1     M         1.296   1.323   1.376   1.349   1.386   1.466   1.367   1.404   1.483
2     -        -0.968  -1.009  -0.914  -1.052  -1.117  -0.974  -0.979  -1.003  -0.877
3     S        -0.879  -0.795  -0.864  -0.852  -0.728  -0.822  -0.887  -0.782  -0.824
4     G         1.296   1.323   1.376   1.200   1.230   1.321   1.367   1.404   1.483
5     N        -0.426  -0.513  -0.433  -0.550  -0.698  -0.571  -0.618  -0.717  -0.605
6     P         1.296   1.323   1.376   1.244   1.282   1.363   1.367   1.404   1.483
7     G         1.296   1.323   1.376   1.215   1.241   1.336   1.367   1.404   1.483
8     S        -0.968  -0.962  -0.914  -1.069  -1.076  -0.989  -0.979  -0.966  -0.877
9     S        -0.322  -0.320  -0.400  -0.282  -0.282  -0.434  -0.452  -0.447  -0.558
10    L         0.150   0.168   0.220  -0.051  -0.025   0.091  -0.192  -0.168  -0.104
11    S        -0.968  -0.964  -0.912  -0.890  -0.861  -0.798  -0.979  -0.968  -0.875
12    A        -0.820  -0.946  -0.910  -0.710  -0.938  -0.867  -0.798  -0.935  -0.872
13    L        -0.426  -0.513  -0.433  -0.435  -0.495  -0.381  -0.618  -0.717  -0.605
14    R        -0.820  -0.866  -0.897  -0.759  -0.870  -0.885  -0.798  -0.854  -0.858
15    P        -0.060  -0.255  -0.373   0.085  -0.170  -0.371  -0.091  -0.356  -0.521
16    T         0.598   0.464   0.343   0.688   0.498   0.312   0.572   0.355   0.125
17    P         0.598   0.530   0.336   0.664   0.593   0.282   0.572   0.463   0.113
18    P         1.296   1.323   1.376   1.267   1.316   1.386   1.367   1.404   1.483
19    E         0.598   0.530   0.336   0.670   0.575   0.255   0.572   0.463   0.113
20    R         1.296   1.323   1.376   1.362   1.395   1.478   1.367   1.404   1.483
21    G         1.296   1.323   1.376   1.215   1.238   1.336   1.367   1.404   1.483
22    S         1.296   1.323   1.376   1.228   1.247   1.348   1.367   1.404   1.483
23    F         1.296   1.323   1.376   1.479   1.508   1.592   1.367   1.404   1.483
24    P         1.296   1.323   1.376   1.267   1.316   1.386   1.367   1.404   1.483
25    L         1.296   1.323   1.376   1.136   1.185   1.259   1.367   1.404   1.483
26    D         1.296   1.323   1.376   1.182   1.221   1.304   1.367   1.404   1.483
27    H         1.296   1.323   1.376   1.473   1.508   1.587   1.367   1.404   1.483
28    D         0.598   0.464   0.343   0.611   0.451   0.292   0.572   0.355   0.125
29    G         0.598   0.530   0.336   0.623   0.527   0.260   0.572   0.463   0.113
30    E         0.277   0.370   0.261   0.182   0.331   0.106   0.041   0.197  -0.026
31    C         1.296   1.323   1.376   1.393   1.429   1.509   1.367   1.404   1.483
32    T        -0.879  -0.867  -0.881  -0.878  -0.877  -0.888  -0.887  -0.866  -0.845
33    K        -1.006  -0.946  -0.913  -0.907  -0.772  -0.744  -1.019  -0.945  -0.876
34    Y        -0.879  -0.970  -0.901  -0.502  -0.589  -0.504  -0.887  -0.962  -0.864
35    M         1.296   1.323   1.376   1.349   1.386   1.466   1.367   1.404   1.483
36    Q        -0.879  -0.957  -0.896  -0.611  -0.732  -0.655  -0.887  -0.957  -0.860
37    E        -0.879  -0.982  -0.893  -0.856  -0.985  -0.873  -0.887  -0.976  -0.856
38    Y         1.296   1.323   1.376   1.455   1.494   1.569   1.367   1.404   1.483
39    L         1.296   1.323   1.376   1.136   1.185   1.259   1.367   1.404   1.483
