1     M         1.685   1.685   1.728   1.964   1.965   2.026   1.799   1.799   1.860
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    C         0.216   0.220   0.183   0.425   0.431   0.352   0.032   0.038  -0.031
16    E        -0.850  -0.849  -0.804  -0.640  -0.629  -0.568  -0.852  -0.850  -0.780
17    S         0.216   0.235   0.190   0.259   0.293   0.200   0.032   0.063  -0.019
18    S        -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    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    N        -0.850  -0.849  -0.804  -0.720  -0.722  -0.648  -0.852  -0.850  -0.780
28    D        -0.714  -0.701  -0.752  -0.737  -0.698  -0.862  -0.686  -0.669  -0.719
29    I         0.387   0.352   0.299   0.456   0.406   0.330   0.308   0.253   0.162
30    V        -1.514  -1.512  -1.467  -1.219  -1.208  -1.145  -1.183  -1.181  -1.110
31    R        -0.714  -0.714  -0.745  -1.001  -1.004  -0.997  -0.686  -0.685  -0.710
32    L         0.387   0.425   0.274   0.382   0.440   0.209   0.308   0.367   0.120
33    S         1.685   1.685   1.728   1.659   1.664   1.723   1.799   1.799   1.860
34    Q        -0.714  -0.714  -0.745  -0.886  -0.891  -0.969  -0.686  -0.685  -0.710
35    A         0.387   0.370   0.254   0.567   0.542   0.334   0.308   0.281   0.087
36    M        -0.714  -0.701  -0.752  -0.479  -0.453  -0.576  -0.686  -0.669  -0.719
37    D         1.685   1.685   1.728   1.872   1.874   1.935   1.799   1.799   1.860
38    V        -0.714  -0.714  -0.745  -0.748  -0.756  -0.832  -0.686  -0.685  -0.710
39    L         0.387   0.352   0.299   0.347   0.296   0.203   0.308   0.253   0.162
40    A         1.685   1.685   1.728   1.837   1.839   1.900   1.799   1.799   1.860
41    K         1.685   1.685   1.728   1.180   1.182   1.245   1.799   1.799   1.860
42    L         0.387   0.370   0.254   0.347   0.324   0.126   0.308   0.281   0.087
43    I         0.085   0.086   0.132   0.017   0.017   0.084  -0.189  -0.189  -0.119
44    I        -0.714  -0.701  -0.752  -0.663  -0.637  -0.721  -0.686  -0.669  -0.719
45    S        -0.714  -0.746  -0.734  -0.647  -0.690  -0.675  -0.686  -0.725  -0.696
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    K         1.685   1.685   1.728   1.180   1.182   1.245   1.799   1.799   1.860
52    Q        -0.714  -0.746  -0.734  -0.450  -0.497  -0.471  -0.686  -0.725  -0.696
53    K        -0.714  -0.712  -0.731  -1.109  -1.101  -1.107  -0.686  -0.684  -0.693
54    D        -0.714  -0.701  -0.752  -0.504  -0.484  -0.584  -0.686  -0.669  -0.719
55    G         0.085   0.086   0.133   0.026   0.032   0.090  -0.189  -0.188  -0.116
56    S        -0.714  -0.701  -0.752  -0.621  -0.603  -0.672  -0.686  -0.669  -0.719
57    Q        -0.850  -0.850  -0.804  -0.832  -0.835  -0.760  -0.852  -0.851  -0.780
58    L         1.685   1.685   1.728   1.565   1.566   1.628   1.799   1.799   1.860
59    Q         0.216   0.207   0.204   0.074   0.053   0.004   0.032   0.017   0.004
60    V        -0.850  -0.850  -0.804  -1.111  -1.117  -1.038  -0.852  -0.851  -0.780
61    E         0.216   0.210   0.201   0.206   0.197   0.183   0.032   0.022  -0.001
62    Y         1.685   1.685   1.728   2.003   2.004   2.065   1.799   1.799   1.860
63    E         0.216   0.210   0.201   0.212   0.205   0.191   0.032   0.022  -0.001
64    H        -0.850  -0.850  -0.804  -0.654  -0.656  -0.582  -0.852  -0.851  -0.780
65    K         1.685   1.685   1.728   1.202   1.203   1.267   1.799   1.799   1.860
66    L         1.685   1.685   1.728   1.565   1.566   1.628   1.799   1.799   1.860
67    K         0.216   0.210   0.201  -0.150  -0.156  -0.143   0.032   0.022  -0.001
68    E        -0.850  -0.850  -0.804  -0.796  -0.793  -0.723  -0.852  -0.851  -0.780
