1     M         0.981   1.033   1.085   1.140   1.191   1.279   1.029   1.095   1.176
2     G         0.981   1.033   1.085   1.071   1.151   1.221   1.029   1.095   1.176
3     K         0.981   1.033   1.085   0.569   0.688   0.802   1.029   1.095   1.176
4     A         0.981   1.033   1.085   0.919   1.009   1.094   1.029   1.095   1.176
5     K         0.088   0.113  -0.164  -0.220  -0.142  -0.531   0.052   0.086  -0.382
6     K         0.088  -0.163  -0.187  -0.197  -0.496  -0.502   0.052  -0.345  -0.421
7     T         0.981   1.033   1.085   1.044   1.122   1.199   1.029   1.095   1.176
8     R         0.981   1.033   1.085   0.933   1.004   1.105   1.029   1.095   1.176
9     K         0.981   1.033   1.085   0.569   0.688   0.802   1.029   1.095   1.176
10    F         0.981   1.033   1.085   1.110   1.175   1.254   1.029   1.095   1.176
11    G         0.088   0.352  -0.152   0.157   0.486  -0.181   0.052   0.418  -0.360
12    L        -1.661  -1.765  -1.531  -1.656  -1.728  -1.404  -1.588  -1.608  -1.320
13    V         0.160   0.281  -0.111   0.231   0.381  -0.135   0.157   0.325  -0.290
14    K         0.981   1.033   1.085   0.585   0.723   0.815   1.029   1.095   1.176
15    R         0.981   1.033   1.085   0.915   0.974   1.091   1.029   1.095   1.176
16    T        -0.980  -1.103  -0.976  -0.808  -1.029  -0.853  -1.090  -1.216  -1.027
17    L        -0.460  -0.386  -0.216  -0.890  -0.777  -0.501  -0.840  -0.726  -0.472
18    N        -0.621  -0.800  -0.934  -0.375  -0.633  -0.950  -0.591  -0.833  -0.973
19    T        -1.661  -1.722  -1.525  -1.681  -1.889  -1.606  -1.588  -1.566  -1.314
20    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    K        -0.621  -0.800  -0.934  -0.763  -0.956  -1.096  -0.591  -0.833  -0.973
22    D         0.981   1.033   1.085   0.963   1.052   1.130   1.029   1.095   1.176
23    Q        -1.661  -1.540  -1.510  -1.369  -1.274  -1.197  -1.588  -1.417  -1.301
24    R         0.981   1.033   1.085   0.915   0.974   1.091   1.029   1.095   1.176
25    L        -0.621  -0.731  -0.928  -0.611  -0.799  -1.086  -0.591  -0.759  -0.965
26    K        -1.357  -1.179  -1.481  -1.399  -1.139  -1.469  -1.214  -0.993  -1.271
27    K        -2.038  -1.736  -1.921  -1.973  -1.618  -1.711  -1.713  -1.408  -1.463
28    N        -0.621  -0.979  -0.958  -0.376  -0.926  -1.000  -0.591  -1.040  -1.003
29    Q        -2.273  -2.200  -1.960  -2.203  -2.150  -1.831  -1.962  -1.793  -1.494
30    E        -1.376  -1.190  -0.997  -1.459  -1.190  -0.920  -1.588  -1.305  -1.050
31    N        -1.661  -1.246  -1.478  -1.869  -1.264  -1.555  -1.588  -1.066  -1.269
32    I        -2.793  -2.186  -2.292  -2.820  -2.074  -2.088  -2.211  -1.627  -1.597
33    K        -2.273  -2.065  -1.948  -2.312  -1.954  -1.754  -1.962  -1.705  -1.485
34    T        -2.650  -2.285  -2.287  -2.546  -2.095  -1.980  -2.087  -1.722  -1.594
35    K        -2.793  -2.556  -2.310  -2.718  -2.396  -2.036  -2.211  -1.910  -1.609
36    -        -1.920  -1.636  -1.516  -1.983  -1.596  -1.468  -1.842  -1.476  -1.305
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    E        -1.283  -0.803  -0.935  -1.662  -0.958  -1.120  -1.464  -0.807  -0.975
49    D        -1.357  -1.580  -1.524  -1.113  -1.554  -1.468  -1.214  -1.434  -1.313
