1     M         2.174   2.191   2.275   2.756   2.786   2.934   2.519   2.546   2.693
2     T        -0.555  -0.532  -0.526  -0.607  -0.581  -0.559  -0.610  -0.578  -0.562
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    -        -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    D        -0.550  -0.529  -0.531  -0.565  -0.524  -0.536  -0.619  -0.594  -0.574
14    A        -1.023  -1.032  -0.997  -0.848  -0.848  -0.788  -0.861  -0.867  -0.808
15    L         2.174   2.191   2.275   1.915   1.928   2.076   2.519   2.546   2.693
16    E        -0.550  -0.583  -0.532  -0.728  -0.770  -0.687  -0.619  -0.651  -0.576
17    Q         0.102   0.127   0.106   0.129   0.171   0.125  -0.136  -0.100  -0.122
18    S         0.397   0.461   0.275   0.994   1.101   0.790   0.346   0.444   0.152
19    V         0.397   0.426   0.257   0.771   0.815   0.544   0.346   0.392   0.123
20    L        -0.371  -0.301  -0.406  -0.429  -0.286  -0.537  -0.378  -0.285  -0.412
21    A         0.870   0.909   0.921   0.793   0.851   0.868   0.588   0.660   0.643
22    L         2.174   2.191   2.275   1.915   1.928   2.076   2.519   2.546   2.693
23    E        -1.023  -1.040  -1.021  -1.040  -1.052  -1.028  -0.861  -0.875  -0.832
24    G        -0.371  -0.399  -0.431  -0.024  -0.083  -0.111  -0.378  -0.414  -0.444
25    T        -0.371  -0.309  -0.447  -0.176  -0.098  -0.267  -0.378  -0.295  -0.464
26    V         0.870   0.840   0.889   1.003   0.932   1.007   0.588   0.520   0.574
27    S        -1.497  -1.488  -1.439  -1.219  -1.176  -1.121  -1.102  -1.091  -1.018
28    V        -1.497  -1.488  -1.439  -1.495  -1.478  -1.402  -1.102  -1.091  -1.018
29    L         1.251   1.280   1.144   1.037   1.066   0.903   1.312   1.360   1.091
30    K        -1.497  -1.488  -1.439  -1.457  -1.450  -1.364  -1.102  -1.091  -1.018
31    D        -1.023  -1.044  -0.994  -0.938  -0.978  -0.893  -0.861  -0.879  -0.805
32    S         1.251   1.280   1.144   1.480   1.513   1.352   1.312   1.360   1.091
33    V        -0.550  -0.583  -0.532  -0.825  -0.881  -0.804  -0.619  -0.651  -0.576
34    E        -1.023  -1.023  -1.024  -1.173  -1.162  -1.178  -0.861  -0.859  -0.835
35    S        -1.023  -0.985  -0.997  -0.843  -0.776  -0.804  -0.861  -0.817  -0.808
36    L         0.397   0.443   0.279   0.053   0.105  -0.143   0.346   0.417   0.159
37    K        -0.550  -0.575  -0.547  -0.716  -0.748  -0.711  -0.619  -0.642  -0.592
38    C        -1.497  -1.488  -1.439  -1.277  -1.282  -1.181  -1.102  -1.091  -1.018
39    A        -0.550  -0.574  -0.516  -0.344  -0.369  -0.275  -0.619  -0.642  -0.559
40    N        -1.023  -1.031  -0.998  -0.936  -0.966  -0.908  -0.861  -0.866  -0.809
41    E        -1.023  -1.040  -1.021  -0.963  -0.946  -0.940  -0.861  -0.875  -0.832
42    P        -0.371  -0.309  -0.447  -0.107  -0.000  -0.214  -0.378  -0.295  -0.464
43    S         0.397   0.347   0.260   0.592   0.510   0.399   0.346   0.267   0.129
44    T         0.102   0.105   0.107   0.335   0.335   0.355  -0.136  -0.139  -0.126
45    N        -0.371  -0.309  -0.447  -0.296  -0.161  -0.463  -0.378  -0.295  -0.464
46    L         1.251   1.168   1.130   0.989   0.850   0.805   1.312   1.160   1.063
47    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    S        -1.023  -0.985  -0.997  -1.138  -1.072  -1.097  -0.861  -0.817  -0.808
49    T        -1.023  -1.023  -1.024  -0.794  -0.765  -0.746  -0.861  -0.859  -0.835
50    M         0.102   0.146   0.126   0.328   0.386   0.380  -0.136  -0.070  -0.093
51    L         2.174   2.191   2.275   1.915   1.928   2.076   2.519   2.546   2.693
