1     M         0.928   0.940   0.996   1.289   1.290   1.330   0.967   0.985   1.068
2     A        -1.374  -1.274  -1.271  -1.358  -1.239  -1.186  -1.437  -1.315  -1.224
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     G         0.928   0.940   0.996   0.699   0.740   0.857   0.967   0.985   1.068
5     V         0.928   0.940   0.996   0.771   0.782   0.915   0.967   0.985   1.068
6     S         0.071  -0.193  -0.387   0.277  -0.032  -0.335   0.131  -0.234  -0.565
7     V         0.928   0.940   0.996   0.771   0.782   0.915   0.967   0.985   1.068
8     R        -0.374  -0.396  -0.394  -0.567  -0.613  -0.620  -0.496  -0.539  -0.578
9     D         0.928   0.940   0.996   0.988   0.998   1.088   0.967   0.985   1.068
10    V         0.928   0.940   0.996   0.771   0.782   0.915   0.967   0.985   1.068
11    A        -2.200  -2.219  -1.894  -2.121  -2.156  -1.760  -1.960  -1.934  -1.541
12    A         0.071  -0.193  -0.387   0.085  -0.224  -0.508   0.131  -0.234  -0.565
13    Q         0.071  -0.193  -0.387   0.326   0.004  -0.300   0.131  -0.234  -0.565
14    D        -2.057  -1.905  -1.863  -2.029  -1.860  -1.731  -1.855  -1.695  -1.514
15    F         0.928   0.940   0.996   1.249   1.257   1.297   0.967   0.985   1.068
16    I         0.071  -0.193  -0.387   0.285  -0.074  -0.479   0.131  -0.234  -0.565
17    N        -0.752  -0.731  -1.217  -0.234  -0.202  -0.951  -0.601  -0.575  -1.158
18    A         0.071   0.221  -0.360   0.092   0.282  -0.444   0.131   0.319  -0.522
19    Y         0.928   0.940   0.996   1.130   1.148   1.202   0.967   0.985   1.068
20    A         0.928   0.940   0.996   0.788   0.828   0.928   0.967   0.985   1.068
21    S        -1.679  -1.511  -1.295  -1.951  -1.725  -1.384  -1.751  -1.554  -1.250
22    F         0.928   0.940   0.996   1.249   1.257   1.297   0.967   0.985   1.068
23    L         0.928   0.940   0.996   0.908   0.943   1.024   0.967   0.985   1.068
24    Q        -0.760  -0.686  -0.443  -1.053  -0.950  -0.564  -1.123  -1.012  -0.658
25    R         0.928   0.940   0.996   0.777   0.797   0.919   0.967   0.985   1.068
26    Q        -0.374  -0.396  -0.394  -0.315  -0.357  -0.423  -0.496  -0.539  -0.578
27    G         0.928   0.940   0.996   0.699   0.740   0.857   0.967   0.985   1.068
28    K         0.928   0.940   0.996   0.902   0.926   1.019   0.967   0.985   1.068
29    L        -0.374  -0.396  -0.394  -0.327  -0.349  -0.357  -0.496  -0.539  -0.578
30    E        -1.157  -1.385  -1.278  -0.934  -1.244  -1.103  -1.123  -1.379  -1.230
31    V        -0.374  -0.396  -0.394  -0.478  -0.529  -0.479  -0.496  -0.539  -0.578
32    P         0.928   0.940   0.996   1.109   1.120   1.185   0.967   0.985   1.068
33    G        -0.374  -0.396  -0.394  -0.610  -0.632  -0.624  -0.496  -0.539  -0.578
34    Y        -0.636  -0.679  -0.455  -0.502  -0.584  -0.275  -0.914  -1.000  -0.677
35    V        -0.374  -0.396  -0.394  -0.535  -0.583  -0.566  -0.496  -0.539  -0.578
36    D         0.071   0.135  -0.369   0.267   0.338  -0.391   0.131   0.213  -0.536
37    I         0.071  -0.193  -0.387   0.341   0.022  -0.291   0.131  -0.234  -0.565
