1     M         1.671   1.697   1.766   1.854   1.889   2.001   1.856   1.894   2.007
2     D        -0.629  -0.606  -0.737  -0.548  -0.523  -0.698  -0.567  -0.542  -0.673
3     S        -0.520  -0.423  -0.447  -0.640  -0.480  -0.523  -0.678  -0.553  -0.571
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     S         1.671   1.697   1.766   1.577   1.619   1.726   1.856   1.894   2.007
7     I         0.923   0.936   0.804   0.983   0.995   0.756   0.877   0.891   0.609
8     T        -0.390  -0.400  -0.431  -0.466  -0.488  -0.536  -0.494  -0.508  -0.544
9     N        -0.152  -0.129  -0.042  -0.433  -0.397  -0.270  -0.494  -0.464  -0.350
10    V         0.085   0.182   0.089  -0.165  -0.018  -0.155  -0.158  -0.012  -0.159
11    K        -0.341  -0.436  -0.411  -0.349  -0.493  -0.465  -0.457  -0.559  -0.529
12    Y        -0.629  -0.637  -0.746  -0.449  -0.443  -0.661  -0.567  -0.575  -0.683
13    L         0.177   0.085   0.082   0.007  -0.131  -0.141  -0.017  -0.150  -0.172
14    D        -0.520  -0.408  -0.444  -0.762  -0.593  -0.636  -0.678  -0.542  -0.565
15    P         0.573   0.628   0.664   0.500   0.597   0.631   0.204   0.300   0.323
16    T        -0.808  -0.765  -0.782  -0.768  -0.711  -0.745  -0.788  -0.735  -0.729
17    E        -1.491  -1.437  -1.407  -1.310  -1.245  -1.203  -1.118  -1.068  -1.004
18    L         1.671   1.697   1.766   1.525   1.571   1.674   1.856   1.894   2.007
19    H        -1.204  -1.124  -1.129  -1.141  -1.048  -1.027  -1.008  -0.935  -0.899
20    R        -1.491  -1.475  -1.425  -1.405  -1.411  -1.291  -1.118  -1.098  -1.016
21    W         1.046   1.043   0.906   1.255   1.286   1.042   1.085   1.074   0.808
22    M        -0.520  -0.539  -0.458  -0.488  -0.521  -0.409  -0.678  -0.683  -0.582
23    Q        -1.491  -1.500  -1.422  -1.368  -1.374  -1.274  -1.118  -1.115  -1.014
24    E        -1.204  -1.163  -1.141  -1.093  -1.040  -1.021  -1.008  -0.967  -0.907
25    G        -0.341  -0.420  -0.410  -0.401  -0.536  -0.516  -0.457  -0.547  -0.529
26    H        -1.204  -1.224  -1.159  -1.120  -1.137  -1.049  -1.008  -1.014  -0.922
27    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    T        -0.007   0.046   0.020  -0.168  -0.093  -0.120  -0.298  -0.221  -0.261
29    T        -0.007   0.044   0.028  -0.018   0.055   0.017  -0.298  -0.229  -0.253
30    L         0.094   0.046   0.032  -0.187  -0.277  -0.304  -0.118  -0.198  -0.237
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -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    R        -0.539  -0.482  -0.475  -0.593  -0.495  -0.503  -0.682  -0.609  -0.597
41    E        -0.918  -0.917  -0.866  -0.985  -0.966  -0.908  -0.886  -0.881  -0.806
42    P        -0.900  -0.915  -0.844  -0.805  -0.839  -0.734  -0.878  -0.883  -0.788
43    F        -0.110  -0.262  -0.348   0.083  -0.151  -0.321  -0.127  -0.328  -0.439
44    Q        -0.520  -0.564  -0.479  -0.524  -0.595  -0.463  -0.678  -0.715  -0.609
45    V         0.738   0.685   0.695   0.660   0.539   0.559   0.534   0.416   0.388
46    V         0.521   0.544   0.624   0.271   0.284   0.429   0.094   0.124   0.238
47    D         1.671   1.697   1.766   1.619   1.678   1.768   1.856   1.894   2.007
