1     M         1.223   1.234   1.241   1.505   1.523   1.526   1.271   1.282   1.290
2     -         1.223   1.234   1.241   1.354   1.364   1.379   1.271   1.282   1.290
3     -        -0.530  -0.512  -0.485  -0.903  -0.846  -0.816  -0.683  -0.649  -0.608
4     -        -0.530  -0.512  -0.485  -0.346  -0.317  -0.274  -0.683  -0.649  -0.608
5     -         1.223   1.234   1.241   1.084   1.091   1.117   1.271   1.282   1.290
6     R        -0.387  -0.450  -0.460  -0.364  -0.454  -0.456  -0.466  -0.556  -0.570
7     A         1.223   1.234   1.241   1.174   1.170   1.204   1.271   1.282   1.290
8     V        -0.387  -0.450  -0.460  -0.212  -0.327  -0.354  -0.466  -0.556  -0.570
9     T        -0.387  -0.450  -0.460  -0.308  -0.389  -0.408  -0.466  -0.556  -0.570
10    R         1.223   1.234   1.241   1.416   1.428   1.440   1.271   1.282   1.290
11    N         1.223   1.234   1.241   1.112   1.152   1.144   1.271   1.282   1.290
12    K        -0.387  -0.450  -0.460  -0.253  -0.379  -0.408  -0.466  -0.556  -0.570
13    I        -1.556  -1.515  -1.494  -1.434  -1.378  -1.333  -1.335  -1.275  -1.241
14    V        -0.387  -0.450  -0.460  -0.212  -0.327  -0.354  -0.466  -0.556  -0.570
15    N         1.223   1.234   1.241   1.112   1.152   1.144   1.271   1.282   1.290
16    N        -0.387  -0.450  -0.460  -0.715  -0.796  -0.827  -0.466  -0.556  -0.570
17    L         1.223   1.234   1.241   1.174   1.177   1.204   1.271   1.282   1.290
18    Y        -0.387  -0.450  -0.460  -0.132  -0.213  -0.225  -0.466  -0.556  -0.570
19    F        -0.387  -0.450  -0.460  -0.595  -0.665  -0.669  -0.466  -0.556  -0.570
20    S         1.223   1.234   1.241   0.953   0.977   0.989   1.271   1.282   1.290
21    T         1.223   1.234   1.241   1.416   1.436   1.440   1.271   1.282   1.290
22    F         1.223   1.234   1.241   1.357   1.374   1.382   1.271   1.282   1.290
23    L        -0.387  -0.450  -0.460  -0.478  -0.610  -0.605  -0.466  -0.556  -0.570
24    I         1.223   1.234   1.241   1.143   1.173   1.174   1.271   1.282   1.290
25    A        -0.387  -0.450  -0.460  -0.172  -0.304  -0.337  -0.466  -0.556  -0.570
26    F        -0.387  -0.450  -0.460  -0.308  -0.413  -0.420  -0.466  -0.556  -0.570
27    A        -0.387  -0.450  -0.460  -0.478  -0.608  -0.605  -0.466  -0.556  -0.570
28    S        -1.556  -1.515  -1.494  -1.548  -1.516  -1.444  -1.335  -1.275  -1.241
29    V         1.223   1.234   1.241   1.266   1.269   1.294   1.271   1.282   1.290
30    A        -0.387  -0.450  -0.460  -0.172  -0.304  -0.337  -0.466  -0.556  -0.570
31    I        -0.387  -0.450  -0.460  -0.492  -0.613  -0.625  -0.466  -0.556  -0.570
32    G        -0.387  -0.450  -0.460  -0.378  -0.428  -0.450  -0.466  -0.556  -0.570
33    S         1.223   1.234   1.241   0.953   0.977   0.989   1.271   1.282   1.290
34    V        -1.556  -1.515  -1.494  -1.568  -1.513  -1.463  -1.335  -1.275  -1.241
35    L        -0.387  -0.315  -0.417  -0.492  -0.375  -0.546  -0.466  -0.356  -0.506
36    P         1.223   1.234   1.241   1.446   1.455   1.469   1.271   1.282   1.290
37    C         1.223   1.234   1.241   1.505   1.523   1.526   1.271   1.282   1.290
38    P         1.223   1.234   1.241   1.446   1.455   1.469   1.271   1.282   1.290
39    A        -1.556  -1.515  -1.494  -1.587  -1.532  -1.482  -1.335  -1.275  -1.241
