1     M         1.528   1.542   1.612   1.783   1.797   1.903   1.647   1.667   1.774
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -0.849  -0.814  -0.729  -1.068  -1.023  -0.872  -0.896  -0.854  -0.743
23    -        -0.849  -0.767  -0.726  -0.969  -0.834  -0.792  -0.896  -0.803  -0.741
24    -         0.635   0.648   0.570   0.650   0.675   0.535   0.517   0.529   0.352
25    -        -0.168  -0.212  -0.200  -0.071  -0.138  -0.140  -0.331  -0.401  -0.398
26    -        -0.168  -0.213  -0.195  -0.417  -0.507  -0.481  -0.331  -0.403  -0.391
27    -        -0.849  -0.771  -0.715  -0.997  -0.878  -0.803  -0.896  -0.804  -0.728
28    -        -1.344  -1.269  -1.145  -1.457  -1.350  -1.161  -1.179  -1.098  -0.950
29    -        -0.168  -0.212  -0.200  -0.371  -0.446  -0.426  -0.331  -0.401  -0.398
30    -        -0.849  -0.814  -0.729  -0.966  -0.930  -0.813  -0.896  -0.854  -0.743
31    -        -0.849  -0.809  -0.730  -1.024  -0.976  -0.858  -0.896  -0.849  -0.745
32    -        -0.355  -0.316  -0.233  -0.728  -0.671  -0.534  -0.614  -0.561  -0.449
33    S        -0.829  -0.822  -0.735  -0.798  -0.780  -0.630  -0.892  -0.872  -0.753
34    F        -0.211  -0.236  -0.190  -0.412  -0.465  -0.365  -0.450  -0.472  -0.399
35    I        -0.713  -0.728  -0.680  -0.796  -0.808  -0.712  -0.781  -0.782  -0.698
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    K        -0.713  -0.763  -0.707  -0.680  -0.746  -0.658  -0.781  -0.808  -0.724
38    N        -0.388  -0.577  -0.652  -0.199  -0.479  -0.652  -0.340  -0.572  -0.657
39    L        -1.255  -1.175  -1.108  -1.347  -1.200  -1.102  -1.113  -1.025  -0.921
40    L        -0.637  -0.682  -0.685  -0.685  -0.767  -0.728  -0.671  -0.721  -0.701
41    F        -1.238  -1.188  -1.116  -1.216  -1.118  -1.023  -1.092  -1.031  -0.925
42    G        -0.177  -0.209  -0.214  -0.257  -0.277  -0.277  -0.371  -0.438  -0.426
43    G        -1.591  -1.568  -1.451  -1.601  -1.558  -1.380  -1.237  -1.202  -1.058
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    V        -1.139  -1.216  -1.117  -1.079  -1.181  -1.048  -1.002  -1.054  -0.927
46    K        -1.139  -1.155  -1.099  -1.007  -1.000  -0.931  -1.002  -1.006  -0.912
47    T        -0.637  -0.725  -0.690  -0.615  -0.741  -0.714  -0.671  -0.756  -0.703
48    S        -0.637  -0.556  -0.662  -0.619  -0.477  -0.654  -0.671  -0.560  -0.671
49    E        -0.829  -0.784  -0.725  -0.968  -0.900  -0.796  -0.892  -0.842  -0.745
50    D        -1.104  -1.203  -1.118  -1.093  -1.240  -1.121  -0.948  -1.039  -0.926
51    P         0.309   0.327   0.427   0.102   0.144   0.293  -0.083  -0.065   0.075
52    T        -0.689  -0.775  -0.732  -0.747  -0.924  -0.876  -0.708  -0.807  -0.747
53    G        -0.168  -0.273  -0.235  -0.428  -0.605  -0.566  -0.331  -0.487  -0.448
54    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    D        -0.277  -0.255  -0.215  -0.469  -0.434  -0.376  -0.512  -0.480  -0.426
65    S         0.107   0.066  -0.103   0.195   0.131  -0.151   0.061  -0.005  -0.259
66    N        -1.591  -1.449  -1.432  -1.554  -1.376  -1.314  -1.237  -1.111  -1.045
67    K        -0.211  -0.063  -0.180  -0.400  -0.190  -0.335  -0.450  -0.270  -0.384
68    G        -2.183  -2.070  -1.951  -1.993  -1.806  -1.668  -1.444  -1.350  -1.205
69    S        -1.565  -1.506  -1.427  -1.553  -1.483  -1.364  -1.223  -1.160  -1.042
70    E        -1.139  -1.128  -1.096  -1.123  -1.092  -1.040  -1.002  -0.987  -0.910
71    P        -0.079  -0.069  -0.143  -0.101  -0.075  -0.207  -0.229  -0.207  -0.321
