1     M         1.047   1.047   1.047   1.309   1.309   1.309   1.047   1.047   1.047
2     I        -0.947  -0.947  -0.947  -1.212  -1.212  -1.212  -0.947  -0.947  -0.947
3     P         1.047   1.047   1.047   1.209   1.209   1.209   1.047   1.047   1.047
4     A        -0.947  -0.947  -0.947  -0.714  -0.714  -0.714  -0.947  -0.947  -0.947
5     P         1.047   1.047   1.047   1.209   1.209   1.209   1.047   1.047   1.047
6     L        -0.947  -0.947  -0.947  -1.072  -1.072  -1.072  -0.947  -0.947  -0.947
7     D         1.047   1.047   1.047   0.952   0.952   0.952   1.047   1.047   1.047
8     A         1.047   1.047   1.047   1.158   1.158   1.158   1.047   1.047   1.047
9     S        -0.947  -0.947  -0.947  -0.899  -0.899  -0.899  -0.947  -0.947  -0.947
10    L         1.047   1.047   1.047   0.872   0.872   0.872   1.047   1.047   1.047
11    L         1.047   1.047   1.047   0.872   0.872   0.872   1.047   1.047   1.047
12    R         1.047   1.047   1.047   1.259   1.259   1.259   1.047   1.047   1.047
13    E         1.047   1.047   1.047   1.158   1.158   1.158   1.047   1.047   1.047
14    H         1.047   1.047   1.047   1.259   1.259   1.259   1.047   1.047   1.047
15    A         1.047   1.047   1.047   1.158   1.158   1.158   1.047   1.047   1.047
16    F        -0.947  -0.947  -0.947  -0.994  -0.994  -0.994  -0.947  -0.947  -0.947
17    Q        -0.947  -0.947  -0.947  -0.625  -0.625  -0.625  -0.947  -0.947  -0.947
18    G        -0.947  -0.947  -0.947  -1.013  -1.013  -1.013  -0.947  -0.947  -0.947
19    T         1.047   1.047   1.047   1.133   1.133   1.133   1.047   1.047   1.047
20    N        -0.947  -0.947  -0.947  -0.769  -0.769  -0.769  -0.947  -0.947  -0.947
21    D        -0.947  -0.947  -0.947  -0.806  -0.806  -0.806  -0.947  -0.947  -0.947
22    L        -0.947  -0.947  -0.947  -1.111  -1.111  -1.111  -0.947  -0.947  -0.947
23    S        -0.947  -0.947  -0.947  -0.769  -0.769  -0.769  -0.947  -0.947  -0.947
24    T        -0.947  -0.947  -0.947  -1.013  -1.013  -1.013  -0.947  -0.947  -0.947
25    V         1.047   1.047   1.047   1.004   1.004   1.004   1.047   1.047   1.047
26    L         1.047   1.047   1.047   0.872   0.872   0.872   1.047   1.047   1.047
27    S        -0.947  -0.947  -0.947  -1.052  -1.052  -1.052  -0.947  -0.947  -0.947
28    P        -0.947  -0.947  -0.947  -0.956  -0.956  -0.956  -0.947  -0.947  -0.947
29    S        -0.947  -0.947  -0.947  -1.052  -1.052  -1.052  -0.947  -0.947  -0.947
30    T         1.047   1.047   1.047   1.133   1.133   1.133   1.047   1.047   1.047
31    F         1.047   1.047   1.047   1.056   1.056   1.056   1.047   1.047   1.047
32    T         1.047   1.047   1.047   1.133   1.133   1.133   1.047   1.047   1.047
33    D         1.047   1.047   1.047   0.952   0.952   0.952   1.047   1.047   1.047
34    E        -0.947  -0.947  -0.947  -0.899  -0.899  -0.899  -0.947  -0.947  -0.947
35    G         1.047   1.047   1.047   1.004   1.004   1.004   1.047   1.047   1.047
36    G         1.047   1.047   1.047   1.004   1.004   1.004   1.047   1.047   1.047
37    Y         1.047   1.047   1.047   0.925   0.925   0.925   1.047   1.047   1.047
38    K         1.047   1.047   1.047   0.952   0.952   0.952   1.047   1.047   1.047
39    P         1.047   1.047   1.047   1.209   1.209   1.209   1.047   1.047   1.047
40    V        -0.947  -0.947  -0.947  -1.111  -1.111  -1.111  -0.947  -0.947  -0.947
41    L        -0.947  -0.947  -0.947  -0.956  -0.956  -0.956  -0.947  -0.947  -0.947
