1     M         1.535   1.541   1.561   1.810   1.819   1.854   1.622   1.629   1.653
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     E         0.001   0.034  -0.023   0.038   0.096  -0.008  -0.129  -0.077  -0.166
4     -        -0.135  -0.132  -0.108  -0.348  -0.341  -0.301  -0.348  -0.342  -0.303
5     -        -0.135  -0.132  -0.108  -0.208  -0.201  -0.161  -0.348  -0.342  -0.303
6     -         1.535   1.541   1.561   1.331   1.340   1.376   1.622   1.629   1.653
7     A         0.001  -0.039  -0.051   0.026  -0.028  -0.056  -0.129  -0.191  -0.211
8     E         1.535   1.541   1.561   1.499   1.512   1.544   1.622   1.629   1.653
9     K        -1.113  -1.106  -1.085  -0.985  -0.992  -0.938  -1.005  -0.993  -0.955
10    Q        -1.113  -1.106  -1.085  -1.287  -1.284  -1.240  -1.005  -0.993  -0.955
11    S         0.001   0.034  -0.023   0.328   0.382   0.282  -0.129  -0.077  -0.166
12    D        -1.113  -1.106  -1.085  -1.166  -1.161  -1.118  -1.005  -0.993  -0.955
13    I        -1.113  -1.106  -1.085  -1.017  -0.993  -0.970  -1.005  -0.993  -0.955
14    K        -1.113  -1.106  -1.085  -1.183  -1.190  -1.135  -1.005  -0.993  -0.955
15    G         1.535   1.541   1.561   1.446   1.454   1.491   1.622   1.629   1.653
16    T        -1.113  -1.106  -1.085  -0.985  -1.001  -0.938  -1.005  -0.993  -0.955
17    I         0.001  -0.039  -0.051   0.133   0.087   0.067  -0.129  -0.191  -0.211
18    A         0.001  -0.039  -0.051   0.050  -0.004  -0.027  -0.129  -0.191  -0.211
19    F         1.535   1.541   1.561   1.835   1.847   1.879   1.622   1.629   1.653
20    D         1.535   1.541   1.561   1.419   1.432   1.464   1.622   1.629   1.653
21    T        -1.113  -1.106  -1.085  -1.033  -1.014  -0.986  -1.005  -0.993  -0.955
22    H        -1.113  -1.106  -1.085  -0.829  -0.823  -0.782  -1.005  -0.993  -0.955
23    G         0.001  -0.039  -0.051  -0.059  -0.124  -0.133  -0.129  -0.191  -0.211
24    N         0.001   0.026  -0.028   0.121   0.158   0.074  -0.129  -0.089  -0.174
25    V        -1.113  -1.106  -1.085  -1.323  -1.314  -1.275  -1.005  -0.993  -0.955
26    I         0.001  -0.039  -0.051  -0.096  -0.172  -0.211  -0.129  -0.191  -0.211
27    E         0.001  -0.039  -0.051  -0.134  -0.205  -0.237  -0.129  -0.191  -0.211
28    S         0.001   0.034  -0.023   0.026   0.083  -0.010  -0.129  -0.077  -0.166
29    T        -1.113  -1.106  -1.085  -1.235  -1.231  -1.187  -1.005  -0.993  -0.955
30    G         1.535   1.541   1.561   1.446   1.454   1.491   1.622   1.629   1.653
31    V         0.001   0.026  -0.028  -0.222  -0.190  -0.262  -0.129  -0.089  -0.174
32    G         0.001  -0.039  -0.051  -0.109  -0.171  -0.193  -0.129  -0.191  -0.211
33    S         0.001   0.034  -0.023   0.074   0.123   0.036  -0.129  -0.077  -0.166
34    Q        -1.113  -1.106  -1.085  -1.149  -1.135  -1.102  -1.005  -0.993  -0.955
35    R         0.001  -0.039  -0.051   0.294   0.225   0.194  -0.129  -0.191  -0.211
36    I        -1.113  -1.106  -1.085  -1.183  -1.190  -1.135  -1.005  -0.993  -0.955
37    E         0.001  -0.039  -0.051  -0.010  -0.073  -0.087  -0.129  -0.191  -0.211
38    D         1.535   1.541   1.561   1.419   1.432   1.464   1.622   1.629   1.653
39    I         0.001   0.026  -0.028  -0.096  -0.044  -0.162  -0.129  -0.089  -0.174
40    G        -1.113  -1.106  -1.085  -1.033  -0.999  -0.986  -1.005  -0.993  -0.955
41    D        -1.113  -1.106  -1.085  -1.149  -1.127  -1.102  -1.005  -0.993  -0.955
