1     M         0.658   0.666   0.704   0.923   0.924   0.940   0.677   0.689   0.739
2     S        -1.401  -1.465  -1.532  -1.226  -1.310  -1.466  -1.418  -1.478  -1.526
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     T        -3.037  -2.949  -2.608  -2.827  -2.699  -2.218  -2.570  -2.476  -2.016
6     K        -0.188  -0.397  -0.680  -0.221  -0.448  -0.873  -0.161  -0.456  -0.910
7     A        -1.401  -1.346  -1.537  -1.245  -1.215  -1.479  -1.418  -1.384  -1.533
8     Q        -0.188  -0.397  -0.680   0.148  -0.119  -0.632  -0.161  -0.456  -0.910
9     N         0.658   0.666   0.704   0.801   0.809   0.843   0.677   0.689   0.739
10    P        -0.627  -0.460  -0.695  -0.426  -0.192  -0.682  -0.789  -0.547  -0.936
11    M         0.658   0.666   0.704   0.923   0.924   0.940   0.677   0.689   0.739
12    R        -0.627  -0.499  -0.678  -0.966  -0.766  -1.054  -0.789  -0.605  -0.908
13    D        -0.188  -0.063  -0.669  -0.061   0.073  -0.730  -0.161  -0.004  -0.892
14    L        -0.188  -0.175  -0.670  -0.021  -0.007  -0.654  -0.161  -0.149  -0.894
15    K        -1.615  -1.457  -1.534  -1.991  -1.709  -1.679  -1.732  -1.513  -1.530
16    I         0.658   0.666   0.704   0.598   0.602   0.682   0.677   0.689   0.739
17    E        -1.401  -1.429  -1.532  -1.293  -1.315  -1.457  -1.418  -1.433  -1.526
18    K         0.658   0.666   0.704   0.478   0.526   0.587   0.677   0.689   0.739
19    L         0.658   0.666   0.704   0.655   0.665   0.727   0.677   0.689   0.739
20    V        -0.188  -0.397  -0.680  -0.118  -0.381  -0.810  -0.161  -0.456  -0.910
21    L         0.658   0.666   0.704   0.655   0.665   0.727   0.677   0.689   0.739
22    N         0.658   0.666   0.704   0.801   0.809   0.843   0.677   0.689   0.739
23    I         0.658   0.666   0.704   0.598   0.602   0.682   0.677   0.689   0.739
24    S        -1.009  -0.956  -0.724  -1.030  -0.940  -0.606  -1.418  -1.347  -0.983
25    V        -0.627  -0.499  -0.678  -0.721  -0.536  -0.835  -0.789  -0.605  -0.908
26    G         0.658   0.666   0.704   0.483   0.508   0.590   0.677   0.689   0.739
27    E         0.658   0.666   0.704   0.633   0.637   0.710   0.677   0.689   0.739
28    S         0.658   0.666   0.704   0.737   0.741   0.792   0.677   0.689   0.739
29    G         0.658   0.666   0.704   0.483   0.508   0.590   0.677   0.689   0.739
30    D         0.658   0.666   0.704   0.779   0.801   0.826   0.677   0.689   0.739
31    R         0.658   0.666   0.704   0.388   0.401   0.515   0.677   0.689   0.739
32    L         0.658   0.666   0.704   0.655   0.665   0.727   0.677   0.689   0.739
33    T         0.658   0.666   0.704   0.715   0.720   0.775   0.677   0.689   0.739
34    R         0.658   0.666   0.704   0.388   0.401   0.515   0.677   0.689   0.739
35    A         0.658   0.666   0.704   0.706   0.716   0.768   0.677   0.689   0.739
36    S        -1.009  -0.902  -0.717  -1.237  -1.063  -0.783  -1.418  -1.254  -0.972
37    K         0.658   0.666   0.704   0.478   0.526   0.587   0.677   0.689   0.739
38    V         0.658   0.666   0.704   0.585   0.597   0.671   0.677   0.689   0.739
39    L         0.658   0.666   0.704   0.655   0.665   0.727   0.677   0.689   0.739
40    E         0.658   0.666   0.704   0.633   0.637   0.710   0.677   0.689   0.739
41    Q         0.658   0.666   0.704   0.851   0.863   0.883   0.677   0.689   0.739
42    L         0.658   0.666   0.704   0.655   0.665   0.727   0.677   0.689   0.739
43    S         0.658   0.666   0.704   0.737   0.741   0.792   0.677   0.689   0.739
44    G         0.658   0.666   0.704   0.483   0.508   0.590   0.677   0.689   0.739
45    Q         0.658   0.666   0.704   0.851   0.863   0.883   0.677   0.689   0.739
46    T         0.658   0.666   0.704   0.715   0.720   0.775   0.677   0.689   0.739
