1     M         1.778   1.790   1.919   2.001   2.016   2.216   1.959   1.975   2.189
2     L        -0.597  -0.618  -0.552  -0.596  -0.633  -0.532  -0.712  -0.716  -0.610
3     R        -0.065  -0.074  -0.015  -0.176  -0.164  -0.105  -0.348  -0.342  -0.256
4     T        -1.048  -0.983  -0.976  -0.862  -0.762  -0.755  -0.955  -0.888  -0.829
5     T        -1.048  -0.996  -0.984  -1.245  -1.158  -1.172  -0.955  -0.896  -0.835
6     R        -1.172  -1.115  -1.026  -1.123  -1.053  -0.931  -1.076  -1.016  -0.877
7     L        -1.154  -1.036  -1.017  -1.124  -0.934  -0.944  -1.054  -0.941  -0.866
8     W        -1.012  -1.018  -1.002  -0.675  -0.698  -0.711  -0.895  -0.897  -0.847
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    T         0.387   0.366   0.147   0.389   0.382   0.108   0.381   0.347   0.008
14    T        -0.720  -0.667  -0.589  -0.982  -0.858  -0.770  -0.833  -0.754  -0.647
15    R         1.065   1.018   0.901   1.348   1.293   1.147   1.109   1.029   0.786
16    M        -1.172  -1.117  -1.026  -1.033  -0.970  -0.818  -1.076  -1.019  -0.877
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -0.638  -0.663  -0.571  -0.784  -0.811  -0.670  -0.737  -0.754  -0.629
35    -        -0.638  -0.599  -0.570  -0.704  -0.654  -0.577  -0.737  -0.697  -0.628
36    P         0.527   0.575   0.668   0.308   0.409   0.501   0.138   0.225   0.327
37    T        -0.516  -0.469  -0.528  -0.547  -0.517  -0.576  -0.590  -0.553  -0.579
38    V        -0.253  -0.238  -0.445  -0.112  -0.087  -0.353  -0.226  -0.209  -0.465
39    S        -1.012  -1.066  -1.001  -1.066  -1.154  -1.055  -0.895  -0.945  -0.846
40    K        -1.154  -1.140  -1.034  -1.079  -1.083  -0.923  -1.054  -1.027  -0.880
41    L        -0.404  -0.494  -0.524  -0.372  -0.501  -0.559  -0.419  -0.531  -0.562
42    F        -0.253  -0.238  -0.445   0.028   0.046  -0.321  -0.226  -0.209  -0.465
43    L        -0.638  -0.696  -0.598  -0.543  -0.590  -0.427  -0.737  -0.793  -0.658
44    R        -0.404  -0.534  -0.538  -0.020  -0.213  -0.241  -0.419  -0.581  -0.580
45    N        -1.828  -1.794  -1.667  -1.446  -1.419  -1.205  -1.319  -1.280  -1.115
46    S        -1.376  -1.386  -1.342  -1.076  -1.101  -1.109  -1.076  -1.077  -0.987
47    S        -0.253  -0.343  -0.460  -0.210  -0.321  -0.475  -0.226  -0.340  -0.484
48    G        -1.500  -1.495  -1.371  -1.423  -1.408  -1.222  -1.197  -1.177  -1.013
49    N        -0.404  -0.526  -0.538  -0.087  -0.272  -0.318  -0.419  -0.572  -0.580
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    A        -1.048  -1.073  -1.007  -1.034  -1.058  -0.947  -0.955  -0.972  -0.858
52    L         0.714   0.677   0.703   0.575   0.523   0.539   0.502   0.425   0.399
53    N        -0.844  -0.965  -0.965  -0.539  -0.738  -0.794  -0.712  -0.839  -0.810
54    K        -0.844  -0.818  -0.915  -0.481  -0.450  -0.574  -0.712  -0.685  -0.759
55    N        -1.154  -1.165  -1.041  -1.175  -1.166  -0.978  -1.054  -1.050  -0.887
56    K        -0.638  -0.602  -0.572  -0.638  -0.574  -0.505  -0.737  -0.678  -0.624
