1     M         1.510   1.519   1.584   1.693   1.719   1.807   1.642   1.652   1.747
2     K         0.473   0.452   0.435   0.403   0.351   0.313   0.239   0.194   0.126
3     V         0.473   0.452   0.435   0.351   0.298   0.259   0.239   0.194   0.126
4     K        -0.232  -0.187  -0.221  -0.413  -0.333  -0.366  -0.462  -0.413  -0.420
5     I         0.129   0.084  -0.138   0.237   0.159  -0.191   0.099   0.033  -0.289
6     N        -1.178  -1.178  -1.137  -1.123  -1.148  -1.047  -1.023  -1.017  -0.935
7     E        -0.491  -0.582  -0.657  -0.463  -0.537  -0.715  -0.462  -0.575  -0.647
8     V        -0.232  -0.269  -0.230  -0.243  -0.303  -0.211  -0.462  -0.498  -0.430
9     H        -0.491  -0.444  -0.655  -0.276  -0.236  -0.529  -0.462  -0.408  -0.645
10    S        -0.835  -0.831  -0.757  -0.857  -0.849  -0.742  -0.883  -0.872  -0.765
11    V         0.129   0.142  -0.100   0.249   0.242  -0.070   0.099   0.107  -0.233
12    F        -1.178  -1.136  -1.127  -1.034  -0.968  -0.958  -1.023  -0.986  -0.928
13    A        -0.705  -0.696  -0.722  -0.611  -0.620  -0.629  -0.743  -0.739  -0.727
14    W         1.510   1.519   1.584   1.666   1.677   1.780   1.642   1.652   1.747
15    S        -1.522  -1.546  -1.469  -1.297  -1.354  -1.225  -1.164  -1.178  -1.067
16    W         1.510   1.519   1.584   1.666   1.677   1.780   1.642   1.652   1.747
17    H         0.129   0.213  -0.105   0.201   0.334  -0.143   0.099   0.215  -0.241
18    I        -0.705  -0.711  -0.712  -0.739  -0.749  -0.737  -0.743  -0.736  -0.713
19    P         0.473   0.561   0.485   0.426   0.570   0.434   0.239   0.396   0.222
20    S        -0.705  -0.626  -0.714  -0.670  -0.568  -0.669  -0.743  -0.646  -0.719
21    T        -0.801  -0.817  -0.773  -0.797  -0.838  -0.770  -0.833  -0.850  -0.778
22    S        -0.801  -0.790  -0.739  -1.052  -1.042  -0.957  -0.833  -0.820  -0.741
23    D        -0.320  -0.330  -0.271  -0.537  -0.556  -0.453  -0.558  -0.568  -0.479
24    E        -0.895  -0.877  -0.786  -1.079  -1.053  -0.913  -0.936  -0.915  -0.792
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    N        -0.293  -0.276  -0.249  -0.468  -0.448  -0.430  -0.506  -0.484  -0.447
48    D         1.510   1.519   1.584   1.404   1.424   1.523   1.642   1.652   1.747
49    P        -0.895  -0.877  -0.786  -1.022  -0.989  -0.857  -0.936  -0.915  -0.792
50    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    D        -0.293  -0.318  -0.260  -0.562  -0.608  -0.521  -0.506  -0.542  -0.463
54    E         0.343   0.376   0.435   0.089   0.139   0.234  -0.008   0.050   0.124
55    D        -0.320  -0.330  -0.271  -0.616  -0.646  -0.558  -0.558  -0.568  -0.479
56    E        -0.148  -0.166  -0.228  -0.259  -0.230  -0.369  -0.322  -0.343  -0.424
57    D         0.326   0.325   0.402  -0.021   0.036   0.097  -0.042  -0.049   0.061
58    V         0.473   0.561   0.485   0.336   0.477   0.335   0.239   0.396   0.222
59    C         1.510   1.519   1.584   1.451   1.439   1.569   1.642   1.652   1.747
60    G         1.510   1.519   1.584   1.518   1.527   1.635   1.642   1.652   1.747
61    I         1.510   1.519   1.584   1.529   1.541   1.646   1.642   1.652   1.747
