1     M         1.184   1.240   1.308   1.567   1.619   1.699   1.251   1.327   1.435
2     A         1.184   1.240   1.308   0.764   0.853   1.004   1.251   1.327   1.435
3     I         1.184   1.240   1.308   1.327   1.391   1.491   1.251   1.327   1.435
4     S        -1.125  -1.354  -1.349  -0.661  -0.994  -1.039  -0.966  -1.209  -1.154
5     K        -0.398  -0.727  -0.755  -0.380  -0.775  -0.776  -0.350  -0.770  -0.807
6     N         0.374   0.141   0.079   0.669   0.318   0.138   0.389   0.032  -0.106
7     L        -1.125  -1.354  -1.349  -0.661  -0.954  -0.929  -0.966  -1.209  -1.154
8     P        -0.025  -0.161  -0.036   0.117  -0.132   0.044  -0.227  -0.480  -0.309
9     I        -0.307  -0.194  -0.033  -0.425  -0.243  -0.014  -0.720  -0.539  -0.303
10    L        -0.752  -0.789  -0.792  -0.596  -0.688  -0.677  -0.843  -0.919  -0.859
11    K        -0.239  -0.209  -0.035  -0.546  -0.431  -0.146  -0.597  -0.565  -0.308
12    N         0.374   0.141   0.079   0.646   0.272   0.074   0.389   0.032  -0.106
13    H         1.184   1.240   1.308   1.483   1.543   1.626   1.251   1.327   1.435
14    F         1.184   1.240   1.308   1.416   1.478   1.568   1.251   1.327   1.435
15    R         0.374   0.141   0.079   0.243  -0.008  -0.052   0.389   0.032  -0.106
16    K         1.184   1.240   1.308   0.941   1.034   1.157   1.251   1.327   1.435
17    H        -0.752  -0.789  -0.792  -0.314  -0.418  -0.419  -0.843  -0.919  -0.859
18    W         1.184   1.240   1.308   1.571   1.623   1.702   1.251   1.327   1.435
19    Q         1.184   1.240   1.308   1.366   1.430   1.525   1.251   1.327   1.435
20    E        -0.025  -0.161  -0.036  -0.154  -0.475  -0.319  -0.227  -0.480  -0.309
21    R         0.374   0.141   0.079   0.244  -0.007  -0.051   0.389   0.032  -0.106
22    V         1.184   1.240   1.308   1.206   1.278   1.386   1.251   1.327   1.435
23    K        -0.025  -0.007  -0.014  -0.408  -0.378  -0.450  -0.227  -0.213  -0.270
24    V        -0.752  -0.896  -0.795  -0.549  -0.707  -0.533  -0.843  -1.011  -0.862
25    H         0.374   0.141   0.079   0.843   0.557   0.440   0.389   0.032  -0.106
26    F         0.374   0.511   0.112   0.733   0.897   0.329   0.389   0.580  -0.050
27    D         0.374   0.141   0.079   0.766   0.473   0.334   0.389   0.032  -0.106
28    Q         1.184   1.240   1.308   1.366   1.430   1.525   1.251   1.327   1.435
29    A        -0.025  -0.097  -0.026  -0.435  -0.525  -0.349  -0.227  -0.367  -0.291
30    G         1.184   1.240   1.308   1.373   1.431   1.531   1.251   1.327   1.435
31    K         0.374   0.141   0.079   0.204  -0.118  -0.257   0.389   0.032  -0.106
32    K         1.184   1.240   1.308   0.941   1.034   1.157   1.251   1.327   1.435
33    V        -2.030  -1.840  -1.783  -2.183  -1.892  -1.716  -1.705  -1.480  -1.337
34    S         0.374   0.141   0.079   0.608   0.255   0.075   0.389   0.032  -0.106
35    R         1.184   1.240   1.308   0.890   0.979   1.114   1.251   1.327   1.435
36    R         1.184   1.240   1.308   0.890   0.979   1.114   1.251   1.327   1.435
37    N        -2.916  -2.550  -2.448  -2.152  -1.716  -1.577  -2.075  -1.744  -1.551
38    A        -0.398  -0.183  -0.691  -0.534  -0.252  -0.780  -0.350  -0.067  -0.724
39    R         1.184   1.240   1.308   0.890   0.979   1.114   1.251   1.327   1.435
40    A        -2.171  -1.841  -1.795  -2.148  -1.538  -1.526  -1.829  -1.482  -1.347
41    T        -2.030  -1.742  -1.763  -2.077  -1.632  -1.761  -1.705  -1.401  -1.323
