1     M         1.132   1.132   1.147   1.435   1.435   1.453   1.176   1.176   1.192
2     L        -0.376  -0.368  -0.432  -0.310  -0.294  -0.446  -0.478  -0.465  -0.558
3     H        -1.471  -1.470  -1.426  -1.402  -1.403  -1.330  -1.305  -1.304  -1.235
4     C        -0.376  -0.368  -0.432  -0.093  -0.082  -0.168  -0.478  -0.465  -0.558
5     T         1.132   1.132   1.147   1.138   1.137   1.162   1.176   1.176   1.192
6     Q        -0.376  -0.368  -0.432  -0.337  -0.324  -0.425  -0.478  -0.465  -0.558
7     V        -0.376  -0.382  -0.433  -0.396  -0.407  -0.492  -0.478  -0.487  -0.560
8     C         1.132   1.132   1.147   1.476   1.476   1.493   1.176   1.176   1.192
9     L         1.132   1.132   1.147   0.902   0.902   0.930   1.176   1.176   1.192
10    S         1.132   1.132   1.147   1.153   1.152   1.176   1.176   1.176   1.192
11    A         1.132   1.132   1.147   1.167   1.166   1.190   1.176   1.176   1.192
12    L         1.132   1.132   1.147   0.902   0.902   0.930   1.176   1.176   1.192
13    T        -0.376  -0.377  -0.433  -0.383  -0.387  -0.481  -0.478  -0.480  -0.561
14    K         1.132   1.132   1.147   0.825   0.826   0.855   1.176   1.176   1.192
15    R         1.132   1.132   1.147   1.239   1.239   1.261   1.176   1.176   1.192
16    T         1.132   1.132   1.147   1.138   1.137   1.162   1.176   1.176   1.192
17    H        -0.376  -0.368  -0.432  -0.553  -0.542  -0.596  -0.478  -0.465  -0.558
18    R         1.132   1.132   1.147   1.239   1.239   1.261   1.176   1.176   1.192
19    V         1.132   1.132   1.147   1.124   1.124   1.148   1.176   1.176   1.192
20    K        -0.376  -0.368  -0.432  -0.450  -0.433  -0.586  -0.478  -0.465  -0.558
21    V         1.132   1.132   1.147   1.124   1.124   1.148   1.176   1.176   1.192
22    Q         1.132   1.132   1.147   1.225   1.225   1.247   1.176   1.176   1.192
23    V        -0.376  -0.368  -0.432  -0.617  -0.603  -0.695  -0.478  -0.465  -0.558
24    L         1.132   1.132   1.147   0.902   0.902   0.930   1.176   1.176   1.192
25    K         1.132   1.132   1.147   0.825   0.826   0.855   1.176   1.176   1.192
26    D         1.132   1.132   1.147   1.310   1.310   1.330   1.176   1.176   1.192
27    F         1.132   1.132   1.147   1.338   1.338   1.357   1.176   1.176   1.192
28    P         1.132   1.132   1.147   1.295   1.295   1.316   1.176   1.176   1.192
29    R        -0.376  -0.382  -0.433  -0.258  -0.269  -0.355  -0.478  -0.487  -0.560
30    F         1.132   1.132   1.147   1.338   1.338   1.357   1.176   1.176   1.192
31    Q        -0.376  -0.377  -0.433  -0.194  -0.196  -0.273  -0.478  -0.480  -0.561
32    L        -0.376  -0.382  -0.433  -0.512  -0.520  -0.568  -0.478  -0.487  -0.560
33    Y        -0.376  -0.382  -0.433  -0.056  -0.065  -0.147  -0.478  -0.487  -0.560
34    K        -0.376  -0.382  -0.433  -0.681  -0.691  -0.753  -0.478  -0.487  -0.560
35    G         1.132   1.132   1.147   1.310   1.310   1.330   1.176   1.176   1.192
36    Q        -0.376  -0.368  -0.432  -0.443  -0.430  -0.522  -0.478  -0.465  -0.558
