1     M         1.913   1.928   2.026   2.187   2.217   2.374   2.127   2.150   2.311
2     S         0.078   0.045  -0.081   0.138   0.084  -0.085   0.051  -0.001  -0.182
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     -        -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    S        -1.389  -1.306  -1.300  -1.270  -1.164  -1.125  -1.102  -1.018  -0.977
12    N        -0.715  -0.691  -0.796  -0.360  -0.330  -0.449  -0.641  -0.612  -0.717
13    E        -0.097  -0.116  -0.167   0.164   0.139   0.061  -0.198  -0.230  -0.305
14    E        -1.492  -1.463  -1.369  -1.247  -1.191  -1.061  -1.194  -1.162  -1.038
15    V        -1.020  -0.977  -0.898  -1.182  -1.099  -0.996  -0.987  -0.938  -0.829
16    F        -0.227  -0.290  -0.218  -0.325  -0.448  -0.335  -0.410  -0.490  -0.388
17    T        -0.900  -0.882  -0.851  -0.858  -0.836  -0.795  -0.871  -0.849  -0.781
18    Q        -1.020  -0.978  -0.898  -0.965  -0.871  -0.778  -0.987  -0.939  -0.829
19    I        -0.286  -0.315  -0.244  -0.619  -0.620  -0.523  -0.468  -0.513  -0.414
20    N        -0.286  -0.339  -0.259  -0.357  -0.504  -0.366  -0.468  -0.544  -0.435
21    A         0.447   0.471   0.570   0.076   0.120   0.286   0.051   0.090   0.229
22    T        -1.389  -1.352  -1.311  -1.338  -1.288  -1.224  -1.102  -1.063  -0.987
23    A        -1.389  -1.418  -1.320  -1.189  -1.220  -1.060  -1.102  -1.124  -0.995
24    N         0.567   0.614   0.642   0.393   0.463   0.511   0.282   0.363   0.370
25    V         0.078   0.031  -0.087   0.077   0.011  -0.194   0.051  -0.016  -0.190
26    V        -1.389  -1.403  -1.349  -1.164  -1.220  -1.131  -1.102  -1.111  -1.021
27    D        -1.389  -1.403  -1.349  -1.266  -1.282  -1.207  -1.102  -1.111  -1.021
28    N         1.913   1.928   2.026   2.114   2.137   2.301   2.127   2.150   2.311
29    K         0.078  -0.045  -0.113   0.373   0.195   0.080   0.051  -0.124  -0.228
30    K         0.078   0.079  -0.075   0.395   0.401   0.176   0.051   0.050  -0.173
31    R        -0.227  -0.225  -0.211  -0.202  -0.205  -0.174  -0.410  -0.409  -0.380
32    L         0.960   0.873   0.795   0.719   0.593   0.461   0.974   0.825   0.659
33    L         0.447   0.463   0.564   0.084   0.112   0.269   0.051   0.074   0.218
34    F        -0.900  -0.910  -0.843  -0.635  -0.654  -0.560  -0.871  -0.874  -0.773
35    V         0.960   0.913   0.803   1.012   0.944   0.761   0.974   0.894   0.674
36    Q        -0.227  -0.249  -0.216   0.050   0.036   0.098  -0.410  -0.425  -0.380
37    D         0.960   0.873   0.795   1.277   1.143   1.001   0.974   0.825   0.659
38    S        -0.227  -0.180  -0.218  -0.478  -0.421  -0.471  -0.410  -0.360  -0.388
39    S        -0.900  -0.829  -0.828  -0.900  -0.822  -0.780  -0.871  -0.797  -0.759
40    A        -0.227  -0.238  -0.192  -0.357  -0.367  -0.279  -0.410  -0.417  -0.354
41    L         1.913   1.928   2.026   1.645   1.671   1.832   2.127   2.150   2.311
42    V        -0.227  -0.234  -0.219  -0.320  -0.324  -0.296  -0.410  -0.410  -0.385
43    L        -0.715  -0.750  -0.782  -1.032  -1.091  -1.156  -0.641  -0.685  -0.701
44    G         1.913   1.928   2.026   1.946   1.976   2.133   2.127   2.150   2.311
