1     M         1.186   1.242   1.310   1.565   1.618   1.699   1.252   1.328   1.436
2     A         1.186   1.242   1.310   0.760   0.850   1.002   1.252   1.328   1.436
3     I         1.186   1.242   1.310   1.325   1.390   1.491   1.252   1.328   1.436
4     S        -1.123  -1.351  -1.343  -0.657  -0.988  -1.033  -0.965  -1.207  -1.150
5     K        -0.396  -0.724  -0.750  -0.377  -0.771  -0.771  -0.350  -0.768  -0.803
6     N         0.376   0.142   0.083   0.673   0.321   0.145   0.389   0.032  -0.102
7     L        -1.123  -1.351  -1.343  -0.657  -0.949  -0.923  -0.965  -1.207  -1.150
8     P        -0.024  -0.159  -0.033   0.119  -0.129   0.047  -0.226  -0.479  -0.306
9     I        -0.305  -0.192  -0.029  -0.422  -0.240  -0.011  -0.719  -0.538  -0.300
10    L        -0.750  -0.787  -0.788  -0.593  -0.684  -0.673  -0.842  -0.918  -0.856
11    K        -0.237  -0.207  -0.032  -0.540  -0.427  -0.141  -0.596  -0.565  -0.306
12    N         0.376   0.142   0.083   0.649   0.275   0.080   0.389   0.032  -0.102
13    H         1.186   1.242   1.310   1.482   1.541   1.626   1.252   1.328   1.436
14    F         1.186   1.242   1.310   1.415   1.477   1.568   1.252   1.328   1.436
15    R         0.376   0.142   0.083   0.245  -0.006  -0.048   0.389   0.032  -0.102
16    K         1.186   1.242   1.310   0.941   1.034   1.158   1.252   1.328   1.436
17    H        -0.750  -0.787  -0.788  -0.311  -0.416  -0.416  -0.842  -0.918  -0.856
18    W         1.186   1.242   1.310   1.569   1.621   1.702   1.252   1.328   1.436
19    Q         1.186   1.242   1.310   1.365   1.429   1.525   1.252   1.328   1.436
20    E        -0.024  -0.159  -0.033  -0.152  -0.471  -0.315  -0.226  -0.479  -0.306
21    R         0.376   0.142   0.083   0.245  -0.006  -0.047   0.389   0.032  -0.102
22    V         1.186   1.242   1.310   1.205   1.277   1.387   1.252   1.328   1.436
23    K        -0.024  -0.005  -0.010  -0.405  -0.373  -0.446  -0.226  -0.210  -0.267
24    V        -0.750  -0.893  -0.791  -0.544  -0.701  -0.527  -0.842  -1.009  -0.859
25    H         0.376   0.142   0.083   0.843   0.557   0.444   0.389   0.032  -0.102
26    F         0.376   0.509   0.115   0.733   0.893   0.331   0.389   0.575  -0.047
27    D         0.376   0.142   0.083   0.763   0.472   0.336   0.389   0.032  -0.102
28    Q         1.186   1.242   1.310   1.365   1.429   1.525   1.252   1.328   1.436
29    A        -0.024  -0.096  -0.022  -0.436  -0.524  -0.348  -0.226  -0.366  -0.288
30    G         1.186   1.242   1.310   1.372   1.430   1.531   1.252   1.328   1.436
31    K         0.376   0.142   0.083   0.206  -0.116  -0.252   0.389   0.032  -0.102
32    K         1.186   1.242   1.310   0.941   1.034   1.158   1.252   1.328   1.436
33    V        -2.027  -1.836  -1.777  -2.179  -1.888  -1.713  -1.704  -1.479  -1.333
34    S         0.376   0.142   0.083   0.609   0.256   0.080   0.389   0.032  -0.102
35    R         1.186   1.242   1.310   0.890   0.979   1.115   1.252   1.328   1.436
36    R         1.186   1.242   1.310   0.890   0.979   1.115   1.252   1.328   1.436
37    N        -2.913  -2.549  -2.442  -2.144  -1.712  -1.571  -2.074  -1.743  -1.548
38    A        -0.396  -0.184  -0.687  -0.534  -0.256  -0.779  -0.350  -0.069  -0.721
39    R         1.186   1.242   1.310   0.890   0.979   1.115   1.252   1.328   1.436
40    A        -2.168  -1.839  -1.790  -2.141  -1.534  -1.521  -1.828  -1.481  -1.343
41    A        -2.027  -1.778  -1.771  -2.261  -1.829  -1.817  -1.704  -1.447  -1.330
