1     M         0.906   0.910   0.991   1.347   1.323   1.377   0.915   0.922   1.028
2     A        -0.339  -0.342  -0.679   0.121   0.102  -0.469  -0.292  -0.296  -0.770
3     A        -0.911  -0.829  -0.716  -0.567  -0.462  -0.455  -1.097  -0.977  -0.826
4     Q        -1.996  -2.101  -1.746  -1.644  -1.754  -1.336  -1.902  -1.993  -1.487
5     K         0.906   0.910   0.991   0.382   0.410   0.636   0.915   0.922   1.028
6     S        -0.911  -0.995  -0.742  -0.584  -0.777  -0.535  -1.097  -1.232  -0.865
7     F         0.906   0.910   0.991   1.412   1.378   1.426   0.915   0.922   1.028
8     R        -0.911  -0.926  -0.738  -1.934  -1.935  -1.579  -1.097  -1.124  -0.858
9     I        -1.996  -1.954  -1.733  -1.644  -1.580  -1.266  -1.902  -1.829  -1.473
10    K         0.906   0.910   0.991   0.382   0.410   0.636   0.915   0.922   1.028
11    Q        -0.339  -0.522  -0.689  -0.015  -0.217  -0.500  -0.292  -0.537  -0.786
12    K         0.906   0.910   0.991   0.382   0.410   0.636   0.915   0.922   1.028
13    M        -0.339  -0.342  -0.679   0.059   0.048  -0.423  -0.292  -0.296  -0.770
14    A         0.906   0.910   0.991   1.061   1.053   1.157   0.915   0.922   1.028
15    K         0.906   0.910   0.991   0.382   0.410   0.636   0.915   0.922   1.028
16    A         0.906   0.910   0.991   1.061   1.053   1.157   0.915   0.922   1.028
17    K        -2.972  -2.971  -2.471  -2.938  -2.871  -2.193  -2.506  -2.462  -1.810
18    K        -0.911  -0.968  -0.740  -1.810  -1.927  -1.567  -1.097  -1.189  -0.862
19    Q         0.906   0.910   0.991   0.994   1.014   1.106   0.915   0.922   1.028
20    N         0.906   0.910   0.991   0.949   0.945   1.071   0.915   0.922   1.028
21    R         0.906   0.910   0.991   0.183   0.226   0.483   0.915   0.922   1.028
22    P        -0.339  -0.207  -0.671   0.114   0.254  -0.475  -0.292  -0.124  -0.759
23    L        -0.911  -0.904  -0.734  -0.770  -0.767  -0.605  -1.097  -1.091  -0.853
24    P         0.906   0.910   0.991   1.173   1.158   1.243   0.915   0.922   1.028
25    Q         0.906   0.910   0.991   0.994   1.014   1.106   0.915   0.922   1.028
26    W         0.906   0.910   0.991   1.282   1.263   1.327   0.915   0.922   1.028
27    I        -0.339  -0.522  -0.689   0.150  -0.063  -0.331  -0.292  -0.537  -0.786
28    R         0.906   0.910   0.991   0.183   0.226   0.483   0.915   0.922   1.028
29    L        -0.339  -0.522  -0.689   0.070  -0.155  -0.410  -0.292  -0.537  -0.786
30    R        -0.339  -0.522  -0.689  -0.997  -1.226  -1.487  -0.292  -0.537  -0.786
31    T        -0.339  -0.080  -0.671   0.007   0.268  -0.461  -0.292   0.031  -0.759
32    N        -2.144  -1.935  -1.738  -1.678  -1.476  -1.134  -2.103  -1.879  -1.480
33    N         0.906   0.910   0.991   0.949   0.945   1.071   0.915   0.922   1.028
34    T        -0.339  -0.140  -0.675  -0.143   0.094  -0.847  -0.292  -0.041  -0.764
35    I        -0.911  -0.968  -0.740  -0.567  -0.654  -0.385  -1.097  -1.189  -0.862
36    R        -0.339  -0.316  -0.679  -0.808  -0.738  -0.976  -0.292  -0.261  -0.770
37    Y         0.906   0.910   0.991   1.433   1.406   1.443   0.915   0.922   1.028
38    N         0.906   0.910   0.991   0.949   0.945   1.071   0.915   0.922   1.028
39    A        -0.339  -0.316  -0.679   0.059   0.077  -0.423  -0.292  -0.261  -0.770
40    K         0.906   0.910   0.991   0.382   0.410   0.636   0.915   0.922   1.028
41    R         0.906   0.910   0.991   0.183   0.226   0.483   0.915   0.922   1.028
42    R         0.906   0.910   0.991   0.183   0.226   0.483   0.915   0.922   1.028
43    N        -0.339  -0.342  -0.679   0.319   0.286  -0.370  -0.292  -0.296  -0.770
44    W         0.906   0.910   0.991   1.282   1.263   1.327   0.915   0.922   1.028
45    R         0.906   0.910   0.991   0.183   0.226   0.483   0.915   0.922   1.028
46    R        -0.339  -0.388  -0.682  -0.997  -1.025  -1.474  -0.292  -0.356  -0.775
47    T         0.906   0.910   0.991   1.017   0.995   1.123   0.915   0.922   1.028
48    K        -0.339  -0.388  -0.682  -0.825  -0.870  -1.419  -0.292  -0.356  -0.775
49    M        -0.911  -0.829  -0.716  -0.686  -0.578  -0.474  -1.097  -0.977  -0.826
50    N        -1.168  -1.119  -0.745  -1.090  -1.007  -0.497  -1.499  -1.427  -0.869
51    I        -0.339  -0.388  -0.682   0.077   0.020  -0.505  -0.292  -0.356  -0.775
* 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/P04650
Output conservation file - output/P04650
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
