1     M         0.996   1.021   1.068   1.289   1.310   1.357   1.043   1.079   1.152
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     K        -0.205  -0.294  -0.164  -0.437  -0.596  -0.387  -0.441  -0.616  -0.445
4     Y        -0.560  -0.734  -0.823  -0.170  -0.425  -0.581  -0.565  -0.799  -0.900
5     I         0.996   1.021   1.068   0.778   0.802   0.931   1.043   1.079   1.152
6     Q        -0.560  -0.786  -0.838  -0.157  -0.452  -0.551  -0.565  -0.857  -0.919
7     T        -0.864  -1.036  -0.872  -0.778  -1.090  -0.883  -0.936  -1.166  -0.964
8     E        -0.347  -0.259  -0.160  -0.463  -0.321  -0.211  -0.689  -0.555  -0.436
9     Q        -0.766  -0.892  -0.864  -0.601  -0.849  -0.885  -0.874  -1.041  -0.955
10    Q        -2.529  -2.228  -2.114  -2.478  -1.961  -1.877  -1.988  -1.695  -1.514
11    I        -0.205  -0.009  -0.101  -0.306   0.012  -0.210  -0.441  -0.134  -0.331
12    E        -1.644  -1.571  -1.383  -1.467  -1.413  -1.168  -1.555  -1.475  -1.235
13    V        -0.416  -0.345  -0.168  -1.089  -0.966  -0.627  -0.812  -0.707  -0.451
14    P         0.996   1.021   1.068   1.245   1.274   1.321   1.043   1.079   1.152
15    E         0.372   0.294  -0.044   0.518   0.433  -0.093   0.424   0.318  -0.233
16    G         0.372   0.238  -0.064   0.511   0.355  -0.084   0.424   0.239  -0.268
17    V         0.996   1.021   1.068   0.653   0.725   0.827   1.043   1.079   1.152
18    T        -0.234  -0.476  -0.789   0.056  -0.235  -0.745  -0.132  -0.434  -0.856
19    V         0.996   1.021   1.068   0.653   0.725   0.827   1.043   1.079   1.152
20    S        -1.238  -1.057  -0.881  -1.240  -0.996  -0.755  -1.431  -1.206  -0.975
21    I         0.996   1.021   1.068   0.778   0.802   0.931   1.043   1.079   1.152
22    K        -0.560  -0.252  -0.777  -0.565  -0.148  -0.852  -0.565  -0.158  -0.841
23    S        -0.416  -0.345  -0.168  -0.495  -0.394  -0.136  -0.812  -0.707  -0.451
24    R         0.996   1.021   1.068   0.987   1.020   1.105   1.043   1.079   1.152
25    I        -2.431  -2.374  -2.104  -2.590  -2.488  -2.004  -1.926  -1.820  -1.509
26    V        -0.347  -0.222  -0.148  -0.956  -0.728  -0.601  -0.689  -0.489  -0.415
27    K        -0.416  -0.318  -0.155  -0.763  -0.549  -0.312  -0.812  -0.659  -0.428
28    V         0.996   1.021   1.068   0.653   0.725   0.827   1.043   1.079   1.152
29    V        -0.819  -0.990  -1.321  -0.477  -0.703  -1.324  -0.627  -0.825  -1.171
30    G         0.996   1.021   1.068   0.998   1.033   1.114   1.043   1.079   1.152
31    P         0.996   1.021   1.068   1.245   1.274   1.321   1.043   1.079   1.152
32    R         0.996   1.021   1.068   0.987   1.020   1.105   1.043   1.079   1.152
33    G         0.996   1.021   1.068   0.998   1.033   1.114   1.043   1.079   1.152
34    T        -1.301  -1.246  -1.339  -1.307  -1.205  -1.405  -1.245  -1.155  -1.194
35    L         0.996   1.021   1.068   1.041   1.088   1.150   1.043   1.079   1.152
36    T        -1.238  -1.089  -0.887  -1.675  -1.442  -1.156  -1.431  -1.235  -0.981
37    K         0.025  -0.086  -0.091  -0.048  -0.179  -0.190  -0.070  -0.258  -0.315
38    N        -1.043  -0.855  -0.848  -1.034  -0.811  -0.787  -1.184  -0.964  -0.936
39    L         0.996   1.021   1.068   1.041   1.088   1.150   1.043   1.079   1.152
