1     M         0.832   0.836   0.872   1.179   1.166   1.182   0.852   0.861   0.911
2     P         0.832   0.836   0.872   0.956   0.955   1.004   0.852   0.861   0.911
3     S        -0.008   0.106  -0.471   0.354   0.468  -0.341   0.044   0.183  -0.646
4     R        -0.444  -0.507  -0.510  -0.565  -0.685  -0.697  -0.562  -0.674  -0.709
5     F        -2.094  -2.029  -1.945  -1.891  -1.750  -1.713  -1.875  -1.758  -1.594
6     T        -0.823  -0.728  -0.536  -0.871  -0.731  -0.454  -1.168  -1.033  -0.752
7     K         0.832   0.836   0.872   0.572   0.625   0.697   0.852   0.861   0.911
8     T         0.832   0.836   0.872   1.046   1.038   1.076   0.852   0.861   0.911
9     R         0.832   0.836   0.872   0.751   0.755   0.840   0.852   0.861   0.911
10    K         0.832   0.836   0.872   0.572   0.625   0.697   0.852   0.861   0.911
11    H        -0.444  -0.507  -0.510  -0.462  -0.587  -0.637  -0.562  -0.674  -0.709
12    R         0.832   0.836   0.872   0.751   0.755   0.840   0.852   0.861   0.911
13    G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
14    H        -0.008   0.110  -0.469   0.188   0.317  -0.430   0.044   0.188  -0.644
15    V         0.832   0.836   0.872   0.762   0.776   0.849   0.852   0.861   0.911
16    S         0.832   0.836   0.872   1.061   1.059   1.088   0.852   0.861   0.911
17    A         0.832   0.836   0.872   0.839   0.853   0.911   0.852   0.861   0.911
18    G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
19    K        -1.212  -1.246  -1.348  -1.387  -1.419  -1.470  -1.168  -1.229  -1.298
20    G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
21    R         0.832   0.836   0.872   0.751   0.755   0.840   0.852   0.861   0.911
22    I        -0.444  -0.449  -0.533  -0.301  -0.336  -0.596  -0.562  -0.584  -0.748
23    G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
24    K         0.832   0.836   0.872   0.572   0.625   0.697   0.852   0.861   0.911
25    H         0.832   0.836   0.872   0.870   0.875   0.935   0.852   0.861   0.911
26    R         0.832   0.836   0.872   0.751   0.755   0.840   0.852   0.861   0.911
27    K         0.832   0.836   0.872   0.572   0.625   0.697   0.852   0.861   0.911
28    H        -0.815  -0.657  -1.311  -0.489  -0.317  -1.145  -0.663  -0.491  -1.255
29    P         0.832   0.836   0.872   0.956   0.955   1.004   0.852   0.861   0.911
30    G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
31    G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
32    R         0.832   0.836   0.872   0.751   0.755   0.840   0.852   0.861   0.911
33    G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
34    M        -0.701  -0.671  -0.546  -0.739  -0.734  -0.653  -0.966  -0.938  -0.769
35    A         0.832   0.836   0.872   0.839   0.853   0.911   0.852   0.861   0.911
36    G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
37    G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
38    Q        -0.701  -0.647  -0.545  -0.631  -0.585  -0.515  -0.966  -0.899  -0.766
39    H        -0.444  -0.507  -0.510  -0.361  -0.464  -0.472  -0.562  -0.674  -0.709
40    H         0.832   0.836   0.872   0.870   0.875   0.935   0.852   0.861   0.911
41    H        -0.444  -0.507  -0.510  -0.462  -0.587  -0.637  -0.562  -0.674  -0.709
42    R         0.832   0.836   0.872   0.751   0.755   0.840   0.852   0.861   0.911
43    I        -1.212  -1.161  -1.341  -0.875  -0.868  -1.116  -1.168  -1.146  -1.290
44    N        -0.444  -0.507  -0.510  -0.185  -0.330  -0.431  -0.562  -0.674  -0.709
45    M        -1.565  -1.517  -1.363  -1.484  -1.429  -1.178  -1.572  -1.522  -1.315
46    D         0.832   0.836   0.872   1.140   1.142   1.151   0.852   0.861   0.911
47    K         0.832   0.836   0.872   0.572   0.625   0.697   0.852   0.861   0.911
48    Y         0.832   0.836   0.872   1.091   1.084   1.112   0.852   0.861   0.911
49    H         0.832   0.836   0.872   0.870   0.875   0.935   0.852   0.861   0.911
50    P         0.832   0.836   0.872   0.956   0.955   1.004   0.852   0.861   0.911
51    G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
52    Y         0.832   0.836   0.872   1.091   1.084   1.112   0.852   0.861   0.911
