1     M         1.152   1.152   1.168   1.207   1.208   1.230   1.198   1.198   1.216
2     T        -1.432  -1.430  -1.388  -1.352  -1.344  -1.273  -1.277  -1.275  -1.206
3     -        -0.478  -0.478  -0.444  -0.456  -0.456  -0.397  -0.659  -0.658  -0.601
4     -        -0.478  -0.478  -0.444  -0.456  -0.456  -0.397  -0.659  -0.658  -0.601
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     -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -0.478  -0.478  -0.444  -0.405  -0.404  -0.347  -0.659  -0.658  -0.601
12    Q        -1.432  -1.430  -1.388  -1.130  -1.136  -1.056  -1.277  -1.275  -1.206
13    H        -1.432  -1.430  -1.388  -1.352  -1.353  -1.273  -1.277  -1.275  -1.206
14    K        -0.345  -0.367  -0.400  -0.296  -0.329  -0.376  -0.452  -0.485  -0.533
15    S        -0.345  -0.367  -0.400  -0.354  -0.389  -0.439  -0.452  -0.485  -0.533
16    S        -0.345  -0.329  -0.392  -0.413  -0.383  -0.497  -0.452  -0.428  -0.520
17    M         1.152   1.152   1.168   1.207   1.208   1.230   1.198   1.198   1.216
18    V        -1.432  -1.430  -1.388  -1.292  -1.293  -1.214  -1.277  -1.275  -1.206
19    Y         1.152   1.152   1.168   1.130   1.130   1.155   1.198   1.198   1.216
20    I        -1.432  -1.430  -1.388  -1.414  -1.414  -1.334  -1.277  -1.275  -1.206
21    P        -0.345  -0.337  -0.398  -0.285  -0.269  -0.435  -0.452  -0.440  -0.529
22    T         1.152   1.152   1.168   1.181   1.183   1.205   1.198   1.198   1.216
23    T        -1.432  -1.430  -1.388  -1.526  -1.514  -1.443  -1.277  -1.275  -1.206
24    K        -0.345  -0.367  -0.400  -0.227  -0.258  -0.292  -0.452  -0.485  -0.533
25    E        -0.345  -0.367  -0.400  -0.116  -0.146  -0.191  -0.452  -0.485  -0.533
26    A        -1.432  -1.430  -1.388  -1.217  -1.221  -1.141  -1.277  -1.275  -1.206
27    K        -1.432  -1.430  -1.388  -1.368  -1.366  -1.289  -1.277  -1.275  -1.206
28    R        -0.345  -0.337  -0.398  -0.160  -0.144  -0.255  -0.452  -0.440  -0.529
29    R        -0.478  -0.478  -0.444  -0.702  -0.702  -0.638  -0.659  -0.658  -0.601
30    N        -0.478  -0.478  -0.444  -0.353  -0.353  -0.296  -0.659  -0.658  -0.601
31    G         1.152   1.152   1.168   1.356   1.356   1.376   1.198   1.198   1.216
32    K         1.152   1.152   1.168   1.208   1.208   1.231   1.198   1.198   1.216
33    S        -0.478  -0.478  -0.444  -0.538  -0.537  -0.476  -0.659  -0.658  -0.601
34    E        -1.432  -1.430  -1.388  -1.322  -1.319  -1.244  -1.277  -1.275  -1.206
35    G        -0.345  -0.337  -0.398  -0.296  -0.283  -0.399  -0.452  -0.440  -0.529
36    I        -0.345  -0.337  -0.398  -0.377  -0.363  -0.470  -0.452  -0.440  -0.529
37    L        -1.432  -1.430  -1.388  -1.625  -1.616  -1.540  -1.277  -1.275  -1.206
38    N        -1.432  -1.430  -1.388  -1.102  -1.101  -1.028  -1.277  -1.275  -1.206
39    T        -1.432  -1.430  -1.388  -1.368  -1.365  -1.289  -1.277  -1.275  -1.206
40    I        -1.432  -1.430  -1.388  -1.625  -1.636  -1.540  -1.277  -1.275  -1.206
41    E        -0.345  -0.367  -0.400  -0.160  -0.193  -0.245  -0.452  -0.485  -0.533
42    E        -0.345  -0.329  -0.392  -0.116  -0.087  -0.204  -0.452  -0.428  -0.520
43    V        -0.345  -0.329  -0.392  -0.521  -0.494  -0.579  -0.452  -0.428  -0.520
44    V        -0.345  -0.337  -0.398  -0.285  -0.271  -0.385  -0.452  -0.440  -0.529
45    E        -1.432  -1.430  -1.388  -1.247  -1.247  -1.170  -1.277  -1.275  -1.206
46    K        -1.432  -1.430  -1.388  -1.188  -1.180  -1.113  -1.277  -1.275  -1.206
47    L        -0.345  -0.337  -0.398  -0.720  -0.711  -0.783  -0.452  -0.440  -0.529
48    Y         1.152   1.152   1.168   1.130   1.130   1.155   1.198   1.198   1.216
