1     M         1.321   1.335   1.361   1.459   1.483   1.515   1.392   1.411   1.449
2     -        -0.854  -0.835  -0.755  -0.970  -0.913  -0.816  -0.942  -0.913  -0.807
3     -        -0.854  -0.835  -0.755  -0.848  -0.801  -0.699  -0.942  -0.913  -0.807
4     -         0.061   0.016   0.050  -0.245  -0.342  -0.276  -0.164  -0.243  -0.200
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -         0.061   0.016   0.050   0.092   0.011   0.083  -0.164  -0.243  -0.200
7     -        -0.854  -0.835  -0.755  -0.957  -0.882  -0.804  -0.942  -0.913  -0.807
8     -         0.061   0.016   0.050  -0.158  -0.257  -0.181  -0.164  -0.243  -0.200
9     -         1.321   1.335   1.361   1.212   1.253   1.278   1.392   1.411   1.449
10    -         1.321   1.335   1.361   1.355   1.364   1.415   1.392   1.411   1.449
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    L         0.061  -0.002   0.042  -0.173  -0.276  -0.193  -0.164  -0.274  -0.215
26    N        -0.854  -0.824  -0.755  -0.740  -0.703  -0.596  -0.942  -0.900  -0.807
27    P        -0.768  -0.803  -0.738  -0.820  -0.873  -0.797  -0.849  -0.879  -0.787
28    S        -1.317  -1.351  -1.297  -1.064  -1.147  -1.054  -1.129  -1.157  -1.077
29    K        -0.768  -0.736  -0.727  -0.991  -0.938  -0.935  -0.849  -0.809  -0.775
30    Y         1.321   1.335   1.361   1.386   1.406   1.445   1.392   1.411   1.449
31    Q        -0.768  -0.803  -0.738  -0.646  -0.716  -0.609  -0.849  -0.879  -0.787
32    D         1.321   1.335   1.361   1.299   1.308   1.361   1.392   1.411   1.449
33    T        -0.561  -0.453  -0.662  -0.499  -0.361  -0.624  -0.569  -0.427  -0.691
34    R        -0.012   0.040   0.049  -0.310  -0.208  -0.204  -0.289  -0.201  -0.202
35    T         1.321   1.335   1.361   1.398   1.423   1.456   1.392   1.411   1.449
36    W        -0.768  -0.772  -0.723  -0.498  -0.518  -0.435  -0.849  -0.843  -0.770
37    K        -0.768  -0.724  -0.721  -0.833  -0.711  -0.717  -0.849  -0.793  -0.767
38    M         0.330   0.303   0.157   0.521   0.479   0.238   0.271   0.229  -0.018
39    T         0.330   0.237   0.147   0.482   0.353   0.203   0.271   0.126  -0.035
40    P         1.321   1.335   1.361   1.236   1.252   1.301   1.392   1.411   1.449
41    A         1.321   1.335   1.361   1.336   1.380   1.397   1.392   1.411   1.449
42    M        -0.012   0.040   0.059  -0.277  -0.207  -0.160  -0.289  -0.201  -0.186
43    I        -0.561  -0.547  -0.675  -0.495  -0.486  -0.723  -0.569  -0.549  -0.708
44    R         1.321   1.335   1.361   1.423   1.435   1.480   1.392   1.411   1.449
45    A        -0.012  -0.000   0.042  -0.095  -0.065  -0.011  -0.289  -0.271  -0.214
46    R         1.321   1.335   1.361   1.423   1.435   1.480   1.392   1.411   1.449
47    K        -1.317  -1.296  -1.289  -1.247  -1.192  -1.210  -1.129  -1.104  -1.070
48    P         1.321   1.335   1.361   1.236   1.252   1.301   1.392   1.411   1.449
49    F         1.321   1.335   1.361   1.435   1.449   1.492   1.392   1.411   1.449
50    F         1.321   1.335   1.361   1.435   1.449   1.492   1.392   1.411   1.449
51    K        -1.317  -1.351  -1.297  -1.253  -1.243  -1.160  -1.129  -1.157  -1.077
52    G        -0.561  -0.453  -0.662  -0.472  -0.312  -0.676  -0.569  -0.427  -0.691
53    N         1.321   1.335   1.361   1.567   1.591   1.619   1.392   1.411   1.449
54    M        -0.561  -0.548  -0.659  -0.433  -0.415  -0.636  -0.569  -0.549  -0.688
55    L        -0.768  -0.736  -0.727  -0.918  -0.895  -0.837  -0.849  -0.809  -0.775
56    G        -0.012  -0.033   0.028  -0.134  -0.188  -0.090  -0.289  -0.328  -0.239
57    L         1.321   1.335   1.361   1.146   1.167   1.215   1.392   1.411   1.449
58    T        -1.317  -1.265  -1.267  -1.157  -1.078  -1.079  -1.129  -1.069  -1.049
59    L        -1.317  -1.351  -1.278  -1.396  -1.452  -1.314  -1.129  -1.157  -1.059
60    L        -0.561  -0.547  -0.675  -0.640  -0.619  -0.791  -0.569  -0.549  -0.708
61    L        -0.768  -0.772  -0.723  -0.909  -0.893  -0.794  -0.849  -0.843  -0.770
