1     M         1.710   1.723   1.788   1.898   1.914   2.018   1.842   1.860   1.957
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    -        -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    K         0.742   0.737   0.710   0.660   0.646   0.566   0.527   0.513   0.420
26    S        -0.079  -0.070  -0.035  -0.294  -0.268  -0.229  -0.349  -0.336  -0.297
27    L        -0.676  -0.668  -0.576  -0.841  -0.826  -0.689  -0.787  -0.775  -0.661
28    F        -0.957  -0.978  -0.907  -0.862  -0.894  -0.775  -0.877  -0.890  -0.794
29    Y        -1.298  -1.302  -1.238  -1.079  -1.103  -0.988  -1.020  -1.019  -0.930
30    L        -0.957  -0.896  -0.902  -1.115  -1.018  -1.023  -0.877  -0.819  -0.789
31    K        -1.298  -1.259  -1.229  -1.075  -1.002  -0.995  -1.020  -0.982  -0.922
32    L        -0.488  -0.462  -0.481  -0.474  -0.429  -0.457  -0.591  -0.554  -0.560
33    L        -0.957  -0.978  -0.912  -1.004  -1.046  -0.952  -0.877  -0.889  -0.798
34    L        -0.276  -0.261  -0.382  -0.209  -0.198  -0.320  -0.304  -0.290  -0.433
35    W        -0.276  -0.330  -0.399  -0.305  -0.391  -0.476  -0.304  -0.374  -0.454
36    V        -0.276  -0.374  -0.424  -0.098  -0.249  -0.354  -0.304  -0.426  -0.484
37    V        -0.488  -0.479  -0.490  -0.539  -0.531  -0.569  -0.591  -0.578  -0.572
38    L        -0.957  -0.929  -0.900  -0.946  -0.884  -0.858  -0.877  -0.845  -0.788
39    L        -0.147  -0.123  -0.066  -0.404  -0.356  -0.296  -0.448  -0.413  -0.343
40    S        -1.298  -1.282  -1.228  -1.344  -1.310  -1.230  -1.020  -1.003  -0.922
41    L        -1.298  -1.260  -1.223  -1.330  -1.285  -1.210  -1.020  -0.983  -0.918
42    C        -0.616  -0.636  -0.545  -0.564  -0.605  -0.453  -0.734  -0.744  -0.632
43    L        -0.488  -0.437  -0.481  -0.659  -0.571  -0.640  -0.591  -0.528  -0.561
44    L        -0.829  -0.886  -0.871  -0.863  -0.949  -0.912  -0.734  -0.792  -0.755
45    M        -0.957  -0.936  -0.903  -1.045  -1.025  -0.939  -0.877  -0.854  -0.790
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    A        -0.018   0.011   0.000  -0.063  -0.035  -0.023  -0.304  -0.270  -0.264
50    H        -0.829  -0.863  -0.866  -0.646  -0.716  -0.769  -0.734  -0.769  -0.750
51    R        -0.957  -0.940  -0.912  -0.878  -0.867  -0.806  -0.877  -0.858  -0.798
52    K         1.004   1.047   0.876   0.988   1.045   0.814   0.983   1.051   0.735
53    T        -0.957  -0.914  -0.907  -0.804  -0.761  -0.722  -0.877  -0.834  -0.793
54    K        -0.276  -0.374  -0.424  -0.082  -0.227  -0.300  -0.304  -0.426  -0.484
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    V        -0.428  -0.406  -0.459  -0.482  -0.454  -0.551  -0.495  -0.466  -0.526
60    A        -0.976  -0.986  -0.920  -1.015  -1.045  -0.947  -0.885  -0.891  -0.803
61    D        -0.976  -0.972  -0.915  -0.911  -0.906  -0.805  -0.885  -0.876  -0.798
62    K        -0.578  -0.591  -0.533  -0.647  -0.667  -0.577  -0.690  -0.697  -0.617
63    F        -0.578  -0.565  -0.528  -0.511  -0.482  -0.435  -0.690  -0.672  -0.612
64    R        -0.031  -0.017  -0.006  -0.329  -0.290  -0.292  -0.300  -0.273  -0.262
65    A        -0.181  -0.172  -0.085  -0.409  -0.406  -0.261  -0.495  -0.482  -0.369
66    L        -0.578  -0.534  -0.532  -0.708  -0.635  -0.658  -0.690  -0.643  -0.616
67    R        -0.428  -0.431  -0.476  -0.394  -0.406  -0.454  -0.495  -0.498  -0.547
68    S        -0.428  -0.385  -0.470  -0.306  -0.227  -0.392  -0.495  -0.440  -0.539
69    R         0.217   0.233   0.107   0.168   0.192  -0.016   0.089   0.112  -0.087
70    I        -0.616  -0.592  -0.547  -0.969  -0.930  -0.862  -0.734  -0.706  -0.633
71    Q         0.340   0.353   0.172   0.387   0.404   0.160   0.268   0.287   0.009
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    L        -0.578  -0.545  -0.523  -0.728  -0.663  -0.637  -0.690  -0.652  -0.607
79    R         0.217   0.205   0.093   0.116   0.093  -0.119   0.089   0.071  -0.108
80    F         0.075  -0.008   0.012   0.047  -0.092  -0.060  -0.121  -0.244  -0.229
