1     M         1.609   1.652   1.746   1.907   1.967   2.117   1.769   1.832   1.993
2     N         0.373   0.365   0.439   0.246   0.207   0.320   0.058   0.025   0.111
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     -        -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     V        -0.871  -0.773  -0.818  -0.814  -0.650  -0.718  -0.902  -0.765  -0.791
10    P         0.282   0.420   0.483   0.035   0.281   0.370  -0.117   0.131   0.197
11    K         1.609   1.652   1.746   1.258   1.348   1.485   1.769   1.832   1.993
12    A        -0.487  -0.416  -0.317  -0.691  -0.575  -0.422  -0.745  -0.647  -0.514
13    R         0.812   0.699   0.647   0.863   0.712   0.640   0.826   0.633   0.510
14    L         0.812   0.881   0.686   0.880   0.972   0.718   0.826   0.930   0.580
15    L        -1.256  -1.359  -1.289  -1.112  -1.259  -1.121  -1.060  -1.147  -1.038
16    K        -1.401  -1.337  -1.275  -1.617  -1.438  -1.345  -1.217  -1.133  -1.027
17    V        -0.342  -0.255  -0.257  -0.486  -0.361  -0.349  -0.588  -0.459  -0.441
18    A        -0.632  -0.668  -0.780  -0.648  -0.699  -0.988  -0.588  -0.628  -0.745
19    E        -0.342  -0.361  -0.281  -0.713  -0.740  -0.599  -0.588  -0.577  -0.469
20    L         0.062   0.229  -0.085   0.188   0.405  -0.000   0.040   0.275  -0.177
21    S         0.812   0.668   0.650   0.949   0.735   0.733   0.826   0.581   0.515
22    A         0.062  -0.012  -0.150   0.198   0.082  -0.132   0.040  -0.069  -0.271
23    K         0.062  -0.038  -0.144  -0.170  -0.278  -0.419   0.040  -0.108  -0.262
24    I         0.447   0.439   0.479   0.539   0.518   0.550   0.197   0.166   0.189
25    F         1.609   1.652   1.746   1.788   1.853   2.002   1.769   1.832   1.993
26    D        -0.247  -0.379  -0.275  -0.146  -0.361  -0.225  -0.431  -0.599  -0.465
27    Q        -0.632  -0.812  -0.792  -0.310  -0.636  -0.604  -0.588  -0.801  -0.759
28    N        -1.256  -1.313  -1.255  -1.047  -1.162  -1.049  -1.060  -1.108  -1.007
29    F        -0.487  -0.458  -0.342  -0.400  -0.358  -0.173  -0.745  -0.701  -0.548
30    N         0.812   0.699   0.647   0.901   0.710   0.574   0.826   0.633   0.510
31    P         0.812   0.699   0.647   0.957   0.805   0.699   0.826   0.633   0.510
32    S        -0.871  -0.792  -0.807  -0.840  -0.717  -0.704  -0.902  -0.789  -0.779
33    G        -0.247  -0.067  -0.180  -0.266   0.039  -0.155  -0.431  -0.153  -0.320
34    I        -1.786  -1.759  -1.656  -1.859  -1.854  -1.683  -1.374  -1.328  -1.185
35    R         1.609   1.652   1.746   1.588   1.649   1.807   1.769   1.832   1.993
36    T        -0.247  -0.324  -0.267  -0.156  -0.306  -0.232  -0.431  -0.514  -0.446
37    G         0.812   0.879   0.680   0.999   1.105   0.803   0.826   0.928   0.570
38    S        -1.256  -1.313  -1.255  -1.159  -1.282  -1.174  -1.060  -1.108  -1.007
39    K         0.812   0.881   0.686   0.512   0.637   0.350   0.826   0.930   0.580
40    I        -0.632  -0.812  -0.792  -0.324  -0.619  -0.601  -0.588  -0.801  -0.759
41    L         0.812   0.699   0.647   0.876   0.721   0.647   0.826   0.633   0.510
42    N        -1.256  -1.065  -1.235  -1.230  -0.942  -1.200  -1.060  -0.856  -0.987
43    E        -0.342  -0.200  -0.271  -0.372  -0.201  -0.240  -0.588  -0.423  -0.461
44    R        -0.342  -0.361  -0.281  -0.541  -0.505  -0.395  -0.588  -0.577  -0.469
45    L         1.609   1.652   1.746   1.606   1.663   1.824   1.769   1.832   1.993
46    K         0.812   0.668   0.650   0.533   0.370   0.334   0.826   0.581   0.515
47    G         1.609   1.652   1.746   1.746   1.815   1.960   1.769   1.832   1.993
48    P         0.062  -0.188  -0.188   0.239  -0.129  -0.162   0.040  -0.314  -0.327
49    S        -1.401  -1.315  -1.284  -1.444  -1.334  -1.287  -1.217  -1.115  -1.035
50    V        -0.871  -0.913  -0.830  -0.740  -0.815  -0.680  -0.902  -0.931  -0.809
51    A        -0.871  -0.778  -0.822  -1.164  -1.113  -1.116  -0.902  -0.804  -0.802
52    S         0.062   0.229  -0.085   0.105   0.337  -0.174   0.040   0.275  -0.177
53    Y         1.609   1.652   1.746   1.831   1.885   2.044   1.769   1.832   1.993
54    Y         1.609   1.652   1.746   1.831   1.885   2.044   1.769   1.832   1.993
55    G         0.734   0.588   0.575   0.889   0.670   0.614   0.699   0.441   0.374
