1     M         1.183   1.232   1.290   1.301   1.343   1.459   1.274   1.345   1.423
2     S        -0.569  -0.525  -0.497  -0.841  -0.780  -0.732  -0.794  -0.718  -0.666
3     N        -0.463  -0.439  -0.485  -0.511  -0.484  -0.585  -0.621  -0.584  -0.646
4     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     D        -0.196  -0.242  -0.453  -0.080  -0.135  -0.445  -0.245  -0.305  -0.601
7     R        -1.844  -1.804  -1.679  -1.717  -1.698  -1.503  -1.488  -1.418  -1.244
8     M         0.472   0.464   0.246   0.650   0.646   0.270   0.445   0.425   0.025
9     D        -0.472  -0.427  -0.482  -0.644  -0.564  -0.643  -0.659  -0.576  -0.646
10    V        -0.472  -0.476  -0.501  -0.553  -0.577  -0.655  -0.659  -0.654  -0.670
11    D         1.183   1.232   1.290   1.146   1.223   1.312   1.274   1.345   1.423
12    E        -1.120  -1.109  -0.996  -1.245  -1.234  -1.055  -1.170  -1.128  -0.965
13    D        -1.920  -1.846  -1.695  -1.890  -1.783  -1.566  -1.545  -1.447  -1.256
14    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    S        -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    Q         0.080   0.121   0.157  -0.169  -0.113  -0.055  -0.230  -0.173  -0.143
19    N        -1.920  -1.849  -1.695  -1.862  -1.769  -1.539  -1.545  -1.450  -1.256
20    I        -1.920  -1.849  -1.695  -1.793  -1.707  -1.474  -1.545  -1.450  -1.256
21    A        -0.569  -0.503  -0.502  -0.730  -0.639  -0.649  -0.794  -0.698  -0.673
22    Q         0.402   0.466   0.254   0.326   0.419   0.106   0.334   0.430   0.040
23    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    P        -1.124  -1.042  -0.993  -1.109  -0.984  -0.931  -1.162  -1.050  -0.961
30    V        -0.644  -0.583  -0.519  -0.962  -0.883  -0.754  -0.891  -0.801  -0.694
31    E        -1.120  -1.068  -1.002  -1.295  -1.217  -1.081  -1.170  -1.087  -0.970
32    T        -1.372  -1.297  -1.347  -1.202  -1.116  -1.202  -1.212  -1.115  -1.111
33    K        -1.029  -0.959  -0.976  -1.071  -0.985  -1.017  -1.074  -0.978  -0.946
34    K         0.472   0.456   0.245   0.502   0.490   0.164   0.445   0.413   0.023
35    K        -0.556  -0.475  -0.495  -0.673  -0.552  -0.542  -0.798  -0.684  -0.664
36    R        -0.505  -0.469  -0.477  -0.613  -0.490  -0.569  -0.735  -0.681  -0.645
37    F        -0.091  -0.289  -0.423   0.189  -0.127  -0.308  -0.101  -0.390  -0.559
38    E        -0.091  -0.163  -0.390  -0.053  -0.256  -0.485  -0.101  -0.241  -0.513
39    I         0.037   0.137   0.143  -0.162  -0.010  -0.011  -0.312  -0.143  -0.170
40    K         0.530   0.571   0.266   0.558   0.619   0.180   0.534   0.592   0.061
41    K         1.183   1.232   1.290   1.125   1.198   1.292   1.274   1.345   1.423
42    W         1.183   1.232   1.290   1.202   1.310   1.365   1.274   1.345   1.423
43    T        -0.376  -0.438  -0.489  -0.346  -0.467  -0.552  -0.524  -0.633  -0.656
44    A         1.183   1.232   1.290   1.046   1.079   1.218   1.274   1.345   1.423
45    V         1.183   1.232   1.290   1.226   1.260   1.388   1.274   1.345   1.423
46    A         1.183   1.232   1.290   1.046   1.079   1.218   1.274   1.345   1.423
47    F        -0.091  -0.285  -0.424   0.191  -0.103  -0.307  -0.101  -0.385  -0.561
48    W         1.183   1.232   1.290   1.202   1.310   1.365   1.274   1.345   1.423
