1     M         2.077   2.138   2.238   2.344   2.435   2.587   2.379   2.488   2.674
2     S        -0.133  -0.084  -0.035  -0.066  -0.003   0.071  -0.415  -0.346  -0.277
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     V        -0.828  -0.782  -0.697  -1.017  -0.934  -0.843  -0.895  -0.841  -0.732
10    I        -0.340  -0.472  -0.543   0.042  -0.158  -0.345  -0.294  -0.461  -0.546
11    P         0.075  -0.029   0.016  -0.259  -0.434  -0.335  -0.115  -0.258  -0.208
12    P        -2.000  -1.964  -1.882  -1.508  -1.552  -1.344  -1.363  -1.328  -1.218
13    K        -0.599  -0.681  -0.621  -0.355  -0.402  -0.308  -0.650  -0.737  -0.650
14    F        -1.170  -1.118  -1.109  -1.413  -1.405  -1.341  -1.007  -0.945  -0.905
15    F         0.409   0.277   0.172   0.461   0.293   0.109   0.419   0.221   0.047
16    K         0.646   0.669   0.771   0.854   0.877   1.027   0.241   0.257   0.405
17    I        -1.170  -1.109  -1.085  -1.365  -1.255  -1.257  -1.007  -0.939  -0.884
18    A        -0.340  -0.287  -0.458  -0.085  -0.010  -0.247  -0.294  -0.221  -0.438
19    N         1.218   1.107   1.066   1.592   1.479   1.438   1.310   1.115   1.008
20    I         0.646   0.668   0.771  -0.036  -0.032   0.132   0.241   0.256   0.405
21    S        -1.170  -1.132  -1.101  -1.218  -1.146  -1.135  -1.007  -0.960  -0.898
22    I         0.075   0.025   0.014  -0.035  -0.138  -0.195  -0.115  -0.204  -0.212
23    G        -0.027  -0.081   0.015  -0.246  -0.292  -0.181  -0.294  -0.347  -0.216
24    C        -0.599  -0.530  -0.562  -0.542  -0.379  -0.442  -0.650  -0.543  -0.575
25    I        -0.340  -0.472  -0.543  -0.504  -0.721  -0.785  -0.294  -0.461  -0.546
26    D        -1.585  -1.542  -1.500  -0.965  -0.984  -0.849  -1.185  -1.144  -1.065
27    I        -0.599  -0.660  -0.589  -0.622  -0.658  -0.580  -0.650  -0.705  -0.613
28    I         0.075   0.133   0.083  -0.357  -0.301  -0.366  -0.115  -0.018  -0.105
29    A        -0.599  -0.577  -0.597  -0.801  -0.821  -0.843  -0.650  -0.636  -0.622
30    A         0.075  -0.029   0.016  -0.106  -0.247  -0.227  -0.115  -0.258  -0.208
31    L         0.409   0.401   0.209   0.139   0.096  -0.174   0.419   0.411   0.105
32    S         0.075   0.034   0.033   0.163   0.111   0.097  -0.115  -0.185  -0.187
33    Q         2.077   2.138   2.238   2.356   2.445   2.599   2.379   2.488   2.674
34    L         0.409   0.290   0.181   0.148  -0.056  -0.204   0.419   0.239   0.061
35    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    I        -0.828  -0.800  -0.697  -0.891  -0.849  -0.714  -0.895  -0.860  -0.732
38    F        -0.340  -0.425  -0.502  -0.274  -0.401  -0.547  -0.294  -0.402  -0.493
39    T        -1.014  -0.871  -1.013  -0.924  -0.780  -0.873  -0.828  -0.668  -0.802
40    N        -1.170  -1.223  -1.120  -0.901  -0.907  -0.777  -1.007  -1.042  -0.915
41    L        -0.184  -0.104  -0.053  -0.825  -0.734  -0.653  -0.472  -0.360  -0.301
