1     M         1.066   1.072   1.140   1.315   1.326   1.423   1.133   1.141   1.246
2     I        -1.214  -1.273  -1.177  -1.449  -1.547  -1.449  -1.210  -1.258  -1.110
3     V        -0.641  -0.593  -0.659  -0.873  -0.789  -0.930  -0.797  -0.726  -0.798
4     K         1.066   1.072   1.140   0.992   0.995   1.122   1.133   1.141   1.246
5     V         0.334   0.241   0.093   0.435   0.305   0.029   0.306   0.161  -0.110
6     K         1.066   1.072   1.140   0.992   0.995   1.122   1.133   1.141   1.246
7     T         1.066   1.072   1.140   1.194   1.211   1.311   1.133   1.141   1.246
8     L         1.066   1.072   1.140   0.842   0.853   0.983   1.133   1.141   1.246
9     T         0.334   0.241   0.093   0.492   0.365   0.079   0.306   0.161  -0.110
10    G         1.066   1.072   1.140   1.031   1.042   1.159   1.133   1.141   1.246
11    K        -0.002   0.047   0.039  -0.137  -0.064  -0.062  -0.245  -0.161  -0.208
12    E        -0.002   0.047   0.039  -0.198  -0.124  -0.133  -0.245  -0.161  -0.208
13    I         0.334   0.384   0.114   0.345   0.408   0.061   0.306   0.380  -0.074
14    S        -0.861  -0.865  -0.717  -0.954  -0.995  -0.764  -1.072  -1.077  -0.870
15    V        -0.641  -0.712  -0.673  -0.761  -0.858  -0.823  -0.797  -0.881  -0.815
16    E        -0.002   0.055   0.024  -0.093   0.015  -0.095  -0.245  -0.147  -0.236
17    L        -0.641  -0.604  -0.662  -0.804  -0.746  -0.906  -0.797  -0.756  -0.802
18    K        -1.568  -1.530  -1.558  -1.603  -1.550  -1.587  -1.348  -1.308  -1.276
19    E        -0.994  -0.907  -1.140  -0.743  -0.607  -1.064  -0.935  -0.831  -1.070
20    S        -1.701  -1.676  -1.567  -1.657  -1.622  -1.437  -1.486  -1.459  -1.285
21    D         0.334   0.346   0.101   0.462   0.483   0.065   0.306   0.324  -0.097
22    L        -0.994  -1.020  -1.135  -1.049  -1.088  -1.308  -0.935  -0.967  -1.064
23    V        -0.153  -0.149  -0.030  -0.442  -0.437  -0.243  -0.521  -0.516  -0.336
24    Y        -0.861  -0.859  -0.715  -0.850  -0.851  -0.660  -1.072  -1.070  -0.868
25    H        -1.214  -1.243  -1.180  -0.892  -0.941  -0.844  -1.210  -1.237  -1.114
26    I         0.334   0.241   0.093   0.264   0.123  -0.160   0.306   0.161  -0.110
27    K         1.066   1.072   1.140   0.992   0.995   1.122   1.133   1.141   1.246
28    E         0.334   0.376   0.108   0.309   0.356  -0.014   0.306   0.368  -0.084
29    L        -1.214  -1.276  -1.187  -1.360  -1.444  -1.264  -1.210  -1.262  -1.120
30    L        -1.214  -1.276  -1.187  -1.408  -1.498  -1.339  -1.210  -1.262  -1.120
31    E         1.066   1.072   1.140   0.982   0.980   1.113   1.133   1.141   1.246
32    E         1.066   1.072   1.140   0.982   0.980   1.113   1.133   1.141   1.246
33    K         0.334   0.241   0.093   0.264   0.118  -0.160   0.306   0.161  -0.110
34    E         1.066   1.072   1.140   0.982   0.980   1.113   1.133   1.141   1.246
35    G         1.066   1.072   1.140   1.031   1.042   1.159   1.133   1.141   1.246
36    I         1.066   1.072   1.140   0.992   0.999   1.122   1.133   1.141   1.246
37    P         0.334   0.384   0.114   0.620   0.686   0.276   0.306   0.380  -0.074
38    P         0.334   0.387   0.106   0.632   0.699   0.290   0.306   0.385  -0.087
39    S        -0.002  -0.026   0.005   0.054   0.013   0.044  -0.245  -0.290  -0.271