62    G        -0.012  -0.000   0.042  -0.050  -0.044   0.029  -0.289  -0.271  -0.214
63    V        -0.768  -0.803  -0.738  -0.684  -0.751  -0.636  -0.849  -0.879  -0.787
64    T        -0.768  -0.803  -0.738  -0.842  -0.896  -0.771  -0.849  -0.879  -0.787
65    G        -0.768  -0.803  -0.738  -0.963  -1.032  -0.908  -0.849  -0.879  -0.787
66    S        -1.317  -1.265  -1.267  -1.152  -1.088  -1.085  -1.129  -1.069  -1.049
67    V        -0.012  -0.019   0.032  -0.016  -0.047   0.031  -0.289  -0.304  -0.232
68    Y         1.321   1.335   1.361   1.386   1.406   1.445   1.392   1.411   1.449
69    Y        -1.317  -1.296  -1.289  -1.374  -1.366  -1.300  -1.129  -1.104  -1.070
70    Y         1.321   1.335   1.361   1.386   1.406   1.445   1.392   1.411   1.449
71    T         1.321   1.335   1.361   1.398   1.423   1.456   1.392   1.411   1.449
72    Y        -1.317  -1.351  -1.297  -1.093  -1.158  -1.056  -1.129  -1.157  -1.077
73    H        -1.317  -1.296  -1.267  -1.336  -1.304  -1.235  -1.129  -1.103  -1.049
74    F        -1.317  -1.335  -1.271  -1.167  -1.197  -1.119  -1.129  -1.142  -1.053
75    L         0.330   0.303   0.157   0.228   0.188  -0.014   0.271   0.229  -0.018
76    H        -1.866  -1.844  -1.740  -1.404  -1.412  -1.234  -1.409  -1.382  -1.258
77    K        -0.561  -0.659  -0.680  -0.698  -0.824  -0.873  -0.569  -0.692  -0.715
78    D         1.321   1.335   1.361   1.299   1.308   1.361   1.392   1.411   1.449
79    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    D         0.330   0.385   0.171   0.370   0.434   0.130   0.271   0.355   0.006
81    F         0.330   0.303   0.157   0.437   0.381   0.115   0.271   0.229  -0.018
82    A        -0.768  -0.724  -0.721  -0.777  -0.711  -0.682  -0.849  -0.793  -0.767
83    D         1.321   1.335   1.361   1.299   1.308   1.361   1.392   1.411   1.449
84    V        -0.012  -0.000   0.042  -0.016  -0.007   0.054  -0.289  -0.271  -0.214
85    P         1.321   1.335   1.361   1.236   1.252   1.301   1.392   1.411   1.449
86    I         1.321   1.335   1.361   1.398   1.414   1.456   1.392   1.411   1.449
87    P         1.321   1.335   1.361   1.236   1.252   1.301   1.392   1.411   1.449
88    P         1.321   1.335   1.361   1.236   1.252   1.301   1.392   1.411   1.449
89    I         0.330   0.237   0.147   0.400   0.236   0.062   0.271   0.126  -0.035
90    D        -0.561  -0.547  -0.675  -0.499  -0.485  -0.675  -0.569  -0.549  -0.708
91    P        -0.768  -0.736  -0.727  -0.940  -0.920  -0.857  -0.849  -0.809  -0.775
92    Q        -1.317  -1.217  -1.263  -1.227  -1.056  -1.165  -1.129  -1.018  -1.046
93    E         1.321   1.335   1.361   1.423   1.452   1.480   1.392   1.411   1.449
94    L         0.330   0.237   0.147   0.212   0.071  -0.056   0.271   0.126  -0.035
95    E        -1.317  -1.351  -1.297  -1.212  -1.263  -1.209  -1.129  -1.157  -1.077
96    A        -0.561  -0.453  -0.662  -0.636  -0.445  -0.760  -0.569  -0.427  -0.691
97    L         1.321   1.335   1.361   1.146   1.167   1.215   1.392   1.411   1.449
98    K         0.330   0.237   0.147   0.238   0.149  -0.002   0.271   0.126  -0.035
99    K        -0.561  -0.659  -0.680  -0.719  -0.835  -0.903  -0.569  -0.692  -0.715
100   E         0.330   0.237   0.147   0.422   0.282   0.079   0.271   0.126  -0.035
101   Y         1.321   1.335   1.361   1.386   1.406   1.445   1.392   1.411   1.449
102   E         0.330   0.237   0.147   0.506   0.380   0.225   0.271   0.126  -0.035
103   A        -1.317  -1.265  -1.267  -1.299  -1.220  -1.228  -1.129  -1.069  -1.049
104   K        -1.317  -1.351  -1.278  -1.347  -1.373  -1.257  -1.129  -1.157  -1.059
105   K         0.330   0.237   0.147   0.222   0.131  -0.029   0.271   0.126  -0.035
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   K        -0.738  -0.733  -0.715  -0.829  -0.824  -0.762  -0.796  -0.787  -0.758
111   A        -0.738  -0.733  -0.715  -0.842  -0.835  -0.825  -0.796  -0.787  -0.758
* 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/Q3E7B2
Output conservation file - output/Q3E7B2
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
