1     M         1.046   1.053   1.063   1.168   1.170   1.191   1.084   1.090   1.101
2     N        -0.439  -0.503  -0.502  -0.450  -0.537  -0.519  -0.551  -0.645  -0.641
3     A        -0.571  -0.563  -0.529  -0.593  -0.581  -0.524  -0.755  -0.738  -0.683
4     N        -0.439  -0.366  -0.475  -0.533  -0.417  -0.583  -0.551  -0.439  -0.599
5     K         1.046   1.053   1.063   1.051   1.056   1.077   1.084   1.090   1.101
6     Q         1.046   1.053   1.063   0.778   0.796   0.811   1.084   1.090   1.101
7     R         1.046   1.053   1.063   1.225   1.225   1.247   1.084   1.090   1.101
8     Q         1.046   1.053   1.063   0.778   0.796   0.811   1.084   1.090   1.101
9     Y         1.046   1.053   1.063   1.310   1.321   1.330   1.084   1.090   1.101
10    N        -0.439  -0.400  -0.482  -0.423  -0.378  -0.520  -0.551  -0.489  -0.610
11    Q        -1.517  -1.493  -1.460  -1.427  -1.382  -1.335  -1.368  -1.331  -1.277
12    L         1.046   1.053   1.063   0.778   0.798   0.811   1.084   1.090   1.101
13    A         1.046   1.053   1.063   1.168   1.150   1.191   1.084   1.090   1.101
14    H        -1.517  -1.493  -1.460  -1.463  -1.417  -1.370  -1.368  -1.331  -1.277
15    E        -1.517  -1.493  -1.460  -1.555  -1.460  -1.460  -1.368  -1.331  -1.277
16    L         1.046   1.053   1.063   0.778   0.798   0.811   1.084   1.090   1.101
17    R        -1.517  -1.493  -1.460  -1.463  -1.435  -1.370  -1.368  -1.331  -1.277
18    E        -0.439  -0.503  -0.502  -0.645  -0.777  -0.794  -0.551  -0.645  -0.641
19    L         1.046   1.053   1.063   0.778   0.798   0.811   1.084   1.090   1.101
20    Q        -1.517  -1.493  -1.460  -1.669  -1.593  -1.571  -1.368  -1.331  -1.277
21    T        -1.517  -1.493  -1.460  -1.689  -1.632  -1.590  -1.368  -1.331  -1.277
22    N         1.046   1.053   1.063   0.961   0.975   0.990   1.084   1.090   1.101
23    L         1.046   1.053   1.063   0.778   0.798   0.811   1.084   1.090   1.101
24    Q        -1.517  -1.493  -1.460  -1.555  -1.482  -1.460  -1.368  -1.331  -1.277
25    E         1.046   1.053   1.063   1.021   1.030   1.048   1.084   1.090   1.101
26    T         1.046   1.053   1.063   1.139   1.144   1.162   1.084   1.090   1.101
27    T         1.046   1.053   1.063   1.139   1.144   1.162   1.084   1.090   1.101
28    K        -1.517  -1.493  -1.460  -1.374  -1.360  -1.283  -1.368  -1.331  -1.277
29    Q        -0.439  -0.366  -0.475  -0.602  -0.498  -0.621  -0.551  -0.439  -0.599
30    L        -0.439  -0.503  -0.502  -0.630  -0.704  -0.682  -0.551  -0.645  -0.641
31    D        -0.439  -0.503  -0.502  -0.265  -0.401  -0.411  -0.551  -0.645  -0.641
32    I        -0.439  -0.366  -0.475  -0.239  -0.129  -0.314  -0.551  -0.439  -0.599
33    M         1.046   1.053   1.063   1.168   1.170   1.191   1.084   1.090   1.101
34    S        -0.439  -0.503  -0.502  -0.330  -0.450  -0.442  -0.551  -0.645  -0.641
35    K        -0.439  -0.503  -0.502  -0.533  -0.655  -0.659  -0.551  -0.645  -0.641
36    Q         1.046   1.053   1.063   0.778   0.796   0.811   1.084   1.090   1.101
