1     M         1.563   1.576   1.625   1.767   1.772   1.868   1.684   1.701   1.778
2     -         0.316   0.340   0.242   0.094   0.237  -0.063   0.204   0.243   0.064
3     -         0.151   0.100   0.158   0.092  -0.002   0.100  -0.071  -0.160  -0.081
4     P         0.453   0.449   0.278   0.534   0.491   0.285   0.421   0.415   0.126
5     P         1.563   1.576   1.625   1.552   1.537   1.659   1.684   1.701   1.778
6     R         0.453   0.376   0.275   0.283   0.199   0.051   0.421   0.300   0.121
7     S         0.453   0.510   0.291   0.662   0.745   0.422   0.421   0.508   0.146
8     I         0.453   0.510   0.288   0.455   0.542   0.232   0.421   0.508   0.142
9     E         0.453   0.376   0.275   0.570   0.429   0.319   0.421   0.300   0.121
10    E         1.563   1.576   1.625   1.581   1.573   1.687   1.684   1.701   1.778
11    W         0.453   0.376   0.275   0.759   0.627   0.475   0.421   0.300   0.121
12    F         0.453   0.510   0.288   0.373   0.467   0.099   0.421   0.508   0.142
13    Y         0.453   0.449   0.278   0.592   0.580   0.284   0.421   0.415   0.126
14    Y        -0.777  -0.747  -0.726  -0.863  -0.832  -0.734  -0.842  -0.806  -0.751
15    K        -0.545  -0.600  -0.662  -0.599  -0.615  -0.781  -0.527  -0.596  -0.668
16    L         1.563   1.576   1.625   1.463   1.495   1.572   1.684   1.701   1.778
17    L        -0.777  -0.812  -0.717  -0.756  -0.797  -0.638  -0.842  -0.874  -0.740
18    S        -0.545  -0.511  -0.641  -0.390  -0.374  -0.531  -0.527  -0.480  -0.640
19    S         1.563   1.576   1.625   1.682   1.713   1.785   1.684   1.701   1.778
20    P        -0.545  -0.511  -0.641  -0.440  -0.439  -0.586  -0.527  -0.480  -0.641
21    G         0.453   0.470   0.288   0.641   0.676   0.323   0.421   0.448   0.142
22    F         1.563   1.576   1.625   1.448   1.460   1.558   1.684   1.701   1.778
23    H         0.453   0.376   0.275   0.745   0.616   0.473   0.421   0.300   0.121
24    R        -0.545  -0.600  -0.662  -0.628  -0.691  -0.750  -0.527  -0.596  -0.668
25    F        -0.545  -0.600  -0.662  -0.495  -0.588  -0.642  -0.527  -0.596  -0.668
26    V         1.563   1.576   1.625   1.711   1.713   1.813   1.684   1.701   1.778
27    R         1.563   1.576   1.625   1.296   1.346   1.410   1.684   1.701   1.778
28    K         0.070   0.076   0.131  -0.408  -0.308  -0.330  -0.211  -0.202  -0.129
29    V         1.563   1.576   1.625   1.711   1.713   1.813   1.684   1.701   1.778
30    Y         0.070   0.056   0.136   0.081   0.041   0.179  -0.211  -0.237  -0.120
31    R        -1.391  -1.346  -1.350  -1.210  -1.148  -1.187  -1.158  -1.104  -1.078
32    K         0.453   0.376   0.275   0.306   0.274  -0.016   0.421   0.300   0.121
33    V         0.070   0.056   0.136   0.104   0.058   0.201  -0.211  -0.237  -0.120
34    N         1.563   1.576   1.625   1.739   1.737   1.841   1.684   1.701   1.778
35    G         0.070   0.056   0.136  -0.107  -0.140  -0.040  -0.211  -0.237  -0.120
36    I         1.563   1.576   1.625   1.767   1.784   1.868   1.684   1.701   1.778
37    K        -0.777  -0.775  -0.727  -0.942  -0.911  -0.838  -0.842  -0.834  -0.753
38    E        -1.391  -1.431  -1.350  -1.227  -1.335  -1.166  -1.158  -1.192  -1.078
39    D        -1.391  -1.383  -1.329  -0.958  -0.966  -0.875  -1.158  -1.145  -1.057
40    P        -0.777  -0.775  -0.727  -0.827  -0.876  -0.728  -0.842  -0.834  -0.753
41    F        -0.743  -0.687  -0.699  -0.883  -0.803  -0.817  -0.783  -0.708  -0.714
42    T        -0.873  -0.858  -0.757  -0.832  -0.883  -0.660  -0.948  -0.924  -0.786
43    D        -0.777  -0.749  -0.710  -0.657  -0.634  -0.548  -0.842  -0.808  -0.733
44    Q        -0.545  -0.600  -0.662  -0.209  -0.328  -0.404  -0.527  -0.596  -0.668
