1     M         1.819   1.824   1.862   2.065   2.071   2.129   1.958   1.965   2.017
2     N        -0.460  -0.478  -0.484  -0.519  -0.546  -0.565  -0.514  -0.537  -0.536
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     K         0.300   0.304   0.341  -0.169  -0.163  -0.112  -0.020  -0.013   0.042
5     D        -0.460  -0.478  -0.484  -0.394  -0.434  -0.446  -0.514  -0.537  -0.536
6     Q        -0.460  -0.478  -0.484  -0.274  -0.306  -0.311  -0.514  -0.537  -0.536
7     A        -1.220  -1.216  -1.181  -1.309  -1.297  -1.242  -1.009  -1.002  -0.947
8     E        -0.460  -0.478  -0.481  -0.377  -0.417  -0.412  -0.514  -0.537  -0.532
9     K         0.300   0.304   0.341  -0.118  -0.093  -0.040  -0.020  -0.013   0.042
10    Y        -0.460  -0.475  -0.483  -0.151  -0.180  -0.187  -0.514  -0.533  -0.534
11    Q        -1.220  -1.216  -1.181  -0.931  -0.925  -0.864  -1.009  -1.002  -0.947
12    E        -0.460  -0.475  -0.483  -0.425  -0.460  -0.479  -0.514  -0.533  -0.534
13    R        -0.460  -0.478  -0.481  -0.555  -0.574  -0.613  -0.514  -0.537  -0.532
14    S        -1.220  -1.216  -1.181  -1.022  -1.001  -0.956  -1.009  -1.002  -0.947
15    L        -0.460  -0.437  -0.467  -0.425  -0.398  -0.422  -0.514  -0.483  -0.515
16    R        -0.460  -0.478  -0.484  -0.287  -0.311  -0.315  -0.514  -0.537  -0.536
17    Q         0.424   0.431   0.408   0.626   0.637   0.586   0.200   0.211   0.160
18    K         1.819   1.824   1.862   1.389   1.391   1.453   1.958   1.965   2.017
19    Y         1.819   1.824   1.862   2.046   2.052   2.110   1.958   1.965   2.017
20    N         0.586   0.606   0.515   0.663   0.686   0.560   0.475   0.507   0.347
21    L         0.586   0.606   0.517   0.580   0.604   0.484   0.475   0.507   0.350
22    L        -0.460  -0.478  -0.484  -0.595  -0.635  -0.635  -0.514  -0.537  -0.536
23    H         1.819   1.824   1.862   2.126   2.133   2.191   1.958   1.965   2.017
24    V        -1.220  -1.216  -1.181  -0.968  -0.973  -0.901  -1.009  -1.002  -0.947
25    L        -0.460  -0.434  -0.467  -0.313  -0.268  -0.329  -0.514  -0.478  -0.515
26    P         0.586   0.606   0.517   0.814   0.842   0.704   0.475   0.507   0.350
27    T        -0.460  -0.478  -0.484  -0.401  -0.443  -0.453  -0.514  -0.537  -0.536
28    L         0.424   0.423   0.409   0.337   0.333   0.316   0.200   0.198   0.163
29    N        -0.589  -0.587  -0.549  -0.500  -0.497  -0.434  -0.679  -0.675  -0.618
30    S        -0.589  -0.587  -0.549  -0.707  -0.696  -0.641  -0.679  -0.675  -0.618
31    R        -0.460  -0.475  -0.483  -0.317  -0.348  -0.364  -0.514  -0.533  -0.534
32    A        -1.220  -1.216  -1.181  -0.906  -0.899  -0.840  -1.009  -1.002  -0.947
33    L         1.819   1.824   1.862   1.754   1.756   1.819   1.958   1.965   2.017
34    S         0.586   0.540   0.493   0.505   0.446   0.375   0.475   0.397   0.308
35    G         0.586   0.540   0.493   0.670   0.582   0.458   0.475   0.397   0.308
36    L        -0.460  -0.478  -0.481  -0.418  -0.445  -0.431  -0.514  -0.537  -0.532
37    Y         1.819   1.824   1.862   2.057   2.063   2.121   1.958   1.965   2.017
38    Y        -0.460  -0.475  -0.483  -0.676  -0.722  -0.724  -0.514  -0.533  -0.534
