1     M         1.474   1.507   1.595   1.726   1.768   1.902   1.613   1.665   1.809
2     P         0.703   0.533   0.479   0.932   0.692   0.610   0.711   0.422   0.287
3     I        -0.413  -0.473  -0.369  -0.421  -0.503  -0.353  -0.642  -0.692  -0.548
4     D         0.766   0.684   0.536   0.898   0.799   0.581   0.807   0.675   0.392
5     Q         0.171   0.217   0.335  -0.013   0.066   0.237  -0.229  -0.161   0.009
6     E         0.092  -0.077  -0.240   0.183  -0.052  -0.325   0.117  -0.118  -0.363
7     K         0.766   0.684   0.536   0.702   0.617   0.443   0.807   0.675   0.392
8     L         1.474   1.507   1.595   1.389   1.437   1.577   1.613   1.665   1.809
9     A         0.766   0.684   0.536   0.602   0.498   0.255   0.807   0.675   0.392
10    K         0.766   0.690   0.527   0.632   0.537   0.261   0.807   0.686   0.376
11    L         1.474   1.507   1.595   1.389   1.437   1.577   1.613   1.665   1.809
12    Q         0.766   0.684   0.536   0.814   0.727   0.491   0.807   0.675   0.392
13    K         0.417   0.334   0.379   0.105  -0.063  -0.034   0.232   0.063   0.095
14    L        -1.782  -1.729  -1.635  -1.651  -1.604  -1.457  -1.380  -1.320  -1.175
15    S         0.417   0.334   0.379   0.416   0.223   0.241   0.232   0.063   0.095
16    A        -0.312  -0.460  -0.386  -0.537  -0.765  -0.650  -0.450  -0.667  -0.570
17    N        -0.427  -0.279  -0.367  -0.672  -0.463  -0.574  -0.638  -0.437  -0.545
18    N        -0.427  -0.502  -0.392  -0.579  -0.708  -0.584  -0.638  -0.724  -0.579
19    K        -0.218  -0.355  -0.349  -0.260  -0.427  -0.375  -0.344  -0.542  -0.523
20    V        -0.218  -0.355  -0.349  -0.119  -0.333  -0.336  -0.344  -0.542  -0.523
21    G         1.474   1.507   1.595   1.440   1.484   1.626   1.613   1.665   1.809
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    G         1.474   1.507   1.595   1.440   1.484   1.626   1.613   1.665   1.809
26    T         0.417   0.532   0.477   0.574   0.740   0.640   0.232   0.421   0.283
27    R         0.231   0.214   0.332   0.314   0.238   0.417  -0.114  -0.168   0.004
28    R         0.417   0.532   0.477   0.610   0.775   0.666   0.232   0.421   0.283
29    K         0.231   0.214   0.332   0.004   0.011   0.207  -0.114  -0.168   0.004
30    L        -1.782  -1.637  -1.650  -1.868  -1.645  -1.617  -1.380  -1.250  -1.186
31    N        -1.456  -1.368  -1.319  -1.642  -1.462  -1.390  -1.265  -1.170  -1.064
32    K         1.474   1.507   1.595   1.268   1.320   1.460   1.613   1.665   1.809
33    K        -0.218  -0.211  -0.266  -0.295  -0.255  -0.310  -0.344  -0.314  -0.400
34    A        -1.782  -1.682  -1.623  -1.571  -1.460  -1.328  -1.380  -1.287  -1.167
35    G        -1.334  -1.431  -1.324  -1.347  -1.483  -1.333  -1.150  -1.214  -1.068
36    S        -1.334  -1.431  -1.324  -1.146  -1.359  -1.258  -1.150  -1.214  -1.068
37    S        -0.427  -0.338  -0.351  -0.335  -0.228  -0.238  -0.638  -0.548  -0.528
38    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    A        -1.029  -0.925  -0.904  -1.038  -0.858  -0.902  -1.039  -0.918  -0.870
41    N        -1.131  -1.047  -0.914  -1.266  -1.184  -0.958  -1.150  -1.053  -0.882
42    K        -1.334  -1.431  -1.324  -1.517  -1.671  -1.539  -1.150  -1.214  -1.068
43    D         1.474   1.507   1.595   1.494   1.540   1.679   1.613   1.665   1.809
44    D         0.766   0.690   0.527   0.884   0.788   0.532   0.807   0.686   0.376