37    V         1.132   1.132   1.147   1.124   1.124   1.148   1.176   1.176   1.192
38    A        -0.376  -0.382  -0.433  -0.370  -0.382  -0.471  -0.478  -0.487  -0.560
39    N        -0.376  -0.377  -0.433  -0.201  -0.203  -0.302  -0.478  -0.480  -0.561
40    V         1.132   1.132   1.147   1.124   1.124   1.148   1.176   1.176   1.192
41    K         1.132   1.132   1.147   0.825   0.826   0.855   1.176   1.176   1.192
42    P         1.132   1.132   1.147   1.295   1.295   1.316   1.176   1.176   1.192
43    S         1.132   1.132   1.147   1.153   1.152   1.176   1.176   1.176   1.192
44    L         1.132   1.132   1.147   0.902   0.902   0.930   1.176   1.176   1.192
45    M         1.132   1.132   1.147   1.435   1.435   1.453   1.176   1.176   1.192
46    R        -0.376  -0.377  -0.433  -0.304  -0.307  -0.413  -0.478  -0.480  -0.561
47    N         1.132   1.132   1.147   1.295   1.295   1.316   1.176   1.176   1.192
48    Y        -0.376  -0.382  -0.433  -0.081  -0.091  -0.178  -0.478  -0.487  -0.560
49    L         1.132   1.132   1.147   0.902   0.902   0.930   1.176   1.176   1.192
50    H         1.132   1.132   1.147   1.393   1.394   1.412   1.176   1.176   1.192
51    N        -0.376  -0.377  -0.433  -0.137  -0.140  -0.224  -0.478  -0.480  -0.561
52    F        -1.471  -1.470  -1.426  -1.071  -1.071  -1.005  -1.305  -1.304  -1.235
53    N         1.132   1.132   1.147   1.295   1.295   1.316   1.176   1.176   1.192
54    G         1.132   1.132   1.147   1.310   1.310   1.330   1.176   1.176   1.192
55    A         1.132   1.132   1.147   1.167   1.166   1.190   1.176   1.176   1.192
56    K        -0.376  -0.368  -0.432  -0.437  -0.420  -0.574  -0.478  -0.465  -0.558
57    Y         1.132   1.132   1.147   1.379   1.380   1.398   1.176   1.176   1.192
58    I         1.132   1.132   1.147   1.310   1.310   1.330   1.176   1.176   1.192
59    L         1.132   1.132   1.147   0.902   0.902   0.930   1.176   1.176   1.192
60    S        -1.471  -1.470  -1.426  -1.493  -1.495  -1.419  -1.305  -1.304  -1.235
61    E         1.132   1.132   1.147   1.036   1.038   1.062   1.176   1.176   1.192
62    E        -1.471  -1.470  -1.426  -1.393  -1.391  -1.321  -1.305  -1.304  -1.235
63    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    D        -0.376  -0.377  -0.433  -0.194  -0.196  -0.298  -0.478  -0.480  -0.561
65    I        -0.376  -0.377  -0.433  -0.239  -0.242  -0.353  -0.478  -0.480  -0.561
66    N        -0.376  -0.368  -0.432  -0.162  -0.149  -0.256  -0.478  -0.465  -0.558
67    T        -0.376  -0.368  -0.432  -0.310  -0.296  -0.413  -0.478  -0.465  -0.558
68    E        -1.471  -1.470  -1.426  -1.375  -1.373  -1.304  -1.305  -1.304  -1.235
69    L         1.132   1.132   1.147   0.902   0.902   0.930   1.176   1.176   1.192
70    L         1.132   1.132   1.147   0.902   0.902   0.930   1.176   1.176   1.192
71    -        -0.510  -0.510  -0.477  -0.667  -0.667  -0.609  -0.685  -0.684  -0.628
72    -        -0.510  -0.510  -0.477  -0.477  -0.477  -0.423  -0.685  -0.684  -0.628
