1     M         1.406   1.415   1.505   1.527   1.531   1.673   1.515   1.527   1.659
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    G        -0.804  -0.775  -0.706  -1.029  -0.975  -0.877  -0.920  -0.886  -0.776
26    I         0.254   0.267   0.387  -0.087  -0.068   0.122  -0.171  -0.152   0.019
27    E        -0.213  -0.149  -0.182  -0.421  -0.313  -0.365  -0.487  -0.400  -0.420
28    D        -0.789  -0.761  -0.691  -0.795  -0.772  -0.646  -0.909  -0.881  -0.762
29    R        -1.077  -1.092  -1.031  -1.197  -1.207  -1.121  -1.014  -1.025  -0.915
30    Q        -0.090  -0.169  -0.170  -0.119  -0.220  -0.218  -0.276  -0.393  -0.395
31    L        -0.680  -0.717  -0.658  -0.770  -0.817  -0.733  -0.803  -0.832  -0.729
32    E        -0.898  -0.845  -0.979  -0.786  -0.706  -0.907  -0.803  -0.744  -0.860
33    A        -1.761  -1.776  -1.620  -1.585  -1.617  -1.406  -1.330  -1.333  -1.146
34    L         0.780   0.752   0.602   0.790   0.758   0.524   0.778   0.731   0.438
35    K        -0.610  -0.667  -0.645  -0.562  -0.647  -0.631  -0.698  -0.759  -0.711
36    R        -1.186  -1.206  -1.068  -1.141  -1.149  -0.961  -1.119  -1.126  -0.948
37    A        -1.761  -1.703  -1.614  -1.754  -1.664  -1.546  -1.330  -1.281  -1.141
38    A        -0.898  -0.882  -0.734  -1.166  -1.156  -0.924  -1.014  -0.993  -0.804
39    L        -0.898  -0.916  -0.983  -0.776  -0.797  -0.917  -0.803  -0.822  -0.863
40    K        -0.090  -0.026  -0.146  -0.166  -0.075  -0.292  -0.276  -0.192  -0.361
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    A         0.780   0.737   0.605   0.735   0.680   0.476   0.778   0.708   0.443
43    C        -0.610  -0.648  -0.630  -0.575  -0.619  -0.608  -0.698  -0.726  -0.692
44    E        -1.474  -1.487  -1.355  -1.425  -1.451  -1.250  -1.225  -1.228  -1.055
45    L        -2.049  -2.024  -1.854  -1.984  -1.939  -1.708  -1.436  -1.412  -1.216
46    S         0.471   0.544   0.495   0.262   0.380   0.270   0.251   0.378   0.234
47    Y         1.406   1.415   1.505   1.506   1.515   1.652   1.515   1.527   1.659
48    S         0.306   0.330   0.409   0.040   0.072   0.195  -0.065  -0.024   0.064
49    P         1.406   1.415   1.505   1.464   1.474   1.611   1.515   1.527   1.659
50    Y         1.406   1.415   1.505   1.506   1.515   1.652   1.515   1.527   1.659
51    S         1.406   1.415   1.505   1.298   1.308   1.451   1.515   1.527   1.659
52    H        -0.378  -0.446  -0.577  -0.156  -0.247  -0.426  -0.382  -0.468  -0.623
53    F         0.780   0.817   0.612   0.914   0.959   0.688   0.778   0.833   0.455
54    R         0.780   0.737   0.605   0.881   0.827   0.614   0.778   0.708   0.443
55    V         1.406   1.415   1.505   1.346   1.360   1.498   1.515   1.527   1.659
56    G         1.406   1.415   1.505   1.320   1.330   1.473   1.515   1.527   1.659
57    C         0.306   0.313   0.404   0.106   0.107   0.229  -0.065  -0.058   0.054
58    S        -0.680  -0.672  -0.654  -0.762  -0.756  -0.712  -0.803  -0.790  -0.725
59    I        -0.213  -0.247  -0.196  -0.429  -0.474  -0.392  -0.487  -0.527  -0.439
60    L         0.183   0.189  -0.047   0.234   0.246  -0.125   0.145   0.150  -0.205
