1     M         1.262   1.271   1.281   1.469   1.494   1.492   1.318   1.325   1.338
2     T        -0.316  -0.238  -0.340  -0.205  -0.093  -0.233  -0.413  -0.292  -0.445
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     K         1.262   1.271   1.281   0.960   0.971   0.995   1.318   1.325   1.338
6     K         1.262   1.271   1.281   0.960   0.971   0.995   1.318   1.325   1.338
7     D        -1.462  -1.437  -1.413  -1.392  -1.348  -1.307  -1.278  -1.239  -1.199
8     K         1.262   1.271   1.281   0.960   0.971   0.995   1.318   1.325   1.338
9     K        -1.462  -1.437  -1.413  -1.528  -1.508  -1.440  -1.278  -1.239  -1.199
10    E        -0.316  -0.272  -0.352  -0.479  -0.417  -0.508  -0.413  -0.343  -0.463
11    V        -1.462  -1.437  -1.413  -1.255  -1.234  -1.173  -1.278  -1.239  -1.199
12    -         1.262   1.271   1.281   1.242   1.256   1.271   1.318   1.325   1.338
13    -        -0.457  -0.449  -0.419  -0.357  -0.340  -0.294  -0.629  -0.613  -0.565
14    -         1.262   1.271   1.281   1.242   1.256   1.271   1.318   1.325   1.338
15    -         1.262   1.271   1.281   1.194   1.209   1.224   1.318   1.325   1.338
16    -         1.262   1.271   1.281   1.242   1.256   1.271   1.318   1.325   1.338
17    -         1.262   1.271   1.281   1.194   1.209   1.224   1.318   1.325   1.338
18    -         1.262   1.271   1.281   1.368   1.382   1.394   1.318   1.325   1.338
19    -        -0.457  -0.449  -0.419  -0.302  -0.285  -0.241  -0.629  -0.613  -0.565
20    -        -0.457  -0.449  -0.419  -0.985  -0.967  -0.909  -0.629  -0.613  -0.565
21    -        -0.457  -0.449  -0.419  -0.760  -0.742  -0.689  -0.629  -0.613  -0.565
22    -        -0.457  -0.449  -0.419  -0.513  -0.496  -0.447  -0.629  -0.613  -0.565
23    -        -0.457  -0.449  -0.419  -0.605  -0.588  -0.537  -0.629  -0.613  -0.565
24    -        -0.457  -0.449  -0.419  -0.335  -0.318  -0.273  -0.629  -0.613  -0.565
25    -         1.262   1.271   1.281   1.242   1.256   1.271   1.318   1.325   1.338
26    -        -0.457  -0.449  -0.419  -0.652  -0.635  -0.583  -0.629  -0.613  -0.565
27    -        -0.457  -0.449  -0.419  -0.712  -0.694  -0.641  -0.629  -0.613  -0.565
28    -        -0.457  -0.449  -0.419  -0.412  -0.395  -0.348  -0.629  -0.613  -0.565
29    -         1.262   1.271   1.281   1.337   1.351   1.363   1.318   1.325   1.338
30    -         1.262   1.271   1.281   0.982   0.997   1.016   1.318   1.325   1.338
31    -        -0.457  -0.449  -0.419  -0.571  -0.553  -0.503  -0.629  -0.613  -0.565
32    K        -0.316  -0.389  -0.378  -0.262  -0.419  -0.424  -0.413  -0.519  -0.502
33    V        -0.316  -0.389  -0.378  -0.288  -0.400  -0.392  -0.413  -0.519  -0.502
34    Q        -0.316  -0.389  -0.378  -0.215  -0.306  -0.302  -0.413  -0.519  -0.502
35    T        -0.316  -0.389  -0.378  -0.298  -0.409  -0.405  -0.413  -0.519  -0.502
36    V        -0.316  -0.389  -0.378  -0.195  -0.322  -0.308  -0.413  -0.519  -0.502
37    T         1.262   1.271   1.281   1.300   1.309   1.328   1.318   1.325   1.338
38    T        -0.316  -0.389  -0.378  -0.298  -0.409  -0.405  -0.413  -0.519  -0.502
39    E        -0.316  -0.389  -0.378  -0.329  -0.482  -0.477  -0.413  -0.519  -0.502
40    D        -0.316  -0.389  -0.378  -0.623  -0.746  -0.718  -0.413  -0.519  -0.502
41    G        -0.316  -0.389  -0.378  -0.205  -0.293  -0.289  -0.413  -0.519  -0.502
42    E        -0.316  -0.238  -0.340  -0.457  -0.353  -0.469  -0.413  -0.292  -0.445
