1     M         1.537   1.596   1.692   1.806   1.893   2.036   1.657   1.738   1.904
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     E         0.204   0.257   0.398   0.398   0.481   0.672  -0.225  -0.146   0.051
5     H        -0.017  -0.279  -0.244   0.459   0.052   0.020  -0.068  -0.433  -0.406
6     P         0.736   0.587   0.575   1.005   0.851   0.804   0.716   0.459   0.392
7     A         0.736   0.879   0.611   0.718   0.908   0.546   0.716   0.929   0.458
8     Y        -0.328  -0.448  -0.308  -0.284  -0.554  -0.392  -0.538  -0.682  -0.505
9     T        -0.328  -0.306  -0.304  -0.289  -0.302  -0.302  -0.538  -0.543  -0.500
10    L         1.537   1.596   1.692   1.126   1.208   1.389   1.657   1.738   1.904
11    S         0.736   0.879   0.611   0.827   1.005   0.623   0.716   0.929   0.458
12    L        -0.955  -0.888  -0.820  -1.351  -1.127  -1.132  -1.009  -0.899  -0.796
13    L         1.537   1.596   1.692   1.126   1.208   1.389   1.657   1.738   1.904
14    T        -0.955  -0.890  -0.827  -0.833  -0.813  -0.746  -1.009  -0.901  -0.804
15    T        -0.328  -0.287  -0.250  -0.333  -0.214  -0.217  -0.538  -0.445  -0.416
16    A        -0.955  -0.953  -0.842  -0.803  -0.820  -0.678  -1.009  -0.987  -0.826
17    G         1.537   1.596   1.692   1.183   1.287   1.443   1.657   1.738   1.904
18    G         1.537   1.596   1.692   1.183   1.287   1.443   1.657   1.738   1.904
19    L        -0.955  -0.851  -0.836  -1.020  -0.943  -0.893  -1.009  -0.884  -0.820
20    M        -0.715  -0.894  -0.833  -0.292  -0.606  -0.556  -0.695  -0.899  -0.810
21    G         1.537   1.596   1.692   1.183   1.287   1.443   1.657   1.738   1.904
22    Y         1.537   1.596   1.692   1.536   1.635   1.779   1.657   1.738   1.904
23    Y        -1.342  -1.274  -1.258  -1.312  -1.311  -1.218  -1.166  -1.078  -1.016
24    R         1.537   1.596   1.692   1.780   1.848   2.010   1.657   1.738   1.904
25    K         0.736   0.626   0.583   0.955   0.811   0.729   0.716   0.525   0.406
26    G         0.204   0.251   0.402  -0.267  -0.113   0.122  -0.225  -0.159   0.060
27    S         1.537   1.596   1.692   1.566   1.635   1.807   1.657   1.738   1.904
28    I        -1.488  -1.248  -1.272  -1.507  -1.113  -1.141  -1.323  -1.063  -1.032
29    P         0.736   0.587   0.575   0.970   0.794   0.730   0.716   0.459   0.392
30    S         1.537   1.596   1.692   1.566   1.635   1.807   1.657   1.738   1.904
31    L         0.736   0.626   0.583   0.432   0.293   0.270   0.716   0.525   0.406
32    V         0.204   0.245   0.397   0.128   0.176   0.419  -0.225  -0.171   0.049
33    S         0.736   0.882   0.612   0.718   0.912   0.549   0.716   0.934   0.460
34    G         1.537   1.596   1.692   1.183   1.287   1.443   1.657   1.738   1.904
35    L        -1.342  -1.328  -1.276  -1.519  -1.409  -1.340  -1.166  -1.141  -1.033
36    V        -0.328  -0.304  -0.307  -0.333  -0.386  -0.356  -0.538  -0.541  -0.504
37    F        -0.715  -0.829  -0.814  -0.400  -0.689  -0.667  -0.695  -0.833  -0.789
