1     M         0.744   0.758   0.776   1.151   1.138   1.112   0.750   0.772   0.800
2     S        -1.541  -1.740  -1.664  -1.299  -1.634  -1.617  -1.416  -1.631  -1.534
3     A        -0.866  -0.735  -0.764  -0.904  -0.724  -0.877  -1.040  -0.870  -0.948
4     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     P        -0.969  -0.980  -0.768  -0.870  -0.964  -0.659  -1.199  -1.252  -0.955
6     S        -0.195  -0.546  -0.737   0.059  -0.423  -0.851  -0.116  -0.593  -0.905
7     V         0.744   0.758   0.776   0.557   0.597   0.656   0.750   0.772   0.800
8     Q         0.744   0.758   0.776   0.889   0.898   0.911   0.750   0.772   0.800
9     T        -1.541  -1.740  -1.664  -1.107  -1.451  -1.411  -1.416  -1.631  -1.534
10    F         0.744   0.758   0.776   0.951   0.966   0.959   0.750   0.772   0.800
11    G         0.744   0.758   0.776   0.622   0.663   0.706   0.750   0.772   0.800
12    K         0.744   0.758   0.776   0.376   0.436   0.516   0.750   0.772   0.800
13    K         0.744   0.758   0.776   0.376   0.436   0.516   0.750   0.772   0.800
14    K        -0.682  -0.598  -0.726  -1.082  -0.931  -1.108  -0.766  -0.668  -0.890
15    S        -2.213  -1.913  -1.674  -2.060  -1.603  -1.339  -2.174  -1.837  -1.545
16    A         0.744   0.758   0.776   0.509   0.530   0.619   0.750   0.772   0.800
17    T         0.744   0.758   0.776   0.946   0.958   0.954   0.750   0.772   0.800
18    A         0.744   0.758   0.776   0.509   0.530   0.619   0.750   0.772   0.800
19    V         0.744   0.758   0.776   0.557   0.597   0.656   0.750   0.772   0.800
20    A         0.744   0.758   0.776   0.509   0.530   0.619   0.750   0.772   0.800
21    H        -0.195  -0.546  -0.737   0.318  -0.176  -0.591  -0.116  -0.593  -0.905
22    V        -0.969  -0.966  -0.773  -1.110  -1.064  -0.732  -1.199  -1.230  -0.963
23    K        -0.195  -0.546  -0.737  -0.425  -0.870  -1.157  -0.116  -0.593  -0.905
24    A        -1.541  -1.740  -1.664  -1.691  -1.964  -1.795  -1.416  -1.631  -1.534
25    G         0.744   0.758   0.776   0.622   0.663   0.706   0.750   0.772   0.800
26    K         0.744   0.758   0.776   0.376   0.436   0.516   0.750   0.772   0.800
27    G         0.744   0.758   0.776   0.622   0.663   0.706   0.750   0.772   0.800
28    L         0.744   0.758   0.776   0.710   0.727   0.774   0.750   0.772   0.800
29    I         0.744   0.758   0.776   0.832   0.851   0.867   0.750   0.772   0.800
30    K         0.744   0.758   0.776   0.376   0.436   0.516   0.750   0.772   0.800
31    V        -1.097  -0.998  -1.634  -0.978  -0.860  -1.689  -0.874  -0.781  -1.501
32    N         0.744   0.758   0.776   1.107   1.098   1.079   0.750   0.772   0.800
33    G         0.744   0.758   0.776   0.622   0.663   0.706   0.750   0.772   0.800
34    S        -2.527  -2.585  -2.313  -2.515  -2.636  -2.198  -2.174  -2.164  -1.838
35    P         0.744   0.758   0.776   0.979   0.986   0.980   0.750   0.772   0.800
36    I        -0.969  -0.966  -0.773  -1.097  -1.163  -0.859  -1.199  -1.230  -0.963
