1     M         1.251   1.251   1.251   1.535   1.535   1.535   1.251   1.251   1.251
2     G         1.251   1.251   1.251   1.143   1.143   1.143   1.251   1.251   1.251
3     A         1.251   1.251   1.251   0.723   0.723   0.723   1.251   1.251   1.251
4     A         1.251   1.251   1.251   0.723   0.723   0.723   1.251   1.251   1.251
5     Y         1.251   1.251   1.251   1.573   1.573   1.573   1.251   1.251   1.251
6     K         1.251   1.251   1.251   1.020   1.020   1.020   1.251   1.251   1.251
7     V        -0.789  -0.789  -0.789  -0.459  -0.459  -0.459  -0.789  -0.789  -0.789
8     F         1.251   1.251   1.251   1.420   1.420   1.420   1.251   1.251   1.251
9     G         1.251   1.251   1.251   1.143   1.143   1.143   1.251   1.251   1.251
10    K        -0.789  -0.789  -0.789  -0.657  -0.657  -0.657  -0.789  -0.789  -0.789
11    T         1.251   1.251   1.251   1.302   1.302   1.302   1.251   1.251   1.251
12    V         1.251   1.251   1.251   1.342   1.342   1.342   1.251   1.251   1.251
13    Q         1.251   1.251   1.251   1.535   1.535   1.535   1.251   1.251   1.251
14    P         1.251   1.251   1.251   1.497   1.497   1.497   1.251   1.251   1.251
15    H         1.251   1.251   1.251   1.648   1.648   1.648   1.251   1.251   1.251
16    V        -0.789  -0.789  -0.789  -0.459  -0.459  -0.459  -0.789  -0.789  -0.789
17    L         1.251   1.251   1.251   1.381   1.381   1.381   1.251   1.251   1.251
18    A         1.251   1.251   1.251   0.723   0.723   0.723   1.251   1.251   1.251
19    I         1.251   1.251   1.251   1.497   1.497   1.497   1.251   1.251   1.251
20    S        -0.789  -0.789  -0.789  -1.182  -1.182  -1.182  -0.789  -0.789  -0.789
21    T         1.251   1.251   1.251   1.302   1.302   1.302   1.251   1.251   1.251
22    F        -0.789  -0.789  -0.789  -0.487  -0.487  -0.487  -0.789  -0.789  -0.789
23    I        -0.789  -0.789  -0.789  -0.600  -0.600  -0.600  -0.789  -0.789  -0.789
24    A        -0.789  -0.789  -0.789  -1.182  -1.182  -1.182  -0.789  -0.789  -0.789
25    T        -0.789  -0.789  -0.789  -0.600  -0.600  -0.600  -0.789  -0.789  -0.789
26    A        -0.789  -0.789  -0.789  -0.957  -0.957  -0.957  -0.789  -0.789  -0.789
27    A        -0.789  -0.789  -0.789  -1.182  -1.182  -1.182  -0.789  -0.789  -0.789
28    V        -0.789  -0.789  -0.789  -0.715  -0.715  -0.715  -0.789  -0.789  -0.789
29    A         1.251   1.251   1.251   0.723   0.723   0.723   1.251   1.251   1.251
30    S        -0.789  -0.789  -0.789  -1.182  -1.182  -1.182  -0.789  -0.789  -0.789
31    Y         1.251   1.251   1.251   1.573   1.573   1.573   1.251   1.251   1.251
32    F        -0.789  -0.789  -0.789  -0.957  -0.957  -0.957  -0.789  -0.789  -0.789
33    T        -0.789  -0.789  -0.789  -0.459  -0.459  -0.459  -0.789  -0.789  -0.789
34    T        -0.789  -0.789  -0.789  -0.745  -0.745  -0.745  -0.789  -0.789  -0.789
35    K        -0.789  -0.789  -0.789  -0.957  -0.957  -0.957  -0.789  -0.789  -0.789
36    P        -0.789  -0.789  -0.789  -0.600  -0.600  -0.600  -0.789  -0.789  -0.789
37    K         1.251   1.251   1.251   1.020   1.020   1.020   1.251   1.251   1.251
38    T        -0.789  -0.789  -0.789  -0.628  -0.628  -0.628  -0.789  -0.789  -0.789
39    K        -0.789  -0.789  -0.789  -1.283  -1.283  -1.283  -0.789  -0.789  -0.789
40    N        -0.789  -0.789  -0.789  -0.404  -0.404  -0.404  -0.789  -0.789  -0.789
