1     M         0.777   0.782   0.828   1.074   1.066   1.095   0.810   0.818   0.883
2     G         0.777   0.782   0.828   0.930   0.932   0.977   0.810   0.818   0.883
3     R         0.777   0.782   0.828   0.462   0.479   0.596   0.810   0.818   0.883
4     V         0.777   0.782   0.828   0.705   0.711   0.795   0.810   0.818   0.883
5     R         0.777   0.782   0.828   0.462   0.479   0.596   0.810   0.818   0.883
6     T         0.777   0.782   0.828   0.786   0.793   0.861   0.810   0.818   0.883
7     K         0.777   0.782   0.828   0.587   0.611   0.699   0.810   0.818   0.883
8     T         0.777   0.782   0.828   0.786   0.793   0.861   0.810   0.818   0.883
9     V        -0.365  -0.467  -0.438  -0.467  -0.640  -0.608  -0.527  -0.702  -0.689
10    K         0.777   0.782   0.828   0.587   0.611   0.699   0.810   0.818   0.883
11    R         0.025  -0.093  -0.404  -0.204  -0.346  -0.819   0.046  -0.121  -0.633
12    A         0.025  -0.093  -0.404   0.259   0.115  -0.394   0.046  -0.121  -0.633
13    S         0.025  -0.093  -0.404   0.212   0.084  -0.411   0.046  -0.121  -0.633
14    K        -0.365  -0.467  -0.438  -0.677  -0.860  -0.852  -0.527  -0.702  -0.689
15    A        -0.595  -0.435  -0.433  -0.810  -0.549  -0.550  -0.909  -0.649  -0.681
16    L        -1.842  -1.844  -1.748  -1.946  -1.918  -1.663  -1.768  -1.745  -1.543
17    I         0.777   0.782   0.828   0.826   0.824   0.893   0.810   0.818   0.883
18    E         0.777   0.782   0.828   0.811   0.808   0.881   0.810   0.818   0.883
19    R        -0.595  -0.607  -0.468  -1.184  -1.205  -0.935  -0.909  -0.942  -0.741
20    Y        -0.365  -0.214  -0.418  -0.112   0.085  -0.259  -0.527  -0.300  -0.655
21    Y         0.777   0.782   0.828   1.002   0.994   1.037   0.810   0.818   0.883
22    P         0.777   0.782   0.828   0.964   0.953   1.005   0.810   0.818   0.883
23    K        -0.365  -0.467  -0.438  -0.677  -0.860  -0.852  -0.527  -0.702  -0.689
24    L         0.777   0.782   0.828   0.660   0.691   0.757   0.810   0.818   0.883
25    T         0.777   0.782   0.828   0.786   0.793   0.861   0.810   0.818   0.883
26    L        -0.365  -0.210  -0.415  -0.428  -0.195  -0.471  -0.527  -0.293  -0.651
27    D         0.777   0.782   0.828   0.876   0.876   0.933   0.810   0.818   0.883
28    F         0.777   0.782   0.828   1.026   1.021   1.056   0.810   0.818   0.883
29    Q        -0.704  -0.648  -0.471  -0.898  -0.810  -0.538  -1.100  -1.013  -0.747
30    T         0.777   0.782   0.828   0.786   0.793   0.861   0.810   0.818   0.883
31    N         0.777   0.782   0.828   0.988   0.993   1.025   0.810   0.818   0.883
32    K         0.777   0.782   0.828   0.587   0.611   0.699   0.810   0.818   0.883
33    R         0.777   0.782   0.828   0.462   0.479   0.596   0.810   0.818   0.883
34    L        -0.595  -0.645  -0.470  -0.883  -0.958  -0.669  -0.909  -1.008  -0.746
35    C        -1.968  -1.876  -1.754  -1.692  -1.613  -1.483  -1.864  -1.765  -1.548
36    D        -0.365  -0.214  -0.418  -0.287  -0.067  -0.429  -0.527  -0.300  -0.655
37    E         0.777   0.782   0.828   0.811   0.808   0.881   0.810   0.818   0.883
38    I        -0.365  -0.467  -0.438  -0.371  -0.563  -0.562  -0.527  -0.702  -0.689
39    A         0.777   0.782   0.828   0.890   0.895   0.945   0.810   0.818   0.883
40    T        -1.592  -1.459  -1.225  -1.885  -1.657  -1.305  -1.768  -1.598  -1.284
41    I         0.777   0.782   0.828   0.826   0.824   0.893   0.810   0.818   0.883
42    Q        -1.243  -1.222  -1.214  -1.165  -1.164  -1.087  -1.386  -1.376  -1.271
43    S         0.777   0.782   0.828   0.836   0.856   0.901   0.810   0.818   0.883
44    K         0.777   0.782   0.828   0.587   0.611   0.699   0.810   0.818   0.883
45    R         0.777   0.782   0.828   0.462   0.479   0.596   0.810   0.818   0.883
46    L         0.777   0.782   0.828   0.660   0.691   0.757   0.810   0.818   0.883
47    R         0.777   0.782   0.828   0.462   0.479   0.596   0.810   0.818   0.883