40    K        -1.216  -1.177  -1.240  -1.065  -1.027  -1.101  -1.019  -0.981  -0.998
41    C         1.296   1.323   1.376   1.393   1.429   1.509   1.367   1.404   1.483
42    M         0.277   0.264   0.244   0.359   0.339   0.303   0.041   0.009  -0.058
43    Q        -0.060   0.114  -0.285   0.048   0.266  -0.243  -0.091   0.145  -0.401
44    L         0.212   0.200   0.231   0.067   0.064   0.118  -0.077  -0.109  -0.082
45    V        -0.541  -0.526  -0.446  -0.474  -0.457  -0.358  -0.754  -0.729  -0.620
46    Q        -1.006  -0.958  -0.915  -0.973  -0.911  -0.837  -1.019  -0.967  -0.879
47    N        -0.331  -0.425  -0.414  -0.386  -0.520  -0.512  -0.489  -0.598  -0.582
48    E        -0.669  -0.708  -0.869  -0.516  -0.569  -0.864  -0.622  -0.663  -0.827
49    N         1.296   1.323   1.376   1.241   1.271   1.361   1.367   1.404   1.483
50    A         0.598   0.464   0.343   0.723   0.558   0.377   0.572   0.355   0.125
51    M        -1.216  -1.239  -1.259  -0.950  -0.995  -1.003  -1.019  -1.041  -1.015
52    N        -0.060  -0.255  -0.373   0.030  -0.257  -0.456  -0.091  -0.356  -0.521
53    C         1.296   1.323   1.376   1.393   1.429   1.509   1.367   1.404   1.483
54    R         1.296   1.323   1.376   1.362   1.395   1.478   1.367   1.404   1.483
55    L        -0.060  -0.025  -0.337   0.030   0.089  -0.280  -0.091  -0.041  -0.472
56    L         1.296   1.323   1.376   1.136   1.185   1.259   1.367   1.404   1.483
57    A         1.296   1.323   1.376   1.305   1.343   1.423   1.367   1.404   1.483
58    K         1.296   1.323   1.376   1.202   1.241   1.323   1.367   1.404   1.483
59    D        -1.006  -0.976  -0.909  -1.085  -1.028  -0.916  -1.019  -0.976  -0.873
60    Y         1.296   1.323   1.376   1.455   1.494   1.569   1.367   1.404   1.483
61    L         1.296   1.323   1.376   1.136   1.185   1.259   1.367   1.404   1.483
62    R        -0.331  -0.431  -0.413  -0.339  -0.455  -0.421  -0.489  -0.606  -0.581
63    C         1.296   1.323   1.376   1.393   1.429   1.509   1.367   1.404   1.483
64    R         1.296   1.323   1.376   1.362   1.395   1.478   1.367   1.404   1.483
65    M         1.296   1.323   1.376   1.349   1.386   1.466   1.367   1.404   1.483
66    D         0.598   0.530   0.336   0.578   0.495   0.201   0.572   0.463   0.113
67    H        -0.331  -0.363  -0.362  -0.282  -0.330  -0.319  -0.489  -0.507  -0.508
68    Q        -0.669  -0.749  -0.879  -0.398  -0.544  -0.799  -0.622  -0.722  -0.839
69    L         1.296   1.323   1.376   1.136   1.185   1.259   1.367   1.404   1.483
70    M         0.598   0.464   0.343   0.776   0.612   0.439   0.572   0.355   0.125
71    D        -0.669  -0.832  -0.879  -0.600  -0.854  -0.926  -0.622  -0.808  -0.839
72    Y        -1.216  -1.110  -1.259  -0.973  -0.835  -1.002  -1.019  -0.909  -1.015
73    D         0.277   0.307   0.251   0.094   0.135   0.018   0.041   0.087  -0.044
74    E        -0.414  -0.442  -0.403  -0.569  -0.610  -0.547  -0.622  -0.636  -0.569
75    W         0.598   0.464   0.343   0.919   0.745   0.536   0.572   0.355   0.125
76    S        -0.414  -0.335  -0.389  -0.637  -0.536  -0.583  -0.622  -0.534  -0.553
77    H        -0.541  -0.455  -0.440  -0.614  -0.512  -0.470  -0.754  -0.635  -0.612
78    L         1.296   1.323   1.376   1.136   1.185   1.259   1.367   1.404   1.483
