1     M         1.578   1.603   1.678   1.673   1.711   1.821   1.720   1.756   1.871
2     V         0.818   0.692   0.616   1.028   0.855   0.728   0.826   0.616   0.453
3     L         0.818   0.692   0.616   0.579   0.419   0.305   0.826   0.616   0.453
4     P         0.818   0.692   0.616   0.998   0.824   0.677   0.826   0.616   0.453
5     I         1.578   1.603   1.678   1.499   1.540   1.651   1.720   1.756   1.871
6     I        -0.192  -0.281  -0.223  -0.325  -0.471  -0.404  -0.365  -0.473  -0.400
7     I        -0.192  -0.267  -0.234  -0.325  -0.449  -0.422  -0.365  -0.452  -0.414
8     G         1.578   1.603   1.678   1.589   1.615   1.739   1.720   1.756   1.871
9     L        -0.281  -0.229  -0.248  -0.573  -0.462  -0.505  -0.514  -0.449  -0.438
10    G         1.578   1.603   1.678   1.589   1.615   1.739   1.720   1.756   1.871
11    V        -0.420  -0.417  -0.314  -0.580  -0.593  -0.452  -0.663  -0.657  -0.517
12    T         0.818   0.692   0.616   0.992   0.817   0.672   0.826   0.616   0.453
13    M        -1.291  -1.279  -1.221  -1.498  -1.488  -1.357  -1.110  -1.091  -0.982
14    V        -0.558  -0.593  -0.710  -0.303  -0.353  -0.578  -0.514  -0.559  -0.676
15    A         1.578   1.603   1.678   1.499   1.517   1.651   1.720   1.756   1.871
16    L        -0.558  -0.583  -0.718  -0.638  -0.692  -0.807  -0.514  -0.548  -0.686
17    S        -1.153  -1.167  -1.175  -0.886  -0.936  -0.952  -0.961  -0.973  -0.938
18    V        -1.153  -1.166  -1.175  -1.109  -1.164  -1.166  -0.961  -0.972  -0.938
19    K        -0.192  -0.130  -0.218  -0.280  -0.198  -0.293  -0.365  -0.282  -0.390
20    S        -0.192  -0.292  -0.230  -0.254  -0.423  -0.350  -0.365  -0.489  -0.408
21    G        -0.192  -0.123  -0.216  -0.195  -0.099  -0.244  -0.365  -0.271  -0.384
22    L        -0.192  -0.271  -0.236  -0.549  -0.629  -0.578  -0.365  -0.458  -0.413
23    N        -1.153  -1.158  -1.184  -0.894  -0.898  -0.936  -0.961  -0.963  -0.946
24    A         1.578   1.603   1.678   1.499   1.517   1.651   1.720   1.756   1.871
25    W        -0.786  -0.861  -0.784  -0.387  -0.478  -0.391  -0.812  -0.879  -0.765
26    T        -1.658  -1.584  -1.544  -1.408  -1.316  -1.247  -1.259  -1.185  -1.098
27    V        -1.153  -1.078  -1.154  -1.027  -0.917  -1.018  -0.961  -0.875  -0.918
28    Y         1.578   1.603   1.678   1.760   1.797   1.907   1.720   1.756   1.871
29    K        -1.291  -1.235  -1.211  -1.373  -1.280  -1.200  -1.110  -1.051  -0.974
30    T        -1.658  -1.669  -1.564  -1.453  -1.460  -1.346  -1.259  -1.257  -1.113
31    L         0.818   0.814   0.631   0.594   0.601   0.360   0.826   0.817   0.481
32    S        -0.028  -0.098  -0.169   0.162   0.054  -0.074  -0.105  -0.217  -0.312
33    P         0.744   0.588   0.595   0.917   0.695   0.682   0.706   0.436   0.415
34    L        -0.884  -0.832  -0.802  -1.084  -0.987  -0.928  -0.916  -0.852  -0.784
35    T        -0.028  -0.098  -0.169   0.213   0.114  -0.004  -0.105  -0.217  -0.312
36    I         0.744   0.588   0.595   0.671   0.436   0.422   0.706   0.436   0.415
