1     M         2.153   2.174   2.316   2.328   2.346   2.586   2.441   2.478   2.739
2     A         2.153   2.174   2.316   2.081   2.079   2.333   2.441   2.478   2.739
3     G         0.163   0.152   0.143   0.062   0.066   0.041  -0.057  -0.060  -0.089
4     K        -0.249  -0.240  -0.383  -0.245  -0.193  -0.424  -0.235  -0.224  -0.400
5     A         0.731   0.739   0.860   0.365   0.344   0.546   0.300   0.305   0.474
6     G        -1.898  -1.877  -1.791  -1.737  -1.727  -1.575  -1.305  -1.284  -1.169
7     R         1.299   1.268   1.188   1.195   1.209   1.059   1.370   1.317   1.143
8     K         1.299   1.249   1.172   1.217   1.201   1.075   1.370   1.284   1.112
9     Q        -0.506  -0.468  -0.493  -0.542  -0.458  -0.528  -0.592  -0.543  -0.550
10    A         2.153   2.174   2.316   2.081   2.079   2.333   2.441   2.478   2.739
11    S        -0.249  -0.303  -0.384  -0.225  -0.328  -0.463  -0.235  -0.305  -0.402
12    S        -0.506  -0.472  -0.486  -0.650  -0.593  -0.621  -0.592  -0.548  -0.541
13    N         2.153   2.174   2.316   2.242   2.269   2.498   2.441   2.478   2.739
14    A        -1.074  -1.089  -1.026  -1.056  -1.088  -0.991  -0.948  -0.957  -0.860
15    K        -1.074  -1.072  -1.009  -0.941  -0.929  -0.849  -0.948  -0.942  -0.845
16    I         0.907   0.919   0.939   0.739   0.733   0.767   0.657   0.671   0.642
17    I         1.299   1.268   1.188   1.109   1.035   0.950   1.370   1.317   1.143
18    Q        -0.506  -0.546  -0.485  -0.625  -0.641  -0.572  -0.592  -0.626  -0.543
19    G        -0.506  -0.565  -0.501  -0.331  -0.415  -0.321  -0.592  -0.654  -0.562
20    L         1.299   1.358   1.195   1.109   1.155   0.962   1.370   1.467   1.157
21    Y        -0.249  -0.308  -0.374   0.205   0.123  -0.001  -0.235  -0.311  -0.389
22    K        -1.074  -1.042  -1.020  -1.299  -1.227  -1.213  -0.948  -0.917  -0.855
23    Q        -1.074  -1.036  -1.009  -1.227  -1.154  -1.112  -0.948  -0.907  -0.845
24    V        -0.661  -0.673  -0.568  -0.813  -0.826  -0.662  -0.770  -0.774  -0.639
25    S        -0.918  -0.921  -0.943  -0.896  -0.916  -0.982  -0.770  -0.773  -0.770
26    L        -1.486  -1.446  -1.412  -1.469  -1.448  -1.365  -1.127  -1.089  -1.017
27    F         0.163   0.136   0.147   0.028  -0.019   0.005  -0.057  -0.093  -0.089
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    L        -0.249  -0.322  -0.403  -0.346  -0.471  -0.573  -0.235  -0.330  -0.426
30    G        -1.074  -1.028  -1.009  -1.253  -1.208  -1.164  -0.948  -0.903  -0.845
31    M        -1.074  -1.128  -1.034  -1.157  -1.226  -1.067  -0.948  -0.989  -0.867
32    A        -1.074  -1.042  -1.020  -1.129  -1.143  -1.056  -0.948  -0.917  -0.855
33    I        -0.918  -0.918  -0.942  -0.984  -1.039  -1.009  -0.770  -0.770  -0.769
34    V        -0.506  -0.523  -0.490  -0.788  -0.829  -0.761  -0.592  -0.609  -0.550
35    R        -0.918  -0.950  -0.982  -0.814  -0.822  -0.974  -0.770  -0.803  -0.811
36    L        -1.486  -1.461  -1.410  -1.461  -1.396  -1.330  -1.127  -1.102  -1.015
37    F        -0.506  -0.395  -0.458  -0.433  -0.276  -0.347  -0.592  -0.454  -0.511
