1     M         0.893   0.894   0.904   1.126   1.126   1.137   0.919   0.921   0.931
2     S        -0.620  -0.571  -0.679  -0.456  -0.381  -0.554  -0.723  -0.649  -0.805
3     K        -0.620  -0.644  -0.690  -0.456  -0.495  -0.569  -0.723  -0.757  -0.821
4     Y         0.893   0.894   0.904   0.853   0.853   0.870   0.919   0.921   0.931
5     A         0.893   0.894   0.904   1.036   1.037   1.049   0.919   0.921   0.931
6     W         0.893   0.894   0.904   1.302   1.301   1.307   0.919   0.921   0.931
7     Y         0.893   0.894   0.904   0.853   0.853   0.870   0.919   0.921   0.931
8     T         0.893   0.894   0.904   0.630   0.637   0.654   0.919   0.921   0.931
9     R         0.893   0.894   0.904   1.156   1.153   1.165   0.919   0.921   0.931
10    V        -1.719  -1.712  -1.661  -1.395  -1.384  -1.316  -1.544  -1.534  -1.455
11    T         0.893   0.894   0.904   0.630   0.637   0.654   0.919   0.921   0.931
12    D         0.893   0.894   0.904   1.185   1.184   1.194   0.919   0.921   0.931
13    T        -0.620  -0.633  -0.684  -0.884  -0.897  -0.960  -0.723  -0.741  -0.812
14    L        -0.620  -0.633  -0.684  -0.914  -0.931  -0.986  -0.723  -0.741  -0.812
15    H         0.893   0.894   0.904   1.302   1.301   1.307   0.919   0.921   0.931
16    R         0.893   0.894   0.904   1.156   1.153   1.165   0.919   0.921   0.931
17    L         0.893   0.894   0.904   0.598   0.601   0.622   0.919   0.921   0.931
18    T         0.893   0.894   0.904   0.630   0.637   0.654   0.919   0.921   0.931
19    V         0.893   0.894   0.904   1.067   1.067   1.078   0.919   0.921   0.931
20    L         0.893   0.894   0.904   0.598   0.601   0.622   0.919   0.921   0.931
21    T         0.893   0.894   0.904   0.630   0.637   0.654   0.919   0.921   0.931
22    L        -0.620  -0.644  -0.690  -0.795  -0.822  -0.838  -0.723  -0.757  -0.821
23    V        -1.719  -1.712  -1.661  -1.647  -1.639  -1.562  -1.544  -1.534  -1.455
24    G         0.893   0.894   0.904   0.884   0.881   0.901   0.919   0.921   0.931
25    G         0.893   0.894   0.904   0.884   0.881   0.901   0.919   0.921   0.931
26    T        -0.620  -0.644  -0.690  -0.824  -0.850  -0.889  -0.723  -0.757  -0.821
27    L         0.893   0.894   0.904   0.598   0.601   0.622   0.919   0.921   0.931
28    Y         0.893   0.894   0.904   0.853   0.853   0.870   0.919   0.921   0.931
29    M         0.893   0.894   0.904   1.126   1.126   1.137   0.919   0.921   0.931
30    S        -1.719  -1.712  -1.661  -1.821  -1.829  -1.731  -1.544  -1.534  -1.455
31    G         0.893   0.894   0.904   0.884   0.881   0.901   0.919   0.921   0.931
32    G         0.893   0.894   0.904   0.884   0.881   0.901   0.919   0.921   0.931
33    L         0.893   0.894   0.904   0.598   0.601   0.622   0.919   0.921   0.931
34    A        -0.620  -0.571  -0.679  -0.483  -0.402  -0.598  -0.723  -0.649  -0.805
35    Y         0.893   0.894   0.904   0.853   0.853   0.870   0.919   0.921   0.931
36    T         0.893   0.894   0.904   0.630   0.637   0.654   0.919   0.921   0.931