37    A         1.578   1.603   1.678   1.500   1.512   1.652   1.720   1.756   1.871
38    K        -1.739  -1.697  -1.585  -1.477  -1.369  -1.260  -1.321  -1.276  -1.128
39    L        -0.028   0.061  -0.163  -0.173  -0.042  -0.321  -0.105   0.023  -0.302
40    N         1.578   1.603   1.678   1.637   1.671   1.786   1.720   1.756   1.871
41    N         0.651   0.676   0.554   0.742   0.779   0.574   0.552   0.589   0.339
42    I         1.578   1.603   1.678   1.454   1.486   1.607   1.720   1.756   1.871
43    R        -0.375  -0.367  -0.285  -0.516  -0.499  -0.367  -0.616  -0.599  -0.482
44    I         0.332   0.353   0.431  -0.250  -0.219  -0.096  -0.032   0.000   0.103
45    E        -1.402  -1.387  -1.253  -1.308  -1.285  -1.095  -1.199  -1.175  -1.008
46    N         0.537   0.586   0.517   0.539   0.615   0.477   0.351   0.433   0.268
47    P        -0.347  -0.343  -0.281  -0.411  -0.405  -0.343  -0.561  -0.554  -0.470
48    T        -0.347  -0.343  -0.281  -0.327  -0.320  -0.244  -0.561  -0.554  -0.470
49    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    A        -0.889  -0.887  -0.820  -1.037  -1.039  -0.962  -0.907  -0.898  -0.800
55    L        -0.889  -0.861  -0.803  -0.940  -0.884  -0.837  -0.907  -0.869  -0.782
56    K        -0.889  -0.887  -0.820  -0.871  -0.856  -0.748  -0.907  -0.898  -0.800
57    F        -0.182  -0.170  -0.240   0.073   0.093  -0.063  -0.324  -0.305  -0.413
58    K        -0.889  -0.871  -0.805  -0.889  -0.857  -0.787  -0.907  -0.880  -0.784
59    S        -0.182  -0.170  -0.240  -0.107  -0.088  -0.222  -0.324  -0.305  -0.413
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    S        -0.889  -0.868  -0.825  -0.755  -0.720  -0.674  -0.907  -0.877  -0.805
64    L        -0.182  -0.129  -0.212  -0.191  -0.103  -0.284  -0.324  -0.246  -0.373
65    I        -0.889  -0.864  -0.815  -1.148  -1.107  -1.003  -0.907  -0.872  -0.795
66    D        -0.889  -0.871  -0.805  -0.827  -0.800  -0.715  -0.907  -0.880  -0.784
67    E        -0.722  -0.657  -0.769  -0.512  -0.405  -0.606  -0.713  -0.628  -0.744
68    E        -0.722  -0.676  -0.770  -0.462  -0.391  -0.538  -0.713  -0.651  -0.745
69    L        -0.722  -0.768  -0.771  -0.990  -1.046  -1.044  -0.713  -0.763  -0.746
70    K        -0.884  -0.859  -0.812  -1.125  -1.099  -0.959  -0.916  -0.879  -0.794
71    N        -0.722  -0.629  -0.766  -0.904  -0.773  -0.922  -0.713  -0.595  -0.741
72    R        -0.722  -0.744  -0.762  -0.591  -0.626  -0.667  -0.713  -0.735  -0.736
73    L        -0.295  -0.288  -0.268  -0.603  -0.581  -0.500  -0.510  -0.507  -0.459
74    N        -0.884  -0.902  -0.818  -0.922  -0.946  -0.804  -0.916  -0.923  -0.799
75    Q        -1.312  -1.291  -1.234  -1.026  -0.985  -0.932  -1.118  -1.090  -0.992
76    Y        -0.295  -0.251  -0.268  -0.138  -0.074  -0.077  -0.510  -0.451  -0.456
77    Q        -2.025  -1.993  -1.866  -1.818  -1.808  -1.594  -1.408  -1.372  -1.214
78    G         0.103   0.154  -0.127   0.268   0.331  -0.070   0.081   0.155  -0.252
79    G         0.818   0.842   0.632   0.929   0.956   0.675   0.826   0.860   0.482
