1     M         1.570   1.577   1.595   1.838   1.848   1.874   1.666   1.673   1.695
2     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    N        -0.230  -0.225  -0.199  -0.419  -0.411  -0.369  -0.419  -0.410  -0.368
30    G        -0.230  -0.225  -0.199  -0.350  -0.342  -0.300  -0.419  -0.410  -0.368
31    P         1.570   1.577   1.595   1.598   1.606   1.636   1.666   1.673   1.695
32    T        -0.230  -0.225  -0.199  -0.547  -0.540  -0.496  -0.419  -0.410  -0.368
33    P         1.570   1.577   1.595   1.598   1.606   1.636   1.666   1.673   1.695
34    A        -0.083  -0.066  -0.115  -0.037  -0.002  -0.075  -0.187  -0.160  -0.235
35    V        -0.230  -0.225  -0.199  -0.106  -0.085  -0.058  -0.419  -0.410  -0.368
36    L        -0.230  -0.225  -0.199  -0.224  -0.217  -0.175  -0.419  -0.410  -0.368
37    P        -0.230  -0.225  -0.199   0.084   0.093   0.131  -0.419  -0.410  -0.368
38    Q         1.570   1.577   1.595   1.456   1.470   1.495   1.666   1.673   1.695
39    K        -0.083  -0.132  -0.139  -0.480  -0.583  -0.598  -0.187  -0.263  -0.274
40    P        -0.083  -0.132  -0.139  -0.024  -0.108  -0.146  -0.187  -0.263  -0.274
41    K         1.570   1.577   1.595   1.255   1.267   1.295   1.666   1.673   1.695
42    L         1.570   1.577   1.595   1.623   1.631   1.660   1.666   1.673   1.695
43    T        -0.083  -0.132  -0.139  -0.063  -0.121  -0.125  -0.187  -0.263  -0.274
44    G        -0.083  -0.132  -0.139   0.109   0.032   0.002  -0.187  -0.263  -0.274
45    W         1.570   1.577   1.595   1.825   1.831   1.861   1.666   1.673   1.695
46    A        -0.083  -0.132  -0.139  -0.011  -0.065  -0.077  -0.187  -0.263  -0.274
47    Q        -0.083  -0.132  -0.139  -0.282  -0.389  -0.411  -0.187  -0.263  -0.274
48    A        -0.083  -0.132  -0.139  -0.018  -0.075  -0.085  -0.187  -0.263  -0.274
49    A        -0.083  -0.132  -0.139  -0.296  -0.400  -0.424  -0.187  -0.263  -0.274
50    A        -0.083  -0.025  -0.104  -0.465  -0.402  -0.488  -0.187  -0.098  -0.218
51    K        -0.230  -0.225  -0.199  -0.363  -0.355  -0.314  -0.419  -0.410  -0.368
52    A         1.570   1.577   1.595   1.442   1.458   1.480   1.666   1.673   1.695
53    L        -0.083  -0.066  -0.115   0.207   0.233   0.172  -0.187  -0.160  -0.235
54    P        -0.083  -0.132  -0.139  -0.024  -0.108  -0.146  -0.187  -0.263  -0.274
55    R        -0.083  -0.025  -0.104  -0.215  -0.131  -0.232  -0.187  -0.098  -0.218
56    Q        -0.083  -0.132  -0.139  -0.208  -0.289  -0.319  -0.187  -0.263  -0.274
57    Q        -0.083  -0.025  -0.104  -0.458  -0.396  -0.480  -0.187  -0.098  -0.218
58    Q        -1.283  -1.273  -1.249  -0.864  -0.819  -0.811  -1.114  -1.097  -1.056
59    Q        -1.283  -1.273  -1.249  -1.108  -1.082  -1.054  -1.114  -1.097  -1.056
60    Q        -1.283  -1.273  -1.249  -1.126  -1.076  -1.071  -1.114  -1.097  -1.056
61    Q        -1.283  -1.273  -1.249  -1.188  -1.154  -1.133  -1.114  -1.097  -1.056
62    Q        -0.083  -0.132  -0.139  -0.148  -0.224  -0.246  -0.187  -0.263  -0.274
63    A         1.570   1.577   1.595   1.426   1.432   1.465   1.666   1.673   1.695
64    R        -0.230  -0.225  -0.199  -0.516  -0.510  -0.465  -0.419  -0.410  -0.368
65    K        -0.230  -0.225  -0.199  -0.292  -0.285  -0.242  -0.419  -0.410  -0.368
