1     M         1.918   1.987   2.058   2.150   2.242   2.358   2.105   2.203   2.320
2     L         0.622   0.600   0.675   0.323   0.246   0.371   0.289   0.211   0.304
3     S        -1.237  -1.264  -1.145  -1.225  -1.136  -0.981  -1.063  -1.047  -0.911
4     A        -0.682  -0.561  -0.618  -0.928  -0.777  -0.866  -0.729  -0.596  -0.622
5     A        -1.237  -1.234  -1.128  -1.442  -1.431  -1.288  -1.063  -1.024  -0.895
6     D         0.297   0.073   0.053   0.778   0.491   0.462   0.271  -0.053  -0.101
7     N        -1.237  -1.093  -1.115  -1.110  -0.907  -0.935  -1.063  -0.912  -0.886
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    L        -0.431  -0.425  -0.554  -0.422  -0.434  -0.649  -0.396  -0.388  -0.535
14    V         0.297   0.223   0.092   0.254   0.127  -0.064   0.271   0.156  -0.044
15    R         1.918   1.987   2.058   2.050   2.144   2.260   2.105   2.203   2.320
16    I        -1.640  -1.551  -1.502  -1.755  -1.591  -1.592  -1.229  -1.130  -1.042
17    I        -1.237  -1.087  -1.103  -1.384  -1.183  -1.184  -1.063  -0.900  -0.876
18    N        -0.027  -0.056  -0.063   0.140   0.078   0.069  -0.229  -0.293  -0.285
19    A        -0.027  -0.042  -0.061  -0.334  -0.409  -0.457  -0.229  -0.277  -0.283
20    V        -0.431  -0.606  -0.604  -0.346  -0.683  -0.644  -0.396  -0.602  -0.594
21    F         0.297   0.312   0.115   0.261   0.279  -0.029   0.271   0.273  -0.010
22    L         0.297   0.205   0.084   0.280   0.164  -0.032   0.271   0.132  -0.055
23    I        -0.682  -0.636  -0.619  -0.867  -0.776  -0.784  -0.729  -0.640  -0.615
24    I         1.918   1.987   2.058   1.788   1.887   2.002   2.105   2.203   2.320
25    S        -1.237  -1.195  -1.120  -1.578  -1.471  -1.365  -1.063  -0.986  -0.888
26    I        -0.431  -0.471  -0.562  -0.342  -0.412  -0.510  -0.396  -0.438  -0.544
27    G         1.083   0.973   0.926   1.089   0.919   0.827   1.104   0.904   0.790
28    L         1.918   1.987   2.058   1.739   1.831   1.955   2.105   2.203   2.320
29    I        -0.834  -0.702  -0.678  -1.162  -1.022  -0.951  -0.896  -0.738  -0.685
30    S        -0.027   0.072  -0.023  -0.189  -0.060  -0.235  -0.229  -0.128  -0.230
31    G        -0.682  -0.716  -0.656  -0.742  -0.795  -0.713  -0.729  -0.748  -0.661
32    L         1.083   0.991   0.929   0.999   0.867   0.788   1.104   0.936   0.795
33    I        -0.126  -0.151  -0.062  -0.593  -0.586  -0.448  -0.396  -0.395  -0.282
34    G        -0.431  -0.484  -0.561  -0.567  -0.612  -0.734  -0.396  -0.455  -0.543
35    T        -0.431  -0.520  -0.566  -0.206  -0.353  -0.433  -0.396  -0.510  -0.549
36    Q        -0.682  -0.625  -0.608  -0.320  -0.193  -0.158  -0.729  -0.627  -0.601
37    -        -0.794  -0.690  -0.662  -0.754  -0.619  -0.557  -0.836  -0.707  -0.661
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    T        -0.027   0.032  -0.036   0.034   0.070   0.029  -0.229  -0.176  -0.246
42    K        -1.237  -1.256  -1.135  -0.730  -0.792  -0.585  -1.063  -1.041  -0.901
