1     M         1.747   1.809   1.900   2.031   2.128   2.260   1.927   2.029   2.194
2     A        -0.271  -0.174  -0.202  -0.160  -0.046  -0.045  -0.492  -0.351  -0.393
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     P         1.747   1.809   1.900   2.002   2.077   2.231   1.927   2.029   2.194
5     T         0.384   0.472   0.550   0.390   0.533   0.627  -0.012   0.133   0.230
6     Q        -0.555  -0.572  -0.704  -0.253  -0.341  -0.461  -0.497  -0.523  -0.664
7     L         0.929   0.881   0.752   0.849   0.819   0.629   0.958   0.876   0.623
8     D        -1.346  -1.384  -1.276  -1.486  -1.529  -1.385  -1.143  -1.163  -1.020
9     I         1.747   1.809   1.900   1.936   1.997   2.165   1.927   2.029   2.194
10    K         0.929   0.781   0.743   0.694   0.516   0.437   0.958   0.706   0.606
11    V        -0.160  -0.191  -0.203  -0.057  -0.109  -0.187  -0.335  -0.407  -0.398
12    K        -1.346  -1.402  -1.278  -1.177  -1.244  -1.070  -1.143  -1.176  -1.022
13    A         0.553   0.524   0.563   0.571   0.480   0.543   0.311   0.235   0.256
14    L         0.929   0.781   0.743   0.835   0.675   0.587   0.958   0.706   0.606
15    K        -0.555  -0.671  -0.729  -0.555  -0.656  -0.726  -0.497  -0.643  -0.694
16    R         1.747   1.809   1.900   1.980   2.061   2.209   1.927   2.029   2.194
17    L         1.747   1.809   1.900   1.537   1.654   1.764   1.927   2.029   2.194
18    T        -0.801  -0.731  -0.782  -0.400  -0.350  -0.352  -0.820  -0.747  -0.764
19    K         0.929   0.781   0.743   0.727   0.572   0.508   0.958   0.706   0.606
20    E         1.747   1.809   1.900   1.415   1.494   1.642   1.927   2.029   2.194
21    E         1.747   1.809   1.900   1.415   1.494   1.642   1.927   2.029   2.194
22    G        -0.801  -0.734  -0.761  -0.803  -0.710  -0.668  -0.820  -0.753  -0.741
23    Y        -0.257  -0.205  -0.206  -0.273  -0.194  -0.137  -0.497  -0.431  -0.402
24    Y         0.929   1.048   0.802   1.258   1.412   1.089   0.958   1.146   0.714
25    Q        -0.801  -0.834  -0.769  -0.923  -0.944  -0.895  -0.820  -0.854  -0.748
26    Q         0.158   0.049  -0.087   0.195  -0.027  -0.322   0.150  -0.013  -0.214
27    E         1.747   1.809   1.900   1.415   1.494   1.642   1.927   2.029   2.194
28    L        -0.801  -0.908  -0.806  -0.832  -0.947  -0.807  -0.820  -0.916  -0.785
29    K        -0.801  -0.825  -0.794  -0.963  -0.946  -1.005  -0.820  -0.828  -0.773
30    D        -0.801  -0.825  -0.794  -0.958  -1.005  -0.917  -0.820  -0.828  -0.773
31    Q         1.747   1.809   1.900   1.756   1.824   1.984   1.927   2.029   2.194
32    E        -0.801  -0.762  -0.748  -1.277  -1.215  -1.185  -0.820  -0.760  -0.721
33    A        -1.196  -1.004  -1.158  -1.017  -0.736  -1.020  -0.981  -0.764  -0.906
34    H        -0.160  -0.166  -0.194   0.308   0.245   0.250  -0.335  -0.380  -0.386
35    V         0.553   0.525   0.572   0.650   0.585   0.642   0.311   0.237   0.273
36    A        -1.346  -1.275  -1.249  -1.365  -1.363  -1.316  -1.143  -1.067  -0.996
37    K        -0.160   0.010  -0.111  -0.583  -0.314  -0.558  -0.335  -0.095  -0.254
