1     M         1.563   1.630   1.708   1.856   1.944   2.063   1.684   1.774   1.898
2     E         0.231   0.115  -0.019   0.011  -0.116  -0.279   0.198   0.033  -0.181
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     L         0.820   0.707   0.660   0.734   0.608   0.550   0.788   0.581   0.452
6     L         1.563   1.630   1.708   1.370   1.480   1.595   1.684   1.774   1.898
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    P         0.479   0.415   0.501   0.656   0.456   0.540   0.191   0.034   0.141
11    Q        -0.527  -0.344  -0.591  -0.835  -0.596  -0.903  -0.555  -0.314  -0.617
12    G         0.820   0.707   0.660   1.100   0.892   0.744   0.788   0.581   0.452
13    Q        -0.527  -0.609  -0.644  -0.235  -0.344  -0.437  -0.555  -0.657  -0.680
14    R        -0.886  -0.836  -0.706  -0.976  -0.910  -0.732  -1.003  -0.912  -0.753
15    N         0.121  -0.078  -0.109   0.491   0.281   0.154   0.042  -0.246  -0.313
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    N        -1.890  -1.843  -1.712  -1.587  -1.625  -1.381  -1.401  -1.323  -1.158
18    T        -0.397  -0.326  -0.215  -0.356  -0.251  -0.112  -0.716  -0.608  -0.467
19    Q        -0.382  -0.252  -0.514  -0.483  -0.325  -0.574  -0.373  -0.230  -0.524
20    V         1.563   1.630   1.708   1.724   1.811   1.936   1.684   1.774   1.898
21    T        -1.144  -1.067  -1.068  -0.897  -0.891  -0.813  -1.059  -0.968  -0.910
22    F        -1.262  -1.201  -1.094  -0.740  -0.645  -0.489  -1.173  -1.073  -0.933
23    E         0.231   0.446   0.065  -0.030   0.240  -0.240   0.198   0.499  -0.057
24    D         1.563   1.630   1.708   1.449   1.554   1.671   1.684   1.774   1.898
25    Q         1.563   1.630   1.708   1.684   1.783   1.897   1.684   1.774   1.898
26    Q        -0.634  -0.716  -0.669  -0.600  -0.751  -0.726  -0.716  -0.802  -0.715
27    K        -0.068  -0.134  -0.106  -0.078  -0.126  -0.096  -0.259  -0.332  -0.317
28    I         0.881   0.751   0.728   0.985   0.831   0.726   0.884   0.656   0.577
29    N         1.563   1.630   1.708   1.768   1.929   1.979   1.684   1.774   1.898
30    E        -0.320  -0.289  -0.200  -0.807  -0.721  -0.570  -0.602  -0.559  -0.446
31    F         1.563   1.630   1.708   1.812   1.910   2.021   1.684   1.774   1.898
32    S         1.563   1.630   1.708   1.704   1.799   1.917   1.684   1.774   1.898
33    K        -1.144  -1.245  -1.097  -0.957  -1.039  -0.817  -1.059  -1.109  -0.934
34    L         1.563   1.630   1.708   1.354   1.454   1.579   1.684   1.774   1.898
35    I        -0.068  -0.176  -0.152   0.127   0.037   0.055  -0.259  -0.429  -0.388
36    M        -1.144  -1.168  -1.079  -0.709  -0.761  -0.632  -1.059  -1.047  -0.919
37    R        -0.068  -0.026  -0.074   0.096   0.197   0.055  -0.259  -0.181  -0.268
38    K         0.231   0.115  -0.019   0.236   0.052  -0.162   0.198   0.033  -0.181
39    D         0.231   0.008  -0.037   0.240  -0.069  -0.166   0.198  -0.121  -0.208
40    A        -0.634  -0.720  -0.643  -0.518  -0.631  -0.545  -0.716  -0.783  -0.683
41    I        -0.830  -0.700  -0.670  -1.007  -0.798  -0.737  -0.944  -0.782  -0.716
42    A        -0.382  -0.141  -0.503  -0.585  -0.281  -0.723  -0.373  -0.060  -0.511
43    Q        -1.144  -1.150  -1.066  -1.321  -1.506  -1.306  -1.059  -1.039  -0.909
44    E        -0.711  -0.596  -0.629  -1.146  -0.974  -0.944  -0.830  -0.684  -0.676
45    L         0.231   0.056  -0.015   0.080  -0.174  -0.350   0.198  -0.055  -0.175
46    S        -0.068   0.207  -0.038  -0.105   0.257  -0.031  -0.259   0.129  -0.216
47    L        -1.576  -1.372  -1.401  -1.594  -1.190  -1.348  -1.287  -1.080  -1.044
48    Q        -1.144  -1.040  -1.047  -1.397  -1.239  -1.297  -1.059  -0.915  -0.888
49    R        -0.711  -0.723  -0.652  -0.637  -0.635  -0.536  -0.830  -0.794  -0.695
