1     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     M         1.361   1.370   1.496   1.675   1.689   1.876   1.513   1.527   1.730
8     -         0.394   0.346   0.291   0.422   0.355   0.254   0.300   0.214   0.066
9     -         0.394   0.467   0.311   0.453   0.571   0.196   0.300   0.419   0.105
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    A        -2.324  -2.285  -2.121  -1.833  -1.762  -1.588  -1.685  -1.653  -1.412
13    G        -0.523  -0.556  -0.499  -0.469  -0.493  -0.406  -0.738  -0.766  -0.648
14    D        -1.989  -1.957  -1.840  -1.768  -1.711  -1.622  -1.567  -1.537  -1.328
15    S        -1.654  -1.647  -1.486  -1.391  -1.368  -1.147  -1.448  -1.436  -1.194
16    D         0.274   0.327   0.302   0.211   0.306   0.161   0.091   0.181   0.087
17    N        -0.061  -0.082  -0.388   0.191   0.145  -0.360  -0.027  -0.059  -0.484
18    V         0.082   0.125   0.227  -0.139  -0.075   0.087  -0.264  -0.187  -0.057
19    S         0.274   0.325   0.276   0.205   0.285   0.200   0.091   0.177   0.038
20    L         1.361   1.370   1.496   1.257   1.270   1.474   1.513   1.527   1.730
21    P         1.361   1.370   1.496   1.675   1.687   1.876   1.513   1.527   1.730
22    K         1.361   1.370   1.496   1.237   1.253   1.455   1.513   1.527   1.730
23    A         1.361   1.370   1.496   1.403   1.403   1.614   1.513   1.527   1.730
24    T         1.361   1.370   1.496   1.597   1.608   1.801   1.513   1.527   1.730
25    V         0.633   0.676   0.390   0.952   1.001   0.577   0.684   0.749   0.252
26    Q         1.361   1.370   1.496   1.564   1.576   1.769   1.513   1.527   1.730
27    K         1.361   1.370   1.496   1.237   1.253   1.455   1.513   1.527   1.730
28    M         0.274   0.263   0.242   0.269   0.260   0.223   0.091   0.067  -0.027
29    I         0.082   0.056   0.204  -0.063  -0.101   0.127  -0.264  -0.321  -0.102
30    S        -0.061   0.018  -0.388   0.100   0.201  -0.308  -0.027   0.080  -0.484
31    E         0.633   0.565   0.374   0.397   0.310   0.062   0.684   0.578   0.222
32    I         0.274   0.325   0.276   0.243   0.323   0.233   0.091   0.177   0.038
33    L         0.633   0.628   0.376   0.604   0.600   0.218   0.684   0.676   0.227
34    D         0.082   0.125   0.227   0.171   0.253   0.363  -0.264  -0.187  -0.057
35    Q        -0.984  -0.968  -1.009  -1.030  -0.984  -1.014  -0.975  -0.949  -0.936
36    D         0.633   0.564   0.375   0.841   0.749   0.425   0.684   0.577   0.224
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    L         0.274   0.327   0.302   0.073   0.161   0.081   0.091   0.181   0.087
40    M        -1.654  -1.648  -1.486  -1.363  -1.373  -1.140  -1.448  -1.438  -1.194
41    F         0.274   0.327   0.302   0.404   0.492   0.384   0.091   0.181   0.087
42    T        -1.192  -1.151  -1.062  -1.182  -1.126  -0.969  -1.211  -1.167  -0.999
43    K         0.633   0.679   0.388   0.620   0.680   0.311   0.684   0.753   0.248
44    D         0.082   0.111   0.216  -0.396  -0.357  -0.169  -0.264  -0.215  -0.078
45    A         0.633   0.628   0.376   0.787   0.771   0.446   0.684   0.676   0.227
46    R         1.361   1.370   1.496   1.587   1.597   1.792   1.513   1.527   1.730
