1     M         1.105   1.115   1.180   1.269   1.283   1.374   1.191   1.204   1.296
2     D        -0.652  -0.614  -0.513  -0.725  -0.673  -0.513  -0.925  -0.874  -0.724
3     Y        -1.734  -1.740  -1.608  -1.871  -1.893  -1.690  -1.440  -1.442  -1.258
4     D        -1.291  -1.333  -1.289  -1.070  -1.155  -1.097  -1.177  -1.221  -1.124
5     S        -1.709  -1.679  -1.590  -1.793  -1.714  -1.583  -1.428  -1.401  -1.245
6     S        -1.428  -1.439  -1.306  -1.329  -1.338  -1.135  -1.327  -1.328  -1.141
7     D        -1.709  -1.717  -1.596  -1.521  -1.504  -1.350  -1.428  -1.429  -1.249
8     T        -2.055  -2.032  -1.855  -1.789  -1.756  -1.506  -1.572  -1.550  -1.335
9     M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    G        -2.055  -2.036  -1.855  -1.813  -1.780  -1.529  -1.572  -1.552  -1.335
13    S        -0.969  -0.943  -0.951  -0.910  -0.875  -0.875  -1.046  -1.025  -0.975
14    S        -1.412  -1.435  -1.318  -1.456  -1.517  -1.370  -1.309  -1.322  -1.150
15    N        -0.865  -0.961  -0.926  -0.631  -0.758  -0.729  -0.925  -1.023  -0.949
16    P        -1.603  -1.657  -1.581  -1.343  -1.409  -1.324  -1.327  -1.372  -1.238
17    L        -0.865  -0.826  -0.903  -0.987  -0.930  -1.074  -0.925  -0.872  -0.924
18    I        -1.428  -1.450  -1.313  -1.423  -1.434  -1.226  -1.327  -1.336  -1.146
19    T        -1.991  -1.952  -1.837  -1.720  -1.670  -1.509  -1.529  -1.496  -1.324
20    K        -1.709  -1.696  -1.588  -1.566  -1.543  -1.385  -1.428  -1.411  -1.244
21    M        -1.991  -1.988  -1.840  -1.893  -1.890  -1.663  -1.529  -1.522  -1.326
22    N        -1.322  -1.236  -1.276  -1.060  -0.932  -0.984  -1.227  -1.142  -1.115
23    T        -0.865  -0.889  -0.914  -0.836  -0.894  -0.931  -0.925  -0.949  -0.936
24    M        -1.709  -1.643  -1.587  -1.834  -1.729  -1.633  -1.428  -1.373  -1.244
25    K        -1.709  -1.737  -1.596  -1.572  -1.616  -1.423  -1.428  -1.442  -1.249
26    L        -1.709  -1.655  -1.594  -1.595  -1.511  -1.422  -1.428  -1.378  -1.248
27    L        -0.865  -0.867  -0.916  -1.044  -1.042  -1.049  -0.925  -0.913  -0.936
28    Y         1.105   1.115   1.180   1.148   1.160   1.259   1.191   1.204   1.296
29    Q         0.493   0.397   0.245   0.696   0.571   0.317   0.486   0.332   0.040
30    H        -1.322  -1.292  -1.283  -1.119  -1.057  -1.099  -1.227  -1.188  -1.120
31    Y        -0.357  -0.442  -0.464  -0.422  -0.547  -0.618  -0.522  -0.631  -0.660
32    L        -0.021  -0.010   0.099  -0.453  -0.442  -0.247  -0.421  -0.406  -0.239
33    D         1.105   1.115   1.180   1.229   1.243   1.336   1.191   1.204   1.296
34    K        -0.934  -0.957  -0.926  -0.875  -0.905  -0.842  -1.025  -1.043  -0.952
35    V        -1.322  -1.323  -1.290  -1.158  -1.145  -1.138  -1.227  -1.226  -1.127
36    T        -0.477  -0.527  -0.481  -0.534  -0.605  -0.538  -0.723  -0.769  -0.685
37    P         1.105   1.115   1.180   1.179   1.192   1.289   1.191   1.204   1.296
38    H         0.031   0.058   0.117  -0.022   0.019   0.111  -0.320  -0.273  -0.204
39    A        -0.934  -0.903  -0.928  -0.889  -0.861  -0.853  -1.025  -0.992  -0.953
40    K        -1.322  -1.286  -1.296  -1.215  -1.165  -1.178  -1.227  -1.200  -1.132
41    E        -1.040  -0.977  -0.945  -1.015  -0.922  -0.862  -1.126  -1.053  -0.970
