1     M         0.960   0.982   1.027   1.245   1.271   1.318   1.020   1.050   1.116
2     A        -0.143  -0.212  -0.135  -0.243  -0.361  -0.239  -0.399  -0.529  -0.431
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     E        -1.915  -1.834  -1.681  -2.018  -1.873  -1.639  -1.696  -1.602  -1.380
10    K        -0.957  -0.997  -0.827  -1.211  -1.299  -1.053  -1.153  -1.199  -0.967
11    R         0.960   0.982   1.027   0.985   1.004   1.087   1.020   1.050   1.116
12    T        -1.595  -1.544  -1.643  -1.376  -1.294  -1.455  -1.370  -1.302  -1.347
13    L        -0.077  -0.080  -0.102  -0.208  -0.198  -0.258  -0.284  -0.293  -0.370
14    I        -0.957  -0.932  -0.815  -1.231  -1.180  -1.016  -1.153  -1.118  -0.952
15    A         0.265   0.080  -0.040   0.320   0.084  -0.097   0.259  -0.027  -0.259
16    V        -0.077   0.003  -0.078  -0.136  -0.016  -0.183  -0.284  -0.153  -0.327
17    I         0.960   0.982   1.027   0.841   0.866   0.959   1.020   1.050   1.116
18    A        -0.260  -0.284  -0.146  -0.465  -0.509  -0.283  -0.610  -0.662  -0.451
19    D         0.960   0.982   1.027   0.824   0.842   0.944   1.020   1.050   1.116
20    E         0.265   0.080  -0.040   0.249  -0.005  -0.231   0.259  -0.027  -0.259
21    D         0.960   0.982   1.027   0.824   0.842   0.944   1.020   1.050   1.116
22    T        -0.260  -0.233  -0.139  -0.435  -0.392  -0.245  -0.610  -0.567  -0.438
23    T        -0.260  -0.163  -0.121  -0.472  -0.301  -0.263  -0.610  -0.441  -0.405
24    T         0.960   0.982   1.027   0.919   0.951   1.028   1.020   1.050   1.116
25    G         0.960   0.982   1.027   1.050   1.078   1.144   1.020   1.050   1.116
26    L         0.265   0.080  -0.040   0.300   0.094  -0.068   0.259  -0.027  -0.259
27    L         0.960   0.982   1.027   0.863   0.909   0.979   1.020   1.050   1.116
28    L         0.960   0.982   1.027   0.863   0.909   0.979   1.020   1.050   1.116
29    A         0.960   0.982   1.027   0.908   0.938   1.018   1.020   1.050   1.116
30    G         0.960   0.982   1.027   1.050   1.078   1.144   1.020   1.050   1.116
31    I        -0.700  -0.781  -0.771  -0.820  -0.933  -0.927  -0.827  -0.907  -0.897
32    G         0.960   0.982   1.027   1.050   1.078   1.144   1.020   1.050   1.116
33    Q        -0.396  -0.417  -0.735   0.018  -0.007  -0.472  -0.393  -0.414  -0.846
34    I        -0.318  -0.271  -0.138  -0.657  -0.569  -0.346  -0.719  -0.638  -0.437
35    T        -0.836  -0.928  -0.793  -0.852  -0.942  -0.758  -1.045  -1.120  -0.928
36    P        -2.234  -2.248  -2.001  -2.054  -2.110  -1.808  -1.805  -1.787  -1.494
37    E        -0.802  -0.858  -0.804  -0.985  -1.049  -0.975  -0.967  -1.023  -0.939
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    T        -2.234  -2.248  -2.001  -2.087  -2.085  -1.771  -1.805  -1.787  -1.494
40    Q        -1.276  -1.348  -1.275  -1.117  -1.200  -1.094  -1.262  -1.311  -1.192
41    E        -1.019  -1.195  -1.271  -0.905  -1.171  -1.287  -0.936  -1.137  -1.186
42    K        -0.396  -0.283  -0.714  -0.244  -0.089  -0.711  -0.393  -0.240  -0.818
43    N         0.960   0.982   1.027   1.114   1.140   1.201   1.020   1.050   1.116
44    F         0.960   0.982   1.027   1.034   1.067   1.130   1.020   1.050   1.116
45    F        -0.836  -0.768  -0.782  -0.958  -0.842  -0.854  -1.045  -0.953  -0.914
46    V        -0.281  -0.266  -0.143  -0.490  -0.475  -0.292  -0.649  -0.627  -0.445
