1     M         1.936   1.955   1.994   2.215   2.247   2.306   2.145   2.172   2.233
2     S         1.936   1.955   1.994   2.027   2.067   2.117   2.145   2.172   2.233
3     R         1.936   1.955   1.994   2.083   2.124   2.173   2.145   2.172   2.233
4     L         0.676   0.722   0.623   0.062   0.139  -0.031   0.579   0.654   0.476
5     R         1.936   1.955   1.994   2.083   2.124   2.173   2.145   2.172   2.233
6     R         0.676   0.593   0.593   0.851   0.720   0.720   0.579   0.433   0.424
7     F        -0.393  -0.440  -0.426  -0.469  -0.563  -0.568  -0.466  -0.524  -0.499
8     N        -0.393  -0.440  -0.426  -0.181  -0.252  -0.225  -0.466  -0.524  -0.499
9     R        -0.393  -0.440  -0.426  -0.251  -0.331  -0.304  -0.466  -0.524  -0.499
10    K        -0.393  -0.440  -0.426  -0.248  -0.326  -0.291  -0.466  -0.524  -0.499
11    I        -0.393  -0.400  -0.410  -0.645  -0.711  -0.720  -0.466  -0.473  -0.478
12    L         1.936   1.955   1.994   1.360   1.397   1.442   2.145   2.172   2.233
13    S        -1.170  -1.157  -1.139  -0.872  -0.856  -0.816  -0.988  -0.967  -0.933
14    -        -0.525  -0.518  -0.489  -0.287  -0.283  -0.224  -0.640  -0.625  -0.581
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    L         0.510   0.500   0.491  -0.062  -0.077  -0.058   0.289   0.267   0.240
19    S        -0.525  -0.519  -0.489  -0.850  -0.871  -0.794  -0.640  -0.627  -0.581
20    S        -0.525  -0.519  -0.489  -0.420  -0.413  -0.358  -0.640  -0.627  -0.581
21    D         0.510   0.523   0.499   0.634   0.657   0.611   0.289   0.308   0.254
22    Y        -0.525  -0.519  -0.489  -0.408  -0.406  -0.346  -0.640  -0.627  -0.581
23    T         0.510   0.542   0.506   0.666   0.720   0.660   0.289   0.343   0.267
24    H        -0.525  -0.519  -0.489  -0.299  -0.294  -0.236  -0.640  -0.627  -0.581
25    D        -0.525  -0.519  -0.489  -0.850  -0.846  -0.794  -0.640  -0.627  -0.581
26    G         0.510   0.500   0.491   0.694   0.673   0.642   0.289   0.267   0.240
27    E        -1.170  -1.157  -1.139  -0.724  -0.703  -0.666  -0.988  -0.967  -0.933
28    S         0.676   0.593   0.593   0.790   0.661   0.658   0.579   0.433   0.424
29    D         1.936   1.955   1.994   2.090   2.124   2.181   2.145   2.172   2.233
30    Q        -0.393  -0.316  -0.393  -0.113  -0.012  -0.099  -0.466  -0.357  -0.456
31    E        -1.170  -1.157  -1.139  -0.897  -0.881  -0.841  -0.988  -0.967  -0.933
32    D         0.676   0.722   0.623   0.787   0.864   0.689   0.579   0.654   0.476
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    V        -0.393  -0.363  -0.401  -0.278  -0.228  -0.290  -0.466  -0.420  -0.467
35    S        -0.393  -0.423  -0.417  -0.162  -0.213  -0.180  -0.466  -0.503  -0.488
36    I        -0.525  -0.519  -0.489  -0.533  -0.520  -0.473  -0.640  -0.627  -0.581
37    L        -1.170  -1.157  -1.139  -1.177  -1.130  -1.124  -0.988  -0.967  -0.933
38    P         1.936   1.955   1.994   2.261   2.290   2.353   2.145   2.172   2.233
39    L        -0.393  -0.363  -0.401  -0.895  -0.853  -0.886  -0.466  -0.420  -0.467
40    D         1.936   1.955   1.994   2.090   2.124   2.181   2.145   2.172   2.233
41    T        -0.393  -0.423  -0.417  -0.201  -0.249  -0.249  -0.466  -0.503  -0.488
42    E        -1.170  -1.157  -1.139  -0.881  -0.849  -0.824  -0.988  -0.967  -0.933