37    L         0.893   0.894   0.904   0.598   0.601   0.622   0.919   0.921   0.931
38    Y         0.893   0.894   0.904   0.853   0.853   0.870   0.919   0.921   0.931
39    M        -0.620  -0.633  -0.684  -0.497  -0.520  -0.644  -0.723  -0.741  -0.812
40    N         0.893   0.894   0.904   1.215   1.214   1.223   0.919   0.921   0.931
41    G         0.893   0.894   0.904   0.884   0.881   0.901   0.919   0.921   0.931
42    K         0.893   0.894   0.904   1.036   1.037   1.049   0.919   0.921   0.931
43    K        -0.620  -0.644  -0.690  -0.456  -0.495  -0.569  -0.723  -0.757  -0.821
44    Y         0.893   0.894   0.904   0.853   0.853   0.870   0.919   0.921   0.931
45    E         0.893   0.894   0.904   1.036   1.037   1.049   0.919   0.921   0.931
46    Q        -0.620  -0.633  -0.684  -0.650  -0.665  -0.753  -0.723  -0.741  -0.812
47    Q        -1.719  -1.712  -1.661  -1.647  -1.625  -1.562  -1.544  -1.534  -1.455
48    V         0.893   0.894   0.904   1.036   1.037   1.048   0.919   0.921   0.931
49    T        -0.755  -0.753  -0.715  -0.910  -0.904  -0.844  -0.928  -0.923  -0.859
50    Q        -0.755  -0.753  -0.715  -1.114  -1.108  -1.044  -0.928  -0.923  -0.859
51    Q        -0.620  -0.644  -0.690  -0.580  -0.608  -0.671  -0.723  -0.757  -0.821
52    K        -0.620  -0.633  -0.684  -0.707  -0.735  -0.883  -0.723  -0.741  -0.812
53    A        -0.755  -0.753  -0.715  -1.092  -1.086  -1.021  -0.928  -0.923  -0.859
54    L         0.893   0.894   0.904   0.539   0.541   0.565   0.919   0.921   0.931
55    E        -1.719  -1.712  -1.661  -1.647  -1.635  -1.562  -1.544  -1.534  -1.455
56    E        -0.620  -0.644  -0.690  -0.442  -0.479  -0.552  -0.723  -0.757  -0.821
57    D        -1.719  -1.712  -1.661  -1.555  -1.550  -1.472  -1.544  -1.534  -1.455
58    N        -1.719  -1.712  -1.661  -1.483  -1.476  -1.402  -1.544  -1.534  -1.455
59    Q        -0.620  -0.644  -0.690  -0.566  -0.593  -0.653  -0.723  -0.757  -0.821
60    Q         0.893   0.894   0.904   0.884   0.891   0.901   0.919   0.921   0.931
61    L        -0.620  -0.633  -0.684  -0.914  -0.931  -0.986  -0.723  -0.741  -0.812
62    Q        -0.620  -0.644  -0.690  -0.650  -0.682  -0.763  -0.723  -0.757  -0.821
63    S        -1.719  -1.712  -1.661  -1.483  -1.482  -1.402  -1.544  -1.534  -1.455
64    P        -1.719  -1.712  -1.661  -1.610  -1.614  -1.526  -1.544  -1.534  -1.455
65    T        -0.755  -0.753  -0.715  -1.080  -1.074  -1.010  -0.928  -0.923  -0.859
66    A        -0.755  -0.753  -0.715  -0.716  -0.710  -0.655  -0.928  -0.923  -0.859
67    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    P        -0.620  -0.571  -0.679  -0.270  -0.199  -0.360  -0.723  -0.649  -0.805
69    T        -1.719  -1.712  -1.661  -1.704  -1.665  -1.617  -1.544  -1.534  -1.455
70    E        -0.620  -0.633  -0.684  -0.429  -0.448  -0.526  -0.723  -0.741  -0.812
* 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/P39103
Output conservation file - output/P39103
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
