1     M         1.431   1.523   1.563   1.673   1.782   1.860   1.516   1.642   1.706
2     R        -1.199  -0.989  -1.036  -0.880  -0.606  -0.640  -1.164  -0.892  -0.904
3     P        -0.209  -0.303  -0.426   0.124  -0.006  -0.252  -0.219  -0.362  -0.510
4     V        -0.209  -0.486  -0.475  -0.458  -0.851  -0.863  -0.219  -0.582  -0.576
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    V         0.587   0.378   0.371   0.353   0.135   0.106   0.570   0.219   0.176
17    S        -0.209  -0.486  -0.475  -0.125  -0.508  -0.525  -0.219  -0.582  -0.576
18    T        -1.607  -1.476  -1.494  -1.305  -1.172  -1.185  -1.322  -1.163  -1.118
19    G        -0.945  -1.067  -1.058  -0.751  -0.881  -0.877  -0.849  -0.965  -0.926
20    K        -0.537  -0.637  -0.510  -0.390  -0.631  -0.410  -0.691  -0.782  -0.627
21    A         1.431   1.523   1.563   1.277   1.411   1.501   1.516   1.642   1.706
22    W        -0.537  -0.571  -0.491  -0.172  -0.217  -0.135  -0.691  -0.693  -0.601
23    C        -1.199  -1.212  -1.064  -1.264  -1.287  -1.061  -1.164  -1.101  -0.934
24    C         1.431   1.523   1.563   1.626   1.742   1.818   1.516   1.642   1.706
25    T         0.587   0.775   0.435   0.763   1.005   0.519   0.570   0.840   0.289
26    V        -0.537  -0.531  -0.476  -0.933  -0.865  -0.789  -0.691  -0.641  -0.582
27    L        -0.209  -0.167  -0.404  -0.257  -0.245  -0.508  -0.219  -0.163  -0.481
28    S         1.431   1.523   1.563   1.366   1.534   1.582   1.516   1.642   1.706
29    A        -0.209  -0.290  -0.421  -0.281  -0.466  -0.639  -0.219  -0.346  -0.504
30    F         0.587   0.378   0.371   0.555   0.290   0.246   0.570   0.219   0.176
31    G         0.199   0.264   0.259  -0.024   0.039   0.017  -0.061   0.020  -0.024
32    V        -0.537  -0.586  -0.502  -0.857  -0.826  -0.671  -0.691  -0.728  -0.618
33    V         0.587   0.522   0.388   0.297   0.258   0.007   0.570   0.457   0.207
34    I         0.587   0.378   0.371   0.637   0.316   0.292   0.570   0.219   0.176
35    L         1.431   1.523   1.563   1.226   1.323   1.455   1.516   1.642   1.706
36    S        -0.209  -0.486  -0.475  -0.188  -0.651  -0.663  -0.219  -0.582  -0.576
37    V         1.431   1.523   1.563   1.093   1.287   1.334   1.516   1.642   1.706
38    I         0.199   0.143   0.231  -0.005  -0.241  -0.058  -0.061  -0.199  -0.077
39    A        -1.199  -1.189  -1.064  -1.315  -1.240  -1.065  -1.164  -1.078  -0.933
40    H        -1.199  -1.101  -1.053  -0.929  -0.799  -0.783  -1.164  -1.002  -0.923
41    L         1.431   1.523   1.563   1.226   1.323   1.455   1.516   1.642   1.706
42    F         1.431   1.523   1.563   1.317   1.489   1.537   1.516   1.642   1.706
43    N        -1.199  -1.102  -1.054  -0.912  -0.782  -0.721  -1.164  -1.003  -0.924
44    T        -0.945  -1.078  -1.056  -0.684  -0.935  -0.921  -0.849  -0.974  -0.923
45    N        -0.209  -0.303  -0.426   0.165   0.044  -0.196  -0.219  -0.362  -0.510
46    H        -0.209  -0.290  -0.421   0.143  -0.033  -0.282  -0.219  -0.346  -0.504
47    E         0.587   0.522   0.388   0.897   0.826   0.614   0.570   0.457   0.207
48    S        -0.209  -0.486  -0.475  -0.075  -0.422  -0.417  -0.219  -0.582  -0.576
49    F        -0.537  -0.449  -0.499  -0.739  -0.694  -0.658  -0.691  -0.590  -0.614
50    V         0.025   0.136   0.232  -0.358  -0.092   0.051  -0.376  -0.211  -0.074
51    G         0.587   0.378   0.371   0.661   0.393   0.405   0.570   0.219   0.176
52    S        -0.209  -0.486  -0.475  -0.098  -0.443  -0.466  -0.219  -0.582  -0.576
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    I        -0.209  -0.486  -0.475  -0.131  -0.615  -0.607  -0.219  -0.582  -0.576
55    N        -0.209  -0.486  -0.475   0.165  -0.254  -0.283  -0.219  -0.582  -0.576