52    Q        -0.077  -0.067   0.002  -0.365  -0.364  -0.249  -0.378  -0.363  -0.270
53    T         0.397   0.339   0.254   0.756   0.656   0.527   0.346   0.256   0.119
54    K         0.102   0.053   0.084  -0.027  -0.092  -0.042  -0.136  -0.198  -0.155
55    R         0.870   0.891   0.919   0.803   0.865   0.857   0.588   0.624   0.638
56    V         1.251   1.168   1.130   1.712   1.600   1.558   1.312   1.160   1.063
57    F         2.174   2.191   2.275   2.762   2.785   2.940   2.519   2.546   2.693
58    R        -1.497  -1.488  -1.439  -1.287  -1.255  -1.190  -1.102  -1.091  -1.018
59    L         2.174   2.191   2.275   1.915   1.928   2.076   2.519   2.546   2.693
60    V         0.870   0.840   0.889   1.003   0.932   1.007   0.588   0.520   0.574
61    P         0.870   0.847   0.880   1.090   1.021   1.044   0.588   0.533   0.556
62    E         2.174   2.191   2.275   2.326   2.361   2.496   2.519   2.546   2.693
63    Y         0.102   0.053   0.084   0.053  -0.039  -0.013  -0.136  -0.198  -0.155
64    D         1.251   1.168   1.130   1.494   1.371   1.284   1.312   1.160   1.063
65    V         0.754   0.767   0.839   0.305   0.292   0.419   0.346   0.365   0.469
66    E        -0.371  -0.419  -0.437  -0.363  -0.452  -0.479  -0.378  -0.439  -0.451
67    R        -0.550  -0.583  -0.531  -0.609  -0.645  -0.574  -0.619  -0.651  -0.574
68    S         0.397   0.364   0.262   0.681   0.625   0.437   0.346   0.292   0.131
69    K         0.102   0.055   0.105  -0.039  -0.088  -0.025  -0.136  -0.194  -0.127
70    L        -0.371  -0.413  -0.473  -0.768  -0.837  -0.916  -0.378  -0.431  -0.497
71    D        -0.550  -0.575  -0.547  -0.574  -0.617  -0.575  -0.619  -0.642  -0.592
72    L         0.102   0.106   0.084  -0.191  -0.179  -0.155  -0.136  -0.141  -0.159
73    I        -1.497  -1.488  -1.439  -1.092  -1.109  -0.991  -1.102  -1.091  -1.018
74    E         0.397   0.426   0.257   0.444   0.501   0.193   0.346   0.392   0.123
75    E        -0.371  -0.419  -0.437  -0.328  -0.400  -0.436  -0.378  -0.439  -0.451
76    V         0.754   0.765   0.838   0.756   0.765   0.894   0.346   0.362   0.467
77    E        -1.023  -1.040  -1.019  -1.071  -1.104  -1.061  -0.861  -0.875  -0.830
78    P         2.174   2.191   2.275   2.775   2.803   2.953   2.519   2.546   2.693
79    L        -0.550  -0.575  -0.547  -0.756  -0.793  -0.713  -0.619  -0.642  -0.592
80    V         0.102   0.146   0.128  -0.304  -0.265  -0.257  -0.136  -0.069  -0.089
81    R        -1.023  -1.023  -1.024  -0.998  -1.006  -1.024  -0.861  -0.859  -0.835
82    T        -0.550  -0.532  -0.524  -0.565  -0.551  -0.522  -0.619  -0.596  -0.567
83    L         0.397   0.322   0.253   0.114  -0.013  -0.098   0.346   0.230   0.118
84    G        -1.023  -1.040  -1.021  -0.672  -0.696  -0.683  -0.861  -0.875  -0.832
85    D        -1.023  -1.040  -1.021  -0.927  -0.956  -0.926  -0.861  -0.875  -0.832
86    K         1.251   1.168   1.130   1.355   1.241   1.164   1.312   1.160   1.063
87    L         0.870   0.901   0.903   0.387   0.416   0.435   0.588   0.643   0.604
88    R         1.251   1.311   1.151   1.390   1.491   1.236   1.312   1.414   1.105
89    K         0.870   0.840   0.889   0.697   0.646   0.702   0.588   0.520   0.574
90    S        -0.077  -0.068   0.001  -0.339  -0.335  -0.217  -0.378  -0.366  -0.271
91    M         0.397   0.364   0.262   0.169   0.096  -0.009   0.346   0.292   0.131
92    G        -0.550  -0.516  -0.516  -0.477  -0.454  -0.404  -0.619  -0.581  -0.559
93    R        -0.550  -0.583  -0.532  -0.691  -0.737  -0.667  -0.619  -0.651  -0.576