66    D        -0.230  -0.225  -0.199  -0.224  -0.217  -0.175  -0.419  -0.410  -0.368
67    D        -1.283  -1.273  -1.249  -1.224  -1.257  -1.169  -1.114  -1.097  -1.056
68    S        -1.283  -1.273  -1.249  -1.452  -1.417  -1.396  -1.114  -1.097  -1.056
69    V        -1.283  -1.273  -1.249  -1.355  -1.383  -1.299  -1.114  -1.097  -1.056
70    A        -0.083  -0.066  -0.115  -0.037  -0.002  -0.075  -0.187  -0.160  -0.235
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    V        -0.083  -0.066  -0.115   0.231   0.261   0.195  -0.187  -0.160  -0.235
76    Q        -1.283  -1.273  -1.249  -1.126  -1.107  -1.071  -1.114  -1.097  -1.056
77    P        -1.283  -1.273  -1.249  -1.442  -1.464  -1.386  -1.114  -1.097  -1.056
78    A        -0.083  -0.132  -0.139  -0.018  -0.075  -0.085  -0.187  -0.263  -0.274
79    N        -0.083  -0.066  -0.115   0.065   0.118   0.022  -0.187  -0.160  -0.235
80    T         1.570   1.577   1.595   1.385   1.393   1.424   1.666   1.673   1.695
81    K        -1.283  -1.273  -1.249  -1.442  -1.447  -1.386  -1.114  -1.097  -1.056
82    T        -0.083  -0.132  -0.139  -0.095  -0.158  -0.164  -0.187  -0.263  -0.274
83    K        -1.283  -1.273  -1.249  -1.584  -1.589  -1.527  -1.114  -1.097  -1.056
84    T        -1.283  -1.273  -1.249  -1.637  -1.651  -1.579  -1.114  -1.097  -1.056
85    I        -0.083  -0.066  -0.115   0.071   0.098  -0.016  -0.187  -0.160  -0.235
86    A        -1.283  -1.273  -1.249  -1.170  -1.188  -1.115  -1.114  -1.097  -1.056
87    S        -0.083  -0.066  -0.115  -0.458  -0.452  -0.495  -0.187  -0.160  -0.235
88    T        -1.283  -1.273  -1.249  -1.099  -1.076  -1.045  -1.114  -1.097  -1.056
89    A        -1.283  -1.273  -1.249  -0.905  -0.862  -0.852  -1.114  -1.097  -1.056
90    P        -1.283  -1.273  -1.249  -1.188  -1.212  -1.133  -1.114  -1.097  -1.056
91    P        -1.283  -1.273  -1.249  -1.188  -1.168  -1.133  -1.114  -1.097  -1.056
92    A        -1.283  -1.273  -1.249  -1.279  -1.294  -1.224  -1.114  -1.097  -1.056
93    N         1.570   1.577   1.595   1.554   1.587   1.592   1.666   1.673   1.695
94    I        -1.283  -1.273  -1.249  -0.946  -0.956  -0.893  -1.114  -1.097  -1.056
95    K        -0.083  -0.066  -0.115  -0.480  -0.455  -0.549  -0.187  -0.160  -0.235
96    G        -1.283  -1.273  -1.249  -1.403  -1.415  -1.347  -1.114  -1.097  -1.056
97    S        -1.283  -1.273  -1.249  -1.384  -1.327  -1.327  -1.114  -1.097  -1.056
98    S        -0.083  -0.132  -0.139  -0.408  -0.477  -0.467  -0.187  -0.263  -0.274
99    T        -0.083  -0.132  -0.139  -0.135  -0.191  -0.212  -0.187  -0.263  -0.274
100   A        -0.083  -0.025  -0.104  -0.465  -0.402  -0.488  -0.187  -0.098  -0.218
101   N        -0.083  -0.066  -0.115   0.065   0.118   0.022  -0.187  -0.160  -0.235
102   G        -0.083  -0.066  -0.115   0.084   0.118   0.019  -0.187  -0.160  -0.235
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   S         1.570   1.577   1.595   1.091   1.075   1.132   1.666   1.673   1.695
106   S        -0.083  -0.132  -0.139  -0.458  -0.545  -0.528  -0.187  -0.263  -0.274
107   T        -0.083  -0.066  -0.115  -0.089  -0.061  -0.124  -0.187  -0.160  -0.235
108   N        -0.083  -0.066  -0.115  -0.188  -0.141  -0.266  -0.187  -0.160  -0.235
109   K        -1.283  -1.273  -1.249  -1.170  -1.134  -1.115  -1.114  -1.097  -1.056