38    L         0.384   0.431   0.536   0.170   0.248   0.388  -0.012   0.053   0.202
39    K         0.553   0.511   0.554   0.145   0.073   0.116   0.311   0.210   0.238
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    E        -0.160  -0.017  -0.148  -0.147   0.039  -0.183  -0.335  -0.135  -0.318
45    D         0.384   0.472   0.550   0.456   0.612   0.696  -0.012   0.133   0.230
46    K        -1.346  -1.307  -1.252  -0.932  -0.864  -0.833  -1.143  -1.095  -0.999
47    S        -0.801  -0.908  -0.806  -0.659  -0.844  -0.713  -0.820  -0.916  -0.785
48    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    D         1.747   1.809   1.900   1.862   1.955   2.090   1.927   2.029   2.194
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    P        -0.257  -0.162  -0.200  -0.497  -0.366  -0.424  -0.497  -0.388  -0.394
56    Y         1.747   1.809   1.900   1.958   2.046   2.187   1.927   2.029   2.194
57    D        -0.160  -0.221  -0.164  -0.198  -0.256  -0.226  -0.335  -0.397  -0.332
58    L         0.929   0.881   0.752   0.849   0.819   0.629   0.958   0.876   0.623
59    K         1.747   1.809   1.900   1.407   1.522   1.634   1.927   2.029   2.194
60    K         0.929   0.781   0.743   0.686   0.506   0.419   0.958   0.706   0.606
61    Q         0.929   0.781   0.743   0.981   0.724   0.641   0.958   0.706   0.606
62    E        -0.801  -0.825  -0.794  -0.765  -0.815  -0.783  -0.820  -0.828  -0.773
63    E        -0.160  -0.221  -0.164  -0.439  -0.508  -0.414  -0.335  -0.397  -0.332
64    V         0.929   0.781   0.743   1.150   0.952   0.878   0.958   0.706   0.606
65    L         0.929   1.010   0.774   0.817   0.951   0.596   0.958   1.085   0.663
66    D        -1.196  -1.103  -1.211  -1.400  -1.326  -1.456  -0.981  -0.875  -0.958
67    D         0.384   0.414   0.528   0.053   0.053   0.221  -0.012   0.019   0.185
68    T         0.553   0.671   0.659   0.711   0.912   0.847   0.311   0.510   0.445
69    K        -0.406  -0.369  -0.254  -1.030  -1.021  -0.858  -0.658  -0.611  -0.461
70    R         0.158  -0.059  -0.113   0.560   0.213   0.117   0.150  -0.161  -0.252
71    L        -0.257  -0.332  -0.225  -0.279  -0.327  -0.208  -0.497  -0.568  -0.426
72    L        -0.257  -0.332  -0.225  -0.345  -0.365  -0.233  -0.497  -0.568  -0.426
73    P         0.929   0.781   0.743   1.326   1.129   1.091   0.958   0.706   0.606
74    T        -0.801  -0.898  -0.790  -0.832  -0.932  -0.757  -0.820  -0.904  -0.768
75    L        -0.160  -0.146  -0.161  -0.254  -0.187  -0.216  -0.335  -0.295  -0.328
76    Y        -1.196  -1.259  -1.247  -0.607  -0.722  -0.686  -0.981  -1.042  -0.992
77    E        -0.801  -0.793  -0.759  -1.220  -1.161  -1.145  -0.820  -0.799  -0.738
78    K         0.929   0.781   0.743   0.727   0.572   0.508   0.958   0.706   0.606
79    I         0.929   1.048   0.802   1.233   1.363   1.063   0.958   1.146   0.714
80    R        -0.801  -0.806  -0.767  -0.937  -0.942  -0.835  -0.820  -0.825  -0.748
81    E        -0.555  -0.601  -0.703  -0.712  -0.761  -0.954  -0.497  -0.557  -0.663
82    F        -1.196  -1.259  -1.247  -0.447  -0.584  -0.537  -0.981  -1.042  -0.992