81    N        -0.428  -0.406  -0.465  -0.490  -0.452  -0.558  -0.495  -0.469  -0.533
82    R         0.615   0.646   0.659   0.408   0.459   0.467   0.284   0.339   0.319
83    H        -0.578  -0.571  -0.534  -0.543  -0.534  -0.507  -0.690  -0.677  -0.618
84    I        -0.957  -0.979  -0.913  -0.754  -0.780  -0.662  -0.877  -0.890  -0.799
85    R        -0.276  -0.330  -0.399  -0.218  -0.287  -0.406  -0.304  -0.374  -0.454
86    L        -1.298  -1.319  -1.248  -1.298  -1.303  -1.197  -1.020  -1.032  -0.937
87    N        -0.957  -0.955  -0.913  -0.978  -0.962  -0.926  -0.877  -0.868  -0.798
88    D        -0.276  -0.242  -0.378  -0.145  -0.096  -0.316  -0.304  -0.261  -0.429
89    S         1.004   1.044   0.871   1.010   1.071   0.825   0.983   1.046   0.725
90    F         1.710   1.723   1.788   1.715   1.730   1.837   1.842   1.860   1.957
91    A        -0.276  -0.210  -0.386  -0.098  -0.008  -0.285  -0.304  -0.221  -0.438
92    D         0.340   0.247   0.152   0.358   0.227   0.085   0.268   0.132  -0.021
93    D         1.710   1.723   1.788   1.626   1.650   1.749   1.842   1.860   1.957
94    L        -0.276  -0.334  -0.407  -0.284  -0.368  -0.457  -0.304  -0.378  -0.464
95    E         0.340   0.293   0.161   0.521   0.452   0.246   0.268   0.196  -0.008
96    N        -0.018  -0.024   0.007  -0.205  -0.205  -0.151  -0.304  -0.306  -0.256
97    G         1.710   1.723   1.788   1.748   1.772   1.869   1.842   1.860   1.957
98    L         1.710   1.723   1.788   1.547   1.572   1.671   1.842   1.860   1.957
99    H        -0.829  -0.829  -0.856  -0.710  -0.713  -0.738  -0.734  -0.734  -0.740
100   S         1.710   1.723   1.788   1.654   1.680   1.777   1.842   1.860   1.957
101   R        -0.488  -0.487  -0.490  -0.683  -0.666  -0.686  -0.591  -0.578  -0.568
102   N        -1.298  -1.303  -1.232  -1.097  -1.124  -0.999  -1.020  -1.020  -0.924
103   F         1.710   1.723   1.788   1.715   1.730   1.837   1.842   1.860   1.957
104   D         1.004   0.990   0.862   0.983   0.970   0.785   0.983   0.957   0.708
105   I         0.535   0.541   0.610   0.142   0.149   0.245   0.125   0.130   0.220
106   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   S        -0.488  -0.499  -0.493  -0.587  -0.611  -0.585  -0.591  -0.606  -0.576
108   E        -0.488  -0.486  -0.476  -0.370  -0.367  -0.350  -0.591  -0.587  -0.557
109   N         1.710   1.723   1.788   1.753   1.773   1.875   1.842   1.860   1.957
110   -         0.849   0.844   0.776   0.845   0.833   0.728   0.720   0.707   0.548
111   -        -0.583  -0.587  -0.532  -0.835  -0.839  -0.766  -0.682  -0.686  -0.612
112   S        -1.298  -1.234  -1.229  -1.242  -1.143  -1.146  -1.020  -0.960  -0.922
113   N        -0.829  -0.863  -0.866  -0.622  -0.677  -0.677  -0.734  -0.769  -0.750
114   D         1.710   1.723   1.788   1.626   1.650   1.749   1.842   1.860   1.957
115   V        -1.639  -1.623  -1.530  -1.432  -1.399  -1.274  -1.163  -1.146  -1.035
116   R         1.710   1.723   1.788   1.632   1.649   1.755   1.842   1.860   1.957
117   G         0.065   0.139   0.060   0.038   0.146   0.050  -0.161  -0.049  -0.164
118   G         1.710   1.723   1.788   1.748   1.772   1.869   1.842   1.860   1.957
119   L         1.710   1.723   1.788   1.547   1.572   1.671   1.842   1.860   1.957
120   D         0.340   0.400   0.168   0.292   0.388   0.007   0.268   0.355   0.003
121   D        -0.616  -0.579  -0.543  -0.656  -0.607  -0.544  -0.734  -0.697  -0.630
122   V        -1.298  -1.283  -1.228  -1.146  -1.131  -1.054  -1.020  -1.004  -0.922
123   S         0.680   0.693   0.678   0.546   0.556   0.506   0.411   0.429   0.356
124   K         1.004   0.925   0.866   1.121   1.022   0.934   0.983   0.849   0.716
125   N        -1.639  -1.623  -1.530  -1.700  -1.665  -1.539  -1.163  -1.146  -1.035
126   E         0.065   0.029   0.027   0.137   0.077   0.077  -0.161  -0.215  -0.218
127   I         1.004   1.044   0.871   1.036   1.090   0.858   0.983   1.046   0.725