47    Y        -1.276  -1.282  -1.277  -1.122  -1.165  -1.146  -1.262  -1.249  -1.194
48    Q        -1.475  -1.381  -1.296  -1.498  -1.396  -1.205  -1.479  -1.365  -1.213
49    E        -1.475  -1.532  -1.310  -1.650  -1.733  -1.394  -1.479  -1.507  -1.227
50    G        -1.019  -1.195  -1.271  -0.684  -0.923  -1.070  -0.936  -1.137  -1.186
51    K         0.960   0.982   1.027   0.946   0.984   1.052   1.020   1.050   1.116
52    T         0.960   0.982   1.027   0.919   0.951   1.028   1.020   1.050   1.116
53    T        -1.019  -0.987  -1.242  -0.891  -0.849  -1.269  -0.936  -0.889  -1.156
54    K        -1.915  -1.903  -1.690  -1.865  -1.870  -1.564  -1.696  -1.661  -1.387
55    E        -0.396  -0.368  -0.724  -0.356  -0.301  -0.875  -0.393  -0.351  -0.831
56    E        -1.475  -1.445  -1.306  -1.585  -1.514  -1.319  -1.479  -1.441  -1.223
57    I        -0.700  -0.572  -0.761  -0.831  -0.639  -0.932  -0.827  -0.643  -0.883
58    T        -1.595  -1.548  -1.652  -1.452  -1.407  -1.548  -1.370  -1.325  -1.355
59    D        -1.276  -1.224  -1.269  -1.406  -1.289  -1.403  -1.262  -1.175  -1.186
60    K        -0.396  -0.201  -0.711  -0.250  -0.010  -0.667  -0.393  -0.134  -0.814
61    F         0.960   0.982   1.027   1.034   1.067   1.130   1.020   1.050   1.116
62    N        -1.595  -1.381  -1.632  -1.521  -1.234  -1.587  -1.370  -1.134  -1.338
63    H        -2.234  -2.201  -1.989  -2.141  -2.147  -1.805  -1.805  -1.758  -1.486
64    F         0.265   0.080  -0.040   0.464   0.240   0.055   0.259  -0.027  -0.259
65    T         0.960   0.982   1.027   0.919   0.951   1.028   1.020   1.050   1.116
66    E        -1.354  -1.289  -1.274  -1.422  -1.305  -1.224  -1.370  -1.281  -1.192
67    E        -1.035  -1.031  -0.832  -1.341  -1.317  -1.016  -1.262  -1.244  -0.973
68    R         0.960   0.982   1.027   0.985   1.004   1.087   1.020   1.050   1.116
69    D        -1.354  -1.234  -1.282  -1.441  -1.261  -1.251  -1.370  -1.232  -1.201
70    D         0.960   0.982   1.027   0.824   0.842   0.944   1.020   1.050   1.116
71    I         0.960   0.982   1.027   0.841   0.866   0.959   1.020   1.050   1.116
72    A         0.265   0.249  -0.026   0.315   0.300  -0.090   0.259   0.236  -0.235
73    I         0.960   0.982   1.027   0.841   0.866   0.959   1.020   1.050   1.116
74    L        -0.077  -0.183  -0.130  -0.226  -0.400  -0.334  -0.284  -0.476  -0.422
75    L         0.960   0.982   1.027   0.863   0.909   0.979   1.020   1.050   1.116
76    I         0.960   0.982   1.027   0.841   0.866   0.959   1.020   1.050   1.116
77    N         0.960   0.982   1.027   1.114   1.140   1.201   1.020   1.050   1.116
78    Q         0.960   0.982   1.027   1.161   1.186   1.244   1.020   1.050   1.116
79    H         0.265   0.080  -0.040   0.602   0.357   0.118   0.259  -0.027  -0.259
80    I        -0.396  -0.526  -0.735  -0.390  -0.585  -0.921  -0.393  -0.574  -0.846
81    A         0.960   0.982   1.027   0.908   0.938   1.018   1.020   1.050   1.116
82    E        -0.260  -0.251  -0.138  -0.636  -0.633  -0.439  -0.610  -0.600  -0.437
83    N        -1.794  -1.713  -1.670  -1.708  -1.611  -1.479  -1.588  -1.510  -1.372
84    I         0.960   0.982   1.027   0.841   0.866   0.959   1.020   1.050   1.116
85    R         0.960   0.982   1.027   0.985   1.004   1.087   1.020   1.050   1.116
86    A        -2.554  -2.483  -2.256  -2.121  -2.069  -1.741  -1.914  -1.843  -1.565
87    R        -0.396  -0.295  -0.716  -0.238  -0.110  -0.756  -0.393  -0.255  -0.820
