1     M         1.240   1.290   1.341   1.430   1.503   1.575   1.321   1.392   1.469
2     K         1.240   1.290   1.341   1.287   1.362   1.442   1.321   1.392   1.469
3     F        -0.025  -0.282  -0.332   0.141  -0.266  -0.420  -0.051  -0.407  -0.493
4     L         0.592   0.456   0.371   0.312   0.139   0.066   0.582   0.357   0.178
5     T         1.240   1.290   1.341   1.340   1.417   1.492   1.321   1.392   1.469
6     T        -0.607  -0.845  -0.855  -0.428  -0.856  -0.909  -0.578  -0.856  -0.856
7     N         1.240   1.290   1.341   1.224   1.314   1.384   1.321   1.392   1.469
8     F         1.240   1.290   1.341   1.350   1.436   1.500   1.321   1.392   1.469
9     L         0.102   0.204   0.239  -0.430  -0.282  -0.184  -0.262  -0.090  -0.070
10    K        -0.607  -0.845  -0.855  -0.400  -0.753  -0.785  -0.578  -0.856  -0.856
11    C         1.240   1.290   1.341   1.383   1.468   1.531   1.321   1.392   1.469
12    S         0.048   0.103   0.207  -0.138  -0.056   0.117  -0.367  -0.285  -0.131
13    V        -0.607  -0.631  -0.811  -0.404  -0.453  -0.740  -0.578  -0.609  -0.806
14    K         1.240   1.290   1.341   1.287   1.362   1.442   1.321   1.392   1.469
15    A        -1.741  -1.732  -1.584  -1.525  -1.534  -1.307  -1.423  -1.376  -1.195
16    C         1.240   1.290   1.341   1.383   1.468   1.531   1.321   1.392   1.469
17    D        -1.144  -1.260  -1.241  -0.942  -1.119  -1.084  -1.000  -1.111  -1.048
18    T        -0.308  -0.093  -0.329  -0.268   0.060  -0.309  -0.473  -0.157  -0.490
19    S         1.240   1.290   1.341   1.307   1.379   1.460   1.321   1.392   1.469
20    N        -1.144  -1.078  -1.221  -1.079  -0.975  -1.251  -1.000  -0.924  -1.030
21    D        -0.607  -0.660  -0.817  -0.561  -0.638  -0.994  -0.578  -0.640  -0.813
22    N        -0.621  -0.584  -0.451  -0.814  -0.741  -0.536  -0.895  -0.834  -0.659
23    F         1.240   1.290   1.341   1.350   1.436   1.500   1.321   1.392   1.469
24    P         1.240   1.290   1.341   1.234   1.313   1.393   1.321   1.392   1.469
25    L         1.240   1.290   1.341   0.868   0.935   1.052   1.321   1.392   1.469
26    Q        -2.039  -1.976  -1.831  -1.650  -1.556  -1.364  -1.528  -1.447  -1.269
27    Y        -0.607  -0.845  -0.855  -0.233  -0.598  -0.669  -0.578  -0.856  -0.856
28    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    S        -1.741  -1.697  -1.564  -1.628  -1.583  -1.347  -1.423  -1.354  -1.182
31    K        -1.330  -1.209  -1.230  -1.374  -1.208  -1.207  -1.212  -1.080  -1.043
32    C        -0.308  -0.403  -0.406  -0.264  -0.464  -0.524  -0.473  -0.625  -0.602
33    Q        -0.308  -0.465  -0.405  -0.262  -0.541  -0.472  -0.473  -0.683  -0.602
34    L         0.592   0.609   0.383   0.312   0.338   0.083   0.582   0.604   0.200
35    V        -0.436  -0.353  -0.389  -0.519  -0.412  -0.439  -0.684  -0.585  -0.585
36    Q        -0.025  -0.282  -0.332   0.217  -0.139  -0.268  -0.051  -0.407  -0.493
37    D        -0.548  -0.478  -0.424  -0.708  -0.572  -0.517  -0.789  -0.697  -0.624
38    E        -0.025  -0.282  -0.332   0.042  -0.321  -0.400  -0.051  -0.407  -0.493
39    S        -1.330  -1.411  -1.276  -1.302  -1.483  -1.281  -1.212  -1.245  -1.080
40    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    E         0.273   0.449   0.332   0.128   0.398   0.209   0.055   0.346   0.106
42    F        -0.846  -0.947  -0.868  -0.755  -0.943  -0.862  -0.895  -0.971  -0.871
43    N        -0.025  -0.151  -0.315   0.073  -0.085  -0.364  -0.051  -0.226  -0.469
44    P         1.240   1.290   1.341   1.234   1.313   1.393   1.321   1.392   1.469
45    E         0.592   0.456   0.371   0.614   0.434   0.318   0.582   0.357   0.178
46    F         0.592   0.456   0.371   0.716   0.506   0.303   0.582   0.357   0.178
