1     M         0.951   0.965   1.004   1.247   1.259   1.281   0.995   1.013   1.072
2     S         0.951   0.965   1.004   1.047   1.059   1.111   0.995   1.013   1.072
3     D        -1.777  -1.745  -1.494  -1.626  -1.575  -1.234  -1.675  -1.602  -1.311
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     F        -1.715  -1.736  -1.493  -1.783  -1.733  -1.347  -1.617  -1.595  -1.311
6     Q        -1.497  -1.392  -1.458  -1.260  -1.071  -1.243  -1.390  -1.243  -1.276
7     K         0.951   0.965   1.004   0.714   0.744   0.827   0.995   1.013   1.072
8     E        -1.015  -0.842  -0.930  -1.052  -0.740  -0.948  -1.163  -0.919  -0.991
9     K        -0.866  -0.893  -0.953  -1.053  -1.092  -1.095  -0.936  -0.999  -1.018
10    V        -0.978  -1.023  -0.970  -1.296  -1.402  -1.242  -1.082  -1.139  -1.039
11    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    Q        -1.227  -1.145  -0.969  -1.318  -1.175  -0.916  -1.378  -1.267  -1.037
14    E        -1.497  -1.538  -1.465  -1.282  -1.266  -1.199  -1.390  -1.393  -1.283
15    Q        -1.497  -1.490  -1.468  -1.295  -1.265  -1.235  -1.390  -1.361  -1.287
16    Q        -1.715  -1.702  -1.489  -1.750  -1.737  -1.459  -1.617  -1.567  -1.307
17    Q        -1.715  -1.617  -1.490  -1.684  -1.542  -1.314  -1.617  -1.511  -1.308
18    Q        -1.497  -1.510  -1.469  -1.320  -1.336  -1.326  -1.390  -1.391  -1.289
19    Q        -1.847  -1.886  -1.878  -1.668  -1.784  -1.907  -1.504  -1.529  -1.457
20    I        -0.866  -0.976  -0.963  -1.116  -1.306  -1.217  -0.936  -1.082  -1.030
21    I        -1.497  -1.336  -1.447  -1.254  -0.984  -1.228  -1.390  -1.186  -1.265
22    K        -0.184  -0.301  -0.233  -0.472  -0.662  -0.521  -0.368  -0.569  -0.492
23    I         0.191   0.015  -0.158   0.065  -0.158  -0.466   0.200  -0.056  -0.363
24    R         0.951   0.965   1.004   1.017   1.023   1.085   0.995   1.013   1.072
25    I         0.191   0.296  -0.140   0.133   0.278  -0.249   0.200   0.343  -0.332
26    T         0.191   0.273  -0.146   0.221   0.329  -0.226   0.200   0.312  -0.343
27    L         0.951   0.965   1.004   1.071   1.070   1.131   0.995   1.013   1.072
28    T         0.951   0.965   1.004   0.865   0.890   0.955   0.995   1.013   1.072
29    S         0.951   0.965   1.004   1.047   1.059   1.111   0.995   1.013   1.072
30    T        -0.184  -0.301  -0.233  -0.325  -0.528  -0.415  -0.368  -0.569  -0.492
31    K         0.191   0.115  -0.153   0.070  -0.006  -0.354   0.200   0.092  -0.354
32    V         0.191   0.162  -0.150   0.171   0.154  -0.234   0.200   0.159  -0.350
33    K        -0.534  -0.766  -0.924  -0.587  -0.882  -1.081  -0.481  -0.773  -0.980
34    Q        -1.216  -1.441  -1.477  -0.837  -1.138  -1.241  -1.049  -1.286  -1.295
35    L         0.951   0.965   1.004   1.071   1.070   1.131   0.995   1.013   1.072
36    E         0.951   0.965   1.004   0.926   0.948   1.008   0.995   1.013   1.072
37    N        -0.184  -0.301  -0.233  -0.167  -0.418  -0.387  -0.368  -0.569  -0.492
38    V         0.951   0.965   1.004   0.796   0.827   0.897   0.995   1.013   1.072
39    S        -0.184  -0.301  -0.233  -0.042  -0.221  -0.115  -0.368  -0.569  -0.492
40    S        -0.384  -0.386  -0.251  -0.466  -0.490  -0.288  -0.709  -0.717  -0.524
41    N        -0.866  -1.036  -0.962  -0.648  -0.908  -0.844  -0.936  -1.132  -1.029
42    I        -0.184  -0.301  -0.233  -0.410  -0.587  -0.460  -0.368  -0.569  -0.492
