1     M         1.479   1.536   1.681   1.446   1.537   1.755   1.597   1.680   1.920
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    N         0.704   0.666   0.505   0.884   0.849   0.602   0.730   0.667   0.359
12    P         0.704   0.876   0.532   0.828   1.043   0.574   0.730   0.978   0.409
13    Q         0.119   0.258   0.342  -0.081   0.176   0.233  -0.261  -0.026   0.054
14    V        -0.525  -0.610  -0.430  -0.766  -0.853  -0.593  -0.756  -0.819  -0.578
15    S        -0.372  -0.526  -0.428  -0.406  -0.646  -0.530  -0.508  -0.694  -0.574
16    N         0.704   0.493   0.482   0.884   0.609   0.564   0.730   0.387   0.319
17    I         0.054   0.123   0.304  -0.460  -0.365  -0.076  -0.384  -0.280  -0.020
18    I        -0.746  -0.704  -0.504  -1.067  -0.999  -0.713  -1.004  -0.936  -0.670
19    I         0.704   0.855   0.529   0.638   0.831   0.414   0.730   0.949   0.404
20    M        -0.034  -0.299  -0.363   0.130  -0.234  -0.391  -0.013  -0.379  -0.475
21    L         0.704   0.493   0.482   0.575   0.266   0.255   0.730   0.387   0.319
22    V        -0.729  -0.863  -0.961  -0.536  -0.721  -0.896  -0.632  -0.802  -0.869
23    M         0.323   0.267   0.334   0.212   0.088   0.121   0.111  -0.009   0.039
24    M         1.479   1.536   1.681   1.446   1.537   1.755   1.597   1.680   1.920
25    Q         0.704   0.493   0.482   0.887   0.616   0.578   0.730   0.387   0.319
26    L        -0.372  -0.347  -0.417  -0.478  -0.511  -0.621  -0.508  -0.521  -0.561
27    S        -0.372  -0.528  -0.431  -0.438  -0.662  -0.572  -0.508  -0.696  -0.577
28    R         0.119   0.193   0.317  -0.024   0.090   0.228  -0.261  -0.146   0.007
29    R        -0.525  -0.627  -0.443  -0.579  -0.723  -0.477  -0.756  -0.845  -0.597
30    I        -0.525  -0.342  -0.402  -0.865  -0.577  -0.645  -0.756  -0.497  -0.540
31    D         0.323   0.362   0.368   0.387   0.440   0.405   0.111   0.163   0.103
32    M        -0.525  -0.347  -0.398  -0.548  -0.279  -0.360  -0.756  -0.516  -0.531
33    E         0.704   0.493   0.482   0.837   0.563   0.521   0.730   0.387   0.319
34    D         0.704   0.493   0.482   0.917   0.658   0.637   0.730   0.387   0.319
35    P         0.704   0.765   0.522   0.857   0.940   0.625   0.730   0.818   0.390
36    T        -1.594  -1.514  -1.460  -1.378  -1.296  -1.163  -1.375  -1.283  -1.140
37    I        -1.015  -1.128  -1.019  -1.086  -1.284  -1.091  -1.004  -1.108  -0.937
38    I        -0.372  -0.164  -0.361  -0.590  -0.318  -0.578  -0.508  -0.227  -0.476
39    M        -1.728  -1.741  -1.500  -1.540  -1.480  -1.173  -1.499  -1.461  -1.173
40    Y        -0.729  -0.896  -0.978  -0.413  -0.671  -0.849  -0.632  -0.836  -0.888
41    I        -1.372  -1.420  -1.454  -1.200  -1.312  -1.312  -1.127  -1.175  -1.131
42    R         1.479   1.536   1.681   1.581   1.655   1.884   1.597   1.680   1.920
43    I         0.119   0.199   0.322  -0.297  -0.157  -0.011  -0.261  -0.135   0.016
44    L         0.054   0.136   0.312  -0.469  -0.346  -0.070  -0.384  -0.254  -0.003
45    Y         1.479   1.536   1.681   1.534   1.618   1.839   1.597   1.680   1.920
46    C        -1.237  -1.110  -1.037  -1.383  -1.239  -1.059  -1.251  -1.109  -0.957
47    S        -2.085  -2.043  -1.862  -2.087  -2.037  -1.784  -1.623  -1.550  -1.304
48    S        -1.015  -1.016  -0.998  -0.856  -0.875  -0.849  -1.004  -0.981  -0.913
