1     M         1.596   1.601   1.624   1.788   1.786   1.833   1.695   1.701   1.729
2     S         0.003  -0.041  -0.046  -0.061  -0.127  -0.141  -0.122  -0.191  -0.199
3     D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     K         1.596   1.601   1.624   1.536   1.546   1.582   1.695   1.701   1.729
5     P         1.596   1.601   1.624   1.670   1.680   1.715   1.695   1.701   1.729
6     D        -0.138  -0.135  -0.109  -0.357  -0.354  -0.308  -0.349  -0.342  -0.300
7     S        -0.138  -0.135  -0.109  -0.492  -0.490  -0.442  -0.349  -0.342  -0.300
8     Q        -1.153  -1.146  -1.123  -1.044  -1.024  -0.993  -1.030  -1.018  -0.976
9     V        -1.153  -1.146  -1.123  -1.252  -1.241  -1.201  -1.030  -1.018  -0.976
10    F        -1.153  -1.146  -1.123  -1.062  -1.061  -1.012  -1.030  -1.018  -0.976
11    C         1.596   1.601   1.624   1.577   1.588   1.623   1.695   1.701   1.729
12    P         1.596   1.601   1.624   1.608   1.612   1.653   1.695   1.701   1.729
13    N         0.003   0.031  -0.023  -0.076  -0.014  -0.129  -0.122  -0.078  -0.163
14    C         1.596   1.601   1.624   1.577   1.588   1.623   1.695   1.701   1.729
15    N        -1.153  -1.146  -1.123  -1.062  -1.034  -1.012  -1.030  -1.018  -0.976
16    E         0.003   0.039  -0.021  -0.061  -0.007  -0.108  -0.122  -0.065  -0.158
17    R        -1.153  -1.146  -1.123  -1.311  -1.303  -1.260  -1.030  -1.018  -0.976
18    L         1.596   1.601   1.624   1.453   1.464   1.499   1.695   1.701   1.729
19    Q         0.003  -0.041  -0.046   0.105   0.048   0.043  -0.122  -0.191  -0.199
20    K         0.003   0.031  -0.023  -0.061  -0.016  -0.113  -0.122  -0.078  -0.163
21    C         0.003  -0.041  -0.046   0.036  -0.031  -0.032  -0.122  -0.191  -0.199
22    L         0.003  -0.041  -0.046  -0.090  -0.160  -0.153  -0.122  -0.191  -0.199
23    V         0.003   0.031  -0.023  -0.005   0.039  -0.055  -0.122  -0.078  -0.163
24    Q         0.003  -0.041  -0.046  -0.033  -0.101  -0.122  -0.122  -0.191  -0.199
25    Q         0.003  -0.041  -0.046   0.050  -0.015  -0.022  -0.122  -0.191  -0.199
26    N         0.003  -0.041  -0.046  -0.147  -0.219  -0.237  -0.122  -0.191  -0.199
27    Y         0.003  -0.041  -0.046   0.265   0.192   0.194  -0.122  -0.191  -0.199
28    A         1.596   1.601   1.624   1.728   1.733   1.773   1.695   1.701   1.729
29    I         0.003   0.031  -0.023  -0.019   0.020  -0.066  -0.122  -0.078  -0.163
30    I        -1.153  -1.146  -1.123  -1.008  -1.009  -0.957  -1.030  -1.018  -0.976
31    I         0.003  -0.041  -0.046   0.077   0.004   0.004  -0.122  -0.191  -0.199
32    C         1.596   1.601   1.624   1.577   1.588   1.623   1.695   1.701   1.729
33    P        -1.153  -1.146  -1.123  -0.954  -0.952  -0.903  -1.030  -1.018  -0.976
34    S         0.003   0.031  -0.023  -0.147  -0.092  -0.196  -0.122  -0.078  -0.163
35    L        -1.153  -1.146  -1.123  -1.213  -1.198  -1.162  -1.030  -1.018  -0.976
36    V        -1.153  -1.146  -1.123  -1.062  -1.067  -1.012  -1.030  -1.018  -0.976
37    C         1.596   1.601   1.624   1.577   1.588   1.623   1.695   1.701   1.729