38    I         0.062   0.052   0.115  -0.262  -0.323  -0.190  -0.235  -0.240  -0.147
39    S        -1.074  -1.061  -1.015  -0.958  -0.949  -0.835  -0.948  -0.932  -0.850
40    R         0.163   0.226   0.164   0.194   0.328   0.189  -0.057   0.025  -0.062
41    K        -0.918  -0.890  -0.948  -0.720  -0.677  -0.803  -0.770  -0.740  -0.776
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    V        -1.898  -1.877  -1.791  -1.828  -1.745  -1.669  -1.305  -1.284  -1.169
44    T         0.907   0.929   0.974   0.771   0.791   0.859   0.657   0.692   0.715
45    I        -0.661  -0.611  -0.561  -0.925  -0.888  -0.769  -0.770  -0.719  -0.633
46    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    I         0.163   0.202   0.152  -0.157  -0.119  -0.228  -0.057  -0.005  -0.081
50    K         0.062   0.037   0.101  -0.131  -0.125  -0.039  -0.235  -0.259  -0.164
51    L        -0.918  -0.822  -0.929  -0.559  -0.431  -0.597  -0.770  -0.662  -0.755
52    V        -0.506  -0.508  -0.483  -0.660  -0.669  -0.633  -0.592  -0.591  -0.537
53    A        -0.506  -0.452  -0.477  -0.724  -0.667  -0.669  -0.592  -0.519  -0.532
54    L         0.907   0.867   0.918   0.752   0.633   0.677   0.657   0.568   0.597
55    N         0.731   0.764   0.878   0.466   0.509   0.687   0.300   0.356   0.514
56    V        -0.506  -0.421  -0.477  -0.592  -0.481  -0.537  -0.592  -0.493  -0.532
57    P         2.153   2.174   2.316   2.276   2.300   2.532   2.441   2.478   2.739
58    M        -0.093  -0.096   0.003  -0.232  -0.274  -0.124  -0.413  -0.419  -0.292
59    F        -0.918  -0.845  -0.913  -0.701  -0.610  -0.699  -0.770  -0.690  -0.738
60    V        -0.661  -0.618  -0.564  -0.906  -0.861  -0.764  -0.770  -0.725  -0.634
61    A        -0.249  -0.308  -0.374   0.108   0.008  -0.132  -0.235  -0.311  -0.389
62    L         0.062   0.033   0.098  -0.119  -0.154  -0.017  -0.235  -0.264  -0.168
63    Y         0.495   0.479   0.318   0.691   0.692   0.440   0.479   0.453   0.197
64    I        -0.249  -0.322  -0.403  -0.104  -0.213  -0.298  -0.235  -0.330  -0.426
65    I         0.907   0.919   0.937   0.507   0.486   0.509   0.657   0.671   0.638
66    V         1.299   1.268   1.188   1.513   1.474   1.370   1.370   1.317   1.143
67    L        -0.249  -0.181  -0.356  -0.296  -0.163  -0.457  -0.235  -0.148  -0.366
68    S         0.163   0.196   0.155   0.182   0.212   0.153  -0.057  -0.015  -0.078
69    G         0.495   0.479   0.318   0.626   0.612   0.396   0.479   0.453   0.197
70    K         1.299   1.268   1.188   1.422   1.437   1.254   1.370   1.317   1.143
71    P         2.153   2.174   2.316   2.276   2.300   2.532   2.441   2.478   2.739
72    K        -0.249  -0.209  -0.355  -0.265  -0.170  -0.411  -0.235  -0.184  -0.364
73    Y         1.299   1.243   1.178   1.440   1.387   1.288   1.370   1.273   1.124
74    D         0.495   0.608   0.350   0.868   1.026   0.682   0.479   0.647   0.248
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -0.615  -0.621  -0.541  -0.702  -0.706  -0.575  -0.715  -0.717  -0.607
82    G        -1.074  -1.094  -1.015  -1.091  -1.046  -0.962  -0.948  -0.961  -0.849
