1     M         0.995   0.995   0.995   0.861   0.861   0.861   0.995   0.995   0.995
2     Q         0.995   0.995   0.995   0.759   0.759   0.759   0.995   0.995   0.995
3     N        -0.995  -0.995  -0.995  -0.699  -0.699  -0.699  -0.995  -0.995  -0.995
4     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     Q         0.995   0.995   0.995   0.759   0.759   0.759   0.995   0.995   0.995
6     D         0.995   0.995   0.995   1.091   1.091   1.091   0.995   0.995   0.995
7     Y        -0.995  -0.995  -0.995  -0.813  -0.813  -0.813  -0.995  -0.995  -0.995
8     F        -0.995  -0.995  -0.995  -0.837  -0.837  -0.837  -0.995  -0.995  -0.995
9     Y        -0.995  -0.995  -0.995  -0.609  -0.609  -0.609  -0.995  -0.995  -0.995
10    A        -0.995  -0.995  -0.995  -0.837  -0.837  -0.837  -0.995  -0.995  -0.995
11    Q        -0.995  -0.995  -0.995  -1.358  -1.358  -1.358  -0.995  -0.995  -0.995
12    N        -0.995  -0.995  -0.995  -1.126  -1.126  -1.126  -0.995  -0.995  -0.995
13    R         0.995   0.995   0.995   1.026   1.026   1.026   0.995   0.995   0.995
14    C        -0.995  -0.995  -0.995  -0.478  -0.478  -0.478  -0.995  -0.995  -0.995
15    Q        -0.995  -0.995  -0.995  -1.102  -1.102  -1.102  -0.995  -0.995  -0.995
16    Q        -0.995  -0.995  -0.995  -1.228  -1.228  -1.228  -0.995  -0.995  -0.995
17    Q        -0.995  -0.995  -0.995  -1.102  -1.102  -1.102  -0.995  -0.995  -0.995
18    Q        -0.995  -0.995  -0.995  -1.028  -1.028  -1.028  -0.995  -0.995  -0.995
19    A        -0.995  -0.995  -0.995  -1.152  -1.152  -1.152  -0.995  -0.995  -0.995
20    P        -0.995  -0.995  -0.995  -1.077  -1.077  -1.077  -0.995  -0.995  -0.995
21    S        -0.995  -0.995  -0.995  -1.052  -1.052  -1.052  -0.995  -0.995  -0.995
22    T        -0.995  -0.995  -0.995  -0.587  -0.587  -0.587  -0.995  -0.995  -0.995
23    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    T        -0.995  -0.995  -0.995  -0.979  -0.979  -0.979  -0.995  -0.995  -0.995
26    V        -0.995  -0.995  -0.995  -0.907  -0.907  -0.907  -0.995  -0.995  -0.995
27    T        -0.995  -0.995  -0.995  -0.767  -0.767  -0.767  -0.995  -0.995  -0.995
28    M        -0.995  -0.995  -0.995  -1.003  -1.003  -1.003  -0.995  -0.995  -0.995
29    A        -0.995  -0.995  -0.995  -1.102  -1.102  -1.102  -0.995  -0.995  -0.995
30    E        -0.995  -0.995  -0.995  -1.228  -1.228  -1.228  -0.995  -0.995  -0.995
31    F         0.995   0.995   0.995   1.155   1.155   1.155   0.995   0.995   0.995
32    R        -0.995  -0.995  -0.995  -1.102  -1.102  -1.102  -0.995  -0.995  -0.995
33    R         0.995   0.995   0.995   1.026   1.026   1.026   0.995   0.995   0.995
34    V         0.995   0.995   0.995   1.123   1.123   1.123   0.995   0.995   0.995
35    P         0.995   0.995   0.995   1.059   1.059   1.059   0.995   0.995   0.995
36    L         0.995   0.995   0.995   0.927   0.927   0.927   0.995   0.995   0.995
37    P         0.995   0.995   0.995   1.059   1.059   1.059   0.995   0.995   0.995
38    P         0.995   0.995   0.995   1.059   1.059   1.059   0.995   0.995   0.995
39    M         0.995   0.995   0.995   0.861   0.861   0.861   0.995   0.995   0.995
40    A         0.995   0.995   0.995   1.026   1.026   1.026   0.995   0.995   0.995
41    E        -0.995  -0.995  -0.995  -1.228  -1.228  -1.228  -0.995  -0.995  -0.995
42    V        -0.995  -0.995  -0.995  -0.837  -0.837  -0.837  -0.995  -0.995  -0.995
43    P         0.995   0.995   0.995   1.059   1.059   1.059   0.995   0.995   0.995
44    M         0.995   0.995   0.995   0.861   0.861   0.861   0.995   0.995   0.995
45    L         0.995   0.995   0.995   0.927   0.927   0.927   0.995   0.995   0.995
46    S        -0.995  -0.995  -0.995  -1.077  -1.077  -1.077  -0.995  -0.995  -0.995
47    T        -0.995  -0.995  -0.995  -0.813  -0.813  -0.813  -0.995  -0.995  -0.995
48    Q        -0.995  -0.995  -0.995  -1.228  -1.228  -1.228  -0.995  -0.995  -0.995
49    N        -0.995  -0.995  -0.995  -0.931  -0.931  -0.931  -0.995  -0.995  -0.995
50    S         0.995   0.995   0.995   0.691   0.691   0.691   0.995   0.995   0.995
51    M        -0.995  -0.995  -0.995  -0.955  -0.955  -0.955  -0.995  -0.995  -0.995
