1     M         1.654   1.709   1.817   1.888   1.972   2.149   1.859   1.935   2.133
2     F        -0.138  -0.374  -0.319   0.019  -0.385  -0.352  -0.194  -0.531  -0.468
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    L        -0.309  -0.458  -0.343  -0.264  -0.499  -0.306  -0.441  -0.651  -0.503
43    R        -0.912  -1.010  -0.929  -0.688  -0.875  -0.803  -0.879  -0.993  -0.865
44    N        -1.092  -1.078  -0.941  -1.192  -1.142  -0.944  -1.107  -1.072  -0.879
45    S        -1.569  -1.466  -1.383  -1.638  -1.453  -1.357  -1.335  -1.220  -1.081
46    V        -1.670  -1.588  -1.424  -1.728  -1.510  -1.364  -1.426  -1.327  -1.117
47    L        -0.912  -0.644  -0.855  -0.822  -0.444  -0.740  -0.879  -0.536  -0.780
48    R        -0.138   0.075  -0.218   0.092   0.414  -0.093  -0.194   0.113  -0.321
49    T        -0.615  -0.525  -0.379  -0.854  -0.704  -0.484  -0.879  -0.748  -0.553
50    A        -0.912  -0.867  -0.896  -1.140  -1.104  -1.146  -0.879  -0.823  -0.827
51    P        -1.097  -0.992  -0.928  -1.243  -1.083  -1.007  -1.097  -0.969  -0.864
52    V        -1.097  -1.147  -0.965  -0.902  -0.991  -0.748  -1.097  -1.138  -0.904
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    L        -1.670  -1.608  -1.424  -1.765  -1.607  -1.399  -1.426  -1.348  -1.117
55    R        -0.525  -0.530  -0.360  -0.610  -0.588  -0.341  -0.769  -0.757  -0.528
56    R        -0.138  -0.374  -0.319   0.230  -0.121  -0.042  -0.194  -0.531  -0.468
57    G        -2.047  -1.972  -1.791  -1.779  -1.728  -1.413  -1.563  -1.480  -1.253
58    I        -1.092  -0.972  -0.922  -1.074  -0.873  -0.837  -1.107  -0.971  -0.862
59    T        -0.939  -0.780  -0.876  -0.849  -0.534  -0.706  -0.964  -0.782  -0.815
60    T         0.223   0.280   0.427  -0.050   0.052   0.265  -0.194  -0.102   0.113
61    L        -1.209  -1.147  -0.964  -1.553  -1.497  -1.196  -1.221  -1.137  -0.903
62    T         0.288   0.288   0.423   0.075   0.003   0.220  -0.066  -0.086   0.106
63    P         1.654   1.709   1.817   1.653   1.734   1.920   1.859   1.935   2.133
64    V        -0.205  -0.344  -0.312  -0.361  -0.581  -0.480  -0.323  -0.503  -0.462
65    S        -1.432  -1.284  -1.348  -1.305  -1.000  -1.146  -1.221  -1.042  -1.051
66    T         0.288   0.286   0.433   0.118   0.099   0.306  -0.066  -0.090   0.125
67    K        -1.925  -1.872  -1.736  -1.887  -1.763  -1.596  -1.477  -1.413  -1.214
68    L        -1.432  -1.270  -1.348  -1.326  -1.062  -1.153  -1.221  -1.034  -1.051
69    A         0.493   0.474   0.491   0.188   0.124   0.167   0.319   0.269   0.240
70    P         0.724   0.599   0.567   0.726   0.496   0.420   0.718   0.494   0.389
71    P        -0.205  -0.344  -0.312  -0.254  -0.457  -0.459  -0.323  -0.503  -0.462
72    A        -0.563  -0.568  -0.823  -0.352  -0.341  -0.760  -0.451  -0.448  -0.742
73    A         0.135  -0.065  -0.214   0.059  -0.271  -0.439   0.191  -0.086  -0.315
74    A         0.288   0.286   0.433  -0.082  -0.143   0.165  -0.066  -0.090   0.125
75    S        -0.358  -0.440  -0.334  -0.624  -0.724  -0.586  -0.579  -0.660  -0.498
76    Y         1.654   1.709   1.817   1.841   1.930   2.103   1.859   1.935   2.133
