1     M         1.520   1.585   1.639   1.773   1.872   1.954   1.687   1.786   1.880
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     T        -0.829  -0.718  -0.804  -0.571  -0.389  -0.526  -0.843  -0.701  -0.774
7     H        -0.660  -0.495  -0.744  -0.610  -0.370  -0.721  -0.633  -0.418  -0.705
8     S        -0.387  -0.444  -0.441  -0.388  -0.496  -0.475  -0.527  -0.578  -0.570
9     L        -1.205  -1.216  -1.147  -1.398  -1.404  -1.304  -1.054  -1.039  -0.948
10    K        -0.829  -0.851  -0.819  -0.952  -0.941  -0.912  -0.843  -0.842  -0.790
11    A        -0.932  -0.900  -0.853  -1.138  -1.104  -1.024  -0.949  -0.891  -0.825
12    L        -0.387  -0.476  -0.447  -0.515  -0.623  -0.597  -0.527  -0.612  -0.577
13    F        -1.102  -0.961  -1.092  -0.983  -0.795  -0.967  -0.949  -0.782  -0.898
14    A        -0.932  -0.957  -0.862  -1.150  -1.200  -1.030  -0.949  -0.944  -0.833
15    L        -0.012   0.025  -0.001  -0.275  -0.220  -0.243  -0.316  -0.271  -0.286
16    L        -1.205  -1.158  -1.142  -1.194  -1.079  -1.091  -1.054  -0.986  -0.944
17    F        -0.829  -0.832  -0.827  -0.770  -0.813  -0.741  -0.843  -0.828  -0.799
18    L        -0.829  -0.833  -0.831  -0.877  -0.906  -0.901  -0.843  -0.828  -0.802
19    Y        -0.829  -0.843  -0.823  -0.875  -0.937  -0.845  -0.843  -0.841  -0.795
20    T        -1.205  -1.182  -1.147  -1.216  -1.164  -1.114  -1.054  -1.013  -0.948
21    A        -1.102  -1.085  -1.115  -0.973  -1.007  -0.987  -0.949  -0.918  -0.918
22    A        -1.205  -1.144  -1.141  -1.224  -1.118  -1.125  -1.054  -0.973  -0.943
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    V        -0.829  -0.751  -0.819  -0.881  -0.809  -0.849  -0.843  -0.758  -0.793
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    N        -0.829  -0.800  -0.818  -0.811  -0.795  -0.777  -0.843  -0.801  -0.792
28    A        -0.932  -0.954  -0.863  -0.837  -0.865  -0.720  -0.949  -0.941  -0.834
29    G        -1.477  -1.447  -1.402  -1.386  -1.281  -1.269  -1.160  -1.113  -1.041
30    V        -1.205  -1.178  -1.151  -1.096  -1.019  -1.038  -1.054  -1.011  -0.952
31    I        -0.488  -0.419  -0.475  -0.633  -0.555  -0.600  -0.654  -0.576  -0.616
32    G        -0.799  -0.839  -0.844  -0.605  -0.687  -0.659  -0.792  -0.825  -0.811
33    I        -0.799  -0.788  -0.820  -0.659  -0.622  -0.701  -0.792  -0.774  -0.786
34    F        -0.917  -0.841  -0.852  -0.947  -0.853  -0.841  -0.929  -0.833  -0.822
35    N        -0.917  -0.845  -0.849  -0.862  -0.731  -0.740  -0.929  -0.837  -0.820
36    -        -0.575  -0.478  -0.485  -0.606  -0.452  -0.477  -0.742  -0.606  -0.620
37    -        -1.010  -0.975  -0.896  -1.145  -1.069  -0.974  -1.012  -0.955  -0.862
38    -        -0.575  -0.585  -0.522  -0.602  -0.656  -0.563  -0.742  -0.742  -0.664
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    -         1.520   1.585   1.639   1.548   1.650   1.727   1.687   1.786   1.880
42    -        -1.010  -0.975  -0.896  -1.062  -1.029  -0.891  -1.012  -0.955  -0.862
43    -         0.026  -0.023  -0.010  -0.038  -0.133  -0.105  -0.202  -0.283  -0.279
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    A        -1.205  -1.202  -1.151  -1.248  -1.251  -1.175  -1.054  -1.028  -0.952
