1     M         1.599   1.609   1.676   1.801   1.812   1.906   1.758   1.772   1.874
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     G         1.599   1.609   1.676   1.750   1.762   1.856   1.758   1.772   1.874
5     L         0.213   0.252   0.020   0.468   0.520   0.205   0.175   0.232  -0.117
6     F         1.599   1.609   1.676   1.613   1.627   1.721   1.758   1.772   1.874
7     S        -0.624  -0.663  -0.643  -0.512  -0.565  -0.538  -0.689  -0.729  -0.683
8     F        -0.410  -0.417  -0.547  -0.606  -0.608  -0.775  -0.401  -0.409  -0.563
9     D        -1.099  -1.093  -1.044  -1.056  -1.030  -0.952  -0.977  -0.968  -0.885
10    G        -0.624  -0.568  -0.608  -0.715  -0.642  -0.691  -0.689  -0.622  -0.644
11    G        -0.969  -0.959  -0.990  -0.978  -0.960  -1.010  -0.833  -0.820  -0.829
12    K        -1.789  -1.785  -1.675  -1.507  -1.488  -1.347  -1.265  -1.258  -1.128
13    K        -1.444  -1.429  -1.373  -1.568  -1.549  -1.431  -1.121  -1.104  -1.017
14    E        -1.521  -1.518  -1.410  -1.563  -1.548  -1.402  -1.181  -1.175  -1.044
15    S        -1.118  -1.133  -1.057  -0.846  -0.866  -0.774  -0.985  -0.995  -0.893
16    Q        -0.720  -0.682  -0.661  -0.634  -0.584  -0.540  -0.781  -0.733  -0.697
17    P        -0.211  -0.197  -0.164  -0.339  -0.301  -0.326  -0.446  -0.426  -0.387
18    P        -0.211  -0.219  -0.173  -0.266  -0.286  -0.195  -0.446  -0.457  -0.400
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    N        -0.065  -0.065  -0.103   0.143   0.160   0.094  -0.257  -0.245  -0.305
26    T        -0.624  -0.641  -0.637  -0.524  -0.556  -0.577  -0.689  -0.707  -0.677
27    R         0.410   0.411   0.486   0.011   0.002   0.089   0.031   0.029   0.129
28    S        -0.410  -0.395  -0.537  -0.278  -0.262  -0.503  -0.401  -0.381  -0.550
29    Q        -1.444  -1.456  -1.374  -1.334  -1.356  -1.255  -1.121  -1.127  -1.018
30    R         1.599   1.609   1.676   1.633   1.643   1.740   1.758   1.772   1.874
31    K        -0.065  -0.085  -0.115  -0.385  -0.412  -0.410  -0.257  -0.297  -0.326
32    L        -1.444  -1.435  -1.375  -1.498  -1.482  -1.357  -1.121  -1.109  -1.018
33    C         1.599   1.609   1.676   1.718   1.730   1.824   1.758   1.772   1.874
34    W         1.599   1.609   1.676   1.795   1.806   1.900   1.758   1.772   1.874
35    E         0.213   0.127  -0.008   0.210   0.100  -0.077   0.175   0.051  -0.158
36    S        -0.065  -0.071  -0.125  -0.153  -0.170  -0.303  -0.257  -0.274  -0.341
37    R         1.599   1.609   1.676   1.633   1.643   1.740   1.758   1.772   1.874
38    D         1.599   1.609   1.676   1.573   1.582   1.682   1.758   1.772   1.874
39    A        -0.624  -0.590  -0.632  -0.647  -0.596  -0.666  -0.689  -0.650  -0.669
40    F         0.885   0.834   0.718   1.021   0.962   0.812   0.895   0.809   0.580
41    F         1.599   1.609   1.676   1.613   1.627   1.721   1.758   1.772   1.874
42    Q        -1.444  -1.398  -1.374  -1.253  -1.188  -1.157  -1.121  -1.077  -1.017
43    C         1.599   1.609   1.676   1.718   1.730   1.824   1.758   1.772   1.874
44    L         1.599   1.609   1.676   1.666   1.678   1.773   1.758   1.772   1.874
