1     M         1.287   1.314   1.378   1.397   1.437   1.531   1.377   1.415   1.510
2     T         0.025  -0.094  -0.269   0.127  -0.037  -0.314   0.006  -0.163  -0.419
3     T        -0.555  -0.642  -0.788  -0.442  -0.589  -0.830  -0.521  -0.632  -0.785
4     I        -0.555  -0.687  -0.795  -0.353  -0.556  -0.770  -0.521  -0.681  -0.793
5     Q        -1.389  -1.290  -1.234  -1.370  -1.235  -1.155  -1.259  -1.154  -1.042
6     P         0.025  -0.157  -0.294   0.239  -0.003  -0.234   0.006  -0.247  -0.455
7     F         1.287   1.314   1.378   1.260   1.301   1.402   1.377   1.415   1.510
8     E        -1.276  -1.348  -1.233  -1.155  -1.255  -1.075  -1.153  -1.195  -1.041
9     P        -0.867  -0.786  -0.816  -0.820  -0.722  -0.716  -0.943  -0.850  -0.826
10    V        -1.276  -1.192  -1.195  -1.329  -1.212  -1.216  -1.153  -1.062  -1.007
11    D         1.287   1.314   1.378   1.213   1.249   1.358   1.377   1.415   1.510
12    L         0.641   0.698   0.433   0.591   0.679   0.299   0.639   0.723   0.262
13    F         0.641   0.516   0.408   0.688   0.526   0.349   0.639   0.437   0.217
14    K        -0.979  -0.875  -0.844  -1.096  -0.966  -0.868  -1.048  -0.935  -0.853
15    T        -0.979  -0.936  -0.863  -1.183  -1.112  -0.982  -1.048  -0.995  -0.873
16    N         0.641   0.516   0.408   0.706   0.545   0.361   0.639   0.437   0.217
17    N        -0.867  -0.894  -0.838  -0.887  -0.920  -0.831  -0.943  -0.951  -0.847
18    V         0.025  -0.157  -0.294   0.155  -0.069  -0.267   0.006  -0.247  -0.455
19    N         1.287   1.314   1.378   1.280   1.326   1.421   1.377   1.415   1.510
20    L         1.287   1.314   1.378   1.166   1.215   1.314   1.377   1.415   1.510
21    D         1.287   1.314   1.378   1.213   1.249   1.358   1.377   1.415   1.510
22    I        -0.794  -0.651  -0.795  -0.733  -0.507  -0.742  -0.837  -0.654  -0.796
23    L         0.322   0.279   0.276   0.127   0.056   0.020   0.112   0.023  -0.031
24    T         1.287   1.314   1.378   1.260   1.305   1.402   1.377   1.415   1.510
25    E         1.287   1.314   1.378   1.243   1.283   1.386   1.377   1.415   1.510
26    N         0.322   0.231   0.271   0.238   0.074   0.101   0.112  -0.066  -0.042
27    F         0.322   0.262   0.282   0.233   0.123   0.132   0.112  -0.010  -0.020
28    P        -0.867  -0.911  -0.840  -0.902  -0.955  -0.858  -0.943  -0.962  -0.848
29    L        -0.384  -0.332  -0.345  -0.588  -0.506  -0.499  -0.626  -0.563  -0.540
30    E        -0.867  -0.882  -0.831  -0.920  -0.932  -0.807  -0.943  -0.936  -0.839
31    F         1.287   1.314   1.378   1.260   1.301   1.402   1.377   1.415   1.510
32    Y         1.287   1.314   1.378   1.306   1.346   1.445   1.377   1.415   1.510
33    F        -0.257  -0.129  -0.313  -0.409  -0.202  -0.493  -0.415  -0.227  -0.487
34    E        -0.384  -0.369  -0.349  -0.418  -0.356  -0.349  -0.626  -0.574  -0.539
35    Y         1.287   1.314   1.378   1.306   1.346   1.445   1.377   1.415   1.510
36    M         0.025  -0.006  -0.254   0.078   0.043  -0.277   0.006  -0.050  -0.397
37    I        -0.257  -0.362  -0.357  -0.209  -0.386  -0.395  -0.415  -0.562  -0.551
38    I        -0.979  -0.897  -0.865  -1.175  -1.060  -0.984  -1.048  -0.960  -0.874
39    W         1.287   1.314   1.378   1.499   1.535   1.627   1.377   1.415   1.510