49    S        -0.091  -0.285  -0.424   0.136  -0.106  -0.349  -0.101  -0.385  -0.561
50    W         1.183   1.232   1.290   1.202   1.310   1.365   1.274   1.345   1.423
51    D         1.183   1.232   1.290   1.149   1.208   1.315   1.274   1.345   1.423
52    I        -0.091  -0.214  -0.413   0.063  -0.104  -0.377  -0.101  -0.300  -0.545
53    A        -1.818  -1.777  -1.680  -1.747  -1.678  -1.521  -1.475  -1.403  -1.245
54    V        -0.091  -0.214  -0.413   0.064  -0.212  -0.460  -0.101  -0.300  -0.545
55    D         0.037   0.137   0.143  -0.254  -0.118  -0.114  -0.312  -0.143  -0.170
56    N        -0.376  -0.506  -0.475  -0.419  -0.578  -0.581  -0.524  -0.678  -0.637
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    C         1.183   1.232   1.290   1.083   1.168   1.252   1.274   1.345   1.423
59    A         0.530   0.303   0.270   0.492   0.151   0.151   0.534   0.156   0.068
60    I         1.183   1.232   1.290   1.167   1.247   1.332   1.274   1.345   1.423
61    C         1.183   1.232   1.290   1.083   1.168   1.252   1.274   1.345   1.423
62    R        -0.091  -0.289  -0.423   0.130  -0.053  -0.385  -0.101  -0.390  -0.559
63    N         0.530   0.303   0.270   0.574   0.298   0.197   0.534   0.156   0.068
64    H         1.183   1.232   1.290   1.255   1.337   1.415   1.274   1.345   1.423
65    I        -0.376  -0.466  -0.472  -0.344  -0.438  -0.466  -0.524  -0.622  -0.630
66    M         0.530   0.303   0.270   0.721   0.355   0.309   0.534   0.156   0.068
67    E        -0.091  -0.285  -0.424  -0.041  -0.366  -0.512  -0.101  -0.385  -0.561
68    P        -0.091  -0.285  -0.424   0.134  -0.127  -0.353  -0.101  -0.385  -0.561
69    C         1.183   1.232   1.290   1.083   1.168   1.252   1.274   1.345   1.423
70    I        -0.091  -0.296  -0.423   0.043  -0.250  -0.440  -0.101  -0.398  -0.560
71    E        -0.676  -0.844  -0.939  -0.618  -0.916  -1.023  -0.629  -0.835  -0.903
72    C         1.183   1.232   1.290   1.083   1.168   1.252   1.274   1.345   1.423
73    Q         0.530   0.303   0.270   0.695   0.379   0.279   0.534   0.156   0.068
74    P        -0.918  -1.036  -0.980  -0.826  -0.968  -0.902  -0.946  -1.057  -0.949
75    K        -0.472  -0.402  -0.466  -0.641  -0.520  -0.654  -0.659  -0.539  -0.620
76    A         0.147   0.181   0.159  -0.089  -0.044  -0.082  -0.107  -0.063  -0.140
77    M        -1.372  -1.395  -1.372  -1.112  -1.165  -1.152  -1.212  -1.209  -1.133
78    T        -1.501  -1.467  -1.375  -1.318  -1.265  -1.139  -1.350  -1.282  -1.135
79    D        -0.569  -0.523  -0.495  -0.818  -0.743  -0.723  -0.794  -0.708  -0.660
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    T        -1.105  -1.057  -0.995  -1.127  -1.062  -0.979  -1.158  -1.085  -0.966
82    D        -2.118  -2.046  -1.951  -1.978  -1.869  -1.738  -1.581  -1.489  -1.332
83    N        -1.818  -1.801  -1.684  -1.838  -1.833  -1.625  -1.475  -1.418  -1.248
84    E         0.530   0.578   0.269   0.503   0.519   0.111   0.534   0.604   0.066
85    C         1.183   1.232   1.290   1.083   1.168   1.252   1.274   1.345   1.423
86    V        -1.405  -1.435  -1.371  -1.317  -1.368  -1.269  -1.264  -1.258  -1.132
87    A        -0.918  -0.977  -0.974  -0.967  -1.071  -0.995  -0.946  -1.004  -0.943
88    A         0.530   0.303   0.270   0.488   0.163   0.140   0.534   0.156   0.068