57    L        -1.012  -1.083  -1.019  -0.910  -1.014  -0.903  -0.895  -0.964  -0.864
58    P         0.075   0.082   0.015   0.111   0.100  -0.040  -0.105  -0.109  -0.205
59    F        -0.516  -0.557  -0.545  -0.344  -0.413  -0.403  -0.590  -0.634  -0.598
60    L        -0.516  -0.452  -0.512  -0.503  -0.395  -0.531  -0.590  -0.493  -0.553
61    Y        -0.253  -0.148  -0.425   0.159   0.275  -0.089  -0.226  -0.100  -0.440
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    S        -0.253  -0.287  -0.454  -0.182  -0.217  -0.419  -0.226  -0.270  -0.476
64    S        -1.828  -1.781  -1.675  -1.779  -1.721  -1.548  -1.319  -1.273  -1.120
65    Q        -1.376  -1.246  -1.308  -1.119  -0.923  -1.053  -1.076  -0.948  -0.958
66    G         0.137   0.019   0.007   0.239   0.073   0.029   0.017  -0.162  -0.204
67    P         1.778   1.790   1.919   1.859   1.876   2.076   1.959   1.975   2.189
68    Q        -1.528  -1.523  -1.388  -1.388  -1.407  -1.215  -1.212  -1.197  -1.025
69    A        -1.154  -1.163  -1.032  -1.360  -1.374  -1.203  -1.054  -1.049  -0.879
70    V        -0.404  -0.521  -0.538  -0.364  -0.532  -0.571  -0.419  -0.565  -0.580
71    R         0.387   0.381   0.146   0.648   0.637   0.362   0.381   0.369   0.008
72    Y         0.467   0.490   0.632   0.424   0.459   0.668   0.017   0.054   0.252
73    T         1.778   1.790   1.919   1.743   1.764   1.962   1.959   1.975   2.189
74    S        -1.048  -1.011  -0.988  -1.200  -1.119  -1.068  -0.955  -0.907  -0.837
75    Q        -0.269  -0.250  -0.111  -0.475  -0.467  -0.267  -0.590  -0.560  -0.379
76    H         1.778   1.790   1.919   1.967   1.985   2.183   1.959   1.975   2.189
77    E         1.065   1.025   0.894   0.931   0.887   0.719   1.109   1.040   0.773
78    W         1.778   1.790   1.919   2.016   2.033   2.230   1.959   1.975   2.189
79    I         0.467   0.487   0.631   0.176   0.203   0.419   0.017   0.048   0.250
80    A        -0.253  -0.361  -0.470  -0.163  -0.320  -0.474  -0.226  -0.363  -0.496
81    V        -0.844  -0.806  -0.653  -1.071  -1.008  -0.788  -0.955  -0.906  -0.715
82    H        -0.844  -0.909  -0.951  -0.381  -0.489  -0.575  -0.712  -0.780  -0.796
83    Q        -1.828  -1.741  -1.667  -1.550  -1.440  -1.336  -1.319  -1.242  -1.115
84    D         1.778   1.790   1.919   1.785   1.802   2.004   1.959   1.975   2.189
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    K        -0.263  -0.256  -0.118  -0.403  -0.397  -0.195  -0.578  -0.569  -0.389
87    T        -0.269  -0.265  -0.119  -0.675  -0.663  -0.457  -0.590  -0.581  -0.391
88    A         0.075   0.058   0.012  -0.063  -0.109  -0.178  -0.105  -0.151  -0.209
89    F         0.387   0.277   0.136   0.710   0.569   0.365   0.381   0.221  -0.008
90    V        -0.189  -0.112  -0.073  -0.434  -0.309  -0.270  -0.469  -0.356  -0.323
91    G         1.778   1.790   1.919   1.758   1.777   1.977   1.959   1.975   2.189
92    I         1.778   1.790   1.919   1.847   1.867   2.064   1.959   1.975   2.189
93    T         1.065   1.002   0.900   1.101   1.024   0.855   1.109   1.004   0.784