37    T        -1.541  -1.740  -1.664  -1.246  -1.611  -1.636  -1.416  -1.631  -1.534
38    L         0.744   0.758   0.776   0.710   0.727   0.774   0.750   0.772   0.800
39    V        -1.097  -1.458  -1.656  -0.939  -1.390  -1.605  -0.874  -1.313  -1.525
40    E        -1.778  -1.853  -1.665  -1.626  -1.779  -1.548  -1.741  -1.769  -1.536
41    P         0.744   0.758   0.776   0.979   0.986   0.980   0.750   0.772   0.800
42    E        -0.195  -0.244  -0.725   0.184   0.101  -0.739  -0.116  -0.185  -0.887
43    I        -0.195  -0.244  -0.725   0.036  -0.028  -0.823  -0.116  -0.185  -0.887
44    L         0.744   0.758   0.776   0.710   0.727   0.774   0.750   0.772   0.800
45    R         0.744   0.758   0.776   0.757   0.780   0.809   0.750   0.772   0.800
46    F        -1.778  -1.908  -1.670  -1.485  -1.719  -1.438  -1.741  -1.838  -1.541
47    K         0.744   0.758   0.776   0.376   0.436   0.516   0.750   0.772   0.800
48    V        -0.195  -0.546  -0.737  -0.221  -0.673  -0.961  -0.116  -0.593  -0.905
49    Y         0.744   0.758   0.776   0.968   0.966   0.972   0.750   0.772   0.800
50    E         0.744   0.758   0.776   0.985   0.991   0.985   0.750   0.772   0.800
51    P         0.744   0.758   0.776   0.979   0.986   0.980   0.750   0.772   0.800
52    L        -0.969  -0.966  -0.773  -1.153  -1.183  -0.861  -1.199  -1.230  -0.963
53    L        -0.682  -0.437  -0.733  -0.657  -0.333  -0.748  -0.766  -0.440  -0.900
54    L        -0.969  -0.892  -0.770  -1.280  -1.191  -1.003  -1.199  -1.113  -0.957
55    V        -1.541  -1.740  -1.664  -1.690  -1.993  -1.873  -1.416  -1.631  -1.534
56    G         0.744   0.758   0.776   0.622   0.663   0.706   0.750   0.772   0.800
57    L        -1.541  -1.740  -1.664  -1.497  -1.782  -1.676  -1.416  -1.631  -1.534
58    D         0.744   0.758   0.776   0.996   0.998   0.993   0.750   0.772   0.800
59    K         0.744   0.758   0.776   0.376   0.436   0.516   0.750   0.772   0.800
60    F         0.744   0.758   0.776   0.951   0.966   0.959   0.750   0.772   0.800
61    S        -1.541  -1.109  -1.636  -1.583  -1.047  -1.634  -1.416  -0.933  -1.504
62    N        -1.778  -1.884  -1.667  -1.540  -1.685  -1.432  -1.741  -1.808  -1.538
63    I        -1.105  -0.946  -0.760  -1.470  -1.260  -0.937  -1.416  -1.198  -0.942
64    D         0.744   0.758   0.776   0.996   0.998   0.993   0.750   0.772   0.800
65    I         0.744   0.758   0.776   0.832   0.851   0.867   0.750   0.772   0.800
66    R         0.744   0.758   0.776   0.757   0.780   0.809   0.750   0.772   0.800
67    V        -1.097  -1.458  -1.656  -0.978  -1.470  -1.717  -0.874  -1.313  -1.525
68    R        -1.105  -0.922  -0.767  -1.714  -1.404  -1.096  -1.416  -1.159  -0.953
69    V         0.744   0.758   0.776   0.557   0.597   0.656   0.750   0.772   0.800
70    T        -1.854  -1.684  -1.655  -1.694  -1.407  -1.338  -1.849  -1.611  -1.524
71    G         0.744   0.758   0.776   0.622   0.663   0.706   0.750   0.772   0.800
72    G         0.744   0.758   0.776   0.622   0.663   0.706   0.750   0.772   0.800
73    G         0.744   0.758   0.776   0.622   0.663   0.706   0.750   0.772   0.800
