1     M         0.850   0.866   0.905   1.112   1.132   1.170   0.882   0.904   0.960
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     E        -1.254  -1.209  -1.183  -1.297  -1.333  -1.317  -1.331  -1.300  -1.201
5     F        -0.653  -0.588  -0.426  -0.692  -0.604  -0.384  -1.014  -0.914  -0.677
6     K        -1.962  -1.975  -1.744  -2.302  -2.291  -1.896  -1.805  -1.782  -1.487
7     A        -1.962  -2.005  -1.747  -2.326  -2.330  -1.892  -1.805  -1.821  -1.489
8     G         0.850   0.866   0.905   0.545   0.573   0.691   0.882   0.904   0.960
9     S        -0.388  -0.494  -0.421  -0.224  -0.415  -0.372  -0.570  -0.753  -0.668
10    A        -1.132  -1.204  -1.179  -1.034  -1.146  -1.153  -1.175  -1.246  -1.195
11    K         0.850   0.866   0.905   0.372   0.431   0.544   0.882   0.904   0.960
12    K         0.850   0.866   0.905   0.372   0.431   0.544   0.882   0.904   0.960
13    G         0.850   0.866   0.905   0.555   0.582   0.699   0.882   0.904   0.960
14    A         0.850   0.866   0.905   0.847   0.858   0.946   0.882   0.904   0.960
15    T        -1.132  -1.224  -1.184  -1.054  -1.196  -1.144  -1.175  -1.280  -1.201
16    L         0.850   0.866   0.905   0.883   0.917   0.976   0.882   0.904   0.960
17    F         0.850   0.866   0.905   1.050   1.061   1.118   0.882   0.904   0.960
18    K         0.850   0.866   0.905   0.372   0.431   0.544   0.882   0.904   0.960
19    T         0.850   0.866   0.905   0.840   0.862   0.940   0.882   0.904   0.960
20    R         0.850   0.866   0.905   1.091   1.106   1.152   0.882   0.904   0.960
21    C         0.850   0.866   0.905   1.139   1.157   1.193   0.882   0.904   0.960
22    L        -0.606  -0.621  -0.428  -0.809  -0.877  -0.574  -0.933  -0.971  -0.679
23    Q         0.850   0.866   0.905   1.152   1.172   1.204   0.882   0.904   0.960
24    C         0.850   0.866   0.905   1.139   1.157   1.193   0.882   0.904   0.960
25    H         0.850   0.866   0.905   1.098   1.120   1.158   0.882   0.904   0.960
26    T         0.850   0.866   0.905   0.840   0.862   0.940   0.882   0.904   0.960
27    V        -0.770  -0.968  -1.160  -0.357  -0.636  -1.067  -0.691  -0.938  -1.170
28    E         0.850   0.866   0.905   0.904   0.922   0.994   0.882   0.904   0.960
29    K        -1.439  -1.408  -1.209  -1.989  -1.931  -1.546  -1.538  -1.496  -1.229
30    G         0.850   0.866   0.905   0.555   0.582   0.699   0.882   0.904   0.960
31    G         0.850   0.866   0.905   0.555   0.582   0.699   0.882   0.904   0.960
32    P        -0.770  -0.983  -1.160  -0.462  -0.797  -1.237  -0.691  -0.956  -1.171
33    H        -0.606  -0.613  -0.430  -0.566  -0.623  -0.380  -0.933  -0.957  -0.683
34    K         0.850   0.866   0.905   0.372   0.431   0.544   0.882   0.904   0.960
35    V         0.021  -0.109  -0.360   0.381   0.226  -0.200   0.035  -0.150  -0.566
36    G         0.850   0.866   0.905   0.555   0.582   0.699   0.882   0.904   0.960
37    P         0.850   0.866   0.905   1.009   1.033   1.083   0.882   0.904   0.960
38    N         0.021  -0.109  -0.360   0.237   0.056  -0.386   0.035  -0.150  -0.566
