1     M         1.203   1.264   1.330   1.489   1.548   1.645   1.270   1.351   1.456
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     W         1.203   1.264   1.330   1.565   1.646   1.713   1.270   1.351   1.456
6     L         0.476   0.579   0.262   0.196   0.350  -0.140   0.470   0.616   0.090
7     T         0.476   0.701   0.277   0.791   1.037   0.516   0.470   0.784   0.116
8     E        -0.073  -0.040   0.095   0.207   0.203   0.387  -0.445  -0.408  -0.212
9     A        -1.679  -1.505  -1.501  -1.269  -1.159  -1.082  -1.474  -1.256  -1.189
10    Q         1.203   1.264   1.330   1.517   1.601   1.670   1.270   1.351   1.456
11    K         0.476   0.598   0.267   0.907   1.054   0.625   0.470   0.642   0.099
12    F        -0.534  -0.571  -0.587  -0.829  -0.935  -0.823  -0.673  -0.752  -0.724
13    G         1.203   1.264   1.330   1.016   1.103   1.219   1.270   1.351   1.456
14    V         0.118   0.244   0.146   0.237   0.409   0.227  -0.102   0.096  -0.118
15    A        -1.137  -0.949  -1.077  -0.939  -0.775  -0.899  -1.131  -0.917  -0.992
16    F         0.476   0.311   0.233   0.282   0.109   0.020   0.470   0.206   0.039
17    T         0.476   0.294   0.247   0.828   0.632   0.545   0.470   0.179   0.063
18    F        -0.677  -0.679  -0.564  -0.806  -0.712  -0.567  -0.902  -0.836  -0.692
19    G         0.476   0.311   0.233   0.350   0.094  -0.061   0.470   0.206   0.039
20    G         1.203   1.264   1.330   1.016   1.103   1.219   1.270   1.351   1.456
21    F        -1.679  -1.568  -1.505  -1.858  -1.797  -1.549  -1.474  -1.332  -1.194
22    L        -0.134  -0.043   0.092  -0.888  -0.738  -0.497  -0.559  -0.414  -0.220
23    F         1.203   1.264   1.330   0.870   0.979   1.087   1.270   1.351   1.456
24    F        -0.868  -1.111  -1.087  -1.019  -1.402  -1.374  -0.788  -1.054  -0.997
25    L        -1.219  -0.960  -1.073  -1.712  -1.256  -1.445  -1.245  -0.927  -0.987
26    F        -0.868  -1.111  -1.087  -1.011  -1.379  -1.356  -0.788  -1.054  -0.997
27    G         1.203   1.264   1.330   1.016   1.103   1.219   1.270   1.351   1.456
28    I         0.476   0.294   0.247   0.380   0.200   0.103   0.470   0.179   0.063
29    F        -0.677  -0.697  -0.576  -0.913  -1.021  -0.790  -0.902  -0.863  -0.709
30    T        -0.868  -1.038  -1.077  -0.417  -0.755  -0.809  -0.788  -0.987  -0.986
31    F         1.203   1.264   1.330   0.870   0.979   1.087   1.270   1.351   1.456
32    F         1.203   1.264   1.330   0.870   0.979   1.087   1.270   1.351   1.456
33    D         1.203   1.264   1.330   1.484   1.559   1.641   1.270   1.351   1.456
34    R        -0.677  -0.687  -0.584  -0.519  -0.558  -0.439  -0.902  -0.849  -0.719
35    A         0.476   0.311   0.233   0.750   0.543   0.416   0.470   0.206   0.039
36    L        -0.216  -0.244  -0.477  -0.370  -0.383  -0.717  -0.216  -0.277  -0.570
37    L         0.476   0.579   0.262   0.292   0.433   0.093   0.470   0.616   0.090
38    A         0.476   0.311   0.233   0.747   0.534   0.409   0.470   0.206   0.039
