1     M         1.134   1.134   1.134   1.363   1.363   1.363   1.134   1.134   1.134
2     S         1.134   1.134   1.134   1.041   1.041   1.041   1.134   1.134   1.134
3     T        -0.870  -0.870  -0.870  -1.112  -1.112  -1.112  -0.870  -0.870  -0.870
4     E        -0.870  -0.870  -0.870  -0.954  -0.954  -0.954  -0.870  -0.870  -0.870
5     K        -0.870  -0.870  -0.870  -0.803  -0.803  -0.803  -0.870  -0.870  -0.870
6     L        -0.870  -0.870  -0.870  -0.832  -0.832  -0.832  -0.870  -0.870  -0.870
7     E        -0.870  -0.870  -0.870  -1.048  -1.048  -1.048  -0.870  -0.870  -0.870
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    A        -0.870  -0.870  -0.870  -0.832  -0.832  -0.832  -0.870  -0.870  -0.870
15    S        -0.870  -0.870  -0.870  -1.048  -1.048  -1.048  -0.870  -0.870  -0.870
16    E         1.134   1.134   1.134   0.915   0.915   0.915   1.134   1.134   1.134
17    E         1.134   1.134   1.134   0.915   0.915   0.915   1.134   1.134   1.134
18    P         1.134   1.134   1.134   1.441   1.441   1.441   1.134   1.134   1.134
19    Q        -0.870  -0.870  -0.870  -0.803  -0.803  -0.803  -0.870  -0.870  -0.870
20    A        -0.870  -0.870  -0.870  -0.832  -0.832  -0.832  -0.870  -0.870  -0.870
21    P        -0.870  -0.870  -0.870  -0.714  -0.714  -0.714  -0.870  -0.870  -0.870
22    L        -0.870  -0.870  -0.870  -0.803  -0.803  -0.803  -0.870  -0.870  -0.870
23    A        -0.870  -0.870  -0.870  -0.570  -0.570  -0.570  -0.870  -0.870  -0.870
24    N        -0.870  -0.870  -0.870  -1.112  -1.112  -1.112  -0.870  -0.870  -0.870
25    T        -0.870  -0.870  -0.870  -1.112  -1.112  -1.112  -0.870  -0.870  -0.870
26    S        -0.870  -0.870  -0.870  -1.048  -1.048  -1.048  -0.870  -0.870  -0.870
27    E        -0.870  -0.870  -0.870  -1.145  -1.145  -1.145  -0.870  -0.870  -0.870
28    T         1.134   1.134   1.134   0.915   0.915   0.915   1.134   1.134   1.134
29    N         1.134   1.134   1.134   0.958   0.958   0.958   1.134   1.134   1.134
30    S        -0.870  -0.870  -0.870  -0.893  -0.893  -0.893  -0.870  -0.870  -0.870
31    I        -0.870  -0.870  -0.870  -1.017  -1.017  -1.017  -0.870  -0.870  -0.870
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    K        -0.870  -0.870  -0.870  -0.954  -0.954  -0.954  -0.870  -0.870  -0.870
36    G        -0.870  -0.870  -0.870  -0.514  -0.514  -0.514  -0.870  -0.870  -0.870
37    D        -0.870  -0.870  -0.870  -0.773  -0.773  -0.773  -0.870  -0.870  -0.870
38    T         1.134   1.134   1.134   0.915   0.915   0.915   1.134   1.134   1.134
39    E        -0.870  -0.870  -0.870  -1.112  -1.112  -1.112  -0.870  -0.870  -0.870
40    N         1.134   1.134   1.134   0.958   0.958   0.958   1.134   1.134   1.134
41    I        -0.870  -0.870  -0.870  -0.685  -0.685  -0.685  -0.870  -0.870  -0.870
42    V        -0.870  -0.870  -0.870  -0.685  -0.685  -0.685  -0.870  -0.870  -0.870
43    T         1.134   1.134   1.134   0.915   0.915   0.915   1.134   1.134   1.134
44    V        -0.870  -0.870  -0.870  -0.487  -0.487  -0.487  -0.870  -0.870  -0.870
45    F         1.134   1.134   1.134   1.441   1.441   1.441   1.134   1.134   1.134
46    D         1.134   1.134   1.134   1.164   1.164   1.164   1.134   1.134   1.134
47    L        -0.870  -0.870  -0.870  -0.803  -0.803  -0.803  -0.870  -0.870  -0.870
