1     M         1.344   1.346   1.367   1.568   1.572   1.598   1.410   1.411   1.435
2     F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     C        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    M         1.344   1.346   1.367   1.583   1.584   1.613   1.410   1.411   1.435
17    P        -0.311  -0.310  -0.278  -0.137  -0.134  -0.085  -0.509  -0.507  -0.454
18    N        -0.176  -0.188  -0.221  -0.041  -0.054  -0.100  -0.296  -0.315  -0.363
19    R        -1.279  -1.276  -1.240  -1.151  -1.146  -1.085  -1.149  -1.144  -1.083
20    S        -0.176  -0.193  -0.221  -0.050  -0.073  -0.124  -0.296  -0.322  -0.363
21    E        -0.176  -0.139  -0.207  -0.101  -0.028  -0.181  -0.296  -0.239  -0.341
22    E         1.344   1.346   1.367   1.226   1.228   1.261   1.410   1.411   1.435
23    L         1.344   1.346   1.367   1.061   1.063   1.098   1.410   1.411   1.435
24    D         1.344   1.346   1.367   1.360   1.362   1.393   1.410   1.411   1.435
25    R        -0.311  -0.310  -0.278  -0.194  -0.190  -0.141  -0.509  -0.507  -0.454
26    L         1.344   1.346   1.367   1.030   1.035   1.067   1.410   1.411   1.435
27    L        -0.176  -0.188  -0.221  -0.394  -0.406  -0.431  -0.296  -0.315  -0.363
28    D        -0.176  -0.193  -0.221  -0.214  -0.243  -0.288  -0.296  -0.322  -0.363
29    K        -0.176  -0.193  -0.221  -0.330  -0.355  -0.379  -0.296  -0.322  -0.363
30    I        -0.176  -0.193  -0.221  -0.385  -0.420  -0.493  -0.296  -0.322  -0.363
31    I        -0.176  -0.188  -0.221  -0.127  -0.145  -0.184  -0.296  -0.315  -0.363
32    N        -0.176  -0.193  -0.221  -0.267  -0.298  -0.370  -0.296  -0.322  -0.363
33    S        -0.176  -0.188  -0.221  -0.127  -0.147  -0.215  -0.296  -0.315  -0.363
34    P        -1.279  -1.276  -1.240  -1.060  -1.062  -0.996  -1.149  -1.144  -1.083
35    H        -1.279  -1.276  -1.240  -0.908  -0.903  -0.846  -1.149  -1.144  -1.083
36    R        -1.279  -1.276  -1.240  -1.415  -1.417  -1.346  -1.149  -1.144  -1.083
37    T        -0.176  -0.188  -0.221   0.034   0.016  -0.050  -0.296  -0.315  -0.363
38    E        -0.176  -0.193  -0.221  -0.285  -0.308  -0.331  -0.296  -0.322  -0.363
39    A        -1.279  -1.276  -1.240  -0.834  -0.829  -0.773  -1.149  -1.144  -1.083
40    S        -0.176  -0.188  -0.221  -0.008  -0.025  -0.073  -0.296  -0.315  -0.363
41    K        -1.279  -1.276  -1.240  -1.440  -1.426  -1.371  -1.149  -1.144  -1.083
42    T        -1.279  -1.276  -1.240  -1.105  -1.104  -1.040  -1.149  -1.144  -1.083
43    L         1.344   1.346   1.367   1.030   1.035   1.067   1.410   1.411   1.435
44    Q        -0.176  -0.139  -0.207  -0.330  -0.280  -0.361  -0.296  -0.239  -0.341
45    E         1.344   1.346   1.367   1.150   1.151   1.186   1.410   1.411   1.435
46    I        -0.176  -0.188  -0.221  -0.385  -0.410  -0.493  -0.296  -0.315  -0.363
47    E        -0.176  -0.188  -0.221  -0.285  -0.303  -0.330  -0.296  -0.315  -0.363
48    N        -1.279  -1.276  -1.240  -1.128  -1.121  -1.063  -1.149  -1.144  -1.083
49    N         1.344   1.346   1.367   1.401   1.406   1.433   1.410   1.411   1.435
50    Q        -1.279  -1.276  -1.240  -1.049  -1.050  -0.985  -1.149  -1.144  -1.083