42    R         1.105   1.115   1.180   1.151   1.162   1.262   1.191   1.204   1.296
43    W         1.105   1.115   1.180   1.306   1.317   1.408   1.191   1.204   1.296
44    A        -0.934  -0.956  -0.933  -1.006  -1.070  -1.043  -1.025  -1.042  -0.958
45    V        -0.934  -0.953  -0.930  -0.821  -0.852  -0.798  -1.025  -1.040  -0.956
46    L        -1.322  -1.370  -1.298  -1.578  -1.642  -1.475  -1.227  -1.263  -1.133
47    G        -0.090  -0.158  -0.394   0.137   0.048  -0.389  -0.119  -0.218  -0.555
48    G        -0.477  -0.441  -0.476  -0.498  -0.456  -0.501  -0.723  -0.682  -0.680
49    L         0.192   0.199   0.147  -0.112  -0.105  -0.169  -0.018  -0.010  -0.145
50    L        -0.638  -0.645  -0.865  -0.824  -0.844  -1.183  -0.622  -0.635  -0.877
51    C        -1.709  -1.661  -1.588  -1.584  -1.539  -1.371  -1.428  -1.386  -1.244
52    L         1.105   1.115   1.180   0.843   0.856   0.972   1.191   1.204   1.296
53    F         1.105   1.115   1.180   0.944   0.949   1.067   1.191   1.204   1.296
54    M        -1.146  -1.122  -0.979  -1.529  -1.499  -1.248  -1.227  -1.198  -1.003
55    V        -0.477  -0.521  -0.475  -0.776  -0.822  -0.758  -0.723  -0.759  -0.677
56    R         1.105   1.115   1.180   1.151   1.162   1.262   1.191   1.204   1.296
57    I         0.192   0.179   0.139   0.067   0.044  -0.043  -0.018  -0.044  -0.161
58    T        -1.322  -1.350  -1.284  -1.459  -1.563  -1.438  -1.227  -1.250  -1.122
59    M        -1.709  -1.676  -1.590  -1.829  -1.806  -1.654  -1.428  -1.398  -1.245
60    A        -1.040  -1.014  -0.951  -1.006  -0.972  -0.859  -1.126  -1.096  -0.977
61    E        -0.090  -0.134  -0.392   0.164   0.100  -0.302  -0.119  -0.187  -0.551
62    G         1.105   1.115   1.180   1.257   1.271   1.362   1.191   1.204   1.296
63    W         1.105   1.115   1.180   1.306   1.317   1.408   1.191   1.204   1.296
64    Y         1.105   1.115   1.180   1.148   1.160   1.259   1.191   1.204   1.296
65    V        -0.021  -0.009   0.100  -0.305  -0.295  -0.110  -0.421  -0.402  -0.238
66    I         0.031   0.085   0.120  -0.180  -0.080  -0.055  -0.320  -0.221  -0.199
67    C         0.493   0.444   0.246   0.830   0.768   0.451   0.486   0.408   0.042
68    Y         1.105   1.115   1.180   1.148   1.160   1.259   1.191   1.204   1.296
69    G        -0.357  -0.362  -0.455  -0.243  -0.280  -0.390  -0.522  -0.550  -0.648
70    L         1.105   1.115   1.180   0.843   0.856   0.972   1.191   1.204   1.296
71    G        -0.090  -0.158  -0.394   0.155   0.059  -0.350  -0.119  -0.218  -0.555
72    L         0.493   0.551   0.255   0.459   0.541   0.052   0.486   0.571   0.057
73    F         0.192   0.241   0.167   0.100   0.182   0.000  -0.018   0.067  -0.106
74    L         1.105   1.115   1.180   0.843   0.856   0.972   1.191   1.204   1.296
75    L         1.105   1.115   1.180   0.843   0.856   0.972   1.191   1.204   1.296
76    N         1.105   1.115   1.180   1.288   1.313   1.391   1.191   1.204   1.296
77    Q         0.031   0.068   0.122  -0.347  -0.291  -0.182  -0.320  -0.253  -0.194
78    F         1.105   1.115   1.180   0.944   0.949   1.067   1.191   1.204   1.296
79    L         1.105   1.115   1.180   0.843   0.856   0.972   1.191   1.204   1.296