40    P         1.287   1.314   1.378   1.352   1.393   1.488   1.377   1.415   1.510
41    D        -0.555  -0.325  -0.724  -0.411  -0.108  -0.671  -0.521  -0.235  -0.712
42    L         1.287   1.314   1.378   1.166   1.215   1.314   1.377   1.415   1.510
43    F         0.025   0.005  -0.253   0.182   0.165  -0.175   0.006  -0.023  -0.397
44    F        -0.555  -0.678  -0.793  -0.397  -0.567  -0.749  -0.521  -0.671  -0.792
45    K        -0.257  -0.329  -0.357  -0.297  -0.436  -0.444  -0.415  -0.534  -0.551
46    S        -0.257  -0.362  -0.357  -0.260  -0.430  -0.398  -0.415  -0.562  -0.551
47    S        -1.686  -1.546  -1.531  -1.704  -1.496  -1.476  -1.364  -1.233  -1.150
48    E        -0.257  -0.362  -0.357  -0.353  -0.538  -0.537  -0.415  -0.562  -0.551
49    M        -1.686  -1.701  -1.534  -1.553  -1.558  -1.348  -1.364  -1.349  -1.153
50    T        -1.686  -1.661  -1.535  -1.604  -1.562  -1.375  -1.364  -1.323  -1.154
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    V        -1.372  -1.332  -1.230  -1.464  -1.394  -1.257  -1.239  -1.188  -1.038
54    D        -0.904  -0.834  -0.828  -0.969  -0.888  -0.830  -0.964  -0.885  -0.836
55    P        -0.998  -0.903  -0.860  -1.048  -0.897  -0.863  -1.052  -0.935  -0.866
56    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    N        -0.844  -0.812  -0.830  -0.843  -0.806  -0.834  -0.872  -0.830  -0.833
61    I        -1.091  -1.021  -1.149  -0.830  -0.740  -0.943  -0.943  -0.861  -0.961
62    S        -0.555  -0.718  -0.800  -0.380  -0.615  -0.733  -0.521  -0.715  -0.800
63    G         1.287   1.314   1.378   1.349   1.382   1.485   1.377   1.415   1.510
64    Y         1.287   1.314   1.378   1.306   1.346   1.445   1.377   1.415   1.510
65    M         0.322   0.231   0.271   0.380   0.214   0.244   0.112  -0.066  -0.042
66    M         1.287   1.314   1.378   1.397   1.437   1.531   1.377   1.415   1.510
67    A         0.152   0.256   0.284   0.012   0.187   0.211  -0.205  -0.020  -0.016
68    K         1.287   1.314   1.378   1.253   1.295   1.396   1.377   1.415   1.510
69    T        -1.091  -1.195  -1.197  -0.983  -1.164  -1.192  -0.943  -1.043  -1.008
70    E         1.287   1.314   1.378   1.243   1.283   1.386   1.377   1.415   1.510
71    G         0.641   0.516   0.408   0.775   0.600   0.423   0.639   0.437   0.217
72    K        -0.555  -0.678  -0.793  -0.408  -0.598  -0.763  -0.521  -0.671  -0.792
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    T        -1.276  -1.260  -1.212  -1.198  -1.170  -1.108  -1.153  -1.121  -1.022
76    T        -1.574  -1.498  -1.508  -1.376  -1.294  -1.284  -1.259  -1.181  -1.132
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    E         0.025  -0.058  -0.258   0.109  -0.005  -0.315   0.006  -0.116  -0.404
87    W         1.287   1.314   1.378   1.499   1.535   1.627   1.377   1.415   1.510
88    H         1.287   1.314   1.378   1.439   1.475   1.570   1.377   1.415   1.510
89    T        -0.497  -0.476  -0.402  -0.671  -0.647  -0.542  -0.732  -0.703  -0.607
90    H         1.287   1.314   1.378   1.439   1.475   1.570   1.377   1.415   1.510
91    I         0.641   0.586   0.413   0.775   0.708   0.425   0.639   0.550   0.225
92    T         1.287   1.314   1.378   1.260   1.305   1.402   1.377   1.415   1.510