53    F         0.832   0.836   0.872   1.140   1.137   1.151   0.852   0.861   0.911
54    G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
55    K         0.832   0.836   0.872   0.572   0.625   0.697   0.852   0.861   0.911
56    V         0.832   0.836   0.872   0.762   0.776   0.849   0.852   0.861   0.911
57    G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
58    M         0.832   0.836   0.872   1.179   1.166   1.182   0.852   0.861   0.911
59    R         0.832   0.836   0.872   0.751   0.755   0.840   0.852   0.861   0.911
60    Y        -1.212  -1.414  -1.359  -0.957  -1.321  -1.324  -1.168  -1.407  -1.310
61    F         0.832   0.836   0.872   1.140   1.137   1.151   0.852   0.861   0.911
62    H         0.832   0.836   0.872   0.870   0.875   0.935   0.852   0.861   0.911
63    K        -0.701  -0.734  -0.549  -1.193  -1.229  -0.894  -0.966  -1.043  -0.773
64    Q        -1.212  -1.414  -1.359  -0.748  -1.087  -1.109  -1.168  -1.407  -1.310
65    Q        -2.234  -2.193  -1.957  -2.147  -2.220  -1.877  -1.976  -1.924  -1.605
66    A        -0.444  -0.226  -0.496  -0.193   0.110  -0.415  -0.562  -0.256  -0.687
67    H        -0.444  -0.507  -0.510  -0.424  -0.541  -0.576  -0.562  -0.674  -0.709
68    F        -1.212  -1.414  -1.359  -0.839  -1.165  -1.137  -1.168  -1.407  -1.310
69    W         0.832   0.836   0.872   1.228   1.212   1.221   0.852   0.861   0.911
70    K        -1.492  -1.519  -1.356  -1.975  -1.931  -1.639  -1.572  -1.550  -1.309
71    P         0.832   0.836   0.872   0.956   0.955   1.004   0.852   0.861   0.911
72    V        -2.234  -2.222  -1.961  -2.165  -2.123  -1.726  -1.976  -1.934  -1.607
73    L        -1.723  -1.550  -1.368  -1.973  -1.749  -1.423  -1.774  -1.581  -1.321
74    N         0.832   0.836   0.872   1.140   1.127   1.151   0.852   0.861   0.911
75    L        -0.815  -0.990  -1.333  -0.591  -0.828  -1.356  -0.663  -0.885  -1.280
76    D        -0.444  -0.541  -0.539  -0.141  -0.320  -0.415  -0.562  -0.727  -0.756
77    K        -1.212  -1.246  -1.348  -1.418  -1.464  -1.501  -1.168  -1.229  -1.298
78    L         0.832   0.836   0.872   0.824   0.827   0.898   0.852   0.861   0.911
79    W         0.832   0.836   0.872   1.228   1.212   1.221   0.852   0.861   0.911
80    T        -0.008   0.004  -0.478   0.326   0.326  -0.444   0.044   0.055  -0.658
81    L         0.832   0.836   0.872   0.824   0.827   0.898   0.852   0.861   0.911
82    I        -1.212  -1.048  -1.314  -1.185  -0.947  -1.339  -1.168  -0.950  -1.258
83    P        -0.444  -0.262  -0.495  -0.289  -0.045  -0.410  -0.562  -0.306  -0.685
84    E        -2.234  -2.149  -1.959  -1.978  -1.938  -1.645  -1.976  -1.899  -1.606
85    D        -0.701  -0.473  -0.511  -0.620  -0.276  -0.383  -0.966  -0.622  -0.712
86    K        -1.936  -2.026  -1.952  -2.006  -2.111  -1.858  -1.673  -1.771  -1.600
87    R        -0.444  -0.262  -0.495  -0.649  -0.361  -0.804  -0.562  -0.306  -0.685
88    D        -0.701  -0.692  -0.548  -0.573  -0.596  -0.437  -0.966  -0.972  -0.772
89    Q        -1.492  -1.257  -1.344  -1.688  -1.389  -1.356  -1.572  -1.286  -1.295
90    Y         0.832   0.836   0.872   1.091   1.084   1.112   0.852   0.861   0.911
91    L        -0.008  -0.212  -0.488   0.094  -0.183  -0.654   0.044  -0.236  -0.674
92    K        -0.813  -0.735  -0.541  -1.266  -1.026  -0.730  -1.152  -1.044  -0.761
93    S        -1.425  -1.320  -1.361  -1.600  -1.585  -1.636  -1.471  -1.384  -1.314
94    A        -1.723  -1.587  -1.360  -1.970  -1.790  -1.455  -1.774  -1.605  -1.312
95    S        -1.212  -1.414  -1.359  -0.868  -1.188  -1.186  -1.168  -1.407  -1.310
96    K        -2.325  -2.071  -1.955  -2.484  -1.983  -1.861  -2.077  -1.798  -1.603
97    E        -0.823  -0.739  -0.540  -0.875  -0.761  -0.470  -1.168  -1.051  -0.759
98    T        -1.565  -1.600  -1.368  -1.658  -1.748  -1.387  -1.572  -1.620  -1.321
99    A         0.832   0.836   0.872   0.839   0.853   0.911   0.852   0.861   0.911
100   P         0.832   0.836   0.872   0.956   0.955   1.004   0.852   0.861   0.911
101   V         0.832   0.836   0.872   0.762   0.776   0.849   0.852   0.861   0.911
