1     M         1.655   1.656   1.671   1.930   1.942   1.955   1.763   1.765   1.783
2     S        -0.020  -0.035  -0.072   0.043   0.010  -0.035  -0.112  -0.135  -0.191
3     S         1.655   1.656   1.671   1.708   1.711   1.734   1.763   1.765   1.783
4     R        -0.169  -0.168  -0.152  -0.123  -0.122  -0.094  -0.346  -0.345  -0.318
5     F         1.655   1.656   1.671   1.957   1.956   1.982   1.763   1.765   1.783
6     A        -1.236  -1.235  -1.218  -1.193  -1.198  -1.162  -1.049  -1.047  -1.019
7     R         1.655   1.656   1.671   1.747   1.745   1.772   1.763   1.765   1.783
8     S        -0.169  -0.168  -0.152  -0.321  -0.326  -0.292  -0.346  -0.345  -0.318
9     N        -0.169  -0.168  -0.152  -0.180  -0.184  -0.151  -0.346  -0.345  -0.318
10    G        -0.169  -0.168  -0.152  -0.258  -0.262  -0.229  -0.346  -0.345  -0.318
11    N        -0.169  -0.168  -0.152  -0.227  -0.231  -0.198  -0.346  -0.345  -0.318
12    P        -0.169  -0.168  -0.152  -0.417  -0.407  -0.388  -0.346  -0.345  -0.318
13    N        -0.169  -0.168  -0.152  -0.321  -0.326  -0.292  -0.346  -0.345  -0.318
14    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    R        -0.020  -0.023  -0.072   0.081   0.075   0.004  -0.112  -0.117  -0.192
17    K         1.655   1.656   1.671   1.605   1.600   1.631   1.763   1.765   1.783
18    R         1.655   1.656   1.671   1.734   1.730   1.760   1.763   1.765   1.783
19    N        -1.236  -1.235  -1.218  -1.123  -1.127  -1.093  -1.049  -1.047  -1.019
20    H        -0.020  -0.023  -0.072   0.220   0.208   0.119  -0.112  -0.117  -0.192
21    S         1.655   1.656   1.671   1.706   1.701   1.731   1.763   1.765   1.783
22    P         1.655   1.656   1.671   1.957   1.955   1.982   1.763   1.765   1.783
23    D         1.655   1.656   1.671   1.293   1.314   1.320   1.763   1.765   1.783
24    P        -0.020  -0.035  -0.072   0.176   0.147   0.074  -0.112  -0.135  -0.191
25    I        -0.020  -0.035  -0.072   0.023  -0.007  -0.049  -0.112  -0.135  -0.191
26    G        -0.020  -0.035  -0.072   0.220   0.196   0.134  -0.112  -0.135  -0.191
27    I         1.655   1.656   1.671   1.663   1.658   1.688   1.763   1.765   1.783
28    D        -0.020  -0.035  -0.072  -0.334  -0.340  -0.394  -0.112  -0.135  -0.191
29    N        -0.020  -0.035  -0.072  -0.049  -0.076  -0.133  -0.112  -0.135  -0.191
30    Y        -0.020  -0.035  -0.072   0.282   0.253   0.198  -0.112  -0.135  -0.191
31    K         1.655   1.656   1.671   1.605   1.600   1.631   1.763   1.765   1.783
32    R        -0.020   0.002  -0.052  -0.128  -0.101  -0.182  -0.112  -0.077  -0.161
33    K        -1.236  -1.235  -1.218  -1.132  -1.138  -1.101  -1.049  -1.047  -1.019
34    R        -0.020  -0.035  -0.072  -0.068  -0.106  -0.169  -0.112  -0.135  -0.191
35    L         1.655   1.656   1.671   1.691   1.700   1.717   1.763   1.765   1.783
36    I         1.655   1.656   1.671   1.663   1.658   1.688   1.763   1.765   1.783
37    I        -1.236  -1.235  -1.218  -1.080  -1.077  -1.050  -1.049  -1.047  -1.019
38    D         1.655   1.656   1.671   1.293   1.314   1.320   1.763   1.765   1.783