38    G        -1.153  -1.146  -1.123  -0.901  -0.896  -0.850  -1.030  -1.018  -0.976
39    Y         1.596   1.601   1.624   1.788   1.798   1.833   1.695   1.701   1.729
40    P         1.596   1.601   1.624   1.608   1.612   1.653   1.695   1.701   1.729
41    F         1.596   1.601   1.624   1.817   1.826   1.862   1.695   1.701   1.729
42    N         1.596   1.601   1.624   1.516   1.533   1.561   1.695   1.701   1.729
43    Q        -1.153  -1.146  -1.123  -1.062  -1.030  -1.012  -1.030  -1.018  -0.976
44    R        -1.153  -1.146  -1.123  -1.213  -1.201  -1.162  -1.030  -1.018  -0.976
45    E         0.003  -0.041  -0.046   0.077  -0.002   0.011  -0.122  -0.191  -0.199
46    V        -1.153  -1.146  -1.123  -0.989  -0.978  -0.939  -1.030  -1.018  -0.976
47    L         0.003   0.031  -0.023  -0.076  -0.025  -0.134  -0.122  -0.078  -0.163
48    E         0.003   0.039  -0.021  -0.076  -0.020  -0.124  -0.122  -0.065  -0.158
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    N         0.003   0.039  -0.021  -0.090  -0.025  -0.126  -0.122  -0.065  -0.158
51    L         1.596   1.601   1.624   1.453   1.464   1.499   1.695   1.701   1.729
52    T        -1.153  -1.146  -1.123  -1.062  -1.058  -1.012  -1.030  -1.018  -0.976
53    Y         0.003   0.039  -0.021   0.225   0.279   0.188  -0.122  -0.065  -0.158
54    V         0.003   0.039  -0.021  -0.019   0.033  -0.061  -0.122  -0.065  -0.158
55    D        -1.153  -1.146  -1.123  -1.156  -1.146  -1.105  -1.030  -1.018  -0.976
56    D         0.003  -0.041  -0.046   0.132   0.063   0.062  -0.122  -0.191  -0.199
57    N        -1.153  -1.146  -1.123  -1.252  -1.236  -1.201  -1.030  -1.018  -0.976
58    D         0.003  -0.041  -0.046   0.022  -0.057  -0.069  -0.122  -0.191  -0.199
59    V        -1.153  -1.146  -1.123  -1.232  -1.235  -1.181  -1.030  -1.018  -0.976
60    L         1.596   1.601   1.624   1.453   1.464   1.499   1.695   1.701   1.729
61    K        -1.153  -1.146  -1.123  -1.194  -1.189  -1.143  -1.030  -1.018  -0.976
62    V         0.003   0.031  -0.023   0.077   0.115   0.025  -0.122  -0.078  -0.163
63    A         0.003  -0.041  -0.046   0.050  -0.037  -0.050  -0.122  -0.191  -0.199
64    K         0.003  -0.041  -0.046   0.009  -0.056  -0.058  -0.122  -0.191  -0.199
65    K         0.003   0.039  -0.021  -0.118  -0.055  -0.163  -0.122  -0.065  -0.158
66    R         0.003  -0.041  -0.046  -0.019  -0.095  -0.105  -0.122  -0.191  -0.199
67    L         0.003  -0.041  -0.046  -0.176  -0.254  -0.257  -0.122  -0.191  -0.199
68    S        -1.153  -1.146  -1.123  -1.232  -1.226  -1.181  -1.030  -1.018  -0.976
69    S        -1.153  -1.146  -1.123  -1.156  -1.144  -1.105  -1.030  -1.018  -0.976
70    R        -1.153  -1.146  -1.123  -1.156  -1.156  -1.105  -1.030  -1.018  -0.976
71    S         0.003   0.039  -0.021  -0.090  -0.021  -0.131  -0.122  -0.065  -0.158
72    K         0.003   0.031  -0.023  -0.061  -0.016  -0.113  -0.122  -0.078  -0.163
73    P        -1.153  -1.146  -1.123  -1.008  -0.989  -0.957  -1.030  -1.018  -0.976
* 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/Q3E7A8
Output conservation file - output/Q3E7A8
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
