1     M         1.152   1.152   1.152   1.502   1.501   1.502   1.152   1.152   1.152
2     S         1.152   1.152   1.152   0.768   0.796   0.768   1.152   1.152   1.152
3     S         1.152   1.152   1.152   0.768   0.796   0.768   1.152   1.152   1.152
4     P        -0.858  -0.858  -0.858  -0.586  -0.591  -0.586  -0.858  -0.858  -0.858
5     T        -0.858  -0.858  -0.858  -0.736  -0.743  -0.736  -0.858  -0.858  -0.858
6     P        -0.858  -0.858  -0.858  -0.918  -0.928  -0.918  -0.858  -0.858  -0.858
7     P        -0.858  -0.858  -0.858  -0.971  -0.955  -0.971  -0.858  -0.858  -0.858
8     G         1.152   1.152   1.152   1.094   1.088   1.094   1.152   1.152   1.152
9     G        -0.858  -0.858  -0.858  -1.081  -1.065  -1.081  -0.858  -0.858  -0.858
10    Q        -0.858  -0.858  -0.858  -0.685  -0.692  -0.685  -0.858  -0.858  -0.858
11    R        -0.858  -0.858  -0.858  -0.710  -0.718  -0.710  -0.858  -0.858  -0.858
12    T        -0.858  -0.858  -0.858  -0.489  -0.493  -0.489  -0.858  -0.858  -0.858
13    L        -0.858  -0.858  -0.858  -1.081  -1.065  -1.081  -0.858  -0.858  -0.858
14    Q        -0.858  -0.858  -0.858  -0.761  -0.769  -0.761  -0.858  -0.858  -0.858
15    K        -0.858  -0.858  -0.858  -1.081  -1.093  -1.081  -0.858  -0.858  -0.858
16    R        -0.858  -0.858  -0.858  -0.891  -0.874  -0.891  -0.858  -0.858  -0.858
17    K        -0.858  -0.858  -0.858  -1.081  -1.093  -1.081  -0.858  -0.858  -0.858
18    Q        -0.858  -0.858  -0.858  -0.489  -0.493  -0.489  -0.858  -0.858  -0.858
19    G         1.152   1.152   1.152   1.094   1.088   1.094   1.152   1.152   1.152
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    S        -0.858  -0.858  -0.858  -1.137  -1.121  -1.137  -0.858  -0.858  -0.858
23    S         1.152   1.152   1.152   0.768   0.796   0.768   1.152   1.152   1.152
24    Q         1.152   1.152   1.152   1.435   1.434   1.435   1.152   1.152   1.152
25    K        -0.858  -0.858  -0.858  -0.710  -0.718  -0.710  -0.858  -0.858  -0.858
26    V        -0.858  -0.858  -0.858  -0.761  -0.769  -0.761  -0.858  -0.858  -0.858
27    A        -0.858  -0.858  -0.858  -0.839  -0.848  -0.839  -0.858  -0.858  -0.858
28    A        -0.858  -0.858  -0.858  -0.839  -0.848  -0.839  -0.858  -0.858  -0.858
29    S        -0.858  -0.858  -0.858  -1.280  -1.266  -1.280  -0.858  -0.858  -0.858
30    A         1.152   1.152   1.152   0.842   0.833   0.842   1.152   1.152   1.152
31    P        -0.858  -0.858  -0.858  -0.839  -0.848  -0.839  -0.858  -0.858  -0.858
32    K        -0.858  -0.858  -0.858  -0.635  -0.616  -0.635  -0.858  -0.858  -0.858
33    K         1.152   1.152   1.152   1.023   1.016   1.023   1.152   1.152   1.152
34    N         1.152   1.152   1.152   1.369   1.366   1.369   1.152   1.152   1.152
35    T         1.152   1.152   1.152   1.301   1.298   1.301   1.152   1.152   1.152
36    N        -0.858  -0.858  -0.858  -0.685  -0.692  -0.685  -0.858  -0.858  -0.858
37    S        -0.858  -0.858  -0.858  -0.813  -0.769  -0.813  -0.858  -0.858  -0.858
38    N        -0.858  -0.858  -0.858  -0.865  -0.848  -0.865  -0.858  -0.858  -0.858
39    N         1.152   1.152   1.152   1.369   1.366   1.369   1.152   1.152   1.152
40    S         1.152   1.152   1.152   0.768   0.796   0.768   1.152   1.152   1.152
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    I        -0.858  -0.858  -0.858  -0.660  -0.667  -0.660  -0.858  -0.858  -0.858
58    L         1.152   1.152   1.152   1.094   1.088   1.094   1.152   1.152   1.152
59    K         1.152   1.152   1.152   1.023   1.016   1.023   1.152   1.152   1.152
