1     M         1.152   1.152   1.152   1.036   1.036   1.036   1.152   1.152   1.152
2     K        -0.858  -0.858  -0.858  -0.808  -0.808  -0.808  -0.858  -0.858  -0.858
3     L        -0.858  -0.858  -0.858  -0.833  -0.833  -0.833  -0.858  -0.858  -0.858
4     D        -0.858  -0.858  -0.858  -0.681  -0.681  -0.681  -0.858  -0.858  -0.858
5     S        -0.858  -0.858  -0.858  -0.833  -0.833  -0.833  -0.858  -0.858  -0.858
6     G        -0.858  -0.858  -0.858  -0.731  -0.731  -0.731  -0.858  -0.858  -0.858
7     I         1.152   1.152   1.152   1.250   1.250   1.250   1.152   1.152   1.152
8     Y         1.152   1.152   1.152   1.144   1.144   1.144   1.152   1.152   1.152
9     S         1.152   1.152   1.152   1.108   1.108   1.108   1.152   1.152   1.152
10    E         1.152   1.152   1.152   1.108   1.108   1.108   1.152   1.152   1.152
11    A         1.152   1.152   1.152   0.963   0.963   0.963   1.152   1.152   1.152
12    Q         1.152   1.152   1.152   1.285   1.285   1.285   1.152   1.152   1.152
13    R        -0.858  -0.858  -0.858  -0.833  -0.833  -0.833  -0.858  -0.858  -0.858
14    V         1.152   1.152   1.152   1.036   1.036   1.036   1.152   1.152   1.152
15    V        -0.858  -0.858  -0.858  -1.100  -1.100  -1.100  -0.858  -0.858  -0.858
16    R        -0.858  -0.858  -0.858  -0.833  -0.833  -0.833  -0.858  -0.858  -0.858
17    T        -0.858  -0.858  -0.858  -0.756  -0.756  -0.756  -0.858  -0.858  -0.858
18    P         1.152   1.152   1.152   1.250   1.250   1.250   1.152   1.152   1.152
19    K        -0.858  -0.858  -0.858  -0.808  -0.808  -0.808  -0.858  -0.858  -0.858
20    F         1.152   1.152   1.152   1.424   1.424   1.424   1.152   1.152   1.152
21    R        -0.858  -0.858  -0.858  -0.833  -0.833  -0.833  -0.858  -0.858  -0.858
22    Y         1.152   1.152   1.152   1.144   1.144   1.144   1.152   1.152   1.152
23    I        -0.858  -0.858  -0.858  -0.833  -0.833  -0.833  -0.858  -0.858  -0.858
24    M        -0.858  -0.858  -0.858  -1.046  -1.046  -1.046  -0.858  -0.858  -0.858
25    L        -0.858  -0.858  -0.858  -1.046  -1.046  -1.046  -0.858  -0.858  -0.858
26    G        -0.858  -0.858  -0.858  -0.938  -0.938  -0.938  -0.858  -0.858  -0.858
27    L        -0.858  -0.858  -0.858  -0.992  -0.992  -0.992  -0.858  -0.858  -0.858
28    V        -0.858  -0.858  -0.858  -0.992  -0.992  -0.992  -0.858  -0.858  -0.858
29    G        -0.858  -0.858  -0.858  -0.533  -0.533  -0.533  -0.858  -0.858  -0.858
30    A         1.152   1.152   1.152   0.963   0.963   0.963   1.152   1.152   1.152
31    A         1.152   1.152   1.152   0.963   0.963   0.963   1.152   1.152   1.152
32    V        -0.858  -0.858  -0.858  -1.046  -1.046  -1.046  -0.858  -0.858  -0.858
33    V         1.152   1.152   1.152   1.036   1.036   1.036   1.152   1.152   1.152
34    P         1.152   1.152   1.152   1.250   1.250   1.250   1.152   1.152   1.152
35    T         1.152   1.152   1.152   1.180   1.180   1.180   1.152   1.152   1.152
36    A         1.152   1.152   1.152   0.963   0.963   0.963   1.152   1.152   1.152
37    Y         1.152   1.152   1.152   1.144   1.144   1.144   1.152   1.152   1.152
38    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    R         1.152   1.152   1.152   1.250   1.250   1.250   1.152   1.152   1.152
40    R         1.152   1.152   1.152   1.250   1.250   1.250   1.152   1.152   1.152
41    G         1.152   1.152   1.152   1.250   1.250   1.250   1.152   1.152   1.152
42    Y        -0.858  -0.858  -0.858  -0.965  -0.965  -0.965  -0.858  -0.858  -0.858
43    T         1.152   1.152   1.152   1.180   1.180   1.180   1.152   1.152   1.152
44    V        -0.858  -0.858  -0.858  -0.992  -0.992  -0.992  -0.858  -0.858  -0.858
45    P         1.152   1.152   1.152   1.250   1.250   1.250   1.152   1.152   1.152
46    A        -0.858  -0.858  -0.858  -0.782  -0.782  -0.782  -0.858  -0.858  -0.858
47    H        -0.858  -0.858  -0.858  -0.656  -0.656  -0.656  -0.858  -0.858  -0.858
