1     M         1.418   1.418   1.418   1.817   1.820   1.817   1.418   1.418   1.418
2     P        -0.699  -0.699  -0.699  -0.388  -0.375  -0.388  -0.699  -0.699  -0.699
3     S        -0.699  -0.699  -0.699  -0.729  -0.722  -0.729  -0.699  -0.699  -0.699
4     L         1.418   1.418   1.418   1.241   1.231   1.241   1.418   1.418   1.418
5     R        -0.699  -0.699  -0.699  -0.708  -0.722  -0.708  -0.699  -0.699  -0.699
6     D        -0.699  -0.699  -0.699  -0.899  -0.873  -0.899  -0.699  -0.699  -0.699
7     L        -0.699  -0.699  -0.699  -0.964  -0.985  -0.964  -0.699  -0.699  -0.699
8     S        -0.699  -0.699  -0.699  -0.447  -0.434  -0.447  -0.699  -0.699  -0.699
9     L        -0.699  -0.699  -0.699  -1.009  -1.030  -1.009  -0.699  -0.699  -0.699
10    E         1.418   1.418   1.418   1.155   1.142   1.155   1.418   1.418   1.418
11    R         1.418   1.418   1.418   1.494   1.489   1.494   1.418   1.418   1.418
12    D        -0.699  -0.699  -0.699  -0.899  -0.873  -0.899  -0.699  -0.699  -0.699
13    Q        -0.699  -0.699  -0.699  -0.771  -0.786  -0.771  -0.699  -0.699  -0.699
14    E        -0.699  -0.699  -0.699  -0.813  -0.829  -0.813  -0.699  -0.699  -0.699
15    L         1.418   1.418   1.418   1.241   1.231   1.241   1.418   1.418   1.418
16    N        -0.699  -0.699  -0.699  -0.667  -0.617  -0.667  -0.699  -0.699  -0.699
17    Q         1.418   1.418   1.418   1.212   1.201   1.212   1.418   1.418   1.418
18    L         1.418   1.418   1.418   1.241   1.231   1.241   1.418   1.418   1.418
19    R         1.418   1.418   1.418   1.494   1.489   1.494   1.418   1.418   1.418
20    A        -0.699  -0.699  -0.699  -0.447  -0.434  -0.447  -0.699  -0.699  -0.699
21    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    I         1.418   1.418   1.418   1.439   1.433   1.439   1.418   1.418   1.418
52    Q        -0.699  -0.699  -0.699  -0.667  -0.680  -0.667  -0.699  -0.699  -0.699
53    T         1.418   1.418   1.418   1.631   1.629   1.631   1.418   1.418   1.418
54    G        -0.699  -0.699  -0.699  -0.408  -0.375  -0.408  -0.699  -0.699  -0.699
55    Q        -0.699  -0.699  -0.699  -0.750  -0.743  -0.750  -0.699  -0.699  -0.699
56    S         1.418   1.418   1.418   1.522   1.546   1.522   1.418   1.418   1.418
57    S        -0.699  -0.699  -0.699  -0.585  -0.576  -0.585  -0.699  -0.699  -0.699
58    N        -0.699  -0.699  -0.699  -0.729  -0.722  -0.729  -0.699  -0.699  -0.699
59    A        -0.699  -0.699  -0.699  -0.312  -0.316  -0.312  -0.699  -0.699  -0.699
60    T        -0.699  -0.699  -0.699  -0.466  -0.474  -0.466  -0.699  -0.699  -0.699
61    N        -0.699  -0.699  -0.699  -0.667  -0.617  -0.667  -0.699  -0.699  -0.699
62    S        -0.699  -0.699  -0.699  -0.792  -0.786  -0.792  -0.699  -0.699  -0.699
63    F        -0.699  -0.699  -0.699  -0.236  -0.239  -0.236  -0.699  -0.699  -0.699
64    V        -0.699  -0.699  -0.699  -0.525  -0.535  -0.525  -0.699  -0.699  -0.699
65    Q        -0.699  -0.699  -0.699  -1.031  -1.053  -1.031  -0.699  -0.699  -0.699