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    T        -0.378  -0.398  -0.568  -0.226  -0.255  -0.545  -0.382  -0.407  -0.612
80    N        -1.474  -1.501  -1.359  -1.474  -1.495  -1.282  -1.225  -1.237  -1.057
81    N        -1.474  -1.485  -1.358  -1.432  -1.439  -1.260  -1.225  -1.226  -1.057
82    D         0.183   0.081  -0.067   0.240   0.100  -0.105   0.145  -0.002  -0.235
83    V        -0.680  -0.675  -0.647  -0.795  -0.769  -0.727  -0.803  -0.791  -0.718
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    I        -1.365  -1.281  -1.313  -1.047  -0.943  -0.990  -1.119  -1.039  -1.018
88    F        -0.610  -0.599  -0.636  -0.632  -0.616  -0.675  -0.698  -0.686  -0.702
89    T        -0.898  -0.849  -0.978  -0.672  -0.604  -0.801  -0.803  -0.750  -0.858
90    G         1.406   1.415   1.505   1.320   1.330   1.473   1.515   1.527   1.659
91    A         0.780   0.752   0.602   0.735   0.700   0.471   0.778   0.731   0.438
92    N         1.406   1.415   1.505   1.481   1.492   1.628   1.515   1.527   1.659
93    V         1.406   1.415   1.505   1.346   1.360   1.498   1.515   1.527   1.659
94    E         1.406   1.415   1.505   1.329   1.356   1.481   1.515   1.527   1.659
95    N         1.406   1.415   1.505   1.481   1.492   1.628   1.515   1.527   1.659
96    A         1.406   1.415   1.505   1.307   1.320   1.460   1.515   1.527   1.659
97    S         0.780   0.752   0.602   0.746   0.710   0.505   0.778   0.731   0.438
98    Y         1.406   1.415   1.505   1.506   1.515   1.652   1.515   1.527   1.659
99    S         0.183   0.116  -0.070   0.209   0.110  -0.172   0.145   0.048  -0.240
100   N        -0.789  -0.787  -0.698  -0.993  -0.981  -0.845  -0.909  -0.903  -0.770
101   C        -0.789  -0.742  -0.687  -0.909  -0.838  -0.758  -0.909  -0.862  -0.758
102   I         0.183   0.237  -0.043   0.256   0.331  -0.082   0.145   0.219  -0.200
103   C         1.406   1.415   1.505   1.472   1.477   1.619   1.515   1.527   1.659
104   A         1.406   1.415   1.505   1.307   1.320   1.460   1.515   1.527   1.659
105   E         1.406   1.415   1.505   1.329   1.356   1.481   1.515   1.527   1.659
106   R         1.406   1.415   1.505   1.451   1.465   1.599   1.515   1.527   1.659
107   S        -0.610  -0.604  -0.638  -0.728  -0.729  -0.789  -0.698  -0.691  -0.703
108   A         0.780   0.837   0.613   0.755   0.827   0.530   0.778   0.863   0.457
109   M         0.183   0.116  -0.070   0.290   0.205  -0.060   0.145   0.048  -0.240
110   I        -0.610  -0.651  -0.643  -0.640  -0.699  -0.724  -0.698  -0.739  -0.709
111   Q        -0.090  -0.119  -0.154  -0.062  -0.091  -0.148  -0.276  -0.306  -0.370
112   V         0.780   0.717   0.598   0.742   0.661   0.478   0.778   0.675   0.429
113   L        -0.610  -0.615  -0.636  -0.665  -0.670  -0.696  -0.698  -0.697  -0.699
114   M        -0.090  -0.132  -0.158  -0.066  -0.132  -0.189  -0.276  -0.332  -0.379
115   A        -1.365  -1.391  -1.332  -1.294  -1.340  -1.259  -1.119  -1.140  -1.035
116   G         0.183   0.184  -0.053   0.189   0.184  -0.183   0.145   0.145  -0.215
117   H         0.183   0.171  -0.051   0.522   0.504   0.155   0.145   0.125  -0.212