49    I        -1.237  -1.118  -1.041  -1.202  -1.031  -0.928  -1.251  -1.120  -0.962
50    G        -1.372  -1.428  -1.447  -1.333  -1.446  -1.519  -1.127  -1.182  -1.124
51    I        -0.372  -0.452  -0.407  -0.561  -0.657  -0.644  -0.508  -0.588  -0.542
52    S        -2.085  -2.038  -1.855  -2.007  -1.912  -1.685  -1.623  -1.547  -1.299
53    W        -1.594  -1.558  -1.463  -1.392  -1.418  -1.192  -1.375  -1.309  -1.140
54    I        -2.441  -2.232  -2.157  -2.237  -1.872  -1.863  -1.746  -1.553  -1.391
55    I        -0.034   0.093  -0.283  -0.034   0.137  -0.410  -0.013   0.161  -0.361
56    Y        -0.034  -0.299  -0.363   0.304  -0.026  -0.112  -0.013  -0.379  -0.475
57    Q        -1.103  -0.903  -0.990  -1.147  -0.931  -0.981  -1.127  -0.900  -0.907
58    M        -0.729  -0.426  -0.881  -0.441  -0.029  -0.728  -0.632  -0.256  -0.777
59    A        -1.015  -0.869  -0.954  -1.040  -0.799  -0.974  -1.004  -0.804  -0.863
60    R        -0.034  -0.299  -0.363   0.274  -0.107  -0.250  -0.013  -0.379  -0.475
61    K        -2.085  -2.031  -1.852  -1.999  -1.919  -1.663  -1.623  -1.543  -1.298
62    R        -1.594  -1.487  -1.460  -1.547  -1.445  -1.322  -1.375  -1.263  -1.141
63    I         0.704   0.765   0.522   0.638   0.727   0.402   0.730   0.818   0.390
64    V        -1.594  -1.567  -1.482  -1.322  -1.291  -1.114  -1.375  -1.329  -1.158
65    A         0.054   0.135   0.313  -0.417  -0.269  -0.014  -0.384  -0.257  -0.001
66    K         1.479   1.536   1.681   1.312   1.395   1.626   1.597   1.680   1.920
67    N         0.704   0.666   0.505   0.872   0.836   0.573   0.730   0.667   0.359
68    D         1.479   1.536   1.681   1.545   1.625   1.850   1.597   1.680   1.920
69    M         0.704   0.863   0.532   0.598   0.772   0.393   0.730   0.960   0.409
70    T         0.704   0.876   0.532   0.751   0.963   0.502   0.730   0.978   0.409
71    T         0.704   0.493   0.482   0.766   0.483   0.453   0.730   0.387   0.319
72    M         0.704   0.863   0.532   0.598   0.772   0.393   0.730   0.960   0.409
73    K         1.479   1.536   1.681   1.312   1.395   1.626   1.597   1.680   1.920
74    Y         1.479   1.536   1.681   1.534   1.618   1.839   1.597   1.680   1.920
75    V         1.479   1.536   1.681   1.387   1.468   1.698   1.597   1.680   1.920
76    E         0.704   0.876   0.532   0.821   1.044   0.567   0.730   0.978   0.409
77    P         0.704   0.765   0.522   0.863   0.945   0.640   0.730   0.818   0.390
78    G        -0.034   0.122  -0.281  -0.015   0.207  -0.355  -0.013   0.199  -0.358
79    N        -0.158  -0.346  -0.397   0.075  -0.214  -0.331  -0.182  -0.456  -0.522
80    A         0.119   0.262   0.343  -0.113   0.148   0.206  -0.261  -0.018   0.057
81    M        -0.372  -0.180  -0.372  -0.321  -0.051  -0.348  -0.508  -0.252  -0.496
82    S         0.119   0.200   0.320  -0.147  -0.021   0.134  -0.261  -0.134   0.012
83    G        -0.034  -0.060  -0.313   0.069   0.052  -0.358  -0.013  -0.046  -0.403
84    E        -1.103  -1.208  -1.018  -0.936  -1.043  -0.786  -1.127  -1.190  -0.938
85    G        -1.103  -0.941  -0.987  -1.094  -0.841  -0.925  -1.127  -0.930  -0.906
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    E        -0.034  -0.214  -0.341   0.222   0.006  -0.202  -0.013  -0.271  -0.443
