1     M         1.785   1.827   1.922   1.924   1.984   2.134   1.970   2.033   2.183
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    Q        -0.721  -0.747  -0.654  -0.846  -0.898  -0.766  -0.775  -0.798  -0.670
25    Q        -1.243  -1.232  -1.122  -1.174  -1.158  -0.997  -1.080  -1.060  -0.915
26    Q        -1.243  -1.232  -1.122  -1.338  -1.309  -1.163  -1.080  -1.060  -0.915
27    Q        -0.717  -0.652  -0.652  -0.875  -0.771  -0.773  -0.783  -0.706  -0.671
28    Q        -1.131  -1.118  -1.073  -1.017  -1.000  -0.901  -0.987  -0.968  -0.873
29    Q        -0.990  -1.046  -1.039  -0.885  -0.981  -0.991  -0.831  -0.882  -0.837
30    L         0.153   0.044   0.002   0.005  -0.159  -0.231   0.064  -0.100  -0.168
31    S        -1.151  -1.157  -1.081  -1.022  -1.044  -0.918  -0.995  -0.994  -0.877
32    L        -0.717  -0.758  -0.656  -0.808  -0.824  -0.685  -0.783  -0.817  -0.675
33    K        -0.118  -0.128  -0.100  -0.291  -0.333  -0.281  -0.360  -0.380  -0.327
34    I         0.287   0.149   0.052   0.404   0.213   0.051   0.258   0.060  -0.094
35    K        -0.245  -0.179  -0.120  -0.432  -0.324  -0.250  -0.520  -0.424  -0.349
36    Q        -1.503  -1.517  -1.430  -1.339  -1.386  -1.224  -1.142  -1.144  -1.015
37    L         0.659   0.694   0.680   0.358   0.411   0.364   0.414   0.466   0.385
38    K         0.659   0.623   0.647   0.492   0.407   0.414   0.414   0.329   0.321
39    L         1.013   0.918   0.834   0.894   0.778   0.670   1.036   0.872   0.685
40    K         0.500   0.527   0.620   0.186   0.215   0.355   0.103   0.139   0.265
41    R         1.785   1.827   1.922   1.677   1.725   1.885   1.970   2.033   2.183
42    I         0.287   0.149   0.052   0.388   0.203   0.021   0.258   0.060  -0.094
43    N        -0.758  -0.765  -0.670  -0.920  -0.923  -0.783  -0.831  -0.825  -0.692
44    E         1.013   0.918   0.834   1.007   0.876   0.756   1.036   0.872   0.685
45    L         0.287   0.210   0.052   0.262   0.160  -0.030   0.258   0.145  -0.093
46    N         0.287   0.196   0.052   0.370   0.261   0.047   0.258   0.126  -0.093
47    N        -0.386  -0.399  -0.543  -0.275  -0.293  -0.504  -0.364  -0.380  -0.539
48    K         0.500   0.564   0.638   0.177   0.274   0.383   0.103   0.213   0.302
49    L         1.785   1.827   1.922   1.549   1.608   1.756   1.970   2.033   2.183
50    R        -0.013  -0.085  -0.067  -0.146  -0.255  -0.234  -0.209  -0.295  -0.277
51    K        -0.990  -0.865  -0.998  -0.949  -0.761  -0.983  -0.831  -0.685  -0.797
52    E        -0.013  -0.031  -0.060  -0.088  -0.113  -0.141  -0.209  -0.225  -0.267
53    L         1.013   0.918   0.834   0.869   0.746   0.619   1.036   0.872   0.685
54    S        -1.503  -1.519  -1.432  -1.413  -1.424  -1.321  -1.142  -1.145  -1.017
55    R         1.785   1.827   1.922   1.677   1.725   1.885   1.970   2.033   2.183
56    E         1.785   1.827   1.922   1.686   1.734   1.894   1.970   2.033   2.183
57    R         1.785   1.827   1.922   1.677   1.725   1.885   1.970   2.033   2.183
58    I         0.287   0.246   0.064   0.442   0.385   0.138   0.258   0.194  -0.076
59    T         0.500   0.518   0.615   0.312   0.333   0.479   0.103   0.122   0.254
60    A         1.013   0.990   0.845   1.104   1.077   0.892   1.036   0.994   0.706
61    S         1.013   0.918   0.834   1.037   0.911   0.771   1.036   0.872   0.685
62    N        -0.013  -0.055  -0.058  -0.124  -0.200  -0.201  -0.209  -0.283  -0.270
63    A         1.785   1.827   1.922   1.761   1.815   1.970   1.970   2.033   2.183
64    C        -0.618  -0.707  -0.643  -0.429  -0.539  -0.457  -0.675  -0.760  -0.662
65    L        -0.386  -0.507  -0.553  -0.407  -0.586  -0.636  -0.364  -0.510  -0.551
66    T        -1.131  -1.121  -1.082  -1.188  -1.152  -1.089  -0.987  -0.970  -0.881
67    I         0.659   0.654   0.656   0.476   0.457   0.388   0.414   0.390   0.338
68    I         1.013   1.060   0.853   1.074   1.146   0.853   1.036   1.109   0.722
69    N        -1.503  -1.515  -1.430  -1.365  -1.377  -1.254  -1.142  -1.142  -1.016
70    Y         1.785   1.827   1.922   1.843   1.898   2.053   1.970   2.033   2.183