47    P         0.658   0.666   0.704   0.906   0.903   0.927   0.677   0.689   0.739
48    V         0.658   0.666   0.704   0.585   0.597   0.671   0.677   0.689   0.739
49    Q        -1.756  -1.769  -1.551  -1.543  -1.609  -1.327  -1.837  -1.875  -1.549
50    S        -0.188  -0.397  -0.680   0.034  -0.239  -0.706  -0.161  -0.456  -0.910
51    K         0.658   0.666   0.704   0.478   0.526   0.587   0.677   0.689   0.739
52    A         0.658   0.666   0.704   0.706   0.716   0.768   0.677   0.689   0.739
53    R         0.658   0.666   0.704   0.388   0.401   0.515   0.677   0.689   0.739
54    Y         0.658   0.666   0.704   0.847   0.846   0.880   0.677   0.689   0.739
55    T         0.658   0.666   0.704   0.715   0.720   0.775   0.677   0.689   0.739
56    V        -0.886  -0.874  -0.720  -1.185  -1.190  -0.939  -1.208  -1.207  -0.976
57    R         0.658   0.666   0.704   0.388   0.401   0.515   0.677   0.689   0.739
58    T        -1.401  -1.465  -1.532  -1.343  -1.416  -1.601  -1.418  -1.478  -1.526
59    F         0.658   0.666   0.704   0.826   0.826   0.863   0.677   0.689   0.739
60    G        -0.188  -0.397  -0.680  -0.217  -0.466  -0.870  -0.161  -0.456  -0.910
61    I         0.658   0.666   0.704   0.598   0.602   0.682   0.677   0.689   0.739
62    R         0.658   0.666   0.704   0.388   0.401   0.515   0.677   0.689   0.739
63    R         0.658   0.666   0.704   0.388   0.401   0.515   0.677   0.689   0.739
64    N         0.658   0.666   0.704   0.801   0.809   0.843   0.677   0.689   0.739
65    E         0.658   0.666   0.704   0.633   0.637   0.710   0.677   0.689   0.739
66    K         0.658   0.666   0.704   0.478   0.526   0.587   0.677   0.689   0.739
67    I         0.658   0.666   0.704   0.598   0.602   0.682   0.677   0.689   0.739
68    A        -0.627  -0.709  -0.716  -0.579  -0.724  -0.782  -0.789  -0.933  -0.971
69    V        -0.627  -0.499  -0.678  -0.615  -0.449  -0.668  -0.789  -0.605  -0.908
70    H         0.658   0.666   0.704   0.960   0.957   0.970   0.677   0.689   0.739
71    V         0.658   0.666   0.704   0.585   0.597   0.671   0.677   0.689   0.739
72    T         0.658   0.666   0.704   0.715   0.720   0.775   0.677   0.689   0.739
73    V        -0.188  -0.175  -0.670  -0.132  -0.118  -0.845  -0.161  -0.149  -0.894
74    R         0.658   0.666   0.704   0.388   0.401   0.515   0.677   0.689   0.739
75    G         0.658   0.666   0.704   0.483   0.508   0.590   0.677   0.689   0.739
76    P         0.658   0.666   0.704   0.906   0.903   0.927   0.677   0.689   0.739
77    K         0.658   0.666   0.704   0.478   0.526   0.587   0.677   0.689   0.739
78    A         0.658   0.666   0.704   0.706   0.716   0.768   0.677   0.689   0.739
79    E         0.658   0.666   0.704   0.633   0.637   0.710   0.677   0.689   0.739
80    E         0.658   0.666   0.704   0.633   0.637   0.710   0.677   0.689   0.739
81    I         0.658   0.666   0.704   0.598   0.602   0.682   0.677   0.689   0.739
82    L         0.658   0.666   0.704   0.655   0.665   0.727   0.677   0.689   0.739
83    E         0.658   0.666   0.704   0.633   0.637   0.710   0.677   0.689   0.739
84    R         0.658   0.666   0.704   0.388   0.401   0.515   0.677   0.689   0.739
85    G         0.658   0.666   0.704   0.483   0.508   0.590   0.677   0.689   0.739
86    L         0.658   0.666   0.704   0.655   0.665   0.727   0.677   0.689   0.739
87    K         0.658   0.666   0.704   0.478   0.526   0.587   0.677   0.689   0.739
88    V         0.658   0.666   0.704   0.585   0.597   0.671   0.677   0.689   0.739
89    K         0.658   0.666   0.704   0.478   0.526   0.587   0.677   0.689   0.739
90    E         0.658   0.666   0.704   0.633   0.637   0.710   0.677   0.689   0.739
