1     M         1.694   1.712   1.779   1.988   2.017   2.130   1.864   1.893   1.999
2     S         1.694   1.712   1.779   1.651   1.677   1.797   1.864   1.893   1.999
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     T         0.935   0.843   0.751   1.194   1.080   0.951   0.954   0.802   0.612
10    V        -0.809  -0.832  -0.718  -0.875  -0.912  -0.761  -0.866  -0.879  -0.736
11    N         1.694   1.712   1.779   1.803   1.832   1.947   1.864   1.893   1.999
12    V         1.694   1.712   1.779   1.755   1.780   1.900   1.864   1.893   1.999
13    L         1.694   1.712   1.779   1.510   1.552   1.658   1.864   1.893   1.999
14    R         1.694   1.712   1.779   1.896   1.924   2.039   1.864   1.893   1.999
15    Y         0.935   0.897   0.763   1.253   1.212   1.051   0.954   0.893   0.633
16    S         1.694   1.712   1.779   1.651   1.677   1.797   1.864   1.893   1.999
17    A         0.586   0.659   0.630   0.102   0.219   0.158   0.347   0.477   0.383
18    L         1.694   1.712   1.779   1.510   1.552   1.658   1.864   1.893   1.999
19    G         0.586   0.573   0.565   0.502   0.460   0.371   0.347   0.316   0.255
20    L         0.429   0.456   0.532  -0.198  -0.158  -0.032   0.044   0.088   0.189
21    G         1.694   1.712   1.779   1.826   1.854   1.970   1.864   1.893   1.999
22    L        -0.304  -0.300  -0.206  -0.428  -0.416  -0.284  -0.563  -0.557  -0.434
23    F        -0.076  -0.101  -0.123  -0.023  -0.068  -0.116  -0.260  -0.303  -0.326
24    F        -0.443  -0.377  -0.581  -0.130  -0.030  -0.389  -0.411  -0.327  -0.574
25    G         1.694   1.712   1.779   1.826   1.854   1.970   1.864   1.893   1.999
26    F        -0.076  -0.020  -0.087  -0.145  -0.028  -0.195  -0.260  -0.169  -0.267
27    R        -1.543  -1.541  -1.456  -1.204  -1.200  -1.056  -1.170  -1.164  -1.048
28    N        -0.166  -0.140  -0.130   0.037   0.082   0.107  -0.411  -0.375  -0.342
29    D        -0.671  -0.727  -0.681  -0.387  -0.454  -0.398  -0.715  -0.762  -0.694
30    M        -1.176  -1.111  -1.097  -0.792  -0.692  -0.686  -1.018  -0.955  -0.901
31    I        -0.443  -0.431  -0.551  -0.224  -0.208  -0.361  -0.411  -0.396  -0.538
32    L         0.219   0.199   0.016   0.219   0.208  -0.041   0.195   0.159  -0.110
33    K        -1.543  -1.546  -1.464  -1.329  -1.331  -1.196  -1.170  -1.168  -1.055
34    C        -0.443  -0.505  -0.595  -0.291  -0.411  -0.520  -0.411  -0.489  -0.591
35    N        -1.038  -0.989  -1.033  -1.166  -1.104  -1.147  -0.866  -0.812  -0.835
36    A        -0.076  -0.037  -0.122  -0.399  -0.377  -0.429  -0.260  -0.223  -0.325
37    K        -1.038  -0.998  -1.027  -1.044  -0.995  -1.052  -0.866  -0.822  -0.829
38    K        -0.076  -0.050  -0.121  -0.399  -0.382  -0.517  -0.260  -0.233  -0.324
39    K        -1.038  -0.984  -1.049  -1.028  -0.988  -1.067  -0.866  -0.811  -0.851
40    E        -1.176  -1.219  -1.126  -1.243  -1.343  -1.234  -1.018  -1.047  -0.925
41    E         0.429   0.456   0.532  -0.096  -0.069   0.070   0.044   0.088   0.189
42    Q        -0.671  -0.666  -0.655  -0.732  -0.686  -0.687  -0.715  -0.696  -0.665
43    A        -1.543  -1.503  -1.443  -1.647  -1.580  -1.489  -1.170  -1.132  -1.039
44    Q        -0.304  -0.310  -0.213  -0.474  -0.492  -0.366  -0.563  -0.571  -0.444
45    Y        -0.809  -0.766  -0.711  -0.556  -0.497  -0.444  -0.866  -0.822  -0.729
46    E        -1.176  -1.111  -1.094  -1.096  -1.029  -0.956  -1.018  -0.957  -0.899
47    E        -1.543  -1.497  -1.447  -1.459  -1.363  -1.325  -1.170  -1.127  -1.042
48    K        -0.809  -0.793  -0.712  -0.862  -0.837  -0.703  -0.866  -0.844  -0.730
49    L        -0.304  -0.297  -0.209  -0.543  -0.510  -0.396  -0.563  -0.554  -0.439
50    K        -0.443  -0.483  -0.581  -0.369  -0.430  -0.567  -0.411  -0.462  -0.574
51    L         1.694   1.712   1.779   1.510   1.552   1.658   1.864   1.893   1.999
52    V         0.586   0.638   0.614   0.688   0.772   0.710   0.347   0.438   0.351
53    E        -1.038  -1.025  -1.067  -1.001  -0.981  -1.099  -0.866  -0.853  -0.868
54    E        -0.443  -0.505  -0.595  -0.188  -0.289  -0.458  -0.411  -0.489  -0.591