94    M         0.397   0.462   0.276   0.099   0.183  -0.085   0.346   0.446   0.153
95    Q        -0.371  -0.323  -0.411  -0.245  -0.152  -0.344  -0.378  -0.313  -0.419
96    R         1.251   1.261   1.149   1.568   1.604   1.418   1.312   1.327   1.100
97    E         0.102   0.053   0.084  -0.125  -0.187  -0.150  -0.136  -0.198  -0.155
98    L        -0.550  -0.575  -0.548  -1.158  -1.184  -1.150  -0.619  -0.643  -0.593
99    D        -0.550  -0.529  -0.531  -0.525  -0.490  -0.499  -0.619  -0.594  -0.574
100   T         0.102   0.058   0.107   0.146   0.062   0.140  -0.136  -0.190  -0.126
101   L         2.174   2.191   2.275   1.915   1.928   2.076   2.519   2.546   2.693
102   Q        -1.497  -1.488  -1.439  -1.416  -1.420  -1.322  -1.102  -1.091  -1.018
103   Q        -0.371  -0.413  -0.473  -0.150  -0.228  -0.343  -0.378  -0.431  -0.497
104   T         0.754   0.767   0.839   0.560   0.572   0.689   0.346   0.365   0.469
105   Y        -1.023  -0.994  -0.994  -0.792  -0.747  -0.765  -0.861  -0.827  -0.805
106   E         0.397   0.426   0.257   0.432   0.491   0.176   0.346   0.392   0.123
107   L         2.174   2.191   2.275   1.915   1.928   2.076   2.519   2.546   2.693
108   N         0.102   0.091   0.085   0.177   0.148   0.151  -0.136  -0.157  -0.159
109   D        -1.497  -1.488  -1.439  -1.577  -1.566  -1.486  -1.102  -1.091  -1.018
110   L         0.102   0.053   0.084  -0.300  -0.373  -0.296  -0.136  -0.198  -0.155
111   R         2.174   2.191   2.275   2.491   2.539   2.664   2.519   2.546   2.693
112   L         1.251   1.280   1.144   1.039   1.066   0.905   1.312   1.360   1.091
113   K        -1.023  -1.032  -0.991  -1.197  -1.197  -1.151  -0.861  -0.867  -0.802
114   K        -0.371  -0.385  -0.445  -0.077  -0.079  -0.188  -0.378  -0.397  -0.462
115   N        -1.497  -1.488  -1.439  -1.410  -1.456  -1.315  -1.102  -1.091  -1.018
116   I        -1.023  -1.019  -0.993  -1.308  -1.317  -1.280  -0.861  -0.854  -0.804
117   S         0.013   0.020   0.039  -0.143  -0.128  -0.065  -0.262  -0.251  -0.220
118   M        -1.123  -1.119  -1.061  -0.952  -0.960  -0.849  -0.957  -0.950  -0.870
119   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   D        -1.123  -1.119  -1.061  -0.980  -0.964  -0.877  -0.957  -0.950  -0.870
121   D        -1.123  -1.119  -1.061  -1.138  -1.122  -1.039  -0.957  -0.950  -0.870
122   D         0.227   0.207   0.170   0.292   0.258   0.168   0.086   0.053  -0.013
123   A        -1.123  -1.119  -1.061  -1.052  -1.047  -0.950  -0.957  -0.950  -0.870
124   L        -0.555  -0.568  -0.523  -1.024  -1.058  -0.961  -0.610  -0.623  -0.559
125   N        -0.666  -0.661  -0.598  -0.707  -0.685  -0.598  -0.740  -0.732  -0.647
126   S         0.044   0.045   0.045   0.152   0.155   0.105  -0.197  -0.196  -0.205
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   P         0.044   0.045   0.045   0.005   0.020   0.032  -0.197  -0.196  -0.205
129   D         0.044   0.059   0.049   0.065   0.097   0.068  -0.197  -0.175  -0.199
130   M         0.044   0.059   0.049   0.425   0.451   0.427  -0.197  -0.175  -0.199
131   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   A        -1.023  -0.970  -0.999  -0.965  -0.874  -0.937  -0.861  -0.802  -0.811
140   D        -1.023  -1.019  -0.993  -0.971  -0.964  -0.915  -0.861  -0.854  -0.804
141   D         0.102   0.053   0.084   0.181   0.130   0.183  -0.136  -0.198  -0.155
142   V        -1.023  -0.980  -0.994  -0.619  -0.544  -0.557  -0.861  -0.812  -0.805
143   V        -0.550  -0.583  -0.531  -0.586  -0.655  -0.582  -0.619  -0.651  -0.574
144   M        -0.371  -0.309  -0.447  -0.189  -0.108  -0.283  -0.378  -0.295  -0.464
