1     M         0.595   0.604   0.643   0.931   0.936   0.945   0.612   0.625   0.676
2     A        -1.711  -1.751  -1.881  -1.798  -1.836  -1.918  -1.663  -1.701  -1.793
3     N        -3.544  -3.406  -3.079  -2.979  -2.857  -2.439  -2.914  -2.801  -2.310
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    D        -3.078  -3.045  -2.564  -2.660  -2.689  -2.132  -2.773  -2.723  -2.123
16    L        -1.261  -1.162  -0.959  -1.381  -1.220  -0.987  -1.644  -1.496  -1.186
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    V        -2.053  -1.998  -1.891  -1.976  -1.883  -1.894  -2.123  -2.032  -1.804
19    Q        -0.429  -0.491  -0.930   0.116   0.033  -0.688  -0.396  -0.484  -1.141
20    A        -2.817  -2.757  -2.559  -2.822  -2.771  -2.461  -2.555  -2.493  -2.119
21    R        -0.429  -0.321  -0.921  -0.496  -0.382  -1.127  -0.396  -0.261  -1.125
22    D        -2.109  -2.155  -1.896  -1.818  -1.917  -1.622  -2.118  -2.193  -1.809
23    N        -2.528  -2.243  -2.545  -2.438  -2.098  -2.593  -2.232  -1.921  -2.107
24    S        -1.272  -1.243  -0.960  -1.257  -1.230  -0.847  -1.663  -1.632  -1.189
25    Q        -1.272  -1.243  -0.960  -1.149  -1.151  -0.791  -1.663  -1.632  -1.189
26    V         0.595   0.604   0.643   0.545   0.570   0.629   0.612   0.625   0.676
27    F         0.595   0.604   0.643   0.915   0.921   0.931   0.612   0.625   0.676
28    G         0.595   0.604   0.643   0.312   0.330   0.439   0.612   0.625   0.676
29    V         0.595   0.604   0.643   0.545   0.570   0.629   0.612   0.625   0.676
30    A         0.595   0.604   0.643   0.227   0.254   0.369   0.612   0.625   0.676
31    R        -0.845  -0.737  -0.934  -0.941  -0.820  -1.000  -0.981  -0.831  -1.146
32    I         0.595   0.604   0.643   0.735   0.743   0.784   0.612   0.625   0.676
33    Y        -0.845  -0.662  -0.938  -0.354  -0.140  -0.595  -0.981  -0.721  -1.153
34    A         0.595   0.604   0.643   0.227   0.254   0.369   0.612   0.625   0.676
35    S         0.595   0.604   0.643   0.689   0.706   0.747   0.612   0.625   0.676
36    F         0.595   0.604   0.643   0.915   0.921   0.931   0.612   0.625   0.676
37    N         0.595   0.604   0.643   1.003   1.008   1.003   0.612   0.625   0.676
38    D         0.595   0.604   0.643   0.712   0.729   0.766   0.612   0.625   0.676
39    T         0.595   0.604   0.643   0.486   0.499   0.581   0.612   0.625   0.676
40    F         0.595   0.604   0.643   0.915   0.921   0.931   0.612   0.625   0.676
41    V         0.595   0.604   0.643   0.545   0.570   0.629   0.612   0.625   0.676
42    H         0.595   0.604   0.643   0.992   1.000   0.994   0.612   0.625   0.676
43    V        -1.135  -1.157  -0.961  -1.236  -1.287  -1.018  -1.436  -1.488  -1.190
44    T         0.595   0.604   0.643   0.486   0.499   0.581   0.612   0.625   0.676
45    D         0.595   0.604   0.643   0.712   0.729   0.766   0.612   0.625   0.676
46    L         0.595   0.604   0.643   0.741   0.749   0.789   0.612   0.625   0.676
47    S        -1.135  -1.157  -0.961  -1.217  -1.295  -1.071  -1.436  -1.488  -1.190
48    G         0.595   0.604   0.643   0.312   0.330   0.439   0.612   0.625   0.676
49    K        -2.027  -1.948  -1.886  -2.116  -2.051  -1.807  -2.118  -2.022  -1.799
50    E         0.595   0.604   0.643   0.865   0.863   0.890   0.612   0.625   0.676
51    T         0.595   0.604   0.643   0.486   0.499   0.581   0.612   0.625   0.676
52    I         0.595   0.604   0.643   0.735   0.743   0.784   0.612   0.625   0.676
53    A        -2.864  -2.903  -2.560  -2.893  -2.905  -2.311  -2.573  -2.603  -2.121
54    R         0.595   0.604   0.643   0.318   0.329   0.444   0.612   0.625   0.676
55    V         0.595   0.604   0.643   0.545   0.570   0.629   0.612   0.625   0.676
56    T         0.595   0.604   0.643   0.486   0.499   0.581   0.612   0.625   0.676
57    G         0.595   0.604   0.643   0.312   0.330   0.439   0.612   0.625   0.676
58    G         0.595   0.604   0.643   0.312   0.330   0.439   0.612   0.625   0.676