62    C         1.510   1.519   1.584   1.451   1.439   1.569   1.642   1.652   1.747
63    R         1.510   1.519   1.584   1.568   1.598   1.684   1.642   1.652   1.747
64    A        -0.148  -0.166  -0.228  -0.159  -0.189  -0.260  -0.322  -0.343  -0.424
65    S        -0.148  -0.203  -0.203  -0.148  -0.242  -0.235  -0.322  -0.403  -0.387
66    Y         0.326   0.329   0.412   0.313   0.333   0.443  -0.042  -0.041   0.080
67    N         0.129   0.151  -0.125   0.221   0.270  -0.139   0.099   0.128  -0.271
68    G         0.473   0.452   0.435   0.415   0.373   0.338   0.239   0.194   0.126
69    T        -0.491  -0.562  -0.655  -0.342  -0.482  -0.628  -0.462  -0.550  -0.646
70    C         1.510   1.519   1.584   1.451   1.439   1.569   1.642   1.652   1.747
71    P         1.510   1.519   1.584   1.529   1.548   1.646   1.642   1.652   1.747
72    S        -0.705  -0.749  -0.717  -0.617  -0.693  -0.643  -0.743  -0.787  -0.723
73    C         1.510   1.519   1.584   1.451   1.439   1.569   1.642   1.652   1.747
74    K        -0.491  -0.593  -0.680  -0.351  -0.520  -0.654  -0.462  -0.586  -0.674
75    F         0.129   0.086  -0.115   0.449   0.397   0.079   0.099   0.033  -0.256
76    P         1.510   1.519   1.584   1.529   1.548   1.646   1.642   1.652   1.747
77    G         1.510   1.519   1.584   1.518   1.527   1.635   1.642   1.652   1.747
78    D         0.129   0.084  -0.138   0.177   0.150  -0.244   0.099   0.033  -0.289
79    Q        -1.178  -1.215  -1.129  -1.123  -1.159  -1.033  -1.023  -1.048  -0.929
80    C         1.510   1.519   1.584   1.451   1.439   1.569   1.642   1.652   1.747
81    P         0.799   0.791   0.587   0.901   0.896   0.604   0.800   0.785   0.412
82    L         0.326   0.351   0.406   0.087   0.123   0.207  -0.042   0.001   0.068
83    V         0.799   0.805   0.586   0.845   0.848   0.533   0.800   0.807   0.412
84    I        -0.148  -0.194  -0.202  -0.196  -0.264  -0.263  -0.322  -0.377  -0.388
85    G         1.510   1.519   1.584   1.518   1.527   1.635   1.642   1.652   1.747
86    L        -1.178  -1.108  -1.128  -1.151  -1.082  -1.067  -1.023  -0.961  -0.929
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    C         1.510   1.519   1.584   1.451   1.439   1.569   1.642   1.652   1.747
89    H        -1.522  -1.546  -1.469  -1.279  -1.352  -1.202  -1.164  -1.178  -1.067
90    H         1.510   1.519   1.584   1.579   1.582   1.695   1.642   1.652   1.747
91    N         0.129   0.057  -0.105   0.357   0.245  -0.003   0.099  -0.007  -0.241
92    F         1.510   1.519   1.584   1.628   1.672   1.743   1.642   1.652   1.747
93    H         1.510   1.519   1.584   1.579   1.582   1.695   1.642   1.652   1.747
94    D        -0.705  -0.737  -0.738  -0.762  -0.813  -0.801  -0.743  -0.778  -0.744
95    H         1.510   1.519   1.584   1.579   1.582   1.695   1.642   1.652   1.747
96    C         1.510   1.519   1.584   1.451   1.439   1.569   1.642   1.652   1.747
97    I         0.799   0.805   0.586   0.878   0.882   0.556   0.800   0.807   0.412
98    Y        -1.049  -1.105  -1.124  -0.882  -0.981  -0.980  -0.883  -0.939  -0.922
