1     M         1.179   1.179   1.179   1.395   1.395   1.395   1.179   1.179   1.179
2     N        -0.840  -0.840  -0.840  -0.926  -0.926  -0.926  -0.840  -0.840  -0.840
3     N        -0.840  -0.840  -0.840  -0.926  -0.926  -0.926  -0.840  -0.840  -0.840
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     N         1.179   1.179   1.179   1.019   1.019   1.019   1.179   1.179   1.179
9     V        -0.840  -0.840  -0.840  -0.696  -0.696  -0.696  -0.840  -0.840  -0.840
10    E        -0.840  -0.840  -0.840  -0.926  -0.926  -0.926  -0.840  -0.840  -0.840
11    E        -0.840  -0.840  -0.840  -0.926  -0.926  -0.926  -0.840  -0.840  -0.840
12    L        -0.840  -0.840  -0.840  -0.926  -0.926  -0.926  -0.840  -0.840  -0.840
13    L         1.179   1.179   1.179   0.987   0.987   0.987   1.179   1.179   1.179
14    R        -0.840  -0.840  -0.840  -0.833  -0.833  -0.833  -0.840  -0.840  -0.840
15    R        -0.840  -0.840  -0.840  -0.833  -0.833  -0.833  -0.840  -0.840  -0.840
16    I         1.179   1.179   1.179   1.210   1.210   1.210   1.179   1.179   1.179
17    P         1.179   1.179   1.179   1.084   1.084   1.084   1.179   1.179   1.179
18    L         1.179   1.179   1.179   0.987   0.987   0.987   1.179   1.179   1.179
19    Y        -0.840  -0.840  -0.840  -0.652  -0.652  -0.652  -0.840  -0.840  -0.840
20    N         1.179   1.179   1.179   1.019   1.019   1.019   1.179   1.179   1.179
21    K         1.179   1.179   1.179   0.889   0.889   0.889   1.179   1.179   1.179
22    Y        -0.840  -0.840  -0.840  -0.608  -0.608  -0.608  -0.840  -0.840  -0.840
23    G         1.179   1.179   1.179   1.303   1.303   1.303   1.179   1.179   1.179
24    K        -0.840  -0.840  -0.840  -1.022  -1.022  -1.022  -0.840  -0.840  -0.840
25    D        -0.840  -0.840  -0.840  -0.926  -0.926  -0.926  -0.840  -0.840  -0.840
26    F        -0.840  -0.840  -0.840  -0.608  -0.608  -0.608  -0.840  -0.840  -0.840
27    P         1.179   1.179   1.179   1.084   1.084   1.084   1.179   1.179   1.179
28    Q        -0.840  -0.840  -0.840  -0.652  -0.652  -0.652  -0.840  -0.840  -0.840
29    E         1.179   1.179   1.179   1.019   1.019   1.019   1.179   1.179   1.179
30    T        -0.840  -0.840  -0.840  -0.564  -0.564  -0.564  -0.840  -0.840  -0.840
31    V        -0.840  -0.840  -0.840  -0.856  -0.856  -0.856  -0.840  -0.840  -0.840
32    T        -0.840  -0.840  -0.840  -0.652  -0.652  -0.652  -0.840  -0.840  -0.840
33    R        -0.840  -0.840  -0.840  -0.926  -0.926  -0.926  -0.840  -0.840  -0.840
34    F        -0.840  -0.840  -0.840  -0.586  -0.586  -0.586  -0.840  -0.840  -0.840
35    Q        -0.840  -0.840  -0.840  -0.856  -0.856  -0.856  -0.840  -0.840  -0.840
36    M        -0.840  -0.840  -0.840  -0.564  -0.564  -0.564  -0.840  -0.840  -0.840
37    P         1.179   1.179   1.179   1.084   1.084   1.084   1.179   1.179   1.179
38    E        -0.840  -0.840  -0.840  -1.070  -1.070  -1.070  -0.840  -0.840  -0.840
39    F        -0.840  -0.840  -0.840  -0.608  -0.608  -0.608  -0.840  -0.840  -0.840
40    K         1.179   1.179   1.179   0.889   0.889   0.889   1.179   1.179   1.179
41    L        -0.840  -0.840  -0.840  -0.926  -0.926  -0.926  -0.840  -0.840  -0.840
42    P        -0.840  -0.840  -0.840  -0.998  -0.998  -0.998  -0.840  -0.840  -0.840
43    A        -0.840  -0.840  -0.840  -0.719  -0.719  -0.719  -0.840  -0.840  -0.840
44    L        -0.840  -0.840  -0.840  -0.926  -0.926  -0.926  -0.840  -0.840  -0.840
45    Q        -0.840  -0.840  -0.840  -0.542  -0.542  -0.542  -0.840  -0.840  -0.840
46    P        -0.840  -0.840  -0.840  -0.879  -0.879  -0.879  -0.840  -0.840  -0.840
47    T        -0.840  -0.840  -0.840  -0.652  -0.652  -0.652  -0.840  -0.840  -0.840
48    R        -0.840  -0.840  -0.840  -0.926  -0.926  -0.926  -0.840  -0.840  -0.840
49    D        -0.840  -0.840  -0.840  -1.022  -1.022  -1.022  -0.840  -0.840  -0.840
50    L        -0.840  -0.840  -0.840  -0.787  -0.787  -0.787  -0.840  -0.840  -0.840
51    L        -0.840  -0.840  -0.840  -0.810  -0.810  -0.810  -0.840  -0.840  -0.840
52    C        -0.840  -0.840  -0.840  -0.741  -0.741  -0.741  -0.840  -0.840  -0.840
53    P         1.179   1.179   1.179   1.084   1.084   1.084   1.179   1.179   1.179
54    W         1.179   1.179   1.179   1.456   1.456   1.456   1.179   1.179   1.179
55    Y         1.179   1.179   1.179   1.272   1.272   1.272   1.179   1.179   1.179
56    E        -0.840  -0.840  -0.840  -1.144  -1.144  -1.144  -0.840  -0.840  -0.840
