1     M         1.309   1.318   1.343   1.452   1.494   1.504   1.372   1.387   1.425
2     D        -1.061  -1.008  -0.999  -0.743  -0.682  -0.644  -1.015  -0.954  -0.930
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     G         0.027   0.093  -0.072  -0.033   0.087  -0.258  -0.060   0.035  -0.232
6     M        -0.271  -0.231  -0.154  -0.165  -0.078   0.022  -0.538  -0.478  -0.365
7     F        -0.225  -0.212  -0.155  -0.369  -0.352  -0.255  -0.461  -0.447  -0.367
8     A        -1.095  -0.996  -1.009  -1.358  -1.193  -1.242  -1.073  -0.968  -0.945
9     M        -1.061  -1.141  -1.038  -0.941  -1.100  -0.959  -1.015  -1.109  -0.975
10    P         0.027  -0.077  -0.099  -0.055  -0.236  -0.273  -0.060  -0.227  -0.275
11    G         1.309   1.318   1.343   1.332   1.361   1.391   1.372   1.387   1.425
12    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    A         1.309   1.318   1.343   0.886   0.907   0.973   1.372   1.387   1.425
15    G        -0.142  -0.231  -0.157  -0.266  -0.452  -0.350  -0.326  -0.477  -0.370
16    A         1.309   1.318   1.343   0.886   0.907   0.973   1.372   1.387   1.425
17    A        -0.142  -0.231  -0.157  -0.716  -0.873  -0.711  -0.326  -0.477  -0.370
18    S        -0.142  -0.005  -0.110  -0.138   0.042  -0.094  -0.326  -0.113  -0.294
19    P        -1.095  -1.038  -1.001  -1.400  -1.322  -1.204  -1.073  -0.998  -0.933
20    Q        -1.095  -1.061  -1.015  -1.194  -1.149  -1.050  -1.073  -1.022  -0.949
21    Q        -1.727  -1.761  -1.664  -1.575  -1.665  -1.504  -1.378  -1.403  -1.278
22    P        -0.857  -0.961  -0.983  -0.799  -0.967  -0.964  -0.767  -0.895  -0.912
23    K        -1.095  -1.061  -1.015  -0.862  -0.809  -0.770  -1.073  -1.022  -0.949
24    S         1.309   1.318   1.343   1.366   1.379   1.423   1.372   1.387   1.425
25    R        -1.095  -1.061  -1.015  -0.687  -0.656  -0.601  -1.073  -1.022  -0.949
26    F         0.169   0.185  -0.030   0.161   0.188  -0.169   0.150   0.172  -0.165
27    Q        -1.095  -1.111  -1.024  -0.847  -0.827  -0.703  -1.073  -1.076  -0.959
28    A        -1.095  -0.990  -1.004  -1.131  -0.966  -1.024  -1.073  -0.959  -0.939
29    F        -0.225  -0.212  -0.155  -0.369  -0.352  -0.255  -0.461  -0.447  -0.367
30    K         1.309   1.318   1.343   1.516   1.533   1.563   1.372   1.387   1.425
31    E        -1.727  -1.761  -1.664  -1.216  -1.293  -1.167  -1.378  -1.403  -1.278
32    S        -0.225  -0.234  -0.159  -0.216  -0.237  -0.113  -0.461  -0.482  -0.373
33    P         1.309   1.318   1.343   1.191   1.203   1.259   1.372   1.387   1.425
34    L        -0.225  -0.117  -0.110  -0.710  -0.516  -0.508  -0.461  -0.291  -0.293
35    Y        -0.225  -0.117  -0.110  -0.198  -0.057  -0.034  -0.461  -0.291  -0.293
36    T         0.169   0.051  -0.055   0.470   0.265   0.045   0.150  -0.028  -0.204
37    I         0.169   0.051  -0.055   0.454   0.281   0.115   0.150  -0.028  -0.204
38    A        -0.857  -0.961  -0.983  -1.071  -1.230  -1.260  -0.767  -0.895  -0.912
39    L        -0.857  -0.961  -0.983  -0.695  -0.844  -0.841  -0.767  -0.895  -0.912
40    N        -0.857  -0.961  -0.983  -0.269  -0.422  -0.509  -0.767  -0.895  -0.912
41    G        -1.095  -1.111  -1.024  -1.267  -1.268  -1.120  -1.073  -1.076  -0.959
42    A         0.169   0.185  -0.030   0.027   0.060  -0.213   0.150   0.172  -0.165
43    F        -0.225  -0.117  -0.110  -0.516  -0.323  -0.325  -0.461  -0.291  -0.293
44    F         1.309   1.318   1.343   1.258   1.280   1.321   1.372   1.387   1.425
45    V        -1.727  -1.582  -1.633  -1.725  -1.552  -1.550  -1.378  -1.232  -1.251
46    A        -0.857  -0.774  -0.943  -1.071  -0.947  -1.200  -0.767  -0.670  -0.863
47    G         1.309   1.318   1.343   1.366   1.399   1.423   1.372   1.387   1.425
48    V         1.309   1.318   1.343   1.557   1.563   1.602   1.372   1.387   1.425
49    A        -0.857  -0.862  -0.980  -1.109  -1.115  -1.313  -0.767  -0.774  -0.908
50    F         1.309   1.318   1.343   1.258   1.280   1.321   1.372   1.387   1.425
51    I         1.309   1.318   1.343   1.473   1.485   1.524   1.372   1.387   1.425
52    Q         1.309   1.318   1.343   1.345   1.368   1.403   1.372   1.387   1.425
53    S         1.309   1.318   1.343   1.366   1.379   1.423   1.372   1.387   1.425
54    P        -0.225  -0.214  -0.156  -0.490  -0.486  -0.375  -0.461  -0.450  -0.368
55    L         0.169   0.051  -0.055   0.221   0.058  -0.084   0.150  -0.028  -0.204
56    M         0.169   0.051  -0.055   0.413   0.264   0.060   0.150  -0.028  -0.204
57    D        -0.225  -0.178  -0.153   0.041   0.103   0.132  -0.461  -0.390  -0.364
58    M         0.169   0.051  -0.055   0.355   0.191  -0.045   0.150  -0.028  -0.204
59    L         1.309   1.318   1.343   1.236   1.252   1.301   1.372   1.387   1.425
60    A        -1.095  -1.111  -1.024  -1.202  -1.184  -1.055  -1.073  -1.076  -0.959
61    P         1.309   1.318   1.343   1.191   1.203   1.259   1.372   1.387   1.425
62    Q         1.309   1.318   1.343   1.345   1.368   1.403   1.372   1.387   1.425
63    L         1.309   1.318   1.343   1.236   1.252   1.301   1.372   1.387   1.425
* 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/P33448
Output conservation file - output/P33448
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