38    G         0.369   0.576   0.528  -0.073   0.258   0.178   0.089   0.440   0.303
39    S        -1.488  -1.385  -1.275  -1.952  -1.853  -1.617  -1.323  -1.197  -1.034
40    V        -0.715  -0.681  -0.778  -0.839  -0.784  -0.833  -0.695  -0.655  -0.748
41    Y         0.802   0.712   0.624   0.923   0.835   0.719   0.817   0.668   0.482
42    G        -0.220  -0.389  -0.267  -0.688  -0.994  -0.829  -0.384  -0.596  -0.451
43    I        -1.845  -1.740  -1.636  -1.707  -1.535  -1.476  -1.465  -1.343  -1.179
44    A         0.101   0.100  -0.146   0.101   0.080  -0.310   0.096   0.094  -0.264
45    G         0.101  -0.182  -0.167  -0.091  -0.477  -0.474   0.096  -0.296  -0.294
46    Y         0.101  -0.182  -0.167   0.300  -0.076  -0.060   0.096  -0.296  -0.294
47    L         0.802   0.740   0.634   0.522   0.458   0.371   0.817   0.713   0.500
48    L         0.101  -0.081  -0.188  -0.077  -0.297  -0.378   0.096  -0.152  -0.325
49    H        -0.830  -0.889  -0.843  -0.388  -0.431  -0.335  -0.864  -0.887  -0.825
50    M        -1.379  -1.298  -1.265  -0.841  -0.742  -0.742  -1.225  -1.120  -1.027
51    N         0.802   0.712   0.624   1.154   1.024   0.830   0.817   0.668   0.482
52    R        -0.830  -0.889  -0.843  -0.691  -0.758  -0.629  -0.864  -0.887  -0.825
53    D         0.101  -0.081  -0.188   0.635   0.397   0.177   0.096  -0.152  -0.325
54    G        -1.169  -1.189  -1.208  -0.793  -0.772  -0.820  -0.984  -1.005  -0.969
55    G         1.537   1.596   1.692   1.200   1.312   1.459   1.657   1.738   1.904
56    L         0.101  -0.081  -0.188  -0.110  -0.349  -0.449   0.096  -0.152  -0.325
57    E         0.802   0.712   0.624   1.240   1.150   1.020   0.817   0.668   0.482
58    M        -1.379  -1.372  -1.239  -1.482  -1.497  -1.222  -1.225  -1.179  -1.002
59    A         0.802   0.740   0.634   0.736   0.647   0.458   0.817   0.713   0.500
60    L         0.101  -0.182  -0.167  -0.085  -0.444  -0.368   0.096  -0.296  -0.294
61    G        -0.558  -0.585  -0.756  -0.785  -0.848  -1.144  -0.504  -0.540  -0.722
62    A        -0.830  -0.700  -0.782  -0.924  -0.744  -0.894  -0.864  -0.668  -0.754
63    S         1.537   1.596   1.692   1.578   1.657   1.819   1.657   1.738   1.904
64    T        -1.169  -1.163  -1.241  -0.953  -0.999  -1.204  -0.984  -0.964  -1.000
65    L        -0.220   0.072  -0.186  -0.265   0.174  -0.238  -0.384   0.021  -0.329
66    L         0.802   0.988   0.674   0.525   0.744   0.432   0.817   1.087   0.572
67    L         0.101   0.100  -0.146  -0.197  -0.214  -0.572   0.096   0.094  -0.264
68    G        -0.913  -0.803  -0.810  -1.130  -1.043  -0.970  -0.984  -0.836  -0.794
69    A        -0.220  -0.104  -0.251  -0.297  -0.174  -0.337  -0.384  -0.251  -0.429
70    G         0.246   0.247   0.397  -0.251  -0.191   0.041  -0.144  -0.168   0.049
71    V        -1.379  -1.317  -1.261  -1.715  -1.652  -1.541  -1.225  -1.144  -1.023
72    I        -1.379  -0.990  -1.201  -1.246  -0.577  -0.984  -1.225  -0.788  -0.966
73    R         1.537   1.596   1.692   1.787   1.863   2.017   1.657   1.738   1.904