39    L        -0.868  -0.908  -1.046  -0.949  -0.989  -1.166  -0.788  -0.827  -0.952
40    G         1.203   1.264   1.330   1.016   1.103   1.219   1.270   1.351   1.456
41    N         1.203   1.264   1.330   1.563   1.642   1.712   1.270   1.351   1.456
42    I        -0.333  -0.438  -0.549  -0.455  -0.699  -0.824  -0.372  -0.546  -0.668
43    L         1.203   1.264   1.330   0.849   0.941   1.069   1.270   1.351   1.456
44    F         0.412   0.153   0.184   0.083  -0.375  -0.324   0.374  -0.059  -0.049
45    L        -0.641  -0.549  -0.594  -0.988  -0.840  -0.876  -0.820  -0.726  -0.733
46    I        -0.333  -0.508  -0.559  -0.558  -0.910  -1.082  -0.372  -0.627  -0.682
47    G         1.203   1.264   1.330   1.042   1.151   1.242   1.270   1.351   1.456
48    V        -1.261  -1.231  -1.127  -1.469  -1.566  -1.468  -1.268  -1.198  -1.039
49    F        -1.787  -1.515  -1.511  -2.013  -1.696  -1.677  -1.567  -1.270  -1.199
50    L         0.412   0.153   0.184   0.209  -0.108  -0.007   0.374  -0.059  -0.049
51    I        -0.333  -0.244  -0.523  -0.413  -0.266  -0.695  -0.372  -0.242  -0.633
52    I         0.412   0.153   0.184   0.306   0.010   0.027   0.374  -0.059  -0.049
53    G         1.203   1.264   1.330   1.042   1.151   1.242   1.270   1.351   1.456
54    S        -0.641  -0.668  -0.579  -0.473  -0.649  -0.503  -0.820  -0.820  -0.709
55    Q        -0.333  -0.508  -0.559   0.242  -0.053  -0.103  -0.372  -0.627  -0.682
56    K         0.049   0.252   0.174   0.309   0.605   0.438  -0.223   0.109  -0.068
57    T         0.412   0.153   0.184   0.717   0.356   0.368   0.374  -0.059  -0.049
58    Y        -1.261  -1.035  -1.104  -1.419  -1.105  -1.106  -1.268  -1.019  -1.018
59    I        -1.787  -1.668  -1.532  -1.531  -1.310  -1.120  -1.567  -1.400  -1.215
60    F         1.203   1.264   1.330   0.843   0.931   1.063   1.270   1.351   1.456
61    F         1.203   1.264   1.330   0.843   0.931   1.063   1.270   1.351   1.456
62    T        -1.261  -1.262  -1.116  -1.031  -1.190  -0.909  -1.268  -1.215  -1.029
63    R         1.203   1.264   1.330   1.404   1.501   1.568   1.270   1.351   1.456
64    P        -0.333  -0.546  -0.567   0.110  -0.191  -0.231  -0.372  -0.671  -0.692
65    N        -1.137  -1.134  -1.100  -0.602  -0.626  -0.523  -1.131  -1.116  -1.014
66    K         0.476   0.311   0.233   0.891   0.684   0.535   0.470   0.206   0.039
67    R        -1.345  -1.327  -1.126  -1.197  -1.155  -0.907  -1.359  -1.275  -1.039
68    R        -0.216  -0.556  -0.537   0.172  -0.339  -0.382  -0.216  -0.664  -0.652
69    G         1.203   1.264   1.330   1.016   1.103   1.219   1.270   1.351   1.456
70    S        -0.134  -0.044   0.092  -0.105   0.015   0.209  -0.559  -0.414  -0.219
71    L        -0.677  -0.689  -0.559  -1.140  -1.032  -0.876  -0.902  -0.851  -0.688
72    F        -1.806  -1.623  -1.523  -1.670  -1.388  -1.316  -1.588  -1.367  -1.208
73    F         0.476   0.598   0.267   0.201   0.383  -0.128   0.470   0.642   0.099