42    L         1.535   1.541   1.561   1.392   1.399   1.437   1.622   1.629   1.653
43    S         0.001   0.026  -0.028   0.098   0.142   0.051  -0.129  -0.089  -0.174
44    K        -1.113  -1.106  -1.085  -1.033  -1.022  -0.986  -1.005  -0.993  -0.955
45    V         1.535   1.541   1.561   1.310   1.306   1.355   1.622   1.629   1.653
46    T        -1.113  -1.106  -1.085  -0.985  -0.962  -0.938  -1.005  -0.993  -0.955
47    L         0.001  -0.039  -0.051   0.014  -0.035  -0.032  -0.129  -0.191  -0.211
48    D         0.001  -0.039  -0.051  -0.084  -0.144  -0.156  -0.129  -0.191  -0.211
49    A         0.001   0.026  -0.028   0.026   0.075  -0.018  -0.129  -0.089  -0.174
50    E         0.001   0.026  -0.028  -0.121  -0.071  -0.177  -0.129  -0.089  -0.174
51    G         1.535   1.541   1.561   1.446   1.454   1.491   1.622   1.629   1.653
52    F         0.001  -0.039  -0.051   0.145   0.056   0.018  -0.129  -0.191  -0.211
53    A         0.001   0.026  -0.028  -0.059  -0.010  -0.115  -0.129  -0.089  -0.174
54    Q        -1.113  -1.106  -1.085  -1.166  -1.166  -1.118  -1.005  -0.993  -0.955
55    V         0.001   0.034  -0.023  -0.274  -0.222  -0.325  -0.129  -0.077  -0.166
56    Q         0.001   0.034  -0.023  -0.022   0.036  -0.057  -0.129  -0.077  -0.166
57    G        -1.113  -1.106  -1.085  -0.891  -0.882  -0.844  -1.005  -0.993  -0.955
58    D         0.001  -0.039  -0.051  -0.184  -0.250  -0.278  -0.129  -0.191  -0.211
59    S        -1.113  -1.106  -1.085  -1.050  -1.053  -1.002  -1.005  -0.993  -0.955
60    L        -1.113  -1.106  -1.085  -1.166  -1.136  -1.118  -1.005  -0.993  -0.955
61    L        -1.113  -1.106  -1.085  -1.116  -1.087  -1.068  -1.005  -0.993  -0.955
62    V         1.535   1.541   1.561   1.310   1.306   1.355   1.622   1.629   1.653
63    H         0.001   0.026  -0.028   0.203   0.252   0.134  -0.129  -0.089  -0.174
64    L        -1.113  -1.106  -1.085  -1.323  -1.322  -1.275  -1.005  -0.993  -0.955
65    Y         0.001  -0.039  -0.051   0.384   0.326   0.314  -0.129  -0.191  -0.211
66    K         1.535   1.541   1.561   1.605   1.610   1.649   1.622   1.629   1.653
67    R         0.001  -0.039  -0.051   0.294   0.225   0.194  -0.129  -0.191  -0.211
68    N        -1.113  -1.106  -1.085  -1.132  -1.130  -1.085  -1.005  -0.993  -0.955
69    D         0.001  -0.039  -0.051  -0.184  -0.250  -0.278  -0.129  -0.191  -0.211
70    I        -1.113  -1.106  -1.085  -0.969  -0.956  -0.922  -1.005  -0.993  -0.955
71    T         1.535   1.541   1.561   1.683   1.695   1.727   1.622   1.629   1.653
72    L         1.535   1.541   1.561   1.392   1.399   1.437   1.622   1.629   1.653
73    A         0.001  -0.039  -0.051  -0.121  -0.202  -0.235  -0.129  -0.191  -0.211
74    V         1.535   1.541   1.561   1.310   1.306   1.355   1.622   1.629   1.653
75    Y         1.535   1.541   1.561   1.810   1.820   1.854   1.622   1.629   1.653
76    T         1.535   1.541   1.561   1.683   1.695   1.727   1.622   1.629   1.653
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     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    S         1.535   1.541   1.561   1.587   1.596   1.631   1.622   1.629   1.653
82    A        -1.113  -1.106  -1.085  -1.235  -1.219  -1.187  -1.005  -0.993  -0.955
83    Q        -1.113  -1.106  -1.085  -1.033  -1.015  -0.986  -1.005  -0.993  -0.955
* 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/Q3E830
Output conservation file - output/Q3E830
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
