1     M         1.640   1.668   1.768   1.861   1.898   2.059   1.803   1.846   2.014
2     A         0.946   0.835   0.734   0.713   0.580   0.422   0.991   0.805   0.594
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     H         0.286   0.133  -0.034   0.796   0.605   0.365   0.295   0.074  -0.183
5     R         1.640   1.668   1.768   1.719   1.762   1.919   1.803   1.846   2.014
6     A         0.364   0.395   0.511  -0.124  -0.061   0.107  -0.053  -0.008   0.157
7     F        -0.792  -0.813  -0.709  -0.688  -0.706  -0.550  -0.864  -0.871  -0.736
8     I        -1.111  -1.183  -1.100  -0.782  -0.880  -0.759  -0.980  -1.028  -0.914
9     Q        -0.593  -0.592  -0.627  -0.425  -0.422  -0.495  -0.633  -0.620  -0.638
10    V         0.286   0.227   0.003   0.600   0.514   0.227   0.295   0.202  -0.127
11    I         0.422   0.429   0.516   0.399   0.390   0.516   0.063   0.059   0.168
12    I        -0.353  -0.339  -0.223  -0.305  -0.298  -0.124  -0.633  -0.613  -0.460
13    T         0.605   0.528   0.553   0.715   0.580   0.591   0.411   0.253   0.243
14    G         1.640   1.668   1.768   1.641   1.692   1.842   1.803   1.846   2.014
15    T        -0.353  -0.347  -0.223  -0.679  -0.658  -0.481  -0.633  -0.624  -0.459
16    Q        -0.274  -0.214  -0.174  -0.312  -0.228  -0.183  -0.517  -0.433  -0.391
17    V         1.640   1.668   1.768   1.738   1.772   1.938   1.803   1.846   2.014
18    F        -0.018  -0.109  -0.122   0.169   0.052   0.006  -0.169  -0.289  -0.323
19    G         0.286   0.120  -0.025   0.400   0.165  -0.125   0.295   0.056  -0.169
20    K        -0.154  -0.107  -0.130  -0.231  -0.210  -0.169  -0.401  -0.354  -0.345
21    A         1.640   1.668   1.768   1.317   1.371   1.522   1.803   1.846   2.014
22    F         1.640   1.668   1.768   1.771   1.816   1.971   1.803   1.846   2.014
23    A        -0.154  -0.216  -0.146  -0.404  -0.455  -0.337  -0.401  -0.463  -0.362
24    E         0.605   0.522   0.550   0.474   0.326   0.365   0.411   0.241   0.237
25    A         0.946   1.060   0.764   0.713   0.866   0.471   0.991   1.161   0.651
26    Y         1.640   1.668   1.768   1.771   1.822   1.971   1.803   1.846   2.014
27    R         0.364   0.414   0.524   0.049   0.098   0.273  -0.053   0.028   0.185
28    Q         1.640   1.668   1.768   1.704   1.737   1.904   1.803   1.846   2.014
29    A         0.946   0.835   0.734   0.758   0.643   0.527   0.991   0.805   0.594
30    A         0.946   0.835   0.734   0.742   0.620   0.489   0.991   0.805   0.594
31    S        -0.593  -0.512  -0.622  -0.901  -0.761  -0.914  -0.633  -0.528  -0.632
32    Q        -0.672  -0.740  -0.682  -0.835  -0.924  -0.822  -0.748  -0.799  -0.707
33    S        -0.593  -0.663  -0.645  -0.576  -0.700  -0.676  -0.633  -0.693  -0.664
34    V         0.286   0.343   0.014   0.167   0.243  -0.172   0.295   0.370  -0.112
35    K        -0.813  -0.832  -0.732  -1.007  -1.019  -0.902  -0.869  -0.890  -0.757
36    Q         0.719   0.803   0.648   0.733   0.845   0.576   0.616   0.752   0.432
37    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    N        -0.792  -0.770  -0.694  -1.101  -1.084  -0.967  -0.864  -0.829  -0.720
42    A        -1.551  -1.515  -1.443  -1.417  -1.316  -1.211  -1.212  -1.168  -1.054
43    S        -1.111  -1.016  -1.066  -1.109  -0.953  -1.071  -0.980  -0.868  -0.882
44    R        -1.111  -1.135  -1.094  -0.910  -0.942  -0.912  -0.980  -0.997  -0.910
45    R        -1.111  -1.069  -1.091  -1.133  -1.145  -1.123  -0.980  -0.943  -0.908
46    G        -0.912  -0.856  -0.748  -1.243  -1.214  -1.020  -0.980  -0.914  -0.774
47    T        -1.111  -1.061  -1.076  -1.018  -1.000  -1.000  -0.980  -0.933  -0.895
48    G        -0.154  -0.209  -0.141  -0.523  -0.581  -0.475  -0.401  -0.452  -0.357
49    K        -0.593  -0.562  -0.635  -0.748  -0.728  -0.840  -0.633  -0.598  -0.653
50    G        -0.353  -0.281  -0.200  -0.788  -0.665  -0.558  -0.633  -0.540  -0.430