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -         1.262   1.271   1.281   1.476   1.490   1.499   1.318   1.325   1.338
47    -        -0.457  -0.449  -0.419  -0.571  -0.553  -0.503  -0.629  -0.613  -0.565
48    -        -0.457  -0.449  -0.419  -0.401  -0.384  -0.337  -0.629  -0.613  -0.565
49    -        -0.457  -0.449  -0.419  -0.652  -0.635  -0.583  -0.629  -0.613  -0.565
50    -        -0.457  -0.449  -0.419  -0.468  -0.451  -0.403  -0.629  -0.613  -0.565
51    -         1.262   1.271   1.281   1.399   1.413   1.424   1.318   1.325   1.338
52    -         1.262   1.271   1.281   1.242   1.256   1.271   1.318   1.325   1.338
53    -        -0.457  -0.449  -0.419  -0.833  -0.815  -0.760  -0.629  -0.613  -0.565
54    -         1.262   1.271   1.281   1.337   1.351   1.363   1.318   1.325   1.338
55    -         1.262   1.271   1.281   1.337   1.351   1.363   1.318   1.325   1.338
56    T        -0.316  -0.272  -0.352  -0.272  -0.200  -0.327  -0.413  -0.343  -0.463
57    V        -1.462  -1.437  -1.413  -1.221  -1.187  -1.140  -1.278  -1.239  -1.199
58    K        -0.316  -0.272  -0.352  -0.517  -0.452  -0.540  -0.413  -0.343  -0.463
59    V        -0.316  -0.389  -0.378  -0.556  -0.671  -0.634  -0.413  -0.519  -0.502
60    F         1.262   1.271   1.281   1.346   1.357   1.372   1.318   1.325   1.338
61    E        -0.316  -0.238  -0.340  -0.623  -0.497  -0.655  -0.413  -0.292  -0.445
62    D        -0.316  -0.238  -0.340  -0.545  -0.402  -0.596  -0.413  -0.292  -0.445
63    L        -0.316  -0.272  -0.352  -0.319  -0.240  -0.377  -0.413  -0.343  -0.463
64    Q        -1.462  -1.437  -1.413  -1.448  -1.373  -1.362  -1.278  -1.239  -1.199
65    G        -1.462  -1.437  -1.413  -1.046  -1.000  -0.969  -1.278  -1.239  -1.199
66    F         1.262   1.271   1.281   1.346   1.357   1.372   1.318   1.325   1.338
67    E         1.262   1.271   1.281   1.021   1.029   1.054   1.318   1.325   1.338
68    T        -0.316  -0.389  -0.378  -0.298  -0.409  -0.405  -0.413  -0.519  -0.502
69    F        -0.316  -0.272  -0.352  -0.175  -0.106  -0.224  -0.413  -0.343  -0.463
70    I        -0.316  -0.238  -0.340  -0.195  -0.063  -0.240  -0.413  -0.292  -0.445
71    A        -0.316  -0.389  -0.378  -0.015  -0.120  -0.115  -0.413  -0.519  -0.502
72    N        -0.316  -0.389  -0.378  -0.356  -0.453  -0.437  -0.413  -0.519  -0.502
73    E         1.262   1.271   1.281   1.021   1.029   1.054   1.318   1.325   1.338
74    T         1.262   1.271   1.281   1.300   1.309   1.328   1.318   1.325   1.338
75    E        -0.316  -0.389  -0.378  -0.155  -0.314  -0.317  -0.413  -0.519  -0.502
76    D         1.262   1.271   1.281   1.185   1.198   1.215   1.318   1.325   1.338
77    D        -0.316  -0.389  -0.378  -0.246  -0.374  -0.376  -0.413  -0.519  -0.502
78    D         1.262   1.271   1.281   1.185   1.198   1.215   1.318   1.325   1.338
79    F         1.262   1.271   1.281   1.346   1.357   1.372   1.318   1.325   1.338
80    D         1.262   1.271   1.281   1.185   1.198   1.215   1.318   1.325   1.338
81    H        -0.316  -0.389  -0.378  -0.104  -0.237  -0.223  -0.413  -0.519  -0.502
82    L        -1.462  -1.437  -1.413  -1.228  -1.190  -1.147  -1.278  -1.239  -1.199
83    H         1.262   1.271   1.281   1.346   1.346   1.372   1.318   1.325   1.338
84    C        -1.462  -1.437  -1.413  -0.996  -0.944  -0.920  -1.278  -1.239  -1.199