69    L        -0.850  -0.850  -0.804  -0.906  -0.901  -0.834  -0.852  -0.851  -0.780
70    E        -0.850  -0.850  -0.804  -0.698  -0.693  -0.626  -0.852  -0.851  -0.780
71    K         0.216   0.207   0.204  -0.318  -0.332  -0.333   0.032   0.017   0.004
72    F        -0.850  -0.850  -0.804  -0.569  -0.573  -0.497  -0.852  -0.851  -0.780
73    I         1.685   1.685   1.728   1.625   1.626   1.689   1.799   1.799   1.860
74    N        -0.850  -0.850  -0.804  -0.851  -0.854  -0.778  -0.852  -0.851  -0.780
75    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    G         0.216   0.232   0.206   0.212   0.237   0.202   0.032   0.059   0.007
79    L        -0.850  -0.850  -0.804  -0.906  -0.901  -0.834  -0.852  -0.851  -0.780
80    H        -0.850  -0.850  -0.804  -0.778  -0.782  -0.705  -0.852  -0.851  -0.780
81    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    M        -0.850  -0.850  -0.804  -0.689  -0.691  -0.617  -0.852  -0.851  -0.780
89    N        -0.850  -0.850  -0.804  -0.535  -0.534  -0.464  -0.852  -0.851  -0.780
90    T        -0.850  -0.850  -0.804  -1.214  -1.221  -1.140  -0.852  -0.851  -0.780
91    S         0.216   0.232   0.206   0.095   0.124   0.064   0.032   0.059   0.007
92    V        -0.850  -0.850  -0.804  -0.992  -0.999  -0.919  -0.852  -0.851  -0.780
93    L         0.216   0.207   0.204   0.206   0.195   0.202   0.032   0.017   0.004
94    D        -0.850  -0.850  -0.804  -0.860  -0.863  -0.787  -0.852  -0.851  -0.780
95    M        -0.850  -0.850  -0.804  -0.897  -0.906  -0.824  -0.852  -0.851  -0.780
96    V        -0.850  -0.850  -0.804  -0.527  -0.523  -0.456  -0.852  -0.851  -0.780
97    L         0.216   0.232   0.206   0.039   0.069   0.004   0.032   0.059   0.007
98    R         0.216   0.232   0.206   0.239   0.262   0.233   0.032   0.059   0.007
99    N         0.216   0.232   0.206  -0.210  -0.190  -0.208   0.032   0.059   0.007
100   G        -0.850  -0.850  -0.804  -0.519  -0.519  -0.447  -0.852  -0.851  -0.780
101   I         1.685   1.685   1.728   1.625   1.626   1.689   1.799   1.799   1.860
102   E         1.685   1.685   1.728   1.655   1.656   1.718   1.799   1.799   1.860
103   I         0.216   0.210   0.201   0.226   0.218   0.212   0.032   0.022  -0.001
104   M        -0.850  -0.850  -0.804  -0.611  -0.614  -0.540  -0.852  -0.851  -0.780
105   E        -0.850  -0.850  -0.804  -0.654  -0.649  -0.582  -0.852  -0.851  -0.780
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   K         0.085   0.088   0.131  -0.393  -0.369  -0.321  -0.189  -0.185  -0.120
115   D         0.085   0.088   0.131   0.034   0.034   0.103  -0.189  -0.185  -0.120
116   D        -1.514  -1.512  -1.467  -1.337  -1.346  -1.262  -1.183  -1.181  -1.110
117   Q         0.387   0.370   0.254   0.499   0.473   0.270   0.308   0.281   0.087
118   K        -1.514  -1.512  -1.467  -1.553  -1.534  -1.478  -1.183  -1.181  -1.110
119   Y        -0.714  -0.746  -0.734  -0.181  -0.229  -0.206  -0.686  -0.725  -0.696
120   A        -0.714  -0.746  -0.734  -0.544  -0.597  -0.589  -0.686  -0.725  -0.696
121   L         0.387   0.352   0.299   0.410   0.363   0.285   0.308   0.253   0.162
122   I         0.387   0.352   0.299   0.429   0.377   0.294   0.308   0.253   0.162
123   P         1.685   1.685   1.728   1.895   1.893   1.958   1.799   1.799   1.860
124   I        -1.514  -1.512  -1.467  -1.575  -1.583  -1.500  -1.183  -1.181  -1.110
125   K        -0.714  -0.725  -0.729  -0.694  -0.701  -0.738  -0.686  -0.699  -0.690
126   A        -1.514  -1.512  -1.467  -1.391  -1.404  -1.316  -1.183  -1.181  -1.110
127   K        -0.714  -0.714  -0.745  -0.858  -0.855  -0.955  -0.686  -0.685  -0.710
128   E        -0.714  -0.714  -0.745  -0.430  -0.429  -0.489  -0.686  -0.685  -0.710
