1     M         1.550   1.559   1.674   1.784   1.795   1.981   1.675   1.689   1.874
2     F         0.318   0.318   0.458   0.117   0.107   0.314  -0.087  -0.092   0.104
3     R         0.323   0.290  -0.024   0.556   0.508   0.046   0.353   0.306  -0.153
4     S        -1.562  -1.583  -1.447  -1.379  -1.395  -1.160  -1.233  -1.242  -1.060
5     V        -0.629  -0.691  -0.682  -0.865  -0.932  -0.917  -0.704  -0.756  -0.704
6     C        -1.182  -1.139  -1.081  -1.209  -1.153  -1.039  -1.057  -1.019  -0.901
7     R        -0.626  -0.660  -0.671  -0.526  -0.576  -0.608  -0.667  -0.703  -0.689
8     I        -1.337  -1.327  -1.151  -1.360  -1.345  -1.102  -1.180  -1.169  -0.959
9     S        -0.626  -0.686  -0.657  -0.806  -0.884  -0.832  -0.667  -0.729  -0.674
10    S        -1.247  -1.233  -1.113  -1.457  -1.431  -1.248  -1.113  -1.098  -0.929
11    R         0.924   0.937   0.675   1.110   1.123   0.810   0.970   0.988   0.524
12    V        -0.519  -0.538  -0.653  -0.616  -0.639  -0.851  -0.510  -0.534  -0.663
13    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    S        -1.230  -1.255  -1.136  -1.210  -1.265  -1.094  -1.092  -1.110  -0.946
16    A        -0.937  -0.961  -1.057  -0.905  -0.951  -1.169  -0.778  -0.804  -0.871
17    Y         0.230   0.206  -0.070   0.218   0.195  -0.137   0.225   0.192  -0.221
18    R         0.924   0.870   0.658   1.074   1.005   0.685   0.970   0.888   0.492
19    T        -1.458  -1.455  -1.410  -1.223  -1.217  -1.138  -1.145  -1.139  -1.031
20    I        -1.130  -1.098  -1.087  -1.108  -1.048  -0.997  -1.001  -0.980  -0.905
21    M        -1.247  -1.199  -1.117  -1.104  -1.067  -0.907  -1.113  -1.072  -0.932
22    G        -1.558  -1.555  -1.434  -1.396  -1.421  -1.236  -1.224  -1.218  -1.051
23    R        -1.130  -1.109  -1.080  -1.019  -0.999  -0.953  -1.001  -0.986  -0.899
24    S        -1.010  -0.962  -1.046  -0.928  -0.863  -0.957  -0.880  -0.839  -0.868
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    V         0.343   0.368   0.482  -0.126  -0.089   0.085  -0.038   0.006   0.153
31    M        -0.839  -0.785  -0.731  -0.656  -0.576  -0.501  -0.894  -0.830  -0.751
32    S        -0.155  -0.090  -0.169   0.026   0.130  -0.050  -0.323  -0.230  -0.366
33    N        -0.839  -0.798  -0.718  -0.714  -0.647  -0.569  -0.894  -0.845  -0.737
34    T        -0.839  -0.840  -0.728  -0.714  -0.727  -0.569  -0.894  -0.896  -0.748
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    I        -1.130  -1.100  -1.098  -1.168  -1.122  -1.139  -1.001  -0.976  -0.915
45    L        -1.247  -1.226  -1.119  -1.190  -1.158  -1.018  -1.113  -1.093  -0.933
46    A        -0.198  -0.218  -0.168  -0.281  -0.282  -0.220  -0.444  -0.454  -0.378
47    Q        -1.130  -1.135  -1.097  -1.115  -1.124  -1.091  -1.001  -1.002  -0.913
48    R         1.550   1.559   1.674   1.611   1.620   1.811   1.675   1.689   1.874
49    F         0.924   0.874   0.658   1.160   1.108   0.859   0.970   0.893   0.492
50    Y         1.550   1.559   1.674   1.784   1.796   1.981   1.675   1.689   1.874
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    S         0.323   0.348  -0.043   0.330   0.357  -0.245   0.353   0.387  -0.181
53    A        -0.741  -0.730  -0.682  -0.899  -0.903  -0.772  -0.801  -0.794  -0.703
54    N        -1.230  -1.237  -1.126  -0.966  -0.989  -0.867  -1.092  -1.096  -0.938
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    L        -0.235  -0.234  -0.177  -0.404  -0.408  -0.357  -0.440  -0.440  -0.378
58    S        -0.733  -0.717  -0.706  -0.896  -0.890  -0.845  -0.792  -0.785  -0.729
