1     M         0.922   0.946   1.005   1.178   1.204   1.269   0.956   0.996   1.080
2     G        -0.243  -0.152  -0.303  -0.230  -0.103  -0.327  -0.343  -0.224  -0.485
3     K        -0.501  -0.526  -0.383  -0.836  -0.870  -0.593  -0.749  -0.827  -0.619
4     S         0.165  -0.123  -0.312   0.406   0.044  -0.307   0.225  -0.182  -0.500
5     H        -2.058  -2.020  -1.762  -1.988  -1.934  -1.608  -1.885  -1.800  -1.465
6     G         0.922   0.946   1.005   0.850   0.903   0.999   0.956   0.996   1.080
7     Y        -0.945  -1.118  -1.156  -0.725  -0.963  -1.056  -0.911  -1.115  -1.141
8     R         0.922   0.946   1.005   0.765   0.810   0.929   0.956   0.996   1.080
9     S        -0.501  -0.526  -0.383  -0.539  -0.640  -0.452  -0.749  -0.827  -0.619
10    R        -0.645  -0.559  -0.386  -1.048  -0.927  -0.632  -0.992  -0.883  -0.624
11    T         0.922   0.946   1.005   0.969   1.005   1.097   0.956   0.996   1.080
12    R         0.922   0.946   1.005   0.765   0.810   0.929   0.956   0.996   1.080
13    Y         0.922   0.946   1.005   0.961   1.006   1.091   0.956   0.996   1.080
14    M        -2.180  -1.993  -1.755  -1.904  -1.739  -1.444  -1.967  -1.780  -1.459
15    F         0.922   0.946   1.005   1.140   1.172   1.238   0.956   0.996   1.080
16    Q        -0.243  -0.460  -0.384  -0.061  -0.424  -0.363  -0.343  -0.714  -0.621
17    R         0.922   0.946   1.005   0.765   0.810   0.929   0.956   0.996   1.080
18    D        -0.945  -1.118  -1.156  -0.563  -0.822  -0.972  -0.911  -1.115  -1.141
19    F         0.922   0.946   1.005   1.140   1.172   1.238   0.956   0.996   1.080
20    R        -0.645  -0.521  -0.381  -1.190  -0.990  -0.762  -0.992  -0.818  -0.616
21    K        -0.501  -0.526  -0.383  -0.860  -0.904  -0.625  -0.749  -0.827  -0.619
22    H        -0.566  -0.964  -1.150  -0.146  -0.719  -1.103  -0.424  -0.925  -1.135
23    G         0.922   0.946   1.005   0.850   0.903   0.999   0.956   0.996   1.080
24    A        -1.614  -1.858  -1.760  -1.306  -1.624  -1.468  -1.398  -1.637  -1.462
25    V         0.165   0.338  -0.283   0.300   0.483  -0.398   0.225   0.439  -0.453
26    H        -2.058  -1.749  -1.756  -1.981  -1.658  -1.567  -1.885  -1.598  -1.460
27    M        -0.243  -0.227  -0.359  -0.028  -0.027  -0.241  -0.343  -0.340  -0.579
28    S         0.922   0.946   1.005   1.012   1.061   1.133   0.956   0.996   1.080
29    T         0.165   0.032  -0.303   0.340   0.169  -0.407   0.225   0.042  -0.485
30    Y         0.922   0.946   1.005   0.961   1.006   1.091   0.956   0.996   1.080
31    L         0.165   0.317  -0.283   0.459   0.614  -0.125   0.225   0.413  -0.453
32    K         0.922   0.946   1.005   0.608   0.666   0.800   0.956   0.996   1.080
33    I        -1.799  -1.703  -1.742  -1.742  -1.571  -1.630  -1.642  -1.518  -1.447
34    Y         0.922   0.946   1.005   0.961   1.006   1.091   0.956   0.996   1.080
35    K        -0.243  -0.012  -0.291  -0.551  -0.218  -0.620  -0.343  -0.020  -0.465
36    V         0.922   0.946   1.005   0.666   0.733   0.848   0.956   0.996   1.080
37    G         0.922   0.946   1.005   0.850   0.903   0.999   0.956   0.996   1.080
38    D         0.922   0.946   1.005   1.151   1.173   1.247   0.956   0.996   1.080
39    I         0.922   0.946   1.005   0.930   0.954   1.065   0.956   0.996   1.080
40    V         0.922   0.946   1.005   0.666   0.733   0.848   0.956   0.996   1.080
41    D         0.922   0.946   1.005   1.151   1.173   1.247   0.956   0.996   1.080