80    F         1.578   1.603   1.678   1.809   1.843   1.954   1.720   1.756   1.871
81    A        -1.658  -1.659  -1.561  -1.391  -1.382  -1.287  -1.259  -1.250  -1.110
82    P        -0.786  -0.807  -0.774  -0.528  -0.560  -0.510  -0.812  -0.829  -0.755
83    R        -0.786  -0.729  -0.756  -0.800  -0.714  -0.739  -0.812  -0.740  -0.737
84    M         1.578   1.603   1.678   1.673   1.711   1.821   1.720   1.756   1.871
85    T         0.313   0.354   0.423   0.182   0.249   0.344  -0.067   0.001   0.087
86    E         0.470   0.407   0.465   0.471   0.351   0.415   0.230   0.103   0.169
87    P        -1.658  -1.638  -1.568  -1.335  -1.337  -1.246  -1.259  -1.234  -1.116
88    E         1.578   1.603   1.678   1.673   1.712   1.821   1.720   1.756   1.871
89    A         1.578   1.603   1.678   1.499   1.517   1.651   1.720   1.756   1.871
90    L         0.818   0.692   0.616   0.558   0.391   0.260   0.826   0.616   0.453
91    L        -0.192  -0.254  -0.227  -0.439  -0.486  -0.431  -0.365  -0.432  -0.405
92    I         1.578   1.603   1.678   1.499   1.540   1.651   1.720   1.756   1.871
93    L         0.818   0.874   0.637   0.589   0.671   0.358   0.826   0.911   0.491
94    D        -0.558  -0.562  -0.717  -0.339  -0.366  -0.571  -0.514  -0.524  -0.684
95    I         0.103  -0.031  -0.126   0.139  -0.066  -0.220   0.081  -0.110  -0.249
96    S        -0.884  -0.906  -0.816  -0.798  -0.824  -0.694  -0.916  -0.930  -0.798
97    A        -0.786  -0.819  -0.784  -0.777  -0.835  -0.733  -0.812  -0.839  -0.764
98    R        -0.558  -0.477  -0.701  -0.374  -0.259  -0.600  -0.514  -0.409  -0.665
99    E         0.744   0.754   0.589   0.916   0.935   0.688   0.706   0.720   0.403
100   I         0.744   0.661   0.595   0.752   0.651   0.555   0.706   0.563   0.415
101   N        -1.312  -1.310  -1.216  -1.255  -1.265  -1.142  -1.118  -1.108  -0.976
102   H        -1.291  -1.306  -1.213  -1.062  -1.078  -0.954  -1.110  -1.111  -0.975
103   L         0.103   0.129  -0.105  -0.046   0.000  -0.306   0.081   0.119  -0.220
104   D        -0.192  -0.198  -0.230  -0.044  -0.075  -0.115  -0.365  -0.396  -0.408
105   E        -1.291  -1.314  -1.222  -1.398  -1.442  -1.328  -1.110  -1.118  -0.983
106   K        -1.153  -1.183  -1.177  -0.987  -1.008  -0.996  -0.961  -0.987  -0.940
107   L        -0.192  -0.292  -0.230  -0.519  -0.652  -0.556  -0.365  -0.489  -0.408
108   L         0.470   0.417   0.448   0.030  -0.057  -0.029   0.230   0.123   0.136
109   K         0.470   0.515   0.465   0.278   0.346   0.241   0.230   0.304   0.169
110   K        -0.925  -0.882  -0.814  -0.866  -0.788  -0.679  -0.961  -0.911  -0.798
111   K        -0.192  -0.271  -0.236  -0.349  -0.473  -0.428  -0.365  -0.458  -0.413
112   H         0.470   0.509   0.492   0.632   0.694   0.639   0.230   0.293   0.221
113   R         1.578   1.603   1.678   1.589   1.619   1.739   1.720   1.756   1.871
114   K        -0.192  -0.179  -0.236  -0.406  -0.399  -0.519  -0.365  -0.365  -0.418
115   A        -0.281  -0.271  -0.253  -0.680  -0.675  -0.596  -0.514  -0.490  -0.443
