1     M         1.526   1.538   1.621   1.862   1.875   2.011   1.671   1.687   1.819
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     D         0.799   0.797   0.629   0.762   0.800   0.527   0.796   0.792   0.471
4     P        -0.739  -0.767  -0.715  -0.935  -0.972  -0.876  -0.807  -0.832  -0.745
5     E         1.526   1.538   1.621   1.494   1.507   1.654   1.671   1.687   1.819
6     L         1.526   1.538   1.621   1.512   1.526   1.671   1.671   1.687   1.819
7     Q        -0.739  -0.739  -0.704  -0.834  -0.842  -0.803  -0.807  -0.795  -0.731
8     A         1.526   1.538   1.621   1.517   1.532   1.677   1.671   1.687   1.819
9     I         0.799   0.858   0.642   0.887   0.968   0.637   0.796   0.888   0.494
10    R         1.526   1.538   1.621   1.470   1.484   1.631   1.671   1.687   1.819
11    E        -0.255  -0.208  -0.208  -0.497  -0.440  -0.397  -0.515  -0.460  -0.427
12    A         1.526   1.538   1.621   1.517   1.532   1.677   1.671   1.687   1.819
13    R         1.526   1.538   1.621   1.470   1.484   1.631   1.671   1.687   1.819
14    L         0.799   0.797   0.629   0.868   0.865   0.660   0.796   0.792   0.471
15    A         0.114   0.147  -0.083   0.122   0.162  -0.209   0.068   0.114  -0.230
16    Q         0.465   0.449   0.463   0.278   0.238   0.249   0.214   0.179   0.151
17    L         1.526   1.538   1.621   1.512   1.526   1.671   1.671   1.687   1.819
18    K         0.315   0.330   0.430   0.149   0.170   0.336  -0.078  -0.054   0.085
19    N        -1.223  -1.240  -1.130  -1.307  -1.342  -1.159  -1.098  -1.102  -0.956
20    N        -1.090  -1.108  -1.091  -0.983  -1.030  -1.031  -0.952  -0.965  -0.917
21    S        -1.090  -1.086  -1.088  -0.902  -0.892  -0.890  -0.952  -0.942  -0.914
22    G         0.114   0.174  -0.080   0.264   0.351  -0.065   0.068   0.154  -0.226
23    G        -0.520  -0.472  -0.628  -0.413  -0.332  -0.631  -0.515  -0.454  -0.637
24    T        -0.739  -0.700  -0.704  -0.772  -0.718  -0.700  -0.807  -0.762  -0.732
25    N        -0.739  -0.730  -0.706  -0.542  -0.521  -0.510  -0.807  -0.787  -0.733
26    G        -0.739  -0.722  -0.707  -0.829  -0.815  -0.806  -0.807  -0.787  -0.737
27    D        -0.871  -0.877  -0.751  -1.083  -1.061  -0.877  -0.952  -0.947  -0.784
28    R        -1.925  -1.906  -1.746  -1.899  -1.885  -1.631  -1.390  -1.365  -1.184
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    N        -0.268  -0.279  -0.225  -0.242  -0.261  -0.182  -0.511  -0.520  -0.446
39    S        -0.159  -0.141  -0.165  -0.151  -0.123  -0.181  -0.329  -0.301  -0.351
40    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    G        -0.159  -0.162  -0.191  -0.165  -0.174  -0.257  -0.329  -0.332  -0.389
45    G         0.727   0.685   0.580   0.861   0.799   0.615   0.679   0.605   0.379
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    G        -0.520  -0.504  -0.644  -0.441  -0.412  -0.706  -0.515  -0.493  -0.656
50    E        -1.090  -1.096  -1.092  -1.081  -1.098  -1.090  -0.952  -0.953  -0.918
51    N        -1.223  -1.173  -1.118  -1.139  -1.087  -0.968  -1.098  -1.047  -0.945
52    S        -0.520  -0.466  -0.638  -0.609  -0.492  -0.815  -0.515  -0.444  -0.649
53    A        -1.090  -1.059  -1.081  -1.181  -1.124  -1.191  -0.952  -0.913  -0.907
54    P        -1.090  -1.075  -1.088  -0.737  -0.713  -0.786  -0.952  -0.930  -0.914
55    V        -1.223  -1.168  -1.124  -1.178  -1.109  -1.014  -1.098  -1.042  -0.951
56    G        -1.223  -1.188  -1.124  -1.239  -1.190  -1.089  -1.098  -1.058  -0.950
57    A        -0.739  -0.730  -0.700  -0.814  -0.793  -0.721  -0.807  -0.783  -0.728
58    A        -1.090  -1.048  -1.082  -1.015  -0.969  -1.020  -0.952  -0.903  -0.908
59    I         0.529   0.600   0.521   0.382   0.482   0.350   0.332   0.456   0.264