40    Q         1.066   1.072   1.140   1.118   1.132   1.240   1.133   1.141   1.246
41    Q         1.066   1.072   1.140   1.118   1.132   1.240   1.133   1.141   1.246
42    R         0.334   0.346   0.101   0.595   0.613   0.185   0.306   0.324  -0.097
43    L         1.066   1.072   1.140   0.842   0.853   0.983   1.133   1.141   1.246
44    I         0.334   0.241   0.093   0.314   0.187  -0.042   0.306   0.161  -0.110
45    F         0.334   0.285   0.093   0.762   0.704   0.412   0.306   0.230  -0.110
46    Q        -1.701  -1.724  -1.580  -1.437  -1.462  -1.244  -1.486  -1.497  -1.295
47    G         1.066   1.072   1.140   1.031   1.042   1.159   1.133   1.141   1.246
48    K        -0.002   0.047   0.039  -0.174  -0.097  -0.107  -0.245  -0.161  -0.208
49    Q         1.066   1.072   1.140   1.118   1.132   1.240   1.133   1.141   1.246
50    I        -0.727  -0.749  -0.693  -1.124  -1.140  -0.974  -0.935  -0.950  -0.842
51    D        -1.214  -1.282  -1.181  -1.029  -1.122  -0.993  -1.210  -1.270  -1.114
52    D         0.334   0.387   0.106   0.518   0.590   0.200   0.306   0.385  -0.087
53    K        -0.994  -1.020  -1.135  -0.843  -0.894  -1.115  -0.935  -0.967  -1.064
54    L        -2.055  -1.964  -1.880  -2.084  -1.941  -1.814  -1.624  -1.544  -1.396
55    T         0.334   0.285   0.093   0.546   0.492   0.203   0.306   0.230  -0.110
56    V        -0.727  -0.747  -0.680  -0.913  -0.933  -0.786  -0.935  -0.948  -0.826
57    T        -2.055  -2.057  -1.894  -1.951  -1.956  -1.722  -1.624  -1.620  -1.406
58    D        -1.214  -1.157  -1.177  -1.291  -1.219  -1.189  -1.210  -1.154  -1.111
59    A        -0.994  -1.074  -1.142  -0.587  -0.700  -0.803  -0.935  -1.029  -1.072
60    H        -1.701  -1.654  -1.561  -1.594  -1.531  -1.386  -1.486  -1.442  -1.281
61    L        -0.153  -0.149  -0.030  -0.695  -0.686  -0.467  -0.521  -0.516  -0.336
62    V        -1.701  -1.629  -1.560  -1.706  -1.623  -1.460  -1.486  -1.420  -1.280
63    E        -1.214  -1.196  -1.180  -1.160  -1.132  -1.169  -1.210  -1.185  -1.113
64    G         1.066   1.072   1.140   1.031   1.042   1.159   1.133   1.141   1.246
65    M        -0.861  -0.838  -0.716  -0.797  -0.768  -0.593  -1.072  -1.042  -0.869
66    Q        -1.214  -1.211  -1.181  -1.258  -1.231  -1.259  -1.210  -1.196  -1.114
67    L         1.066   1.072   1.140   0.842   0.853   0.983   1.133   1.141   1.246
68    H         1.066   1.072   1.140   1.343   1.354   1.449   1.133   1.141   1.246
69    L         1.066   1.072   1.140   0.842   0.853   0.983   1.133   1.141   1.246
70    V         1.066   1.072   1.140   1.137   1.150   1.258   1.133   1.141   1.246
71    L         1.066   1.072   1.140   0.842   0.853   0.983   1.133   1.141   1.246
72    T        -0.002  -0.068  -0.015   0.045  -0.064   0.001  -0.245  -0.365  -0.308
73    L         1.066   1.072   1.140   0.842   0.853   0.983   1.133   1.141   1.246
74    R         1.066   1.072   1.140   1.297   1.306   1.406   1.133   1.141   1.246
75    G         1.066   1.072   1.140   1.031   1.042   1.159   1.133   1.141   1.246
76    G         1.066   1.072   1.140   1.031   1.042   1.159   1.133   1.141   1.246
77    N        -0.994  -0.996  -1.129  -0.528  -0.532  -0.720  -0.935  -0.936  -1.058
78    -        -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/Q03919
Output conservation file - output/Q03919
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