77    S         0.493   0.474   0.491   0.335   0.349   0.305   0.319   0.269   0.240
78    Q         0.876   0.844   0.635   1.152   1.142   0.874   0.960   0.906   0.518
79    A         1.654   1.709   1.817   1.414   1.463   1.688   1.859   1.935   2.133
80    M        -0.205  -0.229  -0.299  -0.249  -0.373  -0.402  -0.323  -0.391  -0.450
81    K         1.654   1.709   1.817   1.590   1.687   1.859   1.859   1.935   2.133
82    A        -0.939  -0.993  -0.878  -1.291  -1.385  -1.134  -0.964  -0.983  -0.813
83    N        -0.205  -0.337  -0.302  -0.148  -0.357  -0.291  -0.323  -0.515  -0.454
84    N        -0.205  -0.148  -0.258  -0.127  -0.063  -0.258  -0.323  -0.212  -0.383
85    F        -0.851  -0.882  -0.873  -0.778  -0.815  -0.897  -0.836  -0.851  -0.810
86    V         0.135   0.085  -0.198   0.255   0.186  -0.269   0.191   0.117  -0.291
87    Y         0.493   0.531   0.472   0.655   0.728   0.582   0.319   0.373   0.203
88    V         0.288   0.286   0.433   0.057   0.029   0.315  -0.066  -0.090   0.125
89    S         1.654   1.709   1.817   1.553   1.681   1.823   1.859   1.935   2.133
90    G         1.654   1.709   1.817   1.776   1.813   2.040   1.859   1.935   2.133
91    Q         1.654   1.709   1.817   1.786   1.877   2.049   1.859   1.935   2.133
92    I         0.135  -0.065  -0.214   0.219  -0.097  -0.382   0.191  -0.086  -0.315
93    P         0.876   0.817   0.637   0.943   0.862   0.569   0.960   0.862   0.522
94    Y        -0.851  -1.009  -0.917  -0.655  -0.928  -0.768  -0.836  -0.995  -0.854
95    T        -0.138  -0.392  -0.319   0.094  -0.308  -0.218  -0.194  -0.557  -0.468
96    P        -0.851  -0.912  -0.875  -0.954  -1.028  -1.042  -0.836  -0.873  -0.810
97    D        -0.205  -0.161  -0.269  -0.012   0.040  -0.133  -0.323  -0.252  -0.405
98    N         0.223   0.297   0.436   0.028   0.145   0.381  -0.194  -0.068   0.131
99    K        -0.205  -0.370  -0.300  -0.279  -0.505  -0.444  -0.323  -0.545  -0.448
100   P        -1.209  -1.409  -1.363  -1.007  -1.310  -1.296  -0.964  -1.154  -1.062
101   V        -0.851  -0.852  -0.862  -0.919  -0.896  -0.865  -0.836  -0.800  -0.790
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   Q        -1.209  -1.053  -1.284  -0.921  -0.723  -1.060  -0.964  -0.782  -0.986
105   G         0.135   0.377  -0.166   0.394   0.669  -0.091   0.191   0.528  -0.244
106   S         0.223   0.264   0.422  -0.050   0.042   0.272  -0.194  -0.134   0.103
107   I         0.135   0.026  -0.198   0.255   0.103  -0.269   0.191   0.038  -0.291
108   S        -1.432  -1.234  -1.338  -1.365  -1.008  -1.218  -1.221  -0.990  -1.042
109   E         0.288   0.394   0.449   0.199   0.331   0.449  -0.066   0.118   0.158
110   K        -0.358  -0.228  -0.293  -0.381  -0.187  -0.225  -0.579  -0.413  -0.443
111   A         0.223   0.297   0.436  -0.150   0.001   0.230  -0.194  -0.068   0.131
112   E        -0.851  -1.009  -0.917  -0.755  -1.019  -0.916  -0.836  -0.995  -0.854
113   Q         0.135   0.007  -0.176   0.401   0.229  -0.108   0.191   0.017  -0.259
114   V        -0.851  -0.846  -0.879  -0.863  -0.884  -0.866  -0.836  -0.827  -0.814
115   F        -0.205  -0.192  -0.291  -0.205  -0.211  -0.329  -0.323  -0.329  -0.439
