1     M         1.621   1.656   1.743   1.889   1.941   2.071   1.767   1.811   1.954
2     S         0.067  -0.135  -0.170   0.135  -0.153  -0.235   0.032  -0.256  -0.327
3     L         0.821   0.685   0.628   0.511   0.323   0.253   0.821   0.587   0.441
4     V         0.067  -0.135  -0.170   0.038  -0.280  -0.391   0.032  -0.256  -0.327
5     K        -1.422  -1.327  -1.229  -1.294  -1.123  -1.008  -1.251  -1.149  -0.993
6     L         0.186   0.040  -0.097  -0.030  -0.222  -0.403   0.198  -0.007  -0.222
7     A        -1.294  -1.343  -1.208  -1.169  -1.234  -1.034  -1.131  -1.160  -0.975
8     N         0.186   0.133  -0.076   0.414   0.356   0.040   0.198   0.123  -0.191
9     T        -1.422  -1.441  -1.239  -1.379  -1.400  -1.141  -1.251  -1.238  -1.001
10    C         0.886   0.819   0.682   1.239   1.166   0.965   0.922   0.809   0.542
11    A         0.330   0.319   0.450   0.111   0.058   0.260  -0.044  -0.084   0.100
12    H         1.621   1.656   1.743   1.868   1.914   2.050   1.767   1.811   1.954
13    L         0.186   0.257  -0.068  -0.058   0.045  -0.412   0.198   0.297  -0.179
14    Q         0.524   0.581   0.558   0.564   0.658   0.567   0.318   0.407   0.310
15    N         1.621   1.656   1.743   1.686   1.734   1.878   1.767   1.811   1.954
16    C        -0.746  -0.880  -0.770  -0.583  -0.800  -0.697  -0.768  -0.901  -0.757
17    S        -1.084  -1.134  -1.170  -0.966  -1.023  -1.133  -0.889  -0.930  -0.935
18    K        -0.136   0.014  -0.153  -0.179   0.030  -0.216  -0.285  -0.090  -0.308
19    V         0.330   0.326   0.449   0.039   0.012   0.222  -0.044  -0.070   0.098
20    R        -0.474  -0.456  -0.671  -0.258  -0.239  -0.531  -0.406  -0.378  -0.635
21    V        -1.294  -1.267  -1.182  -1.684  -1.635  -1.482  -1.131  -1.080  -0.951
22    A        -0.956  -0.936  -0.794  -1.078  -1.042  -0.825  -1.010  -0.967  -0.784
23    L         0.186   0.257  -0.068  -0.038   0.065  -0.373   0.198   0.297  -0.179
24    T         0.886   0.819   0.682   1.079   0.995   0.791   0.922   0.809   0.542
25    S         1.621   1.656   1.743   1.577   1.634   1.775   1.767   1.811   1.954
26    I        -0.491  -0.466  -0.306  -0.967  -0.941  -0.713  -0.768  -0.728  -0.520
27    P         1.621   1.656   1.743   1.700   1.746   1.891   1.767   1.811   1.954
28    Y        -0.746  -0.796  -0.770  -0.423  -0.532  -0.466  -0.768  -0.832  -0.757
29    T        -0.746  -0.777  -0.761  -0.604  -0.639  -0.638  -0.768  -0.796  -0.748
30    K        -0.136  -0.166  -0.177  -0.211  -0.231  -0.277  -0.285  -0.312  -0.341
31    L        -0.136  -0.254  -0.208  -0.503  -0.651  -0.553  -0.285  -0.442  -0.393
32    Q        -0.956  -0.892  -0.781  -0.887  -0.791  -0.638  -1.010  -0.908  -0.767
33    L         1.621   1.656   1.743   1.260   1.310   1.474   1.767   1.811   1.954
34    Q        -0.474  -0.565  -0.695  -0.124  -0.263  -0.479  -0.406  -0.520  -0.663
35    F        -0.956  -0.971  -0.824  -1.141  -1.252  -1.023  -1.010  -1.007  -0.813
36    A         0.886   0.819   0.682   1.069   0.984   0.812   0.922   0.809   0.542
37    Y        -0.829  -0.827  -0.759  -0.930  -0.972  -0.816  -0.889  -0.859  -0.743
38    N        -0.956  -0.995  -0.819  -1.035  -1.109  -0.847  -1.010  -1.030  -0.809
39    L         1.621   1.656   1.743   1.260   1.310   1.474   1.767   1.811   1.954
40    Y         0.886   0.782   0.675   1.240   1.113   0.956   0.922   0.749   0.528
