1     M         1.873   1.899   2.014   2.180   2.211   2.403   2.089   2.124   2.326
2     L         0.676   0.570   0.402   0.839   0.717   0.521   0.693   0.530   0.250
3     P        -0.793  -0.748  -0.744  -1.013  -1.005  -0.924  -0.796  -0.760  -0.709
4     R        -1.063  -1.136  -1.077  -0.932  -0.990  -0.908  -0.889  -0.942  -0.852
5     S        -1.165  -1.137  -1.074  -0.945  -0.852  -0.780  -0.982  -0.947  -0.852
6     A        -0.793  -0.828  -0.739  -0.656  -0.684  -0.571  -0.796  -0.815  -0.704
7     L        -1.047  -1.008  -1.031  -1.004  -0.941  -1.004  -0.855  -0.813  -0.809
8     A        -0.440  -0.383  -0.343  -0.788  -0.708  -0.627  -0.620  -0.546  -0.489
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    -        -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    -         0.695   0.723   0.812   0.616   0.660   0.785   0.280   0.319   0.424
24    -        -0.302  -0.316  -0.301  -0.296  -0.317  -0.298  -0.423  -0.443  -0.428
25    -        -0.860  -0.873  -0.784  -0.929  -0.942  -0.855  -0.842  -0.851  -0.741
26    R         1.263   1.285   1.090   1.317   1.350   1.084   1.345   1.374   1.000
27    S        -1.063  -1.073  -1.021  -0.868  -0.848  -0.768  -0.889  -0.888  -0.806
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    R        -0.860  -0.811  -0.763  -0.658  -0.560  -0.544  -0.842  -0.788  -0.720
36    G        -0.710  -0.605  -0.697  -0.556  -0.418  -0.523  -0.680  -0.561  -0.651
37    V        -0.858  -0.826  -0.762  -0.829  -0.781  -0.710  -0.855  -0.819  -0.724
38    A        -0.251  -0.264  -0.311  -0.150  -0.166  -0.232  -0.384  -0.418  -0.452
39    A        -1.063  -0.954  -1.021  -0.795  -0.622  -0.725  -0.889  -0.780  -0.804
40    R         1.873   1.899   2.014   1.856   1.891   2.077   2.089   2.124   2.326
41    F        -1.063  -1.028  -1.037  -0.821  -0.797  -0.810  -0.889  -0.855  -0.821
42    Y         0.233   0.181   0.204   0.485   0.417   0.467  -0.051  -0.120  -0.092
43    S         1.263   1.227   1.082   1.304   1.270   1.059   1.345   1.278   0.985
44    -        -0.710  -0.678  -0.713  -0.593  -0.554  -0.656  -0.680  -0.645  -0.669
45    -        -0.841  -0.846  -0.751  -0.812  -0.801  -0.663  -0.834  -0.830  -0.713
46    E        -0.793  -0.815  -0.753  -0.935  -0.944  -0.819  -0.796  -0.810  -0.716
47    G        -1.333  -1.402  -1.353  -0.767  -0.868  -0.787  -0.982  -1.033  -0.952
48    S        -0.254  -0.248  -0.279  -0.291  -0.234  -0.264  -0.423  -0.391  -0.415
49    T        -0.422  -0.415  -0.354  -0.453  -0.437  -0.330  -0.610  -0.589  -0.506
50    G         0.118  -0.011  -0.164   0.546   0.380   0.147   0.135  -0.038  -0.249
51    T        -0.793  -0.802  -0.721  -0.727  -0.704  -0.610  -0.796  -0.791  -0.686
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    P        -1.465  -1.428  -1.363  -0.859  -0.800  -0.715  -1.091  -1.056  -0.959
58    R        -0.440  -0.467  -0.376  -0.767  -0.819  -0.712  -0.620  -0.645  -0.530
59    G        -0.743  -0.728  -0.715  -0.593  -0.567  -0.518  -0.738  -0.712  -0.674
60    S        -1.465  -1.418  -1.365  -1.215  -1.140  -1.056  -1.091  -1.047  -0.961
61    G         0.297   0.267   0.224   0.442   0.390   0.281   0.087   0.033  -0.051
62    S        -0.554  -0.633  -0.681  -0.455  -0.584  -0.654  -0.502  -0.594  -0.633
63    E        -1.161  -1.129  -1.075  -1.203  -1.142  -1.099  -0.973  -0.939  -0.851
64    D         0.676   0.570   0.402   0.968   0.829   0.581   0.693   0.530   0.250
65    S        -0.139  -0.118  -0.214  -0.070  -0.012  -0.170  -0.237  -0.196  -0.322
66    F         1.873   1.899   2.014   2.107   2.135   2.330   2.089   2.124   2.326
67    V        -1.435  -1.440  -1.370  -1.246  -1.266  -1.137  -1.075  -1.067  -0.966
68    K        -0.626  -0.727  -0.705  -0.977  -1.144  -1.127  -0.610  -0.708  -0.663
69    R         1.263   1.251   1.109   1.281   1.266   1.037   1.345   1.319   1.036
70    E         1.873   1.899   2.014   1.758   1.788   1.977   2.089   2.124   2.326