71    T        -0.013  -0.031  -0.060   0.040   0.024  -0.001  -0.209  -0.225  -0.267
72    S        -1.131  -1.139  -1.073  -1.137  -1.136  -1.056  -0.987  -0.981  -0.874
73    N        -0.990  -0.906  -1.009  -0.857  -0.717  -0.898  -0.831  -0.730  -0.808
74    T         0.287   0.246   0.064   0.489   0.436   0.221   0.258   0.194  -0.076
75    K        -0.245  -0.224  -0.137  -0.439  -0.415  -0.289  -0.520  -0.488  -0.372
76    D         1.785   1.827   1.922   1.875   1.933   2.086   1.970   2.033   2.183
77    Y         1.013   0.918   0.834   1.208   1.098   1.000   1.036   0.872   0.685
78    T        -0.990  -0.977  -1.030  -0.831  -0.798  -0.910  -0.831  -0.807  -0.829
79    L        -0.245  -0.192  -0.129  -0.417  -0.311  -0.252  -0.520  -0.442  -0.360
80    P         1.785   1.827   1.922   1.835   1.887   2.045   1.970   2.033   2.183
81    E        -0.618  -0.569  -0.608  -0.660  -0.600  -0.631  -0.675  -0.620  -0.625
82    L        -0.013   0.004  -0.038  -0.199  -0.175  -0.226  -0.209  -0.183  -0.236
83    W         1.785   1.827   1.922   2.011   2.072   2.223   1.970   2.033   2.183
84    G         0.287   0.323   0.048   0.598   0.652   0.221   0.258   0.313  -0.099
85    Y        -0.013  -0.031  -0.060  -0.048  -0.069  -0.141  -0.209  -0.225  -0.267
86    P         0.287   0.149   0.052   0.478   0.269   0.113   0.258   0.060  -0.094
87    V         0.287   0.407   0.088   0.549   0.701   0.296   0.258   0.435  -0.041
88    A        -0.721  -0.752  -0.679  -0.695  -0.764  -0.638  -0.775  -0.806  -0.698
89    G        -0.758  -0.763  -0.664  -0.681  -0.705  -0.552  -0.831  -0.822  -0.686
90    S        -1.131  -1.121  -1.082  -1.143  -1.137  -1.070  -0.987  -0.970  -0.881
91    N         1.013   0.990   0.845   1.028   1.015   0.816   1.036   0.994   0.706
92    H        -0.618  -0.563  -0.614  -0.429  -0.353  -0.436  -0.675  -0.596  -0.628
93    F         0.500   0.508   0.614   0.520   0.518   0.676   0.103   0.102   0.253
94    I        -0.721  -0.651  -0.638  -0.816  -0.688  -0.709  -0.775  -0.684  -0.652
95    E        -1.243  -1.228  -1.122  -1.480  -1.472  -1.307  -1.080  -1.056  -0.915
96    G        -0.003   0.072  -0.025   0.139   0.248   0.101  -0.165  -0.053  -0.208
97    L        -0.721  -0.661  -0.638  -0.850  -0.764  -0.732  -0.775  -0.696  -0.652
98    K        -0.721  -0.745  -0.653  -0.875  -0.937  -0.789  -0.775  -0.797  -0.669
99    N        -1.243  -1.228  -1.122  -1.323  -1.307  -1.148  -1.080  -1.056  -0.915
100   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   Q        -0.721  -0.707  -0.656  -0.849  -0.828  -0.769  -0.775  -0.751  -0.672
102   K        -0.200  -0.173  -0.112  -0.403  -0.368  -0.261  -0.470  -0.434  -0.342
103   N        -0.721  -0.723  -0.671  -0.602  -0.602  -0.573  -0.775  -0.770  -0.689
104   S        -0.721  -0.682  -0.670  -0.800  -0.739  -0.736  -0.775  -0.721  -0.689
105   Q        -0.721  -0.682  -0.670  -0.874  -0.811  -0.805  -0.775  -0.721  -0.689
106   M        -1.151  -1.146  -1.077  -1.136  -1.157  -1.030  -0.995  -0.982  -0.874
107   S        -0.717  -0.751  -0.653  -0.620  -0.674  -0.542  -0.783  -0.809  -0.673
108   N        -1.131  -1.066  -1.057  -1.152  -1.056  -1.043  -0.987  -0.921  -0.860
109   S        -1.876  -1.867  -1.759  -1.698  -1.684  -1.527  -1.298  -1.279  -1.136
110   N        -0.386  -0.315  -0.518  -0.224  -0.118  -0.427  -0.364  -0.271  -0.509
111   S        -0.386  -0.410  -0.548  -0.222  -0.258  -0.456  -0.364  -0.394  -0.546
112   V        -0.990  -0.854  -0.999  -0.626  -0.413  -0.662  -0.831  -0.674  -0.798
113   C         1.785   1.827   1.922   1.924   1.984   2.134   1.970   2.033   2.183
114   C         1.785   1.827   1.922   1.924   1.984   2.134   1.970   2.033   2.183
115   T         0.659   0.601   0.652   0.602   0.499   0.570   0.414   0.286   0.330
116   L         0.287   0.306   0.075   0.396   0.436   0.075   0.258   0.286  -0.059
117   M        -0.013  -0.085  -0.067   0.148   0.045   0.054  -0.209  -0.295  -0.277
* 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/P18852
Output conservation file - output/P18852
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