48    V         1.671   1.697   1.766   1.659   1.675   1.808   1.856   1.894   2.007
49    R         1.671   1.697   1.766   1.668   1.696   1.816   1.856   1.894   2.007
50    G         0.054   0.140   0.088  -0.172  -0.011  -0.092  -0.237  -0.108  -0.169
51    S         0.177   0.064   0.068   0.020  -0.153  -0.160  -0.017  -0.185  -0.193
52    D         1.671   1.697   1.766   1.619   1.678   1.768   1.856   1.894   2.007
53    Y         0.450   0.564   0.280   0.662   0.833   0.438   0.424   0.589   0.149
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    M        -0.808  -0.858  -0.815  -0.734  -0.824  -0.724  -0.788  -0.829  -0.760
56    G         1.671   1.697   1.766   1.628   1.666   1.777   1.856   1.894   2.007
57    G         1.046   0.956   0.890   1.073   0.958   0.862   1.085   0.927   0.777
58    H         1.046   0.956   0.890   1.262   1.141   1.039   1.085   0.927   0.777
59    I         1.671   1.697   1.766   1.725   1.759   1.873   1.856   1.894   2.007
60    K         0.450   0.300   0.197   0.584   0.385   0.222   0.424   0.195   0.020
61    D         1.046   1.109   0.915   1.059   1.146   0.876   1.085   1.182   0.824
62    G        -0.412  -0.407  -0.411  -0.431  -0.452  -0.432  -0.567  -0.553  -0.533
63    W        -0.520  -0.525  -0.477  -0.500  -0.512  -0.452  -0.678  -0.679  -0.605
64    H         0.054   0.014   0.064   0.099   0.052   0.123  -0.237  -0.273  -0.207
65    Y        -0.110  -0.262  -0.348   0.104  -0.101  -0.263  -0.127  -0.328  -0.439
66    A         1.046   1.109   0.915   1.257   1.345   1.082   1.085   1.182   0.824
67    Y        -0.124  -0.072  -0.013  -0.373  -0.307  -0.216  -0.457  -0.382  -0.309
68    S        -1.204  -1.196  -1.145  -1.181  -1.172  -1.101  -1.008  -0.991  -0.911
69    R        -0.808  -0.849  -0.819  -0.748  -0.809  -0.764  -0.788  -0.823  -0.765
70    L         0.521   0.550   0.628   0.203   0.274   0.381   0.094   0.138   0.246
71    K        -1.095  -1.153  -1.130  -0.968  -1.075  -1.042  -0.898  -0.947  -0.897
72    Q        -1.491  -1.401  -1.404  -1.343  -1.210  -1.227  -1.118  -1.037  -1.001
73    D        -0.412  -0.378  -0.406  -0.558  -0.508  -0.506  -0.567  -0.519  -0.527
74    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    L        -0.520  -0.479  -0.460  -0.687  -0.648  -0.574  -0.678  -0.638  -0.588
78    R        -1.204  -1.156  -1.126  -1.126  -1.043  -1.006  -1.008  -0.960  -0.897
79    E        -0.341  -0.437  -0.414  -0.291  -0.427  -0.411  -0.457  -0.561  -0.532
80    L         0.450   0.434   0.238   0.467   0.450   0.204   0.424   0.388   0.085
81    K        -0.808  -0.672  -0.779  -0.788  -0.595  -0.744  -0.788  -0.635  -0.725
82    H        -1.204  -1.174  -1.134  -1.141  -1.089  -1.034  -1.008  -0.973  -0.903
83    R        -1.491  -1.475  -1.425  -1.348  -1.332  -1.255  -1.118  -1.098  -1.016
84    L         0.450   0.428   0.237   0.399   0.368   0.083   0.424   0.385   0.082
85    L        -1.491  -1.489  -1.422  -1.348  -1.319  -1.218  -1.118  -1.108  -1.014
86    E        -0.808  -0.785  -0.791  -0.859  -0.817  -0.839  -0.788  -0.756  -0.737
87    K         0.177   0.166   0.120   0.199   0.196   0.120  -0.017  -0.022  -0.107
