1     M         0.900   0.910   0.950   1.030   1.042   1.099   0.959   0.972   1.028
2     L        -1.697  -1.706  -1.596  -1.684  -1.711  -1.522  -1.540  -1.539  -1.369
3     K        -1.033  -1.071  -1.197  -0.839  -0.913  -1.098  -1.014  -1.061  -1.169
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     I        -1.571  -1.606  -1.594  -1.519  -1.565  -1.613  -1.409  -1.440  -1.367
6     V        -1.365  -1.351  -1.244  -1.485  -1.442  -1.256  -1.409  -1.385  -1.219
7     T        -1.697  -1.644  -1.592  -1.833  -1.777  -1.642  -1.540  -1.485  -1.366
8     R         0.900   0.910   0.950   0.956   0.969   1.031   0.959   0.972   1.028
9     A        -1.182  -1.095  -1.209  -1.126  -0.985  -1.240  -1.190  -1.082  -1.182
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    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    T        -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    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    S        -0.042   0.037  -0.094  -0.120  -0.003  -0.212  -0.250  -0.115  -0.367
23    N        -1.423  -1.401  -1.257  -1.426  -1.382  -1.177  -1.458  -1.428  -1.231
24    I        -0.842  -0.857  -0.783  -0.934  -0.969  -0.859  -1.055  -1.074  -0.960
25    A        -1.328  -1.355  -1.244  -1.389  -1.435  -1.256  -1.369  -1.386  -1.219
26    A        -1.715  -1.725  -1.603  -1.782  -1.815  -1.644  -1.548  -1.549  -1.374
27    H        -1.715  -1.708  -1.603  -1.572  -1.573  -1.427  -1.548  -1.534  -1.374
28    L        -1.715  -1.708  -1.603  -1.829  -1.811  -1.620  -1.548  -1.534  -1.374
29    L        -0.794  -0.760  -0.759  -1.042  -0.990  -0.961  -1.011  -0.956  -0.930
30    R        -0.166  -0.140  -0.131  -0.225  -0.184  -0.182  -0.473  -0.427  -0.435
31    T        -1.715  -1.657  -1.593  -1.786  -1.695  -1.601  -1.548  -1.484  -1.366
32    S        -1.571  -1.621  -1.590  -1.425  -1.501  -1.429  -1.409  -1.453  -1.364
33    P        -1.571  -1.480  -1.571  -1.449  -1.295  -1.486  -1.409  -1.308  -1.347
34    S        -1.240  -1.266  -1.223  -1.212  -1.239  -1.165  -1.277  -1.293  -1.198
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -0.261  -0.251  -0.153  -0.478  -0.466  -0.294  -0.652  -0.634  -0.477
46    -        -0.042  -0.105  -0.116  -0.128  -0.251  -0.324  -0.250  -0.364  -0.408
47    L        -1.240  -1.183  -1.217  -1.375  -1.295  -1.341  -1.277  -1.213  -1.192
48    L        -2.028  -2.022  -1.896  -1.926  -1.909  -1.743  -1.672  -1.658  -1.478
49    T        -1.033  -0.991  -1.200  -0.949  -0.893  -1.202  -1.014  -0.959  -1.172
50    R        -2.028  -2.026  -1.897  -1.820  -1.838  -1.634  -1.672  -1.662  -1.478
51    T        -2.028  -2.022  -1.896  -1.834  -1.843  -1.657  -1.672  -1.658  -1.478
52    T        -1.697  -1.632  -1.596  -1.718  -1.623  -1.572  -1.540  -1.476  -1.369
53    T        -2.360  -2.330  -2.148  -2.054  -2.030  -1.759  -1.804  -1.771  -1.553
54    T        -0.908  -0.899  -0.797  -1.263  -1.248  -1.059  -1.146  -1.132  -0.977
55    T        -2.028  -2.013  -1.890  -1.967  -1.935  -1.762  -1.672  -1.652  -1.473
56    R         0.213   0.226  -0.055   0.344   0.362  -0.058   0.170   0.189  -0.295
57    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    P        -1.715  -1.702  -1.600  -1.819  -1.813  -1.610  -1.548  -1.529  -1.371
71    F         0.145   0.041  -0.082   0.297   0.133  -0.142   0.064  -0.108  -0.344
72    S        -1.240  -1.197  -1.226  -1.204  -1.146  -1.145  -1.277  -1.220  -1.201
73    T        -0.434  -0.391  -0.711  -0.380  -0.320  -0.827  -0.488  -0.427  -0.863
74    S         0.213   0.226  -0.055   0.229   0.241  -0.188   0.170   0.189  -0.295
75    S        -2.028  -1.966  -1.886  -1.786  -1.718  -1.563  -1.672  -1.611  -1.470