42    I         0.922   0.946   1.005   0.930   0.954   1.065   0.956   0.996   1.080
43    K         0.165   0.032  -0.303  -0.013  -0.159  -0.642   0.225   0.042  -0.485
44    A        -0.501  -0.526  -0.383  -0.751  -0.868  -0.658  -0.749  -0.827  -0.619
45    N         0.922   0.946   1.005   1.020   1.060   1.139   0.956   0.996   1.080
46    G         0.922   0.946   1.005   0.850   0.903   0.999   0.956   0.996   1.080
47    S        -0.501  -0.526  -0.383  -0.539  -0.640  -0.452  -0.749  -0.827  -0.619
48    I        -0.501  -0.526  -0.383  -0.701  -0.834  -0.624  -0.749  -0.827  -0.619
49    Q         0.165   0.317  -0.283   0.455   0.622  -0.157   0.225   0.413  -0.453
50    K         0.922   0.946   1.005   0.608   0.666   0.800   0.956   0.996   1.080
51    G         0.922   0.946   1.005   0.850   0.903   0.999   0.956   0.996   1.080
52    M         0.922   0.946   1.005   1.178   1.204   1.269   0.956   0.996   1.080
53    P         0.165  -0.123  -0.312   0.472   0.099  -0.258   0.225  -0.182  -0.500
54    H         0.922   0.946   1.005   1.078   1.115   1.187   0.956   0.996   1.080
55    K         0.922   0.946   1.005   0.608   0.666   0.800   0.956   0.996   1.080
56    F        -1.275  -1.359  -1.177  -1.219  -1.348  -1.125  -1.398  -1.439  -1.169
57    Y         0.922   0.946   1.005   0.961   1.006   1.091   0.956   0.996   1.080
58    Q        -0.692  -0.527  -0.364  -0.764  -0.506  -0.285  -1.074  -0.829  -0.587
59    G         0.922   0.946   1.005   0.850   0.903   0.999   0.956   0.996   1.080
60    K         0.165   0.032  -0.303  -0.013  -0.159  -0.642   0.225   0.042  -0.485
61    T         0.922   0.946   1.005   0.969   1.005   1.097   0.956   0.996   1.080
62    G         0.922   0.946   1.005   0.850   0.903   0.999   0.956   0.996   1.080
63    V        -0.645  -0.521  -0.381  -1.086  -0.897  -0.643  -0.992  -0.818  -0.616
64    V         0.165  -0.123  -0.312   0.065  -0.273  -0.540   0.225  -0.182  -0.500
65    Y         0.922   0.946   1.005   0.961   1.006   1.091   0.956   0.996   1.080
66    N         0.922   0.946   1.005   1.020   1.060   1.139   0.956   0.996   1.080
67    V         0.922   0.946   1.005   0.666   0.733   0.848   0.956   0.996   1.080
68    T         0.922   0.946   1.005   0.969   1.005   1.097   0.956   0.996   1.080
69    K        -0.243  -0.152  -0.303  -0.479  -0.346  -0.521  -0.343  -0.224  -0.485
70    S         0.922   0.946   1.005   1.012   1.061   1.133   0.956   0.996   1.080
71    S        -0.645  -0.583  -0.385  -0.818  -0.769  -0.464  -0.992  -0.925  -0.622
72    V         0.922   0.946   1.005   0.666   0.733   0.848   0.956   0.996   1.080
73    G         0.922   0.946   1.005   0.850   0.903   0.999   0.956   0.996   1.080
74    V        -0.243  -0.344  -0.376  -0.450  -0.604  -0.638  -0.343  -0.525  -0.608
75    I        -0.243  -0.152  -0.303  -0.164  -0.067  -0.288  -0.343  -0.224  -0.485
76    I         0.165   0.388  -0.281   0.300   0.535  -0.394   0.225   0.497  -0.450
77    N        -0.692  -0.575  -0.384  -0.862  -0.695  -0.408  -1.074  -0.911  -0.621
78    K         0.922   0.946   1.005   0.608   0.666   0.800   0.956   0.996   1.080
79    M        -1.169  -1.193  -1.153  -1.312  -1.362  -1.299  -1.236  -1.212  -1.138
80    V         0.922   0.946   1.005   0.666   0.733   0.848   0.956   0.996   1.080
81    G         0.165  -0.123  -0.312   0.214  -0.169  -0.541   0.225  -0.182  -0.500