42    R         0.376   0.605   0.123   0.206   0.516  -0.176   0.389   0.702  -0.035
43    A         1.186   1.242   1.310   0.760   0.850   1.002   1.252   1.328   1.436
44    A         1.186   1.242   1.310   0.760   0.850   1.002   1.252   1.328   1.436
45    K        -0.024  -0.023  -0.014  -0.448  -0.459  -0.526  -0.226  -0.241  -0.272
46    I         0.376   0.275   0.092   0.644   0.521   0.220   0.389   0.239  -0.087
47    A         1.186   1.242   1.310   0.760   0.850   1.002   1.252   1.328   1.436
48    P         1.186   1.242   1.310   1.318   1.374   1.485   1.252   1.328   1.436
49    R         1.186   1.242   1.310   0.890   0.979   1.115   1.252   1.328   1.436
50    P         1.186   1.242   1.310   1.318   1.374   1.485   1.252   1.328   1.436
51    L        -1.050  -0.991  -0.814  -1.035  -0.972  -0.726  -1.212  -1.124  -0.885
52    D         0.376   0.142   0.083   0.735   0.422   0.260   0.389   0.032  -0.102
53    L        -1.423  -1.439  -1.344  -1.465  -1.617  -1.468  -1.335  -1.324  -1.153
54    L         0.376   0.142   0.083   0.586   0.298   0.176   0.389   0.032  -0.102
55    R         1.186   1.242   1.310   0.890   0.979   1.115   1.252   1.328   1.436
56    P         1.186   1.242   1.310   1.318   1.374   1.485   1.252   1.328   1.436
57    V        -0.750  -0.938  -0.792  -0.719  -1.060  -0.876  -0.842  -1.050  -0.859
58    V         1.186   1.242   1.310   1.205   1.277   1.387   1.252   1.328   1.436
59    R         0.376   0.142   0.083   0.162  -0.157  -0.274   0.389   0.032  -0.102
60    A        -0.750  -0.930  -0.785  -0.924  -1.076  -0.765  -0.842  -1.039  -0.851
61    P         1.186   1.242   1.310   1.318   1.374   1.485   1.252   1.328   1.436
62    T         1.186   1.242   1.310   1.379   1.450   1.538   1.252   1.328   1.436
63    V        -0.305  -0.142  -0.004  -0.459  -0.165   0.020  -0.719  -0.448  -0.256
64    K        -0.024  -0.096  -0.022  -0.405  -0.551  -0.472  -0.226  -0.366  -0.288
65    Y         1.186   1.242   1.310   1.485   1.544   1.629   1.252   1.328   1.436
66    N         1.186   1.242   1.310   1.397   1.457   1.553   1.252   1.328   1.436
67    R         0.376   0.142   0.083   0.258   0.017  -0.013   0.389   0.032  -0.102
68    K         0.376   0.275   0.092   0.206   0.090  -0.234   0.389   0.239  -0.087
69    V         0.376   0.275   0.092   0.542   0.433   0.171   0.389   0.239  -0.087
70    R         1.186   1.242   1.310   0.890   0.979   1.115   1.252   1.328   1.436
71    A         0.376   0.275   0.092   0.078  -0.017  -0.236   0.389   0.239  -0.087
72    G         1.186   1.242   1.310   1.372   1.430   1.531   1.252   1.328   1.436
73    R         1.186   1.242   1.310   0.890   0.979   1.115   1.252   1.328   1.436
74    G         1.186   1.242   1.310   1.372   1.430   1.531   1.252   1.328   1.436
75    F         1.186   1.242   1.310   1.415   1.477   1.568   1.252   1.328   1.436
76    T        -0.237  -0.145  -0.031  -0.192  -0.053   0.075  -0.596  -0.454  -0.304
77    L         1.186   1.242   1.310   1.256   1.336   1.431   1.252   1.328   1.436
78    A        -0.024  -0.096  -0.022  -0.481  -0.580  -0.424  -0.226  -0.366  -0.288
79    E         1.186   1.242   1.310   1.194   1.268   1.377   1.252   1.328   1.436
80    V        -0.750  -0.328  -0.703  -0.590   0.000  -0.539  -0.842  -0.273  -0.743
81    K         1.186   1.242   1.310   0.941   1.034   1.158   1.252   1.328   1.436
82    A         1.186   1.242   1.310   0.760   0.850   1.002   1.252   1.328   1.436
