1     M         1.519   1.519   1.543   1.828   1.829   1.861   1.604   1.605   1.633
2     I        -1.147  -1.146  -1.120  -1.161  -1.163  -1.113  -1.030  -1.028  -0.981
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     N        -1.147  -1.146  -1.120  -1.118  -1.098  -1.070  -1.030  -1.028  -0.981
5     G        -1.147  -1.146  -1.120  -0.985  -0.989  -0.938  -1.030  -1.028  -0.981
6     V        -0.026  -0.030  -0.065  -0.068  -0.080  -0.146  -0.152  -0.158  -0.213
7     Y        -1.147  -1.146  -1.120  -1.059  -1.066  -1.012  -1.030  -1.028  -0.981
8     Y         1.519   1.519   1.543   1.736   1.737   1.769   1.604   1.605   1.633
9     N        -0.026  -0.037  -0.070  -0.158  -0.182  -0.235  -0.152  -0.169  -0.221
10    E        -0.026  -0.037  -0.070   0.020  -0.001  -0.038  -0.152  -0.169  -0.221
11    I        -0.026  -0.037  -0.070  -0.197  -0.218  -0.260  -0.152  -0.169  -0.221
12    S        -1.147  -1.146  -1.120  -1.294  -1.281  -1.245  -1.030  -1.028  -0.981
13    R        -0.026  -0.007  -0.061   0.094   0.117   0.047  -0.152  -0.123  -0.207
14    D        -0.026  -0.007  -0.061  -0.018   0.005  -0.068  -0.152  -0.123  -0.207
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    L        -0.026  -0.007  -0.061  -0.276  -0.249  -0.338  -0.152  -0.123  -0.207
17    D         1.519   1.519   1.543   1.683   1.684   1.716   1.604   1.605   1.633
18    I        -1.147  -1.146  -1.120  -1.136  -1.134  -1.087  -1.030  -1.028  -0.981
19    S         1.519   1.519   1.543   1.423   1.453   1.458   1.604   1.605   1.633
20    S        -1.147  -1.146  -1.120  -1.223  -1.208  -1.174  -1.030  -1.028  -0.981
21    S        -1.147  -1.146  -1.120  -0.961  -0.941  -0.913  -1.030  -1.028  -0.981
22    T        -1.147  -1.146  -1.120  -1.144  -1.134  -1.096  -1.030  -1.028  -0.981
23    Q        -0.026  -0.030  -0.065   0.082   0.069   0.002  -0.152  -0.158  -0.213
24    C         1.519   1.519   1.543   1.879   1.882   1.912   1.604   1.605   1.633
25    L        -0.026  -0.007  -0.061  -0.197  -0.141  -0.262  -0.152  -0.123  -0.207
26    R        -1.147  -1.146  -1.120  -0.961  -0.970  -0.913  -1.030  -1.028  -0.981
27    F        -0.026  -0.007  -0.061   0.220   0.247   0.162  -0.152  -0.123  -0.207
28    L        -0.026  -0.007  -0.061  -0.276  -0.249  -0.338  -0.152  -0.123  -0.207
29    K         1.519   1.519   1.543   1.282   1.280   1.318   1.604   1.605   1.633
30    E        -0.026  -0.037  -0.070  -0.132  -0.158  -0.216  -0.152  -0.169  -0.221
31    T        -1.147  -1.146  -1.120  -1.144  -1.150  -1.096  -1.030  -1.028  -0.981
32    V        -0.026  -0.007  -0.061  -0.217  -0.192  -0.269  -0.152  -0.123  -0.207
33    I        -0.026  -0.037  -0.070  -0.276  -0.299  -0.354  -0.152  -0.169  -0.221
34    P         1.519   1.519   1.543   1.815   1.816   1.848   1.604   1.605   1.633
35    S        -1.147  -1.146  -1.120  -1.188  -1.173  -1.139  -1.030  -1.028  -0.981
36    L        -1.147  -1.146  -1.120  -0.969  -0.966  -0.921  -1.030  -1.028  -0.981
37    A        -0.026  -0.007  -0.061  -0.049  -0.026  -0.095  -0.152  -0.123  -0.207
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    N        -0.026  -0.037  -0.070  -0.030  -0.048  -0.085  -0.152  -0.169  -0.221
44    N        -0.026  -0.037  -0.070  -0.158  -0.182  -0.235  -0.152  -0.169  -0.221
45    G        -1.147  -1.146  -1.120  -0.718  -0.720  -0.672  -1.030  -1.028  -0.981