80    A         1.105   1.115   1.180   1.204   1.213   1.312   1.191   1.204   1.296
81    F         1.105   1.115   1.180   0.944   0.949   1.067   1.191   1.204   1.296
82    L         1.105   1.115   1.180   0.843   0.856   0.972   1.191   1.204   1.296
83    T         0.493   0.491   0.257   0.683   0.681   0.345   0.486   0.481   0.061
84    P         1.105   1.115   1.180   1.179   1.192   1.289   1.191   1.204   1.296
85    K         1.105   1.115   1.180   1.160   1.176   1.271   1.191   1.204   1.296
86    F         1.105   1.115   1.180   0.944   0.949   1.067   1.191   1.204   1.296
87    D         1.105   1.115   1.180   1.229   1.243   1.336   1.191   1.204   1.296
88    M        -0.357  -0.283  -0.450  -0.287  -0.186  -0.423  -0.522  -0.420  -0.638
89    S         1.105   1.115   1.180   1.189   1.223   1.298   1.191   1.204   1.296
90    L         0.439   0.328   0.218   0.218   0.063  -0.092   0.401   0.217  -0.012
91    Q        -0.526  -0.532  -0.498  -0.555  -0.561  -0.503  -0.783  -0.784  -0.707
92    Q         0.192   0.163   0.147   0.265   0.223   0.149  -0.018  -0.075  -0.146
93    D        -0.865  -0.872  -0.913  -0.693  -0.693  -0.749  -0.925  -0.922  -0.933
94    E        -1.040  -1.066  -0.961  -1.154  -1.184  -1.028  -1.126  -1.145  -0.987
95    E        -0.934  -0.940  -0.934  -0.978  -0.998  -0.983  -1.025  -1.026  -0.959
96    N        -0.357  -0.426  -0.468  -0.158  -0.271  -0.338  -0.522  -0.633  -0.666
97    N        -0.357  -0.363  -0.448  -0.255  -0.251  -0.382  -0.522  -0.516  -0.635
98    E        -0.357  -0.308  -0.438  -0.289  -0.201  -0.404  -0.522  -0.442  -0.620
99    L        -1.040  -1.028  -0.956  -1.253  -1.216  -1.083  -1.126  -1.107  -0.981
100   E         1.105   1.115   1.180   1.170   1.182   1.280   1.191   1.204   1.296
101   A        -0.477  -0.493  -0.479  -0.500  -0.512  -0.469  -0.723  -0.727  -0.682
102   G         1.105   1.115   1.180   1.257   1.271   1.362   1.191   1.204   1.296
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   -         1.105   1.115   1.180   0.877   0.891   1.004   1.191   1.204   1.296
108   -         0.292   0.361   0.192   0.336   0.434   0.165   0.159   0.272  -0.059
109   -        -0.438  -0.315  -0.468  -0.365  -0.179  -0.437  -0.614  -0.437  -0.661
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   E        -0.969  -1.001  -0.949  -0.912  -0.956  -0.871  -1.046  -1.081  -0.973
128   K        -1.603  -1.559  -1.572  -1.303  -1.236  -1.252  -1.327  -1.284  -1.231
129   S        -0.477  -0.438  -0.476  -0.465  -0.396  -0.439  -0.723  -0.671  -0.680
130   E        -0.021  -0.010   0.099  -0.158  -0.144   0.030  -0.421  -0.406  -0.239
131   E         1.105   1.115   1.180   1.170   1.182   1.280   1.191   1.204   1.296
132   F         1.105   1.115   1.180   0.944   0.949   1.067   1.191   1.204   1.296
133   R         0.192   0.227   0.161   0.172   0.226   0.090  -0.018   0.042  -0.119
134   P         1.105   1.115   1.180   1.179   1.192   1.289   1.191   1.204   1.296
135   F         1.105   1.115   1.180   0.944   0.949   1.067   1.191   1.204   1.296
136   I         1.105   1.115   1.180   1.045   1.063   1.163   1.191   1.204   1.296
137   R         1.105   1.115   1.180   1.151   1.162   1.262   1.191   1.204   1.296