93    A         1.287   1.314   1.378   1.313   1.343   1.452   1.377   1.415   1.510
94    V         0.641   0.586   0.413   0.679   0.620   0.364   0.639   0.550   0.225
95    T         1.287   1.314   1.378   1.260   1.305   1.402   1.377   1.415   1.510
96    V         0.641   0.698   0.433   0.679   0.761   0.397   0.639   0.723   0.262
97    A        -0.257  -0.160  -0.318  -0.265  -0.126  -0.379  -0.415  -0.276  -0.496
98    P        -0.555  -0.467  -0.758  -0.339  -0.216  -0.680  -0.521  -0.407  -0.752
99    R        -1.389  -1.375  -1.231  -1.356  -1.336  -1.139  -1.259  -1.220  -1.039
100   F        -1.276  -1.348  -1.233  -1.207  -1.307  -1.120  -1.153  -1.195  -1.041
101   R         1.287   1.314   1.378   1.286   1.326   1.427   1.377   1.415   1.510
102   R         1.287   1.314   1.378   1.286   1.326   1.427   1.377   1.415   1.510
103   I        -0.257  -0.329  -0.357  -0.257  -0.417  -0.462  -0.415  -0.534  -0.551
104   S         0.152   0.252   0.290  -0.014   0.160   0.199  -0.205  -0.029  -0.004
105   L         0.641   0.516   0.408   0.605   0.456   0.291   0.639   0.437   0.217
106   A         0.641   0.516   0.408   0.751   0.580   0.420   0.639   0.437   0.217
107   S        -0.257  -0.362  -0.357  -0.314  -0.495  -0.491  -0.415  -0.562  -0.551
108   K        -1.686  -1.614  -1.518  -1.603  -1.482  -1.370  -1.364  -1.285  -1.141
109   L         0.641   0.586   0.413   0.612   0.559   0.314   0.639   0.550   0.225
110   C         0.025  -0.157  -0.294   0.383   0.128  -0.127   0.006  -0.247  -0.455
111   N        -1.389  -1.387  -1.234  -1.565  -1.551  -1.323  -1.259  -1.230  -1.042
112   T        -1.276  -1.331  -1.226  -1.194  -1.251  -1.081  -1.153  -1.183  -1.036
113   L         1.287   1.314   1.378   1.166   1.215   1.314   1.377   1.415   1.510
114   E         0.641   0.698   0.433   0.668   0.746   0.367   0.639   0.723   0.262
115   T        -0.979  -0.947  -0.855  -1.090  -1.037  -0.894  -1.048  -0.999  -0.864
116   M        -1.686  -1.684  -1.543  -1.618  -1.621  -1.399  -1.364  -1.338  -1.159
117   T        -0.555  -0.680  -0.795  -0.415  -0.598  -0.788  -0.521  -0.674  -0.793
118   D        -1.091  -1.069  -1.177  -0.961  -0.940  -1.088  -0.943  -0.909  -0.989
119   V        -1.276  -1.217  -1.192  -1.274  -1.178  -1.163  -1.153  -1.073  -1.006
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   M        -0.998  -0.848  -0.872  -1.103  -0.867  -0.922  -1.052  -0.868  -0.879
122   P         1.287   1.314   1.378   1.345   1.390   1.481   1.377   1.415   1.510
123   H        -1.276  -1.330  -1.228  -1.128  -1.227  -1.107  -1.153  -1.183  -1.037
124   E        -0.979  -0.975  -0.862  -1.114  -1.113  -0.918  -1.048  -1.031  -0.873
125   V        -0.979  -0.959  -0.870  -1.057  -1.018  -0.851  -1.048  -1.014  -0.879
126   N        -1.276  -1.348  -1.233  -1.255  -1.317  -1.162  -1.153  -1.195  -1.041
127   F         1.287   1.314   1.378   1.260   1.301   1.402   1.377   1.415   1.510
128   I         0.152   0.136   0.244  -0.023  -0.079   0.082  -0.205  -0.250  -0.095
129   D         1.287   1.314   1.378   1.213   1.249   1.358   1.377   1.415   1.510
130   L         1.287   1.314   1.378   1.166   1.215   1.314   1.377   1.415   1.510
131   F         1.287   1.314   1.378   1.260   1.301   1.402   1.377   1.415   1.510
132   V         1.287   1.314   1.378   1.240   1.285   1.383   1.377   1.415   1.510