66    E        -0.699  -0.699  -0.699  -1.031  -1.053  -1.031  -0.699  -0.699  -0.699
67    T        -0.699  -0.699  -0.699  -0.447  -0.434  -0.447  -0.699  -0.699  -0.699
68    I        -0.699  -0.699  -0.699  -0.525  -0.535  -0.525  -0.699  -0.699  -0.699
69    Q        -0.699  -0.699  -0.699  -1.031  -1.053  -1.031  -0.699  -0.699  -0.699
70    K        -0.699  -0.699  -0.699  -0.834  -0.808  -0.834  -0.699  -0.699  -0.699
71    T        -0.699  -0.699  -0.699  -0.447  -0.434  -0.447  -0.699  -0.699  -0.699
72    K        -0.699  -0.699  -0.699  -0.920  -0.940  -0.920  -0.699  -0.699  -0.699
73    Q        -0.699  -0.699  -0.699  -0.687  -0.701  -0.687  -0.699  -0.699  -0.699
74    K         1.418   1.418   1.418   1.298   1.289   1.298   1.418   1.418   1.418
75    E        -0.699  -0.699  -0.699  -0.942  -0.917  -0.942  -0.699  -0.699  -0.699
76    S        -0.699  -0.699  -0.699  -0.792  -0.786  -0.792  -0.699  -0.699  -0.699
77    G         1.418   1.418   1.418   1.685   1.711   1.685   1.418   1.418   1.418
78    Q         1.418   1.418   1.418   1.212   1.201   1.212   1.418   1.418   1.418
79    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    I        -0.699  -0.699  -0.699  -0.792  -0.808  -0.792  -0.699  -0.699  -0.699
82    I        -0.699  -0.699  -0.699  -0.525  -0.535  -0.525  -0.699  -0.699  -0.699
83    P        -0.699  -0.699  -0.699  -0.646  -0.659  -0.646  -0.699  -0.699  -0.699
84    Q        -0.699  -0.699  -0.699  -1.031  -1.053  -1.031  -0.699  -0.699  -0.699
85    K        -0.699  -0.699  -0.699  -0.626  -0.638  -0.626  -0.699  -0.699  -0.699
86    N         1.418   1.418   1.418   1.522   1.546   1.522   1.418   1.418   1.418
87    E        -0.699  -0.699  -0.699  -0.792  -0.786  -0.792  -0.699  -0.699  -0.699
88    H        -0.699  -0.699  -0.699  -0.525  -0.535  -0.525  -0.699  -0.699  -0.699
89    Q         1.418   1.418   1.418   1.212   1.201   1.212   1.418   1.418   1.418
90    R        -0.699  -0.699  -0.699  -0.813  -0.829  -0.813  -0.699  -0.699  -0.699
91    Y        -0.699  -0.699  -0.699  -0.545  -0.555  -0.545  -0.699  -0.699  -0.699
92    I        -0.699  -0.699  -0.699  -0.792  -0.808  -0.792  -0.699  -0.699  -0.699
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   D        -0.699  -0.699  -0.699  -0.899  -0.873  -0.899  -0.699  -0.699  -0.699
103   K        -0.699  -0.699  -0.699  -0.687  -0.680  -0.687  -0.699  -0.699  -0.699
104   V        -0.699  -0.699  -0.699  -0.350  -0.336  -0.350  -0.699  -0.699  -0.699
105   C        -0.699  -0.699  -0.699  -0.255  -0.239  -0.255  -0.699  -0.699  -0.699
106   E         1.418   1.418   1.418   1.155   1.142   1.155   1.418   1.418   1.418
107   T         1.418   1.418   1.418   1.631   1.629   1.631   1.418   1.418   1.418
108   S        -0.699  -0.699  -0.699  -0.447  -0.434  -0.447  -0.699  -0.699  -0.699
109   D         1.418   1.418   1.418   1.327   1.376   1.327   1.418   1.418   1.418
110   L        -0.699  -0.699  -0.699  -0.486  -0.494  -0.486  -0.699  -0.699  -0.699
