1     M         0.661   0.668   0.706   0.927   0.927   0.941   0.678   0.689   0.740
2     S        -1.418  -1.482  -1.544  -1.239  -1.322  -1.474  -1.426  -1.487  -1.531
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     A        -2.458  -2.471  -2.161  -2.342  -2.344  -1.913  -2.267  -2.260  -1.845
6     K        -0.194  -0.404  -0.687  -0.226  -0.453  -0.878  -0.163  -0.460  -0.914
7     A        -1.418  -1.360  -1.549  -1.261  -1.227  -1.487  -1.426  -1.391  -1.537
8     Q        -0.194  -0.404  -0.687   0.145  -0.124  -0.639  -0.163  -0.460  -0.914
9     N         0.661   0.668   0.706   0.804   0.811   0.844   0.678   0.689   0.740
10    P        -0.637  -0.467  -0.703  -0.432  -0.196  -0.687  -0.794  -0.551  -0.939
11    M         0.661   0.668   0.706   0.927   0.927   0.941   0.678   0.689   0.740
12    R        -0.637  -0.508  -0.686  -0.976  -0.776  -1.061  -0.794  -0.611  -0.912
13    D        -0.194  -0.054  -0.675  -0.065   0.084  -0.734  -0.163   0.009  -0.894
14    L        -0.194  -0.179  -0.677  -0.024  -0.008  -0.659  -0.163  -0.150  -0.897
15    K        -1.634  -1.466  -1.546  -2.009  -1.710  -1.685  -1.741  -1.511  -1.533
16    I         0.661   0.668   0.706   0.599   0.603   0.683   0.678   0.689   0.740
17    E        -1.418  -1.447  -1.544  -1.306  -1.330  -1.465  -1.426  -1.444  -1.531
18    K         0.661   0.668   0.706   0.479   0.527   0.587   0.678   0.689   0.740
19    L         0.661   0.668   0.706   0.657   0.666   0.728   0.678   0.689   0.740
20    V        -0.194  -0.404  -0.687  -0.121  -0.386  -0.814  -0.163  -0.460  -0.914
21    L         0.661   0.668   0.706   0.657   0.666   0.728   0.678   0.689   0.740
22    N         0.661   0.668   0.706   0.804   0.811   0.844   0.678   0.689   0.740
23    I         0.661   0.668   0.706   0.599   0.603   0.683   0.678   0.689   0.740
24    S        -1.022  -0.965  -0.730  -1.041  -0.944  -0.609  -1.426  -1.351  -0.985
25    V        -0.637  -0.508  -0.686  -0.730  -0.544  -0.841  -0.794  -0.611  -0.912
26    G         0.661   0.668   0.706   0.484   0.508   0.591   0.678   0.689   0.740
27    E         0.661   0.668   0.706   0.635   0.638   0.710   0.678   0.689   0.740
28    S         0.661   0.668   0.706   0.739   0.743   0.793   0.678   0.689   0.740
29    G         0.661   0.668   0.706   0.484   0.508   0.591   0.678   0.689   0.740
30    D         0.661   0.668   0.706   0.782   0.803   0.827   0.678   0.689   0.740
31    R         0.661   0.668   0.706   0.388   0.401   0.516   0.678   0.689   0.740
32    L         0.661   0.668   0.706   0.657   0.666   0.728   0.678   0.689   0.740
33    T         0.661   0.668   0.706   0.722   0.725   0.779   0.678   0.689   0.740
34    R         0.661   0.668   0.706   0.388   0.401   0.516   0.678   0.689   0.740
35    A         0.661   0.668   0.706   0.705   0.714   0.766   0.678   0.689   0.740
36    S        -1.022  -0.908  -0.723  -1.252  -1.068  -0.789  -1.426  -1.253  -0.973
37    K         0.661   0.668   0.706   0.479   0.527   0.587   0.678   0.689   0.740
38    V         0.661   0.668   0.706   0.586   0.598   0.672   0.678   0.689   0.740
39    L         0.661   0.668   0.706   0.657   0.666   0.728   0.678   0.689   0.740
40    E         0.661   0.668   0.706   0.635   0.638   0.710   0.678   0.689   0.740
41    Q         0.661   0.668   0.706   0.855   0.865   0.885   0.678   0.689   0.740
42    L         0.661   0.668   0.706   0.657   0.666   0.728   0.678   0.689   0.740
43    S         0.661   0.668   0.706   0.739   0.743   0.793   0.678   0.689   0.740
44    G         0.661   0.668   0.706   0.484   0.508   0.591   0.678   0.689   0.740
45    Q         0.661   0.668   0.706   0.855   0.865   0.885   0.678   0.689   0.740
46    T         0.661   0.668   0.706   0.722   0.725   0.779   0.678   0.689   0.740