47    L         0.273   0.449   0.332  -0.168   0.096  -0.054   0.055   0.346   0.106
48    L        -1.032  -0.842  -0.875  -1.297  -0.942  -1.017  -1.106  -0.877  -0.880
49    N        -1.330  -1.290  -1.248  -1.144  -1.076  -0.987  -1.212  -1.137  -1.055
50    I        -0.308  -0.375  -0.372  -0.241  -0.314  -0.331  -0.473  -0.541  -0.555
51    V        -0.607  -0.544  -0.792  -0.799  -0.719  -0.991  -0.578  -0.508  -0.784
52    D        -0.548  -0.552  -0.451  -0.765  -0.791  -0.644  -0.789  -0.795  -0.658
53    R         1.240   1.290   1.341   1.481   1.563   1.623   1.321   1.392   1.469
54    V        -0.621  -0.464  -0.416  -0.978  -0.659  -0.645  -0.895  -0.675  -0.612
55    D         1.240   1.290   1.341   1.254   1.347   1.411   1.321   1.392   1.469
56    W         1.240   1.290   1.341   1.527   1.606   1.666   1.321   1.392   1.469
57    P        -1.442  -1.290  -1.258  -1.469  -1.229  -1.173  -1.317  -1.157  -1.067
58    A         1.240   1.290   1.341   1.326   1.401   1.478   1.321   1.392   1.469
59    V        -0.621  -0.464  -0.416  -1.075  -0.903  -0.775  -0.895  -0.675  -0.612
60    L        -1.032  -1.034  -0.892  -1.242  -1.232  -1.026  -1.106  -1.073  -0.899
61    T        -1.330  -1.135  -1.228  -1.153  -0.913  -0.980  -1.212  -1.016  -1.040
62    V         0.273   0.159   0.232   0.278   0.065   0.170   0.055  -0.176  -0.084
63    A        -0.025  -0.282  -0.332   0.192  -0.174  -0.270  -0.051  -0.407  -0.493
64    A        -2.039  -1.976  -1.831  -1.692  -1.588  -1.400  -1.528  -1.447  -1.269
65    E        -0.308  -0.429  -0.389  -0.352  -0.525  -0.492  -0.473  -0.626  -0.581
66    L         1.240   1.290   1.341   0.868   0.935   1.052   1.321   1.392   1.469
67    G         1.240   1.290   1.341   1.402   1.471   1.549   1.321   1.392   1.469
68    N         0.592   0.456   0.371   0.656   0.498   0.351   0.582   0.357   0.178
69    N        -1.741  -1.693  -1.568  -1.652  -1.563  -1.389  -1.423  -1.352  -1.185
70    A        -0.846  -0.795  -0.849  -0.779  -0.690  -0.790  -0.895  -0.809  -0.850
71    L         1.240   1.290   1.341   0.868   0.935   1.052   1.321   1.392   1.469
72    P         1.240   1.290   1.341   1.234   1.313   1.393   1.321   1.392   1.469
73    P        -0.846  -0.896  -0.877  -0.857  -0.976  -0.894  -0.895  -0.952  -0.884
74    T        -1.330  -1.352  -1.254  -1.265  -1.307  -1.163  -1.212  -1.204  -1.062
75    K         0.592   0.456   0.371   0.703   0.516   0.367   0.582   0.357   0.178
76    P         1.240   1.290   1.341   1.234   1.313   1.393   1.321   1.392   1.469
77    S        -0.308  -0.429  -0.389  -0.395  -0.585  -0.517  -0.473  -0.626  -0.581
78    F        -1.330  -1.411  -1.276  -1.354  -1.532  -1.353  -1.212  -1.245  -1.080
79    P        -1.741  -1.643  -1.561  -1.996  -1.794  -1.625  -1.423  -1.310  -1.179
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    Q        -0.846  -0.627  -0.841  -0.837  -0.527  -0.807  -0.895  -0.637  -0.845
85    E        -0.500  -0.401  -0.430  -0.724  -0.560  -0.622  -0.743  -0.599  -0.631
86    L        -0.650  -0.582  -0.450  -1.087  -0.952  -0.746  -0.930  -0.830  -0.658
87    T        -1.426  -1.411  -1.284  -1.401  -1.510  -1.255  -1.298  -1.252  -1.087
88    D        -0.919  -0.900  -0.870  -1.018  -0.964  -0.885  -1.000  -0.957  -0.877
89    D        -0.846  -0.846  -0.879  -0.821  -0.837  -0.864  -0.895  -0.902  -0.886
90    D        -0.436  -0.275  -0.375  -0.588  -0.323  -0.445  -0.684  -0.468  -0.561
91    M        -1.032  -0.913  -0.903  -1.015  -0.905  -0.835  -1.106  -0.971  -0.910
92    A        -0.436  -0.409  -0.388  -0.471  -0.427  -0.365  -0.684  -0.635  -0.584
93    I        -0.436  -0.321  -0.394  -0.794  -0.730  -0.738  -0.684  -0.547  -0.590
94    L         1.240   1.290   1.341   0.868   0.935   1.052   1.321   1.392   1.469
