1     M         1.809   1.846   1.940   1.981   2.033   2.174   1.974   2.024   2.185
2     S        -0.975  -0.927  -0.948  -0.782  -0.724  -0.759  -0.868  -0.825  -0.799
3     Q        -0.652  -0.589  -0.544  -0.622  -0.508  -0.451  -0.749  -0.656  -0.597
4     S        -1.297  -1.273  -1.301  -0.945  -0.912  -0.973  -0.986  -0.958  -0.944
5     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     P        -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     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    R        -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    L         0.039  -0.075  -0.013  -0.154  -0.375  -0.308  -0.148  -0.319  -0.251
13    A        -0.652  -0.589  -0.544  -0.840  -0.682  -0.670  -0.749  -0.656  -0.597
14    I        -0.652  -0.651  -0.564  -0.759  -0.773  -0.677  -0.749  -0.731  -0.623
15    T        -0.975  -0.931  -0.937  -1.040  -0.999  -0.937  -0.868  -0.817  -0.788
16    T         0.132   0.055   0.048   0.294   0.190   0.164  -0.039  -0.141  -0.172
17    A         0.132   0.122   0.049  -0.189  -0.216  -0.287  -0.039  -0.081  -0.172
18    I        -1.096  -1.055  -0.990  -1.216  -1.221  -1.072  -0.986  -0.931  -0.838
19    A        -0.652  -0.622  -0.578  -0.986  -0.935  -0.827  -0.749  -0.722  -0.640
20    A         1.107   1.223   0.950   0.827   0.967   0.659   1.145   1.318   0.843
21    L        -0.975  -0.835  -0.926  -0.881  -0.672  -0.854  -0.868  -0.728  -0.778
22    S         0.132   0.104   0.033  -0.135  -0.175  -0.226  -0.039  -0.113  -0.195
23    A        -0.975  -0.903  -0.931  -1.150  -1.041  -1.047  -0.868  -0.781  -0.781
24    T        -1.096  -1.013  -0.988  -1.281  -1.148  -1.106  -0.986  -0.901  -0.836
25    G        -0.006  -0.043   0.021  -0.188  -0.233  -0.170  -0.276  -0.309  -0.225
26    Y         1.809   1.846   1.940   1.872   1.920   2.065   1.974   2.024   2.185
27    A         1.107   1.041   0.926   0.804   0.730   0.575   1.145   1.031   0.799
28    I        -0.451  -0.355  -0.485  -0.447  -0.310  -0.547  -0.513  -0.404  -0.534
29    Y         1.809   1.846   1.940   1.872   1.920   2.065   1.974   2.024   2.185
30    F         1.809   1.846   1.940   1.936   1.986   2.128   1.974   2.024   2.185
31    D         1.809   1.846   1.940   1.883   1.931   2.076   1.974   2.024   2.185
32    Y         1.107   1.210   0.945   1.329   1.447   1.162   1.145   1.298   0.835
33    Q         0.577   0.582   0.671   0.399   0.382   0.498   0.198   0.188   0.299
34    R         1.809   1.846   1.940   1.861   1.905   2.054   1.974   2.024   2.185
35    R         1.809   1.846   1.940   1.861   1.905   2.054   1.974   2.024   2.185
36    N         0.132   0.154   0.077   0.402   0.472   0.336  -0.039   0.014  -0.127
37    S        -0.207  -0.202  -0.083  -0.159  -0.147   0.018  -0.513  -0.503  -0.353
38    P         0.762   0.778   0.742   0.661   0.678   0.525   0.553   0.567   0.444
39    Q        -0.530  -0.515  -0.513  -0.419  -0.395  -0.352  -0.631  -0.605  -0.571
40    F         1.809   1.846   1.940   1.936   1.986   2.128   1.974   2.024   2.185
41    R         1.809   1.846   1.940   1.861   1.905   2.054   1.974   2.024   2.185