40    K        -0.864  -1.036  -0.872  -0.937  -1.201  -0.945  -0.936  -1.166  -0.964
41    H         0.372   0.267  -0.046   0.741   0.619   0.119   0.424   0.282  -0.237
42    I         0.025  -0.086  -0.091  -0.215  -0.428  -0.448  -0.070  -0.258  -0.315
43    D        -0.234  -0.447  -0.805   0.095  -0.141  -0.677  -0.132  -0.397  -0.877
44    V         0.025  -0.086  -0.091  -0.314  -0.480  -0.494  -0.070  -0.258  -0.315
45    T        -1.122  -1.383  -1.374  -0.798  -1.176  -1.169  -0.998  -1.282  -1.225
46    F        -0.234  -0.425  -0.799   0.246   0.027  -0.512  -0.132  -0.369  -0.869
47    T        -2.160  -2.231  -2.125  -1.752  -1.938  -1.751  -1.678  -1.722  -1.521
48    K         0.372   0.238  -0.064   0.306   0.166  -0.351   0.424   0.239  -0.268
49    V        -0.864  -0.972  -0.866  -1.145  -1.295  -1.136  -0.936  -1.084  -0.956
50    N        -1.546  -1.606  -1.385  -1.452  -1.582  -1.297  -1.493  -1.512  -1.237
51    N        -1.122  -1.135  -1.335  -0.869  -0.891  -1.230  -0.998  -0.978  -1.186
52    Q        -1.928  -1.984  -1.794  -1.747  -1.823  -1.572  -1.636  -1.651  -1.408
53    L        -2.173  -2.110  -1.801  -1.945  -1.900  -1.532  -1.864  -1.756  -1.414
54    I         0.996   1.021   1.068   0.778   0.802   0.931   1.043   1.079   1.152
55    K         0.372   0.238  -0.064   0.341   0.215  -0.217   0.424   0.239  -0.268
56    V        -1.546  -1.574  -1.384  -1.800  -1.765  -1.470  -1.493  -1.477  -1.235
57    A        -1.122  -1.269  -1.365  -0.861  -1.145  -1.244  -0.998  -1.176  -1.216
58    V         0.025  -0.099  -0.148  -0.314  -0.504  -0.601  -0.070  -0.281  -0.416
59    H        -0.560  -0.734  -0.823  -0.063  -0.297  -0.445  -0.565  -0.799  -0.900
60    N        -0.766  -0.892  -0.864  -0.618  -0.798  -0.723  -0.874  -1.041  -0.955
61    G         0.996   1.021   1.068   0.998   1.033   1.114   1.043   1.079   1.152
62    G        -1.657  -1.733  -1.777  -1.244  -1.403  -1.478  -1.369  -1.451  -1.395
63    R         0.996   1.021   1.068   0.987   1.020   1.105   1.043   1.079   1.152
64    K         0.996   1.021   1.068   0.829   0.892   0.973   1.043   1.079   1.152
65    H         0.372   0.238  -0.064   0.743   0.583   0.093   0.424   0.239  -0.268
66    V         0.025  -0.086  -0.091  -0.261  -0.403  -0.394  -0.070  -0.258  -0.315
67    A         0.996   1.021   1.068   1.144   1.180   1.236   1.043   1.079   1.152
68    A         0.025  -0.086  -0.091   0.293   0.134   0.100  -0.070  -0.258  -0.315
69    L         0.025  -0.086  -0.091   0.077  -0.119  -0.190  -0.070  -0.258  -0.315
70    R         0.996   1.021   1.068   0.987   1.020   1.105   1.043   1.079   1.152
71    T         0.372   0.294  -0.044   0.559   0.486   0.009   0.424   0.318  -0.233
72    V         0.372   0.267  -0.046   0.180   0.107  -0.269   0.424   0.282  -0.237
73    K        -0.560  -0.786  -0.838  -0.514  -0.791  -0.861  -0.565  -0.857  -0.919
74    S        -0.560  -0.625  -0.844  -0.285  -0.425  -0.716  -0.565  -0.687  -0.930
75    L        -0.205  -0.294  -0.164  -0.306  -0.539  -0.363  -0.441  -0.616  -0.445
76    V        -0.205  -0.009  -0.101  -0.610  -0.295  -0.469  -0.441  -0.134  -0.331
77    D        -1.754  -1.400  -1.369  -1.655  -1.191  -1.142  -1.678  -1.289  -1.221
78    N         0.996   1.021   1.068   1.004   1.028   1.119   1.043   1.079   1.152
