1     M         1.704   1.744   1.783   1.934   1.977   2.040   1.872   1.928   1.992
2     H         1.704   1.744   1.783   1.904   1.949   2.012   1.872   1.928   1.992
3     P         1.704   1.744   1.783   1.987   2.036   2.092   1.872   1.928   1.992
4     Q         0.421   0.195   0.141   0.694   0.370   0.272   0.404   0.066  -0.034
5     L         1.047   1.038   0.878   1.063   1.070   0.870   1.082   1.058   0.758
6     E        -0.486  -0.545  -0.486  -0.577  -0.572  -0.488  -0.612  -0.648  -0.573
7     A        -1.205  -1.255  -1.222  -1.040  -1.098  -1.137  -0.950  -0.985  -0.927
8     E        -0.486  -0.486  -0.472  -0.719  -0.745  -0.701  -0.612  -0.599  -0.560
9     R         0.421   0.195   0.141   0.596   0.287   0.209   0.404   0.066  -0.034
10    F         0.421   0.195   0.141   0.828   0.502   0.414   0.404   0.066  -0.034
11    H        -0.903  -0.889  -0.889  -0.788  -0.888  -0.845  -0.837  -0.819  -0.786
12    S        -0.714  -0.780  -0.843  -0.187  -0.339  -0.386  -0.612  -0.688  -0.736
13    C         1.704   1.744   1.783   1.868   1.916   1.977   1.872   1.928   1.992
14    L        -1.319  -1.274  -1.218  -1.364  -1.281  -1.180  -1.063  -1.008  -0.925
15    D         0.134   0.198   0.092   0.186   0.318   0.122  -0.047   0.060  -0.114
16    F        -0.169  -0.135  -0.344   0.051   0.091  -0.142  -0.160  -0.136  -0.389
17    I         0.550   0.573   0.630   0.600   0.616   0.699   0.179   0.197   0.271
18    N        -1.621  -1.552  -1.503  -1.220  -1.121  -1.090  -1.176  -1.106  -1.028
19    A         1.704   1.744   1.783   1.728   1.763   1.841   1.872   1.928   1.992
20    L         1.047   0.905   0.868   1.056   0.894   0.841   1.082   0.830   0.738
21    D         0.495   0.555   0.615   0.121   0.182   0.277   0.066   0.161   0.240
22    K         0.550   0.694   0.691  -0.102   0.203   0.143   0.179   0.439   0.396
23    C         1.704   1.744   1.783   1.868   1.916   1.977   1.872   1.928   1.992
24    H         1.704   1.744   1.783   1.904   1.949   2.012   1.872   1.928   1.992
25    Q        -0.412  -0.506  -0.448  -0.410  -0.581  -0.516  -0.499  -0.586  -0.523
26    K        -0.903  -0.995  -0.909  -1.103  -1.194  -1.092  -0.837  -0.901  -0.803
27    E         0.315   0.108   0.071   0.194  -0.055  -0.104   0.250  -0.070  -0.141
28    Y         0.513   0.627   0.653   0.607   0.786   0.810   0.103   0.307   0.319
29    Y        -0.903  -0.914  -0.892  -0.524  -0.576  -0.525  -0.837  -0.837  -0.789
30    K        -0.169  -0.394  -0.426  -0.133  -0.356  -0.366  -0.160  -0.449  -0.492
31    R         0.004   0.072   0.013  -0.302  -0.260  -0.302  -0.273  -0.199  -0.247
32    I        -1.205  -1.182  -1.171  -0.739  -0.737  -0.684  -0.950  -0.925  -0.884
33    F         0.004  -0.073   0.017  -0.016  -0.070   0.063  -0.273  -0.357  -0.243
34    G         1.704   1.744   1.783   1.934   1.984   2.040   1.872   1.928   1.992
35    L         0.004  -0.037   0.003  -0.123  -0.174  -0.137  -0.273  -0.314  -0.259
