1     M         1.410   1.475   1.525   1.661   1.741   1.818   1.513   1.602   1.679
2     S        -1.209  -1.124  -1.072  -1.244  -1.118  -1.087  -1.168  -1.056  -0.960
3     F        -0.634  -0.575  -0.531  -0.808  -0.734  -0.683  -0.814  -0.723  -0.663
4     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    F         0.159   0.343   0.297   0.062   0.393   0.263  -0.142   0.165   0.052
13    I        -1.248  -1.113  -1.047  -1.091  -0.819  -0.754  -1.222  -1.033  -0.935
14    L         0.604   0.465   0.388   0.297   0.134   0.008   0.601   0.372   0.214
15    S         1.410   1.475   1.525   1.149   1.250   1.340   1.513   1.602   1.679
16    D         0.067   0.142   0.233   0.058   0.107   0.276  -0.311  -0.198  -0.066
17    E         1.410   1.475   1.525   1.468   1.522   1.638   1.513   1.602   1.679
18    S         1.410   1.475   1.525   1.149   1.250   1.340   1.513   1.602   1.679
19    K         0.604   0.522   0.388   0.825   0.729   0.520   0.601   0.465   0.216
20    E         1.410   1.475   1.525   1.468   1.522   1.638   1.513   1.602   1.679
21    R         1.410   1.475   1.525   1.538   1.608   1.703   1.513   1.602   1.679
22    I        -0.156  -0.161  -0.382  -0.138  -0.207  -0.538  -0.159  -0.181  -0.464
23    S        -2.027  -1.851  -1.811  -1.950  -1.741  -1.592  -1.526  -1.346  -1.240
24    K         1.410   1.475   1.525   1.524   1.623   1.690   1.513   1.602   1.679
25    I        -0.712  -0.535  -0.493  -1.097  -0.796  -0.759  -0.918  -0.670  -0.615
26    L        -0.156  -0.331  -0.415  -0.405  -0.621  -0.747  -0.159  -0.392  -0.508
27    T        -0.859  -0.735  -0.943  -0.397  -0.239  -0.548  -0.767  -0.626  -0.823
28    L        -0.712  -0.592  -0.515  -1.170  -0.990  -0.833  -0.918  -0.759  -0.645
29    T        -0.712  -0.610  -0.520  -0.987  -0.812  -0.647  -0.918  -0.778  -0.650
30    H        -1.101  -0.906  -1.023  -0.798  -0.591  -0.643  -1.070  -0.863  -0.914
31    N        -1.101  -0.906  -1.023  -0.926  -0.726  -0.793  -1.070  -0.863  -0.914
32    V        -0.156  -0.095  -0.371   0.030   0.081  -0.291  -0.159  -0.088  -0.449
33    A        -0.859  -1.079  -1.030  -0.628  -1.005  -0.996  -0.767  -0.995  -0.917
34    H         1.410   1.475   1.525   1.647   1.740   1.805   1.513   1.602   1.679
35    Y         1.410   1.475   1.525   1.510   1.597   1.677   1.513   1.602   1.679
36    G         1.410   1.475   1.525   1.510   1.582   1.677   1.513   1.602   1.679
37    W        -0.469  -0.319  -0.429  -0.262   0.002  -0.205  -0.615  -0.375  -0.529
38    I         0.604   0.592   0.392   0.573   0.549   0.191   0.601   0.577   0.222
39    P         1.410   1.475   1.525   1.440   1.569   1.612   1.513   1.602   1.679
40    F         0.234   0.178   0.242   0.024  -0.145  -0.093  -0.007  -0.130  -0.051
41    V         0.234   0.178   0.242   0.145  -0.028   0.095  -0.007  -0.130  -0.051
42    L         0.604   0.522   0.388   0.297   0.218   0.009   0.601   0.465   0.216
43    Y         0.604   0.465   0.388   0.830   0.655   0.546   0.601   0.372   0.214
44    L         0.604   0.522   0.388   0.312   0.234   0.044   0.601   0.465   0.216
45    G         1.410   1.475   1.525   1.510   1.582   1.677   1.513   1.602   1.679
46    W        -0.296  -0.498  -0.484   0.115  -0.188  -0.183  -0.349  -0.621  -0.602
47    A        -0.579  -0.494  -0.481  -0.703  -0.472  -0.525  -0.762  -0.615  -0.599
48    H        -2.027  -1.958  -1.835  -1.506  -1.478  -1.231  -1.526  -1.422  -1.256
49    T        -0.296  -0.493  -0.484  -0.127  -0.474  -0.530  -0.349  -0.612  -0.602
50    S        -1.659  -1.595  -1.492  -1.640  -1.537  -1.401  -1.383  -1.286  -1.137
51    N        -0.296  -0.493  -0.484  -0.123  -0.461  -0.557  -0.349  -0.612  -0.602
52    R        -0.579  -0.568  -0.480  -0.472  -0.470  -0.324  -0.762  -0.714  -0.600
53    P         0.524   0.400   0.332   0.589   0.438   0.303   0.479   0.264   0.116
54    N        -0.469  -0.448  -0.443  -0.605  -0.520  -0.479  -0.615  -0.550  -0.547
55    F        -1.101  -1.014  -1.011  -1.452  -1.319  -1.243  -1.070  -0.949  -0.901
56    L        -1.638  -1.658  -1.472  -1.770  -1.711  -1.462  -1.374  -1.332  -1.123
57    N        -0.859  -1.079  -1.030  -0.545  -0.902  -0.873  -0.767  -0.995  -0.917
58    L        -0.156  -0.387  -0.425  -0.324  -0.578  -0.598  -0.159  -0.467  -0.521
59    L        -0.156  -0.387  -0.425  -0.370  -0.651  -0.691  -0.159  -0.467  -0.521
60    S         1.410   1.475   1.525   1.149   1.250   1.340   1.513   1.602   1.679
61    P        -0.156  -0.387  -0.425   0.033  -0.290  -0.373  -0.159  -0.467  -0.521
62    L         0.067   0.147   0.235  -0.471  -0.324  -0.178  -0.311  -0.188  -0.062
63    P        -0.296  -0.519  -0.484  -0.175  -0.498  -0.484  -0.349  -0.648  -0.602
64    S         0.524   0.364   0.341   0.307   0.097   0.069   0.479   0.200   0.132
65    V        -1.101  -1.102  -1.027  -1.033  -1.030  -0.936  -1.070  -1.020  -0.914
* 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/P53507
Output conservation file - output/P53507
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