41    Q        -0.956  -0.901  -0.786  -1.003  -0.883  -0.720  -1.010  -0.919  -0.773
42    Q        -0.746  -0.758  -0.738  -0.510  -0.547  -0.499  -0.768  -0.778  -0.722
43    G         1.621   1.656   1.743   1.655   1.693   1.848   1.767   1.811   1.954
44    F         1.621   1.656   1.743   1.859   1.904   2.042   1.767   1.811   1.954
45    L         0.330   0.338   0.457  -0.226  -0.208   0.001  -0.044  -0.046   0.113
46    S         1.621   1.656   1.743   1.577   1.634   1.775   1.767   1.811   1.954
47    S         0.886   0.860   0.689   0.925   0.904   0.654   0.922   0.875   0.553
48    L        -0.408  -0.281  -0.252  -0.770  -0.504  -0.556  -0.648  -0.466  -0.445
49    Q         0.186   0.183  -0.083   0.502   0.490   0.111   0.198   0.181  -0.200
50    K         0.524   0.644   0.549   0.407   0.599   0.408   0.318   0.517   0.293
51    G         1.621   1.656   1.743   1.655   1.693   1.848   1.767   1.811   1.954
52    S        -0.136  -0.278  -0.222  -0.148  -0.341  -0.268  -0.285  -0.480  -0.411
53    T        -0.136  -0.278  -0.222  -0.056  -0.278  -0.220  -0.285  -0.480  -0.411
54    M        -2.098  -1.940  -1.867  -1.649  -1.391  -1.359  -1.493  -1.351  -1.217
55    G         0.886   0.782   0.675   1.009   0.866   0.716   0.922   0.749   0.528
56    P         1.621   1.656   1.743   1.700   1.746   1.891   1.767   1.811   1.954
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    D         0.886   0.782   0.675   1.168   1.048   0.866   0.922   0.749   0.528
64    K        -1.760  -1.649  -1.575  -1.836  -1.632  -1.511  -1.372  -1.268  -1.125
65    D        -1.760  -1.704  -1.573  -1.728  -1.689  -1.476  -1.372  -1.308  -1.123
66    F        -0.136  -0.044  -0.138   0.023   0.172   0.044  -0.285  -0.132  -0.284
67    V        -0.829  -0.799  -0.756  -0.879  -0.806  -0.728  -0.889  -0.841  -0.745
68    E        -0.474  -0.565  -0.695  -0.133  -0.278  -0.478  -0.406  -0.520  -0.663
69    V         0.524   0.471   0.506   0.387   0.290   0.336   0.318   0.207   0.209
70    T         1.621   1.656   1.743   1.727   1.775   1.917   1.767   1.811   1.954
71    P         0.186   0.003  -0.114   0.384   0.123  -0.099   0.198  -0.058  -0.246
72    D        -0.136  -0.278  -0.222   0.061  -0.151  -0.104  -0.285  -0.480  -0.411
73    N         1.621   1.656   1.743   1.686   1.734   1.878   1.767   1.811   1.954
74    I         0.330   0.308   0.447   0.068  -0.007   0.207  -0.044  -0.105   0.094
75    S        -0.136  -0.023  -0.164  -0.124   0.060  -0.188  -0.285  -0.113  -0.326
76    T         0.330   0.358   0.466   0.143   0.186   0.327  -0.044  -0.007   0.131
77    R         1.621   1.656   1.743   1.609   1.654   1.805   1.767   1.811   1.954
78    R         0.886   1.005   0.701   0.947   1.099   0.683   0.922   1.094   0.576
79    L         1.621   1.656   1.743   1.260   1.310   1.474   1.767   1.811   1.954
80    W         1.621   1.656   1.743   1.950   1.996   2.128   1.767   1.811   1.954
81    V        -0.491  -0.468  -0.304  -1.065  -1.026  -0.757  -0.768  -0.732  -0.516
82    G         0.186   0.171  -0.074   0.402   0.380   0.052   0.198   0.177  -0.188
83    L         1.621   1.656   1.743   1.260   1.310   1.474   1.767   1.811   1.954
84    K         1.621   1.656   1.743   1.587   1.646   1.784   1.767   1.811   1.954