111   K         1.418   1.418   1.418   1.298   1.289   1.298   1.418   1.418   1.418
112   A         1.418   1.418   1.418   1.631   1.629   1.631   1.418   1.418   1.418
113   K        -0.699  -0.699  -0.699  -0.920  -0.940  -0.920  -0.699  -0.699  -0.699
114   L         1.418   1.418   1.418   1.241   1.231   1.241   1.418   1.418   1.418
115   A        -0.699  -0.699  -0.699  -0.667  -0.680  -0.667  -0.699  -0.699  -0.699
116   P         1.418   1.418   1.418   1.711   1.711   1.711   1.418   1.418   1.418
117   I        -0.699  -0.699  -0.699  -0.813  -0.829  -0.813  -0.699  -0.699  -0.699
118   M        -0.699  -0.699  -0.699  -0.506  -0.515  -0.506  -0.699  -0.699  -0.699
119   E        -0.699  -0.699  -0.699  -0.942  -0.917  -0.942  -0.699  -0.699  -0.699
120   V        -0.699  -0.699  -0.699  -0.667  -0.680  -0.667  -0.699  -0.699  -0.699
121   L         1.418   1.418   1.418   1.241   1.231   1.241   1.418   1.418   1.418
122   E        -0.699  -0.699  -0.699  -0.964  -0.985  -0.964  -0.699  -0.699  -0.699
123   K         1.418   1.418   1.418   1.298   1.289   1.298   1.418   1.418   1.418
124   K         1.418   1.418   1.418   1.298   1.289   1.298   1.418   1.418   1.418
125   T         1.418   1.418   1.418   1.631   1.629   1.631   1.418   1.418   1.418
126   N        -0.699  -0.699  -0.699  -0.667  -0.617  -0.667  -0.699  -0.699  -0.699
127   E         1.418   1.418   1.418   1.155   1.142   1.155   1.418   1.418   1.418
128   K        -0.699  -0.699  -0.699  -0.606  -0.617  -0.606  -0.699  -0.699  -0.699
129   I         1.418   1.418   1.418   1.439   1.433   1.439   1.418   1.418   1.418
130   K         1.418   1.418   1.418   1.298   1.289   1.298   1.418   1.418   1.418
131   G        -0.699  -0.699  -0.699  -0.427  -0.414  -0.427  -0.699  -0.699  -0.699
132   I         1.418   1.418   1.418   1.439   1.433   1.439   1.418   1.418   1.418
133   I        -0.699  -0.699  -0.699  -0.792  -0.808  -0.792  -0.699  -0.699  -0.699
134   R         1.418   1.418   1.418   1.494   1.489   1.494   1.418   1.418   1.418
135   K        -0.699  -0.699  -0.699  -0.708  -0.722  -0.708  -0.699  -0.699  -0.699
136   R        -0.699  -0.699  -0.699  -0.708  -0.722  -0.708  -0.699  -0.699  -0.699
137   V        -0.699  -0.699  -0.699  -0.525  -0.535  -0.525  -0.699  -0.699  -0.699
138   L        -0.699  -0.699  -0.699  -0.506  -0.515  -0.506  -0.699  -0.699  -0.699
139   Q         1.418   1.418   1.418   1.212   1.201   1.212   1.418   1.418   1.418
140   E        -0.699  -0.699  -0.699  -0.942  -0.917  -0.942  -0.699  -0.699  -0.699
141   P        -0.699  -0.699  -0.699  -0.545  -0.555  -0.545  -0.699  -0.699  -0.699
142   D        -0.699  -0.699  -0.699  -0.877  -0.851  -0.877  -0.699  -0.699  -0.699
143   R        -0.699  -0.699  -0.699  -0.687  -0.659  -0.687  -0.699  -0.699  -0.699
144   D         1.418   1.418   1.418   1.327   1.376   1.327   1.418   1.418   1.418
145   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P38302
Output conservation file - output/P38302
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
