1     M         1.244   1.244   1.244   1.599   1.599   1.599   1.244   1.244   1.244
2     S        -0.794  -0.794  -0.794  -0.687  -0.687  -0.687  -0.794  -0.794  -0.794
3     L        -0.794  -0.794  -0.794  -1.018  -1.018  -1.018  -0.794  -0.794  -0.794
4     R        -0.794  -0.794  -0.794  -0.462  -0.462  -0.462  -0.794  -0.794  -0.794
5     N        -0.794  -0.794  -0.794  -0.834  -0.834  -0.834  -0.794  -0.794  -0.794
6     I         1.244   1.244   1.244   1.169   1.169   1.169   1.244   1.244   1.244
7     S        -0.794  -0.794  -0.794  -1.081  -1.081  -1.081  -0.794  -0.794  -0.794
8     M        -0.794  -0.794  -0.794  -0.434  -0.434  -0.434  -0.794  -0.794  -0.794
9     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    L         1.244   1.244   1.244   1.329   1.329   1.329   1.244   1.244   1.244
14    Q        -0.794  -0.794  -0.794  -0.434  -0.434  -0.434  -0.794  -0.794  -0.794
15    T         1.244   1.244   1.244   0.794   0.794   0.794   1.244   1.244   1.244
16    T        -0.794  -0.794  -0.794  -1.344  -1.344  -1.344  -0.794  -0.794  -0.794
17    A        -0.794  -0.794  -0.794  -0.834  -0.834  -0.834  -0.794  -0.794  -0.794
18    K         1.244   1.244   1.244   1.129   1.129   1.129   1.244   1.244   1.244
19    C         1.244   1.244   1.244   1.561   1.561   1.561   1.244   1.244   1.244
20    Y         1.244   1.244   1.244   1.485   1.485   1.485   1.244   1.244   1.244
21    V        -0.794  -0.794  -0.794  -0.895  -0.895  -0.895  -0.794  -0.794  -0.794
22    P         1.244   1.244   1.244   1.329   1.329   1.329   1.244   1.244   1.244
23    K         1.244   1.244   1.244   1.129   1.129   1.129   1.244   1.244   1.244
24    S        -0.794  -0.794  -0.794  -1.081  -1.081  -1.081  -0.794  -0.794  -0.794
25    S        -0.794  -0.794  -0.794  -1.344  -1.344  -1.344  -0.794  -0.794  -0.794
26    P        -0.794  -0.794  -0.794  -0.745  -0.745  -0.745  -0.794  -0.794  -0.794
27    T        -0.794  -0.794  -0.794  -1.178  -1.178  -1.178  -0.794  -0.794  -0.794
28    S         1.244   1.244   1.244   0.921   0.921   0.921   1.244   1.244   1.244
29    T         1.244   1.244   1.244   0.794   0.794   0.794   1.244   1.244   1.244
30    T         1.244   1.244   1.244   0.794   0.794   0.794   1.244   1.244   1.244
31    I        -0.794  -0.794  -0.794  -0.517  -0.517  -0.517  -0.794  -0.794  -0.794
32    P         1.244   1.244   1.244   1.329   1.329   1.329   1.244   1.244   1.244
33    V        -0.794  -0.794  -0.794  -0.925  -0.925  -0.925  -0.794  -0.794  -0.794
34    I        -0.794  -0.794  -0.794  -0.630  -0.630  -0.630  -0.794  -0.794  -0.794
35    R        -0.794  -0.794  -0.794  -0.545  -0.545  -0.545  -0.794  -0.794  -0.794
36    D        -0.794  -0.794  -0.794  -0.407  -0.407  -0.407  -0.794  -0.794  -0.794
37    A        -0.794  -0.794  -0.794  -0.925  -0.925  -0.925  -0.794  -0.794  -0.794
38    S        -0.794  -0.794  -0.794  -0.925  -0.925  -0.925  -0.794  -0.794  -0.794
39    T        -0.794  -0.794  -0.794  -0.775  -0.775  -0.775  -0.794  -0.794  -0.794
40    T        -0.794  -0.794  -0.794  -1.018  -1.018  -1.018  -0.794  -0.794  -0.794
41    Q         1.244   1.244   1.244   1.485   1.485   1.485   1.244   1.244   1.244
42    C        -0.794  -0.794  -0.794  -0.353  -0.353  -0.353  -0.794  -0.794  -0.794
43    R        -0.794  -0.794  -0.794  -0.687  -0.687  -0.687  -0.794  -0.794  -0.794