73    -        -0.510  -0.510  -0.477  -0.716  -0.716  -0.657  -0.685  -0.684  -0.628
74    K         1.132   1.132   1.147   0.825   0.826   0.855   1.176   1.176   1.192
75    Q        -1.471  -1.470  -1.426  -1.511  -1.511  -1.437  -1.305  -1.304  -1.235
76    Y        -0.510  -0.510  -0.477  -0.378  -0.378  -0.326  -0.685  -0.684  -0.628
77    Q        -0.510  -0.510  -0.477  -0.484  -0.484  -0.430  -0.685  -0.684  -0.628
78    T        -0.510  -0.510  -0.477  -0.562  -0.562  -0.506  -0.685  -0.684  -0.628
79    L        -0.510  -0.510  -0.477  -0.772  -0.772  -0.712  -0.685  -0.684  -0.628
80    E        -1.471  -1.470  -1.426  -1.429  -1.427  -1.356  -1.305  -1.304  -1.235
81    A         1.132   1.132   1.147   1.167   1.166   1.190   1.176   1.176   1.192
82    K        -1.471  -1.470  -1.426  -1.684  -1.680  -1.606  -1.305  -1.304  -1.235
83    L         1.132   1.132   1.147   0.902   0.902   0.930   1.176   1.176   1.192
84    E        -1.471  -1.470  -1.426  -1.587  -1.586  -1.511  -1.305  -1.304  -1.235
85    E        -0.376  -0.368  -0.432  -0.732  -0.717  -0.814  -0.478  -0.465  -0.558
86    D        -1.471  -1.470  -1.426  -1.314  -1.316  -1.243  -1.305  -1.304  -1.235
87    H        -1.471  -1.470  -1.426  -1.271  -1.273  -1.201  -1.305  -1.304  -1.235
88    Q        -0.376  -0.382  -0.433  -0.356  -0.367  -0.472  -0.478  -0.487  -0.560
89    Q        -1.471  -1.470  -1.426  -1.279  -1.280  -1.209  -1.305  -1.304  -1.235
90    L        -1.471  -1.470  -1.426  -1.577  -1.576  -1.502  -1.305  -1.304  -1.235
91    S        -1.471  -1.470  -1.426  -1.420  -1.421  -1.347  -1.305  -1.304  -1.235
92    K        -0.376  -0.377  -0.433  -0.674  -0.676  -0.745  -0.478  -0.480  -0.561
93    R        -0.376  -0.368  -0.432  -0.631  -0.619  -0.690  -0.478  -0.465  -0.558
94    H        -1.471  -1.470  -1.426  -1.288  -1.290  -1.218  -1.305  -1.304  -1.235
95    E        -0.376  -0.377  -0.433  -0.491  -0.493  -0.584  -0.478  -0.480  -0.561
96    T        -1.471  -1.470  -1.426  -1.375  -1.375  -1.304  -1.305  -1.304  -1.235
97    E        -0.376  -0.382  -0.433  -0.410  -0.418  -0.482  -0.478  -0.487  -0.560
98    V        -0.376  -0.377  -0.433  -0.403  -0.406  -0.501  -0.478  -0.480  -0.561
99    Q        -1.471  -1.470  -1.426  -1.577  -1.580  -1.502  -1.305  -1.304  -1.235
100   K        -0.376  -0.377  -0.433  -0.666  -0.669  -0.736  -0.478  -0.480  -0.561
101   N        -1.471  -1.470  -1.426  -1.314  -1.316  -1.243  -1.305  -1.304  -1.235
102   M        -1.471  -1.470  -1.426  -1.438  -1.443  -1.365  -1.305  -1.304  -1.235
103   E        -1.471  -1.470  -1.426  -1.429  -1.427  -1.356  -1.305  -1.304  -1.235
104   L        -1.471  -1.470  -1.426  -1.577  -1.575  -1.502  -1.305  -1.304  -1.235
105   R        -1.471  -1.470  -1.426  -1.366  -1.368  -1.295  -1.305  -1.304  -1.235
106   K        -0.510  -0.510  -0.477  -0.789  -0.789  -0.728  -0.685  -0.684  -0.628
107   E        -0.510  -0.510  -0.477  -0.675  -0.675  -0.617  -0.685  -0.684  -0.628
108   S        -0.510  -0.510  -0.477  -0.504  -0.504  -0.449  -0.685  -0.684  -0.628
