1     M         1.703   1.718   1.808   1.993   2.018   2.162   1.882   1.900   2.046
2     P         0.483   0.505   0.438   0.614   0.651   0.535   0.351   0.385   0.244
3     V         0.483   0.505   0.438   0.523   0.559   0.441   0.351   0.385   0.244
4     D         0.618   0.683   0.510   0.752   0.854   0.586   0.575   0.679   0.372
5     Q         0.243   0.236   0.313   0.153   0.131   0.243  -0.078  -0.096   0.014
6     E        -0.358  -0.303  -0.422  -0.399  -0.308  -0.511  -0.405  -0.326  -0.481
7     K         0.618   0.683   0.510   0.497   0.588   0.370   0.575   0.679   0.372
8     L         1.703   1.718   1.808   1.585   1.601   1.753   1.882   1.900   2.046
9     A         0.618   0.683   0.510   0.442   0.552   0.245   0.575   0.679   0.372
10    K         0.618   0.651   0.498   0.392   0.447   0.184   0.575   0.628   0.351
11    L         1.703   1.718   1.808   1.585   1.601   1.753   1.882   1.900   2.046
12    H        -0.358  -0.397  -0.444  -0.207  -0.258  -0.324  -0.405  -0.459  -0.510
13    K         1.703   1.718   1.808   1.486   1.512   1.654   1.882   1.900   2.046
14    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    S         0.323   0.326   0.361   0.211   0.209   0.225   0.067   0.071   0.103
16    A         0.243   0.271   0.329  -0.034   0.015   0.105  -0.078  -0.031   0.043
17    A        -0.585  -0.543  -0.528  -0.808  -0.749  -0.699  -0.732  -0.677  -0.629
18    N        -0.358  -0.416  -0.463  -0.536  -0.624  -0.729  -0.405  -0.484  -0.536
19    K        -0.585  -0.558  -0.534  -0.700  -0.684  -0.626  -0.732  -0.692  -0.635
20    V        -0.585  -0.558  -0.534  -0.537  -0.499  -0.446  -0.732  -0.692  -0.635
21    G         1.703   1.718   1.808   1.690   1.720   1.858   1.882   1.900   2.046
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -         1.703   1.718   1.808   1.644   1.669   1.812   1.882   1.900   2.046
24    -         0.483   0.435   0.412   0.274   0.204   0.172   0.351   0.265   0.197
25    G         0.618   0.658   0.518   0.705   0.768   0.581   0.575   0.638   0.387
26    T         0.618   0.658   0.518   0.851   0.906   0.696   0.575   0.638   0.387
27    R        -0.358  -0.416  -0.463  -0.200  -0.276  -0.392  -0.405  -0.484  -0.536
28    R         0.618   0.658   0.518   0.861   0.929   0.677   0.575   0.638   0.387
29    K         0.243   0.231   0.316   0.115   0.066   0.182  -0.078  -0.105   0.018
30    I        -0.358  -0.421  -0.456  -0.454  -0.537  -0.567  -0.405  -0.490  -0.526
31    N        -0.585  -0.558  -0.534  -0.647  -0.615  -0.565  -0.732  -0.692  -0.635
32    K         0.618   0.658   0.518   0.473   0.532   0.344   0.575   0.638   0.387
33    K         0.618   0.683   0.510   0.497   0.588   0.370   0.575   0.679   0.372
34    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    L        -1.303  -1.272  -1.195  -1.639  -1.585  -1.469  -1.181  -1.139  -1.022
37    Y        -1.303  -1.272  -1.195  -1.154  -1.066  -0.985  -1.181  -1.139  -1.022
38    N        -0.552  -0.599  -0.537  -0.780  -0.857  -0.756  -0.671  -0.732  -0.635
39    N        -0.552  -0.583  -0.524  -0.322  -0.404  -0.288  -0.671  -0.711  -0.618
40    N        -0.585  -0.554  -0.521  -0.529  -0.502  -0.414  -0.732  -0.688  -0.619
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    D        -1.186  -1.205  -1.164  -1.262  -1.273  -1.206  -1.059  -1.072  -0.991
