1     M         0.500   0.508   0.510   0.982   0.974   0.924   0.506   0.519   0.524
2     D         0.500   0.508   0.510   0.770   0.752   0.750   0.506   0.519   0.524
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     S        -2.710  -2.442  -2.357  -2.532  -2.180  -2.058  -2.598  -2.302  -2.211
5     K         0.500   0.508   0.510   0.702   0.710   0.695   0.506   0.519   0.524
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     T        -2.511  -2.492  -2.355  -2.517  -2.526  -2.389  -2.359  -2.370  -2.209
8     P         0.500   0.508   0.510   0.982   0.974   0.924   0.506   0.519   0.524
9     V         0.500   0.508   0.510   0.020   0.065   0.138   0.506   0.519   0.524
10    T        -1.579  -1.434  -1.297  -1.728  -1.518  -1.304  -1.881  -1.697  -1.523
11    L         0.500   0.508   0.510   0.509   0.537   0.538   0.506   0.519   0.524
12    A        -0.555  -0.940  -1.282  -0.033  -0.646  -1.453  -0.449  -0.964  -1.500
13    K         0.500   0.508   0.510   0.702   0.710   0.695   0.506   0.519   0.524
14    V         0.500   0.508   0.510   0.020   0.065   0.138   0.506   0.519   0.524
15    I        -1.569  -2.011  -2.349  -0.966  -1.661  -2.419  -1.285  -1.811  -2.203
16    K        -0.555  -0.940  -1.282  -0.243  -0.855  -1.626  -0.449  -0.964  -1.500
17    V         0.500   0.508   0.510   0.020   0.065   0.138   0.506   0.519   0.524
18    L         0.500   0.508   0.510   0.509   0.537   0.538   0.506   0.519   0.524
19    G         0.500   0.508   0.510   0.606   0.623   0.617   0.506   0.519   0.524
20    R         0.500   0.508   0.510  -0.040   0.008   0.090   0.506   0.519   0.524
21    T         0.500   0.508   0.510   0.647   0.693   0.650   0.506   0.519   0.524
22    G         0.500   0.508   0.510   0.606   0.623   0.617   0.506   0.519   0.524
23    S         0.500   0.508   0.510   0.783   0.779   0.761   0.506   0.519   0.524
24    R         0.500   0.508   0.510  -0.040   0.008   0.090   0.506   0.519   0.524
25    G         0.500   0.508   0.510   0.606   0.623   0.617   0.506   0.519   0.524
26    G         0.500   0.508   0.510   0.606   0.623   0.617   0.506   0.519   0.524
27    V         0.500   0.508   0.510   0.020   0.065   0.138   0.506   0.519   0.524
28    T         0.500   0.508   0.510   0.647   0.693   0.650   0.506   0.519   0.524
29    Q         0.500   0.508   0.510   1.087   1.061   1.009   0.506   0.519   0.524
30    V         0.500   0.508   0.510   0.020   0.065   0.138   0.506   0.519   0.524
31    R         0.500   0.508   0.510  -0.040   0.008   0.090   0.506   0.519   0.524
32    V         0.500   0.508   0.510   0.020   0.065   0.138   0.506   0.519   0.524
33    E         0.500   0.508   0.510   0.537   0.568   0.560   0.506   0.519   0.524
34    F         0.500   0.508   0.510   1.100   1.084   1.019   0.506   0.519   0.524
35    L        -2.335  -2.346  -2.359  -2.133  -2.132  -2.067  -2.239  -2.246  -2.213
36    E        -1.579  -1.434  -1.297  -1.772  -1.561  -1.322  -1.881  -1.697  -1.523
37    D         0.500   0.508   0.510   0.770   0.752   0.750   0.506   0.519   0.524
38    T        -3.177  -3.234  -3.107  -2.697  -2.747  -2.567  -2.717  -2.706  -2.553
39    S        -1.103  -1.261  -1.301  -0.809  -1.135  -1.264  -1.165  -1.430  -1.530
40    R         0.500   0.508   0.510  -0.040   0.008   0.090   0.506   0.519   0.524
41    T        -1.579  -1.434  -1.297  -1.676  -1.461  -1.253  -1.881  -1.697  -1.523
42    I         0.500   0.508   0.510   0.837   0.839   0.805   0.506   0.519   0.524
43    V        -1.426  -1.420  -1.298  -1.961  -1.934  -1.616  -1.643  -1.676  -1.526
44    R         0.500   0.508   0.510  -0.040   0.008   0.090   0.506   0.519   0.524
45    N         0.500   0.508   0.510   1.035   1.032   0.966   0.506   0.519   0.524
46    V         0.500   0.508   0.510   0.020   0.065   0.138   0.506   0.519   0.524
47    K         0.500   0.508   0.510   0.702   0.710   0.695   0.506   0.519   0.524
48    G         0.500   0.508   0.510   0.606   0.623   0.617   0.506   0.519   0.524
49    P         0.500   0.508   0.510   0.982   0.974   0.924   0.506   0.519   0.524
50    V         0.500   0.508   0.510   0.020   0.065   0.138   0.506   0.519   0.524
51    R         0.500   0.508   0.510  -0.040   0.008   0.090   0.506   0.519   0.524
52    E         0.500   0.508   0.510   0.537   0.568   0.560   0.506   0.519   0.524
53    N        -2.335  -2.214  -2.356  -1.835  -1.819  -2.005  -2.239  -2.138  -2.210
54    D         0.500   0.508   0.510   0.770   0.752   0.750   0.506   0.519   0.524
55    I         0.500   0.508   0.510   0.837   0.839   0.805   0.506   0.519   0.524
56    L         0.500   0.508   0.510   0.509   0.537   0.538   0.506   0.519   0.524
57    V        -1.579  -1.394  -1.298  -1.906  -1.715  -1.417  -1.881  -1.635  -1.525
58    L         0.500   0.508   0.510   0.509   0.537   0.538   0.506   0.519   0.524
59    M        -1.426  -1.420  -1.298  -1.231  -1.362  -1.208  -1.643  -1.676  -1.526
60    E         0.500   0.508   0.510   0.537   0.568   0.560   0.506   0.519   0.524
61    S         0.500   0.508   0.510   0.783   0.779   0.761   0.506   0.519   0.524
62    E         0.500   0.508   0.510   0.537   0.568   0.560   0.506   0.519   0.524
63    R         0.500   0.508   0.510  -0.040   0.008   0.090   0.506   0.519   0.524
64    E         0.500   0.508   0.510   0.537   0.568   0.560   0.506   0.519   0.524
65    A         0.500   0.508   0.510   0.903   0.905   0.859   0.506   0.519   0.524
66    R         0.500   0.508   0.510  -0.040   0.008   0.090   0.506   0.519   0.524
67    R         0.500   0.508   0.510  -0.040   0.008   0.090   0.506   0.519   0.524
68    L         0.500   0.508   0.510   0.509   0.537   0.538   0.506   0.519   0.524
69    R         0.500   0.508   0.510  -0.040   0.008   0.090   0.506   0.519   0.524
* 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/P0C0X0
Output conservation file - output/P0C0X0
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