43    E         1.936   1.955   1.994   2.145   2.185   2.236   2.145   2.172   2.233
44    Q         1.936   1.955   1.994   2.268   2.307   2.361   2.145   2.172   2.233
45    E        -0.393  -0.440  -0.426  -0.391  -0.533  -0.479  -0.466  -0.524  -0.499
46    E         0.676   0.693   0.612   0.903   0.932   0.801   0.579   0.605   0.458
47    L         1.936   1.955   1.994   1.360   1.397   1.442   2.145   2.172   2.233
48    I         0.676   0.593   0.593   0.423   0.258   0.216   0.579   0.433   0.424
49    Q        -1.170  -1.157  -1.139  -0.823  -0.826  -0.767  -0.988  -0.967  -0.933
50    K         0.676   0.593   0.593   0.777   0.640   0.639   0.579   0.433   0.424
51    F        -0.393  -0.440  -0.426  -0.423  -0.502  -0.514  -0.466  -0.524  -0.499
52    E         1.936   1.955   1.994   2.145   2.185   2.236   2.145   2.172   2.233
53    T        -1.170  -1.157  -1.139  -1.191  -1.174  -1.139  -0.988  -0.967  -0.933
54    N        -0.393  -0.440  -0.426  -0.224  -0.298  -0.274  -0.466  -0.524  -0.499
55    A        -1.170  -1.157  -1.139  -1.215  -1.174  -1.162  -0.988  -0.967  -0.933
56    H        -1.170  -1.157  -1.139  -1.163  -1.145  -1.110  -0.988  -0.967  -0.933
57    I        -1.170  -1.157  -1.139  -1.452  -1.406  -1.403  -0.988  -0.967  -0.933
58    T        -0.393  -0.400  -0.410  -0.254  -0.285  -0.275  -0.466  -0.473  -0.478
59    N         1.936   1.955   1.994   2.090   2.136   2.181   2.145   2.172   2.233
60    K        -1.170  -1.157  -1.139  -0.918  -0.896  -0.862  -0.988  -0.967  -0.933
61    L        -1.170  -1.157  -1.139  -1.082  -1.017  -1.028  -0.988  -0.967  -0.933
62    Y         0.676   0.593   0.593   0.918   0.788   0.788   0.579   0.433   0.424
63    I        -0.393  -0.440  -0.426  -0.715  -0.778  -0.806  -0.466  -0.524  -0.499
64    N        -0.393  -0.440  -0.426  -0.224  -0.296  -0.274  -0.466  -0.524  -0.499
65    L        -0.393  -0.336  -0.392  -0.593  -0.469  -0.621  -0.466  -0.385  -0.454
66    L        -0.393  -0.423  -0.417  -0.850  -0.873  -0.849  -0.466  -0.503  -0.488
67    S        -0.393  -0.440  -0.426  -0.224  -0.307  -0.263  -0.466  -0.524  -0.499
68    I        -1.170  -1.157  -1.139  -1.385  -1.333  -1.335  -0.988  -0.967  -0.933
69    L         0.676   0.722   0.623   0.147   0.208   0.075   0.579   0.654   0.476
70    Y         0.676   0.593   0.593   0.911   0.773   0.779   0.579   0.433   0.424
71    L        -0.393  -0.423  -0.417  -0.842  -0.836  -0.840  -0.466  -0.503  -0.488
72    L        -0.393  -0.363  -0.401  -0.979  -0.935  -0.979  -0.466  -0.420  -0.467
73    Y        -1.170  -1.157  -1.139  -0.756  -0.748  -0.698  -0.988  -0.967  -0.933
74    G        -1.170  -1.157  -1.139  -0.666  -0.664  -0.608  -0.988  -0.967  -0.933
75    G         0.676   0.593   0.593   1.038   0.913   0.918   0.579   0.433   0.424
76    L        -1.170  -1.157  -1.139  -1.370  -1.323  -1.320  -0.988  -0.967  -0.933
77    L        -0.393  -0.316  -0.393  -0.454  -0.292  -0.476  -0.466  -0.357  -0.456
78    M        -0.393  -0.316  -0.393  -0.649  -0.508  -0.664  -0.466  -0.357  -0.456
79    I        -1.170  -1.157  -1.139  -1.370  -1.343  -1.320  -0.988  -0.967  -0.933
80    L         1.936   1.955   1.994   1.360   1.397   1.442   2.145   2.172   2.233
81    V        -1.170  -1.157  -1.139  -1.205  -1.166  -1.153  -0.988  -0.967  -0.933