56    L        -1.477  -1.402  -1.386  -1.589  -1.445  -1.455  -1.160  -1.070  -1.029
57    P        -1.477  -1.483  -1.412  -1.405  -1.443  -1.302  -1.160  -1.137  -1.048
58    P        -1.477  -1.483  -1.412  -1.323  -1.346  -1.209  -1.160  -1.137  -1.048
59    P        -1.205  -1.156  -1.138  -1.144  -1.066  -1.030  -1.054  -0.985  -0.941
60    N        -0.829  -0.821  -0.821  -0.785  -0.778  -0.782  -0.843  -0.813  -0.793
61    T        -0.829  -0.874  -0.833  -0.796  -0.880  -0.795  -0.843  -0.869  -0.805
62    K         0.105   0.036   0.013   0.057  -0.077  -0.143  -0.105  -0.223  -0.257
63    P         0.105  -0.019   0.019   0.034  -0.142  -0.104  -0.105  -0.275  -0.243
64    I         0.636   0.675   0.630   0.435   0.486   0.381   0.422   0.476   0.344
65    N         0.928   1.057   0.813   0.962   1.137   0.820   0.949   1.155   0.711
66    G         1.520   1.585   1.639   1.569   1.663   1.748   1.687   1.786   1.880
67    E        -0.168  -0.255  -0.364  -0.034  -0.184  -0.355  -0.211  -0.331  -0.465
68    S         0.928   0.786   0.777   1.043   0.837   0.844   0.949   0.688   0.641
69    P         1.520   1.585   1.639   1.478   1.575   1.657   1.687   1.786   1.880
70    L        -0.012  -0.093  -0.006  -0.350  -0.454  -0.334  -0.316  -0.399  -0.291
71    Y        -1.477  -1.372  -1.389  -1.348  -1.166  -1.220  -1.160  -1.045  -1.031
72    Q        -1.102  -1.141  -1.123  -0.774  -0.821  -0.822  -0.949  -0.969  -0.926
73    C         1.520   1.585   1.639   1.708   1.804   1.888   1.687   1.786   1.880
74    D         0.363   0.245   0.133   0.476   0.293   0.113   0.316   0.126  -0.054
75    I        -0.387  -0.404  -0.440  -0.510  -0.538  -0.606  -0.527  -0.533  -0.569
76    L        -1.205  -1.182  -1.147  -1.162  -1.086  -1.069  -1.054  -1.013  -0.948
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    D        -1.477  -1.464  -1.405  -1.331  -1.300  -1.211  -1.160  -1.124  -1.043
81    K        -1.205  -1.119  -1.139  -1.163  -1.020  -1.069  -1.054  -0.950  -0.943
82    Q         0.636   0.563   0.602   0.724   0.578   0.614   0.422   0.251   0.285
83    L        -0.168  -0.258  -0.376  -0.138  -0.236  -0.429  -0.211  -0.334  -0.481
84    V         0.480   0.486   0.553   0.115   0.108   0.201   0.105   0.089   0.179
85    E        -1.102  -1.114  -1.125  -0.956  -1.007  -0.974  -0.949  -0.945  -0.927
86    I        -0.115  -0.100  -0.059  -0.469  -0.456  -0.416  -0.422  -0.401  -0.357
87    K        -0.932  -0.907  -0.857  -0.933  -0.885  -0.807  -0.949  -0.898  -0.828
88    E        -1.102  -1.112  -1.115  -0.874  -0.882  -0.859  -0.949  -0.943  -0.919
89    V         0.105   0.004   0.027  -0.080  -0.240  -0.247  -0.105  -0.237  -0.231
90    N        -0.829  -0.771  -0.814  -0.813  -0.714  -0.799  -0.843  -0.759  -0.785
91    L         0.105   0.212   0.055  -0.119   0.056  -0.223  -0.105   0.054  -0.188
92    D        -0.557  -0.603  -0.502  -0.731  -0.814  -0.660  -0.738  -0.761  -0.645
93    P         1.520   1.585   1.639   1.478   1.575   1.657   1.687   1.786   1.880
94    N         1.520   1.585   1.639   1.636   1.731   1.816   1.687   1.786   1.880
95    P         1.520   1.585   1.639   1.478   1.575   1.657   1.687   1.786   1.880
