1     M         1.527   1.533   1.612   1.700   1.712   1.826   1.629   1.639   1.754
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     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     T        -0.673  -0.594  -0.674  -0.519  -0.393  -0.553  -0.681  -0.587  -0.670
9     K        -0.735  -0.695  -0.713  -0.753  -0.694  -0.731  -0.776  -0.738  -0.722
10    A         0.117   0.043  -0.105   0.092  -0.012  -0.222   0.073  -0.033  -0.252
11    L         1.527   1.533   1.612   1.414   1.429   1.548   1.629   1.639   1.754
12    N        -1.568  -1.557  -1.466  -1.342  -1.334  -1.186  -1.200  -1.189  -1.062
13    A         1.527   1.533   1.612   1.374   1.387   1.510   1.629   1.639   1.754
14    Y         1.527   1.533   1.612   1.731   1.738   1.856   1.629   1.639   1.754
15    R         0.800   0.877   0.645   0.806   0.910   0.559   0.780   0.896   0.491
16    H         0.317   0.338   0.426   0.225   0.254   0.392  -0.068  -0.034   0.083
17    G        -0.735  -0.799  -0.743  -0.863  -0.963  -0.877  -0.776  -0.839  -0.750
18    L         0.800   0.760   0.622   0.789   0.747   0.566   0.780   0.715   0.450
19    R         1.527   1.533   1.612   1.492   1.502   1.624   1.629   1.639   1.754
20    A         1.527   1.533   1.612   1.374   1.387   1.510   1.629   1.639   1.754
21    T         0.317   0.314   0.411   0.060   0.040   0.182  -0.068  -0.081   0.054
22    R         0.117   0.043  -0.105   0.163   0.057  -0.199   0.073  -0.033  -0.252
23    I         0.117   0.080  -0.100   0.300   0.230  -0.041   0.073   0.015  -0.245
24    A         1.527   1.533   1.612   1.374   1.387   1.510   1.629   1.639   1.754
25    F         1.527   1.533   1.612   1.688   1.697   1.814   1.629   1.639   1.754
26    R        -0.384  -0.357  -0.276  -0.732  -0.691  -0.557  -0.634  -0.598  -0.494
27    N        -0.735  -0.723  -0.715  -0.735  -0.728  -0.695  -0.776  -0.766  -0.724
28    D         1.527   1.533   1.612   1.537   1.544   1.667   1.629   1.639   1.754
29    A        -0.735  -0.747  -0.724  -0.828  -0.825  -0.789  -0.776  -0.788  -0.732
30    E        -0.735  -0.747  -0.720  -0.651  -0.657  -0.609  -0.776  -0.787  -0.726
31    V        -0.516  -0.513  -0.641  -0.236  -0.240  -0.410  -0.493  -0.490  -0.632
32    L         1.527   1.533   1.612   1.414   1.429   1.548   1.629   1.639   1.754
33    L        -1.218  -1.249  -1.146  -1.135  -1.167  -1.013  -1.058  -1.079  -0.943
34    A         0.800   0.713   0.609   0.717   0.603   0.444   0.780   0.638   0.427
35    A         1.527   1.533   1.612   1.374   1.387   1.510   1.629   1.639   1.754
36    R         0.117  -0.000  -0.123   0.200   0.029  -0.161   0.073  -0.093  -0.278
37    A        -1.085  -1.068  -1.109  -1.072  -1.048  -1.091  -0.917  -0.899  -0.908
38    K        -1.085  -1.087  -1.106  -0.995  -0.995  -1.049  -0.917  -0.923  -0.905
39    M        -0.252  -0.230  -0.214  -0.224  -0.191  -0.172  -0.493  -0.462  -0.417
40    R         0.467   0.485   0.488   0.262   0.294   0.255   0.214   0.243   0.202
41    S        -1.218  -1.188  -1.143  -1.312  -1.280  -1.178  -1.058  -1.030  -0.941
42    G         0.800   0.844   0.637   0.887   0.936   0.675   0.780   0.847   0.477
43    M        -0.252  -0.230  -0.214  -0.130  -0.094  -0.055  -0.493  -0.462  -0.417
44    L        -0.867  -0.833  -0.762  -0.991  -0.947  -0.834  -0.917  -0.884  -0.772
