1     M         1.174   1.230   1.277   1.381   1.445   1.509   1.233   1.314   1.389
2     G        -1.947  -1.961  -1.787  -1.342  -1.395  -1.235  -1.589  -1.572  -1.342
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     A        -0.848  -0.732  -0.769  -0.711  -0.564  -0.599  -0.961  -0.841  -0.832
7     W        -0.848  -0.936  -0.780  -0.512  -0.691  -0.548  -0.961  -1.045  -0.844
8     L        -0.511  -0.748  -0.750  -0.905  -1.195  -1.054  -0.491  -0.806  -0.803
9     F        -0.092  -0.156  -0.043  -0.240  -0.329  -0.171  -0.334  -0.471  -0.316
10    I         0.307   0.356   0.083   0.250   0.302  -0.219   0.293   0.359  -0.095
11    L        -0.950  -0.980  -0.779  -1.624  -1.518  -1.229  -1.118  -1.103  -0.843
12    A         0.307   0.078   0.051   0.452   0.196   0.134   0.293  -0.072  -0.150
13    V        -0.511  -0.748  -0.750  -0.354  -0.855  -0.938  -0.491  -0.806  -0.803
14    V        -0.950  -0.700  -0.760  -1.440  -1.219  -1.176  -1.118  -0.791  -0.819
15    V        -2.105  -1.933  -1.779  -2.065  -2.075  -1.705  -1.745  -1.555  -1.335
16    N         0.307   0.295   0.079   0.482   0.488   0.182   0.293   0.270  -0.101
17    C        -1.528  -1.580  -1.355  -1.304  -1.433  -1.244  -1.432  -1.439  -1.164
18    I        -0.950  -0.980  -0.779  -0.996  -1.015  -0.742  -1.118  -1.103  -0.843
19    N         1.174   1.230   1.277   1.185   1.279   1.337   1.233   1.314   1.389
20    L         0.307   0.078   0.051  -0.199  -0.464  -0.400   0.293  -0.072  -0.150
21    F         0.307   0.078   0.051   0.176  -0.217  -0.360   0.293  -0.072  -0.150
22    G        -1.528  -1.133  -1.295  -1.791  -1.366  -1.408  -1.432  -0.967  -1.104
23    Q         1.174   1.230   1.277   1.466   1.544   1.583   1.233   1.314   1.389
24    V         0.307   0.078   0.051   0.497   0.159   0.071   0.293  -0.072  -0.150
25    H        -0.271  -0.055   0.010  -0.432  -0.125  -0.035  -0.648  -0.294  -0.221
26    F         0.307   0.078   0.051   0.333   0.078   0.041   0.293  -0.072  -0.150
27    T         0.307   0.078   0.051   0.636   0.305   0.224   0.293  -0.072  -0.150
28    I         1.174   1.230   1.277   1.096   1.170   1.259   1.233   1.314   1.389
29    L        -0.225  -0.002   0.010  -0.516  -0.055  -0.164  -0.567  -0.205  -0.221
30    Y         0.377   0.146   0.057   0.599   0.278   0.068   0.393   0.039  -0.140
31    A        -0.225  -0.002   0.010  -0.190   0.212   0.125  -0.567  -0.205  -0.221
32    D         1.174   1.230   1.277   1.369   1.407   1.499   1.233   1.314   1.389
33    L         1.174   1.230   1.277   0.506   0.555   0.742   1.233   1.314   1.389
34    E         1.174   1.230   1.277   1.323   1.388   1.458   1.233   1.314   1.389
35    A        -0.887  -0.911  -0.777  -0.645  -0.579  -0.480  -1.047  -1.015  -0.839
36    D         1.174   1.230   1.277   1.369   1.407   1.499   1.233   1.314   1.389
37    Y         1.174   1.230   1.277   1.277   1.346   1.418   1.233   1.314   1.389
38    I         1.174   1.230   1.277   1.103   1.212   1.265   1.233   1.314   1.389
39    N         1.174   1.230   1.277   1.177   1.283   1.330   1.233   1.314   1.389
40    P         1.174   1.230   1.277   1.425   1.482   1.548   1.233   1.314   1.389
41    I         1.174   1.230   1.277   1.103   1.212   1.265   1.233   1.314   1.389
42    E        -0.225  -0.197  -0.038  -0.135  -0.160   0.102  -0.567  -0.546  -0.307
43    L         1.174   1.230   1.277   0.506   0.555   0.742   1.233   1.314   1.389
44    C         1.174   1.230   1.277   1.450   1.535   1.570   1.233   1.314   1.389
45    S        -0.225  -0.002   0.010  -0.252   0.095   0.074  -0.567  -0.205  -0.221
46    K        -0.016  -0.036  -0.023   0.184   0.095   0.136  -0.207  -0.262  -0.279
47    V        -0.225  -0.002   0.010  -0.910  -0.627  -0.502  -0.567  -0.205  -0.221
48    N         1.174   1.230   1.277   1.177   1.283   1.330   1.233   1.314   1.389