109   V        -0.510  -0.510  -0.477  -0.535  -0.535  -0.479  -0.685  -0.684  -0.628
110   F        -0.510  -0.510  -0.477  -0.399  -0.399  -0.346  -0.685  -0.684  -0.628
111   G        -0.510  -0.510  -0.477  -0.489  -0.489  -0.434  -0.685  -0.684  -0.628
112   H        -0.510  -0.510  -0.477  -0.369  -0.369  -0.317  -0.685  -0.684  -0.628
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   K         1.132   1.132   1.147   0.825   0.826   0.855   1.176   1.176   1.192
115   K        -0.376  -0.368  -0.432  -0.631  -0.613  -0.753  -0.478  -0.465  -0.558
116   E         1.132   1.132   1.147   1.036   1.038   1.062   1.176   1.176   1.192
117   E        -0.376  -0.382  -0.433  -0.410  -0.418  -0.482  -0.478  -0.487  -0.560
118   K        -0.376  -0.377  -0.433  -0.602  -0.604  -0.658  -0.478  -0.480  -0.561
119   P        -0.376  -0.382  -0.433  -0.245  -0.257  -0.356  -0.478  -0.487  -0.560
120   K        -1.471  -1.470  -1.426  -1.511  -1.508  -1.437  -1.305  -1.304  -1.235
121   E         1.132   1.132   1.147   1.036   1.038   1.062   1.176   1.176   1.192
122   E        -1.471  -1.470  -1.426  -1.704  -1.703  -1.626  -1.305  -1.304  -1.235
123   K        -0.376  -0.382  -0.433  -0.602  -0.611  -0.657  -0.478  -0.487  -0.560
124   K         1.132   1.132   1.147   0.825   0.826   0.855   1.176   1.176   1.192
125   G        -0.376  -0.382  -0.433  -0.226  -0.237  -0.336  -0.478  -0.487  -0.560
126   L        -1.471  -1.470  -1.426  -1.438  -1.436  -1.365  -1.305  -1.304  -1.235
127   L         1.132   1.132   1.147   0.902   0.902   0.930   1.176   1.176   1.192
128   D        -0.376  -0.382  -0.433  -0.162  -0.172  -0.258  -0.478  -0.487  -0.560
129   S        -0.376  -0.382  -0.433  -0.423  -0.435  -0.533  -0.478  -0.487  -0.560
130   G        -1.471  -1.470  -1.426  -1.288  -1.288  -1.218  -1.305  -1.304  -1.235
131   I         1.132   1.132   1.147   1.310   1.310   1.330   1.176   1.176   1.192
132   T         1.132   1.132   1.147   1.138   1.137   1.162   1.176   1.176   1.192
133   I        -0.376  -0.377  -0.433  -0.239  -0.242  -0.353  -0.478  -0.480  -0.561
134   E        -0.376  -0.377  -0.433  -0.410  -0.411  -0.483  -0.478  -0.480  -0.561
135   E        -1.471  -1.470  -1.426  -1.296  -1.293  -1.226  -1.305  -1.304  -1.235
136   V         1.132   1.132   1.147   1.124   1.124   1.148   1.176   1.176   1.192
137   K         1.132   1.132   1.147   0.825   0.826   0.855   1.176   1.176   1.192
138   I         1.132   1.132   1.147   1.310   1.310   1.330   1.176   1.176   1.192
139   P         1.132   1.132   1.147   1.295   1.295   1.316   1.176   1.176   1.192
140   G         1.132   1.132   1.147   1.310   1.310   1.330   1.176   1.176   1.192
141   L         1.132   1.132   1.147   0.902   0.902   0.930   1.176   1.176   1.192
142   D        -0.376  -0.377  -0.433  -0.188  -0.190  -0.290  -0.478  -0.480  -0.561
143   I        -0.376  -0.382  -0.433  -0.337  -0.349  -0.473  -0.478  -0.487  -0.560
* 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/P53724
Output conservation file - output/P53724
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