91    Y         0.658   0.666   0.704   0.847   0.846   0.880   0.677   0.689   0.739
92    Q        -1.009  -0.957  -0.724  -1.186  -1.142  -0.775  -1.418  -1.350  -0.983
93    L         0.658   0.666   0.704   0.655   0.665   0.727   0.677   0.689   0.739
94    R        -0.886  -0.874  -0.720  -1.426  -1.410  -1.130  -1.208  -1.207  -0.976
95    D        -2.896  -2.767  -2.607  -2.751  -2.600  -2.301  -2.465  -2.345  -2.016
96    R        -0.886  -0.883  -0.722  -1.426  -1.427  -1.135  -1.208  -1.222  -0.981
97    N         0.658   0.666   0.704   0.801   0.809   0.843   0.677   0.689   0.739
98    F         0.658   0.666   0.704   0.826   0.826   0.863   0.677   0.689   0.739
99    S         0.658   0.666   0.704   0.737   0.741   0.792   0.677   0.689   0.739
100   A        -1.401  -1.466  -1.544  -1.278  -1.476  -1.541  -1.418  -1.564  -1.541
101   T         0.658   0.666   0.704   0.715   0.720   0.775   0.677   0.689   0.739
102   G         0.658   0.666   0.704   0.483   0.508   0.590   0.677   0.689   0.739
103   N         0.658   0.666   0.704   0.801   0.809   0.843   0.677   0.689   0.739
104   F         0.658   0.666   0.704   0.826   0.826   0.863   0.677   0.689   0.739
105   G         0.658   0.666   0.704   0.483   0.508   0.590   0.677   0.689   0.739
106   F         0.658   0.666   0.704   0.826   0.826   0.863   0.677   0.689   0.739
107   G         0.658   0.666   0.704   0.483   0.508   0.590   0.677   0.689   0.739
108   I        -0.188  -0.175  -0.670  -0.121  -0.114  -0.841  -0.161  -0.149  -0.894
109   D        -2.289  -2.427  -2.144  -2.009  -2.168  -1.815  -2.151  -2.238  -1.840
110   E         0.658   0.666   0.704   0.633   0.637   0.710   0.677   0.689   0.739
111   H         0.658   0.666   0.704   0.960   0.957   0.970   0.677   0.689   0.739
112   I         0.658   0.666   0.704   0.598   0.602   0.682   0.677   0.689   0.739
113   D         0.658   0.666   0.704   0.779   0.801   0.826   0.677   0.689   0.739
114   L         0.658   0.666   0.704   0.655   0.665   0.727   0.677   0.689   0.739
115   G         0.658   0.666   0.704   0.483   0.508   0.590   0.677   0.689   0.739
116   I         0.658   0.666   0.704   0.598   0.602   0.682   0.677   0.689   0.739
117   K         0.658   0.666   0.704   0.478   0.526   0.587   0.677   0.689   0.739
118   Y         0.658   0.666   0.704   0.847   0.846   0.880   0.677   0.689   0.739
119   D         0.658   0.666   0.704   0.779   0.801   0.826   0.677   0.689   0.739
120   P         0.658   0.666   0.704   0.906   0.903   0.927   0.677   0.689   0.739
121   S        -1.615  -1.728  -1.545  -1.704  -1.864  -1.571  -1.732  -1.839  -1.543
122   I         0.658   0.666   0.704   0.598   0.602   0.682   0.677   0.689   0.739
123   G         0.658   0.666   0.704   0.483   0.508   0.590   0.677   0.689   0.739
124   I         0.658   0.666   0.704   0.598   0.602   0.682   0.677   0.689   0.739
125   F        -0.627  -0.477  -0.694  -0.418  -0.222  -0.608  -0.789  -0.573  -0.933
126   G         0.658   0.666   0.704   0.483   0.508   0.590   0.677   0.689   0.739
127   M         0.658   0.666   0.704   0.923   0.924   0.940   0.677   0.689   0.739
128   D         0.658   0.666   0.704   0.779   0.801   0.826   0.677   0.689   0.739
129   F         0.658   0.666   0.704   0.826   0.826   0.863   0.677   0.689   0.739
130   Y        -0.188  -0.397  -0.680   0.158  -0.114  -0.583  -0.161  -0.456  -0.910
131   V        -1.401  -1.377  -1.529  -1.356  -1.279  -1.473  -1.418  -1.367  -1.524
132   V        -1.001  -1.342  -1.532  -0.783  -1.227  -1.470  -0.894  -1.321  -1.527
133   M        -1.001  -1.185  -1.523  -0.500  -0.775  -1.406  -0.894  -1.134  -1.516
134   N        -2.130  -2.055  -2.133  -2.065  -1.960  -1.996  -1.941  -1.856  -1.830