72    V        -0.177  -0.225  -0.206  -0.241  -0.326  -0.335  -0.371  -0.430  -0.415
73    V         0.856   0.730   0.617   0.931   0.765   0.574   0.875   0.668   0.440
74    A        -0.637  -0.650  -0.686  -0.620  -0.647  -0.664  -0.671  -0.703  -0.702
75    G        -0.388  -0.577  -0.652  -0.303  -0.559  -0.681  -0.340  -0.572  -0.657
76    N        -1.448  -1.409  -1.406  -1.248  -1.229  -1.215  -1.113  -1.078  -1.024
77    F         0.525   0.435   0.458   0.512   0.359   0.382   0.323   0.145   0.137
78    F         0.215   0.415  -0.040   0.392   0.643   0.030   0.212   0.480  -0.167
79    P         1.528   1.542   1.612   1.543   1.566   1.676   1.647   1.667   1.774
80    R        -0.388  -0.422  -0.614  -0.095  -0.165  -0.471  -0.340  -0.391  -0.612
81    T        -0.079  -0.136  -0.156  -0.089  -0.168  -0.225  -0.229  -0.295  -0.339
82    L         1.528   1.542   1.612   1.418   1.425   1.558   1.647   1.667   1.774
83    S        -1.139  -1.181  -1.108  -1.131  -1.212  -1.108  -1.002  -1.028  -0.920
84    K         0.215   0.055  -0.099   0.368   0.142  -0.125   0.212  -0.019  -0.253
85    F         0.291   0.335   0.430   0.121   0.202   0.349  -0.119  -0.048   0.082
86    N         1.528   1.542   1.612   1.591   1.639   1.721   1.647   1.667   1.774
87    G         1.528   1.542   1.612   1.436   1.469   1.575   1.647   1.667   1.774
88    H        -1.139  -1.158  -1.099  -0.921  -0.982  -0.925  -1.002  -1.009  -0.912
89    D         0.525   0.442   0.459   0.395   0.254   0.257   0.323   0.157   0.140
90    D         0.215   0.133  -0.081   0.292   0.189  -0.138   0.212   0.086  -0.228
91    E        -0.713  -0.763  -0.707  -0.762  -0.796  -0.688  -0.781  -0.808  -0.724
92    K        -0.388  -0.577  -0.652  -0.205  -0.499  -0.638  -0.340  -0.572  -0.657
93    I         0.347   0.328   0.425   0.192   0.138   0.278  -0.009  -0.063   0.071
94    F         0.215   0.115  -0.078   0.365   0.224  -0.080   0.212   0.068  -0.223
95    I        -0.079  -0.190  -0.195  -0.036  -0.244  -0.242  -0.229  -0.396  -0.400
96    A         0.856   0.798   0.637   0.923   0.848   0.590   0.875   0.780   0.476
97    I         0.347   0.393   0.444   0.165   0.250   0.309  -0.009   0.065   0.110
98    R        -0.211  -0.146  -0.187  -0.267  -0.197  -0.244  -0.450  -0.383  -0.396
99    G         0.525   0.585   0.534   0.368   0.481   0.371   0.323   0.419   0.283
100   K        -0.211  -0.271  -0.201  -0.259  -0.330  -0.223  -0.450  -0.508  -0.412
101   V         1.528   1.542   1.612   1.539   1.566   1.672   1.647   1.667   1.774
102   Y         0.347   0.375   0.444   0.255   0.291   0.383  -0.009   0.030   0.110
103   D         0.525   0.484   0.469   0.402   0.345   0.287   0.323   0.236   0.159
104   C         0.347   0.477   0.492   0.274   0.477   0.495  -0.009   0.222   0.203
105   T         0.856   0.940   0.642   0.964   1.072   0.660   0.875   0.997   0.484
106   R        -0.946  -0.885  -0.762  -0.826  -0.736  -0.562  -1.002  -0.929  -0.779
107   G         1.528   1.542   1.612   1.436   1.469   1.575   1.647   1.667   1.774
108   R        -0.946  -1.011  -1.065  -0.685  -0.806  -0.940  -0.781  -0.851  -0.877
109   Q        -0.829  -0.822  -0.735  -0.776  -0.778  -0.662  -0.892  -0.872  -0.753
110   F         1.528   1.542   1.612   1.556   1.579   1.688   1.647   1.667   1.774
111   Y         1.528   1.542   1.612   1.677   1.690   1.803   1.647   1.667   1.774
