1     M         1.301   1.303   1.322   1.511   1.516   1.537   1.359   1.361   1.383
2     S         1.301   1.303   1.322   1.293   1.298   1.321   1.359   1.361   1.383
3     F        -0.151  -0.176  -0.204   0.071   0.030  -0.022  -0.281  -0.320  -0.360
4     W        -0.151  -0.176  -0.204   0.032  -0.008  -0.050  -0.281  -0.320  -0.360
5     K        -0.151  -0.123  -0.188  -0.320  -0.281  -0.362  -0.281  -0.236  -0.335
6     T         1.301   1.303   1.322   1.293   1.298   1.321   1.359   1.361   1.383
7     L        -0.151  -0.146  -0.194  -0.472  -0.462  -0.521  -0.281  -0.273  -0.345
8     Q         1.301   1.303   1.322   1.278   1.276   1.307   1.359   1.361   1.383
9     R        -0.151  -0.146  -0.194   0.006   0.011  -0.066  -0.281  -0.273  -0.345
10    Q         1.301   1.303   1.322   1.278   1.276   1.307   1.359   1.361   1.383
11    P         1.301   1.303   1.322   1.367   1.370   1.394   1.359   1.361   1.383
12    R         1.301   1.303   1.322   1.439   1.441   1.466   1.359   1.361   1.383
13    T        -0.151  -0.146  -0.194  -0.126  -0.119  -0.190  -0.281  -0.273  -0.345
14    I        -0.151  -0.146  -0.194  -0.060  -0.055  -0.128  -0.281  -0.273  -0.345
15    S        -0.151  -0.146  -0.194  -0.194  -0.184  -0.270  -0.281  -0.273  -0.345
16    L         1.301   1.303   1.322   0.955   0.963   0.988   1.359   1.361   1.383
17    F         1.301   1.303   1.322   1.439   1.443   1.466   1.359   1.361   1.383
18    T         1.301   1.303   1.322   1.293   1.298   1.321   1.359   1.361   1.383
19    N        -0.151  -0.176  -0.204   0.084   0.041  -0.014  -0.281  -0.320  -0.360
20    D        -0.151  -0.146  -0.194  -0.250  -0.244  -0.347  -0.281  -0.273  -0.345
21    I        -0.151  -0.176  -0.204  -0.472  -0.504  -0.533  -0.281  -0.320  -0.360
22    A        -0.151  -0.176  -0.204  -0.033  -0.071  -0.114  -0.281  -0.320  -0.360
23    S        -0.151  -0.123  -0.188  -0.140  -0.095  -0.196  -0.281  -0.236  -0.335
24    N        -0.151  -0.176  -0.204  -0.140  -0.178  -0.221  -0.281  -0.320  -0.360
25    I        -1.205  -1.202  -1.173  -0.932  -0.931  -0.879  -1.101  -1.095  -1.045
26    K        -0.280  -0.279  -0.252  -0.477  -0.475  -0.429  -0.486  -0.483  -0.438
27    S        -1.205  -1.202  -1.173  -0.932  -0.935  -0.879  -1.101  -1.095  -1.045
28    Q        -0.151  -0.123  -0.188  -0.362  -0.310  -0.453  -0.281  -0.236  -0.335
29    K        -1.205  -1.202  -1.173  -1.272  -1.275  -1.215  -1.101  -1.095  -1.045
30    C        -1.205  -1.202  -1.173  -1.187  -1.173  -1.132  -1.101  -1.095  -1.045
31    L         1.301   1.303   1.322   0.955   0.963   0.988   1.359   1.361   1.383
32    Q        -1.205  -1.202  -1.173  -1.169  -1.169  -1.113  -1.101  -1.095  -1.045
33    L        -1.205  -1.202  -1.173  -1.133  -1.146  -1.077  -1.101  -1.095  -1.045
34    L         1.301   1.303   1.322   0.955   0.963   0.988   1.359   1.361   1.383
35    K         1.301   1.303   1.322   1.081   1.083   1.112   1.359   1.361   1.383
36    G        -0.151  -0.176  -0.204  -0.093  -0.129  -0.164  -0.281  -0.320  -0.360
37    D        -1.205  -1.202  -1.173  -0.966  -0.969  -0.912  -1.101  -1.095  -1.045
38    V        -1.205  -1.202  -1.173  -0.974  -0.966  -0.921  -1.101  -1.095  -1.045
39    S        -1.205  -1.202  -1.173  -1.349  -1.341  -1.291  -1.101  -1.095  -1.045
40    H        -0.151  -0.176  -0.204   0.026  -0.012  -0.051  -0.281  -0.320  -0.360
41    R        -0.151  -0.146  -0.194  -0.153  -0.148  -0.256  -0.281  -0.273  -0.345
42    F        -0.151  -0.146  -0.194  -0.027  -0.020  -0.105  -0.281  -0.273  -0.345
43    D        -0.151  -0.146  -0.194  -0.100  -0.095  -0.168  -0.281  -0.273  -0.345
44    V        -1.205  -1.202  -1.173  -1.281  -1.262  -1.224  -1.101  -1.095  -1.045
