1     M         0.585   0.601   0.622   1.106   1.087   1.020   0.586   0.609   0.644
2     S        -0.258  -0.400  -0.987   0.058  -0.070  -0.839  -0.150  -0.321  -1.188
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     G         0.585   0.601   0.622   0.303   0.348   0.443   0.586   0.609   0.644
5     G         0.585   0.601   0.622   0.315   0.355   0.452   0.586   0.609   0.644
6     K         0.585   0.601   0.622   0.498   0.526   0.583   0.586   0.609   0.644
7     G        -1.549  -1.388  -1.010  -1.919  -1.618  -1.129  -1.976  -1.744  -1.224
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     G         0.585   0.601   0.622   0.315   0.355   0.452   0.586   0.609   0.644
10    K        -1.093  -1.248  -1.013  -1.172  -1.474  -1.241  -1.255  -1.518  -1.229
11    A        -1.870  -1.880  -1.967  -2.069  -2.167  -2.053  -1.808  -1.905  -1.853
12    G        -1.333  -1.418  -1.018  -1.847  -2.110  -1.482  -1.624  -1.792  -1.236
13    S        -1.550  -1.566  -1.954  -1.152  -1.305  -1.851  -1.378  -1.472  -1.838
14    A        -3.206  -3.200  -2.654  -3.279  -3.160  -2.560  -2.913  -2.818  -2.174
15    A        -2.472  -2.417  -1.975  -2.673  -2.599  -1.965  -2.483  -2.382  -1.861
16    K         0.585   0.601   0.622   0.498   0.526   0.583   0.586   0.609   0.644
17    A        -2.326  -2.844  -2.653  -2.139  -2.708  -2.350  -1.931  -2.450  -2.173
18    S        -1.093  -1.248  -1.013  -1.112  -1.454  -1.276  -1.255  -1.518  -1.229
19    Q        -2.083  -2.069  -1.966  -1.540  -1.484  -1.597  -2.115  -1.991  -1.851
20    S        -0.749  -0.500  -0.987  -0.444  -0.171  -0.838  -0.764  -0.446  -1.187
21    R         0.585   0.601   0.622   0.611   0.628   0.665   0.586   0.609   0.644
22    S         0.585   0.601   0.622   0.621   0.645   0.671   0.586   0.609   0.644
23    A        -0.258  -0.400  -0.987  -0.495  -0.608  -1.293  -0.150  -0.321  -1.188
24    K         0.585   0.601   0.622   0.498   0.526   0.583   0.586   0.609   0.644
25    A         0.585   0.601   0.622   0.097   0.145   0.295   0.586   0.609   0.644
26    G        -0.258  -0.560  -0.991  -0.240  -0.510  -0.983  -0.150  -0.523  -1.193
27    L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
28    T        -1.093  -1.248  -1.013  -0.802  -1.178  -1.090  -1.255  -1.518  -1.229
29    F         0.585   0.601   0.622   1.106   1.087   1.020   0.586   0.609   0.644
30    P         0.585   0.601   0.622   0.856   0.854   0.840   0.586   0.609   0.644
31    V         0.585   0.601   0.622   0.764   0.759   0.775   0.586   0.609   0.644
32    G         0.585   0.601   0.622   0.315   0.355   0.452   0.586   0.609   0.644
33    R         0.585   0.601   0.622   0.611   0.628   0.665   0.586   0.609   0.644
34    V         0.585   0.601   0.622   0.764   0.759   0.775   0.586   0.609   0.644
35    H         0.585   0.601   0.622   0.964   0.950   0.918   0.586   0.609   0.644
36    R         0.585   0.601   0.622   0.611   0.628   0.665   0.586   0.609   0.644
37    L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
38    L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
39    R         0.585   0.601   0.622   0.611   0.628   0.665   0.586   0.609   0.644
40    R        -1.093  -0.777  -0.993  -1.085  -0.666  -1.062  -1.255  -0.816  -1.197
41    G         0.585   0.601   0.622   0.315   0.355   0.452   0.586   0.609   0.644
42    N         0.585   0.601   0.622   0.732   0.745   0.751   0.586   0.609   0.644
43    Y         0.585   0.601   0.622   0.991   0.981   0.937   0.586   0.609   0.644
44    A         0.585   0.601   0.622   0.097   0.145   0.295   0.586   0.609   0.644
45    Q         0.585   0.601   0.622   0.842   0.845   0.830   0.586   0.609   0.644
46    R         0.585   0.601   0.622   0.611   0.628   0.665   0.586   0.609   0.644
