1     M         1.485   1.491   1.546   1.773   1.783   1.868   1.614   1.622   1.701
2     P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    C         0.321   0.317   0.328   0.345   0.340   0.359   0.058   0.050   0.050
19    M        -0.254  -0.290  -0.354  -0.035  -0.075  -0.231  -0.347  -0.397  -0.479
20    S        -0.445  -0.416  -0.421  -0.527  -0.476  -0.480  -0.627  -0.592  -0.575
21    R         1.485   1.491   1.546   1.635   1.643   1.730   1.614   1.622   1.701
22    I         0.254   0.244   0.292  -0.196  -0.228  -0.153  -0.067  -0.086  -0.019
23    V        -0.953  -0.951  -0.942  -0.974  -0.972  -0.951  -0.907  -0.903  -0.868
24    K         1.485   1.491   1.546   1.609   1.620   1.705   1.614   1.622   1.701
25    E         1.485   1.491   1.546   1.484   1.490   1.581   1.614   1.622   1.701
26    Y         0.254   0.261   0.297   0.046   0.057   0.091  -0.067  -0.054  -0.010
27    K        -1.460  -1.454  -1.392  -1.307  -1.268  -1.193  -1.187  -1.178  -1.086
28    V        -1.052  -1.043  -0.985  -0.960  -0.940  -0.848  -1.012  -1.000  -0.912
29    I        -0.953  -0.986  -0.956  -1.086  -1.138  -1.075  -0.907  -0.940  -0.883
30    L        -0.953  -0.925  -0.933  -0.803  -0.749  -0.782  -0.907  -0.874  -0.859
31    K         0.570   0.539   0.451   0.693   0.649   0.498   0.493   0.442   0.275
32    T        -1.460  -1.454  -1.392  -1.181  -1.161  -1.068  -1.187  -1.178  -1.086
33    L         0.570   0.539   0.451   0.331   0.274   0.129   0.493   0.442   0.275
34    A        -0.953  -0.954  -0.937  -0.966  -0.963  -0.929  -0.907  -0.905  -0.862
35    S        -0.953  -0.946  -0.937  -0.757  -0.748  -0.709  -0.907  -0.897  -0.863
36    D        -1.460  -1.454  -1.392  -1.573  -1.576  -1.458  -1.187  -1.178  -1.086
37    D        -0.445  -0.447  -0.422  -0.615  -0.615  -0.556  -0.627  -0.624  -0.575
38    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    R        -1.460  -1.454  -1.392  -1.279  -1.267  -1.165  -1.187  -1.178  -1.086
45    G        -1.460  -1.454  -1.392  -1.429  -1.419  -1.314  -1.187  -1.178  -1.086
46    I        -1.460  -1.454  -1.392  -1.190  -1.175  -1.077  -1.187  -1.178  -1.086
47    I        -0.254  -0.239  -0.329  -0.460  -0.433  -0.608  -0.347  -0.327  -0.444
48    E        -0.445  -0.454  -0.419  -0.642  -0.657  -0.589  -0.627  -0.634  -0.573
49    S        -0.953  -0.955  -0.939  -0.875  -0.869  -0.841  -0.907  -0.907  -0.865
50    L         1.485   1.491   1.546   1.280   1.280   1.378   1.614   1.622   1.701
51    N        -0.953  -0.958  -0.944  -0.886  -0.886  -0.862  -0.907  -0.910  -0.870
52    P         1.485   1.491   1.546   1.470   1.480   1.567   1.614   1.622   1.701
53    I        -0.445  -0.450  -0.419  -0.797  -0.811  -0.764  -0.627  -0.630  -0.573
54    D        -0.254  -0.290  -0.354  -0.245  -0.299  -0.398  -0.347  -0.397  -0.479
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    E         0.570   0.608   0.463   0.562   0.621   0.384   0.493   0.556   0.295
57    T        -0.953  -0.915  -0.935  -0.933  -0.876  -0.892  -0.907  -0.863  -0.861
58    D        -0.254  -0.290  -0.354  -0.263  -0.322  -0.424  -0.347  -0.397  -0.479
59    L         0.570   0.558   0.455   0.331   0.303   0.135   0.493   0.473   0.281
60    S         0.254   0.244   0.292  -0.070  -0.104  -0.034  -0.067  -0.086  -0.019
61    K        -1.460  -1.454  -1.392  -1.610  -1.626  -1.495  -1.187  -1.178  -1.086
62    W         1.485   1.491   1.546   1.731   1.740   1.826   1.614   1.622   1.701
63    E        -0.254  -0.232  -0.336  -0.234  -0.210  -0.353  -0.347  -0.316  -0.454
64    A         0.570   0.549   0.451   0.692   0.679   0.528   0.493   0.458   0.274