60    A        -0.202  -0.191  -0.184  -0.285  -0.266  -0.245  -0.449  -0.443  -0.398
61    N        -0.071   0.011  -0.143  -0.098   0.046  -0.224  -0.226  -0.100  -0.327
62    F        -0.071   0.012  -0.141   0.041   0.181  -0.040  -0.226  -0.100  -0.323
63    L         1.526   1.538   1.621   1.488   1.488   1.648   1.671   1.687   1.819
64    E        -0.625  -0.721  -0.670  -0.629  -0.740  -0.664  -0.672  -0.772  -0.694
65    P        -1.431  -1.331  -1.411  -0.932  -0.771  -0.933  -1.119  -1.017  -1.047
66    Q        -1.124  -1.041  -1.090  -1.087  -0.976  -0.994  -1.007  -0.919  -0.921
67    A         1.526   1.538   1.621   1.520   1.535   1.679   1.671   1.687   1.819
68    L        -0.625  -0.708  -0.666  -0.822  -0.967  -0.887  -0.672  -0.755  -0.688
69    E         0.529   0.427   0.490   0.325   0.127   0.204   0.332   0.137   0.204
70    R         1.526   1.538   1.621   1.471   1.487   1.632   1.671   1.687   1.819
71    L         1.526   1.538   1.621   1.488   1.488   1.648   1.671   1.687   1.819
72    S         0.221   0.048  -0.059   0.402   0.159  -0.044   0.220  -0.037  -0.196
73    R         1.526   1.538   1.621   1.471   1.487   1.632   1.671   1.687   1.819
74    V         0.353   0.325   0.435   0.265   0.194   0.370  -0.003  -0.064   0.094
75    A        -0.701  -0.624  -0.679  -0.913  -0.820  -0.833  -0.784  -0.705  -0.710
76    L         0.353   0.407   0.446   0.059   0.143   0.208  -0.003   0.098   0.117
77    V         1.526   1.538   1.621   1.720   1.737   1.873   1.671   1.687   1.819
78    R         0.858   0.667   0.659   0.872   0.608   0.609   0.890   0.574   0.525
79    R        -0.933  -1.014  -1.053  -0.556  -0.733  -0.833  -0.784  -0.877  -0.879
80    D         0.529   0.431   0.484   0.289   0.128   0.170   0.332   0.144   0.192
81    R         1.526   1.538   1.621   1.471   1.487   1.632   1.671   1.687   1.819
82    A         0.858   0.876   0.643   0.925   0.948   0.636   0.890   0.917   0.495
83    Q        -1.431  -1.450  -1.420  -1.350  -1.359  -1.383  -1.119  -1.136  -1.055
84    A         0.221   0.084  -0.047   0.277   0.054  -0.149   0.220   0.011  -0.178
85    V         0.858   0.667   0.659   1.108   0.835   0.814   0.890   0.574   0.525
86    E         1.526   1.538   1.621   1.488   1.498   1.648   1.671   1.687   1.819
87    T        -1.431  -1.333  -1.409  -1.299  -1.129  -1.323  -1.119  -1.019  -1.046
88    Y        -0.378  -0.498  -0.612   0.117  -0.109  -0.304  -0.338  -0.497  -0.618
89    L         0.529   0.601   0.516   0.382   0.484   0.341   0.332   0.458   0.255
90    K        -0.817  -0.881  -0.737  -0.890  -0.958  -0.742  -0.896  -0.946  -0.769
91    K        -0.817  -0.879  -0.735  -0.867  -0.925  -0.722  -0.896  -0.943  -0.767
92    L         0.529   0.543   0.471   0.469   0.471   0.394   0.332   0.354   0.165
93    I        -0.625  -0.547  -0.660  -0.571  -0.459  -0.577  -0.672  -0.568  -0.682
94    A        -1.240  -1.209  -1.132  -1.357  -1.291  -1.184  -1.119  -1.079  -0.959
95    T         0.221   0.262  -0.059   0.604   0.659   0.203   0.220   0.278  -0.195
96    N         0.858   0.891   0.649   1.057   1.106   0.764   0.890   0.939   0.508
97    N        -0.071  -0.004  -0.153  -0.048   0.064  -0.194  -0.226  -0.120  -0.343
98    V        -0.071  -0.106  -0.150  -0.100  -0.197  -0.238  -0.226  -0.296  -0.340
99    T        -0.625  -0.559  -0.670  -0.581  -0.487  -0.586  -0.672  -0.580  -0.694
100   H        -1.547  -1.534  -1.437  -1.259  -1.241  -1.115  -1.230  -1.213  -1.071
101   K         1.526   1.538   1.621   1.694   1.710   1.848   1.671   1.687   1.819
102   I        -0.393  -0.372  -0.274  -0.624  -0.585  -0.432  -0.672  -0.639  -0.509
103   T        -0.701  -0.639  -0.670  -0.651  -0.536  -0.593  -0.784  -0.711  -0.702
104   E         1.526   1.538   1.621   1.488   1.498   1.648   1.671   1.687   1.819
