1     M         2.083   2.104   2.248   2.338   2.368   2.593   2.340   2.369   2.611
2     G        -0.403  -0.312  -0.423  -0.327  -0.189  -0.365  -0.459  -0.342  -0.475
3     R         1.182   1.173   1.108   1.409   1.397   1.276   1.174   1.153   0.987
4     D         0.182   0.145   0.150   0.226   0.162   0.144  -0.011  -0.069  -0.083
5     I         1.082   1.081   1.046   0.958   0.963   0.854   0.997   0.988   0.864
6     C         0.171   0.172   0.157   0.052   0.064   0.049  -0.059  -0.055  -0.088
7     T        -1.414  -1.383  -1.352  -1.194  -1.156  -1.099  -1.087  -1.056  -0.981
8     L         1.263   1.267   1.151   1.104   1.109   0.934   1.312   1.315   1.069
9     D         2.083   2.104   2.248   2.176   2.205   2.427   2.340   2.369   2.611
10    N         0.074   0.037   0.116  -0.010  -0.056   0.063  -0.230  -0.265  -0.157
11    V         0.074   0.037   0.116  -0.325  -0.357  -0.251  -0.230  -0.265  -0.157
12    Y         0.074   0.037   0.116  -0.014  -0.054   0.063  -0.230  -0.265  -0.157
13    A        -0.472  -0.452  -0.462  -0.416  -0.396  -0.416  -0.573  -0.551  -0.534
14    N         2.083   2.104   2.248   2.140   2.171   2.390   2.340   2.369   2.611
15    N         2.083   2.104   2.248   2.140   2.171   2.390   2.340   2.369   2.611
16    L         1.263   1.350   1.168   1.104   1.218   0.963   1.312   1.451   1.103
17    G         1.263   1.187   1.157   1.341   1.234   1.177   1.312   1.178   1.081
18    M        -0.472  -0.483  -0.448  -0.345  -0.335  -0.298  -0.573  -0.569  -0.512
19    L         0.171   0.172   0.170   0.010   0.017   0.042  -0.059  -0.048  -0.068
20    T        -0.868  -0.955  -0.933  -0.839  -0.978  -0.922  -0.744  -0.833  -0.781
21    K         0.490   0.440   0.321   0.495   0.417   0.262   0.455   0.377   0.182
22    L         1.263   1.261   1.147   1.212   1.215   1.021   1.312   1.304   1.063
23    A         0.171   0.151   0.129   0.104   0.064   0.003  -0.059  -0.093  -0.129
24    H        -0.868  -0.892  -0.929  -0.790  -0.831  -0.872  -0.744  -0.765  -0.777
25    V         0.490   0.384   0.305   0.511   0.353   0.198   0.455   0.294   0.157
26    T        -0.472  -0.457  -0.447  -0.425  -0.387  -0.357  -0.573  -0.550  -0.518
27    V        -0.225  -0.330  -0.382  -0.294  -0.443  -0.524  -0.230  -0.364  -0.423
28    P         1.263   1.187   1.157   1.521   1.425   1.387   1.312   1.178   1.081
29    N        -1.018  -1.007  -0.966  -0.921  -0.890  -0.840  -0.915  -0.901  -0.819
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    L        -1.414  -1.373  -1.347  -1.299  -1.237  -1.222  -1.087  -1.047  -0.976
34    Y         0.886   0.836   0.904   0.827   0.743   0.826   0.627   0.517   0.575
35    Q        -0.225  -0.246  -0.365   0.105   0.075  -0.109  -0.230  -0.255  -0.401
36    D        -0.472  -0.523  -0.468  -0.520  -0.586  -0.492  -0.573  -0.625  -0.541
37    A         0.490   0.476   0.300   0.608   0.587   0.302   0.455   0.433   0.150
38    F         0.171   0.243   0.194   0.347   0.459   0.391  -0.059   0.063  -0.024
39    F         0.717   0.721   0.839   0.535   0.542   0.715   0.284   0.281   0.437
40    S        -0.472  -0.470  -0.480  -0.634  -0.638  -0.634  -0.573  -0.571  -0.555
41    A        -0.472  -0.423  -0.448  -0.503  -0.451  -0.444  -0.573  -0.520  -0.518
42    L        -1.414  -1.371  -1.355  -1.528  -1.455  -1.428  -1.087  -1.045  -0.983
43    F        -0.472  -0.533  -0.483  -0.675  -0.756  -0.681  -0.573  -0.639  -0.558
44    A        -1.811  -1.793  -1.710  -1.685  -1.663  -1.528  -1.258  -1.239  -1.120