49    K        -1.987  -2.026  -1.787  -1.404  -1.520  -1.179  -1.647  -1.621  -1.342
50    L        -1.026  -0.882  -0.792  -1.434  -1.315  -0.989  -1.167  -0.984  -0.857
51    I        -1.026  -0.931  -0.800  -1.143  -0.921  -0.832  -1.167  -1.055  -0.868
52    T        -1.987  -1.833  -1.766  -2.019  -1.858  -1.672  -1.647  -1.493  -1.326
53    P         1.174   1.230   1.277   1.425   1.482   1.548   1.233   1.314   1.389
54    E         1.174   1.230   1.277   1.323   1.388   1.458   1.233   1.314   1.389
55    A        -1.097  -1.188  -1.306  -0.732  -0.839  -1.045  -0.927  -1.038  -1.114
56    A        -0.730  -0.753  -0.753  -0.576  -0.557  -0.642  -0.807  -0.804  -0.807
57    L        -1.097  -1.363  -1.331  -1.378  -1.660  -1.466  -0.927  -1.212  -1.139
58    H         1.174   1.230   1.277   1.395   1.450   1.521   1.233   1.314   1.389
59    G        -0.887  -0.962  -0.775  -0.708  -0.727  -0.552  -1.047  -1.085  -0.840
60    A        -1.392  -1.368  -1.320  -1.501  -1.555  -1.485  -1.287  -1.250  -1.132
61    L        -1.115  -1.019  -0.816  -1.678  -1.532  -1.180  -1.287  -1.150  -0.886
62    S        -0.225  -0.002   0.010  -0.087   0.242   0.217  -0.567  -0.205  -0.221
63    L        -1.759  -1.589  -1.737  -2.117  -1.926  -1.990  -1.407  -1.224  -1.300
64    L         0.377   0.324   0.079  -0.140  -0.213  -0.422   0.393   0.313  -0.103
65    F        -0.382  -0.439  -0.722  -0.368  -0.520  -0.946  -0.327  -0.435  -0.767
66    L         1.174   1.230   1.277   0.506   0.555   0.742   1.233   1.314   1.389
67    L        -0.730  -0.505  -0.740  -1.291  -1.031  -1.174  -0.807  -0.523  -0.793
68    N        -0.382  -0.670  -0.740  -0.057  -0.384  -0.510  -0.327  -0.701  -0.791
69    G         0.377   0.146   0.057   0.735   0.468   0.257   0.393   0.039  -0.140
70    Y        -0.382  -0.670  -0.740   0.030  -0.380  -0.466  -0.327  -0.701  -0.791
71    W         1.174   1.230   1.277   1.480   1.573   1.596   1.233   1.314   1.389
72    F        -0.730  -0.861  -0.784  -1.059  -1.403  -1.318  -0.807  -0.978  -0.851
73    V        -1.097  -1.172  -1.307  -0.685  -0.919  -1.094  -0.927  -1.024  -1.116
74    F        -0.016  -0.036  -0.023  -0.392  -0.443  -0.581  -0.207  -0.262  -0.279
75    L         0.377   0.381   0.079  -0.140  -0.145  -0.422   0.393   0.397  -0.103
76    L         0.377   0.146   0.057  -0.158  -0.472  -0.503   0.393   0.039  -0.140
77    N         1.174   1.230   1.277   1.177   1.283   1.330   1.233   1.314   1.389
78    L         0.377   0.324   0.079  -0.158  -0.239  -0.473   0.393   0.313  -0.103
79    P         0.377   0.542   0.095   0.797   0.972   0.392   0.393   0.620  -0.075
80    V        -1.026  -0.807  -0.778  -1.638  -1.381  -1.198  -1.167  -0.883  -0.841
81    L        -0.016   0.062  -0.012  -0.735  -0.641  -0.678  -0.207  -0.097  -0.259
82    A         0.377   0.146   0.057   0.515   0.298   0.076   0.393   0.039  -0.140
83    Y        -0.730  -0.783  -0.774  -0.529  -0.634  -0.638  -0.807  -0.878  -0.837
84    N         0.377   0.146   0.057   0.555   0.295   0.146   0.393   0.039  -0.140
85    L        -1.392  -1.072  -1.280  -1.276  -0.763  -1.204  -1.287  -0.934  -1.091
86    N        -0.382  -0.468  -0.725  -0.067  -0.160  -0.514  -0.327  -0.433  -0.771
87    K         0.377   0.146   0.057   0.676   0.373   0.264   0.393   0.039  -0.140
88    I        -0.887  -0.970  -0.779  -1.067  -1.050  -0.845  -1.047  -1.097  -0.844
89    Y        -1.097  -1.188  -1.306  -0.776  -0.946  -1.294  -0.927  -1.038  -1.114
90    N        -1.759  -1.878  -1.771  -1.193  -1.370  -1.197  -1.407  -1.501  -1.329
91    K        -0.016  -0.036  -0.023   0.099   0.005  -0.004  -0.207  -0.262  -0.279
92    V        -2.492  -2.139  -2.115  -1.932  -1.432  -1.479  -1.887  -1.562  -1.443
93    Q        -0.225  -0.002   0.010  -0.019   0.286   0.277  -0.567  -0.205  -0.221
94    L         0.377   0.146   0.057  -0.167  -0.500  -0.529   0.393   0.039  -0.140
95    L         1.174   1.230   1.277   0.506   0.555   0.742   1.233   1.314   1.389