43    V        -0.384  -0.386  -0.251  -0.887  -0.884  -0.649  -0.709  -0.717  -0.524
44    K        -2.065  -2.127  -1.899  -2.052  -2.126  -1.787  -1.731  -1.737  -1.473
45    N        -0.384  -0.399  -0.251  -0.440  -0.502  -0.277  -0.709  -0.741  -0.523
46    A         0.951   0.965   1.004   1.077   1.094   1.136   0.995   1.013   1.072
47    E        -1.583  -1.350  -1.473  -1.871  -1.556  -1.645  -1.504  -1.254  -1.292
48    Q        -1.497  -1.583  -1.481  -1.331  -1.460  -1.311  -1.390  -1.457  -1.299
49    H        -2.547  -2.320  -2.230  -2.162  -1.973  -1.660  -1.958  -1.750  -1.582
50    N        -1.497  -1.589  -1.476  -1.359  -1.438  -1.340  -1.390  -1.446  -1.294
51    L        -0.866  -0.755  -0.916  -0.878  -0.682  -1.034  -0.936  -0.764  -0.970
52    V        -0.866  -0.976  -0.963  -0.972  -1.139  -1.030  -0.936  -1.082  -1.030
53    K        -0.384  -0.399  -0.251  -0.928  -0.956  -0.675  -0.709  -0.741  -0.523
54    K         0.951   0.965   1.004   0.714   0.744   0.827   0.995   1.013   1.072
55    G         0.951   0.965   1.004   1.166   1.174   1.212   0.995   1.013   1.072
56    P         0.951   0.965   1.004   1.119   1.130   1.172   0.995   1.013   1.072
57    V         0.951   0.965   1.004   0.796   0.827   0.897   0.995   1.013   1.072
58    R         0.951   0.965   1.004   1.017   1.023   1.085   0.995   1.013   1.072
59    L        -0.184  -0.019  -0.178  -0.051   0.164  -0.067  -0.368  -0.109  -0.396
60    P         0.951   0.965   1.004   1.119   1.130   1.172   0.995   1.013   1.072
61    T         0.951   0.965   1.004   0.865   0.890   0.955   0.995   1.013   1.072
62    K         0.951   0.965   1.004   0.714   0.744   0.827   0.995   1.013   1.072
63    V        -0.184  -0.301  -0.233  -0.479  -0.697  -0.606  -0.368  -0.569  -0.492
64    L         0.951   0.965   1.004   1.071   1.070   1.131   0.995   1.013   1.072
65    K        -0.534  -0.474  -0.885  -0.577  -0.488  -1.008  -0.481  -0.405  -0.931
66    I         0.951   0.965   1.004   0.758   0.800   0.865   0.995   1.013   1.072
67    S        -0.384  -0.265  -0.224  -0.652  -0.448  -0.384  -0.709  -0.506  -0.476
68    T         0.951   0.965   1.004   0.865   0.890   0.955   0.995   1.013   1.072
69    R         0.951   0.965   1.004   1.017   1.023   1.085   0.995   1.013   1.072
70    K         0.951   0.965   1.004   0.714   0.744   0.827   0.995   1.013   1.072
71    T        -0.184  -0.226  -0.235  -0.315  -0.383  -0.401  -0.368  -0.441  -0.495
72    P         0.951   0.965   1.004   1.119   1.130   1.172   0.995   1.013   1.072
73    N         0.191   0.015  -0.158   0.511   0.307   0.042   0.200  -0.056  -0.363
74    G         0.951   0.965   1.004   1.166   1.174   1.212   0.995   1.013   1.072
75    E         0.951   0.965   1.004   0.926   0.948   1.008   0.995   1.013   1.072
76    G         0.951   0.965   1.004   1.166   1.174   1.212   0.995   1.013   1.072
77    S         0.951   0.965   1.004   1.047   1.059   1.111   0.995   1.013   1.072
78    K         0.951   0.965   1.004   0.714   0.744   0.827   0.995   1.013   1.072
79    T         0.951   0.965   1.004   0.865   0.890   0.955   0.995   1.013   1.072
80    W         0.951   0.965   1.004   1.316   1.323   1.340   0.995   1.013   1.072
81    E        -0.384  -0.321  -0.242  -0.440  -0.339  -0.266  -0.709  -0.604  -0.508
82    T        -1.216  -1.261  -1.445  -1.005  -1.080  -1.264  -1.049  -1.104  -1.263
83    Y        -0.184  -0.283  -0.236   0.187   0.019   0.036  -0.368  -0.537  -0.497