74    L        -2.140  -1.764  -1.842  -2.481  -1.894  -1.956  -1.702  -1.319  -1.318
75    V        -1.679  -1.388  -1.501  -1.747  -1.270  -1.427  -1.474  -1.171  -1.191
76    G         1.203   1.264   1.330   1.016   1.103   1.219   1.270   1.351   1.456
77    A        -0.534  -0.483  -0.578  -0.817  -0.887  -0.910  -0.673  -0.672  -0.712
78    F        -0.677  -0.738  -0.588  -1.242  -1.279  -1.010  -0.902  -0.923  -0.725
79    L         0.476   0.598   0.267   0.292   0.453   0.100   0.470   0.642   0.099
80    I         0.476   0.311   0.233   0.392   0.248   0.113   0.470   0.206   0.039
81    L         1.203   1.264   1.330   0.865   0.968   1.082   1.270   1.351   1.456
82    L        -2.140  -2.036  -1.853  -2.203  -2.017  -1.701  -1.702  -1.546  -1.325
83    K        -0.216  -0.556  -0.537   0.345  -0.091  -0.092  -0.216  -0.664  -0.652
84    W        -1.137  -1.037  -1.090  -0.616  -0.582  -0.648  -1.131  -0.986  -1.003
85    T        -1.219  -0.874  -1.070  -0.860  -0.425  -0.648  -1.245  -0.838  -0.982
86    F        -0.216  -0.556  -0.537  -0.462  -1.019  -1.052  -0.216  -0.664  -0.652
87    L         0.118   0.317   0.189  -0.247   0.120  -0.184  -0.102   0.216  -0.040
88    G         1.203   1.264   1.330   1.016   1.103   1.219   1.270   1.351   1.456
89    F         1.203   1.264   1.330   0.870   0.979   1.087   1.270   1.351   1.456
90    I        -1.471  -1.523  -1.501  -1.463  -1.515  -1.540  -1.245  -1.280  -1.189
91    I        -0.677  -0.495  -0.567  -0.943  -0.622  -0.765  -0.902  -0.682  -0.702
92    E         1.203   1.264   1.330   1.563   1.650   1.712   1.270   1.351   1.456
93    S        -0.803  -0.799  -0.632  -0.715  -0.813  -0.542  -1.016  -0.992  -0.777
94    L        -1.137  -1.079  -1.077  -1.409  -1.219  -1.188  -1.131  -1.016  -0.987
95    G         1.203   1.264   1.330   1.016   1.103   1.219   1.270   1.351   1.456
96    I         0.476   0.311   0.233   0.314   0.113  -0.091   0.470   0.206   0.039
97    I        -1.679  -1.654  -1.520  -1.866  -1.833  -1.626  -1.474  -1.392  -1.206
98    G        -0.868  -1.111  -1.087  -0.750  -1.098  -1.013  -0.788  -1.054  -0.997
99    L         1.203   1.264   1.330   0.865   0.968   1.082   1.270   1.351   1.456
100   F         1.203   1.264   1.330   0.870   0.979   1.087   1.270   1.351   1.456
101   G         0.476   0.311   0.233   0.442   0.252   0.179   0.470   0.206   0.039
102   D         0.476   0.311   0.233   0.883   0.655   0.507   0.470   0.206   0.039
103   F         1.203   1.264   1.330   0.870   0.979   1.087   1.270   1.351   1.456
104   F        -0.216  -0.556  -0.537  -0.350  -0.817  -0.764  -0.216  -0.664  -0.652
105   G        -0.216  -0.319  -0.507  -0.152  -0.288  -0.492  -0.216  -0.359  -0.610
106   V        -1.219  -1.116  -1.098  -1.116  -1.024  -1.047  -1.245  -1.100  -1.012
107   I         1.203   1.264   1.330   0.980   1.119   1.186   1.270   1.351   1.456
108   V        -0.868  -1.098  -1.080  -0.591  -0.996  -1.077  -0.788  -1.042  -0.990
