1     M         1.353   1.363   1.445   1.662   1.680   1.795   1.460   1.475   1.605
2     A         0.426   0.330   0.204   0.544   0.399   0.148   0.418   0.270   0.041
3     P         1.353   1.363   1.445   1.607   1.627   1.742   1.460   1.475   1.605
4     N        -0.818  -0.798  -0.719  -0.985  -0.957  -0.827  -0.942  -0.915  -0.787
5     T         0.323   0.286   0.174   0.366   0.307   0.055   0.259   0.200  -0.012
6     S        -0.908  -0.891  -0.754  -1.199  -1.198  -0.970  -1.042  -1.017  -0.828
7     R        -0.432  -0.395  -0.616  -0.486  -0.439  -0.679  -0.416  -0.364  -0.649
8     K        -0.432  -0.523  -0.650  -0.571  -0.694  -0.864  -0.416  -0.534  -0.694
9     Q        -1.859  -1.834  -1.755  -1.488  -1.454  -1.357  -1.459  -1.432  -1.298
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    K         0.323   0.430   0.199   0.109   0.246  -0.050   0.259   0.425   0.033
16    V        -0.603  -0.484  -0.653  -0.791  -0.624  -0.860  -0.641  -0.481  -0.698
17    I        -1.959  -1.933  -1.777  -1.874  -1.833  -1.625  -1.542  -1.513  -1.315
18    K         0.043   0.010   0.081  -0.302  -0.350  -0.226  -0.208  -0.267  -0.177
19    T         0.426   0.464   0.215   0.226   0.276  -0.049   0.418   0.477   0.060
20    L        -0.908  -0.891  -0.750  -0.851  -0.820  -0.624  -1.042  -1.017  -0.824
21    T        -0.728  -0.781  -0.702  -0.919  -0.979  -0.842  -0.833  -0.884  -0.767
22    V         0.043   0.005   0.079  -0.276  -0.337  -0.214  -0.208  -0.277  -0.182
23    D         0.426   0.423   0.214   0.568   0.568   0.266   0.418   0.414   0.057
24    V        -1.383  -1.325  -1.301  -1.298  -1.215  -1.126  -1.250  -1.191  -1.106
25    S        -1.204  -1.256  -1.252  -1.114  -1.192  -1.231  -1.042  -1.096  -1.055
26    S        -0.432  -0.409  -0.619  -0.171  -0.135  -0.456  -0.416  -0.382  -0.653
27    P         0.426   0.330   0.204   0.812   0.690   0.466   0.418   0.270   0.041
28    T        -1.383  -1.371  -1.287  -1.446  -1.447  -1.314  -1.250  -1.229  -1.092
29    E        -1.204  -1.269  -1.289  -1.017  -1.102  -1.154  -1.042  -1.109  -1.092
30    N        -0.073  -0.058   0.060  -0.187  -0.162   0.010  -0.416  -0.390  -0.215
31    G        -0.728  -0.739  -0.706  -0.831  -0.888  -0.823  -0.833  -0.849  -0.771
32    V        -0.073  -0.058   0.060  -0.425  -0.382  -0.205  -0.416  -0.390  -0.215
33    F         1.353   1.363   1.445   1.494   1.513   1.632   1.460   1.475   1.605
34    D         1.353   1.363   1.445   1.374   1.390   1.516   1.460   1.475   1.605
35    P        -0.728  -0.670  -0.705  -0.784  -0.714  -0.684  -0.833  -0.751  -0.768
36    A        -0.908  -0.894  -0.747  -1.026  -0.996  -0.786  -1.042  -1.020  -0.820
37    S         0.043   0.005   0.079  -0.065  -0.131  -0.028  -0.208  -0.277  -0.182
38    Y        -0.073  -0.058   0.060  -0.095  -0.065   0.102  -0.416  -0.390  -0.215
39    S        -0.728  -0.670  -0.705  -0.946  -0.829  -0.918  -0.833  -0.751  -0.768
40    K         1.353   1.363   1.445   1.036   1.049   1.189   1.460   1.475   1.605
41    Y        -0.073  -0.062   0.059  -0.095  -0.076   0.097  -0.416  -0.396  -0.217
42    L         1.353   1.363   1.445   1.381   1.398   1.523   1.460   1.475   1.605
43    I        -0.728  -0.716  -0.692  -0.736  -0.716  -0.722  -0.833  -0.815  -0.753
44    D         0.043   0.019   0.072  -0.079  -0.116  -0.061  -0.208  -0.252  -0.194
45    H        -1.383  -1.333  -1.298  -1.043  -0.986  -0.978  -1.250  -1.198  -1.103
46    I         0.426   0.443   0.214   0.528   0.554   0.153   0.418   0.444   0.057