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    -        -0.813  -0.789  -0.701  -0.925  -0.895  -0.781  -0.869  -0.839  -0.722
55    E        -1.111  -1.199  -1.112  -1.173  -1.305  -1.185  -0.980  -1.045  -0.924
56    Y        -1.430  -1.484  -1.444  -1.025  -1.102  -1.096  -1.096  -1.138  -1.053
57    G         0.946   0.914   0.738   1.039   1.010   0.744   0.991   0.936   0.603
58    G         0.946   0.835   0.734   1.032   0.892   0.720   0.991   0.805   0.594
59    I        -0.018  -0.129  -0.141   0.201   0.029   0.012  -0.169  -0.339  -0.351
60    T        -0.018  -0.003  -0.086   0.223   0.249   0.130  -0.169  -0.133  -0.264
61    L        -0.337  -0.341  -0.566  -0.066  -0.075  -0.365  -0.285  -0.298  -0.561
62    D         0.286   0.234   0.012   0.585   0.518   0.175   0.295   0.211  -0.114
63    E         1.640   1.668   1.768   1.522   1.562   1.725   1.803   1.846   2.014
64    S         0.422   0.521   0.562  -0.082   0.087   0.130   0.063   0.239   0.262
65    C        -0.912  -0.848  -1.016  -0.342  -0.271  -0.548  -0.748  -0.683  -0.829
66    K         0.946   0.835   0.734   0.844   0.695   0.548   0.991   0.805   0.594
67    I         1.640   1.668   1.768   1.757   1.799   1.957   1.803   1.846   2.014
68    L         1.640   1.668   1.768   1.617   1.667   1.818   1.803   1.846   2.014
69    N         0.422   0.456   0.533   0.420   0.483   0.574   0.063   0.112   0.204
70    I        -0.353  -0.341  -0.224  -0.406  -0.390  -0.218  -0.633  -0.616  -0.461
71    E        -0.792  -0.811  -0.711  -0.911  -0.939  -0.776  -0.864  -0.876  -0.739
72    E        -1.111  -1.078  -1.080  -1.217  -1.161  -1.157  -0.980  -0.945  -0.897
73    S        -1.232  -1.195  -1.113  -1.241  -1.175  -1.079  -1.096  -1.050  -0.928
74    K        -0.302  -0.208  -0.192  -0.791  -0.677  -0.616  -0.572  -0.448  -0.419
75    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    D         0.286   0.234   0.012   0.564   0.490   0.133   0.295   0.211  -0.114
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    L        -0.337  -0.349  -0.573  -0.164  -0.204  -0.549  -0.285  -0.304  -0.569
97    N        -1.111  -1.146  -1.093  -0.985  -1.043  -0.999  -0.980  -1.000  -0.906
98    M        -0.593  -0.618  -0.645  -0.437  -0.491  -0.503  -0.633  -0.656  -0.665
99    D        -0.593  -0.706  -0.673  -0.561  -0.756  -0.779  -0.633  -0.753  -0.695
100   K        -0.018  -0.129  -0.141  -0.207  -0.405  -0.402  -0.169  -0.339  -0.351
101   I        -0.154  -0.214  -0.137  -0.088  -0.173  -0.057  -0.401  -0.460  -0.352
102   N        -0.792  -0.811  -0.712  -0.664  -0.698  -0.557  -0.864  -0.875  -0.740
103   N        -0.593  -0.532  -0.640  -0.668  -0.659  -0.738  -0.633  -0.591  -0.661
104   R         0.422   0.456   0.533   0.215   0.262   0.349   0.063   0.112   0.204
105   F         0.605   0.691   0.637   0.735   0.865   0.767   0.411   0.556   0.410
106   N        -1.870  -1.816  -1.736  -1.769  -1.683  -1.578  -1.328  -1.277  -1.154
107   Y        -0.337  -0.524  -0.621   0.052  -0.217  -0.376  -0.285  -0.518  -0.628
108   L         0.946   0.835   0.734   1.057   0.935   0.809   0.991   0.805   0.594
109   F         0.946   0.899   0.741   1.197   1.149   0.937   0.991   0.912   0.609
110   E        -0.792  -0.784  -0.706  -0.749  -0.725  -0.592  -0.864  -0.841  -0.734
111   V        -0.154  -0.169  -0.137  -0.149  -0.186  -0.154  -0.401  -0.413  -0.353
112   N         1.640   1.668   1.768   1.762   1.818   1.961   1.803   1.846   2.014
113   D         0.422   0.456   0.533   0.326   0.380   0.466   0.063   0.112   0.204
114   K        -0.018  -0.129  -0.141  -0.104  -0.266  -0.256  -0.169  -0.339  -0.351
115   E        -0.337  -0.443  -0.593  -0.180  -0.344  -0.522  -0.285  -0.422  -0.595
116   K         0.946   1.027   0.757   0.863   0.960   0.629   0.991   1.112   0.637
117   G         0.946   0.899   0.741   1.039   0.990   0.749   0.991   0.912   0.609
118   G         0.605   0.691   0.637   0.607   0.744   0.645   0.411   0.556   0.410