79    G         1.296   1.323   1.376   1.215   1.238   1.336   1.367   1.404   1.483
80    L         0.598   0.464   0.343   0.565   0.416   0.250   0.572   0.355   0.125
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    P         0.598   0.464   0.343   0.693   0.544   0.364   0.572   0.355   0.125
85    E        -1.216  -1.073  -1.231  -1.138  -0.949  -1.189  -1.019  -0.872  -0.990
86    D         0.598   0.617   0.356   0.578   0.608   0.233   0.572   0.599   0.147
87    A        -1.681  -1.625  -1.594  -1.594  -1.513  -1.473  -1.284  -1.232  -1.150
88    P        -1.681  -1.696  -1.604  -1.603  -1.625  -1.500  -1.284  -1.284  -1.157
89    G        -1.362  -1.379  -1.290  -1.186  -1.215  -1.090  -1.159  -1.164  -1.042
90    -        -0.475  -0.396  -0.410  -0.567  -0.443  -0.481  -0.663  -0.552  -0.572
91    -        -1.065  -1.042  -0.936  -1.142  -1.104  -0.958  -1.069  -1.035  -0.898
92    -        -0.475  -0.396  -0.410  -0.626  -0.494  -0.546  -0.663  -0.552  -0.572
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -0.475  -0.446  -0.411  -0.739  -0.695  -0.658  -0.663  -0.621  -0.573
100   -        -1.065  -1.042  -0.936  -1.231  -1.182  -1.044  -1.069  -1.035  -0.898
101   -        -1.065  -1.042  -0.936  -1.099  -1.077  -0.916  -1.069  -1.035  -0.898
102   -        -0.475  -0.446  -0.411  -0.669  -0.628  -0.580  -0.663  -0.621  -0.573
103   -        -0.475  -0.463  -0.409  -0.730  -0.717  -0.648  -0.663  -0.646  -0.570
104   -        -1.065  -1.042  -0.936  -1.265  -1.229  -1.077  -1.069  -1.035  -0.898
105   -         0.338   0.409   0.327   0.324   0.421   0.304   0.149   0.263   0.095
106   -        -0.475  -0.441  -0.412  -0.584  -0.551  -0.494  -0.663  -0.615  -0.575
107   -        -1.065  -1.042  -0.936  -1.236  -1.192  -1.049  -1.069  -1.035  -0.898
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   N         0.212   0.229   0.246   0.095   0.111   0.110  -0.077  -0.054  -0.054
119   N         0.529   0.466   0.359   0.507   0.418   0.236   0.465   0.360   0.152
120   G        -0.968  -0.853  -0.897  -1.108  -0.959  -1.013  -0.979  -0.860  -0.861
121   K        -1.362  -1.327  -1.282  -1.299  -1.274  -1.187  -1.159  -1.117  -1.035
122   T        -0.968  -0.931  -0.900  -1.119  -1.069  -1.031  -0.979  -0.924  -0.863
123   I        -1.755  -1.720  -1.612  -1.622  -1.609  -1.425  -1.340  -1.300  -1.163
124   K        -1.755  -1.720  -1.612  -1.584  -1.543  -1.388  -1.340  -1.300  -1.163
125   D        -0.968  -0.943  -0.895  -1.101  -1.082  -1.002  -0.979  -0.944  -0.859
126   A        -1.362  -1.297  -1.273  -1.384  -1.306  -1.266  -1.159  -1.091  -1.027
127   -        -1.065  -1.042  -0.936  -1.137  -1.114  -0.952  -1.069  -1.035  -0.898
128   -        -0.973  -0.948  -0.906  -1.031  -0.994  -0.960  -0.972  -0.937  -0.867
129   T        -0.426  -0.420  -0.407  -0.585  -0.600  -0.577  -0.618  -0.612  -0.575
130   D        -0.968  -0.907  -0.896  -1.121  -1.041  -1.012  -0.979  -0.910  -0.860
131   N        -0.968  -0.907  -0.895  -1.088  -1.000  -0.983  -0.979  -0.909  -0.859
132   K        -1.343  -1.392  -1.284  -1.217  -1.285  -1.153  -1.152  -1.176  -1.038
* 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/Q3E731
Output conservation file - output/Q3E731
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