45    C        -0.673  -0.639  -0.699  -0.538  -0.495  -0.575  -0.681  -0.642  -0.698
46    P        -0.166  -0.196  -0.192  -0.123  -0.164  -0.159  -0.351  -0.380  -0.382
47    P        -1.085  -1.143  -1.127  -0.837  -0.943  -0.966  -0.917  -0.975  -0.925
48    D        -0.252  -0.293  -0.218  -0.411  -0.475  -0.362  -0.493  -0.532  -0.426
49    -         0.531   0.515   0.507   0.431   0.406   0.378   0.329   0.297   0.238
50    -        -0.928  -0.907  -0.791  -1.019  -0.970  -0.810  -0.970  -0.946  -0.798
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    P        -1.568  -1.567  -1.472  -1.385  -1.426  -1.283  -1.200  -1.197  -1.067
53    K        -1.218  -1.136  -1.139  -1.225  -1.108  -1.104  -1.058  -0.986  -0.937
54    L        -0.867  -0.819  -0.760  -0.999  -0.911  -0.837  -0.917  -0.872  -0.770
55    T        -1.085  -1.095  -1.116  -0.850  -0.872  -0.916  -0.917  -0.928  -0.914
56    T        -1.218  -1.211  -1.141  -1.006  -0.997  -0.885  -1.058  -1.049  -0.939
57    E        -1.568  -1.555  -1.458  -1.539  -1.551  -1.384  -1.200  -1.187  -1.056
58    D        -1.085  -1.107  -1.103  -0.912  -0.943  -0.934  -0.917  -0.941  -0.902
59    Q        -0.252  -0.292  -0.232  -0.521  -0.570  -0.472  -0.493  -0.530  -0.441
60    I         0.117   0.043  -0.105   0.315   0.202  -0.039   0.073  -0.033  -0.252
61    Q        -1.085  -1.124  -1.108  -1.093  -1.165  -1.183  -0.917  -0.957  -0.907
62    H        -0.166  -0.120  -0.195  -0.155  -0.080  -0.242  -0.351  -0.293  -0.384
63    L        -0.735  -0.793  -0.725  -0.769  -0.842  -0.738  -0.776  -0.831  -0.733
64    E         0.317   0.338   0.426   0.092   0.128   0.262  -0.068  -0.034   0.083
65    D        -0.166  -0.196  -0.192  -0.239  -0.275  -0.280  -0.351  -0.380  -0.382
66    V         1.527   1.533   1.612   1.600   1.602   1.729   1.629   1.639   1.754
67    A         0.800   0.824   0.635   0.744   0.777   0.539   0.780   0.815   0.475
68    V        -1.568  -1.557  -1.466  -1.349  -1.323  -1.192  -1.200  -1.189  -1.062
69    F         0.800   0.713   0.609   1.044   0.927   0.766   0.780   0.638   0.427
70    L         1.527   1.533   1.612   1.414   1.429   1.548   1.629   1.639   1.754
71    R        -0.166  -0.094  -0.174  -0.254  -0.146  -0.280  -0.351  -0.262  -0.355
72    R        -1.218  -1.244  -1.142  -1.220  -1.238  -1.094  -1.058  -1.075  -0.939
73    N         0.800   0.713   0.609   0.892   0.772   0.609   0.780   0.638   0.427
74    L        -0.384  -0.337  -0.256  -0.519  -0.433  -0.321  -0.634  -0.571  -0.466
75    V         1.527   1.533   1.612   1.600   1.602   1.729   1.629   1.639   1.754
76    Q         1.527   1.533   1.612   1.511   1.523   1.643   1.629   1.639   1.754
77    G         1.527   1.533   1.612   1.518   1.522   1.649   1.629   1.639   1.754
78    K        -0.867  -0.868  -0.768  -1.123  -1.110  -0.958  -0.917  -0.912  -0.777
79    K         0.800   0.844   0.637   0.673   0.731   0.445   0.780   0.847   0.477
80    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    T        -0.828  -0.826  -0.763  -0.793  -0.777  -0.679  -0.874  -0.870  -0.771
86    K        -1.218  -1.159  -1.136  -1.342  -1.240  -1.200  -1.058  -1.004  -0.935
87    E        -0.384  -0.370  -0.288  -0.584  -0.567  -0.439  -0.634  -0.617  -0.508
88    P        -0.735  -0.680  -0.715  -0.725  -0.648  -0.673  -0.776  -0.713  -0.722
89    R         0.117   0.122  -0.084   0.048   0.057  -0.232   0.073   0.077  -0.222
