1     M         1.093   1.092   1.096   1.451   1.473   1.434   1.124   1.123   1.132
2     I         1.093   1.092   1.096   1.060   1.085   1.069   1.124   1.123   1.132
3     F        -0.154  -0.118  -0.286  -0.359  -0.388  -0.562  -0.214  -0.163  -0.424
4     F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     N        -1.212  -1.246  -1.217  -1.067  -1.108  -1.055  -1.106  -1.145  -1.108
7     Q        -0.444  -0.438  -0.369  -0.728  -0.765  -0.595  -0.660  -0.651  -0.555
8     I         1.093   1.092   1.096   1.060   1.085   1.069   1.124   1.123   1.132
9     R         1.093   1.092   1.096   0.983   1.067   0.998   1.124   1.123   1.132
10    S        -1.212  -1.246  -1.217  -1.394  -1.391  -1.415  -1.106  -1.145  -1.108
11    I         1.093   1.092   1.096   1.060   1.085   1.069   1.124   1.123   1.132
12    F         1.093   1.092   1.096   0.879   0.797   0.901   1.124   1.123   1.132
13    T        -1.212  -1.164  -1.213  -0.952  -0.899  -1.035  -1.106  -1.050  -1.104
14    A        -1.212  -1.246  -1.217  -1.187  -1.237  -1.149  -1.106  -1.145  -1.108
15    L        -1.212  -1.246  -1.217  -1.554  -1.697  -1.567  -1.106  -1.145  -1.108
16    H        -0.444  -0.438  -0.369  -0.451  -0.365  -0.332  -0.660  -0.651  -0.555
17    T        -0.154  -0.171  -0.296   0.124   0.066  -0.183  -0.214  -0.240  -0.440
18    P        -1.212  -1.246  -1.217  -0.743  -0.733  -0.748  -1.106  -1.145  -1.108
19    T        -1.212  -1.246  -1.217  -0.762  -0.780  -0.771  -1.106  -1.145  -1.108
20    Q        -1.212  -1.246  -1.217  -1.078  -1.085  -1.162  -1.106  -1.145  -1.108
21    Q        -0.444  -0.438  -0.369  -0.469  -0.459  -0.357  -0.660  -0.651  -0.555
22    I        -1.212  -1.164  -1.213  -1.143  -1.037  -1.133  -1.106  -1.050  -1.104
23    Q        -1.212  -1.164  -1.213  -1.277  -1.215  -1.318  -1.106  -1.050  -1.104
24    L        -0.444  -0.438  -0.369  -0.487  -0.484  -0.377  -0.660  -0.651  -0.555
25    S         1.093   1.092   1.096   0.957   0.945   0.974   1.124   1.123   1.132
26    R         1.093   1.092   1.096   0.983   1.067   0.998   1.124   1.123   1.132
27    R        -1.212  -1.164  -1.213  -1.165  -1.032  -1.130  -1.106  -1.050  -1.104
28    A         1.093   1.092   1.096   1.085   1.118   1.093   1.124   1.123   1.132
29    F         1.093   1.092   1.096   0.879   0.797   0.901   1.124   1.123   1.132
30    F         1.093   1.092   1.096   0.879   0.797   0.901   1.124   1.123   1.132
31    Q        -0.444  -0.438  -0.369  -0.363  -0.391  -0.260  -0.660  -0.651  -0.555
32    F        -0.154  -0.196  -0.299  -0.341  -0.409  -0.610  -0.214  -0.276  -0.445
33    L         1.093   1.092   1.096   0.957   1.001   0.974   1.124   1.123   1.132
34    G         1.093   1.092   1.096   1.379   1.366   1.367   1.124   1.123   1.132
35    Y        -0.154  -0.196  -0.299  -0.230  -0.376  -0.390  -0.214  -0.276  -0.445
36    L         1.093   1.092   1.096   0.957   1.001   0.974   1.124   1.123   1.132
37    G         1.093   1.092   1.096   1.379   1.366   1.367   1.124   1.123   1.132
38    S         1.093   1.092   1.096   0.957   0.945   0.974   1.124   1.123   1.132
39    C         1.093   1.092   1.096   1.474   1.473   1.456   1.124   1.123   1.132
40    V         1.093   1.092   1.096   1.356   1.337   1.345   1.124   1.123   1.132
41    V        -1.212  -1.164  -1.213  -1.067  -0.985  -1.159  -1.106  -1.050  -1.104
42    I        -0.444  -0.438  -0.369  -0.826  -0.860  -0.685  -0.660  -0.651  -0.555
43    S         1.093   1.092   1.096   0.957   0.945   0.974   1.124   1.123   1.132
44    L        -0.444  -0.438  -0.369  -0.906  -0.930  -0.761  -0.660  -0.651  -0.555
45    A        -0.444  -0.438  -0.369  -0.451  -0.454  -0.341  -0.660  -0.651  -0.555
46    A         1.093   1.092   1.096   1.085   1.118   1.093   1.124   1.123   1.132
47    Q         1.093   1.092   1.096   1.110   1.072   1.116   1.124   1.123   1.132
48    S        -1.212  -1.164  -1.213  -1.232  -1.161  -1.201  -1.106  -1.050  -1.104
49    K        -1.212  -1.246  -1.217  -1.025  -1.033  -0.954  -1.106  -1.145  -1.108
50    Y        -0.444  -0.438  -0.369  -0.487  -0.488  -0.366  -0.660  -0.651  -0.555
51    V        -1.212  -1.246  -1.217  -1.266  -1.251  -1.256  -1.106  -1.145  -1.108
52    Q        -0.154  -0.118  -0.286  -0.002   0.007  -0.176  -0.214  -0.163  -0.424
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/Q3E828
Output conservation file - output/Q3E828
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