42    K         0.762   0.682   0.715   0.656   0.530   0.563   0.553   0.385   0.389
43    V        -1.419  -1.354  -1.317  -1.174  -1.096  -1.051  -1.105  -1.040  -0.961
44    L         1.809   1.846   1.940   1.672   1.725   1.866   1.974   2.024   2.185
45    R         0.762   0.748   0.727   0.656   0.634   0.582   0.553   0.511   0.413
46    Q        -0.006   0.060   0.027  -0.050   0.039   0.018  -0.276  -0.189  -0.211
47    R        -0.128  -0.121  -0.062  -0.160  -0.166  -0.105  -0.394  -0.393  -0.323
48    A        -1.742  -1.668  -1.617  -1.713  -1.589  -1.520  -1.223  -1.153  -1.065
49    K        -0.128  -0.104  -0.049  -0.258  -0.222  -0.150  -0.394  -0.371  -0.305
50    E        -0.774  -0.839  -0.912  -0.551  -0.635  -0.746  -0.631  -0.699  -0.755
51    Q        -0.774  -0.785  -0.877  -0.429  -0.468  -0.598  -0.631  -0.640  -0.719
52    A        -0.774  -0.744  -0.886  -0.838  -0.798  -0.961  -0.631  -0.598  -0.728
53    K         0.132   0.055   0.048   0.053  -0.043  -0.083  -0.039  -0.141  -0.172
54    M        -0.530  -0.533  -0.513  -0.787  -0.803  -0.714  -0.631  -0.619  -0.570
55    E        -0.128  -0.034  -0.039  -0.529  -0.347  -0.441  -0.394  -0.261  -0.289
56    E        -0.530  -0.435  -0.506  -0.870  -0.730  -0.799  -0.631  -0.529  -0.563
57    Q        -0.975  -0.986  -0.954  -0.969  -1.011  -0.997  -0.868  -0.860  -0.800
58    A        -0.975  -1.013  -0.969  -1.129  -1.123  -1.038  -0.868  -0.893  -0.817
59    K        -0.652  -0.593  -0.566  -0.918  -0.902  -0.784  -0.749  -0.691  -0.625
60    T        -0.451  -0.432  -0.478  -0.529  -0.497  -0.605  -0.513  -0.496  -0.527
61    H        -1.419  -1.342  -1.320  -1.297  -1.243  -1.144  -1.105  -1.028  -0.963
62    A        -0.451  -0.450  -0.508  -0.691  -0.700  -0.729  -0.513  -0.514  -0.562
63    K         0.439   0.307   0.174   0.546   0.388   0.207   0.435   0.243   0.031
64    E        -0.975  -0.938  -0.930  -0.782  -0.728  -0.716  -0.868  -0.823  -0.781
65    V        -1.742  -1.673  -1.617  -1.614  -1.585  -1.451  -1.223  -1.157  -1.065
66    K        -0.191  -0.383  -0.446   0.014  -0.228  -0.310  -0.157  -0.395  -0.474
67    L        -0.191  -0.383  -0.446  -0.031  -0.288  -0.381  -0.157  -0.395  -0.474
68    Q        -0.975  -0.872  -0.920  -0.818  -0.655  -0.739  -0.868  -0.748  -0.771
69    K        -1.096  -1.113  -0.997  -1.193  -1.152  -0.993  -0.986  -0.978  -0.842
70    V         0.577   0.575   0.665   0.414   0.399   0.526   0.198   0.173   0.288
71    T        -1.419  -1.461  -1.349  -1.137  -1.183  -1.022  -1.105  -1.118  -0.984
72    E        -0.207  -0.190  -0.087  -0.470  -0.443  -0.292  -0.513  -0.488  -0.358
73    F        -1.099  -1.091  -1.021  -1.202  -1.200  -1.022  -0.973  -0.957  -0.861
74    L         0.439   0.307   0.174   0.484   0.317   0.100   0.435   0.243   0.031
75    S        -1.419  -1.430  -1.325  -1.153  -1.173  -1.017  -1.105  -1.095  -0.967
76    M        -0.975  -0.942  -0.932  -1.051  -1.006  -0.949  -0.868  -0.829  -0.782
77    E        -0.451  -0.476  -0.489  -0.405  -0.426  -0.446  -0.513  -0.517  -0.531
