1     M         1.253   1.263   1.300   1.482   1.500   1.554   1.329   1.341   1.390
2     S        -1.708  -1.684  -1.615  -1.652  -1.622  -1.500  -1.416  -1.383  -1.273
3     K        -1.094  -1.075  -1.010  -1.244  -1.206  -1.103  -1.111  -1.082  -0.977
4     N        -1.094  -1.075  -1.010  -1.258  -1.230  -1.116  -1.111  -1.082  -0.977
5     V        -1.094  -1.075  -1.010  -1.057  -1.032  -0.920  -1.111  -1.082  -0.977
6     G        -0.107  -0.061  -0.100  -0.262  -0.188  -0.253  -0.298  -0.223  -0.289
7     K        -1.094  -1.075  -1.010  -1.156  -1.128  -1.017  -1.111  -1.082  -0.977
8     L        -0.107  -0.144  -0.126  -0.360  -0.424  -0.389  -0.298  -0.359  -0.333
9     V        -0.107  -0.061  -0.100  -0.237  -0.161  -0.233  -0.298  -0.223  -0.289
10    K        -1.094  -1.075  -1.010  -1.258  -1.226  -1.116  -1.111  -1.082  -0.977
11    I        -1.094  -1.075  -1.010  -1.176  -1.159  -1.036  -1.111  -1.082  -0.977
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    W         1.253   1.263   1.300   1.490   1.507   1.562   1.329   1.341   1.390
36    N         0.052  -0.022  -0.092   0.109   0.000  -0.108  -0.044  -0.160  -0.276
37    E        -0.968  -0.990  -0.980  -0.922  -0.959  -0.952  -0.959  -0.981  -0.942
38    S         1.253   1.263   1.300   1.193   1.207   1.272   1.329   1.341   1.390
39    E         0.052   0.089  -0.053   0.181   0.235   0.029  -0.044   0.016  -0.211
40    V         1.253   1.263   1.300   1.201   1.216   1.280   1.329   1.341   1.390
41    L        -0.968  -0.990  -0.980  -1.103  -1.141  -1.105  -0.959  -0.981  -0.942
42    V        -0.228  -0.213  -0.156  -0.423  -0.401  -0.297  -0.501  -0.476  -0.382
43    D         1.253   1.263   1.300   1.409   1.424   1.483   1.329   1.341   1.390
44    R         0.052   0.089  -0.053  -0.011   0.047  -0.205  -0.044   0.016  -0.211
45    K         1.253   1.263   1.300   1.064   1.082   1.146   1.329   1.341   1.390
46    S         1.253   1.263   1.300   1.193   1.207   1.272   1.329   1.341   1.390
47    K         1.253   1.263   1.300   1.064   1.082   1.146   1.329   1.341   1.390
48    F         1.253   1.263   1.300   1.466   1.485   1.538   1.329   1.341   1.390
49    Q         1.253   1.263   1.300   1.327   1.352   1.403   1.329   1.341   1.390
50    A         1.253   1.263   1.300   1.269   1.290   1.346   1.329   1.341   1.390
51    R         1.253   1.263   1.300   1.227   1.239   1.305   1.329   1.341   1.390
52    C         0.052  -0.022  -0.092   0.344   0.231   0.099  -0.044  -0.160  -0.276
53    C        -0.968  -1.010  -0.986  -0.723  -0.807  -0.780  -0.959  -1.004  -0.949
54    P        -0.968  -0.944  -0.958  -0.733  -0.679  -0.716  -0.959  -0.922  -0.915
55    L        -0.228  -0.209  -0.151  -0.498  -0.460  -0.353  -0.501  -0.468  -0.374
56    Q        -1.708  -1.684  -1.615  -1.700  -1.667  -1.547  -1.416  -1.383  -1.273
57    N        -0.228  -0.213  -0.156  -0.290  -0.256  -0.164  -0.501  -0.476  -0.382
58    Q        -0.968  -1.010  -0.986  -0.932  -0.998  -0.981  -0.959  -1.004  -0.949
59    K        -0.968  -1.010  -0.986  -1.220  -1.296  -1.244  -0.959  -1.004  -0.949
60    D         0.052   0.055  -0.064   0.243   0.248   0.051  -0.044  -0.038  -0.229
61    I         0.052   0.055  -0.064   0.082   0.079  -0.116  -0.044  -0.038  -0.229
62    P         0.052   0.055  -0.064   0.267   0.291   0.090  -0.044  -0.038  -0.229
63    S        -1.708  -1.684  -1.615  -1.671  -1.638  -1.519  -1.416  -1.383  -1.273
64    I         0.052   0.055  -0.064   0.049   0.046  -0.164  -0.044  -0.038  -0.229
65    L         1.253   1.263   1.300   1.098   1.113   1.180   1.329   1.341   1.390