47    E         0.082   0.056   0.204  -0.396  -0.431  -0.175  -0.264  -0.321  -0.102
48    I        -1.192  -1.196  -1.078  -1.358  -1.378  -1.161  -1.211  -1.214  -1.013
49    I         0.082   0.056   0.204  -0.246  -0.309  -0.098  -0.264  -0.321  -0.102
50    I         0.274   0.327   0.302   0.243   0.328   0.275   0.091   0.181   0.087
51    N        -0.714  -0.701  -0.965  -0.855  -0.841  -1.189  -0.619  -0.606  -0.885
52    S        -0.379  -0.394  -0.449  -0.101  -0.111  -0.303  -0.501  -0.506  -0.573
53    G        -0.731  -0.694  -0.541  -0.598  -0.523  -0.337  -0.975  -0.927  -0.702
54    I         0.082   0.064   0.204  -0.063  -0.089   0.127  -0.264  -0.305  -0.101
55    E         1.361   1.370   1.496   1.029   1.038   1.254   1.513   1.527   1.730
56    F         1.361   1.370   1.496   1.597   1.607   1.801   1.513   1.527   1.730
57    I         1.361   1.370   1.496   1.345   1.365   1.559   1.513   1.527   1.730
58    M        -0.061  -0.192  -0.414   0.421   0.249  -0.131  -0.027  -0.208  -0.520
59    I        -0.731  -0.743  -0.549  -0.862  -0.892  -0.604  -0.975  -0.988  -0.712
60    L         0.274   0.201   0.252   0.158   0.044   0.121   0.091  -0.044  -0.009
61    S         0.633   0.675   0.383   0.662   0.720   0.298   0.684   0.747   0.240
62    S        -0.523  -0.477  -0.493  -0.554  -0.494  -0.452  -0.738  -0.680  -0.641
63    M        -1.192  -1.121  -1.062  -1.366  -1.298  -1.168  -1.211  -1.129  -0.996
64    A        -0.379  -0.328  -0.473  -0.435  -0.366  -0.655  -0.501  -0.433  -0.611
65    S         0.082   0.125   0.227   0.014   0.105   0.203  -0.264  -0.187  -0.057
66    E         0.274   0.327   0.302  -0.098  -0.023  -0.050   0.091   0.181   0.087
67    M         0.274   0.331   0.299   0.269   0.358   0.306   0.091   0.188   0.082
68    A        -0.061  -0.192  -0.414   0.165  -0.016  -0.332  -0.027  -0.208  -0.520
69    D         0.274   0.328   0.281  -0.098  -0.020  -0.083   0.091   0.184   0.047
70    N        -0.061   0.024  -0.382  -0.026   0.087  -0.484  -0.027   0.088  -0.475
71    E         0.633   0.679   0.388   0.397   0.451   0.084   0.684   0.753   0.248
72    A        -0.379  -0.383  -0.464  -0.435  -0.472  -0.635  -0.501  -0.523  -0.598
73    K         1.361   1.370   1.496   1.237   1.253   1.455   1.513   1.527   1.730
74    K         1.361   1.370   1.496   1.237   1.253   1.455   1.513   1.527   1.730
75    T         1.361   1.370   1.496   1.597   1.608   1.801   1.513   1.527   1.730
76    I         1.361   1.370   1.496   1.345   1.365   1.559   1.513   1.527   1.730
77    A         1.361   1.370   1.496   1.403   1.403   1.614   1.513   1.527   1.730
78    P        -0.984  -1.053  -1.030  -0.666  -0.744  -0.743  -0.975  -1.039  -0.960
79    E         0.021   0.033   0.198  -0.441  -0.431  -0.162  -0.382  -0.366  -0.112
80    H         1.361   1.370   1.496   1.688   1.697   1.889   1.513   1.527   1.730
81    V         0.274   0.201   0.252   0.404   0.264   0.275   0.091  -0.044  -0.009
82    I        -0.379  -0.397  -0.453  -0.313  -0.319  -0.387  -0.501  -0.511  -0.578
83    K         0.633   0.564   0.375   0.616   0.537   0.281   0.684   0.577   0.224
