1     M         1.312   1.332   1.431   1.433   1.464   1.607   1.392   1.422   1.572
2     S         1.312   1.332   1.431   1.306   1.339   1.489   1.392   1.422   1.572
3     Q         0.633   0.533   0.404   0.817   0.698   0.482   0.629   0.472   0.217
4     K        -1.070  -1.087  -0.929  -1.388  -1.379  -1.144  -1.117  -1.116  -0.904
5     I        -0.445  -0.479  -0.397  -0.508  -0.532  -0.409  -0.681  -0.700  -0.575
6     G         1.312   1.332   1.431   1.243   1.268   1.430   1.392   1.422   1.572
7     H        -1.696  -1.739  -1.629  -1.448  -1.559  -1.398  -1.335  -1.362  -1.189
8     S        -0.312  -0.278  -0.362  -0.319  -0.252  -0.424  -0.462  -0.398  -0.523
9     G        -0.640  -0.613  -0.455  -0.974  -0.949  -0.691  -0.899  -0.860  -0.645
10    L         0.633   0.680   0.419   0.566   0.639   0.279   0.629   0.698   0.243
11    A         1.312   1.332   1.431   1.212   1.237   1.400   1.392   1.422   1.572
12    F        -0.563  -0.552  -0.438  -0.542  -0.534  -0.399  -0.790  -0.781  -0.622
13    A        -0.445  -0.404  -0.397  -0.636  -0.584  -0.523  -0.681  -0.633  -0.576
14    R         0.633   0.533   0.404   0.613   0.476   0.246   0.629   0.472   0.217
15    L        -0.876  -0.759  -0.862  -0.941  -0.760  -0.892  -0.899  -0.753  -0.832
16    W         1.312   1.332   1.431   1.526   1.552   1.695   1.392   1.422   1.572
17    H         1.312   1.332   1.431   1.352   1.378   1.532   1.392   1.422   1.572
18    H         0.633   0.571   0.398   0.790   0.717   0.489   0.629   0.531   0.205
19    V         0.633   0.575   0.398   0.652   0.583   0.344   0.629   0.538   0.205
20    D         0.572   0.486   0.359   0.692   0.580   0.355   0.537   0.395   0.133
21    V        -0.769  -0.705  -0.868  -0.761  -0.696  -0.943  -0.745  -0.675  -0.836
22    A        -0.312  -0.361  -0.383  -0.417  -0.496  -0.538  -0.462  -0.524  -0.552
23    R        -0.952  -0.911  -0.894  -1.233  -1.159  -1.100  -1.008  -0.955  -0.870
24    D        -0.624  -0.816  -0.873  -0.383  -0.670  -0.796  -0.572  -0.799  -0.841
25    K        -1.383  -1.395  -1.300  -1.365  -1.339  -1.158  -1.226  -1.226  -1.064
26    R        -0.015  -0.170  -0.332   0.068  -0.148  -0.391  -0.026  -0.241  -0.474
27    T        -0.015  -0.077  -0.296   0.163   0.085  -0.237  -0.026  -0.117  -0.424
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    L         1.312   1.332   1.431   1.156   1.196   1.348   1.392   1.422   1.572
44    G         1.312   1.332   1.431   1.243   1.268   1.430   1.392   1.422   1.572
45    R         1.312   1.332   1.431   1.236   1.263   1.423   1.392   1.422   1.572
46    L        -0.312  -0.118  -0.311  -0.466  -0.172  -0.437  -0.462  -0.189  -0.448
47    A         1.312   1.332   1.431   1.212   1.237   1.400   1.392   1.422   1.572
48    S         0.633   0.571   0.398   0.718   0.647   0.382   0.629   0.531   0.205
49    A        -0.876  -0.854  -0.883  -0.824  -0.802  -0.857  -0.899  -0.875  -0.857
50    I         0.633   0.762   0.432   0.801   0.963   0.497   0.629   0.816   0.267
51    A         1.312   1.332   1.431   1.212   1.237   1.400   1.392   1.422   1.572
52    I        -1.501  -1.420  -1.308  -1.503  -1.357  -1.207  -1.335  -1.248  -1.071
53    T        -0.015   0.036  -0.289   0.147   0.214  -0.260  -0.026   0.032  -0.415
54    L         1.312   1.332   1.431   1.156   1.196   1.348   1.392   1.422   1.572
55    I        -0.563  -0.472  -0.417  -0.505  -0.363  -0.308  -0.790  -0.667  -0.594
56    G         1.312   1.332   1.431   1.243   1.268   1.430   1.392   1.422   1.572
