1     M         1.463   1.490   1.550   1.767   1.807   1.882   1.598   1.637   1.727
2     A         1.463   1.490   1.550   1.486   1.530   1.607   1.598   1.637   1.727
3     K         1.463   1.490   1.550   0.827   0.876   0.961   1.598   1.637   1.727
4     S         1.463   1.490   1.550   1.401   1.418   1.524   1.598   1.637   1.727
5     L        -0.125  -0.181  -0.285   0.168   0.084  -0.065  -0.191  -0.275  -0.416
6     R         1.463   1.490   1.550   1.478   1.510   1.599   1.598   1.637   1.727
7     A         0.194   0.227   0.311  -0.000   0.033   0.159  -0.191  -0.137  -0.012
8     S         0.194   0.227   0.311  -0.499  -0.499  -0.366  -0.191  -0.137  -0.012
9     S         0.638   0.674   0.504   0.744   0.771   0.595   0.604   0.659   0.350
10    H        -0.389  -0.454  -0.387  -0.386  -0.473  -0.440  -0.589  -0.659  -0.562
11    L         0.638   0.521   0.470   0.813   0.655   0.552   0.604   0.403   0.287
12    N        -0.389  -0.393  -0.381  -0.168  -0.209  -0.187  -0.589  -0.596  -0.557
13    A         0.638   0.521   0.470   0.800   0.658   0.576   0.604   0.403   0.287
14    K         1.463   1.490   1.550   0.827   0.876   0.961   1.598   1.637   1.727
15    S        -0.125  -0.181  -0.285  -0.179  -0.344  -0.536  -0.191  -0.275  -0.416
16    V        -0.811  -0.749  -0.843  -0.282  -0.200  -0.342  -0.788  -0.703  -0.795
17    K         0.638   0.521   0.470   0.109  -0.026  -0.100   0.604   0.403   0.287
18    R         1.463   1.490   1.550   1.478   1.510   1.599   1.598   1.637   1.727
19    R        -0.811  -0.812  -0.853  -1.220  -1.207  -1.218  -0.788  -0.785  -0.806
20    G        -0.125  -0.196  -0.289   0.314   0.219   0.052  -0.191  -0.294  -0.421
21    V         0.298   0.326   0.347   0.406   0.446   0.432   0.008   0.052   0.058
22    F         1.463   1.490   1.550   1.738   1.775   1.854   1.598   1.637   1.727
23    Q        -0.125  -0.094  -0.275   0.165   0.212  -0.109  -0.191  -0.143  -0.401
24    K        -0.125  -0.213  -0.301  -0.443  -0.509  -0.552  -0.191  -0.316  -0.438
25    A        -1.394  -1.374  -1.310  -0.723  -0.689  -0.626  -1.186  -1.154  -1.049
26    V         0.638   0.521   0.470   0.990   0.840   0.760   0.604   0.403   0.287
27    D         0.638   0.662   0.499   0.867   0.903   0.646   0.604   0.640   0.341
28    A         0.298   0.264   0.313   0.234   0.171   0.205   0.008  -0.065  -0.008
29    R         1.463   1.490   1.550   1.478   1.510   1.599   1.598   1.637   1.727
30    E        -1.394  -1.400  -1.330  -1.063  -1.050  -0.974  -1.186  -1.176  -1.067
31    Q        -0.811  -0.679  -0.838  -1.236  -1.058  -1.228  -0.788  -0.619  -0.789
32    R         1.463   1.490   1.550   1.478   1.510   1.599   1.598   1.637   1.727
33    I        -0.389  -0.361  -0.371  -0.092  -0.078  -0.086  -0.589  -0.561  -0.543
34    S         0.194   0.220   0.304  -0.000   0.023   0.149  -0.191  -0.150  -0.025
35    D        -0.811  -0.833  -0.860  -0.536  -0.573  -0.605  -0.788  -0.810  -0.813
36    K        -0.125  -0.223  -0.302  -0.520  -0.603  -0.678  -0.191  -0.329  -0.440