129   E        -0.850  -0.850  -0.804  -1.214  -1.219  -1.140  -0.852  -0.851  -0.780
130   A        -0.850  -0.850  -0.804  -1.002  -1.006  -0.929  -0.852  -0.851  -0.780
131   D        -0.850  -0.850  -0.804  -0.486  -0.483  -0.415  -0.852  -0.851  -0.780
132   K         0.216   0.210   0.201  -0.202  -0.210  -0.204   0.032   0.022  -0.001
133   T         0.216   0.207   0.204   0.339   0.327   0.329   0.032   0.017   0.004
134   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   I        -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   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   K        -0.714  -0.701  -0.752  -1.036  -1.024  -1.043  -0.686  -0.669  -0.719
152   S        -0.714  -0.714  -0.745  -1.066  -1.061  -1.072  -0.686  -0.685  -0.710
153   S        -0.714  -0.678  -0.733  -1.001  -0.961  -0.988  -0.686  -0.640  -0.695
154   K         0.387   0.370   0.254  -0.040  -0.063  -0.220   0.308   0.281   0.087
155   K         0.387   0.425   0.274  -0.080  -0.023  -0.248   0.308   0.367   0.120
156   K         1.685   1.685   1.728   1.180   1.182   1.245   1.799   1.799   1.860
157   K         0.387   0.425   0.274  -0.014   0.037  -0.157   0.308   0.367   0.120
158   N         0.387   0.370   0.254   0.604   0.576   0.383   0.308   0.281   0.087
159   K         0.085   0.086   0.133  -0.326  -0.333  -0.229  -0.189  -0.188  -0.116
160   I         1.685   1.685   1.728   1.659   1.660   1.723   1.799   1.799   1.860
161   K        -0.714  -0.746  -0.734  -0.908  -0.935  -0.886  -0.686  -0.725  -0.696
162   C         1.685   1.685   1.728   1.941   1.941   2.003   1.799   1.799   1.860
163   S         1.685   1.685   1.728   1.659   1.664   1.723   1.799   1.799   1.860
164   F         0.387   0.405   0.276   0.841   0.865   0.685   0.308   0.336   0.124
165   C         1.685   1.685   1.728   1.941   1.941   2.003   1.799   1.799   1.860
166   H        -0.714  -0.714  -0.745  -0.616  -0.626  -0.695  -0.686  -0.685  -0.710
167   E         0.387   0.370   0.254   0.495   0.474   0.316   0.308   0.281   0.087
168   A        -0.714  -0.725  -0.729  -0.494  -0.513  -0.510  -0.686  -0.699  -0.690
169   G         1.685   1.685   1.728   1.907   1.908   1.969   1.799   1.799   1.860
170   H         1.685   1.685   1.728   1.975   1.975   2.038   1.799   1.799   1.860
171   T         0.387   0.425   0.274   0.460   0.517   0.262   0.308   0.367   0.120
172   R         1.685   1.685   1.728   1.975   1.976   2.038   1.799   1.799   1.860
173   A         0.387   0.425   0.274   0.567   0.628   0.370   0.308   0.367   0.120
174   H        -0.714  -0.725  -0.729  -0.846  -0.855  -0.815  -0.686  -0.699  -0.690
175   C         1.685   1.685   1.728   1.941   1.941   2.003   1.799   1.799   1.860
176   G        -1.514  -1.512  -1.467  -1.041  -1.032  -0.967  -1.183  -1.181  -1.110
177   A         0.387   0.405   0.276  -0.014   0.011  -0.153   0.308   0.336   0.124
178   R         0.085   0.086   0.132  -0.223  -0.223  -0.136  -0.189  -0.189  -0.119
179   L         1.685   1.685   1.728   1.611   1.615   1.674   1.799   1.799   1.860
180   T        -1.514  -1.512  -1.467  -1.213  -1.201  -1.139  -1.183  -1.181  -1.110
181   V        -0.850  -0.849  -0.804  -0.740  -0.744  -0.668  -0.852  -0.850  -0.780
182   I        -0.714  -0.701  -0.752  -0.606  -0.590  -0.654  -0.686  -0.669  -0.719
183   P         0.387   0.352   0.299   0.689   0.636   0.556   0.308   0.253   0.162
184   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
185   K        -1.514  -1.512  -1.467  -1.495  -1.492  -1.420  -1.183  -1.181  -1.110
* 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/P40083
Output conservation file - output/P40083
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
