1     M         1.669   1.730   1.827   1.851   1.930   2.113   1.856   1.941   2.103
2     L        -2.399  -2.177  -2.144  -2.269  -1.916  -1.951  -1.665  -1.461  -1.343
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    K        -0.252  -0.182  -0.296  -0.393  -0.262  -0.472  -0.361  -0.245  -0.406
11    R         0.099  -0.097  -0.248   0.277  -0.003  -0.322   0.161  -0.116  -0.334
12    F         0.257   0.291   0.409  -0.055  -0.012   0.183  -0.100  -0.061   0.096
13    P         0.099   0.157  -0.202   0.149   0.208  -0.207   0.161   0.239  -0.268
14    T        -0.252  -0.329  -0.312  -0.171  -0.267  -0.362  -0.361  -0.436  -0.433
15    P         1.669   1.730   1.827   1.489   1.565   1.766   1.856   1.941   2.103
16    I         0.257   0.304   0.416   0.122   0.210   0.351  -0.100  -0.038   0.109
17    L         0.099   0.168  -0.198   0.351   0.463  -0.072   0.161   0.259  -0.262
18    K         0.865   0.682   0.608   0.908   0.663   0.541   0.943   0.643   0.473
19    V        -0.920  -0.695  -0.883  -0.895  -0.588  -0.779  -0.883  -0.601  -0.781
20    Y        -0.252  -0.358  -0.353  -0.133  -0.323  -0.292  -0.361  -0.528  -0.492
21    W         0.099  -0.138  -0.271   0.533   0.161  -0.116   0.161  -0.169  -0.367
22    P         1.669   1.730   1.827   1.489   1.565   1.766   1.856   1.941   2.103
23    F         0.469   0.528   0.479   0.307   0.396   0.302   0.291   0.377   0.232
24    F         0.257   0.328   0.426  -0.219  -0.118   0.028  -0.100   0.009   0.129
25    V        -1.010  -0.979  -0.934  -1.161  -1.128  -1.007  -1.013  -0.955  -0.842
26    A         0.257   0.289   0.412  -0.135  -0.147   0.068  -0.100  -0.066   0.103
27    G         0.469   0.584   0.525   0.298   0.458   0.334   0.291   0.475   0.319
28    A        -1.150  -1.126  -0.978  -1.421  -1.395  -1.123  -1.143  -1.094  -0.885
29    A        -0.252  -0.195  -0.318  -0.207  -0.151  -0.369  -0.361  -0.317  -0.445
30    V        -1.010  -1.008  -0.946  -0.831  -0.802  -0.709  -1.013  -0.994  -0.854
31    Y        -0.410  -0.515  -0.354  -0.635  -0.831  -0.583  -0.622  -0.720  -0.497
32    Y         0.469   0.532   0.484   0.424   0.520   0.381   0.291   0.385   0.242
33    G        -0.410  -0.252  -0.330  -0.605  -0.400  -0.488  -0.622  -0.428  -0.464
34    M        -1.520  -1.447  -1.397  -1.303  -1.179  -1.127  -1.274  -1.172  -1.060
35    S        -1.520  -1.626  -1.447  -1.397  -1.556  -1.334  -1.274  -1.335  -1.102
36    K         0.865   0.682   0.608   0.922   0.695   0.578   0.943   0.643   0.473
37    A        -0.252  -0.294  -0.340  -0.478  -0.602  -0.595  -0.361  -0.457  -0.473
38    A        -0.920  -1.049  -0.947  -0.988  -1.126  -0.939  -0.883  -0.995  -0.849
39    D        -1.890  -1.877  -1.803  -1.457  -1.434  -1.380  -1.404  -1.372  -1.226
40    L         0.469   0.664   0.528   0.186   0.454   0.277   0.291   0.613   0.325
41    S        -0.252  -0.391  -0.344  -0.121  -0.314  -0.268  -0.361  -0.529  -0.480
42    S        -0.550  -0.344  -0.349  -0.651  -0.305  -0.377  -0.752  -0.457  -0.478
43    N         0.099  -0.138  -0.271   0.429   0.148  -0.054   0.161  -0.169  -0.367
44    T         0.469   0.559   0.485   0.535   0.691   0.541   0.291   0.431   0.244
45    K        -1.520  -1.369  -1.393  -1.239  -0.990  -1.082  -1.274  -1.109  -1.057
46    E         1.669   1.730   1.827   1.889   2.030   2.149   1.856   1.941   2.103
47    F         0.099  -0.138  -0.271   0.219  -0.077  -0.256   0.161  -0.169  -0.367
48    I         0.099  -0.138  -0.271   0.349   0.006  -0.235   0.161  -0.169  -0.367
49    N         1.669   1.730   1.827   1.763   1.855   2.029   1.856   1.941   2.103
50    D         1.669   1.730   1.827   1.826   1.980   2.089   1.856   1.941   2.103
51    P         1.669   1.730   1.827   1.489   1.565   1.766   1.856   1.941   2.103
52    R         1.669   1.730   1.827   1.737   1.852   2.004   1.856   1.941   2.103
53    N         0.865   0.977   0.649   1.098   1.254   0.854   0.943   1.107   0.548
54    P         0.865   0.682   0.608   0.790   0.538   0.457   0.943   0.643   0.473
55    R         0.099  -0.138  -0.271   0.326   0.012  -0.252   0.161  -0.169  -0.367
56    F         0.469   0.358   0.434   0.208  -0.051   0.047   0.291   0.066   0.144
57    A        -0.920  -0.943  -0.933  -1.078  -1.175  -1.040  -0.883  -0.918  -0.841
58    K        -1.520  -1.533  -1.407  -1.523  -1.539  -1.373  -1.274  -1.251  -1.067
59    G         0.099  -0.138  -0.271   0.249  -0.112  -0.319   0.161  -0.169  -0.367
60    G        -0.252  -0.288  -0.303  -0.256  -0.339  -0.364  -0.361  -0.378  -0.416
61    K         1.669   1.730   1.827   1.649   1.737   1.919   1.856   1.941   2.103
62    F        -0.582  -0.543  -0.406  -1.088  -1.060  -0.790  -0.815  -0.753  -0.559
63    V        -0.582  -0.539  -0.415  -0.705  -0.613  -0.446  -0.815  -0.747  -0.571
64    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    V         0.232   0.257   0.404   0.098   0.102   0.345  -0.147  -0.128   0.087
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.174  -1.186  -1.009  -1.263  -1.328  -1.034  -1.149  -1.143  -0.914
68    -        -1.174  -1.095  -0.959  -0.959  -0.823  -0.662  -1.149  -1.041  -0.860
69    D        -0.490  -0.351  -0.337  -0.325  -0.095  -0.108  -0.694  -0.502  -0.468
* 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/P81450
Output conservation file - output/P81450
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