51    S        -1.279  -1.276  -1.240  -1.491  -1.497  -1.421  -1.149  -1.144  -1.083
52    Y         1.344   1.346   1.367   1.605   1.609   1.634   1.410   1.411   1.435
53    I         1.344   1.346   1.367   1.325   1.324   1.358   1.410   1.411   1.435
54    L        -1.279  -1.276  -1.240  -1.491  -1.470  -1.421  -1.149  -1.144  -1.083
55    N        -0.176  -0.139  -0.207  -0.214  -0.156  -0.264  -0.296  -0.239  -0.341
56    V         1.344   1.346   1.367   1.587   1.587   1.616   1.410   1.411   1.435
57    Q         1.344   1.346   1.367   1.531   1.534   1.562   1.410   1.411   1.435
58    L        -0.176  -0.188  -0.221  -0.403  -0.414  -0.442  -0.296  -0.315  -0.363
59    K         1.344   1.346   1.367   1.130   1.129   1.166   1.410   1.411   1.435
60    K         1.344   1.346   1.367   1.130   1.129   1.166   1.410   1.411   1.435
61    L         1.344   1.346   1.367   1.030   1.035   1.067   1.410   1.411   1.435
62    L        -0.176  -0.193  -0.221  -0.622  -0.651  -0.704  -0.296  -0.322  -0.363
63    R        -1.279  -1.276  -1.240  -1.466  -1.472  -1.396  -1.149  -1.144  -1.083
64    L         1.344   1.346   1.367   1.030   1.035   1.067   1.410   1.411   1.435
65    H         1.344   1.346   1.367   1.659   1.662   1.688   1.410   1.411   1.435
66    D         1.344   1.346   1.367   1.325   1.323   1.358   1.410   1.411   1.435
67    D        -1.279  -1.276  -1.240  -1.328  -1.325  -1.260  -1.149  -1.144  -1.083
68    S        -0.176  -0.193  -0.221  -0.214  -0.247  -0.320  -0.296  -0.322  -0.363
69    F         1.344   1.346   1.367   1.713   1.714   1.741   1.410   1.411   1.435
70    K        -0.176  -0.188  -0.221  -0.431  -0.454  -0.500  -0.296  -0.315  -0.363
71    N        -0.176  -0.139  -0.207  -0.376  -0.317  -0.417  -0.296  -0.239  -0.341
72    K        -0.176  -0.188  -0.221  -0.348  -0.366  -0.401  -0.296  -0.315  -0.363
73    C        -0.176  -0.193  -0.221   0.237   0.207   0.153  -0.296  -0.322  -0.363
74    V        -0.176  -0.188  -0.221   0.165   0.147   0.102  -0.296  -0.315  -0.363
75    S        -0.176  -0.139  -0.207   0.034   0.098  -0.025  -0.296  -0.239  -0.341
76    P         1.344   1.346   1.367   1.623   1.626   1.652   1.410   1.411   1.435
77    I        -1.279  -1.276  -1.240  -1.365  -1.358  -1.297  -1.149  -1.144  -1.083
78    N        -1.279  -1.276  -1.240  -1.402  -1.400  -1.334  -1.149  -1.144  -1.083
79    Y        -1.279  -1.276  -1.240  -1.162  -1.161  -1.097  -1.149  -1.144  -1.083
80    M        -0.176  -0.139  -0.207  -0.403  -0.350  -0.427  -0.296  -0.239  -0.341
81    L        -1.279  -1.276  -1.240  -1.466  -1.441  -1.396  -1.149  -1.144  -1.083
82    E        -0.176  -0.188  -0.221  -0.376  -0.392  -0.438  -0.296  -0.315  -0.363
83    K        -0.176  -0.188  -0.221  -0.348  -0.366  -0.401  -0.296  -0.315  -0.363
84    Y         1.344   1.346   1.367   1.605   1.609   1.634   1.410   1.411   1.435
85    T        -1.279  -1.276  -1.240  -0.972  -0.965  -0.909  -1.149  -1.144  -1.083
86    P        -1.279  -1.276  -1.240  -1.094  -1.095  -1.029  -1.149  -1.144  -1.083
87    Y        -1.279  -1.276  -1.240  -0.772  -0.762  -0.712  -1.149  -1.144  -1.083