128   K        -0.276  -0.374  -0.424  -0.169  -0.325  -0.428  -0.304  -0.426  -0.484
129   Q        -0.829  -0.795  -0.845  -0.690  -0.643  -0.729  -0.734  -0.698  -0.730
130   I         1.004   0.925   0.866   0.993   0.879   0.774   0.983   0.849   0.716
131   M         1.710   1.723   1.788   1.898   1.914   2.018   1.842   1.860   1.957
132   E        -0.018   0.016   0.001  -0.120  -0.065  -0.089  -0.304  -0.259  -0.263
133   N        -0.957  -0.942  -0.910  -0.900  -0.882  -0.805  -0.877  -0.859  -0.796
134   D        -1.639  -1.623  -1.530  -1.700  -1.689  -1.539  -1.163  -1.146  -1.035
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   N        -0.957  -0.963  -0.906  -0.846  -0.853  -0.756  -0.877  -0.878  -0.793
137   V        -0.488  -0.535  -0.478  -0.507  -0.544  -0.444  -0.591  -0.634  -0.558
138   D        -0.488  -0.489  -0.484  -0.475  -0.484  -0.472  -0.591  -0.594  -0.564
139   F         1.710   1.723   1.788   1.715   1.730   1.837   1.842   1.860   1.957
140   D         1.710   1.723   1.788   1.626   1.650   1.749   1.842   1.860   1.957
141   K        -0.616  -0.615  -0.543  -0.661  -0.644  -0.541  -0.734  -0.725  -0.629
142   A         1.710   1.723   1.788   1.720   1.729   1.842   1.842   1.860   1.957
143   R         1.710   1.723   1.788   1.632   1.649   1.755   1.842   1.860   1.957
144   L        -0.276  -0.286  -0.408  -0.299  -0.314  -0.481  -0.304  -0.316  -0.465
145   L        -0.829  -0.856  -0.866  -0.840  -0.886  -0.877  -0.734  -0.761  -0.750
146   Y         1.710   1.723   1.788   1.887   1.903   2.007   1.842   1.860   1.957
147   M         0.065   0.008   0.032   0.148   0.060   0.089  -0.161  -0.233  -0.212
148   E        -0.488  -0.492  -0.492  -0.471  -0.494  -0.472  -0.591  -0.597  -0.574
149   R        -0.829  -0.856  -0.866  -0.737  -0.783  -0.778  -0.734  -0.761  -0.750
150   K        -0.957  -0.956  -0.918  -0.905  -0.909  -0.822  -0.877  -0.871  -0.803
151   F         0.065   0.027   0.029  -0.056  -0.093  -0.111  -0.161  -0.202  -0.213
152   G        -0.957  -0.954  -0.915  -1.065  -1.054  -1.011  -0.877  -0.868  -0.800
153   Q        -0.957  -0.930  -0.912  -0.891  -0.874  -0.830  -0.877  -0.846  -0.798
154   N         1.710   1.723   1.788   1.753   1.773   1.875   1.842   1.860   1.957
155   G         0.680   0.657   0.677   0.610   0.569   0.577   0.411   0.361   0.354
156   I         1.004   0.925   0.866   1.036   0.932   0.850   0.983   0.849   0.716
157   A        -0.147  -0.128  -0.061  -0.385  -0.357  -0.262  -0.448  -0.421  -0.336
158   P        -0.957  -0.956  -0.918  -0.834  -0.857  -0.787  -0.877  -0.871  -0.803
159   D         0.340   0.293   0.161   0.369   0.309   0.116   0.268   0.196  -0.008
160   G         1.710   1.723   1.788   1.748   1.772   1.869   1.842   1.860   1.957
161   T        -0.829  -0.887  -0.876  -0.658  -0.757  -0.764  -0.734  -0.793  -0.760
162   P         1.710   1.723   1.788   1.919   1.938   2.039   1.842   1.860   1.957
163   I        -0.616  -0.615  -0.543  -0.919  -0.916  -0.793  -0.734  -0.725  -0.629
164   D         1.710   1.723   1.788   1.626   1.650   1.749   1.842   1.860   1.957
165   P         1.004   0.925   0.866   1.274   1.166   1.072   0.983   0.849   0.716
166   K         1.710   1.723   1.788   1.753   1.777   1.875   1.842   1.860   1.957
167   A        -0.276  -0.244  -0.400  -0.198  -0.161  -0.411  -0.304  -0.263  -0.455
168   F         1.004   1.047   0.876   1.157   1.215   0.972   0.983   1.051   0.735
169   T        -0.276  -0.287  -0.407  -0.055  -0.079  -0.271  -0.304  -0.317  -0.463
170   F         1.004   0.925   0.866   1.071   0.961   0.877   0.983   0.849   0.716
171   D        -0.428  -0.400  -0.462  -0.543  -0.514  -0.634  -0.495  -0.465  -0.530
172   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   R        -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/Q8J0M4
Output conservation file - output/Q8J0M4
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