66    Q        -0.228  -0.209  -0.151  -0.308  -0.270  -0.179  -0.501  -0.468  -0.374
67    E        -1.708  -1.684  -1.615  -1.596  -1.560  -1.446  -1.416  -1.383  -1.273
68    L         0.052   0.089  -0.053   0.002   0.055  -0.120  -0.044   0.016  -0.211
69    T        -1.708  -1.684  -1.615  -1.724  -1.713  -1.571  -1.416  -1.383  -1.273
70    Q        -0.228  -0.209  -0.151  -0.308  -0.270  -0.179  -0.501  -0.468  -0.374
71    N        -1.708  -1.684  -1.615  -1.686  -1.632  -1.533  -1.416  -1.383  -1.273
72    N        -0.968  -0.990  -0.980  -0.844  -0.877  -0.841  -0.959  -0.981  -0.942
73    K         1.253   1.263   1.300   1.064   1.082   1.146   1.329   1.341   1.390
74    S        -1.708  -1.684  -1.615  -1.601  -1.563  -1.450  -1.416  -1.383  -1.273
75    V        -0.228  -0.213  -0.156  -0.423  -0.402  -0.297  -0.501  -0.476  -0.382
76    S        -0.968  -0.944  -0.958  -0.969  -0.927  -0.940  -0.959  -0.922  -0.915
77    K         0.052  -0.022  -0.092  -0.118  -0.233  -0.341  -0.044  -0.160  -0.276
78    A         0.052  -0.022  -0.092   0.071  -0.046  -0.180  -0.044  -0.160  -0.276
79    S         0.052   0.055  -0.064   0.024   0.026  -0.154  -0.044  -0.038  -0.229
80    H         1.253   1.263   1.300   1.360   1.366   1.435   1.329   1.341   1.390
81    M        -0.968  -1.010  -0.986  -0.774  -0.835  -0.838  -0.959  -1.004  -0.949
82    H         1.253   1.263   1.300   1.360   1.366   1.435   1.329   1.341   1.390
83    M         0.052  -0.022  -0.092   0.303   0.182   0.045  -0.044  -0.160  -0.276
84    Y         0.052  -0.022  -0.092   0.318   0.195   0.059  -0.044  -0.160  -0.276
85    A         1.253   1.263   1.300   1.269   1.290   1.346   1.329   1.341   1.390
86    W         1.253   1.263   1.300   1.490   1.507   1.562   1.329   1.341   1.390
87    R         1.253   1.263   1.300   1.227   1.239   1.305   1.329   1.341   1.390
88    T         1.253   1.263   1.300   1.277   1.288   1.354   1.329   1.341   1.390
89    A        -0.228  -0.213  -0.156  -0.423  -0.395  -0.301  -0.501  -0.476  -0.382
90    E        -1.094  -1.075  -1.010  -0.943  -0.912  -0.809  -1.111  -1.082  -0.977
91    V        -0.107  -0.061  -0.100  -0.187  -0.116  -0.186  -0.298  -0.223  -0.289
92    S        -0.107  -0.063  -0.109  -0.191  -0.120  -0.210  -0.298  -0.225  -0.305
93    N        -1.094  -1.075  -1.010  -1.089  -1.062  -0.951  -1.111  -1.082  -0.977
94    N        -1.094  -1.075  -1.010  -1.182  -1.159  -1.042  -1.111  -1.082  -0.977
95    L        -0.107  -0.144  -0.132  -0.234  -0.280  -0.253  -0.298  -0.360  -0.342
96    H        -1.094  -1.075  -1.010  -1.175  -1.139  -1.035  -1.111  -1.082  -0.977
97    L        -1.708  -1.684  -1.615  -1.719  -1.675  -1.566  -1.416  -1.383  -1.273
98    Q        -1.708  -1.684  -1.615  -1.501  -1.453  -1.353  -1.416  -1.383  -1.273
99    Q        -1.708  -1.684  -1.615  -1.510  -1.471  -1.362  -1.416  -1.383  -1.273
100   E        -0.968  -0.990  -0.980  -0.940  -0.975  -0.973  -0.959  -0.981  -0.942
101   Q        -0.968  -1.010  -0.986  -0.784  -0.832  -0.800  -0.959  -1.004  -0.949
102   K        -0.968  -0.944  -0.958  -1.111  -1.072  -1.074  -0.959  -0.922  -0.915
103   K         0.052  -0.022  -0.092  -0.129  -0.246  -0.359  -0.044  -0.160  -0.276
104   K         1.253   1.263   1.300   1.064   1.082   1.146   1.329   1.341   1.390
105   G         0.052   0.089  -0.053  -0.028   0.037  -0.220  -0.044   0.016  -0.211
106   N         0.052  -0.022  -0.092   0.013  -0.109  -0.262  -0.044  -0.160  -0.276
107   K         1.253   1.263   1.300   1.067   1.085   1.149   1.329   1.341   1.390