88    M        -1.279  -1.276  -1.240  -1.128  -1.127  -1.063  -1.149  -1.144  -1.083
89    G        -1.279  -1.276  -1.240  -1.466  -1.479  -1.396  -1.149  -1.144  -1.083
90    H        -1.279  -1.276  -1.240  -0.983  -0.979  -0.920  -1.149  -1.144  -1.083
91    T        -1.279  -1.276  -1.240  -1.105  -1.105  -1.040  -1.149  -1.144  -1.083
92    E        -0.176  -0.139  -0.207  -0.084  -0.016  -0.164  -0.296  -0.239  -0.341
93    A        -0.176  -0.139  -0.207  -0.118  -0.068  -0.155  -0.296  -0.239  -0.341
94    L         1.344   1.346   1.367   1.030   1.035   1.067   1.410   1.411   1.435
95    Q         1.344   1.346   1.367   1.531   1.534   1.562   1.410   1.411   1.435
96    K        -0.176  -0.193  -0.221  -0.394  -0.420  -0.456  -0.296  -0.322  -0.363
97    E        -0.176  -0.193  -0.221  -0.196  -0.215  -0.226  -0.296  -0.322  -0.363
98    A         1.344   1.346   1.367   1.605   1.606   1.634   1.410   1.411   1.435
99    E         1.344   1.346   1.367   1.150   1.151   1.186   1.410   1.411   1.435
100   L         1.344   1.346   1.367   1.030   1.035   1.067   1.410   1.411   1.435
101   V        -0.176  -0.193  -0.221  -0.008  -0.040  -0.104  -0.296  -0.322  -0.363
102   D         1.344   1.346   1.367   1.325   1.323   1.358   1.410   1.411   1.435
103   R         1.344   1.346   1.367   1.494   1.499   1.525   1.410   1.411   1.435
104   D         1.344   1.346   1.367   1.325   1.323   1.358   1.410   1.411   1.435
105   L        -0.176  -0.139  -0.207  -0.385  -0.313  -0.462  -0.296  -0.239  -0.341
106   R         1.344   1.346   1.367   1.494   1.499   1.525   1.410   1.411   1.435
107   I         1.344   1.346   1.367   1.325   1.324   1.358   1.410   1.411   1.435
108   L        -0.176  -0.188  -0.221  -0.525  -0.542  -0.588  -0.296  -0.315  -0.363
109   E         1.344   1.346   1.367   1.150   1.151   1.186   1.410   1.411   1.435
110   M        -0.176  -0.193  -0.221   0.092   0.066   0.019  -0.296  -0.322  -0.363
111   T        -0.176  -0.188  -0.221   0.100   0.083   0.029  -0.296  -0.315  -0.363
112   Y        -0.176  -0.139  -0.207  -0.118  -0.066  -0.155  -0.296  -0.239  -0.341
113   Q        -0.176  -0.193  -0.221  -0.144  -0.178  -0.255  -0.296  -0.322  -0.363
114   L        -1.279  -1.276  -1.240  -1.530  -1.513  -1.460  -1.149  -1.144  -1.083
115   I        -0.176  -0.193  -0.221  -0.385  -0.420  -0.493  -0.296  -0.322  -0.363
116   E        -0.176  -0.188  -0.221  -0.376  -0.392  -0.438  -0.296  -0.315  -0.363
117   K        -0.176  -0.193  -0.221  -0.431  -0.462  -0.500  -0.296  -0.322  -0.363
118   N        -0.176  -0.193  -0.221  -0.258  -0.288  -0.360  -0.296  -0.322  -0.363
119   R        -1.279  -1.276  -1.240  -1.268  -1.265  -1.201  -1.149  -1.144  -1.083
120   N        -0.176  -0.188  -0.221  -0.118  -0.133  -0.192  -0.296  -0.315  -0.363
121   S        -1.279  -1.276  -1.240  -1.151  -1.145  -1.085  -1.149  -1.144  -1.083
122   K        -1.279  -1.276  -1.240  -1.162  -1.143  -1.097  -1.149  -1.144  -1.083
* 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/Q06071
Output conservation file - output/Q06071
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