43    H        -0.682  -0.662  -0.614  -0.563  -0.552  -0.458  -0.729  -0.673  -0.613
44    S        -0.682  -0.778  -0.667  -0.466  -0.547  -0.414  -0.729  -0.802  -0.671
45    S        -0.682  -0.778  -0.667  -0.574  -0.764  -0.633  -0.729  -0.802  -0.671
46    R        -0.682  -0.778  -0.667  -0.426  -0.594  -0.431  -0.729  -0.802  -0.671
47    V         0.528   0.611   0.680   0.161   0.279   0.390   0.104   0.232   0.313
48    N         1.083   1.150   0.953   1.293   1.401   1.108   1.104   1.199   0.840
49    F         1.083   1.150   0.953   1.075   1.186   0.948   1.104   1.199   0.840
50    C        -1.085  -1.120  -1.088  -1.134  -1.170  -1.088  -0.896  -0.918  -0.856
51    M        -0.027   0.044  -0.039  -0.017   0.062  -0.017  -0.229  -0.155  -0.249
52    F         1.083   0.973   0.926   0.973   0.821   0.714   1.104   0.904   0.790
53    A        -0.027  -0.056  -0.063  -0.331  -0.383  -0.314  -0.229  -0.293  -0.285
54    A        -0.027  -0.133  -0.064  -0.407  -0.559  -0.443  -0.229  -0.371  -0.286
55    V        -0.027  -0.059  -0.028  -0.423  -0.448  -0.414  -0.229  -0.251  -0.228
56    Y        -0.431  -0.471  -0.562  -0.265  -0.333  -0.405  -0.396  -0.438  -0.544
57    G        -0.278  -0.253  -0.146  -0.679  -0.658  -0.522  -0.563  -0.524  -0.390
58    L        -0.682  -0.662  -0.614  -0.837  -0.757  -0.722  -0.729  -0.673  -0.613
59    V         0.528   0.582   0.669   0.120   0.175   0.332   0.104   0.174   0.291
60    T        -0.027  -0.054  -0.030  -0.089  -0.121  -0.123  -0.229  -0.245  -0.234
61    D        -0.789  -0.797  -0.696  -0.787  -0.797  -0.658  -0.845  -0.824  -0.701
62    S        -0.431  -0.606  -0.604  -0.456  -0.757  -0.816  -0.396  -0.602  -0.594
63    L         0.528   0.663   0.718   0.074   0.303   0.380   0.104   0.334   0.390
64    Y         0.297   0.073   0.053   0.689   0.352   0.288   0.271  -0.053  -0.101
65    G        -0.027  -0.006  -0.036  -0.164  -0.173  -0.200  -0.229  -0.209  -0.247
66    F        -0.682  -0.550  -0.614  -0.870  -0.711  -0.787  -0.729  -0.578  -0.617
67    L        -1.085  -1.051  -1.067  -1.142  -1.132  -1.149  -0.896  -0.857  -0.835
68    A         1.083   0.973   0.926   0.854   0.735   0.683   1.104   0.904   0.790
69    N        -0.682  -0.729  -0.631  -0.516  -0.646  -0.503  -0.729  -0.743  -0.628
70    F         0.297   0.073   0.053   0.261  -0.076  -0.136   0.271  -0.053  -0.101
71    W        -1.085  -1.084  -1.082  -0.864  -0.869  -0.832  -0.896  -0.888  -0.851
72    T        -1.237  -1.168  -1.116  -1.175  -0.969  -0.902  -1.063  -0.962  -0.884
73    S        -0.027  -0.136  -0.063  -0.439  -0.580  -0.485  -0.229  -0.372  -0.283
74    L        -0.682  -0.625  -0.608  -0.919  -0.817  -0.796  -0.729  -0.627  -0.601
75    T         0.297   0.223   0.092   0.116   0.018  -0.156   0.271   0.156  -0.044
76    Y        -1.085  -1.184  -1.119  -0.557  -0.761  -0.672  -0.896  -0.974  -0.886
77    P         1.918   1.987   2.058   2.154   2.253   2.363   2.105   2.203   2.320
78    A        -1.085  -1.084  -1.082  -1.059  -1.066  -1.086  -0.896  -0.888  -0.851
