1     M         1.096   1.096   1.096   1.496   1.496   1.496   1.096   1.096   1.096
2     N        -0.899  -0.899  -0.899  -0.487  -0.487  -0.487  -0.899  -0.899  -0.899
3     R        -0.899  -0.899  -0.899  -0.459  -0.459  -0.459  -0.899  -0.899  -0.899
4     F         1.096   1.096   1.096   1.177   1.177   1.177   1.096   1.096   1.096
5     V        -0.899  -0.899  -0.899  -0.935  -0.935  -0.935  -0.899  -0.899  -0.899
6     I         1.096   1.096   1.096   0.926   0.926   0.926   1.096   1.096   1.096
7     I         1.096   1.096   1.096   0.926   0.926   0.926   1.096   1.096   1.096
8     C        -0.899  -0.899  -0.899  -0.998  -0.998  -0.998  -0.899  -0.899  -0.899
9     L        -0.899  -0.899  -0.899  -1.031  -1.031  -1.031  -0.899  -0.899  -0.899
10    L         1.096   1.096   1.096   0.434   0.434   0.434   1.096   1.096   1.096
11    F         1.096   1.096   1.096   1.177   1.177   1.177   1.096   1.096   1.096
12    T        -0.899  -0.899  -0.899  -0.872  -0.872  -0.872  -0.899  -0.899  -0.899
13    Y         1.096   1.096   1.096   1.418   1.418   1.418   1.096   1.096   1.096
14    Y         1.096   1.096   1.096   1.418   1.418   1.418   1.096   1.096   1.096
15    V        -0.899  -0.899  -0.899  -0.602  -0.602  -0.602  -0.899  -0.899  -0.899
16    I        -0.899  -0.899  -0.899  -1.031  -1.031  -1.031  -0.899  -0.899  -0.899
17    W         1.096   1.096   1.096   1.496   1.496   1.496   1.096   1.096   1.096
18    S        -0.899  -0.899  -0.899  -1.369  -1.369  -1.369  -0.899  -0.899  -0.899
19    L         1.096   1.096   1.096   0.434   0.434   0.434   1.096   1.096   1.096
20    L         1.096   1.096   1.096   0.434   0.434   0.434   1.096   1.096   1.096
21    P         1.096   1.096   1.096   1.258   1.258   1.258   1.096   1.096   1.096
22    I         1.096   1.096   1.096   0.926   0.926   0.926   1.096   1.096   1.096
23    F         1.096   1.096   1.096   1.177   1.177   1.177   1.096   1.096   1.096
24    E        -0.899  -0.899  -0.899  -0.321  -0.321  -0.321  -0.899  -0.899  -0.899
25    I        -0.899  -0.899  -0.899  -1.477  -1.477  -1.477  -0.899  -0.899  -0.899
26    E        -0.899  -0.899  -0.899  -0.321  -0.321  -0.321  -0.899  -0.899  -0.899
27    N        -0.899  -0.899  -0.899  -0.321  -0.321  -0.321  -0.899  -0.899  -0.899
28    S        -0.899  -0.899  -0.899  -0.720  -0.720  -0.720  -0.899  -0.899  -0.899
29    N        -0.899  -0.899  -0.899  -0.690  -0.690  -0.690  -0.899  -0.899  -0.899
30    P        -0.899  -0.899  -0.899  -0.750  -0.750  -0.750  -0.899  -0.899  -0.899
31    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    L         1.096   1.096   1.096   0.434   0.434   0.434   1.096   1.096   1.096
36    F         1.096   1.096   1.096   1.177   1.177   1.177   1.096   1.096   1.096
37    P         1.096   1.096   1.096   1.258   1.258   1.258   1.096   1.096   1.096
38    I        -0.899  -0.899  -0.899  -1.477  -1.477  -1.477  -0.899  -0.899  -0.899
39    S         1.096   1.096   1.096   1.053   1.053   1.053   1.096   1.096   1.096
40    S         1.096   1.096   1.096   1.053   1.053   1.053   1.096   1.096   1.096
41    N        -0.899  -0.899  -0.899  -0.321  -0.321  -0.321  -0.899  -0.899  -0.899