47    P         0.661   0.668   0.706   0.910   0.906   0.928   0.678   0.689   0.740
48    V         0.661   0.668   0.706   0.586   0.598   0.672   0.678   0.689   0.740
49    Q        -1.777  -1.788  -1.563  -1.557  -1.623  -1.334  -1.846  -1.883  -1.553
50    S        -0.194  -0.404  -0.687   0.032  -0.242  -0.710  -0.163  -0.460  -0.914
51    K         0.661   0.668   0.706   0.479   0.527   0.587   0.678   0.689   0.740
52    A         0.661   0.668   0.706   0.705   0.714   0.766   0.678   0.689   0.740
53    R         0.661   0.668   0.706   0.388   0.401   0.516   0.678   0.689   0.740
54    Y         0.661   0.668   0.706   0.851   0.848   0.881   0.678   0.689   0.740
55    T         0.661   0.668   0.706   0.722   0.725   0.779   0.678   0.689   0.740
56    V        -0.898  -0.885  -0.727  -1.197  -1.200  -0.944  -1.215  -1.213  -0.979
57    R         0.661   0.668   0.706   0.388   0.401   0.516   0.678   0.689   0.740
58    T        -1.418  -1.482  -1.544  -1.352  -1.427  -1.607  -1.426  -1.487  -1.531
59    F         0.661   0.668   0.706   0.829   0.828   0.864   0.678   0.689   0.740
60    G        -0.194  -0.404  -0.687  -0.221  -0.471  -0.875  -0.163  -0.460  -0.914
61    I         0.661   0.668   0.706   0.599   0.603   0.683   0.678   0.689   0.740
62    R         0.661   0.668   0.706   0.388   0.401   0.516   0.678   0.689   0.740
63    R         0.661   0.668   0.706   0.388   0.401   0.516   0.678   0.689   0.740
64    N         0.661   0.668   0.706   0.804   0.811   0.844   0.678   0.689   0.740
65    E         0.661   0.668   0.706   0.635   0.638   0.710   0.678   0.689   0.740
66    K         0.661   0.668   0.706   0.479   0.527   0.587   0.678   0.689   0.740
67    I         0.661   0.668   0.706   0.599   0.603   0.683   0.678   0.689   0.740
68    A        -0.637  -0.718  -0.724  -0.591  -0.735  -0.790  -0.794  -0.939  -0.974
69    V        -0.637  -0.508  -0.686  -0.623  -0.456  -0.673  -0.794  -0.611  -0.912
70    H         0.661   0.668   0.706   0.964   0.960   0.971   0.678   0.689   0.740
71    V         0.661   0.668   0.706   0.586   0.598   0.672   0.678   0.689   0.740
72    T         0.661   0.668   0.706   0.722   0.725   0.779   0.678   0.689   0.740
73    V        -0.194  -0.179  -0.677  -0.136  -0.120  -0.851  -0.163  -0.150  -0.897
74    R         0.661   0.668   0.706   0.388   0.401   0.516   0.678   0.689   0.740
75    G         0.661   0.668   0.706   0.484   0.508   0.591   0.678   0.689   0.740
76    P         0.661   0.668   0.706   0.910   0.906   0.928   0.678   0.689   0.740
77    K         0.661   0.668   0.706   0.479   0.527   0.587   0.678   0.689   0.740
78    A         0.661   0.668   0.706   0.705   0.714   0.766   0.678   0.689   0.740
79    E         0.661   0.668   0.706   0.635   0.638   0.710   0.678   0.689   0.740
80    E         0.661   0.668   0.706   0.635   0.638   0.710   0.678   0.689   0.740
81    I         0.661   0.668   0.706   0.599   0.603   0.683   0.678   0.689   0.740
82    L         0.661   0.668   0.706   0.657   0.666   0.728   0.678   0.689   0.740
83    E         0.661   0.668   0.706   0.635   0.638   0.710   0.678   0.689   0.740
84    R         0.661   0.668   0.706   0.388   0.401   0.516   0.678   0.689   0.740
85    G         0.661   0.668   0.706   0.484   0.508   0.591   0.678   0.689   0.740
86    L         0.661   0.668   0.706   0.657   0.666   0.728   0.678   0.689   0.740
87    K         0.661   0.668   0.706   0.479   0.527   0.587   0.678   0.689   0.740
88    V         0.661   0.668   0.706   0.586   0.598   0.672   0.678   0.689   0.740
89    K         0.661   0.668   0.706   0.479   0.527   0.587   0.678   0.689   0.740
90    E         0.661   0.668   0.706   0.635   0.638   0.710   0.678   0.689   0.740
