1     M         1.513   1.535   1.604   1.790   1.824   1.919   1.653   1.676   1.784
2     L         0.251   0.237   0.283  -0.157  -0.142  -0.085  -0.021  -0.054  -0.006
3     C        -1.123  -1.117  -1.054  -1.151  -1.141  -1.001  -1.067  -1.039  -0.939
4     Q        -0.371  -0.412  -0.426  -0.183  -0.263  -0.331  -0.456  -0.508  -0.528
5     Q        -0.492  -0.542  -0.483  -0.399  -0.503  -0.402  -0.649  -0.704  -0.610
6     M        -0.950  -1.016  -1.018  -0.871  -0.991  -0.990  -0.858  -0.921  -0.900
7     I        -1.581  -1.479  -1.487  -1.255  -1.150  -1.117  -1.276  -1.169  -1.127
8     R        -0.207  -0.314  -0.391  -0.094  -0.266  -0.395  -0.230  -0.374  -0.480
9     T        -1.123  -1.136  -1.044  -1.007  -1.048  -0.896  -1.067  -1.058  -0.929
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    T        -1.581  -1.466  -1.470  -1.502  -1.330  -1.337  -1.276  -1.155  -1.112
19    A        -0.492  -0.537  -0.475  -0.542  -0.650  -0.549  -0.649  -0.697  -0.600
20    K        -0.492  -0.537  -0.475  -0.597  -0.692  -0.563  -0.649  -0.697  -0.600
21    R         1.513   1.535   1.604   1.541   1.563   1.679   1.653   1.676   1.784
22    S        -0.492  -0.398  -0.428  -0.532  -0.348  -0.422  -0.649  -0.500  -0.534
23    S         0.620   0.632   0.452   0.347   0.414   0.104   0.607   0.621   0.302
24    N        -0.492  -0.502  -0.478  -0.465  -0.476  -0.409  -0.649  -0.659  -0.603
25    I        -1.123  -1.104  -1.040  -1.130  -1.072  -0.977  -1.067  -1.025  -0.924
26    M        -0.492  -0.475  -0.458  -0.475  -0.462  -0.388  -0.649  -0.618  -0.578
27    T        -1.123  -1.117  -1.054  -1.255  -1.261  -1.132  -1.067  -1.039  -0.939
28    R         0.398   0.432   0.375   0.370   0.421   0.289   0.241   0.292   0.164
29    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    K        -1.581  -1.582  -1.485  -1.295  -1.300  -1.152  -1.276  -1.261  -1.126
36    R        -1.581  -1.499  -1.480  -1.406  -1.301  -1.254  -1.276  -1.188  -1.121
37    S        -1.581  -1.499  -1.480  -1.609  -1.497  -1.466  -1.276  -1.188  -1.121
38    V        -0.492  -0.434  -0.464  -0.635  -0.566  -0.599  -0.649  -0.586  -0.585
39    H        -0.207  -0.292  -0.399   0.119  -0.018  -0.210  -0.230  -0.342  -0.490
40    F        -0.950  -1.056  -1.028  -1.140  -1.243  -1.199  -0.858  -0.966  -0.910
41    K         0.620   0.565   0.438   0.629   0.540   0.368   0.607   0.513   0.277
42    D        -0.207  -0.259  -0.375   0.253   0.167  -0.018  -0.230  -0.298  -0.458
43    G         1.513   1.535   1.604   1.554   1.580   1.690   1.653   1.676   1.784
44    V         0.251   0.223   0.273   0.127   0.064   0.145  -0.021  -0.080  -0.024
45    Y         1.513   1.535   1.604   1.708   1.733   1.840   1.653   1.676   1.784
46    E        -0.492  -0.533  -0.468  -0.396  -0.441  -0.315  -0.649  -0.690  -0.592
47    N         1.513   1.535   1.604   1.685   1.705   1.817   1.653   1.676   1.784
48    I         0.139   0.160   0.259   0.017   0.048   0.203  -0.230  -0.198  -0.051
49    P         1.513   1.535   1.604   1.626   1.645   1.760   1.653   1.676   1.784
50    F         0.620   0.735   0.467   0.350   0.555   0.132   0.607   0.779   0.328
51    K         1.513   1.535   1.604   1.444   1.463   1.584   1.653   1.676   1.784
52    V         0.139   0.171   0.266  -0.079  -0.027   0.117  -0.230  -0.176  -0.039