50    E        -0.634  -0.504  -0.595  -0.589  -0.360  -0.571  -0.716  -0.538  -0.628
51    E         0.231   0.056  -0.015  -0.005  -0.239  -0.306   0.198  -0.055  -0.175
52    K         0.881   0.751   0.728   0.863   0.700   0.657   0.884   0.656   0.577
53    E         1.563   1.630   1.708   1.168   1.260   1.400   1.684   1.774   1.898
54    Y         0.231   0.008  -0.037   0.583   0.217   0.039   0.198  -0.121  -0.208
55    L         0.881   0.751   0.728   0.752   0.595   0.552   0.884   0.656   0.577
56    D         0.231   0.228   0.027   0.196   0.207  -0.143   0.198   0.170  -0.113
57    D         1.563   1.630   1.708   1.449   1.554   1.671   1.684   1.774   1.898
58    V        -0.202  -0.188  -0.103  -0.400  -0.358  -0.213  -0.487  -0.414  -0.313
59    S        -0.382  -0.619  -0.625  -0.187  -0.625  -0.716  -0.373  -0.656  -0.657
60    L        -0.948  -1.106  -1.064  -0.822  -0.952  -0.881  -0.830  -0.978  -0.902
61    E         1.563   1.630   1.708   1.168   1.260   1.400   1.684   1.774   1.898
62    I        -0.634  -0.764  -0.667  -0.542  -0.680  -0.570  -0.716  -0.840  -0.713
63    E         1.563   1.630   1.708   1.168   1.260   1.400   1.684   1.774   1.898
64    L         1.563   1.630   1.708   1.354   1.454   1.579   1.684   1.774   1.898
65    I        -0.634  -0.743  -0.662  -0.601  -0.773  -0.662  -0.716  -0.821  -0.708
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    D         1.563   1.630   1.708   1.449   1.554   1.671   1.684   1.774   1.898
68    E         0.881   0.986   0.758   0.537   0.678   0.367   0.884   1.036   0.633
69    D         1.563   1.630   1.708   1.449   1.554   1.671   1.684   1.774   1.898
70    E         0.881   0.751   0.728   0.537   0.347   0.315   0.884   0.656   0.577
71    P        -1.458  -1.446  -1.399  -1.358  -1.339  -1.270  -1.173  -1.142  -1.041
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    V        -0.068  -0.124  -0.095   0.125   0.084   0.098  -0.259  -0.316  -0.298
76    Q         0.231   0.056  -0.015   0.493   0.254   0.118   0.198  -0.055  -0.175
77    Y         0.231   0.056  -0.015   0.667   0.407   0.258   0.198  -0.055  -0.175
78    K         1.563   1.630   1.708   1.465   1.559   1.686   1.684   1.774   1.898
79    V        -0.202  -0.059  -0.127  -0.151   0.024  -0.013  -0.487  -0.320  -0.359
80    G         1.563   1.630   1.708   1.856   1.953   2.063   1.684   1.774   1.898
81    D         0.545   0.705   0.618   0.216   0.496   0.270   0.313   0.576   0.371
82    L        -1.144  -1.072  -1.068  -0.821  -0.728  -0.714  -1.059  -0.972  -0.911
83    F         1.563   1.630   1.708   1.812   1.910   2.021   1.684   1.774   1.898
84    I        -0.320  -0.282  -0.201  -0.250  -0.190  -0.091  -0.602  -0.556  -0.448
85    F        -0.382  -0.619  -0.625   0.076  -0.270  -0.315  -0.373  -0.656  -0.657
86    M        -0.830  -0.844  -0.701  -0.924  -0.893  -0.684  -0.944  -0.922  -0.749
87    K        -0.202  -0.268  -0.143  -0.203  -0.226  -0.024  -0.487  -0.543  -0.377
88    Q        -0.634  -0.598  -0.650  -0.636  -0.699  -0.744  -0.716  -0.687  -0.696
89    S        -1.458  -1.432  -1.389  -1.248  -1.224  -1.226  -1.173  -1.127  -1.032
90    K        -0.830  -0.859  -0.701  -1.177  -1.188  -0.961  -0.944  -0.938  -0.750
91    V        -0.068  -0.229  -0.153   0.085  -0.212  -0.106  -0.259  -0.480  -0.386
92    T        -1.576  -1.482  -1.410  -1.446  -1.393  -1.206  -1.287  -1.167  -1.051
93    A        -0.382  -0.426  -0.552  -0.589  -0.706  -0.793  -0.373  -0.436  -0.570
94    Q        -0.711  -0.748  -0.654  -0.677  -0.671  -0.519  -0.830  -0.827  -0.701
95    L         0.545   0.655   0.614   0.272   0.452   0.365   0.313   0.487   0.363
96    E         0.881   0.818   0.727   0.602   0.537   0.455   0.884   0.770   0.577