39    L        -0.020  -0.023  -0.072   0.056   0.054  -0.018  -0.112  -0.117  -0.192
40    E         1.655   1.656   1.671   1.791   1.800   1.816   1.763   1.765   1.783
41    N        -0.020  -0.035  -0.072  -0.075  -0.109  -0.163  -0.112  -0.135  -0.191
42    L         1.655   1.656   1.671   1.691   1.700   1.717   1.763   1.765   1.783
43    S         1.655   1.656   1.671   1.706   1.701   1.731   1.763   1.765   1.783
44    L         1.655   1.656   1.671   1.691   1.700   1.717   1.763   1.765   1.783
45    N         1.655   1.656   1.671   1.639   1.636   1.664   1.763   1.765   1.783
46    D         1.655   1.656   1.671   1.303   1.319   1.329   1.763   1.765   1.783
47    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    G        -0.169  -0.168  -0.152  -0.051  -0.050  -0.023  -0.346  -0.345  -0.318
49    P         1.655   1.656   1.671   1.969   1.971   1.994   1.763   1.765   1.783
50    K        -0.169  -0.168  -0.152  -0.375  -0.374  -0.346  -0.346  -0.345  -0.318
51    N        -0.169  -0.168  -0.152  -0.181  -0.180  -0.152  -0.346  -0.345  -0.318
52    G        -0.169  -0.168  -0.152   0.047   0.048   0.075  -0.346  -0.345  -0.318
53    H        -0.169  -0.168  -0.152  -0.452  -0.451  -0.423  -0.346  -0.345  -0.318
54    A        -0.169  -0.168  -0.152  -0.051  -0.050  -0.023  -0.346  -0.345  -0.318
55    D        -0.169  -0.168  -0.152  -0.676  -0.676  -0.647  -0.346  -0.345  -0.318
56    D        -0.169  -0.168  -0.152  -0.760  -0.759  -0.730  -0.346  -0.345  -0.318
57    N        -0.169  -0.168  -0.152  -0.437  -0.436  -0.407  -0.346  -0.345  -0.318
58    N        -0.169  -0.168  -0.152  -0.152  -0.151  -0.123  -0.346  -0.345  -0.318
59    L        -1.236  -1.235  -1.218  -1.595  -1.590  -1.563  -1.049  -1.047  -1.019
60    I        -0.020  -0.035  -0.072  -0.035  -0.069  -0.117  -0.112  -0.135  -0.191
61    H        -1.236  -1.235  -1.218  -1.255  -1.254  -1.224  -1.049  -1.047  -1.019
62    N        -0.020   0.002  -0.052  -0.068  -0.039  -0.128  -0.112  -0.077  -0.161
63    N        -1.236  -1.235  -1.218  -1.106  -1.103  -1.075  -1.049  -1.047  -1.019
64    I        -1.236  -1.235  -1.218  -1.318  -1.321  -1.287  -1.049  -1.047  -1.019
65    V        -0.020   0.002  -0.052  -0.035  -0.008  -0.086  -0.112  -0.077  -0.161
66    F        -1.236  -1.235  -1.218  -0.980  -0.989  -0.949  -1.049  -1.047  -1.019
67    T        -1.236  -1.235  -1.218  -0.939  -0.942  -0.908  -1.049  -1.047  -1.019
68    D        -1.236  -1.235  -1.218  -1.383  -1.364  -1.352  -1.049  -1.047  -1.019
69    A        -0.020  -0.035  -0.072   0.113   0.091   0.011  -0.112  -0.135  -0.191
70    I        -0.020   0.002  -0.052   0.036   0.067  -0.026  -0.112  -0.077  -0.161
71    D        -0.020  -0.023  -0.072  -0.376  -0.367  -0.443  -0.112  -0.117  -0.192
72    D        -1.236  -1.235  -1.218  -1.355  -1.335  -1.324  -1.049  -1.047  -1.019
73    K        -0.020  -0.035  -0.072  -0.162  -0.198  -0.253  -0.112  -0.135  -0.191
74    V        -1.236  -1.235  -1.218  -1.228  -1.243  -1.197  -1.049  -1.047  -1.019
75    L        -1.236  -1.235  -1.218  -0.971  -0.958  -0.941  -1.049  -1.047  -1.019
