1     M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
2     R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     D        -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     P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     H        -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     E        -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    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    M        -1.379  -1.645  -1.548  -0.797  -1.308  -1.247  -1.414  -1.772  -1.652
17    S         0.531   0.540   0.544  -0.167   0.055   0.077   0.537   0.545   0.552
18    D         0.531   0.540   0.544   0.918   0.870   0.829   0.537   0.545   0.552
19    Q        -1.379  -1.645  -1.548  -1.006  -1.606  -1.456  -1.414  -1.772  -1.652
20    M        -1.379  -1.645  -1.548  -0.797  -1.308  -1.247  -1.414  -1.772  -1.652
21    P         0.531   0.540   0.544   0.562   0.632   0.582   0.537   0.545   0.552
22    F         0.531   0.540   0.544  -0.030   0.099   0.171   0.537   0.545   0.552
23    P         0.531   0.540   0.544   0.562   0.632   0.582   0.537   0.545   0.552
24    F         0.531   0.540   0.544  -0.030   0.099   0.171   0.537   0.545   0.552
25    N         0.531   0.540   0.544   0.583   0.627   0.597   0.537   0.545   0.552
26    N         0.531   0.540   0.544   0.583   0.627   0.597   0.537   0.545   0.552
27    F         0.531   0.540   0.544  -0.030   0.099   0.171   0.537   0.545   0.552
28    T         0.531   0.540   0.544   0.433   0.451   0.493   0.537   0.545   0.552
29    Y         0.531   0.540   0.544   0.939   0.870   0.843   0.537   0.545   0.552
30    F         0.531   0.540   0.544  -0.030   0.099   0.171   0.537   0.545   0.552
31    F         0.531   0.540   0.544  -0.030   0.099   0.171   0.537   0.545   0.552
32    T         0.531   0.540   0.544   0.433   0.451   0.493   0.537   0.545   0.552
33    L         0.531   0.540   0.544   0.647   0.579   0.641   0.537   0.545   0.552
34    F         0.531   0.540   0.544  -0.030   0.099   0.171   0.537   0.545   0.552
35    S         0.531   0.540   0.544  -0.167   0.055   0.077   0.537   0.545   0.552
36    K         0.531   0.540   0.544   0.939   0.870   0.843   0.537   0.545   0.552
37    F         0.531   0.540   0.544  -0.030   0.099   0.171   0.537   0.545   0.552
38    F         0.531   0.540   0.544  -0.030   0.099   0.171   0.537   0.545   0.552
39    S         0.531   0.540   0.544  -0.167   0.055   0.077   0.537   0.545   0.552
40    S         0.531   0.540   0.544  -0.167   0.055   0.077   0.537   0.545   0.552
41    F         0.531   0.540   0.544  -0.030   0.099   0.171   0.537   0.545   0.552
42    H         0.531   0.540   0.544   0.752   0.741   0.714   0.537   0.545   0.552
43    H         0.531   0.540   0.544   0.752   0.741   0.714   0.537   0.545   0.552
44    C         0.531   0.540   0.544   1.020   0.915   0.900   0.537   0.545   0.552
45    T         0.531   0.540   0.544   0.433   0.451   0.493   0.537   0.545   0.552
46    C         0.531   0.540   0.544   1.020   0.915   0.900   0.537   0.545   0.552
47    S         0.531   0.540   0.544  -0.167   0.055   0.077   0.537   0.545   0.552
48    L         0.531   0.540   0.544   0.647   0.579   0.641   0.537   0.545   0.552
49    S         0.531   0.540   0.544  -0.167   0.055   0.077   0.537   0.545   0.552
