1     M         0.824   0.846   0.894   1.184   1.196   1.215   0.846   0.874   0.940
2     A        -1.425  -1.490  -1.298  -1.781  -1.808  -1.505  -1.531  -1.538  -1.271
3     K         0.824   0.846   0.894   0.624   0.669   0.771   0.846   0.874   0.940
4     R         0.824   0.846   0.894   0.551   0.599   0.713   0.846   0.874   0.940
5     T         0.824   0.846   0.894   0.592   0.635   0.745   0.846   0.874   0.940
6     K         0.824   0.846   0.894   0.624   0.669   0.771   0.846   0.874   0.940
7     K         0.824   0.846   0.894   0.624   0.669   0.771   0.846   0.874   0.940
8     V         0.824   0.846   0.894   0.761   0.800   0.880   0.846   0.874   0.940
9     G         0.824   0.846   0.894   0.689   0.735   0.823   0.846   0.874   0.940
10    I        -0.447  -0.438  -0.463  -0.194  -0.211  -0.375  -0.601  -0.596  -0.668
11    T        -0.013  -0.298  -0.446  -0.086  -0.440  -0.641   0.019  -0.382  -0.641
12    G         0.824   0.846   0.894   0.689   0.735   0.823   0.846   0.874   0.940
13    K         0.824   0.846   0.894   0.624   0.669   0.771   0.846   0.874   0.940
14    Y        -0.447  -0.205  -0.446  -0.091   0.201  -0.168  -0.601  -0.247  -0.641
15    G         0.824   0.846   0.894   0.689   0.735   0.823   0.846   0.874   0.940
16    V        -0.013  -0.298  -0.446   0.049  -0.337  -0.643   0.019  -0.382  -0.641
17    R         0.824   0.846   0.894   0.551   0.599   0.713   0.846   0.874   0.940
18    Y         0.824   0.846   0.894   1.064   1.082   1.120   0.846   0.874   0.940
19    G         0.824   0.846   0.894   0.689   0.735   0.823   0.846   0.874   0.940
20    S        -0.704  -0.733  -0.507  -0.914  -1.056  -0.706  -1.014  -1.079  -0.741
21    S         0.824   0.846   0.894   0.872   0.887   0.967   0.846   0.874   0.940
22    L         0.824   0.846   0.894   1.057   1.066   1.114   0.846   0.874   0.940
23    R         0.824   0.846   0.894   0.551   0.599   0.713   0.846   0.874   0.940
24    R        -0.013  -0.298  -0.446  -0.160  -0.531  -0.782   0.019  -0.382  -0.641
25    Q        -1.213  -1.435  -1.305  -0.667  -0.969  -0.868  -1.221  -1.465  -1.278
26    V        -1.213  -0.923  -1.265  -1.196  -0.776  -1.286  -1.221  -0.842  -1.231
27    K        -0.447  -0.438  -0.463  -0.710  -0.705  -0.795  -0.601  -0.596  -0.668
28    K         0.824   0.846   0.894   0.624   0.669   0.771   0.846   0.874   0.940
29    L        -1.213  -1.435  -1.305  -0.741  -1.054  -0.932  -1.221  -1.465  -1.278
30    E         0.824   0.846   0.894   1.125   1.138   1.168   0.846   0.874   0.940
31    I        -0.447  -0.235  -0.458  -0.420  -0.140  -0.445  -0.601  -0.291  -0.660
32    Q        -0.013  -0.298  -0.446   0.417   0.041  -0.291   0.019  -0.382  -0.641
33    Q         0.824   0.846   0.894   1.094   1.121   1.144   0.846   0.874   0.940
34    H         0.824   0.846   0.894   1.229   1.242   1.250   0.846   0.874   0.940
35    A        -0.704  -0.642  -0.502  -1.038  -0.946  -0.709  -1.014  -0.926  -0.732
36    R        -1.213  -1.031  -1.272  -1.468  -1.174  -1.600  -1.221  -0.963  -1.239
37    Y         0.824   0.846   0.894   1.064   1.082   1.120   0.846   0.874   0.940
38    D        -1.934  -2.128  -1.896  -1.215  -1.578  -1.352  -1.737  -1.901  -1.572
39    C         0.824   0.846   0.894   1.003   1.027   1.072   0.846   0.874   0.940
40    S        -1.564  -1.603  -1.317  -1.458  -1.605  -1.203  -1.634  -1.673  -1.292
41    F         0.824   0.846   0.894   1.221   1.236   1.244   0.846   0.874   0.940
42    C         0.824   0.846   0.894   1.003   1.027   1.072   0.846   0.874   0.940
43    G         0.824   0.846   0.894   0.689   0.735   0.823   0.846   0.874   0.940
44    K        -0.447  -0.438  -0.463  -0.710  -0.705  -0.795  -0.601  -0.596  -0.668
45    K        -2.970  -2.712  -2.347  -2.969  -2.449  -2.049  -2.460  -2.188  -1.743
46    T        -0.013  -0.040  -0.433  -0.069  -0.084  -0.564   0.019  -0.018  -0.619
47    V         0.824   0.846   0.894   0.761   0.800   0.880   0.846   0.874   0.940