83    K        -0.801  -0.807  -0.753  -0.895  -0.899  -0.804  -0.820  -0.817  -0.730
84    E        -0.801  -0.749  -0.776  -0.785  -0.732  -0.802  -0.820  -0.747  -0.753
85    D        -1.346  -1.380  -1.276  -1.131  -1.267  -1.055  -1.143  -1.160  -1.020
86    L         1.747   1.809   1.900   1.537   1.654   1.764   1.927   2.029   2.194
87    E        -0.555  -0.394  -0.657  -0.710  -0.498  -0.882  -0.497  -0.288  -0.607
88    Q        -0.555  -0.512  -0.687  -0.712  -0.652  -0.930  -0.497  -0.440  -0.644
89    F        -0.801  -0.904  -0.772  -0.364  -0.549  -0.328  -0.820  -0.911  -0.751
90    L         0.158   0.079  -0.068   0.171   0.084  -0.123   0.150   0.026  -0.186
91    K        -2.136  -2.088  -1.968  -1.916  -1.827  -1.703  -1.466  -1.418  -1.270
92    T        -0.801  -0.804  -0.761  -0.438  -0.441  -0.360  -0.820  -0.807  -0.735
93    Y         0.158  -0.059  -0.113   0.606   0.308   0.228   0.150  -0.161  -0.252
94    Q        -1.346  -1.275  -1.249  -1.573  -1.490  -1.363  -1.143  -1.067  -0.996
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   G         0.929   0.781   0.743   1.330   1.134   1.065   0.958   0.706   0.606
101   T        -1.346  -1.380  -1.276  -0.979  -1.090  -0.896  -1.143  -1.160  -1.020
102   E         0.929   0.881   0.752   0.735   0.674   0.528   0.958   0.876   0.623
103   D         0.929   0.881   0.752   1.107   1.048   0.804   0.958   0.876   0.623
104   V        -0.801  -0.733  -0.741  -0.750  -0.634  -0.631  -0.820  -0.727  -0.717
105   S        -1.346  -1.313  -1.239  -1.357  -1.320  -1.215  -1.143  -1.099  -0.989
106   D        -1.346  -1.222  -1.233  -1.672  -1.507  -1.490  -1.143  -1.013  -0.984
107   A         0.929   0.881   0.752   1.100   1.018   0.856   0.958   0.876   0.623
108   R         0.158   0.185  -0.058   0.071   0.132  -0.177   0.150   0.185  -0.172
109   S        -0.555  -0.512  -0.687  -0.583  -0.549  -0.731  -0.497  -0.440  -0.644
110   A        -0.160  -0.146  -0.161  -0.168  -0.133  -0.160  -0.335  -0.295  -0.328
111   I         0.384   0.481   0.545   0.107   0.237   0.331  -0.012   0.153   0.219
112   T        -0.732  -0.712  -0.746  -0.805  -0.805  -0.799  -0.712  -0.684  -0.713
113   S        -1.367  -1.398  -1.278  -1.040  -1.108  -0.956  -1.152  -1.171  -1.021
114   A        -0.358  -0.230  -0.233  -0.222  -0.047  -0.032  -0.606  -0.440  -0.433
115   Q        -0.911  -0.840  -0.798  -1.040  -0.932  -0.866  -0.923  -0.838  -0.774
116   E         0.404   0.509   0.570  -0.298  -0.113  -0.061   0.027   0.206   0.269
117   L         0.749   0.642   0.674   0.573   0.432   0.455   0.660   0.458   0.473
118   L        -0.149  -0.293  -0.218  -0.215  -0.388  -0.273  -0.290  -0.499  -0.407
119   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   S        -0.732  -0.764  -0.751  -0.966  -1.020  -1.013  -0.712  -0.750  -0.720
121   K        -1.367  -1.231  -1.245  -0.992  -0.812  -0.834  -1.152  -1.008  -0.991
* 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/P48606
Output conservation file - output/P48606
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
