1     M         1.202   1.245   1.295   1.507   1.545   1.618   1.252   1.317   1.398
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     S         0.393   0.455   0.096   0.616   0.676   0.191   0.415   0.501  -0.069
4     D        -0.377  -0.495  -0.730  -0.067  -0.269  -0.638  -0.302  -0.473  -0.760
5     W         1.202   1.245   1.295   1.553   1.590   1.659   1.252   1.317   1.398
6     D        -0.218  -0.086  -0.026  -0.274  -0.061  -0.010  -0.541  -0.334  -0.278
7     T        -0.890  -0.764  -0.775  -0.828  -0.684  -0.645  -1.020  -0.880  -0.824
8     N        -2.378  -2.235  -2.153  -1.969  -1.801  -1.708  -1.737  -1.604  -1.447
9     T         0.393   0.162   0.069   0.566   0.241   0.046   0.415   0.072  -0.115
10    I        -0.890  -0.835  -0.771  -1.001  -0.889  -0.864  -1.020  -0.904  -0.816
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    I         1.202   1.245   1.295   1.276   1.323   1.416   1.252   1.317   1.398
13    G         1.202   1.245   1.295   0.985   1.050   1.160   1.252   1.317   1.398
14    S        -1.493  -1.471  -1.341  -1.437  -1.454  -1.280  -1.378  -1.322  -1.131
15    R        -0.890  -0.986  -0.789  -1.238  -1.275  -0.978  -1.020  -1.092  -0.839
16    A        -0.005  -0.068  -0.033  -0.161  -0.285  -0.243  -0.183  -0.304  -0.292
17    R         0.322   0.074   0.033   0.420   0.079   0.000   0.315  -0.069  -0.175
18    A        -1.700  -1.664  -1.380  -1.789  -1.722  -1.334  -1.559  -1.484  -1.167
19    G         1.202   1.245   1.295   0.988   1.054   1.164   1.252   1.317   1.398
20    G         1.202   1.245   1.295   0.985   1.050   1.160   1.252   1.317   1.398
21    S        -1.402  -1.511  -1.352  -1.439  -1.582  -1.338  -1.259  -1.334  -1.139
22    G         1.202   1.245   1.295   0.985   1.050   1.160   1.252   1.317   1.398
23    P         0.393   0.305   0.083   0.652   0.531   0.144   0.415   0.288  -0.092
24    R         1.202   1.245   1.295   1.174   1.228   1.327   1.252   1.317   1.398
25    A        -1.634  -1.585  -1.371  -1.637  -1.538  -1.243  -1.498  -1.416  -1.159
26    N        -1.402  -1.422  -1.352  -1.078  -1.103  -1.008  -1.259  -1.280  -1.142
27    V         1.202   1.245   1.295   1.184   1.243   1.335   1.252   1.317   1.398
28    A         0.393   0.162   0.069   0.394   0.079  -0.065   0.415   0.072  -0.115
29    R        -0.286  -0.210  -0.048  -0.800  -0.653  -0.395  -0.661  -0.550  -0.318
30    S        -0.377  -0.483  -0.725  -0.113  -0.309  -0.692  -0.302  -0.460  -0.754
31    Q        -0.377  -0.461  -0.720  -0.135  -0.317  -0.726  -0.302  -0.436  -0.747
32    G        -1.121  -0.958  -0.817  -1.433  -1.126  -0.957  -1.259  -1.049  -0.869
33    Q        -0.731  -0.814  -0.776  -0.605  -0.736  -0.735  -0.780  -0.858  -0.821
34    I        -0.218  -0.171  -0.041  -0.316  -0.248  -0.079  -0.541  -0.481  -0.305
35    N         1.202   1.245   1.295   1.291   1.349   1.429   1.252   1.317   1.398
36    A        -0.377  -0.366  -0.710  -0.247  -0.249  -0.692  -0.302  -0.294  -0.735
37    A         1.202   1.245   1.295   1.080   1.121   1.244   1.252   1.317   1.398
38    R        -0.377  -0.561  -0.737  -0.122  -0.369  -0.589  -0.302  -0.547  -0.769
39    R         1.202   1.245   1.295   1.174   1.228   1.327   1.252   1.317   1.398
40    Q        -1.030  -0.873  -0.795  -1.076  -0.857  -0.790  -1.139  -0.939  -0.844