45    T        -0.357  -0.285  -0.344  -0.398  -0.376  -0.397  -0.574  -0.496  -0.519
46    K         1.474   1.507   1.595   1.268   1.320   1.460   1.613   1.665   1.809
47    L         0.766   0.683   0.529   0.792   0.695   0.473   0.807   0.674   0.380
48    Q        -0.805  -0.715  -0.816  -0.625  -0.500  -0.591  -0.805  -0.689  -0.772
49    S        -1.782  -1.640  -1.643  -1.756  -1.611  -1.532  -1.380  -1.252  -1.180
50    Q        -0.560  -0.537  -0.398  -0.837  -0.770  -0.570  -0.805  -0.771  -0.586
51    L         1.474   1.507   1.595   1.389   1.437   1.577   1.613   1.665   1.809
52    A        -1.008  -0.816  -0.867  -1.358  -1.029  -1.135  -1.035  -0.806  -0.831
53    K         1.474   1.507   1.595   1.268   1.320   1.460   1.613   1.665   1.809
54    L         0.092  -0.076  -0.239   0.229   0.021  -0.210   0.117  -0.118  -0.361
55    H        -1.008  -0.816  -0.867  -0.868  -0.588  -0.635  -1.035  -0.806  -0.831
56    A         0.092  -0.082  -0.249   0.089  -0.117  -0.323   0.117  -0.127  -0.375
57    V        -0.357  -0.204  -0.291  -0.426  -0.190  -0.276  -0.574  -0.358  -0.440
58    T        -1.334  -1.431  -1.324  -1.140  -1.276  -1.148  -1.150  -1.214  -1.068
59    I         0.092   0.078  -0.212   0.374   0.345  -0.091   0.117   0.090  -0.321
60    D        -1.334  -1.431  -1.324  -1.258  -1.407  -1.282  -1.150  -1.214  -1.068
61    N        -0.357  -0.342  -0.313  -0.458  -0.427  -0.412  -0.574  -0.520  -0.470
62    V         0.171   0.241   0.347   0.038   0.160   0.310  -0.229  -0.115   0.034
63    A        -1.008  -0.981  -0.886  -1.212  -1.125  -1.001  -1.035  -0.986  -0.854
64    E         0.766   0.864   0.552   0.789   0.912   0.491   0.807   0.952   0.422
65    A         0.231   0.214   0.332  -0.140  -0.154   0.034  -0.114  -0.168   0.004
66    N         1.474   1.507   1.595   1.552   1.600   1.735   1.613   1.665   1.809
67    F         0.231   0.214   0.332   0.335   0.302   0.473  -0.114  -0.168   0.004
68    F         1.474   1.507   1.595   1.638   1.689   1.817   1.613   1.665   1.809
69    K         0.766   0.863   0.560   0.702   0.822   0.477   0.807   0.952   0.436
70    D        -0.357  -0.342  -0.313  -0.458  -0.407  -0.347  -0.574  -0.520  -0.470
71    D         1.474   1.507   1.595   1.494   1.540   1.679   1.613   1.665   1.809
72    G         1.474   1.507   1.595   1.440   1.484   1.626   1.613   1.665   1.809
73    K        -0.805  -0.932  -0.876  -0.811  -0.961  -0.851  -0.805  -0.934  -0.845
74    V         1.474   1.507   1.595   1.499   1.546   1.683   1.613   1.665   1.809
75    M        -0.218  -0.182  -0.314  -0.166  -0.167  -0.260  -0.344  -0.346  -0.474
76    H         0.766   0.683   0.529   1.152   1.055   0.815   0.807   0.674   0.380
77    F         1.474   1.507   1.595   1.638   1.689   1.817   1.613   1.665   1.809
78    N        -0.543  -0.771  -0.850  -0.202  -0.528  -0.679  -0.459  -0.732  -0.810
79    K        -0.480  -0.459  -0.368  -0.749  -0.770  -0.616  -0.689  -0.671  -0.546
80    V         0.417   0.334   0.379   0.446   0.303   0.355   0.232   0.063   0.095
81    G        -0.543  -0.771  -0.850  -0.287  -0.594  -0.713  -0.459  -0.732  -0.810
82    V         1.474   1.507   1.595   1.499   1.546   1.683   1.613   1.665   1.809
83    Q        -0.218  -0.355  -0.349  -0.137  -0.307  -0.313  -0.344  -0.542  -0.523
84    V        -0.885  -0.954  -0.887  -0.899  -0.996  -0.912  -0.920  -0.962  -0.854
