1     M         1.307   1.318   1.408   1.523   1.542   1.668   1.399   1.415   1.551
2     P        -0.104  -0.096  -0.300   0.122   0.132  -0.172  -0.157  -0.143  -0.445
3     R        -0.420  -0.368  -0.376  -0.810  -0.739  -0.696  -0.659  -0.582  -0.562
4     I         0.003  -0.011  -0.268   0.121   0.106  -0.266  -0.009  -0.028  -0.399
5     K        -0.420  -0.424  -0.383  -0.747  -0.771  -0.673  -0.659  -0.665  -0.573
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     T        -0.738  -0.779  -0.846  -0.555  -0.617  -0.743  -0.723  -0.773  -0.832
8     R        -0.956  -0.932  -0.891  -1.064  -1.063  -0.957  -1.006  -0.985  -0.885
9     R        -0.473  -0.457  -0.398  -0.841  -0.829  -0.697  -0.723  -0.701  -0.592
10    S        -1.089  -1.068  -0.922  -1.110  -1.081  -0.873  -1.148  -1.124  -0.917
11    K         0.580   0.492   0.393   0.337   0.218   0.100   0.550   0.408   0.196
12    P        -1.307  -1.283  -1.252  -1.179  -1.139  -1.173  -1.148  -1.117  -1.041
13    A         0.246   0.287   0.293   0.225   0.289   0.257  -0.016   0.054   0.009
14    P         1.307   1.318   1.408   1.377   1.389   1.530   1.399   1.415   1.551
15    D        -0.387  -0.356  -0.370  -0.437  -0.380  -0.414  -0.582  -0.531  -0.549
16    G         1.307   1.318   1.408   1.353   1.367   1.507   1.399   1.415   1.551
17    F         0.134   0.108   0.240   0.157   0.098   0.271  -0.226  -0.279  -0.094
18    E        -1.034  -1.030  -0.905  -1.041  -1.041  -0.861  -1.093  -1.088  -0.900
19    K        -0.843  -0.846  -0.855  -1.068  -1.074  -1.056  -0.876  -0.874  -0.846
20    I         0.639   0.592   0.425   0.700   0.646   0.428   0.641   0.569   0.254
21    K        -0.289  -0.197  -0.344  -0.394  -0.257  -0.528  -0.442  -0.323  -0.514
22    P         0.003   0.028  -0.280   0.247   0.280  -0.183  -0.009   0.027  -0.416
23    T        -0.596  -0.620  -0.805  -0.331  -0.359  -0.642  -0.551  -0.577  -0.784
24    L         1.307   1.318   1.408   1.214   1.230   1.376   1.399   1.415   1.551
25    T        -2.071  -2.055  -1.865  -1.805  -1.776  -1.544  -1.526  -1.507  -1.275
26    D        -0.843  -0.797  -0.855  -0.987  -0.962  -1.018  -0.876  -0.838  -0.846
27    F         0.003  -0.077  -0.286   0.364   0.262  -0.104  -0.009  -0.120  -0.424
28    E        -1.764  -1.779  -1.601  -1.666  -1.686  -1.440  -1.418  -1.421  -1.192
29    I        -1.457  -1.465  -1.291  -1.328  -1.331  -1.087  -1.309  -1.307  -1.078
30    Q        -0.536  -0.493  -0.421  -0.923  -0.865  -0.732  -0.768  -0.707  -0.615
31    L        -0.289  -0.257  -0.352  -0.272  -0.226  -0.344  -0.442  -0.391  -0.524
32    R         0.134   0.175   0.255  -0.359  -0.295  -0.160  -0.226  -0.153  -0.064
33    D        -0.918  -0.943  -0.870  -0.901  -0.935  -0.812  -0.984  -1.002  -0.866
34    A         0.310   0.304   0.297   0.256   0.249   0.187   0.099   0.086   0.017
35    Q        -0.289  -0.295  -0.349  -0.243  -0.230  -0.357  -0.442  -0.437  -0.519
36    K        -1.341  -1.364  -1.270  -1.336  -1.372  -1.242  -1.201  -1.216  -1.060
37    D        -1.764  -1.766  -1.605  -1.646  -1.641  -1.461  -1.418  -1.412  -1.195
38    K        -0.918  -0.893  -0.876  -1.033  -0.994  -0.890  -0.984  -0.955  -0.871
39    S        -1.457  -1.482  -1.296  -1.353  -1.379  -1.127  -1.309  -1.320  -1.083
40    S        -1.341  -1.350  -1.264  -1.475  -1.488  -1.314  -1.201  -1.197  -1.054
