1     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     M         0.407   0.452   0.561   0.143   0.221   0.359   0.005   0.067   0.217
4     N        -0.843  -0.779  -0.715  -0.940  -0.846  -0.763  -0.930  -0.854  -0.752
5     I         0.916   1.019   0.796   1.024   1.170   0.851   0.940   1.098   0.689
6     V         1.683   1.737   1.852   1.654   1.743   1.916   1.874   1.955   2.166
7     P         1.683   1.737   1.852   1.695   1.785   1.958   1.874   1.955   2.166
8     Q        -1.212  -1.149  -1.112  -1.240  -1.130  -1.078  -1.086  -1.013  -0.934
9     D        -1.233  -1.185  -1.125  -1.229  -1.154  -1.086  -1.094  -1.037  -0.943
10    T        -1.233  -1.230  -1.134  -1.254  -1.293  -1.141  -1.094  -1.081  -0.951
11    F        -0.843  -0.864  -0.719  -0.720  -0.747  -0.533  -0.930  -0.931  -0.754
12    K        -0.703  -0.803  -0.678  -0.686  -0.834  -0.668  -0.774  -0.864  -0.710
13    S        -1.073  -1.042  -1.077  -1.064  -1.029  -1.077  -0.930  -0.896  -0.896
14    Q        -1.582  -1.567  -1.498  -1.593  -1.604  -1.462  -1.241  -1.215  -1.105
15    V        -0.103  -0.088  -0.095  -0.200  -0.135  -0.171  -0.307  -0.266  -0.292
16    S        -1.073  -0.989  -1.065  -1.034  -0.906  -1.020  -0.930  -0.831  -0.883
17    T        -0.207  -0.288  -0.171  -0.270  -0.377  -0.230  -0.458  -0.555  -0.404
18    D        -0.801  -0.826  -0.715  -0.952  -0.963  -0.816  -0.882  -0.897  -0.750
19    Q        -1.212  -1.252  -1.147  -1.008  -1.015  -0.878  -1.086  -1.103  -0.964
20    D        -0.703  -0.639  -0.672  -0.703  -0.606  -0.677  -0.774  -0.688  -0.702
21    K        -1.212  -1.146  -1.119  -0.969  -0.916  -0.830  -1.086  -1.010  -0.939
22    S        -0.207  -0.103  -0.105  -0.484  -0.304  -0.346  -0.458  -0.302  -0.308
23    V        -1.233  -1.150  -1.117  -1.174  -1.055  -1.009  -1.094  -0.999  -0.935
24    L        -0.801  -0.779  -0.701  -0.934  -0.930  -0.786  -0.882  -0.843  -0.734
25    S        -0.703  -0.712  -0.681  -0.792  -0.830  -0.776  -0.774  -0.769  -0.711
26    S        -0.703  -0.642  -0.677  -0.855  -0.759  -0.813  -0.774  -0.714  -0.710
27    A        -0.843  -0.753  -0.719  -0.906  -0.813  -0.734  -0.930  -0.821  -0.755
28    V        -0.103  -0.151  -0.098  -0.126  -0.198  -0.124  -0.307  -0.354  -0.298
29    P         0.565   0.665   0.655   0.491   0.645   0.606   0.316   0.485   0.411
30    S        -0.333  -0.329  -0.209  -0.602  -0.594  -0.404  -0.618  -0.615  -0.457
31    L         0.916   0.769   0.758   0.856   0.639   0.621   0.940   0.675   0.615
32    P        -0.333  -0.304  -0.199  -0.431  -0.376  -0.228  -0.618  -0.583  -0.444
33    D         1.683   1.737   1.852   1.647   1.743   1.910   1.874   1.955   2.166
34    T        -0.638  -0.550  -0.654  -0.600  -0.461  -0.668  -0.670  -0.552  -0.675
35    L         0.841   0.908   0.732   0.812   0.900   0.673   0.814   0.916   0.565
36    R         0.841   0.927   0.738   0.863   0.973   0.707   0.814   0.947   0.576
37    Q        -1.212  -1.102  -1.117  -1.261  -1.067  -1.126  -1.086  -0.972  -0.939
38    Q         0.195   0.009  -0.052   0.322   0.035  -0.077   0.161  -0.116  -0.222
39    E        -0.473  -0.592  -0.634  -0.514  -0.822  -0.798  -0.462  -0.614  -0.651
40    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    G         0.916   0.784   0.729   0.997   0.804   0.731   0.940   0.701   0.558