95    N        -0.846  -0.669  -0.837  -0.711  -0.448  -0.693  -0.895  -0.664  -0.837
96    D        -0.308  -0.465  -0.405  -0.363  -0.627  -0.544  -0.473  -0.683  -0.602
97    L         1.240   1.290   1.341   0.868   0.935   1.052   1.321   1.392   1.469
98    H         1.240   1.290   1.341   1.430   1.510   1.575   1.321   1.392   1.469
99    T        -0.846  -0.956  -0.876  -0.802  -1.000  -0.885  -0.895  -0.997  -0.882
100   L         0.592   0.479   0.373   0.292   0.141   0.020   0.582   0.397   0.181
101   L         1.240   1.290   1.341   0.868   0.935   1.052   1.321   1.392   1.469
102   L        -1.032  -1.016  -0.890  -1.374  -1.320  -1.082  -1.106  -1.051  -0.897
103   Q         0.102   0.242   0.265  -0.122   0.103   0.142  -0.262  -0.019  -0.019
104   T         1.240   1.290   1.341   1.340   1.417   1.492   1.321   1.392   1.469
105   S        -1.741  -1.663  -1.565  -1.543  -1.438  -1.287  -1.423  -1.324  -1.182
106   I         0.592   0.456   0.371   0.726   0.573   0.431   0.582   0.357   0.178
107   A        -1.628  -1.568  -1.551  -1.469  -1.364  -1.399  -1.317  -1.251  -1.171
108   E         1.240   1.290   1.341   1.180   1.245   1.342   1.321   1.392   1.469
109   G         1.240   1.290   1.341   1.402   1.471   1.549   1.321   1.392   1.469
110   E        -0.846  -0.669  -0.837  -0.779  -0.505  -0.768  -0.895  -0.664  -0.837
111   M         0.592   0.456   0.371   0.797   0.573   0.376   0.582   0.357   0.178
112   K        -1.741  -1.496  -1.556  -1.569  -1.224  -1.294  -1.423  -1.191  -1.177
113   C         1.240   1.290   1.341   1.383   1.468   1.531   1.321   1.392   1.469
114   R        -1.032  -0.976  -0.903  -0.921  -0.846  -0.760  -1.106  -1.020  -0.911
115   N         0.592   0.456   0.371   0.668   0.515   0.380   0.582   0.357   0.178
116   C         1.240   1.290   1.341   1.383   1.468   1.531   1.321   1.392   1.469
117   G        -0.025   0.186  -0.259   0.250   0.525  -0.117  -0.051   0.239  -0.389
118   H         1.240   1.290   1.341   1.430   1.510   1.575   1.321   1.392   1.469
119   I        -0.607  -0.845  -0.855  -0.425  -0.788  -0.828  -0.578  -0.856  -0.856
120   Y         1.240   1.290   1.341   1.467   1.556   1.610   1.321   1.392   1.469
121   Y        -0.607  -0.845  -0.855  -0.230  -0.591  -0.662  -0.578  -0.856  -0.856
122   I         0.592   0.456   0.371   0.708   0.545   0.388   0.582   0.357   0.178
123   K         0.592   0.479   0.373   0.719   0.579   0.410   0.582   0.397   0.181
124   N         0.592   0.479   0.373   0.632   0.490   0.295   0.582   0.397   0.181
125   G         0.102   0.105   0.207   0.008  -0.005   0.165  -0.262  -0.279  -0.132
126   I         0.592   0.456   0.371   0.708   0.545   0.388   0.582   0.357   0.178
127   P         0.592   0.456   0.371   0.662   0.488   0.352   0.582   0.357   0.178
128   N         1.240   1.290   1.341   1.224   1.314   1.384   1.321   1.392   1.469
129   L        -0.436  -0.444  -0.387  -0.706  -0.612  -0.538  -0.684  -0.649  -0.575
130   L         1.240   1.290   1.341   0.868   0.935   1.052   1.321   1.392   1.469
131   L         1.240   1.290   1.341   0.868   0.935   1.052   1.321   1.392   1.469
132   P         0.592   0.479   0.373   0.660   0.518   0.348   0.582   0.397   0.181
133   P        -0.025  -0.282  -0.332   0.074  -0.305  -0.405  -0.051  -0.407  -0.493
134   H         0.592   0.479   0.373   0.855   0.712   0.520   0.582   0.397   0.181
135   L         0.592   0.479   0.373   0.273   0.108  -0.028   0.582   0.397   0.181
136   V        -0.846  -0.863  -0.859  -0.739  -0.788  -0.757  -0.895  -0.911  -0.865
137   -        -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/P53738
Output conservation file - output/P53738
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
