1     M         1.484   1.489   1.555   1.609   1.621   1.717   1.621   1.629   1.733
2     R        -1.162  -1.134  -1.168  -0.807  -0.762  -0.859  -0.977  -0.948  -0.954
3     S        -0.807  -0.816  -0.808  -1.034  -1.072  -1.041  -0.833  -0.849  -0.802
4     F         0.056   0.098  -0.175   0.183   0.240  -0.152   0.033   0.092  -0.305
5     V        -0.230  -0.245  -0.270  -0.511  -0.535  -0.567  -0.400  -0.419  -0.451
6     T        -0.807  -0.777  -0.789  -0.887  -0.839  -0.853  -0.833  -0.792  -0.778
7     N        -0.586  -0.547  -0.709  -0.393  -0.345  -0.530  -0.544  -0.497  -0.684
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     N        -1.651  -1.638  -1.538  -1.347  -1.320  -1.183  -1.266  -1.253  -1.122
10    D        -0.807  -0.797  -0.813  -0.512  -0.498  -0.550  -0.833  -0.829  -0.807
11    I         0.748   0.802   0.567   0.694   0.772   0.413   0.755   0.837   0.425
12    P         1.484   1.489   1.555   1.619   1.626   1.727   1.621   1.629   1.733
13    V        -0.230  -0.256  -0.264  -0.541  -0.580  -0.599  -0.400  -0.428  -0.441
14    G         1.484   1.489   1.555   1.433   1.444   1.547   1.621   1.629   1.733
15    Y         1.484   1.489   1.555   1.489   1.500   1.602   1.621   1.629   1.733
16    V        -1.296  -1.335  -1.211  -1.151  -1.209  -1.024  -1.121  -1.151  -0.997
17    T         0.411   0.471   0.455   0.235   0.340   0.300   0.178   0.285   0.218
18    P         1.484   1.489   1.555   1.619   1.626   1.727   1.621   1.629   1.733
19    K        -1.296  -1.268  -1.207  -0.900  -0.855  -0.771  -1.121  -1.097  -0.993
20    F         1.484   1.489   1.555   1.474   1.481   1.587   1.621   1.629   1.733
21    P         1.484   1.489   1.555   1.619   1.626   1.727   1.621   1.629   1.733
22    S         1.484   1.489   1.555   1.413   1.419   1.528   1.621   1.629   1.733
23    L         1.484   1.489   1.555   1.355   1.354   1.473   1.621   1.629   1.733
24    Y         0.748   0.699   0.549   0.826   0.765   0.536   0.755   0.675   0.393
25    W         1.484   1.489   1.555   1.629   1.638   1.736   1.621   1.629   1.733
26    P         1.484   1.489   1.555   1.619   1.626   1.727   1.621   1.629   1.733
27    I        -1.296  -1.304  -1.222  -1.468  -1.473  -1.312  -1.121  -1.125  -1.005
28    N         0.259   0.280   0.361   0.138   0.170   0.299  -0.111  -0.074   0.035
29    N        -0.807  -0.795  -0.801  -0.651  -0.640  -0.592  -0.833  -0.819  -0.795
30    S        -0.807  -0.759  -0.786  -0.782  -0.703  -0.737  -0.833  -0.775  -0.780
31    K        -0.807  -0.819  -0.786  -0.450  -0.472  -0.418  -0.833  -0.846  -0.781
32    -        -0.381  -0.377  -0.317  -0.332  -0.341  -0.252  -0.589  -0.586  -0.509
33    -        -1.003  -0.989  -0.865  -0.970  -0.941  -0.766  -1.031  -1.016  -0.860
34    Y         0.411   0.378   0.390   0.313   0.257   0.247   0.178   0.114   0.094
35    N        -1.651  -1.662  -1.543  -1.138  -1.174  -1.000  -1.266  -1.273  -1.126
36    T        -1.296  -1.322  -1.225  -1.330  -1.355  -1.224  -1.121  -1.140  -1.008
37    A        -0.230  -0.279  -0.280  -0.279  -0.363  -0.396  -0.400  -0.463  -0.464