65    I        -0.953  -0.954  -0.937  -0.963  -0.960  -0.930  -0.907  -0.905  -0.862
66    I         0.570   0.549   0.451   0.540   0.516   0.380   0.493   0.458   0.274
67    S        -1.460  -1.454  -1.392  -1.260  -1.237  -1.147  -1.187  -1.178  -1.086
68    G         0.570   0.558   0.455   0.728   0.708   0.547   0.493   0.473   0.281
69    P         0.570   0.539   0.451   0.573   0.530   0.393   0.493   0.442   0.275
70    S        -0.953  -0.951  -0.942  -0.880  -0.871  -0.852  -0.907  -0.903  -0.868
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    D        -0.445  -0.459  -0.420  -0.668  -0.690  -0.618  -0.627  -0.639  -0.574
74    T        -0.445  -0.456  -0.421  -0.454  -0.474  -0.407  -0.627  -0.635  -0.574
75    P         0.570   0.539   0.451   0.578   0.534   0.401   0.493   0.442   0.275
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    Y         0.570   0.549   0.451   0.803   0.776   0.630   0.493   0.458   0.274
78    E        -0.445  -0.459  -0.421  -0.543  -0.567  -0.502  -0.627  -0.639  -0.576
79    N        -0.953  -0.925  -0.933  -0.909  -0.867  -0.884  -0.907  -0.874  -0.859
80    H        -0.953  -0.920  -0.943  -0.693  -0.647  -0.659  -0.907  -0.868  -0.869
81    Q        -0.445  -0.459  -0.420  -0.448  -0.468  -0.392  -0.627  -0.639  -0.574
82    F        -0.445  -0.451  -0.426  -0.397  -0.412  -0.388  -0.627  -0.630  -0.581
83    R        -0.953  -0.962  -0.944  -0.950  -0.981  -0.945  -0.907  -0.915  -0.870
84    I         0.570   0.608   0.463   0.331   0.382   0.150   0.493   0.556   0.295
85    L        -1.460  -1.454  -1.392  -1.412  -1.379  -1.297  -1.187  -1.178  -1.086
86    I         1.485   1.491   1.546   1.403   1.415   1.500   1.614   1.622   1.701
87    E        -0.445  -0.447  -0.422  -0.486  -0.478  -0.424  -0.627  -0.624  -0.575
88    V        -0.254  -0.297  -0.353  -0.390  -0.476  -0.605  -0.347  -0.406  -0.477
89    P         0.570   0.549   0.451   0.544   0.513   0.346   0.493   0.458   0.274
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    S        -1.460  -1.454  -1.392  -1.446  -1.435  -1.331  -1.187  -1.178  -1.086
92    S        -0.254  -0.297  -0.353  -0.168  -0.232  -0.315  -0.347  -0.406  -0.477
93    Y         1.485   1.491   1.546   1.673   1.683   1.769   1.614   1.622   1.701
94    P         1.485   1.491   1.546   1.470   1.480   1.567   1.614   1.622   1.701
95    M        -0.445  -0.456  -0.421  -0.601  -0.625  -0.591  -0.627  -0.635  -0.574
96    N        -1.460  -1.454  -1.392  -1.330  -1.313  -1.216  -1.187  -1.178  -1.086
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    P         0.570   0.549   0.451   0.578   0.548   0.400   0.493   0.458   0.274
99    P         1.485   1.491   1.546   1.470   1.480   1.567   1.614   1.622   1.701
100   K        -0.254  -0.243  -0.336  -0.061  -0.046  -0.194  -0.347  -0.332  -0.454
101   I         0.570   0.549   0.451   0.482   0.453   0.290   0.493   0.458   0.274
102   S        -0.254  -0.243  -0.336  -0.249  -0.237  -0.419  -0.347  -0.332  -0.454
103   F         1.485   1.491   1.546   1.737   1.749   1.832   1.614   1.622   1.701
104   M        -0.953  -0.962  -0.944  -0.985  -1.005  -0.966  -0.907  -0.915  -0.870
105   Q        -0.953  -0.920  -0.943  -0.816  -0.766  -0.804  -0.907  -0.868  -0.869
106   N        -0.953  -0.920  -0.943  -0.969  -0.915  -0.938  -0.907  -0.868  -0.869
107   N        -0.953  -0.920  -0.943  -0.982  -0.927  -0.941  -0.907  -0.868  -0.869
108   I        -0.254  -0.184  -0.327  -0.284  -0.172  -0.413  -0.347  -0.248  -0.441
109   L         0.321   0.342   0.327   0.127   0.168   0.103   0.058   0.096   0.047
