1     M         1.175   1.219   1.252   1.250   1.325   1.376   1.281   1.337   1.390
2     P         0.556   0.380   0.310   0.707   0.453   0.315   0.562   0.268   0.116
3     P         1.175   1.219   1.252   1.270   1.324   1.394   1.281   1.337   1.390
4     L        -0.924  -0.780  -0.879  -1.022  -0.782  -0.932  -1.002  -0.803  -0.896
5     P         0.192   0.316   0.234   0.090   0.302   0.141  -0.061   0.154  -0.028
6     Q        -0.134  -0.175  -0.376  -0.040  -0.083  -0.420  -0.196  -0.250  -0.548
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     N        -1.010  -0.929  -0.915  -1.288  -1.126  -1.130  -1.095  -0.978  -0.935
9     Y        -0.721  -0.832  -0.881  -0.430  -0.592  -0.700  -0.733  -0.851  -0.898
10    A        -0.396  -0.476  -0.441  -0.691  -0.870  -0.836  -0.599  -0.692  -0.645
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    Q        -0.819  -0.836  -0.875  -1.003  -1.029  -1.162  -0.878  -0.880  -0.895
13    Q        -0.589  -0.680  -0.828  -0.424  -0.578  -0.767  -0.569  -0.683  -0.837
14    Q         0.251   0.227   0.203   0.067   0.009  -0.122   0.048  -0.006  -0.087
15    P         1.175   1.219   1.252   1.295   1.366   1.418   1.281   1.337   1.390
16    S         1.175   1.219   1.252   1.192   1.258   1.322   1.281   1.337   1.390
17    N         0.556   0.380   0.310   0.843   0.599   0.459   0.562   0.268   0.116
18    W        -0.426  -0.528  -0.428  -0.357  -0.514  -0.364  -0.672  -0.765  -0.630
19    D         0.088   0.147   0.175   0.166   0.275   0.294  -0.261  -0.158  -0.142
20    K         1.175   1.219   1.252   1.406   1.487   1.523   1.281   1.337   1.390
21    F         0.556   0.380   0.310   0.699   0.437   0.315   0.562   0.268   0.116
22    K         1.175   1.219   1.252   1.406   1.487   1.523   1.281   1.337   1.390
23    M         1.175   1.219   1.252   1.250   1.325   1.376   1.281   1.337   1.390
24    G         1.175   1.219   1.252   0.882   0.958   1.031   1.281   1.337   1.390
25    L         0.036   0.078   0.159  -0.250  -0.202  -0.032  -0.364  -0.294  -0.173
26    M        -0.426  -0.445  -0.427  -0.578  -0.594  -0.542  -0.672  -0.672  -0.628
27    M         1.175   1.219   1.252   1.250   1.325   1.376   1.281   1.337   1.390
28    G         1.175   1.219   1.252   0.882   0.958   1.031   1.281   1.337   1.390
29    T        -0.426  -0.416  -0.418  -0.676  -0.658  -0.679  -0.672  -0.632  -0.616
30    T         0.251   0.146   0.180   0.272   0.041   0.079   0.048  -0.161  -0.132
31    V         0.556   0.380   0.310   0.714   0.460   0.315   0.562   0.268   0.116
32    G         1.175   1.219   1.252   0.882   0.958   1.031   1.281   1.337   1.390
33    V        -0.304  -0.479  -0.426  -0.202  -0.458  -0.373  -0.466  -0.688  -0.623
34    C        -0.034  -0.229  -0.350   0.313  -0.037  -0.299  -0.055  -0.331  -0.510
35    T        -0.534  -0.493  -0.450  -0.617  -0.563  -0.497  -0.775  -0.718  -0.654
36    G         1.175   1.219   1.252   0.882   0.958   1.031   1.281   1.337   1.390
37    I        -0.996  -0.994  -0.913  -1.104  -1.097  -0.958  -1.083  -1.047  -0.935
38    L        -0.034  -0.102  -0.334   0.118   0.020  -0.357  -0.055  -0.142  -0.487
39    F         1.175   1.219   1.252   1.284   1.348   1.407   1.281   1.337   1.390