85    K        -1.462  -1.437  -1.413  -1.448  -1.459  -1.362  -1.278  -1.239  -1.199
86    L         1.262   1.271   1.281   1.278   1.301   1.305   1.318   1.325   1.338
87    N        -1.462  -1.437  -1.413  -1.295  -1.231  -1.212  -1.278  -1.239  -1.199
88    Y         1.262   1.271   1.281   1.502   1.516   1.525   1.318   1.325   1.338
89    Y         1.262   1.271   1.281   1.502   1.516   1.525   1.318   1.325   1.338
90    P         1.262   1.271   1.281   1.379   1.400   1.405   1.318   1.325   1.338
91    P         1.262   1.271   1.281   1.379   1.400   1.405   1.318   1.325   1.338
92    F         1.262   1.271   1.281   1.346   1.357   1.372   1.318   1.325   1.338
93    V        -0.316  -0.272  -0.352  -0.236  -0.172  -0.290  -0.413  -0.343  -0.463
94    L        -1.462  -1.437  -1.413  -1.316  -1.274  -1.232  -1.278  -1.239  -1.199
95    H        -0.316  -0.389  -0.378  -0.601  -0.710  -0.670  -0.413  -0.519  -0.502
96    E        -0.316  -0.238  -0.340  -0.562  -0.437  -0.586  -0.413  -0.292  -0.445
97    S        -1.462  -1.437  -1.413  -1.221  -1.187  -1.140  -1.278  -1.239  -1.199
98    H        -0.316  -0.238  -0.340  -0.185  -0.075  -0.217  -0.413  -0.292  -0.445
99    E        -1.462  -1.437  -1.413  -1.371  -1.364  -1.286  -1.278  -1.239  -1.199
100   D        -0.316  -0.389  -0.378  -0.246  -0.374  -0.376  -0.413  -0.519  -0.502
101   P        -1.462  -1.437  -1.413  -1.268  -1.204  -1.186  -1.278  -1.239  -1.199
102   E        -0.316  -0.272  -0.352  -0.623  -0.552  -0.675  -0.413  -0.343  -0.463
103   K         1.262   1.271   1.281   0.960   0.971   0.995   1.318   1.325   1.338
104   I         1.262   1.271   1.281   1.413   1.431   1.438   1.318   1.325   1.338
105   S        -0.316  -0.389  -0.378  -0.617  -0.713  -0.691  -0.413  -0.519  -0.502
106   D        -0.316  -0.389  -0.378  -0.288  -0.418  -0.414  -0.413  -0.519  -0.502
107   A        -0.316  -0.389  -0.378  -0.205  -0.310  -0.286  -0.413  -0.519  -0.502
108   A        -0.316  -0.389  -0.378  -0.055  -0.154  -0.151  -0.413  -0.519  -0.502
109   N         1.262   1.271   1.281   1.424   1.450   1.449   1.318   1.325   1.338
110   S        -0.316  -0.389  -0.378  -0.617  -0.713  -0.691  -0.413  -0.519  -0.502
111   H        -1.462  -1.437  -1.413  -1.506  -1.455  -1.419  -1.278  -1.239  -1.199
112   S         1.262   1.271   1.281   1.312   1.341   1.339   1.318   1.325   1.338
113   K        -0.316  -0.272  -0.352  -0.517  -0.452  -0.540  -0.413  -0.343  -0.463
114   K         1.262   1.271   1.281   0.960   0.971   0.995   1.318   1.325   1.338
115   F         1.262   1.271   1.281   1.346   1.357   1.372   1.318   1.325   1.338
116   V        -1.462  -1.437  -1.413  -1.463  -1.421  -1.376  -1.278  -1.239  -1.199
117   R         1.262   1.271   1.281   1.513   1.535   1.536   1.318   1.325   1.338
118   H        -1.462  -1.437  -1.413  -1.371  -1.321  -1.286  -1.278  -1.239  -1.199
119   L         1.262   1.271   1.281   1.278   1.301   1.305   1.318   1.325   1.338
120   H        -0.316  -0.389  -0.378  -0.124  -0.255  -0.241  -0.413  -0.519  -0.502
121   Q        -0.316  -0.389  -0.378  -0.185  -0.301  -0.274  -0.413  -0.519  -0.502
122   H         1.262   1.271   1.281   1.346   1.346   1.372   1.318   1.325   1.338
123   I         1.262   1.271   1.281   1.413   1.431   1.438   1.318   1.325   1.338
124   E        -0.316  -0.389  -0.378  -0.267  -0.424  -0.420  -0.413  -0.519  -0.502
125   K         1.262   1.271   1.281   0.960   0.971   0.995   1.318   1.325   1.338
