1     M         1.651   1.697   1.802   1.911   1.977   2.149   1.821   1.898   2.073
2     T        -0.603  -0.507  -0.615  -0.362  -0.216  -0.383  -0.654  -0.531  -0.635
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    K        -1.125  -1.091  -1.092  -1.135  -1.092  -1.077  -1.007  -0.974  -0.920
12    V        -0.722  -0.622  -0.669  -0.864  -0.693  -0.790  -0.795  -0.669  -0.701
13    D        -1.229  -1.158  -1.110  -0.971  -0.843  -0.801  -1.103  -1.027  -0.936
14    F        -0.861  -0.825  -0.719  -0.780  -0.721  -0.579  -0.949  -0.902  -0.757
15    W        -0.022   0.083  -0.055  -0.262  -0.131  -0.257  -0.182  -0.035  -0.231
16    P         0.951   0.790   0.756   1.251   1.030   0.966   0.996   0.728   0.624
17    T        -1.569  -1.583  -1.481  -1.556  -1.636  -1.457  -1.243  -1.241  -1.096
18    L         0.606   0.535   0.582   0.221   0.073   0.136   0.407   0.259   0.282
19    K        -1.125  -1.139  -1.095  -1.133  -1.130  -1.075  -1.007  -1.013  -0.922
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    D        -0.022  -0.133  -0.098   0.024  -0.142  -0.141  -0.182  -0.321  -0.294
23    A        -0.803  -0.786  -0.709  -1.140  -1.110  -0.983  -0.889  -0.869  -0.747
24    Y        -0.803  -0.865  -0.721  -0.896  -0.954  -0.764  -0.889  -0.935  -0.759
25    E        -0.682  -0.644  -0.646  -0.747  -0.677  -0.653  -0.771  -0.719  -0.681
26    P        -0.344  -0.420  -0.570  -0.053  -0.175  -0.493  -0.300  -0.403  -0.575
27    L         0.951   0.790   0.756   0.751   0.522   0.482   0.996   0.728   0.624
28    Y        -0.603  -0.483  -0.623  -0.453  -0.285  -0.459  -0.654  -0.505  -0.648
29    P        -1.569  -1.582  -1.456  -1.352  -1.376  -1.197  -1.243  -1.241  -1.077
30    Q        -0.803  -0.764  -0.710  -0.953  -0.882  -0.797  -0.889  -0.849  -0.750
31    Q         0.422   0.416   0.532   0.203   0.168   0.334   0.054   0.022   0.180
32    L        -0.281  -0.293  -0.191  -0.597  -0.588  -0.418  -0.536  -0.558  -0.428
33    E        -1.569  -1.578  -1.474  -1.563  -1.628  -1.428  -1.243  -1.238  -1.091
34    I        -0.022  -0.132  -0.099  -0.025  -0.171  -0.160  -0.182  -0.319  -0.299
35    L         0.951   0.790   0.756   0.751   0.522   0.482   0.996   0.728   0.624
36    R        -0.159  -0.127  -0.135  -0.311  -0.283  -0.265  -0.418  -0.387  -0.362
37    Q        -0.803  -0.794  -0.704  -0.896  -0.892  -0.768  -0.889  -0.876  -0.742
38    Q         1.651   1.697   1.802   1.723   1.787   1.961   1.821   1.898   2.073
39    V        -0.159  -0.148  -0.131  -0.349  -0.340  -0.333  -0.418  -0.408  -0.357
40    V        -1.247  -1.274  -1.130  -1.311  -1.314  -1.149  -1.125  -1.133  -0.954
41    S        -0.803  -0.790  -0.709  -0.880  -0.880  -0.751  -0.889  -0.871  -0.749
42    E         1.651   1.697   1.802   1.617   1.683   1.856   1.821   1.898   2.073
43    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    G         0.284   0.137   0.004   0.416   0.222  -0.015   0.289   0.072  -0.135
45    P        -0.803  -0.728  -0.683  -0.749  -0.614  -0.566  -0.889  -0.797  -0.718
46    T        -1.891  -1.878  -1.755  -1.576  -1.623  -1.394  -1.361  -1.340  -1.181
47    A        -1.247  -1.274  -1.141  -1.221  -1.246  -1.059  -1.125  -1.133  -0.963
48    T        -0.603  -0.592  -0.628  -0.537  -0.531  -0.590  -0.654  -0.653  -0.659
49    I        -1.125  -1.165  -1.089  -1.150  -1.258  -1.121  -1.007  -1.033  -0.916