42    R         0.374   0.606   0.119   0.204   0.519  -0.179   0.389   0.705  -0.037
43    A         1.184   1.240   1.308   0.764   0.853   1.004   1.251   1.327   1.435
44    A         1.184   1.240   1.308   0.764   0.853   1.004   1.251   1.327   1.435
45    K        -0.025  -0.025  -0.017  -0.450  -0.463  -0.529  -0.227  -0.243  -0.276
46    I         0.374   0.272   0.088   0.644   0.518   0.216   0.389   0.236  -0.091
47    A         1.184   1.240   1.308   0.764   0.853   1.004   1.251   1.327   1.435
48    P         1.184   1.240   1.308   1.319   1.375   1.484   1.251   1.327   1.435
49    R         1.184   1.240   1.308   0.890   0.979   1.114   1.251   1.327   1.435
50    P         1.184   1.240   1.308   1.319   1.375   1.484   1.251   1.327   1.435
51    L        -1.052  -0.992  -0.818  -1.040  -0.974  -0.730  -1.213  -1.124  -0.888
52    D         0.374   0.141   0.079   0.739   0.424   0.259   0.389   0.032  -0.106
53    L        -1.425  -1.440  -1.348  -1.470  -1.619  -1.472  -1.336  -1.324  -1.157
54    L         0.374   0.141   0.079   0.585   0.297   0.172   0.389   0.032  -0.106
55    R         1.184   1.240   1.308   0.890   0.979   1.114   1.251   1.327   1.435
56    P         1.184   1.240   1.308   1.319   1.375   1.484   1.251   1.327   1.435
57    V        -0.752  -0.940  -0.796  -0.722  -1.063  -0.879  -0.843  -1.052  -0.863
58    V         1.184   1.240   1.308   1.206   1.278   1.386   1.251   1.327   1.435
59    R         0.374   0.141   0.079   0.160  -0.158  -0.279   0.389   0.032  -0.106
60    A        -0.752  -0.931  -0.789  -0.925  -1.077  -0.767  -0.843  -1.039  -0.854
61    P         1.184   1.240   1.308   1.319   1.375   1.484   1.251   1.327   1.435
62    T         1.184   1.240   1.308   1.377   1.448   1.534   1.251   1.327   1.435
63    V        -0.307  -0.144  -0.008  -0.462  -0.167   0.016  -0.720  -0.449  -0.260
64    K        -0.025  -0.097  -0.026  -0.408  -0.554  -0.477  -0.227  -0.367  -0.291
65    Y         1.184   1.240   1.308   1.487   1.545   1.629   1.251   1.327   1.435
66    N         1.184   1.240   1.308   1.395   1.456   1.550   1.251   1.327   1.435
67    R         0.374   0.141   0.079   0.256   0.016  -0.017   0.389   0.032  -0.106
68    K         0.374   0.272   0.088   0.204   0.086  -0.239   0.389   0.236  -0.091
69    V         0.374   0.272   0.088   0.541   0.430   0.166   0.389   0.236  -0.091
70    R         1.184   1.240   1.308   0.890   0.979   1.114   1.251   1.327   1.435
71    A         0.374   0.272   0.088   0.080  -0.017  -0.237   0.389   0.236  -0.091
72    G         1.184   1.240   1.308   1.373   1.431   1.531   1.251   1.327   1.435
73    R         1.184   1.240   1.308   0.890   0.979   1.114   1.251   1.327   1.435
74    G         1.184   1.240   1.308   1.373   1.431   1.531   1.251   1.327   1.435
75    F         1.184   1.240   1.308   1.416   1.478   1.568   1.251   1.327   1.435
76    T        -0.239  -0.148  -0.035  -0.198  -0.058   0.069  -0.597  -0.457  -0.307
77    L         1.184   1.240   1.308   1.257   1.337   1.431   1.251   1.327   1.435
78    A        -0.025  -0.097  -0.026  -0.480  -0.580  -0.425  -0.227  -0.367  -0.291
79    E         1.184   1.240   1.308   1.195   1.269   1.377   1.251   1.327   1.435
80    V        -0.752  -0.328  -0.707  -0.593  -0.001  -0.543  -0.843  -0.273  -0.746
81    K         1.184   1.240   1.308   0.941   1.034   1.157   1.251   1.327   1.435
82    A         1.184   1.240   1.308   0.764   0.853   1.004   1.251   1.327   1.435