97    K        -1.144  -1.180  -1.065  -1.082  -1.123  -0.938  -1.059  -1.053  -0.907
98    D        -0.382  -0.619  -0.625  -0.259  -0.573  -0.563  -0.373  -0.656  -0.657
99    A        -0.948  -0.950  -1.001  -0.548  -0.653  -0.691  -0.830  -0.824  -0.840
100   E         0.231   0.214   0.013  -0.030  -0.045  -0.316   0.198   0.169  -0.133
101   R        -1.890  -1.710  -1.684  -1.667  -1.468  -1.399  -1.401  -1.227  -1.140
102   L        -0.068   0.075  -0.034  -0.264  -0.021  -0.186  -0.259  -0.026  -0.207
103   D        -0.634  -0.677  -0.652  -0.885  -1.013  -0.937  -0.716  -0.757  -0.698
104   N        -1.144  -0.994  -1.059  -1.409  -1.210  -1.174  -1.059  -0.908  -0.903
105   K        -0.382  -0.459  -0.572  -0.356  -0.529  -0.682  -0.373  -0.481  -0.594
106   I         0.231   0.056  -0.015   0.403   0.189   0.004   0.198  -0.055  -0.175
107   E        -0.830  -0.742  -0.686  -1.243  -1.124  -0.980  -0.944  -0.831  -0.734
108   T        -1.890  -1.792  -1.696  -1.498  -1.365  -1.198  -1.401  -1.290  -1.148
109   L        -0.068  -0.026  -0.074  -0.243  -0.145  -0.212  -0.259  -0.181  -0.268
110   E        -0.382  -0.619  -0.625  -0.597  -0.916  -0.898  -0.373  -0.656  -0.657
111   D        -0.068   0.020  -0.089  -0.097   0.026  -0.236  -0.259  -0.140  -0.295
112   K        -1.144  -1.041  -1.049  -1.203  -1.031  -1.065  -1.059  -0.944  -0.894
113   Q        -1.576  -1.426  -1.410  -1.434  -1.169  -1.247  -1.287  -1.121  -1.050
114   R        -1.144  -0.994  -1.059  -1.321  -1.253  -1.165  -1.059  -0.908  -0.903
115   D        -1.144  -1.160  -1.057  -1.458  -1.463  -1.239  -1.059  -1.032  -0.897
116   I        -0.634  -0.571  -0.589  -0.676  -0.516  -0.600  -0.716  -0.606  -0.618
117   D        -0.320  -0.340  -0.221  -0.686  -0.723  -0.572  -0.602  -0.628  -0.474
118   S        -1.144  -1.155  -1.056  -1.257  -1.258  -1.162  -1.059  -1.027  -0.896
119   R        -0.202  -0.128  -0.135  -0.458  -0.403  -0.449  -0.487  -0.395  -0.370
120   L        -0.397  -0.358  -0.223  -0.630  -0.506  -0.328  -0.716  -0.652  -0.478
121   D        -1.144  -1.165  -1.071  -1.419  -1.440  -1.310  -1.059  -1.052  -0.912
122   A        -0.948  -0.824  -0.985  -1.077  -0.917  -1.063  -0.830  -0.681  -0.824
123   L         0.881   0.984   0.758   0.791   0.934   0.677   0.884   1.034   0.633
124   K         1.563   1.630   1.708   1.465   1.559   1.686   1.684   1.774   1.898
125   A        -1.262  -1.179  -1.086  -1.079  -1.008  -0.817  -1.173  -1.064  -0.927
126   I        -1.576  -1.561  -1.429  -1.321  -1.298  -1.104  -1.287  -1.230  -1.065
127   L         0.881   0.818   0.727   0.781   0.722   0.614   0.884   0.770   0.577
128   Y         0.881   0.818   0.727   1.284   1.223   1.063   0.884   0.770   0.577
129   A        -0.382  -0.538  -0.595   0.002  -0.240  -0.385  -0.373  -0.565  -0.622
130   K         0.231   0.213   0.015   0.272   0.238  -0.035   0.198   0.168  -0.131
131   F         0.881   0.818   0.727   1.219   1.147   0.999   0.884   0.770   0.577
132   G         0.881   0.751   0.728   1.299   1.150   1.118   0.884   0.656   0.577
133   D         0.479   0.492   0.522   0.302   0.309   0.361   0.191   0.185   0.182
134   N         0.121  -0.120  -0.109   0.433   0.068   0.051   0.042  -0.310  -0.313
135   I         1.563   1.630   1.708   1.622   1.744   1.838   1.684   1.774   1.898
136   N         0.820   0.753   0.675   1.089   1.007   0.861   0.788   0.659   0.479
137   L         1.563   1.630   1.708   1.355   1.447   1.581   1.684   1.774   1.898
138   E         0.820   0.658   0.660   0.480   0.233   0.219   0.788   0.493   0.452
139   R         1.563   1.630   1.708   1.811   1.909   2.019   1.684   1.774   1.898
* 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/P53900
Output conservation file - output/P53900
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