39    K         0.586   0.540   0.493   0.221   0.161   0.092   0.475   0.397   0.308
40    N         0.586   0.540   0.493   0.634   0.556   0.488   0.475   0.397   0.308
41    F         1.819   1.824   1.862   2.088   2.094   2.152   1.958   1.965   2.017
42    H        -0.460  -0.475  -0.483  -0.173  -0.200  -0.207  -0.514  -0.533  -0.534
43    N         0.586   0.540   0.493   0.619   0.540   0.467   0.475   0.397   0.308
44    S        -0.460  -0.478  -0.484  -0.484  -0.500  -0.496  -0.514  -0.537  -0.536
45    V        -0.460  -0.478  -0.484  -0.228  -0.259  -0.262  -0.514  -0.537  -0.536
46    K         0.586   0.540   0.493   0.224   0.165   0.096   0.475   0.397   0.308
47    R         0.586   0.540   0.493   0.714   0.646   0.565   0.475   0.397   0.308
48    Y         0.586   0.540   0.493   0.670   0.581   0.458   0.475   0.397   0.308
49    Q        -0.460  -0.478  -0.484  -0.247  -0.270  -0.281  -0.514  -0.537  -0.536
50    I         0.300   0.304   0.341   0.124   0.129   0.196  -0.020  -0.013   0.042
51    M        -0.460  -0.434  -0.465  -0.333  -0.301  -0.330  -0.514  -0.478  -0.512
52    L         1.819   1.824   1.862   1.754   1.756   1.819   1.958   1.965   2.017
53    P         1.819   1.824   1.862   2.026   2.030   2.090   1.958   1.965   2.017
54    E        -0.460  -0.478  -0.481  -0.290  -0.317  -0.314  -0.514  -0.537  -0.532
55    Q        -1.220  -1.216  -1.181  -1.091  -1.087  -1.024  -1.009  -1.002  -0.947
56    L        -0.460  -0.475  -0.483  -0.330  -0.354  -0.372  -0.514  -0.533  -0.534
57    K        -1.220  -1.216  -1.181  -1.211  -1.180  -1.144  -1.009  -1.002  -0.947
58    S        -1.220  -1.216  -1.181  -1.086  -1.074  -1.020  -1.009  -1.002  -0.947
59    G        -0.460  -0.434  -0.467  -0.225  -0.186  -0.229  -0.514  -0.478  -0.515
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    K         0.586   0.540   0.493   0.224   0.163   0.096   0.475   0.397   0.308
63    F         1.819   1.824   1.862   2.088   2.094   2.152   1.958   1.965   2.017
64    C         1.819   1.824   1.862   2.088   2.093   2.152   1.958   1.965   2.017
65    S        -0.460  -0.475  -0.483  -0.333  -0.353  -0.388  -0.514  -0.533  -0.534
66    H        -1.220  -1.216  -1.181  -1.266  -1.286  -1.200  -1.009  -1.002  -0.947
67    C         1.819   1.824   1.862   2.088   2.093   2.152   1.958   1.965   2.017
68    G         0.586   0.540   0.493   0.824   0.749   0.664   0.475   0.397   0.308
69    C        -0.460  -0.478  -0.481  -0.274  -0.314  -0.322  -0.514  -0.537  -0.532
70    V         0.300   0.304   0.341   0.302   0.306   0.369  -0.020  -0.013   0.042
71    Y        -0.460  -0.437  -0.467  -0.231  -0.190  -0.246  -0.514  -0.483  -0.515
72    V         0.586   0.611   0.519   0.782   0.815   0.676   0.475   0.515   0.353
73    P         0.586   0.606   0.517   0.836   0.864   0.732   0.475   0.507   0.350
74    N        -0.460  -0.434  -0.467  -0.267  -0.223  -0.285  -0.514  -0.478  -0.515
75    F        -1.220  -1.216  -1.181  -0.772  -0.772  -0.705  -1.009  -1.002  -0.947
76    N        -0.460  -0.478  -0.481  -0.523  -0.552  -0.563  -0.514  -0.537  -0.532
77    A        -0.460  -0.434  -0.465  -0.317  -0.272  -0.330  -0.514  -0.478  -0.512
78    S        -0.460  -0.437  -0.467  -0.533  -0.497  -0.531  -0.514  -0.483  -0.515