45    E        -1.018  -1.030  -0.976  -1.118  -1.139  -1.070  -0.915  -0.917  -0.828
46    D        -0.472  -0.399  -0.442  -0.437  -0.329  -0.382  -0.573  -0.484  -0.512
47    S        -1.018  -1.053  -0.960  -0.806  -0.851  -0.711  -0.915  -0.939  -0.814
48    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    H        -0.691  -0.681  -0.572  -0.659  -0.643  -0.477  -0.808  -0.794  -0.653
63    F        -1.018  -1.030  -0.976  -1.101  -1.106  -0.994  -0.915  -0.917  -0.828
64    T         0.171   0.237   0.194   0.067   0.193   0.113  -0.059   0.056  -0.024
65    Q         0.886   0.950   0.950   0.899   1.011   0.951   0.627   0.741   0.670
66    M        -0.225  -0.330  -0.382  -0.274  -0.427  -0.493  -0.230  -0.364  -0.423
67    A         2.083   2.104   2.248   2.067   2.096   2.315   2.340   2.369   2.611
68    Y         1.263   1.350   1.168   1.376   1.494   1.265   1.312   1.451   1.103
69    Y         1.263   1.187   1.157   1.376   1.285   1.248   1.312   1.178   1.081
70    S         0.171   0.147   0.158   0.139   0.094   0.113  -0.059  -0.101  -0.085
71    E         1.263   1.187   1.157   1.283   1.188   1.164   1.312   1.178   1.081
72    I         0.171   0.179   0.189  -0.110  -0.058  -0.090  -0.059  -0.026  -0.031
73    P         0.490   0.411   0.319   0.824   0.723   0.595   0.455   0.334   0.180
74    V         1.263   1.267   1.151   1.276   1.290   1.108   1.312   1.315   1.069
75    G         2.083   2.104   2.248   2.114   2.145   2.363   2.340   2.369   2.611
76    G         0.171   0.177   0.156   0.100   0.122   0.074  -0.059  -0.039  -0.092
77    L         0.074   0.075   0.131  -0.260  -0.251  -0.184  -0.230  -0.224  -0.140
78    V         0.171   0.142   0.155   0.041  -0.003   0.025  -0.059  -0.107  -0.090
79    A        -1.018  -1.000  -0.956  -0.897  -0.868  -0.817  -0.915  -0.893  -0.810
80    K        -0.472  -0.457  -0.440  -0.506  -0.501  -0.440  -0.573  -0.546  -0.508
81    L         0.347   0.483   0.263   0.209   0.393   0.076   0.241   0.444   0.092
82    V        -1.040  -1.046  -0.976  -1.194  -1.229  -1.113  -0.925  -0.928  -0.824
83    P        -1.502  -1.488  -1.396  -1.217  -1.194  -1.049  -1.158  -1.140  -1.016
84    K        -0.577  -0.548  -0.512  -0.728  -0.700  -0.622  -0.692  -0.657  -0.590
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    K         2.083   2.104   2.248   1.945   1.970   2.190   2.340   2.369   2.611
90    Q        -1.040  -1.044  -0.976  -0.935  -0.971  -0.849  -0.925  -0.927  -0.824
91    N        -1.040  -1.056  -0.966  -0.921  -0.944  -0.806  -0.925  -0.938  -0.814
92    E        -1.040  -1.048  -0.969  -0.914  -0.919  -0.811  -0.925  -0.930  -0.818
93    L        -1.502  -1.483  -1.396  -1.486  -1.463  -1.325  -1.158  -1.137  -1.016
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   S        -1.040  -0.971  -0.960  -1.255  -1.163  -1.140  -0.925  -0.851  -0.808
107   L        -0.225  -0.330  -0.382   0.061  -0.099  -0.205  -0.230  -0.364  -0.423
108   K        -1.018  -1.032  -0.977  -1.016  -1.034  -0.936  -0.915  -0.920  -0.828
109   G        -0.868  -0.801  -0.890  -0.701  -0.617  -0.739  -0.744  -0.670  -0.737
110   I        -0.225  -0.186  -0.339  -0.194  -0.137  -0.376  -0.230  -0.181  -0.367
111   Q         0.171   0.112   0.137   0.240   0.161   0.216  -0.059  -0.151  -0.120
112   I         1.263   1.350   1.168   1.212   1.338   1.057   1.312   1.451   1.103
113   E         0.490   0.440   0.321   0.523   0.438   0.274   0.455   0.377   0.182
114   F        -0.868  -0.892  -0.929  -0.753  -0.798  -0.871  -0.744  -0.765  -0.777