40    H        -0.387  -0.450  -0.460  -0.145  -0.241  -0.254  -0.466  -0.556  -0.570
41    S         1.223   1.234   1.241   0.953   0.977   0.989   1.271   1.282   1.290
42    V        -0.387  -0.315  -0.417  -0.421  -0.296  -0.483  -0.466  -0.356  -0.506
43    -        -0.530  -0.512  -0.485  -0.195  -0.165  -0.128  -0.683  -0.649  -0.608
44    -        -0.530  -0.512  -0.485  -0.664  -0.639  -0.584  -0.683  -0.649  -0.608
45    -         1.223   1.234   1.241   0.992   0.998   1.027   1.271   1.282   1.290
46    D         1.223   1.234   1.241   1.387   1.401   1.411   1.271   1.282   1.290
47    S         1.223   1.234   1.241   0.953   0.977   0.989   1.271   1.282   1.290
48    D        -0.530  -0.512  -0.485  -0.558  -0.522  -0.480  -0.683  -0.649  -0.608
49    S        -0.530  -0.512  -0.485  -0.655  -0.619  -0.575  -0.683  -0.649  -0.608
50    P        -0.530  -0.512  -0.485  -0.558  -0.522  -0.480  -0.683  -0.649  -0.608
51    A        -0.530  -0.512  -0.485  -0.788  -0.750  -0.704  -0.683  -0.649  -0.608
52    V        -0.530  -0.512  -0.485  -0.721  -0.684  -0.639  -0.683  -0.649  -0.608
53    Q         1.223   1.234   1.241   1.092   1.110   1.124   1.271   1.282   1.290
54    Q         1.223   1.234   1.241   1.092   1.110   1.124   1.271   1.282   1.290
55    H         1.223   1.234   1.241   1.445   1.459   1.468   1.271   1.282   1.290
56    K         1.223   1.234   1.241   1.137   1.155   1.169   1.271   1.282   1.290
57    L        -0.530  -0.512  -0.485  -0.788  -0.750  -0.704  -0.683  -0.649  -0.608
58    Q        -0.530  -0.512  -0.485  -0.655  -0.619  -0.575  -0.683  -0.649  -0.608
59    L        -1.556  -1.515  -1.494  -1.587  -1.526  -1.482  -1.335  -1.275  -1.241
60    A        -1.556  -1.515  -1.494  -1.607  -1.539  -1.501  -1.335  -1.275  -1.241
61    H        -1.556  -1.515  -1.494  -1.269  -1.187  -1.173  -1.335  -1.275  -1.241
62    E        -0.387  -0.315  -0.417  -0.226  -0.100  -0.295  -0.466  -0.356  -0.506
63    Q        -0.387  -0.315  -0.406  -0.308  -0.194  -0.329  -0.466  -0.356  -0.489
64    E        -1.556  -1.515  -1.494  -1.509  -1.382  -1.406  -1.335  -1.275  -1.241
65    L        -0.387  -0.450  -0.460  -0.507  -0.608  -0.631  -0.466  -0.556  -0.570
66    K        -0.387  -0.315  -0.417  -0.336  -0.237  -0.366  -0.466  -0.356  -0.506
67    R        -1.556  -1.515  -1.494  -1.434  -1.343  -1.333  -1.335  -1.275  -1.241
68    K        -0.387  -0.450  -0.460  -0.685  -0.777  -0.787  -0.466  -0.556  -0.570
69    D        -0.387  -0.450  -0.460  -0.435  -0.498  -0.524  -0.466  -0.556  -0.570
70    A        -1.556  -1.515  -1.494  -1.490  -1.447  -1.388  -1.335  -1.275  -1.241
71    L        -1.556  -1.515  -1.494  -1.252  -1.218  -1.155  -1.335  -1.275  -1.241
72    S        -0.387  -0.450  -0.460  -0.640  -0.739  -0.794  -0.466  -0.556  -0.570
73    K        -0.387  -0.450  -0.460  -0.226  -0.349  -0.384  -0.466  -0.556  -0.570
74    K         1.223   1.234   1.241   1.196   1.205   1.225   1.271   1.282   1.290
75    I         1.223   1.234   1.241   1.143   1.173   1.174   1.271   1.282   1.290
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -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/Q3E823
Output conservation file - output/Q3E823
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
