1     M         2.064   2.114   2.260   2.217   2.278   2.520   2.345   2.423   2.692
2     M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     N        -0.509  -0.492  -0.539  -0.602  -0.574  -0.668  -0.535  -0.508  -0.559
8     D        -1.168  -1.182  -1.089  -1.253  -1.262  -1.140  -1.015  -1.017  -0.892
9     E        -0.735  -0.747  -0.632  -1.165  -1.164  -1.006  -0.829  -0.826  -0.676
10    E        -0.581  -0.464  -0.556  -0.849  -0.719  -0.812  -0.652  -0.526  -0.593
11    K        -0.991  -1.003  -1.028  -0.610  -0.626  -0.673  -0.829  -0.832  -0.830
12    L        -1.168  -1.054  -1.074  -1.233  -1.053  -1.115  -1.015  -0.889  -0.878
13    I        -0.089  -0.105  -0.035  -0.275  -0.305  -0.252  -0.355  -0.389  -0.297
14    S        -0.030  -0.089  -0.003  -0.123  -0.163  -0.027  -0.295  -0.376  -0.258
15    T         0.267   0.154   0.133   0.493   0.325   0.266   0.185   0.014  -0.037
16    T        -1.646  -1.615  -1.525  -1.290  -1.301  -1.118  -1.255  -1.217  -1.092
17    D         1.131   1.094   1.046   1.124   1.063   0.975   1.145   1.071   0.938
18    K         0.267   0.154   0.133   0.346   0.165   0.089   0.185   0.014  -0.037
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    Y         0.825   0.845   0.872   0.948   0.971   0.961   0.582   0.602   0.583
22    F         2.064   2.114   2.260   2.190   2.257   2.492   2.345   2.423   2.692
23    I         0.650   0.663   0.797   0.257   0.247   0.420   0.229   0.232   0.424
24    E        -0.170  -0.176  -0.056  -0.363  -0.346  -0.155  -0.476  -0.486  -0.329
25    Q         1.215   1.139   1.089   1.409   1.325   1.282   1.287   1.151   1.023
26    R         2.064   2.114   2.260   2.208   2.266   2.511   2.345   2.423   2.692
27    N        -0.325  -0.299  -0.450  -0.216  -0.168  -0.433  -0.300  -0.266  -0.446
28    I        -0.991  -0.930  -0.981  -0.781  -0.703  -0.746  -0.829  -0.755  -0.781
29    V        -0.325  -0.278  -0.448  -0.188  -0.114  -0.327  -0.300  -0.236  -0.443
30    L        -0.016  -0.050   0.028  -0.195  -0.198  -0.083  -0.300  -0.326  -0.216
31    Q         0.415   0.267   0.187   0.647   0.438   0.298   0.405   0.185   0.046
32    E         0.415   0.267   0.187   0.303   0.105  -0.032   0.405   0.185   0.046
33    I         1.215   1.354   1.117   1.300   1.481   1.197   1.287   1.511   1.077
34    N        -0.016   0.040   0.047  -0.385  -0.314  -0.268  -0.300  -0.219  -0.187
35    E        -0.991  -1.086  -1.080  -0.907  -1.021  -0.986  -0.829  -0.921  -0.884
36    T        -0.325  -0.209  -0.432  -0.410  -0.245  -0.588  -0.300  -0.144  -0.422
37    M        -0.325  -0.220  -0.438   0.075   0.213  -0.115  -0.300  -0.158  -0.431
38    N        -1.145  -1.061  -1.062  -1.329  -1.252  -1.212  -1.005  -0.920  -0.872
39    S        -0.991  -1.052  -1.050  -1.011  -1.130  -1.100  -0.829  -0.887  -0.853
40    I         0.650   0.730   0.842   0.493   0.631   0.781   0.229   0.370   0.520
41    L         0.085   0.064   0.059  -0.016  -0.048  -0.035  -0.123  -0.162  -0.170
42    N         0.415   0.451   0.219   0.501   0.540   0.288   0.405   0.461   0.097
43    G        -0.581  -0.543  -0.564  -0.590  -0.566  -0.572  -0.652  -0.594  -0.595
44    L         1.215   1.139   1.089   1.150   1.067   1.024   1.287   1.151   1.023
45    N        -0.325  -0.385  -0.486  -0.415  -0.535  -0.749  -0.300  -0.373  -0.492
46    G        -1.145  -1.075  -1.080  -0.707  -0.583  -0.608  -1.005  -0.926  -0.887
47    L         2.064   2.114   2.260   1.837   1.904   2.125   2.345   2.423   2.692
48    N         2.064   2.114   2.260   1.846   1.903   2.135   2.345   2.423   2.692
49    I        -0.016  -0.050   0.028   0.052   0.026   0.151  -0.300  -0.326  -0.216
50    S         0.415   0.417   0.230   0.317   0.305   0.058   0.405   0.401   0.113
51    L         2.064   2.114   2.260   1.837   1.904   2.125   2.345   2.423   2.692
52    E         0.415   0.451   0.219   0.352   0.407   0.105   0.405   0.461   0.097