50    V         0.531   0.540   0.544   1.122   0.976   0.970   0.537   0.545   0.552
51    S         0.531   0.540   0.544  -0.167   0.055   0.077   0.537   0.545   0.552
52    R         0.531   0.540   0.544   0.605   0.605   0.612   0.537   0.545   0.552
53    Q         0.531   0.540   0.544   0.939   0.870   0.843   0.537   0.545   0.552
54    Y         0.531   0.540   0.544   0.939   0.870   0.843   0.537   0.545   0.552
55    L         0.531   0.540   0.544   0.647   0.579   0.641   0.537   0.545   0.552
56    A         0.531   0.540   0.544   0.877   0.839   0.800   0.537   0.545   0.552
57    L         0.531   0.540   0.544   0.647   0.579   0.641   0.537   0.545   0.552
58    D         0.531   0.540   0.544   0.918   0.870   0.829   0.537   0.545   0.552
59    G         0.531   0.540   0.544   1.000   0.920   0.886   0.537   0.545   0.552
60    I         0.531   0.540   0.544   1.102   0.960   0.956   0.537   0.545   0.552
61    Y         0.531   0.540   0.544   0.939   0.870   0.843   0.537   0.545   0.552
62    H         0.531   0.540   0.544   0.752   0.741   0.714   0.537   0.545   0.552
63    P         0.531   0.540   0.544   0.562   0.632   0.582   0.537   0.545   0.552
64    L         0.531   0.540   0.544   0.647   0.579   0.641   0.537   0.545   0.552
65    R         0.531   0.540   0.544   0.605   0.605   0.612   0.537   0.545   0.552
66    A         0.531   0.540   0.544   0.877   0.839   0.800   0.537   0.545   0.552
67    A         0.531   0.540   0.544   0.877   0.839   0.800   0.537   0.545   0.552
68    F         0.531   0.540   0.544  -0.030   0.099   0.171   0.537   0.545   0.552
69    P         0.531   0.540   0.544   0.562   0.632   0.582   0.537   0.545   0.552
70    N         0.531   0.540   0.544   0.583   0.627   0.597   0.537   0.545   0.552
71    N         0.531   0.540   0.544   0.583   0.627   0.597   0.537   0.545   0.552
72    S         0.531   0.540   0.544  -0.167   0.055   0.077   0.537   0.545   0.552
73    T         0.531   0.540   0.544   0.433   0.451   0.493   0.537   0.545   0.552
74    L        -1.379  -1.006  -1.536  -1.334  -0.793  -1.612  -1.414  -0.898  -1.634
75    R         0.531   0.540   0.544   0.605   0.605   0.612   0.537   0.545   0.552
76    R        -2.038  -1.563  -1.531  -2.227  -1.514  -1.474  -2.390  -1.651  -1.627
77    H        -1.379  -1.645  -1.548  -1.204  -1.680  -1.585  -1.414  -1.772  -1.652
78    F         0.531   0.540   0.544  -0.030   0.099   0.171   0.537   0.545   0.552
79    T         0.531   0.540   0.544   0.433   0.451   0.493   0.537   0.545   0.552
80    K        -3.097  -2.788  -2.779  -2.984  -2.428  -2.433  -2.878  -2.433  -2.395
81    N         0.531   0.540   0.544   0.559   0.601   0.580   0.537   0.545   0.552
82    R        -1.616  -1.669  -1.553  -1.107  -1.480  -1.333  -1.750  -1.807  -1.658
83    T        -1.616  -1.669  -1.553  -1.479  -1.746  -1.580  -1.750  -1.807  -1.658
84    P         0.531   0.540   0.544   0.508   0.524   0.545   0.537   0.545   0.552
85    R         0.531   0.540   0.544   0.610   0.601   0.615   0.537   0.545   0.552
86    H         0.531   0.540   0.544   0.736   0.713   0.702   0.537   0.545   0.552
87    T         0.531   0.540   0.544   0.457   0.447   0.509   0.537   0.545   0.552
88    G         0.531   0.540   0.544   0.983   0.861   0.874   0.537   0.545   0.552
