1     M         0.850   0.870   0.904   1.140   1.169   1.189   0.872   0.898   0.951
2     G        -0.671  -0.676  -0.496  -0.825  -0.752  -0.500  -0.960  -0.982  -0.724
3     K         0.850   0.870   0.904   0.660   0.697   0.783   0.872   0.898   0.951
4     K        -2.036  -1.721  -1.880  -1.893  -1.445  -1.564  -1.815  -1.485  -1.548
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     N        -0.671  -0.453  -0.468  -0.966  -0.631  -0.648  -0.960  -0.618  -0.678
8     T        -0.671  -0.453  -0.468  -0.871  -0.565  -0.555  -0.960  -0.618  -0.678
9     K         0.850   0.870   0.904   0.660   0.697   0.783   0.872   0.898   0.951
10    G         0.850   0.870   0.904   0.639   0.685   0.765   0.872   0.898   0.951
11    G         0.850   0.870   0.904   0.639   0.685   0.765   0.872   0.898   0.951
12    K         0.850   0.870   0.904   0.660   0.697   0.783   0.872   0.898   0.951
13    K        -0.671  -0.453  -0.468  -0.874  -0.481  -0.595  -0.960  -0.618  -0.678
14    G        -0.671  -0.453  -0.468  -0.907  -0.516  -0.624  -0.960  -0.618  -0.678
15    R         0.850   0.870   0.904   0.893   0.918   0.979   0.872   0.898   0.951
16    R         0.850   0.870   0.904   0.893   0.918   0.979   0.872   0.898   0.951
17    G         0.850   0.870   0.904   0.639   0.685   0.765   0.872   0.898   0.951
18    K         0.850   0.870   0.904   0.660   0.697   0.783   0.872   0.898   0.951
19    N         0.850   0.870   0.904   0.918   0.950   1.001   0.872   0.898   0.951
20    D        -1.389  -1.224  -1.299  -1.813  -1.598  -1.534  -1.449  -1.269  -1.265
21    S        -0.743  -0.661  -0.496  -0.737  -0.627  -0.403  -1.082  -0.956  -0.723
22    D        -2.584  -2.290  -2.321  -2.711  -2.397  -2.271  -2.059  -1.815  -1.711
23    G        -0.442  -0.587  -0.480  -0.628  -0.853  -0.680  -0.594  -0.833  -0.698
24    P        -2.186  -2.121  -1.893  -1.819  -1.861  -1.508  -1.937  -1.838  -1.559
25    K         0.850   0.870   0.904   0.660   0.697   0.783   0.872   0.898   0.951
26    R         0.850   0.870   0.904   0.893   0.918   0.979   0.872   0.898   0.951
27    E         0.850   0.870   0.904   0.575   0.617   0.711   0.872   0.898   0.951
28    L         0.850   0.870   0.904   0.923   0.936   1.005   0.872   0.898   0.951
29    I        -1.219  -1.389  -1.303  -0.899  -1.136  -1.020  -1.204  -1.412  -1.269
30    Y        -0.016  -0.185  -0.439   0.474   0.262  -0.172   0.017  -0.217  -0.630
31    K        -0.016  -0.175  -0.422  -0.032  -0.219  -0.540   0.017  -0.202  -0.603
32    E        -0.016   0.131  -0.429  -0.185   0.007  -0.829   0.017   0.204  -0.614
33    E         0.850   0.870   0.904   0.575   0.617   0.711   0.872   0.898   0.951
34    G         0.850   0.870   0.904   0.639   0.685   0.765   0.872   0.898   0.951
35    Q         0.850   0.870   0.904   1.067   1.101   1.127   0.872   0.898   0.951
36    E        -0.016  -0.175  -0.422  -0.096  -0.263  -0.540   0.017  -0.202  -0.603
37    Y         0.850   0.870   0.904   1.160   1.181   1.205   0.872   0.898   0.951
38    A         0.850   0.870   0.904   1.003   1.015   1.073   0.872   0.898   0.951
39    Q         0.850   0.870   0.904   1.067   1.101   1.127   0.872   0.898   0.951
40    I        -0.671  -0.676  -0.496  -0.657  -0.672  -0.427  -0.960  -0.982  -0.724