43    K        -1.787  -1.766  -1.679  -2.003  -1.985  -1.833  -1.386  -1.355  -1.227
44    D         1.703   1.718   1.808   1.785   1.818   1.953   1.882   1.900   2.046
45    N        -0.358  -0.421  -0.456  -0.252  -0.353  -0.429  -0.405  -0.490  -0.526
46    T         0.243   0.231   0.316  -0.058  -0.071   0.075  -0.078  -0.105   0.018
47    K         1.703   1.718   1.808   1.478   1.504   1.646   1.882   1.900   2.046
48    L         0.618   0.664   0.507   0.554   0.614   0.392   0.575   0.649   0.368
49    Q        -0.358  -0.308  -0.428  -0.217  -0.147  -0.314  -0.405  -0.333  -0.489
50    A        -0.358  -0.298  -0.405  -0.509  -0.405  -0.592  -0.405  -0.319  -0.457
51    E        -0.585  -0.626  -0.529  -0.732  -0.798  -0.649  -0.732  -0.770  -0.629
52    L         1.703   1.718   1.808   1.585   1.601   1.753   1.882   1.900   2.046
53    H        -0.358  -0.416  -0.463  -0.443  -0.510  -0.562  -0.405  -0.484  -0.536
54    K         1.703   1.718   1.808   1.478   1.504   1.646   1.882   1.900   2.046
55    L        -0.358  -0.288  -0.425  -0.345  -0.252  -0.423  -0.405  -0.305  -0.484
56    H        -0.358  -0.416  -0.463  -0.234  -0.325  -0.410  -0.405  -0.484  -0.536
57    P        -1.186  -1.187  -1.149  -1.120  -1.112  -1.027  -1.059  -1.053  -0.976
58    M        -0.358  -0.416  -0.463  -0.156  -0.239  -0.281  -0.405  -0.484  -0.536
59    T        -1.787  -1.766  -1.679  -1.702  -1.659  -1.532  -1.386  -1.355  -1.227
60    I         0.618   0.664   0.507   0.779   0.854   0.583   0.575   0.649   0.368
61    E        -1.186  -1.118  -1.147  -1.220  -1.112  -1.159  -1.059  -0.975  -0.973
62    N        -0.358  -0.397  -0.444  -0.373  -0.433  -0.534  -0.405  -0.459  -0.510
63    V         0.243   0.231   0.316   0.191   0.162   0.288  -0.078  -0.105   0.018
64    A        -1.186  -1.202  -1.140  -1.245  -1.288  -1.175  -1.059  -1.068  -0.966
65    E         1.703   1.718   1.808   1.642   1.671   1.810   1.882   1.900   2.046
66    A         0.243   0.231   0.316  -0.013  -0.050   0.070  -0.078  -0.105   0.018
67    N         1.703   1.718   1.808   1.769   1.780   1.937   1.882   1.900   2.046
68    F         0.243   0.231   0.316   0.410   0.383   0.514  -0.078  -0.105   0.018
69    F         1.703   1.718   1.808   1.948   1.976   2.116   1.882   1.900   2.046
70    K         0.618   0.658   0.518   0.497   0.555   0.382   0.575   0.638   0.387
71    K        -0.358  -0.397  -0.444  -0.419  -0.505  -0.577  -0.405  -0.459  -0.510
72    N         0.618   0.513   0.478   0.754   0.601   0.535   0.575   0.399   0.316
73    G         1.703   1.718   1.808   1.690   1.720   1.858   1.882   1.900   2.046
74    K        -1.186  -1.118  -1.147  -1.279  -1.194  -1.192  -1.059  -0.975  -0.973
75    V         1.703   1.718   1.808   1.761   1.787   1.930   1.882   1.900   2.046
76    L         0.243   0.284   0.339   0.015   0.071   0.167  -0.078  -0.007   0.062
77    H         0.618   0.664   0.507   0.987   1.047   0.810   0.575   0.649   0.368
78    F         1.703   1.718   1.808   1.948   1.976   2.116   1.882   1.900   2.046
79    N        -1.186  -1.118  -1.147  -1.045  -0.945  -0.984  -1.059  -0.975  -0.973
80    S        -1.186  -1.205  -1.164  -1.258  -1.269  -1.202  -1.059  -1.072  -0.991
81    A        -0.585  -0.626  -0.535  -0.652  -0.726  -0.590  -0.732  -0.770  -0.636
82    V        -1.787  -1.766  -1.679  -1.579  -1.548  -1.409  -1.386  -1.355  -1.227