82    N         0.165  -0.123  -0.312   0.436   0.088  -0.218   0.225  -0.182  -0.500
83    R         0.922   0.946   1.005   0.765   0.810   0.929   0.956   0.996   1.080
84    Y         0.165   0.032  -0.303   0.384   0.244  -0.221   0.225   0.042  -0.485
85    L        -1.476  -1.453  -1.200  -1.338  -1.368  -1.017  -1.561  -1.538  -1.194
86    E         0.922   0.946   1.005   1.024   1.057   1.142   0.956   0.996   1.080
87    K         0.922   0.946   1.005   0.608   0.666   0.800   0.956   0.996   1.080
88    R         0.922   0.946   1.005   0.765   0.810   0.929   0.956   0.996   1.080
89    L        -1.614  -1.356  -1.176  -1.859  -1.494  -1.237  -1.723  -1.419  -1.166
90    N         0.922   0.946   1.005   1.020   1.060   1.139   0.956   0.996   1.080
91    L        -0.501  -0.526  -0.383  -0.603  -0.734  -0.556  -0.749  -0.827  -0.619
92    R         0.922   0.946   1.005   0.765   0.810   0.929   0.956   0.996   1.080
93    V        -0.645  -0.579  -0.378  -1.086  -0.965  -0.609  -0.992  -0.918  -0.611
94    E         0.922   0.946   1.005   1.024   1.057   1.142   0.956   0.996   1.080
95    H         0.922   0.946   1.005   1.078   1.115   1.187   0.956   0.996   1.080
96    I        -0.645  -0.479  -0.374  -1.009  -0.731  -0.599  -0.992  -0.747  -0.604
97    K         0.165  -0.123  -0.312   0.019  -0.308  -0.534   0.225  -0.182  -0.500
98    H         0.165  -0.123  -0.312   0.494   0.142  -0.177   0.225  -0.182  -0.500
99    S         0.922   0.946   1.005   1.012   1.061   1.133   0.956   0.996   1.080
100   K        -1.169  -1.204  -1.163  -1.492  -1.517  -1.433  -1.236  -1.227  -1.150
101   C         0.165  -0.123  -0.312   0.680   0.307  -0.064   0.225  -0.182  -0.500
102   R         0.922   0.946   1.005   0.765   0.810   0.929   0.956   0.996   1.080
103   Q         0.165  -0.123  -0.312   0.463   0.123  -0.174   0.225  -0.182  -0.500
104   E        -0.501  -0.526  -0.383  -0.419  -0.504  -0.294  -0.749  -0.827  -0.619
105   F         0.922   0.946   1.005   1.140   1.172   1.238   0.956   0.996   1.080
106   L        -0.243  -0.012  -0.291  -0.089   0.208  -0.233  -0.343  -0.020  -0.465
107   E        -2.058  -1.956  -1.754  -1.785  -1.690  -1.453  -1.885  -1.739  -1.457
108   R         0.922   0.946   1.005   0.765   0.810   0.929   0.956   0.996   1.080
109   V         0.922   0.946   1.005   0.666   0.733   0.848   0.956   0.996   1.080
110   K         0.922   0.946   1.005   0.608   0.666   0.800   0.956   0.996   1.080
111   A        -1.275  -1.362  -1.173  -1.288  -1.380  -1.094  -1.398  -1.444  -1.163
112   N         0.922   0.946   1.005   1.020   1.060   1.139   0.956   0.996   1.080
113   A        -0.945  -0.989  -1.140  -0.762  -0.818  -0.999  -0.911  -0.958  -1.122
114   A        -0.566  -0.964  -1.150  -0.295  -0.806  -1.062  -0.424  -0.925  -1.135
115   K        -0.501  -0.476  -0.379  -0.856  -0.826  -0.619  -0.749  -0.743  -0.612
116   R        -0.692  -0.583  -0.386  -1.314  -1.147  -0.783  -1.074  -0.925  -0.625
117   A        -1.614  -1.294  -1.168  -2.139  -1.666  -1.445  -1.723  -1.338  -1.156
118   E         0.165  -0.123  -0.312   0.435   0.078  -0.232   0.225  -0.182  -0.500
119   A         0.922   0.946   1.005   0.878   0.916   1.022   0.956   0.996   1.080
120   K         0.922   0.946   1.005   0.608   0.666   0.800   0.956   0.996   1.080
121   A         0.922   0.946   1.005   0.878   0.916   1.022   0.956   0.996   1.080
122   Q        -1.799  -1.920  -1.760  -1.553  -1.732  -1.588  -1.642  -1.706  -1.463