76    K        -1.236  -1.235  -1.218  -1.132  -1.136  -1.101  -1.049  -1.047  -1.019
77    E        -1.236  -1.235  -1.218  -1.439  -1.429  -1.408  -1.049  -1.047  -1.019
78    I        -1.236  -1.235  -1.218  -1.055  -1.058  -1.024  -1.049  -1.047  -1.019
79    I        -1.236  -1.235  -1.218  -1.038  -1.040  -1.008  -1.049  -1.047  -1.019
80    K        -0.020  -0.023  -0.072  -0.101  -0.110  -0.184  -0.112  -0.117  -0.192
81    C        -1.236  -1.235  -1.218  -1.202  -1.210  -1.171  -1.049  -1.047  -1.019
82    S        -1.236  -1.235  -1.218  -1.458  -1.452  -1.427  -1.049  -1.047  -1.019
83    T        -0.020  -0.023  -0.072   0.201   0.196   0.097  -0.112  -0.117  -0.192
84    S         1.655   1.656   1.671   1.706   1.701   1.731   1.763   1.765   1.783
85    K        -1.236  -1.235  -1.218  -1.021  -1.021  -0.991  -1.049  -1.047  -1.019
86    R        -1.236  -1.235  -1.218  -1.080  -1.086  -1.050  -1.049  -1.047  -1.019
87    G        -0.020  -0.023  -0.072   0.113   0.100   0.010  -0.112  -0.117  -0.192
88    D        -0.020  -0.023  -0.072  -0.484  -0.476  -0.568  -0.112  -0.117  -0.192
89    N        -0.020  -0.035  -0.072  -0.075  -0.109  -0.163  -0.112  -0.135  -0.191
90    D        -0.020  -0.035  -0.072  -0.484  -0.496  -0.568  -0.112  -0.135  -0.191
91    L        -1.236  -1.235  -1.218  -1.158  -1.154  -1.127  -1.049  -1.047  -1.019
92    F        -1.236  -1.235  -1.218  -1.055  -1.067  -1.024  -1.049  -1.047  -1.019
93    Y        -0.020  -0.035  -0.072   0.151   0.116   0.047  -0.112  -0.135  -0.191
94    D        -1.236  -1.235  -1.218  -1.273  -1.244  -1.242  -1.049  -1.047  -1.019
95    K        -1.236  -1.235  -1.218  -1.115  -1.117  -1.084  -1.049  -1.047  -1.019
96    I         1.655   1.656   1.671   1.663   1.658   1.688   1.763   1.765   1.783
97    W        -1.236  -1.235  -1.218  -0.874  -0.882  -0.843  -1.049  -1.047  -1.019
98    E        -0.020   0.002  -0.052  -0.390  -0.337  -0.432  -0.112  -0.077  -0.161
99    R        -1.236  -1.235  -1.218  -1.072  -1.072  -1.041  -1.049  -1.047  -1.019
100   L        -1.236  -1.235  -1.218  -1.055  -1.043  -1.024  -1.049  -1.047  -1.019
101   R         1.655   1.656   1.671   1.734   1.730   1.760   1.763   1.765   1.783
102   E        -1.236  -1.235  -1.218  -0.906  -0.894  -0.876  -1.049  -1.047  -1.019
103   K        -1.236  -1.235  -1.218  -1.106  -1.102  -1.075  -1.049  -1.047  -1.019
104   R        -1.236  -1.235  -1.218  -1.264  -1.276  -1.233  -1.049  -1.047  -1.019
105   L        -0.020  -0.023  -0.072  -0.062  -0.066  -0.154  -0.112  -0.117  -0.192
106   Q         1.655   1.656   1.671   1.998   1.996   2.023   1.763   1.765   1.783
107   I        -0.020   0.002  -0.052   0.036   0.067  -0.026  -0.112  -0.077  -0.161
108   I         1.655   1.656   1.671   1.663   1.658   1.688   1.763   1.765   1.783
109   K        -0.020  -0.035  -0.072  -0.022  -0.053  -0.092  -0.112  -0.135  -0.191
110   W         1.655   1.656   1.671   1.971   1.971   1.996   1.763   1.765   1.783
111   V        -1.236  -1.235  -1.218  -1.063  -1.073  -1.033  -1.049  -1.047  -1.019
