1     M         1.423   1.598   1.638   1.523   1.778   1.844   1.524   1.785   1.878
2     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     S        -1.066  -0.900  -0.928  -1.037  -0.815  -0.833  -1.100  -0.876  -0.879
9     K        -1.597  -1.314  -1.370  -1.560  -1.169  -1.247  -1.408  -1.067  -1.092
10    W        -0.476  -0.533  -0.384  -0.500  -0.586  -0.362  -0.721  -0.717  -0.545
11    D         1.423   1.598   1.638   1.385   1.621   1.710   1.524   1.785   1.878
12    Q        -1.024  -0.993  -0.929  -1.093  -1.052  -0.907  -1.076  -0.986  -0.880
13    K        -0.941  -0.758  -0.913  -0.944  -0.722  -0.891  -0.957  -0.756  -0.865
14    G         0.327   0.250   0.326  -0.013  -0.095   0.025   0.106  -0.084   0.006
15    M         0.134   0.212   0.323  -0.034   0.039   0.190  -0.248  -0.159  -0.001
16    D        -1.616  -1.529  -1.398  -1.613  -1.431  -1.251  -1.430  -1.258  -1.117
17    I        -0.669  -0.754  -0.899  -0.574  -0.775  -0.951  -0.603  -0.708  -0.839
18    A         1.423   1.598   1.638   1.418   1.649   1.742   1.524   1.785   1.878
19    Y        -1.151  -0.991  -0.959  -1.101  -0.905  -0.862  -1.194  -0.960  -0.910
20    E        -0.331  -0.313  -0.382  -0.508  -0.524  -0.610  -0.485  -0.494  -0.549
21    E        -0.331  -0.491  -0.388  -0.413  -0.636  -0.471  -0.485  -0.659  -0.552
22    A         0.689   0.420   0.472   0.783   0.382   0.470   0.697   0.231   0.286
23    A        -1.024  -1.071  -0.949  -1.074  -1.044  -0.904  -1.076  -1.042  -0.898
24    L        -0.669  -0.630  -0.876  -0.530  -0.465  -0.849  -0.603  -0.582  -0.813
25    G        -0.534  -0.575  -0.403  -0.894  -0.884  -0.635  -0.791  -0.775  -0.571
26    Y        -0.825  -0.854  -0.915  -0.517  -0.600  -0.688  -0.791  -0.814  -0.858
27    K        -1.597  -1.529  -1.398  -1.666  -1.526  -1.347  -1.408  -1.255  -1.116
28    E        -0.011   0.224  -0.226   0.022   0.364  -0.264  -0.012   0.334  -0.314
29    G         1.423   1.598   1.638   1.093   1.358   1.427   1.524   1.785   1.878
30    G         0.689   0.420   0.472   0.473   0.151   0.220   0.697   0.231   0.286
31    V        -0.476  -0.584  -0.400  -0.627  -0.716  -0.463  -0.721  -0.788  -0.570
32    P         1.423   1.598   1.638   1.569   1.806   1.888   1.524   1.785   1.878
33    I         0.689   0.420   0.472   0.724   0.361   0.447   0.697   0.231   0.286
34    G         1.423   1.598   1.638   1.093   1.358   1.427   1.524   1.785   1.878
35    G        -0.941  -1.022  -0.953  -1.168  -1.186  -1.077  -0.957  -0.998  -0.903
36    C        -0.941  -1.041  -0.946  -0.808  -1.005  -0.873  -0.957  -1.007  -0.895
37    L         0.327   0.266   0.332   0.172   0.012   0.086   0.106  -0.054   0.016
38    I         0.327   0.250   0.326   0.179  -0.012   0.110   0.106  -0.084   0.006
39    N        -1.616  -1.410  -1.377  -1.500  -1.221  -1.143  -1.430  -1.153  -1.099
40    N        -1.151  -1.043  -0.960  -1.293  -1.170  -1.089  -1.194  -1.009  -0.911
41    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    D        -0.331  -0.461  -0.377  -0.354  -0.522  -0.423  -0.485  -0.620  -0.537
43    G         0.689   0.420   0.472   0.442   0.071   0.133   0.697   0.231   0.286
44    S        -1.278  -1.219  -1.345  -1.069  -1.009  -1.218  -1.076  -0.993  -1.067
45    V         0.327   0.628   0.432   0.227   0.688   0.339   0.106   0.593   0.211
