1     M         1.944   1.949   2.087   2.147   2.158   2.372   2.201   2.210   2.464
2     V        -1.295  -1.287  -1.194  -1.188  -1.160  -1.037  -1.092  -1.085  -0.964
3     E        -1.295  -1.287  -1.194  -1.439  -1.452  -1.294  -1.092  -1.085  -0.964
4     P        -0.179  -0.142  -0.104  -0.546  -0.484  -0.413  -0.434  -0.388  -0.328
5     A         0.031   0.104   0.010  -0.261  -0.160  -0.303  -0.104   0.003  -0.149
6     R         0.937   0.972   0.877   1.112   1.165   1.027   0.884   0.944   0.734
7     -        -0.149  -0.155  -0.083  -0.255  -0.230  -0.159  -0.372  -0.383  -0.290
8     -         0.812   0.828   0.831   0.739   0.763   0.762   0.657   0.685   0.645
9     -        -0.149  -0.155  -0.083  -0.366  -0.375  -0.285  -0.372  -0.383  -0.290
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -0.737  -0.738  -0.688  -0.795  -0.755  -0.726  -0.763  -0.764  -0.692
14    -        -0.737  -0.721  -0.671  -0.873  -0.848  -0.757  -0.763  -0.744  -0.672
15    -        -1.295  -1.296  -1.194  -1.025  -0.993  -0.870  -1.092  -1.093  -0.964
16    -        -1.295  -1.296  -1.194  -1.144  -1.164  -0.992  -1.092  -1.093  -0.964
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    K         1.037   1.008   0.909   0.869   0.812   0.722   1.057   1.007   0.797
19    K         1.944   1.949   2.087   1.657   1.647   1.872   2.201   2.210   2.464
20    Q        -0.732  -0.772  -0.682  -0.587  -0.643  -0.511  -0.772  -0.812  -0.690
21    R        -1.197  -1.170  -1.133  -1.374  -1.379  -1.272  -1.001  -0.975  -0.907
22    I        -0.092  -0.094  -0.054  -0.302  -0.330  -0.275  -0.315  -0.311  -0.259
23    D         0.198   0.184   0.056   0.381   0.364   0.121   0.143   0.122  -0.078
24    R        -1.197  -1.169  -1.149  -1.011  -0.990  -0.961  -1.001  -0.974  -0.922
25    D        -1.197  -1.191  -1.133  -1.126  -1.086  -1.052  -1.001  -0.995  -0.907
26    T        -0.557  -0.614  -0.644  -0.575  -0.668  -0.758  -0.544  -0.616  -0.639
27    H        -1.295  -1.290  -1.194  -1.383  -1.428  -1.236  -1.092  -1.088  -0.964
28    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    A        -0.846  -0.836  -0.739  -0.959  -0.902  -0.803  -0.887  -0.876  -0.750
32    E        -0.846  -0.836  -0.739  -0.790  -0.736  -0.630  -0.887  -0.876  -0.750
33    P        -0.737  -0.726  -0.679  -0.700  -0.691  -0.606  -0.763  -0.752  -0.681
34    V        -1.295  -1.290  -1.194  -1.269  -1.245  -1.120  -1.092  -1.088  -0.964
35    T        -1.197  -1.227  -1.166  -1.084  -1.141  -1.030  -1.001  -1.030  -0.938
36    E        -0.732  -0.739  -0.677  -0.911  -0.891  -0.851  -0.772  -0.778  -0.685
37    A        -0.378  -0.289  -0.506   0.020   0.146  -0.187  -0.319  -0.206  -0.469
38    K        -0.626  -0.610  -0.637  -0.784  -0.763  -0.785  -0.656  -0.636  -0.638
39    N        -0.378  -0.408  -0.579  -0.094  -0.127  -0.341  -0.319  -0.359  -0.560
40    T         1.944   1.949   2.087   1.936   1.932   2.157   2.201   2.210   2.464
41    L         1.119   1.109   0.939   1.080   1.057   0.841   1.193   1.177   0.854
42    Y         1.944   1.949   2.087   2.140   2.146   2.365   2.201   2.210   2.464
43    V         1.119   1.112   0.933   1.311   1.296   1.047   1.193   1.181   0.843
44    S        -0.626  -0.588  -0.614  -0.858  -0.826  -0.821  -0.656  -0.608  -0.612
45    Q         1.119   1.164   0.945   1.226   1.299   1.003   1.193   1.267   0.865
46    L         1.944   1.949   2.087   1.805   1.804   2.023   2.201   2.210   2.464
47    N         1.119   1.091   0.929   1.199   1.174   0.923   1.193   1.148   0.836
48    E         0.020  -0.007  -0.028   0.097   0.115   0.008  -0.151  -0.182  -0.216