85    Y         1.621   1.656   1.743   1.863   1.911   2.046   1.767   1.811   1.954
86    R        -0.474  -0.605  -0.690  -0.289  -0.448  -0.614  -0.406  -0.565  -0.658
87    D        -0.956  -0.908  -0.796  -0.869  -0.788  -0.626  -1.010  -0.934  -0.784
88    N         0.186   0.003  -0.114   0.407   0.157  -0.035   0.198  -0.058  -0.246
89    K        -0.280  -0.343  -0.236  -0.374  -0.431  -0.263  -0.527  -0.585  -0.434
90    P         0.524   0.581   0.558   0.492   0.583   0.501   0.318   0.407   0.310
91    V         1.621   1.656   1.743   1.541   1.584   1.740   1.767   1.811   1.954
92    L         0.330   0.400   0.474  -0.226  -0.111   0.020  -0.044   0.073   0.148
93    S        -1.294  -1.401  -1.237  -1.274  -1.397  -1.159  -1.131  -1.203  -0.999
94    S        -1.294  -1.346  -1.203  -1.107  -1.145  -0.931  -1.131  -1.154  -0.971
95    C        -0.829  -0.810  -0.756  -0.945  -0.966  -0.836  -0.889  -0.843  -0.741
96    K        -0.829  -0.770  -0.748  -0.953  -0.860  -0.804  -0.889  -0.815  -0.737
97    L         0.186   0.003  -0.114  -0.023  -0.265  -0.414   0.198  -0.058  -0.246
98    I         0.330   0.333   0.454   0.068   0.054   0.226  -0.044  -0.056   0.108
99    S         0.886   0.954   0.702   0.870   0.973   0.559   0.922   1.018   0.577
100   K         1.621   1.656   1.743   1.587   1.646   1.784   1.767   1.811   1.954
101   P         1.621   1.656   1.743   1.700   1.746   1.891   1.767   1.811   1.954
102   N        -0.280  -0.154  -0.189  -0.455  -0.243  -0.282  -0.527  -0.335  -0.362
103   S        -1.084  -0.820  -1.109  -0.990  -0.596  -1.086  -0.889  -0.592  -0.875
104   R        -0.280  -0.346  -0.234  -0.572  -0.685  -0.536  -0.527  -0.591  -0.433
105   I        -0.280  -0.302  -0.228  -0.424  -0.457  -0.306  -0.527  -0.547  -0.425
106   H        -2.098  -2.011  -1.866  -1.707  -1.605  -1.392  -1.493  -1.408  -1.217
107   L         0.186   0.183  -0.083   0.012  -0.004  -0.299   0.198   0.181  -0.200
108   P        -1.084  -0.931  -1.138  -0.777  -0.580  -0.897  -0.889  -0.724  -0.903
109   M        -1.294  -1.232  -1.180  -1.187  -1.160  -1.040  -1.131  -1.065  -0.950
110   E        -1.084  -0.965  -1.114  -0.697  -0.554  -0.760  -0.889  -0.755  -0.880
111   D        -0.136  -0.118  -0.154   0.037   0.086   0.014  -0.285  -0.233  -0.308
112   M        -0.136   0.014  -0.153  -0.461  -0.265  -0.419  -0.285  -0.090  -0.308
113   K        -0.474  -0.676  -0.718  -0.418  -0.730  -0.877  -0.406  -0.647  -0.691
114   K        -0.956  -1.002  -0.825  -1.034  -1.077  -0.821  -1.010  -1.035  -0.814
115   L        -0.136  -0.210  -0.203  -0.519  -0.613  -0.568  -0.285  -0.380  -0.385
116   C        -0.280  -0.227  -0.201  -0.231  -0.138  -0.085  -0.527  -0.420  -0.379
117   S        -0.474  -0.676  -0.718  -0.447  -0.762  -0.926  -0.406  -0.647  -0.691
118   G         1.621   1.656   1.743   1.655   1.693   1.848   1.767   1.811   1.954
119   V        -1.422  -1.381  -1.240  -1.693  -1.589  -1.349  -1.251  -1.193  -1.001
120   T        -0.956  -0.829  -0.789  -1.100  -0.903  -0.829  -1.010  -0.871  -0.777
121   I         0.186   0.196  -0.074   0.253   0.254  -0.116   0.198   0.197  -0.188
122   R        -0.474  -0.676  -0.718  -0.344  -0.650  -0.761  -0.406  -0.647  -0.691
123   N        -1.294  -1.199  -1.183  -1.065  -0.888  -0.936  -1.131  -1.022  -0.952
124   I        -0.280  -0.347  -0.229  -0.424  -0.495  -0.305  -0.527  -0.592  -0.427