39    L         0.850   0.866   0.905   0.883   0.917   0.976   0.882   0.904   0.960
40    H         0.850   0.866   0.905   1.098   1.120   1.158   0.882   0.904   0.960
41    G         0.850   0.866   0.905   0.555   0.582   0.699   0.882   0.904   0.960
42    I        -1.132  -1.143  -1.160  -0.822  -0.834  -0.962  -1.175  -1.163  -1.171
43    F        -0.770  -0.763  -1.148  -0.301  -0.319  -0.885  -0.691  -0.689  -1.156
44    G         0.021  -0.061  -0.357  -0.146  -0.247  -0.634   0.035  -0.082  -0.561
45    R         0.850   0.866   0.905   1.091   1.106   1.152   0.882   0.904   0.960
46    H        -1.295  -1.159  -1.176  -1.657  -1.479  -1.407  -1.417  -1.251  -1.193
47    S        -0.388  -0.494  -0.421  -0.277  -0.486  -0.463  -0.570  -0.753  -0.668
48    G         0.850   0.866   0.905   0.555   0.582   0.699   0.882   0.904   0.960
49    Q        -2.202  -2.092  -2.165  -1.694  -1.564  -1.921  -1.780  -1.682  -1.647
50    A         0.021  -0.109  -0.360   0.163  -0.008  -0.371   0.035  -0.150  -0.566
51    E        -2.202  -2.089  -2.154  -1.736  -1.639  -1.743  -1.780  -1.669  -1.639
52    G         0.850   0.866   0.905   0.555   0.582   0.699   0.882   0.904   0.960
53    Y        -0.388  -0.386  -0.414  -0.244  -0.258  -0.360  -0.570  -0.576  -0.657
54    S         0.021  -0.109  -0.360   0.313   0.143  -0.329   0.035  -0.150  -0.566
55    Y         0.850   0.866   0.905   0.995   1.020   1.071   0.882   0.904   0.960
56    T         0.021  -0.061  -0.357   0.151   0.050  -0.386   0.035  -0.082  -0.561
57    D         0.021  -0.078  -0.356   0.300   0.164  -0.312   0.035  -0.105  -0.559
58    A         0.850   0.866   0.905   0.847   0.858   0.946   0.882   0.904   0.960
59    N         0.850   0.866   0.905   0.953   0.971   1.036   0.882   0.904   0.960
60    I        -1.295  -1.275  -1.173  -1.605  -1.565  -1.325  -1.417  -1.353  -1.188
61    K        -1.514  -1.762  -1.739  -1.596  -1.862  -1.686  -1.296  -1.557  -1.482
62    K         0.850   0.866   0.905   0.372   0.431   0.544   0.882   0.904   0.960
63    N        -0.606  -0.479  -0.399  -1.041  -0.853  -0.694  -0.933  -0.728  -0.631
64    V        -0.606  -0.621  -0.428  -0.524  -0.577  -0.314  -0.933  -0.971  -0.679
65    L        -1.533  -1.377  -1.200  -1.713  -1.502  -1.254  -1.659  -1.472  -1.219
66    W         0.850   0.866   0.905   1.206   1.220   1.250   0.882   0.904   0.960
67    D        -1.132  -0.996  -1.172  -0.938  -0.772  -1.078  -1.175  -1.009  -1.186
68    E         0.021  -0.061  -0.357   0.187   0.072  -0.420   0.035  -0.082  -0.561
69    N        -2.058  -2.000  -1.751  -1.788  -1.780  -1.457  -1.901  -1.828  -1.494
70    N        -1.295  -1.276  -1.173  -1.316  -1.273  -1.104  -1.417  -1.358  -1.189
71    M        -0.676  -0.584  -0.412  -0.760  -0.636  -0.399  -1.054  -0.907  -0.653
72    S        -0.606  -0.621  -0.428  -0.575  -0.630  -0.359  -0.933  -0.971  -0.679
73    E        -1.295  -1.328  -1.181  -1.261  -1.339  -1.144  -1.417  -1.429  -1.198
74    Y         0.850   0.866   0.905   0.995   1.020   1.071   0.882   0.904   0.960
75    L         0.850   0.866   0.905   0.883   0.917   0.976   0.882   0.904   0.960