59    M         0.595   0.604   0.643   0.931   0.936   0.945   0.612   0.625   0.676
60    K         0.595   0.604   0.643   0.701   0.723   0.756   0.612   0.625   0.676
61    V         0.595   0.604   0.643   0.545   0.570   0.629   0.612   0.625   0.676
62    K         0.595   0.604   0.643   0.701   0.723   0.756   0.612   0.625   0.676
63    A        -0.845  -0.737  -0.934  -1.184  -1.030  -1.330  -0.981  -0.831  -1.146
64    D         0.595   0.604   0.643   0.712   0.729   0.766   0.612   0.625   0.676
65    R         0.595   0.604   0.643   0.318   0.329   0.444   0.612   0.625   0.676
66    D         0.595   0.604   0.643   0.712   0.729   0.766   0.612   0.625   0.676
67    E         0.595   0.604   0.643   0.865   0.863   0.890   0.612   0.625   0.676
68    S        -0.353  -0.616  -0.937  -0.009  -0.302  -0.757  -0.298  -0.656  -1.151
69    S        -0.353  -0.616  -0.937  -0.074  -0.407  -1.013  -0.298  -0.656  -1.151
70    P         0.595   0.604   0.643   0.809   0.810   0.844   0.612   0.625   0.676
71    Y         0.595   0.604   0.643   1.041   1.049   1.034   0.612   0.625   0.676
72    A         0.595   0.604   0.643   0.227   0.254   0.369   0.612   0.625   0.676
73    A         0.595   0.604   0.643   0.227   0.254   0.369   0.612   0.625   0.676
74    M         0.595   0.604   0.643   0.931   0.936   0.945   0.612   0.625   0.676
75    L         0.595   0.604   0.643   0.741   0.749   0.789   0.612   0.625   0.676
76    A         0.595   0.604   0.643   0.227   0.254   0.369   0.612   0.625   0.676
77    A         0.595   0.604   0.643   0.227   0.254   0.369   0.612   0.625   0.676
78    Q         0.595   0.604   0.643   0.926   0.937   0.940   0.612   0.625   0.676
79    D         0.595   0.604   0.643   0.712   0.729   0.766   0.612   0.625   0.676
80    V        -1.135  -1.157  -0.961  -1.471  -1.547  -1.313  -1.436  -1.488  -1.190
81    A        -0.353  -0.616  -0.937  -0.532  -0.844  -1.303  -0.298  -0.656  -1.151
82    A        -1.263  -1.485  -1.880  -1.179  -1.437  -1.779  -1.094  -1.375  -1.791
83    K        -0.353  -0.457  -0.935  -0.083  -0.209  -1.083  -0.298  -0.437  -1.148
84    C        -0.353  -0.616  -0.937   0.254  -0.110  -0.888  -0.298  -0.656  -1.151
85    K        -0.353  -0.266  -0.929  -0.031   0.066  -0.867  -0.298  -0.193  -1.139
86    E         0.595   0.604   0.643   0.865   0.863   0.890   0.612   0.625   0.676
87    V        -0.353  -0.457  -0.935  -0.187  -0.296  -0.981  -0.298  -0.437  -1.148
88    G         0.595   0.604   0.643   0.312   0.330   0.439   0.612   0.625   0.676
89    I         0.595   0.604   0.643   0.735   0.743   0.784   0.612   0.625   0.676
90    T        -0.353  -0.616  -0.937  -0.211  -0.505  -0.888  -0.298  -0.656  -1.151
91    A         0.595   0.604   0.643   0.227   0.254   0.369   0.612   0.625   0.676
92    V        -1.272  -1.243  -0.960  -1.452  -1.409  -1.004  -1.663  -1.632  -1.189
93    H         0.595   0.604   0.643   0.992   1.000   0.994   0.612   0.625   0.676
94    V        -1.135  -1.008  -0.954  -1.148  -0.953  -0.992  -1.436  -1.247  -1.179
95    K        -0.353  -0.616  -0.937  -0.083  -0.423  -1.088  -0.298  -0.656  -1.151
96    I        -0.845  -0.786  -0.937  -0.610  -0.549  -0.858  -0.981  -0.903  -1.152
97    R         0.595   0.604   0.643   0.318   0.329   0.444   0.612   0.625   0.676
98    A         0.595   0.604   0.643   0.227   0.254   0.369   0.612   0.625   0.676
99    T         0.595   0.604   0.643   0.486   0.499   0.581   0.612   0.625   0.676
100   G         0.595   0.604   0.643   0.312   0.330   0.439   0.612   0.625   0.676
101   G         0.595   0.604   0.643   0.312   0.330   0.439   0.612   0.625   0.676
102   T        -0.353  -0.457  -0.935  -0.211  -0.324  -0.886  -0.298  -0.437  -1.148
103   R        -3.544  -3.614  -3.084  -3.698  -3.789  -3.073  -2.914  -2.940  -2.313
104   T        -0.353  -0.217  -0.927  -0.252  -0.112  -1.035  -0.298  -0.133  -1.136
105   K         0.595   0.604   0.643   0.701   0.723   0.756   0.612   0.625   0.676
