1     M         1.994   2.012   2.140   2.297   2.320   2.524   2.260   2.289   2.519
2     G         1.994   2.012   2.140   2.225   2.251   2.451   2.260   2.289   2.519
3     S         0.656   0.677   0.778   0.307   0.331   0.472   0.244   0.277   0.411
4     N        -0.655  -0.656  -0.569  -0.601  -0.601  -0.459  -0.765  -0.758  -0.642
5     T        -0.508  -0.463  -0.491  -0.291  -0.242  -0.235  -0.597  -0.544  -0.553
6     S         1.994   2.012   2.140   1.810   1.833   2.027   2.260   2.289   2.519
7     K         1.994   2.012   2.140   1.731   1.767   1.946   2.260   2.289   2.519
8     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    A        -0.722  -0.705  -0.608  -0.777  -0.753  -0.614  -0.828  -0.805  -0.681
11    G        -0.722  -0.705  -0.608  -0.874  -0.875  -0.713  -0.828  -0.805  -0.681
12    A        -0.073  -0.068   0.016  -0.061  -0.072   0.065  -0.375  -0.366  -0.253
13    E        -0.508  -0.495  -0.507  -0.370  -0.377  -0.406  -0.597  -0.587  -0.573
14    K        -0.120  -0.127  -0.032  -0.616  -0.633  -0.500  -0.429  -0.440  -0.317
15    Q        -0.508  -0.515  -0.511  -0.345  -0.365  -0.352  -0.597  -0.609  -0.577
16    Q        -0.896  -0.949  -0.953  -0.726  -0.763  -0.735  -0.765  -0.820  -0.798
17    V         1.191   1.184   1.071   1.314   1.307   1.133   1.252   1.238   1.007
18    Y         0.122   0.085   0.102   0.504   0.475   0.515  -0.093  -0.134  -0.124
19    T         0.122   0.047   0.074   0.133   0.011   0.017  -0.093  -0.197  -0.170
20    P         1.191   1.114   1.055   1.477   1.369   1.291   1.252   1.118   0.977
21    L        -1.431  -1.373  -1.358  -1.322  -1.205  -1.236  -1.101  -1.046  -0.993
22    T         0.434   0.346   0.230   0.617   0.490   0.289   0.412   0.279   0.089
23    Q         0.434   0.475   0.259   0.750   0.798   0.470   0.412   0.471   0.135
24    I         0.122   0.047   0.074   0.326   0.213   0.227  -0.093  -0.197  -0.170
25    D        -0.508  -0.560  -0.518  -0.439  -0.521  -0.447  -0.597  -0.655  -0.584
26    F         1.191   1.114   1.055   1.514   1.417   1.339   1.252   1.118   0.977
27    S         1.191   1.205   1.068   1.063   1.081   0.868   1.252   1.274   1.001
28    Q        -0.655  -0.667  -0.574  -0.678  -0.686  -0.531  -0.765  -0.767  -0.646
29    S        -0.508  -0.518  -0.500  -0.675  -0.686  -0.674  -0.597  -0.606  -0.563
30    L         0.822   0.913   0.916   0.658   0.807   0.795   0.580   0.748   0.700
31    V        -0.120  -0.125  -0.032  -0.259  -0.235  -0.109  -0.429  -0.438  -0.317
32    S        -0.266  -0.363  -0.438  -0.277  -0.431  -0.550  -0.261  -0.385  -0.474
33    Q         1.191   1.154   1.066   1.314   1.255   1.125   1.252   1.187   0.997
34    L         1.191   1.205   1.068   1.143   1.186   1.012   1.252   1.274   1.001
35    D         0.822   0.863   0.867   0.539   0.592   0.590   0.580   0.653   0.599
36    S         0.122   0.151   0.121   0.032   0.082   0.049  -0.093  -0.040  -0.097
37    S         1.191   1.184   1.071   1.114   1.107   0.965   1.252   1.238   1.007
38    K        -1.043  -1.027  -0.987  -1.067  -1.019  -1.003  -0.933  -0.912  -0.839
39    E         1.994   2.012   2.140   1.752   1.765   1.968   2.260   2.289   2.519
40    S         0.434   0.346   0.230   0.491   0.380   0.252   0.412   0.279   0.089
41    D         1.994   2.012   2.140   2.054   2.082   2.276   2.260   2.289   2.519
42    Y         0.122   0.086   0.095   0.524   0.495   0.507  -0.093  -0.132  -0.138