83    A        -0.024   0.137   0.040  -0.477  -0.222  -0.336  -0.226   0.023  -0.177
84    G         1.186   1.242   1.310   1.372   1.430   1.531   1.252   1.328   1.436
85    L        -0.910  -0.988  -0.778  -0.859  -0.932  -0.649  -1.089  -1.121  -0.843
86    T        -1.655  -1.517  -1.356  -1.499  -1.307  -1.160  -1.581  -1.403  -1.164
87    A        -1.655  -1.582  -1.364  -2.205  -2.095  -1.706  -1.581  -1.444  -1.172
88    A        -2.027  -2.053  -1.809  -2.425  -2.413  -1.946  -1.704  -1.653  -1.358
89    Y        -0.024  -0.159  -0.033   0.229  -0.067   0.067  -0.226  -0.479  -0.306
90    A         1.186   1.242   1.310   0.760   0.850   1.002   1.252   1.328   1.436
91    R        -0.396  -0.724  -0.750  -0.433  -0.826  -0.820  -0.350  -0.768  -0.803
92    T         1.186   1.242   1.310   1.379   1.450   1.538   1.252   1.328   1.436
93    I         0.376   0.629   0.123   0.637   0.929   0.255   0.389   0.733  -0.033
94    G         1.186   1.242   1.310   1.372   1.430   1.531   1.252   1.328   1.436
95    I         1.186   1.242   1.310   1.325   1.390   1.491   1.252   1.328   1.436
96    A        -0.910  -0.989  -0.787  -1.229  -1.210  -0.878  -1.089  -1.121  -0.854
97    V         1.186   1.242   1.310   1.205   1.277   1.387   1.252   1.328   1.436
98    D         1.186   1.242   1.310   1.425   1.498   1.578   1.252   1.328   1.436
99    H         0.376   0.275   0.092   0.808   0.677   0.366   0.389   0.239  -0.087
100   R         1.186   1.242   1.310   0.890   0.979   1.115   1.252   1.328   1.436
101   R         1.186   1.242   1.310   0.890   0.979   1.115   1.252   1.328   1.436
102   Q        -0.396  -0.724  -0.750  -0.122  -0.681  -0.891  -0.350  -0.768  -0.803
103   N         1.186   1.242   1.310   1.397   1.457   1.553   1.252   1.328   1.436
104   R        -0.396  -0.400  -0.704  -0.515  -0.489  -0.951  -0.350  -0.354  -0.744
105   N        -0.237   0.030   0.047  -0.196   0.219   0.211  -0.596  -0.152  -0.165
106   Q        -0.910  -0.777  -0.763  -0.850  -0.690  -0.654  -1.089  -0.903  -0.824
107   E         1.186   1.242   1.310   1.194   1.268   1.377   1.252   1.328   1.436
108   I        -1.655  -1.458  -1.354  -1.354  -1.082  -0.945  -1.581  -1.337  -1.162
109   F        -0.305  -0.164  -0.015  -0.357  -0.141   0.060  -0.719  -0.486  -0.275
110   D        -1.423  -1.566  -1.356  -1.158  -1.395  -1.201  -1.335  -1.424  -1.164
111   A        -0.750  -0.727  -0.731  -1.158  -1.130  -1.109  -0.842  -0.772  -0.779
112   N         1.186   1.242   1.310   1.397   1.457   1.553   1.252   1.328   1.436
113   V         0.376   0.612   0.123   0.534   0.809   0.199   0.389   0.711  -0.035
114   Q        -1.655  -1.489  -1.359  -1.740  -1.491  -1.335  -1.581  -1.364  -1.167
115   R         1.186   1.242   1.310   0.890   0.979   1.115   1.252   1.328   1.436
116   L         0.376   0.142   0.083   0.586   0.298   0.176   0.389   0.032  -0.102
117   K        -0.024   0.137   0.040  -0.243   0.007  -0.118  -0.226   0.023  -0.177
118   E        -0.396  -0.724  -0.750  -0.244  -0.738  -0.890  -0.350  -0.768  -0.803
119   Y         1.186   1.242   1.310   1.485   1.544   1.629   1.252   1.328   1.436
120   Q        -0.750  -0.830  -0.763  -0.619  -0.703  -0.712  -0.842  -0.905  -0.822
121   S        -0.024  -0.159  -0.033  -0.047  -0.416  -0.286  -0.226  -0.479  -0.306
122   K        -0.396  -0.724  -0.750  -0.431  -0.834  -0.902  -0.350  -0.768  -0.803
123   I        -0.024   0.255   0.077   0.047   0.452   0.166  -0.226   0.208  -0.113