83    N        -1.074  -1.040  -1.003  -1.034  -0.953  -0.925  -0.948  -0.915  -0.840
84    R        -0.918  -1.000  -0.962  -0.992  -1.068  -1.067  -0.770  -0.856  -0.790
85    V         0.907   0.929   0.974   0.551   0.563   0.631   0.657   0.692   0.715
86    V        -0.249  -0.314  -0.394  -0.220  -0.309  -0.517  -0.235  -0.319  -0.415
87    K        -1.074  -1.045  -1.005  -1.138  -1.047  -1.033  -0.948  -0.919  -0.841
88    Q        -1.074  -1.087  -1.023  -0.922  -0.947  -0.832  -0.948  -0.954  -0.857
89    G         2.153   2.174   2.316   2.101   2.130   2.353   2.441   2.478   2.739
90    I        -0.249  -0.163  -0.364   0.063   0.167  -0.108  -0.235  -0.125  -0.376
91    D         2.153   2.174   2.316   2.347   2.384   2.606   2.441   2.478   2.739
92    L         0.495   0.573   0.328   0.356   0.436   0.108   0.479   0.595   0.214
93    N        -1.096  -1.073  -1.025  -1.156  -1.097  -1.057  -0.958  -0.932  -0.855
94    D        -1.486  -1.461  -1.416  -1.105  -1.084  -0.997  -1.127  -1.101  -1.020
95    N        -1.486  -1.504  -1.419  -1.255  -1.253  -1.138  -1.127  -1.138  -1.023
96    T         1.299   1.268   1.188   1.351   1.314   1.220   1.370   1.317   1.143
97    N        -0.012  -0.055   0.040  -0.188  -0.276  -0.132  -0.291  -0.360  -0.237
98    L         0.495   0.500   0.322   0.415   0.391   0.192   0.479   0.482   0.204
99    I        -0.506  -0.551  -0.494  -0.390  -0.444  -0.362  -0.592  -0.633  -0.552
100   S         1.299   1.268   1.188   1.501   1.456   1.350   1.370   1.317   1.143
101   Y         2.153   2.174   2.316   2.199   2.248   2.454   2.441   2.478   2.739
102   F        -0.249  -0.308  -0.374   0.043  -0.070  -0.176  -0.235  -0.311  -0.389
103   F         0.907   0.923   0.943   0.772   0.794   0.765   0.657   0.679   0.651
104   D         2.153   2.174   2.316   2.347   2.384   2.606   2.441   2.478   2.739
105   L        -0.661  -0.633  -0.569  -0.950  -0.926  -0.792  -0.770  -0.739  -0.639
106   I         0.062   0.103   0.118  -0.116  -0.062  -0.000  -0.235  -0.186  -0.143
107   Y         1.299   1.249   1.172   1.470   1.432   1.333   1.370   1.284   1.112
108   L         0.062   0.103   0.118  -0.300  -0.245  -0.206  -0.235  -0.186  -0.143
109   S         0.731   0.764   0.878   0.511   0.559   0.735   0.300   0.356   0.514
110   L         0.163   0.237   0.163   0.186   0.283   0.149  -0.057   0.045  -0.060
111   F        -0.506  -0.511  -0.483  -0.611  -0.648  -0.576  -0.592  -0.593  -0.539
112   G        -1.074  -1.054  -1.006  -0.918  -0.913  -0.821  -0.948  -0.926  -0.843
113   N        -0.506  -0.562  -0.519  -0.413  -0.491  -0.454  -0.592  -0.645  -0.580
114   I        -0.249  -0.184  -0.355  -0.237  -0.158  -0.417  -0.235  -0.153  -0.364
115   G         0.062   0.033   0.098  -0.317  -0.365  -0.253  -0.235  -0.264  -0.168
116   I        -1.486  -1.489  -1.432  -1.195  -1.215  -1.131  -1.127  -1.126  -1.034
117   I        -0.249  -0.285  -0.393  -0.179  -0.257  -0.394  -0.235  -0.284  -0.413
118   A        -1.074  -1.072  -1.009  -1.193  -1.223  -1.104  -0.948  -0.942  -0.845