79    M        -0.347  -0.339  -0.170  -0.337  -0.327  -0.078  -0.689  -0.696  -0.455
80    I         0.996   1.021   1.068   0.778   0.802   0.931   1.043   1.079   1.152
81    T        -0.205  -0.294  -0.164  -0.309  -0.543  -0.365  -0.441  -0.616  -0.445
82    G         0.996   1.021   1.068   0.998   1.033   1.114   1.043   1.079   1.152
83    V         0.996   1.021   1.068   0.653   0.725   0.827   1.043   1.079   1.152
84    T         0.996   1.021   1.068   1.038   1.084   1.148   1.043   1.079   1.152
85    K        -0.560  -0.734  -0.823  -0.521  -0.734  -0.853  -0.565  -0.799  -0.900
86    G         0.996   1.021   1.068   0.998   1.033   1.114   1.043   1.079   1.152
87    Y        -0.205  -0.294  -0.164  -0.022  -0.199  -0.043  -0.441  -0.616  -0.445
88    K         0.025  -0.086  -0.091  -0.089  -0.242  -0.267  -0.070  -0.258  -0.315
89    Y         0.996   1.021   1.068   1.191   1.226   1.275   1.043   1.079   1.152
90    K         0.996   1.021   1.068   0.829   0.892   0.973   1.043   1.079   1.152
91    M        -0.347  -0.091  -0.097  -0.244   0.174   0.089  -0.689  -0.267  -0.325
92    R         0.996   1.021   1.068   0.987   1.020   1.105   1.043   1.079   1.152
93    Y        -0.560  -0.582  -0.814  -0.173  -0.263  -0.570  -0.565  -0.637  -0.888
94    V         0.996   1.021   1.068   0.653   0.725   0.827   1.043   1.079   1.152
95    Y         0.996   1.021   1.068   1.191   1.226   1.275   1.043   1.079   1.152
96    A         0.996   1.021   1.068   1.144   1.180   1.236   1.043   1.079   1.152
97    H         0.996   1.021   1.068   1.230   1.262   1.308   1.043   1.079   1.152
98    F         0.996   1.021   1.068   1.183   1.218   1.269   1.043   1.079   1.152
99    P         0.996   1.021   1.068   1.245   1.274   1.321   1.043   1.079   1.152
100   I         0.996   1.021   1.068   0.778   0.802   0.931   1.043   1.079   1.152
101   N         0.996   1.021   1.068   1.004   1.028   1.119   1.043   1.079   1.152
102   V         0.025  -0.086  -0.091  -0.314  -0.480  -0.494  -0.070  -0.258  -0.315
103   N         0.996   1.021   1.068   1.004   1.028   1.119   1.043   1.079   1.152
104   I        -1.754  -1.541  -1.387  -2.094  -1.751  -1.540  -1.678  -1.455  -1.239
105   V        -1.398  -1.501  -1.381  -1.554  -1.712  -1.554  -1.307  -1.400  -1.233
106   E        -0.962  -0.900  -0.873  -0.968  -0.881  -0.935  -1.095  -0.988  -0.964
107   K        -0.560  -0.612  -0.818  -0.600  -0.684  -1.036  -0.565  -0.668  -0.893
108   D        -0.205  -0.294  -0.164  -0.217  -0.405  -0.231  -0.441  -0.616  -0.445
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   G         0.996   1.021   1.068   0.998   1.033   1.114   1.043   1.079   1.152
113   A        -1.711  -1.683  -1.403  -1.626  -1.583  -1.226  -1.646  -1.581  -1.253
114   K        -1.902  -1.956  -1.795  -1.744  -1.798  -1.515  -1.616  -1.649  -1.410
115   F        -1.546  -1.550  -1.392  -1.437  -1.549  -1.288  -1.493  -1.463  -1.243
116   I        -0.416  -0.237  -0.131  -1.089  -0.758  -0.569  -0.812  -0.516  -0.385
117   E         0.996   1.021   1.068   1.022   1.061   1.135   1.043   1.079   1.152
118   V         0.372   0.454  -0.050   0.255   0.342  -0.363   0.424   0.531  -0.243
119   R         0.996   1.021   1.068   0.987   1.020   1.105   1.043   1.079   1.152
120   N         0.996   1.021   1.068   1.004   1.028   1.119   1.043   1.079   1.152