83    A        -0.025   0.137   0.037  -0.476  -0.219  -0.336  -0.227   0.025  -0.180
84    G         1.184   1.240   1.308   1.373   1.431   1.531   1.251   1.327   1.435
85    L        -0.912  -0.990  -0.783  -0.864  -0.935  -0.653  -1.089  -1.121  -0.846
86    T        -1.657  -1.520  -1.361  -1.507  -1.313  -1.165  -1.582  -1.404  -1.168
87    A        -1.657  -1.584  -1.369  -2.209  -2.100  -1.710  -1.582  -1.446  -1.176
88    A        -2.030  -2.056  -1.814  -2.428  -2.416  -1.948  -1.705  -1.654  -1.362
89    Y        -0.025  -0.161  -0.036   0.227  -0.069   0.063  -0.227  -0.480  -0.309
90    A         1.184   1.240   1.308   0.764   0.853   1.004   1.251   1.327   1.435
91    R        -0.398  -0.727  -0.755  -0.437  -0.831  -0.826  -0.350  -0.770  -0.807
92    T         1.184   1.240   1.308   1.377   1.448   1.534   1.251   1.327   1.435
93    I         0.374   0.625   0.119   0.637   0.927   0.252   0.389   0.730  -0.037
94    G         1.184   1.240   1.308   1.373   1.431   1.531   1.251   1.327   1.435
95    I         1.184   1.240   1.308   1.327   1.391   1.491   1.251   1.327   1.435
96    A        -0.912  -0.990  -0.791  -1.231  -1.213  -0.881  -1.089  -1.122  -0.857
97    V         1.184   1.240   1.308   1.206   1.278   1.386   1.251   1.327   1.435
98    D         1.184   1.240   1.308   1.430   1.502   1.580   1.251   1.327   1.435
99    H         0.374   0.272   0.088   0.808   0.675   0.362   0.389   0.236  -0.091
100   R         1.184   1.240   1.308   0.890   0.979   1.114   1.251   1.327   1.435
101   R         1.184   1.240   1.308   0.890   0.979   1.114   1.251   1.327   1.435
102   Q        -0.398  -0.727  -0.755  -0.124  -0.685  -0.897  -0.350  -0.770  -0.807
103   N         1.184   1.240   1.308   1.395   1.456   1.550   1.251   1.327   1.435
104   R        -0.398  -0.403  -0.710  -0.519  -0.494  -0.957  -0.350  -0.358  -0.748
105   N        -0.239   0.028   0.043  -0.201   0.216   0.205  -0.597  -0.153  -0.170
106   Q        -0.912  -0.780  -0.767  -0.855  -0.693  -0.658  -1.089  -0.904  -0.828
107   E         1.184   1.240   1.308   1.195   1.269   1.377   1.251   1.327   1.435
108   I        -1.657  -1.460  -1.359  -1.362  -1.087  -0.951  -1.582  -1.338  -1.166
109   F        -0.307  -0.164  -0.018  -0.360  -0.142   0.058  -0.720  -0.486  -0.277
110   D        -1.425  -1.568  -1.360  -1.159  -1.396  -1.202  -1.336  -1.425  -1.167
111   A        -0.752  -0.730  -0.736  -1.159  -1.133  -1.112  -0.843  -0.775  -0.783
112   N         1.184   1.240   1.308   1.395   1.456   1.550   1.251   1.327   1.435
113   V         0.374   0.609   0.119   0.534   0.808   0.195   0.389   0.709  -0.038
114   Q        -1.657  -1.490  -1.364  -1.745  -1.493  -1.338  -1.582  -1.364  -1.170
115   R         1.184   1.240   1.308   0.890   0.979   1.114   1.251   1.327   1.435
116   L         0.374   0.141   0.079   0.585   0.297   0.172   0.389   0.032  -0.106
117   K        -0.025   0.137   0.037  -0.246   0.007  -0.122  -0.227   0.025  -0.180
118   E        -0.398  -0.727  -0.755  -0.246  -0.742  -0.895  -0.350  -0.770  -0.807
119   Y         1.184   1.240   1.308   1.487   1.545   1.629   1.251   1.327   1.435
120   Q        -0.752  -0.831  -0.767  -0.622  -0.703  -0.715  -0.843  -0.904  -0.824
121   S        -0.025  -0.161  -0.036  -0.048  -0.418  -0.288  -0.227  -0.480  -0.309
122   K        -0.398  -0.727  -0.755  -0.434  -0.839  -0.908  -0.350  -0.770  -0.807
123   I        -0.025   0.254   0.073   0.045   0.453   0.163  -0.227   0.209  -0.116