79    L        -0.460  -0.434  -0.465  -0.327  -0.287  -0.339  -0.514  -0.478  -0.512
80    Q        -1.220  -1.216  -1.181  -1.352  -1.332  -1.285  -1.009  -1.002  -0.947
81    L         0.300   0.304   0.341   0.124   0.130   0.196  -0.020  -0.013   0.042
82    T        -0.460  -0.434  -0.465  -0.367  -0.329  -0.383  -0.514  -0.478  -0.512
83    T        -1.220  -1.216  -1.181  -1.095  -1.075  -1.028  -1.009  -1.002  -0.947
84    N        -0.460  -0.437  -0.467  -0.380  -0.350  -0.384  -0.514  -0.483  -0.515
85    T        -0.460  -0.478  -0.481  -0.330  -0.363  -0.367  -0.514  -0.537  -0.532
86    E        -1.220  -1.216  -1.181  -1.309  -1.322  -1.242  -1.009  -1.002  -0.947
87    Q        -1.220  -1.216  -1.181  -1.243  -1.261  -1.176  -1.009  -1.002  -0.947
88    G        -1.220  -1.216  -1.181  -1.009  -1.007  -0.943  -1.009  -1.002  -0.947
89    D        -0.589  -0.586  -0.549  -0.499  -0.503  -0.432  -0.679  -0.673  -0.618
90    S        -0.589  -0.586  -0.549  -0.587  -0.567  -0.520  -0.679  -0.673  -0.618
91    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    G        -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    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   P        -1.220  -1.216  -1.181  -0.935  -0.931  -0.868  -1.009  -1.002  -0.947
102   K        -1.220  -1.216  -1.181  -1.461  -1.431  -1.394  -1.009  -1.002  -0.947
103   K        -0.460  -0.434  -0.467  -0.694  -0.625  -0.739  -0.514  -0.478  -0.515
104   C        -1.220  -1.216  -1.181  -1.073  -1.085  -1.007  -1.009  -1.002  -0.947
105   I        -0.460  -0.434  -0.467  -0.428  -0.396  -0.425  -0.514  -0.478  -0.515
106   Q        -0.460  -0.434  -0.467  -0.555  -0.497  -0.585  -0.514  -0.478  -0.515
107   V        -0.460  -0.434  -0.467  -0.157  -0.115  -0.165  -0.514  -0.478  -0.515
108   N        -1.220  -1.216  -1.181  -1.323  -1.307  -1.256  -1.009  -1.002  -0.947
109   C         1.819   1.824   1.862   2.088   2.093   2.152   1.958   1.965   2.017
110   L        -0.460  -0.437  -0.467  -0.676  -0.634  -0.696  -0.514  -0.483  -0.515
111   N        -1.220  -1.216  -1.181  -1.266  -1.252  -1.200  -1.009  -1.002  -0.947
112   C         1.819   1.824   1.862   2.088   2.093   2.152   1.958   1.965   2.017
113   E        -1.220  -1.216  -1.181  -0.931  -0.925  -0.864  -1.009  -1.002  -0.947
114   K        -0.460  -0.434  -0.465  -0.505  -0.438  -0.552  -0.514  -0.478  -0.512
115   S        -1.220  -1.216  -1.181  -1.362  -1.370  -1.295  -1.009  -1.002  -0.947
116   K        -0.460  -0.475  -0.483  -0.569  -0.595  -0.658  -0.514  -0.533  -0.534
117   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   F        -0.460  -0.434  -0.465  -0.228  -0.192  -0.230  -0.514  -0.478  -0.512
119   E         0.586   0.540   0.493   0.696   0.623   0.541   0.475   0.397   0.308
120   W        -0.460  -0.434  -0.467  -0.154  -0.116  -0.155  -0.514  -0.478  -0.515
121   -        -0.589  -0.585  -0.549  -0.627  -0.628  -0.561  -0.679  -0.673  -0.618
122   K        -0.460  -0.478  -0.481  -0.897  -0.912  -0.912  -0.514  -0.537  -0.532
123   S        -1.220  -1.216  -1.181  -1.001  -0.985  -0.934  -1.009  -1.002  -0.947
124   E        -0.460  -0.478  -0.481  -0.327  -0.352  -0.355  -0.514  -0.537  -0.532
