1     M         1.891   2.018   2.115   2.122   2.294   2.458   2.080   2.274   2.442
2     L         0.672   0.625   0.714   0.375   0.236   0.369   0.391   0.238   0.343
3     A        -1.154  -1.251  -1.111  -1.220  -1.216  -1.028  -1.024  -1.065  -0.904
4     L        -0.314  -0.149  -0.091  -0.715  -0.473  -0.389  -0.636  -0.419  -0.342
5     A        -1.154  -1.182  -1.098  -1.385  -1.403  -1.284  -1.024  -1.006  -0.891
6     D         0.392   0.097   0.086   0.882   0.520   0.505   0.399  -0.034  -0.074
7     N        -1.154  -1.054  -1.093  -1.016  -0.900  -0.964  -1.024  -0.913  -0.889
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    I        -0.297  -0.227  -0.472  -0.231  -0.156  -0.538  -0.248  -0.170  -0.455
14    L         1.123   1.003   0.977   1.013   0.848   0.806   1.175   0.953   0.866
15    R         1.891   2.018   2.115   1.998   2.173   2.335   2.080   2.274   2.442
16    I        -1.641  -1.566  -1.495  -1.778  -1.644  -1.607  -1.283  -1.178  -1.062
17    I        -1.287  -1.155  -1.104  -1.489  -1.314  -1.219  -1.154  -0.993  -0.901
18    N         0.056  -0.024  -0.031   0.244   0.111   0.101  -0.119  -0.274  -0.266
19    F         0.056   0.087  -0.010  -0.205  -0.256  -0.412  -0.119  -0.154  -0.237
20    L        -0.934  -1.061  -1.065  -0.837  -1.131  -1.102  -0.766  -0.891  -0.857
21    F         0.392   0.383   0.163   0.374   0.362   0.019   0.399   0.361   0.042
22    L         0.392   0.253   0.129   0.378   0.209   0.004   0.399   0.190  -0.009
23    V        -0.668  -0.691  -0.604  -0.873  -0.890  -0.783  -0.766  -0.741  -0.628
24    I         1.891   2.018   2.115   1.772   1.948   2.108   2.080   2.274   2.442
25    S        -1.641  -1.509  -1.480  -1.812  -1.621  -1.522  -1.283  -1.127  -1.049
26    I        -0.581  -0.566  -0.569  -0.641  -0.587  -0.560  -0.636  -0.576  -0.578
27    G         1.123   1.003   0.977   1.135   0.946   0.893   1.175   0.953   0.866
28    L         1.891   2.018   2.115   1.687   1.857   2.023   2.080   2.274   2.442
29    I        -0.801  -0.609  -0.610  -1.161  -0.923  -0.890  -0.895  -0.661  -0.634
30    S        -0.095   0.081   0.006  -0.370  -0.116  -0.239  -0.377  -0.162  -0.218
31    S         0.056  -0.090  -0.017  -0.053  -0.271  -0.201  -0.119  -0.322  -0.244
32    L         1.123   1.017   0.975   1.022   0.878   0.822   1.175   0.978   0.861
33    L        -0.668  -0.608  -0.602  -1.064  -0.970  -0.945  -0.766  -0.676  -0.626
34    N        -0.095  -0.025  -0.010  -0.429  -0.309  -0.276  -0.377  -0.276  -0.241
35    T        -0.297  -0.465  -0.537  -0.030  -0.287  -0.411  -0.248  -0.468  -0.536
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -0.046  -0.036  -0.015  -0.053  -0.098  -0.066  -0.238  -0.236  -0.226
40    Q        -1.641  -1.347  -1.468  -1.330  -0.941  -1.094  -1.283  -0.982  -1.041
41    H        -1.154  -0.913  -1.064  -0.796  -0.563  -0.612  -1.024  -0.781  -0.865
42    R        -1.287  -1.298  -1.129  -0.861  -0.897  -0.628  -1.154  -1.103  -0.920
43    H        -0.668  -0.683  -0.592  -0.546  -0.606  -0.456  -0.766  -0.731  -0.615