50    Q         1.651   1.697   1.802   1.723   1.787   1.961   1.821   1.898   2.073
51    S         0.363   0.404   0.527   0.198   0.266   0.455  -0.064  -0.003   0.169
52    R        -0.159  -0.122  -0.128  -0.310  -0.275  -0.253  -0.418  -0.382  -0.354
53    F         1.651   1.697   1.802   1.936   1.999   2.174   1.821   1.898   2.073
54    N         1.651   1.697   1.802   1.830   1.897   2.068   1.821   1.898   2.073
55    Y         0.951   0.790   0.756   1.039   0.792   0.702   0.996   0.728   0.624
56    A         1.651   1.697   1.802   1.608   1.669   1.847   1.821   1.898   2.073
57    W         1.651   1.697   1.802   1.986   2.052   2.223   1.821   1.898   2.073
58    G         0.951   0.790   0.756   1.031   0.816   0.736   0.996   0.728   0.624
59    L         1.651   1.697   1.802   1.380   1.429   1.620   1.821   1.898   2.073
60    I         0.422   0.415   0.529   0.215   0.186   0.352   0.054   0.021   0.174
61    K         0.606   0.543   0.572   0.513   0.393   0.405   0.407   0.273   0.261
62    S         1.651   1.697   1.802   1.714   1.768   1.952   1.821   1.898   2.073
63    T        -1.569  -1.567  -1.462  -1.315  -1.293  -1.172  -1.243  -1.230  -1.082
64    D        -1.569  -1.506  -1.445  -1.291  -1.202  -1.107  -1.243  -1.178  -1.069
65    V        -1.447  -1.485  -1.444  -1.173  -1.211  -1.164  -1.125  -1.153  -1.066
66    N        -1.569  -1.567  -1.467  -1.525  -1.510  -1.356  -1.243  -1.231  -1.086
67    D        -0.344  -0.442  -0.587   0.044  -0.079  -0.279  -0.300  -0.429  -0.596
68    E         0.284   0.193   0.015   0.463   0.330   0.043   0.289   0.146  -0.118
69    R        -1.125  -1.054  -1.070  -0.944  -0.820  -0.824  -1.007  -0.918  -0.895
70    L        -0.022  -0.067  -0.115  -0.316  -0.403  -0.438  -0.182  -0.266  -0.327
71    G         1.651   1.697   1.802   1.670   1.745   1.909   1.821   1.898   2.073
72    V         0.284   0.173   0.010   0.395   0.197  -0.073   0.289   0.119  -0.126
73    K        -0.803  -0.796  -0.715  -0.867  -0.855  -0.704  -0.889  -0.878  -0.755
74    I         0.422   0.415   0.529   0.051  -0.012   0.142   0.054   0.021   0.174
75    L         0.951   0.790   0.756   0.789   0.582   0.570   0.996   0.728   0.624
76    T        -0.603  -0.672  -0.648  -0.424  -0.490  -0.493  -0.654  -0.724  -0.678
77    D        -0.682  -0.742  -0.679  -0.711  -0.790  -0.689  -0.771  -0.822  -0.715
78    I        -0.022   0.056  -0.068  -0.148  -0.018  -0.254  -0.182  -0.069  -0.249
79    Y         0.951   1.002   0.789   1.117   1.190   0.932   0.996   1.079   0.685
80    K         0.606   0.673   0.621   0.513   0.617   0.500   0.407   0.518   0.361
81    E        -0.682  -0.645  -0.653  -0.689  -0.612  -0.600  -0.771  -0.721  -0.687
82    A        -0.925  -0.801  -1.005  -0.733  -0.545  -0.890  -0.771  -0.622  -0.827
83    E        -0.344  -0.224  -0.529   0.000   0.180  -0.323  -0.300  -0.140  -0.525
84    S        -0.603  -0.589  -0.645  -0.545  -0.568  -0.606  -0.654  -0.656  -0.677
85    R         0.606   0.666   0.643   0.639   0.730   0.689   0.407   0.506   0.405
86    R         1.651   1.697   1.802   1.705   1.767   1.944   1.821   1.898   2.073
87    R         0.951   0.790   0.756   1.034   0.785   0.697   0.996   0.728   0.624
88    E         1.651   1.697   1.802   1.617   1.683   1.856   1.821   1.898   2.073
89    C         0.951   0.992   0.787   1.345   1.406   1.108   0.996   1.062   0.682