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   H         1.485   1.491   1.546   1.750   1.762   1.845   1.614   1.622   1.701
117   C        -0.445  -0.456  -0.421  -0.463  -0.480  -0.430  -0.627  -0.635  -0.574
118   N         1.485   1.491   1.546   1.654   1.666   1.750   1.614   1.622   1.701
119   V         0.570   0.558   0.455   0.562   0.542   0.359   0.493   0.473   0.281
120   K        -0.953  -0.951  -0.942  -0.891  -0.878  -0.876  -0.907  -0.903  -0.868
121   S        -0.953  -0.920  -0.943  -1.069  -1.030  -1.015  -0.907  -0.868  -0.869
122   A        -1.460  -1.454  -1.392  -1.317  -1.305  -1.203  -1.187  -1.178  -1.086
123   T         0.570   0.558   0.455   0.756   0.737   0.565   0.493   0.473   0.281
124   G         1.485   1.491   1.546   1.628   1.634   1.724   1.614   1.622   1.701
125   E         1.485   1.491   1.546   1.484   1.490   1.581   1.614   1.622   1.701
126   I         1.485   1.491   1.546   1.403   1.415   1.500   1.614   1.622   1.701
127   C         1.485   1.491   1.546   1.768   1.787   1.863   1.614   1.622   1.701
128   L         1.485   1.491   1.546   1.280   1.280   1.378   1.614   1.622   1.701
129   N         0.570   0.608   0.463   0.604   0.661   0.448   0.493   0.556   0.295
130   I         0.254   0.242   0.289  -0.196  -0.233  -0.162  -0.067  -0.090  -0.025
131   L         1.485   1.491   1.546   1.280   1.280   1.378   1.614   1.622   1.701
132   K         1.485   1.491   1.546   1.609   1.620   1.705   1.614   1.622   1.701
133   P         0.321   0.290   0.314   0.126   0.066   0.106   0.058  -0.001   0.023
134   E         0.570   0.549   0.451   0.557   0.522   0.359   0.493   0.458   0.274
135   E        -0.953  -0.915  -0.935  -0.955  -0.885  -0.926  -0.907  -0.863  -0.861
136   W         1.485   1.491   1.546   1.731   1.740   1.826   1.614   1.622   1.701
137   T         0.254   0.267   0.301   0.192   0.217   0.259  -0.067  -0.043  -0.003
138   P         1.485   1.491   1.546   1.470   1.480   1.567   1.614   1.622   1.701
139   V        -0.445  -0.424  -0.422  -0.683  -0.636  -0.635  -0.627  -0.600  -0.576
140   W         0.254   0.242   0.289   0.312   0.287   0.358  -0.067  -0.090  -0.025
141   D        -0.953  -0.986  -0.956  -0.915  -0.960  -0.899  -0.907  -0.940  -0.883
142   L        -0.254  -0.239  -0.329  -0.542  -0.526  -0.670  -0.347  -0.327  -0.444
143   L         0.570   0.558   0.455   0.352   0.324   0.168   0.493   0.473   0.281
144   H        -0.254  -0.297  -0.353  -0.070  -0.146  -0.269  -0.347  -0.406  -0.477
145   C        -0.445  -0.450  -0.419  -0.527  -0.533  -0.496  -0.627  -0.630  -0.573
146   V         1.485   1.491   1.546   1.510   1.518   1.607   1.614   1.622   1.701
147   H        -1.460  -1.454  -1.392  -1.181  -1.184  -1.068  -1.187  -1.178  -1.086
148   A         1.485   1.491   1.546   1.550   1.572   1.646   1.614   1.622   1.701
149   V         0.570   0.608   0.463   0.482   0.542   0.311   0.493   0.556   0.295
150   W        -0.953  -0.915  -0.935  -0.839  -0.794  -0.810  -0.907  -0.863  -0.861
151   R        -1.460  -1.454  -1.392  -1.516  -1.500  -1.400  -1.187  -1.178  -1.086
152   L         1.485   1.491   1.546   1.280   1.280   1.378   1.614   1.622   1.701
153   L         1.485   1.491   1.546   1.280   1.280   1.378   1.614   1.622   1.701
154   R        -1.460  -1.454  -1.392  -1.327  -1.323  -1.213  -1.187  -1.178  -1.086
155   E        -0.953  -0.986  -0.956  -0.867  -0.907  -0.842  -0.907  -0.940  -0.883
156   P         1.485   1.491   1.546   1.470   1.480   1.567   1.614   1.622   1.701
157   V        -0.445  -0.447  -0.422  -0.559  -0.559  -0.513  -0.627  -0.624  -0.575