89    W         0.530   0.303   0.270   0.637   0.356   0.259   0.534   0.156   0.068
90    G         1.183   1.232   1.290   1.324   1.387   1.481   1.274   1.345   1.423
91    V        -1.518  -1.382  -1.359  -1.514  -1.385  -1.279  -1.369  -1.212  -1.124
92    C         1.183   1.232   1.290   1.083   1.168   1.252   1.274   1.345   1.423
93    N         0.530   0.303   0.270   0.588   0.335   0.236   0.534   0.156   0.068
94    H         1.183   1.232   1.290   1.255   1.337   1.415   1.274   1.345   1.423
95    A         0.530   0.303   0.270   0.465   0.115   0.078   0.534   0.156   0.068
96    F         1.183   1.232   1.290   1.307   1.364   1.465   1.274   1.345   1.423
97    H         1.183   1.232   1.290   1.255   1.337   1.415   1.274   1.345   1.423
98    L        -0.618  -0.626  -0.536  -0.571  -0.588  -0.469  -0.841  -0.849  -0.715
99    H         1.183   1.232   1.290   1.260   1.333   1.420   1.274   1.345   1.423
100   C         1.183   1.232   1.290   1.094   1.170   1.263   1.274   1.345   1.423
101   I         1.183   1.232   1.290   1.159   1.233   1.324   1.274   1.345   1.423
102   N        -1.372  -1.352  -1.365  -1.315  -1.292  -1.319  -1.212  -1.167  -1.127
103   K        -0.472  -0.402  -0.466  -0.479  -0.347  -0.468  -0.659  -0.539  -0.620
104   W         1.183   1.232   1.290   1.203   1.277   1.366   1.274   1.345   1.423
105   I         0.000   0.069   0.156  -0.160  -0.048   0.082  -0.383  -0.274  -0.146
106   K         0.472   0.456   0.245   0.482   0.465   0.113   0.445   0.413   0.023
107   T         0.000   0.043   0.135  -0.157  -0.102   0.044  -0.383  -0.322  -0.184
108   R         1.183   1.232   1.290   1.260   1.335   1.420   1.274   1.345   1.423
109   D         0.147   0.280   0.228  -0.022   0.194   0.087  -0.107   0.116  -0.008
110   A        -0.556  -0.523  -0.499  -0.778  -0.706  -0.640  -0.798  -0.732  -0.668
111   C         1.183   1.232   1.290   1.094   1.170   1.263   1.274   1.345   1.423
112   P         1.183   1.232   1.290   1.254   1.329   1.414   1.274   1.345   1.423
113   L         1.183   1.232   1.290   1.303   1.377   1.461   1.274   1.345   1.423
114   D         1.183   1.232   1.290   1.159   1.238   1.324   1.274   1.345   1.423
115   N         0.147   0.184   0.159   0.012   0.062   0.005  -0.107  -0.056  -0.139
116   Q        -1.158  -1.077  -0.998  -1.192  -1.089  -0.954  -1.212  -1.103  -0.967
117   P        -1.029  -0.994  -0.996  -1.103  -1.069  -1.092  -1.074  -1.015  -0.966
118   W         1.183   1.232   1.290   1.203   1.277   1.366   1.274   1.345   1.423
119   Q        -1.844  -1.716  -1.678  -1.759  -1.605  -1.502  -1.488  -1.346  -1.244
120   L        -0.686  -0.637  -0.540  -0.610  -0.551  -0.395  -0.936  -0.863  -0.719
121   A        -0.556  -0.530  -0.506  -0.745  -0.696  -0.620  -0.798  -0.743  -0.677
122   R         0.147   0.230   0.169   0.091   0.225   0.066  -0.107   0.027  -0.121
123   C        -1.029  -0.957  -0.995  -0.941  -0.836  -0.829  -1.074  -0.983  -0.965
124   G         1.183   1.232   1.290   1.347   1.417   1.502   1.274   1.345   1.423
125   R        -1.501  -1.499  -1.379  -1.450  -1.447  -1.268  -1.350  -1.307  -1.139
* 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/Q08273
Output conservation file - output/Q08273
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
