1     M         0.874   0.882   0.929   1.269   1.274   1.309   0.922   0.932   1.001
2     V         0.138   0.202  -0.186   0.096   0.180  -0.390   0.134   0.223  -0.400
3     Q        -1.223  -1.323  -1.454  -0.874  -1.019  -1.215  -1.105  -1.223  -1.323
4     A         0.874   0.882   0.929   0.876   0.883   0.970   0.922   0.932   1.001
5     V         0.874   0.882   0.929   0.771   0.783   0.881   0.922   0.932   1.001
6     A         0.874   0.882   0.929   0.876   0.883   0.970   0.922   0.932   1.001
7     V         0.874   0.882   0.929   0.771   0.783   0.881   0.922   0.932   1.001
8     L        -0.224  -0.175  -0.250  -0.215  -0.131  -0.353  -0.429  -0.349  -0.513
9     K        -0.224  -0.193  -0.259  -0.069  -0.024  -0.205  -0.429  -0.380  -0.529
10    G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
11    D         0.138   0.221  -0.181   0.258   0.361  -0.231   0.134   0.249  -0.392
12    A        -0.224  -0.148  -0.233  -0.276  -0.154  -0.341  -0.429  -0.305  -0.483
13    G        -1.495  -1.396  -1.460  -1.624  -1.426  -1.589  -1.443  -1.320  -1.329
14    V         0.874   0.882   0.929   0.771   0.783   0.881   0.922   0.932   1.001
15    S        -0.563  -0.490  -0.907  -0.322  -0.233  -0.810  -0.542  -0.448  -0.990
16    G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
17    V        -1.029  -0.995  -0.963  -1.323  -1.260  -1.136  -1.218  -1.163  -1.066
18    V         0.874   0.882   0.929   0.771   0.783   0.881   0.922   0.932   1.001
19    K        -2.383  -2.267  -2.192  -2.120  -1.953  -1.840  -1.894  -1.780  -1.621
20    F         0.138   0.221  -0.181   0.472   0.569  -0.037   0.134   0.249  -0.392
21    E         0.874   0.882   0.929   1.033   1.046   1.106   0.922   0.932   1.001
22    Q         0.874   0.882   0.929   1.176   1.179   1.229   0.922   0.932   1.001
23    A        -2.045  -2.037  -1.879  -2.019  -2.031  -1.819  -1.781  -1.758  -1.518
24    S         0.138  -0.031  -0.201   0.282   0.041  -0.257   0.134  -0.119  -0.427
25    E         0.138  -0.031  -0.201   0.401   0.185  -0.090   0.134  -0.119  -0.427
26    S        -1.223  -1.295  -1.449  -0.967  -1.099  -1.316  -1.105  -1.194  -1.318
27    E        -2.511  -2.499  -2.210  -2.548  -2.526  -2.108  -2.006  -1.976  -1.633
28    P        -0.224  -0.312  -0.274  -0.040  -0.182  -0.166  -0.429  -0.583  -0.555
29    T        -0.224  -0.297  -0.271  -0.373  -0.512  -0.524  -0.429  -0.556  -0.551
30    T        -0.563  -0.717  -0.930  -0.424  -0.640  -0.981  -0.542  -0.747  -1.021
31    V        -0.418  -0.430  -0.287  -0.627  -0.682  -0.460  -0.767  -0.793  -0.579
32    S        -1.029  -1.120  -0.969  -1.188  -1.295  -1.036  -1.218  -1.299  -1.073
33    Y        -1.029  -1.119  -0.974  -0.714  -0.859  -0.716  -1.218  -1.296  -1.079
34    E        -0.418  -0.427  -0.287  -0.554  -0.584  -0.376  -0.767  -0.788  -0.580
35    I         0.138  -0.031  -0.201   0.387   0.151  -0.140   0.134  -0.119  -0.427
36    A        -2.511  -2.508  -2.212  -2.509  -2.535  -2.072  -2.006  -1.982  -1.635
37    G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
38    N         0.874   0.882   0.929   0.964   0.971   1.046   0.922   0.932   1.001