94    K        -0.189  -0.207  -0.099  -0.291  -0.344  -0.197  -0.469  -0.498  -0.362
95    Y         1.778   1.790   1.919   1.926   1.945   2.143   1.959   1.975   2.189
96    A         1.778   1.790   1.919   1.636   1.653   1.857   1.959   1.975   2.189
97    T         0.387   0.467   0.159   0.382   0.489   0.040   0.381   0.494   0.027
98    D        -1.048  -1.109  -1.012  -0.954  -1.038  -0.887  -0.955  -1.000  -0.861
99    A         1.778   1.790   1.919   1.636   1.653   1.857   1.959   1.975   2.189
100   L         1.778   1.790   1.919   1.652   1.677   1.873   1.959   1.975   2.189
101   G         1.778   1.790   1.919   1.758   1.777   1.977   1.959   1.975   2.189
102   D         0.714   0.712   0.714   0.606   0.595   0.529   0.502   0.490   0.422
103   A         0.527   0.510   0.637   0.142   0.094   0.283   0.138   0.094   0.264
104   T         0.714   0.656   0.704   0.594   0.487   0.514   0.502   0.384   0.400
105   Y         0.527   0.611   0.683   0.531   0.671   0.762   0.138   0.296   0.359
106   V         1.065   1.148   0.907   1.037   1.133   0.850   1.109   1.235   0.797
107   E         1.065   1.061   0.896   0.931   0.931   0.722   1.109   1.098   0.777
108   L         0.387   0.416   0.147   0.430   0.468   0.093   0.381   0.418   0.008
109   P         1.065   1.025   0.894   1.223   1.172   0.960   1.109   1.040   0.773
110   E         1.065   1.190   0.913   0.931   1.082   0.747   1.109   1.298   0.808
111   V        -0.516  -0.587  -0.542  -0.661  -0.770  -0.719  -0.590  -0.662  -0.595
112   G         0.075   0.132   0.061   0.046   0.146   0.001  -0.105  -0.001  -0.126
113   T        -0.516  -0.582  -0.551  -0.428  -0.509  -0.460  -0.590  -0.656  -0.603
114   E         0.075   0.063   0.016  -0.096  -0.108  -0.150  -0.105  -0.125  -0.202
115   I        -0.189  -0.143  -0.085  -0.434  -0.358  -0.290  -0.469  -0.403  -0.340
116   A        -0.516  -0.522  -0.531  -0.743  -0.733  -0.756  -0.590  -0.592  -0.582
117   Q        -1.048  -1.049  -0.996  -1.096  -1.107  -1.001  -0.955  -0.948  -0.847
118   G         0.387   0.336   0.135   0.568   0.506   0.235   0.381   0.306  -0.010
119   E         0.527   0.557   0.653   0.226   0.283   0.384   0.138   0.190   0.297
120   S        -0.516  -0.589  -0.559  -0.716  -0.826  -0.778  -0.590  -0.678  -0.616
121   L        -0.720  -0.653  -0.599  -0.773  -0.679  -0.592  -0.833  -0.759  -0.661
122   G         1.065   1.148   0.907   1.117   1.226   0.882   1.109   1.235   0.797
123   S         0.075  -0.009   0.001  -0.138  -0.265  -0.244  -0.105  -0.234  -0.225
124   I         1.065   1.117   0.901   1.037   1.098   0.842   1.109   1.187   0.786
125   E         1.778   1.790   1.919   1.540   1.561   1.762   1.959   1.975   2.189
126   S         1.778   1.790   1.919   1.556   1.583   1.778   1.959   1.975   2.189
127   V         1.778   1.790   1.919   1.636   1.651   1.857   1.959   1.975   2.189
128   K         1.778   1.790   1.919   1.801   1.812   2.019   1.959   1.975   2.189
