1     M         0.827   0.829   0.838   1.178   1.177   1.177   0.847   0.849   0.858
2     Q         0.827   0.829   0.838   1.276   1.279   1.270   0.847   0.849   0.858
3     L         0.827   0.829   0.838   0.285   0.293   0.334   0.847   0.849   0.858
4     V        -2.076  -2.043  -1.953  -2.047  -2.001  -1.868  -1.836  -1.789  -1.660
5     L        -0.855  -0.924  -0.908  -0.978  -1.015  -0.933  -0.941  -1.038  -1.008
6     A         0.827   0.829   0.838   0.461   0.469   0.500   0.847   0.849   0.858
7     A         0.827   0.829   0.838   0.461   0.469   0.500   0.847   0.849   0.858
8     K         0.827   0.829   0.838   1.281   1.284   1.274   0.847   0.849   0.858
9     Y         0.827   0.829   0.838   1.255   1.256   1.250   0.847   0.849   0.858
10    I         0.827   0.829   0.838   0.719   0.717   0.744   0.847   0.849   0.858
11    G         0.827   0.829   0.838   0.634   0.633   0.664   0.847   0.849   0.858
12    A         0.827   0.829   0.838   0.461   0.469   0.500   0.847   0.849   0.858
13    G        -0.855  -0.777  -0.889  -0.911  -0.813  -0.943  -0.941  -0.824  -0.980
14    I        -0.855  -0.924  -0.908  -1.101  -1.254  -1.261  -0.941  -1.038  -1.008
15    S        -0.855  -0.808  -0.893  -1.074  -1.010  -1.086  -0.941  -0.867  -0.986
16    T         0.827   0.829   0.838   1.126   1.124   1.128   0.847   0.849   0.858
17    I        -0.855  -0.777  -0.889  -1.101  -0.959  -1.211  -0.941  -0.824  -0.980
18    G         0.827   0.829   0.838   0.634   0.633   0.664   0.847   0.849   0.858
19    L        -0.855  -0.924  -0.908  -1.087  -1.142  -1.074  -0.941  -1.038  -1.008
20    L        -2.076  -2.043  -1.953  -2.260  -2.165  -2.069  -1.836  -1.789  -1.660
21    G         0.827   0.829   0.838   0.634   0.633   0.664   0.847   0.849   0.858
22    A         0.827   0.829   0.838   0.461   0.469   0.500   0.847   0.849   0.858
23    G        -0.855  -0.777  -0.889  -1.143  -1.014  -1.232  -0.941  -0.824  -0.980
24    I        -0.855  -0.924  -0.908  -0.768  -0.863  -0.814  -0.941  -1.038  -1.008
25    G         0.827   0.829   0.838   0.634   0.633   0.664   0.847   0.849   0.858
26    I         0.827   0.829   0.838   0.719   0.717   0.744   0.847   0.849   0.858
27    A        -0.855  -0.924  -0.908  -1.229  -1.349  -1.304  -0.941  -1.038  -1.008
28    I        -0.855  -0.808  -0.893  -1.272  -1.190  -1.300  -0.941  -0.867  -0.986
29    V        -0.855  -0.924  -0.908  -0.605  -0.744  -0.761  -0.941  -1.038  -1.008
30    F         0.827   0.829   0.838   0.967   0.971   0.978   0.847   0.849   0.858
31    A        -2.076  -2.043  -1.953  -1.901  -1.850  -1.731  -1.836  -1.789  -1.660
32    A        -0.855  -0.924  -0.908  -0.925  -0.985  -0.903  -0.941  -1.038  -1.008
33    L         0.827   0.829   0.838   0.371   0.394   0.416   0.847   0.849   0.858
34    I         0.827   0.829   0.838   0.719   0.717   0.744   0.847   0.849   0.858
35    N        -0.855  -0.924  -0.908  -0.366  -0.496  -0.513  -0.941  -1.038  -1.008
36    G         0.827   0.829   0.838   0.634   0.633   0.664   0.847   0.849   0.858
37    V        -0.855  -0.808  -0.893  -0.401  -0.340  -0.488  -0.941  -0.867  -0.986
38    S         0.827   0.829   0.838   0.940   0.941   0.952   0.847   0.849   0.858
39    R         0.827   0.829   0.838   1.255   1.256   1.250   0.847   0.849   0.858
