1     M         0.970   0.971   0.984   1.240   1.244   1.255   1.001   1.002   1.016
2     S         0.970   0.971   0.984   0.766   0.770   0.793   1.001   1.002   1.016
3     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     L        -0.438  -0.418  -0.489  -0.396  -0.322  -0.525  -0.567  -0.536  -0.641
6     Y         0.970   0.971   0.984   1.135   1.139   1.153   1.001   1.002   1.016
7     K         0.970   0.971   0.984   0.859   0.855   0.883   1.001   1.002   1.016
8     -        -0.563  -0.561  -0.531  -0.988  -0.996  -0.920  -0.763  -0.759  -0.705
9     Q        -1.459  -1.455  -1.416  -1.383  -1.391  -1.305  -1.351  -1.344  -1.279
10    S        -1.459  -1.455  -1.416  -1.482  -1.445  -1.401  -1.351  -1.344  -1.279
11    T        -1.459  -1.455  -1.416  -1.355  -1.331  -1.278  -1.351  -1.344  -1.279
12    N        -0.438  -0.468  -0.502  -0.273  -0.322  -0.375  -0.567  -0.613  -0.660
13    F        -1.459  -1.455  -1.416  -1.287  -1.282  -1.211  -1.351  -1.344  -1.279
14    T         0.970   0.971   0.984   0.882   0.871   0.906   1.001   1.002   1.016
15    H         0.970   0.971   0.984   1.289   1.293   1.304   1.001   1.002   1.016
16    S         0.970   0.971   0.984   0.929   0.982   0.952   1.001   1.002   1.016
17    T         0.970   0.971   0.984   0.882   0.871   0.906   1.001   1.002   1.016
18    G         0.970   0.971   0.984   0.952   0.947   0.975   1.001   1.002   1.016
19    S         0.970   0.971   0.984   0.929   0.982   0.952   1.001   1.002   1.016
20    F         0.970   0.971   0.984   1.246   1.250   1.261   1.001   1.002   1.016
21    L         0.970   0.971   0.984   0.763   0.759   0.790   1.001   1.002   1.016
22    Q        -0.438  -0.418  -0.490  -0.334  -0.304  -0.418  -0.567  -0.536  -0.642
23    S         0.970   0.971   0.984   0.929   0.982   0.952   1.001   1.002   1.016
24    A         0.970   0.971   0.984   1.090   1.092   1.109   1.001   1.002   1.016
25    P         0.970   0.971   0.984   1.311   1.314   1.325   1.001   1.002   1.016
26    V         0.970   0.971   0.984   1.067   1.070   1.087   1.001   1.002   1.016
27    E         0.970   0.971   0.984   0.906   0.897   0.929   1.001   1.002   1.016
28    L         0.970   0.971   0.984   0.763   0.759   0.790   1.001   1.002   1.016
29    T         0.970   0.971   0.984   0.882   0.871   0.906   1.001   1.002   1.016
30    T        -0.438  -0.418  -0.490  -0.620  -0.579  -0.708  -0.567  -0.536  -0.642
31    V        -1.459  -1.455  -1.416  -1.453  -1.470  -1.373  -1.351  -1.344  -1.279
32    S        -0.438  -0.418  -0.489  -0.642  -0.594  -0.727  -0.567  -0.536  -0.641
33    G         0.970   0.971   0.984   0.952   0.947   0.975   1.001   1.002   1.016
34    Y         0.970   0.971   0.984   1.135   1.139   1.153   1.001   1.002   1.016
35    Q        -0.438  -0.468  -0.502  -0.437  -0.505  -0.570  -0.567  -0.613  -0.660
36    E        -0.438  -0.418  -0.490  -0.480  -0.462  -0.543  -0.567  -0.536  -0.642
37    F         0.970   0.971   0.984   1.246   1.250   1.261   1.001   1.002   1.016
38    L        -1.459  -1.455  -1.416  -1.369  -1.333  -1.291  -1.351  -1.344  -1.279
39    K        -0.438  -0.418  -0.489  -0.458  -0.427  -0.569  -0.567  -0.536  -0.641
40    K         0.970   0.971   0.984   0.859   0.855   0.883   1.001   1.002   1.016
41    Q         0.970   0.971   0.984   1.090   1.092   1.109   1.001   1.002   1.016
42    E        -0.438  -0.418  -0.490  -0.631  -0.612  -0.729  -0.567  -0.536  -0.642
43    K         0.970   0.971   0.984   0.859   0.855   0.883   1.001   1.002   1.016
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    K        -1.459  -1.455  -1.416  -1.645  -1.635  -1.560  -1.351  -1.344  -1.279
50    N        -1.459  -1.455  -1.416  -1.369  -1.333  -1.291  -1.351  -1.344  -1.279