112   G         1.528   1.542   1.612   1.436   1.469   1.575   1.647   1.667   1.774
113   P         1.528   1.542   1.612   1.543   1.566   1.676   1.647   1.667   1.774
114   S        -0.211  -0.216  -0.187  -0.390  -0.335  -0.289  -0.450  -0.419  -0.387
115   G         1.528   1.542   1.612   1.436   1.469   1.575   1.647   1.667   1.774
116   P         1.528   1.542   1.612   1.543   1.566   1.676   1.647   1.667   1.774
117   Y         1.528   1.542   1.612   1.677   1.690   1.803   1.647   1.667   1.774
118   T        -0.713  -0.631  -0.686  -0.806  -0.698  -0.741  -0.781  -0.695  -0.704
119   N         0.856   0.730   0.617   0.990   0.847   0.636   0.875   0.668   0.440
120   F         1.528   1.542   1.612   1.556   1.579   1.688   1.647   1.667   1.774
121   A         1.528   1.542   1.612   1.539   1.559   1.672   1.647   1.667   1.774
122   G         1.528   1.542   1.612   1.436   1.469   1.575   1.647   1.667   1.774
123   H         0.291   0.328   0.426   0.274   0.330   0.475  -0.119  -0.062   0.073
124   D         1.528   1.542   1.612   1.472   1.499   1.609   1.647   1.667   1.774
125   A         1.528   1.542   1.612   1.539   1.559   1.672   1.647   1.667   1.774
126   S         1.528   1.542   1.612   1.569   1.598   1.701   1.647   1.667   1.774
127   R         1.528   1.542   1.612   1.669   1.683   1.795   1.647   1.667   1.774
128   G         1.528   1.542   1.612   1.436   1.469   1.575   1.647   1.667   1.774
129   L         1.528   1.542   1.612   1.418   1.425   1.558   1.647   1.667   1.774
130   A         0.856   0.911   0.653   0.942   1.014   0.658   0.875   0.953   0.505
131   L        -0.637  -0.494  -0.647  -0.604  -0.345  -0.584  -0.671  -0.483  -0.653
132   N         0.215   0.115  -0.078   0.383   0.270  -0.083   0.212   0.068  -0.223
133   S         1.528   1.542   1.612   1.569   1.598   1.701   1.647   1.667   1.774
134   F         1.528   1.542   1.612   1.556   1.579   1.688   1.647   1.667   1.774
135   D         0.525   0.640   0.519   0.371   0.560   0.333   0.323   0.515   0.255
136   L        -1.139  -1.135  -1.089  -1.197  -1.239  -1.094  -1.002  -0.994  -0.903
137   D        -0.211  -0.190  -0.168  -0.447  -0.385  -0.351  -0.450  -0.397  -0.367
138   V        -1.139  -1.124  -1.091  -0.915  -0.887  -0.819  -1.002  -0.984  -0.906
139   I        -0.327  -0.235  -0.233  -0.575  -0.437  -0.423  -0.561  -0.437  -0.447
140   K        -0.637  -0.480  -0.666  -0.590  -0.392  -0.633  -0.671  -0.507  -0.681
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   D        -0.079  -0.015  -0.142  -0.128  -0.051  -0.198  -0.229  -0.161  -0.323
143   W        -1.139  -1.178  -1.107  -0.904  -1.004  -0.931  -1.002  -1.026  -0.919
144   D         0.856   0.903   0.646   0.879   0.950   0.593   0.875   0.941   0.492
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   Q        -0.637  -0.596  -0.669  -0.496  -0.486  -0.608  -0.671  -0.642  -0.685
147   P         0.856   0.730   0.617   0.936   0.766   0.578   0.875   0.668   0.440
148   I        -0.211  -0.106  -0.188  -0.325  -0.252  -0.265  -0.450  -0.346  -0.397
149   D         1.528   1.542   1.612   1.472   1.499   1.609   1.647   1.667   1.774
150   P        -0.327  -0.249  -0.236  -0.513  -0.386  -0.399  -0.561  -0.455  -0.450
151   L         0.856   0.730   0.617   0.860   0.697   0.577   0.875   0.668   0.440
152   D        -1.565  -1.430  -1.415  -1.473  -1.273  -1.242  -1.223  -1.099  -1.034
153   D         0.856   0.911   0.653   0.879   0.959   0.604   0.875   0.953   0.505