116   Q        -0.851  -0.945  -0.908  -0.683  -0.867  -0.812  -0.836  -0.941  -0.848
117   N         1.654   1.709   1.817   1.663   1.774   1.930   1.859   1.935   2.133
118   V         0.223   0.297   0.436  -0.221  -0.076   0.146  -0.194  -0.068   0.131
119   K        -0.851  -0.814  -0.869  -0.934  -0.831  -0.965  -0.836  -0.754  -0.798
120   N        -0.205  -0.282  -0.290  -0.221  -0.348  -0.396  -0.323  -0.425  -0.431
121   I         0.288   0.286   0.433  -0.056  -0.122   0.137  -0.066  -0.090   0.125
122   L         0.876   0.763   0.626   0.953   0.831   0.606   0.960   0.774   0.501
123   A        -1.432  -1.443  -1.360  -1.384  -1.431  -1.285  -1.221  -1.211  -1.064
124   E        -0.358  -0.378  -0.300  -0.639  -0.709  -0.540  -0.579  -0.575  -0.453
125   S         0.288   0.418   0.469  -0.207   0.005   0.083  -0.066   0.163   0.197
126   N         0.223   0.297   0.436   0.028   0.145   0.381  -0.194  -0.068   0.131
127   S         1.654   1.709   1.817   1.553   1.681   1.823   1.859   1.935   2.133
128   S         0.876   1.035   0.658   0.904   1.148   0.657   0.960   1.196   0.561
129   L         0.135  -0.041  -0.213   0.346   0.156  -0.092   0.191  -0.052  -0.313
130   D        -1.074  -0.993  -0.932  -1.005  -0.915  -0.812  -1.092  -1.003  -0.874
131   N        -0.205  -0.002  -0.236  -0.146   0.157  -0.162  -0.323  -0.018  -0.349
132   I         0.135   0.007  -0.176   0.255   0.075  -0.230   0.191   0.017  -0.259
133   V         1.654   1.709   1.817   1.468   1.511   1.741   1.859   1.935   2.133
134   K         1.654   1.709   1.817   1.590   1.687   1.859   1.859   1.935   2.133
135   V         0.493   0.666   0.550   0.169   0.405   0.224   0.319   0.611   0.357
136   N         0.876   0.763   0.626   1.005   0.899   0.687   0.960   0.774   0.501
137   V         0.135   0.160  -0.188   0.219   0.241  -0.332   0.191   0.228  -0.277
138   F         0.876   0.763   0.626   1.146   1.051   0.831   0.960   0.774   0.501
139   L         0.876   0.763   0.626   0.930   0.791   0.548   0.960   0.774   0.501
140   A         0.288   0.379   0.448   0.047   0.200   0.267  -0.066   0.089   0.156
141   D         1.654   1.709   1.817   1.836   1.908   2.098   1.859   1.935   2.133
142   M         0.493   0.531   0.472   0.642   0.736   0.531   0.319   0.373   0.203
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   K        -2.283  -2.189  -2.085  -1.980  -1.829  -1.745  -1.606  -1.513  -1.340
145   N        -1.567  -1.537  -1.393  -1.418  -1.353  -1.186  -1.349  -1.298  -1.093
146   F         1.654   1.709   1.817   1.796   1.912   2.059   1.859   1.935   2.133
147   A        -0.205  -0.113  -0.285  -0.384  -0.324  -0.460  -0.323  -0.215  -0.430
148   E        -0.358  -0.268  -0.312  -0.571  -0.549  -0.457  -0.579  -0.484  -0.471
149   F        -0.851  -0.978  -0.913  -0.619  -0.777  -0.750  -0.836  -0.970  -0.852
150   N         1.654   1.709   1.817   1.663   1.774   1.930   1.859   1.935   2.133
151   S        -1.074  -0.897  -0.911  -1.213  -0.919  -0.959  -1.092  -0.878  -0.850
152   V         0.876   0.844   0.635   0.799   0.726   0.492   0.960   0.906   0.518
153   Y         1.654   1.709   1.817   1.841   1.930   2.103   1.859   1.935   2.133