43    V        -0.266  -0.255  -0.406  -0.165  -0.147  -0.332  -0.261  -0.246  -0.433
44    T         1.191   1.258   1.082   1.490   1.564   1.357   1.252   1.362   1.028
45    K        -0.655  -0.667  -0.574  -0.980  -0.996  -0.861  -0.765  -0.767  -0.646
46    Q         1.191   1.184   1.071   1.305   1.286   1.117   1.252   1.238   1.007
47    N        -0.896  -0.938  -0.953  -0.523  -0.613  -0.681  -0.765  -0.808  -0.798
48    A         0.122   0.121   0.120   0.166   0.182   0.194  -0.093  -0.073  -0.091
49    E         1.191   1.154   1.066   1.088   1.038   0.957   1.252   1.187   0.997
50    K        -0.266  -0.363  -0.438  -0.312  -0.444  -0.553  -0.261  -0.385  -0.474
51    F        -0.896  -0.949  -0.953  -0.331  -0.422  -0.424  -0.765  -0.820  -0.798
52    I         0.122   0.085   0.074   0.292   0.226   0.173  -0.093  -0.160  -0.171
53    E         0.822   0.852   0.868   0.709   0.745   0.725   0.580   0.630   0.601
54    K        -1.043  -1.036  -0.994  -1.045  -1.039  -1.013  -0.933  -0.919  -0.843
55    K         0.656   0.678   0.781   0.352   0.381   0.534   0.244   0.278   0.417
56    V         1.191   1.184   1.071   1.380   1.375   1.252   1.252   1.238   1.007
57    S         0.656   0.678   0.781   0.274   0.297   0.449   0.244   0.278   0.417
58    Q        -0.508  -0.501  -0.513  -0.666  -0.718  -0.708  -0.597  -0.596  -0.579
59    R         0.122   0.145   0.105  -0.081  -0.060  -0.118  -0.093  -0.055  -0.120
60    L         1.994   2.012   2.140   1.810   1.854   2.027   2.260   2.289   2.519
61    S        -0.508  -0.498  -0.508  -0.660  -0.681  -0.655  -0.597  -0.585  -0.573
62    N        -0.896  -0.921  -0.948  -0.883  -0.907  -0.934  -0.765  -0.789  -0.794
63    L         1.191   1.154   1.066   1.114   1.090   0.957   1.252   1.187   0.997
64    E         0.434   0.320   0.222   0.409   0.251   0.144   0.412   0.240   0.076
65    V        -1.431  -1.415  -1.379  -1.229  -1.200  -1.172  -1.101  -1.083  -1.011
66    E         0.122   0.066   0.087  -0.093  -0.185  -0.138  -0.093  -0.165  -0.151
67    T         0.122   0.047   0.074   0.100  -0.035  -0.024  -0.093  -0.197  -0.170
68    L        -0.896  -0.884  -0.944  -0.768  -0.752  -0.809  -0.765  -0.753  -0.789
69    K        -0.896  -0.947  -0.944  -1.032  -1.115  -1.125  -0.765  -0.818  -0.789
70    K        -0.896  -0.829  -0.920  -1.045  -0.943  -1.104  -0.765  -0.689  -0.763
71    F         0.822   0.768   0.825   0.886   0.778   0.807   0.580   0.464   0.512
72    E        -0.655  -0.659  -0.568  -0.990  -0.993  -0.862  -0.765  -0.761  -0.642
73    D        -1.043  -1.014  -0.992  -1.183  -1.145  -1.133  -0.933  -0.902  -0.843
74    T        -0.508  -0.442  -0.491  -0.488  -0.400  -0.483  -0.597  -0.522  -0.553
75    L         0.122   0.153   0.134  -0.093  -0.018  -0.097  -0.093  -0.029  -0.069
76    N        -0.508  -0.487  -0.511  -0.444  -0.449  -0.473  -0.597  -0.581  -0.577
77    N        -0.120  -0.111  -0.022  -0.200  -0.195  -0.085  -0.429  -0.418  -0.303
78    S         0.434   0.451   0.258   0.371   0.390   0.094   0.412   0.434   0.132
79    L        -1.043  -1.085  -0.991  -0.952  -1.002  -0.875  -0.933  -0.962  -0.842
80    L        -0.508  -0.512  -0.499  -0.581  -0.594  -0.549  -0.597  -0.606  -0.564
81    S        -1.819  -1.792  -1.718  -1.611  -1.553  -1.466  -1.269  -1.242  -1.139
82    D         0.822   0.768   0.825   0.714   0.594   0.632   0.580   0.464   0.512
