1     M         1.066   1.086   1.178   1.380   1.405   1.510   1.135   1.164   1.306
2     P        -1.385  -1.422  -1.396  -1.593  -1.622  -1.545  -1.295  -1.309  -1.218
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     -        -0.785  -0.862  -0.858  -0.605  -0.724  -0.736  -0.833  -0.943  -0.923
6     R        -0.993  -1.091  -0.874  -0.948  -1.083  -0.781  -1.197  -1.272  -0.949
7     V        -0.292  -0.263  -0.123  -0.422  -0.389  -0.197  -0.614  -0.573  -0.385
8     A         1.066   1.086   1.178   0.778   0.829   0.995   1.135   1.164   1.306
9     I         1.066   1.086   1.178   1.142   1.178   1.306   1.135   1.164   1.306
10    I        -0.292  -0.330  -0.141  -0.428  -0.523  -0.232  -0.614  -0.694  -0.416
11    I        -0.292  -0.263  -0.123  -0.392  -0.356  -0.158  -0.614  -0.573  -0.385
12    Y         1.066   1.086   1.178   1.234   1.259   1.385   1.135   1.164   1.306
13    T        -0.292  -0.214  -0.118  -0.445  -0.323  -0.226  -0.614  -0.487  -0.376
14    L        -0.993  -1.090  -0.867  -1.036  -1.174  -0.837  -1.197  -1.271  -0.941
15    Y         1.066   1.086   1.178   1.234   1.259   1.385   1.135   1.164   1.306
16    G        -0.064  -0.028  -0.081  -0.382  -0.333  -0.347  -0.226  -0.173  -0.310
17    H         1.066   1.086   1.178   1.314   1.345   1.453   1.135   1.164   1.306
18    V        -0.933  -0.835  -0.864  -1.006  -0.898  -0.910  -1.100  -1.001  -0.937
19    A        -0.933  -1.060  -0.881  -1.185  -1.330  -0.991  -1.100  -1.225  -0.957
20    A        -1.650  -1.549  -1.435  -1.654  -1.519  -1.435  -1.586  -1.489  -1.259
21    T        -1.385  -1.169  -1.386  -1.342  -1.032  -1.304  -1.295  -1.034  -1.208
22    A         1.066   1.086   1.178   0.778   0.829   0.995   1.135   1.164   1.306
23    E        -0.292  -0.263  -0.123  -0.434  -0.398  -0.204  -0.614  -0.573  -0.385
24    A        -0.745  -0.632  -0.836  -0.988  -0.834  -1.041  -0.809  -0.672  -0.897
25    E        -1.385  -1.365  -1.404  -1.150  -1.129  -1.191  -1.295  -1.255  -1.227
26    K        -0.064   0.003  -0.067   0.038   0.144  -0.015  -0.226  -0.122  -0.285
27    K        -1.073  -1.274  -1.394  -0.737  -1.061  -1.296  -0.906  -1.139  -1.215
28    G        -0.064   0.003  -0.067  -0.544  -0.433  -0.579  -0.226  -0.122  -0.285
29    I         0.322   0.447  -0.003   0.502   0.656   0.022   0.358   0.527  -0.174
30    E        -0.064   0.003  -0.067  -0.041   0.058  -0.098  -0.226  -0.122  -0.285
31    A        -1.385  -1.532  -1.426  -1.553  -1.727  -1.486  -1.295  -1.433  -1.248
32    A         1.066   1.086   1.178   0.778   0.829   0.995   1.135   1.164   1.306
33    G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
34    G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
35    S        -2.511  -2.538  -2.213  -2.159  -2.241  -1.775  -1.975  -1.972  -1.558
36    A         1.066   1.086   1.178   0.778   0.829   0.995   1.135   1.164   1.306
37    D         0.322   0.123  -0.028   0.661   0.395   0.101   0.358   0.066  -0.217
38    I        -0.292  -0.263  -0.123  -0.483  -0.446  -0.262  -0.614  -0.573  -0.385
39    Y        -0.400  -0.355  -0.141  -0.552  -0.489  -0.161  -0.809  -0.738  -0.416
40    Q         0.322   0.280  -0.018   0.606   0.551   0.046   0.358   0.299  -0.199
41    V         0.322   0.123  -0.028   0.519   0.255  -0.004   0.358   0.066  -0.217
42    E        -0.393  -0.166  -0.780  -0.101   0.170  -0.668  -0.323  -0.038  -0.822