78    L         0.439   0.307   0.174   0.445   0.255   0.022   0.435   0.243   0.031
79    A        -0.191  -0.158  -0.392  -0.366  -0.327  -0.652  -0.157  -0.120  -0.407
80    K        -1.096  -1.061  -0.992  -1.302  -1.213  -1.140  -0.986  -0.940  -0.839
81    D        -0.975  -1.058  -0.979  -0.630  -0.756  -0.651  -0.868  -0.924  -0.824
82    P         0.439   0.275   0.147   0.709   0.509   0.326   0.435   0.198  -0.011
83    I        -0.451  -0.472  -0.486  -0.290  -0.310  -0.349  -0.513  -0.530  -0.534
84    P         1.809   1.846   1.940   1.840   1.894   2.033   1.974   2.024   2.185
85    S        -0.530  -0.438  -0.505  -0.486  -0.365  -0.468  -0.631  -0.532  -0.562
86    D        -0.451  -0.567  -0.514  -0.189  -0.343  -0.275  -0.513  -0.633  -0.567
87    P        -1.096  -1.131  -1.002  -1.180  -1.196  -1.020  -0.986  -0.994  -0.846
88    S        -0.975  -1.061  -0.953  -0.773  -0.898  -0.757  -0.868  -0.927  -0.802
89    E         1.107   1.179   0.939   1.077   1.171   0.873   1.145   1.251   0.822
90    R         0.518   0.563   0.663   0.284   0.337   0.485   0.079   0.149   0.283
91    E         1.809   1.846   1.940   1.654   1.709   1.848   1.974   2.024   2.185
92    A        -0.774  -0.753  -0.869  -0.866  -0.866  -0.981  -0.631  -0.607  -0.710
93    T        -0.451  -0.426  -0.496  -0.151  -0.109  -0.221  -0.513  -0.473  -0.543
94    F         1.809   1.846   1.940   1.936   1.986   2.128   1.974   2.024   2.185
95    T        -0.652  -0.611  -0.578  -0.494  -0.477  -0.418  -0.749  -0.704  -0.639
96    T        -1.419  -1.372  -1.316  -1.369  -1.346  -1.247  -1.105  -1.053  -0.960
97    N         0.577   0.652   0.702   0.540   0.648   0.716   0.198   0.326   0.362
98    V         1.809   1.846   1.940   1.757   1.810   1.950   1.974   2.024   2.185
99    E        -0.530  -0.614  -0.542  -0.837  -0.920  -0.797  -0.631  -0.698  -0.601
100   N        -1.297  -1.349  -1.297  -1.115  -1.234  -1.133  -0.986  -1.024  -0.941
101   G         1.107   1.041   0.926   1.272   1.183   0.975   1.145   1.031   0.799
102   E         1.107   1.041   0.926   1.085   1.017   0.871   1.145   1.031   0.799
103   R        -0.975  -1.018  -0.971  -0.767  -0.840  -0.788  -0.868  -0.891  -0.817
104   L         0.439   0.453   0.192   0.523   0.550   0.200   0.435   0.445   0.057
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   S        -0.451  -0.508  -0.491  -0.640  -0.694  -0.643  -0.513  -0.559  -0.535
107   M        -0.975  -0.792  -0.930  -0.761  -0.508  -0.737  -0.868  -0.670  -0.778
108   Q        -1.419  -1.417  -1.334  -1.216  -1.244  -1.107  -1.105  -1.086  -0.973
109   Q         0.326   0.334   0.159   0.577   0.594   0.356   0.273   0.278   0.007
110   G        -0.062  -0.074  -0.007   0.034   0.026   0.126  -0.346  -0.345  -0.256
111   K        -1.297  -1.254  -1.260  -0.951  -0.893  -0.886  -0.986  -0.938  -0.909
112   E        -0.451  -0.426  -0.495  -0.649  -0.623  -0.762  -0.513  -0.486  -0.547
113   L        -0.062  -0.083  -0.020  -0.200  -0.211  -0.134  -0.346  -0.358  -0.272
114   E         0.439   0.275   0.147   0.542   0.353   0.190   0.435   0.198  -0.011
