1     M         1.249   1.249   1.249   1.512   1.512   1.512   1.249   1.249   1.249
2     F        -0.795  -0.795  -0.795  -0.592  -0.592  -0.592  -0.795  -0.795  -0.795
3     Y         1.249   1.249   1.249   1.383   1.383   1.383   1.249   1.249   1.249
4     L        -0.795  -0.795  -0.795  -0.959  -0.959  -0.959  -0.795  -0.795  -0.795
5     S        -0.795  -0.795  -0.795  -0.919  -0.919  -0.919  -0.795  -0.795  -0.795
6     D        -0.795  -0.795  -0.795  -0.979  -0.979  -0.979  -0.795  -0.795  -0.795
7     I        -0.795  -0.795  -0.795  -0.555  -0.555  -0.555  -0.795  -0.795  -0.795
8     E        -0.795  -0.795  -0.795  -0.782  -0.782  -0.782  -0.795  -0.795  -0.795
9     E        -0.795  -0.795  -0.795  -0.801  -0.801  -0.801  -0.795  -0.795  -0.795
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    E         1.249   1.249   1.249   1.062   1.062   1.062   1.249   1.249   1.249
13    A        -0.795  -0.795  -0.795  -0.820  -0.820  -0.820  -0.795  -0.795  -0.795
14    S        -0.795  -0.795  -0.795  -0.919  -0.919  -0.919  -0.795  -0.795  -0.795
15    A        -0.795  -0.795  -0.795  -0.743  -0.743  -0.743  -0.795  -0.795  -0.795
16    G         1.249   1.249   1.249   1.537   1.537   1.537   1.249   1.249   1.249
17    A        -0.795  -0.795  -0.795  -0.464  -0.464  -0.464  -0.795  -0.795  -0.795
18    E         1.249   1.249   1.249   1.062   1.062   1.062   1.249   1.249   1.249
19    P        -0.795  -0.795  -0.795  -0.724  -0.724  -0.724  -0.795  -0.795  -0.795
20    T        -0.795  -0.795  -0.795  -1.020  -1.020  -1.020  -0.795  -0.795  -0.795
21    Y        -0.795  -0.795  -0.795  -0.705  -0.705  -0.705  -0.795  -0.795  -0.795
22    N        -0.795  -0.795  -0.795  -0.743  -0.743  -0.743  -0.795  -0.795  -0.795
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    F        -0.795  -0.795  -0.795  -0.879  -0.879  -0.879  -0.795  -0.795  -0.795
36    W        -0.795  -0.795  -0.795  -0.393  -0.393  -0.393  -0.795  -0.795  -0.795
37    E         1.249   1.249   1.249   1.062   1.062   1.062   1.249   1.249   1.249
38    V        -0.795  -0.795  -0.795  -0.519  -0.519  -0.519  -0.795  -0.795  -0.795
39    L        -0.795  -0.795  -0.795  -0.959  -0.959  -0.959  -0.795  -0.795  -0.795
40    L         1.249   1.249   1.249   0.839   0.839   0.839   1.249   1.249   1.249
41    F         1.249   1.249   1.249   1.613   1.613   1.613   1.249   1.249   1.249
42    S        -0.795  -0.795  -0.795  -0.919  -0.919  -0.919  -0.795  -0.795  -0.795
43    N        -0.795  -0.795  -0.795  -0.428  -0.428  -0.428  -0.795  -0.795  -0.795
44    T        -0.795  -0.795  -0.795  -0.840  -0.840  -0.840  -0.795  -0.795  -0.795
45    Q         1.249   1.249   1.249   1.512   1.512   1.512   1.249   1.249   1.249
46    E        -0.795  -0.795  -0.795  -0.801  -0.801  -0.801  -0.795  -0.795  -0.795
47    N         1.249   1.249   1.249   1.588   1.588   1.588   1.249   1.249   1.249
48    L         1.249   1.249   1.249   0.839   0.839   0.839   1.249   1.249   1.249
49    V        -0.795  -0.795  -0.795  -0.537  -0.537  -0.537  -0.795  -0.795  -0.795
50    T        -0.795  -0.795  -0.795  -0.979  -0.979  -0.979  -0.795  -0.795  -0.795
51    V         1.249   1.249   1.249   1.434   1.434   1.434   1.249   1.249   1.249
52    V        -0.795  -0.795  -0.795  -0.840  -0.840  -0.840  -0.795  -0.795  -0.795
53    G        -0.795  -0.795  -0.795  -0.686  -0.686  -0.686  -0.795  -0.795  -0.795
54    E         1.249   1.249   1.249   1.062   1.062   1.062   1.249   1.249   1.249
55    L         1.249   1.249   1.249   0.839   0.839   0.839   1.249   1.249   1.249
56    H        -0.795  -0.795  -0.795  -0.648  -0.648  -0.648  -0.795  -0.795  -0.795