154   L         1.528   1.542   1.612   1.418   1.425   1.558   1.647   1.667   1.774
155   T        -0.637  -0.718  -0.692  -0.630  -0.753  -0.741  -0.671  -0.758  -0.709
156   K        -1.874  -1.789  -1.695  -1.764  -1.641  -1.523  -1.333  -1.256  -1.127
157   E        -1.255  -1.206  -1.108  -1.194  -1.127  -0.976  -1.113  -1.050  -0.921
158   Q         0.347   0.425   0.457   0.196   0.315   0.369  -0.009   0.126   0.135
159   I        -0.829  -0.798  -0.731  -0.888  -0.875  -0.746  -0.892  -0.856  -0.751
160   D        -0.637  -0.556  -0.662  -0.695  -0.530  -0.716  -0.671  -0.560  -0.671
161   A        -0.211  -0.197  -0.174  -0.345  -0.298  -0.262  -0.450  -0.409  -0.374
162   L         1.528   1.542   1.612   1.418   1.425   1.558   1.647   1.667   1.774
163   D        -0.637  -0.612  -0.675  -0.647  -0.595  -0.682  -0.671  -0.646  -0.691
164   E        -1.139  -1.129  -1.071  -1.253  -1.219  -1.137  -1.002  -0.972  -0.884
165   W         1.528   1.542   1.612   1.800   1.816   1.919   1.647   1.667   1.774
166   Q        -0.388  -0.320  -0.607  -0.234  -0.172  -0.547  -0.340  -0.275  -0.604
167   E        -0.637  -0.597  -0.673  -0.585  -0.557  -0.594  -0.671  -0.640  -0.689
168   H        -0.388  -0.577  -0.652   0.028  -0.256  -0.420  -0.340  -0.572  -0.657
169   F         0.856   0.798   0.637   0.967   0.899   0.663   0.875   0.780   0.476
170   E        -0.946  -0.917  -1.049  -0.838  -0.847  -1.022  -0.781  -0.760  -0.862
171   N        -0.946  -1.048  -1.073  -0.704  -0.841  -0.922  -0.781  -0.889  -0.885
172   K         0.856   0.903   0.646   0.987   1.055   0.706   0.875   0.941   0.492
173   Y         1.528   1.542   1.612   1.677   1.690   1.803   1.647   1.667   1.774
174   P        -0.946  -1.072  -1.076  -0.749  -0.936  -0.960  -0.781  -0.911  -0.887
175   C        -0.637  -0.682  -0.669  -0.466  -0.518  -0.486  -0.671  -0.700  -0.679
176   I        -0.079  -0.019  -0.123  -0.029   0.094  -0.060  -0.229  -0.127  -0.292
177   G         1.528   1.542   1.612   1.436   1.469   1.575   1.647   1.667   1.774
178   T        -0.946  -1.048  -1.073  -0.734  -0.893  -0.946  -0.781  -0.889  -0.885
179   L         1.528   1.542   1.612   1.418   1.425   1.558   1.647   1.667   1.774
180   I        -0.829  -0.813  -0.719  -0.832  -0.800  -0.663  -0.892  -0.861  -0.738
181   P        -1.139  -1.125  -1.088  -1.138  -1.114  -1.054  -1.002  -0.981  -0.901
182   E        -0.637  -0.715  -0.686  -0.665  -0.766  -0.738  -0.671  -0.745  -0.698
183   P        -0.751  -0.793  -0.724  -0.866  -0.928  -0.835  -0.804  -0.843  -0.741
184   G        -0.751  -0.833  -0.735  -0.938  -1.057  -0.914  -0.804  -0.878  -0.751
185   V         0.107  -0.081  -0.150   0.192  -0.095  -0.236   0.061  -0.212  -0.327
186   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
192   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
194   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
195   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
197   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
198   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
199   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
200   N        -0.751  -0.817  -0.725  -0.701  -0.782  -0.653  -0.804  -0.863  -0.743
201   V        -1.238  -1.217  -1.109  -1.233  -1.196  -1.046  -1.092  -1.052  -0.919
* 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/Q12091
Output conservation file - output/Q12091
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