121   F         0.996   1.021   1.068   1.183   1.218   1.269   1.043   1.079   1.152
122   L         0.372   0.238  -0.064   0.532   0.376  -0.135   0.424   0.239  -0.268
123   G         0.996   1.021   1.068   0.998   1.033   1.114   1.043   1.079   1.152
124   D        -0.416  -0.237  -0.131  -0.601  -0.300  -0.163  -0.812  -0.516  -0.385
125   K         0.025  -0.086  -0.091  -0.089  -0.242  -0.267  -0.070  -0.258  -0.315
126   K        -1.190  -1.135  -0.892  -1.584  -1.547  -1.129  -1.369  -1.294  -0.988
127   I        -0.560  -0.603  -0.816  -0.758  -0.819  -1.107  -0.565  -0.658  -0.891
128   R         0.996   1.021   1.068   0.987   1.020   1.105   1.043   1.079   1.152
129   N        -2.368  -2.269  -2.116  -2.160  -2.129  -1.832  -1.864  -1.750  -1.515
130   V        -0.205  -0.237  -0.157  -0.689  -0.758  -0.617  -0.441  -0.515  -0.432
131   P        -0.882  -0.944  -0.860  -0.864  -0.999  -0.948  -1.060  -1.098  -0.951
132   V        -1.546  -1.626  -1.392  -1.747  -1.747  -1.329  -1.493  -1.534  -1.243
133   R        -1.902  -1.969  -1.795  -1.526  -1.630  -1.335  -1.616  -1.656  -1.410
134   D        -1.238  -1.137  -0.894  -1.238  -1.065  -0.756  -1.431  -1.297  -0.990
135   G         0.996   1.021   1.068   0.998   1.033   1.114   1.043   1.079   1.152
136   V         0.372   0.300  -0.057   0.198   0.166  -0.217   0.424   0.327  -0.255
137   T        -1.238  -1.119  -0.886  -1.304  -1.136  -0.819  -1.431  -1.275  -0.981
138   I        -0.819  -0.751  -1.316  -0.777  -0.679  -1.326  -0.627  -0.554  -1.166
139   E        -0.864  -0.732  -0.814  -0.733  -0.592  -0.716  -0.936  -0.796  -0.888
140   F        -0.416  -0.323  -0.158  -0.649  -0.595  -0.302  -0.812  -0.668  -0.432
141   S         0.996   1.021   1.068   1.081   1.115   1.184   1.043   1.079   1.152
142   T        -1.301  -1.360  -1.375  -1.093  -1.208  -1.208  -1.245  -1.298  -1.228
143   N        -1.127  -0.965  -0.879  -1.137  -0.927  -0.791  -1.307  -1.117  -0.972
144   V        -0.205  -0.234  -0.160  -0.228  -0.325  -0.328  -0.441  -0.510  -0.437
145   K         0.996   1.021   1.068   0.829   0.892   0.973   1.043   1.079   1.152
146   D         0.996   1.021   1.068   1.052   1.104   1.159   1.043   1.079   1.152
147   E         0.996   1.021   1.068   1.022   1.061   1.135   1.043   1.079   1.152
148   I        -0.882  -0.755  -0.844  -1.153  -0.990  -1.080  -1.060  -0.893  -0.933
149   V        -0.766  -0.847  -0.850  -1.104  -1.210  -1.067  -0.874  -0.971  -0.938
150   L        -0.560  -0.579  -0.826  -0.447  -0.541  -1.005  -0.565  -0.632  -0.909
151   S        -0.560  -0.734  -0.823  -0.333  -0.616  -0.815  -0.565  -0.799  -0.900
152   G         0.996   1.021   1.068   0.998   1.033   1.114   1.043   1.079   1.152
153   N         0.996   1.021   1.068   1.004   1.028   1.119   1.043   1.079   1.152
154   S         0.996   1.021   1.068   1.081   1.115   1.184   1.043   1.079   1.152
155   V        -0.919  -0.855  -0.839  -1.266  -1.039  -1.045  -1.122  -0.983  -0.923
156   E         0.996   1.021   1.068   1.022   1.061   1.135   1.043   1.079   1.152
157   D        -1.546  -1.446  -1.375  -1.416  -1.270  -1.178  -1.493  -1.335  -1.227
158   V         0.996   1.021   1.068   0.653   0.725   0.827   1.043   1.079   1.152
159   S         0.996   1.021   1.068   1.081   1.115   1.184   1.043   1.079   1.152