85    A         0.417   0.337   0.367   0.189   0.063   0.115   0.232   0.069   0.072
86    A        -1.008  -1.008  -0.899  -1.066  -1.061  -0.946  -1.035  -1.017  -0.869
87    Q        -0.480  -0.516  -0.401  -0.669  -0.729  -0.600  -0.689  -0.744  -0.590
88    H        -0.805  -0.932  -0.870  -0.455  -0.674  -0.636  -0.805  -0.934  -0.838
89    N         0.766   0.683   0.529   0.942   0.838   0.590   0.807   0.674   0.380
90    T         1.474   1.507   1.595   1.634   1.680   1.813   1.613   1.665   1.809
91    S        -0.357  -0.343  -0.322  -0.200  -0.139  -0.111  -0.574  -0.520  -0.484
92    V         0.231   0.360   0.406  -0.140   0.068   0.129  -0.114   0.112   0.149
93    F        -0.357  -0.280  -0.340  -0.250  -0.166  -0.244  -0.574  -0.492  -0.516
94    Y        -0.218  -0.205  -0.278   0.189   0.220   0.084  -0.344  -0.307  -0.417
95    G         1.474   1.507   1.595   1.440   1.484   1.626   1.613   1.665   1.809
96    L        -2.108  -2.053  -1.949  -1.506  -1.497  -1.369  -1.495  -1.439  -1.285
97    P        -0.805  -0.922  -0.866  -0.697  -0.894  -0.859  -0.805  -0.921  -0.834
98    Q         0.417   0.334   0.379   0.308   0.161   0.187   0.232   0.063   0.095
99    E         0.092  -0.076  -0.239   0.199  -0.025  -0.287   0.117  -0.118  -0.361
100   K         1.474   1.507   1.595   1.268   1.320   1.460   1.613   1.665   1.809
101   N        -1.334  -1.376  -1.290  -1.067  -1.142  -1.012  -1.150  -1.175  -1.040
102   L        -0.218  -0.147  -0.310  -0.211  -0.128  -0.339  -0.344  -0.266  -0.472
103   Q        -0.885  -0.950  -0.880  -0.814  -0.878  -0.805  -0.920  -0.959  -0.847
104   D        -0.218  -0.012  -0.236  -0.266   0.024  -0.286  -0.344  -0.063  -0.358
105   L         0.766   0.683   0.529   0.804   0.710   0.501   0.807   0.674   0.380
106   F        -0.885  -0.954  -0.887  -0.684  -0.778  -0.711  -0.920  -0.962  -0.854
107   P         1.474   1.507   1.595   1.585   1.622   1.766   1.613   1.665   1.809
108   G        -0.480  -0.408  -0.352  -0.611  -0.498  -0.442  -0.689  -0.593  -0.526
109   I         1.474   1.507   1.595   1.577   1.621   1.758   1.613   1.665   1.809
110   I         0.231   0.360   0.406   0.041   0.244   0.305  -0.114   0.112   0.149
111   S        -0.480  -0.426  -0.357  -0.393  -0.342  -0.240  -0.689  -0.628  -0.531
112   Q         0.766   0.683   0.529   0.830   0.748   0.519   0.807   0.674   0.380
113   L         0.417   0.422   0.380   0.389   0.395   0.343   0.232   0.226   0.098
114   G         1.474   1.507   1.595   1.440   1.484   1.626   1.613   1.665   1.809
115   P        -0.885  -0.829  -0.850  -0.974  -0.866  -0.886  -0.920  -0.850  -0.817
116   E         0.231   0.232   0.333   0.004  -0.011   0.144  -0.114  -0.133   0.006
117   A        -0.480  -0.459  -0.368  -0.692  -0.657  -0.508  -0.689  -0.671  -0.546
118   I         0.231   0.360   0.406   0.041   0.244   0.305  -0.114   0.112   0.149
119   Q        -1.782  -1.801  -1.666  -1.715  -1.748  -1.553  -1.380  -1.370  -1.197
120   A        -0.805  -0.871  -0.852  -0.869  -0.942  -0.904  -0.805  -0.855  -0.813
121   L         1.474   1.507   1.595   1.389   1.437   1.577   1.613   1.665   1.809
122   S        -0.805  -0.708  -0.834  -0.439  -0.302  -0.501  -0.805  -0.669  -0.793
123   Q         0.417   0.422   0.389   0.266   0.275   0.142   0.232   0.225   0.116
124   L        -0.218  -0.296  -0.320  -0.201  -0.316  -0.355  -0.344  -0.447  -0.487