119   F         0.907   0.905   0.940   0.752   0.711   0.730   0.657   0.644   0.644
120   R        -0.506  -0.533  -0.498  -0.515  -0.533  -0.493  -0.592  -0.607  -0.555
121   T         0.828   0.802   0.889   0.735   0.670   0.777   0.498   0.436   0.537
122   F         0.495   0.537   0.331   0.767   0.815   0.555   0.479   0.538   0.218
123   K         0.907   0.856   0.919   0.697   0.655   0.720   0.657   0.545   0.601
124   F        -1.074  -1.128  -1.034  -0.890  -0.986  -0.838  -0.948  -0.989  -0.867
125   W         1.299   1.243   1.178   1.629   1.545   1.477   1.370   1.273   1.124
126   W        -1.074  -1.081  -1.005  -0.881  -0.907  -0.779  -0.948  -0.951  -0.841
127   C        -0.249  -0.303  -0.384  -0.268  -0.363  -0.432  -0.235  -0.305  -0.402
128   L        -0.506  -0.483  -0.493  -0.555  -0.503  -0.510  -0.592  -0.566  -0.549
129   L        -0.249  -0.314  -0.394  -0.361  -0.491  -0.583  -0.235  -0.319  -0.415
130   L        -0.661  -0.675  -0.572  -0.926  -0.944  -0.764  -0.770  -0.777  -0.642
131   C         0.062   0.037   0.101   0.046   0.002   0.108  -0.235  -0.259  -0.164
132   P         2.153   2.174   2.316   2.276   2.300   2.532   2.441   2.478   2.739
133   I        -0.661  -0.675  -0.572  -0.987  -1.050  -0.869  -0.770  -0.777  -0.642
134   Y         0.731   0.777   0.874   0.537   0.629   0.752   0.300   0.384   0.504
135   A        -0.249  -0.179  -0.354  -0.197  -0.121  -0.370  -0.235  -0.146  -0.362
136   G        -0.506  -0.487  -0.498  -0.619  -0.604  -0.591  -0.592  -0.570  -0.555
137   Y         0.495   0.479   0.318   0.691   0.692   0.440   0.479   0.453   0.197
138   K         2.153   2.174   2.316   1.950   2.019   2.199   2.441   2.478   2.739
139   L        -0.249  -0.314  -0.394  -0.375  -0.505  -0.605  -0.235  -0.319  -0.415
140   Y        -0.249  -0.235  -0.398  -0.047  -0.004  -0.284  -0.235  -0.217  -0.420
141   G        -0.918  -0.845  -0.913  -0.758  -0.642  -0.744  -0.770  -0.690  -0.738
142   L         1.299   1.346   1.196   1.136   1.166   1.012   1.370   1.449   1.159
143   K        -0.918  -0.950  -0.982  -0.910  -0.897  -0.986  -0.770  -0.803  -0.811
144   N        -0.621  -0.668  -0.572  -0.630  -0.728  -0.598  -0.706  -0.761  -0.637
145   M        -0.012  -0.059   0.040   0.097   0.019   0.168  -0.291  -0.365  -0.237
146   F        -0.012  -0.059   0.040  -0.080  -0.154  -0.012  -0.291  -0.365  -0.237
147   M        -0.621  -0.671  -0.572  -0.617  -0.704  -0.564  -0.706  -0.765  -0.637
148   P         1.111   1.218   1.092   1.236   1.393   1.192   1.042   1.230   0.956
149   G         0.347   0.421   0.258   0.377   0.477   0.235   0.256   0.368   0.104
150   A        -0.434  -0.364  -0.452  -0.521  -0.454  -0.582  -0.473  -0.382  -0.488
151   Q        -1.096  -1.089  -1.043  -1.163  -1.131  -1.061  -0.958  -0.949  -0.873
152   Q        -0.615  -0.593  -0.541  -0.851  -0.794  -0.730  -0.715  -0.689  -0.607
153   T        -0.615  -0.601  -0.548  -0.573  -0.557  -0.458  -0.715  -0.697  -0.614
154   Q        -0.434  -0.474  -0.480  -0.468  -0.469  -0.508  -0.473  -0.525  -0.525
155   A        -0.434  -0.364  -0.452  -0.446  -0.369  -0.486  -0.473  -0.382  -0.488