42    A        -0.193  -0.199  -0.148  -0.250  -0.176  -0.171  -0.462  -0.454  -0.377
43    V        -0.703  -0.712  -0.695  -0.805  -0.800  -0.770  -0.774  -0.769  -0.727
44    P         0.407   0.452   0.564   0.214   0.330   0.445   0.005   0.068   0.225
45    L         0.565   0.591   0.612   0.359   0.383   0.403   0.316   0.344   0.324
46    S        -1.212  -1.247  -1.147  -1.248  -1.252  -1.166  -1.086  -1.098  -0.964
47    T         0.565   0.682   0.640   0.359   0.666   0.449   0.316   0.516   0.381
48    Q        -0.583  -0.704  -0.658  -0.507  -0.687  -0.628  -0.630  -0.746  -0.683
49    L        -0.583  -0.704  -0.658  -0.631  -0.795  -0.720  -0.630  -0.746  -0.683
50    N         0.308   0.061  -0.016   0.465   0.101  -0.068   0.324  -0.039  -0.168
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    D        -0.663  -0.699  -0.667  -0.700  -0.698  -0.693  -0.750  -0.763  -0.699
69    R         0.308   0.061  -0.016   0.411   0.042  -0.074   0.324  -0.039  -0.168
70    H         1.683   1.737   1.852   1.806   1.910   2.070   1.874   1.955   2.166
71    P         1.683   1.737   1.852   1.700   1.847   1.962   1.874   1.955   2.166
72    L         1.683   1.737   1.852   1.543   1.599   1.804   1.874   1.955   2.166
73    E         0.308   0.384   0.072   0.329   0.340   0.013   0.324   0.431  -0.033
74    S        -0.323  -0.180  -0.501  -0.188   0.113  -0.422  -0.273  -0.086  -0.485
75    T         0.308   0.520   0.071   0.428   0.648   0.103   0.324   0.624  -0.035
76    L        -0.137   0.017  -0.089  -0.366  -0.145  -0.268  -0.392  -0.175  -0.299
77    K        -1.432  -1.230  -1.398  -1.232  -0.914  -1.221  -1.107  -0.897  -1.021
78    N         0.979   0.916   0.787   1.111   1.050   0.851   1.039   0.930   0.671
79    W         1.683   1.737   1.852   1.905   1.987   2.171   1.874   1.955   2.166
80    E         0.979   1.100   0.820   0.915   0.991   0.705   1.039   1.223   0.734
81    T        -0.583  -0.512  -0.644  -0.624  -0.611  -0.683  -0.630  -0.587  -0.674
82    T         0.979   0.812   0.784   1.111   0.924   0.845   1.039   0.752   0.665
83    Q         0.979   0.916   0.787   1.078   0.993   0.806   1.039   0.930   0.671
84    R        -1.554  -1.525  -1.470  -1.352  -1.432  -1.220  -1.227  -1.188  -1.084
85    Q        -1.432  -1.355  -1.405  -1.214  -1.124  -1.195  -1.107  -1.023  -1.026
86    R        -1.432  -1.486  -1.469  -1.247  -1.425  -1.311  -1.107  -1.150  -1.082
87    Q         0.447   0.565   0.604   0.210   0.352   0.441   0.085   0.293   0.308
88    M         0.388   0.429   0.552   0.065   0.084   0.306  -0.034   0.020   0.199
89    E         0.308   0.128   0.020   0.316  -0.020  -0.096   0.324   0.054  -0.113
90    Q        -0.663  -0.750  -0.673  -0.661  -0.734  -0.665  -0.750  -0.820  -0.706
91    Y         0.308   0.061  -0.016   0.670   0.289   0.159   0.324  -0.039  -0.168
92    R         0.979   0.995   0.817   1.028   1.010   0.826   1.039   1.059   0.729
93    Q         0.001   0.187  -0.048  -0.027   0.191  -0.094  -0.153   0.124  -0.222
94    I         0.001   0.049  -0.068   0.051   0.103  -0.068  -0.153  -0.119  -0.260
95    F         0.979   0.812   0.784   1.285   1.111   1.053   1.039   0.752   0.665