116   M         1.578   1.603   1.678   1.673   1.711   1.821   1.720   1.756   1.871
117   V        -0.925  -0.912  -0.815  -1.153  -1.147  -0.980  -0.961  -0.936  -0.799
118   R        -1.291  -1.277  -1.203  -1.478  -1.479  -1.350  -1.110  -1.088  -0.968
119   N         1.578   1.603   1.678   1.640   1.674   1.788   1.720   1.756   1.871
120   H         1.578   1.603   1.678   1.777   1.813   1.923   1.720   1.756   1.871
121   P         1.578   1.603   1.678   1.689   1.732   1.837   1.720   1.756   1.871
122   D         1.578   1.603   1.678   1.722   1.757   1.869   1.720   1.756   1.871
123   R         0.313   0.319   0.420   0.002   0.004   0.164  -0.067  -0.068   0.081
124   G         0.103   0.154  -0.127   0.299   0.361  -0.016   0.081   0.155  -0.252
125   G         1.578   1.603   1.678   1.589   1.615   1.739   1.720   1.756   1.871
126   S         1.578   1.603   1.678   1.617   1.648   1.767   1.720   1.756   1.871
127   P         0.470   0.509   0.492   0.561   0.629   0.577   0.230   0.293   0.221
128   Y         0.470   0.500   0.480   0.635   0.681   0.627   0.230   0.277   0.197
129   M        -0.925  -0.956  -0.817  -1.163  -1.160  -0.990  -0.961  -0.976  -0.801
130   A         0.313   0.348   0.423   0.044   0.084   0.209  -0.067  -0.010   0.086
131   A        -0.925  -0.911  -0.820  -0.937  -0.915  -0.795  -0.961  -0.935  -0.803
132   K         0.818   0.842   0.632   0.793   0.825   0.528   0.826   0.860   0.482
133   I         0.818   0.692   0.616   0.841   0.685   0.569   0.826   0.616   0.453
134   N         1.578   1.603   1.678   1.640   1.674   1.788   1.720   1.756   1.871
135   E         0.470   0.533   0.473   0.545   0.647   0.532   0.230   0.337   0.184
136   A         1.578   1.603   1.678   1.499   1.517   1.651   1.720   1.756   1.871
137   K         0.818   0.886   0.626   0.793   0.881   0.519   0.826   0.929   0.471
138   E        -0.192  -0.239  -0.231  -0.054  -0.105  -0.126  -0.365  -0.408  -0.406
139   V        -0.786  -0.732  -0.765  -1.057  -0.972  -0.972  -0.812  -0.745  -0.744
140   L         1.578   1.603   1.678   1.252   1.293   1.409   1.720   1.756   1.871
141   E        -0.281  -0.231  -0.255  -0.256  -0.179  -0.218  -0.514  -0.451  -0.445
142   R        -0.558  -0.563  -0.712  -0.517  -0.549  -0.761  -0.514  -0.525  -0.678
143   S         0.103  -0.031  -0.126   0.320   0.139  -0.000   0.081  -0.110  -0.249
144   V        -0.192  -0.271  -0.236  -0.041  -0.153  -0.117  -0.365  -0.458  -0.413
145   L        -0.722  -0.793  -0.758  -0.948  -1.034  -0.986  -0.713  -0.797  -0.732
146   L        -1.312  -1.309  -1.227  -1.358  -1.357  -1.185  -1.118  -1.110  -0.986
147   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   K        -0.192  -0.135  -0.213  -0.315  -0.223  -0.338  -0.365  -0.276  -0.382
180   R        -0.558  -0.563  -0.712  -0.496  -0.529  -0.727  -0.514  -0.525  -0.678
* 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/P42834
Output conservation file - output/P42834
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
