1     M         0.928   0.940   0.996   1.291   1.291   1.330   0.967   0.985   1.068
2     P        -1.161  -1.127  -1.254  -0.937  -0.936  -1.121  -1.129  -1.099  -1.202
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     G         0.928   0.940   0.996   0.699   0.739   0.857   0.967   0.985   1.068
5     V         0.928   0.940   0.996   0.771   0.781   0.915   0.967   0.985   1.068
6     S         0.069  -0.194  -0.387   0.275  -0.034  -0.335   0.129  -0.235  -0.565
7     V         0.928   0.940   0.996   0.771   0.781   0.915   0.967   0.985   1.068
8     R        -0.376  -0.401  -0.396  -0.572  -0.622  -0.622  -0.500  -0.546  -0.579
9     D         0.928   0.940   0.996   0.988   0.998   1.088   0.967   0.985   1.068
10    V         0.928   0.940   0.996   0.771   0.781   0.915   0.967   0.985   1.068
11    A        -2.206  -2.222  -1.894  -2.135  -2.163  -1.762  -1.967  -1.938  -1.541
12    A         0.069  -0.194  -0.387   0.086  -0.223  -0.507   0.129  -0.235  -0.565
13    Q         0.069  -0.194  -0.387   0.324   0.002  -0.300   0.129  -0.235  -0.565
14    D        -2.062  -1.909  -1.863  -2.040  -1.867  -1.732  -1.862  -1.699  -1.514
15    F         0.928   0.940   0.996   1.250   1.258   1.297   0.967   0.985   1.068
16    I         0.069  -0.194  -0.387   0.282  -0.076  -0.480   0.129  -0.235  -0.565
17    N        -0.755  -0.735  -1.217  -0.239  -0.207  -0.952  -0.605  -0.581  -1.158
18    A         0.069   0.221  -0.360   0.095   0.286  -0.441   0.129   0.319  -0.522
19    Y         0.928   0.940   0.996   1.131   1.148   1.202   0.967   0.985   1.068
20    A         0.928   0.940   0.996   0.793   0.832   0.932   0.967   0.985   1.068
21    S        -1.683  -1.513  -1.295  -1.958  -1.726  -1.382  -1.758  -1.556  -1.250
22    F         0.928   0.940   0.996   1.250   1.258   1.297   0.967   0.985   1.068
23    L         0.928   0.940   0.996   0.908   0.943   1.024   0.967   0.985   1.068
24    Q        -0.763  -0.687  -0.442  -1.060  -0.953  -0.564  -1.129  -1.014  -0.657
25    R         0.928   0.940   0.996   0.776   0.796   0.919   0.967   0.985   1.068
26    Q        -0.376  -0.401  -0.396  -0.320  -0.366  -0.426  -0.500  -0.546  -0.579
27    G         0.928   0.940   0.996   0.699   0.739   0.857   0.967   0.985   1.068
28    K         0.928   0.940   0.996   0.902   0.926   1.019   0.967   0.985   1.068
29    L        -0.376  -0.401  -0.396  -0.332  -0.357  -0.359  -0.500  -0.546  -0.579
30    E        -1.161  -1.390  -1.279  -0.942  -1.253  -1.108  -1.129  -1.385  -1.231
31    V        -0.376  -0.401  -0.396  -0.483  -0.538  -0.482  -0.500  -0.546  -0.579
32    P         0.928   0.940   0.996   1.105   1.117   1.181   0.967   0.985   1.068
33    G        -0.376  -0.401  -0.396  -0.616  -0.640  -0.626  -0.500  -0.546  -0.579
34    Y        -0.639  -0.681  -0.455  -0.507  -0.588  -0.275  -0.919  -1.003  -0.678
35    V        -0.376  -0.401  -0.396  -0.540  -0.592  -0.569  -0.500  -0.546  -0.579
36    D         0.069   0.135  -0.369   0.265   0.336  -0.391   0.129   0.212  -0.536
37    I         0.069  -0.194  -0.387   0.339   0.020  -0.292   0.129  -0.235  -0.565