41    K        -1.440  -1.441  -1.295  -1.538  -1.505  -1.292  -1.289  -1.282  -1.081
42    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    A        -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    A        -1.764  -1.705  -1.592  -1.830  -1.772  -1.583  -1.418  -1.369  -1.186
46    K        -1.648  -1.694  -1.583  -1.633  -1.693  -1.478  -1.309  -1.346  -1.178
47    S        -0.596  -0.538  -0.799  -0.685  -0.618  -0.930  -0.551  -0.481  -0.778
48    N        -1.341  -1.390  -1.261  -1.178  -1.258  -1.090  -1.201  -1.236  -1.052
49    E        -0.420  -0.476  -0.391  -0.538  -0.601  -0.467  -0.659  -0.715  -0.583
50    Q        -1.648  -1.597  -1.568  -1.323  -1.254  -1.230  -1.309  -1.259  -1.165
51    L         0.003   0.064  -0.268   0.023   0.104  -0.418  -0.009   0.075  -0.399
52    W         0.639   0.681   0.427   0.923   0.979   0.608   0.641   0.704   0.257
53    E        -1.648  -1.660  -1.576  -1.352  -1.381  -1.308  -1.309  -1.317  -1.172
54    I         0.639   0.684   0.428   0.700   0.755   0.433   0.641   0.708   0.260
55    M        -1.341  -1.338  -1.262  -0.973  -0.991  -0.882  -1.201  -1.199  -1.054
56    Q         0.639   0.646   0.424   0.775   0.793   0.459   0.641   0.652   0.253
57    L         0.134   0.145   0.246  -0.141  -0.126   0.009  -0.226  -0.209  -0.083
58    H        -0.289  -0.309  -0.362  -0.055  -0.098  -0.205  -0.442  -0.482  -0.538
59    H         0.003  -0.126  -0.280   0.370   0.201  -0.068  -0.009  -0.186  -0.415
60    Q        -0.289  -0.369  -0.353  -0.311  -0.439  -0.490  -0.442  -0.543  -0.525
61    R         0.310   0.265   0.295   0.208   0.132   0.139   0.099   0.015   0.012
62    S         0.003  -0.077  -0.286   0.197   0.092  -0.215  -0.009  -0.120  -0.424
63    R         1.307   1.318   1.408   1.265   1.286   1.424   1.399   1.415   1.551
64    Y         1.307   1.318   1.408   1.344   1.359   1.499   1.399   1.415   1.551
65    I         0.078   0.092   0.234  -0.097  -0.071   0.142  -0.334  -0.312  -0.104
66    Y         1.307   1.318   1.408   1.344   1.359   1.499   1.399   1.415   1.551
67    T        -1.457  -1.438  -1.291  -1.367  -1.338  -1.122  -1.309  -1.288  -1.079
68    L         0.003  -0.126  -0.280   0.114  -0.048  -0.248  -0.009  -0.186  -0.415
69    Y         0.639   0.684   0.428   0.799   0.853   0.538   0.641   0.708   0.260
70    Y         0.639   0.553   0.415   0.787   0.682   0.490   0.641   0.508   0.235
71    K        -0.289  -0.350  -0.365  -0.611  -0.690  -0.699  -0.442  -0.513  -0.542
72    R         0.134   0.123   0.240  -0.255  -0.293  -0.143  -0.226  -0.251  -0.093
73    K        -0.536  -0.535  -0.427  -0.866  -0.854  -0.735  -0.768  -0.768  -0.623
74    A         0.580   0.517   0.388   0.638   0.558   0.330   0.550   0.449   0.186
75    I         1.307   1.318   1.408   1.257   1.273   1.416   1.399   1.415   1.551
76    S         0.639   0.646   0.424   0.752   0.763   0.453   0.641   0.652   0.253
77    K        -0.843  -0.823  -0.851  -1.081  -1.057  -1.042  -0.876  -0.853  -0.841
78    D         0.003   0.106  -0.262   0.114   0.244  -0.245  -0.009   0.132  -0.390
79    L         1.307   1.318   1.408   1.214   1.230   1.376   1.399   1.415   1.551
80    Y         1.307   1.318   1.408   1.344   1.359   1.499   1.399   1.415   1.551