74    G        -1.379  -1.407  -1.264  -1.562  -1.528  -1.302  -1.225  -1.221  -1.026
75    M        -0.558  -0.474  -0.747  -0.229  -0.148  -0.577  -0.504  -0.399  -0.711
76    P        -0.365  -0.256  -0.266  -0.297  -0.138  -0.138  -0.624  -0.475  -0.453
77    S        -1.845  -1.789  -1.626  -1.921  -1.918  -1.701  -1.465  -1.376  -1.170
78    R        -0.830  -0.656  -0.772  -0.666  -0.478  -0.613  -0.864  -0.676  -0.747
79    F        -0.156  -0.346  -0.287   0.203  -0.097  -0.044  -0.264  -0.544  -0.468
80    T        -1.063  -1.025  -0.885  -1.198  -1.190  -1.015  -1.109  -1.043  -0.867
81    K         1.537   1.596   1.692   1.653   1.731   1.890   1.657   1.738   1.904
82    P         1.537   1.596   1.692   1.673   1.794   1.909   1.657   1.738   1.904
83    V        -0.220   0.092  -0.196  -0.154   0.293  -0.177  -0.384   0.054  -0.345
84    P         1.537   1.596   1.692   1.673   1.794   1.909   1.657   1.738   1.904
85    V        -1.041  -0.902  -0.861  -1.064  -0.781  -0.735  -1.105  -0.936  -0.845
86    V        -1.169  -1.381  -1.258  -0.942  -1.344  -1.217  -0.984  -1.180  -1.017
87    L         1.537   1.596   1.692   1.125   1.206   1.388   1.657   1.738   1.904
88    T        -0.830  -0.887  -0.787  -0.905  -0.928  -0.866  -0.864  -0.883  -0.759
89    A         0.439   0.489   0.465   0.433   0.491   0.396   0.216   0.287   0.184
90    L         0.101   0.100  -0.146  -0.054  -0.063  -0.282   0.096   0.094  -0.264
91    G         0.802   0.740   0.634   0.540   0.490   0.316   0.817   0.713   0.500
92    G        -0.830  -1.024  -0.837  -1.143  -1.378  -1.096  -0.864  -1.045  -0.821
93    L        -1.169  -1.140  -1.243  -1.280  -1.226  -1.300  -0.984  -0.943  -1.003
94    G        -0.365  -0.444  -0.278  -0.686  -0.714  -0.466  -0.624  -0.681  -0.469
95    S        -0.492  -0.463  -0.339  -0.711  -0.785  -0.586  -0.744  -0.707  -0.542
96    Y        -1.041  -0.918  -0.855  -1.141  -0.986  -0.856  -1.105  -0.971  -0.840
97    Y         0.802   0.740   0.634   0.904   0.849   0.693   0.817   0.713   0.500
98    Y         0.439   0.362   0.425   0.444   0.329   0.412   0.216   0.053   0.104
99    Y        -1.717  -1.621  -1.589  -1.478  -1.389  -1.328  -1.345  -1.243  -1.141
100   N        -1.342  -1.414  -1.292  -0.906  -1.033  -0.836  -1.166  -1.218  -1.047
101   K         0.736   0.610   0.558   0.918   0.722   0.607   0.716   0.498   0.360
102   Y         0.736   0.610   0.558   0.837   0.693   0.615   0.716   0.498   0.360
103   K        -0.328  -0.279  -0.272  -0.088  -0.002   0.014  -0.538  -0.433  -0.447
104   E        -0.558  -0.878  -0.792   0.071  -0.351  -0.259  -0.504  -0.873  -0.763
105   F         0.101  -0.081  -0.188   0.446   0.173  -0.082   0.096  -0.152  -0.325
106   Y         0.101  -0.081  -0.188   0.255   0.014  -0.189   0.096  -0.152  -0.325
107   P         0.657   0.551   0.541   0.821   0.658   0.589   0.590   0.397   0.327
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -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/P47131
Output conservation file - output/P47131
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