83    V         1.703   1.718   1.808   1.761   1.787   1.930   1.882   1.900   2.046
84    Q        -0.585  -0.558  -0.534  -0.505  -0.485  -0.441  -0.732  -0.692  -0.635
85    I        -1.186  -1.187  -1.149  -1.149  -1.132  -1.091  -1.059  -1.053  -0.976
86    A         0.243   0.273   0.331  -0.034   0.018   0.107  -0.078  -0.027   0.046
87    P        -0.585  -0.552  -0.530  -0.638  -0.583  -0.560  -0.732  -0.686  -0.631
88    Q        -0.585  -0.626  -0.535  -0.741  -0.796  -0.660  -0.732  -0.770  -0.636
89    C        -1.186  -1.187  -1.149  -0.957  -0.933  -0.900  -1.059  -1.053  -0.976
90    N         0.618   0.664   0.507   0.707   0.764   0.522   0.575   0.649   0.368
91    L         0.618   0.513   0.478   0.809   0.634   0.557   0.575   0.399   0.316
92    T         0.243   0.232   0.311   0.338   0.310   0.430  -0.078  -0.102   0.010
93    M         0.618   0.513   0.478   0.574   0.446   0.406   0.575   0.399   0.316
94    I         0.618   0.658   0.518   0.866   0.930   0.736   0.575   0.638   0.387
95    H        -1.186  -1.205  -1.164  -0.659  -0.692  -0.629  -1.059  -1.072  -0.991
96    G         1.703   1.718   1.808   1.690   1.720   1.858   1.882   1.900   2.046
97    Q        -1.787  -1.766  -1.679  -1.563  -1.546  -1.393  -1.386  -1.355  -1.227
98    P        -1.186  -1.118  -1.147  -1.100  -0.974  -1.060  -1.059  -0.975  -0.973
99    K        -0.585  -0.626  -0.535  -0.837  -0.918  -0.773  -0.732  -0.770  -0.636
100   E        -0.358  -0.288  -0.425  -0.355  -0.246  -0.458  -0.405  -0.305  -0.484
101   N         0.618   0.513   0.478   0.450   0.295   0.246   0.575   0.399   0.316
102   T        -1.186  -1.122  -1.124  -1.003  -0.901  -0.917  -1.059  -0.980  -0.949
103   L         0.243   0.271   0.329   0.015   0.051   0.153  -0.078  -0.031   0.043
104   N        -1.186  -1.202  -1.140  -1.023  -1.066  -0.968  -1.059  -1.068  -0.966
105   G        -0.358  -0.416  -0.463  -0.386  -0.481  -0.563  -0.405  -0.484  -0.536
106   L         0.618   0.664   0.507   0.578   0.638   0.430   0.575   0.649   0.368
107   Y        -1.186  -1.187  -1.149  -0.941  -0.922  -0.886  -1.059  -1.053  -0.976
108   P         1.703   1.718   1.808   1.832   1.862   2.000   1.882   1.900   2.046
109   S        -1.186  -1.205  -1.164  -1.103  -1.124  -1.058  -1.059  -1.072  -0.991
110   V         0.618   0.513   0.478   0.821   0.669   0.598   0.575   0.399   0.316
111   A         0.618   0.513   0.478   0.499   0.326   0.252   0.575   0.399   0.316
112   S        -0.585  -0.626  -0.535  -0.548  -0.609  -0.454  -0.732  -0.770  -0.636
113   Q         0.618   0.664   0.507   0.699   0.760   0.533   0.575   0.649   0.368
114   L         0.618   0.651   0.498   0.614   0.653   0.472   0.575   0.628   0.351
115   G         1.703   1.718   1.808   1.690   1.720   1.858   1.882   1.900   2.046
116   S        -1.186  -1.205  -1.164  -1.084  -1.108  -1.074  -1.059  -1.072  -0.991
117   Q        -0.585  -0.626  -0.529  -0.706  -0.761  -0.612  -0.732  -0.770  -0.629
118   E        -1.186  -1.205  -1.164  -1.146  -1.197  -1.149  -1.059  -1.072  -0.991
119   L         1.703   1.718   1.808   1.585   1.601   1.753   1.882   1.900   2.046
120   E        -1.186  -1.118  -1.147  -1.283  -1.172  -1.230  -1.059  -0.975  -0.973
121   Y        -1.787  -1.766  -1.679  -1.489  -1.424  -1.319  -1.386  -1.355  -1.227