46    N        -0.026  -0.030  -0.065  -0.190  -0.187  -0.264  -0.152  -0.158  -0.213
47    N        -1.147  -1.146  -1.120  -1.179  -1.183  -1.130  -1.030  -1.028  -0.981
48    S        -1.147  -1.146  -1.120  -1.188  -1.174  -1.139  -1.030  -1.028  -0.981
49    T        -1.147  -1.146  -1.120  -1.043  -1.028  -0.995  -1.030  -1.028  -0.981
50    S        -1.147  -1.146  -1.120  -1.249  -1.234  -1.200  -1.030  -1.028  -0.981
51    I        -1.147  -1.146  -1.120  -0.985  -0.979  -0.938  -1.030  -1.028  -0.981
52    Q        -1.147  -1.146  -1.120  -1.034  -1.043  -0.987  -1.030  -1.028  -0.981
53    Y        -1.147  -1.146  -1.120  -1.085  -1.092  -1.037  -1.030  -1.028  -0.981
54    H        -1.147  -1.146  -1.120  -1.026  -1.035  -0.978  -1.030  -1.028  -0.981
55    G        -1.147  -1.146  -1.120  -1.214  -1.208  -1.165  -1.030  -1.028  -0.981
56    I        -1.147  -1.146  -1.120  -1.110  -1.108  -1.062  -1.030  -1.028  -0.981
57    S         1.519   1.519   1.543   1.423   1.453   1.458   1.604   1.605   1.633
58    K         1.519   1.519   1.543   1.282   1.280   1.318   1.604   1.605   1.633
59    N         1.519   1.519   1.543   1.437   1.438   1.472   1.604   1.605   1.633
60    D        -0.026  -0.030  -0.065   0.038   0.041  -0.046  -0.152  -0.158  -0.213
61    N        -0.026  -0.037  -0.070  -0.256  -0.283  -0.351  -0.152  -0.169  -0.221
62    I         1.519   1.519   1.543   1.339   1.339   1.374   1.604   1.605   1.633
63    K         1.519   1.519   1.543   1.282   1.280   1.318   1.604   1.605   1.633
64    K        -1.147  -1.146  -1.120  -1.093  -1.089  -1.045  -1.030  -1.028  -0.981
65    S        -1.147  -1.146  -1.120  -1.136  -1.121  -1.087  -1.030  -1.028  -0.981
66    V         1.519   1.519   1.543   1.561   1.560   1.596   1.604   1.605   1.633
67    N        -1.147  -1.146  -1.120  -1.170  -1.153  -1.122  -1.030  -1.028  -0.981
68    K        -1.147  -1.146  -1.120  -1.258  -1.239  -1.209  -1.030  -1.028  -0.981
69    L         1.519   1.519   1.543   1.437   1.437   1.472   1.604   1.605   1.633
70    D        -1.147  -1.146  -1.120  -0.952  -0.960  -0.905  -1.030  -1.028  -0.981
71    K        -0.026  -0.030  -0.065  -0.190  -0.202  -0.234  -0.152  -0.158  -0.213
72    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    N        -0.026  -0.030  -0.065  -0.230  -0.241  -0.310  -0.152  -0.158  -0.213
75    M        -1.147  -1.146  -1.120  -0.896  -0.905  -0.849  -1.030  -1.028  -0.981
76    A        -0.026  -0.037  -0.070   0.014  -0.015  -0.093  -0.152  -0.169  -0.221
77    D         1.519   1.519   1.543   1.683   1.684   1.716   1.604   1.605   1.633
78    R        -0.163  -0.163  -0.137  -0.217  -0.219  -0.174  -0.371  -0.370  -0.328
79    S        -0.163  -0.163  -0.137  -0.464  -0.452  -0.419  -0.371  -0.370  -0.328
80    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    V        -1.147  -1.146  -1.120  -0.961  -0.963  -0.913  -1.030  -1.028  -0.981
86    V        -0.026  -0.030  -0.065   0.063   0.052   0.006  -0.152  -0.158  -0.213
87    C        -1.147  -1.146  -1.120  -1.018  -1.030  -0.970  -1.030  -1.028  -0.981
88    I        -0.026  -0.030  -0.065  -0.276  -0.287  -0.345  -0.152  -0.158  -0.213
89    F        -1.147  -1.146  -1.120  -0.888  -0.894  -0.841  -1.030  -1.028  -0.981
90    S        -0.026  -0.030  -0.065  -0.062  -0.045  -0.112  -0.152  -0.158  -0.213