88    Q        -1.095  -1.017  -1.088  -0.981  -0.860  -1.001  -0.898  -0.819  -0.859
89    A        -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    D        -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    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    A         0.094   0.121   0.051   0.077   0.115  -0.035  -0.118  -0.080  -0.208
99    L        -0.539  -0.522  -0.490  -0.712  -0.690  -0.625  -0.682  -0.659  -0.615
100   N        -0.808  -0.887  -0.828  -0.721  -0.850  -0.768  -0.788  -0.853  -0.772
101   V        -0.629  -0.566  -0.707  -0.482  -0.445  -0.605  -0.567  -0.499  -0.640
102   I         0.573   0.592   0.644   0.367   0.369   0.463   0.204   0.225   0.281
103   F         1.046   0.956   0.890   1.201   1.083   0.979   1.085   0.927   0.777
104   H         1.671   1.697   1.766   1.824   1.862   1.972   1.856   1.894   2.007
105   C         1.671   1.697   1.766   1.884   1.919   2.030   1.856   1.894   2.007
106   M        -0.341  -0.425  -0.397  -0.210  -0.333  -0.281  -0.457  -0.544  -0.510
107   L        -0.341  -0.401  -0.392  -0.450  -0.495  -0.500  -0.457  -0.510  -0.501
108   S         1.671   1.697   1.766   1.566   1.590   1.714   1.856   1.894   2.007
109   Q         1.671   1.697   1.766   1.712   1.756   1.860   1.856   1.894   2.007
110   Q         0.054   0.085   0.057  -0.073  -0.063  -0.063  -0.237  -0.210  -0.223
111   R         1.671   1.697   1.766   1.668   1.696   1.816   1.856   1.894   2.007
112   G         1.671   1.697   1.766   1.628   1.666   1.777   1.856   1.894   2.007
113   P         1.671   1.697   1.766   1.812   1.855   1.959   1.856   1.894   2.007
114   S        -0.341  -0.352  -0.393  -0.445  -0.484  -0.515  -0.457  -0.480  -0.509
115   A         0.177   0.182   0.121   0.181   0.204   0.091  -0.017   0.005  -0.111
116   A         0.738   0.799   0.769   0.738   0.819   0.773   0.534   0.638   0.539
117   M        -0.124  -0.127  -0.040  -0.345  -0.373  -0.235  -0.457  -0.461  -0.347
118   L        -0.916  -0.952  -0.847  -1.076  -1.110  -0.956  -0.898  -0.914  -0.792
119   L        -0.124  -0.119  -0.034  -0.376  -0.355  -0.245  -0.457  -0.450  -0.339
120   L        -0.629  -0.731  -0.769  -0.613  -0.779  -0.815  -0.567  -0.682  -0.707
121   R         0.450   0.300   0.197   0.542   0.316   0.150   0.424   0.195   0.020
122   S        -1.095  -1.134  -1.118  -1.055  -1.129  -1.090  -0.898  -0.931  -0.886
123   L         0.054   0.058   0.068  -0.198  -0.188  -0.158  -0.237  -0.227  -0.208
124   D        -0.808  -0.838  -0.793  -0.751  -0.785  -0.719  -0.788  -0.804  -0.737
125   T        -1.095  -1.130  -1.120  -0.948  -0.989  -0.977  -0.898  -0.928  -0.888
126   A        -1.491  -1.414  -1.407  -1.573  -1.464  -1.450  -1.118  -1.049  -1.004
127   E        -1.491  -1.439  -1.405  -1.299  -1.215  -1.168  -1.118  -1.070  -1.002
128   L        -0.808  -0.868  -0.820  -0.885  -0.959  -0.888  -0.788  -0.839  -0.766
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   S        -0.916  -0.926  -0.846  -1.013  -1.002  -0.890  -0.898  -0.893  -0.791
168   R        -0.808  -0.879  -0.819  -0.774  -0.896  -0.833  -0.788  -0.844  -0.763
