1     M         1.379   1.405   1.465   1.869   1.872   1.959   1.490   1.527   1.624
2     P         0.006   0.023   0.070   0.243   0.210   0.263  -0.253  -0.233  -0.181
3     Q         1.379   1.405   1.465   1.636   1.645   1.741   1.490   1.527   1.624
4     K        -0.803  -0.878  -0.763  -1.344  -1.306  -1.042  -0.907  -0.974  -0.815
5     P        -1.489  -1.437  -1.351  -0.837  -0.787  -0.696  -1.343  -1.263  -1.127
6     L         1.379   1.405   1.465   1.337   1.388   1.463   1.490   1.527   1.624
7     K         1.379   1.405   1.465   0.527   0.606   0.708   1.490   1.527   1.624
8     V        -0.803  -0.878  -0.763  -0.770  -1.027  -0.997  -0.907  -0.974  -0.815
9     T         0.166  -0.017   0.067   0.439   0.100   0.212   0.019  -0.304  -0.188
10    K         0.166  -0.017   0.067  -0.628  -0.746  -0.587   0.019  -0.304  -0.188
11    K         1.379   1.405   1.465   0.527   0.606   0.708   1.490   1.527   1.624
12    A        -0.492  -0.613  -0.696  -0.094  -0.296  -0.389  -0.471  -0.630  -0.729
13    K         0.006  -0.044   0.050  -0.784  -0.710  -0.523  -0.253  -0.351  -0.218
14    D        -1.301  -1.401  -1.354  -0.695  -1.026  -1.039  -1.125  -1.217  -1.129
15    P        -0.492  -0.613  -0.696   0.121  -0.057  -0.196  -0.471  -0.630  -0.729
16    R        -0.803  -0.778  -0.744  -1.011  -1.162  -1.065  -0.907  -0.872  -0.793
17    R         0.006  -0.044   0.050  -0.281  -0.536  -0.488  -0.253  -0.351  -0.218
18    V        -0.492  -0.613  -0.696   0.181  -0.007  -0.139  -0.471  -0.630  -0.729
19    T         0.407   0.377   0.194   0.840   0.798   0.539   0.400   0.352   0.035
20    K         0.407   0.239   0.166  -0.274  -0.417  -0.459   0.400   0.133  -0.012
21    K         1.379   1.405   1.465   0.527   0.606   0.708   1.490   1.527   1.624
22    Q        -0.492  -0.666  -0.705  -0.008  -0.262  -0.380  -0.471  -0.696  -0.740
23    K        -1.301  -1.401  -1.354  -1.924  -1.951  -1.715  -1.125  -1.217  -1.129
24    N         0.300   0.195   0.124   0.831   0.657   0.509   0.235   0.061  -0.087
25    L        -0.116  -0.028   0.080  -0.127   0.061   0.199  -0.471  -0.322  -0.164
26    R         0.006   0.186   0.157  -0.810  -0.538  -0.544  -0.253   0.045  -0.028
27    K         0.407   0.239   0.166  -0.309  -0.469  -0.534   0.400   0.133  -0.012
28    A         1.379   1.405   1.465   1.499   1.474   1.614   1.490   1.527   1.624
29    A         0.407   0.377   0.194   0.684   0.597   0.379   0.400   0.352   0.035
30    P         1.379   1.405   1.465   1.697   1.696   1.799   1.490   1.527   1.624
31    L        -1.301  -1.276  -1.305  -1.263  -1.227  -1.368  -1.125  -1.094  -1.081
32    Q        -0.803  -0.878  -0.763  -0.645  -0.887  -0.796  -0.907  -0.974  -0.815
33    L         0.407   0.580   0.215   0.852   1.042   0.501   0.400   0.652   0.072
34    K         0.407   0.239   0.166  -0.331  -0.513  -0.582   0.400   0.133  -0.012
35    S        -0.116  -0.028   0.080   0.075   0.211   0.351  -0.471  -0.322  -0.164
36    K         0.407   0.239   0.166  -0.309  -0.469  -0.534   0.400   0.133  -0.012
37    K         0.407   0.239   0.166  -0.309  -0.469  -0.534   0.400   0.133  -0.012
38    K        -1.301  -1.226  -1.307  -1.786  -1.656  -1.579  -1.125  -1.027  -1.083
39    S        -0.492  -0.500  -0.689   0.065   0.055  -0.218  -0.471  -0.475  -0.720
40    L        -0.116  -0.028   0.080  -0.277  -0.132   0.040  -0.471  -0.322  -0.164
41    Q        -0.803  -0.665  -0.727  -1.025  -0.863  -0.937  -0.907  -0.746  -0.772
42    H        -1.301  -1.401  -1.354  -0.531  -0.723  -0.710  -1.125  -1.217  -1.129
43    L        -1.301  -1.401  -1.354  -0.797  -0.831  -0.755  -1.125  -1.217  -1.129
44    K        -0.492  -0.613  -0.696  -1.126  -1.170  -1.247  -0.471  -0.630  -0.729
45    K         0.407   0.239   0.166  -0.298  -0.450  -0.511   0.400   0.133  -0.012