36    C         1.704   1.744   1.783   1.868   1.916   1.977   1.872   1.928   1.992
37    N         1.704   1.744   1.783   1.820   1.856   1.930   1.872   1.928   1.992
38    N        -0.903  -0.995  -0.909  -0.609  -0.802  -0.651  -0.837  -0.901  -0.803
39    E        -0.169  -0.394  -0.426  -0.228  -0.529  -0.552  -0.160  -0.449  -0.492
40    K         1.704   1.744   1.783   1.386   1.462   1.511   1.872   1.928   1.992
41    D        -0.412  -0.420  -0.436  -0.517  -0.486  -0.500  -0.499  -0.483  -0.507
42    A        -0.184  -0.105  -0.058  -0.525  -0.442  -0.352  -0.499  -0.385  -0.333
43    L         1.704   1.744   1.783   1.595   1.661   1.714   1.872   1.928   1.992
44    N        -1.205  -1.147  -1.157  -0.750  -0.785  -0.749  -0.950  -0.896  -0.873
45    K        -0.600  -0.573  -0.525  -0.903  -0.819  -0.767  -0.724  -0.679  -0.617
46    C         1.704   1.744   1.783   1.868   1.916   1.977   1.872   1.928   1.992
47    L         1.704   1.744   1.783   1.595   1.661   1.714   1.872   1.928   1.992
48    K        -0.600  -0.598  -0.518  -0.626  -0.607  -0.499  -0.724  -0.704  -0.609
49    E        -1.017  -0.937  -0.907  -1.123  -1.001  -0.979  -0.950  -0.852  -0.802
50    A        -0.714  -0.780  -0.843  -0.457  -0.647  -0.678  -0.612  -0.688  -0.736
51    S         0.723   0.866   0.774   0.722   0.922   0.786   0.517   0.762   0.559
52    L        -1.319  -1.327  -1.235  -0.967  -0.954  -0.848  -1.063  -1.043  -0.938
53    N        -0.903  -0.893  -0.849  -1.047  -1.103  -0.956  -0.837  -0.814  -0.750
54    N        -1.319  -1.221  -1.208  -0.911  -0.837  -0.780  -1.063  -0.964  -0.918
55    K        -0.903  -0.794  -0.841  -1.018  -0.799  -0.906  -0.837  -0.717  -0.737
56    K        -0.412  -0.354  -0.434  -0.616  -0.525  -0.605  -0.499  -0.426  -0.513
57    R        -1.319  -1.266  -1.212  -1.309  -1.195  -1.169  -1.063  -0.997  -0.921
58    A        -0.600  -0.373  -0.483  -0.534  -0.223  -0.343  -0.724  -0.454  -0.565
59    V        -0.412  -0.464  -0.470  -0.173  -0.306  -0.275  -0.499  -0.573  -0.556
60    I        -1.621  -1.574  -1.489  -1.504  -1.452  -1.328  -1.176  -1.119  -1.019
61    E        -0.714  -0.845  -0.853  -0.806  -0.972  -0.998  -0.612  -0.754  -0.746
62    S        -0.903  -0.887  -0.870  -0.510  -0.541  -0.472  -0.837  -0.817  -0.770
63    R        -0.412  -0.471  -0.441  -0.472  -0.528  -0.534  -0.499  -0.548  -0.521
64    I        -0.714  -0.751  -0.815  -0.731  -0.757  -0.840  -0.612  -0.660  -0.707
65    K         1.047   0.969   0.867   0.809   0.730   0.568   1.082   0.942   0.737
66    R        -0.184  -0.115  -0.064  -0.562  -0.477  -0.391  -0.499  -0.401  -0.342
67    A         0.134   0.186   0.065  -0.149  -0.092  -0.229  -0.047  -0.002  -0.165
68    D        -1.319  -1.273  -1.200  -1.172  -1.081  -1.008  -1.063  -1.005  -0.913
69    V        -0.903  -0.712  -0.839  -0.489  -0.262  -0.407  -0.837  -0.636  -0.740