59    K         0.600   0.588   0.545   0.631   0.620   0.520   0.441   0.418   0.278
60    D        -0.235  -0.240  -0.200  -0.339  -0.350  -0.311  -0.440  -0.448  -0.410
61    Q        -1.010  -1.042  -1.071  -0.887  -0.929  -0.944  -0.880  -0.913  -0.889
62    V        -0.235  -0.265  -0.217  -0.482  -0.537  -0.503  -0.440  -0.485  -0.435
63    S        -1.182  -1.154  -1.109  -1.010  -0.983  -0.913  -1.057  -1.037  -0.925
64    Q        -1.182  -1.183  -1.098  -1.098  -1.084  -0.974  -1.057  -1.050  -0.917
65    R         1.550   1.559   1.674   1.611   1.620   1.811   1.675   1.689   1.874
66    V        -0.235  -0.213  -0.171  -0.409  -0.372  -0.369  -0.440  -0.409  -0.369
67    I        -1.182  -1.211  -1.099  -1.361  -1.400  -1.219  -1.057  -1.078  -0.918
68    D        -0.733  -0.751  -0.701  -0.814  -0.841  -0.764  -0.792  -0.803  -0.723
69    V         0.028  -0.006  -0.114  -0.112  -0.151  -0.359  -0.087  -0.126  -0.287
70    I        -0.131  -0.166  -0.164  -0.277  -0.323  -0.325  -0.352  -0.387  -0.369
71    K        -0.235  -0.244  -0.225  -0.339  -0.352  -0.402  -0.440  -0.454  -0.445
72    A        -0.733  -0.675  -0.675  -0.846  -0.778  -0.731  -0.792  -0.730  -0.691
73    F         0.600   0.619   0.587   0.648   0.677   0.584   0.441   0.471   0.360
74    D         0.600   0.619   0.587   0.449   0.476   0.382   0.441   0.471   0.360
75    K         0.323   0.348  -0.043   0.526   0.565  -0.007   0.353   0.387  -0.181
76    N        -1.286  -1.276  -1.134  -1.277  -1.259  -1.034  -1.145  -1.134  -0.946
77    S        -0.801  -0.793  -0.716  -0.785  -0.758  -0.664  -0.880  -0.870  -0.741
78    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    A        -0.741  -0.693  -0.696  -0.944  -0.864  -0.871  -0.801  -0.745  -0.715
82    N        -1.182  -1.174  -1.106  -1.148  -1.146  -1.063  -1.057  -1.049  -0.922
83    K        -0.733  -0.706  -0.665  -0.841  -0.781  -0.747  -0.792  -0.757  -0.681
84    Q        -1.010  -0.991  -1.039  -0.709  -0.670  -0.813  -0.880  -0.868  -0.863
85    I         0.323   0.273  -0.050   0.490   0.420  -0.078   0.353   0.283  -0.191
86    S         0.600   0.615   0.518   0.645   0.665   0.434   0.441   0.465   0.225
87    S        -1.286  -1.274  -1.128  -1.444  -1.427  -1.237  -1.145  -1.132  -0.941
88    D        -0.733  -0.713  -0.694  -0.674  -0.635  -0.612  -0.792  -0.766  -0.713
89    T        -0.353  -0.358  -0.238  -0.671  -0.684  -0.520  -0.616  -0.622  -0.464
90    Q        -1.458  -1.477  -1.423  -1.145  -1.166  -1.042  -1.145  -1.158  -1.042
91    F         0.924   0.874   0.658   1.113   1.052   0.731   0.970   0.893   0.492
92    H        -1.182  -1.197  -1.113  -1.050  -1.064  -0.935  -1.057  -1.065  -0.927
93    K         0.028  -0.020  -0.147   0.157   0.108  -0.114  -0.087  -0.147  -0.340
94    D         1.550   1.559   1.674   1.470   1.479   1.673   1.675   1.689   1.874
95    L         1.550   1.559   1.674   1.475   1.486   1.678   1.675   1.689   1.874
96    G         0.323   0.365  -0.017   0.777   0.832   0.320   0.353   0.411  -0.142
97    L         1.550   1.559   1.674   1.475   1.486   1.678   1.675   1.689   1.874
98    D         1.550   1.559   1.674   1.470   1.479   1.673   1.675   1.689   1.874
99    S         1.550   1.559   1.674   1.421   1.426   1.625   1.675   1.689   1.874
100   L         1.550   1.559   1.674   1.475   1.486   1.678   1.675   1.689   1.874
101   D         1.550   1.559   1.674   1.470   1.479   1.673   1.675   1.689   1.874
102   T         0.323   0.219  -0.063   0.557   0.416  -0.070   0.353   0.209  -0.210