38    V         0.928   0.940   0.996   0.771   0.782   0.915   0.967   0.985   1.068
39    K         0.928   0.940   0.996   0.902   0.926   1.019   0.967   0.985   1.068
40    T         0.928   0.940   0.996   1.223   1.213   1.277   0.967   0.985   1.068
41    S        -0.636  -0.679  -0.455  -0.931  -1.063  -0.726  -0.914  -1.000  -0.677
42    S        -1.895  -1.988  -1.887  -1.758  -1.874  -1.691  -1.646  -1.736  -1.534
43    G        -1.157  -1.385  -1.278  -1.250  -1.562  -1.397  -1.123  -1.379  -1.230
44    N        -0.636  -0.679  -0.455  -0.656  -0.788  -0.489  -0.914  -1.000  -0.677
45    E         0.071   0.205  -0.360   0.258   0.419  -0.379   0.131   0.300  -0.522
46    M        -0.636  -0.613  -0.452  -0.713  -0.670  -0.421  -0.914  -0.888  -0.672
47    P        -0.374  -0.396  -0.394  -0.271  -0.330  -0.432  -0.496  -0.539  -0.578
48    P         0.928   0.940   0.996   1.109   1.120   1.185   0.967   0.985   1.068
49    Q        -0.374  -0.396  -0.394  -0.270  -0.309  -0.353  -0.496  -0.539  -0.578
50    D        -0.374  -0.176  -0.393  -0.338  -0.059  -0.434  -0.496  -0.209  -0.575
51    A        -2.293  -2.301  -1.893  -2.390  -2.336  -1.776  -2.064  -2.011  -1.540
52    E        -0.636  -0.679  -0.455  -0.790  -0.900  -0.552  -0.914  -1.000  -0.677
53    G        -0.636  -0.534  -0.448  -0.919  -0.761  -0.563  -0.914  -0.758  -0.665
54    W         0.928   0.940   0.996   1.320   1.318   1.354   0.967   0.985   1.068
55    F        -0.636  -0.574  -0.447  -0.481  -0.400  -0.294  -0.914  -0.824  -0.664
56    Y         0.928   0.940   0.996   1.130   1.148   1.202   0.967   0.985   1.068
57    K        -1.374  -1.325  -1.285  -1.538  -1.546  -1.300  -1.437  -1.392  -1.240
58    R         0.928   0.940   0.996   0.777   0.797   0.919   0.967   0.985   1.068
59    A         0.928   0.940   0.996   0.788   0.828   0.928   0.967   0.985   1.068
60    A         0.928   0.940   0.996   0.788   0.828   0.928   0.967   0.985   1.068
61    S        -0.374  -0.396  -0.394  -0.411  -0.446  -0.534  -0.496  -0.539  -0.578
62    V        -0.760  -0.687  -0.455  -1.165  -1.050  -0.648  -1.123  -1.013  -0.677
63    A         0.928   0.940   0.996   0.788   0.828   0.928   0.967   0.985   1.068
64    R         0.928   0.940   0.996   0.777   0.797   0.919   0.967   0.985   1.068
65    H         0.928   0.940   0.996   1.228   1.227   1.281   0.967   0.985   1.068
66    I         0.071  -0.193  -0.387   0.285  -0.074  -0.479   0.131  -0.234  -0.565
67    Y         0.928   0.940   0.996   1.130   1.148   1.202   0.967   0.985   1.068
68    M         0.071   0.198  -0.362   0.227   0.384  -0.311   0.131   0.292  -0.524
69    R         0.928   0.940   0.996   0.777   0.797   0.919   0.967   0.985   1.068
70    K         0.928   0.940   0.996   0.902   0.926   1.019   0.967   0.985   1.068
71    Q        -1.157  -1.249  -1.267  -0.959  -1.051  -1.130  -1.123  -1.204  -1.218
72    V         0.928   0.940   0.996   0.771   0.782   0.915   0.967   0.985   1.068
73    G         0.928   0.940   0.996   0.699   0.740   0.857   0.967   0.985   1.068
74    V         0.928   0.940   0.996   0.771   0.782   0.915   0.967   0.985   1.068