118   R        -0.392  -0.378  -0.259  -0.559  -0.532  -0.359  -0.698  -0.676  -0.517
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   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   G        -0.610  -0.633  -0.651  -0.589  -0.647  -0.648  -0.698  -0.731  -0.719
124   W        -0.680  -0.606  -0.655  -0.527  -0.432  -0.484  -0.803  -0.729  -0.726
125   K        -0.090  -0.127  -0.155  -0.107  -0.162  -0.213  -0.276  -0.325  -0.373
126   C        -0.090  -0.090  -0.161  -0.195  -0.214  -0.306  -0.276  -0.297  -0.383
127   M        -0.610  -0.646  -0.652  -0.657  -0.711  -0.721  -0.698  -0.741  -0.719
128   V        -0.213  -0.249  -0.189  -0.502  -0.548  -0.450  -0.487  -0.521  -0.430
129   I         0.254   0.265   0.385  -0.082  -0.062   0.125  -0.171  -0.155   0.017
130   C        -1.077  -1.102  -1.035  -1.057  -1.091  -0.980  -1.014  -1.035  -0.918
131   G        -0.213  -0.216  -0.190  -0.486  -0.497  -0.427  -0.487  -0.490  -0.432
132   D         0.183   0.200  -0.048   0.361   0.368   0.007   0.145   0.165  -0.207
133   S        -1.045  -1.015  -1.026  -1.070  -1.028  -1.045  -0.962  -0.928  -0.906
134   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   D        -1.186  -1.141  -1.064  -1.222  -1.159  -1.028  -1.119  -1.078  -0.945
136   Q        -1.761  -1.767  -1.617  -1.555  -1.560  -1.365  -1.330  -1.327  -1.144
137   C        -1.077  -1.091  -1.039  -0.947  -0.975  -0.895  -1.014  -1.025  -0.922
138   V        -0.610  -0.607  -0.644  -0.682  -0.705  -0.748  -0.698  -0.709  -0.711
139   S        -0.090  -0.109  -0.154  -0.199  -0.224  -0.287  -0.276  -0.299  -0.372
140   P         1.406   1.415   1.505   1.464   1.474   1.611   1.515   1.527   1.659
141   C         1.406   1.415   1.505   1.472   1.477   1.619   1.515   1.527   1.659
142   G         1.406   1.415   1.505   1.320   1.330   1.473   1.515   1.527   1.659
143   V         0.183   0.116  -0.070   0.272   0.182  -0.095   0.145   0.048  -0.240
144   C         1.406   1.415   1.505   1.472   1.477   1.619   1.515   1.527   1.659
145   R         1.406   1.415   1.505   1.451   1.465   1.599   1.515   1.527   1.659
146   Q         1.406   1.415   1.505   1.561   1.575   1.705   1.515   1.527   1.659
147   F        -0.090  -0.123  -0.157  -0.089  -0.140  -0.216  -0.276  -0.321  -0.376
148   I         1.406   1.415   1.505   1.364   1.381   1.515   1.515   1.527   1.659
149   N         0.780   0.717   0.598   0.906   0.828   0.654   0.778   0.675   0.429
150   E         1.406   1.415   1.505   1.329   1.356   1.481   1.515   1.527   1.659
151   F         0.780   0.845   0.617   0.935   1.011   0.740   0.778   0.877   0.466
152   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   V        -1.761  -1.740  -1.621  -1.833  -1.796  -1.636  -1.330  -1.308  -1.146
157   K        -1.474  -1.439  -1.356  -1.429  -1.380  -1.278  -1.225  -1.190  -1.055
158   D        -0.898  -0.797  -0.968  -0.677  -0.541  -0.813  -0.803  -0.690  -0.848
159   F        -1.077  -1.115  -1.038  -1.086  -1.130  -1.013  -1.014  -1.040  -0.921
160   P         0.780   0.737   0.605   0.919   0.864   0.678   0.778   0.708   0.443
