1     M         1.636   1.699   1.728   1.933   2.010   2.069   1.787   1.872   1.923
2     L        -0.055  -0.143  -0.236   0.209   0.082  -0.109  -0.092  -0.228  -0.348
3     Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     K         0.324   0.345   0.400  -0.032  -0.001   0.087  -0.017  -0.000   0.077
6     F        -0.956  -0.826  -0.881  -0.953  -0.775  -0.864  -0.928  -0.765  -0.804
7     I        -0.956  -0.895  -0.881  -1.169  -1.095  -1.055  -0.928  -0.832  -0.804
8     W        -1.406  -1.363  -1.321  -1.410  -1.412  -1.294  -1.136  -1.071  -1.007
9     P        -0.956  -0.846  -0.872  -0.913  -0.774  -0.783  -0.928  -0.792  -0.797
10    V        -1.406  -1.309  -1.339  -1.308  -1.157  -1.177  -1.136  -1.025  -1.023
11    A        -1.856  -1.763  -1.712  -1.616  -1.553  -1.403  -1.345  -1.235  -1.165
12    R        -0.055   0.204  -0.167   0.094   0.452  -0.060  -0.092   0.271  -0.251
13    I        -1.406  -1.403  -1.349  -1.413  -1.328  -1.262  -1.136  -1.104  -1.030
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    T        -1.501  -1.401  -1.362  -1.462  -1.247  -1.252  -1.220  -1.100  -1.041
18    P        -1.501  -1.401  -1.362  -1.275  -1.144  -1.069  -1.220  -1.100  -1.041
19    I        -0.335  -0.373  -0.303  -0.506  -0.566  -0.462  -0.510  -0.529  -0.444
20    Y        -0.956  -0.843  -0.879  -0.766  -0.612  -0.650  -0.928  -0.778  -0.802
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    R        -1.406  -1.362  -1.319  -1.241  -1.145  -1.106  -1.136  -1.070  -1.005
23    P        -0.956  -0.895  -0.881  -1.011  -0.917  -0.920  -0.928  -0.832  -0.804
24    F        -1.406  -1.389  -1.344  -1.080  -1.059  -1.001  -1.136  -1.093  -1.027
25    T        -1.406  -1.203  -1.304  -1.361  -0.981  -1.225  -1.136  -0.910  -0.991
26    S        -0.956  -0.887  -0.878  -0.883  -0.802  -0.790  -0.928  -0.822  -0.801
27    H        -1.856  -1.763  -1.712  -1.653  -1.503  -1.438  -1.345  -1.235  -1.165
28    P        -0.956  -0.803  -0.871  -1.061  -0.771  -0.910  -0.928  -0.745  -0.796
29    F        -1.856  -1.763  -1.712  -1.796  -1.702  -1.579  -1.345  -1.235  -1.165
30    R        -0.335  -0.318  -0.314  -0.544  -0.537  -0.527  -0.510  -0.484  -0.466
31    N        -0.956  -0.845  -0.882  -1.093  -0.919  -0.977  -0.928  -0.780  -0.805
32    L        -0.786  -0.805  -0.842  -0.864  -0.909  -0.908  -0.719  -0.738  -0.758
33    A        -1.406  -1.246  -1.302  -1.271  -0.998  -1.127  -1.136  -0.954  -0.990
34    T        -0.961  -0.969  -0.918  -0.938  -0.928  -0.869  -0.919  -0.904  -0.840
35    S        -0.420  -0.347  -0.337  -0.801  -0.688  -0.682  -0.619  -0.516  -0.493
36    S        -0.420  -0.347  -0.339  -0.663  -0.563  -0.522  -0.619  -0.517  -0.495
37    S        -0.961  -0.942  -0.912  -0.845  -0.834  -0.756  -0.919  -0.877  -0.834
38    I        -0.216  -0.091  -0.270  -0.349  -0.165  -0.439  -0.318  -0.136  -0.395
39    S        -0.420  -0.354  -0.360  -0.755  -0.659  -0.650  -0.619  -0.519  -0.521
40    S        -0.961  -0.942  -0.912  -0.887  -0.861  -0.805  -0.919  -0.877  -0.834
41    T        -0.420  -0.399  -0.343  -0.573  -0.558  -0.466  -0.619  -0.572  -0.499
42    K        -0.216  -0.270  -0.329  -0.388  -0.482  -0.590  -0.318  -0.386  -0.477
43    A        -0.961  -0.954  -0.914  -0.941  -0.969  -0.916  -0.919  -0.889  -0.836
44    K        -0.216  -0.270  -0.329  -0.284  -0.356  -0.430  -0.318  -0.386  -0.477