129   S         1.065   1.025   0.894   0.925   0.884   0.688   1.109   1.040   0.773
130   A         0.387   0.336   0.135   0.382   0.315  -0.001   0.381   0.306  -0.010
131   S         0.075   0.007   0.001  -0.138  -0.235  -0.244  -0.105  -0.207  -0.225
132   E         0.467   0.501   0.638   0.060   0.145   0.342   0.017   0.077   0.265
133   I         0.527   0.540   0.641   0.332   0.348   0.462   0.138   0.155   0.273
134   Y         0.387   0.283   0.132   0.743   0.615   0.401   0.381   0.230  -0.013
135   Q        -0.516  -0.463  -0.530  -0.671  -0.617  -0.670  -0.590  -0.545  -0.582
136   P         1.778   1.790   1.919   1.866   1.885   2.083   1.959   1.975   2.189
137   A        -0.253  -0.190  -0.440  -0.187  -0.102  -0.471  -0.226  -0.149  -0.459
138   D        -0.269  -0.212  -0.102  -0.643  -0.548  -0.399  -0.590  -0.514  -0.369
139   G         0.387   0.283   0.132   0.616   0.496   0.321   0.381   0.230  -0.013
140   T        -0.065  -0.103  -0.028  -0.322  -0.373  -0.256  -0.348  -0.387  -0.276
141   V         1.065   1.111   0.909   1.037   1.090   0.853   1.109   1.177   0.800
142   E        -0.253  -0.316  -0.457  -0.200  -0.287  -0.519  -0.226  -0.308  -0.480
143   E        -0.516  -0.567  -0.550  -0.778  -0.860  -0.849  -0.590  -0.646  -0.604
144   I        -0.720  -0.684  -0.609  -0.937  -0.904  -0.767  -0.833  -0.798  -0.673
145   N         1.778   1.790   1.919   1.892   1.912   2.109   1.959   1.975   2.189
146   T        -1.048  -1.011  -0.989  -1.205  -1.145  -1.099  -0.955  -0.917  -0.841
147   N        -1.828  -1.837  -1.689  -1.787  -1.808  -1.596  -1.319  -1.310  -1.130
148   L         1.065   1.025   0.894   1.022   0.978   0.782   1.109   1.040   0.773
149   E        -0.253  -0.238  -0.435  -0.337  -0.314  -0.640  -0.226  -0.214  -0.453
150   E        -0.269  -0.244  -0.108  -0.693  -0.646  -0.455  -0.590  -0.554  -0.375
151   N        -0.844  -0.826  -0.932  -0.794  -0.769  -0.912  -0.712  -0.688  -0.776
152   P         1.778   1.790   1.919   1.866   1.885   2.083   1.959   1.975   2.189
153   G        -0.720  -0.743  -0.619  -0.737  -0.793  -0.628  -0.833  -0.848  -0.683
154   V        -0.844  -0.905  -0.951  -0.724  -0.807  -0.895  -0.712  -0.775  -0.796
155   V         0.075   0.065   0.013   0.096   0.077  -0.057  -0.105  -0.120  -0.209
156   N         0.714   0.712   0.714   0.716   0.709   0.634   0.502   0.490   0.422
157   E        -1.500  -1.422  -1.360  -1.463  -1.332  -1.254  -1.197  -1.123  -1.006
158   D        -0.253  -0.388  -0.471  -0.129  -0.347  -0.550  -0.226  -0.397  -0.498
159   P         1.778   1.790   1.919   1.866   1.885   2.083   1.959   1.975   2.189
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   M        -1.500  -1.490  -1.366  -1.339  -1.336  -1.176  -1.197  -1.176  -1.010
165   G        -0.253  -0.361  -0.470  -0.124  -0.293  -0.512  -0.226  -0.363  -0.496
166   D        -0.720  -0.697  -0.615  -0.873  -0.833  -0.683  -0.833  -0.808  -0.678
167   G         1.065   1.111   0.909   1.128   1.189   0.908   1.109   1.177   0.800