44    S        -0.668  -0.787  -0.640  -0.577  -0.635  -0.448  -0.766  -0.840  -0.667
45    S        -0.668  -0.787  -0.640  -0.660  -0.855  -0.648  -0.766  -0.840  -0.667
46    R        -0.668  -0.787  -0.640  -0.446  -0.625  -0.407  -0.766  -0.840  -0.667
47    V         0.478   0.606   0.714   0.072   0.252   0.424   0.011   0.199   0.344
48    N         1.123   1.204   1.005   1.314   1.451   1.153   1.175   1.291   0.918
49    Y         0.745   0.911   0.817   0.623   0.872   0.736   0.528   0.787   0.554
50    C        -1.154  -1.170  -1.085  -1.185  -1.225  -1.078  -1.024  -0.998  -0.878
51    M        -0.581  -0.385  -0.570  -0.525  -0.268  -0.502  -0.636  -0.412  -0.590
52    F         1.123   1.003   0.977   1.016   0.853   0.775   1.175   0.953   0.866
53    A         0.056  -0.024  -0.031  -0.228  -0.377  -0.301  -0.119  -0.274  -0.266
54    C        -0.581  -0.603  -0.611  -0.789  -0.864  -0.759  -0.636  -0.671  -0.636
55    A         0.392   0.357   0.152   0.196   0.140  -0.157   0.399   0.328   0.026
56    Y        -0.581  -0.566  -0.569  -0.491  -0.477  -0.433  -0.636  -0.576  -0.578
57    G        -0.228  -0.238  -0.118  -0.575  -0.668  -0.518  -0.507  -0.529  -0.378
58    I        -0.297  -0.277  -0.488  -0.191  -0.151  -0.495  -0.248  -0.232  -0.475
59    F        -0.581  -0.358  -0.570  -0.830  -0.544  -0.873  -0.636  -0.392  -0.589
60    T         0.056   0.000   0.011   0.047  -0.036  -0.082  -0.119  -0.181  -0.200
61    D        -0.712  -0.762  -0.664  -0.634  -0.740  -0.623  -0.792  -0.811  -0.689
62    S        -0.297  -0.571  -0.576  -0.291  -0.745  -0.829  -0.248  -0.583  -0.583
63    L         0.543   0.720   0.765   0.089   0.372   0.415   0.140   0.427   0.449
64    Y         0.392   0.097   0.086   0.799   0.373   0.319   0.399  -0.034  -0.074
65    G         0.056   0.051   0.004  -0.034  -0.104  -0.165  -0.119  -0.143  -0.214
66    V        -0.228  -0.096  -0.072  -0.546  -0.379  -0.355  -0.507  -0.331  -0.311
67    F        -1.154  -1.216  -1.100  -1.330  -1.440  -1.267  -1.024  -1.042  -0.895
68    A         1.123   1.003   0.977   0.898   0.763   0.747   1.175   0.953   0.866
69    N        -0.581  -0.687  -0.601  -0.392  -0.614  -0.495  -0.636  -0.717  -0.616
70    F         0.392   0.097   0.086   0.374  -0.057  -0.114   0.399  -0.034  -0.074
71    I        -0.581  -0.571  -0.584  -0.623  -0.613  -0.623  -0.636  -0.631  -0.606
72    E        -1.154  -1.182  -1.098  -0.891  -0.864  -0.803  -1.024  -1.006  -0.891
73    P        -0.581  -0.693  -0.602  -0.746  -0.928  -0.767  -0.636  -0.723  -0.618
74    L        -0.581  -0.560  -0.571  -0.787  -0.739  -0.783  -0.636  -0.568  -0.580
75    A         1.123   1.003   0.977   0.872   0.719   0.690   1.175   0.953   0.866
76    W        -0.297  -0.571  -0.576   0.219  -0.215  -0.273  -0.248  -0.583  -0.583
77    P         1.891   2.018   2.115   2.106   2.278   2.443   2.080   2.274   2.442
78    L        -0.668  -0.599  -0.601  -0.811  -0.686  -0.651  -0.766  -0.672  -0.627
79    V         0.056   0.084   0.054  -0.078  -0.039  -0.117  -0.119  -0.052  -0.132