75    G         0.928   0.940   0.996   0.699   0.740   0.857   0.967   0.985   1.068
76    K        -1.374  -1.277  -1.283  -1.628  -1.564  -1.502  -1.437  -1.353  -1.237
77    L         0.928   0.940   0.996   0.908   0.943   1.024   0.967   0.985   1.068
78    N        -1.157  -1.385  -1.278  -0.761  -1.104  -1.067  -1.123  -1.379  -1.230
79    K         0.071  -0.193  -0.387   0.157  -0.201  -0.570   0.131  -0.234  -0.565
80    L        -0.636  -0.679  -0.455  -0.954  -1.086  -0.720  -0.914  -1.000  -0.677
81    Y         0.071  -0.193  -0.387   0.440   0.114  -0.220   0.131  -0.234  -0.565
82    G         0.928   0.940   0.996   0.699   0.740   0.857   0.967   0.985   1.068
83    G        -0.752  -0.845  -1.240  -0.669  -0.785  -1.204  -0.601  -0.742  -1.186
84    A        -0.374  -0.396  -0.394  -0.537  -0.557  -0.583  -0.496  -0.539  -0.578
85    K        -1.895  -1.722  -1.864  -1.852  -1.665  -1.835  -1.646  -1.479  -1.513
86    S        -0.374  -0.179  -0.394  -0.167   0.130  -0.316  -0.496  -0.213  -0.576
87    R         0.928   0.940   0.996   0.777   0.797   0.919   0.967   0.985   1.068
88    G         0.928   0.940   0.996   0.699   0.740   0.857   0.967   0.985   1.068
89    V        -3.335  -3.154  -2.751  -2.934  -2.690  -2.253  -2.482  -2.299  -1.840
90    R         0.928   0.940   0.996   0.777   0.797   0.919   0.967   0.985   1.068
91    P         0.928   0.940   0.996   1.109   1.120   1.185   0.967   0.985   1.068
92    Y        -1.374  -1.107  -1.249  -1.270  -0.899  -1.060  -1.437  -1.095  -1.197
93    K        -0.760  -0.612  -0.430  -0.880  -0.606  -0.379  -1.123  -0.887  -0.636
94    H         0.928   0.940   0.996   1.228   1.227   1.281   0.967   0.985   1.068
95    I        -2.578  -2.320  -2.344  -2.664  -2.358  -2.329  -2.064  -1.829  -1.704
96    D         0.071  -0.193  -0.387   0.267  -0.084  -0.424   0.131  -0.234  -0.565
97    A        -0.374  -0.396  -0.394  -0.613  -0.645  -0.702  -0.496  -0.539  -0.578
98    S         0.928   0.940   0.996   0.967   1.002   1.071   0.967   0.985   1.068
99    G         0.928   0.940   0.996   0.699   0.740   0.857   0.967   0.985   1.068
100   S         0.928   0.940   0.996   0.967   1.002   1.071   0.967   0.985   1.068
101   I        -0.760  -0.611  -0.432  -1.165  -0.933  -0.624  -1.123  -0.886  -0.639
102   N        -1.157  -1.385  -1.278  -0.840  -1.180  -1.133  -1.123  -1.379  -1.230
103   R         0.928   0.940   0.996   0.777   0.797   0.919   0.967   0.985   1.068
104   K        -0.636  -0.462  -0.430  -0.956  -0.648  -0.661  -0.914  -0.643  -0.637
105   V        -0.752  -0.573  -1.221  -0.631  -0.436  -1.224  -0.601  -0.391  -1.163
106   L        -0.636  -0.584  -0.448  -0.954  -0.876  -0.701  -0.914  -0.841  -0.666
107   Q         0.928   0.940   0.996   1.014   1.035   1.109   0.967   0.985   1.068
108   A        -0.760  -0.674  -0.453  -1.194  -1.031  -0.676  -1.123  -0.991  -0.674
109   L         0.928   0.940   0.996   0.908   0.943   1.024   0.967   0.985   1.068
110   E         0.071   0.205  -0.360   0.262   0.423  -0.369   0.131   0.300  -0.522
111   K         0.928   0.940   0.996   0.902   0.926   1.019   0.967   0.985   1.068
112   I        -0.374  -0.236  -0.416  -0.316  -0.101  -0.481  -0.496  -0.296  -0.613
