1     M         1.662   1.726   1.884   1.825   1.905   2.159   1.822   1.923   2.212
2     G         1.662   1.726   1.884   1.694   1.772   2.024   1.822   1.923   2.212
3     R         0.875   0.745   0.701   0.942   0.759   0.703   0.879   0.653   0.523
4     Y         0.133  -0.058  -0.099   0.398   0.156   0.087   0.094  -0.184  -0.257
5     S         0.514   0.442   0.566   0.464   0.316   0.468   0.251   0.088   0.252
6     V         0.133  -0.058  -0.099   0.246  -0.064  -0.171   0.094  -0.184  -0.257
7     K         0.875   0.745   0.701   0.671   0.492   0.413   0.879   0.653   0.523
8     R         0.875   0.745   0.701   0.921   0.726   0.650   0.879   0.653   0.523
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    Y         0.250   0.136  -0.002   0.582   0.463   0.305   0.258   0.099  -0.111
20    K         0.939   0.949   0.770   0.778   0.799   0.550   0.980   0.994   0.658
21    T         1.662   1.726   1.884   1.586   1.677   1.913   1.822   1.923   2.212
22    K         0.583   0.539   0.614   0.286   0.195   0.287   0.379   0.275   0.350
23    R         0.939   0.949   0.770   0.992   0.991   0.779   0.980   0.994   0.658
24    R         0.939   0.949   0.770   0.999   1.000   0.795   0.980   0.994   0.658
25    T         0.250   0.136  -0.002   0.369   0.229   0.013   0.258   0.099  -0.111
26    R         0.583   0.732   0.649   0.418   0.632   0.447   0.379   0.630   0.421
27    D         1.662   1.726   1.884   1.629   1.700   1.957   1.822   1.923   2.212
28    L         0.939   0.862   0.762   0.892   0.815   0.667   0.980   0.852   0.642
29    D         1.662   1.726   1.884   1.629   1.700   1.957   1.822   1.923   2.212
30    L         0.392   0.384   0.537   0.084   0.072   0.277   0.018  -0.029   0.193
31    I         0.939   0.862   0.762   1.119   1.034   0.890   0.980   0.852   0.642
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    Y        -0.667  -0.802  -0.724  -0.427  -0.610  -0.505  -0.704  -0.836  -0.729
34    N        -0.667  -0.759  -0.722  -0.658  -0.777  -0.802  -0.704  -0.781  -0.724
35    D         0.583   0.732   0.649   0.463   0.683   0.497   0.379   0.630   0.421
36    L         0.939   0.847   0.749   0.915   0.826   0.704   0.980   0.827   0.616
37    S        -1.206  -1.262  -1.186  -1.042  -1.080  -1.026  -1.065  -1.100  -0.974
38    T        -0.667  -0.764  -0.720  -0.556  -0.685  -0.673  -0.704  -0.802  -0.726
39    K        -1.332  -1.297  -1.215  -1.319  -1.219  -1.132  -1.185  -1.130  -1.001
40    E        -0.399  -0.518  -0.673  -0.419  -0.594  -0.860  -0.343  -0.492  -0.660
41    S        -0.667  -0.652  -0.685  -0.570  -0.516  -0.600  -0.704  -0.677  -0.684
42    V        -0.399  -0.407  -0.602  -0.049  -0.065  -0.329  -0.343  -0.355  -0.573
43    Q        -1.665  -1.680  -1.575  -1.505  -1.582  -1.382  -1.306  -1.293  -1.143
44    K        -1.539  -1.546  -1.542  -1.523  -1.554  -1.525  -1.185  -1.180  -1.114
45    L         0.939   0.862   0.762   0.899   0.825   0.684   0.980   0.852   0.642
46    L        -0.266  -0.285  -0.197  -0.608  -0.591  -0.462  -0.535  -0.531  -0.412
47    N         0.875   0.701   0.761   0.975   0.720   0.776   0.879   0.575   0.640
48    Q         0.875   0.701   0.761   0.938   0.709   0.767   0.879   0.575   0.640
49    P         0.250   0.046  -0.076   0.489   0.189  -0.084   0.258  -0.029  -0.223
50    L        -0.667  -0.804  -0.728  -0.652  -0.812  -0.711  -0.704  -0.839  -0.733
51    D         0.939   0.862   0.762   1.026   0.926   0.799   0.980   0.852   0.642
52    E         0.939   0.949   0.770   0.840   0.855   0.649   0.980   0.994   0.658
