1     M         0.935   0.944   1.010   1.161   1.166   1.250   0.992   1.003   1.098
2     L         0.238   0.188  -0.055   0.004  -0.045  -0.380   0.227   0.149  -0.271
3     F        -0.105  -0.110  -0.137  -0.240  -0.257  -0.416  -0.320  -0.335  -0.419
4     F        -0.426  -0.566  -0.772  -0.171  -0.353  -0.638  -0.429  -0.619  -0.889
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     S         0.935   0.944   1.010   0.947   0.966   1.061   0.992   1.003   1.098
8     F         0.238   0.143  -0.053   0.330   0.191  -0.209   0.227   0.080  -0.268
9     F         0.935   0.944   1.010   1.003   1.017   1.111   0.992   1.003   1.098
10    K         0.935   0.944   1.010   0.897   0.915   1.017   0.992   1.003   1.098
11    T         0.935   0.944   1.010   1.003   1.016   1.111   0.992   1.003   1.098
12    L         0.935   0.944   1.010   0.626   0.652   0.778   0.992   1.003   1.098
13    V        -0.105  -0.178  -0.145  -0.340  -0.472  -0.398  -0.320  -0.456  -0.434
14    D         0.238   0.143  -0.053   0.320   0.198  -0.129   0.227   0.080  -0.268
15    Q        -0.867  -0.914  -0.820  -0.760  -0.818  -0.686  -1.086  -1.124  -0.956
16    E         0.935   0.944   1.010   1.045   1.051   1.148   0.992   1.003   1.098
17    V         0.238   0.143  -0.053   0.150   0.022  -0.249   0.227   0.080  -0.268
18    V        -0.730  -0.551  -0.768  -0.807  -0.495  -0.905  -0.867  -0.608  -0.885
19    V         0.935   0.944   1.010   0.767   0.776   0.903   0.992   1.003   1.098
20    E         0.238   0.358  -0.038   0.439   0.577   0.034   0.227   0.393  -0.242
21    L         0.935   0.944   1.010   0.626   0.652   0.778   0.992   1.003   1.098
22    K         0.935   0.944   1.010   0.897   0.915   1.017   0.992   1.003   1.098
23    N         0.935   0.944   1.010   0.961   0.989   1.074   0.992   1.003   1.098
24    D         0.238   0.275  -0.047   0.347   0.394  -0.047   0.227   0.276  -0.257
25    I        -0.426  -0.606  -0.770  -0.235  -0.512  -0.830  -0.429  -0.672  -0.887
26    E        -0.730  -0.861  -0.823  -0.628  -0.837  -0.801  -0.867  -1.040  -0.959
27    I         0.238   0.275  -0.047   0.358   0.399  -0.172   0.227   0.276  -0.257
28    K        -0.867  -0.826  -0.820  -1.042  -0.971  -0.919  -1.086  -1.035  -0.957
29    G         0.935   0.944   1.010   1.148   1.154   1.238   0.992   1.003   1.098
30    T        -0.867  -0.884  -0.818  -0.990  -1.025  -0.930  -1.086  -1.094  -0.954
31    L         0.935   0.944   1.010   0.626   0.652   0.778   0.992   1.003   1.098
32    Q        -0.105   0.069  -0.071  -0.187   0.077  -0.139  -0.320  -0.037  -0.300
33    S         0.935   0.944   1.010   0.947   0.966   1.061   0.992   1.003   1.098
34    V         0.935   0.944   1.010   0.767   0.776   0.903   0.992   1.003   1.098
35    D         0.935   0.944   1.010   0.947   0.961   1.061   0.992   1.003   1.098
36    Q         0.935   0.944   1.010   1.113   1.129   1.208   0.992   1.003   1.098
37    F         0.238   0.329  -0.043   0.406   0.516   0.013   0.227   0.354  -0.250
38    L         0.238   0.143  -0.053   0.029  -0.074  -0.311   0.227   0.080  -0.268
39    N         0.935   0.944   1.010   0.961   0.989   1.074   0.992   1.003   1.098
40    L        -0.730  -0.861  -0.823  -1.096  -1.295  -1.198  -0.867  -1.040  -0.959
41    K         0.935   0.944   1.010   0.897   0.915   1.017   0.992   1.003   1.098
42    L         0.935   0.944   1.010   0.626   0.652   0.778   0.992   1.003   1.098
43    D        -0.105  -0.199  -0.146  -0.162  -0.328  -0.260  -0.320  -0.493  -0.435
44    N         0.935   0.944   1.010   0.961   0.989   1.074   0.992   1.003   1.098
45    I         0.238   0.143  -0.053   0.377   0.230  -0.133   0.227   0.080  -0.268
46    S        -0.730  -0.785  -0.809  -0.730  -0.806  -0.839  -0.867  -0.938  -0.942
47    C        -1.309  -1.375  -1.316  -1.125  -1.311  -1.260  -1.304  -1.376  -1.235
48    T        -0.988  -0.823  -0.820  -1.322  -1.058  -1.039  -1.195  -0.968  -0.952
49    D        -1.067  -1.046  -0.853  -1.292  -1.245  -0.949  -1.304  -1.269  -0.996
50    E        -1.629  -1.549  -1.664  -1.314  -1.216  -1.398  -1.414  -1.330  -1.368