124   I        -0.239  -0.163  -0.035  -0.311  -0.204  -0.041  -0.597  -0.482  -0.307
125   V         0.374   0.518   0.111   0.534   0.712   0.183   0.389   0.589  -0.051
126   F         1.184   1.240   1.308   1.416   1.478   1.568   1.251   1.327   1.435
127   P        -0.025   0.137   0.037   0.138   0.358   0.194  -0.227   0.025  -0.180
128   R        -0.025   0.137   0.037  -0.442  -0.165  -0.360  -0.227   0.025  -0.180
129   N        -0.025   0.190   0.032  -0.236   0.086  -0.115  -0.227   0.109  -0.188
130   G        -2.030  -2.056  -1.814  -1.688  -1.831  -1.486  -1.705  -1.654  -1.362
131   K        -0.398  -0.727  -0.755  -0.366  -0.745  -0.744  -0.350  -0.770  -0.807
132   A        -0.752  -0.940  -0.796  -1.193  -1.405  -1.148  -0.843  -1.052  -0.863
133   P        -1.125  -0.879  -1.283  -0.742  -0.419  -1.057  -0.966  -0.662  -1.087
134   E        -0.025  -0.161  -0.036  -0.138  -0.444  -0.289  -0.227  -0.480  -0.309
135   A        -1.657  -1.464  -1.365  -2.061  -1.754  -1.524  -1.582  -1.345  -1.172
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.085  -0.982  -0.804  -1.377  -1.132  -0.865  -1.272  -1.108  -0.871
145   -        -1.085  -0.912  -0.798  -1.168  -0.876  -0.794  -1.272  -1.030  -0.863
146   E        -1.798  -1.756  -1.780  -1.466  -1.531  -1.485  -1.459  -1.394  -1.334
147   Q        -1.425  -1.440  -1.348  -1.170  -1.212  -1.140  -1.336  -1.324  -1.157
148   V        -0.912  -0.709  -0.772  -0.846  -0.592  -0.593  -1.089  -0.858  -0.837
149   L        -1.798  -1.877  -1.798  -1.547  -1.681  -1.719  -1.459  -1.506  -1.349
150   S        -0.239  -0.194  -0.039  -0.182  -0.117   0.092  -0.597  -0.538  -0.315
151   A        -0.752  -0.456  -0.709  -0.818  -0.314  -0.739  -0.843  -0.423  -0.748
152   A        -0.752  -0.746  -0.766  -1.060  -1.010  -0.967  -0.843  -0.797  -0.826
153   A         0.374   0.511   0.112   0.099   0.287  -0.154   0.389   0.580  -0.050
154   T        -0.912  -0.698  -0.767  -0.813  -0.574  -0.596  -1.089  -0.841  -0.830
155   F         0.374   0.141   0.079   0.733   0.418   0.271   0.389   0.032  -0.106
156   P         0.374   0.272   0.088   0.653   0.522   0.253   0.389   0.236  -0.091
157   I        -0.239  -0.163  -0.035  -0.311  -0.204  -0.041  -0.597  -0.482  -0.307
158   A        -1.657  -1.605  -1.357  -1.844  -1.637  -1.336  -1.582  -1.465  -1.164
159   Q         0.374   0.272   0.088   0.634   0.485   0.115   0.389   0.236  -0.091
160   P        -1.125  -1.092  -1.307  -0.772  -0.763  -1.159  -0.966  -0.941  -1.113
161   A        -1.425  -1.216  -1.308  -1.613  -1.308  -1.333  -1.336  -1.068  -1.116
162   T        -1.657  -1.520  -1.361  -1.714  -1.595  -1.333  -1.582  -1.404  -1.168
163   D        -0.752  -0.633  -0.727  -0.587  -0.391  -0.529  -0.843  -0.644  -0.772
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   V        -1.298  -1.160  -1.334  -0.922  -0.804  -1.050  -1.162  -1.022  -1.139
168   E        -1.125  -1.049  -1.304  -0.868  -0.756  -1.189  -0.966  -0.866  -1.109
169   A        -1.657  -1.430  -1.340  -1.685  -1.422  -1.267  -1.582  -1.312  -1.149
170   R        -0.025  -0.161  -0.036  -0.442  -0.707  -0.505  -0.227  -0.480  -0.309
171   A        -0.398  -0.727  -0.755  -0.565  -0.954  -0.916  -0.350  -0.770  -0.807
172   V        -0.752  -0.896  -0.795  -0.644  -0.850  -0.713  -0.843  -1.011  -0.862
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   Q        -0.398  -0.324  -0.698  -0.126  -0.040  -0.515  -0.350  -0.267  -0.734
176   D        -2.030  -1.917  -1.797  -1.803  -1.760  -1.532  -1.705  -1.549  -1.348