50    P        -0.980  -1.103  -0.976  -0.823  -1.044  -0.843  -1.090  -1.216  -1.027
51    E         0.160  -0.124  -0.148   0.369  -0.074  -0.130   0.157  -0.281  -0.354
52    L         0.160  -0.124  -0.148   0.096  -0.278  -0.337   0.157  -0.281  -0.354
53    T        -0.460  -0.386  -0.216  -0.626  -0.577  -0.307  -0.840  -0.726  -0.472
54    R        -0.244   0.045  -0.160  -0.456  -0.009  -0.406  -0.467  -0.014  -0.375
55    N        -1.376  -1.026  -0.959  -1.360  -0.873  -0.784  -1.588  -1.097  -1.004
56    I        -0.460  -0.263  -0.208  -0.818  -0.493  -0.423  -0.840  -0.512  -0.457
57    P         0.981   1.033   1.085   1.017   1.095   1.176   1.029   1.095   1.176
58    Q         0.160   0.281  -0.111   0.373   0.521  -0.056   0.157   0.325  -0.290
59    V        -0.244  -0.376  -0.230  -0.281  -0.510  -0.263  -0.467  -0.708  -0.496
60    S        -0.621  -0.979  -0.958  -0.268  -0.808  -0.846  -0.591  -1.040  -1.003
61    S         0.981   1.033   1.085   1.106   1.176   1.250   1.029   1.095   1.176
62    A        -0.980  -1.094  -0.972  -0.913  -1.072  -0.885  -1.090  -1.202  -1.023
63    L         0.160  -0.124  -0.148   0.130  -0.213  -0.238   0.157  -0.281  -0.354
64    F         0.981   1.033   1.085   1.118   1.191   1.260   1.029   1.095   1.176
65    F         0.981   1.033   1.085   1.118   1.191   1.260   1.029   1.095   1.176
66    Q         0.160   0.347  -0.108   0.328   0.568  -0.168   0.157   0.412  -0.286
67    Y        -0.980  -1.148  -0.976  -0.674  -0.909  -0.704  -1.090  -1.252  -1.027
68    N         0.981   1.033   1.085   1.041   1.124   1.196   1.029   1.095   1.176
69    Q        -0.621  -0.208  -0.871  -0.348   0.118  -0.811  -0.591  -0.066  -0.894
70    A        -0.460  -0.340  -0.226  -0.632  -0.458  -0.282  -0.840  -0.646  -0.489
71    I        -0.244  -0.376  -0.230  -0.484  -0.755  -0.530  -0.467  -0.708  -0.496
72    K        -0.621  -0.979  -0.958  -0.780  -1.224  -1.164  -0.591  -1.040  -1.003
73    P         0.981   1.033   1.085   1.017   1.095   1.176   1.029   1.095   1.176
74    P         0.981   1.033   1.085   1.017   1.095   1.176   1.029   1.095   1.176
75    Y         0.981   1.033   1.085   1.133   1.204   1.273   1.029   1.095   1.176
76    Q        -0.621  -0.979  -0.958  -0.251  -0.747  -0.739  -0.591  -1.040  -1.003
77    V         0.160   0.363  -0.105   0.199   0.449  -0.206   0.157   0.433  -0.281
78    L         0.160   0.058  -0.132   0.083  -0.028  -0.346   0.157   0.004  -0.326
79    I         0.160  -0.124  -0.148   0.120  -0.262  -0.318   0.157  -0.281  -0.354
80    D         0.981   1.033   1.085   0.963   1.052   1.130   1.029   1.095   1.176
81    T         0.981   1.033   1.085   1.037   1.110   1.192   1.029   1.095   1.176
82    N         0.981   1.033   1.085   1.041   1.124   1.196   1.029   1.095   1.176
83    F         0.981   1.033   1.085   1.118   1.191   1.260   1.029   1.095   1.176
84    I         0.160  -0.124  -0.148   0.104  -0.291  -0.367   0.157  -0.281  -0.354
85    N         0.160  -0.124  -0.148   0.369   0.001  -0.072   0.157  -0.281  -0.354
86    F         0.160  -0.124  -0.148   0.419   0.001  -0.091   0.157  -0.281  -0.354
87    S        -0.621  -0.979  -0.958  -0.230  -0.746  -0.750  -0.591  -1.040  -1.003
88    I        -0.621  -0.979  -0.958  -0.591  -1.121  -1.131  -0.591  -1.040  -1.003