82    R        -0.393  -0.400  -0.410  -0.123  -0.141  -0.148  -0.466  -0.473  -0.478
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    K         0.676   0.693   0.612   0.815   0.840   0.720   0.579   0.605   0.458
90    S        -1.170  -1.157  -1.139  -0.811  -0.784  -0.754  -0.988  -0.967  -0.933
91    R        -0.393  -0.316  -0.393  -0.813  -0.729  -0.790  -0.466  -0.357  -0.456
92    G        -0.393  -0.423  -0.417  -0.117  -0.181  -0.160  -0.466  -0.503  -0.488
93    Y        -0.393  -0.363  -0.401  -0.053  -0.017  -0.052  -0.466  -0.420  -0.467
94    I        -1.170  -1.157  -1.139  -0.956  -0.915  -0.901  -0.988  -0.967  -0.933
95    K        -0.393  -0.336  -0.392  -0.301  -0.211  -0.296  -0.466  -0.385  -0.454
96    L        -0.393  -0.363  -0.401  -0.992  -0.947  -0.993  -0.466  -0.420  -0.467
97    A        -1.170  -1.157  -1.139  -0.864  -0.855  -0.808  -0.988  -0.967  -0.933
98    L         0.676   0.593   0.593   0.126   0.006   0.006   0.579   0.433   0.424
99    L         0.676   0.722   0.623   0.062   0.139  -0.031   0.579   0.654   0.476
100   A        -0.525  -0.519  -0.489  -0.801  -0.801  -0.744  -0.640  -0.627  -0.581
101   G         0.510   0.500   0.491   0.694   0.673   0.642   0.289   0.267   0.240
102   A         0.510   0.523   0.499   0.707   0.731   0.681   0.289   0.308   0.254
103   N         0.510   0.500   0.491   0.639   0.625   0.616   0.289   0.267   0.240
104   S         1.936   1.955   1.994   2.016   2.053   2.105   2.145   2.172   2.233
105   L         0.383   0.394   0.428  -0.344  -0.331  -0.288   0.056   0.074   0.123
106   I        -0.393  -0.440  -0.426  -0.433  -0.497  -0.478  -0.466  -0.524  -0.499
107   C         0.676   0.722   0.623   0.851   0.938   0.711   0.579   0.654   0.476
108   S         0.676   0.593   0.593   0.798   0.666   0.669   0.579   0.433   0.424
109   C        -1.170  -1.157  -1.139  -0.760  -0.758  -0.702  -0.988  -0.967  -0.933
110   I         0.676   0.722   0.623   0.423   0.523   0.284   0.579   0.654   0.476
111   T         0.676   0.722   0.623   0.948   1.012   0.864   0.579   0.654   0.476
112   L         1.936   1.955   1.994   1.301   1.328   1.382   2.145   2.172   2.233
113   R         1.936   1.955   1.994   2.078   2.116   2.168   2.145   2.172   2.233
114   Y         1.936   1.955   1.994   2.145   2.181   2.236   2.145   2.172   2.233
115   D        -1.170  -1.157  -1.139  -0.803  -0.805  -0.746  -0.988  -0.967  -0.933
116   I        -1.170  -1.157  -1.139  -1.421  -1.366  -1.371  -0.988  -0.967  -0.933
117   V        -0.393  -0.440  -0.426  -0.356  -0.441  -0.421  -0.466  -0.524  -0.499
118   N        -0.393  -0.440  -0.426  -0.146  -0.224  -0.183  -0.466  -0.524  -0.499
119   D         0.676   0.693   0.612   0.851   0.878   0.750   0.579   0.605   0.458
120   Y         0.676   0.593   0.593   0.903   0.768   0.769   0.579   0.433   0.424
121   L        -1.170  -1.157  -1.139  -1.330  -1.277  -1.279  -0.988  -0.967  -0.933
122   L        -0.393  -0.440  -0.426  -0.874  -0.926  -0.883  -0.466  -0.524  -0.499
123   F        -1.170  -1.157  -1.139  -1.191  -1.148  -1.139  -0.988  -0.967  -0.933
124   K         0.383   0.394   0.428   0.306   0.321   0.376   0.056   0.074   0.123
125   K        -0.393  -0.363  -0.401  -0.298  -0.252  -0.310  -0.466  -0.420  -0.467