42    K         1.047   1.047   1.047   0.952   0.952   0.952   1.047   1.047   1.047
43    Y         1.047   1.047   1.047   0.925   0.925   0.925   1.047   1.047   1.047
44    G         1.047   1.047   1.047   1.004   1.004   1.004   1.047   1.047   1.047
45    L         1.047   1.047   1.047   0.872   0.872   0.872   1.047   1.047   1.047
46    G         1.047   1.047   1.047   1.004   1.004   1.004   1.047   1.047   1.047
47    Y         1.047   1.047   1.047   0.925   0.925   0.925   1.047   1.047   1.047
48    F         1.047   1.047   1.047   1.056   1.056   1.056   1.047   1.047   1.047
49    N         1.047   1.047   1.047   1.284   1.284   1.284   1.047   1.047   1.047
50    Y         1.047   1.047   1.047   0.925   0.925   0.925   1.047   1.047   1.047
51    G        -0.947  -0.947  -0.947  -0.751  -0.751  -0.751  -0.947  -0.947  -0.947
52    L        -0.947  -0.947  -0.947  -1.033  -1.033  -1.033  -0.947  -0.947  -0.947
53    V        -0.947  -0.947  -0.947  -0.861  -0.861  -0.861  -0.947  -0.947  -0.947
54    I        -0.947  -0.947  -0.947  -1.212  -1.212  -1.212  -0.947  -0.947  -0.947
55    D        -0.947  -0.947  -0.947  -0.806  -0.806  -0.806  -0.947  -0.947  -0.947
56    D        -0.947  -0.947  -0.947  -1.052  -1.052  -1.052  -0.947  -0.947  -0.947
57    E        -0.947  -0.947  -0.947  -0.678  -0.678  -0.678  -0.947  -0.947  -0.947
58    V         1.047   1.047   1.047   1.004   1.004   1.004   1.047   1.047   1.047
59    Y        -0.947  -0.947  -0.947  -0.937  -0.937  -0.937  -0.947  -0.947  -0.947
60    D        -0.947  -0.947  -0.947  -0.899  -0.899  -0.899  -0.947  -0.947  -0.947
61    Y        -0.947  -0.947  -0.947  -1.033  -1.033  -1.033  -0.947  -0.947  -0.947
62    S         1.047   1.047   1.047   0.952   0.952   0.952   1.047   1.047   1.047
63    V        -0.947  -0.947  -0.947  -1.072  -1.072  -1.072  -0.947  -0.947  -0.947
64    C        -0.947  -0.947  -0.947  -0.806  -0.806  -0.806  -0.947  -0.947  -0.947
65    D        -0.947  -0.947  -0.947  -0.899  -0.899  -0.899  -0.947  -0.947  -0.947
66    I         1.047   1.047   1.047   0.819   0.819   0.819   1.047   1.047   1.047
67    I         1.047   1.047   1.047   0.819   0.819   0.819   1.047   1.047   1.047
68    R         1.047   1.047   1.047   1.259   1.259   1.259   1.047   1.047   1.047
69    G         1.047   1.047   1.047   1.004   1.004   1.004   1.047   1.047   1.047
70    H         1.047   1.047   1.047   1.259   1.259   1.259   1.047   1.047   1.047
71    V        -0.947  -0.947  -0.947  -1.111  -1.111  -1.111  -0.947  -0.947  -0.947
72    Y         1.047   1.047   1.047   0.925   0.925   0.925   1.047   1.047   1.047
73    D        -0.947  -0.947  -0.947  -0.899  -0.899  -0.899  -0.947  -0.947  -0.947
74    H        -0.947  -0.947  -0.947  -0.843  -0.843  -0.843  -0.947  -0.947  -0.947
75    F         1.047   1.047   1.047   1.056   1.056   1.056   1.047   1.047   1.047
76    W        -0.947  -0.947  -0.947  -0.661  -0.661  -0.661  -0.947  -0.947  -0.947
77    C        -0.947  -0.947  -0.947  -0.899  -0.899  -0.899  -0.947  -0.947  -0.947
78    Y         1.047   1.047   1.047   0.925   0.925   0.925   1.047   1.047   1.047
79    F         1.047   1.047   1.047   1.056   1.056   1.056   1.047   1.047   1.047
80    C        -0.947  -0.947  -0.947  -0.769  -0.769  -0.769  -0.947  -0.947  -0.947
81    C        -0.947  -0.947  -0.947  -0.899  -0.899  -0.899  -0.947  -0.947  -0.947
82    F        -0.947  -0.947  -0.947  -1.072  -1.072  -1.072  -0.947  -0.947  -0.947
83    M        -0.947  -0.947  -0.947  -0.751  -0.751  -0.751  -0.947  -0.947  -0.947