45    L         0.447   0.463   0.564  -0.076  -0.053   0.110   0.051   0.074   0.218
46    V        -0.715  -0.691  -0.796  -0.694  -0.668  -0.857  -0.641  -0.612  -0.717
47    A         0.960   1.021   0.828   1.057   1.142   0.848   0.974   1.070   0.720
48    G         1.913   1.928   2.026   1.946   1.976   2.133   2.127   2.150   2.311
49    F         0.078   0.142  -0.044   0.041   0.142  -0.172   0.051   0.140  -0.128
50    L         1.913   1.928   2.026   1.645   1.671   1.832   2.127   2.150   2.311
51    Q        -0.227  -0.249  -0.216  -0.064  -0.066  -0.013  -0.410  -0.425  -0.380
52    I         0.960   0.964   0.818   0.719   0.728   0.501   0.974   0.978   0.702
53    E         0.960   0.913   0.803   1.268   1.218   1.050   0.974   0.894   0.674
54    S         1.913   1.928   2.026   1.860   1.881   2.047   2.127   2.150   2.311
55    V        -1.389  -1.380  -1.314  -1.186  -1.201  -1.061  -1.102  -1.091  -0.990
56    H        -1.389  -1.344  -1.323  -0.978  -0.931  -0.867  -1.102  -1.055  -0.998
57    G         1.913   1.928   2.026   1.946   1.976   2.133   2.127   2.150   2.311
58    F         1.913   1.928   2.026   1.802   1.831   1.989   2.127   2.150   2.311
59    I        -0.227  -0.244  -0.197  -0.685  -0.702  -0.627  -0.410  -0.425  -0.361
60    W        -0.715  -0.691  -0.796  -0.626  -0.583  -0.700  -0.641  -0.612  -0.717
61    F         0.447   0.463   0.564   0.154   0.179   0.340   0.051   0.074   0.218
62    L        -0.715  -0.762  -0.780  -1.032  -1.112  -1.153  -0.641  -0.697  -0.699
63    I         0.078   0.112  -0.067   0.088   0.143  -0.142   0.051   0.095  -0.162
64    L        -1.389  -1.403  -1.349  -1.369  -1.421  -1.318  -1.102  -1.111  -1.021
65    Y        -0.715  -0.691  -0.794  -0.638  -0.609  -0.840  -0.641  -0.614  -0.715
66    N         0.078   0.031  -0.087   0.278   0.205   0.010   0.051  -0.016  -0.190
67    L        -0.900  -0.823  -0.839  -1.251  -1.153  -1.138  -0.871  -0.793  -0.770
68    I        -0.227  -0.186  -0.179  -0.346  -0.277  -0.273  -0.410  -0.346  -0.329
69    N         0.078   0.077  -0.081   0.375   0.349   0.131   0.051   0.043  -0.182
70    V         0.078  -0.003  -0.096  -0.169  -0.297  -0.452   0.051  -0.066  -0.203
71    I        -0.227  -0.180  -0.218  -0.606  -0.551  -0.610  -0.410  -0.360  -0.388
72    Y         0.078  -0.003  -0.096  -0.027  -0.168  -0.329   0.051  -0.066  -0.203
73    I         0.447   0.463   0.564   0.203   0.231   0.389   0.051   0.074   0.218
74    V        -1.878  -1.844  -1.754  -1.825  -1.763  -1.638  -1.333  -1.300  -1.178
75    W        -0.227  -0.249  -0.216  -0.169  -0.184  -0.165  -0.410  -0.425  -0.380
76    I        -1.389  -1.403  -1.349  -1.211  -1.279  -1.225  -1.102  -1.111  -1.021
77    C         0.078   0.045  -0.081   0.447   0.392   0.153   0.051  -0.001  -0.182
78    Q        -0.900  -0.946  -0.867  -0.659  -0.715  -0.600  -0.871  -0.909  -0.798
79    L        -0.227  -0.234  -0.219  -0.591  -0.588  -0.607  -0.410  -0.410  -0.385
80    Q        -0.715  -0.744  -0.763  -0.330  -0.375  -0.384  -0.641  -0.675  -0.679
81    P         0.960   1.042   0.835   1.327   1.444   1.139   0.974   1.103   0.732