41    T        -0.841  -1.086  -1.278  -0.258  -0.589  -0.959  -0.716  -1.009  -1.240
42    K         0.850   0.870   0.904   0.660   0.697   0.783   0.872   0.898   0.951
43    M         0.850   0.870   0.904   1.140   1.169   1.189   0.872   0.898   0.951
44    L         0.850   0.870   0.904   0.923   0.936   1.005   0.872   0.898   0.951
45    G         0.850   0.870   0.904   0.639   0.685   0.765   0.872   0.898   0.951
46    N         0.850   0.870   0.904   0.918   0.950   1.001   0.872   0.898   0.951
47    G         0.850   0.870   0.904   0.639   0.685   0.765   0.872   0.898   0.951
48    R         0.850   0.870   0.904   0.893   0.918   0.979   0.872   0.898   0.951
49    V        -1.637  -1.565  -1.311  -1.534  -1.476  -1.130  -1.693  -1.592  -1.278
50    E         0.850   0.870   0.904   0.575   0.617   0.711   0.872   0.898   0.951
51    A        -0.442  -0.254  -0.460  -0.235   0.005  -0.327  -0.594  -0.317  -0.664
52    S        -1.618  -1.944  -1.881  -0.891  -1.326  -1.325  -1.326  -1.654  -1.548
53    C         0.850   0.870   0.904   1.208   1.231   1.246   0.872   0.898   0.951
54    F         0.850   0.870   0.904   1.067   1.100   1.127   0.872   0.898   0.951
55    D         0.850   0.870   0.904   0.549   0.606   0.688   0.872   0.898   0.951
56    G        -0.016   0.133  -0.428  -0.120   0.078  -0.776   0.017   0.207  -0.612
57    N        -1.938  -1.491  -1.859  -1.583  -0.971  -1.620  -1.693  -1.213  -1.530
58    K         0.850   0.870   0.904   0.660   0.697   0.783   0.872   0.898   0.951
59    R         0.850   0.870   0.904   0.893   0.918   0.979   0.872   0.898   0.951
60    M        -0.671  -0.676  -0.496  -0.542  -0.635  -0.379  -0.960  -0.982  -0.724
61    A        -0.743  -0.661  -0.496  -1.011  -0.921  -0.638  -1.082  -0.956  -0.723
62    H        -0.016  -0.185  -0.439   0.511   0.290  -0.192   0.017  -0.217  -0.630
63    I         0.850   0.870   0.904   0.933   0.963   1.013   0.872   0.898   0.951
64    R         0.850   0.870   0.904   0.893   0.918   0.979   0.872   0.898   0.951
65    G         0.850   0.870   0.904   0.639   0.685   0.765   0.872   0.898   0.951
66    K         0.850   0.870   0.904   0.660   0.697   0.783   0.872   0.898   0.951
67    L         0.850   0.870   0.904   0.923   0.936   1.005   0.872   0.898   0.951
68    R         0.850   0.870   0.904   0.893   0.918   0.979   0.872   0.898   0.951
69    K         0.850   0.870   0.904   0.660   0.697   0.783   0.872   0.898   0.951
70    K        -0.016   0.133  -0.428  -0.049   0.126  -0.600   0.017   0.207  -0.612
71    V        -0.016  -0.185  -0.439   0.344   0.134  -0.312   0.017  -0.217  -0.630
72    W         0.850   0.870   0.904   1.241   1.262   1.275   0.872   0.898   0.951
73    M        -0.671  -0.676  -0.496  -0.537  -0.615  -0.373  -0.960  -0.982  -0.724
74    G        -1.637  -1.410  -1.312  -1.731  -1.348  -1.243  -1.693  -1.409  -1.279
75    Q        -0.016  -0.185  -0.439   0.361   0.152  -0.305   0.017  -0.217  -0.630
76    G        -0.016  -0.109  -0.439  -0.053  -0.149  -0.580   0.017  -0.110  -0.631
77    D         0.850   0.870   0.904   0.549   0.606   0.688   0.872   0.898   0.951
78    I         0.850   0.870   0.904   0.933   0.963   1.013   0.872   0.898   0.951
79    I         0.850   0.870   0.904   0.933   0.963   1.013   0.872   0.898   0.951