81    D        -1.034  -1.028  -0.903  -1.049  -1.039  -0.850  -1.093  -1.081  -0.898
82    W         0.639   0.646   0.424   0.927   0.940   0.613   0.641   0.652   0.253
83    L         1.307   1.318   1.408   1.214   1.230   1.376   1.399   1.415   1.551
84    I         0.639   0.730   0.432   0.631   0.743   0.341   0.641   0.775   0.267
85    K        -0.596  -0.639  -0.809  -0.734  -0.801  -1.032  -0.551  -0.603  -0.789
86    E        -1.034  -1.000  -0.904  -1.218  -1.168  -1.034  -1.093  -1.052  -0.899
87    K        -0.536  -0.545  -0.434  -0.870  -0.887  -0.678  -0.768  -0.779  -0.633
88    Y         0.003  -0.126  -0.280   0.235   0.069  -0.152  -0.009  -0.186  -0.415
89    A         0.639   0.553   0.415   0.732   0.629   0.403   0.641   0.508   0.235
90    D         0.310   0.265   0.295   0.364   0.289   0.300   0.099   0.015   0.012
91    K        -1.150  -1.147  -1.223  -1.226  -1.227  -1.298  -0.984  -0.978  -1.014
92    L        -1.648  -1.647  -1.573  -1.288  -1.289  -1.218  -1.309  -1.306  -1.170
93    L         1.307   1.318   1.408   1.214   1.230   1.376   1.399   1.415   1.551
94    I         1.307   1.318   1.408   1.257   1.273   1.416   1.399   1.415   1.551
95    A         1.307   1.318   1.408   1.315   1.337   1.472   1.399   1.415   1.551
96    K         1.307   1.318   1.408   0.983   0.996   1.158   1.399   1.415   1.551
97    W         1.307   1.318   1.408   1.499   1.517   1.645   1.399   1.415   1.551
98    R         0.134   0.147   0.253  -0.359  -0.341  -0.162  -0.226  -0.205  -0.068
99    K         1.307   1.318   1.408   0.983   0.996   1.158   1.399   1.415   1.551
100   T        -1.764  -1.725  -1.591  -1.605  -1.546  -1.395  -1.418  -1.384  -1.185
101   G         1.307   1.318   1.408   1.353   1.367   1.507   1.399   1.415   1.551
102   Y         1.307   1.318   1.408   1.344   1.359   1.499   1.399   1.415   1.551
103   E         1.307   1.318   1.408   1.236   1.254   1.396   1.399   1.415   1.551
104   K         0.639   0.646   0.424   0.418   0.425   0.160   0.641   0.652   0.253
105   L         1.307   1.318   1.408   1.214   1.230   1.376   1.399   1.415   1.551
106   C         1.307   1.318   1.408   1.290   1.308   1.448   1.399   1.415   1.551
107   C         1.307   1.318   1.408   1.290   1.308   1.448   1.399   1.415   1.551
108   L         0.639   0.553   0.415   0.631   0.522   0.311   0.641   0.508   0.235
109   R        -0.536  -0.568  -0.428  -0.626  -0.674  -0.475  -0.768  -0.812  -0.624
110   C         1.307   1.318   1.408   1.290   1.308   1.448   1.399   1.415   1.551
111   I         0.639   0.592   0.425   0.700   0.646   0.428   0.641   0.569   0.254
112   Q         0.003  -0.077  -0.286   0.252   0.153  -0.142  -0.009  -0.120  -0.424
113   K        -1.150  -1.101  -1.222  -0.943  -0.859  -1.119  -0.984  -0.930  -1.013
114   N        -0.843  -0.846  -0.855  -0.849  -0.853  -0.902  -0.876  -0.874  -0.846
115   E         1.307   1.318   1.408   1.216   1.229   1.378   1.399   1.415   1.551
116   T        -0.596  -0.565  -0.795  -0.405  -0.362  -0.760  -0.551  -0.511  -0.773
117   N        -0.596  -0.534  -0.792  -0.383  -0.296  -0.756  -0.551  -0.473  -0.770
118   N        -1.034  -1.040  -0.901  -0.778  -0.769  -0.603  -1.093  -1.083  -0.896
119   G         0.003   0.028  -0.280   0.210   0.241  -0.215  -0.009   0.027  -0.416