115   L         0.171   0.270   0.201  -0.072   0.075  -0.030  -0.059   0.100  -0.013
116   G         1.263   1.261   1.147   1.322   1.321   1.164   1.312   1.304   1.063
117   V         2.083   2.104   2.248   2.041   2.075   2.288   2.340   2.369   2.611
118   L         2.083   2.104   2.248   1.869   1.895   2.113   2.340   2.369   2.611
119   P        -0.472  -0.428  -0.447  -0.539  -0.474  -0.498  -0.573  -0.532  -0.518
120   N        -0.225  -0.246  -0.365  -0.106  -0.142  -0.323  -0.230  -0.255  -0.401
121   Y         2.083   2.104   2.248   2.104   2.139   2.353   2.340   2.369   2.611
122   R         1.263   1.237   1.142   1.556   1.527   1.397   1.312   1.263   1.052
123   H        -1.018  -1.024  -0.960  -0.906  -0.905  -0.802  -0.915  -0.914  -0.813
124   K        -1.018  -1.044  -0.975  -1.112  -1.114  -0.987  -0.915  -0.931  -0.826
125   S        -0.472  -0.513  -0.479  -0.491  -0.562  -0.505  -0.573  -0.620  -0.555
126   I         1.263   1.267   1.151   1.245   1.259   1.086   1.312   1.315   1.069
127   G         1.263   1.237   1.142   1.341   1.306   1.151   1.312   1.263   1.052
128   S        -1.414  -1.383  -1.352  -1.364  -1.306  -1.280  -1.087  -1.056  -0.981
129   K         0.490   0.512   0.325   0.470   0.493   0.229   0.455   0.487   0.189
130   L         1.263   1.267   1.151   1.164   1.170   1.042   1.312   1.315   1.069
131   L         2.083   2.104   2.248   1.869   1.895   2.113   2.340   2.369   2.611
132   K        -0.472  -0.398  -0.436  -0.646  -0.555  -0.579  -0.573  -0.492  -0.503
133   F         0.490   0.506   0.325   0.689   0.717   0.480   0.455   0.478   0.188
134   A        -0.472  -0.355  -0.447  -0.673  -0.486  -0.657  -0.573  -0.440  -0.516
135   E        -0.472  -0.502  -0.456  -0.630  -0.645  -0.587  -0.573  -0.591  -0.522
136   D        -0.472  -0.407  -0.450  -0.452  -0.363  -0.414  -0.573  -0.499  -0.522
137   K        -0.472  -0.509  -0.469  -0.655  -0.713  -0.644  -0.573  -0.613  -0.543
138   C        -0.076  -0.038   0.049  -0.048   0.011   0.133  -0.401  -0.349  -0.239
139   S         0.171   0.142   0.155  -0.049  -0.106  -0.080  -0.059  -0.107  -0.090
140   E         0.171   0.256   0.166  -0.014   0.104  -0.024  -0.059   0.060  -0.075
141   C        -1.414  -1.455  -1.375  -0.996  -1.065  -0.933  -1.087  -1.114  -1.000
142   H         0.171   0.092   0.139   0.273   0.145   0.208  -0.059  -0.170  -0.113
143   Q        -0.472  -0.462  -0.452  -0.428  -0.380  -0.396  -0.573  -0.546  -0.518
144   H         0.490   0.440   0.321   0.821   0.741   0.564   0.455   0.377   0.182
145   N        -0.225  -0.271  -0.398  -0.193  -0.267  -0.470  -0.230  -0.287  -0.443
146   V         0.171   0.160   0.147  -0.110  -0.129  -0.195  -0.059  -0.075  -0.106
147   F        -1.018  -0.932  -0.953  -0.867  -0.750  -0.760  -0.915  -0.835  -0.807
148   V        -0.472  -0.447  -0.453  -0.655  -0.606  -0.640  -0.573  -0.545  -0.525
149   Y        -0.225  -0.330  -0.382   0.067  -0.108  -0.222  -0.230  -0.364  -0.423
150   L        -0.472  -0.495  -0.474  -0.672  -0.727  -0.686  -0.573  -0.601  -0.549
151   P        -1.414  -1.400  -1.346  -1.173  -1.150  -1.058  -1.087  -1.068  -0.975
152   A        -1.018  -1.060  -0.976  -0.940  -0.977  -0.853  -0.915  -0.945  -0.827
153   V        -1.414  -1.399  -1.353  -1.370  -1.358  -1.299  -1.087  -1.070  -0.981
154   D         0.074   0.035   0.120  -0.055  -0.114   0.007  -0.230  -0.269  -0.152
155   D        -1.018  -0.931  -0.953  -0.918  -0.815  -0.798  -0.915  -0.834  -0.807