108   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   N        -1.094  -1.075  -1.010  -1.196  -1.160  -1.056  -1.111  -1.082  -0.977
114   S        -1.094  -1.075  -1.010  -1.230  -1.172  -1.089  -1.111  -1.082  -0.977
115   H        -1.094  -1.075  -1.010  -1.149  -1.138  -1.010  -1.111  -1.082  -0.977
116   V        -0.107  -0.144  -0.126  -0.227  -0.295  -0.262  -0.298  -0.359  -0.333
117   N         0.052   0.055  -0.064   0.122   0.141  -0.042  -0.044  -0.038  -0.229
118   K         0.052   0.055  -0.064  -0.124  -0.115  -0.302  -0.044  -0.038  -0.229
119   S        -0.968  -0.883  -0.954  -1.013  -0.865  -1.007  -0.959  -0.848  -0.910
120   R        -0.968  -0.944  -0.958  -1.013  -0.977  -0.997  -0.959  -0.922  -0.915
121   N        -1.708  -1.684  -1.615  -1.506  -1.470  -1.358  -1.416  -1.383  -1.273
122   I        -1.708  -1.684  -1.615  -1.573  -1.531  -1.423  -1.416  -1.383  -1.273
123   T        -1.708  -1.684  -1.615  -1.537  -1.489  -1.388  -1.416  -1.383  -1.273
124   V         0.052   0.055  -0.064   0.030   0.036  -0.151  -0.044  -0.038  -0.229
125   Q        -0.968  -1.010  -0.986  -0.872  -0.947  -0.906  -0.959  -1.004  -0.949
126   P        -0.968  -0.957  -0.974  -0.914  -0.884  -0.876  -0.959  -0.942  -0.935
127   K         0.052  -0.022  -0.092  -0.073  -0.181  -0.268  -0.044  -0.160  -0.276
128   N         1.253   1.263   1.300   1.252   1.274   1.330   1.329   1.341   1.390
129   I        -0.228  -0.213  -0.156  -0.423  -0.408  -0.301  -0.501  -0.476  -0.382
130   E        -0.968  -0.957  -0.974  -0.868  -0.849  -0.882  -0.959  -0.942  -0.935
131   Q         1.253   1.263   1.300   1.327   1.352   1.403   1.329   1.341   1.390
132   G         1.253   1.263   1.300   1.210   1.229   1.289   1.329   1.341   1.390
133   C        -0.968  -0.957  -0.974  -0.809  -0.792  -0.777  -0.959  -0.942  -0.935
134   A        -1.708  -1.684  -1.615  -1.769  -1.742  -1.614  -1.416  -1.383  -1.273
135   D         1.253   1.263   1.300   1.409   1.424   1.483   1.329   1.341   1.390
136   C         0.052  -0.022  -0.092   0.311   0.197   0.046  -0.044  -0.160  -0.276
137   G         1.253   1.263   1.300   1.210   1.229   1.289   1.329   1.341   1.390
138   E         1.253   1.263   1.300   1.310   1.326   1.387   1.329   1.341   1.390
139   A         0.052  -0.022  -0.092   0.030  -0.094  -0.247  -0.044  -0.160  -0.276
140   G         1.253   1.263   1.300   1.210   1.229   1.289   1.329   1.341   1.390
141   A         1.253   1.263   1.300   1.269   1.290   1.346   1.329   1.341   1.390
142   G         1.253   1.263   1.300   1.210   1.229   1.289   1.329   1.341   1.390
143   Q         0.052  -0.022  -0.092   0.127   0.013  -0.130  -0.044  -0.160  -0.276
144   R         0.052  -0.022  -0.092  -0.011  -0.144  -0.284  -0.044  -0.160  -0.276
145   L         1.253   1.263   1.300   1.098   1.113   1.180   1.329   1.341   1.390
146   L         1.253   1.263   1.300   1.098   1.113   1.180   1.329   1.341   1.390
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   T         0.052  -0.022  -0.092   0.122   0.008  -0.104  -0.044  -0.160  -0.276
149   L         0.052  -0.022  -0.092  -0.093  -0.212  -0.324  -0.044  -0.160  -0.276
150   L         1.253   1.263   1.300   1.098   1.113   1.180   1.329   1.341   1.390
151   E         0.052  -0.022  -0.092   0.114  -0.009  -0.140  -0.044  -0.160  -0.276
152   R         0.052  -0.022  -0.092   0.084  -0.033  -0.130  -0.044  -0.160  -0.276
153   A        -0.968  -0.957  -0.974  -0.954  -0.939  -0.947  -0.959  -0.942  -0.935
154   N         0.052   0.055  -0.064   0.109   0.117  -0.062  -0.044  -0.038  -0.229