105   A        -1.547  -1.481  -1.447  -1.454  -1.388  -1.283  -1.230  -1.166  -1.078
106   E        -0.202  -0.315  -0.193  -0.555  -0.684  -0.505  -0.449  -0.571  -0.409
107   I         0.353   0.325   0.435   0.101   0.016   0.207  -0.003  -0.064   0.094
108   V         0.221   0.048  -0.059   0.517   0.261   0.090   0.220  -0.037  -0.196
109   S        -0.817  -0.758  -0.724  -1.001  -0.906  -0.835  -0.896  -0.818  -0.755
110   I         0.353   0.325   0.435   0.101   0.016   0.207  -0.003  -0.064   0.094
111   L         1.526   1.538   1.621   1.488   1.488   1.648   1.671   1.687   1.819
112   N        -0.817  -0.807  -0.738  -1.087  -1.039  -0.930  -0.896  -0.887  -0.771
113   G        -0.933  -1.024  -1.058  -0.717  -0.890  -0.947  -0.784  -0.886  -0.884
114   I        -0.202  -0.188  -0.186  -0.290  -0.274  -0.254  -0.449  -0.438  -0.399
115   A        -0.202  -0.199  -0.188  -0.358  -0.361  -0.309  -0.449  -0.449  -0.401
116   K        -0.625  -0.728  -0.680  -0.733  -0.904  -0.812  -0.672  -0.780  -0.706
117   Q        -0.817  -0.876  -0.735  -1.115  -1.155  -0.960  -0.896  -0.940  -0.768
118   Q        -1.547  -1.563  -1.448  -1.581  -1.576  -1.419  -1.230  -1.233  -1.078
119   N        -1.124  -1.147  -1.090  -1.065  -1.135  -1.016  -1.007  -1.023  -0.920
120   S         0.114   0.132  -0.081   0.333   0.362   0.009   0.068   0.094  -0.228
121   Q        -0.871  -0.860  -0.751  -0.997  -0.991  -0.794  -0.952  -0.931  -0.784
122   N        -0.169  -0.136  -0.180  -0.094  -0.041  -0.114  -0.369  -0.318  -0.381
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   N        -1.240  -1.275  -1.126  -1.302  -1.373  -1.114  -1.119  -1.134  -0.954
125   S        -0.625  -0.686  -0.665  -0.465  -0.576  -0.554  -0.672  -0.733  -0.688
126   K         0.858   0.876   0.643   1.063   1.088   0.721   0.890   0.917   0.495
127   I         1.526   1.538   1.621   1.605   1.628   1.762   1.671   1.687   1.819
128   I        -0.202  -0.188  -0.187  -0.232  -0.216  -0.165  -0.449  -0.439  -0.402
129   F        -0.071  -0.203  -0.165   0.181   0.027   0.003  -0.226  -0.395  -0.360
130   E        -0.701  -0.775  -0.683  -0.831  -0.883  -0.767  -0.784  -0.849  -0.714
131   R         1.526   1.538   1.621   1.471   1.487   1.632   1.671   1.687   1.819
132   K         0.529   0.567   0.492   0.396   0.452   0.326   0.332   0.397   0.208
133   D        -1.431  -1.450  -1.409  -1.335  -1.372  -1.288  -1.119  -1.136  -1.045
134   F        -1.855  -1.858  -1.724  -1.535  -1.549  -1.362  -1.342  -1.335  -1.170
135   S        -1.328  -1.280  -1.164  -1.196  -1.056  -0.950  -1.186  -1.134  -0.984
136   E        -0.837  -0.860  -0.754  -0.988  -1.012  -0.849  -0.900  -0.925  -0.783
137   D        -0.159  -0.250  -0.199  -0.451  -0.643  -0.554  -0.329  -0.469  -0.401
138   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   D         0.727   0.796   0.608   0.617   0.756   0.417   0.679   0.789   0.432
151   D         0.221   0.383  -0.022   0.200   0.454  -0.166   0.220   0.445  -0.140
152   E         0.297   0.313   0.422  -0.171  -0.123   0.043  -0.114  -0.087   0.068
153   D         0.529   0.590   0.499   0.289   0.426   0.201   0.332   0.438   0.221
154   D         1.526   1.538   1.621   1.433   1.487   1.596   1.671   1.687   1.819
155   D         0.858   0.867   0.633   0.874   0.924   0.621   0.890   0.902   0.478
156   D         1.526   1.538   1.621   1.433   1.487   1.596   1.671   1.687   1.819
157   F         0.529   0.427   0.490   0.704   0.524   0.558   0.332   0.137   0.204
158   F         1.526   1.538   1.621   1.840   1.866   1.989   1.671   1.687   1.819
159   D         1.526   1.538   1.621   1.399   1.419   1.563   1.671   1.687   1.819
160   -        -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/Q04773
Output conservation file - output/Q04773
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