48    K        -1.722  -1.518  -1.307  -2.083  -1.836  -1.437  -1.841  -1.594  -1.282
49    R         0.824   0.846   0.894   0.551   0.599   0.713   0.846   0.874   0.940
50    G        -1.213  -1.435  -1.305  -1.290  -1.621  -1.455  -1.221  -1.465  -1.278
51    A        -0.013  -0.298  -0.446  -0.070  -0.411  -0.630   0.019  -0.382  -0.641
52    A        -1.213  -1.169  -1.296  -1.362  -1.356  -1.530  -1.221  -1.217  -1.268
53    G         0.824   0.846   0.894   0.689   0.735   0.823   0.846   0.874   0.940
54    I        -0.013  -0.040  -0.433   0.396   0.355  -0.313   0.019  -0.018  -0.619
55    W         0.824   0.846   0.894   1.221   1.231   1.244   0.846   0.874   0.940
56    T        -2.691  -2.481  -2.336  -2.537  -2.253  -1.977  -2.254  -2.015  -1.735
57    C         0.824   0.846   0.894   1.003   1.027   1.072   0.846   0.874   0.940
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    S        -1.425  -1.121  -1.287  -1.535  -1.186  -1.202  -1.531  -1.180  -1.259
61    C        -2.231  -2.073  -1.894  -2.244  -2.172  -1.817  -2.047  -1.898  -1.571
62    C         0.824   0.846   0.894   1.003   1.027   1.072   0.846   0.874   0.940
63    K        -1.583  -1.449  -1.847  -1.371  -1.199  -1.712  -1.324  -1.176  -1.527
64    K        -0.013  -0.040  -0.433  -0.094  -0.115  -0.734   0.019  -0.018  -0.619
65    T        -0.013  -0.019  -0.422  -0.100  -0.095  -0.650   0.019   0.010  -0.602
66    V        -1.425  -1.426  -1.309  -1.342  -1.318  -1.098  -1.531  -1.515  -1.284
67    A         0.824   0.846   0.894   0.608   0.663   0.758   0.846   0.874   0.940
68    G         0.824   0.846   0.894   0.689   0.735   0.823   0.846   0.874   0.940
69    G         0.824   0.846   0.894   0.689   0.735   0.823   0.846   0.874   0.940
70    A         0.824   0.846   0.894   0.608   0.663   0.758   0.846   0.874   0.940
71    Y        -0.447  -0.438  -0.463  -0.091  -0.103  -0.192  -0.601  -0.596  -0.668
72    T         0.824   0.846   0.894   0.592   0.635   0.745   0.846   0.874   0.940
73    V        -0.013  -0.040  -0.433   0.108   0.087  -0.423   0.019  -0.018  -0.619
74    S        -0.447  -0.438  -0.463  -0.451  -0.478  -0.599  -0.601  -0.596  -0.668
75    T         0.824   0.846   0.894   0.592   0.635   0.745   0.846   0.874   0.940
76    A        -0.013  -0.298  -0.446  -0.014  -0.308  -0.446   0.019  -0.382  -0.641
77    A        -0.013   0.081  -0.424  -0.106   0.030  -0.712   0.019   0.139  -0.605
78    A         0.824   0.846   0.894   0.608   0.663   0.758   0.846   0.874   0.940
79    A        -1.213  -1.132  -1.283  -1.303  -1.217  -1.301  -1.221  -1.129  -1.252
80    T        -1.213  -1.435  -1.305  -1.338  -1.686  -1.501  -1.221  -1.465  -1.278
81    V        -1.213  -1.435  -1.305  -1.159  -1.440  -1.262  -1.221  -1.465  -1.278
82    R         0.824   0.846   0.894   0.551   0.599   0.713   0.846   0.874   0.940
83    S         0.824   0.846   0.894   0.872   0.887   0.967   0.846   0.874   0.940
84    T         0.824   0.846   0.894   0.592   0.635   0.745   0.846   0.874   0.940
85    I        -0.013  -0.298  -0.446   0.432   0.070  -0.221   0.019  -0.382  -0.641
86    R         0.824   0.846   0.894   0.551   0.599   0.713   0.846   0.874   0.940
87    R         0.824   0.846   0.894   0.551   0.599   0.713   0.846   0.874   0.940
88    L         0.824   0.846   0.894   1.057   1.066   1.114   0.846   0.874   0.940
89    R         0.824   0.846   0.894   0.551   0.599   0.713   0.846   0.874   0.940
90    E        -0.704  -0.533  -0.481  -0.406  -0.180  -0.177  -1.014  -0.746  -0.699
91    M        -1.213  -1.311  -1.293  -0.632  -0.775  -0.859  -1.221  -1.307  -1.264
92    V        -1.492  -1.575  -1.308  -1.845  -1.944  -1.545  -1.634  -1.653  -1.282
93    E         0.824   0.846   0.894   1.125   1.138   1.168   0.846   0.874   0.940
94    A        -0.704  -0.733  -0.507  -1.091  -1.151  -0.776  -1.014  -1.079  -0.741
* 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/P0CX26
Output conservation file - output/P0CX26
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
