1     M         0.646   0.647   0.676   0.946   0.943   0.947   0.672   0.674   0.714
2     S        -0.835  -0.773  -0.698  -0.953  -0.854  -0.754  -1.169  -1.073  -0.977
3     T        -0.135  -0.293  -0.663  -0.019  -0.201  -0.739  -0.104  -0.325  -0.918
4     E         0.646   0.647   0.676   0.805   0.802   0.828   0.672   0.674   0.714
5     L         0.646   0.647   0.676   0.780   0.775   0.806   0.672   0.674   0.714
6     T        -1.254  -1.373  -1.486  -1.197  -1.342  -1.515  -1.267  -1.407  -1.526
7     V         0.646   0.647   0.676   0.437   0.445   0.515   0.672   0.674   0.714
8     Q         0.646   0.647   0.676   0.805   0.805   0.828   0.672   0.674   0.714
9     S        -0.135  -0.293  -0.663   0.115  -0.070  -0.610  -0.104  -0.325  -0.918
10    E         0.646   0.647   0.676   0.805   0.802   0.828   0.672   0.674   0.714
11    R         0.646   0.647   0.676   0.526   0.526   0.590   0.672   0.674   0.714
12    A         0.646   0.647   0.676   0.656   0.659   0.701   0.672   0.674   0.714
13    F         0.646   0.647   0.676   0.704   0.705   0.741   0.672   0.674   0.714
14    Q         0.646   0.647   0.676   0.805   0.805   0.828   0.672   0.674   0.714
15    K         0.646   0.647   0.676   0.305   0.314   0.403   0.672   0.674   0.714
16    Q         0.646   0.647   0.676   0.805   0.805   0.828   0.672   0.674   0.714
17    P         0.646   0.647   0.676   0.750   0.752   0.781   0.672   0.674   0.714
18    H         0.646   0.647   0.676   0.822   0.821   0.842   0.672   0.674   0.714
19    I         0.646   0.647   0.676   0.674   0.674   0.716   0.672   0.674   0.714
20    F         0.646   0.647   0.676   0.704   0.705   0.741   0.672   0.674   0.714
21    N        -2.633  -2.572  -2.529  -2.242  -2.159  -2.054  -2.237  -2.186  -2.013
22    N         0.646   0.647   0.676   0.805   0.803   0.828   0.672   0.674   0.714
23    P        -1.451  -1.505  -1.506  -1.342  -1.440  -1.405  -1.558  -1.630  -1.551
24    K         0.646   0.647   0.676   0.305   0.314   0.403   0.672   0.674   0.714
25    V        -3.108  -3.130  -2.897  -2.982  -3.042  -2.687  -2.431  -2.448  -2.130
26    K        -0.540  -0.526  -0.662  -0.848  -0.828  -0.991  -0.686  -0.671  -0.915
27    T        -1.581  -1.613  -1.506  -1.657  -1.748  -1.629  -1.655  -1.709  -1.550
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    S        -1.493  -1.528  -1.500  -1.301  -1.343  -1.362  -1.572  -1.599  -1.543
34    K        -0.883  -0.872  -0.708  -1.481  -1.469  -1.134  -1.252  -1.245  -0.993
35    R        -1.493  -1.528  -1.500  -1.865  -1.893  -1.770  -1.572  -1.599  -1.543
36    T        -0.779  -0.781  -0.697  -0.944  -0.953  -0.832  -1.073  -1.087  -0.974
37    K        -0.779  -0.781  -0.697  -1.280  -1.291  -1.110  -1.073  -1.087  -0.974
38    R         0.646   0.647   0.676   0.526   0.526   0.590   0.672   0.674   0.714
39    W         0.646   0.647   0.676   0.987   0.985   0.982   0.672   0.674   0.714
40    Y        -0.135  -0.128  -0.659   0.187   0.190  -0.588  -0.104  -0.099  -0.910
41    K         0.646   0.647   0.676   0.305   0.314   0.403   0.672   0.674   0.714
42    N        -1.729  -1.726  -1.515  -1.475  -1.487  -1.220  -1.849  -1.848  -1.560
43    A        -0.540  -0.479  -0.673  -0.716  -0.628  -0.908  -0.686  -0.598  -0.935
44    G         0.646   0.647   0.676   0.652   0.652   0.698   0.672   0.674   0.714