168   W         1.065   1.025   0.894   1.425   1.379   1.213   1.109   1.040   0.773
169   L         0.075   0.022   0.011   0.099   0.020  -0.053  -0.105  -0.175  -0.209
170   V        -0.516  -0.452  -0.517  -0.541  -0.456  -0.505  -0.590  -0.516  -0.565
171   K         0.387   0.414   0.150   0.648   0.679   0.366   0.381   0.418   0.014
172   M         0.075   0.066   0.009   0.162   0.112   0.047  -0.105  -0.140  -0.215
173   K         1.065   1.002   0.900   1.214   1.137   1.024   1.109   1.004   0.784
174   L        -0.253  -0.251  -0.440  -0.140  -0.145  -0.403  -0.226  -0.231  -0.459
175   G        -1.828  -1.825  -1.678  -1.611  -1.622  -1.445  -1.319  -1.303  -1.122
176   E        -0.597  -0.568  -0.544  -0.774  -0.743  -0.676  -0.712  -0.675  -0.604
177   G        -0.516  -0.477  -0.524  -0.376  -0.310  -0.408  -0.590  -0.549  -0.574
178   V        -1.376  -1.376  -1.336  -1.368  -1.366  -1.352  -1.076  -1.070  -0.982
179   N        -0.572  -0.510  -0.554  -0.602  -0.508  -0.548  -0.631  -0.556  -0.599
180   V        -0.263  -0.243  -0.115  -0.567  -0.533  -0.344  -0.578  -0.549  -0.385
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   E        -0.572  -0.572  -0.554  -0.764  -0.772  -0.741  -0.631  -0.629  -0.599
183   Q        -1.528  -1.529  -1.392  -1.317  -1.343  -1.166  -1.212  -1.202  -1.028
184   V        -1.154  -1.141  -1.022  -1.261  -1.230  -1.068  -1.054  -1.031  -0.870
185   E         0.387   0.448   0.167   0.334   0.409   0.051   0.381   0.459   0.039
186   G        -1.048  -1.019  -0.989  -1.126  -1.079  -1.069  -0.955  -0.923  -0.841
187   L         1.778   1.790   1.919   1.652   1.677   1.873   1.959   1.975   2.189
188   M         0.527   0.529   0.640   0.355   0.366   0.540   0.138   0.133   0.269
189   S        -0.516  -0.587  -0.542  -0.621  -0.695  -0.624  -0.590  -0.662  -0.595
190   L        -0.597  -0.629  -0.563  -0.886  -0.919  -0.817  -0.712  -0.727  -0.621
191   E         1.065   1.111   0.909   0.924   0.986   0.728   1.109   1.177   0.800
192   Q        -0.253  -0.388  -0.471   0.024  -0.184  -0.408  -0.226  -0.397  -0.498
193   Y         1.778   1.790   1.919   1.926   1.945   2.143   1.959   1.975   2.189
194   E        -0.516  -0.603  -0.560  -0.670  -0.794  -0.719  -0.590  -0.689  -0.616
195   K        -0.720  -0.626  -0.596  -0.864  -0.740  -0.672  -0.833  -0.734  -0.658
196   T        -0.844  -0.637  -0.895  -0.505  -0.214  -0.626  -0.712  -0.475  -0.738
197   L         0.387   0.277   0.136   0.485   0.357   0.180   0.381   0.221  -0.008
198   V        -1.048  -1.017  -0.973  -1.105  -1.064  -1.026  -0.955  -0.914  -0.826
199   H        -0.638  -0.650  -0.564  -0.695  -0.714  -0.578  -0.737  -0.734  -0.618
200   D         0.467   0.502   0.639   0.087   0.132   0.339   0.017   0.078   0.268
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   D         0.387   0.467   0.159   0.774   0.875   0.461   0.381   0.494   0.027
* 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/P39726
Output conservation file - output/P39726
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