177   N        -1.657  -1.597  -1.369  -1.554  -1.523  -1.192  -1.582  -1.456  -1.175
178   G        -0.912  -0.907  -0.759  -0.847  -0.778  -0.576  -1.089  -1.006  -0.814
179   E        -1.517  -1.596  -1.358  -1.277  -1.291  -0.981  -1.459  -1.455  -1.164
180   S        -1.425  -1.438  -1.355  -1.022  -1.046  -0.917  -1.336  -1.325  -1.162
181   A         1.184   1.240   1.308   0.764   0.853   1.004   1.251   1.327   1.435
182   F        -0.239  -0.068  -0.016  -0.089   0.168   0.208  -0.597  -0.316  -0.272
183   R         0.374   0.141   0.079   0.221  -0.049  -0.112   0.389   0.032  -0.106
184   T         0.374   0.272   0.088   0.628   0.480   0.079   0.389   0.236  -0.091
185   L         1.184   1.240   1.308   1.257   1.337   1.431   1.251   1.327   1.435
186   R         0.374   0.141   0.079   0.221  -0.049  -0.112   0.389   0.032  -0.106
187   L        -1.125  -1.354  -1.349  -0.721  -1.048  -1.047  -0.966  -1.209  -1.154
188   A         0.374   0.141   0.079   0.070  -0.216  -0.277   0.389   0.032  -0.106
189   R         0.374   0.511   0.112   0.160   0.358  -0.218   0.389   0.580  -0.050
190   S        -0.398  -0.521  -0.720  -0.068  -0.322  -0.636  -0.350  -0.525  -0.763
191   E        -1.425  -1.404  -1.335  -1.005  -0.918  -0.889  -1.336  -1.264  -1.143
192   K        -0.752  -0.789  -0.792  -1.085  -1.257  -1.143  -0.843  -0.919  -0.859
193   K        -0.239  -0.187  -0.039  -0.830  -0.747  -0.509  -0.597  -0.526  -0.315
194   F        -0.752  -0.624  -0.723  -0.340  -0.143  -0.352  -0.843  -0.632  -0.766
195   R        -1.425  -1.384  -1.350  -1.815  -1.791  -1.720  -1.336  -1.283  -1.158
196   G         1.184   1.240   1.308   1.373   1.431   1.531   1.251   1.327   1.435
197   I        -0.398  -0.727  -0.755  -0.114  -0.652  -0.795  -0.350  -0.770  -0.807
198   R         1.184   1.240   1.308   0.890   0.979   1.114   1.251   1.327   1.435
199   E        -0.025  -0.097  -0.026  -0.194  -0.387  -0.357  -0.227  -0.367  -0.291
200   K         0.374   0.141   0.079   0.186  -0.153  -0.308   0.389   0.032  -0.106
201   R         0.374   0.141   0.079   0.232  -0.028  -0.081   0.389   0.032  -0.106
202   A        -0.398  -0.527  -0.719  -0.549  -0.689  -0.843  -0.350  -0.532  -0.760
203   R        -0.239  -0.015   0.014  -0.830  -0.391  -0.390  -0.597  -0.225  -0.220
204   E        -0.912  -0.990  -0.785  -0.901  -1.000  -0.723  -1.089  -1.122  -0.851
205   K        -0.398  -0.556  -0.734  -0.562  -0.809  -1.196  -0.350  -0.565  -0.780
206   A         1.184   1.240   1.308   0.764   0.853   1.004   1.251   1.327   1.435
207   E        -0.398  -0.440  -0.719  -0.208  -0.287  -0.730  -0.350  -0.401  -0.760
208   A         0.374   0.141   0.079   0.070  -0.216  -0.277   0.389   0.032  -0.106
209   E         0.374   0.141   0.079   0.444   0.085  -0.093   0.389   0.032  -0.106
210   A         0.374   0.141   0.079   0.070  -0.216  -0.277   0.389   0.032  -0.106
211   E        -0.398  -0.527  -0.719  -0.208  -0.457  -0.730  -0.350  -0.532  -0.760
212   K         1.184   1.240   1.308   0.941   1.034   1.157   1.251   1.327   1.435
213   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
214   K         0.374   0.272   0.088   0.272   0.180  -0.059   0.389   0.236  -0.091
215   K         1.184   1.240   1.308   0.941   1.034   1.157   1.251   1.327   1.435
* 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/Q12690
Output conservation file - output/Q12690
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