99    R        -0.705  -0.767  -0.740  -0.661  -0.756  -0.692  -0.743  -0.803  -0.746
100   W         1.510   1.519   1.584   1.666   1.677   1.780   1.642   1.652   1.747
101   L         0.799   0.791   0.587   0.839   0.829   0.519   0.800   0.785   0.412
102   D        -0.705  -0.767  -0.740  -0.808  -0.827  -0.826  -0.743  -0.803  -0.746
103   T         0.473   0.561   0.485   0.442   0.590   0.443   0.239   0.396   0.222
104   P        -0.705  -0.711  -0.717  -0.820  -0.778  -0.823  -0.743  -0.748  -0.721
105   T         0.799   0.719   0.592   0.926   0.813   0.617   0.800   0.667   0.423
106   S         1.510   1.519   1.584   1.568   1.594   1.684   1.642   1.652   1.747
107   K         0.799   0.719   0.592   0.890   0.771   0.591   0.800   0.667   0.423
108   G         1.510   1.519   1.584   1.518   1.527   1.635   1.642   1.652   1.747
109   L         0.799   0.719   0.592   0.851   0.747   0.554   0.800   0.667   0.423
110   C         1.510   1.519   1.584   1.451   1.439   1.569   1.642   1.652   1.747
111   P         1.510   1.519   1.584   1.529   1.548   1.646   1.642   1.652   1.747
112   M         0.799   0.763   0.579   1.040   1.001   0.696   0.800   0.740   0.398
113   C         0.799   0.719   0.592   0.795   0.660   0.484   0.800   0.667   0.423
114   R         1.510   1.519   1.584   1.568   1.598   1.684   1.642   1.652   1.747
115   Q         1.510   1.519   1.584   1.563   1.597   1.679   1.642   1.652   1.747
116   T        -1.178  -1.182  -1.139  -1.121  -1.152  -1.059  -1.023  -1.019  -0.937
117   F         1.510   1.519   1.584   1.628   1.672   1.743   1.642   1.652   1.747
118   Q        -0.705  -0.711  -0.712  -0.708  -0.693  -0.729  -0.743  -0.736  -0.713
119   L        -0.705  -0.711  -0.712  -0.694  -0.704  -0.696  -0.743  -0.736  -0.713
120   Q        -1.178  -1.117  -1.126  -1.057  -0.968  -0.984  -1.023  -0.968  -0.926
121   K        -1.178  -1.144  -1.129  -1.217  -1.148  -1.137  -1.023  -0.990  -0.929
122   G        -1.865  -1.836  -1.743  -1.618  -1.577  -1.443  -1.304  -1.278  -1.154
123   L        -1.522  -1.450  -1.450  -1.383  -1.283  -1.289  -1.164  -1.101  -1.052
124   A        -1.522  -1.523  -1.446  -1.370  -1.368  -1.261  -1.164  -1.161  -1.049
125   I        -0.705  -0.693  -0.712  -0.719  -0.695  -0.730  -0.743  -0.723  -0.716
126   N        -0.705  -0.711  -0.712  -0.604  -0.615  -0.610  -0.743  -0.736  -0.713
127   D        -1.865  -1.836  -1.743  -1.703  -1.636  -1.526  -1.304  -1.278  -1.154
128   A        -1.522  -1.500  -1.453  -1.396  -1.308  -1.278  -1.164  -1.141  -1.054
129   H         0.343   0.376   0.435   0.105   0.177   0.251  -0.008   0.050   0.124
130   V        -0.801  -0.805  -0.748  -0.791  -0.807  -0.711  -0.833  -0.836  -0.750
131   Q        -1.282  -1.263  -1.168  -1.220  -1.214  -1.051  -1.108  -1.087  -0.961
132   K        -0.138  -0.177  -0.212  -0.201  -0.274  -0.376  -0.283  -0.340  -0.395
133   F         0.343   0.376   0.435   0.190   0.258   0.335  -0.008   0.050   0.124
134   V        -0.320  -0.306  -0.255  -0.407  -0.386  -0.308  -0.558  -0.540  -0.460
135   E        -0.320  -0.294  -0.261  -0.562  -0.524  -0.454  -0.558  -0.526  -0.468