48    N         0.777   0.782   0.828   0.988   0.993   1.025   0.810   0.818   0.883
49    K         0.777   0.782   0.828   0.587   0.611   0.699   0.810   0.818   0.883
50    I         0.777   0.782   0.828   0.826   0.824   0.893   0.810   0.818   0.883
51    A         0.777   0.782   0.828   0.890   0.895   0.945   0.810   0.818   0.883
52    G         0.777   0.782   0.828   0.930   0.932   0.977   0.810   0.818   0.883
53    Y         0.777   0.782   0.828   1.002   0.994   1.037   0.810   0.818   0.883
54    T         0.777   0.782   0.828   0.786   0.793   0.861   0.810   0.818   0.883
55    T         0.777   0.782   0.828   0.786   0.793   0.861   0.810   0.818   0.883
56    H         0.777   0.782   0.828   1.103   1.095   1.119   0.810   0.818   0.883
57    L         0.777   0.782   0.828   0.660   0.691   0.757   0.810   0.818   0.883
58    M         0.777   0.782   0.828   1.074   1.066   1.095   0.810   0.818   0.883
59    K         0.025   0.178  -0.391  -0.092   0.113  -0.749   0.046   0.244  -0.609
60    R         0.777   0.782   0.828   0.462   0.479   0.596   0.810   0.818   0.883
61    I         0.777   0.782   0.828   0.826   0.824   0.893   0.810   0.818   0.883
62    Q         0.777   0.782   0.828   0.890   0.892   0.945   0.810   0.818   0.883
63    K        -0.595  -0.645  -0.470  -1.123  -1.251  -0.934  -0.909  -1.008  -0.746
64    G         0.777   0.782   0.828   0.930   0.932   0.977   0.810   0.818   0.883
65    P         0.777   0.782   0.828   0.964   0.953   1.005   0.810   0.818   0.883
66    V         0.777   0.782   0.828   0.705   0.711   0.795   0.810   0.818   0.883
67    R         0.777   0.782   0.828   0.462   0.479   0.596   0.810   0.818   0.883
68    G         0.777   0.782   0.828   0.930   0.932   0.977   0.810   0.818   0.883
69    I         0.777   0.782   0.828   0.826   0.824   0.893   0.810   0.818   0.883
70    S         0.777   0.782   0.828   0.836   0.856   0.901   0.810   0.818   0.883
71    F         0.777   0.782   0.828   1.026   1.021   1.056   0.810   0.818   0.883
72    K         0.777   0.782   0.828   0.587   0.611   0.699   0.810   0.818   0.883
73    L         0.777   0.782   0.828   0.660   0.691   0.757   0.810   0.818   0.883
74    Q         0.777   0.782   0.828   0.890   0.892   0.945   0.810   0.818   0.883
75    E         0.777   0.782   0.828   0.811   0.808   0.881   0.810   0.818   0.883
76    E         0.777   0.782   0.828   0.811   0.808   0.881   0.810   0.818   0.883
77    E         0.777   0.782   0.828   0.811   0.808   0.881   0.810   0.818   0.883
78    R         0.777   0.782   0.828   0.462   0.479   0.596   0.810   0.818   0.883
79    E         0.777   0.782   0.828   0.811   0.808   0.881   0.810   0.818   0.883
80    R         0.777   0.782   0.828   0.462   0.479   0.596   0.810   0.818   0.883
81    K         0.777   0.782   0.828   0.587   0.611   0.699   0.810   0.818   0.883
82    D         0.777   0.782   0.828   0.876   0.876   0.933   0.810   0.818   0.883
83    Q         0.777   0.782   0.828   0.890   0.892   0.945   0.810   0.818   0.883
84    Y         0.777   0.782   0.828   1.002   0.994   1.037   0.810   0.818   0.883
85    V         0.777   0.782   0.828   0.705   0.711   0.795   0.810   0.818   0.883
86    P         0.777   0.782   0.828   0.964   0.953   1.005   0.810   0.818   0.883
87    E        -0.365  -0.210  -0.415  -0.339  -0.124  -0.453  -0.527  -0.293  -0.651
88    V         0.025   0.065  -0.400   0.073   0.119  -0.524   0.046   0.097  -0.625
89    S         0.777   0.782   0.828   0.836   0.856   0.901   0.810   0.818   0.883
90    A        -0.365  -0.467  -0.438  -0.279  -0.459  -0.468  -0.527  -0.702  -0.689
91    L         0.777   0.782   0.828   0.660   0.691   0.757   0.810   0.818   0.883
92    D        -0.365  -0.467  -0.438  -0.294  -0.478  -0.478  -0.527  -0.702  -0.689
93    L        -0.107  -0.369  -0.440  -0.142  -0.470  -0.556  -0.137  -0.542  -0.694
94    S        -0.107  -0.369  -0.440   0.004  -0.369  -0.544  -0.137  -0.542  -0.694