38    F        -0.807  -0.746  -0.789  -0.787  -0.683  -0.731  -0.833  -0.759  -0.778
39    L         1.484   1.489   1.555   1.355   1.354   1.473   1.621   1.629   1.733
40    Y         1.484   1.489   1.555   1.489   1.500   1.602   1.621   1.629   1.733
41    Y         0.748   0.808   0.567   0.826   0.907   0.566   0.755   0.846   0.425
42    I        -0.941  -0.934  -0.847  -1.231  -1.217  -1.080  -0.977  -0.966  -0.842
43    S        -1.651  -1.652  -1.561  -1.351  -1.353  -1.205  -1.266  -1.265  -1.139
44    D         1.484   1.489   1.555   1.727   1.736   1.830   1.621   1.629   1.733
45    I         1.484   1.489   1.555   1.298   1.300   1.417   1.621   1.629   1.733
46    W         1.484   1.489   1.555   1.629   1.638   1.736   1.621   1.629   1.733
47    K         0.259   0.272   0.357   0.367   0.394   0.511  -0.111  -0.090   0.028
48    F         1.484   1.489   1.555   1.474   1.481   1.587   1.621   1.629   1.733
49    S         0.748   0.802   0.567   0.851   0.925   0.580   0.755   0.837   0.425
50    L        -0.230  -0.198  -0.253  -0.483  -0.413  -0.533  -0.400  -0.344  -0.420
51    Y        -0.807  -0.746  -0.789  -0.932  -0.825  -0.930  -0.833  -0.759  -0.778
52    W         1.484   1.489   1.555   1.629   1.638   1.736   1.621   1.629   1.733
53    T         0.411   0.363   0.392   0.324   0.233   0.249   0.178   0.084   0.097
54    L        -0.586  -0.532  -0.709  -0.602  -0.528  -0.800  -0.544  -0.479  -0.684
55    I         0.748   0.699   0.549   0.613   0.539   0.316   0.755   0.675   0.393
56    F         0.259   0.288   0.361  -0.087  -0.045   0.082  -0.111  -0.059   0.037
57    N        -0.230  -0.225  -0.249  -0.199  -0.189  -0.230  -0.400  -0.379  -0.414
58    G        -0.586  -0.564  -0.743  -0.391  -0.358  -0.582  -0.544  -0.518  -0.724
59    A        -1.296  -1.303  -1.219  -1.263  -1.289  -1.154  -1.121  -1.124  -1.002
60    F         0.748   0.734   0.549   0.796   0.778   0.493   0.755   0.731   0.393
61    Y         0.411   0.438   0.430   0.441   0.484   0.478   0.178   0.224   0.170
62    V        -1.296  -1.250  -1.217  -1.411  -1.347  -1.275  -1.121  -1.080  -1.002
63    T        -0.317  -0.277  -0.292  -0.577  -0.523  -0.510  -0.544  -0.502  -0.485
64    A         0.056  -0.005  -0.182   0.237   0.151  -0.144   0.033  -0.053  -0.315
65    G         0.748   0.768   0.558   0.784   0.814   0.527   0.755   0.784   0.409
66    V        -1.651  -1.637  -1.540  -1.687  -1.677  -1.516  -1.266  -1.252  -1.123
67    Y        -0.941  -0.950  -0.840  -1.110  -1.141  -0.978  -0.977  -0.980  -0.834
68    A         1.484   1.489   1.555   1.560   1.567   1.669   1.621   1.629   1.733
69    S        -0.586  -0.628  -0.734  -0.528  -0.590  -0.764  -0.544  -0.596  -0.713
70    L        -1.162  -1.224  -1.195  -1.153  -1.244  -1.199  -0.977  -1.039  -0.979
71    T        -0.807  -0.857  -0.817  -0.805  -0.861  -0.798  -0.833  -0.881  -0.810
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    H         0.259   0.280   0.361   0.401   0.437   0.551  -0.111  -0.074   0.035