109   Q        -0.868  -1.111  -1.087  -0.289  -0.738  -0.730  -0.788  -1.054  -0.997
110   F         0.476   0.598   0.267   0.201   0.383  -0.128   0.470   0.642   0.099
111   L         0.476   0.294   0.247   0.268   0.056   0.014   0.470   0.179   0.063
112   R         1.203   1.264   1.330   1.405   1.500   1.569   1.270   1.351   1.456
113   S        -0.216  -0.556  -0.537   0.244  -0.200  -0.176  -0.216  -0.664  -0.652
114   M        -1.137  -0.999  -1.075  -1.165  -0.954  -1.075  -1.131  -0.950  -0.988
115   P         1.203   1.264   1.330   1.400   1.488   1.565   1.270   1.351   1.456
116   I        -0.885  -0.793  -0.625  -0.885  -0.703  -0.487  -1.131  -0.984  -0.769
117   I         1.203   1.264   1.330   0.980   1.119   1.186   1.270   1.351   1.456
118   G         1.203   1.264   1.330   1.016   1.103   1.219   1.270   1.351   1.456
119   P        -0.025   0.086   0.117   0.159   0.312   0.330  -0.356  -0.177  -0.171
120   I        -0.748  -0.642  -0.610  -1.099  -0.941  -0.904  -0.966  -0.806  -0.750
121   L         1.203   1.264   1.330   0.868   0.974   1.085   1.270   1.351   1.456
122   S         0.334   0.275   0.157   0.653   0.576   0.351   0.254   0.148  -0.099
123   H         1.203   1.264   1.330   1.588   1.673   1.734   1.270   1.351   1.456
124   P         1.203   1.264   1.330   1.402   1.492   1.567   1.270   1.351   1.456
125   A        -1.643  -1.548  -1.521  -1.194  -1.065  -1.058  -1.418  -1.299  -1.205
126   I         0.049   0.208   0.132  -0.227   0.033  -0.092  -0.223   0.035  -0.144
127   A         0.412   0.143   0.184   0.583   0.092   0.150   0.374  -0.076  -0.049
128   P         0.476   0.294   0.247   0.810   0.585   0.486   0.470   0.179   0.063
129   I        -1.806  -1.762  -1.529  -1.546  -1.382  -1.117  -1.588  -1.467  -1.213
130   V        -0.677  -0.545  -0.568  -0.943  -0.728  -0.798  -0.902  -0.719  -0.702
131   D         1.203   1.264   1.330   1.484   1.559   1.641   1.270   1.351   1.456
132   K         0.118   0.401   0.219   0.368   0.756   0.478  -0.102   0.351   0.014
133   L        -0.534  -0.540  -0.535  -0.878  -0.816  -0.828  -0.673  -0.643  -0.651
134   A        -0.216  -0.556  -0.537   0.114  -0.400  -0.415  -0.216  -0.664  -0.652
135   G        -0.216  -0.556  -0.537  -0.160  -0.613  -0.548  -0.216  -0.664  -0.652
136   V        -0.534  -0.502  -0.543  -0.397  -0.275  -0.401  -0.673  -0.592  -0.661
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   R        -1.679  -1.695  -1.523  -1.040  -1.085  -0.851  -1.474  -1.419  -1.207
142   V        -1.679  -1.704  -1.531  -1.255  -1.234  -1.065  -1.474  -1.424  -1.214
143   L         0.476   0.311   0.233   0.275   0.087   0.012   0.470   0.206   0.039
144   P         1.203   1.264   1.330   1.400   1.488   1.565   1.270   1.351   1.456
145   V         1.203   1.264   1.330   1.314   1.401   1.487   1.270   1.351   1.456
* 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/Q03554
Output conservation file - output/Q03554
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