57    R         0.633   0.729   0.421   0.478   0.619   0.187   0.629   0.769   0.247
58    H         1.312   1.332   1.431   1.352   1.378   1.532   1.392   1.422   1.572
59    K         1.312   1.332   1.431   1.079   1.127   1.276   1.392   1.422   1.572
60    P         1.312   1.332   1.431   1.406   1.434   1.582   1.392   1.422   1.572
61    V        -0.563  -0.552  -0.438  -0.714  -0.699  -0.518  -0.790  -0.781  -0.622
62    Y        -0.015   0.006  -0.294   0.312   0.333  -0.045  -0.026  -0.005  -0.422
63    H        -1.188  -1.195  -1.277  -0.895  -0.915  -1.048  -1.008  -1.014  -1.042
64    P         0.633   0.571   0.398   0.817   0.741   0.470   0.629   0.531   0.205
65    S        -0.876  -0.945  -0.886  -0.821  -0.928  -0.861  -0.899  -0.956  -0.858
66    Q        -1.501  -1.495  -1.317  -1.506  -1.501  -1.225  -1.335  -1.305  -1.078
67    D         1.312   1.332   1.431   1.364   1.398   1.543   1.392   1.422   1.572
68    C         0.298   0.381   0.332   0.481   0.607   0.484   0.083   0.219   0.084
69    G         1.312   1.332   1.431   1.243   1.268   1.430   1.392   1.422   1.572
70    D         1.312   1.332   1.431   1.364   1.398   1.543   1.392   1.422   1.572
71    Y         0.633   0.533   0.404   0.816   0.681   0.461   0.629   0.472   0.217
72    V         1.312   1.332   1.431   1.228   1.255   1.415   1.392   1.422   1.572
73    V         1.312   1.332   1.431   1.228   1.255   1.415   1.392   1.422   1.572
74    V         1.312   1.332   1.431   1.228   1.255   1.415   1.392   1.422   1.572
75    T         0.633   0.571   0.398   0.717   0.641   0.360   0.629   0.531   0.205
76    N         0.633   0.533   0.404   0.828   0.706   0.501   0.629   0.472   0.217
77    C         0.633   0.571   0.398   0.941   0.858   0.557   0.629   0.531   0.205
78    Q        -0.952  -1.010  -0.902  -0.961  -1.035  -0.864  -1.008  -1.041  -0.877
79    K        -1.383  -1.365  -1.293  -1.488  -1.452  -1.331  -1.226  -1.196  -1.057
80    I        -0.312  -0.238  -0.369  -0.432  -0.335  -0.505  -0.462  -0.384  -0.533
81    R        -0.876  -0.942  -0.893  -0.990  -1.069  -1.006  -0.899  -0.953  -0.865
82    V        -0.876  -0.964  -0.899  -0.812  -0.922  -0.796  -0.899  -0.986  -0.874
83    T         0.298   0.218   0.268   0.249   0.107   0.149   0.083  -0.072  -0.038
84    G         1.312   1.332   1.431   1.243   1.268   1.430   1.392   1.422   1.572
85    K        -1.383  -1.451  -1.306  -1.347  -1.434  -1.253  -1.226  -1.264  -1.068
86    K         1.312   1.332   1.431   1.079   1.127   1.276   1.392   1.422   1.572
87    F        -0.876  -0.756  -0.867  -0.899  -0.746  -0.873  -0.899  -0.749  -0.837
88    E        -1.383  -1.312  -1.289  -1.174  -1.072  -1.055  -1.226  -1.154  -1.055
89    Q        -1.188  -1.219  -1.273  -0.843  -0.905  -1.001  -1.008  -1.040  -1.037
90    K        -0.015  -0.032  -0.286  -0.097  -0.106  -0.470  -0.026  -0.060  -0.410
91    T        -0.015  -0.174  -0.311   0.124  -0.098  -0.346  -0.026  -0.246  -0.446
92    Y         1.312   1.332   1.431   1.417   1.443   1.593   1.392   1.422   1.572
93    W        -0.312  -0.427  -0.402  -0.031  -0.221  -0.187  -0.462  -0.627  -0.579
94    S        -0.015  -0.137  -0.333   0.110  -0.060  -0.401  -0.026  -0.194  -0.477
95    H         0.633   0.571   0.398   0.777   0.702   0.455   0.629   0.531   0.205
96    S        -0.312  -0.284  -0.356  -0.288  -0.223  -0.349  -0.462  -0.408  -0.514
97    G        -0.563  -0.545  -0.441  -0.710  -0.693  -0.555  -0.790  -0.766  -0.626
