.638   1.525   1.614   1.734
26    A        -0.383  -0.361  -0.396  -0.318  -0.232  -0.397  -0.518  -0.444  -0.515
27    K        -2.025  -1.980  -1.785  -2.081  -1.926  -1.682  -1.599  -1.506  -1.269
28    M        -1.555  -1.547  -1.426  -1.272  -1.287  -1.069  -1.359  -1.310  -1.129
29    S        -1.213  -1.215  -1.014  -1.048  -1.020  -0.765  -1.238  -1.187  -0.946
30    D        -0.383  -0.402  -0.436  -0.305  -0.317  -0.349  -0.518  -0.534  -0.578
31    I         1.393   1.459   1.529   1.315   1.391   1.542   1.525   1.614   1.734
32    V         0.088   0.154   0.252  -0.264  -0.198   0.002  -0.277  -0.173  -0.050
33    L        -0.529  -0.431  -0.445  -1.014  -0.900  -0.743  -0.758  -0.632  -0.594
34    E         0.649   0.681   0.433   0.486   0.618   0.193   0.684   0.728   0.290
35    E         0.649   0.512   0.416   0.486   0.379   0.163   0.684   0.461   0.259
36    L         0.649   0.537   0.420   0.393   0.221   0.061   0.684   0.502   0.265
37    D         1.393   1.459   1.529   1.419   1.524   1.638   1.525   1.614   1.734
38    D         0.088   0.203   0.266  -0.409  -0.142  -0.102  -0.277  -0.080  -0.023
39    T        -0.058  -0.331  -0.384   0.343  -0.064  -0.237  -0.037  -0.401  -0.496
40    H        -0.058  -0.331  -0.384   0.428   0.062  -0.060  -0.037  -0.401  -0.496
41    L         1.393   1.459   1.529   1.089   1.176   1.334   1.525   1.614   1.734
42    L        -0.383  -0.409  -0.438  -0.709  -0.777  -0.705  -0.518  -0.546  -0.580
43    V         0.088   0.186   0.259  -0.219  -0.084   0.040  -0.277  -0.112  -0.037
44    N        -1.684  -1.643  -1.440  -1.535  -1.463  -1.163  -1.479  -1.385  -1.142
45    P        -1.000  -0.923  -0.988  -1.010  -0.982  -1.092  -0.998  -0.923  -0.919
46    S        -1.000  -0.843  -0.960  -0.845  -0.633  -0.785  -0.998  -0.817  -0.890
47    K        -0.383  -0.549  -0.462  -0.284  -0.523  -0.372  -0.518  -0.726  -0.611
48    V         0.649   0.537   0.420   0.715   0.510   0.300   0.684   0.502   0.265
49    E        -0.383  -0.324  -0.429  -0.590  -0.448  -0.588  -0.518  -0.449  -0.568
50    F        -1.342  -1.485  -1.424  -0.864  -1.169  -1.146  -1.118  -1.233  -1.126
51    V        -0.383  -0.386  -0.404  -0.533  -0.576  -0.644  -0.518  -0.479  -0.527
52    K         1.393   1.459   1.529   1.460   1.561   1.676   1.525   1.614   1.734
53    H        -2.367  -2.149  -2.069  -1.764  -1.465  -1.360  -1.719  -1.501  -1.355
54    E         0.283   0.222   0.271  -0.046  -0.091  -0.070   0.083  -0.046  -0.013
55    L         1.393   1.459   1.529   1.089   1.176   1.334   1.525   1.614   1.734
56    N         0.283   0.165   0.259   0.198  -0.049   0.014   0.083  -0.150  -0.036
57    R        -0.058  -0.207  -0.364   0.237   0.004  -0.271  -0.037  -0.235  -0.468
58    L        -0.383  -0.482  -0.461  -0.650  -0.796  -0.635  -0.518  -0.666  -0.611
59    L         1.393   1.459   1.529   1.089   1.176   1.334   1.525   1.614   1.734
60    S        -0.725  -0.978  -0.975  -0.479  -0.854  -0.955  -0.638  -0.916  -0.899
61    K         0.025   0.131   0.259  -0.469  -0.255  -0.088  -0.397  -0.216  -0.036
62    N         1.393   1.459   1.529   1.495   1.602   1.708   1.525   1.614   1.734
63    I         0.088   0.089   0.239  -0.120  -0.105   0.175  -0.277  -0.295  -0.075
64    Y         1.393   1.459   1.529   1.748   1.848   1.942   1.525   1.614   1.734
65    N        -0.058  -0.331  -0.384   0.222  -0.141  -0.240  -0.037  -0.401  -0.496
66    P         0.649   0.537   0.420   0.925   0.768   0.562   0.684   0.502   0.265
67    M        -1.684  -1.520  -1.440  -1.852  -1.601  -1.443  -1.479  -1.279  -1.141
68    D         0.025   0.132   0.262  -0.501  -0.275  -0.108  -0.397  -0.214  -0.030
69    E         0.584   0.360   0.365   0.502   0.223   0.211   0.583   0.203   0.164
70    E        -0.883  -1.015  -1.003  -0.996  -1.251  -1.183  -0.829  -0.973  -0.930
71    E         0.065   0.090   0.239  -0.337  -0.263  -0.008  -0.320  -0.295  -0.075
72    N        -1.235  -1.202  -1.046  -1.457  -1.403  -1.223  -1.243  -1.176  -0.975
73    Q        -1.235  -1.147  -1.021  -1.238  -1.087  -0.932  -1.243  -1.120  -0.949
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/Q3E7C1
Output conservation file - output/Q3E7C1
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