56    D         0.587   0.378   0.371   0.902   0.586   0.530   0.570   0.219   0.176
57    P         0.587   0.378   0.371   0.857   0.550   0.494   0.570   0.219   0.176
58    E         0.587   0.378   0.371   0.834   0.473   0.440   0.570   0.219   0.176
59    D        -0.209  -0.204  -0.413   0.226   0.172  -0.088  -0.219  -0.252  -0.493
60    G         1.431   1.523   1.563   1.376   1.490   1.591   1.516   1.642   1.706
61    P        -0.637  -0.351  -0.441  -0.561  -0.112  -0.276  -0.849  -0.436  -0.534
62    A        -0.209  -0.486  -0.475  -0.143  -0.485  -0.440  -0.219  -0.582  -0.576
63    V         1.431   1.523   1.563   1.093   1.287   1.334   1.516   1.642   1.706
64    A         1.431   1.523   1.563   1.277   1.411   1.501   1.516   1.642   1.706
65    H        -1.199  -0.980  -1.008  -0.987  -0.694  -0.755  -1.164  -0.857  -0.874
66    T         1.431   1.523   1.563   1.541   1.648   1.740   1.516   1.642   1.706
67    V        -0.945  -1.001  -1.047  -1.118  -1.138  -1.209  -0.849  -0.907  -0.915
68    Y        -1.199  -1.189  -1.064  -1.270  -1.325  -1.096  -1.164  -1.078  -0.933
69    L        -1.199  -1.234  -1.085  -1.375  -1.369  -1.111  -1.164  -1.123  -0.953
70    A         1.431   1.523   1.563   1.277   1.411   1.501   1.516   1.642   1.706
71    A        -0.537  -0.358  -0.431  -0.993  -0.611  -0.773  -0.691  -0.406  -0.518
72    L        -1.761  -1.606  -1.518  -2.172  -1.976  -1.813  -1.480  -1.263  -1.138
73    V         0.199   0.143   0.231  -0.243  -0.295  -0.150  -0.061  -0.199  -0.077
74    Y         1.431   1.523   1.563   1.635   1.757   1.826   1.516   1.642   1.706
75    L         0.025   0.149   0.248  -0.509  -0.324  -0.114  -0.376  -0.187  -0.045
76    V        -0.537  -0.474  -0.479  -1.041  -0.887  -0.937  -0.691  -0.566  -0.585
77    F         1.431   1.523   1.563   1.317   1.489   1.537   1.516   1.642   1.706
78    F         0.587   0.758   0.428   0.523   0.801   0.279   0.570   0.816   0.276
79    V        -0.945  -1.067  -1.058  -1.168  -1.344  -1.310  -0.849  -0.965  -0.926
80    F         1.431   1.523   1.563   1.317   1.489   1.537   1.516   1.642   1.706
81    C         1.431   1.523   1.563   1.626   1.742   1.818   1.516   1.642   1.706
82    G         1.431   1.523   1.563   1.376   1.490   1.591   1.516   1.642   1.706
83    F        -0.791  -0.564  -0.512  -1.257  -0.882  -0.794  -1.007  -0.700  -0.629
84    Q         1.431   1.523   1.563   1.635   1.753   1.826   1.516   1.642   1.706
85    V        -1.199  -0.999  -1.039  -1.586  -1.245  -1.309  -1.164  -0.902  -0.908
86    Y        -1.199  -1.152  -1.067  -1.253  -1.285  -1.183  -1.164  -1.057  -0.937
87    L        -0.209  -0.303  -0.426  -0.349  -0.587  -0.723  -0.219  -0.362  -0.510
88    A        -1.199  -0.964  -1.031  -1.250  -0.840  -0.970  -1.164  -0.872  -0.900
89    R        -1.199  -0.960  -1.014  -0.964  -0.634  -0.725  -1.164  -0.853  -0.884
90    R         0.587   0.378   0.371   0.908   0.659   0.597   0.570   0.219   0.176
91    K        -1.199  -0.901  -1.017  -0.854  -0.424  -0.580  -1.164  -0.781  -0.884
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     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    P        -2.169  -1.957  -1.876  -1.698  -1.426  -1.321  -1.637  -1.381  -1.263
96    S        -0.945  -1.078  -1.056  -0.791  -0.937  -0.932  -0.849  -0.974  -0.923
97    I         0.199   0.218   0.247  -0.055  -0.076  -0.086  -0.061  -0.062  -0.047
98    E        -1.761  -1.609  -1.517  -1.393  -1.197  -1.072  -1.480  -1.264  -1.137
99    L         0.587   0.378   0.371   0.464   0.127   0.169   0.570   0.219   0.176
100   R         0.273   0.219   0.245   0.418   0.325   0.333   0.067  -0.059  -0.050
* 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/P0C5R9
Output conservation file - output/P0C5R9
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