98    R        -0.312  -0.297  -0.378  -0.383  -0.385  -0.506  -0.462  -0.483  -0.547
99    P         1.312   1.332   1.431   1.406   1.434   1.582   1.392   1.422   1.572
100   G         1.312   1.332   1.431   1.243   1.268   1.430   1.392   1.422   1.572
101   Q        -1.383  -1.265  -1.276  -1.220  -1.087  -1.050  -1.226  -1.121  -1.044
102   L         0.633   0.571   0.398   0.566   0.501   0.244   0.629   0.531   0.205
103   K        -0.624  -0.705  -0.854  -0.644  -0.735  -0.944  -0.572  -0.669  -0.820
104   L        -0.624  -0.816  -0.873  -0.574  -0.841  -0.924  -0.572  -0.799  -0.841
105   Q        -1.383  -1.360  -1.300  -1.246  -1.192  -1.066  -1.226  -1.185  -1.063
106   T        -0.312  -0.303  -0.364  -0.281  -0.260  -0.379  -0.462  -0.435  -0.522
107   M         0.633   0.571   0.398   0.831   0.754   0.463   0.629   0.531   0.205
108   N        -0.876  -0.846  -0.886  -0.815  -0.784  -0.855  -0.899  -0.864  -0.860
109   K        -1.696  -1.607  -1.614  -1.599  -1.488  -1.511  -1.335  -1.254  -1.178
110   V        -0.312  -0.355  -0.389  -0.249  -0.321  -0.449  -0.462  -0.515  -0.561
111   V        -0.876  -0.860  -0.888  -0.776  -0.770  -0.826  -0.899  -0.883  -0.863
112   A        -0.952  -0.832  -0.873  -0.969  -0.821  -0.821  -1.008  -0.885  -0.850
113   D        -0.312  -0.306  -0.390  -0.286  -0.343  -0.476  -0.462  -0.491  -0.563
114   K        -0.624  -0.816  -0.873  -0.644  -0.897  -0.969  -0.572  -0.799  -0.841
115   G         1.312   1.332   1.431   1.243   1.268   1.430   1.392   1.422   1.572
116   F        -1.188  -1.290  -1.283  -0.850  -1.045  -1.039  -1.008  -1.111  -1.047
117   G        -1.070  -1.089  -0.924  -1.294  -1.341  -1.090  -1.117  -1.118  -0.900
118   E         0.633   0.533   0.404   0.813   0.685   0.488   0.629   0.472   0.217
119   I        -0.563  -0.509  -0.434  -0.784  -0.712  -0.602  -0.790  -0.718  -0.616
120   L         0.633   0.680   0.419   0.580   0.652   0.313   0.629   0.698   0.243
121   K         0.062   0.116   0.249  -0.414  -0.293  -0.089  -0.353  -0.264  -0.073
122   K         0.062   0.103   0.240  -0.414  -0.328  -0.116  -0.353  -0.289  -0.091
123   A         0.633   0.571   0.398   0.624   0.545   0.298   0.629   0.531   0.205
124   V         1.312   1.332   1.431   1.228   1.255   1.415   1.392   1.422   1.572
125   S        -0.876  -0.945  -0.886  -0.972  -1.066  -1.023  -0.899  -0.956  -0.858
126   G         1.312   1.332   1.431   1.243   1.268   1.430   1.392   1.422   1.572
127   M         1.312   1.332   1.431   1.433   1.464   1.607   1.392   1.422   1.572
128   L         0.298   0.381   0.332   0.125   0.258   0.176   0.083   0.219   0.084
129   P         1.312   1.332   1.431   1.406   1.434   1.582   1.392   1.422   1.572
130   K         0.298   0.218   0.268  -0.007  -0.137  -0.082   0.083  -0.072  -0.038
131   N         1.312   1.332   1.431   1.410   1.441   1.586   1.392   1.422   1.572
132   K         0.298   0.322   0.284  -0.007   0.044  -0.053   0.083   0.116  -0.006
133   L         0.633   0.680   0.419   0.573   0.645   0.295   0.629   0.698   0.243
134   R        -0.015  -0.174  -0.311   0.065  -0.147  -0.365  -0.026  -0.246  -0.446
135   K        -1.070  -1.072  -0.929  -1.383  -1.328  -1.121  -1.117  -1.103  -0.904
136   Q        -1.814  -1.814  -1.624  -1.759  -1.812  -1.510  -1.444  -1.422  -1.187
137   R         1.312   1.332   1.431   1.236   1.263   1.423   1.392   1.422   1.572
138   L        -0.445  -0.471  -0.399  -0.583  -0.589  -0.456  -0.681  -0.700  -0.577