90    Y         1.527   1.533   1.612   1.731   1.738   1.856   1.629   1.639   1.754
91    H        -0.735  -0.799  -0.743  -0.567  -0.676  -0.623  -0.776  -0.839  -0.750
92    L         1.527   1.533   1.612   1.414   1.429   1.548   1.629   1.639   1.754
93    N         0.117   0.144  -0.081   0.209   0.246  -0.123   0.073   0.107  -0.218
94    I        -0.166  -0.220  -0.207  -0.090  -0.171  -0.171  -0.351  -0.416  -0.401
95    H         1.527   1.533   1.612   1.719   1.728   1.844   1.629   1.639   1.754
96    K        -0.166  -0.185  -0.203  -0.414  -0.437  -0.458  -0.351  -0.372  -0.396
97    D         0.117   0.142  -0.100   0.196   0.230  -0.170   0.073   0.107  -0.245
98    T         0.117   0.102  -0.099   0.355   0.334   0.053   0.073   0.044  -0.243
99    E         1.527   1.533   1.612   1.505   1.514   1.636   1.629   1.639   1.754
100   L         0.117  -0.000  -0.123   0.147  -0.003  -0.186   0.073  -0.093  -0.278
101   G         1.527   1.533   1.612   1.518   1.522   1.649   1.629   1.639   1.754
102   D         1.527   1.533   1.612   1.537   1.544   1.667   1.629   1.639   1.754
103   N         1.527   1.533   1.612   1.550   1.556   1.680   1.629   1.639   1.754
104   E         0.800   0.760   0.622   0.852   0.799   0.596   0.780   0.715   0.450
105   T         0.467   0.458   0.464   0.498   0.482   0.473   0.214   0.193   0.157
106   I         1.527   1.533   1.612   1.619   1.628   1.747   1.629   1.639   1.754
107   A         0.800   0.852   0.638   0.653   0.723   0.409   0.780   0.858   0.479
108   D        -1.085  -1.107  -1.103  -0.943  -0.978  -0.976  -0.917  -0.941  -0.902
109   P        -0.735  -0.700  -0.723  -0.560  -0.522  -0.543  -0.776  -0.743  -0.732
110   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   K        -0.735  -0.756  -0.718  -0.879  -0.900  -0.827  -0.776  -0.798  -0.726
115   T        -0.516  -0.496  -0.626  -0.601  -0.573  -0.770  -0.493  -0.471  -0.615
116   N        -0.828  -0.835  -0.756  -0.849  -0.863  -0.740  -0.874  -0.878  -0.764
117   L        -1.218  -1.224  -1.149  -1.131  -1.150  -1.027  -1.058  -1.061  -0.946
118   K        -0.166  -0.120  -0.195  -0.441  -0.374  -0.490  -0.351  -0.293  -0.384
119   A        -0.735  -0.799  -0.743  -0.780  -0.863  -0.755  -0.776  -0.839  -0.750
120   R        -1.218  -1.236  -1.155  -1.381  -1.422  -1.291  -1.058  -1.069  -0.951
121   P        -0.867  -0.882  -0.769  -1.015  -1.057  -0.880  -0.917  -0.924  -0.778
122   F        -0.735  -0.779  -0.726  -0.662  -0.728  -0.640  -0.776  -0.813  -0.732
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   K         0.117   0.173  -0.079   0.005   0.082  -0.298   0.073   0.149  -0.214
125   C         0.117   0.142  -0.100   0.432   0.465   0.045   0.073   0.107  -0.245
126   S        -0.735  -0.680  -0.704  -0.520  -0.429  -0.501  -0.776  -0.707  -0.708
127   D        -0.735  -0.657  -0.697  -0.688  -0.558  -0.645  -0.776  -0.683  -0.700
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   K        -0.928  -0.909  -0.791  -1.029  -1.016  -0.820  -0.970  -0.949  -0.798
133   K        -0.314  -0.286  -0.242  -0.506  -0.466  -0.381  -0.537  -0.499  -0.447
134   Q        -1.568  -1.557  -1.466  -1.688  -1.681  -1.524  -1.200  -1.189  -1.062
* 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/Q03429
Output conservation file - output/Q03429
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