169   C        -1.204  -1.173  -1.145  -1.024  -0.969  -0.935  -1.008  -0.972  -0.911
170   R        -1.204  -1.205  -1.137  -1.089  -1.092  -0.978  -1.008  -1.000  -0.905
171   L         0.054   0.141   0.085  -0.117   0.002  -0.066  -0.237  -0.106  -0.176
172   W        -0.341  -0.420  -0.417  -0.128  -0.209  -0.240  -0.457  -0.552  -0.537
173   V         1.046   0.956   0.890   1.106   0.967   0.895   1.085   0.927   0.777
174   L         1.671   1.697   1.766   1.525   1.571   1.674   1.856   1.894   2.007
175   R        -1.204  -1.175  -1.139  -1.135  -1.092  -1.047  -1.008  -0.974  -0.906
176   G         1.046   1.043   0.906   1.066   1.064   0.875   1.085   1.074   0.808
177   G         1.671   1.697   1.766   1.628   1.666   1.777   1.856   1.894   2.007
178   F         1.671   1.697   1.766   1.764   1.807   1.912   1.856   1.894   2.007
179   S        -0.412  -0.389  -0.401  -0.462  -0.455  -0.431  -0.567  -0.537  -0.524
180   R        -1.491  -1.475  -1.425  -1.370  -1.376  -1.280  -1.118  -1.098  -1.016
181   W         1.671   1.697   1.766   1.837   1.906   1.984   1.856   1.894   2.007
182   Q         0.450   0.300   0.197   0.608   0.411   0.234   0.424   0.195   0.020
183   S        -0.916  -0.916  -0.840  -1.065  -1.051  -0.938  -0.898  -0.887  -0.786
184   V        -1.095  -1.049  -1.111  -0.900  -0.853  -0.939  -0.898  -0.852  -0.880
185   Y         0.738   0.704   0.701   0.748   0.709   0.659   0.534   0.454   0.401
186   G         1.046   0.992   0.894   1.075   1.006   0.872   1.085   0.988   0.785
187   D        -1.204  -1.218  -1.144  -1.179  -1.178  -1.074  -1.008  -1.009  -0.910
188   D         0.450   0.300   0.197   0.527   0.342   0.170   0.424   0.195   0.020
189   E        -0.520  -0.500  -0.473  -0.613  -0.589  -0.548  -0.678  -0.657  -0.603
190   S        -1.491  -1.488  -1.411  -1.424  -1.419  -1.325  -1.118  -1.106  -1.007
191   V         0.054   0.015   0.053  -0.200  -0.278  -0.199  -0.237  -0.285  -0.227
192   T         0.450   0.300   0.197   0.671   0.448   0.297   0.424   0.195   0.020
193   A         0.450   0.437   0.233   0.604   0.585   0.286   0.424   0.397   0.076
194   G        -0.390  -0.335  -0.412  -0.438  -0.342  -0.482  -0.494  -0.421  -0.520
195   Y         1.671   1.697   1.766   1.737   1.771   1.885   1.856   1.894   2.007
196   L        -0.776  -0.676  -0.795  -0.869  -0.703  -0.941  -0.734  -0.619  -0.735
197   P        -0.007  -0.007   0.007  -0.044  -0.060  -0.048  -0.298  -0.303  -0.283
198   D         0.521   0.546   0.626   0.223   0.266   0.386   0.094   0.130   0.241
199   L         0.615   0.643   0.658   0.307   0.334   0.363   0.289   0.330   0.309
200   W         1.671   1.697   1.766   1.830   1.875   1.977   1.856   1.894   2.007
201   R        -0.539  -0.480  -0.475  -0.666  -0.579  -0.583  -0.682  -0.607  -0.597
202   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
203   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
204   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
205   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
206   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P42937
Output conservation file - output/P42937
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