112   D         1.655   1.656   1.671   1.293   1.314   1.320   1.763   1.765   1.783
113   Y        -0.020  -0.023  -0.072   0.288   0.279   0.205  -0.112  -0.117  -0.192
114   K        -0.020  -0.023  -0.072  -0.128  -0.144  -0.215  -0.112  -0.117  -0.192
115   E        -1.236  -1.235  -1.218  -1.021  -1.020  -0.991  -1.049  -1.047  -1.019
116   I        -1.236  -1.235  -1.218  -1.055  -1.058  -1.024  -1.049  -1.047  -1.019
117   A        -0.020  -0.023  -0.072   0.183   0.184   0.090  -0.112  -0.117  -0.192
118   Y        -0.020  -0.023  -0.072   0.257   0.254   0.169  -0.112  -0.117  -0.192
119   L        -1.236  -1.235  -1.218  -1.291  -1.295  -1.260  -1.049  -1.047  -1.019
120   S        -1.236  -1.235  -1.218  -1.211  -1.204  -1.180  -1.049  -1.047  -1.019
121   W         1.655   1.656   1.671   1.971   1.971   1.996   1.763   1.765   1.783
122   W        -1.236  -1.235  -1.218  -1.030  -1.035  -0.999  -1.049  -1.047  -1.019
123   K         1.655   1.656   1.671   1.605   1.600   1.631   1.763   1.765   1.783
124   W         1.655   1.656   1.671   1.971   1.971   1.996   1.763   1.765   1.783
125   F        -0.020   0.002  -0.052   0.282   0.313   0.230  -0.112  -0.077  -0.161
126   H        -1.236  -1.235  -1.218  -0.963  -0.976  -0.933  -1.049  -1.047  -1.019
127   -        -0.169  -0.168  -0.152  -0.122  -0.127  -0.093  -0.346  -0.345  -0.318
128   -        -0.169  -0.168  -0.152  -0.151  -0.156  -0.122  -0.346  -0.345  -0.318
129   -        -0.169  -0.168  -0.152  -0.357  -0.349  -0.328  -0.346  -0.345  -0.318
130   -        -0.169  -0.168  -0.152  -0.180  -0.171  -0.151  -0.346  -0.345  -0.318
131   -        -0.169  -0.168  -0.152  -0.372  -0.380  -0.343  -0.346  -0.345  -0.318
132   -        -0.169  -0.168  -0.152  -0.686  -0.665  -0.656  -0.346  -0.345  -0.318
133   -         1.655   1.656   1.671   1.247   1.261   1.273   1.763   1.765   1.783
134   -        -0.169  -0.168  -0.152  -0.051  -0.041  -0.022  -0.346  -0.345  -0.318
135   -        -0.169  -0.168  -0.152  -0.282  -0.274  -0.253  -0.346  -0.345  -0.318
136   -        -0.169  -0.168  -0.152  -0.495  -0.488  -0.465  -0.346  -0.345  -0.318
137   -        -0.169  -0.168  -0.152  -0.165  -0.171  -0.136  -0.346  -0.345  -0.318
138   -        -0.169  -0.168  -0.152  -0.638  -0.632  -0.608  -0.346  -0.345  -0.318
139   -        -0.169  -0.168  -0.152  -0.253  -0.259  -0.223  -0.346  -0.345  -0.318
140   -        -0.169  -0.168  -0.152  -0.605  -0.584  -0.576  -0.346  -0.345  -0.318
141   -        -0.169  -0.168  -0.152  -0.079  -0.084  -0.051  -0.346  -0.345  -0.318
142   -        -0.169  -0.168  -0.152  -0.180  -0.171  -0.151  -0.346  -0.345  -0.318
143   -        -0.169  -0.168  -0.152  -0.180  -0.171  -0.151  -0.346  -0.345  -0.318
144   -        -0.169  -0.168  -0.152  -0.605  -0.584  -0.576  -0.346  -0.345  -0.318
145   -        -0.169  -0.168  -0.152  -0.312  -0.319  -0.283  -0.346  -0.345  -0.318
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -         1.655   1.656   1.671   1.750   1.748   1.776   1.763   1.765   1.783
151   -         1.655   1.656   1.671   1.790   1.788   1.816   1.763   1.765   1.783