91    Y         0.661   0.668   0.706   0.851   0.848   0.881   0.678   0.689   0.740
92    Q        -1.022  -0.967  -0.731  -1.198  -1.149  -0.779  -1.426  -1.354  -0.985
93    L         0.661   0.668   0.706   0.657   0.666   0.728   0.678   0.689   0.740
94    R        -0.898  -0.885  -0.727  -1.439  -1.421  -1.136  -1.215  -1.213  -0.979
95    D        -2.927  -2.785  -2.626  -2.776  -2.610  -2.312  -2.478  -2.348  -2.020
96    R        -0.898  -0.893  -0.730  -1.439  -1.437  -1.141  -1.215  -1.227  -0.984
97    N         0.661   0.668   0.706   0.804   0.811   0.844   0.678   0.689   0.740
98    F         0.661   0.668   0.706   0.829   0.828   0.864   0.678   0.689   0.740
99    S         0.661   0.668   0.706   0.739   0.743   0.793   0.678   0.689   0.740
100   A        -1.418  -1.481  -1.556  -1.294  -1.490  -1.549  -1.426  -1.571  -1.545
101   T         0.661   0.668   0.706   0.722   0.725   0.779   0.678   0.689   0.740
102   G         0.661   0.668   0.706   0.484   0.508   0.591   0.678   0.689   0.740
103   N         0.661   0.668   0.706   0.804   0.811   0.844   0.678   0.689   0.740
104   F         0.661   0.668   0.706   0.829   0.828   0.864   0.678   0.689   0.740
105   G         0.661   0.668   0.706   0.484   0.508   0.591   0.678   0.689   0.740
106   F         0.661   0.668   0.706   0.829   0.828   0.864   0.678   0.689   0.740
107   G         0.661   0.668   0.706   0.484   0.508   0.591   0.678   0.689   0.740
108   I        -0.194  -0.179  -0.677  -0.125  -0.116  -0.847  -0.163  -0.150  -0.897
109   D        -2.315  -2.450  -2.160  -2.027  -2.181  -1.823  -2.162  -2.246  -1.844
110   E         0.661   0.668   0.706   0.635   0.638   0.710   0.678   0.689   0.740
111   H         0.661   0.668   0.706   0.964   0.960   0.971   0.678   0.689   0.740
112   I         0.661   0.668   0.706   0.599   0.603   0.683   0.678   0.689   0.740
113   D         0.661   0.668   0.706   0.782   0.803   0.827   0.678   0.689   0.740
114   L         0.661   0.668   0.706   0.657   0.666   0.728   0.678   0.689   0.740
115   G         0.661   0.668   0.706   0.484   0.508   0.591   0.678   0.689   0.740
116   I         0.661   0.668   0.706   0.599   0.603   0.683   0.678   0.689   0.740
117   K         0.661   0.668   0.706   0.479   0.527   0.587   0.678   0.689   0.740
118   Y         0.661   0.668   0.706   0.851   0.848   0.881   0.678   0.689   0.740
119   D         0.661   0.668   0.706   0.782   0.803   0.827   0.678   0.689   0.740
120   P         0.661   0.668   0.706   0.910   0.906   0.928   0.678   0.689   0.740
121   S        -1.634  -1.745  -1.557  -1.720  -1.876  -1.578  -1.741  -1.846  -1.547
122   I         0.661   0.668   0.706   0.599   0.603   0.683   0.678   0.689   0.740
123   G         0.661   0.668   0.706   0.484   0.508   0.591   0.678   0.689   0.740
124   I         0.661   0.668   0.706   0.599   0.603   0.683   0.678   0.689   0.740
125   F        -0.637  -0.475  -0.699  -0.424  -0.214  -0.610  -0.794  -0.564  -0.934
126   G         0.661   0.668   0.706   0.484   0.508   0.591   0.678   0.689   0.740
127   M         0.661   0.668   0.706   0.927   0.927   0.941   0.678   0.689   0.740
128   D         0.661   0.668   0.706   0.782   0.803   0.827   0.678   0.689   0.740
129   F         0.661   0.668   0.706   0.829   0.828   0.864   0.678   0.689   0.740
130   Y        -0.194  -0.404  -0.687   0.156  -0.118  -0.588  -0.163  -0.460  -0.914
131   V        -1.418  -1.393  -1.542  -1.369  -1.290  -1.480  -1.426  -1.374  -1.528
132   V        -1.014  -1.358  -1.545  -0.792  -1.239  -1.477  -0.900  -1.330  -1.531
133   M        -1.014  -1.197  -1.536  -0.507  -0.781  -1.414  -0.900  -1.139  -1.521
134   N        -2.154  -2.068  -2.149  -2.082  -1.966  -2.003  -1.952  -1.858  -1.834