53    T        -1.206  -1.219  -1.202  -1.173  -1.213  -1.191  -1.065  -1.066  -0.989
54    K         0.583   0.539   0.614   0.252   0.167   0.233   0.379   0.275   0.350
55    P         0.939   1.025   0.768   1.149   1.265   0.907   0.980   1.113   0.653
56    G         1.662   1.726   1.884   1.709   1.793   2.040   1.822   1.923   2.212
57    L         1.662   1.726   1.884   1.494   1.588   1.819   1.822   1.923   2.212
58    G         0.939   0.847   0.749   1.090   0.974   0.815   0.980   0.827   0.616
59    Q         0.939   0.862   0.762   1.024   0.938   0.780   0.980   0.852   0.642
60    H        -0.208  -0.240  -0.167  -0.061  -0.059   0.045  -0.464  -0.473  -0.375
61    Y         1.662   1.726   1.884   1.717   1.808   2.048   1.822   1.923   2.212
62    C         1.662   1.726   1.884   1.858   1.943   2.193   1.822   1.923   2.212
63    I         0.939   0.862   0.762   1.119   1.034   0.890   0.980   0.852   0.642
64    H        -0.748  -0.737  -0.723  -0.709  -0.709  -0.654  -0.825  -0.790  -0.729
65    C         1.662   1.726   1.884   1.858   1.943   2.193   1.822   1.923   2.212
66    A         1.662   1.726   1.884   1.555   1.635   1.882   1.822   1.923   2.212
67    K         0.583   0.531   0.583   0.286   0.182   0.233   0.379   0.260   0.287
68    Y         0.939   0.862   0.762   1.150   1.080   0.971   0.980   0.852   0.642
69    M         0.250   0.436  -0.012   0.680   0.907   0.355   0.258   0.521  -0.125
70    E         0.583   0.539   0.614   0.332   0.235   0.339   0.379   0.275   0.350
71    T        -0.667  -0.720  -0.712  -0.523  -0.550  -0.535  -0.704  -0.741  -0.711
72    A        -1.332  -1.249  -1.219  -1.363  -1.263  -1.179  -1.185  -1.089  -1.004
73    I        -1.539  -1.612  -1.550  -1.111  -1.188  -1.131  -1.185  -1.235  -1.122
74    A         0.250   0.231  -0.027   0.353   0.326  -0.024   0.258   0.228  -0.148
75    L         0.939   0.847   0.749   0.852   0.739   0.542   0.980   0.827   0.616
76    K        -1.206  -1.317  -1.213  -1.288  -1.404  -1.270  -1.065  -1.142  -0.998
77    T        -0.667  -0.720  -0.712  -0.676  -0.751  -0.768  -0.704  -0.741  -0.711
78    H         1.662   1.726   1.884   1.801   1.886   2.134   1.822   1.923   2.212
79    L        -0.748  -0.802  -0.744  -0.893  -0.915  -0.873  -0.825  -0.852  -0.752
80    K         0.939   0.847   0.749   0.778   0.666   0.515   0.980   0.827   0.616
81    G         0.250   0.428  -0.003   0.506   0.737   0.158   0.258   0.513  -0.113
82    K         1.662   1.726   1.884   1.392   1.480   1.715   1.822   1.923   2.212
83    V        -0.208  -0.217  -0.151  -0.177  -0.149  -0.054  -0.464  -0.441  -0.352
84    H         1.662   1.726   1.884   1.801   1.886   2.134   1.822   1.923   2.212
85    K         0.939   1.080   0.784   0.778   0.956   0.572   0.980   1.196   0.684
86    R         1.662   1.726   1.884   1.594   1.655   1.922   1.822   1.923   2.212
87    R         1.662   1.726   1.884   1.594   1.655   1.922   1.822   1.923   2.212
88    V        -0.208  -0.160  -0.172  -0.359  -0.320  -0.321  -0.464  -0.409  -0.384
89    K         0.939   1.025   0.768   0.778   0.892   0.547   0.980   1.113   0.653
90    E        -0.399  -0.321  -0.647  -0.335  -0.234  -0.654  -0.343  -0.236  -0.628
91    L         0.939   0.847   0.749   0.900   0.806   0.664   0.980   0.827   0.616
92    R        -0.208  -0.135  -0.158  -0.500  -0.421  -0.391  -0.464  -0.380  -0.364
93    G        -0.667  -0.458  -0.684  -0.702  -0.420  -0.694  -0.704  -0.430  -0.679
94    V        -1.206  -1.202  -1.177  -1.053  -1.050  -1.004  -1.065  -1.040  -0.964