90    L         1.651   1.697   1.802   1.380   1.429   1.620   1.821   1.898   2.073
91    Y         1.651   1.697   1.802   1.709   1.774   1.948   1.821   1.898   2.073
92    Y         1.651   1.697   1.802   1.709   1.774   1.948   1.821   1.898   2.073
93    L         0.951   0.790   0.756   0.751   0.522   0.482   0.996   0.728   0.624
94    T        -0.159  -0.105  -0.113  -0.285  -0.201  -0.193  -0.418  -0.332  -0.326
95    I        -0.159  -0.075  -0.117  -0.558  -0.448  -0.465  -0.418  -0.299  -0.336
96    G         0.951   0.790   0.756   1.046   0.839   0.771   0.996   0.728   0.624
97    C        -0.682  -0.754  -0.679  -0.435  -0.503  -0.383  -0.771  -0.832  -0.716
98    Y         0.951   0.992   0.787   1.039   1.098   0.761   0.996   1.062   0.682
99    K         1.651   1.697   1.802   1.643   1.707   1.882   1.821   1.898   2.073
100   L         0.606   0.666   0.643   0.250   0.331   0.289   0.407   0.506   0.405
101   G         0.606   0.549   0.572   0.518   0.415   0.395   0.407   0.284   0.261
102   E        -0.603  -0.690  -0.656  -0.569  -0.681  -0.620  -0.654  -0.743  -0.684
103   Y         1.651   1.697   1.802   1.709   1.774   1.948   1.821   1.898   2.073
104   S        -0.603  -0.693  -0.651  -0.548  -0.694  -0.646  -0.654  -0.747  -0.681
105   M        -1.569  -1.583  -1.481  -1.218  -1.253  -1.108  -1.243  -1.241  -1.096
106   A         0.951   0.790   0.756   0.984   0.763   0.711   0.996   0.728   0.624
107   K        -0.159  -0.121  -0.129  -0.303  -0.258  -0.225  -0.418  -0.380  -0.355
108   R         0.606   0.668   0.630   0.552   0.649   0.546   0.407   0.509   0.379
109   Y         1.651   1.697   1.802   1.709   1.774   1.948   1.821   1.898   2.073
110   V        -0.925  -0.978  -1.045  -0.735  -0.871  -0.947  -0.771  -0.830  -0.867
111   D         0.284   0.137   0.004   0.559   0.361   0.138   0.289   0.072  -0.135
112   T        -0.682  -0.742  -0.658  -0.736  -0.787  -0.699  -0.771  -0.821  -0.694
113   L         1.651   1.697   1.802   1.380   1.429   1.620   1.821   1.898   2.073
114   F        -0.344  -0.200  -0.545  -0.360  -0.185  -0.574  -0.300  -0.109  -0.544
115   E        -0.925  -0.966  -1.037  -0.747  -0.813  -0.903  -0.771  -0.817  -0.859
116   H        -1.247  -1.269  -1.128  -1.079  -1.116  -0.924  -1.125  -1.130  -0.953
117   E         0.951   0.790   0.756   1.005   0.798   0.748   0.996   0.728   0.624
118   R         0.951   1.055   0.796   1.251   1.389   1.033   0.996   1.161   0.698
119   N        -0.682  -0.631  -0.655  -0.693  -0.601  -0.633  -0.771  -0.710  -0.691
120   N         0.284   0.165   0.003   0.603   0.431   0.187   0.289   0.109  -0.137
121   K        -0.603  -0.626  -0.649  -0.608  -0.638  -0.697  -0.654  -0.691  -0.681
122   Q         0.951   0.790   0.756   1.085   0.861   0.790   0.996   0.728   0.624
123   V        -0.022   0.090  -0.047  -0.107   0.068  -0.142  -0.182  -0.012  -0.217
124   G        -1.569  -1.490  -1.451  -1.784  -1.689  -1.602  -1.243  -1.167  -1.074
125   A        -1.569  -1.513  -1.459  -1.445  -1.350  -1.246  -1.243  -1.183  -1.079
126   L         1.651   1.697   1.802   1.380   1.429   1.620   1.821   1.898   2.073
127   K        -0.603  -0.540  -0.618  -0.690  -0.586  -0.747  -0.654  -0.568  -0.641
128   S        -1.891  -1.870  -1.772  -1.729  -1.659  -1.553  -1.361  -1.334  -1.192