38    V         0.928   0.940   0.996   0.771   0.781   0.915   0.967   0.985   1.068
39    K         0.928   0.940   0.996   0.902   0.926   1.019   0.967   0.985   1.068
40    T         0.928   0.940   0.996   1.224   1.213   1.277   0.967   0.985   1.068
41    S        -0.639  -0.681  -0.455  -0.938  -1.069  -0.727  -0.919  -1.003  -0.678
42    S        -1.900  -1.990  -1.887  -1.763  -1.877  -1.691  -1.653  -1.739  -1.534
43    G        -1.161  -1.390  -1.279  -1.257  -1.569  -1.397  -1.129  -1.385  -1.231
44    N        -0.639  -0.681  -0.455  -0.661  -0.793  -0.490  -0.919  -1.003  -0.678
45    E         0.069   0.205  -0.360   0.256   0.419  -0.380   0.129   0.300  -0.522
46    M        -0.639  -0.613  -0.451  -0.719  -0.671  -0.422  -0.919  -0.888  -0.672
47    P        -0.376  -0.401  -0.396  -0.279  -0.341  -0.436  -0.500  -0.546  -0.579
48    P         0.928   0.940   0.996   1.105   1.117   1.181   0.967   0.985   1.068
49    Q        -0.376  -0.401  -0.396  -0.274  -0.317  -0.356  -0.500  -0.546  -0.579
50    D        -0.376  -0.176  -0.393  -0.343  -0.060  -0.435  -0.500  -0.209  -0.575
51    A        -2.299  -2.304  -1.894  -2.401  -2.342  -1.777  -2.072  -2.015  -1.541
52    E        -0.639  -0.681  -0.455  -0.796  -0.905  -0.553  -0.919  -1.003  -0.678
53    G        -0.639  -0.536  -0.448  -0.925  -0.767  -0.564  -0.919  -0.763  -0.666
54    W         0.928   0.940   0.996   1.321   1.318   1.355   0.967   0.985   1.068
55    F        -0.639  -0.577  -0.447  -0.486  -0.406  -0.296  -0.919  -0.829  -0.665
56    Y         0.928   0.940   0.996   1.131   1.148   1.202   0.967   0.985   1.068
57    K        -1.378  -1.328  -1.285  -1.547  -1.551  -1.301  -1.443  -1.395  -1.240
58    R         0.928   0.940   0.996   0.776   0.796   0.919   0.967   0.985   1.068
59    A         0.928   0.940   0.996   0.793   0.832   0.932   0.967   0.985   1.068
60    A         0.928   0.940   0.996   0.793   0.832   0.932   0.967   0.985   1.068
61    S        -0.376  -0.401  -0.396  -0.415  -0.453  -0.535  -0.500  -0.546  -0.579
62    V        -0.763  -0.689  -0.455  -1.173  -1.054  -0.648  -1.129  -1.016  -0.678
63    A         0.928   0.940   0.996   0.793   0.832   0.932   0.967   0.985   1.068
64    R         0.928   0.940   0.996   0.776   0.796   0.919   0.967   0.985   1.068
65    H         0.928   0.940   0.996   1.229   1.227   1.281   0.967   0.985   1.068
66    I         0.069  -0.194  -0.387   0.282  -0.076  -0.480   0.129  -0.235  -0.565
67    Y         0.928   0.940   0.996   1.131   1.148   1.202   0.967   0.985   1.068
68    M         0.069   0.202  -0.362   0.225   0.387  -0.312   0.129   0.296  -0.524
69    R         0.928   0.940   0.996   0.776   0.796   0.919   0.967   0.985   1.068
70    K         0.928   0.940   0.996   0.902   0.926   1.019   0.967   0.985   1.068
71    Q        -1.161  -1.250  -1.267  -0.966  -1.054  -1.132  -1.129  -1.205  -1.218
72    V         0.928   0.940   0.996   0.771   0.781   0.915   0.967   0.985   1.068
73    G         0.928   0.940   0.996   0.699   0.739   0.857   0.967   0.985   1.068
74    V         0.928   0.940   0.996   0.771   0.781   0.915   0.967   0.985   1.068