80    L         0.056  -0.113  -0.032  -0.082  -0.331  -0.190  -0.119  -0.363  -0.266
81    F        -0.801  -0.705  -0.662  -1.275  -1.193  -1.109  -0.895  -0.778  -0.693
82    T        -1.641  -1.459  -1.474  -1.796  -1.513  -1.581  -1.283  -1.087  -1.047
83    L        -0.581  -0.688  -0.610  -0.703  -0.827  -0.726  -0.636  -0.738  -0.635
84    D         1.891   2.018   2.115   2.110   2.297   2.447   2.080   2.274   2.442
85    F         0.392   0.396   0.167   0.348   0.330  -0.026   0.399   0.381   0.048
86    L        -0.297  -0.571  -0.576  -0.346  -0.838  -0.865  -0.248  -0.583  -0.583
87    N         0.392   0.266   0.128   0.614   0.424   0.156   0.399   0.209  -0.011
88    F        -0.668  -0.590  -0.582  -0.577  -0.378  -0.397  -0.766  -0.642  -0.603
89    V         0.392   0.396   0.167   0.438   0.409   0.088   0.399   0.381   0.048
90    F         1.123   1.204   1.005   1.039   1.173   0.872   1.175   1.291   0.918
91    T         1.123   1.003   0.977   1.215   1.034   0.971   1.175   0.953   0.866
92    F         0.056  -0.113  -0.032  -0.155  -0.459  -0.357  -0.119  -0.363  -0.266
93    T        -0.668  -0.635  -0.610  -0.931  -0.858  -0.818  -0.766  -0.698  -0.636
94    A         0.745   0.711   0.752   0.346   0.256   0.320   0.528   0.409   0.423
95    G         0.543   0.769   0.787   0.125   0.522   0.502   0.140   0.521   0.494
96    T        -0.297  -0.571  -0.576  -0.044  -0.445  -0.505  -0.248  -0.583  -0.583
97    V        -0.095  -0.149  -0.030  -0.479  -0.493  -0.298  -0.377  -0.418  -0.266
98    L         0.543   0.645   0.731   0.120   0.249   0.381   0.140   0.278   0.380
99    A         1.891   2.018   2.115   1.531   1.706   1.866   2.080   2.274   2.442
100   V        -0.095  -0.021  -0.014  -0.475  -0.380  -0.338  -0.377  -0.268  -0.245
101   G         0.056  -0.113  -0.032  -0.034  -0.346  -0.233  -0.119  -0.363  -0.266
102   I         1.123   1.017   0.975   1.094   0.947   0.875   1.175   0.978   0.861
103   R         1.123   1.017   0.975   1.341   1.203   1.143   1.175   0.978   0.861
104   A        -1.154  -1.216  -1.100  -1.176  -1.238  -1.031  -1.024  -1.042  -0.895
105   H         0.392   0.370   0.151   0.901   0.889   0.580   0.399   0.348   0.025
106   S         0.392   0.097   0.086   0.419   0.019  -0.057   0.399  -0.034  -0.074
107   C         1.891   2.018   2.115   2.129   2.311   2.466   2.080   2.274   2.442
108   N        -1.287  -1.184  -1.117  -1.163  -0.958  -0.876  -1.154  -1.009  -0.910
109   N         1.891   2.018   2.115   1.982   2.172   2.319   2.080   2.274   2.442
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   S        -1.641  -1.534  -1.473  -1.023  -0.861  -0.773  -1.283  -1.147  -1.045
113   S        -1.154  -1.088  -1.079  -0.763  -0.597  -0.620  -1.024  -0.917  -0.874
114   Y         0.392   0.370   0.151   0.840   0.841   0.516   0.399   0.348   0.025
115   V        -0.668  -0.637  -0.582  -0.788  -0.719  -0.604  -0.766  -0.700  -0.607
116   D        -0.934  -0.879  -1.016  -0.369  -0.316  -0.500  -0.766  -0.692  -0.806