40    N         0.827   0.829   0.838   1.229   1.231   1.226   0.847   0.849   0.858
41    P         0.827   0.829   0.838   1.229   1.231   1.226   0.847   0.849   0.858
42    S         0.827   0.829   0.838   0.940   0.941   0.952   0.847   0.849   0.858
43    I        -2.076  -2.043  -1.953  -2.103  -1.991  -1.922  -1.836  -1.789  -1.660
44    K        -0.855  -0.808  -0.893  -0.195  -0.138  -0.276  -0.941  -0.867  -0.986
45    D        -2.076  -2.043  -1.953  -1.277  -1.232  -1.141  -1.836  -1.789  -1.660
46    T        -0.855  -0.924  -0.908  -0.274  -0.369  -0.345  -0.941  -1.038  -1.008
47    V        -0.855  -0.808  -0.893  -1.087  -1.014  -1.070  -0.941  -0.867  -0.986
48    F         0.827   0.829   0.838   0.967   0.971   0.978   0.847   0.849   0.858
49    P        -0.855  -0.924  -0.908  -0.366  -0.496  -0.513  -0.941  -1.038  -1.008
50    M        -0.855  -0.777  -0.889  -0.263  -0.167  -0.328  -0.941  -0.824  -0.980
51    A         0.827   0.829   0.838   0.461   0.469   0.500   0.847   0.849   0.858
52    I         0.827   0.829   0.838   0.719   0.717   0.744   0.847   0.849   0.858
53    L         0.827   0.829   0.838   0.371   0.394   0.416   0.847   0.849   0.858
54    G         0.827   0.829   0.838   0.634   0.633   0.664   0.847   0.849   0.858
55    F         0.827   0.829   0.838   0.967   0.971   0.978   0.847   0.849   0.858
56    A         0.827   0.829   0.838   0.461   0.469   0.500   0.847   0.849   0.858
57    L         0.827   0.829   0.838   0.371   0.394   0.416   0.847   0.849   0.858
58    S        -0.855  -0.924  -0.908  -0.544  -0.647  -0.618  -0.941  -1.038  -1.008
59    E         0.827   0.829   0.838   1.306   1.308   1.298   0.847   0.849   0.858
60    A         0.827   0.829   0.838   0.461   0.469   0.500   0.847   0.849   0.858
61    T        -0.855  -0.777  -0.889  -0.309  -0.215  -0.367  -0.941  -0.824  -0.980
62    G         0.827   0.829   0.838   0.634   0.633   0.664   0.847   0.849   0.858
63    L         0.827   0.829   0.838   0.371   0.394   0.416   0.847   0.849   0.858
64    F         0.827   0.829   0.838   0.967   0.971   0.978   0.847   0.849   0.858
65    C         0.827   0.829   0.838   1.281   1.285   1.274   0.847   0.849   0.858
66    L         0.827   0.829   0.838   0.371   0.394   0.416   0.847   0.849   0.858
67    M         0.827   0.829   0.838   1.178   1.177   1.177   0.847   0.849   0.858
68    V        -2.076  -2.043  -1.953  -2.103  -2.098  -1.922  -1.836  -1.789  -1.660
69    S        -0.855  -0.924  -0.908  -0.846  -1.002  -1.022  -0.941  -1.038  -1.008
70    F         0.827   0.829   0.838   0.967   0.971   0.978   0.847   0.849   0.858
71    L         0.827   0.829   0.838   0.371   0.394   0.416   0.847   0.849   0.858
72    L        -0.855  -0.924  -0.908  -1.272  -1.367  -1.318  -0.941  -1.038  -1.008
73    L        -0.855  -0.924  -0.908  -1.272  -1.367  -1.318  -0.941  -1.038  -1.008
74    F        -0.855  -0.808  -0.893  -0.332  -0.264  -0.447  -0.941  -0.867  -0.986
75    G        -0.855  -0.808  -0.893  -1.229  -1.156  -1.280  -0.941  -0.867  -0.986
76    V        -0.855  -0.924  -0.908  -0.717  -0.874  -0.913  -0.941  -1.038  -1.008
* 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/P61829
Output conservation file - output/P61829
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
