1     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    M         0.056  -0.025  -0.157   0.325   0.217  -0.025  -0.028  -0.138  -0.350
36    S        -0.716  -0.709  -0.692  -0.671  -0.663  -0.619  -0.827  -0.809  -0.764
37    L         1.334   1.372   1.423   1.249   1.305   1.392   1.437   1.489   1.569
38    P         0.676   0.698   0.520   0.920   0.964   0.669   0.638   0.671   0.333
39    D        -0.716  -0.701  -0.689  -0.710  -0.675  -0.649  -0.827  -0.797  -0.760
40    G         0.676   0.698   0.520   0.646   0.677   0.431   0.638   0.671   0.333
41    F         0.676   0.693   0.520   0.795   0.826   0.573   0.638   0.663   0.333
42    Y        -1.034  -1.044  -1.039  -1.025  -1.041  -1.070  -0.960  -0.952  -0.927
43    I        -0.200  -0.199  -0.212  -0.329  -0.324  -0.357  -0.427  -0.402  -0.435
44    R         1.334   1.372   1.423   1.467   1.514   1.602   1.437   1.489   1.569
45    R        -1.034  -1.035  -1.048  -0.829  -0.822  -0.867  -0.960  -0.944  -0.935
46    M        -0.200  -0.158  -0.222  -0.314  -0.248  -0.330  -0.427  -0.366  -0.452
47    E        -1.154  -1.182  -1.074  -1.177  -1.193  -1.047  -1.093  -1.094  -0.961
48    E        -1.789  -1.787  -1.629  -1.681  -1.632  -1.442  -1.359  -1.332  -1.166
49    G        -1.472  -1.453  -1.364  -1.449  -1.411  -1.294  -1.226  -1.186  -1.073
50    D         1.334   1.372   1.423   1.373   1.423   1.511   1.437   1.489   1.569
51    L         0.056   0.104  -0.127   0.168   0.240  -0.129  -0.028   0.048  -0.307
52    E        -0.836  -0.840  -0.731  -0.943  -0.935  -0.759  -0.960  -0.942  -0.805
53    Q        -1.154  -1.193  -1.079  -1.145  -1.193  -1.016  -1.093  -1.103  -0.965
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    V        -0.200  -0.199  -0.212  -0.368  -0.341  -0.358  -0.427  -0.402  -0.435
56    T        -0.200  -0.177  -0.223  -0.423  -0.379  -0.472  -0.427  -0.382  -0.454
57    E        -1.034  -1.074  -1.048  -1.025  -1.080  -1.057  -0.960  -0.982  -0.935
58    T        -0.518  -0.534  -0.641  -0.419  -0.430  -0.626  -0.560  -0.568  -0.699
59    L         1.334   1.372   1.423   1.249   1.305   1.392   1.437   1.489   1.569
60    K        -0.518  -0.596  -0.654  -0.466  -0.565  -0.652  -0.560  -0.643  -0.714
61    V         1.334   1.372   1.423   1.236   1.293   1.379   1.437   1.489   1.569
62    L         1.334   1.372   1.423   1.249   1.305   1.392   1.437   1.489   1.569
63    T         1.334   1.372   1.423   1.377   1.431   1.516   1.437   1.489   1.569
64    T         0.056   0.108  -0.126   0.194   0.271  -0.067  -0.028   0.054  -0.305
65    V         1.334   1.372   1.423   1.236   1.293   1.379   1.437   1.489   1.569
66    G         1.334   1.372   1.423   1.249   1.300   1.392   1.437   1.489   1.569
67    T        -0.278  -0.267  -0.237  -0.476  -0.451  -0.390  -0.560  -0.532  -0.480
68    I         0.374   0.416   0.397   0.146   0.214   0.145   0.105   0.177   0.095
69    T         0.374   0.356   0.372   0.317   0.280   0.270   0.105   0.063   0.045
70    P        -0.613  -0.489  -0.646  -0.622  -0.438  -0.645  -0.704  -0.534  -0.711
71    E        -0.389  -0.494  -0.593  -0.315  -0.506  -0.642  -0.398  -0.540  -0.641
72    S        -1.064  -0.983  -1.034  -1.011  -0.897  -0.990  -1.010  -0.930  -0.927