43    E         1.066   1.086   1.178   1.135   1.171   1.300   1.135   1.164   1.306
44    T         1.066   1.086   1.178   1.007   1.036   1.191   1.135   1.164   1.306
45    L         1.066   1.086   1.178   1.035   1.065   1.215   1.135   1.164   1.306
46    S        -0.393  -0.302  -0.792  -0.096   0.004  -0.741  -0.323  -0.207  -0.838
47    P        -0.933  -0.905  -0.862  -0.958  -0.933  -0.805  -1.100  -1.066  -0.933
48    E         0.322   0.354  -0.010   0.514   0.558   0.058   0.358   0.401  -0.185
49    V        -0.393  -0.629  -0.822  -0.086  -0.411  -0.690  -0.323  -0.631  -0.877
50    V        -0.064   0.096  -0.043  -0.138   0.093  -0.132  -0.226   0.024  -0.242
51    K        -1.650  -1.741  -1.445  -1.818  -1.969  -1.571  -1.586  -1.653  -1.268
52    A        -1.057  -0.876  -0.860  -1.238  -0.906  -1.015  -1.197  -0.955  -0.927
53    L        -0.400  -0.334  -0.130  -0.523  -0.402  -0.112  -0.809  -0.701  -0.398
54    G        -0.400  -0.376  -0.143  -0.853  -0.798  -0.382  -0.809  -0.778  -0.421
55    G        -0.064   0.096  -0.043  -0.514  -0.235  -0.512  -0.226   0.024  -0.242
56    A        -0.292  -0.279  -0.129  -0.582  -0.579  -0.399  -0.614  -0.602  -0.395
57    P        -0.292  -0.228  -0.118  -0.582  -0.462  -0.369  -0.614  -0.512  -0.376
58    K         1.066   1.086   1.178   1.186   1.230   1.344   1.135   1.164   1.306
59    P        -0.064   0.003  -0.067  -0.006   0.088  -0.062  -0.226  -0.122  -0.285
60    D        -1.526  -1.377  -1.404  -1.323  -1.101  -1.231  -1.489  -1.305  -1.227
61    Y        -0.292  -0.263  -0.123  -0.279  -0.251  -0.060  -0.614  -0.573  -0.385
62    P         1.066   1.086   1.178   1.159   1.192   1.321   1.135   1.164   1.306
63    I        -0.745  -0.854  -0.862  -0.660  -0.850  -0.896  -0.809  -0.959  -0.934
64    A        -0.064  -0.199  -0.126  -0.391  -0.605  -0.458  -0.226  -0.462  -0.389
65    T        -0.064   0.058  -0.091  -0.154   0.018  -0.219  -0.226  -0.035  -0.328
66    Q        -1.978  -1.899  -1.839  -1.605  -1.523  -1.514  -1.683  -1.592  -1.417
67    D        -1.385  -1.346  -1.407  -1.197  -1.153  -1.313  -1.295  -1.244  -1.230
68    T        -0.745  -0.880  -0.865  -0.773  -1.006  -0.949  -0.809  -0.997  -0.937
69    L         1.066   1.086   1.178   1.035   1.065   1.215   1.135   1.164   1.306
70    T        -0.393  -0.302  -0.792  -0.252  -0.145  -0.799  -0.323  -0.207  -0.838
71    E        -1.073  -1.215  -1.390  -0.800  -1.010  -1.352  -0.906  -1.074  -1.211
72    Y         1.066   1.086   1.178   1.234   1.259   1.385   1.135   1.164   1.306
73    D         0.322   0.353  -0.011   0.684   0.722   0.200   0.358   0.400  -0.188
74    A         1.066   1.086   1.178   0.778   0.829   0.995   1.135   1.164   1.306
75    F        -0.064   0.019  -0.086   0.021   0.142  -0.068  -0.226  -0.098  -0.319
76    L         0.322   0.353  -0.011   0.424   0.463   0.008   0.358   0.400  -0.188
77    F         1.066   1.086   1.178   1.176   1.212   1.335   1.135   1.164   1.306
78    G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
79    I        -0.393  -0.494  -0.809  -0.119  -0.266  -0.729  -0.323  -0.470  -0.859
80    P         1.066   1.086   1.178   1.159   1.192   1.321   1.135   1.164   1.306
81    T         1.066   1.086   1.178   1.007   1.036   1.191   1.135   1.164   1.306
82    R         1.066   1.086   1.178   1.357   1.382   1.490   1.135   1.164   1.306