156   L        -0.577  -0.586  -0.505  -0.662  -0.678  -0.554  -0.692  -0.696  -0.582
157   T        -0.472  -0.512  -0.477  -0.608  -0.680  -0.632  -0.573  -0.617  -0.552
158   K        -0.225  -0.330  -0.382  -0.158  -0.306  -0.392  -0.230  -0.364  -0.423
159   Q        -0.225  -0.191  -0.351  -0.123  -0.077  -0.293  -0.230  -0.187  -0.383
160   W         2.083   2.104   2.248   2.393   2.426   2.649   2.340   2.369   2.611
161   F         0.886   0.847   0.911   0.827   0.761   0.838   0.627   0.538   0.588
162   I        -0.472  -0.448  -0.447  -0.796  -0.770  -0.782  -0.573  -0.553  -0.518
163   A        -0.225  -0.330  -0.382  -0.218  -0.371  -0.452  -0.230  -0.364  -0.423
164   H        -0.472  -0.429  -0.443  -0.178  -0.129  -0.115  -0.573  -0.530  -0.511
165   G         2.083   2.104   2.248   2.114   2.145   2.363   2.340   2.369   2.611
166   F         2.083   2.104   2.248   2.222   2.251   2.474   2.340   2.369   2.611
167   E        -0.577  -0.563  -0.507  -0.720  -0.694  -0.612  -0.692  -0.673  -0.584
168   Q        -1.040  -1.043  -0.966  -0.925  -0.932  -0.829  -0.925  -0.924  -0.814
169   V        -1.040  -0.996  -0.970  -1.010  -0.942  -0.899  -0.925  -0.877  -0.818
170   G         0.347   0.408   0.269   0.399   0.489   0.262   0.241   0.329   0.102
171   E        -0.403  -0.382  -0.418  -0.497  -0.459  -0.543  -0.459  -0.432  -0.469
172   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   V         0.347   0.305   0.236   0.248   0.174   0.014   0.241   0.175   0.050
174   N        -1.040  -1.039  -0.981  -1.138  -1.147  -1.046  -0.925  -0.921  -0.829
175   N        -0.577  -0.542  -0.503  -0.695  -0.649  -0.579  -0.692  -0.652  -0.580
176   F         0.347   0.279   0.214   0.480   0.388   0.294   0.241   0.135   0.016
177   I         0.171   0.112   0.137   0.049  -0.055  -0.043  -0.059  -0.151  -0.120
178   K         0.490   0.384   0.305   0.463   0.306   0.184   0.455   0.294   0.157
179   G        -1.414  -1.400  -1.346  -1.269  -1.253  -1.171  -1.087  -1.068  -0.975
180   V        -1.414  -1.455  -1.375  -1.263  -1.354  -1.249  -1.087  -1.114  -1.000
181   N        -1.018  -1.060  -0.976  -0.896  -0.947  -0.815  -0.915  -0.945  -0.827
182   G        -0.028  -0.050   0.053  -0.387  -0.400  -0.255  -0.347  -0.371  -0.236
183   D        -1.811  -1.793  -1.710  -1.605  -1.586  -1.447  -1.258  -1.239  -1.120
184   E        -0.868  -0.870  -0.886  -0.733  -0.739  -0.772  -0.744  -0.745  -0.732
185   Q        -1.018  -1.002  -0.966  -0.937  -0.929  -0.862  -0.915  -0.891  -0.817
186   D         0.886   0.924   0.923   0.812   0.873   0.812   0.627   0.690   0.613
187   A         0.490   0.384   0.305   0.607   0.457   0.341   0.455   0.294   0.157
188   I        -0.472  -0.453  -0.436  -0.547  -0.500  -0.484  -0.573  -0.537  -0.503
189   L         0.171   0.243   0.194  -0.171  -0.042  -0.141  -0.059   0.063  -0.024
190   L        -0.225  -0.135  -0.309  -0.217  -0.102  -0.309  -0.230  -0.113  -0.330
191   K        -1.018  -0.980  -0.958  -1.127  -1.084  -1.033  -0.915  -0.877  -0.812
192   K         0.171   0.218   0.186  -0.038   0.059   0.008  -0.059   0.029  -0.035
193   H        -0.868  -0.848  -0.909  -0.858  -0.834  -0.912  -0.744  -0.720  -0.756
194   I         0.074   0.081   0.122  -0.325  -0.320  -0.258  -0.230  -0.215  -0.148
195   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
197   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
198   S        -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/Q08689
Output conservation file - output/Q08689
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