46    L         0.689   0.420   0.472   0.707   0.307   0.364   0.697   0.231   0.286
47    G         0.689   0.420   0.472   0.464   0.133   0.192   0.697   0.231   0.286
48    R        -0.941  -0.872  -0.925  -0.799  -0.750  -0.781  -0.957  -0.852  -0.876
49    G         0.689   0.420   0.472   0.447   0.082   0.147   0.697   0.231   0.286
50    H         0.689   0.420   0.472   0.925   0.457   0.500   0.697   0.231   0.286
51    N         1.423   1.598   1.638   1.514   1.757   1.835   1.524   1.785   1.878
52    M        -0.825  -0.903  -0.951  -0.579  -0.663  -0.812  -0.791  -0.828  -0.897
53    R         1.423   1.598   1.638   1.492   1.709   1.813   1.524   1.785   1.878
54    F        -0.603  -0.550  -0.442  -0.650  -0.622  -0.494  -0.839  -0.747  -0.623
55    Q         0.689   0.420   0.472   0.962   0.583   0.654   0.697   0.231   0.286
56    K        -1.278  -1.349  -1.369  -1.092  -1.208  -1.221  -1.076  -1.103  -1.089
57    G        -0.669  -0.400  -0.819  -0.759  -0.357  -0.919  -0.603  -0.225  -0.746
58    S         0.689   0.420   0.472   0.833   0.405   0.490   0.697   0.231   0.286
59    A        -0.476  -0.566  -0.386  -0.529  -0.652  -0.375  -0.721  -0.763  -0.553
60    T        -0.331  -0.172  -0.342  -0.356  -0.102  -0.407  -0.485  -0.231  -0.488
61    L        -0.331  -0.515  -0.393  -0.295  -0.502  -0.337  -0.485  -0.692  -0.560
62    H         1.423   1.598   1.638   1.614   1.853   1.931   1.524   1.785   1.878
63    G         0.689   0.420   0.472   0.447   0.082   0.147   0.697   0.231   0.286
64    E         1.423   1.598   1.638   1.282   1.527   1.610   1.524   1.785   1.878
65    I        -0.476  -0.313  -0.367  -0.647  -0.409  -0.432  -0.721  -0.495  -0.530
66    S        -0.669  -0.863  -0.918  -0.412  -0.741  -0.822  -0.603  -0.815  -0.861
67    T         0.134   0.212   0.325  -0.078  -0.009   0.178  -0.248  -0.159   0.002
68    L         0.689   0.420   0.472   0.718   0.338   0.394   0.697   0.231   0.286
69    E        -0.669  -0.863  -0.918  -0.659  -1.039  -1.083  -0.603  -0.815  -0.861
70    N         0.689   0.420   0.472   0.862   0.455   0.510   0.697   0.231   0.286
71    C        -0.331  -0.386  -0.346  -0.310  -0.428  -0.351  -0.485  -0.522  -0.488
72    G         0.689   0.420   0.472   0.451   0.095   0.157   0.697   0.231   0.286
73    R         0.689   0.420   0.472   0.839   0.413   0.489   0.697   0.231   0.286
74    L         0.689   0.420   0.472   0.721   0.346   0.403   0.697   0.231   0.286
75    E        -1.616  -1.556  -1.400  -1.634  -1.457  -1.284  -1.430  -1.276  -1.118
76    G        -0.011  -0.247  -0.319  -0.175  -0.490  -0.587  -0.012  -0.352  -0.448
77    K        -0.476  -0.572  -0.389  -0.634  -0.751  -0.483  -0.721  -0.771  -0.557
78    V        -0.941  -0.985  -0.939  -0.938  -1.028  -0.969  -0.957  -0.961  -0.888
79    Y         0.689   0.420   0.472   0.905   0.487   0.529   0.697   0.231   0.286
80    K         0.689   0.843   0.535   0.718   0.968   0.503   0.697   0.933   0.403
81    D        -0.825  -0.726  -0.915  -0.676  -0.508  -0.807  -0.791  -0.622  -0.857
82    T        -0.941  -0.696  -0.867  -0.768  -0.348  -0.660  -0.957  -0.586  -0.804
83    T         1.423   1.598   1.638   1.441   1.681   1.764   1.524   1.785   1.878
84    L        -0.476  -0.322  -0.371  -0.584  -0.368  -0.439  -0.721  -0.510  -0.537