115   A         0.762   0.777   0.749   0.354   0.375   0.327   0.553   0.566   0.458
116   A         1.107   1.025   0.922   0.812   0.719   0.587   1.145   1.004   0.792
117   S        -0.652  -0.609  -0.559  -0.893  -0.837  -0.758  -0.749  -0.699  -0.619
118   K        -0.207  -0.208  -0.090  -0.361  -0.415  -0.256  -0.513  -0.511  -0.362
119   F         1.107   1.041   0.926   1.364   1.290   1.138   1.145   1.031   0.799
120   Y         1.809   1.846   1.940   1.872   1.920   2.065   1.974   2.024   2.185
121   K         1.107   1.077   0.943   1.104   1.080   0.902   1.145   1.089   0.830
122   A         1.809   1.846   1.940   1.393   1.446   1.588   1.974   2.024   2.185
123   L         1.809   1.846   1.940   1.672   1.725   1.866   1.974   2.024   2.185
124   T        -0.774  -0.726  -0.615  -1.017  -0.923  -0.774  -0.868  -0.809  -0.674
125   V         1.809   1.846   1.940   1.757   1.810   1.950   1.974   2.024   2.185
126   Y         1.809   1.846   1.940   1.872   1.920   2.065   1.974   2.024   2.185
127   P         1.809   1.846   1.940   1.840   1.894   2.033   1.974   2.024   2.185
128   Q        -0.451  -0.574  -0.518  -0.151  -0.327  -0.268  -0.513  -0.643  -0.571
129   P         1.809   1.846   1.940   1.840   1.894   2.033   1.974   2.024   2.185
130   A        -0.975  -1.000  -0.961  -0.913  -0.915  -0.884  -0.868  -0.874  -0.808
131   D         1.107   1.077   0.943   1.281   1.244   1.052   1.145   1.089   0.830
132   L         0.762   0.891   0.810   0.636   0.824   0.693   0.553   0.774   0.577
133   L         0.439   0.307   0.174   0.549   0.391   0.223   0.435   0.243   0.031
134   G         0.439   0.307   0.174   0.691   0.510   0.268   0.435   0.243   0.031
135   I         1.809   1.846   1.940   1.833   1.884   2.026   1.974   2.024   2.185
136   Y         1.809   1.846   1.940   1.872   1.920   2.065   1.974   2.024   2.185
137   Q         0.132   0.003   0.025   0.197  -0.016   0.005  -0.039  -0.226  -0.208
138   R         0.132   0.060   0.037   0.228   0.118   0.051  -0.039  -0.136  -0.190
139   S         0.577   0.582   0.670   0.472   0.465   0.590   0.198   0.188   0.297
140   I         0.439   0.542   0.198   0.588   0.723   0.255   0.435   0.580   0.067
141   P        -0.191  -0.304  -0.443   0.040  -0.149  -0.400  -0.157  -0.301  -0.471
142   E         0.439   0.275   0.147   0.486   0.277   0.079   0.435   0.198  -0.011
143   A        -0.530  -0.417  -0.509  -0.580  -0.394  -0.539  -0.631  -0.500  -0.565
144   I         0.762   0.891   0.810   0.766   0.961   0.812   0.553   0.774   0.577
145   Y         0.132   0.024   0.025   0.263   0.074   0.085  -0.039  -0.207  -0.207
146   E         0.439   0.307   0.174   0.542   0.391   0.228   0.435   0.243   0.031
147   Y        -0.652  -0.586  -0.558  -0.603  -0.525  -0.450  -0.749  -0.670  -0.616
148   I        -0.207  -0.205  -0.088  -0.367  -0.383  -0.219  -0.513  -0.507  -0.359
149   I        -0.774  -0.906  -0.917  -0.592  -0.832  -0.869  -0.631  -0.768  -0.760
150   L        -0.975  -1.058  -0.979  -0.908  -1.060  -0.964  -0.868  -0.924  -0.824
151   M         1.809   1.846   1.940   1.981   2.033   2.174   1.974   2.024   2.185