126   F        -1.170  -1.157  -1.139  -1.168  -1.134  -1.115  -0.988  -0.967  -0.933
127   K        -0.393  -0.440  -0.426  -0.574  -0.718  -0.672  -0.466  -0.524  -0.499
128   L         0.676   0.693   0.612   0.156   0.182   0.072   0.579   0.605   0.458
129   R        -1.170  -1.157  -1.139  -0.827  -0.803  -0.771  -0.988  -0.967  -0.933
130   V        -0.393  -0.400  -0.410  -0.809  -0.804  -0.799  -0.466  -0.473  -0.478
131   S        -0.393  -0.423  -0.417  -0.224  -0.283  -0.251  -0.466  -0.503  -0.488
132   N         0.383   0.401   0.431   0.306   0.337   0.379   0.056   0.086   0.128
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   F        -1.170  -1.157  -1.139  -1.173  -1.227  -1.120  -0.988  -0.967  -0.933
135   S        -1.170  -1.157  -1.139  -0.889  -0.880  -0.833  -0.988  -0.967  -0.933
136   I        -0.393  -0.440  -0.426  -0.726  -0.796  -0.820  -0.466  -0.524  -0.499
137   N        -0.393  -0.423  -0.417  -0.523  -0.634  -0.603  -0.466  -0.503  -0.488
138   I         1.936   1.955   1.994   1.891   1.941   1.979   2.145   2.172   2.233
139   I         0.676   0.761   0.634   0.062   0.198  -0.013   0.579   0.719   0.496
140   N         0.676   0.593   0.593   0.841   0.713   0.704   0.579   0.433   0.424
141   I        -0.393  -0.440  -0.426  -0.291  -0.335  -0.315  -0.466  -0.524  -0.499
142   I        -1.170  -1.157  -1.139  -0.973  -0.955  -0.918  -0.988  -0.967  -0.933
143   L        -1.170  -1.157  -1.139  -1.091  -1.039  -1.037  -0.988  -0.967  -0.933
144   L         1.936   1.955   1.994   1.360   1.397   1.442   2.145   2.172   2.233
145   V        -0.393  -0.400  -0.410  -0.430  -0.439  -0.451  -0.466  -0.473  -0.478
146   L        -1.170  -1.157  -1.139  -1.077  -1.009  -1.024  -0.988  -0.967  -0.933
147   M        -1.170  -1.157  -1.139  -1.335  -1.322  -1.284  -0.988  -0.967  -0.933
148   A        -1.170  -1.157  -1.139  -0.815  -0.799  -0.758  -0.988  -0.967  -0.933
149   W         1.936   1.955   1.994   2.336   2.375   2.429   2.145   2.172   2.233
150   I         0.676   0.593   0.593   0.648   0.530   0.516   0.579   0.433   0.424
151   S        -1.170  -1.157  -1.139  -0.994  -0.955  -0.939  -0.988  -0.967  -0.933
152   F        -1.170  -1.157  -1.139  -1.365  -1.330  -1.315  -0.988  -0.967  -0.933
153   N         0.383   0.397   0.429   0.352   0.375   0.426   0.056   0.079   0.126
154   H        -1.170  -1.157  -1.139  -0.686  -0.684  -0.627  -0.988  -0.967  -0.933
155   V        -1.170  -1.157  -1.139  -1.205  -1.263  -1.153  -0.988  -0.967  -0.933
156   V        -1.170  -1.157  -1.139  -0.732  -0.695  -0.674  -0.988  -0.967  -0.933
157   E         0.510   0.542   0.506   0.540   0.593   0.532   0.289   0.343   0.267
158   D         0.510   0.500   0.491   0.666   0.652   0.636   0.289   0.267   0.240
159   K        -0.525  -0.519  -0.489  -0.287  -0.274  -0.224  -0.640  -0.627  -0.581
160   K         0.510   0.542   0.506  -0.152  -0.115  -0.149   0.289   0.343   0.267
161   T        -0.525  -0.519  -0.489  -1.004  -1.031  -0.950  -0.640  -0.627  -0.581
162   V         0.510   0.542   0.506  -0.152  -0.115  -0.149   0.289   0.343   0.267
163   L         0.510   0.523   0.499  -0.152  -0.141  -0.156   0.289   0.308   0.254
164   C         0.510   0.523   0.499   0.824   0.848   0.794   0.289   0.308   0.254