45    S        -1.391  -1.367  -1.329  -1.045  -1.019  -0.956  -1.158  -1.127  -1.057
46    T        -1.391  -1.346  -1.350  -1.275  -1.156  -1.182  -1.158  -1.104  -1.078
47    A        -2.006  -2.002  -1.865  -1.943  -1.966  -1.740  -1.474  -1.463  -1.299
48    F        -1.391  -1.334  -1.313  -1.129  -1.042  -1.033  -1.158  -1.092  -1.042
49    Q        -0.545  -0.511  -0.641  -0.345  -0.328  -0.470  -0.527  -0.480  -0.640
50    Y        -1.391  -1.367  -1.322  -1.454  -1.434  -1.352  -1.158  -1.127  -1.050
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    L         0.070   0.056   0.136  -0.087  -0.087   0.029  -0.211  -0.237  -0.120
55    Y         0.070   0.052   0.124  -0.099  -0.161  -0.052  -0.211  -0.245  -0.141
56    K        -0.545  -0.543  -0.643  -0.509  -0.437  -0.629  -0.527  -0.520  -0.643
57    P         1.563   1.576   1.625   1.552   1.537   1.659   1.684   1.701   1.778
58    T         1.563   1.576   1.625   1.753   1.772   1.855   1.684   1.701   1.778
59    P        -0.545  -0.511  -0.641  -0.691  -0.625  -0.810  -0.527  -0.480  -0.640
60    R        -1.391  -1.403  -1.347  -1.391  -1.389  -1.319  -1.158  -1.164  -1.075
61    Q         0.070   0.095   0.139   0.152   0.165   0.249  -0.211  -0.169  -0.115
62    K         1.563   1.576   1.625   1.433   1.540   1.543   1.684   1.701   1.778
63    F         0.453   0.376   0.275   0.433   0.311   0.188   0.421   0.300   0.121
64    K        -0.777  -0.747  -0.726  -0.963  -0.855  -0.914  -0.842  -0.806  -0.751
65    A         1.563   1.576   1.625   1.739   1.739   1.841   1.684   1.701   1.778
66    L        -0.777  -0.747  -0.726  -0.937  -0.908  -0.865  -0.842  -0.806  -0.751
67    R         1.563   1.576   1.625   1.296   1.346   1.410   1.684   1.701   1.778
68    L        -1.391  -1.413  -1.336  -1.263  -1.314  -1.225  -1.158  -1.174  -1.064
69    L         0.070   0.056   0.136  -0.103  -0.118   0.011  -0.211  -0.237  -0.120
70    F         0.070   0.056   0.136  -0.099  -0.138   0.018  -0.211  -0.237  -0.120
71    W        -0.545  -0.600  -0.662  -0.345  -0.462  -0.612  -0.527  -0.596  -0.668
72    D         0.453   0.376   0.275   0.779   0.679   0.509   0.421   0.300   0.121
73    E         1.563   1.576   1.625   1.581   1.573   1.687   1.684   1.701   1.778
74    M        -0.545  -0.543  -0.643  -0.296  -0.318  -0.491  -0.527  -0.520  -0.643
75    R         0.070   0.056   0.136  -0.449  -0.399  -0.340  -0.211  -0.237  -0.120
76    S        -1.391  -1.403  -1.347  -1.221  -1.239  -1.180  -1.158  -1.164  -1.075
77    T        -0.777  -0.778  -0.712  -0.637  -0.641  -0.537  -0.842  -0.838  -0.736
78    F        -0.545  -0.511  -0.641  -0.594  -0.554  -0.749  -0.527  -0.480  -0.641
79    G        -0.545  -0.570  -0.638  -0.331  -0.390  -0.530  -0.527  -0.558  -0.637
80    F         0.070   0.088   0.143  -0.296  -0.269  -0.185  -0.211  -0.181  -0.109
81    R        -1.391  -1.403  -1.347  -1.305  -1.333  -1.243  -1.158  -1.164  -1.075
82    R         0.026   0.034   0.123  -0.566  -0.494  -0.397  -0.290  -0.275  -0.143
83    R        -0.743  -0.689  -0.701  -1.039  -0.956  -0.962  -0.783  -0.710  -0.717
84    L        -0.873  -0.871  -0.757  -0.996  -1.000  -0.819  -0.948  -0.939  -0.786
85    G        -0.873  -0.871  -0.757  -0.745  -0.746  -0.575  -0.948  -0.939  -0.786
86    D         0.151   0.161   0.162  -0.076  -0.025  -0.037  -0.071  -0.055  -0.075
87    R        -0.873  -0.871  -0.757  -1.207  -1.214  -1.024  -0.948  -0.939  -0.786
88    F         0.151   0.161   0.162  -0.212  -0.207  -0.211  -0.071  -0.055  -0.075
89    K         1.563   1.576   1.625   1.346   1.410   1.459   1.684   1.701   1.778
90    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P53869
Output conservation file - output/P53869
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