84    E         0.951   0.965   1.004   0.926   0.948   1.008   0.995   1.013   1.072
85    M         0.951   0.965   1.004   1.247   1.259   1.281   0.995   1.013   1.072
86    R         0.951   0.965   1.004   1.017   1.023   1.085   0.995   1.013   1.072
87    I         0.951   0.965   1.004   0.758   0.800   0.865   0.995   1.013   1.072
88    H         0.951   0.965   1.004   1.259   1.263   1.291   0.995   1.013   1.072
89    K         0.951   0.965   1.004   0.714   0.744   0.827   0.995   1.013   1.072
90    R         0.951   0.965   1.004   1.017   1.023   1.085   0.995   1.013   1.072
91    Y        -1.233  -1.078  -0.967  -1.241  -1.011  -0.881  -1.390  -1.185  -1.035
92    I         0.951   0.965   1.004   0.758   0.800   0.865   0.995   1.013   1.072
93    D         0.951   0.965   1.004   1.177   1.182   1.222   0.995   1.013   1.072
94    L         0.191   0.296  -0.140   0.455   0.556   0.019   0.200   0.343  -0.332
95    E        -1.715  -1.714  -1.494  -1.666  -1.636  -1.330  -1.617  -1.575  -1.311
96    A        -0.184  -0.233  -0.231  -0.110  -0.202  -0.247  -0.368  -0.453  -0.489
97    P         0.191   0.301  -0.141   0.446   0.577  -0.095   0.200   0.350  -0.334
98    V        -1.497  -1.568  -1.477  -1.445  -1.533  -1.461  -1.390  -1.423  -1.295
99    Q        -1.583  -1.371  -1.473  -1.509  -1.239  -1.275  -1.504  -1.269  -1.292
100   I        -0.534  -0.422  -0.890  -0.617  -0.452  -1.177  -0.481  -0.345  -0.937
101   V         0.951   0.965   1.004   0.796   0.827   0.897   0.995   1.013   1.072
102   K         0.951   0.965   1.004   0.714   0.744   0.827   0.995   1.013   1.072
103   R        -1.148  -1.159  -0.984  -1.322  -1.346  -1.119  -1.276  -1.281  -1.054
104   I         0.951   0.965   1.004   0.758   0.800   0.865   0.995   1.013   1.072
105   T         0.191   0.015  -0.158   0.167  -0.073  -0.396   0.200  -0.056  -0.363
106   Q        -0.256  -0.366  -0.249  -0.258  -0.469  -0.302  -0.488  -0.682  -0.521
107   I         0.191   0.015  -0.158   0.065  -0.158  -0.466   0.200  -0.056  -0.363
108   T        -0.866  -0.998  -0.961  -0.846  -1.010  -0.889  -0.936  -1.100  -1.029
109   I         0.951   0.965   1.004   0.758   0.800   0.865   0.995   1.013   1.072
110   E         0.951   0.965   1.004   0.926   0.948   1.008   0.995   1.013   1.072
111   P         0.191   0.015  -0.158   0.467   0.232  -0.069   0.200  -0.056  -0.363
112   G         0.951   0.965   1.004   1.166   1.174   1.212   0.995   1.013   1.072
113   V         0.951   0.965   1.004   0.796   0.827   0.897   0.995   1.013   1.072
114   D        -0.184  -0.301  -0.233  -0.051  -0.296  -0.241  -0.368  -0.569  -0.492
115   V         0.951   0.965   1.004   0.796   0.827   0.897   0.995   1.013   1.072
116   E         0.951   0.965   1.004   0.926   0.948   1.008   0.995   1.013   1.072
117   V         0.951   0.965   1.004   0.796   0.827   0.897   0.995   1.013   1.072
118   V        -0.866  -0.670  -0.916  -1.074  -0.740  -1.188  -0.936  -0.667  -0.970
119   V        -0.184  -0.032  -0.180  -0.504  -0.231  -0.509  -0.368  -0.128  -0.401
120   A         0.951   0.965   1.004   1.077   1.094   1.136   0.995   1.013   1.072
121   S        -0.866  -0.805  -0.917  -0.714  -0.597  -0.807  -0.936  -0.826  -0.972
122   N        -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/P38701
Output conservation file - output/P38701
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