96    G         1.683   1.737   1.852   1.686   1.753   1.948   1.874   1.955   2.166
97    I        -1.231  -1.118  -1.120  -1.227  -1.105  -1.065  -1.107  -0.998  -0.942
98    A        -0.137  -0.224  -0.119  -0.181  -0.257  -0.116  -0.392  -0.477  -0.338
99    E         0.979   1.110   0.814   0.926   1.014   0.719   1.039   1.239   0.722
100   P         1.683   1.737   1.852   1.700   1.847   1.962   1.874   1.955   2.166
101   M        -0.137  -0.205  -0.115  -0.196  -0.265  -0.144  -0.392  -0.445  -0.330
102   K         0.388   0.459   0.562   0.134   0.201   0.390  -0.034   0.082   0.219
103   R         1.683   1.737   1.852   1.629   1.660   1.891   1.874   1.955   2.166
104   T        -1.432  -1.444  -1.438  -1.190  -1.273  -1.228  -1.107  -1.114  -1.055
105   M         1.683   1.737   1.852   1.728   1.803   1.991   1.874   1.955   2.166
106   E         1.683   1.737   1.852   1.529   1.526   1.789   1.874   1.955   2.166
107   M        -0.583  -0.625  -0.625  -0.622  -0.727  -0.664  -0.630  -0.671  -0.648
108   E        -0.663  -0.582  -0.628  -0.745  -0.632  -0.650  -0.750  -0.642  -0.658
109   I         0.447   0.467   0.558   0.205   0.190   0.322   0.085   0.098   0.213
110   V         0.979   0.812   0.784   1.060   0.917   0.802   1.039   0.752   0.665
111   N        -1.878  -1.865  -1.789  -1.800  -1.821  -1.656  -1.346  -1.320  -1.200
112   R        -1.878  -1.861  -1.775  -1.723  -1.714  -1.599  -1.346  -1.317  -1.191
113   T         0.001  -0.115  -0.109   0.005  -0.124  -0.214  -0.153  -0.323  -0.322
114   D        -0.583  -0.690  -0.655  -0.631  -0.770  -0.779  -0.630  -0.751  -0.686
115   F         0.195   0.009  -0.052   0.514   0.268   0.131   0.161  -0.116  -0.222
116   N        -0.785  -0.798  -0.711  -0.801  -0.863  -0.694  -0.869  -0.872  -0.749
117   P         1.683   1.737   1.852   1.700   1.847   1.962   1.874   1.955   2.166
118   L        -0.907  -0.720  -0.992  -0.832  -0.560  -0.969  -0.750  -0.529  -0.808
119   S        -1.231  -1.141  -1.131  -1.322  -1.066  -1.144  -1.107  -1.003  -0.951
120   T        -0.473  -0.355  -0.580  -0.464  -0.298  -0.624  -0.462  -0.306  -0.584
121   -         1.683   1.737   1.852   1.649   1.719   1.911   1.874   1.955   2.166
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -         0.841   0.900   0.768   0.875   0.958   0.770   0.814   0.903   0.635
130   N        -1.554  -1.497  -1.466  -1.448  -1.275  -1.310  -1.227  -1.162  -1.081
131   G        -0.907  -0.846  -0.741  -1.064  -0.892  -0.813  -0.988  -0.912  -0.777
132   S         0.388   0.459   0.561   0.079   0.284   0.352  -0.034   0.081   0.218
133   I        -1.109  -1.165  -1.105  -0.956  -1.001  -0.946  -0.988  -1.024  -0.926
134   H         1.683   1.737   1.852   1.806   1.910   2.070   1.874   1.955   2.166
135   R        -0.785  -0.802  -0.703  -0.936  -1.072  -0.850  -0.869  -0.871  -0.739
136   D         0.979   0.916   0.787   1.022   0.950   0.732   1.039   0.930   0.671
137   I         0.632   0.774   0.646   0.603   0.836   0.581   0.443   0.683   0.393
138   L         1.683   1.737   1.852   1.543   1.599   1.804   1.874   1.955   2.166
139   L        -0.663  -0.748  -0.651  -0.721  -0.822  -0.661  -0.750  -0.816  -0.684
140   N         0.979   0.916   0.787   1.110   1.046   0.848   1.039   0.930   0.671
