1     M         1.189   1.204   1.227   1.385   1.394   1.433   1.268   1.287   1.320
2     S        -0.254  -0.376  -0.541  -0.127  -0.293  -0.571  -0.248  -0.409  -0.640
3     D        -0.067  -0.028   0.051  -0.312  -0.236  -0.106  -0.420  -0.351  -0.241
4     E        -0.067  -0.050   0.042  -0.470  -0.434  -0.272  -0.420  -0.393  -0.258
5     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     K        -0.695  -0.663  -0.622  -0.908  -0.859  -0.812  -0.842  -0.798  -0.748
10    S        -0.695  -0.669  -0.624  -0.864  -0.845  -0.766  -0.842  -0.807  -0.749
11    T        -1.640  -1.594  -1.499  -1.716  -1.641  -1.490  -1.358  -1.306  -1.185
12    P        -0.383  -0.519  -0.583  -0.085  -0.302  -0.484  -0.420  -0.599  -0.697
13    I        -0.049  -0.045   0.043  -0.381  -0.391  -0.222  -0.386  -0.384  -0.257
14    V        -0.767  -0.775  -0.650  -1.016  -1.048  -0.845  -0.937  -0.943  -0.783
15    K         1.189   1.204   1.227   1.049   1.065   1.124   1.268   1.287   1.320
16    A         0.446   0.424   0.185   0.509   0.489   0.117   0.441   0.408  -0.001
17    S         0.105   0.042   0.072  -0.011  -0.128  -0.101  -0.110  -0.225  -0.204
18    D         1.189   1.204   1.227   1.265   1.281   1.323   1.268   1.287   1.320
19    I        -0.767  -0.685  -0.622  -0.852  -0.695  -0.634  -0.937  -0.823  -0.747
20    T        -1.620  -1.628  -1.501  -1.491  -1.493  -1.301  -1.350  -1.342  -1.187
21    D        -0.049  -0.034   0.049  -0.262  -0.241  -0.106  -0.386  -0.363  -0.245
22    K        -0.543  -0.595  -0.600  -0.705  -0.807  -0.802  -0.661  -0.730  -0.724
23    L        -0.543  -0.430  -0.566  -0.447  -0.272  -0.517  -0.661  -0.511  -0.676
24    K        -0.254  -0.159  -0.517   0.029   0.151  -0.398  -0.248  -0.121  -0.608
25    E        -1.620  -1.566  -1.500  -1.401  -1.308  -1.226  -1.350  -1.289  -1.186
26    D        -1.485  -1.394  -1.459  -1.409  -1.278  -1.387  -1.212  -1.114  -1.150
27    I        -0.254  -0.376  -0.541  -0.232  -0.414  -0.682  -0.248  -0.409  -0.640
28    L        -0.543  -0.572  -0.601  -0.663  -0.746  -0.759  -0.661  -0.710  -0.723
29    T        -1.485  -1.566  -1.497  -1.265  -1.369  -1.249  -1.212  -1.279  -1.183
30    I        -0.543  -0.627  -0.598  -0.632  -0.751  -0.737  -0.661  -0.755  -0.720
31    S        -0.543  -0.605  -0.606  -0.600  -0.699  -0.700  -0.661  -0.745  -0.731
32    K        -1.979  -1.991  -1.824  -1.807  -1.845  -1.587  -1.488  -1.483  -1.302
33    D        -1.126  -1.044  -1.090  -0.968  -0.852  -0.906  -1.075  -0.981  -0.998
34    A         1.189   1.204   1.227   1.183   1.209   1.247   1.268   1.287   1.320
35    L        -1.620  -1.506  -1.489  -1.505  -1.328  -1.333  -1.350  -1.246  -1.179
36    D        -1.620  -1.623  -1.497  -1.529  -1.527  -1.338  -1.350  -1.338  -1.184
37    K        -1.126  -1.038  -1.085  -1.128  -1.024  -1.053  -1.075  -0.966  -0.992
38    Y        -0.254  -0.376  -0.541  -0.042  -0.215  -0.478  -0.248  -0.409  -0.640
39    Q        -1.126  -1.144  -1.107  -1.213  -1.227  -1.127  -1.075  -1.089  -1.015
40    L        -0.049  -0.022   0.047  -0.344  -0.296  -0.178  -0.386  -0.341  -0.249
41    E         1.189   1.204   1.227   1.150   1.173   1.217   1.268   1.287   1.320
42    R        -0.049  -0.022   0.047  -0.270  -0.243  -0.097  -0.386  -0.341  -0.249
43    D         0.105   0.143   0.086   0.049   0.111  -0.023  -0.110  -0.047  -0.178
44    I         1.189   1.204   1.227   1.117   1.134   1.186   1.268   1.287   1.320
45    A         1.189   1.204   1.227   1.183   1.209   1.247   1.268   1.287   1.320
46    G        -0.902  -0.848  -1.045  -0.771  -0.680  -1.000  -0.799  -0.731  -0.946
47    T        -1.126  -1.130  -1.091  -1.117  -1.135  -1.073  -1.075  -1.071  -0.999
48    V        -0.767  -0.717  -0.625  -1.043  -0.967  -0.815  -0.937  -0.868  -0.753
49    K         1.189   1.204   1.227   1.049   1.065   1.124   1.268   1.287   1.320
50    K         0.446   0.333   0.181   0.413   0.265   0.078   0.441   0.266  -0.009