51    K        -2.270  -2.223  -2.021  -2.336  -2.274  -1.964  -1.851  -1.786  -1.514
52    K         0.238   0.298  -0.043   0.277   0.358  -0.133   0.227   0.310  -0.250
53    Y         0.238   0.143  -0.053   0.546   0.416   0.067   0.227   0.080  -0.268
54    P         0.935   0.944   1.010   1.228   1.228   1.310   0.992   1.003   1.098
55    H         0.238   0.298  -0.043   0.589   0.649   0.162   0.227   0.310  -0.250
56    L         0.238   0.137  -0.061   0.029  -0.082  -0.321   0.227   0.071  -0.281
57    G        -1.829  -1.812  -1.693  -1.634  -1.616  -1.413  -1.632  -1.593  -1.394
58    S        -0.347  -0.287  -0.155  -0.510  -0.396  -0.188  -0.758  -0.654  -0.453
59    V         0.935   0.944   1.010   0.767   0.776   0.903   0.992   1.003   1.098
60    R        -0.347  -0.310  -0.164  -0.647  -0.587  -0.345  -0.758  -0.698  -0.468
61    N        -0.105  -0.199  -0.146  -0.180  -0.343  -0.303  -0.320  -0.493  -0.435
62    I        -1.309  -1.199  -1.285  -1.596  -1.433  -1.493  -1.304  -1.153  -1.201
63    F         0.935   0.944   1.010   1.003   1.017   1.111   0.992   1.003   1.098
64    I         0.935   0.944   1.010   1.031   1.033   1.135   0.992   1.003   1.098
65    R         0.935   0.944   1.010   1.010   1.019   1.117   0.992   1.003   1.098
66    G         0.935   0.944   1.010   1.148   1.154   1.238   0.992   1.003   1.098
67    S         0.935   0.944   1.010   0.947   0.966   1.061   0.992   1.003   1.098
68    T        -0.867  -0.812  -0.820  -1.113  -1.081  -1.028  -1.086  -1.023  -0.957
69    V         0.935   0.944   1.010   0.767   0.776   0.903   0.992   1.003   1.098
70    R         0.935   0.944   1.010   1.010   1.019   1.117   0.992   1.003   1.098
71    Y         0.935   0.944   1.010   1.168   1.177   1.256   0.992   1.003   1.098
72    V         0.935   0.944   1.010   0.767   0.776   0.903   0.992   1.003   1.098
73    Y        -0.105   0.069  -0.071   0.108   0.354   0.113  -0.320  -0.037  -0.300
74    L        -0.289  -0.264  -0.159  -0.699  -0.648  -0.433  -0.648  -0.612  -0.460
75    N        -1.309  -1.377  -1.317  -1.215  -1.300  -1.234  -1.304  -1.378  -1.235
76    K        -1.508  -1.509  -1.331  -1.525  -1.496  -1.208  -1.523  -1.505  -1.249
77    N        -1.629  -1.763  -1.698  -1.372  -1.553  -1.463  -1.414  -1.539  -1.397
78    M        -1.387  -1.451  -1.315  -1.253  -1.323  -1.102  -1.414  -1.446  -1.232
79    V         0.935   0.944   1.010   0.767   0.776   0.903   0.992   1.003   1.098
80    D         0.935   0.944   1.010   0.947   0.961   1.061   0.992   1.003   1.098
81    T        -0.730  -0.697  -0.790  -0.595  -0.543  -0.679  -0.867  -0.805  -0.915
82    N        -1.387  -1.427  -1.316  -1.395  -1.414  -1.233  -1.414  -1.424  -1.234
83    L         0.935   0.944   1.010   0.626   0.652   0.778   0.992   1.003   1.098
84    L         0.935   0.944   1.010   0.626   0.652   0.778   0.992   1.003   1.098
85    Q        -0.730  -0.861  -0.823  -0.553  -0.766  -0.717  -0.867  -1.040  -0.959
86    D         0.935   0.944   1.010   0.947   0.961   1.061   0.992   1.003   1.098
87    A         0.935   0.944   1.010   1.148   1.133   1.238   0.992   1.003   1.098
88    T        -0.730  -0.739  -0.795  -0.670  -0.645  -0.742  -0.867  -0.858  -0.922
89    R         0.935   0.944   1.010   1.010   1.019   1.117   0.992   1.003   1.098
90    R         0.935   0.944   1.010   1.010   1.019   1.117   0.992   1.003   1.098
91    E        -0.730  -0.793  -0.811  -0.616  -0.712  -0.765  -0.867  -0.937  -0.944
92    V        -2.270  -2.095  -2.010  -2.239  -2.024  -1.835  -1.851  -1.704  -1.507
93    M        -1.508  -1.520  -1.327  -1.587  -1.621  -1.337  -1.523  -1.512  -1.245
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   T        -2.591  -2.512  -2.289  -2.507  -2.388  -2.086  -1.961  -1.882  -1.594
106   E        -2.270  -2.188  -2.018  -2.081  -1.959  -1.760  -1.851  -1.765  -1.512
107   R        -1.629  -1.625  -1.683  -1.512  -1.517  -1.718  -1.414  -1.407  -1.385
108   K        -1.051  -1.105  -1.284  -0.890  -0.957  -1.206  -0.976  -1.043  -1.199
* 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/P38203
Output conservation file - output/P38203
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