103   V         1.550   1.559   1.674   1.431   1.444   1.634   1.675   1.689   1.874
104   E         1.550   1.559   1.674   1.485   1.497   1.688   1.675   1.689   1.874
105   L        -0.353  -0.337  -0.215  -0.737  -0.707  -0.544  -0.616  -0.595  -0.435
106   L         0.318   0.322   0.458  -0.051  -0.048   0.156  -0.087  -0.084   0.105
107   V         0.408   0.394   0.469   0.265   0.246   0.377   0.089   0.058   0.127
108   A         0.924   0.937   0.676   0.795   0.813   0.449   0.970   0.990   0.527
109   I         0.600   0.619   0.587   0.575   0.599   0.522   0.441   0.471   0.360
110   E         1.550   1.559   1.674   1.485   1.497   1.688   1.675   1.689   1.874
111   E         1.550   1.559   1.674   1.485   1.497   1.688   1.675   1.689   1.874
112   E         1.550   1.559   1.674   1.485   1.497   1.688   1.675   1.689   1.874
113   F         1.550   1.559   1.674   1.644   1.657   1.844   1.675   1.689   1.874
114   D        -0.235  -0.244  -0.225  -0.323  -0.340  -0.319  -0.440  -0.454  -0.445
115   I        -0.131  -0.131  -0.158  -0.247  -0.258  -0.297  -0.352  -0.357  -0.362
116   E         0.924   0.870   0.658   0.985   0.925   0.667   0.970   0.888   0.492
117   I         0.600   0.613   0.551   0.622   0.637   0.529   0.441   0.462   0.290
118   P         1.550   1.559   1.674   1.687   1.696   1.885   1.675   1.689   1.874
119   D         1.550   1.559   1.674   1.470   1.479   1.673   1.675   1.689   1.874
120   K         0.924   0.874   0.658   1.094   1.049   0.798   0.970   0.893   0.492
121   V        -0.801  -0.773  -0.707  -1.012  -0.975  -0.864  -0.880  -0.853  -0.729
122   A         0.600   0.619   0.587   0.338   0.366   0.290   0.441   0.471   0.360
123   D         1.550   1.559   1.674   1.470   1.479   1.673   1.675   1.689   1.874
124   E         0.323   0.387  -0.037   0.458   0.531  -0.023   0.353   0.439  -0.171
125   L         0.408   0.423   0.494   0.236   0.257   0.335   0.089   0.113   0.177
126   R        -0.249  -0.234  -0.588   0.101   0.121  -0.324  -0.175  -0.159  -0.586
127   S         0.408   0.402   0.482   0.188   0.170   0.295   0.089   0.072   0.152
128   V         1.550   1.559   1.674   1.431   1.444   1.634   1.675   1.689   1.874
129   G        -0.787  -0.752  -1.007  -0.214  -0.159  -0.555  -0.616  -0.578  -0.823
130   E        -0.511  -0.519  -0.665  -0.401  -0.418  -0.616  -0.528  -0.542  -0.682
131   T         0.408   0.423   0.494   0.110   0.133   0.243   0.089   0.113   0.177
132   V         0.600   0.538   0.508   0.473   0.373   0.297   0.441   0.326   0.204
133   D        -0.629  -0.649  -0.649  -0.711  -0.727  -0.703  -0.704  -0.714  -0.671
134   Y         1.550   1.559   1.674   1.784   1.796   1.981   1.675   1.689   1.874
135   I         0.924   0.874   0.658   1.021   0.955   0.635   0.970   0.893   0.492
136   A        -1.182  -1.230  -1.107  -1.183  -1.243  -1.086  -1.057  -1.091  -0.921
137   S        -0.733  -0.751  -0.707  -0.950  -0.984  -0.927  -0.792  -0.814  -0.730
138   N        -0.801  -0.789  -0.702  -0.669  -0.636  -0.540  -0.880  -0.866  -0.725
139   P         0.600   0.619   0.587   0.704   0.729   0.644   0.441   0.471   0.360
140   D        -1.010  -1.049  -1.067  -1.004  -1.078  -1.124  -0.880  -0.921  -0.887
141   A         0.600   0.619   0.587   0.384   0.415   0.359   0.441   0.471   0.360
142   N        -0.626  -0.728  -0.678  -0.432  -0.591  -0.575  -0.667  -0.776  -0.696
* 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/P32463
Output conservation file - output/P32463
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
