1     M         1.644   1.662   1.790   1.892   1.912   2.123   1.825   1.859   2.078
2     S        -0.764  -0.741  -0.711  -0.972  -0.976  -0.919  -0.826  -0.811  -0.733
3     Q        -1.137  -1.165  -1.122  -0.956  -1.016  -0.956  -0.982  -1.013  -0.929
4     D        -0.345  -0.337  -0.223  -0.724  -0.707  -0.517  -0.620  -0.611  -0.451
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    F         0.444   0.479   0.542   0.369   0.424   0.501   0.127   0.184   0.237
14    V         0.584   0.531   0.549   0.482   0.381   0.366   0.392   0.285   0.253
15    T        -0.970  -0.988  -1.106  -0.616  -0.650  -0.868  -0.802  -0.825  -0.913
16    L         1.644   1.662   1.790   1.447   1.476   1.683   1.825   1.859   2.078
17    V         0.584   0.567   0.569   0.482   0.445   0.405   0.392   0.353   0.293
18    S         1.644   1.662   1.790   1.664   1.699   1.897   1.825   1.859   2.078
19    K        -0.723  -0.713  -0.694  -0.791  -0.764  -0.716  -0.802  -0.791  -0.717
20    D         0.934   0.900   0.737   0.982   0.945   0.724   0.990   0.935   0.621
21    D        -0.053   0.055  -0.068   0.093   0.256   0.053  -0.205  -0.044  -0.218
22    K        -0.970  -0.908  -1.094  -0.594  -0.511  -0.812  -0.802  -0.736  -0.901
23    E        -0.643  -0.671  -0.668  -0.874  -0.907  -0.918  -0.682  -0.701  -0.675
24    Y         0.257   0.260  -0.025   0.612   0.614   0.202   0.273   0.274  -0.151
25    E        -1.623  -1.579  -1.497  -1.561  -1.495  -1.368  -1.279  -1.243  -1.102
26    I        -0.193  -0.236  -0.162  -0.439  -0.518  -0.420  -0.443  -0.495  -0.377
27    S        -1.623  -1.616  -1.507  -1.724  -1.729  -1.527  -1.279  -1.270  -1.109
28    R         0.337   0.357   0.501   0.217   0.243   0.476  -0.085  -0.059   0.153
29    S        -0.053  -0.003  -0.116  -0.336  -0.268  -0.460  -0.205  -0.141  -0.299
30    A        -0.193  -0.219  -0.160  -0.323  -0.353  -0.262  -0.443  -0.466  -0.369
31    A         0.934   0.872   0.735   1.150   1.069   0.881   0.990   0.891   0.618
32    M        -0.846  -0.808  -0.744  -0.943  -0.881  -0.764  -0.921  -0.889  -0.768
33    I        -1.173  -1.248  -1.154  -1.129  -1.227  -1.082  -1.040  -1.104  -0.964
34    S         1.644   1.662   1.790   1.664   1.699   1.897   1.825   1.859   2.078
35    P        -1.173  -1.203  -1.143  -1.060  -1.086  -1.033  -1.040  -1.060  -0.952
36    T        -0.193  -0.207  -0.153  -0.242  -0.239  -0.159  -0.443  -0.444  -0.358
37    L         0.584   0.518   0.550   0.278   0.160   0.184   0.392   0.260   0.255
38    K         0.337   0.357   0.499   0.217   0.244   0.462  -0.085  -0.059   0.148
39    A        -1.623  -1.614  -1.498  -1.363  -1.341  -1.155  -1.279  -1.268  -1.103
40    M         0.795   0.759   0.694   1.025   0.968   0.841   0.764   0.700   0.538
41    I         0.008   0.092  -0.070  -0.209  -0.082  -0.353  -0.085   0.034  -0.218
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    E        -0.970  -0.908  -1.063  -0.889  -0.812  -0.982  -0.802  -0.738  -0.870
44    G        -0.643  -0.672  -0.670  -0.406  -0.437  -0.443  -0.682  -0.702  -0.677
45    P        -1.623  -1.661  -1.526  -1.406  -1.460  -1.289  -1.279  -1.302  -1.123
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    F         0.934   0.872   0.735   1.236   1.159   0.969   0.990   0.891   0.618
49    R        -1.623  -1.646  -1.520  -1.573  -1.601  -1.395  -1.279  -1.293  -1.119
50    E         1.644   1.662   1.790   1.484   1.502   1.719   1.825   1.859   2.078
51    S        -1.296  -1.237  -1.171  -1.248  -1.165  -1.056  -1.160  -1.108  -0.979
52    -        -0.868  -0.911  -0.784  -0.905  -0.963  -0.794  -0.926  -0.977  -0.808
53    K        -0.846  -0.848  -0.755  -0.853  -0.840  -0.716  -0.921  -0.919  -0.781
54    G         0.584   0.567   0.569   0.708   0.673   0.657   0.392   0.353   0.293
55    R        -1.173  -1.198  -1.147  -0.988  -1.046  -0.931  -1.040  -1.066  -0.958
56    I         0.584   0.518   0.550   0.622   0.514   0.568   0.392   0.260   0.255
57    E        -1.623  -1.578  -1.499  -1.599  -1.544  -1.392  -1.279  -1.243  -1.104
58    L         0.934   0.873   0.730   0.822   0.751   0.561   0.990   0.893   0.608
59    K        -0.863  -0.848  -0.740  -0.830  -0.812  -0.678  -0.934  -0.918  -0.764
60    Q        -0.053  -0.004  -0.135  -0.206  -0.138  -0.344  -0.205  -0.142  -0.326
61    F        -0.396  -0.371  -0.245  -0.462  -0.440  -0.242  -0.682  -0.650  -0.480