47    K         1.353   1.363   1.445   1.036   1.049   1.189   1.460   1.475   1.605
48    V         1.353   1.363   1.445   1.084   1.098   1.236   1.460   1.475   1.605
49    D        -0.073  -0.062   0.059  -0.281  -0.254  -0.080  -0.416  -0.396  -0.217
50    G         1.353   1.363   1.445   1.449   1.465   1.589   1.460   1.475   1.605
51    A        -1.383  -1.401  -1.307  -1.235  -1.288  -1.168  -1.250  -1.259  -1.111
52    V        -0.728  -0.679  -0.692  -0.851  -0.799  -0.739  -0.833  -0.785  -0.755
53    G         0.426   0.439   0.221   0.642   0.663   0.346   0.418   0.439   0.070
54    N         0.426   0.439   0.221   0.653   0.680   0.373   0.418   0.439   0.070
55    L         1.353   1.363   1.445   1.381   1.398   1.523   1.460   1.475   1.605
56    G         1.353   1.363   1.445   1.449   1.465   1.589   1.460   1.475   1.605
57    N        -1.204  -1.269  -1.289  -0.951  -1.053  -1.142  -1.042  -1.109  -1.092
58    A        -0.908  -0.898  -0.754  -0.988  -0.977  -0.769  -1.042  -1.025  -0.828
59    I         0.426   0.330   0.204   0.528   0.386   0.134   0.418   0.270   0.041
60    E        -1.383  -1.401  -1.307  -1.696  -1.751  -1.604  -1.250  -1.259  -1.111
61    V        -0.073  -0.061   0.058  -0.425  -0.419  -0.228  -0.416  -0.396  -0.219
62    T        -0.073  -0.058   0.060  -0.253  -0.229  -0.056  -0.416  -0.390  -0.215
63    E        -1.859  -1.889  -1.761  -1.535  -1.555  -1.388  -1.459  -1.477  -1.303
64    D        -1.204  -1.181  -1.245  -1.099  -1.059  -1.202  -1.042  -1.011  -1.047
65    G         0.426   0.443   0.214   0.616   0.640   0.280   0.418   0.444   0.057
66    S        -1.383  -1.326  -1.288  -1.277  -1.209  -1.132  -1.250  -1.193  -1.094
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    I         0.043   0.067   0.089  -0.321  -0.288  -0.240  -0.208  -0.167  -0.162
69    V         0.043   0.005   0.079  -0.276  -0.337  -0.214  -0.208  -0.277  -0.182
70    T        -1.383  -1.419  -1.302  -1.443  -1.470  -1.294  -1.250  -1.274  -1.106
71    V         0.426   0.423   0.214   0.272   0.268  -0.013   0.418   0.414   0.057
72    V        -0.432  -0.507  -0.630  -0.502  -0.606  -0.761  -0.416  -0.513  -0.668
73    S        -0.728  -0.739  -0.706  -0.822  -0.842  -0.822  -0.833  -0.849  -0.771
74    S        -1.383  -1.325  -1.301  -1.070  -0.974  -0.958  -1.250  -1.191  -1.106
75    A        -1.859  -1.879  -1.751  -1.622  -1.651  -1.501  -1.459  -1.469  -1.294
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    K        -1.859  -1.889  -1.761  -1.869  -1.890  -1.683  -1.459  -1.477  -1.303
79    F         0.426   0.423   0.214   0.675   0.676   0.350   0.418   0.414   0.057
80    S         1.353   1.363   1.445   1.305   1.322   1.449   1.460   1.475   1.605
81    G         1.353   1.363   1.445   1.449   1.465   1.589   1.460   1.475   1.605
82    K         0.043   0.005   0.079  -0.257  -0.311  -0.171  -0.208  -0.277  -0.182
83    Y         1.353   1.363   1.445   1.449   1.467   1.589   1.460   1.475   1.605
84    L         1.353   1.363   1.445   1.381   1.398   1.523   1.460   1.475   1.605
85    K         1.353   1.363   1.445   1.036   1.049   1.189   1.460   1.475   1.605
86    Y         1.353   1.363   1.445   1.449   1.467   1.589   1.460   1.475   1.605
87    L         1.353   1.363   1.445   1.381   1.398   1.523   1.460   1.475   1.605
88    T         1.353   1.363   1.445   1.419   1.442   1.560   1.460   1.475   1.605
89    K         0.426   0.443   0.214   0.251   0.271  -0.002   0.418   0.444   0.057