45    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    T        -1.501  -1.429  -1.362  -1.504  -1.340  -1.293  -1.220  -1.122  -1.041
49    D        -0.786  -0.805  -0.842  -0.447  -0.490  -0.536  -0.719  -0.738  -0.758
50    T        -0.055  -0.143  -0.236  -0.243  -0.376  -0.536  -0.092  -0.228  -0.348
51    T        -0.786  -0.812  -0.842  -0.848  -0.938  -0.946  -0.719  -0.745  -0.758
52    P         0.395   0.447   0.445   0.308   0.389   0.346   0.116   0.192   0.162
53    L         1.636   1.699   1.728   1.414   1.514   1.561   1.787   1.872   1.923
54    K         0.758   0.577   0.567   0.637   0.336   0.296   0.743   0.426   0.390
55    L         1.636   1.699   1.728   1.414   1.514   1.561   1.787   1.872   1.923
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    S         0.758   0.577   0.567   0.858   0.595   0.574   0.743   0.426   0.390
61    N        -0.786  -0.881  -0.887  -0.520  -0.657  -0.677  -0.719  -0.815  -0.808
62    E        -0.786  -0.881  -0.887  -0.467  -0.610  -0.627  -0.719  -0.815  -0.808
63    L         0.758   0.577   0.567   0.590   0.330   0.310   0.743   0.426   0.390
64    Y         0.758   0.577   0.567   1.051   0.786   0.767   0.743   0.426   0.390
65    A         1.636   1.699   1.728   1.791   1.873   1.930   1.787   1.872   1.923
66    I        -0.055  -0.102  -0.220   0.006  -0.118  -0.305  -0.092  -0.178  -0.326
67    F         0.758   0.577   0.567   0.995   0.696   0.666   0.743   0.426   0.390
68    K        -0.335  -0.405  -0.317  -0.511  -0.564  -0.443  -0.510  -0.574  -0.468
69    I        -0.335  -0.427  -0.346  -0.487  -0.600  -0.484  -0.510  -0.605  -0.503
70    H         1.636   1.699   1.728   1.911   1.977   2.047   1.787   1.872   1.923
71    N         0.758   0.926   0.622   0.966   1.201   0.772   0.743   0.997   0.488
72    R        -0.786  -0.881  -0.887  -0.770  -0.913  -0.975  -0.719  -0.815  -0.808
73    P         0.758   0.577   0.567   0.984   0.715   0.695   0.743   0.426   0.390
74    Y         1.636   1.699   1.728   1.849   1.937   1.986   1.787   1.872   1.923
75    L         1.636   1.699   1.728   1.414   1.514   1.561   1.787   1.872   1.923
76    V         1.636   1.699   1.728   1.585   1.676   1.728   1.787   1.872   1.923
77    T         1.636   1.699   1.728   1.543   1.640   1.687   1.787   1.872   1.923
78    E         0.395   0.542   0.484   0.183   0.419   0.321   0.116   0.364   0.235
79    G         1.636   1.699   1.728   1.837   1.914   1.974   1.787   1.872   1.923
80    D         1.636   1.699   1.728   1.826   1.912   1.963   1.787   1.872   1.923
81    R        -0.055  -0.143  -0.236  -0.061  -0.179  -0.316  -0.092  -0.228  -0.348
82    V        -0.055  -0.201  -0.249   0.027  -0.173  -0.241  -0.092  -0.301  -0.367
83    I        -0.786  -0.881  -0.887  -0.666  -0.842  -0.848  -0.719  -0.815  -0.808
84    L         1.636   1.699   1.728   1.414   1.514   1.561   1.787   1.872   1.923
85    P         1.636   1.699   1.728   1.791   1.882   1.930   1.787   1.872   1.923
86    F         0.395   0.359   0.408   0.492   0.404   0.480   0.116   0.026   0.091
87    K         0.758   0.577   0.567   0.686   0.419   0.391   0.743   0.426   0.390
88    L         0.758   0.577   0.567   0.621   0.382   0.370   0.743   0.426   0.390
89    K         1.636   1.699   1.728   1.519   1.616   1.663   1.787   1.872   1.923
90    Q        -0.956  -0.983  -0.892  -0.694  -0.738  -0.595  -0.928  -0.924  -0.815
91    A         0.758   0.577   0.567   0.912   0.590   0.556   0.743   0.426   0.390