70    E         0.421   0.254   0.161   0.263   0.040  -0.105   0.404   0.150  -0.004
71    K        -0.903  -0.753  -0.847  -0.994  -0.805  -0.977  -0.837  -0.693  -0.749
72    R         0.134   0.161   0.080  -0.164  -0.086  -0.228  -0.047   0.013  -0.140
73    W        -0.412  -0.382  -0.459  -0.106  -0.079  -0.256  -0.499  -0.465  -0.543
74    K         0.723   0.776   0.699   0.348   0.443   0.294   0.517   0.595   0.411
75    K        -0.412  -0.404  -0.459  -0.823  -0.829  -0.899  -0.499  -0.497  -0.543
76    I        -1.205  -1.096  -1.174  -0.894  -0.774  -0.916  -0.950  -0.840  -0.887
77    E         0.723   0.644   0.664   0.417   0.303   0.330   0.517   0.340   0.341
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    E         1.704   1.744   1.783   1.406   1.477   1.531   1.872   1.928   1.992
80    E         1.704   1.744   1.783   1.390   1.455   1.516   1.872   1.928   1.992
81    E        -0.524  -0.557  -0.518  -0.856  -0.884  -0.816  -0.635  -0.665  -0.607
82    Y         0.989   0.856   0.805   1.313   1.141   1.038   0.987   0.743   0.620
83    G         0.989   0.856   0.805   1.270   1.064   0.953   0.987   0.743   0.620
84    E        -0.524  -0.604  -0.531  -0.863  -0.872  -0.755  -0.635  -0.706  -0.620
85    D         0.513   0.552   0.614   0.459   0.491   0.593   0.103   0.153   0.237
86    A        -0.869  -0.927  -0.909  -0.724  -0.895  -0.850  -0.782  -0.836  -0.801
87    I         0.661   0.734   0.707   0.789   0.900   0.835   0.397   0.516   0.427
88    L         1.704   1.744   1.783   1.587   1.650   1.706   1.872   1.928   1.992
89    K         0.315   0.132   0.071   0.087  -0.158  -0.280   0.250  -0.031  -0.141
90    T        -1.345  -1.304  -1.225  -1.228  -1.151  -1.022  -1.077  -1.025  -0.930
91    I        -0.309  -0.348  -0.454   0.009  -0.116  -0.250  -0.340  -0.398  -0.527
92    L         0.037   0.014   0.023  -0.070  -0.102  -0.095  -0.192  -0.206  -0.222
93    D        -1.000  -0.977  -0.926  -1.198  -1.247  -1.117  -0.929  -0.893  -0.818
94    R         0.037   0.046  -0.003  -0.186  -0.239  -0.320  -0.192  -0.201  -0.263
95    Q         0.037   0.034   0.043  -0.214  -0.183  -0.169  -0.192  -0.177  -0.188
96    Y        -1.000  -0.994  -0.922  -1.010  -0.994  -0.900  -0.929  -0.904  -0.815
97    A        -0.524  -0.448  -0.460  -0.759  -0.578  -0.685  -0.635  -0.529  -0.541
98    K        -0.524  -0.604  -0.531  -0.614  -0.664  -0.538  -0.635  -0.706  -0.620
99    K        -0.060  -0.089  -0.019  -0.585  -0.652  -0.542  -0.336  -0.366  -0.285
100   K        -1.019  -0.856  -0.901  -1.015  -0.680  -0.904  -0.938  -0.762  -0.794
101   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   S        -0.600  -0.515  -0.518  -0.574  -0.463  -0.445  -0.724  -0.631  -0.608
118   K        -0.903  -0.948  -0.877  -1.198  -1.180  -1.100  -0.837  -0.864  -0.776
* 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/Q3E7A4
Output conservation file - output/Q3E7A4
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