155   I        -0.968  -0.990  -0.980  -0.994  -1.052  -1.029  -0.959  -0.981  -0.942
156   F        -0.968  -1.010  -0.986  -0.673  -0.730  -0.708  -0.959  -1.004  -0.949
157   N         1.253   1.263   1.300   1.252   1.274   1.330   1.329   1.341   1.390
158   V         0.052  -0.022  -0.092   0.033  -0.086  -0.195  -0.044  -0.160  -0.276
159   L         0.052   0.089  -0.053  -0.067  -0.014  -0.220  -0.044   0.016  -0.211
160   V         1.253   1.263   1.300   1.201   1.216   1.280   1.329   1.341   1.390
161   I         0.052   0.055  -0.064   0.082   0.079  -0.116  -0.044  -0.038  -0.229
162   V         1.253   1.263   1.300   1.201   1.216   1.280   1.329   1.341   1.390
163   T         1.253   1.263   1.300   1.277   1.288   1.354   1.329   1.341   1.390
164   R         1.253   1.263   1.300   1.227   1.239   1.305   1.329   1.341   1.390
165   W         1.253   1.263   1.300   1.490   1.507   1.562   1.329   1.341   1.390
166   Y         1.253   1.263   1.300   1.498   1.515   1.570   1.329   1.341   1.390
167   G         1.253   1.263   1.300   1.210   1.229   1.289   1.329   1.341   1.390
168   G         1.253   1.263   1.300   1.210   1.229   1.289   1.329   1.341   1.390
169   T         0.052  -0.022  -0.092   0.079  -0.049  -0.173  -0.044  -0.160  -0.276
170   P         0.052   0.055  -0.064   0.223   0.249   0.025  -0.044  -0.038  -0.229
171   L         1.253   1.263   1.300   1.098   1.113   1.180   1.329   1.341   1.390
172   G         1.253   1.263   1.300   1.210   1.229   1.289   1.329   1.341   1.390
173   S         0.052   0.144  -0.052   0.199   0.361   0.013  -0.044   0.099  -0.210
174   S        -0.968  -0.957  -0.974  -1.035  -1.027  -1.064  -0.959  -0.942  -0.935
175   R         1.253   1.263   1.300   1.227   1.239   1.305   1.329   1.341   1.390
176   F         1.253   1.263   1.300   1.466   1.485   1.538   1.329   1.341   1.390
177   R         1.253   1.263   1.300   1.227   1.239   1.305   1.329   1.341   1.390
178   H         1.253   1.263   1.300   1.360   1.366   1.435   1.329   1.341   1.390
179   I         1.253   1.263   1.300   1.277   1.286   1.354   1.329   1.341   1.390
180   S        -0.968  -0.990  -0.980  -0.889  -0.930  -0.878  -0.959  -0.981  -0.942
181   T        -0.968  -0.990  -0.980  -0.961  -1.003  -0.990  -0.959  -0.981  -0.942
182   C        -0.968  -0.883  -0.954  -0.823  -0.704  -0.787  -0.959  -0.848  -0.910
183   A         0.052  -0.022  -0.092   0.071  -0.046  -0.180  -0.044  -0.160  -0.276
184   V        -0.228  -0.213  -0.156  -0.555  -0.537  -0.431  -0.501  -0.476  -0.382
185   E        -0.968  -0.990  -0.980  -0.809  -0.836  -0.816  -0.959  -0.981  -0.942
186   T         0.052   0.144  -0.052   0.024   0.157  -0.134  -0.044   0.099  -0.210
187   L         1.253   1.263   1.300   1.098   1.113   1.180   1.329   1.341   1.390
188   K        -0.228  -0.213  -0.156  -0.562  -0.532  -0.429  -0.501  -0.476  -0.382
189   K         0.052   0.089  -0.053  -0.101  -0.045  -0.251  -0.044   0.016  -0.211
190   G         0.052  -0.022  -0.092   0.013  -0.105  -0.232  -0.044  -0.160  -0.276
191   G        -0.968  -1.010  -0.986  -1.076  -1.142  -1.118  -0.959  -1.004  -0.949
192   F         0.052  -0.022  -0.092   0.287   0.168   0.031  -0.044  -0.160  -0.276
193   L         0.052   0.089  -0.053  -0.093  -0.036  -0.256  -0.044   0.016  -0.211
194   P         1.253   1.263   1.300   1.422   1.438   1.496   1.329   1.341   1.390
* 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/Q12257
Output conservation file - output/Q12257
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