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    D         0.122   0.075   0.097   0.250   0.197   0.220  -0.093  -0.149  -0.135
85    D        -1.431  -1.415  -1.379  -1.352  -1.338  -1.316  -1.101  -1.083  -1.011
86    K        -1.064  -1.084  -1.012  -1.123  -1.137  -1.029  -0.942  -0.957  -0.858
87    D        -0.611  -0.632  -0.548  -0.703  -0.736  -0.609  -0.713  -0.729  -0.617
88    A        -0.616  -0.637  -0.565  -0.643  -0.700  -0.582  -0.704  -0.727  -0.631
89    V        -1.159  -1.138  -1.051  -1.172  -1.161  -1.017  -1.034  -1.008  -0.895
90    D        -0.508  -0.431  -0.497  -0.264  -0.171  -0.224  -0.597  -0.521  -0.561
91    G        -1.431  -1.453  -1.376  -1.175  -1.225  -1.137  -1.101  -1.114  -1.008
92    I        -0.508  -0.547  -0.512  -0.488  -0.508  -0.458  -0.597  -0.638  -0.578
93    S         1.191   1.184   1.071   1.156   1.152   1.039   1.252   1.238   1.007
94    S        -0.655  -0.668  -0.570  -0.673  -0.683  -0.538  -0.765  -0.769  -0.642
95    S        -1.431  -1.404  -1.367  -1.305  -1.271  -1.199  -1.101  -1.073  -1.000
96    S        -1.043  -1.020  -0.994  -1.268  -1.231  -1.228  -0.933  -0.903  -0.843
97    L        -0.508  -0.427  -0.494  -0.629  -0.503  -0.603  -0.597  -0.515  -0.558
98    N        -0.266  -0.320  -0.418   0.048  -0.028  -0.217  -0.261  -0.333  -0.448
99    N        -0.896  -0.904  -0.929  -0.945  -0.992  -0.997  -0.765  -0.773  -0.773
100   Q         0.434   0.412   0.251   0.296   0.259   0.012   0.412   0.373   0.122
101   I        -0.508  -0.514  -0.488  -0.311  -0.280  -0.269  -0.597  -0.594  -0.548
102   E        -0.266  -0.229  -0.381  -0.284  -0.242  -0.442  -0.261  -0.211  -0.401
103   S        -1.043  -1.006  -0.998  -1.173  -1.088  -1.082  -0.933  -0.890  -0.847
104   L         1.994   2.012   2.140   1.810   1.854   2.027   2.260   2.289   2.519
105   N        -1.043  -1.044  -1.001  -1.019  -1.024  -0.952  -0.933  -0.927  -0.850
106   K        -1.431  -1.453  -1.376  -1.312  -1.329  -1.200  -1.101  -1.114  -1.008
107   K        -0.266  -0.144  -0.371  -0.206  -0.042  -0.309  -0.261  -0.100  -0.387
108   L         1.191   1.154   1.066   1.143   1.124   1.009   1.252   1.187   0.997
109   T        -0.896  -0.873  -0.918  -1.035  -0.999  -1.098  -0.765  -0.739  -0.762
110   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   D        -0.073  -0.039   0.003  -0.595  -0.557  -0.484  -0.375  -0.329  -0.268
113   Q        -0.616  -0.630  -0.585  -0.694  -0.743  -0.724  -0.704  -0.719  -0.655
114   L        -0.616  -0.589  -0.566  -0.676  -0.631  -0.586  -0.704  -0.670  -0.633
115   E        -0.266  -0.185  -0.380  -0.411  -0.283  -0.623  -0.261  -0.156  -0.399
116   L        -0.896  -0.979  -0.963  -0.898  -1.000  -1.008  -0.765  -0.850  -0.809
117   Q        -1.819  -1.792  -1.718  -1.160  -1.127  -1.004  -1.269  -1.242  -1.139
118   K         1.191   1.154   1.066   1.077   1.050   0.953   1.252   1.187   0.997
119   L        -0.266  -0.232  -0.400  -0.129  -0.076  -0.396  -0.261  -0.214  -0.426
120   E        -1.431  -1.453  -1.376  -1.379  -1.392  -1.279  -1.101  -1.114  -1.008
121   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   K        -1.819  -1.792  -1.718  -1.549  -1.501  -1.401  -1.269  -1.242  -1.139
129   S        -0.508  -0.421  -0.476  -0.658  -0.502  -0.584  -0.597  -0.482  -0.533
130   D        -0.508  -0.466  -0.499  -0.446  -0.380  -0.467  -0.597  -0.552  -0.562
131   K        -0.508  -0.431  -0.497  -0.774  -0.694  -0.740  -0.597  -0.521  -0.561