39    S         0.138   0.185  -0.184   0.258   0.317  -0.237   0.134   0.200  -0.397
40    P        -0.418  -0.433  -0.289  -0.522  -0.569  -0.367  -0.767  -0.799  -0.583
41    N         0.874   0.882   0.929   0.964   0.971   1.046   0.922   0.932   1.001
42    A         0.874   0.882   0.929   0.876   0.883   0.970   0.922   0.932   1.001
43    E        -1.240  -1.233  -1.001  -1.315  -1.303  -0.960  -1.443  -1.426  -1.111
44    R         0.874   0.882   0.929   1.123   1.127   1.183   0.922   0.932   1.001
45    G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
46    F         0.874   0.882   0.929   1.123   1.128   1.183   0.922   0.932   1.001
47    H         0.874   0.882   0.929   1.069   1.078   1.137   0.922   0.932   1.001
48    I        -0.224  -0.162  -0.250  -0.224  -0.125  -0.361  -0.429  -0.329  -0.514
49    H         0.874   0.882   0.929   1.069   1.078   1.137   0.922   0.932   1.001
50    E        -1.240  -1.237  -1.002  -1.344  -1.318  -0.959  -1.443  -1.430  -1.111
51    F         0.874   0.882   0.929   1.123   1.128   1.183   0.922   0.932   1.001
52    G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
53    D         0.874   0.882   0.929   0.922   0.931   1.011   0.922   0.932   1.001
54    A        -0.563  -0.448  -0.906  -0.396  -0.242  -0.999  -0.542  -0.394  -0.989
55    T         0.874   0.882   0.929   0.885   0.902   0.978   0.922   0.932   1.001
56    N         0.874   0.882   0.929   0.964   0.971   1.046   0.922   0.932   1.001
57    G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
58    C         0.874   0.882   0.929   1.238   1.244   1.282   0.922   0.932   1.001
59    V        -0.224  -0.148  -0.233  -0.373  -0.235  -0.438  -0.429  -0.305  -0.483
60    S         0.874   0.882   0.929   0.950   0.955   1.035   0.922   0.932   1.001
61    A         0.874   0.882   0.929   0.876   0.883   0.970   0.922   0.932   1.001
62    G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
63    P         0.874   0.882   0.929   1.096   1.114   1.160   0.922   0.932   1.001
64    H         0.874   0.882   0.929   1.069   1.078   1.137   0.922   0.932   1.001
65    F         0.874   0.882   0.929   1.123   1.128   1.183   0.922   0.932   1.001
66    N         0.874   0.882   0.929   0.964   0.971   1.046   0.922   0.932   1.001
67    P         0.874   0.882   0.929   1.096   1.114   1.160   0.922   0.932   1.001
68    F        -0.563  -0.664  -0.926  -0.165  -0.320  -0.751  -0.542  -0.684  -1.016
69    K        -1.578  -1.515  -1.476  -1.957  -1.888  -1.731  -1.556  -1.481  -1.347
70    K         0.138   0.202  -0.183   0.332   0.420  -0.194   0.134   0.223  -0.395
71    T        -1.495  -1.418  -1.470  -1.440  -1.328  -1.353  -1.443  -1.352  -1.341
72    H         0.874   0.882   0.929   1.069   1.078   1.137   0.922   0.932   1.001
73    G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
74    A        -0.884  -0.904  -0.962  -1.046  -1.101  -1.273  -0.993  -1.034  -1.063
75    P        -0.224  -0.287  -0.267  -0.057  -0.160  -0.182  -0.429  -0.540  -0.544
76    T        -1.029  -0.945  -0.962  -1.107  -0.992  -0.930  -1.218  -1.116  -1.065
77    D        -0.224  -0.287  -0.267  -0.303  -0.426  -0.433  -0.429  -0.540  -0.544
78    E        -1.495  -1.550  -1.476  -1.413  -1.506  -1.436  -1.443  -1.488  -1.346