125   F        -1.220  -1.216  -1.181  -1.157  -1.145  -1.090  -1.009  -1.002  -0.947
126   V        -1.220  -1.216  -1.181  -1.401  -1.391  -1.334  -1.009  -1.002  -0.947
127   V         0.586   0.611   0.519   0.230   0.272   0.141   0.475   0.515   0.353
128   P        -1.220  -1.216  -1.181  -0.906  -0.901  -0.840  -1.009  -1.002  -0.947
129   T        -0.460  -0.475  -0.483  -0.337  -0.373  -0.392  -0.514  -0.533  -0.534
130   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   S         0.424   0.402   0.409   0.190   0.161   0.167   0.200   0.161   0.163
136   P         1.819   1.824   1.862   2.019   2.023   2.083   1.958   1.965   2.017
137   M        -0.589  -0.586  -0.549  -0.697  -0.682  -0.631  -0.679  -0.673  -0.618
138   I        -0.589  -0.586  -0.549  -0.401  -0.399  -0.335  -0.679  -0.673  -0.618
139   N         0.424   0.440   0.422   0.383   0.402   0.380   0.200   0.227   0.185
140   S         0.424   0.442   0.422   0.416   0.451   0.389   0.200   0.231   0.185
141   T        -0.589  -0.586  -0.549  -0.449  -0.443  -0.383  -0.679  -0.673  -0.618
142   S        -0.460  -0.437  -0.467  -0.415  -0.380  -0.402  -0.514  -0.483  -0.515
143   S        -0.460  -0.478  -0.484  -0.509  -0.529  -0.524  -0.514  -0.537  -0.536
144   G        -1.220  -1.216  -1.181  -0.898  -0.893  -0.832  -1.009  -1.002  -0.947
145   K        -1.220  -1.216  -1.181  -1.271  -1.245  -1.204  -1.009  -1.002  -0.947
146   V        -1.220  -1.216  -1.181  -1.043  -1.026  -0.977  -1.009  -1.002  -0.947
147   S         0.586   0.540   0.493   0.460   0.398   0.314   0.475   0.397   0.308
148   Y        -1.220  -1.216  -1.181  -1.248  -1.241  -1.181  -1.009  -1.002  -0.947
149   A        -1.220  -1.216  -1.181  -1.229  -1.248  -1.163  -1.009  -1.002  -0.947
150   V        -0.460  -0.478  -0.481  -0.257  -0.290  -0.290  -0.514  -0.537  -0.532
151   K        -1.220  -1.216  -1.181  -1.280  -1.263  -1.214  -1.009  -1.002  -0.947
152   K        -0.460  -0.437  -0.467  -0.755  -0.721  -0.740  -0.514  -0.483  -0.515
153   P        -0.460  -0.437  -0.467  -0.228  -0.192  -0.239  -0.514  -0.483  -0.515
154   Q        -0.460  -0.475  -0.483  -0.782  -0.795  -0.785  -0.514  -0.533  -0.534
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   K         0.424   0.440   0.422   0.045   0.072   0.054   0.200   0.227   0.185
163   S        -0.460  -0.475  -0.483  -0.865  -0.862  -0.878  -0.514  -0.533  -0.534
164   K         0.586   0.540   0.493   0.221   0.161   0.092   0.475   0.397   0.308
165   T         0.586   0.606   0.517   0.716   0.741   0.596   0.475   0.507   0.350
166   S        -0.460  -0.437  -0.467  -0.595  -0.558  -0.598  -0.514  -0.483  -0.515
167   T        -0.460  -0.478  -0.481  -0.577  -0.633  -0.646  -0.514  -0.537  -0.532
168   G        -0.460  -0.475  -0.483  -0.300  -0.335  -0.350  -0.514  -0.533  -0.534
169   K         1.819   1.824   1.862   1.416   1.429   1.480   1.958   1.965   2.017
170   E        -0.460  -0.478  -0.481  -0.283  -0.313  -0.307  -0.514  -0.537  -0.532
171   R         1.819   1.824   1.862   1.923   1.935   1.988   1.958   1.965   2.017
172   S        -0.460  -0.475  -0.483  -0.428  -0.459  -0.496  -0.514  -0.533  -0.534
173   K         1.819   1.824   1.862   1.416   1.429   1.480   1.958   1.965   2.017