48    S         1.152   1.152   1.152   1.108   1.108   1.108   1.152   1.152   1.152
49    L        -0.858  -0.858  -0.858  -0.808  -0.808  -0.808  -0.858  -0.858  -0.858
50    D        -0.858  -0.858  -0.858  -0.808  -0.808  -0.808  -0.858  -0.858  -0.858
51    N        -0.858  -0.858  -0.858  -0.859  -0.859  -0.859  -0.858  -0.858  -0.858
52    I        -0.858  -0.858  -0.858  -0.833  -0.833  -0.833  -0.858  -0.858  -0.858
53    N        -0.858  -0.858  -0.858  -0.808  -0.808  -0.808  -0.858  -0.858  -0.858
54    G        -0.858  -0.858  -0.858  -0.833  -0.833  -0.833  -0.858  -0.858  -0.858
55    V         1.152   1.152   1.152   1.036   1.036   1.036   1.152   1.152   1.152
56    D        -0.858  -0.858  -0.858  -0.681  -0.681  -0.681  -0.858  -0.858  -0.858
57    T        -0.858  -0.858  -0.858  -0.886  -0.886  -0.886  -0.858  -0.858  -0.858
58    T        -0.858  -0.858  -0.858  -0.756  -0.756  -0.756  -0.858  -0.858  -0.858
59    K        -0.858  -0.858  -0.858  -0.833  -0.833  -0.833  -0.858  -0.858  -0.858
60    A         1.152   1.152   1.152   0.963   0.963   0.963   1.152   1.152   1.152
61    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    E        -0.858  -0.858  -0.858  -0.681  -0.681  -0.681  -0.858  -0.858  -0.858
67    Q        -0.858  -0.858  -0.858  -0.808  -0.808  -0.808  -0.858  -0.858  -0.858
68    R        -0.858  -0.858  -0.858  -0.731  -0.731  -0.731  -0.858  -0.858  -0.858
69    A        -0.858  -0.858  -0.858  -0.938  -0.938  -0.938  -0.858  -0.858  -0.858
70    A        -0.858  -0.858  -0.858  -1.046  -1.046  -1.046  -0.858  -0.858  -0.858
71    M        -0.858  -0.858  -0.858  -0.992  -0.992  -0.992  -0.858  -0.858  -0.858
72    T        -0.858  -0.858  -0.858  -0.886  -0.886  -0.886  -0.858  -0.858  -0.858
73    K         1.152   1.152   1.152   1.108   1.108   1.108   1.152   1.152   1.152
74    G        -0.858  -0.858  -0.858  -0.706  -0.706  -0.706  -0.858  -0.858  -0.858
75    K        -0.858  -0.858  -0.858  -0.833  -0.833  -0.833  -0.858  -0.858  -0.858
76    S         1.152   1.152   1.152   1.108   1.108   1.108   1.152   1.152   1.152
77    L        -0.858  -0.858  -0.858  -0.992  -0.992  -0.992  -0.858  -0.858  -0.858
78    Q        -0.858  -0.858  -0.858  -0.509  -0.509  -0.509  -0.858  -0.858  -0.858
79    E        -0.858  -0.858  -0.858  -0.833  -0.833  -0.833  -0.858  -0.858  -0.858
80    M         1.152   1.152   1.152   1.036   1.036   1.036   1.152   1.152   1.152
81    M        -0.858  -0.858  -0.858  -0.992  -0.992  -0.992  -0.858  -0.858  -0.858
82    D        -0.858  -0.858  -0.858  -0.808  -0.808  -0.808  -0.858  -0.858  -0.858
83    D         1.152   1.152   1.152   1.285   1.285   1.285   1.152   1.152   1.152
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    D        -0.858  -0.858  -0.858  -0.808  -0.808  -0.808  -0.858  -0.858  -0.858
92    E         1.152   1.152   1.152   1.108   1.108   1.108   1.152   1.152   1.152
93    V        -0.858  -0.858  -0.858  -0.965  -0.965  -0.965  -0.858  -0.858  -0.858
94    T         1.152   1.152   1.152   1.180   1.180   1.180   1.152   1.152   1.152
95    Y         1.152   1.152   1.152   1.144   1.144   1.144   1.152   1.152   1.152
96    L        -0.858  -0.858  -0.858  -0.938  -0.938  -0.938  -0.858  -0.858  -0.858
97    M        -0.858  -0.858  -0.858  -0.992  -0.992  -0.992  -0.858  -0.858  -0.858
98    F         1.152   1.152   1.152   1.424   1.424   1.424   1.152   1.152   1.152
99    S         1.152   1.152   1.152   1.108   1.108   1.108   1.152   1.152   1.152
100   S         1.152   1.152   1.152   1.108   1.108   1.108   1.152   1.152   1.152
101   I         1.152   1.152   1.152   1.250   1.250   1.250   1.152   1.152   1.152
102   M         1.152   1.152   1.152   1.036   1.036   1.036   1.152   1.152   1.152
* 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/P50088
Output conservation file - output/P50088
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