91    Y         1.519   1.519   1.543   1.736   1.737   1.769   1.604   1.605   1.633
92    G         1.519   1.519   1.543   1.762   1.764   1.795   1.604   1.605   1.633
93    P        -1.147  -1.146  -1.120  -0.857  -0.863  -0.810  -1.030  -1.028  -0.981
94    H         1.519   1.519   1.543   1.828   1.829   1.861   1.604   1.605   1.633
95    I        -0.026  -0.030  -0.065  -0.217  -0.227  -0.276  -0.152  -0.158  -0.213
96    Q         1.519   1.519   1.543   1.696   1.696   1.730   1.604   1.605   1.633
97    K         1.519   1.519   1.543   1.282   1.280   1.318   1.604   1.605   1.633
98    M        -0.026  -0.030  -0.065   0.302   0.293   0.234  -0.152  -0.158  -0.213
99    L        -0.026  -0.037  -0.070  -0.126  -0.148  -0.197  -0.152  -0.169  -0.221
100   S        -0.026  -0.037  -0.070  -0.119  -0.114  -0.186  -0.152  -0.169  -0.221
101   I         1.519   1.519   1.543   1.339   1.339   1.374   1.604   1.605   1.633
102   L        -1.147  -1.146  -1.120  -1.303  -1.307  -1.254  -1.030  -1.028  -0.981
103   E         1.519   1.519   1.543   1.493   1.490   1.527   1.604   1.605   1.633
104   I         1.519   1.519   1.543   1.339   1.339   1.374   1.604   1.605   1.633
105   F        -0.026  -0.037  -0.070   0.082   0.057  -0.013  -0.152  -0.169  -0.221
106   K         1.519   1.519   1.543   1.282   1.280   1.318   1.604   1.605   1.633
107   K        -0.026  -0.030  -0.065  -0.250  -0.262  -0.303  -0.152  -0.158  -0.213
108   G        -0.163  -0.163  -0.137  -0.231  -0.233  -0.188  -0.371  -0.370  -0.328
109   Y        -0.163  -0.163  -0.137   0.001   0.001   0.044  -0.371  -0.370  -0.328
110   I        -1.147  -1.146  -1.120  -1.093  -1.092  -1.045  -1.030  -1.028  -0.981
111   K        -0.026  -0.030  -0.065  -0.303  -0.317  -0.365  -0.152  -0.158  -0.213
112   N        -0.026  -0.037  -0.070  -0.068  -0.087  -0.129  -0.152  -0.169  -0.221
113   N        -0.163  -0.163  -0.137  -0.215  -0.217  -0.172  -0.371  -0.370  -0.328
114   K        -0.026  -0.037  -0.070  -0.250  -0.273  -0.310  -0.152  -0.169  -0.221
115   K        -0.026  -0.030  -0.065  -0.190  -0.202  -0.234  -0.152  -0.158  -0.213
116   I        -0.026  -0.007  -0.061  -0.230  -0.200  -0.303  -0.152  -0.123  -0.207
117   Y        -0.026  -0.007  -0.061   0.308   0.336   0.247  -0.152  -0.123  -0.207
118   Q         1.519   1.519   1.543   1.696   1.696   1.730   1.604   1.605   1.633
119   W        -0.026  -0.030  -0.065   0.383   0.375   0.310  -0.152  -0.158  -0.213
120   N         1.519   1.519   1.543   1.437   1.438   1.472   1.604   1.605   1.633
121   K        -0.026  -0.037  -0.070  -0.158  -0.177  -0.202  -0.152  -0.169  -0.221
122   L         1.519   1.519   1.543   1.437   1.437   1.472   1.604   1.605   1.633
123   T        -1.147  -1.146  -1.120  -0.825  -0.825  -0.779  -1.030  -1.028  -0.981
124   S         1.519   1.519   1.543   1.423   1.453   1.458   1.604   1.605   1.633
125   F         1.519   1.519   1.543   1.722   1.723   1.756   1.604   1.605   1.633
126   D        -1.147  -1.146  -1.120  -1.188  -1.197  -1.139  -1.030  -1.028  -0.981
127   I        -1.147  -1.146  -1.120  -1.093  -1.090  -1.045  -1.030  -1.028  -0.981
128   K        -0.026  -0.007  -0.061  -0.351  -0.321  -0.424  -0.152  -0.123  -0.207
129   R        -0.026  -0.007  -0.061  -0.158  -0.138  -0.192  -0.152  -0.123  -0.207