89    F         0.531   0.540   0.544   0.011   0.172   0.200   0.537   0.545   0.552
90    S         0.531   0.540   0.544  -0.179   0.050   0.068   0.537   0.545   0.552
91    P         0.531   0.540   0.544   0.508   0.524   0.545   0.537   0.545   0.552
92    S         0.531   0.540   0.544  -0.179   0.050   0.068   0.537   0.545   0.552
93    M         0.531   0.540   0.544   1.031   0.934   0.908   0.537   0.545   0.552
94    T         0.531   0.540   0.544   0.457   0.447   0.509   0.537   0.545   0.552
95    S         0.531   0.540   0.544  -0.179   0.050   0.068   0.537   0.545   0.552
96    C         0.531   0.540   0.544   1.031   0.934   0.908   0.537   0.545   0.552
97    S         0.531   0.540   0.544  -0.179   0.050   0.068   0.537   0.545   0.552
98    K         0.531   0.540   0.544   0.934   0.861   0.840   0.537   0.545   0.552
99    E         0.531   0.540   0.544   1.128   1.007   0.975   0.537   0.545   0.552
100   H         0.531   0.540   0.544   0.736   0.713   0.702   0.537   0.545   0.552
101   R         0.531   0.540   0.544   0.610   0.601   0.615   0.537   0.545   0.552
102   Q         0.531   0.540   0.544   0.934   0.861   0.840   0.537   0.545   0.552
103   G         0.531   0.540   0.544   0.983   0.861   0.874   0.537   0.545   0.552
104   T        -1.616  -1.669  -1.553  -1.868  -2.026  -1.786  -1.750  -1.807  -1.658
105   A         0.531   0.540   0.544   0.860   0.825   0.789   0.537   0.545   0.552
106   P        -1.379  -1.006  -1.536  -1.524  -0.934  -1.746  -1.414  -0.898  -1.634
107   K        -1.379  -1.645  -1.548  -1.016  -1.590  -1.476  -1.414  -1.772  -1.652
108   L        -1.379  -1.645  -1.548  -1.174  -1.589  -1.384  -1.414  -1.772  -1.652
109   P        -1.379  -1.645  -1.548  -1.261  -1.557  -1.437  -1.414  -1.772  -1.652
110   S         0.531   0.540   0.544  -0.167   0.055   0.077   0.537   0.545   0.552
111   P        -1.379  -1.006  -1.536  -2.123  -1.329  -2.085  -1.414  -0.898  -1.634
112   N        -1.379  -1.645  -1.548  -1.329  -1.700  -1.594  -1.414  -1.772  -1.652
113   Y        -1.379  -1.645  -1.548  -0.921  -1.396  -1.292  -1.414  -1.772  -1.652
114   N        -1.379  -1.645  -1.548  -1.240  -1.561  -1.426  -1.414  -1.772  -1.652
115   S        -1.379  -1.645  -1.548  -2.100  -2.275  -2.045  -1.414  -1.772  -1.652
116   G        -3.097  -2.788  -2.779  -2.811  -2.567  -2.476  -2.878  -2.433  -2.395
117   T        -3.097  -2.788  -2.779  -2.729  -2.556  -2.537  -2.878  -2.433  -2.395
118   E        -1.379  -1.645  -1.548  -0.700  -1.246  -1.168  -1.414  -1.772  -1.652
119   G        -1.379  -1.006  -1.536  -0.941  -0.455  -1.284  -1.414  -0.898  -1.634
120   T        -3.097  -2.788  -2.779  -2.811  -2.348  -2.442  -2.878  -2.433  -2.395
121   R        -1.379  -1.645  -1.548  -1.529  -2.155  -2.024  -1.414  -1.772  -1.652
122   F         0.531   0.540   0.544  -0.030   0.099   0.171   0.537   0.545   0.552
123   Q         0.531   0.540   0.544   0.939   0.870   0.843   0.537   0.545   0.552
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   I        -1.379  -1.645  -1.548  -0.896  -1.610  -1.467  -1.414  -1.772  -1.652
* 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/Q8TGM6
Output conservation file - output/Q8TGM6
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