45    E         1.301   1.303   1.322   1.381   1.387   1.409   1.359   1.361   1.383
46    I        -0.151  -0.123  -0.188  -0.277  -0.220  -0.372  -0.281  -0.236  -0.335
47    A        -1.205  -1.202  -1.173  -0.932  -0.922  -0.879  -1.101  -1.095  -1.045
48    N        -1.205  -1.202  -1.173  -1.151  -1.145  -1.095  -1.101  -1.095  -1.045
49    R        -0.151  -0.176  -0.204  -0.320  -0.357  -0.383  -0.281  -0.320  -0.360
50    F         1.301   1.303   1.322   1.439   1.443   1.466   1.359   1.361   1.383
51    P         1.301   1.303   1.322   1.367   1.370   1.394   1.359   1.361   1.383
52    T         1.301   1.303   1.322   1.293   1.298   1.321   1.359   1.361   1.383
53    W        -1.205  -1.202  -1.173  -1.197  -1.176  -1.141  -1.101  -1.095  -1.045
54    D         1.301   1.303   1.322   1.337   1.338   1.365   1.359   1.361   1.383
55    Q         1.301   1.303   1.322   1.278   1.276   1.307   1.359   1.361   1.383
56    L        -0.151  -0.123  -0.188  -0.435  -0.394  -0.470  -0.281  -0.236  -0.335
57    Q        -1.205  -1.202  -1.173  -1.017  -1.022  -0.963  -1.101  -1.095  -1.045
58    Y         1.301   1.303   1.322   1.568   1.571   1.594   1.359   1.361   1.383
59    M        -0.151  -0.146  -0.194  -0.140  -0.128  -0.257  -0.281  -0.273  -0.345
60    R        -1.205  -1.202  -1.173  -0.949  -0.945  -0.895  -1.101  -1.095  -1.045
61    T        -1.205  -1.202  -1.173  -1.234  -1.233  -1.178  -1.101  -1.095  -1.045
62    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    C        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    Q        -0.151  -0.176  -0.204  -0.133  -0.182  -0.232  -0.281  -0.320  -0.360
66    G        -1.205  -1.202  -1.173  -0.983  -0.978  -0.929  -1.101  -1.095  -1.045
67    P        -0.151  -0.146  -0.194  -0.222  -0.215  -0.320  -0.281  -0.273  -0.345
68    V        -1.205  -1.202  -1.173  -0.949  -0.948  -0.895  -1.101  -1.095  -1.045
69    S        -1.205  -1.202  -1.173  -1.142  -1.140  -1.086  -1.101  -1.095  -1.045
70    L         1.301   1.303   1.322   0.955   0.963   0.988   1.359   1.361   1.383
71    Q        -1.205  -1.202  -1.173  -1.000  -1.005  -0.946  -1.101  -1.095  -1.045
72    R        -1.205  -1.202  -1.173  -0.966  -0.962  -0.912  -1.101  -1.095  -1.045
73    Q         1.301   1.303   1.322   1.278   1.276   1.307   1.359   1.361   1.383
74    I         1.301   1.303   1.322   1.367   1.369   1.394   1.359   1.361   1.383
75    P         1.301   1.303   1.322   1.367   1.370   1.394   1.359   1.361   1.383
76    K        -0.151  -0.123  -0.188  -0.270  -0.233  -0.305  -0.281  -0.236  -0.335
77    L        -0.151  -0.146  -0.194  -0.509  -0.497  -0.565  -0.281  -0.273  -0.345
78    D        -1.205  -1.202  -1.173  -1.133  -1.126  -1.077  -1.101  -1.095  -1.045
79    S        -0.151  -0.123  -0.188  -0.292  -0.237  -0.373  -0.281  -0.236  -0.335
80    V        -1.205  -1.202  -1.173  -1.281  -1.273  -1.224  -1.101  -1.095  -1.045
81    L        -0.151  -0.123  -0.188  -0.398  -0.358  -0.428  -0.281  -0.236  -0.335
82    K         1.301   1.303   1.322   1.081   1.083   1.112   1.359   1.361   1.383
83    Y        -1.205  -1.202  -1.173  -1.378  -1.350  -1.320  -1.101  -1.095  -1.045
84    K        -0.151  -0.146  -0.194  -0.306  -0.300  -0.354  -0.281  -0.273  -0.345
85    H        -1.205  -1.202  -1.173  -0.957  -0.944  -0.904  -1.101  -1.095  -1.045
86    T        -1.205  -1.202  -1.173  -0.991  -0.993  -0.938  -1.101  -1.095  -1.045
87    D         1.301   1.303   1.322   1.337   1.338   1.365   1.359   1.361   1.383
88    P         1.301   1.303   1.322   1.367   1.370   1.394   1.359   1.361   1.383
89    T        -0.151  -0.176  -0.204  -0.509  -0.542  -0.578  -0.281  -0.320  -0.360
90    F         1.301   1.303   1.322   1.439   1.443   1.466   1.359   1.361   1.383