136   I        -0.244  -0.282  -0.242  -0.406  -0.487  -0.402  -0.458  -0.504  -0.442
137   V        -0.293  -0.254  -0.245  -0.577  -0.487  -0.507  -0.506  -0.452  -0.441
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   S        -0.645  -0.702  -0.707  -0.566  -0.680  -0.676  -0.649  -0.718  -0.705
141   R        -0.244  -0.204  -0.224  -0.365  -0.260  -0.324  -0.458  -0.391  -0.414
142   R        -0.796  -0.825  -0.759  -0.837  -0.895  -0.778  -0.840  -0.863  -0.764
143   R         0.005   0.005  -0.175   0.180   0.156  -0.091  -0.077  -0.079  -0.341
144   E        -1.197  -1.177  -1.128  -1.106  -1.088  -1.019  -1.031  -1.011  -0.926
145   E        -1.598  -1.570  -1.480  -1.506  -1.464  -1.332  -1.222  -1.196  -1.074
146   M        -0.645  -0.723  -0.711  -0.446  -0.594  -0.588  -0.649  -0.742  -0.710
147   I        -0.645  -0.673  -0.737  -0.492  -0.536  -0.635  -0.649  -0.682  -0.739
148   E         0.005  -0.083  -0.155  -0.071  -0.149  -0.315  -0.077  -0.205  -0.314
149   E        -0.796  -0.771  -0.743  -0.932  -0.879  -0.828  -0.840  -0.815  -0.749
150   G        -1.197  -1.155  -1.132  -1.151  -1.119  -1.059  -1.031  -0.990  -0.930
151   V         0.005   0.076  -0.141  -0.076   0.082  -0.300  -0.077   0.022  -0.293
152   A        -0.801  -0.816  -0.756  -0.756  -0.795  -0.707  -0.833  -0.849  -0.760
153   E        -1.282  -1.263  -1.168  -1.363  -1.357  -1.191  -1.108  -1.087  -0.961
154   E        -1.282  -1.263  -1.168  -1.234  -1.215  -1.065  -1.108  -1.087  -0.961
155   F        -0.895  -0.877  -0.786  -1.017  -0.978  -0.852  -0.936  -0.915  -0.792
156   V        -0.320  -0.303  -0.267  -0.489  -0.477  -0.415  -0.558  -0.536  -0.474
157   D        -0.801  -0.798  -0.746  -0.962  -0.961  -0.883  -0.833  -0.829  -0.749
158   F        -0.138  -0.177  -0.212  -0.033  -0.095  -0.173  -0.283  -0.340  -0.395
159   D         0.343   0.340   0.406  -0.068  -0.078   0.026  -0.008  -0.020   0.068
160   E        -0.138  -0.145  -0.197  -0.340  -0.359  -0.443  -0.283  -0.296  -0.373
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   P        -0.293  -0.241  -0.260  -0.285  -0.209  -0.235  -0.506  -0.432  -0.463
165   I        -0.895  -0.877  -0.786  -0.969  -0.957  -0.805  -0.936  -0.915  -0.792
166   R        -0.293  -0.241  -0.260  -0.328  -0.252  -0.289  -0.506  -0.432  -0.463
167   Q         0.535   0.532   0.484   0.322   0.318   0.241   0.353   0.343   0.219
168   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
183   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
184   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
185   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
186   F        -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   L        -1.282  -1.263  -1.168  -1.120  -1.100  -0.953  -1.108  -1.087  -0.961
189   L        -0.796  -0.815  -0.737  -0.838  -0.870  -0.745  -0.840  -0.856  -0.743
190   R        -1.197  -1.167  -1.132  -1.123  -1.079  -1.037  -1.031  -1.003  -0.930
* 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/Q12157
Output conservation file - output/Q12157
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