73    F         1.334   1.372   1.423   1.485   1.536   1.619   1.437   1.489   1.569
74    S        -1.726  -1.631  -1.603  -1.481  -1.308  -1.315  -1.315  -1.217  -1.149
75    K        -0.716  -0.661  -0.690  -0.865  -0.774  -0.814  -0.827  -0.752  -0.761
76    L        -0.200  -0.176  -0.229  -0.380  -0.352  -0.429  -0.427  -0.407  -0.464
77    I        -0.836  -0.830  -0.731  -0.981  -0.966  -0.823  -0.960  -0.935  -0.805
78    K        -0.716  -0.698  -0.699  -0.677  -0.642  -0.670  -0.827  -0.794  -0.771
79    Y        -0.716  -0.691  -0.692  -0.596  -0.542  -0.527  -0.827  -0.778  -0.762
80    W         0.676   0.631   0.510   0.976   0.917   0.688   0.638   0.561   0.314
81    N        -0.836  -0.832  -0.731  -0.870  -0.853  -0.697  -0.960  -0.936  -0.805
82    E        -0.518  -0.600  -0.653  -0.389  -0.505  -0.624  -0.560  -0.647  -0.713
83    A        -1.472  -1.502  -1.378  -1.476  -1.485  -1.308  -1.226  -1.227  -1.083
84    T        -1.154  -1.192  -1.079  -1.087  -1.133  -0.990  -1.093  -1.102  -0.965
85    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    M        -1.726  -1.626  -1.602  -1.506  -1.342  -1.325  -1.315  -1.213  -1.149
97    Q        -1.169  -1.122  -1.070  -1.183  -1.082  -1.019  -1.112  -1.042  -0.959
98    Y         1.334   1.372   1.423   1.401   1.457   1.538   1.437   1.489   1.569
99    N        -1.064  -1.004  -1.043  -0.864  -0.801  -0.816  -1.010  -0.948  -0.935
100   P        -0.613  -0.612  -0.669  -0.471  -0.536  -0.583  -0.704  -0.720  -0.739
101   M        -1.726  -1.715  -1.612  -1.622  -1.644  -1.460  -1.315  -1.287  -1.155
102   V         1.334   1.372   1.423   1.245   1.303   1.388   1.437   1.489   1.569
103   I         0.729   0.518   0.547   0.715   0.388   0.434   0.723   0.364   0.383
104   V        -0.786  -0.749  -0.707  -1.013  -0.954  -0.873  -0.908  -0.857  -0.780
105   D         0.272   0.344   0.358   0.142   0.273   0.272  -0.092   0.040   0.018
106   K        -1.343  -1.348  -1.328  -1.232  -1.290  -1.237  -1.112  -1.108  -1.044
107   R        -1.448  -1.354  -1.349  -1.370  -1.235  -1.223  -1.214  -1.115  -1.063
108   T        -0.786  -0.784  -0.722  -0.967  -0.937  -0.842  -0.908  -0.890  -0.796
109   E        -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   T        -1.448  -1.427  -1.352  -1.333  -1.271  -1.192  -1.214  -1.180  -1.066
113   V         1.334   1.372   1.423   1.245   1.303   1.388   1.437   1.489   1.569
114   A        -0.111  -0.250  -0.190  -0.251  -0.467  -0.376  -0.296  -0.469  -0.406
115   A         0.431   0.321   0.392   0.396   0.162   0.265   0.214  -0.005   0.085
116   T         0.153   0.217  -0.100   0.307   0.403  -0.070   0.112   0.209  -0.267
117   G         0.729   0.518   0.547   0.717   0.420   0.469   0.723   0.364   0.383
118   N        -1.064  -1.140  -1.053  -0.865  -0.963  -0.851  -1.010  -1.058  -0.942
119   I        -0.403  -0.368  -0.284  -0.841  -0.786  -0.646  -0.704  -0.647  -0.537
120   I        -0.786  -0.739  -0.713  -0.958  -0.856  -0.866  -0.908  -0.833  -0.787
121   I        -0.230  -0.349  -0.223  -0.549  -0.734  -0.528  -0.500  -0.620  -0.461
122   E         1.334   1.372   1.423   1.319   1.375   1.460   1.437   1.489   1.569
123   R         0.431   0.552   0.425   0.438   0.638   0.378   0.214   0.424   0.151