42    V        -0.899  -0.899  -0.899  -0.661  -0.661  -0.661  -0.899  -0.899  -0.899
43    A         1.096   1.096   1.096   1.457   1.457   1.457   1.096   1.096   1.096
44    I        -0.899  -0.899  -0.899  -1.031  -1.031  -1.031  -0.899  -0.899  -0.899
45    F        -0.899  -0.899  -0.899  -0.573  -0.573  -0.573  -0.899  -0.899  -0.899
46    L        -0.899  -0.899  -0.899  -1.477  -1.477  -1.477  -0.899  -0.899  -0.899
47    P         1.096   1.096   1.096   1.258   1.258   1.258   1.096   1.096   1.096
48    I         1.096   1.096   1.096   0.926   0.926   0.926   1.096   1.096   1.096
49    F        -0.899  -0.899  -0.899  -1.264  -1.264  -1.264  -0.899  -0.899  -0.899
50    L         1.096   1.096   1.096   0.434   0.434   0.434   1.096   1.096   1.096
51    L         1.096   1.096   1.096   0.434   0.434   0.434   1.096   1.096   1.096
52    L         1.096   1.096   1.096   0.434   0.434   0.434   1.096   1.096   1.096
53    I        -0.899  -0.899  -0.899  -1.477  -1.477  -1.477  -0.899  -0.899  -0.899
54    G         1.096   1.096   1.096   1.378   1.378   1.378   1.096   1.096   1.096
55    F        -0.899  -0.899  -0.899  -0.690  -0.690  -0.690  -0.899  -0.899  -0.899
56    T        -0.899  -0.899  -0.899  -0.780  -0.780  -0.780  -0.899  -0.899  -0.899
57    L        -0.899  -0.899  -0.899  -1.477  -1.477  -1.477  -0.899  -0.899  -0.899
58    T        -0.899  -0.899  -0.899  -0.811  -0.811  -0.811  -0.899  -0.899  -0.899
59    G         1.096   1.096   1.096   1.378   1.378   1.378   1.096   1.096   1.096
60    S        -0.899  -0.899  -0.899  -0.780  -0.780  -0.780  -0.899  -0.899  -0.899
61    V        -0.899  -0.899  -0.899  -0.935  -0.935  -0.935  -0.899  -0.899  -0.899
62    L        -0.899  -0.899  -0.899  -1.404  -1.404  -1.404  -0.899  -0.899  -0.899
63    G        -0.899  -0.899  -0.899  -0.376  -0.376  -0.376  -0.899  -0.899  -0.899
64    V         1.096   1.096   1.096   1.011   1.011   1.011   1.096   1.096   1.096
65    L        -0.899  -0.899  -0.899  -0.998  -0.998  -0.998  -0.899  -0.899  -0.899
66    L         1.096   1.096   1.096   0.434   0.434   0.434   1.096   1.096   1.096
67    I        -0.899  -0.899  -0.899  -0.661  -0.661  -0.661  -0.899  -0.899  -0.899
68    R        -0.899  -0.899  -0.899  -0.348  -0.348  -0.348  -0.899  -0.899  -0.899
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    S         1.096   1.096   1.096   1.053   1.053   1.053   1.096   1.096   1.096
72    D         1.096   1.096   1.096   1.378   1.378   1.378   1.096   1.096   1.096
73    K        -0.899  -0.899  -0.899  -0.750  -0.750  -0.750  -0.899  -0.899  -0.899
74    K        -0.899  -0.899  -0.899  -0.573  -0.573  -0.573  -0.899  -0.899  -0.899
75    K         1.096   1.096   1.096   1.299   1.299   1.299   1.096   1.096   1.096
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    K        -0.899  -0.899  -0.899  -0.487  -0.487  -0.487  -0.899  -0.899  -0.899
85    V        -0.899  -0.899  -0.899  -0.811  -0.811  -0.811  -0.899  -0.899  -0.899
* 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/Q2V2P5
Output conservation file - output/Q2V2P5
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