92    -        -1.554  -1.594  -1.479  -1.318  -1.410  -1.277  -1.314  -1.335  -1.154
93    K         0.704   0.851   0.530   0.686   0.868   0.500   0.730   0.943   0.406
94    L        -0.659  -0.612  -0.475  -0.940  -0.863  -0.653  -0.880  -0.822  -0.633
95    Q        -0.729  -0.483  -0.897  -0.472  -0.159  -0.682  -0.632  -0.327  -0.796
96    V        -0.372  -0.534  -0.434  -0.422  -0.668  -0.560  -0.508  -0.706  -0.581
97    T         1.479   1.536   1.681   1.421   1.494   1.730   1.597   1.680   1.920
98    T         1.479   1.536   1.681   1.421   1.494   1.730   1.597   1.680   1.920
99    V         0.323   0.362   0.368   0.170   0.224   0.169   0.111   0.163   0.103
100   R        -0.372  -0.313  -0.391  -0.206  -0.085  -0.244  -0.508  -0.401  -0.520
101   D        -0.525  -0.482  -0.428  -0.523  -0.424  -0.390  -0.756  -0.661  -0.575
102   Y         1.479   1.536   1.681   1.534   1.618   1.839   1.597   1.680   1.920
103   D         1.479   1.536   1.681   1.545   1.625   1.850   1.597   1.680   1.920
104   L         0.704   0.832   0.529   0.575   0.717   0.334   0.730   0.916   0.402
105   K        -1.015  -1.118  -1.004  -1.023  -1.166  -1.014  -1.004  -1.081  -0.921
106   E        -0.372  -0.478  -0.402  -0.251  -0.405  -0.338  -0.508  -0.625  -0.533
107   I        -1.237  -1.203  -1.040  -1.469  -1.449  -1.199  -1.251  -1.184  -0.960
108   D        -1.103  -1.209  -1.030  -0.997  -1.181  -0.939  -1.127  -1.191  -0.950
109   S        -0.659  -0.662  -0.500  -0.756  -0.782  -0.539  -0.880  -0.882  -0.665
110   A        -1.015  -1.126  -1.015  -1.060  -1.213  -1.072  -1.004  -1.090  -0.931
111   I        -0.034  -0.299  -0.363  -0.004  -0.357  -0.477  -0.013  -0.379  -0.475
112   K         0.119   0.194   0.318  -0.118  -0.007   0.182  -0.261  -0.144   0.007
113   S        -0.372  -0.452  -0.407  -0.376  -0.455  -0.427  -0.508  -0.588  -0.542
114   I        -0.729  -0.896  -0.978  -0.603  -0.831  -0.943  -0.632  -0.836  -0.888
115   Y        -1.103  -1.209  -1.030  -0.961  -1.137  -0.881  -1.127  -1.191  -0.950
116   T        -0.034  -0.299  -0.363   0.128  -0.240  -0.357  -0.013  -0.379  -0.475
117   G        -0.034  -0.136  -0.329   0.092  -0.054  -0.335  -0.013  -0.175  -0.427
118   M        -1.237  -1.154  -1.043  -1.495  -1.405  -1.191  -1.251  -1.157  -0.965
119   A        -0.034  -0.060  -0.313  -0.016  -0.023  -0.406  -0.013  -0.046  -0.403
120   M         0.704   0.493   0.482   0.796   0.531   0.489   0.730   0.387   0.319
121   M         0.704   0.493   0.482   0.796   0.531   0.489   0.730   0.387   0.319
122   G        -0.034  -0.139  -0.329   0.063  -0.114  -0.401  -0.013  -0.179  -0.427
123   F         0.704   0.666   0.505   0.900   0.855   0.615   0.730   0.667   0.359
124   M         1.479   1.536   1.681   1.446   1.537   1.755   1.597   1.680   1.920
125   H         1.479   1.536   1.681   1.669   1.746   1.970   1.597   1.680   1.920
126   L        -0.372  -0.227  -0.364  -0.556  -0.351  -0.525  -0.508  -0.291  -0.482
127   Y         1.479   1.536   1.681   1.534   1.618   1.839   1.597   1.680   1.920
128   L        -0.034   0.029  -0.299   0.148   0.246  -0.238  -0.013   0.069  -0.383
129   K         0.323   0.235   0.327   0.127  -0.027   0.079   0.111  -0.067   0.026
130   Y         1.479   1.536   1.681   1.534   1.618   1.839   1.597   1.680   1.920
131   T        -0.034  -0.214  -0.341   0.101  -0.168  -0.381  -0.013  -0.271  -0.443