53    S        -0.991  -0.973  -1.035  -0.972  -0.920  -1.029  -0.829  -0.801  -0.838
54    S         0.415   0.267   0.187   0.351   0.171   0.056   0.405   0.185   0.046
55    I        -0.325  -0.465  -0.514  -0.110  -0.314  -0.404  -0.300  -0.473  -0.527
56    A        -0.735  -0.707  -0.628  -0.626  -0.555  -0.471  -0.829  -0.784  -0.673
57    V         0.415   0.353   0.197   0.634   0.545   0.292   0.405   0.313   0.062
58    G         1.215   1.167   1.087   1.390   1.336   1.189   1.287   1.199   1.018
59    R         0.415   0.399   0.234   0.697   0.669   0.481   0.405   0.380   0.120
60    E         1.215   1.167   1.087   1.037   0.984   0.882   1.287   1.199   1.018
61    F         1.215   1.167   1.087   1.426   1.360   1.226   1.287   1.199   1.018
62    Q         0.085   0.142   0.096  -0.169  -0.094  -0.145  -0.123  -0.045  -0.106
63    S        -0.991  -0.955  -0.999  -1.070  -1.046  -1.142  -0.829  -0.782  -0.800
64    V         1.215   1.167   1.087   1.349   1.285   1.160   1.287   1.199   1.018
65    S        -0.016   0.040   0.047  -0.067   0.065   0.110  -0.300  -0.219  -0.187
66    D        -1.555  -1.531  -1.497  -1.255  -1.287  -1.225  -1.181  -1.150  -1.070
67    L         0.415   0.441   0.222   0.449   0.490   0.210   0.405   0.440   0.101
68    W         2.064   2.114   2.260   2.315   2.386   2.621   2.345   2.423   2.692
69    K         0.650   0.671   0.799   0.313   0.316   0.483   0.229   0.249   0.428
70    T        -1.145  -1.098  -1.064  -0.904  -0.826  -0.832  -1.005  -0.953  -0.874
71    L         1.215   1.290   1.111   1.439   1.540   1.293   1.287   1.408   1.064
72    Y         1.215   1.139   1.089   1.552   1.466   1.409   1.287   1.151   1.023
73    D         0.650   0.666   0.796   0.269   0.262   0.445   0.229   0.239   0.423
74    G         0.415   0.267   0.187   0.702   0.504   0.354   0.405   0.185   0.046
75    L         0.085   0.033   0.042   0.013  -0.064  -0.009  -0.123  -0.215  -0.195
76    E        -0.016  -0.050   0.028  -0.471  -0.514  -0.415  -0.300  -0.326  -0.216
77    S        -0.030  -0.069  -0.002  -0.230  -0.261  -0.140  -0.295  -0.350  -0.256
78    L        -1.168  -1.155  -1.087  -1.086  -1.055  -0.968  -1.015  -0.995  -0.891
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    S        -0.689  -0.687  -0.631  -1.052  -1.081  -1.045  -0.775  -0.762  -0.674
97    D        -0.030   0.028   0.049  -0.329  -0.247  -0.254  -0.295  -0.213  -0.183
98    E        -0.509  -0.585  -0.601  -0.693  -0.811  -0.843  -0.535  -0.624  -0.635
99    A        -1.168  -1.192  -1.116  -0.656  -0.707  -0.604  -1.015  -1.028  -0.919
100   P        -0.695  -0.689  -0.633  -0.687  -0.675  -0.563  -0.765  -0.751  -0.673
101   I        -0.121  -0.089  -0.013  -0.351  -0.305  -0.188  -0.420  -0.377  -0.270
102   D        -0.121  -0.089  -0.013  -0.667  -0.634  -0.530  -0.420  -0.377  -0.270
103   E         1.028   1.079   1.003   0.919   0.991   0.826   0.963   1.043   0.853
104   Q        -0.807  -0.787  -0.668  -0.781  -0.740  -0.590  -0.895  -0.865  -0.713
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   P        -0.695  -0.735  -0.633  -0.706  -0.750  -0.595  -0.765  -0.805  -0.673
111   T        -0.695  -0.662  -0.595  -0.739  -0.675  -0.611  -0.765  -0.720  -0.628
112   L        -0.695  -0.685  -0.605  -0.825  -0.821  -0.704  -0.765  -0.749  -0.639
113   S        -1.145  -1.167  -1.086  -1.295  -1.332  -1.227  -1.005  -1.010  -0.892
114   Q        -0.735  -0.758  -0.621  -0.758  -0.776  -0.590  -0.829  -0.836  -0.667
115   S        -1.555  -1.580  -1.507  -1.464  -1.511  -1.363  -1.181  -1.189  -1.078
116   K        -1.966  -1.943  -1.850  -1.643  -1.607  -1.484  -1.358  -1.327  -1.200
117   T        -1.145  -1.119  -1.074  -0.938  -0.873  -0.793  -1.005  -0.969  -0.883
118   K        -1.555  -1.573  -1.501  -1.300  -1.321  -1.252  -1.181  -1.184  -1.073
* 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/Q12248
Output conservation file - output/Q12248
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