41    G         1.202   1.245   1.295   0.985   1.050   1.160   1.252   1.317   1.398
42    L        -1.493  -1.402  -1.335  -1.314  -1.173  -1.080  -1.378  -1.255  -1.126
43    V        -0.005  -0.146  -0.045  -0.030  -0.268  -0.135  -0.183  -0.437  -0.312
44    V        -0.890  -0.963  -0.789  -0.935  -0.980  -0.761  -1.020  -1.060  -0.839
45    S        -0.890  -0.979  -0.795  -1.056  -1.191  -0.936  -1.020  -1.081  -0.847
46    V        -0.218  -0.052  -0.012  -0.360  -0.074  -0.064  -0.541  -0.277  -0.254
47    D        -0.286  -0.192  -0.044  -0.401  -0.252  -0.043  -0.661  -0.519  -0.310
48    K         1.202   1.245   1.295   0.877   0.950   1.066   1.252   1.317   1.398
49    K         1.202   1.245   1.295   0.877   0.950   1.066   1.252   1.317   1.398
50    Y         1.202   1.245   1.295   1.521   1.560   1.630   1.252   1.317   1.398
51    G        -0.218  -0.211  -0.046  -0.669  -0.672  -0.386  -0.541  -0.552  -0.313
52    S        -0.890  -0.958  -0.783  -0.887  -0.983  -0.751  -1.020  -1.052  -0.833
53    T        -1.121  -1.054  -0.836  -1.425  -1.366  -1.034  -1.259  -1.165  -0.892
54    N         1.202   1.245   1.295   1.291   1.349   1.429   1.252   1.317   1.398
55    T        -0.731  -0.731  -0.769  -0.643  -0.647  -0.798  -0.780  -0.757  -0.812
56    R        -1.103  -1.277  -1.329  -1.161  -1.420  -1.471  -0.900  -1.101  -1.116
57    G        -1.402  -1.324  -1.331  -1.271  -1.118  -1.196  -1.259  -1.141  -1.118
58    D        -2.006  -1.929  -1.795  -1.836  -1.787  -1.660  -1.617  -1.517  -1.326
59    N        -1.103  -0.830  -1.279  -0.717  -0.356  -1.108  -0.900  -0.589  -1.065
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    E        -0.377  -0.435  -0.719  -0.063  -0.154  -0.616  -0.302  -0.375  -0.746
63    G         1.202   1.245   1.295   0.985   1.050   1.160   1.252   1.317   1.398
64    Q         1.202   1.245   1.295   1.262   1.311   1.403   1.252   1.317   1.398
65    R         0.393   0.305   0.083   0.547   0.458   0.190   0.415   0.288  -0.092
66    L         1.202   1.245   1.295   1.252   1.315   1.395   1.252   1.317   1.398
67    T         1.202   1.245   1.295   1.267   1.317   1.407   1.252   1.317   1.398
68    K         0.393   0.162   0.069   0.240  -0.004  -0.093   0.415   0.072  -0.115
69    V        -1.030  -0.889  -0.797  -1.084  -0.864  -0.768  -1.139  -0.964  -0.846
70    D         1.202   1.245   1.295   1.296   1.346   1.433   1.252   1.317   1.398
71    R        -0.005   0.219   0.059  -0.103   0.238  -0.048  -0.183   0.160  -0.132
72    E        -1.402  -1.212  -1.337  -1.149  -0.959  -1.110  -1.259  -1.096  -1.128
73    T        -0.890  -0.850  -0.778  -0.833  -0.723  -0.657  -1.020  -0.927  -0.824
74    D         0.393   0.305   0.083   0.626   0.521   0.178   0.415   0.288  -0.092
75    I        -0.218  -0.123  -0.030  -0.352  -0.196  -0.095  -0.541  -0.398  -0.286
76    V        -0.377  -0.435  -0.719  -0.215  -0.296  -0.788  -0.302  -0.375  -0.746
77    K        -1.030  -0.907  -0.819  -1.394  -1.186  -1.041  -1.139  -0.980  -0.871
78    P        -0.377  -0.059  -0.680   0.001   0.383  -0.484  -0.302   0.091  -0.695
79    K        -0.377  -0.435  -0.719  -0.442  -0.489  -0.837  -0.302  -0.375  -0.746
80    K        -0.005  -0.146  -0.045  -0.331  -0.530  -0.349  -0.183  -0.437  -0.312