79    I        -0.126  -0.153  -0.051  -0.406  -0.454  -0.280  -0.396  -0.399  -0.270
80    L        -0.027  -0.133  -0.064  -0.185  -0.343  -0.213  -0.229  -0.371  -0.286
81    L        -0.682  -0.467  -0.600  -1.053  -0.766  -0.945  -0.729  -0.494  -0.602
82    V        -1.237  -1.134  -1.113  -1.476  -1.309  -1.317  -1.063  -0.940  -0.884
83    L        -0.682  -0.718  -0.638  -0.818  -0.837  -0.727  -0.729  -0.746  -0.643
84    D         1.918   1.987   2.058   2.141   2.246   2.349   2.105   2.203   2.320
85    F         0.297   0.329   0.122   0.225   0.254  -0.078   0.271   0.299   0.001
86    L        -0.431  -0.606  -0.604  -0.524  -0.863  -0.870  -0.396  -0.602  -0.594
87    N         0.297   0.221   0.092   0.511   0.388   0.142   0.271   0.157  -0.044
88    F        -0.682  -0.581  -0.610  -0.492  -0.302  -0.403  -0.729  -0.591  -0.609
89    I        -0.027  -0.028  -0.016  -0.199  -0.208  -0.205  -0.229  -0.205  -0.213
90    F         1.083   1.150   0.953   1.003   1.113   0.818   1.104   1.199   0.840
91    T         1.083   0.973   0.926   1.156   0.989   0.891   1.104   0.904   0.790
92    F        -0.027  -0.133  -0.064  -0.269  -0.458  -0.355  -0.229  -0.371  -0.286
93    V        -0.682  -0.689  -0.655  -0.999  -0.978  -0.909  -0.729  -0.725  -0.660
94    A         0.700   0.678   0.710   0.270   0.226   0.274   0.438   0.363   0.375
95    A         0.528   0.576   0.671  -0.006   0.101   0.255   0.104   0.162   0.295
96    T        -0.431  -0.606  -0.604  -0.234  -0.499  -0.543  -0.396  -0.602  -0.594
97    A         0.297   0.073   0.053   0.157  -0.124  -0.136   0.271  -0.053  -0.101
98    L         0.528   0.608   0.687   0.092   0.204   0.337   0.104   0.226   0.328
99    A         1.918   1.987   2.058   1.556   1.667   1.775   2.105   2.203   2.320
100   V        -0.126  -0.060  -0.050  -0.529  -0.423  -0.367  -0.396  -0.299  -0.271
101   G        -0.027  -0.133  -0.064  -0.168  -0.358  -0.257  -0.229  -0.371  -0.286
102   I         1.083   0.991   0.929   1.032   0.903   0.806   1.104   0.936   0.795
103   R         1.083   0.991   0.929   1.317   1.190   1.099   1.104   0.936   0.795
104   C        -1.085  -1.051  -1.067  -0.744  -0.730  -0.798  -0.896  -0.857  -0.835
105   H         0.297   0.289   0.105   0.798   0.795   0.526   0.271   0.248  -0.024
106   S         0.297   0.073   0.053   0.330   0.025  -0.057   0.271  -0.053  -0.101
107   C         1.918   1.987   2.058   2.168   2.266   2.376   2.105   2.203   2.320
108   K        -1.237  -1.165  -1.122  -1.029  -0.874  -0.807  -1.063  -0.960  -0.890
109   N         1.918   1.987   2.058   2.036   2.143   2.247   2.105   2.203   2.320
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   K        -1.237  -1.193  -1.112  -0.659  -0.611  -0.468  -1.063  -0.990  -0.884
113   T        -1.085  -1.064  -1.084  -0.564  -0.518  -0.588  -0.896  -0.857  -0.852
114   Y         0.297   0.289   0.105   0.739   0.747   0.465   0.271   0.248  -0.024
115   L        -0.682  -0.635  -0.611  -0.732  -0.652  -0.588  -0.729  -0.653  -0.611