37    L         0.638   0.674   0.504   0.871   0.925   0.708   0.604   0.659   0.350
38    K        -0.811  -0.874  -0.890  -1.279  -1.334  -1.319  -0.788  -0.854  -0.848
39    E        -0.971  -0.997  -0.911  -0.927  -0.953  -0.911  -0.987  -0.997  -0.872
40    D        -0.389  -0.427  -0.357  -0.287  -0.314  -0.235  -0.589  -0.618  -0.521
41    L        -0.389  -0.454  -0.387  -0.146  -0.215  -0.128  -0.589  -0.659  -0.562
42    L        -0.468  -0.438  -0.404  -0.846  -0.849  -0.720  -0.692  -0.645  -0.584
43    K        -0.277  -0.284  -0.342  -0.800  -0.812  -0.827  -0.406  -0.412  -0.496
44    Q         1.463   1.490   1.550   1.609   1.646   1.728   1.598   1.637   1.727
45    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    E        -0.811  -0.828  -0.862  -0.730  -0.729  -0.871  -0.788  -0.803  -0.816
48    D         0.194   0.218   0.302   0.117   0.161   0.264  -0.191  -0.154  -0.028
49    L         0.638   0.662   0.499   0.815   0.855   0.603   0.604   0.640   0.341
50    K        -0.125  -0.196  -0.289  -0.546  -0.605  -0.708  -0.191  -0.294  -0.421
51    K        -0.811  -0.726  -0.828  -1.216  -1.084  -1.194  -0.788  -0.675  -0.777
52    K        -0.811  -0.874  -0.890  -1.236  -1.311  -1.258  -0.788  -0.854  -0.848
53    E        -1.394  -1.400  -1.330  -1.093  -1.125  -1.008  -1.186  -1.176  -1.067
54    E        -1.817  -1.780  -1.676  -1.633  -1.608  -1.453  -1.384  -1.336  -1.198
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    Q        -1.394  -1.390  -1.325  -1.040  -1.056  -0.943  -1.186  -1.168  -1.063
61    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -0.277  -0.203  -0.291  -0.090   0.021  -0.109  -0.406  -0.298  -0.425
68    -        -0.277  -0.226  -0.299  -0.113  -0.033  -0.148  -0.406  -0.330  -0.435
69    -        -0.440  -0.363  -0.373  -0.259  -0.125  -0.203  -0.639  -0.524  -0.539
70    -        -0.440  -0.384  -0.366  -0.154  -0.062  -0.074  -0.639  -0.555  -0.529
71    -        -1.483  -1.450  -1.347  -1.028  -0.986  -0.860  -1.265  -1.218  -1.081
72    V        -1.817  -1.780  -1.676  -1.633  -1.526  -1.453  -1.384  -1.336  -1.198
73    D        -0.971  -1.002  -0.909  -0.672  -0.690  -0.566  -0.987  -1.001  -0.870
74    E        -0.125  -0.196  -0.289   0.060  -0.053  -0.181  -0.191  -0.294  -0.421
75    K        -0.811  -0.861  -0.869  -1.252  -1.276  -1.271  -0.788  -0.840  -0.824
76    K        -0.971  -0.913  -0.900  -1.003  -0.961  -0.920  -0.987  -0.915  -0.861
77    S        -1.394  -1.319  -1.302  -1.452  -1.296  -1.366  -1.186  -1.098  -1.042
78    N        -1.394  -1.299  -1.304  -0.774  -0.657  -0.668  -1.186  -1.078  -1.044
79    E        -1.394  -1.387  -1.317  -1.348  -1.349  -1.281  -1.186  -1.165  -1.056
80    E        -1.394  -1.407  -1.330  -1.348  -1.371  -1.305  -1.186  -1.182  -1.067
81    A        -0.971  -0.903  -0.896  -0.851  -0.780  -0.771  -0.987  -0.903  -0.857
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    P        -1.394  -1.360  -1.324  -1.556  -1.501  -1.358  -1.186  -1.141  -1.061
93    R        -1.817  -1.780  -1.676  -1.747  -1.637  -1.565  -1.384  -1.336  -1.198
94    K        -0.125  -0.196  -0.289  -0.520  -0.565  -0.667  -0.191  -0.294  -0.421
