1     M         0.845   0.845   0.845   1.344   1.344   1.344   0.845   0.845   0.845
2     A        -1.168  -1.168  -1.168  -1.873  -1.873  -1.873  -1.168  -1.168  -1.168
3     S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
4     S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
5     T        -1.168  -1.168  -1.168  -1.300  -1.300  -1.300  -1.168  -1.168  -1.168
6     S        -1.168  -1.168  -1.168  -1.027  -1.027  -1.027  -1.168  -1.168  -1.168
7     T        -1.168  -1.168  -1.168  -0.477  -0.477  -0.477  -1.168  -1.168  -1.168
8     S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
9     A        -1.168  -1.168  -1.168  -1.873  -1.873  -1.873  -1.168  -1.168  -1.168
10    S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    A        -1.168  -1.168  -1.168  -0.900  -0.900  -0.900  -1.168  -1.168  -1.168
19    S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
20    S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
21    S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
22    I         0.845   0.845   0.845   1.284   1.284   1.284   0.845   0.845   0.845
23    K        -1.168  -1.168  -1.168  -0.283  -0.283  -0.283  -1.168  -1.168  -1.168
24    T         0.845   0.845   0.845   1.164   1.164   1.164   0.845   0.845   0.845
25    N         0.845   0.845   0.845   1.225   1.225   1.225   0.845   0.845   0.845
26    S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
27    A         0.845   0.845   0.845   0.584   0.584   0.584   0.845   0.845   0.845
28    L         0.845   0.845   0.845   1.344   1.344   1.344   0.845   0.845   0.845
29    V         0.845   0.845   0.845   1.010   1.010   1.010   0.845   0.845   0.845
30    S        -1.168  -1.168  -1.168  -1.300  -1.300  -1.300  -1.168  -1.168  -1.168
31    N         0.845   0.845   0.845   1.225   1.225   1.225   0.845   0.845   0.845
32    N        -1.168  -1.168  -1.168  -0.325  -0.325  -0.325  -1.168  -1.168  -1.168
33    V        -1.168  -1.168  -1.168  -0.900  -0.900  -0.900  -1.168  -1.168  -1.168
34    V         0.845   0.845   0.845   1.010   1.010   1.010   0.845   0.845   0.845
35    A         0.845   0.845   0.845   0.584   0.584   0.584   0.845   0.845   0.845
36    A         0.845   0.845   0.845   0.584   0.584   0.584   0.845   0.845   0.845
37    S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
38    S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
39    V         0.845   0.845   0.845   1.010   1.010   1.010   0.845   0.845   0.845
40    S        -1.168  -1.168  -1.168  -1.873  -1.873  -1.873  -1.168  -1.168  -1.168
41    A         0.845   0.845   0.845   0.584   0.584   0.584   0.845   0.845   0.845
42    T        -1.168  -1.168  -1.168  -1.300  -1.300  -1.300  -1.168  -1.168  -1.168
43    S        -1.168  -1.168  -1.168  -1.873  -1.873  -1.873  -1.168  -1.168  -1.168
44    T        -1.168  -1.168  -1.168  -0.325  -0.325  -0.325  -1.168  -1.168  -1.168
45    A        -1.168  -1.168  -1.168  -1.873  -1.873  -1.873  -1.168  -1.168  -1.168
46    S        -1.168  -1.168  -1.168  -1.300  -1.300  -1.300  -1.168  -1.168  -1.168
47    S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
48    S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
49    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    N        -1.168  -1.168  -1.168  -0.099  -0.099  -0.099  -1.168  -1.168  -1.168
53    T        -1.168  -1.168  -1.168  -0.283  -0.283  -0.283  -1.168  -1.168  -1.168