53    K         0.139   0.168   0.265  -0.018  -0.000   0.164  -0.230  -0.183  -0.040
54    G         0.620   0.632   0.452   0.853   0.861   0.587   0.607   0.621   0.302
55    R         1.513   1.535   1.604   1.541   1.563   1.679   1.653   1.676   1.784
56    K         1.513   1.535   1.604   1.444   1.463   1.584   1.653   1.676   1.784
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    T        -0.207  -0.235  -0.369  -0.015  -0.051  -0.275  -0.230  -0.265  -0.450
59    P         1.513   1.535   1.604   1.626   1.645   1.760   1.653   1.676   1.784
60    Y        -0.492  -0.500  -0.464  -0.611  -0.574  -0.590  -0.649  -0.641  -0.586
61    A         0.620   0.564   0.446   0.589   0.510   0.319   0.607   0.513   0.290
62    L        -0.492  -0.467  -0.447  -0.834  -0.765  -0.741  -0.649  -0.597  -0.563
63    S        -1.581  -1.479  -1.487  -1.250  -1.096  -1.150  -1.276  -1.169  -1.127
64    H        -0.207  -0.292  -0.399   0.060  -0.072  -0.309  -0.230  -0.342  -0.490
65    F         0.251   0.223   0.284  -0.062  -0.056   0.036  -0.021  -0.080  -0.005
66    G         1.513   1.535   1.604   1.554   1.580   1.690   1.653   1.676   1.784
67    F        -0.207  -0.292  -0.399  -0.440  -0.510  -0.708  -0.230  -0.342  -0.490
68    F        -0.207  -0.292  -0.399  -0.384  -0.458  -0.615  -0.230  -0.342  -0.490
69    A        -0.492  -0.501  -0.457  -0.604  -0.607  -0.538  -0.649  -0.641  -0.576
70    I        -2.040  -1.994  -1.872  -2.124  -2.067  -1.869  -1.485  -1.432  -1.275
71    G        -0.207  -0.292  -0.399  -0.145  -0.277  -0.503  -0.230  -0.342  -0.490
72    F         1.513   1.535   1.604   1.190   1.271   1.339   1.653   1.676   1.784
73    A         0.620   0.565   0.438   0.619   0.544   0.361   0.607   0.513   0.277
74    V        -0.492  -0.542  -0.483  -0.846  -0.936  -0.872  -0.649  -0.704  -0.610
75    P         1.513   1.535   1.604   1.626   1.645   1.760   1.653   1.676   1.784
76    F         1.513   1.535   1.604   1.190   1.271   1.339   1.653   1.676   1.784
77    V        -1.123  -1.136  -1.044  -1.101  -1.121  -0.974  -1.067  -1.058  -0.929
78    A        -1.123  -1.149  -1.039  -1.199  -1.225  -1.042  -1.067  -1.073  -0.926
79    C        -1.123  -1.160  -1.043  -0.936  -1.011  -0.827  -1.067  -1.083  -0.929
80    Y         0.620   0.593   0.448   0.930   0.889   0.697   0.607   0.558   0.294
81    V         0.251   0.223   0.284   0.220   0.171   0.281  -0.021  -0.080  -0.005
82    Q         0.251   0.214   0.274   0.395   0.326   0.401  -0.021  -0.097  -0.023
83    L        -0.207  -0.126  -0.357   0.091   0.172  -0.116  -0.230  -0.128  -0.434
84    K         1.513   1.535   1.604   1.444   1.463   1.584   1.653   1.676   1.784
85    K         0.620   0.565   0.438   0.611   0.520   0.336   0.607   0.513   0.277
86    S        -0.492  -0.420  -0.448  -0.804  -0.685  -0.759  -0.649  -0.563  -0.567
87    G         0.620   0.565   0.438   0.721   0.637   0.437   0.607   0.513   0.277
88    A        -0.950  -0.931  -0.983  -0.921  -0.926  -0.969  -0.858  -0.834  -0.862
89    F         0.521   0.627   0.417   0.209   0.364   0.062   0.448   0.613   0.240
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -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/P04039
Output conservation file - output/P04039
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