160   Q         0.996   1.021   1.068   1.165   1.207   1.254   1.043   1.079   1.152
161   N        -0.766  -0.892  -0.864  -0.680  -0.894  -0.809  -0.874  -1.041  -0.955
162   A         0.372   0.300  -0.057   0.687   0.618   0.150   0.424   0.327  -0.255
163   A         0.996   1.021   1.068   1.144   1.180   1.236   1.043   1.079   1.152
164   D         0.025  -0.086  -0.091   0.136  -0.033  -0.091  -0.070  -0.258  -0.315
165   L        -0.560  -0.293  -0.784  -0.696  -0.336  -1.011  -0.565  -0.213  -0.849
166   Q         0.025  -0.086  -0.091   0.211   0.025  -0.075  -0.070  -0.258  -0.315
167   Q         0.996   1.021   1.068   1.165   1.207   1.254   1.043   1.079   1.152
168   I        -0.234  -0.255  -0.789  -0.231  -0.266  -1.020  -0.132  -0.161  -0.856
169   C         0.996   1.021   1.068   1.307   1.328   1.372   1.043   1.079   1.152
170   R         0.025  -0.086  -0.091   0.072  -0.115  -0.140  -0.070  -0.258  -0.315
171   V         0.996   1.021   1.068   0.653   0.725   0.827   1.043   1.079   1.152
172   R         0.996   1.021   1.068   0.987   1.020   1.105   1.043   1.079   1.152
173   N         0.996   1.021   1.068   1.004   1.028   1.119   1.043   1.079   1.152
174   K         0.996   1.021   1.068   0.829   0.892   0.973   1.043   1.079   1.152
175   D         0.996   1.021   1.068   1.052   1.104   1.159   1.043   1.079   1.152
176   I         0.996   1.021   1.068   0.778   0.802   0.931   1.043   1.079   1.152
177   R         0.996   1.021   1.068   0.987   1.020   1.105   1.043   1.079   1.152
178   K         0.996   1.021   1.068   0.829   0.892   0.973   1.043   1.079   1.152
179   F         0.996   1.021   1.068   1.183   1.218   1.269   1.043   1.079   1.152
180   L         0.996   1.021   1.068   1.041   1.088   1.150   1.043   1.079   1.152
181   D         0.996   1.021   1.068   1.052   1.104   1.159   1.043   1.079   1.152
182   G         0.996   1.021   1.068   0.998   1.033   1.114   1.043   1.079   1.152
183   I         0.996   1.021   1.068   0.778   0.802   0.931   1.043   1.079   1.152
184   Y         0.996   1.021   1.068   1.191   1.226   1.275   1.043   1.079   1.152
185   V         0.996   1.021   1.068   0.653   0.725   0.827   1.043   1.079   1.152
186   S         0.996   1.021   1.068   1.081   1.115   1.184   1.043   1.079   1.152
187   H        -0.205  -0.009  -0.101  -0.163   0.108  -0.035  -0.441  -0.134  -0.331
188   K        -0.347  -0.318  -0.168  -0.681  -0.637  -0.391  -0.689  -0.659  -0.450
189   G         0.372   0.300  -0.057   0.515   0.439  -0.059   0.424   0.327  -0.255
190   F        -2.012  -1.625  -1.761  -1.802  -1.301  -1.537  -1.740  -1.337  -1.382
191   I         0.372   0.300  -0.057   0.255   0.158  -0.378   0.424   0.327  -0.255
192   T        -1.657  -1.642  -1.768  -1.433  -1.492  -1.741  -1.369  -1.351  -1.390
193   E         0.996   1.021   1.068   1.022   1.061   1.135   1.043   1.079   1.152
194   D        -1.043  -1.071  -0.866  -1.029  -1.090  -0.817  -1.184  -1.213  -0.958
195   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   L        -1.911  -1.838  -1.784  -1.665  -1.558  -1.491  -1.651  -1.537  -1.401
* 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/P05738
Output conservation file - output/P05738
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