40    G         1.175   1.219   1.252   0.882   0.958   1.031   1.281   1.337   1.390
41    G         0.556   0.551   0.325   0.308   0.321   0.007   0.562   0.550   0.143
42    F        -0.426  -0.446  -0.421  -0.519  -0.523  -0.455  -0.672  -0.673  -0.621
43    A        -0.819  -0.677  -0.845  -0.883  -0.641  -0.869  -0.878  -0.669  -0.858
44    I         0.556   0.380   0.310   0.726   0.476   0.345   0.562   0.268   0.116
45    A        -0.819  -0.735  -0.860  -0.846  -0.748  -0.909  -0.878  -0.779  -0.879
46    T        -0.534  -0.493  -0.450  -0.634  -0.572  -0.511  -0.775  -0.718  -0.654
47    Q        -0.996  -0.976  -0.908  -0.957  -0.874  -0.759  -1.083  -1.029  -0.930
48    G         1.175   1.219   1.252   0.882   0.958   1.031   1.281   1.337   1.390
49    P         0.088   0.096   0.165  -0.138  -0.149  -0.011  -0.261  -0.258  -0.162
50    G         1.175   1.219   1.252   0.882   0.958   1.031   1.281   1.337   1.390
51    P         1.175   1.219   1.252   1.295   1.366   1.418   1.281   1.337   1.390
52    D        -0.304  -0.372  -0.393  -0.119  -0.206  -0.263  -0.466  -0.528  -0.575
53    G         1.175   1.219   1.252   0.882   0.958   1.031   1.281   1.337   1.390
54    V        -0.534  -0.549  -0.473  -0.665  -0.702  -0.579  -0.775  -0.786  -0.684
55    V        -0.304  -0.384  -0.393  -0.341  -0.443  -0.480  -0.466  -0.545  -0.575
56    R         0.556   0.525   0.320   0.757   0.727   0.413   0.562   0.509   0.134
57    T         1.175   1.219   1.252   1.351   1.425   1.471   1.281   1.337   1.390
58    L         1.175   1.219   1.252   1.278   1.339   1.402   1.281   1.337   1.390
59    G         1.175   1.219   1.252   0.882   0.958   1.031   1.281   1.337   1.390
60    K         0.251   0.377   0.241   0.234   0.456   0.212   0.048   0.263  -0.013
61    Y         1.175   1.219   1.252   1.428   1.506   1.543   1.281   1.337   1.390
62    I        -0.304  -0.424  -0.426  -0.304  -0.526  -0.521  -0.466  -0.636  -0.625
63    A        -0.534  -0.493  -0.450  -0.765  -0.726  -0.627  -0.775  -0.718  -0.654
64    G         0.556   0.380   0.310   0.308   0.074  -0.017   0.562   0.268   0.116
65    S         1.175   1.219   1.252   1.192   1.258   1.322   1.281   1.337   1.390
66    A        -0.304  -0.194  -0.366  -0.442  -0.258  -0.593  -0.466  -0.277  -0.534
67    G         0.088   0.226   0.196  -0.357  -0.053  -0.166  -0.261  -0.009  -0.100
68    T         1.175   1.219   1.252   1.351   1.425   1.471   1.281   1.337   1.390
69    F         1.175   1.219   1.252   1.284   1.348   1.407   1.281   1.337   1.390
70    G         1.175   1.219   1.252   0.882   0.958   1.031   1.281   1.337   1.390
71    L         0.251   0.155   0.187   0.222   0.019   0.071   0.048  -0.143  -0.118
72    F         1.175   1.219   1.252   1.284   1.348   1.407   1.281   1.337   1.390
73    M         1.175   1.219   1.252   1.250   1.325   1.376   1.281   1.337   1.390
74    S         1.175   1.219   1.252   1.192   1.258   1.322   1.281   1.337   1.390
75    I         0.556   0.525   0.320   0.726   0.696   0.363   0.562   0.509   0.134
76    G         1.175   1.219   1.252   0.882   0.958   1.031   1.281   1.337   1.390
77    S         1.175   1.219   1.252   1.192   1.258   1.322   1.281   1.337   1.390
78    I         0.088   0.144   0.174  -0.057   0.054   0.079  -0.261  -0.163  -0.143