124   K         1.334   1.372   1.423   1.266   1.319   1.408   1.437   1.489   1.569
125   I        -0.891  -0.845  -0.750  -1.188  -1.060  -0.958  -1.010  -0.942  -0.823
126   I         0.729   0.518   0.547   0.715   0.384   0.434   0.723   0.364   0.383
127   H         0.729   0.518   0.547   0.972   0.669   0.714   0.723   0.364   0.383
128   E        -0.613  -0.667  -0.672  -0.663  -0.777  -0.731  -0.704  -0.769  -0.742
129   L        -0.613  -0.721  -0.670  -0.569  -0.773  -0.708  -0.704  -0.816  -0.740
130   G         0.729   0.763   0.535   0.717   0.766   0.449   0.723   0.774   0.360
131   L        -1.064  -1.086  -1.038  -1.117  -1.164  -1.077  -1.010  -1.015  -0.929
132   C        -0.230  -0.226  -0.229  -0.370  -0.334  -0.324  -0.500  -0.492  -0.471
133   G         1.334   1.372   1.423   1.257   1.310   1.400   1.437   1.489   1.569
134   H         1.334   1.372   1.423   1.508   1.555   1.642   1.437   1.489   1.569
135   I         1.334   1.372   1.423   1.282   1.327   1.424   1.437   1.489   1.569
136   E         1.334   1.372   1.423   1.319   1.375   1.460   1.437   1.489   1.569
137   D         0.729   0.518   0.547   0.820   0.514   0.546   0.723   0.364   0.383
138   I         0.729   0.518   0.547   0.715   0.388   0.434   0.723   0.364   0.383
139   A         0.153   0.023  -0.086   0.328   0.101  -0.047   0.112  -0.096  -0.247
140   V         0.729   0.748   0.541   0.682   0.717   0.399   0.723   0.751   0.371
141   N        -0.891  -0.933  -1.002  -0.617  -0.687  -0.775  -0.806  -0.853  -0.891
142   S        -0.111  -0.266  -0.198  -0.190  -0.382  -0.295  -0.296  -0.493  -0.419
143   K        -0.681  -0.615  -0.681  -0.726  -0.622  -0.701  -0.806  -0.716  -0.754
144   Y        -0.786  -0.774  -0.720  -0.813  -0.771  -0.685  -0.908  -0.883  -0.795
145   Q         1.334   1.372   1.423   1.477   1.546   1.612   1.437   1.489   1.569
146   G         0.729   0.518   0.547   0.722   0.431   0.481   0.723   0.364   0.383
147   Q         0.729   0.789   0.547   0.732   0.816   0.491   0.723   0.814   0.382
148   G        -0.389  -0.507  -0.601  -0.345  -0.529  -0.661  -0.398  -0.554  -0.650
149   L         0.729   0.518   0.547   0.682   0.358   0.410   0.723   0.364   0.383
150   G         1.334   1.372   1.423   1.257   1.310   1.400   1.437   1.489   1.569
151   K        -0.681  -0.567  -0.667  -0.893  -0.749  -0.821  -0.806  -0.677  -0.740
152   L        -1.448  -1.337  -1.347  -1.386  -1.257  -1.233  -1.214  -1.103  -1.061
153   L         0.272   0.253   0.346   0.051   0.035   0.178  -0.092  -0.141  -0.007
154   I         0.431   0.350   0.400   0.249   0.076   0.148   0.214   0.052   0.101
155   D        -1.726  -1.699  -1.607  -1.574  -1.560  -1.418  -1.315  -1.277  -1.152
156   Q        -1.726  -1.589  -1.599  -1.538  -1.304  -1.352  -1.315  -1.183  -1.147
157   L         1.334   1.372   1.423   1.245   1.291   1.388   1.437   1.489   1.569
158   V        -0.891  -0.967  -1.001  -0.785  -0.939  -1.002  -0.806  -0.888  -0.890
159   T        -1.064  -1.012  -1.035  -1.125  -1.024  -1.047  -1.010  -0.928  -0.927
160   I        -0.335  -0.321  -0.253  -0.682  -0.682  -0.571  -0.602  -0.581  -0.493
161   G         0.431   0.498   0.421   0.396   0.508   0.329   0.214   0.329   0.142
162   F        -1.064  -0.909  -1.037  -0.966  -0.729  -0.928  -1.010  -0.843  -0.930