135   R         0.658   0.666   0.704   0.388   0.401   0.515   0.677   0.689   0.739
136   P        -0.627  -0.522  -0.694  -0.394  -0.257  -0.625  -0.789  -0.640  -0.934
137   G         0.658   0.666   0.704   0.483   0.508   0.590   0.677   0.689   0.739
138   A        -2.804  -2.863  -2.608  -2.380  -2.490  -2.139  -2.360  -2.393  -2.016
139   R         0.658   0.666   0.704   0.388   0.401   0.515   0.677   0.689   0.739
140   V        -0.188  -0.082  -0.668  -0.132  -0.010  -0.841  -0.161  -0.029  -0.891
141   T        -1.683  -1.714  -1.545  -1.753  -1.767  -1.494  -1.837  -1.831  -1.543
142   R         0.658   0.666   0.704   0.388   0.401   0.515   0.677   0.689   0.739
143   R         0.658   0.666   0.704   0.388   0.401   0.515   0.677   0.689   0.739
144   K        -0.188  -0.353  -0.678  -0.266  -0.454  -1.031  -0.161  -0.393  -0.907
145   R        -0.627  -0.499  -0.678  -0.899  -0.718  -0.947  -0.789  -0.605  -0.908
146   C        -1.756  -1.657  -1.542  -1.433  -1.327  -1.277  -1.837  -1.723  -1.540
147   K        -1.401  -1.263  -1.535  -1.617  -1.480  -1.731  -1.418  -1.295  -1.531
148   G        -1.916  -1.875  -1.561  -2.202  -2.138  -1.631  -2.046  -1.995  -1.561
149   T        -2.289  -2.242  -2.143  -2.422  -2.390  -2.188  -2.151  -2.104  -1.839
150   V        -0.886  -0.740  -0.705  -1.185  -0.942  -0.911  -1.208  -0.983  -0.952
151   G         0.658   0.666   0.704   0.483   0.508   0.590   0.677   0.689   0.739
152   N        -2.130  -2.297  -2.143  -1.782  -2.044  -1.900  -1.941  -2.090  -1.838
153   S        -1.916  -1.897  -1.562  -1.980  -1.971  -1.472  -2.046  -2.021  -1.561
154   H         0.658   0.666   0.704   0.960   0.957   0.970   0.677   0.689   0.739
155   K        -0.627  -0.813  -0.721  -0.902  -1.234  -1.125  -0.789  -1.105  -0.978
156   T        -1.615  -1.727  -1.551  -1.702  -1.885  -1.621  -1.732  -1.838  -1.550
157   T        -1.916  -1.771  -1.551  -1.955  -1.781  -1.456  -2.046  -1.890  -1.549
158   K        -1.401  -1.429  -1.532  -1.530  -1.541  -1.763  -1.418  -1.433  -1.526
159   E        -0.188  -0.353  -0.678  -0.061  -0.268  -0.745  -0.161  -0.393  -0.907
160   D         0.658   0.666   0.704   0.779   0.801   0.826   0.677   0.689   0.739
161   T        -0.188  -0.175  -0.670   0.016   0.023  -0.694  -0.161  -0.149  -0.894
162   V        -0.627  -0.654  -0.714  -0.728  -0.793  -0.926  -0.789  -0.846  -0.966
163   S        -3.178  -2.945  -2.609  -3.043  -2.777  -2.278  -2.675  -2.468  -2.017
164   W         0.658   0.666   0.704   1.038   1.033   1.032   0.677   0.689   0.739
165   F         0.658   0.666   0.704   0.826   0.826   0.863   0.677   0.689   0.739
166   K         0.658   0.666   0.704   0.478   0.526   0.587   0.677   0.689   0.739
167   Q        -1.001  -1.017  -1.518  -0.544  -0.588  -1.361  -0.894  -0.938  -1.510
168   K        -1.009  -0.952  -0.726  -1.667  -1.557  -1.139  -1.418  -1.341  -0.986
169   Y        -0.188  -0.353  -0.678   0.158  -0.057  -0.580  -0.161  -0.393  -0.907
170   D         0.658   0.666   0.704   0.779   0.801   0.826   0.677   0.689   0.739
171   A         0.658   0.666   0.704   0.706   0.716   0.768   0.677   0.689   0.739
172   D        -3.037  -3.028  -2.609  -2.928  -2.906  -2.355  -2.570  -2.519  -2.017
173   V         0.658   0.666   0.704   0.585   0.597   0.671   0.677   0.689   0.739
174   L         0.658   0.666   0.704   0.649   0.657   0.723   0.677   0.689   0.739
175   D        -1.661  -1.679  -1.553  -1.677  -1.725  -1.551  -1.747  -1.766  -1.551
176   K        -0.256  -0.516  -0.695  -0.354  -0.722  -1.069  -0.251  -0.631  -0.935
* 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/Q3E757
Output conservation file - output/Q3E757
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