47    I        -1.485  -1.408  -1.019  -1.380  -1.323  -0.873  -1.869  -1.775  -1.238
48    G         0.585   0.601   0.622   0.315   0.355   0.452   0.586   0.609   0.644
49    S        -1.333  -1.418  -1.018  -1.547  -1.865  -1.312  -1.624  -1.792  -1.236
50    G         0.585   0.601   0.622   0.315   0.355   0.452   0.586   0.609   0.644
51    A         0.585   0.601   0.622   0.097   0.145   0.295   0.586   0.609   0.644
52    P         0.585   0.601   0.622   0.856   0.854   0.840   0.586   0.609   0.644
53    V        -0.258  -0.560  -0.991   0.188  -0.145  -0.827  -0.150  -0.523  -1.193
54    Y         0.585   0.601   0.622   0.991   0.981   0.937   0.586   0.609   0.644
55    L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
56    T        -1.333  -1.418  -1.018  -1.246  -1.623  -1.140  -1.624  -1.792  -1.236
57    A        -1.333  -1.030  -1.004  -1.828  -1.381  -1.309  -1.624  -1.182  -1.214
58    V         0.585   0.601   0.622   0.764   0.759   0.775   0.586   0.609   0.644
59    L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
60    E         0.585   0.601   0.622   0.819   0.821   0.814   0.586   0.609   0.644
61    Y         0.585   0.601   0.622   0.991   0.981   0.937   0.586   0.609   0.644
62    L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
63    A         0.585   0.601   0.622   0.097   0.145   0.295   0.586   0.609   0.644
64    A        -0.258  -0.560  -0.991  -0.482  -0.763  -1.227  -0.150  -0.523  -1.193
65    E         0.585   0.601   0.622   0.819   0.821   0.814   0.586   0.609   0.644
66    I         0.585   0.601   0.622   0.778   0.788   0.784   0.586   0.609   0.644
67    L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
68    E         0.585   0.601   0.622   0.819   0.821   0.814   0.586   0.609   0.644
69    L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
70    A        -0.258  -0.560  -0.991  -0.495  -0.782  -1.296  -0.150  -0.523  -1.193
71    G         0.585   0.601   0.622   0.315   0.355   0.452   0.586   0.609   0.644
72    N         0.585   0.601   0.622   0.732   0.745   0.751   0.586   0.609   0.644
73    A         0.585   0.601   0.622   0.097   0.145   0.295   0.586   0.609   0.644
74    A         0.585   0.601   0.622   0.097   0.145   0.295   0.586   0.609   0.644
75    R         0.585   0.601   0.622   0.611   0.628   0.665   0.586   0.609   0.644
76    D         0.585   0.601   0.622   1.013   1.005   0.953   0.586   0.609   0.644
77    N         0.585   0.601   0.622   0.732   0.745   0.751   0.586   0.609   0.644
78    K         0.585   0.601   0.622   0.498   0.526   0.583   0.586   0.609   0.644
79    K         0.585   0.601   0.622   0.498   0.526   0.583   0.586   0.609   0.644
80    T        -1.559  -1.425  -1.019  -1.520  -1.333  -0.867  -1.992  -1.804  -1.238
81    R         0.585   0.601   0.622   0.611   0.628   0.665   0.586   0.609   0.644
82    I         0.585   0.601   0.622   0.778   0.788   0.784   0.586   0.609   0.644
83    I        -0.258  -0.560  -0.991   0.201  -0.121  -0.825  -0.150  -0.523  -1.193
84    P         0.585   0.601   0.622   0.856   0.854   0.840   0.586   0.609   0.644
85    R         0.585   0.601   0.622   0.611   0.628   0.665   0.586   0.609   0.644
86    H         0.585   0.601   0.622   0.964   0.950   0.918   0.586   0.609   0.644
87    L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
88    Q         0.585   0.601   0.622   0.842   0.845   0.830   0.586   0.609   0.644
89    L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
90    A         0.585   0.601   0.622   0.097   0.145   0.295   0.586   0.609   0.644
91    I         0.585   0.601   0.622   0.778   0.788   0.784   0.586   0.609   0.644
92    R         0.585   0.601   0.622   0.611   0.628   0.665   0.586   0.609   0.644