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   S        -1.641  -1.592  -1.498  -1.138  -1.030  -0.904  -1.283  -1.194  -1.063
119   N         0.392   0.401   0.162   0.732   0.766   0.452   0.399   0.388   0.041
120   K        -0.581  -0.687  -0.601  -0.111  -0.179  -0.070  -0.636  -0.717  -0.616
121   I         0.392   0.253   0.129   0.504   0.344   0.170   0.399   0.190  -0.009
122   T        -0.095   0.087   0.010  -0.387  -0.153  -0.237  -0.377  -0.155  -0.216
123   Q         0.392   0.370   0.151   0.868   0.851   0.610   0.399   0.348   0.025
124   G         1.891   2.018   2.115   1.835   2.003   2.171   2.080   2.274   2.442
125   S         1.891   2.018   2.115   1.751   1.965   2.087   2.080   2.274   2.442
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   G        -1.287  -1.298  -1.129  -1.194  -1.175  -0.932  -1.154  -1.103  -0.920
130   T        -1.154  -1.185  -1.107  -0.862  -0.862  -0.708  -1.024  -1.010  -0.900
131   R         1.891   2.018   2.115   1.998   2.173   2.335   2.080   2.274   2.442
132   C         1.891   2.018   2.115   2.129   2.311   2.466   2.080   2.274   2.442
133   R         1.123   1.003   0.977   1.375   1.241   1.222   1.175   0.953   0.866
134   Q        -0.228  -0.145  -0.081   0.072   0.193   0.295  -0.507  -0.414  -0.329
135   A         0.392   0.097   0.086   0.183  -0.264  -0.295   0.399  -0.034  -0.074
136   Q         1.123   1.003   0.977   1.455   1.329   1.304   1.175   0.953   0.866
137   A         1.891   2.018   2.115   1.531   1.706   1.866   2.080   2.274   2.442
138   A        -1.154  -1.131  -1.087  -1.330  -1.293  -1.271  -1.024  -0.973  -0.884
139   V        -0.095  -0.150  -0.019  -0.187  -0.216  -0.011  -0.377  -0.420  -0.253
140   A         0.056  -0.090  -0.017  -0.316  -0.558  -0.451  -0.119  -0.322  -0.244
141   F         1.891   2.018   2.115   1.717   1.911   2.053   2.080   2.274   2.442
142   L         0.392   0.401   0.162   0.411   0.438   0.121   0.399   0.388   0.041
143   Y         0.056  -0.024  -0.031   0.394   0.258   0.244  -0.119  -0.274  -0.266
144   F         0.392   0.396   0.167   0.374   0.370   0.026   0.399   0.381   0.048
145   S        -0.297  -0.571  -0.576  -0.224  -0.601  -0.686  -0.248  -0.583  -0.583
146   C        -1.507  -1.316  -1.418  -1.211  -1.023  -1.048  -1.154  -0.951  -0.996
147   A        -0.095  -0.117  -0.020  -0.591  -0.594  -0.451  -0.377  -0.367  -0.248
148   I        -0.297  -0.571  -0.576  -0.282  -0.779  -0.835  -0.248  -0.583  -0.583
149   F         1.123   1.003   0.977   1.102   0.996   0.967   1.175   0.953   0.866
150   L        -0.581  -0.568  -0.600  -0.763  -0.793  -0.817  -0.636  -0.629  -0.624
151   A         0.392   0.680   0.224   0.190   0.572  -0.053   0.399   0.810   0.135
152   K        -0.668  -0.693  -0.622  -0.641  -0.711  -0.612  -0.766  -0.746  -0.647
153   T        -1.287  -1.177  -1.107  -1.290  -1.171  -1.065  -1.154  -1.013  -0.904
154   L        -0.297  -0.175  -0.456  -0.198  -0.043  -0.455  -0.248  -0.107  -0.436
155   M        -0.801  -0.690  -0.610  -0.945  -0.804  -0.667  -0.895  -0.721  -0.627