90    K         0.426   0.529   0.226   0.251   0.373   0.015   0.418   0.572   0.078
91    Y         0.043   0.005   0.079   0.100   0.037   0.130  -0.208  -0.277  -0.182
92    L         1.353   1.363   1.445   1.381   1.398   1.523   1.460   1.475   1.605
93    K         0.426   0.443   0.214   0.223   0.244  -0.057   0.418   0.444   0.057
94    K         1.353   1.363   1.445   1.036   1.049   1.189   1.460   1.475   1.605
95    N        -1.859  -1.889  -1.761  -1.253  -1.265  -1.105  -1.459  -1.477  -1.303
96    Q         0.426   0.330   0.204   0.697   0.573   0.337   0.418   0.270   0.041
97    L        -0.432  -0.335  -0.620  -0.238  -0.107  -0.542  -0.416  -0.287  -0.655
98    R         1.353   1.363   1.445   1.531   1.545   1.668   1.460   1.475   1.605
99    D         0.426   0.443   0.214   0.563   0.587   0.257   0.418   0.444   0.057
100   W         1.353   1.363   1.445   1.669   1.688   1.802   1.460   1.475   1.605
101   I         0.043   0.005   0.079   0.008  -0.063   0.028  -0.208  -0.277  -0.182
102   R         1.353   1.363   1.445   1.531   1.545   1.668   1.460   1.475   1.605
103   F        -0.073  -0.058   0.060  -0.355  -0.353  -0.166  -0.416  -0.390  -0.215
104   V         0.426   0.439   0.221   0.272   0.289  -0.001   0.418   0.439   0.070
105   S         1.353   1.363   1.445   1.305   1.322   1.449   1.460   1.475   1.605
106   I        -0.728  -0.670  -0.705  -0.822  -0.705  -0.787  -0.833  -0.751  -0.768
107   R        -0.728  -0.701  -0.693  -0.991  -0.963  -0.888  -0.833  -0.799  -0.755
108   Q        -0.728  -0.749  -0.719  -0.713  -0.774  -0.734  -0.833  -0.859  -0.788
109   N        -0.073  -0.058   0.060  -0.133  -0.104   0.065  -0.416  -0.390  -0.215
110   Q        -0.728  -0.741  -0.721  -0.713  -0.763  -0.741  -0.833  -0.852  -0.789
111   Y         1.353   1.363   1.445   1.449   1.467   1.589   1.460   1.475   1.605
112   K        -1.383  -1.325  -1.301  -1.474  -1.389  -1.304  -1.250  -1.191  -1.106
113   L         1.353   1.363   1.445   1.381   1.398   1.523   1.460   1.475   1.605
114   V        -1.383  -1.401  -1.307  -1.431  -1.452  -1.336  -1.250  -1.259  -1.111
115   F         0.426   0.330   0.204   0.688   0.565   0.360   0.418   0.270   0.041
116   Y         0.426   0.423   0.214   0.653   0.654   0.354   0.418   0.414   0.057
117   Q        -1.204  -1.102  -1.265  -0.871  -0.718  -0.986  -1.042  -0.924  -1.068
118   V         1.353   1.363   1.445   1.084   1.098   1.236   1.460   1.475   1.605
119   T        -0.728  -0.670  -0.705  -0.914  -0.839  -0.845  -0.833  -0.751  -0.768
120   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   D         0.196   0.066   0.105   0.252   0.054   0.087   0.053  -0.168  -0.134
123   A        -0.603  -0.654  -0.674  -0.570  -0.681  -0.746  -0.641  -0.711  -0.726
124   D        -1.204  -1.242  -1.258  -0.993  -1.041  -1.077  -1.042  -1.081  -1.060
125   E        -0.728  -0.749  -0.719  -0.708  -0.729  -0.678  -0.833  -0.859  -0.788
126   E         0.426   0.330   0.204   0.493   0.374   0.167   0.418   0.270   0.041
127   E         1.353   1.363   1.445   1.312   1.338   1.457   1.460   1.475   1.605
128   D         0.426   0.330   0.204   0.542   0.413   0.197   0.418   0.270   0.041
129   D         0.426   0.464   0.215   0.493   0.555   0.185   0.418   0.477   0.060
130   E         0.426   0.330   0.204   0.525   0.417   0.232   0.418   0.270   0.041
* 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/P56628
Output conservation file - output/P56628
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