120   S        -0.843  -0.846  -0.861  -0.808  -0.823  -0.885  -0.876  -0.887  -0.854
121   T         1.307   1.318   1.408   1.336   1.356   1.491   1.399   1.415   1.551
122   C         1.307   1.318   1.408   1.290   1.308   1.448   1.399   1.415   1.551
123   I         0.639   0.553   0.415   0.700   0.597   0.412   0.641   0.508   0.235
124   C         1.307   1.318   1.408   1.290   1.308   1.448   1.399   1.415   1.551
125   R         1.307   1.318   1.408   1.265   1.286   1.424   1.399   1.415   1.551
126   V         1.307   1.318   1.408   1.438   1.450   1.588   1.399   1.415   1.551
127   P         1.307   1.318   1.408   1.390   1.404   1.542   1.399   1.415   1.551
128   R         0.078   0.087   0.235  -0.427  -0.420  -0.178  -0.334  -0.320  -0.104
129   A        -1.150  -1.164  -1.218  -1.002  -1.024  -1.189  -0.984  -0.995  -1.009
130   Q        -1.457  -1.443  -1.288  -1.558  -1.553  -1.313  -1.309  -1.292  -1.076
131   L         0.639   0.646   0.424   0.631   0.642   0.327   0.641   0.652   0.253
132   E        -0.377  -0.415  -0.403  -0.451  -0.517  -0.518  -0.542  -0.595  -0.590
133   E        -0.563  -0.558  -0.426  -0.868  -0.859  -0.699  -0.820  -0.810  -0.624
134   E        -0.563  -0.581  -0.429  -0.839  -0.886  -0.672  -0.820  -0.837  -0.627
135   A         0.114   0.107   0.238   0.018   0.008   0.199  -0.265  -0.283  -0.097
136   R        -1.054  -1.074  -0.912  -1.079  -1.107  -0.886  -1.097  -1.115  -0.904
137   K        -0.596  -0.641  -0.814  -0.710  -0.782  -0.995  -0.551  -0.606  -0.795
138   K        -0.289  -0.274  -0.359  -0.596  -0.575  -0.664  -0.442  -0.418  -0.533
139   G        -0.486  -0.469  -0.409  -0.605  -0.579  -0.537  -0.719  -0.695  -0.602
140   T        -1.440  -1.365  -1.284  -1.371  -1.252  -1.189  -1.289  -1.220  -1.072
141   Q        -1.341  -1.322  -1.262  -1.139  -1.112  -1.030  -1.201  -1.179  -1.053
142   V         0.639   0.553   0.415   0.855   0.740   0.514   0.641   0.508   0.235
143   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   Q        -0.420  -0.362  -0.376  -0.551  -0.461  -0.468  -0.659  -0.577  -0.562
147   C         1.307   1.318   1.408   1.290   1.308   1.448   1.399   1.415   1.551
148   V        -0.420  -0.399  -0.382  -0.431  -0.420  -0.374  -0.659  -0.639  -0.572
149   H        -0.918  -0.925  -0.874  -0.741  -0.751  -0.675  -0.984  -0.981  -0.869
150   C         1.307   1.318   1.408   1.290   1.308   1.448   1.399   1.415   1.551
151   G         1.307   1.318   1.408   1.353   1.367   1.507   1.399   1.415   1.551
152   C         1.307   1.318   1.408   1.290   1.308   1.448   1.399   1.415   1.551
153   R        -0.596  -0.579  -0.797  -0.374  -0.344  -0.641  -0.551  -0.529  -0.775
154   G         1.307   1.318   1.408   1.353   1.367   1.507   1.399   1.415   1.551
155   C         1.307   1.318   1.408   1.290   1.308   1.448   1.399   1.415   1.551
156   A         1.307   1.318   1.408   1.315   1.337   1.472   1.399   1.415   1.551
157   S         0.639   0.670   0.421   0.752   0.792   0.448   0.641   0.687   0.247
158   T        -0.918  -0.881  -0.864  -0.884  -0.836  -0.791  -0.984  -0.945  -0.860
159   D         1.307   1.318   1.408   1.385   1.404   1.538   1.399   1.415   1.551
* 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/P25337
Output conservation file - output/P25337
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