84    A         0.633   0.675   0.383   0.745   0.789   0.352   0.684   0.747   0.240
85    L         1.361   1.370   1.496   1.257   1.270   1.474   1.513   1.527   1.730
86    E        -0.379  -0.329  -0.464  -0.700  -0.631  -0.808  -0.501  -0.435  -0.600
87    E        -0.714  -0.802  -0.986  -0.778  -0.890  -1.065  -0.619  -0.728  -0.909
88    L         1.361   1.370   1.496   1.257   1.270   1.474   1.513   1.527   1.730
89    E        -0.523  -0.491  -0.493  -0.778  -0.735  -0.653  -0.738  -0.707  -0.645
90    Y         0.274   0.331   0.299   0.533   0.613   0.557   0.091   0.188   0.082
91    N        -1.989  -1.978  -1.831  -1.770  -1.782  -1.558  -1.567  -1.553  -1.321
92    E        -0.984  -0.951  -1.027  -1.215  -1.178  -1.203  -0.975  -0.950  -0.960
93    F         0.082   0.125   0.227   0.291   0.368   0.481  -0.264  -0.187  -0.057
94    I        -0.379  -0.397  -0.453  -0.444  -0.439  -0.544  -0.501  -0.511  -0.578
95    P        -0.984  -0.991  -1.027  -0.837  -0.852  -0.997  -0.975  -0.979  -0.960
96    F        -1.989  -1.995  -1.835  -1.865  -1.902  -1.688  -1.567  -1.565  -1.325
97    L        -1.066  -1.136  -1.057  -1.214  -1.288  -1.135  -1.093  -1.151  -0.992
98    E        -1.192  -1.196  -1.078  -1.602  -1.618  -1.423  -1.211  -1.214  -1.013
99    E        -1.319  -1.236  -1.425  -1.414  -1.304  -1.514  -1.093  -1.004  -1.135
100   I        -0.714  -0.839  -1.000  -0.552  -0.725  -1.011  -0.619  -0.772  -0.926
101   L        -0.379  -0.446  -0.488  -0.522  -0.645  -0.712  -0.501  -0.608  -0.631
102   L        -1.989  -1.929  -1.843  -1.749  -1.678  -1.544  -1.567  -1.516  -1.330
103   N        -0.061   0.020  -0.378  -0.190  -0.094  -0.561  -0.027   0.083  -0.469
104   F         0.274   0.331   0.299   0.569   0.653   0.565   0.091   0.188   0.082
105   K         1.361   1.370   1.496   1.237   1.253   1.455   1.513   1.527   1.730
106   G         0.274   0.331   0.299  -0.048   0.029   0.015   0.091   0.188   0.082
107   S        -2.324  -2.322  -2.143  -2.026  -2.009  -1.726  -1.685  -1.679  -1.426
108   Q         0.082   0.109   0.220  -0.048   0.005   0.122  -0.264  -0.218  -0.071
109   K         1.361   1.370   1.496   1.237   1.253   1.455   1.513   1.527   1.730
110   V        -1.527  -1.524  -1.474  -1.229  -1.207  -1.171  -1.330  -1.320  -1.182
111   K         0.021   0.038   0.201  -0.223  -0.173   0.069  -0.382  -0.354  -0.107
112   E         1.361   1.370   1.496   1.029   1.038   1.254   1.513   1.527   1.730
113   T        -0.061   0.020  -0.378   0.021   0.124  -0.376  -0.027   0.083  -0.469
114   R         0.082   0.126   0.220  -0.162  -0.093   0.056  -0.264  -0.185  -0.070
115   D        -1.527  -1.588  -1.473  -1.229  -1.329  -1.190  -1.330  -1.377  -1.182
116   S        -1.066  -1.042  -1.036  -0.975  -0.939  -0.900  -1.093  -1.067  -0.972
117   K         1.361   1.370   1.496   1.237   1.253   1.455   1.513   1.527   1.730
118   F         0.633   0.628   0.376   0.932   0.925   0.501   0.684   0.676   0.227
119   K        -0.731  -0.694  -0.541  -1.252  -1.218  -0.951  -0.975  -0.927  -0.702
120   K        -0.731  -0.694  -0.541  -0.854  -0.778  -0.554  -0.975  -0.927  -0.702
121   S         1.361   1.370   1.496   1.306   1.324   1.521   1.513   1.527   1.730