85    Y         1.423   1.598   1.638   1.569   1.825   1.888   1.524   1.785   1.878
86    T         1.423   1.598   1.638   1.441   1.681   1.764   1.524   1.785   1.878
87    T         0.689   0.420   0.472   0.806   0.413   0.491   0.697   0.231   0.286
88    L         0.689   0.420   0.472   0.721   0.346   0.403   0.697   0.231   0.286
89    S         0.689   0.420   0.472   0.819   0.371   0.450   0.697   0.231   0.286
90    P         1.423   1.598   1.638   1.569   1.806   1.888   1.524   1.785   1.878
91    C         1.423   1.598   1.638   1.560   1.806   1.879   1.524   1.785   1.878
92    D        -0.669  -0.733  -0.887  -0.463  -0.621  -0.761  -0.603  -0.684  -0.826
93    M         1.423   1.598   1.638   1.523   1.778   1.844   1.524   1.785   1.878
94    C         1.423   1.598   1.638   1.560   1.806   1.879   1.524   1.785   1.878
95    T         0.689   0.420   0.472   0.806   0.413   0.491   0.697   0.231   0.286
96    G         1.423   1.598   1.638   1.093   1.358   1.427   1.524   1.785   1.878
97    A         1.423   1.598   1.638   1.418   1.649   1.742   1.524   1.785   1.878
98    I         0.327   0.532   0.408   0.225   0.520   0.329   0.106   0.429   0.164
99    I        -0.476  -0.571  -0.388  -0.678  -0.720  -0.492  -0.721  -0.769  -0.556
100   M        -0.476  -0.571  -0.388  -0.549  -0.565  -0.347  -0.721  -0.769  -0.556
101   Y        -0.011  -0.249  -0.327   0.325  -0.024  -0.136  -0.012  -0.353  -0.461
102   G         0.689   0.843   0.535   0.439   0.693   0.230   0.697   0.933   0.403
103   I        -0.011   0.190  -0.248   0.093   0.371  -0.223  -0.012   0.289  -0.347
104   P        -1.151  -0.913  -0.947  -1.259  -0.886  -0.980  -1.194  -0.896  -0.898
105   R         1.423   1.598   1.638   1.492   1.709   1.813   1.524   1.785   1.878
106   C        -0.331  -0.386  -0.346  -0.276  -0.328  -0.282  -0.485  -0.522  -0.488
107   V         0.689   0.420   0.472   0.763   0.344   0.415   0.697   0.231   0.286
108   V        -1.616  -1.525  -1.396  -1.579  -1.338  -1.236  -1.430  -1.257  -1.115
109   G         1.423   1.598   1.638   1.093   1.358   1.427   1.524   1.785   1.878
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   E         0.689   0.420   0.472   0.647   0.266   0.347   0.697   0.231   0.286
112   N         0.689   0.994   0.547   0.879   1.278   0.686   0.697   1.149   0.426
113   V        -1.024  -1.076  -0.942  -1.121  -1.218  -0.986  -1.076  -1.048  -0.893
114   N         0.327   0.471   0.386   0.351   0.565   0.378   0.106   0.323   0.122
115   F         0.689   0.420   0.472   0.938   0.532   0.580   0.697   0.231   0.286
116   K        -0.941  -0.998  -0.943  -1.000  -1.092  -1.029  -0.957  -0.970  -0.892
117   S        -1.024  -1.071  -0.951  -1.281  -1.324  -1.158  -1.076  -1.041  -0.900
118   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   G         0.624   0.758   0.452   0.364   0.568   0.142   0.598   0.802   0.249
120   E         0.624   0.652   0.438   0.552   0.615   0.251   0.598   0.631   0.222
121   K        -0.534  -0.334  -0.401  -0.809  -0.492  -0.610  -0.791  -0.511  -0.571
122   Y         0.257   0.405   0.361   0.243   0.471   0.320  -0.019   0.205   0.075
123   L         1.423   1.598   1.638   1.362   1.620   1.688   1.524   1.785   1.878
124   Q        -1.954  -1.774  -1.740  -1.801  -1.536  -1.480  -1.548  -1.319  -1.242