81    L        -1.493  -1.398  -1.335  -1.402  -1.237  -1.164  -1.378  -1.249  -1.125
82    D        -1.103  -1.343  -1.342  -0.732  -1.103  -1.183  -0.900  -1.163  -1.129
83    P        -2.518  -2.412  -2.160  -2.350  -2.310  -1.867  -1.856  -1.739  -1.452
84    N        -0.890  -0.932  -0.778  -0.824  -0.841  -0.649  -1.020  -1.017  -0.825
85    V         1.202   1.245   1.295   1.184   1.243   1.335   1.252   1.317   1.398
86    G         0.393   0.305   0.083   0.283   0.181  -0.161   0.415   0.288  -0.092
87    R        -1.103  -1.277  -1.329  -1.166  -1.423  -1.482  -0.900  -1.101  -1.116
88    A         0.393   0.574   0.106   0.406   0.606   0.029   0.415   0.659  -0.052
89    I         1.202   1.245   1.295   1.276   1.323   1.416   1.252   1.317   1.398
90    S        -1.103  -0.830  -1.279  -0.752  -0.401  -1.076  -0.900  -0.589  -1.065
91    R        -1.030  -0.734  -0.762  -1.394  -0.935  -0.981  -1.139  -0.754  -0.801
92    A        -0.890  -0.726  -0.777  -1.212  -1.002  -1.007  -1.020  -0.841  -0.827
93    R         1.202   1.245   1.295   1.174   1.228   1.327   1.252   1.317   1.398
94    T        -1.030  -0.952  -0.813  -1.007  -0.911  -0.732  -1.139  -1.047  -0.866
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   D        -0.890  -0.911  -0.782  -0.853  -0.881  -0.723  -1.020  -1.016  -0.833
101   K         1.202   1.245   1.295   0.877   0.950   1.066   1.252   1.317   1.398
102   K        -1.402  -1.472  -1.359  -1.710  -1.829  -1.609  -1.259  -1.323  -1.148
103   M        -0.890  -0.911  -0.787  -0.669  -0.636  -0.468  -1.020  -1.016  -0.839
104   S        -0.731  -0.664  -0.749  -0.606  -0.501  -0.694  -0.780  -0.666  -0.785
105   Q         1.202   1.245   1.295   1.262   1.311   1.403   1.252   1.317   1.398
106   K         1.202   1.245   1.295   0.877   0.950   1.066   1.252   1.317   1.398
107   D        -0.218  -0.193  -0.049  -0.274  -0.253  -0.053  -0.541  -0.520  -0.319
108   L         1.202   1.245   1.295   1.252   1.315   1.395   1.252   1.317   1.398
109   A         0.393   0.305   0.083   0.409   0.292  -0.001   0.415   0.288  -0.092
110   T        -0.377  -0.435  -0.719  -0.085  -0.156  -0.617  -0.302  -0.375  -0.746
111   K        -0.005  -0.146  -0.045  -0.364  -0.581  -0.409  -0.183  -0.437  -0.312
112   I        -0.377  -0.461  -0.720  -0.021  -0.117  -0.488  -0.302  -0.436  -0.747
113   N         1.202   1.245   1.295   1.291   1.349   1.429   1.252   1.317   1.398
114   E         0.393   0.162   0.069   0.628   0.319   0.153   0.415   0.072  -0.115
115   K         0.393   0.162   0.069   0.202  -0.069  -0.197   0.415   0.072  -0.115
116   P         0.393   0.162   0.069   0.677   0.371   0.186   0.415   0.072  -0.115
117   T        -1.634  -1.625  -1.375  -1.547  -1.552  -1.227  -1.498  -1.450  -1.162
118   V        -0.005  -0.068  -0.033  -0.030  -0.136  -0.116  -0.183  -0.304  -0.292
119   V        -0.286  -0.211  -0.049  -0.498  -0.377  -0.140  -0.661  -0.552  -0.320
120   N         0.393   0.162   0.069   0.590   0.272   0.066   0.415   0.072  -0.115
121   D         0.393   0.162   0.069   0.620   0.319   0.140   0.415   0.072  -0.115
122   Y         1.202   1.245   1.295   1.521   1.560   1.630   1.252   1.317   1.398
123   E         1.202   1.245   1.295   1.300   1.344   1.437   1.252   1.317   1.398