119   S         1.640   1.668   1.768   1.572   1.614   1.774   1.803   1.846   2.014
120   F         1.640   1.668   1.768   1.771   1.816   1.971   1.803   1.846   2.014
121   Y         1.640   1.668   1.768   1.771   1.822   1.971   1.803   1.846   2.014
122   L         1.640   1.668   1.768   1.617   1.667   1.818   1.803   1.846   2.014
123   Q         1.640   1.668   1.768   1.704   1.737   1.904   1.803   1.846   2.014
124   S         1.640   1.668   1.768   1.572   1.614   1.774   1.803   1.846   2.014
125   K         1.640   1.668   1.768   1.447   1.486   1.650   1.803   1.846   2.014
126   V         0.605   0.710   0.623   0.698   0.845   0.706   0.411   0.589   0.383
127   Y         0.286   0.133  -0.034   0.630   0.441   0.192   0.295   0.074  -0.183
128   R         0.605   0.691   0.637   0.685   0.814   0.719   0.411   0.556   0.410
129   A         1.640   1.668   1.768   1.317   1.371   1.522   1.803   1.846   2.014
130   A        -1.111  -1.119  -1.099  -0.896  -0.843  -0.871  -0.980  -0.970  -0.912
131   E         0.605   0.691   0.637   0.496   0.619   0.541   0.411   0.556   0.410
132   R        -0.337  -0.341  -0.566  -0.059  -0.094  -0.438  -0.285  -0.298  -0.561
133   L         0.946   0.899   0.741   1.041   0.998   0.786   0.991   0.912   0.609
134   K        -0.018  -0.053  -0.110  -0.164  -0.223  -0.306  -0.169  -0.217  -0.305
135   W        -1.551  -1.565  -1.465  -1.376  -1.456  -1.288  -1.212  -1.208  -1.071
136   E         1.640   1.668   1.768   1.522   1.562   1.725   1.803   1.846   2.014
137   L         0.946   0.914   0.738   1.041   1.016   0.781   0.991   0.936   0.603
138   A        -0.792  -0.811  -0.713  -1.125  -1.121  -0.973  -0.864  -0.875  -0.741
139   Q        -1.111  -1.083  -1.086  -0.844  -0.807  -0.815  -0.980  -0.940  -0.900
140   R        -0.347  -0.265  -0.186  -0.613  -0.500  -0.378  -0.621  -0.506  -0.407
141   E        -0.484  -0.604  -0.658  -0.310  -0.473  -0.508  -0.469  -0.620  -0.671
142   K         0.174   0.008  -0.089   0.133  -0.110  -0.270   0.137  -0.107  -0.265
143   N        -0.711  -0.553  -0.658  -0.868  -0.634  -0.808  -0.772  -0.592  -0.675
144   A        -0.222  -0.283  -0.181  -0.675  -0.758  -0.592  -0.465  -0.544  -0.406
145   K        -1.234  -1.191  -1.119  -1.406  -1.356  -1.254  -1.084  -1.038  -0.929
146   A        -0.302  -0.239  -0.187  -0.545  -0.431  -0.382  -0.572  -0.492  -0.414
147   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   N        -0.813  -0.760  -0.708  -0.954  -0.854  -0.807  -0.869  -0.811  -0.729
160   S        -0.813  -0.747  -0.710  -1.018  -0.962  -0.883  -0.869  -0.797  -0.732
161   T        -1.234  -1.198  -1.119  -1.124  -1.065  -0.991  -1.084  -1.043  -0.929
162   N        -1.234  -1.196  -1.122  -1.404  -1.364  -1.250  -1.084  -1.042  -0.932
163   S        -0.648  -0.747  -0.697  -0.594  -0.755  -0.698  -0.671  -0.788  -0.717
164   S        -0.222  -0.171  -0.147  -0.421  -0.318  -0.306  -0.465  -0.377  -0.355
165   G        -0.808  -0.788  -0.705  -0.869  -0.846  -0.723  -0.877  -0.849  -0.730
166   A        -1.214  -1.213  -1.131  -0.928  -0.884  -0.811  -1.075  -1.063  -0.941
167   D        -1.214  -1.146  -1.102  -1.052  -0.977  -0.900  -1.075  -1.007  -0.917
168   N        -0.912  -1.003  -1.061  -0.816  -1.010  -1.076  -0.748  -0.848  -0.873
169   S        -0.018   0.142  -0.045  -0.264  -0.017  -0.343  -0.169   0.069  -0.204
170   A        -1.551  -1.507  -1.449  -1.355  -1.274  -1.248  -1.212  -1.164  -1.058
171   S        -1.551  -1.523  -1.437  -1.348  -1.305  -1.208  -1.212  -1.178  -1.050
172   S        -1.870  -1.795  -1.733  -1.795  -1.719  -1.626  -1.328  -1.259  -1.152
173   N        -1.111  -1.032  -1.059  -1.093  -0.992  -1.004  -0.980  -0.899  -0.879
174   Q        -1.870  -1.811  -1.734  -1.550  -1.469  -1.342  -1.328  -1.273  -1.153
* 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/P42949
Output conservation file - output/P42949
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