124   I        -0.237  -0.161  -0.032  -0.308  -0.203  -0.038  -0.596  -0.482  -0.305
125   V         0.376   0.520   0.115   0.534   0.713   0.187   0.389   0.590  -0.047
126   F         1.186   1.242   1.310   1.415   1.477   1.568   1.252   1.328   1.436
127   P        -0.024   0.137   0.040   0.138   0.356   0.195  -0.226   0.023  -0.177
128   R        -0.024   0.137   0.040  -0.439  -0.165  -0.357  -0.226   0.023  -0.177
129   D        -0.396  -0.104  -0.668  -0.353   0.013  -0.621  -0.350   0.026  -0.696
130   G        -2.027  -2.053  -1.809  -1.681  -1.826  -1.481  -1.704  -1.653  -1.358
131   K        -0.396  -0.724  -0.750  -0.363  -0.740  -0.737  -0.350  -0.768  -0.803
132   A        -0.750  -0.938  -0.792  -1.191  -1.402  -1.145  -0.842  -1.050  -0.859
133   P        -1.123  -0.879  -1.278  -0.739  -0.420  -1.054  -0.965  -0.663  -1.084
134   E        -0.024  -0.159  -0.033  -0.136  -0.440  -0.285  -0.226  -0.479  -0.306
135   A        -1.655  -1.462  -1.360  -2.054  -1.750  -1.520  -1.581  -1.344  -1.169
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.083  -0.980  -0.800  -1.372  -1.129  -0.861  -1.271  -1.108  -0.867
145   -        -1.083  -0.911  -0.794  -1.163  -0.873  -0.790  -1.271  -1.029  -0.860
146   E        -1.795  -1.756  -1.775  -1.461  -1.529  -1.482  -1.458  -1.394  -1.331
147   Q        -1.423  -1.439  -1.344  -1.164  -1.210  -1.136  -1.335  -1.324  -1.153
148   V        -0.910  -0.706  -0.768  -0.841  -0.588  -0.588  -1.089  -0.856  -0.834
149   L        -1.795  -1.876  -1.793  -1.541  -1.677  -1.714  -1.458  -1.506  -1.345
150   S        -0.237  -0.192  -0.036  -0.181  -0.118   0.092  -0.596  -0.538  -0.312
151   A        -0.750  -0.454  -0.705  -0.815  -0.313  -0.735  -0.842  -0.423  -0.745
152   A        -0.750  -0.742  -0.762  -1.059  -1.007  -0.965  -0.842  -0.794  -0.822
153   A         0.376   0.509   0.115   0.097   0.281  -0.153   0.389   0.575  -0.047
154   T        -0.910  -0.696  -0.763  -0.805  -0.569  -0.590  -1.089  -0.839  -0.827
155   F         0.376   0.142   0.083   0.733   0.419   0.275   0.389   0.032  -0.102
156   P         0.376   0.275   0.092   0.654   0.525   0.257   0.389   0.239  -0.087
157   I        -0.237  -0.161  -0.032  -0.308  -0.203  -0.038  -0.596  -0.482  -0.305
158   A        -1.655  -1.603  -1.352  -1.838  -1.632  -1.330  -1.581  -1.464  -1.161
159   Q         0.376   0.275   0.092   0.634   0.488   0.119   0.389   0.239  -0.087
160   P        -1.123  -1.088  -1.302  -0.769  -0.758  -1.154  -0.965  -0.939  -1.108
161   A        -1.423  -1.213  -1.303  -1.610  -1.305  -1.330  -1.335  -1.067  -1.111
162   T        -1.655  -1.517  -1.356  -1.706  -1.589  -1.328  -1.581  -1.403  -1.164
163   D        -0.750  -0.631  -0.723  -0.584  -0.389  -0.527  -0.842  -0.643  -0.769
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   V        -1.295  -1.157  -1.329  -0.918  -0.799  -1.045  -1.162  -1.020  -1.136
168   E        -1.123  -1.049  -1.299  -0.864  -0.755  -1.185  -0.965  -0.866  -1.106
169   A        -1.655  -1.427  -1.335  -1.679  -1.417  -1.263  -1.581  -1.311  -1.146
170   R        -0.024  -0.159  -0.033  -0.439  -0.703  -0.501  -0.226  -0.479  -0.306
171   A        -0.396  -0.724  -0.750  -0.565  -0.952  -0.913  -0.350  -0.768  -0.803
172   V        -0.750  -0.893  -0.791  -0.640  -0.845  -0.708  -0.842  -1.009  -0.859
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   Q        -0.396  -0.324  -0.694  -0.123  -0.039  -0.511  -0.350  -0.267  -0.731
176   D        -2.027  -1.916  -1.791  -1.800  -1.758  -1.530  -1.704  -1.548  -1.345