75    G         0.928   0.940   0.996   0.699   0.739   0.857   0.967   0.985   1.068
76    K        -1.378  -1.279  -1.283  -1.636  -1.568  -1.502  -1.443  -1.356  -1.238
77    L         0.928   0.940   0.996   0.908   0.943   1.024   0.967   0.985   1.068
78    N        -1.161  -1.390  -1.279  -0.767  -1.112  -1.070  -1.129  -1.385  -1.231
79    K         0.069  -0.194  -0.387   0.154  -0.203  -0.571   0.129  -0.235  -0.565
80    L        -0.639  -0.681  -0.455  -0.961  -1.092  -0.721  -0.919  -1.003  -0.678
81    Y         0.069  -0.194  -0.387   0.439   0.113  -0.221   0.129  -0.235  -0.565
82    G         0.928   0.940   0.996   0.699   0.739   0.857   0.967   0.985   1.068
83    G        -0.755  -0.846  -1.240  -0.675  -0.787  -1.205  -0.605  -0.743  -1.186
84    A        -0.376  -0.401  -0.396  -0.537  -0.562  -0.582  -0.500  -0.546  -0.579
85    K        -1.900  -1.727  -1.865  -1.862  -1.675  -1.838  -1.653  -1.485  -1.514
86    S        -0.376  -0.177  -0.392  -0.171   0.133  -0.313  -0.500  -0.210  -0.574
87    R         0.928   0.940   0.996   0.776   0.796   0.919   0.967   0.985   1.068
88    G         0.928   0.940   0.996   0.699   0.739   0.857   0.967   0.985   1.068
89    V        -3.343  -3.157  -2.752  -2.947  -2.693  -2.253  -2.491  -2.302  -1.840
90    R         0.928   0.940   0.996   0.776   0.796   0.919   0.967   0.985   1.068
91    P         0.928   0.940   0.996   1.105   1.117   1.181   0.967   0.985   1.068
92    Y        -1.378  -1.105  -1.249  -1.278  -0.898  -1.061  -1.443  -1.093  -1.197
93    K        -0.763  -0.612  -0.429  -0.886  -0.606  -0.378  -1.129  -0.887  -0.634
94    H         0.928   0.940   0.996   1.229   1.227   1.281   0.967   0.985   1.068
95    I        -2.585  -2.322  -2.344  -2.676  -2.364  -2.329  -2.072  -1.832  -1.705
96    D         0.069  -0.194  -0.387   0.265  -0.085  -0.425   0.129  -0.235  -0.565
97    A        -0.376  -0.401  -0.396  -0.613  -0.650  -0.701  -0.500  -0.546  -0.579
98    S         0.928   0.940   0.996   0.967   1.002   1.071   0.967   0.985   1.068
99    G         0.928   0.940   0.996   0.699   0.739   0.857   0.967   0.985   1.068
100   S         0.928   0.940   0.996   0.967   1.002   1.071   0.967   0.985   1.068
101   I        -0.763  -0.611  -0.431  -1.173  -0.935  -0.623  -1.129  -0.886  -0.637
102   N        -1.161  -1.390  -1.279  -0.847  -1.188  -1.136  -1.129  -1.385  -1.231
103   R         0.928   0.940   0.996   0.776   0.796   0.919   0.967   0.985   1.068
104   K        -0.639  -0.463  -0.430  -0.963  -0.650  -0.662  -0.919  -0.644  -0.637
105   V        -0.755  -0.574  -1.221  -0.636  -0.437  -1.223  -0.605  -0.392  -1.163
106   L        -0.639  -0.587  -0.448  -0.961  -0.883  -0.702  -0.919  -0.846  -0.667
107   Q         0.928   0.940   0.996   1.015   1.035   1.109   0.967   0.985   1.068
108   A        -0.763  -0.676  -0.453  -1.198  -1.032  -0.674  -1.129  -0.995  -0.674
109   L         0.928   0.940   0.996   0.908   0.943   1.024   0.967   0.985   1.068
110   E         0.069   0.205  -0.360   0.259   0.423  -0.370   0.129   0.300  -0.522
111   K         0.928   0.940   0.996   0.902   0.926   1.019   0.967   0.985   1.068
112   I        -0.376  -0.236  -0.416  -0.320  -0.103  -0.481  -0.500  -0.297  -0.613