41    E        -0.789  -0.789  -0.789  -0.775  -0.775  -0.775  -0.789  -0.789  -0.789
42    G        -0.789  -0.789  -0.789  -1.182  -1.182  -1.182  -0.789  -0.789  -0.789
43    K         1.251   1.251   1.251   1.020   1.020   1.020   1.251   1.251   1.251
44    N        -0.789  -0.789  -0.789  -0.323  -0.323  -0.323  -0.789  -0.789  -0.789
45    S        -0.789  -0.789  -0.789  -1.182  -1.182  -1.182  -0.789  -0.789  -0.789
46    S        -0.789  -0.789  -0.789  -0.715  -0.715  -0.715  -0.789  -0.789  -0.789
47    A         1.251   1.251   1.251   0.723   0.723   0.723   1.251   1.251   1.251
48    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    K        -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    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    S        -0.789  -0.789  -0.789  -0.745  -0.745  -0.745  -0.789  -0.789  -0.789
57    S        -0.789  -0.789  -0.789  -0.600  -0.600  -0.600  -0.789  -0.789  -0.789
58    N        -0.789  -0.789  -0.789  -0.865  -0.865  -0.865  -0.789  -0.789  -0.789
59    S        -0.789  -0.789  -0.789  -1.182  -1.182  -1.182  -0.789  -0.789  -0.789
60    D        -0.789  -0.789  -0.789  -0.487  -0.487  -0.487  -0.789  -0.789  -0.789
61    A         1.251   1.251   1.251   0.723   0.723   0.723   1.251   1.251   1.251
62    M        -0.789  -0.789  -0.789  -0.865  -0.865  -0.865  -0.789  -0.789  -0.789
63    G         1.251   1.251   1.251   1.143   1.143   1.143   1.251   1.251   1.251
64    K        -0.789  -0.789  -0.789  -0.957  -0.957  -0.957  -0.789  -0.789  -0.789
65    D        -0.789  -0.789  -0.789  -0.745  -0.745  -0.745  -0.789  -0.789  -0.789
66    D         1.251   1.251   1.251   1.302   1.302   1.302   1.251   1.251   1.251
67    D        -0.789  -0.789  -0.789  -0.571  -0.571  -0.571  -0.789  -0.789  -0.789
68    V        -0.789  -0.789  -0.789  -0.515  -0.515  -0.515  -0.789  -0.789  -0.789
69    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    S        -0.789  -0.789  -0.789  -0.745  -0.745  -0.745  -0.789  -0.789  -0.789
72    I        -0.789  -0.789  -0.789  -0.459  -0.459  -0.459  -0.789  -0.789  -0.789
73    E         1.251   1.251   1.251   1.381   1.381   1.381   1.251   1.251   1.251
74    G        -0.789  -0.789  -0.789  -0.957  -0.957  -0.957  -0.789  -0.789  -0.789
75    F        -0.789  -0.789  -0.789  -0.487  -0.487  -0.487  -0.789  -0.789  -0.789
76    L         1.251   1.251   1.251   1.381   1.381   1.381   1.251   1.251   1.251
77    N        -0.789  -0.789  -0.789  -0.571  -0.571  -0.571  -0.789  -0.789  -0.789
78    D         1.251   1.251   1.251   1.302   1.302   1.302   1.251   1.251   1.251
79    L        -0.789  -0.789  -0.789  -0.487  -0.487  -0.487  -0.789  -0.789  -0.789
80    E        -0.789  -0.789  -0.789  -0.515  -0.515  -0.515  -0.789  -0.789  -0.789
81    K         1.251   1.251   1.251   1.020   1.020   1.020   1.251   1.251   1.251
82    D        -0.789  -0.789  -0.789  -0.571  -0.571  -0.571  -0.789  -0.789  -0.789
83    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    K        -0.789  -0.789  -0.789  -0.775  -0.775  -0.775  -0.789  -0.789  -0.789
89    A        -0.789  -0.789  -0.789  -1.182  -1.182  -1.182  -0.789  -0.789  -0.789
90    N        -0.789  -0.789  -0.789  -0.657  -0.657  -0.657  -0.789  -0.789  -0.789
* 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/Q3E824
Output conservation file - output/Q3E824
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