76    T        -0.388  -0.269  -0.370  -0.398  -0.228  -0.444  -0.570  -0.390  -0.582
77    N         0.850   0.866   0.905   0.953   0.971   1.036   0.882   0.904   0.960
78    P         0.850   0.866   0.905   1.009   1.033   1.083   0.882   0.904   0.960
79    K         0.850   0.866   0.905   0.372   0.431   0.544   0.882   0.904   0.960
80    K         0.850   0.866   0.905   0.372   0.431   0.544   0.882   0.904   0.960
81    Y         0.850   0.866   0.905   0.995   1.020   1.071   0.882   0.904   0.960
82    I         0.850   0.866   0.905   1.091   1.100   1.152   0.882   0.904   0.960
83    P         0.850   0.866   0.905   1.009   1.033   1.083   0.882   0.904   0.960
84    G         0.850   0.866   0.905   0.555   0.582   0.699   0.882   0.904   0.960
85    T         0.850   0.866   0.905   0.840   0.862   0.940   0.882   0.904   0.960
86    K         0.850   0.866   0.905   0.372   0.431   0.544   0.882   0.904   0.960
87    M         0.850   0.866   0.905   1.112   1.132   1.170   0.882   0.904   0.960
88    A         0.850   0.866   0.905   0.847   0.858   0.946   0.882   0.904   0.960
89    F         0.850   0.866   0.905   1.050   1.061   1.118   0.882   0.904   0.960
90    G         0.021  -0.078  -0.356  -0.162  -0.291  -0.682   0.035  -0.105  -0.559
91    G         0.850   0.866   0.905   0.555   0.582   0.699   0.882   0.904   0.960
92    L         0.021  -0.078  -0.356   0.196   0.083  -0.343   0.035  -0.105  -0.559
93    K         0.850   0.866   0.905   0.372   0.431   0.544   0.882   0.904   0.960
94    K         0.850   0.866   0.905   0.372   0.431   0.544   0.882   0.904   0.960
95    E        -1.914  -1.869  -1.737  -1.750  -1.689  -1.534  -1.780  -1.709  -1.481
96    K         0.021  -0.078  -0.356  -0.348  -0.443  -0.824   0.035  -0.105  -0.559
97    D         0.850   0.866   0.905   1.009   1.026   1.083   0.882   0.904   0.960
98    R         0.850   0.866   0.905   1.091   1.106   1.152   0.882   0.904   0.960
99    N         0.021   0.060  -0.339   0.173   0.220  -0.534   0.035   0.087  -0.531
100   D         0.021  -0.078  -0.356   0.307   0.173  -0.291   0.035  -0.105  -0.559
101   L        -1.132  -1.205  -1.180  -0.955  -1.050  -1.029  -1.175  -1.253  -1.197
102   I        -0.388  -0.161  -0.381  -0.148   0.161  -0.228  -0.570  -0.226  -0.601
103   T        -0.770  -0.651  -1.127  -0.553  -0.419  -1.103  -0.691  -0.546  -1.131
104   Y        -0.770  -0.968  -1.160  -0.338  -0.596  -0.897  -0.691  -0.938  -1.170
105   L        -0.606  -0.596  -0.430  -0.668  -0.654  -0.413  -0.933  -0.928  -0.683
106   K        -1.132  -0.995  -1.173  -1.484  -1.288  -1.425  -1.175  -1.028  -1.188
107   K        -0.388  -0.487  -0.422  -0.897  -1.032  -0.872  -0.570  -0.741  -0.669
108   A         0.850   0.866   0.905   0.845   0.852   0.944   0.882   0.904   0.960
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   C        -2.058  -1.996  -1.747  -1.877  -1.813  -1.483  -1.901  -1.812  -1.490
111   E        -2.965  -2.861  -2.532  -2.888  -2.720  -2.242  -2.264  -2.156  -1.771
* 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/P00044
Output conservation file - output/P00044
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