130   E        -1.147  -1.146  -1.120  -0.872  -0.872  -0.826  -1.030  -1.028  -0.981
131   G        -0.026  -0.037  -0.070   0.142   0.118   0.050  -0.152  -0.169  -0.221
132   R        -0.026  -0.037  -0.070   0.075   0.049  -0.034  -0.152  -0.169  -0.221
133   N         1.519   1.519   1.543   1.437   1.438   1.472   1.604   1.605   1.633
134   E         1.519   1.519   1.543   1.493   1.490   1.527   1.604   1.605   1.633
135   L         1.519   1.519   1.543   1.437   1.437   1.472   1.604   1.605   1.633
136   Q        -0.026  -0.007  -0.061  -0.062  -0.038  -0.109  -0.152  -0.123  -0.207
137   E        -0.026  -0.030  -0.065  -0.018  -0.029  -0.074  -0.152  -0.158  -0.213
138   E        -1.147  -1.146  -1.120  -0.985  -0.987  -0.938  -1.030  -1.028  -0.981
139   R        -0.026  -0.030  -0.065   0.075   0.064  -0.023  -0.152  -0.158  -0.213
140   L        -1.147  -1.146  -1.120  -1.136  -1.138  -1.087  -1.030  -1.028  -0.981
141   K        -0.026  -0.030  -0.065  -0.330  -0.343  -0.396  -0.152  -0.158  -0.213
142   V        -0.026  -0.030  -0.065  -0.068  -0.080  -0.146  -0.152  -0.158  -0.213
143   P         1.519   1.519   1.543   1.815   1.816   1.848   1.604   1.605   1.633
144   I         1.519   1.519   1.543   1.339   1.339   1.374   1.604   1.605   1.633
145   L        -0.026  -0.037  -0.070   0.001  -0.017  -0.048  -0.152  -0.169  -0.221
146   V        -0.026  -0.030  -0.065  -0.113  -0.126  -0.198  -0.152  -0.158  -0.213
147   T         1.519   1.519   1.543   1.602   1.601   1.636   1.604   1.605   1.633
148   L        -0.026  -0.037  -0.070  -0.049  -0.069  -0.107  -0.152  -0.169  -0.221
149   V        -1.147  -1.146  -1.120  -1.059  -1.064  -1.012  -1.030  -1.028  -0.981
150   S        -0.026  -0.030  -0.065  -0.119  -0.103  -0.179  -0.152  -0.158  -0.213
151   D        -1.147  -1.146  -1.120  -1.258  -1.268  -1.209  -1.030  -1.028  -0.981
152   S        -1.147  -1.146  -1.120  -0.985  -0.967  -0.938  -1.030  -1.028  -0.981
153   E        -0.026  -0.037  -0.070  -0.018  -0.040  -0.082  -0.152  -0.169  -0.221
154   I        -1.147  -1.146  -1.120  -1.267  -1.270  -1.218  -1.030  -1.028  -0.981
155   I        -0.026  -0.007  -0.061  -0.378  -0.351  -0.445  -0.152  -0.123  -0.207
156   D        -0.163  -0.163  -0.137  -0.203  -0.205  -0.160  -0.371  -0.370  -0.328
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   L        -0.163  -0.163  -0.137  -0.189  -0.191  -0.146  -0.371  -0.370  -0.328
164   N        -1.147  -1.146  -1.120  -1.144  -1.126  -1.096  -1.030  -1.028  -0.981
165   L        -0.026  -0.037  -0.070  -0.190  -0.200  -0.273  -0.152  -0.169  -0.221
166   H        -0.026  -0.007  -0.061   0.001   0.024  -0.037  -0.152  -0.123  -0.207
167   S        -1.147  -1.146  -1.120  -1.258  -1.242  -1.209  -1.030  -1.028  -0.981
168   F         1.519   1.519   1.543   1.722   1.723   1.756   1.604   1.605   1.633
169   T        -0.026  -0.037  -0.070   0.106   0.085   0.041  -0.152  -0.169  -0.221
170   K        -0.026  -0.037  -0.070  -0.158  -0.177  -0.202  -0.152  -0.169  -0.221
171   Q         1.519   1.519   1.543   1.696   1.696   1.730   1.604   1.605   1.633
172   -         1.519   1.519   1.543   1.459   1.461   1.494   1.604   1.605   1.633
* 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/P53218
Output conservation file - output/P53218
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