110   K        -1.283  -1.273  -1.249  -1.345  -1.303  -1.289  -1.114  -1.097  -1.056
111   F        -1.283  -1.273  -1.249  -1.047  -1.082  -0.993  -1.114  -1.097  -1.056
112   K        -0.083  -0.132  -0.139  -0.148  -0.196  -0.195  -0.187  -0.263  -0.274
113   R        -1.283  -1.273  -1.249  -1.091  -1.058  -1.036  -1.114  -1.097  -1.056
114   A        -0.230  -0.225  -0.199  -0.067  -0.059  -0.019  -0.419  -0.410  -0.368
115   N        -0.230  -0.225  -0.199  -0.648  -0.629  -0.597  -0.419  -0.410  -0.368
116   K        -0.083  -0.066  -0.115  -0.303  -0.269  -0.347  -0.187  -0.160  -0.235
117   Q        -1.283  -1.273  -1.249  -0.971  -0.931  -0.917  -1.114  -1.097  -1.056
118   P         1.570   1.577   1.595   1.650   1.667   1.687   1.666   1.673   1.695
119   Y        -0.083  -0.132  -0.139   0.350   0.287   0.278  -0.187  -0.263  -0.274
120   N         1.570   1.577   1.595   1.554   1.587   1.592   1.666   1.673   1.695
121   R        -0.083  -0.132  -0.139   0.237   0.181   0.174  -0.187  -0.263  -0.274
122   E        -0.083  -0.025  -0.104   0.279   0.364   0.247  -0.187  -0.098  -0.218
123   E         1.570   1.577   1.595   1.691   1.698   1.728   1.666   1.673   1.695
124   V         1.570   1.577   1.595   1.650   1.662   1.687   1.666   1.673   1.695
125   R        -0.083  -0.132  -0.139  -0.037  -0.125  -0.158  -0.187  -0.263  -0.274
126   S        -1.283  -1.273  -1.249  -1.279  -1.254  -1.224  -1.114  -1.097  -1.056
127   Y        -0.083  -0.132  -0.139   0.350   0.287   0.278  -0.187  -0.263  -0.274
128   M        -0.083  -0.132  -0.139   0.309   0.233   0.212  -0.187  -0.263  -0.274
129   H        -1.283  -1.273  -1.249  -0.729  -0.702  -0.677  -1.114  -1.097  -1.056
130   K        -0.083  -0.025  -0.104  -0.560  -0.489  -0.593  -0.187  -0.098  -0.218
131   L        -0.083  -0.132  -0.139   0.040  -0.039  -0.061  -0.187  -0.263  -0.274
132   F         1.570   1.577   1.595   1.851   1.859   1.887   1.666   1.673   1.695
133   Q        -1.283  -1.273  -1.249  -1.179  -1.136  -1.124  -1.114  -1.097  -1.056
134   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   E        -0.083  -0.132  -0.139   0.102   0.021  -0.002  -0.187  -0.263  -0.274
140   K        -1.283  -1.273  -1.249  -1.126  -1.069  -1.071  -1.114  -1.097  -1.056
141   S         1.570   1.577   1.595   1.091   1.075   1.132   1.666   1.673   1.695
142   H        -0.083  -0.025  -0.104   0.237   0.316   0.218  -0.187  -0.098  -0.218
143   S        -0.083  -0.066  -0.115  -0.408  -0.394  -0.438  -0.187  -0.160  -0.235
144   M        -1.283  -1.273  -1.249  -1.188  -1.221  -1.133  -1.114  -1.097  -1.056
145   K        -0.083  -0.132  -0.139  -0.208  -0.262  -0.268  -0.187  -0.263  -0.274
146   T         1.570   1.577   1.595   1.385   1.393   1.424   1.666   1.673   1.695
147   Y        -0.083  -0.132  -0.139   0.249   0.174   0.156  -0.187  -0.263  -0.274
148   K        -0.083  -0.132  -0.139  -0.338  -0.410  -0.425  -0.187  -0.263  -0.274
149   Q        -0.083  -0.132  -0.139  -0.148  -0.224  -0.246  -0.187  -0.263  -0.274
150   V         1.570   1.577   1.595   1.634   1.642   1.672   1.666   1.673   1.695
151   L         1.570   1.577   1.595   1.616   1.624   1.654   1.666   1.673   1.695
152   S        -0.230  -0.225  -0.199  -0.665  -0.658  -0.613  -0.419  -0.410  -0.368
153   E         1.570   1.577   1.595   1.723   1.731   1.760   1.666   1.673   1.695