122   G         1.361   1.370   1.496   1.638   1.651   1.841   1.513   1.527   1.730
123   L        -0.061  -0.134  -0.400   0.056  -0.033  -0.356  -0.027  -0.129  -0.502
124   S         0.021   0.035   0.199  -0.167  -0.152   0.100  -0.382  -0.362  -0.112
125   E        -0.061  -0.192  -0.414  -0.250  -0.429  -0.745  -0.027  -0.208  -0.520
126   E         0.633   0.565   0.374   0.397   0.310   0.062   0.684   0.578   0.222
127   E         1.361   1.370   1.496   1.029   1.038   1.254   1.513   1.527   1.730
128   L         1.361   1.370   1.496   1.257   1.270   1.474   1.513   1.527   1.730
129   L         0.633   0.564   0.375   0.559   0.460   0.097   0.684   0.577   0.224
130   R        -0.061   0.015  -0.368   0.304   0.403  -0.192  -0.027   0.077  -0.455
131   Q        -0.061  -0.135  -0.396   0.246   0.142  -0.343  -0.027  -0.130  -0.496
132   Q         1.361   1.370   1.496   1.564   1.576   1.769   1.513   1.527   1.730
133   E         0.633   0.564   0.375   0.411   0.326   0.100   0.684   0.577   0.224
134   E         1.361   1.370   1.496   1.029   1.038   1.254   1.513   1.527   1.730
135   L        -0.061  -0.135  -0.396   0.050  -0.040  -0.363  -0.027  -0.130  -0.496
136   F         0.633   0.565   0.374   0.932   0.839   0.496   0.684   0.578   0.222
137   R        -1.192  -1.221  -1.077  -1.251  -1.305  -1.126  -1.211  -1.233  -1.012
138   Q        -1.527  -1.588  -1.473  -1.442  -1.512  -1.323  -1.330  -1.377  -1.182
139   S         0.082   0.056   0.204  -0.202  -0.260  -0.031  -0.264  -0.321  -0.102
140   R         0.633   0.564   0.375   0.943   0.849   0.540   0.684   0.577   0.224
141   S        -0.984  -1.016  -1.030  -1.102  -1.176  -1.225  -0.975  -1.012  -0.965
142   R         0.633   0.628   0.376   0.920   0.912   0.485   0.684   0.676   0.227
143   L         0.568   0.440   0.337   0.565   0.400   0.255   0.584   0.375   0.153
144   H        -1.108  -1.191  -1.051  -0.814  -0.959  -0.786  -1.117  -1.196  -0.986
145   H        -1.108  -1.008  -1.041  -0.843  -0.696  -0.759  -1.117  -1.003  -0.974
146   N        -0.763  -0.736  -0.552  -0.680  -0.647  -0.379  -1.014  -0.979  -0.715
147   S         0.490   0.322   0.302   0.512   0.290   0.241   0.460   0.173   0.088
148   V        -0.476  -0.615  -0.524  -0.280  -0.517  -0.419  -0.610  -0.810  -0.676
149   S         0.394   0.274   0.284   0.348   0.172   0.143   0.300   0.087   0.054
150   D        -1.214  -1.249  -1.084  -1.054  -1.112  -0.878  -1.216  -1.257  -1.018
151   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   K        -1.750  -1.713  -1.517  -2.060  -1.937  -1.719  -1.519  -1.483  -1.218
167   S        -1.656  -1.642  -1.492  -1.911  -1.969  -1.680  -1.435  -1.424  -1.196
168   E        -1.656  -1.566  -1.481  -1.583  -1.415  -1.380  -1.435  -1.345  -1.187
169   D        -1.209  -1.249  -1.074  -1.493  -1.593  -1.302  -1.225  -1.261  -1.009
170   S        -1.527  -1.525  -1.448  -1.622  -1.602  -1.382  -1.330  -1.319  -1.158
171   S        -1.654  -1.630  -1.479  -1.442  -1.399  -1.186  -1.448  -1.424  -1.189
* 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/Q92317
Output conservation file - output/Q92317
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
