1     M         1.706   1.748   1.823   1.898   1.954   2.068   1.873   1.929   2.061
2     F         0.300   0.289   0.063   0.482   0.455   0.162   0.300   0.256  -0.064
3     R        -0.818  -0.836  -0.683  -1.026  -1.018  -0.819  -0.910  -0.894  -0.717
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -0.840  -0.803  -0.694  -0.931  -0.873  -0.730  -0.915  -0.854  -0.724
9     -        -0.110   0.030  -0.049  -0.117   0.093  -0.031  -0.296  -0.092  -0.231
10    -        -0.110  -0.101  -0.076  -0.001   0.006   0.012  -0.296  -0.286  -0.272
11    Q        -1.481  -1.543  -1.443  -1.047  -1.144  -1.035  -1.152  -1.177  -1.049
12    C        -1.150  -1.083  -1.048  -1.038  -0.905  -0.838  -1.031  -0.937  -0.865
13    A        -0.943  -0.557  -0.945  -0.764  -0.212  -0.808  -0.789  -0.347  -0.760
14    K        -1.150  -1.061  -1.054  -1.217  -1.130  -1.115  -1.031  -0.933  -0.875
15    R         0.986   0.838   0.791   1.060   0.865   0.806   1.026   0.770   0.654
16    Y        -1.275  -1.262  -1.103  -1.360  -1.331  -1.114  -1.152  -1.094  -0.917
17    A        -1.150  -1.097  -1.069  -1.209  -1.122  -1.045  -1.031  -0.961  -0.887
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    S         0.401   0.507   0.583   0.208   0.377   0.492  -0.024   0.161   0.250
22    L         0.048  -0.129  -0.108   0.081  -0.213  -0.183  -0.063  -0.331  -0.318
23    P         0.048   0.023  -0.065   0.139   0.122  -0.043  -0.063  -0.102  -0.255
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    P        -1.150  -1.079  -1.028  -1.259  -1.142  -1.094  -1.031  -0.918  -0.846
35    N        -1.606  -1.421  -1.404  -1.513  -1.284  -1.235  -1.273  -1.090  -1.021
36    A        -0.612  -0.572  -0.622  -0.791  -0.737  -0.768  -0.668  -0.622  -0.650
37    L        -0.346  -0.505  -0.571  -0.235  -0.469  -0.593  -0.305  -0.504  -0.580
38    K        -1.150  -1.210  -1.078  -1.338  -1.433  -1.243  -1.031  -1.048  -0.896
39    P        -0.943  -1.008  -1.035  -0.735  -0.842  -0.920  -0.789  -0.847  -0.851
40    A        -0.346  -0.463  -0.548  -0.355  -0.509  -0.616  -0.305  -0.452  -0.553
41    F        -0.346  -0.396  -0.537  -0.184  -0.245  -0.511  -0.305  -0.362  -0.538
42    G        -0.818  -0.755  -0.685  -0.768  -0.719  -0.589  -0.910  -0.824  -0.718
43    P        -0.346  -0.407  -0.555  -0.297  -0.408  -0.607  -0.305  -0.399  -0.560
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    P        -0.943  -1.052  -1.045  -0.725  -0.897  -0.920  -0.789  -0.892  -0.861
55    D        -0.156  -0.173  -0.080  -0.216  -0.194  -0.072  -0.426  -0.402  -0.291
56    K        -0.612  -0.583  -0.607  -0.768  -0.732  -0.760  -0.668  -0.633  -0.632
57    V        -1.150  -1.142  -1.078  -1.202  -1.184  -1.070  -1.031  -1.003  -0.896
58    A        -0.014  -0.031  -0.070  -0.200  -0.210  -0.250  -0.184  -0.214  -0.273
59    A        -0.281  -0.294  -0.182  -0.632  -0.655  -0.472  -0.547  -0.568  -0.426
60    Q        -1.150  -1.090  -1.048  -1.135  -1.057  -0.994  -1.031  -0.940  -0.865
61    K        -0.346  -0.351  -0.521  -0.429  -0.436  -0.701  -0.305  -0.327  -0.519
62    F        -0.014  -0.050  -0.055   0.043   0.024  -0.003  -0.184  -0.211  -0.248
63    K        -0.943  -1.086  -1.055  -0.887  -1.106  -1.072  -0.789  -0.926  -0.871
64    E        -1.606  -1.452  -1.416  -1.663  -1.461  -1.371  -1.273  -1.117  -1.030
65    S        -1.150  -0.914  -1.020  -1.229  -0.891  -1.053  -1.031  -0.754  -0.837
66    L        -1.606  -1.535  -1.426  -1.378  -1.310  -1.101  -1.273  -1.176  -1.036
67    M        -1.481  -1.326  -1.364  -1.319  -1.105  -1.147  -1.152  -0.995  -0.984
68    A        -0.014   0.149  -0.031  -0.288  -0.060  -0.296  -0.184   0.023  -0.212
69    T        -1.150  -1.150  -1.082  -1.130  -1.170  -1.054  -1.031  -1.008  -0.899
