1     M         1.991   2.034   2.157   2.213   2.283   2.485   2.309   2.382   2.617
2     T        -0.864  -0.851  -0.807  -0.930  -0.909  -0.831  -0.873  -0.848  -0.772
3     S        -1.464  -1.425  -1.367  -1.397  -1.317  -1.251  -1.216  -1.168  -1.078
4     K        -0.241  -0.217  -0.179  -0.107  -0.071  -0.003  -0.445  -0.412  -0.358
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     R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     K        -0.985  -0.945  -0.879  -1.113  -1.053  -0.957  -0.996  -0.943  -0.847
10    S        -0.241  -0.270  -0.209  -0.621  -0.688  -0.588  -0.445  -0.490  -0.404
11    L         0.917   0.968   0.837   0.825   0.881   0.720   0.899   0.983   0.713
12    D        -0.869  -0.773  -0.804  -0.893  -0.709  -0.825  -0.863  -0.742  -0.761
13    H         0.625   0.667   0.700   0.883   0.945   0.999   0.351   0.417   0.435
14    T        -0.676  -0.692  -0.758  -0.531  -0.555  -0.667  -0.628  -0.648  -0.705
15    L         0.625   0.614   0.667   0.261   0.196   0.285   0.351   0.311   0.366
16    E        -1.360  -1.384  -1.333  -1.305  -1.350  -1.265  -1.118  -1.131  -1.047
17    L        -0.180  -0.160  -0.169  -0.524  -0.534  -0.521  -0.384  -0.372  -0.358
18    K        -0.368  -0.330  -0.240  -0.510  -0.458  -0.325  -0.628  -0.577  -0.450
19    I         1.024   0.917   0.868   0.981   0.846   0.734   1.085   0.890   0.774
20    P         1.991   2.034   2.157   2.159   2.233   2.429   2.309   2.382   2.617
21    F         1.024   0.917   0.868   1.256   1.092   0.987   1.085   0.890   0.774
22    E         0.129  -0.024  -0.084   0.251   0.034  -0.044   0.106  -0.123  -0.215
23    T        -0.180  -0.151  -0.131  -0.404  -0.339  -0.314  -0.384  -0.323  -0.296
24    E        -1.360  -1.358  -1.321  -1.282  -1.283  -1.221  -1.118  -1.109  -1.035
25    R        -0.864  -0.844  -0.811  -0.769  -0.767  -0.685  -0.873  -0.846  -0.777
26    Q         1.024   0.917   0.868   1.307   1.153   1.056   1.085   0.890   0.774
27    A         1.991   2.034   2.157   2.127   2.197   2.396   2.309   2.382   2.617
28    T        -1.856  -1.810  -1.767  -1.716  -1.656  -1.581  -1.363  -1.312  -1.232
29    I         0.129   0.067  -0.056   0.140   0.070  -0.145   0.106   0.008  -0.173
30    A         0.129  -0.024  -0.084   0.405   0.178   0.088   0.106  -0.123  -0.215
31    T        -1.360  -1.297  -1.308  -1.060  -1.007  -0.995  -1.118  -1.049  -1.022
32    K        -0.864  -0.918  -0.841  -0.710  -0.766  -0.653  -0.873  -0.916  -0.807
33    V        -0.180  -0.116  -0.150  -0.384  -0.298  -0.358  -0.384  -0.296  -0.327
34    L         1.024   0.983   0.885   0.891   0.817   0.666   1.085   1.008   0.807
35    S         0.129   0.067  -0.056   0.029  -0.058  -0.273   0.106   0.008  -0.173
36    P         1.024   0.983   0.885   1.303   1.260   1.132   1.085   1.008   0.807
37    D         1.991   2.034   2.157   1.916   1.994   2.177   2.309   2.382   2.617
38    P        -0.676  -0.762  -0.774  -0.439  -0.586  -0.627  -0.628  -0.733  -0.725
39    I         0.129  -0.024  -0.084   0.152  -0.056  -0.171   0.106  -0.123  -0.215
40    L         1.024   1.095   0.912   0.958   1.035   0.828   1.085   1.202   0.859
41    K         0.625   0.728   0.745   0.579   0.757   0.763   0.351   0.537   0.528
42    P        -0.864  -0.918  -0.841  -0.907  -0.980  -0.858  -0.873  -0.916  -0.807
43    Q        -0.864  -0.783  -0.808  -0.922  -0.817  -0.818  -0.873  -0.780  -0.773
44    D        -0.180  -0.218  -0.165  -0.440  -0.511  -0.447  -0.384  -0.419  -0.346
45    F        -0.180  -0.218  -0.165  -0.358  -0.444  -0.332  -0.384  -0.419  -0.346
46    Q        -0.180  -0.086  -0.151  -0.197  -0.065  -0.178  -0.384  -0.267  -0.331
47    V        -0.676  -0.721  -0.764  -0.541  -0.604  -0.653  -0.628  -0.687  -0.713
48    D        -1.360  -1.384  -1.333  -1.404  -1.426  -1.375  -1.118  -1.131  -1.047