154   T         1.570   1.577   1.595   1.264   1.271   1.303   1.666   1.673   1.695
155   A        -0.230  -0.225  -0.199  -0.419  -0.397  -0.369  -0.419  -0.410  -0.368
156   S        -0.230  -0.225  -0.199  -0.405  -0.397  -0.355  -0.419  -0.410  -0.368
157   G         1.570   1.577   1.595   1.652   1.660   1.689   1.666   1.673   1.695
158   R        -0.230  -0.225  -0.199   0.004   0.013   0.052  -0.419  -0.410  -0.368
159   V        -0.230  -0.225  -0.199  -0.110  -0.102  -0.062  -0.419  -0.410  -0.368
160   S        -1.283  -1.273  -1.249  -1.270  -1.223  -1.215  -1.114  -1.097  -1.056
161   T        -1.283  -1.273  -1.249  -0.905  -0.867  -0.852  -1.114  -1.097  -1.056
162   A        -1.283  -1.273  -1.249  -1.502  -1.517  -1.445  -1.114  -1.097  -1.056
163   T        -0.083  -0.066  -0.115  -0.352  -0.331  -0.425  -0.187  -0.160  -0.235
164   D         1.570   1.577   1.595   1.772   1.779   1.808   1.666   1.673   1.695
165   W         1.570   1.577   1.595   1.825   1.831   1.861   1.666   1.673   1.695
166   G        -0.083  -0.132  -0.139   0.158   0.096   0.062  -0.187  -0.263  -0.274
167   T         1.570   1.577   1.595   1.385   1.393   1.424   1.666   1.673   1.695
168   V        -0.083  -0.132  -0.139  -0.095  -0.207  -0.233  -0.187  -0.263  -0.274
169   S        -1.283  -1.273  -1.249  -1.492  -1.460  -1.435  -1.114  -1.097  -1.056
170   S        -0.083  -0.066  -0.115  -0.408  -0.394  -0.438  -0.187  -0.160  -0.235
171   S        -0.083  -0.025  -0.104  -0.480  -0.382  -0.527  -0.187  -0.098  -0.218
172   K        -1.283  -1.273  -1.249  -1.317  -1.272  -1.261  -1.114  -1.097  -1.056
173   N        -1.283  -1.273  -1.249  -0.954  -0.903  -0.901  -1.114  -1.097  -1.056
174   K        -0.083  -0.066  -0.115  -0.215  -0.184  -0.246  -0.187  -0.160  -0.235
175   N        -0.083  -0.132  -0.139  -0.188  -0.277  -0.321  -0.187  -0.263  -0.274
176   K         1.570   1.577   1.595   1.255   1.267   1.295   1.666   1.673   1.695
177   K         1.570   1.577   1.595   1.255   1.267   1.295   1.666   1.673   1.695
178   Y         1.570   1.577   1.595   1.772   1.781   1.808   1.666   1.673   1.695
179   G         1.570   1.577   1.595   1.704   1.717   1.741   1.666   1.673   1.695
180   C        -0.083  -0.066  -0.115   0.267   0.300   0.195  -0.187  -0.160  -0.235
181   L         1.570   1.577   1.595   1.623   1.631   1.660   1.666   1.673   1.695
182   S        -0.083  -0.066  -0.115  -0.465  -0.458  -0.503  -0.187  -0.160  -0.235
183   D        -0.083  -0.025  -0.104   0.243   0.322   0.218  -0.187  -0.098  -0.218
184   I        -0.083  -0.132  -0.139   0.297   0.221   0.200  -0.187  -0.263  -0.274
185   A        -0.083  -0.132  -0.139  -0.018  -0.075  -0.085  -0.187  -0.263  -0.274
186   K        -0.083  -0.025  -0.104  -0.037   0.070  -0.086  -0.187  -0.098  -0.218
187   V         1.570   1.577   1.595   1.650   1.662   1.687   1.666   1.673   1.695
188   L         1.570   1.577   1.595   1.623   1.631   1.660   1.666   1.673   1.695
189   R         1.570   1.577   1.595   1.636   1.648   1.674   1.666   1.673   1.695
190   N         1.570   1.577   1.595   1.598   1.606   1.636   1.666   1.673   1.695
191   Q        -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/Q07362
Output conservation file - output/Q07362
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