76    F        -2.028  -1.996  -1.891  -1.767  -1.735  -1.569  -1.672  -1.639  -1.475
77    L        -1.571  -1.504  -1.579  -1.602  -1.505  -1.570  -1.409  -1.333  -1.354
78    N        -2.028  -1.996  -1.891  -1.771  -1.714  -1.602  -1.672  -1.639  -1.475
79    H         0.900   0.910   0.950   1.014   1.029   1.084   0.959   0.972   1.028
80    G         0.900   0.910   0.950   0.889   0.907   0.969   0.959   0.972   1.028
81    H         0.900   0.910   0.950   1.014   1.029   1.084   0.959   0.972   1.028
82    L        -0.701  -0.721  -0.759  -0.900  -0.937  -0.942  -0.883  -0.923  -0.930
83    K        -0.782  -0.850  -0.768  -0.818  -0.919  -0.806  -1.014  -1.077  -0.943
84    K         0.213   0.083  -0.067   0.370   0.194  -0.068   0.170  -0.038  -0.318
85    P         0.900   0.910   0.950   0.952   0.967   1.027   0.959   0.972   1.028
86    K        -0.244  -0.217  -0.144  -0.357  -0.301  -0.198  -0.620  -0.570  -0.459
87    P         0.900   0.910   0.950   0.952   0.967   1.027   0.959   0.972   1.028
88    G         0.900   0.910   0.950   0.889   0.907   0.969   0.959   0.972   1.028
89    E         0.900   0.910   0.950   0.898   0.914   0.977   0.959   0.972   1.028
90    E         0.900   0.910   0.950   0.898   0.914   0.977   0.959   0.972   1.028
91    L         0.213   0.215  -0.056   0.097   0.103  -0.287   0.170   0.173  -0.297
92    K        -0.701  -0.781  -0.767  -0.588  -0.683  -0.675  -0.883  -0.972  -0.940
93    I        -0.244  -0.213  -0.150  -0.400  -0.338  -0.253  -0.620  -0.563  -0.471
94    T         0.900   0.910   0.950   0.873   0.885   0.953   0.959   0.972   1.028
95    F         0.213   0.252  -0.036   0.463   0.515   0.104   0.170   0.229  -0.261
96    I         0.900   0.910   0.950   0.931   0.958   1.008   0.959   0.972   1.028
97    L        -0.782  -0.851  -0.773  -1.121  -1.222  -1.078  -1.014  -1.078  -0.948
98    K         0.900   0.910   0.950   0.989   1.006   1.061   0.959   0.972   1.028
99    D         0.900   0.910   0.950   0.775   0.786   0.863   0.959   0.972   1.028
100   G         0.213   0.083  -0.067   0.276   0.105  -0.139   0.170  -0.038  -0.318
101   S        -1.697  -1.693  -1.599  -1.677  -1.666  -1.502  -1.540  -1.529  -1.371
102   Q         0.213   0.083  -0.067   0.386   0.193  -0.077   0.170  -0.038  -0.318
103   K        -1.240  -1.299  -1.238  -1.273  -1.338  -1.260  -1.277  -1.327  -1.212
104   T        -1.033  -1.129  -1.218  -0.958  -1.108  -1.258  -1.014  -1.127  -1.191
105   Y        -1.240  -1.304  -1.233  -1.068  -1.188  -1.107  -1.277  -1.333  -1.208
106   E        -0.434  -0.554  -0.733  -0.368  -0.548  -0.874  -0.488  -0.655  -0.893
107   V         0.213   0.215  -0.056   0.341   0.341  -0.093   0.170   0.173  -0.297
108   C        -0.701  -0.781  -0.767  -0.728  -0.852  -0.829  -0.883  -0.972  -0.940
109   E         0.213   0.252  -0.036   0.250   0.306  -0.158   0.170   0.229  -0.261
110   G         0.900   0.910   0.950   0.889   0.907   0.969   0.959   0.972   1.028
111   E         0.213   0.269  -0.049   0.147   0.219  -0.241   0.170   0.254  -0.284
112   T        -0.701  -0.633  -0.744  -0.722  -0.603  -0.808  -0.883  -0.784  -0.908
113   I        -0.701  -0.644  -0.753  -0.910  -0.813  -0.942  -0.883  -0.792  -0.922
114   L         0.900   0.910   0.950   0.718   0.732   0.810   0.959   0.972   1.028
115   D         0.900   0.910   0.950   0.775   0.786   0.863   0.959   0.972   1.028
116   I         0.900   0.910   0.950   0.931   0.958   1.008   0.959   0.972   1.028
117   A         0.900   0.910   0.950   0.902   0.911   0.981   0.959   0.972   1.028
118   Q         0.900   0.910   0.950   1.018   1.024   1.088   0.959   0.972   1.028