132   N         0.704   0.493   0.482   0.898   0.634   0.600   0.730   0.387   0.319
133   P         1.479   1.536   1.681   1.498   1.574   1.804   1.597   1.680   1.920
134   L         1.479   1.536   1.681   1.244   1.300   1.560   1.597   1.680   1.920
135   F        -0.525  -0.415  -0.427  -0.641  -0.575  -0.525  -0.756  -0.633  -0.577
136   M        -0.372  -0.480  -0.435  -0.430  -0.642  -0.622  -0.508  -0.659  -0.585
137   Q         1.479   1.536   1.681   1.534   1.613   1.839   1.597   1.680   1.920
138   S         0.704   0.876   0.532   0.748   0.954   0.527   0.730   0.978   0.409
139   I         0.704   0.493   0.482   0.638   0.366   0.337   0.730   0.387   0.319
140   S        -0.034   0.001  -0.307   0.090   0.129  -0.317  -0.013   0.033  -0.395
141   P        -0.372  -0.441  -0.398  -0.325  -0.420  -0.415  -0.508  -0.572  -0.527
142   V        -1.237  -1.261  -1.048  -1.502  -1.550  -1.256  -1.251  -1.236  -0.968
143   K         0.704   0.493   0.482   0.686   0.434   0.428   0.730   0.387   0.319
144   S         0.323   0.201   0.319   0.211  -0.019   0.133   0.111  -0.132   0.011
145   A         0.704   0.493   0.482   0.606   0.328   0.272   0.730   0.387   0.319
146   L        -0.372  -0.397  -0.435  -0.503  -0.578  -0.577  -0.508  -0.589  -0.585
147   E         0.704   0.493   0.482   0.858   0.602   0.575   0.730   0.387   0.319
148   H        -1.594  -1.567  -1.482  -1.247  -1.223  -1.141  -1.375  -1.329  -1.158
149   N         0.704   0.493   0.482   0.884   0.609   0.564   0.730   0.387   0.319
150   E        -1.103  -1.075  -1.004  -1.195  -1.129  -1.047  -1.127  -1.061  -0.924
151   V         0.704   0.666   0.505   0.717   0.680   0.424   0.730   0.667   0.359
152   K         0.119   0.147   0.306  -0.144  -0.102   0.139  -0.261  -0.233  -0.015
153   I         1.479   1.536   1.681   1.294   1.376   1.608   1.597   1.680   1.920
154   H         1.479   1.536   1.681   1.669   1.746   1.970   1.597   1.680   1.920
155   L        -0.372  -0.480  -0.435  -0.571  -0.768  -0.688  -0.508  -0.659  -0.585
156   F         0.704   0.493   0.482   0.921   0.650   0.629   0.730   0.387   0.319
157   G         0.323   0.235   0.327   0.249   0.115   0.227   0.111  -0.067   0.026
158   K        -0.729  -0.596  -0.922  -0.590  -0.411  -0.858  -0.632  -0.468  -0.824
159   P         1.479   1.536   1.681   1.498   1.574   1.804   1.597   1.680   1.920
160   A         1.479   1.536   1.681   1.282   1.382   1.597   1.597   1.680   1.920
161   T        -1.237  -1.158  -1.033  -1.369  -1.278  -1.085  -1.251  -1.147  -0.954
162   G         0.704   0.493   0.482   0.755   0.505   0.482   0.730   0.387   0.319
163   D         0.704   0.493   0.482   0.904   0.637   0.604   0.730   0.387   0.319
164   L         1.479   1.536   1.681   1.244   1.300   1.560   1.597   1.680   1.920
165   K         0.704   0.493   0.482   0.686   0.434   0.428   0.730   0.387   0.319
166   R         1.479   1.536   1.681   1.581   1.655   1.884   1.597   1.680   1.920
167   P         1.479   1.536   1.681   1.498   1.574   1.804   1.597   1.680   1.920
168   F         1.479   1.536   1.681   1.555   1.628   1.860   1.597   1.680   1.920
169   K         0.704   0.765   0.522   0.657   0.746   0.419   0.730   0.818   0.390
170   A        -1.015  -1.000  -0.998  -1.051  -1.036  -0.998  -1.004  -0.993  -0.918