49    W         1.152   1.152   1.168   1.529   1.530   1.546   1.198   1.198   1.216
50    T        -1.432  -1.430  -1.388  -1.414  -1.409  -1.334  -1.277  -1.275  -1.206
51    Y         1.152   1.152   1.168   1.130   1.130   1.155   1.198   1.198   1.216
52    Y         1.152   1.152   1.168   1.130   1.130   1.155   1.198   1.198   1.216
53    I         1.152   1.152   1.168   1.207   1.208   1.230   1.198   1.198   1.216
54    H         1.152   1.152   1.168   1.407   1.409   1.426   1.198   1.198   1.216
55    L        -0.345  -0.337  -0.398  -0.720  -0.711  -0.783  -0.452  -0.440  -0.529
56    P         1.152   1.152   1.168   1.481   1.481   1.498   1.198   1.198   1.216
57    F        -0.345  -0.337  -0.398  -0.607  -0.590  -0.691  -0.452  -0.440  -0.529
58    Y         1.152   1.152   1.168   1.130   1.130   1.155   1.198   1.198   1.216
59    L         1.152   1.152   1.168   0.838   0.835   0.869   1.198   1.198   1.216
60    M         1.152   1.152   1.168   1.207   1.208   1.230   1.198   1.198   1.216
61    A        -0.345  -0.329  -0.392  -0.296  -0.272  -0.357  -0.452  -0.428  -0.520
62    S         1.152   1.152   1.168   1.181   1.183   1.205   1.198   1.198   1.216
63    F        -0.345  -0.367  -0.400  -0.746  -0.790  -0.868  -0.452  -0.485  -0.533
64    D         1.152   1.152   1.168   1.432   1.432   1.450   1.198   1.198   1.216
65    S        -0.345  -0.329  -0.392  -0.182  -0.154  -0.284  -0.452  -0.428  -0.520
66    F         1.152   1.152   1.168   0.999   1.003   1.027   1.198   1.198   1.216
67    F        -0.345  -0.329  -0.392  -0.194  -0.159  -0.317  -0.452  -0.428  -0.520
68    L         1.152   1.152   1.168   0.838   0.835   0.869   1.198   1.198   1.216
69    H         1.152   1.152   1.168   1.407   1.409   1.426   1.198   1.198   1.216
70    V        -0.345  -0.329  -0.392  -0.354  -0.328  -0.426  -0.452  -0.428  -0.520
71    F        -0.345  -0.367  -0.400  -0.570  -0.602  -0.650  -0.452  -0.485  -0.533
72    F         1.152   1.152   1.168   0.999   1.003   1.027   1.198   1.198   1.216
73    L         1.152   1.152   1.168   0.838   0.835   0.869   1.198   1.198   1.216
74    T        -1.432  -1.430  -1.388  -1.414  -1.409  -1.334  -1.277  -1.275  -1.206
75    I        -0.345  -0.367  -0.400  -0.331  -0.367  -0.418  -0.452  -0.485  -0.533
76    F        -0.345  -0.367  -0.400  -0.521  -0.552  -0.590  -0.452  -0.485  -0.533
77    S         1.152   1.152   1.168   1.181   1.183   1.205   1.198   1.198   1.216
78    L         1.152   1.152   1.168   0.838   0.835   0.869   1.198   1.198   1.216
79    S         1.152   1.152   1.168   1.181   1.183   1.205   1.198   1.198   1.216
80    F        -0.345  -0.329  -0.392  -0.824  -0.797  -0.900  -0.452  -0.428  -0.520
81    F         1.152   1.152   1.168   0.999   1.003   1.027   1.198   1.198   1.216
82    G         1.152   1.152   1.168   1.308   1.307   1.329   1.198   1.198   1.216
83    I        -0.345  -0.367  -0.400  -0.545  -0.593  -0.683  -0.452  -0.485  -0.533
84    L        -0.345  -0.337  -0.398  -0.669  -0.662  -0.722  -0.452  -0.440  -0.529
85    K         1.152   1.152   1.168   1.207   1.208   1.230   1.198   1.198   1.216
86    Y         1.152   1.152   1.168   1.130   1.130   1.155   1.198   1.198   1.216
87    C        -0.345  -0.367  -0.400  -0.105  -0.145  -0.227  -0.452  -0.485  -0.533
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    F         1.152   1.152   1.168   0.999   1.003   1.027   1.198   1.198   1.216
90    L         1.152   1.152   1.168   0.838   0.835   0.869   1.198   1.198   1.216
* 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/Q3E790
Output conservation file - output/Q3E790
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