46    L         0.407   0.239   0.166   0.543   0.353   0.241   0.400   0.133  -0.012
47    K        -1.988  -1.822  -1.807  -1.648  -1.383  -1.494  -1.561  -1.394  -1.314
48    K         1.379   1.405   1.465   0.527   0.606   0.708   1.490   1.527   1.624
49    S        -1.988  -1.943  -1.818  -1.566  -1.676  -1.426  -1.561  -1.493  -1.323
50    S        -1.489  -1.376  -1.331  -0.745  -0.588  -0.535  -1.343  -1.199  -1.108
51    S         0.006  -0.044   0.050   0.238   0.144   0.249  -0.253  -0.351  -0.218
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    L         0.407   0.532   0.211   0.543   0.707   0.301   0.400   0.583   0.064
55    T         0.006   0.023   0.070   0.353   0.367   0.423  -0.253  -0.233  -0.181
56    E        -1.301  -1.401  -1.354  -0.986  -1.189  -1.271  -1.125  -1.217  -1.129
57    T        -0.803  -0.675  -0.723  -0.464  -0.307  -0.389  -0.907  -0.761  -0.771
58    T         1.379   1.405   1.465   1.636   1.655   1.741   1.490   1.527   1.624
59    E         1.379   1.405   1.465   1.625   1.635   1.732   1.490   1.527   1.624
60    R        -0.803  -0.817  -0.748  -1.059  -1.227  -1.140  -0.907  -0.910  -0.797
61    L         1.379   1.405   1.465   1.337   1.388   1.463   1.490   1.527   1.624
62    V        -0.803  -0.801  -0.712  -0.361  -0.395  -0.306  -0.907  -0.870  -0.750
63    A         0.407   0.532   0.211   0.681   0.782   0.400   0.400   0.583   0.064
64    S         0.407   0.377   0.194   0.824   0.790   0.519   0.400   0.352   0.035
65    K         0.006   0.186   0.157  -0.281   0.113  -0.064  -0.253   0.045  -0.028
66    V         1.379   1.405   1.465   1.748   1.760   1.846   1.490   1.527   1.624
67    G         1.379   1.405   1.465   1.718   1.715   1.818   1.490   1.527   1.624
68    H         1.379   1.405   1.465   1.819   1.823   1.912   1.490   1.527   1.624
69    L         1.379   1.405   1.465   1.337   1.388   1.463   1.490   1.527   1.624
70    E         1.379   1.405   1.465   1.625   1.635   1.732   1.490   1.527   1.624
71    L         0.407   0.239   0.166   0.543   0.353   0.241   0.400   0.133  -0.012
72    L         0.006   0.023   0.070   0.022   0.059   0.122  -0.253  -0.233  -0.181
73    R         0.006   0.186   0.157  -0.810  -0.538  -0.544  -0.253   0.045  -0.028
74    G         1.379   1.405   1.465   1.718   1.715   1.818   1.490   1.527   1.624
75    T        -0.803  -0.878  -0.763  -0.386  -0.460  -0.328  -0.907  -0.974  -0.815
76    R         1.379   1.405   1.465   1.583   1.587   1.693   1.490   1.527   1.624
77    K        -0.116  -0.028   0.080  -0.798  -0.470  -0.321  -0.471  -0.322  -0.164
78    E         0.006   0.023   0.070   0.238   0.238   0.284  -0.253  -0.233  -0.181
79    L        -1.489  -1.433  -1.329  -0.994  -0.871  -0.736  -1.343  -1.253  -1.107
80    E         0.407   0.532   0.211   0.781   0.911   0.462   0.400   0.583   0.064
81    K        -0.492  -0.382  -0.639  -1.129  -0.946  -1.214  -0.471  -0.329  -0.654
82    G        -1.988  -1.822  -1.807  -1.680  -1.640  -1.526  -1.561  -1.394  -1.314
83    K        -0.803  -0.647  -0.708  -0.579  -0.322  -0.577  -0.907  -0.716  -0.752
84    K         1.379   1.405   1.465   0.527   0.606   0.708   1.490   1.527   1.624
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -0.864  -0.764  -0.727  -0.782  -0.651  -0.615  -0.961  -0.825  -0.768
96    -        -1.612  -1.521  -1.369  -1.623  -1.402  -1.295  -1.452  -1.335  -1.144
97    -         0.166   0.173   0.143   0.308   0.300   0.259   0.019   0.024  -0.052
98    N        -1.495  -1.449  -1.332  -1.217  -1.118  -1.090  -1.334  -1.266  -1.108
99    S        -0.492  -0.504  -0.674  -1.049  -0.996  -1.105  -0.471  -0.502  -0.700
100   K         1.379   1.405   1.465   0.527   0.606   0.708   1.490   1.527   1.624
* 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/Q3E747
Output conservation file - output/Q3E747
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
