1     M         1.025   1.025   1.025   1.502   1.502   1.502   1.025   1.025   1.025
2     K        -0.966  -0.966  -0.966  -0.171  -0.171  -0.171  -0.966  -0.966  -0.966
3     F         1.025   1.025   1.025   1.502   1.502   1.502   1.025   1.025   1.025
4     S         1.025   1.025   1.025   0.767   0.767   0.767   1.025   1.025   1.025
5     T         1.025   1.025   1.025   0.443   0.443   0.443   1.025   1.025   1.025
6     L        -0.966  -0.966  -0.966  -0.827  -0.827  -0.827  -0.966  -0.966  -0.966
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    S        -0.966  -0.966  -0.966  -0.895  -0.895  -0.895  -0.966  -0.966  -0.966
11    T         1.025   1.025   1.025   0.443   0.443   0.443   1.025   1.025   1.025
12    V        -0.966  -0.966  -0.966  -0.827  -0.827  -0.827  -0.966  -0.966  -0.966
13    A        -0.966  -0.966  -0.966  -1.227  -1.227  -1.227  -0.966  -0.966  -0.966
14    A         1.025   1.025   1.025   0.798   0.798   0.798   1.025   1.025   1.025
15    I        -0.966  -0.966  -0.966  -0.632  -0.632  -0.632  -0.966  -0.966  -0.966
16    A         1.025   1.025   1.025   0.798   0.798   0.798   1.025   1.025   1.025
17    A        -0.966  -0.966  -0.966  -1.153  -1.153  -1.153  -0.966  -0.966  -0.966
18    F         1.025   1.025   1.025   1.502   1.502   1.502   1.025   1.025   1.025
19    A         1.025   1.025   1.025   0.798   0.798   0.798   1.025   1.025   1.025
20    S        -0.966  -0.966  -0.966  -0.674  -0.674  -0.674  -0.966  -0.966  -0.966
21    A        -0.966  -0.966  -0.966  -0.739  -0.739  -0.739  -0.966  -0.966  -0.966
22    D        -0.966  -0.966  -0.966  -0.918  -0.918  -0.918  -0.966  -0.966  -0.966
23    S        -0.966  -0.966  -0.966  -1.178  -1.178  -1.178  -0.966  -0.966  -0.966
24    T        -0.966  -0.966  -0.966  -1.433  -1.433  -1.433  -0.966  -0.966  -0.966
25    S         1.025   1.025   1.025   0.767   0.767   0.767   1.025   1.025   1.025
26    D         1.025   1.025   1.025   1.474   1.474   1.474   1.025   1.025   1.025
27    G         1.025   1.025   1.025   1.334   1.334   1.334   1.025   1.025   1.025
28    V         1.025   1.025   1.025   0.860   0.860   0.860   1.025   1.025   1.025
29    T         1.025   1.025   1.025   0.443   0.443   0.443   1.025   1.025   1.025
30    Y         1.025   1.025   1.025   1.446   1.446   1.446   1.025   1.025   1.025
31    V         1.025   1.025   1.025   0.860   0.860   0.860   1.025   1.025   1.025
32    D         1.025   1.025   1.025   1.474   1.474   1.474   1.025   1.025   1.025
33    V         1.025   1.025   1.025   0.860   0.860   0.860   1.025   1.025   1.025
34    T         1.025   1.025   1.025   0.443   0.443   0.443   1.025   1.025   1.025
35    T        -0.966  -0.966  -0.966  -0.987  -0.987  -0.987  -0.966  -0.966  -0.966
36    T         1.025   1.025   1.025   0.443   0.443   0.443   1.025   1.025   1.025
37    P         1.025   1.025   1.025   1.502   1.502   1.502   1.025   1.025   1.025
38    Q        -0.966  -0.966  -0.966  -0.247  -0.247  -0.247  -0.966  -0.966  -0.966
39    S        -0.966  -0.966  -0.966  -1.178  -1.178  -1.178  -0.966  -0.966  -0.966
40    T         1.025   1.025   1.025   0.443   0.443   0.443   1.025   1.025   1.025
41    T        -0.966  -0.966  -0.966  -1.433  -1.433  -1.433  -0.966  -0.966  -0.966
42    S         1.025   1.025   1.025   0.767   0.767   0.767   1.025   1.025   1.025
43    M        -0.966  -0.966  -0.966  -0.653  -0.653  -0.653  -0.966  -0.966  -0.966
44    V         1.025   1.025   1.025   0.860   0.860   0.860   1.025   1.025   1.025
45    S         1.025   1.025   1.025   0.767   0.767   0.767   1.025   1.025   1.025
46    T         1.025   1.025   1.025   0.443   0.443   0.443   1.025   1.025   1.025
47    V        -0.966  -0.966  -0.966  -0.696  -0.696  -0.696  -0.966  -0.966  -0.966
48    K        -0.966  -0.966  -0.966  -0.365  -0.365  -0.365  -0.966  -0.966  -0.966
49    T        -0.966  -0.966  -0.966  -1.514  -1.514  -1.514  -0.966  -0.966  -0.966
50    T         1.025   1.025   1.025   0.443   0.443   0.443   1.025   1.025   1.025
51    S         1.025   1.025   1.025   0.767   0.767   0.767   1.025   1.025   1.025
52    T         1.025   1.025   1.025   0.443   0.443   0.443   1.025   1.025   1.025
53    P         1.025   1.025   1.025   1.502   1.502   1.502   1.025   1.025   1.025
54    Y         1.025   1.025   1.025   1.446   1.446   1.446   1.025   1.025   1.025
55    T        -0.966  -0.966  -0.966  -1.514  -1.514  -1.514  -0.966  -0.966  -0.966