88    R        -0.586  -0.597  -0.723  -0.142  -0.159  -0.366  -0.544  -0.560  -0.700
89    K        -0.807  -0.832  -0.811  -0.448  -0.482  -0.449  -0.833  -0.860  -0.805
90    K        -1.651  -1.606  -1.544  -1.516  -1.472  -1.330  -1.266  -1.227  -1.126
91    A        -1.651  -1.606  -1.544  -1.409  -1.352  -1.227  -1.266  -1.227  -1.126
92    G        -1.162  -1.176  -1.192  -0.924  -0.944  -0.934  -0.977  -0.991  -0.976
93    S        -0.807  -0.784  -0.790  -0.724  -0.678  -0.689  -0.833  -0.817  -0.784
94    V        -0.807  -0.848  -0.799  -1.065  -1.140  -1.061  -0.833  -0.874  -0.794
95    W        -1.162  -1.197  -1.203  -0.979  -1.043  -1.121  -0.977  -1.013  -0.986
96    I         0.056  -0.008  -0.185  -0.014  -0.110  -0.364   0.033  -0.057  -0.319
97    F        -0.807  -0.816  -0.808  -0.916  -0.949  -0.925  -0.833  -0.849  -0.802
98    V        -1.651  -1.636  -1.539  -1.633  -1.610  -1.464  -1.266  -1.251  -1.122
99    M        -1.296  -1.282  -1.209  -1.394  -1.365  -1.273  -1.121  -1.108  -0.995
100   Y         1.484   1.489   1.555   1.489   1.500   1.602   1.621   1.629   1.733
101   V        -0.807  -0.800  -0.780  -1.030  -1.029  -0.977  -0.833  -0.826  -0.773
102   L        -1.162  -1.176  -1.192  -1.183  -1.205  -1.236  -0.977  -0.991  -0.976
103   Y        -0.807  -0.843  -0.804  -1.010  -1.062  -0.988  -0.833  -0.861  -0.795
104   G         0.411   0.459   0.410   0.293   0.375   0.280   0.178   0.263   0.132
105   G        -0.230  -0.278  -0.292  -0.364  -0.455  -0.454  -0.400  -0.473  -0.479
106   V        -0.452  -0.436  -0.341  -0.799  -0.766  -0.606  -0.688  -0.669  -0.543
107   Q        -0.230  -0.251  -0.268   0.144   0.124   0.100  -0.400  -0.419  -0.442
108   G         0.259   0.268   0.351   0.032   0.051   0.181  -0.111  -0.097   0.016
109   L        -1.162  -1.063  -1.172  -1.149  -0.986  -1.213  -0.977  -0.874  -0.958
110   T        -0.317  -0.280  -0.292  -0.661  -0.615  -0.585  -0.544  -0.504  -0.485
111   T        -1.162  -1.160  -1.189  -1.092  -1.077  -1.138  -0.977  -0.976  -0.974
112   G         1.484   1.489   1.555   1.433   1.444   1.547   1.621   1.629   1.733
113   T        -0.230  -0.253  -0.279  -0.231  -0.275  -0.319  -0.400  -0.444  -0.462
114   V         0.259   0.280   0.361  -0.193  -0.156  -0.022  -0.111  -0.074   0.035
115   M        -0.452  -0.442  -0.342  -0.747  -0.749  -0.588  -0.688  -0.678  -0.543
116   G         1.484   1.489   1.555   1.433   1.444   1.547   1.621   1.629   1.733
117   F        -0.807  -0.820  -0.795  -1.038  -1.063  -1.037  -0.833  -0.838  -0.785
118   L         0.259   0.262   0.351  -0.201  -0.208  -0.054  -0.111  -0.108   0.016
119   I         0.411   0.394   0.391   0.082   0.041   0.019   0.178   0.143   0.095
120   G        -0.941  -0.950  -0.840  -1.048  -1.053  -0.890  -0.977  -0.980  -0.834
121   A        -0.230  -0.224  -0.270  -0.282  -0.264  -0.380  -0.400  -0.385  -0.446
122   I         0.411   0.438   0.430   0.094   0.138   0.111   0.178   0.224   0.170
123   Y         1.484   1.489   1.555   1.489   1.500   1.602   1.621   1.629   1.733
124   R        -0.230  -0.293  -0.293   0.097   0.013   0.013  -0.400  -0.486  -0.481