171   P        -0.746  -0.710  -0.504  -0.991  -0.932  -0.646  -1.004  -0.944  -0.670
172   S        -1.015  -1.126  -1.015  -0.964  -1.124  -0.995  -1.004  -1.090  -0.931
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   L        -0.034   0.173  -0.274  -0.020   0.215  -0.310  -0.013   0.268  -0.349
175   F        -0.659  -0.662  -0.500  -0.733  -0.801  -0.585  -0.880  -0.881  -0.665
176   G        -0.729  -0.596  -0.922  -0.522  -0.348  -0.808  -0.632  -0.468  -0.824
177   G        -0.372  -0.441  -0.398  -0.453  -0.513  -0.520  -0.508  -0.572  -0.527
178   M        -1.594  -1.559  -1.469  -1.652  -1.577  -1.433  -1.375  -1.313  -1.147
179   -        -1.261  -1.190  -1.056  -1.385  -1.294  -1.125  -1.256  -1.160  -0.973
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   G         0.553   0.442   0.407   0.533   0.381   0.322   0.496   0.300   0.178
182   Q        -0.601  -0.551  -0.468  -0.870  -0.810  -0.649  -0.825  -0.763  -0.625
183   T        -0.486  -0.277  -0.392  -0.590  -0.266  -0.457  -0.667  -0.367  -0.520
184   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
185   G        -2.085  -2.055  -1.857  -1.846  -1.789  -1.549  -1.623  -1.558  -1.301
186   P        -1.594  -1.481  -1.453  -1.488  -1.316  -1.307  -1.375  -1.228  -1.131
187   K        -1.015  -1.124  -1.012  -1.032  -1.222  -1.035  -1.004  -1.103  -0.931
188   T         0.704   0.666   0.505   0.767   0.723   0.495   0.730   0.667   0.359
189   D         0.704   0.765   0.522   0.905   0.990   0.671   0.730   0.818   0.390
190   K         0.704   0.765   0.522   0.642   0.733   0.383   0.730   0.818   0.390
191   K        -0.729  -0.511  -0.894  -0.568  -0.283  -0.779  -0.632  -0.360  -0.792
192   S        -0.372  -0.298  -0.401  -0.438  -0.357  -0.522  -0.508  -0.424  -0.538
193   I         0.054   0.149   0.321  -0.353  -0.181   0.071  -0.384  -0.231   0.014
194   E        -0.034  -0.156  -0.335   0.215   0.056  -0.209  -0.013  -0.200  -0.434
195   E        -2.085  -1.886  -1.839  -1.938  -1.649  -1.591  -1.623  -1.435  -1.289
196   A         1.479   1.536   1.681   1.282   1.382   1.597   1.597   1.680   1.920
197   E         1.479   1.536   1.681   1.490   1.575   1.797   1.597   1.680   1.920
198   R        -1.728  -1.683  -1.491  -1.723  -1.696  -1.403  -1.499  -1.422  -1.167
199   A        -0.034  -0.136  -0.329  -0.013  -0.147  -0.427  -0.013  -0.175  -0.427
200   G         1.479   1.536   1.681   1.385   1.465   1.696   1.597   1.680   1.920
201   N        -0.586  -0.619  -0.467  -0.726  -0.737  -0.507  -0.829  -0.838  -0.624
202   A         0.636   0.770   0.468   0.623   0.803   0.343   0.626   0.826   0.292
203   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
204   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
205   G         0.704   0.493   0.482   0.722   0.446   0.395   0.730   0.387   0.319
206   V        -1.103  -1.208  -1.018  -1.300  -1.469  -1.197  -1.127  -1.190  -0.938
207   K         1.479   1.536   1.681   1.312   1.395   1.626   1.597   1.680   1.920
208   A        -1.103  -1.114  -1.014  -1.105  -1.083  -0.908  -1.127  -1.112  -0.932
209   E        -0.372  -0.441  -0.398  -0.252  -0.333  -0.301  -0.508  -0.572  -0.527
* 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/P38264
Output conservation file - output/P38264
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