95    P         1.662   1.726   1.884   1.768   1.854   2.100   1.822   1.923   2.212
96    Y         1.662   1.726   1.884   1.717   1.808   2.048   1.822   1.923   2.212
97    T         0.939   1.025   0.768   0.988   1.110   0.779   0.980   1.113   0.653
98    Q        -0.399  -0.392  -0.664  -0.083  -0.054  -0.405  -0.343  -0.332  -0.649
99    E        -0.667  -0.631  -0.713  -0.883  -0.838  -0.980  -0.704  -0.647  -0.711
100   V         0.392   0.533   0.587   0.044   0.251   0.319   0.018   0.264   0.296
101   S         0.583   0.720   0.614   0.481   0.679   0.496   0.379   0.609   0.349
102   D        -0.208  -0.260  -0.177  -0.405  -0.471  -0.343  -0.464  -0.508  -0.388
103   A         0.939   0.847   0.749   0.976   0.873   0.763   0.980   0.827   0.616
104   A         1.662   1.726   1.884   1.555   1.635   1.882   1.822   1.923   2.212
105   A        -0.208  -0.158  -0.149  -0.339  -0.273  -0.238  -0.464  -0.405  -0.354
106   G         0.939   0.949   0.770   1.110   1.134   0.900   0.980   0.994   0.658
107   Y        -1.539  -1.567  -1.551  -1.111  -1.168  -1.108  -1.185  -1.200  -1.122
108   N         0.797   0.903   0.731   0.918   1.068   0.826   0.753   0.921   0.581
109   L        -0.447  -0.385  -0.248  -0.542  -0.427  -0.257  -0.744  -0.660  -0.479
110   N        -0.723  -0.785  -0.771  -0.702  -0.833  -0.890  -0.744  -0.820  -0.777
111   K        -0.003  -0.097  -0.137  -0.132  -0.277  -0.330  -0.103  -0.256  -0.315
112   F         0.797   0.633   0.681   1.079   0.837   0.894   0.753   0.451   0.485
113   L        -0.003   0.087  -0.118   0.031   0.172  -0.108  -0.103   0.030  -0.286
114   N        -0.280  -0.175  -0.163  -0.466  -0.315  -0.323  -0.530  -0.371  -0.358
115   R         0.331   0.386   0.535   0.128   0.194   0.419  -0.103  -0.024   0.188
116   V         0.797   0.633   0.681   0.905   0.675   0.722   0.753   0.451   0.485
117   Q        -0.003  -0.063  -0.128  -0.138  -0.263  -0.338  -0.103  -0.211  -0.301
118   E        -0.723  -0.725  -0.746  -0.907  -0.891  -0.969  -0.744  -0.755  -0.747
119   I        -0.891  -0.892  -0.796  -0.723  -0.743  -0.565  -0.958  -0.948  -0.807
120   T         0.797   0.946   0.738   0.597   0.807   0.494   0.753   0.990   0.595
121   Q        -1.334  -1.314  -1.220  -1.315  -1.333  -1.170  -1.172  -1.141  -1.002
122   S        -0.895  -0.836  -0.803  -0.998  -0.910  -0.853  -0.950  -0.870  -0.813
123   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   G        -0.790  -0.766  -0.761  -0.787  -0.757  -0.747  -0.849  -0.811  -0.768
125   P        -0.790  -0.753  -0.740  -0.712  -0.663  -0.644  -0.849  -0.786  -0.744
126   E        -1.694  -1.577  -1.563  -1.406  -1.226  -1.213  -1.320  -1.208  -1.132
127   K         0.875   0.762   0.701   0.676   0.520   0.368   0.879   0.683   0.523
128   E         0.514   0.503   0.600   0.209   0.169   0.301   0.251   0.205   0.322
129   S        -0.790  -0.688  -0.717  -0.916  -0.777  -0.804  -0.849  -0.736  -0.721
130   N         0.514   0.422   0.564   0.486   0.308   0.505   0.251   0.047   0.247
131   E        -0.790  -0.912  -0.778  -1.110  -1.271  -1.099  -0.849  -0.959  -0.787
132   A        -1.694  -1.593  -1.568  -1.536  -1.346  -1.360  -1.320  -1.221  -1.136
133   L        -1.313  -1.344  -1.233  -1.428  -1.445  -1.273  -1.163  -1.171  -1.015
134   L        -0.399  -0.392  -0.664  -0.177  -0.141  -0.442  -0.343  -0.332  -0.649
135   K        -0.874  -0.784  -0.753  -1.066  -0.884  -0.892  -0.945  -0.818  -0.759
136   E        -0.748  -0.600  -0.723  -0.914  -0.683  -0.863  -0.825  -0.651  -0.732