161   I         0.306   0.330   0.409   0.030   0.077   0.175  -0.065  -0.024   0.064
162   V        -1.077  -1.075  -1.037  -1.013  -1.027  -0.976  -1.014  -1.011  -0.920
163   M         0.780   0.845   0.617   0.965   1.039   0.722   0.778   0.877   0.466
164   L         0.183   0.094  -0.074   0.348   0.225  -0.047   0.145   0.016  -0.246
165   N        -0.378  -0.374  -0.569  -0.100  -0.097  -0.372  -0.382  -0.378  -0.613
166   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   T        -0.610  -0.592  -0.631  -0.559  -0.532  -0.609  -0.698  -0.672  -0.693
168   G        -0.680  -0.656  -0.656  -0.776  -0.746  -0.727  -0.803  -0.776  -0.726
169   S        -0.610  -0.565  -0.632  -0.749  -0.691  -0.779  -0.698  -0.646  -0.694
170   R        -1.186  -1.201  -1.060  -1.190  -1.215  -1.014  -1.119  -1.122  -0.942
171   S        -0.680  -0.728  -0.661  -0.664  -0.734  -0.638  -0.803  -0.842  -0.732
172   K        -1.077  -1.043  -1.033  -1.073  -1.012  -1.010  -1.014  -0.970  -0.915
173   V        -0.789  -0.811  -0.701  -0.866  -0.911  -0.742  -0.909  -0.927  -0.773
174   M        -1.077  -1.085  -1.042  -1.002  -1.021  -0.931  -1.014  -1.023  -0.925
175   T        -0.898  -0.797  -0.968  -0.700  -0.558  -0.827  -0.803  -0.690  -0.848
176   M        -0.090  -0.139  -0.153  -0.154  -0.213  -0.246  -0.276  -0.337  -0.369
177   G        -1.077  -1.068  -1.023  -1.030  -1.016  -0.952  -1.014  -0.996  -0.906
178   E         0.306   0.343   0.410   0.065   0.135   0.220  -0.065   0.001   0.068
179   L         0.780   0.817   0.612   0.798   0.851   0.557   0.778   0.833   0.455
180   L         1.406   1.415   1.505   1.359   1.377   1.511   1.515   1.527   1.659
181   P         1.406   1.415   1.505   1.464   1.474   1.611   1.515   1.527   1.659
182   M        -0.610  -0.676  -0.651  -0.598  -0.692  -0.654  -0.698  -0.772  -0.717
183   A         0.780   0.717   0.598   0.728   0.642   0.457   0.778   0.675   0.429
184   F         1.406   1.415   1.505   1.455   1.467   1.603   1.515   1.527   1.659
185   G         1.406   1.415   1.505   1.320   1.330   1.473   1.515   1.527   1.659
186   P         1.406   1.415   1.505   1.464   1.474   1.611   1.515   1.527   1.659
187   S        -0.213  -0.261  -0.194  -0.399  -0.458  -0.355  -0.487  -0.543  -0.437
188   H        -1.077  -1.028  -1.022  -0.814  -0.749  -0.752  -1.014  -0.964  -0.906
189   L         0.183   0.148  -0.063   0.285   0.242  -0.052   0.145   0.094  -0.229
190   N        -1.365  -1.393  -1.337  -1.220  -1.262  -1.168  -1.119  -1.142  -1.039
191   -        -1.188  -1.177  -1.070  -1.267  -1.263  -1.101  -1.108  -1.094  -0.948
192   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
194   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
195   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
197   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
198   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
202   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
203   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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/Q06549
Output conservation file - output/Q06549
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