70    E        -0.943  -0.865  -0.994  -0.942  -0.839  -1.061  -0.789  -0.695  -0.810
71    K        -0.693  -0.689  -0.618  -0.881  -0.822  -0.704  -0.789  -0.746  -0.646
72    H         1.706   1.748   1.823   1.710   1.778   1.890   1.873   1.929   2.061
73    A         0.631   0.675   0.658   0.354   0.429   0.396   0.421   0.480   0.399
74    K        -0.693  -0.608  -0.617  -0.990  -0.872  -0.861  -0.789  -0.682  -0.648
75    D        -1.481  -1.395  -1.396  -1.133  -1.078  -1.054  -1.152  -1.061  -1.011
76    T        -0.014  -0.117  -0.079   0.070  -0.060  -0.025  -0.184  -0.314  -0.281
77    S         0.381   0.440   0.552   0.175   0.266   0.438  -0.063   0.027   0.187
78    N        -0.818  -0.700  -0.676  -0.999  -0.885  -0.796  -0.910  -0.781  -0.710
79    M        -0.346  -0.218  -0.503  -0.170  -0.042  -0.378  -0.305  -0.170  -0.498
80    W         1.706   1.748   1.823   1.812   1.870   1.987   1.873   1.929   2.061
81    V        -0.362  -0.275  -0.168  -0.684  -0.546  -0.388  -0.668  -0.539  -0.405
82    K         0.986   0.998   0.820   0.924   0.955   0.716   1.026   1.035   0.707
83    I         0.300   0.146   0.037   0.533   0.318   0.130   0.300   0.070  -0.103
84    S         0.442   0.452   0.555   0.293   0.287   0.443   0.058   0.051   0.193
85    V        -0.818  -0.618  -0.659  -0.817  -0.550  -0.590  -0.910  -0.680  -0.691
86    W        -1.150  -0.910  -1.021  -0.984  -0.640  -0.795  -1.031  -0.752  -0.840
87    V        -0.014  -0.121  -0.105   0.013  -0.132  -0.105  -0.184  -0.340  -0.326
88    A        -0.346  -0.516  -0.589  -0.274  -0.477  -0.526  -0.305  -0.517  -0.602
89    L        -1.481  -1.490  -1.417  -1.297  -1.289  -1.217  -1.152  -1.138  -1.028
90    P         1.706   1.748   1.823   1.700   1.774   1.880   1.873   1.929   2.061
91    A         0.631   0.699   0.638   0.328   0.448   0.326   0.421   0.525   0.360
92    I        -0.281  -0.294  -0.182  -0.375  -0.442  -0.284  -0.547  -0.568  -0.426
93    A        -0.156  -0.222  -0.109  -0.490  -0.533  -0.353  -0.426  -0.481  -0.336
94    L         0.986   1.040   0.825   0.967   1.038   0.732   1.026   1.102   0.717
95    T        -0.014  -0.099  -0.099  -0.065  -0.254  -0.268  -0.184  -0.328  -0.317
96    A        -0.346  -0.516  -0.589  -0.284  -0.497  -0.543  -0.305  -0.517  -0.602
97    V        -0.612  -0.743  -0.656  -0.580  -0.779  -0.659  -0.668  -0.793  -0.685
98    N         0.631   0.675   0.658   0.584   0.640   0.597   0.421   0.480   0.399
99    T        -0.612  -0.628  -0.648  -0.611  -0.699  -0.709  -0.668  -0.692  -0.679
100   Y         0.300   0.341   0.064   0.508   0.552   0.149   0.300   0.355  -0.063
101   F        -0.943  -1.077  -1.060  -0.718  -0.918  -0.929  -0.789  -0.917  -0.876
102   V        -0.014  -0.117  -0.094  -0.019  -0.168  -0.145  -0.184  -0.333  -0.311
103   E         0.631   0.532   0.591   0.452   0.282   0.378   0.421   0.209   0.266
104   K        -1.606  -1.596  -1.440  -1.553  -1.443  -1.244  -1.273  -1.218  -1.047
105   E        -0.943  -1.008  -1.035  -0.927  -1.045  -1.106  -0.789  -0.847  -0.851
106   H         1.706   1.748   1.823   1.710   1.778   1.890   1.873   1.929   2.061
107   A         0.300   0.084   0.003   0.269   0.018  -0.083   0.300  -0.016  -0.153
108   E         0.986   1.160   0.839   0.935   1.155   0.767   1.026   1.281   0.743
109   H         1.706   1.748   1.823   1.710   1.778   1.890   1.873   1.929   2.061
110   R         0.300   0.084   0.003   0.424   0.110  -0.023   0.300  -0.016  -0.153
111   E        -0.156  -0.174  -0.112  -0.471  -0.474  -0.358  -0.426  -0.428  -0.337
112   H         1.706   1.748   1.823   1.710   1.778   1.890   1.873   1.929   2.061
113   L         0.184  -0.015  -0.043   0.263  -0.037  -0.065   0.134  -0.167  -0.222
114   K        -0.668  -0.764  -0.694  -0.801  -0.954  -0.861  -0.709  -0.810  -0.724