57    T        -0.795  -0.795  -0.795  -0.979  -0.979  -0.979  -0.795  -0.795  -0.795
58    L        -0.795  -0.795  -0.795  -1.020  -1.020  -1.020  -0.795  -0.795  -0.795
59    T         1.249   1.249   1.249   1.089   1.089   1.089   1.249   1.249   1.249
60    D         1.249   1.249   1.249   1.251   1.251   1.251   1.249   1.249   1.249
61    R        -0.795  -0.795  -0.795  -0.705  -0.705  -0.705  -0.795  -0.795  -0.795
62    V        -0.795  -0.795  -0.795  -0.519  -0.519  -0.519  -0.795  -0.795  -0.795
63    V        -0.795  -0.795  -0.795  -0.630  -0.630  -0.630  -0.795  -0.795  -0.795
64    H        -0.795  -0.795  -0.795  -0.555  -0.555  -0.555  -0.795  -0.795  -0.795
65    Y         1.249   1.249   1.249   1.383   1.383   1.383   1.249   1.249   1.249
66    K        -0.795  -0.795  -0.795  -0.705  -0.705  -0.705  -0.795  -0.795  -0.795
67    I        -0.795  -0.795  -0.795  -0.782  -0.782  -0.782  -0.795  -0.795  -0.795
68    E        -0.795  -0.795  -0.795  -0.939  -0.939  -0.939  -0.795  -0.795  -0.795
69    P         1.249   1.249   1.249   1.588   1.588   1.588   1.249   1.249   1.249
70    E        -0.795  -0.795  -0.795  -0.782  -0.782  -0.782  -0.795  -0.795  -0.795
71    S         1.249   1.249   1.249   1.330   1.330   1.330   1.249   1.249   1.249
72    R        -0.795  -0.795  -0.795  -0.762  -0.762  -0.762  -0.795  -0.795  -0.795
73    E        -0.795  -0.795  -0.795  -0.840  -0.840  -0.840  -0.795  -0.795  -0.795
74    V        -0.795  -0.795  -0.795  -0.375  -0.375  -0.375  -0.795  -0.795  -0.795
75    T         1.249   1.249   1.249   1.089   1.089   1.089   1.249   1.249   1.249
76    A        -0.795  -0.795  -0.795  -0.519  -0.519  -0.519  -0.795  -0.795  -0.795
77    T        -0.795  -0.795  -0.795  -0.979  -0.979  -0.979  -0.795  -0.795  -0.795
78    T         1.249   1.249   1.249   1.089   1.089   1.089   1.249   1.249   1.249
79    L         1.249   1.249   1.249   0.839   0.839   0.839   1.249   1.249   1.249
80    P         1.249   1.249   1.249   1.588   1.588   1.588   1.249   1.249   1.249
81    S        -0.795  -0.795  -0.795  -0.919  -0.919  -0.919  -0.795  -0.795  -0.795
82    L         1.249   1.249   1.249   0.839   0.839   0.839   1.249   1.249   1.249
83    L        -0.795  -0.795  -0.795  -0.959  -0.959  -0.959  -0.795  -0.795  -0.795
84    A         1.249   1.249   1.249   1.460   1.460   1.460   1.249   1.249   1.249
85    L        -0.795  -0.795  -0.795  -0.959  -0.959  -0.959  -0.795  -0.795  -0.795
86    L         1.249   1.249   1.249   0.839   0.839   0.839   1.249   1.249   1.249
87    L        -0.795  -0.795  -0.795  -0.959  -0.959  -0.959  -0.795  -0.795  -0.795
88    E        -0.795  -0.795  -0.795  -1.000  -1.000  -1.000  -0.795  -0.795  -0.795
89    K        -0.795  -0.795  -0.795  -0.428  -0.428  -0.428  -0.795  -0.795  -0.795
90    R         1.249   1.249   1.249   1.198   1.198   1.198   1.249   1.249   1.249
91    N        -0.795  -0.795  -0.795  -0.743  -0.743  -0.743  -0.795  -0.795  -0.795
92    Q        -0.795  -0.795  -0.795  -0.705  -0.705  -0.705  -0.795  -0.795  -0.795
93    A         1.249   1.249   1.249   1.460   1.460   1.460   1.249   1.249   1.249
94    R         1.249   1.249   1.249   1.198   1.198   1.198   1.249   1.249   1.249
95    R         1.249   1.249   1.249   1.198   1.198   1.198   1.249   1.249   1.249
96    L        -0.795  -0.795  -0.795  -0.959  -0.959  -0.959  -0.795  -0.795  -0.795
97    Y         1.249   1.249   1.249   1.383   1.383   1.383   1.249   1.249   1.249
98    R        -0.795  -0.795  -0.795  -0.705  -0.705  -0.705  -0.795  -0.795  -0.795
99    D         1.249   1.249   1.249   1.251   1.251   1.251   1.249   1.249   1.249