45    D         0.213   0.230  -0.004   0.300   0.323  -0.046   0.175   0.201  -0.152
46    K         0.885   0.834   0.718   0.582   0.520   0.367   0.895   0.809   0.580
47    A        -0.410  -0.400  -0.552  -0.059  -0.040  -0.249  -0.401  -0.388  -0.569
48    D        -1.099  -1.079  -1.052  -1.019  -0.977  -0.958  -0.977  -0.955  -0.891
49    I         0.885   0.915   0.723   1.117   1.154   0.898   0.895   0.941   0.589
50    L        -0.755  -0.772  -0.688  -0.649  -0.664  -0.535  -0.833  -0.844  -0.730
51    D         0.392   0.400   0.484   0.244   0.252   0.374  -0.005   0.007   0.126
52    A         0.491   0.515   0.551   0.357   0.389   0.435   0.191   0.234   0.261
53    M         0.089   0.066  -0.047   0.336   0.308   0.151  -0.005  -0.038  -0.215
54    D         1.599   1.609   1.676   1.586   1.597   1.694   1.758   1.772   1.874
55    P         0.620   0.645   0.589   0.706   0.745   0.621   0.436   0.478   0.335
56    K         1.599   1.609   1.676   1.203   1.216   1.318   1.758   1.772   1.874
57    N        -1.099  -1.057  -1.055  -0.965  -0.917  -0.844  -0.977  -0.937  -0.894
58    S        -0.624  -0.612  -0.631  -0.647  -0.637  -0.659  -0.689  -0.678  -0.671
59    K        -0.149  -0.171  -0.140  -0.593  -0.630  -0.583  -0.401  -0.422  -0.366
60    S        -1.444  -1.426  -1.378  -1.245  -1.220  -1.155  -1.121  -1.102  -1.021
61    I        -0.280  -0.284  -0.206  -0.252  -0.275  -0.159  -0.545  -0.551  -0.447
62    K        -0.564  -0.593  -0.609  -0.746  -0.786  -0.768  -0.593  -0.626  -0.636
63    S        -0.280  -0.263  -0.199  -0.711  -0.695  -0.576  -0.545  -0.521  -0.437
64    H        -1.444  -1.440  -1.384  -1.390  -1.390  -1.243  -1.121  -1.114  -1.026
65    C         1.599   1.609   1.676   1.718   1.730   1.824   1.758   1.772   1.874
66    K        -0.624  -0.632  -0.634  -0.773  -0.771  -0.740  -0.689  -0.693  -0.670
67    V        -0.969  -0.968  -1.011  -0.823  -0.850  -0.912  -0.833  -0.829  -0.849
68    E         0.885   0.891   0.720   0.796   0.802   0.580   0.895   0.903   0.583
69    N        -1.099  -1.113  -1.057  -1.196  -1.210  -1.156  -0.977  -0.984  -0.895
70    E        -1.099  -1.069  -1.041  -1.350  -1.317  -1.264  -0.977  -0.948  -0.883
71    K        -0.755  -0.752  -0.682  -1.094  -1.076  -0.962  -0.833  -0.827  -0.725
72    F         0.557   0.562   0.560   0.581   0.590   0.576   0.319   0.324   0.279
73    E         0.885   0.891   0.720   0.792   0.799   0.573   0.895   0.903   0.583
74    E        -1.444  -1.453  -1.376  -1.339  -1.382  -1.264  -1.121  -1.125  -1.019
75    N        -0.065  -0.044  -0.117  -0.144  -0.108  -0.266  -0.257  -0.222  -0.330
76    C         1.599   1.609   1.676   1.718   1.730   1.824   1.758   1.772   1.874
77    A        -0.065  -0.078  -0.101   0.005  -0.018  -0.034  -0.257  -0.267  -0.304
78    H        -0.624  -0.565  -0.608  -0.418  -0.355  -0.374  -0.689  -0.619  -0.644
79    S         0.885   0.834   0.718   0.989   0.932   0.759   0.895   0.809   0.580
80    W         1.599   1.609   1.676   1.795   1.806   1.900   1.758   1.772   1.874
81    I        -0.149  -0.146  -0.131  -0.056  -0.051  -0.022  -0.401  -0.396  -0.356