113   G         0.928   0.940   0.996   0.699   0.739   0.857   0.967   0.985   1.068
114   I         0.069   0.202  -0.362   0.055   0.200  -0.514   0.129   0.296  -0.524
115   V        -0.639  -0.442  -0.415  -0.961  -0.602  -0.626  -0.919  -0.612  -0.611
116   E         0.928   0.940   0.996   0.977   1.002   1.080   0.967   0.985   1.068
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   I        -2.585  -2.558  -2.364  -2.380  -2.401  -2.184  -2.072  -2.032  -1.720
119   S        -0.755  -0.944  -1.248  -0.511  -0.762  -1.334  -0.605  -0.847  -1.195
120   P        -1.900  -2.036  -1.892  -1.598  -1.846  -1.707  -1.653  -1.777  -1.539
121   K        -0.376  -0.401  -0.396  -0.373  -0.405  -0.417  -0.500  -0.546  -0.579
122   G         0.928   0.940   0.996   0.699   0.739   0.857   0.967   0.985   1.068
123   G         0.928   0.940   0.996   0.699   0.739   0.857   0.967   0.985   1.068
124   R         0.928   0.940   0.996   0.776   0.796   0.919   0.967   0.985   1.068
125   R         0.069   0.243  -0.359   0.044   0.246  -0.558   0.129   0.345  -0.520
126   I         0.928   0.940   0.996   1.031   1.057   1.122   0.967   0.985   1.068
127   S         0.069  -0.194  -0.387   0.275  -0.034  -0.335   0.129  -0.235  -0.565
128   E        -1.378  -1.268  -1.283  -1.407  -1.302  -1.252  -1.443  -1.347  -1.237
129   N        -0.639  -0.681  -0.455  -0.612  -0.726  -0.427  -0.919  -1.003  -0.678
130   G         0.928   0.940   0.996   0.699   0.739   0.857   0.967   0.985   1.068
131   Q         0.069   0.221  -0.360   0.283   0.463  -0.384   0.129   0.319  -0.522
132   R         0.928   0.940   0.996   0.776   0.796   0.919   0.967   0.985   1.068
133   D         0.928   0.940   0.996   0.988   0.998   1.088   0.967   0.985   1.068
134   L         0.928   0.940   0.996   0.908   0.943   1.024   0.967   0.985   1.068
135   D         0.928   0.940   0.996   0.988   0.998   1.088   0.967   0.985   1.068
136   R         0.928   0.940   0.996   0.776   0.796   0.919   0.967   0.985   1.068
137   I         0.928   0.940   0.996   1.031   1.057   1.122   0.967   0.985   1.068
138   A         0.928   0.940   0.996   0.793   0.832   0.932   0.967   0.985   1.068
139   A        -1.161  -1.390  -1.279  -1.163  -1.457  -1.291  -1.129  -1.385  -1.231
140   Q        -1.900  -1.976  -1.886  -1.665  -1.784  -1.698  -1.653  -1.729  -1.534
141   T        -1.161  -1.390  -1.279  -0.858  -1.271  -1.235  -1.129  -1.385  -1.231
142   L         0.069  -0.194  -0.387   0.191  -0.127  -0.459   0.129  -0.235  -0.565
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   E         0.928   0.940   0.996   0.977   1.002   1.080   0.967   0.985   1.068
148   E        -0.639  -0.522  -0.444  -0.791  -0.607  -0.531  -0.919  -0.739  -0.659
149   D        -0.763  -0.676  -0.453  -1.033  -0.895  -0.550  -1.129  -0.995  -0.675
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   E         0.928   0.940   0.996   0.977   1.002   1.080   0.967   0.985   1.068
* 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/P07280
Output conservation file - output/P07280
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