135   R         0.661   0.668   0.706   0.388   0.401   0.516   0.678   0.689   0.740
136   P        -0.637  -0.529  -0.702  -0.401  -0.262  -0.632  -0.794  -0.644  -0.938
137   G         0.661   0.668   0.706   0.484   0.508   0.591   0.678   0.689   0.740
138   A        -2.835  -2.891  -2.627  -2.404  -2.511  -2.150  -2.373  -2.402  -2.020
139   R         0.661   0.668   0.706   0.388   0.401   0.516   0.678   0.689   0.740
140   V        -0.194  -0.085  -0.675  -0.136  -0.011  -0.847  -0.163  -0.029  -0.894
141   T        -1.703  -1.731  -1.557  -1.769  -1.778  -1.501  -1.846  -1.837  -1.546
142   R         0.661   0.668   0.706   0.388   0.401   0.516   0.678   0.689   0.740
143   R         0.661   0.668   0.706   0.388   0.401   0.516   0.678   0.689   0.740
144   K        -0.194  -0.362  -0.686  -0.271  -0.462  -1.037  -0.163  -0.399  -0.911
145   R        -0.637  -0.508  -0.686  -0.910  -0.728  -0.955  -0.794  -0.611  -0.912
146   C        -1.777  -1.677  -1.555  -1.448  -1.343  -1.286  -1.846  -1.733  -1.544
147   K        -1.418  -1.272  -1.547  -1.632  -1.483  -1.738  -1.426  -1.294  -1.534
148   G        -1.938  -1.893  -1.574  -2.223  -2.152  -1.640  -2.057  -2.002  -1.564
149   T        -2.315  -2.263  -2.159  -2.440  -2.403  -2.195  -2.162  -2.111  -1.843
150   V        -0.898  -0.748  -0.713  -1.197  -0.949  -0.917  -1.215  -0.987  -0.956
151   G         0.661   0.668   0.706   0.484   0.508   0.591   0.678   0.689   0.740
152   N        -2.154  -2.322  -2.160  -1.799  -2.063  -1.910  -1.952  -2.101  -1.843
153   S        -1.938  -1.914  -1.574  -1.995  -1.980  -1.477  -2.057  -2.027  -1.565
154   H         0.661   0.668   0.706   0.964   0.960   0.971   0.678   0.689   0.740
155   K        -0.637  -0.824  -0.728  -0.912  -1.245  -1.131  -0.794  -1.112  -0.981
156   T        -1.634  -1.745  -1.563  -1.714  -1.896  -1.627  -1.741  -1.846  -1.553
157   T        -1.938  -1.787  -1.563  -1.970  -1.788  -1.460  -2.057  -1.896  -1.553
158   K        -1.418  -1.447  -1.544  -1.545  -1.558  -1.774  -1.426  -1.444  -1.531
159   E        -0.194  -0.362  -0.686  -0.065  -0.275  -0.751  -0.163  -0.399  -0.911
160   D         0.661   0.668   0.706   0.782   0.803   0.827   0.678   0.689   0.740
161   T        -0.194  -0.179  -0.677   0.017   0.026  -0.696  -0.163  -0.150  -0.897
162   V        -0.637  -0.658  -0.721  -0.736  -0.792  -0.930  -0.794  -0.843  -0.969
163   S        -3.212  -2.965  -2.628  -3.071  -2.787  -2.289  -2.688  -2.472  -2.021
164   W         0.661   0.668   0.706   1.043   1.036   1.034   0.678   0.689   0.740
165   F         0.661   0.668   0.706   0.829   0.828   0.864   0.678   0.689   0.740
166   K         0.661   0.668   0.706   0.479   0.527   0.587   0.678   0.689   0.740
167   Q        -1.014  -1.032  -1.531  -0.550  -0.598  -1.367  -0.900  -0.947  -1.515
168   K        -1.022  -0.961  -0.733  -1.683  -1.565  -1.144  -1.426  -1.344  -0.989
169   Y        -0.194  -0.362  -0.686   0.156  -0.063  -0.585  -0.163  -0.399  -0.911
170   D         0.661   0.668   0.706   0.782   0.803   0.827   0.678   0.689   0.740
171   A         0.661   0.668   0.706   0.705   0.714   0.766   0.678   0.689   0.740
172   D        -3.070  -3.056  -2.629  -2.953  -2.926  -2.365  -2.583  -2.528  -2.022
173   V         0.661   0.668   0.706   0.586   0.598   0.672   0.678   0.689   0.740
174   L         0.661   0.668   0.706   0.651   0.659   0.723   0.678   0.689   0.740
175   D        -1.680  -1.696  -1.565  -1.692  -1.739  -1.559  -1.756  -1.775  -1.555
176   K        -0.262  -0.525  -0.702  -0.360  -0.731  -1.076  -0.254  -0.638  -0.938
* 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/P0C0W9
Output conservation file - output/P0C0W9
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