96    P         1.520   1.585   1.639   1.478   1.575   1.657   1.687   1.786   1.880
97    V        -1.205  -1.142  -1.136  -1.273  -1.172  -1.162  -1.054  -0.971  -0.940
98    R        -0.012   0.018  -0.003  -0.019  -0.017  -0.015  -0.316  -0.279  -0.289
99    G         1.520   1.585   1.639   1.569   1.663   1.748   1.687   1.786   1.880
100   E        -0.454  -0.509  -0.462  -0.448  -0.504  -0.439  -0.633  -0.672  -0.602
101   N         0.363   0.398   0.165   0.586   0.642   0.294   0.316   0.373  -0.003
102   L         1.520   1.585   1.639   1.395   1.502   1.573   1.687   1.786   1.880
103   T         0.928   1.005   0.803   0.994   1.100   0.811   0.949   1.071   0.692
104   I         0.636   0.731   0.662   0.515   0.654   0.548   0.422   0.585   0.409
105   S        -1.102  -0.928  -1.091  -1.071  -0.790  -1.071  -0.949  -0.747  -0.897
106   A         0.928   0.786   0.777   0.954   0.745   0.740   0.949   0.688   0.641
107   N        -1.102  -1.054  -1.108  -0.986  -0.954  -1.022  -0.949  -0.890  -0.912
108   G         0.928   0.786   0.777   1.022   0.815   0.789   0.949   0.688   0.641
109   E        -1.205  -1.222  -1.152  -1.241  -1.236  -1.145  -1.054  -1.043  -0.952
110   V        -0.012   0.023   0.003  -0.344  -0.294  -0.321  -0.316  -0.273  -0.282
111   F        -1.477  -1.468  -1.411  -1.138  -1.143  -1.049  -1.160  -1.127  -1.048
112   E        -0.387  -0.349  -0.439  -0.407  -0.368  -0.467  -0.527  -0.488  -0.572
113   T         0.105   0.131   0.049   0.075   0.114  -0.029  -0.105  -0.055  -0.198
114   I         0.636   0.581   0.599   0.435   0.311   0.319   0.422   0.287   0.279
115   E         0.928   0.786   0.777   0.924   0.726   0.687   0.949   0.688   0.641
116   E         0.363   0.245   0.133   0.440   0.286   0.116   0.316   0.126  -0.054
117   G         1.520   1.585   1.639   1.569   1.663   1.748   1.687   1.786   1.880
118   A         0.928   0.786   0.777   0.957   0.746   0.747   0.949   0.688   0.641
119   Y         1.520   1.585   1.639   1.636   1.730   1.816   1.687   1.786   1.880
120   I         0.480   0.574   0.589   0.150   0.311   0.308   0.105   0.273   0.257
121   D        -0.012   0.016   0.005  -0.152  -0.087  -0.104  -0.316  -0.259  -0.275
122   V         0.105   0.052   0.018  -0.074  -0.187  -0.264  -0.105  -0.193  -0.249
123   E         0.105   0.061   0.018   0.081   0.016  -0.040  -0.105  -0.199  -0.249
124   V         1.520   1.585   1.639   1.451   1.540   1.630   1.687   1.786   1.880
125   R         0.636   0.563   0.602   0.762   0.612   0.652   0.422   0.251   0.285
126   L         0.480   0.577   0.594   0.303   0.492   0.472   0.105   0.280   0.268
127   G         1.520   1.585   1.639   1.569   1.663   1.748   1.687   1.786   1.880
128   Y         0.480   0.492   0.555   0.455   0.457   0.554   0.105   0.101   0.183
129   I         0.928   0.786   0.777   0.878   0.673   0.652   0.949   0.688   0.641
130   R         0.430   0.483   0.550   0.341   0.435   0.529   0.000   0.082   0.173
131   L         0.928   0.786   0.777   0.847   0.655   0.616   0.949   0.688   0.641
132   L        -0.012  -0.090  -0.003  -0.351  -0.454  -0.334  -0.316  -0.394  -0.285