156   D        -0.621  -0.619  -0.559  -0.463  -0.462  -0.383  -0.706  -0.704  -0.621
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   N        -1.074  -1.079  -1.014  -0.950  -0.955  -0.852  -0.948  -0.948  -0.849
160   R        -1.486  -1.508  -1.422  -1.147  -1.122  -1.046  -1.127  -1.141  -1.025
161   S        -1.074  -1.040  -1.003  -1.031  -0.992  -0.926  -0.948  -0.912  -0.839
162   K        -0.249  -0.379  -0.404  -0.048  -0.256  -0.339  -0.235  -0.401  -0.428
163   N        -0.918  -0.972  -0.960  -0.605  -0.690  -0.677  -0.770  -0.828  -0.788
164   A        -0.249  -0.379  -0.404  -0.012  -0.229  -0.287  -0.235  -0.401  -0.428
165   N        -0.621  -0.569  -0.541  -0.583  -0.507  -0.454  -0.706  -0.644  -0.599
166   E        -0.621  -0.605  -0.540  -0.456  -0.434  -0.337  -0.706  -0.686  -0.598
167   G         0.175   0.112   0.148   0.062  -0.058   0.008  -0.007  -0.104  -0.069
168   Q        -0.615  -0.599  -0.540  -0.577  -0.576  -0.449  -0.715  -0.693  -0.606
169   S        -1.074  -1.097  -1.015  -0.942  -0.983  -0.835  -0.948  -0.964  -0.850
170   K         0.495   0.384   0.288   0.444   0.328   0.153   0.479   0.312   0.151
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   S         1.299   1.249   1.172   1.333   1.260   1.176   1.370   1.284   1.112
178   K         1.299   1.249   1.172   1.195   1.184   1.035   1.370   1.284   1.112
179   R         1.299   1.249   1.172   1.422   1.410   1.226   1.370   1.284   1.112
180   Q         2.153   2.174   2.316   2.304   2.333   2.562   2.441   2.478   2.739
181   M        -1.486  -1.470  -1.432  -1.189  -1.143  -1.124  -1.127  -1.110  -1.034
182   K         1.299   1.249   1.172   1.195   1.184   1.035   1.370   1.284   1.112
183   R        -0.249  -0.322  -0.403  -0.058  -0.128  -0.321  -0.235  -0.330  -0.426
184   E         0.495   0.475   0.303   0.775   0.736   0.501   0.479   0.447   0.175
185   R        -0.093  -0.069   0.019  -0.422  -0.337  -0.254  -0.413  -0.382  -0.270
186   R         1.215   1.241   1.127   1.358   1.392   1.237   1.227   1.270   1.025
187   G         0.347   0.357   0.221   0.364   0.382   0.139   0.256   0.271   0.045
188   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   D        -0.012  -0.043   0.046   0.052  -0.007   0.113  -0.291  -0.340  -0.228
191   S        -1.096  -1.133  -1.048  -0.922  -0.985  -0.879  -0.958  -0.991  -0.878
192   K         1.215   1.220   1.124   1.039   1.053   0.901   1.227   1.233   1.019
193   I        -0.434  -0.403  -0.451  -0.401  -0.355  -0.449  -0.473  -0.433  -0.488
194   K        -1.096  -1.092  -1.043  -1.129  -1.108  -1.021  -0.958  -0.952  -0.873
195   Y         0.047   0.082   0.095  -0.043   0.019   0.030  -0.230  -0.177  -0.166
196   K         0.047   0.060   0.096  -0.217  -0.191  -0.128  -0.230  -0.215  -0.164
197   Y         1.111   1.107   1.061   1.155   1.150   1.063   1.042   1.031   0.893
198   R         1.215   1.143   1.112   1.332   1.221   1.167   1.227   1.095   0.995
* 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/Q99382
Output conservation file - output/Q99382
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