102   I         0.832   0.836   0.872   1.051   1.049   1.080   0.852   0.861   0.911
103   D        -0.444  -0.507  -0.510  -0.112  -0.228  -0.312  -0.562  -0.674  -0.709
104   T        -1.212  -1.414  -1.359  -1.004  -1.367  -1.366  -1.168  -1.407  -1.310
105   L         0.832   0.836   0.872   0.824   0.827   0.898   0.852   0.861   0.911
106   A        -1.212  -1.414  -1.359  -1.030  -1.295  -1.202  -1.168  -1.407  -1.310
107   A        -1.723  -1.573  -1.357  -1.887  -1.633  -1.333  -1.774  -1.588  -1.308
108   G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
109   Y         0.832   0.836   0.872   1.091   1.084   1.112   0.852   0.861   0.911
110   G        -0.008  -0.212  -0.488  -0.242  -0.482  -0.866   0.044  -0.236  -0.674
111   K         0.832   0.836   0.872   0.572   0.625   0.697   0.852   0.861   0.911
112   I        -0.815  -0.898  -1.325  -0.645  -0.779  -1.358  -0.663  -0.785  -1.271
113   L         0.832   0.836   0.872   0.824   0.827   0.898   0.852   0.861   0.911
114   G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
115   K         0.832   0.836   0.872   0.572   0.625   0.697   0.852   0.861   0.911
116   G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
117   R        -0.008   0.004  -0.478  -0.002   0.012  -0.768   0.044   0.055  -0.658
118   I        -0.701  -0.446  -0.503  -0.852  -0.458  -0.553  -0.966  -0.580  -0.699
119   P         0.832   0.836   0.872   0.956   0.955   1.004   0.852   0.861   0.911
120   N        -2.465  -2.318  -1.969  -2.085  -1.910  -1.477  -2.178  -2.017  -1.614
121   V        -0.444  -0.507  -0.510  -0.504  -0.604  -0.606  -0.562  -0.674  -0.709
122   P         0.832   0.836   0.872   0.956   0.955   1.004   0.852   0.861   0.911
123   V        -0.008  -0.212  -0.488   0.069  -0.176  -0.571   0.044  -0.236  -0.674
124   I        -0.008  -0.212  -0.488   0.322   0.038  -0.492   0.044  -0.236  -0.674
125   V        -0.008  -0.089  -0.469   0.069  -0.019  -0.543   0.044  -0.066  -0.644
126   K        -1.212  -1.414  -1.359  -1.337  -1.584  -1.485  -1.168  -1.407  -1.310
127   A        -0.444  -0.507  -0.510  -0.429  -0.531  -0.554  -0.562  -0.674  -0.709
128   R         0.832   0.836   0.872   0.751   0.755   0.840   0.852   0.861   0.911
129   F        -0.701  -0.734  -0.549  -0.549  -0.654  -0.409  -0.966  -1.043  -0.773
130   V         0.832   0.836   0.872   0.762   0.776   0.849   0.852   0.861   0.911
131   S         0.832   0.836   0.872   1.061   1.059   1.088   0.852   0.861   0.911
132   K        -2.234  -2.252  -1.962  -2.508  -2.510  -2.019  -1.976  -1.961  -1.608
133   L        -1.936  -2.072  -1.960  -1.819  -2.058  -1.818  -1.673  -1.805  -1.606
134   A         0.832   0.836   0.872   0.839   0.853   0.911   0.852   0.861   0.911
135   E         0.832   0.836   0.872   1.036   1.029   1.068   0.852   0.861   0.911
136   E        -0.815  -0.990  -1.333  -0.447  -0.722  -1.420  -0.663  -0.885  -1.280
137   K         0.832   0.836   0.872   0.572   0.625   0.697   0.852   0.861   0.911
138   I         0.832   0.836   0.872   1.051   1.049   1.080   0.852   0.861   0.911
139   R        -0.701  -0.526  -0.523  -1.228  -0.891  -0.903  -0.966  -0.704  -0.731
140   A        -1.212  -1.414  -1.359  -1.034  -1.304  -1.213  -1.168  -1.407  -1.310
141   A        -0.444  -0.262  -0.495  -0.509  -0.229  -0.657  -0.562  -0.306  -0.685
142   G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
143   G         0.832   0.836   0.872   0.480   0.513   0.623   0.852   0.861   0.911
144   V         0.832   0.836   0.872   0.762   0.776   0.849   0.852   0.861   0.911
145   V        -0.008  -0.212  -0.488   0.069  -0.176  -0.571   0.044  -0.236  -0.674
146   E         0.832   0.836   0.872   1.036   1.029   1.068   0.852   0.861   0.911
147   L         0.832   0.836   0.872   0.824   0.827   0.898   0.852   0.861   0.911
148   I        -0.701  -0.654  -0.544  -0.775  -0.728  -0.626  -0.966  -0.910  -0.765
149   A         0.832   0.836   0.872   0.839   0.853   0.911   0.852   0.861   0.911
* 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/P02406
Output conservation file - output/P02406
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