126   H         1.262   1.271   1.281   1.346   1.346   1.372   1.318   1.325   1.338
127   L         1.262   1.271   1.281   1.278   1.301   1.305   1.318   1.325   1.338
128   L        -1.462  -1.437  -1.413  -1.248  -1.204  -1.166  -1.278  -1.239  -1.199
129   K        -0.316  -0.272  -0.352  -0.584  -0.515  -0.617  -0.413  -0.343  -0.463
130   D        -0.316  -0.272  -0.352  -0.545  -0.463  -0.620  -0.413  -0.343  -0.463
131   I        -1.462  -1.437  -1.413  -1.248  -1.182  -1.166  -1.278  -1.239  -1.199
132   K        -0.316  -0.389  -0.378  -0.732  -0.880  -0.855  -0.413  -0.519  -0.502
133   Q        -0.316  -0.389  -0.378  -0.534  -0.620  -0.587  -0.413  -0.519  -0.502
134   A        -0.316  -0.389  -0.378   0.033  -0.078  -0.072  -0.413  -0.519  -0.502
135   V        -1.462  -1.437  -1.413  -1.221  -1.189  -1.140  -1.278  -1.239  -1.199
136   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   K        -0.316  -0.389  -0.378  -0.272  -0.433  -0.434  -0.413  -0.519  -0.502
138   P        -1.462  -1.437  -1.413  -1.208  -1.166  -1.127  -1.278  -1.239  -1.199
139   E        -0.316  -0.272  -0.352  -0.567  -0.502  -0.610  -0.413  -0.343  -0.463
140   L        -0.316  -0.272  -0.352  -0.251  -0.167  -0.298  -0.413  -0.343  -0.463
141   K        -1.462  -1.437  -1.413  -1.609  -1.598  -1.520  -1.278  -1.239  -1.199
142   F         1.262   1.271   1.281   1.346   1.357   1.372   1.318   1.325   1.338
143   H        -0.316  -0.389  -0.378  -0.104  -0.235  -0.223  -0.413  -0.519  -0.502
144   E        -0.316  -0.389  -0.378  -0.761  -0.899  -0.871  -0.413  -0.519  -0.502
145   K        -1.462  -1.437  -1.413  -1.343  -1.354  -1.259  -1.278  -1.239  -1.199
146   S        -1.462  -1.437  -1.413  -1.441  -1.372  -1.355  -1.278  -1.239  -1.199
147   K        -0.316  -0.389  -0.378  -0.441  -0.608  -0.589  -0.413  -0.519  -0.502
148   E        -0.316  -0.238  -0.340  -0.556  -0.443  -0.580  -0.413  -0.292  -0.445
149   E         1.262   1.271   1.281   1.021   1.029   1.054   1.318   1.325   1.338
150   T         1.262   1.271   1.281   1.300   1.309   1.328   1.318   1.325   1.338
151   F        -1.462  -1.437  -1.413  -1.399  -1.341  -1.314  -1.278  -1.239  -1.199
152   D        -1.462  -1.437  -1.413  -1.399  -1.370  -1.314  -1.278  -1.239  -1.199
153   K        -0.316  -0.272  -0.352  -0.539  -0.471  -0.565  -0.413  -0.343  -0.463
154   I        -1.462  -1.437  -1.413  -1.336  -1.278  -1.253  -1.278  -1.239  -1.199
155   T        -0.316  -0.272  -0.352  -0.463  -0.381  -0.549  -0.413  -0.343  -0.463
156   W         1.262   1.271   1.281   1.600   1.618   1.621   1.318   1.325   1.338
157   H        -0.316  -0.389  -0.378  -0.601  -0.710  -0.670  -0.413  -0.519  -0.502
158   Y        -0.316  -0.389  -0.378  -0.175  -0.280  -0.262  -0.413  -0.519  -0.502
159   G        -1.462  -1.437  -1.413  -1.662  -1.558  -1.572  -1.278  -1.239  -1.199
160   E        -0.316  -0.389  -0.378  -0.545  -0.691  -0.674  -0.413  -0.519  -0.502
161   E        -0.316  -0.272  -0.352  -0.567  -0.502  -0.610  -0.413  -0.343  -0.463
162   T        -0.316  -0.272  -0.352  -0.303  -0.225  -0.363  -0.413  -0.343  -0.463
163   E        -0.316  -0.389  -0.378  -0.545  -0.691  -0.674  -0.413  -0.519  -0.502
164   Y        -0.316  -0.389  -0.378  -0.175  -0.290  -0.262  -0.413  -0.519  -0.502
165   -         1.262   1.271   1.281   1.476   1.490   1.499   1.318   1.325   1.338