116   E        -1.085  -1.055  -1.088  -0.552  -0.521  -0.578  -0.896  -0.846  -0.856
117   Q        -1.640  -1.630  -1.532  -1.048  -1.018  -0.913  -1.229  -1.184  -1.065
118   N         1.083   0.991   0.929   1.347   1.250   1.169   1.104   0.936   0.795
119   K        -0.682  -0.729  -0.631  -0.216  -0.225  -0.091  -0.729  -0.743  -0.628
120   I         0.297   0.205   0.084   0.385   0.275   0.112   0.271   0.132  -0.055
121   I        -0.126  -0.048  -0.045  -0.482  -0.354  -0.340  -0.396  -0.289  -0.265
122   Q         0.297   0.289   0.105   0.760   0.748   0.544   0.271   0.248  -0.024
123   G         1.918   1.987   2.058   1.873   1.971   2.087   2.105   2.203   2.320
124   S         1.918   1.987   2.058   1.812   1.946   2.026   2.105   2.203   2.320
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   S        -0.682  -0.781  -0.658  -0.600  -0.720  -0.542  -0.729  -0.806  -0.663
129   S        -1.085  -1.145  -1.115  -0.732  -0.796  -0.734  -0.896  -0.939  -0.882
130   R         1.918   1.987   2.058   2.050   2.144   2.260   2.105   2.203   2.320
131   C         1.918   1.987   2.058   2.168   2.266   2.376   2.105   2.203   2.320
132   H         0.297   0.223   0.092   0.701   0.601   0.457   0.271   0.156  -0.044
133   Q        -0.027  -0.042  -0.061   0.362   0.327   0.335  -0.229  -0.277  -0.283
134   S        -0.431  -0.592  -0.600  -0.673  -0.937  -0.964  -0.396  -0.586  -0.590
135   Q         1.083   0.973   0.926   1.401   1.271   1.216   1.104   0.904   0.790
136   A         1.918   1.987   2.058   1.556   1.667   1.775   2.105   2.203   2.320
137   A        -1.085  -1.184  -1.119  -1.115  -1.295  -1.243  -0.896  -0.974  -0.886
138   V        -0.126  -0.163  -0.051  -0.186  -0.205  -0.029  -0.396  -0.415  -0.273
139   A        -0.027  -0.124  -0.054  -0.437  -0.583  -0.472  -0.229  -0.352  -0.270
140   F         1.918   1.987   2.058   1.759   1.874   1.974   2.105   2.203   2.320
141   F         0.297   0.239   0.088   0.322   0.253   0.047   0.271   0.181  -0.049
142   Y        -0.027  -0.056  -0.063   0.289   0.232   0.216  -0.229  -0.293  -0.285
143   F         0.297   0.329   0.122   0.261   0.299  -0.016   0.271   0.299   0.001
144   S        -0.431  -0.606  -0.604  -0.377  -0.615  -0.680  -0.396  -0.602  -0.594
145   C        -1.085  -0.987  -1.047  -0.913  -0.809  -0.839  -0.896  -0.783  -0.815
146   F        -0.027  -0.124  -0.054  -0.345  -0.506  -0.435  -0.229  -0.352  -0.270
147   L        -0.682  -0.722  -0.652  -0.963  -1.080  -0.968  -0.729  -0.752  -0.657
148   F         1.083   0.973   0.926   1.075   0.968   0.910   1.104   0.904   0.790
149   L        -0.682  -0.612  -0.627  -0.881  -0.809  -0.802  -0.729  -0.652  -0.631
150   I        -0.431  -0.189  -0.483  -0.662  -0.305  -0.755  -0.396  -0.084  -0.448
151   K        -0.682  -0.688  -0.646  -0.661  -0.681  -0.622  -0.729  -0.708  -0.649
152   V        -1.640  -1.491  -1.487  -1.655  -1.431  -1.436  -1.229  -1.075  -1.030
153   T        -0.027   0.078  -0.021  -0.146  -0.027  -0.137  -0.229  -0.116  -0.225