83    F        -0.064  -0.167  -0.119   0.021  -0.157  -0.127  -0.226  -0.406  -0.378
84    G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
85    N        -0.064  -0.171  -0.123   0.122  -0.091  -0.131  -0.226  -0.412  -0.384
86    F        -0.745  -0.892  -0.855  -0.583  -0.793  -0.779  -0.809  -0.980  -0.922
87    P         1.066   1.086   1.178   1.159   1.192   1.321   1.135   1.164   1.306
88    A         0.322   0.344  -0.009   0.118   0.167  -0.336   0.358   0.389  -0.183
89    Q         1.066   1.086   1.178   1.260   1.289   1.408   1.135   1.164   1.306
90    W        -0.292  -0.327  -0.138  -0.200  -0.298  -0.057  -0.614  -0.687  -0.412
91    K        -0.064  -0.171  -0.123   0.065  -0.100  -0.062  -0.226  -0.412  -0.384
92    A         0.322   0.123  -0.028   0.118  -0.135  -0.371   0.358   0.066  -0.217
93    F         0.322   0.280  -0.018   0.522   0.474  -0.021   0.358   0.299  -0.199
94    W         1.066   1.086   1.178   1.383   1.415   1.513   1.135   1.164   1.306
95    D         1.066   1.086   1.178   1.301   1.331   1.442   1.135   1.164   1.306
96    R        -1.978  -2.014  -1.853  -1.751  -1.844  -1.659  -1.683  -1.707  -1.429
97    T         1.066   1.086   1.178   1.007   1.036   1.191   1.135   1.164   1.306
98    G         0.322   0.344  -0.009   0.128   0.161  -0.221   0.358   0.389  -0.183
99    G         0.322   0.353  -0.011   0.103   0.145  -0.298   0.358   0.400  -0.188
100   L         1.066   1.086   1.178   1.035   1.065   1.215   1.135   1.164   1.306
101   W         1.066   1.086   1.178   1.383   1.415   1.513   1.135   1.164   1.306
102   A         0.322   0.123  -0.028   0.138  -0.103  -0.309   0.358   0.066  -0.217
103   K        -1.526  -1.416  -1.403  -1.329  -1.156  -1.115  -1.489  -1.346  -1.228
104   G         0.322   0.344  -0.009   0.125   0.157  -0.230   0.358   0.389  -0.183
105   A        -0.064  -0.038  -0.088  -0.379  -0.331  -0.384  -0.226  -0.189  -0.322
106   L         1.066   1.086   1.178   1.035   1.065   1.215   1.135   1.164   1.306
107   H        -1.385  -1.340  -1.399  -1.166  -1.114  -1.247  -1.295  -1.238  -1.222
108   G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
109   K         1.066   1.086   1.178   1.186   1.230   1.344   1.135   1.164   1.306
110   V        -2.059  -2.020  -1.856  -1.839  -1.785  -1.531  -1.781  -1.718  -1.432
111   A         0.322   0.123  -0.028   0.140  -0.097  -0.301   0.358   0.066  -0.217
112   G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
113   C        -2.840  -2.701  -2.507  -2.467  -2.295  -2.057  -2.072  -1.958  -1.641
114   F         1.066   1.086   1.178   1.176   1.212   1.335   1.135   1.164   1.306
115   V         0.322   0.123  -0.028   0.519   0.255  -0.004   0.358   0.066  -0.217
116   S         1.066   1.086   1.178   1.196   1.219   1.353   1.135   1.164   1.306
117   T         1.066   1.086   1.178   1.007   1.036   1.191   1.135   1.164   1.306
118   G         0.322   0.354  -0.010   0.103   0.145  -0.296   0.358   0.401  -0.185
119   T         0.322   0.354  -0.010   0.315   0.355  -0.251   0.358   0.401  -0.185
120   -        -0.785  -0.874  -0.858  -0.685  -0.851  -0.871  -0.833  -0.958  -0.924
121   G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
122   G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
123   G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