123   G         0.165   0.032  -0.303   0.259   0.122  -0.352   0.225   0.042  -0.485
124   V        -1.535  -1.304  -1.176  -1.913  -1.607  -1.399  -1.642  -1.385  -1.167
125   A        -2.582  -2.540  -2.214  -2.321  -2.263  -1.812  -2.129  -2.032  -1.641
126   V         0.922   0.946   1.005   0.666   0.733   0.848   0.956   0.996   1.080
127   Q        -0.945  -0.595  -1.112  -0.617  -0.190  -0.906  -0.911  -0.489  -1.089
128   L         0.922   0.946   1.005   1.032   1.065   1.149   0.956   0.996   1.080
129   K        -0.501  -0.473  -0.377  -0.972  -0.951  -0.772  -0.749  -0.737  -0.609
130   R         0.922   0.946   1.005   0.765   0.810   0.929   0.956   0.996   1.080
131   Q         0.922   0.946   1.005   1.040   1.081   1.155   0.956   0.996   1.080
132   P        -0.243  -0.338  -0.376  -0.056  -0.238  -0.392  -0.343  -0.515  -0.607
133   A        -1.614  -1.766  -1.744  -1.470  -1.673  -1.705  -1.398  -1.539  -1.448
134   Q        -2.582  -2.573  -2.223  -2.472  -2.434  -1.949  -2.129  -2.058  -1.647
135   P         0.165   0.032  -0.303   0.482   0.325  -0.205   0.225   0.042  -0.485
136   R        -0.945  -0.739  -1.118  -0.993  -0.740  -1.318  -0.911  -0.682  -1.095
137   E        -2.243  -1.862  -2.175  -1.784  -1.326  -1.855  -1.804  -1.425  -1.611
138   S        -0.501  -0.273  -0.344  -0.611  -0.279  -0.403  -0.749  -0.411  -0.555
139   R        -0.945  -0.989  -1.140  -0.933  -1.013  -1.270  -0.911  -0.958  -1.122
140   I        -2.180  -2.014  -1.763  -2.250  -2.017  -1.628  -1.967  -1.803  -1.466
141   V        -0.945  -1.142  -1.170  -1.014  -1.291  -1.260  -0.911  -1.169  -1.161
142   S        -0.945  -0.867  -1.126  -0.685  -0.573  -1.019  -0.911  -0.799  -1.106
143   T        -0.566  -0.964  -1.150  -0.260  -0.832  -1.191  -0.424  -0.925  -1.135
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   E        -0.945  -1.002  -1.137  -0.800  -0.899  -1.256  -0.911  -0.971  -1.118
146   G        -2.503  -2.516  -2.217  -2.206  -2.205  -1.791  -2.048  -2.012  -1.643
147   N         0.922   0.946   1.005   1.020   1.060   1.139   0.956   0.996   1.080
148   V        -2.243  -2.330  -2.215  -2.164  -2.381  -2.141  -1.804  -1.875  -1.641
149   P         0.922   0.946   1.005   1.078   1.116   1.187   0.956   0.996   1.080
150   Q        -1.614  -1.858  -1.760  -1.283  -1.643  -1.565  -1.398  -1.637  -1.462
151   T         0.922   0.946   1.005   0.969   1.005   1.097   0.956   0.996   1.080
152   L        -0.243  -0.460  -0.384  -0.151  -0.586  -0.561  -0.343  -0.714  -0.621
153   A        -0.243  -0.152  -0.303  -0.203  -0.091  -0.306  -0.343  -0.224  -0.485
154   P         0.922   0.946   1.005   1.078   1.116   1.187   0.956   0.996   1.080
155   V         0.165   0.032  -0.303   0.077  -0.047  -0.482   0.225   0.042  -0.485
156   P        -0.645  -0.434  -0.353  -0.818  -0.507  -0.384  -0.992  -0.672  -0.568
157   Y         0.922   0.946   1.005   0.961   1.006   1.091   0.956   0.996   1.080
158   E        -0.243  -0.152  -0.303  -0.042   0.061  -0.171  -0.343  -0.224  -0.485
159   T         0.922   0.946   1.005   0.969   1.005   1.097   0.956   0.996   1.080
160   F        -0.501  -0.526  -0.383  -0.384  -0.496  -0.321  -0.749  -0.827  -0.619
161   I         0.922   0.946   1.005   0.930   0.954   1.065   0.956   0.996   1.080
* 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/Q12672
Output conservation file - output/Q12672
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