132   K        -0.508  -0.572  -0.518  -0.693  -0.814  -0.775  -0.597  -0.661  -0.583
133   T         0.122   0.215   0.119   0.070   0.202   0.041  -0.093   0.035  -0.102
134   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   S        -1.043  -1.067  -1.001  -1.148  -1.163  -1.039  -0.933  -0.946  -0.850
140   I        -1.431  -1.404  -1.366  -1.110  -1.075  -1.005  -1.101  -1.072  -1.000
141   K         0.822   0.863   0.867   0.835   0.898   0.845   0.580   0.653   0.599
142   A        -1.431  -1.415  -1.379  -1.363  -1.402  -1.310  -1.101  -1.083  -1.011
143   K        -0.655  -0.617  -0.569  -0.987  -0.930  -0.857  -0.765  -0.724  -0.643
144   L         0.656   0.678   0.781   0.326   0.372   0.504   0.244   0.278   0.417
145   T        -0.120  -0.099  -0.013  -0.077  -0.054   0.072  -0.429  -0.401  -0.290
146   E        -0.508  -0.510  -0.508  -0.834  -0.822  -0.836  -0.597  -0.595  -0.573
147   C         1.994   2.012   2.140   2.283   2.306   2.509   2.260   2.289   2.519
148   L         1.994   2.012   2.140   1.810   1.854   2.027   2.260   2.289   2.519
149   L        -1.043  -1.085  -1.010  -1.087  -1.080  -0.969  -0.933  -0.962  -0.859
150   A        -0.655  -0.619  -0.567  -0.987  -0.949  -0.859  -0.765  -0.726  -0.641
151   N         1.191   1.114   1.055   1.503   1.426   1.368   1.252   1.118   0.977
152   K         0.434   0.415   0.243   0.359   0.344   0.104   0.412   0.378   0.108
153   G         0.434   0.365   0.230   0.818   0.723   0.507   0.412   0.305   0.089
154   K         0.822   0.768   0.825   0.573   0.501   0.582   0.580   0.464   0.512
155   P         0.822   0.913   0.916   0.863   1.018   0.984   0.580   0.748   0.700
156   L         1.994   2.012   2.140   1.810   1.854   2.027   2.260   2.289   2.519
157   N         0.822   0.768   0.825   0.919   0.830   0.882   0.580   0.464   0.512
158   C         1.994   2.012   2.140   2.283   2.306   2.509   2.260   2.289   2.519
159   Y         0.026   0.028   0.059   0.383   0.388   0.447  -0.261  -0.254  -0.199
160   E         0.026  -0.013   0.068  -0.267  -0.330  -0.222  -0.261  -0.301  -0.188
161   E         1.994   2.012   2.140   1.752   1.765   1.968   2.260   2.289   2.519
162   M         0.434   0.475   0.259   0.755   0.805   0.564   0.412   0.471   0.135
163   E         0.434   0.427   0.251   0.363   0.343   0.109   0.412   0.401   0.121
164   E        -0.508  -0.439  -0.491  -0.508  -0.431  -0.493  -0.597  -0.523  -0.553
165   F         1.994   2.012   2.140   2.211   2.237   2.436   2.260   2.289   2.519
166   K         1.191   1.290   1.091   1.036   1.171   0.917   1.252   1.414   1.046
167   K        -0.508  -0.512  -0.505  -0.790  -0.825  -0.772  -0.597  -0.607  -0.571
168   L        -0.896  -0.979  -0.963  -0.969  -1.107  -1.106  -0.765  -0.850  -0.809
169   V        -0.266  -0.246  -0.375   0.067   0.087  -0.070  -0.261  -0.236  -0.392
170   M        -1.043  -1.006  -0.998  -0.919  -0.825  -0.804  -0.933  -0.890  -0.847
171   G        -1.431  -1.435  -1.370  -1.268  -1.274  -1.152  -1.101  -1.099  -1.003
172   -         0.294   0.260   0.181   0.240   0.190   0.061   0.202   0.148   0.012
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -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     *
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   -        -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/P43594
Output conservation file - output/P43594
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