163   D        -1.448  -1.468  -1.362  -1.336  -1.342  -1.178  -1.214  -1.208  -1.073
164   Y        -1.726  -1.711  -1.612  -1.672  -1.685  -1.519  -1.315  -1.285  -1.155
165   G         0.153   0.023  -0.086   0.186   0.000  -0.147   0.112  -0.096  -0.247
166   C         0.153  -0.038  -0.107   0.434   0.150   0.038   0.112  -0.173  -0.277
167   Y         1.334   1.372   1.423   1.401   1.457   1.538   1.437   1.489   1.569
168   K         1.334   1.372   1.423   1.266   1.319   1.408   1.437   1.489   1.569
169   I        -0.111  -0.045  -0.185  -0.288  -0.162  -0.407  -0.296  -0.181  -0.401
170   I         1.334   1.372   1.423   1.282   1.327   1.424   1.437   1.489   1.569
171   L         1.334   1.372   1.423   1.245   1.291   1.388   1.437   1.489   1.569
172   D         1.334   1.372   1.423   1.377   1.435   1.515   1.437   1.489   1.569
173   C         1.334   1.372   1.423   1.512   1.570   1.646   1.437   1.489   1.569
174   D         0.272   0.342   0.362   0.108   0.239   0.239  -0.092   0.036   0.026
175   E        -0.335  -0.335  -0.264  -0.457  -0.471  -0.354  -0.602  -0.603  -0.510
176   K        -1.064  -1.003  -1.037  -1.092  -1.011  -1.019  -1.010  -0.946  -0.929
177   N         1.334   1.372   1.423   1.481   1.545   1.616   1.437   1.489   1.569
178   V         0.729   0.748   0.541   0.688   0.724   0.411   0.723   0.751   0.371
179   K        -0.613  -0.522  -0.657  -0.719  -0.561  -0.751  -0.704  -0.570  -0.724
180   F         1.334   1.372   1.423   1.485   1.536   1.619   1.437   1.489   1.569
181   Y         1.334   1.372   1.423   1.401   1.457   1.538   1.437   1.489   1.569
182   E         0.729   0.748   0.541   0.752   0.786   0.458   0.723   0.751   0.371
183   K         1.334   1.372   1.423   1.266   1.319   1.408   1.437   1.489   1.569
184   C         1.334   1.372   1.423   1.512   1.570   1.646   1.437   1.489   1.569
185   G         1.334   1.372   1.423   1.257   1.310   1.400   1.437   1.489   1.569
186   F        -0.335  -0.370  -0.281  -0.470  -0.563  -0.411  -0.602  -0.646  -0.532
187   S        -0.111  -0.185  -0.201  -0.221  -0.355  -0.355  -0.296  -0.420  -0.425
188   N        -1.064  -0.924  -1.032  -0.913  -0.684  -0.868  -1.010  -0.844  -0.924
189   A        -0.389  -0.236  -0.604  -0.208   0.017  -0.569  -0.398  -0.192  -0.654
190   G         1.334   1.372   1.423   1.257   1.310   1.400   1.437   1.489   1.569
191   V        -0.389  -0.567  -0.616  -0.396  -0.688  -0.759  -0.398  -0.621  -0.669
192   E         1.334   1.372   1.423   1.319   1.375   1.460   1.437   1.489   1.569
193   M         1.334   1.372   1.423   1.524   1.600   1.658   1.437   1.489   1.569
194   Q        -0.681  -0.788  -0.689  -0.783  -0.936  -0.774  -0.806  -0.893  -0.762
195   I        -1.169  -1.147  -1.067  -1.257  -1.234  -1.089  -1.112  -1.066  -0.957
196   R        -0.111  -0.195  -0.209  -0.052  -0.226  -0.246  -0.296  -0.437  -0.436
197   K        -0.891  -0.996  -1.011  -0.684  -0.860  -0.928  -0.806  -0.914  -0.899
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   -        -1.249  -1.220  -1.101  -1.408  -1.356  -1.178  -1.173  -1.124  -0.984
* 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/P43577
Output conservation file - output/P43577
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