106   T         0.595   0.604   0.643   0.486   0.499   0.581   0.612   0.625   0.676
107   P         0.595   0.604   0.643   0.809   0.810   0.844   0.612   0.625   0.676
108   G         0.595   0.604   0.643   0.312   0.330   0.439   0.612   0.625   0.676
109   P         0.595   0.604   0.643   0.809   0.810   0.844   0.612   0.625   0.676
110   G         0.595   0.604   0.643   0.312   0.330   0.439   0.612   0.625   0.676
111   G        -1.951  -2.109  -1.897  -2.283  -2.443  -1.994  -2.004  -2.155  -1.811
112   Q         0.595   0.604   0.643   0.926   0.937   0.940   0.612   0.625   0.676
113   A        -1.272  -1.240  -0.962  -1.741  -1.652  -1.226  -1.663  -1.628  -1.192
114   A         0.595   0.604   0.643   0.227   0.254   0.369   0.612   0.625   0.676
115   L        -0.353  -0.616  -0.937  -0.015  -0.350  -0.949  -0.298  -0.656  -1.151
116   R         0.595   0.604   0.643   0.318   0.329   0.444   0.612   0.625   0.676
117   A         0.595   0.604   0.643   0.227   0.254   0.369   0.612   0.625   0.676
118   L         0.595   0.604   0.643   0.741   0.749   0.789   0.612   0.625   0.676
119   A         0.595   0.604   0.643   0.227   0.254   0.369   0.612   0.625   0.676
120   R         0.595   0.604   0.643   0.318   0.329   0.444   0.612   0.625   0.676
121   S        -1.135  -1.157  -0.961  -1.333  -1.421  -1.217  -1.436  -1.488  -1.190
122   G         0.595   0.604   0.643   0.312   0.330   0.439   0.612   0.625   0.676
123   L        -1.272  -1.243  -0.960  -1.175  -1.147  -0.778  -1.663  -1.632  -1.189
124   R        -0.353  -0.457  -0.935  -0.419  -0.542  -1.154  -0.298  -0.437  -1.148
125   I         0.595   0.604   0.643   0.735   0.743   0.784   0.612   0.625   0.676
126   G         0.595   0.604   0.643   0.312   0.330   0.439   0.612   0.625   0.676
127   R         0.595   0.604   0.643   0.318   0.329   0.444   0.612   0.625   0.676
128   I         0.595   0.604   0.643   0.735   0.743   0.784   0.612   0.625   0.676
129   E         0.595   0.604   0.643   0.865   0.863   0.890   0.612   0.625   0.676
130   D         0.595   0.604   0.643   0.712   0.729   0.766   0.612   0.625   0.676
131   V         0.595   0.604   0.643   0.545   0.570   0.629   0.612   0.625   0.676
132   T         0.595   0.604   0.643   0.486   0.499   0.581   0.612   0.625   0.676
133   P         0.595   0.604   0.643   0.809   0.810   0.844   0.612   0.625   0.676
134   V        -1.711  -1.709  -1.883  -1.527  -1.521  -1.860  -1.663  -1.645  -1.795
135   P         0.595   0.604   0.643   0.809   0.810   0.844   0.612   0.625   0.676
136   S        -0.845  -0.737  -0.934  -0.725  -0.579  -1.007  -0.981  -0.831  -1.146
137   D         0.595   0.604   0.643   0.712   0.729   0.766   0.612   0.625   0.676
138   S         0.595   0.604   0.643   0.689   0.706   0.747   0.612   0.625   0.676
139   T         0.595   0.604   0.643   0.486   0.499   0.581   0.612   0.625   0.676
140   R         0.595   0.604   0.643   0.318   0.329   0.444   0.612   0.625   0.676
141   K        -1.135  -0.963  -0.948  -1.460  -1.217  -1.169  -1.436  -1.175  -1.169
142   K         0.595   0.604   0.643   0.701   0.723   0.756   0.612   0.625   0.676
143   G         0.595   0.604   0.643   0.312   0.330   0.439   0.612   0.625   0.676
144   G         0.595   0.604   0.643   0.312   0.330   0.439   0.612   0.625   0.676
145   R         0.595   0.604   0.643   0.318   0.329   0.444   0.612   0.625   0.676
146   R         0.595   0.604   0.643   0.318   0.329   0.444   0.612   0.625   0.676
147   G         0.595   0.604   0.643   0.312   0.330   0.439   0.612   0.625   0.676
148   R         0.595   0.604   0.643   0.318   0.329   0.444   0.612   0.625   0.676
149   R         0.595   0.604   0.643   0.318   0.329   0.444   0.612   0.625   0.676
150   L         0.595   0.604   0.643   0.741   0.749   0.789   0.612   0.625   0.676
* 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/P39516
Output conservation file - output/P39516
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