57    E         1.179   1.179   1.179   1.019   1.019   1.019   1.179   1.179   1.179
58    C         1.179   1.179   1.179   1.425   1.425   1.425   1.179   1.179   1.179
59    D         1.179   1.179   1.179   1.179   1.179   1.179   1.179   1.179   1.179
60    N        -0.840  -0.840  -0.840  -1.046  -1.046  -1.046  -0.840  -0.840  -0.840
61    I         1.179   1.179   1.179   1.210   1.210   1.210   1.179   1.179   1.179
62    T        -0.840  -0.840  -0.840  -0.630  -0.630  -0.630  -0.840  -0.840  -0.840
63    K        -0.840  -0.840  -0.840  -0.810  -0.810  -0.810  -0.840  -0.840  -0.840
64    V        -0.840  -0.840  -0.840  -0.521  -0.521  -0.521  -0.840  -0.840  -0.840
65    C         1.179   1.179   1.179   1.425   1.425   1.425   1.179   1.179   1.179
66    Q        -0.840  -0.840  -0.840  -0.856  -0.856  -0.856  -0.840  -0.840  -0.840
67    L        -0.840  -0.840  -0.840  -0.856  -0.856  -0.856  -0.840  -0.840  -0.840
68    H         1.179   1.179   1.179   1.486   1.486   1.486   1.179   1.179   1.179
69    D         1.179   1.179   1.179   1.179   1.179   1.179   1.179   1.179   1.179
70    S        -0.840  -0.840  -0.840  -0.741  -0.741  -0.741  -0.840  -0.840  -0.840
71    S        -0.840  -0.840  -0.840  -0.950  -0.950  -0.950  -0.840  -0.840  -0.840
72    N        -0.840  -0.840  -0.840  -0.833  -0.833  -0.833  -0.840  -0.840  -0.840
73    K        -0.840  -0.840  -0.840  -0.926  -0.926  -0.926  -0.840  -0.840  -0.840
74    K        -0.840  -0.840  -0.840  -1.144  -1.144  -1.144  -0.840  -0.840  -0.840
75    F         1.179   1.179   1.179   1.365   1.365   1.365   1.179   1.179   1.179
76    D        -0.840  -0.840  -0.840  -0.926  -0.926  -0.926  -0.840  -0.840  -0.840
77    Q         1.179   1.179   1.179   1.272   1.272   1.272   1.179   1.179   1.179
78    W         1.179   1.179   1.179   1.456   1.456   1.456   1.179   1.179   1.179
79    Y         1.179   1.179   1.179   1.272   1.272   1.272   1.179   1.179   1.179
80    K        -0.840  -0.840  -0.840  -1.144  -1.144  -1.144  -0.840  -0.840  -0.840
81    E         1.179   1.179   1.179   1.019   1.019   1.019   1.179   1.179   1.179
82    Q        -0.840  -0.840  -0.840  -0.950  -0.950  -0.950  -0.840  -0.840  -0.840
83    Y         1.179   1.179   1.179   1.272   1.272   1.272   1.179   1.179   1.179
84    L        -0.840  -0.840  -0.840  -0.926  -0.926  -0.926  -0.840  -0.840  -0.840
85    S         1.179   1.179   1.179   1.179   1.179   1.179   1.179   1.179   1.179
86    K        -0.840  -0.840  -0.840  -0.856  -0.856  -0.856  -0.840  -0.840  -0.840
87    K         1.179   1.179   1.179   0.889   0.889   0.889   1.179   1.179   1.179
88    P         1.179   1.179   1.179   1.084   1.084   1.084   1.179   1.179   1.179
89    P         1.179   1.179   1.179   1.084   1.084   1.084   1.179   1.179   1.179
90    G         1.179   1.179   1.179   1.303   1.303   1.303   1.179   1.179   1.179
91    I        -0.840  -0.840  -0.840  -0.630  -0.630  -0.630  -0.840  -0.840  -0.840
92    V         1.179   1.179   1.179   1.303   1.303   1.303   1.179   1.179   1.179
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    G         1.179   1.179   1.179   1.303   1.303   1.303   1.179   1.179   1.179
95    N         1.179   1.179   1.179   1.019   1.019   1.019   1.179   1.179   1.179
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    T        -0.840  -0.840  -0.840  -0.652  -0.652  -0.652  -0.840  -0.840  -0.840
100   L        -0.840  -0.840  -0.840  -0.856  -0.856  -0.856  -0.840  -0.840  -0.840
101   L         1.179   1.179   1.179   0.987   0.987   0.987   1.179   1.179   1.179
102   S         1.179   1.179   1.179   1.179   1.179   1.179   1.179   1.179   1.179
103   P         1.179   1.179   1.179   1.084   1.084   1.084   1.179   1.179   1.179
104   S         1.179   1.179   1.179   1.179   1.179   1.179   1.179   1.179   1.179
105   R        -0.840  -0.840  -0.840  -0.926  -0.926  -0.926  -0.840  -0.840  -0.840
106   K         1.179   1.179   1.179   0.889   0.889   0.889   1.179   1.179   1.179
107   D        -0.840  -0.840  -0.840  -0.586  -0.586  -0.586  -0.840  -0.840  -0.840
108   N        -0.840  -0.840  -0.840  -0.833  -0.833  -0.833  -0.840  -0.840  -0.840
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   S        -0.840  -0.840  -0.840  -1.022  -1.022  -1.022  -0.840  -0.840  -0.840
* 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/P42939
Output conservation file - output/P42939
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
