1     M         1.802   1.842   1.904   2.045   2.111   2.221   1.983   2.043   2.145
2     K         0.267   0.294   0.368  -0.367  -0.326  -0.203  -0.087  -0.047   0.062
3     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    M         0.392   0.447   0.428   0.263   0.348   0.329   0.143   0.233   0.175
19    S         0.311   0.332   0.376   0.021   0.056   0.110  -0.004   0.023   0.078
20    V        -1.148  -1.065  -1.104  -0.946  -0.837  -0.842  -0.998  -0.896  -0.914
21    F        -0.302  -0.424  -0.424   0.112  -0.061  -0.051  -0.335  -0.495  -0.491
22    N        -0.302  -0.328  -0.391  -0.104  -0.130  -0.242  -0.335  -0.371  -0.446
23    V        -0.631  -0.610  -0.532  -0.491  -0.462  -0.334  -0.777  -0.743  -0.634
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    L         1.802   1.842   1.904   1.741   1.808   1.915   1.983   2.043   2.145
29    K        -0.631  -0.610  -0.532  -1.053  -1.002  -0.900  -0.777  -0.743  -0.634
30    P        -1.148  -1.105  -1.109  -0.791  -0.699  -0.748  -0.998  -0.939  -0.920
31    L        -0.500  -0.447  -0.469  -0.639  -0.561  -0.574  -0.605  -0.525  -0.551
32    L        -1.268  -1.243  -1.170  -1.204  -1.158  -1.053  -1.122  -1.083  -0.982
33    K        -1.268  -1.243  -1.170  -1.557  -1.512  -1.408  -1.122  -1.083  -0.982
34    G        -1.268  -1.243  -1.170  -1.352  -1.338  -1.201  -1.122  -1.083  -0.982
35    S        -0.500  -0.536  -0.493  -0.464  -0.511  -0.413  -0.605  -0.647  -0.583
36    N        -1.268  -1.243  -1.170  -1.361  -1.337  -1.210  -1.122  -1.083  -0.982
37    S        -0.500  -0.509  -0.492  -0.862  -0.902  -0.894  -0.605  -0.612  -0.581
38    F        -1.268  -1.243  -1.170  -1.424  -1.408  -1.274  -1.122  -1.083  -0.982
39    K        -1.268  -1.243  -1.170  -1.471  -1.383  -1.321  -1.122  -1.083  -0.982
40    V         0.392   0.473   0.442   0.254   0.376   0.345   0.143   0.280   0.201
41    K         0.392   0.419   0.431  -0.021   0.013   0.031   0.143   0.183   0.180
42    L         0.267   0.301   0.373   0.022   0.106   0.216  -0.087  -0.033   0.072
43    N        -1.268  -1.243  -1.170  -1.397  -1.322  -1.247  -1.122  -1.083  -0.982
44    G         0.311   0.311   0.375  -0.002  -0.021   0.087  -0.004  -0.015   0.076
45    F        -1.148  -1.121  -1.116  -0.951  -0.901  -0.872  -0.998  -0.961  -0.927
46    L        -1.148  -1.140  -1.113  -1.445  -1.410  -1.411  -0.998  -0.979  -0.924
47    F        -1.148  -1.140  -1.113  -0.830  -0.816  -0.780  -0.998  -0.979  -0.924
48    N        -0.302  -0.296  -0.394  -0.096  -0.075  -0.236  -0.335  -0.321  -0.450
49    N        -0.534  -0.477  -0.475  -0.579  -0.501  -0.468  -0.667  -0.594  -0.567
50    V        -1.148  -1.105  -1.109  -0.860  -0.790  -0.814  -0.998  -0.939  -0.920
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    S        -1.148  -1.197  -1.136  -1.254  -1.323  -1.248  -0.998  -1.037  -0.947
64    T        -1.148  -1.121  -1.116  -1.093  -1.020  -1.016  -0.998  -0.961  -0.927
65    I        -0.302  -0.355  -0.400   0.093   0.005  -0.050  -0.335  -0.405  -0.458
66    T        -1.148  -1.065  -1.104  -0.930  -0.765  -0.876  -0.998  -0.896  -0.914
67    I        -1.148  -1.121  -1.116  -0.825  -0.799  -0.736  -0.998  -0.961  -0.927
68    R         1.802   1.842   1.904   1.775   1.850   1.949   1.983   2.043   2.145
69    T         0.311   0.388   0.408   0.156   0.297   0.311  -0.004   0.126   0.138
70    L        -0.302  -0.424  -0.424  -0.534  -0.755  -0.792  -0.335  -0.495  -0.491
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    M         0.694   0.590   0.560   1.014   0.867   0.830   0.658   0.482   0.414
77    K         1.802   1.842   1.904   1.573   1.617   1.746   1.983   2.043   2.145
78    T         1.802   1.842   1.904   1.814   1.871   1.988   1.983   2.043   2.145
79    H         0.694   0.590   0.560   0.909   0.732   0.645   0.658   0.482   0.414
80    K         0.694   0.762   0.570   0.460   0.550   0.255   0.658   0.766   0.430
81    G         0.311   0.298   0.369   0.074   0.044   0.169  -0.004  -0.040   0.065
82    T        -0.302  -0.301  -0.377  -0.116  -0.114  -0.235  -0.335  -0.337  -0.427
83    A         0.694   0.762   0.570   0.811   0.917   0.586   0.658   0.766   0.430
84    K         0.694   0.590   0.560   0.505   0.336   0.311   0.658   0.482   0.414
85    R         1.802   1.842   1.904   1.775   1.850   1.949   1.983   2.043   2.145
86    W        -0.302  -0.424  -0.424   0.215   0.033   0.020  -0.335  -0.495  -0.491
