1     M         2.153   2.172   2.292   2.446   2.477   2.665   2.390   2.422   2.631
2     S        -0.739  -0.724  -0.693  -0.913  -0.899  -0.834  -0.729  -0.714  -0.662
3     E        -0.856  -0.836  -0.765  -1.101  -1.037  -0.977  -0.859  -0.836  -0.741
4     V        -0.739  -0.732  -0.721  -0.529  -0.540  -0.530  -0.729  -0.721  -0.694
5     A        -1.340  -1.325  -1.257  -1.449  -1.418  -1.335  -1.076  -1.058  -0.966
6     E        -0.739  -0.740  -0.700  -0.951  -0.939  -0.884  -0.729  -0.729  -0.670
7     T         0.090   0.100   0.027   0.179   0.178   0.061  -0.036  -0.025  -0.139
8     W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     V        -0.856  -0.839  -0.765  -0.820  -0.792  -0.689  -0.859  -0.838  -0.741
10    D         0.649   0.663   0.764   0.467   0.488   0.638   0.224   0.244   0.383
11    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    M        -1.235  -1.235  -1.218  -0.837  -0.865  -0.823  -0.979  -0.979  -0.932
14    A        -1.235  -1.208  -1.190  -1.034  -0.996  -0.956  -0.979  -0.953  -0.905
15    K        -0.544  -0.487  -0.597  -0.187  -0.097  -0.275  -0.498  -0.429  -0.549
16    L        -0.733  -0.738  -0.696  -0.666  -0.669  -0.592  -0.739  -0.739  -0.672
17    V        -1.235  -1.235  -1.218  -1.071  -1.081  -1.029  -0.979  -0.979  -0.932
18    N        -1.235  -1.168  -1.190  -0.877  -0.810  -0.807  -0.979  -0.912  -0.905
19    Y        -0.232  -0.218  -0.128  -0.338  -0.319  -0.183  -0.498  -0.481  -0.363
20    D        -0.733  -0.725  -0.691  -0.815  -0.804  -0.758  -0.739  -0.726  -0.666
21    Y        -0.733  -0.674  -0.699  -0.492  -0.439  -0.420  -0.739  -0.677  -0.675
22    K        -1.235  -1.213  -1.201  -1.031  -1.002  -0.969  -0.979  -0.955  -0.916
23    H        -0.733  -0.766  -0.701  -0.585  -0.643  -0.551  -0.739  -0.767  -0.677
24    F        -0.733  -0.720  -0.698  -0.419  -0.395  -0.340  -0.739  -0.724  -0.673
25    I        -0.042  -0.020  -0.029  -0.082  -0.037  -0.055  -0.257  -0.221  -0.233
26    R         2.153   2.172   2.292   2.061   2.089   2.270   2.390   2.422   2.631
27    L         0.771   0.744   0.808   0.552   0.504   0.581   0.465   0.403   0.472
28    V        -0.733  -0.691  -0.697  -0.580  -0.522  -0.528  -0.739  -0.692  -0.672
29    I        -0.042  -0.063  -0.034  -0.026  -0.058  -0.022  -0.257  -0.291  -0.242
30    I         0.270   0.188   0.118   0.518   0.408   0.319   0.224   0.104  -0.003
31    V         2.153   2.172   2.292   2.290   2.322   2.505   2.390   2.422   2.631
32    G         1.175   1.181   1.058   1.470   1.475   1.351   1.187   1.195   0.956
33    G        -0.544  -0.496  -0.613  -0.134  -0.077  -0.221  -0.498  -0.438  -0.568
34    Y         2.153   2.172   2.292   2.320   2.350   2.536   2.390   2.422   2.631
35    L        -0.042  -0.070  -0.035   0.027   0.008   0.079  -0.257  -0.298  -0.244
36    L        -0.544  -0.515  -0.614  -0.331  -0.296  -0.398  -0.498  -0.462  -0.569
37    L        -0.733  -0.734  -0.692  -0.517  -0.525  -0.424  -0.739  -0.737  -0.668
38    R         2.153   2.172   2.292   2.061   2.089   2.270   2.390   2.422   2.631
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    N        -0.042  -0.071  -0.033   0.041  -0.023   0.026  -0.257  -0.301  -0.242
48    I         0.270   0.274   0.134   0.457   0.466   0.254   0.224   0.231   0.020
49    A        -0.733  -0.762  -0.710  -0.530  -0.565  -0.485  -0.739  -0.763  -0.686
50    S        -0.544  -0.617  -0.624  -0.369  -0.517  -0.531  -0.498  -0.586  -0.581
51    R         0.270   0.329   0.118   0.249   0.342  -0.019   0.224   0.309  -0.003
52    E        -0.544  -0.496  -0.613  -0.632  -0.578  -0.693  -0.498  -0.438  -0.568
53    L        -0.733  -0.762  -0.710  -0.658  -0.666  -0.593  -0.739  -0.763  -0.686
54    A        -1.235  -1.242  -1.210  -1.040  -1.050  -1.010  -0.979  -0.984  -0.925