88    V         0.265   0.080  -0.040   0.357   0.087  -0.136   0.259  -0.027  -0.259
89    D         0.265   0.080  -0.040   0.205  -0.060  -0.253   0.259  -0.027  -0.259
90    S        -1.475  -1.532  -1.307  -1.401  -1.467  -1.156  -1.479  -1.506  -1.224
91    F        -0.957  -0.949  -0.819  -0.757  -0.745  -0.604  -1.153  -1.144  -0.957
92    T        -0.396  -0.526  -0.735  -0.261  -0.448  -0.742  -0.393  -0.574  -0.846
93    N        -1.276  -1.289  -1.283  -1.032  -1.073  -1.098  -1.262  -1.284  -1.202
94    A         0.265   0.361  -0.019   0.319   0.437  -0.067   0.259   0.397  -0.222
95    F         0.960   0.982   1.027   1.034   1.067   1.130   1.020   1.050   1.116
96    P         0.960   0.982   1.027   1.077   1.110   1.168   1.020   1.050   1.116
97    A         0.265   0.249  -0.026   0.296   0.279  -0.140   0.259   0.236  -0.235
98    I        -0.700  -0.783  -0.796  -0.831  -0.985  -0.987  -0.827  -0.955  -0.931
99    L         0.960   0.982   1.027   0.863   0.909   0.979   1.020   1.050   1.116
100   E         0.960   0.982   1.027   0.874   0.916   0.989   1.020   1.050   1.116
101   I         0.960   0.982   1.027   0.841   0.866   0.959   1.020   1.050   1.116
102   P         0.960   0.982   1.027   1.077   1.110   1.168   1.020   1.050   1.116
103   S         0.960   0.982   1.027   1.087   1.116   1.178   1.020   1.050   1.116
104   K         0.960   0.982   1.027   0.946   0.984   1.052   1.020   1.050   1.116
105   D         0.960   0.982   1.027   0.824   0.842   0.944   1.020   1.050   1.116
106   H         0.265   0.080  -0.040   0.573   0.307   0.040   0.259  -0.027  -0.259
107   P         0.960   0.982   1.027   1.077   1.110   1.168   1.020   1.050   1.116
108   Y         0.960   0.982   1.027   1.214   1.243   1.290   1.020   1.050   1.116
109   D         0.265   0.279  -0.026   0.221   0.229  -0.187   0.259   0.279  -0.235
110   P         0.960   0.982   1.027   1.077   1.110   1.168   1.020   1.050   1.116
111   E         0.960   0.982   1.027   0.874   0.916   0.989   1.020   1.050   1.116
112   K         0.960   0.982   1.027   0.946   0.984   1.052   1.020   1.050   1.116
113   D         0.960   0.982   1.027   0.824   0.842   0.944   1.020   1.050   1.116
114   S         0.960   0.982   1.027   1.087   1.116   1.178   1.020   1.050   1.116
115   V        -0.260  -0.266  -0.142  -0.513  -0.556  -0.354  -0.610  -0.628  -0.443
116   L         0.960   0.982   1.027   0.863   0.909   0.979   1.020   1.050   1.116
117   K        -0.318  -0.271  -0.138  -0.576  -0.495  -0.281  -0.719  -0.638  -0.437
118   R        -0.077   0.003  -0.078  -0.119  -0.001  -0.161  -0.284  -0.153  -0.327
119   V         0.960   0.982   1.027   0.979   1.002   1.082   1.020   1.050   1.116
120   R         0.960   0.982   1.027   0.985   1.004   1.087   1.020   1.050   1.116
121   K        -0.318  -0.290  -0.147  -0.576  -0.535  -0.299  -0.719  -0.673  -0.452
122   L         0.265   0.080  -0.040   0.240  -0.005  -0.233   0.259  -0.027  -0.259
123   F         0.265   0.080  -0.040   0.411   0.152  -0.091   0.259  -0.027  -0.259
124   G         0.960   0.982   1.027   1.050   1.078   1.144   1.020   1.050   1.116
125   E        -0.077  -0.026  -0.105  -0.266  -0.178  -0.361  -0.284  -0.202  -0.376
126   -        -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/P39111
Output conservation file - output/P39111
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