129   M        -1.891  -1.892  -1.774  -1.669  -1.678  -1.565  -1.361  -1.349  -1.194
130   V        -0.159  -0.246  -0.140  -0.360  -0.501  -0.361  -0.418  -0.502  -0.364
131   E        -0.603  -0.679  -0.656  -0.539  -0.645  -0.573  -0.654  -0.736  -0.688
132   D         0.284   0.383   0.048   0.559   0.699   0.211   0.289   0.435  -0.070
133   K         0.951   0.790   0.756   1.004   0.778   0.711   0.996   0.728   0.624
134   I        -0.159  -0.127  -0.126  -0.360  -0.319  -0.335  -0.418  -0.386  -0.351
135   Q        -0.022   0.090  -0.047   0.079   0.265   0.021  -0.182  -0.012  -0.217
136   K        -0.603  -0.510  -0.618  -0.564  -0.423  -0.578  -0.654  -0.534  -0.645
137   E         0.951   1.020   0.785   0.994   1.092   0.771   0.996   1.106   0.678
138   T         0.606   0.706   0.660   0.574   0.739   0.643   0.407   0.578   0.438
139   L        -0.344  -0.415  -0.576  -0.423  -0.541  -0.724  -0.300  -0.397  -0.582
140   K        -0.159  -0.097  -0.116  -0.281  -0.165  -0.160  -0.418  -0.323  -0.329
141   G         1.651   1.697   1.802   1.670   1.745   1.909   1.821   1.898   2.073
142   V        -0.603  -0.657  -0.643  -0.606  -0.644  -0.690  -0.654  -0.705  -0.672
143   V        -0.281  -0.290  -0.188  -0.522  -0.538  -0.399  -0.536  -0.552  -0.424
144   V        -0.603  -0.578  -0.649  -0.606  -0.589  -0.705  -0.654  -0.638  -0.683
145   A        -0.360  -0.321  -0.205  -0.646  -0.574  -0.408  -0.654  -0.599  -0.448
146   G        -0.603  -0.668  -0.646  -0.589  -0.689  -0.658  -0.654  -0.722  -0.676
147   G         0.951   1.020   0.785   1.031   1.139   0.787   0.996   1.106   0.678
148   V        -0.125  -0.042  -0.101  -0.245  -0.107  -0.219  -0.334  -0.209  -0.303
149   L        -0.360  -0.365  -0.219  -0.804  -0.805  -0.580  -0.654  -0.658  -0.468
150   A         0.606   0.549   0.572   0.474   0.362   0.367   0.407   0.284   0.261
151   G        -0.603  -0.655  -0.652  -0.593  -0.653  -0.673  -0.654  -0.700  -0.678
152   A        -0.603  -0.657  -0.643  -0.647  -0.706  -0.726  -0.654  -0.705  -0.672
153   V        -0.022   0.062  -0.072  -0.171  -0.032  -0.299  -0.182  -0.049  -0.261
154   A        -0.682  -0.615  -0.646  -0.788  -0.689  -0.700  -0.771  -0.695  -0.681
155   V        -0.803  -0.779  -0.705  -1.042  -1.058  -0.910  -0.889  -0.861  -0.745
156   A        -0.803  -0.845  -0.698  -1.122  -1.155  -0.972  -0.889  -0.912  -0.734
157   S         0.951   1.055   0.796   1.046   1.195   0.836   0.996   1.161   0.698
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   F        -1.447  -1.450  -1.440  -1.375  -1.388  -1.386  -1.125  -1.123  -1.061
163   F        -0.344  -0.197  -0.529  -0.418  -0.230  -0.651  -0.300  -0.105  -0.525
164   L        -0.925  -0.986  -1.037  -0.931  -0.996  -1.029  -0.771  -0.838  -0.859
165   R         0.606   0.544   0.577   0.575   0.452   0.473   0.407   0.276   0.271
166   N        -0.820  -0.741  -0.698  -0.858  -0.741  -0.683  -0.902  -0.811  -0.734
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   K        -0.159  -0.105  -0.112  -0.287  -0.184  -0.184  -0.418  -0.331  -0.330
170   R         0.422   0.480   0.555   0.201   0.301   0.390   0.054   0.150   0.228
171   R        -0.022  -0.132  -0.103  -0.001  -0.134  -0.134  -0.182  -0.319  -0.308
* 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/P40515
Output conservation file - output/P40515
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