124   N        -0.292  -0.150  -0.091  -0.236  -0.014   0.036  -0.614  -0.376  -0.327
125   E         1.066   1.086   1.178   1.135   1.171   1.300   1.135   1.164   1.306
126   A        -2.307  -2.197  -1.874  -2.457  -2.295  -1.752  -1.975  -1.869  -1.446
127   T         1.066   1.086   1.178   1.007   1.036   1.191   1.135   1.164   1.306
128   I        -0.292  -0.150  -0.091  -0.769  -0.523  -0.415  -0.614  -0.376  -0.327
129   M        -2.183  -2.065  -1.861  -2.154  -2.032  -1.713  -1.878  -1.753  -1.437
130   N        -0.393  -0.629  -0.822   0.070  -0.272  -0.637  -0.323  -0.631  -0.877
131   S        -0.292  -0.156  -0.107  -0.742  -0.519  -0.412  -0.614  -0.388  -0.356
132   L        -0.064  -0.171  -0.123  -0.074  -0.245  -0.153  -0.226  -0.412  -0.384
133   S         0.322   0.123  -0.028   0.539   0.255  -0.036   0.358   0.066  -0.217
134   T        -1.073  -1.215  -1.390  -0.822  -1.037  -1.204  -0.906  -1.074  -1.211
135   L         0.322   0.123  -0.028   0.398   0.139  -0.098   0.358   0.066  -0.217
136   A        -0.933  -0.943  -0.869  -1.329  -1.337  -1.131  -1.100  -1.128  -0.943
137   H         1.066   1.086   1.178   1.314   1.345   1.453   1.135   1.164   1.306
138   H         1.066   1.086   1.178   1.314   1.345   1.453   1.135   1.164   1.306
139   G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
140   I        -0.064  -0.199  -0.126   0.029  -0.185  -0.084  -0.226  -0.462  -0.389
141   I         0.322   0.280  -0.018   0.487   0.440  -0.048   0.358   0.299  -0.199
142   F        -0.400  -0.370  -0.142  -0.552  -0.522  -0.164  -0.809  -0.767  -0.419
143   V         1.066   1.086   1.178   1.156   1.183   1.318   1.135   1.164   1.306
144   P         1.066   1.086   1.178   1.159   1.192   1.321   1.135   1.164   1.306
145   L         1.066   1.086   1.178   1.035   1.065   1.215   1.135   1.164   1.306
146   G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
147   Y         1.066   1.086   1.178   1.234   1.259   1.385   1.135   1.164   1.306
148   K        -0.064  -0.028  -0.081  -0.093  -0.028  -0.251  -0.226  -0.173  -0.310
149   N        -1.073  -1.092  -1.368  -0.523  -0.559  -1.016  -0.906  -0.922  -1.188
150   V        -1.730  -1.631  -1.431  -2.045  -1.908  -1.477  -1.683  -1.569  -1.256
151   F         1.066   1.086   1.178   1.176   1.212   1.335   1.135   1.164   1.306
152   A        -1.978  -1.985  -1.840  -2.238  -2.232  -2.019  -1.683  -1.675  -1.419
153   E        -1.197  -1.210  -0.915  -1.343  -1.398  -0.944  -1.392  -1.399  -0.995
154   L        -1.385  -1.480  -1.410  -1.262  -1.384  -1.231  -1.295  -1.382  -1.233
155   T        -0.064  -0.167  -0.119  -0.272  -0.485  -0.485  -0.226  -0.406  -0.378
156   N         0.322   0.280  -0.018   0.708   0.656   0.169   0.358   0.299  -0.199
157   M        -0.393  -0.472  -0.802  -0.203  -0.341  -0.741  -0.323  -0.444  -0.851
158   D        -0.292  -0.193  -0.118  -0.368  -0.212  -0.119  -0.614  -0.451  -0.376
159   E         0.322   0.123  -0.028   0.501   0.244  -0.012   0.358   0.066  -0.217
160   V        -0.745  -0.754  -0.857  -0.691  -0.758  -0.973  -0.809  -0.861  -0.926
161   H         1.066   1.086   1.178   1.314   1.345   1.453   1.135   1.164   1.306
162   G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
163   G         0.322   0.353  -0.011   0.103   0.145  -0.298   0.358   0.400  -0.188
164   S         1.066   1.086   1.178   1.196   1.219   1.353   1.135   1.164   1.306