165   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   Q        -0.393  -0.400  -0.410   0.013  -0.022  -0.012  -0.466  -0.473  -0.478
167   V        -0.393  -0.316  -0.393  -0.726  -0.573  -0.748  -0.466  -0.357  -0.456
168   P         1.936   1.955   1.994   2.261   2.290   2.353   2.145   2.172   2.233
169   M        -1.170  -1.157  -1.139  -0.744  -0.749  -0.686  -0.988  -0.967  -0.933
170   F         0.383   0.394   0.428  -0.138  -0.103  -0.064   0.056   0.074   0.123
171   L         0.676   0.593   0.593   0.173   0.063   0.069   0.579   0.433   0.424
172   F         0.676   0.593   0.593   0.967   0.851   0.856   0.579   0.433   0.424
173   W        -1.170  -1.157  -1.139  -1.243  -1.208  -1.191  -0.988  -0.967  -0.933
174   V         0.676   0.593   0.593   0.851   0.722   0.728   0.579   0.433   0.424
175   A        -0.393  -0.423  -0.417  -0.088  -0.151  -0.110  -0.466  -0.503  -0.488
176   V        -1.170  -1.157  -1.139  -0.827  -0.814  -0.771  -0.988  -0.967  -0.933
177   L        -0.393  -0.440  -0.426  -0.979  -1.021  -1.003  -0.466  -0.524  -0.499
178   V         0.383   0.397   0.429   0.184   0.205   0.251   0.056   0.079   0.126
179   K         0.676   0.593   0.593   0.795   0.663   0.663   0.579   0.433   0.424
180   R        -0.393  -0.423  -0.417  -0.433  -0.456  -0.498  -0.466  -0.503  -0.488
181   W         0.383   0.394   0.428   0.027   0.065   0.104   0.056   0.074   0.123
182   A        -1.170  -1.157  -1.139  -1.335  -1.322  -1.284  -0.988  -0.967  -0.933
183   R        -0.393  -0.336  -0.392  -0.238  -0.152  -0.228  -0.466  -0.385  -0.454
184   N        -0.393  -0.336  -0.392  -0.201  -0.106  -0.198  -0.466  -0.385  -0.454
185   I        -0.393  -0.440  -0.426  -0.742  -0.812  -0.839  -0.466  -0.524  -0.499
186   E        -0.393  -0.400  -0.410  -0.224  -0.251  -0.249  -0.466  -0.473  -0.478
187   D        -0.393  -0.336  -0.392  -0.254  -0.169  -0.246  -0.466  -0.385  -0.454
188   E         0.383   0.397   0.429   0.391   0.408   0.464   0.056   0.079   0.126
189   I         0.676   0.761   0.634   0.062   0.198  -0.013   0.579   0.719   0.496
190   A        -1.170  -1.157  -1.139  -0.752  -0.727  -0.694  -0.988  -0.967  -0.933
191   D        -1.170  -1.157  -1.139  -0.848  -0.844  -0.791  -0.988  -0.967  -0.933
192   L         1.936   1.955   1.994   1.360   1.397   1.442   2.145   2.172   2.233
193   R         0.676   0.593   0.593   0.826   0.694   0.687   0.579   0.433   0.424
194   C        -1.170  -1.157  -1.139  -0.713  -0.709  -0.655  -0.988  -0.967  -0.933
195   L         0.676   0.593   0.593   0.185   0.077   0.085   0.579   0.433   0.424
196   K        -0.393  -0.440  -0.426  -0.152  -0.226  -0.181  -0.466  -0.524  -0.499
197   Y         1.936   1.955   1.994   2.145   2.181   2.236   2.145   2.172   2.233
198   K         0.676   0.722   0.623   0.798   0.868   0.715   0.579   0.654   0.476
199   Y        -0.393  -0.440  -0.426  -0.451  -0.599  -0.549  -0.466  -0.524  -0.499
200   K         1.936   1.955   1.994   2.035   2.069   2.125   2.145   2.172   2.233
201   N         0.676   0.593   0.593   0.896   0.782   0.777   0.579   0.433   0.424
202   A         0.676   0.693   0.612   0.863   0.876   0.759   0.579   0.605   0.458
* 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/P53209
Output conservation file - output/P53209
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