92    E        -0.786  -0.812  -0.842  -0.600  -0.703  -0.735  -0.719  -0.745  -0.758
93    V         1.636   1.699   1.728   1.585   1.676   1.728   1.787   1.872   1.923
94    G         1.636   1.699   1.728   1.837   1.914   1.974   1.787   1.872   1.923
95    D         1.636   1.699   1.728   1.826   1.912   1.963   1.787   1.872   1.923
96    I        -0.335  -0.231  -0.276  -0.575  -0.397  -0.494  -0.510  -0.347  -0.408
97    L         0.758   0.577   0.567   0.590   0.330   0.310   0.743   0.426   0.390
98    N         0.758   0.811   0.602   0.943   1.030   0.700   0.743   0.820   0.452
99    M        -0.055  -0.143  -0.236  -0.102  -0.221  -0.307  -0.092  -0.228  -0.348
100   T        -0.335  -0.427  -0.346  -0.455  -0.545  -0.427  -0.510  -0.605  -0.503
101   D         0.758   0.577   0.567   1.042   0.779   0.772   0.743   0.426   0.390
102   V         1.636   1.699   1.728   1.585   1.676   1.728   1.787   1.872   1.923
103   T        -0.335  -0.427  -0.346  -0.605  -0.735  -0.613  -0.510  -0.605  -0.503
104   T         0.758   0.577   0.567   0.758   0.510   0.504   0.743   0.426   0.390
105   L         0.285   0.338   0.397  -0.131  -0.039   0.050  -0.092  -0.014   0.071
106   G         1.636   1.699   1.728   1.837   1.914   1.974   1.787   1.872   1.923
107   S         1.636   1.699   1.728   1.669   1.758   1.810   1.787   1.872   1.923
108   R         0.395   0.447   0.445   0.298   0.381   0.364   0.116   0.192   0.162
109   N        -0.786  -0.881  -0.887  -0.474  -0.616  -0.610  -0.719  -0.815  -0.808
110   Y        -0.335  -0.406  -0.313  -0.137  -0.228  -0.091  -0.510  -0.575  -0.464
111   K        -0.335  -0.427  -0.346  -0.677  -0.819  -0.699  -0.510  -0.605  -0.503
112   L        -0.055  -0.201  -0.249  -0.124  -0.313  -0.360  -0.092  -0.301  -0.367
113   V        -0.335  -0.427  -0.346  -0.400  -0.497  -0.368  -0.510  -0.605  -0.503
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   G        -0.055   0.058  -0.187   0.193   0.354  -0.036  -0.092   0.071  -0.279
116   H        -1.406  -1.363  -1.321  -1.178  -1.184  -1.065  -1.136  -1.071  -1.007
117   P        -0.335  -0.427  -0.346  -0.203  -0.329  -0.202  -0.510  -0.605  -0.503
118   I         1.636   1.699   1.728   1.698   1.782   1.838   1.787   1.872   1.923
119   N        -0.956  -0.845  -0.882  -0.841  -0.688  -0.728  -0.928  -0.780  -0.805
120   T        -0.956  -0.957  -0.881  -1.009  -0.969  -0.884  -0.928  -0.902  -0.806
121   S        -0.335  -0.427  -0.346  -0.321  -0.432  -0.308  -0.510  -0.605  -0.503
122   L        -0.055  -0.111  -0.227  -0.146  -0.214  -0.364  -0.092  -0.189  -0.335
123   Y         0.285   0.369   0.413   0.290   0.423   0.491  -0.092   0.045   0.102
124   T        -0.956  -0.934  -0.906  -0.965  -0.897  -0.875  -0.928  -0.883  -0.830
125   L         0.395   0.386   0.414   0.030   0.009   0.059   0.116   0.077   0.103
126   K         1.636   1.699   1.728   1.519   1.616   1.663   1.787   1.872   1.923
127   A         0.758   0.577   0.567   0.993   0.720   0.712   0.743   0.426   0.390
128   T        -0.956  -0.895  -0.881  -1.138  -1.018  -0.996  -0.928  -0.832  -0.804
129   V         1.636   1.699   1.728   1.585   1.676   1.728   1.787   1.872   1.923
130   V        -0.335  -0.373  -0.303  -0.707  -0.738  -0.652  -0.510  -0.529  -0.444
131   G        -0.055  -0.143  -0.236   0.245   0.093  -0.031  -0.092  -0.228  -0.348
132   K        -0.335  -0.427  -0.346  -0.634  -0.806  -0.673  -0.510  -0.605  -0.503