79    I         1.175   1.219   1.252   1.306   1.375   1.429   1.281   1.337   1.390
80    R         1.175   1.219   1.252   1.323   1.389   1.444   1.281   1.337   1.390
81    S         0.556   0.380   0.310   0.629   0.389   0.285   0.562   0.268   0.116
82    D         0.088   0.082   0.160   0.166   0.148   0.266  -0.261  -0.285  -0.172
83    S        -0.819  -0.752  -0.865  -0.935  -0.828  -1.023  -0.878  -0.820  -0.886
84    E        -1.958  -1.917  -1.811  -1.811  -1.763  -1.629  -1.495  -1.426  -1.287
85    S        -0.996  -0.812  -0.883  -1.178  -0.845  -0.974  -1.083  -0.841  -0.902
86    S        -1.958  -1.939  -1.816  -1.863  -1.827  -1.623  -1.495  -1.439  -1.290
87    P        -1.958  -1.916  -1.803  -1.844  -1.794  -1.627  -1.495  -1.426  -1.282
88    M        -1.673  -1.689  -1.564  -1.677  -1.717  -1.517  -1.392  -1.361  -1.209
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        -1.673  -1.521  -1.542  -1.558  -1.353  -1.327  -1.392  -1.238  -1.194
97    H        -1.565  -1.399  -1.523  -1.351  -1.100  -1.280  -1.289  -1.102  -1.178
98    P        -1.958  -1.883  -1.799  -2.071  -1.977  -1.834  -1.495  -1.404  -1.279
99    N        -1.103  -1.157  -1.222  -0.953  -1.063  -1.118  -0.981  -1.026  -1.054
100   L        -1.958  -1.824  -1.801  -1.872  -1.631  -1.628  -1.495  -1.361  -1.280
101   N        -1.958  -1.812  -1.793  -1.590  -1.375  -1.350  -1.495  -1.345  -1.275
102   L        -1.281  -1.311  -1.253  -1.341  -1.382  -1.280  -1.186  -1.185  -1.085
103   Q        -0.304  -0.424  -0.426  -0.365  -0.591  -0.572  -0.466  -0.636  -0.625
104   Q        -0.819  -0.914  -0.872  -0.773  -0.862  -0.800  -0.878  -0.948  -0.891
105   Q        -0.819  -0.833  -0.870  -0.899  -0.952  -0.978  -0.878  -0.871  -0.888
106   A        -0.630  -0.582  -0.475  -0.973  -0.901  -0.699  -0.912  -0.830  -0.688
107   R         1.175   1.219   1.252   1.316   1.381   1.437   1.281   1.337   1.390
108   L        -1.014  -1.023  -0.925  -1.162  -1.183  -1.012  -1.087  -1.073  -0.946
109   E        -0.387  -0.494  -0.446  -0.250  -0.476  -0.426  -0.561  -0.706  -0.646
110   M        -1.014  -1.016  -0.921  -1.059  -1.084  -0.919  -1.087  -1.067  -0.941
111   W        -0.387  -0.494  -0.446  -0.176  -0.381  -0.335  -0.561  -0.706  -0.646
112   K        -0.134  -0.347  -0.395   0.090  -0.263  -0.377  -0.196  -0.497  -0.575
113   L        -1.249  -1.304  -1.262  -1.230  -1.350  -1.262  -1.136  -1.170  -1.091
114   R        -0.134  -0.237  -0.376   0.038  -0.149  -0.363  -0.196  -0.355  -0.548
115   A        -0.487  -0.450  -0.451  -0.674  -0.653  -0.590  -0.729  -0.679  -0.657
116   K        -1.390  -1.351  -1.285  -1.406  -1.392  -1.238  -1.278  -1.212  -1.110
117   Y         0.435   0.227   0.242   0.704   0.376   0.365   0.368  -0.007  -0.012
118   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   R        -1.103  -1.183  -1.223  -0.909  -1.069  -1.108  -0.981  -1.050  -1.055
128   K        -1.958  -1.909  -1.811  -1.657  -1.584  -1.438  -1.495  -1.422  -1.287
129   D        -1.281  -1.303  -1.247  -0.960  -0.968  -0.894  -1.186  -1.169  -1.078
* 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/Q02889
Output conservation file - output/Q02889
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
