1     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    M         1.771   1.831   1.948   2.090   2.183   2.382   1.966   2.063   2.290
24    S         0.217   0.246   0.407  -0.146  -0.173   0.093  -0.153  -0.136   0.103
25    F        -0.422  -0.567  -0.470  -0.597  -0.822  -0.631  -0.507  -0.716  -0.595
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    S        -0.067  -0.069  -0.285   0.243   0.270  -0.074  -0.017  -0.021  -0.333
28    S        -0.435  -0.344  -0.329  -0.410  -0.245  -0.282  -0.557  -0.403  -0.398
29    L        -0.892  -0.989  -1.032  -0.576  -0.750  -0.894  -0.737  -0.848  -0.883
30    Y         0.473   0.597   0.545   0.699   0.883   0.780   0.310   0.503   0.368
31    K        -1.127  -0.920  -1.040  -1.161  -0.814  -0.979  -1.070  -0.819  -0.896
32    T        -2.228  -2.199  -2.012  -1.895  -1.844  -1.602  -1.622  -1.562  -1.344
33    F        -1.127  -1.056  -1.037  -1.179  -1.103  -1.036  -1.070  -0.981  -0.897
34    F         0.073   0.103  -0.253   0.080   0.128  -0.358   0.172   0.214  -0.288
35    K        -0.307  -0.385  -0.409  -0.287  -0.413  -0.404  -0.380  -0.528  -0.523
36    R         0.901   0.754   0.633   1.273   1.064   0.898   1.000   0.766   0.532
37    N         1.771   1.831   1.948   1.849   1.934   2.149   1.966   2.063   2.290
38    A         0.073   0.080  -0.264   0.390   0.409  -0.133   0.172   0.158  -0.302
39    V        -1.278  -1.281  -1.108  -1.356  -1.401  -1.102  -1.208  -1.182  -0.971
40    F         0.473   0.597   0.545   0.283   0.460   0.411   0.310   0.503   0.368
41    V         0.901   0.769   0.615   1.045   0.911   0.701   1.000   0.790   0.499
42    G         0.171   0.253   0.408  -0.310  -0.189   0.063  -0.242  -0.124   0.105
43    T         0.901   0.754   0.633   1.131   0.937   0.713   1.000   0.766   0.532
44    I         0.473   0.488   0.462   0.568   0.566   0.470   0.310   0.312   0.210
45    F         0.244   0.380   0.440  -0.115   0.093   0.197  -0.104   0.116   0.167
46    A        -0.307  -0.348  -0.374  -0.491  -0.545  -0.599  -0.380  -0.414  -0.463
47    G         0.171   0.245   0.403  -0.088   0.055   0.277  -0.242  -0.138   0.096
48    A         1.771   1.831   1.948   1.598   1.672   1.906   1.966   2.063   2.290
49    F         1.771   1.831   1.948   1.559   1.655   1.869   1.966   2.063   2.290
50    V        -0.478  -0.539  -0.423  -0.793  -0.927  -0.741  -0.656  -0.707  -0.542
51    F         0.901   0.769   0.615   0.778   0.595   0.349   1.000   0.790   0.499
52    Q        -0.707  -0.978  -1.047  -0.154  -0.597  -0.833  -0.518  -0.837  -0.900
53    T        -2.077  -2.049  -2.006  -1.692  -1.630  -1.587  -1.484  -1.451  -1.339
54    V        -1.678  -1.614  -1.570  -1.860  -1.783  -1.679  -1.346  -1.267  -1.162
55    F         0.901   0.754   0.633   0.843   0.675   0.543   1.000   0.766   0.532
56    D         0.901   0.924   0.651   0.885   0.936   0.558   1.000   1.032   0.565
57    T        -0.478  -0.547  -0.423  -0.506  -0.596  -0.413  -0.656  -0.715  -0.542
58    A        -0.478  -0.532  -0.405  -0.845  -0.928  -0.732  -0.656  -0.696  -0.521
59    I        -1.029  -1.182  -1.072  -0.810  -0.980  -0.810  -0.932  -1.071  -0.933
60    T        -0.727  -0.558  -0.450  -0.946  -0.722  -0.557  -0.932  -0.704  -0.568
61    S        -0.478  -0.445  -0.416  -0.562  -0.515  -0.458  -0.656  -0.609  -0.534
62    W        -0.307  -0.416  -0.429  -0.126  -0.378  -0.455  -0.380  -0.560  -0.548
63    Y         0.171   0.307   0.443   0.200   0.414   0.625  -0.242  -0.020   0.174
64    E        -0.307  -0.486  -0.433  -0.349  -0.681  -0.640  -0.380  -0.623  -0.551
65    N        -1.029  -1.143  -1.075  -0.815  -1.028  -0.906  -0.932  -1.053  -0.936
66    H        -0.307  -0.486  -0.433   0.069  -0.266  -0.236  -0.380  -0.623  -0.551
67    N         1.771   1.831   1.948   1.849   1.934   2.149   1.966   2.063   2.290
68    K         0.473   0.413   0.441   0.263   0.132   0.114   0.310   0.178   0.169
69    G         0.901   0.966   0.654   0.957   1.088   0.589   1.000   1.095   0.571
70    K         0.073  -0.220  -0.328   0.252  -0.108  -0.260   0.172  -0.229  -0.394
71    L        -0.307  -0.486  -0.433  -0.007  -0.245  -0.171  -0.380  -0.623  -0.551
72    W         1.771   1.831   1.948   2.006   2.102   2.302   1.966   2.063   2.290
73    K         0.901   0.769   0.615   0.912   0.760   0.484   1.000   0.790   0.499
74    D         0.073  -0.037  -0.297   0.151   0.005  -0.372   0.172   0.017  -0.350
75    V         0.244   0.283   0.408   0.076   0.127   0.328  -0.104  -0.066   0.106
76    K         0.473   0.406   0.450   0.402   0.301   0.373   0.310   0.163   0.188
77    A        -1.278  -1.251  -1.103  -1.192  -1.020  -0.843  -1.208  -1.153  -0.964
78    R        -1.029  -0.742  -1.024  -0.873  -0.525  -0.815  -0.932  -0.635  -0.883
79    I        -0.727  -0.655  -0.488  -0.887  -0.811  -0.530  -0.932  -0.835  -0.619
80    A        -2.077  -1.850  -1.975  -1.626  -1.338  -1.548  -1.484  -1.279  -1.315
81    A        -0.629  -0.450  -0.442  -0.820  -0.546  -0.562  -0.794  -0.561  -0.560
82    G        -0.478  -0.539  -0.420  -0.788  -0.879  -0.708  -0.656  -0.706  -0.538
83    D        -1.176  -1.108  -1.053  -1.411  -1.302  -1.239  -1.098  -0.991  -0.909
84    G        -0.435  -0.351  -0.412  -0.571  -0.444  -0.579  -0.557  -0.474  -0.524
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -         0.302   0.432   0.450  -0.063   0.144   0.150   0.003   0.212   0.187
88    D        -0.435  -0.495  -0.426  -0.675  -0.797  -0.686  -0.557  -0.619  -0.541
89    D         0.390   0.619   0.534   0.231   0.607   0.426   0.164   0.541   0.348
90    D         1.771   1.831   1.948   1.617   1.710   1.925   1.966   2.063   2.290
91    D         0.901   0.754   0.633   0.885   0.708   0.528   1.000   0.766   0.532
92    E         1.771   1.831   1.948   1.799   1.890   2.101   1.966   2.063   2.290
* 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/P22289
Output conservation file - output/P22289
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