52    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    A        -0.995  -0.995  -0.995  -1.152  -1.152  -1.152  -0.995  -0.995  -0.995
58    S         0.995   0.995   0.995   0.691   0.691   0.691   0.995   0.995   0.995
59    A        -0.995  -0.995  -0.995  -0.790  -0.790  -0.790  -0.995  -0.995  -0.995
60    S         0.995   0.995   0.995   0.691   0.691   0.691   0.995   0.995   0.995
61    S         0.995   0.995   0.995   0.691   0.691   0.691   0.995   0.995   0.995
62    L         0.995   0.995   0.995   0.927   0.927   0.927   0.995   0.995   0.995
63    E         0.995   0.995   0.995   0.861   0.861   0.861   0.995   0.995   0.995
64    M         0.995   0.995   0.995   0.861   0.861   0.861   0.995   0.995   0.995
65    W         0.995   0.995   0.995   1.344   1.344   1.344   0.995   0.995   0.995
66    E         0.995   0.995   0.995   0.861   0.861   0.861   0.995   0.995   0.995
67    K         0.995   0.995   0.995   1.187   1.187   1.187   0.995   0.995   0.995
68    D         0.995   0.995   0.995   1.091   1.091   1.091   0.995   0.995   0.995
69    L         0.995   0.995   0.995   0.927   0.927   0.927   0.995   0.995   0.995
70    E        -0.995  -0.995  -0.995  -0.979  -0.979  -0.979  -0.995  -0.995  -0.995
71    E         0.995   0.995   0.995   0.861   0.861   0.861   0.995   0.995   0.995
72    R         0.995   0.995   0.995   1.026   1.026   1.026   0.995   0.995   0.995
73    L         0.995   0.995   0.995   0.927   0.927   0.927   0.995   0.995   0.995
74    N        -0.995  -0.995  -0.995  -1.126  -1.126  -1.126  -0.995  -0.995  -0.995
75    S        -0.995  -0.995  -0.995  -1.279  -1.279  -1.279  -0.995  -0.995  -0.995
76    I         0.995   0.995   0.995   1.282   1.282   1.282   0.995   0.995   0.995
77    D         0.995   0.995   0.995   1.091   1.091   1.091   0.995   0.995   0.995
78    H        -0.995  -0.995  -0.995  -0.860  -0.860  -0.860  -0.995  -0.995  -0.995
79    D        -0.995  -0.995  -0.995  -0.884  -0.884  -0.884  -0.995  -0.995  -0.995
80    M        -0.995  -0.995  -0.995  -0.837  -0.837  -0.837  -0.995  -0.995  -0.995
81    N        -0.995  -0.995  -0.995  -1.177  -1.177  -1.177  -0.995  -0.995  -0.995
82    N        -0.995  -0.995  -0.995  -0.931  -0.931  -0.931  -0.995  -0.995  -0.995
83    N         0.995   0.995   0.995   0.993   0.993   0.993   0.995   0.995   0.995
84    K         0.995   0.995   0.995   1.187   1.187   1.187   0.995   0.995   0.995
85    F        -0.995  -0.995  -0.995  -0.837  -0.837  -0.837  -0.995  -0.995  -0.995
86    G         0.995   0.995   0.995   1.155   1.155   1.155   0.995   0.995   0.995
87    S        -0.995  -0.995  -0.995  -1.152  -1.152  -1.152  -0.995  -0.995  -0.995
88    G        -0.995  -0.995  -0.995  -0.813  -0.813  -0.813  -0.995  -0.995  -0.995
89    E         0.995   0.995   0.995   0.861   0.861   0.861   0.995   0.995   0.995
90    L         0.995   0.995   0.995   0.927   0.927   0.927   0.995   0.995   0.995
91    K        -0.995  -0.995  -0.995  -0.676  -0.676  -0.676  -0.995  -0.995  -0.995
92    S        -0.995  -0.995  -0.995  -1.028  -1.028  -1.028  -0.995  -0.995  -0.995
93    M         0.995   0.995   0.995   0.861   0.861   0.861   0.995   0.995   0.995
94    F         0.995   0.995   0.995   1.155   1.155   1.155   0.995   0.995   0.995
95    N        -0.995  -0.995  -0.995  -0.931  -0.931  -0.931  -0.995  -0.995  -0.995
96    Q        -0.995  -0.995  -0.995  -1.358  -1.358  -1.358  -0.995  -0.995  -0.995
97    G         0.995   0.995   0.995   1.155   1.155   1.155   0.995   0.995   0.995
98    K         0.995   0.995   0.995   1.187   1.187   1.187   0.995   0.995   0.995
99    V        -0.995  -0.995  -0.995  -0.907  -0.907  -0.907  -0.995  -0.995  -0.995
100   E         0.995   0.995   0.995   0.861   0.861   0.861   0.995   0.995   0.995
101   E         0.995   0.995   0.995   0.861   0.861   0.861   0.995   0.995   0.995
102   M         0.995   0.995   0.995   0.861   0.861   0.861   0.995   0.995   0.995
103   D         0.995   0.995   0.995   1.091   1.091   1.091   0.995   0.995   0.995
104   F         0.995   0.995   0.995   1.155   1.155   1.155   0.995   0.995   0.995
* 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/Q04964
Output conservation file - output/Q04964
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