166   -         1.262   1.271   1.281   1.368   1.382   1.394   1.318   1.325   1.338
167   -         1.262   1.271   1.281   1.242   1.256   1.271   1.318   1.325   1.338
168   -         1.262   1.271   1.281   0.982   0.997   1.016   1.318   1.325   1.338
169   -         1.262   1.271   1.281   1.048   1.063   1.081   1.318   1.325   1.338
170   -         1.262   1.271   1.281   1.048   1.063   1.081   1.318   1.325   1.338
171   -         1.262   1.271   1.281   1.048   1.063   1.081   1.318   1.325   1.338
172   -        -0.457  -0.449  -0.419  -0.582  -0.565  -0.515  -0.629  -0.613  -0.565
173   -        -0.457  -0.449  -0.419  -0.346  -0.329  -0.283  -0.629  -0.613  -0.565
174   H        -1.462  -1.437  -1.413  -1.228  -1.203  -1.147  -1.278  -1.239  -1.199
175   G        -0.316  -0.389  -0.378  -0.319  -0.413  -0.391  -0.413  -0.519  -0.502
176   R         1.262   1.271   1.281   1.513   1.535   1.536   1.318   1.325   1.338
177   P        -0.316  -0.389  -0.378  -0.231  -0.354  -0.332  -0.413  -0.519  -0.502
178   F        -0.316  -0.389  -0.378  -0.015  -0.144  -0.142  -0.413  -0.519  -0.502
179   K        -0.316  -0.238  -0.340  -0.517  -0.408  -0.526  -0.413  -0.292  -0.445
180   I        -0.316  -0.389  -0.378  -0.277  -0.376  -0.368  -0.413  -0.519  -0.502
181   D        -1.462  -1.437  -1.413  -1.535  -1.490  -1.447  -1.278  -1.239  -1.199
182   V        -0.316  -0.389  -0.378  -0.319  -0.434  -0.420  -0.413  -0.519  -0.502
183   Q        -1.462  -1.437  -1.413  -1.535  -1.451  -1.447  -1.278  -1.239  -1.199
184   V         1.262   1.271   1.281   1.323   1.325   1.350   1.318   1.325   1.338
185   V        -1.462  -1.437  -1.413  -1.385  -1.340  -1.300  -1.278  -1.239  -1.199
186   C         1.262   1.271   1.281   1.567   1.585   1.589   1.318   1.325   1.338
187   T        -0.316  -0.272  -0.352  -0.251  -0.179  -0.303  -0.413  -0.343  -0.463
188   H        -0.316  -0.389  -0.378  -0.175  -0.295  -0.286  -0.413  -0.519  -0.502
189   E         1.262   1.271   1.281   1.021   1.029   1.054   1.318   1.325   1.338
190   D        -1.462  -1.437  -1.413  -1.392  -1.348  -1.307  -1.278  -1.239  -1.199
191   A        -0.316  -0.272  -0.352  -0.070   0.009  -0.139  -0.413  -0.343  -0.463
192   M        -0.316  -0.272  -0.352  -0.165  -0.071  -0.237  -0.413  -0.343  -0.463
193   V         1.262   1.271   1.281   1.323   1.325   1.350   1.318   1.325   1.338
194   F        -1.462  -1.437  -1.413  -1.624  -1.557  -1.535  -1.278  -1.239  -1.199
195   V         1.262   1.271   1.281   1.323   1.325   1.350   1.318   1.325   1.338
196   D        -0.316  -0.238  -0.340  -0.545  -0.402  -0.596  -0.413  -0.292  -0.445
197   Y         1.262   1.271   1.281   1.502   1.516   1.525   1.318   1.325   1.338
198   K        -0.316  -0.272  -0.352  -0.539  -0.471  -0.565  -0.413  -0.343  -0.463
199   T        -1.462  -1.437  -1.413  -1.261  -1.221  -1.179  -1.278  -1.239  -1.199
200   H        -0.316  -0.389  -0.378  -0.185  -0.311  -0.296  -0.413  -0.519  -0.502
201   P         1.262   1.271   1.281   1.379   1.400   1.405   1.318   1.325   1.338
202   V        -1.462  -1.437  -1.413  -1.221  -1.189  -1.140  -1.278  -1.239  -1.199
203   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
204   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
205   N        -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/P40043
Output conservation file - output/P40043
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