74    H         0.744   0.758   0.776   1.091   1.089   1.066   0.750   0.772   0.800
75    V         0.744   0.758   0.776   0.557   0.597   0.656   0.750   0.772   0.800
76    S         0.744   0.758   0.776   0.861   0.901   0.889   0.750   0.772   0.800
77    Q         0.744   0.758   0.776   0.889   0.898   0.911   0.750   0.772   0.800
78    V        -0.969  -0.892  -0.770  -1.294  -1.174  -0.947  -1.199  -1.113  -0.957
79    Y         0.744   0.758   0.776   0.968   0.966   0.972   0.750   0.772   0.800
80    A         0.744   0.758   0.776   0.509   0.530   0.619   0.750   0.772   0.800
81    I        -0.195  -0.546  -0.737   0.036  -0.455  -0.849  -0.116  -0.593  -0.905
82    R         0.744   0.758   0.776   0.757   0.780   0.809   0.750   0.772   0.800
83    Q         0.744   0.758   0.776   0.889   0.898   0.911   0.750   0.772   0.800
84    A         0.744   0.758   0.776   0.509   0.530   0.619   0.750   0.772   0.800
85    I         0.744   0.758   0.776   0.832   0.851   0.867   0.750   0.772   0.800
86    A        -0.682  -0.598  -0.726  -0.878  -0.763  -0.908  -0.766  -0.668  -0.890
87    K         0.744   0.758   0.776   0.376   0.436   0.516   0.750   0.772   0.800
88    G        -0.969  -0.966  -0.773  -1.386  -1.448  -1.094  -1.199  -1.230  -0.963
89    L        -0.969  -0.966  -0.773  -1.153  -1.183  -0.861  -1.199  -1.230  -0.963
90    V         0.744   0.758   0.776   0.557   0.597   0.656   0.750   0.772   0.800
91    A         0.744   0.758   0.776   0.509   0.530   0.619   0.750   0.772   0.800
92    Y        -0.195  -0.244  -0.725   0.220   0.143  -0.565  -0.116  -0.185  -0.887
93    H        -0.969  -0.966  -0.773  -0.747  -0.825  -0.574  -1.199  -1.230  -0.963
94    Q        -0.195  -0.546  -0.737   0.087  -0.426  -0.831  -0.116  -0.593  -0.905
95    K         0.744   0.758   0.776   0.376   0.436   0.516   0.750   0.772   0.800
96    Y        -0.969  -0.923  -0.774  -0.872  -0.843  -0.652  -1.199  -1.161  -0.964
97    V         0.744   0.758   0.776   0.557   0.597   0.656   0.750   0.772   0.800
98    D         0.744   0.758   0.776   0.996   0.998   0.993   0.750   0.772   0.800
99    E         0.744   0.758   0.776   0.985   0.991   0.985   0.750   0.772   0.800
100   Q        -2.112  -1.848  -1.674  -2.074  -1.676  -1.513  -2.065  -1.780  -1.546
101   S         0.744   0.758   0.776   0.861   0.901   0.889   0.750   0.772   0.800
102   K         0.744   0.758   0.776   0.376   0.436   0.516   0.750   0.772   0.800
103   N        -0.682  -0.598  -0.726  -0.388  -0.315  -0.660  -0.766  -0.668  -0.890
104   E        -0.195  -0.546  -0.737   0.236  -0.224  -0.577  -0.116  -0.593  -0.905
105   L         0.744   0.758   0.776   0.710   0.727   0.774   0.750   0.772   0.800
106   K         0.744   0.758   0.776   0.376   0.436   0.516   0.750   0.772   0.800
107   K        -0.195  -0.546  -0.737  -0.373  -0.766  -0.968  -0.116  -0.593  -0.905
108   A        -1.097  -0.755  -1.630  -1.049  -0.654  -1.775  -0.874  -0.508  -1.496
109   F        -0.969  -0.966  -0.773  -0.987  -1.070  -0.790  -1.199  -1.230  -0.963