84    I         1.047   1.047   1.047   0.819   0.819   0.819   1.047   1.047   1.047
85    L        -0.947  -0.947  -0.947  -1.212  -1.212  -1.212  -0.947  -0.947  -0.947
86    F        -0.947  -0.947  -0.947  -1.033  -1.033  -1.033  -0.947  -0.947  -0.947
87    T        -0.947  -0.947  -0.947  -0.769  -0.769  -0.769  -0.947  -0.947  -0.947
88    I         1.047   1.047   1.047   0.819   0.819   0.819   1.047   1.047   1.047
89    W         1.047   1.047   1.047   1.309   1.309   1.309   1.047   1.047   1.047
90    L        -0.947  -0.947  -0.947  -1.212  -1.212  -1.212  -0.947  -0.947  -0.947
91    I        -0.947  -0.947  -0.947  -1.212  -1.212  -1.212  -0.947  -0.947  -0.947
92    S         1.047   1.047   1.047   0.952   0.952   0.952   1.047   1.047   1.047
93    L        -0.947  -0.947  -0.947  -1.072  -1.072  -1.072  -0.947  -0.947  -0.947
94    N        -0.947  -0.947  -0.947  -0.806  -0.806  -0.806  -0.947  -0.947  -0.947
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    W        -0.947  -0.947  -0.947  -0.643  -0.643  -0.643  -0.947  -0.947  -0.947
99    C         1.047   1.047   1.047   1.284   1.284   1.284   1.047   1.047   1.047
100   P        -0.947  -0.947  -0.947  -0.918  -0.918  -0.918  -0.947  -0.947  -0.947
101   S        -0.947  -0.947  -0.947  -0.918  -0.918  -0.918  -0.947  -0.947  -0.947
102   S        -0.947  -0.947  -0.947  -1.052  -1.052  -1.052  -0.947  -0.947  -0.947
103   K        -0.947  -0.947  -0.947  -0.824  -0.824  -0.824  -0.947  -0.947  -0.947
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   K        -0.947  -0.947  -0.947  -0.824  -0.824  -0.824  -0.947  -0.947  -0.947
106   S         1.047   1.047   1.047   0.952   0.952   0.952   1.047   1.047   1.047
107   K        -0.947  -0.947  -0.947  -0.899  -0.899  -0.899  -0.947  -0.947  -0.947
108   F         1.047   1.047   1.047   1.056   1.056   1.056   1.047   1.047   1.047
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   D        -0.947  -0.947  -0.947  -1.052  -1.052  -1.052  -0.947  -0.947  -0.947
114   W        -0.947  -0.947  -0.947  -0.806  -0.806  -0.806  -0.947  -0.947  -0.947
115   S         1.047   1.047   1.047   0.952   0.952   0.952   1.047   1.047   1.047
116   K         1.047   1.047   1.047   0.952   0.952   0.952   1.047   1.047   1.047
117   K         1.047   1.047   1.047   0.952   0.952   0.952   1.047   1.047   1.047
118   K        -0.947  -0.947  -0.947  -1.013  -1.013  -1.013  -0.947  -0.947  -0.947
119   D         1.047   1.047   1.047   0.952   0.952   0.952   1.047   1.047   1.047
120   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   D        -0.947  -0.947  -0.947  -1.013  -1.013  -1.013  -0.947  -0.947  -0.947
128   L        -0.947  -0.947  -0.947  -1.212  -1.212  -1.212  -0.947  -0.947  -0.947
129   E        -0.947  -0.947  -0.947  -0.899  -0.899  -0.899  -0.947  -0.947  -0.947
130   Y         1.047   1.047   1.047   0.925   0.925   0.925   1.047   1.047   1.047
131   Q        -0.947  -0.947  -0.947  -0.769  -0.769  -0.769  -0.947  -0.947  -0.947
132   H         1.047   1.047   1.047   1.259   1.259   1.259   1.047   1.047   1.047
133   V         1.047   1.047   1.047   1.004   1.004   1.004   1.047   1.047   1.047
134   K        -0.947  -0.947  -0.947  -0.769  -0.769  -0.769  -0.947  -0.947  -0.947
135   I        -0.947  -0.947  -0.947  -1.111  -1.111  -1.111  -0.947  -0.947  -0.947
* 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/P25361
Output conservation file - output/P25361
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