156   S         0.392   0.097   0.086   0.435   0.049  -0.020   0.399  -0.034  -0.074
157   V        -0.228   0.024  -0.037  -0.620  -0.202  -0.365  -0.507  -0.143  -0.260
158   F        -0.801  -0.795  -0.662  -0.972  -0.917  -0.742  -0.895  -0.847  -0.692
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   -        -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   N         0.543   0.635   0.720   0.292   0.452   0.550   0.140   0.257   0.356
163   M        -1.994  -1.852  -1.812  -1.691  -1.390  -1.419  -1.412  -1.263  -1.167
164   I        -1.641  -1.508  -1.479  -1.432  -1.188  -1.172  -1.283  -1.129  -1.049
165   S        -1.641  -1.637  -1.520  -1.175  -1.098  -0.949  -1.283  -1.223  -1.080
166   N        -1.154  -1.087  -1.075  -1.019  -0.885  -0.926  -1.024  -0.911  -0.868
167   G         1.123   1.003   0.977   1.219   1.086   1.079   1.175   0.953   0.866
168   A        -0.581  -0.687  -0.601  -0.905  -1.025  -0.905  -0.636  -0.717  -0.616
169   F         1.123   1.017   0.975   1.048   0.935   0.841   1.175   0.978   0.861
170   G        -0.297  -0.571  -0.576  -0.073  -0.483  -0.475  -0.248  -0.583  -0.583
171   S        -1.994  -1.792  -1.800  -1.792  -1.491  -1.520  -1.412  -1.212  -1.159
172   G        -0.934  -0.848  -1.009  -0.636  -0.501  -0.680  -0.766  -0.665  -0.800
173   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   S         0.268   0.202   0.061   0.234   0.137  -0.112   0.222   0.092  -0.112
176   K        -0.819  -0.680  -0.641  -0.627  -0.424  -0.367  -0.909  -0.732  -0.668
177   R         1.055   0.888   0.895   1.256   1.002   1.007   1.067   0.745   0.707
178   R        -0.712  -0.411  -0.590  -0.581  -0.197  -0.368  -0.792  -0.420  -0.607
179   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   T        -0.819  -0.775  -0.665  -0.867  -0.768  -0.589  -0.909  -0.833  -0.693
181   G        -0.864  -0.703  -0.670  -0.952  -0.787  -0.691  -0.961  -0.769  -0.700
182   Q        -0.712  -0.683  -0.649  -0.419  -0.439  -0.305  -0.792  -0.736  -0.675
183   V        -0.057  -0.145  -0.044  -0.226  -0.424  -0.262  -0.285  -0.394  -0.277
184   G         1.055   0.888   0.895   1.147   0.931   0.963   1.067   0.745   0.707
185   V         0.268   0.061   0.021   0.335   0.032  -0.033   0.222  -0.095  -0.173
186   P         1.891   2.018   2.115   2.106   2.278   2.443   2.080   2.274   2.442
187   T         0.056   0.078   0.050   0.060   0.121   0.015  -0.119  -0.061  -0.139
188   I         0.543   0.763   0.791   0.508   0.882   0.892   0.140   0.509   0.502
189   S         1.891   2.018   2.115   1.751   1.965   2.087   2.080   2.274   2.442
190   Q         1.123   1.003   0.977   1.377   1.198   1.131   1.175   0.953   0.866
191   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
192   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   V         1.891   2.018   2.115   1.780   1.950   2.116   2.080   2.274   2.442
* 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/Q12207
Output conservation file - output/Q12207
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