133   S        -0.557  -0.530  -0.505  -0.474  -0.450  -0.387  -0.738  -0.696  -0.649
134   Q         0.363   0.202   0.128   0.621   0.387   0.251   0.316   0.065  -0.061
135   T         0.363   0.202   0.128   0.517   0.299   0.197   0.316   0.065  -0.061
136   F        -0.557  -0.555  -0.502  -0.596  -0.628  -0.536  -0.738  -0.719  -0.647
137   D         1.520   1.585   1.639   1.549   1.643   1.729   1.687   1.786   1.880
138   L         0.928   0.786   0.777   0.847   0.655   0.616   0.949   0.688   0.641
139   C         1.520   1.585   1.639   1.708   1.804   1.888   1.687   1.786   1.880
140   E         0.363   0.202   0.128   0.427   0.206   0.085   0.316   0.065  -0.061
141   T        -0.829  -0.833  -0.831  -0.810  -0.807  -0.810  -0.843  -0.828  -0.802
142   L        -0.829  -0.896  -0.846  -0.945  -1.030  -0.928  -0.843  -0.885  -0.816
143   E        -0.660  -0.730  -0.791  -0.574  -0.665  -0.783  -0.633  -0.705  -0.755
144   D        -0.932  -0.909  -0.861  -0.922  -0.876  -0.792  -0.949  -0.900  -0.831
145   N        -0.454  -0.512  -0.469  -0.575  -0.683  -0.621  -0.633  -0.674  -0.609
146   D         0.363   0.202   0.128   0.476   0.232   0.105   0.316   0.065  -0.061
147   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   L         0.363   0.242   0.132   0.372   0.201   0.063   0.316   0.123  -0.055
151   S        -0.829  -0.684  -0.795  -0.808  -0.599  -0.738  -0.843  -0.665  -0.766
152   C         1.520   1.585   1.639   1.708   1.804   1.888   1.687   1.786   1.880
153   P         1.520   1.585   1.639   1.478   1.575   1.657   1.687   1.786   1.880
154   I         0.928   0.786   0.777   0.878   0.673   0.652   0.949   0.688   0.641
155   E        -0.012   0.024   0.001  -0.155  -0.110  -0.128  -0.316  -0.268  -0.283
156   P        -0.829  -0.748  -0.807  -0.854  -0.751  -0.836  -0.843  -0.752  -0.781
157   G         1.520   1.585   1.639   1.569   1.663   1.748   1.687   1.786   1.880
158   E        -1.477  -1.464  -1.405  -1.319  -1.306  -1.215  -1.160  -1.124  -1.043
159   Y        -0.557  -0.612  -0.512  -0.613  -0.714  -0.573  -0.738  -0.773  -0.657
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   N        -1.205  -1.154  -1.139  -1.133  -1.060  -1.049  -1.054  -0.983  -0.942
162   I        -0.012  -0.091  -0.006  -0.326  -0.410  -0.301  -0.316  -0.395  -0.291
163   K        -1.205  -1.200  -1.147  -1.056  -1.027  -0.964  -1.054  -1.026  -0.949
164   K         0.928   0.786   0.777   1.028   0.828   0.804   0.949   0.688   0.641
165   I        -1.205  -1.219  -1.153  -1.113  -1.118  -1.014  -1.054  -1.039  -0.953
166   V         0.636   0.581   0.599   0.455   0.325   0.330   0.422   0.287   0.279
167   E         0.363   0.250   0.134   0.426   0.265   0.092   0.316   0.134  -0.052
168   I         0.480   0.480   0.551   0.108   0.077   0.180   0.105   0.075   0.176
169   P         1.520   1.585   1.639   1.478   1.575   1.657   1.687   1.786   1.880
170   G        -1.749  -1.710  -1.636  -1.408  -1.290  -1.238  -1.265  -1.209  -1.119
171   E         0.928   0.786   0.777   0.936   0.741   0.715   0.949   0.688   0.641
172   V         0.480   0.480   0.551   0.150   0.107   0.223   0.105   0.075   0.176
173   P         1.520   1.585   1.639   1.478   1.575   1.657   1.687   1.786   1.880