154   A        -1.209  -1.236  -1.316  -1.191  -1.277  -1.327  -0.964  -0.979  -1.018
155   K         0.493   0.474   0.491   0.383   0.345   0.355   0.319   0.269   0.240
156   H        -1.209  -1.268  -1.323  -0.635  -0.696  -0.780  -0.964  -1.009  -1.025
157   F         0.493   0.474   0.491   0.560   0.554   0.499   0.319   0.269   0.240
158   H        -1.925  -1.900  -1.771  -1.661  -1.576  -1.370  -1.477  -1.430  -1.239
159   T        -1.547  -1.490  -1.403  -1.346  -1.274  -1.145  -1.325  -1.250  -1.100
160   H         0.493   0.474   0.491   0.715   0.682   0.641   0.319   0.269   0.240
161   K         0.135  -0.065  -0.214   0.324   0.126  -0.088   0.191  -0.086  -0.315
162   P         0.876   0.763   0.626   0.943   0.783   0.548   0.960   0.774   0.501
163   A         1.654   1.709   1.817   1.414   1.463   1.688   1.859   1.935   2.133
164   R         1.654   1.709   1.817   1.876   2.036   2.137   1.859   1.935   2.133
165   S         0.493   0.399   0.456   0.372   0.253   0.308   0.319   0.127   0.173
166   C         0.493   0.399   0.456   0.743   0.561   0.622   0.319   0.127   0.173
167   V         0.876   0.763   0.626   0.789   0.610   0.453   0.960   0.774   0.501
168   G         0.493   0.475   0.467   0.238   0.157   0.209   0.319   0.270   0.194
169   V         0.493   0.531   0.472   0.169   0.174   0.058   0.319   0.373   0.203
170   A        -0.851  -0.977  -0.887  -0.900  -1.111  -0.931  -0.836  -0.961  -0.824
171   S        -1.790  -1.774  -1.721  -1.747  -1.746  -1.619  -1.349  -1.313  -1.199
172   L         0.135   0.074  -0.209   0.255   0.189  -0.289   0.191   0.110  -0.307
173   P         1.654   1.709   1.817   1.653   1.734   1.920   1.859   1.935   2.133
174   L         0.876   0.844   0.635   0.947   0.938   0.606   0.960   0.906   0.518
175   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   N         0.493   0.640   0.541   0.550   0.744   0.595   0.319   0.566   0.338
179   V         0.135  -0.065  -0.214   0.171  -0.119  -0.263   0.191  -0.086  -0.315
180   D        -0.851  -0.889  -0.897  -0.638  -0.720  -0.724  -0.836  -0.879  -0.833
181   L        -0.493  -0.557  -0.387  -0.753  -0.916  -0.647  -0.707  -0.792  -0.564
182   E         1.654   1.709   1.817   1.699   1.748   1.965   1.859   1.935   2.133
183   M         0.223   0.264   0.422   0.083   0.161   0.393  -0.194  -0.134   0.103
184   E         0.876   0.763   0.626   1.050   0.885   0.741   0.960   0.774   0.501
185   V        -0.358  -0.440  -0.334  -0.507  -0.624  -0.434  -0.579  -0.660  -0.498
186   I         0.493   0.495   0.466   0.349   0.324   0.218   0.319   0.308   0.191
187   A         0.876   0.763   0.626   0.710   0.519   0.340   0.960   0.774   0.501
188   V        -1.074  -0.999  -0.907  -1.348  -1.204  -1.104  -1.092  -0.970  -0.843
189   E         0.876   0.844   0.635   1.023   0.960   0.691   0.960   0.906   0.518
190   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
192   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
194   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
195   -        -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/P40185
Output conservation file - output/P40185
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