54    T        -1.168  -1.168  -1.168  -1.300  -1.300  -1.300  -1.168  -1.168  -1.168
55    S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
56    S        -1.168  -1.168  -1.168  -1.188  -1.188  -1.188  -1.168  -1.168  -1.168
57    S        -1.168  -1.168  -1.168  -1.300  -1.300  -1.300  -1.168  -1.168  -1.168
58    K         0.845   0.845   0.845   1.284   1.284   1.284   0.845   0.845   0.845
59    N         0.845   0.845   0.845   1.225   1.225   1.225   0.845   0.845   0.845
60    A        -1.168  -1.168  -1.168  -0.777  -0.777  -0.777  -1.168  -1.168  -1.168
61    A         0.845   0.845   0.845   0.584   0.584   0.584   0.845   0.845   0.845
62    P        -1.168  -1.168  -1.168  -0.283  -0.283  -0.283  -1.168  -1.168  -1.168
63    G        -1.168  -1.168  -1.168  -1.300  -1.300  -1.300  -1.168  -1.168  -1.168
64    M         0.845   0.845   0.845   1.344   1.344   1.344   0.845   0.845   0.845
65    V        -1.168  -1.168  -1.168  -0.390  -0.390  -0.390  -1.168  -1.168  -1.168
66    A         0.845   0.845   0.845   0.584   0.584   0.584   0.845   0.845   0.845
67    N        -1.168  -1.168  -1.168  -1.243  -1.243  -1.243  -1.168  -1.168  -1.168
68    P         0.845   0.845   0.845   1.431   1.431   1.431   0.845   0.845   0.845
69    V         0.845   0.845   0.845   1.010   1.010   1.010   0.845   0.845   0.845
70    S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
71    S        -1.168  -1.168  -1.168  -1.001  -1.001  -1.001  -1.168  -1.168  -1.168
72    K         0.845   0.845   0.845   1.284   1.284   1.284   0.845   0.845   0.845
73    Y         0.845   0.845   0.845   1.460   1.460   1.460   0.845   0.845   0.845
74    G         0.845   0.845   0.845   1.164   1.164   1.164   0.845   0.845   0.845
75    I        -1.168  -1.168  -1.168  -0.390  -0.390  -0.390  -1.168  -1.168  -1.168
76    I        -1.168  -1.168  -1.168  -0.682  -0.682  -0.682  -1.168  -1.168  -1.168
77    M        -1.168  -1.168  -1.168  -0.159  -0.159  -0.159  -1.168  -1.168  -1.168
78    A        -1.168  -1.168  -1.168  -0.777  -0.777  -0.777  -1.168  -1.168  -1.168
79    A         0.845   0.845   0.845   0.584   0.584   0.584   0.845   0.845   0.845
80    F         0.845   0.845   0.845   1.402   1.402   1.402   0.845   0.845   0.845
81    A        -1.168  -1.168  -1.168  -0.635  -0.635  -0.635  -1.168  -1.168  -1.168
82    A         0.845   0.845   0.845   0.584   0.584   0.584   0.845   0.845   0.845
83    V        -1.168  -1.168  -1.168  -0.477  -0.477  -0.477  -1.168  -1.168  -1.168
84    S         0.845   0.845   0.845  -0.159  -0.159  -0.159   0.845   0.845   0.845
85    F         0.845   0.845   0.845   1.402   1.402   1.402   0.845   0.845   0.845
86    V         0.845   0.845   0.845   1.010   1.010   1.010   0.845   0.845   0.845
87    L         0.845   0.845   0.845   1.344   1.344   1.344   0.845   0.845   0.845
88    G         0.845   0.845   0.845   1.164   1.164   1.164   0.845   0.845   0.845
89    T        -1.168  -1.168  -1.168  -0.777  -0.777  -0.777  -1.168  -1.168  -1.168
90    G         0.845   0.845   0.845   1.164   1.164   1.164   0.845   0.845   0.845
91    I         0.845   0.845   0.845   1.284   1.284   1.284   0.845   0.845   0.845
* 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/Q3E842
Output conservation file - output/Q3E842
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