100   V        -0.795  -0.795  -0.795  -0.519  -0.519  -0.519  -0.795  -0.795  -0.795
101   L         1.249   1.249   1.249   0.839   0.839   0.839   1.249   1.249   1.249
102   S        -0.795  -0.795  -0.795  -0.648  -0.648  -0.648  -0.795  -0.795  -0.795
103   M        -0.795  -0.795  -0.795  -0.782  -0.782  -0.782  -0.795  -0.795  -0.795
104   K         1.249   1.249   1.249   1.512   1.512   1.512   1.249   1.249   1.249
105   M        -0.795  -0.795  -0.795  -0.574  -0.574  -0.574  -0.795  -0.795  -0.795
106   S         1.249   1.249   1.249   1.330   1.330   1.330   1.249   1.249   1.249
107   E         1.249   1.249   1.249   1.062   1.062   1.062   1.249   1.249   1.249
108   L        -0.795  -0.795  -0.795  -0.899  -0.899  -0.899  -0.795  -0.795  -0.795
109   D        -0.795  -0.795  -0.795  -0.611  -0.611  -0.611  -0.795  -0.795  -0.795
110   W         1.249   1.249   1.249   1.688   1.688   1.688   1.249   1.249   1.249
111   D         1.249   1.249   1.249   1.251   1.251   1.251   1.249   1.249   1.249
112   I        -0.795  -0.795  -0.795  -0.939  -0.939  -0.939  -0.795  -0.795  -0.795
113   D        -0.795  -0.795  -0.795  -1.000  -1.000  -1.000  -0.795  -0.795  -0.795
114   D        -0.795  -0.795  -0.795  -0.611  -0.611  -0.611  -0.795  -0.795  -0.795
115   L        -0.795  -0.795  -0.795  -0.939  -0.939  -0.939  -0.795  -0.795  -0.795
116   F        -0.795  -0.795  -0.795  -0.464  -0.464  -0.464  -0.795  -0.795  -0.795
117   T        -0.795  -0.795  -0.795  -0.782  -0.782  -0.782  -0.795  -0.795  -0.795
118   Q        -0.795  -0.795  -0.795  -0.801  -0.801  -0.801  -0.795  -0.795  -0.795
119   L         1.249   1.249   1.249   0.839   0.839   0.839   1.249   1.249   1.249
120   Q        -0.795  -0.795  -0.795  -0.801  -0.801  -0.801  -0.795  -0.795  -0.795
121   E        -0.795  -0.795  -0.795  -0.840  -0.840  -0.840  -0.795  -0.795  -0.795
122   E         1.249   1.249   1.249   1.062   1.062   1.062   1.249   1.249   1.249
123   L         1.249   1.249   1.249   0.839   0.839   0.839   1.249   1.249   1.249
124   T        -0.795  -0.795  -0.795  -0.919  -0.919  -0.919  -0.795  -0.795  -0.795
125   R         1.249   1.249   1.249   1.198   1.198   1.198   1.249   1.249   1.249
126   T         1.249   1.249   1.249   1.089   1.089   1.089   1.249   1.249   1.249
127   D         1.249   1.249   1.249   1.251   1.251   1.251   1.249   1.249   1.249
128   D        -0.795  -0.795  -0.795  -1.000  -1.000  -1.000  -0.795  -0.795  -0.795
129   T        -0.795  -0.795  -0.795  -1.294  -1.294  -1.294  -0.795  -0.795  -0.795
130   L         1.249   1.249   1.249   0.839   0.839   0.839   1.249   1.249   1.249
131   S         1.249   1.249   1.249   1.330   1.330   1.330   1.249   1.249   1.249
132   M        -0.795  -0.795  -0.795  -0.959  -0.959  -0.959  -0.795  -0.795  -0.795
133   Y         1.249   1.249   1.249   1.383   1.383   1.383   1.249   1.249   1.249
134   P         1.249   1.249   1.249   1.588   1.588   1.588   1.249   1.249   1.249
135   R        -0.795  -0.795  -0.795  -0.648  -0.648  -0.648  -0.795  -0.795  -0.795
136   R         1.249   1.249   1.249   1.198   1.198   1.198   1.249   1.249   1.249
137   R        -0.795  -0.795  -0.795  -0.686  -0.686  -0.686  -0.795  -0.795  -0.795
138   F        -0.795  -0.795  -0.795  -0.705  -0.705  -0.705  -0.795  -0.795  -0.795
139   Y        -0.795  -0.795  -0.795  -1.061  -1.061  -1.061  -0.795  -0.795  -0.795
140   H        -0.795  -0.795  -0.795  -0.648  -0.648  -0.648  -0.795  -0.795  -0.795
* 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/P53130
Output conservation file - output/P53130
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