152   I         1.107   1.077   0.943   1.256   1.225   1.053   1.145   1.089   0.830
153   A         1.107   1.041   0.926   0.812   0.739   0.592   1.145   1.031   0.799
154   I        -1.078  -1.117  -1.011  -1.068  -1.157  -1.020  -0.964  -0.983  -0.853
155   L        -1.447  -1.433  -1.351  -0.976  -0.974  -0.870  -1.119  -1.096  -0.985
156   P         1.045   0.961   0.896   1.199   1.099   1.003   1.046   0.896   0.744
157   P         1.045   0.942   0.894   1.192   1.064   0.984   1.046   0.863   0.738
158   A        -0.340  -0.469  -0.499  -0.608  -0.816  -0.851  -0.346  -0.508  -0.539
159   N        -0.570  -0.588  -0.556  -0.488  -0.524  -0.549  -0.655  -0.673  -0.614
160   V         0.326   0.136   0.096   0.449   0.183   0.098   0.273  -0.007  -0.087
161   A        -0.939  -0.986  -0.948  -0.791  -0.879  -0.865  -0.810  -0.856  -0.792
162   S        -0.570  -0.581  -0.539  -0.510  -0.576  -0.491  -0.655  -0.667  -0.597
163   F        -0.570  -0.653  -0.565  -0.299  -0.396  -0.286  -0.655  -0.728  -0.620
164   V        -0.340  -0.331  -0.458  -0.223  -0.213  -0.387  -0.346  -0.339  -0.489
165   K        -1.078  -0.976  -0.975  -0.769  -0.642  -0.627  -0.964  -0.863  -0.822
166   G         0.029   0.090   0.017  -0.068  -0.005  -0.169  -0.191  -0.122  -0.218
167   V        -0.570  -0.560  -0.543  -0.666  -0.626  -0.655  -0.655  -0.630  -0.598
168   V        -0.709  -0.712  -0.588  -0.942  -0.926  -0.769  -0.810  -0.795  -0.649
169   G        -1.078  -0.967  -0.982  -1.101  -0.889  -0.934  -0.964  -0.846  -0.828
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   S        -0.673  -0.635  -0.581  -0.495  -0.464  -0.379  -0.754  -0.710  -0.636
174   K         0.877   0.970   0.837   0.480   0.610   0.411   0.761   0.911   0.631
175   A        -0.156  -0.184  -0.058  -0.533  -0.561  -0.383  -0.451  -0.480  -0.320
176   E        -0.156  -0.184  -0.056  -0.703  -0.718  -0.549  -0.451  -0.479  -0.317
177   S        -0.673  -0.680  -0.594  -0.543  -0.533  -0.440  -0.754  -0.760  -0.651
178   D        -0.668  -0.686  -0.579  -0.786  -0.801  -0.685  -0.763  -0.772  -0.637
179   A        -1.099  -1.081  -1.010  -1.398  -1.376  -1.246  -0.973  -0.948  -0.851
180   V        -0.939  -0.910  -0.966  -0.784  -0.720  -0.827  -0.810  -0.778  -0.809
181   A        -0.709  -0.658  -0.587  -1.005  -0.971  -0.851  -0.810  -0.748  -0.647
182   E        -0.340  -0.201  -0.433  -0.211  -0.003  -0.413  -0.346  -0.165  -0.458
183   A        -1.078  -1.033  -0.988  -1.289  -1.240  -1.143  -0.964  -0.909  -0.832
184   N        -1.096  -1.026  -0.988  -1.219  -1.102  -1.045  -0.986  -0.911  -0.835
185   D        -0.451  -0.521  -0.521  -0.233  -0.351  -0.356  -0.513  -0.600  -0.576
186   I        -0.128  -0.001  -0.003  -0.244  -0.037  -0.073  -0.394  -0.210  -0.236
187   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   D         0.518   0.550   0.658   0.279   0.317   0.478   0.079   0.124   0.273
* 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/P35180
Output conservation file - output/P35180
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