115   H         0.845   0.844   0.699   0.847   0.847   0.593   0.797   0.782   0.479
116   V         0.401   0.442   0.556   0.078   0.131   0.311  -0.024   0.030   0.195
117   P         0.563   0.574   0.587   0.472   0.492   0.481   0.292   0.289   0.258
118   D         0.184   0.047  -0.052   0.339   0.166  -0.066   0.134  -0.073  -0.236
119   S        -0.612  -0.539  -0.564  -0.669  -0.536  -0.579  -0.668  -0.541  -0.574
120   E         0.631   0.578   0.601   0.447   0.376   0.387   0.421   0.297   0.287
121   W        -0.346  -0.516  -0.589  -0.038  -0.295  -0.451  -0.305  -0.517  -0.602
122   P         0.300   0.084   0.003   0.474   0.207   0.049   0.300  -0.016  -0.153
123   R        -0.818  -0.790  -0.682  -0.827  -0.763  -0.602  -0.910  -0.856  -0.715
124   D        -0.818  -0.845  -0.692  -0.808  -0.820  -0.628  -0.910  -0.904  -0.725
125   Y         1.706   1.748   1.823   1.761   1.802   1.939   1.873   1.929   2.061
126   E        -0.346  -0.547  -0.580  -0.257  -0.519  -0.574  -0.305  -0.553  -0.591
127   F         0.442   0.468   0.560   0.273   0.303   0.441   0.058   0.083   0.203
128   M         0.300   0.309   0.060   0.605   0.572   0.260   0.300   0.281  -0.069
129   N         1.706   1.748   1.823   1.705   1.752   1.885   1.873   1.929   2.061
130   I        -0.156  -0.099  -0.088  -0.245  -0.171  -0.141  -0.426  -0.347  -0.311
131   R         1.706   1.748   1.823   1.674   1.727   1.856   1.873   1.929   2.061
132   S        -0.818  -0.825  -0.682  -0.751  -0.755  -0.550  -0.910  -0.883  -0.716
133   K         0.986   0.926   0.804   0.924   0.861   0.692   1.026   0.918   0.678
134   P        -0.281  -0.299  -0.186  -0.457  -0.512  -0.359  -0.547  -0.572  -0.430
135   F         0.442   0.442   0.552   0.273   0.254   0.431   0.058   0.029   0.187
136   F         0.631   0.532   0.591   0.574   0.406   0.463   0.421   0.209   0.266
137   W         1.706   1.748   1.823   1.812   1.870   1.987   1.873   1.929   2.061
138   G         1.706   1.748   1.823   1.792   1.838   1.968   1.873   1.929   2.061
139   D         0.986   1.160   0.839   1.127   1.377   0.939   1.026   1.281   0.743
140   G         1.706   1.748   1.823   1.792   1.838   1.968   1.873   1.929   2.061
141   D         0.986   0.838   0.791   1.132   0.979   0.872   1.026   0.770   0.654
142   K         1.706   1.748   1.823   1.547   1.614   1.736   1.873   1.929   2.061
143   T         1.706   1.748   1.823   1.731   1.799   1.910   1.873   1.929   2.061
144   L         1.706   1.748   1.823   1.621   1.672   1.806   1.873   1.929   2.061
145   F         1.706   1.748   1.823   1.694   1.763   1.876   1.873   1.929   2.061
146   W         1.706   1.748   1.823   1.812   1.870   1.987   1.873   1.929   2.061
147   N         1.706   1.748   1.823   1.705   1.752   1.885   1.873   1.929   2.061
148   P        -0.612  -0.743  -0.656  -0.547  -0.716  -0.628  -0.668  -0.793  -0.685
149   V        -1.150  -1.210  -1.099  -1.136  -1.205  -1.096  -1.031  -1.053  -0.913
150   V         0.631   0.842   0.727   0.566   0.883   0.706   0.421   0.777   0.534
151   N         1.706   1.748   1.823   1.705   1.752   1.885   1.873   1.929   2.061
152   R         0.300   0.084   0.003   0.457   0.161   0.045   0.300  -0.016  -0.153
153   H         0.986   0.838   0.791   1.080   0.890   0.805   1.026   0.770   0.654
154   I        -0.612  -0.715  -0.624  -0.517  -0.674  -0.575  -0.668  -0.757  -0.651
155   E        -1.606  -1.480  -1.416  -1.595  -1.443  -1.317  -1.273  -1.138  -1.030
156   H        -1.150  -1.095  -1.082  -1.092  -0.974  -1.030  -1.031  -0.952  -0.899
157   D         0.922   0.875   0.779   1.018   0.964   0.794   0.925   0.833   0.632
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P32799
Output conservation file - output/P32799
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