95    K         1.463   1.490   1.550   0.827   0.876   0.961   1.598   1.637   1.727
96    I         0.638   0.738   0.520   0.990   1.108   0.832   0.604   0.759   0.378
97    S         1.463   1.490   1.550   1.401   1.418   1.524   1.598   1.637   1.727
98    T         1.463   1.490   1.550   1.694   1.732   1.811   1.598   1.637   1.727
99    S         1.463   1.490   1.550   1.401   1.418   1.524   1.598   1.637   1.727
100   G         1.463   1.490   1.550   1.702   1.741   1.818   1.598   1.637   1.727
101   W         0.638   0.521   0.470   1.142   0.999   0.916   0.604   0.403   0.287
102   R         1.463   1.490   1.550   1.478   1.510   1.599   1.598   1.637   1.727
103   D         1.463   1.490   1.550   1.599   1.637   1.717   1.598   1.637   1.727
104   G        -0.971  -0.970  -0.915  -0.775  -0.777  -0.667  -0.987  -0.973  -0.876
105   R         0.638   0.521   0.470   0.792   0.639   0.569   0.604   0.403   0.287
106   H        -0.811  -0.874  -0.890  -0.536  -0.663  -0.840  -0.788  -0.854  -0.848
107   H        -0.389  -0.454  -0.387   0.003  -0.082  -0.013  -0.589  -0.659  -0.562
108   T        -1.817  -1.780  -1.676  -1.436  -1.505  -1.260  -1.384  -1.336  -1.198
109   Y         0.638   0.521   0.470   1.143   1.005   0.919   0.604   0.403   0.287
110   K         0.638   0.521   0.470   0.096  -0.044  -0.124   0.604   0.403   0.287
111   K         0.298   0.326   0.347  -0.294  -0.242  -0.192   0.008   0.052   0.058
112   A        -0.389  -0.393  -0.381  -0.733  -0.811  -0.825  -0.589  -0.596  -0.557
113   K        -0.125  -0.181  -0.285  -0.520  -0.552  -0.663  -0.191  -0.275  -0.416
114   L         0.638   0.695   0.509   0.693   0.785   0.406   0.604   0.693   0.358
115   M        -0.971  -0.895  -0.892  -1.014  -0.990  -0.888  -0.987  -0.896  -0.854
116   K         0.638   0.662   0.499   0.142   0.185  -0.001   0.604   0.640   0.341
117   Q        -0.811  -0.800  -0.848  -1.036  -0.994  -0.979  -0.788  -0.772  -0.801
118   S        -0.389  -0.336  -0.340  -0.934  -0.877  -0.822  -0.589  -0.504  -0.498
119   K        -0.389  -0.443  -0.372  -0.810  -0.871  -0.718  -0.589  -0.643  -0.544
120   K         0.547   0.436   0.423   0.014  -0.127  -0.158   0.453   0.254   0.201
121   K         1.463   1.490   1.550   0.868   0.915   1.000   1.598   1.637   1.727
122   T        -0.468  -0.503  -0.399  -0.139  -0.187  -0.053  -0.692  -0.723  -0.578
123   S         1.463   1.490   1.550   1.375   1.378   1.498   1.598   1.637   1.727
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   F         1.463   1.490   1.550   1.716   1.753   1.833   1.598   1.637   1.727
126   T        -0.811  -0.874  -0.890  -0.329  -0.450  -0.485  -0.788  -0.854  -0.848
127   R         0.298   0.370   0.380  -0.375  -0.265  -0.251   0.008   0.135   0.120
128   F         1.463   1.490   1.550   1.738   1.775   1.854   1.598   1.637   1.727
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -        -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/P38202
Output conservation file - output/P38202
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