95    R        -0.940  -1.044  -1.205  -0.531  -0.723  -1.135  -0.926  -1.094  -1.259
96    S        -1.388  -1.463  -1.224  -1.507  -1.557  -1.194  -1.558  -1.608  -1.283
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    N        -2.300  -2.364  -2.172  -2.045  -2.165  -1.969  -1.959  -1.991  -1.714
100   G        -1.243  -1.205  -1.204  -1.134  -1.107  -1.051  -1.386  -1.350  -1.260
101   V        -1.842  -1.867  -1.747  -1.929  -1.947  -1.868  -1.768  -1.744  -1.541
102   L        -0.697  -0.881  -1.176  -0.617  -0.837  -1.304  -0.622  -0.854  -1.224
103   N        -1.700  -1.639  -1.741  -1.356  -1.251  -1.475  -1.577  -1.487  -1.536
104   V         0.025   0.136  -0.393   0.073   0.200  -0.513   0.046   0.190  -0.613
105   D         0.777   0.782   0.828   0.876   0.876   0.933   0.810   0.818   0.883
106   N        -2.506  -2.343  -2.177  -2.243  -2.061  -1.817  -2.150  -2.005  -1.717
107   Q        -1.510  -1.397  -1.216  -1.581  -1.406  -1.163  -1.673  -1.520  -1.273
108   T         0.777   0.782   0.828   0.786   0.793   0.861   0.810   0.818   0.883
109   S        -1.243  -1.152  -1.210  -1.343  -1.302  -1.291  -1.386  -1.318  -1.268
110   D         0.025   0.111  -0.393   0.241   0.335  -0.394   0.046   0.157  -0.613
111   L        -0.365  -0.467  -0.438  -0.428  -0.551  -0.499  -0.527  -0.702  -0.689
112   V        -0.704  -0.654  -0.467  -1.147  -1.050  -0.734  -1.100  -1.024  -0.740
113   K         0.025   0.111  -0.393  -0.024   0.091  -0.530   0.046   0.157  -0.613
114   S        -1.700  -1.764  -1.741  -1.463  -1.500  -1.489  -1.577  -1.618  -1.536
115   L         0.777   0.782   0.828   0.660   0.691   0.757   0.810   0.818   0.883
116   G         0.777   0.782   0.828   0.930   0.932   0.977   0.810   0.818   0.883
117   L        -1.510  -1.453  -1.216  -1.521  -1.394  -1.090  -1.673  -1.591  -1.273
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   K        -1.243  -1.317  -1.209  -1.472  -1.519  -1.295  -1.386  -1.460  -1.266
120   L        -0.704  -0.601  -0.462  -1.047  -0.836  -0.639  -1.100  -0.931  -0.731
121   P         0.777   0.782   0.828   0.964   0.953   1.005   0.810   0.818   0.883
122   L        -1.842  -1.776  -1.743  -2.009  -1.905  -1.773  -1.768  -1.692  -1.539
123   S        -2.838  -2.858  -2.528  -2.678  -2.735  -2.343  -2.245  -2.217  -1.833
124   V        -0.365  -0.214  -0.418  -0.467  -0.245  -0.573  -0.527  -0.300  -0.655
125   I        -1.842  -1.798  -1.742  -1.918  -1.853  -1.730  -1.768  -1.701  -1.538
126   N        -2.506  -2.368  -2.171  -2.161  -1.948  -1.677  -2.150  -1.991  -1.713
127   V        -1.842  -1.865  -1.743  -1.842  -1.828  -1.598  -1.768  -1.742  -1.538
128   S        -0.697  -0.912  -1.178  -0.419  -0.684  -1.131  -0.622  -0.894  -1.226
129   A        -0.513  -0.612  -0.470  -0.498  -0.689  -0.493  -0.769  -0.951  -0.746
130   Q        -0.940  -1.116  -1.207  -0.692  -0.969  -1.172  -0.926  -1.174  -1.262
131   R        -0.809  -0.886  -1.189  -0.907  -0.994  -1.358  -0.761  -0.868  -1.240
132   -        -1.404  -1.261  -1.213  -1.327  -1.103  -1.071  -1.553  -1.359  -1.270
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   D        -2.506  -2.504  -2.180  -2.255  -2.251  -1.797  -2.150  -2.105  -1.720
137   R         0.025  -0.091  -0.401  -0.174  -0.307  -0.712   0.046  -0.118  -0.626
138   R         0.025  -0.058  -0.400  -0.153  -0.239  -0.642   0.046  -0.070  -0.625
139   Y         0.025   0.163  -0.393   0.415   0.555  -0.210   0.046   0.224  -0.613
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   R        -1.385  -1.287  -1.725  -1.401  -1.274  -1.768  -1.195  -1.098  -1.520
144   K        -1.053  -1.213  -1.210  -1.263  -1.532  -1.457  -1.100  -1.314  -1.267
145   R         0.777   0.782   0.828   0.462   0.479   0.596   0.810   0.818   0.883
146   V        -2.032  -2.149  -2.168  -1.443  -1.615  -1.725  -1.673  -1.787  -1.711
* 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/P02407
Output conservation file - output/P02407
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