49    Y        -0.180  -0.160  -0.169  -0.054  -0.120  -0.072  -0.384  -0.372  -0.358
50    S        -1.360  -1.355  -1.337  -1.250  -1.228  -1.172  -1.118  -1.106  -1.050
51    S        -0.180  -0.215  -0.150  -0.394  -0.436  -0.368  -0.384  -0.416  -0.327
52    E        -1.360  -1.302  -1.301  -1.342  -1.243  -1.255  -1.118  -1.051  -1.015
53    K        -0.676  -0.578  -0.709  -0.621  -0.449  -0.670  -0.628  -0.504  -0.645
54    N        -0.676  -0.650  -0.731  -0.490  -0.465  -0.598  -0.628  -0.592  -0.672
55    V        -1.360  -1.372  -1.342  -1.149  -1.167  -1.135  -1.118  -1.122  -1.055
56    M         1.024   1.133   0.923   0.958   1.082   0.844   1.085   1.265   0.880
57    L        -0.864  -0.844  -0.811  -1.132  -1.130  -1.052  -0.873  -0.846  -0.777
58    V        -0.180  -0.183  -0.149  -0.215  -0.233  -0.163  -0.384  -0.375  -0.327
59    Q        -1.856  -1.810  -1.767  -1.467  -1.384  -1.323  -1.363  -1.312  -1.232
60    F         1.024   0.917   0.868   1.351   1.226   1.168   1.085   0.890   0.774
61    R        -0.676  -0.629  -0.743  -0.700  -0.631  -0.789  -0.628  -0.567  -0.687
62    S        -0.864  -0.918  -0.841  -0.718  -0.767  -0.646  -0.873  -0.916  -0.807
63    I        -0.864  -0.829  -0.805  -1.090  -1.038  -1.001  -0.873  -0.825  -0.770
64    D         0.625   0.708   0.726   0.250   0.399   0.385   0.351   0.497   0.489
65    D        -0.676  -0.767  -0.788  -0.607  -0.735  -0.770  -0.628  -0.738  -0.742
66    R         1.991   2.034   2.157   2.127   2.195   2.396   2.309   2.382   2.617
67    V        -0.676  -0.767  -0.788  -0.671  -0.822  -0.875  -0.628  -0.738  -0.742
68    L        -0.180  -0.206  -0.154  -0.511  -0.539  -0.465  -0.384  -0.400  -0.328
69    R         1.991   2.034   2.157   2.127   2.195   2.396   2.309   2.382   2.617
70    V         1.991   2.034   2.157   1.938   1.993   2.200   2.309   2.382   2.617
71    G        -0.180  -0.206  -0.154   0.007  -0.019   0.054  -0.384  -0.400  -0.328
72    V         0.625   0.728   0.745   0.358   0.533   0.530   0.351   0.537   0.528
73    S         0.503   0.553   0.656   0.179   0.291   0.446   0.106   0.187   0.345
74    S         0.625   0.667   0.700   0.347   0.417   0.452   0.351   0.417   0.435
75    I        -0.864  -0.860  -0.818  -0.911  -0.945  -0.867  -0.873  -0.861  -0.783
76    I         0.129  -0.024  -0.084   0.226   0.045  -0.043   0.106  -0.123  -0.215
77    D         0.625   0.611   0.662   0.363   0.328   0.373   0.351   0.306   0.356
78    S         0.625   0.708   0.726   0.488   0.641   0.619   0.351   0.497   0.489
79    I         0.625   0.614   0.667   0.277   0.242   0.275   0.351   0.311   0.366
80    K         0.129  -0.024  -0.084   0.429   0.242   0.175   0.106  -0.123  -0.215
81    T         1.024   0.917   0.868   1.092   0.928   0.823   1.085   0.890   0.774
82    I         1.024   0.983   0.885   1.020   0.996   0.835   1.085   1.008   0.807
83    V         0.625   0.708   0.726   0.336   0.492   0.473   0.351   0.497   0.489
84    E         1.024   0.917   0.868   1.033   0.879   0.782   1.085   0.890   0.774
85    A        -0.180  -0.128  -0.165  -0.010   0.039   0.002  -0.384  -0.327  -0.351
86    M         0.129   0.122  -0.034   0.369   0.346   0.060   0.106   0.095  -0.138
87    D         1.024   0.917   0.868   1.080   0.958   0.901   1.085   0.890   0.774
88    V         1.024   1.133   0.923   1.038   1.192   0.886   1.085   1.265   0.880
89    L         0.625   0.728   0.745   0.384   0.520   0.565   0.351   0.537   0.528
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -0.985  -0.940  -0.879  -1.051  -0.994  -0.893  -0.996  -0.938  -0.847
105   -        -0.985  -0.940  -0.879  -1.051  -0.993  -0.893  -0.996  -0.938  -0.847
106   S        -1.856  -1.810  -1.767  -1.518  -1.508  -1.375  -1.363  -1.312  -1.232
* 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/Q3E833
Output conservation file - output/Q3E833
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