79    V        -1.240  -1.179  -0.995  -1.516  -1.430  -1.121  -1.443  -1.364  -1.104
80    R         0.874   0.882   0.929   1.123   1.127   1.183   0.922   0.932   1.001
81    H         0.874   0.882   0.929   1.069   1.078   1.137   0.922   0.932   1.001
82    V         0.874   0.882   0.929   0.771   0.783   0.881   0.922   0.932   1.001
83    G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
84    D         0.874   0.882   0.929   0.922   0.931   1.011   0.922   0.932   1.001
85    M         0.138   0.185  -0.184   0.428   0.483  -0.017   0.134   0.200  -0.397
86    G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
87    N         0.874   0.882   0.929   0.964   0.971   1.046   0.922   0.932   1.001
88    V        -1.029  -1.110  -0.968  -1.168  -1.261  -1.034  -1.218  -1.283  -1.072
89    K        -2.045  -2.005  -1.882  -1.879  -1.820  -1.659  -1.781  -1.739  -1.521
90    T         0.138  -0.031  -0.201   0.221  -0.006  -0.297   0.134  -0.119  -0.427
91    D         0.874   0.882   0.929   0.922   0.931   1.011   0.922   0.932   1.001
92    E        -1.834  -1.716  -1.851  -1.811  -1.633  -1.938  -1.556  -1.428  -1.495
93    N        -1.495  -1.394  -1.462  -1.233  -1.088  -1.248  -1.443  -1.326  -1.333
94    G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
95    V        -0.884  -0.933  -0.964  -1.019  -1.108  -1.095  -0.993  -1.065  -1.067
96    A        -0.563  -0.717  -0.930  -0.428  -0.649  -0.975  -0.542  -0.747  -1.021
97    K         0.874   0.882   0.929   1.005   1.020   1.082   0.922   0.932   1.001
98    G         0.138  -0.031  -0.201  -0.221  -0.443  -0.668   0.134  -0.119  -0.427
99    S        -1.240  -1.183  -0.996  -1.585  -1.486  -1.194  -1.443  -1.367  -1.104
100   F        -2.173  -2.079  -1.884  -2.031  -1.892  -1.638  -1.894  -1.805  -1.523
101   K        -1.706  -1.742  -1.492  -1.706  -1.747  -1.375  -1.668  -1.678  -1.362
102   D         0.874   0.882   0.929   0.922   0.931   1.011   0.922   0.932   1.001
103   S        -1.495  -1.414  -1.468  -1.400  -1.284  -1.361  -1.443  -1.344  -1.338
104   L        -1.223  -1.310  -1.454  -0.892  -1.056  -1.298  -1.105  -1.209  -1.323
105   I        -1.029  -0.950  -0.956  -1.168  -1.023  -1.007  -1.218  -1.106  -1.057
106   K         0.138  -0.031  -0.201   0.341   0.111  -0.203   0.134  -0.119  -0.427
107   L         0.874   0.882   0.929   1.046   1.055   1.117   0.922   0.932   1.001
108   I        -1.223  -1.328  -1.458  -0.884  -1.042  -1.279  -1.105  -1.228  -1.327
109   G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
110   P        -1.834  -1.866  -1.867  -1.445  -1.523  -1.580  -1.556  -1.586  -1.508
111   T        -2.045  -1.955  -1.869  -1.973  -1.827  -1.701  -1.781  -1.681  -1.510
112   S         0.874   0.882   0.929   0.950   0.955   1.035   0.922   0.932   1.001
113   V        -0.418  -0.353  -0.268  -0.627  -0.500  -0.404  -0.767  -0.655  -0.545
114   V        -1.157  -1.157  -0.994  -1.374  -1.377  -1.084  -1.331  -1.329  -1.101
115   G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
116   R         0.874   0.882   0.929   1.123   1.127   1.183   0.922   0.932   1.001
117   S        -0.224  -0.148  -0.233  -0.315  -0.186  -0.357  -0.429  -0.305  -0.483