119   G        -0.102  -0.050  -0.117  -0.212  -0.126  -0.262  -0.356  -0.265  -0.408
120   H        -0.102  -0.082  -0.120  -0.072  -0.034  -0.134  -0.356  -0.321  -0.415
121   N         0.213   0.083  -0.067   0.333   0.147  -0.149   0.170  -0.038  -0.318
122   L         0.900   0.910   0.950   0.718   0.732   0.810   0.959   0.972   1.028
123   D         0.213   0.083  -0.067   0.147  -0.036  -0.273   0.170  -0.038  -0.318
124   M         0.900   0.910   0.950   1.030   1.042   1.099   0.959   0.972   1.028
125   E         0.900   0.910   0.950   0.898   0.914   0.977   0.959   0.972   1.028
126   G         0.900   0.910   0.950   0.889   0.907   0.969   0.959   0.972   1.028
127   A         0.900   0.910   0.950   0.902   0.911   0.981   0.959   0.972   1.028
128   C         0.900   0.910   0.950   1.018   1.034   1.088   0.959   0.972   1.028
129   G         0.900   0.910   0.950   0.889   0.907   0.969   0.959   0.972   1.028
130   G         0.900   0.910   0.950   0.889   0.907   0.969   0.959   0.972   1.028
131   S         0.900   0.910   0.950   0.860   0.869   0.942   0.959   0.972   1.028
132   C         0.900   0.910   0.950   1.018   1.034   1.088   0.959   0.972   1.028
133   A         0.900   0.910   0.950   0.902   0.911   0.981   0.959   0.972   1.028
134   C         0.900   0.910   0.950   1.018   1.034   1.088   0.959   0.972   1.028
135   S         0.900   0.910   0.950   0.860   0.869   0.942   0.959   0.972   1.028
136   T         0.900   0.910   0.950   0.873   0.885   0.953   0.959   0.972   1.028
137   C         0.900   0.910   0.950   1.018   1.034   1.088   0.959   0.972   1.028
138   H         0.900   0.910   0.950   1.014   1.029   1.084   0.959   0.972   1.028
139   V         0.900   0.910   0.950   0.973   0.982   1.046   0.959   0.972   1.028
140   I         0.900   0.910   0.950   0.931   0.958   1.008   0.959   0.972   1.028
141   V         0.900   0.910   0.950   0.973   0.982   1.046   0.959   0.972   1.028
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   D         0.900   0.910   0.950   0.775   0.786   0.863   0.959   0.972   1.028
144   P         0.213   0.083  -0.067   0.344   0.169  -0.071   0.170  -0.038  -0.318
145   D        -0.244  -0.225  -0.151  -0.585  -0.553  -0.418  -0.620  -0.584  -0.473
146   Y        -0.434  -0.545  -0.730  -0.092  -0.246  -0.544  -0.488  -0.643  -0.888
147   Y         0.900   0.910   0.950   1.099   1.116   1.163   0.959   0.972   1.028
148   D         0.900   0.910   0.950   0.775   0.786   0.863   0.959   0.972   1.028
149   A        -1.240  -1.249  -1.233  -1.232  -1.252  -1.203  -1.277  -1.284  -1.208
150   L        -0.701  -0.783  -0.755  -0.896  -0.990  -0.920  -0.883  -0.975  -0.924
151   P        -0.244  -0.218  -0.150  -0.438  -0.386  -0.288  -0.620  -0.572  -0.471
152   E         0.900   0.910   0.950   0.898   0.914   0.977   0.959   0.972   1.028
153   P         0.900   0.910   0.950   0.952   0.967   1.027   0.959   0.972   1.028
154   E        -0.102  -0.053  -0.101  -0.330  -0.249  -0.333  -0.356  -0.269  -0.380
155   D         0.900   0.910   0.950   0.775   0.786   0.863   0.959   0.972   1.028
156   D         0.900   0.910   0.950   0.775   0.786   0.863   0.959   0.972   1.028
157   E         0.900   0.910   0.950   0.898   0.914   0.977   0.959   0.972   1.028
158   N         0.900   0.910   0.950   0.981   1.001   1.054   0.959   0.972   1.028
159   D         0.900   0.910   0.950   0.775   0.786   0.863   0.959   0.972   1.028
160   M         0.900   0.910   0.950   1.030   1.042   1.099   0.959   0.972   1.028
161   L         0.900   0.910   0.950   0.718   0.732   0.810   0.959   0.972   1.028
162   D         0.900   0.910   0.950   0.775   0.786   0.863   0.959   0.972   1.028