174   K         0.586   0.606   0.515   0.252   0.287   0.165   0.475   0.507   0.347
175   R         1.819   1.824   1.862   1.923   1.935   1.988   1.958   1.965   2.017
176   K         1.819   1.824   1.862   1.416   1.429   1.480   1.958   1.965   2.017
177   L         0.586   0.611   0.519   0.703   0.743   0.578   0.475   0.515   0.353
178   N         0.586   0.606   0.517   0.540   0.570   0.409   0.475   0.507   0.350
179   S        -0.460  -0.478  -0.484  -0.595  -0.623  -0.621  -0.514  -0.537  -0.536
180   L         1.819   1.824   1.862   1.754   1.756   1.819   1.958   1.965   2.017
181   T         0.300   0.304   0.342   0.059   0.061   0.121  -0.020  -0.013   0.043
182   N         0.586   0.606   0.515   0.540   0.570   0.405   0.475   0.507   0.347
183   L         1.819   1.824   1.862   1.754   1.756   1.819   1.958   1.965   2.017
184   L         1.819   1.824   1.862   1.754   1.756   1.819   1.958   1.965   2.017
185   S         0.300   0.304   0.342   0.124   0.144   0.200  -0.020  -0.013   0.043
186   K        -0.460  -0.478  -0.484  -1.021  -1.040  -1.057  -0.514  -0.537  -0.536
187   R         0.586   0.611   0.519   0.201   0.246   0.105   0.475   0.515   0.353
188   N        -0.589  -0.585  -0.549  -0.901  -0.912  -0.834  -0.679  -0.673  -0.618
189   Q         0.586   0.611   0.519   0.224   0.266   0.134   0.475   0.515   0.353
190   E         1.819   1.824   1.862   1.923   1.928   1.988   1.958   1.965   2.017
191   K         1.819   1.824   1.862   1.416   1.429   1.480   1.958   1.965   2.017
192   K         0.300   0.304   0.342  -0.169  -0.146  -0.090  -0.020  -0.013   0.043
193   M        -1.220  -1.216  -1.181  -1.001  -1.005  -0.934  -1.009  -1.002  -0.947
194   E        -0.460  -0.437  -0.467  -0.439  -0.396  -0.457  -0.514  -0.483  -0.515
195   K        -0.460  -0.478  -0.481  -0.909  -0.934  -0.925  -0.514  -0.537  -0.532
196   K         1.819   1.824   1.862   1.416   1.429   1.480   1.958   1.965   2.017
197   K        -0.460  -0.478  -0.481  -0.901  -0.907  -0.916  -0.514  -0.537  -0.532
198   S        -1.220  -1.216  -1.181  -1.073  -1.054  -1.007  -1.009  -1.002  -0.947
199   S        -0.460  -0.478  -0.484  -0.580  -0.606  -0.605  -0.514  -0.537  -0.536
200   S         0.586   0.606   0.515   0.508   0.543   0.412   0.475   0.507   0.347
201   L         1.819   1.824   1.862   1.754   1.756   1.819   1.958   1.965   2.017
202   S         1.819   1.824   1.862   1.680   1.693   1.744   1.958   1.965   2.017
203   L         1.819   1.824   1.862   1.754   1.756   1.819   1.958   1.965   2.017
204   E        -0.460  -0.434  -0.467  -0.228  -0.184  -0.243  -0.514  -0.478  -0.515
205   S        -0.460  -0.478  -0.484  -0.555  -0.577  -0.576  -0.514  -0.537  -0.536
206   F         1.819   1.824   1.862   2.088   2.094   2.152   1.958   1.965   2.017
207   M         1.819   1.824   1.862   2.065   2.071   2.129   1.958   1.965   2.017
208   K         0.586   0.540   0.493   0.172   0.106   0.027   0.475   0.397   0.308
209   S        -0.589  -0.585  -0.549  -1.068  -1.070  -1.002  -0.679  -0.673  -0.618
* 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/P40993
Output conservation file - output/P40993
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