138   R         1.105   1.115   1.180   1.151   1.162   1.262   1.191   1.204   1.296
139   L         1.105   1.115   1.180   0.843   0.856   0.972   1.191   1.204   1.296
140   P         1.105   1.115   1.180   1.179   1.192   1.289   1.191   1.204   1.296
141   E         1.105   1.115   1.180   1.170   1.182   1.280   1.191   1.204   1.296
142   F         1.105   1.115   1.180   0.944   0.949   1.067   1.191   1.204   1.296
143   K         0.493   0.524   0.252   0.618   0.659   0.260   0.486   0.531   0.053
144   F         1.105   1.115   1.180   0.944   0.949   1.067   1.191   1.204   1.296
145   W         1.105   1.115   1.180   1.306   1.317   1.408   1.191   1.204   1.296
146   Y        -0.021  -0.011   0.099  -0.087  -0.070   0.098  -0.421  -0.406  -0.239
147   N         0.031   0.003   0.103   0.015  -0.030   0.094  -0.320  -0.379  -0.231
148   S        -0.477  -0.458  -0.477  -0.454  -0.427  -0.406  -0.723  -0.703  -0.682
149   I        -0.357  -0.462  -0.467  -0.388  -0.531  -0.519  -0.522  -0.663  -0.663
150   R         1.105   1.115   1.180   1.151   1.162   1.262   1.191   1.204   1.296
151   A         1.105   1.115   1.180   1.204   1.213   1.312   1.191   1.204   1.296
152   T        -0.090  -0.109  -0.391   0.145   0.113  -0.309  -0.119  -0.147  -0.550
153   V        -0.865  -0.932  -0.926  -0.918  -1.032  -1.054  -0.925  -0.986  -0.948
154   I        -0.477  -0.524  -0.469  -0.893  -0.947  -0.876  -0.723  -0.763  -0.672
155   S        -0.357  -0.358  -0.453  -0.240  -0.241  -0.364  -0.522  -0.535  -0.645
156   L        -0.357  -0.345  -0.456  -0.691  -0.690  -0.810  -0.522  -0.512  -0.648
157   L        -1.040  -1.029  -0.953  -1.453  -1.449  -1.301  -1.126  -1.118  -0.980
158   L        -0.865  -0.929  -0.926  -0.946  -1.020  -0.932  -0.925  -1.000  -0.949
159   S         0.192   0.241   0.153   0.225   0.321   0.131  -0.018   0.066  -0.135
160   L        -0.357  -0.363  -0.448  -0.623  -0.614  -0.739  -0.522  -0.516  -0.635
161   F         0.493   0.491   0.257   0.385   0.376   0.034   0.486   0.481   0.061
162   S        -1.709  -1.681  -1.590  -1.488  -1.447  -1.302  -1.428  -1.400  -1.245
163   I        -0.090  -0.065  -0.379  -0.022   0.012  -0.432  -0.119  -0.085  -0.533
164   F         0.493   0.524   0.252   0.356   0.390  -0.048   0.486   0.531   0.053
165   D         0.493   0.444   0.246   0.706   0.649   0.359   0.486   0.408   0.042
166   I         0.493   0.397   0.245   0.503   0.378   0.145   0.486   0.332   0.040
167   P         1.105   1.115   1.180   1.179   1.192   1.289   1.191   1.204   1.296
168   V         1.105   1.115   1.180   1.151   1.155   1.262   1.191   1.204   1.296
169   F         1.105   1.115   1.180   0.944   0.949   1.067   1.191   1.204   1.296
170   W         1.105   1.115   1.180   1.306   1.317   1.408   1.191   1.204   1.296
171   P         1.105   1.115   1.180   1.179   1.192   1.289   1.191   1.204   1.296
172   I         0.493   0.444   0.246   0.503   0.443   0.147   0.486   0.408   0.042
173   L         1.105   1.115   1.180   0.843   0.856   0.972   1.191   1.204   1.296
174   L         0.192   0.115   0.133  -0.131  -0.265  -0.220  -0.018  -0.164  -0.173
175   M        -0.638  -0.707  -0.874  -0.391  -0.499  -0.833  -0.622  -0.709  -0.887