177   N        -1.655  -1.595  -1.364  -1.545  -1.516  -1.186  -1.581  -1.456  -1.172
178   G        -0.910  -0.905  -0.755  -0.842  -0.774  -0.571  -1.089  -1.005  -0.810
179   E        -1.514  -1.593  -1.353  -1.272  -1.286  -0.976  -1.458  -1.454  -1.160
180   S        -1.423  -1.435  -1.350  -1.015  -1.039  -0.909  -1.335  -1.323  -1.159
181   A         1.186   1.242   1.310   0.760   0.850   1.002   1.252   1.328   1.436
182   F        -0.237  -0.065  -0.012  -0.087   0.171   0.211  -0.596  -0.313  -0.269
183   R         0.376   0.142   0.083   0.222  -0.047  -0.108   0.389   0.032  -0.102
184   T         0.376   0.275   0.092   0.631   0.484   0.085   0.389   0.239  -0.087
185   L         1.186   1.242   1.310   1.256   1.336   1.431   1.252   1.328   1.436
186   R         0.376   0.142   0.083   0.222  -0.047  -0.108   0.389   0.032  -0.102
187   L        -1.123  -1.351  -1.343  -0.716  -1.042  -1.040  -0.965  -1.207  -1.150
188   A         0.376   0.142   0.083   0.068  -0.217  -0.276   0.389   0.032  -0.102
189   R         0.376   0.509   0.115   0.162   0.355  -0.214   0.389   0.575  -0.047
190   S        -0.396  -0.519  -0.715  -0.066  -0.319  -0.630  -0.350  -0.524  -0.758
191   E        -1.423  -1.402  -1.330  -1.003  -0.916  -0.886  -1.335  -1.264  -1.139
192   K        -0.750  -0.787  -0.788  -1.081  -1.254  -1.140  -0.842  -0.918  -0.856
193   K        -0.237  -0.185  -0.036  -0.825  -0.743  -0.505  -0.596  -0.525  -0.312
194   F        -0.750  -0.622  -0.718  -0.337  -0.140  -0.348  -0.842  -0.630  -0.762
195   R        -1.423  -1.383  -1.345  -1.810  -1.789  -1.716  -1.335  -1.283  -1.154
196   G         1.186   1.242   1.310   1.372   1.430   1.531   1.252   1.328   1.436
197   I        -0.396  -0.724  -0.750  -0.112  -0.648  -0.790  -0.350  -0.768  -0.803
198   R         1.186   1.242   1.310   0.890   0.979   1.115   1.252   1.328   1.436
199   E        -0.024  -0.096  -0.022  -0.192  -0.385  -0.354  -0.226  -0.366  -0.288
200   K         0.376   0.142   0.083   0.187  -0.152  -0.305   0.389   0.032  -0.102
201   R         0.376   0.142   0.083   0.234  -0.026  -0.076   0.389   0.032  -0.102
202   A        -0.396  -0.528  -0.715  -0.549  -0.691  -0.841  -0.350  -0.535  -0.758
203   R        -0.237  -0.015   0.016  -0.825  -0.392  -0.388  -0.596  -0.227  -0.219
204   E        -0.910  -0.988  -0.781  -0.899  -0.998  -0.721  -1.089  -1.121  -0.848
205   K        -0.396  -0.554  -0.729  -0.559  -0.806  -1.191  -0.350  -0.564  -0.776
206   A         1.186   1.242   1.310   0.760   0.850   1.002   1.252   1.328   1.436
207   E        -0.396  -0.436  -0.714  -0.206  -0.283  -0.727  -0.350  -0.397  -0.756
208   A         0.376   0.142   0.083   0.068  -0.217  -0.276   0.389   0.032  -0.102
209   E         0.376   0.142   0.083   0.445   0.085  -0.090   0.389   0.032  -0.102
210   A         0.376   0.142   0.083   0.068  -0.217  -0.276   0.389   0.032  -0.102
211   E        -0.396  -0.528  -0.715  -0.206  -0.460  -0.730  -0.350  -0.535  -0.758
212   K         1.186   1.242   1.310   0.941   1.034   1.158   1.252   1.328   1.436
213   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
214   K         0.376   0.275   0.092   0.273   0.183  -0.055   0.389   0.239  -0.087
215   K         1.186   1.242   1.310   0.941   1.034   1.158   1.252   1.328   1.436
* 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/P40212
Output conservation file - output/P40212
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