80    L         0.850   0.870   0.904   0.923   0.936   1.005   0.872   0.898   0.951
81    V        -0.442  -0.557  -0.478  -0.232  -0.451  -0.392  -0.594  -0.784  -0.694
82    S         0.850   0.870   0.904   1.106   1.143   1.160   0.872   0.898   0.951
83    L         0.850   0.870   0.904   0.923   0.936   1.005   0.872   0.898   0.951
84    R         0.850   0.870   0.904   0.893   0.918   0.979   0.872   0.898   0.951
85    D        -0.442  -0.587  -0.480  -0.835  -1.103  -0.940  -0.594  -0.833  -0.698
86    F        -0.016  -0.185  -0.439   0.395   0.200  -0.197   0.017  -0.217  -0.630
87    Q        -0.016  -0.109  -0.439   0.315   0.192  -0.455   0.017  -0.110  -0.631
88    D         0.850   0.870   0.904   0.549   0.606   0.688   0.872   0.898   0.951
89    D        -0.442  -0.587  -0.480  -0.835  -1.103  -0.940  -0.594  -0.833  -0.698
90    Q        -0.671  -0.676  -0.496  -0.739  -0.858  -0.583  -0.960  -0.982  -0.724
91    C        -1.219  -1.389  -1.303  -0.825  -1.204  -1.122  -1.204  -1.412  -1.269
92    D         0.850   0.870   0.904   0.549   0.606   0.688   0.872   0.898   0.951
93    V         0.850   0.870   0.904   1.047   1.079   1.110   0.872   0.898   0.951
94    V        -0.743  -0.612  -0.487  -0.769  -0.579  -0.419  -1.082  -0.874  -0.710
95    H        -1.219  -1.389  -1.303  -0.694  -1.014  -0.923  -1.204  -1.412  -1.269
96    K         0.850   0.870   0.904   0.660   0.697   0.783   0.872   0.898   0.951
97    Y         0.850   0.870   0.904   1.160   1.181   1.205   0.872   0.898   0.951
98    N        -1.618  -1.944  -1.881  -1.023  -1.415  -1.329  -1.326  -1.654  -1.548
99    L        -2.735  -2.531  -2.343  -2.108  -1.870  -1.623  -2.181  -1.974  -1.727
100   D         0.850   0.870   0.904   0.549   0.606   0.688   0.872   0.898   0.951
101   E         0.850   0.870   0.904   0.575   0.617   0.711   0.872   0.898   0.951
102   A         0.850   0.870   0.904   1.003   1.015   1.073   0.872   0.898   0.951
103   R         0.850   0.870   0.904   0.893   0.918   0.979   0.872   0.898   0.951
104   T        -0.841  -1.086  -1.278  -0.238  -0.557  -0.906  -0.716  -1.009  -1.240
105   L         0.850   0.870   0.904   0.923   0.936   1.005   0.872   0.898   0.951
106   K         0.850   0.870   0.904   0.660   0.697   0.783   0.872   0.898   0.951
107   N        -1.540  -1.451  -1.304  -1.351  -1.272  -1.065  -1.571  -1.470  -1.271
108   Q        -1.219  -1.207  -1.281  -0.783  -0.739  -0.905  -1.204  -1.157  -1.244
109   G         0.850   0.870   0.904   0.639   0.685   0.765   0.872   0.898   0.951
110   E         0.850   0.870   0.904   0.575   0.617   0.711   0.872   0.898   0.951
111   L         0.850   0.870   0.904   0.923   0.936   1.005   0.872   0.898   0.951
112   P         0.850   0.870   0.904   1.203   1.220   1.242   0.872   0.898   0.951
113   E        -0.016  -0.185  -0.439  -0.185  -0.406  -0.850   0.017  -0.217  -0.630
114   N        -1.219  -1.389  -1.303  -0.901  -1.130  -1.003  -1.204  -1.412  -1.269
115   A         0.850   0.870   0.904   1.003   1.015   1.073   0.872   0.898   0.951
116   K         0.850   0.870   0.904   0.660   0.697   0.783   0.872   0.898   0.951
117   I         0.850   0.870   0.904   0.933   0.963   1.013   0.872   0.898   0.951
118   N         0.850   0.870   0.904   0.918   0.950   1.001   0.872   0.898   0.951
