1     M         1.641   1.724   1.830   1.870   1.991   2.174   1.783   1.903   2.081
2     G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     N        -1.977  -1.824  -1.732  -1.742  -1.560  -1.405  -1.540  -1.379  -1.215
4     F         0.792   0.646   0.618   0.873   0.642   0.546   0.786   0.528   0.428
5     R         1.641   1.724   1.830   1.347   1.485   1.672   1.783   1.903   2.081
6     F         0.708   0.542   0.559   0.764   0.487   0.444   0.652   0.344   0.317
7     P         0.792   0.755   0.627   0.933   0.891   0.649   0.786   0.712   0.445
8     I        -0.453  -0.445  -0.321  -0.597  -0.587  -0.419  -0.704  -0.669  -0.509
9     K         0.792   0.849   0.655   0.746   0.824   0.564   0.786   0.865   0.496
10    T        -0.438  -0.392  -0.297  -0.622  -0.527  -0.420  -0.709  -0.612  -0.479
11    K        -0.337  -0.327  -0.283  -0.472  -0.441  -0.342  -0.543  -0.509  -0.457
12    L        -0.007  -0.063  -0.204  -0.083  -0.173  -0.361  -0.044  -0.141  -0.340
13    P         0.792   0.755   0.627   0.976   0.946   0.745   0.786   0.712   0.445
14    P        -0.633  -0.531  -0.350  -0.938  -0.798  -0.491  -0.930  -0.786  -0.547
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    G        -0.958  -0.699  -0.819  -0.797  -0.441  -0.589  -1.015  -0.738  -0.779
17    F        -0.599  -0.530  -0.353  -0.572  -0.445  -0.189  -0.888  -0.785  -0.551
18    I        -0.870  -0.877  -0.836  -1.020  -1.019  -0.918  -0.888  -0.878  -0.793
19    N         0.118  -0.139  -0.177   0.335  -0.015  -0.105   0.129  -0.229  -0.301
20    A        -0.581  -0.717  -0.781  -0.440  -0.610  -0.685  -0.506  -0.660  -0.721
21    R         0.477   0.374   0.469   0.020  -0.197  -0.042   0.257   0.032   0.141
22    I         0.118   0.099  -0.133   0.305   0.271  -0.086   0.129   0.089  -0.238
23    L        -0.376  -0.361  -0.236  -0.672  -0.621  -0.418  -0.634  -0.560  -0.398
24    R         0.477   0.455   0.498   0.020  -0.044   0.012   0.257   0.184   0.199
25    D         1.641   1.724   1.830   1.896   2.025   2.199   1.783   1.903   2.081
26    N        -0.870  -0.933  -0.851  -0.784  -0.873  -0.766  -0.888  -0.921  -0.804
27    F        -0.581  -0.847  -0.828  -0.391  -0.832  -0.865  -0.506  -0.814  -0.775
28    K         0.118  -0.139  -0.177   0.200  -0.136  -0.167   0.129  -0.229  -0.301
29    R         1.641   1.724   1.830   1.323   1.447   1.649   1.783   1.903   2.081
30    Q        -1.452  -1.556  -1.354  -1.538  -1.735  -1.460  -1.270  -1.313  -1.070
31    Q        -0.581  -0.847  -0.828  -0.366  -0.800  -0.863  -0.506  -0.814  -0.775
32    F        -0.870  -0.810  -0.822  -0.730  -0.585  -0.635  -0.888  -0.775  -0.774
33    K         0.118   0.213  -0.110   0.086   0.211  -0.304   0.129   0.259  -0.204
34    E         0.118   0.178  -0.114   0.412   0.473   0.107   0.129   0.190  -0.210
35    N        -0.870  -0.870  -0.823  -0.633  -0.608  -0.606  -0.888  -0.842  -0.773
36    E         1.641   1.724   1.830   1.745   1.860   2.054   1.783   1.903   2.081
37    I        -0.376  -0.336  -0.265  -0.449  -0.362  -0.250  -0.634  -0.556  -0.443
38    L        -0.870  -0.913  -0.863  -0.820  -0.907  -0.860  -0.888  -0.935  -0.822
39    V        -0.223   0.172  -0.167  -0.591  -0.018  -0.494  -0.379   0.165  -0.291
40    K        -1.093  -1.094  -0.905  -1.352  -1.330  -1.072  -1.142  -1.100  -0.864