87    R        -0.302  -0.424  -0.424  -0.359  -0.574  -0.578  -0.335  -0.495  -0.491
88    R        -1.148  -1.121  -1.116  -1.186  -1.142  -1.099  -0.998  -0.961  -0.927
89    T         0.694   0.590   0.560   0.830   0.696   0.680   0.658   0.482   0.414
90    G        -0.302  -0.191  -0.369  -0.355  -0.179  -0.470  -0.335  -0.177  -0.416
91    N        -0.302  -0.355  -0.400  -0.221  -0.318  -0.418  -0.335  -0.405  -0.458
92    T        -0.302  -0.132  -0.357  -0.398  -0.124  -0.505  -0.335  -0.097  -0.399
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    F         0.694   0.590   0.560   1.032   0.886   0.843   0.658   0.482   0.414
95    K         0.694   0.590   0.560   0.470   0.289   0.255   0.658   0.482   0.414
96    R         1.802   1.842   1.904   1.775   1.850   1.949   1.983   2.043   2.145
97    G         0.694   0.667   0.545   0.599   0.546   0.310   0.658   0.611   0.386
98    I        -0.534  -0.536  -0.480  -0.584  -0.618  -0.491  -0.667  -0.654  -0.571
99    A         0.694   0.590   0.560   0.840   0.667   0.614   0.658   0.482   0.414
100   G         1.802   1.842   1.904   1.761   1.822   1.935   1.983   2.043   2.145
101   R         1.802   1.842   1.904   1.775   1.850   1.949   1.983   2.043   2.145
102   K         0.311   0.341   0.378  -0.088  -0.061   0.029  -0.004   0.040   0.082
103   H         1.802   1.842   1.904   2.070   2.146   2.246   1.983   2.043   2.145
104   G         1.802   1.842   1.904   1.761   1.822   1.935   1.983   2.043   2.145
105   N         1.802   1.842   1.904   1.943   2.006   2.119   1.983   2.043   2.145
106   I        -1.148  -1.182  -1.134  -0.992  -1.091  -1.014  -0.998  -1.023  -0.946
107   G         1.802   1.842   1.904   1.761   1.822   1.935   1.983   2.043   2.145
108   W         0.694   0.667   0.545   1.182   1.156   0.956   0.658   0.611   0.386
109   S         1.802   1.842   1.904   1.788   1.864   1.962   1.983   2.043   2.145
110   H        -0.534  -0.460  -0.479  -0.503  -0.385  -0.428  -0.667  -0.568  -0.570
111   R        -0.534  -0.572  -0.489  -0.653  -0.689  -0.566  -0.667  -0.697  -0.583
112   S         0.694   0.590   0.560   0.656   0.499   0.416   0.658   0.482   0.414
113   L         0.694   0.667   0.545   0.665   0.644   0.468   0.658   0.611   0.386
114   K         0.311   0.298   0.369  -0.193  -0.227  -0.103  -0.004  -0.040   0.065
115   A        -1.148  -1.165  -1.125  -1.159  -1.217  -1.120  -0.998  -1.007  -0.936
116   L         0.694   0.590   0.560   0.532   0.354   0.275   0.658   0.482   0.414
117   T        -0.302  -0.269  -0.407  -0.197  -0.130  -0.338  -0.335  -0.285  -0.467
118   G         0.694   0.667   0.545   0.652   0.614   0.400   0.658   0.611   0.386
119   R        -0.302  -0.424  -0.424  -0.217  -0.375  -0.374  -0.335  -0.495  -0.491
120   K        -1.148  -1.065  -1.104  -1.243  -1.085  -1.187  -0.998  -0.896  -0.914
121   I        -1.762  -1.731  -1.665  -1.137  -1.045  -0.984  -1.329  -1.286  -1.190
122   A        -0.302  -0.424  -0.424  -0.152  -0.368  -0.365  -0.335  -0.495  -0.491
123   H        -0.534  -0.460  -0.479  -0.419  -0.339  -0.312  -0.667  -0.568  -0.570
124   P        -1.148  -1.182  -1.134  -0.791  -0.856  -0.799  -0.998  -1.023  -0.946
125   A        -0.500  -0.506  -0.482  -0.529  -0.534  -0.485  -0.605  -0.612  -0.568
126   Y        -1.148  -1.065  -1.104  -0.766  -0.669  -0.713  -0.998  -0.896  -0.914
127   S        -1.148  -1.165  -1.125  -1.198  -1.283  -1.224  -0.998  -1.007  -0.936
128   K        -0.302  -0.269  -0.407  -0.503  -0.477  -0.654  -0.335  -0.285  -0.467
129   H         0.311   0.375   0.398   0.244   0.386   0.374  -0.004   0.102   0.119
130   L         0.694   0.590   0.560   0.672   0.538   0.502   0.658   0.482   0.414
131   K         0.694   0.762   0.570   0.460   0.550   0.255   0.658   0.766   0.430
132   R         0.311   0.298   0.369  -0.132  -0.203  -0.089  -0.004  -0.040   0.065
133   L         0.694   0.590   0.560   0.695   0.572   0.539   0.658   0.482   0.414
134   L        -1.148  -1.197  -1.136  -1.232  -1.298  -1.196  -0.998  -1.037  -0.947
135   P         0.694   0.667   0.545   1.116   1.082   0.873   0.658   0.611   0.386
136   Y        -0.302  -0.424  -0.424   0.104  -0.094  -0.127  -0.335  -0.495  -0.491
137   H        -0.534  -0.531  -0.483  -0.791  -0.829  -0.744  -0.667  -0.647  -0.575
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P53921
Output conservation file - output/P53921
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