145   M        -1.023  -1.028  -1.012  -0.817  -0.833  -0.800  -0.861  -0.863  -0.823
146   A        -1.023  -1.040  -1.021  -0.605  -0.626  -0.577  -0.861  -0.875  -0.832
147   S         0.870   0.891   0.919   0.749   0.780   0.814   0.588   0.624   0.638
148   S        -0.550  -0.575  -0.547  -0.530  -0.574  -0.507  -0.619  -0.642  -0.592
149   T         0.870   0.891   0.919   0.949   0.985   1.012   0.588   0.624   0.638
150   N        -1.023  -1.032  -0.991  -0.802  -0.808  -0.745  -0.861  -0.867  -0.802
151   E         0.102   0.128   0.116  -0.341  -0.292  -0.305  -0.136  -0.098  -0.107
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   E         0.102   0.053   0.084  -0.186  -0.263  -0.236  -0.136  -0.198  -0.155
165   L         1.251   1.168   1.130   0.945   0.796   0.734   1.312   1.160   1.063
166   E        -0.371  -0.337  -0.426  -0.224  -0.159  -0.291  -0.378  -0.331  -0.437
167   E        -0.077  -0.065   0.000  -0.254  -0.212  -0.124  -0.378  -0.361  -0.273
168   L         2.174   2.191   2.275   1.915   1.928   2.076   2.519   2.546   2.693
169   K         0.870   0.888   0.896   0.710   0.755   0.732   0.588   0.617   0.590
170   K        -1.023  -0.980  -0.994  -1.049  -0.952  -1.023  -0.861  -0.812  -0.805
171   L         1.251   1.168   1.130   0.989   0.850   0.805   1.312   1.160   1.063
172   K        -0.371  -0.413  -0.473  -0.339  -0.399  -0.496  -0.378  -0.431  -0.497
173   E        -0.550  -0.523  -0.518  -0.530  -0.477  -0.484  -0.619  -0.588  -0.562
174   K         0.870   0.896   0.912   0.710   0.771   0.763   0.588   0.634   0.623
175   K         0.870   0.848   0.884   0.710   0.680   0.710   0.588   0.535   0.565
176   K        -1.023  -1.031  -0.998  -1.032  -1.031  -0.987  -0.861  -0.866  -0.809
177   Q        -0.550  -0.562  -0.543  -0.687  -0.699  -0.681  -0.619  -0.630  -0.587
178   L         2.174   2.191   2.275   1.915   1.928   2.076   2.519   2.546   2.693
179   E        -1.023  -1.020  -0.990  -0.938  -0.923  -0.895  -0.861  -0.855  -0.802
180   N         0.227   0.243   0.160   0.656   0.683   0.518   0.086   0.110  -0.027
181   K        -0.555  -0.579  -0.556  -0.711  -0.744  -0.727  -0.610  -0.637  -0.599
182   L         1.149   1.167   1.086   0.836   0.849   0.732   1.128   1.158   0.976
183   -        -0.666  -0.653  -0.598  -0.850  -0.820  -0.745  -0.740  -0.724  -0.647
184   E         0.754   0.767   0.839   0.530   0.578   0.670   0.346   0.365   0.469
185   I         0.397   0.364   0.262   0.178   0.123   0.004   0.346   0.292   0.131
186   L        -0.550  -0.575  -0.548  -0.753  -0.781  -0.700  -0.619  -0.643  -0.593
187   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
192   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
197   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
198   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
199   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
200   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
201   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
202   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
203   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
204   K        -0.555  -0.468  -0.526  -0.703  -0.525  -0.680  -0.610  -0.499  -0.562
205   Q        -0.555  -0.520  -0.523  -0.377  -0.306  -0.342  -0.610  -0.566  -0.559
206   K        -0.555  -0.578  -0.543  -0.533  -0.567  -0.522  -0.610  -0.638  -0.582
* 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/Q03954
Output conservation file - output/Q03954
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