55    A         1.694   1.712   1.779   1.365   1.378   1.515   1.864   1.893   1.999
56    K         1.694   1.712   1.779   1.569   1.598   1.716   1.864   1.893   1.999
57    K         0.219   0.148  -0.003  -0.014  -0.130  -0.356   0.195   0.090  -0.139
58    E         0.935   0.843   0.751   0.928   0.792   0.623   0.954   0.802   0.612
59    Y        -0.076  -0.053  -0.101   0.222   0.247   0.199  -0.260  -0.238  -0.294
60    A         1.694   1.712   1.779   1.365   1.378   1.515   1.864   1.893   1.999
61    K         0.586   0.607   0.591   0.456   0.489   0.471   0.347   0.380   0.307
62    L         0.219   0.174   0.004   0.133   0.081  -0.207   0.195   0.126  -0.129
63    H         0.219   0.174   0.004   0.617   0.540   0.269   0.195   0.126  -0.129
64    P        -0.076  -0.037  -0.122   0.032   0.082  -0.096  -0.260  -0.223  -0.325
65    V         0.860   0.887   0.732   1.122   1.164   0.938   0.832   0.876   0.576
66    V         0.515   0.484   0.538   0.286   0.238   0.319   0.212   0.144   0.201
67    T        -0.179  -0.219  -0.141  -0.239  -0.286  -0.202  -0.407  -0.447  -0.350
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    P        -0.179  -0.105  -0.138  -0.422  -0.351  -0.319  -0.407  -0.309  -0.348
72    K        -1.196  -1.214  -1.113  -1.426  -1.431  -1.285  -1.026  -1.040  -0.912
73    D        -1.196  -1.163  -1.106  -0.976  -0.939  -0.839  -1.026  -0.990  -0.905
74    V        -1.038  -1.060  -1.053  -1.144  -1.178  -1.142  -0.866  -0.888  -0.855
75    P        -1.176  -1.123  -1.095  -1.063  -0.988  -0.960  -1.018  -0.967  -0.900
76    A        -0.076  -0.075  -0.123  -0.065  -0.078  -0.215  -0.260  -0.265  -0.329
77    N        -0.671  -0.680  -0.672  -0.565  -0.571  -0.536  -0.715  -0.729  -0.689
78    A        -1.176  -1.219  -1.126  -1.255  -1.311  -1.180  -1.018  -1.047  -0.925
79    S        -1.038  -1.084  -1.066  -0.918  -0.976  -0.985  -0.866  -0.913  -0.868
80    F        -0.443  -0.541  -0.603  -0.029  -0.174  -0.271  -0.411  -0.532  -0.601
81    N         0.586   0.603   0.591   0.654   0.682   0.646   0.347   0.372   0.305
82    L        -1.176  -1.219  -1.126  -0.898  -0.939  -0.813  -1.018  -1.047  -0.925
83    E        -0.076  -0.141  -0.131  -0.091  -0.184  -0.171  -0.260  -0.354  -0.338
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    D         0.935   0.843   0.751   1.158   1.037   0.889   0.954   0.802   0.612
87    P         0.935   0.897   0.763   1.227   1.186   1.004   0.954   0.893   0.633
88    N         0.935   0.897   0.763   1.105   1.059   0.847   0.954   0.893   0.633
89    I        -0.076  -0.108  -0.127  -0.162  -0.196  -0.189  -0.260  -0.321  -0.333
90    D         1.694   1.712   1.779   1.842   1.872   1.985   1.864   1.893   1.999
91    F        -0.166  -0.111  -0.128   0.002   0.067   0.079  -0.411  -0.347  -0.340
92    E        -0.166  -0.108  -0.134  -0.297  -0.219  -0.278  -0.411  -0.342  -0.346
93    R        -1.176  -1.127  -1.108  -1.426  -1.385  -1.306  -1.018  -0.967  -0.909
94    V        -0.809  -0.786  -0.716  -0.996  -0.922  -0.840  -0.866  -0.836  -0.733
95    I        -0.166  -0.215  -0.153  -0.248  -0.291  -0.195  -0.411  -0.460  -0.370
96    L        -1.176  -1.219  -1.126  -1.249  -1.291  -1.157  -1.018  -1.047  -0.925
97    N        -0.671  -0.748  -0.678  -0.663  -0.790  -0.676  -0.715  -0.790  -0.693
98    A         0.429   0.442   0.523  -0.198  -0.182  -0.047   0.044   0.061   0.171
99    V        -0.443  -0.498  -0.583  -0.190  -0.290  -0.412  -0.411  -0.483  -0.577
100   E        -1.176  -1.219  -1.126  -1.093  -1.182  -1.040  -1.018  -1.047  -0.925
101   S        -0.671  -0.676  -0.668  -0.920  -0.925  -0.955  -0.715  -0.710  -0.682
102   L         0.860   0.799   0.703   0.657   0.571   0.403   0.832   0.726   0.521
103   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   E        -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   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   T        -0.671  -0.582  -0.642  -0.789  -0.699  -0.717  -0.715  -0.605  -0.650
* 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/P81449
Output conservation file - output/P81449
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