37    C         1.046   1.053   1.063   1.371   1.379   1.388   1.084   1.090   1.101
38    N         1.046   1.053   1.063   0.950   0.959   0.979   1.084   1.090   1.101
39    E        -0.439  -0.503  -0.502  -0.464  -0.564  -0.559  -0.551  -0.645  -0.641
40    N         1.046   1.053   1.063   0.961   0.975   0.990   1.084   1.090   1.101
41    L        -0.439  -0.503  -0.502  -0.688  -0.771  -0.755  -0.551  -0.645  -0.641
42    V        -0.439  -0.503  -0.502  -0.176  -0.291  -0.284  -0.551  -0.645  -0.641
43    G        -0.439  -0.503  -0.502  -0.370  -0.472  -0.482  -0.551  -0.645  -0.641
44    Q        -0.439  -0.503  -0.502  -0.746  -0.840  -0.830  -0.551  -0.645  -0.641
45    L         1.046   1.053   1.063   0.778   0.798   0.811   1.084   1.090   1.101
46    G         1.046   1.053   1.063   1.139   1.158   1.162   1.084   1.090   1.101
47    K        -0.439  -0.503  -0.502  -0.437  -0.557  -0.535  -0.551  -0.645  -0.641
48    V         1.046   1.053   1.063   1.282   1.283   1.302   1.084   1.090   1.101
49    H        -1.517  -1.493  -1.460  -1.593  -1.573  -1.496  -1.368  -1.331  -1.277
50    G        -1.517  -1.493  -1.460  -1.356  -1.327  -1.266  -1.368  -1.331  -1.277
51    S         1.046   1.053   1.063   1.168   1.179   1.191   1.084   1.090   1.101
52    W        -0.439  -0.503  -0.502  -0.113  -0.236  -0.255  -0.551  -0.645  -0.641
53    L        -0.439  -0.503  -0.502  -0.574  -0.638  -0.610  -0.551  -0.645  -0.641
54    I         1.046   1.053   1.063   1.282   1.282   1.302   1.084   1.090   1.101
55    G         1.046   1.053   1.063   1.139   1.158   1.162   1.084   1.090   1.101
56    S         1.046   1.053   1.063   1.168   1.179   1.191   1.084   1.090   1.101
57    Y        -1.517  -1.493  -1.460  -1.374  -1.354  -1.283  -1.368  -1.331  -1.277
58    I        -0.439  -0.400  -0.482  -0.227  -0.179  -0.297  -0.551  -0.489  -0.610
59    Y        -1.517  -1.493  -1.460  -1.056  -1.028  -0.974  -1.368  -1.331  -1.277
60    Y        -0.439  -0.400  -0.482  -0.063  -0.009  -0.145  -0.551  -0.489  -0.610
61    M        -0.439  -0.400  -0.482  -0.464  -0.407  -0.528  -0.551  -0.489  -0.610
62    E        -0.439  -0.400  -0.482  -0.265  -0.205  -0.367  -0.551  -0.489  -0.610
63    Q        -0.439  -0.503  -0.502  -0.760  -0.855  -0.849  -0.551  -0.645  -0.641
64    M         1.046   1.053   1.063   1.168   1.170   1.191   1.084   1.090   1.101
65    L         1.046   1.053   1.063   0.778   0.798   0.811   1.084   1.090   1.101
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    G         1.046   1.053   1.063   1.037   1.045   1.063   1.084   1.090   1.101
68    K        -0.571  -0.563  -0.529  -0.718  -0.705  -0.645  -0.755  -0.738  -0.683
69    T        -1.517  -1.493  -1.460  -1.518  -1.483  -1.423  -1.368  -1.331  -1.277
70    Q        -0.439  -0.400  -0.482  -0.616  -0.543  -0.722  -0.551  -0.489  -0.610
* 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/P69852
Output conservation file - output/P69852
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