42    N        -1.014  -1.068  -1.070  -0.328  -0.407  -0.409  -0.828  -0.884  -0.861
43    V        -2.000  -1.964  -1.882  -1.814  -1.805  -1.656  -1.363  -1.328  -1.218
44    F         0.824   0.871   0.867   0.559   0.633   0.567   0.597   0.670   0.609
45    L        -0.027  -0.006   0.023  -0.474  -0.474  -0.423  -0.294  -0.262  -0.208
46    L         0.409   0.377   0.212   0.234   0.133  -0.010   0.419   0.362   0.110
47    A         0.075   0.040   0.037  -0.067  -0.107  -0.138  -0.115  -0.179  -0.182
48    V        -1.014  -0.900  -1.010  -1.146  -0.999  -1.139  -0.828  -0.699  -0.798
49    Y         1.218   1.107   1.066   1.433   1.278   1.200   1.310   1.115   1.008
50    G        -1.170  -1.139  -1.110  -1.347  -1.256  -1.262  -1.007  -0.961  -0.904
51    L         0.646   0.666   0.770   0.014  -0.022   0.136   0.241   0.252   0.404
52    A        -1.014  -1.031  -1.047  -1.046  -1.098  -1.200  -0.828  -0.845  -0.837
53    L         0.646   0.666   0.770   0.065   0.017   0.183   0.241   0.252   0.404
54    S         0.075   0.022   0.014   0.001  -0.064  -0.064  -0.115  -0.208  -0.215
55    V        -0.755  -0.698  -0.653  -0.946  -0.841  -0.782  -0.828  -0.760  -0.687
56    P        -1.170  -1.189  -1.126  -1.073  -1.141  -1.051  -1.007  -1.011  -0.920
57    I         0.409   0.290   0.181   0.382   0.192   0.030   0.419   0.239   0.061
58    V        -0.340  -0.337  -0.481  -0.318  -0.287  -0.565  -0.294  -0.283  -0.467
59    Y        -1.585  -1.602  -1.525  -1.461  -1.459  -1.319  -1.185  -1.190  -1.086
60    L         2.077   2.138   2.238   1.657   1.702   1.885   2.379   2.488   2.674
61    E         2.077   2.138   2.238   2.286   2.383   2.528   2.379   2.488   2.674
62    F         2.077   2.138   2.238   1.938   2.026   2.172   2.379   2.488   2.674
63    K        -1.014  -0.953  -1.031  -0.288  -0.194  -0.298  -0.828  -0.754  -0.821
64    V        -0.340  -0.425  -0.502  -0.053  -0.149  -0.272  -0.294  -0.402  -0.493
65    P         1.218   1.107   1.066   1.428   1.255   1.163   1.310   1.115   1.008
66    S        -0.599  -0.530  -0.562  -0.311  -0.162  -0.219  -0.650  -0.543  -0.575
67    N        -1.585  -1.633  -1.540  -1.006  -1.137  -0.960  -1.185  -1.214  -1.098
68    L        -0.027   0.014   0.012  -0.443  -0.441  -0.403  -0.294  -0.227  -0.219
69    Y         0.409   0.329   0.196   0.844   0.743   0.603   0.419   0.294   0.085
70    R        -0.184  -0.093  -0.041   0.051   0.219   0.271  -0.472  -0.346  -0.284
71    Y         2.077   2.138   2.238   2.204   2.287   2.444   2.379   2.488   2.674
72    A         1.218   1.294   1.096   1.263   1.378   1.084   1.310   1.437   1.065
73    S         2.077   2.138   2.238   2.067   2.159   2.304   2.379   2.488   2.674
74    F         1.218   1.234   1.086   1.239   1.273   1.100   1.310   1.337   1.047
75    Y        -0.027   0.014   0.012  -0.225  -0.116  -0.084  -0.294  -0.227  -0.219
76    F         1.218   1.107   1.066   1.220   1.091   1.037   1.310   1.115   1.008