49    K         1.119   1.109   0.939   0.955   0.920   0.725   1.193   1.177   0.854
50    I         1.119   1.091   0.929   1.292   1.259   1.082   1.193   1.148   0.836
51    N        -0.378  -0.378  -0.554  -0.266  -0.272  -0.570  -0.319  -0.320  -0.528
52    M        -1.025  -0.987  -1.088  -1.136  -1.127  -1.223  -0.824  -0.783  -0.862
53    Q        -1.175  -1.159  -1.135  -1.250  -1.253  -1.203  -0.992  -0.978  -0.912
54    R        -0.777  -0.796  -0.705  -0.722  -0.750  -0.616  -0.824  -0.840  -0.716
55    L         1.119   1.109   0.939   1.080   1.057   0.841   1.193   1.177   0.854
56    R         0.020  -0.014  -0.046  -0.061  -0.133  -0.251  -0.151  -0.195  -0.246
57    V        -1.025  -1.010  -1.062  -0.556  -0.515  -0.628  -0.824  -0.808  -0.835
58    N        -1.025  -1.042  -1.072  -0.781  -0.797  -0.840  -0.824  -0.842  -0.845
59    L         1.944   1.949   2.087   1.805   1.804   2.023   2.201   2.210   2.464
60    F         0.740   0.759   0.760   0.848   0.873   0.847   0.521   0.555   0.501
61    L         0.020   0.050  -0.030   0.104   0.130  -0.009  -0.151  -0.117  -0.224
62    L         0.341   0.354   0.088   0.404   0.405   0.077   0.353   0.370  -0.029
63    F         1.944   1.949   2.087   2.036   2.045   2.258   2.201   2.210   2.464
64    A         0.740   0.757   0.759   0.619   0.657   0.612   0.521   0.552   0.498
65    T        -0.378  -0.449  -0.565  -0.238  -0.361  -0.542  -0.319  -0.409  -0.543
66    F         0.740   0.736   0.734   0.848   0.833   0.796   0.521   0.511   0.447
67    G         1.944   1.949   2.087   2.140   2.149   2.365   2.201   2.210   2.464
68    E        -0.626  -0.631  -0.657  -0.474  -0.401  -0.487  -0.656  -0.662  -0.662
69    V         0.570   0.565   0.676   0.412   0.390   0.555   0.185   0.174   0.326
70    L        -0.077  -0.060  -0.048  -0.291  -0.289  -0.224  -0.319  -0.301  -0.259
71    K        -0.077  -0.108  -0.070  -0.333  -0.380  -0.307  -0.319  -0.353  -0.286
72    V         0.570   0.575   0.683   0.396   0.394   0.562   0.185   0.193   0.341
73    S        -0.626  -0.658  -0.652  -0.583  -0.636  -0.632  -0.656  -0.687  -0.655
74    M        -0.626  -0.665  -0.641  -0.512  -0.584  -0.555  -0.656  -0.697  -0.643
75    N        -1.197  -1.207  -1.166  -1.246  -1.269  -1.237  -1.001  -1.011  -0.938
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    F        -0.737  -0.732  -0.707  -0.638  -0.635  -0.602  -0.763  -0.758  -0.713
78    K        -0.732  -0.746  -0.691  -0.776  -0.795  -0.682  -0.772  -0.786  -0.699
79    K         0.198   0.151   0.032   0.015  -0.073  -0.234   0.143   0.072  -0.115
80    Q        -0.077  -0.082  -0.058  -0.011  -0.018   0.015  -0.319  -0.325  -0.270
81    R         1.119   1.070   0.938   1.348   1.288   1.087   1.193   1.111   0.853
82    G         1.119   1.112   0.933   1.399   1.390   1.131   1.193   1.181   0.843
83    Q         1.119   1.070   0.938   1.370   1.318   1.124   1.193   1.111   0.853
84    A         1.944   1.949   2.087   1.958   1.979   2.179   2.201   2.210   2.464
85    F         0.570   0.578   0.686   0.562   0.572   0.741   0.185   0.200   0.349
86    I         0.740   0.740   0.765   0.695   0.686   0.710   0.521   0.519   0.511
87    T        -0.228  -0.231  -0.142  -0.377  -0.406  -0.255  -0.488  -0.493  -0.378
88    M         0.341   0.372   0.091   0.575   0.608   0.198   0.353   0.396  -0.025
89    R        -1.574  -1.584  -1.540  -1.427  -1.462  -1.419  -1.160  -1.169  -1.087
90    T        -0.777  -0.760  -0.706  -0.826  -0.793  -0.722  -0.824  -0.810  -0.717
91    I        -0.626  -0.639  -0.627  -0.528  -0.573  -0.531  -0.656  -0.669  -0.632
92    D        -1.025  -1.021  -1.074  -0.705  -0.660  -0.793  -0.824  -0.820  -0.848