137   H        -0.874  -0.914  -0.787  -0.799  -0.855  -0.690  -0.945  -0.966  -0.798
138   L        -0.162  -0.153  -0.204  -0.360  -0.356  -0.488  -0.334  -0.321  -0.415
139   D         0.701   0.745   0.652   0.753   0.810   0.648   0.590   0.652   0.426
140   S        -0.790  -0.654  -0.750  -0.702  -0.516  -0.638  -0.849  -0.717  -0.759
141   T        -0.790  -0.917  -0.778  -0.935  -1.096  -0.909  -0.849  -0.965  -0.787
142   L        -0.173  -0.249  -0.158  -0.401  -0.455  -0.373  -0.378  -0.464  -0.350
143   A        -0.933  -0.950  -0.789  -1.151  -1.201  -0.956  -1.006  -0.999  -0.800
144   N         0.875   0.788   0.717   0.975   0.858   0.693   0.879   0.727   0.554
145   V        -0.790  -0.786  -0.740  -0.780  -0.775  -0.700  -0.849  -0.836  -0.744
146   K        -0.891  -0.778  -0.775  -1.116  -0.982  -0.976  -0.958  -0.829  -0.783
147   T        -0.280  -0.358  -0.222  -0.463  -0.576  -0.394  -0.530  -0.623  -0.443
148   T        -0.280  -0.358  -0.222  -0.392  -0.514  -0.325  -0.530  -0.623  -0.443
149   E        -0.280  -0.358  -0.222  -0.582  -0.737  -0.532  -0.530  -0.623  -0.443
150   P        -0.891  -0.901  -0.798  -0.848  -0.882  -0.720  -0.958  -0.956  -0.809
151   T        -0.280  -0.358  -0.222  -0.380  -0.499  -0.312  -0.530  -0.623  -0.443
152   L        -0.280  -0.358  -0.222  -0.414  -0.492  -0.314  -0.530  -0.623  -0.443
153   P         0.797   0.633   0.681   0.997   0.765   0.812   0.753   0.451   0.485
154   W        -0.891  -0.901  -0.798  -0.573  -0.566  -0.419  -0.958  -0.956  -0.809
155   A        -0.723  -0.612  -0.727  -0.776  -0.610  -0.833  -0.744  -0.598  -0.725
156   A        -0.891  -0.885  -0.796  -1.083  -1.106  -0.944  -0.958  -0.942  -0.807
157   A        -1.334  -1.304  -1.220  -1.222  -1.252  -1.048  -1.172  -1.132  -1.002
158   D        -1.334  -1.184  -1.202  -1.203  -0.973  -1.014  -1.172  -1.005  -0.985
159   A        -1.334  -1.280  -1.239  -1.437  -1.401  -1.358  -1.172  -1.111  -1.020
160   E        -0.891  -0.893  -0.775  -1.190  -1.204  -1.049  -0.958  -0.950  -0.785
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   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   T        -0.895  -0.888  -0.800  -1.020  -1.069  -0.921  -0.950  -0.936  -0.810
175   A        -1.428  -1.363  -1.253  -1.507  -1.398  -1.261  -1.258  -1.180  -1.032
176   A        -1.334  -1.306  -1.219  -1.428  -1.423  -1.293  -1.172  -1.134  -1.001
177   V        -0.891  -0.918  -0.783  -0.864  -0.880  -0.684  -0.958  -0.971  -0.793
178   T        -0.003   0.160  -0.066   0.136   0.378   0.023  -0.103   0.135  -0.207
179   E        -1.334  -1.327  -1.237  -1.268  -1.230  -1.077  -1.172  -1.152  -1.018
180   A        -1.334  -1.318  -1.235  -1.293  -1.253  -1.150  -1.172  -1.145  -1.016
181   E        -0.723  -0.595  -0.723  -0.833  -0.663  -0.836  -0.744  -0.577  -0.720
182   S        -0.874  -0.749  -0.756  -0.965  -0.769  -0.769  -0.945  -0.796  -0.765
183   T        -1.206  -1.261  -1.177  -1.294  -1.375  -1.239  -1.065  -1.097  -0.967
184   A        -1.332  -1.303  -1.210  -1.362  -1.335  -1.170  -1.185  -1.138  -0.997
185   S        -1.665  -1.646  -1.575  -1.306  -1.306  -1.192  -1.306  -1.272  -1.143
186   A        -0.667  -0.604  -0.724  -0.426  -0.405  -0.557  -0.704  -0.662  -0.730
187   S        -1.665  -1.502  -1.559  -1.382  -1.127  -1.225  -1.306  -1.156  -1.132
188   T        -1.539  -1.525  -1.539  -1.203  -1.187  -1.198  -1.185  -1.163  -1.112
* 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/Q08004
Output conservation file - output/Q08004
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