176   Y         1.105   1.115   1.180   1.148   1.160   1.259   1.191   1.204   1.296
177   F        -0.090  -0.229  -0.407  -0.106  -0.299  -0.522  -0.119  -0.314  -0.573
178   I        -0.865  -0.872  -0.922  -1.104  -1.178  -1.237  -0.925  -0.950  -0.946
179   L        -1.322  -1.319  -1.292  -1.365  -1.356  -1.306  -1.227  -1.225  -1.129
180   L         1.105   1.115   1.180   0.843   0.856   0.972   1.191   1.204   1.296
181   F         0.493   0.397   0.245   0.407   0.278   0.068   0.486   0.332   0.040
182   F        -1.322  -1.307  -1.285  -1.387  -1.379  -1.291  -1.227  -1.203  -1.122
183   L         0.493   0.397   0.245   0.268   0.129  -0.118   0.486   0.332   0.040
184   T         0.493   0.397   0.245   0.702   0.583   0.372   0.486   0.332   0.040
185   M         0.493   0.397   0.245   0.698   0.559   0.274   0.486   0.332   0.040
186   R         0.493   0.491   0.257   0.610   0.607   0.263   0.486   0.481   0.061
187   R         0.031   0.036   0.111  -0.119  -0.115  -0.007  -0.320  -0.315  -0.216
188   Q         1.105   1.115   1.180   1.238   1.256   1.345   1.191   1.204   1.296
189   I         1.105   1.115   1.180   1.045   1.063   1.163   1.191   1.204   1.296
190   Q         0.493   0.530   0.257   0.715   0.767   0.385   0.486   0.541   0.062
191   H         1.105   1.115   1.180   1.349   1.364   1.448   1.191   1.204   1.296
192   M         1.105   1.115   1.180   1.269   1.283   1.374   1.191   1.204   1.296
193   I        -0.090  -0.124  -0.388  -0.082  -0.149  -0.578  -0.119  -0.174  -0.547
194   K         1.105   1.115   1.180   1.160   1.176   1.271   1.191   1.204   1.296
195   Y         1.105   1.115   1.180   1.148   1.160   1.259   1.191   1.204   1.296
196   R         0.031   0.078   0.121  -0.119  -0.035   0.013  -0.320  -0.234  -0.196
197   Y         1.105   1.115   1.180   1.148   1.160   1.259   1.191   1.204   1.296
198   I        -0.652  -0.621  -0.518  -1.075  -1.008  -0.835  -0.925  -0.882  -0.730
199   P         1.105   1.115   1.180   1.179   1.192   1.289   1.191   1.204   1.296
200   L        -0.357  -0.292  -0.449  -0.678  -0.572  -0.853  -0.522  -0.426  -0.637
201   D         0.493   0.444   0.246   0.695   0.634   0.333   0.486   0.408   0.042
202   I        -0.090   0.012  -0.383  -0.118   0.030  -0.647  -0.119   0.021  -0.539
203   G         1.105   1.115   1.180   1.257   1.271   1.362   1.191   1.204   1.296
204   K         1.105   1.115   1.180   1.160   1.176   1.271   1.191   1.204   1.296
205   K        -0.357  -0.347  -0.443  -0.293  -0.265  -0.418  -0.522  -0.493  -0.628
206   K        -0.477  -0.476  -0.469  -0.544  -0.541  -0.501  -0.723  -0.718  -0.672
207   Y         0.493   0.397   0.245   0.576   0.436   0.163   0.486   0.332   0.040
208   S        -1.709  -1.721  -1.596  -1.479  -1.473  -1.288  -1.428  -1.430  -1.249
209   H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
210   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
211   S        -0.447  -0.386  -0.458  -0.416  -0.316  -0.428  -0.651  -0.560  -0.648
212   N        -1.734  -1.703  -1.595  -1.438  -1.381  -1.254  -1.440  -1.412  -1.248
* 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/P25560
Output conservation file - output/P25560
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