122   L         1.703   1.718   1.808   1.585   1.601   1.753   1.882   1.900   2.046
123   T        -0.358  -0.421  -0.456  -0.037  -0.135  -0.204  -0.405  -0.490  -0.526
124   G        -0.358  -0.397  -0.444  -0.381  -0.450  -0.563  -0.405  -0.459  -0.510
125   L        -0.358  -0.303  -0.422  -0.399  -0.325  -0.490  -0.405  -0.326  -0.481
126   A         1.703   1.718   1.808   1.544   1.578   1.712   1.882   1.900   2.046
127   H        -0.358  -0.421  -0.456  -0.267  -0.345  -0.384  -0.405  -0.490  -0.526
128   N        -0.358  -0.397  -0.444  -0.244  -0.322  -0.375  -0.405  -0.459  -0.510
129   L        -1.186  -1.122  -1.124  -0.972  -0.906  -0.848  -1.059  -0.980  -0.949
130   E        -1.186  -1.202  -1.140  -1.234  -1.274  -1.179  -1.059  -1.068  -0.966
131   N        -1.186  -1.133  -1.128  -1.272  -1.187  -1.205  -1.059  -0.991  -0.953
132   E        -1.787  -1.766  -1.679  -1.631  -1.623  -1.462  -1.386  -1.355  -1.227
133   Q        -0.358  -0.298  -0.405  -0.396  -0.299  -0.508  -0.405  -0.319  -0.457
134   T        -1.186  -1.118  -1.147  -1.160  -1.031  -1.140  -1.059  -0.975  -0.973
135   -        -1.303  -1.288  -1.195  -1.250  -1.225  -1.081  -1.181  -1.156  -1.022
136   -         0.323   0.355   0.364  -0.151  -0.095  -0.113   0.067   0.121   0.109
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   V        -1.186  -1.187  -1.149  -1.336  -1.323  -1.274  -1.059  -1.053  -0.976
147   L        -0.585  -0.626  -0.529  -1.064  -1.127  -0.972  -0.732  -0.770  -0.629
148   D         0.618   0.651   0.498   0.723   0.783   0.520   0.575   0.628   0.351
149   Q         0.618   0.513   0.478   0.505   0.358   0.292   0.575   0.399   0.316
150   L        -1.186  -1.187  -1.149  -1.269  -1.289  -1.228  -1.059  -1.053  -0.976
151   G        -1.186  -1.118  -1.147  -1.262  -1.135  -1.216  -1.059  -0.975  -0.973
152   D         0.618   0.658   0.518   0.723   0.792   0.556   0.575   0.638   0.387
153   R        -0.358  -0.421  -0.456  -0.195  -0.275  -0.350  -0.405  -0.490  -0.526
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   C         0.618   0.513   0.478   0.904   0.773   0.735   0.575   0.399   0.316
157   S         0.618   0.513   0.478   0.815   0.668   0.605   0.575   0.399   0.316
158   E        -0.358  -0.421  -0.456  -0.252  -0.362  -0.429  -0.405  -0.490  -0.526
159   T         0.618   0.513   0.478   0.586   0.432   0.397   0.575   0.399   0.316
160   K         0.618   0.513   0.478   0.660   0.487   0.396   0.575   0.399   0.316
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   Q         0.243   0.231   0.316  -0.011  -0.037   0.097  -0.078  -0.105   0.018
164   Q        -0.585  -0.626  -0.529  -0.834  -0.905  -0.739  -0.732  -0.770  -0.629
165   V         0.618   0.513   0.478   0.911   0.756   0.684   0.575   0.399   0.316
166   M         0.323   0.285   0.355   0.256   0.205   0.318   0.067  -0.004   0.092
167   N        -0.358  -0.397  -0.444  -0.192  -0.260  -0.328  -0.405  -0.459  -0.510
168   -        -1.303  -1.288  -1.195  -1.452  -1.418  -1.282  -1.181  -1.156  -1.022
169   -         0.483   0.532   0.425   0.542   0.618   0.433   0.351   0.430   0.221
170   S        -0.358  -0.411  -0.448  -0.322  -0.397  -0.449  -0.405  -0.478  -0.516
* 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/P40314
Output conservation file - output/P40314
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