125   S         0.411   0.471   0.455   0.358   0.465   0.408   0.178   0.285   0.218
126   G         1.484   1.489   1.555   1.433   1.444   1.547   1.621   1.629   1.733
127   L         0.411   0.363   0.392   0.161   0.063   0.104   0.178   0.084   0.097
128   F        -0.452  -0.457  -0.353  -0.571  -0.601  -0.429  -0.688  -0.697  -0.558
129   S        -0.586  -0.679  -0.763  -0.437  -0.561  -0.666  -0.544  -0.657  -0.747
130   M         0.056   0.098  -0.175   0.243   0.309  -0.163   0.033   0.092  -0.305
131   S         1.484   1.489   1.555   1.413   1.419   1.528   1.621   1.629   1.733
132   T         1.484   1.489   1.555   1.525   1.535   1.636   1.621   1.629   1.733
133   W         1.484   1.489   1.555   1.629   1.638   1.736   1.621   1.629   1.733
134   V         0.411   0.471   0.455   0.094   0.196   0.158   0.178   0.285   0.218
135   P         1.484   1.489   1.555   1.619   1.626   1.727   1.621   1.629   1.733
136   L        -0.230  -0.242  -0.255  -0.348  -0.364  -0.368  -0.400  -0.404  -0.430
137   C         0.056   0.036  -0.168   0.425   0.399   0.049   0.033   0.004  -0.296
138   C         0.259   0.280   0.361   0.308   0.342   0.462  -0.111  -0.074   0.035
139   A         0.748   0.697   0.551   0.890   0.821   0.592   0.755   0.671   0.397
140   V         0.056  -0.038  -0.195   0.064  -0.064  -0.320   0.033  -0.099  -0.333
141   V         0.056  -0.038  -0.195   0.053  -0.077  -0.340   0.033  -0.099  -0.333
142   Q         0.748   0.697   0.551   1.144   1.081   0.889   0.755   0.671   0.397
143   I         0.748   0.699   0.549   0.619   0.548   0.326   0.755   0.675   0.393
144   L         1.484   1.489   1.555   1.355   1.354   1.473   1.621   1.629   1.733
145   F        -0.807  -0.790  -0.787  -0.795  -0.767  -0.777  -0.833  -0.812  -0.778
146   D        -0.452  -0.452  -0.349  -0.272  -0.265  -0.125  -0.688  -0.690  -0.553
147   V         0.748   0.699   0.549   0.694   0.630   0.381   0.755   0.675   0.393
148   V        -1.296  -1.296  -1.218  -1.278  -1.263  -1.137  -1.121  -1.119  -1.002
149   L        -1.162  -1.160  -1.189  -0.950  -0.942  -1.004  -0.977  -0.976  -0.974
150   S         0.748   0.697   0.551   0.729   0.656   0.428   0.755   0.671   0.397
151   Y         1.484   1.489   1.555   1.489   1.500   1.602   1.621   1.629   1.733
152   S         0.748   0.697   0.551   0.729   0.656   0.428   0.755   0.671   0.397
153   M         0.411   0.363   0.392   0.447   0.364   0.379   0.178   0.084   0.097
154   V        -0.941  -0.934  -0.847  -1.062  -1.043  -0.904  -0.977  -0.966  -0.842
155   G        -1.296  -1.335  -1.239  -1.126  -1.175  -1.047  -1.121  -1.150  -1.020
156   S        -0.807  -0.820  -0.795  -0.976  -0.984  -0.943  -0.833  -0.838  -0.785
157   V        -0.230  -0.170  -0.245  -0.490  -0.401  -0.505  -0.400  -0.319  -0.410
158   M        -0.317  -0.319  -0.296  -0.503  -0.520  -0.478  -0.544  -0.542  -0.489
* 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/Q06537
Output conservation file - output/Q06537
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