89    Q         0.160  -0.124  -0.148   0.395   0.012  -0.063   0.157  -0.281  -0.354
90    K        -0.621  -0.979  -0.958  -0.780  -1.222  -1.164  -0.591  -1.040  -1.003
91    K         0.981   1.033   1.085   0.585   0.723   0.815   1.029   1.095   1.176
92    V        -0.980  -0.830  -0.959  -1.146  -1.035  -1.147  -1.090  -0.951  -1.008
93    D         0.160  -0.124  -0.148   0.279  -0.095  -0.166   0.157  -0.281  -0.354
94    I        -0.244  -0.376  -0.230  -0.484  -0.755  -0.530  -0.467  -0.708  -0.496
95    V        -2.650  -2.511  -2.313  -2.204  -2.019  -1.767  -2.087  -1.881  -1.611
96    R        -1.376  -1.187  -0.996  -1.786  -1.410  -1.146  -1.588  -1.302  -1.050
97    G        -0.621  -0.800  -0.934  -0.288  -0.554  -0.792  -0.591  -0.833  -0.973
98    M        -0.980  -1.151  -0.976  -0.837  -1.181  -0.979  -1.090  -1.257  -1.027
99    M         0.981   1.033   1.085   1.140   1.191   1.279   1.029   1.095   1.176
100   D         0.160   0.058  -0.132   0.282   0.170  -0.131   0.157   0.004  -0.326
101   C         0.160   0.363  -0.105   0.447   0.677   0.040   0.157   0.433  -0.281
102   L         0.981   1.033   1.085   0.795   0.896   0.991   1.029   1.095   1.176
103   L        -1.896  -1.665  -1.523  -1.814  -1.451  -1.231  -1.837  -1.539  -1.314
104   A         0.981   1.033   1.085   0.911   0.995   1.088   1.029   1.095   1.176
105   K         0.160  -0.124  -0.148  -0.086  -0.385  -0.410   0.157  -0.281  -0.354
106   C        -1.357  -1.580  -1.524  -0.920  -1.339  -1.308  -1.214  -1.434  -1.313
107   N        -0.460  -0.340  -0.226  -0.670  -0.487  -0.359  -0.840  -0.646  -0.489
108   P        -0.244  -0.280  -0.222  -0.282  -0.390  -0.363  -0.467  -0.542  -0.481
109   L        -1.753  -1.523  -1.496  -1.857  -1.482  -1.379  -1.713  -1.383  -1.286
110   I         0.160   0.281  -0.111   0.120   0.293  -0.253   0.157   0.325  -0.290
111   T         0.160   0.058  -0.132   0.365   0.242  -0.048   0.157   0.004  -0.326
112   D         0.160  -0.124  -0.148   0.292  -0.068  -0.129   0.157  -0.281  -0.354
113   C         0.981   1.033   1.085   1.129   1.193   1.269   1.029   1.095   1.176
114   V         0.981   1.033   1.085   0.911   0.986   1.088   1.029   1.095   1.176
115   M        -0.244   0.052  -0.161  -0.163   0.258  -0.138  -0.467  -0.004  -0.376
116   A         0.981   1.033   1.085   0.911   0.995   1.088   1.029   1.095   1.176
117   E         0.981   1.033   1.085   1.068   1.106   1.218   1.029   1.095   1.176
118   L         0.981   1.033   1.085   0.795   0.896   0.991   1.029   1.095   1.176
119   E         0.981   1.033   1.085   1.068   1.106   1.218   1.029   1.095   1.176
120   K         0.981   1.033   1.085   0.585   0.723   0.815   1.029   1.095   1.176
121   L         0.981   1.033   1.085   0.795   0.896   0.991   1.029   1.095   1.176
122   G         0.981   1.033   1.085   1.072   1.149   1.221   1.029   1.095   1.176
123   P        -0.621  -0.583  -0.912  -0.356  -0.340  -0.826  -0.591  -0.541  -0.945
124   K         0.160   0.058  -0.132  -0.115  -0.188  -0.470   0.157   0.004  -0.326
125   Y         0.981   1.033   1.085   1.133   1.204   1.273   1.029   1.095   1.176
126   R         0.981   1.033   1.085   0.915   0.974   1.091   1.029   1.095   1.176
127   I         0.160  -0.124  -0.148   0.120  -0.262  -0.318   0.157  -0.281  -0.354