165   P         0.322   0.123  -0.028   0.525   0.265   0.007   0.358   0.066  -0.217
166   W         0.322   0.354  -0.010   0.752   0.792   0.228   0.358   0.401  -0.185
167   G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
168   A         0.322   0.280  -0.018   0.143   0.113  -0.276   0.358   0.299  -0.199
169   G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
170   T         0.322   0.123  -0.028   0.373   0.111  -0.112   0.358   0.066  -0.217
171   I        -0.933  -0.986  -0.861  -0.943  -0.970  -0.803  -1.100  -1.114  -0.929
172   A         0.322   0.280  -0.018   0.118   0.084  -0.352   0.358   0.299  -0.199
173   G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
174   S        -1.978  -1.878  -1.838  -2.199  -2.080  -1.963  -1.683  -1.574  -1.417
175   D         1.066   1.086   1.178   1.301   1.331   1.442   1.135   1.164   1.306
176   G         0.322   0.344  -0.009   0.047   0.082  -0.459   0.358   0.389  -0.183
177   S         1.066   1.086   1.178   1.196   1.219   1.353   1.135   1.164   1.306
178   R         1.066   1.086   1.178   1.357   1.382   1.490   1.135   1.164   1.306
179   S        -1.650  -1.559  -1.428  -1.465  -1.363  -1.190  -1.586  -1.502  -1.252
180   P         0.322   0.123  -0.028   0.519   0.258  -0.009   0.358   0.066  -0.217
181   S        -0.292  -0.233  -0.124  -0.445  -0.362  -0.239  -0.614  -0.521  -0.386
182   A        -1.730  -1.668  -1.442  -1.925  -1.800  -1.421  -1.683  -1.616  -1.266
183   L         0.322   0.123  -0.028   0.414   0.164  -0.049   0.358   0.066  -0.217
184   E         1.066   1.086   1.178   1.135   1.171   1.300   1.135   1.164   1.306
185   L         0.322   0.354  -0.010   0.399   0.441  -0.063   0.358   0.401  -0.185
186   Q        -1.650  -1.486  -1.420  -1.538  -1.326  -1.195  -1.586  -1.413  -1.243
187   V        -0.400  -0.327  -0.133  -0.638  -0.516  -0.217  -0.809  -0.688  -0.402
188   H        -0.292  -0.150  -0.091  -0.684  -0.458  -0.329  -0.614  -0.376  -0.327
189   E        -2.183  -2.141  -1.871  -1.905  -1.842  -1.441  -1.878  -1.826  -1.444
190   I         1.066   1.086   1.178   1.142   1.178   1.306   1.135   1.164   1.306
191   Q         1.066   1.086   1.178   1.260   1.289   1.408   1.135   1.164   1.306
192   G         1.066   1.086   1.178   0.738   0.772   0.961   1.135   1.164   1.306
193   K        -0.933  -1.060  -0.881  -0.840  -1.010  -0.758  -1.100  -1.225  -0.957
194   T        -1.385  -1.365  -1.404  -1.425  -1.410  -1.495  -1.295  -1.254  -1.226
195   F         1.066   1.086   1.178   1.176   1.212   1.335   1.135   1.164   1.306
196   Y        -0.064  -0.124  -0.114   0.061  -0.056  -0.106  -0.226  -0.333  -0.369
197   E        -1.978  -2.086  -1.865  -1.773  -1.928  -1.584  -1.683  -1.761  -1.439
198   T         0.322   0.280  -0.018   0.366   0.314  -0.115   0.358   0.299  -0.199
199   V        -0.393  -0.279  -0.788  -0.170  -0.033  -0.848  -0.323  -0.179  -0.832
200   A        -2.511  -2.492  -2.216  -2.315  -2.313  -1.966  -1.975  -1.945  -1.559
201   K        -0.064  -0.199  -0.126   0.065  -0.147  -0.066  -0.226  -0.462  -0.389
202   F        -1.152  -1.161  -0.906  -1.376  -1.411  -1.044  -1.325  -1.340  -0.985
203   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
204   -        -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/Q12335
Output conservation file - output/Q12335
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