174   P         1.520   1.585   1.639   1.478   1.575   1.657   1.687   1.786   1.880
175   G         1.520   1.585   1.639   1.569   1.663   1.748   1.687   1.786   1.880
176   K         0.928   0.786   0.777   1.062   0.890   0.876   0.949   0.688   0.641
177   Y         1.520   1.585   1.639   1.636   1.730   1.816   1.687   1.786   1.880
178   V        -1.205  -1.218  -1.150  -1.269  -1.217  -1.160  -1.054  -1.040  -0.951
179   V         0.928   0.996   0.806   0.913   1.006   0.741   0.949   1.056   0.699
180   V        -1.102  -1.136  -1.120  -1.162  -1.252  -1.230  -0.949  -0.964  -0.923
181   A         1.520   1.585   1.639   1.484   1.564   1.663   1.687   1.786   1.880
182   R         0.363   0.202   0.128   0.667   0.430   0.306   0.316   0.065  -0.061
183   A         0.928   0.949   0.801   0.942   0.965   0.756   0.949   0.978   0.689
184   Y         1.520   1.585   1.639   1.636   1.730   1.816   1.687   1.786   1.880
185   T         0.480   0.486   0.552   0.341   0.331   0.438   0.105   0.088   0.177
186   E        -1.205  -1.215  -1.152  -1.204  -1.237  -1.121  -1.054  -1.038  -0.952
187   K         0.928   1.057   0.813   1.023   1.197   0.871   0.949   1.155   0.711
188   D         0.928   0.786   0.777   1.024   0.832   0.814   0.949   0.688   0.641
189   D        -0.454  -0.432  -0.447  -0.582  -0.538  -0.566  -0.633  -0.586  -0.586
190   L        -0.829  -0.804  -0.827  -0.712  -0.640  -0.638  -0.843  -0.805  -0.799
191   I         0.928   0.786   0.777   0.870   0.663   0.635   0.949   0.688   0.641
192   T         1.520   1.585   1.639   1.536   1.625   1.716   1.687   1.786   1.880
193   C         1.520   1.585   1.639   1.708   1.804   1.888   1.687   1.786   1.880
194   L         0.363   0.250   0.134   0.306   0.142  -0.064   0.316   0.134  -0.052
195   T         0.105   0.073   0.018   0.062  -0.029  -0.111  -0.105  -0.176  -0.251
196   G        -0.012   0.069   0.015  -0.168  -0.050  -0.109  -0.316  -0.183  -0.256
197   E        -0.454  -0.512  -0.469  -0.506  -0.581  -0.474  -0.633  -0.674  -0.609
198   V         0.928   1.046   0.813   0.904   1.063   0.734   0.949   1.137   0.711
199   I        -1.102  -1.165  -1.125  -1.024  -1.121  -1.040  -0.949  -0.989  -0.927
200   F         1.520   1.585   1.639   1.690   1.780   1.869   1.687   1.786   1.880
201   P         0.363   0.202   0.128   0.433   0.202   0.092   0.316   0.065  -0.061
202   P        -0.829  -0.869  -0.832  -0.798  -0.799  -0.762  -0.843  -0.862  -0.804
203   R        -1.749  -1.710  -1.636  -1.425  -1.348  -1.255  -1.265  -1.209  -1.119
204   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
205   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
206   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
207   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
208   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
209   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
210   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
211   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
212   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/Q12408
Output conservation file - output/Q12408
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
