1     M         2.082   2.087   2.171   2.325   2.330   2.457   2.353   2.362   2.499
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     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     E         0.960   0.902   0.912   1.022   0.923   0.919   0.801   0.690   0.671
7     I         0.006  -0.025   0.014  -0.421  -0.497  -0.473  -0.233  -0.281  -0.232
8     L         2.082   2.087   2.171   1.722   1.718   1.848   2.353   2.362   2.499
9     Q        -0.573  -0.588  -0.554  -0.351  -0.343  -0.304  -0.636  -0.650  -0.594
10    D        -1.034  -1.048  -1.019  -0.665  -0.673  -0.645  -0.866  -0.879  -0.826
11    V         0.063   0.062   0.065  -0.441  -0.460  -0.468  -0.176  -0.180  -0.172
12    Q        -0.399  -0.358  -0.453  -0.019   0.049  -0.111  -0.406  -0.354  -0.465
13    R        -1.034  -1.048  -1.019  -0.588  -0.569  -0.567  -0.866  -0.879  -0.826
14    K        -1.496  -1.489  -1.433  -1.116  -1.078  -1.018  -1.095  -1.088  -1.011
15    L         1.183   1.188   1.080   0.894   0.873   0.760   1.203   1.213   0.995
16    V         0.698   0.704   0.777   0.407   0.451   0.528   0.284   0.293   0.395
17    F        -0.399  -0.427  -0.465  -0.318  -0.377  -0.446  -0.406  -0.441  -0.481
18    P        -0.399  -0.430  -0.485  -0.305  -0.364  -0.478  -0.406  -0.445  -0.505
19    I         1.183   1.195   1.074   1.099   1.118   0.925   1.203   1.225   0.985
20    D         2.082   2.087   2.171   2.265   2.282   2.397   2.353   2.362   2.499
21    F         2.082   2.087   2.171   2.104   2.100   2.234   2.353   2.362   2.499
22    P         0.063   0.084   0.070   0.118   0.202   0.130  -0.176  -0.147  -0.163
23    S         0.063   0.086   0.065   0.126   0.155   0.136  -0.176  -0.140  -0.167
24    Q         2.082   2.087   2.171   2.083   2.083   2.213   2.353   2.362   2.499
25    R        -0.573  -0.546  -0.549  -0.377  -0.287  -0.323  -0.636  -0.607  -0.589
26    K        -0.573  -0.552  -0.550  -0.665  -0.625  -0.592  -0.636  -0.613  -0.590
27    T        -1.034  -1.048  -1.019  -0.905  -0.938  -0.900  -0.866  -0.879  -0.826
28    E         1.183   1.130   1.068   1.401   1.362   1.256   1.203   1.112   0.973
29    K        -0.573  -0.553  -0.560  -0.722  -0.684  -0.678  -0.636  -0.615  -0.600
30    F        -0.573  -0.583  -0.549  -0.905  -0.933  -0.855  -0.636  -0.645  -0.588
31    Q        -1.034  -1.029  -1.014  -0.990  -0.961  -0.944  -0.866  -0.860  -0.822
32    Q        -1.034  -1.040  -1.005  -0.552  -0.560  -0.502  -0.866  -0.871  -0.813
33    L        -0.573  -0.583  -0.549  -0.726  -0.693  -0.694  -0.636  -0.645  -0.588
34    S        -1.034  -1.037  -1.007  -0.995  -1.035  -0.971  -0.866  -0.868  -0.815
35    L         1.183   1.190   1.077   0.918   0.904   0.793   1.203   1.217   0.991
36    M        -1.034  -1.041  -1.016  -0.696  -0.710  -0.671  -0.866  -0.872  -0.824
37    I         0.811   0.828   0.853   0.260   0.268   0.305   0.514   0.545   0.550
38    G         0.063   0.076   0.073   0.027   0.043   0.046  -0.176  -0.155  -0.157
39    A        -0.399  -0.372  -0.448  -0.182  -0.160  -0.264  -0.406  -0.372  -0.459
40    L        -1.034  -1.031  -1.006  -1.260  -1.259  -1.229  -0.866  -0.862  -0.815
41    V        -1.034  -1.036  -1.002  -1.245  -1.281  -1.206  -0.866  -0.867  -0.811
42    A         1.183   1.208   1.078   1.339   1.370   1.198   1.203   1.247   0.992
43    C        -0.399  -0.417  -0.452  -0.247  -0.289  -0.336  -0.406  -0.429  -0.464
44    I         0.350   0.362   0.230   0.273   0.286   0.068   0.284   0.301   0.096
45    L        -1.034  -1.032  -1.005  -1.196  -1.189  -1.165  -0.866  -0.863  -0.813
46    G         2.082   2.087   2.171   2.175   2.165   2.306   2.353   2.362   2.499
47    F         0.063   0.077   0.072   0.165   0.192   0.197  -0.176  -0.154  -0.161
48    A        -0.573  -0.564  -0.544  -0.905  -0.902  -0.858  -0.636  -0.625  -0.584
49    Q         0.063   0.068   0.068  -0.142  -0.181  -0.144  -0.176  -0.175  -0.163
50    Q         0.350   0.330   0.227   0.515   0.490   0.344   0.284   0.252   0.091
51    S         0.698   0.704   0.777   0.644   0.670   0.764   0.284   0.293   0.395