56    N        -0.356  -0.422  -0.319  -0.324  -0.412  -0.242  -0.584  -0.654  -0.518
57    P        -0.247  -0.324  -0.267  -0.285  -0.394  -0.331  -0.431  -0.514  -0.446
58    D        -0.247  -0.302  -0.263  -0.169  -0.244  -0.222  -0.431  -0.485  -0.441
59    I        -0.871  -0.816  -0.821  -0.769  -0.687  -0.662  -0.902  -0.831  -0.796
60    L        -0.974  -0.883  -0.847  -0.828  -0.680  -0.630  -1.012  -0.899  -0.825
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    K        -1.401  -1.405  -1.303  -1.630  -1.579  -1.451  -1.217  -1.193  -1.051
63    F         0.062  -0.188  -0.188   0.372   0.019   0.012   0.040  -0.314  -0.327
64    R         0.282   0.337   0.438  -0.390  -0.279  -0.130  -0.117  -0.029   0.108
65    H        -1.401  -1.306  -1.279  -1.056  -0.986  -0.855  -1.217  -1.116  -1.031
66    L        -0.247  -0.093  -0.219  -0.311  -0.096  -0.242  -0.431  -0.224  -0.377
67    K         0.282   0.307   0.425  -0.390  -0.306  -0.123  -0.117  -0.090   0.081
68    T        -0.487  -0.475  -0.345  -0.893  -0.820  -0.614  -0.745  -0.723  -0.551
69    L        -0.247  -0.324  -0.267  -0.242  -0.357  -0.253  -0.431  -0.514  -0.446
70    Y        -0.871  -0.993  -0.862  -0.721  -0.905  -0.709  -0.902  -1.005  -0.840
71    P         0.062   0.065  -0.133   0.227   0.232  -0.089   0.040   0.032  -0.247
72    D        -0.871  -0.775  -0.821  -0.672  -0.545  -0.593  -0.902  -0.799  -0.800
73    I        -1.401  -1.405  -1.303  -1.423  -1.494  -1.287  -1.217  -1.193  -1.051
74    E        -1.786  -1.619  -1.637  -1.723  -1.434  -1.513  -1.374  -1.213  -1.170
75    F         0.062   0.230  -0.092   0.329   0.561   0.092   0.040   0.277  -0.188
76    V        -0.632  -0.751  -0.778  -0.399  -0.607  -0.678  -0.588  -0.738  -0.742
77    D         1.609   1.652   1.746   1.839   1.908   2.052   1.769   1.832   1.993
78    L        -1.256  -1.245  -1.249  -1.109  -1.109  -1.118  -1.060  -1.048  -1.001
79    E        -1.256  -1.359  -1.289  -1.138  -1.296  -1.268  -1.060  -1.147  -1.038
80    E         1.609   1.652   1.746   1.780   1.832   1.994   1.769   1.832   1.993
81    Q        -1.786  -1.771  -1.659  -1.359  -1.322  -1.173  -1.374  -1.335  -1.187
82    Y         0.062  -0.012  -0.150   0.397   0.264   0.080   0.040  -0.069  -0.271
83    R         1.609   1.652   1.746   1.588   1.649   1.807   1.769   1.832   1.993
84    L        -0.247  -0.302  -0.263  -0.285  -0.339  -0.270  -0.431  -0.485  -0.441
85    S        -1.786  -1.662  -1.635  -1.599  -1.416  -1.395  -1.374  -1.249  -1.168
86    M        -0.247  -0.379  -0.276  -0.049  -0.272  -0.125  -0.431  -0.600  -0.465
87    V         0.062   0.064  -0.128   0.283   0.276  -0.060   0.040   0.031  -0.240
88    E        -1.422  -1.405  -1.309  -1.513  -1.586  -1.394  -1.225  -1.188  -1.056
89    A        -0.974  -0.967  -0.877  -1.013  -0.978  -0.866  -1.012  -0.983  -0.856
90    K         0.734   0.872   0.632   0.650   0.870   0.402   0.699   0.917   0.482
91    K         0.734   0.606   0.575   0.308   0.142   0.111   0.699   0.472   0.374
92    R         0.734   0.763   0.612   0.650   0.694   0.356   0.699   0.741   0.444
93    R         0.734   0.606   0.575   0.800   0.619   0.575   0.699   0.472   0.374
94    G         0.373   0.415   0.461   0.288   0.353   0.401   0.058   0.121   0.154
95    K         1.609   1.652   1.746   1.136   1.208   1.366   1.769   1.832   1.993
96    G         1.609   1.652   1.746   1.731   1.795   1.946   1.769   1.832   1.993
97    A         1.609   1.652   1.746   1.656   1.729   1.872   1.769   1.832   1.993
98    P         0.734   0.606   0.575   0.879   0.690   0.600   0.699   0.472   0.374
99    K         0.734   0.819   0.624   0.323   0.451   0.209   0.699   0.831   0.466
100   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   K         0.734   0.606   0.575   0.272   0.088   0.037   0.699   0.472   0.374
115   K         1.609   1.652   1.746   1.136   1.208   1.366   1.769   1.832   1.993
116   K        -0.632  -0.624  -0.736  -0.939  -0.889  -1.078  -0.588  -0.583  -0.693
117   K        -0.247  -0.245  -0.272  -0.631  -0.596  -0.592  -0.431  -0.442  -0.459
* 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/P53305
Output conservation file - output/P53305
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