163   L         0.900   0.910   0.950   0.718   0.732   0.810   0.959   0.972   1.028
164   A         0.900   0.910   0.950   0.902   0.911   0.981   0.959   0.972   1.028
165   Y        -0.244  -0.213  -0.139  -0.230  -0.174  -0.071  -0.620  -0.562  -0.451
166   G         0.900   0.910   0.950   0.889   0.907   0.969   0.959   0.972   1.028
167   L         0.900   0.910   0.950   0.718   0.732   0.810   0.959   0.972   1.028
168   T         0.900   0.910   0.950   0.873   0.885   0.953   0.959   0.972   1.028
169   E         0.900   0.910   0.950   0.898   0.914   0.977   0.959   0.972   1.028
170   T         0.900   0.910   0.950   0.873   0.885   0.953   0.959   0.972   1.028
171   S         0.900   0.910   0.950   0.860   0.869   0.942   0.959   0.972   1.028
172   R         0.900   0.910   0.950   0.956   0.969   1.031   0.959   0.972   1.028
173   L         0.900   0.910   0.950   0.718   0.732   0.810   0.959   0.972   1.028
174   G         0.900   0.910   0.950   0.889   0.907   0.969   0.959   0.972   1.028
175   C         0.900   0.910   0.950   1.018   1.034   1.088   0.959   0.972   1.028
176   Q         0.213   0.257  -0.050   0.409   0.459   0.015   0.170   0.236  -0.286
177   I        -0.244  -0.219  -0.150  -0.400  -0.349  -0.252  -0.620  -0.573  -0.471
178   K        -0.434  -0.554  -0.733  -0.209  -0.374  -0.654  -0.488  -0.655  -0.893
179   M         0.900   0.910   0.950   1.030   1.042   1.099   0.959   0.972   1.028
180   S        -0.701  -0.699  -0.762  -0.805  -0.826  -0.885  -0.883  -0.890  -0.935
181   K         0.900   0.910   0.950   0.989   1.006   1.061   0.959   0.972   1.028
182   D        -0.244  -0.246  -0.154  -0.585  -0.589  -0.419  -0.620  -0.625  -0.478
183   I        -0.244  -0.247  -0.154  -0.565  -0.578  -0.433  -0.620  -0.627  -0.478
184   D         0.900   0.910   0.950   0.775   0.786   0.863   0.959   0.972   1.028
185   G         0.900   0.910   0.950   0.889   0.907   0.969   0.959   0.972   1.028
186   I         0.213   0.083  -0.067   0.275   0.092  -0.216   0.170  -0.038  -0.318
187   R         0.213   0.083  -0.067   0.341   0.162  -0.087   0.170  -0.038  -0.318
188   V         0.213   0.215  -0.056   0.350   0.353  -0.069   0.170   0.173  -0.297
189   A         0.213   0.083  -0.067   0.290   0.110  -0.125   0.170  -0.038  -0.318
190   L         0.900   0.910   0.950   0.718   0.732   0.810   0.959   0.972   1.028
191   P         0.900   0.910   0.950   0.952   0.967   1.027   0.959   0.972   1.028
192   Q        -0.701  -0.697  -0.761  -0.764  -0.795  -0.847  -0.883  -0.892  -0.934
193   M         0.900   0.910   0.950   1.030   1.042   1.099   0.959   0.972   1.028
194   T         0.900   0.910   0.950   0.873   0.885   0.953   0.959   0.972   1.028
195   R         0.900   0.910   0.950   0.956   0.969   1.031   0.959   0.972   1.028
196   N         0.900   0.910   0.950   0.981   1.001   1.054   0.959   0.972   1.028
197   V        -0.244  -0.213  -0.139  -0.583  -0.539  -0.398  -0.620  -0.562  -0.451
198   N        -0.701  -0.628  -0.744  -0.667  -0.559  -0.741  -0.883  -0.780  -0.909
199   N        -0.908  -0.902  -0.797  -1.062  -1.059  -0.902  -1.146  -1.135  -0.977
200   N        -1.240  -1.168  -1.217  -1.237  -1.135  -1.174  -1.277  -1.190  -1.192
201   D         0.900   0.910   0.950   0.775   0.786   0.863   0.959   0.972   1.028
202   F         0.900   0.910   0.950   1.058   1.074   1.125   0.959   0.972   1.028
203   S        -1.033  -1.067  -1.205  -0.846  -0.894  -1.147  -1.014  -1.057  -1.178
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/Q12184
Output conservation file - output/Q12184
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