119   E        -0.016  -0.109  -0.439  -0.185  -0.298  -0.850   0.017  -0.110  -0.631
120   T        -0.016  -0.109  -0.439   0.426   0.308  -0.228   0.017  -0.110  -0.631
121   D         0.850   0.870   0.904   0.549   0.606   0.688   0.872   0.898   0.951
122   N        -1.389  -1.303  -1.289  -1.116  -0.933  -0.981  -1.449  -1.291  -1.253
123   F        -0.016  -0.109  -0.439   0.323   0.203  -0.427   0.017  -0.110  -0.631
124   G         0.850   0.870   0.904   0.639   0.685   0.765   0.872   0.898   0.951
125   F        -1.458  -1.501  -1.302  -1.165  -1.195  -0.937  -1.521  -1.520  -1.268
126   E        -1.347  -1.386  -1.297  -1.690  -1.691  -1.579  -1.361  -1.375  -1.262
127   S        -2.036  -1.929  -1.863  -2.068  -1.998  -1.973  -1.815  -1.677  -1.533
128   D        -0.016  -0.175  -0.422  -0.209  -0.400  -0.825   0.017  -0.202  -0.603
129   E        -1.389  -1.448  -1.291  -1.904  -1.978  -1.725  -1.449  -1.473  -1.256
130   D        -0.671  -0.590  -0.495  -1.261  -1.111  -0.969  -0.960  -0.839  -0.722
131   V        -1.938  -1.939  -1.880  -1.372  -1.424  -1.366  -1.693  -1.704  -1.548
132   N        -0.841  -1.142  -1.271  -0.587  -1.047  -1.420  -0.716  -1.075  -1.231
133   F         0.850   0.870   0.904   1.067   1.100   1.127   0.872   0.898   0.951
134   E         0.850   0.870   0.904   0.575   0.617   0.711   0.872   0.898   0.951
135   F         0.850   0.870   0.904   1.067   1.100   1.127   0.872   0.898   0.951
136   G        -0.525  -0.662  -0.496  -0.910  -1.222  -0.947  -0.723  -0.958  -0.724
137   N        -1.802  -1.801  -1.874  -1.519  -1.639  -1.811  -1.521  -1.537  -1.542
138   A        -1.347  -1.318  -1.303  -1.363  -1.520  -1.511  -1.361  -1.361  -1.269
139   D        -0.093  -0.374  -0.451  -0.284  -0.650  -0.739  -0.085  -0.496  -0.649
140   E        -1.630  -1.513  -1.315  -2.000  -1.887  -1.511  -1.680  -1.533  -1.282
141   D        -0.093  -0.374  -0.451  -0.249  -0.582  -0.640  -0.085  -0.496  -0.649
142   D        -0.720  -0.630  -0.489  -1.377  -1.214  -0.973  -1.042  -0.905  -0.712
143   E        -1.347  -1.220  -1.285  -1.666  -1.532  -1.519  -1.361  -1.225  -1.250
144   E         0.850   0.870   0.904   0.577   0.617   0.712   0.872   0.898   0.951
145   G        -1.630  -1.510  -1.309  -2.269  -2.102  -1.772  -1.680  -1.534  -1.275
146   E        -1.458  -1.525  -1.294  -2.041  -2.127  -1.750  -1.521  -1.547  -1.259
147   D        -1.575  -1.566  -1.309  -2.035  -1.882  -1.542  -1.629  -1.593  -1.276
148   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   E        -1.347  -1.426  -1.293  -1.685  -1.737  -1.554  -1.361  -1.424  -1.258
154   L        -1.347  -1.390  -1.286  -1.085  -1.145  -1.026  -1.361  -1.380  -1.250
155   D         0.850   0.870   0.904   0.549   0.606   0.688   0.872   0.898   0.951
156   I        -0.016  -0.175  -0.422   0.246   0.058  -0.318   0.017  -0.202  -0.603
157   D         0.850   0.870   0.904   0.549   0.606   0.688   0.872   0.898   0.951
158   D        -0.016  -0.175  -0.422  -0.144  -0.310  -0.625   0.017  -0.202  -0.603
159   I         0.850   0.870   0.904   0.933   0.963   1.013   0.872   0.898   0.951
* 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/P38912
Output conservation file - output/P38912
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