128   A         0.981   1.033   1.085   0.911   0.995   1.088   1.029   1.095   1.176
129   L         0.981   1.033   1.085   0.795   0.896   0.991   1.029   1.095   1.176
130   K        -0.621  -0.979  -0.958  -0.766  -1.190  -1.129  -0.591  -1.040  -1.003
131   L        -0.244  -0.376  -0.230  -0.500  -0.759  -0.531  -0.467  -0.708  -0.496
132   A         0.981   1.033   1.085   0.911   0.995   1.088   1.029   1.095   1.176
133   R        -0.460  -0.340  -0.226  -0.906  -0.726  -0.576  -0.840  -0.646  -0.489
134   D         0.981   1.033   1.085   0.963   1.052   1.130   1.029   1.095   1.176
135   P        -0.244  -0.376  -0.230  -0.203  -0.475  -0.242  -0.467  -0.708  -0.496
136   R         0.981   1.033   1.085   0.915   0.974   1.091   1.029   1.095   1.176
137   I        -0.621  -0.979  -0.958  -0.468  -0.879  -0.822  -0.591  -1.040  -1.003
138   K        -1.661  -1.745  -1.531  -1.795  -1.826  -1.478  -1.588  -1.588  -1.320
139   R         0.981   1.033   1.085   0.915   0.974   1.091   1.029   1.095   1.176
140   L         0.981   1.033   1.085   0.795   0.896   0.991   1.029   1.095   1.176
141   S        -1.753  -1.558  -1.505  -1.635  -1.357  -1.365  -1.713  -1.423  -1.296
142   C         0.981   1.033   1.085   1.129   1.193   1.269   1.029   1.095   1.176
143   S        -1.141  -1.197  -0.971  -1.065  -1.154  -0.847  -1.339  -1.318  -1.021
144   H         0.981   1.033   1.085   1.205   1.268   1.333   1.029   1.095   1.176
145   K         0.160   0.347  -0.108  -0.116   0.174  -0.434   0.157   0.412  -0.286
146   G         0.981   1.033   1.085   1.072   1.149   1.221   1.029   1.095   1.176
147   T         0.981   1.033   1.085   1.037   1.110   1.192   1.029   1.095   1.176
148   Y         0.981   1.033   1.085   1.133   1.204   1.273   1.029   1.095   1.176
149   A         0.981   1.033   1.085   0.911   0.995   1.088   1.029   1.095   1.176
150   D         0.981   1.033   1.085   0.963   1.052   1.130   1.029   1.095   1.176
151   D         0.981   1.033   1.085   0.963   1.052   1.130   1.029   1.095   1.176
152   C         0.981   1.033   1.085   1.129   1.193   1.269   1.029   1.095   1.176
153   L        -0.529  -0.359  -0.218  -1.027  -0.720  -0.505  -0.965  -0.678  -0.475
154   V         0.981   1.033   1.085   0.911   0.986   1.088   1.029   1.095   1.176
155   H        -1.661  -1.692  -1.520  -1.322  -1.400  -1.159  -1.588  -1.537  -1.309
156   R         0.981   1.033   1.085   0.915   0.974   1.091   1.029   1.095   1.176
157   V         0.160  -0.124  -0.148   0.199  -0.216  -0.287   0.157  -0.281  -0.354
158   L        -1.661  -1.745  -1.531  -1.696  -1.741  -1.443  -1.588  -1.588  -1.320
159   Q         0.160  -0.124  -0.148   0.328  -0.120  -0.257   0.157  -0.281  -0.354
160   H         0.981   1.033   1.085   1.205   1.268   1.333   1.029   1.095   1.176
161   K         0.160  -0.124  -0.148  -0.115  -0.455  -0.496   0.157  -0.281  -0.354
162   C         0.160  -0.124  -0.148   0.417  -0.014  -0.121   0.157  -0.281  -0.354
163   Y         0.981   1.033   1.085   1.133   1.204   1.273   1.029   1.095   1.176
164   I         0.160   0.058  -0.132   0.104  -0.012  -0.337   0.157   0.004  -0.326
165   V         0.981   1.033   1.085   0.911   0.986   1.088   1.029   1.095   1.176
166   A         0.981   1.033   1.085   0.911   0.995   1.088   1.029   1.095   1.176