93    Q        -1.175  -1.162  -1.144  -0.987  -0.917  -0.910  -0.992  -0.981  -0.921
94    A         1.119   1.091   0.929   1.212   1.188   0.935   1.193   1.148   0.836
95    S        -1.175  -1.182  -1.147  -1.172  -1.191  -1.127  -0.992  -0.998  -0.924
96    L        -0.378  -0.347  -0.544  -0.371  -0.341  -0.633  -0.319  -0.281  -0.516
97    A         1.944   1.949   2.087   1.958   1.979   2.179   2.201   2.210   2.464
98    Q        -0.626  -0.588  -0.614  -0.692  -0.670  -0.678  -0.656  -0.608  -0.612
99    I        -1.574  -1.598  -1.533  -1.688  -1.743  -1.609  -1.160  -1.180  -1.082
100   S        -0.626  -0.672  -0.638  -0.610  -0.664  -0.611  -0.656  -0.704  -0.642
101   L         1.944   1.949   2.087   1.805   1.804   2.023   2.201   2.210   2.464
102   N        -0.626  -0.604  -0.637  -0.793  -0.757  -0.785  -0.656  -0.631  -0.640
103   G        -0.626  -0.658  -0.643  -0.530  -0.591  -0.585  -0.656  -0.691  -0.648
104   E        -1.025  -1.033  -1.108  -0.879  -0.808  -1.042  -0.824  -0.833  -0.882
105   R        -1.973  -1.971  -1.880  -1.579  -1.553  -1.436  -1.328  -1.327  -1.209
106   F         1.944   1.949   2.087   2.036   2.045   2.258   2.201   2.210   2.464
107   F         1.119   1.091   0.929   1.326   1.292   1.085   1.193   1.148   0.836
108   G        -0.626  -0.636  -0.639  -0.449  -0.439  -0.466  -0.656  -0.669  -0.643
109   K         1.119   1.112   0.933   0.932   0.896   0.670   1.193   1.181   0.843
110   P         0.020   0.053  -0.017   0.217   0.297   0.160  -0.151  -0.111  -0.200
111   L         0.740   0.740   0.765   0.576   0.562   0.608   0.521   0.519   0.511
112   K        -0.626  -0.588  -0.613  -0.641  -0.592  -0.609  -0.656  -0.608  -0.613
113   V         0.020   0.030  -0.025  -0.058  -0.080  -0.152  -0.151  -0.151  -0.218
114   E         0.020  -0.013  -0.021   0.058   0.098  -0.005  -0.151  -0.193  -0.209
115   F         0.570   0.575   0.683   0.524   0.526   0.687   0.185   0.193   0.341
116   S         0.570   0.563   0.680   0.303   0.299   0.458   0.185   0.170   0.334
117   K        -1.025  -1.033  -1.108  -1.024  -1.070  -1.097  -0.824  -0.833  -0.882
118   S        -0.626  -0.643  -0.639  -0.780  -0.818  -0.796  -0.656  -0.674  -0.643
119   E        -0.626  -0.643  -0.646  -0.880  -0.875  -0.890  -0.656  -0.675  -0.652
120   T         0.570   0.575   0.683   0.290   0.292   0.450   0.185   0.193   0.341
121   K         0.341   0.304   0.093   0.259   0.180  -0.064   0.353   0.299  -0.021
122   T        -1.175  -1.165  -1.134  -1.187  -1.184  -1.137  -0.992  -0.982  -0.912
123   L         0.570   0.575   0.683   0.244   0.241   0.397   0.185   0.193   0.341
124   -        -0.149  -0.141  -0.101  -0.339  -0.334  -0.282  -0.372  -0.362  -0.316
125   -        -0.846  -0.844  -0.739  -0.915  -0.913  -0.758  -0.887  -0.885  -0.750
126   -        -0.149  -0.160  -0.096  -0.375  -0.396  -0.305  -0.372  -0.390  -0.309
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -         0.549   0.551   0.674   0.311   0.317   0.498   0.143   0.145   0.323
138   -        -0.149  -0.141  -0.101  -0.206  -0.196  -0.141  -0.372  -0.362  -0.316
139   -        -0.149  -0.141  -0.101  -0.220  -0.206  -0.168  -0.372  -0.362  -0.316
140   -        -0.149  -0.114  -0.085  -0.119  -0.064  -0.030  -0.372  -0.321  -0.293
141   -         0.549   0.551   0.674   0.269   0.269   0.456   0.143   0.145   0.323
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -         0.937   0.999   0.863   1.037   1.129   0.915   0.884   0.992   0.706
* 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/P40567
Output conservation file - output/P40567
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