45    L         0.646   0.647   0.676   0.780   0.775   0.806   0.672   0.674   0.714
46    G         0.646   0.647   0.676   0.652   0.652   0.698   0.672   0.674   0.714
47    F         0.646   0.647   0.676   0.704   0.705   0.741   0.672   0.674   0.714
48    K        -0.135  -0.184  -0.658  -0.342  -0.397  -1.049  -0.104  -0.172  -0.909
49    T         0.646   0.647   0.676   0.600   0.610   0.653   0.672   0.674   0.714
50    P         0.646   0.647   0.676   0.750   0.752   0.781   0.672   0.674   0.714
51    K        -1.451  -1.563  -1.507  -1.738  -1.865  -1.665  -1.558  -1.677  -1.551
52    T        -1.729  -1.669  -1.498  -1.784  -1.693  -1.438  -1.849  -1.779  -1.541
53    A         0.646   0.647   0.676   0.656   0.659   0.701   0.672   0.674   0.714
54    I         0.646   0.647   0.676   0.674   0.674   0.716   0.672   0.674   0.714
55    E        -1.254  -1.373  -1.486  -0.917  -1.087  -1.318  -1.267  -1.407  -1.526
56    G         0.646   0.647   0.676   0.652   0.652   0.698   0.672   0.674   0.714
57    S        -2.548  -2.653  -2.531  -1.985  -2.120  -1.925  -2.140  -2.231  -2.014
58    Y         0.646   0.647   0.676   0.809   0.810   0.831   0.672   0.674   0.714
59    I        -0.540  -0.526  -0.662  -0.543  -0.530  -0.819  -0.686  -0.671  -0.915
60    D         0.646   0.647   0.676   0.909   0.907   0.916   0.672   0.674   0.714
61    K         0.646   0.647   0.676   0.305   0.314   0.403   0.672   0.674   0.714
62    K         0.646   0.647   0.676   0.305   0.314   0.403   0.672   0.674   0.714
63    C         0.646   0.647   0.676   0.950   0.949   0.951   0.672   0.674   0.714
64    P         0.646   0.647   0.676   0.750   0.752   0.781   0.672   0.674   0.714
65    F         0.646   0.647   0.676   0.704   0.705   0.741   0.672   0.674   0.714
66    T        -1.729  -1.690  -1.512  -1.987  -1.954  -1.647  -1.849  -1.816  -1.556
67    G         0.646   0.647   0.676   0.652   0.652   0.698   0.672   0.674   0.714
68    L        -2.633  -2.625  -2.534  -2.137  -2.127  -2.007  -2.237  -2.230  -2.016
69    V        -0.135  -0.293  -0.663  -0.190  -0.375  -0.884  -0.104  -0.325  -0.918
70    S         0.646   0.647   0.676   0.725   0.728   0.759   0.672   0.674   0.714
71    I         0.646   0.647   0.676   0.674   0.674   0.716   0.672   0.674   0.714
72    R         0.646   0.647   0.676   0.526   0.526   0.590   0.672   0.674   0.714
73    G         0.646   0.647   0.676   0.652   0.652   0.698   0.672   0.674   0.714
74    K        -0.779  -0.781  -0.697  -1.280  -1.291  -1.110  -1.073  -1.087  -0.974
75    I         0.646   0.647   0.676   0.674   0.674   0.716   0.672   0.674   0.714
76    L         0.646   0.647   0.676   0.780   0.775   0.806   0.672   0.674   0.714
77    T        -0.540  -0.522  -0.695  -0.536  -0.509  -0.790  -0.686  -0.665  -0.972
78    G         0.646   0.647   0.676   0.652   0.652   0.698   0.672   0.674   0.714
79    T        -0.135  -0.293  -0.663  -0.071  -0.274  -0.941  -0.104  -0.325  -0.918
80    V         0.646   0.647   0.676   0.437   0.445   0.515   0.672   0.674   0.714
81    V         0.646   0.647   0.676   0.437   0.445   0.515   0.672   0.674   0.714
82    S         0.646   0.647   0.676   0.725   0.728   0.759   0.672   0.674   0.714
83    T         0.646   0.647   0.676   0.600   0.610   0.653   0.672   0.674   0.714
84    K        -0.135  -0.024  -0.653  -0.342  -0.214  -1.041  -0.104   0.035  -0.901