52    L         0.063   0.036   0.064  -0.482  -0.538  -0.488  -0.176  -0.206  -0.172
53    K        -0.399  -0.425  -0.452  -0.157  -0.149  -0.231  -0.406  -0.440  -0.464
54    V        -1.034  -1.048  -1.019  -1.177  -1.205  -1.156  -0.866  -0.879  -0.826
55    L        -1.034  -1.039  -1.025  -1.186  -1.222  -1.136  -0.866  -0.870  -0.832
56    L        -0.399  -0.411  -0.460  -0.596  -0.629  -0.665  -0.406  -0.422  -0.474
57    T        -1.034  -1.041  -1.016  -1.048  -1.057  -1.019  -0.866  -0.872  -0.824
58    A        -1.496  -1.489  -1.433  -1.134  -1.105  -1.036  -1.095  -1.088  -1.011
59    Y         0.350   0.373   0.243   0.549   0.577   0.408   0.284   0.318   0.116
60    G        -0.573  -0.580  -0.558  -0.816  -0.847  -0.799  -0.636  -0.641  -0.597
61    I        -1.496  -1.489  -1.433  -1.585  -1.580  -1.492  -1.095  -1.088  -1.011
62    S        -1.034  -1.040  -1.005  -0.881  -0.906  -0.847  -0.866  -0.871  -0.813
63    C        -1.034  -1.032  -1.005  -0.852  -0.862  -0.808  -0.866  -0.863  -0.813
64    V        -0.573  -0.580  -0.558  -0.658  -0.668  -0.625  -0.636  -0.641  -0.597
65    I         0.063   0.077   0.078  -0.341  -0.311  -0.344  -0.176  -0.153  -0.150
66    T         0.811   0.830   0.844   0.682   0.703   0.697   0.514   0.549   0.533
67    L         0.350   0.306   0.211   0.157   0.083  -0.013   0.284   0.218   0.067
68    I         0.063   0.074   0.065  -0.401  -0.407  -0.431  -0.176  -0.168  -0.171
69    C        -0.573  -0.555  -0.555  -0.897  -0.895  -0.847  -0.636  -0.616  -0.595
70    V         1.183   1.195   1.074   1.093   1.106   0.950   1.203   1.225   0.985
71    L         0.811   0.792   0.839   0.228   0.170   0.242   0.514   0.473   0.522
72    P         2.082   2.087   2.171   2.145   2.145   2.276   2.353   2.362   2.499
73    A         0.350   0.375   0.238   0.593   0.623   0.444   0.284   0.321   0.107
74    Y         0.698   0.704   0.777   0.750   0.769   0.870   0.284   0.293   0.395
75    P         0.811   0.832   0.845   0.766   0.801   0.802   0.514   0.553   0.535
76    W        -1.034  -1.003  -1.018  -0.796  -0.768  -0.765  -0.866  -0.833  -0.826
77    Y         1.183   1.130   1.068   1.426   1.368   1.263   1.203   1.112   0.973
78    N         0.350   0.312   0.221   0.684   0.633   0.493   0.284   0.226   0.082
79    K         0.350   0.306   0.211   0.564   0.544   0.373   0.284   0.218   0.067
80    Q         0.063   0.073   0.067   0.321   0.334   0.332  -0.176  -0.165  -0.169
81    K        -0.399  -0.355  -0.461  -0.136  -0.058  -0.223  -0.406  -0.350  -0.475
82    L         0.063   0.095   0.066  -0.380  -0.336  -0.369  -0.176  -0.132  -0.164
83    R        -0.573  -0.558  -0.540  -0.444  -0.392  -0.381  -0.636  -0.619  -0.580
84    W         2.082   2.087   2.171   2.315   2.311   2.447   2.353   2.362   2.499
85    A        -1.034  -1.048  -1.019  -1.134  -1.179  -1.157  -0.866  -0.879  -0.826
86    Q         0.350   0.330   0.227   0.537   0.501   0.375   0.284   0.252   0.091
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    P         2.082   2.087   2.171   2.137   2.140   2.267   2.353   2.362   2.499
95    K        -0.578  -0.597  -0.571  -0.481  -0.484  -0.476  -0.626  -0.649  -0.607
96    I        -0.578  -0.585  -0.557  -0.661  -0.641  -0.616  -0.626  -0.636  -0.591
97    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    I        -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   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   V        -0.686  -0.680  -0.618  -0.719  -0.710  -0.617  -0.751  -0.743  -0.660
102   D        -0.578  -0.541  -0.558  -0.525  -0.462  -0.500  -0.626  -0.582  -0.592
103   Q        -1.131  -1.125  -1.066  -0.996  -0.973  -0.896  -0.957  -0.950  -0.870
104   Y        -1.131  -1.125  -1.066  -0.882  -0.865  -0.781  -0.957  -0.950  -0.870
105   D        -0.578  -0.589  -0.557  -0.530  -0.546  -0.504  -0.626  -0.640  -0.591
* 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/P46965
Output conservation file - output/P46965
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