110   T        -2.112  -1.848  -1.674  -2.182  -1.820  -1.618  -2.065  -1.780  -1.546
111   S        -1.935  -1.928  -1.666  -1.758  -1.791  -1.438  -1.849  -1.856  -1.536
112   Y        -0.682  -0.868  -0.774  -0.406  -0.748  -0.651  -0.766  -1.075  -0.963
113   D         0.744   0.758   0.776   0.996   0.998   0.993   0.750   0.772   0.800
114   R        -0.682  -0.437  -0.733  -0.770  -0.396  -0.973  -0.766  -0.440  -0.900
115   T         0.744   0.758   0.776   0.946   0.958   0.954   0.750   0.772   0.800
116   L         0.744   0.758   0.776   0.710   0.727   0.774   0.750   0.772   0.800
117   L         0.744   0.758   0.776   0.710   0.727   0.774   0.750   0.772   0.800
118   I        -1.105  -0.896  -0.762  -1.515  -1.180  -0.940  -1.416  -1.119  -0.946
119   A         0.744   0.758   0.776   0.509   0.530   0.619   0.750   0.772   0.800
120   D         0.744   0.758   0.776   0.996   0.998   0.993   0.750   0.772   0.800
121   S        -1.854  -1.450  -1.653  -1.774  -1.198  -1.530  -1.849  -1.412  -1.522
122   R         0.744   0.758   0.776   0.757   0.780   0.809   0.750   0.772   0.800
123   R         0.744   0.758   0.776   0.757   0.780   0.809   0.750   0.772   0.800
124   P        -1.778  -1.746  -1.655  -1.289  -1.184  -1.130  -1.741  -1.639  -1.524
125   E         0.744   0.758   0.776   0.985   0.991   0.985   0.750   0.772   0.800
126   P         0.744   0.758   0.776   0.979   0.986   0.980   0.750   0.772   0.800
127   K         0.744   0.758   0.776   0.376   0.436   0.516   0.750   0.772   0.800
128   K         0.744   0.758   0.776   0.376   0.436   0.516   0.750   0.772   0.800
129   F         0.744   0.758   0.776   0.951   0.966   0.959   0.750   0.772   0.800
130   G         0.744   0.758   0.776   0.622   0.663   0.706   0.750   0.772   0.800
131   G         0.744   0.758   0.776   0.622   0.663   0.706   0.750   0.772   0.800
132   K        -2.785  -2.572  -2.308  -2.853  -2.548  -2.085  -2.390  -2.149  -1.833
133   G         0.744   0.758   0.776   0.622   0.663   0.706   0.750   0.772   0.800
134   A         0.744   0.758   0.776   0.509   0.530   0.619   0.750   0.772   0.800
135   R         0.744   0.758   0.776   0.757   0.780   0.809   0.750   0.772   0.800
136   S        -0.969  -0.896  -0.772  -1.324  -1.212  -0.961  -1.199  -1.119  -0.961
137   R         0.744   0.758   0.776   0.757   0.780   0.809   0.750   0.772   0.800
138   F        -1.541  -1.502  -1.647  -1.141  -1.105  -1.352  -1.416  -1.369  -1.515
139   Q         0.744   0.758   0.776   0.889   0.898   0.911   0.750   0.772   0.800
140   K         0.744   0.758   0.776   0.376   0.436   0.516   0.750   0.772   0.800
141   S         0.744   0.758   0.776   0.861   0.901   0.889   0.750   0.772   0.800
142   Y         0.744   0.758   0.776   0.968   0.966   0.972   0.750   0.772   0.800
143   R         0.744   0.758   0.776   0.757   0.780   0.809   0.750   0.772   0.800
* 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/P0CX51
Output conservation file - output/P0CX51
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