85    M         0.646   0.647   0.676   0.946   0.943   0.947   0.672   0.674   0.714
86    H         0.646   0.647   0.676   0.822   0.821   0.842   0.672   0.674   0.714
87    R         0.646   0.647   0.676   0.526   0.526   0.590   0.672   0.674   0.714
88    T         0.646   0.647   0.676   0.600   0.610   0.653   0.672   0.674   0.714
89    I         0.646   0.647   0.676   0.674   0.674   0.716   0.672   0.674   0.714
90    V        -0.540  -0.459  -0.676  -0.543  -0.425  -0.851  -0.686  -0.568  -0.940
91    I         0.646   0.647   0.676   0.674   0.674   0.716   0.672   0.674   0.714
92    R         0.646   0.647   0.676   0.526   0.526   0.590   0.672   0.674   0.714
93    R         0.646   0.647   0.676   0.526   0.526   0.590   0.672   0.674   0.714
94    A        -1.514  -1.468  -1.504  -1.269  -1.226  -1.266  -1.655  -1.602  -1.548
95    Y         0.646   0.647   0.676   0.809   0.810   0.831   0.672   0.674   0.714
96    L         0.646   0.647   0.676   0.780   0.775   0.806   0.672   0.674   0.714
97    H         0.646   0.647   0.676   0.822   0.821   0.842   0.672   0.674   0.714
98    Y        -0.779  -0.781  -0.697  -0.729  -0.748  -0.662  -1.073  -1.087  -0.974
99    I        -0.892  -0.834  -0.702  -1.227  -1.109  -0.915  -1.267  -1.178  -0.984
100   P         0.646   0.647   0.676   0.750   0.752   0.781   0.672   0.674   0.714
101   K         0.646   0.647   0.676   0.305   0.314   0.403   0.672   0.674   0.714
102   Y         0.646   0.647   0.676   0.809   0.810   0.831   0.672   0.674   0.714
103   N         0.646   0.647   0.676   0.805   0.803   0.828   0.672   0.674   0.714
104   R         0.646   0.647   0.676   0.526   0.526   0.590   0.672   0.674   0.714
105   Y         0.646   0.647   0.676   0.809   0.810   0.831   0.672   0.674   0.714
106   E         0.646   0.647   0.676   0.805   0.802   0.828   0.672   0.674   0.714
107   K         0.646   0.647   0.676   0.305   0.314   0.403   0.672   0.674   0.714
108   R         0.646   0.647   0.676   0.526   0.526   0.590   0.672   0.674   0.714
109   H         0.646   0.647   0.676   0.822   0.821   0.842   0.672   0.674   0.714
110   K         0.646   0.647   0.676   0.305   0.314   0.403   0.672   0.674   0.714
111   N         0.646   0.647   0.676   0.805   0.803   0.828   0.672   0.674   0.714
112   V        -0.892  -0.831  -0.703  -1.138  -1.013  -0.842  -1.267  -1.174  -0.984
113   P        -0.779  -0.698  -0.690  -0.846  -0.723  -0.728  -1.073  -0.948  -0.962
114   V        -0.540  -0.479  -0.673  -0.561  -0.471  -0.857  -0.686  -0.598  -0.935
115   H         0.646   0.647   0.676   0.822   0.821   0.842   0.672   0.674   0.714
116   V         0.646   0.647   0.676   0.437   0.445   0.515   0.672   0.674   0.714
117   S         0.646   0.647   0.676   0.725   0.728   0.759   0.672   0.674   0.714
118   P         0.646   0.647   0.676   0.750   0.752   0.781   0.672   0.674   0.714
119   A         0.646   0.647   0.676   0.656   0.659   0.701   0.672   0.674   0.714
120   F         0.646   0.647   0.676   0.704   0.705   0.741   0.672   0.674   0.714
121   R         0.646   0.647   0.676   0.526   0.526   0.590   0.672   0.674   0.714
122   V        -0.540  -0.526  -0.662  -0.711  -0.691  -0.882  -0.686  -0.671  -0.915
123   Q        -1.729  -1.715  -1.504  -1.552  -1.556  -1.260  -1.849  -1.842  -1.548