55    K         0.270   0.338   0.149   0.300   0.405   0.111   0.224   0.322   0.043
56    K        -0.232  -0.217  -0.130  -0.453  -0.424  -0.308  -0.498  -0.479  -0.366
57    Q         1.175   1.089   1.054   1.277   1.157   1.090   1.187   1.039   0.949
58    L         0.270   0.329   0.118   0.371   0.454   0.175   0.224   0.309  -0.003
59    A        -0.042  -0.089  -0.029  -0.257  -0.335  -0.286  -0.257  -0.311  -0.235
60    A        -1.235  -1.239  -1.204  -0.944  -0.942  -0.876  -0.979  -0.982  -0.919
61    Q         1.175   1.089   1.054   1.225   1.091   1.003   1.187   1.039   0.949
62    V        -0.042   0.005  -0.029  -0.037   0.023  -0.040  -0.257  -0.204  -0.237
63    E        -0.137  -0.128  -0.071  -0.558  -0.538  -0.472  -0.383  -0.370  -0.291
64    K        -0.104  -0.069  -0.047  -0.252  -0.192  -0.197  -0.318  -0.268  -0.247
65    D         1.067   1.091   0.999   0.896   0.925   0.732   1.004   1.042   0.847
66    K        -0.042  -0.077  -0.015  -0.455  -0.489  -0.405  -0.257  -0.292  -0.215
67    R        -0.733  -0.762  -0.690  -0.929  -0.955  -0.880  -0.739  -0.763  -0.666
68    D        -0.733  -0.762  -0.710  -1.166  -1.218  -1.139  -0.739  -0.763  -0.686
69    K        -0.042  -0.063  -0.034  -0.246  -0.288  -0.243  -0.257  -0.291  -0.242
70    E        -1.235  -1.242  -1.210  -1.314  -1.284  -1.247  -0.979  -0.984  -0.925
71    E         1.175   1.162   1.057   0.880   0.865   0.713   1.187   1.164   0.954
72    K        -0.544  -0.617  -0.624  -0.495  -0.584  -0.631  -0.498  -0.586  -0.581
73    R        -0.544  -0.564  -0.626  -0.303  -0.340  -0.384  -0.498  -0.524  -0.583
74    S        -0.733  -0.734  -0.692  -0.795  -0.787  -0.725  -0.739  -0.737  -0.668
75    K         0.090   0.023   0.023   0.032  -0.062  -0.081  -0.036  -0.137  -0.144
76    D        -0.137  -0.094  -0.074  -0.470  -0.382  -0.362  -0.383  -0.329  -0.294
77    L        -1.235  -1.252  -1.212  -1.310  -1.318  -1.301  -0.979  -0.994  -0.927
78    I        -1.736  -1.715  -1.659  -1.485  -1.419  -1.372  -1.220  -1.199  -1.116
79    D        -0.544  -0.555  -0.619  -0.837  -0.859  -0.970  -0.498  -0.515  -0.575
80    K        -1.235  -1.239  -1.204  -1.259  -1.298  -1.231  -0.979  -0.982  -0.919
81    P        -1.235  -1.252  -1.212  -0.695  -0.713  -0.670  -0.979  -0.994  -0.927
82    D        -0.544  -0.555  -0.619  -0.727  -0.741  -0.824  -0.498  -0.515  -0.575
83    D        -0.042  -0.084  -0.035  -0.376  -0.457  -0.414  -0.257  -0.303  -0.239
84    -         0.090   0.154   0.080   0.237   0.351   0.184  -0.036   0.054  -0.061
85    -        -0.137  -0.135  -0.066  -0.605  -0.588  -0.493  -0.383  -0.377  -0.285
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    A        -0.733  -0.716  -0.692  -0.909  -0.911  -0.839  -0.739  -0.714  -0.668
92    A        -1.235  -1.252  -1.212  -1.222  -1.278  -1.224  -0.979  -0.994  -0.927
93    T        -0.733  -0.679  -0.676  -0.900  -0.844  -0.813  -0.739  -0.683  -0.652
94    A        -0.733  -0.690  -0.687  -0.555  -0.471  -0.480  -0.739  -0.691  -0.663
95    E        -1.235  -1.249  -1.199  -1.176  -1.156  -1.088  -0.979  -0.990  -0.914
96    T        -0.733  -0.773  -0.711  -0.598  -0.666  -0.565  -0.739  -0.773  -0.687
97    T        -0.733  -0.736  -0.691  -0.606  -0.607  -0.550  -0.739  -0.736  -0.667
98    S         0.649   0.668   0.766   0.194   0.196   0.340   0.224   0.254   0.389
99    F         1.175   1.191   1.067   1.489   1.512   1.359   1.187   1.211   0.974
100   G         1.175   1.089   1.054   1.379   1.250   1.196   1.187   1.039   0.949
101   W         2.153   2.172   2.292   2.468   2.499   2.687   2.390   2.422   2.631
102   G         2.153   2.172   2.292   2.283   2.305   2.498   2.390   2.422   2.631
103   K         0.270   0.173   0.106   0.412   0.296   0.211   0.224   0.083  -0.022