71    R         0.946   0.998   0.913   0.619   0.687   0.522   0.786   0.871   0.640
72    A         1.873   1.899   2.014   1.925   1.958   2.147   2.089   2.124   2.326
73    T        -0.626  -0.626  -0.691  -0.636  -0.684  -0.754  -0.610  -0.624  -0.653
74    E         1.873   1.899   2.014   1.758   1.788   1.977   2.089   2.124   2.326
75    D         0.946   0.974   0.950   1.090   1.129   1.085   0.786   0.825   0.718
76    F        -0.356  -0.342  -0.316  -0.106  -0.088  -0.054  -0.517  -0.504  -0.455
77    F         0.184   0.171   0.202   0.338   0.322   0.381  -0.144  -0.151  -0.099
78    V         0.670   0.684   0.800   0.675   0.683   0.861   0.228   0.236   0.397
79    R         0.233   0.185   0.218  -0.132  -0.193  -0.110  -0.051  -0.114  -0.074
80    Q         0.946   0.974   0.950   0.846   0.890   0.784   0.786   0.825   0.718
81    R         0.387   0.432   0.272   0.630   0.692   0.401   0.228   0.291   0.027
82    E         1.873   1.899   2.014   1.758   1.788   1.977   2.089   2.124   2.326
83    K        -0.139  -0.219  -0.248  -0.355  -0.471  -0.504  -0.237  -0.331  -0.367
84    E         1.263   1.251   1.109   1.219   1.205   1.018   1.345   1.319   1.036
85    Q         0.946   0.941   0.888   0.846   0.828   0.640   0.786   0.761   0.587
86    L         1.873   1.899   2.014   1.835   1.869   2.056   2.089   2.124   2.326
87    R        -1.063  -1.028  -1.041  -1.307  -1.272  -1.264  -0.889  -0.855  -0.823
88    H        -1.063  -0.940  -1.015  -1.172  -1.042  -1.077  -0.889  -0.771  -0.802
89    L         1.873   1.899   2.014   1.835   1.869   2.056   2.089   2.124   2.326
90    K         0.670   0.720   0.811   0.128   0.195   0.336   0.228   0.313   0.422
91    E         0.946   0.941   0.888   0.684   0.657   0.484   0.786   0.761   0.587
92    Q         0.233   0.181   0.204  -0.051  -0.142  -0.144  -0.051  -0.120  -0.092
93    L         1.873   1.899   2.014   1.835   1.869   2.056   2.089   2.124   2.326
94    E        -0.793  -0.790  -0.731  -1.125  -1.118  -1.009  -0.796  -0.783  -0.695
95    K        -0.793  -0.832  -0.748  -0.937  -0.977  -0.888  -0.796  -0.819  -0.711
96    Q         0.233   0.236   0.222   0.237   0.241   0.231  -0.051  -0.067  -0.067
97    R        -0.356  -0.342  -0.317  -0.778  -0.762  -0.737  -0.517  -0.492  -0.459
98    K        -0.254  -0.238  -0.269  -0.672  -0.621  -0.691  -0.423  -0.389  -0.408
99    K        -1.333  -1.371  -1.331  -1.402  -1.455  -1.382  -0.982  -1.007  -0.935
100   I        -0.254  -0.271  -0.276  -0.184  -0.228  -0.205  -0.423  -0.443  -0.420
101   D        -0.793  -0.782  -0.742  -0.805  -0.828  -0.770  -0.796  -0.783  -0.706
102   S        -1.063  -0.997  -1.043  -1.065  -0.991  -1.041  -0.889  -0.830  -0.823
103   L         1.263   1.230   1.113   1.316   1.280   1.143   1.345   1.283   1.045
104   E         0.676   0.591   0.401   0.671   0.557   0.263   0.693   0.561   0.247
105   N        -0.793  -0.774  -0.735  -1.047  -1.045  -0.953  -0.796  -0.776  -0.701
106   K        -0.356  -0.399  -0.336  -0.675  -0.738  -0.615  -0.517  -0.561  -0.482
107   I         0.233   0.216   0.238   0.250   0.254   0.277  -0.051  -0.057  -0.039
108   D         0.676   0.739   0.414   0.961   1.040   0.586   0.693   0.782   0.268
109   S        -0.793  -0.757  -0.733  -1.029  -1.000  -0.926  -0.796  -0.739  -0.696
110   M        -0.554  -0.590  -0.638  -0.258  -0.342  -0.419  -0.502  -0.543  -0.586
111   T        -0.251  -0.285  -0.284  -0.260  -0.297  -0.323  -0.384  -0.417  -0.413
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -         0.354   0.329   0.287   0.028  -0.018  -0.104   0.205   0.158   0.065
114   K         0.118   0.017  -0.194   0.015  -0.144  -0.461   0.135  -0.002  -0.289
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     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -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/P01097
Output conservation file - output/P01097
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