60    I        -0.858  -0.858  -0.858  -0.660  -0.667  -0.660  -0.858  -0.858  -0.858
61    Y         1.152   1.152   1.152   1.534   1.534   1.534   1.152   1.152   1.152
62    S        -0.858  -0.858  -0.858  -0.918  -0.901  -0.918  -0.858  -0.858  -0.858
63    D         1.152   1.152   1.152   1.469   1.467   1.469   1.152   1.152   1.152
64    E         1.152   1.152   1.152   1.435   1.467   1.435   1.152   1.152   1.152
65    A         1.152   1.152   1.152   0.842   0.833   0.842   1.152   1.152   1.152
66    T        -0.858  -0.858  -0.858  -0.918  -0.901  -0.918  -0.858  -0.858  -0.858
67    G         1.152   1.152   1.152   1.094   1.088   1.094   1.152   1.152   1.152
68    L        -0.858  -0.858  -0.858  -0.660  -0.667  -0.660  -0.858  -0.858  -0.858
69    R        -0.858  -0.858  -0.858  -0.710  -0.718  -0.710  -0.858  -0.858  -0.858
70    V         1.152   1.152   1.152   0.951   0.944   0.951   1.152   1.152   1.152
71    D         1.152   1.152   1.152   1.469   1.467   1.469   1.152   1.152   1.152
72    P         1.152   1.152   1.152   1.233   1.229   1.233   1.152   1.152   1.152
73    L        -0.858  -0.858  -0.858  -0.944  -0.955  -0.944  -0.858  -0.858  -0.858
74    V         1.152   1.152   1.152   0.951   0.944   0.951   1.152   1.152   1.152
75    V         1.152   1.152   1.152   0.951   0.944   0.951   1.152   1.152   1.152
76    L        -0.858  -0.858  -0.858  -0.537  -0.542  -0.537  -0.858  -0.858  -0.858
77    F        -0.858  -0.858  -0.858  -0.761  -0.769  -0.761  -0.858  -0.858  -0.858
78    L         1.152   1.152   1.152   1.094   1.088   1.094   1.152   1.152   1.152
79    A        -0.858  -0.858  -0.858  -1.280  -1.266  -1.280  -0.858  -0.858  -0.858
80    V         1.152   1.152   1.152   0.951   0.944   0.951   1.152   1.152   1.152
81    G         1.152   1.152   1.152   1.094   1.088   1.094   1.152   1.152   1.152
82    F         1.152   1.152   1.152   1.335   1.332   1.335   1.152   1.152   1.152
83    I         1.152   1.152   1.152   1.335   1.332   1.335   1.152   1.152   1.152
84    F        -0.858  -0.858  -0.858  -0.839  -0.848  -0.839  -0.858  -0.858  -0.858
85    S         1.152   1.152   1.152   0.768   0.796   0.768   1.152   1.152   1.152
86    V         1.152   1.152   1.152   0.951   0.944   0.951   1.152   1.152   1.152
87    V        -0.858  -0.858  -0.858  -0.761  -0.769  -0.761  -0.858  -0.858  -0.858
88    A        -0.858  -0.858  -0.858  -1.026  -1.037  -1.026  -0.858  -0.858  -0.858
89    L         1.152   1.152   1.152   1.094   1.088   1.094   1.152   1.152   1.152
90    H         1.152   1.152   1.152   1.534   1.534   1.534   1.152   1.152   1.152
91    V        -0.858  -0.858  -0.858  -0.761  -0.769  -0.761  -0.858  -0.858  -0.858
92    I        -0.858  -0.858  -0.858  -0.761  -0.769  -0.761  -0.858  -0.858  -0.858
93    S        -0.858  -0.858  -0.858  -1.280  -1.266  -1.280  -0.858  -0.858  -0.858
94    K        -0.858  -0.858  -0.858  -0.710  -0.718  -0.710  -0.858  -0.858  -0.858
95    V        -0.858  -0.858  -0.858  -0.761  -0.769  -0.761  -0.858  -0.858  -0.858
96    A        -0.858  -0.858  -0.858  -1.026  -1.037  -1.026  -0.858  -0.858  -0.858
97    G        -0.858  -0.858  -0.858  -0.891  -0.901  -0.891  -0.858  -0.858  -0.858
98    K         1.152   1.152   1.152   1.023   1.016   1.023   1.152   1.152   1.152
99    L        -0.858  -0.858  -0.858  -0.660  -0.667  -0.660  -0.858  -0.858  -0.858
100   F        -0.858  -0.858  -0.858  -0.839  -0.848  -0.839  -0.858  -0.858  -0.858
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P52870
Output conservation file - output/P52870
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