77    S         1.218   1.107   1.066   1.366   1.246   1.198   1.310   1.115   1.008
78    F         1.218   1.107   1.066   1.220   1.091   1.037   1.310   1.115   1.008
79    L        -0.599  -0.586  -0.564  -1.025  -1.012  -0.969  -0.650  -0.614  -0.577
80    G         2.077   2.138   2.238   1.913   2.018   2.147   2.379   2.488   2.674
81    R         2.077   2.138   2.238   2.344   2.435   2.587   2.379   2.488   2.674
82    G         1.218   1.234   1.086   1.165   1.215   0.986   1.310   1.337   1.047
83    L        -0.599  -0.666  -0.586  -0.830  -0.929  -0.856  -0.650  -0.715  -0.609
84    S        -0.599  -0.631  -0.610  -0.941  -1.057  -1.034  -0.650  -0.685  -0.639
85    Y         1.218   1.107   1.066   1.442   1.289   1.217   1.310   1.115   1.008
86    I        -0.027  -0.015   0.022  -0.153  -0.152  -0.121  -0.294  -0.272  -0.210
87    L         0.824   0.899   0.878   0.304   0.380   0.345   0.597   0.725   0.632
88    L         0.075   0.172   0.093  -0.401  -0.266  -0.385  -0.115   0.047  -0.089
89    S        -0.599  -0.657  -0.620  -0.628  -0.671  -0.639  -0.650  -0.713  -0.649
90    L        -0.340  -0.282  -0.463  -0.150  -0.067  -0.349  -0.294  -0.213  -0.444
91    I        -0.599  -0.623  -0.576  -0.718  -0.774  -0.694  -0.650  -0.655  -0.592
92    I        -0.027  -0.012   0.027  -0.490  -0.494  -0.387  -0.294  -0.268  -0.204
93    S        -1.170  -1.145  -1.092  -0.623  -0.570  -0.488  -1.007  -0.980  -0.890
94    F        -1.170  -1.135  -1.118  -0.957  -0.845  -0.848  -1.007  -0.958  -0.913
95    G         1.218   1.107   1.066   1.210   1.104   1.039   1.310   1.115   1.008
96    G        -0.027   0.005   0.027  -0.129  -0.065  -0.015  -0.294  -0.242  -0.201
97    I        -1.585  -1.585  -1.521  -1.543  -1.553  -1.470  -1.185  -1.179  -1.082
98    Y         0.409   0.408   0.204   0.490   0.500   0.210   0.419   0.421   0.097
99    N        -0.599  -0.681  -0.621  -0.125  -0.244  -0.154  -0.650  -0.737  -0.650
100   I        -0.340  -0.252  -0.447  -0.209  -0.063  -0.341  -0.294  -0.174  -0.424
101   L        -0.027   0.057   0.032  -0.597  -0.510  -0.521  -0.294  -0.195  -0.199
102   A        -0.599  -0.679  -0.602  -0.606  -0.704  -0.605  -0.650  -0.732  -0.628
103   G         0.409   0.441   0.226   0.437   0.508   0.171   0.419   0.471   0.131
104   M        -1.170  -1.135  -1.118  -1.274  -1.151  -1.142  -1.007  -0.958  -0.913
105   F        -0.599  -0.536  -0.575  -1.057  -1.001  -1.035  -0.650  -0.574  -0.596
106   T        -0.599  -0.571  -0.601  -0.859  -0.887  -0.863  -0.650  -0.628  -0.628
107   F         0.409   0.277   0.172   0.605   0.470   0.361   0.419   0.221   0.047
108   I        -1.170  -1.145  -1.097  -1.462  -1.423  -1.367  -1.007  -0.979  -0.894
109   L        -1.170  -1.223  -1.120  -1.121  -1.150  -1.037  -1.007  -1.042  -0.915
110   G         1.218   1.107   1.066   1.165   1.044   0.954   1.310   1.115   1.008
111   V         0.075   0.112   0.053  -0.319  -0.304  -0.352  -0.115  -0.071  -0.156