139   D        -0.445  -0.466  -0.389  -0.648  -0.674  -0.566  -0.681  -0.679  -0.563
140   R         1.312   1.332   1.431   1.236   1.263   1.423   1.392   1.422   1.572
141   L         1.312   1.332   1.431   1.156   1.196   1.348   1.392   1.422   1.572
142   K         0.633   0.533   0.404   0.506   0.405   0.228   0.629   0.472   0.217
143   V        -1.070  -1.056  -0.920  -1.249  -1.219  -1.011  -1.117  -1.085  -0.895
144   F         0.298   0.291   0.287   0.459   0.440   0.390   0.083   0.060  -0.000
145   D         0.298   0.238   0.261   0.322   0.219   0.221   0.083  -0.036  -0.051
146   G         1.312   1.332   1.431   1.243   1.268   1.430   1.392   1.422   1.572
147   S        -1.070  -1.041  -0.919  -1.137  -1.087  -0.918  -1.117  -1.068  -0.895
148   E        -0.015  -0.039  -0.303   0.217   0.174  -0.233  -0.026  -0.063  -0.435
149   N         0.633   0.729   0.421   0.777   0.892   0.493   0.629   0.769   0.247
150   P         1.312   1.332   1.431   1.406   1.434   1.582   1.392   1.422   1.572
151   Y         1.312   1.332   1.431   1.417   1.443   1.593   1.392   1.422   1.572
152   K         0.633   0.741   0.426   0.479   0.634   0.198   0.629   0.786   0.255
153   Q        -1.383  -1.362  -1.281  -1.193  -1.174  -1.064  -1.226  -1.193  -1.048
154   N         1.312   1.332   1.431   1.410   1.441   1.586   1.392   1.422   1.572
155   I        -0.445  -0.341  -0.389  -0.582  -0.451  -0.432  -0.681  -0.558  -0.564
156   T        -1.070  -1.087  -0.929  -1.068  -1.088  -0.842  -1.117  -1.116  -0.904
157   A         0.298   0.220   0.261   0.123  -0.030   0.013   0.083  -0.069  -0.050
158   F         0.080   0.110   0.243   0.067   0.107   0.300  -0.318  -0.275  -0.085
159   A        -0.124  -0.309  -0.370  -0.088  -0.363  -0.472  -0.175  -0.434  -0.529
160   H        -0.769  -0.725  -0.876  -0.628  -0.577  -0.857  -0.745  -0.698  -0.844
161   E        -0.412  -0.336  -0.399  -0.448  -0.363  -0.473  -0.603  -0.518  -0.574
162   Q        -0.929  -0.963  -0.925  -0.732  -0.805  -0.767  -0.935  -0.977  -0.898
163   S        -1.503  -1.441  -1.313  -1.563  -1.474  -1.333  -1.323  -1.257  -1.074
164   S        -1.503  -1.464  -1.320  -1.491  -1.453  -1.263  -1.323  -1.278  -1.080
165   I        -1.503  -1.435  -1.330  -1.455  -1.382  -1.256  -1.323  -1.252  -1.088
166   P        -1.086  -1.019  -0.926  -1.116  -1.008  -0.922  -1.129  -1.048  -0.900
167   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   L        -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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
183   K        -0.929  -0.895  -0.895  -0.979  -0.924  -0.953  -0.935  -0.898  -0.866
184   E        -0.499  -0.412  -0.392  -0.672  -0.564  -0.502  -0.745  -0.643  -0.570
185   S        -1.349  -1.293  -1.287  -1.467  -1.399  -1.375  -1.173  -1.113  -1.051
186   I        -1.841  -1.808  -1.644  -1.536  -1.519  -1.281  -1.458  -1.416  -1.200
187   F        -0.991  -0.943  -0.903  -1.085  -1.019  -0.897  -1.030  -0.972  -0.878
188   N        -1.091  -1.028  -0.926  -1.127  -1.074  -0.896  -1.121  -1.052  -0.899
189   Q        -1.349  -1.438  -1.312  -1.105  -1.253  -1.097  -1.173  -1.250  -1.073
190   L        -1.814  -1.783  -1.619  -1.819  -1.783  -1.535  -1.444  -1.400  -1.183
191   K        -1.696  -1.636  -1.610  -1.725  -1.634  -1.584  -1.335  -1.275  -1.175
* 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/Q12487
Output conservation file - output/Q12487
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