48    A        -0.870  -0.870  -0.870  -0.627  -0.627  -0.627  -0.870  -0.870  -0.870
49    N        -0.870  -0.870  -0.870  -1.017  -1.017  -1.017  -0.870  -0.870  -0.870
50    E         1.134   1.134   1.134   0.915   0.915   0.915   1.134   1.134   1.134
51    I         1.134   1.134   1.134   1.082   1.082   1.082   1.134   1.134   1.134
52    E         1.134   1.134   1.134   0.915   0.915   0.915   1.134   1.134   1.134
53    K        -0.870  -0.870  -0.870  -0.542  -0.542  -0.542  -0.870  -0.870  -0.870
54    S        -0.870  -0.870  -0.870  -0.832  -0.832  -0.832  -0.870  -0.870  -0.870
55    L         1.134   1.134   1.134   1.204   1.204   1.204   1.134   1.134   1.134
56    K         1.134   1.134   1.134   1.123   1.123   1.123   1.134   1.134   1.134
57    D        -0.870  -0.870  -0.870  -0.924  -0.924  -0.924  -0.870  -0.870  -0.870
58    V         1.134   1.134   1.134   1.363   1.363   1.363   1.134   1.134   1.134
59    Q         1.134   1.134   1.134   1.082   1.082   1.082   1.134   1.134   1.134
60    R        -0.870  -0.870  -0.870  -0.627  -0.627  -0.627  -0.870  -0.870  -0.870
61    Q         1.134   1.134   1.134   1.082   1.082   1.082   1.134   1.134   1.134
62    M         1.134   1.134   1.134   1.363   1.363   1.363   1.134   1.134   1.134
63    K        -0.870  -0.870  -0.870  -0.985  -0.985  -0.985  -0.870  -0.870  -0.870
64    E        -0.870  -0.870  -0.870  -0.954  -0.954  -0.954  -0.870  -0.870  -0.870
65    N         1.134   1.134   1.134   0.958   0.958   0.958   1.134   1.134   1.134
66    D         1.134   1.134   1.134   1.164   1.164   1.164   1.134   1.134   1.134
67    D        -0.870  -0.870  -0.870  -0.773  -0.773  -0.773  -0.870  -0.870  -0.870
68    E        -0.870  -0.870  -0.870  -1.017  -1.017  -1.017  -0.870  -0.870  -0.870
69    F         1.134   1.134   1.134   1.441   1.441   1.441   1.134   1.134   1.134
70    S        -0.870  -0.870  -0.870  -0.924  -0.924  -0.924  -0.870  -0.870  -0.870
71    R        -0.870  -0.870  -0.870  -0.627  -0.627  -0.627  -0.870  -0.870  -0.870
72    S         1.134   1.134   1.134   1.041   1.041   1.041   1.134   1.134   1.134
73    I         1.134   1.134   1.134   1.082   1.082   1.082   1.134   1.134   1.134
74    Q        -0.870  -0.870  -0.870  -1.017  -1.017  -1.017  -0.870  -0.870  -0.870
75    A         1.134   1.134   1.134   1.164   1.164   1.164   1.134   1.134   1.134
76    I         1.134   1.134   1.134   1.082   1.082   1.082   1.134   1.134   1.134
77    E         1.134   1.134   1.134   0.915   0.915   0.915   1.134   1.134   1.134
78    D         1.134   1.134   1.134   1.164   1.164   1.164   1.134   1.134   1.134
79    K         1.134   1.134   1.134   1.123   1.123   1.123   1.134   1.134   1.134
80    L         1.134   1.134   1.134   1.204   1.204   1.204   1.134   1.134   1.134
81    N        -0.870  -0.870  -0.870  -0.743  -0.743  -0.743  -0.870  -0.870  -0.870
82    K        -0.870  -0.870  -0.870  -0.985  -0.985  -0.985  -0.870  -0.870  -0.870
83    M        -0.870  -0.870  -0.870  -0.599  -0.599  -0.599  -0.870  -0.870  -0.870
84    S        -0.870  -0.870  -0.870  -0.924  -0.924  -0.924  -0.870  -0.870  -0.870
85    R         1.134   1.134   1.134   1.402   1.402   1.402   1.134   1.134   1.134
* 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/O14468
Output conservation file - output/O14468
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