125   T        -1.489  -1.115  -1.322  -1.345  -0.736  -1.096  -1.312  -0.857  -1.049
126   R        -0.331  -0.300  -0.373  -0.283  -0.323  -0.396  -0.485  -0.471  -0.538
127   G         0.689   0.420   0.472   0.457   0.104   0.174   0.697   0.231   0.286
128   H        -1.024  -0.996  -0.931  -1.163  -1.230  -1.014  -1.076  -0.989  -0.882
129   E         1.423   1.598   1.638   1.282   1.527   1.610   1.524   1.785   1.878
130   V         0.689   0.420   0.472   0.794   0.429   0.501   0.697   0.231   0.286
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   V        -0.011  -0.123  -0.305   0.116  -0.112  -0.366  -0.012  -0.211  -0.428
136   V        -0.476  -0.163  -0.344  -0.509  -0.035  -0.266  -0.721  -0.279  -0.496
137   V        -1.151  -1.119  -0.964  -1.223  -1.120  -0.920  -1.194  -1.077  -0.914
138   D        -1.024  -1.079  -0.943  -1.030  -1.073  -0.890  -1.076  -1.050  -0.894
139   D         0.689   0.842   0.526   0.755   0.973   0.544   0.697   0.931   0.387
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   E        -1.489  -1.477  -1.394  -1.458  -1.387  -1.283  -1.312  -1.222  -1.113
146   R        -1.489  -1.353  -1.369  -1.417  -1.180  -1.188  -1.312  -1.118  -1.090
147   C         0.689   0.420   0.472   0.936   0.567   0.630   0.697   0.231   0.286
148   K        -0.476  -0.364  -0.368  -0.699  -0.529  -0.505  -0.721  -0.545  -0.531
149   K        -1.954  -1.690  -1.719  -1.919  -1.517  -1.563  -1.548  -1.235  -1.226
150   I        -0.476  -0.533  -0.384  -0.715  -0.740  -0.544  -0.721  -0.717  -0.545
151   M         0.689   0.420   0.472   0.879   0.488   0.540   0.697   0.231   0.286
152   K        -1.826  -1.798  -1.751  -1.817  -1.889  -1.786  -1.430  -1.326  -1.248
153   Q        -1.826  -1.733  -1.730  -1.614  -1.435  -1.466  -1.430  -1.283  -1.233
154   F         0.689   0.420   0.472   0.967   0.604   0.658   0.697   0.231   0.286
155   I         0.689   0.843   0.535   0.699   0.913   0.485   0.697   0.933   0.403
156   D        -1.954  -1.852  -1.753  -1.925  -1.783  -1.624  -1.548  -1.367  -1.250
157   E        -1.278  -1.229  -1.341  -1.229  -1.198  -1.341  -1.076  -1.001  -1.063
158   R        -1.278  -1.370  -1.380  -0.993  -1.220  -1.192  -1.076  -1.120  -1.099
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   P         1.423   1.598   1.638   1.569   1.806   1.888   1.524   1.785   1.878
163   Q        -1.024  -1.076  -0.941  -1.082  -1.078  -0.967  -1.076  -1.048  -0.892
164   D        -0.669  -0.863  -0.918  -0.553  -0.875  -0.995  -0.603  -0.815  -0.861
165   W         0.689   0.420   0.472   0.987   0.523   0.558   0.697   0.231   0.286
166   F        -0.941  -0.724  -0.902  -0.636  -0.296  -0.555  -0.957  -0.650  -0.848
167   E         0.689   0.420   0.472   0.676   0.349   0.427   0.697   0.231   0.286
168   D         1.423   1.598   1.638   1.385   1.621   1.710   1.524   1.785   1.878
169   I         0.689   0.420   0.472   0.653   0.184   0.247   0.697   0.231   0.286
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   G         1.423   1.598   1.638   1.093   1.358   1.427   1.524   1.785   1.878
181   E        -0.331  -0.365  -0.387  -0.450  -0.522  -0.516  -0.485  -0.546  -0.556
* 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/Q12178
Output conservation file - output/Q12178
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