82    G        -0.900  -0.811  -0.819  -1.052  -0.930  -0.920  -0.871  -0.781  -0.751
83    K        -0.715  -0.762  -0.780  -0.464  -0.545  -0.584  -0.641  -0.697  -0.699
84    F         0.447   0.469   0.569   0.154   0.208   0.364   0.051   0.086   0.227
85    Y         0.960   0.964   0.818   0.922   0.933   0.733   0.974   0.978   0.702
86    Q        -1.389  -1.388  -1.344  -1.025  -1.049  -0.960  -1.102  -1.097  -1.017
87    S        -0.900  -0.893  -0.840  -0.848  -0.838  -0.720  -0.871  -0.860  -0.771
88    P         1.913   1.928   2.026   2.232   2.258   2.419   2.127   2.150   2.311
89    L        -0.227  -0.187  -0.209  -0.668  -0.612  -0.624  -0.410  -0.378  -0.378
90    H        -0.227  -0.244  -0.193   0.048   0.044   0.104  -0.410  -0.417  -0.354
91    D        -0.900  -0.946  -0.867  -0.588  -0.642  -0.524  -0.871  -0.909  -0.798
92    I         0.078   0.045  -0.081   0.002  -0.063  -0.299   0.051  -0.001  -0.182
93    F         0.960   0.913   0.803   0.955   0.901   0.766   0.974   0.894   0.674
94    F        -0.227  -0.180  -0.189  -0.469  -0.376  -0.424  -0.410  -0.337  -0.349
95    E        -0.900  -0.887  -0.850  -0.677  -0.647  -0.606  -0.871  -0.853  -0.781
96    S        -0.900  -0.946  -0.867  -0.919  -0.962  -0.818  -0.871  -0.909  -0.798
97    F        -0.900  -0.867  -0.845  -1.350  -1.296  -1.259  -0.871  -0.834  -0.776
98    F         0.960   1.042   0.835   0.901   1.018   0.724   0.974   1.103   0.732
99    R        -0.227  -0.249  -0.216  -0.154  -0.174  -0.145  -0.410  -0.425  -0.380
100   E        -0.227  -0.249  -0.216  -0.118  -0.139  -0.107  -0.410  -0.425  -0.380
101   I        -0.227  -0.154  -0.190  -0.688  -0.580  -0.622  -0.410  -0.317  -0.352
102   T        -0.900  -0.903  -0.844  -0.842  -0.871  -0.745  -0.871  -0.869  -0.774
103   G         0.960   0.873   0.795   1.020   0.892   0.752   0.974   0.825   0.659
104   F         1.913   1.928   2.026   1.802   1.831   1.989   2.127   2.150   2.311
105   V        -0.227  -0.190  -0.218  -0.580  -0.538  -0.602  -0.410  -0.369  -0.388
106   M         0.960   0.873   0.795   1.219   1.083   0.913   0.974   0.825   0.659
107   A        -0.227  -0.234  -0.219  -0.123  -0.121  -0.111  -0.410  -0.410  -0.385
108   W         1.913   1.928   2.026   2.241   2.267   2.428   2.127   2.150   2.311
109   T         0.567   0.634   0.659   0.635   0.745   0.783   0.282   0.401   0.403
110   F         0.567   0.614   0.642   0.041   0.126   0.147   0.282   0.363   0.370
111   G        -1.389  -1.403  -1.349  -1.485  -1.531  -1.453  -1.102  -1.111  -1.021
112   Y         0.567   0.582   0.608   0.458   0.481   0.473   0.282   0.303   0.305
113   A         0.078  -0.045  -0.113   0.264   0.087  -0.015   0.051  -0.124  -0.228
114   L         1.913   1.928   2.026   1.645   1.671   1.832   2.127   2.150   2.311
115   I         0.960   0.964   0.818   1.012   1.019   0.788   0.974   0.978   0.702
116   G        -0.900  -0.946  -0.867  -0.710  -0.748  -0.611  -0.871  -0.909  -0.798
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     *
* 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/Q12431
Output conservation file - output/Q12431
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