118   V        -0.224  -0.306  -0.274  -0.396  -0.535  -0.465  -0.429  -0.572  -0.556
119   V         0.874   0.882   0.929   0.771   0.783   0.881   0.922   0.932   1.001
120   I        -0.480  -0.455  -0.289  -0.804  -0.755  -0.466  -0.880  -0.838  -0.582
121   H         0.874   0.882   0.929   1.069   1.078   1.137   0.922   0.932   1.001
122   A         0.138   0.179  -0.188   0.143   0.199  -0.474   0.134   0.191  -0.404
123   G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
124   Q        -1.157  -1.173  -0.997  -1.223  -1.246  -0.960  -1.331  -1.349  -1.105
125   D         0.874   0.882   0.929   0.922   0.931   1.011   0.922   0.932   1.001
126   D         0.874   0.882   0.929   0.922   0.931   1.011   0.922   0.932   1.001
127   L         0.138   0.159  -0.187   0.430   0.455  -0.014   0.134   0.162  -0.402
128   G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
129   K         0.874   0.882   0.929   1.005   1.020   1.082   0.922   0.932   1.001
130   G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
131   D        -0.563  -0.679  -0.921  -0.886  -1.047  -1.350  -0.542  -0.702  -1.009
132   T        -2.383  -2.403  -2.202  -2.124  -2.179  -1.898  -1.894  -1.899  -1.628
133   E        -0.418  -0.379  -0.283  -0.578  -0.504  -0.390  -0.767  -0.701  -0.571
134   E        -0.224  -0.188  -0.256  -0.182  -0.120  -0.304  -0.429  -0.371  -0.523
135   S         0.874   0.882   0.929   0.950   0.955   1.035   0.922   0.932   1.001
136   L        -0.224  -0.175  -0.248  -0.142  -0.062  -0.239  -0.429  -0.349  -0.510
137   K         0.138   0.159  -0.187   0.332   0.365  -0.201   0.134   0.162  -0.402
138   T         0.874   0.882   0.929   0.885   0.902   0.978   0.922   0.932   1.001
139   G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
140   N         0.138   0.159  -0.187   0.317   0.341  -0.163   0.134   0.162  -0.402
141   A         0.874   0.882   0.929   0.876   0.883   0.970   0.922   0.932   1.001
142   G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
143   P        -0.480  -0.450  -0.286  -0.686  -0.644  -0.375  -0.880  -0.829  -0.578
144   R         0.874   0.882   0.929   1.123   1.127   1.183   0.922   0.932   1.001
145   P        -0.563  -0.717  -0.930  -0.203  -0.420  -0.803  -0.542  -0.747  -1.021
146   A         0.874   0.882   0.929   0.876   0.883   0.970   0.922   0.932   1.001
147   C         0.874   0.882   0.929   1.238   1.244   1.282   0.922   0.932   1.001
148   G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
149   V         0.874   0.882   0.929   0.771   0.783   0.881   0.922   0.932   1.001
150   I         0.874   0.882   0.929   1.037   1.039   1.109   0.922   0.932   1.001
151   G         0.874   0.882   0.929   0.456   0.478   0.609   0.922   0.932   1.001
152   L        -0.418  -0.433  -0.289  -0.482  -0.526  -0.303  -0.767  -0.799  -0.582
153   T        -1.029  -1.113  -0.971  -1.221  -1.331  -1.102  -1.218  -1.288  -1.076
154   N        -2.045  -2.047  -1.881  -1.900  -1.943  -1.702  -1.781  -1.769  -1.520
155   -        -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/P00445
Output conservation file - output/P00445
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