93    N         0.585   0.601   0.622   0.732   0.745   0.751   0.586   0.609   0.644
94    D         0.585   0.601   0.622   1.013   1.005   0.953   0.586   0.609   0.644
95    D        -1.485  -1.161  -1.000  -1.212  -0.789  -0.707  -1.869  -1.381  -1.208
96    E         0.585   0.601   0.622   0.819   0.821   0.814   0.586   0.609   0.644
97    L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
98    N         0.585   0.601   0.622   0.732   0.745   0.751   0.586   0.609   0.644
99    K         0.585   0.601   0.622   0.498   0.526   0.583   0.586   0.609   0.644
100   L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
101   L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
102   G         0.585   0.601   0.622   0.315   0.355   0.452   0.586   0.609   0.644
103   N        -2.560  -2.144  -1.963  -2.037  -1.499  -1.422  -2.606  -2.103  -1.848
104   V         0.585   0.601   0.622   0.764   0.759   0.775   0.586   0.609   0.644
105   T         0.585   0.601   0.622   0.933   0.934   0.895   0.586   0.609   0.644
106   I         0.585   0.601   0.622   0.778   0.788   0.784   0.586   0.609   0.644
107   A         0.585   0.601   0.622   0.097   0.145   0.295   0.586   0.609   0.644
108   Q         0.585   0.601   0.622   0.842   0.845   0.830   0.586   0.609   0.644
109   G         0.585   0.601   0.622   0.315   0.355   0.452   0.586   0.609   0.644
110   G         0.585   0.601   0.622   0.315   0.355   0.452   0.586   0.609   0.644
111   V         0.585   0.601   0.622   0.764   0.759   0.775   0.586   0.609   0.644
112   L        -0.749  -0.939  -0.994  -0.952  -1.164  -1.203  -0.764  -1.046  -1.198
113   P         0.585   0.601   0.622   0.856   0.854   0.840   0.586   0.609   0.644
114   N         0.585   0.601   0.622   0.732   0.745   0.751   0.586   0.609   0.644
115   I         0.585   0.601   0.622   0.778   0.788   0.784   0.586   0.609   0.644
116   H        -0.749  -0.939  -0.994  -0.142  -0.438  -0.736  -0.764  -1.046  -1.198
117   Q        -0.749  -0.939  -0.994  -0.371  -0.695  -1.078  -0.764  -1.046  -1.198
118   N        -1.995  -1.981  -1.960  -1.410  -1.430  -1.590  -1.869  -1.879  -1.845
119   L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
120   L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
121   P         0.585   0.601   0.622   0.856   0.854   0.840   0.586   0.609   0.644
122   K        -1.550  -1.646  -1.958  -1.310  -1.387  -2.065  -1.378  -1.463  -1.843
123   K        -1.080  -1.384  -1.952  -0.630  -0.921  -1.626  -0.826  -1.163  -1.836
124   S        -1.550  -1.499  -1.956  -1.075  -0.985  -1.701  -1.378  -1.297  -1.840
125   A        -2.472  -2.198  -1.966  -2.957  -2.647  -2.203  -2.483  -2.220  -1.852
126   K        -0.258  -0.438  -0.984  -0.092  -0.267  -1.047  -0.150  -0.368  -1.183
127   A        -3.480  -3.315  -2.657  -3.557  -3.242  -2.406  -3.088  -2.912  -2.176
128   T        -1.700  -1.782  -1.960  -1.586  -1.710  -2.036  -1.521  -1.627  -1.845
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   K        -2.326  -1.861  -2.636  -1.829  -1.310  -2.473  -1.931  -1.443  -2.159
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   A        -0.749  -0.939  -0.994  -0.979  -1.191  -1.186  -0.764  -1.046  -1.198
133   S         0.585   0.601   0.622   0.621   0.645   0.671   0.586   0.609   0.644
134   Q         0.585   0.601   0.622   0.842   0.845   0.830   0.586   0.609   0.644
135   E         0.585   0.601   0.622   0.819   0.821   0.814   0.586   0.609   0.644
136   L         0.585   0.601   0.622   0.142   0.201   0.328   0.586   0.609   0.644
* 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/P04911
Output conservation file - output/P04911
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