152   -        -0.169  -0.168  -0.152  -0.605  -0.584  -0.576  -0.346  -0.345  -0.318
153   -        -0.169  -0.168  -0.152  -0.180  -0.171  -0.151  -0.346  -0.345  -0.318
154   -        -0.169  -0.168  -0.152   0.060   0.057   0.088  -0.346  -0.345  -0.318
155   -        -0.169  -0.168  -0.152  -0.165  -0.171  -0.136  -0.346  -0.345  -0.318
156   N         1.655   1.656   1.671   1.663   1.659   1.688   1.763   1.765   1.783
157   Q        -0.169  -0.168  -0.152  -0.051  -0.050  -0.023  -0.346  -0.345  -0.318
158   M         1.655   1.656   1.671   1.909   1.912   1.935   1.763   1.765   1.783
159   T        -0.169  -0.168  -0.152   0.074   0.076   0.103  -0.346  -0.345  -0.318
160   S        -0.169  -0.168  -0.152  -0.285  -0.283  -0.255  -0.346  -0.345  -0.318
161   K        -0.169  -0.168  -0.152  -0.437  -0.436  -0.407  -0.346  -0.345  -0.318
162   Y        -0.169  -0.168  -0.152  -0.484  -0.483  -0.454  -0.346  -0.345  -0.318
163   T        -0.169  -0.168  -0.152  -0.009  -0.008   0.020  -0.346  -0.345  -0.318
164   Y        -0.020  -0.023  -0.072   0.282   0.272   0.198  -0.112  -0.117  -0.192
165   D        -0.020  -0.035  -0.072  -0.419  -0.429  -0.492  -0.112  -0.135  -0.191
166   G        -0.020  -0.023  -0.072   0.257   0.247   0.177  -0.112  -0.117  -0.192
167   E        -1.236  -1.235  -1.218  -1.047  -1.044  -1.016  -1.049  -1.047  -1.019
168   A        -0.020  -0.035  -0.072   0.113   0.091   0.011  -0.112  -0.135  -0.191
169   D        -0.020  -0.035  -0.072  -0.390  -0.393  -0.459  -0.112  -0.135  -0.191
170   T        -1.236  -1.235  -1.218  -0.834  -0.832  -0.804  -1.049  -1.047  -1.019
171   D        -0.020  -0.035  -0.072  -0.455  -0.466  -0.534  -0.112  -0.135  -0.191
172   V        -1.236  -1.235  -1.218  -1.237  -1.251  -1.206  -1.049  -1.047  -1.019
173   E        -0.020  -0.023  -0.072  -0.155  -0.148  -0.282  -0.112  -0.117  -0.192
174   M        -0.020  -0.035  -0.072   0.282   0.265   0.201  -0.112  -0.135  -0.191
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   M        -1.236  -1.235  -1.218  -0.947  -0.931  -0.916  -1.049  -1.047  -1.019
183   A        -0.020   0.002  -0.052  -0.334  -0.281  -0.370  -0.112  -0.077  -0.161
184   V        -1.236  -1.235  -1.218  -0.930  -0.918  -0.900  -1.049  -1.047  -1.019
185   D         1.655   1.656   1.671   1.293   1.314   1.320   1.763   1.765   1.783
186   T        -1.236  -1.235  -1.218  -0.971  -0.975  -0.941  -1.049  -1.047  -1.019
187   D         1.655   1.656   1.671   1.293   1.314   1.320   1.763   1.765   1.783
188   V        -0.020   0.002  -0.052  -0.035  -0.009  -0.086  -0.112  -0.077  -0.161
189   D        -0.020  -0.023  -0.072  -0.390  -0.375  -0.460  -0.112  -0.117  -0.192
190   M        -0.169  -0.168  -0.152  -0.137  -0.136  -0.109  -0.346  -0.345  -0.318
191   D         1.655   1.656   1.671   1.241   1.243   1.267   1.763   1.765   1.783
192   A        -0.169  -0.168  -0.152  -0.109  -0.107  -0.080  -0.346  -0.345  -0.318
* 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/Q02864
Output conservation file - output/Q02864
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