44    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    N        -0.794  -0.794  -0.794  -0.925  -0.925  -0.925  -0.794  -0.794  -0.794
51    I        -0.794  -0.794  -0.794  -0.630  -0.630  -0.630  -0.794  -0.794  -0.794
52    T        -0.794  -0.794  -0.794  -1.018  -1.018  -1.018  -0.794  -0.794  -0.794
53    S         1.244   1.244   1.244   0.921   0.921   0.921   1.244   1.244   1.244
54    L        -0.794  -0.794  -0.794  -0.775  -0.775  -0.775  -0.794  -0.794  -0.794
55    K        -0.794  -0.794  -0.794  -0.687  -0.687  -0.687  -0.794  -0.794  -0.794
56    G        -0.794  -0.794  -0.794  -0.326  -0.326  -0.326  -0.794  -0.794  -0.794
57    Y         1.244   1.244   1.244   1.485   1.485   1.485   1.244   1.244   1.244
58    S         1.244   1.244   1.244   0.921   0.921   0.921   1.244   1.244   1.244
59    P        -0.794  -0.794  -0.794  -0.517  -0.517  -0.517  -0.794  -0.794  -0.794
60    S        -0.794  -0.794  -0.794  -0.834  -0.834  -0.834  -0.794  -0.794  -0.794
61    P        -0.794  -0.794  -0.794  -0.630  -0.630  -0.630  -0.794  -0.794  -0.794
62    R        -0.794  -0.794  -0.794  -0.462  -0.462  -0.462  -0.794  -0.794  -0.794
63    T        -0.794  -0.794  -0.794  -1.018  -1.018  -1.018  -0.794  -0.794  -0.794
64    V        -0.794  -0.794  -0.794  -0.925  -0.925  -0.925  -0.794  -0.794  -0.794
65    H        -0.794  -0.794  -0.794  -0.380  -0.380  -0.380  -0.794  -0.794  -0.794
66    D         1.244   1.244   1.244   1.407   1.407   1.407   1.244   1.244   1.244
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    K        -0.794  -0.794  -0.794  -0.687  -0.687  -0.687  -0.794  -0.794  -0.794
72    P         1.244   1.244   1.244   1.329   1.329   1.329   1.244   1.244   1.244
73    I        -0.794  -0.794  -0.794  -1.145  -1.145  -1.145  -0.794  -0.794  -0.794
74    V         1.244   1.244   1.244   1.129   1.129   1.129   1.244   1.244   1.244
75    I         1.244   1.244   1.244   1.169   1.169   1.169   1.244   1.244   1.244
76    C        -0.794  -0.794  -0.794  -0.745  -0.745  -0.745  -0.794  -0.794  -0.794
77    T        -0.794  -0.794  -0.794  -1.344  -1.344  -1.344  -0.794  -0.794  -0.794
78    D         1.244   1.244   1.244   1.407   1.407   1.407   1.244   1.244   1.244
79    N        -0.794  -0.794  -0.794  -0.834  -0.834  -0.834  -0.794  -0.794  -0.794
80    E        -0.794  -0.794  -0.794  -0.434  -0.434  -0.434  -0.794  -0.794  -0.794
81    E         1.244   1.244   1.244   1.523   1.523   1.523   1.244   1.244   1.244
82    V         1.244   1.244   1.244   1.129   1.129   1.129   1.244   1.244   1.244
83    E        -0.794  -0.794  -0.794  -0.407  -0.407  -0.407  -0.794  -0.794  -0.794
84    T         1.244   1.244   1.244   0.794   0.794   0.794   1.244   1.244   1.244
85    V         1.244   1.244   1.244   1.129   1.129   1.129   1.244   1.244   1.244
86    S         1.244   1.244   1.244   0.921   0.921   0.921   1.244   1.244   1.244
87    E        -0.794  -0.794  -0.794  -0.434  -0.434  -0.434  -0.794  -0.794  -0.794
88    H         1.244   1.244   1.244   1.561   1.561   1.561   1.244   1.244   1.244
89    V         1.244   1.244   1.244   1.129   1.129   1.129   1.244   1.244   1.244
90    K        -0.794  -0.794  -0.794  -0.687  -0.687  -0.687  -0.794  -0.794  -0.794
91    V         1.244   1.244   1.244   1.129   1.129   1.129   1.244   1.244   1.244
* 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/Q3E825
Output conservation file - output/Q3E825
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