91    G         1.301   1.303   1.322   1.511   1.513   1.537   1.359   1.361   1.383
92    M        -0.151  -0.176  -0.204  -0.093  -0.127  -0.164  -0.281  -0.320  -0.360
93    D        -1.205  -1.202  -1.173  -1.151  -1.149  -1.095  -1.101  -1.095  -1.045
94    L         1.301   1.303   1.322   0.955   0.963   0.988   1.359   1.361   1.383
95    Q        -0.151  -0.123  -0.188  -0.208  -0.165  -0.272  -0.281  -0.236  -0.335
96    K        -0.151  -0.123  -0.188  -0.370  -0.328  -0.420  -0.281  -0.236  -0.335
97    C         1.301   1.303   1.322   1.582   1.585   1.608   1.359   1.361   1.383
98    V         1.301   1.303   1.322   1.439   1.440   1.466   1.359   1.361   1.383
99    Q        -1.205  -1.202  -1.173  -1.169  -1.166  -1.113  -1.101  -1.095  -1.045
100   R        -1.205  -1.202  -1.173  -1.178  -1.166  -1.123  -1.101  -1.095  -1.045
101   G         1.301   1.303   1.322   1.511   1.513   1.537   1.359   1.361   1.383
102   L        -1.205  -1.202  -1.173  -1.329  -1.337  -1.272  -1.101  -1.095  -1.045
103   W         1.301   1.303   1.322   1.497   1.499   1.523   1.359   1.361   1.383
104   N         1.301   1.303   1.322   1.410   1.413   1.438   1.359   1.361   1.383
105   P        -0.151  -0.176  -0.204  -0.355  -0.394  -0.426  -0.281  -0.320  -0.360
106   K        -1.205  -1.202  -1.173  -1.300  -1.308  -1.243  -1.101  -1.095  -1.045
107   E        -1.205  -1.202  -1.173  -1.052  -1.048  -0.998  -1.101  -1.095  -1.045
108   A        -1.205  -1.202  -1.173  -1.061  -1.052  -1.007  -1.101  -1.095  -1.045
109   L         1.301   1.303   1.322   0.955   0.963   0.988   1.359   1.361   1.383
110   W         1.301   1.303   1.322   1.497   1.499   1.523   1.359   1.361   1.383
111   V         1.301   1.303   1.322   1.439   1.440   1.466   1.359   1.361   1.383
112   D         1.301   1.303   1.322   1.337   1.338   1.365   1.359   1.361   1.383
113   W         1.301   1.303   1.322   1.497   1.499   1.523   1.359   1.361   1.383
114   E         1.301   1.303   1.322   1.381   1.387   1.409   1.359   1.361   1.383
115   N        -0.151  -0.176  -0.204  -0.334  -0.372  -0.400  -0.281  -0.320  -0.360
116   K        -0.151  -0.146  -0.194  -0.306  -0.300  -0.354  -0.281  -0.273  -0.345
117   L        -1.205  -1.202  -1.173  -1.215  -1.227  -1.159  -1.101  -1.095  -1.045
118   V        -0.151  -0.176  -0.204  -0.435  -0.466  -0.489  -0.281  -0.320  -0.360
119   G         1.301   1.303   1.322   1.511   1.513   1.537   1.359   1.361   1.383
120   N        -0.151  -0.176  -0.204  -0.140  -0.178  -0.221  -0.281  -0.320  -0.360
121   E        -1.205  -1.202  -1.173  -1.133  -1.125  -1.077  -1.101  -1.095  -1.045
122   P        -1.205  -1.202  -1.173  -1.281  -1.264  -1.224  -1.101  -1.095  -1.045
123   A        -0.151  -0.176  -0.204  -0.126  -0.169  -0.200  -0.281  -0.320  -0.360
124   D        -0.151  -0.176  -0.204  -0.174  -0.215  -0.262  -0.281  -0.320  -0.360
125   I        -0.151  -0.146  -0.194  -0.277  -0.268  -0.387  -0.281  -0.273  -0.345
126   D        -0.151  -0.176  -0.204  -0.370  -0.411  -0.443  -0.281  -0.320  -0.360
127   K        -0.151  -0.176  -0.204  -0.208  -0.258  -0.328  -0.281  -0.320  -0.360
128   Y        -0.280  -0.279  -0.252  -0.390  -0.388  -0.343  -0.486  -0.483  -0.438
129   I        -1.205  -1.202  -1.173  -1.243  -1.227  -1.187  -1.101  -1.095  -1.045
130   I        -0.151  -0.176  -0.204  -0.472  -0.504  -0.533  -0.281  -0.320  -0.360
131   Q        -1.205  -1.202  -1.173  -1.124  -1.125  -1.069  -1.101  -1.095  -1.045
132   R        -0.151  -0.176  -0.204  -0.320  -0.357  -0.383  -0.281  -0.320  -0.360
133   K        -1.205  -1.202  -1.173  -1.243  -1.250  -1.187  -1.101  -1.095  -1.045
* 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/P36141
Output conservation file - output/P36141
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