96    D         1.174   1.230   1.277   1.369   1.407   1.499   1.233   1.314   1.389
97    A         1.174   1.230   1.277   1.156   1.298   1.312   1.233   1.314   1.389
98    T         1.174   1.230   1.277   1.369   1.441   1.499   1.233   1.314   1.389
99    E         1.174   1.230   1.277   1.323   1.388   1.458   1.233   1.314   1.389
100   I         1.174   1.230   1.277   1.103   1.212   1.265   1.233   1.314   1.389
101   F         1.174   1.230   1.277   1.005   1.165   1.180   1.233   1.314   1.389
102   R         1.174   1.230   1.277   1.445   1.503   1.565   1.233   1.314   1.389
103   T        -0.382  -0.622  -0.744   0.134  -0.177  -0.376  -0.327  -0.643  -0.795
104   L         1.174   1.230   1.277   0.506   0.555   0.742   1.233   1.314   1.389
105   G        -1.392  -1.315  -1.312  -0.909  -0.775  -0.871  -1.287  -1.155  -1.121
106   K        -0.382  -0.622  -0.744   0.045  -0.290  -0.451  -0.327  -0.643  -0.795
107   H         1.174   1.230   1.277   1.395   1.450   1.521   1.233   1.314   1.389
108   K         1.174   1.230   1.277   1.287   1.327   1.427   1.233   1.314   1.389
109   R        -0.887  -0.842  -0.772  -0.555  -0.502  -0.389  -1.047  -0.949  -0.835
110   E         0.377   0.146   0.057   0.696   0.385   0.250   0.393   0.039  -0.140
111   S         0.377   0.146   0.057   0.730   0.443   0.222   0.393   0.039  -0.140
112   F         1.174   1.230   1.277   1.005   1.165   1.180   1.233   1.314   1.389
113   L        -0.887  -0.727  -0.745  -1.335  -0.940  -0.983  -1.047  -0.795  -0.801
114   K         1.174   1.230   1.277   1.287   1.327   1.427   1.233   1.314   1.389
115   L         0.377   0.146   0.057  -0.140  -0.434  -0.449   0.393   0.039  -0.140
116   G        -0.730  -0.884  -0.777  -0.405  -0.572  -0.544  -0.807  -0.978  -0.841
117   F         0.377   0.324   0.079   0.393   0.424   0.064   0.393   0.313  -0.103
118   H        -0.292  -0.176  -0.038  -0.259  -0.132   0.080  -0.687  -0.507  -0.306
119   L         1.174   1.230   1.277   0.506   0.555   0.742   1.233   1.314   1.389
120   L        -1.392  -1.376  -1.331  -1.911  -1.785  -1.631  -1.287  -1.267  -1.142
121   M        -0.887  -0.846  -0.771  -1.160  -1.061  -1.041  -1.047  -0.956  -0.836
122   F         1.174   1.230   1.277   1.005   1.165   1.180   1.233   1.314   1.389
123   F         1.174   1.230   1.277   1.005   1.165   1.180   1.233   1.314   1.389
124   F        -0.382  -0.670  -0.740  -0.370  -0.724  -0.986  -0.327  -0.701  -0.791
125   Y        -0.382  -0.463  -0.720  -0.155  -0.406  -0.881  -0.327  -0.461  -0.765
126   L         1.174   1.230   1.277   0.506   0.555   0.742   1.233   1.314   1.389
127   Y         1.174   1.230   1.277   1.277   1.346   1.418   1.233   1.314   1.389
128   R        -0.730  -0.831  -0.784  -0.233  -0.416  -0.357  -0.807  -0.951  -0.850
129   M         1.174   1.230   1.277   1.380   1.472   1.508   1.233   1.314   1.389
130   I         0.377   0.146   0.057   0.462   0.215   0.034   0.393   0.039  -0.140
131   M        -0.382  -0.468  -0.725   0.089   0.005  -0.467  -0.327  -0.433  -0.771
132   A        -0.016  -0.067  -0.037   0.040   0.013  -0.006  -0.207  -0.316  -0.304
133   L         1.174   1.230   1.277   0.506   0.555   0.742   1.233   1.314   1.389
134   I        -0.016   0.062  -0.012  -0.050   0.097  -0.073  -0.207  -0.097  -0.259
135   A        -1.392  -1.418  -1.340  -1.028  -0.996  -0.926  -1.287  -1.309  -1.150
136   E        -0.887  -0.737  -0.761  -0.656  -0.527  -0.516  -1.047  -0.873  -0.824
137   S        -1.115  -0.967  -0.798  -0.881  -0.717  -0.487  -1.287  -1.084  -0.864
138   G        -2.128  -1.978  -1.792  -1.530  -1.396  -1.146  -1.754  -1.585  -1.345
139   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   F        -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/P53173
Output conservation file - output/P53173
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