51    Q         0.105   0.166   0.104   0.018   0.116   0.017  -0.110  -0.007  -0.146
52    L        -0.254  -0.376  -0.541  -0.089  -0.258  -0.514  -0.248  -0.409  -0.640
53    D         1.189   1.204   1.227   1.265   1.281   1.323   1.268   1.287   1.320
54    V        -1.126  -1.178  -1.106  -1.096  -1.189  -1.109  -1.075  -1.110  -1.012
55    K        -1.261  -1.200  -1.117  -1.325  -1.243  -1.104  -1.212  -1.147  -1.024
56    Y        -0.543  -0.527  -0.589  -0.521  -0.538  -0.588  -0.661  -0.662  -0.708
57    G         0.446   0.333   0.181   0.566   0.439   0.160   0.441   0.266  -0.009
58    N        -1.979  -1.922  -1.815  -1.571  -1.474  -1.381  -1.488  -1.429  -1.296
59    T         1.189   1.204   1.227   1.257   1.277   1.315   1.268   1.287   1.320
60    W         1.189   1.204   1.227   1.479   1.498   1.520   1.268   1.287   1.320
61    H         1.189   1.204   1.227   1.377   1.389   1.426   1.268   1.287   1.320
62    V         0.105   0.042   0.072   0.090  -0.009   0.063  -0.110  -0.225  -0.204
63    I         1.189   1.204   1.227   1.117   1.134   1.186   1.268   1.287   1.320
64    V         1.189   1.204   1.227   1.158   1.168   1.224   1.268   1.287   1.320
65    G         1.189   1.204   1.227   1.241   1.287   1.300   1.268   1.287   1.320
66    K        -0.049  -0.050   0.042  -0.270  -0.257  -0.084  -0.386  -0.393  -0.258
67    N        -0.049  -0.040   0.044  -0.116  -0.088   0.041  -0.386  -0.374  -0.255
68    F         1.189   1.204   1.227   1.175   1.184   1.240   1.268   1.287   1.320
69    G         1.189   1.204   1.227   1.241   1.287   1.300   1.268   1.287   1.320
70    S         1.189   1.204   1.227   1.200   1.231   1.262   1.268   1.287   1.320
71    Y         0.446   0.333   0.181   0.586   0.434   0.172   0.441   0.266  -0.009
72    V         1.189   1.204   1.227   1.158   1.168   1.224   1.268   1.287   1.320
73    T         1.189   1.204   1.227   1.257   1.277   1.315   1.268   1.287   1.320
74    H         1.189   1.204   1.227   1.377   1.389   1.426   1.268   1.287   1.320
75    E         1.189   1.204   1.227   1.150   1.173   1.217   1.268   1.287   1.320
76    K        -1.126  -1.171  -1.104  -1.184  -1.247  -1.125  -1.075  -1.100  -1.009
77    G        -0.254  -0.384  -0.539  -0.082  -0.237  -0.526  -0.248  -0.419  -0.637
78    H        -1.126  -1.042  -1.085  -1.025  -0.885  -1.004  -1.075  -0.969  -0.992
79    F         1.189   1.204   1.227   1.175   1.184   1.240   1.268   1.287   1.320
80    V        -0.631  -0.572  -0.603  -0.856  -0.789  -0.768  -0.799  -0.729  -0.728
81    Y         1.189   1.204   1.227   1.265   1.293   1.323   1.268   1.287   1.320
82    F         1.189   1.204   1.227   1.175   1.184   1.240   1.268   1.287   1.320
83    Y         1.189   1.204   1.227   1.265   1.293   1.323   1.268   1.287   1.320
84    I        -0.543  -0.642  -0.607  -0.698  -0.854  -0.789  -0.661  -0.778  -0.731
85    G         1.189   1.204   1.227   1.241   1.287   1.300   1.268   1.287   1.320
86    P        -1.126  -1.131  -1.100  -0.837  -0.850  -0.833  -1.075  -1.072  -1.008
87    L        -0.902  -0.952  -1.060  -0.747  -0.840  -1.013  -0.799  -0.856  -0.963
88    A         1.189   1.204   1.227   1.183   1.209   1.247   1.268   1.287   1.320
89    F        -0.254  -0.296  -0.531  -0.175  -0.243  -0.620  -0.248  -0.300  -0.627
90    L         1.189   1.204   1.227   1.216   1.247   1.278   1.268   1.287   1.320
91    V        -0.543  -0.569  -0.577  -0.678  -0.699  -0.721  -0.661  -0.671  -0.689
92    F         1.189   1.204   1.227   1.175   1.184   1.240   1.268   1.287   1.320
93    K         1.189   1.204   1.227   1.049   1.065   1.124   1.268   1.287   1.320
94    T        -0.049  -0.034   0.049  -0.238  -0.209  -0.082  -0.386  -0.363  -0.245
95    A        -0.644  -0.640  -0.616  -0.745  -0.728  -0.705  -0.795  -0.778  -0.741
* 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/Q02647
Output conservation file - output/Q02647
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