82    K        -0.410  -0.467  -0.567  -0.583  -0.652  -0.766  -0.401  -0.472  -0.587
83    Y         1.599   1.609   1.676   1.795   1.806   1.900   1.758   1.772   1.874
84    F         1.599   1.609   1.676   1.613   1.627   1.721   1.758   1.772   1.874
85    K        -0.065  -0.021  -0.091  -0.394  -0.336  -0.397  -0.257  -0.199  -0.286
86    E         0.213   0.127  -0.008   0.102  -0.027  -0.265   0.175   0.051  -0.158
87    K         0.885   0.834   0.718   0.613   0.555   0.424   0.895   0.809   0.580
88    R         1.599   1.609   1.676   1.633   1.643   1.740   1.758   1.772   1.874
89    V        -0.624  -0.618  -0.630  -0.308  -0.299  -0.298  -0.689  -0.680  -0.665
90    I        -1.099  -1.123  -1.066  -0.751  -0.775  -0.686  -0.977  -0.993  -0.903
91    D         0.885   0.848   0.718   0.917   0.863   0.655   0.895   0.833   0.580
92    F        -0.624  -0.679  -0.652  -0.444  -0.502  -0.448  -0.689  -0.743  -0.691
93    K        -0.969  -1.020  -1.032  -1.028  -1.079  -1.032  -0.833  -0.883  -0.869
94    R         0.557   0.514   0.533   0.379   0.278   0.243   0.319   0.232   0.225
95    E        -0.065  -0.100  -0.114  -0.315  -0.374  -0.430  -0.257  -0.298  -0.320
96    Q        -0.624  -0.640  -0.636  -0.630  -0.650  -0.689  -0.689  -0.703  -0.673
97    T        -1.099  -1.099  -1.064  -0.674  -0.676  -0.631  -0.977  -0.974  -0.901
98    I         0.410   0.424   0.489   0.356   0.377   0.466   0.031   0.054   0.136
99    K         0.213   0.230  -0.004  -0.085  -0.059  -0.415   0.175   0.201  -0.152
100   R        -0.624  -0.585  -0.626  -1.022  -0.975  -0.983  -0.689  -0.648  -0.664
101   I        -0.969  -0.935  -1.007  -0.585  -0.541  -0.631  -0.833  -0.794  -0.846
102   E         1.599   1.609   1.676   1.409   1.419   1.521   1.758   1.772   1.874
103   Q        -0.624  -0.636  -0.642  -0.725  -0.740  -0.727  -0.689  -0.698  -0.679
104   E         0.410   0.424   0.489   0.148   0.175   0.248   0.031   0.054   0.136
105   A        -0.162  -0.136  -0.133  -0.083  -0.035  -0.048  -0.397  -0.355  -0.350
106   K         0.815   0.825   0.684   0.800   0.797   0.548   0.779   0.793   0.517
107   Q        -0.162  -0.146  -0.152  -0.224  -0.197  -0.250  -0.397  -0.386  -0.379
108   R        -0.716  -0.708  -0.671  -0.697  -0.698  -0.668  -0.789  -0.778  -0.711
109   -        -0.211  -0.257  -0.192  -0.116  -0.179  -0.089  -0.446  -0.511  -0.428
110   -        -0.211  -0.257  -0.192  -0.247  -0.342  -0.281  -0.446  -0.511  -0.428
111   -        -0.211  -0.257  -0.192  -0.151  -0.210  -0.128  -0.446  -0.511  -0.428
112   -         0.392   0.406   0.488  -0.014   0.049   0.158  -0.005   0.019   0.134
113   -        -0.815  -0.805  -0.711  -0.650  -0.634  -0.504  -0.887  -0.874  -0.753
114   -        -0.815  -0.805  -0.711  -0.880  -0.848  -0.731  -0.887  -0.874  -0.753
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   N        -1.789  -1.785  -1.675  -1.558  -1.533  -1.397  -1.265  -1.258  -1.128
119   Q        -0.410  -0.430  -0.551  -0.655  -0.689  -0.854  -0.401  -0.425  -0.568
* 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/Q3E846
Output conservation file - output/Q3E846
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