125   A         1.474   1.507   1.595   1.233   1.284   1.426   1.613   1.665   1.809
126   A        -0.805  -0.708  -0.834  -0.860  -0.683  -0.877  -0.805  -0.669  -0.793
127   Q         0.766   0.684   0.536   0.834   0.752   0.540   0.807   0.675   0.392
128   M        -1.456  -1.461  -1.305  -1.087  -1.082  -0.873  -1.265  -1.241  -1.052
129   E        -0.805  -0.838  -0.829  -0.818  -0.833  -0.867  -0.805  -0.813  -0.787
130   K        -1.334  -1.347  -1.286  -1.454  -1.442  -1.315  -1.150  -1.143  -1.034
131   H        -1.782  -1.784  -1.663  -1.587  -1.566  -1.341  -1.380  -1.360  -1.195
132   E        -0.480  -0.394  -0.341  -0.740  -0.581  -0.555  -0.689  -0.573  -0.510
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   A        -1.659  -1.711  -1.657  -1.640  -1.763  -1.618  -1.265  -1.300  -1.190
135   K        -1.334  -1.313  -1.276  -1.160  -1.137  -1.144  -1.150  -1.115  -1.025
136   A        -1.066  -0.974  -0.898  -1.456  -1.328  -1.204  -1.094  -0.996  -0.869
137   P        -2.108  -1.920  -1.925  -1.982  -1.746  -1.721  -1.495  -1.338  -1.269
138   A        -0.694  -0.659  -0.841  -0.781  -0.758  -1.021  -0.642  -0.607  -0.800
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   D        -1.298  -1.154  -1.251  -1.168  -0.978  -1.160  -1.094  -0.940  -1.001
147   A         0.092   0.121  -0.202  -0.003   0.025  -0.453   0.117   0.146  -0.307
148   E         0.092   0.077  -0.199   0.209   0.183  -0.201   0.117   0.089  -0.303
149   K        -0.805  -0.710  -0.800  -1.022  -0.874  -1.033  -0.805  -0.685  -0.760
150   K        -1.008  -1.014  -0.912  -1.319  -1.277  -1.138  -1.035  -1.024  -0.880
151   D         0.092   0.252  -0.195   0.250   0.461  -0.223   0.117   0.335  -0.297
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   E        -0.694  -0.846  -0.875  -0.557  -0.814  -0.838  -0.642  -0.834  -0.838
157   A        -0.554  -0.488  -0.388  -0.838  -0.737  -0.610  -0.793  -0.712  -0.574
158   I         1.474   1.507   1.595   1.577   1.621   1.758   1.613   1.665   1.809
159   P         1.474   1.507   1.595   1.585   1.622   1.766   1.613   1.665   1.809
160   E        -0.357  -0.337  -0.325  -0.444  -0.367  -0.350  -0.574  -0.514  -0.487
161   L         1.474   1.507   1.595   1.389   1.437   1.577   1.613   1.665   1.809
162   V         0.766   0.871   0.562   0.913   1.042   0.652   0.807   0.963   0.440
163   E         0.092   0.078  -0.193   0.168   0.132  -0.276   0.117   0.090  -0.294
164   G         1.474   1.507   1.595   1.455   1.500   1.640   1.613   1.665   1.809
165   Q         0.627   0.408   0.419   0.610   0.286   0.253   0.590   0.202   0.174
166   T        -1.008  -0.895  -0.892  -1.026  -0.891  -0.827  -1.035  -0.920  -0.861
167   F         1.474   1.507   1.595   1.638   1.689   1.817   1.613   1.665   1.809
168   D         0.231   0.232   0.333   0.038   0.010   0.150  -0.114  -0.133   0.006
169   A        -0.312  -0.470  -0.386  -0.499  -0.725  -0.592  -0.450  -0.679  -0.570
170   D        -0.805  -0.922  -0.866  -0.754  -0.943  -0.900  -0.805  -0.921  -0.834
171   V         0.766   0.683   0.529   0.891   0.791   0.547   0.807   0.674   0.380
172   E         0.766   0.683   0.529   0.800   0.698   0.479   0.807   0.674   0.380
* 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/Q02642
Output conservation file - output/Q02642
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