56    T         1.025   1.025   1.025   0.443   0.443   0.443   1.025   1.025   1.025
57    S        -0.966  -0.966  -0.966  -1.514  -1.514  -1.514  -0.966  -0.966  -0.966
58    T         1.025   1.025   1.025   0.443   0.443   0.443   1.025   1.025   1.025
59    I        -0.966  -0.966  -0.966  -0.385  -0.385  -0.385  -0.966  -0.966  -0.966
60    A         1.025   1.025   1.025   0.798   0.798   0.798   1.025   1.025   1.025
61    T        -0.966  -0.966  -0.966  -1.433  -1.433  -1.433  -0.966  -0.966  -0.966
62    L        -0.966  -0.966  -0.966  -0.872  -0.872  -0.872  -0.966  -0.966  -0.966
63    S        -0.966  -0.966  -0.966  -1.514  -1.514  -1.514  -0.966  -0.966  -0.966
64    T        -0.966  -0.966  -0.966  -1.129  -1.129  -1.129  -0.966  -0.966  -0.966
65    K        -0.966  -0.966  -0.966  -0.247  -0.247  -0.247  -0.966  -0.966  -0.966
66    S        -0.966  -0.966  -0.966  -1.514  -1.514  -1.514  -0.966  -0.966  -0.966
67    I        -0.966  -0.966  -0.966  -0.228  -0.228  -0.228  -0.966  -0.966  -0.966
68    S        -0.966  -0.966  -0.966  -1.227  -1.227  -1.227  -0.966  -0.966  -0.966
69    S        -0.966  -0.966  -0.966  -0.805  -0.805  -0.805  -0.966  -0.966  -0.966
70    Q        -0.966  -0.966  -0.966  -0.190  -0.190  -0.190  -0.966  -0.966  -0.966
71    A        -0.966  -0.966  -0.966  -0.590  -0.590  -0.590  -0.966  -0.966  -0.966
72    N        -0.966  -0.966  -0.966  -0.611  -0.611  -0.611  -0.966  -0.966  -0.966
73    T         1.025   1.025   1.025   0.443   0.443   0.443   1.025   1.025   1.025
74    T        -0.966  -0.966  -0.966  -1.514  -1.514  -1.514  -0.966  -0.966  -0.966
75    T         1.025   1.025   1.025   0.443   0.443   0.443   1.025   1.025   1.025
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    H         1.025   1.025   1.025   1.584   1.584   1.584   1.025   1.025   1.025
78    E        -0.966  -0.966  -0.966  -0.987  -0.987  -0.987  -0.966  -0.966  -0.966
79    I        -0.966  -0.966  -0.966  -0.632  -0.632  -0.632  -0.966  -0.966  -0.966
80    S        -0.966  -0.966  -0.966  -0.761  -0.761  -0.761  -0.966  -0.966  -0.966
81    T        -0.966  -0.966  -0.966  -0.895  -0.895  -0.895  -0.966  -0.966  -0.966
82    Y         1.025   1.025   1.025   1.446   1.446   1.446   1.025   1.025   1.025
83    V        -0.966  -0.966  -0.966  -1.178  -1.178  -1.178  -0.966  -0.966  -0.966
84    G         1.025   1.025   1.025   1.334   1.334   1.334   1.025   1.025   1.025
85    A         1.025   1.025   1.025   0.798   0.798   0.798   1.025   1.025   1.025
86    A         1.025   1.025   1.025   0.798   0.798   0.798   1.025   1.025   1.025
87    V        -0.966  -0.966  -0.966  -0.827  -0.827  -0.827  -0.966  -0.966  -0.966
88    K         1.025   1.025   1.025   1.502   1.502   1.502   1.025   1.025   1.025
89    G        -0.966  -0.966  -0.966  -0.286  -0.286  -0.286  -0.966  -0.966  -0.966
90    S        -0.966  -0.966  -0.966  -0.761  -0.761  -0.761  -0.966  -0.966  -0.966
91    V         1.025   1.025   1.025   0.860   0.860   0.860   1.025   1.025   1.025
92    A        -0.966  -0.966  -0.966  -0.872  -0.872  -0.872  -0.966  -0.966  -0.966
93    G         1.025   1.025   1.025   1.334   1.334   1.334   1.025   1.025   1.025
94    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    G        -0.966  -0.966  -0.966  -0.805  -0.805  -0.805  -0.966  -0.966  -0.966
96    A        -0.966  -0.966  -0.966  -1.227  -1.227  -1.227  -0.966  -0.966  -0.966
97    I        -0.966  -0.966  -0.966  -0.385  -0.385  -0.385  -0.966  -0.966  -0.966
98    M        -0.966  -0.966  -0.966  -0.611  -0.611  -0.611  -0.966  -0.966  -0.966
99    G         1.025   1.025   1.025   1.334   1.334   1.334   1.025   1.025   1.025
100   A        -0.966  -0.966  -0.966  -1.153  -1.153  -1.153  -0.966  -0.966  -0.966
101   A        -0.966  -0.966  -0.966  -1.153  -1.153  -1.153  -0.966  -0.966  -0.966
102   A         1.025   1.025   1.025   0.798   0.798   0.798   1.025   1.025   1.025
103   F        -0.966  -0.966  -0.966  -0.365  -0.365  -0.365  -0.966  -0.966  -0.966
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   A         1.025   1.025   1.025   0.798   0.798   0.798   1.025   1.025   1.025
107   L         1.025   1.025   1.025   1.219   1.219   1.219   1.025   1.025   1.025
108   L         1.025   1.025   1.025   1.219   1.219   1.219   1.025   1.025   1.025
* 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/P48560
Output conservation file - output/P48560
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