141   K         0.632   0.515   0.589   0.615   0.375   0.468   0.443   0.195   0.276
142   E         0.388   0.429   0.552  -0.002  -0.001   0.239  -0.034   0.020   0.199
143   C        -1.432  -1.339  -1.402  -1.136  -0.982  -1.104  -1.107  -1.009  -1.024
144   S         0.001  -0.184  -0.111  -0.109  -0.271  -0.296  -0.153  -0.411  -0.323
145   I        -0.137  -0.237  -0.118  -0.271  -0.387  -0.243  -0.392  -0.497  -0.341
146   D         0.979   0.916   0.787   1.049   1.007   0.795   1.039   0.930   0.671
147   W         0.979   0.812   0.784   1.275   1.017   0.974   1.039   0.752   0.665
148   E         0.979   0.812   0.784   0.925   0.632   0.668   1.039   0.752   0.665
149   D         1.683   1.737   1.852   1.653   1.760   1.915   1.874   1.955   2.166
150   V         0.447   0.466   0.560   0.249   0.313   0.398   0.085   0.096   0.217
151   Y         1.683   1.737   1.852   1.896   1.970   2.162   1.874   1.955   2.166
152   P        -0.583  -0.668  -0.652  -0.497  -0.580  -0.604  -0.630  -0.738  -0.682
153   G         0.195   0.324  -0.006   0.286   0.421  -0.044   0.161   0.347  -0.153
154   T        -1.664  -1.612  -1.510  -1.625  -1.523  -1.403  -1.306  -1.246  -1.113
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   G        -0.583  -0.747  -0.655  -0.568  -0.838  -0.706  -0.630  -0.801  -0.685
157   L        -1.109  -1.221  -1.097  -1.043  -1.186  -1.003  -0.988  -1.072  -0.921
158   Q        -1.554  -1.443  -1.455  -1.478  -1.304  -1.353  -1.227  -1.117  -1.073
159   A        -0.703  -0.747  -0.677  -0.838  -0.931  -0.794  -0.774  -0.816  -0.710
160   S        -0.103  -0.078  -0.129  -0.245  -0.289  -0.354  -0.307  -0.319  -0.350
161   T        -1.324  -1.300  -1.168  -1.386  -1.347  -1.162  -1.179  -1.140  -0.982
162   M        -0.093  -0.082  -0.152  -0.010   0.022  -0.131  -0.263  -0.250  -0.373
163   V         1.683   1.737   1.852   1.642   1.729   1.904   1.874   1.955   2.166
164   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   D        -1.432  -1.486  -1.469  -1.242  -1.329  -1.318  -1.107  -1.150  -1.082
166   D         0.308   0.061  -0.016   0.431   0.135  -0.059   0.324  -0.039  -0.168
167   V        -0.137  -0.224  -0.119  -0.106  -0.136  -0.024  -0.392  -0.477  -0.338
168   H         0.979   0.812   0.784   1.198   0.997   0.930   1.039   0.752   0.665
169   S        -0.663  -0.790  -0.660  -0.760  -0.870  -0.748  -0.750  -0.857  -0.693
170   K         0.001   0.187  -0.048  -0.111   0.075  -0.172  -0.153   0.124  -0.222
171   I        -0.137  -0.074  -0.097  -0.217  -0.124  -0.150  -0.392  -0.280  -0.304
172   E         0.979   0.812   0.784   0.926   0.635   0.671   1.039   0.752   0.665
173   K         0.001  -0.151  -0.108   0.049  -0.189  -0.153  -0.153  -0.359  -0.321
174   Q        -0.339  -0.253  -0.192  -0.520  -0.436  -0.307  -0.630  -0.518  -0.434
175   L        -0.583  -0.652  -0.648  -0.503  -0.620  -0.605  -0.630  -0.710  -0.678
176   G         0.979   0.916   0.787   1.069   0.968   0.797   1.039   0.930   0.671
177   I         0.308   0.236   0.029   0.489   0.346   0.069   0.324   0.197  -0.099
178   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   -        -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/P38293
Output conservation file - output/P38293
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