51    Y        -1.459  -1.455  -1.416  -1.355  -1.364  -1.278  -1.351  -1.344  -1.279
52    E        -1.459  -1.455  -1.416  -1.584  -1.600  -1.501  -1.351  -1.344  -1.279
53    I        -0.438  -0.418  -0.490  -0.243  -0.209  -0.345  -0.567  -0.536  -0.642
54    Q        -0.438  -0.418  -0.489  -0.544  -0.529  -0.613  -0.567  -0.536  -0.641
55    T         0.970   0.971   0.984   0.882   0.871   0.906   1.001   1.002   1.016
56    V        -1.459  -1.455  -1.416  -1.260  -1.251  -1.185  -1.351  -1.344  -1.279
57    L         0.970   0.971   0.984   0.763   0.759   0.790   1.001   1.002   1.016
58    S        -0.438  -0.468  -0.502  -0.609  -0.626  -0.733  -0.567  -0.613  -0.660
59    E         0.970   0.971   0.984   0.906   0.897   0.929   1.001   1.002   1.016
60    D        -0.438  -0.468  -0.502  -0.354  -0.420  -0.496  -0.567  -0.613  -0.660
61    K        -0.438  -0.468  -0.502  -0.458  -0.505  -0.515  -0.567  -0.613  -0.660
62    S        -0.438  -0.468  -0.502  -0.598  -0.618  -0.718  -0.567  -0.613  -0.660
63    H        -1.459  -1.455  -1.416  -1.328  -1.343  -1.251  -1.351  -1.344  -1.279
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    G         0.970   0.971   0.984   0.952   0.947   0.975   1.001   1.002   1.016
66    Y         0.970   0.971   0.984   1.135   1.139   1.153   1.001   1.002   1.016
67    V        -0.438  -0.468  -0.502  -0.522  -0.592  -0.672  -0.567  -0.613  -0.660
68    L         0.970   0.971   0.984   0.763   0.759   0.790   1.001   1.002   1.016
69    K        -1.459  -1.455  -1.416  -1.260  -1.244  -1.185  -1.351  -1.344  -1.279
70    D         0.970   0.971   0.984   1.179   1.185   1.196   1.001   1.002   1.016
71    G        -0.438  -0.418  -0.490  -0.555  -0.507  -0.649  -0.567  -0.536  -0.642
72    E         0.970   0.971   0.984   0.906   0.897   0.929   1.001   1.002   1.016
73    V         0.970   0.971   0.984   1.067   1.070   1.087   1.001   1.002   1.016
74    I        -1.459  -1.455  -1.416  -1.453  -1.451  -1.373  -1.351  -1.344  -1.279
75    A         0.970   0.971   0.984   1.090   1.092   1.109   1.001   1.002   1.016
76    N        -0.438  -0.418  -0.489  -0.522  -0.507  -0.587  -0.567  -0.536  -0.641
77    I        -0.438  -0.418  -0.489  -0.313  -0.285  -0.385  -0.567  -0.536  -0.641
78    I        -1.459  -1.455  -1.416  -1.341  -1.309  -1.264  -1.351  -1.344  -1.279
79    G         0.970   0.971   0.984   0.952   0.947   0.975   1.001   1.002   1.016
80    E         0.970   0.971   0.984   0.906   0.897   0.929   1.001   1.002   1.016
81    A        -0.438  -0.468  -0.502  -0.501  -0.572  -0.652  -0.567  -0.613  -0.660
82    K         0.970   0.971   0.984   0.859   0.855   0.883   1.001   1.002   1.016
83    D        -0.438  -0.468  -0.502  -0.273  -0.327  -0.391  -0.567  -0.613  -0.660
84    Y        -0.438  -0.468  -0.502  -0.223  -0.269  -0.311  -0.567  -0.613  -0.660
85    L         0.970   0.971   0.984   0.763   0.759   0.790   1.001   1.002   1.016
86    L         0.970   0.971   0.984   0.763   0.759   0.790   1.001   1.002   1.016
87    D        -1.459  -1.455  -1.416  -1.411  -1.422  -1.332  -1.351  -1.344  -1.279
88    L        -0.438  -0.468  -0.502  -0.654  -0.709  -0.729  -0.567  -0.613  -0.660
89    A        -1.459  -1.455  -1.416  -1.554  -1.536  -1.472  -1.351  -1.344  -1.279
90    G        -0.438  -0.468  -0.502  -0.566  -0.638  -0.685  -0.567  -0.613  -0.660
91    Q        -1.459  -1.455  -1.416  -1.525  -1.537  -1.444  -1.351  -1.344  -1.279
92    A        -1.459  -1.455  -1.416  -1.234  -1.201  -1.159  -1.351  -1.344  -1.279
* 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/O43137
Output conservation file - output/O43137
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