133   K         0.152   0.136   0.244  -0.086  -0.129   0.043  -0.205  -0.250  -0.095
134   C        -1.276  -1.348  -1.233  -1.093  -1.215  -1.081  -1.153  -1.195  -1.041
135   N        -0.384  -0.369  -0.349  -0.552  -0.493  -0.472  -0.626  -0.574  -0.539
136   N         1.287   1.314   1.378   1.280   1.326   1.421   1.377   1.415   1.510
137   Q        -1.574  -1.557  -1.518  -1.265  -1.246  -1.250  -1.259  -1.234  -1.139
138   L         0.025  -0.094  -0.269   0.046  -0.111  -0.367   0.006  -0.163  -0.419
139   A         0.641   0.710   0.432   0.751   0.832   0.460   0.639   0.741   0.260
140   I         0.025   0.128  -0.245   0.245   0.381  -0.144   0.006   0.149  -0.386
141   K        -1.686  -1.640  -1.533  -1.563  -1.487  -1.312  -1.364  -1.304  -1.152
142   L        -0.257  -0.329  -0.357  -0.383  -0.508  -0.517  -0.415  -0.534  -0.551
143   Y         1.287   1.314   1.378   1.306   1.346   1.445   1.377   1.415   1.510
144   E         0.322   0.231   0.271   0.200   0.029   0.068   0.112  -0.066  -0.042
145   K        -0.257  -0.387  -0.357  -0.292  -0.490  -0.452  -0.415  -0.584  -0.550
146   L         0.025  -0.094  -0.269   0.047  -0.099  -0.364   0.006  -0.163  -0.419
147   G         0.322   0.366   0.316   0.290   0.350   0.227   0.112   0.180   0.044
148   Y         1.287   1.314   1.378   1.306   1.346   1.445   1.377   1.415   1.510
149   S         1.287   1.314   1.378   1.263   1.297   1.405   1.377   1.415   1.510
150   V         0.641   0.516   0.408   0.679   0.525   0.356   0.639   0.437   0.217
151   Y         0.152   0.174   0.250  -0.053  -0.024   0.078  -0.205  -0.176  -0.082
152   R         1.287   1.314   1.378   1.286   1.326   1.427   1.377   1.415   1.510
153   R         0.641   0.516   0.408   0.712   0.547   0.366   0.639   0.437   0.217
154   V         1.287   1.314   1.378   1.240   1.285   1.383   1.377   1.415   1.510
155   V        -0.555  -0.718  -0.800  -0.446  -0.682  -0.833  -0.521  -0.715  -0.800
156   G         0.641   0.516   0.408   0.768   0.590   0.406   0.639   0.437   0.217
157   Y         1.287   1.314   1.378   1.306   1.346   1.445   1.377   1.415   1.510
158   Y         1.287   1.314   1.378   1.306   1.346   1.445   1.377   1.415   1.510
159   N        -0.384  -0.369  -0.349  -0.478  -0.426  -0.405  -0.626  -0.574  -0.539
160   S        -0.904  -0.993  -0.867  -1.007  -1.153  -0.963  -0.964  -1.037  -0.875
161   A        -1.712  -1.687  -1.547  -1.459  -1.429  -1.262  -1.377  -1.338  -1.161
162   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   Y        -0.523  -0.499  -0.400  -0.639  -0.598  -0.449  -0.782  -0.740  -0.604
166   P         0.429   0.415   0.321   0.513   0.494   0.333   0.297   0.266   0.055
167   D        -0.998  -0.975  -0.880  -1.152  -1.118  -1.003  -1.052  -1.015  -0.888
168   T        -0.994  -0.900  -0.860  -1.160  -1.019  -0.943  -1.060  -0.949  -0.868
169   L        -0.994  -0.897  -0.856  -1.204  -1.023  -0.975  -1.060  -0.937  -0.863
170   K        -0.994  -1.008  -0.881  -1.186  -1.214  -1.018  -1.060  -1.058  -0.889
171   K        -0.201  -0.323  -0.348  -0.203  -0.407  -0.436  -0.310  -0.497  -0.531
172   V        -1.372  -1.314  -1.225  -1.335  -1.226  -1.095  -1.239  -1.164  -1.033
173   D        -0.904  -0.977  -0.854  -1.026  -1.129  -0.939  -0.964  -1.018  -0.861