113   G         0.928   0.940   0.996   0.699   0.740   0.857   0.967   0.985   1.068
114   I         0.071   0.198  -0.362   0.058   0.197  -0.513   0.131   0.292  -0.524
115   V        -0.636  -0.443  -0.416  -0.954  -0.603  -0.628  -0.914  -0.613  -0.613
116   E         0.928   0.940   0.996   0.977   1.002   1.080   0.967   0.985   1.068
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   I        -2.578  -2.554  -2.364  -2.369  -2.394  -2.183  -2.064  -2.028  -1.719
119   S        -0.752  -0.943  -1.248  -0.506  -0.759  -1.332  -0.601  -0.845  -1.195
120   P        -1.895  -2.032  -1.892  -1.584  -1.834  -1.701  -1.646  -1.771  -1.538
121   K        -0.374  -0.396  -0.394  -0.368  -0.398  -0.415  -0.496  -0.539  -0.578
122   G         0.928   0.940   0.996   0.699   0.740   0.857   0.967   0.985   1.068
123   G         0.928   0.940   0.996   0.699   0.740   0.857   0.967   0.985   1.068
124   R         0.928   0.940   0.996   0.777   0.797   0.919   0.967   0.985   1.068
125   R         0.071   0.242  -0.359   0.047   0.247  -0.557   0.131   0.345  -0.520
126   I         0.928   0.940   0.996   1.030   1.057   1.122   0.967   0.985   1.068
127   S         0.071  -0.193  -0.387   0.277  -0.032  -0.335   0.131  -0.234  -0.565
128   E        -1.374  -1.266  -1.282  -1.399  -1.298  -1.250  -1.437  -1.344  -1.237
129   N        -0.636  -0.679  -0.455  -0.606  -0.721  -0.426  -0.914  -1.000  -0.677
130   G         0.928   0.940   0.996   0.699   0.740   0.857   0.967   0.985   1.068
131   Q         0.071   0.221  -0.360   0.285   0.464  -0.384   0.131   0.319  -0.522
132   R         0.928   0.940   0.996   0.777   0.797   0.919   0.967   0.985   1.068
133   D         0.928   0.940   0.996   0.988   0.998   1.088   0.967   0.985   1.068
134   L         0.928   0.940   0.996   0.908   0.943   1.024   0.967   0.985   1.068
135   D         0.928   0.940   0.996   0.988   0.998   1.088   0.967   0.985   1.068
136   R         0.928   0.940   0.996   0.777   0.797   0.919   0.967   0.985   1.068
137   I         0.928   0.940   0.996   1.030   1.057   1.122   0.967   0.985   1.068
138   A         0.928   0.940   0.996   0.788   0.828   0.928   0.967   0.985   1.068
139   A        -1.157  -1.385  -1.278  -1.161  -1.453  -1.292  -1.123  -1.379  -1.230
140   Q        -1.895  -1.972  -1.885  -1.656  -1.776  -1.697  -1.646  -1.723  -1.533
141   T        -1.157  -1.385  -1.278  -0.852  -1.262  -1.232  -1.123  -1.379  -1.230
142   L         0.071  -0.193  -0.387   0.194  -0.126  -0.458   0.131  -0.234  -0.565
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   E         0.928   0.940   0.996   0.977   1.002   1.080   0.967   0.985   1.068
148   E        -0.636  -0.521  -0.444  -0.785  -0.605  -0.530  -0.914  -0.738  -0.659
149   D        -0.760  -0.674  -0.453  -1.026  -0.890  -0.549  -1.123  -0.991  -0.675
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   E         0.928   0.940   0.996   0.977   1.002   1.080   0.967   0.985   1.068
* 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/P07281
Output conservation file - output/P07281
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