167   T         0.981   1.033   1.085   1.037   1.110   1.192   1.029   1.095   1.176
168   N         0.981   1.033   1.085   1.041   1.124   1.196   1.029   1.095   1.176
169   D         0.981   1.033   1.085   0.963   1.052   1.130   1.029   1.095   1.176
170   A        -1.357  -1.580  -1.524  -1.189  -1.618  -1.552  -1.214  -1.434  -1.313
171   G        -1.141  -0.977  -0.936  -1.143  -0.858  -0.831  -1.339  -1.036  -0.976
172   L         0.981   1.033   1.085   0.795   0.896   0.991   1.029   1.095   1.176
173   K         0.981   1.033   1.085   0.585   0.723   0.815   1.029   1.095   1.176
174   Q        -0.529  -0.375  -0.223  -0.751  -0.548  -0.295  -0.965  -0.707  -0.484
175   R         0.981   1.033   1.085   0.915   0.974   1.091   1.029   1.095   1.176
176   I        -0.980  -0.593  -0.898  -1.123  -0.545  -1.028  -1.090  -0.542  -0.928
177   R         0.981   1.033   1.085   0.915   0.974   1.091   1.029   1.095   1.176
178   K         0.981   1.033   1.085   0.585   0.723   0.815   1.029   1.095   1.176
179   I        -0.529  -0.384  -0.227  -0.940  -0.702  -0.448  -0.965  -0.723  -0.491
180   P         0.981   1.033   1.085   1.017   1.095   1.176   1.029   1.095   1.176
181   G         0.981   1.033   1.085   1.072   1.149   1.221   1.029   1.095   1.176
182   I        -0.244  -0.300  -0.224  -0.446  -0.560  -0.450  -0.467  -0.576  -0.486
183   P         0.981   1.033   1.085   1.017   1.095   1.176   1.029   1.095   1.176
184   L        -0.529  -0.321  -0.201  -1.027  -0.646  -0.470  -0.965  -0.613  -0.445
185   M         0.160   0.058  -0.132   0.425   0.262  -0.088   0.157   0.004  -0.326
186   S         0.160   0.281  -0.111   0.429   0.575   0.026   0.157   0.325  -0.290
187   V         0.160  -0.124  -0.148   0.244  -0.126  -0.158   0.157  -0.281  -0.354
188   G         0.160   0.058  -0.132   0.372   0.241  -0.097   0.157   0.004  -0.326
189   G        -0.980  -1.165  -0.978  -0.870  -1.242  -1.017  -1.090  -1.276  -1.029
190   H        -0.621  -0.800  -0.934  -0.212  -0.498  -0.836  -0.591  -0.833  -0.973
191   A        -1.896  -1.609  -1.528  -2.028  -1.721  -1.520  -1.837  -1.467  -1.318
192   Y         0.160   0.058  -0.132   0.421   0.279  -0.085   0.157   0.004  -0.326
193   V        -0.621  -0.979  -0.958  -0.478  -1.028  -1.017  -0.591  -1.040  -1.003
194   I         0.160   0.058  -0.132   0.120   0.008  -0.290   0.157   0.004  -0.326
195   E         0.981   1.033   1.085   1.068   1.106   1.218   1.029   1.095   1.176
196   K        -0.460  -0.121  -0.154  -0.906  -0.283  -0.392  -0.840  -0.275  -0.364
197   L         0.981   1.033   1.085   0.795   0.896   0.991   1.029   1.095   1.176
198   P         0.160   0.058  -0.132   0.318   0.186  -0.138   0.157   0.004  -0.326
199   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
200   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
201   D        -0.621  -0.671  -0.922  -0.384  -0.505  -0.819  -0.591  -0.698  -0.958
202   V         0.160  -0.124  -0.148   0.212  -0.190  -0.248   0.157  -0.281  -0.354
203   F        -0.621  -0.979  -0.958  -0.243  -0.765  -0.802  -0.591  -1.040  -1.003
204   -        -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/Q05498
Output conservation file - output/Q05498
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