125   K        -0.136  -0.166  -0.202  -0.179  -0.233  -0.281  -0.285  -0.345  -0.382
126   P        -0.136  -0.195  -0.207  -0.086  -0.220  -0.223  -0.285  -0.393  -0.390
127   L         0.886   0.860   0.689   0.613   0.588   0.375   0.922   0.875   0.553
128   Q        -0.474  -0.503  -0.678  -0.143  -0.189  -0.484  -0.406  -0.441  -0.644
129   P         0.186   0.040  -0.097   0.343   0.117  -0.154   0.198  -0.007  -0.222
130   G         0.330   0.347   0.461   0.139   0.144   0.326  -0.044  -0.029   0.121
131   E         1.621   1.656   1.743   1.753   1.794   1.942   1.767   1.811   1.954
132   L        -0.491  -0.469  -0.300  -0.883  -0.788  -0.544  -0.768  -0.731  -0.512
133   I        -0.474  -0.553  -0.689  -0.289  -0.444  -0.662  -0.406  -0.508  -0.656
134   L        -0.280  -0.326  -0.234  -0.598  -0.613  -0.443  -0.527  -0.570  -0.433
135   V         0.524   0.528   0.517   0.366   0.365   0.324   0.318   0.311   0.231
136   R        -0.829  -0.916  -0.761  -0.926  -1.014  -0.784  -0.889  -0.948  -0.749
137   A        -0.474  -0.266  -0.624  -0.166   0.118  -0.400  -0.406  -0.146  -0.580
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   H        -1.632  -1.456  -1.513  -1.259  -0.999  -1.136  -1.251  -1.076  -1.074
142   N        -1.632  -1.725  -1.584  -1.332  -1.470  -1.285  -1.251  -1.313  -1.130
143   N        -1.422  -1.328  -1.227  -1.293  -1.180  -1.001  -1.251  -1.152  -0.993
144   I         0.330   0.326   0.452   0.068   0.036   0.221  -0.044  -0.071   0.103
145   M        -0.829  -0.768  -0.760  -1.005  -0.938  -0.894  -0.889  -0.816  -0.749
146   D        -0.280  -0.326  -0.234  -0.240  -0.301  -0.180  -0.527  -0.570  -0.433
147   I        -0.280  -0.300  -0.232  -0.554  -0.597  -0.523  -0.527  -0.542  -0.431
148   N        -1.422  -1.394  -1.232  -1.211  -1.179  -0.936  -1.251  -1.207  -0.996
149   E         0.524   0.542   0.517   0.618   0.640   0.573   0.318   0.337   0.231
150   A         1.621   1.656   1.743   1.691   1.729   1.883   1.767   1.811   1.954
151   I        -0.746  -0.833  -0.765  -0.666  -0.783  -0.693  -0.768  -0.846  -0.749
152   S        -1.294  -1.258  -1.196  -1.278  -1.203  -1.134  -1.131  -1.072  -0.962
153   K        -0.746  -0.770  -0.762  -0.761  -0.823  -0.777  -0.768  -0.808  -0.749
154   K        -1.632  -1.608  -1.544  -1.393  -1.340  -1.263  -1.251  -1.213  -1.098
155   L        -0.746  -0.660  -0.729  -1.080  -0.982  -0.991  -0.768  -0.675  -0.712
156   D        -0.474  -0.310  -0.642  -0.267  -0.051  -0.539  -0.406  -0.200  -0.601
157   G         1.621   1.656   1.743   1.655   1.693   1.848   1.767   1.811   1.954
158   E        -1.084  -1.183  -1.178  -0.779  -0.980  -0.985  -0.889  -0.985  -0.943
159   V         0.186   0.318  -0.052   0.186   0.371  -0.206   0.198   0.378  -0.155
160   L         0.524   0.471   0.506   0.091   0.006   0.066   0.318   0.207   0.209
161   C         0.186   0.171  -0.074   0.538   0.519   0.100   0.198   0.177  -0.188
162   R         0.886   0.782   0.675   0.947   0.807   0.639   0.922   0.749   0.528
163   V        -0.136  -0.094  -0.168  -0.233  -0.156  -0.279  -0.285  -0.209  -0.334
164   K        -0.136  -0.108  -0.174  -0.232  -0.163  -0.314  -0.285  -0.230  -0.342
* 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/Q03799
Output conservation file - output/Q03799
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