154   V        -0.278  -0.160  -0.098  -0.671  -0.498  -0.392  -0.563  -0.404  -0.326
155   A        -0.027  -0.136  -0.063  -0.239  -0.390  -0.322  -0.229  -0.372  -0.283
156   T        -0.682  -0.469  -0.588  -0.949  -0.591  -0.784  -0.729  -0.460  -0.584
157   M        -0.682  -0.689  -0.655  -0.651  -0.659  -0.588  -0.729  -0.725  -0.660
158   G        -0.431  -0.425  -0.554  -0.318  -0.309  -0.505  -0.396  -0.388  -0.535
159   M        -1.640  -1.491  -1.487  -1.604  -1.361  -1.359  -1.229  -1.075  -1.030
160   M        -1.640  -1.452  -1.489  -1.148  -0.856  -0.947  -1.229  -1.042  -1.031
161   Q        -1.237  -1.234  -1.128  -0.748  -0.751  -0.595  -1.063  -1.024  -0.895
162   N        -1.640  -1.630  -1.532  -1.375  -1.314  -1.209  -1.229  -1.184  -1.065
163   G         1.083   0.973   0.926   1.152   1.008   0.948   1.104   0.904   0.790
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   G        -0.789  -0.791  -0.685  -1.137  -1.112  -0.962  -0.845  -0.818  -0.689
168   F         1.918   1.987   2.058   1.731   1.838   1.947   2.105   2.203   2.320
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   G         1.918   1.987   2.058   1.873   1.971   2.087   2.105   2.203   2.320
173   S        -1.259  -1.041  -1.116  -0.950  -0.647  -0.754  -1.072  -0.829  -0.883
174   N         0.152   0.033  -0.013   0.163  -0.006  -0.078   0.063  -0.120  -0.197
175   T        -0.611  -0.703  -0.664  -0.471  -0.557  -0.500  -0.618  -0.717  -0.664
176   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   R         0.152   0.081   0.004   0.360   0.190   0.073   0.063  -0.054  -0.174
182   A        -1.259  -1.183  -1.137  -1.226  -1.164  -1.042  -1.072  -0.979  -0.902
183   R        -1.085  -0.978  -1.051  -1.083  -0.953  -0.987  -0.896  -0.770  -0.820
184   R        -1.085  -0.978  -1.051  -0.705  -0.561  -0.712  -0.896  -0.770  -0.820
185   Q         0.700   0.818   0.774   0.824   0.992   0.922   0.438   0.628   0.501
186   M        -0.789  -0.797  -0.683  -0.759  -0.785  -0.589  -0.845  -0.826  -0.688
187   G         1.918   1.987   2.058   1.882   1.981   2.095   2.105   2.203   2.320
188   I         0.548   0.576   0.666   0.244   0.250   0.395   0.144   0.162   0.286
189   P         1.918   1.987   2.058   2.154   2.253   2.363   2.105   2.203   2.320
190   T         0.297   0.312   0.115   0.466   0.471   0.180   0.271   0.273  -0.010
191   I         0.700   0.818   0.774   0.807   0.987   0.878   0.438   0.628   0.501
192   S         1.918   1.987   2.058   1.812   1.946   2.026   2.105   2.203   2.320
193   Q         1.083   0.973   0.926   1.309   1.139   1.039   1.104   0.904   0.790
194   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
195   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   V         1.918   1.987   2.058   1.831   1.919   2.045   2.105   2.203   2.320
* 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/P53279
Output conservation file - output/P53279
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