41    S         0.477   0.487   0.504   0.311   0.310   0.337   0.257   0.243   0.210
42    L         0.861   0.745   0.680   0.738   0.593   0.513   0.893   0.696   0.543
43    K        -0.223  -0.330  -0.257  -0.560  -0.778  -0.723  -0.379  -0.512  -0.427
44    F        -0.223  -0.168  -0.209  -0.000   0.127   0.007  -0.379  -0.271  -0.351
45    I         0.861   0.869   0.697   1.059   1.082   0.837   0.893   0.897   0.574
46    A        -0.581  -0.847  -0.828  -0.438  -0.789  -0.742  -0.506  -0.814  -0.775
47    R         0.861   0.758   0.683   0.639   0.524   0.437   0.893   0.718   0.548
48    N         1.641   1.724   1.830   1.705   1.836   2.015   1.783   1.903   2.081
49    M        -0.581  -0.497  -0.745  -0.265  -0.166  -0.496  -0.506  -0.408  -0.678
50    N        -0.376  -0.245  -0.265  -0.439  -0.268  -0.248  -0.634  -0.476  -0.445
51    L         1.641   1.724   1.830   1.430   1.547   1.751   1.783   1.903   2.081
52    P         0.861   0.940   0.717   1.008   1.131   0.778   0.893   1.006   0.609
53    T        -1.452  -1.419  -1.320  -1.484  -1.447  -1.278  -1.270  -1.191  -1.039
54    K         0.477   0.495   0.497   0.020   0.029   0.010   0.257   0.257   0.196
55    L        -1.946  -1.807  -1.695  -1.938  -1.667  -1.560  -1.524  -1.364  -1.189
56    R         1.641   1.724   1.830   1.323   1.447   1.649   1.783   1.903   2.081
57    L        -1.229  -1.128  -1.244  -1.221  -1.113  -1.225  -1.015  -0.901  -0.965
58    E         0.118  -0.033  -0.155   0.379   0.179  -0.024   0.129  -0.080  -0.269
59    A         1.641   1.724   1.830   1.534   1.650   1.852   1.783   1.903   2.081
60    Q         0.118  -0.139  -0.177   0.391   0.038  -0.052   0.129  -0.229  -0.301
61    L         0.861   0.745   0.680   0.711   0.548   0.452   0.893   0.696   0.543
62    K         0.118   0.099  -0.133   0.295   0.248  -0.177   0.129   0.089  -0.238
63    L         0.861   0.745   0.680   0.745   0.600   0.529   0.893   0.696   0.543
64    N        -1.452  -1.243  -1.272  -1.322  -0.993  -1.069  -1.270  -1.019  -0.993
65    A        -0.958  -0.814  -0.815  -1.027  -0.840  -0.787  -1.015  -0.846  -0.775
66    L         0.477   0.487   0.504   0.528   0.507   0.445   0.257   0.243   0.210
67    P         0.861   0.869   0.697   1.076   1.112   0.893   0.893   0.897   0.574
68    N        -1.452  -1.556  -1.354  -1.480  -1.626  -1.360  -1.270  -1.313  -1.070
69    Y         0.118  -0.139  -0.177   0.516   0.159   0.050   0.129  -0.229  -0.301
70    M        -0.581  -0.729  -0.797  -0.299  -0.547  -0.638  -0.506  -0.685  -0.739
71    R        -0.870  -1.000  -0.863  -1.059  -1.178  -0.944  -0.888  -0.993  -0.817
72    S        -2.305  -2.029  -2.014  -1.997  -1.572  -1.601  -1.651  -1.402  -1.294
73    T        -0.581  -0.561  -0.768  -0.249  -0.217  -0.502  -0.506  -0.480  -0.705
74    Q         0.118  -0.139  -0.177   0.329  -0.060  -0.190   0.129  -0.229  -0.301
75    I         0.118   0.217  -0.108   0.350   0.445  -0.011   0.129   0.235  -0.201
76    K         0.861   0.869   0.697   0.781   0.792   0.509   0.893   0.897   0.574
77    N         0.118   0.132  -0.123   0.369   0.391   0.053   0.129   0.133  -0.223
78    R         1.641   1.724   1.830   1.323   1.447   1.649   1.783   1.903   2.081
79    C         1.641   1.724   1.830   1.916   2.032   2.218   1.783   1.903   2.081