62    D        -0.970  -1.006  -1.098  -0.778  -0.818  -0.934  -0.802  -0.846  -0.905
63    S        -1.173  -1.195  -1.153  -0.968  -0.983  -0.911  -1.040  -1.054  -0.962
64    H        -0.970  -1.069  -1.115  -0.761  -0.906  -0.929  -0.802  -0.912  -0.922
65    I        -0.053  -0.063  -0.133  -0.148  -0.159  -0.347  -0.205  -0.206  -0.321
66    L         0.257   0.346  -0.006   0.162   0.285  -0.227   0.273   0.398  -0.122
67    E         0.257   0.281  -0.029   0.221   0.239  -0.183   0.273   0.304  -0.157
68    K         0.584   0.672   0.659   0.642   0.776   0.757   0.392   0.547   0.471
69    A        -0.380  -0.266  -0.559  -0.296  -0.133  -0.614  -0.324  -0.181  -0.538
70    V        -0.316  -0.318  -0.234  -0.412  -0.416  -0.285  -0.563  -0.571  -0.464
71    E         1.644   1.662   1.790   1.484   1.502   1.719   1.825   1.859   2.078
72    Y         1.644   1.662   1.790   1.762   1.782   1.994   1.825   1.859   2.078
73    L         0.257   0.155  -0.038   0.219   0.092  -0.161   0.273   0.126  -0.171
74    N        -0.846  -0.831  -0.757  -0.849  -0.825  -0.691  -0.921  -0.912  -0.783
75    Y         1.644   1.662   1.790   1.762   1.782   1.994   1.825   1.859   2.078
76    N        -1.296  -1.276  -1.163  -1.006  -0.969  -0.815  -1.160  -1.139  -0.973
77    L         0.397   0.447   0.525   0.095   0.198   0.257   0.034   0.122   0.203
78    K         0.934   0.873   0.730   1.102   1.032   0.838   0.990   0.893   0.608
79    Y         1.644   1.662   1.790   1.762   1.782   1.994   1.825   1.859   2.078
80    S        -0.643  -0.566  -0.660  -0.499  -0.399  -0.509  -0.682  -0.601  -0.673
81    G         0.257   0.235  -0.032   0.375   0.353  -0.012   0.273   0.238  -0.161
82    V        -1.173  -1.142  -1.129  -0.912  -0.861  -0.870  -1.040  -1.012  -0.940
83    S        -1.623  -1.619  -1.511  -1.885  -1.915  -1.756  -1.279  -1.273  -1.113
84    E        -1.298  -1.289  -1.174  -1.493  -1.512  -1.302  -1.146  -1.138  -0.979
85    D        -0.868  -0.796  -0.756  -1.118  -0.996  -0.964  -0.926  -0.843  -0.776
86    D        -0.868  -0.892  -0.784  -0.965  -1.024  -0.910  -0.926  -0.956  -0.808
87    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    E        -0.053   0.005  -0.112  -0.211  -0.141  -0.316  -0.205  -0.136  -0.292
89    I         0.337   0.356   0.499   0.014   0.040   0.264  -0.085  -0.060   0.149
90    P         1.644   1.662   1.790   1.865   1.890   2.096   1.825   1.859   2.078
91    E         0.257   0.132  -0.048   0.181  -0.003  -0.300   0.273   0.093  -0.185
92    F         0.934   0.872   0.735   1.236   1.159   0.969   0.990   0.891   0.618
93    E        -0.396  -0.381  -0.249  -0.697  -0.693  -0.507  -0.682  -0.665  -0.485
94    I         0.584   0.604   0.577   0.510   0.536   0.438   0.392   0.422   0.308
95    P         0.934   0.900   0.737   1.211   1.168   0.907   0.990   0.935   0.621
96    T        -0.193  -0.239  -0.167  -0.139  -0.211  -0.101  -0.443  -0.500  -0.382
97    E        -0.053  -0.019  -0.084  -0.186  -0.143  -0.232  -0.205  -0.141  -0.243
98    M        -0.643  -0.672  -0.670  -0.547  -0.557  -0.584  -0.682  -0.702  -0.677
99    S        -0.723  -0.787  -0.714  -0.734  -0.804  -0.682  -0.802  -0.858  -0.737
100   L         1.644   1.662   1.790   1.447   1.476   1.683   1.825   1.859   2.078
101   E         0.934   0.900   0.737   0.821   0.769   0.520   0.990   0.935   0.621
102   L         1.644   1.662   1.790   1.447   1.476   1.683   1.825   1.859   2.078
103   L         0.934   0.872   0.735   0.791   0.712   0.499   0.990   0.891   0.618
104   L         0.397   0.425   0.515  -0.001   0.052   0.136   0.034   0.079   0.181
105   A        -0.053  -0.041  -0.086   0.026   0.067  -0.014  -0.205  -0.171  -0.245
106   A         1.644   1.662   1.790   1.776   1.797   2.008   1.825   1.859   2.078
107   D         0.934   0.873   0.730   0.927   0.845   0.587   0.990   0.893   0.608
108   Y         0.934   1.010   0.763   1.136   1.228   0.913   0.990   1.109   0.670
109   L         1.644   1.662   1.790   1.447   1.476   1.683   1.825   1.859   2.078
110   S        -0.723  -0.722  -0.703  -0.868  -0.858  -0.848  -0.802  -0.796  -0.724
111   I        -0.380  -0.475  -0.631  -0.174  -0.312  -0.559  -0.324  -0.447  -0.627
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/Q03071
Output conservation file - output/Q03071
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