174   D         0.025  -0.157  -0.294   0.070  -0.193  -0.420   0.006  -0.247  -0.455
175   N        -1.686  -1.589  -1.515  -1.666  -1.534  -1.411  -1.364  -1.268  -1.139
176   K        -0.867  -0.763  -0.829  -0.978  -0.821  -0.888  -0.943  -0.816  -0.836
177   D         1.287   1.314   1.378   1.213   1.249   1.358   1.377   1.415   1.510
178   A         0.641   0.586   0.413   0.739   0.660   0.398   0.639   0.550   0.225
179   F         0.322   0.262   0.282   0.233   0.123   0.132   0.112  -0.010  -0.020
180   D         1.287   1.314   1.378   1.213   1.249   1.358   1.377   1.415   1.510
181   M         1.287   1.314   1.378   1.397   1.437   1.531   1.377   1.415   1.510
182   R         1.287   1.314   1.378   1.286   1.326   1.427   1.377   1.415   1.510
183   K         0.641   0.698   0.433   0.705   0.782   0.437   0.639   0.723   0.262
184   A        -1.389  -1.300  -1.229  -1.394  -1.253  -1.161  -1.259  -1.160  -1.039
185   M         0.098   0.130   0.243  -0.171  -0.117   0.058  -0.310  -0.261  -0.096
186   A        -1.276  -1.307  -1.213  -1.220  -1.289  -1.148  -1.153  -1.166  -1.025
187   R         0.641   0.707   0.430   0.711   0.800   0.401   0.639   0.736   0.256
188   D         1.287   1.314   1.378   1.213   1.249   1.358   1.377   1.415   1.510
189   R        -0.555  -0.336  -0.741  -0.417  -0.120  -0.689  -0.521  -0.248  -0.732
190   N        -0.497  -0.457  -0.383  -0.642  -0.589  -0.490  -0.732  -0.678  -0.582
191   R        -0.570  -0.517  -0.397  -0.810  -0.726  -0.544  -0.837  -0.764  -0.602
192   -         1.287   1.314   1.378   1.220   1.265   1.365   1.377   1.415   1.510
193   S        -0.384  -0.446  -0.367  -0.524  -0.584  -0.447  -0.626  -0.677  -0.564
194   V        -0.794  -0.736  -0.826  -0.830  -0.766  -0.892  -0.837  -0.795  -0.833
195   R         1.287   1.314   1.378   1.286   1.326   1.427   1.377   1.415   1.510
196   P        -1.276  -1.112  -1.184  -1.274  -1.046  -1.139  -1.153  -0.980  -0.999
197   D         0.098   0.141   0.251  -0.225  -0.143   0.031  -0.310  -0.239  -0.080
198   G         1.287   1.314   1.378   1.349   1.382   1.485   1.377   1.415   1.510
199   R         0.152   0.141   0.243  -0.079  -0.121   0.036  -0.205  -0.239  -0.096
200   S        -1.091  -1.035  -1.155  -0.995  -0.918  -1.135  -0.943  -0.875  -0.968
201   H        -0.497  -0.503  -0.404  -0.549  -0.590  -0.465  -0.732  -0.742  -0.610
202   K        -0.794  -0.813  -0.815  -0.823  -0.848  -0.861  -0.837  -0.843  -0.822
203   C         0.098   0.134   0.245  -0.039   0.010   0.180  -0.310  -0.253  -0.092
204   Y        -1.686  -1.699  -1.534  -1.737  -1.768  -1.526  -1.364  -1.347  -1.153
205   P         1.287   1.314   1.378   1.352   1.393   1.488   1.377   1.415   1.510
206   H        -1.574  -1.622  -1.520  -1.193  -1.298  -1.156  -1.259  -1.285  -1.141
207   D         0.152   0.201   0.268  -0.144  -0.066   0.032  -0.205  -0.124  -0.048
208   V         0.322   0.392   0.309   0.229   0.343   0.188   0.112   0.227   0.032
209   R        -0.904  -0.941  -0.861  -0.985  -1.059  -0.924  -0.964  -0.992  -0.870
210   F         0.641   0.516   0.408   0.720   0.571   0.426   0.639   0.437   0.217
* 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/Q06504
Output conservation file - output/Q06504
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