133   T         1.636   1.699   1.728   1.543   1.640   1.687   1.787   1.872   1.923
134   K        -0.055  -0.201  -0.249  -0.085  -0.296  -0.375  -0.092  -0.301  -0.367
135   R         0.285   0.369   0.413   0.133   0.300   0.354  -0.092   0.045   0.102
136   A         0.395   0.537   0.483   0.419   0.649   0.548   0.116   0.354   0.235
137   F        -1.406  -1.357  -1.320  -1.156  -1.043  -1.044  -1.136  -1.067  -1.006
138   Q        -0.956  -0.930  -0.906  -0.800  -0.819  -0.758  -0.928  -0.879  -0.829
139   T        -0.956  -0.887  -0.878  -1.042  -0.927  -0.882  -0.928  -0.822  -0.801
140   R        -0.335  -0.427  -0.346  -0.435  -0.542  -0.419  -0.510  -0.605  -0.503
141   E        -0.786  -0.881  -0.887  -0.593  -0.790  -0.813  -0.719  -0.815  -0.808
142   V        -0.335  -0.427  -0.346  -0.455  -0.552  -0.425  -0.510  -0.605  -0.503
143   T        -0.335  -0.427  -0.346  -0.570  -0.663  -0.541  -0.510  -0.605  -0.503
144   K         0.758   0.577   0.567   0.686   0.419   0.391   0.743   0.426   0.390
145   R        -0.335  -0.427  -0.346  -0.328  -0.469  -0.328  -0.510  -0.605  -0.503
146   R         0.758   0.577   0.567   0.797   0.506   0.467   0.743   0.426   0.390
147   N        -0.335  -0.427  -0.346  -0.129  -0.239  -0.118  -0.510  -0.605  -0.503
148   R         0.758   0.577   0.567   0.797   0.506   0.467   0.743   0.426   0.390
149   R        -0.786  -0.805  -0.842  -0.764  -0.778  -0.886  -0.719  -0.738  -0.758
150   V        -0.786  -0.881  -0.887  -0.862  -0.989  -1.066  -0.719  -0.815  -0.808
151   R        -0.335  -0.427  -0.346  -0.581  -0.744  -0.631  -0.510  -0.605  -0.503
152   H        -0.335  -0.427  -0.346  -0.313  -0.501  -0.376  -0.510  -0.605  -0.503
153   A        -0.335  -0.323  -0.332  -0.364  -0.399  -0.382  -0.510  -0.491  -0.488
154   K        -0.956  -0.845  -0.882  -0.939  -0.719  -0.805  -0.928  -0.780  -0.805
155   S        -0.956  -0.949  -0.909  -1.017  -1.015  -0.948  -0.928  -0.893  -0.832
156   K        -0.055  -0.007  -0.227  -0.021   0.056  -0.239  -0.092  -0.018  -0.335
157   G        -1.406  -1.403  -1.349  -1.154  -1.202  -1.078  -1.136  -1.104  -1.030
158   D        -0.786  -0.881  -0.887  -0.435  -0.591  -0.588  -0.719  -0.815  -0.808
159   L         0.395   0.542   0.484   0.338   0.599   0.456   0.116   0.364   0.235
160   T         1.636   1.699   1.728   1.543   1.640   1.687   1.787   1.872   1.923
161   I         0.395   0.498   0.444   0.241   0.412   0.286   0.116   0.285   0.161
162   L         0.395   0.383   0.414   0.030   0.004   0.058   0.116   0.072   0.103
163   R         0.395   0.447   0.445   0.364   0.441   0.442   0.116   0.192   0.162
164   I         1.636   1.699   1.728   1.698   1.782   1.838   1.787   1.872   1.923
165   S         0.395   0.447   0.445   0.298   0.379   0.362   0.116   0.192   0.162
166   E         1.636   1.699   1.728   1.814   1.906   1.952   1.787   1.872   1.923
167   L         1.636   1.699   1.728   1.414   1.514   1.561   1.787   1.872   1.923
168   S        -0.055  -0.143  -0.236  -0.076  -0.197  -0.340  -0.092  -0.228  -0.348
169   M        -0.335  -0.153  -0.291  -0.636  -0.348  -0.514  -0.510  -0.244  -0.428
170   N         0.285   0.369   0.413  -0.001   0.120   0.187  -0.092   0.045   0.102
171   -        -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/P40858
Output conservation file - output/P40858
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