124   A        -0.890  -0.986  -0.794  -1.020  -1.133  -0.842  -1.020  -1.092  -0.846
125   A         0.393   0.545   0.102   0.283   0.480  -0.128   0.415   0.621  -0.059
126   R         0.393   0.162   0.069   0.505   0.211   0.058   0.415   0.072  -0.115
127   A        -0.005  -0.068  -0.033  -0.226  -0.371  -0.356  -0.183  -0.304  -0.292
128   I        -0.731  -0.733  -0.778  -0.602  -0.634  -0.725  -0.780  -0.798  -0.825
129   P         1.202   1.245   1.295   1.353   1.400   1.483   1.252   1.317   1.398
130   N         0.393   0.162   0.069   0.620   0.330   0.149   0.415   0.072  -0.115
131   Q         1.202   1.245   1.295   1.262   1.311   1.403   1.252   1.317   1.398
132   Q         0.393   0.162   0.069   0.534   0.192  -0.035   0.415   0.072  -0.115
133   V        -0.890  -0.760  -0.781  -0.935  -0.750  -0.751  -1.020  -0.873  -0.831
134   L         1.202   1.245   1.295   1.252   1.315   1.395   1.252   1.317   1.398
135   S        -0.890  -0.728  -0.772  -1.119  -0.903  -0.914  -1.020  -0.841  -0.822
136   K         0.393   0.162   0.069   0.206  -0.060  -0.187   0.415   0.072  -0.115
137   L        -0.286  -0.211  -0.049  -0.282  -0.167   0.050  -0.661  -0.552  -0.320
138   E         1.202   1.245   1.295   1.300   1.344   1.437   1.252   1.317   1.398
139   R         1.202   1.245   1.295   1.174   1.228   1.327   1.252   1.317   1.398
140   A        -0.005  -0.096  -0.038  -0.161  -0.332  -0.250  -0.183  -0.351  -0.299
141   L         1.202   1.245   1.295   1.252   1.315   1.395   1.252   1.317   1.398
142   G         0.393   0.162   0.069   0.314   0.038  -0.099   0.415   0.072  -0.115
143   V        -0.218  -0.166  -0.044  -0.384  -0.302  -0.134  -0.541  -0.472  -0.311
144   K         1.202   1.245   1.295   0.877   0.950   1.066   1.252   1.317   1.398
145   L         1.202   1.245   1.295   1.252   1.315   1.395   1.252   1.317   1.398
146   R         1.202   1.245   1.295   1.174   1.228   1.327   1.252   1.317   1.398
147   G         1.202   1.245   1.295   0.985   1.050   1.160   1.252   1.317   1.398
148   N        -1.103  -1.277  -1.329  -1.096  -1.315  -1.342  -0.900  -1.101  -1.116
149   N        -0.731  -0.677  -0.777  -0.580  -0.550  -0.720  -0.780  -0.764  -0.826
150   I         1.202   1.245   1.295   1.276   1.323   1.416   1.252   1.317   1.398
151   G         1.202   1.245   1.295   0.985   1.050   1.160   1.252   1.317   1.398
152   S        -1.774  -1.879  -1.792  -1.436  -1.718  -1.637  -1.378  -1.470  -1.324
153   P         1.202   1.245   1.295   1.353   1.400   1.483   1.252   1.317   1.398
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   L         0.393   0.162   0.069   0.624   0.370   0.231   0.415   0.072  -0.115
156   G        -0.731  -0.756  -0.752  -0.711  -0.731  -0.687  -0.780  -0.783  -0.788
157   A        -1.493  -1.519  -1.351  -1.757  -1.816  -1.527  -1.378  -1.362  -1.140
158   P        -0.286  -0.208  -0.048  -0.661  -0.542  -0.291  -0.661  -0.547  -0.318
159   K        -0.838  -0.859  -0.791  -1.124  -1.130  -1.056  -0.890  -0.925  -0.837
160   K         1.202   1.245   1.295   0.877   0.950   1.066   1.252   1.317   1.398
161   K         1.202   1.245   1.295   0.877   0.950   1.066   1.252   1.317   1.398
* 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/O14467
Output conservation file - output/O14467
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