124   V        -1.451  -1.508  -1.500  -1.391  -1.425  -1.428  -1.558  -1.597  -1.543
125   G         0.646   0.647   0.676   0.652   0.652   0.698   0.672   0.674   0.714
126   D         0.646   0.647   0.676   0.909   0.907   0.916   0.672   0.674   0.714
127   I        -2.073  -2.159  -2.081  -2.126  -2.214  -2.053  -1.946  -2.010  -1.838
128   V         0.646   0.647   0.676   0.437   0.445   0.515   0.672   0.674   0.714
129   T        -0.135  -0.128  -0.659  -0.055  -0.042  -0.869  -0.104  -0.099  -0.910
130   V         0.646   0.647   0.676   0.437   0.445   0.515   0.672   0.674   0.714
131   G         0.646   0.647   0.676   0.652   0.652   0.698   0.672   0.674   0.714
132   Q         0.646   0.647   0.676   0.805   0.805   0.828   0.672   0.674   0.714
133   C         0.646   0.647   0.676   0.950   0.949   0.951   0.672   0.674   0.714
134   R         0.646   0.647   0.676   0.526   0.526   0.590   0.672   0.674   0.714
135   P         0.646   0.647   0.676   0.750   0.752   0.781   0.672   0.674   0.714
136   I        -0.892  -0.886  -0.708  -1.006  -1.008  -0.725  -1.267  -1.269  -0.994
137   S         0.646   0.647   0.676   0.725   0.728   0.759   0.672   0.674   0.714
138   K         0.646   0.647   0.676   0.305   0.314   0.403   0.672   0.674   0.714
139   T         0.646   0.647   0.676   0.600   0.610   0.653   0.672   0.674   0.714
140   V         0.646   0.647   0.676   0.437   0.445   0.515   0.672   0.674   0.714
141   R         0.646   0.647   0.676   0.526   0.526   0.590   0.672   0.674   0.714
142   F         0.646   0.647   0.676   0.704   0.705   0.741   0.672   0.674   0.714
143   N         0.646   0.647   0.676   0.805   0.803   0.828   0.672   0.674   0.714
144   V         0.646   0.647   0.676   0.437   0.445   0.515   0.672   0.674   0.714
145   V        -0.135  -0.116  -0.655   0.126   0.138  -0.723  -0.104  -0.083  -0.904
146   K        -0.892  -0.886  -0.708  -1.476  -1.461  -1.118  -1.267  -1.269  -0.994
147   V         0.646   0.647   0.676   0.437   0.445   0.515   0.672   0.674   0.714
148   S        -2.418  -2.392  -2.087  -2.400  -2.373  -1.924  -2.237  -2.216  -1.844
149   A        -2.763  -2.699  -2.530  -2.727  -2.665  -2.390  -2.334  -2.295  -2.013
150   A        -2.548  -2.492  -2.525  -2.172  -2.124  -2.182  -2.140  -2.096  -2.009
151   A        -1.254  -1.182  -1.489  -1.210  -1.104  -1.647  -1.267  -1.176  -1.530
152   G        -0.693  -0.618  -0.689  -0.705  -0.600  -0.739  -0.931  -0.818  -0.961
153   K        -1.254  -1.154  -1.475  -1.414  -1.298  -1.665  -1.267  -1.165  -1.513
154   A        -1.729  -1.697  -1.504  -1.771  -1.737  -1.450  -1.849  -1.817  -1.548
155   N        -1.493  -1.475  -1.500  -1.332  -1.312  -1.448  -1.572  -1.545  -1.543
156   K         0.646   0.647   0.676   0.305   0.314   0.403   0.672   0.674   0.714
157   Q        -1.254  -1.361  -1.497  -1.063  -1.210  -1.559  -1.267  -1.390  -1.540
158   F         0.646   0.647   0.676   0.704   0.705   0.741   0.672   0.674   0.714
159   A        -2.763  -2.704  -2.524  -2.495  -2.446  -2.150  -2.334  -2.293  -2.009
160   K         0.646   0.647   0.676   0.305   0.314   0.403   0.672   0.674   0.714
161   F         0.646   0.647   0.676   0.704   0.705   0.741   0.672   0.674   0.714
* 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/P0CX47
Output conservation file - output/P0CX47
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