104   K         0.270   0.173   0.106   0.314   0.184   0.061   0.224   0.083  -0.022
105   T         1.175   1.089   1.054   1.414   1.298   1.243   1.187   1.039   0.949
106   R         2.153   2.172   2.292   2.061   2.089   2.270   2.390   2.422   2.631
107   R        -0.733  -0.698  -0.690  -0.706  -0.653  -0.633  -0.739  -0.701  -0.666
108   R         0.771   0.809   0.837   0.663   0.718   0.757   0.465   0.530   0.530
109   V         1.175   1.089   1.054   1.411   1.296   1.243   1.187   1.039   0.949
110   K         1.175   1.089   1.054   1.150   1.039   0.966   1.187   1.039   0.949
111   R        -0.733  -0.691  -0.697  -0.874  -0.811  -0.824  -0.739  -0.692  -0.672
112   Q         1.175   1.181   1.058   1.329   1.341   1.182   1.187   1.195   0.956
113   Q        -0.042  -0.074  -0.019  -0.443  -0.494  -0.413  -0.257  -0.287  -0.217
114   E         0.270   0.329   0.118   0.052   0.129  -0.160   0.224   0.309  -0.003
115   L        -0.137  -0.101  -0.072  -0.237  -0.191  -0.134  -0.383  -0.340  -0.292
116   F         1.067   1.142   1.016   1.027   1.127   0.966   1.004   1.130   0.879
117   E         0.090   0.119   0.020  -0.212  -0.170  -0.330  -0.036   0.005  -0.149
118   N        -1.340  -1.325  -1.257  -1.319  -1.319  -1.201  -1.076  -1.058  -0.966
119   A        -0.137  -0.135  -0.076  -0.451  -0.448  -0.360  -0.383  -0.378  -0.296
120   L        -0.739  -0.732  -0.721  -0.617  -0.609  -0.610  -0.729  -0.721  -0.694
121   E         0.270   0.259   0.130   0.002  -0.019  -0.217   0.224   0.208   0.015
122   E        -1.235  -1.239  -1.204  -1.289  -1.272  -1.261  -0.979  -0.982  -0.919
123   A        -0.544  -0.543  -0.590  -0.421  -0.411  -0.481  -0.498  -0.501  -0.541
124   K        -0.042  -0.036  -0.027  -0.228  -0.203  -0.204  -0.257  -0.242  -0.228
125   R        -0.733  -0.773  -0.711  -0.804  -0.853  -0.784  -0.739  -0.773  -0.687
126   R        -0.544  -0.617  -0.624  -0.294  -0.397  -0.370  -0.498  -0.586  -0.581
127   N        -1.235  -1.249  -1.199  -0.973  -1.033  -0.948  -0.979  -0.990  -0.914
128   Q         0.270   0.173   0.106   0.422   0.279   0.154   0.224   0.083  -0.022
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -         0.933   0.977   0.933   1.044   1.114   1.039   0.766   0.841   0.721
133   G        -0.544  -0.624  -0.622  -0.110  -0.221  -0.203  -0.498  -0.593  -0.579
134   L        -0.042  -0.016  -0.027  -0.058  -0.020  -0.015  -0.257  -0.218  -0.227
135   D         1.175   1.191   1.067   1.172   1.189   1.038   1.187   1.211   0.974
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   P        -0.042  -0.013  -0.018   0.128   0.172   0.186  -0.257  -0.213  -0.216
139   D        -0.544  -0.515  -0.614  -0.614  -0.584  -0.763  -0.498  -0.462  -0.569
140   S        -0.232  -0.212  -0.128  -0.655  -0.636  -0.510  -0.498  -0.472  -0.364
141   D         2.153   2.172   2.292   2.029   2.053   2.237   2.390   2.422   2.631
142   A        -0.733  -0.701  -0.687  -0.891  -0.881  -0.815  -0.739  -0.703  -0.663
143   D         1.175   1.191   1.067   1.068   1.085   0.869   1.187   1.211   0.974
144   I         2.153   2.172   2.292   2.184   2.215   2.397   2.390   2.422   2.631
145   E         1.175   1.181   1.058   0.852   0.857   0.667   1.187   1.195   0.956
146   E         0.649   0.663   0.764   0.029   0.038   0.187   0.224   0.244   0.383
147   L         1.175   1.089   1.054   1.219   1.121   1.090   1.187   1.039   0.949
148   L         2.153   2.172   2.292   2.037   2.071   2.246   2.390   2.422   2.631
149   E         1.175   1.162   1.057   0.885   0.868   0.721   1.187   1.164   0.954
150   E         1.175   1.285   1.091   1.068   1.220   0.910   1.187   1.364   1.016
* 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/P53903
Output conservation file - output/P53903
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