158   C        -0.953  -0.962  -0.944  -1.103  -1.135  -1.092  -0.907  -0.915  -0.870
159   D         1.485   1.491   1.546   1.490   1.501   1.587   1.614   1.622   1.701
160   S         1.485   1.491   1.546   1.543   1.555   1.640   1.614   1.622   1.701
161   P         1.485   1.491   1.546   1.470   1.480   1.567   1.614   1.622   1.701
162   L         1.485   1.491   1.546   1.280   1.280   1.378   1.614   1.622   1.701
163   D         0.254   0.244   0.292   0.099   0.085   0.164  -0.067  -0.086  -0.019
164   V        -0.254  -0.283  -0.344  -0.390  -0.449  -0.586  -0.347  -0.386  -0.465
165   D         1.485   1.491   1.546   1.490   1.501   1.587   1.614   1.622   1.701
166   I        -0.953  -0.951  -0.942  -1.002  -0.993  -0.962  -0.907  -0.903  -0.868
167   G         0.570   0.608   0.463   0.656   0.724   0.494   0.493   0.556   0.295
168   N        -0.254  -0.297  -0.353  -0.065  -0.126  -0.221  -0.347  -0.406  -0.477
169   I         0.254   0.244   0.292  -0.196  -0.228  -0.153  -0.067  -0.086  -0.019
170   I        -0.445  -0.416  -0.415  -0.673  -0.619  -0.631  -0.627  -0.593  -0.569
171   R        -0.254  -0.232  -0.336  -0.140  -0.108  -0.285  -0.347  -0.316  -0.454
172   C        -0.525  -0.516  -0.460  -0.381  -0.339  -0.273  -0.720  -0.706  -0.622
173   G        -0.953  -0.946  -0.937  -0.778  -0.766  -0.745  -0.907  -0.897  -0.863
174   D         1.485   1.491   1.546   1.490   1.501   1.587   1.614   1.622   1.701
175   M        -0.953  -0.986  -0.956  -0.635  -0.669  -0.641  -0.907  -0.940  -0.883
176   S        -0.445  -0.451  -0.426  -0.620  -0.630  -0.585  -0.627  -0.630  -0.581
177   A         1.485   1.491   1.546   1.550   1.572   1.646   1.614   1.622   1.701
178   Y         0.570   0.539   0.451   0.758   0.716   0.561   0.493   0.442   0.275
179   Q        -1.460  -1.454  -1.392  -1.295  -1.297  -1.181  -1.187  -1.178  -1.086
180   G        -0.254  -0.283  -0.344  -0.090  -0.137  -0.230  -0.347  -0.386  -0.465
181   I         0.570   0.539   0.451   0.424   0.373   0.201   0.493   0.442   0.275
182   V         0.570   0.623   0.465   0.562   0.644   0.377   0.493   0.580   0.299
183   K        -0.953  -0.958  -0.944  -0.816  -0.829  -0.799  -0.907  -0.910  -0.870
184   Y        -0.254  -0.290  -0.354  -0.126  -0.194  -0.315  -0.347  -0.397  -0.479
185   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
186   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
192   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
194   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
195   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   F        -0.254  -0.297  -0.353   0.034  -0.031  -0.121  -0.347  -0.406  -0.477
197   L         0.254   0.244   0.292  -0.168  -0.193  -0.100  -0.067  -0.086  -0.019
198   A        -0.953  -0.915  -0.935  -0.925  -0.870  -0.883  -0.907  -0.863  -0.861
199   E         0.570   0.558   0.455   0.557   0.535   0.366   0.493   0.473   0.281
200   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
201   E        -0.417  -0.421  -0.407  -0.555  -0.555  -0.537  -0.574  -0.577  -0.551
202   R         0.456   0.458   0.402   0.538   0.545   0.441   0.301   0.303   0.186
203   I        -0.953  -0.986  -0.956  -1.159  -1.216  -1.161  -0.907  -0.940  -0.883
204   N        -1.460  -1.454  -1.392  -1.399  -1.385  -1.284  -1.187  -1.178  -1.086
205   N        -0.953  -0.962  -0.944  -0.854  -0.868  -0.825  -0.907  -0.915  -0.870
206   H        -1.460  -1.454  -1.392  -1.530  -1.533  -1.414  -1.187  -1.178  -1.086
* 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/P29340
Output conservation file - output/P29340
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