112   A        -0.027   0.022   0.027  -0.245  -0.174  -0.198  -0.294  -0.232  -0.204
113   F         0.075  -0.010   0.039   0.233   0.135   0.174  -0.115  -0.227  -0.176
114   I        -0.184  -0.158  -0.078  -0.643  -0.662  -0.553  -0.472  -0.443  -0.339
115   V        -0.599  -0.519  -0.581  -0.626  -0.544  -0.617  -0.650  -0.578  -0.605
116   F         1.218   1.242   1.085   0.890   0.888   0.693   1.310   1.350   1.045
117   H         0.646   0.666   0.770   0.823   0.859   1.008   0.241   0.252   0.404
118   F        -0.599  -0.587  -0.577  -0.702  -0.743  -0.685  -0.650  -0.628  -0.599
119   S        -0.755  -0.778  -0.663  -0.823  -0.789  -0.673  -0.828  -0.837  -0.697
120   Q         0.409   0.395   0.200   0.819   0.814   0.547   0.419   0.402   0.091
121   F        -0.340  -0.472  -0.543  -0.126  -0.300  -0.465  -0.294  -0.461  -0.546
122   V         0.824   0.778   0.823   0.570   0.493   0.523   0.597   0.483   0.516
123   E        -0.599  -0.623  -0.576  -0.323  -0.324  -0.282  -0.650  -0.655  -0.592
124   E         0.646   0.666   0.770   0.705   0.734   0.880   0.241   0.252   0.404
125   P         2.077   2.138   2.238   2.234   2.322   2.475   2.379   2.488   2.674
126   A        -1.014  -1.060  -1.045  -0.395  -0.452  -0.435  -0.828  -0.876  -0.835
127   N         1.218   1.107   1.066   1.555   1.425   1.367   1.310   1.115   1.008
128   F         0.646   0.666   0.770   0.589   0.571   0.714   0.241   0.252   0.404
129   R        -0.184  -0.125  -0.048   0.156   0.247   0.356  -0.472  -0.399  -0.295
130   A        -1.585  -1.633  -1.540  -1.016  -1.063  -0.958  -1.185  -1.214  -1.098
131   P        -1.585  -1.615  -1.521  -0.839  -0.864  -0.738  -1.185  -1.201  -1.083
132   G        -0.599  -0.599  -0.599  -0.425  -0.383  -0.370  -0.650  -0.655  -0.626
133   S        -0.042  -0.026   0.018  -0.240  -0.207  -0.176  -0.289  -0.267  -0.208
134   S        -0.709  -0.664  -0.628  -0.782  -0.702  -0.683  -0.774  -0.721  -0.657
135   L        -0.599  -0.499  -0.559  -0.882  -0.764  -0.792  -0.650  -0.522  -0.578
136   S        -0.599  -0.606  -0.611  -0.603  -0.595  -0.590  -0.650  -0.662  -0.640
137   I        -0.755  -0.709  -0.646  -1.128  -1.051  -0.962  -0.828  -0.773  -0.681
138   G        -1.014  -0.953  -1.031  -0.412  -0.318  -0.432  -0.828  -0.754  -0.821
139   D         0.409   0.454   0.218   0.911   0.979   0.689   0.419   0.491   0.119
140   D         0.625   0.679   0.779   0.689   0.771   0.914   0.196   0.280   0.423
141   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   D         2.077   2.138   2.238   2.221   2.310   2.461   2.379   2.488   2.674
148   M         0.899   0.954   0.924   0.744   0.821   0.789   0.742   0.831   0.726
149   I         0.646   0.704   0.786   0.304   0.410   0.491   0.241   0.331   0.438
* 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/Q03860
Output conservation file - output/Q03860
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