80    V         0.206   0.290   0.449  -0.024   0.110   0.359  -0.252  -0.132   0.101
81    D        -0.870  -0.736  -0.796  -0.852  -0.655  -0.749  -0.888  -0.706  -0.742
82    S        -0.376  -0.356  -0.262  -0.397  -0.365  -0.201  -0.634  -0.590  -0.440
83    G         1.641   1.724   1.830   1.785   1.907   2.092   1.783   1.903   2.081
84    H        -0.870  -0.848  -0.852  -0.808  -0.953  -0.943  -0.888  -0.875  -0.812
85    A        -0.376  -0.429  -0.275  -0.559  -0.591  -0.334  -0.634  -0.669  -0.457
86    R         0.272   0.330   0.459  -0.359  -0.283  -0.058  -0.125  -0.054   0.122
87    F        -0.958  -0.649  -0.814  -0.899  -0.455  -0.678  -1.015  -0.669  -0.771
88    V         0.477   0.425   0.484   0.461   0.364   0.424   0.257   0.128   0.170
89    L        -0.223  -0.338  -0.263  -0.429  -0.584  -0.453  -0.379  -0.524  -0.436
90    S        -0.958  -0.936  -0.845  -1.228  -1.241  -1.072  -1.015  -0.939  -0.800
91    D         0.118  -0.139  -0.177   0.500   0.124   0.006   0.129  -0.229  -0.301
92    F         1.641   1.724   1.830   1.718   1.853   2.028   1.783   1.903   2.081
93    R        -0.376  -0.332  -0.242  -0.850  -0.667  -0.542  -0.634  -0.516  -0.402
94    L         0.861   0.869   0.697   0.763   0.791   0.597   0.893   0.897   0.574
95    C        -0.870  -0.933  -0.851  -0.640  -0.744  -0.671  -0.888  -0.921  -0.804
96    R         1.641   1.724   1.830   1.323   1.447   1.649   1.783   1.903   2.081
97    Y        -1.452  -1.339  -1.312  -1.170  -1.046  -0.995  -1.270  -1.149  -1.036
98    Q        -1.811  -1.876  -1.722  -1.402  -1.495  -1.284  -1.397  -1.415  -1.208
99    F         0.118   0.029  -0.139   0.304   0.197  -0.122   0.129   0.002  -0.247
100   R         0.118   0.029  -0.139  -0.013  -0.119  -0.310   0.129   0.002  -0.247
101   E        -1.229  -1.253  -1.288  -0.939  -1.017  -1.079  -1.015  -1.023  -1.008
102   N        -1.567  -1.515  -1.341  -2.017  -1.913  -1.686  -1.373  -1.288  -1.059
103   A         0.792   0.657   0.649   0.719   0.500   0.486   0.786   0.547   0.485
104   L        -0.337  -0.325  -0.260  -0.802  -0.717  -0.686  -0.543  -0.495  -0.427
105   K        -0.337  -0.340  -0.290  -0.586  -0.616  -0.498  -0.543  -0.547  -0.472
106   G         0.792   0.701   0.655   0.988   0.873   0.783   0.786   0.622   0.496
107   N        -1.590  -1.432  -1.344  -1.601  -1.425  -1.262  -1.383  -1.210  -1.060
108   L         0.323   0.367   0.464  -0.053   0.003   0.180  -0.026   0.018   0.132
109   P         1.641   1.724   1.830   1.732   1.861   2.042   1.783   1.903   2.081
110   G         1.641   1.724   1.830   1.759   1.879   2.067   1.783   1.903   2.081
111   V         1.641   1.724   1.830   1.724   1.858   2.033   1.783   1.903   2.081
112   K        -0.007  -0.192  -0.217  -0.058  -0.381  -0.450  -0.044  -0.309  -0.358
113   K        -0.223  -0.241  -0.230  -0.413  -0.444  -0.457  -0.379  -0.379  -0.381
114   G        -0.958  -0.936  -0.845  -1.013  -0.973  -0.822  -1.015  -0.939  -0.800
115   I        -1.452  -1.311  -1.290  -1.223  -0.982  -0.964  -1.270  -1.082  -1.011
116   W         0.118   0.029  -0.139   0.618   0.499   0.213   0.129   0.002  -0.247
* 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/P10663
Output conservation file - output/P10663
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
